Immunohistochemistry - In Situ Hybridization

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  • Immunohistochemistry - In Situ Hybridization Images:

  • Immunohistochemistry Image Gallery

  • Immunofluorescence Image Gallery

  • In Situ Hybridization Image Gallery

  • Immunohistochemistry - In Situ Hybridization Staining Protocols:

  • ABC Protocol for Monoclonal Antibodies

  • ABC Protocol for Polyclonal Antibodies

  • ABC Protocol Monoclonal Antibodies (Frozen Sections)

  • ABC Protocol Polyclonal Antibodies (Frosen Sections)

  • ABC Px DAB for FFPWs for all species of Primary Abs

  • Actin (Muscle Actin) Protocol for ES/NexES

  • Actin (Smooth Muscle) Protocol for Autostainer (Cytospins)

  • Actin alpha. Muscle - specific

  • Adrenocorticotropin (ACTH) Protocol for ES/NexES

  • ALK Protein Protocol for ES/NexES

  • Alpha-1-Antitrypsin Protocol for ES/NexES

  • Alpha-Sarcoglycan (Adhalin) Protocol for NexES/ES

  • Alpha-Synuclein Protocol for ES/NexES

  • Amyloid A Component Protocol for ES/NexES

  • Antigen Retrieval Tris pH 10 using M/waveable pressure cooker

  • APAAP General Protocol (Mouse Primary)

  • APAAP General Protocol (Rabbit Primary)

  • Apolipoprotein D Protocol for ES/NexES

  • Aspergillus Protocol for ES/NexES

  • B-catenin staining FFPET

  • Bcl-2 Oncoprotein Protocol for ES/NexES

  • Bcl-6

  • Bcl-6 Protocol for ES/NexES

  • BCL6 on FFPET

  • Beta Tubulin Monoclonal in FFPW tissues 1

  • Beta tubulin Polyclonal in FFPWs 2

  • Beta-Dystroglycan Protocol for NexES/ES

  • Beta-Sarcoglycan Protocol for NexES/ES

  • Blocking solution for non-specific binding in pwax sections

  • Bob-1 Protocol for ES/NexES

  • BrdU

  • BrdU Ag retrieval Pwax sections

  • BRDU in FFPE Mouse Tissue

  • BrdU in FFPWs Rat,mouse, chick, human

  • C4d Complement

  • Calbindin D detection stABC pxDAB

  • Calcitonin Protocol for ES/NexES

  • Calretinin Protocol for Autostainer

  • Calretinin Protocol for Autostainer (Cytospins)

  • Candida Albicans Protocol for ES/NexES

  • Carcinoembryonic Antigen (CEA) Protocol for ES/NexES

  • CD10 on FFPET

  • CD10 Protocol for Autostainer

  • CD10 Protocol for ES/NexES

  • CD117 (c-kit) Protocol for ES/NexES

  • CD133 localisation in FFPWs of rat adult brain

  • CD138 on FFPET

  • CD138 Protocol for ES/NexES

  • CD14

  • CD15 Protocol for ES/NexES

  • CD1a Protocol for ES/NexES

  • CD20 Protocol for ES/NexES

  • CD21 Protocol for ES/NexES

  • CD22 Protocol for ES/NexES

  • CD23 Protocol for ES/NexES

  • CD3 Polyclonal

  • CD3 Protocol for ES/NexES

  • CD3 Rabbit monoclonal in mouse FFPW section

  • CD3 Rabbit polyclonal on mouse FFPW sections

  • CD30 Protocol for ES/NexES

  • CD31 Protocol for ES/NexES

  • CD34

  • CD34 Protocol for ES/NexES

  • CD4 Protocol for ES/NexES

  • CD40 Protocol for ES/NexES

  • CD42b Protocol for ES/NexES

  • CD43 Protocol for ES/NexES

  • CD45T0 Protocol for ES/NexES

  • CD5 Protocol for ES/NexES

  • CD56 (NCAM) Protocol for ES/NexES

  • CD56 ERIC NCAM on FFPWs

  • CD56 H28 NCAM on FFPW sections of mouse

  • CD57 localisation in FFPWs of mouse, rat and chick sections

  • CD57 Protocol for ES/NexES

  • CD68 Protocol for ES/NexES

  • CD79a Protocol for ES/NexES

  • CD8 Protocol for ES/NexES

  • CD99 Protocol for ES/NexES

  • Chromogranin A Protocol for ES/NexES

  • Cyclin D1

  • Cyclin D1 Protocol for ES/NexES

  • Cytokeratin 19 Protocol for ES/NexES

  • Cytokeratin High Molecular Weight Protocol for ES/NexES

  • Cytokeratin MNF116 Protocol for ES/NexES

  • Cytokeratin Pan- Protocol for Autostainer (Cytospins)

  • Cytomegalovirus (CMV) Protocol for ES/NexES

  • DAB Stock solution

  • Delta-Sarcoglycan Protocol for NexES/ES

  • Desmin Protocol for Autostainer (Cytospins)

  • Desmin Protocol for ES/NexES

  • Dewaxing slides for immunostaining

  • Drosophila embryo sections for BP102

  • Drosophila menanogaster Processing for Immunostaining ( Fruit fly embryos)

  • Dysferlin Protocol for NexES/ES

  • Dystrophin (c-terminus) Protocol for NexES/ES

  • Dystrophin (n-terminus) Protocol for NexES/ES

  • Dystrophin (rod domain) Protocol for NexES/ES

  • Emerin Protocol for NexES/ES

  • Epithelial Antigen (Ber-EP4) Protocol for ES/NexES

  • Epithelial Membrane Antigen (EMA) Protocol for ES/NexES

  • Epstein-Barr Virus (EBNA2) Protocol for ES/NexES

  • Epstein-Barr virus (Latent Membrane Protein) Protocol for ES/NexES

  • Estrogen Receptor (cytospin) Protocol for Autostainer

  • Estrogen Receptor (ER) Protocol for ES/NexES

  • Estrogen Receptor (Smears and Cytospins) Protocol for ES/NexES

  • Fasciclin II in Fruit fly FFPWs

  • Fixing GFP expressing tissue

  • Gamma-Sarcoglycan Protocol for NexES/ES

  • GAP43 Immunostaining in FFPWs

  • GAP43 phosphospecific inFFPWs Mouse, rat and chick

  • Gastrin Protocol for ES/NexES

  • GFAP for Astrocytes FFPWS

  • GFAP Protocol for Autostainer (Cytospins)

  • GFP localisation in FFPW sections

  • Glial Fibrillary Acidic Protein (GFAP) Protocol for ES/NexES

  • Glucagon Protocol for ES/NexES

  • Glycophorin A Protocol for ES/NexES

  • Granzyme B Protocol for ES/NexES (1)

  • Granzyme B Protocol for ES/NexES (2)

  • Heat Induced Epitope Retrieval (HIER) Microwave Method

  • Heat Induced Epitope Retrieval (HIER) Pressure Cooker

  • Helicobacter Pylori Protocol for ES/NexES

  • Hepatitis B Core Antigen (HBcAg) Protocol for ES/NexES

  • Hepatitis B Surface Antigen (HBsAg) Protocol for ES/NexES

  • Hepatocyte Protocol for ES/NexES

  • HIER M/W pressure- cooker with TRIS 10mM pH10

  • Histone H3 ( phospho) Mitosis marker FFPWs

  • HLA-DR Alpha Chain Protocol for ES/NexES

  • HMB45 Protocol for ES/NexES

  • HuC/D antigens demonstration in FFPWs

  • Human Chorionic Gonadotropin (hCG) Protocol for Autostainer

  • Human Chorionic Gonadotropin (hCG) Protocol for ES/NexES

  • Human Growth Hormone (hGH) Protocol for ES/NexES

  • Human Herpesvirus (type 8) Protocol for ES/NexES

  • Immuno Gold Silver (IGS)

  • Immuno Gold Silver Staining (with Colloidal Gold)

  • Immunofluorescence Labeling of Cells

  • Immunoglobulin A (IgA) Protocol for ES/NexES

  • Immunoglobulin G (IgG) Protocol for ES/NexES

  • Immunoglobulin M (IgM) Protocol for ES/NexES

  • Indirect Immunoenzyme Technique

  • Ki67 (cytospin) Protocol for Autostainer

  • Ki67 (Smears and Cytospins) Protocol for ES/NexES

  • Ki67 for FFPWs

  • Ki67 Protocol for ES/NexES

  • Labeled Streptavidin Biotin (LSAB) General Method

  • Lamin A&C Protocol for NexES/ES

  • Laminin detection in FFPWs

  • LCA Protocol for ES/NexES

  • Lysozyme (Muramidase) Protocol for ES/NexES

  • M. Tuberculosis on FFPET

  • Mast Cell Tryptase (MCT) Protocol for ES/NexES

  • MCAD localisation in FFPWs

  • Melan-A Protocol for ES/NexES

  • Melanoma Cocktail Rapid immunostaining protocol

  • Melanoma Marker (Pan) Protocol for ES/NexES

  • Merosin Laminin Alpha 2 Chain Protocol for NexES/ES

  • Merosin M-chain Protocol for NexES/ES

  • Mesothelial Cell (HBME-1) Protocol for ES/NexES

  • Microtubule-associated Protein, Neurone-specific in FFPWs

  • MLH-1 on FFPET

  • Mowiol Mountant Firm set Immunofluorescence

  • MSH-2 on FFPET

  • Myogenin in FFPWs

  • Myosin heavy chain typeII ( fast) in FFPWs

  • Nestin localisation in FFPWs

  • Neurofilament 160 ( RMO ) in FFPWs

  • Neurofilament 160 (NN18) in FFPWs

  • Neurofilament associated protein

  • Neurofilament Protein Protocol for ES/NexES

  • Neuron Specific Enolase (NSE)

  • Neuronal Nuclei (NeuN) Protocol for ES/NexES

  • Neurotactin in fly embryo FFPWs

  • Oct-2 Protocol for ES/NexES

  • p16 INK4a Protocol for ES/NexES

  • p21 WAF1/CIP1 in FFPWs of developing mouse muscle

  • p53 (cytospins) Protocol for Autostainer

  • p53 Protocol for ES/NexES

  • PAP General Protocol (Mouse Primary)

  • Parvovirus B19 Protocol for ES/NexES

  • Pax-5 Protocol for ES/NexES

  • PGP 9.5 in FFPWs

  • Placental Alkaline Phosphatase (PLAP) Protocol for ES/NexES

  • Pneumocystis carinii Protocol for ES/NexES

  • Progesterone Receptor (Cytospins) Protocol for Autostainer

  • Progesterone Receptor (PGR) Protocol for ES/NexES

  • Progesterone Receptor (Smears and Cytospins) Protocol for ES/NexES

  • Prolactin

  • Prostate Specific Antigen (PSA) Protocol for ES/NexES

  • Proteinase K Digestion

  • PU.1 Protocol for ES/NexES

  • Renal cell Carcinoma Marker on FFPET

  • Resin sectioning of wholemount in situ/immuno labelled specimens

  • Respiratory Syncytial Virus (RSV) Protocol for ES/NexES

  • S 100 Protocol for ES/NexES

  • Semi-permanent mounting medium for immunofluorescence

  • Serotonin

  • Somatostatin Protocol for ES/NexES

  • Spectrin Protocol for NexES/ES

  • StABC (Streptavidin Biotin Complex Method)

  • streptABC Peroxidase Dako kit/DAB method for FFPWs for all species of primary Antibody

  • Streptavidin-Nanogold-Silver-Staining

  • SV40 T-Ag (Ab-1) Protocol for ES/NexES

  • SV40 T-Ag (Ab-2) Protocol for ES/NexES

  • SV40 T-Ag Ab-2 (Cytospins) Protocol for ES/NexES

  • Synaptophysin Protocol for ES/NexES

  • Terminal Deoxynucleotidyl Transferase (TdT) Protocol for ES/NexES

  • Toxoplasma Gondii Protocol for ES/NexES

  • Trk (C-14) on pwax mouse embyro section

  • Trypsin Digestion

  • Trypsin Treatment

  • TTF-1 Protocol for Autostainer (Cytospins)

  • Tyramide amplification ABC- DAB - Px method

  • Tyrosine hydroxylase in HIER FFPWs mouse

  • ubiquitin on FFPET

  • VGLUT1 on human rat mouse pwax sections

  • Vimentin Protocol for Autostainer (Cytospins)

  • Vimentin Protocol for ES/NexES

  • Vimentin V9 on rat pwax sections

  • Von Willebrand Factor (Factor VIII) Protocol for ES/NexES


  • Immunohistochemistry - In Situ Hybridization News:

  • 225,000 PRIMARY ANTIBODIES and Where to Get Them

  • A Simple, Reliable, and Sensitive Method for Multiple Immunoenzyme Staining

  • A Universal Antigen Retrieval Method

  • Abbott and BioGenex Enter Agreement for Automated Molecular Diagnostics System

  • ALCAM/CD166 in in breast cancer

  • Anaplastic Lymphoma Kinase (ALK)

  • Apoptosis, Cell Death and Cell Proliferation

  • Application of microarray technology in pulmonary diseases

  • Applied Immunohistochemistry & Molecular Morphology

  • Autofluorescence Eliminator Reagent

  • BCL-2

  • Biotinyl-tyramide-based In Situ Hybridization

  • Breast Carcinoma vs. Pulmonary Adenocarcinoma

  • Calretinin

  • CD10 (CALLA) Immunohistochemistry

  • CD155/PVR

  • CD56 (NCAM)

  • cDNA microarrays

  • CDX2

  • CDX2

  • Chromogenic in situ hybridization (CISH)

  • Claudin 7

  • Claudin-1, -3 and -4 proteins and mRNA expression

  • Coexistence of HER2 over-expression and p53 protein

  • Collecting duct carcinoma of the kidney (CDC)

  • Cutaneous Basal Cell Carcinoma and Squamous Cell Carcinoma

  • Cyclin A and cyclin D1

  • Cytokeratin 5/6

  • Cytokeratin AE1/AE3

  • Cytopathology - from an Immunohistochemist’s Perspective

  • D2-40

  • Dako goes Rabbit

  • DAX-1 expression in human breast cancer

  • Desmoplastic small round cell tumor

  • Differential Diagnosis of Cytokeratin “Dots”

  • Double-label Fluorescent Immunohistochemistry

  • Dual Fluorescent In Situ Hybridization and Immunohistochemical Detection

  • Endocervical vs. Endometrial Adenocarcinoma

  • Endogenous Biotin Artifact

  • Enhanced diagnostic immunofluorescence using biopsies transported in saline

  • Enrichment methods to detect bone marrow micrometastases

  • Epidermal Growth Factor Receptor and Erbitux

  • Evaluation of Follicular or Nodular Lymphoid Lesions

  • Evaluation of Hydropic Placentas (Hydropic Degeneration vs. Partial Mole vs. Com

  • Expression of pS2 in prostate cancer

  • FISH Solution for Lymphoma

  • HER-2/neu and c-Kit (CD117) in malignant melanoma

  • High Molecular Weight Cytokeratin (34βE12)

  • Histologic Spring 2004

  • hMLH1 and hMSH2

  • Human CD57+ germinal center-T cells

  • Human Herpesvirus Type 8 (HHV8)

  • ImmPRESS™ - New Staining System from Vector Laboratories

  • Immunohistochemical markers of prostate carcinoma

  • Immunohistochemistry

  • Immunohistochemistry in Amyloidosis

  • Immunohistochemistry in Clear Cell Carcinomas

  • Immunohistochemistry in DFSP vs. DF-FH

  • Immunohistochemistry in Lymph Node Histiocytosis

  • Immunohistochemistry in the Differential Diagnosis of Schwannoma and Neurofibrom

  • Immunohistochemistry in the Evaluation of Atypical Epithelial Cells in Effusions

  • Immunohistochemistry in thyroid carcinoma

  • Immunohistochemistry in Urothelial Dysplasia

  • Immunohistochemistry Staining Protocols

  • Immunohistochemistry Staining Protocols

  • Immunohistochemistry: New Visualization System

  • Immunostaining of imprint smears with the 'MCW melanoma cocktail'

  • Immunostains for b-catenin in Diagnostic Pathology

  • In Situ Hybridization

  • In Situ Hybridization with Nanogold-Streptavidin

  • Interleukin-2 and its receptor complex (a, ß and γ chains)

  • KATP channel subunits

  • Ki-67 clone K-2: A useful marker of fat cells and lipoblasts

  • MCM2

  • Metallothionein expression in renal cell carcinoma

  • Microarray analysis in clinical oncology

  • MMP-13 and TIMP-1 in head and neck squamous cell carcinomas

  • Multicolor-FICTION

  • New Instrument for Cancer Diagnostics

  • New Web site!

  • Oct3/4 A New Marker of Embryonal Carcinoma and Seminoma

  • Oncotech Offers New Genomic Test for Lung Cancer

  • ONE-STEP RNA probe synthesis templates

  • Optimal Titering of Primary Antibodies

  • p14ARF expression in invasive breast cancers and ductal carcinoma in

  • p16INK4a

  • p21WAF1/CIP1 and HER-2/ neu

  • p27Kip1

  • P504S (a-Methylacyl-CoA-Racemase)

  • p63

  • p63/P504S Antibody Cocktail in Prostate Biopsies

  • Perivascular Epithelioid Cell Tumores

  • Platelet derived growth factor receptor alpha (PDGFR-α)

  • Polysomy of chromosome 17 and overexpression of ERBB2

  • Prostate stem cell antigen (PSCA)

  • Protein p16

  • Recognition of Early Myocardial Infarction

  • Respiratory Syncytial Virus (RSV) Immunohistochemistry

  • S100A7 (psoriasin) and Jab1 in ductal carcinoma in situ of the breast

  • Simultaneous Detection of EGFP and Cell Surface Markers by Fluorescence

  • TFE3 Immunostains in the Diagnosis of Alveolar Soft Part Sarcoma and Other Tumor

  • The Antigen–Antibody Reaction in Immunohistochemistry

  • The utility of cytokeratins 7 and 20 (CK7/20) immunohistochemistry

  • Tissue Micro Array (TMA)

  • Tissue Protection Immunohistochemistry

  • Traps in Sentinel Lymph Node Biopsies

  • True Positive vs. False Positive Staining

  • Ubiquitin Immunohistochemistry in Alzheimer’s Disease

  • Ultrarapid Ki-67 immunostaining in frozen section interpretation of gliomas

  • UroVysion FISH

  • Utility of Ki-67 (MIB-1) Immunostaining in Cervical Biopsies

  • Utility of p16 (INK4a) Immunostaining in Cervical Biopsies

  • Vascular endothelial growth factor (VEGF)-C

  • Villin Immunohistochemistry

  • Wilms Tumor Gene Protein (WT1)

  • XHM

  • Xmatrx(TM)

  • ZAP-70 in Chronic Lymphocytic Leukemia

  • “Basal-like” or “Basaloid” Breast Carcinoma


  • Immunohistochemistry - In Situ Hybridization Forum Categories:

  • Immunohistochemistry

  • In Situ Hybridization

  • Welcome


  • Immunohistochemistry - In Situ Hybridization Forums:

  • Automated Immunohistochemistry - Here you can discuss anything related to Automated Immunohistochemistry.

  • Automated In Situ Hybridization - Here you can discuss anything related to Automated ISH and FISH.

  • General Immunohistochemistry - This forum is open for all to discuss anything related to Immunohistochemistry and Immunofluorescence techniques.

  • General In Situ Hybridization - This forum is open for all to discuss anything related to In Situ Hybridization (ISH) and Fluorescent In Situ Hybridization (FISH) techniques.


  • Immunohistochemistry - In Situ Hybridization Topics / Posts:

  • about storage of embryos

  • About the TSA system (Perkin)

  • Abs towards human HLA class I antigens

  • adressing the sense probe signal problem

  • AEC a better substrate in IHC

  • alternative mounting solution (to DEPEX)

  • Alu probe

  • amti rat MMP12 or MMP14

  • anti Cathepsin S on rat

  • anti Cy5

  • anti integrin alpha v beta 3 on mouse tissue

  • Anti TNFa mouse tissues

  • anti-Tet-repressor antibody

  • anti-VP16 antibody

  • antibodies against C5b-9 Complement Terminal Complex

  • Antibody Diluents, Help!

  • Antibody penetration issues

  • antibody VEGF

  • antigen recognition

  • Antigen retreavel

  • Any protocols for removing lipids in sections prior to ISH?

  • aquaporins

  • Artifacts

  • Aspergillus

  • autofluorescence

  • Autofluorescence in rat brain tissue after lesions

  • automated ISH

  • Background problems

  • background problems with isotope probes

  • Background Staining on frozen embryo liver

  • background staining with hrp detection

  • Background staining.

  • Base mismatch

  • basic equipment(s) for ISH

  • Basic Questions

  • Basic theory of ISH

  • Best mounting media?

  • Best way finding antibodies

  • bibliography about probe design

  • biotin blocking kits

  • Blimp-1

  • blood vessels in brain

  • bone problems

  • Books for ISH

  • Botulinum Toxin A (BOTOX) IHC?

  • Bouin fixation with ISH

  • BrdU double labelling

  • Brdu in vivo @ in vitro

  • Bubbles on the brain sections

  • c-Kit antibody

  • can BSA increase background???

  • Can you do FISH on live bacterial cells?

  • CD3

  • CD38 Formalin Fixed Tissue

  • CD45 antigen not just in leukocytes??

  • Cells appear brown in BF microscopy in abscence of DAB

  • checking RNA -probes

  • Citraconic Anhydride

  • Citraconic anhydride recipe

  • Citraconic revisited

  • Colormetric detection and quantification

  • Combination ISH/Immunofluorescence

  • Commercial source for gene probes - recommendations?

  • Compatibility of non-perfused tissue and Immuno...

  • control probe

  • Control probe for Aedes mosquitoes or Drosophila

  • counterstain nucleus

  • Counterstaining of DIG-labelled riboprobes

  • course

  • Cross-Hybridization

  • Crystalline silica induced inflammation

  • Cyclin D2 detection

  • Cytokeratin stains

  • DAB Away Recipe

  • DakoCytomation GenPoint TSA System!!!

  • DAPI

  • DC-SIGN

  • Debris after development

  • decalcification

  • Decalcification

  • decalcification

  • detect nuclear mRNA

  • DIG control riboprobes

  • Dig-RNA probes

  • Disposal of used DAB solution

  • dispose PF

  • DNAse to reduce sense probe staining

  • double immunofluorescence protocol about bone

  • Double Immunofluorescence with two mouse mAb

  • Double ISH

  • Double ISH problem

  • Double stain, incompatible pretreatments

  • Draq5

  • Endogenous Alkaline Phosphatase

  • Factor XIIIa

  • Feulgen kit?

  • few questions about ish?

  • FISH

  • FISH in embryos or spermatozoa

  • Fixation and postfixation

  • Frozen brain.

  • fuzzy signal

  • General in situ protocol

  • general info on ISH

  • GFP fluorescence in mouse brain tissue

  • glutamatergic cell body marker

  • Gold medal for Ole.........

  • good anti-Biotin antibody?

  • Happy, belated, birthday Hogne!

  • HEEEELLLLPPP!

  • HELP with FISH

  • help! anyone has experience of caveolin immunostaining

  • Hi Ventana users

  • High background in ovaries

  • how to design RNA probe

  • how to reduce background staining?

  • hyaluronic acid detection

  • hybridization buffer

  • Hybridization buffer recipes...

  • hydrolysis of probe

  • I just ordered some new Abs...need user comments, please

  • IF nuclear stain other than DAPI

  • IgG biotynilation

  • IHC of cytoplasmic antigen as readout for RNAi

  • IHC problem! everything turning brown, even negative control

  • Immuno in frozen sections

  • immunofluorescence

  • Immunofluorescence AND ISH on mouse tissue

  • Immunohistochem apoptotic markers

  • Immunohistochemistry Protocols

  • immunohistochemistry vs. immunofluorensce

  • immunostaining H&E

  • Impressed?

  • In situ and immuno together

  • In situ hybridization on culture cells

  • In situ PCR

  • in situ RT-PCR - fixatives

  • Interleukin 6

  • interleukins staining IHC

  • ISH background in glass

  • ISH for free floating sections and cryoprotection

  • ISH for IFNgamma mRNA

  • ISH for new a gene

  • ISH in Bone

  • ISH on bovine prions

  • ISH on Cryosections

  • ISH on embryo cryosection

  • ISH on plants tissue

  • just the biochemicals do

  • just the biochemicals do

  • Ki-67 Quantitation in Mouse Bronchioles

  • LacZ activity and ISH

  • LacZ staining hard tissue

  • large amount of osteopontin background staining

  • Lectin PNA conjugates

  • Localisation of mRNA

  • Localization in Plant Tissue using ISH

  • Loss of signal in DIG in-situs

  • Low signal with DRD2 radioactive

  • Low signal with Isotopic In situ hybridization

  • Making anitsense riboprobes

  • Mallory-staining

  • mast cells in mice

  • MCM2

  • Melanin pigment removal

  • Mitochondrial Probe problems

  • MLH-1

  • Most appropriate protein blocking solution ?

  • mouse probe

  • mRNA degradation in frozen tissue

  • mRNA degradation in frozen tissue

  • multi probes

  • Need contract IHC for panel of human tissue

  • Need some antibodies

  • new guy

  • New to IF! Please review my protocol!

  • New to IHC - startup equipment?

  • newbie Q: negative control is stained

  • Nitrotyrosine Staining

  • no signal in in situ using b-actin

  • non-specific binding

  • OCT compound

  • Ole's New HRP kit

  • oligo dT hybridization to mRNA in stress granules

  • Omiting Normal Serum in blocking lessen background?

  • optimum amount of probe-please help!

  • Organ Culture & BrdU

  • P53 immunistainning

  • Paul - a question of sense and nuclear negative controls

  • PCNA brown background

  • PCNA brown background

  • PCR DIG Probe Kit for RNA detection?

  • per1 in hamster brains

  • perfusion of liver tissue

  • Phosphoantibodies

  • pink background with DIG staining

  • Please Help; Non-specific stainning everywhere

  • Poly d(T) probe

  • positive blank sections

  • Positive sense probe

  • Positive signal in sense probe

  • probe design and label for FISH

  • Problem with erys

  • Problem with Fluorojade-B

  • problem:precipitate/debris with any chromogen

  • problems with bone tissue

  • Problems with DAPI

  • problems with sectioning.

  • Problems with Staining

  • Problems with the background...IHC in chick embryos

  • Proteinase k alternative for ISH/IHC

  • protocol ER beta

  • Protocol for ER, PR and Her-2

  • protocols

  • radioactive in-situ

  • radioactive in-situ hybridization

  • Radioactive Labeling of Probe

  • rat-specific nuclear stain

  • Resources to locate those proficient in immunohistochemistry

  • Retina IF

  • Retriever EMS

  • Revised Mowiol formulation in "Protocols"

  • rhodamine at 37 degrees

  • Riboprobe without cloning for ISH

  • Riboprobes or Oligoprobes..?

  • RNALater

  • Search for canine antibodies of TNF, IFN, IL

  • sections ad slides

  • Sensitive Dig in situ protocol

  • Sensitive TSA ISH combined with IHC

  • Sensitivity X-ray film vs liquid emulsion

  • Signal amplification

  • signal in nucleaus

  • skipping the protease step

  • slide-coating protocol

  • slides for in-situ

  • SlowFade Gold/Prolong Gold vs. Permount

  • software to organise IHC slides

  • Some problem in signal....

  • some very basic questions

  • storage

  • Storage of embryonic and adult tissues for wax ISH

  • Storage of Frozen OCT blocks

  • Storing fixed cells

  • Tissue Preparation for ISH

  • TMA artifact

  • transcription factor in mouse lymphoid tissue sections

  • Trilogy Ag retrieval soln

  • trouble with ISH

  • TUNEL staining

  • Tween and (NH4)2SO4

  • Tween and (NH4)2SO4

  • Tyramide Signal Amplification and blurry DAPI

  • Urovysion-SpectrumGold Problems

  • use of citrate buffer

  • Use of TSA kits

  • Very Basic Question

  • Very useful form for beginers

  • Washed tissue?

  • What concentration to use for anti-DIG-POD Ab?

  • what label?

  • Which is more specific?

  • whole (bacterial) cell FISH

  • Whole mout in situ hybridization using 60mer oligos

  • why bubbles can cause background?

  • WT1 and PTEN

  • Y chromosome

  • y-chromosome specific antibody

  • ZAP-70


  • Immunohistochemistry - In Situ Hybridization Downloads:

  • ABC Technique - PowerPoint presentation of Avidin Biotin Complex (ABC) Technique.

  • Adobe Acrobat Reader - To read some of the files hosted on this web site, you may nead Adobe Acrobat Reader.
    Adobe Reader 6.0 is the newest version of the familiar Adobe Acrobat Reader software. It also replaces Adobe Acrobat eBook Reader, software for viewing high-fidelity eBooks on your notebook or desktop computer.

  • APAAP Technique - PowerPoint presentation of Alkaline Anti-Alkaline Phosphatase (APAAP) Technique.

  • DAKO Handbook - Theory and application of immunlabelling techniques

  • EBER In Situ Hybridization - PowerPoint presentation of Epstein Barr Virus (EBER) In Situ Hybridization.

  • EBER In Situ Hybridization and CD20 Immunohistochemistry - PowerPoint presentation of Epstein Barr Virus (EBER) In Situ Hybridization combined with CD20 Immunohistochemistry

  • EBER In Situ Hybridization and CK Immunohistochemistry - PowerPoint presentation of Epstein Barr Virus (EBER) In Situ Hybridization in combination with Cytokeratin Immunohistochemistry.

  • EBER In Situ Hybridization and Kappa/Lambda Double Immunofluorescence - PowrPoint presentation of Epstein Barr Virus (EBER) In Situ Hybridization combined with Kappa and Lambda Light Chain Double Immunofluorescence

  • HPV In Situ Hybridization and CK Immunohistochemistry - PowerPoint presentation of Human Papilloma Virus (HPV) In Situ Hybridization combined with Cytokeratin Immunofluorescence

  • Immuno Gold Silver Technique - PowerPoint presentation of Immuno Gold Silver (IGS) Technique.

  • Immunohistochemistry vade mecum - An excellent piece of work by Dr. Paul W. Bishop You can search for tumours to find out their pattern of immunoreactivity or look for individual antibodies to check their specification. There are links to all the references through PubMed. This amazing programme is small, easy to install and runs on any PC.
    To download the latest version, go to author's Home Page

  • LSAB Technique - PowerPoint presentation of Labelled Streptavidin Biotin (LSAB) Technique.

  • Non Biotin Amplification - PowerPoint presentation of Non Biotin Amplification using Fluorecein-labelled antibody.

  • PAP Technique - PowerPoint presentation of Peroxidase Anti-Peroxidase (PAP) Technique

  • Polymer Detection - PowerPoint presentation of Polymer Detection.

  • Technical Immunohistochemistry - TECHNICAL IMMUNOHISTOCHEMISTRY: Achieving Reliability and Reproducibility of Immunostains.
    By Rodney T. Miller, M.D. Director of Immunohistochemistry ProPath Laboratory, Inc.


  • Immunohistochemistry - In Situ Hybridization Web Links:

  • 35S-labeled probe - In Situ Hybridization using 35S-labeled probe, Detection by emulsion or film autoradiography. Frozen Sections.

  • A Concise Guide to cDNA Microarray Analysis - Standard protocol including Array Fabrication, Probe Preparation and Hybridization, and Data Collection, Normalization and Analysis. This is a 27-page PDF file. (The Institute for Genomic Research)

  • A New Blocking Method for Application of Murine Monoclonal Antibody to Mouse Tissue Sections - A New Blocking Method for Application of Murine Monoclonal Antibody to Mouse Tissue Sections

  • A New Rapid Immunohistochemical Staining Technique Using the EnVision Antibody Complex - A New Rapid Immunohistochemical Staining Technique Using the EnVision Antibody Complex

  • A Novel Quality Control Slide for Quantitative Immunohistochemistry Testing - We introduce a novel quality control technology that may improve intra- and interlaboratory immunohistochemistry (IHC) standardization. The technology involves the creation of standardized antibody targets that are attached to the same slides as the patient sample. After IHC staining, the targets turn the same color as the stained cells or tissue elements. Unlike current clinical practice, our proposed targets are neither cells nor tissue sections.

  • Abazyme - A variety of antibodies including anti-human cytokine and anti-human CD antigens antibodies

  • Abcam - Mission:"...to build the largest catalog of the best antibodies in the world"

  • Abgent - Abgent develops innovative reagents and technologies to profile post-translational modifications of the proteome.

  • Abkem Iberia - Polyclonal antibodies for food and environmental contaminants, allergens, and growth promoters

  • Abnova Corporation - Abnova is the world largest monoclonal antibody manufacturer. We have a capacity of generating 500 mouse monoclonal antibodies per month. Rather than the traditional method of monoclonal antibody production, Abnova is taking a genomic/proteomic approach for the antibody development. Our goal is to have at least one antibody to every human expressed gene in human genome. We manufacture all our products, recombinant proteins and antibodies, in house in our stat-of-art facility in Taiwan. In most cases, we have multiple clones for our monoclonal antibodies, and their access is available to our industrial partners and collaborators from the academic institutions.

  • Academy Bio-Medical Co - Specializing in Human Lipoproteins, Apolipoproteins and Polyclonal Antibodies.

  • Accurate Chemical & Scientific - Accurate has specialized in products for basic and R&D research as well as routine laboratory work. Polyclonal and monoclonal antibodies

  • Acris - Where ever your research interests may be and what ever animal model you work with you will have a good chance to find what you need.

  • ACTIgen - Develops and markets rProteinL for detection and purification of antibodies

  • Active Motif - Kits and reagents for monitoring phosphorylation and other events that change the activation state of transcription factors, signalling proteins and receptors.

  • ADI - Custom peptides and antbodies. They also sell a unique collection of antibodies to receptors, transporters, neurobiologicals, and much more.

  • Advanced Biotechnologies Inc - Supplier of monoclonal antibodies to the following viruses: HIV-1, SIV, HSV-1, HSV-2, CMV, EBV, VZV, HHV-6, HHV-7, HHV-8 and polyclonal antibodies to HIV-1, HTLV-1, HHV-8 vIL-6, and SIV

  • Advanced ImmunoChemical Inc. - Immunological Reagents worldwide for diagnostics sector & research needs.

  • Advanced Targeting Systems - An international supplier of neuroendocrine and neuroscience polyclonal and monoclonal antibodies. ATS also provides agents for the targeting and elimination of specific cell types

  • Advances in Cytochemical Methods for Detection of Apoptosis - Key Words: apoptosis, cytochemistry, TUNEL, ISNT, annexin V, caspases, ricin

  • Affibody - Affibody is a biotech company that uses innovative protein-engineering technologies for the development of products for biotherapeutics and biotechnology applications. The Affibody® molecule, which is a key component of the company’s technology, mimics a monoclonal antibody in many ways, and its properties make it a superior choice for many applications.

  • Affinity BioReagents - ABR—Affinity BioReagents, a privately held corporation, offers over 2,600 industry leading research reagents and custom antibody production services to the worldwide research community. The ABR product portfolio includes primary and secondary antibodies, proteins, peptides and viral expression kits supporting 34 distinct research areas. Cutting-edge antibody production services allow researchers the flexibility to create a custom antibody to meet their specific research needs.

  • Agdia - Easy-to-use test kits, reagents and laboratory testing services for agricultural diagnostics

  • AgriSera - Antibodies to mammalian, insect and bacterial antigens as well as antibodies in the area of photosynthetic research.

  • Ah Receptor (AhR) - Detection of Ah Receptor (AhR) in Formalin-Fixed, Paraffin-Embedded Rat Tissue

  • Alexa Dyes, a Series of New Fluorescent Dyes that Yield Exceptionally Bright, Photostable Conjugates - We report here the superior, largely unparalleled fluorescence emission and photostability of conjugates of a new series of sulfonated compounds named Alexa 350, Alexa 430, Alexa 488, Alexa 532, Alexa 546, Alexa 568, and Alexa 594 dyes. The number in each of their names refers to the approximate excitation maxima of the dyes, which nearly match the principal wavelength of several commonly used excitation sources. All of the Alexa dyes exhibit pH-insensitivity over a very broad range, and those that absorb at wavelengths greater than 480 nm have the high molar extinction coefficient typical of fluoresceins or rhodamines.

  • Alexis - Apoptosis, Cell Cycle & DNA Transactions, Combinatorial Chemistry Reagents, Cytoskeletal Research, Growth Factors, Cytokines & Chemokines, Immunology & Cancer Research, Neurochemicals, Nitric Oxide & Oxidative Stress, Signal Transduction.

  • Alomone Labs - Supplying innovative biochemicals which serve the neuroscience research community.

  • Alpha Diagnostic International - Alpha Diagnostic Intl., Inc., (ADI) located in San Antonio, Texas, USA, is one of the major providers of custom services such as peptides synthesis, and polyclonal antibodies. ADI maintains an USDA inspected and approved, animal facility. We have NIH/OPRR Assurance on file. Other antibody related services (affinity purification, conjugation to enzymes, dyes, fluorochromes, etc, ELISA, Western blots) are also provided.

  • ALT Inc - Novel, site specific nucleotide based photoaffinity reagents for labeling of antibodies

  • American Qualex - Labeled primary and secondary antibodies in addition to antibodies for signal transduction.

  • American Research Products - Mono- and polyclonal Antibodies, Antigens and Tissue Arrays

  • Amplification Methods to Increase the Sensitivity of In Situ Hybridization - Here we outline the principles of tyramide signal amplification using the catalyzed reporter deposition (CARD) technique, present practical suggestions to efficiently enhance the sensitivity of ISH with CARD, and discuss some applications and possible future directions of in situ nucleic acid detection using such an amplification strategy.

  • Amylase - Identification of Amylase (C-20) in Formalin-Fixed, Paraffin-Embedded Rat Tissue

  • An Optimized Method for ISH with Signal Amplification That Allows the Detection of Rare mRNAs - Using biotinyl–tyramide and streptavidin conjugated to alkaline phosphatase (AP) to introduce an additional round of amplification, we have now achieved a considerable enhancement of signal intensity relative to standard chromogenic ISH detection systems. We term this protocol TSA-AP (tyramide signal amplification using AP). In addition, we have optimized critical parameters to improve hybridization with digoxigenin (DIG)-labeled probes and to reduce nonspecific binding of probes, both strategies being essential for successful detection of rare mRNAs.

  • AnaSpec - Life science company providing innovative products (peptides, antibodies, fluorescent reagents, assay kits, synthesis resins and reagents) and custom manufacturing. AnaSpec offers a broad product line of these biochemicals and reagents for basic research, high-throughput screening and drug discovery. In conjunction, AnaSpec provides premier custom services including peptide synthesis, antibody production, and assay development.

  • Anaspec - An international manufacturer of antibodies in the areas of apoptosis, cancer research, and signal transduction; and secondary antibodies.

  • Anawa - Custom antibody production and a large selection of antibodies

  • Ancell - Anti-CD antibodies and more

  • Anderson Lab In Situ Hybridization Protocols - In Situ Hybridization of Frozen Sections, Whole Mount In Situ Hybridization, In Situ Hybridization on Cultured Cells and Additional Techniques

  • AngioBio - Provider of reagents for angiogenesis and lymphangiogenesis research, including many antibodies.

  • Anogen - Antibodies to cytokines, viral proteins, tumor markers and growth factors; and custom monoclonal antibody services.

  • Anti-Human CD Antibodies - Anti-Human CD Clustered Antibodies

  • Anti-Mouse CD Antibodies - Anti-Mouse CD Clustered and other Antibodies

  • Anti-Rat CD Antibodies - Anti-Rat CD Clustered and other antibodies

  • Antibodies - Structure and Sequence - This page attempts to summarise useful information on antibody structure and sequence. It provides a query interface to the Kabat antibody sequence data, general information on antibodies and crystal structures and links to other antibody-related information.

  • Antibodies Incorporated - Antibodies Incorporated is owned and operated by employees who have many years of experience in animal care, antiserum production, immunochemistry and related services applicable to aiding the academic or industry research scientist to save time and money in pursuit of their scientific goals. Having developed and manufactured our own diagnostic kits for many years has given us experience that is highly regarded in developing new assays and for contract manufacturing.

  • Antibody Directory - We are striving to include as many companies or products as possible, but we do not make a claim to being comprehensive.

  • Antibody Purification Handbook - The purpose of this handbook is to present the most effective and most frequently used strategies for sample preparation and purification of the many different forms of antibodies and antibody fragments used in the laboratory.

  • Antibody Staining of Drosophila Adult Retina - The following protocol has been adapted from Larry Zipursky's lab. It detects antigen in retinas that have been sectioned in plastic.

  • Antibody Structure - Antibody Structure - nicely illustrated

  • AntibodyShop - Large selection of monoclonal antibodies available online. The main antigens are: mannan binding lectin, complement system components, blood coagulation cascade components, immunoglobulins, albumins, cytokines, hormones, enzymes, haptens, human plasma proteins, and bacterial antigens.

  • Antigen Retrieval by Heating En Bloc for Pre-fixed Frozen Material - This article describes a simple alternative method for AR that can be used for aldehyde-fixed frozen sections.

  • Antigen Retrieval Immunohistochemistry - Antigen Retrieval Immunohistochemistry: Past, Present, and Future

  • Antigen Retrieval in Prion Protein Immunohistochemistry - Many different protocols for the detection of prions in brain tissue have been used. Thus far, picric and/or formic acid, steam autoclaving at 121C of sections, microwave treatment, and 4 M guanidine thiocyanate treatment have been suggested. The objective of our experiment was to obtain the standard pretreatment(s) resulting in optimal immunostaining. In the experiment, successive tissue slides of brain specimens of several Creutzfeldt–Jakob disease and control patients were stained using different combinations of pretreatments.

  • Antigen Retrieval of Basement Membrane Proteins from Archival Eye Tissues - Antigen retrieval (AR) methods can unmask tissue antigens that have been altered by fixation, processing, storage, or resin interactions. This is particularly important in the study of archival tissues, because primary fixatives and storage times may vary among specimens.

  • Antigen Retrieval Techniques - Antigen Retrieval Techniques: Current Perspectives

  • Antigen Retrieval Trial for Post-embedding Immunoelectron Microscopy by Heating - Antigen Retrieval Trial for Post-embedding Immunoelectron Microscopy by Heating with Several Unmasking Solutions

  • APC Formalin-Fixed Paraffin-Embedded MouseTissue - Identification of Adenomatous Polyposis Coli in Formalin-Fixed Paraffin-Embedded MouseTissue

  • Apotech - Antibodies for apoptosis and inflammation research

  • Application of Microwave Technology - Application of Microwave Technology to the Processing and Immunolabeling of Plastic-embedded and Cryosections

  • Applied Immunohistochemistry & Molecular Morphology - Applied Immunohistochemistry & Molecular Morphology provides complete coverage of the diagnostic and prognostic applications of immunohistochemistry (IHC), its contributions to the understanding of the biology of tumors and other lesions, and the technical aspects of setting up a laboratory and interpreting results.

  • Aptec Diagnostics - Polyclonal antibodies for use in quantitative turbidimetric and nephelometric determinations in human serum

  • Aquatic Diagnostics - Monoclonal antibodies for aquaculture. Antibodies to detect pathogens in fish and IgM in different fish species.

  • Araclon Biotech - Makers of 3 polyclonal antibodies: AB1 recognizes both Ab40 and Ab42, AB2 recognizes specifically Ab40, and AB3 recognizes specifically Ab42. They also make an ELISA kit to detect beta-amyloid protein in blood.

  • Argene Biosoft - Argene: development and production of diagnostic and/or research use reagents in the microbiology field by using immunology or molecular biology methods

  • Arista Biologicals - Monoclonal and polyclonal antibodies, and colloidal gold conjugates for fertility, infectious diseases, drugs of abuse, etc., as well as antigens for rapid diagnostic tests.

  • ASMA - 1A4 - ASMA (1A4) Optimax Immunostainer

  • ASMA - 1A4 - ASMA (1A4) Protocol for Techmate. NordiQC

  • ASMA - 1A4 - ASMA(1A4) Protocol for Autostainer. NordiQC

  • Assay Designs - Antibodies for research and diagnostic purposes (Immunoassays and Kits)

  • Assessment of Methods for Tissue-Based Detection of the HER-2/neu Alteration in Human Breast Cancer - Assessment of Methods for Tissue-Based Detection of the HER-2/neu Alteration in Human Breast Cancer: A Direct Comparison of Fluorescence In Situ Hybridization and Immunohistochemistry

  • Athens Research & Technology - Polyclonal sera to purified human proteins.

  • Aurion - AURION is a research oriented company dedicated to and specializing in the development and production of Ultra Small ImmunoGold Reagents, Silver Enhancement Reagents, Blocking Reagents, Incubation Solutions and Conventional ImmunoGold Reagents

  • Autoradiography for mRNA detection in mouse embryo tissue sections - Protocols from Oxford Practical Approach Series

  • Aves Labs - Specializing in chicken antibodies. They sell blocking reagents (BlokHen®) and reagents designed for immunoprecipitation (PrecipHen®) of chicken antibodies; a variety of enzyme- and fluorescence-tagged anti-chicken antibody reagents; and chicken antibodies against epitope tags such as c-myc, hemagglutinin, and FLAG.

  • Aviva Systems Biology - Aviva Systems Biology (ASB) develops, manufactures and markets reagent tools for gene transcription regulation research. We are best known for high quality novel antibodies, Innovative innovative Gene Regulatory Elements mapping and Analysis (GREMA) Technology and reliable custom gene transcription regulation mapping services

  • B-Catenin - Identification of B-Catenin in Formalin-Fixed, Paraffin Embedded Rodent Tissue

  • Bachem - Offers a comprehensive selection of sevices to meet your needs in immunochemicals of your choice.

  • Bcl-2 - Bcl-2 clone 124 staining protocol for Ventana Nexes. NordiQC

  • Bcl-2 - Bcl-2 clone bcl-2/100/D5 Staining protocol for Autostainer, DakoCytomation. NordiQC

  • Bcl-2 - Bcl-2 clone 100 Staining Protocol for I6000, BioGenex. NordiQC

  • Bcl-2 - Bcl-2 clone 8C8 Staining Protocol for LabVision Immunostainer. NordiQC

  • BCL2 - BCL2 Protocol for Autostainer

  • BCL2 - BCL2 Protocol for Techmate. NordiQC

  • BCL6 - BCL6 Protocol for Autostainer. NordiQC

  • BD Bioscience Clontech - Provider of GFP, GAL4, cell cycle, phosphoamino acid, phosphokeratin, and other antibodies, as well as many other innovative molecular and cell biology-related products

  • BD Biosciences - Immunocytometry systems

  • Beckman Coulter - Monoclonal and polyclonal antibodies to human and animal antigens.

  • Beecher Instruments - Beecher develops microarray technologies that facilitate high-throughput genomic and proteomic research. Offers automated and manual tissue microarray instruments and accessory tissue arrayer products.

  • Beta Polymerase - Identification of Beta Polymerase by an 8K Domain Antibody in Paraffin Embedded Rodent Tissue

  • Bethyl Laboratories - Primary and secondary antibodies to human, rodent and domestic animal serum proteins, affinity purified and conjugated, epitope tags, ELISA kits

  • Biocare Medical - BIOCARE is a unique manufacturer and supplier of immunostaining systems, histopathology products, monoclonal and polyclonal antibodies and automated staining equipment.

  • BioCore - BioCore supplies over 10,000 research related products including Antibodies, Immunoassay Kits, Enzymes, Immunotoxins, Reagents, and much more.

  • BioCytex - Thrombosis and Haemostasis field

  • Biodesign International - Broad range of antigens and antibodies

  • Biogenesis - Operating from the South Coast of England and New Hampshire in the US we are able to offer a wide range of Custom Services, in addition to our comprehensive catalogue of over 6,000 products.

  • BioGenex - BioGenex offers a broad range of reagents, detection kits, antibodies, probes, special stains, tissue microarrays, automated staining and imaging systems to streamline and standardize cellular and molecular analysis.

  • Biognostik - Supplier of custom-designed, high-quality ANTISENSE sequences and HybriProbes™ for in situ hybridization.

  • BioLegend - We offer products covering the areas of cell immunophenotyping, cytokines and chemokines, adhesion, phosphorylation, cancer research, cell-cycle analysis, and apoptosis. Our aggressive product development program, through technology licensing, collaborations, and internal hybridoma development, produces strategic reagents for use in a variety of applications including flow cytometry, ELISA, immunoprecipitation, Western blotting, immunofluorescence microscopy, immunohistochemistry, and in vitro / in vivo functional assays.

  • BioLink International - Provide Recombinant HIV, HCV and Syphilis antigens for purpose of research and manufacturing. We also provide laboratory consumables to distributors, hospitals and research communities.

  • Biomarket - Biomarket offers more than 100 products in the field of infectious diseases, monoclonal antibodies, antigens, extracellular matrix, integrin and molecular biology products including modifying enzymes and PCR reagents.

  • BioMed Central - BioMed Central. Over 100 Open Access journals covering all areas of Biology and Medicine

  • Biomeda - Full range of detection kits, a diversified line of monoclonal and polyclonal antibodies,

  • Biomedica - Supplier of endothelin and big endothelin antibodies.

  • Biomedical Technologies - BTI prepares over 35 different antibodies. Antibodies to the cytoskeletal proteins, growth & attachment factors, lipoproteins, hormones and keratinocyte differentiation markers are also offered. All our products are produced in the USA. Labeled second antibodies and precipitating antibodies are available in convenient packaging.

  • BIOMOL International - BIOMOL offers a range of biochemicals with applications in signal transduction, immunohistochemistry, gene regulation, apoptosis, neuroscience and drug discovery. In addition to purified enzymes, antibodies, and assay kits, BIOMOL’s innovative products include Nupherin-neuron transfection reagent, Fluor de Lys HDAC assay kit, and Screen-Well compound libraries. www.biomol.com 800-942-0430

  • Biomol International - The BIOMOL International worldwide network offers specialised reagents for signal transduction research (including antibodies, peptides, enzymes, enzyme activators and inhibitors, second messengers, and assay kits as well as a comprehensive offering of bioactive lipids and neuropharmacologics) and a range of compound libraries for screening (previously available from BIOMOL Research Laboratories) with the innovative products and services for cell biological research available from AFFINITI. This includes a wide range of products for neuroscience research and the world's most comprehensive range of substrates, inhibitors, enzymes, proteins and antibodies for use in ubiquitin, proteasome and COP9-signalosome research. AFFINITI staff also specialise in the manufacture of high quality synthetic peptides and in the synthetic peptide approach to protein-reactive antibody production.

  • BioProcessing - Antibodies to Ca15-3, Ca27.29, breast tumor antigens, Ca125, ovarian tumor antigen, Ca19-9, GI tumor antigen, CEA, carcinoembryonic antigen, AFP, alpha fetoprotein, Ca72.4, Tag-72, NSE, neuron specific enolase, Cyfra21-1, cytokeratin-19, PSA, prostate specific antigen using cell culture technologies.

  • Biosense Laboratories - Producers of antibodies and ELISA kits for the detection of biomarker proteins in fish. Products include monoclonal and polyclonal antibodies for the detection of responses to oil hydrocarbons, PAHs, PCBs, dioxins, endocrine disruptors, etc...

  • Biosonda - Featuring anti-human acrosin and anti-gizzerosine antibodies and Blue Carrier, a highly soluble and purified carrier protein from the hemocyanin family

  • Biosource - Biosource International, Inc. is a broad based life sciences company focused on providing solutions in the areas of functional proteomics and advanced drug discovery through the development, manufacturing, marketing, and distribution of unique biologically active reagent systems which facilitate, enable, and accelerate pharmaceutical development as well as biomedical research.

  • BioSource International - Develops, manufactures, markets and distributes monoclonal and polyclonal antibodies, recombinant proteins, custom oligonucleotides and quantitative cDNA amplification kits for the study of immunology and molecular biology

  • BiosPacific - Antibodies and antigens for the development of diagnostic assays

  • Biostride - East Coast Biologics - Monoclonal and polyclonal antibodies to drugs of abuse, environmental compounds, hormones and steroids, tumor markers, infectious diseases, therapeutic drugs, and other miscellaneous compounds

  • Biotin and Digoxigenin as Labels for Light and Electron Microscopy in Situ Hybridization Probes - Biotin and Digoxigenin as Labels for Light and Electron Microscopy in Situ Hybridization Probes: Where Do We Stand?

  • Biotinylation of Antibodies - Biotin is used in two-step detection systems in concert with conjugated avidin. Biotin is typically conjugated to proteins via primary amines (i.e., lysines). Usually, between 3 and 6 biotin molecules are conjugated to each antibody.

  • Biotrend - BIOTREND is specialised in Immunology, Neuroscience, Pharmacology and Radiochemistry, supplying biomedical and pharmaceutical research with a large range of antibodies, radiolabelled products, custom synthesis and antibody production services.

  • BioVendor Laboratory Medicine - Specializes in the production and distribution of in vitro research products for molecular and cellular laboratory medicine

  • BMA Biomedicals - Monoclonal antibodies, polyclonal antibodies, and ELISA kits for macrophage and inflammation typing in mouse, human and rats

  • Boston Biochem - Antibodies and assay kits for the ubiquitin proteasome pathway

  • BRDU Mouse - Detection of BRDU in formalin-fixed, paraffin-embedded mouse tissue

  • BRDU Rat - Detection of BRDU in formalin-fixed, paraffin-embedded rat tissue

  • Calbindin-D-28K in Formalin-Fixed Paraffin-embedded Mouse Tissue - Detection of Calbindin-D-28K in Formalin-Fixed Paraffin-embedded Mouse Tissue

  • Calbiochem - Distributor of an extensive range of monoclonal and polyclonal antibodies, secondary antibodies and their conjugates, plus many accessory products for immunoassay and immunoseparation.

  • Calcium-induced Modification of Protein Conformation Demonstrated by Immunohistochemistry - Calcium-induced Modification of Protein Conformation Demonstrated by Immunohistochemistry: What Is the Signal?

  • Calgranulin in Formalin-Fixed, Paraffin Embedded Rat Tissue - Identification of Calgranulin in Formalin-Fixed, Paraffin Embedded Rat Tissue

  • Calretinin - Calretinin Protocol for DakoCytomation Horizon. NordiQC

  • Calretinin clone 5A5 - Calretinin clone 5A5 Protocol for DakoCytomation Autostainer. NordiQC

  • Calretinin in Formalin-Fixed, Paraffin Embedded Rodent Tissue - Identification of Calretinin in Formalin-Fixed, Paraffin Embedded Rodent Tissue

  • Caltag Laboratories - Antibodies to cell markers for flow cytometric applications

  • Cambio - STAR*FISH Chromosome Painting

  • CanAg Diagnostics - A biotechnology company specialising in the development of specific reagents (monoclonal antibodies) and laboratory tests that can be used for sensitive and specific determination of tumor markers and biochemical markers of brain disease

  • Capralogics - Capralogics produces high quality polyclonal antibodies. Chemokine Receptors, Interleukins, Nuclear Components, Apoptosis, Cell Membrane, Protein Kinases, Signaling Intermediates, Lymphocyte Signaling

  • Capricorn - Manufacturer and distributor of immunodiagnostic products including monoclonal and polyclonal antibodies to infectious diseases, hormones. steroids, tumor markers, and serum proteins.

  • Carcinoembryonic antigen - CEA - Carcinoembryonic antigen (CEA) Protocol for DakoCytomation Autostainer

  • Caspase-3 - Detection of Cleaved Caspase-3 in Formalin-Fixed, Paraffin-Embedded Human and Rodent Tissue

  • Catalase in Formalin-Fixed, Paraffin Embedded Rat Tissue - Detection of Catalase in Formalin-Fixed, Paraffin Embedded Rat Tissue

  • Cayman Chemical - Cayman Chemical Company is helping make research possible by supplying scientists worldwide with biochemical tools in research disciplines such as cancer, nitric oxide, neuroscience, apoptosis, oxidative injury, endocrinology, and much more. We specialize in assay kits for the measurement of eicosanoids, free radical biomarkers, cyclic nucleotides, cytokines, hormones and nitric oxide. In addition, Cayman offers a broad range of quality biochemicals including eicosanoids, nitric oxide reagents, and a variety of related lipids, fatty acids, enzymes, and antibodies.

  • CC10 using LSAB Kit in Formalin-Fixed, Paraffin Embedded Rodent Tissue - Identification of CC10 using LSAB Kit in Formalin-Fixed, Paraffin Embedded Rodent Tissue

  • CCK-A Receptor - Detection of CCK-A Receptor (G-17) in Formalin-Fixed, Paraffin-Embedded Rat Tissue

  • CD10 - CD10 clone 56C6 Protocol for DakoCytomation Autostainer. NordiQC

  • CD10 - CD10 clone 56C6 Protocol for DakoCytomation Autostainer. NordiQC

  • CD10 is expressed in a subset of chromophobe renal cell carcinomas - CD10 has been considered a useful marker in the diagnosis of renal carcinomas, because of its expression in clear cell and papillary renal cell carcinomas and its absence in chromophobe renal cell carcinomas.

  • CD117 - CD117 (polyclonal) Staining Protocol for Autostainer

  • CD117 - CD117 (polyclonal) Staining Protocol for Ventana BenchMark XT

  • CD117 c-kit - CD117 (c-kit) Polyclonal, Protocol for DakoCytomation Autostainer. NordiQC

  • CD117 c-kit - CD117 (c-kit) Polyclonal, Protocol for DakoCytomation TechMate

  • CD117 c-kit - CD117 (c-kit) Polyclonal, Protocol for Ventana BenchMark. NordiQC

  • CD117 c-kit - CD117 (c-kit) Polyclonal, Protocol for DakoCytomation TechMate. NordiQC

  • CD14 - CD14 clone 7 Protocol

  • CD14 - CD14 clone 7 Protocol for TechMate

  • CD15 - CD15 clone MMA Protocol for DakoCytomation Autostainer. NordiQC

  • CD15 - CD15 clone Tu9 Protocol for GenoMx i6000, BioGenex. NordiQC

  • CD15 - CD15 clone MMA Staining Protocol for TechMate 500

  • CD15 - CD15 clone MMA Staining Protocol for Ventana ES

  • CD15 - CD15 clone C3D-1 Staining Protocol for TechMate 500

  • CD15 C3D-1 - CD15(C3D-1) Protocol for Autostainer LabVision

  • CD19 - Detection of CD19 in Frozen Mouse Tissue

  • CD20 - CD20 clone L26 Protocol for DakoCytomation Horizon. NordiQC

  • CD20 Expression in Hodgkin and Reed-Sternberg Cells of Classical Hodgkin’s Disease - CD20 can be expressed in Hodgkin and Reed-Sternberg (HRS) cells of classical Hodgkin’s disease (HD), but its clinical significance remains controversial. Therefore, we correlated CD20 expression with presenting features and clinical outcome of untreated patients with classical HD.

  • CD23 - CD23 clone 1B12 Protocol for DakoCytomation Autostainer. NordiQC

  • CD23 - CD23 clone 1B12 Protocol for DakoCytomation Autostainer. NordiQC

  • CD23 - CD23 clone 1B12 Protocol for Ventana NexES. NordiQC

  • CD23 - CD23 clone MHM6 Protocol for DakoCytomation Autostainer. NordiQC

  • CD3 - CD3 clone PS1 Protocol for DakoCytomation Autostainer. NordiQC

  • CD3 - CD3 clone F7.2.38 Staining Protocol for DakoCytomation Autostainer.

  • CD3 - CD3 clone PS1 Staining Protocol for Ventana Benchmark.

  • CD3 - CD3 clone PS1 Staining Protocol for DakoCytomation Autostainer

  • CD3 - CD3 clone SP7 Manual Staining Protocol

  • CD3 - CD3 (polyclonal) Staining Protocol for LabVision Autostainer

  • CD3 - CD3 (polyclonal) Staining Protocol for LabVision Immunostainer

  • CD3 - Detection of CD3 in Formalin-Fixed, Paraffin-Embedded Human and Mouse Tissue

  • CD3 Polyclonal - CD3 Polyclonal Protocol for Dako TechMate

  • CD30 - CD30 clone Ber-H2 Protocol for DakoCytomation Autostainer. NordiQC

  • CD30 - CD30 clone Ber-H2 Protocol for DakoCytomation TechMate. NordiQC

  • CD30 - CD30 clone Ber-H2 Protocol for Ventana NexES. NordiQC

  • CD30 - CD30 clone Ber-H2 Protocol for DakoCytomation TechMate

  • CD30 - CD30 clone Ber-H2 Protocol for Ventana BenchMark. NordiQC

  • CD31 - CD31 clone JC/70A Protocol for DakoCytomation Autostainer. NordiQC

  • CD31 - CD31 clone JC/70A Protocol for DakoCytomation TechMate. NordiQC

  • CD31 - CD31 clone JC/70A for Autostainer. NordiQC

  • CD31 - CD31 clone JC/70A Protocol for Ventana BenchMark. NordiQC

  • CD34 - CD34 clone QBEnd 10 Protocol for Labvision Autostainer. NordiQC

  • CD34 - CD34 clone My10 Protocol for DakoCytomation TechMate

  • CD34 - CD34 clone QBEnd 10 manual protocol. NordiQC

  • CD34 - CD34 clone QBEnd 10 for DakoCytomation Autostainer. NordiQC

  • CD4 - CD4 clone 1F6 Staining Protocol for Ventana NexES

  • CD4 - CD4 clone 1F6 Staining Protocol for TechMate

  • CD4 - CD4 clone 4B12 Staining Protocol for DakoCytomation Autostainer

  • CD4 - CD4 clone 4B12 Staining Protocol for DakoCytomation TM500

  • CD40 in Formalin Fixed Paraffin Embedded Mouse Tissue - Detection of CD-40 in Formalin Fixed Paraffin Embedded Mouse Tissue

  • CD40 in Frozen Mouse Tissue - Detection of CD-40 in Frozen Mouse Tissue

  • CD5 4C7 - CD5 (4C7) Protocol for Autostainer Lab Vision. NordiQC

  • CD5 4C7 - CD5 (4C7) Protocol for Ventana NexES. NordiQC

  • CD5 CD5/54/F6 - CD5 (CD5/54/F6) Protocol for DakoCytomation Autostainer

  • CD68 - CD68 clone KP1 for DakoCytomation Autostainer. NordiQC

  • CD68 - CD68 clone KP1 Protocol for Ventana NexES. NordiQC

  • CD68 - CD68 clone PG-M1 for Ventana NexES. NordiQC

  • CD68 - CD68 clone PG-M1 Protocol for DakoCytomation Autostainer. NordiQC

  • CD79a - CD79a clone JCB117 Protocol for LabVision Autostainer. NordiQC

  • CD79a - CD79a clone JCB117 for Ventana NexES. NordiQC

  • CD8 - CD8 clone 1A5 Staining Protocol for Ventana BenchMark

  • CD8 - CD8 clone 4B11 Staining Protocol for TechMate 500

  • CD8 - CD8 clone CD8/144B Staining Protocol for DakoCytomation Autostainer

  • CD99 - CD99 (12E7) NordiQC

  • CD99 12E7 - CD99 (12E7) Protocol for Autostainer. NordiQC

  • cDNA Microarray Protocol - This set of protocols is intended to serve as a basic introduction to making and using cDNA microarrays. There are three fundamental types of operations required in a cDNA microarray experiment. The first operation, BASIC PROTOCOL 1, cDNA AMPLIFICATION AND PRINTING, deals with making the cDNA microarray itself. BASIC PROTOCOL 2, RNA EXTRACTION AND LABELING, RNA is extracted from the cell samples to be examined, purified, and used as the substrate for reverse transcription in the presence of fluor-derivatized nucleotides. BASIC PROTOCOL 3, HYBRIDIZATION AND DATA EXTRACTION, covers the steps in which fluor-labeled cDNAs hybridize to their complements on the microarray, and the resulting localized concentrations of fluorescent molecules are detected and quantitated. (National Human Genome Research Institute)

  • CEA - CEA (ll-7) Protocol for Autostainer. NordiQC

  • CEA - CEA (ll-7) Protocol for Ventana Benchmark. NordiQC

  • CEA - CEA (Col-1) Protocol for Autostainer. NordiQC

  • Cedarlane Laboratories - Complement, Lympholyte cell separation media, cell purification Immunocolumns and a wide range of Antibodies. Custom Antibody Services.

  • Cell Marque - Antibodies, Bio Reagents, Detection Systems and Declere/Trilogy

  • Cell Pellet Protocol - Special Techniques Cell Pellet Protocol

  • Cell Sciences - Cell Sciences offers immunochemicals for life science research including recombinant cytokines, cytokine receptors, recombinant chemokines, chemically synthesized chemokines, cytokine ELISA and ELISPOT kits, plus associated monoclonal and polyclonal antibodies

  • Cell Signaling Technologies - Signal Transduction Research

  • Cemines - Antibodies to different transcription factors

  • Chemicon - Broad range of antibodies.

  • Chick, mouse, and Xenopus two colour whole mount ISH - Protocols from Oxford Practical Approach Series. Chick, mouse, and Xenopus two colour whole mount in situ hybridization staining with Fast Red and TrueBlue

  • Cholecystokinin (CCK) - Detection of Cholecystokinin (CCK) in Formalin-Fixed, Paraffin-Embedded, Rat Tissue

  • Chromogranin A - Chromogranin polyclonal, Protocol for DakoCytomation Autostainer

  • Chromogranin A - Chromogranin clone LK2H10 Protocol for DakoCytomation Autostainer. NordiQC

  • Chromogranin A - Chromogranin Polyclonal. Protocol for LabVision Autostainer. NordiQC

  • Chromogranin A - Chromogranin clone LK2H10+PHE5 Protocol for LabVision Immunostainer. NordiQC

  • Chromogranin A - Chromogranin clone LK2H10 + PHE5 Staining Protocol for LabVision Immunostainer. NordiQC

  • Chromogranin A - Chromogranin A clone LK2H10 Staining Protocol for Autostainer. NordiQC

  • Chromogranin A - Chromogranin A (polyclonal) Staining Protocol for Autostainer. NordiQC

  • Chromogranin A in Formalin-Fixed, Paraffin-Embedded Mouse Tissue - Identification of Chromogranin A in Formalin-Fixed, Paraffin-Embedded Mouse Tissue

  • Chromosome In Situ Hybridization using biotin labeled probes - Chromosome In Situ Hybridization using biotin labeled probes. Preparation of Chromosome Squashes

  • Chromosome preparation for ISH - Chromosome preparation for in situ hybridization (ISH)

  • Clonegene - Clonegene is your source for RNAi reagents. We have recently launched our monoclonal antibody to human Dicer , a key enzyme in RNAi and siRNA biology. Other products include monoclonal antibodies to HuR, HuD and Hu.

  • Co-labeling Using In Situ PCR - Co-labeling Using In Situ PCR: A Review

  • Co-Localization of Multiple Antigens and Specific DNA - Co-localization of proteins and nucleic acid sequences by in situ hybridization and immunohistochemistry is frequently difficult as the process necessary to detect the target structure of one technique may negatively affect the target of the other. Morphological impairment may also limit the application of the two techniques on sensitive tissue. To overcome these problems we developed a method to perform in situ hybridization and immunohistochemistry on semithin sections of methyl methacrylate-embedded tissue.

  • Complete Chromogen Separation and Analysis in Double Immunohistochemical Stains Using Photoshop - Complete Chromogen Separation and Analysis in Double Immunohistochemical Stains Using Photoshop-based Image Analysis

  • Conjugation of monoclonal antibodies - In this series of web pages, protocols, notes, and various illustrations are given to aid in the conjugation of proteins--principally monoclonal antibodies--to fluorescent dyes. These conjugation procedures are commonly performed in our laboratory--we have conjugated several hundred different monoclonals using almost all of the various dyes listed. The procedures are relatively straightforward and require only minimal familiarity with standard laboratory techniques (gel filtration and spectrophotometry are the most difficult!).

  • Control of Autofluorescence of Archival Formaldehyde-fixed, Paraffin-embedded Tissue - Confocal laser scanning microscopy (CLSM) offers the advantage of quasi-theoretical resolution due to absence of interference with out-of-focus light. Prerequisites include minimal tissue autofluorescence, either intrinsic or induced by fixation and tissue processing, and minimal background fluorescence due to nonspecific binding of the fluorescent label. To eliminate or reduce autofluorescence, three different reagents, ammonia–ethanol, sodium borohydride, and Sudan Black B were tested on paraffin sections of archival formaldehyde-fixed tissue.

  • Cortex Biochem - Cortex Biochem is a leading developer and manufacturer of innovative, versatile, and reliable products for Molecular Biology, Magnetic Separation and Immunodiagnostics. Our worldwide business channels support research scientists as well as molecular and clinical laboratories in their quest to advance basic research and improve commercial operations. The Company has proprietary molecular biology products as well as a wide array of purified antigens, proteins, enzymes, hormones and antibodies. Antibody for Infectious Disease and Reporter Gene research.

  • CovalAb - Manufacturer and supplier of polyclonal and monoclonal antibodies and synthetic peptides.

  • Covance Research Products - Provides antibody products and services.

  • Cox-1 - Detection of Cox-1 in Formalin-Fixed, Paraffin-Embedded in Mouse Tissue

  • Cox-2 - Detection of Cox2 in Formalin-Fixed, Paraffin-Embedded Rat and Mouse Tissue

  • Creating an interactive database for image viewing and data input - The major problem of using tissue microarray is how to simultaneously examine each core at the microscope, know its identity and input the score in a database next to the correct identifier. Here offers you simple methods of using Excel to achieve these goals. (Giorgio Cattoretti, Institute for Cancer Genetics, Columbia University)

  • Culture and harvesting of human metaphase chromosomes - Protocols from Oxford Practical Approach Series.

  • CureVac - CureVac is specialized in the production of all kinds of chemically and enzymatically synthesized RNA molecules for research and therapeutic use. The mission of the RNA peopleTM is to deliver reliable and innovative RNA-related services, products and pharmaceutical ingredients under GMP conditions for the life-science community.

  • Cyclin D1 - Detection of Cyclin D1 in Formalin-Fixed, Paraffin-Embedded, Rodent Tissue

  • Cyclin D1 - Cyclin D1 clone P2D11F11. Manual Protocol. NordiQC

  • Cyclin D1 - Cyclin D1 Rabbit Monoclonal SP4. Protocol for DakoCytomation Autostainer. NordiQC

  • Cyclin D1 - Cyclin D1 clone PD211F11. Protocol for DakoCytomation Autostainer. NordiQC

  • Cyclin D1 - Cyclin D1 clone P2D11F11. Protocol for DakoCytomation TechMate. NordiQC

  • Cyp1A1 - Detection of Cyp1A1 in Formalin-Fixed, Paraffin-Embedded, Rat Tissue

  • CYP4A in Formalin-Fixed, Paraffin Embedded Mouse Tissue - Detection of CYP4A in Formalin-Fixed, Paraffin Embedded Mouse Tissue

  • CYP4A in Formalin-Fixed, Paraffin Embedded Rat Tissue - Detection of CYP4A in Formalin-Fixed, Paraffin Embedded Rat Tissue

  • Cytokeratin (Wide Spectrum) in Formali-fixed, Paraffin-embedded Mouse Tissue - Detection of Cytokeratin (Wide Spectrum) in Formali-fixed, Paraffin-embedded Mouse Tissue

  • Cytokeratin (Wide Spectrum) in formali-fixed, paraffin-embedded rat tissue - Detection of Cytokeratin (Wide Spectrum) in formali-fixed, paraffin-embedded rat tissue

  • Cytokeratin 15 in Formalin-Fixed, Paraffin Embedded Mouse Tissue - Identification of Cytokeratin 15 in Formalin-Fixed, Paraffin Embedded Mouse Tissue

  • Cytokeratin 15 in Formalin-Fixed, Paraffin Embedded Rat Tissue - Identification of Cytokeratin 15 in Formalin-Fixed, Paraffin Embedded Rat Tissue

  • Cytokeratin 20 - Cytokeratin 20 clone Ks 20.8. Protocol for DakoCytomation Autostainer. NordiQC

  • Cytokeratin 20 - Cytokeratin 20 clone Ks 20.8. Protocol for Ventana NexES. NordiQC

  • Cytokeratin 20 - Cytokeratin 20 clone Ks 20.8. Protocol for TechMate. NordiQC

  • Cytokeratin 5 - Cytokeratin 5 (34BE12) Protocol for Ventana Benchmark

  • Cytokeratin 5 - Cytokeratin 5 (34BE12) Protocol for Ventana NexES. NordiQC

  • Cytokeratin 5 - Cytokeratin 5 (D5/16 B4) Protocol for DakoCytomation TechMate. NordiQC.

  • Cytokeratin 5 - Cytokeratin 5 (D5/16 B4) Protocol for Sequenza (manuel) NordiQC

  • Cytokeratin 5 - Cytokeratin 5 (XM26) Protocol for DakoCytomation TechMate. NordiQC

  • Cytokeratin 5 - Cytokeratin 5 (XM26) Protocol for Ventana BenchMark. NordiQC

  • Cytokeratin 5 and 8 in Formalin-Fixed, Paraffin Embedded in Rat Tissue - Detection of Cytokeratin 5 and 8 in Formalin-Fixed, Paraffin Embedded in Rat Tissue

  • Cytokeratin 5 in Formalin-Fixed, Paraffin Embedded Rodent Tissue - Identification of Cytokeratin 5 (Basal Cells) in Formalin-Fixed, Paraffin Embedded Rodent Tissue

  • Cytokeratin 7 - Cytokeratin 7 clone OV-TL 12/30. Protocol for DakoCytomation Autostainer. NordiQC

  • Cytokeratin 7 - Cytokeratin 7 clone OV-TL 12/30. Protocol for Ventana NexES. NordiQC

  • Cytokeratin 7 - Cytokeratin 7 clone K72.7. Protocol for LabVision Immunostainer

  • Cytokeratin 7 - Cytokeratin 7 clone K72. Protocol for Ventana BenchMark. NordiQC

  • Cytokeratin High Molecular Weight - Cytokeratin High Molecular Weight clone 34BE12. Protocol for DakoCytomation TechMate

  • Cytokeratin High Molecular Weight - Cytokeratin High Molecular Weight clone 34BE12. Manual Protocol. NordiQC

  • Cytokeratin Low Molecuar Weight - Cytokeratin Low Molecuar Weight clone DC 10. Protocol for DakoCytomation TechMate/Horizon. NordiQC

  • Cytokeratin Low Molecular Weight - Cytokeratin Low Molecular Weight clone 5D3. Protocol for TechMate. NordiQC

  • Cytokeratin Low Molecular Weight - Cytokeratin Low Molecular Weight clone CAM 5.2. Protocol for TechMate. NordiQC

  • Cytokeratin Low Molecular Weight - Cytokeratin Low Molecular Weight clone C-51. Protocol for TechMate. NordiQC

  • Cytokeratin Pan- - Pan Cytokeratin clone AE1/AE3 + 5D3. Protocol for TechMate. NordiQC

  • Cytokeratin Pan- - Pan Cytokeratin clone AE1/AE3. Protocol for DakoCytomation Autostainer. NordiQC

  • Cytokeratin Pan- - Pan Cytokeratin clone KL1. Protocol For DakoCytomation Horizon/TechMate. NordiQC

  • CytoLab - Cytokines and anti-cytokine antibodies

  • Cytoshop - Cytoshop specializes in on-line marketing and sale of biological recombinant products, such as Cytokines, Chemokines, Growth Factors, Neurotrophins, Hormones and Monoclonal Antibodies

  • Cytoskeleton - Cytoskeleton is pleased to offer researchers a continually expanding line for kits and products in signal transduction, tubulin, actin, drug sreening and antibodies.

  • CytoStore - CytoStore's mandate is to produce and market products for use within advanced medical and biomedical research laboratories world wide.

  • DAKO Handbook - Theory and application of immunlabelling techniques.

  • DakoCytomation - Development and production of antibodies, detection reagents and instruments for the diagnostic industry.

  • Delta Biolabs - Apoptosis - Cell Cycle - Protein Kinases -Transcription Regulation

  • Denaturation of DNA in ultrathin sections of Lowicryl K4M embedded material - Protocols from Oxford Practical Approach Series.

  • Desmin - Desmin clone D33. Protocol for TechMate. NordiQC

  • Desmin - Desmin clone DE-R-11. Protocol for DakoCytomation Autostainer. NordiQC

  • Desmin in Formalin-Fixed, Paraffin Embedded Rat and Mouse Tissue - Detection of Desmin in Formalin-Fixed, Paraffin Embedded Rat and Mouse Tissue

  • Detection and amplification of FISH signal - Protocols from Oxford Practical Approach Series.

  • Detection of Glucagon in Formalin-Fixed, Paraffin-Embedded, Rodent and Human Pancreas - Detection of Glucagon in Formalin-Fixed, Paraffin-Embedded, Rodent and Human Pancreas

  • Detection of Integrins in Formalin-fixed, Paraffin-embedded Tissues - The purpose of this study was to determine the optimal conditions for detection of integrins in formalin-fixed, paraffin-embedded tissues. We utilized microwave heating and enzyme digestion in routinely processed, surgically removed tissues. Our results demonstrate that integrins can be reliably detected in archival material.

  • Detection of mRNA by in situ hybridization - The following page describes the current favorite non-radioactive in situ hybridization technique used by Dr. G.V. Childs at the University of Arkansas for Medical Sciences to detect mRNAs in whole pituitary cells grown in culture.

  • Detection of multiply spliced HIV-1 tat mRNA by RT-PCR in situ hybridization - Protocols from Oxford Practical Approach Series.

  • Detection of single-copy HIV-1 DNA by PCR in situ hybridization - Protocols from Oxford Practical Approach Series.

  • Detection of single-copy HIV-1 DNA using Real-Time (Taqman) PCR in situ - Protocols from Oxford Practical Approach Series.

  • Detection of Viral Infection and Gene Expression in Clinical Tissue Specimens Using Branched DNA - Detection of Viral Infection and Gene Expression in Clinical Tissue Specimens Using Branched DNA (bDNA) In Situ Hybridization

  • Diaclone - Diaclone produces a large panel of monoclonal antibodies and kits to detect human, mouse and rat molecules playing key roles in the immune system (CDs, cytokines and adhesion molecules).

  • Diagnostic Biosystems - Antibodies, Kits and Accessory Products

  • Diagnostic Systems Laboratories - IGF and IGFBP polyclonal and monoclonal antibodies

  • DiaSorin - Large selection of antibodies.

  • Diatec - Broad range of Antibobodies

  • Differential Expression of RNA and Protein of the Three Pore-forming Subunits of the Amiloride-sensi - Differential Expression of RNA and Protein of the Three Pore-forming Subunits of the Amiloride-sensitive Epithelial Sodium Channel in Taste Buds of the Rat

  • DIG & Biotin RNA Double Labeling - Whole Mount In Situ Protocol for DIG & Biotin RNA Double Labeling

  • DIG-labeled probe - In Situ Hybridization using DIG-labeled probe, Detection by AP (alkaline phosphatase), FITC or rhodamine. Paraffin Sections.

  • Distinct expression patterns of ER and ERß in normal human mammary gland - Two oestrogen receptors (ERs) have been identified to date—the "classic" ER and the more recently described ERß. Although much is known about ER at the mRNA and protein levels, our knowledge of the expression and distribution of ERß protein is much more limited. The aim of this study was to compare the cellular distribution of ER and ERß in normal human mammary gland.

  • DNA Extraction from Archival Formalin-fixed, Paraffin-embedded Tissue Sections - DNA Extraction from Archival Formalin-fixed, Paraffin-embedded Tissue Sections Based on the Antigen Retrieval Principle: Heating Under the Influence of pH

  • Double Autoimmunostaining with Glycine Treatment - Double Autoimmunostaining with Glycine Treatment

  • Double immunofluorescence - Any type of tissue is suitable for this technique, as long as the antigenicity for your antigen(s) is preserved. Use cytocentrifuged cells or frozen or paraffin dewaxed sections.

  • Double Immunofluorescent Procedure - Double Immunofluorescent Procedure Using Two Biotinylated Secondary Antibodies and Avidin D Fluorochrome Conjugates (Fluorescein and Texas Red)

  • Dss1 in Formalin-fixed, Paraffin-embedded Mouse Tissue - Detection of Dss1 in Formalin-fixed, Paraffin-embedded Mouse Tissue

  • Dual Fluorescent In Situ Hybridization and Immunohistochemical Detection with TSA - In this article we describe a method for performing dual mRNA ISH and antigen IHC on either frozen or paraffin-embedded sections using fluorescent TSA techniques. We used this method to examine the relationship between GFR2 mRNA expression and Ret protein immunoreactivity in the developing mouse nervous system and GFR2 mRNA expression and NeuN immunoreactivity in the adult mouse brain.

  • Dutch Diagnostics - A worldwide (OEM) distributor of immunodiagnostic products for use in clinical laboratories

  • E-cadherin on Formalin-Fixed, Paraffin-Embedded Rat Tissue - Detection of E-cadherin on Formalin-Fixed, Paraffin-Embedded Rat Tissue

  • eBioscience - Human, Mouse and Rat Immunology and Cytokine Research

  • Echelon Biosciences - Phosphoinositide monoclonal antibodies

  • ED2 in Formali-Fixed, Paraffin-Embedded Rat Tissue - Identification of ED2 in Formali-Fixed, Paraffin-Embedded Rat Tissue

  • Effect of Fixation and Epitope Retrieval on BrdU Indices in Mammary Carcinomas - As with all IHC methods, a persistent concern is choosing the correct fixative and duration of fixation that will provide minimal loss of antigenicity with maximal preservation of tissue morphology. This issue is particularly relevant to the detection of the BrdU epitope because studies in which BrdU is used are conducted prospectively. Therefore, the opportunity exists to select conditions that optimize epitope detection.

  • Effect of Fixatives and Tissue Processing on the Content and Integrity of Nucleic Acids - The purpose of this review is to provide an overview of the methods of human tissue acquisition, fixation, and preservation. In addition, the parameters of procurement and fixation that affect the quality of the tissues at the molecular level are discussed.

  • EnCor Biotechnology - Specializing in monoclonal antibodies to yeast proteins and mammalian cytoskeletal proteins, including chicken antibodies suitable for double and triple label immunocytochemistry

  • Endocrine Technologies - Endocrine Technologies is dedicated to research, development, manufacture and distributiong of innovative new scientific discovery tools, diagnostic products and therapies for researchers and physicians in both human healthcare and veterinary healthcare.

  • eNOS in Formalin-Fixed, Paraffin-Embedded Rat Tissue - Detection of eNOS in Formalin-Fixed, Paraffin-Embedded Rat Tissue

  • EnVision+, a New Dextran Polymer-based Signal Enhancement Technique for In Situ Hybridization - Key Words: EnVision+, dextran polymer conjugate, biotinyl–tyramide, GenPoint+, in situ signal amplification, In Situ Hybridization (ISH)

  • Enzo - Enzo Life Sciences, the source for nonradioactive labeling and detection, is a leading worldwide enabler of microarray technologies in gene expression and genomic analysis applications.

  • Epithelial antigen Ber-EP4 - Epithelial antigen clone Ber-EP4. Protocol for DakoCytomation TechMate. NordiQC

  • Epithelial antigen Ber-EP4 - Epithelial antigen clone Ber-EP4. Protocol for TechMate. NordiQC

  • Epithelial Membrane Antigen (EMA) - Epithelial Membrane Antigen (EMA) clone E29. Protocol for DakoCytomation Autostainer. NordiQC

  • Epithelial Membrane Antigen (EMA) - Epithelial Membran Antigen (EMA) clone E29. Manual Protocol

  • Epithelial Membrane Antigen (EMA) - Epithelial Membran Antigen (EMA) clone E29. Protocol for DakoCytomation Autostainer. NordiQC

  • Epithelial Membrane Antigen (EMA) - Epithelial Membrane Antigen (EMA) clone E29. Protocol for TechMate. NordiQC

  • Epitomics - Rabbit and mouse monoclonal antibodies

  • ePitope Informatics - An Internet-based, applied bioinformatics company specialising in the prediction and analysis of protein B cell epitopes

  • Estrogen Receptor (ER) - Estrogen Receptor (ER) clone SP1. Protocol for DakoCytomation Autostainer. NordiQC

  • Estrogen Receptor (ER) - Estrogen Receptor (ER) clone 1D5. Protocol for DakoCytomation Autostainer. NordiQC

  • Estrogen Receptor (ER) - Estrogen Receptor (ER) clone 6F11. Protocol for DakoCytomation Autostainer. NordiQC

  • Estrogen Receptor (ER) - Estrogen Receptor (ER) clone 6F11. Protocol for Ventana NexES. NordiQC

  • Estrogen Receptor (ER) - Estrogen Receptor clone 6F11 Staining Protocol for Autostainer. NordiQC

  • Estrogen Receptor (ER) - Estrogen Receptor clone 1D5 Staining Protocol for TechMate 500+. NordiQC

  • Estrogen Receptor (ER) - Estrogen Receptor clone SP1 Staining Protocol for BenchMark XT. NordiQC

  • Estrogen Receptor (ER) Alpha in Formalin-Fixed, Paraffin-Embedded Mouse Tissue - Detection of Estrogen Receptor Alpha in Formalin-Fixed, Paraffin-Embedded Mouse Tissue

  • Estrogen Receptor (ER) Alpha in Formalin-Fixed, Paraffin-Embedded Rat Tissue - Detection of Estrogen Receptor (ER) Alpha in Formalin-Fixed, Paraffin-Embedded Rat Tissue

  • Eurogentec - Custom oligos, RNAi - siRNA, Real-Time PCR and Custom protein tools and services

  • Exbio - EXBIO manufactures and supplies antibodies for world-wide distribution. Sales on an OEM basis and in bulk quantity is the core business activity of the company. Strong Research & Development (hybridoma technology, construction of recombinant proteins and antibodies) in co-operation with academic institutions ensures the continuous addition of important new products.

  • Exiqon - Provider of high performance technologies for nucleic acid detection and identification in the life-sciences market.

  • Expression of vascular endothelial growth factor C and chemokine receptor CCR7 in gastric carcinoma - AIM: To study the expression of vascular endothelial growth factor C (VEGF-C) and chemokine receptor CCR7 in gastric carcinoma and to investigate their associations with lymph node metastasis of gastric carcinoma and their values in predicting lymph node metastasis.

  • EY Laboratories - Manufacturer of biochemical reagents serving the needs of biochemical research in glycobiology, immunology, and microbiology.

  • FISH hybridization and subsequent washes - Protocols from Oxford Practical Approach Series.

  • Fixation and pre-treatment of embryos for whole mount hybridization - Protocols from Oxford Practical Approach Series.

  • Fixation and sectioning of cryosections for mRNA detetcion - Protocols from Oxford Practical Approach Series.

  • Fixation and storage of mouse embryos for mRNA detection - Protocols from Oxford Practical Approach Series.

  • FLAG in Formalin-Fixed, Paraffin Embedded RodentTissue - Detection of FLAG in Formalin-Fixed, Paraffin Embedded RodentTissue

  • Fluorescence In Situ Hybridization (FISH) - Fluorescence In Situ Hybridization (FISH) on human chromosomes and interphase nuclei.

  • Fluorescence In Situ Hybridization and Catalyzed Reporter Deposition - Fluorescence In Situ Hybridization and Catalyzed Reporter Deposition for the Identification of Marine Bacteria

  • Fluorescence in situ hybridization: past, present and future - Fluorescence in situ hybridization (FISH), the assay of choice for localization of specific nucleic acids sequences in native context, is a 20-year-old technology that has developed continuously.

  • Fluorescence Mounting Medium (Antifade) - Fluorescence Mounting Medium (Antifade) from Spector Lab

  • Fluorescent Histochemical Techniques for Analysis of Intracellular Signaling - Intracellular signaling relies on the orchestrated cooperation of signaling proteins and modules, their intracellular localization, and membrane trafficking. Recently, a repertoire of fluorescence-based techniques, which significantly increases our potential for detailed studies of the involved mechanisms, has been introduced. Microscopic techniques with increased resolution have been combined with improved techniques for detection of signaling proteins. Transfections of fluorescently tagged proteins have allowed in vivo microscopy of their trafficking and interactions with other proteins and intracellular structures. We present an overview of general signaling principles and a description of techniques based on fluorescent microscopy suited for studies of signaling mechanisms.

  • Fluorescent in situ Hybridization (FISH) - This page briefly presents the fluorescent in situ hybridization technique (FISH). This technique is used for the detection of target molecules with a system of coupled antibodies and fluorochromes.

  • Fluorescent in situ Hybridization (FISH) - Fluorescent in situ Hybridization (FISH) protocol from Sigma-Aldrich

  • Fluorescent in situ hybridization (FISH) - ULS(TM)-dGreen and ULS(TM)-Rhodamine labeled probes for translocation, locus specific and chromosome copy number detection

  • Focus: Monoclonal Antibodies and therapies - Since they were first reported in 1975, monoclonal antibodies have developed from tools in basic research, to diagnostic agents, and more recently, with humanization, to the status of bona fide therapeutic agents. Nature Biotechnology, Nature Medicine and Nature Cell Biology present a focus on monoclonal antibodies, covering basic, technological and clinical aspects of their use, and stretching across fields that range from transplantation tolerance to colon cancer.

  • Frimorfo - Frimorfo’s focus and expertise lies in phenotyping of genetically engineered animals and diagnostic pathology of animal and human tissues. In addition Frimorfo leverages a network of experts in the field of genetically engineered animals (GEA). This network covers GEA generation, breeding and chararcterization.
    Offers comprehensive histological analysis and diagnosis worldwide.

  • Gene Tex Inc - Our very first products were directed toward breast cancer research and prognosis. More recently, we have added tools for scientists studying basic mechanisms common to many forms of cancer. These research tools include immunological reagents used to study specific proteins and events involved in the regulation of the cell cycle and DNA repair and replication.

  • GeneDetect - World's largest selection of gene probes.

  • GeneDetect Laboratory Protocols - In Situ Hybridization protocols optimized for use with GeneDetect ® products.

  • General Drosophila Whole-Mount Histochemical Staining Method - General Drosophila Whole-Mount Immunohistochemistry Protocol

  • Genesis Biotech - Products covering synthesis of peptides and phosphopeptides, generation of anti-peptide mono-/poly- clonal antibody and hundreds of catalog antibodies to tumor marker (TEM, PRL-3), growth factor, G-protein receptors, SARS-Co-V, influenza A virus, human/animal disease (WSSV), oxidative stress (8-OH dG). We can produce peptides on the large scale and we synthesize modified peptides or peptide libraries.

  • GFAP in Formalin-Fixed, Paraffin-Embedded Mouse Tissue - Detection of GFAP in Formalin-Fixed, Paraffin-Embedded Mouse Tissue

  • GFAP in Formalin-Fixed, Paraffin-Embedded Rat Tissue - Detection of GFAP in Formalin-Fixed, Paraffin-Embedded Rat Tissue

  • Glial Fibrillary Acidic Protein (GFAP) - Glial Fibrillary Acidic Protein (GFAP) polyclonal. Protocol for DakoCytomation Autostainer. NordiQC

  • Glial Fibrillary Acidic Protein (GFAP) - Glial Fibrillary Acidic Protein (GFAP) clone 6F2. Protocol for DakoCytomation Autostainer. NordiQC

  • Glial Fibrillary Acidic Protein (GFAP) - Glial Fibrillary Acidic Protein (GFAP) clone 6F2 Staining Protocol for Autostainer. NordiQC

  • Glial Fibrillary Acidic Protein (GFAP) - Glial Fibrillary Acidic Protein (GFAP) clone GA5 Protocol for manual staining. NordiQC

  • Glial Fibrillary Acidic Protein (GFAP) - Glial Fibrillary Acidic Protein (GFAP) PolyclonalStaining Protocol for TechMate500+. NordiQC

  • Glial Fibrillary Acidic Protein (GFAP) - Glial Fibrillary Acidic Protein (GFAP) Polyclonal. Protocol for manual staining. NordiQC

  • GreenStar* BIOTIN-labeled probe - In Situ Hybridization using GreenStar* BIOTIN-labeled probe in paraffin sections. Detection by AP (alkaline phosphatase) or HRP (Horseradish Peroxidase) with or without tyramide signal amplification (TSA).

  • GreenStar* BIOTIN-labeled probe - In Situ Hybridization using GreenStar* BIOTIN-labeled probe in frozen sections. Detection by AP (alkaline phosphatase) or HRP (Horseradish Peroxidase) with or without tyramide signal amplification (TSA).

  • GreenStar* DIG-labeled probe - In Situ Hybridization using GreenStar* DIG-labeled probe in paraffin sections. Detection by direct fluorescence, AP (alkaline phosphatase) or tyramide signal amplification (TSA).

  • GreenStar* DIG-labeled probe - In Situ Hybridization using GreenStar* DIG-labeled probe in frozen sections. Detection by direct fluorescence, AP (alkaline phosphatase) or tyramide signal amplification (TSA).

  • GreenStar* FITC-labeled probe - In Situ Hybridization using GreenStar* FITC-labeled probe, Detection by direct fluorescence, AP (alkaline phosphatase) or tyramide signal amplification (TSA). Frozen Sections.

  • Griffonia Simplicifolia Isolectin B4 (IB4) - Griffonia Simplicifolia Isolectin B4 (IB4) HRP-Conjugate Protocol

  • Groovy Blue Genes Biotech Ltd. - We offer products covering the areas of cell immunophenotyping, cytokines and chemokines, cell biology, adhesion, phosphorylation, cancer research, and apoptosis. Reagents are for use in a variety of research applications including flow cytometry, ELISA, IP, Western blotting, immunofluorescence microscopy, IHC, and functional assays

  • GSTpi in Formalin-Fixed, Paraffin-Embedded Rat Tissue - Detection of GSTpi in Formalin-Fixed, Paraffin-Embedded Rat Tissue

  • HA.11 in Formalin-Fixed, Paraffin-Embedded in Mouse Tissue - Detection of HA.11 in Formalin-Fixed, Paraffin-Embedded in Mouse Tissue

  • Handbook of Fluorescent Probes and Research Products - This Web Edition of the Handbook is an updated version of the Ninth Edition and is presented in two formats. Sections in "standard" format load into browsers quickly and contain links to all of the tables, figures and images. Sections in "printer-friendly" format include tables, figures and images together with the text and are specifically designed for printing and offline reading.

  • High-density Hapten Labeling and HRP Conjugation of Oligonucleotides for Use as ISH Probes - High-density Hapten Labeling and HRP Conjugation of Oligonucleotides for Use as In Situ Hybridization Probes to Detect mRNA Targets in Cells and Tissues

  • High-resolution In Situ Hybridization and TUNEL Staining with Free-floating Brain Sections - High-resolution In Situ Hybridization and TUNEL Staining with Free-floating Brain Sections

  • Histone H2A.X in Formalin-Fixed, Paraffin-Embedded MouseTissue - Detection of Histone H2A.X in Formalin-Fixed, Paraffin-Embedded MouseTissue

  • Human Chorionic Gonadotropin (HCG) - Human Chorionic Gonadotropin (HCG) polyclonal. Protocol for DakoCytomation Autostainer. NordiQC

  • Human Chorionic Gonadotropin (HCG) - Human Chorionic Gonadotropin (HCG) polyclonal. Protocol for DakoCytomation Autostainer. NordiQC

  • Human Chorionic Gonadotropin (HCG) - Human Chorionic Gonadotropin (HCG) polyclonal. Protocol for DakoCytomation TechMate. NordiQC

  • Human Chorionic Gonadotropin (HCG) - Human Chorionic Gonadotropin (HCG) polyclonal. Protocol for DakoCytomation Autostainer. NordiQC

  • Hybridization of mouse embryo sections for mRNA detection - Protocols from Oxford Practical Approach Series.

  • Hybridization of sections, washing, and detection of probe - Protocols from Oxford Practical Approach Series.

  • Hybridization solution: composition, heat treatment prior to post-embedding ish - Protocols from Oxford Practical Approach Series.

  • HyCult biotechnology - HyCult biotechnology (Hbt) is a leading supplier of antibodies and reagents for research laboratories. HyCult biotechnology specializes in PLUS QUALITY reagents for studies in the following fields: Innate immunity, TLR, complement, scavenger receptors,,Endotoxin & other microbial toxins,,Cell- and tissue damage,,Coagulation,,Tight junctions and adhesion molecules,,Cell biology, oxidation damage and tumor markers,,Inflammation, Cytokines and chemokines

  • Ian's Home Page - Exploring the functional neuroanatomy of neuronal nicotinic acetylcholine receptors

  • ICAM (M-19) Formalin-Fixed, Paraffin Embedded Rodent - Identification of ICAM (M-19) in Formalin-Fixed, Paraffin Embedded Rodent Tissue

  • Identification of Neomycin in Formalin-Fixed Paraffin Embedded Mouse Tissue - Identification of Neomycin in Formalin-Fixed Paraffin Embedded Mouse Tissue

  • IGF-1 in Formalin-Fixed, Paraffin-Embedded Rat Tissue - Identification of IGF-1 in Formalin-Fixed, Paraffin-Embedded Rat Tissue

  • IGF-1 receptor-beta in Formalin-Fixed, Paraffin Embedded Mouse Tissue - Identification of IGF-1 receptor-beta in Formalin-Fixed, Paraffin Embedded Mouse Tissue

  • IgG in Formalin Fixed Paraffin Embedded Mouse Tissue - Detection of Mouse IgG in Formalin Fixed Paraffin Embedded Mouse Tissue

  • IHC protocol for free floating brain sections - IHC protocol for free floating brain sections

  • IL1 alpha in PLP Fixed Mouse Tissue - Identification of IL1 alpha in PLP Fixed Mouse Tissue

  • IL1 beta in PLP-Fixed, Paraffin-Embedded Mouse Tissue - Identification of IL1 beta in PLP-Fixed, Paraffin-Embedded Mouse Tissue

  • Immunofluorescence - Immunofluorescence of C. elegans Embryos

  • Immunofluorescence labelling of neurobiotin-filled electrophysiology slices - Integrating electrophysiological studies with immunolabelling is an easy way to generate more data from an experiment. During electrophysiological recordings, neurones are filled with neurobiotin and then subsequently fixed. This protocol describes how to detect the neurobiotin using immunofluorescence and co-label with other proteins. Ian Jones, PhD University of Bath, UK

  • Immunofluorescence Procedure for Staining Cryosection with Two Mouse Monoclonal Promary Antibodies - An Indirect Immunofluorescence Procedure for Staining the Same Cryosection with Two Mouse Monoclonal Primary Antibodies

  • Immunofluorescence Protocol for Cells - This protocol describes our method for preparing cells for immunofluorescence, in which all incubations and washes are performed in microtiter dishes. Two dishes can be processed simultaneously. The last step is to transfer each sample to a well on a polylysine coated 8-well slide for visualization. The protocol can also easily be adapted for preparing cells for immunofluorescence in microfuge tubes.

  • Immunofluorescence Protocol for Confocal Microscopy - Immunofluorescence Protocol for Confocal Microscopy

  • Immunofluorescence Protocol for Cultured Cells - Immunofluorescence Protocol for Cultured Cells

  • Immunofluorescence Protocols - Immunofluorescence Protocols from Biovisa

  • Immunofluorescence Technique - Immunofluorescence Technique (Spector Lab)

  • Immunofluorescence- Whole Mount - Immunohistochemistry allows visualization of antigens (usually proteins) within an embryo. Typically, a primary antibody binds specifically to an antigen (e.g. Luciferase); then a secondary antibody conjugated to a flourochrome or enzyme is bound to the heavy chain constant region of the primary antibody with specificity to the species of origin of the primary (e.g. anti-rabbit conjugated to Rhodamine).

  • Immunofluroescence Technique - Immunofluroescence Technique (Spector Lab)

  • Immunoflurorescence Analysis - Staining Protocols - Antigen expression, both extracellular and intracellular, can be quantitated using fluorescently-labelled antibodies or ligands directed towards these biomolecules. Over the past few years, the introduction of novel fluorochromes with unique spectral (excitation and emission) properties has facilitated the use of multicolour immunofluorescence analysis permitting the identification and characterisation of specific subpopulations of cells. Furthermore, this has also facilitated the combination of flow cytometric assays for both phenotype and function.

  • Immunohistochemical Detection of Interferon-gamma: Fake or Fact? - Immunohistochemistry is a widely accepted tool to investigate the presence and immunolocalization of cytokines in tissue sections at the protein level. We have tested the specificity and reproducibility of IFN immunohistochemistry on tissue sections with a large panel of anti-IFN antibodies. Thirteen different commercially available anti-IFN antibodies, including seven advertised and/or regularly applied for immunohistochemistry/-cytochemistry, were tested using a three-step streptavidin–biotin–peroxidase technique and a two-step immunofluorescence (FACS) analysis.

  • Immunohistochemical Identification of Estrogen and Progesterone Receptor - This article describes an immunohistochemical protocol used in our laboratory for the detection of ER and PR in routinely processed, paraffinembedded tissue that has produced consistent, reproducible, and easy-to-interpret results.

  • Immunohistochemical Recognition of Human Follicular Dendritic Cells - Immunohistochemical Recognition of Human Follicular Dendritic Cells (FDCs) in Routinely Processed Paraffin Sections

  • Immunohistochemistry Protocol - General immunohistochemistry protocol for formalin fixed paraffin embedded tissues.

  • Immunohistochemistry vade mecum - An excellent piece of work by Dr. Paul W. Bishop
    You can search for tumours to find out their pattern of immunoreactivity or look for individual antibodies to check their specification. There are links to all the references through PubMed. This amazing programme is small, easy to install and runs on any PC.

  • Immunohistochemistry/Immunocytochemistry Procedures (Chemicon) - Specimen Preparation, Antigen Retrieval, Antibody Staining, Antibody Detection, General Protocol for Immunohistochemical Staining and Troubleshooting

  • Immunolocalization by avidin biotinylated enzyme complex staining of zebrafish embryos after ish - Protocols from Oxford Practical Approach Series.

  • Immunolocalization by the peroxidase anti-peroxidase (PAP) method after ish - Protocols from Oxford Practical Approach Series.

  • Immunolocalization with a horse-radish peroxidase-conjugated secondary antibody after ish - Protocols from Oxford Practical Approach Series.

  • ImmunologicalsDirect - Buy antibodies online! Choose from thousands of antibodies in stock

  • Immunophenotyping simultaneously with RT-PCR in situ hybridization, DNA-PCR ish, and ish - Protocols from Oxford Practical Approach Series.

  • ImmunoQuest - We manufacture and license cutting edge antibodies in the Cell Biology field, in areas that are emerging as foci for basic scientific research. Nuclear Processes, Cell Cycle, Protein folding & Human disease, Phenotypic markers for cancer and Stem Cell Differentiation

  • Immunostaining Drosophila Embryos - Immunohistochemistry Protocol for Drosophila Embryos

  • ImmunoStar - Antibodies for Neuroscience Research

  • ImmunoVision Technologies - Primary Antibodies and PowerVision Detection Systems

  • Improved Immunodetection of Nuclear Antigens - Improved Immunodetection of Nuclear Antigens After Sodium Dodecyl Sulfate Treatment of Formaldehyde-fixed Cells

  • In Situ Characterization of Genetically Targeted (Green Fluorescent) Single Cells - In Situ Characterization of Genetically Targeted (Green Fluorescent) Single Cells and Their Microenvironment in an Adoptive Host

  • In Situ Hybridization - Collection of ISH/FISH Protocols from Protocol Online.

  • In Situ Hybridization AT-Tailing with Catalyzed Signal Amplification - In Situ Hybridization AT-Tailing with Catalyzed Signal Amplification for Sensitive and Specific in Situ Detection of Human Immunodeficiency Virus-1 mRNA in Formalin-Fixed and Paraffin-Embedded Tissues

  • In Situ Hybridization Detection Systems (Vector Laboratories) - Several different fluorescent or enzyme-based systems are used for detecting labeled nucleic acid probes. These options provide the researcher with flexibility in optimizing experimental systems to achieve highest sensitivity, to avoid potential problems such as endogenous biotin or enzyme activity, or to introduce multiple labels in a single experiment. Such factors as tissue fixation, endogenous biotin or enzyme activity, desired sensitivity, and permanency of record should all be considered when choosing both the optimal probe label and subsequent detection system.

  • In Situ Hybridization Digoxigenin and Fluorecein labeled cRNA Probes - In Situ Hybridization Digoxigenin and Fluorecein labeled cRNA Probes with double label addendum

  • In situ hybridization of DIG-labelled RNA probes - Paraffin and Cryo-sections Protocols by Carin Lundmark

  • In situ hybridization of mammalian cells - In situ hybridization of mammalian cells (RNA and Oligonucleotide probes)

  • In Situ Hybridization of mRNA and Immunofluorescence - Corbett Lab: In Situ Hybridization of mRNA and Immunofluorescence

  • In situ hybridization of yeast cells - In situ hybridization of yeast cells (RNA and Oligonucleotide probes)

  • In Situ Hybridization on Frozen Sections - Protocol by Josiah N. Wilcox, Ph.D.

  • In situ Hybridization on imaginal discs - In situ Hybridization on imaginal discs, with option of histochemical or fluorescence visualization.

  • In Situ Hybridization to Tissue Sections - In Situ Hybridization to Tissue Sections (Kornberg et al., Cell 40:45, 1985)

  • In Situ Hybridization Using Digoxigenin Labeled Probes - Berkeley Drosophila Genome Project

  • In Situ Hybridization with Nanogold®-Streptavidin - The small size of Nanogold® probes, their lack of aggregation and their consequent ability to access nuclear antigens makes them an excellent reagent for ultrasensitive in situ hybridization detection of specific DNA sequences both with and without in situ PCR.

  • In Situ Hybridization with RNA Probes - Embryo fixation, Preparing DNA to make RNA probes, Probe synthesis and Hybridization

  • Increased Concentrations of Radioisotopically-labeled Complementary Ribonucleic Acid Probe, Dextran - Increased Concentrations of Radioisotopically-labeled Complementary Ribonucleic Acid Probe, Dextran Sulfate, and Dithiothreitol in the Hybridization Buffer Can Improve Results of In Situ Hybridization Histochemistry

  • iNOS in Formalin-Fixed, Paraffin Embedded Rat Tissue - Detection of iNOS in Formalin-Fixed, Paraffin Embedded Rat Tissue

  • Insitus Biotechnologies - FISH and Tissue Microarray

  • Insulin Rodent and Human Tissues - Detection of Insulin in Formalin-Fixed, Paraffin-Embedded, Rodent and Human Pancreas

  • Introduction to Antibodies - An online technical resource describing the basics behind various antibody based protocols such as immunoprecipitation, Western blotting, ELISA, and immunohistochemistry

  • Invitrogen (Zymed) - Antibodies, Probes, Automation, Detection Kits and Ancillary Reagents

  • Jackson ImmunoResearch Laboratories - Jackson ImmunoResearch Laboratories, Inc., specialises in the production and conjugation of affinity-purified, secondary antibodies and purified immunoglobulins.

  • Journal of Clinical Pathology - Journal of Clinical Pathology is a leading international journal covering all aspects of pathology. Diagnostic and research areas covered include histopathology, virology, haematology, microbiology, cytopathology, chemical pathology, molecular pathology, forensic pathology, dermatopathology, neuropathology and immunopathology. Each issue contains Reviews, Original articles, Short reports, Case reports, Correspondence, Book reviews and more. JCP has Editorial Board members from all around to world to ensure coverage of global research.

  • Journal of Histochemistry and Cytochemistry - The Journal of Histochemistry and Cytochemistry, the official Journal of the Histochemical Society, publishes papers that report the development of new histochemical and cytochemical methods, significant modifications of existing techniques, or original research in which histochemical and cytochemical methods make a significant contribution.

  • Ki 67 (MIB 5) in Formalin-Fixed, Paraffin-Embedded Rat Tissue - Detection of Ki 67 (MIB 5) in Formalin-Fixed, Paraffin-Embedded Rat Tissue

  • Ki 67 (TEC-3) in Formalin-Fixed, Paraffin-Embedded Mouse Tissue - Detection of Ki 67 (TEC-3) in Formalin-Fixed, Paraffin-Embedded Mouse Tissue

  • Ki67 - Ki67 clone MIB-1. Protocol for DakoCytomation Autostainer. NordiQC

  • Ki67 - Ki67 clone MIB-1. Protocol for TechMate. NordiQC

  • Kreatech Diagnostics - Probes and detection kits

  • Lab Vision - Antibodies, Instrumentation, IHC Detection Systems and Ancillary Products

  • Labelling of probes for FISH by nick translation - Protocols from Oxford Practical Approach Series.

  • Labfrontier - ROS - Signaling (Reactive Oxygen Species Signaling) - Antibodies and Antigens

  • List of Antibodies tested on Mouse Tissue - List of antibodies tested on mouse

  • Localization of Monoamine Oxidase mRNA in Human Placenta - Localization of Monoamine Oxidase mRNA in Human Placenta

  • Making Monoclonal Antibodies - How to make a monoclonal antibody - a techniques oriented guide

  • Marck’s Protein in Rodent Tissue - Detection of Marck’s Protein in Formalin-Fixed, Paraffin Embedded Rodent Tissue

  • Melan-A - Melan-A clone A103. Protocol for DakoCytomation Autostainer. NordiQC

  • Melan-A - Melan-A clone A103. Protocl (2) for DakoCytomation Autostainer. NordiQC

  • Melan-A - Melan-A clone M2-7C10 + M2-9E3. Protocol for LabVision Immunostainer. NordiQC

  • Melanosoma antigen (HMB-45) - Melanosoma antigen clone HMB-45. Protocol for Optimax Immunostainer. NordiQC

  • Melanosoma antigen (HMB-45) - Melanosoma antigen clone HMB-45. Protocol for DakoCytomation Autostainer. NordiQC

  • Melanosoma antigen (HMB-45) - Melanosoma antigen clone HMB-45. Protocol (2) for DakoCytomation Autostainer. NordiQC

  • Melanosoma antigen (HMB-45) - Melanosoma antigen clone HMB-45. Protocol for LabVision Immunostainer. NordiQC

  • Merck Biosciences - Distributor of an extensive range of monoclonal and polyclonal antibodies, secondary antibodies and their conjugates, plus many accessory products for immunoassay and immunoseparation.

  • Microarray Protocol - A set of protocols for microarray experiments: Reagents & Equipments/Labelling/Purification/Hybridisation/Washing

  • Microarray Protocols - Detailed protocols for microarray experiments. Overview, Slide Preparation, Directions for Printing Arrays, DNA Preparation, Nucleic Acid Preparation, Nucleic Acid Labelling, Array Post Processing, Array Hybridization, Scanning Microarrays, Tips & Tricks (microarrays.org)

  • Mike's Immunoglobulin Structure/Function Home Page - Contains animated pictures of antibodies, downloadable PDB files of antibodies, a review on the humanisation of monoclonal antibodies, and many more educational links

  • Mismatch repair in appendiceal tumors - We investigated whether tumors arising in the appendix are associated with defective DNA mismatch repair using immunohistochemistry for mismatch repair enzymes hMLH-1, hMSH-2, hMSH-6, and hPMS-2.

  • MLH1 - Mismatch repair proteins MLH1 clone G168-15 Staining Protocol for Autostainer. NordiQC

  • MLH1 - Mismatch repair proteins MLH1 clone G168-15 Staining Protocol for Autostainer. NordiQC

  • MLH1 - Mismatch repair proteins MLH1 clone G168-15 (BD Pharmingen) Staining Protocol for Autostainer. NordiQC

  • MLH1 - Mismatch repair proteins MLH1 clone G168-15 Staining Protocol for TechMate 500. NordiQC

  • Modern Pathology - Modern Pathology is the official journal of the United States and Canadian Academy of Pathology (USCAP). Modern Pathology is available as both a print and online journal. After 17 years, the journal's main focus remains the publication of peer-reviewed original papers reporting innovative clinical and translational research in the pathology of human disease.

  • Molecular Probes - Provider of fluorescence-based detection products

  • Monoclonal Antibodies - Monoclonal Antibodies: A nice over overview

  • Monoclonal Antibodies to Rabbit Leucocyte Antigens - Monoclonal Antibodies to Rabbit Leucocyte Antigens. The following monoclonals are available which have been shown to react with RABBIT systems

  • Mouse Pathology Lab Protocols - Mouse Pathology Lab Protocols by Giorgio Cattoretti, MD, Columbia University

  • Mouse Tumor Biology Database - The Mouse Tumor Biology (MTB) Database supports the use of the mouse as a model system of hereditary cancer by providing electronic access to: Descriptions of tumors (data are organized by strain and organ of tumor origin), Tumor frequency and latency data, Information on genetic factors associated with tumors and tumor development, Tumor pathology reports and images, References, both published and unpublished, and Links to related online resources

  • mRNA In Situ Hybridization with Nick-Translated Probes - mRNA In Situ Hybridization with Nick-Translated Probes (Spector Lab)

  • MSH2 - Mismatch repair proteins MSH2 clone 25D12 Staining Protocol for Autostainer. NordiQC

  • MSH2 - Mismatch repair proteins MSH2 clone 27 Staining Protocol for Autostainer. NordiQC

  • MSH2 - Mismatch repair proteins MSH2 clone FE11 Staining Protocol for Autostainer. NordiQC

  • MSRS Catalog of Primary Antibodies - The MSRS web site, www.antibodies-probes.com, offers an interactive searchable database containing a listing of 225,000+ PRIMARY ANTIBODIES. SUBSCRIPTIONS - are for unlimited searching for one full year and cost $98.00. Large laboratories, departments, companies and library subscriptions are $255.00 for unlimited access. The database is constantly updated and should soon grow to 300,000 primary antibodies.

  • Multicolor-FICTION - Phenotypic and genotypic analyses of cells are increasingly essential for understanding pathogenetic mechanisms as well as for diagnosing and classifying malignancies and other diseases. We report a novel multicolor approach based on the FICTION (fluorescence immunophenotyping and interphase cytogenetics as a tool for the investigation of neoplasms) technique, which enables the simultaneous detection of morphological, immunophenotypic, and genetic characteristics of single cells. As prerequisite, multicolor interphase fluorescence in situ hybridization assays for B-cell non-Hodgkin’s lymphoma and anaplastic large-cell lymphoma have been developed. These assays allow the simultaneous detection of the most frequent primary chromosomal aberrations in these neoplasms, such as t(8;14), t(11;14), t(14;18), and t(3;14), and the various rearrangements of the ALK gene, respectively. To establish the multicolor FICTION technique, these assays were combined with the immunophenotypic detection of lineage- or tumor-specific antigens, namely CD20 and ALK, respectively.

  • Multiplex Fluorescent mRNA In Situ Hybridization - Presents information on how to do multiplex fluorescent mRNA in situ hybridization on Drosophila embryos.

  • Nanogold DNA In Situ Hybridization - This molecular morphological procedure is based on silver/gold-enhanced Nanogold (Nanoprobes, Inc.) and allowed a reliable and very sensitive detection of few copies of human papillomavirus (HPV), cytomegalovirus (CMV), Epstein Barr Virus (EBV), herpes simplex virus (HSV) and other DNA-viruses in routinely formalin-fixed and paraffin-embedded tissues. Other DNA sequences, as well as RNA stainings, have not yet been tested by us. The method described below can be applied as a robust and fast routine method for diagnostic purposes in all cases where "conventional ISH" is not sensitive enough, and where real single-copy sensitivity is not neded. The protocol also works well with Fluoro-Nanogold™ (Nanoprobes, Inc.), thus allowing visualization of the very same preparation by fluorescent microscopy (FISH) and transmitted light microscopy. Nanogold-preparations can be transferred to the electron microscope

  • Nanoprobes - Nanogold Labelling Reagents, Conjugates, Fluoro Nanogold and Silver Enhancement reagents

  • NeoMarkers - Antibodies, Instrumentation, IHC Detection Systems and Ancillary Products

  • Neurofilament in Formalin-Fixed, Paraffin-Embedded Rodent Tissue - Identification of Neurofilament in Formalin-Fixed, Paraffin-Embedded Rodent Tissue

  • Neuromics Antibodies - Neuromics has a reputation of providing quality antibody products for Central Nervous System research.

  • Neuron Specific Enolase (NSE) in Formalin-Fixed, Paraffin-Embedded Rat Tissue - Identification of Neuron Specific Enolase (NSE) in Formalin-Fixed, Paraffin-Embedded Rat Tissue

  • Neuron Specific Enolase in Formalin-Fixed, Paraffin-Embedded Mouse Tissue - Identification of Neuron Specific Enolase in Formalin-Fixed, Paraffin-Embedded Mouse Tissue

  • NeuroScience Associates (NSA) - NeuroScience Associates (NSA) has earned a reputation for providing high-throughput neurohistology which produces unsurpassed quality of stained sections and accelerated image analysis.

  • NFkB (p65) Paraffin-embedded Rat Tissue - Detection of NFkB (p65) Paraffin-embedded Rat Tissue

  • Nonradioactive In Situ Hybridization Application Manual - This manual concentrates on two labeling systems:
    -Indirect methods using digoxigenin (detected by specific antibodies) and biotin (detected by streptavidin)
    -Direct methods using fluorescein or other fluorochromes directly coupled to the nucleotide

  • NordiQC - Nordic immunohistochemical Quality Control. Capacity to include a limited number of laboratories outside the Nordic countries.

  • NordiQC Protocols - Protocols from Nordic immunohistochemical Quality Control

  • Novel Application of Tyramide Signal Amplification (TSA) - Novel Application of Tyramide Signal Amplification (TSA): Ultrastructural Visualization of Double-labeled Immunofluorescent Axonal Profiles

  • Novocastra Laboratories Ltd - Antibodies, Probes, Automation, IHC Detection Systems and Ancillary Products

  • Novocastra TechnoBase - Collection of Protocols

  • Novus Biologicals - Antibodies, Controls, Tissue Microarrays and Kit. DNA repair, hypoxia, neuroscience and cancer research

  • Nuclear Localization of Thyroid Transcription Factor-1 - Nuclear Localization of Thyroid Transcription Factor-1 Correlates with Serum Thyrotropin Activity and May Be Increased in Differentiated Thyroid Carcinomas with Aggressive Clinical Course

  • Ophthalmic Histology Service - 25 years experience in sectioning whole eye specimens.

  • Osmium-free Embedment Protocol for Antigenic Preservation - Osmium is often used as an additional fixative in preparing samples for electron microscopy. However, osmium is detremental to antigenicity and therefore only a few antibodies tend to work in post-embedding labelling of osmium fixed tissue. To overcome this, Aldo Rustioni and Kris Phend at the University of Noth Carolina have developed an osmium-free embedding protocol which better retains tissue antigenicity (Phend et al., 1995, J. Histochem. Cytochem. 43: 283-292).

  • p15 in Formalin-Fixed, Paraffin Embedded Mouse Tissue - Detection of p15 in Formalin-Fixed, Paraffin Embedded Mouse Tissue

  • p16INK4A Immunohistochemical Overexpression in Premalignant and Malignant Oral Lesions - p16INK4A Immunohistochemical Overexpression in Premalignant and Malignant Oral Lesions Infected with Human Papillomavirus

  • p16INK4a in squamous skin cancer - Retinoblastoma protein function and p16INK4a expression in actinic keratosis, squamous cell carcinoma in situ and invasive squamous cell carcinoma of the skin and links between p16INK4a expression and infiltrative behavior

  • p19arf in Formalin-Fixed, Paraffin-Embedded Mouse Tissue - Detection of p19arf in Formalin-Fixed, Paraffin-Embedded Mouse Tissue

  • p21 in Formalin-Fixed, Paraffin-Embedded Rat Tissue - Detection of p21 in Formalin-Fixed, Paraffin-Embedded Rat Tissue

  • p53 in Formalin-Fixed, Paraffin-Embedded Human and MouseTissue - Detection of p53 in Formalin-Fixed, Paraffin-Embedded Human and MouseTissue

  • Pan-MCM in Formalin-Fixed, Paraffin Embedded Rat Tissue - Detection of Pan-MCM in Formalin-Fixed, Paraffin Embedded Rat Tissue

  • Pathbase - Pathbase is a database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice. Images can be retrieved by searching for specific lesions or class of lesion, by genetic locus, or by a wide set of parameters shown on an Advanced Search Interface.

  • PCNA in Formalin-Fixed, Paraffin Embedded Rat and Mouse Tissue - Detection of PCNA in Formalin-Fixed, Paraffin Embedded Rat and Mouse Tissue

  • PCR in situ hybridization for a representative tissue control (HLA-DQalpha amplification) - Protocols from Oxford Practical Approach Series.

  • Peroxidase -anti-peroxidase (PAP) - Peroxidase-anti-peroxidase technique for the identification of antigens in paraffin wax sections

  • PhenoPath Laboratories - PhenoPath Laboratories is a physician-owned and directed national reference pathology laboratory providing comprehensive diagnostic immunohistochemical and in situ hybridization (e.g., FISH) services. PhenoPath Laboratories’ specialties include breast cancer markers, carcinomas of unknown primary, hematolymphoid malignancies, large cell undifferentiated malignant neoplasms, and other difficult diagnostic cases. PhenoPath Laboratories’ pathologists are nationally recognized experts in their fields, publishing papers, giving lectures and workshops at national meetings.

  • Phoenix Biotechnologies - Custom RNA Synthesis, LNA Oligos, Probes, In Situ Hybridization and Immunohistochemistry Reagents

  • Phospho-eNOS in Formalin-Fixed, Paraffin Embedded Rat - Detection of Phospho-eNOS in Formalin-Fixed, Paraffin Embedded Rat Tissue

  • Phylogeny Inc. - Phylogeny, Inc. provides the highest-quality 35S labeled and digoxigenin (DIG) labeled in situ hybridization (ISH) service available to the scientific community. We have provided this service to pharmaceutical, biotechnology, institute and academic organizations through our premier distributors for many years but now we are able to offer this service directly to customers at a reduced price.

  • Placental alkaline phosphatase PLAP - Placental alkaline phosphatase (PLAP) clone PL8-F6 Staining Protocol for BioGenex I6000

  • Placental alkaline phosphatase PLAP - Placental alkaline phosphatase (PLAP) clone PL8-F6 Staining Protocol for Autostainer

  • Placental alkaline phosphatase PLAP - Placental alkaline phosphatase (PLAP) clone NB10 Staining Protocol for Ventana BenchMark XT

  • Post-embedding in situ hybridization and detection of hybrids - Protocols from Oxford Practical Approach Series.

  • Post-hybridization washes after mRNA detection in mouse embryo tissue sections - Protocols from Oxford Practical Approach Series.

  • Pre-absorption of antibody - Protocols from Oxford Practical Approach Series.

  • Pre-treatment of cryosections for mRNA detection in tissue sections - Protocols from Oxford Practical Approach Series.

  • Pre-treatment of sections before mRNA detection - Protocols from Oxford Practical Approach Series.

  • Pre-treatment of sections or cells on slides - Protocols from Oxford Practical Approach Series.

  • Preparation of Formvar carbon coated grids for ultrathin sections of Lowicryl embedded cells prior t - Protocols from Oxford Practical Approach Series.

  • Preparation of labelled whole chromosome paints by DOP-PCR - Protocols from Oxford Practical Approach Series.

  • Preparation of lymphoid cells and tissue for molecular and immunological applications - Protocols from Oxford Practical Approach Series.

  • Preparation of probes for in situ hybridization - Preparation of probes for in situ hybridization from Singer Lab

  • Preparation of sections for in situ hybridization - Protocols from Oxford Practical Approach Series.

  • Preparation of stock solutions for FISH - Preparation of stock solutions for FISH

  • Pretreatment in a High-pressure Microwave Processor for MIB-1 Immunostaining - Pretreatment in a High-pressure Microwave Processor for MIB-1 Immunostaining of Cytological Smears and Paraffin Tissue Sections to Visualize the Various Phases of the Mitotic Cycle

  • Progesterone Receptor (PGR) - Progesteron Receptor clone PR88. Protocol for i6000, Sakura Prohosp. NordiQC

  • Progesterone Receptor (PGR) - Progesteron Receptor (PGR) clone PgR 636. Protocol for DakoCytomation Autostainer. NordiQC

  • Progesterone Receptor (PGR) - Progesterone Receptor (PGR) clone 16. Protocol for DakoCytomation Autostainer. NordiQC

  • Progesterone Receptor (PGR) - Progesterone Receptor (PGR) clone 1A6. Protocol for Ventana NexES. NordiQC

  • Progesterone Receptor in Formalin-Fixed, Paraffin-Embedded Rat Tissue - Detection of Progesterone Receptor in Formalin-Fixed, Paraffin-Embedded Rat Tissue

  • ProPath Laboratory - Providing pathology services of unsurpassed quality is the singular intent of ProPath. For over 35 years, our pathologists have partnered with physicians and hospitals to diagnose disease and help patients find their unique road to recovery.

  • Prostate Specific Anantigen (PSA) - Prostate Specific Anantigen (PSA) 35H9 Protocol for DakoCytomation Autostainer. NordiQC

  • Prostate Specific Anantigen (PSA) - Prostate Specific Anantigen (PSA) ER-PR8. Protocol for DakoCytomation Autostainer. NordiQC

  • Prostate Specific Anantigen (PSA) - Prostate Specific Anantigen (PSA) ER-PR8+PA05. Protocol for LabVision Immunostainer. NordiQC

  • Prostate Specific Anantigen (PSA) - Prostate Specific Anantigen (PSA) polyclonal 760-2506. Protocol for Ventana BenchMark. NordiQC

  • Prostate Specific Anantigen (PSA) - Prostate Specific Anantigen (PSA) polyclonal A0562. Protocol for Ventana Benchmark. NordiQC

  • Prostate Specific Anantigen (PSA) - Prostate Specific Anantigen (PSA) polyclonal A0562. Protocol for DakoCytomation Autostainer. NordiQC

  • Prostatic Acid Phosphatase (PAP) - Prostatic Acid Phosphatase (PAP) PASE/4LJ. Protocol for DakoCytomation Autostainer. NordiQC

  • Prostatic Acid Phosphatase (PAP) - Prostatic Acid Phosphatase (PAP) PASE/4LJ. Protocol for DakoCytomation TechMate. NordiQC

  • Prostatic Acid Phosphatase (PAP) - Prostatic Acid Phosphatase (PAP) polyclonal A0627. Protocol for Ventana NexES

  • Prostatic Acid Phosphatase (PAP) - Prostatic Acid Phosphatase (PAP) polyclonal A0627. Protocol for DakoCytomation Autostainer. NordiQC

  • Protocol for IHC Staining of Frozen Tissue Sections - Immunohistochemistry Staining, Frozen Tissues (Acetone-Fixed)

  • Protocol for pre-embedding gold-αBgt - Here is a basic method for pre-embedding labelling using the conjugate (could be used for any gold tagged marker).The protocol describes embedding for electron microscopy, but is easily changed for light microscopy analysis. Ian Jones, PhD University of Bath, UK

  • Protocols for microarray development - Protocols for microarray development in use in the Vodkin Laboratory For the NSF Soybean Functional Genomics Project. Preparation of DNA for microarrays,PCR Data/Reaction Sheet, Electrophoresis of PCR products, Purification of PCR products with Sephadex, Transferring PCR DNA from 96 to 384 well plates, Preparing poly-L-lysine coated slides, Postprint slide treatments, Postprint blocking of amine slides, Postprint blocking of aldehyde slides, Reverse transcriptase labeling with Cy3/Cy5,Staining of total DNA on slides,Microarray construction, Laser scanning, Spot quantitation, Statistics of expression, Sample tracking

  • Quantitative Comparison of Anti-Fading Mounting Media - In this study, we examined the fluorescence fading phenomenon quantitatively, obtained an equation to express the phenomenon, compared the ability of various anti-fading media, and tried to restore already faded images to their original state with a computer.

  • Quantitative Comparison of Pretreatment Regimens Used to Sensitize In Situ Hybridization - Quantitative Comparison of Pretreatment Regimens Used to Sensitize In Situ Hybridization Using Oligonucleotide Probes on Paraffin-embedded Brain Tissue

  • R&D Systems - Extensive selection of cytokine-related reagents

  • Rapid Synthesis of Biotin-, Digoxigenin-, Trinitrophenyl-, and Fluorochrome-labeled Tyramides - Rapid Synthesis of Biotin-, Digoxigenin-, Trinitrophenyl-, and Fluorochrome-labeled Tyramides and Their Application for In Situ Hybridization Using CARD Amplification

  • Re-evaluation of Epoxy Resin Sections for Light and Electron Microscopic Immunostaining - Epoxy resins provide optimal tissue morphology at both the light and the electron microscopic level and therefore enable correlative studies on semithin and thin sections from the same tissue block. Here we report on an approach to retain these advantages for immunolabeling studies by adapting and combining well-known techniques, i.e., surface etching with sodium ethoxide and heat-mediated antigen retrieval.

  • Reduction of Lipofuscin-like Autofluorescence in Fluorescently Labeled Tissue - In this study we examined several chemical treatments of tissue sections for their ability to reduce or eliminate lipofuscin-like autofluorescence without adversely affecting other fluorescent labels.

  • Richard-Allan Scientific - Richard-Allan Scientific develops and produces a complete portfolio of consumable and supplies for the histology, cytology and hematology lab community. We are the leading histology and cytology supplies manufacturer for the North American market. We specialize in high performance stains, reagents, paraffin, prefilled specimen containers, tissue cassettes and disposable microtome blades.

  • RNA In Situ Hybridization of Dissected Gonads - RNA In Situ Hybridization of Dissected Gonads with Digoxygenin-Labeled Probes

  • Rockland Immunochemicals - Any signal transduction antibodies you need: monoclonal and polyclonal antibodies, secondary antibody conjugates, epitope tags, GFP and GST epitope antibodies, AKT signaling and ATM antibodies, NFkB and phospho specific antibodies, ubiquitin, and custom antibody production from Rockland Immunochemicals.

  • Routine Acid Decalcification of Bone Marrow Samples Can Preserve DNA for FISH and CGH - Production of paraffin-section material from tissue samples that contain bone requires decalcification. Techniques such as acidic decalcification or EDTA chelation are suitable methods. Acid decalcification is generally quicker than EDTA chelation but studies have suggested that it may result in hydrolysis of DNA. Here we show that limited acid decalcification (less than 24 hr) in 5% formic acid can preserve DNA sufficient for fluorescent in situ hybridization (FISH) or comparative genomic hybridization (CGH) and that prolonged 10% formic acid decalcification results in failure of FISH and only limited retrieval of DNA for CGH studies. (J Histochem Cytochem 50:113–115, 2002)

  • S-100 Protein - S-100 Protein polyclonal. Protocol for DakoCytomation Autostainer. NordiQC

  • S-100 Protein - S-100 Protein polyclonal. Protocol (2) for DakoCytomation Autostainer. NordiQC

  • S-100 Protein - S-100 Protein polyclonal. Protocol for Ventana NexES. NordiQC

  • S100 in Formalin-Fixed, Paraffin-Embedded in Rat Tissue - Detection of S100 in Formalin-Fixed, Paraffin-Embedded in Rat Tissue

  • S100 in Formalin-Fixed, Paraffin-Embedded Mouse Tissue - Detection of S100 in Formalin-Fixed, Paraffin-Embedded Mouse Tissue

  • Santa Cruz Biotechnology - Broad range of research antibodies

  • ScyTek Laboratories - Products for Life Sciences

  • Sectioning mouse embryos for mRNA detection - Protocols from Oxford Practical Approach Series.

  • Sectioning of whole mount hybridized embryos - Protocols from Oxford Practical Approach Series.

  • Sensitive Chemiluminescence In Situ Hybridization for the Detection of Human Papillomavirus Genomes - Sensitive Chemiluminescence In Situ Hybridization for the Detection of Human Papillomavirus Genomes in Biopsy Specimens

  • Sensitive mRNA Detection by Fluorescence In Situ Hybridization - Sensitive mRNA Detection by Fluorescence In Situ Hybridization Using Horseradish Peroxidase-labeled Oligodeoxynucleotides and Tyramide Signal Amplification

  • Sensitive Nonradioactive Detection of mRNA in Tissue Sections - Sensitive Nonradioactive Detection of mRNA in Tissue Sections: Novel Application of the Whole-mount In Situ Hybridization Protocol

  • Serotec - Manufacturer and supplier of high quality antibodies and immunological reagents for medical research

  • Signal Amplification in Immunohistochemistry Using Biotinylated Tyramide and Nanogold–Silver - Signal Amplification in Immunohistochemistry at the Light Microscopic Level Using Biotinylated Tyramide and Nanogold–Silver Staining

  • Signet Laboratories - Signet Laboratories is a leading medical diagnostic/research company specializing in the development of monoclonal antibodies for cancer, infectious disease, and neurodegenerative disease applications

  • Simple Method for Reduction of Autofluorescence in Fluorescence Microscopy - Autofluorescence of aldehyde-fixed neural tissue often complicates the use of fluorescence microscopy. Background fluorescence can be notably reduced or eliminated by irradiation with light before treatment with fluorescence probes, resulting in a higher contrast without adversely affecting the staining probabilities.

  • Simultaneous Detection of EGFP and Cell Surface Markers - Simultaneous Detection of EGFP and Cell Surface Markers by Fluorescence Microscopy in Lymphoid Tissues

  • Single and Double FISH protocols for Drosophila - This procedure is taken from a recently published book chapter. The reference is: Hughes, S. and Krause, H.M. (1998) Single and double FISH protocols for Drosophila. in: Protocols in confocal microscopy., ed. Stephen Paddock, Humana Press Inc., in press.

  • Single-copy Gene Detection Using Branched DNA (bDNA) In Situ Hybridization - Single-copy Gene Detection Using Branched DNA (bDNA) In Situ Hybridization

  • Software Tools for High-Throughput Analysis and Archiving Tissue Microarrays - A comprehensive system for high-throughput analysis and storage of TMA immunostaining data, using a combination of commercially available systems and novel software application. Staining results are recorded directly into an Excel worksheet and are reformatted by a novel program (TMA-Deconvoluter) into a format suitable for hierarchical clustering analysis or other statistical analysis

  • Somatostatin in Rodent and Human Tissue - Detection of Somatostatin in Formalin-Fixed, Paraffin-Embedded, Rodent and Human Tissue

  • Southern Biotech - Secondary Antibodies and other immunochemicals. Produce a broad range of Monoclonal Antibodies, Collagen, and Collagen Antibodies.

  • SP-A in Formalin-Fixed, Paraffin-Embedded Rodent Tissue - Identification of SP-A in Formalin-Fixed, Paraffin-Embedded Rodent Tissue

  • Specific detection of double-stranded DNA sequences in Lowicryl K4M sections by ish - Protocols from Oxford Practical Approach Series.

  • Spring Bioscience - Spring Bioscience, your source for high quality products, tools, and services for gene cloning, target screening and protein expression analysis.

  • Subbing of slides for mouse embryo sections for mRNA detection - Protocols from Oxford Practical Approach Series.

  • Successive steps for Lowicryl K4M embedding and ultrathin sectioning of somatic mammalian cells prio - Protocols from Oxford Practical Approach Series.

  • Successive steps for specific detection of DNA sequences by post-embedding in situ hybridization - Protocols from Oxford Practical Approach Series.

  • Successive steps for specific detection of RNA molecules in Lowicryl K4M sections by in situ hybridi - Protocols from Oxford Practical Approach Series.

  • SV40 Large T antigen in Paraffin Embedded Mouse Tissue - Identification of SV40 Large T antigen in Paraffin Embedded Mouse Tissue

  • Swant - Antibodies against Ca2+ - binding proteins, Ca2+ - channels, Ca2+ - exchangers and Ca2+ - pumps. Antibodies against insulin-like growth factors, neurotransmitters and components of the renin-angiotensin system

  • Synaptophysin - Synaptophysin polyclonal. Protocol for DakoCytomation Autostainer. NordiQC

  • Synaptophysin - Synaptophysin clone Snp88. Manual Protocol. NordiQCr

  • Synaptophysin in Formalin-Fixed, Paraffin-Embedded Rodent Tissue - Detection of Synaptophysin in Formalin-Fixed, Paraffin-Embedded Rodent Tissue

  • Synaptosome Immunocytochemistry Protocol. - Synaptosomes (essentially free-floating axon terminals) can be treated very much like cell cultures. I've included them as a separate immunofluorescence method as there are a few extra steps needed to stick them to slides. Ian Jones, PhD University of Bath, UK

  • Synthesis of digoxigenin or fluorescein labelled RNA probe - Protocols from Oxford Practical Approach Series.

  • Synthesis of single-stranded RNA probe for mRNA detection in tissue sections - Protocols from Oxford Practical Approach Series.

  • The Animal Research Kit Can Be Used in a Multistep Double Staining Method for Human Tissue Specimens - The Animal Research Kit (ARK) Can Be Used in a Multistep Double Staining Method for Human Tissue Specimens

  • The Antibody Resource Page - Your complete guide to antibody research and suppliers.

  • The Antibody Resource Page - Your complete guide to antibody research and suppliers.

  • The Antigen–Antibody Reaction in Immunohistochemistry - The problems of major concern in immunohistochemical practice are discussed in the following order: (a) the mechanism of the Ag–Ab reaction in fixed tissue as opposed to the in vitro reaction; (b) the chemistry of fixation and its influence on the final result of the immunohistochemical reaction; (c) the various procedures used for antigen retrieval in formaldehyde-fixed tissue; and (d) the consideration of the possible mechanism underlying heat-induced antigen retrieval.

  • The Binding Site - The Binding Site is a UK manufacturer which specialises in the research, development and production of immunodiagnostic kits and reagents for use in the investigation of human and veterinary diseases

  • The Biotech Source - Supplying bulk antibodies & antigens for human, animal, environmental, plant and other diagnostic applications

  • The ELF-97 Alkaline Phosphatase Substrate Provides a Bright, Photostable, Fluorescent Signal - The ELF-97 Alkaline Phosphatase Substrate Provides a Bright, Photostable, Fluorescent Signal Amplification Method for FISH

  • The Journal of Histotechnology - The Web Site of The Journal of Histotechnology, a quarterly publication dedicated to technological innovation and enhancements in the field of histology.

  • The Mouse in Science: Monoclonal Antibodies - In 1975, Kohler and Milstein first fused lymphocytes to produce a cell line which was both immortal and a producer of specific antibodies. The two scientists were awarded the Nobel Prize for Medicine in 1984 for the development of this "hybridoma." The value of hybridomas to the field was not truly appreciated until about 1987, when MAbs were regularly produced in rodents for diagnostics.

  • The PHL Murine Immunohistochemistry Database - The PHL Murine Immunohistochemistry Database features 450 different immunohistochemical techniques optimized in mouse tissues. The information is constantly updated and improved. The database may be searched by Antibody, Manufacturer, and Fixative.

  • The Power and Versatility of In Situ Hybridization - The Power and Versatility of In Situ Hybridization

  • Thyroglobulin in Formalin-Fixed, Paraffin-Embedded in Rat Tissue - Detection of Thyroglobulin in Formalin-Fixed, Paraffin-Embedded in Rat Tissue

  • Thyroid Transcription Factor-1 (TTF-1) - Thyroid Transcription Factor-1 (TTF-1) clone 8G7G3/1. Protocol for DakoCytomation Autostainer. NordiQC

  • Thyroid Transcription Factor-1 (TTF-1) - Thyroid Transcription Factor-1 (TTF-1) clone SPT24. Protocol for DakoCytomation Autostainer. NordiQC

  • Thyroid Transcription Factor-1 (TTF-1) - Thyroid Transcription Factor-1 (TTF-1) clone SPT24. Protocol for Ventana NexES. NordiQC

  • Thyroid Transcription Factor-1 (TTF-1) - Thyroid Transcription Factor-1 (TTF-1) clone 8G7G3/1. Protocol for LabVision Immunostainer. NordiQC

  • Tissue Array Workshop - This is the cheapest and easiest way to construct Tissue Microarrays without purchasing expensive equipment especially if you are only planning to make a couple arrays a year. At the bottom of this page is a list of places you can purchase supplies.

  • Tissue Immunolabelling – ABC / DAB reaction - This protocol describes a standard method for immunolabelling vibratome sections using the HRP substrate diaminobenzidine (DAB). The labelled sections can be viewed at the light microscope level or processed for electron microscopy for subcellular analysis.
    Ian Jones, PhD University of Bath, UK www.bath.ac.uk/~bssiwj

  • Tissue Microarray Construction Protocols - Yale Tissue Microarray Construction Protocols

  • TMA Builder - Device for Producing Tissue Micro Arrays

  • TNF alpha in PLP Fixed Mouse Tissue - Identification of TNF alpha in PLP Fixed Mouse Tissue

  • TNFa in Frozen Mouse Tissue - Identification of TNFa in Frozen Mouse Tissue

  • Torrey Pines Biolabs - Antibodies against Chemokines and their receptors, Antibodies against Cytokines, Antibodies against Green Fluorescent Protein (GFP)

  • Towards Quantitative In Situ Hybridization - In situ hybridization analysis of tissue mRNA concentrations remains to be accepted as a quantitative technique, even though exposure of tissue sections to photographic emulsion is equivalent to Northern blot analysis. Because of the biological importance of in situ quantification of RNA sequences within a morphological context, we evaluated the quantitative aspects of this technique

  • Treatment of slides prior to FISH - Protocols from Oxford Practical Approach Series.

  • Triple Immunofluorescence Staining with Antibodies Raised in the Same Species - A general problem in immunocytochemistry is the development of a reliable multiple immunolabeling method when primary antibodies must be used that originate in the same species. We have developed a protocol for the immunodetection of three antigens in a single tissue preparation, using unconjugated primary antibodies raised in the same species. Immunocytochemical detection of neuronal nitric oxide synthase, calcitonin gene-related peptide, and calbindin D28k in the lung of rats demonstrated that part of the pulmonary neuroepithelial bodies are selectively contacted by at least three different nerve fiber populations. The first antigen was detected using tyramide signal amplification, a very sensitive method allowing a dilution of the first primary antibody far beyond the detection limit of fluorescently labeled secondary antibodies. The second antigen was visualized by a fluorophore-conjugated secondary monovalent Fab antibody that at the same time blocks the access of the third secondary antibody to the second primary antibody. Moreover, the monovalence of the Fab fragment prevents the third primary antibody from binding with the second-step secondary antibody. The triple staining technique described here is generally applicable, uses commercially available products only, and allows the detection of three antigens in the same preparation with primary antibodies that are raised in the same species. (J Histochem Cytochem 50:575–582, 2002)

  • Triple Point Biologics - Antibodies to MMP´s, TIMP´s, ADAM´s und Calpain´s

  • Triple-Labelling Immunofluorescence Protocol (Tissue Sections) - Immunofluorescence (confocal) microscopy is used extensively within the group for multiple labelling studies, often using three different primary antibodies. The protocol outlines the basic labelling methods used with cell cultures and tissue sections. Ian Jones, PhD University of Bath, UK

  • TUNEL Apoptotic Cell Detection in Tissue Sections: Critical Evaluation and Improvement - We reviewed the limitations and artifacts of TUNEL and designed a comprehensive protocol to reassess the various procedures in use for five crosslinking and/or precipitating fixatives. By introducing microwave heating in extreme pH-value solutions (pH 3 for formalin and pH 10.6 for Bouin's fixative) coupled with proteolysis, we obtained an intense staining of 70–80% of apoptotic cells and bodies on archival tissue blocks, with little or no background.

  • Two colour in situ hybridization - Two colour in situ hybridization - sequential alkaline phosphatase staining with chromogenic substrates of zebrafish embryos. Protocols from Oxford Practical Approach Series.

  • Two colour ISH - Two colour ISH - sequential alkaline phosphatase staining with chromogenic substrates of chick, mouse, and Xenopus embryos. Protocols from Oxford Practical Approach Series.

  • Tyramide Amplification Allows Anterograde Tracing by Horseradish Peroxidase-conjugated Lectins.. - Tyramide Amplification Allows Anterograde Tracing by Horseradish Peroxidase-conjugated Lectins in Conjunction with Simultaneous Immunohistochemistry

  • Tyramine Amplification Technique in Routine Immunohistochemistry - Signal amplification in immunohistochemistry via binding of biotinylated tyramine to proteins near the site of peroxidase-labeled antibodies is a promising new technique, but studies investigating a wide range of markers are lacking. The tyramine amplification technique (TAT) was investigated on 85 antibodies using a simple and fast protocol, and TAT results were compared to those obtained with conventional immunohistochemistry.

  • UK NEQAS - A main aim of the scheme is to provide useful information on methods and reagents that allow for improved quality of immunocytochemistry. The scheme currently attracts members from over 30 different countries and welcomes participation from both UK and non-UK based laboratories.

  • Ultrastructural Localization of ß-Actin and Amphoterin mRNA in Cultured Cells - Ultrastructural Localization of ß-Actin and Amphoterin mRNA in Cultured Cells: Application of Tyramide Signal Amplification and Comparison of Detection Methods

  • Upstate - Upstate develops innovative cell signaling products, technology platforms and services to accelerate your life science research and drug discovery efforts.

  • USBio - Antibodies, Biochemicals, Growth Factors, Cytokines, Kits and Assays

  • Use of Methacrylate De-embedding Protocols for In Situ Hybridization on Semithin Plastic Sections - Use of Methacrylate De-embedding Protocols for In Situ Hybridization on Semithin Plastic Sections with Multiple Detection Strategies

  • Use of Microwave Oven Heating to Block Antibody Crossreactivity and Retrieve Antigens - We report a simple and reliable method for detection of two or more antigens within tissue sections by indirect immunuenzyme staining using mouse monoclonal antibodies (MAbs). This technique involves treating sections with two 5-min Microwave (MW) Oven heatings between sequential rounds of three-layer immunoenzyme staining (mouse MAb, goat anti-mouse IgG, and mouse PAP or mouse APAAP) and color development.

  • VCAM in Formalin-Fixed, Paraffin Embedded Mouse Tissue - Identification of VCAM in Formalin-Fixed, Paraffin Embedded Mouse Tissue

  • Vector Laboratories - Developing innovative labeling and detection systems for biological and medical science

  • VEGF in paraffin-embedded rat tissue - Detection of Rabbit anti-VEGF in paraffin-embedded rat tissue

  • Ventana Discovery - Ventana’s Molecular Discovery Systems (MDS) division offers solutions for slide-based applications including immunohistochemistry, in situ hybridization, and microarrays

  • Ventana Medical Systems - Automation, Antibodies and Detection Systems

  • Veterinary Medical Research & Development, VMRD Inc. - Antibodies against bovine, porcine, sheep, equine, dog and cat antigens for veterinary research

  • Vimentin - Vimentin clone 3B4. Protocol for DakoCytomation Autostainer. NordiQC

  • Vimentin - Vimentin 3B4. Protocol for LabVision Immunostainer. NordiQC

  • Vimentin - Vimentin SP20. Protocol for DakoCytomation Autostainer. NordiQC

  • Vimentin - Vimentin V9. Protocol for DakoCytomation Autostainer. NordiQC

  • Vimentin - Vimentin V9. Protocol for Ventana NexES. NordiQC

  • Vimentin in Formalin-Fixed, Paraffin Embedded Mouse Tissue - Detection of Vimentin in Formalin-Fixed, Paraffin Embedded Mouse Tissue

  • Vimentin in Formalin-Fixed, Paraffin Embedded Rat Tissue - Detection of Vimentin in Formalin-Fixed, Paraffin Embedded Rat Tissue

  • Vision BioSystems - Bond™-maX Automated Immunohistochemistry System. With onboard dewaxing, epitope retrieval and Immunohistochemistry (IHC) staining through to counterstaining the Bond-maX system offers true walk away capability. Unique features such as continuous batch processing, optimized reagents, including Bond Polymer detection system and NovoCastra primary antibodies means the laboratory productivity is maximized.

  • Von Willebrand Factor (Factor 8) in Formalin Fixed, Paraffin-Embedded Rodent Tissue - Detection of Von Willebrand Factor (Factor 8) in Formalin Fixed, Paraffin-Embedded Rodent Tissue

  • Von Willebrand factor (Factor VIII) - Factor VIII polyclonal. Protocol for Ventana NexES

  • Von Willebrand factor (Factor VIII) - Factor VIII polyclonal. Protocol for DakoCytomation TechMate

  • Von Willebrand factor (Factor VIII) - Factor VIII polyclonal. Protocol (2) for Ventana NexES. NordiQC

  • Von Willebrand factor (Factor VIII) - Factor VIII polyclonal. Protocol for TechMate. NordiQC

  • Vysis - CEP and Telomerase Probes, WCP Whole Chromosome Paint DNS FISH Probes, Gene, Locus and Chromosome Amplification and Deletion Research. FISH Reagents, Controls and Laboratory Materials

  • What are tissue microarrays? - Tissue microarrays are produced by a method of re-locating tissue from conventional histologic paraffin blocks such that tissue from multiple patients or blocks can be seen on the same slide.

  • Whole mount hybridization, washing, and detection of probe (method 1) - Protocols from Oxford Practical Approach Series.

  • Whole mount hybridization, washing, and detection of probe (method 2) - Protocols from Oxford Practical Approach Series.

  • Whole Mount ISH - Whole Mount In Situ Hybridization, Mouse Embryos

  • Whole-mount in situ hybridization - Whole-mount in situ hybridization for the detection of RNA in C. elegans embryos

  • WT-1 in Formalin-Fixed, Paraffin-Embedded Rat Tissue - Identification of WT-1 in Formalin-Fixed, Paraffin-Embedded Rat Tissue

  • Zebrafish or Drosophila two colour whole mount in situ hybridization staining with DAB and BCIP/NBT - Protocols from Oxford Practical Approach Series.


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  • BMC Cell Biology - Latest articles - The latest articles from BMC Cell Biology (ISSN 1471-2121) published by BioMed Central

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  • Immunohistochemistry - In Situ Hybridization Latest Articles:

  • Tim50a, a nuclear isoform of the mitochondrial Tim50, interacts with proteins involved in snRNP biogenesis - Background: The Cajal body (CB) is a nuclear suborganelle involved in the biogenesis of small nuclear ribonucleoproteins (snRNPs), which are vital for pre-mRNA splicing. Newly imported Sm-class snRNPs traffic through CBs, where the snRNA component of the snRNP is modified, and then target to other nuclear domains such as speckles and perichromatin fibrils. It is not known how nascent snRNPs localize to the CB and are released from this structure after modification. The marker protein for CBs, coilin, may play a role in snRNP biogenesis given that it can interact with snRNPs and SMN, the protein mutated in Spinal Muscular Atrophy. Loss of coilin function in mice leads to significant viability and fertility problems and altered CB formation. Results: In this report, we identify a minor isoform of the mitochondrial Tim50, Tim50a, as a coilin interacting protein. The Tim50a transcript can be detected in some cancer cell lines and normal brain tissue. The Tim50a protein differs only from Tim50 in that it contains an additional 103 aa N-terminal to the translation start of Tim50. Importantly, a putative nuclear localization signal is found within these 103 residues. In contrast to Tim50, which localizes to the cytoplasm and mitochondria, Tim50a is strictly nuclear and is enriched in speckles with snRNPs. In addition to coilin, Tim50a interacts with snRNPs and SMN. Competition binding experiments demonstrate that coilin competes with Sm proteins of snRNPs and SMN for binding sites on Tim50a. Conclusions: Tim50a may play a role in snRNP biogenesis given its cellular localization and protein interaction characteristics. We hypothesize that Tim50a takes part in the release of snRNPs and SMN from the CB.

  • 14th Workshop on Fetal Cells and Fetal DNA - (No abstract is available for this citation)

  • 25-Hydroxyvitamin D3 1α-hydroxylase expression in breast cancer and use of non-1α-hydroxylated vitamin D analogue - IntroductionThe cytochrome P450 mitochondrial enzyme 25-hydroxyvitamin D3 1α-hydroxylase (1α-hydroxylase) of renal tubule cells hydroxylates the major circulating form of vitamin D (25(OH)D3) to the active systemic hormone 1,25(OH)2D3. Local production of 1,25(OH)2D3 appears to occur also at other sites where 1α-hydroxylase is expressed for autocrine/paracrine regulation. To reduce risks of hypercalcemia during treatment with vitamin D, we have previously suggested use of non-1α-hydroxylated vitamin D analogues to target tissues where 1α-hydroxylase is expressed, including the parathyroid glands in secondary hyperparathyroidism. The present study was undertaken to examine expression of 1α-hydroxylase in breast cancer and to investigate whether a non-1α-hydroxylated vitamin D analogue displayed biological function. In addition, expression of the 25-hydroxyvitamin D3 24-hydroxylase (24-hydroxylase) and the vitamin D receptor (VDR) was investigated. Methods: The expression of 1α-hydroxylase, 24-hydroxylase and VDR was investigated in breast cancer specimens (n = 19) and normal breast tissues (n = 10) by immunohistochemistry and/or RT-PCR. Consecutive cryosections of 6 μm essentially free of immune cells were used in the analyses. The effect of vitamin D analogues on transcriptional activation was analyzed in transiently transfected MCF-7 breast cancer cells. Results: 1α-hydroxylase protein was demonstrated in 79% and 100% of breast cancer specimens and normal breast, respectively. The overall relative mRNA levels of 1α-hydroxylase and 24-hydroxylase in normal breast compared to breast tumors were: 1α-hydroxylase, 1 ± 0.07 versus 0.7 ± 0.05, respectively (p < 0.001); 24-hydroxylase, 1 ± 0.08 verus 2.1 ± 0.2, respectively (p < 0.001). The VDR was expressed in 95% of the tumors as expected, with mRNA levels of 1 ± 0.09 and 1.4 ± 0.12 (p < 0.05) in breast cancer and normal breast, respectively. The ketoconazole-sensitive transcription activation potential of the non-1α-hydroxylated vitamin D analogue prodrug of EB1089 (EB1285) was demonstrated in MCF-7 cells, which express 1α-hydroxylase. The activity of EB1285 was about 20% of 1,25(OH)2D3. Conclusion: These results demonstrate nearly normal expression levels of 1α-hydroxylase, 24-hydroxylase and VDR in the majority of investigated breast cancer specimens. A non-1α-hydroxylated vitamin D analogue displayed activity in breast cancer cells. Such analogues may present future therapeutic options for proliferative disorders where 1α-hydroxylase is expressed.

  • 5-Hydroxytryptamine (5HT) Receptors in the Heart Valves of Cynomolgus Monkeys and Sprague-Dawley Rats -

    5-Hydroxytryptamine-2B receptor (5HT2BR) stimulation is known to cause fibroblast mitogenesis, and the mitogenic effect has been proposed to trigger valvular heart disease in humans. In this study, we used real-time polymerase chain reaction (TaqMan) to quantify transcript levels of 5HT2B, 5HT2C, and 5HT1B receptors and immunohistochemistry (IHC) to detect the tissue localization of these receptors in the normal heart valves of cynomolgus (CM) monkeys and Sprague-Dawley (S-D) rats. In both species, positive immunostaining was noted for 5HT1B and 5HT2B receptors in mitral, tricuspid, aortic, and pulmonary valves, and the cell types showing positive staining were interstitial cells and endothelial cells lining the valve leaflet. In CM monkeys, 5HT2CR was expressed only in the endothelial cells lining the leaflet, whereas S-D valves were negative for this receptor. IHC results were correlated with 5HT2B and 5HT1B receptor transcripts for all four valves. However, 5HT2C receptor transcripts were lower than 5HT2B or 5HT1B in all CM monkey valves, whereas 5HT2C transcripts were below the level of detection in any of the S-D rat valves. Our data showed the expression of 5HT2B, 5HT1B, and 5HT2C receptors in the normal heart valves of CM monkeys and S-D rats, and IHC and TaqMan techniques may be used to study the potential mechanism of compounds with 5HT2BR agonist activity.

    (J Histochem Cytochem 53:671–677, 2005)


  • 5-Hydroxytryptamine (5HT) Receptors in the Heart Valves of Cynomolgus Monkeys and Sprague-Dawley Rats -

    5-Hydroxytryptamine-2B receptor (5HT2BR) stimulation is known to cause fibroblast mitogenesis, and the mitogenic effect has been proposed to trigger valvular heart disease in humans. In this study, we used real-time polymerase chain reaction (TaqMan) to quantify transcript levels of 5HT2B, 5HT2C, and 5HT1B receptors and immunohistochemistry (IHC) to detect the tissue localization of these receptors in the normal heart valves of cynomolgus (CM) monkeys and Sprague-Dawley (S-D) rats. In both species, positive immunostaining was noted for 5HT1B and 5HT2B receptors in mitral, tricuspid, aortic, and pulmonary valves, and the cell types showing positive staining were interstitial cells and endothelial cells lining the valve leaflet. In CM monkeys, 5HT2CR was expressed only in the endothelial cells lining the leaflet, whereas S-D valves were negative for this receptor. IHC results were correlated with 5HT2B and 5HT1B receptor transcripts for all four valves. However, 5HT2C receptor transcripts were lower than 5HT2B or 5HT1B in all CM monkey valves, whereas 5HT2C transcripts were below the level of detection in any of the S-D rat valves. Our data showed the expression of 5HT2B, 5HT1B, and 5HT2C receptors in the normal heart valves of CM monkeys and S-D rats, and IHC and TaqMan techniques may be used to study the potential mechanism of compounds with 5HT2BR agonist activity.

    (J Histochem Cytochem 53:671–677, 2005)


  • 5-Hydroxytryptamine (5HT) Receptors in the Heart Valves of Cynomolgus Monkeys and Sprague-Dawley Rats -

    5-Hydroxytryptamine-2B receptor (5HT2BR) stimulation is known to cause fibroblast mitogenesis, and the mitogenic effect has been proposed to trigger valvular heart disease in humans. In this study, we used real-time polymerase chain reaction (TaqMan) to quantify transcript levels of 5HT2B, 5HT2C, and 5HT1B receptors and immunohistochemistry (IHC) to detect the tissue localization of these receptors in the normal heart valves of cynomolgus (CM) monkeys and Sprague-Dawley (S-D) rats. In both species, positive immunostaining was noted for 5HT1B and 5HT2B receptors in mitral, tricuspid, aortic, and pulmonary valves, and the cell types showing positive staining were interstitial cells and endothelial cells lining the valve leaflet. In CM monkeys, 5HT2CR was expressed only in the endothelial cells lining the leaflet, whereas S-D valves were negative for this receptor. IHC results were correlated with 5HT2B and 5HT1B receptor transcripts for all four valves. However, 5HT2C receptor transcripts were lower than 5HT2B or 5HT1B in all CM monkey valves, whereas 5HT2C transcripts were below the level of detection in any of the S-D rat valves. Our data showed the expression of 5HT2B, 5HT1B, and 5HT2C receptors in the normal heart valves of CM monkeys and S-D rats, and IHC and TaqMan techniques may be used to study the potential mechanism of compounds with 5HT2BR agonist activity.

    (J Histochem Cytochem 53:671–677, 2005)


  • A cell behavior screen: identification, sorting, and enrichment of cells based on motility - Background: Identifying and isolating cells with specific behavioral characteristics will facilitate the understanding of the molecular basis regulating these behaviors. Although many approaches exist to characterize cell motility, retrieving cells of specific motility following analysis remains challenging. Results: Cells migrating on substrates coated with fluorescent microspheres generate non-fluorescent tracks as they move and ingest the spheres. The area cleared by each cell allows for quantitation of single cell and population motility; because individual cell fluorescence is proportional to motility, cells can be sorted according to their degree of movement. Using this approach, we sorted a glioblastoma cell line into high motility and low motility populations and found stable differences in motility following sorting. Conclusion: We describe an approach to identify, sort, and enrich populations of cells possessing specific levels of motility. Unlike existing assays of cell motility, this approach enables recovery of characterized cell populations, and can enable screens to identify factors that might regulate motility differences even within clonal population of cells.

  • A cluster of genes located in 1p36 are down-regulated in neuroblastomas with poor prognosis, but not due to CpG island methylation - Background: A common feature of neuroblastoma tumours are partial deletions of the short arm of chromosome 1 (1p-deletions). This is indicative of a neuroblastoma tumour suppressor gene being located in the region. Several groups including our have been studying candidate neuroblastoma genes in the region, but no gene/genes have yet been found that fulfil the criteria for being a neuroblastoma tumour suppressor. Since frequent mutations have not been detected, we have now analyzed the expression and promoter CpG island methylation status of the genes UBE4B, KIF1B, PGD, APITD1, DFFA and PEX14 in the 1p36.22 region in order to find an explanation for a possible down-regulation of this region. Results: The current study shows that gene transcripts in high stage neuroblastoma tumours are significantly down-regulated compared to those in low stage tumours in the 1p36.22 region. CpG island methylation does not seem to be the mechanism of down-regulation for most of the genes tested, since no methylation was detected in the fragments analyzed. One exception is the CpG island of APITD1. Methylation of this gene is also seen in blood from control individuals and is therefore not believed to participate in tumour development. Conclusion: The genes UBE4B, KIF1B, PGD, APITD1, DFFA and PEX14 are down-regulated in high stage NB tumours, a feature that can not be explained by CpG island methylation.

  • A conserved lysine in the estrogen receptor DNA binding domain regulates ligand activation profiles at AP-1 sites, possibly by controlling interactions with a modulating repressor - Background: Estrogen receptors alpha and beta (ERα and ERβ) differentially activate genes with AP-1 elements. ERα activates AP-1 targets via activation functions with estrogens (the AF-dependent pathway), whereas ERβ, and a short version of ERα (ERα DBD-LBD) activate only with anti-estrogens (AF-independent pathway). The DNA binding domain (DBD) plays an important role in both pathways, even though neither pathway requires ERE recognition. Results: Mutations of a highly conserved DBD lysine (ERα.K206A/G), lead to super-activation of AP-1 through activation function dependent pathways, up to 200 fold. This super-activity can be elicited either through ER AFs 1 or 2, or that of a heterologous activation function (VP16). The homologous substitution in ERβ, K170A, or in ERα DBD-LBD leads to estrogen-dependent AP-1 activation and loss of the usually potent anti-estrogen effects. Each of numerous K206 substitutions in ERα, except K206R, eliminates anti-estrogen activation and this loss correlates perfectly with a loss of ability to titrate a repressive function from the RU486 bound progesterone receptor. Conclusion: We conclude that ER DBDs contain a complex regulatory function that influences ligand activation profiles at AP-1. This function, which requires the integrity of the conserved lysine, both allows for activation at AP-1 with anti-estrogens (with ERβ and ERα DBD-LBD), and prevents ERα from becoming superactive at AP-1 with estrogens. We discuss the possibility that a repressor interaction with the DBD both mediates the AF-independent pathway and dampens the AF dependent pathway. Mutations in the conserved lysine might, by this model, disrupt the binding or function of the repressor.

  • A HEV-restricted sulfotransferase is expressed in rheumatoid arthritis synovium and is induced by lymphotoxin-α/β and TNF-α in cultured endothelial cells - Background: The recruitment of lymphocytes to secondary lymphoid organs relies on interactions of circulating cells with high endothelial venules (HEV). HEV are exclusive to these organs under physiological conditions, but they can develop in chronically-inflamed tissues. The interaction of L-selectin on lymphocytes with sulfated glycoprotein ligands on HEV results in lymphocyte rolling, which represents the initial step in lymphocyte homing. HEV expression of GlcNAc6ST-2 (also known as HEC-GlcNAc6ST, GST-3, LSST or CHST4), an HEV-restricted sulfotransferase, is essential for the elaboration of L-selectin functional ligands as well as a critical epitope recognized by MECA-79 mAb. Results: We examined the expression of GlcNAc6ST-2 in relationship to the MECA-79 epitope in rheumatoid arthritis (RA) synovial vessels. Expression of GlcNAc6ST-2 was specific to RA synovial tissues as compared to osteoarthritis synovial tissues and localized to endothelial cells of HEV-like vessels and small flat-walled vessels. Double MECA-79 and GlcNAc6ST-2 staining showed colocalization of the MECA-79 epitope and GlcNAc6ST-2. We further found that both TNF-α and lymphotoxin-αβ induced GlcNAc6ST-2 mRNA and protein in cultured human umbilical vein endothelial cells. Conclusion: These observations demonstrate that GlcNAc6ST-2 is induced in RA vessels and provide potential cytokine pathways for its induction. GlcNAc6ST-2 is a novel marker of activated vessels within RA ectopic lymphoid aggregates. This enzyme represents a potential therapeutic target for RA.

  • A Highly Complex Chromosomal Rearrangement between Five Chromosomes in a Healthy Female Diagnosed in Preparation for Intracytoplasmatic Sperm Injection -

    We report a case of a de novo complex chromosomal rearrangement among five chromosomes found in a clinically healthy woman. The only indication for chromosome analysis was a planned intracytoplasmatic sperm injection. Physical examination, including internal and external genitals, and ovaries and hormone status were normal. Banding cytogenetics showed a rearrangement among chromosomes #3, #4, #7, #9, and #17. Twenty-four-color fluorescence in situ hybridization and multicolor banding were applied to characterize the translocations and breakpoints more precisely. This confirmed the involved chromosomes and revealed two breakpoints in chromosome #4. This six-breakpoint rearrangement [der(3)t(3;4), der(4)t(17;4;7), der(7)t(3;7), der(9)t(4;9), and der(17)t(9;17)] seemed to be balanced on a molecular cytogenetic level, although submicroscopic deletions or duplications close to the breakpoints cannot be excluded. (J Histochem Cytochem 53:355–357, 2005)


  • A Mapping Study of Caspase-3 Activation Following Acute Spinal Cord Contusion in Rats -

    Spinal cord injury (SCI) initiates a cascade of biochemical changes that results in necrotic and apoptotic cell death. There is evidence that caspase-3 activation and apoptotic cell death occur within hours after SCI. However, the time course and cellular localization of activated caspase-3 has not been examined. Such information is essential because caspase-3–independent apoptotic pathways do exist. In this experiment, we describe the distribution of and cell types containing activated caspase-3 at 4 hr, 1 day, 2 days, 4 days, and 8 days following SCI in rats. Numerous caspase-3–positive cells were observed at 4 hr and 1 day postinjury and colocalized most often with CC1, a marker for oligodendroglia. Both markers disappeared near the injury epicenter over the next several days. Activated caspase-3 was again present in the injured spinal cord on postoperative day 8, which coincided with a reemergence of CC1-positive cells. Many of these CC1-positive cells again colocalized activated caspase-3. NeuN-positive neurons of the dorsal horn were occasionally immunopositive for activated caspase-3 at early time points. OX42-positive microglia/macrophages rarely contained activated caspase-3. The results indicate a biphasic pattern of caspase-3 activation during the first 8 days postinjury, suggesting that at least two mechanisms activate caspase-3 following SCI. This time-course study provides a framework for investigating and understanding the different signaling events contributing to this biphasic pattern of caspase-3 activation. (J Histochem Cytochem 53:809–819, 2005)


  • A Mapping Study of Caspase-3 Activation Following Acute Spinal Cord Contusion in Rats -

    Spinal cord injury (SCI) initiates a cascade of biochemical changes that results in necrotic and apoptotic cell death. There is evidence that caspase-3 activation and apoptotic cell death occur within hours after SCI. However, the time course and cellular localization of activated caspase-3 has not been examined. Such information is essential because caspase-3–independent apoptotic pathways do exist. In this experiment, we describe the distribution of and cell types containing activated caspase-3 at 4 hr, 1 day, 2 days, 4 days, and 8 days following SCI in rats. Numerous caspase-3–positive cells were observed at 4 hr and 1 day postinjury and colocalized most often with CC1, a marker for oligodendroglia. Both markers disappeared near the injury epicenter over the next several days. Activated caspase-3 was again present in the injured spinal cord on postoperative day 8, which coincided with a reemergence of CC1-positive cells. Many of these CC1-positive cells again colocalized activated caspase-3. NeuN-positive neurons of the dorsal horn were occasionally immunopositive for activated caspase-3 at early time points. OX42-positive microglia/macrophages rarely contained activated caspase-3. The results indicate a biphasic pattern of caspase-3 activation during the first 8 days postinjury, suggesting that at least two mechanisms activate caspase-3 following SCI. This time-course study provides a framework for investigating and understanding the different signaling events contributing to this biphasic pattern of caspase-3 activation. (J Histochem Cytochem 53:809–819, 2005)


  • A mathematical model for the effect of a false-negative sentinel node biopsy on breast cancer mortality: a tool for everyday use - One of the concerns of using sentinel node biopsy (SNB) is the risks of a false-negative result (FNR). We have created a mathematical model to estimate the effects of FNR on mortality because of excess local recurrence and adjuvant therapy inappropriately withheld. With a FNR of 9.7%, the absolute effect on 10-year mortality is estimated to be less than 0.6% for all patients with tumours <2 cm in size. Since the impact of FNR on mortality is small and FNR rates do not improve with training, we suggest that detection rate alone is an adequate criterion for judging competence in SNB.

  • A molecular mechanism of formalin fixation and antigen retrieval. -
    Related Articles

    A molecular mechanism of formalin fixation and antigen retrieval.

    Am J Clin Pathol. 2004 Jul;122(1):154; author reply 154-5

    Authors: O'Leary TJ, Mason JT

    PMID: 15272544 [PubMed - indexed for MEDLINE]


  • A Monoclonal Antibody with Potential for Aiding Non-invasive Prenatal Diagnosis: Utility in Screening of Pregnant Women at Risk of Preeclampsia -

    The development of a non-invasive method of prenatal diagnosis in maternal blood has been the goal of our investigations during the last years. We have developed several anti-CD71 monoclonal antibodies and optimized a protocol for the isolation of nucleated red blood cells (NRBC) from peripheral maternal blood. The enhanced traffic of fetal erythroblasts into the maternal circulation in preeclampsia has been investigated by several groups. In this study, we compared one of our antibodies, 2F6.3, with a commercial anti-CD71 antibody in blood samples from pregnant women suffering pregnancy-induced hypertension (PIH) and in a control group of pregnant women without clinical features suggestive of an increased risk of developing preeclampsia. The mAb 2F6.3, developed by our group, has succeeded in isolating a significantly higher number of erythroblasts with less maternal cell contamination than the commercial antibody in both women with PIH and in the control group (p<0.01; Wilcoxon Signed Ranks Test). Florescence in situ hybridization analysis also demonstrated that 2F6.3 is a better antibody for the isolation of fetal NRBC in maternal blood than the commercial anti-CD71 antibody.

    (J Histochem Cytochem 53:345–350, 2005)


  • A new option for early breast cancer patients previously irradiated for Hodgkin's disease: intraoperative radiotherapy with electrons (ELIOT) - IntroductionPatients who have undergone mantle radiotherapy for Hodgkin's disease (HD) are at increased risk of developing breast cancer. In such patients, breast conserving surgery (BCS) followed by breast irradiation is generally considered contraindicated owing to the high cumulative radiation dose. Mastectomy is therefore recommended as the first option treatment in these women. Methods: Six patients affected by early breast cancer previously treated with mantle radiation for HD underwent BCS associated with full-dose intraoperative radiotherapy with electrons (ELIOT). Results: A total dose of 21 Gy (prescribed at 90% isodose) in five cases and 17 Gy (at 100% isodose) in one case were delivered directly to the mammary gland without acute complications and with good cosmetic results. After an average of 30.8 months of follow up, no late sequelae were observed and the patients are free of disease. Conclusion: In patients previously irradiated for HD, ELIOT can avoid repeat irradiation of the whole breast, permit BCS and decrease the number of avoidable mastectomies.

  • A novel EB-1/AIDA-1 isoform, AIDA-1c, interacts with the Cajal body protein coilin - Background: Cajal bodies (CBs) are nuclear suborganelles that play a role in the biogenesis of small nuclear ribonucleoproteins (snRNPs), which are crucial for pre-mRNA splicing. Upon nuclear reentry, Sm-class snRNPs localize first to the CB, where the snRNA moiety of the snRNP is modified. It is not clear how snRNPs target to the CB and are released from this structure after their modification. Coilin, the CB marker protein, may participate in snRNP biogenesis given that it can interact with snRNPs and SMN. SMN is crucial for snRNP assembly and is the protein mutated in the neurodegenerative disease Spinal Muscular Atrophy. Coilin knockout mice display significant viability problems and altered CB formation. Thus characterization of the CB and its associated proteins will give insight into snRNP biogenesis and clarify the dynamic organization of the nucleus. Results: In this report, we identify a novel protein isoform of EB-1/AIDA-1, termed AIDA-1c, that interacts with the CB marker protein, coilin. Northern and nested PCR experiments reveal that the AIDA-1c isoform is expressed in brain and several cancer cell lines. Competition binding experiments demonstrate that AIDA-1c competes with SmB' for coilin binding sites, but does not bind SMN. When ectopically expressed, AIDA-1c is predominantly nuclear with no obvious accumulations in CBs. Interestingly, another EB-1/AIDA-1 nuclear isoform, AIDA-1a, does not bind coilin in vivo as efficiently as AIDA-1c. Conclusions: These data suggest that specific EB-1/AIDA-1 isoforms, such as AIDA-1c, may participate in the regulation of nucleoplasmic coilin protein interactions in neuronal and transformed cells.

  • A Novel Marker for Purkinje Cells, KIAA0864 Protein. An Analysis Based on a Monoclonal Antibody HFB-16 in Developing Human Cerebellum -

    In the search for immunohistochemical markers of the developing human brain, a monoclonal antibody, HFB-16, was raised against homogenates from the cerebrum of a 15-gestational-week-old (GW) human fetus and screened on paraffin-embedded human embryonic brain specimens. This antibody was particularly useful as a marker for Purkinje cells in the developing human cerebellum. Positive immunoreactivities with HFB-16 first appeared in the Purkinje cell layer at 17 GW. From 20 to 24 GW, positive immunoreactivities were found above the lamina dissecans. After 25 GW, dendrites of Purkinje cells were found with the HFB-16 antibody, and the nerve fibers of the Purkinje cells became positive after 35 GW. Neurons in the dentate nucleus and external and internal granular layers reacted negatively to this antibody. After 1 year, when the external granular layer faded out, the dendrites of the Purkinje cells reached the pial surface of the cerebellum, and nerve fibers began to develop in the white matter. This antibody was also useful for characterization of components in heterotopic neurons found in various anomaly syndromes such as trisomy 13. Expressional cloning indicated the antigen against HFB-16 to be human KIAA0864 protein, which is supposed to be an alternative splicing product of p116Rip, whose function has not yet been elucidated. The antigenicity of the KIAA0864 protein was confirmed using human cDNA of the KIAA0864 protein, a protein expression vector, and an HFB-16 antibody. (J Histochem Cytochem 53:423–430, 2005)


  • A Novel Marker for Purkinje Cells, KIAA0864 Protein. An Analysis Based on a Monoclonal Antibody HFB-16 in Developing Human Cerebellum -

    In the search for immunohistochemical markers of the developing human brain, a monoclonal antibody, HFB-16, was raised against homogenates from the cerebrum of a 15-gestational-week-old (GW) human fetus and screened on paraffin-embedded human embryonic brain specimens. This antibody was particularly useful as a marker for Purkinje cells in the developing human cerebellum. Positive immunoreactivities with HFB-16 first appeared in the Purkinje cell layer at 17 GW. From 20 to 24 GW, positive immunoreactivities were found above the lamina dissecans. After 25 GW, dendrites of Purkinje cells were found with the HFB-16 antibody, and the nerve fibers of the Purkinje cells became positive after 35 GW. Neurons in the dentate nucleus and external and internal granular layers reacted negatively to this antibody. After 1 year, when the external granular layer faded out, the dendrites of the Purkinje cells reached the pial surface of the cerebellum, and nerve fibers began to develop in the white matter. This antibody was also useful for characterization of components in heterotopic neurons found in various anomaly syndromes such as trisomy 13. Expressional cloning indicated the antigen against HFB-16 to be human KIAA0864 protein, which is supposed to be an alternative splicing product of p116Rip, whose function has not yet been elucidated. The antigenicity of the KIAA0864 protein was confirmed using human cDNA of the KIAA0864 protein, a protein expression vector, and an HFB-16 antibody. (J Histochem Cytochem 53:423–430, 2005)


  • A Novel Marker for Purkinje Cells, KIAA0864 Protein. An Analysis Based on a Monoclonal Antibody HFB-16 in Developing Human Cerebellum -

    In the search for immunohistochemical markers of the developing human brain, a monoclonal antibody, HFB-16, was raised against homogenates from the cerebrum of a 15-gestational-week-old (GW) human fetus and screened on paraffin-embedded human embryonic brain specimens. This antibody was particularly useful as a marker for Purkinje cells in the developing human cerebellum. Positive immunoreactivities with HFB-16 first appeared in the Purkinje cell layer at 17 GW. From 20 to 24 GW, positive immunoreactivities were found above the lamina dissecans. After 25 GW, dendrites of Purkinje cells were found with the HFB-16 antibody, and the nerve fibers of the Purkinje cells became positive after 35 GW. Neurons in the dentate nucleus and external and internal granular layers reacted negatively to this antibody. After 1 year, when the external granular layer faded out, the dendrites of the Purkinje cells reached the pial surface of the cerebellum, and nerve fibers began to develop in the white matter. This antibody was also useful for characterization of components in heterotopic neurons found in various anomaly syndromes such as trisomy 13. Expressional cloning indicated the antigen against HFB-16 to be human KIAA0864 protein, which is supposed to be an alternative splicing product of p116Rip, whose function has not yet been elucidated. The antigenicity of the KIAA0864 protein was confirmed using human cDNA of the KIAA0864 protein, a protein expression vector, and an HFB-16 antibody. (J Histochem Cytochem 53:423–430, 2005)


  • A role for the Tec family kinase ITK in regulating SEB induced Interleukin-2 production in vivovia c-jun phosphorylation - Background: Exposure to Staphylococcal Enterotoxin B (SEB), a bacterial superantigen secreted by the Gram-positive bacteria Staphyloccocus aureus, results in the expansion and eventual clonal deletion and anergy of Vb8+ T cells, as well as massive cytokine release, including Interleukin-2 (IL-2). This IL-2 is rapidly secreted following exposure to SEB and may contribute to the symptoms seen following exposure to this bacterial toxin. The Tec family kinase ITK has been shown to be important for the production of IL-2 by T cells stimulated in vitro and may represent a good target for blocking the production of this cytokine in vivo. In order to determine if ITK represents such a target, mice lacking ITK were analyzed for their response to SEB exposure. Results: It was found that T cells from mice lacking ITK exhibited significantly reduced proliferative responses to SEB exposure in vitro, as well as in vivo. Examination of IL-2 production revealed that ITK null mice produced reduced levels of this cytokine in vitro, and more dramatically, in vivo. In vivo analysis of c-jun phosphorylation, previously shown to be critical for regulating IL-2 production, revealed that this pathway was specifically activated in SEB reactive Vb8+ (but not non-reactive Vb6+) T cells from WT mice, but not in Vb8+ T cells from ITK null mice. However, toxicity analysis indicated that both WT and ITK null animals were similarly affected by SEB exposure. Conclusions: These data show that ITK is required for IL-2 production induced by SEB in vivo, and may regulate signals leading IL-2 production, in part by regulating phosphorylation of c-jun. The data also suggest that perturbing T cell activation pathways leading to IL-2 does not necessarily lead to improved responses to SEB toxicity.

  • A Simple Antigen Retrieval Method for the Optimal Demonstration of Cyclin-D1 Overexpression in Formalin-Fixed Paraffin-Embedded Cases of Mantle Cell Lymphoma. -

  • A strategy to study tyrosinase transgenes in mouse melanocytes - Background: A number of transgenic mice carrying different deletions in the Locus Control Region (LCR) of the mouse tyrosinase (Tyr) gene have been developed and analysed in our laboratory. We require melanocytes from these mice, to further study, at the cellular level, the effect of these deletions on the expression of the Tyr transgene, without potential interference with or from the endogenous Tyr alleles. It has been previously reported that it is possible to obtain and immortalise melanocyte cell cultures from postnatal mouse skin. Results: Here, we describe the efforts towards obtaining melanocyte cultures from our Tyr transgenic mice. We have bred our Tyr transgenic mice into Tyr c-32DSD mutant background, lacking the endogenous Tyr locus. In these conditions, we failed to obtain immortalised melanocytes. We decided to include the inactivation of the Ink4a-Arf locus to promote melanocyte immortalisation. For this purpose, we report the segregation of the Ink4a-Arf null allele from the brown (Tyrp1b) mutation in mice. Finally, we found that Ink4a-Arf +/- and Ink4a-Arf -/- melanocytes had undistinguishable tyrosine hydroxylase activities, although the latter showed reduced cellular pigmentation content. Conclusion: The simultaneous presence of precise genomic deletions that include the tyrosinase locus, such as the Tyr c-32DSD allele, the Tyr transgene itself and the inactivated Ink4a-Arf locus in Tyrp1B genetic background appear as the crucial combination to perform forthcoming experiments. We cannot exclude that Ink4a-Arf mutations could affect the melanin biosynthetic pathway. Therefore, subsequent experiments with melanocytes will have to be performed in a normalized genetic background regarding the Ink4a-Arf locus.

  • A Transcriptome Map of Cellular Transformation by the Fos Oncogene - Background: The c-fos gene was originally identified as the cellular homolog of the oncogene v-fos carried by the Finkel-Biskis-Jenkins and Finkel-Biskis-Reilly murine osteogenic sarcoma retroviruses. Sustained expression of fos is sufficient to induce cellular transformation in vitro and tumorigenesis in vivo. Fos functions as a component of the AP-1 transcription factor complex to regulate gene transcription and several differentially expressed genes have been identified in cells transformed by fos. We have extended these studies by constructing a cellular system for conditional transformation by v-fos. Using Affymetrix-based DNA microarray technology, we analyzed transcriptional changes over the course of transformation and reversion in an inducible v-fos system. Results: Microarray analyses of temporal gene expression during the process of v-fos mediated cellular transformation and morphological reversion revealed a remarkably dynamic transcriptome. Of the more than 8000 genes analyzed in this study, 3766 genes were categorized into 18 gene-expression patterns by using self-organizing map analysis. By combining the analysis of gene expression profiles in stably transformed cells with the analysis of sequential expression patterns during conditional transformation, we identified a relatively small cohort of genes implicated in v-fos mediated cellular transformation. Conclusions: This approach defines a general conditional cell transformation system that can be used to study the endogenous transcription regulatory mechanisms involved in transformation and tumorigenesis. In addition, this study is the first reported analysis of dynamic changes in gene expression throughout experimentally controlled morphological transformation mediated by v-fos.

  • ABC transporters as multidrug resistance mechanisms and the development of chemosensitizers for their reversal - One of the major problems related with anticancer chemotherapy is resistance against anticancer drugs. The ATP-binding cassette (ABC) transporters are a family of transporter proteins that are responsible for drug resistance and a low bioavailablity of drugs by pumping a variety of drugs out cells at the expense of ATP hydrolysis. One strategy for reversal of the resistance of tumor cells expressing ABC transporters is combined use of anticancer drugs with chemosensitizers. In this review, the physiological functions and structures of ABC transporters, and development of chemosensitizers are described focusing on well-known proteins including P-glycoprotein, multidrug resistance protein, and breast cancer resistance protein.

  • ABCC5, ERCC2, XPA and XRCC1 transcript abundance levels correlate with cisplatin chemoresistance in non-small cell lung cancer cell lines - Background: Although 40-50% of non-small cell lung cancer (NSCLC) tumors respond to cisplatin chemotherapy, there currently is no way to prospectively identify potential responders. The purpose of this study was to determine whether transcript abundance (TA) levels of twelve selected DNA repair or multi-drug resistance genes (LIG1, ERCC2, ERCC3, DDIT3, ABCC1, ABCC4, ABCC5, ABCC10, GTF2H2, XPA, XPC and XRCC1*) were associated with cisplatin chemoresistance and could therefore contribute to the development of a predictive marker. Standardized RT (StaRT)-PCR, was employed to assess these genes in a set of NSCLC cell lines with a previously published range of sensitivity to cisplatin. Data were obtained in the form of target gene molecules relative to 10E+06 beta-actin (ACTB) molecules. To cancel the effect of ACTB variation among the different cell lines individual gene expression values were incorporated into ratios of one gene to another. Each two-gene ratio was compared as a single variable to chemoresistance for each of eight NSCLC cell lines using multiple regression. In an effort to validate these results, six additional lines then were evaluated. Results: Following validation, single variable models best correlated with chemoresistance (p < 0.001), were ERCC2/XPC, ABCC5/GTF2H2, ERCC2/GTF2H2, XPA/XPC and XRCC1/XPC. All single variable models were examined hierarchically to achieve two variable models. The two variable model with the highest correlation was (ABCC5/GTF2H2, ERCC2/GTF2H2) with an R2 value of 0.96 (p < 0.001). Conclusions: These results provide markers suitable for assessment of small fine needle aspirate biopsies in an effort to prospectively identify cisplatin resistant tumors.

  • Accelerated partial breast irradiation: a valid choice - Doctor Ross puts forth a series of cogent arguments in favor of careful study of partial breast irradiation prior to its generalized use. (1) The title of Dr. Ross's article-particularly the phrase "who will benefit" begs a different perspective than the presentation of existing data for or against the use of any given therapy. Instead, the question asks for a more profound view of the role of any healthcare provider within any healthcare system in helping a patient deal with the medical, social, psychological and financial impact of a disease process.

  • Accelerated partial breast irradiation: technically feasible but who will benefit? - Modern breast cancer radiotherapy aims to increase uncomplicated cure rates. A priority is reduction of late effects which include chronic chest wall or breast pain, poor cosmesis, and cardiac toxicity. As breast screening detects early cancers we may be able to safely restrict irradiation postlumpectomy to the tumour bed with a margin, defining a 'partial breast' target volume for treatment. Differing technical approaches to partial breast irradiation are being evaluated in phase III studies with standard whole breast irradiation. These include intra-operative single doses, hypo-fractionated accelerated brachytherapy, and LINAC (linear accelerator)-based three-dimensional external beam therapy.

  • Accumulation and Loss of Extracellular Matrix During Shear Stress-mediated Intimal Growth and Regression in Baboon Vascular Grafts -

    The composition of extracellular matrix during growth and regression of the neointima was analyzed during healing in a baboon aorto-iliac polytetrafluoroethylene graft. Graft neointimal thickening can be modulated by altering blood flow by construction of downstream arteriovenous fistulas. Normal flow with normal shear stress induces neointimal thickening, whereas high flow with high shear stress upstream of a fistula induces regression of established neointima. The neointima formed under normal shear stress is enriched in hyaluronan and proteoglycans, particularly versican. On the other hand, the neointima near the graft material is enriched in collagen and biglycan. Neointimal regression in response to high shear stress is associated with a loss of proteoglycans as detected by histochemical staining. Immunostaining with an antibody against an ADAMTS cleavage neoepitope of versican increases after switching to high flow, although immunostaining for versican core protein is not appreciably changed by high flow. The present data demonstrate that the graft neointima is enriched with proteoglycans, particularly versican and hyaluronan, as well as collagen, and there is a differential distribution of each. Neointimal atrophy occurs with an apparent loss of proteoglycans and evidence of versican degradation. (J Histochem Cytochem 53:131–140, 2005)


  • Accumulation of marginal zone B cells and accelerated loss of follicular dendritic cells in NF-kappaB p50-deficient mice - Background: Marginal zone (MZ) B cells play important roles in the early phases of humoral immune responses. In addition to possessing an inherent capacity to rapidly differentiate into antibody secreting cells, MZ B cells also help to regulate the fate of both T-independent and T-dependent blood-borne antigens in the spleen. For T-dependent antigens, MZ B cells bind IgM-antigen complexes in a complement-dependent manner. Once MZ B cells bind IgM-containing immune complexes (IgM-IC), they transport them into B cell follicles for deposition onto follicular dendritic cells (FDCs), an important component of secreted IgM's ability to enhance adaptive immune responses. To further define the requirement for MZ B cells in IgM-IC deposition, mice deficient in the NF-kB protein p50, which have been reported to lack MZ B cells, were analyzed for their ability to trap IgM-IC onto FDCs. Results: Mice (2 months of age) deficient in p50 (p50-/-) had small numbers of MZ B cells, as determined by cell surface phenotype and localization in the splenic MZ. These cells bound high levels of IgM-IC both in vivo and in vitro. Subsequent to the binding of IgM-IC by the MZ B cells in p50-/- mice, small amounts of IgM-IC were found localized on FDCs, suggesting that the MZ B cells retained their ability to transport these complexes into splenic follicles. Strikingly, MZ B cells accumulated with age in p50-/- mice. By 6 months of age, p50-/- mice contained normal numbers of these cells as defined by CD21/CD23 profile and high level expression of CD1d, CD9, and IgM, and by their positioning around the marginal sinus. However, FDCs from these older p50-/- mice exhibited a reduced capacity to trap IgM-IC and retain complement components. Conclusions: These results demonstrate that while the p50 component of the NF-kB transcription complex plays an important role in the early development of MZ B cells, MZ B cells can develop and accumulate in mice lacking this protein. These results highlight the interface between genetic deficiencies and age, and suggest that different transcription factors may play distinct roles in the development and maintenance of cell populations at different ages.

  • Activation of focal adhesion kinase enhances the adhesion and invasion of pancreatic cancer cells via extracellular signal-regulated kinase-1/2 signaling pathway activation. - Background: Interaction with integrin and focal adhesion kinase (FAK) regulates the cancer cell adhesion and invasion into extracellular matrix (ECM). In addition, phosphorylation of FAK correlates with the increase of cell motility and invasion. Adhesion and spreading of cancer cells on a variety of ECM proteins, including collagen type IV (Coll IV), leads to an increase in tyrosine phosphorylation and activation of FAK. In this study, we investigated the mechanism of activation of FAK and its downstream extracellular signal-regulated kinase (ERK)-1/2 signaling following stimulation by interleukin (IL)-1alpha and adhesion to ECM with subsequent enhancement of pancreatic cancer cell adhesion and invasion. Results: In immunoblotting analysis, all three pancreatic cancer cell lines (AsPC-1, BxPC-3, and Capan-2) expressed the protein of FAK and beta1 integrin. Enhancement of FAK protein association with beta1 integrin when cells were plated on Coll IV was more increased by stimulation with IL-1alpha. Preincubation with anti-beta1 integrin antibody and FAK siRNA transfection inhibited the association of FAK with beta1 integrin of pancreatic cancer cells. FAK phosphorylation was observed by adhesion to Coll IV, furthermore, stronger FAK phosphorylation was observed by stimulation with IL-1alpha of pancreatic cancer cells adhered to Coll IV in time-dependent manner. Genistein, a tyrosine kinase inhibitor, markedly inhibited the FAK phosphorylation. IL-1alpha stimulation and Coll IV adhesion enhanced the activation of Ras, as evidenced by the increased Ras-GTP levels in pancreatic cancer cells. Activation of Ras correlated with the phosphorylation of ERK. While not statistical affecting the apoptosis of pancreatic cancer cells, IL-1alpha-induced adhesion and invasion on Coll IV were inhibited with FAK gene silencing by siRNA, beta1 integrin blocking, and inhibition of FAK phosphorylation. PD98059, a MEK inhibitor, also inhibited IL-1alpha-induced enhancement of adhesion and invasion in pancreatic cancer cells. Conclusions: Our results demonstrated that activation of FAK is involved with the aggressive capability in pancreatic cancer through Ras/ERK signaling pathway. Based on our results, we suggest that the modification of IL-1, FAK, and integrins functions might be a novel therapeutic approach to aggressive spread of pancreatic cancer.

  • Activation of p53, inhibition of telomerase activity and induction of estrogen receptor beta are associated with the anti-growth effects of combination of ovarian hormones and retinoids in immortalized human mammary epithelial cells - Background: A full-term pregnancy has been associated with reduced risk for developing breast cancer. In rodent models, the protective effect of pregnancy can be mimicked with a defined regimen of estrogen and progesterone combination (E/P). However, the effects of pregnancy levels of E/P in humans and their underlying mechanisms are not fully understood. In this report, we investigated the growth inhibitory effects of pregnancy levels of E/P and both natural and synthetic retinoids in an immortalized human mammary epithelial cell line, 76N TERT cell line. Results: We observed that cell growth was modestly inhibited by E/P, 9-cis-retinoic acid (9-cis RA) or all-trans-retinoic acid (ATRA), and strongly inhibited by N-(4-hydroxyphenyl) retinamide (HPR). The growth inhibitory effects of retinoids were further increased in the presence of E/P, suggesting their effects are additive. In addition, our results showed that both E/P and retinoid treatments resulted in increased RARE and p53 gene activity. We further demonstrated that p53 and p21 protein expression were induced following the E/P and retinoid treatments. Furthermore, we demonstrated that while the telomerase activity was moderately inhibited by E/P, 9-cis RA and ATRA, it was almost completely abolished by HPR treatment. These inhibitions on telomerase activity by retinoids were potentiated by co-treatment with E/P, and correlated well with their observed growth inhibitory effects. Finally, this study provides the first evidence that estrogen receptor beta is up-regulated in response to E/P and retinoid treatments. Conclusion: Taken together, our studies show that part of the anti-growth effects of E/P and retinoids is p53 dependent, and involve activation of p53 and subsequent induction of p21 expression. Inhibition of telomerase activity and up-regulation of estrogen receptor beta are also associated with the E/P- and retinoid-mediated growth inhibition. Our studies also demonstrate that the potency of retinoids on cell growth inhibition may be increased through combination of estrogen and progesterone treatment.

  • Activation of PAR4 Induces a Distinct Actin Fiber Formation via p38 MAPK in Human Lung Endothelial Cells -

    Protease-activated receptors (PARs) are multifunctional G protein–coupled receptors. Among the four existing PARs, PAR4 is preferentially expressed in the human lung tissue. However, the function of PAR4 has not been defined in the lung endothelial cells. Because PAR1-mediated cellular effects are deeply related to the morphological changes, we focused on the actin fiber and p38 mitogen-activated protein kinase (MAPK) signaling involved in actin polymerization to elucidate the role of PAR4. RT-PCR and Western blot analyses identified PAR4 expression in human pulmonary artery endothelial cells and in human microvascular endothelial cells from lung. We then examined the changes in actin fibers in endothelial cells treated with PAR4-activating peptide. PAR1-activating peptide was used for comparison. Activation of PAR4 and PAR1 by their corresponding peptides induced actin fiber formation; however, the actin filaments were broadly bundled in PAR4 as compared with the ringlike actin filaments in PAR1 activation. Correspondingly, the magnitude of p38 MAPK phosphorylation was different between cells treated with PAR4 and PAR1, with PAR4-activating peptide showing a significantly higher sensitivity to p38 MAPK inhibitor, SB203580. Taken together, these results demonstrate that activation of PAR4 results in the formation of actin fiber distinct from that by PAR1 activation, suggesting PAR4 may play specific roles in the lung endothelial cells. (J Histochem Cytochem 53:1121–1129, 2005)


  • Acupuncture prevents cognitive deficits and oxidative stress in cerebral multi-infarction rats. -
    Related Articles

    Acupuncture prevents cognitive deficits and oxidative stress in cerebral multi-infarction rats.

    Neurosci Lett. 2005 Oct 14;

    Authors: Liu CZ, Yu JC, Zhang XZ, Fu WW, Wang T, Han JX

    The aim of this study is to investigate the effects of acupuncture on cognitive deficits and oxidative stress in cerebral multi-infarction rats. The results showed that acupunctural treatment attenuated memory impairment induced by cerebral multi-infarction, as evaluated by shortened escape latency and increased swimming time of rats with memory impairment in the target quadrant. The data additionally suggested that acupunctural treatment ameliorated oxidative injuries induced by cerebral multi-infarction by increasing the activities of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) in the hippocampus. Further investigation by in situ hybridization and immunohistochemistry revealed that acupunctural treatment significantly increased the expression of CuZnSOD mRNA and protein in the hippocampus of the impaired rats. The findings demonstrate that acupuncture can exert beneficial effects on spatial memory and antioxidant status of cerebral multi-infarction rats.

    PMID: 16236447 [PubMed - as supplied by publisher]


  • ADAMTS13, Thrombotic Thrombocytopenic Purpura, and Hemolytic Uremic Syndrome - No abstract available

  • Addition of 5-fluorouracil to doxorubicin-paclitaxel sequence increases caspase-dependent apoptosis in breast cancer cell lines - IntroductionThe aim of the study was to evaluate the activity of a combination of doxorubicin (Dox), paclitaxel (Pacl) and 5-fluorouracil (5-FU), to define the most effective schedule, and to investigate the mechanisms of action in human breast cancer cells. Methods: The study was performed on MCF-7 and BRC-230 cell lines. The cytotoxic activity was evaluated by sulphorhodamine B assay and the type of drug interaction was assessed by the median effect principle. Cell cycle perturbation and apoptosis were evaluated by flow cytometry, and apoptosis-related marker (p53, bcl-2, bax, p21), caspase and thymidylate synthase (TS) expression were assessed by western blot. Results: 5-FU, used as a single agent, exerted a low cytotoxic activity in both cell lines. The Dox→Pacl sequence produced a synergistic cytocidal effect and enhanced the efficacy of subsequent exposure to 5-FU in both cell lines. Specifically, the Dox→Pacl sequence blocked cells in the G2-M phase, and the addition of 5-FU forced the cells to progress through the cell cycle or killed them. Furthermore, Dox→Pacl pretreatment produced a significant reduction in basal TS expression in both cell lines, probably favoring the increase in 5-FU activity. The sequence Dox→Pacl→48-h washout→5-FU produced a synergistic and highly schedule-dependent interaction (combination index < 1), resulting in an induction of apoptosis in both experimental models regardless of hormonal, p53, bcl-2 or bax status. Apoptosis in MCF-7 cells was induced through caspase-9 activation and anti-apoptosis-inducing factor hyperexpression. In the BRC-230 cell line, the apoptotic process was triggered only by a caspase-dependent mechanism. In particular, at the end of the three-drug treatment, caspase-8 activation triggered downstream executioner caspase-3 and, to a lesser degree, caspase-7. Conclusion: In our experimental models, characterized by different biomolecular profiles representing the different biology of human breast cancers, the schedule Dox→Pacl→48-h washout→5-FU was highly active and schedule-dependent and has recently been used to plan a phase I/II clinical protocol.

  • Age-related differences in 1p and 19q deletions in oligodendrogliomas - Background: Recent reports indicate that anaplastic oligodendrogliomas frequently show allelic losses on chromosome arms 1p and 19q, and that these deletions are associated with better chemotherapeutic response and overall patient survival. Because of the diversified genetic makeup of the population and the centralized provincial referral system for brain tumor patients in Manitoba, the epidemiological features of such tumors sometimes differ from the published data acquired from non-community based settings. In this study, we assessed the prevalence of allelic deletions for chromosome arms 1p and 19q in anaplastic and in low-grade oligodendrogliomas in the Manitoba population. Methods: Loss of heterozygosity (LOH) analysis of brain tumors was carried out using 4 microsatellite markers (D1S508, D1S2734, D19S219 and D19S412) and a PCR based assay. The tumors were consecutively acquired during the period September 1999–March 2001 and a total of 63 tumors were assessed. Results: We found that allelic loss of chromosome 1p and 19q was higher in oligodendrogliomas than in other diffuse gliomas and that for anaplastic oligodendrogliomas, younger patients exhibited significantly more deletions than older patients (>60 years of age). Conclusions: These studies suggest that age may be a factor in the genetic alterations of oligodendrogliomas. In addition, these studies demonstrate that this assay can easily be carried out in a cost-effective manner in a small tertiary center.

  • Altered Expression Patterns of Heterogeneous Nuclear Ribonucleoproteins A2 and B1 in the Adrenal Cortex -

    Several proteins implicated in hormonogenesis of the adrenal cortex have alternatively spliced isoforms, which respond differently to adrenocorticotropic hormone (ACTH). Heterogeneous nuclear ribonucleoproteins A2 and B1 are among the abundant pre-mRNA-binding proteins involved in alternative splicing. We examined the expression of A2 and B1 in normal adrenal cortex and tumors. B1 was variably expressed in the zona fasciculata-reticularis, although A2 was diffusely expressed in the three zones. B1 was more abundant in compact cells than clear cells, and B1 expression was frequent in the zona reticularis, which consists mainly of compact cells. In three kinds of cortical adenomas autonomously producing hormones, B1 was generally overexpressed and there were no significant differences among them. In cortisol-producing tumors, non-tumor parts of the cortex, which were generally atrophic due to low ACTH, had less B1 protein than normal adrenals. These results suggested a correlation between B1 expression and the hormonal activity responding to ACTH. In vitro ACTH stimulation induced a biphasic expression of B1 in an H295R cortical carcinoma cell line, and it paralleled hormonogenesis. Conclusively, B1 expression varied in relation to the hormonal activity responding to the ACTH, and it may provide a key to elucidating the splicing mechanisms involved in hormonogenesis.

    (J Histochem Cytochem 53:487–495, 2005)


  • Altered Expression Patterns of Heterogeneous Nuclear Ribonucleoproteins A2 and B1 in the Adrenal Cortex -

    Several proteins implicated in hormonogenesis of the adrenal cortex have alternatively spliced isoforms, which respond differently to adrenocorticotropic hormone (ACTH). Heterogeneous nuclear ribonucleoproteins A2 and B1 are among the abundant pre-mRNA-binding proteins involved in alternative splicing. We examined the expression of A2 and B1 in normal adrenal cortex and tumors. B1 was variably expressed in the zona fasciculata-reticularis, although A2 was diffusely expressed in the three zones. B1 was more abundant in compact cells than clear cells, and B1 expression was frequent in the zona reticularis, which consists mainly of compact cells. In three kinds of cortical adenomas autonomously producing hormones, B1 was generally overexpressed and there were no significant differences among them. In cortisol-producing tumors, non-tumor parts of the cortex, which were generally atrophic due to low ACTH, had less B1 protein than normal adrenals. These results suggested a correlation between B1 expression and the hormonal activity responding to ACTH. In vitro ACTH stimulation induced a biphasic expression of B1 in an H295R cortical carcinoma cell line, and it paralleled hormonogenesis. Conclusively, B1 expression varied in relation to the hormonal activity responding to the ACTH, and it may provide a key to elucidating the splicing mechanisms involved in hormonogenesis.

    (J Histochem Cytochem 53:487–495, 2005)


  • Altered Expression Patterns of Heterogeneous Nuclear Ribonucleoproteins A2 and B1 in the Adrenal Cortex -

    Several proteins implicated in hormonogenesis of the adrenal cortex have alternatively spliced isoforms, which respond differently to adrenocorticotropic hormone (ACTH). Heterogeneous nuclear ribonucleoproteins A2 and B1 are among the abundant pre-mRNA-binding proteins involved in alternative splicing. We examined the expression of A2 and B1 in normal adrenal cortex and tumors. B1 was variably expressed in the zona fasciculata-reticularis, although A2 was diffusely expressed in the three zones. B1 was more abundant in compact cells than clear cells, and B1 expression was frequent in the zona reticularis, which consists mainly of compact cells. In three kinds of cortical adenomas autonomously producing hormones, B1 was generally overexpressed and there were no significant differences among them. In cortisol-producing tumors, non-tumor parts of the cortex, which were generally atrophic due to low ACTH, had less B1 protein than normal adrenals. These results suggested a correlation between B1 expression and the hormonal activity responding to ACTH. In vitro ACTH stimulation induced a biphasic expression of B1 in an H295R cortical carcinoma cell line, and it paralleled hormonogenesis. Conclusively, B1 expression varied in relation to the hormonal activity responding to the ACTH, and it may provide a key to elucidating the splicing mechanisms involved in hormonogenesis.

    (J Histochem Cytochem 53:487–495, 2005)


  • Alternative initiation and splicing in dicer gene expression in human breast cells - IntroductionDicer is a ribonuclease that mediates RNA interference both at the transcriptional and the post-transcriptional levels. Human dicer gene expression is regulated in different tissues. Dicer is responsible for the synthesis of microRNAs and short temporal (st)RNAs that regulate the expression of many genes. Thus, understanding the control of the expression of the dicer gene is essential for the appreciation of double-stranded (ds)RNA-mediated pathways of gene expression. Human dicer mRNA has many upstream open reading frames (uORFs) at the 5'-leader sequences (the nucleotide sequence between the 5'-end and the start codon of the major ORF), and we studied whether these elements at the 5'-leader sequences regulate the expression of the dicer gene.MethodWe determined the 5'-leader sequences of the dicer mRNAs in human breast cells by 5'-RACE and S1-nuclease protection analysis. We have analyzed the functions of the 5'-leader variants by reporter gene expression in vitro and in vivo. Results: We found that the dicer transcripts in human breast cells vary in the sequence of their 5'-leader sequences, and that alternative promoter selection along with alternative splicing of the 5'-terminal exons apparently generate these variations. The breast cell has at least two predominant forms of dicer mRNAs, one of which has an additional 110 nucleotides at the 5'-end. Sequence comparison revealed that the first 80 nucleotides of these mRNA isoforms are encoded by a new exon located approximately 16 kb upstream of the reported start site. There are 30 extra nucleotides added to the previously reported exon 1. The human breast cells studied predominantly express two 5'-leader variants of dicer mRNAs, one with the exons 2 and 3 (long form) and the other without them (short form). By reporter gene expression analysis we found that the exon 2 and 3 sequences at the 5'-leader sequences are greatly inhibitory for the translation of the mRNA into protein. Conclusion: Dicer gene expression in human breast cells is regulated by alternative promoter selection to alter the length and composition of the 5'-leader sequence of its mRNA. Furthermore, alternative splicing of its exon 2 and 3 sequences of their pre-mRNA creates a more translationally competent mRNA in these cells.

  • Alternative splicing affects the function and tissue-specific expression of the human constitutive androstane receptor - Background: The constitutive androstane receptor (CAR) plays a key role in the control of drug metabolism and transport by mediating the phenobarbital-type induction of many phase I and II drug metabolizing enzymes and drug transporters. Results: We identified transcripts generated by four different alternative splicing events in the human CAR gene. Two of the corresponding ligand binding domain isoforms demonstrated novel functional properties: First, CAR(SV3), which is encoded by a transcript containing an lengthened exon 7, differentially transactivated target gene promoters. Second, CAR(SV2), which results from the use of an alternative 3' splice site lengthening exon 8, showed ligand-dependent instead of constitutive interaction with coactivators. Furthermore, alternatively spliced transcripts demonstrated a tissue-specific expression pattern. In most tissues, only transcripts generated by alternative splicing within exon 9 were expressed. The encoded variant demonstrated a loss-of-function phenotype. Correct splicing of exon 8 to exon 9 is restricted to only a few tissues, among them liver and small intestine for which CAR function has been demonstrated, and is associated with the induction of CAR expression during differentiation of intestinal cells. Conclusion: Due to their specific activities, CAR variant proteins SV2 and SV3 may modulate the activity of reference CAR(SV1). Furthermore, we propose that transcriptional activation and regulation of splicing of exon 9 may be coupled to ensure appropriate tissue- and differentiation state-specific expression of transcripts encoding functional CAR protein. Altogether, alternative splicing seems to be of utmost importance for the regulation of CAR expression and function.

  • Amplification and overexpression of the ID4gene at 6p22.3 in bladder cancer - Background: Amplifications at 6p22.3 are prevalent in advanced stage bladder cancer (TCC). Previous studies have identified SOX4, CDKAL, and E2F3 as targets of this amplification and therefore potential oncogenes, but the more telomeric DEK gene too has been reported as overexpressed and amplified. We have therefore investigated whether the intermediate region harboring the oncogene candidate ID4 is also part of the amplicon. Results: Expression of E2F3, DEK, and ID4 was investigated by real-time RT-PCR in 28 TCC compared to 6 normal bladder tissues and in 15 TCC cell lines compared to cultured normal urothelial cells. Expression of E2F3 as well as DEK increased on average in tumor vs. normal tissues (3-fold and 2.5-fold, resp.), but only the increase for E2F3 was statistically significant (p=0.039). ID4 overexpression was observed in selected specimens. Each of the three genes was overexpressed in several cell lines, up to 150-fold (ID4), 30-fold (E2F3), and 9-fold (DEK), but these increases were not correlated to each other. Instead, moderate (DEK) to excellent (ID4) correlations were observed with copy number increases of microsatellites near each gene. Microsatellite copy number increases were highly heterogeneous across the investigated several Mb region revealing at least three subregions of amplification. Conclusions: Extending previous reports, our data indicate that the 6p22.3 amplicon in TCC is highly heterogeneous and targets several genes in a variable fashion. Among these, expression of E2F3 and DEK appear to be generally increased in TCC, with additional increases caused by amplifications. In contrast, over-expression of ID4, which is normally predominantly expressed in testes and brain, appears to depend more strictly on gene amplification. Accordingly, the effect of amplifications at 6p22.3 in bladder cancer is expected to be non-uniform, thereby contributing to the highly variable biological and clinical behavior of advanced stage tumors. ID4 is a potential oncogene in a small subset of bladder cancers.

  • Amplification of EMSY, a novel oncogene on 11q13, in high grade ovarian surface epithelial carcinomas. -
    Related Articles

    Amplification of EMSY, a novel oncogene on 11q13, in high grade ovarian surface epithelial carcinomas.

    Gynecol Oncol. 2005 Oct 14;

    Authors: Brown LA, Irving J, Parker R, Kim H, Press JZ, Longacre TA, Chia S, Magliocco A, Makretsov N, Gilks B, Pollack J, Huntsman D

    OBJECTIVES.: Amplification of the 11q13 locus is commonly observed in a number of human cancers including both breast and ovarian cancer. Cyclin D1 and EMS1 have been implicated as candidate oncogenes involved in the emergence of amplification at this locus. Detailed analysis of the 11q13 amplicon in breast cancer led to the discovery of four regions of amplification suggesting the involvement of other genes. Here, we investigate the role of EMSY, a recently described BRCA2 interacting protein, as a key element of the 11q13 amplicon in ovarian cancer. EMSY maps to 11q13.5 and is amplified in 13% of breast and 17% of ovarian carcinomas. METHODS.: EMSY amplification was assessed by fluorescent in-situ hybridization (FISH) in 674 ovarian cancers in a tissue microarray and correlated with histopathological subtype and tumor grade. A detailed map of the 11q13 amplicon in 51 cases of ovarian cancer was obtained using cDNA-array-based comparative genomic hybridization (aCGH). To further characterize the role of EMSY within this amplicon, we evaluated both the amplification profiles and RNA expression levels of EMSY and two other genes from the 11q13 amplicon in an additional series of 22 ovarian carcinomas. RESULTS.: EMSY amplification was seen in 52/285 (18%) high grade papillary serous carcinomas, 4/27 (15%) high grade endometrioid carcinomas, 3/38 (8%) clear cell carcinomas, and 3/10 (30%) undifferentiated carcinomas. aCGH mapping of 11q13 in ovarian cancer showed that EMSY localized to the region with the highest frequency of copy number gain. Cyclin D1 and EMS1 showed a lower frequency of copy number gain. A highly significant correlation between EMSY gene amplification and RNA expression was also observed (P = 0.0001). This was a stronger correlation than for other genes at 11q13 including Cyclin D1 and PAK1. CONCLUSIONS.: These findings support the role of EMSY as a key oncogene within the 11q13 amplicon in ovarian cancer.

    PMID: 16236351 [PubMed - as supplied by publisher]


  • Amplitude-dependency of response of SI cortex to flutter stimulation - Background: It is established that increasing the amplitude of a flutter stimulus increases its perceived intensity. Although many studies have examined this phenomenon with regard to the responding afferent population, the way in which the intensity of a stimulus is coded in primary somatosensory cortex (SI) remains unclear. Results: Optical intrinsic signal (OIS) imaging was used to study the evoked responses in SI of anesthetized squirrel monkeys by 25 Hz sinusoidal vertical skin displacement stimulation. Stimuli were 10sec duration with a 50sec inter-stimulus interval. Stimulus amplitude ranged from 50 to 400 microns and different amplitudes were interleaved. Control levels of activity were measured in the absence of stimulation, and used to compare with activation levels evoked by the different stimulus amplitudes. Stimulation of a discrete skin site on the forelimb evoked a prominent increase in absorbance within the forelimb representational region in cytoarchitectonic areas 3b and 1 of the contralateral hemisphere. An increase in stimulus amplitude led to a proportional increase in the magnitude of the absorbance increase in this region of areas 3b and 1 while surrounding cortex underwent a decrease in absorbance. Correlation maps revealed that as stimulus amplitude is increased, the spatial extent of the activated region in SI remains relatively constant, and the activity within this region increases progressively. Additionally, as stimulus amplitude is increased to suprathreshold levels, correlated activity in the surround of the activated SI territory becomes negative, suggesting an increase in inhibition of neuronal activity within these regions. Conclusions: Increasing the amplitude of a flutter stimulus leads to a proportional increase in absorbance within the forelimb representational region of SI. This most likely reflects an increase in the firing rate of neurons in this region of SI. The relatively constant spatial extent of this stimulus-evoked increase in absorbance suggests that an increase in the amplitude of a 25 Hz skin stimulus does not evoke a larger area of SI neuronal activation due to an amplitude-dependent lateral inhibitory effect that spatially funnels the responding SI neuronal population.

  • An Alternative Pretreatment Procedure in Animal Transmissible Spongiform Encephalopathies Diagnosis Using PrPsc Immunohistochemistry -

    Because of its sensitivity, immunohistochemistry (IHC) of abnormal prion protein (PrPsc) is used more often in the diagnosis of transmissible spongiform encephalopathies (TSEs), such as scrapie and bovine spongiform encephalopathy (BSE). PrPsc IHC requires a combination of pretreatments (chemical, heating, and enzymatic). The method of application may depend on the anti-prion antibody considered. If these pretreatments are efficient for diagnostic purpose, it may, however, be interesting to use an alternative method to efficiently detect PrPsc IHC immunohistochemically using chemical pretreatments solely. Here we describe such pretreatments reporting the difficulty (section adhesion) but also the potential advantages of such methods (easy, quick, inexpensive, and amplifying effect). (J Histochem Cytochem 53:1199–1202, 2005)


  • An Alternative Pretreatment Procedure in Animal Transmissible Spongiform Encephalopathies Diagnosis Using PrPsc Immunohistochemistry -

    Because of its sensitivity, immunohistochemistry (IHC) of abnormal prion protein (PrPsc) is used more often in the diagnosis of transmissible spongiform encephalopathies (TSEs), such as scrapie and bovine spongiform encephalopathy (BSE). PrPsc IHC requires a combination of pretreatments (chemical, heating, and enzymatic). The method of application may depend on the anti-prion antibody considered. If these pretreatments are efficient for diagnostic purpose, it may, however, be interesting to use an alternative method to efficiently detect PrPsc IHC immunohistochemically using chemical pretreatments solely. Here we describe such pretreatments reporting the difficulty (section adhesion) but also the potential advantages of such methods (easy, quick, inexpensive, and amplifying effect). (J Histochem Cytochem 53:1199–1202, 2005)


  • An Approach for Quantitative Assessment of Fluorescence In Situ Hybridization (FISH) Signals for Applied Human Molecular Cytogenetics -

    A number of applied molecular cytogenetic studies require the quantitative assessment of fluorescence in situ hybridization (FISH) signals (for example, interphase FISH analysis of aneuploidy by chromosome enumeration DNA probes; analysis of somatic pairing of homologous chromosomes in interphase nuclei; identification of chromosomal heteromorphism after FISH with satellite DNA probes for differentiation of parental origin of homologous chromosome, etc.). We have performed a pilot study to develop a simple technique for quantitative assessment of FISH signals by means of the digital capturing of microscopic images and the intensity measuring of hybridization signals using Scion Image software, commonly used for quantification of electrophoresis gels. We have tested this approach by quantitative analysis of FISH signals after application of chromosome-specific DNA probes for aneuploidy scoring in interphase nuclei in cells of different human tissues. This approach allowed us to exclude or confirm a low-level mosaic form of aneuploidy by quantification of FISH signals (for example, discrimination of pseudo-monosomy and artifact signals due to over-position of hybridization signals). Quantification of FISH signals was also used for analysis of somatic pairing of homologous chromosomes in nuclei of postmortem brain tissues after FISH with "classical" satellite DNA probes for chromosomes 1, 9, and 16. This approach has shown a relatively high efficiency for the quantitative registration of chromosomal heteromorphism due to variations of centromeric alphoid DNA in homologous parental chromosomes. We propose this approach to be efficient and to be considered as a useful tool in addition to visual FISH signal analysis for applied molecular cytogenetic studies. (J Histochem Cytochem 53:401–408, 2005)


  • An extrahippocampal projection from the dentate gyrus to the olfactory tubercle - Background: The dentate gyrus is well known for its mossy fiber projection to the hippocampal field 3 (CA3) and its extensive associational and commissural connections. The dentate gyrus, on the other hand, has only few projections to the CA1 and the subiculum, and none have clearly been shown to extrahippocampal target regions. Results: Using anterograde and retrograde tracer techniques in the Madagascan lesser hedgehog tenrec (Afrosoricidae, Afrotheria) it was shown in this study that the dentate hilar region gave rise to a faint, but distinct, bilateral projection to the most rostromedial portion of the olfactory tubercle, particularly its molecular layer. Unlike the CA1 and the subiculum the dentate gyrus did not project to the accumbens nucleus. A control injection into the medial septum-diagonal band complex also retrogradely labeled cells in the dentate hilus, but these neurons were found immediately adjacent to the heavily labeled CA3, while the tracer injections into the rostromedial tubercle did not reveal any labeling in CA3. Conclusions: The dentate hilar neurons projecting to the olfactory tubercle cannot be considered displaced cells of CA3 but represent true dentato-tubercular projection neurons. This projection supplements the subiculo-tubercular projection. Both terminal fields overlap among one another as well as with the fiber terminations arising in the anteromedial frontal cortex. The rostromedial olfactory tubercle might represent a distinct ventral striatal target area worth investigating in studies of the parallel processing of cortico-limbic information in tenrec as well as in cat and monkey.

  • An Update on Gene Therapy for Hemophilia - More than two thirds of the world's hemophiliacs currently face a drastically shortened life of pain and disability because they do not have access to safe factor concentrates, as these products are highly expensive and in limited supply. For these individuals, gene therapy remains an important avenue of hope because of its potential for a durable cure following a single therapeutic manipulation. The results of recent hemophilia gene clinical trials are encouraging, although they have failed to demonstrate sustained correction of the bleeding diathesis. Although many obstacles still remain, continuing technologic improvements have resulted in impressive advances in this field, which bodes well for patients with hemophilia and other genetic disorders.

  • Anal screening cytology - This issue of CytoJournal contains an article on screening for anal intraepithelial neoplasia in high-risk male patients. This accompanying Editorial focuses on current understanding of this relatively new disease entity, with insights as to the potential role of screening cytopathology in the epidemiology, pathophysiology and clinical management of this HIV and HPV related anal lesion, which predominates in male patients living long-term with AIDS. Mention is made of techniques of obtaining samples, methods of preparation, and morphologic classification. Issues of anoscopic confirmation, as well as topical and surgical management are emphasized. The similarity of initial experiences in anal screening to problems encountered early in cervical cancer screening programs several decades ago, are highlighted.

  • Analysis of Cell-free Fetal DNA in Plasma and Serum of Pregnant Women -

    Sixty blood samples from pregnant women during gestational weeks 9–28 were investigated. Cell-free fetal DNA was extracted from maternal plasma or serum to be detected by nested PCR for determination of fetal gender. The SRY gene as a marker for fetal Y chromosome was detected in 34/36 women carrying a male fetus. In 3/24 women carrying female fetuses, the SRY sequence was also detected. Overall, fetal sex was correctly predicted in 91.7% of the cases. Therefore, the new, non-invasive method of prenatal diagnosis of fetal gender for women at risk of producing children with X-linked disorders is reliable, secure, and can substantially reduce invasive prenatal tests.

    (J Histochem Cytochem 53:297–299, 2005)


  • Analysis of Green Fluorescent Protein Expression in Transgenic Rats for Tracking Transplanted Neural Stem/Progenitor Cells -

    Green fluorescent protein (GFP) expression was evaluated in tissues of different transgenic rodents—Sprague-Dawley (SD) rat strain [SD-Tg(GFP)Bal], W rat strain [Wistar-TgN(CAG-GFP)184ys], and M mouse strain [Tg(GFPU)5Nagy/J]—by direct fluorescence of native GFP expression and by immunohistochemistry. The constitutively expressing GFP transgenic strains showed tissue-specific differences in GFP expression, and GFP immunohistochemistry amplified the fluorescent signal. The fluorescence of stem/progenitor cells cultured as neurospheres from the ependymal region of the adult spinal cord from the GFP SD and W rat strains was assessed in vitro. After transplantation of the cells into wild-type spinal cord, the ability to track the grafted cells was evaluated in vivo. Cultured stem/progenitor cells from the SD strain required GFP immunostaining to be visualized. Likewise, after transplantation of SD cells into the spinal cord, immunohistochemical amplification of the GFP signal was required for detection. In contrast, GFP expression of stem/progenitor cells generated from the W strain was readily detected by direct fluorescence both in vitro and in vivo without the need for immunohistochemical amplification. The cultured stem/progenitor cells transplanted into the spinal cord survived for at least 49 days after transplantation, and continued to express GFP, demonstrating stable expression of the GFP transgene in vivo. (J Histochem Cytochem 53:1215–1226, 2005)


  • Analysis of Green Fluorescent Protein Expression in Transgenic Rats for Tracking Transplanted Neural Stem/Progenitor Cells -

    Green fluorescent protein (GFP) expression was evaluated in tissues of different transgenic rodents—Sprague-Dawley (SD) rat strain [SD-Tg(GFP)Bal], W rat strain [Wistar-TgN(CAG-GFP)184ys], and M mouse strain [Tg(GFPU)5Nagy/J]—by direct fluorescence of native GFP expression and by immunohistochemistry. The constitutively expressing GFP transgenic strains showed tissue-specific differences in GFP expression, and GFP immunohistochemistry amplified the fluorescent signal. The fluorescence of stem/progenitor cells cultured as neurospheres from the ependymal region of the adult spinal cord from the GFP SD and W rat strains was assessed in vitro. After transplantation of the cells into wild-type spinal cord, the ability to track the grafted cells was evaluated in vivo. Cultured stem/progenitor cells from the SD strain required GFP immunostaining to be visualized. Likewise, after transplantation of SD cells into the spinal cord, immunohistochemical amplification of the GFP signal was required for detection. In contrast, GFP expression of stem/progenitor cells generated from the W strain was readily detected by direct fluorescence both in vitro and in vivo without the need for immunohistochemical amplification. The cultured stem/progenitor cells transplanted into the spinal cord survived for at least 49 days after transplantation, and continued to express GFP, demonstrating stable expression of the GFP transgene in vivo. (J Histochem Cytochem 53:1215–1226, 2005)


  • Analysis of the CCR3 promoter reveals a regulatory region in exon 1 that binds GATA-1 - Background: CC Chemokine Receptor 3 (CCR3), the major chemokine receptor expressed on eosinophils, binds promiscuously to several ligands including eotaxins 1, 2, and 3. Even though the only cells that consistently accumulate following eotaxin administration in vivo are myeloid cells (primarily eosinophils), other cell types have recently been shown to express CCR3. It is therefore important to elucidate the molecular mechanisms regulating receptor expression. Results: In order to define regions responsible for CCR3 transcription, a DNAse hypersensitive site was identified in the vicinity of exon 1. Coupled with our previous data implicating exon 1 in CCR3 transcription, we hypothesized that transcription factors bind to exon-1. Electrophoretic mobility shift analysis revealed that nuclear proteins in eosinophilic cells bound to exon 1. Furthermore, antibody interference and mutation studies demonstrated GATA-1 binding to exon 1. In order to test the 1.6-kb CCR3 promoter element (that includes exon 1) for in vivo function, this region was used to generate transgenic mice that expressed a reporter protein. Strong transgene expression was achieved, with the pattern of expression suggesting a broad acting promoter. Conclusion: The transcription factor GATA-1 binds to CCR3 exon 1. The 1.6-kb CCR3 promoter element, that includes exon 1, is a strong promoter in vivo.

  • Androgen receptor signaling is required for androgen-sensitive human prostate cancer cell proliferation and survival - Background: Androgens and androgen receptors (AR) regulate normal prostate development and growth. They also are involved in pathological development of prostatic diseases, including benign prostatic hyperplasia (BPH) and prostate cancer (PCa). Antiandrogen therapy for PCa, in conjunction with chemical or surgical castration, offers initial positive responses and leads to massive prostate cell death. However, cancer cells later appear as androgen-independent PCa. To investigate the role of AR in prostate cell proliferation and survival, we introduced a vector-based small interfering RNA (siRNA). This siRNA targeted 5'-untranslated region of AR mRNA for extended suppression of AR expression in androgen-sensitive human prostate LNCaP cells. Results: The siRNA design successfully suppressed endogenous AR expression, as revealed by western blotting and immunofluorescence staining in LNCaP cells. LNCaP cells did not proliferate in the absence of AR and underwent apoptosis, based on elevated phospho-Histone H2B expression and higher number of apoptotic body as compared to control cells. Conclusion: We demonstrated that AR is vital for prostate cell proliferation and survival in this androgen-sensitive prostate cell line. These results further strengthen the hypothesis that AR can be a therapeutic target for treating androgen-sensitive stages of PCa. Unlike antiandorgens, however, siRNA targeting AR provides a direct inactivation of AR function through the suppression of AR protein expression.

  • Anemia in HIV-Infected Adults: -Epidemiology, Pathogenesis, and -Clinical Management - Anemia is the most common cytopenia seen in people with HIV. Independent of CD4 count and HIV-viral load, anemia has been shown to correlate with increased mortality. -Furthermore, successful treatment of anemia has been shown to reduce this risk of death in a comparison with paitents with similar immunologic and virologic parameters who are not treated. Women, blacks, injection drug users, and people with advanced disease suffer disproportionally from anemia and should be screened. The pathogenesis of anemia in HIV is complex and may result from opportunistic infections, -nutritional deficiencies, AIDS-associated malignancies, -medications, or alteration in hematopoeisis induced by HIV itself. A careful review of the patient's past medical history, medications, symptoms, and basic laboratory studies often leads to a treatable cause(s). For patients without secondary causes of anemia, a combination of highly active antiretroviral therapy (HAART) and supplemental erythropoietin leads to improved outcomes. Given the importance of completing therapy on adequate doses of both interferon and ribavirin, effective management of anemia in HIV/Hepatitis C (HCV)-coinfected patients is particularly important.

  • Another Small Supernumerary Marker Chromosome (sSMC) Derived from Chromosome 2: Towards a Genotype/Phenotype Correlation -

    Here we report a prenatally detected small supernumerary marker chromosome (sSMC) derived from chromosome 2 as demonstrated by cenM-FISH (centromere-specific multicolor fluorescence in situ hybridization). By application of a recently described subcentromere-specific probe set (subcenM-FISH) for chromosome 2, the presence of a small partial trisomy due to a karyotype 47,XX,+r(2)(::p11.1->q11.2::) was demonstrated. Including this case, a total of 11 patients with sSMC(2) are described throughout the literature. Based on that data, a first genotype/phenotype correlation according to the size and structure of the marker is suggested. (J Histochem Cytochem 53:367–370, 2005)


  • Anthrax vaccine design: strategies to achieve comprehensive protection against spore, bacillus, and toxin - The successful use of Bacillus anthracis as a lethal biological weapon has prompted renewed research interest in the development of more effective vaccines against anthrax. The disease consists of three critical components: spore, bacillus, and toxin, elimination of any of which confers at least partial protection against anthrax. Current remedies rely on postexposure antibiotics to eliminate bacilli and pre- and postexposure vaccination to target primarily toxins. Vaccines effective against toxin have been licensed for human use, but need improvement. Vaccines against bacilli have recently been developed by us and others. Whether effective vaccines will be developed against spores is still an open question. An ideal vaccine would confer simultaneous protection against spores, bacilli, and toxins. One step towards this goal is our dually active vaccine, designed to destroy both bacilli and toxin. Existing and potential strategies towards potent and effective anthrax vaccines are discussed in this review.

  • Anti-lipid phosphate phosphohydrolase-3 (LPP3) antibody inhibits bFGF and VEGF induced capillary morphogenesis of endothelial cells - Background: Angiogenesis, or the remodeling of existing vasculature serves as a lifeline to nourish developing embryos and starved tissues, and to accelerate wound healing, diabetic retinopathy, and tumor progression. Recent studies indicate that angiogenesis requires growth factor activity as well as cell adhesion events mediated by alpha5 beta1 and alphav beta3 integrins. We previously demonstrated that human lipid phosphate phosphohydrolase-3 (LPP3) acts as a cell-associated ligand for alpha5 beta1 and alphav beta3 integrins. Here, we test the hypothesis that an anti-LPP3 antibody can inhibit basic fibroblast growth factor (bFGF)- and vascular endothelial growth factor (VEGF)-induced capillary morphogenesis of endothelial cells (ECs). Results: We report that bFGF and VEGF up-regulate LPP3 protein expression in ECs. Immunoprecipitation analyses show that LPP3 is a cell surface protein and undergoes N-glycosylation. Fluorescent activated cell sorting (FACS) data suggest that anti-LPP3-RGD detects native neoepitope on the surface of activated ECs. Moreover, we demonstrate LPP3 protein expression in tumor endothelium alongside VEGF. The embedding of ECs into three-dimensional type I collagen in the presence of bFGF and VEGF induces capillary formation. Importantly, we show that the addition of an anti-LPP3 antibody specifically and significantly blocks bFGF- and VEGF-induced capillary morphogenesis of ECs. Conclusion: These data suggest that activated ECs as well as tumor endothelium express LPP3 protein. In an in vitro assay, the anti-LPP3-RGD specifically blocks bFGF and VEGF induced capillary morphogenesis of ECs. Our results, therefore, suggest a role for LPP3 in angiogenesis.

  • Antibodies that label paraffin-embedded mouse tissues: a collaborative endeavor. -
    Related Articles

    Antibodies that label paraffin-embedded mouse tissues: a collaborative endeavor.

    Toxicol Pathol. 2004 Mar-Apr;32(2):181-91

    Authors: Mikaelian I, Nanney LB, Parman KS, Kusewitt DF, Ward JM, Näf D, Krupke DM, Eppig JT, Bult CJ, Seymour R, Ichiki T, Sundberg JP

    Histology and immunohistochemistry are important tools in the study of human diseases and their respective animal models. The study of mouse models has been hampered by the absence of a large set of mouse-specific antibodies adapted to paraffin-embedded tissues. A total of 196 antibodies were tested on paraffin-embedded mouse tissues preserved in five different fixatives (Fekete's acid-alcohol-formalin, 10% neutral buffered formalin, 4% paraformaldehyde, IHC Zinc Fixative, and Bouin's fixative). The antibodies were targeted to proteins of the cytoplasm (n = 100), plasma membrane (n = 48), nucleus (n = 36), extracellular compartment (n = 5), cytoplasm/cell membrane (n = 4), and viral proteins (n = 3). A total of 83 antibodies provided an adequate signal to noise ratio. Of these, adequate labeling required heat-mediated epitope retrieval or enzymatic digestion for 32 and 8 antibodies, respectively. Epitope recognition was best for tissues fixed with Fekete's acid-alcohol-formalin. However, some proteins could be detected only in IHC Zinc Fixative, confirming that there is no single fixative suitable for the preservation of all epitopes. Four of 13 antibodies that failed to label their cellular targets on tissue sections successfully labeled whole-mount tissues, indicating that tissue processing plays an important role in epitope degradation. Regularly updated information on immunohistochemistry of normal and neoplastic mouse tissues is accessible online at (http://tumor.informatics.jax.org); links to antibody suppliers' web sites are provided.

    PMID: 15200156 [PubMed - indexed for MEDLINE]


  • Antibody selection in immunohistochemical detection of cyclin d1 in mantle cell lymphoma. -
    Related Articles

    Antibody selection in immunohistochemical detection of cyclin d1 in mantle cell lymphoma.

    Am J Clin Pathol. 2005 Nov;124(5):1-8

    Authors: Torlakovic E, Nielsen S, Vyberg M

    An assessment in Nordic immunohistochemical Quality Control (NordiQC) revealed that only 23% participant laboratories performed optimal staining for detection of cyclin D1 (CyD1) in mantle cell lymphoma (MCL). False-negative results were secondary to suboptimal protocols. We compared the 5 anti-CyD1 antibodies (monoclonal SP4, P2D11F11, and DCS-6 and polyclonal CP236 and 06-137) used in the Scandinavian laboratories. Evaluated were 31 MCLs, 16 other malignant lymphomas, and 19 samples of normal tissues. Sensitivity was as follows: CP236, 100%; SP4, 95%; P2D11F11, 90%; DCS-6, 84%; and 06-137, 53%. SP4 produced the strongest staining. Correlation of CyD1 with the proliferative index was best with polyclonal antibodies CP236 and 06-137. The use of heat-induced epitope retrieval in an alkaline buffer such as 1/10 mmol/L of Tris-EDTA buffer, pH 9, seemed mandatory. For the optimal detection of CyD1 expression, both SP4 and CP236 antibodies should be available in the laboratory.

    PMID: 16203276 [PubMed - in process]


  • Anticancer properties of propofol-docosahexaenoate and propofol-eicosapentaenoate on breast cancer cells - IntroductionEpidemiological evidence strongly links fish oil, which is rich in docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), with low incidences of several types of cancer. The inhibitory effects of omega-3 polyunsaturated fatty acids on cancer development and progression are supported by studies with cultured cells and animal models. Propofol (2,6-diisopropylphenol) is the most extensively used general anesthetic–sedative agent employed today and is nontoxic to humans at high levels (50 μg/ml). Clinically relevant concentrations of propofol (3 to 8 μg/ml; 20 to 50 μM) have also been reported to have anticancer activities. The present study describes the synthesis, purification, characterization and evaluation of two novel anticancer conjugates, propofol-docosahexaenoate (propofol-DHA) and propofol-eicosapentaenoate (propofol-EPA). Methods: The conjugates linking an omega-3 fatty acid, either DHA or EPA, with propofol were synthesized and tested for their effects on migration, adhesion and apoptosis on MDA-MB-231 breast cancer cells. Results: At low concentrations (25 μM), DHA, EPA or propofol alone or in combination had minimal effect on cell adhesion to vitronectin, cell migration against serum and the induction of apoptosis (only 5 to 15% of the cells became apoptotic). In contrast, the propofol-DHA or propofol-EPA conjugates significantly inhibited cell adhesion (15 to 30%) and migration (about 50%) and induced apoptosis (about 40%) in breast cancer cells. Conclusion: These results suggest that the novel propofol-DHA and propofol-EPA conjugates reported here may be useful for the treatment of breast cancer.

  • APC: the toll road to continued high quality communication - In this article we briefly review the reasons and advantages that underly our publisher's decision to introduce article-processing charges (APC) for manuscripts submitted to Cell Communication and Signaling. The charge is an attempt to develop a new business model for distributing biomedical information and has been accepted in a number of other journals. APCs will enable BioMed Central to continue to provide their excellent service and will help to establish our journal.

  • Apolipoprotein D Expression in Primary Brain Tumors: Analysis by Quantitative RT-PCR in Formalin-fixed, Paraffin-embedded Tissue -

    Apolipoprotein D (apoD) expression has been shown to correlate both with cell cycle arrest and with prognosis in several types of malignancy, including central nervous system astrocytomas and medulloblastomas. ApoD expression was investigated by real-time quantitative RT-PCR using RNA extracted from 68 formalin-fixed, paraffin-embedded brain specimens. Glyceraldehyde phosphate dehydrogenase was used as an internal control. Quantitation was achieved on all specimens. Sixteen poorly infiltrating WHO grade I glial neoplasms (i.e., pilocytic astrocytomas and gangliogliomas) showed an average 20-fold higher apoD expression level compared with the 20 diffusely infiltrating glial neoplasms (i.e., glioblastoma, anaplastic astrocytoma, oligodendrogliomas; p=0.00004). A small number of exceptions (i.e., two high-expressing glioblastomas and three low-expressing gangliogliomas) were identified. Analyzed as individual tumor groups, poorly infiltrating grade I pilocytic astrocytomas and gangliogliomas differed significantly from each tumor type within the diffusely infiltrating higher-grade category (p<0.05 for each comparison) but not from each other (p>0.05). Conversely, each individual tumor type within the diffusely infiltrating category differed significantly from both pilocytic astrocytomas and gangliogliomas (p<0.05) but did not vary from other infiltrating tumors (p>0.05). Ependymomas, non-infiltrating grade II neoplasms, expressed levels of apoD similar to or lower than levels expressed by the diffusely infiltrating gliomas. Ten medulloblastomas with survival longer than 3 years averaged slightly higher apoD expression than four fatal medulloblastomas; however, this result was not statistically significant and individual exceptions were notable. In 17 of the medulloblastomas, MIB-1 proliferation rates quantitated by image cytometry did not correlate with apoD expression. In addition, apoD expression was 5-fold higher in the slowly proliferating grade I glial neoplasms compared with non-proliferating normal brain tissue (p=0.01), suggesting that apoD expression is not simply an inverse measure of proliferation. ApoD expression measured by quantitative RT-PCR may be useful in the differential diagnosis of primary brain tumors, particularly pilocytic astrocytomas and gangliogliomas. (J Histochem Cytochem 53:963–969, 2005)


  • Apolipoprotein D Expression in Primary Brain Tumors: Analysis by Quantitative RT-PCR in Formalin-fixed, Paraffin-embedded Tissue -

    Apolipoprotein D (apoD) expression has been shown to correlate both with cell cycle arrest and with prognosis in several types of malignancy, including central nervous system astrocytomas and medulloblastomas. ApoD expression was investigated by real-time quantitative RT-PCR using RNA extracted from 68 formalin-fixed, paraffin-embedded brain specimens. Glyceraldehyde phosphate dehydrogenase was used as an internal control. Quantitation was achieved on all specimens. Sixteen poorly infiltrating WHO grade I glial neoplasms (i.e., pilocytic astrocytomas and gangliogliomas) showed an average 20-fold higher apoD expression level compared with the 20 diffusely infiltrating glial neoplasms (i.e., glioblastoma, anaplastic astrocytoma, oligodendrogliomas; p=0.00004). A small number of exceptions (i.e., two high-expressing glioblastomas and three low-expressing gangliogliomas) were identified. Analyzed as individual tumor groups, poorly infiltrating grade I pilocytic astrocytomas and gangliogliomas differed significantly from each tumor type within the diffusely infiltrating higher-grade category (p<0.05 for each comparison) but not from each other (p>0.05). Conversely, each individual tumor type within the diffusely infiltrating category differed significantly from both pilocytic astrocytomas and gangliogliomas (p<0.05) but did not vary from other infiltrating tumors (p>0.05). Ependymomas, non-infiltrating grade II neoplasms, expressed levels of apoD similar to or lower than levels expressed by the diffusely infiltrating gliomas. Ten medulloblastomas with survival longer than 3 years averaged slightly higher apoD expression than four fatal medulloblastomas; however, this result was not statistically significant and individual exceptions were notable. In 17 of the medulloblastomas, MIB-1 proliferation rates quantitated by image cytometry did not correlate with apoD expression. In addition, apoD expression was 5-fold higher in the slowly proliferating grade I glial neoplasms compared with non-proliferating normal brain tissue (p=0.01), suggesting that apoD expression is not simply an inverse measure of proliferation. ApoD expression measured by quantitative RT-PCR may be useful in the differential diagnosis of primary brain tumors, particularly pilocytic astrocytomas and gangliogliomas. (J Histochem Cytochem 53:963–969, 2005)


  • Application of Cryotechniques with Freeze-substitution for the Immunohistochemical Demonstration of Intranuclear pCREB and Chromosome Territory -

    Intranuclear localization of signal molecules and chromosome territories has become more attractive in relation to postgenomic analyses of cellular functions. Cryotechniques and freeze-substitution (CrT-FS) have been generally used for electron microscopic observation to obtain better ultrastructure and immunoreactivity. To investigate benefits of applying the CrT-FS method to immunostaining of intranuclear signal molecules and FISH for chromosome territories, we performed an immunohistochemical study of phosphorylated cAMP-responsive element binding protein (pCREB) in mouse cerebellar tissues and a FISH study of chromosome 18 territory in human thyroid tissues using various cryotechniques. The immunoreactivity of pCREB was more clearly detected without antigen retrieval treatment on sections prepared by the CrT-FS method than those prepared by the conventional dehydration method. In the FISH study, more definite probe labeling of the chromosome territory could be obtained on paraffin sections by the CrT-FS method without microwave treatment, although such labeling was not clear even with microwave treatment on sections prepared by the routine dehydration method. The CrT-FS preserved relatively native morphology by preventing shrinkage of nuclei, and produced better immunoreactivity. Because the reduction of routine pretreatments in the present study might reveal more native morphology, the CrT-FS method would be a useful technique for intranuclear immunostaining and FISH. (J Histochem Cytochem 53:55–62, 2005)


  • Application of Fetal DNA Detection in Maternal Plasma: A Prenatal Diagnosis Unit Experience -

    Non-invasive prenatal diagnosis tests based on the analysis of fetal DNA in maternal plasma have potential to be a safer alternative to invasive methods. So far, different studies have shown mainly fetal sex, fetal RhD, and quantitative variations of fetal DNA during gestation with fetal chromosomal anomalies or gestations at risk for preeclampsia. The objective of our research was to evaluate the use of fetal DNA in maternal plasma for clinical application. In our study, we have established the methodology needed for the analysis of fetal DNA. Different methods were used, according to the requirements of the assay. We have used quantitative fluorescent polymerase chain reaction (QF-PCR) to perform fetal sex detection with 90% sensitivity. The same technique permitted the detection of fetal DNA from the 10th week of gestation to hours after delivery. We have successfully carried out the diagnosis of two inherited disorders, cystic fibrosis (conventional PCR and restriction analysis) and Huntington disease (QF-PCR). Ninety percent of the cases studied for fetal RhD by real-time PCR were correctly diagnosed. The detection of fetal DNA sequences is a reality and could reduce the risk of invasive techniques for certain fetal disorders in the near future. (J Histochem Cytochem 53:307–314, 2005)


  • Artificial Neural Networks for Diagnosis and Survival Prediction in Colon Cancer - ANNs are nonlinear regression computational devices that have been used for over 45 years in classification and survival prediction in several biomedical systems, including colon cancer. Described in this article is the theory behind the three-layer free forward artificial neural networks with backpropagation error, which is widely used in biomedical fields, and a methodological approach to its application for cancer research, as exemplified by colon cancer. Review of the literature shows that applications of these networks have improved the accuracy of colon cancer classification and survival prediction when compared to other statistical or clinicopathological methods. Accuracy, however, must be exercised when designing, using and publishing biomedical results employing machine-learning devices such as ANNs in worldwide literature in order to enhance confidence in the quality and reliability of reported data.

  • Arylamine N-acetyltransferase 2 Expression in the Developing Heart -

    Murine arylamine N-acetyltransferase 2 (NAT2) is expressed in the developing heart and in the neural tube at the time of closure. Classically described as a xenobiotic metabolizing enzyme, there is increasing evidence for a distinct biological role for murine NAT2. We have characterized the expression of arylamine N-acetyltransferase 2 during cardiogenesis, mapping its expression in vivo, using a lacZ insertion deletion, and also in vitro, by measuring NAT2 enzyme activity. These findings show that cardiac Nat2 expression is both temporally and spatially regulated during development. In neonatal mice, cardiac Nat2 expression is most extensive in the central fibrous body and is evident in the atrioventricular valves and the valves of the great vessels. Whereas Nat2 expression is not detected in ventricular myocardial cells, Nat2 is strongly expressed in scattered cells in the region of the sinus node, the epicardium of the right atrial appendage, and in the pulmonary artery. Expression of active NAT2 protein is maximal when the developing heart attains the adult circulation pattern and moves from metabolizing glucose to fatty acids. NAT2 acetylating activity in cardiac tissue from Nat2–/– and Nat2+/– mice indicates a lack of compensating acetylating activity either from other acetylating enzymes or by NAT2 encoded by the wild-type Nat2 allele in Nat2+/– heterozygotes. The temporal and spatial control of murine Nat2 expression points to an endogenous role distinct from xenobiotic metabolism and indicates that Nat2 expression may be useful as a marker in cardiac development.

    (J Histochem Cytochem 53:583–592, 2005)


  • Arylamine N-acetyltransferase 2 Expression in the Developing Heart -

    Murine arylamine N-acetyltransferase 2 (NAT2) is expressed in the developing heart and in the neural tube at the time of closure. Classically described as a xenobiotic metabolizing enzyme, there is increasing evidence for a distinct biological role for murine NAT2. We have characterized the expression of arylamine N-acetyltransferase 2 during cardiogenesis, mapping its expression in vivo, using a lacZ insertion deletion, and also in vitro, by measuring NAT2 enzyme activity. These findings show that cardiac Nat2 expression is both temporally and spatially regulated during development. In neonatal mice, cardiac Nat2 expression is most extensive in the central fibrous body and is evident in the atrioventricular valves and the valves of the great vessels. Whereas Nat2 expression is not detected in ventricular myocardial cells, Nat2 is strongly expressed in scattered cells in the region of the sinus node, the epicardium of the right atrial appendage, and in the pulmonary artery. Expression of active NAT2 protein is maximal when the developing heart attains the adult circulation pattern and moves from metabolizing glucose to fatty acids. NAT2 acetylating activity in cardiac tissue from Nat2–/– and Nat2+/– mice indicates a lack of compensating acetylating activity either from other acetylating enzymes or by NAT2 encoded by the wild-type Nat2 allele in Nat2+/– heterozygotes. The temporal and spatial control of murine Nat2 expression points to an endogenous role distinct from xenobiotic metabolism and indicates that Nat2 expression may be useful as a marker in cardiac development.

    (J Histochem Cytochem 53:583–592, 2005)


  • Arylamine N-acetyltransferase 2 Expression in the Developing Heart -

    Murine arylamine N-acetyltransferase 2 (NAT2) is expressed in the developing heart and in the neural tube at the time of closure. Classically described as a xenobiotic metabolizing enzyme, there is increasing evidence for a distinct biological role for murine NAT2. We have characterized the expression of arylamine N-acetyltransferase 2 during cardiogenesis, mapping its expression in vivo, using a lacZ insertion deletion, and also in vitro, by measuring NAT2 enzyme activity. These findings show that cardiac Nat2 expression is both temporally and spatially regulated during development. In neonatal mice, cardiac Nat2 expression is most extensive in the central fibrous body and is evident in the atrioventricular valves and the valves of the great vessels. Whereas Nat2 expression is not detected in ventricular myocardial cells, Nat2 is strongly expressed in scattered cells in the region of the sinus node, the epicardium of the right atrial appendage, and in the pulmonary artery. Expression of active NAT2 protein is maximal when the developing heart attains the adult circulation pattern and moves from metabolizing glucose to fatty acids. NAT2 acetylating activity in cardiac tissue from Nat2–/– and Nat2+/– mice indicates a lack of compensating acetylating activity either from other acetylating enzymes or by NAT2 encoded by the wild-type Nat2 allele in Nat2+/– heterozygotes. The temporal and spatial control of murine Nat2 expression points to an endogenous role distinct from xenobiotic metabolism and indicates that Nat2 expression may be useful as a marker in cardiac development.

    (J Histochem Cytochem 53:583–592, 2005)


  • Assessment of Apoptosis by Immunohistochemical Markers Compared to Cellular Morphology in Ex Vivo-stressed Colonic Mucosa -

    Apoptosis competence is central to the prevention of cancer. Frequency of apoptotic cells, after a sample of colonic tissue is stressed, can be used to gauge apoptosis competence and, thus, possible susceptibility to colon cancer. The gold standard for assessment of apoptosis is morphological evaluation, but this requires an experienced microscopist. Easier-to-use immunohistochemical markers of apoptosis, applicable in archived paraffin-embedded tissue, have been commercially developed. Potentially useful apoptosis markers include cleaved cytokeratin-18 (c-CK18), cleaved caspase-3 (c-cas-3), cleaved lamin A (c-lam-A), phosphorylated histone H2AX (H2AX), cleaved poly(ADP ribose) polymerase (c-PARP), and translocation of apoptosis-inducing factor (AIF). When tissue samples from freshly resected colon segments were challenged ex vivo with the bile acid deoxycholate, ~50% of goblet cells became apoptotic by morphologic criteria. This high level of morphologic apoptosis allowed quantitative comparison with the usefulness and specificity of immunohistochemical markers of apoptosis. The antibody to c-CK18 was almost as useful and about as specific as morphology for identifying apoptotic colonic epithelial cells. Antibodies to c-cas-3, c-lam-A, and H2AX, though specific for apoptotic cells, were less useful. The antibody to c-PARP, though specific for apoptotic cells, had low usefulness, and the antibody to AIF was relatively nonspecific, under our conditions.

    (J Histochem Cytochem 53:229–235, 2005)


  • Assessment of Human Pancreatic Islet Architecture and Composition by Laser Scanning Confocal Microscopy -

    The recent success of pancreatic islet transplantation has generated considerable enthusiasm. To better understand the quality and characteristics of human islets used for transplantation, we performed detailed analysis of islet architecture and composition using confocal laser scanning microscopy. Human islets from six separate isolations provided by three different islet isolation centers were compared with isolated mouse and non-human primate islets. As expected from histological sections of murine pancreas, in isolated murine islets and cells resided at the periphery of the ßbeta;-cell core. However, human islets were markedly different in that , ßbeta;, and cells were dispersed throughout the islet. This pattern of cell distribution was present in all human islet preparations and islets of various sizes and was also seen in histological sections of human pancreas. The architecture of isolated non-human primate islets was very similar to that of human islets. Using an image analysis program, we calculated the volume of , ßbeta;, and cells. In contrast to murine islets, we found that populations of islet cell types varied considerably in human islets. The results indicate that human islets not only are quite heterogeneous in terms of cell composition but also have a substantially different architecture from widely studied murine islets.

    (J Histochem Cytochem 53:1087–1097, 2005)


  • Association between Endocrine Pancreas and Ductal System. More than an Epiphenomenon of Endocrine Differentiation and Development? -

    Traditional histological descriptions of the pancreas distinguish between the exocrine and the endocrine pancreas, as if they were two functionally distinct glands. This view has been proven incorrect and can be considered obsolete. Interactions between acinar and islet tissues have been well established through numerous studies that reveal the existence of anatomical and functional relationships between these compartments of the gland. Less attention, however, has traditionally been paid to the relationships occurring between the endocrine pancreas and the ductal system. Associations between islet tissue and ducts are considered by most researchers as only a transient epiphenomenon of endocrine development. This article reviews the evidence that has emerged in the last 10 years demonstrating the existence of stable, close, and systematic relationships between these two pancreatic compartments. Functional and pathophysiological implications are considered, and the existence of an "acinar–duct–islet" axis is put forward. The pancreas appears at present to be an integrated organ composed of three functionally related components of well-orchestrated endocrine and exocrine physiological responses. (J Histochem Cytochem 53:1071–1086, 2005)


  • Association of the Hermansky-Pudlak syndrome type-3 protein with clathrin - Background: Hermansky-Pudlak syndrome (HPS) is a disorder of lysosome-related organelle biogenesis characterized by oculocutaneous albinism and prolonged bleeding. These clinical findings reflect defects in the formation of melanosomes in melanocytes and dense bodies in platelets. HPS type-3 (HPS-3) results from mutations in the HPS3 gene, which encodes a 1004 amino acid protein of unknown function that contains a predicted clathrin-binding motif (LLDFE) at residues 172-176. Results: Clathrin was co-immunoprecipitated by HPS3 antibodies from normal but not HPS3 null melanocytes. Normal melanocytes expressing a GFP-HPS3 fusion protein demonstrated partial co-localization of GFP-HPS3 with clathrin following a 20o C temperature block. GFP-HPS3 in which the predicted clathrin-binding domain of HPS3 was mutated (GFP-HPS3-delCBD) did not co-localize with clathrin under the same conditions. Immunoelectron microscopy of normal melanocytes expressing GFP-HPS3 showed co-localization of GFP-HPS3 with clathrin, predominantly on small vesicles in the perinuclear region. In contrast, GFP-HPS3-delCBD did not co-localize with clathrin and exhibited a largely cytoplasmic distribution. Conclusion: HPS3 associates with clathrin, predominantly on small clathrin-containing vesicles in the perinuclear region. This association most likely occurs directly via a functional clathrin-binding domain in HPS3. These results suggest a role for HPS3 and its protein complex, BLOC-2, in vesicle formation and trafficking.

  • Ataxia and peripheral nerve hypomyelination in ADAM22-deficient mice - Background: ADAM22 is a member of the ADAM gene family, but the fact that it is expressed only in the nervous systems makes it unique. ADAM22's sequence similarity to other ADAMs suggests it to be an integrin binder and thus to have a role in cell-cell or cell-matrix interactions. To elucidate the physiological functions of ADAM22, we employed gene targeting to generate ADAM22 knockout mice. Results: ADAM22-deficient mice were produced in a good accordance with the Mendelian ratio and appeared normal at birth. After one week, severe ataxia was observed, and all homozygotes died before weaning, probably due to convulsions. No major histological abnormalities were detected in the cerebral cortex or cerebellum of the homozygous mutants; however, marked hypomyelination of the peripheral nerves was observed. Conclusion: The results of our study demonstrate that ADAM22 is closely involved in the correct functioning of the nervous system. Further analysis of ADAM22 will provide clues to understanding the mechanisms of human diseases such as epileptic seizures and peripheral neuropathy.

  • Attenuated Expression of DFFBis a Hallmark of Oligodendrogliomas with 1p-Allelic Loss - Allelic loss of chromosome 1p is frequently observed in oligodendrogliomas. We screened 177 oligodendroglial tumors for 1p deletions and found 6 tumors with localized 1p36 deletions. Several apoptosis regulation genes have been mapped to this region, including Tumor Protein 73 (p73), DNA Fragmentation Factor subunits alpha (DFFA) and beta (DFFB), and Tumor Necrosis Factor Receptor Superfamily Members 9 and 25 (TNFRSF9, TNFRSF25). We compared expression levels of these 5 genes in pairs of 1p-loss and 1p-intact tumors using quantitative reverse-transcriptase PCR (QRTPCR) to test if 1p deletions had an effect on expression. Only the DFFB gene demonstrated decreased expression in all tumor pairs tested. Mutational analysis did not reveal DFFB mutations in 12 tested samples. However, it is possible that DFFB haploinsufficiency from 1p allelic loss is a contributing factor in oligodendroglioma development.

  • Attenuation of Accumulation of Neointimal Lipid by Pioglitazone in Mice Genetically Deficient in Insulin Receptor Substrate-2 and Apolipoprotein E -

    Rupture of vulnerable atherosclerotic plaques that are characterized by extensive neointimal accumulation of lipid is a cause of acute coronary syndromes. To identify whether insulin resistance alters atherogenesis, we characterized the composition of atherosclerotic lesions in the proximal aortas in mice deficient in apolipoprotein E (ApoE–/–) and in ApoE–/– mice in which insulin resistance was intensified by a concomitant heterozygous deficiency in insulin receptor substrate type 2 (IRS2+/– ApoE–/– mice). In addition, we characterized the effect of an insulin sensitizer, pioglitazone, on the atherogenesis in IRS2+/– ApoE–/– mice. The extent of the aortic intima occupied by lesion was increased in the IRS2+/– ApoE–/– compared with ApoE–/– mice (79 ± 3% compared with 68 ± 8%, p<0.05). Treatment with pioglitazone decreased the neointimal content of lipid in 20-week-old mice from 50 ± 6% to 30 ± 7%, p=0.005 and decreased the cellularity reflected by the multisection cross-sectional areas of lesions comprising cells in atheroma from 24 ± 1% to 19 ± 3%, p=0.018. Accordingly, genetically induced intensification of insulin resistance increases atheroma formation. Furthermore, attenuation of insulin resistance by treatment with pioglitazone decreases accumulation of lipid in the neointima.

    (J Histochem Cytochem 53:603–610, 2005)


  • Attenuation of Accumulation of Neointimal Lipid by Pioglitazone in Mice Genetically Deficient in Insulin Receptor Substrate-2 and Apolipoprotein E -

    Rupture of vulnerable atherosclerotic plaques that are characterized by extensive neointimal accumulation of lipid is a cause of acute coronary syndromes. To identify whether insulin resistance alters atherogenesis, we characterized the composition of atherosclerotic lesions in the proximal aortas in mice deficient in apolipoprotein E (ApoE–/–) and in ApoE–/– mice in which insulin resistance was intensified by a concomitant heterozygous deficiency in insulin receptor substrate type 2 (IRS2+/– ApoE–/– mice). In addition, we characterized the effect of an insulin sensitizer, pioglitazone, on the atherogenesis in IRS2+/– ApoE–/– mice. The extent of the aortic intima occupied by lesion was increased in the IRS2+/– ApoE–/– compared with ApoE–/– mice (79 ± 3% compared with 68 ± 8%, p<0.05). Treatment with pioglitazone decreased the neointimal content of lipid in 20-week-old mice from 50 ± 6% to 30 ± 7%, p=0.005 and decreased the cellularity reflected by the multisection cross-sectional areas of lesions comprising cells in atheroma from 24 ± 1% to 19 ± 3%, p=0.018. Accordingly, genetically induced intensification of insulin resistance increases atheroma formation. Furthermore, attenuation of insulin resistance by treatment with pioglitazone decreases accumulation of lipid in the neointima.

    (J Histochem Cytochem 53:603–610, 2005)


  • Attenuation of Accumulation of Neointimal Lipid by Pioglitazone in Mice Genetically Deficient in Insulin Receptor Substrate-2 and Apolipoprotein E -

    Rupture of vulnerable atherosclerotic plaques that are characterized by extensive neointimal accumulation of lipid is a cause of acute coronary syndromes. To identify whether insulin resistance alters atherogenesis, we characterized the composition of atherosclerotic lesions in the proximal aortas in mice deficient in apolipoprotein E (ApoE–/–) and in ApoE–/– mice in which insulin resistance was intensified by a concomitant heterozygous deficiency in insulin receptor substrate type 2 (IRS2+/– ApoE–/– mice). In addition, we characterized the effect of an insulin sensitizer, pioglitazone, on the atherogenesis in IRS2+/– ApoE–/– mice. The extent of the aortic intima occupied by lesion was increased in the IRS2+/– ApoE–/– compared with ApoE–/– mice (79 ± 3% compared with 68 ± 8%, p<0.05). Treatment with pioglitazone decreased the neointimal content of lipid in 20-week-old mice from 50 ± 6% to 30 ± 7%, p=0.005 and decreased the cellularity reflected by the multisection cross-sectional areas of lesions comprising cells in atheroma from 24 ± 1% to 19 ± 3%, p=0.018. Accordingly, genetically induced intensification of insulin resistance increases atheroma formation. Furthermore, attenuation of insulin resistance by treatment with pioglitazone decreases accumulation of lipid in the neointima.

    (J Histochem Cytochem 53:603–610, 2005)


  • Automated measurement of cell motility and proliferation - Background: Time-lapse microscopic imaging provides a powerful approach for following changes in cell phenotype over time. Visible responses of whole cells can yield insight into functional changes that underlie physiological processes in health and disease. For example, features of cell motility accompany molecular changes that are central to the immune response, to carcinogenesis and metastasis, to wound healing and tissue regeneration, and to the myriad developmental processes that generate an organism. Previously reported image processing methods for motility analysis require custom viewing devices and manual interactions that may introduce bias, that slow throughput, and that constrain the scope of experiments in terms of the number of treatment variables, time period of observation, replication and statistical options. Here we describe a fully automated system in which images are acquired 24/7 from 384 well plates and are automatically processed to yield high-content motility and morphological data. Results: We have applied this technology to study the effects of different extracellular matrix compounds on human osteoblast-like cell lines to explore functional changes that may underlie processes involved in bone formation and maintenance. We show dose-response and kinetic data for significant increases in motility induced by laminin and collagen type I without significant effects on growth rate or morphology. Differential motility response was evident within 4 hours of plating cells; long-term responses differed depending upon cell type and surface coating. Average velocities were increased approximately 0.1 um/min by ten-fold increases in laminin coating concentration in some cases. Exponential growth was profiled by total cell area, and while not linearly correlated with absolute cell number, cell growth monitoring provided valuable supplementary data. Conclusions: These results demonstrate the applicability of a system for fully automated image acquisition and analysis for the study of cell motility and growth, enabling investigation of cellular response in an unbiased and comparatively high throughput manner. The output and database management of abundant ancillary data provide opportunities for uniform filtering according to criteria that select for biological relevance and for providing insight into features of system performance.

  • B(7) molecule mRNA expression in colorectal carcinoma. -
    Related Articles

    B(7) molecule mRNA expression in colorectal carcinoma.

    World J Gastroenterol. 2005 Sep 28;11(36):5655-8

    Authors: Xiao JX, Bai PS, Lai BC, Li L, Zhu J, Wang YL

    AIM: To observe the status of tumor-associated B(7) molecule mRNA expression in human colorectal cancer tissue by in situ hybridization. METHODS: The mRNA expression patterns of cancer-associated B(7-1),B(7)H(1),B(7)H(2),ICOS in 22 specimens of human colorectal cancer tissue were monitored by in situ hybridization (ISH) with digoxin-labeled oligonucleotide probes. RESULTS: B(7-1),B(7)H(1),B(7)H(2),ICOS mRNA were detected in both cancer cells and tumor infiltrating lymphocytes (TIL). The mRNA expression level of these molecules in tumor cells was higher than that in TIL (0.76+/-0.54-1.62+/-0.82 vs 0.38+/-0.19-0.65+/-0.33, P<0.001). There was no relationship between expression level of tested B(7) family molecules and patients' sex, age, differentiation status of cancer and regional lymph node metastasis. CONCLUSION: Th2 cytokine predominant in tumor microenvironment might be related to the expression of B(7)H(1),B(7)H(2) co-signal molecules in tumor cells and TIL.

    PMID: 16237760 [PubMed - in process]


  • Basal cytokeratins and their relationship to the cellular origin and functional classification of breast cancer - Recent publications have classified breast cancers on the basis of expression of cytokeratin-5 and -17 at the RNA and protein levels, and demonstrated the importance of these markers in defining sporadic tumours with bad prognosis and an association with BRCA1-related breast cancers. These important observations using different technology platforms produce a new functional classification of breast carcinoma. However, it is important in developing hypotheses about the pathogenesis of this tumour type to review the nomenclature that is being used to emphasize potential confusion between terminology that defines clinical subgroups and markers of cell lineage. This article reviews the lineages in the normal breast in relation to what have become known as the 'basal-like' carcinomas.

  • Basal Lamina Visualization Using Color Image Processing and Pattern Recognition. -

  • Behavior of Transplanted Bone Marrow-derived GFP Mesenchymal Cells in Osteochondral Defect as a Simulation of Autologous Transplantation -

    To elucidate the behavior of autologously transplanted mesenchymal cells in osteochondral defects, we followed transplanted cells using green fluorescent protein (GFP) transgenic rats, in which all cells express GFP signals in their cytoplasm and nuclei as transplantation donors. Bone marrow–derived mesenchymal cells, which contain mesenchymal stem cells (MSCs), were obtained from transgenic rats. Then, dense mesenchymal cell masses created by hanging-drop culture were transplanted and fixed with fibrin glue into osteochondral defects of wild-type rats. At 24 weeks after surgery, the defects were repaired with hyaline-like cartilage and subchondral bone. GFP positive cells, indicating transplanted mesenchymal-derived cells, were observed in the regenerated tissues for 24 weeks although GFP positive cells decreased in number with time. Because GFP causes no immunological rejection and requires no chemicals for visualization, transplantation between transgenic and wild-type rats can be regarded as a simulation of autologous transplantation, and the survivability of transplanted cells are able to be followed easily and reliably. Thus, the behavior of transplanted mesenchymal cells was able to be elucidated in vivo by this strategy, and the results could be essential in future tissue engineering for the regeneration of osteochondral defects with original hyaline cartilage and subchondral bone. (J Histochem Cytochem 53:207–216, 2005)


  • Benign breast disease, recent alcohol consumption, and risk of breast cancer: a nested case–control study - IntroductionAlcohol consumption is a well-established risk factor for breast cancer. Some studies have suggested that the risk of breast cancer associated with alcohol consumption is greater for women with a history of benign breast disease (BBD). We hypothesized that among women with biopsy-confirmed BBD, recent alcohol consumption would increase the risk of breast cancer in women with proliferative breast disease to a greater extent than in women with nonproliferative breast disease. Methods: We conducted a nested case–control study in the Nurses' Health Study I and II. The cases (n = 282) were women diagnosed with incident breast cancer, with a prior biopsy-confirmed breast disease. The controls (n = 1,223) were participants with a previous BBD biopsy, but without a diagnosis of breast cancer. Pathologists reviewed benign breast biopsy slides in a blinded fashion and classified the BBD as nonproliferative, proliferative without atypia, or atypical hyperplasia, according to standard criteria. Results: Women with nonproliferative breast disease consuming ≥ 15 g of alcohol per day had a nonsignificant 67% increased risk of breast cancer (odds ratio = 1.67; 95% confidence interval 0.65 to 4.34) compared with nondrinkers. There was no evidence that recent alcohol consumption increased the risk of breast cancer to a greater extent in women with proliferative BBD than among women with nonproliferative BBD (P for interactio n = 0.20). Conclusion: Contrary to our a priori hypothesis, there was no evidence that recent alcohol consumption increased the risk of breast cancer to a greater extent among women with proliferative BBD than among women with nonproliferative BBD.

  • Beta-Adrenergic Receptor Activation in Immortalized Human Urothelial Cells Stimulates Inflammatory Responses by PKA-Independent Mechanisms - Background: Interstitial cystitis (IC) is a debilitating disease characterized by chronic inflammation of the urinary bladder, yet specific cellular mechanisms of inflammation in IC are largely unknown. Multiple lines of evidence suggest that beta-adrenergic receptor (AR) signaling is increased in the inflamed urothelium, however the precise effects of these urothelial cell signals have not been studied. In order to better elucidate the AR signaling mechanisms of inflammation associated with IC, we have examined the effects of beta-AR stimulation in an immortalized human urothelial cell line (UROtsa). For these studies, UROtsa cells were treated with effective concentrations of the selective beta-AR agonist isoproterenol, in the absence or presence of selective inhibitors of protein kinase A (PKA). Cell lysates were analyzed by radioimmunoassay for generation of cAMP or by Western blotting for induction of protein products associated with inflammatory responses. Results: Radioligand binding demonstrated the presence of beta-ARs on human urothelial UROtsa cell membranes. Stimulating UROtsa cells with isoproterenol led to concentration-dependent increases of cAMP production that could be inhibited by pretreatment with a blocking concentration of the selective beta-AR antagonist propranolol. In addition, isoproterenol activation of these same cells led to significant increases in the amount of phosphorylated extracellular signal-regulated kinase (pERK), inducible nitric oxide synthase (iNOS) and the induced form of cyclooxygenase (COX-2) when compared to control. Moreover, preincubation of UROtsa cells with the selective PKA inhibitors H-89 or Rp-cAMPs did not diminish this isoproterenol mediated phosphorylation of ERK or production of iNOS and COX-2. Conclusions: Functional beta-ARs expressed on human urothelial UROtsa cell membranes increase the generation of cAMP and production of protein products associated with inflammation when activated by the selective beta-AR agonist isoproterenol. However, the increased production of iNOS and COX-2 by isoproterenol is not blocked when UROtsa cells are preincubated with inhibitors of PKA. Therefore, UROtsa cell beta-AR activation significantly increases the amount of iNOS and COX-2 produced by a PKA-independent mechanism. Consequently, this immortalized human urothelial cell line can be useful in characterizing potential AR signaling mechanisms associated with chronic inflammatory diseases of the bladder.

  • Binding of estrogen receptor with estrogen conjugated to bovine serum albumin (BSA) - Background: The classic model of estrogen action requires that the estrogen receptor (ER) activates gene expression by binding directly or indirectly to DNA. Recent studies, however, strongly suggest that ER can act through nongenomic signal transduction pathways and may be mediated by a membrane bound form of the ER. Estradiol covalently linked to membrane impermeable BSA (E2-BSA) has been widely used as an agent to study these novel membrane-associated ER events. However, a recent report suggests that E2-BSA does not compete for E2 binding to purified ER in vitro. To resolve this apparent discrepancy, we performed competition studies examining the binding of E2 and E2-BSA to both purified ER preparations and ER within intact cells. To eliminate potential artifacts due to contamination of commercially available E2-BSA preparations with unconjugated E2 (usually between 3–5%), the latter was carefully removed by ultrafiltration. Results: As previously reported, a 10-to 1000-fold molar excess of E2-BSA was unable to compete with 3H-E2 binding to ER when added simultaneously. However, when ER was pre-incubated with the same concentrations of E2-BSA, the binding of 3H-E2 was significantly reduced. E2-BSA binding to a putative membrane-associated ER was directly visualized using fluorescein labeled E2-BSA (E2-BSA-FITC). Staining was restricted to the cell membrane when E2-BSA-FITC was incubated with stable transfectants of the murine ERα within ER-negative HeLa cells and with MC7 cells that endogenously produce ERα. This staining appeared highly specific since it was competed by pre-incubation with E2 in a dose dependent manner and with the competitor ICI-182,780. Conclusions: These results demonstrate that E2-BSA does bind to purified ER in vitro and to ER in intact cells. It seems likely that the size and structure of E2-BSA requires more energy for it to bind to the ER and consequently binds more slowly than E2. More importantly, these findings demonstrate that in intact cells that express ER, E2-BSA binding is localized to the cell membrane, strongly suggesting a membrane bound form of the ER.

  • Biological dosimetry in a group of radiologists by the analysis of dicentrics and translocations. -
    Related Articles

    Biological dosimetry in a group of radiologists by the analysis of dicentrics and translocations.

    Radiat Res. 2005 Nov;164(5):612-7

    Authors: Montoro A, Rodríguez P, Almonacid M, Villaescusa JI, Verdú G, Caballín MR, Barrios L, Barquinero JF

    Montoro, A., Rodríguez, P., Almonacid, M., Villaescusa, J. I., Verdú, G., Caballín, M. R., Barrios, L. and Barquinero, J. F. Biological Dosimetry in a Group of Radiologists by the Analysis of Dicentrics and Translocations. Radiat. Res. 164, 612-617 (2005). The results of a cytogenetic study carried out in a group of nine radiologists are presented. Chromosome aberrations were detected by fluorescence plus Giemsa staining and fluorescence in situ hybridization. Dose estimates were obtained by extrapolating the yield of dicentrics and translocations to their respective dose-effect curves. In seven individuals, the 95% confidence limits of the doses estimated by dicentrics did not include 0 Gy. The 99 dicentrics observed in 17,626 cells gave a collective estimated dose of 115 mGy (95% confidence limits 73-171). For translocations, five individuals had estimated doses that were clearly higher than the total accumulated recorded dose. The 82 total apparently simple translocations observed in 9722 cells gave a collective estimated dose of 275 mGy (132-496). The mean genomic frequencies (x100 +/- SE) of complete and total apparently simple translocations observed in the group of radiologists (1.91 +/- 0.30 and 2.67 +/- 0.34, respectively) were significantly higher than those observed in a matched control group (0.53 +/- 0.10 and 0.87 +/- 0.13, P < 0.01 in both cases) and in another occupationally exposed matched group (0.79 +/- 0.12 and 1.14 +/-0.14, P < 0.03 and P < 0.01, respectively). The discrepancies observed between the physically recorded doses and the biologically estimated doses indicate that the radiologists did not always wear their dosimeters or that the dosimeters were not always in the radiation field.

    PMID: 16238438 [PubMed - in process]


  • Bioluminescent human breast cancer cell lines that permit rapid and sensitive in vivo detection of mammary tumors and multiple metastases in immune deficient mice - IntroductionOur goal was to generate xenograft mouse models of human breast cancer based on luciferase-expressing MDA-MB-231 tumor cells that would provide rapid mammary tumor growth; produce metastasis to clinically relevant tissues such as lymph nodes, lung, and bone; and permit sensitive in vivo detection of both primary and secondary tumor sites by bioluminescent imaging.MethodTwo clonal cell sublines of human MDA-MB-231 cells that stably expressed firefly luciferase were isolated following transfection of the parental cells with luciferase cDNA. Each subline was passaged once or twice in vivo to enhance primary tumor growth and to increase metastasis. The resulting luciferase-expressing D3H1 and D3H2LN cells were analyzed for long-term bioluminescent stability, primary tumor growth, and distal metastasis to lymph nodes, lungs, bone and soft tissues by bioluminescent imaging. Cells were injected into the mammary fat pad of nude and nude-beige mice or were delivered systemically via intracardiac injection. Metastasis was also evaluated by ex vivo imaging and histologic analysis postmortem. Results: The D3H1 and D3H2LN cell lines exhibited long-term stable luciferase expression for up to 4–6 months of accumulative tumor growth time in vivo. Bioluminescent imaging quantified primary mammary fat pad tumor development and detected early spontaneous lymph node metastasis in vivo. Increased frequency of spontaneous lymph node metastasis was observed with D3H2LN tumors as compared with D3H1 tumors. With postmortem ex vivo imaging, we detected additional lung micrometastasis in mice with D3H2LN mammary tumors. Subsequent histologic evaluation of tissue sections from lymph nodes and lung lobes confirmed spontaneous tumor metastasis at these sites. Following intracardiac injection of the MDA-MB-231-luc tumor cells, early metastasis to skeletal tissues, lymph nodes, brain and various visceral organs was detected. Weekly in vivo imaging data permitted longitudinal analysis of metastasis at multiple sites simultaneously. Ex vivo imaging data from sampled tissues verified both skeletal and multiple soft tissue tumor metastasis. Conclusion: This study characterized two new bioluminescent MDA-MB-231-luc human breast carcinoma cell lines with enhanced tumor growth and widespread metastasis in mice. Their application to current xenograft models of breast cancer offers rapid and highly sensitive detection options for preclinical assessment of anticancer therapies in vivo.

  • BMP-6 inhibits growth of mature human B cells; induction of Smad phosphorylation and upregulation of Id1 - Background: Bone morphogenetic proteins (BMPs) belong to the TGF-beta superfamily and are secreted proteins with pleiotropic roles in many different cell types. A potential role of BMP-6 in the immune system has been implied by various studies of malignant and rheumatoid diseases. In the present study, we explored the role of BMP-6 in normal human peripheral blood B cells. Results: The B cells were found to express BMP type I and type II receptors and BMP-6 rapidly induced phosphorylation of Smad1/5/8. Furthermore, Smad-phosphorylation was followed by upregulation of Id1 mRNA and Id1 protein, whereas Id2 and Id3 expression was not affected. Furthermore, we found that BMP-6 had an antiproliferative effect both in naive (CD19+CD27-) and memory B cells (CD19+CD27+) stimulated with anti-IgM alone or the combined action of anti-IgM and CD40L. Additionally, BMP-6 induced cell death in activated memory B cells. Importantly, the antiproliferative effect of BMP-6 in B-cells was completely neutralized by the natural antagonist, noggin. Furthermore, B cells were demonstrated to upregulate BMP-6 mRNA upon stimulation with anti-IgM. Conclusions: In mature human B cells, BMP-6 inhibited cell growth, and rapidly induced phosphorylation of Smad1/5/8 followed by an upregulation of Id1.

  • Bone Marrow Transplant in -Myelodysplastic Syndromes: New Technologies, Same Questions - Myelodysplastic syndrome (MDS) comprises a hetero-geneous group of hematologic disorders characterized by a clonal abnormality of hematopoietic stem cells that results in a -varying degree of cytopenias and risk of transformation into acute leukemia. Only allogeneic transplant has been shown to cure this disease. However, high nonrelapse mortality rates limit the applicability of conventional allografts and, even in young patients, long-term disease control ranging from only 30% to 50% has been reported. Novel transplant regimens, availability of alternative donors, and busulfan targeting -promise to increase transplant applicability and reduce -nonrelapse mortality rates. However, high relapse rates in patients with high-risk disease limit the success of this -procedure to the point that a definite advantage of allografting over standard therapy remains controversial. New agents being developed for MDS may have a potential impact on transplant outcomes. Therefore, design and implementation of clinical trials of transplant for MDS should be encouraged to improve the natural history of this disease.

  • BOOK REVIEW - "Fine Needle Aspiration Cytology of the Liver: Diagnostic algorithm a Southeast Asian Perspective" - This a review of Wee, A and Sampatankul, P: Fine Needle Aspiration Cytology of the Liver: Diagnostic algorithm a Southeast Asian Perspective, first edition.

  • BRCA1 Gene Expression in Breast Cancer: A Correlative Study between Real-time RT-PCR and Immunohistochemistry -

    Breast cancer is a major cause of cancer-related mortality in women. There are major discrepancies concerning the usefulness of various antibodies in detecting breast cancer susceptibility gene 1 (BRCA1) protein and its subcellular localization. The aim of the present study was to determine the specificity and sensitivity of immunohistochemistry (IHC) as a screening method for demonstrating BRCA1 expression. BRCA1 gene expression in archival paraffin-embedded breast cancer tissues was studied simultaneously at the protein and mRNA levels, and the two findings were compared. Forty-eight archival paraffin-embedded breast cancer tissues were studied for BRCA1 gene expression at protein level by IHC using four different antibodies against different BRCA1 epitopes and at mRNA level using real-time RT-PCR. BRCA1 mRNA expression was reduced or absent in 79% of the samples, and this finding correlated significantly with loss of BRCA1 protein expression in 83% of breast cancer tissues using one BRCA1 antibody studied (AB-1, against N-terminus epitope). The specificity of this antibody was 91.3%, and its sensitivity was 66.6%. There was no significant correlation between BRCA1 mRNA and protein expression as demonstrated by the remaining three antibodies. Antibody 8F7 had the highest sensitivity of 100%, but its specificity was 30.4% if mRNA levels were considered as the reference standard. (J Histochem Cytochem 53:621–629, 2005)


  • BRCA1 Gene Expression in Breast Cancer: A Correlative Study between Real-time RT-PCR and Immunohistochemistry -

    Breast cancer is a major cause of cancer-related mortality in women. There are major discrepancies concerning the usefulness of various antibodies in detecting breast cancer susceptibility gene 1 (BRCA1) protein and its subcellular localization. The aim of the present study was to determine the specificity and sensitivity of immunohistochemistry (IHC) as a screening method for demonstrating BRCA1 expression. BRCA1 gene expression in archival paraffin-embedded breast cancer tissues was studied simultaneously at the protein and mRNA levels, and the two findings were compared. Forty-eight archival paraffin-embedded breast cancer tissues were studied for BRCA1 gene expression at protein level by IHC using four different antibodies against different BRCA1 epitopes and at mRNA level using real-time RT-PCR. BRCA1 mRNA expression was reduced or absent in 79% of the samples, and this finding correlated significantly with loss of BRCA1 protein expression in 83% of breast cancer tissues using one BRCA1 antibody studied (AB-1, against N-terminus epitope). The specificity of this antibody was 91.3%, and its sensitivity was 66.6%. There was no significant correlation between BRCA1 mRNA and protein expression as demonstrated by the remaining three antibodies. Antibody 8F7 had the highest sensitivity of 100%, but its specificity was 30.4% if mRNA levels were considered as the reference standard. (J Histochem Cytochem 53:621–629, 2005)


  • BRCA1 Gene Expression in Breast Cancer: A Correlative Study between Real-time RT-PCR and Immunohistochemistry -

    Breast cancer is a major cause of cancer-related mortality in women. There are major discrepancies concerning the usefulness of various antibodies in detecting breast cancer susceptibility gene 1 (BRCA1) protein and its subcellular localization. The aim of the present study was to determine the specificity and sensitivity of immunohistochemistry (IHC) as a screening method for demonstrating BRCA1 expression. BRCA1 gene expression in archival paraffin-embedded breast cancer tissues was studied simultaneously at the protein and mRNA levels, and the two findings were compared. Forty-eight archival paraffin-embedded breast cancer tissues were studied for BRCA1 gene expression at protein level by IHC using four different antibodies against different BRCA1 epitopes and at mRNA level using real-time RT-PCR. BRCA1 mRNA expression was reduced or absent in 79% of the samples, and this finding correlated significantly with loss of BRCA1 protein expression in 83% of breast cancer tissues using one BRCA1 antibody studied (AB-1, against N-terminus epitope). The specificity of this antibody was 91.3%, and its sensitivity was 66.6%. There was no significant correlation between BRCA1 mRNA and protein expression as demonstrated by the remaining three antibodies. Antibody 8F7 had the highest sensitivity of 100%, but its specificity was 30.4% if mRNA levels were considered as the reference standard. (J Histochem Cytochem 53:621–629, 2005)


  • Bridging of Oral Anticoagulation Therapy for Invasive Procedures - The management of patients who need temporary interruption of chronic oral anticoagulant (OAC) therapy for an elective surgical or invasive procedure is problematic and complex. Patient and procedural risk factors for thrombosis and bleeding, anticoagulant-related risks of bleeding, and clinical consequences of a thrombotic or bleeding event need to be assessed and properly risk-stratified in the perioperative period. Certain procedures, such as dental, endoscopic, and cutaneous procedures, can be completed without discontinuing OAC, but most procedures with a high bleeding risk (including major surgeries) will necessitate temporary discontinuation of OAC. Bridging therapy with shorter-acting anticoagulants, such as heparin, for patients at intermediate to high risk of thromboembolism represents one strategy to maintain functional anticoagulation during this period. Large, prospective cohort studies and registries of patients on chronic OAC who underwent bridging therapy mostly with low-molecular-weight heparin have been completed recently. This paper reviews these clinical data on bridging therapy and provides an evidence-based perioperative management strategy for the at-risk patient on chronic OAC.

  • Ca2+ regulation in the absence of the iplA gene product in Dictyostelium discoideum - Background: Stimulation of Dictyostelium discoideum with cAMP evokes an elevation of the cytosolic free Ca2+ concentration ([Ca2+]i). The [Ca2+]i-change is composed of liberation of stored Ca2+ and extracellular Ca2+-entry. The significance of the [Ca2+]i-transient for chemotaxis is under debate. Abolition of chemotactic orientation and migration by Ca2+-buffers in the cytosol indicates that a [Ca2+]i-increase is required for chemotaxis. Yet, the iplA- mutant disrupted in a gene bearing similarity to IP3-receptors of higher eukaryotes aggregates despite the absence of a cAMP-induced [Ca2+]i-transient which favours the view that [Ca2+]i-changes are insignificant for chemotaxis. Results: We investigated Ca2+-fluxes and the effect of their disturbance on chemotaxis and development of iplA- cells. Differentiation was altered as compared to wild type amoebae and sensitive towards manipulation of the level of stored Ca2+. Chemotaxis was impaired when [Ca2+]i-transients were suppressed by the presence of a Ca2+-chelator in the cytosol of the cells. Analysis of ion fluxes revealed that capacitative Ca2+-entry was fully operative in the mutant. In suspensions of intact and permeabilized cells cAMP elicited extracellular Ca2+-influx and liberation of stored Ca2+, respectively, yet to a lesser extent than in wild type. In suspensions of partially purified storage vesicles ATP-induced Ca2+-uptake and Ca2+-release activated by fatty acids or Ca2+-ATPase inhibitors were similar to wild type. Mn2+-quenching of fura2 fluorescence allows to study Ca2+-influx indirectly and revealed that the responsiveness of mutant cells was shifted to higher concentrations: roughly 100 times more Mn2+ was necessary to observe agonist-induced Mn2+-influx. cAMP evoked a [Ca2+]i-elevation when stores were strongly loaded with Ca2+, again with a similar shift in sensitivity in the mutant. In addition, basal [Ca2+]i was significantly lower in iplA- than in wild type amoebae. Conclusion: These results support the view that [Ca2+]i-transients are essential for chemotaxis and differentiation. Moreover, capacitative and agonist-activated ion fluxes are regulated by separate pathways that are mediated either by two types of channels in the plasma membrane or by distinct mechanisms coupling Ca2+-release from stores to Ca2+-entry in Dictyostelium. The iplA- strain retains the capacitative Ca2+-entry pathway and an impaired agonist-activated pathway that operates with reduced efficiency or at higher ionic pressure.

  • Cancer and Thrombosis - The risk of venous thromboembolic events (VTE) in patients with cancer is well established. Malignancy screening in patients who present with their first episode of VTE is recommended only if the history or physical findings are suggestive of an underlying problem, however. Thrombotic events remain a significant cause of death in cancer patients and their treatment remains a major challenge in the management of cancer. Low-molecular-weight heparins are safe, effective options for treatment and prophylaxis and may prolong survival in this patient population. It remains to be seen, however, if this treatment will influence cancer outcomes.

  • Cancer/testis antigens and gametogenesis: a review and "brain-storming" session - Genes expressed both in normal testis and in malignancies (Cancer/ Testis associated genes – CTA) have become the most extensively studied antigen group in the field of tumour immunology. Despite this, many fundamentally important questions remain unanswered: what is the connection between germ-cell specific genes and tumours? Is the expression of these genes yet another proof for the importance of genome destabilisation in the process of tumorigenesis?, or maybe activation of these genes is not quite random but instead related to some programme giving tumours a survival advantage?This review collates most of the recent information available about CTAs expression, function, and regulation. The data suggests a programme related to ontogenesis, mostly to gametogenesis. In the "brain-storming" part, facts in conflict with the hypothesis of random CTA gene activation are discussed. We propose a programme borrowed from organisms phylogenetically much older than humans, which existed before the differentiation of sexes. It is a programme that has served as a life cycle with prominent ploidy changes, and from which, as we know, the germ-cell ploidy cycle – meiosis – has evolved. Further work may show whether this hypothesis can lead to a novel anti-tumour strategy.

  • Cardiac apoptosis in severe relapsing Fever borreliosis. -
    Related Articles

    Cardiac apoptosis in severe relapsing Fever borreliosis.

    Infect Immun. 2005 Nov;73(11):7669-76

    Authors: Londoño D, Bai Y, Zückert WR, Gelderblom H, Cadavid D

    Previous studies revealed that the heart suffers significant injury during experimental Lyme and relapsing fever borreliosis when the immune response is impaired (D. Cadavid, Y. Bai, E. Hodzic, K. Narayan, S. W. Barthold, and A. R. Pachner, Lab. Investig. 84:1439-1450, 2004; D. Cadavid, T. O'Neill, H. Schaefer, and A. R. Pachner, Lab. Investig. 80:1043-1054, 2000; and D. Cadavid, D. D. Thomas, R. Crawley, and A. G. Barbour, J. Exp. Med. 179:631-642, 1994). To investigate cardiac injury in borrelia carditis, we used antibody-deficient mice persistently infected with isogenic serotypes of the relapsing fever agent Borrelia turicatae. We studied infection in hearts 1 to 2 months after inoculation by TaqMan reverse transcription-PCR and immunohistochemistry (IHC) and inflammation by hematoxylin and eosin and trichrome staining, IHC, and in situ hybridization (ISH). We studied apoptosis by terminal transferase-mediated DNA nick end labeling assay and measured expression of apoptotic molecules by RNase protection assay, immunofluorescence, and immunoblot. All antibody-deficient mice, but none of the immunocompetent controls, developed persistent infection of the heart. Antibody-deficient mice infected with serotype 2 had more severe cardiac infection and injury than serotype 1-infected mice. The injury was more severe around the base of the heart and pericardium, corresponding to sites of marked infiltration by activated macrophages and upregulation of interleukin-6 (IL-6). Infected hearts showed evidence of apoptosis of macrophages and cardiomyocytes as well as significant upregulation of caspases, most notably caspase-1. We conclude that persistent infection with relapsing fever borrelias causes significant loss of cardiomyocytes associated with prominent infiltration by activated macrophages, upregulation of IL-6, induction of caspase-1, and apoptosis.

    PMID: 16239571 [PubMed - in process]


  • Cardiac apoptosis in severe relapsing Fever borreliosis. -
    Related Articles

    Cardiac apoptosis in severe relapsing Fever borreliosis.

    Infect Immun. 2005 Nov;73(11):7669-76

    Authors: Londoño D, Bai Y, Zückert WR, Gelderblom H, Cadavid D

    Previous studies revealed that the heart suffers significant injury during experimental Lyme and relapsing fever borreliosis when the immune response is impaired (D. Cadavid, Y. Bai, E. Hodzic, K. Narayan, S. W. Barthold, and A. R. Pachner, Lab. Investig. 84:1439-1450, 2004; D. Cadavid, T. O'Neill, H. Schaefer, and A. R. Pachner, Lab. Investig. 80:1043-1054, 2000; and D. Cadavid, D. D. Thomas, R. Crawley, and A. G. Barbour, J. Exp. Med. 179:631-642, 1994). To investigate cardiac injury in borrelia carditis, we used antibody-deficient mice persistently infected with isogenic serotypes of the relapsing fever agent Borrelia turicatae. We studied infection in hearts 1 to 2 months after inoculation by TaqMan reverse transcription-PCR and immunohistochemistry (IHC) and inflammation by hematoxylin and eosin and trichrome staining, IHC, and in situ hybridization (ISH). We studied apoptosis by terminal transferase-mediated DNA nick end labeling assay and measured expression of apoptotic molecules by RNase protection assay, immunofluorescence, and immunoblot. All antibody-deficient mice, but none of the immunocompetent controls, developed persistent infection of the heart. Antibody-deficient mice infected with serotype 2 had more severe cardiac infection and injury than serotype 1-infected mice. The injury was more severe around the base of the heart and pericardium, corresponding to sites of marked infiltration by activated macrophages and upregulation of interleukin-6 (IL-6). Infected hearts showed evidence of apoptosis of macrophages and cardiomyocytes as well as significant upregulation of caspases, most notably caspase-1. We conclude that persistent infection with relapsing fever borrelias causes significant loss of cardiomyocytes associated with prominent infiltration by activated macrophages, upregulation of IL-6, induction of caspase-1, and apoptosis.

    PMID: 16239571 [PubMed - in process]


  • Cardiomyocyte Remodeling and Sarcomere Addition after Uniaxial Static Strain In Vitro -

    Individual cardiomyocytes are lengthened in dilated cardiomyopathy. However, it is not known how the new sarcomeres are added to preexisting myofibrils. Using a three-dimensional microtextured culturing system, a 10% mechanical static strain was applied to aligned, well-attached cardiomyocytes from neonatal rat. The morphology of the myofibrils and the ends of the myocytes were examined. Disruptions of the sarcomeric pattern for actin showed a progression from weak to intense staining over 4 hr. The lightly stained sarcomeres were common at 1 hr after being strained, peaked at 2 hr, and then subsided. In contrast, the numbers of intensely stained sarcomeres were initially low, peaked at 3 hr, and then began to decline when compared with control values. The myocyte ends showed elongations and convolutions after 3 hr and 4 hr of mechanical strain when observed with -actinin and N-cadherin staining. We suggest that myocytes from neonatal rat hearts remodel by insertion of new sarcomeres throughout the cell length and also by enhancement at the intercalated discs. (J Histochem Cytochem 53:839–844, 2005)


  • Cardiomyocyte Remodeling and Sarcomere Addition after Uniaxial Static Strain In Vitro -

    Individual cardiomyocytes are lengthened in dilated cardiomyopathy. However, it is not known how the new sarcomeres are added to preexisting myofibrils. Using a three-dimensional microtextured culturing system, a 10% mechanical static strain was applied to aligned, well-attached cardiomyocytes from neonatal rat. The morphology of the myofibrils and the ends of the myocytes were examined. Disruptions of the sarcomeric pattern for actin showed a progression from weak to intense staining over 4 hr. The lightly stained sarcomeres were common at 1 hr after being strained, peaked at 2 hr, and then subsided. In contrast, the numbers of intensely stained sarcomeres were initially low, peaked at 3 hr, and then began to decline when compared with control values. The myocyte ends showed elongations and convolutions after 3 hr and 4 hr of mechanical strain when observed with -actinin and N-cadherin staining. We suggest that myocytes from neonatal rat hearts remodel by insertion of new sarcomeres throughout the cell length and also by enhancement at the intercalated discs. (J Histochem Cytochem 53:839–844, 2005)


  • Cardiomyocytes of Chronically Ischemic Pig Hearts Express the MDR-1 Gene-encoded P-glycoprotein -

    The multidrug-resistant (MDR)-1 gene-encoded P-glycoprotein (Pgp-170) is not normally present in the cardiomyocyte. Given that in other tissues Pgp-170 is not found under normoxic conditions but is expressed during hypoxia, we searched for Pgp-170 in chronically ischemic porcine cardiomyocytes. Pgp-170 was detected and localized via immunohistochemistry in ischemic and nonischemic cardiomyocytes of eight adult pigs 8 weeks after placement of an Ameroid constrictor at the origin of the left circumflex artery (Cx). Regional myocardial ischemia in the Cx bed was documented with nuclear perfusion scans. Pgp-170 mass was quantified using Western blot analysis. In all pigs, Pgp-170 was consistently present in the sarcolemma and T invaginations of the cardiomyocytes of the ischemic zone. Pgp-170 expression decreased toward the border of the ischemic zone and was negative in nonischemic regions as well as in the myocardium of sham-operated animals. Western blot analysis yielded significantly higher Pgp-170 mass in ischemic than in nonischemic areas. We conclude that Pgp-170 is consistently expressed in the cardiomyocytes of chronically ischemic porcine myocardium. Its role in the ischemic heart as well as in conditions such as myocardial hibernation, stunning, and preconditioning may have potentially relevant clinical implications and merits further investigation.

    (J Histochem Cytochem 53:845–850, 2005)


  • Cardiomyocytes of Chronically Ischemic Pig Hearts Express the MDR-1 Gene-encoded P-glycoprotein -

    The multidrug-resistant (MDR)-1 gene-encoded P-glycoprotein (Pgp-170) is not normally present in the cardiomyocyte. Given that in other tissues Pgp-170 is not found under normoxic conditions but is expressed during hypoxia, we searched for Pgp-170 in chronically ischemic porcine cardiomyocytes. Pgp-170 was detected and localized via immunohistochemistry in ischemic and nonischemic cardiomyocytes of eight adult pigs 8 weeks after placement of an Ameroid constrictor at the origin of the left circumflex artery (Cx). Regional myocardial ischemia in the Cx bed was documented with nuclear perfusion scans. Pgp-170 mass was quantified using Western blot analysis. In all pigs, Pgp-170 was consistently present in the sarcolemma and T invaginations of the cardiomyocytes of the ischemic zone. Pgp-170 expression decreased toward the border of the ischemic zone and was negative in nonischemic regions as well as in the myocardium of sham-operated animals. Western blot analysis yielded significantly higher Pgp-170 mass in ischemic than in nonischemic areas. We conclude that Pgp-170 is consistently expressed in the cardiomyocytes of chronically ischemic porcine myocardium. Its role in the ischemic heart as well as in conditions such as myocardial hibernation, stunning, and preconditioning may have potentially relevant clinical implications and merits further investigation.

    (J Histochem Cytochem 53:845–850, 2005)


  • Caveolin-3 Is a Sensitive and Specific Marker for Rhabdomyosarcoma. -

  • CD117/c-kit positive interstitial (Cajal-like) cells in human pancreas. -
    Related Articles

    CD117/c-kit positive interstitial (Cajal-like) cells in human pancreas.

    J Cell Mol Med. 2005 Jul-Sep;9(3):738-9

    Authors: Popescu LM, Hinescu ME, Radu E, Ciontea SM, Cretoiu D, Leabu M, Ardeleanu C

    We provide evidence that interstitial Cajal-like cells, previously described in human pancreas - pICC (J Cel Mol Med, 9: 169, 2005), are positive for c-kit irrespective of immunohistochemical procedures used. Various sample types (fresh cryosections or formalin-fixed, paraffin-embedded specimens), various slide pretreatments (with or without heat-induced epitope retrieval) or different antibodies used (Dako polyclonal or Santa Cruz monoclonal), all showed CD117-positive pICC.

    PMID: 16202222 [PubMed - in process]


  • Celecoxib analogues disrupt Akt signaling, which is commonly activated in primary breast tumours - IntroductionPhosphorylated Akt (P-Akt) is an attractive molecular target because it contributes to the development of breast cancer and confers resistance to conventional therapies. Akt also serves as a signalling intermediate for receptors such as human epidermal growth factor receptor (HER)-2, which is overexpressed in 30% of breast cancers; therefore, inhibitors to this pathway are being sought. New celecoxib analogues reportedly inhibit P-Akt in prostate cancer cells. We therefore examined the potential of these compounds in the treatment of breast cancer. The analogues were characterized in MDA-MB-453 cells because they overexpress HER-2 and have very high levels of P-Akt. Methods: To evaluate the effect of the celecoxib analogues, immunoblotting was used to identify changes in the phosphorylation of Akt and its downstream substrates glycogen synthase kinase (GSK) and 4E binding protein (4EBP-1). In vitro kinase assays were then used to assess the effect of the drugs on Akt activity. Cell death was evaluated by poly(ADP-ribose) polymerase cleavage, nucleosomal fragmentation and MTS assays. Finally, tumour tissue microarrays were screened for P-Akt and HER-2 expression. Results: OSU-03012 and OSU-O3013 inhibited P-Akt and its downstream signalling through 4EBP-1 and GSK at concentrations well below that of celecoxib. Disruption of P-Akt was followed by induction of apoptosis and more than 90% cell death. We also noted that the cytotoxicity of the celecoxib analogues was not significantly affected by serum. In contrast, the presence of 5% serum protected cells from celecoxib induced death. Thus, the structural modification of the celecoxib analogues increased P-Akt inhibition and enhanced the bioavailability of the drugs in vitro. To assess how many patients may potentially benefit from such drugs we screened tumour tissue microarrays. P-Akt was highly activated in 58% (225/390) of cases, whereas it was only similarly expressed in 35% (9/26) of normal breast tissues. Furthermore, HER-2 positive tumours expressed high levels of P-Akt (P < 0.01), supporting in vitro signal transduction. Conclusion: We determined that Celecoxib analogues are potent inhibitors of P-Akt signalling and kill breast cancer cells that overexpress HER-2. We also defined an association between HER-2 and P-Akt in primary breast tissues, suggesting that these inhibitors may benefit patients in need of new treatment options.

  • Change in Renal Heme Oxygenase Expression in Cyclosporine A-induced Injury -

    Cyclosporine A (CsA) is the first immunosuppressant used in allotransplantation. Its use is associated with side effects that include nephrotoxicity. This study explored the anatomic structures involved in CsA nephrotoxicity and the effect of heme oxygenase (HO) in preventing CsA injury. Rats were divided into four groups, which were treated with olive oil, CsA (15 mg/kg/day), CsA plus the HO inhibitor (SnMP; 30 µM/kg/day), and with the HO inducer (CoPP; 5 mg/100 g bw). Renal tissue was treated for morphological, biochemical, and immunohistochemical studies. CsA-treated rats showed degenerative changes with renal fibrosis localized mainly around proximal tubules. Collapsed vessels were sometimes seen in glomeruli. No HO-1 expression and increased expression of endothelin-1 (ET-1) were observed in CsA-treated rats compared with controls. In CsA plus SnMP-treated rats, HO-1 expression was further reduced and the morphology was not changed compared to the CsA group, whereas CsA plus CoPP-treated animals again showed normal morphology and with restoration and an increase in HO-1 levels. HO activity and immunohistochemical data showed similar alterations as HO expression. No changes were observed for HO-2 analysis. The observations indicate that HO-1 downregulation and ET-1 upregulation by CsA might be one mechanism underlying CsA-induced nephrotoxicity. Therefore, attempts to preserve HO levels attenuate CsA nephrotoxicity. (J Histochem Cytochem 53:105–112, 2005)


  • Changes in body weight and the risk of breast cancer in BRCA1 and BRCA2 mutation carriers - Background: Several anthropometric measures have been found to be associated with the risk of breast cancer. Current weight, body mass index, and adult weight gain appear to be predictors of postmenopausal breast cancer. These factors have been associated with a reduced risk of premenopausal breast cancer. We asked whether there is an association between changes in body weight and the risk of breast cancer in women who carry a mutation in either breast cancer susceptibility gene, BRCA1 or BRCA2. Methods: A matched case–control study was conducted in 1,073 pairs of women carrying a deleterious mutation in either BRCA1 (n = 797 pairs) or BRCA2 (n = 276 pairs). Women diagnosed with breast cancer were matched to control subjects by year of birth, mutation, country of residence, and history of ovarian cancer. Information about weight was derived from a questionnaire routinely administered to women who were carriers of a mutation in either gene. Conditional logistic regression was used to estimate the association between weight gain or loss and the risk of breast cancer, stratified by age at diagnosis or menopausal status. Results: A loss of at least 10 pounds in the period from age 18 to 30 years was associated with a decreased risk of breast cancer between age 30 and 49 (odds ratio (OR) = 0.47; 95% confidence interval (CI) 0.28–0.79); weight gain during the same interval did not influence the overall risk. Among the subgroup of BRCA1 mutation carriers who had at least two children, weight gain of more than 10 pounds between age 18 and 30 was associated with an increased risk of breast cancer diagnosed between age 30 and 40 (OR = 1.44, 95% CI 1.01–2.04). Change in body weight later in life (at age 30 to 40) did not influence the risk of either premenopausal or postmenopausal breast cancer. Conclusion: The results from this study suggest that weight loss in early adult life (age 18 to 30) protects against early-onset BRCA-associated breast cancers. Weight gain should also be avoided, particularly among BRCA1 mutation carriers who elect to have at least two pregnancies.

  • Changes in P-glycoprotein activity are mediated by the growth of a tumour cell line as multicellular spheroids - Background: Expression of P-glycoprotein (P-gp), the multidrug resistance (MDR) 1 gene product, can lead to multidrug resistance in tumours. However, the physiological role of P-gp in tumours growing as multicellular spheroids is not well understood. Recent evidence suggests that P-gp activity may be modulated by cellular components such as membrane proteins, membrane-anchoring proteins or membrane-lipid composition. Since, multicellular spheroids studies have evidenced alterations in numerous cellular components, including those related to the plasma membrane function, result plausible that some of these changes might modulate P-gp function and be responsible for the acquisition of multicellular drug resistance. In the present study, we asked if a human lung cancer cell line (INER-51) grown as multicellular spheroids can modify the P-gp activity to decrease the levels of doxorubicin (DXR) retained and increase their drug resistance. Results: Our results showed that INER-51 spheroids retain 3-folds lower doxorubicin than the same cells as monolayers however; differences in retention were not observed when the P-gp substrate Rho-123 was used. Interestingly, neither the use of the P-gp-modulating agent cyclosporin-A (Cs-A) nor a decrease in ATP-pools were able to increase DXR retention in the multicellular spheroids. Only the lack of P-gp expression throughout the pharmacological selection of a P-gp negative (P-gpneg) mutant clone (PSC-1) derived from INER-51 cells, allow increase of DXR retention in spheroids. Conclusion: Thus, multicellular arrangement appears to alter the P-gp activity to maintain lower levels of DXR. However, the non expression of P-gp by cells forming multicellular spheroids has only a minor impact in the resistance to chemotherapeutic agents.

  • Characterization of Osteocrin Expression in Human Bone -

    Osteocrin (Ostn), a bone-active molecule, has been shown in animals to be highly expressed in cells of the osteoblast lineage. We have characterized this protein in human cultured primary human osteoblasts, in developing human neonatal bone, and in iliac crest bone biopsies from adult women. In vivo, Ostn expression was localized in developing human neonatal rib bone, with intense immunoreactivity in osteoblasts on bone-forming surfaces, in newly incorporated osteocytes, and in some late hypertrophic chondrocytes. In adult bone, Ostn expression was specifically localized to osteoblasts and young osteocytes at bone-forming sites. In vitro, Ostn expression decreased time dependently (p<0.02) in osteoblasts cultured for 2, 3, and 6 days. Expression was further decreased in cultures containing 200 nM hydrocortisone by 1.5-, 2.3-, and 3.1-fold (p<0.05) at the same time points. In contrast, alkaline phosphatase expression increased with osteoblast differentiation (p<0.05). Low-dose estradiol decreased Ostn expression time dependently (p<0.05), whereas Ostn expression in cultures treated with high-dose estradiol was not significantly changed. These results demonstrate that Ostn is expressed in human skeletal tissue, particularly in osteoblasts in developing bone and at sites of bone remodeling, suggesting a role in bone formation. Thus, Ostn provides a marker of osteoblast lineage cells and appears to correlate with osteoblast activity. (J Histochem Cytochem 53:1181–1187, 2005)


  • Characterization of Osteocrin Expression in Human Bone -

    Osteocrin (Ostn), a bone-active molecule, has been shown in animals to be highly expressed in cells of the osteoblast lineage. We have characterized this protein in human cultured primary human osteoblasts, in developing human neonatal bone, and in iliac crest bone biopsies from adult women. In vivo, Ostn expression was localized in developing human neonatal rib bone, with intense immunoreactivity in osteoblasts on bone-forming surfaces, in newly incorporated osteocytes, and in some late hypertrophic chondrocytes. In adult bone, Ostn expression was specifically localized to osteoblasts and young osteocytes at bone-forming sites. In vitro, Ostn expression decreased time dependently (p<0.02) in osteoblasts cultured for 2, 3, and 6 days. Expression was further decreased in cultures containing 200 nM hydrocortisone by 1.5-, 2.3-, and 3.1-fold (p<0.05) at the same time points. In contrast, alkaline phosphatase expression increased with osteoblast differentiation (p<0.05). Low-dose estradiol decreased Ostn expression time dependently (p<0.05), whereas Ostn expression in cultures treated with high-dose estradiol was not significantly changed. These results demonstrate that Ostn is expressed in human skeletal tissue, particularly in osteoblasts in developing bone and at sites of bone remodeling, suggesting a role in bone formation. Thus, Ostn provides a marker of osteoblast lineage cells and appears to correlate with osteoblast activity. (J Histochem Cytochem 53:1181–1187, 2005)


  • Chondrogenic Potential of Mouse Calvarial Mesenchyme -

    Facial and calvarial bones form intramembranously without a cartilagenous model; however, cultured chick calvarial mesenchyme cells may differentiate into both osteoblasts and chondroblasts and, in rodents, small cartilages occasionally form at the sutures in vivo. Therefore, we wanted to investigate what factors regulate normal differentiation of calvarial mesenchymal cells directly into osteoblasts. In embryonic mouse heads and in cultured tissue explants, we analyzed the expression of selected transcription factors and extracellular matrix molecules associated with bone and cartilage development. Cartilage markers Sox9 and type II collagen were expressed in all craniofacial cartilages. In addition, Msx2 and type I collagen were expressed in sense capsule cartilages. We also observed that the undifferentiated calvarial mesenchyme and the osteogenic fronts in the jaw expressed Col2A1. Moreover, we found that cultured mouse calvarial mesenchyme could develop into cartilage. Of the 49 explants that contained mesenchyme, intramembranous ossification occurred in 35%. Only cartilage formed in 4%, and both cartilage and bone formed in 4%. Our study confirms that calvarial mesenchyme, which normally gives rise to intramembranous bone, also has chondrogenic potential.

    (J Histochem Cytochem 53:653–663, 2005)


  • Chondrogenic Potential of Mouse Calvarial Mesenchyme -

    Facial and calvarial bones form intramembranously without a cartilagenous model; however, cultured chick calvarial mesenchyme cells may differentiate into both osteoblasts and chondroblasts and, in rodents, small cartilages occasionally form at the sutures in vivo. Therefore, we wanted to investigate what factors regulate normal differentiation of calvarial mesenchymal cells directly into osteoblasts. In embryonic mouse heads and in cultured tissue explants, we analyzed the expression of selected transcription factors and extracellular matrix molecules associated with bone and cartilage development. Cartilage markers Sox9 and type II collagen were expressed in all craniofacial cartilages. In addition, Msx2 and type I collagen were expressed in sense capsule cartilages. We also observed that the undifferentiated calvarial mesenchyme and the osteogenic fronts in the jaw expressed Col2A1. Moreover, we found that cultured mouse calvarial mesenchyme could develop into cartilage. Of the 49 explants that contained mesenchyme, intramembranous ossification occurred in 35%. Only cartilage formed in 4%, and both cartilage and bone formed in 4%. Our study confirms that calvarial mesenchyme, which normally gives rise to intramembranous bone, also has chondrogenic potential.

    (J Histochem Cytochem 53:653–663, 2005)


  • Chondrogenic Potential of Mouse Calvarial Mesenchyme -

    Facial and calvarial bones form intramembranously without a cartilagenous model; however, cultured chick calvarial mesenchyme cells may differentiate into both osteoblasts and chondroblasts and, in rodents, small cartilages occasionally form at the sutures in vivo. Therefore, we wanted to investigate what factors regulate normal differentiation of calvarial mesenchymal cells directly into osteoblasts. In embryonic mouse heads and in cultured tissue explants, we analyzed the expression of selected transcription factors and extracellular matrix molecules associated with bone and cartilage development. Cartilage markers Sox9 and type II collagen were expressed in all craniofacial cartilages. In addition, Msx2 and type I collagen were expressed in sense capsule cartilages. We also observed that the undifferentiated calvarial mesenchyme and the osteogenic fronts in the jaw expressed Col2A1. Moreover, we found that cultured mouse calvarial mesenchyme could develop into cartilage. Of the 49 explants that contained mesenchyme, intramembranous ossification occurred in 35%. Only cartilage formed in 4%, and both cartilage and bone formed in 4%. Our study confirms that calvarial mesenchyme, which normally gives rise to intramembranous bone, also has chondrogenic potential.

    (J Histochem Cytochem 53:653–663, 2005)


  • Chromatoid Bodies: Aggresome-like Characteristics and Degradation Sites for Organelles of Spermiogenic Cells -

    We investigated the localization of several markers for lysosomes and aggresomes in the chromatoid bodies (CBs) by immunoelectron microscopy. We found so-called aggresomal markers such as Hsp70 and ubiquitin in the core of the CBs and vimentin and proteasome subunit around the CBs. Ubiquitin-conjugating enzyme (E2) was also found in the CBs. In tubulovesicular structures surrounding the CBs, lysosomal markers were detected but an endoplasmic reticulum retention signal (KDEL) was not. Moreover, proteins located in each subcellular compartment, including the cytosol, mitochondria, and nucleus, were detected in the CBs. Signals for cytochrome oxidase I (COXI) coded on mitochondrial DNA were also found in the CBs. Quantitative analysis of labeling density showed that all proteins examined were concentrated in the CBs to some extent. These results show that the CBs have some aggresomal features, suggesting that they are not a synthetic site as proposed previously but a degradation site where unnecessary DNA, RNA, and proteins are digested. (J Histochem Cytochem 53:455–465, 2005)


  • Chromatoid Bodies: Aggresome-like Characteristics and Degradation Sites for Organelles of Spermiogenic Cells -

    We investigated the localization of several markers for lysosomes and aggresomes in the chromatoid bodies (CBs) by immunoelectron microscopy. We found so-called aggresomal markers such as Hsp70 and ubiquitin in the core of the CBs and vimentin and proteasome subunit around the CBs. Ubiquitin-conjugating enzyme (E2) was also found in the CBs. In tubulovesicular structures surrounding the CBs, lysosomal markers were detected but an endoplasmic reticulum retention signal (KDEL) was not. Moreover, proteins located in each subcellular compartment, including the cytosol, mitochondria, and nucleus, were detected in the CBs. Signals for cytochrome oxidase I (COXI) coded on mitochondrial DNA were also found in the CBs. Quantitative analysis of labeling density showed that all proteins examined were concentrated in the CBs to some extent. These results show that the CBs have some aggresomal features, suggesting that they are not a synthetic site as proposed previously but a degradation site where unnecessary DNA, RNA, and proteins are digested. (J Histochem Cytochem 53:455–465, 2005)


  • Chromatoid Bodies: Aggresome-like Characteristics and Degradation Sites for Organelles of Spermiogenic Cells -

    We investigated the localization of several markers for lysosomes and aggresomes in the chromatoid bodies (CBs) by immunoelectron microscopy. We found so-called aggresomal markers such as Hsp70 and ubiquitin in the core of the CBs and vimentin and proteasome subunit around the CBs. Ubiquitin-conjugating enzyme (E2) was also found in the CBs. In tubulovesicular structures surrounding the CBs, lysosomal markers were detected but an endoplasmic reticulum retention signal (KDEL) was not. Moreover, proteins located in each subcellular compartment, including the cytosol, mitochondria, and nucleus, were detected in the CBs. Signals for cytochrome oxidase I (COXI) coded on mitochondrial DNA were also found in the CBs. Quantitative analysis of labeling density showed that all proteins examined were concentrated in the CBs to some extent. These results show that the CBs have some aggresomal features, suggesting that they are not a synthetic site as proposed previously but a degradation site where unnecessary DNA, RNA, and proteins are digested. (J Histochem Cytochem 53:455–465, 2005)


  • Chromosomal changes in uroepithelial carcinomas - This article reviews and summarizes chromosomal changes responsible for the initiation and progression of uroepithelial carcinomas. Characterization of these alterations may lead to a better understanding of the genetic mechanisms and open the door for molecular markers that can be used for better diagnosis and prognosis of the disease. Such information might even help in designing new therapeutic strategies geared towards prevention of tumor recurrences and more aggressive approach in progression-prone cases. The revision of 205 cases of uroepithelial carcinomas reported with abnormal karyotypes showed karyotypic profile characterized by nonrandom chromosomal aberrations varying from one or few changes in low-grade and early stage tumors to massively rearranged karyotypes in muscle invasive ones. In general, the karyotypic profile was dominated by losses of chromosomal material seen as loss of entire chromosome and/or deletions of genetic materials. Rearrangements of chromosome 9 resulting in loss of material from 9p, 9q, or of the entire chromosome were the most frequent cytogenetic alterations, seen in 45% of the cases. Whereas loss of material from chromosome arms 1p, 8p, and 11p, and gains of chromosome 7, and chromosome arm 1q, and 8q seem to be an early, but secondary, changes appearing in superficial and well differentiated tumors, the formation of an isochromosome for 5p and loss of material from 17p are associated with more aggressive tumor phenotypes. Upper urinary tract TCCs have identical karyotypic profile to that of bladder TCCs, indicating the same pathogenetic mechanisms are at work in both locales. Intratumor cytogenetic heterogeneity was not seen except in a few post-radiation uroepithelial carcinomas in which distinct karyotypic and clonal pattern were characterized by massive intratumor heterogeneity (cytogenetic polyclonality) with near-diploid clones and simple balanced and/or unbalanced translocations. In the vast majority of cases strong correlation between the tumors grade/stage and karyotypic complexity was seen, indicating that progressive accumulation of acquired genetic alterations is the driving force behind multistep bladder TCC carcinogenesis. Although most of these cytogenetic alterations have been identified for many years, the molecular consequences and relevant cancer genes of these alterations have not yet been identified. However, loss of TSG(s) from chromosome 9 seems to be the primary and important event(s) in uroepithelial carcinogenesis

  • Chromosome loops arising from intrachromosomal tethering of telomeres occur at high frequency in G1 (non-cycling) mitotic cells: Implications for telomere capture - Background: To investigate potential mechanisms for telomere capture the spatial arrangement of telomeres and chromosomes was examined in G1 (non-cycling) mitotic cells with diploid or triploid genomes. This was examined firstly by directly labelling the respective short arm (p) and long arm subtelomeres (q) with different fluorophores and probing cell preparations using a number of subtelomere probe pairs, those for chromosomes 1, 3, 4, 5, 6, 7, 9, 10, 12, 17, 18, and 20. In addition some interstitial probes (CEN15, PML and SNRPN on chromosome 15) and whole chromosome paint probes (e.g. WCP12) were jointly hybridised to investigate the co-localization of interphase chromosome domains and tethered subtelomeres. Cells were prepared by omitting exposure to colcemid and hypotonic treatments. Results: In these cells a specific interphase chromosome topology was detected. It was shown that the p and q telomeres of the each chromosome associate frequently (80% pairing) in an intrachromosomal manner, i.e. looped chromosomes with homologues usually widely spaced within the nucleus. This p-q tethering of the telomeres from the one chromosome was observed with large (chromosomes 3, 4, 5), medium sized (6, 7, 9, 10, 12), or small chromosomes (17, 18, 20). When triploid nuclei were probed there were three tetherings of p-q subtelomere signals representing the three widely separated looped chromosome homologues. The separate subtelomere pairings were shown to coincide with separate chromosome domains as defined by the WCP and interstitial probes. The 20% of apparently unpaired subtelomeric signals in diploid nuclei were partially documented to be pairings with the telomeres of other chromosomes. Conclusions: A topology for telomeres was detected where looped chromosome homologues were present at G1 interphase. These homologues were spatially arranged with respect to one-another independently of other chromosomes, i.e. there was no chromosome order on different sides of the cell nuclei and no segregation into haploid sets was detected. The normal function of this high frequency of intrachromosomal loops is unknown but a potential role is likely in the genesis of telomere captures whether of the intrachromosomal type or between non-homologues. This intrachromosomal tethering of telomeres cannot be related to telomeric or subtelomeric sequences since these are shared in varying degree with other chromosomes. In our view, these intrachromosomal telomeric tetherings with the resulting looped chromosomes arranged in a regular topology must be important to normal cell function since non-cycling cells in G1 are far from quiescent, are in fact metabolically active, and these cells represent the majority status since only a small proportion of cells are normally dividing.

  • clc is co-expressed with clf or cntfr in developing mouse muscles - Background: The ciliary neurotrophic factor (CNTF) receptor is composed of two signalling receptor chains, gp130 and the leukaemia inhibitory factor receptor, associated with a non-signalling CNTF binding receptor α component (CNTFR). This tripartite receptor has been shown to play important roles in the development of motor neurons, but the identity of the relevant ligand(s) is still not clearly established. Recently, we have identified two new ligands for the CNTF receptor complex. These are heterodimeric cytokines composed of cardiotrophin-like cytokine (CLC) associated either with the soluble receptor subunit cytokine-like factor-1 (CLF) or the soluble form of the binding receptor itself (sCNTFR). Results: Here we show that, during development, clc is expressed in lung, kidney, vibrissae, tooth, epithelia and muscles during the period of development corresponding to when motoneuron loss is observed in mice lacking a functional CNTF receptor. In addition, we demonstrate that it is co-expressed at the single cell level with clf and cntfr, supporting the idea that CLC might be co-secreted with either CLF or sCNTFR. Conclusion: This expression pattern is in favor of CLC, associated either with CLF or sCNTFR, being an important player in the signal triggered by the CNTF receptor being required for motoneuron development.

  • Clinical and biological characteristics of cervical neoplasias with FGFR3 mutation - Background: We have previously reported activating mutations of the gene coding for the fibroblast growth factor receptor 3 (FGFR3) in invasive cervical carcinoma. To further analyze the role of FGFR3 in cervical tumor progression, we extended our study to screen a total of 75 invasive tumors and 80 cervical intraepithelial neoplasias (40 low-grade and 40 high-grade lesions). Results: Using single strand conformation polymorphism (SSCP) followed by DNA sequencing, we found FGFR3 mutation (S249C in all cases) in 5% of invasive cervical carcinomas and no mutation in intraepithelial lesions. These results suggest that, unlike in bladder carcinoma, FGFR3 mutation does not occur in non invasive lesions. Compared to patients with wildtype FGFR3 tumor, patients with S249C FGFR3 mutated tumors were older (mean age 64 vs. 49.4 years, P = 0.02), and were more likely to be associated with a non-16/18 HPV type in their tumor. Gene expression analysis demonstrated that FGFR3 mutated tumors were associated with higher FGFR3b mRNA expression levels compared to wildtype FGFR3 tumors. Supervised analysis of Affymetrix expression data identified a significant number of genes specifically differentially expressed in tumors with respect to FGFR3 mutation status. Conclusions: This study suggest that tumors with FGFR3 mutation appear to have distinctive clinical and biological characteristics that may help in defining a population of patients for FGFR3 mutation screening.

  • Clinical trial update: International Breast Cancer Study Group - The International Breast Cancer Study Group (IBCSG) has been conducting large, phase III clinical trials since 1978. Prior to 1986, these activities were carried out under the name of Ludwig Breast Cancer Study Group. Seven trials of adjuvant therapies are currently open for patient accrual, five of which are described in this report. The IBCSG has been a leader in the field of tailored treatment approaches for specific subpopulations of patients with breast cancer, believing that what is best for the majority may not be best for a defined minority.

  • Clinical utility of serum HER2/neu in monitoring and prediction of progression-free survival in metastatic breast cancer patients treated with trastuzumab-based therapies - IntroductionThe purpose of this retrospective study was to determine the clinical utility of serum HER2/neu in monitoring metastatic breast cancer patients undergoing trastuzumab-based therapy and to compare these results with those obtained using cancer antigen (CA) 15-3. We also sought to determine whether early changes in serum HER2/neu concentrations could be a predictor of progression-free survival. Methods: Sera were obtained retrospectively from 103 women at four medical institutions. Patients eligible for participation were women with metastatic breast cancer who had HER2/neu tissue overexpression and were scheduled to be treated with trastuzumab with or without additional therapies as per the established practices of the treating physicians. A baseline serum sample for each patient was taken before trastuzumab-based therapy was started. Patients were subsequently monitored over 12 to 20 months and serum samples were taken at the time of clinical assessment and tested with Bayer's HER2/neu and CA15-3 assays. Results: Concordance between clinical status in patients undergoing trastuzumab-based treatment and HER2/neu and CA15-3 used as single tests was 0.793 and 0.627, respectively, and increased to 0.829 when the tests were used in combination. Progression-free survival times did not differ significantly in patients with elevated baseline HER2/neu concentrations (≥ 15 ng/mL) and those with normal concentrations (<15 ng/mL). However, progression-free survival differed significantly (P = 0.043) according to whether the patient's HER2/neu concentration at 2 to 4 weeks after the start of therapy was >77% or ≤ 77% of her baseline concentration. The median progression-free survival times for these two groups were 217 and 587 days, respectively. A similar trend was observed for a subcohort of patients treated specifically with a combination of trastuzumab and taxane. Conclusion: These findings indicate that serum HER2/neu testing is clinically valuable in monitoring metastatic breast cancer patients undergoing trastuzumab-based treatment and provides additional value over the commonly used CA15-3 test. The percentage of baseline HER2/neu concentrations in the early weeks after the start of therapy may be an early predictor of progression-free-survival.

  • Clioquinol and pyrrolidine dithiocarbamate complex with copper to form proteasome inhibitors and apoptosis inducers in human breast cancer cells - IntroductionA physiological feature of many tumor tissues and cells is the tendency to accumulate high concentrations of copper. While the precise role of copper in tumors is cryptic, copper, but not other trace metals, is required for angiogenesis. We have recently reported that organic copper-containing compounds, including 8-hydroxyquinoline-copper(II) and 5,7-dichloro-8-hydroxyquinoline-copper(II), comprise a novel class of proteasome inhibitors and tumor cell apoptosis inducers. In the current study, we investigate whether clioquinol (CQ), an analog of 8-hydroxyquinoline and an Alzheimer's disease drug, and pyrrolidine dithiocarbamate (PDTC), a known copper-binding compound and antioxidant, can interact with copper to form cancer-specific proteasome inhibitors and apoptosis inducers in human breast cancer cells. Tetrathiomolybdate (TM), a strong copper chelator currently being tested in clinical trials, is used as a comparison. Methods: Breast cell lines, normal, immortalized MCF-10A, premalignant MCF10AT1K.cl2, and malignant MCF10DCIS.com and MDA-MB-231, were treated with CQ or PDTC with or without prior interaction with copper, followed by measurement of proteasome inhibition and cell death. Inhibition of the proteasome was determined by levels of the proteasomal chymotrypsin-like activity and ubiquitinated proteins in protein extracts of the treated cells. Apoptotic cell death was measured by morphological changes, Hoechst staining, and poly(ADP-ribose) polymerase cleavage. Results: When in complex with copper, both CQ and PDTC, but not TM, can inhibit the proteasome chymotrypsin-like activity, block proliferation, and induce apoptotic cell death preferentially in breast cancer cells, less in premalignant breast cells, but are non-toxic to normal/non-transformed breast cells at the concentrations tested. In contrast, CQ, PDTC, TM or copper alone had no effects on any of the cells. Breast premalignant or cancer cells that contain copper at concentrations similar to those found in patients, when treated with just CQ or PDTC alone, but not TM, undergo proteasome inhibition and apoptosis. Conclusion: The feature of breast cancer cells and tissues to accumulate copper can be used as a targeting method for anticancer therapy through treatment with novel compounds such as CQ and PDTC that become active proteasome inhibitors and breast cancer cell killers in the presence of copper.

  • Cloning and functional characterization of the rabbit C-C chemokine receptor 2 - Background: CC-family chemokine receptor 2 (CCR2) is implicated in the trafficking of blood-borne monocytes to sites of inflammation and is implicated in the pathogenesis of several inflammatory diseases such as rheumatoid arthritis, multiple sclerosis and atherosclerosis. The major challenge in the development of small molecule chemokine receptor antagonists is the lack of cross-species activity to the receptor in the preclinical species. Rabbit models have been widely used to study the role of various inflammatory molecules in the development of inflammatory processes. Therefore, in this study, we report the cloning and characterization of rabbit CCR2. Results: Sequence alignment indicated that rabbit CCR2 shares 80 % identity to human CCR2b. Tissue distribution indicated that rabbit CCR2 is abundantly expressed in spleen and lung. Recombinant rabbit CCR2 expressed as stable transfectants in U-937 cells binds radiolabeled 125I-mouse JE (murine MCP-1) with a calculated Kd of 0.1 nM. In competition binding assays, binding of radiolabeled mouse JE to rabbit CCR2 is differentially competed by human MCP-1, -2, -3 and -4, but not by RANTES, MIP-1alpha or MIP-1beta. U-937/rabbit CCR2 stable transfectants undergo chemotaxis in response to both human MCP-1 and mouse JE with potencies comparable to those reported for human CCR2b. Finally, TAK-779, a dual CCR2/CCR5 antagonist effectively inhibits the binding of 125I-mouse JE (Ki = 2.3 nM) to rabbit CCR2 and effectively blocks CCR2-mediated chemotaxis. Conclusions: In this study, we report the cloning of rabbit CCR2 and demonstrate that this receptor is a functional chemotactic receptor for MCP-1. Data regarding the activity of the CCR2 antagonists against rabbit CCR2 will provide valuable tools to perform toxicology and efficacy studies in this species.

  • Cloning and transcription analysis of an AGAMOUS- and SEEDSTICK ortholog in the orchid Dendrobium thyrsiflorum (Reichb. f.). -
    Related Articles

    Cloning and transcription analysis of an AGAMOUS- and SEEDSTICK ortholog in the orchid Dendrobium thyrsiflorum (Reichb. f.).

    Gene. 2005 Oct 15;

    Authors: Skipper M, Johansen LB, Pedersen KB, Frederiksen S, Johansen BB

    Studies have shown that several plant species posses AGAMOUS (AG) and SEEDSTICK (STK) orthologs. These genes are part of the so-called C- and D MADS-box gene lineages and play key roles in ovule development in Arabidopsis thaliana. We have cloned an AG- and STK ortholog in the orchid Dendrobium thyrsiflorum, named DthyrAG1 and DthyrAG2, respectively, and analyzed their expression patterns. Quantification by real-time RT-PCR analysis shows that both are transcribed in the mature flowers and during ovule development. Localization of the transcripts by in situ hybridization analysis in flowers reveals that both genes are transcribed in the rostellum, stigma, and stylar canal. Expression analysis during ovule development shows that DthyrAG1 is expressed only in the initial periods of placenta- and ovule development, whereas the DthyrAG2 is transcribed throughout ovule development. These results suggest that both C- and D lineage orthologs are involved in various aspects of flower development and that DthyrAG2 have a more prominent role than DthyrAG1 in late ovule development in D. thyrsiflorum.

    PMID: 16236468 [PubMed - as supplied by publisher]


  • Co-accumulation of Dendritic Cells and Natural Killer T Cells within Rupture-prone Regions in Human Atherosclerotic Plaques -

    We previously reported that CD1d, a molecule responsible for the presentation of lipid antigens, is expressed in atherosclerotic lesions and that its expression is restricted to dendritic cells. Recent studies demonstrating that CD1d-restricted natural killer T (NKT) cells are involved in atherogenesis prompted the present study investigating whether NKT cells are present in human atherosclerotic lesions and, if so, whether there is an association between NKT cells and dendritic cells. We found that NKT cells do accumulate in rupture-prone shoulders of atherosclerotic plaques and observed direct contacts of dendritic cells with NKT cells in rupture-prone regions of plaque.

    (J Histochem Cytochem 53:781–785, 2005)


  • Co-accumulation of Dendritic Cells and Natural Killer T Cells within Rupture-prone Regions in Human Atherosclerotic Plaques -

    We previously reported that CD1d, a molecule responsible for the presentation of lipid antigens, is expressed in atherosclerotic lesions and that its expression is restricted to dendritic cells. Recent studies demonstrating that CD1d-restricted natural killer T (NKT) cells are involved in atherogenesis prompted the present study investigating whether NKT cells are present in human atherosclerotic lesions and, if so, whether there is an association between NKT cells and dendritic cells. We found that NKT cells do accumulate in rupture-prone shoulders of atherosclerotic plaques and observed direct contacts of dendritic cells with NKT cells in rupture-prone regions of plaque.

    (J Histochem Cytochem 53:781–785, 2005)


  • Co-accumulation of Dendritic Cells and Natural Killer T Cells within Rupture-prone Regions in Human Atherosclerotic Plaques -

    We previously reported that CD1d, a molecule responsible for the presentation of lipid antigens, is expressed in atherosclerotic lesions and that its expression is restricted to dendritic cells. Recent studies demonstrating that CD1d-restricted natural killer T (NKT) cells are involved in atherogenesis prompted the present study investigating whether NKT cells are present in human atherosclerotic lesions and, if so, whether there is an association between NKT cells and dendritic cells. We found that NKT cells do accumulate in rupture-prone shoulders of atherosclerotic plaques and observed direct contacts of dendritic cells with NKT cells in rupture-prone regions of plaque.

    (J Histochem Cytochem 53:781–785, 2005)


  • Co-release of noradrenaline and dopamine in the cerebral cortex elicited by single train and repeated train stimulation of the locus coeruleus - Background: Previous studies by our group suggest that extracellular dopamine (DA) and noradrenaline (NA) may be co-released from noradrenergic nerve terminals in the cerebral cortex. We recently demonstrated that the concomitant release of DA and NA could be elicited in the cerebral cortex by electrical stimulation of the locus coeruleus (LC). This study analyzes the effect of both single train and repeated electrical stimulation of LC on NA and DA release in the medial prefrontal cortex (mPFC), occipital cortex (Occ), and caudate nucleus. To rule out possible stressful effects of electrical stimulation, experiments were performed on chloral hydrate anaesthetised rats. Results: Twenty min electrical stimulation of the LC, with burst type pattern of pulses, increased NA and DA both in the mPFC and in the Occ. NA in both cortices and DA in the mPFC returned to baseline within 20 min after the end of the stimulation period, while DA in the Occ reached a maximum increase during 20 min post-stimulation and remained higher than baseline values at 220 min post-stimulation. Local perfusion with tetrodotoxin (TTX, 10 microM) markedly reduced baseline NA and DA in the mPFC and Occ and totally suppressed the effect of electrical stimulation in both areas. A sequence of five 20 min stimulation at 20 min interval were delivered to the LC. Each stimulus increased NA to the same extent and duration as the first stimulus, whereas DA remained elevated at the time next stimulus was delivered, so that baseline DA progressively increased in the mPFC and Occ to reach about 130 and 200% the initial level, respectively. In the presence of the NA transport blocker desipramine (DMI, 100 microM), multiple LC stimulation still increased extracellular NA and DA levels. Electrical stimulation of the LC increased NA levels in the homolateral caudate nucleus, but failed to modify DA level. Conclusion: The results confirm and extend that LC stimulation induces a concomitant release of DA and NA in the mPFC and Occ. The different time-course of LC-induced elevation of DA and NA suggests that their co-release may be differentially controlled.

  • Colocalization of Apolipoprotein AI in Various Kinds of Systemic Amyloidosis -

    Apolipoprotein AI (apoAI), a major component of high-density lipoproteins, is one of the major amyloid fibril proteins and a minor constituent of the senile plaques observed in Alzheimer's disease. We examined colocalization of apoAI in various kinds of systemic amyloidosis in this study. Forty-three of 48 formalin-fixed paraffin-embedded heart specimens with various forms of systemic amyloidosis reacted immunohistochemically with anti-human apoAI antibody. ApoAI was also detected in water-extracted amyloid material by immunoblotting. In addition, we observed colocalization of apoAI and murine amyloid A (AA) amyloidosis in human apoAI transgenic mice. This is the first report of colocalization of apoAI with amyloid deposits in various forms of human systemic amyloidosis and murine AA amyloidosis in human apoAI transgenic mice. ApoAI may not always be a major component of amyloid fibrils, even when it is present in systemic amyloid deposits.

    (J Histochem Cytochem 53:237–242, 2005)


  • Comments on the NIH Enhanced Public Access Policy - (No abstract is available for this citation)

  • Comparable response of ccn1with ccn2genes upon arthritis: An in vitroevaluation with a human chondrocytic cell line stimulated by a set of cytokines - Background: The chondrosarcoma-derived HCS-2/8 has been known to be an excellent model of human articular chondrocytes. By mimicking the arthritic conditions through the treatment of HCS-2/8 cells with cytokines, we estimated the gene expression response of ccn1 and ccn2 during the course of joint inflammation in vitro. Results: In order to mimic the initiation of inflammation, HCS-2/8 cells were treated with tumor necrosis factor (TNF)-alpha. To induce pro-inflammatory or reparative responses, TGF-alpha was employed. Effects of an anti-inflammatory glucocorticoid were also evaluated. After stimulation, expression levels of ccn1 and ccn2 were quantitatively analyzed. Surprisingly, not only ccn2, but also ccn1 expression was repressed upon TNF-alpha stimulation, whereas both mRNAs were uniformly induced by transforming growth factor (TGF)-beta and a glucocorticoid. Conclusions: These results describing the same response during the course of inflammation suggests similar and co-operative roles of these 2 ccn family members in the course of arthritis.

  • Complex de novo cryptic subtelomeric rearrangements in a fetus with multiple ultrasonographic abnormalities and a normal karyotype at amniocentesis. -
    Related Articles

    Complex de novo cryptic subtelomeric rearrangements in a fetus with multiple ultrasonographic abnormalities and a normal karyotype at amniocentesis.

    Prenat Diagn. 2005 Oct 21;

    Authors: Iqbal MA, Ramadan S, Ali FA, Kurdi W

    OBJECTIVE: Prenatal diagnosis is usually offered to the majority of pregnancies with fetal structural abnormalities detected by prenatal ultrasound; however, only a small proportion show an abnormal karyotype. We wanted to detect cryptic subtelomeric rearrangements (CSTR) in a fetus with multiple abnormal ultrasonographic findings that revealed a normal karyotype at amniocentesis. METHODS: Fetal chromosome analysis was performed from amniotic fluid cells. Parental chromosome analysis was done on PHA stimulated lymphocyte cultures. For fluorescence in situ hybridization (FISH) analysis, ToTelVysion multicolor DNA probe mixture was used to hybridize the p and q telomeres of each chromosome. RESULTS: The amniotic fluid chromosome analysis revealed an apparently normal 46,XY karyotype. A follow-up FISH analysis showed three apparently balanced complex translocations involving (1) the chromosome 4p and 22q telomeres (2) 4q and 11q telomeres and (3) 8p, 20p and 20q telomeres. Parental chromosome and subtelomere FISH analysis was found to be normal. CONCLUSION: To our knowledge, this is the first report of complex de novo cryptic translocations in an abnormal fetus. These CSTR identified by FISH with subtelomere-specific probes are not detected by other cytogenetic and/or molecular cytogenetic approaches. However, to confirm the balanced nature of CSTR, array-CGH can be helpful. Further studies are in progress to determine the frequency of CSTR and its significance in the etiology of fetal abnormalities. Copyright (c) 2005 John Wiley & Sons, Ltd.

    PMID: 16240463 [PubMed - as supplied by publisher]


  • Connective Tissue Growth Factor and Cardiac Fibrosis after Myocardial Infarction -

    The temporal and spatial expression of transforming growth factor (TGF)-ßbeta;1 and connective tissue growth factor (CTGF) was assessed in the left ventricle of a myocardial infarction (MI) model of injury with and without angiotensin-converting enzyme (ACE) inhibition. Coronary artery ligated rats were killed 1, 3, 7, 28, and 180 days after MI. TGF-ßbeta;1, CTGF, and procollagen 1(I) mRNA were localized by in situ hybridization, and TGF-ßbeta;1 and CTGF protein levels by immunohistochemistry. Collagen protein was measured using picrosirius red staining. In a separate group, rats were treated for 6 months with an ACE inhibitor. There were temporal and regional differences in the expression of TGF-ßbeta;1, CTGF, and collagen after MI. Procollagen 1(I) mRNA expression increased in the border zone and scar peaking 1 week after MI, whereas collagen protein increased in all areas of the heart over the 180 days. Expression of TGF-ßbeta;1 mRNA and protein showed major increases in the border zone and scar peaking 1 week after MI. The major increases in CTGF mRNA and protein occurred in the viable myocardium at 180 days after MI. Long-term ACE inhibition reduced left ventricular mass and decreased fibrosis in the viable myocardium, but had no effect on cardiac TGF-ßbeta;1 or CTGF. TGF-ßbeta;1 is involved in the initial, acute phase of inflammation and repair after MI, whereas CTGF is involved in the ongoing fibrosis of the heart. The antifibrotic benefits of captopril are not mediated through a reduction in CTGF.

    (J Histochem Cytochem 53:1245–1256, 2005)


  • Connective Tissue Growth Factor and Cardiac Fibrosis after Myocardial Infarction -

    The temporal and spatial expression of transforming growth factor (TGF)-ßbeta;1 and connective tissue growth factor (CTGF) was assessed in the left ventricle of a myocardial infarction (MI) model of injury with and without angiotensin-converting enzyme (ACE) inhibition. Coronary artery ligated rats were killed 1, 3, 7, 28, and 180 days after MI. TGF-ßbeta;1, CTGF, and procollagen 1(I) mRNA were localized by in situ hybridization, and TGF-ßbeta;1 and CTGF protein levels by immunohistochemistry. Collagen protein was measured using picrosirius red staining. In a separate group, rats were treated for 6 months with an ACE inhibitor. There were temporal and regional differences in the expression of TGF-ßbeta;1, CTGF, and collagen after MI. Procollagen 1(I) mRNA expression increased in the border zone and scar peaking 1 week after MI, whereas collagen protein increased in all areas of the heart over the 180 days. Expression of TGF-ßbeta;1 mRNA and protein showed major increases in the border zone and scar peaking 1 week after MI. The major increases in CTGF mRNA and protein occurred in the viable myocardium at 180 days after MI. Long-term ACE inhibition reduced left ventricular mass and decreased fibrosis in the viable myocardium, but had no effect on cardiac TGF-ßbeta;1 or CTGF. TGF-ßbeta;1 is involved in the initial, acute phase of inflammation and repair after MI, whereas CTGF is involved in the ongoing fibrosis of the heart. The antifibrotic benefits of captopril are not mediated through a reduction in CTGF.

    (J Histochem Cytochem 53:1245–1256, 2005)


  • Connexin 43 mediated gap junctional communication enhances breast tumor cell diapedesis in culture - IntroductionMetastasis involves the emigration of tumor cells through the vascular endothelium, a process also known as diapedesis. The molecular mechanisms regulating tumor cell diapedesis are poorly understood, but may involve heterocellular gap junctional intercellular communication (GJIC) between tumor cells and endothelial cells.MethodTo test this hypothesis we expressed connexin 43 (Cx43) in GJIC-deficient mammary epithelial tumor cells (HBL100) and examined their ability to form gap junctions, establish heterocellular GJIC and migrate through monolayers of human microvascular endothelial cells (HMVEC) grown on matrigel-coated coverslips. Results: HBL100 cells expressing Cx43 formed functional heterocellular gap junctions with HMVEC monolayers within 30 minutes. In addition, immunocytochemistry revealed Cx43 localized to contact sites between Cx43 expressing tumor cells and endothelial cells. Quantitative analysis of diapedesis revealed a two-fold increase in diapedesis of Cx43 expressing cells compared to empty vector control cells. The expression of a functionally inactive Cx43 chimeric protein in HBL100 cells failed to increase migration efficiency, suggesting that the observed up-regulation of diapedesis in Cx43 expressing cells required heterocellular GJIC. This finding is further supported by the observation that blocking homocellular and heterocellular GJIC with carbenoxolone in co-cultures also reduced diapedesis of Cx43 expressing HBL100 tumor cells. Conclusion: Collectively, our results suggest that heterocellular GJIC between breast tumor cells and endothelial cells may be an important regulatory step during metastasis.

  • Conventional liquid-based techniques versus Cytyc Thinprep(R)processing of urinary samples: a qualitative approach - Background: The aim of our study was to objectively compare Cytyc Thinprep* and other methods of obtaining thin layer cytologic preparations(cytocentrifugation, direct smearing and Millipore* filtration) in urine cytopathology. Methods: Thinprep slides were compared to direct smears in 79 cases.Cytocentrifugation carried out with the Thermo Shandon Cytospin* 4 was compared to Thinprep in 106 cases, and comparison with Millipore filtration followed by blotting was obtained in 22 cases. Quality was assessed by scoring cellularity, fixation, red blood cells, leukocytes and nuclear abnormalities. Results: The data show that 1) smearing allows good overall results to be obtained, 2) Cytocentrifugation with reusable TPX* chambers should be avoided, 3)Cytocentrifugation using disposable chambers (Cytofunnels* or Megafunnel* chambers) gives excellent results equalling or surpassing Thinprep and 4)Millipore filtration should be avoided, owing to its poor global quality. Despite differences in quality, the techniques studied have no impact on the diagnostic accuracy as evaluated by the rate of abnormalities. Conclusion: We conclude that conventional methods such as cytocentrifugation remain the most appropriate ones for current treatment of urinary samples. Cytyc Thinprep processing, owing to its cost, could be used essentially for cytology-based molecular studies.

  • Correction for Vol. 52, p. 1098 - (No abstract is available for this citation)

  • Correction for Vol. 52, p. 1098 - (No abstract is available for this citation)

  • Correction for Vol. 52, p. 1098 - (No abstract is available for this citation)

  • Cortactin overexpression results in sustained epidermal growth factor receptor signaling by preventing ligand-induced receptor degradation in human carcinoma cells - The chromosome 11q13 region is frequently amplified in human carcinomas and results in an increased expression of various genes including cortactin, and is also associated with an increased invasive potential. Cortactin acts as an important regulator of the actin cytoskeleton. It is therefore very tempting to speculate that cortactin is the crucial gene within the 11q13 amplicon that mediates the invasive potential of these carcinomas. Cortactin also participates in receptor-mediated endocytosis, and recent findings have shown that, during receptor internalization, cortactin overexpression inhibits the ubiquitylation-mediated degradation of the epidermal growth factor receptor, resulting in a sustained ligand-induced epidermal growth factor receptor activity.

  • Crosstalk between the actin cytoskeleton and Ran-mediated nuclear transport - Background: Transport of macromolecules into and out of the nucleus is a highly regulated process. The RanGTP/RanGDP gradient controls the trafficking of molecules exceeding the diffusion limit of the nuclear pore across the nuclear envelope. Results: We found genetic interaction between genes establishing the Ran gradient, nuclear transport factor 2 (ntf-2), Ran GTPase activating protein (Sd), and the gene encoding Drosophila Profilin, chickadee (chic). The severe eye phenotype caused by reduction of NTF2 is suppressed by loss of function mutations in chic and gain of function mutations in Sd (RanGAP). We show that in chic mutants, as in Sd-RanGAP, nuclear export is impaired. Conclusions: Our data suggest that Profilin and the organization of the actin cytoskeleton play an important role in nuclear trafficking.

  • Cyclical up-regulated iNOS and long-term down-regulated nNOS are the basis for relapse and quiescent phases in a rat model of IBD. -
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    Cyclical up-regulated iNOS and long-term down-regulated nNOS are the basis for relapse and quiescent phases in a rat model of IBD.

    Am J Physiol Gastrointest Liver Physiol. 2005 Oct 20;

    Authors: Porras M, Martin MT, Torres R, Vergara P

    Background: We previously reported that indomethacin induces a chronic intestinal inflammation in the rat where the cyclical characteristic phases of Crohn's disease are manifested with a few days' interval and lasting for several months: active phase (high inflammation, hypomotility, bacterial traslocation) and reactive phase (low inflammation, hypermotility, no bacterial traslocation). Aims: In this study we investigated the possible role of both constitutive and inducible isoforms of nitric oxide synthase (NOS) and cyclooxygenase (COX) in the cyclicity of active and reactive phases in rats with chronic intestinal inflammation. Methods: Rats selected at either active or reactive phases and from 2 to 60 days after indomethacin treatment were used. mRNA expression of both constitutive and inducible NOS and COX isoforms in each phase was evaluated by RT-PCR and cellular enzyme localization by immunohistochemistry. The effects of different COX and NOS inhibitors on the intestinal motor activity were tested. Results: mRNA expression of COX-1 was not modified by inflammation whereas mRNA expression of nNOS was reduced in all indomethacin treated rats. In contrast, NOS and COX inducible forms showed a cyclical oscillation. mRNA expression and protein of both iNOS and COX-2 increased only during active phases. The intestinal hypomotility associated with active phases was turned into hypermotility after the administration of selective iNOS inhibitors. Conclusions: Sustained down-regulation of constitutive NOS caused hypermotility, possibly as a defense mechanism. However, this reaction was masked during the active phases due to the inhibitory effects of nitric oxide resulting from the increased levels of inducible NOS isoform.

    PMID: 16239401 [PubMed - as supplied by publisher]


  • CYP17 5'-UTR MspA1 polymorphism and the risk of premenopausal breast cancer in a German population-based case–control study - IntroductionStudies on the association between the cytochrome P450c17α gene (CYP17) 5'-untranslated region MspA1 genetic polymorphism and breast cancer risk have yielded inconsistent results. Higher levels of estrogen have been reported among young nulliparous women with the A2 allele. Therefore we assessed the impact of CYP17 genotypes on the risk of premenopausal breast cancer, with emphasis on parity. Methods: We used data from a population-based case–control study of women aged below 51 years conducted from 1992 to 1995 in Germany. Analyses were restricted to clearly premenopausal women with complete information on CYP17 and encompassed 527 case subjects and 904 controls, 99.5% of whom were of European descent. The MspA1 polymorphism was analyzed using PCR-RFLP (PCR–restriction fragment length polymorphism) assay. Results: The frequencies of the variant allele among the cases and controls were 43% and 41%, respectively. Overall, CYP17 A1/A2 and A2/A2 genotypes compared with the A1/A1 genotype were not associated with breast cancer, with adjusted odds ratios (ORs) of 1.04 and 1.23, respectively. Among nulliparous women, however, breast cancer risk was elevated for the A1/A2 (OR = 1.31; 95% confidence interval (CI) 0.74 to 2.32) and the A2/A2 genotype (OR = 2.12; 95% CI 1.04 to 4.32) compared with the A1/A1 genotype, with a trend towards increasing risk associated with number of A2 alleles (P = 0.04). Otherwise, the CYP17 polymorphism was found neither to be an effect modifier of breast cancer risks nor to be associated with stage of disease. Conclusion: Our results do not indicate a major influence of CYP17 MspA1 polymorphism on the risk of premenopausal breast cancer, but suggest that it may have an impact on breast cancer risk among nulliparous women. The finding, however, needs to be confirmed in further studies.

  • CYP17 and breast cancer: no overall effect, but what about interactions? - Three large studies published in recent issues of Breast Cancer Research reported no overall evidence of an association between the CYP17 5'-untranslated region MspA1 polymorphism and breast cancer. The present commentary briefly highlights a few important observations and discusses some additional approaches to further assessment of associations between CYP17 common variants and breast cancer risk. In particular, the evolution of evidence on breast cancer and the CYP17 MspA1 variant suggests that determination of possible interactions between gene variants postulated to influence risk and nongenetic risk factors would be more efficiently accomplished by pooled analyses, ideally involving all studies of breast cancer, than by attempting to synthesize published information. Furthermore, such analyses would also be relevant to investigation of potential gene–gene interactions between CYP17 and other common variants in genes encoding enzymes that are involved in the synthesis and inactivation of sex steroid hormones, preferably using optimal sets of single nucleotide polymorphisms.

  • CYP17 gene polymorphism in relation to breast cancer risk: a case-control study - IntroductionThe c.1-34T>C 5' promoter region polymorphism in cytochrome P450c17 (CYP17), a key enzyme in the biosynthesis of estrogen, has been associated with breast cancer risk, but most previous studies have been relatively small. Methods: We genotyped 1,544 incident cases of primary breast cancer and 1,502 population controls, all postmenopausal Swedish women, for the CYP17 c.1-34T>C polymorphism and calculated odds ratios (ORs) and 95% confidence intervals (CIs) from logistic regression models. Results: No overall association was found between CYP17 c.1-34T>C and breast cancer risk, OR 1.0 (95% CI 0.8–1.3) for the A2/A2 (CC) carriers compared to the A1/A1 (TT) carriers, regardless of histopathology. We detected an interaction between CYP17 c.1-34T>C and age at menarche (P = 0.026) but regarded that as a chance finding as no dose-response pattern was evident. Other breast cancer risk factors, including menopausal hormone use and diabetes mellitus, did not modify the overall results. Conclusion: It is unlikely that CYP17 c.1-34T>C has a role in breast cancer etiology, overall or in combination with established non-genetic breast cancer risk factors.

  • CYP17 genetic polymorphism, breast cancer, and breast cancer risk factors: Australian Breast Cancer Family Study - IntroductionBecause CYP17 can influence the degree of exposure of breast tissues to oestrogen, the interaction between polymorphisms in this gene and hormonal risk factors is of particular interest. We attempted to replicate the findings of studies assessing such interactions with the -34T→C polymorphism. Methods: Risk factor and CYP17 genotyping data were derived from a large Australian population-based case-control-family study of 1,284 breast cancer cases and 679 controls. Crude and adjusted odds ratio (OR) estimates and 95% confidence intervals (CIs) were calculated by unconditional logistic regression analyses. Results: We found no associations between the CYP17 genotype and breast cancer overall. Premenopausal controls with A2/A2 genotype had a later age at menarche (P < 0.01). The only associations near statistical significance were that postmenopausal women with A1/A1 (wild-type) genotype had an increased risk of breast cancer if they had ever used hormone replacement therapy (OR 2.40, 95% CI 1.0 to 5.7; P = 0.05) and if they had menopause after age 47 years (OR 2.59, 95% CI 1.0 to 7.0; P = 0.06). We found no associations in common with any other studies, and no evidence for interactions. Conclusion: We observed no evidence of effect modification of reproductive risk factors by CYP17 genotype, although the experiment did not have sufficient statistical power to detect small main effects and modest effects in subgroups. Associations found only in subgroup analyses based on relatively small numbers require cautious interpretation without confirmation by other studies. This emphasizes the need for replication in multiple and large population-based studies to provide convincing evidence for gene–environment interactions.

  • CYP2D6 genotype and tamoxifen response - none

  • CYP2D6 variants and the prediction of tamoxifen response in randomized patients: author response - No abstract

  • CyProQuant-PCR: a real time RT-PCR technique for profiling human cytokines, based on external RNA standards, readily automatable for clinical use - Background: Real-time PCR is becoming a common tool for detecting and quantifying expression profiling of selected genes. Cytokines mRNA quantification is widely used in immunological research to dissect the early steps of immune responses or pathophysiological pathways. It is also growing to be of clinical relevancy to immuno-monitoring and evaluation of the disease status of patients. The techniques currently used for "absolute quantification" of cytokine mRNA are based on a DNA standard curve and do not take into account the critical impact of RT efficiency. Results: To overcome this pitfall, we designed a strategy using external RNA as standard in the RT-PCR. Use of synthetic RNA standards, by comparison with the corresponding DNA standard, showed significant variations in the yield of retro-transcription depending the target amplified and the experiment. We then developed primers to be used under one single experimental condition for the specific amplification of human IL-1β, IL-4, IL-10, IL-12p40, IL-13, IL-15, IL-18, IFN-γ, MIF, TGF-β1 and TNF-α mRNA. We showed that the beta-2 microglobulin (β2-MG) gene was suitable for data normalisation since the level of β2-MG transcripts in naïve PBMC varied less than 5 times between individuals and was not affected by LPS or PHA stimulation. The technique, we named CyProQuant-PCR (Cytokine Profiling Quantitative PCR) was validated using a kinetic measurement of cytokine transcripts under in vitro stimulation of human PBMC by lipopolysaccharide (LPS) or Staphylococcus aureus strain Cowan (SAC). Results obtained show that CyProQuant-PCR is powerful enough to precociously detect slight cytokine induction. Finally, having demonstrated the reproducibility of the method, it was applied to malaria patients and asymptomatic controls for the quantification of TGF-β1 transcripts and showed an increased capacity of cells from malaria patients to accumulate TGF-β1 mRNA in response to LPS. Conclusion: The real-time RT-PCR technique based on a RNA standard curve, CyProQuant-PCR, outlined here, allows for a genuine absolute quantification and a simultaneous analysis of a large panel of human cytokine mRNA. It represents a potent and attractive tool for immunomonitoring, lending itself readily to automation and with a high throughput. This opens the possibility of an easy and reliable cytokine profiling for clinical applications.

  • CytoJournal's move to fund Open Access - CytoJournal is published by an independent publisher BioMed Central, which is committed to ensuring that the peer-reviewed biomedical research is Open Access. Since its launch, BioMed Central has graciously supported the processing of all the articles published during CytoJournal's first 6 months. However, for long term viability, CytoJournal has to achieve financial viability to support publication expenses. From 1st March, 2005, authors will be asked by the publisher to pay a flat article-processing charge. This editorial discusses how a significant proportion of authors may not have to pay this fee directly under a variety of different mechanisms such as institutional and society memberships with BioMed Central.

  • Cytomegalovirus-Associated Pulmonary Septal Capillary Injury Sine Inclusion Body Change: A Distinctive Cause of Occult or Macroscopic Pulmonary Hemorrhage in the Immunocompetent Host. -

  • DAPI Fluorescence in Nuclei Isolated from Tumors -

    In DNA histograms of some human solid tumors stained with nuclear isolation medium–4,6-diamidino-2-phenylindole dihydrochloride (NIM-DAPI), the coefficient of variation (CV) of the G0/G1 peak was broad, and in nuclear volume vs DNA scattergrams, a prominent slope was seen. To determine the cause for this, nuclei from frozen breast tumors were stained with NIM-DAPI and analyzed after dilution or resuspension in PBS. In two-color (blue vs red) analysis, most of the slope and broad CV was due to red fluorescence of nuclei stained with NIM-DAPI, which was reduced on dilution or resuspension in PBS, resulting in elimination of the slope and tightening of the CV.

    (J Histochem Cytochem 53:1033–1036, 2005)


  • DAPI Fluorescence in Nuclei Isolated from Tumors -

    In DNA histograms of some human solid tumors stained with nuclear isolation medium–4,6-diamidino-2-phenylindole dihydrochloride (NIM-DAPI), the coefficient of variation (CV) of the G0/G1 peak was broad, and in nuclear volume vs DNA scattergrams, a prominent slope was seen. To determine the cause for this, nuclei from frozen breast tumors were stained with NIM-DAPI and analyzed after dilution or resuspension in PBS. In two-color (blue vs red) analysis, most of the slope and broad CV was due to red fluorescence of nuclei stained with NIM-DAPI, which was reduced on dilution or resuspension in PBS, resulting in elimination of the slope and tightening of the CV.

    (J Histochem Cytochem 53:1033–1036, 2005)


  • Depth-varying Density and Organization of Chondrocytes in Immature and Mature Bovine Articular Cartilage Assessed by 3D Imaging and Analysis -

    Articular cartilage is a heterogeneous tissue, with cell density and organization varying with depth from the surface. The objectives of the present study were to establish a method for localizing individual cells in three-dimensional (3D) images of cartilage and quantifying depth-associated variation in cellularity and cell organization at different stages of growth. Accuracy of nucleus localization was high, with 99% sensitivity relative to manual localization. Cellularity (million cells per cm3) decreased from 290, 310, and 150 near the articular surface in fetal, calf, and adult samples, respectively, to 120, 110, and 50 at a depth of 1.0 mm. The distance/angle to the nearest neighboring cell was 7.9 µm/31°, 7.1 µm/31°, and 9.1 µm/31° for cells at the articular surface of fetal, calf, and adult samples, respectively, and increased/decreased to 11.6 µm/31°, 12.0 µm/30°, and 19.2 µm/25° at a depth of 0.7 mm. The methodologies described here may be useful for analyzing the 3D cellular organization of cartilage during growth, maturation, aging, degeneration, and regeneration. (J Histochem Cytochem 53:1109–1119, 2005)


  • Dermal fibroblasts in Hutchinson-Gilford progeria syndrome with the lamin A G608G mutation have dysmorphic nuclei and are hypersensitive to heat stress - Background: Hutchinson-Gilford progeria syndrome (HGPS, OMIM 176670) is a rare sporadic disorder with an incidence of approximately 1 per 8 million live births. The phenotypic appearance consists of short stature, sculptured nose, alopecia, prominent scalp veins, small face, loss of subcutaneous fat, faint mid-facial cyanosis, and dystrophic nails. HGPS is caused by mutations in LMNA, the gene that encodes nuclear lamins A and C. The most common mutation in subjects with HGPS is a de novo single-base pair substitution, G608G (GGC>GGT), within exon 11 of LMNA. This creates an abnormal splice donor site, leading to expression of a truncated protein. Results: We studied a new case of a 5 year-old girl with HGPS and found a heterozygous point mutation, G608G, in LMNA. Complementary DNA sequencing of RNA showed that this mutation resulted in the deletion of 50 amino acids in the carboxyl-terminal tail domain of prelamin A. We characterized a primary dermal fibroblast cell line derived from the subject's skin. These cells expressed the mutant protein and exhibited a normal growth rate at early passage in primary culture but showed alterations in nuclear morphology. Expression levels and overall distributions of nuclear lamins and emerin, an integral protein of the inner nuclear membrane, were not dramatically altered. Ultrastructural analysis of the nuclear envelope using electron microscopy showed that chromatin is in close association to the nuclear lamina, even in areas with abnormal nuclear envelope morphology. The fibroblasts were hypersensitive to heat shock, and demonstrated a delayed response to heat stress. Conclusions: Dermal fibroblasts from a subject with HGPS expressing a mutant truncated lamin A have dysmorphic nuclei, hypersensitivity to heat shock, and delayed response to heat stress. This suggests that the mutant protein, even when expressed at low levels, causes defective cell stability, which may be responsible for phenotypic abnormalities in the disease.

  • Design and assessment of a tissue-engineered model of human phalanges and a small joint. -
    Related Articles

    Design and assessment of a tissue-engineered model of human phalanges and a small joint.

    Orthod Craniofac Res. 2005 Nov;8(4):303-12

    Authors: Landis W, Jacquet R, Hillyer J, Lowder E, Yanke A, Siperko L, Asamura S, Kusuhara H, Enjo M, Chubinskaya S, Potter K, Isogai N

    Objectives - To develop models of human phalanges and small joints by suturing different cell-polymer constructs that are then implanted in athymic (nude) mice. Design - Models consisted of bovine periosteum, cartilage, and/or tendon cells seeded onto biodegradable polymer scaffolds of either polyglycolic acid (PGA) or copolymers of PGA and poly-L-lactic acid (PLLA) or poly-epsilon-caprolactone (PCL) and PLLA. Constructs were fabricated to produce a distal phalanx, middle phalanx, or distal interphalangeal joint. Setting and Sample Population - Studies of more than 250 harvested implants were conducted at the Northeastern Ohio Universities College of Medicine. Experimental Variable - Polymer scaffold, cell type, and implantation time were examined. Outcome Measure - Tissue-engineered specimens were characterized by histology, transmission electron microscopy, in situ hybridization, laser capture microdissection and qualitative and quantitative polymerase chain reaction analysis, magnetic resonance microscopy, and X-ray microtomography. Results - Over periods to 60 weeks of implantation, constructs developed through vascularity from host mice; formed new cartilage, bone, and/or tendon; expressed characteristic genes of bovine origin, including type I, II and X collagen, osteopontin, aggrecan, biglycan, and bone sialoprotein; secreted corresponding proteins; responded to applied mechanical stimuli; and maintained shapes of human phalanges with small joints. Conclusion - Results give insight into construct processes of tissue regeneration and development and suggest more complete tissue-engineered cartilage, bone, and tendon models. These should have significant future scientific and clinical applications in medicine, including their use in plastic surgery, orthopaedics, craniofacial reconstruction, and teratology.

    PMID: 16238611 [PubMed - in process]


  • Designing a HER2/neu promoter to drive α1,3galactosyltransferase expression for targeted anti-αGal antibody-mediated tumor cell killing - IntroductionOur goal was to specifically render tumor cells susceptible to natural cytolytic anti-αGal antibodies by using a murine α1,3galactosyltransferase (mαGalT) transgene driven by a designed form of HER2/neu promoter (pNeu), the transcription of which is frequently observed to be above basal in breast tumors. Indeed, the αGalT activity that promotes Galα1,3Galβ1,4GlcNAc-R (αGal) epitope expression has been mutationally disrupted during the course of evolution, starting from Old World primates, and this has led to the counter-production of large amounts of cytotoxic anti-αGal antibodies in recent primates, including man.MethodExpression of the endogenous c-erbB-2 gene was investigated in various cell lines by northern blotting. A mαGalT cDNA was constructed into pcDNA3 vector downstream of the original CMV promoter (pCMV/mαGalT) and various forms of pNeu were prepared by PCR amplification and inserted in the pCMV/mαGalT construct upstream of the mαGalT cDNA, in the place of the CMV promoter. These constructs were transferred into HEK-293 control and breast tumor cell lines. Stably transfected cells were analyzed by northern blotting for their expression of αGalT and c-erbB-2, and by flow cytometry for their binding with fluorescein isothiocyanate-conjugated Griffonia simplicifolia/isolectin B4. Results: We show that expression of the mαGalT was up- or down-modulated according to the level of endogenous pNeu activity and the particular form of constructed pNeu. Among several constructs, two particular forms of the promoter, pNeu250 containing the CCAAT box and the PEA3 motif adjacent to the TATAA box, and pNeu664, which has three additional PEA3 motifs upstream of the CCAAT box, were found to promote differential αGalT expression. Conclusion: Our results strengthen current concepts about the crucial role played by the proximal PEA3 motif of pNeu, and may represent a novel therapeutic approach for the development of targeted transgene expression.

  • Desmoplastic Infantile Ganglioglioma: cytologic findings and differential diagnosis on aspiration material - Background: Desmoplastic infantile ganglioglioma (DIG) is a rare WHO Grade I tumor of infancy that is characterized by large volume, superficial location, invariable supratentoriality, fronto-parietal lobe predilection and morphologically, by an admixture of astroglial and neuroepithelial elements in a desmoplastic milieu. With over 50 cases described, the histologic and radiographic spectrum of DIG has been well-characterized. The superficial location of DIGs may render them greatly amenable to preoperative assessment utilizing aspiration cytology; however, the cytologic features of this rare tumor have only been reported once previously.Case PresentationWe present herein cytomorphologic findings from the intraoperative aspiration of a typical case of DIG diagnosed in a 1-year-old male. As evaluated on a single liquid-based preparation, the specimen showed low cellularity and was comprised predominantly of a population of dispersed (occasionally clustered) large neuronal cells with eccentrically located hyperchromatic nuclei (which were occasionally binucleated) and abundant unipolar cytoplasm. Rare smaller astroglial cells were intermixed. Despite the tumor's characteristic desmoplastic histologic appearance, no stromal fragments were identified on the aspiration material. Conclusions: A differential diagnosis is presented and analyzed in detail and it is concluded that when these large neuronal cells are encountered in an aspirate of a brain mass in a child, a combination of clinical, radiologic and immunohistochemical parameters can eliminate most of the differential possibilities.

  • Desmoplastic small round cell tumour: Cytological and immunocytochemical features - Background: Desmoplastic small round cell tumor (DSRCT) is a rare and highly aggressive neoplasm. The cytological diagnosis of these tumors can be difficult because they show morphological features quite similar to other small round blue cells tumors. We described four cases of DSRCT with cytological sampling: one obtained by fine needle aspiration biopsy (FNAB) and three from serous effusions. The corresponding immunocytochemical panel was also reviewed. Methods: Papanicolaou stained samples from FNAB and effusions were morphologically described. Immunoreaction with WT1 antibody was performed in all cytological samples. An immunohistochemical panel including the following antibodies was performed in the corresponding biopsies: 34BE12, AE1/AE3, Chromogranin A, CK20, CK7, CK8, Desmin, EMA, NSE, Vimentin and WT1. Results: The smears showed high cellularity with minor size alteration. Nuclei were round to oval, some of them with inconspicuous nucleoli. Tumor cells are clustered, showing rosette-like feature. Tumor cells in effusions and FNA were positive to WT1 in 3 of 4 cytology specimens (2 out 3 effusions and one FNA). Immunohistochemical reactions for vimentin, NSE, AE1/AE3 and WT1 were positive in all cases in tissue sections. Conclusion: The use of an adjunct immunocytochemical panel coupled with the cytomorphological characteristics allows the diagnosis of DSRCT in cytological specimens.

  • Determinants of Bleeding Severity in von Willebrand Disease - von Willebrand disease (VWD) is one of the most common bleeding disorders. It is caused by abnormalities in the von Willebrand factor (VWF) protein, and is characterized by incomplete penetrance and variable expressivity. VWF levels vary widely in the population. The best-characterized human genetic modifier of VWF is the ABO blood group. Patients with VWD show considerable variation in bleeding tendency even within the same family, independently of VWF levels. It is possible that several modifier genes influence the phenotype. Variants of genes that encode for platelet receptors as well as those that encode for clotting factor levels have been proposed as modifiers. It is hoped that new clinical-genetic studies will shed light on these issues and help practitioners to determine the population at risk for bleeding.

  • Development of In Situ Zymography to Localize Active Matrix Metalloproteinase-7 (Matrilysin-1) -

    Matrix metalloproteinase-7 (MMP-7) is upregulated during carcinogenesis and its expression correlates with metastasis of human endometrial and gastrointestinal carcinomas. In the present study, we have developed a new method to localize the activity of MMP-7 within tissues. Polyethylene terephthalate films were uniformly coated with crosslinked carboxymethylated transferrin (CCm-Tf) as a substrate and incubated with frozen tissue sections mounted on the films. CCm-Tf on the films was degraded selectively by MMP-7, but showed little or no susceptibility to MMP-1, -2, -3, -9, or -13; MT1-MMP; MT3-MMP; or ADAMTS4. Although some serine proteinases such as elastase also digested CCm-Tf, CCm-Tf films impregnated with serine proteinase inhibitors prevented the digestion. When frozen sections of human endometrial carcinoma and lung carcinoma tissues were incubated on CCm-Tf films or those treated with proteinase inhibitors, the activity was detected in the carcinoma cell nests, where MMP-7 was immunolocalized. The present in situ zymography using CCm-Tf may be a useful method to analyze the functions of MMP-7 in pathophysiological conditions. (J Histochem Cytochem 53:1227–1234, 2005)


  • Development of In Situ Zymography to Localize Active Matrix Metalloproteinase-7 (Matrilysin-1) -

    Matrix metalloproteinase-7 (MMP-7) is upregulated during carcinogenesis and its expression correlates with metastasis of human endometrial and gastrointestinal carcinomas. In the present study, we have developed a new method to localize the activity of MMP-7 within tissues. Polyethylene terephthalate films were uniformly coated with crosslinked carboxymethylated transferrin (CCm-Tf) as a substrate and incubated with frozen tissue sections mounted on the films. CCm-Tf on the films was degraded selectively by MMP-7, but showed little or no susceptibility to MMP-1, -2, -3, -9, or -13; MT1-MMP; MT3-MMP; or ADAMTS4. Although some serine proteinases such as elastase also digested CCm-Tf, CCm-Tf films impregnated with serine proteinase inhibitors prevented the digestion. When frozen sections of human endometrial carcinoma and lung carcinoma tissues were incubated on CCm-Tf films or those treated with proteinase inhibitors, the activity was detected in the carcinoma cell nests, where MMP-7 was immunolocalized. The present in situ zymography using CCm-Tf may be a useful method to analyze the functions of MMP-7 in pathophysiological conditions. (J Histochem Cytochem 53:1227–1234, 2005)


  • Development of Species-specific rDNA Probes for Giardia by Multiple Fluorescent In Situ Hybridization Combined with Immunocytochemical Identification of Cyst Wall Antigens -

    In this study, we describe the development of fluorescent oligonucleotide probes to variable regions in the small subunit of 16S rRNA in three distinct Giardia species. Sense and antisense probes (17–22 mer) to variable regions 1, 3, and 8 were labeled with digoxygenin or selected fluorochomes (FluorX, Cy3, or Cy5). Optimal results were obtained with fluorochome-labeled oligonucleotides for detection of rRNA in Giardia cysts. Specificity of fluorescent in situ hybridization (FISH) was shown using RNase digestion and high stringency to diminish the hybridization signal, and oligonucleotide probes for rRNA in Giardia lamblia, Giardia muris, and Giardia ardeae were shown to specifically stain rRNA only within cysts or trophozoites of those species. The fluorescent oligonucleotide specific for rRNA in human isolates of Giardia was positive for ten different strains. A method for simultaneous FISH detection of cysts using fluorescent antibody (genotype marker) and two oligonucleotide probes (species marker) permitted visualization of G. lamblia and G. muris cysts in the same preparation. Testing of an environmental water sample revealed the presence of FISH-positive G. lamblia cysts with a specific rDNA probe for rRNA, while negative cysts were presumed to be of animal or bird origin. (J Histochem Cytochem 53:917–927, 2005)


  • Development of Species-specific rDNA Probes for Giardia by Multiple Fluorescent In Situ Hybridization Combined with Immunocytochemical Identification of Cyst Wall Antigens -

    In this study, we describe the development of fluorescent oligonucleotide probes to variable regions in the small subunit of 16S rRNA in three distinct Giardia species. Sense and antisense probes (17–22 mer) to variable regions 1, 3, and 8 were labeled with digoxygenin or selected fluorochomes (FluorX, Cy3, or Cy5). Optimal results were obtained with fluorochome-labeled oligonucleotides for detection of rRNA in Giardia cysts. Specificity of fluorescent in situ hybridization (FISH) was shown using RNase digestion and high stringency to diminish the hybridization signal, and oligonucleotide probes for rRNA in Giardia lamblia, Giardia muris, and Giardia ardeae were shown to specifically stain rRNA only within cysts or trophozoites of those species. The fluorescent oligonucleotide specific for rRNA in human isolates of Giardia was positive for ten different strains. A method for simultaneous FISH detection of cysts using fluorescent antibody (genotype marker) and two oligonucleotide probes (species marker) permitted visualization of G. lamblia and G. muris cysts in the same preparation. Testing of an environmental water sample revealed the presence of FISH-positive G. lamblia cysts with a specific rDNA probe for rRNA, while negative cysts were presumed to be of animal or bird origin. (J Histochem Cytochem 53:917–927, 2005)


  • Diagnosis of Polycythemia Vera Based on Bone Marrow Pathology - The diagnostic criteria of the Polycythemia Vera Study Group (PVSG) do not include bone marrow (BM) examinations. The aim of this review is to elucidate whether distinctive patterns of histopathology exist which discriminate reactive (secondary polycythemia [SP]) from autonomous (polycythemia vera [PV]) erythrocytosis. When accompanied by an elevated platelet count, the initial stages of PV may clinically mimic essential thrombocythemia because they are not recognized by the conventional diagnostic criteria. Our data are derived from previous studies and evaluations of 362 patients with a borderline to marked increase in hemoglobin. PV revealed a trilineage myeloproliferation (panmyelosis) with a pleomorphous appearance (ie, differences in size) of loosely clustered megakaryocytes that failed to show gross cytological anomalies. Distinction from SP was accomplished by regarding megakaryopoiesis and the stromal changes (perivascular plasmacytosis, eosinophils, cell debris, and iron deposits). Discriminant analysis of standardized BM features, based on semiquantitative evaluation, yielded a sensitivity of 96% concerning the clear-cut separation of PV from SP.

  • Diagnostic utility of CDX-2 expression in separating metastatic gastrointestinal adenocarcinoma from other metastatic adenocarcinoma in fine-needle aspiration cytology using cell blocks. -
    Related Articles

    Diagnostic utility of CDX-2 expression in separating metastatic gastrointestinal adenocarcinoma from other metastatic adenocarcinoma in fine-needle aspiration cytology using cell blocks.

    Cancer. 2004 Jun 25;102(3):168-73

    Authors: Saad RS, Essig DL, Silverman JF, Liu Y

    BACKGROUND: CDX-2 gene is a transcription factor that is involved in the proliferation and differentiation of intestinal epithelial cells. Recent studies have shown that CDX-2 could be used as an immunohistochemical marker to differentiate metastatic gastrointestinal adenocarcinoma from other metastatic adenocarcinomas in surgical pathology. The objective of the current study was to investigate the diagnostic value of CDX-2 to separate metastatic gastrointestinal adenocarcinoma from other metastatic adenocarcinomas in fine-needle aspiration cytology (FNAC). METHODS: Sixty-two FNAC specimens of metastatic adenocarcinomas with corresponding cell blocks were retrieved from the hospital computer system. There were 22 specimens of metastatic gastrointestinal adenocarcinoma, 20 specimens of metastatic pulmonary adenocarcinoma, and 20 specimens of metastatic adenocarcinomas from other sites, including 10 from the breast, 3 from the ovaries, 4 from the pancreas, and 3 from the prostate. Radiology and histologic evaluation confirmed all cases. Sections were immunostained for CDX-2 and thyroid transcription factor-1 (TTF-1) using a heat-induced epitope retrieval technique. RESULTS: In metastatic gastrointestinal adenocarcinoma, CDX-2 demonstrated positive nuclear staining in 19 of 22 specimens (86%). Other specimens of metastatic adenocarcinoma were negative for CDX-2. TTF-1 expression was detected in 0%, 80%, and 0% of metastatic gastrointestinal adenocarcinoma, pulmonary adenocarcinoma, and other adenocarcinoma specimens, respectively. CONCLUSIONS: The results of the current study demonstrated that CDX-2 is a sensitive and a specific marker to separate metastatic gastrointestinal adenocarcinoma from other metastatic adenocarcinomas in FNAC specimens.

    PMID: 15211476 [PubMed - indexed for MEDLINE]


  • Diagnostic utility of p16 immunocytochemistry for Trichomonas in urine cytology - We present a case in which p16 immunocytochemistry helped establish the diagnosis of Trichomonas in urine from a male patient. Based on this finding, we recommend p16 immunocytochemistry as a diagnostic tool for unexpected patients or specimen types in which potential trichomonads are identified following routine cytologic evaluation.

  • Diagnostic utility of p75 neurotrophin receptor (p75NTR) as a marker of breast myoepithelial cells - Nikolay K Popnikolov, Sharon M Cavone, Pauline M Schultz & Fernando U Garcia

  • Dietary omega-3 fatty acids and ionizing irradiation on human breast cancer xenograft growth and angiogenesis - Background: The effects of an omega-3 (n-3) fatty acid enriched diet alone and in combination with gamma irradiation (IR) therapy in nude mice bearing a human MDA-MB231 breast cancer xenograft were tested. The omega-3 fatty acid enriched diet proved to be a safe means for retarding tumor growth and vascularization. Methods: The cancer cells were injected into the mammary fat pad of young female mice. Six weeks later, mice were randomly divided into two diet groups: 1) mice with 10% corn oil (rich in omega 6 fatty acids) in their food, 2) mice consuming a 10% fat diet that was enriched in n-3 fatty acids. After two weeks on the diet, treatment with 200cGy of IR every second day for four treatments (total 800 cGy) was initiated on half of the mice from each diet group. Some mice in each of the 4 groups were euthanized 24 hours after the end of IR while the remaining mice were followed for 3 additional weeks. Tumor sections were stained for endothelial cells with CD31 and PAS and for hypoxia inducible factor 1a (HIF-a). Results: The tumor cortex within 100 microns of the well-vascularized capsule had little vascularization. Blood vessels, capillaries, and endothelial pseudopods were found at areas greater than 100 microns from the capsule (subcortex). Mice on the corn oil diet and treated with IR 24 hours previously or non-irradiated mice fed the n-3 diet had tumors with fewer blood vessels in the subcortex and more endothelial pseudopods projecting into hypoxic (HIF- a positive) areas than did mice from the non-irradiated corn oil fed group. The tumor growth rate of mice that received IR or that were fed the n-3 fatty acid enriched diet was significantly slower than in the mice fed the 10% corn oil diet. Harmful side effects were found only in the IR treated mice. The omega-3 fatty acid enriched diet proved to be a safe means for retarding tumor growth and vascularization.

  • Difference in trafficking of brain-derived neurotrophic factor between axons and dendrites of cortical neurons, revealed by live-cell imaging - Background: Brain-derived neurotrophic factor (BDNF), which is sorted into a regulated secretory pathway of neurons, is supposed to act retrogradely through dendrites on presynaptic neurons or anterogradely through axons on postsynaptic neurons. Depending on which is the case, the pattern and direction of trafficking of BDNF in dendrites and axons are expected to be different. To address this issue, we analyzed movements of green fluorescent protein (GFP)-tagged BDNF in axons and dendrites of living cortical neurons by time-lapse imaging. In part of the experiments, the expression of BDNF tagged with cyan fluorescent protein (CFP) was compared with that of nerve growth factor (NGF) tagged with yellow fluorescent protein (YFP), to see whether fluorescent protein-tagged BDNF is expressed in a manner specific to this neurotrophin. Results: We found that BDNF tagged with GFP or CFP was expressed in a punctated manner in dendrites and axons in about two-thirds of neurons into which plasmid cDNAs had been injected, while NGF tagged with GFP or YFP was diffusely expressed even in dendrites in about 70% of the plasmid-injected neurons. In neurons in which BDNF-GFP was expressed as vesicular puncta in axons, 59 and 23% of the puncta were moving rapidly in the anterograde and retrograde directions, respectively. On the other hand, 64% of BDNF-GFP puncta in dendrites did not move at all or fluttered back and forth within a short distance. The rest of the puncta in dendrites were moving relatively smoothly in either direction, but their mean velocity of transport, 0.47 +/- 0.23 (SD) um/s, was slower than that of the moving puncta in axons (0.73 +/- 0.26 um/s). Conclusions: The present results show that the pattern and velocity of the trafficking of fluorescence protein-tagged BDNF are different between axons and dendrites, and suggest that the anterograde transport in axons may be the dominant stream of BDNF to release sites.

  • Differential effects of ERK and p38 signaling in BMP-2 stimulated hypertrophy of cultured chick sternal chondrocytes - Background: During endochondral bone formation, the hypertrophy of chondrocytes is accompanied by selective expression of several genes including type X collagen and alkaline phosphatase. This expression is stimulated by inducers including BMPs and ascorbate. A 316 base pair region of the type X collagen (Col X) promoter has been previously characterized as the site required for BMP regulation. The intent of this study was to examine the role of Mitogen Activated Protein (MAP) and related kinase pathways in the regulation of Col X transcription and alkaline phosphatase activity in pre-hypertrophic chick chondrocytes. Results: Using a luciferase reporter regulated by the BMP-responsive region of the type X collagen promoter, we show that promoter activity is increased by inhibition of extra-cellular signal regulated kinases 1 or 2 (ERK1/2). In contrast the ability of BMP-2 to induce alkaline phosphatase activity is little affected by ERK1/2 inhibition. The previously demonstrated stimulatory affect of p38 on Col X was shown to act specifically at the BMP responsive region of the promoter. The inhibitory effect of the ERK1/2 pathway and stimulatory effect of the p38 pathway on the Col X promoter were confirmed by the use of mutant kinases. Inhibition of upstream kinases: protein kinase C (PKC) and phosphatidylinositol 3-(PI3) kinase pathways increased basal Col X activity but had no effect on the BMP-2 induced increase. In contrast, ascorbate had no effect on the BMP-2 responsive region of the Col X promoter nor did it alter the increase in promoter activity induced by ERK1/2 inhibition. The previously shown increase in alkaline phosphatase activity induced by ascorbate was not affected by any kinase inhibitors examined. However some reduction in the alkaline phosphatase activity induced by the combination of BMP-2 and ascorbate was observed with ERK1/2 inhibition. Conclusion: Our results demonstrate that ERK1/2 plays a negative role while p38 plays a positive role in the BMP-2 activated transcription of type X collagen. This regulation occurs specifically at the BMP-2 responsive promoter region of Col X. Ascorbate does not modulate Col X at this region indicating that BMP-2 and ascorbate exert their action on chondrocyte hypertrophy via different transcriptional pathways. MAP kinases seem to have only a modest effect on alkaline phosphatase when activity is induced by the combination of both BMP-2 and ascorbate.

  • Differential effects of intragastric acid and capsaicin on gastric emptying and afferent input to the rat spinal cord and brainstem - Background: Hydrochloric acid (HCl) is a potential threat to the integrity of the gastric mucosa and is known to contribute to upper abdominal pain. We have previously found that gastric mucosal challenge with excess HCl is signalled to the rat brainstem, but not spinal cord, as visualized by expression of c-fos messenger ribonucleic acid (mRNA), a surrogate marker of neuronal excitation. This study examined whether gastric mucosal exposure to capsaicin, a stimulant of nociceptive afferents that does not damage the gastric mucosa, is signalled to both brainstem and spinal cord and whether differences in the afferent signalling of gastric HCl and capsaicin challenge are related to different effects on gastric emptying. Results: Rats were treated intragastrically with vehicle, HCl or capsaicin, activation of neurons in the brainstem and spinal cord was visualized by in situ hybridization autoradiography for c-fos mRNA, and gastric emptying deduced from the retention of intragastrically administered fluid. Relative to vehicle, HCl (0.5 M) and capsaicin (3.2 mM) increased c-fos transcription in the nucleus tractus solitarii by factors of 7.0 and 2.1, respectively. Capsaicin also caused a 5.2-fold rise of c-fos mRNA expression in lamina I of the caudal thoracic spinal cord, although the number of c-fos mRNA-positive cells in this lamina was very small. Thus, on average only 0.13 and 0.68 c-fos mRNA-positive cells were counted in 0.01 mm sections of the unilateral lamina I following intragastric administration of vehicle and capsaicin, respectively. In contrast, intragastric HCl failed to induce c-fos mRNA in the spinal cord. Measurement of gastric fluid retention revealed that HCl suppressed gastric emptying while capsaicin did not. Conclusion: The findings of this study show that gastric mucosal exposure to HCl and capsaicin is differentially transmitted to the brainstem and spinal cord. Since only HCl blocks gastric emptying, it is hypothesized that the two stimuli are transduced by different afferent pathways. We infer that HCl is exclusively signalled by gastric vagal afferents whereas capsaicin is processed both by gastric vagal and intestinal spinal afferents.

  • Differential expression of CCN-family members in primary human bone marrow-derived mesenchymal stem cells during osteogenic, chondrogenic and adipogenic differentiation - Background: The human cysteine rich protein 61 (CYR61, CCN1) as well as the other members of the CCN family of genes play important roles in cellular processes such as proliferation, adhesion, migration and survival. These cellular events are of special importance within the complex cellular interactions ongoing in bone remodeling. Previously, we analyzed the role of CYR61/CCN1 as an extracellular signaling molecule in human osteoblasts. Since mesenchymal stem cells of bone marrow are important progenitors for various differentiation pathways in bone and possess increasing potential for regenerative medicine, here we aimed to analyze the expression of CCN family members in bone marrow-derived human mesenchymal stem cells and along the osteogenic, the adipogenic and the chondrogenic differentiation. Results: Primary cultures of human mesenchymal stem cells were obtained from the femoral head of patients undergoing total hip arthroplasty. Differentiation into adipocytes and osteoblasts was done in monolayer culture, differentiation into chondrocytes was induced in high density cell pellet cultures. For either pathway, established differentiation markers and CCN-members were analyzed at the mRNA level by RT-PCR and the CYR61/CCN1 protein was analyzed by immunocytochemistry.RT-PCR and histochemical analysis revealed the appropriate phenotype of differentiated cells (Alizarin-red S, Oil Red O, Alcian blue, alkaline phosphatase; osteocalcin, collagen types I, II, IX, X, cbfa1, PPARγ, aggrecan). Mesenchymal stem cells expressed CYR61/CCN1, CTGF/CCN2, CTGF-L/WISP2/CCN5 and WISP3/CCN6. The CYR61/CCN1 expression decreased markedly during osteogenic differentiation, adipogenic differentiation and chondrogenic differentiation. These results were confirmed by immuncytochemical analyses. WISP2/CCN5 RNA expression declined during adipogenic differentiation and WISP3/CCN6 RNA expression was markedly reduced in chondrogenic differentiation. Conclusion: The decrease in CYR61/CCN1 expression during the differentiation pathways of mesenchymal stem cells into osteoblasts, adipocytes and chondrocytes suggests a specific role of CYR61/CCN1 for maintenance of the stem cell phenotype. The differential expression of CTGF/CCN2, WISP2/CCN5, WISP3/CCN6 and mainly CYR61/CCN1 indicates, that these members of the CCN-family might be important regulators for bone marrow-derived mesenchymal stem cells in the regulation of proliferation and initiation of specific differentiation pathways.

  • Differential Expression of Laminin Isoforms in Ovarian Epithelial Carcinomas Suggesting Different Origin and Providing Tools for Differential Diagnosis -

    Immunohistochemistry was used to study the distribution of laminin (Ln) chains, collagen types IV ( 1/2), VII, and XVIII and Lutheran antigen (Lu) in 36 frozen ovarian carcinoma samples. Surface epithelial basement membrane (BM) of the normal ovary showed immunoreactivity for Ln 1, 3-5, ßbeta;1-3, 1, and 2 chains and type IV and XVIII collagens. Chains of Ln-5 (3ßbeta;32) and Ln-10 (5ßbeta;11) as well as type IV and XVIII collagens were found in most tumor BMs, but Ln 2 chain and type VII collagen were detected only in few tumors. Contrary to serous tumors, BMs of mucinous carcinomas showed Ln 4 chain, but not Ln 1 and ßbeta;2 chains. Ln 1 chain was found in most endometrioid carcinomas, whereas chains of Ln-5 were only moderately detectable in comparison with serous and mucinous carcinomas. In the normal ovary, Lu immunoreactivity was confined to basal aspect in the ovarian epithelial cells, but in tumor specimens Lu immunostainings showed variable polarized and nonpolarized patterns. The results suggest that the three types of ovarian carcinoma have distinct differences in their Ln distribution and can be grouped based on their expression pattern. This suggests that they may have histogenetically different precursors and may help to distinguish these tumors from each other.

    (J Histochem Cytochem 53:1293–1300, 2005)


  • Differential Expression of Laminin Isoforms in Ovarian Epithelial Carcinomas Suggesting Different Origin and Providing Tools for Differential Diagnosis -

    Immunohistochemistry was used to study the distribution of laminin (Ln) chains, collagen types IV ( 1/2), VII, and XVIII and Lutheran antigen (Lu) in 36 frozen ovarian carcinoma samples. Surface epithelial basement membrane (BM) of the normal ovary showed immunoreactivity for Ln 1, 3-5, ßbeta;1-3, 1, and 2 chains and type IV and XVIII collagens. Chains of Ln-5 (3ßbeta;32) and Ln-10 (5ßbeta;11) as well as type IV and XVIII collagens were found in most tumor BMs, but Ln 2 chain and type VII collagen were detected only in few tumors. Contrary to serous tumors, BMs of mucinous carcinomas showed Ln 4 chain, but not Ln 1 and ßbeta;2 chains. Ln 1 chain was found in most endometrioid carcinomas, whereas chains of Ln-5 were only moderately detectable in comparison with serous and mucinous carcinomas. In the normal ovary, Lu immunoreactivity was confined to basal aspect in the ovarian epithelial cells, but in tumor specimens Lu immunostainings showed variable polarized and nonpolarized patterns. The results suggest that the three types of ovarian carcinoma have distinct differences in their Ln distribution and can be grouped based on their expression pattern. This suggests that they may have histogenetically different precursors and may help to distinguish these tumors from each other.

    (J Histochem Cytochem 53:1293–1300, 2005)


  • Differential Intracellular Distributions of Inositol Trisphosphate and Ryanodine Receptors Within and Among Hematopoietic Cells -

    To better understand the mechanism(s) of leukocyte Ca2+ signaling, we have studied the intracellular locations of two Ca2+-mobilizing receptors, the inositol 1,4,5-trisphosphate receptor and ryanodine receptor, by immunofluorescence microscopy. Our results show that localization differs not only between receptor classes within a cell, but among leukocyte types as well. We also illustrate the importance of preserving labile cellular filaments in maintaining cell integrity by fixation with the Safiejko-Mroczka and Bell protocol, because conventional fixation methods distort receptor patterns. We suggest that the observed differences influence intracellular Ca2+ signaling.

    (J Histochem Cytochem 53:913–916, 2005)


  • Differential Intracellular Distributions of Inositol Trisphosphate and Ryanodine Receptors Within and Among Hematopoietic Cells -

    To better understand the mechanism(s) of leukocyte Ca2+ signaling, we have studied the intracellular locations of two Ca2+-mobilizing receptors, the inositol 1,4,5-trisphosphate receptor and ryanodine receptor, by immunofluorescence microscopy. Our results show that localization differs not only between receptor classes within a cell, but among leukocyte types as well. We also illustrate the importance of preserving labile cellular filaments in maintaining cell integrity by fixation with the Safiejko-Mroczka and Bell protocol, because conventional fixation methods distort receptor patterns. We suggest that the observed differences influence intracellular Ca2+ signaling.

    (J Histochem Cytochem 53:913–916, 2005)


  • Differential responses to doxorubicin-induced phosphorylation and activation of Akt in human breast cancer cells - IntroductionWe have shown previously that overexpression of constitutively active Akt or activation of Akt caused by constitutively active Ras or human epidermal growth factor receptor-2 (HER2) confers on breast cancer cells resistance to chemotherapy or radiotherapy. As an expanded study we here report differential responses in terms of phosphorylation and activation of Akt as a result of treatment with doxorubicin in a panel of breast cancer cell lines. Methods: The levels of Akt phosphorylation and activity were measured by Western blot analysis with an anti-Ser473-phosphorylated Akt antibody and by in vitro Akt kinase assay using glycogen synthase kinase-3 as a substrate. Results: Within 24 hours after exposure to doxorubicin, MCF7, MDA468 and T47D cells showed a drug-dose-dependent increase in the levels of phosphorylated Akt; in contrast, SKBR3 and MDA231 cells showed a decrease in the levels of phosphorylated Akt, and minimal or no changes were detected in MDA361, MDA157 and BT474 cells. The doxorubicin-induced Akt phosphorylation was correlated with increased kinase activity and was dependent on phosphoinositide 3-kinase (PI3-K). An increased baseline level of Akt was also found in MCF7 cells treated with ionizing radiation. The cellular responses to doxorubicin-induced Akt phosphorylation were potentiated after the expression of Akt upstream activators including HER2, HER3 and focal adhesion kinase. Conclusion: Taken together with our recent published results showing that constitutive Akt mediates resistance to chemotherapy or radiotherapy, our present data suggest that the doxorubicin-induced phosphorylation and activation of Akt might reflect a cellular defensive mechanism of cancer cells to overcome doxorubicin-induced cytotoxic effects, which further supports the current efforts of targeting PI3-K/Akt for enhancing the therapeutic responses of breast cancer cells to chemotherapy and radiotherapy.

  • Disentangling the effects of phonation and articulation: Hemispheric asymmetries in the auditory N1m response of the human brain - Background: The cortical activity underlying the perception of vowel identity has typically been addressed by manipulating the first and second formant frequency (F1 & F2) of the speech stimuli. These two values, originating from articulation, are already sufficient for the phonetic characterization of vowel category. In the present study, we investigated how the spectral cues caused by articulation are reflected in cortical speech processing when combined with phonation, the other major part of speech production manifested as the fundamental frequency (F0) and its harmonic integer multiples. To study the combined effects of articulation and phonation we presented vowels with either high (/a/) or low (/u/) formant frequencies which were driven by three different types of excitation: a natural periodic pulseform reflecting the vibration of the vocal folds, an aperiodic noise excitation, or a tonal waveform. The auditory N1m response was recorded with whole-head magnetoencephalography (MEG) from ten human subjects in order to resolve whether brain events reflecting articulation and phonation are specific to the left or right hemisphere of the human brain. Results: The N1m responses for the six stimulus types displayed a considerable dynamic range of 115-135 ms, and were elicited faster (~10 ms) by the high-formant /a/ than by the low-formant /u/, indicating an effect of articulation. While excitation type had no effect on the latency of the right-hemispheric N1m, the left-hemispheric N1m elicited by the tonally excited /a/ was some 10 ms earlier than that elicited by the periodic and the aperiodic excitation. The amplitude of the N1m in both hemispheres was systematically stronger to stimulation with natural periodic excitation. Also, stimulus type had a marked (up to 7 mm) effect on the source location of the N1m, with periodic excitation resulting in more anterior sources than aperiodic and tonal excitation. Conclusions: The auditory brain areas of the two hemispheres exhibit differential tuning to natural speech signals, observable already in the passive recording condition. The variations in the latency and strength of the auditory N1m response can be traced back to the spectral structure of the stimuli. More specifically, the combined effects of the harmonic comb structure originating from the natural voice excitation caused by the fluctuating vocal folds and the location of the formant frequencies originating from the vocal tract leads to asymmetric behaviour of the left and right hemisphere.

  • Disseminated primary diffuse leptomeningeal gliomatosis: a case report with liquid based and conventional smear cytology - Background: Primary diffuse leptomeningeal gliomatosis is a rare neoplasm confined to the meninges without evidence of primary tumor in the brain or spinal cord parenchyma. Cerebrospinal fluid diversion via ventriculoperitoneal shunt may be used as a therapeutic modality. Herein, we describe the first report of cytologic findings of a case of this neoplasm with shunt-related peritoneal metastasis.Case presentationA 19-year-old male presented with a 6-month history of severe headaches. He had bilateral papilledema on physical exam. Cerebrospinal fluid examination was negative. Four months later a ventriculoperitoneal shunt was placed. Shortly thereafter, he was diagnosed with primary diffuse leptomeningeal gliomatosis based on the biopsy of an intradural extramedullary lesion adjacent to the lumbar spinal cord at a referral cancer center. The histology featured an infiltrating growth pattern of pleomorphic astrocytes with diffuse positivity for glial fibrillary acidic protein. A couple of months later he presented at our institution with ascites and an anterior peritoneal mass. Repeat cerebrospinal fluid cytology and fine needle aspiration of the mass confirmed disseminated gliomatosis. Cytologic characteristics included clusters of anaplastic cells of variable size, high nuclear to cytoplasm ratio and scant to moderate cytoplasm. Occasional single bizarre multinucleated cells were seen with eccentric "partial wreath-like" nuclei, clumped chromatin and prominent nucleoli. Patient expired 13 months after initial presentation. Conclusion: Disseminated primary diffuse leptomeningeal gliomatosis should be considered in the differential diagnosis of chronic aseptic meningitis and in the presence of a peritoneal tumor in patients with ventriculoperitoneal shunts. Immunocytochemistry may be of diagnostic value.

  • Distinct but overlapping T helper epitopes in the 37-58 region of SSX-2. -
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    Distinct but overlapping T helper epitopes in the 37-58 region of SSX-2.

    Clin Immunol. 2005 Jan;114(1):70-8

    Authors: Ayyoub M, Merlo A, Hesdorffer CS, Speiser D, Rimoldi D, Cerottini JC, Ritter G, Chen YT, Old LJ, Stevanovic S, Valmori D

    Because of their specific expression in tumors of different histological types, the products of the SSX genes are important candidate targets for development of cancer vaccines. We have previously identified two immunodominant SSX-2-derived T cell epitopes recognized by HLA-A2-restricted CD8+ T cells (SSX-2 41-49) and HLA-DR11-restricted CD4+ T cells (SSX-2 45-59), respectively. In this study, we report the identification of an HLA-DR3-restricted epitope mapping to the 37-51 region of SSX-2, overlapping both previously identified epitopes. As about one fifth of individuals from several major ethnic groups express HLA-DR3, the identification of this epitope significantly increases the percent of patients that are expected to mount specific CD4+ T cell responses following vaccination with peptides in this region of SSX-2. Retrieval of multiple overlapping epitopes in a defined region of SSX-2 protein suggests the presence of a "hot spot" for T cell recognition that may prove sufficient for the induction of immune responses.

    PMID: 15596411 [PubMed - indexed for MEDLINE]


  • Distinct functions of S. pombe Rec12 (Spo11) protein and Rec12-dependent crossover recombination (chiasmata) in meiosis I; and a requirement for Rec12 in meiosis II - Background: In most organisms proper reductional chromosome segregation during meiosis I is strongly correlated with the presence of crossover recombination structures (chiasmata); recombination deficient mutants lack crossovers and suffer meiosis I nondisjunction. We report that these functions are separable in the fission yeast Schizosaccharomyces pombe. Results: Intron mapping and expression studies confirmed that Rec12 is a member of the Spo11/Top6A topoisomerase family required for the formation of meiotic dsDNA breaks and recombination. rec12-117, rec12-D15 (null), and rec12-Y98F (active site) mutants lacked most crossover recombination and chromosomes segregated abnormally to generate aneuploid meiotic products. Since S. pombe contains only three chromosome pairs, many of those aneuploid products were viable. The types of aberrant chromosome segregation were inferred from the inheritance patterns of centromere linked markers in diploid meiotic products. The rec12-117 and rec12-D15 mutants manifest segregation errors during both meiosis I and meiosis II. Remarkably, the rec12-Y98F (active site) mutant exhibited essentially normal meiosis I segregation patterns, but still exhibited meiosis II segregation errors. Conclusions: Rec12 is a 345 amino acid protein required for most crossover recombination and for chiasmatic segregation of chromosomes during meiosis I. Rec12 also participates in a backup distributive (achiasmatic) system of chromosome segregation during meiosis I. In addition, catalytically-active Rec12 mediates some signal that is required for faithful equational segregation of chromosomes during meiosis II.

  • Diurnal difference in CAR mRNA expression - Background: The constitutive androstane receptor (CAR, NR1I3) plays a key role in the transcriptional activation of genes that encode xenobiotic/steroid and drug metabolizing enzymes. Results: The expression of CAR mRNA throughout the circadian rhythm is reported for the first time in phase with the clock gene Bmal1 and in antiphase with the clock-controlled gene Rev-erbα mRNAs, with a peak at Zeitgeber time (ZT) 20 and a trough at ZT8, and a peak/trough ratio of 2.0. The diurnal difference in CAR mRNA expression might underlie the 1.7-fold difference in the magnitude of the PB-dependent induction of CYP2B1/2 mRNA. Conclusion: The circadian oscillation of xenosensor gene CAR mRNA expression is partially responsible for chronopharmacokinetics and chronopharmacology in disease.

  • DNA and the chromosome – varied targets for chemotherapy - The nucleus of the cell serves to maintain, regulate, and replicate the critical genetic information encoded by the genome. Genomic DNA is highly associated with proteins that enable simple nuclear structures such as nucleosomes to form higher-order organisation such as chromatin fibres. The temporal association of regulatory proteins with DNA creates a dynamic environment capable of quickly responding to cellular requirements and distress. The response is often mediated through alterations in the chromatin structure, resulting in changed accessibility of specific DNA sequences that are then recognized by specific proteins. Anti-cancer drugs that target cellular DNA have been used clinically for over four decades, but it is only recently that nuclease specific drugs have been developed to not only target the DNA but also other components of the nuclear structure and its regulation. In this review, we discuss some of the new drugs aimed at primary DNA sequences, DNA secondary structures, and associated proteins, keeping in mind that these agents are not only important from a clinical perspective but also as tools for understanding the nuclear environment in normal and cancer cells.

  • DNA index determination with Automated Cellular Imaging System (ACIS) in Barrett's esophagus: Comparison with CAS 200 - Background: For solid tumors, image cytometry has been shown to be more sensitive for diagnosing DNA content abnormalities (aneuploidy) than flow cytometry. Image cytometry has often been performed using the semi-automated CAS 200 system. Recently, an Automated Cellular Imaging System (ACIS) has been introduced for DNA content ( DNA index) determination, but its results have not been validated. Methods: We performed a comparative study of DNA index (DI) determination using the conventional CAS 200 system and ACIS in the same archived formalin-fixed and paraffin embedded tissues with Barrett esophagus related lesions, including specialized intestinal metaplasia without dysplasia, low-grade dysplasia, high-grade dysplasia and adenocarcinoma. Results: There was a very good correlation between the DI values determined by ACIS and CAS 200. However, in comparison to CAS 200, ACIS was 25% more sensitive in detecting aneuploidy. . ACIS yielded mean DI value that was 18% higher than CAS 200 (p < 0.001; paired t test). In addition, average time required to perform DNA ploidy analysis was shorter with the ACIS (30-40 min) than with the CAS 200 (40-70 min). Results obtained by ACIS showed excellent intra-observer and intra-observer variability (coefficient of correlation >0.9 for both, p<0.0001) Conclusions: Compared to CAS 200, the ACIS is more sensitive and less time consuming for DNA ploidy determination. Results obtained by ACIS are also highly reproducible.

  • Does Vasculogenic Mimicry Exist in Astrocytoma? -

    Vasculogenic mimicry (VM) has been observed in melanoma and in some nonmelanoma tumor types. It is unknown whether a similar VM phenomenon exists in astrocytoma. The present study was to examine 45 astrocytomas (including World Health Organization grade II 15 cases, grade III 15 cases, and grade IV 15 cases) by CD34 endothelial marker periodic acid–Schiff (PAS) dual staining to see if VM existing in these tumors. The results demonstrated that endothelium-lined vessels dominated the tumor microvasculature and stained positively for PAS, laminin, and endothelial marker. PAS-positive pattern of VM was found in two grade IV astrocytomas. Channels stained positively for PAS, laminin, and negatively for CD34 of the VM entrapped in the tumor tissue. Erythrocytes could be observed in some of these channels. In these networks of PAS-positive pattern, spots of weak reaction for CD34 were observed, suggesting the incorporation of VM channel and normal vessel. Furthermore, in astrocytoma, especially glioblastoma, focus of anaplastic tumor cells appeared with CD34 expression, whereas some tumor cells lost glial fibrillary acid protein expression. It is assumed that genetically deregulated tumor cells in astrocytoma could lose the astrocyte-specific protein and express inappropriate markers not expected in cells of astrocyte lineage. The present results suggest that VM phenomenon exists in some malignant astrocytoma. (J Histochem Cytochem 53:997–1002, 2005)


  • Does Vasculogenic Mimicry Exist in Astrocytoma? -

    Vasculogenic mimicry (VM) has been observed in melanoma and in some nonmelanoma tumor types. It is unknown whether a similar VM phenomenon exists in astrocytoma. The present study was to examine 45 astrocytomas (including World Health Organization grade II 15 cases, grade III 15 cases, and grade IV 15 cases) by CD34 endothelial marker periodic acid–Schiff (PAS) dual staining to see if VM existing in these tumors. The results demonstrated that endothelium-lined vessels dominated the tumor microvasculature and stained positively for PAS, laminin, and endothelial marker. PAS-positive pattern of VM was found in two grade IV astrocytomas. Channels stained positively for PAS, laminin, and negatively for CD34 of the VM entrapped in the tumor tissue. Erythrocytes could be observed in some of these channels. In these networks of PAS-positive pattern, spots of weak reaction for CD34 were observed, suggesting the incorporation of VM channel and normal vessel. Furthermore, in astrocytoma, especially glioblastoma, focus of anaplastic tumor cells appeared with CD34 expression, whereas some tumor cells lost glial fibrillary acid protein expression. It is assumed that genetically deregulated tumor cells in astrocytoma could lose the astrocyte-specific protein and express inappropriate markers not expected in cells of astrocyte lineage. The present results suggest that VM phenomenon exists in some malignant astrocytoma. (J Histochem Cytochem 53:997–1002, 2005)


  • Downregulation of calcineurin activity in cervical carcinoma - Background: Calcineurin (CaN) is an important serine-threonine phosphatase (PP2B), which plays a crucial role in calcium-calmodulin mediated signal transduction events. Calcineurin has been implicated in pathogenesis of various diseases cardiac hypertrophy, diabetic neuropathy and Alzheimer's, however its role in neoplasia remains unclear. Results: In view of this we evaluated the calcineurin activity in serum and biopsy samples collected from women diagnosed with invasive squamous cell carcinoma of cervix. A significant reduction was observed in the calcineurin activity in cancer cervix patients compared to the control group. However the calcineurin activity remained unaltered in the cervical scrapes obtained from patients diagnosed with low-grade squamous intra epithelial lesions (LSIL). Interestingly the downregulation of calcineurin activity in squamous cell carcinomas was not accompanied by any change in DNA-binding affinity of the transcriptional factor NFAT (Nuclear Factor of Activated T-cells). All the squamous cell carcinoma samples used in the present study were positive for high-risk human pappilomavirus (HPV) types. Conclusions: The present study demonstrates the downregulation of calcineurin activity in squamous cell carcinoma of cervix with high risk HPV infection. We conclude that perturbations in calcineurin-mediated pathway may be involved in development of cervical neoplasia. Key words: cervical neoplasia, squamous cell carcinoma (SCC), calcineurin (PP2B/CaN), calmodulin (CaM),

  • Dual-color, break-apart fluorescence in situ hybridization for EWS gene rearrangement distinguishes clear cell sarcoma of soft tissue from malignant melanoma - Rajiv M Patel, Erinn Downs-Kelly, Sharon W Weiss, Andrew L Folpe, Raymond R Tubbs, Ralph J Tuthill, John R Goldblum & Marek Skacel

  • Dup(13)(q14.2-q14.3): Yet Another New Differential Diagnostic Aspect for Short Stature-like Phenotype -

    We report on the case of a pregnant woman with hyposomia who was previously suspected of having Turner syndrome. Prenatal cytogenetic diagnostics showed a fetal karyotype of 46,XX,dup(13)(q14.2q21.1) ish.13q14(RB1 x 3). Parental and grandparental chromosome analyses were performed and the dup(13) was found to be of maternal origin (de novo). The pregnancy was continued and a healthy female child was born with normal development apart from growth retardation. The reported chromosomal aberration is, together with two other cases reported in the literature, the first hint of a short stature–like phenotype due to dup(13)(q14.2q14.3). (J Histochem Cytochem 53:365–366, 2005)


  • Dynamic assembly, localization and proteolysis of the Bacillus subtilis SMC complex - Background: SMC proteins are key components of several protein complexes that perform vital tasks in different chromosome dynamics. Bacterial SMC forms a complex with ScpA and ScpB that is essential for chromosome arrangement and segregation. The complex localizes to discrete centres on the nucleoids that during most of the time of the cell cycle localize in a bipolar manner. The complex binds to DNA and condenses DNA in an as yet unknown manner. Results: We show that in vitro, ScpA and ScpB form different complexes with each other, among which the level of the putative 2 ScpA/4 ScpB complex showed a pronounced decrease in level upon addition of SMC protein. Different mutations of the ATPase-binding pocket of SMC reduced, but did not abolish interaction of mutant SMC with ScpA and ScpB. The loss of SMC ATPase activity led to a loss of function in vivo, and abolished proper localization of the SMC complex. The formation of bipolar SMC centres was also lost after repression of gyrase activity, and was abnormal during inhibition of replication, resulting in single central clusters. Resumption of replication quickly re-established bipolar SMC centres, showing that proper localization depends on ongoing replication. We also found that the SMC protein is subject to induced proteolysis, most strikingly as cells enter stationary phase, which is partly achieved by ClpX and LonA proteases. Atomic force microscopy revealed the existence of high order rosette-like SMC structures in vitro, which might explain the formation of the SMC centres in vivo. Conclusions: Our data suggest that a ScpA/ScpB sub-complex is directly recruited into the SMC complex. This process does not require SMC ATPase activity, which, however, appears to facilitate loading of ScpA and ScpB. Thus, the activity of SMC could be regulated through binding and release of ScpA and ScpB, which has been shown to affect SMC ATPase activity. The proper bipolar localization of the SMC complex depends on a variety of physiological aspects: ongoing replication, ATPase activity and chromosome supercoiling. Because the cellular concentration of SMC protein is also regulated at the posttranscriptional level, the activity of SMC is apparently regulated at multiple levels.

  • Dynamin-dependent NMDAR endocytosis during LTD and its dependence on synaptic state - Background: The N-methyl-D-aspartate (NMDA)-type glutamate receptor expressed at excitatory glutamatergic synapses is required for learning and memory and is critical for normal brain function. At a cellular level, this receptor plays a pivotal role in triggering and controlling synaptic plasticity. While it has been long recognized that this receptor plays a regulatory role, it was considered by many to be itself immune to synaptic activity-induced plasticity. More recently, we and others have shown that NMDA receptor-mediated synaptic responses can be subject to activity-dependent depression. Results: Here we show that depression of synaptic transmission mediated by NMDA receptors displays a state-dependence in its plasticity; NMDA receptors are resistant to activity-induced changes at silent and recently-silent synapses. Once synapses transition to the active state however, NMDA receptors become fully 'plastic'. This state-dependence is identical to that shown by the -amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA) receptor. Furthermore, the down-regulation of NMDAR-mediated responses during synaptic depression is prevented by disruption of dynamin-dependent endocytosis. Conclusions: NMDA receptor-mediated synaptic responses are plastic in a state-dependent manner. Depending on the plasticity state in which a synapse currently resides, NMDA receptors will either be available or unavailable for down-regulation. The mechanism underlying the down-regulation of NMDA receptor-mediated synaptic responses is endocytosis of the NMDA receptor. Other potential mechanisms, such as receptor diffusion along the plane of the membrane, or changes in the activity of the channel are not supported. The mechanisms of AMPA receptor and NMDA receptor endocytosis appear to be tightly coupled, as both are either available or unavailable for endocytosis in the same synaptic states. Endocytosis of NMDA receptors would serve as a potent mechanism for metaplasticity. Such state-dependent regulation of NMDAR endocytosis will provide fundamental control over downstream NMDA receptor-dependent plasticity of neuronal circuitry

  • Early and late skin reactions to radiotherapy for breast cancer and their correlation with radiation-induced DNA damage in lymphocytes - IntroductionRadiotherapy outcomes might be further improved by a greater understanding of the individual variations in normal tissue reactions that determine tolerance. Most published studies on radiation toxicity have been performed retrospectively. Our prospective study was launched in 1996 to measure the in vitro radiosensitivity of peripheral blood lymphocytes before treatment with radical radiotherapy in patients with breast cancer, and to assess the early and the late radiation skin side effects in the same group of patients. We prospectively recruited consecutive breast cancer patients receiving radiation therapy after breast surgery. To evaluate whether early and late side effects of radiotherapy can be predicted by the assay, a study was conducted of the association between the results of in vitro radiosensitivity tests and acute and late adverse radiation effects. Methods: Intrinsic molecular radiosensitivity was measured by using an initial radiation-induced DNA damage assay on lymphocytes obtained from breast cancer patients before radiotherapy. Acute reactions were assessed in 108 of these patients on the last treatment day. Late morbidity was assessed after 7 years of follow-up in some of these patients. The Radiation Therapy Oncology Group (RTOG) morbidity score system was used for both assessments. Results: Radiosensitivity values obtained using the in vitro test showed no relation with the acute or late adverse skin reactions observed. There was no evidence of a relation between acute and late normal tissue reactions assessed in the same patients. A positive relation was found between the treatment volume and both early and late side effects. Conclusion: After radiation treatment, a number of cells containing major changes can have a long survival and disappear very slowly, becoming a chronic focus of immunological system stimulation. This stimulation can produce, in a stochastic manner, late radiation-related adverse effects of varying severity. Further research is warranted to identify the major determinants of normal tissue radiation response to make it possible to individualize treatments and improve the outcome of radiotherapy in cancer patients.

  • Early detection of breast cancer based on gene-expression patterns in peripheral blood cells - IntroductionExisting methods to detect breast cancer in asymptomatic patients have limitations, and there is a need to develop more accurate and convenient methods. In this study, we investigated whether early detection of breast cancer is possible by analyzing gene-expression patterns in peripheral blood cells. Methods: Using macroarrays and nearest-shrunken-centroid method, we analyzed the expression pattern of 1,368 genes in peripheral blood cells of 24 women with breast cancer and 32 women with no signs of this disease. The results were validated using a standard leave-one-out cross-validation approach. Results: We identified a set of 37 genes that correctly predicted the diagnostic class in at least 82% of the samples. The majority of these genes had a decreased expression in samples from breast cancer patients, and predominantly encoded proteins implicated in ribosome production and translation control. In contrast, the expression of some defense-related genes was increased in samples from breast cancer patients. Conclusion: The results show that a blood-based gene-expression test can be developed to detect breast cancer early in asymptomatic patients. Additional studies with a large sample size, from women both with and without the disease, are warranted to confirm or refute this finding.

  • Early stopping of clinical trials - Early stopping of clinical trials in favour of a new treatment creates ethical and scientific difficulties, which are different from those associated with early stopping due to toxicity or futility. Two major breast cancer trials have recently taken such a decision, and the problem is relevant for several ongoing trials. Here we argue that such a decision should be taken with the utmost gravity and should be based on a clear overall clinical benefit for the new treatment, and not as an automatic response to crossing a predefined threshold. Predefined rules can be used to trigger a debate within the Independent Data Monitoring and Safety Committee (IDMC) about early stopping, but the IDMC should retain the responsibility of assessing overall clinical benefit in making its recommendation.

  • Effect of connective tissue growth factor (CCN2/CTGF) on proliferation and differentiation of mouse periodontal ligament-derived cells - Background: CCN2/CTGF is known to be involved in tooth germ development and periodontal tissue remodeling, as well as in mesenchymal tissue development and regeneration. In this present study, we investigated the roles of CCN2/CTGF in the proliferation and differentiation of mouse periodontal ligament (MPL) cells in vitro. Results: In cell cultures of MPL, the mRNA expression of the CCN2/CTGF gene was stronger in sparse cultures than in confluent ones and was significantly enhanced by TGF-b. The addition of recombinant CCN2/CTGF (rCCN2) to MPL cultures stimulated DNA synthesis and cell growth in a dose-dependent manner. Moreover, rCCN2 addition also enhanced the mRNA expression of alkaline phosphatase (ALPase), type I collagen, and periostin, the latter of which is considered to be a specific marker of the periosteum and periodontium; whereas it showed little effect on the mRNA expression of typical osteoblastic markers, e.g., osteopontin and osteocalcin. Finally, rCCN2/CTGF also stimulated ALPase activity and collagen synthesis. Conclusions: These results taken together suggest important roles of CCN2/CTGF in the development and regeneration of periodontal tissue including the periodontal ligament.

  • Effect of Heat-Induced Antigen Retrieval Following Inconsistent Formalin Fixation. -

  • Effect of neutrophil depletion on gelatinase expression, edema formation and hemorrhagic transformation after focal ischemic stroke - Background: While gelatinase (MMP-2 and -9) activity is increased after focal ischemia/reperfusion injury in the brain, the relative contribution of neutrophils to the MMP activity and to the development of hemorrhagic transformation remains unknown. Results: Anti-PMN treatment caused successful depletion of neutrophils in treated animals. There was no difference in either infarct volume or hemorrhage between control and PMN depleted animals. While there were significant increases in gelatinase (MMP-2 and MMP-9) expression and activity and edema formation associated with ischemia, neutrophil depletion failed to cause any change. Conclusions: The main finding of this study is that, in the absence of circulating neutrophils, MMP-2 and MMP-9 expression and activity are still up-regulated following focal cerebral ischemia. Additionally, neutrophil depletion had no influence on indicators of ischemic brain damage including edema, hemorrhage, and infarct size. These findings indicate that, at least acutely, neutrophils are not a significant contributor of gelatinase activity associated with acute neurovascular damage after stroke.

  • Effect of reproductive factors on stage, grade and hormone receptor status in early-onset breast cancer - IntroductionWomen younger than 35 years who are diagnosed with breast cancer tend to have more advanced stage tumors and poorer prognoses than do older women. Pregnancy is associated with elevated exposure to estrogen, which may influence the progression of breast cancer in young women. The objective of the present study was to examine the relationship between reproductive events and tumor stage, grade, estrogen receptor and progesterone receptor status, and survival in women diagnosed with early-onset breast cancer. Methods: In a population-based, case–case study of 254 women diagnosed with invasive breast cancer at age under 35 years, odds ratios (ORs) and 95% confidence intervals (CIs) were estimated using unconditional logistic regression with tumor characteristics as dependent variables and adjusting for age and education. Survival analyses also examined the relationship between reproductive events and overall survival. Results: Compared with nulliparous women, women with three or more childbirths were more likely to be diagnosed with nonlocalized tumors (OR = 3.1, 95% CI = 1.3–7.7), and early age (<20 years) at first full-term pregnancy was also associated with a diagnosis of breast cancer that was nonlocalized (OR = 3.0, 95% CI = 1.2–7.4) and of higher grade (OR = 3.2, 95% CI 1.0–9.9). The hazard ratio for death among women with two or more full-term pregnancies, as compared with those with one full-term pregnancy or none, was 2.1 (95% CI = 1.0–4.5), adjusting for stage. Among parous women, those who lactated were at decreased risk for both estrogen receptor and progesterone receptor negative tumors (OR = 0.2, 95% CI = 0.1–0.5, and OR = 0.4, 95% CI = 0.2–0.8, respectively). Conclusion: The results of the present study suggest that pregnancy and lactation may influence tumor presentation and survival in women with early-onset breast cancer.

  • Effective antigen-retrieval method for immunohistochemical detection of abnormal isoform of prion proteins in animals. -
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    Effective antigen-retrieval method for immunohistochemical detection of abnormal isoform of prion proteins in animals.

    Acta Neuropathol (Berl). 2005 Mar;109(3):263-71

    Authors: Furuoka H, Yabuzoe A, Horiuchi M, Tagawa Y, Yokoyama T, Yamakawa Y, Shinagawa M, Sata T

    For immunohistochemistry of the prion diseases, several pretreatment methods to enhance the immunoreactivity of human and animal abnormal proteinase-resistant prion protein (PrP(Sc)) on the tissue sections have been employed. The method of 121 degree C hydrated autoclaving pretreatment or the combination method of 121 degree C hydrated autoclaving with a certain chemical reagent (formic acid or proteinase K, etc) are now widely used. We found that an improved hydrated autoclaving method at 135 degrees C, more effectively enhanced PrP(Sc) immunoreactivity for the antibodies recognizing the linear epitope. In addition, this method was more effective for the long-term fixation samples as compared with other previous methods. However, this modified method could not retrieve PrP(Sc) antigenic epitopes composed of conformational structures or several discontinuous epitopes. We describe the comparative studies between our improved method and other antigen-retrieval procedures reported previously. Based on the differences of reaction among the antibodies, we also discuss the mechanisms of the hydrated autoclaving methods to retrieve PrP(Sc) immunoreactivity.

    PMID: 15616789 [PubMed - indexed for MEDLINE]


  • Effects of lesions of the nucleus accumbens core on choice between small certain rewards and large uncertain rewards in rats - Background: Animals must frequently make choices between alternative courses of action, seeking to maximize the benefit obtained. They must therefore evaluate the magnitude and the likelihood of the available outcomes. Little is known of the neural basis of this process, or what might predispose individuals to be overly conservative or to take risks excessively (avoiding or preferring uncertainty, respectively). The nucleus accumbens core (AcbC) is known to contribute to rats' ability to choose large, delayed rewards over small, immediate rewards; AcbC lesions cause impulsive choice and an impairment in learning with delayed reinforcement. However, it is not known how the AcbC contributes to choice involving probabilistic reinforcement, such as between a large, uncertain reward and a small, certain reward. We examined the effects of excitotoxic lesions of the AcbC on probabilistic choice in rats. Results: Rats chose between a single food pellet delivered with certainty (p = 1) and four food pellets delivered with varying degrees of uncertainty (p = 1, 0.5, 0.25, 0.125, and 0.0625) in a discrete-trial task, with the large-reinforcer probability decreasing or increasing across the session. Subjects were trained on this task and then received excitotoxic or sham lesions of the AcbC before being retested. After a transient period during which AcbC-lesioned rats exhibited relative indifference between the two alternatives compared to controls, AcbC-lesioned rats came to exhibit risk-averse choice, choosing the large reinforcer less often than controls when it was uncertain, to the extent that they obtained less food as a result. Rats behaved as if indifferent between a single certain pellet and four pellets at p = 0.32 (sham-operated) or at p = 0.70 (AcbC-lesioned) by the end of testing. When the probabilities did not vary across the session, AcbC-lesioned rats and controls strongly preferred the large reinforcer when it was certain, and strongly preferred the small reinforcer when the large reinforcer was very unlikely (p = 0.0625), with no differences between AcbC-lesioned and sham-operated groups. Conclusions: These results support the view that the AcbC contributes to action selection by promoting the choice of uncertain, as well as delayed, reinforcement.

  • Effects of milk fermented by Lactobacillus helveticus R389 on a murine breast cancer model - IntroductionAntitumour activity is one of the health-promoting effects attributed to the lactic acid bacteria and their products of fermentation. Previous studies in mice demonstrated that bioactive compounds released in milk fermented by Lactobacillus helveticus R389 contribute to its immunoenhancing and antitumour properties. The aim of the present work was to study the effects of the consumption of milk fermented by L. helveticus R389 or its proteolytic-deficient variant, L. helveticus L89, on a murine hormone-dependent breast cancer model. Methods: Mice were fed with milk fermented by L. helveticus R389 or L. helveticus L89, during 2 or 7 days. The tumour control group received no special feeding. At the end of the feeding period, the mice were challenged by a subcutaneous injection of tumour cells in the mammary gland. Four days post-injection, the mice received fermented milk on a cyclical basis. The rate of tumour development and the cytokines in serum, mammary gland tissue and tumour-isolated cells were monitored. Bcl-2-positive cells in mammary glands and cellular apoptosis in tumour tissue were also studied. Results: Seven days of cyclical administration of milk fermented by either bacterial strain delayed or stopped the tumour development. Cytokines demonstrated that L. helveticus R389 modulated the immune response challenged by the tumour. IL-10 and IL-4 were increased in all the samples from this group. In comparison with the tumour control, all test groups showed a decrease of IL-6, a cytokine involved in oestrogen synthesis. Seven days of cyclical feeding with milk fermented by L. helveticus R389 produced an increase in the number of apoptotic cells, compared with all other groups. Conclusion: This study demonstrated that 7 days of cyclical administration of milk fermented by both strains of L. helveticus diminishes tumour growth, stimulating an antitumour immune response. Compounds released during milk fermentation with L. helveticus R389 would be implicated in its immunoregulatory capacity on the immune response in mammary glands and tumour, which were correlated with the cytokines found at the systemic level. The milk fermented by L. helveticus R389 was able to modulate the relationship between immune and endocrine systems (by IL-6 diminution), which is very important in oestrogen-dependent tumour and induced cellular apoptosis.

  • Efficiency of an inexpensive liquid-based cytology performed by cytocentrifugations: a comparative study using the histology as reference standard - Background: Although liquid-based cytology (LBC) is now recommended for cervical cancer screening, it requires expensive automated devices and materials. To evaluate the efficiency of inexpensive LBC methods relying on an inexpensive fixative liquid, Easyfix(R), we compared the results obtained by the liquid-based cytology (LBC) diagnoses performed by cytocentrifugations (Papspin(R) and Turbitec(R)) with those obtained by histology. Furthermore, we evaluated the efficiency of the fixative liquid, Easyfix(R), to preserve HPV DNA in the collected samples. Method266 LBC were compared with 174 colposcopies and 91 Loop Electrosurgical Excision Procedure (LEEP). Among the LBC, 51 were performed using the Papspin(R) system and 215 were performed using the Turbitec(R) system. To control the quality of the preservation liquid, Easyfix(R), we correlated the results of HCII assays with those of HPV PCR. Results: For Papspin(R) and Turbitec(R) systems, the sensitivities were respectively 82.6% (95% CI: 61.2-95.0%, p<0.001) and 75.0% (95% CI: 64.4-89.8%, p<0.001) and the specificities were 92.6% (95%CI: 76.5-99.1%, p<0.001) and 96.2% (95% CI: 91.3-98.7%, p<0.001). We find no statistical difference between the results of the both systems (p=ns). The sensitivity of the HCII was 86.4% (95% IC: 77.4-92.8%, p<0.001) and the specificity was 39.4% (95% CI: 31.2-48.1%, p<0.001). The comparison between HCII and HPV-PCR shows a good correlation: the kappa was 0.89. Conclusion: LBC performed by cytocentrifugations are inexpensive, reduce inadequate smears, show excellent efficiency and allow HPV detection by molecular biology. The Easyfix(R) fixative liquid also preserves HPV DNA.

  • Electron microscopic localisation of P2X4 receptor subunit immunoreactivity to pre- and post-synaptic neuronal elements and glial processes in the dorsal vagal complex of the rat. -
    Related Articles

    Electron microscopic localisation of P2X4 receptor subunit immunoreactivity to pre- and post-synaptic neuronal elements and glial processes in the dorsal vagal complex of the rat.

    Brain Res. 2004 Nov 5;1026(1):44-55

    Authors: Ashour F, Deuchars J

    P2X receptors are ligand gated ion channels activated by extracellular ATP. There are seven P2X subunits, P2X(1-7), and all are expressed in the CNS. The P2X(4) receptor subunit (P2X(4)R) is likely to be important in the CNS as it has been reported to be expressed throughout the brain and spinal cord. However, P2X(4)Rs have been identified as restricted to neurones, only in glia or expressed in both neurones and glia with no discernible relationship to CNS region or epitope target of antibodies used for staining. In addition, although there are particularly high levels of mRNA encoding P2X(4)R in the brainstem, previous immunohistochemical studies have revealed only indistinct staining. We therefore examined the distribution of P2X(4)R in the dorsal vagal complex (DVC) of the brainstem using immunohistochemistry in sections obtained from adult Wistar rats transcardially perfused with aldehyde fixatives. When this revealed staining identifiable only as small puncta at the light microscope level, we examined the area with electron microscopy. This ultrastructural study revealed that P2X(4)R immunoreactivity (IR) was present in neurones at both pre- and post-synaptic sites as well as in glial cell processes and somata. This P2X(4)R-IR was localised adjacent to plasma membranes, as well as internally in membrane bound structures resembling endosomes. Immunoreactivity in endosomes was more prominent following antigen retrieval protocols. Localisation of P2X(4)R-IR in astrocytes, identified by the presence of glial fibrillary acidic protein (GFAP), was confirmed using immunofluorescence. The presence of P2X(4)Rs in the dorsal vagal complex is consistent with expression studies, but some reasons for a lack of correlation with pharmacological studies are discussed. The P2X(4)R is therefore expressed by neurones and glia in the dorsal vagal complex and may play a role in mediating extracellular signalling by ATP in this region.

    PMID: 15476696 [PubMed - indexed for MEDLINE]


  • Elevated ex vivomonocyte chemotactic protein-1 (CCL2) in pulmonary as compared with extra-pulmonary tuberculosis - Background: Tuberculosis causes 3 million deaths annually. The most common site of tuberculosis is pulmonary however; extra-pulmonary forms of the disease also remain prevalent. Restriction of Mycobacterium tuberculosis depends on effective recruitment and subsequent activation of T lymphocytes, mononuclear and polymorphonuclear cells to the site of infection. Tumor necrosis factor (TNF) -a is essential for granuloma formation and is a potent activator of monocyte chemotactic protein (MCP-1, CCL2). CCL2 is essential for recruitment of monocytes and T cells and has been shown to play a role in protection against tuberculosis. Interleukin -8 (CXCL8) is a potent activator of neutrophils. Increased levels of CCL2, CXCL8 and TNFa are reported in tuberculosis but their significance in different forms of tuberculosis is as yet unclear. We have used an ex vivo assay to investigate differences in immune parameters in patients with either pulmonary or extra-pulmonary tuberculosis. Methods: Serum levels of CCL2, CXCL8 and TNFa were measured in patients with pulmonary tuberculosis (N=12), extra-pulmonary tuberculosis (N=8) and BCG-vaccinated healthy volunteers (N=12). Whole blood cells were stimulated with non-pathogenic Mycobacterium bovis bacille-Calmette Guerin (BCG) vaccine strain or bacterial lipopolysaccharide (LPS) and cyto/chemokines were monitored in supernatants. Results: Circulating serum levels of CXCL8 and TNFa were raised in all tuberculosis patients, while CCL2 levels were not. There was no difference in spontaneous cytokine secretion from whole blood cells between patients and controls. M. bovis BCG-induced ex vivo CCL2 secretion was significantly greater in pulmonary as compared with both extra-pulmonary tuberculosis patients and endemic controls. In response to LPS stimulation, patients with pulmonary tuberculosis showed increased CCL2 and TNFa responses as compared with the extra-pulmonary group. BCG-, and LPS-induced CXCL8 secretion was comparable between patients and controls. Conclusions: CCL2 is activated by TNFa and is essential for recruitment of monocytes and T cells to the site of mycobacterial infection. Increased CCL2 activation in pulmonary tuberculosis may result in a stronger cellular response as compared with extra-pulmonary tuberculosis patients, and this may contribute to the localization of infection to the pulmonary site.

  • Elongation of Peroxisomes as an Indicator for Efficient Dynamin-like Protein 1 Knock Down in Mammalian Cells -

    RNA interference has become a valuable tool to identify and investigate proteins involved in the formation of peroxisomes. We demonstrate that the elongation of peroxisomes serves as an excellent indicator for efficient knock down of dynamin-like protein 1 (DLP1) in mammalian cells. We took advantage of the silencing-dependent morphological changes of peroxisomes to compare different transfection methods and show that a single transfection of DLP1 siRNA by electroporation is sufficient to effectively silence DLP1. We present a fast, easy, and convenient protocol for efficient gene silencing in a large number of cells, which can be used for quantitative and biochemical studies.

    (J Histochem Cytochem 53:1037–1040, 2005)


  • Elongation of Peroxisomes as an Indicator for Efficient Dynamin-like Protein 1 Knock Down in Mammalian Cells -

    RNA interference has become a valuable tool to identify and investigate proteins involved in the formation of peroxisomes. We demonstrate that the elongation of peroxisomes serves as an excellent indicator for efficient knock down of dynamin-like protein 1 (DLP1) in mammalian cells. We took advantage of the silencing-dependent morphological changes of peroxisomes to compare different transfection methods and show that a single transfection of DLP1 siRNA by electroporation is sufficient to effectively silence DLP1. We present a fast, easy, and convenient protocol for efficient gene silencing in a large number of cells, which can be used for quantitative and biochemical studies.

    (J Histochem Cytochem 53:1037–1040, 2005)


  • Endocrine and Exocrine Secretion of Leptin by the Gastric Mucosa -

    Leptin is a hormone that plays important roles in nutritional status and in obesity. By means of immunocytochemistry, two populations of leptin-secreting cells were found in the lower half of the gastric mucosa. One consists of numerous large cells located around the gastric pits, the Chief epithelial cells, whereas the second refers to much smaller cells, strongly stained, few in number, and scattered between the gastric pits, the endocrine cells. By double immunostaining, leptin and pepsinogen were colocalized in the Chief cells, whereas the endocrine cells were positive only for leptin. Immunoelectron microscopy showed that leptin is present along the rough endoplasmic reticulum–Golgi-granules secretory pathways of the Chief and endocrine cells. On the other hand, leptin-receptor (long and short forms) immunolabelings, although absent in the gastric epithelial cell plasma membranes, were present in enterocytes at the level of their apical and basolateral membranes. Duodenal, jejunal, and ileal enterocytes displayed similar labelings for the leptin receptor. Thus, exocrine and endocrine secretions of leptin together with the presence of leptin receptors on enterocyte plasma membranes constitute a gastroenteric axis that coordinates the role played by leptin in the digestive tract.

    (J Histochem Cytochem 53:851–860, 2005)


  • Endocrine and Exocrine Secretion of Leptin by the Gastric Mucosa -

    Leptin is a hormone that plays important roles in nutritional status and in obesity. By means of immunocytochemistry, two populations of leptin-secreting cells were found in the lower half of the gastric mucosa. One consists of numerous large cells located around the gastric pits, the Chief epithelial cells, whereas the second refers to much smaller cells, strongly stained, few in number, and scattered between the gastric pits, the endocrine cells. By double immunostaining, leptin and pepsinogen were colocalized in the Chief cells, whereas the endocrine cells were positive only for leptin. Immunoelectron microscopy showed that leptin is present along the rough endoplasmic reticulum–Golgi-granules secretory pathways of the Chief and endocrine cells. On the other hand, leptin-receptor (long and short forms) immunolabelings, although absent in the gastric epithelial cell plasma membranes, were present in enterocytes at the level of their apical and basolateral membranes. Duodenal, jejunal, and ileal enterocytes displayed similar labelings for the leptin receptor. Thus, exocrine and endocrine secretions of leptin together with the presence of leptin receptors on enterocyte plasma membranes constitute a gastroenteric axis that coordinates the role played by leptin in the digestive tract.

    (J Histochem Cytochem 53:851–860, 2005)


  • Endocrinology and hormone therapy in breast cancer: New insight into estrogen receptor-α function and its implication for endocrine therapy resistance in breast cancer - Estrogen and its receptor (ER) are critical for development and progression of breast cancer. This pathway is targeted by endocrine therapies that either block ER functions or deplete ER's estrogen ligand. While endocrine therapies are very effective, de novo and acquired resistance are still common. Laboratory and clinical data now indicate that bidirectional molecular crosstalk between nuclear or membrane ER and growth factor receptor pathways such as HER2/neu is involved in endocrine resistance. Preclinical data suggest that blockade of selected growth factor receptor signaling can overcome this type of resistance, and this strategy is already being tested in clinical trials

  • Endocrinology and hormone therapy in breast cancer: Selective oestrogen receptor modulators and downregulators for breast cancer – have they lost their way? - Although tamoxifen has been an effective treatment for breast cancer, several novel anti-oestrogen compounds have been developed with a reduced agonist profile on breast and gynaecological tissues. These include selective oestrogen receptor modulators (SERMs; both 'tamoxifen-like' and 'fixed-ring' SERMs) and selective oestrogen receptor downregulators (SERDs), although none has been proved superior in efficacy to tamoxifen in various advanced breast cancer trials. Thus, many have questioned whether a need for SERMs in breast cancer still exists, although chemoprevention remains a possible niche setting. In contrast, SERDs may have useful efficacy following aromatase inhibitors because of their unique mechanism of action, and clinical trials to determine their optimal use or sequence are ongoing.

  • Endothelial cell pseudopods and angiogenesis of breast cancer tumors - Background: A neoplastic tumor cannot grow beyond a millimeter or so in diameter without recruitment of endothelial cells and new blood vessels to supply nutrition and oxygen for tumor cell survival. This study was designed to investigate formation of new blood vessels within a human growing breast cancer tumor model (MDA MB231 in mammary fat pad of nude female mouse). Once the tumor grew to 35mm3, it developed a well-vascularized capsule. Histological sections of tumors greater than 35mm3 were stained with PAS, with CD-31 antibody (an endothelial cell maker), or with hypoxia inducible factor 1-alpha antibody (HIF). The extent of blood vessel and endothelial cell pseudopod volume density was measured by ocular grid intercept counting in the PAS stained slides. Results: The tumor area within 100-150mm of the well-vascularized capsule had few blood vessels and only occasional endothelial cell pseudopods, whereas the area greater than 150mm from the capsule had more blood vessels, capillaries, and a three-fold increase in volume density of pseudopods sprouting from the capillary endothelial cells. This subcortical region, rich in pseudopods, some of which were observed to have vacuoles/lumens, was strongly positive for presence of HIF. In some larger tumors, pseudopods were observed to insinuate for mm distances through hypoxic regions of the tumor. Conclusions: The positive correlation between presence of HIF and the increased extent of pseudopods suggests volume density measure of the latter as a quantifiable marker of tumor hypoxia. Apparently, hypoxic regions of the tumor produce HIF leading to production of vascular endothelial growth factors that stimulate sprouting of capillary endothelial cells and formation of endothelial cell pseudopods.

  • Endotoxin leads to rapid subcellular re-localization of hepatic RXRα: A novel mechanism for reduced hepatic gene expression in inflammation - Background: Lipopolysaccharide (LPS) treatment of animals down-regulates the expression of hepatic genes involved in a broad variety of physiological processes, collectively known as the negative hepatic acute phase response (APR). Retinoid X receptor α (RXRα), the most highly expressed RXR isoform in liver, plays a central role in regulating bile acid, cholesterol, fatty acid, steroid and xenobiotic metabolism and homeostasis. Many of the genes regulated by RXRα are repressed during the negative hepatic APR, although the underlying mechanism is not known. We hypothesized that inflammation-induced alteration of the subcellular location of RXRα was a common mechanism underlying the negative hepatic APR. Results: Nuclear RXRα protein levels were significantly reduced (~50%) within 1–2 hours after low-dose LPS treatment and remained so for at least 16 hours. RXRα was never detected in cytosolic extracts from saline-treated mice, yet was rapidly and profoundly detectable in the cytosol from 1 hour, to at least 4 hours, after LPS administration. These effects were specific, since the subcellular localization of the RXRα partner, the retinoic acid receptor (RARα), was unaffected by LPS. A potential cell-signaling modulator of RXRα activity, c-Jun-N-terminal kinase (JNK) was maximally activated at 1–2 hours, coincident with maximal levels of cytoplasmic RXRα. RNA levels of RXRα were unchanged, while expression of 6 sentinel hepatic genes regulated by RXRα were all markedly repressed after LPS treatment. This is likely due to reduced nuclear binding activities of regulatory RXRα-containing heterodimer pairs. Conclusion: The subcellular localization of native RXRα rapidly changes in response to LPS administration, correlating with induction of cell signaling pathways. This provides a novel and broad-ranging molecular mechanism for the suppression of RXRα-regulated genes in inflammation.

  • Enhanced levels of Hsulf-1 interfere with heparin-binding growth factor signaling in pancreatic cancer - Background: Hsulf-1 is a newly identified enzyme, which has the ability to decrease the growth of hepatocellular, ovarian, and head and neck squamous cell carcinoma cells by interfering with heparin-binding growth factor signaling. Since pancreatic cancers over-express a number of heparin-binding growth factors and their receptors, the expression and function of this enzyme in pancreatic cancer was analyzed. Results: Pancreatic cancer samples expressed significantly (22.5-fold) increased Hsulf-1 mRNA levels compared to normal controls, and Hsulf-1 mRNA was localized in the cancer cells themselves as well as in peritumoral fibroblasts. 4 out of 8 examined pancreatic cancer cell lines expressed Hsulf-1, whereas its expression was below the level of detection in the other cell lines. Stable transfection of the Hsulf-1 negative Panc-1 pancreatic cancer cell line with a full length Hsulf-1 expression vector resulted in increased sulfatase activity and decreased cell-surface heparan-sulfate proteoglycan (HSPG) sulfation. Hsulf-1 expression reduced both anchorage-dependent and -independent cell growth and decreased FGF-2 mediated cell growth and invasion in this cell line. Conclusion: High expression of Hsulf-1 occurs in the stromal elements as well as in the tumor cells in pancreatic cancer and interferes with heparin-binding growth factor signaling.

  • Eosinophilic esophagitis in adults: distinguishing features from gastroesophageal reflux disease: a study of 41 patients - Jeremy R Parfitt, James C Gregor, Neville G Suskin, Hani A Jawa & David K Driman

  • Epidermal growth factor (EGF) withdrawal masks gene expression differences in the study of pituitary adenylate cyclase-activating polypeptide (PACAP) activation of primary neural stem cell proliferation - Background: The recently discovered adult neural stem cells, which maintain continuous generation of new neuronal and glial cells throughout adulthood, are a promising and expandable source of cells for use in cell replacement therapies within the central nervous system. These cells could either be induced to proliferate and differentiate endogenously, or expanded and differentiated in culture before being transplanted into the damaged site of the brain. In order to achieve these goals effective strategies to isolate, expand and differentiate neural stem cells into the desired specific phenotypes must be developed. However, little is known as yet about the factors and mechanisms influencing these processes. It has recently been reported that pituitary adenylate cyclase-activating polypeptide (PACAP) promotes neural stem cell proliferation both in vivo and in vitro. Results: We used cDNA microarrays with the aim of analysing the transcriptional changes underlying PACAP induced proliferation of neural stem cells. The primary neural stem/progenitor cells used were neurospheres, generated from the lateral ventricle wall of the adult mouse brain. The results were compared to both differentiation and proliferation controls, which revealed an unexpected and significant differential expression relating to withdrawal of epidermal growth factor (EGF) from the neurosphere growth medium. The effect of EGF removal was so pronounced that it masked the changes in gene expression patterns produced by the addition of PACAP. Conclusions: Experimental models aiming at transcriptional analysis of induced proliferation in primary neural stem cells need to take into consideration the significant effect on transcription caused by removal of EGF. Alternatively, EGF-free culture conditions need to be developed.

  • Epigenetic alterations in neuroendocrine tumors: methylation of RAS-association domain family 1, isoform A and p16 genes are associated with metastasis - Lixia Liu, Russell R Broaddus, James C Yao, SuSu Xie, Jill A White, Tsung-Teh Wu, Stanley R Hamilton & Asif Rashid

  • Epigenetic inactivation and aberrant transcription of CSMD1in squamous cell carcinoma cell lines - Background: The p23.2 region of human chromosome 8 is frequently deleted in several types of epithelial cancer and those deletions appear to be associated with poor prognosis. Cub and Sushi Multiple Domains 1 (CSMD1) was positionally cloned as a candidate for the 8p23 suppressor but point mutations in this gene are rare relative to the frequency of allelic loss. In an effort to identify alternative mechanisms of inactivation, we have characterized CSMD1 expression and epigenetic modifications in head and neck squamous cell carcinoma cell lines. Results: Only 1 of the 20 cell lines examined appears to express a structurally normal CSMD1 transcript. The rest express transcripts which either lack internal exons, terminate abnormally or initiate at cryptic promoters. None of these truncated transcripts is predicted to encode a functional CSMD1 protein. Cell lines that express little or no CSMD1 RNA exhibit DNA methylation of a specific region of the CpG island surrounding CSMD1's first exon. Conclusions: Correlating methylation patterns and expression suggests that it is modification of the genomic DNA preceding the first exon that is associated with gene silencing and that methylation of CpG dinucleotides further 3' does not contribute to inactivation of the gene. Taken together, the cell line data suggest that epigenetic silencing and aberrant splicing rather than point mutations may be contributing to the reduction in CSMD1 expression in squamous cancers. These mechanisms can now serve as a focus for further analysis of primary squamous cancers.

  • Epigenetic silencing of DSC3 is a common event in human breast cancer - IntroductionDesmocollin 3 (DSC3) is a member of the cadherin superfamily of calcium-dependent cell adhesion molecules and a principle component of desmosomes. Desmosomal proteins such as DSC3 are integral to the maintenance of tissue architecture and the loss of these components leads to a lack of adhesion and a gain of cellular mobility. DSC3 expression is down-regulated in breast cancer cell lines and primary breast tumors; however, the loss of DSC3 is not due to gene deletion or gross rearrangement of the gene. In this study, we examined the prevalence of epigenetic silencing of DSC3 gene expression in primary breast tumor specimens. Methods: We used bisulfite genomic sequencing to analyze the methylation state of the DSC3 promoter region from 32 primary breast tumor specimens. We also used a quantitative real-time RT-PCR approach, and analyzed all breast tumor specimens for DSC3 expression. Finally, in addition to bisulfite sequencing and RT-PCR, we used an in vivo nuclease accessibility assay to determine the chromatin architecture of the CpG island region from DSC3-negative breast cancer cells lines. Results: DSC3 expression was downregulated in 23 of 32 (72%) breast cancer specimens comprising: 22 invasive ductal carcinomas, 7 invasive lobular breast carcinomas, 2 invasive ductal carcinomas that metastasized to the lymph node, and a mucoid ductal carcinoma. Of the 23 specimens showing a loss of DSC3 expression, 13 (56%) were associated with cytosine hypermethylation of the promoter region. Furthermore, DSC3 expression is limited to cells of epithelial origin and its expression of mRNA and protein is lost in a high proportion of breast tumor cell lines (79%). Lastly, DNA hypermethylation of the DSC3 promoter is highly correlated with a closed chromatin structure. Conclusion: These results indicate that the loss of DSC3 expression is a common event in primary breast tumor specimens, and that DSC3 gene silencing in breast tumors is frequently linked to aberrant cytosine methylation and concomitant changes in chromatin structure.

  • EPIMHC: a curated database of MHC-binding peptides for customized computational vaccinology. -
    Related Articles

    EPIMHC: a curated database of MHC-binding peptides for customized computational vaccinology.

    Bioinformatics. 2005 May 1;21(9):2140-1

    Authors: Reche PA, Zhang H, Glutting JP, Reinherz EL

    SUMMARY: EPIMHC is a relational database of MHC-binding peptides and T cell epitopes that are observed in real proteins. Currently, the database contains 4867 distinct peptide sequences from various sources, including 84 tumor-associated antigens. The EPIMHC database is accessible through a web server that has been designed to facilitate research in computational vaccinology. Importantly, peptides resulting from a query can be selected to derive specific motif-matrices. Subsequently, these motif-matrices can be used in combination with a dynamic algorithm for predicting MHC-binding peptides from user-provided protein queries. AVAILABILITY: The EPIMHC database server is hosted by the Dana-Farber Cancer Institute at the site http://immunax.dfci.harvard.edu/bioinformatics/epimhc/

    PMID: 15657103 [PubMed - indexed for MEDLINE]


  • Epithelioid trophoblastic tumor: clinicopathological features with an emphasis on uterine cervical involvement - Oluwole Fadare, Vinita Parkash, Maria-Luisa Carcangiu & Pei Hui

  • Establishment of Stable GH3 Cell Line Expressing Enhanced Yellow Fluorescein Protein-Growth Hormone Fusion Protein -

    To investigate, in real time, the transport and secretion of pituitary hormone, we have developed an experimental pituitary cell line, GH3 cell, which has secretory granules of growth hormone (GH) linked to enhanced yellow fluorescein protein (EYFP). This stable GH3 cell secretes secretory granules of GH linked to EYFP on stimulation by Ca2+ influx or Ca2 release from storage. This GH3 cell will be useful for the real-time visualization of the intracellular transport and secretion of GH. (J Histochem Cytochem 53:1177–1180, 2005)


  • Estren promotes androgen phenotypes in primary lymphoid organs and submandibular glands - Background: Estrogens and androgens have extensive effects on the immune system, for example they suppress both T and B lymphopoiesis in thymus and bone marrow. Submandibular glands are sexually dimorphic in rodents, resulting in larger granular convoluted tubules in males compared to females. The aim of the present experiments was to investigate the estrogenic and androgenic effects of 4-estren-3alpha,17beta-diol (estren) on thymus, bone marrow and submandibular glands, and compare the effects to those of 17beta-estradiol (E2) and 5alpha-dihydrotestosterone (DHT), respectively. Estrogen receptors (ERs) were blocked by treatment of mice with the ER-antagonist ICI 182,780; also, knock-out mice lacking one or both ERs were used. Results: As expected, the presence of functional ERs was mandatory for all the effects of E2. Similar to DHT-treatment, estren-treatment resulted in decreased thymus weight or cellularity, as well as decreased frequency of bone marrow B cells. Treatment with estren or DHT also resulted in a shift in submandibular glands towards an androgen phenotype. All the effects of estren and DHT were independent of ERs. Conclusions: Our study is the first to show that estren has similar effects as the androgen DHT on lymphopoiesis in thymus and bone marrow, and on submandibular glands, and that these effects are independent of estrogen receptors. This supports the hypothesis of estren being able to signal through the androgen receptor.

  • Estrogen receptor-dependent activation of AP-1 via non-genomic signalling - Background: Ligand-bound estrogen receptor α (ERα) and estrogen receptor β (ERβ) modulate AP-1-dependent transcription via protein-protein interactions on DNA, in a manner that depends on the type of cells and the subtype of ER. We present here evidence for an additional mechanism by which ERs modulate the transcriptional activity of AP-1. Results: We show that ERs located in the cytoplasm efficiently activate transcription at AP-1 sites in response to 17β-estradiol, while ERs present in the nucleus repress transcription under the same conditions. 17β-estradiol-induced activation of the coll-73-luc reporter correlated with cytoplasmic localization of various ERα and ERβ mutant receptors, and was inhibited in the presence of the full estrogen antagonist ICI 182,780 and the MAP-kinase inhibitor UO126. We also show that the selective estrogen receptor modulator (SERM) tamoxifen is as potent as 17β-estradiol in inducing activation of AP-1 when ERα is present in the cytoplasm. Conclusions: These results suggest that non-genomic signalling is involved in the mechanism by which ERα and ERβ influence AP-1-dependent transcription. We have previously shown that Stat3 and Stat5 are targeted by non-genomic actions of ERs, and the results presented here allow us to conclude that ERs bound to 17β-estradiol mediate the transcriptional activation of promoters regulated by AP-1 and by Stat proteins via different combinations of signal transduction pathways. Our observations thereby provide new insights into the mechanisms by which ERs act at alternate response elements, and suggest a mechanism by which tamoxifen exerts its action as a tissue-selective agonist.

  • Estrogen-repressed genes – key mediators of estrogen action? - No abstract available

  • Ethanol induces cell-cycle activity and reduces stem cell diversity to alter both regenerative capacity and differentiation potential of cerebral cortical neuroepithelial precursors - Background: The fetal cortical neuroepithelium is a mosaic of distinct progenitor populations that elaborate diverse cellular fates. Ethanol induces apoptosis and interferes with the survival of differentiating neurons. However, we know little about ethanol's effects on neuronal progenitors. We therefore exposed neurosphere cultures from fetal rat cerebral cortex, to varying ethanol concentrations, to examine the impact of ethanol on stem cell fate. Results: Ethanol promoted cell cycle progression, increased neurosphere number and increased diversity in neurosphere size, without inducing apoptosis. Unlike controls, dissociated cortical progenitors exposed to ethanol exhibited morphological evidence for asymmetric cell division, and cells derived from ethanol pre-treated neurospheres exhibited decreased proliferation capacity. Ethanol significantly reduced the numbers of cells expressing the stem cell markers CD117, CD133, Sca-1 and ABCG2, without decreasing nestin expression. Furthermore, ethanol-induced neurosphere proliferation was not accompanied by a commensurate increase in telomerase activity. Finally, cells derived from ethanol-pretreated neurospheres exhibited decreased differentiation in response to retinoic acid. Conclusions: The reduction in stem cell number along with a transient ethanol-driven increase in cell proliferation, suggests that ethanol promotes stem to blast cell maturation, ultimately depleting the reserve proliferation capacity of neuroepithelial cells. However, the lack of a concomitant change in telomerase activity suggests that neuroepithelial maturation is accompanied by an increased potential for genomic instability. Finally, the cellular phenotype that emerges from ethanol pre-treated, stem cell depleted neurospheres is refractory to additional differentiation stimuli, suggesting that ethanol exposure ablates or delays subsequent neuronal differentiation.

  • Euploidy in somatic cells from R6/2 transgenic Huntington's disease mice - Background: Huntington's disease (HD) is a hereditary neurodegenerative disorder caused by a CAG repeat expansion in the HD gene. The huntingtin protein expressed from HD has an unknown function but is suggested to interact with proteins involved in the cell division machinery. The R6/2 transgenic mouse is the most widely used model to study HD. In R6/2 fibroblast cultures, a reduced mitotic index and high frequencies of multiple centrosomes and aneuploid cells have recently been reported. Aneuploidy is normally a feature closely connected to neoplastic disease. To further explore this unexpected aspect of HD, we studied cultures derived from 6- and 12-week-old R6/2 fibroblasts, skeletal muscle cells, and liver cells. Results: Cytogenetic analyses revealed a high frequency of polyploid cells in cultures from both R6/2 and wild-type mice with the greatest proportions of polyploid cells in cultures derived from skeletal muscle cells of both genotypes. The presence of polyploid cells in skeletal muscle in vivo was confirmed by fluorescence in situ hybridisation with centromeric probes. Enlarged and supernumerary centrosomes were found in cultures from both R6/2 and wild-type mice. However, no aneuploid cells could be found in any of the tissues. Conclusion: We conclude that polyploid cells are found in fibroblast and skeletal muscle cultures derived from both R6/2 and wild-type littermate mice and that aneuploidy is unlikely to be a hallmark of HD.

  • Evaluation and Management of Bleeding During Cardiac Surgery - Patients undergoing cardiac surgery with and potentially without cardiopulmonary bypass (CPB) are at risk for excessive microvascular bleeding. This bleeding often leads to transfusion of allogeneic blood and blood components as well as reexploration. Excessive bleeding after cardiac surgery occurs because of alterations in the hemostatic system pertaining to dilutional thrombocytopenia, excessive hemostatic activation, and exposure to long-acting antiplatelet or antithrombotic agents. Pharmacologic interventions have been extensively reported as means to attenuate the alterations in the hemostatic system during CPB in an attempt to reduce excessive bleeding, transfusion, and reexploration. Prophylactic administration of agents with antifibrinolytic and antiinflammatory properties can decrease blood loss and transfusion. Aprotinin is the most extensively studied and effective blood conservation agent and has the most potent antifibrinolytic and antiinflam-matory effects. Other agents, including the lysine analogues with isolated antifibrinolytic properties, may be effective in low-risk patients. The ability to reduce blood product transfusions and to decrease operative times and reexplor-ation rates favorably affects patient outcomes, availability of blood products, and overall health care costs.

  • Evaluation of a Soybean Lectin-based Method for the Enrichment of Erythroblasts -

    We performed a comparative study of the enrichment of erythroblasts by a soybean agglutinin galactose-specific lectin method and a standardized magnetic cell-sorting (MACS) protocol. Blood samples, obtained from 11 pregnant women at between 11 and 40 weeks of gestation, were split and examined by each method in parallel. The number of erythroblasts recovered by the lectin method was approximately eightfold higher than the number obtained by MACS. Our data suggest that the lectin-based method may provide a better approach for the enrichment of rare fetal erythroblasts from maternal blood.

    (J Histochem Cytochem 53:329330, 2005)


  • Evaluation of genome-wide chromatin library of Stat5 binding sites in human breast cancer - Background: There is considerable interest in identifying target genes and chromatin binding sites for transcription factors in a genome-wide manner. Such information may become useful in diagnosis and treatment of disease, drug target identification, and for prognostication. In cancer diagnosis, patterns of transcription factor binding to specific regulatory chromatin elements are expected to complement and enhance current diagnostic predictions of tumor behavior based on protein and mRNA analyses. Signal transducer and activator of transcription-5 (Stat5) is a cytokine-activated transcription factor implicated in growth and progression of many malignancies, including hematopoietic, prostate, and breast cancer. We have explored immunoaffinity purification of Stat5-bound chromatin from breast cancer cells to identify Stat5 target sites in an unbiased, genome-wide manner. Results: In this report, we evaluate the efficacy of a Stat5-bound chromatin library to identify valid Stat5 chromatin binding sites within the oncogenome of T-47D human breast cancer cells. A general problem with cloning of immunocaptured, transcription factor-bound chromatin fragments is contamination with non-specific chromatin. However, using an optimized strategy, five out of ten randomly selected clones could be experimentally verified to bind Stat5 both in vitro and in vivo as tested by electrophoretic mobility shift assay and chromatin immunoprecipitation, respectively. While there was no binding to fragments lacking a Stat5 consensus binding sequence, presence of a Stat5 binding sequence did not assure binding. Conclusion: A chromatin library coupled with experimental validation may productively identify novel in vivo Stat5 chromatin binding sites in cancer, including abnormal regulatory sites in tumor-specific neochromatin.

  • Evaluation of Pancreatic Amylase mRNA upon Cholinergic Stimulation of Secretion -

    The primary function of the exocrine pancreas consists of the synthesis and secretion of several digestive enzymes. It is well established that amylase secretion by rat pancreatic tissue or by isolated acinar cells in culture can be stimulated by the cholinergic agonist carbachol. However, the effect of this secretagogue on enzyme synthesis remains unclear. Some studies demonstrated increases in rates of synthesis, whereas others reported increases in secretion with or without decreases in synthesis. We have evaluated changes in pancreatic amylase mRNA and total RNA after a single injection of carbachol and under fasting conditions. Two approaches in molecular morphology were applied on rat pancreatic tissue: in situ hybridization and RNase A–gold. Both revealed decreases in RNA labeling at the level of the rough endoplasmic reticulum (RER) 5 min after stimulation of secretion and after fasting. Gradual recovery was registered 15 and 30 min after stimulation of secretion. Northern blotting confirmed drastic decreases in amylase mRNA 5 min after stimulation and after fasting. The combination of such different approaches has demonstrated drastic decreases in RNA at the RER level, reflecting declines in rates of synthesis at the translational level under all conditions tested. (J Histochem Cytochem 53:93–103, 2005)


  • Evidence for High Frequency of Chromosomal Mosaicism in Spontaneous Abortions Revealed by Interphase FISH Analysis -

    Numerical chromosomal imbalances are a common feature of spontaneous abortions. However, the incidence of mosaic forms of chromosomal abnormalities has not been evaluated. We have applied interphase multicolor fluorescence in situ hybridization using original DNA probes for chromosomes 1, 9, 13, 14, 15, 16, 18, 21, 22, X, and Y to study chromosomal abnormalities in 148 specimens of spontaneous abortions. We have detected chromosomal abnormalities in 89/148 (60.1%) of specimens. Among them, aneuploidy was detected in 74 samples (83.1%). In the remaining samples, polyploidy was detected. The mosaic forms of chromosome abnormality, including autosomal and sex chromosomal aneuploidies and polyploidy (31 and 12 cases, respectively), were observed in 43/89 (48.3%) of specimens. The most frequent mosaic form of aneuploidy was related to chromosome X (19 cases). The frequency of mosaic forms of chromosomal abnormalities in samples with male chromosomal complement was 50% (16/32 chromosomally abnormal), and in samples with female chromosomal complement, it was 47.4% (27/57 chromosomally abnormal). The present study demonstrates that the postzygotic or mitotic errors leading to chromosomal mosaicism in spontaneous abortions are more frequent than previously suspected. Chromosomal mosaicsm may contribute significantly to both pregnancy complications and spontaneous fetal loss. (J Histochem Cytochem 53:375–380, 2005)


  • Evidence for proteolytic cleavage of brevican by the ADAMTSs in the dentate gyrus after excitotoxic lesion of the mouse entorhinal cortex - Background: Brevican is a member of the lectican family of aggregating extracellular matrix (ECM) proteoglycans that bear chondroitin sulfate (CS) chains. It is highly expressed in the central nervous system (CNS) and is thought to stabilize synapses and inhibit neural plasticity and as such, neuritic or synaptic remodeling would be less likely to occur in regions with intact and abundant, lectican-containing, ECM complexes. Neural plasticity may occur more readily when these ECM complexes are broken down by endogenous proteases, the ADAMTSs (a disintegrin and metalloproteinase with thrombospondin motifs), that selectively cleave the lecticans. The purpose of these experiments was to determine whether the production of brevican or ADAMTS-cleaved fragments of brevican were altered after deafferentation and reinnervation of the dentate gyrus via entorhinal cortex lesion (ECL). Results: In the C57Bl6J mouse, synaptic density in the molecular layer of the dentate gyrus, as measured by synaptophysin levels in ELISA, was significantly attenuated 2 days (nearly 50% of contralateral) and 7 days after lesion and returned to levels not different from the contralateral region at 30 days. Immunoreactive brevican in immunoblot was elevated 2 days after lesion, whereas there was a significant increase in the proteolytic product at 7, but not 30 days post-lesion. ADAMTS activity, estimated using the ratio of the specific ADAMTS-derived brevican fragment and intact brevican levels was increased at 7 days, but was not different from the contralateral side at 2 or 30 days after deafferentation. Conclusion: These findings indicate that ADAMTS activity in the dentate outer molecular layer (OML) is elevated during the initial synaptic reinnervation period (7 days after lesion). Therefore, proteolytic processing of brevican appears to be a significant extracellular event in the remodeling of the dentate after EC lesion, and may modulate the process of sprouting and/or synaptogenesis.

  • Evolutionary conservation analysis increases the colocalization of predicted exonic splicing enhancers in the BRCA1 gene with missense sequence changes and in-frame deletions, but not polymorphisms - IntroductionAberrant pre-mRNA splicing can be more detrimental to the function of a gene than changes in the length or nature of the encoded amino acid sequence. Although predicting the effects of changes in consensus 5' and 3' splice sites near intron:exon boundaries is relatively straightforward, predicting the possible effects of changes in exonic splicing enhancers (ESEs) remains a challenge. Methods: As an initial step toward determining which ESEs predicted by the web-based tool ESEfinder in the breast cancer susceptibility gene BRCA1 are likely to be functional, we have determined their evolutionary conservation and compared their location with known BRCA1 sequence variants. Results: Using the default settings of ESEfinder, we initially detected 669 potential ESEs in the coding region of the BRCA1 gene. Increasing the threshold score reduced the total number to 464, while taking into consideration the proximity to splice donor and acceptor sites reduced the number to 211. Approximately 11% of these ESEs (23/211) either are identical at the nucleotide level in human, primates, mouse, cow, dog and opossum Brca1 (conserved) or are detectable by ESEfinder in the same position in the Brca1 sequence (shared). The frequency of conserved and shared predicted ESEs between human and mouse is higher in BRCA1 exons (2.8 per 100 nucleotides) than in introns (0.6 per 100 nucleotides). Of conserved or shared putative ESEs, 61% (14/23) were predicted to be affected by sequence variants reported in the Breast Cancer Information Core database. Applying the filters described above increased the colocalization of predicted ESEs with missense changes, in-frame deletions and unclassified variants predicted to be deleterious to protein function, whereas they decreased the colocalization with known polymorphisms or unclassified variants predicted to be neutral. Conclusion: In this report we show that evolutionary conservation analysis may be used to improve the specificity of an ESE prediction tool. This is the first report on the prediction of the frequency and distribution of ESEs in the BRCA1 gene, and it is the first reported attempt to predict which ESEs are most likely to be functional and therefore which sequence variants in ESEs are most likely to be pathogenic.

  • Evolutionary selection across the nuclear hormone receptor superfamily with a focus on the NR1I subfamily (vitamin D, pregnane X, and constitutive androstane receptors) - Background: The nuclear hormone receptor (NR) superfamily complement in humans is composed of 48 genes with diverse roles in metabolic homeostasis, development, and detoxification. In general, NRs are strongly conserved between vertebrate species, and few examples of molecular adaptation (positive selection) within this superfamily have been demonstrated. Previous studies utilizing two-species comparisons reveal strong purifying (negative) selection of most NR genes, with two possible exceptions being the ligand-binding domains (LBDs) of the pregnane X receptor (PXR, NR1I2) and the constitutive androstane receptor (CAR, NR1I3), two proteins involved in the regulation of toxic compound metabolism and elimination. The aim of this study was to apply detailed phylogenetic analysis using maximum likelihood methods to the entire complement of genes in the vertebrate NR superfamily. Analyses were carried out both across all vertebrates and limited to mammals and also separately for the two major domains of NRs, the DNA-binding domain (DBD) and LBD, in addition to the full-length sequences. Additional functional data is also reported for activation of PXR and the vitamin D receptor (VDR; NR1I1) to gain further insight into the evolution of the NR1I subfamily. Results: The NR genes appear to be subject to strong purifying selection, particularly in the DBDs. Estimates of the ratio of the non-synonymous to synonymous nucleotide substitution rates (the omega ratio) revealed that only the PXR LBD had a sub-population of codons with an estimated omega ratio greater than 1. CAR was also unusual in showing high relative omega ratios in both the DBD and LBD, a finding that may relate to the recent appearance of the CAR gene (presumably by duplication of a pre-mammalian PXR gene) just prior to the evolution of mammals. Functional analyses of the NR1I subfamily show that human and zebrafish PXRs show similar activation by steroid hormones and early bile salts, properties not shared by sea lamprey, mouse, or human VDRs, or by Xenopus laevis PXRs. Conclusions: NR genes generally show strong sequence conservation and little evidence for positive selection. The main exceptions are PXR and CAR, genes that may have adapted to cross-species differences in toxic compound exposure.

  • Ex Vivo Modeling of Oral HIV Transmission in Human Palatine Tonsil -

    The majority of newly acquired HIV infections are believed to occur following transmission of virus infectivity across mucosal surfaces, although many mechanistic details still remain unresolved. We have used human ex vivo organ cultures and primary cell populations to analyze the cellular and molecular basis for mucosal HIV transmission. By using human palatine tonsil from routine tonsillectomies and semen from HIV-positive donors, we have created an experimental equivalent to oral HIV transmission. HIV infection was readily transferred into tonsillar lymphocytes, but this transmission into lymphocytes was dramatically reduced when the exposed lymphocyte populations were protected by intact mucosal surfaces. In this study, we consider the impact that leukocyte activation and morphological aberrations in surface structure may have on susceptibility to primary HIV infection and introduce novel time-lapse confocal microscopy procedures that begin to reveal the dynamic complexity associated with cell-mediated HIV transmission. This manuscript contains online supplemental material at http://www.jhc.org. Please visit this article online to view these materials. (J Histochem Cytochem 53:631–642, 2005)


  • Ex Vivo Modeling of Oral HIV Transmission in Human Palatine Tonsil -

    The majority of newly acquired HIV infections are believed to occur following transmission of virus infectivity across mucosal surfaces, although many mechanistic details still remain unresolved. We have used human ex vivo organ cultures and primary cell populations to analyze the cellular and molecular basis for mucosal HIV transmission. By using human palatine tonsil from routine tonsillectomies and semen from HIV-positive donors, we have created an experimental equivalent to oral HIV transmission. HIV infection was readily transferred into tonsillar lymphocytes, but this transmission into lymphocytes was dramatically reduced when the exposed lymphocyte populations were protected by intact mucosal surfaces. In this study, we consider the impact that leukocyte activation and morphological aberrations in surface structure may have on susceptibility to primary HIV infection and introduce novel time-lapse confocal microscopy procedures that begin to reveal the dynamic complexity associated with cell-mediated HIV transmission. This manuscript contains online supplemental material at http://www.jhc.org. Please visit this article online to view these materials. (J Histochem Cytochem 53:631–642, 2005)


  • Ex Vivo Modeling of Oral HIV Transmission in Human Palatine Tonsil -

    The majority of newly acquired HIV infections are believed to occur following transmission of virus infectivity across mucosal surfaces, although many mechanistic details still remain unresolved. We have used human ex vivo organ cultures and primary cell populations to analyze the cellular and molecular basis for mucosal HIV transmission. By using human palatine tonsil from routine tonsillectomies and semen from HIV-positive donors, we have created an experimental equivalent to oral HIV transmission. HIV infection was readily transferred into tonsillar lymphocytes, but this transmission into lymphocytes was dramatically reduced when the exposed lymphocyte populations were protected by intact mucosal surfaces. In this study, we consider the impact that leukocyte activation and morphological aberrations in surface structure may have on susceptibility to primary HIV infection and introduce novel time-lapse confocal microscopy procedures that begin to reveal the dynamic complexity associated with cell-mediated HIV transmission. This manuscript contains online supplemental material at http://www.jhc.org. Please visit this article online to view these materials. (J Histochem Cytochem 53:631–642, 2005)


  • Exposure of nuclear antigens in formalin-fixed, paraffin-embedded necropsy human spinal cord tissue: Detection of NeuN. -
    Related Articles

    Exposure of nuclear antigens in formalin-fixed, paraffin-embedded necropsy human spinal cord tissue: Detection of NeuN.

    J Neurosci Methods. 2005 Oct 15;148(1):26-35

    Authors: Gill SK, Ishak M, Rylett RJ

    Immunohistochemical and immunofluorescence staining approaches are powerful tools for characterization of the endogenous protein expression and subcellular compartmentalization. However, several technical problems hamper identification of low-abundance nuclear proteins in archival formalin-fixed, paraffin-embedded human neural tissue. These include loss of protein antigenicity during tissue fixation and processing, and intrinsic auto-fluorescence associated with the tissue related to its fixation and the presence of lipofuscin. We evaluated several antigen retrieval methods to establish a strategy for detection of neuronal nuclear proteins in human spinal cord formalin-fixed, paraffin-embedded tissue. Thus, using immunostaining of the neuron-specific nuclear protein NeuN as the outcome measure, we found that heating tissue sections in an alkaline pH buffer unmasked protein epitopes most effectively. Moreover, staining by immunohistochemistry with diaminobenzidine tetrahydrochloride chromagen was superior to immunofluorescence labeling, likely due to the signal amplification steps included in the former approach. Auto-fluorescence in the tissue sections can be effectively reduced, but a sufficient fluorescence signal associated with specific antibody labeling could not be detected above this background for NeuN in the nucleus.

    PMID: 16176837 [PubMed - in process]


  • Expression analysis of candidate breast tumour suppressor genes on chromosome 16q - IntroductionChromosome arm 16q is the second most frequent target of loss of heterozygosity in breast cancer and is, therefore, a candidate to contain one or more classic tumour suppressor genes (TSGs). E-cadherin at 16q22 was identified as a TSG in lobular breast cancer, but TSGs in ductal breast cancer remain elusive. Several genes have been suggested as potential candidates (e.g. CBFA2T3, CTCF and WWOX) but no inactivating mutations could be identified in these genes and they thus fail to fit the classic two-hit model for a TSG. With the completion of the human transcriptome, new candidate genes can be distinguished. Besides mutational inactivation, a TSG could, at least in a subset of the tumours, be transcriptionally suppressed or even inactivated. Studying candidate genes for expression and somatic mutations could thus identify the TSGs. Methods: Possible candidates CBFA2T3, TERF2 and TERF2IP, FBXL8 and LRRC29 and FANCA were studied for insertion and deletion mutations and for expression differences using quantitative RT-PCR in a panel of tumour cell lines and primary tumours with and without loss of 16q. Results: None of the genes showed mutations or obvious expression differences. FANCA expression increased with tumour grade. Conclusion: Apparently, the underlying genetics at chromosome 16q are complex or the TSGs remain to be identified. Multiple mechanisms, such as mutations, promoter hypermethylation or haploinsufficiency, might lead to the inactivation of a TSG.

  • Expression Analysis of PMP22/Gas3 in Premalignant and Malignant Pancreatic Lesions -

    PMP22 is a structural protein of Schwann cells, but it also influences cell proliferation. In the present study, quantitative RT-PCR (QRT-PCR) and immunohistochemistry were used to determine PMP22 mRNA levels and to localize PMP22 in the normal pancreas (n=20), chronic pancreatitis (CP) (n=22), pancreatic ductal adenocarcinoma (PDAC) (n=31), intraductal papillary mucinous neoplasms (IPMN) (n=9), mucinous cystic tumors (MCN) (n=4), and in a panel of PanIN lesions (n=29). PMP22 mRNA levels were significantly higher in CP (3-fold) and PDAC (2.5-fold), compared to normal pancreatic tissues. PMP22 expression was restricted to nerves in the normal pancreas, while in CP and PDAC PMP22 was also expressed in PanIN lesions and in a small percentage of pancreatic cancer cells. PMP22 was weak to absent in the tumor cells of IPMNs and MCNs. PMP22 mRNA was present at different levels in cultured pancreatic cancer cells and up-regulated by transforming growth factor (TGF)-ßbeta;1 in 2 of 8 of these cell lines. In conclusion, PMP22 expression is present in both CP and PDAC tissues. Its expression in PanIN lesions and some pancreatic cancer cells in vitro and in vivo suggests a role of PMP22 in the neoplastic transformation process from the normal pancreas to pre-malignant lesions to pancreatic cancer.

    (J Histochem Cytochem 53:885–893, 2005)


  • Expression Analysis of PMP22/Gas3 in Premalignant and Malignant Pancreatic Lesions -

    PMP22 is a structural protein of Schwann cells, but it also influences cell proliferation. In the present study, quantitative RT-PCR (QRT-PCR) and immunohistochemistry were used to determine PMP22 mRNA levels and to localize PMP22 in the normal pancreas (n=20), chronic pancreatitis (CP) (n=22), pancreatic ductal adenocarcinoma (PDAC) (n=31), intraductal papillary mucinous neoplasms (IPMN) (n=9), mucinous cystic tumors (MCN) (n=4), and in a panel of PanIN lesions (n=29). PMP22 mRNA levels were significantly higher in CP (3-fold) and PDAC (2.5-fold), compared to normal pancreatic tissues. PMP22 expression was restricted to nerves in the normal pancreas, while in CP and PDAC PMP22 was also expressed in PanIN lesions and in a small percentage of pancreatic cancer cells. PMP22 was weak to absent in the tumor cells of IPMNs and MCNs. PMP22 mRNA was present at different levels in cultured pancreatic cancer cells and up-regulated by transforming growth factor (TGF)-ßbeta;1 in 2 of 8 of these cell lines. In conclusion, PMP22 expression is present in both CP and PDAC tissues. Its expression in PanIN lesions and some pancreatic cancer cells in vitro and in vivo suggests a role of PMP22 in the neoplastic transformation process from the normal pancreas to pre-malignant lesions to pancreatic cancer.

    (J Histochem Cytochem 53:885–893, 2005)


  • Expression of Cellular Prion Protein in the Frontal and Occipital Lobe in Alzheimer's Disease, Diffuse Lewy Body Disease, and in Normal Brain: An Immunohistochemical Study -

    Cellular prion protein (PrPc) is a glycoprotein expressed at low to moderate levels within the nervous system. Recent studies suggest that PrPc may possess neuroprotective functions and that its expression is upregulated in certain neurodegenerative disorders. We investigated whether PrPc expression is altered in the frontal and occipital cortex in two well-characterized neurodegenerative disorders—Alzheimer's disease (AD) and diffuse Lewy body disease (DLBD)—compared with that in normal human brain using immunohistochemistry and computerized image analysis. The distribution of PrPc was further tested for correlation with glial reactivity. We found that PrPc was localized mainly in the gray matter (predominantly in neurons) and expressed at higher levels within the occipital cortex in the normal human brain. Image analysis revealed no significant variability in PrPc expression between DLBD and control cases. However, blood vessels within the white matter of DLBD cases showed immunoreactivity to PrPc. By contrast, this protein was differentially expressed in the frontal and occipital cortex of AD cases; it was markedly overexpressed in the former and significantly reduced in the latter. Epitope specificity of antibodies appeared important when detecting PrPc. The distribution of PrPc did not correlate with glial immunoreactivity. In conclusion, this study supports the proposal that regional changes in expression of PrPc may occur in certain neurodegenerative disorders such as AD, but not in other disorders such as DLBD. (J Histochem Cytochem 53:929–940, 2005)


  • Expression of Cellular Prion Protein in the Frontal and Occipital Lobe in Alzheimer's Disease, Diffuse Lewy Body Disease, and in Normal Brain: An Immunohistochemical Study -

    Cellular prion protein (PrPc) is a glycoprotein expressed at low to moderate levels within the nervous system. Recent studies suggest that PrPc may possess neuroprotective functions and that its expression is upregulated in certain neurodegenerative disorders. We investigated whether PrPc expression is altered in the frontal and occipital cortex in two well-characterized neurodegenerative disorders—Alzheimer's disease (AD) and diffuse Lewy body disease (DLBD)—compared with that in normal human brain using immunohistochemistry and computerized image analysis. The distribution of PrPc was further tested for correlation with glial reactivity. We found that PrPc was localized mainly in the gray matter (predominantly in neurons) and expressed at higher levels within the occipital cortex in the normal human brain. Image analysis revealed no significant variability in PrPc expression between DLBD and control cases. However, blood vessels within the white matter of DLBD cases showed immunoreactivity to PrPc. By contrast, this protein was differentially expressed in the frontal and occipital cortex of AD cases; it was markedly overexpressed in the former and significantly reduced in the latter. Epitope specificity of antibodies appeared important when detecting PrPc. The distribution of PrPc did not correlate with glial immunoreactivity. In conclusion, this study supports the proposal that regional changes in expression of PrPc may occur in certain neurodegenerative disorders such as AD, but not in other disorders such as DLBD. (J Histochem Cytochem 53:929–940, 2005)


  • Expression of Components of the Renin-angiotensin System in Autosomal Recessive Polycystic Kidney Disease -

    Hypertension is a common complication in children with autosomal recessive polycystic kidney disease (ARPKD) who have survived the neonatal period. No information is available regarding the mechanism of hypertension in this condition. The renin-angiotensin system (RAS) is thought to play a role in hypertension associated with the more common autosomal dominant polycystic kidney disease (ADPKD). Occasional reports have documented increased activity of the intrarenal RAS in ADPKD, with ectopic renin expression within cysts and dilated tubules. Because of similarities between ARPKD and ADPKD, we hypothesized that increased intrarenal RAS activity might also be found in ARPKD. We performed immunohistochemical studies on kidney tissues from two infants with ARPKD and two control kidneys. The cystic dilated tubules showed staining with the peanut lectin arachis hypogaea, a marker of distal tubules and collecting ducts, but not with lotus tetragonolobus, a marker of proximal tubules. Strong renin staining was seen in many cysts and tubules of ARPKD kidneys, but only in the afferent arterioles of the normal control kidneys. Angiotensinogen staining was also observed in some cysts and in proximal tubules. Staining for angiotensin-converting enzyme, angiotensin II type 1 receptor, and angiotensin II peptide was present in many cystic dilated tubules. These immunohistochemical studies document for the first time ectopic expression of components of the RAS in cystic-dilated tubules of ARPKD and suggest that overactivity of RAS could result in increased intrarenal angiotensin II production, which may contribute to the development of hypertension in ARPKD. (J Histochem Cytochem 53:979–988, 2005)


  • Expression of Components of the Renin-angiotensin System in Autosomal Recessive Polycystic Kidney Disease -

    Hypertension is a common complication in children with autosomal recessive polycystic kidney disease (ARPKD) who have survived the neonatal period. No information is available regarding the mechanism of hypertension in this condition. The renin-angiotensin system (RAS) is thought to play a role in hypertension associated with the more common autosomal dominant polycystic kidney disease (ADPKD). Occasional reports have documented increased activity of the intrarenal RAS in ADPKD, with ectopic renin expression within cysts and dilated tubules. Because of similarities between ARPKD and ADPKD, we hypothesized that increased intrarenal RAS activity might also be found in ARPKD. We performed immunohistochemical studies on kidney tissues from two infants with ARPKD and two control kidneys. The cystic dilated tubules showed staining with the peanut lectin arachis hypogaea, a marker of distal tubules and collecting ducts, but not with lotus tetragonolobus, a marker of proximal tubules. Strong renin staining was seen in many cysts and tubules of ARPKD kidneys, but only in the afferent arterioles of the normal control kidneys. Angiotensinogen staining was also observed in some cysts and in proximal tubules. Staining for angiotensin-converting enzyme, angiotensin II type 1 receptor, and angiotensin II peptide was present in many cystic dilated tubules. These immunohistochemical studies document for the first time ectopic expression of components of the RAS in cystic-dilated tubules of ARPKD and suggest that overactivity of RAS could result in increased intrarenal angiotensin II production, which may contribute to the development of hypertension in ARPKD. (J Histochem Cytochem 53:979–988, 2005)


  • Expression of CXCR4 is associated with axillary lymph node status in patients with early breast cancer. -
    Related Articles

    Expression of CXCR4 is associated with axillary lymph node status in patients with early breast cancer.

    Breast. 2005 Oct 17;

    Authors: Su YC, Wu MT, Huang CJ, Hou MF, Yang SF, Chai CY

    Recent studies have discovered that CXCR4 is associated with tumor metastasis. It is worth understanding the association between CXCR4 expression and axillary lymph node involvement in early breast cancer. Eighty-five patients with early breast cancers were divided into three groups based on their axillary lymph node status. CXCR4 expression was assessed by immunohistochemistry in all cases and its correlation with axillary lymph node involvement was evaluated. There was a significant difference in nuclear CXCR4 expression among these three groups and high nuclear expression of CXCR4 was associated with cases with no lymph node involvement. However, high cytoplasmic expression of CXCR4 was associated with patients who developed high-level axillary lymph node involvement. In conclusion, the different staining locations of CXCR4 have varying biological significance for the metastatic potential of axillary lymph nodes. In particular, it provided information that high cytoplasmic expression of CXCR4 was related to axillary internodal metastasis, and adjuvant radio-chemotherapy was suggested.

    PMID: 16239110 [PubMed - as supplied by publisher]


  • Expression of D2-40 in lymphatic endothelium of normal tissues and in vascular tumours. -
    Related Articles

    Expression of D2-40 in lymphatic endothelium of normal tissues and in vascular tumours.

    Histopathology. 2005 Apr;46(4):396-402

    Authors: Fukunaga M

    AIMS: To evaluate the expression of D2-40 in normal lymphatic endothelium and vascular tumours or tumour-like lesions of the skin and soft tissue. D2-40 is a novel monoclonal antibody to a Mr 40 000 O-linked sialoglycoprotein that reacts with a fixation-resistant epitope in lymphatic endothelium. METHODS AND RESULTS: Formalin-fixed paraffin-embedded sections from 30 normal tissue samples, including skin, soft tissue, stomach, and colon, and 84 vascular tumours or vascular tumour-like lesions were immunostained with monoclonal antibodies to D2-40 and CD31. Normal lymphatic endothelial cells in all normal tissues expressed D2-40. Its positive staining delineated flattened channels or open spaces lined by a single layer of endothelial cells whose lumena were sometimes filled with lymphocytes. Ten of 10 cases of lymphangioma, nine of 10 Kaposi's sarcomas (KSs), one of five spindle cell haemangiomas, one of one reactive angioenodotheliomatosis, one of one vascular transformation of lymph node sinuses, three of three Dabska tumours, one of 10 epithelioid haemangioendotheliomas (HEs) and seven of 15 angiosarcomas were positive for D2-40. Positively staining angiosarcomas were characterized by epithelioid or papillary endothelial cells. Twenty-two non-spindle cell haemangiomas, one retiform HE and one Kaposiform HE, and five glomus tumours were negative for D2-40. In comparison, CD31 was expressed in five of 10 lymphangiomas, nine of 10 KSs, 27 of 27 haemangiomas, three of three Dabska tumours, 10 of 10 epithelioid HEs, 15 of 15 angiosarcomas and one of one each of retiform HE, Kaposiform HE, reactive angioendotheliomatosis, and vascular transformation of node sinuses. Five glomus tumours were negative for CD31. CONCLUSIONS: The monoclonal antibody D2-40 is a highly sensitive and specific marker of lymphatic endothelium in normal tissue and a subset of vascular lesions, including KS, Dabska tumour, and lymphangioma. The findings support the concept that these tumours show at least partial lymphatic endothelial differentiation. Subsets of angiosarcomas and HEs show both vascular and lymphatic endothelial differentiation. D2-40 can be used in a panel of markers to classify vascular tumours. There is no requirement for epitope retrieval. This novel monoclonal antibody also has the potential for increasing the accuracy of detection of lymphatic invasion in primary tumours and could be widely applied for this purpose in surgical pathology.

    PMID: 15810951 [PubMed - indexed for MEDLINE]


  • Expression of HBsAg and HBcAg in the ovaries and ova of patients with chronic hepatitis B. -
    Related Articles

    Expression of HBsAg and HBcAg in the ovaries and ova of patients with chronic hepatitis B.

    World J Gastroenterol. 2005 Sep 28;11(36):5718-20

    Authors: Ye F, Yue YF, Li SH, Chen TY, Zhang SL, Bai GQ, Liu M

    AIM: To investigate the expression and distribution of HBV in the ovaries and ova. METHODS: The immunohistochemistry method was used to detect the HBsAg and HBcAg in the ovaries of patients with chronic hepatitis B. RESULTS: Expression of HBsAg in the ova, granular and interstitial cells of the ovaries was located in the cytomembrane and cytoplasm. Expression of HBcAg in the ova, granular, interstitial and endothelial cells of interstitial blood vessels of the ovaries was found in the cytomembrane, cytoplasm, and nuclei. CONCLUSION: HBV can infect the ova at different stages of development and replicate in it.

    PMID: 16237773 [PubMed - in process]


  • Expression of hepatocyte nuclear factor-1beta (HNF-1beta) in clear cell tumors and endometriosis of the ovary - Noriko Kato, Shun-ichi Sasou & Teiichi Motoyama

  • Expression of human AID in yeast induces mutations in context similar to the context of somatic hypermutation at G-C pairs in immunoglobulin genes - Background: Antibody genes are diversified by somatic hypermutation (SHM), gene conversion and class-switch recombination. All three processes are initiated by the activation induced deaminase (AID). According to a DNA deamination model of SHM, AID converts cytosine to uracil in DNA sequences. The initial deamination of cytosine leads to mutation and recombination in pathways involving replication, DNA mismatch repair and possibly base excision repair. The DNA sequence context of mutation hotspots at G-C pairs during SHM is DGYW/WRCH (G-C is a mutable position, R = A/G, Y = T/C, W = A/T, D = A/G/T). Results: To investigate the mechanisms of AID-induced mutagenesis in a model system, we studied the genetic consequences of AID expression in yeast. We constructed a yeast vector with an artificially synthesized human AID gene insert using codons common to highly expressed yeast genes. We found that expression of the artificial hAIDSc gene was moderately mutagenic in a wild-type strain and highly mutagenic in an ung1 uracil-DNA glycosylase-deficient strain. A majority of mutations were at G-C pairs. In the ung1 strain, C-G to T-A transitions were found almost exclusively, while a mixture of transitions with 12% transversions was characteristic in the wild-type strain. In the ung1 strain mutations that could have originated from deamination of the transcribed stand were found more frequently. In the wild-type strain, the strand bias was reversed. DGYW/WRCH motifs were preferential sites of mutations. Conclusions: The results are consistent with the hypothesis that AID-mediated deamination of DNA is a major cause of mutations at G-C base pairs in immunoglobulin genes during SHM. The sequence contexts of mutations in yeast induced by AID and those of somatic mutations at G-C pairs in immunoglobulin genes are significantly similar. This indicates that the intrinsic substrate specificity of AID itself is a primary determinant of mutational hotspots at G-C base pairs during SHM.

  • Expression of hypoxia-inducible factor 1 alpha and its downstream targets in fibroepithelial tumors of the breast - IntroductionHypoxia-inducible factor 1 (HIF-1) alpha and its downstream targets carbonic anhydrase IX (CAIX) and vascular endothelial growth factor (VEGF) are key factors in the survival of proliferating tumor cells in a hypoxic microenvironment. We studied the expression and prognostic relevance of HIF-1α and its downstream targets in phyllodes tumors and fibroadenomas of the breast. Methods: The expression of HIF-1α, CAIX, VEGF and p53 was investigated by immunohistochemistry in a group of 37 primary phyllodes tumors and 30 fibroadenomas with known clinical follow-up. The tumor microvasculature was visualized by immunohistochemistry for CD31. Proliferation was assessed by Ki67 immunostaining and mitotic counts. Being biphasic tumors, immunoquantification was performed in the stroma and epithelium. Results: Only two fibroadenomas displayed low-level stromal HIF-1α reactivity in the absence of CAIX expression. Stromal HIF-1α expression was positively correlated with phyllodes tumor grade (P = 0.001), with proliferation as measured by Ki67 expression (P < 0.001) and number of mitoses (P < 0.001), with p53 accumulation (P = 0.003), and with global (P = 0.015) and hot-spot (P = 0.031) microvessel counts, but not with CAIX expression. Interestingly, concerted CAIX and HIF-1α expression was frequently found in morphologically normal epithelium of phyllodes tumors. The distance from the epithelium to the nearest microvessels was higher in phyllodes tumors as compared with in fibroadenomas. Microvessel counts as such did not differ between fibroadenomas and phyllodes tumors, however. High expression of VEGF was regularly found in both tumors, with only a positive relation between stromal VEGF and grade in phyllodes tumors (P = 0.016). Stromal HIF-1α overexpression in phyllodes tumors was predictive of disease-free survival (P = 0.032). Conclusion: These results indicate that HIF-1α expression is associated with diminished disease-free survival and may play an important role in stromal progression of breast phyllodes tumors. In view of the absence of stromal CAIX expression in phyllodes tumors, stromal upregulation of HIF-1α most probably arises from hypoxia-independent pathways, with p53 inactivation as one possible cause. In contrast, coexpression of HIF-1α and CAIX in the epithelium in phyllodes tumors points to epithelial hypoxia, most probably caused by relatively distant blood vessels. On the other hand, HIF-1α and CAIX seem to be of minor relevance in breast fibroadenomas.

  • Expression of Neuronal Nuclear Antigen (NeuN) in Epithelial Neuroendocrine Carcinoma. -

  • Expression of Nkx6 Genes in the Hindbrain and Gut of the Developing Mouse -

    The Nkx6 gene family of homeodomain transcription factors consists of three members. For two, Nkx6.1 and Nkx6.2, important developmental roles in the central nervous system and pancreas have been demonstrated. Here we introduce the third member of the Nkx6 gene family, Nkx6.3, and identify similar and distinct patterns of expression for all three Nkx6 genes in the hindbrain and gut of the developing mouse embryo.

    (J Histochem Cytochem 53:787–790, 2005)


  • Expression of Nkx6 Genes in the Hindbrain and Gut of the Developing Mouse -

    The Nkx6 gene family of homeodomain transcription factors consists of three members. For two, Nkx6.1 and Nkx6.2, important developmental roles in the central nervous system and pancreas have been demonstrated. Here we introduce the third member of the Nkx6 gene family, Nkx6.3, and identify similar and distinct patterns of expression for all three Nkx6 genes in the hindbrain and gut of the developing mouse embryo.

    (J Histochem Cytochem 53:787–790, 2005)


  • Expression of Nkx6 Genes in the Hindbrain and Gut of the Developing Mouse -

    The Nkx6 gene family of homeodomain transcription factors consists of three members. For two, Nkx6.1 and Nkx6.2, important developmental roles in the central nervous system and pancreas have been demonstrated. Here we introduce the third member of the Nkx6 gene family, Nkx6.3, and identify similar and distinct patterns of expression for all three Nkx6 genes in the hindbrain and gut of the developing mouse embryo.

    (J Histochem Cytochem 53:787–790, 2005)


  • Expression of p63 in Diffuse Large B-Cell Lymphoma. -

  • Expression of PDE11A in Normal and Malignant Human Tissues -

    Cyclic nucleotide phosphodiesterase 11A (PDE11A) is the newest member in the PDE family. Although the tissue distribution of PDE11A mRNA has been shown, its protein expression pattern has not been well studied. The goal of this report is to investigate the distribution of PDE11A proteins in a wide range of normal and malignant human tissues. We utilized a polyclonal antibody that recognized all four PDE11A isoforms. Its specificity was demonstrated by Western blot analysis on a recombinant human PDE11A protein and native PDE11A proteins in various human tissues. Immunohistochemistry showed that PDE11A is widely expressed. Various degrees of immunoreactivity were observed in the epithelial cells, endothelial cells, and smooth muscle cells of all tissues examined. The highest expression was in the epithelial, endothelial, and smooth muscle cells of the prostate, Leydig, and spermatogenic cells of the testis, the tubule epithelial cells in the kidney, the epithelial and endothelial cells in the adrenal, the epithelial cells and macrophages in the colon, and the epidermis in the skin. Furthermore, PDE11A expression was also detected in several human carcinomas. Our results suggest that PDE11A might be involved in multiple physiological processes in various organs via its ability to modulate intracellular cAMP and cGMP levels. (J Histochem Cytochem 53:895–903, 2005)


  • Expression of PDE11A in Normal and Malignant Human Tissues -

    Cyclic nucleotide phosphodiesterase 11A (PDE11A) is the newest member in the PDE family. Although the tissue distribution of PDE11A mRNA has been shown, its protein expression pattern has not been well studied. The goal of this report is to investigate the distribution of PDE11A proteins in a wide range of normal and malignant human tissues. We utilized a polyclonal antibody that recognized all four PDE11A isoforms. Its specificity was demonstrated by Western blot analysis on a recombinant human PDE11A protein and native PDE11A proteins in various human tissues. Immunohistochemistry showed that PDE11A is widely expressed. Various degrees of immunoreactivity were observed in the epithelial cells, endothelial cells, and smooth muscle cells of all tissues examined. The highest expression was in the epithelial, endothelial, and smooth muscle cells of the prostate, Leydig, and spermatogenic cells of the testis, the tubule epithelial cells in the kidney, the epithelial and endothelial cells in the adrenal, the epithelial cells and macrophages in the colon, and the epidermis in the skin. Furthermore, PDE11A expression was also detected in several human carcinomas. Our results suggest that PDE11A might be involved in multiple physiological processes in various organs via its ability to modulate intracellular cAMP and cGMP levels. (J Histochem Cytochem 53:895–903, 2005)


  • Expression profile of immune response genes in patients with Severe Acute Respiratory Syndrome - Background: Severe acute respiratory syndrome (SARS) emerged in later February 2003, as a new epidemic form of life-threatening infection caused by a novel coronavirus. However, the immune-pathogenesis of SARS is poorly understood. To understand the host response to this pathogen, we investigated the gene expression profiles of peripheral blood mononuclear cells (PBMCs) derived from SARS patients, and compared with healthy controls. Results: The number of differentially expressed genes was found to be 186 under stringent filtering criteria of microarray data analysis. Several genes were highly up-regulated in patients with SARS, such as, the genes coding for Lactoferrin, S100A9 and Lipocalin 2. The real-time PCR method verified the results of the gene array analysis and showed that those genes that were up-regulated as determined by microarray analysis were also found to be comparatively up-regulated by real-time PCR analysis. Conclusions: This differential gene expression profiling of PBMCs from patients with SARS strongly suggests that the response of SARS affected patients seems to be mainly an innate inflammatory response, rather than a specific immune response against a viral infection, as we observed a complete lack of cytokine genes usually triggered during a viral infection. Our study shows for the first time how the immune system responds to the SARS infection, and opens new possibilities for designing new diagnostics and treatments for this new life-threatening disease.

  • FADD adaptor in cancer - FADD (Fas Associated protein with Death Domain) is a key adaptor molecule transmitting the death signal mediated by death receptors. In addition, this multiple functional protein is implicated in survival/proliferation and cell cycle progression. FADD functions are regulated via cellular sublocalization, protein phosphorylation, and inhibitory molecules. In the present review, we focus on the role of the FADD adaptor in cancer. Increasing evidence shows that defects in FADD protein expression are associated with tumor progression both in mice and humans. Better knowledge of the mechanisms leading to regulation of FADD functions will improve understanding of tumor growth and the immune escape mechanisms, and could open a new field for therapeutic interventions.

  • Farnesyltransferase Inhibitor Therapy in Acute Myelogenous Leukemia - Acute myelogenous leukemia (AML) remains a clinical -challenge with poor long-term survival. Low remission rates and high treatment-related mortality persist as major -obstacles, particularly in older patients. The design of novel agents based on the identification of genetic lesions and aberrant signaling pathways provides opportunity to improve the standard treatment paradigm of intensive cytotoxic -chemotherapy. Farnesyltransferase inhibitors (FTIs) show potential to fill this niche. The preclinical concept of farnesyltransferase blockade as a targeted therapy against oncogenic Ras has clearly evolved with the recognition that many -proteins involved signaling pathways in tumor cells undergo farnesylation. Phase I/II trials of FTI monotherapy in AML demonstrate encouraging responses and good tolerability. The FTI tipifarnib (R115777, Zarnestra; Johnson Johnson, Titusville, NJ) has advanced the furthest in clinical trials, with the most promising activity in previously untreated, high-risk AML patients. A major emphasis of current clinical studies has been to analyze potential candidate genes and signaling pathways modified by FTIs in order to identify mechanisms of response and resistance. Preclinical concepts related to the development of FTIs, the rationale for their use in AML, and efficacy and safety results from recent clinical trials are evaluated in this paper.

  • Farnesyltransferase Inhibitors in Myelodysplastic Syndrome - The farnesyltransferase inhibitors (FTIs) are in active clinical development in a variety of human malignancies. The most promising activity to date has been demonstrated in patients with hematological malignancies, in particular acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). In patients with MDS, two non-peptidomimetic agents, tipifarnib (Zarnestra, Johnson Johnson, New Brunswick, NJ) and lonafarnib (Sarasar, Schering-Plough, Kenilworth, NJ) have been the most extensively studied. In both phase I and phase II trials, tipifarnib has demonstrated significant efficacy with overall response rates of 30%, with complete remissions in about 15%. Dose-limiting side effects have been primarily myelosuppression, although fatigue, neurotoxicity, and occasional renal dysfunction have required dose reductions. Lonafarnib in patients with MDS has also resulted in clinical responses in approximately 30%, including significant improvements in platelet counts. Lonafarnib has been associated with primarily diarrhea and other gastro-intestinal toxicity, anorexia, and nausea, which has limited its efficacy. Clinical response correlation with documentation of inhibition of farnesyltransferase and/or evidence of decreased farnesylation of downstream protein targets has not been demonstrated with either agent. In addition, the presence of an activating Ras mutation has not predicted response to therapy with FTIs in MDS and AML. Despite this, significant clinical efficacy of the FTIs in MDS, on par with that of currently available chemotherapeutic agents, has been observed, leading to further development of this new class of drugs in MDS and AML.

  • Fetal Gender Determination and BclI Polymorphism Using Nucleated Erythrocytes in Maternal Blood -

    This study demonstrated determination of fetal gender from nucleated red blood cells (NRBCs) in maternal blood and attempted to apply prenatal diagnosis of hemophilia A using BclI DNA polymorphism. Venous blood was drawn from 20 pregnant women, and NRBCs were recovered by magnetic activated cell sorting and anti-GPA (glycophorin A) immunostaining. After microdissector isolation of the NRBCs, primer extension preamplification (PEP) and nested PCR of the amelogenin gene were performed to determine fetal gender. We also performed PEP and nested PCR of BclI polymorphism to verify the validity of prenatal diagnosis of hemophilia A. DNA amplification was achieved in 107 cells (51.9%) and fetal gender determined with 65.0% accuracy. Unfortunately, we could not verify the validity within the scope of this study. However, in a larger number of cases that are informative in BclI polymorphism, we will be able to identify patients affected by hemophilia A using fetal NRBCs in maternal blood. (J Histochem Cytochem 53:323–327, 2005)


  • Fiber Content and Myosin Heavy Chain Composition of Muscle Spindles in Aged Human Biceps Brachii -

    The present study investigated potential age-related changes in human muscle spindles with respect to the intrafusal fiber-type content and myosin heavy chain (MyHC) composition in biceps brachii muscle. The total number of intrafusal fibers per spindle decreased significantly with aging, due to a significant reduction in the number of nuclear chain fibers. Nuclear chain fibers in old spindles were short and some showed novel expression of MyHC -cardiac. The expression of MyHC -cardiac in bag1 and bag2 fibers was greatly decreased in the A region. The expression of slow MyHC was increased in nuclear bag1 fibers and that of fetal MyHC decreased in bag2 fibers whereas the patterns of distribution of the remaining MyHC isoforms were generally not affected by aging. We conclude that aging appears to have an important impact on muscle spindle composition. These changes in muscle spindle phenotype may reflect an age-related deterioration in sensory and motor innervation and are likely to have an impact in motor control in the elderly. (J Histochem Cytochem 53:445–454, 2005)


  • Fiber Content and Myosin Heavy Chain Composition of Muscle Spindles in Aged Human Biceps Brachii -

    The present study investigated potential age-related changes in human muscle spindles with respect to the intrafusal fiber-type content and myosin heavy chain (MyHC) composition in biceps brachii muscle. The total number of intrafusal fibers per spindle decreased significantly with aging, due to a significant reduction in the number of nuclear chain fibers. Nuclear chain fibers in old spindles were short and some showed novel expression of MyHC -cardiac. The expression of MyHC -cardiac in bag1 and bag2 fibers was greatly decreased in the A region. The expression of slow MyHC was increased in nuclear bag1 fibers and that of fetal MyHC decreased in bag2 fibers whereas the patterns of distribution of the remaining MyHC isoforms were generally not affected by aging. We conclude that aging appears to have an important impact on muscle spindle composition. These changes in muscle spindle phenotype may reflect an age-related deterioration in sensory and motor innervation and are likely to have an impact in motor control in the elderly. (J Histochem Cytochem 53:445–454, 2005)


  • Fiber Content and Myosin Heavy Chain Composition of Muscle Spindles in Aged Human Biceps Brachii -

    The present study investigated potential age-related changes in human muscle spindles with respect to the intrafusal fiber-type content and myosin heavy chain (MyHC) composition in biceps brachii muscle. The total number of intrafusal fibers per spindle decreased significantly with aging, due to a significant reduction in the number of nuclear chain fibers. Nuclear chain fibers in old spindles were short and some showed novel expression of MyHC -cardiac. The expression of MyHC -cardiac in bag1 and bag2 fibers was greatly decreased in the A region. The expression of slow MyHC was increased in nuclear bag1 fibers and that of fetal MyHC decreased in bag2 fibers whereas the patterns of distribution of the remaining MyHC isoforms were generally not affected by aging. We conclude that aging appears to have an important impact on muscle spindle composition. These changes in muscle spindle phenotype may reflect an age-related deterioration in sensory and motor innervation and are likely to have an impact in motor control in the elderly. (J Histochem Cytochem 53:445–454, 2005)


  • Fine needle aspiration biopsy diagnosis of metastatic neoplasms of the breast. A three-case report - Metastases to the breast are unusual lesions that make up approximately 2% of all malignant mammary neoplasms and may mimic both benign and malignant primary neoplasms from a clinical point of view, as well as in imaging studies. Arriving at a correct diagnosis is therefore essential in order to establish appropriate management. We present three cases of metastatic neoplasms diagnosed through fine needle aspiration biopsy and immunocytochemistry. The cytological diagnoses were: medulloblastoma in an 18-year-old woman, melanoma in a 26-year-old man, and an exceptional case of ovarian sarcoma originating from a granulosa cell tumor with metastases to both breasts. A metastatic disease should be considered in the differential diagnosis of a palpable mass in the breast, especially if there is a history of an extramammary malignant neoplasm. Fine needle aspiration biopsy is the method of choice for the management of these cases. Whenever possible the exam of the material obtained should be compared to the previous biopsy, which is usually enough to arrive at a correct diagnosis, thus preventing unnecessary surgical procedures.

  • Fine Needle Aspiration Biopsy of the Liver Algorithmic approach and current issues in the diagnosis of hepatocellular carcinoma - The role of fine needle aspiration biopsy (FNAB) in the evaluation of focal liver lesions has evolved. Guided FNAB is still useful to procure a tissue diagnosis if clinical, biochemical and radiologic findings are inconclusive. Major diagnostic issues include: (i) Distinction of benign hepatocellular nodular lesions from reactive hepatocytes, (ii) Distinction of well-differentiated hepatocellular carcinoma (WD-HCC) from benign hepatocellular nodular lesions, (iii) Distinction of poorly differentiated HCC from cholangiocarcinoma and metastatic carcinomas, (iv) Determination of histogenesis of malignant tumor, and (v) Determination of primary site of origin of malignant tumor. This review gives a general overview of hepatic FNAB; outlines an algorithmic approach to cytodiagnosis with emphasis on HCC, its variants and their mimics; and addresses current diagnostic issues. Close radiologic surveillance of high-risk cirrhotic patients has resulted in the increasing detection of smaller lesions with many subjected to biopsy for tissue characterization. The need for tissue confirmation in clinically obvious HCC is questioned due to risk of malignant seeding. When a biopsy is indicated, core needle biopsy is favored over FNAB. The inherent difficulty of distinguishing small/early HCC from benign hepatocellular nodular lesions has resulted in indeterminate reports. Changing concepts in the understanding of the biological behavior and morphologic evolution of HCC and its precursors; and the current lack of agreement on the morphologic criteria for distinguishing high-grade dysplastic lesions (with small cell change) from WD-HCC, have profound impact on nomenclature, cytohistologic interpretation and management. Optimization of hepatic FNAB to enhance the yield and accuracy of diagnoses requires close clinicopathologic correlation; combined cytohistologic approach; judicious use of ancillary tests; and skilled healthcare teams.KeywordsDiagnostic algorithm, fine needle aspiration biopsy, hepatocellular carcinoma, immunohistochemistry, liver

  • Fine-needle aspiration of the thyroid: an overview - Thyroid nodules (TN) are a common clinical problem. Fine-needle aspiration (FNA) of the thyroid now is practiced worldwide and proves to be the most economical and reliable diagnostic procedure to identify TNs that need surgical excision and TNs that can be managed conservatively. The key for the success of thyroid FNA consist of an adequate or representative cell sample and the expertise in thyroid cytology. The FNA cytologic manifestations of TNs may be classified into seven working cytodiagnostic groups consisting of a few heterogenous lesions each to facilitate the differential diagnosis. Application of diagnostic molecular techniques to aspirated thyroid cells proved to be useful in separating benign from malignant TNs in several cases of indeterminate lesions.

  • First results of chronic wasting disease (CWD) surveillance in the south-eastern part of Belgium. -
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    First results of chronic wasting disease (CWD) surveillance in the south-eastern part of Belgium.

    Vet Q. 2005 Sep;27(3):98-104

    Authors: Roels S, Saegerman C, De Bosschere H, Berkvens D, Gregoire F, Hoyoux A, Mousset B, Desmecht D, Vanopdenbosch E, Linden A

    Chronic wasting disease (CWD) has not been reported in Europe, whereas it is considered to be enzootic in free-ranging mule deer, Rocky mountain elk and white-tailed deer in the area of Colorado, Wyoming, and Nebraska, and new foci of CWD have been detected in other parts of the United States. However, no large-scale active epidemiosurveillance of European wild cervids has been installed in Europe. In accordance with the opinion of the European Scientific Steering Committee, a preliminary (active) surveillance scheme was installed, in order to improve the knowledge of the CWD status of the Belgian free-ranging cervids (roe deer and red deer). Spleen samples (n=866) of roe deer and red deer collected in the south-eastern part of Belgium, were examined for CWD using a enzyme-linked immunosorbent assay of Bio-Rad. Afterwards, the ELISA was systematically confirmed by immunohistochemistry using three antibodies, namely R524, 2G11 and 12F10. There were no indications on the occurrence of transmissible spongiform enncephalopathy (TSE) in any of the samples. A Bayesian framework was used for the estimation of the true prevalence of CWD in south-eastern part of Belgium that was estimated to have a median value of zero with a 95% percentile value of 0.00115.

    PMID: 16238109 [PubMed - in process]


  • First Systematic CGH-based Analyses of Ancient DNA Samples of Malformed Fetuses Preserved in the Meckel Anatomical Collection in Halle/Saale (Germany) -

    We present the first data on our comparative genomic hybridization (CGH)–based strategy for the analysis of ancient DNA (aDNA) samples extracted from fetuses preserved in the Meckel Anatomical Collection in Halle, Germany. The collection contains numerous differently fixed ancient samples of fetal malformations collected from the middle of the 18th to the early 19th century. The main objective of this study is to establish a "standard" aDNA extraction and amplification protocol as a prerequisite for successful CGH analyses to detect or exclude chromosomal imbalances possibly causative for the malformations described for the fetuses. (J Histochem Cytochem 53:381–384, 2005)


  • First-trimester NRBC Count in Maternal Circulation: Correlation with Doppler Ultrasound Studies -

    This study aimed to determine whether the number of nucleated red blood cells (NRBCs) in maternal circulation during the first trimester of pregnancy could identify pregnancies that will have an anomalous Doppler in the second trimester. A total of 85 blood samples were obtained at 11–14 weeks of gestation with mean uterine arterial perfusion index >1.6, as noted by Doppler ultrasonography. NRBCs were enriched by magnetic automated cell sorting using anti-CD71 and were stained with May/Grunwald/Giemsa. A total of 4.8 NRBCs (range 1–75) were identified in 68 cases. Follow-up scans at 22–24 weeks were available in 46 cases. In 39 women, blood flow in the uterine arteries normalized, whereas in seven, high resistance was noted. One woman in the high-resistance group developed preeclampsia (PET; four NRBCs) and another delivered an intrauterine growth restriction (IUGR) baby (75 NRBCs). The number of NRBCs in women whose Doppler indices later normalized and in those who continued to have increased impedance was similar. The study indicates that NRBC number in maternal circulation during the first trimester cannot be used to screen pregnancies at high risk for developing preeclampsia (PET)/IUGR. High-impedance blood flow in the uterine arteries in the first trimester may be due to an unfinished process of trophoblastic invasion, most likely to be completed successfully by 22–24 weeks. (J Histochem Cytochem 53:315–317, 2005)


  • First-trimester Screening: An Overview -

    An improvement in prenatal screening for chromosomal defects has been achieved by combining sonography and biochemical markers. Analyzing markers taken from maternal blood such as pregnancy-associated plasma protein A and free ßbeta;-human chorionic gonadotropin in combination with the ultrasound marker nuchal translucency provides detection rates of 90% for the most important chromosomal anomalies. In addition, nuchal translucency is a marker for severe heart defects. This report discusses the potential of new markers such as the nasal bone. (J Histochem Cytochem 53:281–283, 2005)


  • FISH Analysis of All Fetal Nucleated Cells in Maternal Whole Blood: Improved Specificity by the Use of Two Y-chromosome Probes -

    Current cytogenetic approaches in noninvasive prenatal diagnosis focus on fetal nucleated red blood cells in maternal blood. This practice may be too restrictive because a vast proportion of other fetal cells is ignored. Recent studies have indicated that fetal cells can be directly detected, without prior enrichment, in maternal blood samples by fluorescence in situ hybridization (FISH) analysis for chromosomes X and Y (XY-FISH). In our blinded analysis of 40 maternal blood samples, we therefore examined all fetal cells without any enrichment. Initial examinations using conventional XY-FISH indicated a low specificity of 69.4%, which could be improved to 89.5% by the use of two different Y-chromosome-specific probes (YY-FISH) with only a slight concomitant decrease in sensitivity (52.4% vs 42.9%). On average, 12–20 male fetal cells/ml of maternal blood were identified by XY- and YY-FISH, respectively. (J Histochem Cytochem 53:319–322, 2005)


  • Fluorescence In Situ Hybridization and Spectral Imaging Analysis of Human Oocytes and First Polar Bodies -

    We investigated the frequencies of abnormalities involving either chromosome 1, 16, 18, or 21 in failed-fertilized human oocytes. Although abnormalities involving chromosome 16 showed an age-dependent increase, results for the other chromosomes did not show statistically significant differences among the three age groups, <35 years, 35–39 years, and >39 years. The scoring of four chromosomes is likely to underestimate the true rate of aneuploid cells. Therefore, for a pilot study investigating a more-comprehensive analysis of oocytes and their corresponding first polar bodies, we developed a novel eight-probe chromosome enumeration scheme using fluorescence in situ hybridization and spectral imaging analysis. (J Histochem Cytochem 53:269–272, 2005)


  • Fluorescence in situ hybridization, comparative genomic hybridization, and other molecular biology techniques in the analysis of effusions. -
    Related Articles

    Fluorescence in situ hybridization, comparative genomic hybridization, and other molecular biology techniques in the analysis of effusions.

    Diagn Cytopathol. 2005 Oct 20;33(5):294-299

    Authors: Reis-Filho JS, de Landér Schmitt FC

    Over the last 20 yr, the introduction of immunocytochemistry as a diagnostic tool has dramatically revolutionized diagnostic pathology. With the introduction of molecular methods as part of the diagnostic armamentarium, the practicing pathologist is facing the new challenge of grasping novel concepts of the molecular cytogenetics era. Herein, we review the diagnostic contribution of ancillary molecular techniques, including fluorescent and chromogenic in situ hybridization, telomerase assays, loss of heterozygosity, comparative genomic hybridization (CGH), and microarray-based CGH, for the practicing cytopathologists and discuss how these techniques will help pathologists in decision-making. Diagn. Cytopathol. 2005;33:294-299. (c) 2005 Wiley-Liss, Inc.

    PMID: 16240394 [PubMed - as supplied by publisher]


  • Fluorescent two-color whole mount in situ hybridization in Platynereis dumerilii (Polychaeta, Annelida), an emerging marine molecular model for evolution and development. -
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    Fluorescent two-color whole mount in situ hybridization in Platynereis dumerilii (Polychaeta, Annelida), an emerging marine molecular model for evolution and development.

    Biotechniques. 2005 Oct;39(4):460, 462, 464

    Authors: Tessmar-Raible K, Steinmetz PR, Snyman H, Hassel M, Arendt D

    PMID: 16235555 [PubMed - in process]


  • FNAB cytology of extra-cranial metastasis of glioblastoma multiforme may resemble a lung primary: A diagnostic pitfall - Background: As extra-cranial metastasis of glioblastoma multiforme (GBM) is rare, it may create a diagnostic dilemma especially during interpretation of fine needle aspiration biopsy (FNAB) cytology. Case presentationWe present transbronchial FNAB findings in a 62-year-old smoker with lung mass clinically suspicious for a lung primary. The smears of transbronchial FNAB showed groups of cells with ill-defined cell margins and cytological features overlapping with poorly differentiated non-small cell carcinoma. The tumor cells demonstrated lack of immunoreactivity for cytokeratin, thyroid transcription factor-1, and usual neuroendocrine markers- synaptophysin and chromogranin in formalin-fixed cellblock sections. However, they were immunoreactive for the other neuroendocrine immunomarker, CD56, suggesting neural nature of the cells. Further scrutiny of clinical details revealed a history of GBM, 13 months status-post surgical excision with radiation therapy and systemic chemotherapy. The tumor recurred 7 months earlier and was debulked surgically and with intra-cranial chemotherapy. Additional evaluation of tumor cells for glial fibrillary acidic protein (GFAP) immunoreactivity with clinical details resulted in final interpretation of metastatic GBM. Conclusion: Lack of clinical history and immunophenotyping may lead to a diagnostic pitfall with possible misinterpretation of metastatic GBM as poorly differentiated non-small cell carcinoma of lung in a smoker. Key words: Glioblastoma multiforme, Fine needle aspiration biopsy cytology, FNA, lung tumor, GFAP

  • FNAC of Bacillus- Calmette- Guerin lymphadenitis masquerading as Langerhans cell histiocytosis. - Bacillus Calmette Guerin (BCG) lymphadenitis is a well known entity. Disseminated BCG infection usually presents as generalized lymphadenopathy, skin rash and hepatosplenomegaly and at times, can pose a diagnostic challenge to clinicians. There are only a few published studies on the cytological findings of BCG lymphadenitis. In this letter we report the fine needle aspiration cytology (FNAC) of BCG lymphadenitis clinically masquerading as Langerhans cell histiocytosis (LCH). FNA smears showed sheets of foamy macrophages and many polymorphs in a dirty necrotic background with many macrophages as well as polymorphs showing negatively stained rod like structures within their cytoplasm. Zeihl Neelson stain revealed that these cells were heavily loaded with acid fast bacilli (AFB). In the index case, AFB were also seen within the cytoplasm of polymorphs, which has not been documented earlier in the literature.

  • Follicular dendritic-like cells derived from human monocytes - Background: Follicular dendritic cells (FDCs) play a central role in controlling B-cell response maturation, isotype switching and the maintenance of B-cell memory. These functions are based on prolonged preservation of antigen and its presentation in its native form by FDCs. However, when entrapping entire pathogens, FDCs can turn into dangerous long-term reservoirs that may preserve viruses or prions in highly infectious form. Despite various efforts, the ontogeny of FDCs has remained elusive. They have been proposed to derive either from bone marrow stromal cells, myeloid cells or local mesenchymal precursors. Still, differentiating FDCs from their precursors in vitro may allow addressing many unsolved issues associated with the (patho-) biology of these important antigen-presenting cells. The aim of our study was to demonstrate that FDC-like cells can be deduced from monocytes, and to develop a protocol in order to quantitatively generate them in vitro. Results: Employing highly purified human monocytes as a starter population, low concentrations of Il-4 (25 U/ml) and GM-CSF (3 U/ml) in combination with Dexamethasone (Dex) (0.5 uM) in serum-free medium trigger the differentiation into FDC-like cells. After transient de-novo membrane expression of alkaline phosphatase (AP), such cells highly up-regulate surface expression of complement receptor I (CD35). Co-expression of CD68 confirms the monocytic origin of both, APpos and CD35pos cells. The common leukocyte antigen CD45 is strongly down-regulated. Successive stimulation with TNF-a up-regulates adhesion molecules ICAM-1 (CD54) and VCAM (CD106). Importantly, both, APpos as well as APneg FDC-like cells, heterotypically cluster with and emperipolese B cells and exhibit the FDC characteristic ability to entrap functionally preserved antigen for prolonged times. Identical characteristics are found in monocytes which were highly expanded in vitro by higher doses of GM-CSF (25 U/ml) in the absence of Dex and Il-4 before employing the above differentiation cocktail. Conclusions: In this work we provide evidence that FDC-like cells can be derived from monocytes in vitro. Monocyte-derived FDC-like cells quantitatively produced offer a broad utility covering basic research as well as clinical application.

  • Formation of nonculturable Escherichia coli in drinking water. -
    Related Articles

    Formation of nonculturable Escherichia coli in drinking water.

    J Appl Microbiol. 2005 Nov;99(5):1090-1098

    Authors: Bjergbæk LA, Roslev P

    Aims: To examine whether incubation of Escherichia coli in nondisinfected drinking water result in development of cells that are not detectable using standard procedures but maintain a potential for metabolic activity and cell division. Methods and Results: Survival and detectability of four different E. coli strains were studied using drinking water microcosms and samples from contaminated drinking water wells. Recovery of E. coli was compared using different cultivation-dependent methods, fluorescence in situ hybridization (FISH) using specific oligonucleotide probes, direct viable counts (DVC), and by enumeration of gfp-tagged E. coli (green fluorescent protein, GFP). Two levels of stress responses were observed after incubation of E. coli in nondisinfected drinking water: (i) the presence of cells that were not detected using standard cultivation methods but could be cultivated after gentle resuscitation on nonselective nutrient-rich media, and (ii) the presence of cells that responded to nutrient addition but could only be detected by cultivation-independent methods (DVC, FISH and GFP). Collectively, the experiments demonstrated that incubation for 20-60 days in nondisinfected drinking water resulted in detection of only 0.7-5% of the initial E. coli population using standard cultivation methods, whereas 1-20% could be resuscitated to a culturable state, and 17-49% could be clearly detected using cultivation-independent methods. Conclusions: Resuscitation of stressed E. coli on nonselective nutrient-rich media increased cell counts in drinking water using both traditional (CFU), and cultivation-independent methods (DVC, FISH and GFP). The cultivation-independent methods resulted in detection of 10-20 times more E. coli than the traditional methods. The results indicate that a subpopulation of substrate-responsive but apparent nonculturable E. coli may develop in drinking water during long-term starvation survival. Significance and Impact of the Study: The existence of substrate-responsive but nonculturable cells should be considered when evaluating the survival potential of E. coli in nondisinfected drinking water.

    PMID: 16238739 [PubMed - as supplied by publisher]


  • Fully automated synthesis of (phospho)peptide arrays in microtiter plate wells provides efficient access to protein tyrosine kinase characterization - Background: Synthetic peptides have played a useful role in studies of protein kinase substrates and interaction domains. Synthetic peptide arrays and libraries, in particular, have accelerated the process. Several factors have hindered or limited the applicability of various techniques, such as the need for deconvolution of combinatorial libraries, the inability or impracticality of achieving full automation using two-dimensional or pin solid phases, the lack of convenient interfacing with standard analytical platforms, or the difficulty of compartmentalization of a planar surface when contact between assay components needs to be avoided. This paper describes a process for synthesis of peptides and phosphopeptides on microtiter plate wells that overcomes previous limitations and demonstrates utility in determination of the epitope of an autophosphorylation site phospho-motif antibody and utility in substrate utilization assays of the protein tyrosine kinase, p60c-src. Results: The overall reproducibility of phospho-peptide synthesis and multiplexed EGF receptor (EGFR) autophosphorylation site (pY1173) antibody ELISA (9H2) was within 5.5 to 8.0%. Mass spectrometric analyses of the released (phospho)peptides showed homogeneous peaks of the expected molecular weights. An overlapping peptide array of the complete EGFR cytoplasmic sequence revealed a high redundancy of 9H2 reactive sites. The eight reactive phospopeptides were structurally related and interestingly, the most conserved antibody reactive peptide motif coincided with a subset of other known EGFR autophosphorylation and SH2 binding motifs and an EGFR optimal substrate motif. Finally, peptides based on known substrate specificities of c-src and related enzymes were synthesized in microtiter plate array format and were phosphorylated by c-Src with the predicted specificities. The level of phosphorylation was proportional to c-Src concentration with sensitivities below 0.1 Units of enzyme. Conclusions: The ability of this method to interface with various robotics and instrumentation is highly flexible since the microtiter plate is an industry standard. It is highly scalable by increasing the surface area within the well or the number of wells and does not require specialized robotics. The microtiter plate array system is well suited to the study of protein kinase substrates, antigens, binding molecules, and inhibitors since these all can be quantitatively studied at a single uniform, reproducible interface.

  • Functional and structural characteristics of anticancer peptide Pep27 analogues - Background: A secreted peptide Pep27 initiates the cell death program in S. pneumoniae through signal transduction. This study was undertaken to evaluate the relation between the structure and cytotoxic activity of Pep27 and its analogues on cancer cells. Results: Pep27anal2 characterized substituting (2R->W), (4E->W), (11S->W) and (13Q->W) in native Pep27, exhibited greater hydrophobicity and anticancer activity than natural Pep27 and other analogues. The IC50 values of Pep27anal2 were approximately 10 - 30 muM in a number of cell lines (AML-2, HL-60, Jurkat, MCF-7 and SNU-601). Confocal microscopy showed that Pep27anal2-FITC was localized in the plasma membrane, and then moving from the membrane to subcellular compartments with the initiation of membrane blebbing. Flow cytometric analysis using propidium iodide and Annexin V also revealed that Pep27anal2 induced apoptosis with minor membrane damage. Electron microscopy revealed that Pep27 induced apoptosis in Jurkat cells. The anticancer activity of Pep27anal2 was neither abrogated by pan-caspase inhibitor (Z-VAD-fmk) nor related to cytochrome c release from mitochondria. The 3D solution structures of these two Pep27 peptides revealed that both form a random coil conformation in water; however, they adopted stable -helical conformations in solutions. Conclusion: The results indicate that Pep27anal2 can penetrate the plasma membrane, and then induce apoptosis in both caspase- and cytochrome c-independent manner. The hydrophobicity of Pep27anal2 appears to play an important role in membrane permeabilization and/or anticancer properties. The structure-functional relationships of these peptides are also discussed. It is proposed that Pep27 anal2 is a potential candidate for anticancer therapeutic agents.KeywordsPeptide Pep27, Pep27 analogues, S. pneumoniae, apoptosis, anticancer activity, 3D structure

  • Functional Dissociation of the Basolateral Transcytotic Compartment from the Apical Phago-lysosomal Compartment in Human Osteoclasts -

    Tartrate-resistant acid phosphatase (TRAP) is essential for elimination of Staphylococcus aureus, the main infectious agent responsible for osteomyelitis. This in vitro study investigated uptake and processing of fluorescence-labeled S. aureus by human osteoclasts and dendritic cells. The cells were stained for TRAP and the acidic compartment using a fluorescence-based protocol. In dendritic cells, TRAP and bacteria were colocalized. In osteoclasts, there was no colocalization of bacteria, TRAP, or the acidic compartment, indicating that there are three distinct vesicular compartments: the apical phago-lysosomal compartment, the basal secretory compartment, and the basolateral transcytotic compartment. Dissociation of the TRAP-containing transcytotic vesicles from the apical phago-lysosomal compartment may restrain osteoclasts from eliminating S. aureus.

    (J Histochem Cytochem 53:665–670, 2005)


  • Functional Dissociation of the Basolateral Transcytotic Compartment from the Apical Phago-lysosomal Compartment in Human Osteoclasts -

    Tartrate-resistant acid phosphatase (TRAP) is essential for elimination of Staphylococcus aureus, the main infectious agent responsible for osteomyelitis. This in vitro study investigated uptake and processing of fluorescence-labeled S. aureus by human osteoclasts and dendritic cells. The cells were stained for TRAP and the acidic compartment using a fluorescence-based protocol. In dendritic cells, TRAP and bacteria were colocalized. In osteoclasts, there was no colocalization of bacteria, TRAP, or the acidic compartment, indicating that there are three distinct vesicular compartments: the apical phago-lysosomal compartment, the basal secretory compartment, and the basolateral transcytotic compartment. Dissociation of the TRAP-containing transcytotic vesicles from the apical phago-lysosomal compartment may restrain osteoclasts from eliminating S. aureus.

    (J Histochem Cytochem 53:665–670, 2005)


  • Functional Dissociation of the Basolateral Transcytotic Compartment from the Apical Phago-lysosomal Compartment in Human Osteoclasts -

    Tartrate-resistant acid phosphatase (TRAP) is essential for elimination of Staphylococcus aureus, the main infectious agent responsible for osteomyelitis. This in vitro study investigated uptake and processing of fluorescence-labeled S. aureus by human osteoclasts and dendritic cells. The cells were stained for TRAP and the acidic compartment using a fluorescence-based protocol. In dendritic cells, TRAP and bacteria were colocalized. In osteoclasts, there was no colocalization of bacteria, TRAP, or the acidic compartment, indicating that there are three distinct vesicular compartments: the apical phago-lysosomal compartment, the basal secretory compartment, and the basolateral transcytotic compartment. Dissociation of the TRAP-containing transcytotic vesicles from the apical phago-lysosomal compartment may restrain osteoclasts from eliminating S. aureus.

    (J Histochem Cytochem 53:665–670, 2005)


  • Functional interaction between mouse erbB3 and wild-type rat c-neu in transgenic mouse mammary tumor cells - IntroductionCo-expression of several receptor tyrosine kinases (RTKs), including erbB2 and erbB3, is frequently identified in breast cancers. A member of the RTK family, the kinase-deficient erbB3 can activate downstream signaling via heterodimer formation with erbB2. We studied the expression of RTK receptors in mammary tumors from the wild-type (wt) rat c-neu transgenic model. We hypothesized that physical and functional interactions between the wt rat neu/ErbB2 transgene and mouse ErbB3-encoded proteins could occur, activating downstream signaling and promoting mammary oncogenesis. Methods: Immunohistochemical and Western blot analyses were performed to study the expression of rat c-neu/ErbB2 and mouse erbB3 in mammary tumors and tumor-derived cell lines from the wt rat c-neu transgenic mice. Co-immunoprecipitation methods were employed to quantitate heterodimerization between the transgene-encoded protein erbB2 and the endogenous mouse erbB3. Tumor cell growth in response to growth factors, such as Heregulin (HRG), epidermal growth factor (EGF), or insulin-like growth factor-1 (IGF-1), was also studied. Post-HRG stimulation, activation of the RTK downstream signaling was determined by Western blot analyses using antibodies against phosphorylated Akt and mitogen-activated protein kinase (MAPK), respectively. Specific inhibitors were then used with cell proliferation assays to study the phosphoinositide-3 kinase (PI-3K)/Akt and MAPK kinase (MEK)/MAPK pathways as possible mechanisms of HRG-induced tumor cell proliferation. Results: Mammary tumors and tumor-derived cell lines frequently exhibited elevated co-expression of erbB2 and erbB3. The transgene-encoded protein erbB2 formed a stable heterodimer complex with endogenous mouse erbB3. HRG stimulation promoted physical and functional erbB2/erbB3 interactions and tumor cell growth, whereas no response to EGF or IGF-1 was observed. HRG treatment activated both the Akt and MAPK pathways in a dose- and time-dependent manner. Both the PI-3K inhibitor LY 294002 and MEK inhibitor PD 98059 significantly decreased the stimulatory effect of HRG on tumor cell proliferation. Conclusion: The co-expression of wt rat neu/ErbB2 transgene and mouse ErbB3, with physical and functional interactions between these two species of RTK receptors, was demonstrated. These data strongly suggest a role for erbB3 in c-neu (ErbB2)-associated mammary tumorigenesis, as has been reported in human breast cancers.

  • GABAAreceptor gamma2 subunit knockdown mice have enhanced anxiety-like behavior but unaltered hypnotic response to benzodiazepines - Background: Gamma-aminobutyric acid type A receptors (GABAA-Rs) are the major inhibitory receptors in the mammalian brain and are modulated by a number of sedative/hypnotic drugs including benzodiazepines and anesthetics. The significance of specific GABAA-Rs subunits with respect to behavior and in vivo drug responses is incompletely understood. The gamma2 subunit is highly expressed throughout the brain. Global gamma2 knockout mice are insensitive to the hypnotic effects of diazepam and die perinatally. Heterozygous gamma2 global knockout mice are viable and have increased anxiety-like behaviors. To further investigate the role of the gamma2 subunit in behavior and whole animal drug action, we used gene targeting to create a novel mouse line with attenuated gamma2 expression, i.e., gamma2 knockdown mice. Results: Knockdown mice were created by inserting a neomycin resistance cassette into intron 8 of the gamma2 gene. Knockdown mice, on average, showed a 65% reduction of gamma2 subunit mRNA compared to controls; however gamma2 gene expression was highly variable in these mice, ranging from 10-95% of normal. Immunohistochemical studies demonstrated that gamma2 protein levels were also variably reduced. Pharmacological studies using autoradiography on frozen brain sections demonstrated that binding of the benzodiazepine site ligand Ro15-4513 was decreased in mutant mice compared to controls. Behaviorally, knockdown mice displayed enhanced anxiety-like behaviors on the elevated plus maze and forced novelty exploration tests. Surprisingly, mutant mice had an unaltered response to hypnotic doses of the benzodiazepine site ligands diazepam, midazolam and zolpidem as well as ethanol and pentobarbital. Lastly, we demonstrated that the gamma2 knockdown mouse line can be used to create gamma2 global knockout mice by crossing to a general deleter cre-expressing mouse line. Conclusions: We conclude that: 1) insertion of a neomycin resistance gene into intron 8 of the gamma2 gene variably reduced the amount of gamma2, and that 2) attenuated expression of gamma2 increased anxiety-like behaviors but did not lead to differences in the hypnotic response to benzodiazepine site ligands. This suggests that reduced synaptic inhibition can lead to a phenotype of increased anxiety-like behavior. In contrast, normal drug effects can be maintained despite a dramatic reduction in GABAA-R targets.

  • Galanin-mediated anxiolytic effect in rat central amygdala is not a result of corelease from noradrenergic terminals. -
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    Galanin-mediated anxiolytic effect in rat central amygdala is not a result of corelease from noradrenergic terminals.

    Synapse. 2005 Oct 19;59(1):27-40

    Authors: Barrera G, Hernandez A, Poulin JF, Laforest S, Drolet G, Morilak DA

    Galanin is colocalized extensively with norepinephrine in brain. Although this suggests possible activity-dependent neurotransmitter interactions, the functional significance of such colocalization remains elusive. Previously, we showed that enhancing stress-activation of the noradrenergic system by yohimbine pretreatment released galanin in central amygdala, attenuating the anxiety-like behavioral response to stress on the elevated plus-maze. The present study was conducted to determine, in this context, whether galanin was indeed coreleased from noradrenergic terminals, or instead from another galanin afferent or local stress-responsive galanin neurons in the amygdala. In experiment 1, galanin-mediated anxiolytic effects on the plus-maze following yohimbine + stress were unaltered by lesioning the noradrenergic innervation of central amygdala. In experiment 2, combining immunohistochemistry and in situ hybridization, galanin neurons specifically activated by yohimbine + stress treatment were found only in the locus coeruleus and intraamygdalar bed nucleus of the stria terminalis, adjacent to central amygdala. In experiment 3, retrograde tracing combined with in situ hybridization revealed few if any galanin cells projecting to central amygdala in locus coeruleus or nucleus tractus solitarius, sources of noradrenergic innervation. Indeed, few retrogradely-labeled galanin neurons were observed anywhere in the brain, including a small number in the intraamygdalar bed nucleus. Together, these results suggest that stress following yohimbine may have induced galanin release from an afferent to central amygdala originating in the bed nucleus, or from local neurons in the intraamygdalar bed nucleus, but that anxiolytic effects exerted by galanin in this context of elevated noradrenergic activity were not the result of corelease from noradrenergic terminals innervating central amygdala. Synapse 59:27-40, 2006. (c) 2005 Wiley-Liss, Inc.

    PMID: 16237681 [PubMed - as supplied by publisher]


  • Galanin-mediated anxiolytic effect in rat central amygdala is not a result of corelease from noradrenergic terminals. -
    Related Articles

    Galanin-mediated anxiolytic effect in rat central amygdala is not a result of corelease from noradrenergic terminals.

    Synapse. 2005 Oct 19;59(1):27-40

    Authors: Barrera G, Hernandez A, Poulin JF, Laforest S, Drolet G, Morilak DA

    Galanin is colocalized extensively with norepinephrine in brain. Although this suggests possible activity-dependent neurotransmitter interactions, the functional significance of such colocalization remains elusive. Previously, we showed that enhancing stress-activation of the noradrenergic system by yohimbine pretreatment released galanin in central amygdala, attenuating the anxiety-like behavioral response to stress on the elevated plus-maze. The present study was conducted to determine, in this context, whether galanin was indeed coreleased from noradrenergic terminals, or instead from another galanin afferent or local stress-responsive galanin neurons in the amygdala. In experiment 1, galanin-mediated anxiolytic effects on the plus-maze following yohimbine + stress were unaltered by lesioning the noradrenergic innervation of central amygdala. In experiment 2, combining immunohistochemistry and in situ hybridization, galanin neurons specifically activated by yohimbine + stress treatment were found only in the locus coeruleus and intraamygdalar bed nucleus of the stria terminalis, adjacent to central amygdala. In experiment 3, retrograde tracing combined with in situ hybridization revealed few if any galanin cells projecting to central amygdala in locus coeruleus or nucleus tractus solitarius, sources of noradrenergic innervation. Indeed, few retrogradely-labeled galanin neurons were observed anywhere in the brain, including a small number in the intraamygdalar bed nucleus. Together, these results suggest that stress following yohimbine may have induced galanin release from an afferent to central amygdala originating in the bed nucleus, or from local neurons in the intraamygdalar bed nucleus, but that anxiolytic effects exerted by galanin in this context of elevated noradrenergic activity were not the result of corelease from noradrenergic terminals innervating central amygdala. Synapse 59:27-40, 2006. (c) 2005 Wiley-Liss, Inc.

    PMID: 16237681 [PubMed - as supplied by publisher]


  • Gastrointestinal [beta]2microglobulin amyloidosis in hemodialysis patients: biochemical analysis of amyloid proteins in small formalin-fixed paraffin-embedded tissue specimens - Batia Kaplan, Brian M Martin, Alejandro Livoff, Dimitri Yeremenko, Avi Livneh & Hector I Cohen

  • Gender dimorphism in differential peripheral blood leukocyte counts in mice using cardiac, tail, foot, and saphenous vein puncture methods - Background: In many animal models that investigate the pathology of various diseases, there is a need to monitor leukocyte counts and differentials. However, various researchers use a range of different techniques in male and female laboratory animals to collect such blood variable information. These studies are then compared to one another without consideration of the possibility that different bleeding sites or techniques as well as gender may produce varying results. In light of this, the peripheral blood leukocyte counts and differentials of C57BL/6 male and female mice were determined using four blood-sampling techniques: cardiac, tail, foot, and saphenous vein punctures. Methods: Blood smears were prepared and stained with Wright-stain for differential cell analysis. The total number of peripheral blood leukocytes was determined with the aid of a hemocytometer. Applying ANOVA and Student t-test analysis made comparisons between groups. Results: The total leukocyte counts obtained using the cardiac puncture method were significantly lower as compared to the other three blood sources; saphenous, tail and foot. There were no significant differences between leukocyte counts of blood samples collected from the tail, saphenous, and foot. Additionally, no significant differences were observed in total leukocyte counts between male and female mice. Differential analysis showed lymphocytes as the predominant cell type present in the peripheral blood of both male and female mice, comprising 75–90% of the total leukocytes. While no significant differences were observed between male and female differential counts of blood collected from saphenous and tail veins, a significant difference in differential counts of blood obtained via cardiac puncture was observed between the male and female groups, suggesting the role of sex hormones. Further, of the four methods, cardiac puncture appeared to be the fastest and more reliable technique, yielding the maximum blood volume with the least amount of stress being exerted on the sampling site. Conclusions: This information suggests that in studies concerning leukocyte counts and differentials, the animal gender and the sampling site of blood collection should be kept consistent as to avoid introducing any misleading experimental variation, and that cardiac puncture is the best method of blood collection in mice.

  • Gene deletion of P-Selectin and ICAM-1 does not inhibit neutrophil infiltration into peritoneal cavity following cecal ligation-puncture - Background: Neutrophil infiltration is one of the critical cellular components of an inflammatory response during peritonitis. The adhesion molecules, P-selectin and intercellular adhesion molecule (ICAM)-1, mediate neutrophil-endothelial cell interactions and the subsequent neutrophil transendothelial migration during the inflammatory response. Despite very strong preclinical data, recent clinical trials failed to show a protective effect of anti-adhesion therapy, suggesting that the length of injury might be a critical factor in neutrophil infiltration. Therefore, the objective of this study was to determine the role of P-selectin and ICAM-1 in neutrophil infiltration into the peritoneal cavity during early and late phases of peritonitis. Methods: Peritonitis was induced in both male wild-type and P-selectin/ICAM-1 double deficient (P/I null) mice by cecal ligation-puncture (CLP). Peripheral blood and peritoneal lavage were collected at 6 and 24 hours after CLP. The total leukocyte and neutrophil contents were determined, and neutrophils were identified with the aid of in situ immunohistochemical staining. Comparisons between groups were made by applying ANOVA and student t-test analysis. Results: CLP induced a severe inflammatory response associated with a significant leukopenia in both wild-type and P/I null mice. Additionally, CLP caused a significant neutrophil infiltration into the peritoneal cavity that was detected in both groups of mice. However, neutrophil infiltration in the P/I null mice at 6 hours of CLP was significantly lower than the corresponding wild-type mice, which reached a similar magnitude at 24 hours of CLP. In contrast, in peritonitis induced by intraperitoneal inoculation of 2% glycogen, no significant difference in neutrophil infiltration was observed between the P/I null and wild-type mice at 6 hours of peritonitis. Conclusions: The data suggest that alternative adhesion pathway(s) independent of P-selectin and ICAM-1 can participate in neutrophil migration during peritonitis and that the mode of stimuli and duration of the injury modulate the neutrophil infiltration.

  • Gene expression in human keloids is altered from dermal to chondrocytic and osteogenic lineage. -
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    Gene expression in human keloids is altered from dermal to chondrocytic and osteogenic lineage.

    Genes Cells. 2005 Nov;10(11):1081-91

    Authors: Naitoh M, Kubota H, Ikeda M, Tanaka T, Shirane H, Suzuki S, Nagata K

    Keloids are a dermal fibrotic disease whose etiology remains totally unknown and for which there is no successful treatment. Here, we employed cDNA microarray analysis to examine gene expression in keloid lesions and control skin. We found that 32 genes among the 9000 tested were strongly up-regulated in keloid lesions, of which 21 were confirmed by Northern blotting. These included at least seven chondrocyte/osteoblast marker genes, and RT-PCR analysis revealed that transcription factors specific for these genes, SOX9 and CBFA1, were induced. Immunostaining and in situ hybridization further supported that these markers are expressed in keloid lesions. Intriguingly, scleraxis, a transcription factor known as a marker of tendons and ligaments, was also induced in keloid fibroblasts. We propose that reprogramming of gene expression or disordered differentiation from a dermal pattern to that of a chondrocytic/osteogenic lineage, probably closer to that of tendon/ligament lineage, may be involved in the etiology of keloids.

    PMID: 16236136 [PubMed - in process]


  • Gene expression profiling of potential peroxisome proliferator-activated receptor (PPAR) target genes in human hepatoblastoma cell lines inducibly expressing PPAR isoform - Background: Peroxisome proliferator-activated receptors (PPARs) are ligand-activated transcription factors and commonly play an important role in the regulation of lipid homeostasis. To identify human PPARs-responsive genes, we established tetracycline-regulated human hepatoblastoma cell lines that can be induced to express each human PPAR and investigated the gene expression profiles of these cells. Results: The expression of each introduced PPAR gene was investigated using the various concentrations of doxycycline in the culture media. We found that the expression of each PPAR subtype was tightly controlled by the concentration of doxycycline in these established cell lines. DNA microarray analyses using these cell lines were performed with or without adding each subtype ligand and provided much important information on the PPAR target genes involved in lipid metabolism, transport, storage and other activities. Interestingly, it was noted that while ligand-activated PPAR delta induced target gene expression, unliganded PPAR delta repressed these genes. The real-time RT-PCR was used to verify the altered expression of selected genes by PPARs and we found that these genes were induced to express in the same pattern as detected in the microarray analyses. Furthermore, we analysed the 5'-flanking region of the human adipose differentiation-related protein (adrp) gene that responded to all subtypes of PPARs. From the detailed analyses by reporter assays, the EMSAs, and ChIP assays, we determined the functional PPRE of the human adrp gene. Conclusions: The results suggest that these cell lines are important tools used to identify the human PPARs-responsive genes.

  • Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts - IntroductionAdjuvant breast cancer therapy significantly improves survival, but overtreatment and undertreatment are major problems. Breast cancer expression profiling has so far mainly been used to identify women with a poor prognosis as candidates for adjuvant therapy but without demonstrated value for therapy prediction. Methods: We obtained the gene expression profiles of 159 population-derived breast cancer patients, and used hierarchical clustering to identify the signature associated with prognosis and impact of adjuvant therapies, defined as distant metastasis or death within 5 years. Independent datasets of 76 treated population-derived Swedish patients, 135 untreated population-derived Swedish patients and 78 Dutch patients were used for validation. The inclusion and exclusion criteria for the studies of population-derived Swedish patients were defined. Results: Among the 159 patients, a subset of 64 genes was found to give an optimal separation of patients with good and poor outcomes. Hierarchical clustering revealed three subgroups: patients who did well with therapy, patients who did well without therapy, and patients that failed to benefit from given therapy. The expression profile gave significantly better prognostication (odds ratio, 4.19; P = 0.007) (breast cancer end-points odds ratio, 10.64) compared with the Elston–Ellis histological grading (odds ratio of grade 2 vs 1 and grade 3 vs 1, 2.81 and 3.32 respectively; P = 0.24 and 0.16), tumor stage (odds ratio of stage 2 vs 1 and stage 3 vs 1, 1.11 and 1.28; P = 0.83 and 0.68) and age (odds ratio, 0.11; P = 0.55). The risk groups were consistent and validated in the independent Swedish and Dutch data sets used with 211 and 78 patients, respectively. Conclusion: We have identified discriminatory gene expression signatures working both on untreated and systematically treated primary breast cancer patients with the potential to spare them from adjuvant therapy.

  • Gene Therapy for Lympho-hematopoietic Disorders - Inherited lympho-hematopoietic disorders are considered to be some of the most amenable targets for development of gene therapy because of their defined molecular biology and pathophysiology and the potential for corrected cells to exhibit profound growth and survival advantages. Recently, several clinical studies have shown that conventional gene transfer technology can produce major beneficial therapeutic effects.

  • Generation of competent bone marrow-derived antigen presenting cells from the deer mouse (Peromyscus maniculatus) - Background: Human infections with Sin Nombre virus (SNV) and related New World hantaviruses often lead to hantavirus cardiopulmonary syndrome (HCPS), a sometimes fatal illness. Lungs of patients who die from HCPS exhibit cytokine-producing mononuclear infiltrates and pronounced pulmonary inflammation. Deer mice (Peromyscus maniculatus) are the principal natural hosts of SNV, in which the virus establishes life-long persistence without conspicuous pathology. Little is known about the mechanisms SNV employs to evade the immune response of deer mice, and experimental examination of this question has been difficult because of a lack of methodologies for examining such responses during infection. One such deficiency is our inability to characterize T cell responses because susceptible syngeneic deer mice are not available. Results: To solve this problem, we have developed an in vitro method of expanding and generating competent antigen presenting cells (APC) from deer mouse bone marrow using commercially-available house mouse (Mus musculus) granulocyte-macrophage colony stimulating factor. These cells are capable of processing and presenting soluble protein to antigen-specific autologous helper T cells in vitro. Inclusion of antigen-specific deer mouse antibody augments T cell stimulation, presumably through Fc receptor-mediated endocytosis. Conclusions: The use of these APC has allowed us to dramatically expand deer mouse helper T cells in culture and should permit extensive characterization of T cell epitopes. Considering the evolutionary divergence between deer mice and house mice, it is probable that this method will be useful to other investigators using unconventional models of rodent-borne diseases.

  • Genes involved in Drosophilaglutamate receptor expression and localization - Background: A clear picture of the mechanisms controlling glutamate receptor expression, localization, and stability remains elusive, possibly due to an incomplete understanding of the proteins involved. We screened transposon mutants generated by the ongoing Drosophila Gene Disruption Project in an effort to identify the different types of genes required for glutamate receptor cluster development. Results: To enrich for non-silent insertions with severe disruptions in glutamate receptor clustering, we identified and focused on homozygous lethal mutants in a collection of 2185 BG and KG transposon mutants generated by the BDGP Gene Disruption Project. 202 lethal mutant lines were individually dissected to expose glutamatergic neuromuscular junctions, stained using antibodies that recognize neuronal membrane and the glutamate receptor subunit GluRIIA, and viewed using laser-scanning confocal microscopy. We identified 57 mutants with qualitative differences in GluRIIA expression and/or localization. 84% of mutants showed loss of receptors and/or clusters; 16% of mutants showed an increase in receptors. Insertion loci encode a variety of protein types, including cytoskeleton proteins and regulators, kinases, phosphatases, ubiquitin ligases, mucins, cell adhesion proteins, transporters, proteins controlling gene expression and protein translation, and proteins of unknown/novel function. Expression pattern analyses and complementation tests, however, suggest that any single mutant - even if a mutant gene is uniquely tagged -- must be interpreted with caution until the mutation is validated genetically and phenotypically. Conclusions: Our study identified 57 transposon mutants with qualitative differences in glutamate receptor expression and localization. Despite transposon tagging of every insertion locus, extensive validation is needed before one can have confidence in the role of any individual gene. Alternatively, one can focus on the types of genes identified, rather than the identities of individual genes. This genomic approach, which circumvents many technical caveats in favor of a wider perspective, suggests that glutamate receptor cluster formation involves many cellular processes, including: 1) cell adhesion and signaling, 2) extensive and relatively specific regulation of gene expression and RNA, 3) the actin and microtubule cytoskeletons, and 4) many novel/unexplored processes, such as those involving mucin/polycystin-like proteins and proteins of unknown function.

  • Genetic Modification of Hematopoietic Cells Using Retroviral and Lentiviral Vectors: Safety Considerations for Vector Design and Delivery Into Target Cells - The recent development of leukemia in three patients following retroviral vector gene transfer in hematopoietic stem cells, resulting in the death of one patient, has raised safety concerns for the use of integrating gene transfer vectors for human gene therapy. This review discusses these serious adverse events from the perspective of whether restrictions on vector design and vector-modified target cells are warranted at this time. A case is made against presently establishing specific restrictions for vector design and transduced cells; rather, their safety should be ascertained by empiric evaluation in appropriate preclinical models on a case-by-case basis. Such preclinical data, coupled with proper informed patient consent and a risk-benefit ratio analysis, provide the best available prospective evaluation of gene transfer vectors prior to their translation into the clinic.

  • Genetic polymorphisms in human SULT1A1 and UGT1A1 genes associate with breast tumor characteristics: a case-series study - IntroductionEstrogens are important in breast cancer development. SULT1A1 and UGT1A1 catalyze estrogen metabolism and are polymorphic. The SULT1A1*2 protein exhibits low activity, and a TA repeat within the UGT1A1 promoter alters the level of expression of the protein. We hypothesized that the SULT1A1*2 allozyme has decreased capacity to sulfate estrogens, that the SULT1A1*2 allele conferred increased capacity of cells to proliferate in response to estrogens, and that individuals with the variant SULT1A1 and UGT1A1 genotypes exhibited different breast tumor characteristics. Methods: The capacity for SULT1A1*2 to sulfate 17β-estradiol and the capacity for cells expressing SULT1A1*1 or SULT1A1*2 to proliferate in response to 17β-estradiol was evaluated. A case-series study was performed in a total of 210 women with incident breast cancer, including 177 Caucasians, 25 African-Americans and eight women of other ethnic background. The SULT1A1 and UGT1A1 genotypes were determined and a logistic regression model was used to analyze genotype–phenotype associations. Results: We determined that the SULT1A1*1/*1 high-activity genotype was associated with tumor size ≤2 cm (odds ratio = 2.63, 95% confidence interval = 1.25–5.56, P = 0.02). Individuals with low-activity UGT1A1 genotypes (UGT1A1*28/*28 or UGT1A1*28/*34) were more likely to have an age at diagnosis ≥60 years (odds ratio = 3.70, 95% confidence interval = 1.33–10.00, P = 0.01). Individuals with both SULT1A1 and UGT1A1 high-activity genotypes had low tumor grade (odds ratio = 2.56, 95% confidence interval = 1.04–6.25, P = 0.05). Upon stratification by estrogen receptor status, significant associations were observed predominantly in estrogen receptor-negative tumors. Conclusion: The data suggest that genetic variation in SULT1A1 and UGT1A1 may influence breast cancer characteristics and might be important for breast cancer prognosis.

  • Genetic polymorphisms in the matrix metalloproteinase 12 gene (MMP12) and breast cancer risk and survival: the Shanghai Breast Cancer Study - IntroductionMatrix metalloproteinase 12 (MMP12) is a proteolytic enzyme responsible for cleavage of plasminogen to angiotensin, which has an angiostatic effect. Using data from a population-based case–control study conducted among Chinese women in Shanghai, we evaluated the association of breast cancer risk and survival with two common polymorphisms in the MMP12 gene: A-82G in the promoter region and A1082G in exon, resulting in an amino acid change of asparagine to serine. Methods: Included in the study were 1,129 cases and 1,229 age-frequency-matched population controls. Breast cancer patients were followed up to determine the intervals of overall survival and disease-free survival. Results: The frequencies of the G allele in the A-82G and A1082G polymorphism among controls were 0.029 and 0.107, respectively. There were no associations between MMP12 polymorphisms and breast cancer risk. Patients with the AG or GG genotype of the A1082G polymorphism showed poorer overall survival (though the difference was not statistically significant) than patients with the AA genotype (hazard ratio 1.36, 95% CI 0.92 to 2.00). Conclusion: This result suggests that MMP12 A1082G polymorphism may be related to prognosis in breast cancer patients. Additional studies with larger sample sizes are warranted.

  • Genotypes and haplotypes of the methyl-CpG-binding domain 2 modify breast cancer risk dependent upon menopausal status - IntroductionMBD2, the gene encoding methyl-CpG-binding domain (MBD)2, is a major methylation related gene and functions as a transcriptional repressor that can specifically bind to the methylated regions of other genes. MBD2 may also mediate gene activation because of its potential DNA demethylase activity. The present case-control study investigated associations between two single nucleotide polymorphisms (SNPs) in the MBD2 gene and breast cancer risk. Methods: DNA samples from 393 Caucasian patients with breast cancer (cases) and 436 matched control individuals, collected in a recently completed breast cancer case–control study conducted in Connecticut, were included in the study. Because no coding SNPs were found in the MBD2 gene, one SNP in the noncoding exon (rs1259938) and another in the intron 3 (rs609791) were genotyped. Odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to estimate cancer risk associated with the variant genotypes and the reconstructed haplotypes. Results: The variant genotypes at both SNP loci were significantly associated with reduced risk among premenopausal women (OR = 0.41 for rs1259938; OR = 0.54 for rs609791). Further haplotype analyses showed that the two rare haplotypes (A-C and A-G) were significantly associated with reduced breast cancer risk (OR = 0.40, 95% CI = 0.20–0.83 for A-C; OR = 0.47, 95% CI = 0.26–0.84 for A-G) in premenopausal women. No significant associations were detected in the postmenopausal women and the whole population. Conclusion: Our results demonstrate a role for the MBD2 gene in breast carcinogenesis in premenopausal women. These findings suggest that genetic variations in methylation related genes may potentially serve as a biomarker in risk estimates for breast cancer.

  • Global gene expression in neuroendocrine tumors from patients with the MEN1 syndrome - Background: Multiple Endocrine Neoplasia type 1 (MEN1, OMIM 131100) is an autosomal dominant disorder characterized by endocrine tumors of the parathyroids, pancreatic islets and pituitary. The disease is caused by the functional loss of the tumor suppressor protein menin, coded by the MEN1 gene. The protein sequence has no significant homology to known consensus motifs. In vitro studies have shown menin binding to JunD, Pem, Smad3, NF-kappaB, nm23H1, and RPA2 proteins. However, none of these binding studies have led to a convincing theory of how loss-of-menin leads to neoplasia. Results: Global gene expression studies on eight neuroendocrine tumors from MEN1 patients and 4 normal islet controls was performed utilizing Affymetrix U95Av2 chips. Overall hierarchical clustering placed all tumors in one group separate from the group of normal islets. Within the group of tumors, those of the same type were mostly clustered together. The clustering analysis also revealed 19 apoptosis-related genes that were under-expressed in the group of tumors. There were 193 genes that were increased/decreased by at least 2-fold in the tumors relative to the normal islets and that had a t-test significance value of p < = 0.005. Forty-five of these genes were increased and 148 were decreased in the tumors relative to the controls. One hundred and four of the genes could be classified as being involved in cell growth, cell death, or signal transduction. The results from 11 genes were selected for validation by quantitative RT-PCR. The average correlation coefficient was 0.655 (range 0.235–0.964). Conclusion: This is the first analysis of global gene expression in MEN1-associated neuroendocrine tumors. Many genes were identified which were differentially expressed in neuroendocrine tumors arising in patients with the MEN1 syndrome, as compared with normal human islet cells. The expression of a group of apoptosis-related genes was significantly suppressed, suggesting that these genes may play crucial roles in tumorigenesis in this syndrome. We identified a number of genes which are attractive candidates for further investigation into the mechanisms by which menin loss causes tumors in pancreatic islets. Of particular interest are: FGF9 which may stimulate the growth of prostate cancer, brain cancer and endometrium; and IER3 (IEX-1), PHLDA2 (TSS3), IAPP (amylin), and SST, all of which may play roles in apoptosis.

  • Global gene expression profiling of cells overexpressing SMC3 - Background: The Structural Maintenance of Chromosome 3 protein (SMC3) plays an essential role during the sister chromatid separation, is involved in DNA repair and recombination and participates in microtubule-mediated intracellular transport. SMC3 is frequently elevated in human colon carcinoma and overexpression of the protein transforms murine NIH3T3 fibroblasts. In order to gain insight into the mechanism of SMC3-mediated tumorigenesis a gene expression profiling was performed on human 293 cells line stably overexpressing SMC3. Results: Biotinylated complementary RNA (cRNA) was used for hybridization of a cDNA microarray chip harboring 18,861 65-mer oligos derived from the published dEST sequences. After filtering, the hybridization data were normalized and statistically analyzed. Sixty-five genes for which a putative function could be assigned displayed at least two-fold change in their expression level. Eighteen of the affected genes is either a transcriptional factor or is involved in DNA and chromatin related mechanisms whereas most of those involved in signal transduction are members or modulators of the ras-rho/GTPase and cAMP signaling pathways. In particular the expression of RhoB and CRE-BPa, two mediators of cellular transformation, was significantly enhanced. This association was confirmed by analyzing the RhoB and CRE-BPa transcript levels in cells transiently transfected with an SMC3 expression vector. Consistent with the idea that the activation of ras-rho/GTPase and cAMP pathways is relevant in the context of the cellular changes following SMC3 overexpression, gene transactivation through the related serum (SRE) and cAMP (CRE) cis-acting response elements was significantly increased. Conclusions: We have documented a selective effect of the ectopic expression of SMC3 on a set of genes and transcriptional signaling pathways that are relevant for tumorigenesis. The results lead to postulate that RhoB and CRE-BPa two known oncogenic mediators whose expression is significantly increased following SMC3 overexpression play a significant role in mediating SMC3 tumorigenesis.

  • Glycosaminoglycans modulate C6 glioma cell adhesion to extracellular matrix components and alter cell proliferation and cell migration - Background: Adhesion to extracellular matrix (ECM) components has been implicated in the proliferative and invasive properties of tumor cells. We investigated the ability of C6 glioma cells to attach to ECM components in vitro and described the regulatory role of glycosaminoglycans (GAGs) on their adhesion to the substrate, proliferation and migration. Results: ECM proteins (type IV collagen, laminin and fibronectin) stimulate rat C6 glioma cell line adhesion in vitro, in a dose-dependent manner. The higher adhesion values were achieved with type IV collagen. Exogenous heparin or chondroitin sulfate impaired, in a dose-dependent manner the attachment of C6 glioma cell line to laminin and fibronectin, but not to type IV collagen. Dextran sulfate did not affect C6 adhesion to any ECM protein analyzed, indicating a specific role of GAGs in mediating glioma adhesion to laminin and fibronectin. GAGs and dextran sulfate did not induce C6 glioma detachment from any tested substrate suggesting specific effect in the initial step of cell adhesion. Furthermore, heparin and chondroitin sulfate impaired C6 cells proliferation on fibronectin, but not on type IV collagen or laminin. In contrast, both GAGs stimulate the glioma migration on laminin without effect on type IV collagen or fibronectin. Conclusions: The results suggest that GAGs and proteoglycans regulate glioma cell adhesion to ECM proteins in specific manner leading to cell proliferation or cell migration, according to the ECM composition, thus modulating tumor cell properties.

  • Gonadal steroids differentially modulate neurotoxicity of HIV and cocaine: testosterone and ICI 182,780 sensitive mechanism - Background: HIV Associated Dementia (HAD) is a common complication of human immunodeficiency virus (HIV) infection that erodes the quality of life for patients and burdens health care providers. Intravenous drug use is a major route of HIV transmission, and drug use is associated with increased HAD. Specific proteins released as a consequence of HIV infection (e.g., gp120, the HIV envelope protein and Tat, the nuclear transactivating protein) have been implicated in the pathogenesis of HAD. In primary cultures of human fetal brain tissue, subtoxic doses of gp120 and Tat are capable of interacting with a physiologically relevant dose of cocaine, to produce a significant synergistic neurotoxicity. Using this model system, the neuroprotective potential of gonadal steroids was investigated. Results: 17beta-Estradiol (17beta-E2), but not 17alpha-estradiol (17alpha-E2), was protective against this combined neurotoxicity. Progesterone (PROG) afforded limited neuroprotection, as did dihydrotestosterone (DHT). The efficacy of 5alpha-testosterone (T)-mediated neuroprotection was robust, similar to that provided by 17beta-E2. In the presence of the specific estrogen receptor (ER) antagonist, ICI-182,780, T's neuroprotection was completely blocked. Thus, T acts through the ER to provide neuroprotection against HIV proteins and cocaine. Interestingly, cholesterol also demonstrated concentration-dependent neuroprotection, possibly attributable to cholesterol's serving as a steroid hormone precursor in neurons. Conclusions: Collectively, the present data indicate that cocaine has a robust interaction with the HIV proteins gp120 and Tat that produces severe neurotoxicity, and this toxicity can be blocked through pretreatment with ER agonists.

  • Greatly increased occurrence of breast cancers in areas of mammographically dense tissue - IntroductionMammographic density is a strong, independent risk factor for breast cancer. A critical unanswered question is whether cancers tend to arise in mammographically dense tissue (i.e. are densities directly related to risk or are they simply a marker of risk). This question cannot be addressed by studying invasive tumors because they manifest as densities and cannot be confidently differentiated from the densities representing fibrous and glandular tissue. We addressed this question by studying ductal carcinoma in situ (DCIS), as revealed by microcalcifications.MethodWe studied the cranio-caudal and the mediolateral-oblique mammograms of 28 breasts with a solitary DCIS lesion. Two experienced radiologists independently judged whether the DCIS occurred in a mammographically dense area, and determined the density of different areas of the mammograms. Results: It was not possible to determine whether the DCIS was or was not in a dense area for six of the tumors. Of the remaining 22 lesions, 21 occurred in dense tissue (test for difference from expected taken as the percentage of density of the 'mammographic quadrant' containing DCIS; P < 0.0001). A preponderance of DCIS (17 out of 28) occurred in the mammographic quadrant with the highest percentage density. Conclusion: DCIS occurs overwhelmingly in the mammographically dense areas of the breast, and pre-DCIS mammograms showed that this relationship was not brought about by the presence of the DCIS. This strongly suggests that some aspect of stromal tissue comprising the mammographically dense tissue directly influences the carcinogenic process in the local breast glandular tissue.

  • Guanylic nucleotide starvation affects Saccharomyces cerevisiae mother-daughter separation and may be a signal for entry into quiescence - Background: Guanylic nucleotides are both macromolecules constituents and crucial regulators for a variety of cellular processes. Therefore, their intracellular concentration must be strictly controlled. Consistently both yeast and mammalian cells tightly correlate the transcription of genes encoding enzymes critical for guanylic nucleotides biosynthesis with the proliferation state of the cell population. Results: To gain insight into the molecular relationships connecting intracellular guanylic nucleotide levels and cellular proliferation, we have studied the consequences of guanylic nucleotide limitation on Saccharomyces cerevisiae cell cycle progression. We first utilized mycophenolic acid, an immunosuppressive drug that specifically inhibits inosine monophosphate dehydrogenase, the enzyme catalyzing the first committed step in de novo GMP biosynthesis. To approach this system physiologically, we next developed yeast mutants for which the intracellular guanylic nucleotide pools can be modulated through changes of growth conditions. In both the pharmacological and genetic approaches, we found that guanylic nucleotide limitation generated a mother-daughter separation defect, characterized by cells with two unseparated daughters. We then showed that this separation defect resulted from cell wall perturbations but not from impaired cytokinesis. Importantly, cells with similar separation defects were found in a wild type untreated yeast population entering quiescence upon nutrient limitation. Conclusions: Our results demonstrate that guanylic nucleotide limitation slows budding yeast cell cycle progression, with a severe pause in telophase. At the cellular level, guanylic nucleotide limitation causes the emergence of cells with two unseparated daughters. By fluorescence and electron microscopy, we demonstrate that this phenotype arises from defects in cell wall partition between mother and daughter cells. Because cells with two unseparated daughters are also observed in a wild type population entering quiescence, our results reinforce the hypothesis that guanylic nucleotide intracellular pools contribute to a signal regulating both cell proliferation and entry into quiescence.

  • Heat shock protein 72 expression allows permissive replication of oncolytic adenovirus dl1520 (ONYX-015) in rat glioblastoma cells - In this study we have made novel observations with regards to potentiation of the tumoricidal activity of the oncolytic adenovirus, dl1520 (ONYX-015) in rat glioblastoma cell lines expressing heat shock protein 72 (HSP72) due to permissive virus replication. ONYX-015 is a conditionally replicating adenovirus that is deleted for the E1B 55 kDA gene product whose normal function is to interact with cell-cycle regulatory proteins to permit virus replication. However, many murine and rodent cell lines are not permissive for adenovirus replication. Previously, it has been reported that the heat shock response is necessary for adenovirus replication and that induction of heat shock proteins is mediated by E1 region gene products. Therefore, we hypothesized that HSP72 expression may allow for permissive replication of ONYX-015 in previously non-permissive cells. Rat glioma cell lines 9L and RT2 were transfected with a plasmids expressing HSP72 or GFP. After infection with ONYX-015, no tumoricidal activity is observed in GFP expressing cell lines despite adequate transduction. In contrast, HSP72 transfected cells show cytopathic effects by 72 hours and greater than 75% loss of viability by 96 hours. Burst assays show active virus replication in the HSP72 expressing cell lines. Therefore, 9L-HSP72 and RT2-HSP72 are ideal models to evaluate the efficacy of ONYX-015 in an immunocompetent rat model. Our study has implications for creating rodent tumor models for pre-clinical studies with E1 region deleted conditionally replicating adenovirus.

  • Hematopoietic Stem Cell Transplantation in the Treatment of Peripheral T-cell Lymphomas - Peripheral T-cell lymphomas (PTCL) are a rare group of heterogeneous lymphoproliferative disorders with their origin in the post-thymic T cells. Most PTCL have a relatively poor outcome, with a 5-year overall survival of less than 30%. Anaplastic large cell lymphoma (ALCL) has a better prognosis compared with other subtypes of PTCL. As with aggressive B-cell non-Hodgkin's lymphoma, high-dose chemotherapy followed by autologous stem cell transplantation should be offered to patients with PTCL in their first relapse. Patients with poor-risk features (alk-negative ALCL, histologic subtypes other than ALCL, and high International Prognostic Index score at presentation) may be candidates for autologous stem cell transplantation as first-line therapy. Initial results of allogeneic stem cell transplantation, both with standard and nonmyelo-ablative conditioning, look promising. Randomized, multi-institutional clinical trials are needed to optimally define the role of stem cell transplantation in PTCL.

  • Hemispheric biases and the control of visuospatial attention: an ERP study - Background: We examined whether individual differences in hemispheric utilization can interact with the intrinsic attentional biases of the cerebral hemispheres. Evidence suggests that the hemispheres have competing biases to direct attention contralaterally, with the left hemisphere (LH) having a stronger bias than the right hemisphere. There is also evidence that individuals have characteristic biases to utilize one hemisphere more than the other for processing information, which can induce a bias to direct attention to contralateral space. We predicted that LH-biased individuals would display a strong rightward attentional bias, which would create difficulty in selectively attending to target stimuli in the left visual field (LVF) as compared to right in the performance of a bilateral flanker task. Results: Consistent with our hypothesis, flanker interference effects were found on the N2c event-related brain potential and error rate for LH-biased individuals in the Attend-LVF condition. The error rate effect was correlated with the degree of hemispheric utilization bias for the LH-Bias group. Conclusions: We conclude that hemispheric utilization bias can enhance a hemisphere's contralateral attentional bias, at least for individuals with a LH utilization bias. Hemispheric utilization bias may play an important and largely unrecognized role in visuospatial attention.

  • Hemolytic Anemia-associated Pulmonary Hypertension in Sickle Cell Disease - Pulmonary hypertension is one of the leading causes of death in adult sickle cell patients, with a prevalence of 20% to 40%. Although these patients have lower pulmonary pressures than patients with primary pulmonary hypertension, both groups suffer high 2-year mortality rates. Pulmonary hypertension may go undetected until the disease is advanced. Therefore, all adult patients with sickle cell disease should be screened with transthoracic Doppler echocardiogram and the tricuspid regurgitant jet (TRJ) velocity measured to -estimate pulmonary artery pressures. A regurgitant jet (RJ) velocity of 2.5 m/s or higher establishes diagnosis and -suggests a high risk of death (rate ratio of 10.1; CI 2.2-47). Basic and epidemiologic studies suggest that pulmonary hypertension in sickle cell disease is mechanistically linked to chronic hemolytic anemia. Hemolysis results in the release of hemoglobin and arginase from the erythrocyte, increasing the consumption and decreasing the production of nitric oxide (NO), respectively. NO is a critical regulator of -vasodilation and vascular homeostasis whose inactivation produces vasoconstriction and proliferative vasculopathy. Finally, we review suggested therapies including the -established treatments and new pulmonary vasodilator and remodeling agents in the management of pulmonary -hypertension in hemolytic anemias.

  • Heterogeneous chloride homeostasis and GABAA responses in the median preoptic nucleus of the rat. -
    Related Articles

    Heterogeneous chloride homeostasis and GABAA responses in the median preoptic nucleus of the rat.

    J Physiol. 2005 Oct 20;

    Authors: Grob M, Mouginot D

    The median preoptic nucleus (MnPO) is an integrative structure of the hypothalamus receiving periphery-derived information pertinent to hydromineral and cardiovascular homeostasis. In this context, excitability of MnPO neurons is controlled by fast GABAergic, glutamatergic and angiotensinergic projection from the subfornical organ (SFO). Taking advantage of a brain slice preparation preserving synaptic connection between the SFO and the MnPO and appropriate bicarbonate-free artificial CSF, we investigated the role of the neuron-specific K(+)/Cl(-) cotransporter, KCC2, in regulating efficacy of the GABAA receptor-mediated inhibitory response at the SFO-MnPO synapse. When somata of the MnPO neurons was loaded with 18 mM chloride, stimulation of the SFO evoked outward IPSCs in 81% of the MnPO neurons held at -60 mV. Accordingly, EIPSC was found 25 mV hyperpolarized from the theoretical value calculated from the Nernst equation, indicating that IPSC polarity and amplitude were driven by an active Cl(-) extrusion system in these neurons. EIPSC estimated with gramicidin-based perforated-patch recordings amounted -89.2 +/- 4.3 mV. Furosemide (100microM), a pharmacological compound known to block the activity of the neuron-specific K(+)/Cl(-) cotransporter, KCC2, reversed IPSC polarity and shifted EIPSC towards theoretical value. Presence of the KCC2 protein in the MnPO was further detected with immunohistochemistry, revealing a dense network of KCC2 positive intermingled fibers. In the presence of a GABAB receptor antagonist, high frequency stimulation (5Hz) of the SFO evoked a train of IPSCs or IPSPs, whose amplitude was maintained throughout the sustained stimulation. Contrastingly, similar 5Hz stimulation carried out in the presence of furosemide (50microM) evoked IPSCs/IPSPs, whose amplitude collapsed during the high-frequency stimulation. Similar reduction in inhibitory neurotransmission was also observed in MnPO neurons lacking the functional Cl(-) extrusion mechanism. We conclude that a majority of MnPO neurons were characterized by a functional Cl(-) transporter that insured efficient activity-dependent Cl(-) transport rate, allowing sustained synaptic inhibition of these neurons. Pharmacological and anatomical data strongly suggested the involvement of KCC2, as an essential postsynaptic determinant of the inhibitory neurotransmission afferent to the MnPO, a key-structure in the physiology of the hydromineral and cardiovascular homeostasis.

    PMID: 16239278 [PubMed - as supplied by publisher]


  • High expression of Lewisy/b antigens is associated with decreased survival in lymph node negative breast carcinomas - IntroductionThere is sufficient evidence that blood group related Lewis antigens are tumour-associated molecules. The Lewisy and Lewisb antigens are complex carbohydrates that are over-expressed by breast, lung, colon and ovarian cancers. The SC101 mAb is a unique Lewisy/b binding antibody that binds to native and extended Lewisy and Lewisb haptens, displaying no cross reactivity with H type 1, H type 2, Lewisx or normal blood group antigens. Methods: Immunohistochemical detection of Lewisy/b was performed on 660 formalin-fixed, paraffin embedded breast tumour specimens using a streptavidin-biotin peroxidase technique. Tissue from these patients had previously been included in tissue microarrays. This cohort comprises a well characterized series of patients with primary operable breast cancer diagnosed between 1987 and 1992, obtained from the Nottingham Tenovus Primary Breast Carcinoma Series. This includes patients 70 years of age or less, with a mean follow up of 7 years. Results: Of the breast carcinomas, 370 of 660 (56%) were negative for Lewisy/b expression, 110 (17%) cases showed a low level of expression (<25% of positive cells) and only 54 cases (8%) showed extensive expression of Lewisy/b (>75% of positive cells). We found significant positive associations between histological grade (p < 0.001), Nottingham Prognostic Index (p = 0.016), tumour type (p = 0.007) and the level of Lewis y/b expression. There was a significant correlation between the proportion of Lewisy/b positive tumour cells and survival in lymph-node negative patients (p = 0.006). Conclusion: The unique epitope recognised by SC101 mAb on Lewisy/b hapten is over-expressed on breast tumour tissue compared with normal breast. In this large series of invasive breast cancers, higher expression of Lewisy/b was more often found in high grade and poor prognosis tumours compared to good prognosis cancers. Moreover, in lymph node negative breast carcinomas, over-expression of Lewisy/b hapten was associated with significantly decreased patient survival.

  • High proportion of recurrent germline mutations in the BRCA1 gene in breast and ovarian cancer patients from the Prague area - Background: Germline mutations in the BRCA1 and BRCA2 genes have been shown to account for the majority of hereditary breast and ovarian cancers. The purpose of our study was to estimate the incidence and spectrum of pathogenic mutations in BRCA1/2 genes in high-risk Czech families. Methods: A total of 96 Czech families with recurrent breast and/or ovarian cancer and 55 patients considered to be at high-risk but with no reported family history of cancer were screened for mutations in the BRCA1/2 genes. The entire coding sequence of each gene was analyzed using a combination of the protein truncation test and direct DNA sequencing. Results: A total of 35 mutations in the BRCA1/2 genes were identified in high-risk families (36.5%). Pathogenic mutations were found in 23.3% of breast cancer families and in 59.4% of families with the occurrence of both breast and ovarian cancer. In addition, four mutations were detected in 31 (12.9%) women with early onset breast cancer. One mutation was detected in seven (14.3%) patients affected with both a primary breast and ovarian cancer and another in three (33.3%) patients with a bilateral breast cancer. A total of 3 mutations in BRCA1 were identified among 14 (21.4%) women with a medullary breast carcinoma. Of 151 analyzed individuals, 35 (23.2%) carried a BRCA1 mutation and 9 (6.0%) a BRCA2 mutation. One novel truncating mutation was found in BRCA1 (c.1747A>T) and two in BRCA2 (c.3939delC and c.5763dupT). The 35 identified BRCA1 mutations comprised 13 different alterations. Three recurrent mutations accounted for 71.4% of unrelated individuals with detected gene alterations. The BRCA1 c.5266dupC (5382insC) was detected in 51.4% of mutation positive women. The mutations c.3700_3704del5 and c.181T>G (300T>G) contributed to 11.4% and 8.6% of pathogenic mutations, respectively. A total of eight different mutations were identified in BRCA2. The novel c.5763dupT mutation, which appeared in two unrelated families, was the only recurrent alteration of the BRCA2 gene identified in this study. Conclusion: Mutational analysis of BRCA1/2 genes in 151 high-risk patients characterized the spectrum of gene alterations and demonstrated the dominant role of the BRCA1 c.5266dupC allele in hereditary breast and ovarian cancer.

  • High-resolution Light Microscopy (HRLM) and Digital Analysis of Pompe Disease Pathology -

    Pompe disease is an autosomal recessive lysosomal storage disorder caused by a deficiency of the lysosomal enzyme acid -glucosidase, responsible for the degradation of lysosomal glycogen. Absent or low levels of the enzyme leads to lysosomal glycogen accumulation in cardiac and skeletal muscle cells, resulting in progressive muscle weakness and death from cardiac or respiratory failure. Recombinant enzyme replacement and gene therapy are now being investigated as treatment modalities for this disease. A knockout mouse model for Pompe disease, induced by the disruption of exon 6 within the acid -glucosidase gene, mimics the human disease and has been used to evaluate the efficacy of treatment modalities for clearing glycogen. However, for accurate histopathological assessment of glycogen clearance, maximal preservation of in situ lysosomal glycogen is essential. To improve retention of glycogen in Pompe tissues, several fixation and embedding regimens were evaluated. The best glycogen preservation was obtained when tissues fixed with 3% glutaraldehyde and postfixed with 1% osmium tetroxide were processed into epon–araldite. Preservation was confirmed by staining with the Periodic acid–Schiff's reaction and by electron microscopy. This methodology resulted in high-resolution light microscopy (HRLM) sections suitable for digital quantification of glycogen content in heart and skeletal muscle. Combining this method of tissue fixation with computer-assisted histomorphometry has provided us with what we believe is the most objective and reproducible means of evaluating histological glycogen load in Pompe disease.

    (J Histochem Cytochem 53:63–73, 2005)


  • Hippocampal lesions facilitate instrumental learning with delayed reinforcement but induce impulsive choice in rats - Background: Animals must frequently act to influence the world even when the reinforcing outcomes of their actions are delayed. Learning with action-outcome delays is a complex problem, and little is known of the neural mechanisms that bridge such delays. When outcomes are delayed, they may be attributed to (or associated with) the action that caused them, or mistakenly attributed to other stimuli, such as the environmental context. Consequently, animals that are poor at forming context-outcome associations might learn action-outcome associations better with delayed reinforcement than normal animals. The hippocampus contributes to the representation of environmental context, being required for aspects of contextual conditioning. We therefore hypothesized that animals with hippocampal lesions would be better than normal animals at learning to act on the basis of delayed reinforcement. We tested the ability of hippocampal-lesioned rats to learn a free-operant instrumental response using delayed reinforcement, and what is potentially a related ability -- the ability to exhibit self-controlled choice, or to sacrifice an immediate, small reward in order to obtain a delayed but larger reward. Results: Rats with sham or excitotoxic hippocampal lesions acquired an instrumental response with different delays (0, 10, or 20 s) between the response and reinforcer delivery. These delays retarded learning in normal rats. Hippocampal-lesioned rats responded slightly less than sham-operated controls in the absence of delays, but they became better at learning (relative to shams) as the delays increased; delays impaired learning less in hippocampal-lesioned rats than in shams. In contrast, lesioned rats exhibited impulsive choice, preferring an immediate, small reward to a delayed, larger reward, even though they preferred the large reward when it was not delayed. Conclusions: These results support the view that the hippocampus hinders action-outcome learning with delayed outcomes, perhaps because it promotes the formation of context-outcome associations instead. However, although lesioned rats were better at learning with delayed reinforcement, they were worse at choosing it, suggesting that self-controlled choice and learning with delayed reinforcement tax different psychological processes.

  • Histological Analysis of GFP Expression in Murine Bone -

    The power for appreciating complex cellular interactions during embryonic development using green fluorescent protein (GFP) as a visual histological marker has not been applied to adult tissues due to loss of GFP signal during paraffin embedding and a high autofluorescent background, particularly in section of bone and bone marrow. Here we demonstrate that the GFP signal is well preserved in frozen sections of adult decalcified bone. Using a tape-transfer system that preserves histological relationships, GFP expression can be related to standard histological stains used in bone biology research. The choice of a dual-filter cube and a strong GFP signal makes it possible to readily distinguish at least four different GFP colors that are distinctly different from the autofluorescent background. An additional advantage of the frozen sections is better preservation of immunological epitopes that allow colocalization of an immunostained section with an endogenous GFP and a strong lacZ signal emanating from a ßbeta;-gal marker gene. We present an approach for recording multiple images from the same histological section that allows colocalization of a GFP signal with subsequent stains and procedures that destroy GFP. Examples that illustrate the flexibility for dual imaging of various fluorescent signals are described in this study. The same imaging approach can serve as a vehicle for archiving, retrieving, and sharing histological images among research groups. (J Histochem Cytochem 53:593–602, 2005)


  • Histological Analysis of GFP Expression in Murine Bone -

    The power for appreciating complex cellular interactions during embryonic development using green fluorescent protein (GFP) as a visual histological marker has not been applied to adult tissues due to loss of GFP signal during paraffin embedding and a high autofluorescent background, particularly in section of bone and bone marrow. Here we demonstrate that the GFP signal is well preserved in frozen sections of adult decalcified bone. Using a tape-transfer system that preserves histological relationships, GFP expression can be related to standard histological stains used in bone biology research. The choice of a dual-filter cube and a strong GFP signal makes it possible to readily distinguish at least four different GFP colors that are distinctly different from the autofluorescent background. An additional advantage of the frozen sections is better preservation of immunological epitopes that allow colocalization of an immunostained section with an endogenous GFP and a strong lacZ signal emanating from a ßbeta;-gal marker gene. We present an approach for recording multiple images from the same histological section that allows colocalization of a GFP signal with subsequent stains and procedures that destroy GFP. Examples that illustrate the flexibility for dual imaging of various fluorescent signals are described in this study. The same imaging approach can serve as a vehicle for archiving, retrieving, and sharing histological images among research groups. (J Histochem Cytochem 53:593–602, 2005)


  • Histological Analysis of GFP Expression in Murine Bone -

    The power for appreciating complex cellular interactions during embryonic development using green fluorescent protein (GFP) as a visual histological marker has not been applied to adult tissues due to loss of GFP signal during paraffin embedding and a high autofluorescent background, particularly in section of bone and bone marrow. Here we demonstrate that the GFP signal is well preserved in frozen sections of adult decalcified bone. Using a tape-transfer system that preserves histological relationships, GFP expression can be related to standard histological stains used in bone biology research. The choice of a dual-filter cube and a strong GFP signal makes it possible to readily distinguish at least four different GFP colors that are distinctly different from the autofluorescent background. An additional advantage of the frozen sections is better preservation of immunological epitopes that allow colocalization of an immunostained section with an endogenous GFP and a strong lacZ signal emanating from a ßbeta;-gal marker gene. We present an approach for recording multiple images from the same histological section that allows colocalization of a GFP signal with subsequent stains and procedures that destroy GFP. Examples that illustrate the flexibility for dual imaging of various fluorescent signals are described in this study. The same imaging approach can serve as a vehicle for archiving, retrieving, and sharing histological images among research groups. (J Histochem Cytochem 53:593–602, 2005)


  • Histomathematical Analysis of Clinical Specimens: Challenges and Progress -

    Proteomic analysis of clinical tissue specimens is a difficult undertaking. Described here is a multiplex study of protein expression levels in histological sections of human prostate that addresses many of the associated challenges. Whole-mount sections from 10 prostatectomy specimens were studied using 15 antibodies, immunohistochemical staining, digital imaging, and mathematical analysis of the data sets. The approach was successful in stratifying cell lineages present in the samples based on proteomic patterns, including differentiating normal epithelium from cancer. This strategy likely will be a useful method for extending the number of proteins that can be analyzed in clinical cancer specimens using currently available laboratory techniques.

    (J Histochem Cytochem 53:177–185, 2005)


  • Histone acetylation and histone deacetylase activity of magnesium valproate in tumor and peripheral blood of patients with cervical cancer. A phase I study - Background: The development of cancer has been associated with epigenetic alterations such as aberrant histone deacetylase (HDAC) activity. It was recently reported that valproic acid is an effective inhibitor of histone deacetylases and as such induces tumor cell differentiation, apoptosis, or growth arrest. Methods: Twelve newly diagnosed patients with cervical cancer were treated with magnesium valproate after a baseline tumor biopsy and blood sampling at the following dose levels (four patients each): 20 mg/kg; 30 mg/kg, or 40 mg/kg for 5 days via oral route. At day 6, tumor and blood sampling were repeated and the study protocol ended. Tumor acetylation of H3 and H4 histones and HDAC activity were evaluated by Western blot and colorimetric HDAC assay respectively. Blood levels of valproic acid were determined. Toxicity of treatment was evaluated at the end of study period. Results: All patients completed the study medication. Mean daily dose for all patients was 1,890 mg. Corresponding means for the doses 20-, 30-, and 40-mg/kg were 1245, 2000, and 2425 mg, respectively. Depressed level of consciousness grade 2 was registered in nine patients. Ten patients were evaluated for H3 and H4 acetylation and HDAC activity. After treatment, we observed hyperacetylation of H3 and H4 in the tumors of nine and seven patients, respectively, whereas six patients demonstrated hyperacetylation of both histones. Serum levels of valproic acid ranged from 73.6-170.49 ug/mL. Tumor deacetylase activity decreased in eight patients (80%), whereas two had either no change or a mild increase. There was a statistically significant difference between pre and post-treatment values of HDAC activity (mean, 0.36 vs. 0.21, two-tailed t test p <0.0264). There was no correlation between H3 and H4 tumor hyperacetylation with serum levels of valproic acid. Conclusions: Magnesium valproate at a dose between 20 and 40 mg/kg is an effective and well-tolerated HDAC inhibitor for patients with cancer.

  • HIV Infection and Thrombocytopenia - Thrombocytopenia is a common complication of HIV -infection. The low platelet count can be caused by multiple mechanisms including immune-mediated destruction, decreased platelet production, effects of drugs on -progenitors, or by the development of a form of thrombotic thrombocytopenic purpura (TTP). Bleeding problems -associated with the thrombocytopenia can be accentuated by the presence of platelet dysfunction produced by drugs used to treat HIV/AIDs or its complications. Therapy should be directed at reducing the load of the HIV virus of the patient supplemented by other therapies chosen depending on the specific underlying cause.

  • HLA-DR- and CD11c-positive Dendritic Cells Penetrate beyond Well-developed Epithelial Tight Junctions in Human Nasal Mucosa of Allergic Rhinitis -

    The epithelial barrier of the upper respiratory tract plays a crucial role in host defense. In this study, to elucidate whether there is antigen monitoring by dendritic cells (DCs) beyond the epithelial tight-junction barrier in allergic rhinitis, we investigated the expression and function of tight junctions and characterized DCs in the epithelium of nasal mucosa from patients with allergic rhinitis. In reverse transcription-polymerase chain reaction, mRNAs of tight-junction proteins occludin, JAM-1, ZO-1, and claudin-1, -4, -7, -8, -12, -13, and -14 were detected in the nasal mucosa. Occludin, JAM-1, and ZO-1 were colocalized in the uppermost layer in the pseudostratified epithelium of the nasal mucosa, whereas claudin-1, -4, and -7 were found throughout the epithelium. In freeze-fracture replicas of the nasal mucosa, continuous tight-junction strands formed well-developed networks. Epithelial barrier function measured by a dye tracer was well maintained in occludin-positive tight junctions in the epithelium of the nasal mucosa. HLA-DR- and CD11c-positive DCs expressed claudin-1 and penetrated beyond occludin in the epithelium of the nasal mucosa with, but not without, allergic rhinitis. These results indicate that DCs may easily access antigens beyond epithelial tight junctions in the human nasal mucosa of allergic rhinitis.

    (J Histochem Cytochem 53:611–619, 2005)


  • HLA-DR- and CD11c-positive Dendritic Cells Penetrate beyond Well-developed Epithelial Tight Junctions in Human Nasal Mucosa of Allergic Rhinitis -

    The epithelial barrier of the upper respiratory tract plays a crucial role in host defense. In this study, to elucidate whether there is antigen monitoring by dendritic cells (DCs) beyond the epithelial tight-junction barrier in allergic rhinitis, we investigated the expression and function of tight junctions and characterized DCs in the epithelium of nasal mucosa from patients with allergic rhinitis. In reverse transcription-polymerase chain reaction, mRNAs of tight-junction proteins occludin, JAM-1, ZO-1, and claudin-1, -4, -7, -8, -12, -13, and -14 were detected in the nasal mucosa. Occludin, JAM-1, and ZO-1 were colocalized in the uppermost layer in the pseudostratified epithelium of the nasal mucosa, whereas claudin-1, -4, and -7 were found throughout the epithelium. In freeze-fracture replicas of the nasal mucosa, continuous tight-junction strands formed well-developed networks. Epithelial barrier function measured by a dye tracer was well maintained in occludin-positive tight junctions in the epithelium of the nasal mucosa. HLA-DR- and CD11c-positive DCs expressed claudin-1 and penetrated beyond occludin in the epithelium of the nasal mucosa with, but not without, allergic rhinitis. These results indicate that DCs may easily access antigens beyond epithelial tight junctions in the human nasal mucosa of allergic rhinitis.

    (J Histochem Cytochem 53:611–619, 2005)


  • HLA-DR- and CD11c-positive Dendritic Cells Penetrate beyond Well-developed Epithelial Tight Junctions in Human Nasal Mucosa of Allergic Rhinitis -

    The epithelial barrier of the upper respiratory tract plays a crucial role in host defense. In this study, to elucidate whether there is antigen monitoring by dendritic cells (DCs) beyond the epithelial tight-junction barrier in allergic rhinitis, we investigated the expression and function of tight junctions and characterized DCs in the epithelium of nasal mucosa from patients with allergic rhinitis. In reverse transcription-polymerase chain reaction, mRNAs of tight-junction proteins occludin, JAM-1, ZO-1, and claudin-1, -4, -7, -8, -12, -13, and -14 were detected in the nasal mucosa. Occludin, JAM-1, and ZO-1 were colocalized in the uppermost layer in the pseudostratified epithelium of the nasal mucosa, whereas claudin-1, -4, and -7 were found throughout the epithelium. In freeze-fracture replicas of the nasal mucosa, continuous tight-junction strands formed well-developed networks. Epithelial barrier function measured by a dye tracer was well maintained in occludin-positive tight junctions in the epithelium of the nasal mucosa. HLA-DR- and CD11c-positive DCs expressed claudin-1 and penetrated beyond occludin in the epithelium of the nasal mucosa with, but not without, allergic rhinitis. These results indicate that DCs may easily access antigens beyond epithelial tight junctions in the human nasal mucosa of allergic rhinitis.

    (J Histochem Cytochem 53:611–619, 2005)


  • Hodgkin lymphoma: flow me? - Combining fine needle aspirate cytology with flow cytometry immunophenotyping for the rapid diagnosis of lymphoproliferative lesions is commonplace practice in many institutions. Yet, a definitive diagnosis of Hodgkin lymphoma in many cases remains elusive, requiring subsequent tissue biopsy confirmation. In this issue of CytoJournal, Hernandez et al explore the potential role of using the increased CD4/CD8 T-cell ratio in lymph node fine needle aspiration specimens as a specific feature in diagnosing Hodgkin lymphoma. CD4/CD8 T-cell ratio comparisons are made with cytomorphologic diagnoses of reactive, atypical, non-Hodgkin lymphoma, and Hodgkin lymphoma cases.

  • Hodgkin's lymphoma of the thyroid: a clinicopathologic study of five cases and review of the literature - Sa A Wang, Aliyah Rahemtullah, William C Faquin, Janet Roepke, Nancy Lee Harris & Robert P Hasserjian

  • Human CD57+ germinal center-T cells are the major helpers for GC-B cells and induce class switch recombination - Background: The function of CD57+ CD4+ T cells, constituting a major subset of germinal center T (GC-Th) cells in human lymphoid tissues, has been unclear. There have been contradictory reports regarding the B cell helping function of CD57+ GC-Th cells in production of immunoglobulin (Ig). Furthermore, the cytokine and co-stimulation requirement for their helper activity remains largely unknown. To clarify and gain more insight into their function in helping B cells, we systematically investigated the capacity of human tonsil CD57+ GC-Th cells in inducing B cell Ig synthesis. Results: We demonstrated that CD57+ GC-Th cells are highly efficient in helping B cell production of all four subsets of Ig (IgM, IgG, IgA and IgE) compared to other T-helper cells located in germinal centers or interfollicular areas. CD57+ GC-Th cells were particularly more efficient than other T cells in helping GC-B cells but not naïve B cells. CD57+ GC-Th cells induced the expression of activation-induced cytosine deaminase (AID) and class switch recombination in developing B cells. IgG1-3 and IgA1 were the major Ig isotypes induced by CD57+ GC-Th cells. CD40L, but not IL-4, IL-10 and IFN-γ, was critical in CD57+ GC-Th cell-driven B cell production of Ig. However, IL-10, when added exogenously, significantly enhanced the helper activity of CD57+ GC-Th cells, while TGF-β1 completely and IFN-γ partially suppressed the CD57+ GC-Th cell-driven Ig production. Conclusions: CD57+CD4+ T cells in the germinal centers of human lymphoid tissues are the major T helper cell subset for GC-B cells in Ig synthesis. Their helper activity is consistent with their capacity to induce AID and class switch recombination, and can be regulated by CD40L, IL-4, IL-10 and TGF-β.

  • hZIP1 zinc uptake transporter down regulation and zinc depletion in prostate cancer - Background: The genetic and molecular mechanisms responsible for and associated with the development and progression of prostate malignancy are largely unidentified. The peripheral zone is the major region of the human prostate gland where malignancy develops. The normal peripheral zone glandular epithelium has the unique function of accumulating high levels of zinc. In contrast, the ability to accumulate zinc is lost in the malignant cells. The lost ability of the neoplastic epithelial cells to accumulate zinc is a consistent factor in their development of malignancy. Recent studies identified ZIP1 (SLC39A1) as an important zinc transporter involved in zinc accumulation in prostate cells. Therefore, we investigated the possibility that down-regulation of hZIP1 gene expression might be involved in the inability of malignant prostate cells to accumulate zinc. To address this issue, the expression of hZIP1 and the depletion of zinc in malignant versus non-malignant prostate glands of prostate cancer tissue sections were analyzed. hZIP1 expression was also determined in malignant prostate cell lines. Results: hZIP1 gene expression, ZIP1 transporter protein, and cellular zinc were prominent in normal peripheral zone glandular epithelium and in benign hyperplastic glands (also zinc accumulating glands). In contrast, hZIP1 gene expression and transporter protein were markedly down-regulated and zinc was depleted in adenocarcinomatous glands and in prostate intra-epithelial neoplastic foci (PIN). These changes occur early in malignancy and are sustained during its progression in the peripheral zone. hZIP1 is also expressed in the malignant cell lines LNCaP, PC-3, DU-145; and in the nonmalignant cell lines HPr-1 and BPH-1. Conclusion: The studies clearly establish that hZIP1 gene expression is down regulated and zinc is depleted in adenocarcinomatous glands. The fact that all the malignant cell lines express hZIP1 indicates that the down-regulation in adenocarcinomatous glands is likely due to in situ gene silencing. These observations, coupled with the numerous and consistent reports of loss of zinc accumulation in malignant cells in prostate cancer, lead to the plausible proposal that down regulation of hZIP1 is a critical early event in the development prostate cancer.

  • Id4 and FABP7 are preferentially expressed in cells with astrocytic features in oligodendrogliomas and oligoastrocytomas - Background: Oligodendroglioma (ODG) and oligoastrocytoma (OAC) are diffusely infiltrating primary brain tumors whose pathogenesis remains unclear. We previously identified a group of genes whose expression was inversely correlated with survival in a cohort of patients with glioblastoma (GBM), and some of these genes are also reportedly expressed in ODG and OAC. We examined the expression patterns and localization of these survival-associated genes in ODG and OAC in order to analyze their possible roles in the oncogenesis of these two tumor types. Methods: We used UniGene libraries derived from GBM and ODG specimens to examine the expression levels of the transcripts for each of the 50 GBM survival-associated genes. We used immunohistochemistry and cDNA microarrays to examine expression of selected survival-associated genes and Id4, a gene believed to control the timing of oligodendrocyte development. The expression of FABP7 and Id4 and the survival of patients with ODG and OAC were also analyzed. Results: Transcripts of most survival-associated genes as well as Id4 were present in both GBM and ODG tumors, whereas protein expression of Id4 and one of the survival-associated genes, brain-type fatty acid-binding protein (FABP7), was present in cells with astrocytic features, including reactive and neoplastic astrocytes, but not in neoplastic oligodendrocytes. Id4 was co-expressed with FABP7 in microgemistocytes in ODG and in neoplastic astrocytes in OAC. Id4 and FABP7 expression, however, did not correlate with the clinical outcome of patients with ODG or OAC tumors. Conclusions: Expression of Id4 and some of our previously identified GBM survival-associated genes is present in developing or mature oligodendrocytes. However, protein expression of Id4 and FABP7 in GBM, ODG, and OAC suggests that this group of functionally important genes might demonstrate two patterns of expression in these glioma subtypes: one group is universally expressed in glioma cells, and the other group of genes is expressed primarily in neoplastic astrocytes but not in neoplastic oligodendrocytes. Differential expression of these two groups of genes in ODG and OAC may be related to the cellular origins and the histological features of the neoplastic cells.

  • Identification of a new neuropeptide precursor reveals a novel source of extrinsic modulation in the feeding system of Aplysia. -
    Related Articles

    Identification of a new neuropeptide precursor reveals a novel source of extrinsic modulation in the feeding system of Aplysia.

    J Neurosci. 2005 Oct 19;25(42):9637-48

    Authors: Proekt A, Vilim FS, Alexeeva V, Brezina V, Friedman A, Jing J, Li L, Zhurov Y, Sweedler JV, Weiss KR

    The Aplysia feeding system is advantageous for investigating the role of neuropeptides in behavioral plasticity. One family of Aplysia neuropeptides is the myomodulins (MMs), originally purified from one of the feeding muscles, the accessory radula closer (ARC). However, two MMs, MMc and MMe, are not encoded on the only known MM gene. Here, we identify MM gene 2 (MMG2), which encodes MMc and MMe and four new neuropeptides. We use matrix-assisted laser desorption/ionization time-of-flight mass spectrometry to verify that these novel MMG2-derived peptides (MMG2-DPs), as well as MMc and MMe, are synthesized from the precursor. Using antibodies against the MMG2-DPs, we demonstrate that neuronal processes that stain for MMG2-DPs are found in the buccal ganglion, which contains the feeding network, and in the buccal musculature including the ARC muscle. Surprisingly, however, no immunostaining is observed in buccal neurons including the ARC motoneurons. In situ hybridization reveals only few MMG2-expressing neurons that are mostly located in the pedal ganglion. Using immunohistochemical and electrophysiological techniques, we demonstrate that some of these pedal neurons project to the buccal ganglion and are the likely source of the MMG2-DP innervation of the feeding network and musculature. We show that the MMG2-DPs are bioactive both centrally and peripherally: they bias egestive feeding programs toward ingestive ones, and they modulate ARC muscle contractions. The multiple actions of the MMG2-DPs suggest that these peptides play a broad role in behavioral plasticity and that the pedal-buccal projection neurons that express them are a novel source of extrinsic modulation of the feeding system of Aplysia.

    PMID: 16237168 [PubMed - in process]


  • Identification of a novel Rev-interacting cellular protein - Background: Human cell types respond differently to infection by human immunodeficiency virus (HIV). Defining specific interactions between host cells and viral proteins is essential in understanding how viruses exploit cellular functions and the innate strategies underlying cellular control of HIV replication. The HIV Rev protein is a post-transcriptional inducer of HIV gene expression and an important target for interaction with cellular proteins. Identification of Rev-modulating cellular factors may eventually contribute to the design of novel antiviral therapies. Results: Yeast-two hybrid screening of a T-cell cDNA library with Rev as bait led to isolation of a novel human cDNA product (16.4.1). 16.4.1-containing fusion proteins showed predominant cytoplasmic localization, which was dependent on CRM1-mediated export from the nucleus. Nuclear export activity of 16.4.1 was mapped to a 60 amino acid region and a novel transport signal identified. Interaction of 16.4.1 with Rev in human cells was shown in a mammalian two-hybrid assay and by colocalization of Rev and 16.4.1 in nucleoli, indicating that Rev can recruit 16.4.1 to the nucleus/nucleoli. Rev-dependent reporter expression was inhibited by overexpressing 16.4.1 and stimulated by siRNAs targeted to 16.4.1 sequences, demonstrating that 16.4.1 expression influences the transactivation function of Rev. Conclusion: These results suggest that 16.4.1 may act as a modulator of Rev activity. The experimental strategies outlined in this study are applicable to the identification and biological characterization of further novel Rev-interacting cellular factors.

  • Identification of Adrenomedullin in Avian Type II Pneumocytes: Increased Expression after Exposure to Air Pollutants -

    Adrenomedullin (AM) is a potent vasodilator peptide present in the lung of mammals where it is expressed mainly in the columnar epithelium and alveolar macrophages. AM increases the secretion of phosphatidylcholine by type II pneumocytes, which suggests a role as an autocrine modulator of surfactant secretion. In this study we show the expression of an AM-like protein in the lung of the pigeon, Columba livia. Using an antibody against its human ortholog, AM-like immunoreactivity was found to be associated with membranous structures of the multivesicular bodies of type II pneumocytes. We also studied the differential expression of AM-like peptide in the lung of pigeons exposed to polluted city air vs cleaner countryside conditions and found that AM-like expression was higher in city animals. Similar results were obtained in an experimental study in which pigeons were exposed to increasing concentrations of a single pollutant, ozone. Taken together, our findings support the implication of AM in the response of type II pneumocytes to air pollutants.

    (J Histochem Cytochem 53:773–780, 2005)


  • Identification of Adrenomedullin in Avian Type II Pneumocytes: Increased Expression after Exposure to Air Pollutants -

    Adrenomedullin (AM) is a potent vasodilator peptide present in the lung of mammals where it is expressed mainly in the columnar epithelium and alveolar macrophages. AM increases the secretion of phosphatidylcholine by type II pneumocytes, which suggests a role as an autocrine modulator of surfactant secretion. In this study we show the expression of an AM-like protein in the lung of the pigeon, Columba livia. Using an antibody against its human ortholog, AM-like immunoreactivity was found to be associated with membranous structures of the multivesicular bodies of type II pneumocytes. We also studied the differential expression of AM-like peptide in the lung of pigeons exposed to polluted city air vs cleaner countryside conditions and found that AM-like expression was higher in city animals. Similar results were obtained in an experimental study in which pigeons were exposed to increasing concentrations of a single pollutant, ozone. Taken together, our findings support the implication of AM in the response of type II pneumocytes to air pollutants.

    (J Histochem Cytochem 53:773–780, 2005)


  • Identification of Adrenomedullin in Avian Type II Pneumocytes: Increased Expression after Exposure to Air Pollutants -

    Adrenomedullin (AM) is a potent vasodilator peptide present in the lung of mammals where it is expressed mainly in the columnar epithelium and alveolar macrophages. AM increases the secretion of phosphatidylcholine by type II pneumocytes, which suggests a role as an autocrine modulator of surfactant secretion. In this study we show the expression of an AM-like protein in the lung of the pigeon, Columba livia. Using an antibody against its human ortholog, AM-like immunoreactivity was found to be associated with membranous structures of the multivesicular bodies of type II pneumocytes. We also studied the differential expression of AM-like peptide in the lung of pigeons exposed to polluted city air vs cleaner countryside conditions and found that AM-like expression was higher in city animals. Similar results were obtained in an experimental study in which pigeons were exposed to increasing concentrations of a single pollutant, ozone. Taken together, our findings support the implication of AM in the response of type II pneumocytes to air pollutants.

    (J Histochem Cytochem 53:773–780, 2005)


  • Identification of amplified and highly expressed genes in amplicons of the T-cell line huT78 detected by cDNA microarray CGH - Background: Conventional Comparative Genomic Hybridization (CGH) has been widely used for detecting copy number alterations in cancer and for identifying regions containing candidate tumor responsible genes. Recently, several studies have shown the utility of cDNA microarray CGH for studing gene copy changes in various types of tumors. However, no such studies on T-cell lymphomas have been performed. To date T-cell lymphomas analyzed by the use of chromosome CGH have revealed only slight copy number alterations and not gene amplifications. Results: In the present study, we describe the characterization of three amplicons of the T-cell line huT78 located at 2q34-q37, 8q23-q24 and 20p, where new amplified and overexpressed genes are found. The use of a cDNA microarray containing 7.657 transcripts allowed the identification of certain genes, such as BCLX, PCNA, FKBP1A, IGFBP2 and cMYC, that are amplified, highly expressed, and also contained in the amplicons on 20p and 2q. The expresion of these genes was analyzed in 39 T-cell lymphomas and 3 other T-cell lines. Conclusion: By the use of conventional CGH and CGH and expression cDNA microarrays we defined three amplicons in the T-cell line huT78 and identified several novel gene amplifications (BCLX, PCNA, FKBP1A, IGFBP2 and cMYC). We showed that overexpression of the amplified genes could be attributable to gene dosage. We speculate that deregulation of those genes could be important in the development of T-cell lymphomas and/or in the maintenance of T-cell lines.

  • Identification of Vascular Progenitor Cells in Pulmonary Arteries of Patients with COPD. -
    Related Articles

    Identification of Vascular Progenitor Cells in Pulmonary Arteries of Patients with COPD.

    Am J Respir Cell Mol Biol. 2005 Oct 20;

    Authors: Peinado VI, Ramirez J, Roca J, Rodriguez-Roisin R, Barbera JA

    Progenitor cells of bone marrow origin migrate to injured vessels, where they may contribute to endothelial maintenance and vessel remodeling, through vascular endothelial growth factor (VEGF) related signals. To what extent progenitor cells may play a role in vascular changes occurring in patients with chronic obstructive pulmonary disease (COPD) remains unsettled. The study was addressed to identify vascular progenitor cells in pulmonary arteries of patients with COPD and to investigate whether the presence of these cells could be related to changes in endothelial function or the expression of VEGF. Pulmonary arteries of 9 patients with COPD and 6 controls were studied. Scanning electron microscopy demonstrated areas of denuded endothelium in arteries of COPD patients. Vascular progenitor cells were identified by immunohistochemistry and immunogold using antibodies against AC133, CD34 and CD45. AC133(+) cells were localized in the endothelial surface, close to denuded areas. The number of AC133(+) and CD45(+) cells in pulmonary arteries was greater in COPD patients than in controls. The number of AC133(+) cells correlated with the response of pulmonary artery rings to hypoxic stimulus. AC133(+) and CD45(+) cells were also identified in the intimal layer. The wall thickness correlated with the number of progenitor cells in the intima, as well as with VEGF and VEGF receptor-2 mRNA expression. We conclude that COPD patients show an increased number of bone marrow-derived progenitor cells in pulmonary arteries. These cells seem to contribute to ongoing endothelial repair, but they might also be involved in the pathogenesis of pulmonary vascular remodeling.

    PMID: 16239642 [PubMed - as supplied by publisher]


  • IHC Comparison of Antibodies 1D5 and 6F11 for Estrogen Receptor. -

  • Imaging genome abnormalities in cancer research - Increasing attention is focusing on chromosomal and genome structure in cancer research due to the fact that genomic instability plays a principal role in cancer initiation, progression and response to chemotherapeutic agents. The integrity of the genome (including structural, behavioral and functional aspects) of normal and cancer cells can be monitored with direct visualization by using a variety of cutting edge molecular cytogenetic technologies that are now available in the field of cancer research. Examples are presented in this review by grouping these methodologies into four categories visualizing different yet closely related major levels of genome structures. An integrated discussion is also presented on several ongoing projects involving the illustration of mitotic and meiotic chromatin loops; the identification of defective mitotic figures (DMF), a new type of chromosomal aberration capable of monitoring condensation defects in cancer; the establishment of a method that uses Non-Clonal Chromosomal Aberrations (NCCAs) as an index to monitor genomic instability; and the characterization of apoptosis related chromosomal fragmentations caused by drug treatments.

  • Imaging in breast cancer: Magnetic resonance imaging - Over the past 5 years there has been a marked increase in the use of magnetic resonance imaging (MRI) of the breast. Multiple research studies have confirmed improved cancer detection, diagnosis, and evaluation of response to therapy with breast MRI compared with mammography and ultrasound. As this exciting new technology advances, focused work in optimal scan protocols, appropriate clinical applications, and image interpretation are needed. Both the potential benefits and harms need to be evaluated to guide optimal use of this imaging modality in select patient populations.

  • Immunocytochemical Localization of Atrial Natriuretic Peptide, Vessel Dilator, Long-acting Natriuretic Peptide, and Kaliuretic Peptide in Human Pancreatic Adenocarcinomas -

    We recently found that four peptide hormones synthesized by the same gene completely inhibit the growth of human pancreatic adenocarcinomas in athymic mice. The present immunocytochemical investigation was designed to determine where in the adenocarcinomas these peptide hormones localize. Atrial natriuretic peptide, vessel dilator, long-acting natriuretic peptide, and kaliuretic peptide localized to the cytoplasm and nucleus of the human pancreatic adenocarcinomas, which is consistent with their ability to decrease DNA synthesis in the nucleus of this cancer. In this first investigation of where these peptide hormones with anticancer effects localize in any cancer, these peptide hormones also localized to the endothelium of capillaries and fibroblasts within these cancers. This is the first demonstration of growth-inhibiting peptide hormones localizing to the nucleus, where they inhibit DNA synthesis and may interact with growth-promoting hormones that localize there as the etiology of their ability to inhibit the growth of adenocarcinomas both in vitro and in vivo. (J Histochem Cytochem 53:989–995, 2005)


  • Immunocytochemical Localization of Atrial Natriuretic Peptide, Vessel Dilator, Long-acting Natriuretic Peptide, and Kaliuretic Peptide in Human Pancreatic Adenocarcinomas -

    We recently found that four peptide hormones synthesized by the same gene completely inhibit the growth of human pancreatic adenocarcinomas in athymic mice. The present immunocytochemical investigation was designed to determine where in the adenocarcinomas these peptide hormones localize. Atrial natriuretic peptide, vessel dilator, long-acting natriuretic peptide, and kaliuretic peptide localized to the cytoplasm and nucleus of the human pancreatic adenocarcinomas, which is consistent with their ability to decrease DNA synthesis in the nucleus of this cancer. In this first investigation of where these peptide hormones with anticancer effects localize in any cancer, these peptide hormones also localized to the endothelium of capillaries and fibroblasts within these cancers. This is the first demonstration of growth-inhibiting peptide hormones localizing to the nucleus, where they inhibit DNA synthesis and may interact with growth-promoting hormones that localize there as the etiology of their ability to inhibit the growth of adenocarcinomas both in vitro and in vivo. (J Histochem Cytochem 53:989–995, 2005)


  • Immunocytochemistry for Drugs Containing an Aliphatic Primary Amino Group in the Molecule, Anticancer Antibiotic Daunomycin as a Model -

    An immunocytochemistry (ICC) for the anticancer antibiotic daunomycin (DM) was developed using a combination of anti-DM serum produced against N-(gamma-maleimidobutyryloxy)succinimide (GMBS)-conjugated DM, and DM-uptake human melanoma BD cells. The antiserum was demonstrated to be specific for DM and the structurally related analogs adriamicin and epirubicin by an ICC model system of the enzyme immunoassay (EIA) using glutaraldehyde (GA)-conjugated DM as a solid phase antigen. No cross-reaction occurred with any of the other antibiotics tested such as bleomycin, pepleomycin, and mitomycin C. Successful DM ICC required a series of processes prior to the immunocytochemical reaction: the cells were first fixed with GA, then reduced with NaBH4, treated with hydrochloric acid, and finally digested with protease. The cell specimens were then subjected to immunoreaction with anti-DM serum followed by peroxidase-labeled goat anti-rabbit IgG/Fab', and in both immune reagents the detergent Triton X-100 was contained as well. The present ICC covering all these processes successfully stained for DM in the nucleus and in the perinuclear Golgi region of the cytoplasm of the BD cells, consistent with the results obtained by the DM autofluorescence method. This ICC was found to be three times as sensitive as the cytofluorometric method and applicable to the paraffin sections of the liver of rats 24 hr after an IV injection of DM. The principle used in the present study for developing DM ICC might be applied to other drugs containing the primary amino group(s) in the molecule. Thus, these ICCs for drugs are direct, precise and easy new methods that should have potential for pharmacology and toxicology studies of drugs, revealing the localization of a drug in cells and tissues. (J Histochem Cytochem 53:467–474, 2005)


  • Immunocytochemistry for Drugs Containing an Aliphatic Primary Amino Group in the Molecule, Anticancer Antibiotic Daunomycin as a Model -

    An immunocytochemistry (ICC) for the anticancer antibiotic daunomycin (DM) was developed using a combination of anti-DM serum produced against N-(gamma-maleimidobutyryloxy)succinimide (GMBS)-conjugated DM, and DM-uptake human melanoma BD cells. The antiserum was demonstrated to be specific for DM and the structurally related analogs adriamicin and epirubicin by an ICC model system of the enzyme immunoassay (EIA) using glutaraldehyde (GA)-conjugated DM as a solid phase antigen. No cross-reaction occurred with any of the other antibiotics tested such as bleomycin, pepleomycin, and mitomycin C. Successful DM ICC required a series of processes prior to the immunocytochemical reaction: the cells were first fixed with GA, then reduced with NaBH4, treated with hydrochloric acid, and finally digested with protease. The cell specimens were then subjected to immunoreaction with anti-DM serum followed by peroxidase-labeled goat anti-rabbit IgG/Fab', and in both immune reagents the detergent Triton X-100 was contained as well. The present ICC covering all these processes successfully stained for DM in the nucleus and in the perinuclear Golgi region of the cytoplasm of the BD cells, consistent with the results obtained by the DM autofluorescence method. This ICC was found to be three times as sensitive as the cytofluorometric method and applicable to the paraffin sections of the liver of rats 24 hr after an IV injection of DM. The principle used in the present study for developing DM ICC might be applied to other drugs containing the primary amino group(s) in the molecule. Thus, these ICCs for drugs are direct, precise and easy new methods that should have potential for pharmacology and toxicology studies of drugs, revealing the localization of a drug in cells and tissues. (J Histochem Cytochem 53:467–474, 2005)


  • Immunocytochemistry for Drugs Containing an Aliphatic Primary Amino Group in the Molecule, Anticancer Antibiotic Daunomycin as a Model -

    An immunocytochemistry (ICC) for the anticancer antibiotic daunomycin (DM) was developed using a combination of anti-DM serum produced against N-(gamma-maleimidobutyryloxy)succinimide (GMBS)-conjugated DM, and DM-uptake human melanoma BD cells. The antiserum was demonstrated to be specific for DM and the structurally related analogs adriamicin and epirubicin by an ICC model system of the enzyme immunoassay (EIA) using glutaraldehyde (GA)-conjugated DM as a solid phase antigen. No cross-reaction occurred with any of the other antibiotics tested such as bleomycin, pepleomycin, and mitomycin C. Successful DM ICC required a series of processes prior to the immunocytochemical reaction: the cells were first fixed with GA, then reduced with NaBH4, treated with hydrochloric acid, and finally digested with protease. The cell specimens were then subjected to immunoreaction with anti-DM serum followed by peroxidase-labeled goat anti-rabbit IgG/Fab', and in both immune reagents the detergent Triton X-100 was contained as well. The present ICC covering all these processes successfully stained for DM in the nucleus and in the perinuclear Golgi region of the cytoplasm of the BD cells, consistent with the results obtained by the DM autofluorescence method. This ICC was found to be three times as sensitive as the cytofluorometric method and applicable to the paraffin sections of the liver of rats 24 hr after an IV injection of DM. The principle used in the present study for developing DM ICC might be applied to other drugs containing the primary amino group(s) in the molecule. Thus, these ICCs for drugs are direct, precise and easy new methods that should have potential for pharmacology and toxicology studies of drugs, revealing the localization of a drug in cells and tissues. (J Histochem Cytochem 53:467–474, 2005)


  • Immunohistochemical Characterization of the Distribution of Galectin-4 in Porcine Small Intestine -

    Galectins are an evolutionarily conserved family of 15 different lectins found in various combinations in virtually every type of animal cell. One of the primary galectins expressed in intestinal epithelium is galectin-4, a tandem-repeat galectin with two carbohydrate-recognition domains in a single polypeptide chain. In the current study, we produced an anti-galectin-4 monoclonal antibody (MAb) for determining the distribution of galectin-4 in porcine small intestine to enhance our understanding of where galectin-4 performs its functions in the small intestine. In immunohistochemistry studies, this MAb detected galectin-4 primarily in the cytoplasm of absorptive epithelial cells lining intestinal villi. Mature epithelial cells at the villous tips stained the most intensely with this MAb, with progressively less intense staining observed along the sides of villi and into the crypts. In addition to its cytoplasmic localization, galectin-4 was also associated with nuclei in villous tip cells, indicating that some galectin-4 may migrate to the nucleus during terminal maturation of these cells. In intestinal crypts, a specific subset of cells, which may be enteroendocrine cells, expressed galectin-4 at a relatively high level. Galectin-4 distribution patterns were similar in all three regions (duodenum, jejunum, and ileum) of porcine small intestine. (J Histochem Cytochem 53:197–205, 2005)


  • Immunohistochemical Detection of the {beta}4 Integrin Subunit in Pancreatic Adenocarcinoma -

    The expression of the ßbeta;4 integrin subunit protein in pancreatic cancer was investigated using routine immunohistochemical methods on paraffin-embedded archival material. Forty-eight cases of pancreatic ductal adenocarcinoma were immunostained with a monoclonal antibody to the ßbeta;4 integrin subunit, and the extent of staining was compared with that seen in non-cancerous pancreatic tissues, including 15 separate cases of chronic pancreatitis and 6 sections from normal pancreas. We found that the ßbeta;4 integrin subunit protein was overexpressed in the majority of pancreatic carcinoma cases tested, whereas chronic pancreatitis and normal pancreas did not display substantial levels of expression. (J Histochem Cytochem 53:799–801, 2005)


  • Immunohistochemical Detection of the {beta}4 Integrin Subunit in Pancreatic Adenocarcinoma -

    The expression of the ßbeta;4 integrin subunit protein in pancreatic cancer was investigated using routine immunohistochemical methods on paraffin-embedded archival material. Forty-eight cases of pancreatic ductal adenocarcinoma were immunostained with a monoclonal antibody to the ßbeta;4 integrin subunit, and the extent of staining was compared with that seen in non-cancerous pancreatic tissues, including 15 separate cases of chronic pancreatitis and 6 sections from normal pancreas. We found that the ßbeta;4 integrin subunit protein was overexpressed in the majority of pancreatic carcinoma cases tested, whereas chronic pancreatitis and normal pancreas did not display substantial levels of expression. (J Histochem Cytochem 53:799–801, 2005)


  • Immunohistochemical Detection of the {beta}4 Integrin Subunit in Pancreatic Adenocarcinoma -

    The expression of the ßbeta;4 integrin subunit protein in pancreatic cancer was investigated using routine immunohistochemical methods on paraffin-embedded archival material. Forty-eight cases of pancreatic ductal adenocarcinoma were immunostained with a monoclonal antibody to the ßbeta;4 integrin subunit, and the extent of staining was compared with that seen in non-cancerous pancreatic tissues, including 15 separate cases of chronic pancreatitis and 6 sections from normal pancreas. We found that the ßbeta;4 integrin subunit protein was overexpressed in the majority of pancreatic carcinoma cases tested, whereas chronic pancreatitis and normal pancreas did not display substantial levels of expression. (J Histochem Cytochem 53:799–801, 2005)


  • Immunohistochemical Determination of Cytosolic Cytochrome c Concentration in Cardiomyocytes -

    Cytochrome c release from the intermembrane space of mitochondria is one of the triggers of apoptosis. There is no histochemical method available to demonstrate cytochrome c in cryostat sections, possibly because small cytosolic proteins diffuse readily into aqueous fixation media. This report shows that it is possible to demonstrate cytochrome c release in cardiomyocytes in failing myocardium using vapor fixation of cryostat sections and immunohistochemistry. The method is calibrated using sections from gelatin blocks containing known concentrations of cytochrome c. The method is applied to the hypertrophied right ventricular wall of rats in which pulmonary hypertension was induced by monocrotaline. Cytochrome c release is found in a fraction of the cardiomyocytes, leading to a mosaic-staining pattern. Cytochrome c release was found in myocytes over the full range of cross-sectional area (from 1 to 3.9 times control) in the hypertrophied myocardium. Cytosolic cytochrome c concentrations up to 0.4–0.5 mM occur frequently.

    (J Histochem Cytochem 53:803–807, 2005)


  • Immunohistochemical Determination of Cytosolic Cytochrome c Concentration in Cardiomyocytes -

    Cytochrome c release from the intermembrane space of mitochondria is one of the triggers of apoptosis. There is no histochemical method available to demonstrate cytochrome c in cryostat sections, possibly because small cytosolic proteins diffuse readily into aqueous fixation media. This report shows that it is possible to demonstrate cytochrome c release in cardiomyocytes in failing myocardium using vapor fixation of cryostat sections and immunohistochemistry. The method is calibrated using sections from gelatin blocks containing known concentrations of cytochrome c. The method is applied to the hypertrophied right ventricular wall of rats in which pulmonary hypertension was induced by monocrotaline. Cytochrome c release is found in a fraction of the cardiomyocytes, leading to a mosaic-staining pattern. Cytochrome c release was found in myocytes over the full range of cross-sectional area (from 1 to 3.9 times control) in the hypertrophied myocardium. Cytosolic cytochrome c concentrations up to 0.4–0.5 mM occur frequently.

    (J Histochem Cytochem 53:803–807, 2005)


  • Immunohistochemical Distribution of Sphingosine Kinase 1 in Normal and Tumor Lung Tissue -

    Sphingosine kinase 1 (SK1) is a key enzyme critical to the sphingolipid metabolic pathway responsible for catalyzing the formation of the bioactive lipid sphingosine-1-phosphate. SK1-mediated production of sphingosine-1-phosphate has been shown to stimulate such biological processes as cell growth, differentiation, migration, angiogenesis, and inhibition of apoptosis. In this study, cell type–specific immunolocalization of SK1 was examined in the bronchus/terminal bronchiole of the lung. Strong immunopositive staining was evident at the apical surface of pseudostratified epithelial cells of the bronchus and underlying smooth muscle cells, submucosal serous glands, immature chondrocytes, type II alveolar cells, foamy macrophages, endothelial cells of blood vessels, and neural bundles. Immunohistochemical screening for SK1 expression was performed in 25 samples of normal/tumor patient matched non–small-cell lung cancer tissue and found that 25 of 25 tumor samples (carcinoid [5 samples], squamous [10 samples], and adenocarcinoma tumors [10 samples]), exhibited overwhelmingly positive immunostaining for SK1 as compared with patient-matched normal tissue. In addition, an approximately 2-fold elevation of SK1 mRNA expression was observed in lung cancer tissue versus normal tissue, as well as in several other solid tumors. Taken together, these findings define the localization of SK1 in lung and provide clues as to how SK1 may play a role in normal lung physiology and the pathophysiology of lung cancer. (J Histochem Cytochem 53:1159–1166, 2005)


  • Immunohistochemical evaluation of human epidermal growth factor receptor 2 and estrogen and progesterone receptors in breast carcinoma in Jordan - IntroductionAlthough breast carcinoma (BC) is the most common malignancy affecting Jordanian females and the affected population in Jordan is younger than that in the West, no information is available on its biological characteristics. Our aims in this study are to evaluate the expression of estrogen receptor (ER) and progesterone receptor (PR) and Her-2/neu overexpression in BC in Jordan, and to compare the expression of these with other prognostic parameters for BC such as histological type, histological grade, tumor size, patients' age, and number of lymph node metastases.MethodThis is a retrospective study conducted in the Department of Pathology at Jordan University of Science and Technology. A confirmed 91 cases of BC diagnosed in the period 1995 to 1998 were reviewed and graded. We used immunohistochemistry to evaluate the expression of ER, PR, and Her-2. Immunohistochemical findings were correlated with age, tumor size, grade and axillary lymph node status. Results: Her-2 was overexpressed in 24% of the cases. The mean age of Her-2 positive cases was 42 years as opposed to 53 years among Her-2 negative cases (p = 0.0001). Her-2 expression was inversely related to ER and PR expression. Her-2 positive tumors tended to be larger than Her-2 negative tumors with 35% overexpression among T3 tumors as opposed to 22% among T2 tumors (p = 0.13). Her-2 positive cases tended to have higher rates of axillary metastases, but this did not reach statistical significance. ER and PR positive cases were seen in older patients with smaller tumor sizes. Conclusion: Her-2 overexpression was seen in 24% of BC affecting Jordanian females. Her-2 overexpression was associated with young age at presentation, larger tumor size, and was inversely related to ER and PR expression. One-fifth of the carcinomas were Her-2 positive and ER negative. This group appears to represent an aggressive form of BC presenting at a young age with large primary tumors and a high rate of four or more axillary lymph node metastases.

  • Immunohistochemical Expression of p16INK4a and bcl-2 According to HPV Type and to the Progression of Cervical Squamous Intraepithelial Lesions -

    Inactivation of the cell cycle inhibitor gene p16MTS1 seems to be involved in human papillomavirus (HPV)-related carcinogenesis because E6 and E7 oncoproteins may impair p16INK4a and, indirectly, bcl-2 functions. In this study, we analyzed the role of immunohistochemical expression of p16INK4a and bcl-2 in HPV-infected cervical biopsies as prognostic markers of the progression of squamous intraepithelial lesion (SIL). Sixty-five cervical biopsies were stratified into two subgroups according to the second biopsy: 27 of them maintained a low-grade (LG)-SIL diagnosis, and 38 progressed from LG-SIL to high-grade (HG)-SIL. p16INK4a and bcl-2 quantitative expression levels were measured by the immunoperoxidase method. PCR-DNA techniques were used to detect and type HPV. The Wilcoxon and Fisher exact tests were employed for the statistical analysis. In the group with an LG-SIL diagnosis at the second biopsy, no significant associations were found between p16INK4a and bcl-2 expression and presence of HPV16/18. In the group that progressed to HG-SIL, a significant association was observed between p16INK4a overexpression and HPV16/18 presence (p=0.021), but none with bcl-2 levels. It is concluded that immunohistochemical bcl-2 expression may not be useful for predicting the progression of HPV-related SIL. In contrast, p16INK4a overexpression seemed to be associated with HPV 16 and 18, suggesting that it may be a good marker for predicting SIL progression.

    (J Histochem Cytochem 53:509–516, 2005)


  • Immunohistochemical Expression of p16INK4a and bcl-2 According to HPV Type and to the Progression of Cervical Squamous Intraepithelial Lesions -

    Inactivation of the cell cycle inhibitor gene p16MTS1 seems to be involved in human papillomavirus (HPV)-related carcinogenesis because E6 and E7 oncoproteins may impair p16INK4a and, indirectly, bcl-2 functions. In this study, we analyzed the role of immunohistochemical expression of p16INK4a and bcl-2 in HPV-infected cervical biopsies as prognostic markers of the progression of squamous intraepithelial lesion (SIL). Sixty-five cervical biopsies were stratified into two subgroups according to the second biopsy: 27 of them maintained a low-grade (LG)-SIL diagnosis, and 38 progressed from LG-SIL to high-grade (HG)-SIL. p16INK4a and bcl-2 quantitative expression levels were measured by the immunoperoxidase method. PCR-DNA techniques were used to detect and type HPV. The Wilcoxon and Fisher exact tests were employed for the statistical analysis. In the group with an LG-SIL diagnosis at the second biopsy, no significant associations were found between p16INK4a and bcl-2 expression and presence of HPV16/18. In the group that progressed to HG-SIL, a significant association was observed between p16INK4a overexpression and HPV16/18 presence (p=0.021), but none with bcl-2 levels. It is concluded that immunohistochemical bcl-2 expression may not be useful for predicting the progression of HPV-related SIL. In contrast, p16INK4a overexpression seemed to be associated with HPV 16 and 18, suggesting that it may be a good marker for predicting SIL progression.

    (J Histochem Cytochem 53:509–516, 2005)


  • Immunohistochemical Expression of p16INK4a and bcl-2 According to HPV Type and to the Progression of Cervical Squamous Intraepithelial Lesions -

    Inactivation of the cell cycle inhibitor gene p16MTS1 seems to be involved in human papillomavirus (HPV)-related carcinogenesis because E6 and E7 oncoproteins may impair p16INK4a and, indirectly, bcl-2 functions. In this study, we analyzed the role of immunohistochemical expression of p16INK4a and bcl-2 in HPV-infected cervical biopsies as prognostic markers of the progression of squamous intraepithelial lesion (SIL). Sixty-five cervical biopsies were stratified into two subgroups according to the second biopsy: 27 of them maintained a low-grade (LG)-SIL diagnosis, and 38 progressed from LG-SIL to high-grade (HG)-SIL. p16INK4a and bcl-2 quantitative expression levels were measured by the immunoperoxidase method. PCR-DNA techniques were used to detect and type HPV. The Wilcoxon and Fisher exact tests were employed for the statistical analysis. In the group with an LG-SIL diagnosis at the second biopsy, no significant associations were found between p16INK4a and bcl-2 expression and presence of HPV16/18. In the group that progressed to HG-SIL, a significant association was observed between p16INK4a overexpression and HPV16/18 presence (p=0.021), but none with bcl-2 levels. It is concluded that immunohistochemical bcl-2 expression may not be useful for predicting the progression of HPV-related SIL. In contrast, p16INK4a overexpression seemed to be associated with HPV 16 and 18, suggesting that it may be a good marker for predicting SIL progression.

    (J Histochem Cytochem 53:509–516, 2005)


  • Immunohistochemical localization of calcitonin gene-related peptide and substance P in the rat knee cartilage at birth. -
    Related Articles

    Immunohistochemical localization of calcitonin gene-related peptide and substance P in the rat knee cartilage at birth.

    Physiol Res. 2005;55(5):549-56

    Authors: Oliva F, Tarantino U, Maffulli N

    Substance P (SP) and calcitonin gene-related peptide (CGRP) have been found in the perichondrium and within the cartilage canals. It is still unknown whether they exert a direct effect on chondrocytes during joint development. We processed 28 knees of newborn Wistar rats in 7 different fashions to perform histology and immunohistochemistry studies. Positive immunoreactivity against CGRP and SP was found in the inner aspect of the perichondrium in a close contact with chondrocytes. The presence of CGRP and SP indicates the presence of nerves fibers, and precedes the development of cartilage canals. Nerve fibers may play a role in the development of synovial joints before and during the presence of cartilage canals. The presence of CGRP and SP in the cartilage at birth may be involved in the early postnatal maturation of synovial joints. It remains to be determined whether autonomic innervation is later involved in age-related degenerative joint disease.

    PMID: 16238469 [PubMed - in process]


  • Immunohistochemical Localization of Monoamine Oxidase Type B in Pancreatic Islets of the Rat -

    Monoamine oxidase (MAO) is regarded as a mitochondrial enzyme. This enzyme localizes on the outer membrane of mitochondria. There are two kinds of MAO isozymes, MAO type A (MAOA) and type B (MAOB). Previous studies have shown that MAOB activity is found in the pancreatic islets. This activity in the islets is increased by the fasting-induced decrease of plasma glucose level. Islet B cells contain monoamines in their secretory granules. These monoamines inhibit the secretion of insulin from the B cells. MAOB is active in degrading monoamines. Therefore, MAOB may influence the insulin-secretory process by regulating the stores of monoamines in the B cells. However, it has not been determined whether MAOB is localized on B cells or other cell types of the islets. In the present study, we used both double-labeling immunofluorescence histochemical and electron microscopic immunohistochemical methods to examine the subcellular localization of MAOB in rat pancreatic islets. MAOB was found in the mitochondrial outer membranes of glucagon-secreting cells (A cells), insulin-secreting cells (B cells), and some pancreatic polypeptide (PP)-secreting cells (PP cells), but no MAOB was found in somatostatin-secreting cells (D cells), nor in certain other PP cells. There were two kinds of mitochondria in pancreatic islet B cells: one contains MAOB on their outer membranes, but a substantial proportion of them lack this enzyme. Our findings indicate that pancreatic islet B cells contain MAOB on their mitochondrial outer membranes, and this enzyme may be involved in the regulation of monoamine levels and insulin secretion in the B cells.

    (J Histochem Cytochem 53:1149–1158, 2005)


  • Immunohistochemical Localization of P-glycoprotein in Rat Brain and Detection of Its Increased Expression by Seizures Are Sensitive to Fixation and Staining Variables -

    The MDR1 gene product, P-glycoprotein (P-gp), was shown to confer multidrug resistance to cancer cells, but its overexpression is also suggested to be involved in pharmacoresistance of epilepsy by acting as an energy-dependent drug-efflux pump in the blood–brain barrier (BBB). In normal brain tissue, P-gp is almost exclusively expressed by capillary endothelial cells (EC) of the BBB, whereas little or no expression is detected in other cell types. Increased P-gp expression was observed after seizures, but localization of this increase, i.e., within brain capillary EC or within parenchymal or perivascular astrocytes, which contribute to the BBB function, is controversial. To test whether these antithetic data arise from unusual properties of the antigen itself, we compared different immunohistochemical techniques and monoclonal or polyclonal antibodies to P-gp in normal rat brain and rat brain after kainate-induced seizures. Using acetone-fixed cryostat sections of snap-frozen tissue, strong P-gp labeling was detected in EC and, after seizures, in hippocampal neurons, but not in astrocytes. In contrast, EC and neuronal P-gp immunolabeling were not seen in paraformaldehyde-fixed sections, whereas both perivascular and parenchymal astrocytes exhibited strong P-gp labeling after seizures. The lack of P-gp labeling in EC by paraformaldehyde fixation, was reversed by treatment of the sections with acetate/ethanol. These experiments demonstrate that various fixation conditions have a striking effect on the immunohistochemical localization of P-gp in rat brain and detection of its increased expression by seizures. When data obtained from different immunohistochemical techniques are taken together, seizures seem to induce overexpression of P-gp in four different cell types, i.e., EC, perivascular astrocytes, parenchymal astrocytes, and neurons. (J Histochem Cytochem 53:517–531, 2005)


  • Immunohistochemical Localization of P-glycoprotein in Rat Brain and Detection of Its Increased Expression by Seizures Are Sensitive to Fixation and Staining Variables -

    The MDR1 gene product, P-glycoprotein (P-gp), was shown to confer multidrug resistance to cancer cells, but its overexpression is also suggested to be involved in pharmacoresistance of epilepsy by acting as an energy-dependent drug-efflux pump in the blood–brain barrier (BBB). In normal brain tissue, P-gp is almost exclusively expressed by capillary endothelial cells (EC) of the BBB, whereas little or no expression is detected in other cell types. Increased P-gp expression was observed after seizures, but localization of this increase, i.e., within brain capillary EC or within parenchymal or perivascular astrocytes, which contribute to the BBB function, is controversial. To test whether these antithetic data arise from unusual properties of the antigen itself, we compared different immunohistochemical techniques and monoclonal or polyclonal antibodies to P-gp in normal rat brain and rat brain after kainate-induced seizures. Using acetone-fixed cryostat sections of snap-frozen tissue, strong P-gp labeling was detected in EC and, after seizures, in hippocampal neurons, but not in astrocytes. In contrast, EC and neuronal P-gp immunolabeling were not seen in paraformaldehyde-fixed sections, whereas both perivascular and parenchymal astrocytes exhibited strong P-gp labeling after seizures. The lack of P-gp labeling in EC by paraformaldehyde fixation, was reversed by treatment of the sections with acetate/ethanol. These experiments demonstrate that various fixation conditions have a striking effect on the immunohistochemical localization of P-gp in rat brain and detection of its increased expression by seizures. When data obtained from different immunohistochemical techniques are taken together, seizures seem to induce overexpression of P-gp in four different cell types, i.e., EC, perivascular astrocytes, parenchymal astrocytes, and neurons. (J Histochem Cytochem 53:517–531, 2005)


  • Immunohistochemical Localization of P-glycoprotein in Rat Brain and Detection of Its Increased Expression by Seizures Are Sensitive to Fixation and Staining Variables -

    The MDR1 gene product, P-glycoprotein (P-gp), was shown to confer multidrug resistance to cancer cells, but its overexpression is also suggested to be involved in pharmacoresistance of epilepsy by acting as an energy-dependent drug-efflux pump in the blood–brain barrier (BBB). In normal brain tissue, P-gp is almost exclusively expressed by capillary endothelial cells (EC) of the BBB, whereas little or no expression is detected in other cell types. Increased P-gp expression was observed after seizures, but localization of this increase, i.e., within brain capillary EC or within parenchymal or perivascular astrocytes, which contribute to the BBB function, is controversial. To test whether these antithetic data arise from unusual properties of the antigen itself, we compared different immunohistochemical techniques and monoclonal or polyclonal antibodies to P-gp in normal rat brain and rat brain after kainate-induced seizures. Using acetone-fixed cryostat sections of snap-frozen tissue, strong P-gp labeling was detected in EC and, after seizures, in hippocampal neurons, but not in astrocytes. In contrast, EC and neuronal P-gp immunolabeling were not seen in paraformaldehyde-fixed sections, whereas both perivascular and parenchymal astrocytes exhibited strong P-gp labeling after seizures. The lack of P-gp labeling in EC by paraformaldehyde fixation, was reversed by treatment of the sections with acetate/ethanol. These experiments demonstrate that various fixation conditions have a striking effect on the immunohistochemical localization of P-gp in rat brain and detection of its increased expression by seizures. When data obtained from different immunohistochemical techniques are taken together, seizures seem to induce overexpression of P-gp in four different cell types, i.e., EC, perivascular astrocytes, parenchymal astrocytes, and neurons. (J Histochem Cytochem 53:517–531, 2005)


  • Immunohistochemical Staining of Epoxy Resin Sections of Peripheral Nerve. -

  • Immunohistochemistry of Tissue Prepared by a Molecular-Friendly Fixation and Processing System. -

  • Immunoreactivity of the Septins SEPT4, SEPT5, and SEPT8 in the Human Eye -

    We aimed to examine the distribution of SEPT4, SEPT5, and SEPT8 in the human eye. For each septin, five to six normal human eyes were examined by immunohistochemical staining of paraffin sections using polyclonal antibodies against SEPT4, SEPT5, and SEPT8 and an avidin biotin complex immunodetection system. SEPT4 immunoreactivity (IR) was detected primarily in the epithelium of cornea, lens, and nonpigmented ciliary epithelium; in the endothelium of cornea and vessels of iris and retina; and in the retinal nerve fiber layer, the outer plexiform layer, the outer segments of the photoreceptor cells, the inner limiting membrane of the optic nerve head, and optic nerve axons. SEPT5-IR was present in corneal endothelial cells, iris tissue, nonpigmented ciliary epithelium, and epithelial cells of the lens. SEPT8-IR almost paralleled that of SEPT4, except for a lower SEPT8-IR of the outer photoreceptor segments and a positive staining of the meningothelial cell nests in the subarachnoidal space of the bulbar segment of the orbital optic nerve. In conclusion, SEPT4, SEPT5, and SEPT8 are expressed in various ocular tissues, each revealing a distinct expression pattern. Both physiological and potential pathophysiological role of septins in the human eye deserve further investigation. (J Histochem Cytochem 53:1139–1147, 2005)


  • Impact of cryopreservation on tetramer, cytokine flow cytometry, and ELISPOT - Background: Cryopreservation of PBMC and/or overnight shipping of samples are required for many clinical trials, despite their potentially adverse effects upon immune monitoring assays such as MHC-peptide tetramer staining, cytokine flow cytometry (CFC), and ELISPOT. In this study, we compared the performance of these assays on leukapheresed PBMC shipped overnight in medium versus cryopreserved PBMC from matched donors. Results: Using CMV pp65 peptide pool stimulation or pp65 HLA-A2 tetramer staining, there was significant correlation between shipped and cryopreserved samples for each assay (p[less than or equal to]0.001). The differences in response magnitude between cryopreserved and shipped PBMC specimens were not significant for most antigens and assays. There was significant correlation between CFC and ELISPOT assay using pp65 peptide pool stimulation, in both shipped and cryopreserved samples (p[less than or equal to]0.001). Strong correlation was observed between CFC (using HLA-A2-restricted pp65 peptide stimulation) and tetramer staining (p<0.001). Roughly similar sensitivity and specificity were observed between the three assays and between shipped and cryopreserved samples for each assay. Conclusions: We conclude that all three assays show concordant results on shipped versus cryopreserved specimens, when using a peptide-based readout. The assays are also concordant with each other in pairwise comparisons using equivalent antigen systems.

  • Impact of intercensal population projections and error of closure on breast cancer surveillance: examples from 10 California counties - IntroductionIn 2001, data from the California Cancer Registry suggested that breast cancer incidence rates among non-Hispanic white (nHW) women in Marin County, California, had increased almost 60% between 1991 and 1999. This analysis examines the extent to which these and other breast cancer incidence trends could have been impacted by bias in intercensal population projections.MethodWe obtained population projections for the year 2000 projected from the 1990 census from the California Department of Finance (DOF) and population counts from the 2000 US Census for nHW women living in 10 California counties and quantified age-specific differences in counts. We also computed age-adjusted incidence rates of invasive breast cancer in order to examine and quantify the impact of differences between the population data sources. Results: Differences between year 2000 DOF projections and year 2000 census counts varied by county and age and ranged from underestimates of 60% to overestimates of 64%. For Marin County, the DOF underestimated the number of nHW women aged 45 to 64 years by 32% compared to the 2000 US census. This difference produced a significant 22% discrepancy between breast cancer incidence rates calculated using the two population data sources. In Los Angeles and Santa Clara counties, DOF-based incidence rates were significantly lower than rates based on census data. Rates did not differ significantly by population data source in the remaining seven counties examined. Conclusion: Although year 2000 population estimates from the DOF did not differ markedly from census counts at the state or county levels, greater discrepancies were observed for race-stratified, age-specific groups within counties. Because breast cancer incidence rates must be calculated with age-specific data, differences between population data sources at the age-race level may lead to mis-estimation of breast cancer incidence rates in county populations affected by these differences, as was observed in Marin County. Although intercensal rates based on population projections are important for timely breast cancer surveillance, these rates are prone to bias due to the error of closure between population projections and decennial census population counts. Intercensal rates should be interpreted with this potential bias in mind.

  • Improving Treatment Approach in Patients With Chronic Lymphocytic Leukemia - No abstract available

  • In vitro analysis of the invasive phenotype of SUM 149, an inflammatory breast cancer cell line - Background: Inflammatory breast cancer (IBC) is the most lethal form of locally invasive breast cancer known. However, very little information is available on the cellular mechanisms responsible for manifestation of the IBC phenotype. To understand the unique phenotype of IBC, we compared the motile and adhesive interactions of an IBC cell line, SUM 149, to the non-IBC cell line SUM 102. Results: Our results demonstrate that both IBC and non-IBC cell lines exhibit similar adhesive properties to basal lamina, but SUM 149 showed a marked increase in adhesion to collagen I. In vitro haptotaxis assays demonstrate that SUM 149 was less invasive, while wound healing assays show a less in vitro migratory phenotype for SUM 149 cells relative to SUM 102 cells. We also demonstrate a role for Rho and E-cadherin in the unique invasive phenotype of IBC. Immunoblotting reveals higher E-cadherin and RhoA expression in the IBC cell line but similar RhoC expression. Rhodamine phalloidin staining demonstrates increased formation of actin stress fibers and larger focal adhesions in SUM 149 relative to the SUM 102 cell line. Conclusions: The observed unique actin and cellular architecture as well as the invasive and adhesive responses to the extracellular matrix of SUM 149 IBC cells suggest that the preference of IBC cells for connective tissue, possibly a mediator important for the vasculogenic mimicry via tubulogenesis seen in IBC pathological specimens. Overexpression of E-cadherin and RhoA may contribute to passive dissemination of IBC by promoting cell-cell adhesion and actin cytoskeletal structures that maintain tissue integrity. Therefore, we believe that these findings indicate a passive metastatic mechanism by which IBC cells invade the circulatory system as tumor emboli rather than by active migratory mechanisms.

  • In vitro mutation artifacts after formalin fixation and error prone translesion synthesis during PCR - Background: Clinical specimens are routinely fixed in 10% buffered formalin and paraffin embedded. Although DNA is commonly extracted from fixed tissues and amplified by PCR, the effects of formalin fixation are relatively unknown. Formalin fixation is known to impair PCR, presumably through damage that blocks polymerase elongation, but an insidious possibility is error prone translesion synthesis across sites of damage, producing in vitro artifactual mutations during PCR. Methods: To better understand the consequences of fixation, DNA specimens extracted from fresh or fixed tissues were amplified with Taq DNA polymerase, and their PCR products were cloned and sequenced. Results: Significantly more (3- to 4-fold) mutations were observed with fixed DNA specimens. The majority of mutations were transitions, predominantly at A:T base pairs, randomly distributed along the template. Conclusions: Formalin fixation appears to cause random base damage, which can be bridged during PCR by Taq DNA polymerase through error prone translesion synthesis. Fixed DNA is a damaged but "readable" template.

  • Inactivation of MAP kinase signalling in Myc Transformed Cells and Rescue by LiCl inhibition of GSK3 - c-Myc oncogene is an important regulator of cell cycle and apoptosis, and its dysregulated expression is associated with many malignancies. Myc is instrumental in directly or indirectly regulating the progression through the G1 phase and G1/S transition, and transformation by Myc results in perturbed cell cycle. Also contributory to the control of G1 is the Ras effector pathway Raf/MEK/ERK MAP kinase. Together with GSK3, ERK plays an important role in the critical hierarchical phosphorylation of S62/T58 controlling Myc protein levels. Therefore, our main aim was to examine the levels of MAPK in Myc transformed cells in light of the roles of ERK in cell cycle and control of Myc protein levels. We found that active forms of ERK were barely detectable in v-Myc (MC29) transformed cells. Furthermore, we could only detect reduced levels of activated ERK in c-Myc transformed cells compared to the non-transformed primary chick embryo fibroblast cells. The addition of LiCl inhibited GSK3 and successfully restored the levels of ERK in v-Myc and c-Myc transformed cells to those found in non-transformed cells. In addition, LiCl stabilised Myc protein in the non-transformed and c-Myc transformed cells but not in v-Myc transformed cells. These results can provide an important insight into the role of MAPK in the mechanism of Myc induced transformation and carcinogenesis.

  • Increased copy number at 3p14 in breast cancer - IntroductionThe present study was conducted to investigate if chromosome band 3p14 is of any pathogenic significance in the malignant process of breast cancer. Genetic studies have implicated a tumour suppressor gene on chromosome arm 3p and we have proposed LRIG1 at 3p14 as a candidate tumour suppressor. The LRIG1 gene encodes an integral membrane protein that counteracts signalling by receptor tyrosine kinases belonging to the ERBB family. LRIG1 mRNA and protein are expressed in many tissues, including breast tissue. Methods: In the present report we analysed the LRIG1 gene by fluorescence in situ hybridisation (FISH), LRIG1 mRNA by quantitative RT-PCR, and LRIG1 protein by western blot analysis. Two tumour series were analysed; one series consisted of 19 tumour samples collected between 1987 and 1995 and the other series consisted of 9 tumour samples with corresponding non-neoplastic breast tissues collected consecutively. Results: The LRIG1 gene showed increased copy number in 11 out of 28 tumours (39%) and only one tumour showed a deletion at this locus. Increased LRIG1 copy number was associated with increased levels of LRIG1 mRNA (two of three tumours) and protein (four of four tumours) in the tumours compared to matched non-neoplastic breast tissue, as assessed by RT-PCR and western blot analysis. Conclusion: The molecular function of LRIG1 as a negative regulator of ERBB receptors questions the biological significance of increased LRIG1 copy number in breast cancer. We propose that a common, but hitherto unrecognised, breast cancer linked gene is located within an amplicon containing the LRIG1 locus at 3p14.3.

  • Increased Efficiency of Fluorescence In Situ Hybridization (FISH) Using the Microwave -

    A new method is described for performing fluorescence in situ hybridization (FISH). FISH signals are enhanced by microwave pulses applied during the DNA-DNA hybridization process. It is the first description of FISH with a single/low-copy probe done more efficiently by application of microwave; the latter leads to quick results or enhancement of weak signals. Microwave FISH has been compared systematically with normal FISH, and we could demonstrate the efficiency of microwave irradiation especially in the first 100 min of hybridization. (J Histochem Cytochem 53:1301–1303, 2005)


  • Increased Efficiency of Fluorescence In Situ Hybridization (FISH) Using the Microwave -

    A new method is described for performing fluorescence in situ hybridization (FISH). FISH signals are enhanced by microwave pulses applied during the DNA-DNA hybridization process. It is the first description of FISH with a single/low-copy probe done more efficiently by application of microwave; the latter leads to quick results or enhancement of weak signals. Microwave FISH has been compared systematically with normal FISH, and we could demonstrate the efficiency of microwave irradiation especially in the first 100 min of hybridization. (J Histochem Cytochem 53:1301–1303, 2005)


  • Influence of photoperiod and running wheel access on the entrainment of split circadian rhythms in hamsters - Background: In the laboratory, behavioral and physiological states of nocturnal rodents alternate, with a period near 24 h, between those appropriate for the night (e.g., elevated wheel-running activity and high melatonin secretion) and for the day (e.g., rest and low melatonin secretion). Under appropriate 24 h light:dark:light:dark conditions, however, rodents may be readily induced to express bimodal rest/activity cycles that reflect a global temporal reorganization of the central neural pacemaker in the hypothalamus. We examine here how the relative length of the light and dark phases of the environmental cycle influences this rhythm splitting and the necessity of a running wheel for expression of this entrainment condition. Results: Rhythm splitting was observed in wheel-running and general locomotion of Siberian and Syrian hamsters. The latter also manifest split rhythms in body temperature. Access to a running wheel was necessary neither for the induction nor maintenance of this entrainment pattern. While rhythms were only transiently split in many animals with two 5 h nights, the incidence of splitting was greater with twice daily nights of shorter duration. Removal of running wheels altered the body temperature rhythm but did not eliminate its clear bimodality. Conclusions: The expression of entrained, split circadian rhythms exhibits no strict dependence on access to a running wheel, but can be facilitated by manipulation of ambient lighting conditions. These circadian entrainment patterns may be of therapeutic value to human shift-workers and others facing chronobiological challenges.

  • Influence of RARa gene on MDR1 expression and P-glycoprotein function in human leukemic cells - Background: Multidrug resistance (MDR) phenotype of malignant cells is the major problem in the chemotherapy of neoplasia. The treatment of leukemia with retinoids is aimed on the induction of leukemic cells differentiation. However the interconnections between retinoid regulated differentiation of leukemic cells and regulation of MDR remains unclear. Methods: Four lines of cultured leukemic cells of diverse types of differentiation were infected with RARa gene and stable transfectants were isolated. We investigated the differentiation of these cells as well as the expression of RARalpha and MDR1 genes and P-glycoprotein (Pgp, MDR protein) functional activity in these cells. Results: All RARa transfected sublines demonstrated the increase in the quantity of RARa mRNA. All these sublines became more differentiated. Intrinsic activity of MDR1 gene (but not Pgp functional activity) was increased in one of the transfectants. All-trans-retinoic acid (ATRA) induced Pgp activity in two of three infectants to a larger extent than in parental cells. Conclusions: The data show that RARa regulates MDR1/ Pgp activity in human leukemic cells, in the first place, Pgp activity induced by ATRA. These results show that RARa overexpression in leukemic cells could result in MDR.

  • Inhibition of chemokine expression in rat inflamed paws by systemic use of the antihyperalgesic oxidized ATP - . Background: We previously showed that local use of periodate oxidized ATP (oATP, a selective inhibitor of P2X7 receptors for ATP) in rat paws treated with Freund's adjuvant induced a significant reduction of hyperalgesia. Herein we investigate the effect of oATP administration in the rat paws inflamed by carrageenan: such condition mimics acute inflammation in humans. Results: Local, oral or intravenous administration of a single dose of oATP significantly reduced thermal hyperalgesia in hind paws of rats for 24 hours, and such effect was greater than that induced by diclofenac or indomethacin. Following oATP treatment, the expression of the pro-inflammatory chemokines interferon-gamma-inducible protein-10 (IP-10), monocyte chemoattractant protein-1 (MCP-1) and interleukin-8 (IL-8) within the inflamed tissues markedly decreased on vessels and infiltrated cells. In parallel, the immunohistochemical findings showed an impairment, with respect to the untreated rats, in P2X7 expression, mainly on nerves and vessels close to the site of inflammation. Finally, oATP treatment significantly reduced the presence of infiltrating inflammatory macrophages in the paw tissue. Conclusions: Taken together these results clearly show that oATP reduces carrageenan- induced inflammation in rats.

  • Inhibition of dynamin-dependent endocytosis increases shedding of the amyloid precursor protein ectodomain and reduces generation of amyloid beta protein - Background: The amyloid precursor protein (APP) is transported via the secretory pathway to the cell surface, where it may be cleaved within its ectodomain by alpha-secretase, or internalized within clathrin-coated vesicles. An alternative proteolytic pathway occurs within the endocytic compartment, where the sequential action of beta- and gamma-secretases generates the amyloid beta protein (Abeta). In this study, we investigated the effects of modulators of endocytosis on APP processing. Results: Human embryonic kidney cells were transfected with a dominant negative mutant of dynamin I, an important mediator of clathrin-dependent endocytosis, and APP proteolysis was analyzed. Overexpression of the mutant dynamin (dyn I K44A) resulted in increased shedding of the APP ectodomain (sAPPalpha), accumulation of the C-terminal alpha-secretase product C83, and a reduction in the release of Abeta. Levels of mature APP on the cell surface were increased in cells expressing dyn I K44A, and internalization of surface-immunolabeled APP, assessed by fluorescence microscopy, was inhibited. Dynamin is a substrate for protein kinase C (PKC), and it was hypothesized that activators of PKC, which are known to stimulate alpha-secretase-mediated cleavage of APP, might exert their effects by inhibiting dynamin-dependent endocytosis. However, the internalization of surface-biotinylated APP was unaffected by treatment of cells with phorbol 12-myristate 13-acetate in the presence of the alpha-secretase inhibitor TAPI-1. Conclusions: The results indicate that APP is internalized by a dynamin-dependent process, and suggest that alterations in the activity of proteins that mediate endocytosis might lead to significant changes in Abeta production.

  • Inhibition of insulin-like growth factor-1 receptor signaling enhances growth-inhibitory and proapoptotic effects of gefitinib (Iressa) in human breast cancer cells - IntroductionGefitinib (Iressa, ZD 1839, AstraZeneca) blocks the tyrosine kinase activity of the epidermal growth factor receptor (EGFR) and inhibits proliferation of several human cancer cell types including breast cancer. Phase II clinical trials with gefitinib monotherapy showed an objective response of 9 to 19% in non-small-cell lung cancer patients and less than 10% for breast cancer, and phase III results have indicated no benefit of gefitinib in combination with chemotherapy over chemotherapy alone. In order to improve the antineoplastic activity of gefitinib, we investigated the effects of blocking the signalling of the insulin-like growth factor 1 receptor (IGF-1R), a tyrosine kinase with a crucial role in malignancy that is coexpressed with EGFR in most human primary breast carcinomas. Methods: AG1024 (an inhibitor of IGF-1R) was used with gefitinib for treatment of MDA468, MDA231, SK-BR-3, and MCF-7 breast cancer lines, which express similar levels of IGF-1R but varying levels of EGFR. Proliferation assays, apoptosis induction studies, and Western blot analyses were conducted with cells treated with AG1024 and gefitinib as single agents and in combination. Results: Gefitinib and AG1024 reduced proliferation in all lines when used as single agents, and when used in combination revealed an additive-to-synergistic effect on cell growth inhibition. Flow cytometry measurements of cells stained with annexin V-propidium iodide and cells stained for caspase-3 activation indicated that adding an IGF-1R-targeting strategy to gefitinib results in higher levels of apoptosis than are achieved with gefitinib alone. Gefitinib either reduced or completely inhibited p42/p44 Erk kinase phosphorylation, depending on the cell line, while Akt phosphorylation was reduced by a combination of the two agents. Overexpression of IGF-1R in SK-BR-3 cells was sufficient to cause a marked enhancement in gefitinib resistance. Conclusion: These results indicate that IGF-1R signaling reduces the antiproliferative effects of gefitinib in several breast cancer cell lines, and that the addition of an anti-IGF-1R strategy to gefitinib treatment may be more effective than a single-agent approach.

  • Insulin-like growth factor binding protein 2 promotes ovarian cancer cell invasion - Background: Insulin-like growth factor binding protein 2 (IGFBP2) is overexpressed in ovarian malignant tissues and in the serum and cystic fluid of ovarian cancer patients, suggesting an important role of IGFBP2 in the biology of ovarian cancer. The purpose of this study was to assess the role of increased IGFBP2 in ovarian cancer cells. Results: Using western blotting and tissue microarray analyses, we showed that IGFBP2 was frequently overexpressed in ovarian carcinomas compared with normal ovarian tissues. Furthermore, IGFBP2 was significantly overexpressed in invasive serous ovarian carcinomas compared with borderline serous ovarian tumors. To test whether increased IGFBP2 contributes to the highly invasive nature of ovarian cancer cells, we generated IGFBP2-overexpressing cells from an SKOV3 ovarian cancer cell line, which has a very low level of endogenous IGFBP2. A Matrigel invasion assay showed that these IGFBP2-overexpressing cells were more invasive than the control cells. We then designed small interference RNA (siRNA) molecules that attenuated IGFBP2 expression in PA-1 ovarian cancer cells, which have a high level of endogenous IGFBP2. The Matrigel invasion assay showed that the attenuation of IGFBP2 expression indeed decreased the invasiveness of PA-1 cells. Conclusions: We therefore showed that IGFBP2 enhances the invasion capacity of ovarian cancer cells. Blockage of IGFBP2 may thus constitute a viable strategy for targeted cancer therapy.

  • Interaction between spontaneous and neurally-mediated regulation of smooth muscle tone in the rabbit corpus cavernosum. -
    Related Articles

    Interaction between spontaneous and neurally-mediated regulation of smooth muscle tone in the rabbit corpus cavernosum.

    J Physiol. 2005 Oct 20;

    Authors: Hashitani H, Yanai Y, Shirasawa N, Soji T, Tomita A, Kohri K, Suzuki H

    Interaction between spontaneous and neurally-mediated regulation of tone in the corpus cavernosum smooth muscle (CCSM) of the rabbit was investigated. Changes in isometric muscle tension, intracellular concentration of Ca(2+) ([Ca(2+)]i) and membrane potential were recorded. CCSM developed spontaneous contractions, transient increases in [Ca(2+)]i (Ca transients) and depolarizations. This spontaneous activity was abolished by blocking L-type Ca channels (nicardipine 1 microM), sarcoplasmic reticulum Ca pump activity (cyclopiazonic acid 10 microM), Ca-activated Cl channels (niflumic acid 10 microM) or cyclooxygenase-2 (COX-2; NS-398 1 microM). Transmural nerve stimulation initiated either alpha-adrenergic contractions or nitrergic relaxations of CCSM depending on the level of muscle tone. NS-398 suppressed nerve-evoked contractions by about 70 % but caused only a 40 % reduction in the corresponding Ca transient. Blocking nitric oxide synthase with N(omega)-nitro-L-arginine (LNA 100 microM) reinforced nerve-evoked Ca transients by about 150 %, whilst increasing the corresponding Ca transients by only 20 %. In CCSM preparations which had been pre-contracted with either noradrenaline (0.3 microM) or prostaglandin F2alpha (0.1 microM), nerve stimulation inhibited about 70% of the contraction and caused only a 20 % decrease in [Ca(2+)]i. Fluorescent immunohistochemistry with COX-2 antibodies and the reverse transcriptase (RT)-polymerase chain reaction (PCR) method showed that the enzyme and its mRNA were highly expressed in the CCSM. These results suggest that spontaneously produced prostaglandins (PGs) not only contribute to the generation of spontaneous contractions but also facilitate nerve-evoked contractions. Conversely, spontaneously released nitric oxide (NO) suppresses excitation. Thus, interaction between spontaneous and neurally-mediated regulation of CCSM tone may be fundamental to maintaining the muscle contractility. In addition, both PGs and NO appear to alter CCSM tone with only small changes in [Ca(2+)]i.

    PMID: 16239265 [PubMed - as supplied by publisher]


  • Intercellular communication, NO and the biology of Chinese medicine - New multiple categories of health disciplines have become popular in the west and integration between the medicinal approaches became essential. The hypothesis presented here suggests a novel integrative view that combines Western biochemistry with the Chinese medicinal concept of qi. The core for this hypothesis is that transmission of qi along the meridians is based on informational molecules that travel via an intercellular communication system. Acupuncture at specific points, enhances the flow of the signaling molecules through this communication system. Nitric oxide is suggested as a prime candidate for such a signaling molecule in the meridian system. The biochemistry of nitric oxide can shed light on the biology underlying Chinese medicine while Chinese medicinal data can provide a clue to the sought after framework for nitric oxide.

  • Intercellular junctions in Ewing sarcoma/primitive neuroectodermal tumor: additional evidence of epithelial differentiation. -
    Related Articles

    Intercellular junctions in Ewing sarcoma/primitive neuroectodermal tumor: additional evidence of epithelial differentiation.

    Mod Pathol. 2005 Nov;18(11):1403-10

    Authors: Schuetz AN, Rubin BP, Goldblum JR, Shehata B, Weiss SW, Liu W, Wick MR, Folpe AL

    Ewing sarcoma/primitive neuroectodermal tumor (ES/PNET) has recently been shown to frequently express cytokeratins, suggesting partial epithelial differentiation. Older ultrastructural studies have documented primitive cell-cell junctions in ES/PNET, reportedly resembling poorly formed desmosomes. Recently, paraffin-reactive antibodies have become available to proteins found in a variety of intercellular junctions indicative of epithelial differentiation, including tight junctions, desmosomes and adherens junctions. We examined intercellular junction protein expression in a large number of genetically confirmed ES/PNET. Formalin-fixed, paraffin-embedded sections from 23 primary and seven recurrent or metastatic cases of genetically confirmed ES/PNET were immunostained for claudin-1 and occludin (tight junction structural proteins), zonula occludens-1 (ZO-1, tight junction linker protein), desmoglein 1/2 (desmosomal adherens protein), desmoplakin (desmosomal structural protein) and E-cadherin (epithelial adherens junction protein), using steam heat-induced epitope retrieval and the Dako Envision system. Cases with >5% positive cells were scored as 'positive'. Normal colonic epithelium and skin served as external positive controls. Claudin-1 was expressed by 19 of 30 specimens (63%), ZO-1 was expressed by 15 of 29 specimens (51%), and occludin was expressed by three of 28 specimens (11%). In 28 specimens all three tight junction markers were evaluable. In all, 15 samples (54%) expressed only one tight junction marker, and 10 samples (36%) expressed two tight junction markers. No case expressed all three tight junction markers. Desmoglein was expressed in one of 30 (3%) samples. Desmoplakin was expressed in two of 28 (7%) samples. E-cadherin was negative in all cases. Our data suggest that many of the previously described cell-cell junctions in ES/PNET are poorly formed tight junctions, given the high frequency of claudin-1 and ZO-1 expression. This may underestimate the true frequency of tight junction protein expression in ES/PNET, as there are at least 20 different claudins and other ZO proteins. These tight junctions are almost certainly abnormal, given the absence of occludin expression in most cases. Desmosomal and adherens junction protein expression was rare to absent. Our findings provide additional evidence that ES/PNET frequently show partial epithelial differentiation.Modern Pathology (2005) 18, 1403-1410. doi:10.1038/modpathol.3800435; published online 6 May 2005.

    PMID: 15920547 [PubMed - in process]


  • Intracellular Distribution of Desmoplakin in Human Odontoblasts -

    Coexpression of desmosomal proteins and vimentin has been reported in a specific mesenchymal phenotype. This study investigated the expression of vimentin-binding desmosomal proteins in human dental pulp fibroblasts (DPF) and odontoblasts. The dental pulp has no cells expressing desmocollin (DSC) 1-3, desmoglein (DSG) 1-3, junction plakoglobin (JUP), or desmoplakin (DPK) 1 and 2 except for odontoblasts expressing DPK. A confocal image by laser-scanning microscopy demonstrated the diffuse distribution of DPK in the cytoplasm throughout the odontoblast processes. In culture, the mRNA expression of JUP and DPK1, but not DSC1-3 and DSG1-3, was detected in all DPF clones tested and also in odontoblast-like cells (OB) expressing osteocalcin and dentin sialophosphoprotein mRNAs established in the differentiation medium. The DPF having the potential to differentiate into OB expressed vimentin, but not DPK before culturing in the differentiation medium, whereas OB expressed vimentin-binding DPK1. These results suggest that DPF usually expresses DPK1 mRNA, and that the DPK1 production and the bonding of vimentin to DPK1 occur in DPF with the differentiation into odontoblasts.

    (J Histochem Cytochem 53:1099–1108, 2005)


  • Intracellular Localization of Oxidized Low-density Lipoproteins in Atherosclerotic Plaque Cells Revealed by Electron Microscopy Combined with Laser Capture Microdissection -

    Recently, laser capture microdissection (LCM) has become a powerful tool for investigating the genome and protein contents of cells populating normal and pathologically altered tissues. The present work reports a technique for the preparation of tissue specimens for further LCM combined with electron microscopy. In this work, atherosclerotic plaque cells containing oxidized low-density lipoproteins (LDL) were microdissected from human carotid arteries and the intracellular distribution of oxidized LDL was examined, providing novel information about the association of microvesicles containing oxidized LDL with "lipid droplets" in macrophage foam cells.

    (J Histochem Cytochem 53:793–797, 2005)


  • Intracellular Localization of Oxidized Low-density Lipoproteins in Atherosclerotic Plaque Cells Revealed by Electron Microscopy Combined with Laser Capture Microdissection -

    Recently, laser capture microdissection (LCM) has become a powerful tool for investigating the genome and protein contents of cells populating normal and pathologically altered tissues. The present work reports a technique for the preparation of tissue specimens for further LCM combined with electron microscopy. In this work, atherosclerotic plaque cells containing oxidized low-density lipoproteins (LDL) were microdissected from human carotid arteries and the intracellular distribution of oxidized LDL was examined, providing novel information about the association of microvesicles containing oxidized LDL with "lipid droplets" in macrophage foam cells.

    (J Histochem Cytochem 53:793–797, 2005)


  • Intracellular Localization of Oxidized Low-density Lipoproteins in Atherosclerotic Plaque Cells Revealed by Electron Microscopy Combined with Laser Capture Microdissection -

    Recently, laser capture microdissection (LCM) has become a powerful tool for investigating the genome and protein contents of cells populating normal and pathologically altered tissues. The present work reports a technique for the preparation of tissue specimens for further LCM combined with electron microscopy. In this work, atherosclerotic plaque cells containing oxidized low-density lipoproteins (LDL) were microdissected from human carotid arteries and the intracellular distribution of oxidized LDL was examined, providing novel information about the association of microvesicles containing oxidized LDL with "lipid droplets" in macrophage foam cells.

    (J Histochem Cytochem 53:793–797, 2005)


  • Introduction of Tyramide Signal Amplification (TSA) to Pre-embedding Nanogold-Silver Staining at the Electron Microscopic Level -

    The tyramide signal amplification (TSA) technique has been shown to detect scarce tissue antigens in light and electron microscopy. In this study we applied the TSA technique at the electron microscopic level to pre-embedding immunocytochemistry. This protocol was compared to the non-amplified protocol. With the TSA protocol, the labeling of GM130, a cis-Golgi matrix protein, was tested in a cell line and found to be highly sensitive and more enhanced than that with the simple protocol. Moreover, the gold particles were well localized to the cis-side of the Golgi apparatus in both the TSA and the simple protocol. (J Histochem Cytochem 53:249–252, 2005)


  • Iron Chelation Therapy - Although iron chelation therapy with deferoxamine (DFO) has changed life expectancy in thalassemic patients, -compliance with the rigorous requirements of long-term -subcutaneous DFO infusions is unsatisfactory. This problem underlines the current efforts for developing alternative, orally effective chelators to improve compliance and treatment results. For the patient with transfusional iron overload in whom results of DFO treatment are unsatisfactory, several orally effective agents are now available. The most important of the new generation of oral chelators are deferiprone and ICL670. Total iron excretion with deferiprone is less than with DFO, but deferiprone has a better ability to penetrate cell membranes and may have a better cardioprotective effect than DFO. Current studies of the clinical efficacy and tolerability of ICL670 indicate that at a single oral dose of 20 mg/kg daily, it may be as effective as parenteral DFO used at the standard dose of 40 mg/kg daily. Combined chelation treatment, employing a weak chelator that penetrates cells better, and a stronger chelator with efficient urinary excretion, may result in improved therapeutic effect through iron shuttling between the two compounds. The efficacy of combined -chelation treatment is additive and offers an increased -likelihood of success in patients previously failing DFO or deferiprone monotherapy.

  • Is an increase in CD4/CD8 T-cell ratio in lymph node fine needle aspiration helpful for diagnosing Hodgkin lymphoma? A study of 85 lymph node FNAs with increased CD4/CD8 ratio - Background: An elevated CD4/CD8 T-cell ratio on flow cytometry (FCM) analysis has been reported in the literature to be associated with Hodgkin lymphoma (HL). The purpose of our study was to determine the diagnostic significance of an elevated CD4/CD8 ratio in lymph node fine needle aspiration (FNA) specimens.DesignBetween 1996 and 2002, out of 837 lymph node FNAs submitted for flow cytometry analysis, 85 cases showed an elevated CD4/CD8 ratio, defined as greater than or equal to 4, without definitive evidence of a lymphoproliferative disorder. The cytologic diagnoses of these 85 cases were grouped into four categories: reactive, atypical, Hodgkin lymphoma (HL), and non-Hodgkin lymphoma (NHL). Histologic follow-up was available in 17/85 (20%) of the cases. Results: 5 of the 64 cases in which FCM and cytology did not reveal evidence of a lymphoproliferative disease had tissue follow-up because of persistent lymphadenopathy and high clinical suspicion. 3/5 (60%) confirmed the diagnosis of reactive lymphadenopathy. The two remaining cases (40%) were positive for lymphoma (1HL, 1NHL). 8/15 cases called atypical on cytology had histologic follow-up. 7/8 (87.5%) cases were positive for lymphoma (3HL, 4NHL). 3/4 cases called HL on cytology had tissue follow-up and all 3 (100%) confirmed the diagnosis of HL. One case diagnosed as NHL on cytology was found to be a diffuse large B-cell lymphoma. In summary, out of 17 cases with histologic follow-up 4/17 (24%) were reactive with CD4/CD8 T-cell ratio of 4.1-29, 7/17 (41%) were HLs with CD4/CD8 T-cell ratio of 5.3 - 11, and 6/17 (35%) were NHLs with CD4/CD8 T-cell ratio of 4.2 - 14. Conclusion: An elevated CD4/CD8 ratio on FCM is a nonspecific finding which may be seen in both reactive and lymphoproliferative disorders. Cytology diagnosis is more pertinent when an increased CD4/CD8 ratio is the only finding on FCM. KEY WORDS: lymph node, FNA, cytology, Hodgkin lymphoma

  • Karyotype and Molecular Cytogenetic Studies in Polycythemia Vera - A minority of patients with newly diagnosed polycythemia vera (PV) have an abnormal karyotype in their myeloid cells but no invariant chromosomal aberration has been found. The most frequent visible alteration is a 20q deletion, also characterized in other myeloproliferative diseases (MPD) and myeloid malignancies; among other chromosomal changes, trisomy 9 appears more common in PV than in other MPDs. When a myelofibrosis complicates the course of the disease, cytogenetic anomalies become quite common with a striking frequency of partial duplication 1q; an evolution towards myelodysplasia or acute leukemia is almost always associated with nonspecific chromosomal aberrations. Modern cytogenetic methods have disclosed cryptic anomalies and pointed out the high frequency of 9p alterations affecting a restricted region, thus stimulating an active search for candidate genes or specific mutations.

  • Key stages in mammary gland development: The mammary end bud as a motile organ - In the rodent, epithelial end buds define the tips of elongating mammary ducts. These highly motile structures undergo repeated dichotomous branching as they aggressively advance through fatty stroma and, turning to avoid other ducts, they finally cease growth leaving behind the open, tree-like framework on which secretory alveoli develop during pregnancy. This review identifies the motility of end buds as a unique developmental marker that represents the successful integration of systemic and local mammotrophic influences, and covers relevant advances in ductal growth regulation, extracellular matrix (ECM) remodeling, and cell adhesion in the inner end bud. An unexpected growth-promoting synergy between insulin-like growth factor-1 and progesterone, in which ducts elongate without forming new end buds, is described as well as evidence strongly supporting self-inhibition of ductal elongation by end-bud-secreted transforming growth factor-β acting on stromal targets. The influence of the matrix metalloproteinase ECM-remodeling enzymes, notably matrix metalloproteinase-2, on end bud growth is discussed in the broader context of enzymes that regulate the polysaccharide-rich glycosaminoglycan elements of the ECM. Finally, a critical, motility-enabling role for the cellular architecture of the end bud is identified and the contribution of cadherins, the netrin/neogenin system, and ErbB2 to the structure and motility of end buds is discussed.

  • Key stages of mammary gland development: Molecular mechanisms involved in the formation of the embryonic mammary gland - The development of the embryonic mammary gland involves communication between the epidermis and mesenchyme and is coordinated temporally and spatially by various signaling pathways. Although many more genes are likely to control mammary gland development, functional roles have been identified for Wnt, fibroblast growth factor, and parathyroid hormone-related protein signaling. This review describes what is known about the molecular mechanisms that regulate embryonic mammary gland development.

  • Keystone symposium: The role of microenvironment in tumor induction and progression, Banff, Canada, 5–10 February 2005 - The first Keystone symposium on the role of microenvironment in tumor induction and progression attracted 274 delegates from 13 countries to Banff in the heart of the Canadian Rockies. The meeting was organized by Mina Bissell, Ronald DePinho and Luis Parada, and was held concurrently with the Keystone symposium on cancer and development, chaired by Matthew Scott and Roeland Nusse. The 30 oral presentations and over 130 posters provided an excellent forum for discussing emerging data in this rapidly advancing field.

  • KIT (CD117): A Review on Expression in Normal and Neoplastic Tissues, and Mutations and Their Clinicopathologic Correlation. -

  • KIT is highly expressed in adenoid cystic carcinoma of the breast, a basal-like carcinoma associated with a favorable outcome - Sandy Azoulay, Marick Lae, Paul Freneaux, Solange Merle, Abir Al Ghuzlan, Caroline Chnecker, Christophe Rosty, Jerzy Klijanienko, Brigitte Sigal-Zafrani, Remy Salmon, Alain Fourquet, Xavier Sastre-Garau & Anne Vincent-Salomon

  • Laminin isoform expression in breast tumors - Certain laminins of vascular basement membranes have been identified in human breast tumors and brain gliomas that share the same β1 chain. These laminins are new carcinoma angiogenic markers and might represent potential targets for antiangiogenic therapy.

  • Late stage inhibition of hematogenous melanoma metastasis by cystatin C over-expression - Background: Tumor metastasis is a frequent cause of treatment failure for cancer patients. A key feature of metastatic cancer cells is their invasive ability. Cysteine proteases contribute to invasive properties of many cancer cell types. To analyze the contribution of cysteine proteases to metastasis we have over-expressed in B16 melanoma cells the natural cysteine protease inhibitor, cystatin C. We measured in vitro invasion of cystatin over-expression clones with Boyden chamber type assays. Tail-vein injections of cells were used to compare lung tumor colonization. Subcutaneous tumor growth and tumor cell metastasis from primary tumors were also analyzed. Apoptosis of tumor cells was measured in lung tissues following melanoma cell injection. Results: Results show the in vitro invasion of cystatin C over-expressing cells was dramatically inhibited. Lung tumor colonization was also reduced. Increased tumor cell apoptosis was found to be an important factor and may be related to the reduced tumor burden noted in this system of melanoma metastasis. Conclusions: Cysteine proteases therefore, may be a target for future anti-metastatic therapies.

  • Lenalidomide (Revlimid, CC-5013) in Myelodysplastic Syndromes: Is It Any Good? - The myelodysplastic syndromes (MDS) can be divided into 'early' and 'advanced' disease by evaluation of prognostic variables such as the number of cytopenias, karyotype, and percentage of myeloblasts. Patients with an isolated interstitial deletion of chromosome 5q31 represent a distinct subset who may derive particular benefit from immunomodulatory drugs. Goals of therapy for early MDS focus on hematologic improvement and maximizing quality of life. Thalidomide, the prototype of the immunomo-dulatory drugs, yields major erythroid responses in some patients with early MDS, but dose-limiting neurologic toxicities limit its potential clinical benefit. Lenalidomide, a more potent and non-neurotoxic derivative, has shown promising results in early MDS, yielding hematologic improvement in almost half of patients, and transfusion independence with cytogenetic remissions in approximately two thirds of patients harboring the chromosome 5q31 deletion.

  • Light and Electron Microscopic Immunohistochemical Detection of Bromodeoxyuridine-labeled Cells in the Brain: Different Fixation and Processing Protocols -

    Bromodeoxyuridine (BrdU) immunohistochemistry is the method of choice for labeling newly generated cells in the brain. Most BrdU studies utilize paraformaldehyde-fixed brain tissue because of its compatibility with both BrdU and other immunohistochemical methods. However, stronger fixation is required for electron microscopic studies, and unfixed tissue is needed for biochemical and molecular studies. Because there are no systematic studies comparing the effects of different fixatives on BrdU immunohistochemistry in brain tissue, we compared BrdU immunohistochemical methods in brain tissue fixed with 4% paraformaldehyde, a mixed glutaraldehyde–paraformaldehyde fixative for electron microscopy, and unfixed tissue from brains perfused only with buffer and flash frozen. After optimizing immunostaining protocols, qualitative assessments of light microscopic diaminobenzidine labeling and of double-label immunofluorescence with confocal microscopy demonstrated excellent BrdU labeling in each of the three groups. Quantitative stereological assessment of the number of BrdU-labeled cells in rat dentate gyrus showed no significant difference in the number of labeled cells detected with each perfusion protocol. Additionally, we developed a protocol to visualize BrdU-labeled cells in the electron microscope with adequate preservation of fine structure in both rat and monkey brain.

    (J Histochem Cytochem 53:821–832, 2005)


  • Light and Electron Microscopic Immunohistochemical Detection of Bromodeoxyuridine-labeled Cells in the Brain: Different Fixation and Processing Protocols -

    Bromodeoxyuridine (BrdU) immunohistochemistry is the method of choice for labeling newly generated cells in the brain. Most BrdU studies utilize paraformaldehyde-fixed brain tissue because of its compatibility with both BrdU and other immunohistochemical methods. However, stronger fixation is required for electron microscopic studies, and unfixed tissue is needed for biochemical and molecular studies. Because there are no systematic studies comparing the effects of different fixatives on BrdU immunohistochemistry in brain tissue, we compared BrdU immunohistochemical methods in brain tissue fixed with 4% paraformaldehyde, a mixed glutaraldehyde–paraformaldehyde fixative for electron microscopy, and unfixed tissue from brains perfused only with buffer and flash frozen. After optimizing immunostaining protocols, qualitative assessments of light microscopic diaminobenzidine labeling and of double-label immunofluorescence with confocal microscopy demonstrated excellent BrdU labeling in each of the three groups. Quantitative stereological assessment of the number of BrdU-labeled cells in rat dentate gyrus showed no significant difference in the number of labeled cells detected with each perfusion protocol. Additionally, we developed a protocol to visualize BrdU-labeled cells in the electron microscope with adequate preservation of fine structure in both rat and monkey brain.

    (J Histochem Cytochem 53:821–832, 2005)


  • Light microscopic demonstration of the microlumen of ependymoma: a study of the usefulness of antigen retrieval for epithelial membrane antigen (EMA) immunostaining. -
    Related Articles

    Light microscopic demonstration of the microlumen of ependymoma: a study of the usefulness of antigen retrieval for epithelial membrane antigen (EMA) immunostaining.

    Brain Tumor Pathol. 2004;21(1):17-21

    Authors: Kawano N, Yasui Y, Utsuki S, Oka H, Fujii K, Yamashina S

    To determine the origin of dotlike epithelial membrane antigen (EMA) immunoreactivity of ependymoma, which is consistent with the eosinophilic globular body in hematoxylin and eosin (H&E) stain, an immunoelectron microscopic study was undertaken. The usefulness of antigen retrieval pretreatment in detecting the dotlike EMA immunoreactivity in ependymomas was also studied. The materials were 29 ependymomas, 7 autopsy brains as a normal control, and 50 brain tumors of various types. The study confirmed that most of the brown dots in EMA immunostain in ependymoma represented microlumina of tumor cells. In ependymomas, plain EMA immunostaining showed dotlike positivity in only six cases (21%), and antigen retrieval pretreatment increased the number of positives up to 26 cases (90%). Antigen retrieved CD99 detected 23 positive cases (80%) in ependymomas. On the basis of the results, although some false positive findings were raised by antigen retrieval pretreatment, the authors positively recommend adoption of the technique, especially when ependymoma remains as one of the differential diagnoses of the tumor.

    PMID: 15696964 [PubMed - indexed for MEDLINE]


  • lin-12Notch functions in the adult nervous system of C. elegans - Background: Notch signaling pathways are conserved across species and traditionally have been implicated in cell fate determination during embryonic development. Notch signaling components are also expressed postdevelopmentally in the brains of adult mice and Drosophila. Recent studies suggest that Notch signaling may play a role in the physiological, rather than developmental, regulation of neurons. Here, we investigate a new non-developmental role for Caenorhabditis elegans lin-12 Notch signaling in neurons regulating the spontaneous reversal rate during locomotion. Results: The spontaneous reversal rate of C. elegans during normal locomotion is constant. Both lin-12 gain and loss of function mutant animals had significantly increased reversal rates compared to wild type controls. These defects were caused by lin-12 activity, because the loss of function defect could be rescued by a wild type lin-12 transgene. Furthermore, overexpression of lin-12 recapitulated the gain-of-function defect. Increasing or decreasing lin-12 activity in the postdevelopmental adult animal was sufficient to rapidly and reversibly increase reversals, thereby excluding a developmental role for lin-12. Although lin-12 is expressed in the vulval and somatic gonad lineages, we find that these tissues play no role in regulating reversal rates. In contrast, altering lin-12 activity specifically in the nervous system was sufficient to increase reversals. These behavioral changes require components of the canonical lin-12 signaling cascade, including the ligand lag-2 and the transcriptional effector lag-1. Finally, the C. elegans AMPA/kainate glutamate receptor homolog glr-1 shows strong genetic interactions with lin-12, suggesting that glr-1 and/or other glutamate gated channels may be targets of lin-12 regulation. Conclusions: Our results demonstrate a neuronal role for lin-12 Notch in C. elegans and suggest that lin-12 acutely regulates neuronal physiology to modulate animal behavior, without altering neuronal cell fate specification or neurite outgrowth. This is consistent with a role for Notch signaling in neurological disease with late onset symptoms.

  • Localization of CD44 (Hyaluronan Receptor) and Hyaluronan in Rat Mandibular Condyle -

    CD44 is a multifunctional adhesion molecule that binds to hyaluronan (HA), type I collagen, and fibronectin. We investigated localization of CD44 and HA in mandibular condylar cartilage compared with the growth plate and the articular cartilage, to clarify the characteristics of chondrocytes. We also performed Western blotting using a lysate of mandibular condyle. In mandibular condyle, CD44-positive cells were seen in the surface region of the fibrous cell layer and in the proliferative cell layer. Western blotting revealed that the molecular weight of CD44 in condyle was 78 to 86 kD. Intense reactivity for HA was detected on the surface of the condyle and the lacunae of the hypertrophic cell layer. Moderate labeling was seen in cartilage matrix of the proliferative and maturative layer. Weak labeling was also seen in the fibrous cell layer. In growth plate and articular cartilage, HA was detected in all cell layers. However, chondrocytes of these cartilages did not exhibit reactivity for CD44. These results suggest that chondrocytes in the mandibular condylar cartilage differ in expression of CD44 from those in tibial growth plate and articular cartilage. Cell-matrix interaction between CD44 and HA may play an important role in the proliferation of chondrocytes in the mandibular condyle.

    (J Histochem Cytochem 53:113–120, 2005)


  • Localization of Cytochrome P450 CYP2S1 Expression in Human Tissues by In Situ Hybridization and Immunohistochemistry -

    CYP2S1 is a recently discovered dioxin-inducible member of the cytochrome P450 superfamily. It has been shown to be involved in the metabolism of some aromatic hydrocarbons as well as retinoic acid, suggesting a role in biotransformation of both exogenous and endogenous compounds. In this study, we used mRNA in situ hybridization and immunohistochemistry to investigate the cellular localization of CYP2S1 in various human tissues using tissue microarrays. High expression levels were observed mainly in epithelial cell types, especially in the epithelia frequently exposed to xenobiotics. In the respiratory tract, the expression was strong in nasal cavity, bronchi, and bronchioli, whereas it was low in the alveolar lining cells. Similarly, CYP2S1 was highly expressed in the epithelial cells throughout the gastrointestinal tract. Strong epithelial expression was also observed in uterine cervix, urinary bladder, and skin. In many exocrine glands (e.g., adrenal gland and pancreas), secretory epithelial cells showed moderate to strong expression levels. In the liver, the expression was low. CYP2S1 was highly expressed in epithelial cells that are major targets for carcinogen exposure and common progenitor cells to tumor development. Indeed, we found strong CYP2S1 expression in many tumors of epithelial origin.

    (J Histochem Cytochem 53:549–556, 2005)


  • Localization of Cytochrome P450 CYP2S1 Expression in Human Tissues by In Situ Hybridization and Immunohistochemistry -

    CYP2S1 is a recently discovered dioxin-inducible member of the cytochrome P450 superfamily. It has been shown to be involved in the metabolism of some aromatic hydrocarbons as well as retinoic acid, suggesting a role in biotransformation of both exogenous and endogenous compounds. In this study, we used mRNA in situ hybridization and immunohistochemistry to investigate the cellular localization of CYP2S1 in various human tissues using tissue microarrays. High expression levels were observed mainly in epithelial cell types, especially in the epithelia frequently exposed to xenobiotics. In the respiratory tract, the expression was strong in nasal cavity, bronchi, and bronchioli, whereas it was low in the alveolar lining cells. Similarly, CYP2S1 was highly expressed in the epithelial cells throughout the gastrointestinal tract. Strong epithelial expression was also observed in uterine cervix, urinary bladder, and skin. In many exocrine glands (e.g., adrenal gland and pancreas), secretory epithelial cells showed moderate to strong expression levels. In the liver, the expression was low. CYP2S1 was highly expressed in epithelial cells that are major targets for carcinogen exposure and common progenitor cells to tumor development. Indeed, we found strong CYP2S1 expression in many tumors of epithelial origin.

    (J Histochem Cytochem 53:549–556, 2005)


  • Localization of Cytochrome P450 CYP2S1 Expression in Human Tissues by In Situ Hybridization and Immunohistochemistry -

    CYP2S1 is a recently discovered dioxin-inducible member of the cytochrome P450 superfamily. It has been shown to be involved in the metabolism of some aromatic hydrocarbons as well as retinoic acid, suggesting a role in biotransformation of both exogenous and endogenous compounds. In this study, we used mRNA in situ hybridization and immunohistochemistry to investigate the cellular localization of CYP2S1 in various human tissues using tissue microarrays. High expression levels were observed mainly in epithelial cell types, especially in the epithelia frequently exposed to xenobiotics. In the respiratory tract, the expression was strong in nasal cavity, bronchi, and bronchioli, whereas it was low in the alveolar lining cells. Similarly, CYP2S1 was highly expressed in the epithelial cells throughout the gastrointestinal tract. Strong epithelial expression was also observed in uterine cervix, urinary bladder, and skin. In many exocrine glands (e.g., adrenal gland and pancreas), secretory epithelial cells showed moderate to strong expression levels. In the liver, the expression was low. CYP2S1 was highly expressed in epithelial cells that are major targets for carcinogen exposure and common progenitor cells to tumor development. Indeed, we found strong CYP2S1 expression in many tumors of epithelial origin.

    (J Histochem Cytochem 53:549–556, 2005)


  • Localization of Mesothelin in Epithelial Ovarian Cancer. -

  • Localization of P2X and P2Y Receptors in Dorsal Root Ganglia of the Cat -

    The distribution of P2X and P2Y receptor subtypes in upper lumbosacral cat dorsal root ganglia (DRG) has been investigated using immunohistochemistry. Intensity of immunoreactivity for six P2X receptors (P2X5 receptors were immuno-negative) and the three P2Y receptors examined in cat DRG was in the order of P2Y2 = P2Y4>P2X3>P2X2 = P2X7>P2X6>P2X1 = P2X4>P2Y1. P2X3, P2Y2, and P2Y4 receptor polyclonal antibodies stained 33.8%, 35.3%, and 47.6% of DRG neurons, respectively. Most P2Y2, P2X1, P2X3, P2X4, and P2X6 receptor staining was detected in small- and medium-diameter neurons. However, P2Y4, P2X2, and P2X7 staining was present in large- and small-diameter neurons. Double-labeling immunohistochemistry showed that 90.8%, 32.1%, and 2.4% of P2X3 receptor-positive neurons coexpressed IB4, CGRP, and NF200, respectively; whereas 67.4%, 41.3%, and 39.1% of P2Y4 receptor-positive neurons coexpressed IB4, CGRP, and NF200, respectively. A total of 18.8%, 16.6%, and 63.5% of P2Y2 receptor-positive neurons also stained for IB4, CGRP, and NF200, respectively. Only 30% of DRG neurons in cat were P2X3-immunoreactive compared with 90% in rat and in mouse. A further difference was the low expression of P2Y1 receptors in cat DRG neurons compared with more than 80% of the neurons in rat. Many small-diameter neurons were NF200-positive in cat, again differing from rat and mouse. (J Histochem Cytochem 53:1273–1282, 2005)


  • Localization of P2X and P2Y Receptors in Dorsal Root Ganglia of the Cat -

    The distribution of P2X and P2Y receptor subtypes in upper lumbosacral cat dorsal root ganglia (DRG) has been investigated using immunohistochemistry. Intensity of immunoreactivity for six P2X receptors (P2X5 receptors were immuno-negative) and the three P2Y receptors examined in cat DRG was in the order of P2Y2 = P2Y4>P2X3>P2X2 = P2X7>P2X6>P2X1 = P2X4>P2Y1. P2X3, P2Y2, and P2Y4 receptor polyclonal antibodies stained 33.8%, 35.3%, and 47.6% of DRG neurons, respectively. Most P2Y2, P2X1, P2X3, P2X4, and P2X6 receptor staining was detected in small- and medium-diameter neurons. However, P2Y4, P2X2, and P2X7 staining was present in large- and small-diameter neurons. Double-labeling immunohistochemistry showed that 90.8%, 32.1%, and 2.4% of P2X3 receptor-positive neurons coexpressed IB4, CGRP, and NF200, respectively; whereas 67.4%, 41.3%, and 39.1% of P2Y4 receptor-positive neurons coexpressed IB4, CGRP, and NF200, respectively. A total of 18.8%, 16.6%, and 63.5% of P2Y2 receptor-positive neurons also stained for IB4, CGRP, and NF200, respectively. Only 30% of DRG neurons in cat were P2X3-immunoreactive compared with 90% in rat and in mouse. A further difference was the low expression of P2Y1 receptors in cat DRG neurons compared with more than 80% of the neurons in rat. Many small-diameter neurons were NF200-positive in cat, again differing from rat and mouse. (J Histochem Cytochem 53:1273–1282, 2005)


  • Localization of plasma membrane t-SNAREs syntaxin 2 and 3 in intracellular compartments - Background: Membrane fusion requires the formation of a complex between a vesicle protein (v-SNARE) and the target membrane proteins (t-SNAREs). Syntaxin 2 and 3 are t-SNAREs that, according to previous over-expression studies, are predominantly localized at the plasma membrane. In the present study we investigated localization of the endogenous syntaxin 2 and 3. Results: Endogenous syntaxin 2 and 3 were found in NRK cells in intracellular vesicular structures in addition to regions of the plasma membrane. Treatment of these cells with N-ethylmaleimide (NEM), which is known to inactivate membrane fusion, caused syntaxin 3 to accumulate in the trans-Golgi network and syntaxin 2 in perinuclear membrane vesicles. Kinetic analysis in the presence of NEM indicated that this redistribution of syntaxin 2 and 3 takes place via actin containing structures. Conclusions: Our data suggest that syntaxin 2 cycles between the plasma membrane and the perinuclear compartment whereas syntaxin 3 cycles between the plasma membrane and the trans-Golgi network. It is possible that this cycling has an important role in the regulation of t-SNARE function

  • Localization of Sphingosine Kinase-1 in Mouse Sperm Acrosomes -

    Sphingosine kinase (SPHK) catalyzes sphingosine phosphorylation to form a bioactive lipid mediator, sphingosine-1-phosphate (S1P). In the current study, we report the presence of SPHK-1 in mouse spermatozoa. SPHK-1 was localized to the acrosomes of spermatozoa, and its expression was proven by RT-PCR and Western blot analysis. SPHK activity of mouse spermatozoa was 18.1 pmol/min/mg protein. Furthermore, we identified the presence of the S1P receptors S1P1, S1P2, S1P3, and S1P5, in mouse spermatozoa by RT-PCR. These results suggest that S1P produced by SPHK-1 would play a role in the acrosomal reaction through S1P receptors. (J Histochem Cytochem 53:243–247, 2005)


  • Localization of Type 8 17{beta}-hydroxysteroid Dehydrogenase mRNA in Mouse Tissues as Studied by In Situ Hybridization -

    The enzyme type 8 17ßbeta;-hydroxysteroid dehydrogenase (17ßbeta;-HSD) selectively catalyzes the conversion of estradiol (E2) to estrone (E1). To obtain detailed information on the sites of action of type 8 17ßbeta;-HSD, we have studied the cellular localization of type 8 17ßbeta;-HSD mRNA in mouse tissues using in situ hybridization. In the ovary, hybridization signal was detected in granulosa cells of growing follicles and luteal cells. In the uterus, type 8 17ßbeta;-HSD mRNA was found in the epithelial (luminal and glandular) and stromal cells. In the female mammary gland, the enzyme mRNA was seen in ductal epithelial cells and stromal cells. In the testis, hybridization signal was observed in the seminiferous tubule. In the prostate, type 8 17ßbeta;-HSD was detected in the epithelial cells of the acini and stromal cells. In the clitoral and preputial glands, labeling was detected in the epithelial cells of acini and small ducts. The three lobes of the pituitary gland were labeled. In the adrenal gland, hybridization signal was observed in the three zones of the cortex, the medulla being unlabeled. In the kidney, the enzyme mRNA was found to be expressed in the epithelial cells of proximal convoluted tubules. In the liver, all the hepatocytes exhibited a positive signal. In the lung, type 8 17ßbeta;-HSD mRNA was detected in bronchial epithelial cells and walls of pulmonary arteries. The present data suggest that type 8 17ßbeta;-HSD can exert its action to downregulate E2 levels in a large variety of tissues. (J Histochem Cytochem 53:1257–1271, 2005)


  • Localization of Type 8 17{beta}-hydroxysteroid Dehydrogenase mRNA in Mouse Tissues as Studied by In Situ Hybridization -

    The enzyme type 8 17ßbeta;-hydroxysteroid dehydrogenase (17ßbeta;-HSD) selectively catalyzes the conversion of estradiol (E2) to estrone (E1). To obtain detailed information on the sites of action of type 8 17ßbeta;-HSD, we have studied the cellular localization of type 8 17ßbeta;-HSD mRNA in mouse tissues using in situ hybridization. In the ovary, hybridization signal was detected in granulosa cells of growing follicles and luteal cells. In the uterus, type 8 17ßbeta;-HSD mRNA was found in the epithelial (luminal and glandular) and stromal cells. In the female mammary gland, the enzyme mRNA was seen in ductal epithelial cells and stromal cells. In the testis, hybridization signal was observed in the seminiferous tubule. In the prostate, type 8 17ßbeta;-HSD was detected in the epithelial cells of the acini and stromal cells. In the clitoral and preputial glands, labeling was detected in the epithelial cells of acini and small ducts. The three lobes of the pituitary gland were labeled. In the adrenal gland, hybridization signal was observed in the three zones of the cortex, the medulla being unlabeled. In the kidney, the enzyme mRNA was found to be expressed in the epithelial cells of proximal convoluted tubules. In the liver, all the hepatocytes exhibited a positive signal. In the lung, type 8 17ßbeta;-HSD mRNA was detected in bronchial epithelial cells and walls of pulmonary arteries. The present data suggest that type 8 17ßbeta;-HSD can exert its action to downregulate E2 levels in a large variety of tissues. (J Histochem Cytochem 53:1257–1271, 2005)


  • Loss of expression and nuclear/cytoplasmic localization of the FOXP1 forkhead transcription factor are common events in early endometrial cancer: relationship with estrogen receptors and HIF-1[alpha] expression - Alexandra Giatromanolaki, Michael I Koukourakis, Efthimios Sivridis, Kevin C Gatter, Adrian L Harris & Alison H Banham

  • Mammary epithelial cell transformation: insights from cell culture and mouse models - Normal human mammary epithelial cells (HMECs) have a finite life span and do not undergo spontaneous immortalization in culture. Critical to oncogenic transformation is the ability of cells to overcome the senescence checkpoints that define their replicative life span and to multiply indefinitely – a phenomenon referred to as immortalization. HMECs can be immortalized by exposing them to chemicals or radiation, or by causing them to overexpress certain cellular genes or viral oncogenes. However, the most efficient and reproducible model of HMEC immortalization remains expression of high-risk human papillomavirus (HPV) oncogenes E6 and E7. Cell culture models have defined the role of tumor suppressor proteins (pRb and p53), inhibitors of cyclin-dependent kinases (p16INK4a, p21, p27 and p57), p14ARF, telomerase, and small G proteins Rap, Rho and Ras in immortalization and transformation of HMECs. These cell culture models have also provided evidence that multiple epithelial cell subtypes with distinct patterns of susceptibility to oncogenesis exist in the normal mammary tissue. Coupled with information from distinct molecular portraits of primary breast cancers, these findings suggest that various subtypes of mammary cells may be precursors of different subtypes of breast cancers. Full oncogenic transformation of HMECs in culture requires the expression of multiple gene products, such as SV40 large T and small t, hTERT (catalytic subunit of human telomerase), Raf, phosphatidylinositol 3-kinase, and Ral-GEFs (Ral guanine nucleotide exchange factors). However, when implanted into nude mice these transformed cells typically produce poorly differentiated carcinomas and not adenocarcinomas. On the other hand, transgenic mouse models using ErbB2/neu, Ras, Myc, SV40 T or polyomavirus T develop adenocarcinomas, raising the possibility that the parental normal cell subtype may determine the pathological type of breast tumors. Availability of three-dimensional and mammosphere models has led to the identification of putative stem cells, but more studies are needed to define their biologic role and potential as precursor cells for distinct breast cancers. The combined use of transformation strategies in cell culture and mouse models together with molecular definition of human breast cancer subtypes should help to elucidate the nature of breast cancer diversity and to develop individualized therapies.

  • Marked Differences in Tissue-specific Expression of Chitinases in Mouse and Man -

    Two distinct chitinases have been identified in mammals: a phagocyte-specific enzyme named chitotriosidase and an acidic mammalian chitinase (AMCase) expressed in the lungs and gastrointestinal tract. Increased expression of both chitinases has been observed in different pathological conditions: chitotriosidase in lysosomal lipid storage disorders like Gaucher disease and AMCase in asthmatic lung disease. Recently, it was reported that AMCase activity is involved in the pathogenesis of asthma in an induced mouse model. Inhibition of chitinase activity was found to alleviate the inflammation-driven pathology. We studied the tissue-specific expression of both chitinases in mice and compared it to the situation in man. In both species AMCase is expressed in alveolar macrophages and in the gastrointestinal tract. In mice, chitotriosidase is expressed only in the gastrointestinal tract, the tongue, fore-stomach, and Paneth cells in the small intestine, whereas in man the enzyme is expressed exclusively by professional phagocytes. This species difference seems to be mediated by distinct promoter usage. In conclusion, the pattern of expression of chitinases in the lung differs between mouse and man. The implications for the development of anti-asthma drugs with chitinases as targets are discussed.

    (J Histochem Cytochem 53:1283–1292, 2005)


  • Marked Differences in Tissue-specific Expression of Chitinases in Mouse and Man -

    Two distinct chitinases have been identified in mammals: a phagocyte-specific enzyme named chitotriosidase and an acidic mammalian chitinase (AMCase) expressed in the lungs and gastrointestinal tract. Increased expression of both chitinases has been observed in different pathological conditions: chitotriosidase in lysosomal lipid storage disorders like Gaucher disease and AMCase in asthmatic lung disease. Recently, it was reported that AMCase activity is involved in the pathogenesis of asthma in an induced mouse model. Inhibition of chitinase activity was found to alleviate the inflammation-driven pathology. We studied the tissue-specific expression of both chitinases in mice and compared it to the situation in man. In both species AMCase is expressed in alveolar macrophages and in the gastrointestinal tract. In mice, chitotriosidase is expressed only in the gastrointestinal tract, the tongue, fore-stomach, and Paneth cells in the small intestine, whereas in man the enzyme is expressed exclusively by professional phagocytes. This species difference seems to be mediated by distinct promoter usage. In conclusion, the pattern of expression of chitinases in the lung differs between mouse and man. The implications for the development of anti-asthma drugs with chitinases as targets are discussed.

    (J Histochem Cytochem 53:1283–1292, 2005)


  • MDM2 protein expression is a negative prognostic marker in breast carcinoma - Dmitry A Turbin, Maggie C U Cheang, Chris D Bajdik, Karen A Gelmon, Erika Yorida, Alessandro De Luca, Torsten O Nielsen, David G Huntsman & C Blake Gilks

  • Mechanisms of Heat-induced Antigen Retrieval: Analyses In Vitro Employing SDS-PAGE and Immunohistochemistry -

    In this study, we examined the mechanism of heat-induced antigen retrieval using analytical procedures involving SDS-PAGE, Western blotting, and immunohistochemistry. Five proteins were treated with 4% formaldehyde in the presence or absence of 25 mM CaCl2, then heated under various conditions after removal of formaldehyde and analyzed on SDS-PAGE. Formaldehyde produced inter- and intramolecular cross-links in the proteins. Heating at high temperatures cleaved these cross-links at all pH ranges examined (pH 3.0, 6.0, 7.5, 9.0) and produced almost the same electrophoregrams as the native proteins. Proteins treated with formaldehyde containing CaCl2 showed similar electrophoretic patterns, observed without heating or after heating at pH 6.0 and pH 9.0 in the presence or absence of 10 mM EDTA. Western blot analyses demonstrated that the soluble forms of ßbeta;-actin (monomer and oligomers) and fibronectin were present in extracts from deparaffinized mouse uterine sections autoclaved for 15 min but not in extracts from unheated specimens. Nine of ten antigens, independent of their isoelectric points, exhibited much stronger immunoreaction in the sections heated at pH 9.0 than in those heated at pH 6.0. The second heating at pH 6.0 significantly decreased the immunostaining of the antigens that had been boiled at pH 9.0, but the immunostaining was recovered after a third heating at pH 9.0. These results suggest that the main mechanism of heat-induced antigen retrieval is disruption of the cross-links and that pH is an essential factor for a proper refolding of epitopes. (J Histochem Cytochem 53:13–21, 2005)


  • Mechanisms of heat-induced antigen retrieval: analyses in vitro employing SDS-PAGE and immunohistochemistry. -
    Related Articles

    Mechanisms of heat-induced antigen retrieval: analyses in vitro employing SDS-PAGE and immunohistochemistry.

    J Histochem Cytochem. 2005 Jan;53(1):13-21

    Authors: Yamashita S, Okada Y

    In this study, we examined the mechanism of heat-induced antigen retrieval using analytical procedures involving SDS-PAGE, Western blotting, and immunohistochemistry. Five proteins were treated with 4% formaldehyde in the presence or absence of 25 mM CaCl2, then heated under various conditions after removal of formaldehyde and analyzed on SDS-PAGE. Formaldehyde produced inter- and intramolecular cross-links in the proteins. Heating at high temperatures cleaved these cross-links at all pH ranges examined (pH 3.0, 6.0, 7.5, 9.0) and produced almost the same electrophoregrams as the native proteins. Proteins treated with formaldehyde containing CaCl2 showed similar electrophoretic patterns, observed without heating or after heating at pH 6.0 and pH 9.0 in the presence or absence of 10 mM EDTA. Western blot analyses demonstrated that the soluble forms of beta-actin (monomer and oligomers) and fibronectin were present in extracts from deparaffinized mouse uterine sections autoclaved for 15 min but not in extracts from unheated specimens. Nine of ten antigens, independent of their isoelectric points, exhibited much stronger immunoreaction in the sections heated at pH 9.0 than in those heated at pH 6.0. The second heating at pH 6.0 significantly decreased the immunostaining of the antigens that had been boiled at pH 9.0, but the immunostaining was recovered after a third heating at pH 9.0. These results suggest that the main mechanism of heat-induced antigen retrieval is disruption of the cross-links and that pH is an essential factor for a proper refolding of epitopes.

    PMID: 15637334 [PubMed - indexed for MEDLINE]


  • Melanoma Inhibitory Activity (MIA) increases the invasiveness of pancreatic cancer cells - Background: Melanoma inhibitory activity (MIA) is a small secreted protein that interacts with extracellular matrix proteins. Its over-expression promotes the metastatic behavior of malignant melanoma, thus making it a potential prognostic marker in this disease. In the present study, the expression and functional role of MIA was analyzed in pancreatic cancer by quantitative real-time PCR (QRT-PCR), immunohistochemistry, immunoblot analysis and ELISA. To determine the effects of MIA on tumor cell growth and invasion, MTT cell growth assays and modified Boyden chamber invasion assays were used. Results: The mRNA expression of MIA was 42-fold increased in pancreatic cancers in comparison to normal pancreatic tissues (p < 0.01). In contrast, MIA serum levels were not significantly different between healthy donors and pancreatic cancer patients. In pancreatic tissues, MIA was predominantly localized in malignant cells and in tubular complexes of cancer specimens, whereas normal ductal cells, acinar cells and islets were devoid of MIA immunoreactivity. MIA significantly promoted the invasiveness of cultured pancreatic cancer cells without influencing cell proliferation. Conclusion: MIA is over-expressed in pancreatic cancer and has the potential of promoting the invasiveness of pancreatic cancer cells.

  • Menopausal hormone therapy after breast cancer: a meta-analysis and critical appraisal of the evidence - IntroductionMenopausal hormone therapy (HT) is typically withheld from breast cancer survivors because of concerns about risk for recurrence. Our objectives were to estimate the effects of HT on recurrence in breast cancer survivors and to examine the reliability of these estimates. Methods: In a systematic review of the literature we identified all reports of HT use in breast cancer survivors that included comparison groups. Study design features that might affect selection of participants, detection of recurrence, and manuscript publication were assessed. The relative risks for breast cancer recurrence associated with HT were combined with random effects models. Results: Two randomized and eight observational studies included 1,316 breast cancer survivors who used HT and 2,839 nonusers. In the observational studies, HT users were younger and more commonly node negative; only two reported balanced restaging for HT and control groups. Randomized trials suggest that HT increased the risk for recurrence (relative risk 3.41, 95% confidence interval 1.59–7.33), whereas observational studies suggest that HT decreased this risk (relative risk 0.64, 95% confidence interval 0.50–0.82). Conclusion: Results from observational studies of HT conducted in breast cancer survivors are discrepant with results from randomized trials. Observational studies of HT use in breast cancer survivors have design limitations that cannot be controlled for using standard statistical methods. Therefore, the randomized clinical trial data provide the only reliable estimates of the effect of HT use on recurrence risks in breast cancer survivors.

  • Merkel cell carcinoma in a malignant pleural effusion: case report - Background: Merkel cell (neuroendocrine) carcinoma is a small round blue cell malignant neoplasm that primarily presents in the skin. The diagnosis of Merkel cell carcinoma in a pleural fluid is challenging because of the morphological similarity to many other malignant neoplasms. Immunohistochemical stains can be essential to establish the diagnosis of Merkel cell carcinoma.Case presentationA 77 year-old woman presented with a mass in her right buttock thought clinically to be a boil or sebaceous cyst. Upon histopathologic review including immunohistochemical analysis, a diagnosis of Merkel cell carcinoma was rendered. Wide-excision and sentinel lymph node biopsy revealed negative margins and no evidence of metastasis. Ten months later she complained of bone pain and a bone scan revealed multiple lesions. An abdominal CT scan revealed a T4 vertebral mass and local radiotherapy was administered. Two months later the patient presented with shortness of breath. A chest radiograph showed an effusion and thoracentesis was performed. The fluid was confirmed to contain metastatic Merkel cell carcinoma by cytology and immunohistochemical analysis. Conclusions: Merkel cell carcinoma is an aggressive neoplasm that can, despite careful surgical management, occasionally present as a malignant pleural effusion in a relatively short time period. Immunohistochemical analysis can aid in confirming this rare outcome.

  • Metallothionein mediates leukocyte chemotaxis - Background: Metallothionein (MT) is a cysteine-rich, metal-binding protein that can be induced by a variety of agents. Modulation of MT levels has also been shown to alter specific immune functions. We have noticed that the MT genes map close to the chemokines Ccl17 and Cx3cl1. Cysteine motifs that characterize these chemokines are also found in the MT sequence suggesting that MT might also act as a chemotactic factor. Results: In the experiments reported here, we show that immune cells migrate chemotactically in the presence of a gradient of MT. This response can be specifically blocked by two different monoclonal anti-MT antibodies. Exposure of cells to MT also leads to a rapid increase in F-actin content. Incubation of Jurkat T cells with cholera toxin or pertussis toxin completely abrogates the chemotactic response to MT. Thus MT may act via G-protein coupled receptors and through the cyclic AMP signaling pathway to initiate chemotaxis. Conclusions: These results suggest that under inflammatory conditions metallothionein in the extracellular environment may support the beneficial movement of leukocytes to the site of inflammation. MT may therefore represent a "danger signal"; modifying the character of the immune response when cells sense cellular stress. Excess metallothionein produced in the context of exposure to environmental toxicants, or as a result of chronic inflammatory disease, may alter the normal chemotactic responses that regulate leukocyte trafficking. Thus, inappropriate MT synthesis may represent an important factor in immunosuppression that is associated with autoimmune disease and toxicant exposure.

  • Metastasis of hormone-independent breast cancer to lung and bone is decreased by α-difluoromethylornithine treatment - IntroductionPolyamines affect proliferation, differentiation, migration and apoptosis of cells, indicating their potential as a target for cancer chemotherapy. Ornithine decarboxylase converts ornithine to putrescine and is the rate-limiting step in polyamine synthesis.α-Difluoromethylornithine (DFMO) irreversibly inhibits ornithine decarboxylase and MDA-MB-435 human breast cancer metastasis to the lung without blocking orthotopic tumor growth. This study tested the effects of DFMO on orthotopic tumor growth and lung colonization of another breast cancer cell line (MDA-MB-231) and the effects on bone metastasis of MDA-MB-435 cells. Methods: MDA-MB-231 cells were injected into the mammary fat pad of athymic mice. DFMO treatment (2% per orally) began at the day of tumor cell injection or 21 days post injection. Tumor growth was measured weekly. MDA-MB-231 cells were injected into the tail vein of athymic mice. DFMO treatment began 7 days prior to injection, or 7 or 14 days post injection. The number and incidence of lung metastases were determined. Green fluorescent protein-tagged MDA-MB-435 cells were injected into the left cardiac ventricle in order to assess the incidence and extent of metastasis to the femur. DFMO treatment began 7 days prior to injection. Results: DFMO treatment delayed MDA-MB-231 orthotopic tumor growth to a greater extent than growth of MDA-MB-435 tumors. The most substantial effect on lung colonization by MDA-MB-231 cells occurred when DFMO treatment began 7 days before intravenous injection of tumor cells (incidence decreased 28% and number of metastases per lung decreased 35–40%). When DFMO treatment began 7 days post injection, the incidence and number of metastases decreased less than 10%. Surprisingly, treatment initiated 14 days after tumor cell inoculation resulted in a nearly 50% reduction in the number of lung metastases without diminishing the incidence. After intracardiac injection, DFMO treatment decreased the incidence of bone metastases (55% vs 87%) and the area occupied by the tumor (1.66 mm2 vs 4.51 mm2, P < 0.05). Conclusion: Taken together, these data demonstrate that DFMO exerts an anti-metastatic effect in more than one hormone-independent breast cancer, for which no standard form of biologically-based treatment exists. Importantly, the data show that DFMO is effective against metastasis to multiple sites and that treatment is generally more effective when administered early.

  • MG-132, an inhibitor of proteasomes and calpains, induced inhibition of oocyte maturation and aneuploidy in mouse oocytes - Background: Although chromosome missegregation during oocyte maturation (OM) is a significant contributor to human morbidity and mortality, very little is known about the causes and mechanisms of aneuploidy. Several investigators have proposed that temporal perturbations during OM predispose oocytes to aberrant chromosome segregation. One approach for testing this proposal is to temporarily inhibit the activity of protein proteolysis during OM. We used the reversible proteasome inhibitor MG-132 to transiently perturb the temporal sequence of events during OM and subsequently analyzed mouse metaphase II (MII) for cytogenetic abnormalities. The transient inhibition of proteasome activity by MG-132 resulted in elevated levels of oocytes containing extra chromatids and chromosomes. Results: The transient inhibition of proteasome-mediated proteolysis during OM by MG-132 resulted in dose-response delays during OM and elevated levels of aneuploid MII oocytes. Oocytes exposed in vitro to MG-132 exhibited greater delays during metaphase I (MI) as demonstrated by significantly (p < 0.01) higher levels of MI arrested oocytes and lower frequencies of premature sister chromatid separation in MII oocytes. Furthermore, the proportions of MII oocytes containing single chromatids and extra chromosomes significantly (p < 0.01) increased with MG-132 dosage. Conclusions: These data suggest that the MG-132-induced transient delay of proteasomal activity during mouse OM in vitro predisposed oocytes to abnormal chromosome segregation. Although these findings support a relationship between disturbed proteasomal activity and chromosome segregation, considerable additional data are needed to further investigate the roles of proteasome-mediated proteolysis and other potential molecular mechanisms on chromosome segregation during OM.

  • Microarray analysis of gene expression during the cell cycle - Microarrays have been applied to the determination of genome-wide expression patterns during the cell cycle of a number of different cells. Both eukaryotic and prokaryotic cells have been studied using whole-culture and selective synchronization methods. The published microarray data on yeast, mammalian, and bacterial cells have been uniformly interpreted as indicating that a large number of genes are expressed in a cell-cycle-dependent manner. These conclusions are reconsidered using explicit criteria for synchronization and precise criteria for identifying gene expression patterns during the cell cycle. The conclusions regarding cell-cycle-dependent gene expression based on microarray analysis are weakened by arguably problematic choices for synchronization methodology (e.g., whole-culture methods that do not synchronize cells) and questionable statistical rigor for identifying cell-cycle-dependent gene expression. Because of the uncertainties in synchrony methodology, as well as uncertainties in microarray analysis, one should be somewhat skeptical of claims that there are a large number of genes expressed in a cell-cycle-dependent manner.

  • Microdissection-derived Murine Mcb Probes from Somatic Cell Hybrids -

    The multicolor-banding (mcb) technique is a fluorescence in situ hybridization (FISH)-banding approach, which is based on region-specific microdissection libraries producing changing fluorescence intensity ratios along the chromosomes. The latter are used to assign different pseudocolors to specific chromosomal regions. Here we present the first three available mcb-probe sets for the Mus musculus chromosomes 3, 6, and 18. In the present work, the creation of the microdissection libraries was done for the first time on mouse/human somatic cell hybrids. During creation of the mcb-probes, the latter enabled an unambiguous identification of the, otherwise in GTG-banding, hardly distinguishable murine chromosomes. (J Histochem Cytochem 53:791–792, 2005)


  • Microdissection-derived Murine Mcb Probes from Somatic Cell Hybrids -

    The multicolor-banding (mcb) technique is a fluorescence in situ hybridization (FISH)-banding approach, which is based on region-specific microdissection libraries producing changing fluorescence intensity ratios along the chromosomes. The latter are used to assign different pseudocolors to specific chromosomal regions. Here we present the first three available mcb-probe sets for the Mus musculus chromosomes 3, 6, and 18. In the present work, the creation of the microdissection libraries was done for the first time on mouse/human somatic cell hybrids. During creation of the mcb-probes, the latter enabled an unambiguous identification of the, otherwise in GTG-banding, hardly distinguishable murine chromosomes. (J Histochem Cytochem 53:791–792, 2005)


  • Microdissection-derived Murine Mcb Probes from Somatic Cell Hybrids -

    The multicolor-banding (mcb) technique is a fluorescence in situ hybridization (FISH)-banding approach, which is based on region-specific microdissection libraries producing changing fluorescence intensity ratios along the chromosomes. The latter are used to assign different pseudocolors to specific chromosomal regions. Here we present the first three available mcb-probe sets for the Mus musculus chromosomes 3, 6, and 18. In the present work, the creation of the microdissection libraries was done for the first time on mouse/human somatic cell hybrids. During creation of the mcb-probes, the latter enabled an unambiguous identification of the, otherwise in GTG-banding, hardly distinguishable murine chromosomes. (J Histochem Cytochem 53:791–792, 2005)


  • Mitochondrial Expression of Arginase II in Male and Female Rat Inner Medullary Collecting Ducts -

    Microdissected rat proximal straight tubules (PST) and inner medullary collecting ducts (IMCD) highly produce urea from l-arginine, supporting the expression of the mitochondrial arginase II. However, IMCD contain a very low density of mitochondria compared with PST. Recently, arginase II has been localized by immunohistochemistry in rat PST but not IMCD. This study was designed to verify whether rat IMCD express arginase II and to identify its subcellular localization. We developed an antibody raised against arginase II that allowed the detection of a band of 38 kDa corresponding to arginase II on immunoblots. In male and female rat kidneys, Western blot analyses revealed that arginase II was highly expressed in the inner medulla (IM), the outer stripe of the outer medulla (osOM), and the deep cortex. Immunocytochemistry demonstrated that arginase II was homogeneously expressed in IMCD. Proteins of the cytosolic and mitochondrial fractions extracted from osOM and IM and analyzed by Western blot showed that 86% of arginase II was associated with mitochondria. The molecular weight of arginase II was similar in the cytosolic and mitochondrial fractions. Immunoelectron microscopy confirmed the presence of arginase II in the mitochondria of IMCD. In conclusion, arginase II is expressed in mitochondria of male and female rat IMCD. (J Histochem Cytochem 53:533–541, 2005)


  • Mitochondrial Expression of Arginase II in Male and Female Rat Inner Medullary Collecting Ducts -

    Microdissected rat proximal straight tubules (PST) and inner medullary collecting ducts (IMCD) highly produce urea from l-arginine, supporting the expression of the mitochondrial arginase II. However, IMCD contain a very low density of mitochondria compared with PST. Recently, arginase II has been localized by immunohistochemistry in rat PST but not IMCD. This study was designed to verify whether rat IMCD express arginase II and to identify its subcellular localization. We developed an antibody raised against arginase II that allowed the detection of a band of 38 kDa corresponding to arginase II on immunoblots. In male and female rat kidneys, Western blot analyses revealed that arginase II was highly expressed in the inner medulla (IM), the outer stripe of the outer medulla (osOM), and the deep cortex. Immunocytochemistry demonstrated that arginase II was homogeneously expressed in IMCD. Proteins of the cytosolic and mitochondrial fractions extracted from osOM and IM and analyzed by Western blot showed that 86% of arginase II was associated with mitochondria. The molecular weight of arginase II was similar in the cytosolic and mitochondrial fractions. Immunoelectron microscopy confirmed the presence of arginase II in the mitochondria of IMCD. In conclusion, arginase II is expressed in mitochondria of male and female rat IMCD. (J Histochem Cytochem 53:533–541, 2005)


  • Mitochondrial Expression of Arginase II in Male and Female Rat Inner Medullary Collecting Ducts -

    Microdissected rat proximal straight tubules (PST) and inner medullary collecting ducts (IMCD) highly produce urea from l-arginine, supporting the expression of the mitochondrial arginase II. However, IMCD contain a very low density of mitochondria compared with PST. Recently, arginase II has been localized by immunohistochemistry in rat PST but not IMCD. This study was designed to verify whether rat IMCD express arginase II and to identify its subcellular localization. We developed an antibody raised against arginase II that allowed the detection of a band of 38 kDa corresponding to arginase II on immunoblots. In male and female rat kidneys, Western blot analyses revealed that arginase II was highly expressed in the inner medulla (IM), the outer stripe of the outer medulla (osOM), and the deep cortex. Immunocytochemistry demonstrated that arginase II was homogeneously expressed in IMCD. Proteins of the cytosolic and mitochondrial fractions extracted from osOM and IM and analyzed by Western blot showed that 86% of arginase II was associated with mitochondria. The molecular weight of arginase II was similar in the cytosolic and mitochondrial fractions. Immunoelectron microscopy confirmed the presence of arginase II in the mitochondria of IMCD. In conclusion, arginase II is expressed in mitochondria of male and female rat IMCD. (J Histochem Cytochem 53:533–541, 2005)


  • Mixed Gastric- and Intestinal-type Metaplasia Is Formed by Cells with Dual Intestinal and Gastric Differentiation -

    We have proposed to divide intestinal metaplasia (IM) into two categories, i.e., a mixed gastric and intestinal (GI) type, and a solely intestinal (I) type, based on the residual gastric phenotype cells. The GI-mixed-type IM can be identified by the presence of both cells with either gastric or intestinal phenotypes in a single gland. This study is conducted to elucidate whether cells in the GI-mixed-type IM glands can simultaneously present both gastric and intestinal phenotypes. MUC5AC, MUC2, CD10 and villin expressions were investigated in 20 samples from five gastric cancer cases, directly using either AlexaFluor 488- or 568-labeled specific monoclonal antibodies and observed by fluorescent microscopy and confocal laser-scanning microscopy. GI-mixed IM glands comprise a population expressing MUC5AC and MUC2, MUC5AC and villin, and MUC5AC and CD10. MUC2 and villin expressions were reciprocally increased with decreasing MUC5AC expression, while CD10 expression was limited to cells with only a residual MUC5AC expression or no expression. These results suggest that a heterogeneous cell population with both gastric and intestinal phenotypes would develop into a single intestinal phenotype, as reflected in the progression of intestinal metaplasia from GI-mixed-type- to I-type IM-type glands.

    (J Histochem Cytochem 53:75–85, 2005)


  • Modulation of monocyte matrix metalloproteinase-2 by breast adenocarcinoma cells - IntroductionThe presence of monocyte and macrophage cells in growing breast tumors, and the positive relationship between the degree of immune cell infiltration and tumor growth, suggest a possible paracrine growth regulatory function of immune cells in breast cancer.MethodTo better understand the interaction between monocytes and breast cancer cells, in vitro matrix metalloproteinase and tissue inhibitor of metalloproteinase activity was assessed from the THP-1 myeloid cell line in response to conditioned media from two breast cancer cell lines, MCF-7 and MDA-MB-231. Results: Enzymography and immunoblotting revealed increased MMP-2 as well as increased levels of TIMP-1 and TIMP-2. Furthermore, a significant increase in the invasive potential of MCF-7 and MDA-MB-231 cells was noted in response to THP-1 cell-conditioned media. Conclusion: These data demonstrate that monocyte cells in the breast tumor microenvironment play an important role in the modulation of MMPs, which may have a significant effect on the control of tumor growth and metastatic spread.

  • Modulation of p53 activity by I-kappa B alpha: Evidence suggesting a common phylogeny between NF-kappa B and p53 transcription factors - Background: In this work we present evidence that the p53 tumor suppressor protein and NF-kappa B transcription factors could be related through common descent from a family of ancestral transcription factors regulating cellular proliferation and apoptosis. P53 is a homotetrameric transcription factor known to interact with the ankyrin protein 53BP2 (a fragment of the ASPP2 protein). NF-kappa B is also regulated by ankyrin proteins, the prototype of which is I-kappa B alpha of the I kappa B family. The DNA binding sequences of the two transcription factors are similar, sharing 8 out of 10 nucleotides. Interactions between the two proteins, both direct and indirect, have been noted previously and the two proteins play central roles in the control of proliferation and apoptosis. Results: Using previously published structural data, we noted a significant degree of structural alignment between p53 and NF-kappa B p65. We also determined that I-kappa B alpha and p53 bind in vitro through a specific interaction in part involving the DNA binding region of p53, or a region proximal to it, and the amino terminus of I-kappa B alpha, independently or cooperatively with the ankyrin 3 domain of I-kappa B alpha. In cotransfection experiments, I-kappa B alpha could significantly inhibit the transcriptional activity of p53. Inhibition of p53-mediated transcription was increased by deletion of the ankyrin 2, 4, or 5 domains of I-kappa B alpha. Co-precipitation experiments using the stably transfected ankyrin 5 deletion mutant of I-kappa B alpha and endogenous wild-type p53 further support the hypothesis that p53 and I-kappa B alpha can physically interact in vivo. Conclusions: The collective results obtained using bacterially produced I-kappa B alpha and p53, as well as reticulocyte lysate produced proteins, suggest a correlation between in vitro co-precipitation in at least one of the systems and in vivo p53 inhibitory activity. These observations argue for a mechanism involving direct binding of I-kappa B alpha to p53 in the inhibition of p53 transcriptional activity, analogous to the inhibition of NF-kappa B by I-kappa B proteins and p53 by 53BP2/ASPP2, and suggest a role for ankyrin proteins in the regulation of p53 activity. Finally, these data showing (1) similarity in structure between NF-kappa B and p53; (2) similarity in DNA binding sites; and, (3)binding and regulation by ankyrin proteins, support our hypothesis that the two proteins share common descent from an ancestral transcriptional factor.

  • Molecular Diagnosis in Lymphoma - The evolution of our ability to diagnose and classify lymphomas in an increasingly refined manner has paralleled the development of novel technologic approaches, with contemporary practice dependent upon the harnessing of a plethora of data that include microscopic, immunophenotypic, and genetic information. Although each of these components is currently indispensable, there is a purported progressive improvement in biologic objectivity as one maneuvers through these respective technologies. Accordingly, and in particular given the rapid pace at which key insights into lymphoma biology are emerging with microarray and other cutting-edge technologies, the role of molecular genetic testing is assuming even greater relevance. The ability to diagnose and classify lymphomas more accurately, precisely, and rationally by incorporating molecular data ought to lead to the development of more appropriate directed therapies.

  • Molecular diagnosis of Ewing sarcoma/primitive neuroectodermal tumor in routinely processed tissue: a comparison of two FISH strategies and RT-PCR in malignant round cell tumors - Robert S Bridge, Veena Rajaram, Louis P Dehner, John D Pfeifer & Arie Perry

  • Molecular Karyotyping: Array CGH Quality Criteria for Constitutional Genetic Diagnosis -

    Array CGH (comparative genomic hybridization) enables the identification of chromosomal copy number changes. The availability of clone sets covering the human genome opens the possibility for the widespread use of array CGH for both research and diagnostic purposes. In this manuscript we report on the parameters that were critical for successful implementation of the technology, assess quality criteria, and discuss the potential benefits and pitfalls of the technology for improved pre- and postnatal constitutional genetic diagnosis. We propose to name the genome-wide array CGH "molecular karyotyping," in analogy with conventional karyotyping that uses staining methods to visualize chromosomes. (J Histochem Cytochem 53:413–422, 2005)


  • Monoclonal Antibodies to Plant Cell Wall Xylans and Arabinoxylans -

    Two rat monoclonal antibodies have been generated to plant cell wall (1->4)-ßbeta;-D-xylans using a penta-1,4-xylanoside–containing neoglycoprotein as an immunogen. The monoclonal antibodies, designated LM10 and LM11, have different specificities to xylans in relation to the substitution of the xylan backbone as indicated by immunodot assays and competitive-inhibition ELISAs. LM10 is specific to unsubstituted or low-substituted xylans, whereas LM11 binds to wheat arabinoxylan in addition to unsubstituted xylans. Immunocytochemical analyses indicated the presence of both epitopes in secondary cell walls of xylem but differences in occurrence in other cell types.

    (J Histochem Cytochem 53:543–546, 2005)


  • Monoclonal Antibodies to Plant Cell Wall Xylans and Arabinoxylans -

    Two rat monoclonal antibodies have been generated to plant cell wall (1->4)-ßbeta;-D-xylans using a penta-1,4-xylanoside–containing neoglycoprotein as an immunogen. The monoclonal antibodies, designated LM10 and LM11, have different specificities to xylans in relation to the substitution of the xylan backbone as indicated by immunodot assays and competitive-inhibition ELISAs. LM10 is specific to unsubstituted or low-substituted xylans, whereas LM11 binds to wheat arabinoxylan in addition to unsubstituted xylans. Immunocytochemical analyses indicated the presence of both epitopes in secondary cell walls of xylem but differences in occurrence in other cell types.

    (J Histochem Cytochem 53:543–546, 2005)


  • Monoclonal Antibodies to Plant Cell Wall Xylans and Arabinoxylans -

    Two rat monoclonal antibodies have been generated to plant cell wall (1->4)-ßbeta;-D-xylans using a penta-1,4-xylanoside–containing neoglycoprotein as an immunogen. The monoclonal antibodies, designated LM10 and LM11, have different specificities to xylans in relation to the substitution of the xylan backbone as indicated by immunodot assays and competitive-inhibition ELISAs. LM10 is specific to unsubstituted or low-substituted xylans, whereas LM11 binds to wheat arabinoxylan in addition to unsubstituted xylans. Immunocytochemical analyses indicated the presence of both epitopes in secondary cell walls of xylem but differences in occurrence in other cell types.

    (J Histochem Cytochem 53:543–546, 2005)


  • Morphologic and immunophenotypic diversity in Ewing family tumors: a study of 66 genetically confirmed cases. -
    Related Articles

    Morphologic and immunophenotypic diversity in Ewing family tumors: a study of 66 genetically confirmed cases.

    Am J Surg Pathol. 2005 Aug;29(8):1025-33

    Authors: Folpe AL, Goldblum JR, Rubin BP, Shehata BM, Liu W, Dei Tos AP, Weiss SW

    More than 85% of Ewing sarcoma/primitive neuroectodermal tumor (ES/PNET), or "Ewing family of tumors" (EFTs), have the translocation, t (11;22) (q24;q12), with others having variant translocations. Identification of these by cytogenetic and/or molecular genetic techniques is specific for EFT and is increasingly recognized as the "gold standard" for diagnosis. However, these techniques are not universally available. We therefore studied a large group of genetically confirmed EFTs to more completely understand the morphologic and immunophenotypic spectrum of this rare sarcoma. Sixty-six cytogenetically, FISH or RT-PCR proven-EFTs were retrieved. In 56 cases, immunohistochemistry (IHC) was performed for pan-cytokeratins (PanCK), high molecular weight cytokeratins (HMWCK), desmin (DES), CD99, CD117, and FLI1 protein using heat-induced epitope retrieval and the Dako Envision system. The cases arose chiefly in children and young adults (median 18 years; range, 3-65 years) of both sexes (male, 32; female, 31; unknown, 3) in a variety of bone (N = 39) and soft tissue (N = 27) sites. Histologically, 46 cases (73%) showed only typical features of ES, 9 cases (16%) showed features of PNET, 3 cases (5%) showed "adamantinoma-like" features, 3 cases (5%) corresponded to "atypical Ewing sarcoma," 3 cases (5%) showed principally intersecting fascicles of spindled cells, and 2 cases had abundant hyalinized matrix. IHC results were as follows: PanCK (18 of 56, 32%), HMWCK (3 of 55, 5%), DES (1 of 56, 2%), CD99 (52 of 52, 100%), CD117 (13 of 54, 24%), and FLI1 (44 of 47, 94%). HMWCK was expressed only in "adamantinoma-like" EFTs, none of which expressed DES. In conclusion, most, but not all, EFTs can be accurately diagnosed using time-honored morphologic criteria and ancillary immunohistochemistry. However, genetic confirmation remains essential for the diagnosis of unusual morphologic variants of EFT, including "adamantinoma-like," spindled, sclerosing, and clear cell/anaplastic variants. Therefore, to exclude or confirm the diagnosis of Ewing's sarcoma in round cell sarcomas having a variety of patterns but not specifically conforming to a tumor of known lineage (eg, rhabdomyosarcoma), cytogenetics, and/or molecular analysis is required.

    PMID: 16006796 [PubMed - indexed for MEDLINE]


  • Morphological characterization of a human glioma cell line. - A human malignant continuous cell line, named NG97, was recently established in our laboratory. This cell line has been serially subcultured over 100 times in standard culture media presenting no sign of cell senescence. The NG97 cell line has a doubling time of about 24 h. Immunocytochemical analysis of glial markers demonstrated that cells are positive for glial fibrillary acidic protein (GFAP) and S-100 protein, and negative for vimentin. Under phase-contrast microscope, cultures of NG97 showed cells with variable morphological features, such as small rounded cells, fusiform cells (fibroblastic-like cells), and dendritic-like cells. However, at confluence just small rounded and fusiform cells can be observed. At scanning electron microscopy (SEM) small rounded cells showed heterogeneous microextentions, including blebs and filopodia. Dendritic-like cells were flat and presented extensive prolongations, making several contacts with small rounded cells, while fusiform cells presented their surfaces dominated by microvilli. We believe that the knowledge about NG97 cell line may be useful for a deeper understanding of biological and immunological characteristics of gliomas.

  • Mosquito Phenoloxidase and Defensin Colocalize in Melanization Innate Immune Responses -

    Mosquitoes mount strong humoral and cellular immune responses against foreign organisms. Two components of the mosquito immune response that have received much attention are the phenoloxidase cascade that leads to melanization and antimicrobial peptides. The purpose of the current study was to use immunocytochemistry and transmission electron microscopy to identify the location of the melanization rate-limiting enzyme phenoloxidase and the antimicrobial peptide defensin in innate immune reactions against Escherichia coli and Micrococcus luteus by the mosquito Aedes aegypti. Our results show that both phenoloxidase and defensin are present at the sites of melanin biosynthesis in immune reactions against bacteria. Furthermore, both proteins are often present inside the same melanotic capsules. When hemocytes were analyzed, phenoloxidase was present in the cytosol of oenocytoids, but no significant amounts of defensin were detected inside any hemocytes. In summary, these data show that phenoloxidase and defensin colocalize in melanization reactions against bacteria and argue for further studies into the potential role of defensin in phenoloxidase-based melanization innate immune responses in mosquitoes.

    (J Histochem Cytochem 53:689–698, 2005)


  • Mosquito Phenoloxidase and Defensin Colocalize in Melanization Innate Immune Responses -

    Mosquitoes mount strong humoral and cellular immune responses against foreign organisms. Two components of the mosquito immune response that have received much attention are the phenoloxidase cascade that leads to melanization and antimicrobial peptides. The purpose of the current study was to use immunocytochemistry and transmission electron microscopy to identify the location of the melanization rate-limiting enzyme phenoloxidase and the antimicrobial peptide defensin in innate immune reactions against Escherichia coli and Micrococcus luteus by the mosquito Aedes aegypti. Our results show that both phenoloxidase and defensin are present at the sites of melanin biosynthesis in immune reactions against bacteria. Furthermore, both proteins are often present inside the same melanotic capsules. When hemocytes were analyzed, phenoloxidase was present in the cytosol of oenocytoids, but no significant amounts of defensin were detected inside any hemocytes. In summary, these data show that phenoloxidase and defensin colocalize in melanization reactions against bacteria and argue for further studies into the potential role of defensin in phenoloxidase-based melanization innate immune responses in mosquitoes.

    (J Histochem Cytochem 53:689–698, 2005)


  • Mosquito Phenoloxidase and Defensin Colocalize in Melanization Innate Immune Responses -

    Mosquitoes mount strong humoral and cellular immune responses against foreign organisms. Two components of the mosquito immune response that have received much attention are the phenoloxidase cascade that leads to melanization and antimicrobial peptides. The purpose of the current study was to use immunocytochemistry and transmission electron microscopy to identify the location of the melanization rate-limiting enzyme phenoloxidase and the antimicrobial peptide defensin in innate immune reactions against Escherichia coli and Micrococcus luteus by the mosquito Aedes aegypti. Our results show that both phenoloxidase and defensin are present at the sites of melanin biosynthesis in immune reactions against bacteria. Furthermore, both proteins are often present inside the same melanotic capsules. When hemocytes were analyzed, phenoloxidase was present in the cytosol of oenocytoids, but no significant amounts of defensin were detected inside any hemocytes. In summary, these data show that phenoloxidase and defensin colocalize in melanization reactions against bacteria and argue for further studies into the potential role of defensin in phenoloxidase-based melanization innate immune responses in mosquitoes.

    (J Histochem Cytochem 53:689–698, 2005)


  • Mucin Granules are in Close Contact with Tubular Elements of the Endoplasmic Reticulum -

    Live cell imaging methods were used to characterize goblet cells expressing a MUC5AC domain fused to enhanced green fluorescent protein that labels the granule lumen. Golgi complex and endosome/lysosome elements largely resided in the periphery of the granular mass. On the contrary, a tubular meshwork of endoplasmic reticulum (ER) was in close contact with the mucin granules. This meshwork could be identified in fixed native human bronchial goblet cells labeled with an anti-calreticulin antibody. The potential biological significance of this ER network for mucin secretion is discussed.

    (J Histochem Cytochem 53:1305–1309, 2005)


  • Mucin Granules are in Close Contact with Tubular Elements of the Endoplasmic Reticulum -

    Live cell imaging methods were used to characterize goblet cells expressing a MUC5AC domain fused to enhanced green fluorescent protein that labels the granule lumen. Golgi complex and endosome/lysosome elements largely resided in the periphery of the granular mass. On the contrary, a tubular meshwork of endoplasmic reticulum (ER) was in close contact with the mucin granules. This meshwork could be identified in fixed native human bronchial goblet cells labeled with an anti-calreticulin antibody. The potential biological significance of this ER network for mucin secretion is discussed.

    (J Histochem Cytochem 53:1305–1309, 2005)


  • Multidrug Resistance-Associated Protein 1 (MRP1) mediated vincristine resistance: effects of N-acetylcysteine and Buthionine Sulfoximine - Background: Multidrug resistance mediated by the multidrug resistance-associated protein 1 (MRP1) decreases cellular drug accumulation. The exact mechanism of MRP1 involved multidrug resistance has not been clarified yet, though glutathione (GSH) is likely to have a role for the resistance to occur. N-acetylcysteine (NAC) is a pro-glutathione drug. DL-Buthionine (S,R)-sulfoximine (BSO) is an inhibitor of GSH synthesis. The aim of our study was to investigate the effect of NAC and BSO on MRP1-mediated vincristine resistance in Human Embryonic Kidney (HEK293) and its MRP1 transfected 293MRP cells. Human Embryonic Kidney (HEK293) cells were transfected with a plasmid encoding whole MRP1 gene. Both cells were incubated with vincristine in the presence or absence of NAC and/or BSO. The viability of both cells was determined under different incubation conditions. GSH, Glutathione S-Transferase (GST) and glutathione peroxidase (GPx) levels were measured in the cell extracts obtained from both cells incubated with different drugs. Results: N-acetylcysteine increased the resistance of both cells against vincristine and BSO decreased NAC-enhanced MRP1-mediated vincristine resistance, indicating that induction of MRP1-mediated vincristine resistance depends on GSH. Vincristine decreased cellular GSH concentration and increased GPx activity. Glutathione S-Transferase activity was decreased by NAC. Conclusion: Our results demonstrate that NAC and BSO have opposite effects in MRP1 mediated vincristine resistance and BSO seems a promising chemotherapy improving agent in MRP1 overexpressing tumor cells.

  • Multiple Roles for Elastic Fibers in the Skin -

    Dermal elastic fibers are believed to have a primary role in providing elastic stretch and recoil to the skin. Here we compare the structural arrangement of dermal elastic fibers of chick skin and different animal species. Most elastic fibers in chick skin are derived from cells that line the feather follicle and/or smooth muscle that connects the pterial and apterial muscle bundles to feather follicles. Elastic fibers in the dermis of animals with single, primary hair follicles are derived from cells lining the hair follicle or from the ends of the pili muscle, which anchors the muscle to the matrix or to the hair follicle. Each follicle is interconnected with elastic fibers. Follicles of animals with primary and secondary (wool) hair follicles are also interconnected by elastic fibers, yet only the elastic fibers derived from the primary follicle are connected to each primary follicle. Only the primary hair follicles are connected to the pili muscle. Human skin, but not the skin of other primates, is significantly different from other animals with respect to elastic fiber organization and probably cell of origin. The data suggest that the primary role for elastic fibers in animals, with the possible exception of humans, is movement and/or placement of feathers or hair. (J Histochem Cytochem 53:431–443, 2005)


  • Multiple Roles for Elastic Fibers in the Skin -

    Dermal elastic fibers are believed to have a primary role in providing elastic stretch and recoil to the skin. Here we compare the structural arrangement of dermal elastic fibers of chick skin and different animal species. Most elastic fibers in chick skin are derived from cells that line the feather follicle and/or smooth muscle that connects the pterial and apterial muscle bundles to feather follicles. Elastic fibers in the dermis of animals with single, primary hair follicles are derived from cells lining the hair follicle or from the ends of the pili muscle, which anchors the muscle to the matrix or to the hair follicle. Each follicle is interconnected with elastic fibers. Follicles of animals with primary and secondary (wool) hair follicles are also interconnected by elastic fibers, yet only the elastic fibers derived from the primary follicle are connected to each primary follicle. Only the primary hair follicles are connected to the pili muscle. Human skin, but not the skin of other primates, is significantly different from other animals with respect to elastic fiber organization and probably cell of origin. The data suggest that the primary role for elastic fibers in animals, with the possible exception of humans, is movement and/or placement of feathers or hair. (J Histochem Cytochem 53:431–443, 2005)


  • Multiple Roles for Elastic Fibers in the Skin -

    Dermal elastic fibers are believed to have a primary role in providing elastic stretch and recoil to the skin. Here we compare the structural arrangement of dermal elastic fibers of chick skin and different animal species. Most elastic fibers in chick skin are derived from cells that line the feather follicle and/or smooth muscle that connects the pterial and apterial muscle bundles to feather follicles. Elastic fibers in the dermis of animals with single, primary hair follicles are derived from cells lining the hair follicle or from the ends of the pili muscle, which anchors the muscle to the matrix or to the hair follicle. Each follicle is interconnected with elastic fibers. Follicles of animals with primary and secondary (wool) hair follicles are also interconnected by elastic fibers, yet only the elastic fibers derived from the primary follicle are connected to each primary follicle. Only the primary hair follicles are connected to the pili muscle. Human skin, but not the skin of other primates, is significantly different from other animals with respect to elastic fiber organization and probably cell of origin. The data suggest that the primary role for elastic fibers in animals, with the possible exception of humans, is movement and/or placement of feathers or hair. (J Histochem Cytochem 53:431–443, 2005)


  • Muscular ETB Receptors Develop Postnatally and Are Differentially Distributed in Specific Segments of the Rat Vasculature -

    The endothelin/endothelin–receptor system is a key player in the regulation of vascular tone in mammals. We raised and characterized an antiserum against rat ETB receptor and investigated the distribution of ETB receptors in different vascular beds during postnatal development (day 0 through day 28) and in the adult rat. We report the tissue-specific and age-dependent presence of vasoconstrictor ETB receptors. At the time of birth, vascular smooth muscle cells from all tissues examined did not exhibit ETB receptor immunoreactivity. The occurrence of ETB receptor immunoreactivity in the postnatal development was time dependent and started in small coronary and meningeal arteries at day 5, followed by small mesenteric arteries as well as brachial artery and vein at day 14. At day 21, ETB receptors were present in the media of muscular segments of pulmonary artery, large coronary arteries, and intracerebral arterioles. At day 28, ETB receptor immunoreactivity was evident in interlobular renal arteries, vas afferens, and efferens. Large renal arteries, mesenteric artery, and elastic segments of pulmonary arteries, as well as coronary and mesenteric veins, did not exhibit ETB receptor immunoreactivity. These data demonstrate the age-dependent and tissue-specific presence of ETB receptors, mainly on arterial smooth muscle cells in the vascular system of the rat. (J Histochem Cytochem 53:187–196, 2005)


  • Mutation analysis of the ATR gene in breast and ovarian cancer families - IntroductionMutations in BRCA1, BRCA2, ATM, TP53, CHK2 and PTEN account for only 20–30% of the familial aggregation of breast cancer, which suggests the involvement of additional susceptibility genes. The ATR (ataxia-telangiectasia- and Rad3-related) kinase is essential for the maintenance of genomic integrity. It functions both in parallel and cooperatively with ATM, but whereas ATM is primarily activated by DNA double-strand breaks induced by ionizing radiation, ATR has been shown to respond to a much broader range of DNA damage. Upon activation, ATR phosphorylates several important tumor suppressors, including p53, BRCA1 and CHK1. Based on its central function in the DNA damage response, ATR is a plausible candidate gene for susceptibility to cancer. Methods: We screened the entire coding region of the ATR gene for mutations in affected index cases from 126 Finnish families with breast and/or ovarian cancer, 75 of which were classified as high-risk and 51 as moderate-risk families, by using conformation sensitive gel electrophoresis and direct sequencing. Results: A large number of novel sequence variants were identified, four of which – Glu254Gly, Ser1142Gly, IVS24-48G>A and IVS26+15C>T – were absent from the tested control individuals (n = 300). However, the segregation of these mutations with the cancer phenotype could not be confirmed, partly because of the lack of suitable DNA samples. Conclusion: The present study does not support a major role for ATR mutations in hereditary susceptibility to breast and ovarian cancer.

  • Myoepithelial cells: good fences make good neighbors - The mammary gland consists of an extensively branched ductal network contained within a distinctive basement membrane and encompassed by a stromal compartment. During lactation, production of milk depends on the action of the two epithelial cell types that make up the ductal network: luminal cells, which secrete the milk components into the ductal lumen; and myoepithelial cells, which contract to aid in the ejection of milk. There is increasing evidence that the myoepithelial cells also play a key role in the organizational development of the mammary gland, and that the loss and/or change of myoepithelial cell function is a key step in the development of breast cancer. In this review we briefly address the characteristics of breast myoepithelial cells from human breast and mouse mammary gland, how they function in normal mammary gland development, and their recently appreciated role in tumor suppression.

  • Myogenic Potential of Muscle Side and Main Population Cells after Intravenous Injection into Sub-lethally Irradiated mdx Mice -

    Muscle side population (SP) cells have demonstrated hematopoietic and myogenic activities in vivo upon intravenous (IV) injection into lethally irradiated mdx mice. In contrast, muscle main population (MP) cells were unable to rescue the bone marrow of lethally irradiated mice and, consequently, their in vivo myogenic potential could not be assessed using this method. In the current study, muscle SP or MP cells derived from syngeneic wild-type male mice were delivered to sub-lethally irradiated mdx female mice by single or serial IV injections. Recipient mice were euthanized 12 weeks after transplantation at which time the quadriceps and diaphragm muscles were analyzed for the presence of donor-derived cells. Mice injected with 104 muscle SP cells or with 106 MP cells appeared to have similar numbers of dystrophin-positive myofibers containing fused donor nuclei. Analysis of the remaining tissue via real-time quantitative PCR indicated that mice injected with muscle SP cells had a higher percentage of donor-derived Y-DNA in the quadriceps than mice injected with MP cells, suggesting that muscle SP cells may be enriched for progenitors able to engraft dystrophic skeletal muscles from the circulation. Although the overall engraftment did not reach therapeutically significant levels, these results indicate that further optimization of cell delivery techniques may lead to improved efficacy of cell-mediated therapy using muscle SP cells. (J Histochem Cytochem 53:861–873, 2005)


  • Myogenic Potential of Muscle Side and Main Population Cells after Intravenous Injection into Sub-lethally Irradiated mdx Mice -

    Muscle side population (SP) cells have demonstrated hematopoietic and myogenic activities in vivo upon intravenous (IV) injection into lethally irradiated mdx mice. In contrast, muscle main population (MP) cells were unable to rescue the bone marrow of lethally irradiated mice and, consequently, their in vivo myogenic potential could not be assessed using this method. In the current study, muscle SP or MP cells derived from syngeneic wild-type male mice were delivered to sub-lethally irradiated mdx female mice by single or serial IV injections. Recipient mice were euthanized 12 weeks after transplantation at which time the quadriceps and diaphragm muscles were analyzed for the presence of donor-derived cells. Mice injected with 104 muscle SP cells or with 106 MP cells appeared to have similar numbers of dystrophin-positive myofibers containing fused donor nuclei. Analysis of the remaining tissue via real-time quantitative PCR indicated that mice injected with muscle SP cells had a higher percentage of donor-derived Y-DNA in the quadriceps than mice injected with MP cells, suggesting that muscle SP cells may be enriched for progenitors able to engraft dystrophic skeletal muscles from the circulation. Although the overall engraftment did not reach therapeutically significant levels, these results indicate that further optimization of cell delivery techniques may lead to improved efficacy of cell-mediated therapy using muscle SP cells. (J Histochem Cytochem 53:861–873, 2005)


  • Neuregulin Receptor ErbB2 Localization at T-tubule in Cardiac and Skeletal Muscle -

    Previous studies have indicated that ErbB receptors for neuregulins play an important role in cardiac development and muscle spindle formation during embryogenesis; however, little is known about their functions in adulthood. Recent reports indicate that breast cancer therapy with humanized monoclonal ErbB2 antibody induces cardiomyopathy, suggesting that ErbB2 serves as a crucial signaling receptor, even in the adult heart. Here, we examine ErbB2 expression and localization in both cardiac and skeletal muscle of adult mice via immunoblot and immunohistochemistry. ErbB2 was detected as a band ~185 kD molecular mass in each cardiac and skeletal muscle extraction. Confocal images of double labeling showed that ErbB2 was colocalized with caveolin-3 in cardiac muscle and with dihydropyridine receptor in skeletal muscle, suggesting that ErbB2 was localized at the T-tubule. In addition, immunoelectron micrographs clearly demonstrated that ErbB2 was located at the T-tubule in both types of muscle. Taken together, the results of the present study suggest that neuregulin-ErbB2 signaling plays a role in the physiological function of cardiac and skeletal muscle, even in adulthood.

    (J Histochem Cytochem 53:87–91, 2005)


  • Neuroanatomy of sea spiders implies an appendicular origin of the protocerebral segment. -
    Related Articles

    Neuroanatomy of sea spiders implies an appendicular origin of the protocerebral segment.

    Nature. 2005 Oct 20;437(7062):1144-8

    Authors: Maxmen A, Browne WE, Martindale MQ, Giribet G

    Independent specialization of arthropod body segments has led to more than a century of debate on the homology of morphologically diverse segments, each defined by a lateral appendage and a ganglion of the central nervous system. The plesiomorphic composition of the arthropod head remains enigmatic because variation in segments and corresponding appendages is extreme. Within extant arthropod classes (Chelicerata, Myriapoda, Crustacea and Hexapoda--including the insects), correspondences between the appendage-bearing second (deutocerebral) and third (tritocerebral) cephalic neuromeres have been recently resolved on the basis of immunohistochemistry and Hox gene expression patterns. However, no appendage targets the first ganglion, the protocerebrum, and the corresponding segmental identity of this anterior region remains unclear. Reconstructions of stem-group arthropods indicate that the anteriormost region originally might have borne an ocular apparatus and a frontal appendage innervated by the protocerebrum. However, no study of the central nervous system in extant arthropods has been able to corroborate this idea directly, although recent analyses of cephalic gene expression patterns in insects suggest a segmental status for the protocerebral region. Here we investigate the developmental neuroanatomy of a putative basal arthropod, the pycnogonid sea spider, with immunohistochemical techniques. We show that the first pair of appendages, the chelifores, are innervated at an anterior position on the protocerebrum. This is the first true appendage shown to be innervated by the protocerebrum, and thus pycnogonid chelifores are not positionally homologous to appendages of extant arthropods but might, in fact, be homologous to the 'great appendages' of certain Cambrian stem-group arthropods.

    PMID: 16237442 [PubMed - in process]


  • Neuromagnetic brain responses to words from semantic sub- and supercategories - Background: We explored spatio-temporal patterns of cortical activity evoked by written words from super-ordinate and sub-ordinate semantic categories and hoped to find a differential cortical and/or temporal distribution of the brain response depending on the level of the categories. Twenty-three subjects saw 360 words belonging to six sub-ordinate categories (mammals, birds, fish, fruit, flowers, trees) within two super-ordinate categories (fauna, flora). Visually evoked magnetic fields were determined from whole-head (148-sensor) magnetoencephalography and analyzed in the source space (Minimum Norm Estimate). Results: Activity (MNE amplitudes) 100-150ms after stimulus onset in the left occipito-temporal area distinguished super-ordinate categories, while later activity (300-550ms) in the left temporal area distinguished the six sub-ordinate categories. Conclusions: Our results document temporally and spatially distinct processing and representation of words according to their categorical information. If further studies can rule out possible confounds then our results may help constructing a theory about the internal structure of entries in the mental lexicon and its access.

  • New Agents in Myelodysplastic Syndromes - Myelodysplastic syndromes (MDS) are a heterogeneous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis resulting in peripheral cytopenia and by increased progression to acute myeloid leukemia (AML). Therapeutic interventions for MDS other than allogeneic stem cell transplantation have been palliative. Novel and targeted therapeutic agents such as the inhibition of farnesyl transferases and receptor tyrosine kinases, more potent thalidomide analogs, arsenic trioxide, immunomo-dulating agents, hypomethylating agents, and histone deacetylase inhibitors have shown encouraging results and may offer durable benefit to patients with MDS. Further development of rational therapies and improvements in the outcome of patients with MDS are likely to emerge from an increased understanding of the pathophysiology of these diseases.

  • New Anticoagulant Drugs: A Critical Perspective - No abstract available

  • New approaches to eliciting protective immunity through T cell repertoire manipulation: the concept of thymic vaccination - Conventional vaccines afford protection against infectious diseases by expanding existing pathogen-specific peripheral lymphocytes, both CD8 cytotoxic effector (CTL) and CD4 helper T cells. The latter induce B cell maturation and antibody production. As a consequence, lymphocytes within the memory pool are poised to rapidly proliferate at the time of a subsequent infection. The "thymic vaccination" concept offers a novel way to alter the primary T cell repertoire through exposure of thymocytes to altered peptide ligands (APL) with reduced T cell receptor (TCR) affinity relative to cognate antigens recognized by those same TCRs. Thymocyte maturation (i.e. positive selection) is enhanced by low affinity interaction between a TCR and an MHC-bound peptide in the thymus and subsequent emigration of mature cells into the peripheral T lymphocyte pool follows. In principal, such variants of antigens derived from infectious agents could be utilized for peptide-driven maturation of thymocytes bearing pathogen-specific TCRs. To test this idea, APLs of gp33–41, a Db-restricted peptide derived from the lymphocytic choriomeningitis virus (LCMV) glycoprotein, and of VSV8, a Kb-restricted peptide from the vesicular stomatitis virus (VSV) nucleoprotein, have been designed and their influence on thymic maturation of specific TCR-bearing transgenic thymocytes examined in vivo using irradiation chimeras. Injection of APL resulted in positive selection of CD8 T cells expressing the relevant viral specificity and in the export of those virus-specific CTL to lymph nodes without inducing T cell proliferation. Thus, exogenous APL administration offers the potential of expanding repertoires in vivo in a manner useful to the organism. To efficiently peripheralize antigen-specific T cells, concomitant enhancement of mechanisms promoting thymocyte migration appears to be required. This commentary describes the rationale for thymic vaccination and addresses the potential prophylactic and therapeutic applications of this approach for treatment of infectious diseases and cancer. Thymic vaccination-induced peptide-specific T cells might generate effective immune protection against disease-causing agents, including those for which no effective natural protection exists.

  • New Aspects of Laser Microdissection in Research and Routine -

    Laser microdissection has opened a window to new technologies. The scientific fields of genomics, transcriptomics, and proteomics need pure samples for rendering reliable results. Homogeneous sample preparation is a prerequisite for modern molecular analyses, both qualitative and quantitative. Laser microdissection and pressure catapulting (LMPC) is a tool for isolating specific cells from complex tissues in a non-contact and contamination-free manner. Because LMPC technology is an optimal method for obtaining fast and reliable access to single cells, the possibility of automatic isolation of single fetal cells has the promise of being a big step forward in developing protocols for non-invasive prenatal diagnosis. (J Histochem Cytochem 53:409–412, 2005)


  • New insights into the possible role of bacteriophages in host defense and disease - Background: While the ability of bacteriophages to kill bacteria is well known and has been used in some centers to combat antibiotics – resistant infections, our knowledge about phage interactions with mammalian cells is very limited and phages have been believed to have no intrinsic tropism for those cells.Presentation of the hypothesisAt least some phages (e.g., T4 coliphage) express Lys-Arg-Gly (KGD) sequence which binds β3 integrins (primarily αIIbβ3). Therefore, phages could bind β3+ cells (platelets, monocytes, some lymphocytes and some neoplastic cells) and downregulate activities of those cells by inhibiting integrin functions.Testing the hypothesisBinding of KGD+ phages to β3 integrin+ cells may be detected using standard techniques involving phage – mediated bacterial lysis and plaque formation. Furthermore, the binding may be visualized by electron microscopy and fluorescence using labelled phages. Binding specificity can be confirmed with the aid of specific blocking peptides and monoclonal antibodies. In vivo effects of phage – cell interactions may be assessed by examining the possible biological effects of β3 blockade (e.g., anti-metastatic activity).Implication of the hypothesisIf, indeed, phages can modify functions of β3+ cells (platelets, monocytes, lymphocytes, cancer cells) they could be important biological response modifiers regulating migration and activities of those cells. Such novel understanding of their role could open novel perspectives in their potential use in treatment of cardiovascular and autoimmune disease, graft rejection and cancer.

  • New Methods to Evaluate Colocalization of Fluorophores in Immunocytochemical Preparations as Exemplified by a Study on A2A and D2 Receptors in Chinese Hamster Ovary Cells -

    An important aspect of the image analysis of immunocytochemical preparations is the evaluation of colocalization of different molecules. The aim of the present study is to introduce image analysis methods to identify double-labeled locations exhibiting the highest association of two fluorophores and to characterize their pattern of distribution. These methods will be applied to the analysis of the cotrafficking of adenosine A2A and dopamine D2 receptors belonging to the G protein–coupled receptor family and visualized by means of fluorescence immunocytochemistry in Chinese hamster ovary cells after agonist treatment. The present procedures for colocalization have the great advantage that they are, to a large extent, insensitive to the need for a balanced staining with the two fluorophores. Thus, these procedures involve image processing, visualization, and analysis of colocalized events, using a covariance method and a multiply method and the evaluation of the identified colocalization patterns. Moreover, the covariance method offers the possibility of detecting and quantitatively characterizing anticorrelated patterns of intensities, whereas the immediate detection of colocalized clusters with a high concentration of labeling is a possibility offered by the multiply method. The present methods offer a new and sensitive approach to detecting and quantitatively characterizing strongly associated fluorescence events, such as those generated by receptor–receptor interaction, and their distribution patterns in dual-color confocal laser microscopy.

    (J Histochem Cytochem 53:941–953, 2005)


  • New Methods to Evaluate Colocalization of Fluorophores in Immunocytochemical Preparations as Exemplified by a Study on A2A and D2 Receptors in Chinese Hamster Ovary Cells -

    An important aspect of the image analysis of immunocytochemical preparations is the evaluation of colocalization of different molecules. The aim of the present study is to introduce image analysis methods to identify double-labeled locations exhibiting the highest association of two fluorophores and to characterize their pattern of distribution. These methods will be applied to the analysis of the cotrafficking of adenosine A2A and dopamine D2 receptors belonging to the G protein–coupled receptor family and visualized by means of fluorescence immunocytochemistry in Chinese hamster ovary cells after agonist treatment. The present procedures for colocalization have the great advantage that they are, to a large extent, insensitive to the need for a balanced staining with the two fluorophores. Thus, these procedures involve image processing, visualization, and analysis of colocalized events, using a covariance method and a multiply method and the evaluation of the identified colocalization patterns. Moreover, the covariance method offers the possibility of detecting and quantitatively characterizing anticorrelated patterns of intensities, whereas the immediate detection of colocalized clusters with a high concentration of labeling is a possibility offered by the multiply method. The present methods offer a new and sensitive approach to detecting and quantitatively characterizing strongly associated fluorescence events, such as those generated by receptor–receptor interaction, and their distribution patterns in dual-color confocal laser microscopy.

    (J Histochem Cytochem 53:941–953, 2005)


  • NF-kB inhibitor blocks B cell development at two checkpoints - Members of the NF-kB transcription factor family are differentially expressed in the B cell lineage. Disruption of individual or two NF-kB subunits exhibits distinct defects in B lymphocyte development, activation, and survival. However, the role each NF-kB plays during B cell development has been obscured by molecular compensation. To address this issue, a trans-dominant form of IkBα was transduced into bone marrow cells to act as a pan-inhibitor of NF-kB using a retroviral system. While the development of T-lymphocytes and myeloid cell lineages was not grossly affected by the transduced IkBα gene, a significant reduction in the number and percentage of B lineage cells was apparent in IkBα transduced chimeric mice. IkBα expression decreased the percentage of pre-B and immature B cell subsets in the bone marrow and further impaired the development of follicular mature B cells and marginal zone B cells in the periphery. Introduction of the Bcl-X transgene completely restored the pre-B and immature B cell pool in the bone marrow. However, despite a significant improvement of overall viability of the B cell lineage, Bcl-X expression was insufficient to overcome the maturation block resulting from NF-kB inhibition. Together, our study suggests that NF-kB activity is required for two distinct checkpoints during B cell development: one is for pre-B/immature B cell viability, the other is to provide both survival and maturation signals to ensure the proper development of follicular mature B cells.

  • Non-invasive Fetal RHD and RHCE Genotyping Using Real-time PCR Testing of Maternal Plasma in RhD-negative Pregnancies -

    We assessed the feasibility of fetal RHD and RHCE genotyping by analysis of DNA extracted from plasma samples of RhD-negative pregnant women using real-time PCR and primers and probes targeted toward RHD and RHCE genes. We analyzed 45 pregnant women in the 11th to 40th weeks of pregnancy and correlated the results with serological analysis of cord blood after delivery. Non-invasive prenatal fetal RHD exon 7, RHD exon 10, RHCE exon 2 (C allele), and RHCE exon 5 (E allele) genotyping analysis of maternal plasma samples was correctly performed in 45 out of 45 RhD-negative pregnant women delivering 24 RhD-, 17 RhC-, and 7 RhE-positive newborns. Detection of fetal RHD and the C and E alleles of RHCE gene from maternal plasma is highly accurate and enables implementation into clinical routine. We recommend performing fetal RHD and RHCE genotyping together with fetal sex determination in alloimmunized D-negative pregnancies at risk of hemolytic disease of the newborn. In case of D-negative fetus, amplification of another paternally inherited allele (SRY and/or RhC and/or RhE positivity) proves the presence of fetal DNA in maternal circulation. (J Histochem Cytochem 53:301–305, 2005)


  • Non-obstructive azoospermia and maturation arrest with complex translocation 46,XY t(9;13;14)(p22;q21.2;p13) is consistent with the Luciani-Guo hypothesis of latent aberrant autosomal regions and infertility - ObjectiveTo describe clinical and histological features observed in the setting of an unusual complex translocation involving three autosomes (9, 13, and 14) identified in an otherwise healthy male referred for infertility consultation. Material and methods: The patient was age 30 and no family history was available (adopted). Total azoospermia was confirmed on multiple semen analyses. Peripheral karyotype showed a 46,XY t(9;13;14)(p22:q21.2;p13) genotype; no Y-chromosome microdeletions were identified. Cystic fibrosis screening was negative. Bilateral testis biopsy revealed uniform maturation arrest and peritubular fibrosis. Results: Formal genetic counseling was obtained and the extant literature reviewed with the couple. Given the low probability of obtaining sperm on testicular biopsy, as well as the high risk of any retrieved sperm having an unbalanced genetic rearrangement, the couple elected to proceed with fertility treatment using anonymous donor sperm for insemination. Conclusion: Although genes mapped to the Y-chromosome have been established as critical to normal testicular development and spermatogenesis, certain autosomal genes are now also recognized as important in these processes. Here we present clinical evidence to support the Luciani-Guo hypothesis (first advanced in 1984 and refined in 2002), which predicts severe spermatogenic impairment with aberrations involving chromosomes 9, 13, and/or 14, independent of Y-chromosome status. Additional study including fluorescent in situ hybridization and molecular analysis of specific chromosomal regions is needed to characterize more fully the contribution(s) of these autosomes to male testicular development and spermatogenesis.

  • NOSIP and Its Interacting Protein, eNOS, in the Rat Trachea and Lung -

    Endothelial nitric oxide synthase (eNOS), the major nitric oxide (NO)-generating enzyme of the vasculature, is regulated through multiple interactions with proteins, including caveolin-1, Hsp90, Ca2+-calmodulin, and the recently discovered eNOS-interacting protein, NOSIP. Previous studies indicate that NOSIP may contribute to the intricate regulation of eNOS activity and availability. Because eNOS has been shown to be abundantly expressed in the airways, we determined the expression and cellular localization of NOSIP in rat trachea and lung by RT-PCR and immunohistochemistry and examined the interaction of NOSIP with eNOS in lung by coimmunoprecipitation. In tracheal epithelium and lung, NOSIP mRNA expression was prevalent, as shown by RT-PCR, and the corresponding protein interacted with eNOS, as demonstrated by coimmunoprecipitation. Using immunohistochemistry, we found both NOSIP and eNOS immunoreactivity in ciliated epithelial cells of trachea and bronchi, while Clara cells showed immunoreactivity for NOSIP only. NOSIP and eNOS were present in vascular and bronchial smooth muscle cells of large arteries and airways, whereas endothelial cells, as well as bronchiolar and arteriolar smooth muscle cells, exclusively stained for NOSIP. Our results point to functional role(s) of NOSIP in the control of airway and vascular diameter, mucosal secretion, NO synthesis in ciliated epithelium, and, therefore, of mucociliary and bronchial function. (J Histochem Cytochem 53:155–164, 2005)


  • Nuclear localization of Annexin A7 during murine brain development - Background: Annexin A7 is a member of the annexin protein family, which is characterized by its ability to interact with phospholipids in the presence of Ca2+-ions and which is thought to function in Ca2+-homeostasis. Results from mutant mice showed altered Ca2+-wave propagation in astrocytes. As the appearance and distribution of Annexin A7 during brain development has not been investigated so far, we focused on the distribution of Annexin A7 protein during mouse embryogenesis in the developing central nervous system and in the adult mouse brain. Results: Annexin A7 is expressed in cells of the developing brain where a change in its subcellular localization from cytoplasm to nucleus was observed. In the adult CNS, the subcellular distribution of Annexin A7 depends on the cell type. By immunohistochemistry analysis Annexin A7 was detected in the cytosol of undifferentiated cells at embryonic days E5–E8. At E11–E15 the protein is still present in the cytosol of cells predominantly located in the ventricular germinative zone surrounding the lateral ventricle. Later on, at embryonic day E16, Annexin A7 in cells of the intermediate and marginal zone of the neopallium translocates to the nucleus. Neuronal cells of all areas in the adult brain present Annexin A7 in the nucleus, whereas glial fibrillary acidic protein (GFAP)-positive astrocytes exhibit both, a cytoplasmic and nuclear staining. The presence of nuclear Annexin A7 was confirmed by extraction of the nucleoplasm from isolated nuclei obtained from neuronal and astroglial cell lines. Conclusion: We have demonstrated a translocation of Annexin A7 to nuclei of cells in early murine brain development and the presence of Annexin A7 in nuclei of neuronal cells in the adult animal. The role of Annexin A7 in nuclei of differentiating and mature neuronal cells remains elusive.

  • Nuclear telomerase is less accessible to antibody probing than known nuclear antigens: retrieval with new immunostaining buffer. -
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    Nuclear telomerase is less accessible to antibody probing than known nuclear antigens: retrieval with new immunostaining buffer.

    Histochem Cell Biol. 2005 Jan;123(1):105-12

    Authors: Leung DT, Ma CH, Niu H, Liew CT, Tang JT, Lim PL

    Telomerase is an important tumor marker but few antibodies to the enzyme have been described or used without difficulty in histochemical detection. Here we report specific detection of the enzyme in cell and tissue preparations using a new monoclonal antibody (mAb 476) and a new antigen-retrieval buffer (Enhancing buffer). When used to detect telomerase under normal immunostaining conditions in HL-60 cells or tissue sections of hepatocellular carcinoma or metastatic choriocarcinoma, unexpectedly, the antibody stained the cytoplasm rather than the nucleus. Nuclear staining, however, was revealed using the Enhancing buffer. Since other nuclear antigens in the HL-60 cell could be stained both ordinarily and in the Enhancing buffer, nuclear telomerase appears to be shrouded by the nuclear matrix or blocked by accessory proteins. The cytoplasmic activity seen in normal buffer but absent largely from the Enhancing buffer may be an artifact or the nascent, "naked" enzyme. With a known cytoplasmic antigen (proteinase-3) chosen arbitrarily for comparison, the antigenicity was found enhanced, instead, by the Enhancing buffer. The mode of action of the Enhancing buffer differs from that of microwave irradiation or the signal amplification (CSA) used by some investigators. The latter was found to enhance the cytoplasmic reactivity rather than the nuclear reactivity of mAb 476.

    PMID: 15538612 [PubMed - indexed for MEDLINE]


  • Nuclear [beta]-Catenin Expression Is Rare and its Potential Association With Short Survival in Colorectal Signet-Ring Cell Carcinoma. -

  • Number and Distribution of Intraganglionic Laminar Endings in the Mouse Esophagus as Demonstrated with Two Different Immunohistochemical Markers -

    Intraganglionic laminar endings (IGLEs) represent the only vagal mechanosensory terminals in the tunica muscularis of the esophagus. Two specific markers for IGLEs were recently described in mouse: the purinergic P2x2 receptor and the vesicular glutamate transporter 2 (VGLUT2). This study aimed at comparing both markers with respect to their suitability for quantitative analysis. We counted IGLEs immunostained for VGLUT2 and P2x2, respectively, and mapped their distribution in esophageal wholemounts of C57Bl/6 mice. Numbers and distribution of IGLEs were compared with those of myenteric ganglia as demonstrated by cuprolinic blue histochemistry. Whereas the distribution of VGLUT2-immunopositive IGLEs closely matched that of myenteric ganglia, P2x2-immunopositive IGLEs were rarely found in upper and middle esophagus but increasingly in its lower parts. P2x2 stained only half the number of IGLEs found with VGLUT2 immunostaining. We also investigated the correlation between anterograde tracing and immunohistochemistry for identifying IGLEs. Confocal microscopy revealed colocalization of all three markers in ~50% of IGLEs. The remaining IGLEs showed only tracer and VGLUT2 labeling but no P2x2 immunoreactivity. Thus, VGLUT2 and P2x2 represent two specific markers for qualitative demonstration of esophageal IGLEs. However, VGLUT2 may be superior to P2x2 as a quantitative marker for IGLEs in the esophagus of C57Bl/6 mice. (J Histochem Cytochem 53:1023–1031, 2005)


  • Number and Distribution of Intraganglionic Laminar Endings in the Mouse Esophagus as Demonstrated with Two Different Immunohistochemical Markers -

    Intraganglionic laminar endings (IGLEs) represent the only vagal mechanosensory terminals in the tunica muscularis of the esophagus. Two specific markers for IGLEs were recently described in mouse: the purinergic P2x2 receptor and the vesicular glutamate transporter 2 (VGLUT2). This study aimed at comparing both markers with respect to their suitability for quantitative analysis. We counted IGLEs immunostained for VGLUT2 and P2x2, respectively, and mapped their distribution in esophageal wholemounts of C57Bl/6 mice. Numbers and distribution of IGLEs were compared with those of myenteric ganglia as demonstrated by cuprolinic blue histochemistry. Whereas the distribution of VGLUT2-immunopositive IGLEs closely matched that of myenteric ganglia, P2x2-immunopositive IGLEs were rarely found in upper and middle esophagus but increasingly in its lower parts. P2x2 stained only half the number of IGLEs found with VGLUT2 immunostaining. We also investigated the correlation between anterograde tracing and immunohistochemistry for identifying IGLEs. Confocal microscopy revealed colocalization of all three markers in ~50% of IGLEs. The remaining IGLEs showed only tracer and VGLUT2 labeling but no P2x2 immunoreactivity. Thus, VGLUT2 and P2x2 represent two specific markers for qualitative demonstration of esophageal IGLEs. However, VGLUT2 may be superior to P2x2 as a quantitative marker for IGLEs in the esophagus of C57Bl/6 mice. (J Histochem Cytochem 53:1023–1031, 2005)


  • Obesity promotes 7,12-dimethylbenz(a)anthracene-induced mammary tumor development in female zucker rats - IntroductionHigh body mass index has been associated with increased risk for various cancers, including breast cancer. Here we describe studies using 7,12-dimethylbenz(a)anthracene (DMBA) to investigate the role of obesity in DMBA-induced mammary tumor susceptibility in the female Zucker rat (fa/fa), which is the most widely used rat model of genetic obesity.MethodFifty-day-old female obese (n = 25) and lean (n = 28) Zucker rats were orally gavaged with 65 mg/kg DMBA. Rats were weighed and palpated twice weekly for detection of mammary tumors. Rats were killed 139 days after DMBA treatment. Results: The first mammary tumor was detected in the obese group at 49 days after DMBA treatment, as compared with 86 days in the lean group (P < 0.001). The median tumor-free time was significantly lower in the obese group (P < 0.001). Using the days after DMBA treatment at which 25% of the rats had developed mammary tumors as the marker of tumor latency, the obese group had a significantly shorter latency period (66 days) than did the lean group (118 days). At the end of the study, obese rats had developed a significantly (P < 0.001) greater mammary tumor incidence (68% versus 32%) compared with the lean group. The tumor histology of the mammary tumors revealed that obesity was associated with a significant (P < 0.05) increase in the number of rats with at least one invasive ductal and lobular carcinoma compared with lean rats. Conclusion: Our results indicate that obesity increases the susceptibility of female Zucker rats to DMBA-induced mammary tumors, further supporting the hypothesis that obesity and some of its mediators play a significant role in carcinogenesis.

  • On evolutionary origin of cancer - Background: The necessary and sufficient capabilities of cancer cell have been identified. Strikingly, this list does not include one that would seem to be a key property, namely the ability of cancer cells to kill their "host". This is believed to be a self-evident consequence of the other capabilities (e.g., metastasis), although the available evidence suggests a distinct killer function. Taking into account this unlisted property can significantly affect the current paradigm of carcinogenesis.Presentation of the hypothesisOn the assumption that killer function is a key capability of the cancer cell, it is suggested that cancer has evolved as a mechanism of negative selection of mutant alleles of vitally important genes present in population. Similarly to apoptosis, which is an altruistic suicidal act of a damaged cell, cancer is an altruistic suicidal act of an individual who carries dangerous alleles and presents a hazard for genetic stability of the population. From this point of view, apoptosis is not a protection means against cancer as generally believed, but rather they are the first and second lines of defense against genome instability, respectively.Testing the hypothesisThe modern DNA array technology is capable of revealing gene expression profiles responsible for killer function of cancer cell as well as those specific targets in the body that are most strongly affected by the tumor growth.Implications of the hypothesisThis hypothesis suggests new avenues of cancer research as well as principally new therapeutic strategies.

  • On the Nature of Cancer and why Anticancer Vaccines don't work - In this essay I suggest that the major difficulty in producing effective anti-cancer vaccines lies in the fact that most cancers have little immunogenicity because of a basic paucity of tumor-specific antigenicity. The lack of antigenicity, despite extensive genomic instability, could be explained if most tumor mutations occur in silenced genes. A further problem is that an immune reaction against tumor antigens, especially in moderate or low amount, may be stimulatory rather than inhibitory to tumor growth.

  • Open Access - (No abstract is available for this citation)

  • Optimal clinical trial designs for immune-based therapies in persistent viral infections - There is now effective therapy for infection by the Human Immunodeficiency Virus (HIV), but there is no cure. Consequently, antiviral drugs must be administered continuously to suppress viral replication. Recently, a large phase III international immune-based therapy trial was discontinued because it is difficult to measure clinical endpoints while antivirals are administered. Since the immune system has evolved under the selective force of microbial infections, the immune reaction is antiviral. This commentary explores the rationale of using "Diagnostic Treatment Interruptions" of antiviral therapies to determine efficacies of immune-based therapies.

  • Optimal conditions for the retrieval of CD4 and CD8 antigens in formalin-fixed, paraffin-embedded tissues. -
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    Optimal conditions for the retrieval of CD4 and CD8 antigens in formalin-fixed, paraffin-embedded tissues.

    J Mol Histol. 2004 May;35(4):403-8

    Authors: Kim SH, Kook MC, Song HG

    The effects of buffer, NaCl, EDTA, and urea on the retrieval of CD4 and CD8 antigens in formaldehyde-fixed, paraffin-embedded tissues with a microwave pressure-cooker were evaluated. The optimal retrieval conditions were found to be borate buffer at pH 8 containing 1 mM NaCl and 1 mM EDTA. Urea was found to be less effective.

    PMID: 15503814 [PubMed - indexed for MEDLINE]


  • Optimal Processing Method to Obtain Four-color Confocal Fluorescent Images of the Cytoskeleton and Nucleus in Three-dimensional Chondrocyte Cultures -

    Tissue engineering of articular cartilage requires accurate imaging of the chondrocyte cytoskeleton. Past studies have applied various fixation and permeabilization protocols without optimization of parameters. In this study, we have examined procedures using glutaraldehyde and paraformaldehyde as fixatives and Triton X-100 and Octyl-POE as permeabilizing detergents. A four-color fluorescence confocal method was developed to simultaneously image actin, tubulin, vimentin, and the nucleus. We found optimal preservation and morphology of the chondrocyte cytoskeleton after simultaneous fixation and permeabilization with glutaraldehyde and Triton X-100. These images displayed less cellular shrinkage and higher-resolution filamentous structures than with paraformaldehyde or when permeabilization followed fixation. (J Histochem Cytochem 53:1171–1175, 2005)


  • Orchitis: A Complication of Severe Acute Respiratory Syndrome (SARS). -
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    Orchitis: A Complication of Severe Acute Respiratory Syndrome (SARS).

    Biol Reprod. 2005 Oct 19;

    Authors: Xu J, Qi L, Chi X, Yang J, Wei X, Gong E, Peh S, Gu J

    Severe acute respiratory syndrome (SARS) coronavirus has been known to damage multiple organs, however, little is known about its impact on the reproductive system. In the present study, we analyzed the pathological changes of testes from 6 patients who died of SARS. Results suggested that SARS caused orchitis. All SARS testes displayed wide spread germ cell destruction, few or no spermatozoon in the seminiferous tubule, thickened basement membrane, and leukocyte infiltration. The numbers of CD3+ T lymphocyte and CD68+ macrophage increased significantly in the interstitial tissue comparing to the control group (P<0.05). SARS viral genomic sequences was not detected in the testes by in situ hybridization. Immunohistochemistry demonstrated abundant IgG precipitation in the seminiferous epithelium of SARS testes indicating possible immune response as the cause for the damages. Our findings indicated that orchitis is a complication of SARS. It further suggests that the reproductive functions should be followed and evaluated in recovered male SARS patients.

    PMID: 16237152 [PubMed - as supplied by publisher]


  • Overcoming cisplatin resistance by mTOR inhibitor in lung cancer - Background: Cisplatin resistance is complex and involves several different mechanisms. Employing cDNA microarray analysis, we have found that cisplatin resistant cells share the common characteristic of increase in ribosomal proteins and elongation factors. We hypothesize that in order to survive cisplatin treatment, cells have to synthesize DNA repair proteins, antiapoptotic proteins and growth-stimulating proteins. Thus, by blocking the translation of these proteins, one should be able to restore cisplatin sensitivity. We have studied the role of CCI-779, an ester analog of rapamycin which is known to inhibit translation by disabling mTOR, in restoring cisplatin sensitivity in a panel of cisplatin resistant cell lines. We have also determined the role of CCI-779 in P-gp1 and MRP1 mediated resistance. Results: Our data show that CCI-779 possess antiproliferative effects in both cisplatin sensitive and resistant cell lines, but shows no effect in P-gp1 and MRP1 overexpressing cell lines. Importantly, CCI-779 at 10 ng/ml (less that 10% of the growth inhibitory effect) can increase the growth inhibition of cisplatin by 2.5–6 fold. Moreover, CCI-779 also enhances the apoptotic effect of cisplatin in cisplatin resistant cell lines. In these resistant cells, adding CCI-779 decreases the amount of 4E-BP phosphorylation and p-70S6 kinase phosphorylation as well as lower the amount of elongation factor while cisplatin alone has no effect. However, CCI-779 can only reverse P-gp mediated drug resistance at a higher dose(1 ug/ml). Conclusion: We conclude that CCI-779 is able to restore cisplatin sensitivity in small cell lung cancer cell lines selected for cisplatin resistance as well as cell lines derived from patients who failed cisplatin. These findings can be further explored for future clinical use. On the other hand, CCI-779 at achievable clinical concentration, has no growth inhibitory effect in P-gp1 or MRP1 overexpressing cells. Furthermore, CCI-779 also appears to be a weak MDR1 reversal agent. Thus, it is not a candidate to use in MDR1 or MRP1 overexpressing cells.

  • Overdiagnosis and overtreatment of breast cancer: Overdiagnosis in randomised controlled trials of breast cancer screening - Data from randomised controlled trials of mammographic screening can be used to determine the extent of any overdiagnosis, as soon as either a time equivalent to the lead-time has elapsed after the final screen, or the control arm has been offered screening. This paper reviews those randomised trials for which breast cancer incidence data are available. In recent trials in which the control group has not been offered screening, an excess incidence of breast cancer remains after many years of follow-up. In those trials in which the control arm has been offered screening, although there is a possible shift from invasive to in situ disease, there is no evidence of overdiagnosis as a result of incident screens.

  • Overexpression of eCLCA1 in Small Airways of Horses with Recurrent Airway Obstruction -

    The human hCLCA1 and murine mCLCA3 (chloride channels, calcium-activated) have recently been identified as promising therapeutic targets in asthma. Recurrent airway obstruction in horses is an important animal model of human asthma. Here, we have cloned and characterized the first equine CLCA family member, eCLCA1. The 913 amino acids eCLCA1 polypeptide forms a 120-kDa transmembrane glycoprotein that is processed to an 80-kDa protein in vivo. Three single nucleotide polymorphisms were detected in the eCLCA1 coding region in 14 horses, resulting in two amino acid changes (485H/R and 490V/L). However, no functional differences were recorded between the channel properties of the two variants in transfected HEK293 cells. The eCLCA1 protein was detected immunohistochemically in mucin-producing cells in the respiratory and intestinal tracts, cutaneous sweat glands, and renal mucous glands. Strong overexpression of eCLCA1 was observed in the airways of horses with recurrent airway obstruction using Northern blot hybridization, Western blotting, immunohistochemistry, and real-time quantitative RT-PCR. The results suggest that spontaneous or experimental recurrent airway obstruction in horses may serve as a model to study the role of CLCA homologs in chronic airway disease with overproduction of mucins. (J Histochem Cytochem 53:1011–1021, 2005)


  • Overexpression of eCLCA1 in Small Airways of Horses with Recurrent Airway Obstruction -

    The human hCLCA1 and murine mCLCA3 (chloride channels, calcium-activated) have recently been identified as promising therapeutic targets in asthma. Recurrent airway obstruction in horses is an important animal model of human asthma. Here, we have cloned and characterized the first equine CLCA family member, eCLCA1. The 913 amino acids eCLCA1 polypeptide forms a 120-kDa transmembrane glycoprotein that is processed to an 80-kDa protein in vivo. Three single nucleotide polymorphisms were detected in the eCLCA1 coding region in 14 horses, resulting in two amino acid changes (485H/R and 490V/L). However, no functional differences were recorded between the channel properties of the two variants in transfected HEK293 cells. The eCLCA1 protein was detected immunohistochemically in mucin-producing cells in the respiratory and intestinal tracts, cutaneous sweat glands, and renal mucous glands. Strong overexpression of eCLCA1 was observed in the airways of horses with recurrent airway obstruction using Northern blot hybridization, Western blotting, immunohistochemistry, and real-time quantitative RT-PCR. The results suggest that spontaneous or experimental recurrent airway obstruction in horses may serve as a model to study the role of CLCA homologs in chronic airway disease with overproduction of mucins. (J Histochem Cytochem 53:1011–1021, 2005)


  • Overexpression of β1-chain-containing laminins in capillary basement membranes of human breast cancer and its metastases - IntroductionLaminins are the major components of vascular and parenchymal basement membranes. We previously documented a switch in the expression of vascular laminins containing the α4 chain from predominantly laminin-9 (α4β2γ1) to predominantly laminin-8 (α4β1γ1) during progression of human brain gliomas to high-grade glioblastoma multiforme. Here, differential expression of laminins was studied in blood vessels and ductal epithelium of the breast.MethodIn the present study the expressions of laminin isoforms α1–α5, β1–β3, γ1, and γ2 were examined during progression of breast cancer. Forty-five clinical samples of breast tissues including normal breast, ductal carcinomas in situ, invasive ductal carcinomas, and their metastases to the brain were compared using Western blot analysis and immunohistochemistry for various chains of laminin, in particular laminin-8 and laminin-9. Results: Laminin α4 chain was observed in vascular basement membranes of most studied tissues, with the highest expression in metastases. At the same time, the expression of laminin β2 chain (a constituent of laminin-9) was mostly seen in normal breast and carcinomas in situ but not in invasive carcinomas or metastases. In contrast, laminin β1 chain (a constituent of laminin-8) was typically found in vessel walls of carcinomas and their metastases but not in those of normal breast. The expression of laminin-8 increased in a progression-dependent manner. A similar change was observed from laminin-11 (α5β2γ1) to laminin-10 (α5β1γ1) during breast tumor progression. Additionally, laminin-2 (α2β1γ1) appeared in vascular basement membranes of invasive carcinomas and metastases. Chains of laminin-5 (α3β3γ2) were expressed in the ductal epithelium basement membranes of the breast and diminished with tumor progression. Conclusion: These results suggest that laminin-2, laminin-8, and laminin-10 are important components of tumor microvessels and may associate with breast tumor progression. Angiogenic switch from laminin-9 and laminin-11 to laminin-8 and laminin-10 first occurs in carcinomas in situ and becomes more pronounced with progression of carcinomas to the invasive stage. Similar to high-grade brain gliomas, the expression of laminin-8 (and laminin-10) in breast cancer tissue may be a predictive factor for tumor neovascularization and invasion.

  • Overexpression of platelet-derived growth factor receptor α in breast cancer is associated with tumour progression - IntroductionReceptor tyrosine kinases have been extensively studied owing to their frequently abnormal activation in the development and progression of human cancers. Platelet-derived growth factor receptors (PDGFRs) are receptors with intrinsic tyrosine kinase activity that regulate several functions in normal cells and are widely expressed in a variety of malignancies. After the demonstration that gastrointestinal stromal tumours without c-Kit mutations harbour PDGFR-α-activating mutations and that PDGFR-α is also a therapeutic target for imatinib mesylate, the interest for this receptor has increased considerably. Because breast cancer is one of the most frequent neoplasias in women worldwide, and only one study has reported PDGFR-α expression in breast carcinomas, the aim of this work was to investigate the potential significance of PDGFR-α expression in invasive mammary carcinomas. Methods: We used immunohistochemistry to detect PDGFR-α overexpression on a series of 181 formalin-fixed paraffin-embedded invasive ductal breast carcinomas and in two breast cancer cell lines: MCF-7 and HS578T. We associated its expression with known prognostic factors and we also performed polymerase chain reaction–single-stranded conformational polymorphism and direct sequencing to screen for PDGFR-α mutations. Results: PDGFR-α expression was observed in 39.2% of the breast carcinomas and showed an association with lymph node metastasis (P = 0.0079), HER-2 expression (P = 0.0265) and Bcl2 expression (P = 0.0121). A correlation was also found with the expression of platelet-derived growth factor A (PDGF-A; P = 0.0194). The two cell lines tested did not express PDGFR-α. Screening for mutations revealed alterations in the PDGFR-α gene at the following locations: 2500A→G, 2529T→A and 2472C→T in exon 18 and 1701G→A in exon 12. We also found an intronic insertion IVS17-50insA at exon 18 in all sequenced cases. None of these genetic alterations was correlated with PDGFR-α expression. The cell lines did not reveal any alterations in the PDGFR-α gene sequence. Conclusion: PDGFR-α is expressed in invasive breast carcinomas and is associated with biological aggressiveness. The genetic alterations described were not correlated with protein expression, but other mechanisms such as gene amplification or constitutive activation of a signalling pathway inducing this receptor could still sustain PDGFR-α as a potential therapeutic target.

  • p27Kip1 is expressed in proliferating cells in its form phosphorylated on threonine 187 - Background: G1/S cell cycle progression requires p27Kip1 (p27) proteolysis, which is triggered by its phosphorylation on threonine (Thr) 187. Since its levels are abundant in quiescent and scarce in cycling cells, p27 is an approved marker for quiescent cells, extensively used in histopathology and cancer research. Methods: However here we showed that by using a specific phosphorylation site (pThr187) antibody, p27 is detectable also in proliferative compartments of normal, dysplastic and neoplastic tissues. Results: In fact, whereas un-phosphorylated p27 and MIB-1 showed a significant inverse correlation (Spearman R = -0.55; p < 0,001), pThr187-p27 was positively and significantly correlated with MIB-1 expression (Spearman R = 0.88; p < 0,001). Thus proliferating cells only stain for pThr187-p27, whereas they are un-reactive with the regular p27 antibodies. However increasing the sensitivity of the immunocytochemistry (ICH) by the use of an ultra sensitive detection system based on tiramide signal amplification, simultaneous expression and colocalisation of both forms of p27 was shown in proliferating compartments nuclei by double immunofluorescence and laser scanning confocal microscopy studies. Conclusion: Overall, our data suggest that p27 expression also occurs in proliferating cells compartments and the combined use of both regular and phospho- p27 antibodies is suggested.

  • P53 and Beta-Catenin Activity during Estrogen treatment of Osteoblasts - Background: This study was undertaken to examine the relationship between the tumor suppressor gene p53 and the nuclear signaling protein beta-catenin during bone differentiation. Cross talk between p53 and beta- catenin pathways has been demonstrated and is important during tumorigenesis and DNA damage, where deregulation of beta catenin activates p53. In this study, we used estrogen treatment of osteoblasts as a paradigm to study the relationship between the two proteins during osteoblast differentiation. Results: We exposed osteoblast-like ROS17/2.8 cells to 17-beta estradiol (E2), in a short term assay, and studied the cellular distribution and expression of beta-catenin. We found beta-catenin to be up regulated several fold following E2 treatment. Levels of p53 and its functional activity mirrored the quantitative changes seen in beta-catenin. Alkaline phosphatase, an early marker of osteoblast differentiation, was increased in a manner similar to beta-catenin and p53. In order to determine if there was a direct relationship between alkaline phosphatase expression and beta-catenin, we used two different approaches. In the first approach, treatment with LiCl, which is known to activate beta-catenin, caused a several fold increase in alkaline phosphatase activity. In the second approach, transient transfection of wild type beta-catenin into osteoblasts increased alkaline phosphatase activity two fold over basal levels, showing that beta catenin expression can directly affect alkaline phosphatase expression. However increase in beta catenin activity was not associated with an increase in its signaling activity through TCF/LEF mediated transcription. Immunofluorescence analyses of p53 and beta-catenin localization showed that E2 first caused an increase in cytosolic beta-catenin followed by the accumulation of beta-catenin in the nucleus. Nuclear p53 localization was detected in several cells. Expression of p53 was accompanied by distribution of beta-catenin to the cytoplasm and cell borders. A sub population of cells staining strongly for both proteins appeared to be apoptotic. Conclusions: These results suggest that interactions between p53 and beta-catenin signaling pathways may play a key role in osteoblast differentiation and maintenance of tissue homeostasis.

  • p53 and c-kit (CD117) protein expression as prognostic indicators in breast phyllodes tumors: a tissue microarray study - Puay-Hoon Tan, Thiyagarajan Jayabaskar, George Yip, Yen Tan, Maryam Hilmy, Sathiyamoorthy Selvarajan & Boon-Huat Bay

  • Pallister-Killian Syndrome: Rapid Decrease of Isochromosome 12p Frequency during Amniocyte Subculturing. Conclusion for Strategy of Prenatal Cytogenetic Diagnostics -

    Pallister-Killian syndrome (PKS) is characterized cytogenetically by mosaic tetrasomy of chromosome 12p. Routine prenatal diagnosis of PKS is still complicated because of the difficulties of discriminating between the supernumerary isochromosome 12p and the duplication 21q and because of the variable level of mosaicism. The frequency of cells with an extra metacentric chromosome i(12)(p10) is usually determined by tissue-limited or tissue-specific mosaicism. We demonstrated a decrease of the abnormal clone with extra i(12p) in the amniotic fluid cells of the PKS fetus during amniocyte subculturing. The rapid loss of the i(12p) in the course of amniocyte subculturing should be the focus of attention during prenatal karyotyping. This is especially necessary for cultures with slow growth, which require further interpretation of the result during cytogenetic diagnosis of PKS.

    (J Histochem Cytochem 53:361–364, 2005)


  • Pancreatic Stellate Cells (PSCs) Express Cyclooxygenase-2 (COX-2) and Pancreatic Cancer Stimulates COX-2 in PSCs - Background: Cyclooxygenase 2 (COX-2), the inducible form of prostaglandin G/H synthase, is associated with several human cancers inducing pancreatic adenocarcinoma. Pancreatic stellate cells (PSCs) play a central role in the intense desmoplastic reaction that surrounds pancreatic adenocarcinoma. The present study examined COX-2 expression in PSCs, PSCs isolated from normal rats, were cultured and exposed to conditioned medium (CM) from the human pancreatic cell line, PANC-1. Results: COX-2 expression was evaluated by immunostaining and western blotting. Proliferation of PSCs was determined by thymidine incorporation and cell counting. COX-2 was found to be constitutively expressed in PSCs, and COX-2 protein was up-regulated by PANC-1 CM. Moreover, the induction of COX-2 by PANC-1 CM was prevented by U0126, an extracellular signal-regulated kinase (ERK) 1/2 inhibitor suggesting that activation of ERK 1/2 is needed for stimulation of COX-2. Finally, NS398, a selective COX-2 inhibitor, reduced the growth of PSCs by PANC-1 CM, indicating that activation of COX-2 is required for cancer stimulated PSC proliferation. Conclusions: The results suggest that COX-2 may play an important role in the regulation of PSC proliferation in response to pancreatic cancer.

  • Parallel organization of contralateral and ipsilateral prefrontal cortical projections in the rhesus monkey - Background: The neocortical commissures have a fundamental role in functional integration across the cerebral hemispheres. We investigated whether commissural projections in prefrontal cortices are organized according to the same or different rules as those within the same hemisphere, by quantitatively comparing density, topography, and laminar origin of contralateral and ipsilateral projections, labeled after unilateral injection of retrograde tracers in prefrontal areas. Results: Commissural projection neurons constituted less than one third of the ipsilateral. Nevertheless, projections from the two hemispheres were strongly correlated in topography and relative density. We investigated to what extent the distribution of contralateral projections depended on: (a) geographic proximity of projection areas to the area homotopic to the injection site; (b) the structural type of the linked areas, based on the number and neuronal density of their layers. Although both measures were good predictors, structural type was a comparatively stronger determinant of the relative distribution and density of projections. Ipsilateral projection neurons were distributed in the superficial (II-III) and deep (V-VI) layers, in proportions that varied across areas. In contrast, contralateral projection neurons were found mostly in the superficial layers, but still showed a gradient in their distribution within cortical layers that correlated significantly with cortical type, but not with geographic proximity to the homotopic area. Conclusions: The organization of ipsilateral and contralateral prefrontal projections is similar in topography and relative density, differing only by higher overall density and more widespread laminar origin of ipsilateral than contralateral projections. The projections on both sides are highly correlated with the structural architecture of the linked areas, and their remarkable organization is likely established by punctuated development of distinct cortical types. The preponderance of contralateral projections from layer III may be traced to the late development of the callosal system, whose function may be compromised in diseases that have their root late in ontogeny.

  • Parathyroid Hormone-related Peptide (hPTHrP) and Parathyroid Hormone-related Peptide Receptor Type 1 (PTHR1) Expression in Human Thymus -

    Parathyroid hormone-related peptide (hPTHrP) is expressed in human tissues and regulates cellular proliferation, differentiation, and apoptosis by an autocrine/paracrine loop. In rodent thymus, both parathormone and parathyroid hormone-related peptide (PTHrP) are expressed by thymic epithelial cells (TECs). The present study demonstrated by RT-PCR and immunohistochemistry that hPTHrP and parathyroid hormone-related peptide receptor type 1 (PTHR1) were expressed in human thymus at both RNA and protein levels. hPTHrP was expressed mainly in the thymic medulla by epithelial (cytokeratin-positive), mature dendritic (CD40+/86+) and plasmacytoid interleukin (IL)-3R1 cells. This protein was also present in some cells forming Hassall's bodies and a few subcapsular and cortical TECs. PTHR1 was expressed by scattered subcapsular and cortical TECs and by rare TECs in the medulla. Thymocytes did not express either hPTHrP or PTHR1. Primary cultures of human TECs revealed the presence of both hPTHrP and PTHR1 mRNAs, confirming the capacity of TECs to synthesize both peptides. Moreover, synthetic (1-39) hPTHrP peptide administered on cultured TECs induced the expression of IL-6 mRNA, suggesting that hPTHrP can regulate thymic functions by inducing in TECs the expression of IL-6, which is involved in the development and maturation of thymocytes. (J Histochem Cytochem 53:955–962, 2005)


  • Parathyroid Hormone-related Peptide (hPTHrP) and Parathyroid Hormone-related Peptide Receptor Type 1 (PTHR1) Expression in Human Thymus -

    Parathyroid hormone-related peptide (hPTHrP) is expressed in human tissues and regulates cellular proliferation, differentiation, and apoptosis by an autocrine/paracrine loop. In rodent thymus, both parathormone and parathyroid hormone-related peptide (PTHrP) are expressed by thymic epithelial cells (TECs). The present study demonstrated by RT-PCR and immunohistochemistry that hPTHrP and parathyroid hormone-related peptide receptor type 1 (PTHR1) were expressed in human thymus at both RNA and protein levels. hPTHrP was expressed mainly in the thymic medulla by epithelial (cytokeratin-positive), mature dendritic (CD40+/86+) and plasmacytoid interleukin (IL)-3R1 cells. This protein was also present in some cells forming Hassall's bodies and a few subcapsular and cortical TECs. PTHR1 was expressed by scattered subcapsular and cortical TECs and by rare TECs in the medulla. Thymocytes did not express either hPTHrP or PTHR1. Primary cultures of human TECs revealed the presence of both hPTHrP and PTHR1 mRNAs, confirming the capacity of TECs to synthesize both peptides. Moreover, synthetic (1-39) hPTHrP peptide administered on cultured TECs induced the expression of IL-6 mRNA, suggesting that hPTHrP can regulate thymic functions by inducing in TECs the expression of IL-6, which is involved in the development and maturation of thymocytes. (J Histochem Cytochem 53:955–962, 2005)


  • Paroxysmal Nocturnal Hemoglobinuria: Current Issues in Pathophysiology and Treatment - Paroxysmal nocturnal hemoglobinuria (PNH) is an acquired genetic disorder of the bone marrow that produces -intravascular hemolysis, proclivity to venous thrombosis, and hematopoietic failure. Mutation in the PIG-A gene in a stem cell aborts synthesis of glycosyl-phosphoinositol (GPI) anchors and therefore expression of all GPI-anchored -proteins on the surface of progeny erythrocytes, leukocytes, and platelets. The hemolytic anemia of PNH is well understood, and erythrocyte susceptibility to complement may be treated with anti-C5a monoclonal antibody. The pathophysiology of PNH cell clonal expansion and its association with immune-mediated marrow failure are not understood, but PNH/aplasia responds to immunosuppressive regimens such as antithymocyte globulin and cyclosporine. The mechanism of thrombosis in PNH is also obscure, but frequently fatal clotting episodes may be prevented by Coumadin (Bristol-Myers Squibb Pharma Co., Wilmington, DE) prophylaxis.

  • Pediatric Transplantation: Results in Solid Tumors - Solid tumors are one of the leading causes of disease-related mortality in children today. Although overall survival of children with solid tumors has improved over time, certain high-risk patients continue to respond poorly to conventional therapy. Recent studies have investigated using dose-intensified myeloablative therapy with auto-logous hematopoietic progenitor cell transplantation (AHPCT) in hopes of eradicating disease and improving the long-term survival of these patients. Results of high-dose therapy with AHPCT have been encouraging in treatment of metastatic neuroblastoma and recurrent Wilms' tumor, but little benefit has been demonstrated with Ewing's sarcoma. In this article, we examine the role of autologous transplant with each solid tumor and discuss some of the recent transplant-related controversies still under debate.

  • Pep-1 as a Novel Probe for the In Situ Detection of Hyaluronan -

    Hyaluronan (HA) is expressed by most tissues, including skin. Localization of HA in the skin is assessed by histology with HA-binding protein (HABP) serving as the probe. Reports have suggested that HA expression in skin is altered in a number of diseases. However, interlaboratory variations in HABP staining profiles, even in normal skin, suggest a need to standardize methods and/or identify new probes. We report the staining patterns of a HA-binding peptide (termed "Pep-1") in human and mouse skin. After acetone fixation, Pep-1 stained HA in the intercellular spaces of the epidermis, whereas staining in the dermis was weak and diffuse in both human and mouse skin. HABP staining of the epidermis and dermis were comparable in human skin but failed to stain the vital epidermis of mouse skin. In human skin, Pep-1 stained the basal, spinous, and granular layers, whereas HABP failed to stain the basal layer. Precipitation of HA in situ resulted in dermal staining but weak staining in the epidermis for HABP and Pep-1. Our results may suggest that Pep-1 is sensitive to HA conformation. Furthermore, Pep-1 may represent a new probe to study HA expression in the skin. (J Histochem Cytochem 53:745–751, 2005)


  • Pep-1 as a Novel Probe for the In Situ Detection of Hyaluronan -

    Hyaluronan (HA) is expressed by most tissues, including skin. Localization of HA in the skin is assessed by histology with HA-binding protein (HABP) serving as the probe. Reports have suggested that HA expression in skin is altered in a number of diseases. However, interlaboratory variations in HABP staining profiles, even in normal skin, suggest a need to standardize methods and/or identify new probes. We report the staining patterns of a HA-binding peptide (termed "Pep-1") in human and mouse skin. After acetone fixation, Pep-1 stained HA in the intercellular spaces of the epidermis, whereas staining in the dermis was weak and diffuse in both human and mouse skin. HABP staining of the epidermis and dermis were comparable in human skin but failed to stain the vital epidermis of mouse skin. In human skin, Pep-1 stained the basal, spinous, and granular layers, whereas HABP failed to stain the basal layer. Precipitation of HA in situ resulted in dermal staining but weak staining in the epidermis for HABP and Pep-1. Our results may suggest that Pep-1 is sensitive to HA conformation. Furthermore, Pep-1 may represent a new probe to study HA expression in the skin. (J Histochem Cytochem 53:745–751, 2005)


  • Pep-1 as a Novel Probe for the In Situ Detection of Hyaluronan -

    Hyaluronan (HA) is expressed by most tissues, including skin. Localization of HA in the skin is assessed by histology with HA-binding protein (HABP) serving as the probe. Reports have suggested that HA expression in skin is altered in a number of diseases. However, interlaboratory variations in HABP staining profiles, even in normal skin, suggest a need to standardize methods and/or identify new probes. We report the staining patterns of a HA-binding peptide (termed "Pep-1") in human and mouse skin. After acetone fixation, Pep-1 stained HA in the intercellular spaces of the epidermis, whereas staining in the dermis was weak and diffuse in both human and mouse skin. HABP staining of the epidermis and dermis were comparable in human skin but failed to stain the vital epidermis of mouse skin. In human skin, Pep-1 stained the basal, spinous, and granular layers, whereas HABP failed to stain the basal layer. Precipitation of HA in situ resulted in dermal staining but weak staining in the epidermis for HABP and Pep-1. Our results may suggest that Pep-1 is sensitive to HA conformation. Furthermore, Pep-1 may represent a new probe to study HA expression in the skin. (J Histochem Cytochem 53:745–751, 2005)


  • Percentage density, Wolfe's and Tabár's mammographic patterns: agreement and association with risk factors for breast cancer - IntroductionThe purpose of this report was to classify mammograms according to four methods and to examine their agreement and their relationship to selected risk factors for breast cancer.MethodMammograms and epidemiological data were collected from 987 women, aged 55 to 71 years, attending the Norwegian Breast Cancer Screening Program. Two readers each classified the mammograms according to a quantitative method (Cumulus or Madena software) and one reader according to two qualitative methods (Wolfe and Tabár patterns). Mammograms classified in the reader-specific upper quartile of percentage density, Wolfe's P2 and DY patterns, or Tabár's IV and V patterns, were categorized as high-risk density patterns and the remaining mammograms as low-risk density patterns. We calculated intra-reader and inter-reader agreement and estimated prevalence odds ratios of having high-risk mammographic density patterns according to selected risk factors for breast cancer. Results: The Pearson correlation coefficient was 0.86 for the two quantitative density measurements. There was moderate agreement between the Wolfe and Tabár classifications (Kappa = 0.51; 95% confidence interval 0.46 to 0.56). Age at screening, number of children and body mass index (BMI) showed a statistically significant inverse relationship with high-risk density patterns for all four methods (all P < 0.05). After adjustment for percentage density, the Wolfe classification was not associated with any of the risk factors for breast cancer, whereas the association with number of children and BMI remained statistically significant for the Tabár classification. Adjustment for Wolfe or Tabár patterns did not alter the associations between these risk factors and percentage mammographic density. Conclusion: The four assessments methods seem to capture the same overall associations with risk factors for breast cancer. Our results indicate that the quantitative methods convey additional information over the qualitative methods.

  • Perlecan, a Basement Membrane-type Heparan Sulfate Proteoglycan, in the Enamel Organ: Its Intraepithelial Localization in the Stellate Reticulum -

    The localization and biosynthesis of perlecan, a basement membrane–type heparan sulfate proteoglycan, were studied in developing tooth germs by using murine molars in neonatal and postnatal stages and primary cultured cells of the enamel organ and dental papilla to demonstrate the role of perlecan in normal odontogenesis. Perlecan was immunolocalized mainly in the intercellular spaces of the enamel organ as well as in the dental papilla/pulp or in the dental follicle. By in situ hybridization, mRNA signals for perlecan core protein were intensely demonstrated in the cytoplasm of stellate reticulum cells and in dental papilla/pulp cells, including odontoblasts and fibroblastic cells in the dental follicle. Furthermore, the in vitro biosyntheses of perlecan core protein by the enamel organ and dental papilla/pulp cells were confirmed by immunofluorescence, immunoprecipitation, and reverse transcriptase–polymerase chain reaction. The results indicate that perlecan is synthesized by the dental epithelial cells and is accumulated in their intercellular spaces to form the characteristic stellate reticulum, whose function is still unknown. (J Histochem Cytochem 53:763–772, 2005)


  • Perlecan, a Basement Membrane-type Heparan Sulfate Proteoglycan, in the Enamel Organ: Its Intraepithelial Localization in the Stellate Reticulum -

    The localization and biosynthesis of perlecan, a basement membrane–type heparan sulfate proteoglycan, were studied in developing tooth germs by using murine molars in neonatal and postnatal stages and primary cultured cells of the enamel organ and dental papilla to demonstrate the role of perlecan in normal odontogenesis. Perlecan was immunolocalized mainly in the intercellular spaces of the enamel organ as well as in the dental papilla/pulp or in the dental follicle. By in situ hybridization, mRNA signals for perlecan core protein were intensely demonstrated in the cytoplasm of stellate reticulum cells and in dental papilla/pulp cells, including odontoblasts and fibroblastic cells in the dental follicle. Furthermore, the in vitro biosyntheses of perlecan core protein by the enamel organ and dental papilla/pulp cells were confirmed by immunofluorescence, immunoprecipitation, and reverse transcriptase–polymerase chain reaction. The results indicate that perlecan is synthesized by the dental epithelial cells and is accumulated in their intercellular spaces to form the characteristic stellate reticulum, whose function is still unknown. (J Histochem Cytochem 53:763–772, 2005)


  • Perlecan, a Basement Membrane-type Heparan Sulfate Proteoglycan, in the Enamel Organ: Its Intraepithelial Localization in the Stellate Reticulum -

    The localization and biosynthesis of perlecan, a basement membrane–type heparan sulfate proteoglycan, were studied in developing tooth germs by using murine molars in neonatal and postnatal stages and primary cultured cells of the enamel organ and dental papilla to demonstrate the role of perlecan in normal odontogenesis. Perlecan was immunolocalized mainly in the intercellular spaces of the enamel organ as well as in the dental papilla/pulp or in the dental follicle. By in situ hybridization, mRNA signals for perlecan core protein were intensely demonstrated in the cytoplasm of stellate reticulum cells and in dental papilla/pulp cells, including odontoblasts and fibroblastic cells in the dental follicle. Furthermore, the in vitro biosyntheses of perlecan core protein by the enamel organ and dental papilla/pulp cells were confirmed by immunofluorescence, immunoprecipitation, and reverse transcriptase–polymerase chain reaction. The results indicate that perlecan is synthesized by the dental epithelial cells and is accumulated in their intercellular spaces to form the characteristic stellate reticulum, whose function is still unknown. (J Histochem Cytochem 53:763–772, 2005)


  • Persistence of Natural Killer (NK) cell lymphocytosis with hyposplenism without development of leukaemia - Background: Natural killer (NK) cell lymphocytosis usually has an indolent course and can progress into massive lymphocytosis with development of cytopenias and neoplastic diseases. NK-cells usually express one or more "NK-associated" antigens (CD16, CD56, CD57). Reactive expansions are seen in autoimmune diseases, viral infections, solid tumours and non-Hodgkin's lymphoma.Case presentationWe report a lady with a benign clinical course over 10 years and persistent CD8+/CD3-/CD57+/CD16+ LGL proliferation with presence of Howell-Jolly bodies (functional hyposplenism), an association not previously described. Conclusion: We discuss the possible causes of clonal expansion and conclude that this may be part of the spectrum of immune dysregulation associated with NK-cell lymphocytosis.

  • Phase I clinical study of the recombinant antibody toxin scFv(FRP5)-ETA specific for the ErbB2/HER2 receptor in patients with advanced solid malignomas - IntroductionScFv(FRP5)-ETA is a recombinant antibody toxin with binding specificity for ErbB2 (HER2). It consists of an N-terminal single-chain antibody fragment (scFv), genetically linked to truncated Pseudomonas exotoxin A (ETA). Potent antitumoral activity of scFv(FRP5)-ETA against ErbB2-overexpressing tumor cells was previously demonstrated in vitro and in animal models. Here we report the first systemic application of scFv(FRP5)-ETA in human cancer patients. Methods: We have performed a phase I dose-finding study, with the objective to assess the maximum tolerated dose and the dose-limiting toxicity of intravenously injected scFv(FRP5)-ETA. Eighteen patients suffering from ErbB2-expressing metastatic breast cancers, prostate cancers, head and neck cancer, non small cell lung cancer, or transitional cell carcinoma were treated. Dose levels of 2, 4, 10, 12.5, and 20 μg/kg scFv(FRP5)-ETA were administered as five daily infusions each for two consecutive weeks. Results: No hematologic, renal, and/or cardiovascular toxicities were noted in any of the patients treated. However, transient elevation of liver enzymes was observed, and considered dose limiting, in one of six patients at the maximum tolerated dose of 12.5 μg/kg, and in two of three patients at 20 μg/kg. Fifteen minutes after injection, peak concentrations of more than 100 ng/ml scFv(FRP5)-ETA were obtained at a dose of 10 μg/kg, indicating that predicted therapeutic levels of the recombinant protein can be applied without inducing toxic side effects. Induction of antibodies against scFv(FRP5)-ETA was observed 8 days after initiation of therapy in 13 patients investigated, but only in five of these patients could neutralizing activity be detected. Two patients showed stable disease and in three patients clinical signs of activity in terms of signs and symptoms were observed (all treated at doses ≥ 10 μg/kg). Disease progression occurred in 11 of the patients. Conclusion: Our results demonstrate that systemic therapy with scFv(FRP5)-ETA can be safely administered up to a maximum tolerated dose of 12.5 μg/kg in patients with ErbB2-expressing tumors, justifying further clinical development.

  • Phenotypic heterogeneity within a new family with the MAPT p301s mutation. -
    Related Articles

    Phenotypic heterogeneity within a new family with the MAPT p301s mutation.

    Ann Neurol. 2005 Oct 20;

    Authors: Yasuda M, Nakamura Y, Kawamata T, Kaneyuki H, Maeda K, Komure O

    Mutations in the gene encoding the microtubule-associated protein tau (MAPT) cause frontotemporal dementia and parkinsonism linked to chromosome 17. Clinical variability is seen not only among families with different mutations, but also among family members with the same mutation. We investigated a newly identified familial frontotemporal dementia and parkinsonism family. The disease was of early onset and was inherited as an autosomal dominant trait. Clinically, parkinsonism was the prominent and often early feature, and it preceded dementia. Three autopsied cases shared involvement predominantly in the frontal and temporal lobes and also in the subcortical nuclei, including substantia nigra, globus pallidus, and subthalamic nucleus, that microscopically consisted of neuronal loss, microvacuolation, and astrocytic fibrosis. Immunohistochemistry demonstrated neuropil threads, ballooned cells, and glial fibrillary tangles. Sequencing analysis of the MAPT gene showed an alteration in one allele, resulting in a P301S substitution. These findings suggest that the MAPT P301S mutation can cause pathologically subcortical-predominant, neuropil thread-rich, tau-containing lesions, which could result in consistent parkinsonism. Our study confirms the notion that the phenotype observed in affected individuals from P301S MAPT mutation families is heterogeneous and is broader than the phenotypes seen to date in affected family members carrying other MAPT mutations. Ann Neurol 2005.

    PMID: 16240366 [PubMed - as supplied by publisher]


  • Phosphorylation of estrogen receptor α serine 167 is predictive of response to endocrine therapy and increases postrelapse survival in metastatic breast cancer - IntroductionEndocrine therapy is the most important treatment option for women with hormone-receptor-positive breast cancer. The potential mechanisms for endocrine resistance involve estrogen receptor (ER)-coregulatory proteins and crosstalk between ER and other growth factor signaling networks. However, the factors and pathways responsible for endocrine resistance are still poorly identified. Methods: Using immunohistochemical techniques, we focused on the expression and phosphorylation of hormone receptors themselves and examined the phosphorylation of ER-α Ser118 and ER-α Ser167 and the expression of ER-α, ER-β1, ER-βcx/β2, progesterone receptor (PR), PRA, and PRB in the primary breast carcinomas of 75 patients with metastatic breast cancer who received first-line treatment with endocrine therapy after relapse. Results: Phosphorylation of ER-α Ser118, but not Ser167, was positively associated with overexpression of HER2, and HER2-positive tumors showed resistance to endocrine therapy. The present study has shown for the first time that phosphorylation of ER-α Ser167, but not Ser118, and expression of PRA and PRB, as well as ER-α and PR in primary breast tumors are predictive of response to endocrine therapy, whereas expression of ER-β1 and ER-βcx/β2 did not affect response to the therapy. In addition, patients with either high phosphorylation of ER-α Ser167, or high expression of ER-α, PR, PRA, or PRB had a significantly longer survival after relapse. Conclusion: These data suggest that phosphorylation of ER-α Ser167 is helpful in selecting patients who may benefit from endocrine therapy and is a prognostic marker in metastatic breast cancer.

  • Platelet Bleeding Disorders and Approach to Their Management - No abstract available

  • Platelet Inhibitor Therapy for Patients with Cardiovascular Disease: Looking Toward the Future - Understanding platelet function and the role of platelets in the response to vascular injury has led to the development of novel platelet-inhibiting therapies that have been proven effective in the treatment of acute and chronic vascular disease. Antiplatelet therapies are cornerstone treatments for patients with acute coronary syndromes and have been essential in reducing the acute and subacute ischemic complications of percutaneous coronary intervention. Furthermore, an increased understanding of the pathobiology behind the platelet's role in atherothrombosis has offered up many new avenues of research and many new targets for therapeutic drug development. This review briefly summarizes the state of available anticoagulant and antiplatelet treatments in cardiovascular disease management and provides a perspective on the key issues in developing new antiplatelet strategies in the future.

  • Platelet-derived growth factor modulates rat vascular smooth muscle cell responses on laminin-5 via mitogen-activated protein kinase-sensitive pathways - Background: A treatment to remove vascular blockages, angioplasty, can cause damage to the vessel wall and a subsequent abnormal wound healing response, known as restenosis. Vascular smooth muscle cells (VSMC) lining the vessel wall respond to growth factors and other stimuli released by injured cells. However, the extracellular matrix (ECM) may differentially modulate VSMC responses to these growth factors, such as proliferation, migration and adhesion. Our previous reports of low-level expression of one ECM molecule, laminin-5, in normal and injured vessels suggest that laminin-5, in addition to growth factors, may mediate VSMC response following vascular injury. To elucidate VSMC response on laminin-5 we investigated-the role of platelet-derived growth factor (PDGF-BB) in activating the mitogen-activated protein kinase (MAPK) signaling cascade as a possible link between growth-factor initiated phenotypic changes in vitro and the ECM. Results: Using a system of in vitro assays we assessed rat vascular smooth muscle cell (rVSMC) responses plated on laminin-5 to the addition of exogenous, soluble PDGF-BB. Our results indicate that although laminin-5 induces haptotactic migration of rVSMC, the addition of PDGF-BB significantly increases rVSMC migration on laminin-5, which is inhibited in a dose-dependent manner by the MAPK inhibitor, PD98059, and transforming growth factor (TGF-β1). In addition, PDGF-BB greatly reduces rVSMC adhesion to laminin-5, an effect that is reversible by MAPK inhibition or the addition of TGF-β1. In addition, this reduction in adhesion is less significant on another ECM substrate, fibronectin and is reversible using TGF-β1 but not MAPK inhibition. PDGF-BB also strongly increased rVSMC proliferation on laminin-5, but had no effect on rVSMC plated on fibronectin. Finally, plating rVSMC on laminin-5 did not induce an increase in MAPK activation, while plating on fibronectin or the addition of soluble PDGF-BB did. Conclusion: These results suggest that rVSMC binding to laminin-5 activates integrin-dependent intracellular signaling cascades that are different from those of fibronectin or PDGF-BB, causing rVSMC to respond more acutely to the inhibition of MAPK. In contrast, our results suggest that fibronectin and PDGF-BB may activate parallel, reinforcing intracellular signaling cascades that converge in the activation of MAPK and are therefore less sensitive to MAPK inhibition. These results suggest a partial mechanism to explain the regulation of rVSMC behaviors, including migration, adhesion, and proliferation that may be responsible for the progression of restenosis.

  • Pleiotrophin Cellular Localization in Nerve Regeneration after Peripheral Nerve Injury -

    Pleiotrophin (PTN) is a member of the family of heparin-binding growth factors that displays mitogenic activities and promotes neurite outgrowth in vitro. In vivo, PTN is widely expressed along pathways of developing axons during the late embryonic and early postnatal period. Although the level of PTN gene expression is very low during adulthood, activation of the gene may occur during recovery from injury and seems to play an important role in tissue regeneration processes. In this study, we investigated whether PTN was involved in the regenerative process of injured peripheral nerves. To refer localization of the fluorescent markers to myelinated axons, we developed a specific computer tool for colocalization of fluorescence images with phase contrast images. Immunohistochemical analysis showed PTN in different types of nonneural cells in distal nerve segments, including Schwann cells, macrophages, and endothelial cells, but not in axons. Schwann cells exhibited PTN immunoreactivity as early as 2 days after injury, whereas PTN-positive macrophages were found 1 week later. Strong PTN immunoreactivity was noted in endothelial cells at all time points. These findings support the idea that PTN participates in the adaptive response to peripheral nerve injury. A better understanding of its contribution may suggest new strategies for enhancing peripheral nerve regeneration.

    (J Histochem Cytochem 53:971–977, 2005)


  • Pleiotrophin Cellular Localization in Nerve Regeneration after Peripheral Nerve Injury -

    Pleiotrophin (PTN) is a member of the family of heparin-binding growth factors that displays mitogenic activities and promotes neurite outgrowth in vitro. In vivo, PTN is widely expressed along pathways of developing axons during the late embryonic and early postnatal period. Although the level of PTN gene expression is very low during adulthood, activation of the gene may occur during recovery from injury and seems to play an important role in tissue regeneration processes. In this study, we investigated whether PTN was involved in the regenerative process of injured peripheral nerves. To refer localization of the fluorescent markers to myelinated axons, we developed a specific computer tool for colocalization of fluorescence images with phase contrast images. Immunohistochemical analysis showed PTN in different types of nonneural cells in distal nerve segments, including Schwann cells, macrophages, and endothelial cells, but not in axons. Schwann cells exhibited PTN immunoreactivity as early as 2 days after injury, whereas PTN-positive macrophages were found 1 week later. Strong PTN immunoreactivity was noted in endothelial cells at all time points. These findings support the idea that PTN participates in the adaptive response to peripheral nerve injury. A better understanding of its contribution may suggest new strategies for enhancing peripheral nerve regeneration.

    (J Histochem Cytochem 53:971–977, 2005)


  • Plexin B3 promotes neurite outgrowth, interacts homophilically, and interacts with Rin - Background: Plexins, known to date as receptors of semaphorins, are implicated in semaphorin-mediated axon repulsion and growth cone collapse. However, subtype-specific functions of the majority of the nine members of the mammalian plexin family are largely unknown. In order to investigate functional properties of B-plexins, we analyzed the expression of human and murine plexin B3 and expressed full-length human plexins B2 (B2) and B3 (B3) in NIH-3T3 cells. Results: Unexpectedly, B3 strongly and B2 moderately stimulate neurite outgrowth of primary murine cerebellar neurons. Both plexins mediate Ca2+/Mg2+-dependent cell aggregation due to homophilic trans-interaction, which is strong in the case of B3 and moderate for B2. Using different deletion constructs we show that the sema domain of B3 is essential for homophilic interaction. Using yeast two-hybrid analysis, we identified the neuron-specific and calmodulin-binding Ras-related GTPase Rin as an interaction partner of the intracellular part of B3, but not of B2. Rin, also known for its neurite outgrowth-inducing characteristics, co-localizes and co-immunoprecipitates with B3 in co-transfected COS-7 cells. Conclusions: Our data suggest an involvement of homophilic interaction of B3 in semaphorin-independent signaling mechanisms positively influencing neuronal morphogenesis or function. Furthermore, the neuron-specific small GTPase Rin is involved in downstream signaling of plexin B3.

  • Polar Body Diagnosis for Hemophilia A Using Multiplex PCR for Linked Polymorphic Markers -

    Preimplantation genetic diagnosis (PGD) is usually performed on blastomeres. In Germany, the only possibility to perform PGD is by analysis of polar bodies. We performed PGD using polar bodies in a woman who is a carrier of hemophilia A. Multiplex PCR followed by nested fluorescent PCR for five linked polymorphic markers was established. From 11 analyzed polar bodies, only 1 showed alleles linked to the mutation. The corresponding oocyte was transferred and no pregnancy was established. As seen in other investigations, the rate of heterozygous first polar bodies is surprisingly high.

    (J Histochem Cytochem 53:277–280, 2005)


  • Polo-like kinase 1 expression is a prognostic factor in human colon cancer. -
    Related Articles

    Polo-like kinase 1 expression is a prognostic factor in human colon cancer.

    World J Gastroenterol. 2005 Sep 28;11(36):5644-50

    Authors: Weichert W, Kristiansen G, Schmidt M, Gekeler V, Noske A, Niesporek S, Dietel M, Denkert C

    AIM: To clarify the expression patterns and prognostic implications of the mitotic regulator Polo-like kinase 1 (PLK1) in colon cancer. METHODS: Expression of PLK1 was investigated by immunohistochemistry (158 cases) and immunoblotting in tissue of colon adenomas and adenocarcinomas. PLK1 expression patterns were correlated with clinicopathological parameters and patient prognosis. In addition, expression of PLK1 was evaluated by immunoblot and PCR in colon carcinoma cell lines, and coexpression of PLK1 with the proliferation marker Ki-67 was investigated. RESULTS: Weak PLK1 expression was observed in normal colon mucosa and adenomas. In contrast, 66.7% of carcinomas showed strong expression of PLK1. Overexpression of PLK1 correlated positively with Dukes stage (P<0.001), tumor stage (P = 0.001) and nodal status (P<0.05). Additionally, PLK1 expression was a prognostic marker in univariate survival analysis (P<0.01) and had independent prognostic significance (RR = 3.3, P = 0.02) in patients with locoregional disease. Expression of PLK1 mRNA and protein was detected in all cell lines investigated. Coexpression of PLK1 and Ki-67 was observed in the majority of colon cancer cells, but a considerable proportion of cells showed PLK1 positivity without Ki-67 expression. CONCLUSION: PLK1 is a new prognostic marker for colon carcinoma patients and may be involved in tumorigenesis and progression of colon cancer. Strategies focusing on PLK1 inhibition in vivo might therefore represent a promising new therapeutic approach for this tumor entity.

    PMID: 16237758 [PubMed - in process]


  • Polycythemia Vera: Plethora, From Prehistory to Present - The term polycythemia (literally, 'many blood cell disease') and its obsolete synonym, erythremia, postdate Robert Hooke's 17th century discovery of cells, but the concept of a clinically problematic excess of blood was formulated in antiquity. Observation of plethoric patients by clinicians of the Hippocratic school informed the classical humoral framework that dominated theoretical constructs of human disease for more than a thousand years. In the golden era of disease description at the end of the 19th century, the idiopathic entity polycythemia rubra vera (PRV) was first described and distinguished from secondary and relative polycythemia (red cell excess not caused by a primary bone marrow disorder, and artifactual red cell excess caused by plasma volume contraction, respectively). This review traces some of the principal events in the history of polycythemia vera (PV) as a discrete clinical entity.

  • Polyploid Formation via Chromosome Duplication Induced by CTP:Phosphocholine Cytidylyltransferase Deficiency and Bcl-2 Overexpression: Identification of Two Novel Endogenous Factors -

    Polyploidy is a profound phenotype found in tumors and its mechanism is unknown. We report here that when B-cell lymphoma gene-2 (Bcl-2) was overexpressed in a Chinese hamster ovary cell line that was deficient in CTP:phosphocholine cytidylyltransferase (CT), cellular DNA content doubled. The higher DNA content was due to a permanent conversion from diploid cells to tetraploid cells. The mechanism of polyploid formation could be attributed to the duplication of 18 parental chromosomes. The rate of conversion from diploid to tetraploid was Bcl-2 dose dependent. The diploid genome was not affected by Bcl-2 expression or by CT deficiency alone. Endogenous CT or expression of recombinant rat liver CT prior to Bcl-2 expression prevented the formation of polyploid cells. This conversion was irreversible even when both initiating factors were removed. In this study, we have identified Bcl-2 as a positive regulator and CT as a negative regulator of polyploid formation. (J Histochem Cytochem 53:725–733, 2005)


  • Polyploid Formation via Chromosome Duplication Induced by CTP:Phosphocholine Cytidylyltransferase Deficiency and Bcl-2 Overexpression: Identification of Two Novel Endogenous Factors -

    Polyploidy is a profound phenotype found in tumors and its mechanism is unknown. We report here that when B-cell lymphoma gene-2 (Bcl-2) was overexpressed in a Chinese hamster ovary cell line that was deficient in CTP:phosphocholine cytidylyltransferase (CT), cellular DNA content doubled. The higher DNA content was due to a permanent conversion from diploid cells to tetraploid cells. The mechanism of polyploid formation could be attributed to the duplication of 18 parental chromosomes. The rate of conversion from diploid to tetraploid was Bcl-2 dose dependent. The diploid genome was not affected by Bcl-2 expression or by CT deficiency alone. Endogenous CT or expression of recombinant rat liver CT prior to Bcl-2 expression prevented the formation of polyploid cells. This conversion was irreversible even when both initiating factors were removed. In this study, we have identified Bcl-2 as a positive regulator and CT as a negative regulator of polyploid formation. (J Histochem Cytochem 53:725–733, 2005)


  • Polyploid Formation via Chromosome Duplication Induced by CTP:Phosphocholine Cytidylyltransferase Deficiency and Bcl-2 Overexpression: Identification of Two Novel Endogenous Factors -

    Polyploidy is a profound phenotype found in tumors and its mechanism is unknown. We report here that when B-cell lymphoma gene-2 (Bcl-2) was overexpressed in a Chinese hamster ovary cell line that was deficient in CTP:phosphocholine cytidylyltransferase (CT), cellular DNA content doubled. The higher DNA content was due to a permanent conversion from diploid cells to tetraploid cells. The mechanism of polyploid formation could be attributed to the duplication of 18 parental chromosomes. The rate of conversion from diploid to tetraploid was Bcl-2 dose dependent. The diploid genome was not affected by Bcl-2 expression or by CT deficiency alone. Endogenous CT or expression of recombinant rat liver CT prior to Bcl-2 expression prevented the formation of polyploid cells. This conversion was irreversible even when both initiating factors were removed. In this study, we have identified Bcl-2 as a positive regulator and CT as a negative regulator of polyploid formation. (J Histochem Cytochem 53:725–733, 2005)


  • Positive association between mammographic breast density and bone mineral density in the Postmenopausal Estrogen/Progestin Interventions Study - IntroductionMammographic breast density is a strong independent risk factor for breast cancer. We hypothesized that demonstration of an association between mammographic breast density and bone mineral density (BMD) would suggest a unifying underlying mechanism influencing both breast density and BMD. Methods: In a cross-sectional analysis of baseline data from the Postmenopausal Estrogen/Progestin Interventions Study (PEPI), participants were aged 45 to 64 years and were at least 1 year postmenopausal. Mammographic breast density (percentage of the breast composed of dense tissue), the outcome, was assessed with a computer-assisted percentage-density method. BMD, the primary predictor, was measured with dual-energy X-ray absorptiometry. Women quitting menopausal hormone therapy to join PEPI were designated recent hormone users. Results: The mean age of the 594 women was 56 years. The average time since menopause was 5.6 years. After adjustment for age, body mass index, and cigarette smoking, in women who were not recent hormone users before trial enrollment (n = 415), mammographic density was positively associated with total hip (P = 0.04) and lumbar (P = 0.08) BMD. Mammographic density of recent hormone users (n = 171) was not significantly related to either total hip (P = 0.51) or lumbar (P = 0.44) BMD. In participants who were not recent hormone users, mammographic density was 4% greater in the highest quartile of total hip BMD than in the lowest. In participants who were not recent hormone users, mammographic density was 5% greater in the highest quartile of lumbar spine BMD than in the lowest. Conclusion: Mammographic density and BMD are positively associated in women who have not recently used postmenopausal hormones. A unifying biological mechanism may link mammographic density and BMD. Recent exogenous postmenopausal hormone use may obscure the association between mammographic density and BMD by having a persistent effect on breast tissue.

  • Possibility of selection against mtDNA mutations in tumors - Several studies of tumors have revealed substantial numbers of clonally expanded somatic mutations in mitochondrial DNA (mtDNA), not observed in adjacent intact tissues. These findings were interpreted as indicating the involvement of mtDNA mutations in tumorigenesis. Such comparisons, however, ignore an important confounding factor: the monoclonal origin of tumors as opposed to the highly polyclonal nature of normal tissues. Analysis of recently published data on the incidence of somatic mutations in nontumor monoclonal cells suggests that, contrary to the prevailing view, the process of tumorigenesis may be accompanied by active selection against detrimental mtDNA mutations.

  • Post-transfusion Purpura - Post-transfusion purpura (PTP) is a rare bleeding disorder caused by alloantibodies specific to platelet antigens. The -antibody against the human platelet alloantigen (HPA)-1a is responsible for most of the cases. The majority of affected patients are multiparous women who presumably have been previously sensitized during pregnancy. Blood transfusions rarely have been implicated as the primary cause for -alloimmunization in PTP. Thrombocytopenia is usually severe and resolves spontaneously within several weeks. However, patients may develop severe if not fatal bleeding during the course of this disease. The diagnosis is confirmed by -demonstrating that the patient's serum contains antibodies to platelet-specific antigens. Treatments for PTP include intra-venous immunoglobulin, corticosteroids, and plasmapheresis.

  • Potential cellular conformations of the CCN3(NOV) protein - AimTo study the cellular distribution of CCN3(NOV) and to determine if the carboxyterminus of CCN3 is hidden or masked due to high affinity interactions with other partners. CCN3 was detected using affinity purified antibodies (anti-K19M-AF) as well as a Protein A purified anti-K19M antibodies (anti-K19M IgG) against a C-terminal 19-aminoacid peptide (K19M) of human CCN3 protein. The antibodies were applied in indirect immunofluorescence tests and immunoenzyme assays on glial tumor cell line, G59, and its CCN3-transfected variant G59/540 and the adrenocortical cell line, NCI-H295R. Results: Anti-K19M-AF antibodies reacted against K19M peptide in ELISA and recognized two bands of 51 kDa and 30 kDa in H295R (adrenocortical carcinoma) cell culture supernatants by immunoblotting. H295R culture supernatants which contained CCN3 as shown by immunoblotting did not react with anti-CCN3 antibodies in liquid phase. Anti-CCN3 antibodies stained the surface membranes of non-permeabilized H295R and cytoplasm in permeabilized H295R cells. Similarly, anti-CCN3 stained surface membranes of G59/540, but did not react with G59 cells. Prominent cytoplasmic staining was observed in G59/540, as well as the cell footprints of G59/540 and H295R were strongly labeled. Conclusions: The K19M-AF antibody directed against the C-terminal 19-aminoacid peptide of CCN3 recognized the secreted protein under denaturing conditions. However, the C-terminal motif of secreted CCN3 was not accessible to K19M-AF in liquid phase. These anti-CCN3 antibodies stained CCN3 protein which was localized to cytoplasmic stores, cell membranes and extracellular matrix. This would suggest that cytoplasmic and cell membrane bound CCN3 has an exposed C-terminus while secreted CCN3 has a sequestered C-terminus which could be due to interaction with other proteins or itself (dimerization). Thus the K19M-AF antibodies revealed at least two conformational states of the native CCN3 protein.

  • Preclinical evaluation of the proteasome inhibitor bortezomib in cancer therapy - Bortezomib is a highly selective, reversible inhibitor of the 26S proteasome that is indicated for single-agent use in the treatment of patients with multiple myeloma who have received at least 2 prior therapies and are progressing on their most recent therapy. Clinical investigations have been completed or are under way to evaluate the safety and efficacy of bortezomib alone or in combination with chemotherapy in multiple myeloma, both at relapse and presentation, as well as in other cancer types. The antiproliferative, proapoptotic, antiangiogenic, and antitumor activities of bortezomib result from proteasome inhibition and depend on the altered degradation of a host of regulatory proteins. Exposure to bortezomib has been shown to stabilize p21, p27, and p53, as well as the proapoptotic Bid and Bax proteins, caveolin-1, and inhibitor κB-α, which prevents activation of nuclear factor κBinduced cell survival pathways. Bortezomib also promoted the activation of the proapoptotic c-Jun-NH2 terminal kinase, as well as the endoplasmic reticulum stress response. The anticancer effects of bortezomib as a single agent have been demonstrated in xenograft models of multiple myeloma, adult T-cell leukemia, lung, breast, prostate, pancreatic, head and neck, and colon cancer, and in melanoma. In these preclinical in vivo studies, bortezomib treatment resulted in decreased tumor growth, angiogenesis, and metastasis, as well as increased survival and tumor apoptosis. In several in vitro and/or in vivo cancer models, bortezomib has also been shown to enhance the antitumor properties of several antineoplastic treatments. Importantly, bortezomib was generally well tolerated and did not appear to produce additive toxicities when combined with other therapies in the dosing regimens used in these preclinical in vivo investigations. These findings provide a rationale for further clinical trials using bortezomib alone or in combination regimens with chemotherapy, radiation therapy, immunotherapy, or novel agents in patients with hematologic malignancies or solid tumors.

  • Preimplantation Genetic Diagnosis--An Overview -

    Since the early 1990s, preimplantation genetic diagnosis (PGD) has been expanding in scope and applications. Selection of female embryos to avoid X-linked disease was carried out first by polymerase chain reaction, then by fluorescence in situ hybridization (FISH), and an ever-increasing number of tests for monogenic diseases have been developed. Couples with chromosome rearrangements such as Robertsonian and reciprocal translocations form a large referral group for most PGD centers and present a special challenge, due to the large number of genetically unbalanced embryos generated by meiotic segregation. Early protocols used blastomeres biopsied from cleavage-stage embryos; testing of first and second polar bodies is now a routine alternative, and blastocyst biopsy can also be used. More recently, the technology has been harnessed to provide PGD-AS, or aneuploidy screening. FISH probes specific for chromosomes commonly found to be aneuploid in early pregnancy loss are used to test blastomeres for aneuploidy, with the aim of replacing euploid embryos and increasing pregnancy rates in groups of women who have poor IVF success rates. More recent application of PGD to areas such as HLA typing and social sex selection have stoked public controversy and concern, while provoking interesting ethical debates and keeping PGD firmly in the public eye. (J Histochem Cytochem 53:255–260, 2005)


  • Prenatal Diagnosis and Molecular Cytogenetic Characterization of an Unusual Complex Structural Rearrangement in a Pregnancy Following Intracytoplasmic Sperm Injection (ICSI) -

    We report on a balanced complex chromosomal aberration detected in a fetus after amniocentesis. The pregnancy was achieved after intracytoplasmic sperm injection. GTG-banding revealed a complex structurally rearranged karyotype with a translocation between chromosomes 5 and 15 and an additional paracentric inversion in the der(15) between bands 5q11.2 and 5q15. Ag-NOR staining showed an interstitial active nuclear organizer region in the der(15). Molecular cytogenetic analyses using whole-chromosome–painting probes, comparative genomic hybridization, and multicolor banding did not point to further structural aberrations or imbalances. Therefore, a complex rearrangement with three breakpoints has occurred, and the karyotype can be described as 46,XX,der(5)t(5;15) (q11.2;p12),der(15)t(5;15)(q11.2;p12)inv(5)(q11.2q15). (J Histochem Cytochem 53:351–354, 2005)


  • Preoperative Diagnosis of a Mediastinal Granular Cell Tumor by EUS-FNA: a case report and review of the literature - We report the first case of a posterior mediastinal granular cell tumor initially diagnosed on cytologic material obtained via endoscopic ultrasound-guided fine needle aspiration (EUS-FNA) in a 51-year-old male with a prior history of colon cancer. Aspirates obtained were cellular and composed of polygonal cells with abundant granular cytoplasm and small, round dark nuclei. An immunoperoxidase stain performed on the cell block for antibodies to S-100 protein showed strong, diffuse staining of the cytoplasmic granules. Electron microscopy performed on the cell block revealed numerous cytoplasmic lysosomes. This is the first case report in the English literature of a definitive preoperative diagnosis of a mediastinal granular cell tumor utilizing material obtained via EUS-FNA.

  • Presence of Anti-cystatin C-positive Dendritic Cells or Macrophages and Localization of Cysteine Proteases in the Apical Bud of the Enamel Organ in the Rat Incisor -

    Cystatin C, a cysteine protease inhibitor, was examined in the apical buds of rat incisors by immunohistochemistry, because in transition and maturation zones most of the dendritic cells in the papillary layer are anti-cystatin C–positive. Anti-cystatin C–labeled cells were sparse and localized to the proliferation and differentiation zones, constituting the apical bud of 5-week-old rat incisors. These cells were considered macrophages or dendritic cells, based on their reactivity with OX6 and ED1, as well as their ultrastructure. Basement membrane at the periphery of apical bud was also labeled by anti-cystatin C antibody. The apical buds included a few apoptotic fragments and weak reactivity with antibody to cathepsin L, a cysteine protease. Reactivity to anti-cystatin C and anti-cathepsin L antibodies was also detected in the apical bud of newborn rat incisors. These results suggest that the cystatin C–positive macrophages or dendritic cells are involved in normal incisor formation. They may be related to the clearance of apoptotic cells or protection from putative cysteine protease activity. (J Histochem Cytochem 53:643–651, 2005)


  • Presence of Anti-cystatin C-positive Dendritic Cells or Macrophages and Localization of Cysteine Proteases in the Apical Bud of the Enamel Organ in the Rat Incisor -

    Cystatin C, a cysteine protease inhibitor, was examined in the apical buds of rat incisors by immunohistochemistry, because in transition and maturation zones most of the dendritic cells in the papillary layer are anti-cystatin C–positive. Anti-cystatin C–labeled cells were sparse and localized to the proliferation and differentiation zones, constituting the apical bud of 5-week-old rat incisors. These cells were considered macrophages or dendritic cells, based on their reactivity with OX6 and ED1, as well as their ultrastructure. Basement membrane at the periphery of apical bud was also labeled by anti-cystatin C antibody. The apical buds included a few apoptotic fragments and weak reactivity with antibody to cathepsin L, a cysteine protease. Reactivity to anti-cystatin C and anti-cathepsin L antibodies was also detected in the apical bud of newborn rat incisors. These results suggest that the cystatin C–positive macrophages or dendritic cells are involved in normal incisor formation. They may be related to the clearance of apoptotic cells or protection from putative cysteine protease activity. (J Histochem Cytochem 53:643–651, 2005)


  • Presence of Anti-cystatin C-positive Dendritic Cells or Macrophages and Localization of Cysteine Proteases in the Apical Bud of the Enamel Organ in the Rat Incisor -

    Cystatin C, a cysteine protease inhibitor, was examined in the apical buds of rat incisors by immunohistochemistry, because in transition and maturation zones most of the dendritic cells in the papillary layer are anti-cystatin C–positive. Anti-cystatin C–labeled cells were sparse and localized to the proliferation and differentiation zones, constituting the apical bud of 5-week-old rat incisors. These cells were considered macrophages or dendritic cells, based on their reactivity with OX6 and ED1, as well as their ultrastructure. Basement membrane at the periphery of apical bud was also labeled by anti-cystatin C antibody. The apical buds included a few apoptotic fragments and weak reactivity with antibody to cathepsin L, a cysteine protease. Reactivity to anti-cystatin C and anti-cathepsin L antibodies was also detected in the apical bud of newborn rat incisors. These results suggest that the cystatin C–positive macrophages or dendritic cells are involved in normal incisor formation. They may be related to the clearance of apoptotic cells or protection from putative cysteine protease activity. (J Histochem Cytochem 53:643–651, 2005)


  • Preventive and curative effect of melatonin on mammary carcinogenesis induced by dimethylbenz[a]anthracene in the female Sprague–Dawley rat - IntroductionIt has been well documented that the pineal hormone, melatonin, which plays a major role in the control of reproduction in mammals, also plays a role in the incidence and growth of breast and mammary cancer. The curative effect of melatonin on the growth of dimethylbenz [a]anthracene-induced (DMBA-induced) mammary adenocarcinoma (ADK) has been previously well documented in the female Sprague–Dawley rat. However, the preventive effect of melatonin in limiting the frequency of cancer initiation has not been well documented. Methods: The aim of this study was to compare the potency of melatonin to limit the frequency of mammary cancer initiation with its potency to inhibit tumor progression once initiation, at 55 days of age, was achieved. The present study compared the effect of preventive treatment with melatonin (10 mg/kg daily) administered for only 15 days before the administration of DMBA with the effect of long-term (6-month) curative treatment with the same dose of melatonin starting the day after DMBA administration. The rats were followed up for a year after the administration of the DMBA. Results: The results clearly showed almost identical preventive and curative effects of melatonin on the growth of DMBA-induced mammary ADK. Many hypotheses have been proposed to explain the inhibitory effects of melatonin. However, the mechanisms responsible for its strong preventive effect are still a matter of debate. At least, it can be envisaged that the artificial amplification of the intensity of the circadian rhythm of melatonin could markedly reduce the DNA damage provoked by DMBA and therefore the frequency of cancer initiation. Conclusion: In view of the present results, obtained in the female Sprague–Dawley rat, it can be envisaged that the long-term inhibition of mammary ADK promotion by a brief, preventive treatment with melatonin could also reduce the risk of breast cancer induced in women by unidentified environmental factors.

  • Primary lymphoepithelioma-like carcinoma of minor salivary gland: A case report with immunohistochemical and in situ hybridization studies. -
    Related Articles

    Primary lymphoepithelioma-like carcinoma of minor salivary gland: A case report with immunohistochemical and in situ hybridization studies.

    Head Neck. 2005 Oct 20;

    Authors: Lu SY, Huang CC, Hsiung CY, Eng HL, Huang HY

    BACKGROUND.: Lymphoepithelioma-like carcinomas (LEC) of salivary glands represent rare epithelial malignancies, with most cases affecting the parotid gland. To our knowledge, there was only one LEC arising from the minor salivary gland described in the English-language literature. METHODS.: We report the second LEC of the minor salivary gland in the buccal area of a 50-year-old Taiwanese woman, who underwent surgical resection and adjuvant radiotherapy and remained alive and well after 120 months of follow-up. Histologically, irregular tumor nests of undifferentiated epithelial cells with syncytial cell boundaries were found embedded within rich lymphoplasmacytic stroma. The tumor cells also showed strong c-KIT expression and evidence of Epstein-Barr virus (EBV) infection. CONCLUSIONS.: Our case suggests potential pathogenic implications of both c-KIT and EBV in LEC of the minor salivary gland that can be cured by the combination of surgery and radiotherapy and has a very favorable long-term prognosis. (c) 2005 Wiley Periodicals, Inc. Head Neck 27: XXX-XXX, 2005.

    PMID: 16240326 [PubMed - as supplied by publisher]


  • Prime–boost vaccination with plasmid and adenovirus gene vaccines control HER2/neu+ metastatic breast cancer in mice - IntroductionOnce metastasis has occurred, the possibility of completely curing breast cancer is unlikely, particularly for the 30 to 40% of cancers overexpressing the gene for HER2/neu. A vaccine targeting p185, the protein product of the HER2/neu gene, could have therapeutic application by controlling the growth and metastasis of highly aggressive HER2/neu+ cells. The purpose of this study was to determine the effectiveness of two gene vaccines targeting HER2/neu in preventive and therapeutic tumor models. Methods: The mouse breast cancer cell line A2L2, which expresses the gene for rat HER2/neu and hence p185, was injected into the mammary fat pad of mice as a model of solid tumor growth or was injected intravenously as a model of lung metastasis. SINCP-neu, a plasmid containing Sindbis virus genes and the gene for rat HER2/neu, and Adeno-neu, an E1,E2a-deleted adenovirus also containing the gene for rat HER2/neu, were tested as preventive and therapeutic vaccines. Results: Vaccination with SINCP-neu or Adeno-neu before tumor challenge with A2L2 cells significantly inhibited the growth of the cells injected into the mammary fat or intravenously. Vaccination 2 days after tumor challenge with either vaccine was ineffective in both tumor models. However, therapeutic vaccination in a prime–boost protocol with SINCP-neu followed by Adeno-neu significantly prolonged the overall survival rate of mice injected intravenously with the tumor cells. Naive mice vaccinated using the same prime–boost protocol demonstrated a strong serum immunoglobulin G response and p185-specific cellular immunity, as shown by the results of ELISPOT (enzyme-linked immunospot) analysis for IFNγ. Conclusion: We report herein that vaccination of mice with a plasmid gene vaccine and an adenovirus gene vaccine, each containing the gene for HER2/neu, prevented growth of a HER2/neu-expressing breast cancer cell line injected into the mammary fat pad or intravenously. Sequential administration of the vaccines in a prime–boost protocol was therapeutically effective when tumor cells were injected intravenously before the vaccination. The vaccines induced high levels of both cellular and humoral immunity as determined by in vitro assessment. These findings indicate that clinical evaluation of these vaccines, particularly when used sequentially in a prime–boost protocol, is justified.

  • Profiles of PrKX Expression in Developmental Mouse Embryo and Human Tissues -

    Protein kinase X (PrKX), karyotypically located on the human X chromosome, is a type I cAMP-dependent protein kinase. Although a specific role for PrKX has not yet been defined, PrKX gene expression in mouse and human tissues has been profiled only by in situ hybridization and Northern blot analyses and not by protein expression. To determine more precisely the PrKX protein levels, we developed specific anti-PrKX antibodies and examined gestationally staged mouse embryo sections by immunohistochemistry. These results showed that PrKX is ubiquitously distributed and highly expressed in murine central nervous system and heart tissues in early developmental stages and in most organs at later stages but was not detected in either connective tissues or bone. Using Western blots to detect PrKX, total protein extracts from eight different adult or fetal human tissues including brain, heart, kidney, liver, lung, pancreas, spleen, and thymus were analyzed. Although PrKX protein was present in each of the tissues tested, the protein levels varied depending on tissue type and developmental stage. Very low protein levels were found in heart tissues from a 5-month-old fetus and from an adult, whereas PrKX proteins were more abundant in fetal brain, kidney, and liver tissues compared with adult samples of the same tissue type. (J Histochem Cytochem 53:1003–1009, 2005)


  • Profiles of PrKX Expression in Developmental Mouse Embryo and Human Tissues -

    Protein kinase X (PrKX), karyotypically located on the human X chromosome, is a type I cAMP-dependent protein kinase. Although a specific role for PrKX has not yet been defined, PrKX gene expression in mouse and human tissues has been profiled only by in situ hybridization and Northern blot analyses and not by protein expression. To determine more precisely the PrKX protein levels, we developed specific anti-PrKX antibodies and examined gestationally staged mouse embryo sections by immunohistochemistry. These results showed that PrKX is ubiquitously distributed and highly expressed in murine central nervous system and heart tissues in early developmental stages and in most organs at later stages but was not detected in either connective tissues or bone. Using Western blots to detect PrKX, total protein extracts from eight different adult or fetal human tissues including brain, heart, kidney, liver, lung, pancreas, spleen, and thymus were analyzed. Although PrKX protein was present in each of the tissues tested, the protein levels varied depending on tissue type and developmental stage. Very low protein levels were found in heart tissues from a 5-month-old fetus and from an adult, whereas PrKX proteins were more abundant in fetal brain, kidney, and liver tissues compared with adult samples of the same tissue type. (J Histochem Cytochem 53:1003–1009, 2005)


  • Prognostic value of serum CA-125 measurements on stimulation day 1 and on the day of oocyte pickup in the prediction of IVF treatment outcome. -
    Related Articles

    Prognostic value of serum CA-125 measurements on stimulation day 1 and on the day of oocyte pickup in the prediction of IVF treatment outcome.

    J Assist Reprod Genet. 2005 Jun;22(6):265-8

    Authors: Hauzman EE, Lagarde AR, Nagy K, Fancsovits P, Murber A, Jánoki G, Papp Z, Urbancsek J

    PURPOSE: To assess whether serum levels of CA-125, a proposed marker of endometrial receptivity, are associated with pregnancy after IVF. METHODS: 42 IVF pregnancies were matched with nonpregnant controls. Twenty-eight additional unmatched pregnancies were included for the comparison of pregnancy outcomes. CA-125 concentrations were measured on stimulation day 1 (SD1) and at oocyte pickup (OPU). We analyzed association between CA-125 levels and establishment of pregnancy and its outcome; correlation between CA-125 concentrations and other parameters; differences in CA-125 levels between SD1 and OPU. RESULTS: In pregnant, but not in nonpregnant patients, CA-125 levels decreased significantly from SD1 to OPU. There was no significant difference in CA-125 levels at either time point between pregnant and nonpregnant subjects. No significant correlation was found between CA-125 levels and any other clinical or laboratory parameters. CONCLUSIONS: CA-125 measurements at the beginning of stimulation or at oocyte retrieval are not useful in predicting IVF outcome.

    PMID: 16021856 [PubMed - indexed for MEDLINE]


  • Proliferation dynamics of germinative zone cells in the intact and excitotoxically lesioned postnatal rat brain - Background: The forebrain subventricular zone (SVZ)-olfactory bulb pathway and hippocampal subgranular zone (SGZ) generate neurons into adulthood in the mammalian brain. Neurogenesis increases after injury to the adult brain, but few studies examine the effect of injury on neural and glial precursors in the postnatal brain. To characterize the spatio-temporal dynamics of cell proliferation in the germinative zones, this study utilized a model of postnatal damage induced by NMDA injection in the right sensorimotor cortex at postnatal day 9.Dividing cell populations were labeled with 5-Bromodeoxyuridine (BrdU) in the intact and damaged postnatal brain. Identity of proliferating cells was determined by double immunolabeling with nestin, GFAP, NeuN and tomato lectin (TL). Results: In the control brain, grouped BrdU+ cells were observed in the Rostral Migratory Stream (RMS), SVZ and SGZ. Maximal proliferation was seen at P12, persisted until P23 and diminished by P49. After injury, a striking reduction in the number of BrdU+ cells was observed in the ipsilateral SVZ from 10 hours (58% decrease) until 14 days post-lesion (88% decrease). In contrast, an increase in grouped BrdU+ cells was seen in the striatum adjacent to the depleted SVZ. Significantly reduced numbers of BrdU+ cells were also seen in the RMS until 3 days post-lesion. No changes were noted in the SGZ. Both in controls and lesioned hemispheres, BrdU+ cells located in the germinal zones were mostly nestin positive and negative for GFAP, NeuN, and TL. In the SVZ area lining the ventricle, BrdU+/nestin+ cells were mainly located between TL+ ependyma and parenchymal GFAP+ astrocytes. After excitotoxicity, a decrease in the number and orientation of GFAP/nestin+ prolongations leaving the SVZ to the cortex, corpus callosum and striatum was noted until 5 days post-lesion. Conclusion: Postnatal excitotoxic injury differentially affects proliferating cells in the germinative zones: no change is observed in the dentate gyrus whereas excitotoxicity causes a significant decrease in proliferating cells in the SVZ and RMS. Depletion of BrdU+ cells in the postnatal SVZ and RMS differs from previous studies after adult brain injury and may affect the SVZ-RMS migration and is suggestive of progenitor recruitment to injured areas.

  • Prostaglandin H2 Synthase-1 and -2 Expression in Guinea Pig Gestational Tissues during Late Pregnancy and Parturition. -
    Related Articles

    Prostaglandin H2 Synthase-1 and -2 Expression in Guinea Pig Gestational Tissues during Late Pregnancy and Parturition.

    J Physiol. 2005 Oct 20;

    Authors: Welsh TN, Mitchell CM, Walters WA, Mesiano S, Zakar T

    Increased intrauterine prostaglandin (PG) production is crucial for the initiation of parturition. To investigate the mechanisms controlling intrauterine PG synthesis, we examined the expression of the key PG biosynthetic isoenzymes, PG-H2 synthase (PTGS)-1 and -2, in the amnion, visceral yolk sac (VYS), placenta and myo-endometrium of pregnant guinea pigs. This animal model was chosen because the hormonal milieu of pregnancy and the role of PGs in the hormonal control of parturition are similar to those in the human. PTGS1 mRNA abundance, measured by real-time RT-PCR, increased in the amnion and the placenta during the last third of gestation. During labour, PTGS1 mRNA levels decreased precipitously in all four tissues. PTGS1 protein abundance, assessed by immunoblotting, increased to high levels in the amnion and the placenta by the end of pregnancy and remained high during labour. PTGS2 mRNA expression was higher in the placenta than in the other tissues, but did not change before and during labour. PTGS2 protein expression decreased in the placenta and remained low in the other tissues during labour. Immunohistochemistry showed pervasive PTGS1 protein expression in the amnion and strong expression in the parietal yolk sac membrane (PYS) covering the placenta. PTGS2 was expressed in the PYS and the endometrium. The PTGS inhibitor piroxicam, administered in doses that inhibited PTGS1 but not PTGS2, significantly prolonged gestation. These data suggest that PGs generated by intrauterine PTGS1 are involved in the timing of birth in guinea pigs. The induction of PTGS1 in the amnion and the PYS is a critical event leading to labour in guinea pigs and models analogous changes in the human gestational tissues before labour.

    PMID: 16239272 [PubMed - as supplied by publisher]


  • Protection of cortical cells by equine estrogens against glutamate-induced excitotoxicity is mediated through a calcium independent mechanism - Background: High concentrations of glutamate can accumulate in the brain and may be involved in the pathogenesis of neurodegenerative disorders such as Alzheimer's disease. This form of neurotoxicity involves changes in the regulation of cellular calcium (Ca2+) and generation of free radicals such as peroxynitrite (ONOO-). Estrogen may protect against glutamate-induced cell death by reducing the excitotoxic Ca2+ influx associated with glutamate excitotoxicity. In this study, the inhibition of N-methyl-D-aspartate (NMDA) receptor and nitric oxide synthase (NOS) along with the effect of 17beta-estradiol (17beta-E2) and a more potent antioxidant delta8,17beta-estradiol (delta8,17beta-E2) on cell viability and intracellular Ca2+ ([Ca2+]i), following treatment of rat cortical cells with glutamate, was investigated. Results: Primary rat cortical cells were cultured for 7-12 days in Neurobasal medium containing B27 supplements. Addition of glutamate (200 microM) decreased cell viability to 51.3 +/- 0.7% compared to control. Treatment with the noncompetitive NMDAR antagonist, MK-801, and the NOS inhibitor, L-NAME, completely prevented cell death. Pretreatment (24 hrs) with 17beta-E2 and delta8,17beta-E2 (0.01 to 10 microM) significantly reduced cell death. 17beta-E2 was more potent than delta8,17beta-E2. Glutamate caused a rapid 2.5 fold increase in [Ca2+]i. Treatment with 0.001 to 10 microM MK-801 reduced the initial Ca2+ influx by 14-41% and increased cell viability significantly. Pretreatment with 17beta-E2 and delta8,17beta-E2 had no effect on Ca2+ influx but protected the cortical cells against glutamate-induced cell death. Conclusions: Glutamate-induced cell death in cortical cultures can occur through NMDAR and NOS-linked mechanisms by increasing nitric oxide and ONOO-. Equine estrogens: 17beta-E2 and delta8,17beta-E2, significantly protected cortical cells against glutamate-induced excitotoxicity by a mechanism that appears to be independent of Ca2+ influx. To our knowledge, this is a first such observation. Whether the decrease in NOS related products such as ONOO-, is a mechanism by which estrogens protect against glutamate toxicity, remains to be investigated. Estrogen replacement therapy in healthy and young postmenopausal women may protect against neurodegenerative diseases by these mechanisms.

  • Protein-embedding Technique: A Potential Approach to Standardization of Immunohistochemistry for Formalin-fixed, Paraffin-embedded Tissue Sections -

    A serial study was performed to develop a protein-embedding technique for standardization of immunohistochemistry (IHC) on formalin-fixed, paraffin-embedded (FFPE) tissue sections. A protein carrier matrix must have two phases, a liquid phase to allow uniform mixing of a protein and a solid phase forming a ‘block’ that can be fixed and processed in the same manner as human tissue. This standardized protein block would serve as a source of thin sections for control of IHC and therefore must also withstand the boiling conditions of antigen retrieval (AR). After multiple experiments, a method was developed utilizing polymer microsphere (beads) as a support medium for protein. The method showed particular promise for quantitative IHC.

    (J Histochem Cytochem 53:1167–1170, 2005)


  • Proteoglycan-Collagen XV in Human Tissues Is Seen Linking Banded Collagen Fibers Subjacent to the Basement Membrane -

    Type XV is a large collagen-proteoglycan found in all human tissues examined. By light microscopy it was localized to most epithelial and all nerve, muscle, fat and endothelial basement membrane zones except for the glomerular capillaries or hepatic/splenic sinusoids. This widespread distribution suggested that type XV may be a discrete structural component that acts to adhere basement membrane to the underlying connective tissue. To address these issues, immunogold ultrastructural analysis of type XV collagen in human kidney, placenta, and colon was conducted. Surprisingly, type XV was found almost exclusively associated with the fibrillar collagen network in very close proximity to the basement membrane. Type XV exhibited a focal appearance directly on the surface of, or extending from, the fibers in a linear or clustered array. The most common single arrangement was a bridge of type XV gold particles linking thick-banded fibers. The function of type XV in this restricted microenvironment is expected to have an intrinsic dependence upon its modification with glycosaminoglycan chains. Present biochemical characterization showed that the type XV core protein in vivo carries chains of chondroitin/dermatan sulfate alone, or chondroitin/dermatan sulfate together with heparan sulfate in a differential ratio. Thus, type XV collagen may serve as a structural organizer to maintain a porous meshwork subjacent to the basement membrane, and in this domain may play a key role in signal transduction pathways. (J Histochem Cytochem 53:165–176, 2005)


  • Proteome Analysis of Maternal Serum Samples for Trisomy 21 Pregnancies Using ProteinChip Arrays and Bioinformatics -

    A surface-enhanced laser desorption/ionization time of flight (SELDI-TOF)-based ProteinChip System was used as a tool for rapid discovery and identification of protein patterns in serum that discriminate between trisomy 21 and unaffected pregnancies. We analyzed 24 serum samples from women carrying a trisomy 21 pregnancy and 32 with an unaffected pregnancy, ranging from 10.0 to 14.0 weeks of gestation. The resulting protein profiles were submitted to a clustering algorithm, a rule extraction, a rating, and a rule base construction step. For the generated combined rule base, the specificity and sensitivity for the prediction of a trisomy 21 pregnancy reach 97% and 91%, respectively.

    (J Histochem Cytochem 53:341343, 2005)


  • Proteomic identification of heat shock protein 90 as a candidate target for p53 mutation reactivation by PRIMA-1 in breast cancer cells - IntroductionA loss of p53 function resulting from mutation is prevalent in human cancers. Thus, restoration of p53 function to mutant p53 using small compounds has been extensively studied for cancer therapy. We previously reported that PRIMA-1 (for 'p53 reactivation and induction of massive apoptosis') restored the transcriptional activity of p53 target genes in breast cancer cells with a p53 mutation. By using functional proteomics approach, we sought to identify molecular targets that are involved in the restoration of normal function to mutant p53. Methods: PRIMA-1 treated cell lysates were subjected to immunoprecipitation with DO-1 primary antibody against p53 protein, and proteins bound to p53 were separated on a denaturing gel. Bands expressed differentially between control and PRIMA-1-treated cells were then identified by matrix-assisted laser desorption ionization-time-of-flight spectrometry. Protein expression in whole cell lysates and nuclear extracts were confirmed by Western blotting. The effect of combined treatment of PRIMA-1 and adriamycin in breast cancer cells was determined with a cytotoxicity assay in vitro. Results: PRIMA-1 treated cells distinctly expressed a protein band of 90 kDa that was identified as heat shock protein 90 (Hsp90) by the analysis of the 90 kDa band tryptic digest. Immunoblotting with isoform-specific antibodies against Hsp90 identified this band as the α isoform of Hsp90 (Hsp90α). Co-immunoprecipitation with anti-Hsp90α antibody followed by immunoblotting with DO-1 confirmed that p53 and Hsp90α were interacting proteins. PRIMA-1 treatment also resulted in the translocation of Hsp90α to the nucleus by 8 hours. Treatment of cells with PRIMA-1 alone or in combination with adriamycin, a DNA-targeted agent, resulted in increased sensitivity of tumor cells. Conclusion: The studies demonstrate that PRIMA-1 restores the p53-Hsp90α interaction, enhances the translocation of the p53-Hsp90α complex and reactivates p53 transcriptional activity. Our preliminary evidence also suggests that PRIMA-1 could be considered in combination therapy with DNA-targeted agents for the treatment of breast cancer, especially for tumors with aberrant p53 function.

  • Proton Induced X ray Emission (PIXE) Analysis and DNA-chain Break study in rat hepatocarcinogenesis: A possible chemopreventive role by combined supplementation of vanadium and beta-carotene - Background: Combined effect of vanadium and beta-carotene on rat liver DNA-chain break and Proton induced X-ray emission (PIXE) analysis was studied during a necrogenic dose (200 mg/kg of body weight) of Diethyl Nitrosamine (DENA) induced rat liver carcinogenesis. Morphological and histopathological changes were observed as an end point biomarker. Method:Supplementation of vanadium (0.5 ppm ad libitum) in drinking water and beta-carotene in the basal diet (120mg/Kg of body weight) were performed four weeks before DENA treatment and continued till the end of the experiment (16 weeks). Result: PIXE analysis revealed the restoration of near normal value of zinc, copper, and iron, which were substantially altered when compared to carcinogen treated groups. Supplementation of both vanadium and beta-carotene four weeks before DENA injection was found to offer significant (64.73%, P<0.001) protection against generation of single-strand breaks when compared with the carcinogen control counter parts. A significant stabilization of hepatic architecture of the cells was observed as compared to carcinogen control in vanadium plus beta-carotene treated group. Conclusion: This study thus suggests that vanadium, a prooxidant but potential therapeutic agent yield safe and effective pharmacological formulation with beta-carotene, an antioxidant, in the inhibition of experimental rat hepatocarcinogenesis.

  • Proton NMR visible mobile lipid signals in sensitive and multidrug-resistant K562 cells are modulated by rafts - Background: Most cancer cells are characterized by mobile lipids visible on proton NMR (1H-NMR), these being comprised mainly of methyl and methylene signals from lipid acyl chains. Erythroleukemia K562 cells show narrow signals at 1.3 and 0.9 ppm, corresponding to mobile lipids (methylene and methyl, respectively), which are reduced when K562 cells are multidrug resistant (MDR). While the significance of the mobile lipids is unknown, their subcellular localization is still a matter of debate and may lie in the membrane or the cytoplasm. In this study, we investigate the role of cholesterol in the generation of mobile lipid signals. Results: The proportion of esterified cholesterol was found to be higher in K562-sensitive cells than in resistant cells, while the total cholesterol content was identical in both cell lines. Cholesterol extraction in the K562 wild type (K562wt) cell line and its MDR counterpart (K562adr), using methyl-β-cyclodextrin, was accompanied by a rise of mobile lipids in K562wt cells only. The absence of caveolae was checked by searching for the caveolin-1 protein in K562wt and K562adr cells. However, cholesterol was enriched in another membrane microdomain designated as "detergent-insoluble glycosphingomyelin complexes" or rafts. These microdomains were studied after extraction with triton X-100, a mild non-ionic detergent, revealing mobile lipid signals preserved only in the K562wt spectra. Moreover, following perturbation/disruption of these microdomains using sphingomyelinase, mobile lipids increased only in K562wt cells. Conclusion: These results suggest that cholesterol and sphingomyelin are involved in mobile lipid generation via microdomains of detergent-insoluble glycosphingomyelin complexes such as rafts. Increasing our knowledge of membrane microdomains in sensitive and resistant cell lines may open up new possibilities in resistance reversion.

  • Proximal-Type Epithelioid Sarcoma: Report of Two Cases in the Perineum: Differential Diagnosis and Review of Soft Tissue Tumors With Epithelioid and/or Rhabdoid Features. -

  • PTEN levels in Alzheimer's disease medial temporal cortex. -
    Related Articles

    PTEN levels in Alzheimer's disease medial temporal cortex.

    Neurochem Int. 2005 Oct 17;

    Authors: Rickle A, Bogdanovic N, Volkmann I, Zhou X, Pei JJ, Winblad B, Cowburn RF

    Phosphatase and tensin homologue deleted from chromosome 10 (PTEN) is a dual (protein tyrosine and lipid) phosphatase one of the functions of which is to dephosphorylate phosphatidylinositol 3,4,5-trisphosphate to phosphatidylinositol-3,4-biphosphate thereby inhibiting phosphoinositide-dependent kinase activation of the cell survival kinase Akt. Akt activity is up regulated in Alzheimer's disease (AD) brain in parallel to the progression of neurofibrillary pathology. The present study determined whether altered expression of PTEN occurs in Alzheimer's disease brain. Western immunoblotting revealed no significant changes of PTEN protein levels in nuclear and membrane fractions of medial temporal cortex from a series of Alzheimer's disease and control cases. Similarly, no changes in PTEN protein levels, as determined by dot-blotting, were seen in temporal cortex homogenates from a separate series of Alzheimer's disease and control brains. A small but significant decrease in the levels of Ser(380) p-PTEN was seen in homogenates of Alzheimer's disease temporal cortex. Immunohistochemistry revealed PTEN immunoreactivity in a number of brain structures including neurons, capillaries and structures resembling oligodendrocytes and astrocytes. The majority of temporal cortex pyramidal neurons (93-100%) were PTEN immunopositive. The Alzheimer's disease cases had significantly lower numbers of total ( approximately 12% loss, P<0.02) and PTEN immunopositive ( approximately 15% loss, P<0.01) pyramidal neurons as compared to the control cases.

    PMID: 16239049 [PubMed - as supplied by publisher]


  • QF-PCR Examination of Parental and Meiotic Origin of Trisomy 21 in Central and Eastern Europe -

    Study of parental/meiotic origin of free trisomy 21 in nuclear families from Russia (70 cases), Ukraine (32 cases), and 22 from Germany revealed maternal nondisjunction in 77.3% (Germany), 93.8% (Ukraine), and 91.4% (Russia), paternal origin in 13.6%, 6.2%, and 8.6%, respectively. Maternal meiosis I errors were found in 84.4% (Ukraine), 77.1% (Russia), paternal origin in 3.1% (Ukraine), 2.9% (Russia). Maternal meiosis II errors occurred in 9.4% and 14.3% and paternal in 3.1% and 5.7% in Ukraine and Russia, respectively. No significant differences were found in maternal/paternal origin among Ukraine, Russia, Germany, and published data from other European regions.

    (J Histochem Cytochem 53:371–373, 2005)


  • Quantification of the response of circulating epithelial cells to neodadjuvant treatment for breast cancer: a new tool for therapy monitoring - IntroductionIn adjuvant treatment for breast cancer there is no tool available with which to measure the efficacy of the therapy. In contrast, in neoadjuvant therapy reduction in tumour size is used as an indicator of the sensitivity of tumour cells to the agents applied. If circulating epithelial (tumour) cells can be shown to react to therapy in the same way as the primary tumour, then this response may be exploited to monitor the effect of therapy in the adjuvant setting.MethodWe used MAINTRAC® analysis to monitor the reduction in circulating epithelial cells during the first three to four cycles of neoadjuvant therapy in 30 breast cancer patients. Results: MAINTRAC® analysis revealed a patient-specific response. Comparison of this response with the decline in size of the primary tumour showed that the reduction in number of circulating epithelial cells accurately predicted final tumour reduction at surgery if the entire neoadjuvant regimen consisted of chemotherapy. However, the response of the circulating tumour cells was unable to predict the response to additional antibody therapy. Conclusion: The response of circulating epithelial cells faithfully reflects the response of the whole tumour to adjuvant therapy, indicating that these cells may be considered part of the tumour and can be used for therapy monitoring.

  • Quantification of Viability in Organotypic Multicellular Spheroids of Human Malignant Glioma using Lactate Dehydrogenase Activity: A Rapid and Reliable Automated Assay -

    Organotypic spheroids from malignant glioma resemble the biological complexity of the original tumor and are therefore appealing to study anticancer drug responses. Accurate and reproducible quantification of response effect has been lacking to determine drug responses in this three-dimensional tumor model. Lactate dehydrogenase (LDH) activity was demonstrated in cryostat sections of spheroids using the tetrazolium salt method. Calibrated digital image acquisition of the stained cryostat sections enables quantification of LDH activity. Fully automated image cytometry reliably demarcates LDH-active and LDH-inactive tissue areas by thresholding at specific absorbance values. The viability index (VI) was calculated as ratio of LDH-active areas and total spheroid tissue areas. Duplicate staining and processing on the same tissue showed good correlation and therefore reproducibility. Sodium azide incubation of spheroids induced reduction in VI to almost zero. We conclude that quantification of viability in cryostat sections of organotypic multicellular spheroids from malignant glioma can be performed reliably and reproducibly with this approach. (J Histochem Cytochem 53:23–34, 2005)


  • Quantifying Estrogen and Progesterone Receptor Expression in Breast Cancer by Digital Imaging -

    Developments in digital imaging and fluorescent microscopy provide a new method and opportunities for quantification of protein expression in human tissue. Archived collections of paraffin-embedded tumors can be used to study the relationship between quantitative differences in protein expression in tumors and patient outcome. In this report we describe the use of a DeltaVision Restoration deconvolution microscope, combined with fluorescent immunohistochemistry, to obtain reproducible and quantitative estimates of protein expression in a formalin-fixed paraffin-embedded tissue. As proof of principle, we used antibodies to the estrogen and progesterone receptors in a hormone receptor–positive breast cancer specimen. We provide guidelines for control of day-to-day variability in camera and microscope performance to ensure that image acquisition leads to reproducible quantitative estimates of protein expression. We show that background autofluorescence related to formalin fixation can be controlled and that for proteins that are expressed in nearly every cell, multiplexing two primary antibodies on the same slide does not significantly affect the results obtained. We demonstrate that for proteins whose expression varies markedly from cell to cell, data reproducibility, as assessed by imaging successive tissue sections, is more difficult to determine.

    (J Histochem Cytochem 53:753–762, 2005)


  • Quantifying Estrogen and Progesterone Receptor Expression in Breast Cancer by Digital Imaging -

    Developments in digital imaging and fluorescent microscopy provide a new method and opportunities for quantification of protein expression in human tissue. Archived collections of paraffin-embedded tumors can be used to study the relationship between quantitative differences in protein expression in tumors and patient outcome. In this report we describe the use of a DeltaVision Restoration deconvolution microscope, combined with fluorescent immunohistochemistry, to obtain reproducible and quantitative estimates of protein expression in a formalin-fixed paraffin-embedded tissue. As proof of principle, we used antibodies to the estrogen and progesterone receptors in a hormone receptor–positive breast cancer specimen. We provide guidelines for control of day-to-day variability in camera and microscope performance to ensure that image acquisition leads to reproducible quantitative estimates of protein expression. We show that background autofluorescence related to formalin fixation can be controlled and that for proteins that are expressed in nearly every cell, multiplexing two primary antibodies on the same slide does not significantly affect the results obtained. We demonstrate that for proteins whose expression varies markedly from cell to cell, data reproducibility, as assessed by imaging successive tissue sections, is more difficult to determine.

    (J Histochem Cytochem 53:753–762, 2005)


  • Quantifying Estrogen and Progesterone Receptor Expression in Breast Cancer by Digital Imaging -

    Developments in digital imaging and fluorescent microscopy provide a new method and opportunities for quantification of protein expression in human tissue. Archived collections of paraffin-embedded tumors can be used to study the relationship between quantitative differences in protein expression in tumors and patient outcome. In this report we describe the use of a DeltaVision Restoration deconvolution microscope, combined with fluorescent immunohistochemistry, to obtain reproducible and quantitative estimates of protein expression in a formalin-fixed paraffin-embedded tissue. As proof of principle, we used antibodies to the estrogen and progesterone receptors in a hormone receptor–positive breast cancer specimen. We provide guidelines for control of day-to-day variability in camera and microscope performance to ensure that image acquisition leads to reproducible quantitative estimates of protein expression. We show that background autofluorescence related to formalin fixation can be controlled and that for proteins that are expressed in nearly every cell, multiplexing two primary antibodies on the same slide does not significantly affect the results obtained. We demonstrate that for proteins whose expression varies markedly from cell to cell, data reproducibility, as assessed by imaging successive tissue sections, is more difficult to determine.

    (J Histochem Cytochem 53:753–762, 2005)


  • Quantitative PCR for detection of the OT-1 transgene - Background: Transgenic TCR mice are often used experimentally as a source of T cells of a defined specificity. One of the most widely used transgenic TCR models is the OT-1 transgenic mouse in which the CD8+ T cells express a TCR specific for the SIINFEKL peptide of ovalbumin presented on kb [1]. Although OT-1 CD8+ can be used in a variety of different experimental settings, we principally employ adoptive transfer and peptide-driven expansion of OT-1 cells in order to explore the distribution and fate of these antigen-specific OT-1 T cells. We set out to develop a quantitative PCR assay for OT-1 cells in order to assess the distribution of OT-1 CD8+ T cells in tissues that are either intrinsically difficult to dissociate for flow cytometric analysis or rendered incompatible with flow cytometric analysis through freezing or fixation. Because the OT-1 mouse was made by micronuclear injection of genomic DNA, which did not contain unique transgene non-coding sequence, we based a quantitative PCR strategy on the DNA sequence encoding the rearranged VDJ sequences corresponding to the CDR3 region of the TCR Beta chain. The utility and sensitivity of a qPCR assay designed to detect the OT-1 transgene was compared to the standard method of flow cytometry to track and quantify activated OT-1 cells in both in vitro dilution and in vivo adoptive transfer experiments. Results: We show excellent correlation between flow cytometric assessment of OT-1 cells and OT-1 qPCR assays in cell dilutions as well as in in vivo adoptive transfer experiments. We also demonstrate that qPCR can be performed from archival formalin-fixed paraffin-embedded tissue sections. In addition, the non-quantitative PCR using the OT-1-specific primers without the real-time probe is a valuable tool for OT-1 genotyping, obviating the need for peripheral blood collection and subsequent flow cytometric analysis. Conclusions: An OT-1 specific qPCR assay has been developed to quantify adoptively transferred OT-1 cells. OT-1 qPCR is a valuable adjunct to the standard flow cytometric analysis of OT-1 cell number, particularly in experimental settings where tissue disaggregation is not desirable or in tissues which are not readily disassociated

  • Rac1 and Rac3 isoform activation is involved in the invasive and metastatic phenotype of human breast cancer cells - IntroductionThe metastatic progression of cancer is a direct result of the disregulation of numerous cellular signaling pathways, including those associated with adhesion, migration, and invasion. Members of the Rac family of small GTPases are known to act as regulators of actin cytoskeletal structures and strongly influence the cellular processes of integrin-mediated adhesion and migration. Even though hyperactivated Rac proteins have been shown to influence metastatic processes, these proteins have never been directly linked to metastatic progression. Methods: To investigate a role for Rac and Cdc42 in metastatic breast cancer cell invasion and migration, relative endogenous Rac or Cdc42 activity was determined in a panel of metastatic variants of the MDA-MB-435 metastatic human breast cancer cell line using a p21-binding domain-PAK pull down assay. To investigate the migratory and invasive potential of the Rac isoforms in human breast cancer, namely Rac1 and the subsequently cloned Rac3, we stably expressed either dominant active Rac1 or dominant active Rac3 into the least metastatic cell variant. Dominant negative Rac1 or dominant negative Rac3 were stably expressed in the most metastatic cell variant. Cell lines expressing mutant Rac1 or Rac3 were analyzed using in vitro adhesion, migration and invasion assays. Results: We show that increased activation of Rac proteins directly correlates with increasing metastatic potential in a panel of cell variants derived from a single metastatic breast cancer cell line (MDA-MB-435). The same correlation could not be found with activated Cdc42. Expression of a dominant active Rac1 or a dominant active Rac3 resulted in a more invasive and motile phenotype. Moreover, expression of either dominant negative Rac1 or dominant negative Rac3 into the most metastatic cell variant resulted in decreased invasive and motile properties. Conclusion: This study correlates endogenous Rac activity with high metastatic potential and implicates Rac in the regulation of cell migration and invasion in metastatic breast cancer cells. Taken together, these results suggest a role for both the Rac1 and Rac3 GTPases in human breast cancer progression.

  • Raman Spectroscopic Evaluation of Efficacy of Current Paraffin Wax Section Dewaxing Agents -

    During a spectroscopic study to identify biochemical changes in cervical tissue with the onset of carcinogenesis, residual paraffin wax contributions were observed on almost all dewaxed formalin-fixed paraffin-processed (FFPP) tissue sections examined. Subsequently, the present study was formulated to evaluate the efficacy of current dewaxing agents using Raman spectroscopy. Three cervical FFPP sections were subjected to each of the protocols. Sections were dewaxed using four common dewaxing protocols, namely, xylene, Histoclear, heat-mediated antigen retrieval (HMAR) using xylene and citrate buffer, and Trilogy (combined deparaffinization and unmasking of antigens). The potential for hexane as a dewaxing agent was also evaluated. Sections were dewaxed in multiple dewaxing cycles using xylene, Histoclear, and hexane. Residual paraffin wax contributions remained at 1062 cm–1, 1296 cm–1, and 1441 cm–1. HMAR using xylene and citrate buffer, and HMAR using Trilogy, showed a similar efficacy, resulting in incomplete removal of wax. Hexane was shown to be the most effective dewaxing agent, resulting in almost complete removal of wax. Immunohistochemistry was carried out on dewaxed slides, and those dewaxed with hexane displayed a stronger positivity (28%). Implications for histopathology and immunohistochemistry are considered, as well as problems that residual wax poses for spectroscopic evaluation of dewaxed FFPP sections with a view to disease diagnosis.

    (J Histochem Cytochem 53:121–129, 2005)


  • Rapid in vivoTaxotere quantitative chemosensitivity response by 4.23 Tesla sodium MRI and histo-immunostaining features in N-Methyl-N-Nitrosourea induced breast tumors in rats - Background: Sodium weighted images can indicate sodium signal intensities from different features in the tumor before and 24 hours following administration of Taxotere. Aim: To evaluate the association of in vivo intracellular sodium magnetic resonance image intensities with immuno-biomarkers and histopathological features to monitor the early tumor response to Taxotere chemotherapy in Methyl-Nitroso-Urea induced rat xenograft breast tumors. Methods and Materials: Methyl-Nitroso-Urea (MNU) induced rat xenograft breast tumors were imaged for sodium MRI and compared with tumor histology, immunostaining after 24 hours chemotherapy. Results: Sodium MRI signal intensities represented sodium concentrations. Excised tumor histological sections showed different in vitro histological end points i.e. single strand s-DNA content of cell nuclei during cell cycle (G1/S-G2/M), distinct S or M histograms (Feulgen labeling to nuclear DNA content by CAS 200), mitotic figures and apoptosis at different locations of breast tumors. Necrosis and cystic fluid appeared gray on intracellular (IC) sodium images while apoptosis rich regions appeared brighter on IC sodium images. After 24 hours Taxotere-treated tumors showed lower 'IC/EC ratio' of viable cells (65-76%) with higher mitotic index; apoptotic tumor cells at high risk due to cytotoxicity ( > 70% with high apoptotic index); reduced proliferation index (270 vs 120 per high power field) associated with enhanced IC sodium in vivo MR image intensities and decreased tumor size (3 %; p < 0.001; n=16) than that of pre-treated tumors. IC-Na MR signal intensities possibly indicated Taxotere chemosensitivity response in vivo associated with apoptosis and different pre-malignant features within 24 hours of exposure of cancer cells to anti-neoplastic Taxotere drug. Conclusion: Sodium MRI imaging may be used as in vivo rapid drug monitoring method to evaluate Taxotere chemosensitivity response associated with neoplasia, apoptosis and tumor histology features.

  • Rapid Prenatal Diagnosis of Aneuploidy Using Quantitative Fluorescence-PCR (QF-PCR) -

    Molecular cytogenetic aneuploidy testing for pregnant women at increased risk of chromosome abnormality leads to rapid reassurance for those with normal results and earlier decisions on pregnancy management in the case of abnormality. We tested 9080 prenatal samples using a one-tube QF-PCR test for trisomies 13, 18, and 21; the abnormality rate was 5.9%. There were no misdiagnoses for non-mosaic trisomy. A sex chromosome multiplex was developed that detects structural sex chromosome abnormalities as well as aneuploidies. The sex chromosome test was targeted at pregnancies (272) with specific abnormalities suggestive of Turner syndrome; 13.2% showed 45,X, confirmed by follow-up analysis. (J Histochem Cytochem 53:285–288, 2005)


  • Rapid Prenatal Diagnostics in the Interphase Nucleus: Procedure and Cut-off Rates -

    Results of a rapid prenatal aneuploidy screening in uncultured amniocytes using FISH are available within 24 hr. However, care has to be taken of possible pitfalls in connection with the commercially available probe sets and in the interpretation of results in general. Here we present our cut-off rates for and the way in which we handle the Aneu Vysion kit (ABBOTT/Vysis), based on the experience of 1200 studied cases. In summary, the method is reliable, and the risk for misdiagnosis is low (~0.4%). Nonetheless, the test should be used exclusively as a preamble to full chromosome analysis by microscopy.

    (J Histochem Cytochem 53:289291, 2005)


  • Real-time reverse transcription-PCR and fluorescence in-situ hybridization are complementary to understand the mechanisms involved in HER-2/neu overexpression in human breast carcinomas. -
    Related Articles

    Real-time reverse transcription-PCR and fluorescence in-situ hybridization are complementary to understand the mechanisms involved in HER-2/neu overexpression in human breast carcinomas.

    Histopathology. 2005 Apr;46(4):431-41

    Authors: Vanden Bempt I, Vanhentenrijk V, Drijkoningen M, Wlodarska I, Vandenberghe P, De Wolf-Peeters C

    AIMS: To evaluate the HER-2/neu status at the mRNA and DNA level of breast carcinomas and to compare it with HER-2/neu receptor overexpression by immunohistochemistry (IHC). METHODS AND RESULTS: In 32 invasive breast carcinomas, frozen tissue was available for real-time detection of HER-2/neu mRNA levels by reverse transcription-polymerase chain reaction (RT-PCR). Corresponding paraffin sections were examined by IHC and fluorescence in-situ hybridization (FISH). Thereby, different IHC and FISH procedures were compared. Using microwave epitope retrieval, all 32 cases scored 3+ on IHC, whereas only 28 out of 32 cases scored IHC 3+ using water bath epitope retrieval. All of these 28 cases showed increased levels of HER-2/neu mRNA. Dual-colour FISH analysis showed corresponding gene amplification in all 28 cases, with two cases showing a peculiar amplification pattern. In the remaining four cases, scoring IHC 2+ using water bath epitope retrieval, mRNA levels were not elevated. Three cases did not have gene amplification and one case showed low-level HER-2/neu gene amplification. All four carcinomas showed chromosome 17 polysomy. CONCLUSIONS: Real-time RT-PCR is accurate in selecting breast carcinoma cases scoring 3+ by IHC with high-level gene amplification. Results obtained by dual-colour FISH suggest that mechanisms leading to HER-2/neu receptor overexpression may be different between carcinomas scoring 2+ and 3+ on IHC, with polysomy 17 found in the former and gene amplification in the latter.

    PMID: 15810955 [PubMed - indexed for MEDLINE]


  • Recent Advances in Fetal Nucleic Acids in Maternal Plasma -

    The discovery of cell-free fetal DNA in maternal plasma in 1997 has opened up new possibilities for noninvasive prenatal diagnosis. Circulating fetal DNA molecules have been detected in maternal plasma from the first trimester onwards and can be robustly detected using a variety of molecular methods. This approach has been used for the prenatal investigation of sex-linked diseases, fetal RhD status, and prenatal exclusion of ßbeta;-thalassemia major. Recently, fetal RNA has also been found in maternal plasma. Such fetal RNA has been shown to originate from the placenta and to be remarkably stable. The use of microarray-based approaches has made it feasible to rapidly generate new circulating RNA markers. It is hoped that further developments in this field will make the routine and widespread practice of noninvasive nucleic acid–based prenatal diagnosis for common pregnancy-associated disorders feasible in the near future.

    (J Histochem Cytochem 53:293296, 2005)


  • Recent Advances in the Molecular Biology of Congenital Polycythemias and Polycythemia Vera - This review will focus on the molecular basis of certain polycythemic disorders. Primary polycythemias are characterized by acquired somatic or inherited germ- line mutations expressed within hematopoietic progenitors that cause increased accumulation of red blood cells. Polycythemia vera (PV), an acquired condition, is the most common primary polycythemia; although some progress has been made in the understanding of PV, its molecular basis remains unknown. In contrast, recent advances in delineating the molecular defects of some inherited polycythemias have greatly furthered our knowledge of the regulation of erythropoiesis and hypoxia sensing; however, more work needs to be done.

  • Reciprocal role of cyclins and cyclin kinase inhibitor p21WAF1/CIP1on lymphocyte proliferation, allo-immune activation and inflammation - Background: : Immune activation that results due to the aberrant proliferation of lymphocytes leads to inflammation and graft rejection in organ transplant recipients. We hypothesize that the cell cycle control and inflammation are parallel events, inhibition of cellular proliferation by cyclin kinase inhibitor specifically p21 will limit inflammation and prevent allograft rejection. MethodS: We performed in vitro and in vivo studies using lymphocytes, and rat heart transplant model to understand the role of cyclins and p21 on mitogen and allo-induced lymphocyte activation and inflammation. Lymphocyte proliferation was studied by 3H-thymidine uptake assay and mRNA expression was studied RT-PCR. Activation of allo- and mitogen stimulated lymphocytes resulted in increased expression of cyclins, IL-2 and pro-inflammatory cytokines, which was inhibited by cyclosporine. The over-expression of p21 prolonged graft survival in a completely mismatched rat heart transplant model by inhibiting circulating and intra-graft expression of proinflammatory cytokines. Conclusions: : Cyclins play a significant role in transplant-induced immune activation and p21 over-expression has potential to inhibit T cell activation and inflammation. The results from this study will permit the design of alternate strategies by controlling cell cycle progression to achieve immunosuppression in transplantation.

  • Recognizing scientific excellence in the biology of cell adhesion - The prestigious 2005 Japan Prize for Cell Biology has been awarded to Dr. Masatoshi Takeichi, Director of RIKEN Developmental Biology, Kobe, Japan, and Dr. Erkki Ruoslahti, Distinguished Professor, The Burnham Institute, La Jolla, USA for their "Fundamental contribution in elucidating the molecular mechanisms of cell adhesion". The award is scheduled to be presented to the scientists in ceremonies in Tokyo on April 20, 2005 as part of a week-long celebration of "Japan Prize Week".

  • Reduced expression of multiple gap junction proteins is a feature of cervical dysplasia. - Cervical dysplasia is a premalignant lesion associated with human papillomavirus (HPV) infection which, over time, can turn cancerous. Previous studies have indicated that loss of gap junctions may be a feature of cervical cancer and premalignant dysplasia. Loss of the gap junction protein connexin43 has been demonstrated in dysplastic cervix, but other connexins have not been investigated. In contrast we previously showed that HPV-associated cutaneous warts - and other hyperproliferative skin conditions - display a dramatic upregulation of certain connexins, in particular connexin26. By performing immunofluorescence staining after antigen retrieval of paraffin-embedded cervical tissue samples, this study reports for the first time that connexin26 and connexin30, in addition to connexin43, are expressed in differentiating cells of normal human cervical epithelia. Moreover, in dysplastic ectocervix, all connexins studied display a dramatic loss of expression compared to adjacent normal epithelia. The role of connexins in keratinocyte differentiation and carcinogenesis is discussed.

  • Reduction of Colitis by Prebiotics in HLA-B27 Transgenic Rats Is Associated with Microflora Changes and Immunomodulation. -
    Related Articles

    Reduction of Colitis by Prebiotics in HLA-B27 Transgenic Rats Is Associated with Microflora Changes and Immunomodulation.

    Inflamm Bowel Dis. 2005 Nov;11(11):977-985

    Authors: Hoentjen F, Welling GW, Harmsen HJ, Zhang X, Snart J, Tannock GW, Lien K, Churchill TA, Lupicki M, Dieleman LA

    HLA-B27 transgenic rats develop spontaneous colitis under specific pathogen-free conditions (SPF) but germ-free rats remain disease-free, emphasizing a role for intestinal bacteria in the pathogenesis of chronic intestinal inflammation. Prebiotics are dietary substances that affect the host by stimulating growth and/or activity of potentially health promoting bacteria. The aims of this study were to investigate whether prebiotics can prevent colitis in SPF HLA-B27 rats, and secondly, to explore mechanisms of protection. SPF HLA-B27 transgenic rats received orally the prebiotic combination long-chain inulin and oligofructose (Synergy 1), or not, prior to the development of clinically detectable colitis. After seven weeks, cecal and colonic tissues were collected for gross cecal scores (GCS), histologic inflammatory scores (scale 0-4), and mucosal cytokine measurement. Cecal and colonic contents were collected for analysis of the gut microbiota by PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and fluorescent in-situ hybridization (FISH), and analysis of short-chain fatty acid composition. Prebiotic treatment significantly decreased GCS and inflammatory histologic scores in the cecum and colon. Prebiotic treatment also decreased cecal IL-1beta, but increased cecal TGF-beta concentrations. Inulin/oligofructose altered the cecal and colonic PCR-DGGE profiles, and FISH analysis showed significant increases in cecal Lactobacillus and Bifidobacterium populations after prebiotic treatment compared with water-treated rats. In conclusion, the prebiotic combination Synergy 1 reduced colitis in HLA-B27 transgenic rats, which effect was associated with alterations to the gut microbiota, decreased tissue proinflammatory cytokines and increased immunomodulatory molecules. These results show promise for prebiotics as primary or adjuvant maintenance therapy for chronic inflammatory bowel diseases.

    PMID: 16239843 [PubMed - as supplied by publisher]


  • Reduction of the hand representation in the homolateral primary motor cortex following unilateral section of the corticospinal tract at cervical level in monkeys - Background: After sub-total hemi-section of cervical cord at level C7/C8 in monkeys, the homolateral hand exhibited a paralysis for a couple weeks, rapidly followed by incomplete recovery of manual dexterity, reaching a plateau after 40-50 days. Recently, we demonstrated that the level of the plateau was related to the size of the lesion and, following a comparable time course, progressive plastic changes of the motor map in the contralesional motor cortex took place, in particular the hand representation. The goal of the present study was to assess, in three macaque monkeys, whether the hand representation in the ipsilesional primary motor cortex (M1) was also affected by the cervical hemi-section. Results: Very unexpectedly, based on the minor contribution of the ipsilesional hemisphere to the transected CS tract, a considerable reduction of the hand representation was also observed in the ipsilesional M1. Mapping control experiments provided evidence ruling out the possibility that changes of motor maps are due to variability of the intracortical microstimulation mapping technique. The extent of the size reduction of the hand area was nearly as large as in the contralesional hemisphere in two of the three monkeys. In the third monkey, it represented a reduction by a factor of half the change observed in the contralesional hemisphere. Although the hand representation was modified in the ipsilesional hemisphere, such changes were not correlated with a contribution of this hemisphere to the incomplete recovery of the manual dexterity for the hand affected by the lesion, as demonstrated by reversible inactivation experiments (in contrast to the contralesional hemisphere). Moreover, despite the size reduction of M1 hand area in the ipsilesional hemisphere, no deficit of manual dexterity for the hand opposite to the cervical hemi-section was detected. Conclusions: After cervical hemi-section, the ispilesional motor cortex exhibits a substantial reduction of the hand representation, whose extent does not match the small amount of axotomized CS neurons. We hypothesize that the paradoxical reduction of hand representation in the ipsilesional hemisphere is secondary to the changes taking place on the contralesional hemisphere, possibly corresponding to re-adjustments aimed at re-establishing a balance between the two hemispheres.

  • Region- and Cell-specific Differences in the Distribution of Carbonic Anhydrases II, III, XII, and XIV in the Adult Rat Epididymis -

    We employed RT-PCR followed by light microscope immunocytochemistry on St. Marie's- and Bouin's-fixed tissues to define the distribution of carbonic anhydrase (CA) isoforms in the male reproductive tract. The data revealed that CA II, III, IV, XII, and XIV were expressed in rat epididymis. Whereas CA III was found in principal cells of all epididymal regions, CA II was localized in narrow cells of the initial segment and principal cells of all regions. CA XII expression was most intense in the corpus and proximal cauda regions, where it appeared over the basolateral plasma membranes of principal cells. Narrow cells of the initial segment also revealed intense reactions, as did basal cells of the corpus and proximal cauda regions. Principal cells of the initial segment and proximal caput regions showed diffuse apical cytosolic reactions and occasional basolateral staining for CA XIV, whereas principal cells of distal regions showed more diffuse cytosolic reactions highlighting both apical and basal regions of the cell, with basal cells also being reactive. These data suggest subtle differences in cell type and subcellular- and region-specific distributions for CAs in their role of fine-tuning pH in the lumen, cell cytosol, and intervening intercellular spaces of the epididymis. (J Histochem Cytochem 53:699–713, 2005)


  • Region- and Cell-specific Differences in the Distribution of Carbonic Anhydrases II, III, XII, and XIV in the Adult Rat Epididymis -

    We employed RT-PCR followed by light microscope immunocytochemistry on St. Marie's- and Bouin's-fixed tissues to define the distribution of carbonic anhydrase (CA) isoforms in the male reproductive tract. The data revealed that CA II, III, IV, XII, and XIV were expressed in rat epididymis. Whereas CA III was found in principal cells of all epididymal regions, CA II was localized in narrow cells of the initial segment and principal cells of all regions. CA XII expression was most intense in the corpus and proximal cauda regions, where it appeared over the basolateral plasma membranes of principal cells. Narrow cells of the initial segment also revealed intense reactions, as did basal cells of the corpus and proximal cauda regions. Principal cells of the initial segment and proximal caput regions showed diffuse apical cytosolic reactions and occasional basolateral staining for CA XIV, whereas principal cells of distal regions showed more diffuse cytosolic reactions highlighting both apical and basal regions of the cell, with basal cells also being reactive. These data suggest subtle differences in cell type and subcellular- and region-specific distributions for CAs in their role of fine-tuning pH in the lumen, cell cytosol, and intervening intercellular spaces of the epididymis. (J Histochem Cytochem 53:699–713, 2005)


  • Region- and Cell-specific Differences in the Distribution of Carbonic Anhydrases II, III, XII, and XIV in the Adult Rat Epididymis -

    We employed RT-PCR followed by light microscope immunocytochemistry on St. Marie's- and Bouin's-fixed tissues to define the distribution of carbonic anhydrase (CA) isoforms in the male reproductive tract. The data revealed that CA II, III, IV, XII, and XIV were expressed in rat epididymis. Whereas CA III was found in principal cells of all epididymal regions, CA II was localized in narrow cells of the initial segment and principal cells of all regions. CA XII expression was most intense in the corpus and proximal cauda regions, where it appeared over the basolateral plasma membranes of principal cells. Narrow cells of the initial segment also revealed intense reactions, as did basal cells of the corpus and proximal cauda regions. Principal cells of the initial segment and proximal caput regions showed diffuse apical cytosolic reactions and occasional basolateral staining for CA XIV, whereas principal cells of distal regions showed more diffuse cytosolic reactions highlighting both apical and basal regions of the cell, with basal cells also being reactive. These data suggest subtle differences in cell type and subcellular- and region-specific distributions for CAs in their role of fine-tuning pH in the lumen, cell cytosol, and intervening intercellular spaces of the epididymis. (J Histochem Cytochem 53:699–713, 2005)


  • Regional-dependent Increase of Sympathetic Innervation in Rat White Adipose Tissue during Prolonged Fasting -

    White adipose tissue (WAT) is innervated by the sympathetic nervous system. A role for WAT sympathetic noradrenergic nerves in lipid mobilization has been suggested. To gain insight into the involvement of nerve activity in the delipidation process, WAT nerves were investigated in rat retroperitoneal and epididymal depots after prolonged fasting. A significant increase in tyrosine hydroxylase (TH) content was found in epididymal and, especially, retroperitoneal WAT by Western blotting. Accordingly, an increased immunoreactivity for TH was detected by immunohistochemistry in epididymal and, especially, retroperitoneal vascular and parenchymal noradrenergic nerves. Neuropeptide Y (NPY)-containing nerves were found around arteries and in the parenchyma. Double-staining experiments and confocal microscopy showed that most perivascular and some parenchymal noradrenergic nerves also contained NPY. Detection of protein gene product (PGP) 9.5, a general marker of peripheral nerves, by Western blotting and PGP 9.5-TH by double-staining experiments showed significantly increased noradrenergic nerve density in fasted retroperitoneal, but not epididymal depots, suggesting that formation of new nerves takes place in retroperitoneal WAT in fasting conditions. On the whole, these data confirm the important role of sympathetic noradrenergic nerves in WAT lipid mobilization during fasting but also raise questions about the physiological role of regional-dependent nerve adjustments and their functional significance in relation to white adipocyte secretory products.

    (J Histochem Cytochem 53:679–687, 2005)


  • Regional-dependent Increase of Sympathetic Innervation in Rat White Adipose Tissue during Prolonged Fasting -

    White adipose tissue (WAT) is innervated by the sympathetic nervous system. A role for WAT sympathetic noradrenergic nerves in lipid mobilization has been suggested. To gain insight into the involvement of nerve activity in the delipidation process, WAT nerves were investigated in rat retroperitoneal and epididymal depots after prolonged fasting. A significant increase in tyrosine hydroxylase (TH) content was found in epididymal and, especially, retroperitoneal WAT by Western blotting. Accordingly, an increased immunoreactivity for TH was detected by immunohistochemistry in epididymal and, especially, retroperitoneal vascular and parenchymal noradrenergic nerves. Neuropeptide Y (NPY)-containing nerves were found around arteries and in the parenchyma. Double-staining experiments and confocal microscopy showed that most perivascular and some parenchymal noradrenergic nerves also contained NPY. Detection of protein gene product (PGP) 9.5, a general marker of peripheral nerves, by Western blotting and PGP 9.5-TH by double-staining experiments showed significantly increased noradrenergic nerve density in fasted retroperitoneal, but not epididymal depots, suggesting that formation of new nerves takes place in retroperitoneal WAT in fasting conditions. On the whole, these data confirm the important role of sympathetic noradrenergic nerves in WAT lipid mobilization during fasting but also raise questions about the physiological role of regional-dependent nerve adjustments and their functional significance in relation to white adipocyte secretory products.

    (J Histochem Cytochem 53:679–687, 2005)


  • Regional-dependent Increase of Sympathetic Innervation in Rat White Adipose Tissue during Prolonged Fasting -

    White adipose tissue (WAT) is innervated by the sympathetic nervous system. A role for WAT sympathetic noradrenergic nerves in lipid mobilization has been suggested. To gain insight into the involvement of nerve activity in the delipidation process, WAT nerves were investigated in rat retroperitoneal and epididymal depots after prolonged fasting. A significant increase in tyrosine hydroxylase (TH) content was found in epididymal and, especially, retroperitoneal WAT by Western blotting. Accordingly, an increased immunoreactivity for TH was detected by immunohistochemistry in epididymal and, especially, retroperitoneal vascular and parenchymal noradrenergic nerves. Neuropeptide Y (NPY)-containing nerves were found around arteries and in the parenchyma. Double-staining experiments and confocal microscopy showed that most perivascular and some parenchymal noradrenergic nerves also contained NPY. Detection of protein gene product (PGP) 9.5, a general marker of peripheral nerves, by Western blotting and PGP 9.5-TH by double-staining experiments showed significantly increased noradrenergic nerve density in fasted retroperitoneal, but not epididymal depots, suggesting that formation of new nerves takes place in retroperitoneal WAT in fasting conditions. On the whole, these data confirm the important role of sympathetic noradrenergic nerves in WAT lipid mobilization during fasting but also raise questions about the physiological role of regional-dependent nerve adjustments and their functional significance in relation to white adipocyte secretory products.

    (J Histochem Cytochem 53:679–687, 2005)


  • Regulation of actin cytoskeleton architecture by Eps8 and Abi1 - Background: The actin cytoskeleton participates in many fundamental processes including the regulation of cell shape, motility, and adhesion. The remodeling of the actin cytoskeleton is dependent on actin binding proteins, which organize actin filaments into specific structures that allow them to perform various specialized functions. The Eps8 family of proteins is implicated in the regulation of actin cytoskeleton remodeling during cell migration, yet the precise mechanism by which Eps8 regulates actin organization and remodeling remains elusive. Results: Here, we show that Eps8 promotes the assembly of actin rich filopodia-like structures and actin cables in cultured mammalian cells and Xenopus embryos, respectively. The morphology of actin structures induced by Eps8 was modulated by interactions with Abi1, which stimulated formation of actin cables in cultured cells and star-like structures in Xenopus. The actin stars observed in Xenopus animal cap cells assembled at the apical surface of epithelial cells in a Rac-independent manner and their formation was accompanied by recruitment of N-WASP, suggesting that the Eps8/Abi1 complex is capable of regulating the localization and/or activity of actin nucleators. We also found that Eps8 recruits Dishevelled to the plasma membrane and actin filaments suggesting that Eps8 might participate in non-canonical Wnt/Polarity signaling. Consistent with this idea, mis-expression of Eps8 in dorsal regions of Xenopus embryos resulted in gastrulation defects. Conclusions: Together, these results suggest that Eps8 plays multiple roles in modulating actin filament organization, possibly through its interaction with distinct sets of actin regulatory complexes. Furthermore, the finding that Eps8 interacts with Dsh and induced gastrulation defects provides evidence that Eps8 might participate in non-canonical Wnt signaling to control cell movements during vertebrate development.

  • Regulation of Pancreatic Cancer Cell Migration and Invasion by RhoC GTPase and Caveolin-1 - Background: : In the current study we investigated the role of cav-1 in pancreatic adenocarcinoma (PC) cell migration and invasion; initial steps in metastasis. Caveolin-1 (cav-1) is the major structural protein in caveolae; small Omega-shaped invaginations within the plasma membrane. Caveolae are involved in signal transduction, wherein cav-1 acts as a scaffolding protein to organize multiple molecular complexes regulating a variety of cellular events. Recent evidence suggests a role for cav-1 in promoting cancer cell migration, invasion and metastasis; however, the molecular mechanisms have not been described. The small monomeric GTPases are among several molecules which associate with cav-1. Classically, the Rho GTPases control actin cytoskeletal reorganization during cell migration and invasion. RhoC GTPase is overexpressed in aggressive cancers that metastasize and is the predominant GTPase in PC. Like several GTPases, RhoC contains a putative cav-1 binding motif. Results: : Analysis of 10 PC cell lines revealed high levels of cav-1 expression in lines derived from primary tumors and low expression in those derived from metastases. Comparison of the BxPC-3 (derived from a primary tumor) and HPAF-II (derived from a metastasis) demonstrates a reciprocal relationship between cav-1 expression and p42/p44 Erk activation with PC cell migration, invasion, RhoC GTPase and p38 MAPK activation. Furthermore, inhibition of RhoC or p38 activity in HPAF-II cells leads to partial restoration of cav-1 expression. Conclusions: : Cav-1 expression restricts RhoC GTPase activation and subsequent activation of the p38 MAPK pathway in primary PC cells thus restricting migration and invasion. In contrast, loss of cav-1 expression leads to RhoC-mediated migration and invasion in metastatic PC cells.

  • Rel/Nuclear factor-kappa B Apoptosis Pathways in Human Cervical Cancer Cells - Cervical cancer is considered a common yet preventable cause of death in women. It has been estimated that about 420 women out of the 1400 women diagnosed with cervical cancer will die during 5 years from diagnosis. This review addresses the pathogenesis of cervical cancer in humans with a special emphasis on the human papilloma virus as a predominant cause of cervical cancer in humans. The current understanding of apoptosis and regulators of apoptosis as well as their implication in carcinogenesis will follow. A special focus will be given to the role of Rel/NF-kappa B family of genes in the growth and chemotherapeutic treatment of the malignant HeLa cervical cells emphasizing on Xrel3, a cRel homologue.

  • Relationship between the expression of cyclooxygenase 2 and MDR1/P-glycoprotein in invasive breast cancers and their prognostic significance - IntroductionRecent reports suggest that expression of the cyclooxygenase 2 (COX-2) enzyme may up-regulate expression of MDR1/P-glycoprotein (MDR1/P-gp), an exponent of resistance to cytostatic drugs. The present study aimed at examining the relationship between the expression of COX-2 and of MDR1/P-gp in a group of breast cancer cases. Methods: Immunohistochemical reactions were performed using monoclonal antibodies against COX-2 and MDR1/P-gp on samples originating from 104 cases of primary invasive breast cancer. Results: COX-2-positive cases were shown to demonstrate higher expression of MDR1/P-gp (P < 0.0001). The studies also demonstrate that COX-2 expression was typical for cases of a higher grade (P = 0.01), a shorter overall survival time (P < 0.0001) and a shorter progression-free time (P < 0.0001). In the case of MDR1/P-gp, its higher expression characterised cases of a higher grade (P < 0001), with lymph node involvement (P < 0001), and shorter overall survival (P < 0.0001) and progression-free time (P < 0.0001). Conclusion: Our studies confirmed the unfavourable prognostic significance of COX-2 and MDR1/P-gp. We also document a relationship between COX-2 and MDR1/P-gp, which suggests that COX-2 inhibitors should be investigated in trials as a treatment supplementary to chemotherapy of breast cancers.

  • Relationship of patients' age to histopathological features of breast tumours in BRCA1 and BRCA2 and mutation-negative breast cancer families - IntroductionOur aim was to evaluate the relationship of patients' age to histopathological features of hereditary breast tumours in a series of breast cancer families not selected for age at diagnosis. In sporadic breast cancer, tumours from premenopausal patients have been shown to differ from those of postmenopausal patients, but this phenomenon has been little studied among familial patients. Methods: Representative areas of all available breast cancer tissue specimens (n = 262) from 25 BRCA1, 20 BRCA2, and 74 non-BRCA1/2 breast cancer families were punched into a tissue microarray. Immunohistochemical staining of oestrogen receptor, progesterone receptor, ERBB2, and p53 as well as the histology and grade of tumours in these three groups of families were studied in different age groups and compared with each other. Results: We found that only breast cancers from young (<50 years) BRCA1+ patients represent features documented as being typical of BRCA1-associated cancers, such as high tumour grade, negativity for oestrogen and progesterone receptors, and overexpression of p53. Among the BRCA2 families, the opposite was found, with a significantly higher frequency of tumours negative for oestrogen and progesterone receptors among the older patients than among the other groups, but no distinctive tumour characteristics among the younger BRCA2 patients. Conclusion: Tumours of BRCA1 and BRCA2 carriers aged 50 years or more differed significantly from those of younger carriers. This difference may reflect different biological behaviour and pathways of tumour development among the older and the younger BRCA1 and BRCA2 patients, with impact also on prognosis and survival.

  • Remembering George L. Wied, M.D., February 7, 1921-July 25, 2004 - A personal tribute to George L. Wied, M.D., a founder of the medical subspecialty, cytopathology, who died July 25, 2004.

  • Resin Tissue Microarrays: a Universal Format for Immunohistochemistry -

    Tissue microarray (TMA) technology allows the miniaturization and characterization of multiple tissue samples on a single slide and commonly uses formalin-fixed paraffin-embedded (FFPE) tissue or acetone-fixed frozen tissue. The former provides good morphology but can compromise antigenicity, whereas the latter provides compromised morphology with good antigenicity. Here, we report the development of TMAs in glycol methacrylate resin, which combine the advantages of both methods in one embedding format. Freshly collected tissue fixed in –20C acetone or 10% neutral buffered formaldehyde were cored and arrayed into an intermediary medium of 2% agarose before infiltration of the agarose array with glycol methacrylate resin. Acetone-fixed resin TMA demonstrated improved morphology over acetone-fixed frozen TMA, with no loss of antigenicity. Staining for extracellular, cell surface, and nuclear antigens could be realized with monoclonal and polyclonal antibodies as well as with monomeric single-chain Fv preparations. In addition, when compared with FFPE TMA, formalin-fixed tissue in a resin TMA gave enhanced morphology and subcellular detail. Therefore, resin provides a universal format for the construction of TMAs, providing improved tissue morphology while retaining antigenicity, allows thin-section preparation, and could be used to replace preparation of frozen and FFPE TMAs for freshly collected tissue. (J Histochem Cytochem 53:1189–1197, 2005)


  • Resin Tissue Microarrays: a Universal Format for Immunohistochemistry -

    Tissue microarray (TMA) technology allows the miniaturization and characterization of multiple tissue samples on a single slide and commonly uses formalin-fixed paraffin-embedded (FFPE) tissue or acetone-fixed frozen tissue. The former provides good morphology but can compromise antigenicity, whereas the latter provides compromised morphology with good antigenicity. Here, we report the development of TMAs in glycol methacrylate resin, which combine the advantages of both methods in one embedding format. Freshly collected tissue fixed in –20C acetone or 10% neutral buffered formaldehyde were cored and arrayed into an intermediary medium of 2% agarose before infiltration of the agarose array with glycol methacrylate resin. Acetone-fixed resin TMA demonstrated improved morphology over acetone-fixed frozen TMA, with no loss of antigenicity. Staining for extracellular, cell surface, and nuclear antigens could be realized with monoclonal and polyclonal antibodies as well as with monomeric single-chain Fv preparations. In addition, when compared with FFPE TMA, formalin-fixed tissue in a resin TMA gave enhanced morphology and subcellular detail. Therefore, resin provides a universal format for the construction of TMAs, providing improved tissue morphology while retaining antigenicity, allows thin-section preparation, and could be used to replace preparation of frozen and FFPE TMAs for freshly collected tissue. (J Histochem Cytochem 53:1189–1197, 2005)


  • Response of SI cortex to ipsilateral, contralateral and bilateral flutter stimulation in the cat - Background: While SII cortex is considered to be the first cortical stage of the pathway that integrates tactile information arising from both sides of the body, SI cortex is generally not considered as a region in which neuronal response is modulated by simultaneous stimulation of bilateral (and mirror-image) skin sites. Results: Optical intrinsic signal imaging was used to evaluate the response of SI and SII in the same hemisphere to 25 Hz sinusoidal vertical skin displacement stimulation ("skin flutter") applied contralaterally, ipsilaterally, and bilaterally (simultaneously) to the central pads of the forepaws. A localized increase in absorbance in both SI and SII occurred in response to both contralateral and bilateral flutter stimulation. Ipsilateral flutter stimulation evoked a localized increase in absorbance in SII, but little or no change in SI absorbance. In the forepaw representational region of SI, however, bilateral stimulation of the central pads evoked a response substantially smaller (approximately 30–35% smaller) than the response to flutter stimulation of the contralateral central pad. Conclusion: The finding that the response of SI cortex to bilateral central pad flutter stimulation is substantially smaller than the response evoked by a contralateral flutter stimulus, together with the recently published observation that a region located posteriorly in SII responds with a substantially larger response to a bilateral flutter stimulus than the response evoked from the contralateral central pad, lead us to propose that the SI activity evoked by contralateral skin stimulation is suppressed/inhibited (via corticocortical connections between SII and SI in the same hemisphere) by the activity a simultaneous ipsilateral skin stimulus evokes in posterior SII.

  • Responses of genes involved in cell cycle control to diverse DNA damaging chemicals in human lung adenocarcinoma A549 cells - Background: Many anticancer agents and carcinogens are DNA damaging chemicals and exposure to such chemicals results in the deregulation of cell cycle progression. The molecular mechanisms of DNA damage-induced cell cycle alteration are not well understood. We have studied the effects of etoposide (an anticancer agent), cryptolepine (CLP, a cytotoxic alkaloid), benzo[a]pyrene (BaP, a carcinogenic polycyclic aromatic hydrocarbon) and 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP, a cooked-meat derived carcinogen) on the expression of cell cycle regulatory genes to understand the molecular mechanisms of the cell cycle disturbance. Results: A549 cells were treated with DMSO or chemicals for up to 72 h and periodically sampled for cell cycle analysis, mRNA and protein expression. DMSO treated cells showed a dominant G1 peak in cell cycle at all times examined. Etoposide and CLP both induced G2/M phase arrest yet the former altered the expression of genes functioning at multiple phases, whilst the latter was more effective in inhibiting the expression of genes in G2-M transition. Both etoposide and CLP induced an accumulation of p53 protein and upregulation of p53 transcriptional target genes. Neither BaP nor PhIP had substantial phase-specific cell cycle effect, however, they induced distinctive changes in gene expression. BaP upregulated the expression of CYP1B1 at 6-24 h and downregulated many cell cycle regulatory genes at 48-72 h. By contrast, PhIP increased the expression of many cell cycle regulatory genes. Changes in the expression of key mRNAs were confirmed at protein level. Conclusion: Our experiments show that DNA damaging agents with different mechanisms of action induced distinctive changes in the expression pattern of a panel of cell cycle regulatory genes. We suggest that examining the genomic response to chemical exposure provides an exceptional opportunity to understand the molecular mechanism involved in cellular response to toxicants.

  • Restricted Distribution of mRNAs Encoding a Sarcoplasmic Reticulum or Transverse Tubule Protein in Skeletal Myofibers -

    Calsequestrin (CSQ) and dihydropyridine receptor (DHPR) are muscle cell proteins that are directed into the endoplasmic reticulum (ER) during translation. The former is subsequently found in the sarcoplasmic reticulum (SR) and the latter in the transverse tubule membrane. To elucidate the potential role of mRNA targeting within muscle cells, we have analyzed the localization of CSQ and DHPR proteins and mRNAs in primary cultured rat myotubes, in skeletal muscle cryosections, and in isolated flexor digitorum brevis muscle fibers. In the myotube stage of differentiation, the mRNAs distributed throughout the cell, mimicking the distribution of the endogenous ER marker proteins. In the adult skeletal myofibers, however, both CSQ and DHPR1 transcripts located perinuclearly and in cross-striations flanking Z lines beneath the sarcolemma, a distribution pattern that sharply contrasted the interfibrillar distribution of typical ER proteins. Interestingly, all nuclei of the myofibers were transcriptionally active. In summary, the mRNAs encoding either a resident SR protein or a transverse tubule protein were located beneath the sarcolemma, implying that translocation of the respective proteins to the lumen of ER takes place at this location. (J Histochem Cytochem 53:217–227, 2005)


  • Rethinking the Coagulation Cascade - The concept of coagulation as a 'cascade' of proteolytic reactions was a conceptual breakthrough in understanding how the coagulation process acts as a biologic amplifier. The model that it evolved into, with 'extrinsic' and 'intrinsic' pathways meeting in a common pathway, delineates the interactions between the coagulation proteins and provides a framework for interpreting the common screening coagulation tests. The coagulation 'cascade' has significant limitations as a model of how hemostasis occurs in vivo, however. This article describes how the modern view of hemostasis has evolved to emphasize the role of cells in controlling and directing the coagulation reactions. It also highlights how host factors that are not part of the coagulation process per se can influence the effectiveness of coagulation.

  • Retraction: Inactivation of MAP kinase signalling in Myc Transformed Cells and Rescue by LiCl inhibition of GSK3 - The corresponding author submitted this article [1] to Molecular Cancer on the assumption that the co-author had agreed to the submission. Since this is not the case, the authors are retracting the article. The corresponding author is deeply sorry for any inconvenience this may have caused to the editorial and publishing staff. An apology is also extended to the readers.

  • Reversing the Effects of Formalin Fixation with Citraconic Anhydride and Heat: A Universal Antigen Retrieval Method -

    Formalin is a commonly used fixative for tissue preservation in pathology laboratories. A major adverse effect of this fixative is the concealing of tissue antigens by protein cross-linking. To achieve a universal antigen retrieval method for immunohistochemistry under a constant condition, we developed a new method in which the effects of formalin fixation were reversed with citraconic anhydride (a reversible protein cross-linking agent) plus heating. Formalin-fixed, paraffin-embedded tissues from various organs were examined for immunohistochemical localization of a wide variety of antigens. Deparaffinized tissue sections were placed in an electric kitchen pot containing 0.05% citraconic anhydride solution, pH 7.4, and the pot was set at "keep warm" temperature mode of 98C for 45 min. This mode allowed heating the sections at a constant temperature. The sections were then washed in buffer solution and immunostained using a labeled streptavidin–biotin method using an automated stainer. In general, formalin-fixed tissues demonstrated specific immunostainings comparable to that in fresh frozen tissues and significantly more enhanced than after conventional antigen retrieval methods. In particular, even difficult-to-detect antigens such as CD4, cyclin D1, granzyme ßbeta;, bcl-6, CD25, and lambda chain revealed distinct immunostainings. Different classes of antigens such as cellular markers and receptors, as well as cytoplasmic and nuclear proteins, consistently produced enhanced reactions. This method provides efficient antigen retrieval for successful immunostaining of a wide variety of antigens under an optimized condition. It also allows standardization of immunohistochemistry for formalin-fixed tissues in pathology laboratories, eliminating inter-laboratory discrepancies in results for accurate clinical and research studies.

    (J Histochem Cytochem 53:3–11, 2005)


  • RLIP76, a non-ABC transporter, and drug resistance in epilepsy - Background: Permeability of the blood-brain barrier is one of the factors determining the bioavailability of therapeutic drugs and resistance to chemically different antiepileptic drugs is a consequence of decreased intracerebral accumulation. The ABC transporters, particularly P-glycoprotein, are known to play a role in antiepileptic drug extrusion, but are not by themselves sufficient to fully explain the phenomenon of drug-resistant epilepsy. Proteomic analyses of membrane protein differentially expressed in epileptic foci brain tissue revealed the frequently increased expression of RLIP76/RALBP1, a recently described non-ABC multi-specific transporter. Because of a significant overlap in substrates between P-glycoprotein and RLIP76, present studies were carried out to determine the potential role of RLIP76 in AED transport in the brain. Results: RLIP76 was expressed in brain tissue, preferentially in the lumenal surface of endothelial cell membranes. The expression was most prominent in blood brain barrier tissue from excised epileptic foci. Saturable, energy-dependent, anti-gradient transport of both phenytoin and carbamazepine were demonstrated using recombinant RLIP76 reconstituted into artificial membrane liposomes. Immunotitration studies of transport activity in crude membrane vesicles prepared from whole-brain tissue endothelium showed that RLIP76 represented the dominant transport mechanism for both drugs. RLIP76-/- knockout mice exhibited dramatic toxicity upon phenytoin administration due to decreased drug extrusion mechanisms at the blood-brain barrier. Conclusions: We conclude that RLIP76 is the predominant transporter of AED in the blood brain barrier, and that it may be a transporter involved in mechanisms of drug-resistant epilepsy.

  • Role of Immunohistochemistry in the Diagnosis and Progression of Follicular Epithelium-Derived Thyroid Carcinoma. -

  • S-Nitrosothiols modulate G protein-coupled receptor signaling in a reversible and highly receptor-specific manner - Background: Recent studies indicate that the G protein-coupled receptor (GPCR) signaling machinery can serve as direct target of reactive oxygen species, including nitric oxide (NO) and S-nitrosothiols (RSNOs). To gain a broader view, as how receptor-dependent G protein activation - an early step in signal transduction - might be affected by RSNOs, we have studied several receptors coupling to the Gi family of G proteins in their native cellular environment using the powerful functional approach of [35S]GTP-gamma-S autoradiography with brain cryostat sections in combination with classical G protein activation assays. Results: We demonstrate that RSNOs, like S-nitrosoglutathione (GSNO) and S-nitrosocysteine (CysNO), can modulate GPCR signaling via reversible, thiol-sensitive mechanisms likely involving S-nitrosylation. RSNOs are capable of very targeted regulation, as they potentiate the signaling of some receptors (exemplified by the M2/M4 muscarinic acetylcholine receptors), inhibit that of others (P2Y12 purinergic, LPA1 lysophosphatidic acid, and cannabinoid CB1 receptors), and yet only marginally affect that of others, such as adenosine A1, mu-opioid, and opiate related receptors. Amplification of M2/M4 muscarinic responses is explained by an accelerated rate of guanine nucleotide exchange, as well as an increased number of high-affinity [35S]GTP-gamma-S binding sites available for the agonist-liganded receptor. GSNO amplified human M4 receptor signaling also under heterologous expression in CHO cells, but the effect diminished with increasing constitutive receptor activity. RSNOs markedly inhibited P2Y12 receptor signaling in native tissues (rat brain and human platelets), but failed to affect human P2Y12 receptor signaling under heterologous expression in CHO cells, indicating that the native cellular signaling partners, rather than the P2Y12 receptor protein, act as molecular target of this action. Conclusion: These in vitro studies show for the first time in a broader general context that RSNOs are capable of modulating GPCR signaling in a reversible and highly receptor-specific manner. Given that the enzymatic machinery responsible for endogenous NO production is apposed in close proximity with the GPCR signaling complex, especially with that for several receptors whose signaling is shown here to be modulated by exogenous RSNOs, our data suggest that GPCR signaling in vivo is likely subject to substantial, and highly receptor-specific modulation by NO-derived RSNOs.

  • Salivary changes and dental caries as potential oral markers of autoimmune salivary gland dysfunction in primary Sjögren's syndrome - Background: the classification criteria for primary Sjögren's syndrome (pSS) include a number of oral components. In this study we evaluated if salivary flow and composition as well as dental caries are oral markers of disease severity in pSS. Methods: in 20 patients fulfilling the American-European Consensus criteria for pSS and 20 age-matched healthy controls whole and parotid saliva flow rates and composition, measures of oral dryness, scores of decayed, missing and filled tooth surfaces (DMFS), periodontal indices, oral hygiene, and dietary habits were examined. Results: in pSS, salivary flow rates, pH, and buffer capacities were lower, and DMFS, salivary sodium and chloride concentrations higher than in the healthy controls. DMFS also correlated inversely to salivary flow rates and positively to oral dryness. Apart from slightly increased gingival index, and more frequent dental visits in pSS, the periodontal condition, oral hygiene or sugar intake did not differ between these two groups. In pSS, findings were correlated to labial salivary gland focus score (FS) and presence of serum-autoantibodies to SSA/SSB (AB). The patients having both presence of AB and the highest FS (>2) also had the highest salivary sodium and chloride concentrations, the lowest salivary phosphate concentrations, lowest salivary flow rates, and highest DMFS compared to those with normal salivary concentrations of sodium and chloride at a given flow rate. Conclusion: the salivary changes observed in some pSS patients reflect impaired ductal salt reabsorption, but unaffected acinar transport mechanisms, despite low salivary secretion. Our results suggest that changes in salivary flow and composition as well as dental caries may serve as potential markers of the extent of autoimmune-mediated salivary gland dysfunction in pSS. The study also indicates that the ductal epithelium is functionally affected in some pSS patients, which calls for future pathophysiological studies on the mechanisms underlying this impaired salt reabsorption.

  • Screening and Identification of Differentially Expressed Transcripts in Circulating Cells of Prostate Cancer Patients Using Suppression Subtractive Hybridization - Background: Tumor metastasis and changes in host immunosurveillance are important components in cancer development. Tumor cell invasion into the bloodstream is an essential step for systemic metastasis. Currently, the detection of tumor cells in the circulation is mainly dependent upon the utilization of known epithelial cell markers. However, expression of these molecules is not limited to cancer patients; healthy people also have a small number of epithelial cells in their circulation. Utilizing these markers to detect circulating tumor cells (CTCs) cannot adequately explain the mechanisms of tumor cell survival or their development of metastatic potential in peripheral blood. The immune system can also evolve along with the cancer, actually promoting or selecting the outgrowth of tumor variants. Unfortunately, both metastasis and immunosurveillance remain mysterious and are debatable because we have yet to define the molecules that participate in these processes. We are interested in identifying the existence of expressed genes, or mRNA species, that are specifically associated with circulating cells of cancer-bearing patients using prostate cancer (PCa) as a model. Results: We established two comprehensive subtracted cDNA libraries using a molecular technique called suppression subtractive hybridization. This technique selectively amplifies transcripts that are specifically expressed in circulating cells of either PCa patients or healthy men. Following sequencing reaction, we showed that 17 out of 23 (73.9%) sequenced clones did not match any mRNAs in the GenBank database. This result suggests that genes associated with alterations in circulating cells of cancer-bearing patients are largely unknown. Semi-quantitative RT-PCR confirmed that two genes are up-regulated in circulating cells of PCa patients, whereas another two genes are down-regulated in the same patients. Conclusions: The comprehensive gene expression analysis is capable of identifying differentially expressed genes in circulating cells of healthy men and PCa patients. We did not attempt to enrich specific cell types in this study because phenotypes of CTCs and subsets of leukocytes participating in immunosurveillance remain largely unknown. Continuous studies of these differentially expressed genes will eventually lead us to understand the mechanisms involved in tumor metastasis and immune modulation during cancer development.

  • Se-methylselenocysteine inhibits phosphatidylinositol 3-kinase activity of mouse mammary epithelial tumor cells in vitro - IntroductionSe-methylselenocysteine (MSC), a naturally occurring selenium compound, is a promising chemopreventive agent against in vivo and in vitro models of carcinogen-induced mouse and rat mammary tumorigenesis. We have demonstrated previously that MSC induces apoptosis after a cell growth arrest in S phase in a mouse mammary epithelial tumor cell model (TM6 cells) in vitro. The present study was designed to examine the involvement of the phosphatidylinositol 3-kinase (PI3-K) pathway in TM6 tumor model in vitro after treatment with MSC. Methods: Synchronized TM6 cells treated with MSC and collected at different time points were examined for PI3-K activity and Akt phosphorylation along with phosphorylations of Raf, MAP kinase/ERK kinase (MEK), extracellular signal-related kinase (ERK) and p38 mitogen-activated protein kinase (MAPK). The growth inhibition was determined with a [3H]thymidine incorporation assay. Immunoblotting and a kinase assay were used to examine the molecules of the survival pathway. Results: PI3-K activity was inhibited by MSC followed by dephosphorylation of Akt. The phosphorylation of p38 MAPK was also downregulated after these cells were treated with MSC. In parallel experiments MSC inhibited the Raf–MEK–ERK signaling pathway. Conclusion: These studies suggest that MSC blocks multiple signaling pathways in mouse mammary tumor cells. MSC inhibits cell growth by inhibiting the activity of PI3-K and its downstream effector molecules in mouse mammary tumor cells in vitro.

  • Second edition of 'The Bethesda System for reporting cervical cytology' – atlas, website, and Bethesda interobserver reproducibility project - A joint task force of the American Society of Cytopathology (ASC) and the National Cancer Institute (NCI) recently completed a 2-year effort to revise the Bethesda System "blue book" atlas and develop a complementary web-based collection of cervical cytology images. The web-based collection of images is housed on the ASC website, which went live on November 5th, 2003; it can be directly accessed at http://www.cytopathology.org/NIH/.

  • Selection of Unrelated Donors for Hematopoietic Cell Transplantation - Transplants from partially human leukocyte antigens (HLA)-incompatible relatives are associated with an increased risk of graft rejection, graft-versus-host disease (GVHD), and lower survival, which are correlated with the degree of disparity. For patients without an HLA-matched sibling, the preferred donors of hematopoietic cells remain HLA-compatible, unrelated volunteers. The hurdle for a wider application of hematopoietic cell transplantation is the enormous polymorphism of HLA genes that makes unrelated individuals unlikely to match randomly. The identification of functional HLA genes and their poly-morphic alleles, the development of precise and effective tissue typing techniques, and the assembly of large volunteer registries worldwide that exceed 9 million HLA-typed individuals have made it feasible to transplant hemato-poietic stem cells from well-matched, unrelated donors for most patients.

  • Selective estrogen receptor modulators inhibit growth and progression of premalignant lesions in a mouse model of ductal carcinoma in situ - IntroductionDuctal carcinoma in situ (DCIS) is a noninvasive premalignant lesion and is considered a precursor to invasive carcinoma. DCIS accounts for nearly 20% of newly diagnosed breast cancer, but the lack of experimentally amenable in vivo DCIS models hinders the development of treatment strategies. Here, we demonstrate the utility of a mouse transplantation model of DCIS for chemoprevention studies using selective estrogen receptor modulators (SERMs). This model consists of a set of serially transplanted lines of genetically engineered mouse mammary intraepithelial neoplasia (MIN) outgrowth (MIN-O) tissue that have stable characteristics. We studied the ovarian-hormone-responsiveness of one of the lines with a particular focus on the effects of two related SERMs, tamoxifen and ospemifene. Methods: The estrogen receptor (ER) status and ovarian-hormone-dependence of the mouse MIN outgrowth tissue were determined by immunohistochemistry and ovarian ablation. The effects of tamoxifen and ospemifene on the growth and tumorigenesis of MIN outgrowth were assessed at 3 and 10 weeks after transplantation. The effects on ER status, cell proliferation, and apoptosis were studied with immunohistochemistry. Results: The MIN-O was ER-positive and ovarian ablation resulted in reduced MIN-O growth and tumor development. Likewise, tamoxifen and ospemifene treatments decreased the MIN growth and tumor incidence in comparison with the control (P < 0.01). Both SERMs significantly decreased cell proliferation. Between the two SERM treatment groups, there were no statistically significant differences in MIN-O size, tumor latency, or proliferation rate. In contrast, the ospemifene treatment significantly increased ER levels while tamoxifen significantly decreased them. Conclusion: Tamoxifen and ospemifene inhibit the growth of premalignant mammary lesions and the progression to invasive carcinoma in a transplantable mouse model of DCIS. The inhibitory effects of these two SERMs are similar except for their effects on ER modulation. These differences in ER modulation may suggest different mechanisms of action between the two related SERMs and may portend different long-term outcomes. These data demonstrate the value of this model system for preclinical testing of antiestrogen or other therapies designed to prevent or delay the malignant transformation of premalignant mammary lesions in chemoprevention.

  • SF-1 a key player in the development and differentiation of steroidogenic tissues - Since its discovery in the early 1990s, the orphan nuclear receptor SF-1 has been attributed a central role in the development and differentiation of steroidogenic tissues. SF-1 controls the expression of all the steroidogenic enzymes and cholesterol transporters required for steroidogenesis as well as the expression of steroidogenesis-stimulating hormones and their cognate receptors. SF-1 is also an essential regulator of genes involved in the sex determination cascade. The study of SF-1 null mice and of human mutants has been of great value to demonstrate the essential role of this factor in vivo, although the complete adrenal and gonadal agenesis in knock-out animals has impeded studies of its function as a transcriptional regulator. In particular, the role of SF-1 in the hormonal responsiveness of steroidogenic genes promoters is still a subject of debate. This extensive review takes into account recent data obtained from SF-1 haploinsufficient mice, pituitary-specific knock-outs and from transgenic mice experiments carried out with SF-1 target gene promoters. It also summarizes the pros and cons regarding the presumed role of SF-1 in cAMP signalling.

  • Smooth Muscle-specific {alpha} Tropomyosin Is a Marker of Fully Differentiated Smooth Muscle in Lung -

    Tropomyosin (Tm) is one of the major components of smooth muscle. Currently it is impossible to easily distinguish the two major smooth muscle (sm) forms of Tm at a protein level by immunohistochemistry due to lack of specific antibodies. -sm Tm contains a unique 2a exon not found in any other Tm. We have produced a polyclonal antibody to this exon that specifically detects -sm Tm. We demonstrate here the utility of this antibody for the study of smooth muscle. The tissue distribution of -sm Tm was shown to be highly specific to smooth muscle. -sm Tm showed an identical profile and tissue colocalization with -sm actin both by Western blotting and immunohistochemistry. Using lung as a model organ system, we examined the developmental appearance of -sm Tm in comparison to -sm actin in both the mouse and human. -sm Tm is a late-onset protein, appearing much later than actin in both species. There were some differences in onset of appearance in vascular and airway smooth muscle with airway appearing earlier. -sm Tm can therefore be used as a good marker of mature differentiated smooth muscle cells. Along with -sm actin and sm-myosin antibodies, -sm Tm is a valuable tool for the study of smooth muscle. (J Histochem Cytochem 53:875–883, 2005)


  • Smooth Muscle-specific {alpha} Tropomyosin Is a Marker of Fully Differentiated Smooth Muscle in Lung -

    Tropomyosin (Tm) is one of the major components of smooth muscle. Currently it is impossible to easily distinguish the two major smooth muscle (sm) forms of Tm at a protein level by immunohistochemistry due to lack of specific antibodies. -sm Tm contains a unique 2a exon not found in any other Tm. We have produced a polyclonal antibody to this exon that specifically detects -sm Tm. We demonstrate here the utility of this antibody for the study of smooth muscle. The tissue distribution of -sm Tm was shown to be highly specific to smooth muscle. -sm Tm showed an identical profile and tissue colocalization with -sm actin both by Western blotting and immunohistochemistry. Using lung as a model organ system, we examined the developmental appearance of -sm Tm in comparison to -sm actin in both the mouse and human. -sm Tm is a late-onset protein, appearing much later than actin in both species. There were some differences in onset of appearance in vascular and airway smooth muscle with airway appearing earlier. -sm Tm can therefore be used as a good marker of mature differentiated smooth muscle cells. Along with -sm actin and sm-myosin antibodies, -sm Tm is a valuable tool for the study of smooth muscle. (J Histochem Cytochem 53:875–883, 2005)


  • Somatic mutation and gain of copy number of PIK3CA in human breast cancer - IntroductionPhosphatidylinositol 3-kinases (PI3Ks) are a group of lipid kinases that regulate signaling pathways involved in cell proliferation, adhesion, survival, and motility. Even though PIK3CA amplification and somatic mutation have been reported previously in various kinds of human cancers, the genetic change in PIK3CA in human breast cancer has not been clearly identified. Methods: Fifteen breast cancer cell lines and 92 primary breast tumors (33 with matched normal tissue) were used to check somatic mutation and gene copy number of PIK3CA. For the somatic mutation study, we specifically checked exons 1, 9, and 20, which have been reported to be hot spots in colon cancer. For the analysis of the gene copy number, we used quantitative real-time PCR and fluorescence in situ hybridization. We also treated several breast cancer cells with the PIK3CA inhibitor LY294002 and compared the apoptosis status in cells with and without PIK3CA mutation. Results: We identified a 20.6% (19 of 92) and 33.3% (5 of 15) PIK3CA somatic mutation frequency in primary breast tumors and cell lines, respectively. We also found that 8.7% (8 of 92) of the tumors harbored a gain of PIK3CA gene copy number. Only four cases in this study contained both an increase in the gene copy number and a somatic mutation. In addition, mutation of PIK3CA correlated with the status of Akt phosphorylation in some breast cancer cells and inhibition of PIK3CA-induced increased apoptosis in breast cancer cells with PIK3CA mutation. Conclusion: Somatic mutation rather than a gain of gene copy number of PIK3CA is the frequent genetic alteration that contributes to human breast cancer progression. The frequent and clustered mutations within PIK3CA make it an attractive molecular marker for early detection and a promising therapeutic target in breast cancer.

  • Soy isoflavone glycitein protects against beta amyloid-induced toxicity and oxidative stress in transgenic Caenorhabditis elegans - Background: Epidemiological studies have associated estrogen replacement therapy with a lower risk of developing Alzheimer's disease, but a higher risk of developing breast cancer and certain cardiovascular disorders. The neuroprotective effect of estrogen prompted us to determine potential therapeutic impact of soy-derived estrogenic compounds. Transgenic C. elegans, that express human beta amyloid (A-beta), were fed with soy derived isoflavones genistein, daidzin and glycitein (100 ug/ml) and then examined for A-beta induced paralysis and oxidative stress. Results: Among the three compounds tested, only glycitein alleviated A-beta expression-induced paralysis in the transgenic C. elegans. This activity of glycitein correlated with a reduced level of hydrogen peroxide in the transgenic C. elegans. In vitro scavenging effects of glycitein on three types of reactive oxygen species confirmed its antioxidant properties. Furthermore, the transgenic C. elegans fed with glycitein exhibited reduced formation of beta amyloid. Conclusions: These findings suggest that a specific soy isoflavone glycitein can suppress A-beta toxicity through antioxidative activity, thus may have therapeutic potential for prevention of beta amyloid associated neurodegenerative disorders.

  • SPARC-thrombospondin-2-double-null Mice Exhibit Enhanced Cutaneous Wound Healing and Increased Fibrovascular Invasion of Subcutaneous Polyvinyl Alcohol Sponges -

    Secreted protein acidic and rich in cysteine (SPARC) and thrombospondin-2 (TSP-2) are structurally unrelated matricellular proteins that have important roles in cell–extracellular matrix (ECM) interactions and tissue repair. SPARC-null mice exhibit accelerated wound closure, and TSP-2-null mice show an overall enhancement in wound healing. To assess potential compensation of one protein for the other, we examined cutaneous wound healing and fibrovascular invasion of subcutaneous sponges in SPARC-TSP-2 (ST) double-null and wild-type (WT) mice. Epidermal closure of cutaneous wounds was found to occur significantly faster in ST-double-null mice, compared with WT animals: histological analysis of dermal wound repair revealed significantly more mature phases of healing at 1, 4, 7, 10, and 14 days after wounding, and electron microscopy showed disrupted ECM at 14 days in these mice. ST-double-null dermal fibroblasts displayed accelerated migration, relative to WT fibroblasts, in a wounding assay in vitro, as well as enhanced contraction of native collagen gels. Zymography indicated that fibroblasts from ST-double-null mice also produced higher levels of matrix metalloproteinase (MMP)-2. These data are consistent with the increased fibrovascular invasion of subcutaneous sponge implants seen in the double-null mice. The generally accelerated wound healing of ST-double-null mice reflects that described for the single-null animals. Importantly, the absence of both proteins results in elevated MMP-2 levels. SPARC and TSP-2 therefore perform similar functions in the regulation of cutaneous wound healing, but fine-tuning with respect to ECM production and remodeling could account for the enhanced response seen in ST-double-null mice.

    (J Histochem Cytochem 53:571–581, 2005)


  • SPARC-thrombospondin-2-double-null Mice Exhibit Enhanced Cutaneous Wound Healing and Increased Fibrovascular Invasion of Subcutaneous Polyvinyl Alcohol Sponges -

    Secreted protein acidic and rich in cysteine (SPARC) and thrombospondin-2 (TSP-2) are structurally unrelated matricellular proteins that have important roles in cell–extracellular matrix (ECM) interactions and tissue repair. SPARC-null mice exhibit accelerated wound closure, and TSP-2-null mice show an overall enhancement in wound healing. To assess potential compensation of one protein for the other, we examined cutaneous wound healing and fibrovascular invasion of subcutaneous sponges in SPARC-TSP-2 (ST) double-null and wild-type (WT) mice. Epidermal closure of cutaneous wounds was found to occur significantly faster in ST-double-null mice, compared with WT animals: histological analysis of dermal wound repair revealed significantly more mature phases of healing at 1, 4, 7, 10, and 14 days after wounding, and electron microscopy showed disrupted ECM at 14 days in these mice. ST-double-null dermal fibroblasts displayed accelerated migration, relative to WT fibroblasts, in a wounding assay in vitro, as well as enhanced contraction of native collagen gels. Zymography indicated that fibroblasts from ST-double-null mice also produced higher levels of matrix metalloproteinase (MMP)-2. These data are consistent with the increased fibrovascular invasion of subcutaneous sponge implants seen in the double-null mice. The generally accelerated wound healing of ST-double-null mice reflects that described for the single-null animals. Importantly, the absence of both proteins results in elevated MMP-2 levels. SPARC and TSP-2 therefore perform similar functions in the regulation of cutaneous wound healing, but fine-tuning with respect to ECM production and remodeling could account for the enhanced response seen in ST-double-null mice.

    (J Histochem Cytochem 53:571–581, 2005)


  • SPARC-thrombospondin-2-double-null Mice Exhibit Enhanced Cutaneous Wound Healing and Increased Fibrovascular Invasion of Subcutaneous Polyvinyl Alcohol Sponges -

    Secreted protein acidic and rich in cysteine (SPARC) and thrombospondin-2 (TSP-2) are structurally unrelated matricellular proteins that have important roles in cell–extracellular matrix (ECM) interactions and tissue repair. SPARC-null mice exhibit accelerated wound closure, and TSP-2-null mice show an overall enhancement in wound healing. To assess potential compensation of one protein for the other, we examined cutaneous wound healing and fibrovascular invasion of subcutaneous sponges in SPARC-TSP-2 (ST) double-null and wild-type (WT) mice. Epidermal closure of cutaneous wounds was found to occur significantly faster in ST-double-null mice, compared with WT animals: histological analysis of dermal wound repair revealed significantly more mature phases of healing at 1, 4, 7, 10, and 14 days after wounding, and electron microscopy showed disrupted ECM at 14 days in these mice. ST-double-null dermal fibroblasts displayed accelerated migration, relative to WT fibroblasts, in a wounding assay in vitro, as well as enhanced contraction of native collagen gels. Zymography indicated that fibroblasts from ST-double-null mice also produced higher levels of matrix metalloproteinase (MMP)-2. These data are consistent with the increased fibrovascular invasion of subcutaneous sponge implants seen in the double-null mice. The generally accelerated wound healing of ST-double-null mice reflects that described for the single-null animals. Importantly, the absence of both proteins results in elevated MMP-2 levels. SPARC and TSP-2 therefore perform similar functions in the regulation of cutaneous wound healing, but fine-tuning with respect to ECM production and remodeling could account for the enhanced response seen in ST-double-null mice.

    (J Histochem Cytochem 53:571–581, 2005)


  • Spatiotemporal receptive field properties of epiretinally recorded spikes and local electroretinograms in cats - Background: Receptive fields of retinal neural signals of different origin can be determined from extracellular microelectrode recordings at the inner retinal surface. However, locations and types of neural processes generating the different signal components are difficult to separate and identify. We here report epiretinal receptive fields (RFs) from simultaneously recorded spikes and local electroretinograms (LERGs) using a semi-chronic multi-electrode in vivo recording technique in cats. Broadband recordings were filtered to yield LERG and multi unit as well as single unit spike signals. RFs were calculated from responses to multifocal pseudo-random spatiotemporal visual stimuli registered at the retinal surface by a 7-electrode array. Results: LERGs exhibit spatially unimodal RFs always centered at the location of the electrode tip. Spike-RFs are either congruent with LERG-RFs (N=26/61) or shifted distally (N=35/61) but never proximally with respect to the optic disk. LERG-RFs appear at shorter latencies (11.9 ms +/- 0.5 ms, N=18) than those of spikes (18.6 ms +/- 0.4 ms, N=53). Furthermore, OFF-center spike-RFs precede and have shorter response rise times than ON-center spike-RFs. Our results indicate that displaced spike-RFs result from action potentials of ganglion cell axons passing the recording electrode en route to the optic disk while LERG-RFs are related to superimposed postsynaptic potentials of cells near the electrode tip. Conclusions: Besides contributing to the understanding of retinal function we demonstrate the caveats that come with recordings from the retinal surface, i.e., the likelihood of recordings from mixed sets of retinal neurons. Implications for the design of an epiretinal visual implant are discussed.

  • Sperm and Blastomere Aneuploidy Detection in Reproductive Genetics and Medicine -

    The use of multiple probes in fluorescence in situ hybridization (FISH) permits the simultaneous analysis of several chromosomes in both blastomeres and spermatozoa. Preimplantation genetic diagnosis (PGD) for aneuploidy provides information on embryonic chromosomal status, enabling the selection of embryos carrying aneuploid condition. This strategy directly affects implantation, as documented for patients with a poor prognosis for pregnancy, who have the tendency to generate high proportions of chromosomally abnormal embryos. PGD for aneuploidy also has contributed information on early phases in human embryology by clarifying the molecular basis in some cases of irregular development. Multicolor FISH has also been used to study chromosomes on spermatozoa. Experimental strategies and modifications enabled the analysis of samples with a very low number of sperm cells, including samples retrieved from the genital tract or directly from the testicular tissue. The results confirmed that the incidence of aneuploidy increases proportionally with the severity of the male-factor condition. This observation suggests that, in selected cases, the paternal contribution to aneuploidy in the developing conceptus could be more relevant than expected from general data from aborted fetuses and live births.

    (J Histochem Cytochem 53:261–267, 2005)


  • Stage-specific Expression of Dynein Light Chain-1 and Its Interacting Kinase, p21-activated Kinase-1, in Rodent Testes: Implications in Spermiogenesis -

    Mammalian spermatogenesis is a complex process involving regulatory interactions of many gene products. In this study, we found that dynein light chain-1 (DLC1), a component of the dynein motor complex, is highly expressed in mouse and rat testes. Immunohistochemically detectable levels of DLC1 are observed specifically in spermatids in steps 9–16 in distinct subcellular compartments: in steps 9–11, DLC1 is predominantly localized in the nucleus; in steps 12 and 13, it is found in both nucleus and cytoplasm; and in step 14–16, it is present exclusively in the cytoplasm. In addition, we found p21-activated kinase 1 (Pak1), a protein kinase that activates DLC1 by phosphorylating DLC1 at Serine 88, was also expressed during these stages of spermatogenesis. Pak1 was also expressed in Leydig cells, in preleptotene primary spermatocytes, and in round spermatids. The spermiogenic stage–specific expression of DLC1 suggests a role for DLC1 in chromatin condensation, spermatid shaping, and the final release of sperm from the spermatogenic epithelium. Further, Pak1 may also play a role in spermiogenesis by regulating DLC1 phosphorylation and, consequently, its function. (J Histochem Cytochem 53:1235–1243, 2005)


  • Stage-specific Expression of Dynein Light Chain-1 and Its Interacting Kinase, p21-activated Kinase-1, in Rodent Testes: Implications in Spermiogenesis -

    Mammalian spermatogenesis is a complex process involving regulatory interactions of many gene products. In this study, we found that dynein light chain-1 (DLC1), a component of the dynein motor complex, is highly expressed in mouse and rat testes. Immunohistochemically detectable levels of DLC1 are observed specifically in spermatids in steps 9–16 in distinct subcellular compartments: in steps 9–11, DLC1 is predominantly localized in the nucleus; in steps 12 and 13, it is found in both nucleus and cytoplasm; and in step 14–16, it is present exclusively in the cytoplasm. In addition, we found p21-activated kinase 1 (Pak1), a protein kinase that activates DLC1 by phosphorylating DLC1 at Serine 88, was also expressed during these stages of spermatogenesis. Pak1 was also expressed in Leydig cells, in preleptotene primary spermatocytes, and in round spermatids. The spermiogenic stage–specific expression of DLC1 suggests a role for DLC1 in chromatin condensation, spermatid shaping, and the final release of sperm from the spermatogenic epithelium. Further, Pak1 may also play a role in spermiogenesis by regulating DLC1 phosphorylation and, consequently, its function. (J Histochem Cytochem 53:1235–1243, 2005)


  • Stainable hepatic iron in 341 African American adults at coroner/medical examiner autopsy - Background: Results of previous autopsy studies indicate that increased hepatic iron stores or hepatic iron overload is common in African Americans dying in hospitals, but there are no reports of hepatic iron content in other cohorts of African Americans. Methods: We investigated the prevalence of heavy liver iron deposition in African American adults. Using established histochemical criteria, we graded Perls' acid ferrocyanide-reactive iron in the hepatocytes and Kupffer cells of 341 consecutive African American adults who were autopsied in the coroner/medical examiner office. Heavy staining was defined as grade 3 or 4 hepatocyte iron or grade 3 Kupffer cell iron. Results: There were 254 men and 85 women (mean age ± 1 SD: 44 ± 13 y vs. 48 ± 14 y, respectively; p = 0.0255); gender was unstated or unknown in two subjects. Approximately one-third of subjects died of natural causes. Heavy staining was observed in 10.2% of men and 4.7% of women. 23 subjects had heavy hepatocyte staining only, six had heavy Kupffer cell staining only, and one had a mixed pattern of heavy staining. 15 subjects had histories of chronic alcoholism; three had heavy staining confined to hepatocytes. We analyzed the relationships of three continuous variables (age at death in years, hepatocyte iron grade, Kupffer cell iron grade) and two categorical variables (sex, cause of death (natural and non-natural causes)) in all 341 subjects using a correlation matrix with Bonferroni correction. This revealed two positive correlations: hepatocyte with Kupffer cell iron grades (p < 0.01), and male sex with hepatocyte iron grade (p < 0.05). We also analyzed the relationship of steatosis, inflammation, and fibrosis/cirrhosis in 30 subjects with heavy iron staining using a correlation matrix with Bonferroni correction. There were significant positive correlations of steatosis with inflammation (r = 0.5641; p < 0.01), and of inflammation with fibrosis/cirrhosis (r = 0.6124; p < 0.01). Conclusions: The present results confirm and extend previous observations that heavy liver iron staining is relatively common in African Americans. The pertinence of these observations to genetic and acquired causes of iron overload in African Americans is discussed.

  • Standardization of cytokine flow cytometry assays - Background: Cytokine flow cytometry (CFC) or intracellular cytokine staining (ICS) can quantitate antigen-specific T cell responses in settings such as experimental vaccination. Standardization of ICS among laboratories performing vaccine studies would provide a common platform by which to compare the immunogenicity of different vaccine candidates across multiple international organizations conducting clinical trials. As such, a study was carried out among several laboratories involved in HIV clinical trials, to define the inter-lab precision of ICS using various sample types, and using a common protocol for each experiment (see additional files online). Results: Three sample types (activated, fixed, and frozen whole blood; fresh whole blood; and cryopreserved PBMC) were shipped to various sites, where ICS assays using cytomegalovirus (CMV) pp65 peptide mix or control antigens were performed in parallel in 96-well plates. For one experiment, antigens and antibody cocktails were lyophilised into 96-well plates to simplify and standardize the assay setup. Results (CD4+cytokine+ cells and CD8+cytokine+ cells) were determined by each site. Raw data were also sent to a central site for batch analysis with a dynamic gating template. Mean inter-laboratory coefficient of variation (C.V.) ranged from 17-44% depending upon the sample type and analysis method. Cryopreserved peripheral blood mononuclear cells (PBMC) yielded lower inter-lab C.V.'s than whole blood. Centralized analysis (using a dynamic gating template) reduced the inter-lab C.V. by 5-20%, depending upon the experiment. The inter-lab C.V. was lowest (18-24%) for samples with a mean of >0.5% IFN+ T cells, and highest (57-82%) for samples with a mean of <0.1% IFN+ cells. Conclusions: ICS assays can be performed by multiple laboratories using a common protocol with good inter-laboratory precision, which improves as the frequency of responding cells increases. Cryopreserved PBMC may yield slightly more consistent results than shipped whole blood. Analysis, particularly gating, is a significant source of variability, and can be reduced by centralized analysis and/or use of a standardized dynamic gating template. Use of pre-aliquoted lyophilized reagents for stimulation and staining can provide further standardization to these assays.

  • Stem Cell Transplantation and Gene Therapy for Hemoglobinopathies - The b-thalassemias and sickle cell disorders are the most common genetic diseases worldwide. Although -improvements in conservative treatment have considerably improved the prognosis of hemoglobinopathies, stem cell transplantation remains the only cure for thalassemia and sickle cell disease. Results of transplants in these diseases have steadily improved over the last two decades due to improvements in preventive strategies, effective control of transplant-related complications and development of new preparative regimens. High-resolution human leukocyte antigen (HLA) typing has enabled physicians to perform transplant from unrelated volunteer donors for thalassemia with results comparable with those obtained employing an HLA-identical sibling. Current understandings of stable mixed chimerism (MC) in patients with hemoglobinopathies provide a rationale for the use of less intensive conditioning regimens and future gene therapy. Despite recent advances in animal models, the clinical application of gene therapy for hemoglobinopathies is unlikely to be a reality for at least near future. With the advances in transplantation for -thalassemia, all sickle cell disease patients should be offered stem cell transplantation with an human leukocyte antigen (HLA)-identical donor. This review focuses on the current status of stem cell transplantation for hemoglobinopathies.

  • Stimulus-dependent spatial patterns of response in SI cortex - Background: Recently we reported that vibrotactile flutter stimulation of a skin locus at different amplitudes evokes an optical response confined to the same local region of the primary somatosensory cortex (SI), where its overall magnitude varies proportionally to the flutter amplitude. In this report, we characterize the impact of the flutter amplitude on the spatial patterns of activity evoked within the responding SI region. Results: In order to characterize the spatial pattern of activity within the responding SI region, images of the flutter-evoked SI optical response were segmented and analyzed with spatial frequency analysis. The analysis revealed that: (1) dominant spatial frequencies in the optical intrinsic signal emerge within the responding SI region within 3-5sec of stimulus onset; (2) the stimulus-evoked activity is spatially organized in a form of several roughly parallel, anterior-posteriorly extended waves, spaced 0.4-0.5 mm apart; (3) the waves themselves exhibit spatial periodicities along their long axis; and (4) depending on the flutter stimulus amplitude, these periodicities can range from fine 0.15mm "ripples" at 50microns amplitude to well-developed 0.5mm fluctuations at the amplitude of 400microns. Conclusions: The observed spatiointensive fractionation on a sub-macrocolumnar scale of the SI response to skin stimulation might be the product of local competitive interactions within the stimulus-activated SI region and may be a feature that could yield novel insights into the functional interactions that take place in SI cortex.

  • Strong evidence that the common variant S384F in BRCA2 has no pathogenic relevance in hereditary breast cancer - IntroductionUnclassified variants (UVs) of unknown clinical significance are frequently detected in the BRCA2 gene. In this study, we have investigated the potential pathogenic relevance of the recurrent UV S384F (BRCA2, exon 10). Methods: For co-segregation, four women from a large kindred (BN326) suffering from breast cancer were analysed. Moreover, paraffin-embedded tumours from two patients were analysed for loss of heterozygosity. Co-occurrence of the variant with a deleterious mutation was further determined in a large data set of 43,029 index cases. Nature and position of the UV and conservation among species were evaluated. Results: We identified the unclassified variant S384F in three of the four breast cancer patients (the three were diagnosed at 41, 43 and 57 years of age). One woman with bilateral breast cancer (diagnosed at ages 32 and 50) did not carry the variant. Both tumours were heterozygous for the S384F variant, so loss of the wild-type allele could be excluded. Ser384 is not located in a region of functional importance and cross-species sequence comparison revealed incomplete conservation in the human, dog, rodent and chicken BRCA2 homologues. Overall, the variant was detected in 116 patients, five of which co-occurred with different deleterious mutations. The combined likelihood ratio of co-occurrence, co-segregation and loss of heterozygosity revealed a value of 1.4 × 10-8 in favour of neutrality of the variant. Conclusion: Our data provide conclusive evidence that the S384F variant is not a disease causing mutation.

  • Survivin 2α: a novel Survivin splice variant expressed in human malignancies - Background: Survivin and its alternative splice forms are involved in critical cellular processes, including cell division and programmed cell death. Survivin is expressed in the majority of human cancers, but minimally in differentiated normal tissues. Expression levels correlate with tumor aggressiveness and resistance to therapy. Results: In the present study, we identify and characterize a novel survivin isoform that we designate survivin 2α. Structurally, the transcript consists of 2 exons: exon 1 and exon 2, as well as a 3' 197 bp region of intron 2. Acquisition of a new in-frame stop codon within intron 2 results in an open reading frame of 225 nucleotides, predicting a truncated 74 amino acid protein. Survivin 2α is expressed at high levels in several malignant cell lines and primary tumors. Functional assays show that survivin 2α attenuates the anti-apoptotic activity of survivin. Subcellular localization and immunoprecipitation of survivin 2α suggests a physical interaction with survivin. Conclusion: We characterized a novel survivin splice variant that we designated survivin 2α. We hypothesize that survivin 2α can alter the anti-apoptotic functions of survivin in malignant cells. Thus survivin 2α may be useful as a therapeutic tool in sensitizing chemoresistant tumor cells to chemotherapy.

  • Synaptic and genomic responses to JNK and AP-1 signaling in Drosophila neurons - Background: The transcription factor AP-1 positively controls synaptic plasticity at the Drosophila neuromuscular junction. Although in motor neurons, JNK has been shown to activate AP-1, a positive regulator of growth and strength at the larval NMJ, the consequences of JNK activation are poorly studied. In addition, the downstream transcriptional targets of JNK and AP-1 signaling in the Drosophila nervous system have yet to be identified. Here, we further investigated the role of JNK signaling at this model synapse employing an activated form of JNK-kinase; and using Serial Analysis of Gene Expression and oligonucleotide microarrays, searched for candidate early targets of JNK or AP-1 dependent transcription in neurons. Results: Temporally-controlled JNK induction in postembryonic motor neurons triggers synaptic growth at the NMJ indicating a role in developmental plasticity rather than synaptogenesis. An unexpected observation that JNK activation also causes a reduction in transmitter release is inconsistent with JNK functioning solely through AP-1 and suggests an additional, yet-unidentified pathway for JNK signaling in motor neurons. SAGE profiling of mRNA expression helps define the neural transcriptome in Drosophila. Though many putative AP-1 and JNK target genes arose from the genomic screens, few were confirmed in subsequent validation experiments. One potentially important neuronal AP-1 target discovered, CG6044, was previously implicated in olfactory associative memory. In addition, 5 mRNAs regulated by RU486, a steroid used to trigger conditional gene expression were identified. Conclusions: This study demonstrates a novel role for JNK signaling at the larval neuromuscular junction and provides a quantitative profile of gene transcription in Drosophila neurons. While identifying potential JNK/AP-1 targets it reveals the limitations of genome-wide analyses using complex tissues like the whole brain.

  • Synergistic effect of bromocriptine and tumor necrosis factor-alpha on reversing hepatocellular carcinoma multidrug resistance in nude mouse MDR1 model of liver neoplasm. -
    Related Articles

    Synergistic effect of bromocriptine and tumor necrosis factor-alpha on reversing hepatocellular carcinoma multidrug resistance in nude mouse MDR1 model of liver neoplasm.

    World J Gastroenterol. 2005 Sep 28;11(36):5621-6

    Authors: Ding L, Chen XP, Zhang ZW, Guan J, Zhang WG, Wang HP, Wang ZH, Li CL

    AIM: To investigate the effect of bromocriptine (BCT) and tumor necrosis factor-alpha (TNF-alpha) on hepatocellular carcinoma (HCC) multidrug resistance (MDR) in nude mouse MDR model of liver neoplasm. METHODS: Human hepatocarcinoma cell line HepG(2), drug resistant hepatocarcinoma cell line HepG(2)/adriamycin (ADM) and hepatocarcinoma cell line transfected with TNF-alpha gene HepG(2)/ADM/TNF were injected into the liver of nude mice via orthotopic implantation and MDR model of liver neoplasm in vivo was established (HepG(2), ADM, TNF, BCT groups). Among these groups, BCT group and TNF group were treated with BCT through gastric canal. Each group was divided into control group and chemotherapy group. Size and weight of the tumor were measured. Furthermore, tumor histological character and growth of the nude mice were observed and their chemosensitivity was tested. MDR-associated genes and proteins (MRP, LRP) of implanted tumors were detected by immunohistochemistry, reverse transcriptase polymerase chain reaction, and apoptosis rate of hepatocarcinoma cells was detected by TUNEL assay. RESULTS: The nude mouse model of each cell line was inoculated successfully. The tumor growth rate and weight were significantly different among groups. After chemotherapy, abdominal cavity tumor growth inhibition rate was higher in BCT group (67%) compared to ADM and TNF groups, and similar to HepG(2) group (54%). MDR1 and LRPmRNA could be detected in all groups, but TNF-alpha was detected only in TNF and BCT groups. Furthermore, MDR1 and LRP protein expression of tumors in TNF and BCT groups was low similar to HepG(2) group. The apoptosis rate of hepatocarcinoma cells was much higher in BCT group than in other groups with TUNEL assay. CONCLUSION: BCT and TNF-alpha can reverse HCC MDR in nude mouse MDR1 model of liver neoplasm.

    PMID: 16237754 [PubMed - in process]


  • Targeted Deletion of the SPARC Gene Accelerates Disc Degeneration in the Aging Mouse -

    SPARC (secreted protein, acidic, and rich in cysteine) is a matricellular protein that is present in the intervertebral disc; in man, levels of SPARC decrease with aging and degeneration. In this study, we asked whether targeted deletion of SPARC in the mouse influenced disc morphology. SPARC-null and wild-type (WT) mice were studied at 0.3–21 months of age. Radiologic examination of spines from 2-month-old SPARC-null mice revealed wedging, endplate calcification, and sclerosis, features absent in age-matched WT spines. Discs from 3-month-old SPARC-null mice had a greater number of annulus cells than those of WT animals (1884.6 ± 397.9 [mean ± SD] vs 1500.2 ± 188.2, p=0.031). By 19 months discs from SPARC-null mice contained fewer cells than WT counterparts (1383.6 ± 363.3 vs 1466.8 ± 148.0, p=0.033). Histology of midsagittal spines showed herniations of lower lumbar discs of SPARC-null mice ages 14–19 months; in contrast, no herniations were seen in WT age-matched animals. Ultrastructural studies showed uniform collagen fibril diameters in the WT annulus, whereas in SPARC-null disc fibrils were of variable size with irregular margins. Consistent with the connective tissue deficits observed in other tissues of SPARC-null mice, our findings support a fundamental role for SPARC in the production, assembly, or maintenance of the disc extracellular matrix.

    (J Histochem Cytochem 53:1131–1138, 2005)


  • Targeted therapy against Bcl-2-related proteins in breast cancer cells - IntroductionBcl-2 and Bcl-xL confer resistance to apoptosis, thereby reducing the effectiveness of chemotherapy. We examined the relationship between the expression of Bcl-2 and Bcl-xL and chemosensitivity of breast cancer cells, with the aim of developing specific targeted therapy. Methods: Four human breast cancer cell lines were examined, and the effects of antisense (AS) Bcl-2 and AS Bcl-xL phosphorothioate oligodeoxynucleotides (ODNs) on chemosensitivity were tested in vitro and in vivo. Chemosensitivity was evaluated by the MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide) assay, and the antitumor effect was assessed in vivo by the success of xenograft transplantation into athymic mice. Results: Treatment with AS Bcl-2 and Bcl-xL ODNs resulted in a sequence-specific decrease in protein expression, compared with controls. Treatment of BT-474, ZR-75-1, and MDA-MB-231 cells with AS Bcl-2 increased chemosensitivity to doxorubicin (DOX), mitomycin C (MMC), paclitaxel (TXL), and docetaxel (TXT). Transfection of the Bcl-2 gene into MDA-MB-453 cells decreased sensitivity to DOX and MMC. Treatment of MDA-MB-231, BT-474, and ZR-75-1 cells with AS Bcl-xL increased chemosensitivity to DOX, MMC and taxanes to a smaller extent than AS Bcl-2. This occurred in the setting of increased Bax and cleaved poly(ADP-ribose) polymerase, as well as decreased Bcl-2 and pAkt. AS Bcl-2 ODNs induced splenomegaly in association with increased serum IL-12, which was attenuated by methylation of the CpG motifs of AS Bcl-2; however, methylated CpG failed to negate the increased antitumor effect of AS Bcl-2. Bcl-2 and Bcl-xL, to a smaller extent, are major determinants of chemosensitivity in breast cancer cells. Conclusion: Targeted therapy against Bcl-2 protein with the use of AS ODNs might enhance the effects of chemotherapy in patients with breast cancer.

  • Telomerase inhibition by siRNA causes senescence and apoptosis in Barrett's adenocarcinoma cells: mechanism and therapeutic potential. - Background: In cancer cells, telomerase induction helps maintain telomere length and thereby bypasses senescence and provides enhanced replicative potential. Chemical inhibitors of telomerase have been shown to reactivate telomere shortening and cause replicative senescence and apoptotic cell death of tumor cells while having little or no effect on normal diploid cells. Results: We designed siRNAs against two different regions of telomerase gene and evaluated their effect on telomere length, proliferative potential, and gene expression in Barrett's adenocarcinoma SEG-1 cells. The mixture of siRNAs in nanomolar concentrations caused a loss of telomerase activity that appeared as early as day 1 and was essentially complete at day 3. Inhibition of telomerase activity was associated with marked reduction in median telomere length and complete loss of detectable telomeres in more than 50% of the treated cells. Telomere loss caused senescence in 40% and apoptosis in 86% of the treated cells. These responses appeared to be associated with activation of DNA sensor HR23B and subsequent activation of p53 homolog p73 and p63 and E2F1. Changes in these gene regulators were probably the source of observed up-regulation of cell cycle inhibitors, p16 and GADD45. Elevated transcript levels of FasL, Fas and caspase 8 that activate death receptors and CARD 9 that interacts with Bcl10 and NFKB to enhance mitochondrial translocation and activation of caspase 9 were also observed. Conclusion: These studies show that telomerase siRNAs can cause effective suppression of telomerase and telomere shortening leading to both cell cycle arrest and apoptosis via mechanisms that include up-regulation of several genes involved in cell cycle arrest and apoptosis. Telomerase siRNAs may therefore be strong candidates for highly selective therapy for chemoprevention and treatment of Barrett's adenocarcinoma.

  • Temporal Expression of Alpha-Smooth Muscle Actin and Drebrin in Septal Interstitial Cells during Alveolar Maturation -

    In rat lung, the definitive alveoli are established during development by the outgrowth of secondary septa from the primary septa present in newborn; however, the mechanism of alveolar formation has not yet been fully clarified. In this study, we characterize the septal interstitial cells in developing alveoli. During the perinatal period, alpha-SMA–containing slender cells were found in the primitive alveolar septa. Alpha-SMA–containing cells were detected at the tips of the septa until postnatal day 21, when the alveolar formation was almost completed, but disappeared in adult. Immunoelectron microscopy demonstrated that alpha-SMA is localized mainly in the cellular protrusions, which are connected with the elastic fibers around the interstitial cells. Developmentally regulated brain protein (drebrin) is also located in the cell extensions containing alpha-SMA in immature alveolar interstitial cells. In adult lung, alpha-SMA–positive cells are located only at the alveolar ducts but are not found in the secondary septa. Desmin is expressed only in alpha-SMA–containing cells at the alveolar ducts but not in those at the tip of alveolar septa. These results suggest that a part of the septal interstitial cells are temporarily alpha-SMA– and drebrin-positive during maturation. Alpha-SMA– and drebrin-containing septal interstitial cells (termed septal myofibroblast-like cells) may play an important role in alveolar formation.

    (J Histochem Cytochem 53:735–744, 2005)


  • Temporal Expression of Alpha-Smooth Muscle Actin and Drebrin in Septal Interstitial Cells during Alveolar Maturation -

    In rat lung, the definitive alveoli are established during development by the outgrowth of secondary septa from the primary septa present in newborn; however, the mechanism of alveolar formation has not yet been fully clarified. In this study, we characterize the septal interstitial cells in developing alveoli. During the perinatal period, alpha-SMA–containing slender cells were found in the primitive alveolar septa. Alpha-SMA–containing cells were detected at the tips of the septa until postnatal day 21, when the alveolar formation was almost completed, but disappeared in adult. Immunoelectron microscopy demonstrated that alpha-SMA is localized mainly in the cellular protrusions, which are connected with the elastic fibers around the interstitial cells. Developmentally regulated brain protein (drebrin) is also located in the cell extensions containing alpha-SMA in immature alveolar interstitial cells. In adult lung, alpha-SMA–positive cells are located only at the alveolar ducts but are not found in the secondary septa. Desmin is expressed only in alpha-SMA–containing cells at the alveolar ducts but not in those at the tip of alveolar septa. These results suggest that a part of the septal interstitial cells are temporarily alpha-SMA– and drebrin-positive during maturation. Alpha-SMA– and drebrin-containing septal interstitial cells (termed septal myofibroblast-like cells) may play an important role in alveolar formation.

    (J Histochem Cytochem 53:735–744, 2005)


  • Temporal Expression of Alpha-Smooth Muscle Actin and Drebrin in Septal Interstitial Cells during Alveolar Maturation -

    In rat lung, the definitive alveoli are established during development by the outgrowth of secondary septa from the primary septa present in newborn; however, the mechanism of alveolar formation has not yet been fully clarified. In this study, we characterize the septal interstitial cells in developing alveoli. During the perinatal period, alpha-SMA–containing slender cells were found in the primitive alveolar septa. Alpha-SMA–containing cells were detected at the tips of the septa until postnatal day 21, when the alveolar formation was almost completed, but disappeared in adult. Immunoelectron microscopy demonstrated that alpha-SMA is localized mainly in the cellular protrusions, which are connected with the elastic fibers around the interstitial cells. Developmentally regulated brain protein (drebrin) is also located in the cell extensions containing alpha-SMA in immature alveolar interstitial cells. In adult lung, alpha-SMA–positive cells are located only at the alveolar ducts but are not found in the secondary septa. Desmin is expressed only in alpha-SMA–containing cells at the alveolar ducts but not in those at the tip of alveolar septa. These results suggest that a part of the septal interstitial cells are temporarily alpha-SMA– and drebrin-positive during maturation. Alpha-SMA– and drebrin-containing septal interstitial cells (termed septal myofibroblast-like cells) may play an important role in alveolar formation.

    (J Histochem Cytochem 53:735–744, 2005)


  • The allergy adjuvant effect of particles - genetic factors influence antibody and cytokine responses - Background: There is increasing epidemiological and experimental evidence for an aggravating effect of particulate air pollution on asthma and allergic symptoms and, to a lesser extent, on allergic sensitization. Genetic factors appear to influence not only the magnitude, but also the quality of the adjuvant effect of particles with respect to allergen-specific IgE (Th2-associated) and IgG2a (Th1-associated) responses. In the present study, we aimed to investigate how the genetic background influences the responses to the allergen and particles alone and in combination. We examined how polystyrene particles (PSP) affected the IgE and IgG2a responses against the model allergen ovalbumin (OVA), after subcutaneous injection into the footpad of BALB/cA, BALB/cJ, NIH and C3H/HeN mice, Further, ex vivo IL-4, IFN-gamma and IL-10 cytokine secretion by Con A-stimulated cells from the draining popliteal lymph node (PLN) five days after injection of OVA and PSP separately or in combination was determined. Results: PSP injected with OVA increased the levels of OVA-specific IgE antibodies in all strains examined. In contrast, the IgG2a levels were significantly increased only in NIH and C3H/HeN mice. PSP in the presence of OVA increased cell numbers and IL-4, IL-10 and IFN-gamma levels in BALB/cA, NIH and C3H/HeN mice, with the exception of IFN-gamma in NIH mice. However, each mouse strain had their unique pattern of response to OVA+PSP, OVA and PSP, and also their unique background cytokine response (i.e. the cytokine response in cells from mice injected with buffer only). Conclusions: Genetic factors (i.e. the strain of mice) influenced the susceptibility to the adjuvant effect of PSP on both secondary antibody responses and primary cellular responses in the lymph node, as well as the cellular responses to both OVA and PSP given separately. Interestingly, PSP alone induced cytokine responses in the lymph node in some of the mouse strains. Furthermore, we found that the ex vivo cytokine patterns did not predict the in vivo Th2- and Th1-associated antibody response patterns in the different mouse strains. The results indicate that insoluble particles act by increasing the inherent response to the allergen, and that the genetic background may determine whether an additional Th1-associated component is added to the response.

  • The Anal Pap Smear: Cytomorphology of squamous intraepithelial lesions - Background: Anal smears are increasingly being used as a screening test for anal squamous intraepithelial lesions (ASILs). This study was undertaken to assess the usefulness and limitations of anal smears in screening for ASILs. Methods: The cytomorphological features of 200 consecutive anal smears collected in liquid medium from 198 patients were studied and findings were correlated with results of surgical biopsies and/or repeat smears that became available for 71 patients within six months. Results: Adequate cellularity was defined as an average of 6 or more nucleated squamous cells/hpf. A glandular/transitional component was not required for adequacy. Dysplastic cells, atypical parakeratotic cells and bi/multinucleated cells were frequent findings in ASIL while koilocytes were infrequent. Smears from LSIL cases most frequently showed mildly dysplastic and bi/multinucleate squamous cells followed by parakeratotic cells (PK), atypical parakeratotic cells (APK), and koilocytes. HSIL smears contained squamous cells with features of moderate/severe dysplasia and many APKs. Features of LSIL were also found in most HSIL smears. Conclusions: In this study liquid based anal smears had a high sensitivity (98%) for detection of ASIL but a low specificity (50%) for predicting the severity of the abnormality in subsequent biopsy. Patients with cytologic diagnoses of ASC-US and LSIL had a significant risk (46–56%) of HSIL at biopsy. We suggest that all patients with a diagnosis of ASC-US and above be recommended for high resolution anoscopy with biopsy.

  • The big problem of the missing cytology slides - Cytology slides are often unique and irreplaceable. Unlike surgical pathology cases, where additional paraffin sections can be cut, cytology slides often cannot be duplicated because there are only a few direct smears or the diagnostic material is present on a single slide. Cytology slides are often "sent out" to other physicians, laboratories or hospitals, typically so that the pathologist at the institution where the patient will receive treatment can review the slides. Less often, a cytology lab sends out the slides for a second opinion or as part of the discovery process in a lawsuit, where they may or may not be defendants. Rarely, unique and irreplaceable cytology slides are lost. This article presents a hypothetical scenario that is based on reported state appellate court decisions. The article discusses some of the legal issues that will affect the defendant cytologist/cytology lab and the "expert cytologist," and suggests some steps a cytologist/cytology lab can take to minimize the risk of repercussions from a lost unique and irreplaceable cytology slide.

  • THE CDX2 TRANSCRIPTION FACTOR REGULATES FURIN EXPRESSION DURING INTESTINAL EPITHELIAL CELL DIFFERENTIATION. -
    Related Articles

    THE CDX2 TRANSCRIPTION FACTOR REGULATES FURIN EXPRESSION DURING INTESTINAL EPITHELIAL CELL DIFFERENTIATION.

    Am J Physiol Gastrointest Liver Physiol. 2005 Oct 20;

    Authors: Gendron FP, Mongrain S, Laprise P, McMahon S, Dubois CM, Blais M, Asselin C, Rivard N

    CDX2, a member of the caudal family of transcription factors, is involved in enterocyte lineage specification. CDX2 activates many intestine-specific genes such as sucrase-isomaltase and lactase-phlorizin hydrolase (LPH), and adhesion proteins, namely LI-cadherin and claudin-2. In this study, we show that the pro-protein convertase furin, involved in proteolytic maturation of pro-protein substrates including LPH and cell surface proteins, is a CDX2 target. Indeed, expression of the rat furin homolog was induced 1.5-fold, as determined by microarray experiments which compared control to CDX2-expressing intestinal epithelial cells (IEC-6). As determined by transient transfection assays in Caco-2/15 cells, the furin P1 promoter 1.3 kb fragment between SacI and NheI was essential for CDX2 transcriptional activation. Electrophoretic mobility shift/supershift assays followed by site-specific mutagenesis and chromatin immunoprecipitation identified the CBS2 sequence from nt -1827 to nt -1821 as the major CDX2 DNA-binding site involved in furin P1 promoter activation. Increased furin mRNA and protein expression correlated with both CDX2 expression and intestinal epithelial cell differentiation. In addition, furin mRNAs were detected predominantly in differentiated epithelial cells of the villus, as determined by in situ hybridization. Treatment of Caco-2/15 cells with a furin inhibitor led to inhibition of LPH activity. Morphological differentiation of enterocyte-like features in Caco-2/15 such as epithelial cell polarity and brush border formation were strongly attenuated by furin inhibition. These results suggest that CDX2 regulates furin expression in intestinal epithelial cells. Furin may be important in modulating the maturation and/or activation of key factors involved in enterocyte differentiation.

    PMID: 16239403 [PubMed - as supplied by publisher]


  • The Classics of Immunology - Medical Immunology will be publishing invited Reviews and Commentaries from investigators who are at the forefront of their fields, to up-date our readers as to the current state of their art. These Reviews and Commentaries will be accompanied by Editorials that place the current work into the perspective of the first contribution in an area, which resulted in a "Classic" paper. Where possible, links will be provided to the original publication, so that the modern student of immunology can read the original and draw their own conclusions as to the value of the "Classic" contribution, and its relationship to our contemporary views as to how the immune system functions. To begin this process at the very dawn of immunology, we highlight Sir Edward Jenner's first descriptions of the use of cowpox to immunize individuals against the dread disease smallpox.

  • The Clinical Implications of the World Health Organization's Classification of Myelodysplastic Syndromes - Myelodysplastic syndromes (MDS) are a heterogeneous group of neoplastic clonal stem cell diseases characterized by dysplastic morphological features with a varying percentage of leukemic blasts and clinical bone marrow failure. The French-American-British (FAB) system served as the gold standard of MDS classification for more than two decades. The World Health Organization (WHO) classification, built on the backbone of the FAB classification, is an attempt to further improve the prognostic value of MDS classification as well as to establish its clinical utility as a tool to select different treatments. In this article we highlight the major differences between the FAB classification and the WHO MDS classification. We discuss in more details the experience of using the new WHO classification since its publications and review the studies that tried to either validate the prognostic value of the new classification or apply it to predict clinical responses to various treatments.

  • The continuing HIV vaccine saga: naked emperors alongside fairy godmothers - The latest developments in the HIV vaccine field were aired at a Keystone Symposium recently. This Commentary summarizes some of the highlights from this meeting, and focuses on some of the developments that appeared particularly promising, as well as those that do not. Unfortunately, the "saga" continues.

  • The cysteine-rich with EGF-Like domains 2 (CRELD2) protein interacts with the large cytoplasmic domain of human neuronal nicotinic acetylcholine receptor alpha4 and beta2 subunits. -
    Related Articles

    The cysteine-rich with EGF-Like domains 2 (CRELD2) protein interacts with the large cytoplasmic domain of human neuronal nicotinic acetylcholine receptor alpha4 and beta2 subunits.

    J Neurochem. 2005 Oct 20;

    Authors: Ortiz JA, Castillo M, Del Toro ED, Mulet J, Gerber S, Valor LM, Sala S, Sala F, Gutiérrez LM, Criado M

    Using a yeast two-hybrid screening we report the isolation of a novel human protein, hCRELD2beta, that interacts specifically with the large cytoplasmic regions of human nicotinic acetylcholine receptor (nAChR) alpha4 and beta2 subunits, both in yeast cells and in vitro. This interaction is not detected with nAChR alpha7 and alpha3 subunits. The hCRELD2 gene encodes for multiple transcripts, likely to produce multiple protein isoforms. A previously reported one has been renamed as CRELD2alpha. Isoforms alpha and beta are expressed in all tissues examined and have the same N-terminal and central regions but alternative C-terminal regions. Both isoforms interact with the alpha4 subunit. Within this subunit the interaction was localized to the N-terminal region of the large cytoplasmic loop. The CRELD2beta protein is present at the endoplasmic reticulum where colocalized with alpha4beta2 nAChRs upon cell transfection. Immunohistochemistry experiments demonstrated the presence of CRELD2 in the rat brain at sites where alpha4beta2 receptors have been previously detected. Labeling was restricted to neuronal perikarya. Finally, CRELD2 decreases the functional expression and impairs membrane transport of alpha4beta2 nAChRs in Xenopus leavis oocytes, without affecting alpha3beta4 and alpha7 nAChR expression. These results suggest that CRELD2 can act as a specific regulator of alpha4beta2 nAChR expression.

    PMID: 16238698 [PubMed - as supplied by publisher]


  • The effect of nimesulide, a selective cyclooxygenase-2 inhibitor, on Ets-1 and Ets-2 expression in head and neck cancer cell lines. -
    Related Articles

    The effect of nimesulide, a selective cyclooxygenase-2 inhibitor, on Ets-1 and Ets-2 expression in head and neck cancer cell lines.

    Head Neck. 2005 Oct 20;

    Authors: Lamm W, Vormittag L, Turhani D, Erovic BM, Czembirek C, Eder-Czembirek C, Thurnher D

    BACKGROUND.: The protooncogenes Ets-1 and Ets-2 are involved in carcinogenesis of different tumors. Nimesulide, a selective cyclooxygenase-2 (COX-2) inhibitor, has antiproliferative effects on tumor cells. The question arises whether nimesulide influences Ets-1 and Ets-2 synthesis in head and neck tumors. METHODS.: Expression of Ets-1 and Ets-2 was analyzed in tumor tissues by immunohistochemistry. The influence of nimesulide and an extracellular signal-regulated kinase (ERK) inhibitor on cell proliferation of two head and neck cancer cell lines and Ets-1 and Ets-2 expression was determined by automated cell counting and Western blotting, respectively. RESULTS.: Immunohistochemistry showed a high expression of Ets-1 and Ets-2 in tumor tissues. In both cell lines, Ets-1 and Ets-2 expression were reduced after 24 and 48 hours by nimesulide. CONCLUSION.: Both Ets-1 and Ets-2 are overexpressed in head and neck cancer specimens. Inhibition of Ets-1 and Ets-2 expression in head and neck cancer cell lines by nimesulide might explain the proapoptotic property of this COX-2 inhibitor. (c) 2005 Wiley Periodicals, Inc. Head Neck 27: XXX-XXX, 2005.

    PMID: 16240325 [PubMed - as supplied by publisher]


  • The establishment of a doxycycline-regulated cell line of inducible, double-stable expression of wild-type p53 gene in a p53-deleted hepatocellular carcinoma cell line - Although p53 is an important molecule in both development and therapy of hepatocellular carcinoma (HCC), how p53 functions to inhibit the growth of HCC is still a hot area to be explored. The establishment of a good cell model for study of p53 will be very useful in addressing unresolved issues. The present study aimed to establish a HCC cell system in which p53 can be timely and quantitatively regulated. The full-length cDNA of wild-type p53 obtained by PCR was cloned into a retroviral response vector controlled by the tetracycline responsive element (RevTRE-p53). The regulatory vector RevTet-Off and RevTRE-p53 were transfected into a packaging cell line PT67, respectively. Hep3B cells, of which p53 gene was deleted, were then infected by the RevTet-off viral particles from PT67. Having tested luciferase activity in G418-resistant cell clones, we selected three clones with high expression of luciferase and low background to be infected by RevTRE-p53. By screening dozens of RevTRE-p53-infected cell clones with hygromycin, we identified a clone that had the highest expression of p53 and the lowest background after doxycycline treatment. The result showed that the expression of p53 in this cell clone could be simply turned on or off by removing or adding doxycycline. Furthermore, it was found that the level of p53 protein was negatively and finely associated with the concentration of doxycycline. In conclusion, we have established a HCC cell line in which the expression of p53 can be not only switched on or off but regulated in both dose- and temporal-dependent manners.

  • The evolution of drug-activated nuclear receptors: one ancestral gene diverged into two xenosensor genes in mammals - Background: Drugs and other xenobiotics alter gene expression of cytochromes P450 (CYP) by activating the pregnane X receptor (PXR) and constitutive androstane receptor (CAR) in mammals. In non-mammalian species, only one xenosensor gene has been found. Using chicken as a model organism, the aim of our study was to elucidate whether non-mammalian species only have one or two xenosensors like mammals. Results: To explore the evolutionary aspect of this divergence, we tried to identify additional xenobiotic sensing nuclear receptors in chicken using various experimental approaches. However, none of those revealed novel candidates. Ablation of chicken xenobiotic receptor (CXR) function by RNAi or dominant-negative alleles drastically reduced drug-induction in a chicken hepatoma cell line. Subsequently, we functionally and structurally characterized CXR and compared our results to PXR and CAR. Despite the high similarity in their amino acid sequence, PXR and CAR have very distinct modes of activation. Some aspects of CXR function, e.g. direct ligand activation and high promiscuity are very reminiscent of PXR. On the other hand, cellular localization studies revealed common characteristics of CXR and CAR in terms of cytoplasmic-nuclear distribution. Finally, CXR has unique properties regarding its regulation in comparison to PXR and CAR. Conclusion: Our finding thus strongly suggest that CXR constitutes an ancestral gene which has evolved into PXR and CAR in mammals. Future studies should elucidate the reason for this divergence in mammalian versus non-mammalian species.

  • The Expression of Mannose Receptors in Skin Fibroblast and Their Involvement in Leishmania (L.) amazonensis Invasion -

    Leishmania are protozoa that invade mononuclear phagocytes with the involvement of different ligand-receptor systems, including mannose receptors. Until now, scant data are available concerning the mechanisms that govern the infection of Leishmania in other host cell types such as fibroblasts. Our aim was to analyze the expression of mannose receptors in primary cultures of skin fibroblasts (SF) further characterizing their role during the invasion of promastigotes of Leishmania (L.) amazonensis. Both fluorescent, light, and electron microscopy assays revealed that SF have mannose receptors since they bound and internalized mannosylated ligands in addition to being positively labeled by fuc-BSA-FITC probes. d-mannose competition assays revealed the participation of mannose receptors during the parasite association with SF presenting upregulated receptor expression during the initial steps of the infection. After longer periods of Leishmania:fibroblasts contact, the modulation noted in the host mannose receptors was reverted concomitantly to the infection control, suggesting that the parasites were required for the alteration maintenance and providing evidences that the SF may display microbicidal mechanisms to control the Leishmania infection. (J Histochem Cytochem 53:35–44, 2005)


  • The expression of the ubiquitin ligase subunit Cks1 in human breast cancer - IntroductionLoss of the cell-cycle inhibitory protein p27Kip1 is associated with a poor prognosis in breast cancer. The decrease in the levels of this protein is the result of increased proteasome-dependent degradation, mediated and rate-limited by its specific ubiquitin ligase subunits S-phase kinase protein 2 (Skp2) and cyclin-dependent kinase subunit 1 (Cks1). Skp2 was recently found to be overexpressed in breast cancers, but the role of Cks1 in these cancers is unknown. The present study was undertaken to examine the role of Cks1 expression in breast cancer and its relation to p27Kip1 and Skp2 expression and to tumor aggressiveness. Methods: The expressions of Cks1, Skp2, and p27Kip1 were examined immunohistochemically on formalin-fixed, paraffin-wax-embedded tissue sections from 50 patients with breast cancer and by immunoblot analysis on breast cancer cell lines. The relation between Cks1 levels and patients' clinical and histological parameters were examined by Cox regression and the Kaplan–Meier method. Results: The expression of Cks1 was strongly associated with Skp2 expression (r = 0.477; P = 0.001) and inversely with p27Kip1 (r = -0.726; P < 0.0001). Overexpression of Cks1 was associated with loss of tumor differentiation, young age, lack of expression of estrogen receptors and of progesterone receptors, and decreased disease-free (P = 0.0007) and overall (P = 0.041) survival. In addition, Cks1 and Skp2 expression were increased by estradiol in estrogen-dependent cell lines but were down-regulated by tamoxifen. Conclusion: These results suggest that Cks1 is involved in p27Kip1 down-regulation and may have an important role in the development of aggressive tumor behavior in breast cancer.

  • The expression of the ubiquitin ligase subunit Cks1 in human breast cancer - IntroductionLoss of the cell-cycle inhibitory protein p27Kip1 is associated with a poor prognosis in breast cancer. The decrease in the levels of this protein is the result of increased proteasome-dependent degradation, mediated and rate-limited by its specific ubiquitin ligase subunits S-phase kinase protein 2 (Skp2) and cyclin-dependent kinase subunit 1 (Cks1). Skp2 was recently found to be overexpressed in breast cancers, but the role of Cks1 in these cancers is unknown. The present study was undertaken to examine the role of Cks1 expression in breast cancer and its relation to p27Kip1 and Skp2 expression and to tumor aggressiveness. Methods: The expressions of Cks1, Skp2, and p27Kip1 were examined immunohistochemically on formalin-fixed, paraffin-wax-embedded tissue sections from 50 patients with breast cancer and by immunoblot analysis on breast cancer cell lines. The relation between Cks1 levels and patients' clinical and histological parameters were examined by Cox regression and the Kaplan–Meier method. Results: The expression of Cks1 was strongly associated with Skp2 expression (r = 0.477; P = 0.001) and inversely with p27Kip1 (r = -0.726; P < 0.0001). Overexpression of Cks1 was associated with loss of tumor differentiation, young age, lack of expression of estrogen receptors and of progesterone receptors, and decreased disease-free (P = 0.0007) and overall (P = 0.041) survival. In addition, Cks1 and Skp2 expression were increased by estradiol in estrogen-dependent cell lines but were down-regulated by tamoxifen. Conclusion: These results suggest that Cks1 is involved in p27Kip1 down-regulation and may have an important role in the development of aggressive tumor behavior in breast cancer.

  • The Fetal Erythroblast Is Not the Optimal Target for Non-invasive Prenatal Diagnosis: Preliminary Results -

    Fetal cells, present in the blood of pregnant women, are potential targets for non-invasive prenatal diagnosis. The fetal erythroblast has been the favorite target cell type. We investigated four methods of enrichment for fetal erythroblasts, identifying only three fetal erythroblasts in 573 ml of maternal blood. This is much less than the expected two to six fetal cells per ml of maternal blood. Hamada and Krabchi used a cell type-independent marker, i.e., the Y chromosome in maternal blood from male pregnancies after Carnoy fixation, leaving the nuclei for hybridization with X-and Y-chromosome-specific probes. We found with a similar technique 28 fetal cells in 15 ml of maternal blood. The fetal origin of cells was confirmed by hybridizing the nuclei with X- and Y-chromosome-specific probes, using two consecutive hybridizations with the two probes in opposite colors (reverse FISH). Candidate fetal cells were inspected after each hybridization. Only cells that were found to change the color of both probe signals from first to second hybridization were diagnosed as fetal. To reduce the labor-intensive slide screening load, we used semiautomated scanning microscopy to search for candidate cells. We conclude that erythroblasts form only a small fraction of fetal cells present in maternal blood.

    (J Histochem Cytochem 53:331336, 2005)


  • The Fourth International Symposium on the Intraductal Approach to Breast Cancer, Santa Barbara, California, 10–13 March 2005 - Intraductal approaches encompass procedures and technologies that are designed to access and interrogate the ductal–alveolar systems of the human breast, and include nipple aspiration, ductal lavage, random periareolar fine needle aspiration, and ductoscopy. These approaches are being used to collect and analyze fluids and cells to develop methods for breast cancer detection and risk assessment; to introduce imaging technologies to explore the mammary tree for abnormalities; to administer therapeutic and/or preventive agents directly to the breast tissue; and to explore the biology of the normal mammary gland. The latest research findings in these areas, presented at The 4th International Symposium on the Intraductal Approach to Breast Cancer in 2005, are summarized in this report.

  • The Future of Smallpox Vaccination: is MVA the key? - Eradication of the smallpox virus through extensive global vaccination efforts has resulted in one of the most important breakthroughs in medical history, saving countless lives from the severe morbidity and mortality that is associated with this disease. Although smallpox is now extinct in nature, laboratory stocks of this virus still remain and the subject of smallpox vaccination has gained renewed attention due to the potential risk that smallpox may be used as a biological weapon by terrorists or rogue states. Despite having the longest history of any modern vaccine, there is still much to be learned about smallpox vaccination and the correlates of protection remain to be formally defined. This Commentary will discuss the strengths and weaknesses of traditional smallpox vaccination in comparison with immunization using modified vaccinia virus Ankura (MVA), a non-replicating virus with a strong safety record but weakened immunogenicity.

  • The HIV vaccine saga - The development of a vaccine that can prevent infection by the Human immunodeficiency virus or prevent the Acquired Immunodeficiency Syndrome has remained elusive despite 20 years of scientific effort. This "Commentary" analyzes the reasons that the development of a vaccine has been so difficult, and proposes a plan to work towards an immunological approach to investigate the best vaccine candidates in the first world in individuals who are already infected, before taking the most promising vaccines to the developing world to attempt to prevent infection and disease. SAGA: (Old Norse) "a long, continued heroic story that is action-packed, but not especially romantic, and that is historical or legendary or both".

  • The involvement of CD147 in overexpression of MMP-2 and MMP-9 and enhancement of invasive potential of PMA-differentiated THP-1 - Background: During infection and inflammation, circulating blood monocytes migrate from the intravascular compartments to the extravascular compartments, where they mature into tissue macrophages. The maturation process prepares the cells to actively participate in the inflammatory and immune responses, and many factors have been reported to be involved in the process. We found in our study that CD147 played a very important role in this process. Results: By using PMA-differentiated human monocyte cells line THP-1, we found that CD147 mediated matrix metalloproteinases (MMPs) expression of the leukemic THP-1 cells and thus enhanced the invasiveness of THP-1 cells. After 24 hours of PMA-induced monocyte differentiation, the mean fluorescence intensity of CD147 in differentiated THP-1 cells (289.61+/-31.63) was higher than that of the undifferentiated THP-1 cells (205.1+/-19.25). There was a significant increase of the levels of proMMP-2, proMMP-9 and their activated forms in the differentiated THP-1 cells. Invasion assays using reconstituted basement membrane showed a good correlation between the invasiveness of THP-1 cells and the production of MMP-2 and MMP-9. The difference in the MMPs expression and the invasive ability was significantly blocked by HAb18G/CD147 antagonistic peptide AP-9. The inhibitory rate of the secretion of proMMP-9 in the undifferentiated THP-1 cells was 45.07%. The inhibitory rate of the secretion of proMMP-9, the activated MMP-9 and proMMP-2 in the differentiated THP-1 cells was 52.90%, 53.79% and 47.80%, respectively. The inhibitory rate of invasive potential in the undifferentiated cells and the differentiated THP-1 cells was 41.82 % and 25.15%, respectively. Conclusions: The results suggest that the expression of CD147 is upregulated during the differentiation of monocyte THP-1 cells to macrophage cells, and CD147 induces the secretion and activation of MMP-2 and MMP-9 and enhances the invasive ability of THP-1 cells. The matured monocytes / macrophages, via their high expression of CD147, may play an important role in promoting the tissue repair or tissue damage during their inflammatory response.

  • The LIM Domain Protein Lmo4 Is Highly Expressed in Proliferating Mouse Epithelial Tissues -

    LMO4 belongs to the LIM-only family of zinc finger proteins that have been implicated in oncogenesis. The LMO4 gene is overexpressed in breast cancer and oral cavity carcinomas, and high levels of this protein inhibit mammary epithelial differentiation. Targeted deletion of Lmo4 in mice leads to complex phenotypic abnormalities and perinatal lethality. To further understand the role of LMO4, we have characterized Lmo4 expression in adult mouse tissues by immunohistochemical staining using monoclonal anti-Lmo4 antibodies. Lmo4 was highly expressed within specific cell types in diverse tissues. Expression was prevalent in epithelial-derived tissues, including the mammary gland, tongue, skin, small intestine, lung, and brain. High levels of Lmo4 were frequently observed in proliferating cells, such as the crypt cells of the small intestine and the basal cells of the skin and tongue. Lmo4 was highly expressed in the proliferative cap cell layer of the terminal end buds in the peripubertal mammary gland and in the lobuloalveolar units during pregnancy. The expression profile of Lmo4 suggests that this cofactor is an important regulator of epithelial proliferation and has implications for its role in the pathogenicity of cancer.

    (J Histochem Cytochem 53:475–486, 2005)


  • The LIM Domain Protein Lmo4 Is Highly Expressed in Proliferating Mouse Epithelial Tissues -

    LMO4 belongs to the LIM-only family of zinc finger proteins that have been implicated in oncogenesis. The LMO4 gene is overexpressed in breast cancer and oral cavity carcinomas, and high levels of this protein inhibit mammary epithelial differentiation. Targeted deletion of Lmo4 in mice leads to complex phenotypic abnormalities and perinatal lethality. To further understand the role of LMO4, we have characterized Lmo4 expression in adult mouse tissues by immunohistochemical staining using monoclonal anti-Lmo4 antibodies. Lmo4 was highly expressed within specific cell types in diverse tissues. Expression was prevalent in epithelial-derived tissues, including the mammary gland, tongue, skin, small intestine, lung, and brain. High levels of Lmo4 were frequently observed in proliferating cells, such as the crypt cells of the small intestine and the basal cells of the skin and tongue. Lmo4 was highly expressed in the proliferative cap cell layer of the terminal end buds in the peripubertal mammary gland and in the lobuloalveolar units during pregnancy. The expression profile of Lmo4 suggests that this cofactor is an important regulator of epithelial proliferation and has implications for its role in the pathogenicity of cancer.

    (J Histochem Cytochem 53:475–486, 2005)


  • The LIM Domain Protein Lmo4 Is Highly Expressed in Proliferating Mouse Epithelial Tissues -

    LMO4 belongs to the LIM-only family of zinc finger proteins that have been implicated in oncogenesis. The LMO4 gene is overexpressed in breast cancer and oral cavity carcinomas, and high levels of this protein inhibit mammary epithelial differentiation. Targeted deletion of Lmo4 in mice leads to complex phenotypic abnormalities and perinatal lethality. To further understand the role of LMO4, we have characterized Lmo4 expression in adult mouse tissues by immunohistochemical staining using monoclonal anti-Lmo4 antibodies. Lmo4 was highly expressed within specific cell types in diverse tissues. Expression was prevalent in epithelial-derived tissues, including the mammary gland, tongue, skin, small intestine, lung, and brain. High levels of Lmo4 were frequently observed in proliferating cells, such as the crypt cells of the small intestine and the basal cells of the skin and tongue. Lmo4 was highly expressed in the proliferative cap cell layer of the terminal end buds in the peripubertal mammary gland and in the lobuloalveolar units during pregnancy. The expression profile of Lmo4 suggests that this cofactor is an important regulator of epithelial proliferation and has implications for its role in the pathogenicity of cancer.

    (J Histochem Cytochem 53:475–486, 2005)


  • The loss of NKX3.1 expression in testicular – and prostate – cancers is not caused by promoter hypermethylation - Background: Recent studies have demonstrated that the NKX3.1 protein is commonly down-regulated in testicular germ cell tumors (TGCTs) and prostate carcinomas. The homeobox gene NKX3.1 maps to chromosome band 8p21, which is a region frequently lost in prostate cancer, but not in TGCT. Mutations have not been reported in the NKX3.1 sequence, and the gene is hypothesized to be epigenetically inactivated. In the present study we examined the methylation status of the NKX3.1 promoter in relevant primary tumors and cell lines: primary TGCTs (n = 55), intratubular germ cell neoplasias (n = 7), germ cell tumor cell lines (n = 3), primary prostate adenocarcinomas (n = 20), and prostate cancer cell lines (n = 3) by methylation-specific PCR and bisulphite sequencing.Results and ConclusionsDown-regulation of NKX3.1 expression was generally not caused by promoter hypermethylation, which was only found in one TGCT. However, other epigenetic mechanisms, such as modulation of chromatin structure or modifications of histones, may explain the lack of NKX3.1 expression, which is seen in most TGCTs and prostate cancer specimens.

  • The Lymphomas: Molecular Pathways and Novel Therapeutic Targets - In recent years, several molecular mechanisms involved in promoting cancer cell survival and growth have been identified. These discoveries helped in designing and testing novel drugs that target specific cellular pathways. In this review, we focus on new molecular targets that are currently being explored for the treatment of non-Hodgkin's lymphoma and Hodgkin's lymphoma.

  • The Macrophage-derived Lectin, MNCF, Activates Neutrophil Migration through a Pertussis Toxin-sensitive Pathway -

    The macrophage-derived neutrophil chemotactic factor (MNCF) is a d-galactose-binding lectin that induces neutrophil migration in vitro and in vivo. Neutrophil recruitment induced by MNCF is resistant to glucocorticoid treatment and is inhibited by the lectin-specific sugar, d-galactose. In the present study, we characterized the binding of MNCF to neutrophils and the responses triggered by this binding. Exposure to MNCF resulted in cell polarization, formation of a lamellipodium, and deep ruffles on the cell surface. By confocal microscopy, we observed that MNCF was evenly distributed on the cell surface after 30 min of incubation. The labeling intensity progressively diminished with longer incubations. Internalization kinetics showed that MNCF/ligand complexes were rapidly internalized, reaching maximum intracellular concentrations at 120 min and then decreased thereafter. The binding and internalization of MNCF were selectively inhibited by d-galactose. MNCF-induced neutrophil chemotaxis was inhibited by pertussis toxin. This fact strongly suggests that the MNCF–ligand on the neutrophil surface is a G-protein-coupled receptor (GPCR), similar to receptors for well-established neutrophil attractants. Our observations on the ability of MNCF to activate neutrophils are consistent with the increasing evidence for the participation of animal lectins in the innate immune response.

    (J Histochem Cytochem 53:715–723, 2005)


  • The Macrophage-derived Lectin, MNCF, Activates Neutrophil Migration through a Pertussis Toxin-sensitive Pathway -

    The macrophage-derived neutrophil chemotactic factor (MNCF) is a d-galactose-binding lectin that induces neutrophil migration in vitro and in vivo. Neutrophil recruitment induced by MNCF is resistant to glucocorticoid treatment and is inhibited by the lectin-specific sugar, d-galactose. In the present study, we characterized the binding of MNCF to neutrophils and the responses triggered by this binding. Exposure to MNCF resulted in cell polarization, formation of a lamellipodium, and deep ruffles on the cell surface. By confocal microscopy, we observed that MNCF was evenly distributed on the cell surface after 30 min of incubation. The labeling intensity progressively diminished with longer incubations. Internalization kinetics showed that MNCF/ligand complexes were rapidly internalized, reaching maximum intracellular concentrations at 120 min and then decreased thereafter. The binding and internalization of MNCF were selectively inhibited by d-galactose. MNCF-induced neutrophil chemotaxis was inhibited by pertussis toxin. This fact strongly suggests that the MNCF–ligand on the neutrophil surface is a G-protein-coupled receptor (GPCR), similar to receptors for well-established neutrophil attractants. Our observations on the ability of MNCF to activate neutrophils are consistent with the increasing evidence for the participation of animal lectins in the innate immune response.

    (J Histochem Cytochem 53:715–723, 2005)


  • The Macrophage-derived Lectin, MNCF, Activates Neutrophil Migration through a Pertussis Toxin-sensitive Pathway -

    The macrophage-derived neutrophil chemotactic factor (MNCF) is a d-galactose-binding lectin that induces neutrophil migration in vitro and in vivo. Neutrophil recruitment induced by MNCF is resistant to glucocorticoid treatment and is inhibited by the lectin-specific sugar, d-galactose. In the present study, we characterized the binding of MNCF to neutrophils and the responses triggered by this binding. Exposure to MNCF resulted in cell polarization, formation of a lamellipodium, and deep ruffles on the cell surface. By confocal microscopy, we observed that MNCF was evenly distributed on the cell surface after 30 min of incubation. The labeling intensity progressively diminished with longer incubations. Internalization kinetics showed that MNCF/ligand complexes were rapidly internalized, reaching maximum intracellular concentrations at 120 min and then decreased thereafter. The binding and internalization of MNCF were selectively inhibited by d-galactose. MNCF-induced neutrophil chemotaxis was inhibited by pertussis toxin. This fact strongly suggests that the MNCF–ligand on the neutrophil surface is a G-protein-coupled receptor (GPCR), similar to receptors for well-established neutrophil attractants. Our observations on the ability of MNCF to activate neutrophils are consistent with the increasing evidence for the participation of animal lectins in the innate immune response.

    (J Histochem Cytochem 53:715–723, 2005)


  • The mannose receptor is expressed by subsets of APC in non-lymphoid organs - Background: The mannose receptor (MR) is an endocytic receptor of Mφ and endothelial cell subsets whose natural ligands include both self glycoproteins and microbial glycans. It is also expressed by immature cultured dendritic cells (DC), where it mediates high efficiency uptake of glycosylated antigens, yet its role in antigen handling in vivo is unknown. Knowledge of which APC subsets express MR will assist the design of experiments to address its immunological functions. Here the expression of MR by MHC class II positive APC in non-lymphoid organs of the mouse is described. Results: MR positive APC were identified in several peripheral organs: skin, liver, cardiac and skeletal muscle and tongue. MR positive cells in salivary gland, thyroid and pancreas coexpressed MHC class II and the myeloid markers macrosialin and sialoadhesin, but not the dendritic cell markers CD11c or DEC-205. MR and MHC class II colocalised in confocal microscope images, implying that antigen capture may be the primary role of MR in these cells. Distinct ligands of MR were found in salivary gland and pancreas tissue lysates that are candidate physiological ligands of MR positive APC in these organs. Conclusions: The tissue and subcellular distribution of MR suggest it is appropriately located to serve as a high efficiency antigen uptake receptor of APC.

  • The neuronal ceroid lipofuscinosis Cln8 gene expression is developmentally regulated in mouse brain and up-regulated in the hippocampal kindling model of epilepsy - Background: The neuronal ceroid lipofuscinoses (NCLs) are a group of inherited neurodegenerative disorders characterized by accumulation of autofluorescent material in many tissues, especially in neurons. Mutations in the CLN8 gene, encoding an endoplasmic reticulum (ER) transmembrane protein of unknown function, underlie NCL phenotypes in humans and mice. The human phenotype is characterized by epilepsy, progressive psychomotor deterioration and visual loss, while motor neuron degeneration (mnd) mice with a Cln8 mutation show progressive motor neuron dysfunction and retinal degeneration. Results: We investigated spatial and temporal expression of Cln8 messenger ribonucleic acid (mRNA) using in situ hybridization, reverse transcriptase polymerase chain reaction (RT-PCR) and northern blotting. Cln8 is ubiquitously expressed at low levels in embryonic and adult tissues. In prenatal embryos Cln8 is most prominently expressed in the developing gastrointestinal tract, dorsal root ganglia (DRG) and brain. In postnatal brain the highest expression is in the cortex and hippocampus. Expression of Cln8 mRNA in the central nervous system (CNS) was also analyzed in the hippocampal electrical kindling model of epilepsy, in which Cln8 expression was rapidly up-regulated in hippocampal pyramidal and granular neurons. Conclusion: Expression of Cln8 in the developing and mature brain suggests roles for Cln8 in maturation, differentiation and supporting the survival of different neuronal populations. The relevance of Cln8 up-regulation in hippocampal neurons of kindled mice should be further explored.

  • The neurotrophin receptor p75NTR mediates early anti-inflammatory effects of estrogen in the forebrain of young adult rats - Background: Estrogen suppresses microglial activation and extravasation of circulating monocytes in young animals, supporting an anti-inflammatory role for this hormone. However, the mechanisms underlying estrogen's anti-inflammatory effects, especially in vivo, are not well understood. The present study tests the hypothesis that anti-inflammatory effects of estrogen are mediated by the pan-neurotrophin receptor p75NTR. Previously, we reported that estrogen attenuated local increases of interleukin(IL)-1β in the NMDA-lesioned olfactory bulb, while further increasing NGF expression. Results: The present studies show that this lesion enhances expression of the neurotrophin receptor p75NTR at the lesion site, and p75NTR expression is further enhanced by estrogen treatment to lesioned animals. Specifically, estrogen stimulates p75NTR expression in cells of microvessels adjacent to the lesion site. To determine the role of this receptor in mediating estrogen's anti-inflammatory effects, a p75NTR neutralizing antibody was administered at the same time the lesion was created (by stereotaxic injections of NMDA) and specific markers of the inflammatory cascade were measured. Olfactory bulb injections of NMDA+vehicle (preimmune serum) increased IL-1β and activated the signaling molecule c-jun terminal kinase (JNK)-2 at 6 h. At 24 h, the lesion significantly increased matrix metalloproteinase (MMP)-9 and prostaglandin (PG)E2, a COX-2 mediated metabolite of arachadonic acid. All of these markers were significantly attenuated by estrogen in a time-dependent manner. However, estrogen's effects on all these markers were abolished in animals that received anti-p75NTR. Conclusion: These data support the hypothesis that estrogen's anti-inflammatory effects may be, in part, mediated by this neurotrophin receptor. In view of the novel estrogen-dependent expression of p75NTR in cells associated with microvessels, these data also suggest that the blood brain barrier is a critical locus of estrogen's neuro-immune effects.

  • The NMDA antagonist memantine affects training induced motor cortex plasticity - a study using transcranial magnetic stimulation [ISRCTN65784760] - Background: Training of a repetitive synchronised movement of two limb muscles leads to short-term plastic changes in the primary motor cortex, which can be assessed by transcranial magnetic stimulation (TMS) mapping. We used this paradigm to study the effect of memantine, a NDMA antagonist, on short-term motor cortex plasticity in 20 healthy human subjects, and we were especially interested in possible differential effects of different treatment regimens. In a randomised double-blinded cross over study design we therefore administered placebo or memantine either as a single dosage or as an ascending dosage over 8 days. Before and after one hour of motor training, which consisted of a repetitive co-contraction of the abductor pollicis brevis (APB) and the deltoid muscle, we assessed the motor output map of the APB muscle by TMS under the different conditions. Results: We found a significant medial shift of the APB motor output map after training in the placebo condition, indicating training-induced short-term plastic changes in the motor cortex. A single dosage of memantine had no significant effect on this training-induced plasticity, whereas memantine administered in an ascending dosage over 8 days was able to block the cortical effect of the motor training. The memantine serum levels after 8 days were markedly higher than the serum levels after a single dosage of memantine, but there was no individual correlation between the shift of the motor output map and the memantine serum level. Besides, repeated administration of a low memantine dosage also led to an effective blockade of training-induced cortical plasticity in spite of serum levels comparable to those reached after single dose administration, suggesting that the repeated administration was more important for the blocking effect than the memantine serum levels. Conclusion: We conclude that the NMDA-antagonist memantine is able to block training-induced motor cortex plasticity when administered over 8 days, but not after administration of a single dose. This differential effect might be mainly due to the prolonged action of memantine at the NMDA receptor. These findings must be considered if clinical studies are designed, which aim at evaluating the potency of memantine to prevent "maladaptive" plasticity, e.g. after limb amputation.

  • The novel protein KBP regulates mitochondria localization by interaction with a kinesin-like protein - Background: Members of the Kinesin-3 family of kinesin-like proteins mediate transport of axonal vesicles (KIF1A, KIF1Bbeta), distribution of mitochondria (KIF1Balpha) and anterograde Golgi to ER vesicle transport (KIF1C). Until now, little is known about the regulation of kinesin-like proteins. Several proteins interact with members of this protein family. Here we report on a novel, KIF1 binding protein (KBP) that was identified in yeast two-hybrid screens. Results: KBP was identified by using the yeast-two-hybrid system with an amino-terminal fragment of KIF1C as a bait that is strongly homologous to KIF1B. Here we investigated the interaction of KBP and KIF1B. The full length proteins coimmunoprecipitated after overexpression and in untransfected 293 cells. Immunofluorescence experiments revealed that KBP was mainly localized to mitochondria, as has been described for KIF1Balpha. Overexpression of a deletion mutant or reduction of the KBP protein level using an anti-sense construct led to an aggregation of mitochondria. Such an effect is probably due to the lower activity of KIF1Balpha in the absence of KBP, as was revealed in motility assays. Conclusions: KBP is a new binding partner for KIF1Balpha that is a regulator of its transport function and thus represents a new type of kinesin interacting protein.

  • The peroxisome proliferator activated receptor δ is required for the differentiation of THP-1 monocytic cells by phorbol ester - Background: PPARδ (NR1C2) promotes lipid accumulation in human macrophages in vitro and has been implicated in the response of macrophages to vLDL. We have investigated the role of PPARδ in PMA-stimulated macrophage differentiation.The THP-1 monocytic cell line which displays macrophage like differentiation in response to phorbol esters was used as a model system. We manipulated the response to PMA using a potent synthetic agonist of PPARδ , compound F. THP-1 sub-lines that either over-expressed PPARδ protein, or expressed PPARδ anti-sense RNA were generated. We then explored the effects of these genetic modulations on the differentiation process. Results: The PPARδ agonist, compound F, stimulated differentiation in the presence of sub-nanomolar concentrations of phorbol ester. Several markers of differentiation were induced by compound F in a synergistic fashion with phorbol ester, including CD68 and IL8. Over-expression of PPARδ also sensitised THP-1 cells to phorbol ester and correspondingly, inhibition of PPARδ by anti-sense RNA completely abolished this response. Conclusions: These data collectively demonstrate that PPARδ plays a fundamental role in mediating a subset of cellular effects of phorbol ester and supports observations from mouse knockout models that PPARδ is involved in macrophage-mediated inflammatory responses.

  • The protective role of pregnancy in breast cancer - Epidemiological, clinical, and experimental data indicate that the risk of developing breast cancer is strongly dependent on the ovary and on endocrine conditions modulated by ovarian function, such as early menarche, late menopause, and parity. Women who gave birth to a child when they were younger than 24 years of age exhibit a decrease in their lifetime risk of developing breast cancer, and additional pregnancies increase the protection. The breast tissue of normally cycling women contains three identifiable types of lobules, the undifferentiated Lobules type 1 (Lob 1) and the more developed Lobules type 2 and Lobules type 3. The breast attains its maximum development during pregnancy and lactation (Lobules type 4). After menopause the breast regresses in both nulliparous and parous women containing only Lob 1. Despite the similarity in the lobular composition of the breast at menopause, the fact that nulliparous women are at higher risk of developing breast cancer than parous women indicates that Lob 1 in these two groups of women might be biologically different, or might exhibit different susceptibility to carcinogenesis. Based on these observations it was postulated that Lob 1 found in the breast of nulliparous women and of parous women with breast cancer never went through the process of differentiation, retaining a high concentration of epithelial cells that are targets for carcinogens and are therefore susceptible to undergo neoplastic transformation. These epithelial cells are called Stem cells 1, whereas Lob 1 structures found in the breast of early parous postmenopausal women free of mammary pathology, on the contrary, are composed of an epithelial cell population that is refractory to transformation, called Stem cells 2. It was further postulated that the degree of differentiation acquired through early pregnancy has changed the 'genomic signature' that differentiates Lob 1 of the early parous women from that of the nulliparous women by shifting the Stem cells 1 to Stem cells 2 that are refractory to carcinogenesis, making this the postulated mechanism of protection conferred by early full-term pregnancy. The identification of a putative breast stem cell (Stem cells 1) has, in the past decade, reached a significant impulse, and several markers also reported for other tissues have been found in the mammary epithelial cells of both rodents and humans. Although further work needs to be carried out in order to better understand the role of the Stem cells 2 and their interaction with the genes that confer them a specific signature, collectively the data presently available provide evidence that pregnancy, through the process of cell differentiation, shifts Stem cells 1 to Stem cells 2 – cells that exhibit a specific genomic signature that could be responsible for the refractoriness of the mammary gland to carcinogenesis.

  • The quantal theory of how the immune system discriminates between "self and non-self" - In the past 50 years, immunologists have accumulated an amazing amount of information as to how the immune system functions. However, one of the most fundamental aspects of immunity, how the immune system discriminates between self vs. non-self, still remains an enigma. Any attempt to explain this most intriguing and fundamental characteristic must account for this decision at the level of the whole immune system, but as well, at the level of the individual cells making up the immune system. Moreover, it must provide for a molecular explanation as to how and why the cells behave as they do. The "Quantal Theory", proposed herein, is based upon the "Clonal Selection Theory", first proposed by Sir McFarland Burnet in 1955, in which he explained the remarkable specificity as well as diversity of recognition of everything foreign in the environment. The "Quantal Theory" is built upon Burnet's premise that after antigen selection of cell clones, a proliferative expansion of the selected cells ensues. Furthermore, it is derived from experiments which indicate that the proliferation of antigen-selected cell clones is determined by a quantal, "all-or-none", decision promulgated by a critical number of cellular receptors triggered by the T Cell Growth Factor (TCGF), interleukin 2 (IL2). An extraordinary number of experiments reported especially in the past 20 years, and detailed herein, indicate that the T cell Antigen Receptor (TCR) behaves similarly, and also that there are several critical numbers of triggered TCRs that determine different fates of the T cells. Moreover, the fates of the cells appear ultimately to be determined by the TCR triggering of the IL2 and IL2 receptor (IL2R) genes, which are also expressed in a very quantal fashion. The "Quantal Theory" states that the fundamental decisions of the T cell immune system are dependent upon the cells receiving a critical number of triggered TCRs and IL2Rs and that the cells respond in an all-or-none fashion. The "Quantal Theory" accounts fully for the development of T cells in the thymus, and such fundamental cellular fates as both "positive" and "negative" selection, as well as the decision to differentiate into a "Regulatory T cell" (T-Reg). In the periphery, the "Quantal Theory" accounts for the decision to proliferate or not in response to the presence of an antigen, either non-self or self, or to differentiate into a T-Reg. Since the immune system discriminates between self and non-self antigens by the accumulated number of triggered TCRs and IL2Rs, therapeutic manipulation of the determinants of these quantal decisions should permit new approaches to either enhance or dampen antigen-specific immune responses.

  • The recombination activation gene 1(Rag1) is expressed in a subset of zebrafish olfactory neurons but is not essential for axon targeting or amino acid detection - Background: Rag1 (Recombination activation gene-1) mediates genomic rearrangement and is essential for adaptive immunity in vertebrates. This gene is also expressed in the olfactory epithelium, but its function there is unknown. Results: Using a transgenic zebrafish line and immunofluorescence, we show that Rag1 is expressed and translated in a subset of olfactory sensory neurons (OSNs). Neurons expressing GFP under the Rag1 promoter project their axons to the lateral region of the olfactory bulb only, and axons with the highest levels of GFP terminate in a single glomerular structure. A subset of GFP-expressing neurons contain Galphao, a marker for microvillous neurons. None of the GFP-positive neurons express Galphaolf, Galphaq or the olfactory marker protein OMP. Depletion of RAG1, by morpholino-mediated knockdown or mutation, did not affect axon targeting. Calcium imaging indicates that amino acids evoke chemotopically organized glomerular activity patterns in a Rag1 mutant. Conclusions: Rag1expression is restricted to a subpopulation of zebrafish olfactory neurons projecting to the lateral olfactory bulb. RAG1 catalytic activity is not essential for axon targeting, nor is it likely to be required for regulation of odorant receptor expression or the response of OSNs to amino acids.

  • The Rise and Fall of Red Cell Mass Measurement in Polycythemia Vera - The total blood volume (BV) consists of the part occupied by red blood cells (RBC), which is referred to as red cell mass (RCM), and that occupied by plasma (ie, plasma volume). Quantitative laboratory measurements that are pertinent to RBC, including RBC count, hematocrit (Hct), and hemo-globin (Hgb) are expressed in reference to a given volume of whole blood and are therefore influenced by plasma volume. Consequently, a 'direct' RCM measurement has been promoted as a more accurate indicator of the body's red cell content. In accordance with this view, an international group of investigators, then identified as the Polycythemia Vera Study Group (PVSG), recommended that RCM be measured and only if elevated should a patient be considered for participation in a series of clinical trials in PV that were conducted more than 30 years ago. By default, the 'study eligibility' criteria used in these studies became 'diagnostic' criteria without any systematic evaluation for diagnostic accuracy. Furthermore, over the years, it has become evident that RCM measurement is a cumbersome and costly test that is also suboptimal in its diagnostic accuracy. As a result, the specific procedure has been abandoned by the majority of hematologists in certain countries and instead physicians are increasingly using bone marrow histology, serum erythro-poietin level, and other disease-characteristic biologic markers as diagnostic tools.

  • The Role of Antiplatelet Autoantibody Assays in the Diagnosis of Immune Thrombocytopenic Purpura - Immune thrombocytopenic purpura (ITP) is a disorder almost always manifested by antibody-induced thrombo-cytopenia. In 1987, two clinically useful antigen-specific assays were reported, the immunobead assay and the monoclonal antibody-specific immobilization of platelet antigens (MAIPA) assay. These two assays and their variations give similar results and can measure both platelet-associated and plasma antibodies. Three prospective studies have reported assay results with sensitivities ranging from 49% to 66% and -specificities ranging from 78% to 93%. Most antibodies react with either platelet glycoprotein (GP) IIb/IIIa or GPIb/IX. Recent evidence suggests that antiplatelet antibody assays may also be useful in predicting disease prognosis. Rare ITP patients have bleeding with normal or near-normal platelet counts, a prolonged bleeding time, and aggregation -abnormalities due to autoantibodies that affect platelet -function. Incubation of patient plasma, IgG or eluate with normal platelet-rich plasma reproduces the patient's -aggregation abnormalities.

  • The role of mutation in the new cancer paradigm - The almost universal belief that cancer is caused by mutation may gradually be giving way to the belief that cancer begins as a cellular adaptation that involves the local epigenetic suppression of various genes. In my own interpretation of the new paradigm, the genes epigenetically suppressed are genes that normally serve in post-embryonic life to silence and keep silenced those other genes upon which embryonic development depends. Those other genes, if not silenced or repressed in the post-embryonic animal, are, I suggest, the basis of neoplasia. Mutations that occur in silenced genes go unrepaired and are, therefore, postulated to accumulate; however, such mutations probably play little or no causative role in neoplasia because they occur in already epigenetically silenced genes. However, these mutations probably serve to make the silencing relatively irreversible.

  • The Role of the Anti-CD20 Antibody Rituximab in Hematopoietic Stem Cell Transplantation for Non-Hodgkin's Lymphoma - Autologous hematopoietic stem cell transplantation is widely accepted as effective therapy for patients with relapsed aggressive B-cell non-Hodgkin's lymphoma, and to a lesser extent, for indolent and mantle cell lymphoma, resulting in prolonged disease-free survival. Despite these advances, disease recurrence remains a problem and a major clinical challenge. Allogeneic transplantation has also been increasingly utilized in patients with relapsed aggressive and indolent lymphoma but is associated with high toxicity and graft-versus-host disease. Recently, nonmyelo-abla--tive preparatory regimens have shown encouraging results, attributed to graft-versus-lymphoma effects. Rituximab, a monoclonal antibody targeted against the CD20 antigen, is a potent therapeutic tool with documented efficacy in B-cell lymphomas. It is effective when used alone or in combination with chemotherapy, resulting in a significantly improved response rate compared with chemotherapy alone, in both aggressive and indolent lymphomas. Increasing evidence suggests that rituximab is also effective at in vivo purging prior to transplantation and may prevent relapse by eradication of residual disease when administered after transplantation. This review summarizes the available data on the use of rituximab and discusses the current evidence for its role in conjunction with auto- and allotransplantation.

  • The STATs in cell stress-type responses - In the early 1990's, a new cell signaling pathway was described. This new paradigm, now known as the JAK/STAT pathway, has been extensively investigated in immune-type cells in response to interferons and interleukins. However, recent evidence suggests that the JAK/STAT pathway also mediates diverse cellular responses to various forms of biological stress including hypoxia/reperfusion, endotoxin, ultraviolet light, and hyperosmolarity. The current literature describing the JAK/STAT pathway's role in cellular stress responses has been reviewed herein, but it is clear that our knowledge in this area is far from complete.

  • The use of cystatin C to inhibit epithelial–mesenchymal transition and morphological transformation stimulated by transforming growth factor-β - IntroductionTransforming growth factor-β (TGF-β) is a potent suppressor of mammary epithelial cell (MEC) proliferation and is thus an inhibitor of mammary tumor formation. Malignant MECs typically evolve resistance to TGF-β-mediated growth arrest, enhancing their proliferation, invasion, and metastasis when stimulated by TGF-β. Recent findings suggest that therapeutics designed to antagonize TGF-β signaling may alleviate breast cancer progression, thereby improving the prognosis and treatment of breast cancer patients. We identified the cysteine protease inhibitor cystatin C (CystC) as a novel TGF-β type II receptor antagonist that inhibits TGF-β binding and signaling in normal and cancer cells. We hypothesized that the oncogenic activities of TGF-β, particularly its stimulation of mammary epithelial–mesenchymal transition (EMT), can be prevented by CystC.MethodRetroviral infection was used to constitutively express CystC or a CystC mutant impaired in its ability to inhibit cathepsin protease activity (namely Δ14CystC) in murine NMuMG MECs and in normal rat kidney (NRK) fibroblasts. The effect of recombinant CystC administration or CystC expression on TGF-β stimulation of NMuMG cell EMT in vitro was determined with immunofluorescence to monitor rearrangements of actin cytoskeletal architecture and E-cadherin expression. Soft-agar growth assays were performed to determine the effectiveness of CystC in preventing TGF-β stimulation of morphological transformation and anchorage-independent growth in NRK fibroblasts. Matrigel invasion assays were performed to determine the ability of CystC to inhibit NMuMG and NRK motility stimulated by TGF-β. Results: CystC and Δ14CystC both inhibited NMuMG cell EMT and invasion stimulated by TGF-β by preventing actin cytoskeletal rearrangements and E-cadherin downregulation. Moreover, both CystC molecules completely antagonized TGF-β-mediated morphological transformation and anchorage-independent growth of NRK cells, and inhibited their invasion through synthetic basement membranes. Both CystC and Δ14CystC also inhibited TGF-β signaling in two tumorigenic human breast cancer cell lines. Conclusion: Our findings show that TGF-β stimulation of initiating metastatic events, including decreased cell polarization, reduced cell–cell contact, and elevated cell invasion and migration, are prevented by CystC treatment. Our findings also suggest that the future development of CystC or its peptide mimetics hold the potential to improve the therapeutic response of human breast cancers regulated by TGF-β.

  • The Use of Peptide Nucleic Acids for In Situ Identification of Human Chromosomes -

    The peptide nucleic acids (PNAs) constitute a remarkable new class of synthetic nucleic acid analogues, based on their peptide-like backbone. This structure gives to PNAs the capacity to hybridize with high affinity and specificity to complementary RNA and DNA sequences and a great resistance to nucleases and proteinases. Originally conceived as ligands for the study of double-stranded DNA, the unique physicochemical properties of PNAs have led to the development of a large variety of research and diagnostic assays, including antigene and antisense therapy, genome mapping, and mutation detection. Over the past few years, PNAs have been shown to be powerful tools in cytogenetics for the rapid in situ identification of human chromosomes and the detection of aneuploidies. Recent studies have reported the successful use of chromosome-specific PNA probes on human lymphocytes, amniocytes, and spermatozoa, as well as on isolated oocytes and blastomeres. Multicolor PNA protocols have been described for the identification of several human chromosomes, indicating that PNAs could become a powerful complement to FISH for in situ chromosomal investigation. (J Histochem Cytochem 53:395–400, 2005)


  • The use of time-resolved fluorescence imaging in the study of protein kinase C localisation in cells - Background: Two-photon-excitation fluorescence lifetime imaging (2P-FLIM) was used to investigate the association of protein kinase C alpha (PKCa) with caveolin in CHO cells. PKCa is found widely in the cytoplasm and nucleus in most cells. Upon activation, as a result of increased intracellular Ca2+ and production of DAG, through G-protein coupled-phospholipase C signalling, PKC translocates to a variety of regions in the cell where it phosphorylates and interacts with many signalling pathways. Due to its wide distribution, discerning a particular interaction from others within the cell is extremely difficult Results: Fluorescence energy transfer (FRET), between GFP-PKCa and DsRed-caveolin, was used to investigate the interaction between caveolin and PKC, an aspect of signalling that is poorly understood. Using 2P-FLIM measurements, the lifetime of GFP was found to decrease (quench) in certain regions of the cell from ~2.2 ns to ~1.5 ns when the GFP and DsRed were sufficiently close for FRET to occur. This only occurred when intracellular Ca2+ increased or in the presence of phorbol ester, and was an indication of PKC and caveolin co-localisation under these conditions. In the case of phorbol ester stimulated PKC translocation, as commonly used to model PKC activation, three PKC areas could be delineated. These included PKCa that was not associated with caveolin in the nucleus and cytoplasm, PKCa associated with caveolin in the cytoplasm/perinuclear regions and probably in endosomes, and PKC in the peripheral regions of the cell, possibly indirectly interacting with caveolin. Conclusions: Based on the extent of lifetime quenching observed, the results are consistent with a direct interaction between PKCa and caveolin in the endosomes, and possibly an indirect interaction in the peripheral regions of the cell. The results show that 2P-FLIM-FRET imaging offers an approach that can provide information not only confirming the occurrence of specific protein-protein interactions but where they occur within the cell.

  • The Usefulness of Calyculin A for Cytogenetic Prenatal Diagnosis -

    An increased number of chromosome plates can be obtained by use of calyculin A (CLA). CLA is an inhibitor of protein phosphatases (type 1 and type 2A serine/threonine). Inactivation of these phosphatases leads to premature chromosome condensation (PCC) in all phases of the cell cycle; thus, it is possible to investigate both metaphase and G2-PCC chromosomes. Amniotic fluid (AF) cultures were treated with calyculin A (CLA). GTG banding was obtained. Using this method it is possible to investigate all cell cycle phases, GTG banding, chromosomal breaks, and rates of PCD on the same preparation. Analyses of AF cultures treated with CLA allow complex studies on fetal genetic material. This work presents potential usefulness of CLA for cytogenetic prenatal diagnosis.

    (J Histochem Cytochem 53:391–394, 2005)


  • The utility of cytokeratins 7 and 20 (CK7/20) immunohistochemistry in the distinction of short-segment Barrett esophagus from gastric intestinal metaplasia: Is it reliable? - Background: The purpose of the present correlative immunohistochemical study was to assess the utility of cytokeratin (CK7 and CK20) expression in the diagnosis of short-segment Barrett esophagus, particularly its efficacy in differentiating Barrett mucosa from intestinal metaplasia of the gastric cardia and corpus. Methods: Two groups of endoscopic biopsy specimens were examined, including 20 endoscopic biopsy specimens of short-segment Barrett esophagus (Group A) and equal number exhibiting Helicobacter pylori associated intestinal metaplasia of the gastric cardia and corpus (Group B). All were investigated by immunohistochemistry using the standard ABC method for CK7 and CK20 expression. Fisher's exact test was used for statistical analysis of Barrett CK7/20 and gastric CK7/20 patterns between the groups. Results: The anticipated pattern of reactivity in Barrett mucosa (CK7: strong diffuse positivity in superficial and deep glands; CK20: positivity in surface epithelium and superficial glands) was seen in 2 cases of Group A specimens. The expected gastric pattern (CK7: patchy immunostaining with variable involvement of deep glands; CK20: patchy immunostaining of superficial and deep glands in incomplete intestinal metaplasia / absence of CK7 immunoreactivity with strong CK20 staining in superficial and deep glands in complete intestinal metaplasia) was seen in 8 cases of Group B specimens. The respective sensitivity and false-negativity values of CK7/20 staining for Barrett pattern in Group A were 10% and 90%, respectively. These values for gastric pattern in Group B were 40% and 60%, respectively. The specificity and false-positivity values of both patterns were same (100% and 0%, respectively). There was no statistically significant difference for Barrett pattern between the two groups (P = 0.487), while the observation of gastric pattern was significantly higher in Group B than in Group A (P = 0.02). Conclusions: We concluded that these hypothesized and recently applied diagnostic criteria involving CK7 and CK20 immunoreactivity are not reliable in distinguishing short-segment Barrett esophagus from intestinal metaplasia as seen in gastric cardia and corpus.

  • The Variation of Aneuploidy Frequency in the Developing and Adult Human Brain Revealed by an Interphase FISH Study -

    Despite the lack of direct cytogenetic studies, the neuronal cells of the normal human brain have been postulated to contain normal (diploid) chromosomal complement. Direct proof of a chromosomal mutation presence leading to large-scale genomic alterations in neuronal cells has been missing in the human brain. Large-scale genomic variations due to chromosomal complement instability in developing neuronal cells may lead to the variable level of chromosomal mosaicism probably having a substantial effect on brain development. The aim of the present study was the pilot assessment of chromosome complement variations in neuronal cells of developing and adult human brain tissues using interphase multicolor fluorescence in situ hybridization (mFISH). Chromosome-enumerating DNA probes from the original collection (chromosomes 1, 13 and 21, 18, X, and Y) were used for the present pilot FISH study. As a source of fetal brain tissue, the medulla oblongata was used. FISH studies were performed using uncultured fetal brain samples as well as organotypic cultures of medulla oblongata tissue. Cortex tissues of postmortem adult brain samples (Brodmann area 10) were also studied. In cultured in vitro embryonic neuronal brain cells, an increased level of aneuploidy was found (mean rate in the range of 1.3–7.0% per individual chromosome, in contrast to 0.6–3.0% and 0.1–0.8% in uncultured fetal and postmortem adult brain cells, respectively). The data obtained support the hypothesis regarding aneuploidy occurrence in normal developing and adult human brain.

    (J Histochem Cytochem 53:385–390, 2005)


  • Therapeutic Electromagnetic Field (TEMF) and gamma irradiation on human breast cancer xenograft growth, angiogenesis and metastasis - Background: The effects of a rectified semi-sinewave signal (15 mT amplitude, 120 pulses per second, EMF Therapeutics, Inc.) (TEMF) alone and in combination with gamma irradiation (IR) therapy in nude mice bearing a human MDA MB231 breast cancer xenograft were tested. Green fluorescence protein transfected cancer cells were injected into the mammary fat pad of young female mice. Six weeks later, mice were randomly divided into four treatment groups: untreated controls; 10 minute daily TEMF; 200 cGy of IR every other day (total 800 cGy); IR plus daily TEMF. Some mice in each group were euthanized 24 hours after the end of IR. TEMF treatment continued for 3 additional weeks. Tumor sections were stained for: endothelial cells with CD31 and PAS or hypoxia inducible factor 1a (HIF). Results: Most tumors <35 mm3 were white but tumors >35 mm3 were pink and had a vascularized capsule. The cortex within 100 microns of the capsule had little vascularization. Blood vessels, capillaries, and endothelial pseudopods were found at >100 microns from the capsule (subcortex). Tumors >35mm3 treated with IR 24 hours previously or with TEMF had decreased blood vessels in the subcortex and more endothelial pseudopods projecting into hypoxic, HIF positive areas than tumors from the control group. Mice that received either IR or TEMF had significantly fewer lung metastatic sites and slower tumor growth than did untreated mice. No harmful side effects were attributed to TEMF. Conclusion: TEMF therapy provided a safe means for retarding tumor vascularization, growth and metastasis.

  • Three Cases with Enlarged Acrocentric p-arms and Two Cases with Cryptic Partial Trisomies -

    In three cases, banding analysis revealed a normal karyotype except for an enlarged short arm of one chromosome 13 or 15. To clarify whether this enlargement was due to a heteromorphism or to a cryptic chromosomal trisomy, so-called cenM-FISH probe sets containing a microdissection-derived probe specific for the acrocentric human p-arms were applied. The results enabled us to confirm in one case and to exclude in two cases that the enlargement on the suspect chromosome was due to a p-arm polymorphism. M-FISH and/or microdissection were used to resolve the nature of the rearrangements, i.e., partial trisomies 6 and 19. (J Histochem Cytochem 53:359–360, 2005)


  • Three-dimensional Imaging of the Intracellular Localization of Growth Hormone and Prolactin and Their mRNA Using Nanocrystal (Quantum Dot) and Confocal Laser Scanning Microscopy Techniques -

    Semiconductor nanocrystals (Quantum dots, Qdots) have recently been used in biological research, because they do not fade on exposure to light, and they enable us to obtain multicolor imaging because of a narrow emission peak that can be excited via a single wavelength of light. There have been no reports of simultaneous localization of mRNA and protein using Qdots. We successfully applied these advantages of Qdot and confocal laser scanning microscopy (CLSM) to three-dimensional images of the intracellular localization of growth hormone and prolactin and to their mRNA. In situ hybridization and immunohistochemistry using Qdots combined with CLSM can optimally illustrate the relationship between protein and mRNA simultaneously in three dimensions. Such an approach enables us to visualize functional images of proteins in relation with mRNA synthesis and localization.

    (J Histochem Cytochem 53:833–838, 2005)


  • Three-dimensional Imaging of the Intracellular Localization of Growth Hormone and Prolactin and Their mRNA Using Nanocrystal (Quantum Dot) and Confocal Laser Scanning Microscopy Techniques -

    Semiconductor nanocrystals (Quantum dots, Qdots) have recently been used in biological research, because they do not fade on exposure to light, and they enable us to obtain multicolor imaging because of a narrow emission peak that can be excited via a single wavelength of light. There have been no reports of simultaneous localization of mRNA and protein using Qdots. We successfully applied these advantages of Qdot and confocal laser scanning microscopy (CLSM) to three-dimensional images of the intracellular localization of growth hormone and prolactin and to their mRNA. In situ hybridization and immunohistochemistry using Qdots combined with CLSM can optimally illustrate the relationship between protein and mRNA simultaneously in three dimensions. Such an approach enables us to visualize functional images of proteins in relation with mRNA synthesis and localization.

    (J Histochem Cytochem 53:833–838, 2005)


  • Thrombocytopenia in Dengue Fever - Dengue is probably the most important arthropod-borne viral disease in terms of human morbidity and mortality. We review the pathophysiology of thrombocytopenia and clinical bleeding in dengue across the spectrum of disease. The mechanisms of thrombocytopenia and coagulopathy are complex, involving platelet activation, procoagulant and anticoagulant arms of the coagulation system, complement, cytokines, and endothelial cells. Platelet counts do not correlate well with clinical -bleeding. Although serious bleeding is rare, patients should be monitored closely for hemorrhagic manifestations and -thrombocytopenia. Symptomatic thrombocytopenia may require platelet transfusion.

  • Thrombopoietic Growth Factors and Cytokines - Chemotherapy-induced thrombocytopenia is largely -managed with platelet transfusions and reductions of chemotherapy doses. In the last decade, several thrombopoietic cytokines have been investigated without much success. Thrombopoietin (TPO), a key physiologic regulator of -platelet production, is found to be the most potent -thrombopoietic cytokine studied so far. Unfortunately, the clinical development of recombinant human thrombopietin has met challenges related to the biology of TPO with a delayed peak platelet response and the findings of -neutralizing antibodies to the pegylated molecule. Recent clinical studies showed the importance of TPO schedule in relation to chemotherapy. Also, recombinant TPO facilitated collection of platelets in normal donors and patients for transfusions. The initial trials in leukemia or transplant -settings did not impact the need for platelet transfusions. Future developments of TPO and mimetics will require carefully designed clinical trials with the consideration of unique biology of TPO and the time lag for a peak platelet response.

  • Thymus-derived glucocorticoids are insufficient for normal thymus homeostasis in the adult mouse - Background: It is unclear if thymus-derived glucocorticoids reach sufficient local concentrations to support normal thymus homeostasis, or if adrenal-derived glucocorticoids from the circulation are required. Modern approaches to this issue (transgenic mice that under or over express glucocorticoid receptor in the thymus) have yielded irreconcilably contradictory results, suggesting fundamental problems with one or more the transgenic mouse strains used. In the present study, a more direct approach was used, in which mice were adrenalectomized with or without restoration of circulating corticosterone using timed release pellets. Reversal of the increased number of thymocytes caused by adrenalectomy following restoration of physiological corticosterone concentrations would indicate that corticosterone is the major adrenal product involved in thymic homeostasis. Results: A clear relationship was observed between systemic corticosterone concentration, thymus cell number, and percentage of apoptotic thymocytes. Physiological concentrations of corticosterone in adrenalectomized mice restored thymus cell number to normal values and revealed differential sensitivity of thymocyte subpopulations to physiological and stress-inducible corticosterone concentrations. Conclusion: This indicates that thymus-derived glucocorticoids are not sufficient to maintain normal levels of death by neglect in the thymus, but that apoptosis and possibly other mechanisms induced by physiological, non stress-induced levels of adrenal-derived corticosterone are responsible for keeping the total number of thymocytes within the normal range.

  • Thyroid hormone receptor binding to DNA and T3-dependent transcriptional activation are inhibited by uremic toxins - Background: There is a substantial clinical overlap between chronic renal failure and hypothyroidism, suggesting the presence of hypothyroidism in uremic patients. Although CRF patients have low T3 and T4 levels with normal TSH, they show a higher prevalence of goiter and evidence for blunted tissue responsiveness to T3 action. However, there are no studies examining whether thyroid hormone receptors (TRs) play a role in thyroid hormone dysfunction in CRF patients. To evaluate the effects of an uremic environment on TR function, we investigated the effect of uremic plasma on TRbeta1 binding to DNA as heterodimers with the retinoid X receptor alpha (RXR) and on T3-dependent transcriptional activity. Results: We demonstrated that uremic plasma collected prior to hemodialysis (Pre-HD) significantly reduced TR-RXR binding to DNA. Such inhibition was also observed with a vitamin D receptor (VDR) but not with a peroxisome proliferator-activated receptor gamma (PPAR). A cell-based assay confirmed this effect where uremic pre-HD ultrafiltrate inhibited the transcriptional activation induced by T3, in U937 cells. In both cases, the inhibitory effects were reversed when the uremic plasma and the uremic ultrafiltrate were collected and used after hemodialysis (Post-HD). Conclusions: These results suggest that dialyzable toxins in uremic plasma selectively block the binding of TR-RXR to DNA and impair T3 transcriptional activity. These findings may explain some features of hypothyroidism and thyroid hormone resistance observed in CRF patients.

  • Tissue eosinophilia: a morphologic marker for assessing stromal invasion in laryngeal squamous neoplasms - Background: The assessment of tumor invasion of underlying benign stroma in neoplastic squamous proliferation of the larynx may pose a diagnostic challenge, particularly in small biopsy specimens that are frequently tangentially sectioned. We studied whether thresholds of an eosinophilic response to laryngeal squamous neoplasms provides an adjunctive histologic criterion for determining the presence of invasion. Methods: Eighty-seven(n = 87) cases of invasive squamous cell carcinoma and preinvasive squamous neoplasia were evaluated. In each case, the number of eosinophils per high power field(eosinophils/hpf), and per 10 hpf in the tissue adjacent to the neoplastic epithelium, were counted and tabulated. For statistical purposes, the elevated eosinophils were defined and categorized as: focally and moderately elevated (5–9 eos/hpf), focally and markedly increased(>10/hpf), diffusely and moderately elevated(5–19 eos/10hpf), and diffusely and markedly increased (>20/10hpf). Results: In the invasive carcinoma, eosinophil counts were elevated focally and /or diffusely, more frequently seen than in non-invasive neoplastic lesions. The increased eosinophil counts, specifically >10hpf, and >20/10hpf, were all statistically significantly associated with stromal invasion. Greater than 10 eosinophils/hpf and/or >20 eosinophils/10hpf had highest predictive power, with a sensitivity, specificity and positive predictive value of 82%, 93%, 96% and 80%, 100% and 100%, respectively. Virtually, greater than 20 eosinophils/10 hpf was diagnostic for tumor invasion in our series. Conclusion: Our study suggests for the first time that the elevated eosinophil count in squamous neoplasia of the larynx is a morphologic feature associated with tumor invasion. When the number of infiltrating eosinophils exceeds 10/hpf and or >20/10 hpf in a laryngeal biopsy with squamous neoplasia, it represents an indicator for the possibility of tumor invasion. Similarly, the presence of eosinophils meeting these thresholds in an excisional specimen should prompt a thorough evaluation for invasiveness, when evidence of invasion is absent, or when invasion is suspected by conventional criteria in the initial sections.

  • Tissue transglutaminase-induced alterations in extracellular matrix inhibit tumor invasion - Background: Alterations in the extracellular matrix (ECM) can affect host-tumor interactions and tumor growth and metastasis. Tissue transglutaminase (TG2, EC 2.3.2.13), a calcium-dependent enzyme that catalyzes covalent cross-linking of proteins, can render the ECM highly stable and resistant to proteolytic degradation. So we determined whether TG2 expression in a tumor or nontumor (stroma) environment could affect the process of metastasis. Two hundred archived samples from patients with breast cancer were studied for the TG2 expression. Also, in an in vitro model the invasive behavior of MDA-MB-231 cells in the presence or absence of exogenous TG2 was determined. Results: Tumors associated with negative nodes showed significantly higher expression of TG2 in the stroma (P < 0.001). TG2 in the stroma was catalytically active, as revealed by the presence of isopeptide cross-links. Pretreatment of Matrigel with catalytically active TG2 resulted in strong inhibition of invasion of MDA-MB-231 cells through the Matrigel Transwell filters. Conclusion: TG2-induced alterations in the ECM could effectively inhibit the process of metastasis. Therefore, selective induction of catalytically active TG2 at the site of tumor may offer promising approach for limiting the metastasis.

  • Tissue-specific Tropomyosin Isoform Composition -

    Four distinct genes encode tropomyosin (Tm) proteins, integral components of the actin microfilament system. In non-muscle cells, over 40 Tm isoforms are derived using alternative splicing. Distinct populations of actin filaments characterized by the composition of these Tm isoforms are found differentially sorted within cells (Gunning et al. 1998b). We hypothesized that these distinct intracellular compartments defined by the association of Tm isoforms may allow for independent regulation of microfilament function. Consequently, to understand the molecular mechanisms that give rise to these different microfilaments and their regulation, a cohort of fully characterized isoform-specific Tm antibodies was required. The characterization protocol initially involved testing the specificity of the antibodies on bacterially produced Tm proteins. We then confirmed that these Tm antibodies can be used to probe the expression and subcellular localization of different Tm isoforms by Western blot analysis, immunofluorescence staining of cells in culture, and immunohistochemistry of paraffin wax–embedded mouse tissues. These Tm antibodies, therefore, have the capacity to monitor specific actin filament populations in a range of experimental systems. (J Histochem Cytochem 53:557–570, 2005)


  • Tissue-specific Tropomyosin Isoform Composition -

    Four distinct genes encode tropomyosin (Tm) proteins, integral components of the actin microfilament system. In non-muscle cells, over 40 Tm isoforms are derived using alternative splicing. Distinct populations of actin filaments characterized by the composition of these Tm isoforms are found differentially sorted within cells (Gunning et al. 1998b). We hypothesized that these distinct intracellular compartments defined by the association of Tm isoforms may allow for independent regulation of microfilament function. Consequently, to understand the molecular mechanisms that give rise to these different microfilaments and their regulation, a cohort of fully characterized isoform-specific Tm antibodies was required. The characterization protocol initially involved testing the specificity of the antibodies on bacterially produced Tm proteins. We then confirmed that these Tm antibodies can be used to probe the expression and subcellular localization of different Tm isoforms by Western blot analysis, immunofluorescence staining of cells in culture, and immunohistochemistry of paraffin wax–embedded mouse tissues. These Tm antibodies, therefore, have the capacity to monitor specific actin filament populations in a range of experimental systems. (J Histochem Cytochem 53:557–570, 2005)


  • Tissue-specific Tropomyosin Isoform Composition -

    Four distinct genes encode tropomyosin (Tm) proteins, integral components of the actin microfilament system. In non-muscle cells, over 40 Tm isoforms are derived using alternative splicing. Distinct populations of actin filaments characterized by the composition of these Tm isoforms are found differentially sorted within cells (Gunning et al. 1998b). We hypothesized that these distinct intracellular compartments defined by the association of Tm isoforms may allow for independent regulation of microfilament function. Consequently, to understand the molecular mechanisms that give rise to these different microfilaments and their regulation, a cohort of fully characterized isoform-specific Tm antibodies was required. The characterization protocol initially involved testing the specificity of the antibodies on bacterially produced Tm proteins. We then confirmed that these Tm antibodies can be used to probe the expression and subcellular localization of different Tm isoforms by Western blot analysis, immunofluorescence staining of cells in culture, and immunohistochemistry of paraffin wax–embedded mouse tissues. These Tm antibodies, therefore, have the capacity to monitor specific actin filament populations in a range of experimental systems. (J Histochem Cytochem 53:557–570, 2005)


  • TMA-Combiner, a simple software tool to permit analysis of replicate cores on tissue microarrays - Chih Long Liu, Kelli D Montgomery, Yasodha Natkunam, Robert B West, Torsten O Nielsen, Maggie C U Cheang, Dmitry A Turbin, Robert J Marinelli, Matt van de Rijn & John P T Higgins

  • Topographical expression of class IA and class II phosphoinositide 3-kinase enzymes in normal human tissues is consistent with a role in differentiation - Background: Growth factor, cytokine and chemokine-induced activation of PI3K enzymes constitutes the start of a complex signalling cascade, which ultimately mediates cellular activities such as proliferation, differentiation, chemotaxis, survival, trafficking, and glucose homeostasis. The PI3K enzyme family is divided into 3 classes; class I (subdivided into IA and IB), class II (PI3K-C2α, PI3K-C2β and PI3K-C2γ) and class III PI3K. Expression of these enzymes in human tissue has not been clearly defined. Methods: In this study, we analysed the immunohistochemical topographical expression profile of class IA (anti-p85 adaptor) and class II PI3K (PI3K-C2α and PI3K-C2β) enzymes in 104 formalin-fixed, paraffin embedded normal adult human (age 33–71 years, median 44 years) tissue specimens including those from the gastrointestinal, genitourinary, hepatobiliary, endocrine, integument and lymphoid systems. Antibody specificity was verified by Western blotting of cell lysates and peptide blocking studies. Immunohistochemistry intensity was scored from undetectable to strong. Results: PI3K enzymes were expressed in selected cell populations of epithelial or mesenchymal origin. Columnar epithelium and transitional epithelia were reactive but mucous secreting and stratified squamous epithelia were not. Mesenchymal elements (smooth muscle and endothelial cells) and glomerular epithelium were only expressed PI3K-C2α while ganglion cells expressed p85 and PI3K-C2β. All three enzymes were detected in macrophages, which served as an internal positive control. None of the three PI3K isozymes was detected in the stem cell/progenitor compartments or in B lymphocyte aggregates. Conclusions: Taken together, these data suggest that PI3K enzyme distribution is not ubiquitous but expressed selectively in fully differentiated, non-proliferating cells. Identification of the normal in vivo expression pattern of class IA and class II PI3K paves the way for further analyses which will clarify the role played by these enzymes in inflammatory, neoplastic and other human disease conditions.

  • Topology of Chromosomes 18 and X in Human Blastomeres from 3- to 4-Day-old Embryos -

    The positions of chromosomes 18 and X fluorescence in situ hybridization signals were analyzed in blastomeres generated from human in vitro fertilization 3- to 4-day-old embryos after preimplantation screening of aneuploidy of chromosomes 13, 16, 18, 21, 22, X, and Y. Fluorescent signal localization compared with a three-dimensional sphere model of random signal distribution revealed significant differences, providing evidence of peripheral localization of chromosome 18 in aneuploid (p=0.0013) and aneuploid/euploid blastomeres (p=0.0011). No differences were found in localization of chromosome 18 in euploid and in chromosome X in euploid and aneuploid blastomeres.

    (J Histochem Cytochem 53:273–276, 2005)


  • tortuga refines Notch pathway gene expression in the zebrafish presomitic mesoderm at the post-transcriptional level. -
    Related Articles

    tortuga refines Notch pathway gene expression in the zebrafish presomitic mesoderm at the post-transcriptional level.

    Dev Biol. 2005 Oct 14;

    Authors: Dill KK, Amacher SL

    We have identified the zebrafish tortuga (tor) gene by an ENU-induced mutation that disrupts the presomitic mesoderm (PSM) expression of Notch pathway genes. In tor mutants, Notch pathway gene expression persists in regions of the PSM where expression is normally off in wild type embryos. The expression of hairy/Enhancer of split-related 1 (her1) is affected first, followed by the delta genes deltaC and deltaD, and finally, by another hairy/Enhancer of split-related gene, her7. In situ hybridization with intron-specific probes for her1 and deltaC indicates that transcriptional bursts of expression are normal in tor mutants, suggesting that tor normally functions to refine her1 and deltaC message levels downstream of transcription. Despite the striking defects in Notch pathway gene expression, somite boundaries form normally in tor mutant embryos, although somitic mesoderm defects are apparent later, when cells mature to form muscle fibers. Thus, while the function of Notch pathway genes is required for proper somite formation, the tor mutant phenotype suggests that precise oscillations of Notch pathway transcripts are not essential for establishing segmental pattern in the presomitic mesoderm.

    PMID: 16236276 [PubMed - as supplied by publisher]


  • Towards Open Access - No abstract.

  • TP53-binding protein variants and breast cancer risk: a case-control study - IntroductionThe TP53-binding protein (53BP1) has been shown to influence TP53-mediated transcriptional activation, thus playing a pivotal role in DNA damage signalling. Genetic aberrations in TP53 and in ATM and CHEK2 predispose to cancer. We have therefore examined the effects of 53BP1 single nucleotide polymorphisms (D353E, G412S, and K1136Q) and the novel 53BP1 6bp deletion (1347_1352delTATCCC) on breast cancer risk. Methods: Allelic discrimination was performed to investigate the frequencies of 53BP1 D353E, G412S, and K1136Q and of 1347_1352delTATCCC in 353 patients with breast cancer and 960 control individuals. Results: No significant association of 53BP1 D353E, G412S, or K1136Q with breast cancer risk was detected. 53BP1 1347_1352delTATCCC, leading to the loss of an isoleucine and a proline residue, showed a nonsignificant inverse association with breast cancer risk (odds ratio = 0.61, 95% confidence interval = 0.22 to 1.68, P = 0.34). Conclusion: The lack of association casts doubt on the putative effects of D353E, G412S, and K1136Q on breast cancer risk. Investigating a larger study cohort might elucidate the influence of the 6bp deletion 1347_1352delTATCCC. Studying the functional effect and the impact of this variant on the risk of other cancers may be revealing.

  • TPO/Mpl Studies in Agnogenic Myeloid Metaplasia - Background: Agnogenic myeloid metaplasia (AMM) is one of the Philadelphia chromosome negative myeloproliferative disorder and is diagnosed by hyperplasia of atypical megakaryocytes, hepatosplenomegaly, extramedullary hematopoiesis and bone marrow fibrosis. Fibrosis is considered to be a secondary consequence of enhanced levels of fibrogenic growth factors such as TGF β1, bFGF and PDGF produced by enhanced numbers of megakaryocytes, while the primary cause is considered to be the enhanced proliferation of a defective stem cell. We have previously reported that thrombopoietin (TPO) is elevated in patients with AMM. Others have reported that Mpl protein is decreased in these patients. Since TPO is essential for the development of megakaryocytes, and Mpl protein is the receptor for TPO, we extended the study of TPO/Mpl to in vitro and in vivo cell culture systems to better understand the mechanism that leads to reduced Mpl protein in AMM patients. Results: Plasma TPO levels were significantly elevated and Mpl protein levels were significantly reduced in AMM patients in concordance with previous studies. Platelet Mpl transcripts in AMM were however similar to those in controls. We also cloned Mpl cDNA from AMM patients and tested for their ability to make functional proteins in vitro and in the in vivo system of 293 T human embryonic kidney cells. Their expression including the glycosylated forms was similar to those from the controls. We also measured the level of translation initiation factor, eIF4E and found it to be increased in patients with AMM demonstrating that the reduced Mpl protein may not be due to translation defects. Conclusions: Our studies using the in vitro and in vivo systems further confirm that reduced Mpl protein levels are not due to defects in its transcription/translation. Reduced Mpl protein could be due to its increased internalisation owing to enhanced plasma TPO or in vivo intrinsic defects in patients with AMM.

  • Transcriptome analysis in primary neural stem cells using a tag cDNA amplification method - Background: Neural stem cells (NSCs) can be isolated from the adult mammalian brain and expanded in culture, in the form of cellular aggregates called neurospheres. Neurospheres provide an in vitro model for studying NSC behaviour and give information on the factors and mechanisms that govern their proliferation and differentiation. They are also a promising source for cell replacement therapies of the central nervous system. Neurospheres are complex structures consisting of several cell types of varying degrees of differentiation. One way of characterising neurospheres is to analyse their gene expression profiles. The value of such studies is however uncertain since they are heterogeneous structures and different populations of neurospheres may vary significantly in their gene expression. Results: To address this issue, we have used cDNA microarrays and a recently reported tag cDNA amplification method to analyse the gene expression profiles of neurospheres originating from separate isolations of the lateral ventricle wall of adult mice and passaged to varying degrees. Separate isolations as well as consecutive passages yield a high variability in gene expression while parallel cultures yield the lowest variability. Conclusions: We demonstrate a low technical amplification variability using the employed amplification strategy and conclude that neurospheres from the same isolation and passage are sufficiently similar to be used for comparative gene expression analysis.

  • Translocation-excision-deletion-amplification mechanism leading to nonsyntenic coamplification of MYC and ATBF1. -
    Related Articles

    Translocation-excision-deletion-amplification mechanism leading to nonsyntenic coamplification of MYC and ATBF1.

    Genes Chromosomes Cancer. 2005 Oct 18;

    Authors: Van Roy N, Vandesompele J, Menten B, Nilsson H, De Smet E, Rocchi M, De Paepe A, PÃ¥hlman S, Speleman F

    Despite oncogene amplification being a characteristic of many tumor types, the mechanisms leading to amplicon formation have remained largely unresolved. In this study, we used a combinatorial approach of fluorescence in situ hybridization and single-nucleotide polymorphism chip gene copy number analyses to unravel the mechanism leading to nonsyntenic coamplification of MYC and ATBF1 in SJNB-12 cells. To explain our findings, we propose a complex series of events consisting of multiple double-strand breaks, accompanied (or triggered) by the formation of a reciprocal translocation t(8;16), as well as excisions and deletions near the translocation breakpoints. This study provides evidence for a translocation-excision-deletion-amplification sequence of events rather than a breakage-fusion-bridge model, which has been more frequently proposed to explain proto-oncogene amplification. Furthermore, it illustrates the power of presently available tools for detailed analysis of the complex rearrangements that accompany amplicon formation. (c) 2005 Wiley-Liss, Inc.

    PMID: 16235245 [PubMed - as supplied by publisher]


  • Trapping of normal EB1 ligands in aggresomes formed by an EB1 deletion mutant - Background: EB1 is a microtubule tip-associated protein that interacts with the APC tumour suppressor protein and the p150glued subunit of dynactin. We previously reported that an EB1 deletion mutant that retains both of these interactions but does not directly associate with microtubules (EB1-deltaN2-GFP) spontaneously formed perinuclear aggregates when expressed in COS-7 cells. Results: In the present study live imaging indicated that EB1-deltaN2-GFP aggregates underwent dynamic microtubule-dependent changes in morphology and appeared to be internally cohesive. EB1-deltaN2-GFP aggregates were phase-dense structures that displayed microtubule-dependent accumulation around the centrosome, were immunoreactive for both the 20s subunit of the proteasome and ubiquitin, and induced the collapse of the vimentin cytoskeleton. Fractionation studies revealed that a proportion of EB1-deltaN2-GFP was detergent-insoluble and ubiquitylated, indicating that EB1-deltaN2-GFP aggregates are aggresomes. Immunostaining also revealed that APC and p150glued were present in EB1-deltaN2-GFP aggregates, whereas EB3 was not. Furthermore, evidence for p150glued degradation was found in the insoluble fraction of EB1-deltaN2-GFP transfected cultures. Conclusions: Our data indicate that aggresomes can be internally cohesive and may not represent a simple "aggregate of aggregates" assembled around the centrosome. Our observations also indicate that a partially misfolded protein may retain the ability to interact with its normal physiological ligands, leading to their co-assembly into aggresomes. This supports the idea that the trapping and degradation of co-aggregated proteins might contribute to human pathologies characterised by aggresome formation.

  • Treating breast cancer through novel inhibitors of the phosphatidylinositol 3'-kinase pathway - Recent studies indicate that constitutive signaling through the phosphatidylinositol 3'-kinase (PI3K) pathway is a cause of treatment resistance in breast cancer patients. This implies that patients with tumors that exhibit aberrant PI3K signaling may benefit from targeted pathway inhibitors. The first agents to make it to the clinic are the rapamycin analogs. These compounds inhibit the downstream PI3K effector mTOR (mammalian target of rapamycin). A study presented in this issue of Breast Cancer Research suggests that recently developed inhibitors of phosphoinositide-dependent protein kinase 1, a more proximal target of the PI3K pathway, may provide an alternative route to effective PI3K pathway inhibition for breast cancer treatment.

  • Treatment of Polycythemia Vera with Recombinant Interferon a (rIFNa) or Imatinib Mesylate - Polycythemia vera (PV) is a myeloproliferative disease which if untreated leads to thrombohemorrhagic compli-cations and eventually to progressive myelofibrosis of the marrow, anemia, and splenomegaly. Two new drugs are now available, interferon and imatinib mesylate, which may alter the course of this disease. Used as single agents, each produces lasting remissions in about 75% of the cases.

  • Treatment of solid tumors with immunotoxins - Immunotoxins are hybrid molecules that generally consist of a toxin coupled with a tumor-specific antibody or antibody fragment that is intended to target and concentrate the toxin within the tumor tissue. The biodistribution, specificity, immunogenicity, and cytotoxic activity of the immunotoxin are but a few of the factors that govern the effectiveness of these compounds in the treatment of patients with cancer. Improvements in design, synthesis, and delivery of these molecules may permit them to become significant components in the arsenal of targeted therapies for cancer.

  • Trial Report - Anemia - No abstract available

  • Trial Report - Bleeding Disorders - No abstract available

  • Trial Report - Bone Marrow Transplantation - No abstract available

  • Trial Report - Myelodysplastic Syndrome - No abstract available

  • Trial Report - Myeloproliferative Syndromes - No abstract available

  • Trial Report - Thrombocytopenias - No abstract available

  • Trial Report - Thrombotic Disorders - No abstract available

  • Trophoblasts Isolated from the Maternal Circulation: In Vitro Expansion and Potential Application in Non-invasive Prenatal Diagnosis -

    Prenatal diagnosis based on rare fetal cells in maternal blood is currently not a feasible option. An effort was made to improve cell yields by targeting trophoblast cells. After sorting, the HLA-G-positive cell fraction was analyzed directly or after culture. In situ hybridization technology was applied to prove fetal cell source in samples from women carrying a male fetus and to predict gender in samples without previous knowledge of fetal sex. In vitro culture led to a significant increase in fetal cells and accurate gender prediction in 93% of these samples. This approach might be useful for non-invasive prenatal diagnosis. (J Histochem Cytochem 53:337–339, 2005)


  • Tumor suppressor in lung cancer 1 (TSLC1)alters tumorigenic growth properties and gene expression - Background: Introduction of cDNA or genomic clones of the tumor suppressor in lung cancer 1 (TSLC1) gene into the non-small cell lung cancer line, A549, reverses tumorigenic growth properties of these cells. These results and the observation that TSLC1 is down-regulated in a number of tumors suggest that TSLC1 functions as a critical switch mediating repression of tumorigenesis. Results: To investigate this mechanism, we compared growth properties of A549 with the TSLC1-containing derivative. We found a G1/S phase transition delay in 12.2. Subtractive hybridization, quantitative PCR, and TranSignal Protein/DNA arrays were used to identify genes whose expression changed when TSLC1 was up-regulated. Members of common G1/S phase regulatory pathways such as TP53, MYC, RB1 and HRAS were not differentially expressed, indicating that TSLC1 may function through an alternative pathway(s). A number of genes involved in cell proliferation and tumorigenesis were differentially expressed, notably genes in the Ras-induced senescence pathway. We examined expression of several of these key genes in human tumors and normal lung tissue, and found similar changes in expression, validating the physiological relevance of the A549 and 12.2 cell lines. Conclusions: Gene expression and cell cycle differences provide insights into potential downstream pathways of TSLC1 that mediate the suppression of tumor properties in A549 cells.

  • Type 2N von Willebrand Disease - Type 2N von Willebrand disease (VWD) refers to patients with a factor VIII (FVIII) deficiency caused by a markedly decreased affinity of von Willebrand factor (VWF) for FVIII. It is inherited as an autosomal recessive trait but is clinically similar to mild hemophilia. The differential biologic diagnosis, which is of major importance for providing relevant genetic counseling and optimal treatment, is based on the measurement of plasma VWF capacity to bind FVIII. Molecular biology techniques have allowed the identification of 20 missense mutations in the VWF gene that cause type 2N VWD. All of them induce changes in amino acid residues located in the N-terminal part of mature VWF, which contains the FVIII binding site. Their identification may provide a genetic diagnosis. Theoretically, patients with type 2N VWD should be treated with products containing VWF that is able to stabilize their endogenous normal FVIII.

  • U94 alters FN1 and ANGPTL4 gene expression and inhibits tumorigenesis of prostate cancer cell line PC3. - Background: Insensitivity of advanced-stage prostate cancer to androgen ablation therapy is a serious problem in clinical practice because it is associated with aggressive progression and poor prognosis. Targeted therapeutic drug discovery efforts are thwarted by lack of adequate knowledge of gene(s) associated with prostate tumorigenesis. Therefore there is the need for studies to provide leads to targeted intervention measures. Here we propose that stable expression of U94, a tumor suppressor gene encoded by human herpesvirus 6A (HHV-6A), could alter gene expression and thereby inhibit the tumorigenicity of PC3 cell line. Microarray gene expression profiling on U94 recombinant PC3 cell line could reveal genes that would elucidate prostate cancer biology, and hopefully identify potential therapeutic targets. Results: We have shown that stable expression of U94 gene in PC3 cell line inhibited its focus formation in culture, and tumorigenesis in nude mice. Moreover gene expression profiling revealed dramatic upregulation of FN 1 (fibronectin, 91+/-16-fold), and profound downregulation of ANGPTL 4 (angiopoietin-like-4, 20+/-4-fold) in U94 recombinant PC3 cell line. Quantitative real-time polymerase chain reaction (QRT-PCR) analysis showed that the pattern of expression of FN 1 and ANGPTL 4 mRNA were consistent with the microarray data. Based on previous reports, the findings in this study implicate upregulation of FN 1 and downregulation of ANGPTL 4 in the anti tumor activity of U94. Genes with cancer inhibitory activities that were also upregulated include SERPINE 2 (serine/cysteine protease inhibitor 2, 7+/-1-fold increase) and ADAMTS 1 (a disintegrin-like and metalloprotease with thrombospondin type 1 motif, 7+/-2-fold increase). Additionally, SPUVE 23 (serine protease 23) that is pro-tumorigenic was significantly downregulated (10+/-1-fold). Conclusion: The dramatic upregulation of FN 1 and downregulation of ANGPTL 4 genes in PC3 cell line stably expressing U94 implicate up-regulation of FN 1 and downregulation of ANGPTL 4 in anti tumor activity of U94. Further studies are necessary to determine functional roles of differentially expressed genes in U94 recombinant PC3 cell line, and hopefully provide leads to potential therapeutic targets in prostate cancer.

  • Ultrastructural Studies and Na+,K+-ATPase Immunolocalization in the Antennal Urinary Glands of the Lobster Homarus gammarus (Crustacea, Decapoda) -

    Unlike in crustacean freshwater species, the structure and ultrastructure of the excretory antennal gland is poorly documented in marine species. The general organization and ultrastructure of the cells and the localization of Na+,K+-ATPase were examined in the antennal gland of the adult lobster Homarus gammarus. Each gland is composed of a centrally located coelomosac surrounded ventrally by a labyrinth divided into two parts (I and II) and dorsally by a voluminous bladder. There is no differentiated nephridal tubule between them. The labyrinth and bladder cells have in common a number of ultrastructural cytological features, including basal membrane infoldings associated with mitochondria, apical microvilli, and cytoplasmic extrusions, and a cytoplasm packed with numerous vacuoles, vesicles, lysosome-like bodies, and swollen mitochondria. Each type of cell also presents distinctive characters. Na+,K+-ATPase was detected through immunofluorescence in the basal part of the cells of the labyrinth and in the bladder cells with an increasing immunostaining from labyrinth I to the bladder. No immunoreactivity was detected in the coelomosac. The cells of the labyrinth and of the bladder present morphological and enzymatic features of ionocytes. The antennal glands of the lobster thus possess active ion exchanges capabilities. (J Histochem Cytochem 53:1203–1214, 2005)


  • Ultrastructural Studies and Na+,K+-ATPase Immunolocalization in the Antennal Urinary Glands of the Lobster Homarus gammarus (Crustacea, Decapoda) -

    Unlike in crustacean freshwater species, the structure and ultrastructure of the excretory antennal gland is poorly documented in marine species. The general organization and ultrastructure of the cells and the localization of Na+,K+-ATPase were examined in the antennal gland of the adult lobster Homarus gammarus. Each gland is composed of a centrally located coelomosac surrounded ventrally by a labyrinth divided into two parts (I and II) and dorsally by a voluminous bladder. There is no differentiated nephridal tubule between them. The labyrinth and bladder cells have in common a number of ultrastructural cytological features, including basal membrane infoldings associated with mitochondria, apical microvilli, and cytoplasmic extrusions, and a cytoplasm packed with numerous vacuoles, vesicles, lysosome-like bodies, and swollen mitochondria. Each type of cell also presents distinctive characters. Na+,K+-ATPase was detected through immunofluorescence in the basal part of the cells of the labyrinth and in the bladder cells with an increasing immunostaining from labyrinth I to the bladder. No immunoreactivity was detected in the coelomosac. The cells of the labyrinth and of the bladder present morphological and enzymatic features of ionocytes. The antennal glands of the lobster thus possess active ion exchanges capabilities. (J Histochem Cytochem 53:1203–1214, 2005)


  • Ultrastructural Studies of Human Basophils and Mast Cells -

    Ultrastructural studies of human mast cells (HMCs) and basophils (HBs) are reviewed. Sources of HMCs include biopsies of tissue sites and in situ study of excised diseased organs; isolated, partially purified samples from excised organs; and growth-factor-stimulated mast cells that develop de novo in cultures of cord blood cells. Sources of HBs for study include partially purified peripheral blood basophils, basophils in tissue biopsies, and specific growth factor-stimulated basophils arising de novo from cord blood cells. The ultrastructural studies reviewed deal with identity, secretion, vesicles, recovery, and synthesis issues related to the biology of these similar cells.

    (J Histochem Cytochem 53:1043–1070, 2005)


  • Understanding endocrine resistance: the critical need for sequential samples from clinical breast cancer and novel in vitro models - No abstract available

  • Understanding the Antiphospholipid Syndrome and Its Treatment - The antiphospholipid syndrome (APS) is a clinicopathologic disorder characterized by the persistent presence of anticardiolipin antibodies, lupus anticoagulants, or both in the plasma of patients with arterial or venous thrombosis or obstetric complications. The antiphospholipid antibodies involved in this syndrome have a relatively weak affinity for phospholipid-binding proteins such as b2 glycoprotein I and prothrombin. In certain conditions they form bivalent -antibody-protein complexes that bind with a relatively high affinity to negatively charged phospholipid surfaces. Evidence is accumulating for a pathogenetic role of antiphospholipid antibodies via interference with surface-mediated anticoagulant and procoagulant processes. The syndrome is characterized by the recurrence of thrombotic and obstetric complications. Retrospective studies have suggested that patients with APS and thrombosis need a high-intensity anticoagulant treatment. A few small prospective studies support treatment with a targeted INR of 2 to 3.

  • Unexpected combination of acute croup and myocarditis: Case report - Background: Lower vaccination coverage among foreign-born children is of concern because they live in households and communities characterized by more intense exposure to infectious diseases. Because of their higher prevalence rates, there is an increasing occurrence of infectious diseases imported into developed countries. This case report emphasizes the emerging necessity for new clinicians and pathologists of having competence with old infectious disease pathology.Case presentationA 3.5 year-old unvaccinated immigrant girl, who presented with croup history of 5 days and has been in severe respiratory distress, was admitted to the Pediatric Intensive Care Unit in shock and acute respiratory failure. The patient was immediately intubated, and a grayish nonadherent membrane extending through the glottis down into the larynx was apparent during the procedure. Echocardiographic findings, which were consistent with acute myocarditis, confirmed poor left ventricular contractility despite escalating high doses of inotropes. Autopsy showed numerous strains of toxigenic corynobacterium diphtheriae, which also grew on the Loeffler cultures of membranes received during the intubation. Conclusions: It is critical that new generations of clinicians and bio-pathologists not only be trained in the subspecialty of infectious disease pathology, but that they also be willing participants in the diagnosis and investigation of infectious diseases.

  • Update on Gene Therapy Approaches for Cancer - The goal of cancer gene therapy is the selective and efficient eradication of tumor cells without significant systemic toxicity. Although several different gene therapy approaches have been developed and tested both in preclinical and clinical trials, none of these methods are suitable for the safe and efficient treatment of cancer. Recent advances in tumor cell biology have accelerated the identification of novel proteins as targets for gene transfer strategies. However, the development of vectors and delivery systems for specific and efficient gene therapy has not kept pace with these discoveries. Below, we describe the most widely used gene therapy approaches and discuss the caveats of using these techniques in the clinic.

  • Upregulation of Neuronal Nitric Oxide Synthase mRNA and Protein in Adrenal Medulla of Water-deprived Rats -

    Experiments were performed to investigate whether adrenal neuronal nitric oxide synthase (nNOS) mRNA and protein expression are responsive to alterations in body volume. Using an RT-PCR technique, the relative quantities of nNOS mRNA as well as the tyrosine hydroxylase and phenylethanolamine N-methyltransferase mRNA in the adrenals of water-deprived rats significantly increased from 12 hr to 4 days. In situ hybridization and immunohistochemical study showed that water deprivation activated nNOS mRNA and protein expression in the adrenal medulla. Four days after water deprivation, nNOS protein expression determined by Western blot significantly increased in the adrenal gland. Our results are the first to demonstrate that nNOS syntheses in the adrenal medulla are markedly increased in water-deprived rats. This study also indicates that the upregulation of nNOS synthesis of the adrenal medulla is associated with the activation of adrenal medullary function in the face of volume depletion. (J Histochem Cytochem 53:45–53, 2005)


  • Uremic Platelet Dysfunction: Past and Present - Uremic patients develop an acquired platelet dysfunction that results in bleeding complications. The pathogenesis of this hemostatic dysfunction is multifactorial and includes effects of circulating toxins, alterations of the vessel wall, anemia, and other factors, complicated by unwanted effects of hemodialysis procedures. This review seeks to place in perspective the evolution of knowledge on uremic platelet dysfunction. It examines how investigations of the altered hemostasis in these patients have led to a better understanding of the mechanisms involved and how these advances have contributed to the development of effective therapeutic strategies. It also comments upon the fact that elevated rates of thrombotic complications are apparently emerging as the bleeding tendency is better controlled. Emphasized is the delicate balance of hemostasis in the uremic condition, in which deficient hemostasis paradoxically coexists with accelerated atherosclerosis and an enhanced risk of thrombosis.

  • Utility of [alpha]-Methylacyl Coenzyme A Racemase (P504S Antibody) as a Diagnostic Immunohistochemical Marker for Cancer. -

  • Variation in gene expression patterns in effusions and primary tumors from serous ovarian cancer patients - Background: While numerous studies have characterized primary ovarian tumors, little information is available regarding expression patterns of metastatic sites of this cancer. To define sets of genes that distinguish primary and metastatic ovarian tumors, we used cDNA microarrays to characterize global gene expression patterns in 38 effusions (28 peritoneal, 10 pleural) and 8 corresponding primary ovarian tumors, and searched for associations between expression patterns and clinical parameters. Results: We observed multidimensional variation in expression patterns among the cancers. Coordinate variation in expression of genes from two chromosomal regions, 8q and 19q, was seen in subsets of the cancers indicating possible amplifications in these regions. A set of 112 unique genes of known function was differentially expressed between primary tumors and effusions using supervised analysis. Relatively few differences were seen between effusions isolated from the pleural and peritoneal cavities or between effusions from patients diagnosed with stage III and stage IV cancers. A set of 84 unique genes was identified that distinguished high from lower grade ovarian cancers. The results were corroborated using immunocytochemistry, mRNA in situ hybridization, and immunoblotting. Conclusions: The extensive variation in expression patterns observed underscores the molecular heterogeneity of ovarian cancer, but suggests a similar molecular profile for ovarian carcinoma cells in serosal cavities.

  • Variation in transcriptional regulation of cyclin dependent kinase inhibitor p21waf1/cip1among human bronchogenic carcinomas - Background: Cell proliferation control depends in part on the carefully ordered regulation of transcription factors. The p53 homolog p73, contributes to this control by directly upregulating the cyclin dependent kinase inhibitor, p21waf1/cip1. E2F1, an inducer of cell proliferation, directly upregulates p73 and in some systems upregulates p21 directly. Because of its central role in controlling cell proliferation, upregulation of p21 has been explored as a modality for treating bronchogenic carcinoma (BC). Improved understanding of p21 transcriptional regulation will facilitate identification of BC tissues that are responsive to p21-directed therapies. Toward this goal, we investigated the role that E2F1 and p73 each play in the transcriptional regulation of p21. Results: Among BC samples (N=21) p21 transcript abundance (TA) levels varied over two orders of magnitude with values ranging from 400 to 120,000 (in units of molecules/10^6 molecules beta-actin). The p21 values in many BC were high compared to those observed in normal bronchial epithelial cells (BEC) (N=18). Among all BC samples, there was no correlation between E2F1 and p21 TA but there was positive correlation between E2F1 and p73alpha (p<0.001) TA. Among BC cell lines with inactivated p53 and wild type p73 (N=7) there was positive correlation between p73alpha and p21 TA (p<0.05). Additionally, in a BC cell line in which both p53 and p73 were inactivated (H1155), E2F1 TA level was high (50,000), but p21 TA level was low (470). Transiently expressed exogenous p73alpha in the BC cell line Calu-1, was associated with a significant (p<0.05) 90% increase in p21 TA and a 20% reduction in E2F1 TA. siRNA mediated reduction of p73 TA in the N417 BC cell line was associated with a significant reduction in p21 TA level (p<0.01). Conclusion: p21 TA levels vary considerably among BC patients which may be attributable to 1) genetic alterations in Rb and p53 and 2) variation in TA levels of upstream transcription factors E2F1 and p73. Here we provide evidence that p73 upregulates p21 TA in BC tissues and upregulated p21 TA may result from E2F1 upregulation of p73 but not from E2F1 directly.

  • Visualization of the Nuclear Lamina in Mouse Anterior Pituitary Cells and Immunocytochemical Detection of Lamin A/C by Quick-freeze Freeze-substitution Electron Microscopy -

    We examined the nuclear lamina in the quickly frozen anterior pituitary cells by electron microscopic techniques combined with freeze substitution, deep etching, and immunocytochemistry and compared it with that in the chemically fixed cells. By quick-freeze freeze-substitution electron microscopy, an electron-lucent layer, as thick as 20 nm, was revealed just inside the inner nuclear membrane, whereas in the conventionally glutaraldehyde-fixed cells the layer was not seen. By quick-freeze deep-etch electron microscopy, we could not distinguish definitively the layer corresponding to the nuclear lamina in either fresh unfixed or glutaraldehyde-fixed cells. Immunofluorescence microscopy showed that lamin A/C in the nucleus was detected in the acetone-fixed cells and briefly in paraformaldehyde-fixed cells but not in the cells with prolonged paraformaldehyde fixation. Nuclear localization of lamin A/C was revealed by immunogold electron microscopy also in the quickly frozen and freeze-substituted cells, but not in the paraformaldehyde-fixed cells. Lamin A/C was localized mainly in the peripheral nucleoplasm within 60 nm from the inner nuclear membrane, which corresponded to the nuclear lamina. These results suggest that the nuclear lamina can be preserved both ultrastructurally and immunocytochemically by quick-freezing fixation, rather than by conventional chemical fixation.

    (J Histochem Cytochem 53:497–507, 2005)


  • Visualization of the Nuclear Lamina in Mouse Anterior Pituitary Cells and Immunocytochemical Detection of Lamin A/C by Quick-freeze Freeze-substitution Electron Microscopy -

    We examined the nuclear lamina in the quickly frozen anterior pituitary cells by electron microscopic techniques combined with freeze substitution, deep etching, and immunocytochemistry and compared it with that in the chemically fixed cells. By quick-freeze freeze-substitution electron microscopy, an electron-lucent layer, as thick as 20 nm, was revealed just inside the inner nuclear membrane, whereas in the conventionally glutaraldehyde-fixed cells the layer was not seen. By quick-freeze deep-etch electron microscopy, we could not distinguish definitively the layer corresponding to the nuclear lamina in either fresh unfixed or glutaraldehyde-fixed cells. Immunofluorescence microscopy showed that lamin A/C in the nucleus was detected in the acetone-fixed cells and briefly in paraformaldehyde-fixed cells but not in the cells with prolonged paraformaldehyde fixation. Nuclear localization of lamin A/C was revealed by immunogold electron microscopy also in the quickly frozen and freeze-substituted cells, but not in the paraformaldehyde-fixed cells. Lamin A/C was localized mainly in the peripheral nucleoplasm within 60 nm from the inner nuclear membrane, which corresponded to the nuclear lamina. These results suggest that the nuclear lamina can be preserved both ultrastructurally and immunocytochemically by quick-freezing fixation, rather than by conventional chemical fixation.

    (J Histochem Cytochem 53:497–507, 2005)


  • Visualization of the Nuclear Lamina in Mouse Anterior Pituitary Cells and Immunocytochemical Detection of Lamin A/C by Quick-freeze Freeze-substitution Electron Microscopy -

    We examined the nuclear lamina in the quickly frozen anterior pituitary cells by electron microscopic techniques combined with freeze substitution, deep etching, and immunocytochemistry and compared it with that in the chemically fixed cells. By quick-freeze freeze-substitution electron microscopy, an electron-lucent layer, as thick as 20 nm, was revealed just inside the inner nuclear membrane, whereas in the conventionally glutaraldehyde-fixed cells the layer was not seen. By quick-freeze deep-etch electron microscopy, we could not distinguish definitively the layer corresponding to the nuclear lamina in either fresh unfixed or glutaraldehyde-fixed cells. Immunofluorescence microscopy showed that lamin A/C in the nucleus was detected in the acetone-fixed cells and briefly in paraformaldehyde-fixed cells but not in the cells with prolonged paraformaldehyde fixation. Nuclear localization of lamin A/C was revealed by immunogold electron microscopy also in the quickly frozen and freeze-substituted cells, but not in the paraformaldehyde-fixed cells. Lamin A/C was localized mainly in the peripheral nucleoplasm within 60 nm from the inner nuclear membrane, which corresponded to the nuclear lamina. These results suggest that the nuclear lamina can be preserved both ultrastructurally and immunocytochemically by quick-freezing fixation, rather than by conventional chemical fixation.

    (J Histochem Cytochem 53:497–507, 2005)


  • Wanted, an Anthrax vaccine: Dead or Alive? - It has been more than 100 years since the realization that microbes are capable of causing disease. In that time, we have learned a great deal as to how each organism has adapted to the immune system so as to avoid elimination. As well, we have also learned an immense amount since Louis Pasteur first proposed that the solution to infectious diseases was to culture the microbes and attenuate their virulence, so as to use them as vaccines. From the optimism and promise of the 19th century and immunization as the ultimate answer to the invasion by the microbial world, to the scientific realities of the 21st century, it is of interest to retrace the steps of the earliest microbiologists cum immunologists, to realize how far we've come, as well as how far we yet have to go. This editorial focuses on the history of anthrax as a microbial disease, and the earliest efforts at producing a vaccine for its prevention.

  • Web Alert - No abstract available

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  • What does an orphan G-protein-coupled receptor have to do with estrogen? - Estrogen affects multiple aspects of human physiology, including the normal growth and development of female reproductive tissues, bone integrity, cardiovascular and central nervous system functions, and plays a central role in normal mammary development and breast pathogenesis. It modulates diverse cell signaling pathways, some of which appear to be independent of the known estrogen receptors (ERs). Although many of estrogen's actions can be explained by the nuclear ERs (ER-α and ER-β) functioning as ligand-activated RNA transcription factors, there are numerous rapid biochemical and physiological responses that cannot be explained by the classical genomic effects of estrogen signaling. It has long been postulated that the rapid effects of estrogen are due to a membrane-bound ER, and two recent reports suggest that it is in fact a G-protein-coupled receptor named 'GPR30'.

  • White matter damage and chemokine induction in developing rat brain after intrauterine infection. -
    Related Articles

    White matter damage and chemokine induction in developing rat brain after intrauterine infection.

    J Perinat Med. 2005;33(5):415-22

    Authors: Yuan TM, Yu HM, Gu WZ, Li JP

    In order to investigate the neuropathological effects on the developing rat brain after intrauterine infection, identification of glail fibrillary acidic protein (GFAP), 2', 3'-cyclic nucleotide phosphodiesterase (CNPase), and neurofilament (NF) was observed. Escherichia coli (E. coli) was inoculated into uterine horn of pregnant rats when gestation was 70% complete (15 days) and the control group was inoculated with normal saline. Immunohistochemistry was used for evaluation of GFAP, CNPase, and NF expression in pup brains at postnatal day 7 (P7) and reverse transcriptase-PCR (RT-PCR) to analyze macrophage inflammatory protein-1 alpha mRNA (MIP-1 alpha mRNA), macrophage inflammatory protein-1 beta mRNA (MIP-1beta mRNA), the regulated upon activation normal T expressed and secreted chemokine mRNA (RANTES mRNA) and Eotaxin mRNA expression in pup brains at P1, P3 and P7. The numbers of GFAP-positive cells of the E. coli-treated group pups were marked increased in periventricular white matter and hippocampus at P7 compared with the control group but no significant different levels of GFAP expression in corpus callosum were found between two groups. The integrate density (ID) of CNPase-positive staining of the Escherichia coli-treated group pups were marked decreased in periventricular white matter and corpus callosum at P7 compared with the control group. The ID of NF-positive staining of the Escherichia coli-treated group pups were marked decreased in periventricular white matter at P7 compared with the control group and no significant different levels of NF expression in corpus callosum were found between two groups. The expression of MIP-1 alpha mRNA and MIP-1 beta mRNA in brain of the E. coli-treated pup rat were higher than the control at P1, but the expression of MIP-1 alpha mRNA and MIP-1 beta mRNA in brain of the pup rat at P3 and P7 had no significant difference between two groups. The alteration of expression of GFAP, CNPase, and NF in the brain of neonatal rats after intrauterine infection suggested that intrauterine infection could cause neonatal white matter damage. Moreover, the transient increase in expression of chemokine such as MIP-1 alpha, MIP-1 beta in neonatal brain after intrauterine infection indicated that MIP-1 alpha, MIP-1 beta may be a mechanism mediating between the neonatal white matter damage and the intrauterine infection.

    PMID: 16238536 [PubMed - in process]


  • Wilms tumor gene product: sensitive and contextually specific marker of serous carcinomas of ovarian surface epithelial origin. -
    Related Articles

    Wilms tumor gene product: sensitive and contextually specific marker of serous carcinomas of ovarian surface epithelial origin.

    Appl Immunohistochem Mol Morphol. 2004 Jun;12(2):122-6

    Authors: Hwang H, Quenneville L, Yaziji H, Gown AM

    Carcinomas of ovarian surface epithelial origin can arise from, and often present at, extraovarian sites. There are few available markers for the positive identification of carcinomas of ovarian surface epithelial origin, which might aid in distinguishing them from metastatic carcinomas, such as of breast, colon, or lung origin. Recently, the Wilms tumor gene product (WT-1) has been shown to be expressed in ovarian surface and mesothelial epithelium. We tested the hypothesis that WT-1 would be a sensitive and specific marker of ovarian surface epithelium carcinomas. An archived series of 116 ovarian carcinomas (57 serous [43 ovarian, 14 extraovarian], 31 mucinous, 15 clear cell, 13 endometrioid), 118 breast carcinomas, 46 colonic carcinomas, and 45 nonsmall cell lung cancers were selected. A polyclonal antibody to the WT-1 gene product was applied to deparaffinized, formalin-fixed tissue sections after epitope retrieval. Fifty-two of 57 (93%) serous carcinomas of ovarian surface epithelial origin were WT-1-positive, in a nuclear pattern, with virtually all the tumor cell population positive in the majority of cases. None of the mucinous, clear cell, or endometrioid ovarian cancers were positive, and only 8 of 118 breast, 0 of 46 colonic, and 0 of 45 lung nonsmall cell carcinomas were WT-1-positive. These findings demonstrate that WT-1 is a highly sensitive and specific marker of serous carcinomas of ovarian surface epithelial origin (both ovarian and extraovarian). These results also contradict recent reports demonstrating WT-1 expression in both breast and lung carcinomas.

    PMID: 15354736 [PubMed - indexed for MEDLINE]


  • Xenopus frizzled-4S, a splicing variant of Xfz4 is a context-dependent activator and inhibitor of Wnt/beta-catenin signaling - Background: Secreted Frizzled related proteins (SFRPs) are extracellular regulators of Wnt signaling. These proteins contain an N-terminal cysteine rich domain (CRD) highly similar to the CRDs of the Frizzled family of seven-transmembrane proteins that act as Wnt receptors. SFRPs can bind to Wnts and prevent their interaction with the Frizzled receptor. Recently it has been reported that a splice variant of human Frizzled-4 (FZD4S) lacking the transmembrane and the cytoplasmic domains of Frizzled-4 can activate rather than inhibit Wnt-8 activity in Xenopus embryos. This indicates that secreted CRD containing proteins such as Frizzled ecto-domains and SFRPs may not always act as Wnt inhibitors. It is not known how FZD4S can activate Wnt/beta-catenin signaling and what biological role these molecules play in vivo. Results: Here we report that the Xenopus frizzled-4 is alternatively spliced to give rise to a putative secreted protein that lacks the seven-transmembrane and the cytoplasmic domains. We performed functional experiments in Xenopus embryos to investigate how this novel splicing variant, Xfz4S, can modulate the Wnt/beta-catenin pathway. We show that Xfz4S as well as the extracellular domain of Xfz8 (ECD8) can act as both activators and inhibitors of Wnt/beta-catenin signaling dependent on the Wnt ligand presented. The positive regulation of Wnt/beta-catenin signaling by the extracellular domains of Frizzled receptors is mediated by the members of low density lipoprotein receptor-related protein (LRP-5/6) that act as Wnt coreceptors. Conclusions: This work provides evidence that the secreted extracellular domains of Frizzled receptors may act both as inhibitors and activators of Wnt signaling dependent on the Wnt ligand presented.

  • XRCC1 and XPD genetic polymorphisms, smoking and breast cancer risk in a Finnish case-control study - IntroductionIt has been suggested that individuals with reduced DNA repair capacities might have increased susceptibility to environmentally induced cancer. In this study, we evaluated if polymorphisms in DNA repair genes XRCC1 (Arg280His, Arg399Gln) and XPD (Lys751Gln) modify individual breast cancer risk, with emphasis on tobacco smoking. Methods: The study population consisted of 483 incident breast cancer cases and 482 population controls of Finnish Caucasian origin. The genotypes were determined by PCR-RFLP-based methods. Odds ratio (OR) and confidence intervals (CIs) were calculated by unconditional logistic regression analyses. Results: No statistically significant overall effect in the breast cancer risk was seen for any of the studied polymorphisms. However, a significant increase in breast cancer risk was seen among ever smoking women if they carried at least one XRCC1-399 Gln allele (OR 2.33, 95% CI 1.30–4.19, pint 0.025) or XPD-751 Gln/Gln genotype (OR 2.52, 95% CI 1.27–5.03, pint 0.011) compared to smoking women not carrying these genotypes. The risks were found to be confined to women smoking at least five pack-years; the respective ORs were 4.14 (95% CI 1.66–10.3) and 4.41 (95% CI 1.62–12.0). Moreover, a significant trend of increasing risk with increasing number of the putative at-risk genotypes (p for trend 0.042) was seen. Women with at least two at-risk genotypes had an OR of 1.54 (95% CI 1.00–2.41) compared to women with no at-risk genotypes. Even higher estimates were seen for ever actively smoking women with at least two at-risk genotypes. Conclusion: Our results do not indicate a major role for XRCC1 and XPD polymorphisms in breast cancer susceptibility, but suggest that they may modify the risk especially among smoking women.

  • Zinc-regulating Proteins, ZnT-1, and Metallothionein I/II Are Present in Different Cell Populations in the Mouse Testis -

    Zinc ions play an important role in testis development and spermatogenesis. Thus, nutritional zinc deficiency leads to aberrant testicular development, reduced spermatogenesis, and male sterility. The precise actions of zinc in mediating these functions and the mechanisms by which zinc is itself regulated in the testis, however, have not been adequately elucidated. We have assessed the distribution of the zinc-regulating proteins ZnT-1 and metallothionein I/II (MT I/II) in the mouse seminiferous tubule. Colabeling for ZnT-1 and MT I/II demonstrated unique patterns of distribution for these proteins, with ZnT-1 present in Sertoli cells in addition to luminal spermatozoa and MT I/II restricted to spermatocytes. These findings were confirmed by dual-label immunofluorescence for ZnT-1 and the Sertoli cell marker, vimentin, and by immunoelectron microscopy. The differential expression patterns of ZnT-1 and MTs support the hypothesis that ZnT-1 and MTs play different roles in the regulation of intracellular zinc in this organ. The specific expression of ZnT-1 in the Sertoli cells, moreover, is consistent with their role in maintaining a nurturing, closely regulated environment for spermatogenesis.

    (J Histochem Cytochem 53:905–912, 2005)


  • Zinc-regulating Proteins, ZnT-1, and Metallothionein I/II Are Present in Different Cell Populations in the Mouse Testis -

    Zinc ions play an important role in testis development and spermatogenesis. Thus, nutritional zinc deficiency leads to aberrant testicular development, reduced spermatogenesis, and male sterility. The precise actions of zinc in mediating these functions and the mechanisms by which zinc is itself regulated in the testis, however, have not been adequately elucidated. We have assessed the distribution of the zinc-regulating proteins ZnT-1 and metallothionein I/II (MT I/II) in the mouse seminiferous tubule. Colabeling for ZnT-1 and MT I/II demonstrated unique patterns of distribution for these proteins, with ZnT-1 present in Sertoli cells in addition to luminal spermatozoa and MT I/II restricted to spermatocytes. These findings were confirmed by dual-label immunofluorescence for ZnT-1 and the Sertoli cell marker, vimentin, and by immunoelectron microscopy. The differential expression patterns of ZnT-1 and MTs support the hypothesis that ZnT-1 and MTs play different roles in the regulation of intracellular zinc in this organ. The specific expression of ZnT-1 in the Sertoli cells, moreover, is consistent with their role in maintaining a nurturing, closely regulated environment for spermatogenesis.

    (J Histochem Cytochem 53:905–912, 2005)


  • Zinc-specific Autometallographic In Vivo Selenium Methods: Tracing of Zinc-enriched (ZEN) Terminals, ZEN Pathways, and Pools of Zinc Ions in a Multitude of Other ZEN Cells -

    In vivo–applied sodium selenide or sodium selenite causes the appearance of zinc–selenium nanocrystals in places where free or loosely bound zinc ions are present. These nanocrystals can in turn be silver enhanced by autometallographic (AMG) development. The selenium method was introduced in 1982 as a tool for zinc-ion tracing, e.g., in vesicular compartments such as synaptic vesicles of zinc-enriched (ZEN) terminals in the central nervous system, and for visualization of zinc ions in ZEN secretory vesicles of, e.g., somatotrophic cells in the pituitary, zymogene granules in pancreatic acinar cells, beta-cells of the islets of Langerhans, Paneth cells of the crypts of Lieberkühn, secretory cells of the tubuloacinar glands of prostate, epithelium of parts of ductus epididymidis, and osteoblasts. If sodium selenide/selenite is injected into brain, spinal cord, spinal nerves containing sympathetic axons, or intraperitoneally, retrograde axonal transport of zinc–selenium nanocrystals takes place in ZEN neurons, resulting in accumulation of zinc–selenium nanocrystals in lysosomes of the neuronal somata. The technique is, therefore, also a highly specific tool for tracing ZEN pathways. The present review includes an update of the 1982 paper and presents evidence that only zinc ions are traced with the AMG selenium techniques if the protocols are followed to the letter. (J Histochem Cytochem 53:141–153, 2005)


  • [Abstracts] CCN abstracts - (No abstract is available for this citation)

  • [Articles] 5-Halogenated pyrimidine lesions within a CpG sequence context mimic 5-methylcytosine by enhancing the binding of the methyl-CpG-binding domain of methyl-CpG-binding protein 2 (MeCP2) -

    Perturbations in cytosine methylation signals are observed in the majority of human tumors; however, it is as yet unknown how methylation patterns become altered. Epigenetic changes can result in the activation of transforming genes as well as in the silencing of tumor suppressor genes. We report that methyl-CpG-binding proteins (MBPs), specific for methyl-CpG dinucleotides, bind with high affinity to halogenated pyrimidine lesions, previously shown to result from peroxidase-mediated inflammatory processes. Emerging data suggest that the initial binding of MBPs to methyl-CpG sequences may be a seeding event that recruits chromatin-modifying enzymes and DNA methyltransferase, initiating a cascade of events that result in gene silencing. MBD4, a protein with both methyl-binding and glycosylase activity demonstrated repair activity against a series of 5-substituted pyrimidines, with the greatest efficiency against 5-chlorouracil, but undetectable activity against 5-chlorocytosine. The data presented here suggest that halogenated pyrimidine damage products can potentially accumulate and mimic endogenous methylation signals.


  • [Articles] 8-Oxoguanine incorporation into DNA repeats in vitro and mismatch recognition by MutS{alpha} -

    DNA 8-oxoguanine (8-oxoG) causes transversions and is also implicated in frameshifts. We previously identified the dNTP pool as a likely source of mutagenic DNA 8-oxoG and demonstrated that DNA mismatch repair prevented oxidation-related frameshifts in mononucleotide repeats. Here, we show that both Klenow fragment and DNA polymerase can utilize 8-oxodGTP and incorporate the oxidized purine into model frameshift targets. Both polymerases incorporated 8-oxodGMP opposite C and A in repetitive DNA sequences and efficiently extended a terminal 8-oxoG. The human MutS mismatch repair factor recognized DNA 8-oxoG efficiently in some contexts that resembled frameshift intermediates in the same C or A repeats. DNA 8-oxoG in other slipped/mispaired structures in the same repeats adopted configurations that prevented recognition by MutS and by the OGG1 DNA glycosylase thereby rendering it invisible to DNA repair. These findings are consistent with a contribution of oxidative DNA damage to frameshifts. They also suggest how mismatch repair might reduce the burden of DNA 8-oxoG and prevent frameshift formation.


  • [Articles] A diminutive and specific RNA binding site for L-tryptophan -

    Selection for amino acid affinity by elution of RNAs from tryptophan–Sepharose using free L-tryptophan evokes one sequence predominantly (KD = 12 µM), a symmetrical internal loop of 3 nt per side. Though we have also isolated larger sequences with affinity for tryptophan, successively squeezed selection in randomized tracts of 70, 60, 40, 20 and 17 nt show that this internal loop is the simplest sequence that can meet the column affinity selection. From sequence variation in ~50 independent isolates, only 26 bits of information are required to describe this loop (equivalent to only 13 fully conserved nucleotides). Thus, it is among the simplest amino acid binding sites known, as well as selective among hydrophobic side chains. Among site sequences defined as essential to affinity by conservation, protection and modification-interference, there is a recurring CCA sequence (a tryptophan anticodon triplet) which apparently forms one side of the binding site. Such conserved juxtaposition of tryptophan with a cognate coding triplet supports a stereochemical origin for the genetic code.


  • [Articles] A highly distinctive mechanical property found in the majority of human promoters and its transcriptional relevance -

    A recent study revealed that TATA boxes and initiator sequences have a common anomalous mechanical property, i.e. they comprise distinctive flexible and rigid sequences when compared with the other parts of the promoter region. In the present study, using the flexibility parameters from two different models, we calculated the average flexibility profiles of 1004 human promoters that do not contain canonical promoter elements, such as a TATA box, initiator (Inr) sequence, downstream promoter element or a GC box, and those of 382 human promoters that contain the GC box only. Here, we show that they have a common characteristic mechanical property that is strikingly similar to those of the TATA box-containing or Inr-containing promoters. Their most interesting feature is that the TATA- or Inr-corresponding region lies in the several nucleotides around the transcription start site. We have also found that a dinucleotide step from –1 to +1 (transcription start site) has a slight tendency to adopt CA that is known to be flexible. We also demonstrate that certain synthetic DNA fragments designed to mimic the average mechanical property of these 1386 promoters can drive transcription. This distinctive mechanical property may be the hallmark of a promoter.


  • [Articles] A host-guest approach for determining drug-DNA interactions: an example using netropsin -

    Netropsin is a well-characterized DNA minor groove binding compound that serves as a model for the study of drug–DNA interactions. Our laboratory has developed a novel host–guest approach to study drug–DNA interactions in which the host, the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase (MMLV RT) is co-crystallized with a DNA oligonucleotide guest in the presence and absence of drug. We have co-crystallized netropsin with the RT fragment bound to the symmetric 16mer d(CTTAATTCGAATTAAG)2 and determined the structure of the complex at 1.85 Å. In contrast to previously reported netropsin–DNA structures, our oligonucleotide contains two AATT sites that bind netropsin with flanking 5' and 3' sequences that are not symmetric. The asymmetric unit of the RT fragment–DNA–netropsin crystals contains one protein molecule and one-half of the 16mer with one netropsin molecule bound. The guanidinium moiety of netropsin binds in a narrow part of the minor groove, while the amidinium is bound in the widest region within the site. We compare this structure to other Class I netropsin–DNA structures and find that the asymmetry of minor groove widths in the AATT site contributes to the orientation of netropsin within the groove while hydrogen bonding patterns vary in the different structures.


  • [Articles] A human-Tetrahymena pseudoknot chimeric telomerase RNA reconstitutes a nonprocessive enzyme in vitro that is defective in telomere elongation -

    The phylogenetically-derived secondary structures of telomerase RNAs (TR) from ciliates, yeasts and vertebrates are surprisingly conserved and contain a pseudoknot domain at a similar location downstream of the template. As the pseudoknot domains of Tetrahymena TR (tTR) and human TR (hTR) mediate certain similar functions, we hypothesized that they might be functionally interchangeable. We constructed a chimeric TR (htTR) by exchanging the hTR pseudoknot sequences for the tTR pseudoknot region. The chimeric RNA reconstituted human telomerase activity when coexpressed with hTERT in vitro, but exhibited defects in repeat addition processivity and levels of DNA synthesis compared to hTR. Activity was dependent on tTR sequences within the chimeric RNA. htTR interacted with hTERT in vitro and dimerized predominantly via a region of its hTR backbone, the J7b/8a loop. Introduction of htTR in telomerase-negative cells stably expressing hTERT did not reconstitute an active enzyme able to elongate telomeres. Thus, our results indicate that the chimeric RNA reconstituted a weakly active nonprocessive human telomerase enzyme in vitro that was defective in telomere elongation in vivo. This suggests that there may be species-specific requirements for pseudoknot functions.


  • [Articles] A monoclonal antibody that inhibits mycobacterial DNA gyrase by a novel mechanism -

    DNA gyrase is a DNA topoisomerase indispensable for cellular functions in bacteria. We describe a novel, hitherto unknown, mechanism of specific inhibition of Mycobacterium smegmatis and Mycobacterium tuberculosis DNA gyrase by a monoclonal antibody (mAb). Binding of the mAb did not affect either GyrA–GyrB or gyrase–DNA interactions. More importantly, the ternary complex of gyrase–DNA–mAb retained the ATPase activity of the enzyme and was competent to catalyse DNA cleavage–religation reactions, implying a new mode of action different from other classes of gyrase inhibitors. DNA gyrase purified from fluoroquinolone-resistant strains of M.tuberculosis and M.smegmatis were inhibited by the mAb. The absence of cross-resistance of the drug-resistant enzymes from two different sources to the antibody-mediated inhibition corroborates the new mechanism of inhibition. We suggest that binding of the mAb in the proximity of the primary dimer interface region of GyrA in the heterotetrameric enzyme appears to block the release of the transported segment after strand passage, leading to enzyme inhibition. The specific inhibition of mycobacterial DNA gyrase with the mAb opens up new avenues for designing novel lead molecules for drug discovery and for probing gyrase mechanism.


  • [Articles] A new mechanism for mtDNA pathogenesis: impairment of post-transcriptional maturation leads to severe depletion of mitochondrial tRNASer(UCN) caused by T7512C and G7497A point mutations -

    We have studied the consequences of two homoplasmic, pathogenic point mutations (T7512C and G7497A) in the tRNASer(UCN) gene of mitochondrial (mt) DNA using osteosarcoma cybrids. We identified a severe reduction of tRNASer(UCN) to levels below 10% of controls for both mutations, resulting in a 40% reduction in mitochondrial protein synthesis rate and in a respiratory chain deficiency resembling that in the patients muscle. Aminoacylation was apparently unaffected. On non-denaturating northern blots we detected an altered electrophoretic mobility for G7497A containing tRNA molecules suggesting a structural impact of this mutation, which was confirmed by structural probing. By comparing in vitro transcribed molecules with native RNA in such gels, we also identified tRNASer(UCN) being present in two isoforms in vivo, probably corresponding to the nascent, unmodified transcripts co-migrating with the in vitro transcripts and a second, faster moving isoform corresponding to the mature tRNA. In cybrids containing either mutations the unmodified isoforms were severely reduced. We hypothesize that both mutations lead to an impairment of post-transcriptional modification processes, ultimately leading to a preponderance of degradation by nucleases over maturation by modifying enzymes, resulting in severely reduced tRNASer(UCN) steady state levels. We infer that an increased degradation rate, caused by disturbance of tRNA maturation and, in the case of the G7497A mutant, alteration of tRNA structure, is a new pathogenic mechanism of mt tRNA point mutations.


  • [Articles] A peripheral element assembles the compact core structure essential for group I intron self-splicing -

    The presence of non-conserved peripheral elements in all naturally occurring group I introns underline their importance in ensuring the natural intron function. Recently, we reported that some peripheral elements are conserved in group I introns of IE subgroup. Using self-splicing activity as a readout, our initial screening revealed that one such conserved peripheral elements, P2.1, is mainly required to fold the catalytically active structure of the Candida ribozyme, an IE intron. Unexpectedly, the essential function of P2.1 resides in a sequence-conserved short stem of P2.1 but not in a long-range interaction associated with the loop of P2.1 that stabilizes the ribozyme structure. The P2.1 stem is indispensable in folding the compact ribozyme core, most probably by forming a triple helical interaction with two core helices, P3 and P6. Surprisingly, although the ribozyme lacking the P2.1 stem renders a loosely folded core and the loss of self-splicing activity requires two consecutive transesterifications, the mutant ribozyme efficiently catalyzes the first transesterification reaction. These results suggest that the intron self-splicing demands much more ordered structure than does one independent transesterification, highlighting that the universally present peripheral elements achieve their functional importance by enabling the highly ordered structure through diverse tertiary interactions.


  • [Articles] A real-time semi-quantitative RT-PCR assay demonstrates that the pilE sequence dictates the frequency and characteristics of pilin antigenic variation in Neisseria gonorrhoeae -

    A semi-quantitative real-time RT–PCR assay was designed to measure gonococcal pilin antigenicvariation (SQ-PCR Av assay). This assay employs 17 hybridization probe sets that quantitate subpopulations of pilin transcripts carrying different silent pilin copy sequences and one set that detects total pilE transcript levels. Mixtures of a DNA standard carrying the silent copy being detected and a clone encoding the starting pilE sequence, which is the majority pilE template, provided amplification curves that closely matched the experimental data and allowed an analysis of the contribution of different silent pilin copies to variation. The SQ-PCR Av assay was verified using DNA sequence analysis to demonstrate that this methodology allowed an accurate analysis of pilin variation. Both assays showed that with a specific starting pilE sequence, only a subset of the silent pilin copies recombine into pilE at a detectable level, and that this limited subset was reproducibly detected in replicate cultures. When an isogenic pilE sequence variant was examined using both assays, a new subset of silent copy sequences were detected recombining into pilE and the overall frequency of variation was increased. Thus, the parental pilE sequence influences the frequency of variation and the repertoire of pilin variants produced.


  • [Articles] A sensitive, support-vector-machine method for the detection of horizontal gene transfers in viral, archaeal and bacterial genomes -

    In earlier work, we introduced and discussed a generalized computational framework for identifying horizontal transfers. This framework relied on a gene's nucleotide composition, obviated the need for knowledge of codon boundaries and database searches, and was shown to perform very well across a wide range of archaeal and bacterial genomes when compared with previously published approaches, such as Codon Adaptation Index and C + G content. Nonetheless, two considerations remained outstanding: we wanted to further increase the sensitivity of detecting horizontal transfers and also to be able to apply the method to increasingly smaller genomes. In the discussion that follows, we present such a method, Wn-SVM, and show that it exhibits a very significant improvement in sensitivity compared with earlier approaches. Wn-SVM uses a one-class support-vector machine and can learn using rather small training sets. This property makes Wn-SVM particularly suitable for studying small-size genomes, similar to those of viruses, as well as the typically larger archaeal and bacterial genomes. We show experimentally that the new method results in a superior performance across a wide range of organisms and that it improves even upon our own earlier method by an average of 10% across all examined genomes. As a small-genome case study, we analyze the genome of the human cytomegalovirus and demonstrate that Wn-SVM correctly identifies regions that are known to be conserved and prototypical of all beta-herpesvirinae, regions that are known to have been acquired horizontally from the human host and, finally, regions that had not up to now been suspected to be horizontally transferred. Atypical region predictions for many eukaryotic viruses, including the -, ßbeta;- and -herpesvirinae, and 123 archaeal and bacterial genomes, have been made available online at http://cbcsrv.watson.ibm.com/HGT_SVM/.


  • [Articles] A sequence sub-sampling algorithm increases the power to detect distant homologues -

    Searching databases for distant homologues using alignments instead of individual sequences increases the power of detection. However, most methods assume that protein evolution proceeds in a regular fashion, with the inferred tree of sequences providing a good estimation of the evolutionary process. We investigated the combined HMMER search results from random alignment subsets (with three sequences each) drawn from the parent alignment (Rand-shuffle algorithm), using the SCOP structural classification to determine true similarities. At false-positive rates of 5%, the Rand-shuffle algorithm improved HMMER's sensitivity, with a 37.5% greater sensitivity compared with HMMER alone, when easily identified similarities (identifiable by BLAST) were excluded from consideration. An extension of the Rand-shuffle algorithm (Ali-shuffle) weighted towards more informative sequence subsets. This approach improved the performance over HMMER alone and PSI-BLAST, particularly at higher false-positive rates. The improvements in performance of these sequence sub-sampling methods may reflect lower sensitivity to alignment error and irregular evolutionary patterns. The Ali-shuffle and Rand-shuffle sequence homology search programs are available by request from the authors.


  • [Articles] A spontaneous tRNA suppressor of a mutation in the Chlamydomonas reinhardtii nuclear MCD1 gene required for stability of the chloroplast petD mRNA -

    Numerous nuclear gene products are required for the correct expression of organellar genes. One such gene in the green alga Chlamydomonas reinhardtii is MCD1, whose product is required for stability of the chloroplast-encoded petD mRNA. In mcd1 mutants, which are non-photosynthetic, petD mRNA is degraded by a 5'–3' exonuclease activity, resulting in a failure to synthesize its product, subunit IV of the cytochrome b 6/f complex. Here, we report the sequence of the wild-type MCD1 gene, which encodes a large and novel putative protein. Analysis of three mutant alleles showed that two harbored large deletions, but that one allele, mcd1-2, had a single base change resulting in a nonsense codon near the N-terminus. This same mutant allele can be suppressed by a second-site mutation in the nuclear MCD2 gene, whereas mcd2-1 cannot suppress the deletion in mcd1-1 (Esposito,D. Higgs,D.C. Drager,R.G. Stern, D.B. and Girard-Bascou,J. (2001) Curr. Genet., 39, 40–48). We report the cloning of mcd2-1, and show that the mutation lies in a tRNASer(CGA), which has been modified to translate the nonsense codon in mcd1-2. We discuss how the existence of a large tRNASer gene family may permit this suppression without pleiotropic consequences.


  • [Articles] A universally applicable method of operon map prediction on minimally annotated genomes using conserved genomic context -

    An important step in understanding the regulation of a prokaryotic genome is the generation of its transcription unit map. The current strongest operon predictor depends on the distributions of intergenic distances (IGD) separating adjacent genes within and between operons. Unfortunately, experimental data on these distance distributions are limited to Escherichia coli and Bacillus subtilis. We suggest a new graph algorithmic approach based on comparative genomics to identify clusters of conserved genes independent of IGD and conservation of gene order. As a consequence, distance distributions of operon pairs for any arbitrary prokaryotic genome can be inferred. For E.coli, the algorithm predicts 854 conserved adjacent pairs with a precision of 85%. The IGD distribution for these pairs is virtually identical to the E.coli operon pair distribution. Statistical analysis of the predicted pair IGD distribution allows estimation of a genome-specific operon IGD cut-off, obviating the requirement for a training set in IGD-based operon prediction. We apply the method to a representative set of eight genomes, and show that these genome-specific IGD distributions differ considerably from each other and from the distribution in E.coli.


  • [Articles] A-tract clusters may facilitate DNA packaging in bacterial nucleoid -

    Molecular mechanisms of bacterial chromosome packaging are still unclear, as bacteria lack nucleosomes or other apparent basic elements of DNA compaction. Among the factors facilitating DNA condensation may be a propensity of the DNA molecule for folding due to its intrinsic curvature. As suggested previously, the sequence correlations in genome reflect such a propensity [Trifonov and Sussman (1980) Proc. Natl Acad. Sci. USA, 77, 3816–3820]. To further elaborate this concept, we analyzed positioning of A-tracts (the sequence motifs introducing the most pronounced DNA curvature) in the Escherichia coli genome. First, we observed that the A-tracts are over-represented and distributed ‘quasi-regularly’ throughout the genome, including both the coding and intergenic sequences. Second, there is a 10–12 bp periodicity in the A-tract positioning indicating that the A-tracts are phased with respect to the DNA helical repeat. Third, the phased A-tracts are organized in ~100 bp long clusters. The latter feature was revealed with the help of a novel approach based on the Fourier series expansion of the A-tract distance autocorrelation function. Since the A-tracts introduce local bends of the DNA duplex and these bends accumulate when properly phased, the observed clusters would facilitate DNA looping. Also, such clusters may serve as binding sites for the nucleoid-associated proteins that have affinities for curved DNA (such as HU, H-NS, Hfq and CbpA). Therefore, we suggest that the ~100 bp long clusters of the phased A-tracts constitute the ‘structural code’ for DNA compaction by providing the long-range intrinsic curvature and increasing stability of the DNA complexes with architectural proteins.


  • [Articles] Acinetobacter sp. ADP1: an ideal model organism for genetic analysis and genome engineering -

    Acinetobacter sp. strain ADP1 is a naturally transformable gram-negative bacterium with simple culture requirements, a prototrophic metabolism and a compact genome of 3.7 Mb which has recently been sequenced. Wild-type ADP1 can be genetically manipulated by the direct addition of linear DNA constructs to log-phase cultures. This makes it an ideal organism for the automation of complex strain construction. Here, we demonstrate the flexibility and versatility of ADP1 as a genetic model through the construction of a broad variety of mutants. These include marked and unmarked insertions and deletions, complementary replacements, chromosomal expression tags and complex combinations thereof. In the process of these constructions, we demonstrate that ADP1 can effectively express a wide variety of foreign genes including antibiotic resistance cassettes, essential metabolic genes, negatively selectable catabolic genes and even intact operons from highly divergent bacteria. All of the described mutations were achieved by the same process of splicing PCR, direct transformation of growing cultures and plating on selective media. The simplicity of these tools make genetic analysis and engineering with Acinetobacter ADP1 accessible to laboratories with minimal microbial genetics expertise and very little equipment. They are also compatible with complete automation of genetic analysis and engineering protocols.


  • [Articles] Activation of APE1/Ref-1 is dependent on reactive oxygen species generated after purinergic receptor stimulation by ATP -

    Apurinic apyrimidinic endonuclease redox effector factor-1 (APE1/Ref-1) is involved both in the base excision repair (BER) of DNA lesions and in the eukaryotic transcriptional regulation. APE1/Ref-1 is regulated at both the transcriptional and post-translational levels, through control of subcellular localization and post-translational modification. In response to stress conditions, several cell types release ATP, which exerts stimulatory effects on eukaryotic cells via the purinergic receptors (P2) family. By using western blot and immunofluorescence analysis on a human tumour thyroid cell line (ARO), we demonstrate that purinergic stimulation by extracellular ATP induces quick cytoplasm to nucleus translocation of the protein at early times and its neosynthesis at later times. Continuous purinergic triggering by extracellular ATP released by ARO cells is responsible for the control of APE1/Ref-1 intracellular level. Interference with intracellular pathways activated by P2 triggering demonstrates that Ca2+ mobilization and intracellular reactive oxygen species (ROS) production are responsible for APE1/Ref-1 translocation. The APE1/Ref-1 activities on activator protein-1 (AP-1) DNA binding and DNA repair perfectly match its nuclear enrichment upon ATP stimulation. The biological relevance of our data is reinforced by the observation that APE1/Ref-1 stimulation by ATP protects ARO cells by H2O2-induced cell death. Our data provide new insights into the complex mechanisms regulating APE1/Ref-1 functions.


  • [Articles] Activity of 3'-thioAMP derivatives as ribosomal P-site substrates -

    The ribosome is a large RNP complex but its main enzymatic activity, the peptidyl transferase, is a ribozyme. As many RNA enzymes use divalent metal ions in catalysis, one of the hypotheses put forward proposed that metal ions might aid peptide bond formation. To be able to test a possible coordination of a metal ion to the 3'-bridging oxygen of P-site substrates, a 3'-thioAMP was synthesized. Its chemical acylation with N-acetyl-l-leucine yielded both mono and diaminoacylated 3'-thioAMP. These thioated substrates were tested for peptide bond formation in an optimized fragment reaction in comparison with their unmodified counterparts. As the amino acid was predominantly linked to the unproductive 2'-OH in AcLeu-thioAMP (5), this substrate was barely active and not used for further analysis. In contrast, Di(AcLeu)-thioAMP (4) was more active than Di(AcLeu)-AMP (2) which is in line with the higher energy of thioesters. Both activities were slightly enhanced when Mn2+ containing buffers were employed in the assay. These data show that thioated P-site substrates are active in peptide bond formation and can in principle be used for metal-ion-rescue experiments in a full translation system.


  • [Articles] Alleviation of restriction by DNA condensation and non-specific DNA binding ligands -

    During conditions of cell stress, the type I restriction and modification enzymes of bacteria show reduced, but not zero, levels of restriction of unmethylated foreign DNA. In such conditions, chemically identical unmethylated recognition sequences also occur on the chromosome of the host but restriction alleviation prevents the enzymes from destroying the host DNA. How is this distinction between chemically identical DNA molecules achieved? For some, but not all, type I restriction enzymes, alleviation is partially due to proteolytic degradation of a subunit of the enzyme. We identify that the additional alleviation factor is attributable to the structural difference between foreign DNA entering the cell as a random coil and host DNA, which exists in a condensed nucleoid structure coated with many non-specific ligands. The type I restriction enzyme is able to destroy the ‘naked’ DNA using a complex reaction linked to DNA translocation, but this essential translocation process is inhibited by DNA condensation and the presence of non-specific ligands bound along the DNA.


  • [Articles] Alteration of the nucleosomal DNA path in the crystal structure of a human nucleosome core particle -

    Gene expression in eukaryotes depends upon positioning, mobility and packaging of nucleosomes; thus, we need the detailed information of the human nucleosome core particle (NCP) structure, which could clarify chromatin properties. Here, we report the 2.5 Å crystal structure of a human NCP. The overall structure is similar to those of other NCPs reported previously. However, the DNA path of human NCP is remarkably different from that taken within other NCPs with an identical DNA sequence. A comparison of the structural parameters between human and Xenopus laevis DNA reveals that the DNA path of human NCP consecutively shifts by 1 bp in the regions of superhelix axis location –5.0 to –2.0 and 5.0 to 7.0. This alteration of the human DNA path is caused predominantly by tight DNA–DNA contacts within the crystal. It is also likely that the conformational change in the human H2B tail induces the local alteration of the DNA path. In human NCP, the region with the altered DNA path lacks Mn2+ ions and the B-factors of the DNA phosphate groups are substantially high. Therefore, in contrast to the histone octamer, the nucleosomal DNA is sufficiently flexible and mobile and can undergo drastic conformational changes, depending upon the environment.


  • [Articles] An atypical RNA pseudoknot stimulator and an upstream attenuation signal for -1 ribosomal frameshifting of SARS coronavirus -

    The –1 ribosomal frameshifting requires the existence of an in cis RNA slippery sequence and is promoted by a downstream stimulator RNA. An atypical RNA pseudoknot with an extra stem formed by complementary sequences within loop 2 of an H-type pseudoknot is characterized in the severe acute respiratory syndrome coronavirus (SARS CoV) genome. This pseudoknot can serve as an efficient stimulator for –1 frameshifting in vitro. Mutational analysis of the extra stem suggests frameshift efficiency can be modulated via manipulation of the secondary structure within the loop 2 of an infectious bronchitis virus-type pseudoknot. More importantly, an upstream RNA sequence separated by a linker 5' to the slippery site is also identified to be capable of modulating the –1 frameshift efficiency. RNA sequence containing this attenuation element can downregulate –1 frameshifting promoted by an atypical pseudoknot of SARS CoV and two other pseudoknot stimulators. Furthermore, frameshift efficiency can be reduced to half in the presence of the attenuation signal in vivo. Therefore, this in cis RNA attenuator represents a novel negative determinant of general importance for the regulation of –1 frameshift efficiency, and is thus a potential antiviral target.


  • [Articles] An Oct-1 binding site mediates activation of the gata2 promoter by BMP signaling -

    The gata2 gene encodes a transcription factor implicated in regulating early patterning of ectoderm and mesoderm, and later in numerous cell-specific gene expression programs. Activation of the gata2 gene during embryogenesis is dependent on the bone morphogenetic protein (BMP) signaling pathway, but the mechanism for how signaling controls gene activity has not been defined. We developed an assay in Xenopus embryos to analyze regulatory sequences of the zebrafish gata2 promoter that are necessary to mediate the response to BMP signaling during embryogenesis. We show that activation is Smad dependent, since it is blocked by expression of the inhibitory Smad6. Deletion analysis identified an octamer binding site that is necessary for BMP-mediated induction, and that interacts with the POU homeodomain protein Oct-1. However, this element is not sufficient to transfer a BMP response to a heterologous promoter, requiring an additional more proximal cooperating element. Based on recent studies with other BMP-dependent promoters (Drosophila vestigial and Xenopus Xvent-2), our studies of the gata2 gene suggest that POU-domain proteins comprise a common component of the BMP signaling pathway, cooperating with Smad proteins and other transcriptional activators.


  • [Articles] Analysis of nuclear transport signals in the human apurinic/apyrimidinic endonuclease (APE1/Ref1) -

    The mammalian abasic-endonuclease1/redox-factor1 (APE1/Ref1) is an essential protein whose subcellular distribution depends on the cellular physiological status. However, its nuclear localization signals have not been studied in detail. We examined nuclear translocation of APE1, by monitoring enhanced green fluorescent protein (EGFP) fused to APE1. APE1's nuclear localization was significantly decreased by deleting 20 amino acid residues from its N-terminus. Fusion of APE1's N-terminal 20 residues directed nuclear localization of EGFP. An APE1 mutant lacking the seven N-terminal residues (ND7 APE1) showed nearly normal nuclear localization, which was drastically reduced when the deletion was combined with the E12A/D13A double mutation. On the other hand, nearly normal nuclear localization of the full-length E12A/D13A mutant suggests that the first 7 residues and residues 8–13 can independently promote nuclear import. Both far-western analyses and immuno-pull-down assays indicate interaction of APE1 with karyopherin alpha 1 and 2, which requires the 20 N-terminal residues and implicates nuclear importins in APE1's nuclear translocation. Nuclear accumulation of the ND7 APE1(E12A/D13A) mutant after treatment with the nuclear export inhibitor leptomycin B suggests the presence of a previously unidentified nuclear export signal, and the subcellular distribution of APE1 may be regulated by both nuclear import and export.


  • [Articles] Analysis of the transcriptome of the protozoan Theileria parva using MPSS reveals that the majority of genes are transcriptionally active in the schizont stage -

    Massively parallel signature sequencing (MPSS) was used to analyze the transcriptome of the intracellular protozoan Theileria parva. In total 1 095 000, 20 bp sequences representing 4371 different signatures were generated from T.parva schizonts. Reproducible signatures were identified within 73% of potentially detectable predicted genes and 83% had signatures in at least one MPSS cycle. A predicted leader peptide was detected on 405 expressed genes. The quantitative range of signatures was 4–52 256 transcripts per million (t.p.m.). Rare transcripts (<50 t.p.m.) were detected from 36% of genes. Sequence signatures approximated a lognormal distribution, as in microarray. Transcripts were widely distributed throughout the genome, although only 47% of 138 telomere-associated open reading frames exhibited signatures. Antisense signatures comprised 13.8% of the total, comparable with Plasmodium. Eighty five predicted genes with antisense signatures lacked a sense signature. Antisense transcripts were independently amplified from schizont cDNA and verified by sequencing. The MPSS transcripts per million for seven genes encoding schizont antigens recognized by bovine CD8 T cells varied 1000-fold. There was concordance between transcription and protein expression for heat shock proteins that were very highly expressed according to MPSS and proteomics. The data suggests a low level of baseline transcription from the majority of protein-coding genes.


  • [Articles] Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell -

    Gene duplication is a crucial mechanism of evolutionary innovation. A substantial fraction of eukaryotic genomes consists of paralogous gene families. We assess the extent of ancestral paralogy, which dates back to the last common ancestor of all eukaryotes, and examine the origins of the ancestral paralogs and their potential roles in the emergence of the eukaryotic cell complexity. A parsimonious reconstruction of ancestral gene repertoires shows that 4137 orthologous gene sets in the last eukaryotic common ancestor (LECA) map back to 2150 orthologous sets in the hypothetical first eukaryotic common ancestor (FECA) [paralogy quotient (PQ) of 1.92]. Analogous reconstructions show significantly lower levels of paralogy in prokaryotes, 1.19 for archaea and 1.25 for bacteria. The only functional class of eukaryotic proteins with a significant excess of paralogous clusters over the mean includes molecular chaperones and proteins with related functions. Almost all genes in this category underwent multiple duplications during early eukaryotic evolution. In structural terms, the most prominent sets of paralogs are superstructure-forming proteins with repetitive domains, such as WD-40 and TPR. In addition to the true ancestral paralogs which evolved via duplication at the onset of eukaryotic evolution, numerous pseudoparalogs were detected, i.e. homologous genes that apparently were acquired by early eukaryotes via different routes, including horizontal gene transfer (HGT) from diverse bacteria. The results of this study demonstrate a major increase in the level of gene paralogy as a hallmark of the early evolution of eukaryotes.


  • [Articles] Anti-HIV-1 activity of anti-TAR polyamide nucleic acid conjugated with various membrane transducing peptides -

    The transactivator responsive region (TAR) present in the 5'-NTR of the HIV-1 genome represents a potential target for antiretroviral intervention and a model system for the development of specific inhibitors of RNA–protein interaction. Earlier, we have shown that an anti-TAR polyamide nucleotide analog (PNATAR) conjugated to a membrane transducing (MTD) peptide, transportan, is efficiently taken up by the cells and displays potent antiviral and virucidal activity [B. Chaubey, S. Tripathi, S. Ganguly, D. Harris, R. A. Casale and V. N. Pandey (2005) Virology, 331, 418–428]. In the present communication, we have conjugated five different MTD peptides, penetratin, tat peptide, transportan-27, and two of its truncated derivatives, transportan-21 and transportan-22, to a 16mer PNA targeted to the TAR region of the HIV-1 genome. The individual conjugates were examined for their uptake efficiency as judged by FACScan analysis, uptake kinetics using radiolabeled conjugate, virucidal activity and antiviral efficacy assessed by inhibition of HIV-1 infection/replication. While FACScan analysis revealed concentration-dependent cellular uptake of all the PNATAR–peptide conjugates where uptake of the PNATAR–penetratin conjugate was most efficient as >90% MTD was observed within 1 min at a concentration of 200 nM. The conjugates with penetratin, transportan-21 and tat-peptides were most effective as an anti-HIV virucidal agents with IC50 values in the range of 28–37 nM while IC50 for inhibition of HIV-1 replication was lowest with PNATAR–transportan-27 (0.4 µM) followed by PNATAR–tat (0.72 µM) and PNATAR–penetratin (0.8 µM). These results indicate that anti-HIV-1 PNA conjugated with MTD peptides are not only inhibitory to HIV-1 replication in vitro but are also potent virucidal agents which render HIV-1 virions non-infectious upon brief exposure.


  • [Articles] Application of locked nucleic acids to improve aptamer in vivo stability and targeting function -

    Aptamers are powerful candidates for molecular imaging applications due to a number of attractive features, including rapid blood clearance and tumor penetration. We carried out structure–activity relationship (SAR) studies with the Tenascin-C binding aptamer TTA1, which is a promising candidate for application in tumor imaging with radioisotopes. The aim was to improve its in vivo stability and target binding. We investigated the effect of thermal stabilization of the presumed non-binding double-stranded stem region on binding affinity and resistance against nucleolytic degradation. To achieve maximal thermal stem stabilization melting experiments with model hexanucleotide duplexes consisting of unmodified RNA, 2'-O-methyl RNA (2'-OMe), 2'-Fluoro RNA (2'-F) or Locked Nucleic Acids (LNAs) were initially carried out. Extremely high melting temperatures have been found for an LNA/LNA duplex. TTA1 derivatives with LNA and 2'-OMe modifications within the non-binding stem have subsequently been synthesized. Especially, the LNA-modified TTA1 derivative exhibited significant stem stabilization and markedly improved plasma stability while maintaining its binding affinity to the target. In addition, higher tumor uptake and longer blood retention was found in tumor-bearing nude mice. Thus, our strategy to introduce LNA modifications after the selection procedure is likely to be generally applicable to improve the in vivo stability of aptamers without compromising their binding properties.


  • [Articles] Assigning functions to genes: identification of S-phase expressed genes in Leishmania major based on post-transcriptional control elements -

    Assigning functions to genes is one of the major challenges of the post-genomic era. Usually, functions are assigned based on similarity of the coding sequences to sequences of known genes, or by identification of transcriptional cis-regulatory elements that are known to be associated with specific pathways or conditions. In trypanosomatids, where regulation of gene expression takes place mainly at the post-transcriptional level, new approaches for function assignment are needed. Here we demonstrate the identification of novel S-phase expressed genes in Leishmania major, based on a post-transcriptional control element that was recognized in Crithidia fasciculata as involved in the cell cycle-dependent expression of several nuclear and mitochondrial S-phase expressed genes. Hypothesizing that a similar regulatory mechanism is manifested in L.major, we have applied a computational search for similar control elements in the genome of L.major. Our computational scan yielded 132 genes, of which 33% are homologues of known DNA metabolism genes and 63% lack any annotation. Experimental testing of seven of these genes revealed that their mRNAs cycle throughout the cell cycle, reaching a maximum level during S-phase or just prior to it. It is suggested that screening for post-transcriptional control elements associated with a specific function provides an efficient method for assigning functions to trypanosomatid genes.


  • [Articles] Automated band mapping in electrophoretic gel images using background information -

    Some popular methods for polymorphism and mutation discovery involve ascertainment of novel bands by the examination of electrophoretic gel images. Although existing strategies for mapping bands work well for specific applications, such as DNA sequencing, these strategies are not well suited for novel band detection. Here, we describe a general strategy for band mapping that uses background banding patterns to facilitate lane calling and size calibration. We have implemented this strategy in GelBuddy, a user-friendly Java-based program for PC and Macintosh computers, which includes several utilities to assist discovery of mutations and polymorphisms. We demonstrate the use of GelBuddy in applications based on single-base mismatch cleavage of heteroduplexed PCR products. Use of software designed to facilitate novel band detection can significantly shorten the time needed for image analysis and data entry in a high-throughput setting. Furthermore, the interactive strategy implemented in GelBuddy has been successfully applied to DNA fingerprinting applications, such as AFLP. GelBuddy promises to make electrophoretic gel analysis a viable alternative to DNA resequencing for discovery of mutations and polymorphisms.


  • [Articles] Bacillus cereus DNA topoisomerase I and III{alpha}: purification, characterization and complementation of Escherichia coli TopoIII activity -

    The Bacillus cereus genome possesses three type IA topoisomerase genes. These genes, encoding DNA topoisomerase I and III (bcTopo I, bcTopo III), have been cloned into T7 RNA polymerase-regulated plasmid expression vectors and the enzymes have been overexpressed, purified and characterized. The proteins exhibit similar biochemical activity to their Escherichia coli counterparts, DNA topoisomerase I and III (ecTopo I, ecTopo III). bcTopo I is capable of efficiently relaxing negatively supercoiled DNA in the presence of Mg2+ but does not possess an efficient DNA decatenation activity. bcTopo III is an active topoisomerase that is capable of relaxing supercoiled DNA at a broad range of Mg2+ concentrations; however, its DNA relaxation activity is not as efficient as that of bcTopo I. In addition, bcTopo III is a potent DNA decatenase that resolves oriC-based plasmid replication intermediates in vitro. Interestingly, bcTopo I and bcTopo III are both able to compensate for the loss of ecTopo III in E.coli cells that lack ecTopo I. In contrast, ecTopo I cannot substitute for ecTopo III under these conditions.


  • [Articles] Bacillus subtilis RecU Holliday-junction resolvase modulates RecA activities -

    The Bacillus subtilis RecU protein is able to catalyze in vitro DNA strand annealing and Holliday-junction resolution. The interaction between the RecA and RecU proteins, in the presence or absence of a single-stranded binding (SSB) protein, was studied. Substoichiometric amounts of RecU enhanced RecA loading onto single-stranded DNA (ssDNA) and stimulated RecA-catalyzed D-loop formation. However, RecU inhibited the RecA-mediated three-strand exchange reaction and ssDNA-dependent dATP or rATP hydrolysis. The addition of an SSB protein did not reverse the negative effect exerted by RecU on RecA function. Annealing of circular ssDNA and homologous linear 3'-tailed double-stranded DNA by RecU was not affected by the addition of RecA both in the presence and in the absence of SSB. We propose that RecU modulates RecA activities by promoting RecA-catalyzed strand invasion and inhibiting RecA-mediated branch migration, by preventing RecA filament disassembly, and suggest a potential mechanism for the control of resolvasome assembly.


  • [Articles] Base excision repair intermediates are mutagenic in mammalian cells -

    Base excision repair (BER) is the main pathway for repair of DNA damage in mammalian cells. This pathway leads to the formation of DNA repair intermediates which, if still unsolved, cause cell lethality and mutagenesis. To characterize mutations induced by BER intermediates in mammalian cells, an SV-40 derived shuttle vector was constructed carrying a site-specific lesion within the recognition sequence of a restriction endonuclease. The mutation spectra of abasic (AP) sites, 5'-deoxyribose-5-phosphate (5'dRp) and 3'-[2,3-didehydro-2,3-dideoxy-ribose] (3'ddR5p) single-strand breaks (ssb) in mammalian cells was analysed by RFLP/PCR and mutation frequency was estimated by quantitative PCR. Point mutations were the predominant events occurring at all BER intermediates. The AP site-induced mutation spectrum supports evidence for the ‘A-rule’ and is also consistent with the use of the 5' neighbouring base to instruct nucleotide incorporation (5'-rule). Preferential adenine insertion was also observed after in vivo replication of 5'dRp or 3'ddR5p ssb. We provide original evidence that not only the abasic site but also its derivatives ‘faceless’ BER intermediates are mutagenic, with a similar mutation frequency, in mammalian cells. Our findings support the hypothesis that unattended BER intermediates could be a constant threat for genome integrity as well as a spontaneous source of mutations.


  • [Articles] Binding of serum response factor to cystic fibrosis transmembrane conductance regulator CArG-like elements, as a new potential CFTR transcriptional regulation pathway -

    CFTR expression is tightly controlled by a complex network of ubiquitous and tissue-specific cis-elements and trans-factors. To better understand mechanisms that regulate transcription of CFTR, we examined transcription factors that specifically bind a CFTR CArG-like motif we have previously shown to modulate CFTR expression. Gel mobility shift assays and chromatin immunoprecipitation analyses demonstrated the CFTR CArG-like motif binds serum response factor both in vitro and in vivo. Transient co-transfections with various SRF expression vector, including dominant-negative forms and small interfering RNA, demonstrated that SRF significantly increases CFTR transcriptional activity in bronchial epithelial cells. Mutagenesis studies suggested that in addition to SRF other co-factors, such as Yin Yang 1 (YY1) previously shown to bind the CFTR promoter, are potentially involved in the CFTR regulation. Here, we show that functional interplay between SRF and YY1 might provide interesting perspectives to further characterize the underlying molecular mechanism of the basal CFTR transcriptional activity. Furthermore, the identification of multiple CArG binding sites in highly conserved CFTR untranslated regions, which form specific SRF complexes, provides direct evidence for a considerable role of SRF in the CFTR transcriptional regulation into specialized epithelial lung cells.


  • [Articles] cAMP-responsive element in TATA-less core promoter is essential for haploid-specific gene expression in mouse testis -

    Promoters, including neither TATA box nor initiator, have been frequently found in testicular germ cell-specific genes in mice. These investigations imply that unique forms of the polymerase II transcription initiation machinery play a role in selective activation of germ cell-specific gene expression programs during spermatogenesis. However, there is little information about testis-specific core promoters, because useful germ cell culture system is not available. In this study, we characterize the regulatory region of the haploid-specific Oxct2b gene in detail by using in vivo transient transfection assay in combination with a transgenic approach, with electrophoretic mobility shift and chromatin immunoprecipitation assays. Expression studies using mutant constructs demonstrate that a 34 bp region, which extends from –49 to –16, acts as a core promoter in an orientation-dependent manner. This promoter region includes the cAMP-responsive element (CRE)-like sequence TGACGCAG, but contains no other motifs, such as a TATA box or initiator. The CRE-like element is indispensable for the core promoter activity, but not for activator in testicular germ cells, through the binding of a testis-specific CRE modulator transcription factor. These results indicate the presence of alternative transcriptional initiation machinery for cell-type-specific gene expression in testicular germ cells.


  • [Articles] Cell-type-specific epigenetic marking of the IL2 gene at a distal cis-regulatory region in competent, nontranscribing T-cells -

    T-cells retain cell-type-specific programming for IL-2 inducibility through many rounds of division without being stimulated to transcribe the locus. To understand the layering of controls needed to poise this gene heritably for activation, we have used chromatin immunoprecipitation to map histone modifications across the murine IL2 locus, from –10.2 through +0.25 kb, in induction-competent and incompetent cells. In highly inducible EL4 T-lineage cells, stimulation with PMA/A23187 induced strong acetylation of histone H3 and H4, in parallel with transcriptional activation, from –4.6 through +0.25 kb. However, dimethylation of histone H3/K4 was already fully elevated across the same restricted domain before stimulation, with little change after stimulation. RNA polymerase II binding, in contrast, was only found at the known promoter region after stimulation. Similar patterns of histone modifications were seen also in normal IL-2-inducible T-lineage cells. However, neither acetylated histone H3, H4 nor dimethylated histone H3/K4 marking was detected, with or without stimulation, in expression-incompetent cells (NIH/3T3 or Scid.adh). These results identify a discrete new domain of IL2 regulatory sequence marked by dimethylated histone H3/K4 in expression-permissive T-cells even when they are not transcribing IL2, setting boundaries for histone H3 and H4 acetylation when the IL2 gene is transcriptionally activated.


  • [Articles] Centromere parC of plasmid R1 is curved -

    The centromere sequence parC of Escherichia coli low-copy-number plasmid R1 consists of two sets of 11 bp iterated sequences. Here we analysed the intrinsic sequence-directed curvature of parC by its migration anomaly in polyacrylamide gels. The 159 bp long parC is strongly curved with anomaly values (k-factors) close to 2. The properties of the parC curvature agree with those of other curved DNA sequences. parC contains two regions of 5-fold repeated iterons separated by 39 bp. We modified 4 bp within this intermediate sequence so that we could analyse the two 5-fold repeated regions independently. The analysis shows that the two repeat regions are not independently curved parts of parC but that the overall curvature is a property of the whole fragment. Since the centromere sequence of an E.coli plasmid as well as eukaryotic centromere sequences show DNA curvature, we speculate that curvature might be a general property of centromeres.


  • [Articles] Characterization of a novel transcriptionally active domain in the transforming growth factor {beta}-regulated Smad3 protein -

    Transforming growth factor ßbeta; (TGFßbeta;) regulates transcriptional responses via activation of cytoplasmic effector proteins termed Smads. Following their phosphorylation by the type I TGFßbeta; receptor, Smads form oligomers and translocate to the nucleus where they activate the transcription of TGFßbeta; target genes in cooperation with nuclear cofactors and coactivators. In the present study, we have undertaken a deletion analysis of human Smad3 protein in order to characterize domains that are essential for transcriptional activation in mammalian cells. With this analysis, we showed that Smad3 contains two domains with transcriptional activation function: the MH2 domain and a second middle domain that includes the linker region and the first two ßbeta; strands of the MH2 domain. Using a protein–protein interaction assay based on biotinylation in vivo, we were able to show that a Smad3 protein bearing an internal deletion in the middle transactivation domain is characterized by normal oligomerization and receptor activation properties. However, this mutant has reduced transactivation capacity on synthetic or natural promoters and is unable to interact physically and functionally with the histone acetyltransferase p/CAF. The loss of interaction with p/CAF or other coactivators could account, at least in part, for the reduced transactivation capacity of this Smad3 mutant. Our data support an essential role of the previously uncharacterized middle region of Smad3 for nuclear functions, such as transcriptional activation and interaction with coactivators.


  • [Articles] Characterization of E2F8, a novel E2F-like cell-cycle regulated repressor of E2F-activated transcription -

    The E2F family of transcription factors are downstream effectors of the retinoblastoma protein, pRB, pathway and are essential for the timely regulation of genes necessary for cell-cycle progression. Here we describe the characterization of human and murine E2F8, a new member of the E2F family. Sequence analysis of E2F8 predicts the presence of two distinct E2F-related DNA binding domains suggesting that E2F8 and, the recently, identified E2F7 form a subgroup within the E2F family. We show that E2F transcription factors bind the E2F8 promoter in vivo and that expression of E2F8 is being induced at the G1/S transition. Purified recombinant E2F8 binds specifically to a consensus E2F-DNA-binding site indicating that E2F8, like E2F7, binds DNA without the requirement of co-factors such as DP1. E2F8 inhibits E2F-driven promoters suggesting that E2F8 is transcriptional repressor like E2F7. Ectopic expression of E2F8 in diploid human fibroblasts reduces expression of E2F-target genes and inhibits cell growth consistent with a role for repressing E2F transcriptional activity. Taken together, these data suggest that E2F8 has an important role in turning of the expression of E2F-target genes in the S-phase of the cell cycle.


  • [Articles] Characterization of the bisintercalative DNA binding mode of a bifunctional platinum-acridine agent -

    The DNA interactions of PT-BIS(ACRAMTU) ([Pt(en)(ACRAMTU)2](NO3)4; ACRAMTU = 1-[2-(acridin-9-ylamino)ethyl]-1,3-dimethylthiourea, en = ethylenediamine), a bifunctional platinum–acridine conjugate, have been studied in native and synthetic double-stranded DNAs and model duplexes using various biophysical techniques. These include ethidium-DNA fluorescence quenching and thermal melting experiments, circular dichroism (CD) spectroscopy and plasmid unwinding assays. In addition, the binding mode was studied in a short octamer by NMR spectroscopy in conjunction with molecular modeling. In alternating copolymers, PT-BIS(ACRAMTU) shows a distinct preference for poly(dA-dT)2, which is ~3-fold higher than that of ACRAMTU. In the ligand-oligomer complex, d(GCTATAGC)2·PT-BIS(ACRAMTU) (complex I*), PT-BIS(ACRAMTU) increases the thermal stability of the B-form host duplex by Tm > 30 K (CD and UV melting experiments). The agent unwinds pSP73 plasmid DNA by 44(±2)° per bound molecule, indicating bisintercalative binding. A 2-D NMR study unequivocally demonstrates that PT-BIS(ACRAMTU)'s chromophores deeply bisintercalate into the 5'-TA/TA base pair steps in I*, while the platinum linker lies in the minor groove. An AMBER model reflecting the NMR results shows that bracketing of the central AT base pairs in a classical nearest neighbor excluded fashion is feasible. PT-BIS(ACRAMTU) inhibits DNA hydrolysis by BstZ17 I at the enzyme's restriction site, GTATAC. Possible consequences for other relevant DNA–protein interactions, such as those involved in TATA-box-mediated transcription initiation and the utility of the platinum-intercalator technology for the design of sequence-specific agents are discussed.


  • [Articles] Characterization of the metal ion binding site in the anti-terminator protein, HutP, of Bacillus subtilis -

    HutP is an RNA-binding protein that regulates the expression of the histidine utilization (hut) operon in Bacillus subtilis, by binding to cis-acting regulatory sequences on hut mRNA. It requires L-histidine and an Mg2+ ion for binding to the specific sequence within the hut mRNA. In the present study, we show that several divalent cations can mediate the HutP–RNA interactions. The best divalent cations were Mn2+, Zn2+ and Cd2+, followed by Mg2+, Co2+ and Ni2+, while Cu2+, Yb2+ and Hg2+ were ineffective. In the HutP–RNA interactions, divalent cations cannot be replaced by monovalent cations, suggesting that a divalent metal ion is required for mediating the protein–RNA interactions. To clarify their importance, we have crystallized HutP in the presence of three different metal ions (Mg2+, Mn2+ and Ba2+), which revealed the importance of the metal ion binding site. Furthermore, these analyses clearly demonstrated how the metal ions cause the structural rearrangements that are required for the hut mRNA recognition.


  • [Articles] Cis-acting regulatory sequences promote high-frequency gene conversion between repeated sequences in mammalian cells -

    In mammalian cells, little is known about the nature of recombination-prone regions of the genome. Previously, we reported that the immunoglobulin heavy chain (IgH) µ locus behaved as a hotspot for mitotic, intrachromosomal gene conversion (GC) between repeated µ constant (Cµ) regions in mouse hybridoma cells. To investigate whether elements within the µ gene regulatory region were required for hotspot activity, gene targeting was used to delete a 9.1 kb segment encompassing the µ gene promoter (Pµ), enhancer (Eµ) and switch region (Sµ) from the locus. In these cell lines, GC between the Cµ repeats was significantly reduced, indicating that this ‘recombination-enhancing sequence’ (RES) is necessary for GC hotspot activity at the IgH locus. Importantly, the RES fragment stimulated GC when appended to the same Cµ repeats integrated at ectopic genomic sites. We also show that deletion of Eµ and flanking matrix attachment regions (MARs) from the RES abolishes GC hotspot activity at the IgH locus. However, no stimulation of ectopic GC was observed with the Eµ/MARs fragment alone. Finally, we provide evidence that no correlation exists between the level of transcription and GC promoted by the RES. We suggest a model whereby Eµ/MARS enhances mitotic GC at the endogenous IgH µ locus by effecting chromatin modifications in adjacent DNA.


  • [Articles] Cleavage of double-stranded RNA by RNase HI from a thermoacidophilic archaeon, Sulfolobus tokodaii 7 -

    ST0753, the orthologous gene of Type 1 RNase H found in a thermoacidophilic archaeon, Sulfolobus tokodaii, was analyzed. The recombinant ST0753 protein exhibited RNase H activity in both in vivo and in vitro assays. The protein expressed in an RNase H-deficient mutant Escherichia coli strain functioned to suppress the temperature-sensitive phenotype associated with the lack of RNase H. The in vitro characteristics of the gene's RNase H activity were similar to those of Halobacterium RNase HI, the first archaeal Type 1 RNase H to be characterized. Surprisingly, the S.tokodaii RNase HI cleaved not only the RNA strand of an RNA/DNA hybrid but also an RNA strand of an RNA/RNA duplex in the presence of Mn2+ or Co2+. The result of gel filtration column chromatography showed this double-stranded RNA-dependent RNase (dsRNase) activity was coincident with S.tokodaii RNase HI. A site-directed mutagenesis study of essential amino acids for RNase H activity indicated that this activity also affected dsRNase activity. A single amino acid replacement of Asp-125 by Asn resulted in loss of dsRNase activity but not RNase H activity, suggesting that amino acid residues required for dsRNase activity seemed slightly different from those of RNase H activity. Some reverse transcriptases from retroelements can cleave double-stranded RNA, and this activity requires the RNase H domain. Similarities in primary structure and biochemical characteristics between S.tokodaii RNase HI and reverse transcriptases imply that the S.tokodaii enzyme might be derived from the RNase H domain of reverse transcriptase.


  • [Articles] Cloning and characterization of the Schizosaccharomyces pombe homologs of the human protein Translin and the Translin-associated protein TRAX -

    Translin is a human octameric protein that specifically binds the single-stranded microsatellite repeats d(GT)n and the corresponding transcripts (GU)n. It also binds, with lesser affinities, other single-stranded G-rich DNA and RNA sequences. TRAX is a human protein that bears a homology to Translin and interacts with it. Translin and TRAX have been proposed to be involved in DNA recombination, chromosomal translocation and mRNA transport and translation. Both proteins are highly conserved in eukaryotes, including the fission yeast Schizosaccharomyces pombe, which is amenable to genetic analysis. Here, we report the first study of the S.pombe Translin and TRAX homologs. We have deleted the genes encoding Translin and TRAX in S.pombe and found that the proliferation of the mutant cells was slightly stimulated, suggesting that these genes are not essential for the fission yeast. We have also shown that the S.pombe Translin and TRAX interact. Biochemical analysis of the S.pombe Translin, which was cloned and expressed in Escherichia coli, revealed that it is octameric and that it selectively binds d(GT)n and d(GTT)n microsatellite repeats. However, unlike the human protein, it has much higher affinities for the homologous RNA sequences (GU)n and (GUU)n. These data suggest that the S.pombe Translin is primarily involved in functions related to RNA metabolism.


  • [Articles] Cobalt hexammine induced tautomeric shift in Z-DNA: the structure of d(CGCGCA).d(TGCGCG) in two crystal forms -

    We report here the crystal structure of the DNA hexamer duplex d(CGCGCA).d(TGCGCG) at 1.71 Å resolution. The crystals, in orthorhombic space group, were grown in the presence of cobalt hexammine, a known inducer of the left-handed Z form of DNA. The interaction of this ion with the DNA helix results in a change of the adenine base from the common amino tautomeric form to the imino tautomer. Consequently the A:T base pair is disrupted from the normal Watson–Crick base pairing to a ‘wobble’ like base pairing. This change is accommodated easily within the helix, and the helical parameters are those expected for Z-DNA. When the cobalt hexammine concentration is decreased slightly in the crystallization conditions, the duplex crystallizes in a different, hexagonal space group, with two hexamer duplexes in the asymmetric unit. One of these is situated on a crystallographic 6-fold screw axis, leading to disorder. The tautomeric shift is not observed in this space group. We show that the change in inter-helix interactions that lead to the two different space groups probably arise from the small decrease in ion concentration, and consequently disordered positions for the ion.


  • [Articles] Common and specific amino acid residues in the prokaryotic polypeptide release factors RF1 and RF2: possible functional implications -

    Termination of protein synthesis is promoted in ribosomes by proper stop codon discrimination by class 1 polypeptide release factors (RFs). A large set of prokaryotic RFs differing in stop codon specificity, RF1 for UAG and UAA, and RF2 for UGA and UAA, was analyzed by means of a recently developed computational method allowing identification of the specificity-determining positions (SDPs) in families composed of proteins with similar but not identical function. Fifteen SDPs were identified within the RF1/2 superdomain II/IV known to be implicated in stop codon decoding. Three of these SDPs had particularly high scores. Five residues invariant for RF1 and RF2 [invariant amino acid residues (IRs)] were spatially clustered with the highest-scoring SDPs that in turn were located in two zones within the SDP/IR area. Zone 1 (domain II) included PxT and SPF motifs identified earlier by others as ‘discriminator tripeptides’. We suggest that IRs in this zone take part in the recognition of U, the first base of all stop codons. Zone 2 (domain IV) possessed two SDPs with the highest scores not identified earlier. Presumably, they also take part in stop codon binding and discrimination. Elucidation of potential functional role(s) of the newly identified SDP/IR zones requires further experiments.


  • [Articles] Competition between trans-translation and termination or elongation of translation -

    The effects of tRNA, RF1 and RRF on trans-translation by tmRNA were examined using a stalled complex of ribosome prepared using a synthetic mRNA and pure Escherichia coli translation factors. No endoribonucleolytic cleavage of mRNA around the A site was found in the stalled ribosome and was required for the tmRNA action. When the A site was occupied by a stop codon, alanyl-tmRNA competed with RF1 with the efficiency of peptidyl-transfer to alanyl-tmRNA for trans-translation inversely correlated to the efficiency of translation termination. The competition was not affected by RF3. A sense codon also serves as a target for alanyl-tmRNA with competition of aminoacyl-tRNA. The extent of inhibition was decreased with the length of the 3'-extension of mRNA. RRF, only at a high concentration, slightly affected peptidyl-transfer for trans-translation, although it did not affect the canonical elongation. These results indicate that alanyl-tmRNA does not absolutely require the truncation of mRNA around the A site but prefers an mRNA of a short 3'-extension from the A site and that it can operate on either a sense or termination codon at the A site, at which alanyl-tmRNA competes with aminoacyl-tRNA, RF and RRF.


  • [Articles] Complex patterns of transcription at the insertion site of a retrotransposon in the mouse -

    Here we report that transcriptional effects of the insertion of a retrotransposon can occur simultaneously both upstream and downstream of the insertion site. We have identified an intra-cisternal A particle (IAP) retrotransposon in intron 6 of a gene that we have named Cabp (CDK5 activator binding protein). The presence of the IAP is associated with an aberrant transcript initiating from a cryptic promoter in the IAP, reading out into the adjacent Cabp gene sequence. The expression of this transcript is highly variable among isogenic mice within the C57BL/6J strain and so CabpIAP can be classified as a metastable epiallele. As expected, the presence or absence of the transcript correlates with differential DNA methylation of the 5' LTR of the IAP. More surprisingly, in mice where the retrotransposon is unmethylated and presumably transcriptionally active, we find a number of short Cabp transcripts which initiate at the normal 5' end of the gene but terminate prematurely, just 5' of the retrotransposon. This is the first report of a retrotransposon having both upstream and downstream effects on transcription at the site of insertion and it suggests that alternative polyadenylation may sometimes be caused by a downstream convergent transcription unit.


  • [Articles] Complicated water orientations in the minor groove of the B-DNA decamer d(CCATTAATGG)2 observed by neutron diffraction measurements -

    It has long been suspected that the structure and function of a DNA duplex can be strongly dependent on its degree of hydration. By neutron diffraction experiments, we have succeeded in determining most of the hydrogen (H) and deuterium (D) atomic positions in the decameric d(CCATTAATGG)2 duplex. Moreover, the D positions in 27 D2O molecules have been determined. In particular, the complex water network in the minor groove has been observed in detail. By a combined structural analysis using 2.0 Å resolution X-ray and 3.0 Å resolution neutron data, it is clear that the spine of hydration is built up, not only by a simple hexagonal hydration pattern (as reported in earlier X-ray studies), but also by many other water bridges hydrogen-bonded to the DNA strands. The complexity of the hydration pattern in the minor groove is derived from an extraordinary variety of orientations displayed by the water molecules.


  • [Articles] Composite genome map and recombination parameters derived from three archetypal lineages of Toxoplasma gondii -

    Toxoplasma gondii is a highly successful protozoan parasite in the phylum Apicomplexa, which contains numerous animal and human pathogens. T.gondii is amenable to cellular, biochemical, molecular and genetic studies, making it a model for the biology of this important group of parasites. To facilitate forward genetic analysis, we have developed a high-resolution genetic linkage map for T.gondii. The genetic map was used to assemble the scaffolds from a 10X shotgun whole genome sequence, thus defining 14 chromosomes with markers spaced at ~300 kb intervals across the genome. Fourteen chromosomes were identified comprising a total genetic size of ~592 cM and an average map unit of ~104 kb/cM. Analysis of the genetic parameters in T.gondii revealed a high frequency of closely adjacent, apparent double crossover events that may represent gene conversions. In addition, we detected large regions of genetic homogeneity among the archetypal clonal lineages, reflecting the relatively few genetic outbreeding events that have occurred since their recent origin. Despite these unusual features, linkage analysis proved to be effective in mapping the loci determining several drug resistances. The resulting genome map provides a framework for analysis of complex traits such as virulence and transmission, and for comparative population genetic studies.


  • [Articles] Computer identification of snoRNA genes using a Mammalian Orthologous Intron Database -

    Based on comparative genomics, we created a bioinformatic package for computer prediction of small nucleolar RNA (snoRNA) genes in mammalian introns. The core of our approach was the use of the Mammalian Orthologous Intron Database (MOID), which contains all known introns within the human, mouse and rat genomes. Introns from orthologous genes from these three species, that have the same position relative to the reading frame, are grouped in a special orthologous intron table. Our program SNO.pl searches for conserved snoRNA motifs within MOID and reports all cases when characteristic snoRNA-like structures are present in all three orthologous introns of human, mouse and rat sequences. Here we report an example of the SNO.pl usage for searching a particular pattern of conserved C/D-box snoRNA motifs (canonical C- and D-boxes and the 6 nt long terminal stem). In this computer analysis, we detected 57 triplets of snoRNA-like structures in three mammals. Among them were 15 triplets that represented known C/D-box snoRNA genes. Six triplets represented snoRNA genes that had only been partially characterized in the mouse genome. One case represented a novel snoRNA gene, and another three cases, putative snoRNAs. Our programs are publicly available and can be easily adapted and/or modified for searching any conserved motifs within mammalian introns.


  • [Articles] Contrahelicase activity of the mitochondrial transcription termination factor mtDBP -

    The sea urchin mitochondrial D-loop binding protein (mtDBP) is a transcription termination factor that is able to arrest bidirectionally mitochondrial RNA chain elongation. The observation that the mtDBP binding site in the main non-coding region is located in correspondence of the 3' end of the triplex structure, where the synthesis of heavy strand mitochondrial (mt) DNA is either prematurely terminated or allowed to continue, raised the question whether mtDBP could also regulate mtDNA replication. By using a helicase assay in the presence of the replicative helicase of SV40, we show that mtDBP is able to inhibit the enzyme thus acting as a contrahelicase. The impairing activity of mtDBP is bidirectional as it is independent of the orientation of the protein binding site. The inhibition is increased by the presence of the guanosine-rich sequence that flanks mtDBP binding site. Finally, a mechanism of abrogation of mtDBP contrahelicase activity is suggested that is based on the dissociation of mtDBP from DNA caused by the passage of the RNA polymerase through the protein–DNA complex. All these findings favour the view that mtDBP, besides serving as transcription termination factor, could also act as a negative regulator of mtDNA synthesis at the level of D-loop expansion.


  • [Articles] Contrasting effects of Elg1-RFC and Ctf18-RFC inactivation in the absence of fully functional RFC in fission yeast -

    Proliferating cell nuclear antigen loading onto DNA by replication factor C (RFC) is a key step in eukaryotic DNA replication and repair processes. In this study, the C-terminal domain (CTD) of the large subunit of fission yeast RFC is shown to be essential for its function in vivo. Cells carrying a temperature-sensitive mutation in the CTD, rfc1-44, arrest with incompletely replicated chromosomes, are sensitive to DNA damaging agents, are synthetically lethal with other DNA replication mutants, and can be suppressed by mutations in rfc5. To assess the contribution of the RFC-like complexes Elg1–RFC and Ctf18–RFC to the viability of rfc1-44, genes encoding the large subunits of these complexes have been deleted and overexpressed. Inactivation of Ctf18–RFC by the deletion of ctf18+, dcc1+ or ctf8+ is lethal in an rfc1-44 background showing that full Ctf18–RFC function is required in the absence of fully functional RFC. In contrast, rfc1-44 elg1 cells are viable and overproduction of Elg1 in rfc1-44 is lethal, suggesting that Elg1–RFC plays a negative role when RFC function is inhibited. Consistent with this, the deletion of elg1+ is shown to restore viability to rfc1-44 ctf18 cells.


  • [Articles] Cooperative binding of DNA and CBF{beta} to the Runt domain of the CBF{alpha} studied via MD simulations -

    The Runt domain (RD) is the DNA-binding region of the Runx genes. A related protein, known as core binding factor ßbeta; (CBFßbeta;) also binds to the RD to enhance RD–DNA interaction by 6- to 10-fold. Here, we report results from molecular dynamics (MD) simulations of RD alone, as a dimer in complexes with DNA and CBFßbeta; and in a ternary complex with DNA and CBFßbeta;. Consistent with the experimental findings, in the presence of CBFßbeta; the estimated free energy of binding of RD to the DNA is more favorable, which is shown to be due to more favorable intermolecular interactions and desolvation contributions. Also contributing to the enhanced binding are favorable intramolecular interactions between the ‘wing’ residues (RD residues 139–145) and the ‘wing1’ residues (RD residues 104–116). The simulation studies also indicate that the RD–CBFßbeta; binding is more favorable in the presence of DNA due to a more favorable RD–CBFßbeta; interaction energy. In addition, it is predicted that long-range interactions involving ionic residues contribute to binding cooperativity. Results from the MD calculations are used to interpret a variety of experimental mutagenesis data. A novel role for RD Glu116 to the RD–CBFßbeta; interaction is predicted.


  • [Articles] Core promoter elements of eukaryotic genes have a highly distinctive mechanical property -

    In spite of the abundant data on DNA sequence, the mechanical aspects of promoter DNA remain poorly understood. We classified 1871 human and 196 mouse RNA polymerase II promoters and investigated average flexibility profiles of the human promoters containing either a TATA box or an initiator (Inr) sequence only. Here, we show that TATA boxes and Inr sequences have a common anomalous mechanical property: they are comprised of distinctively flexible and rigid sequences, compared with the other parts of the promoter region. The +2 position in the Inr consensus sequence does not favor adenine to keep the high flexibility and thus this position is more accurately represented as ‘T, G, C>>A’. Additionally, it was also found that DNA region upstream of TATA box or Inr sequence is more rigid than region downstream of each element. These properties may function as a marker for recognition by TATA-binding protein and Inr-binding protein.


  • [Articles] Covalent ligation studies on the human telomere quadruplex -

    Recent X-ray crystallographic studies on the human telomere sequence d[AGGG(TTAGGG)3] revealed a unimolecular, parallel quadruplex structure in the presence of potassium ions, while earlier NMR results in the presence of sodium ions indicated a unimolecular, antiparallel quadruplex. In an effort to identify and isolate the parallel form in solution, we have successfully ligated into circular products the single-stranded human telomere and several modified human telomere sequences in potassium-containing solutions. Using these sequences with one or two terminal phosphates, we have made chemically ligated products via creation of an additional loop. Circular products have been identified by polyacrylamide gel electrophoresis, enzymatic digestion with exonuclease VII and electrospray mass spectrometry in negative ion mode. Optimum pH for the ligation reaction of the human telomere sequence ranges from 4.5 to 6.0. Several buffers were also examined, with MES yielding the greatest ligation efficiency. Human telomere sequences with two phosphate groups, one each at the 3' and 5' ends, were more efficient at ligation, via pyrophosphate bond formation, than the corresponding sequences with only one phosphate group, at the 5' end. Circular dichroism spectra showed that the ligation product was derived from an antiparallel, single-stranded guanine quadruplex rather than a parallel single-stranded guanine quadruplex structure.


  • [Articles] CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome -

    An effective tool for the global analysis of both DNA methylation status and protein–chromatin interactions is a microarray constructed with sequences containing regulatory elements. One type of array suited for this purpose takes advantage of the strong association between CpG Islands (CGIs) and gene regulatory regions. We have obtained 20 736 clones from a CGI Library and used these to construct CGI arrays. The utility of this library requires proper annotation and assessment of the clones, including CpG content, genomic origin and proximity to neighboring genes. Alignment of clone sequences to the human genome (UCSC hg17) identified 9595 distinct genomic loci; 64% were defined by a single clone while the remaining 36% were represented by multiple, redundant clones. Approximately 68% of the loci were located near a transcription start site. The distribution of these loci covered all 23 chromosomes, with 63% overlapping a bioinformatically identified CGI. The high representation of genomic CGI in this rich collection of clones supports the utilization of microarrays produced with this library for the study of global epigenetic mechanisms and protein–chromatin interactions. A browsable database is available on-line to facilitate exploration of the CGIs in this library and their association with annotated genes or promoter elements.


  • [Articles] Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding -

    The crystal structures of six complexes between aminoglycoside antibiotics (neamine, gentamicin C1A, kanamycin A, ribostamycin, lividomycin A and neomycin B) and oligonucleotides containing the decoding A site of bacterial ribosomes are reported at resolutions between 2.2 and 3.0 Å. Although the number of contacts between the RNA and the aminoglycosides varies between 20 and 31, up to eight direct hydrogen bonds between rings I and II of the neamine moiety are conserved in the observed complexes. The puckered sugar ring I is inserted into the A site helix by stacking against G1491 and forms a pseudo base pair with two H-bonds to the Watson–Crick sites of the universally conserved A1408. This central interaction helps to maintain A1492 and A1493 in a bulged-out conformation. All these structures of the minimal A site RNA complexed to various aminoglycosides display crystal packings with intermolecular contacts between the bulging A1492 and A1493 and the shallow/minor groove of Watson–Crick pairs in a neighbouring helix. In one crystal, one empty A site is observed. In two crystals, two aminoglycosides are bound to the same A site with one bound specifically and the other bound in various ways in the deep/major groove at the edge of the A sites.


  • [Articles] CTD kinase I is involved in RNA polymerase I transcription -

    RNA polymerase II carboxy terminal domain (CTD) kinases are key elements in the control of mRNA synthesis. Yeast CTD kinase I (CTDK-I), is a non-essential complex involved in the regulation of mRNA synthesis at the level of transcription elongation, pre-mRNA 3' formation and nuclear export. Here, we report that CTDK-I is also involved in ribosomal RNA synthesis. We show that CTDK-I is localized in part in the nucleolus. In its absence, nucleolar structure and RNA polymerase I transcription are affected. In vitro experiments show an impairment of the Pol I transcription machinery. Remarkably, RNA polymerase I co-precipitates from cellular extracts with Ctk1, the kinase subunit of the CTDK-I complex. In vitro analysis further demonstrates a direct interaction between RNA polymerase I and Ctk1. The results suggest that CTDK-I might participate in the regulation of distinct nuclear transcriptional machineries, thus playing a role in the adaptation of the global transcriptional response to growth signalling.


  • [Articles] Curved DNA molecules migrate anomalously slowly in free solution -

    The electrophoretic mobility of a curved DNA restriction fragment taken from the VP1 gene in the SV40 minichromosome has been measured in polyacrylamide gels and free solution, using capillary electrophoresis. The 199 bp restriction fragment has an apparent bend angle of 46 ± 2° located at SV40 sequence position 1922 ± 2 bp [Lu Y.J., Weers B.D. and Stellwagen N. C. (2005) Biophys. J., 88, 1191–1206]. The ‘curvature module’ surrounding the apparent bend center contains five unevenly spaced A- and T-tracts, which are responsible for the observed curvature. The parent 199 bp fragment and sequence mutants containing at least one A-tract in the curvature module migrate anomalously slowly in free solution, as well as in polyacrylamide gels. Hence, the anomalously slow mobilities observed for curved DNA molecules in polyacrylamide gels are due in part to their anomalously slow mobilities in free solution. Analysis of the gel and free solution mobility decrements indicates that each A- or T-tract contributes independently, but not equally, to the curvature of the 199 bp fragment and its A-tract mutants. The relative contribution of each A- or T-tract to the observed curvature depends on its spacing with respect to the first A-tract in the curvature module.


  • [Articles] Deacylated tRNA is released from the E site upon A site occupation but before GTP is hydrolyzed by EF-Tu -

    The presence or absence of deacylated tRNA at the E site sharply influences the activation energy required for binding of a ternary complex to the ribosomal A site indicating the different conformations that the E-tRNA imparts on the ribosome. Here we address two questions: (i) whether or not peptidyltransferase—the essential catalytic activity of the large ribosomal subunit—also depends on the occupancy state of the E site and (ii) at what stage the E-tRNA is released during an elongation cycle. Kinetics of the puromycin reaction on various functional states of the ribosome indicate that the A-site substrate of the peptidyltransferase center, puromycin, requires the same activation energy for peptide-bond formation under all conditions tested. We further demonstrate that deacylated tRNA is released from the E site by binding a ternary complex aminoacyl-tRNA•EF-Tu•GDPNP to the A site. This observation indicates that the E-tRNA is released after the decoding step but before both GTP hydrolysis by EF-Tu and accommodation of the A-tRNA. Collectively these results reveal that the reciprocal linkage between the E and A sites affects the decoding center on the 30S subunit, but does not influence the rate of peptide-bond formation at the active center of the 50S subunit.


  • [Articles] Determination of protein-DNA binding constants and specificities from statistical analyses of single molecules: MutS-DNA interactions -

    Atomic force microscopy (AFM) is a powerful technique for examining the conformations of protein–DNA complexes and determining the stoichiometries and affinities of protein–protein complexes. We extend the capabilities of AFM to the determination of protein–DNA binding constants and specificities. The distribution of positions of the protein on the DNA fragments provides a direct measure of specificity and requires no knowledge of the absolute binding constants. The fractional occupancies of the protein at a given position in conjunction with the protein and DNA concentrations permit the determination of the absolute binding constants. We present the theoretical basis for this analysis and demonstrate its utility by characterizing the interaction of MutS with DNA fragments containing either no mismatch or a single mismatch. We show that MutS has significantly higher specificities for mismatches than was previously suggested from bulk studies and that the apparent low specificities are the result of high affinity binding to DNA ends. These results resolve the puzzle of the apparent low binding specificity of MutS with the expected high repair specificities. In conclusion, from a single set of AFM experiments, it is possible to determine the binding affinity, specificity and stoichiometry, as well as the conformational properties of the protein–DNA complexes.


  • [Articles] Differential and collaborative actions of Rad51 paralog proteins in cellular response to DNA damage -

    Metazoan Rad51 plays a central role in homologous DNA recombination, and its activity is controlled by a number of Rad51 cofactors. These include five Rad51 paralogs, Rad51B, Rad51C, Rad51D, XRCC2 and XRCC3. We previously hypothesized that all five paralogs participate collaboratively in repair. However, this idea was challenged by the biochemical identification of two independent complexes composed of either Rad51B/C/D/XRCC2 or Rad51C/XRCC3. To investigate if this biochemical finding is matched by genetic interactions, we made double mutants in either the same complex (rad51b/rad51d) or in both complexes (xrcc3/rad51d). In agreement with the biochemical findings the double deletion involving both complexes had an additive effect on the sensitivity to camptothecin and cisplatin. The double deletion of genes in the same complex, on the other hand, did not further increase the sensitivity to these agents. Conversely, all mutants tested displayed comparatively mild sensitivity to -irradiation and attenuated -irradiation-induced Rad51 foci formation. Thus, in accord with our previous conclusion, all paralogs appear to collaboratively facilitate Rad51 action. In conclusion, our detailed genetic study reveals a complex interplay between the five Rad51 paralogs and suggests that some of the Rad51 paralogs can separately operate in later step of homologous recombination.


  • [Articles] Discovery of new genes and deletion editing in Physarum mitochondria enabled by a novel algorithm for finding edited mRNAs -

    Gene finding is complicated in organisms that exhibit insertional RNA editing. Here, we demonstrate how our new algorithm Predictor of Insertional Editing (PIE) can be used to locate genes whose mRNAs are subjected to multiple frameshifting events, and extend the algorithm to include probabilistic predictions for sites of nucleotide insertion; this feature is particularly useful when designing primers for sequencing edited RNAs. Applying this algorithm, we successfully identified the nad2, nad4L, nad6 and atp8 genes within the mitochondrial genome of Physarum polycephalum, which had gone undetected by existing programs. Characterization of their mRNA products led to the unanticipated discovery of nucleotide deletion editing in Physarum. The deletion event, which results in the removal of three adjacent A residues, was confirmed by primer extension sequencing of total RNA. This finding is remarkable in that it comprises the first known instance of nucleotide deletion in this organelle, to be contrasted with nearly 500 sites of single and dinucleotide addition in characterized mitochondrial RNAs. Statistical analysis of this larger pool of editing sites indicates that there are significant biases in the 2 nt immediately upstream of editing sites, including a reduced incidence of nucleotide repeats, in addition to the previously identified purine-U bias.


  • [Articles] Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains -

    The comparative genomics of apicomplexans, such as the malarial parasite Plasmodium, the cattle parasite Theileria and the emerging human parasite Cryptosporidium, have suggested an unexpected paucity of specific transcription factors (TFs) with DNA binding domains that are closely related to those found in the major families of TFs from other eukaryotes. This apparent lack of specific TFs is paradoxical, given that the apicomplexans show a complex developmental cycle in one or more hosts and a reproducible pattern of differential gene expression in course of this cycle. Using sensitive sequence profile searches, we show that the apicomplexans possess a lineage-specific expansion of a novel family of proteins with a version of the AP2 (Apetala2)-integrase DNA binding domain, which is present in numerous plant TFs. About 20–27 members of this apicomplexan AP2 (ApiAP2) family are encoded in different apicomplexan genomes, with each protein containing one to four copies of the AP2 DNA binding domain. Using gene expression data from Plasmodium falciparum, we show that guilds of ApiAP2 genes are expressed in different stages of intraerythrocytic development. By analogy to the plant AP2 proteins and based on the expression patterns, we predict that the ApiAP2 proteins are likely to function as previously unknown specific TFs in the apicomplexans and regulate the progression of their developmental cycle. In addition to the ApiAP2 family, we also identified two other novel families of AP2 DNA binding domains in bacteria and transposons. Using structure similarity searches, we also identified divergent versions of the AP2-integrase DNA binding domain fold in the DNA binding region of the PI-SceI homing endonuclease and the C-terminal domain of the pleckstrin homology (PH) domain-like modules of eukaryotes. Integrating these findings, we present a reconstruction of the evolutionary scenario of the AP2-integrase DNA binding domain fold, which suggests that it underwent multiple independent combinations with different types of mobile endonucleases or recombinases. It appears that the eukaryotic versions have emerged from versions of the domain associated with mobile elements, followed by independent lineage-specific expansions, which accompanied their recruitment to transcription regulation functions.


  • [Articles] Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes -

    Exonic splicing enhancers (ESEs) are pre-mRNA cis-acting elements required for splice-site recognition. We previously developed a web-based program called ESEfinder that scores any sequence for the presence of ESE motifs recognized by the human SR proteins SF2/ASF, SRp40, SRp55 and SC35 (http://rulai.cshl.edu/tools/ESE/). Using ESEfinder, we have undertaken a large-scale analysis of ESE motif distribution in human protein-coding genes. Significantly higher frequencies of ESE motifs were observed in constitutive internal protein-coding exons, compared with both their flanking intronic regions and with pseudo exons. Statistical analysis of ESE motif frequency distributions revealed a complex relationship between splice-site strength and increased or decreased frequencies of particular SR protein motifs. Comparison of constitutively and alternatively spliced exons demonstrated slightly weaker splice-site scores, as well as significantly fewer ESE motifs, in the alternatively spliced group. Our results underline the importance of ESE-mediated SR protein function in the process of exon definition, in the context of both constitutive splicing and regulated alternative splicing.


  • [Articles] DNA bending by M.EcoKI methyltransferase is coupled to nucleotide flipping -

    The maintenance methyltransferase M.EcoKI recognizes the bipartite DNA sequence 5'-AACNNNNNNGTGC-3', where N is any nucleotide. M.EcoKI preferentially methylates a sequence already containing a methylated adenine at or complementary to the underlined bases in the sequence. We find that the introduction of a single-stranded gap in the middle of the non-specific spacer, of up to 4 nt in length, does not reduce the binding affinity of M.EcoKI despite the removal of non-sequence-specific contacts between the protein and the DNA phosphate backbone. Surprisingly, binding affinity is enhanced in a manner predicted by simple polymer models of DNA flexibility. However, the activity of the enzyme declines to zero once the single-stranded region reaches 4 nt in length. This indicates that the recognition of methylation of the DNA is communicated between the two methylation targets not only through the protein structure but also through the DNA structure. Furthermore, methylation recognition requires base flipping in which the bases targeted for methylation are swung out of the DNA helix into the enzyme. By using 2-aminopurine fluorescence as the base flipping probe we find that, although flipping occurs for the intact duplex, no flipping is observed upon introduction of a gap. Our data and polymer model indicate that M.EcoKI bends the non-specific spacer and that the energy stored in a double-stranded bend is utilized to force or flip out the bases. This energy is not stored in gapped duplexes. In this way, M.EcoKI can determine the methylation status of two adenine bases separated by a considerable distance in double-stranded DNA and select the required enzymatic response.


  • [Articles] DNA binding and helicase actions of mouse MCM4/6/7 helicase -

    Helicases play central roles in initiation and elongation of DNA replication. We previously reported that helicase and ATPase activities of the mammalian Mcm4/6/7 complex are activated specifically by thymine-rich single-stranded DNA. Here, we examined its substrate preference and helicase actions using various synthetic DNAs. On a bubble substrate, Mcm4/6/7 makes symmetric dual contacts with the 5'-proximal 25 nt single-stranded segments adjacent to the branch points, presumably generating double hexamers. Loss of thymine residues from one single-strand results in significant decrease of unwinding efficacy, suggesting that concurrent bidirectional unwinding by a single double hexameric Mcm4/6/7 may play a role in efficient unwinding of the bubble. Mcm4/6/7 binds and unwinds various fork and extension structures carrying a single-stranded 3'-tail DNA. The extent of helicase activation depends on the sequence context of the 3'-tail, and the maximum level is achieved by DNA with 50% or more thymine content. Strand displacement by Mcm4/6/7 is inhibited, as the GC content of the duplex region increases. Replacement of cytosine–guanine pairs with cytosine–inosine pairs in the duplex restored unwinding, suggesting that mammalian Mcm4/6/7 helicase has difficulties in unwinding stably base-paired duplex. Taken together, these findings reveal important features on activation and substrate preference of the eukaryotic replicative helicase.


  • [Articles] DNA condensation and self-aggregation of Escherichia coli Dps are coupled phenomena related to the properties of the N-terminus -

    Escherichia coli Dps (DNA-binding proteins from starved cells) is the prototype of a DNA-protecting protein family expressed by bacteria under nutritional and oxidative stress. The role of the lysine-rich and highly mobile Dps N-terminus in DNA protection has been investigated by comparing the self-aggregation and DNA-condensation capacity of wild-type Dps and two N-terminal deletion mutants, Dps8 and Dps18, lacking two or all three lysine residues, respectively. Gel mobility and atomic force microscopy imaging showed that at pH 6.3, both wild type and Dps8 self-aggregate, leading to formation of oligomers of variable size, and condense DNA with formation of large Dps–DNA complexes. Conversely, Dps18 does not self-aggregate and binds DNA without causing condensation. At pH 8.2, Dps8 and Dps18 neither self-aggregate nor cause DNA condensation, a behavior also displayed by wild-type Dps at pH 8.7. Thus, Dps self-aggregation and Dps-driven DNA condensation are parallel phenomena that reflect the properties of the N-terminus. DNA protection against the toxic action of Fe(II) and H2O2 is not affected by the N-terminal deletions either in vitro or in vivo, in accordance with the different structural basis of this property.


  • [Articles] DNA damage response and Ku80 function in the vertebrate embryo -

    Cellular responses to DNA damage reflect the dynamic integration of cell cycle control, cell–cell interactions and tissue-specific patterns of gene regulation that occurs in vivo but is not recapitulated in cell culture models. Here we describe use of the zebrafish embryo as a model system to identify determinants of the in vivo response to ionizing radiation-induced DNA damage. To demonstrate the utility of the model we cloned and characterized the embryonic function of the XRCC5 gene, which encodes Ku80, an essential component of the nonhomologous end joining pathway of DNA repair. After the onset of zygotic transcription, Ku80 mRNA accumulates in a tissue-specific pattern, which includes proliferative zones of the retina and central nervous system. In the absence of genotoxic stress, zebrafish embryos with reduced Ku80 function develop normally. However, low dose irradiation of these embryos during gastrulation leads to marked apoptosis throughout the developing central nervous system. Apoptosis is p53 dependent, indicating that it is a downstream consequence of unrepaired DNA damage. Results suggest that nonhomologous end joining components mediate DNA repair to promote survival of irradiated cells during embryogenesis.


  • [Articles] DNA looping induced by a transcriptional enhancer in vivo -

    Enhancers are DNA sequences that can activate gene transcription from remote positions. In yeast, regulatory sequences that are functionally equivalent to the metazoan enhancers are called upstream activating sequences (UASs). UASs show a lower degree of flexibility than their metazoan counterparts, but can nevertheless activate transcription from a distance of >1000 bp from the promoter. One of several models for the mechanism of action of transcriptional enhancers proposes that enhancer-bound activating proteins contact promoter-bound transcription factors and thereby get in close proximity to the promoter region with concomitant looping of the intervening DNA. We tested the mode of enhancer activity in yeast. A polymerase II-transcribed gene was paired with a remote, inducible enhancer. An independent reporter system was inserted next to the promoter to monitor the potential modes of enhancer activity. Our results show that the enhancer activated the reporter system only in the presence of a functional promoter. We also demonstrate that the heterologous expression of GAGA, a factor known to facilitate DNA loop formation, allows enhancer action in yeast over a distance of 3000 bp.


  • [Articles] DNA repair factor XPC is modified by SUMO-1 and ubiquitin following UV irradiation -

    Nucleotide excision repair (NER) is the major DNA repair process that removes diverse DNA lesions including UV-induced photoproducts. There are more than 20 proteins involved in NER. Among them, XPC is thought to be one of the first proteins to recognize DNA damage during global genomic repair (GGR), a sub-pathway of NER. In order to study the mechanism through which XPC participates in GGR, we investigated the possible modifications of XPC protein upon UV irradiation in mammalian cells. Western blot analysis of cell lysates from UV-irradiated normal human fibroblast, prepared by direct boiling in an SDS lysis buffer, showed several anti-XPC antibody-reactive bands with molecular weight higher than the original XPC protein. The reciprocal immunoprecipitation and siRNA transfection analysis demonstrated that XPC protein is modified by SUMO-1 and ubiquitin. By using several NER-deficient cell lines, we found that DDB2 and XPA are required for UV-induced XPC modifications. Interestingly, both the inactivation of ubiquitylation and the treatment of proteasome inhibitors quantitatively inhibited the UV-induced XPC modifications. Furthermore, XPC protein is degraded significantly following UV irradiation in XP-A cells in which sumoylation of XPC does not occur. Taken together, we conclude that XPC protein is modified by SUMO-1 and ubiquitin following UV irradiation and these modifications require the functions of DDB2 and XPA, as well as the ubiquitin–proteasome system. Our results also suggest that at least one function of UV-induced XPC sumoylation is related to the stabilization of XPC protein.


  • [Articles] DNA-dependent conversion of Oct-1 and Oct-2 into transcriptional repressors by Groucho/TLE -

    POU domain proteins contain a bipartite DNA-binding element that can confer allosteric control of coactivator recruitment. Dimerization of Oct-1 and Oct-2 on palindromic response elements results in the conformational dependent inclusion or exclusion of the transcriptional coactivator OBF-1. In this paper, we demonstrate that Oct-1 and Oct-2 can function as transcriptional repressors by recruiting and physically interacting with members of the Grg/TLE family of corepressors. In accordance with a model of DNA induced cofactor assembly, and analogous to the recruitment of the OBF-1 coactivator, the different Grg/TLE members can discriminate between both Oct-1 and Oct-2, and the monomeric or dimeric nature of the POU/DNA complex.


  • [Articles] Dnmt1 deficiency leads to enhanced microsatellite instability in mouse embryonic stem cells -

    DNA hypomethylation is frequently seen in cancer and imparts genomic instability in mouse models and some tissue culture systems. However, the effects of genomic DNA hypomethylation on mutation rates are still elusive. We have developed a model system to analyze the effects of DNA methyltransferase 1 (Dnmt1) deficiency on DNA mismatch repair (MMR) in mouse embryonic stem (ES) cells. We generated sibling ES cell clones with and without functional Dnmt1 expression, containing a stable reporter gene that allowed us to measure the slippage rate at a mononucleotide repeat. We found that Dnmt1 deficiency led to a 7-fold increase in the microsatellite slippage rate. Interestingly, the region flanking the mononucleotide repeat was unmethylated regardless of Dnmt1 status, suggesting that it is not the local levels of DNA methylation that direct the increase in microsatellite instability (MSI). The enhanced MSI was associated with higher levels of histone H3 acetylation and lower MeCP2 binding at regions near the assayed microsatellite, suggesting that Dnmt1 loss may decrease MMR efficiency by modifying chromatin structure.


  • [Articles] Domain organization of the yeast histone chaperone FACT: the conserved N-terminal domain of FACT subunit Spt16 mediates recovery from replication stress -

    The abundant nuclear complex termed FACT affects several DNA transactions in a chromatin context, including transcription, replication, and repair. Earlier studies of yeast FACT, which indicated the apparent dispensability of conserved sequences at the N terminus of the FACT subunit Cdc68/Spt16, prompted genetic and biochemical studies reported here that suggest the domain organization for Spt16 and the other FACT subunit Pob3, the yeast homolog of the metazoan SSRP1 protein. Our findings suggest that each FACT subunit is a multidomain protein, and that FACT integrity depends on Pob3 interactions with the Spt16 Mid domain. The conserved Spt16 N-terminal domain (NTD) is shown to be without essential function during normal growth, but becomes important under conditions of replication stress. Genetic interactions suggest that some functions carried out by the Spt16 NTD may be partially redundant within FACT.


  • [Articles] Effect of 6-thioguanine on the stability of duplex DNA -

    The incorporation of 6-thioguanine (S6G) into DNA is a prerequisite for its cytotoxic action, but duplex structure is not significantly perturbed by the presence of the lesion [J. Bohon and C. R. de los Santos (2003) Nucleic Acids Res., 31, 1331–1338]. It is therefore possible that the mechanism of cytotoxicity relies on a loss of stability rather than a pathway involving direct structural recognition. The research described here focuses on the changes in thermodynamic properties of duplex DNA owing to the introduction of S6G as well as the kinetic properties of base pairs involving S6G. Replacement of a guanine in a G•C pair by S6G results in ~1 kcal/mol less favorable Gibbs free energy of duplex formation at 37°C. S6G•T and G•T mismatch-containing duplexes have almost identical Gibbs free energy at 37°C, with values ~3 kcal/mol less favorable than that of the control. Base pair stability is affected by S6G. The lifetime of the normal G•C base pair is ~125 ms, whereas that of the G•T mismatch is below the detection limit. The lifetimes of S6G•C and S6G•T pairs are ~7 and 2 ms, respectively, demonstrating that, although S6G significantly decreases the stability of the pairing with cytosine, it slightly increases that of a mismatch.


  • [Articles] Effect on DNA relaxation of the single Thr718Ala mutation in human topoisomerase I: a functional and molecular dynamics study -

    The functional and dynamical properties of the human topoisomerase I Thr718Ala mutant have been compared to that of the wild-type enzyme using functional assays and molecular dynamics (MD) simulations. At physiological ionic strength, the cleavage and religation rates, evaluated on oligonucleotides containing the preferred topoisomerase I DNA sequence, are almost identical for the wild-type and the mutated enzymes, as is the cleavage/religation equilibrium. On the other hand, the Thr718Ala mutant shows a decreased efficiency in a DNA plasmid relaxation assay. The MD simulation, carried out on the enzyme complexed with its preferred DNA substrate, indicates that the mutant has a different dynamic behavior compared to the wild-type enzyme. Interestingly, no changes are observed in the proximity of the mutation site, whilst a different flexibility is detected in regions contacting the DNA scissile strand, such as the linker and the V-shaped helices. Taken together, the functional and simulation results indicate a direct communication between the mutation site and regions located relatively far away, such as the linker domain, that with their altered flexibility confer a reduced DNA relaxation efficiency. These results provide evidence that the comprehension of the topoisomerase I dynamical properties are an important element in the understanding of its complex catalytic cycle.


  • [Articles] Evidence for a preferential targeting of 3'-UTRs by cis-encoded natural antisense transcripts -

    Although both the 5'- and 3'-untranslated regions (5'- and 3'-UTRs) of eukaryotic mRNAs may play a crucial role in posttranscriptional gene regulation, we observe that cis-encoded natural antisense RNAs have a striking preferential complementarity to the 3'-UTRs of their target genes in mammalian (human and mouse) genomes. A null neutral model, evoking differences in the rate of 3'-UTR and 5'-UTR extension, could potentially explain high rates of 3'-to-3' overlap compared with 5'-to-5' overlap. However, employing a simulation model we show that this null model probably cannot explain the finding that 3'-to-3' overlapping pairs have a much higher probability (>5 times) of conservation in both mouse and human genomes with the same overlapping pattern than do 5'-to-5' overlaps. Furthermore, it certainly cannot explain the finding that overlapping pairs seen in both genomes have a significantly higher probability of having co-expression and inverse expression (i.e. characteristic of sense–antisense regulation) than do overlapping pairs seen in only one of the two species. We infer that the function of many 3'-to-3' overlaps is indeed antisense regulation. These findings underscore the preference for, and conservation of, 3'-UTR-targeted antisense regulation, and the importance of 3'-UTRs in gene regulation.


  • [Articles] Evidence for a role of initiation factor 3 in recycling of ribosomal complexes stalled on mRNAs in Escherichia coli -

    Specific interactions between ribosome recycling factor (RRF) and elongation factor-G (EFG) mediate disassembly of post-termination ribosomal complexes for new rounds of initiation. The interactions between RRF and EFG are also important in peptidyl-tRNA release from stalled pre-termination complexes. Unlike the post-termination complexes (harboring deacylated tRNA), the pre-termination complexes (harboring peptidyl-tRNA) are not recycled by RRF and EFG in vitro, suggesting participation of additional factor(s) in the process. Using a combination of biochemical and genetic approaches, we show that, (i) Inclusion of IF3 with RRF and EFG results in recycling of the pre-termination complexes; (ii) IF3 overexpression in Escherichia coli LJ14 rescues its temperature sensitive phenotype for RRF; (iii) Transduction of infC135 (which encodes a functionally compromised IF3) in E.coli LJ14 generates a ‘synthetic severe’ phenotype; (iv) The infC135 and frr1 (containing an insertion in the RRF gene promoter) alleles synergistically rescue a temperature sensitive mutation in peptidyl-tRNA hydrolase in E.coli; and (v) IF3 facilitates ribosome recycling by Thermus thermophilus RRF and E.coli EFG in vivo and in vitro. These lines of evidence clearly demonstrate the physiological importance of IF3 in the overall mechanism of ribosome recycling in E.coli.


  • [Articles] Evidence for rolling circle replication of tandem genes in Drosophila -

    Extrachromosomal circular DNA (eccDNA) is one characteristic of the plasticity of the eukaryotic genome. It is found in various organisms and contains sequences derived primarily from repetitive chromosomal DNA. Using 2D gel electrophoresis, we have previously detected eccDNA composed of chromosomal tandem repeats throughout the life cycle of Drosophila. Here, we report for the first time evidence suggesting the occurrence of rolling circle replication of eccDNA in Drosophila. We show, on 2D gels, specific structures that can be enriched by benzoylated naphthoylated DEAE-cellulose chromatography and were identified in other systems as rolling circle intermediates (RCIs). These RCIs are homologous to histone genes, Stellate and Suppressor of Stellate, which are all organized in the chromosomes as tandem repeats. RCIs are detected throughout the life cycle of Drosophila and in cultured fly cells. These structures are found regardless of the expression of the replicated gene or of its chromosomal copy number.


  • [Articles] Evidence that public database records for many cancer-associated genes reflect a splice form found in tumors and lack normal splice forms -

    Alternative splicing is widespread in the human genome, and it appears that many genes display different splice forms in cancerous tissue than in normal human tissues. However, since cDNAs for many cancer-associated genes were originally cloned from tumor samples, it is important to ask whether this repertoire of cDNAs provides a complete or representative picture of the transcript isoforms found in normal tissues. To answer this, we used bioinformatics and RT–PCR to identify novel splice forms, focusing on in-frame exonskips, for a panel of 50 cancer-associated genes in normal tissue samples. These data show that in nearly two-thirds of the genes, normal tissues expressed previously unknown splice forms, of which 40% were normally a dominant splice form. Surprisingly, the tumor-associated splice forms were twice as likely to be represented in GenBank than their normal tissue-associated splice forms, most likely because 70% of the mRNAs in GenBank for these genes were cloned from tumor samples. As an example, we describe a novel normal splice form of IKBßbeta;, an important regulator of the NFB pathway. Our data suggest that systematic re-evaluation of cancer genes' splice forms in normal tissue will yield insights into their distinct functions in normal tissues and in cancer. Our database contains 1308 novel normal splice forms, including many known cancer genes.


  • [Articles] Evidence that the Tfg1/Tfg2 dimer interface of TFIIF lies near the active center of the RNA polymerase II initiation complex -

    The ssu71 alleles of the TFG1 gene, which encodes the largest subunit of TFIIF, were isolated as suppressors of a TFIIB defect that affects the accuracy of transcription start site selection in the yeast Saccharomyces cerevisiae. Here we report that ssu71-1 also suppresses the cell growth and start site defects associated with an altered form of the Rpb1 subunit of RNA polymerase II (RNAP II). The ssu71-1 and ssu71-2 alleles were cloned and found to encode single amino acid replacements of glycine-363, either glycine to aspartic acid (G363D) or glycine to arginine (G363R). Two other charged replacements, G363E and G363K, were constructed by site-directed mutagenesis and suppress both TFIIB E62K and Rpb1 N445S, whereas neither G363A nor G363P exhibited any effect. G363 is phylogenetically conserved and its counterpart in human TFIIF (RAP74 G112) is located within the RAP74/RAP30 dimerization domain. We propose that the TFIIF dimerization domain is located in proximity to the B-finger of TFIIB near the active center of RNAP II where the TFIIB–TFIIF–RNAP II interface plays a key role in start site selection.


  • [Articles] Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles -

    To better decipher the functional impact of alternative splicing, we classified alternative splicing events in 10 818 pairs of human and mouse genes based on conservation at genome and transcript levels. Expression levels of conserved alternative splices in human and mouse expressed sequence tag databases show strong correlation, indicating that alternative splicing is similarly regulated in both species. A total of 43% (8921) of mouse alternative splices could be found in the human genome but not in human transcripts. Five of eleven tested mouse predictions were observed in human tissues, demonstrating that mouse transcripts provide a valuable resource for identifying alternative splicing events in human genes. Combining gene-specific measures of conserved and diverged alternative splicing with both gene classification based on Gene Ontology (GO) and microarray-determined gene expression in 52 diverse human tissues and cell lines, we found conserved alternative splicing most enriched in brain-expressed signaling pathways. Diverged alternative splicing is more prevalent in testis and cancerous cell line up-regulated processes, including protein biosynthesis, responses to stress and responses to endogenous stimuli. Using conservation as a surrogate for functional significance, these results suggest that alternative splicing plays an important role in enhancing the functional capacity of central nervous systems, while non-functional splicing more frequently occurs in testis and cell lines, possibly as a result of cellular stress and rapid proliferation.


  • [Articles] Evolutionary conservation suggests a regulatory function of AUG triplets in 5'-UTRs of eukaryotic genes -

    By comparing sequences of human, mouse and rat orthologous genes, we show that in 5'-untranslated regions (5'-UTRs) of mammalian cDNAs but not in 3'-UTRs or coding sequences, AUG is conserved to a significantly greater extent than any of the other 63 nt triplets. This effect is likely to reflect, primarily, bona fide evolutionary conservation, rather than cDNA annotation artifacts, because the excess of conserved upstream AUGs (uAUGs) is seen in 5'-UTRs containing stop codons in-frame with the start AUG and many of the conserved AUGs are found in different frames, consistent with the location in authentic non-coding sequences. Altogether, conserved uAUGs are present in at least 20–30% of mammalian genes. Qualitatively similar results were obtained by comparison of orthologous genes from different species of the yeast genus Saccharomyces. Together with the observation that mammalian and yeast 5'-UTRs are significantly depleted in overall AUG content, these findings suggest that AUG triplets in 5'-UTRs are subject to the pressure of purifying selection in two opposite directions: the uAUGs that have no specific function tend to be deleterious and get eliminated during evolution, whereas those uAUGs that do serve a function are conserved. Most probably, the principal role of the conserved uAUGs is attenuation of translation at the initiation stage, which is often additionally regulated by alternative splicing in the mammalian 5'-UTRs. Consistent with this hypothesis, we found that open reading frames starting from conserved uAUGs are significantly shorter than those starting from non-conserved uAUGs, possibly, owing to selection for optimization of the level of attenuation.


  • [Articles] Excision of formamidopyrimidine lesions by endonucleases III and VIII is not a major DNA repair pathway in Escherichia coli -

    Proper maintenance of the genome is of great importance. Consequently, damaged nucleotides are repaired through redundant pathways. We considered whether the genome is protected from formamidopyrimidine nucleosides (Fapy•dA, Fapy•dG) via a pathway distinct from the Escherichia coli guanine oxidation system. The formamidopyrimidines are produced in significant quantities in DNA as a result of oxidative stress and are efficiently excised by formamidopyrimidine DNA glycosylase. Previous reports suggest that the formamidopyrimidine nucleosides are substrates for endonucleases III and VIII, enzymes that are typically associated with pyrimidine lesion repair in E.coli. We investigated the possibility that Endo III and/or Endo VIII play a role in formamidopyrimidine nucleoside repair by examining Fapy•dA and Fapy•dG excision opposite all four native 2'-deoxyribonucleotides. Endo VIII excises both lesions more efficiently than does Endo III, but the enzymes exhibit similar selectivity with respect to their action on duplexes containing the formamidopyrimidines opposite native deoxyribonucleotides. Fapy•dA is removed more rapidly than Fapy•dG, and duplexes containing purine nucleotides opposite the lesions are superior substrates compared with those containing formamidopyrimidine–pyrimidine base pairs. This dependence upon opposing nucleotide indicates that Endo III and Endo VIII do not serve as back up enzymes to formamidopyrimidine DNA glycosylase in the repair of formamidopyrimidines. When considered in conjunction with cellular studies [J. O. Blaisdell, Z. Hatahet and S. S. Wallace (1999) J. Bacteriol., 181, 6396–6402], these results also suggest that Endo III and Endo VIII do not protect E.coli against possible mutations attributable to formamidopyrimidine lesions.


  • [Articles] Exonization of AluYa5 in the human ACE gene requires mutations in both 3' and 5' splice sites and is facilitated by a conserved splicing enhancer -

    Ancient Alu elements have been shown to be included in mature transcripts by point mutations that improve their 5' or 3' splice sites. We have examined requirements for exonization of a younger, disease-associated AluYa5 in intron 16 of the human ACE gene. A single G>C transversion in position –3 of the new Alu exon was insufficient for Alu exonization and a significant inclusion in mRNA was only observed when improving several potential splice donor sites in the presence of 3' CAG. Since complete Alu exonization was not achieved by optimizing traditional splicing signals, including the branch site, we tested whether auxiliary elements in AluYa5 were required for constitutive inclusion. Exonization was promoted by a SELEX-predicted heptamer in Alu consensus sequence 222–228 and point mutations in highly conserved nucleotides of this heptamer decreased Alu inclusion. In addition, we show that Alu exonization was facilitated by a subset of serine/arginine-rich (SR) proteins through activation of the optimized 3' splice site. Finally, the haplotype- and allele-specific ACE minigenes generated similar splicing patterns in both ACE-expressing and non-expressing cells, suggesting that previously reported allelic association with plasma ACE activity and cardiovascular disease is not attributable to differential splicing of introns 16 and 17.


  • [Articles] Extended base pair complementarity between U1 snRNA and the 5' splice site does not inhibit splicing in higher eukaryotes, but rather increases 5' splice site recognition -

    Spliceosome formation is initiated by the recognition of the 5' splice site through formation of an RNA duplex between the 5' splice site and U1 snRNA. We have previously shown that RNA duplex formation between U1 snRNA and the 5' splice site can protect pre-mRNAs from degradation prior to splicing. This initial RNA duplex must be disrupted to expose the 5' splice site sequence for base pairing with U6 snRNA and to form the active spliceosome. Here, we investigated whether hyperstabilization of the U1 snRNA/5' splice site duplex interferes with splicing efficiency in human cell lines or nuclear extracts. Unlike observations in Saccharomyces cerevisiae, we demonstrate that an extended U1 snRNA/5' splice site interaction does not decrease splicing efficiency, but rather increases 5' splice site recognition and exon inclusion. However, low complementarity of the 5' splice site to U1 snRNA significantly increases exon skipping and RNA degradation. Although the splicing mechanisms are conserved between human and S.cerevisiae, these results demonstrate that distinct differences exist in the activation of the spliceosome.


  • [Articles] FAST DB: a website resource for the study of the expression regulation of human gene products -

    Human genes use various mechanisms to generate different transcripts having different exon content, which in turn generate multiple protein isoforms having differential and even opposite biological activities. To understand the biological consequences of gene transcriptional activity modulation, it is necessary to integrate the capability of genes to generate distinct functional products, particularly because transcriptional stimuli also affect the exon content of their target gene products. For this purpose, we have developed a bioinformatics suite, FAST DB, which defines easily and accurately the exon content of all known transcripts produced by human genes. In addition, several tools have been developed, including a graphical presentation of all gene products, a sequence multi-alignment of all gene transcripts and an in silico PCR computer program. The FAST DB interface also offers extensive links to website resources for promoter analysis and transcription factor binding site prediction, splicing regulatory sequence prediction, as well as 5'- and 3'-untranslated region analysis. FAST DB has been designed to facilitate studies that integrate transcriptional and post-transcriptional events to investigate the expression regulation of human gene products.


  • [Articles] Fluorescent properties of DNA base analogue tC upon incorporation into DNA -- negligible influence of neighbouring bases on fluorescence quantum yield -

    The quantum yield of the fluorescent tricyclic cytosine analogue, 1,3-diaza-2-oxophenothiazine, tC, is high and virtually unaffected by incorporation into both single- and double-stranded DNA irrespective of neighbouring bases (0.17–0.24 and 0.16–0.21, respectively) and the corresponding fluorescence decay curves are all mono-exponential, properties that are unmatched by any base analogue so far. The fluorescence lifetimes increase when going from tC free in solution (3.2 ns) to single- and double-stranded DNA (on average 5.7 and 6.3 ns, respectively). The mono-exponential decays further support previous NMR results where it was found that tC has a well-defined position and geometry within the DNA helix. Furthermore, we find that the oxidation potential of tC is 0.4 V lower than for deoxyguanosine, the natural base with the lowest oxidation potential. This suggests that tC may be of interest in charge transfer studies in DNA as an electron hole acceptor. We also present a novel synthetic route to the phosphoramidite form of tC. The results presented here together with previous work show that tC is a very good C-analogue that induces minimal perturbation to the native structure of DNA. This makes tC unique as a fluorescent base analogue and is thus highly interesting in a range of applications for studying e.g. structure, dynamics and kinetics in nucleic acid systems.


  • [Articles] Formation and properties of hairpin and tetraplex structures of guanine-rich regulatory sequences of muscle-specific genes -

    Clustered guanine residues in DNA readily generate hairpin or a variety of tetrahelical structures. The myogenic determination protein MyoD was reported to bind to a tetrahelical structure of guanine-rich enhancer sequence of muscle creatine kinase (MCK) more tightly than to its target E-box motif [K. Walsh and A. Gualberto (1992) J. Biol. Chem., 267, 13714–13718], suggesting that tetraplex structures of regulatory sequences of muscle-specific genes could contribute to transcriptional regulation. In the current study we show that promoter or enhancer sequences of various muscle-specific genes display a disproportionately high incidence of guanine clusters. The sequences derived from the guanine-rich promoter or enhancer regions of three muscle-specific genes, human sarcomeric mitochondrial creatine kinase (sMtCK), mouse MCK and 7 integrin formed diverse secondary structures. The sMtCK sequence folded into a hairpin structure; the 7 integrin oligonucleotide generated a unimolecular tetraplex; and sequences from all three genes associated to generate bimolecular tetraplexes. Furthermore, two neighboring non-contiguous guanine-rich tracts in the 7 integrin promoter region also paired to form a tetraplex structure. We also show that homodimeric MyoD bound bimolecular tetraplex structures of muscle-specific regulatory sequences more efficiently than its target E-box motif. These results are consistent with a role of tetrahelical structures of DNA in the regulation of muscle-specific gene expression.


  • [Articles] Formation of a large, complex domain of histone hyperacetylation at human 14q32.1 requires the serpin locus control region -

    The human serine protease inhibitor (serpin) gene cluster at 14q32.1 is a useful model system to study cell-type-specific gene expression and chromatin structure. Activation of the serpin locus can be induced in vitro by transferring human chromosome 14 from non-expressing to expressing cells. Serpin gene activation in expressing cells is correlated with locus-wide alterations in chromatin structure, including the de novo formation of 17 expression-associated DNase I-hypersensitive sites (DHSs). In this study, we investigated histone acetylation throughout the proximal serpin subcluster. We report that gene activation is correlated with high levels of histone H3 and H4 acetylation at serpin gene promoters and other regulatory regions. However, the locus is not uniformly hyperacetylated, as there are regions of hypoacetylation between genes. Furthermore, genetic tests indicate that locus-wide controls regulate both gene expression and chromatin structure. For example, deletion of a previously identified serpin locus control region (LCR) upstream of the proximal subcluster reduces both gene expression and histone acetylation throughout the ~130 kb region. A similar down regulation phenotype is displayed by transactivator-deficient cell variants, but this phenotype can be rescued by transfecting the cells with expression cassettes encoding hepatocyte nuclear factor-1 (HNF-1) or HNF-4. Taken together, these results suggest that histone acetylation depends on interactions between the HNF-1/HNF-4 signaling cascade and the serpin LCR.


  • [Articles] Four base recognition by triplex-forming oligonucleotides at physiological pH -

    We have achieved recognition of all 4 bp by triple helix formation at physiological pH, using triplex-forming oligonucleotides that contain four different synthetic nucleotides. BAU [2'-aminoethoxy-5-(3-aminoprop-1-ynyl)uridine] recognizes AT base pairs with high affinity, MeP (3-methyl-2 aminopyridine) binds to GC at higher pHs than cytosine, while APP (6-(3-aminopropyl)-7-methyl-3H-pyrrolo[2,3-d]pyrimidin-2(7H)-one) and S [N-(4-(3-acetamidophenyl)thiazol-2-yl-acetamide)] bind to CG and TA base pairs, respectively. Fluorescence melting and DNase I footprinting demonstrate successful triplex formation at a 19mer oligopurine sequence that contains two CG and two TA interruptions. The complexes are pH dependent, but are still stable at pH 7.0. BAU, MeP and APP retain considerable selectivity, and single base pair changes opposite these residues cause a large reduction in affinity. In contrast, S is less selective and tolerates CG pairs as well as TA.


  • [Articles] Functional analysis of the N- and C-terminus of mammalian G9a histone H3 methyltransferase -

    Methylation of lysine 9 (K9) in the N-terminus tail of histone H3 (H3) in chromatin is associated with transcriptionally silenced genes and is mediated by histone methyltransferases. Murine G9a is a 1263 amino acid H3-K9 methyltransferase that possesses characteristic SET domain and ANK repeats. In this paper, we have used a series of green fluorescent protein-tagged deletion constructs to identify two nuclear localization signals (NLS), the first NLS embedded between amino acids 24 and 109 and the second between amino acids 394 and 401 of murine G9a. Our data show that both long and short G9a isoforms were capable of entering the nucleus to methylate chromatin. Full-length or N-terminus-deleted G9a isoforms were also catalytically active enzymes that methylated recombinant H3 or synthetic peptides representing the N-terminus tail of H3. In vitro methylation reactions using N-terminus tail peptides resulted in tri-methylation of K9 that remained processive, even in G9a enzymes that lacked an N-terminus region by deletion. Co-expression of G9a and H3 resulted in di- and tri-methylation of H3-K9, while siRNA-mediated knockdown of G9a in HeLa cells resulted in reduction of global H3-K9 di- and tri-methylation. A recombinant deletion mutant enzyme fused with maltose-binding protein (MBP-G9a634) was used for steady-state kinetic analysis with various substrates and was compared with full-length G9a (G9aFL). Turnover numbers of MBP-G9a634 for various substrates was ~3-fold less compared with G9aFL, while their Michaelis constants (Km) for recombinant H3 were similar. The $${K}_{\hbox{ m }}^{\hbox{ AdoMet }}$$ for MBP-G9a634 was ~2.3–2.65 µM with various substrates. Catalytic efficiencies (kcat/Km) for both MBP-G9a634 and G9aFL were similar, suggesting that the N-terminus is not essential for catalysis. Furthermore, mutation of conserved amino acids R1097A, W1103A, Y1120A, Y1138A and R1162A, or the metal binding C1168A in the catalytic region, resulted in catalytically impaired enzymes, thereby confirming the involvement of the C-terminus of G9a in catalysis. Thus, distinct domains modulate nuclear targeting and catalytic functions of G9a.


  • [Articles] Functional polarity is introduced by Dicer processing of short substrate RNAs -

    Synthetic RNA duplexes that are substrates for Dicer are potent triggers of RNA interference (RNAi). Blunt 27mer duplexes can be up to 100-fold more potent than traditional 21mer duplexes (1). Not all 27mer duplexes show increased potency. Evaluation of the products of in vitro dicing reactions using electrospray ionization mass spectrometry reveals that a variety of products can be produced by Dicer cleavage. Use of asymmetric duplexes having a single 2-base 3'-overhang restricts the heterogeneity that results from dicing. Inclusion of DNA residues at the ends of blunt duplexes also limits heterogeneity. Combination of asymmetric 2-base 3'-overhang with 3'-DNA residues on the blunt end result in a duplex form which directs dicing to predictably yield a single primary cleavage product. It is therefore possible to design a 27mer duplex which is processed by Dicer to yield a specific, desired 21mer species. Using this strategy, two different 27mers can be designed that result in the same 21mer after dicing, one where the 3'-overhang resides on the antisense (AS) strand and dicing proceeds to the ‘right’ (‘R’) and one where the 3'-overhang resides on the sense (S) strand and dicing proceeds to the ‘left’ (‘L’). Interestingly, the ‘R’ version of the asymmetric 27mer is generally more potent in reducing target gene levels than the ‘L’ version 27mer. Strand targeting experiments show asymmetric strand utilization between the two different 27mer forms, with the ‘R’ form favoring S strand and the ‘L’ form favoring AS strand silencing. Thus, Dicer processing confers functional polarity within the RNAi pathway.


  • [Articles] Functional studies on the ATM intronic splicing processing element -

    In disease-associated genes, the understanding of the functional significance of deep intronic nucleotide variants may represent a difficult challenge. We have previously reported a new disease-causing mechanism that involves an intronic splicing processing element (ISPE) in ATM, composed of adjacent consensus 5' and 3' splice sites. A GTAA deletion within ISPE maintains potential adjacent splice sites, disrupts a non-canonical U1 snRNP interaction and activates an aberrant exon. In this paper, we demonstrate that binding of U1 snRNA through complementarity within a ~40 nt window downstream of the ISPE prevents aberrant splicing. By selective mutagenesis at the adjacent consensus ISPE splice sites, we show that this effect is not due to a resplicing process occurring at the ISPE. Functional comparison of the ATM mouse counterpart and evaluation of the pre-mRNA splicing intermediates derived from affected cell lines and hybrid minigene assays indicate that U1 snRNP binding at the ISPE interferes with the cryptic acceptor site. Activation of this site results in a stringent 5'–3' order of intron sequence removal around the cryptic exon. Artificial U1 snRNA loading by complementarity to heterologous exonic sequences represents a potential therapeutic method to prevent the usage of an aberrant CFTR cryptic exon. Our results suggest that ISPE-like intronic elements binding U1 snRNPs may regulate correct intron processing.


  • [Articles] Futile short-patch DNA base excision repair of adenine:8-oxoguanine mispair -

    8-Oxo-7, 8-dihydrodeoxyguanosine (8-oxo-dG), one of the representative oxidative DNA lesions, frequently mispairs with the incoming dAMP during mammalian DNA replication. Mispaired dA is removed by post-replicative base excision repair (BER) initiated by adenine DNA glycosylase, MYH, creating an apurinic (AP) site. The subsequent mechanism ensuring a dC:8-oxo-dG pair, a substrate for 8-oxoguanine DNA glycosylase (OGG1), remains to be elucidated. At the nucleotide insertion step, none of the mammalian DNA polymerases examined exclusively inserted dC opposite 8-oxo-dG that was located in a gap. AP endonuclease 1, which possesses 3'->5' exonuclease activity and potentially serves as a proofreader, did not discriminate dA from dC that was located opposite 8-oxo-dG. However, human DNA ligases I and III joined 3'-dA terminus much more efficiently than 3'-dC terminus when paired to 8-oxo-dG. In reconstituted short-patch BER, repair products contained only dA opposite 8-oxo-dG. These results indicate that human DNA ligases discriminate dC from dA and that MYH-initiated short-patch BER is futile and hence this BER must proceed to long-patch repair, even if it is initiated as short-patch repair, through strand displacement synthesis from the ligation-resistant dC terminus to generate the OGG1 substrate, dC:8-oxo-dG pair.


  • [Articles] GANA--a genetic algorithm for NMR backbone resonance assignment -

    NMR data from different experiments often contain errors; thus, automated backbone resonance assignment is a very challenging issue. In this paper, we present a method called GANA that uses a genetic algorithm to automatically perform backbone resonance assignment with a high degree of precision and recall. Precision is the number of correctly assigned residues divided by the number of assigned residues, and recall is the number of correctly assigned residues divided by the number of residues with known human curated answers. GANA takes spin systems as input data and uses two data structures, candidate lists and adjacency lists, to assign the spin systems to each amino acid of a target protein. Using GANA, almost all spin systems can be mapped correctly onto a target protein, even if the data are noisy. We use the BioMagResBank (BMRB) dataset (901 proteins) to test the performance of GANA. To evaluate the robustness of GANA, we generate four additional datasets from the BMRB dataset to simulate data errors of false positives, false negatives and linking errors. We also use a combination of these three error types to examine the fault tolerance of our method. The average precision rates of GANA on BMRB and the four simulated test cases are 99.61, 99.55, 99.34, 99.35 and 98.60%, respectively. The average recall rates of GANA on BMRB and the four simulated test cases are 99.26, 99.19, 98.85, 98.87 and 97.78%, respectively. We also test GANA on two real wet-lab datasets, hbSBD and hbLBD. The precision and recall rates of GANA on hbSBD are 95.12 and 92.86%, respectively, and those of hbLBD are 100 and 97.40%, respectively.


  • [Articles] GATA-1 mediates auto-regulation of Gfi-1B transcription in K562 cells -

    Gfi-1B (growth factor independence-1B) gene is an erythroid-specific transcription factor, whose expression plays an essential role in erythropoiesis. Our laboratory has previously defined the human Gfi-1B promoter region and shown that GATA-1 mediates erythroid-specific Gfi-1B transcription. By further investigating the regulation of the Gfi-1B promoter, here we report that (i) Gfi-1B transcription is negatively regulated by its own gene product, (ii) GATA-1, instead of Gfi-1B, binds directly to the Gfi-1-like sites in the Gfi-1B promoter and (iii) Gfi-1B suppresses GATA-1-mediated stimulation of Gfi-1B promoter through their protein interaction. These results not only demonstrate that interaction of GATA-1 and Gfi-1B participates in a feedback regulatory pathway in controlling the expression of the Gfi-1B gene, but also provide the first evidence that Gfi-1B can exert its repression function by acting on GATA-1-mediated transcription without direct binding to the Gfi-1 site of the target genes. Based on these data, we propose that this negative auto-regulatory feedback loop is important in restricting the expression level of Gfi-1B, thus optimizing its function in erythroid cells.


  • [Articles] GDNF-inducible zinc finger protein 1 is a sequence-specific transcriptional repressor that binds to the HOXA10 gene regulatory region -

    The RET tyrosine kinase receptor and its ligand, glial cell line-derived neurotrophic factor (GDNF) are critical regulators of renal and neural development. It has been demonstrated that RET activates a variety of downstream signaling cascades, including the RAS/mitogen-activated protein kinase and phosphatidylinositol-3-kinase(PI3-K)/AKT pathways. However, nuclear targets specific to RET-triggered signaling still remain elusive. We have previously identified a novel zinc finger protein, GZF1, whose expression is induced during GDNF/RET signaling and may play a role in renal branching morphogenesis. Here, we report the DNA binding property of GZF1 and its potential target gene. Using the cyclic amplification and selection of targets technique, the consensus DNA sequence to which GZF1 binds was determined. This sequence was found in the 5' regulatory region of the HOXA10 gene. Electrophoretic mobility shift assay revealed that GZF1 specifically binds to the determined consensus sequence and suppresses transcription of the luciferase gene from the HOXA10 gene regulatory element. These findings thus suggest that GZF1 may regulate the spatial and temporal expression of the HOXA10 gene which plays a role in morphogenesis.


  • [Articles] GeMS: an advanced software package for designing synthetic genes -

    A user-friendly, advanced software package for gene design is described. The software comprises an integrated suite of programs—also provided as stand-alone tools—that automatically performs the following tasks in gene design: restriction site prediction, codon optimization for any expression host, restriction site inclusion and exclusion, separation of long sequences into synthesizable fragments, Tm and stem–loop determinations, optimal oligonucleotide component design and design verification/error-checking. The output is a complete design report and a list of optimized oligonucleotides to be prepared for subsequent gene synthesis. The user interface accommodates both inexperienced and experienced users. For inexperienced users, explanatory notes are provided such that detailed instructions are not necessary; for experienced users, a streamlined interface is provided without such notes. The software has been extensively tested in the design and successful synthesis of over 400 kb of genes, many of which exceeded 5 kb in length.


  • [Articles] Gene targeting using randomly inserted group II introns (targetrons) recovered from an Escherichia coli gene disruption library -

    The Lactococcus lactis Ll.LtrB group II intron retrohomes by reverse-splicing into one strand of a double-stranded DNA target site, while the intron-encoded protein cleaves the opposite strand and uses it to prime reverse transcription of the inserted intron RNA. The protein and intron RNA function in a ribonucleoprotein particle, with much of the DNA target sequence recognized by base-pairing of the intron RNA. Consequently, group II introns can be reprogrammed to insert into specific or random DNA sites by substituting specific or random nucleotide residues in the intron RNA. Here, we show that an Escherichia coli gene disruption library obtained using such randomly inserting Ll.LtrB introns contains most viable E.coli gene disruptions. Further, each inserted intron is targeted to a specific site by its unique base-pairing regions, and in most cases, could be recovered by PCR and used unmodified to obtain the desired single disruptant. Additionally, we identified a subset of introns that insert at sites lacking T+5, a nucleotide residue critical for second-strand cleavage. All such introns tested individually gave the desired specific disruption, some by switching to an alternate retrohoming mechanism targeting single-stranded DNA and using a nascent lagging DNA strand to prime reverse transcription.


  • [Articles] Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers -

    We report on a new type of systematic annotation error in genome and pathway databases that results from the misinterpretation of partial Enzyme Commission (EC) numbers such as ‘1.1.1.-’. This error results in the assignment of genes annotated with a partial EC number to many or all biochemical reactions that are annotated with the same partial EC number. That inference is faulty because of the ambiguous nature of partial EC numbers. We have observed this type of error in multiple databases, including KEGG, VIMSS and IMG, all of which assign genes to KEGG pathways. The Escherichia coli subset of the KEGG database exhibits this error for 6.8% of its gene-reaction assignments. For example, KEGG contains 17 reactions that are annotated with EC 1.1.1.-. A group of three E.coli genes, b1580 [putative dehydrogenase, NAD(P)-binding, starvation-sensing protein], b3787 (UDP-N-acetyl-d-mannosaminuronic acid dehydrogenase) and b0207 (2,5-diketo-d-gluconate reductase B), is assigned to 15 of those reactions, despite experimental evidence indicating different single functions for two of the three genes. Furthermore, the databases (DBs) are internally inconsistent in that the description of gene functions for genes with partial EC numbers is inconsistent with the activities implied by reactions to which the genes were assigned. We infer that these inconsistencies result from the processing used to match gene products to reactions within KEGG's metabolic pathways. These errors affect scientists who use these DBs as online encyclopedias and they affect bioinformaticists who use these DBs to train and validate newly developed algorithms.


  • [Articles] Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages -

    Long INterspersed Elements (LINE-1s or L1s) are abundant non-LTR retrotransposons in mammalian genomes that are capable of insertional mutagenesis. They have been associated with target site deletions upon insertion in cell culture studies of retrotransposition. Here, we report 50 deletion events in the human and chimpanzee genomes directly linked to the insertion of L1 elements, resulting in the loss of ~18 kb of sequence from the human genome and ~15 kb from the chimpanzee genome. Our data suggest that during the primate radiation, L1 insertions may have deleted up to 7.5 Mb of target genomic sequences. While the results of our in vivo analysis differ from those of previous cell culture assays of L1 insertion-mediated deletions in terms of the size and rate of sequence deletion, evolutionary factors can reconcile the differences. We report a pattern of genomic deletion sizes similar to those created during the retrotransposition of Alu elements. Our study provides support for the existence of different mechanisms for small and large L1-mediated deletions, and we present a model for the correlation of L1 element size and the corresponding deletion size. In addition, we show that internal rearrangements can modify L1 structure during retrotransposition events associated with large deletions.


  • [Articles] Gibbs sampling and helix-cap motifs -

    Protein backbones have characteristic secondary structures, including -helices and ßbeta;-sheets. Which structure is adopted locally is strongly biased by the local amino acid sequence of the protein. Accurate (probabilistic) mappings from sequence to structure are valuable for both secondary-structure prediction and protein design. For the case of -helix caps, we test whether the information content of the sequence–structure mapping can be self-consistently improved by using a relaxed definition of the structure. We derive helix-cap sequence motifs using database helix assignments for proteins of known structure. These motifs are refined using Gibbs sampling in competition with a null motif. Then Gibbs sampling is repeated, allowing for frameshifts of ±1 amino acid residue, in order to find sequence motifs of higher total information content. All helix-cap motifs were found to have good generalization capability, as judged by training on a small set of non-redundant proteins and testing on a larger set. For overall prediction purposes, frameshift motifs using all training examples yielded the best results. Frameshift motifs using a fraction of all training examples performed best in terms of true positives among top predictions. However, motifs without frameshifts also performed well, despite a roughly one-third lower total information content.


  • [Articles] Global analysis of yeast RNA processing identifies new targets of RNase III and uncovers a link between tRNA 5' end processing and tRNA splicing -

    We used a microarray containing probes that tile all known yeast noncoding RNAs (ncRNAs) to investigate RNA biogenesis on a global scale. The microarray verified a general loss of Box C/D snoRNAs in the TetO7-BCD1 mutant, which had previously been shown for only a handful of snoRNAs. We also monitored the accumulation of improperly processed flank sequences of pre-RNAs in strains depleted for known RNA nucleases, including RNase III, Dbr1p, Xrn1p, Rat1p and components of the exosome and RNase P complexes. Among the hundreds of aberrant RNA processing events detected, two novel substrates of Rnt1p (the RUF1 and RUF3 snoRNAs) were identified. We also identified a relationship between tRNA 5' end processing and tRNA splicing, processes that were previously thought to be independent. This analysis demonstrates the applicability of microarray technology to the study of global analysis of ncRNA synthesis and provides an extensive directory of processing events mediated by yeast ncRNA processing enzymes.


  • [Articles] Group 13 HOX proteins interact with the MH2 domain of R-Smads and modulate Smad transcriptional activation functions independent of HOX DNA-binding capability -

    Interactions with co-factors provide a means by which HOX proteins exert specificity. To identify candidate protein interactors of HOXA13, we created and screened an E11.5–E12.5, distal limb bud yeast two-hybrid prey library. Among the interactors, we isolated the BMP-signaling effector Smad5, which interacted with the paralogous HOXD13 but not with HOXA11 or HOXA9, revealing unique interaction capabilities of the AbdB-like HOX proteins. Using deletion mutants, we determined that the MH2 domain of Smad5 is necessary for HOXA13 interaction. This is the first report demonstrating an interaction between HOX proteins and the MH2 domain of Smad proteins. HOXA13 and HOXD13 also bind to other BMP and TGF-ßbeta;/Activin-regulated Smad proteins including Smad1 and Smad2, but not Smad4. Furthermore, HOXD13 could be co-immunoprecipitated with Smad1 from cells. Expression of HOXA13, HOXD13 or a HOXD13 homeodomain mutant (HOXD13IQN>AAA) antagonized TGF-ßbeta;-stimulated transcriptional activation of the pAdtrack-3TP-Lux reporter vector in Mv1Lu cells as well as the Smad3/Smad4-activated pTRS6-E1b promoter in Hep3B cells. Finally, using mammalian one-hybrid assay, we show that transcriptional activation by a GAL4/Smad3-C-terminus fusion protein is specifically inhibited by HOXA13. Our results identify a new co-factor for HOX group 13 proteins and suggest that HOX proteins may modulate Smad-mediated transcriptional activity through protein–protein interactions without the requirement for HOX monomeric DNA-binding capability.


  • [Articles] Guanosine tetra- and pentaphosphate synthase activity in chloroplasts of a higher plant: association with 70S ribosomes and inhibition by tetracycline -

    Chloroplasts possess bacterial-type systems for transcription and translation. On the basis of the identification of a Chlamydomonas reinhardtii gene encoding a RelA-SpoT homolog (RSH) that catalyzes the synthesis of guanosine tetra- or pentaphosphate [(p)ppGpp], we have previously suggested the operation of stringent control in the chloroplast genetic system. Although RSH genes have also been identified in several higher plants, the activities of the encoded enzymes and their mode of action in chloroplasts have remained uncharacterized. We have now characterized the intrinsic (p)ppGpp synthase activity of chloroplast extracts prepared from pea (Pisum sativum). Fractionation by ultracentrifugation suggested that the (p)ppGpp synthase activity of a translationally active chloroplast stromal extract was associated with 70S ribosomes. Furthermore, this enzymatic activity was inhibited by tetracycline, as was the peptide elongation activity of the extract. Structural comparisons between rRNA molecules of Escherichia coli and pea chloroplasts revealed the conservation of putative tetracycline-binding sites. These observations demonstrate the presence of a ribosome-associated (p)ppGpp synthase activity in the chloroplasts of a higher plant, further implicating (p)ppGpp in a genetic system of chloroplasts similar to that operative in bacteria.


  • [Articles] Heterologous gene expression using self-assembled supra-molecules with high affinity for HSP70 chaperone -

    Contrary to the results of direct expression, various human proteins (ferritin light-chain, epithermal growth factor, interleukin-2, prepro-ghrelin, deletion mutants of glutamate decarboxylase and arginine deiminase, and mini-proinsulin) were all soluble in Escherichia coli cytoplasm when expressed with the N-terminus fusion of ferritin heavy-chain (FTN-H). Through systematic investigations, we have found that a specific peptide motif within FTN-H has a high affinity to HSP70 chaperone DnaK, and that the peptide motif was composed of a hydrophobic core of three residues (Ile, Phe and Leu) and two flanking regions enriched with polar residues (Gly, Gln and Arg). It was also observed that all the recombinant proteins expressed with the fusion of FTN-H formed spherical nanoparticles with diameters of 10–15 nm, as confirmed by the transmission electron microscopy image. The protein nanoparticles are non-covalently cross-linked supra-molecules formed by the self-assembly function of FTN-H. Upon the formation of the supra-molecule, its size is likely to be limited by the assembly properties of FTN-H, thereby keeping the self-assembled particles soluble. This study reports on the dual function of FTN-H for fusion expression and solubility enhancement of heterologous proteins: (i) high-affinity interaction with DnaK and (ii) formation of self-assembled supra-molecules with limited and constant sizes, thereby avoiding the undesirable formation of insoluble macro-aggregates of heterologous proteins.


  • [Articles] Highly prevalent putative quadruplex sequence motifs in human DNA -

    We report here the results of a systematic search for the existence and prevalence of potential intramolecular G-quadruplex forming sequences in the human genome. We have also examined the tendency for particular sequences of ‘loop’ regions to occur in particular positions with respect to the G-tracts in a quadruplex. Using arithmetic ratio and probability techniques we have discovered frequent and systematic occurrence of certain sequence types, the most prominent being a potential quadruplex containing CCTGT in the first ‘loop’ position. Being able to highlight types of potential quadruplex sequences in G-rich regions is an important step in searching for biologically relevant sequences and finding their function.


  • [Articles] HnRNP H inhibits nuclear export of mRNA containing expanded CUG repeats and a distal branch point sequence -

    Myotonic dystrophy type 1 (DM1) is an autosomal dominant neuromuscular disorder associated with a (CUG)n expansion in the 3'-untranslated region of the DMPK (DM1 protein kinase) gene. Mutant DMPK mRNAs containing the trinucleotide expansion are retained in the nucleus of DM1 cells and form discrete foci. The nuclear sequestration of RNA binding proteins and associated factors binding to the CUG expansions is believed to be responsible for several of the splicing defects observed in DM1 patients and could ultimately be linked to DM1 muscular pathogenesis. Several RNA binding proteins capable of co-localizing with the nuclear-retained mutant DMPK mRNAs have already been identified but none can account for the nuclear retention of the mutant transcripts. Here, we have employed a modified UV crosslinking assay to isolate proteins bound to mutant DMPK-derived RNA and have identified hnRNP H as an abundant candidate. The specific binding of hnRNP H requires not only a CUG repeat expansion but also a splicing branch point distal to the repeats. Suppression of hnRNP H expression by RNAi rescued nuclear retention of RNA with CUG repeat expansions. The identification of hnRNP H as a factor capable of binding and possibly modulating nuclear retention of mutant DMPK mRNA may prove to be an important link in our understanding of the molecular mechanisms that lead to DM1 pathogenesis.


  • [Articles] HP1 modulates the transcription of cell-cycle regulators in Drosophila melanogaster -

    Heterochromatin protein 1 (HP1) was originally described as a non-histone chromosomal protein and is required for transcriptional gene silencing and the formation of heterochromatin. Although it is localized primarily at pericentric heterochromatin, a scattered distribution over a large number of euchromatic loci is also evident. Here, we provide evidence that Drosophila HP1 is essential for the maintenance of active transcription of euchromatic genes functionally involved in cell-cycle progression, including those required for DNA replication and mitosis. Depletion of HP1 in proliferating embryonic cells caused aberrant progression of the cell cycle at S phase and G2/M phase, linked to aberrant chromosome segregation, cytokinesis, and an increase in apoptosis. The chromosomal distribution of Aurora B, and the level of phosphorylation of histone H3 serine 10 were also altered in the absence of HP1. Using chromatin immunoprecipitation analysis, we further demonstrate that the promoters of a number of cell-cycle regulator genes are bound to HP1, supporting a direct role for HP1 in their active transcription. Overall, our data suggest that HP1 is essential for the maintenance of cell-cycle progression and the transcription of cell-cycle regulatory genes. The results also support the view that HP1 is a positive regulator of transcription in euchromatin.


  • [Articles] Human AP endonuclease suppresses DNA mismatch repair activity leading to microsatellite instability -

    The multifunctional mammalian apurinic/apyrimidinic (AP) endonuclease (APE) participates in the repair of AP sites in the cellular DNA as well as participating in the redox regulation of the transcription factor function. The function of APE is considered as the rate-limiting step in DNA base excision repair. Paradoxically, an unbalanced increase in APE protein leads to genetic instability. Therefore, we investigated the mechanisms of genetic instability that are induced by APE. Here, we report that the overexpression of APE protein disrupts the repair of DNA mismatches, which results in microsatellite instability (MSI). We found that expression of APE protein led to the suppression of the repair of DNA mismatches in the normal human fibroblast cells. Western blot analysis revealed that hMSH6 protein was markedly reduced in the APE-expressing cells. Moreover, the addition of purified Mut (MSH2 and MSH6 complex) to the extracts from the APE-expressing cells led to the restoration of mismatch repair (MMR) activity. By performing MMR activity assay and MSI analysis, we found that the co-expression of hMSH6 and APE exhibited the microsatellite stability, whereas the expression of APE alone generated the MSI-high phenotype. The APE-mediated decrease in MMR activity described here demonstrates the presence of a new and highly effective APE-mediated mechanism for MSI.


  • [Articles] Human Rad51 filaments on double- and single-stranded DNA: correlating regular and irregular forms with recombination function -

    Recombinase proteins assembled into helical filaments on DNA are believed to be the catalytic core of homologous recombination. The assembly, disassembly and dynamic rearrangements of this structure must drive the DNA strand exchange reactions of homologous recombination. The sensitivity of eukaryotic recombinase activity to reaction conditions in vitro suggests that the status of bound nucleotide cofactors is important for function and possibly for filament structure. We analyzed nucleoprotein filaments formed by the human recombinase Rad51 in a variety of conditions on double-stranded and single-stranded DNA by scanning force microscopy. Regular filaments with extended double-stranded DNA correlated with active in vitro recombination, possibly due to stabilizing the DNA products of these assays. Though filaments formed readily on single-stranded DNA, they were very rarely regular structures. The irregular structure of filaments on single-stranded DNA suggests that Rad51 monomers are dynamic in filaments and that regular filaments are transient. Indeed, single molecule force spectroscopy of Rad51 filament assembly and disassembly in magnetic tweezers revealed protein association and disassociation from many points along the DNA, with kinetics different from those of RecA. The dynamic rearrangements of proteins and DNA within Rad51 nucleoprotein filaments could be key events driving strand exchange in homologous recombination.


  • [Articles] Human XPC-hHR23B interacts with XPA-RPA in the recognition of triplex-directed psoralen DNA interstrand crosslinks -

    DNA interstrand crosslinks (ICLs) represent a severe form of damage that blocks DNA metabolic processes and can lead to cell death or carcinogenesis. The repair of DNA ICLs in mammals is not well characterized. We have reported previously that a key protein complex of nucleotide excision repair (NER), XPA-RPA, recognizes DNA ICLs. We now report the use of triplex technology to direct a site-specific psoralen ICL to a target DNA substrate to determine whether the human global genome NER damage recognition complex, XPC-hHR23B, recognizes this lesion. Our results demonstrate that XPC-hHR23B recognizes psoralen ICLs, which have a structure fundamentally different from other lesions that XPC-hHR23B is known to bind, with high affinity and specificity. XPC-hHR23B and XPA-RPA protein complexes were also observed to bind psoralen ICLs simultaneously, demonstrating not only that psoralen ICLs are recognized by XPC-hHR23B alone, but also that XPA-RPA may interact cooperatively with XPC-hHR23B on damaged DNA, forming a multimeric complex. Since XPC-hHR23B and XPA-RPA participate in the recognition and verification of DNA damage, these results support the hypothesis that interplay between components of the global genome repair sub-pathway of NER is critical for the recognition of psoralen DNA ICLs in the mammalian genome.


  • [Articles] Human-zebrafish non-coding conserved elements act in vivo to regulate transcription -

    Whole genome comparisons of distantly related species effectively predict biologically important sequences—core genes and cis-acting regulatory elements (REs)—but require experimentation to verify biological activity. To examine the efficacy of comparative genomics in identification of active REs from anonymous, non-coding (NC) sequences, we generated a novel alignment of the human and draft zebrafish genomes, and contrasted this set to existing human and fugu datasets. We tested the transcriptional regulatory potential of candidate sequences using two in vivo assays. Strict selection of non-genic elements which are deeply conserved in vertebrate evolution identifies 1744 core vertebrate REs in human and two fish genomes. We tested 16 elements in vivo for cis-acting gene regulatory properties using zebrafish transient transgenesis and found that 10 (63%) strongly modulate tissue-specific expression of a green fluorescent protein reporter vector. We also report a novel quantitative enhancer assay with potential for increased throughput based on normalized luciferase activity in vivo. This complementary system identified 11 (69%; including 9 of 10 GFP-confirmed elements) with cis-acting function. Together, these data support the utility of comparative genomics of distantly related vertebrate species to identify REs and provide a scaleable, in vivo quantitative assay to define functional activity of candidate REs.


  • [Articles] Identification and analysis of ribonuclease P and MRP RNA in a broad range of eukaryotes -

    RNases P and MRP are ribonucleoprotein complexes involved in tRNA and rRNA processing, respectively. The RNA subunits of these two enzymes are structurally related to each other and play an essential role in the enzymatic reaction. Both of the RNAs have a highly conserved helical region, P4, which is important in the catalytic reaction. We have used a bioinformatics approach based on conserved elements to computationally analyze available genomic sequences of eukaryotic organisms and have identified a large number of novel nuclear RNase P and MRP RNA genes. For MRP RNA for instance, this investigation increases the number of known sequences by a factor of three. We present secondary structure models of many of the predicted RNAs. Although all sequences are able to fold into the consensus secondary structure of P and MRP RNAs, a striking variation in size is observed, ranging from a Nosema locustae MRP RNA of 160 nt to much larger RNAs, e.g. a Plasmodium knowlesi P RNA of 696 nt. The P and MRP RNA genes appear in tandem in some protists, further emphasizing the close evolutionary relationship of these RNAs.


  • [Articles] Identification and characterization of endogenous small interfering RNAs from rice -

    RNA silencing-mediated small interfering RNAs (siRNAs) and microRNAs (miRNAs) have diverse natural roles, ranging from regulation of gene expression and heterochromatin formation to genome defense against transposons and viruses. Unlike miRNAs, endogenous siRNAs are generally not conserved between species; consequently, their identification requires experimental approaches. Thus far, endogenous siRNAs have not been reported from rice, which is a model species for monocotyledonous plants. We identified a large set of putative endogenous siRNAs from root, shoot and inflorescence small RNA cDNA libraries of rice. Most of these siRNAs are from intergenic regions, although a substantial proportion (22%) originates from the introns and exons of protein-coding genes. Northern and RT–PCR analysis revealed that the expression of some of the siRNAs is tissue specific or developmental stage specific. A total of 25 transposons and 21 protein-coding genes were predicted to be cis-targets of some of the siRNAs. Based on sequence homology, we also predicted 111 putative trans-targets for 44 of the siRNAs. Interestingly, ~46% of the predicted trans-targets are transposable elements, which suggests that endogenous siRNAs may play an important role in the suppression of transposon proliferation. Using RNA ligase-mediated-5' rapid amplification of cDNA end assays, we validated three of the predicted targets and provided evidence for both cis- and trans-silencing of target genes by siRNAs-guided mRNA cleavage.


  • [Articles] Identification and characterization of the mouse nuclear export factor (Nxf) family members -

    TAP/hNXF1 is a key factor that mediates general cellular mRNA export from the nucleus, and its orthologs are structurally and functionally conserved from yeast to humans. Metazoans encode additional proteins that share homology and domain organization with TAP/hNXF1, suggesting their participation in mRNA metabolism; however, the precise role(s) of these proteins is not well understood. Here, we found that the human mRNA export factor hNXF2 is specifically expressed in the brain, suggesting a brain-specific role in mRNA metabolism. To address the roles of additional NXF factors, we have identified and characterized the two Nxf genes, Nxf2 and Nxf7, which together with the TAP/hNXF1's ortholog Nxf1 comprise the murine Nxf family. Both mNXF2 and mNXF7 have a domain structure typical of the NXF family. We found that mNXF2 protein is expressed during mouse brain development. Similar to TAP/hNXF1, the mNXF2 protein is found in the nucleus, the nuclear envelope and cytoplasm, and is an active mRNA export receptor. In contrast, mNXF7 localizes exclusively to cytoplasmic granules and, despite its overall conserved sequence, lacks mRNA export activity. We concluded that mNXF2 is an active mRNA export receptor similar to the prototype TAP/hNXF1, whereas mNXF7 may have a more specialized role in the cytoplasm.


  • [Articles] Identification of a novel gene encoding a flavin-dependent tRNA:m5U methyltransferase in bacteria--evolutionary implications -

    Formation of 5-methyluridine (ribothymidine) at position 54 of the T-psi loop of tRNA is catalyzed by site-specific tRNA methyltransferases (tRNA:m5U-54 MTase). In all Eukarya and many Gram-negative Bacteria, the methyl donor for this reaction is S-adenosyl-l-methionine (S-AdoMet), while in several Gram-positive Bacteria, the source of carbon is N5, N10-methylenetetrahydrofolate (CH2H4folate). We have identified the gene for Bacillus subtilis tRNA:m5U-54 MTase. The encoded recombinant protein contains tightly bound flavin and is active in Escherichia coli mutant lacking m5U-54 in tRNAs and in vitro using T7 tRNA transcript as substrate. This gene is currently annotated gid in Genome Data Banks and it is here renamed trmFO. TrmFO (Gid) orthologs have also been identified in many other bacterial genomes and comparison of their amino acid sequences reveals that they are phylogenetically distinct from either ThyA or ThyX class of thymidylate synthases, which catalyze folate-dependent formation of deoxyribothymine monophosphate, the universal DNA precursor.


  • [Articles] Identification of CELF splicing activation and repression domains in vivo -

    CUG-BP and ETR-3 like factor (CELF) proteins are regulators of pre-mRNA alternative splicing. We created a series of truncation mutants to identify the regions of CELF proteins that are required to activate and to repress alternative splicing of different exons. This analysis was performed in parallel on two CELF proteins, ETR-3 (CUG-BP2, NAPOR, BRUNOL3) and CELF4 (BRUNOL4). We identified a 20-residue region of CELF4 required for repression or activation, in contrast to ETR-3, for which the required residues are more disperse. For both ETR-3 and CELF4, distinct regions were required to activate splicing of two different alternative exons, while regions required for repression of an additional third exon overlapped with regions required for activation. Our results suggest that activation of different splicing events by individual CELF proteins requires separable regions, implying the nature of the protein–protein interactions required for activation are target-dependent. The finding that residues required for activation and repression overlap suggests either that the same region interacts with different proteins to mediate different effects or that interactions with the same proteins can have different effects on splicing due to yet-to-be defined downstream events. These results provide a foundation for identifying CELF-interacting proteins involved in activated and/or repressed splicing.


  • [Articles] Identification of RNA editing sites in the SNP database -

    The relationship between human inherited genomic variations and phenotypic differences has been the focus of much research effort in recent years. These studies benefit from millions of single-nucleotide polymorphism (SNP) records available in public databases, such as dbSNP. The importance of identifying false dbSNP records increases with the growing role played by SNPs in linkage analysis for disease traits. In particular, the emerging understanding of the abundance of DNA and RNA editing calls for a careful distinction between inherited SNPs and somatic DNA and RNA modifications. In order to demonstrate that some of the SNP database records are actually somatic modification, we focus on one type of these modifications, namely A-to-I RNA editing, and present evidence for hundreds of dbSNP records that are actually editing sites. We provide a list of 102 RNA editing sites previously annotated in dbSNP database as SNPs, and experimentally validate seven of these. Interestingly, we show how dbSNP can serve as a starting point to look for new editing sites. Our results, for this particular type of RNA editing, demonstrate the need for a careful analysis of SNP databases in light of the increasing recognition of the significance of somatic sequence modifications.


  • [Articles] Identification of the CRP regulon using in vitro and in vivo transcriptional profiling -

    The Escherichia coli cyclic AMP receptor protein (CRP) is a global regulator that controls transcription initiation from more than 100 promoters by binding to a specific DNA sequence within cognate promoters. Many genes in the CRP regulon have been predicted simply based on the presence of DNA-binding sites within gene promoters. In this study, we have exploited a newly developed technique, run-off transcription/microarray analysis (ROMA) to define CRP-regulated promoters. Using ROMA, we identified 176 operons that were activated by CRP in vitro and 16 operons that were repressed. Using positive control mutants in different regions of CRP, we were able to classify the different promoters into class I or class II/III. A total of 104 operons were predicted to contain Class II CRP-binding sites. Sequence analysis of the operons that were repressed by CRP revealed different mechanisms for CRP inhibition. In contrast, the in vivo transcriptional profiles failed to identify most CRP-dependent regulation because of the complexity of the regulatory network. Analysis of these operons supports the hypothesis that CRP is not only a regulator of genes required for catabolism of sugars other than glucose, but also regulates the expression of a large number of other genes in E.coli. ROMA has revealed 152 hitherto unknown CRP regulons.


  • [Articles] In vitro selection of RNA aptamers against a composite small molecule-protein surface -

    A particularly challenging problem in chemical biology entails developing systems for modulating the activity of RNA using small molecules. One promising new approach towards this problem exploits the phenomenon of ‘surface borrowing,’ in which the small molecule is presented to the RNA in complex with a protein, thereby expanding the overall surface area available for interaction with RNA. To extend the utility of surface borrowing to include potential applications in synthetic biology, we set out to create an ‘orthogonal’ RNA-targeting system, one in which all components are foreign to the cell. Here we report the identification of small RNA modules selected in vitro to bind a surface-engineered protein, but only when the two macromolecules are bound to a synthetic bifunctional small molecule.


  • [Articles] Incorporation of non-nucleoside triphosphate analogues opposite to an abasic site by human DNA polymerases {beta} and {lambda} -

    A novel class of non-nucleoside triphosphate analogues, bearing hydrophobic groups sterically similar to nucleosides linked to the -phosphate but lacking the chemical functional groups of nucleic acids, were tested against six different DNA polymerases (polymerases). Human polymerases , ßbeta; and , and Saccharomyces cerevisiae polymerase IV, were inhibited with different potencies by these analogues. On the contrary, Escherichia coli polymerase I and HIV-1 reverse transcriptase were not. Polymerase ßbeta; incorporated these derivatives in a strictly Mn++-dependent manner. On the other hand, polymerase could incorporate some alkyltriphosphate derivatives with both Mg++ and Mn++, but only opposite to an abasic site on the template strand. The active site mutant polymerase Y505A showed an increased ability to incorporate the analogues. These results show for the first time that neither the base nor the sugar moieties of nucleotides are required for incorporation by family X DNA polymerases.


  • [Articles] Induction of transcription within chromosomal DNA loops flanked by MAR elements causes an association of loop DNA with the nuclear matrix -

    The spatial organization of an ~170 kb region of human chromosome 19, including CD22 and GPR40–GPR43 genes, was studied using in situ hybridization of a set of cosmid and PAC probes with nuclear halos prepared from proliferating and differentiated HL60 cells. The whole region under study was found to be looped out into the nuclear halo in proliferating cells. It is likely that the loop observed was attached to the nuclear matrix via MAR elements present at the flanks of the area under study. Upon dimethyl sulfoxide-induced differentiation of the cells the looped fragment became associated with the nuclear matrix. This change in the spatial organization correlated with the activation of transcription of at least two (CD22 and GPR43) genes present within the loop. The data obtained are discussed in the framework of the hypothesis postulating that the spatial organization of chromosomal DNA is maintained via constitutive (basic) and facultative (transcription-related) interactions of the latter with the nuclear matrix.


  • [Articles] Inferring the connectivity of a regulatory network from mRNA quantification in Synechocystis PCC6803 -

    A major task of contemporary biology is to understand and predict the functioning of regulatory networks. We use expression data to deduce the regulation network connecting the sigma factors of Synechocystis PCC6803, the most global regulators in bacteria. Synechocystis contains one group 1 (SigA) and four group 2 (SigB, SigC, SigD and SigE) sigma factors. From the relative abundance of the sig mRNA measured in the wild-type and the four group 2 sigma mutants, we derive a network of the influences of each sigma factor on the transcription of all other sigma factors. Internal or external stimuli acting on only one of the sigma factors will thus indirectly modify the expression of most of the others. From this model, we predict the control points through which the circadian time modulates the expression of the sigma factors. Our results show that the cross regulation between the group 1 and group 2 sigma factors is very important for the adaptation of the bacterium to different environmental and physiological conditions.


  • [Articles] Inhibition of O6-methylguanine-DNA methyltransferase by an alkyltransferase-like protein from Escherichia coli -

    The alkyltransferase-like (ATL) proteins contain primary sequence motifs resembling those found in DNA repair O6-alkylguanine-DNA alkyltransferase proteins. However, in the putative active site of ATL proteins, a tryptophan (W83) residue replaces the cysteine at the known active site of alkyltransferases. The Escherichia coli atl gene was expressed as a fusion protein and purified. Neither ATL nor C83 or A83 mutants transferred [3H] from [3H]-methylated DNA to themselves, and the levels of O6-methyl guanine (O6-meG) in substrate DNA were not affected by ATL. However, ATL inhibited the transfer of methyl groups to human alkyltransferase (MGMT). Inhibition was reduced by prolonged incubation in the presence of MGMT, again suggesting that O6-meG in the substrate is not changed by ATL. Gel-shift assays show that ATL binds to short single- or double-stranded oligonucleotides containing O6-meG, but not to oligonucleotides containing 8-oxoguanine, ethenoadenine, 5-hydroxycytosine or O4-methylthymine. There was no evidence of demethylation of O6-meG or of glycosylase or endonuclease activity. Overexpression of ATL in E.coli increased, or did not affect, the toxicity of N-methyl-N'-nitro-N-nitrosoguanidine in an alklyltransferase-proficient and -deficient strain, respectively. These results suggest that ATL may act as a damage sensor that flags O6-meG and possibly other O6-alkylation lesions for processing by other repair pathways.


  • [Articles] Initiation of DNA replication at the human {beta}-globin 3' enhancer -

    The origin of DNA replication in the human ßbeta;-globin gene contains an initiation region (IR) and two flanking auxiliary elements. Two replicator modules are located within the upstream auxiliary sequence and the IR core, but the functional sequences in the downstream auxiliary element are unknown. Here, we use a combination of benzoylated-naphthoylated DEAE (BND) cellulose purification and nascent strand abundance assays to show that replication initiation occurs at the ßbeta;-globin 3' enhancer on human chromosome 11 in the Hu11 hybrid murine erythroleukemia (MEL) cell line. To examine replicator function, 3' enhancer fragments were inserted into an ectopic site in MEL cells via an optimized FRT/EGFP-FLP integration system. These experiments demonstrate that the 1.6 kb downstream auxiliary element is a third replicator module called bGRep-E in erythroid cells. The minimal 260 bp 3' enhancer is required but not sufficient to initiate efficient replication, suggesting cooperation with adjacent sequences. The minimal 3' enhancer also cooperates with elements in an expressing HS3ßbeta;/-globin construct to initiate replication. These data indicate that the ßbeta;-globin replicator has multiple initiation sites in three closely spaced replicator modules. We conclude that a mammalian enhancer can cooperate with adjacent sequences to create an efficient replicator module.


  • [Articles] Intercalator conjugates of pyrimidine locked nucleic acid-modified triplex-forming oligonucleotides: improving DNA binding properties and reaching cellular activities -

    Triplex-forming oligonucleotides (TFOs) are powerful tools to interfere sequence-specifically with DNA-associated biological functions. (A/T,G)-containing TFOs are more commonly used in cells than (T,C)-containing TFOs, especially C-rich sequences; indeed the low intracellular stability of the non-covalent pyrimidine triplexes make the latter less active. In this work we studied the possibility to enhance DNA binding of (T,C)-containing TFOs, aiming to reach cellular activities; to this end, we used locked nucleic acid-modified TFOs (TFO/LNAs) in association with 5'-conjugation of an intercalating agent, an acridine derivative. In vitro a stable triplex was formed with the TFO-acridine conjugate: by SPR measurements at 37°C and neutral pH, the dissociation equilibrium constant was found in the nanomolar range and the triplex half-life ~10 h (50-fold longer compared with the unconjugated TFO/LNA). Moreover to further understand DNA binding of (T,C)-containing TFO/LNAs, hybridization studies were performed at different pH values: triplex stabilization associated with pH decrease was mainly due to a slower dissociation process. Finally, biological activity of pyrimidine TFO/LNAs was evaluated in a cellular context: it occurred at concentrations ~0.1 µM for acridine-conjugated TFO/LNA (or ~2 µM for the unconjugated TFO/LNA) whereas the corresponding phosphodiester TFO was inactive, and it was demonstrated to be triplex-mediated.


  • [Articles] Internal initiation of translation of the TrkB mRNA is mediated by multiple regions within the 5' leader -

    Translational regulation of the dendritically localized mRNA encoding for the neurotrophin receptor TrkB has important ramifications for synaptic function. We examined whether the TrkB mRNA is translated through an internal initiation entry site (IRES). The human TrkB 5' leaders are derived from the use of alternative promoters and alternative splicing, but all 5' leaders share a common exon. Insertion of a full-length 5' leader, as well as the common exon into the intercistronic region of a dicistronic luciferase construct, yielded luciferase activity generated from the second cistron that was either equivalent or higher than that observed from the encephalomyocarditis virus IRES. Moreover, inhibiting cap-dependent translation ex vivo and in in vitro lysates had only a minimal effect on the translation of mRNA containing the TrkB 5' leader. Dissecting the 5' leader showed that the IRES is located in the exon common to all TrkB 5' leaders. Moreover, six regions ranging from 2 to 25 nt were identified that either promoted or inhibited IRES activity. Taken together, these results suggest that the 5' leader of the human TrkB mRNA contains multiple cis-elements that regulate internal initiation of translation and that this mechanism may contribute significantly to the translation of the TrkB mRNA in neuronal dendrites.


  • [Articles] Interplay between GCN2 and GCN4 expression, translation elongation factor 1 mutations and translational fidelity in yeast -

    Genetic screens in Saccharomyces cerevisiae have identified the roles of ribosome components, tRNAs and translation factors in translational fidelity. These screens rely on the suppression of altered start codons, nonsense codons or frameshift mutations in genes involved in amino acid or nucleotide metabolism. Many of these genes are regulated by the General Amino Acid Control (GAAC) pathway. Upon amino acid starvation, the kinase GCN2 induces the GAAC cascade via increased translation of the transcriptional activator GCN4 controlled by upstream open reading frames (uORFs). Overexpression of the GCN2 or GCN4 genes enhances the sensitivity of translation fidelity assays that utilize genes regulated by GCN4, such as the suppression of a +1 insertion by S.cerevisiae translation elongation factor 1A (eEF1A) mutants. Paromomycin and the prion [PSI+], which reduce translational fidelity, do not increase GCN4 expression to induce the suppression phenotype and in fact reduce derepression. eEF1A mutations that reduce translation, however, reduce expression of GCN4 under non-starvation conditions. These eEF1A mutants also reduce HIS4 mRNA expression. Taken together, this system improves in vivo strategies for the analysis of translational fidelity and further provides new information on the interplay among translation fidelity, altered elongation and translational control via uORFs.


  • [Articles] Interplay between positive and negative activities that influence the role of Bicoid in transcription -

    The Drosophila mophogenetic protein Bicoid (Bcd) can activate transcription in a concentration-dependent manner in embryos. It contains a self-inhibitory domain that can interact with the co-repressor Sin3A. In this report, we study a Bcd mutant, Bcd(A57–61), which has a strengthened self-inhibitory function and is unable to activate the hb-CAT reporter in Drosophila cells, to analyze the role of co-factors in regulating Bcd function. We show that increased concentrations of the co-activator dCBP in cells can switch this protein from its inactive state to an active state on the hb-CAT reporter. The C-terminal portion of Bcd(A57–61) is required to mediate such activity-rescuing function of dCBP. Although capable of binding to DNA in vitro, Bcd(A57–61) is unable to access the hb enhancer element in cells, suggesting that its DNA binding defect is only manifested in a cellular context. Increased concentrations of dCBP restore not only the ability of Bcd(A57–61) to access the hb enhancer element in cells but also the occupancy of the general transcription factors TBP and TFIIB at the reporter promoter. These and other results suggest that an activator can undergo switches between its active and inactive states through sensing the opposing actions of positive and negative co-factors.


  • [Articles] Interruptions in gene expression drive highly expressed operons to the leading strand of DNA replication -

    In bacteria, most genes are on the leading strand of replication, a phenomenon attributed to collisions between the DNA and RNA polymerases. In Escherichia coli, these collisions slow the movement of the replication fork through actively transcribed genes only if they are coded on the lagging strand. For genes on both strands, however, these collisions sever nascent transcripts and interrupt gene expression. Based on these observations, we propose a new theory to explain strand bias: genes whose expression is important for fitness are selected to the leading strand because this reduces the duration of these interruptions. Our theory predicts that multi-gene operons, which are subject to longer interruptions, should be more strongly selected to the leading strand than singleton transcripts. We show that this is true even after controlling for the tendency for essential genes, which are strongly biased to the leading strand, to occur in operons. Our theory also predicts that other factors that are associated with strand bias should have stronger effects for genes that are in operons. We find that expression level and phylogenetic ubiquity are correlated with strand bias for both essential and non-essential genes, but only for genes in operons.


  • [Articles] Inverted repeat-stimulated sister-chromatid exchange events are RAD1-independent but reduced in a msh2 mutant -

    Inverted repeats (IRs) and trinucleotide repeats (TNRs) that have the potential to form secondary structures in vivo are known to cause genome rearrangements. Expansions of TNRs in humans are associated with several neurological disorders. Both IRs and TNRs stimulate spontaneous unequal sister-chromatid exchange (SCE) in yeast. Secondary structure-associated SCE events occur via double-strand break repair. Here we show that the rate of spontaneous IR-stimulated unequal SCE events in yeast is significantly reduced in strains with mutations in the mismatch repair genes MSH2 or MSH3, but unaffected by a mutation in the nucleotide excision-repair gene RAD1. Non-IR-associated unequal SCE events are increased in both MMR- and rad1-mutant cells; however, SCE events for both IR- and non-IR-containing substrates occur at a higher level in the exo1 background. Our results suggest that spontaneous SCE occurs by a template switching mechanism. Like IRs, TNRs have been shown to generate double-strand breaks (DSBs) in yeast. TNR expansions in mice are MSH2-dependent. Since IR-mediated SCE events are reduced in msh2 cells, we propose that TNR expansion mutations arise when DSBs are repaired using the sister or the homolog as a template.


  • [Articles] Investigation of the DNA-dependent cyclohexenyl nucleic acid polymerization and the cyclohexenyl nucleic acid-dependent DNA polymerization -

    DNA polymerases from different evolutionary families [Vent (exo–) DNA polymerase from the B-family polymerases, Taq DNA polymerase from the A-family polymerases and HIV reverse transcriptase from the reverse transcriptase family] were examined for their ability to incorporate the sugar-modified cyclohexenyl nucleoside triphosphates. All enzymes were able to use the cyclohexenyl nucleotides as a substrate. Using Vent (exo–) DNA polymerase and HIV reverse transcriptase, we were even able to incorporate seven consecutive cyclohexenyl nucleotides. Using a cyclohexenyl nucleic acid (CeNA) template, all enzymes tested were also able to synthesize a short DNA fragment. Since the DNA-dependent CeNA polymerization and the CeNA-dependent DNA polymerization is possible to a limited extend, we suggest CeNA as an ideal candidate to use in directed evolution methods for the development of a polymerase capable of replicating CeNA.


  • [Articles] Kinetic analysis of the role of the tyrosine 13, phenylalanine 56 and glutamine 54 network in the U1A/U1 hairpin II interaction -

    The A protein of the U1 small nuclear ribonucleoprotein particle, interacting with its stem–loop RNA target (U1hpII), is frequently used as a paradigm for RNA binding by recognition motif domains (RRMs). U1A/U1hpII complex formation has been proposed to consist of at least two steps: electrostatically mediated alignment of both molecules followed by locking into place, based on the establishment of close-range interactions. The sequence of events between alignment and locking remains obscure. Here we examine the roles of three critical residues, Tyr13, Phe56 and Gln54, in complex formation and stability using Biacore. Our mutational and kinetic data suggest that Tyr13 plays a more important role than Phe56 in complex formation. Mutational analysis of Gln54, combined with molecular dynamics studies, points to Arg52 as another key residue in association. Based on our data and previous structural and modeling studies, we propose that electrostatic alignment of the molecules is followed by hydrogen bond formation between the RNA and Arg52, and the sequential establishment of interactions with loop bases (including Tyr13). A quadruple stack, sandwiching two bases between Phe56 and Asp92, would occur last and coincide with the rearrangement of a C-terminal helix that partially occludes the RRM surface in the free protein.


  • [Articles] Kinetic resolution of bimolecular hybridization versus intramolecular folding in nucleic acids by surface plasmon resonance: application to G-quadruplex/duplex competition in human c-myc promoter -

    The human oncogene c-myc is regulated by G-quadruplex formation within the nuclease hypersensitive element (NHE IIII) in the c-myc promoter, making the quadruplex a strong anti-cancer target. With respect to this, the competing equilibrium between intramolecular quadruplex folding and bimolecular duplex formation is poorly understood and very few techniques have addressed this problem. We present a method for simultaneously determining the kinetic constants for G-quadruplex folding/unfolding and hybridization in the presence of the complementary strand from a single reaction using an optical biosensor based on surface plasmon resonance (SPR). Using this technique, we demonstrate for the first time that quadruplex formation in the c-myc promoter is favored at low strand concentrations. Our results indicate favorable quadruplex folding (equilibrium folding constant KF of 2.09 calculated from the kinetic parameters: folding rate constant, kf = 1.65 x 10–2 s–1 and unfolding rate constant, ku = 7.90 x 10–3 s–1) in 150 mM K+. The hybridization rate constants detected concurrently gave a bimolecular association constant, ka = 1.37 x 105 M–1 s–1 and dissociation constant, kd = 4.94 x 10–5 s–1. Interestingly, in the presence of Na+ we observed that G-quadruplex folding was unfavorable (KF = 0.54). Implication of our results on the c-myc transcription activation model is discussed in light of aberrant c-myc expression observed on destabilization of the G-quadruplex.


  • [Articles] Kinetics of substrate recognition and cleavage by human 8-oxoguanine-DNA glycosylase -

    Human 8-oxoguanine-DNA glycosylase (hOgg1) excises 8-oxo-7,8-dihydroguanine (8-oxoG) from damaged DNA. We report a pre-steady-state kinetic analysis of hOgg1 mechanism using stopped-flow and enzyme fluorescence monitoring. The kinetic scheme for hOgg1 processing an 8-oxoG:C-containing substrate was found to include at least three fast equilibrium steps followed by two slow, irreversible steps and another equilibrium step. The second irreversible step was rate-limiting overall. By comparing data from Ogg1 intrinsic fluorescence traces and from accumulation of products of different types, the irreversible steps were attributed to two main chemical steps of the Ogg1-catalyzed reaction: cleavage of the N-glycosidic bond of the damaged nucleotide and ßbeta;-elimination of its 3'-phosphate. The fast equilibrium steps were attributed to enzyme conformational changes during the recognition of 8-oxoG, and the final equilibrium, to binding of the reaction product by the enzyme. hOgg1 interacted with a substrate containing an aldehydic AP site very slowly, but the addition of 8-bromoguanine (8-BrG) greatly accelerated the reaction, which was best described by two initial equilibrium steps followed by one irreversible chemical step and a final product release equilibrium step. The irreversible step may correspond to ßbeta;-elimination since it is the very step facilitated by 8-BrG.


  • [Articles] Large-scale structural analysis of the core promoter in mammalian and plant genomes -

    DNA encodes at least two independent levels of functional information. The first level is for encoding proteins and sequence targets for DNA-binding factors, while the second one is contained in the physical and structural properties of the DNA molecule itself. Although the physical and structural properties are ultimately determined by the nucleotide sequence itself, the cell exploits these properties in a way in which the sequence itself plays no role other than to support or facilitate certain spatial structures. In this work, we focus on these structural properties, comparing them between different organisms and assessing their ability to describe the core promoter. We prove the existence of distinct types of core promoters, based on a clustering of their structural profiles. These results indicate that the structural profiles are much conserved within plants (Arabidopsis and rice) and animals (human and mouse), but differ considerably between plants and animals. Furthermore, we demonstrate that these structural profiles can be an alternative way of describing the core promoter, in addition to more classical motif or IUPAC-based approaches. Using the structural profiles as discriminatory elements to separate promoter regions from non-promoter regions, reliable models can be built to identify core-promoter regions using a strictly computational approach.


  • [Articles] Length-dependent energetics of (CTG)n and (CAG)n trinucleotide repeats -

    Trinucleotide repeats are involved in a number of debilitating diseases such as myotonic dystrophy. Twelve to seventy-five base-long (CTG)n oligodeoxynucleotides were analysed using a combination of biophysical [UV-absorbance, circular dichroism and differential scanning calorimetry (DSC)] and biochemical methods (non-denaturing gel electrophoresis and enzymatic footprinting). All oligomers formed stable intramolecular structures under near physiological conditions with a melting temperature that was only weakly dependent on oligomer length. Thermodynamic analysis of the denaturation process by UV-melting and calorimetric experiments revealed an unprecedented length-dependent discrepancy between the enthalpy values deduced from model-dependent (UV-melting) and model-independent (calorimetry) experiments. Evidence for non-zero molar heat capacity changes was also derived from the analysis of the Arrhenius plots and DSC profiles. Such behaviour is analysed in the framework of an intramolecular ‘branched-hairpin’ model, in which long CTG oligomers do not fold into a simple long hairpin–stem intramolecular structure, but allow the formation of several independent folding units of unequal stability. We demonstrate that, for sequences ranging from 12 to 25 CTG repeats, an intramolecular structure with two loops is formed which we will call ‘bis-hairpin’. Similar results were also found for CAG oligomers, suggesting that this observation may be extended to various trinucleotide repeats-containing sequences.


  • [Articles] Localization of mitochondrial DNA base excision repair to an inner membrane-associated particulate fraction -

    Mitochondrial DNA (mtDNA) contains high levels of oxidative damage relative to nuclear DNA. A full, functional DNA base excision repair (BER) pathway is present in mitochondria, to repair oxidative DNA lesions. However, little is known about the organization of this pathway within mitochondria. Here, we provide evidence that the mitochondrial BER proteins are not freely soluble, but strongly associated with an inner membrane-containing particulate fraction. Uracil DNA glycosylase, oxoguanine DNA glycosylase and DNA polymerase activities all co-sedimented with this particulate fraction and were not dissociated from it by detergent (0.1% or 1.0% NP40) treatment. The particulate associations of these activities were not due to their binding mtDNA, which is itself associated with the inner membrane, as they also localized to the particulate fraction of mitochondria from 143B (TK) 0 cells, which lack mtDNA. However, all of the BER activities were at least partially solubilized from the particulate fraction by treatment with 150–300 mM NaCl, suggesting that electrostatic interactions are involved in the association. The biological implications of the apparent immobilization of BER proteins are discussed.


  • [Articles] Localization of spermine binding sites in 23S rRNA by photoaffinity labeling: parsing the spermine contribution to ribosomal 50S subunit functions -

    Polyamine binding to 23S rRNA was investigated, using a photoaffinity labeling approach. This was based on the covalent binding of a photoreactive analog of spermine, N1-azidobenzamidino (ABA)-spermine, to Escherichia coli ribosomes or naked 23S rRNA under mild irradiation conditions. The cross-linking sites of ABA-spermine in 23S rRNA were determined by RNase H digestion and primer-extension analysis. Domains I, II, IV and V in naked 23S rRNA were identified as discrete regions of preferred cross-linking. When 50S ribosomal subunits were targeted, the interaction of the photoprobe with the above 23S rRNA domains was elevated, except for helix H38 in domain II whose susceptibility to cross-linking was greatly reduced. In addition, cross-linking sites were identified in domains III and VI. Association of 30S with 50S subunits, poly(U), tRNAPhe and AcPhe-tRNA to form a post-translocation complex further altered the cross-linking, in particular to helices H11–H13, H21, H63, H80, H84, H90 and H97. Poly(U)-programmed 70S ribosomes, reconstituted from photolabeled 50S subunits and untreated 30S subunits, bound AcPhe-tRNA in a similar fashion to native ribosomes. However, they exhibited higher reactivity toward puromycin and enhanced tRNA-translocation efficiency. These results suggest an essential role for polyamines in the structural and functional integrity of the large ribosomal subunit.


  • [Articles] Localization, mobility and fidelity of retrotransposed Group II introns in rRNA genes -

    We previously showed that the group II Lactococcus lactis Ll.LtrB intron could retrotranspose into ectopic locations on the genome of its native host. Two integration events, which had been mapped to unique sequences, were localized in the present study to separate copies of the six L.lactis 23S rRNA genes, within operon B or D. Although further movement within the bacterial chromosome was undetectable, the retrotransposed introns were able to re-integrate into their original homing site provided on a plasmid. This finding indicates not only that retrotransposed group II introns retain mobility properties, but also that movement occurs back into sequence that is heterologous to the sequence of the chromosomal location. Sequence analysis of the retrotransposed introns and the secondary mobility events back to the homing site showed that the introns retain sequence integrity. These results are illuminating, since the reverse transcriptase (RT) of the intron-encoded protein, LtrA, has no known proofreading function, yet the mobility events have a low error rate. Enzymatic digests were used to monitor sequence changes from the wild-type intron. The results indicate that retromobility events have ~10–5 misincorporations per nucleotide inserted. In contrast to the high RT error rates for retroviruses that must escape host defenses, the infrequent mutations of group II introns would ensure intron spread through retention of sequences essential for mobility.


  • [Articles] Loss of G-A base pairs is insufficient for achieving a large opening of U4 snRNA K-turn motif -

    Upon binding to the 15.5K protein, two tandem-sheared G–A base pairs are formed in the internal loop of the kink-turn motif of U4 snRNA (Kt-U4). We have reported that the folding of Kt-U4 is assisted by protein binding. Unstable interactions that contribute to a large opening of the free RNA (‘k–e motion’) were identified using locally enhanced sampling molecular dynamics simulations, results that agree with experiments. A detailed analysis of the simulations reveals that the k–e motion in Kt-U4 is triggered both by loss of G–A base pairs in the internal loop and backbone flexibility in the stems. Essential dynamics show that the loss of G–A base pairs is correlated along the first mode but anti-correlated along the third mode with the k–e motion. Moreover, when enhanced sampling was confined to the internal loop, the RNA adopted an alternative conformation characterized by a sharper kink, opening of G–A base pairs and modified stacking interactions. Thus, loss of G–A base pairs is insufficient for achieving a large opening of the free RNA. These findings, supported by previously published RNA structure probing experiments, suggest that G–A base pair formation occurs upon protein binding, thereby stabilizing a selective orientation of the stems.


  • [Articles] Mammalian enzymes for preventing transcriptional errors caused by oxidative damage -

    8-Oxo-7,8-dihydroguanine (8-oxoGua) is produced in cells by reactive oxygen species normally formed during cellular metabolic processes. This oxidized base can pair with both adenine and cytosine, and thus the existence of this base in messenger RNA would cause translational errors. The MutT protein of Escherichia coli degrades 8-oxoGua-containing ribonucleoside di- and triphosphates to the monophosphate, thereby preventing the misincorporation of 8-oxoGua into RNA. Here, we show that for human the MutT-related proteins, NUDT5 and MTH1 have the ability to prevent translational errors caused by oxidative damage. The increase in the production of erroneous proteins by oxidative damage is 28-fold over the wild-type cells in E.coli mutT deficient cells. By the expression of NUDT5 or MTH1 in the cells, it is reduced to 1.4- or 1.2-fold, respectively. NUDT5 and MTH1 hydrolyze 8-oxoGDP to 8-oxoGMP with Vmax/Km values of 1.3 x 10–3 and 1.7 x 10–3, respectively, values which are considerably higher than those for its normal counterpart, GDP (0.1–0.5 x 10–3). MTH1, but not NUDT5, possesses an additional activity to degrade 8-oxoGTP to the monophosphate. These results indicate that the elimination of 8-oxoGua-containing ribonucleotides from the precursor pool is important to ensure accurate protein synthesis and that both NUDT5 and MTH1 are involved in this process in human cells.


  • [Articles] MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences -

    The application of high-throughput techniques such as genomics, proteomics or transcriptomics means that vast amounts of heterogeneous data are now available in the public databases. Bioinformatics is responding to the challenge with new integrated management systems for data collection, validation and analysis. Multiple alignments of genomic and protein sequences provide an ideal environment for the integration of this mass of information. In the context of the sequence family, structural and functional data can be evaluated and propagated from known to unknown sequences. However, effective integration is being hindered by syntactic and semantic differences between the different data resources and the alignment techniques employed. One solution to this problem is the development of an ontology that systematically defines the terms used in a specific domain. Ontologies are used to share data from different resources, to automatically analyse information and to represent domain knowledge for non-experts. Here, we present MAO, a new ontology for multiple alignments of nucleic and protein sequences. MAO is designed to improve interoperation and data sharing between different alignment protocols for the construction of a high quality, reliable multiple alignment in order to facilitate knowledge extraction and the presentation of the most pertinent information to the biologist.


  • [Articles] Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE -

    A minimally addressed area in Saccharomyces cerevisiae research is the mapping of transcription start sites (TSS). Mapping of TSS in S.cerevisiae has the potential to contribute to our understanding of gene regulation, transcription, mRNA stability and aspects of RNA biology. Here, we use 5' SAGE to map 5' TSS in S.cerevisiae. Tags identifying the first 15–17 bases of the transcripts are created, ligated to form ditags, amplified, concatemerized and ligated into a vector to create a library. Each clone sequenced from this library identifies 10–20 TSS. We have identified 13 746 unique, unambiguous sequence tags from 2231 S.cerevisiae genes. TSS identified in this study are consistent with published results, with primer extension results described here, and are consistent with expectations based on previous work on transcription initiation. We have aligned the sequence flanking 4637 TSS to identify the consensus sequence A(Arich)5NPyA(A/T)NN(Arich)6, which confirms and expands the previous reported PyA(A/T)Pu consensus pattern. The TSS data allowed the identification of a previously unrecognized gene, uncovered errors in previous annotation, and identified potential regulatory RNAs and upstream open reading frames in 5'-untranslated region.


  • [Articles] Maternal disruption of Ube3a leads to increased expression of Ube3a-ATS in trans -

    Angelman syndrome (AS) is a neurogenetic disorder characterized by severe mental retardation, ‘puppet-like’ ataxic gait with jerky arm movements, seizures, EEG abnormalities, hyperactivity and bouts of inappropriate laughter. Individuals with AS fail to inherit a normal active maternal copy of the gene encoding ubiquitin protein ligase E3A (UBE3A). UBE3A is transcribed predominantly from the maternal allele in brain, but is expressed from both alleles in most other tissues. It has been proposed that brain-specific silencing of the paternal UBE3A allele is mediated by a large (>500 kb) paternal non-coding antisense transcript (UBE3A-ATS). There are several other examples of imprinting regulation involving antisense transcripts that share two main properties: (i) the sense transcript is repressed by antisense and (ii) the interaction between sense and antisense occurs in cis. We show here that, in a mouse model of AS, maternal transmission of Ube3a mutation leads to increased expression of the paternal Ube3a-ATS, suggesting that the antisense is modulated by sense rather than the reciprocal mode of regulation. Our observation that Ube3a regulates expression of Ube3a-ATS in trans is in contrast to the other cases of sense–antisense epigenetic cis-interactions and argues against a major role for Ube3a-ATS in the imprinting of Ube3a.


  • [Articles] Mechanistic features of CAG*CTG repeat contractions in cultured cells revealed by a novel genetic assay -

    Trinucleotide repeats (TNRs) undergo high frequency mutagenesis to cause at least 15 neurodegenerative diseases. To understand better the molecular mechanisms of TNR instability in cultured cells, a new genetic assay was created using a shuttle vector. The shuttle vector contains a promoter-TNR-reporter gene construct whose expression is dependent on TNR length. The vector harbors the SV40 ori and large T antigen gene, allowing portability between primate cell lines. The shuttle vector is propagated in cultured cells, then recovered and analyzed in yeast using selection for reporter gene expression. We show that (CAG•CTG)25–33 contracts at frequencies as high as 1% in 293T and 293 human cells and in COS-1 monkey cells, provided that the plasmid undergoes replication. Hairpin-forming capacity of the repeat sequence stimulated contractions. Evidence for a threshold was observed between 25 and 33 repeats in COS-1 cells, where contraction frequencies increased sharply (up 720%) over a narrow range of repeat lengths. Expression of the mismatch repair protein Mlh1 does not correlate with repeat instability, suggesting contractions are independent of mismatch repair in our system. Together, these findings recapitulate certain features of human genetics and therefore establish a novel cell culture system to help provide new mechanistic insights into CAG•CTG repeat instability.


  • [Articles] Mechanistic studies on DNA damage by minor groove binding copper-phenanthroline conjugates -

    Copper–phenanthroline complexes oxidatively damage and cleave nucleic acids. Copper bis-phenanthroline and copper complexes of mono- and bis-phenanthroline conjugates are used as research tools for studying nucleic acid structure and binding interactions. The mechanism of DNA oxidation and cleavage by these complexes was examined using two copper–phenanthroline conjugates of the sequence-specific binding molecule, distamycin. The complexes contained either one or two phenanthroline units that were bonded to the DNA-binding domain through a linker via the 3-position of the copper ligand. A duplex containing independently generated 2-deoxyribonolactone facilitated kinetic analysis of DNA cleavage. Oxidation rate constants were highly dependent upon the ligand environment but rate constants describing elimination of the alkali-labile 2-deoxyribonolactone intermediate were not. Rate constants describing DNA cleavage induced by each molecule were 11–54 times larger than the respective oxidation rate constants. The experiments indicate that DNA cleavage resulting from ßbeta;-elimination of 2-deoxyribonolactone by copper–phenanthroline complexes is a general mechanism utilized by this family of molecules. In addition, the experiments confirm that DNA damage mediated by mono- and bis-phenanthroline copper complexes proceeds through distinct species, albeit with similar outcomes.


  • [Articles] Methyl methanesulfonate (MMS) produces heat-labile DNA damage but no detectable in vivo DNA double-strand breaks -

    Homologous recombination (HR) deficient cells are sensitive to methyl methanesulfonate (MMS). HR is usually involved in the repair of DNA double-strand breaks (DSBs) in Saccharomyces cerevisiae implying that MMS somehow induces DSBs in vivo. Indeed there is evidence, based on pulsed-field gel electrophoresis (PFGE), that MMS causes DNA fragmentation. However, the mechanism through which MMS induces DSBs has not been demonstrated. Here, we show that DNA fragmentation following MMS treatment, and detected by PFGE is not the consequence of production of cellular DSBs. Instead, DSBs seen following MMS treatment are produced during sample preparation where heat-labile methylated DNA is converted into DSBs. Furthermore, we show that the repair of MMS-induced heat-labile damage requires the base excision repair protein XRCC1, and is independent of HR in both S.cerevisiae and mammalian cells. We speculate that the reason for recombination-deficient cells being sensitive to MMS is due to the role of HR in repair of MMS-induced stalled replication forks, rather than for repair of cellular DSBs or heat-labile damage.


  • [Articles] miBLAST: scalable evaluation of a batch of nucleotide sequence queries with BLAST -

    A common task in many modern bioinformatics applications is to match a set of nucleotide query sequences against a large sequence dataset. Exis-ting tools, such as BLAST, are designed to evaluate a single query at a time and can be unacceptably slow when the number of sequences in the query set is large. In this paper, we present a new algorithm, called miBLAST, that evaluates such batch workloads efficiently. At the core, miBLAST employs a q-gram filtering and an index join for efficiently detecting similarity between the query sequences and database sequences. This set-oriented technique, which indexes both the query and the database sets, results in substantial performance improvements over existing methods. Our results show that miBLAST is significantly faster than BLAST in many cases. For example, miBLAST aligned 247 965 oligonucleotide sequences in the Affymetrix probe set against the Human UniGene in 1.26 days, compared with 27.27 days with BLAST (an improvement by a factor of 22). The relative performance of miBLAST increases for larger word sizes; however, it decreases for longer queries. miBLAST employs the familiar BLAST statistical model and output format, guaranteeing the same accuracy as BLAST and facilitating a seamless transition for existing BLAST users.


  • [Articles] Modulation of ADAR1 editing activity by Z-RNA in vitro -

    RNA editing by A-to-I modification has been recognized as an important molecular mechanism for generating RNA and protein diversity. In mammals, it is mediated by a family of adenosine deaminases that act on RNAs (ADARs). The large version of the editing enzyme ADAR1 (ADAR1-L), expressed from an interferon-responsible promoter, has a Z-DNA/Z-RNA binding domain at its N-terminus. We have tested the in vitro ability of the enzyme to act on a 50 bp segment of dsRNA with or without a Z-RNA forming nucleotide sequence. A-to-I editing efficiency is markedly enhanced in presence of the sequence favoring Z-RNA. In addition, an alteration in the pattern of modification along the RNA duplex becomes evident as reaction times decrease. These results suggest that the local conformation of dsRNA molecules might be an important feature for target selectivity by ADAR1 and other proteins with Z-RNA binding domains.


  • [Articles] MSH2 missense mutations alter cisplatin cytotoxicity and promote cisplatin-induced genome instability -

    Defects in the mismatch repair protein MSH2 cause tolerance to DNA damage. We report how cancer-derived and polymorphic MSH2 missense mutations affect cisplatin cytotoxicity. The chemotolerance phenotype was compared with the mutator phenotype in a yeast model system. MSH2 missense mutations display a strikingly different effect on cell death and genome instability. A mutator phenotype does not predict chemotolerance or vice versa. MSH2 mutations that were identified in tumors (Y109C) or as genetic variations (L402F) promote tolerance to cisplatin, but leave the initial mutation rate of cells unaltered. A secondary increase in the mutation rate is observed after cisplatin exposure in these strains. The mutation spectrum of cisplatin-resistant mutators identifies persistent cisplatin adduction as the cause for this acquired genome instability. Our results demonstrate that MSH2 missense mutations that were identified in tumors or as polymorphic variations can cause increased cisplatin tolerance independent of an initial mutator phenotype. Cisplatin exposure promotes drug-induced genome instability. From a mechanistical standpoint, these data demonstrate functional separation between MSH2-dependent cisplatin cytotoxicity and repair. From a clinical standpoint, these data provide valuable information on the consequences of point mutations for the success of chemotherapy and the risk for secondary carcinogenesis.


  • [Articles] Multiple defects in translation associated with altered ribosomal protein L4 -

    The ribosomal proteins L4 and L22 form part of the peptide exit tunnel in the large ribosomal subunit. In Escherichia coli, alterations in either of these proteins can confer resistance to the macrolide antibiotic, erythromycin. The structures of the 30S as well as the 50S subunits from each antibiotic resistant mutant differ from wild type in distinct ways and L4 mutant ribosomes have decreased peptide bond-forming activity. Our analyses of the decoding properties of both mutants show that ribosomes carrying the altered L4 protein support increased levels of frameshifting, missense decoding and readthrough of stop codons during the elongation phase of protein synthesis and stimulate utilization of non-AUG codons and mutant initiator tRNAs at initiation. L4 mutant ribosomes are also altered in their interactions with a range of 30S-targeted antibiotics. In contrast, the L22 mutant is relatively unaffected in both decoding activities and antibiotic interactions. These results suggest that mutations in the large subunit protein L4 not only alter the structure of the 50S subunit, but upon subunit association, also affect the structure and function of the 30S subunit.


  • [Articles] Mutational analysis of BTAF1-TBP interaction: BTAF1 can rescue DNA-binding defective TBP mutants -

    The BTAF1 transcription factor interacts with TATA-binding protein (TBP) to form the B–TFIID complex, which is involved in RNA polymerase II transcription. Here, we present an extensive mapping study of TBP residues involved in BTAF1 interaction. This shows that residues in the concave, DNA-binding surface of TBP are important for BTAF1 binding. In addition, BTAF1 interacts with residues in helix 2 on the convex side of TBP as assayed in protein–protein and in DNA-binding assays. BTAF1 drastically changes the TATA-box binding specificity of TBP, as it is able to recruit DNA-binding defective TBP mutants to both TATA-containing and TATA-less DNA. Interestingly, other helix 2 interacting factors, such as TFIIA and NC2, can also stabilize mutant TBP binding to DNA. In contrast, TFIIB which interacts with a distinct surface of TBP does not display this activity. Since many proteins contact helix 2 of TBP, this provides a molecular basis for mutually exclusive TBP interactions and stresses the importance of this structural element for eukaryotic transcription.


  • [Articles] N-methylpurine DNA glycosylase overexpression increases alkylation sensitivity by rapidly removing non-toxic 7-methylguanine adducts -

    Previous studies indicate that overexpression of N-methylpurine DNA glycosylase (MPG) dramatically sensitizes cells to alkylating agent-induced cytotoxicity. We recently demonstrated that this sensitivity is preceded by an increased production of AP sites and strand breaks, confirming that overexpression of MPG disrupts normal base excision repair and causes cell death through overproduction of toxic repair intermediates. Here we establish through site-directed mutagenesis that MPG-induced sensitivity to alkylation is dependent on enzyme glycosylase activity. However, in contrast to the sensitivity seen to heterogeneous alkylating agents, MPG overexpression generates no cellular sensitivity to MeOSO2(CH2)2-lexitropsin, an alkylator which exclusively induces 3-meA lesions. Indeed, MPG overexpression has been shown to increase the toxicity of alkylating agents that produce 7-meG adducts, and here we demonstrate that MPG-overexpressing cells have dramatically increased removal of 7-meG from their DNA. These data suggest that the mechanism of MPG-induced cytotoxicity involves the conversion of non-toxic 7-meG lesions into highly toxic repair intermediates. This study establishes a mechanism by which a benign DNA modification can be made toxic through the overexpression of an otherwise well-tolerated gene product, and the application of this principle could lead to improved chemotherapeutic strategies that reduce the peripheral toxicity of alkylating agents.


  • [Articles] New NTP analogs: the synthesis of 4'-thioUTP and 4'-thioCTP and their utility for SELEX -

    The synthesis of the triphosphates of 4'-thiouridine and 4'-thiocytidine, 4'-thioUTP (7; thioUTP) and 4'-thioCTP (8; thioCTP), and their utility for SELEX (systematic evolution of ligands by exponential enrichment) is described. The new nucleoside triphosphate (NTP) analogs 7 and 8 were prepared from appropriately protected 4'-thiouridine and -cytidine derivatives using the one-pot method reported by J. Ludwig and F. Eckstein [(1989) J. Org. Chem., 54, 631–635]. Because SELEX requires both in vitro transcription and reverse transcription, we examined the ability of 7 and 8 for SELEX by focusing on the two steps. Incorporation of 7 and 8 by T7 RNA polymerase to give 4'-thioRNA (thioRNA) proceeded well and was superior to those of the two sets of frequently used modified NTP analogs for SELEX (2'-NH2dUTP and 2'-NH2dCTP; 2'-FdUTP and 2'-FdCTP), when an adequate leader sequence of DNA template was selected. We revealed that a leader sequence of about +15 of DNA template is important for the effective incorporation of modified NTP analogs by T7 RNA polymerase. In addition, reverse transcription of the resulting thioRNA into the complementary DNA in the presence of 2'-deoxynucleoside triphosphates (dNTPs) also proceeded smoothly and precisely. The stability of the thioRNA toward RNase A was 50 times greater than that of the corresponding natural RNA. With these successful results in hand, we attempted the selection of thioRNA aptamers to human -thrombin using thioUTP and thioCTP, and found a thioRNA aptamer with high binding affinity (Kd = 4.7 nM).


  • [Articles] NF-{kappa}B controls the global pro-inflammatory response in endothelial cells: evidence for the regulation of a pro-atherogenic program -

    Activation of the transcription factor NF-B is critical for the tumor necrosis factor- (TNF-)-induced inflammatory response. Here we report the complete gene expression profile from activated microvascular endothelial cells emphasizing the direct contribution of the NF-B pathway. Human microvascular endothelial cell line-1 (HMEC-1) cells were modified to express dominant interfering mutants of the IKK/NF-B signaling module and expression profiles were determined. Our results provide compelling evidence for the virtually absolute dependence of TNF--regulated genes on NF-B. A constitutively active IKK2 was sufficient for maximal induction of most target genes, whereas a transdominant IB suppressed gene expression. Several genes with a critical role in atherogenesis were identified. The endothelial lipase (EL) gene, a key enzyme involved in lipoprotein metabolism, was investigated more in detail. Binding sites interacting with NF-B in vitro and in vivo were identified and co-transfection experiments demonstrated the direct regulation of the EL promoter by NF-B. We conclude that targeting the IKK/NF-B pathway or specific genes downstream may be effective for the control or prevention of chronic inflammatory diseases such as atherosclerosis.


  • [Articles] NFAT5 binds to the TNF promoter distinctly from NFATp, c, 3 and 4, and activates TNF transcription during hypertonic stress alone -

    Tumor necrosis factor (TNF) is a pro-inflammatory cytokine that plays an important role in a variety of infectious and autoimmune disorders. Its transcription is regulated in a stimulus- and cell-type-specific manner via the recruitment of distinct DNA/activator complexes forming secondary structures or enhanceosomes. NFATp, a member of the nuclear factor of activated T cells (NFAT) family of transcription factors, plays a critical role in TNF gene regulation under a variety of conditions. In this study, we show that NFAT5, the most recently described NFAT family member, binds to the TNF promoter in a manner distinct from other NFAT proteins and is a key mediator in the activation of TNF gene transcription during hypertonic stress alone.


  • [Articles] NMR structure and Mg2+ binding of an RNA segment that underlies the L7/L12 stalk in the E.coli 50S ribosomal subunit -

    Helix 42 of Domain II of Escherichia coli 23S ribosomal RNA underlies the L7/L12 stalk in the ribosome and may be significant in positioning this feature relative to the rest of the 50S ribosomal subunit. Unlike the Haloarcula marismortui and Deinococcus radiodurans examples, the lower portion of helix 42 in E.coli contains two consecutive G•A oppositions with both adenines on the same side of the stem. Herein, the structure of an analog of positions 1037–1043 and 1112–1118 in the helix 42 region is reported. NMR spectra and structure calculations support a cis Watson–Crick/Watson–Crick (cis W.C.) G•A conformation for the tandem (G•A)2 in the analog and a minimally perturbed helical duplex stem. Mg2+ titration studies imply that the cis W.C. geometry of the tandem (G•A)2 probably allows O6 of G20 and N1 of A4 to coordinate with a Mg2+ ion as indicated by the largest chemical shift changes associated with the imino group of G20 and the H8 of G20 and A4. A cross-strand bridging Mg2+ coordination has also been found in a different sequence context in the crystal structure of H.marismortui 23S rRNA, and therefore it may be a rare but general motif in Mg2+ coordination.


  • [Articles] Non-EST based prediction of exon skipping and intron retention events using Pfam information -

    Most of the known alternative splice events have been detected by the comparison of expressed sequence tags (ESTs) and cDNAs. However, not all splice events are represented in EST databases since ESTs have several biases. Therefore, non-EST based approaches are needed to extend our view of a transcriptome. Here, we describe a novel method for the ab initio prediction of alternative splice events that is solely based on the annotation of Pfam domains. Furthermore, we applied this approach in a genome-wide manner to all human RefSeq transcripts and predicted a total of 321 exon skipping and intron retention events. We show that this method is very reliable as 78% (250 of 321) of our predictions are confirmed by ESTs or cDNAs. Subsequent analyses of splice events within Pfam domains revealed a significant preference of alternative exon junctions to be located at the protein surface and to avoid secondary structure elements. Thus, splice events within Pfams are probable to alter the structure and function of a domain which makes them highly interesting for detailed biological investigation. As Pfam domains are annotated in many other species, our strategy to predict exon skipping and intron retention events might be important for species with a lower number of ESTs.


  • [Articles] Non-homologous end joining, but not homologous recombination, enables survival for cells exposed to a histone deacetylase inhibitor -

    Non-homologous end joining (NHEJ) and homologous recombination (HR) are pathways that repair DNA double-strand breaks (DSBs). In Saccharomyces cerevisiae, the repair of these breaks is influenced by histone acetylation. Therefore, we tested mammalian cells deleted for NHEJ (Ku80 or DNA Ligase IV) or altered for HR (breast cancer associated gene, Brca2, or Bloom's syndrome, Blm) for sensitivity to trichostatin A (TSA), a histone deacetylase inhibitor that is being investigated as an anti-cancer therapeutic. We show that cells mutated for Ku80 (ku80–/–) or DNA Ligase IV (lig 4–/–), but not cells mutated for Brca2 (brca2lex1/lex2) or Blm (blmtm3Brd/tm4Brd), are hypersensitive to TSA in a dose-dependent manner. TSA-induced toxicity stimulates apoptosis and cell cycle checkpoint responses independent of p53, but does not increase phosphorylated histone H2AX (-H2AX) as compared with a clastogenic agent, camptothecin, indicating that the quantity of DSBs is not the primary cause of TSA-induced cell death. In addition, we show that potential anti-cancer drugs (LY-294002 and vanillin) that inhibit the family of phosphatidylinositol 3 kinases that include the NHEJ protein, DNA–PKCS act in synergy with TSA to reduce the viability of HeLa cells in tissue culture presenting the possibility of using the two drugs in combination to treat cancer.


  • [Articles] Not so crystal clear: the structure of the human telomere G-quadruplex in solution differs from that present in a crystal -

    The structure of human telomere DNA is of intense interest because of its role in the biology of both cancer and aging. The sequence [5'-AGGG(TTAGGG)3] has been used as a model for telomere DNA in both NMR and X-ray crystallographic studies, the results of which show dramatically different structures. In Na+ solution, NMR revealed an antiparallel G-quadruplex structure that featured both diagonal and lateral TTA loops. Crystallographic studies in the presence of K+ revealed a flattened, propeller-shaped structure featuring a parallel-stranded G-quadruplex with symmetrical external TTA loops. We report the results of biophysical experiments in solution and computational studies that are inconsistent with the reported crystal structure, indicating that a different structure exists in K+ solutions. Sedimentation coefficients were determined experimentally in both Na+ and K+ solutions and were compared with values calculated using bead models for the reported NMR and crystal structures. Although the solution NMR structure accurately predicted the observed S-value in Na+ solution, the crystal structure predicted an S-value that differed dramatically from that experimentally observed in K+ solution. The environments of loop adenines were probed by quantitative fluorescence studies using strategic and systematic single-substitutions of 2-aminopurine for adenine bases. Both fluorescence intensity and quenching experiments in K+ yielded results at odds with quantitative predictions from the reported crystal structure. Circular dichroism and fluorescence quenching studies in the presence of the crowding agent polyethylene glycol showed dramatic changes in the quadruplex structure in K+ solutions, but not in Na+ solutions, suggesting that the crystal environment may have selected for a particular conformational form. Molecular dynamics simulations were performed to yield model structures for the K+ quadruplex form that are consistent with our biophysical results and with previously reported chemical modification studies. These models suggest that the biologically relevant structure of the human telomere quadruplex in K+ solution is not the one determined in the published crystalline state.


  • [Articles] Novel DNA-binding properties of the RNA-binding protein TIAR -

    TIA-1 related protein binds avidly to uridine-rich elements in mRNA and pre-mRNAs of a wide range of genes, including interleukin (IL)-8 and vascular endothelial growth factor (VEGF). The protein has diverse regulatory roles, which in part depend on the locus of binding within the transcript, including translational control, splicing and apoptosis. Here, we observed selective and potent inhibition of TIAR–RNP complex formation with IL-8 and VEGF 3'-untranslated regions (3'-UTRs) using thymidine-rich deoxyoligonucleotide (ODN) sequences derived from the VEFG 3'-UTR. We show by ultraviolet crosslinking and electrophoretic mobility shift assays that TIAR can bind directly to single-stranded, thymidine-rich ODNs but not to double-stranded ODNs containing the same sequence. TIAR had a nearly 6-fold greater affinity for DNA than RNA ( $${K}_{{\hbox{ d }}_{\hbox{ app }}}=1.6\times {10}^{-9}\hbox{ M }$$ versus 9.4 x 10–9 M). Truncation of TIAR indicated that the high affinity DNA-binding site overlaps with the RNA-binding site involving RNA recognition motif 2 (RRM2). However, RRM1 alone could also bind to DNA. Finally, we show that TIAR can be displaced from single-stranded DNA by active transcription through the binding site. These results provide a potential mechanism by which TIAR can shuttle between RNA and DNA ligands.


  • [Articles] Nucleic acid melting by Escherichia coli CspE -

    Escherichia coli contains nine members of the CspA family. CspA and some of its homologues play critical role in cold acclimation of cells by acting as RNA chaperones, destabilizing nucleicacid secondary structures. Disruption of nucleic acid melting activity of CspE led to loss of its transcription antitermination activity and consequently its cold acclimation activity. To date, the melting activity of Csp proteins was studied using partially double-stranded model nucleic acids substrates forming stem–loop structures. Here, we studied the mechanism of nucleic acid melting by CspE. We show that CspE melts the stem region in two directions, that CspE-induced melting does not require the continuity of the substrate's loop region, and CspE can efficiently melt model substrates with single-stranded overhangs as short as 4 nt. We further show that preferential binding of CspE at the stem–loop junction site initiates melting; binding of additional CspE molecules that fully cover the single-stranded region of a melting substrate leads to complete melting of the stem.


  • [Articles] Open reading frames provide a rich pool of potential natural antisense transcripts in fungal genomes -

    Natural antisense transcripts are reported from all kingdoms of life and several recent reports of genomewide screens indicate that they are widely distributed. These transcripts seem to be involved in various biological functions and may govern the expression of their respective sense partner. Very little, however, is known about the degree of evolutionary conservation of antisense transcripts. Furthermore, none of the earlier analyses has studied whether antisense relationships are solely dual or involved in more complex relationships. Here we present a systematic screen for cis- and trans-located antisense transcripts based on open reading frames (ORFs) from five fungal species. The relative number of ORFs involved in antisense relationships varies greatly between the five species. In addition, other significant differences are found between the species, such as the mean length of the antisense region. The majority of trans-located antisense transcripts is found to be involved in complex relationships, resulting in highly connected networks. The analysis of the degree of evolutionary conservation of antisense transcripts shows that most antisense transcripts have no ortholog in any other species. An annotation of antisense transcripts based on Gene Ontology directs to common terms and shows that proteins of genes involved in antisense relationships preferentially localize to the nucleus with common functions in the regulation or maintenance of nucleic acids.


  • [Articles] oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes -

    Targeted transcript profiling studies can identify sets of co-expressed genes; however, identification of the underlying functional mechanism(s) is a significant challenge. Established methods for the analysis of gene annotations, particularly those based on the Gene Ontology, can identify functional linkages between genes. Similar methods for the identification of over-represented transcription factor binding sites (TFBSs) have been successful in yeast, but extension to human genomics has largely proved ineffective. Creation of a system for the efficient identification of common regulatory mechanisms in a subset of co-expressed human genes promises to break a roadblock in functional genomics research. We have developed an integrated system that searches for evidence of co-regulation by one or more transcription factors (TFs). oPOSSUM combines a pre-computed database of conserved TFBSs in human and mouse promoters with statistical methods for identification of sites over-represented in a set of co-expressed genes. The algorithm successfully identified mediating TFs in control sets of tissue-specific genes and in sets of co-expressed genes from three transcript profiling studies. Simulation studies indicate that oPOSSUM produces few false positives using empirically defined thresholds and can tolerate up to 50% noise in a set of co-expressed genes.


  • [Articles] Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members -

    We report an in-depth computational study of the protein sequences and structures of the superfamily of archaeo-eukaryotic primases (AEPs). This analysis greatly expands the range of diversity of the AEPs and reveals the unique active site shared by all members of this superfamily. In particular, it is shown that eukaryotic nucleo-cytoplasmic large DNA viruses, including poxviruses, asfarviruses, iridoviruses, phycodnaviruses and the mimivirus, encode AEPs of a distinct family, which also includes the herpesvirus primases whose relationship to AEPs has not been recognized previously. Many eukaryotic genomes, including chordates and plants, encode previously uncharacterized homologs of these predicted viral primases, which might be involved in novel DNA repair pathways. At a deeper level of evolutionary connections, structural comparisons indicate that AEPs, the nucleases involved in the initiation of rolling circle replication in plasmids and viruses, and origin-binding domains of papilloma and polyoma viruses evolved from a common ancestral protein that might have been involved in a protein-priming mechanism of initiation of DNA replication. Contextual analysis of multidomain protein architectures and gene neighborhoods in prokaryotes and viruses reveals remarkable parallels between AEPs and the unrelated DnaG-type primases, in particular, tight associations with the same repertoire of helicases. These observations point to a functional equivalence of the two classes of primases, which seem to have repeatedly displaced each other in various extrachromosomal replicons.


  • [Articles] Overexpression of human DNA polymerase {micro} (Pol {micro}) in a Burkitt's lymphoma cell line affects the somatic hypermutation rate -

    DNA polymerase µ (Pol µ) is a DNA-dependent DNA polymerase closely related to terminal deoxynucleotidyl transferase (TdT), and prone to induce template/primer misalignments and misincorporation. In addition to a proposed general role in non-homologous end joining of double-strand breaks, its mutagenic potential and preferential expression in secondary lymphoid tissues support a role in somatic hypermutation (SHM) of immunoglobulin genes. Here, we show that human Pol µ protein is expressed in the nucleus of centroblasts obtained from human tonsils, forming a characteristic foci pattern resembling that of other DNA repair proteins in response to DNA damage. Overexpression of human Pol µ in Ramos cells, in which the SHM process is constitutive, augmented the somatic mutations specifically at the variable (V) region of the immunoglobulin genes. The nature of the mutations introduced, mostly base substitutions, supports the contribution of Pol µ to mutation of G and C residues during SHM. In vitro analysis of Pol µ misincorporation on specific templates, that mimic DNA repair intermediates and correspond to mutational hotspots, indicated that many of the mutations observed in vivo can be explained by the capacity of Pol µ to induce transient template/primer misalignments.


  • [Articles] Oxetane modified, conformationally constrained, antisense oligodeoxyribonucleotides function efficiently as gene silencing molecules -

    Incorporation of nucleosides with novel base-constraining oxetane (OXE) modifications [oxetane, 1-(1',3'-O-anhydro-ßbeta;-d-psicofuranosyl nucleosides)] into antisense (AS) oligodeoxyribonucleotides (ODNs) should greatly improve the gene silencing efficiency of these molecules. This is because OXE modified bases provide nuclease protection to the natural backbone ODNs, can impart Tm values similar to those predicted for RNA–RNA hybrids, and not only permit but also accelerate RNase H mediated catalytic activity. We tested this assumption in living cells by directly comparing the ability of OXE and phosphorothioate (PS) ODNs to target c-myb gene expression. The ODNs were targeted to two different sites within the c-myb mRNA. One site was chosen arbitrarily. The other was a ‘rational’ choice based on predicted hybridization accessibility after physical mapping with self-quenching reporter molecules (SQRM). The Myb mRNA and protein levels were equally diminished by OXE and PS ODNs, but the latter were delivered to cells with approximately six times greater efficiency, suggesting that OXE modified ODNs were more potent on a molar basis. The rationally targeted molecules demonstrated greater silencing efficiency than those directed to an arbitrarily chosen mRNA sequence. We conclude that rationally targeted, OXE modified ODNs, can function efficiently as gene silencing agents, and hypothesize that they will prove useful for therapeutic purposes.


  • [Articles] Oxidative stress-induced apoptosis in neurons correlates with mitochondrial DNA base excision repair pathway imbalance -

    Neurodegeneration can occur as a result of endogenous oxidative stress. Primary cerebellar granule cells were used in this study to determine if mitochondrial DNA (mtDNA) repair deficiencies correlate with oxidative stress-induced apoptosis in neuronal cells. Granule cells exhibited a significantly higher intracellular oxidative state compared with primary astrocytes as well as increases in reductants, such as glutathione, and redox sensitive signaling molecules, such as AP endonuclease/redox effector factor-1. Cerebellar granule cultures also exhibited an increased susceptibility to exogenous oxidative stress. Menadione (50 µM) produced twice as many lesions in granule cell mtDNA compared with astrocytes, and granule cell mtDNA repair was significantly less efficient. A decreased capacity to repair oxidative mtDNA damage correlates strongly with mitochondrial initiated apoptosis in these neuronal cultures. Interestingly, the mitochondrial activities of initiators for base excision repair (BER), the bifunctional glycosylase/AP lyases as well as AP endonuclease, were significantly higher in cerebellar granule cells compared with astrocytes. The increased mitochondrial AP endonuclease activity in combination with decreased polymerase activity may cause an imbalance in oxidative BER leading to an increased production and persistence of mtDNA damage in neurons when treated with menadione. This study provides evidence linking neuronal mtDNA repair capacity with oxidative stress-related neurodegeneration.


  • [Articles] PCNA-MutS{alpha}-mediated binding of MutL{alpha} to replicative DNA with mismatched bases to induce apoptosis in human cells -

    Modified bases, such as O6-methylguanines, are produced in cells exposed to alkylating agents and cause apoptosis. In human cells treated with N-methyl-N-nitrosourea, we detected a protein complex composed of MutS, MutL and PCNA on damaged DNA by immunoprecipitation method using chromatin extracts, in which protein–protein interactions were stabilized by chemical crosslinking. Time course experiments revealed that MutS, consisting of MSH2 and MSH6 proteins, and PCNA bind to DNA to form an initial complex, and MutL, composed of MLH1 and PMS2, binds to the complex when the DNA is damaged. This sequential mode of binding was further confirmed by the findings that the association of PCNA–MutS complex on chromatin was observed even in the cells that lack MLH1, whereas in the absence of MSH2 no association of MutL with the chromatin was achieved. Moreover, reduction in the PCNA content by small-interfering RNA or inhibition of DNA replication by aphidicolin, an inhibitor of DNA polymerase, significantly reduced the levels of the PCNA–MutS–MutL complex and also suppressed an increase in the caspase-3 activity, a hallmark for the induction of apoptosis. These observations imply that the induction of apoptosis is coupled with the progression of DNA replication through the action of PCNA.


  • [Articles] Phosphorylation of human DNA polymerase {lambda} by the cyclin-dependent kinase Cdk2/cyclin A complex is modulated by its association with proliferating cell nuclear antigen -

    DNA polymerase (Pol) is a member of the Pol X family and possesses four different enzymatic activities, being DNA polymerase, terminal transferase, deoxyribose phosphate lyase and polynucleotide synthetase, all localized in its C-terminal region. On the basis of its biochemical properties, Pol has been implicated in various DNA repair pathways, such as abasic site translesion DNA synthesis, base excision repair and non-homologous end joining of double strand breaks. However, its role in vivo has not yet been elucidated. In addition, Pol has been shown to interact with the replication clamp proliferating cell nuclear antigen (PCNA) in vitro and in vivo. In this work, we searched by affinity chromatography for novel partners and we identified the cyclin-dependent kinase Cdk2 as novel partner of Pol . Pol is phosphorylated in vitro by several Cdk/cyclin complexes, including Cdk2/cyclin A, in its proline-serine-rich domain. While the polymerase activity of Pol was not affected by Cdk2/cyclin A phosphorylation, phosphorylation of Pol was decreased by its interaction with PCNA. Finally, Pol is also phosphorylated in vivo in human cells and this phosphorylation is modulated during the cell cycle.


  • [Articles] Phosphorylation of human oxoguanine DNA glycosylase ({alpha}-OGG1) modulates its function -

    Oxoguanine DNA glycosylase (OGG1) initiates the repair of 8-oxoguanine (8-oxoG), a major oxidative DNA base modification that has been directly implicated in cancer and aging. OGG1 functions in the base excision repair pathway, for which a molecular hand-off mechanism has been proposed. To date, only one functional and a few physical protein interactions have been reported for OGG1. Using the yeast two-hybrid system and a protein array membrane, we identified two novel protein interactions of OGG1, with two different protein kinases: Cdk4, a serine-threonine kinase, and c-Abl, a tyrosine kinase. We confirmed these interactions in vitro using recombinant proteins and in vivo by co-immunoprecipitation from whole cell extracts. OGG1 is phosphorylated in vitro by Cdk4, resulting in a 2.5-fold increase in the 8-oxoG/C incision activity of OGG1. C-Abl tyrosine phosphorylates OGG1 in vitro; however, this phosphorylation event does not affect OGG1 8-oxoG/C incision activity. These results provide the first evidence that a post-translational modification of OGG1 can affect its catalytic activity. The distinct functional outcomes from serine/threonine or tyrosine phosphorylation may indicate that activation of different signal transduction pathways modulate OGG1 activity in different ways.


  • [Articles] Plasmodium interspersed repeats: the major multigene superfamily of malaria parasites -

    Functionally related homologues of known genes can be difficult to identify in divergent species. In this paper, we show how multi-character analysis can be used to elucidate the relationships among divergent members of gene superfamilies. We used probabilistic modelling in conjunction with protein structural predictions and gene-structure analyses on a whole-genome scale to find gene homologies that are missed by conventional similarity-search strategies and identified a variant gene superfamily in six species of malaria (Plasmodium interspersed repeats, pir). The superfamily includes rif in P.falciparum, vir in P.vivax, a novel family kir in P.knowlesi and the cir/bir/yir family in three rodent malarias. Our data indicate that this is the major multi-gene family in malaria parasites. Protein localization of products from pir members to the infected erythrocyte membrane in the rodent malaria parasite P.chabaudi, demonstrates phenotypic similarity to the products of pir in other malaria species. The results give critical insight into the evolutionary adaptation of malaria parasites to their host and provide important data for comparative immunology between malaria parasites obtained from laboratory models and their human counterparts.


  • [Articles] Potentiation of gene targeting in human cells by expression of Saccharomyces cerevisiae Rad52 -

    When exogenous DNA is stably introduced in mammalian cells, it is typically integrated in random positions, and only a minor fraction enters a pathway of homologous recombination (HR). The complex Rad51/Rad52 is a major player in the management of exogenous DNA in eukaryotic organisms and plays a critical role in the choice of repair system. In Saccharomyces cerevisiae, the pathway of choice is HR, mediated by Rad52 (ScRad52), which differs slightly from its human homologue. Here, we present an approach that utilizes ScRad52 to enhance HR in human cells containing a specific substrate for recombination. Clones of HeLa cells were produced expressing functional ScRad52. These cells showed enhanced resistance to DNA damaging treatments and revealed a different distribution of Rad51 foci (a marker of recombination complex formation). More significantly, ScRad52 expression resulted in an up to 37-fold increase in gene targeting by HR. In the same cells, random integration of exogenous DNA was significantly reduced, consistent with the view that HR and non-homologous end joining are alternative competing pathways. Expression of ScRad52 could offer a major improvement for experiments requiring gene targeting by HR, both in basic research and in gene therapy studies.


  • [Articles] Predicting non-coding RNA genes in Escherichia coli with boosted genetic programming -

    Several methods exist for predicting non-coding RNA (ncRNA) genes in Escherichia coli (E.coli). In addition to about sixty known ncRNA genes excluding tRNAs and rRNAs, various methods have predicted more than thousand ncRNA genes, but only 95 of these candidates were confirmed by more than one study. Here, we introduce a new method that uses automatic discovery of sequence patterns to predict ncRNA genes. The method predicts 135 novel candidates. In addition, the method predicts 152 genes that overlap with predictions in the literature. We test sixteen predictions experimentally, and show that twelve of these are actual ncRNA transcripts. Six of the twelve verified candidates were novel predictions. The relatively high confirmation rate indicates that many of the untested novel predictions are also ncRNAs, and we therefore speculate that E.coli contains more ncRNA genes than previously estimated.


  • [Articles] Predicting specificity-determining residues in two large eukaryotic transcription factor families -

    Certain amino acid residues in a protein, when mutated, change the protein's function. We present an improved method of finding these specificity-determining positions that uses all the protein sequence data available for a family of homologous proteins. We study in detail two families of eukaryotic transcription factors, basic leucine zippers and nuclear receptors, because of the large amount of sequences and experimental data available. These protein families also have a clear definition of functional specificity: DNA-binding specificity. We compare our results to three other methods, including the evolutionary trace algorithm and a method that depends on orthology relationships. All of the predictions are compared to the available mutational and crystallographic data. We find that our method provides superior predictions of the known specificity-determining residues and also predicts residue positions within these families that deserve further study for their roles in functional specificity.


  • [Articles] Prediction of functional modules based on comparative genome analysis and Gene Ontology application -

    We present a computational method for the prediction of functional modules encoded in microbial genomes. In this work, we have also developed a formal measure to quantify the degree of consistency between the predicted and the known modules, and have carried out statistical significance analysis of consistency measures. We first evaluate the functional relationship between two genes from three different perspectives—phylogenetic profile analysis, gene neighborhood analysis and Gene Ontology assignments. We then combine the three different sources of information in the framework of Bayesian inference, and we use the combined information to measure the strength of gene functional relationship. Finally, we apply a threshold-based method to predict functional modules. By applying this method to Escherichia coli K12, we have predicted 185 functional modules. Our predictions are highly consistent with the previously known functional modules in E.coli. The application results have demonstrated that our approach is highly promising for the prediction of functional modules encoded in a microbial genome.


  • [Articles] Prediction of solvent accessibility and sites of deleterious mutations from protein sequence -

    Residues that form the hydrophobic core of a protein are critical for its stability. A number of approaches have been developed to classify residues as buried or exposed. In order to optimize the classification, we have refined a suite of five methods over a large dataset and proposed a metamethod based on an ensemble average of the individual methods, leading to a two-state classification accuracy of 80%. Many studies have suggested that hydrophobic core residues are likely sites of deleterious mutations, so we wanted to see to what extent these sites can be predicted from the putative buried residues. Residues that were most confidently classified as buried were proposed as sites of deleterious mutations. This proposition was tested on six proteins for which sites of deleterious mutations have previously been identified by stability measurement or functional assay. Of the total of 130 residues predicted as sites of deleterious mutations, 104 (or 80%) were correct.


  • [Articles] Preferential binding of a G-quadruplex ligand to human chromosome ends -

    The G-overhangs of telomeres are thought to adopt particular conformations, such as T-loops or G-quadruplexes. It has been suggested that G-quadruplex structures could be stabilized by specific ligands in a new approach to cancer treatment consisting in inhibition of telomerase, an enzyme involved in telomere maintenance and cell immortality. Although the formation of G-quadruplexes was demonstrated in vitro many years ago, it has not been definitively demonstrated in living human cells. We therefore investigated the chromosomal binding of a tritiated G-quadruplex ligand, 3H-360A (2,6-N,N'-methyl-quinolinio-3-yl)-pyridine dicarboxamide [methyl-3H]. We verified the in vitro selectivity of 3H-360A for G-quadruplex structures by equilibrium dialysis. We then showed by binding experiments with human genomic DNA that 3H-360A has a very potent selectivity toward G-quadruplex structures of the telomeric 3'-overhang. Finally, we performed autoradiography of metaphase spreads from cells cultured with 3H-360A. We found that 3H-360A was preferentially bound to chromosome terminal regions of both human normal (peripheral blood lymphocytes) and tumor cells (T98G and CEM1301). In conclusion, our results provide evidence that a specific G-quadruplex ligand interacts with the terminal ends of human chromosomes. They support the hypothesis that G-quadruplex ligands induce and/or stabilize G-quadruplex structures at telomeres of human cells.


  • [Articles] Prevalence of quadruplexes in the human genome -

    Guanine-rich DNA sequences of a particular form have the ability to fold into four-stranded structures called G-quadruplexes. In this paper, we present a working rule to predict which primary sequences can form this structure, and describe a search algorithm to identify such sequences in genomic DNA. We count the number of quadruplexes found in the human genome and compare that with the figure predicted by modelling DNA as a Bernoulli stream or as a Markov chain, using windows of various sizes. We demonstrate that the distribution of loop lengths is significantly different from what would be expected in a random case, providing an indication of the number of potentially relevant quadruplex-forming sequences. In particular, we show that there is a significant repression of quadruplexes in the coding strand of exonic regions, which suggests that quadruplex-forming patterns are disfavoured in sequences that will form RNA.


  • [Articles] Protein length in eukaryotic and prokaryotic proteomes -

    We analyzed length differences of eukaryotic, bacterial and archaeal proteins in relation to function, conservation and environmental factors. Comparing Eukaryotes and Prokaryotes, we found that the greater length of eukaryotic proteins is pervasive over all functional categories and involves the vast majority of protein families. The magnitude of these differences suggests that the evolution of eukaryotic proteins was influenced by processes of fusion of single-function proteins into extended multi-functional and multi-domain proteins. Comparing Bacteria and Archaea, we determined that the small but significant length difference observed between their proteins results from a combination of three factors: (i) bacterial proteomes include a greater proportion than archaeal proteomes of longer proteins involved in metabolism or cellular processes, (ii) within most functional classes, protein families unique to Bacteria are generally longer than protein families unique to Archaea and (iii) within the same protein family, homologs from Bacteria tend to be longer than the corresponding homologs from Archaea. These differences are interpreted with respect to evolutionary trends and prevailing environmental conditions within the two prokaryotic groups.


  • [Articles] Real-time expression profiling of microRNA precursors in human cancer cell lines -

    Our previous study described a real-time PCR method to quantify microRNA (miRNA) precursors using SYBR green detection [T. D. Schmittgen, J. Jiang, Q. Liu and L. Yang (2004) Nucleic Acids Res., 32, e43]. The present study adapted the assay to a 384-well format and expanded it to include primers to 222 human miRNA precursors. TaqMan minor groove binder probes were used to discriminate nearly identical members of the let-7 family of miRNA isoforms. The miRNA precursor expression was profiled in 32 human cell lines from lung, breast, colorectal, hematologic, prostate, pancreatic, and head and neck cancers. Some miRNA precursors were expressed at similar levels in many of the cell lines, while others were differentially expressed. Clustering analysis of the miRNA precursor expression data revealed that most of the cell lines clustered into their respective tissues from which each cell line was ostensibly derived. miRNA precursor expression by PCR paralleled the mature miRNA expression by northern blotting for most of the conditions studied. Our study provides PCR primer sequences to all of the known human miRNA precursors as of December 2004 and provides a database of the miRNA precursor expression in many commonly used human cancer cell lines.


  • [Articles] Recognizing the pseudogenes in bacterial genomes -

    Pseudogenes are now known to be a regular feature of bacterial genomes and are found in particularly high numbers within the genomes of recently emerged bacterial pathogens. As most pseudogenes are recognized by sequence alignments, we use newly available genomic sequences to identify the pseudogenes in 11 genomes from 4 bacterial genera, each of which contains at least 1 human pathogen. The numbers of pseudogenes range from 27 in Staphylococcus aureus MW2 to 337 in Yersinia pestis CO92 (e.g. 1–8% of the annotated genes in the genome). Most pseudogenes are formed by small frameshifting indels, but because stop codons are A + T-rich, the two low-G + C Gram-positive taxa (Streptococcus and Staphylococcus) have relatively high fractions of pseudogenes generated by nonsense mutations when compared with more G + C-rich genomes. Over half of the pseudogenes are produced from genes whose original functions were annotated as ‘hypothetical’ or ‘unknown’; however, several broadly distributed genes involved in nucleotide processing, repair or replication have become pseudogenes in one of the sequenced Vibrio vulnificus genomes. Although many of our comparisons involved closely related strains with broadly overlapping gene inventories, each genome contains a largely unique set of pseudogenes, suggesting that pseudogenes are formed and eliminated relatively rapidly from most bacterial genomes.


  • [Articles] Reconstitution of archaeal H/ACA small ribonucleoprotein complexes active in pseudouridylation -

    Pseudouridine () are frequently modified residues in RNA. In Eukarya, their formation is catalyzed by enzymes or by ribonucleoprotein complexes (RNPs) containing H/ACA snoRNAs. H/ACA sRNA and putative ORFs for H/ACA sRNP proteins (L7Ae, aCBF5, aNOP10 and aGAR1) were found in Archaea. Here, by using Pyrococcus abyssi recombinant proteins and an in vitro transcribed P.abyssi H/ACA sRNA, we obtained the first complete in vitro reconstitution of an active H/ACA RNP. Both L7Ae and the aCBF5 RNA: synthase bind directly the sRNA; aCBF5 also interacts directly and independently with aNOP10 and aGAR1. Presence of aCBF5, aNOP10 and a U residue at the pseudouridylation site in the target RNA are required for RNA target recruitment. In agreement, we found that the aCBF5–aNOP10 pair is the minimal set of proteins needed for the formation of a particle active for pseudouridylation. However, particles more efficient in targeted pseudouridylation can be formed with the addition of proteins L7Ae and/or aGAR1. Although necessary for optimal activity, the conserved ACA motif in the sRNA was found to be not essential.


  • [Articles] Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization -

    Prediction of structural changes resulting from complex formation, both in ligands and receptors, is an important and unsolved problem in structural biology. In this work, we use all-atom normal modes calculated with the Elastic Network Model as a basis set to model structural flexibility during formation of macromolecular complexes and refine the non-bonded intermolecular energy between the two partners (protein–ligand or protein–DNA) along 5–10 of the lowest frequency normal mode directions. The method handles motions unrelated to the docking transparently by first applying the modes that improve non-bonded energy most and optionally restraining amplitudes; in addition, the method can correct small errors in the ligand position when the first six rigid-body modes are switched on. For a test set of six protein receptors that show an open-to-close transition when binding small ligands, our refinement scheme reduces the protein coordinate cRMS by 0.3–3.2 Å. For two test cases of DNA structures interacting with proteins, the program correctly refines the docked B-DNA starting form into the expected bent DNA, reducing the DNA cRMS from 8.4 to 4.8 Å and from 8.7 to 5.4 Å, respectively. A public web server implementation of the refinement method is available at http://lorentz.immstr.pasteur.fr.


  • [Articles] Regulation of expression by promoters versus internal ribosome entry site in the 5'-untranslated sequence of the human cyclin-dependent kinase inhibitor p27kip1 -

    p27kip1 regulates cell proliferation by binding to and inhibiting the activity of cyclin-dependent kinases and its expression oscillates with cell cycle. Recently, it has been suggested from studies using the traditional dicistronic DNA assay that the expression of p27kip1 is regulated by internal ribosome entry site (IRES)-mediated translation initiation, and several RNA-binding protein factors were thought to play some role in this regulation. Considering the inevitable drawbacks of the dicistronic DNA assay, which could mislead a promoter activity or alternative splicing to IRES as previously demonstrated, we decided to reanalyze the 5'-untranslated region (5'-UTR) sequence of p27kip1 and test whether it contains an IRES element or a promoter using more stringent methods, such as dicistronic RNA and promoterless dicistronic and monocistronic DNA assays. We found that the 5'-UTR sequence of human p27kip1 does not have any significant IRES activity. The previously observed IRES activities are likely generated from the promoter activities present in the 5'-UTR sequences of p27kip1. The findings in this study indicate that transcriptional regulation likely plays an important role in p27kip1 expression, and the mechanism of regulation of p27 expression by RNA-binding factors needs to be re-examined. The findings in this study also further enforce the importance that more stringent studies, such as promoterless dicistronic and monocistronic DNA and dicistronic RNA tests, are required to safeguard any future claims of cellular IRES.


  • [Articles] Regulation of multiple insulin-like growth factor binding protein genes by 1{alpha},25-dihydroxyvitamin D3 -

    Recently, insulin-like growth factor binding proteins (IGFBPs) have been found to be primary mediators of the anti-proliferative actions of the nuclear hormone 1,25-dihydroxyvitamin D3 [1,25(OH)2D3], but dependent on cellular context IGFBPs can also have a mitogenic effect. In this study, we performed expression profiling of all six human IGFBP genes in prostate and bone cancer cells and demonstrated that IGFBP1, 3 and 5 are primary 1,25(OH)2D3 target genes. In silico screening of the 174 kb of genomic sequence surrounding all six IGFBP genes identified 15 candidate vitamin D response elements (VDREs) close to or in IGFBP1, 2, 3 and 5 but not in the IGFBP4 and 6 genes. The putative VDREs were evaluated in vitro by gelshift assays and in living cells by reporter gene and chromatin immuno-precipitation (ChIP) assays. Of these 10 VDREs appear to be functional. ChIP assays demonstrated for each of these an individual, stimulation time-dependent association profile not only with the vitamin D receptor, but also with first heterodimeric partner the retinoid X receptor, other regulatory complex components and phosphorylated RNA polymerase II. Some of the VDREs are located distantly from the transcription start sites of IGFBP1, 3 and 5, but all 10 VDREs seem to contribute to the regulation of the genes by 1,25(OH)2D3. In conclusion, IGFBP1, 3 and 5 are primary 1,25(OH)2D3 target genes that in intact cells are each under the control of multiple VDREs.


  • [Articles] Replication-mediated instability of the GAA triplet repeat mutation in Friedreich ataxia -

    Friedreich ataxia is caused by the expansion of a polymorphic and unstable GAA triplet repeat in the FRDA gene, but the mechanisms for its instability are poorly understood. Replication of (GAA•TTC)n sequences (9–105 triplets) in plasmids propagated in Escherichia coli displayed length- and orientation-dependent instability. There were small length variations upon replication in both orientations, but large contractions were frequently observed when GAA was the lagging strand template. DNA replication was also significantly slower in this orientation. To evaluate the physiological relevance of our findings, we analyzed peripheral leukocytes from human subjects carrying repeats of similar length (8–107 triplets). Analysis of 9400 somatic FRDA molecules using small-pool PCR revealed a similar mutational spectrum, including large contractions. The threshold length for the initiation of somatic instability in vivo was between 40 and 44 triplets, corresponding to the length of a eukaryotic Okazaki fragment. Consistent with the stabilization of premutation alleles during germline transmission, we also found that instability of somatic cells in vivo and repeats propagated in E.coli were abrogated by (GAGGAA)n hexanucleotide interruptions. Our data demonstrate that the GAA triplet repeat mutation in Friedreich ataxia is destabilized, frequently undergoing large contractions, during DNA replication.


  • [Articles] REV1 accumulates in DNA damage-induced nuclear foci in human cells and is implicated in mutagenesis by benzo[a]pyrenediolepoxide -

    The REV1 gene encodes a Y-family DNA polymerase that has been postulated to have both catalytic and structural functions in translesion replication past UV photoproducts in mammalian cells. To examine if REV1 is implicated in DNA damage tolerance mechanisms after exposure of human cells to a chemical carcinogen, we generated a plasmid expressing REV1 protein fused at its C-terminus with green fluorescent protein (GFP). In transient transfection experiments, virtually all of the transfected cells had a diffuse nuclear pattern in the absence of carcinogen exposure. In contrast, in cells exposed to benzo[a]pyrenediolepoxide, the fusion protein accumulated in a focal pattern in the nucleus in 25% of the cells, and co-localized with PCNA. These data support the idea that REV1 is present at stalled replication forks. We also examined the mutagenic response at the HPRT locus of human cells that had greatly reduced levels of REV1 mRNA due to the stable expression of gene-specific ribozymes, and compared them to wild-type cells. The mutant frequency was greatly reduced in the ribozyme-expressing cells. These data indicate that REV1 is implicated in the mutagenic DNA damage tolerance response to BPDE and support the development of strategies to target this protein to prevent such mutations.


  • [Articles] RNase III cleavage demonstrates a long range RNA: RNA duplex element flanking the hepatitis C virus internal ribosome entry site -

    Here, we show that Escherichia coli Ribonuclease III cleaves specifically the RNA genome of hepatitis C virus (HCV) within the first 570 nt with similar efficiency within two sequences which are ~400 bases apart in the linear HCV map. Demonstrations include determination of the specificity of the cleavage sites at positions C27 and U33 in the first (5') motif and G439 in the second (3') motif, complete competition inhibition of 5' and 3' HCV RNA cleavages by added double-stranded RNA in a 1:6 to 1:8 weight ratio, respectively, 50% reverse competition inhibition of the RNase III T7 R1.1 mRNA substrate cleavage by HCV RNA at 1:1 molar ratio, and determination of the 5' phosphate and 3' hydroxyl end groups of the newly generated termini after cleavage. By comparing the activity and specificity of the commercial RNase III enzyme, used in this study, with the natural E.coli RNase III enzyme, on the natural bacteriophage T7 R1.1 mRNA substrate, we demonstrated that the HCV cuts fall into the category of specific, secondary RNase III cleavages. This reaction identifies regions of unusual RNA structure, and we further showed that blocking or deletion of one of the two RNase III-sensitive sequence motifs impeded cleavage at the other, providing direct evidence that both sequence motifs, besides being far apart in the linear RNA sequence, occur in a single RNA structural motif, which encloses the HCV internal ribosome entry site in a large RNA loop.


  • [Articles] RNase P: role of distinct protein cofactors in tRNA substrate recognition and RNA-based catalysis -

    The Escherichia coli ribonuclease P (RNase P) has a protein component, termed C5, which acts as a cofactor for the catalytic M1 RNA subunit that processes the 5' leader sequence of precursor tRNA. Rpp29, a conserved protein subunit of human RNase P, can substitute for C5 protein in reconstitution assays of M1 RNA activity. To better understand the role of the former protein, we compare the mode of action of Rpp29 to that of the C5 protein in activation of M1 RNA. Enzyme kinetic analyses reveal that complexes of M1 RNA–Rpp29 and M1 RNA–C5 exhibit comparable binding affinities to precursor tRNA but different catalytic efficiencies. High concentrations of substrate impede the activity of the former complex. Rpp29 itself exhibits high affinity in substrate binding, which seems to reduce the catalytic efficiency of the reconstituted ribonucleoprotein. Rpp29 has a conserved C-terminal domain with an Sm-like fold that mediates interaction with M1 RNA and precursor tRNA and can activate M1 RNA. The results suggest that distinct protein folds in two unrelated protein cofactors can facilitate transition from RNA- to ribonucleoprotein-based catalysis by RNase P.


  • [Articles] Selection of novel mediators of E2F1-induced apoptosis through retroviral expression of an antisense cDNA library -

    The E2F1 transcription factor is an essential mediator of p53-dependent and p53-independent apoptosis as part of an anti-tumour safeguard mechanism. In this study, a functional so-called technical knockout (TKO) approach was applied to Saos-2ERE2F1 cells that conditionally activate E2F1 by the addition of 4-hydroxytamoxifen to search for p53-independent pro-apoptotic E2F1 targets. The approach was based on random inactivation of genes after retroviral transfer of an antisense cDNA library enriched of E2F1-induced genes, followed by the selection of Saos-2ERE2F1 cells that survive in the presence of the apoptotic stimulus. We identified 13 novel E2F1 target genes encoding proteins of known cellular function, including apoptosis and RNA binding. FACS analysis revealed that E2F1-induced apoptosis was significantly attenuated in cell clones containing the antisense cDNA fragments of these genes, demonstrating their participation in E2F1 death pathways. Moreover, inactivation of the target genes resulted in a clear increase of cell viability (>80%) in response to E2F1 activation compared with controls (~30%). Four genes showed an increase in expression intensity in the presence of cycloheximide, suggesting a direct effect of E2F1 on gene transcription, whereas one gene was identified as an indirect target. Our data provide new insight in the regulation of E2F1-induced apoptosis.


  • [Articles] Sequence determination of nucleic acids containing 5-methylisocytosine and isoguanine: identification and insight into polymerase replication of the non-natural nucleobases -

    Nucleobase analogs 5-methylisocytosine (MeisoC) and isoguanine (isoG) form a non-natural base pair in duplex nucleic acids with base pairing specificity orthogonal to the natural nucleobase pairs. Sequencing reactions were conducted with oligodeoxyribonucleotides (ODNs) containing dMeisoC and disoG using modified pyrosequencing and dye terminator methods. Modified dye terminator sequencing was generally useful for the sequence identification of ODNs containing the non-natural nucleobases. The two sequencing methods were also used to monitor nucleotide incorporation and subsequent extension by Family A polymerases used in the sequencing methods with a six-nucleobase system that includes dMeisoC and disoG. Nucleic acids containing the six-nucleobase system could be replicated well, but not as well as natural nucleic acids, especially in regions of high dMeisoC–disoG content. Challenges in replication with dMeisoC–disoG are consistent with nucleobase tautomerism in the insertion step and disrupted minor groove nucleobase pair–polymerase contacts in subsequent extension.


  • [Articles] siRNA-mediated off-target gene silencing triggered by a 7 nt complementation -

    A growing body of evidence suggests that siRNA could generate off-target effects through different mechanisms. However, the full impact of off-target gene regulation on phenotypic induction and accordingly on data interpretation in the context of large-scale siRNA library screen has not been reported. Here we report on off-target gene silencing effects observed in a large-scale knockdown experiment designed to identify novel regulators of the HIF-1 pathway. All of the three ‘top hits’ from our screen have been demonstrated to result from off-target gene silencing. Two of the three ‘siRNA hits’ were found to directly trigger down-regulation of hif-1 mRNA through a 7 nt motif, AGGCAGT, that is present in both the hif-1 mRNA and the siRNAs. Further analysis revealed that the generation of off-target gene silencing via this 7 nt motif depends on the characteristics of the target mRNA, including the sequence context surrounding the complementary region, the position of the complementary region in the mRNA and the copy number of the complementary region. Interestingly, the off-target siRNA against hif-1 was also shown to trigger mRNA degradation with high probability of other genes that possess multiple copies of the AGGCAGT motif in the 3'-untranslated region. Lessons learned from this study will be a valuable asset to aid in designing siRNAs with more stringent target selectivity and improving ‘hits-follow-up’ strategies for future large-scale knockdown experiments.


  • [Articles] Solution structure of the DNA-binding domain of RPA from Saccharomyces cerevisiae and its interaction with single-stranded DNA and SV40 T antigen -

    Replication protein A (RPA) is a three-subunit complex with multiple roles in DNA metabolism. DNA-binding domain A in the large subunit of human RPA (hRPA70A) binds to single-stranded DNA (ssDNA) and is responsible for the species-specific RPA–T antigen (T-ag) interaction required for Simian virus 40 replication. Although Saccharomyces cerevisiae RPA70A (scRPA70A) shares high sequence homology with hRPA70A, the two are not functionally equivalent. To elucidate the similarities and differences between these two homologous proteins, we determined the solution structure of scRPA70A, which closely resembled the structure of hRPA70A. The structure of ssDNA-bound scRPA70A, as simulated by residual dipolar coupling-based homology modeling, suggested that the positioning of the ssDNA is the same for scRPA70A and hRPA70A, although the conformational changes that occur in the two proteins upon ssDNA binding are not identical. NMR titrations of hRPA70A with T-ag showed that the T-ag binding surface is separate from the ssDNA-binding region and is more neutral than the corresponding part of scRPA70A. These differences might account for the species-specific nature of the hRPA70A–T-ag interaction. Our results provide insight into how these two homologous RPA proteins can exhibit functional differences, but still both retain their ability to bind ssDNA.


  • [Articles] Specific binding of the methyl binding domain protein 2 at the BRCA1-NBR2 locus -

    The methyl-CpG binding domain (MBD) proteins are key molecules in the interpretation of DNA methylation signals leading to gene silencing. We investigated their binding specificity at the constitutively methylated region of a CpG island containing the bidirectional promoter of the Breast cancer predisposition gene 1, BRCA1, and the Near BRCA1 2 (NBR2) gene. In HeLa cells, quantitative chromatin immunoprecipitation assays indicated that MBD2 is associated with the methylated region, while MeCP2 and MBD1 were not detected at this locus. MBD2 depletion (~90%), mediated by a transgene expressing a small interfering RNA (siRNA), did not induce MeCP2 or MBD1 binding at the methylated area. Furthermore, the lack of MBD2 at the BRCA1-NBR2 CpG island is associated with an elevated level of NBR2 transcripts and with a significant reduction of induced-DNA-hypomethylation response. In MBD2 knockdown cells, transient expression of a Mbd2 cDNA, refractory to siRNA-mediated decay, shifted down the NBR2 mRNA level to that observed in unmodified HeLa cells. Variations in MBD2 levels did not affect BRCA1 expression despite its stimulation by DNA hypomethylation. Collectively, our data indicate that MBD2 has specific targets and its presence at these targets is indispensable for gene repression.


  • [Articles] sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes -

    Small non-coding bacterial RNAs (sRNAs) play important regulatory roles in a variety of cellular processes. Nearly all known sRNAs have been identified in Escherichia coli and most of these are not conserved in the majority of other bacterial species. Many of the E.coli sRNAs were initially predicted through bioinformatic approaches based on their common features, namely that they are encoded between annotated open reading frames and are flanked by predictable transcription signals. Because promoter consensus sequences are undetermined for most species, the successful use of bioinformatics to identify sRNAs in bacteria other than E.coli has been limited. We have created a program, sRNAPredict, which uses coordinate-based algorithms to integrate the respective positions of individual predictive features of sRNAs and rapidly identify putative intergenic sRNAs. Relying only on sequence conservation and predicted Rho-independent terminators, sRNAPredict was used to search for sRNAs in Vibrio cholerae. This search identified 9 of the 10 known or putative V.cholerae sRNAs and 32 candidates for novel sRNAs. Small transcripts for 6 out of 9 candidate sRNAs were observed by Northern analysis. Our findings suggest that sRNAPredict can be used to efficiently identify novel sRNAs even in bacteria for which promoter consensus sequences are not available.


  • [Articles] Stabilizing contributions of sulfur-modified nucleotides: crystal structure of a DNA duplex with 2'-O-[2-(methoxy)ethyl]-2-thiothymidines -

    Substitution of oxygen atoms by sulfur at various locations in the nucleic acid framework has led to analogs such as the DNA phosphorothioates and 4'-thio RNA. The phosphorothioates are excellent mimics of DNA, exhibit increased resistance to nuclease degradation compared with the natural counterpart, and have been widely used as first-generation antisense nucleic acid analogs for applications in vitro and in vivo. The 4'-thio RNA analog exhibits significantly enhanced RNA affinity compared with RNA, and shows potential for incorporation into siRNAs. 2-Thiouridine (s2U) and 5-methyl-2-thiouridine (m5s2U) are natural nucleotide analogs. s2U in tRNA confers greater specificity of codon–anticodon interactions by discriminating more strongly between A and G compared with U. 2-Thio modification preorganizes the ribose and 2'-deoxyribose sugars for a C3'-endo conformation, and stabilizes heteroduplexes composed of modified DNA and complementary RNA. Combination of the 2-thio and sugar 2'-O-modifications has been demonstrated to boost both thermodynamic stability and nuclease resistance. Using the 2'-O-[2-(methoxy)ethyl]-2-thiothymidine (m5s2Umoe) analog, we have investigated the consequences of the replacement of the 2-oxygen by sulfur for base-pair geometry and duplex conformation. The crystal structure of the A-form DNA duplex with sequence GCGTAT*ACGC (T* = m5s2Umoe) was determined at high resolution and compared with the structure of the corresponding duplex with T* = m5Umoe. Notable changes as a result of the incorporation of sulfur concern the base-pair parameter ‘opening’, an improvement of stacking in the vicinity of modified nucleotides as measured by base overlap, and a van der Waals interaction between sulfur atoms from adjacent m5s2Umoe residues in the minor groove. The structural data indicate only minor adjustments in the water structure as a result of the presence of sulfur. The observed small structural perturbations combined with the favorable consequences for pairing stability and nuclease resistance (when combined with 2'-O-modification) render 2-thiouracil-modified RNA a promising candidate for applications in RNAi.


  • [Articles] Stable transmission of targeted gene modification using single-stranded oligonucleotides with flanking LNAs -

    Targeted mutagenesis directed by oligonucleotides (ONs) is a promising method for manipulating the genome in higher eukaryotes. In this study, we have compared gene editing by different ONs on two new target sequences, the eBFP and the rd1 mutant photoreceptor ßbeta;PDE cDNAs, which were integrated as single copy transgenes at the same genomic site in 293T cells. Interestingly, antisense ONs were superior to sense ONs for one target only, showing that target sequence can by itself impart strand-bias in gene editing. The most efficient ONs were short 25 nt ONs with flanking locked nucleic acids (LNAs), a chemistry that had only been tested for targeted nucleotide mutagenesis in yeast, and 25 nt ONs with phosphorothioate linkages. We showed that LNA-modified ONs mediate dose-dependent target modification and analyzed the importance of LNA position and content. Importantly, when using ONs with flanking LNAs, targeted gene modification was stably transmitted during cell division, which allowed reliable cloning of modified cells, a feature essential for further applications in functional genomics and gene therapy. Finally, we showed that ONs with flanking LNAs aimed at correcting the rd1 stop mutation could promote survival of photoreceptors in retinas of rd1 mutant mice, suggesting that they are also active in vivo.


  • [Articles] Stimulation of the XPB ATP-dependent helicase by the beta subunit of TFIIE -

    TFIIE and TFIIH are essential for the promoter opening and escape that occurs as RNA polymerase II transits into early elongation. XPB, a subunit of TFIIH, contains an ATP-dependent helicase activity that is used in both of these processes. Here, we show that the smaller beta subunit of TFIIE stimulates the XPB helicase and ATPase activities. The larger alpha subunit can use its known inhibitory activity to moderate the stimulation by the beta subunit. Regions of TFIIE beta required for the helicase stimulation were identified. Mutants were constructed that are defective in stimulating the XPB helicase but still allow intact TFIIE to bind and recruit XPB and TFIIH to form the pre-initiation complex. In a test for the functional significance of the stimulatory effect of TFIIE beta, these mutant forms of TFIIE were shown to be defective in a transcription assay on linear DNA. The data suggest that the beta subunit of TFIIE is an ATPase and helicase co-factor that can assist the XPB subunit of TFIIH during transcription initiation and the transition to early elongation, enhancing the potential diversity of regulatory targets.


  • [Articles] Structural and DNA-binding studies on the bovine antimicrobial peptide, indolicidin: evidence for multiple conformations involved in binding to membranes and DNA -

    Indolicidin, a l3-residue antimicrobial peptide-amide, which is unusually rich in tryptophan and proline, is isolated from the cytoplasmic granules of bovine neutrophils. In this study, the structures of indolicidin in 50% D3-trifluoroethanol and in the absence and presence of SDS and D38-dodecylphosphocholine were determined using NMR spectroscopy. Multiple conformations were found and were shown to be due to different combinations of contact between the two WPW motifs. Although indolicidin is bactericidal and able to permeabilize bacterial membranes, it does not lead to cell wall lysis, showing that there is more than one mechanism of antimicrobial action. The structure of indolicidin in aqueous solution was a globular and amphipathic conformation, differing from the wedge shape adopted in lipid micelles, and these two structures were predicted to have different functions. Indolicidin, which is known to inhibit DNA synthesis and induce filamentation of bacteria, was shown to bind DNA in gel retardation and fluorescence quenching experiments. Further investigations using surface plasmon resonance confirmed the DNA-binding ability and showed the sequence preference of indolicidin. Based on our biophysical studies and previous results, we present a diagram illustrating the DNA-binding mechanism of the antimicrobial action of indolicidin and explaining the roles of the peptide when interacting with lipid bilayers at different concentrations.


  • [Articles] Structural and functional characterizations reveal the importance of a zinc binding domain in Bloom's syndrome helicase -

    Bloom's syndrome (BS) is an autosomal recessive human disorder characterized by genomic instability and a predisposition to a wide variety of cancers. The gene mutated in BS, BLM, encodes a protein containing three domains: an N-terminal domain whose function remains elusive, a helicase domain characterized by seven ‘signature’ motifs conserved in a wide range of helicases and a C-terminal extension that can be further divided into two sub-domains: RecQ-Ct and HRDC. The RecQ-Ct domain appears essential because two point-mutations altering highly conserved cysteine residues within this domain have been found in BS patients. We report herein that BLM contains a zinc ion. Modelling studies suggest that four conserved cysteine residues within the RecQ-Ct domain coordinate this zinc ion and subsequent mutagenesis studies further confirm this prediction. Biochemical and biophysical studies show that the ATPase, helicase and DNA binding activities of the mutants are severely modified. Structural analysis of both wild-type and mutant proteins reveal that alteration of cysteine residues does not significantly change the overall conformation. The observed defects in ATPase and helicase activities were inferred to result from a compromise of DNA binding. Our results implicate an important role of this zinc binding domain in both DNA binding and protein conformation. They could be pivotal for understanding the molecular basis of BS disease.


  • [Articles] Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes -

    During the process of transcription, RNA polymerase can exactly locate a promoter sequence in the complex maze of a genome. Several experimental studies and computational analyses have shown that the promoter sequences apparently possess some special properties, such as unusual DNA structures and low stability, which make them distinct from the rest of the genome. But most of these studies have been carried out on a particular set of promoter sequences or on promoter sequences from similar organisms. To examine whether the promoters from a wide variety of organisms share these special properties, we have carried out an analysis of sets of promoters from bacteria, vertebrates and plants. These promoters were analyzed with respect to the prediction of three different properties, such as DNA curvature, bendability and stability, which are relevant to transcription. All the promoter sequences are predicted to share certain features, such as stability and bendability profiles, but there are significant differences in DNA curvature profiles and nucleotide composition between the different organisms. These similarities and differences are correlated with some of the known facts about transcription process in the promoters from the three groups of organisms.


  • [Articles] Structure of RadB recombinase from a hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1: an implication for the formation of a near-7-fold helical assembly -

    The X-ray crystal structure of RadB from Thermococcus kodakaraensis KOD1, an archaeal homologue of the RecA/Rad51 family proteins, have been determined in two crystal forms. The structure represents the core ATPase domain of the RecA/Rad51 proteins. Two independent molecules in the type 1 crystal were roughly related by 7-fold screw symmetry whereas non-crystallographic 2-fold symmetry was observed in the type 2 crystal. The dimer structure in the type 1 crystal is extended to construct a helical assembly, which resembles the filamentous structures reported for other RecA/Rad51 proteins. The molecular interface in the type 1 dimer is formed by facing a basic surface patch of one monomer to an acidic one of the other. The empty ATP binding pocket is located at the interface and barely concealed from the outside similarly to that in the active form of the RecA filament. The model assembly has a positively charged belt on one surface bordering the helical groove suitable for facile binding of DNA. Electron microscopy has revealed that, in the absence of ATP and DNA, RadB forms a filament with a similar diameter to that of the hypothetical assembly, although its helical properties were not confirmed.


  • [Articles] Structure, internal motions and association-dissociation kinetics of the i-motif dimer of d(5mCCTCACTCC) -

    At slightly acidic pH, the association of two d(5mCCTCACTCC) strands results in the formation of an i-motif dimer. Using NMR methods, we investigated the structure of [d(5mCCTCACTCC)]2, the internal motion of the base pairs stacked in the i-motif core, the dimer formation and dissociation kinetics versus pH. The excellent resolution of the 1H and 31P spectra provided the determination of dihedral angles, which together with a large set of distance restraints, improve substantially the definition of the sugar-phosphate backbone by comparison with previous NMR studies of i-motif structures. [d(5mCCTCACTCC)]2 is built by intercalation of two symmetrical hairpins held together by six symmetrical C•C+ pairs and by pair T7•T7. The hairpin loops that are formed by a single residue, A5, cross the narrow grooves on the same side of the i-motif core. The base pair intercalation order is C9•C9+/5mC1•5mC1+/C8•C8+/C2•C2+/T7.T7/C6•C6+/C4•C4+. The T3 bases are flipped out in the wide grooves. The core of the structure includes four long-lived pairs whose lifetimes at 15°C range from 100 s (C8•C8+) to 0.18 s (T7•T7). The formation rate and the lifetime of [d(5mCCTCACTCC)]2 were measured between pH 6.8 and 4.8. The dimer formation rate is three to four magnitude orders slower than that of a B-DNA duplex. It depends on pH, as it must occur for a bimolecular process involving non cooperative association of neutral and protonated residues. In the range of pH investigated, the dimer lifetime, 500 s at 0°C, pH 6.8, varies approximately as 10–pH.


  • [Articles] Sub-array normalization subject to differentiation -

    From microarray measurement, we seek differentiation of mRNA expressions among different biological samples. However, each array has a ‘block effect’ due to uncontrolled variation. The statistical treatment of reducing the block effect is usually referred to as normalization. Our perspective is to find a transformation that matches the distributions of hybridization levels of those probes corresponding to undifferentiated genes between arrays. We address two important issues. First, array-specific spatial patterns exist due to uneven hybridization and measurement process. Second, in some cases a substantially large portion of genes are differentially expressed between a target and a reference array. For the purpose of normalization we need to identify a subset that exclude those probes corresponding to differentially expressed genes and abnormal probes due to experimental variation. Least trimmed squares (LTS) is a natural choice to achieve this goal. Substantial differentiation is protected in LTS by setting an appropriate trimming fraction. To take into account any spatial pattern of hybridization, we divide each array into sub-arrays and normalize probe intensities within each sub-array. We illustrate the problem and solution through an Affymetrix spike-in dataset with defined perturbation and a dataset of primate brain expression.


  • [Articles] Synergistic defect in 60S ribosomal subunit assembly caused by a mutation of Rrs1p, a ribosomal protein L11-binding protein, and 3'-extension of 5S rRNA in Saccharomyces cerevisiae -

    Rrs1p, a ribosomal protein L11-binding protein, has an essential role in biogenesis of 60S ribosomal subunits. We obtained conditionally synthetic lethal allele with the rrs1-5 mutation and determined that the mutation is in REX1, which encodes an exonuclease. The highly conserved leucine at 305 was substituted with tryptophan in rex1-1. The rex1-1 allele resulted in 3'-extended 5S rRNA. Polysome analysis revealed that rex1-1 and rrs1-5 caused a synergistic defect in the assembly of 60S ribosomal subunits. In vivo and in vitro binding assays indicate that Rrs1p interacts with the ribosomal protein L5–5S rRNA complex. The rrs1-5 mutation weakens the interaction between Rrs1p with both L5 and L11. These data suggest that the assembly of L5–5S rRNA on 60S ribosomal subunits coordinates with assembly of L11 via Rrs1p.


  • [Articles] Syntheses of 4'-thioribonucleosides and thermodynamic stability and crystal structure of RNA oligomers with incorporated 4'-thiocytosine -

    A facile synthetic route for the 4'-thioribonucleoside building block 4'SN (N = U, C, A and G) with the ribose O4' replaced by sulfur is presented. Conversion of l-lyxose to 1,5-di-O-acetyl-2,3-di-O-benzoyl-4-thio-d-ribofuranose was achieved via an efficient four-step synthesis with high yield. Conversion of the thiosugar into the four ribonucleoside phosphoramidite building blocks was accomplished with additional four steps in each case. Incorporation of 4'-thiocytidines into oligoribonucleotides improved the thermal stability of the corresponding duplexes by ~1°C per modification, irrespective of whether the strand contained a single modification or a consecutive stretch of 4'SC residues. The gain in thermodynamic stability is comparable to that observed with oligoribonucleotides containing 2'-O-methylated residues. To establish potential conformational changes in RNA as a result of the 4'-thio modification and to better understand the origins of the observed stability changes, the crystal structure of the oligonucleotide 5'-r(CC4'SCCGGGG) was determined and analyzed using the previously solved structure of the native RNA octamer as a reference. The two 4'-thioriboses adopt conformations that are very similar to the C3'-endo pucker observed for the corresponding sugars in the native duplex. Subtle changes in the local geometry of the modified duplex are mostly due to the larger radius of sulfur compared to oxygen or appear to be lattice-induced. The significantly increased RNA affinity of 4'-thio-modified RNA relative to RNA, and the relatively minor conformational changes caused by the modification render this nucleic acid analog an interesting candidate for in vitro and in vivo applications, including use in RNA interference (RNAi), antisense, ribozyme, decoy and aptamer technologies.


  • [Articles] Telomere structure and shortening in telomerase-deficient Trypanosoma brucei -

    Telomerase consists of a reverse transcriptase (TERT) and an RNA that contains a template for telomere-repeat extension. Telomerase is required to prevent telomere erosion and its activity or lack thereof is important for tumorigenesis and ageing. Telomerase has been identified in numerous organisms but it has not been studied in kinetoplastid protozoa. Trypanosoma brucei, the causative agent of African sleeping sickness, evades the host immune response by frequently changing its variant surface glycoprotein (VSG). The single expressed VSG is transcribed from one of ~20 subtelomeric ‘Expression Sites’, but the role telomeres might play in regulating VSG transcription and switching is unknown. We identified and sequenced the T.brucei TERT gene. Deleting TERT resulted in progressive telomere shortening of 3–6 bp per generation. In other organisms, the rate of telomere shortening is proportional to the length of the terminal 3' single-strand overhang. In T.brucei, G-overhangs were undetectable (<30 nt) by in-gel hybridization. The rate of telomere shortening therefore, agrees with the predicted shortening due to the end replication problem, and is consistent with our observation that G-overhangs are short. Trypanosomes whose telomere length can be manipulated provide a new tool to investigate the role of telomeres in antigenic variation.


  • [Articles] Testing the conservation of the translational machinery over evolution in diverse environments: assaying Thermus thermophilus ribosomes and initiation factors in a coupled transcription-translation system from Escherichia coli -

    Ribosomes from the extreme thermophile Thermus thermophilus are capable of translation in a coupled transcription–translation system derived from Escherichia coli. At 45°C, T.thermophilus ribosomes translate at ~25–30% of the maximal rate of E.coli ribosomes, and synthesize full-length protein. T.thermophilus and E.coli subunits can be combined to effect translation, with the spectrum of proteins produced depending upon the source of the 30S subunit. In this system, T.thermophilus ribosomes function in concert with E.coli translational factors and tRNAs, with elongation and release factors being supplied from the E.coli extract, and purified initiation factors (IFs) being added exogenously. Cloned and purified T.thermophilus IF1, IF2 and IF3 supported the synthesis of the same products in vitro as the E.coli factors, although the relative levels of some polypeptides were factor dependent. We conclude that, at least between these two phylogenetically distant species, translational factor function and subunit–subunit interactions are conserved. This functional compatibility is remarkable given the extreme and highly divergent environments to which these species have adapted.


  • [Articles] The 5S rRNA maturase, ribonuclease M5, is a Toprim domain family member -

    The maturation of 5S ribosomal RNA in low G+C Gram-positive bacteria is catalyzed by a highly conserved, ~190 residue, enzyme, called ribonuclease M5 (RNase M5). Sequence alignment had predicted that the N-terminal half of RNase M5 would consist of a Toprim domain, a protein fold found in type IA and type II topoisomerases, DnaG-like primases, OLD family nucleases and RecR proteins [L. Aravind, D. D. Leipe and E. V. Koonin (1998) Nucleic Acids Res., 26, 4205–4213]. Here, we present structural modelling data and a mutational analysis of RNase M5 that confirms this hypothesis. The N-terminal half of RNase M5 can be fitted to the Toprim domain of the DnaG catalytic core. Mutation of amino acid residues highly conserved among RNase M5 enzymes and members of the Toprim domain family showed that alteration of residues critical for topoisomerase and primase activity also had a dramatic effect on the cleavage of 5S rRNA precursor by RNase M5 both in vivo and in vitro. This suggests that the mechanisms of double-stranded RNA cleavage by RNase M5 and double-stranded DNA cleavage by members of the topoisomerase family are related.


  • [Articles] The Bloom's syndrome helicase promotes the annealing of complementary single-stranded DNA -

    The product of the gene mutated in Bloom's syndrome, BLM, is a 3'–5' DNA helicase belonging to the highly conserved RecQ family. In addition to a conventional DNA strand separation activity, BLM catalyzes both the disruption of non-B-form DNA, such as G-quadruplexes, and the branch migration of Holliday junctions. Here, we have characterized a new activity for BLM: the promotion of single-stranded DNA (ssDNA) annealing. This activity does not require Mg2+, is inhibited by ssDNA binding proteins and ATP, and is dependent on DNA length. Through analysis of various truncation mutants of BLM, we show that the C-terminal domain is essential for strand annealing and identify a 60 amino acid stretch of this domain as being important for both ssDNA binding and strand annealing. We present a model in which the ssDNA annealing activity of BLM facilitates its role in the processing of DNA intermediates that arise during repair of damaged replication forks.


  • [Articles] The CHD remodeling factor Hrp1 stimulates CENP-A loading to centromeres -

    Centromeres of fission yeast are arranged with a central core DNA sequence flanked by repeated sequences. The centromere-associated histone H3 variant Cnp1 (SpCENP-A) binds exclusively to central core DNA, while the heterochromatin proteins and cohesins bind the surrounding outer repeats. CHD (chromo-helicase/ATPase DNA binding) chromatin remodeling factors were recently shown to affect chromatin assembly in vitro. Here, we report that the CHD protein Hrp1 plays a key role at fission yeast centromeres. The hrp1 mutant disrupts silencing of the outer repeats and central core regions of the centromere and displays chromosome segregation defects characteristic for dysfunction of both regions. Importantly, Hrp1 is required to maintain high levels of Cnp1 and low levels of histone H3 and H4 acetylation at the central core region. Hrp1 interacts directly with the centromere in early S-phase when centromeres are replicated, suggesting that Hrp1 plays a direct role in chromatin assembly during DNA replication.


  • [Articles] The ELAV RNA-stability factor HuR binds the 5'-untranslated region of the human IGF-IR transcript and differentially represses cap-dependent and IRES-mediated translation -

    The type I insulin-like growth factor receptor (IGF-IR) is an integral component in the control of cell proliferation, differentiation and apoptosis. The IGF-IR mRNA contains an extraordinarily long (1038 nt) 5'-untranslated region (5'-UTR), and we have characterized a diverse series of proteins interacting with this RNA sequence which may provide for intricate regulation of IGF-IR gene expression at the translational level. Here, we report the purification and identification of one of these IGF-IR 5'-UTR-binding proteins as HuR, using a novel RNA crosslinking/RNase elution strategy. Because HuR has been predominantly characterized as a 3'-UTR-binding protein, enhancing mRNA stability and generally increasing gene expression, we sought to determine whether HuR might serve a different function in the context of its binding the IGF-IR 5'-UTR. We found that HuR consistently repressed translation initiation through the IGF-IR 5'-UTR. The inhibition of translation by HuR was concentration dependent, and could be reversed in trans by addition of a fragment of the IGF-IR 5'-UTR containing the HuR binding sites as a specific competitor, or abrogated by deletion of the third RNA recognition motif of HuR. We determined that HuR repressed translation initiation through the IGF-IR 5'-UTR in cells as well, and that siRNA knockdown of HuR markedly increased IGF-IR protein levels. Interestingly, we also found that HuR potently inhibited IGF-IR translation mediated through internal ribosome entry. Kinetic assays were performed to investigate the mechanism of translation repression by HuR and the dynamic interplay between HuR and the translation apparatus. We found that HuR, occupying a cap-distal position, significantly delayed translation initiation mediated by cap-dependent scanning, but was eventually displaced from its binding site, directly or indirectly, as a consequence of ribosomal scanning. However, HuR perpetually blocked the activity of the IGF-IR IRES, apparently arresting the IRES-associated translation pre-initiation complex in an inactive state. This function of HuR as a 5'-UTR-binding protein and dual-purpose translation repressor may be critical for the precise regulation of IGF-IR expression essential to normal cellular homeostasis.


  • [Articles] The genes encoding Arabidopsis ORC subunits are E2F targets and the two ORC1 genes are differently expressed in proliferating and endoreplicating cells -

    Initiation of eukaryotic DNA replication depends on the function of pre-replication complexes (pre-RC), one of its key component being the six subunits origin recognition complex (ORC). In spite of a significant degree of conservation among ORC proteins from different eukaryotic sources, the regulation of their availability varies considerably in different model systems and cell types. Here, we show that the six ORC genes of Arabidopsis thaliana are regulated at the transcriptional level during cell cycle and development. We found that Arabidopsis ORC genes, except AtORC5, contain binding sites for the E2F family of transcription factors. Expression of AtORC genes containing E2F binding sites peaks at the G1/S-phase. Analysis of AtORC gene expression in plants with reduced E2F activity, obtained by expressing a dominant negative version of DP, the E2F heterodimerization partner, and with increased E2F activity, obtained by inactivation of the retinoblastoma protein, led us to conclude that all AtORC genes, except AtORC5 are E2F targets. Interestingly, Arabidopsis contains two AtORC1 (a and b) genes, highly conserved at the amino acid level but with unrelated promoter sequences. AtORC1b expression is restricted to proliferating cells. However, AtORC1a is preferentially expressed in endoreplicating cells based on our analysis in endoreplicating tissues and in a mutant with altered endocycle pattern. This suggests a differential expression of the two ORC1 genes in Arabidopsis.


  • [Articles] The importance of being divisible by three in alternative splicing -

    Alternative splicing events that are conserved in orthologous genes in different species are commonly viewed as reliable evidence of authentic, functionally significant alternative splicing events. Several recent bioinformatic analyses have shown that conserved alternative exons possess several features that distinguish them from alternative exons that are species-specific. One of the most striking differences between conserved and species-specific alternative exons is the high percentage of exons that preserve the reading frame (exons whose length is an exact multiple of 3, termed symmetrical exons) among the conserved alternative exons. Here, we examined conserved alternative exons and found several features that differentiate between symmetrical and non-symmetrical alternative exons. We show that symmetrical alternative exons have a strong tendency not to disrupt protein domain structures, whereas the tendency of non-symmetrical alternative exons to overlap with different fractions of protein domains is similar to that of constitutive exons. Additionally, skipping isoforms of non-symmetrical alternative exons are strongly underrepresented, compared with their including isoforms, suggesting that skipping of a large fraction of non-symmetrical alternative exons produces transcripts that are degraded by the nonsense-mediated mRNA decay mechanism. Non-symmetrical alternative exons also show a tendency to reside in the 5' half of the CDS. These findings suggest that alternative splicing of symmetrical and non-symmetrical exons is governed by different selective pressures and serves different purposes.


  • [Articles] The influence of locked nucleic acid residues on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes -

    The influence of locked nucleic acid (LNA) residues on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes is reported. Optical melting studies indicate that LNA incorporated into an otherwise 2'-O-methyl RNA oligonucleotide usually, but not always, enhances the stabilities of complementary duplexes formed with RNA. Several trends are apparent, including: (i) a 3' terminal U LNA and 5' terminal LNAs are less stabilizing than interior and other 3' terminal LNAs; (ii) most of the stability enhancement is achieved when LNA nucleotides are separated by at least one 2'-O-methyl nucleotide; and (iii) the effects of LNA substitutions are approximately additive when the LNA nucleotides are separated by at least one 2'-O-methyl nucleotide. An equation is proposed to approximate the stabilities of complementary duplexes formed with RNA when at least one 2'-O-methyl nucleotide separates LNA nucleotides. The sequence dependence of 2'-O-methyl RNA/RNA duplexes appears to be similar to that of RNA/RNA duplexes, and preliminary nearest-neighbor free energy increments at 37°C are presented for 2'-O-methyl RNA/RNA duplexes. Internal mismatches with LNA nucleotides significantly destabilize duplexes with RNA.


  • [Articles] The involvement of the aspartate triad of the active center in all catalytic activities of multisubunit RNA polymerase -

    Three conserved aspartate residues in the largest subunit of multisubunit RNA polymerases (RNAPs) coordinate two Mg2+ ions involved in the catalysis of phosphodiester bond synthesis. A structural model based on the stereochemistry of nucleotidyl transfer reaction as well as recent crystallographic data predict that these Mg2+ ions should also be involved in the reverse reaction of pyrophosphorolysis as well as in the endo- and exonucleolytic cleavage of the nascent RNA. Here, we check these predictions by constructing point substitutions of each of the three Asp residues in the ßbeta;' subunit of Escherichia coli RNAP and testing the mutant enzymes' functions. Using artificially assembled elongation complexes, we demonstrate that substitutions of any of the three aspartates dramatically reduce all known RNAP catalytic activities, supporting the model's predictions that same amino acids participate in all RNAP catalytic reactions. We demonstrate that though substitutions in the DFDGD motif decrease Mg2+ binding to free RNAP below detection limits, the apparent affinity to Mg2+ in transcription complexes formed by the mutant and wild-type RNAPs is similar, suggesting that NTP substrates and/or nucleic acids actively contribute to the retention of active center Mg2+.


  • [Articles] The proliferating cell nuclear antigen regulates retinoic acid receptor transcriptional activity through direct protein-protein interaction -

    Retinoic acid receptors (RARs) interact, in a ligand-dependent fashion, with many coregulators that participate in a wide spectrum of biological responses, ranging from embryonic development to cellular growth control. The transactivating function of these ligand-inducible transcription factors reside mainly, but not exclusively, in their ligand-binding domain (AF2), which recruits or dismiss coregulators in a ligand-dependent fashion. However, little is known about AF2-independent function(s) of RARs. We have isolated the proliferating cell nuclear antigen (PCNA) as a repressor of RAR transcriptional activity, able to interact with an AF2-crippled RAR. The N-terminus of PCNA interacts directly with the DNA-binding domain of RAR, and PCNA is recruited to a retinoid-regulated promoter in intact cells. This interaction affects the transcriptional response to retinoic acid in a promoter-specific manner, conferring an unanticipated role to PCNA in transcriptional regulation. Our findings also suggest a role for RAR as a factor coordinating DNA transcription and repair.


  • [Articles] The replacement histone H2A.Z in a hyperacetylated form is a feature of active genes in the chicken -

    The replacement histone H2A.Z is variously reported as being linked to gene expression and preventing the spread of heterochromatin in yeast, or concentrated at heterochromatin in mammals. To resolve this apparent dichotomy, affinity-purified antibodies against the N-terminal region of H2A.Z, in both a triacetylated and non-acetylated state, are used in native chromatin immmuno-precipitation experiments with mononucleosomes from three chicken cell types. The hyperacetylated species concentrates at the 5' end of active genes, both tissue specific and housekeeping but is absent from inactive genes, while the unacetylated form is absent from both active and inactive genes. A concentration of H2A.Z is also found at insulators under circumstances implying a link to barrier activity but not to enhancer blocking. Although acetylated H2A.Z is widespread throughout the interphase genome, at mitosis its acetylation is erased, the unmodified form remaining. Thus, although H2A.Z may operate as an epigenetic marker for active genes, its N-terminal acetylation does not.


  • [Articles] The Rhodomonas salina mitochondrial genome: bacteria-like operons, compact gene arrangement and complex repeat region -

    To gain insight into the mitochondrial genome structure and gene content of a putatively ancestral group of eukaryotes, the cryptophytes, we sequenced the complete mitochondrial DNA of Rhodomonas salina. The 48 063 bp circular-mapping molecule codes for 2 rRNAs, 27 tRNAs and 40 proteins including 23 components of oxidative phosphorylation, 15 ribosomal proteins and two subunits of tat translocase. One potential protein (ORF161) is without assigned function. Only two introns occur in the genome; both are present within cox1 belong to group II and contain RT open reading frames. Primitive genome features include bacteria-like rRNAs and tRNAs, ribosomal protein genes organized in large clusters resembling bacterial operons and the presence of the otherwise rare genes such as rps1 and tatA. The highly compact gene organization contrasts with the presence of a 4.7 kb long, repeat-containing intergenic region. Repeat motifs ~40–700 bp long occur up to 31 times, forming a complex repeat structure. Tandem repeats are the major arrangement but the region also includes a large, ~3 kb, inverted repeat and several potentially stable ~40–80 bp long hairpin structures. We provide evidence that the large repeat region is involved in replication and transcription initiation, predict a promoter motif that occurs in three locations and discuss two likely scenarios of how this highly structured repeat region might have evolved.


  • [Articles] The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes -

    The release of the 1000th complete microbial genome will occur in the next two to three years. In anticipation of this milestone, the Fellowship for Interpretation of Genomes (FIG) launched the Project to Annotate 1000 Genomes. The project is built around the principle that the key to improved accuracy in high-throughput annotation technology is to have experts annotate single subsystems over the complete collection of genomes, rather than having an annotation expert attempt to annotate all of the genes in a single genome. Using the subsystems approach, all of the genes implementing the subsystem are analyzed by an expert in that subsystem. An annotation environment was created where populated subsystems are curated and projected to new genomes. A portable notion of a populated subsystem was defined, and tools developed for exchanging and curating these objects. Tools were also developed to resolve conflicts between populated subsystems. The SEED is the first annotation environment that supports this model of annotation. Here, we describe the subsystem approach, and offer the first release of our growing library of populated subsystems. The initial release of data includes 180 177 distinct proteins with 2133 distinct functional roles. This data comes from 173 subsystems and 383 different organisms.


  • [Articles] The use of thymidine analogs to improve the replication of an extra DNA base pair: a synthetic biological system -

    Synthetic biology based on a six-letter genetic alphabet that includes the two non-standard nucleobases isoguanine (isoG) and isocytosine (isoC), as well as the standard A, T, G and C, is known to suffer as a consequence of a minor tautomeric form of isoguanine that pairs with thymine, and therefore leads to infidelity during repeated cycles of the PCR. Reported here is a solution to this problem. The solution replaces thymidine triphosphate by 2-thiothymidine triphosphate (2-thioTTP). Because of the bulk and hydrogen bonding properties of the thione unit in 2-thioT, 2-thioT does not mispair effectively with the minor tautomer of isoG. To test whether this might allow PCR amplification of a six-letter artificially expanded genetic information system, we examined the relative rates of misincorporation of 2-thioTTP and TTP opposite isoG using affinity electrophoresis. The concentrations of isoCTP and 2-thioTTP were optimal to best support PCR amplification using thermostable polymerases of a six-letter alphabet that includes the isoC–isoG pair. The fidelity-per-round of amplification was found to be ~98% in trial PCRs with this six-letter DNA alphabet. The analogous PCR employing TTP had a fidelity-per-round of only ~93%. Thus, the A, 2-thioT, G, C, isoC, isoG alphabet is an artificial genetic system capable of Darwinian evolution.


  • [Articles] The XPF-ERCC1 endonuclease and homologous recombination contribute to the repair of minor groove DNA interstrand crosslinks in mammalian cells produced by the pyrrolo[2,1-c][1,4]benzodiazepine dimer SJG-136 -

    SJG-136, a pyrrolo[2,1-c][1,4]benzodiazepine (PBD) dimer, is a highly efficient interstrand crosslinking agent that reacts with guanine bases in a 5'-GATC-3' sequence in the DNA minor groove. SJG-136 crosslinks form rapidly and persist compared to those produced by conventional crosslinking agents such as nitrogen mustard, melphalan or cisplatin which bind in the DNA major groove. A panel of Chinese hamster ovary (CHO) cells with defined defects in specific DNA repair pathways were exposed to the bi-functional agents SJG-136 and melphalan, and to their mono-functional analogues mmy-SJG and mono-functional melphalan. SJG-136 was >100 times more cytotoxic than melphalan, and the bi-functional agents were much more cytotoxic than their respective mono-functional analogues. Cellular sensitivity of both SJG-136 and melphalan was dependent on the XPF-ERCC1 heterodimer, and homologous recombination repair factors XRCC2 and XRCC3. The relative level of sensitivity of these repair mutant cell lines to SJG-136 was, however, significantly less than with major groove crosslinking agents. In contrast to melphalan, there was no clear correlation between sensitivity to SJG-136 and crosslink unhooking capacity measured using a modified comet assay. Furthermore, repair of SJG-136 crosslinks did not involve the formation of DNA double-strand breaks. SJG-136 cytotoxicity is likely to result from the poor recognition of DNA damage by repair proteins resulting in the slow repair of both mono-adducts and more importantly crosslinks in the minor groove.


  • [Articles] Topological constraints in nucleic acid hybridization kinetics -

    A theoretical examination of kinetic mechanisms for forming knots and links in nucleic acid structures suggests that molecules involving base pairs between loops are likely to become topologically trapped in persistent frustrated states through the mechanism of ‘helix-driven wrapping’. Augmentation of the state space to include both secondary structure and topology in describing the free energy landscape illustrates the potential for topological effects to influence the kinetics and function of nucleic acid strands. An experimental study of metastable complementary ‘kissing hairpins’ demonstrates that the topological constraint of zero linking number between the loops effectively prevents conversion to the minimum free energy helical state. Introduction of short catalyst strands that break the topological constraint causes rapid conversion to full duplex.


  • [Articles] Transcription factor binding sites in the pol gene intragenic regulatory region of HIV-1 are important for virus infectivity -

    We have previously identified in the pol gene of human immunodeficiency virus type 1 (HIV-1) a new positive transcriptional regulatory element (nt 4481–4982) containing recognition sites for nuclear proteins (sites B, C, D and a GC-box) [C. Van Lint, J. Ghysdael, P. Paras, Jr, A. Burny and E. Verdin (1994) J. Virol. 68, 2632–2648]. In this study, we have further physically characterized each binding site and have shown that the transcription factors Oct-1, Oct-2, PU.1, Sp1 and Sp3 interact in vitro with the pol region. Chromatin immunoprecipitation assays using HIV-infected cell lines demonstrated in the context of chromatin that Sp1, Sp3, Oct-1 and PU.1 are recruited to the HS7 region in vivo. For each site, we have identified mutations abolishing factor binding to their cognate DNA sequences without altering the underlying amino acid sequence of the integrase. By transient transfection assays, we have demonstrated the involvement of the pol binding sites in the transcriptional enhancing activity of the intragenic region. Our functional results with multimerized wild-type and mutated pol binding sites separately (i.e. in the absence of the other sites) have demonstrated that the PU.1, Sp1, Sp3 and Oct-1 transcription factors regulate the transcriptional activity of a heterologous promoter through their respective HS7 binding sites. Finally, we have investigated the physiological role of the HS7 binding sites in HIV-1 replication and have shown that these sites are important for viral infectivity.


  • [Articles] Triplex targeted genomic crosslinks enter separable deletion and base substitution pathways -

    We have synthesized triple helix forming oligonucleotides (TFOs) that target a psoralen (pso) interstrand crosslink to a specific chromosomal site in mammalian cells. Mutagenesis of the targeted crosslinks results in base substitutions and deletions. Identification of the gene products involved in mutation formation is important for developing practical applications of pso-TFOs, and may be informative about the metabolism of other interstrand crosslinks. We have studied mutagenesis of a pso-TFO genomic crosslink in repair proficient and deficient cells. Deficiencies in non homologous end joining and mismatch repair do not influence mutation patterns. In contrast, the frequency of base substitutions is dependent on the activity of ERCC1/XPF and polymerase , but independent of other nucleotide excision repair (NER) or transcription coupled repair (TCR) genes. In NER/TCR deficient cells the frequency of deletions rises, indicating that in wild-type cells NER/TCR functions divert pso-TFO crosslinks from processes that result in deletions. We conclude that targeted pso-TFO crosslinks can enter genetically distinct mutational routes that resolve to base substitutions or deletions.


  • [Articles] Two clustered 8-oxo-7,8-dihydroguanine (8-oxodG) lesions increase the point mutation frequency of 8-oxodG, but do not result in double strand breaks or deletions in Escherichia coli -

    Multiply damaged sites (MDSs) are generated in DNA by ionizing radiation. In vitro studies predict that base excision repair in cells will convert MDSs to lethal double strand breaks (DSBs) when two opposing base damages are situated ≥2 bp apart. If the lesions are situated immediately 5' or 3' to each other, repair is predicted to occur sequentially due to inhibition of the DNA glycosylase by a single strand break repair intermediate. In this study, we examined how the distance between two opposing lesions alters the mutation frequency of an 8-oxodG in an MDS, and whether repair generates DSBs and deletions in bacteria. The 8-oxodG mutation frequency declined in MutY-deficient bacteria when the opposing 8-oxodG was 6 bp away, and was similar to a single 8-oxodG when the lesions were separated by 14 bp. However, the number of deletions detected for the MDSs was equivalent to the undamaged sequence. Using a separate assay, MDSs consisting of two 8-oxodG or an 8-oxodG opposite a uracil were not converted to DSBs in the absence of DNA replication in wild-type and transcription-coupled repair-deficient bacteria. This is the first study showing that DSB-repair intermediates and deletions are not formed during repair of clustered 8-oxodGs in cells.


  • [Articles] U3 snoRNP and Rrp5p associate independently with Saccharomyces cerevisiae 35S pre-rRNA, but Rrp5p is essential for association of Rok1p -

    Biogenesis of eukaryotic ribosomal subunits proceeds via a series of precursor ribonucleoprotein particles that correspond to different stages in the maturation pathway. The different pre-ribosomal particles each contain a distinct complement of non-ribosomal, trans-acting factors that are crucial for correct and efficient progress of the maturation process. Although in recent years we have gained considerable insight into the composition of the pre-ribosomal particles, our knowledge how the ordered association with and their dissociation from the pre-ribosome of these trans-acting factors is controlled is still quite limited. Here, we have studied the mutual dependence between three of these factors, Rrp5p, U3 snoRNP and Rok1p, all essential for the early stages of pre-rRNA processing/assembly, for association with the 35S pre-rRNA in Saccharomyces cerevisiae. Using co-immunoprecipitation assays, we show that Rrp5p and U3 snoRNP associate independently of each other and that the two factors do not detectably interact prior to incorporation into the pre-ribosome. In contrast, association of the putative RNA helicase Rok1p, which is known to genetically interact with Rrp5p, is absolutely dependent on the presence of the latter protein but does not require U3.


  • [Articles] Unfolding of DNA quadruplexes induced by HIV-1 nucleocapsid protein -

    The human immunodeficiency virus type 1 nucleocapsid protein (NC) is a nucleic acid chaperone that catalyzes the rearrangement of nucleic acids into their thermodynamically most stable structures. In the present study, a combination of optical and thermodynamic techniques were used to characterize the influence of NC on the secondary structure, thermal stability and energetics of monomolecular DNA quadruplexes formed by the sequence d(GGTTGGTGTGGTTGG) in the presence of K+ or Sr2+. Circular dichroism studies demonstrate that NC effectively unfolds the quadruplexes. Studies carried out with NC variants suggest that destabilization is mediated by the zinc fingers of NC. Calorimetric studies reveal that NC destabilization is enthalpic in origin, probably owing to unstacking of the G-quartets upon protein binding. In contrast, parallel studies performed on a related DNA duplex reveal that under conditions where NC readily destabilizes and unfolds the quadruplexes, its effect on the DNA duplex is much less pronounced. The differences in NC's ability to destabilize quadruplex versus duplex is in accordance with the higher G of melting for the latter, and with the inverse correlation between nucleic acid stability and the destabilizing activity of NC.


  • [Articles] Unidirectional translocation from recognition site and a necessary interaction with DNA end for cleavage by Type III restriction enzyme -

    Type III restriction enzymes have been demonstrated to require two unmethylated asymmetric recognition sites oriented head-to-head to elicit double-strand break 25–27 bp downstream of one of the two sites. The proposed DNA cleavage mechanism involves ATP-dependent DNA translocation. The sequence context of the recognition site was suggested to influence the site of DNA cleavage by the enzyme. In this investigation, we demonstrate that the cleavage site of the R.EcoP15I restriction enzyme does not depend on the sequence context of the recognition site. Strikingly, this study demonstrates that the enzyme can cleave linear DNA having either recognition sites in the same orientation or a single recognition site. Cleavage occurs predominantly at a site proximal to the DNA end in the case of multiple site substrates. Such cleavage can be abolished by the binding of Lac repressor downstream (3' side) but not upstream (5' side) of the recognition site. Binding of HU protein has also been observed to interfere with R.EcoP15I cleavage activity. In accordance with a mechanism requiring two enzyme molecules cooperating to elicit double-strand break on DNA, our results convincingly demonstrate that the enzyme translocates on DNA in a 5' to 3' direction from its recognition site and indicate a switch in the direction of enzyme motion at the DNA ends. This study demonstrates a new facet in the mode of action of these restriction enzymes.


  • [Articles] Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium -

    Acinetobacter sp. strain ADP1 is a nutritionally versatile soil bacterium closely related to representatives of the well-characterized Pseudomonas aeruginosa and Pseudomonas putida. Unlike these bacteria, the Acinetobacter ADP1 is highly competent for natural transformation which affords extraordinary convenience for genetic manipulation. The circular chromosome of the Acinetobacter ADP1, presented here, encodes 3325 predicted coding sequences, of which 60% have been classified based on sequence similarity to other documented proteins. The close evolutionary proximity of Acinetobacter and Pseudomonas species, as judged by the sequences of their 16S RNA genes and by the highest level of bidirectional best hits, contrasts with the extensive divergence in the GC content of their DNA (40 versus 62%). The chromosomes also differ significantly in size, with the Acinetobacter ADP1 chromosome <60% of the length of the Pseudomonas counterparts. Genome analysis of the Acinetobacter ADP1 revealed genes for metabolic pathways involved in utilization of a large variety of compounds. Almost all of these genes, with orthologs that are scattered in other species, are located in five major ‘islands of catabolic diversity’, now an apparent ‘archipelago of catabolic diversity’, within one-quarter of the overall genome. Acinetobacter ADP1 displays many features of other aerobic soil bacteria with metabolism oriented toward the degradation of organic compounds found in their natural habitat. A distinguishing feature of this genome is the absence of a gene corresponding to pyruvate kinase, the enzyme that generally catalyzes the terminal step in conversion of carbohydrates to pyruvate for respiration by the citric acid cycle. This finding supports the view that the cycle itself is centrally geared to the catabolic capabilities of this exceptionally versatile organism.


  • [Articles] UNR translation can be driven by an IRES element that is negatively regulated by polypyrimidine tract binding protein -

    Upstream of N-ras (Unr) has been described as an internal initiation trans-acting factor (ITAF) in the cap-independent translation of some particular viral and cellular mRNAs. Two factors led us to hypothesize that the UNR 5'-untranslated region (5'-UTR) may contain an internal ribosome entry site (IRES). The first was the requirement for persisting Unr expression under conditions that correlate with cap-independent translation. The other was the observation that the primary UNR transcript contains a 447 nt long 5'-UTR including two upstream AUGs that may restrict translation initiation via cap-dependent ribosome scanning. Here we report that the UNR 5'-UTR allows IRES-dependent translation, as revealed by a dicistronic reporter assay. Various controls ruled out the contribution of leaky scanning, cryptic promoter sequences or RNA processing events to the ability of the UNR 5'-UTR to mediate internal initiation of translation. Ultraviolet cross-linking analysis and RNA affinity chromatography revealed the binding of polypyrimidine tract binding protein (PTB) to the UNR IRES, requiring a pyrimidine-rich region (nucleotides 335–355). Whereas overexpression of PTB in several cell lines inhibited UNR IRES activity and UNR protein expression, depletion of endogenous PTB using RNAi increased UNR IRES activity. Moreover, a mutant version of the UNR IRES lacking the PTB binding site was more efficient at directing IRES-mediated translation. In conclusion, our results demonstrate that translation of the ITAF Unr can itself be regulated by an IRES that is downregulated by PTB.


  • [Articles] Unusual features of fibrillarin cDNA and gene structure in Euglena gracilis: evolutionary conservation of core proteins and structural predictions for methylation-guide box C/D snoRNPs throughout the domain Eucarya -

    Box C/D ribonucleoprotein (RNP) particles mediate O2'-methylation of rRNA and other cellular RNA species. In higher eukaryotic taxa, these RNPs are more complex than their archaeal counterparts, containing four core protein components (Snu13p, Nop56p, Nop58p and fibrillarin) compared with three in Archaea. This increase in complexity raises questions about the evolutionary emergence of the eukaryote-specific proteins and structural conservation in these RNPs throughout the eukaryotic domain. In protists, the primarily unicellular organisms comprising the bulk of eukaryotic diversity, the protein composition of box C/D RNPs has not yet been extensively explored. This study describes the complete gene, cDNA and protein sequences of the fibrillarin homolog from the protozoon Euglena gracilis, the first such information to be obtained for a nucleolus-localized protein in this organism. The E.gracilis fibrillarin gene contains a mixture of intron types exhibiting markedly different sizes. In contrast to most other E.gracilis mRNAs characterized to date, the fibrillarin mRNA lacks a spliced leader (SL) sequence. The predicted fibrillarin protein sequence itself is unusual in that it contains a glycine-lysine (GK)-rich domain at its N-terminus rather than the glycine-arginine-rich (GAR) domain found in most other eukaryotic fibrillarins. In an evolutionarily diverse collection of protists that includes E.gracilis, we have also identified putative homologs of the other core protein components of box C/D RNPs, thereby providing evidence that the protein composition seen in the higher eukaryotic complexes was established very early in eukaryotic cell evolution.


  • [Articles] Uracil content of 16S rRNA of thermophilic and psychrophilic prokaryotes correlates inversely with their optimal growth temperatures -

    We report here the finding of a highly significant inverse correlation of the uracil content of 16S rRNA and the optimum growth temperature (Topt) of cultured thermophilic and psychrophilic prokaryotes. This correlation was significantly different from the weaker correlations between the contents of other nucleotides and Topt. Analysis of the 16S rRNA secondary structure regions revealed a fall in the A:U base-pair content in step with the increase in Topt that was much steeper than that of mismatched base-pairs, which are thermodynamically less stable. These findings indicate that the 16S rRNA sequences of thermophiles and psychrophiles are under a strong thermo-adaptive pressure, and that structure–function constraints play a crucial role in determining their 16S rRNA nucleotide composition. The derived relationship between uracil content and Topt was used to develop an algorithm to predict the Topt values of uncultured prokaryotes lacking cultured close relatives and belonging to the phyla predominantly containing thermophiles. This algorithm may be useful in guiding the design of cultivation conditions for hitherto uncultured microbes.


  • [Articles] Using multiple alignments to improve seeded local alignment algorithms -

    Multiple alignments among genomes are becoming increasingly prevalent. This trend motivates the development of tools for efficient homology search between a query sequence and a database of multiple alignments. In this paper, we present an algorithm that uses the information implicit in a multiple alignment to dynamically build an index that is weighted most heavily towards the promising regions of the multiple alignment. We have implemented Typhon, a local alignment tool that incorporates our indexing algorithm, which our test results show to be more sensitive than algorithms that index only a sequence. This suggests that when applied on a whole-genome scale, Typhon should provide improved homology searches in time comparable to existing algorithms.


  • [Articles] UVA-visible photo-excitation of guanine radical cations produces sugar radicals in DNA and model structures -

    This work presents evidence that photo-excitation of guanine radical cations results in high yields of deoxyribose sugar radicals in DNA, guanine deoxyribonucleosides and deoxyribonucleotides. In dsDNA at low temperatures, formation of C1'• is observed from photo-excitation of G•+ in the 310–480 nm range with no C1'• formation observed ≥520 nm. Illumination of guanine radical cations in 2'dG, 3'-dGMP and 5'-dGMP in aqueous LiCl glasses at 143 K is found to result in remarkably high yields (~85–95%) of sugar radicals, namely C1'•, C3'• and C5'•. The amount of each of the sugar radicals formed varies dramatically with compound structure and temperature of illumination. Radical assignments were confirmed using selective deuteration at C5' or C3' in 2'-dG and at C8 in all the guanine nucleosides/tides. Studies of the effect of temperature, pH, and wavelength of excitation provide important information about the mechanism of formation of these sugar radicals. Time-dependent density functional theory calculations verify that specific excited states in G•+ show considerable hole delocalization into the sugar structure, in accord with our proposed mechanism of action, namely deprotonation from the sugar moiety of the excited molecular radical cation.


  • [Articles] Viral mutations enhance the Max binding properties of the vMyc b-HLH-LZ domain -

    Interaction with Max via the helix–loop–helix/leucine zipper (HLH-LZ) domain is essential for Myc to function as a transcription factor. Myc is commonly upregulated in tumours, however, its activity can also be potentiated by virally derived mutations. vMyc, derived from the virus, MC29 gag-Myc, differs from its cellular counterpart by five amino acids. The N-terminal mutation stabilizes the protein, however, the significance of the other mutations is not known. We now show that vMyc can sustain longer deletions in the LZ domain than cMyc before complete loss in transforming activity, implicating the viral mutations in contributing to Myc:Max complex formation. We confirmed this both in vitro and in vivo, with loss of Max binding correlating with a loss in the biological activity of Myc. A specific viral mutation, isoleucine383>leucine (I383>L) in helix 2 of the HLH domain, extends the LZ domain from four to five heptad repeats. Significantly, introduction of I383>L into a Myc mutant that is defective for Max binding substantially restored its ability to complex with Max in vitro and in vivo. We therefore propose that this virally derived mutation is functional by significantly contributing to establishing a more hydrophobic interface between the LZs of Myc and Max.


  • [Articles] Visualizing the dynamic behavior of poliovirus plus-strand RNA in living host cells -

    Dynamic analysis of viral nucleic acids in host cells is important for understanding virus–host interaction. By labeling endogenous RNA with molecular beacon, we have realized the direct visualization of viral nucleic acids in living host cells and have studied the dynamic behavior of poliovirus plus-strand RNA. Poliovirus plus-strand RNA was observed to display different distribution patterns in living Vero cells at different post-infection time points. Real-time imaging suggested that the translocation of poliovirus plus-strand RNA is a characteristic rearrangement process requiring intact microtubule network of host cells. Confocal-FRAP measurements showed that 49.4 ± 3.2% of the poliovirus plus-strand RNA molecules diffused freely (with a D-value of 9.6 ± 1.6 x 10–10 cm2/s) within their distribution region, while the remaining (50.5 ± 2.9%) were almost immobile and moved very slowly only with change of the RNA distribution region. Under the electron microscope, it was found that virus-induced membrane rearrangement is microtubule-associated in poliovirus-infected Vero cells. These results reveal an entrapment and diffusion mechanism for the movement of poliovirus plus-strand RNA in living mammalian cells, and demonstrate that the mechanism is mainly associated with microtubules and virus-induced membrane structures.


  • [Article] A conditional feedback loop regulates Ras activity through EphA2 - By Madhu Macrae, Richard M. Neve, Pablo Rodriguez-Viciana, Christopher Haqq, Jennifer Yeh, Chira Chen, Joe W. Gray, and Frank McCormick. The EphA2 receptor tyrosine kinase is frequently overexpressed in many cancers, including 40% of breast cancers. Here, we show that EphA2 is a direct transcriptional...

  • [Article] A Cxcl12-Cxcr4 Chemokine Signaling Pathway Defines the Initial Trajectory of Mammalian Motor Axons - By Ivo Lieberam, Dritan Agalliu, Takashi Nagasawa, Johan Ericson, and Thomas M. Jessell. Motor neurons, alone among neurons in the vertebrate CNS, extend axons out of the neural tube to innervate peripheral targets. Two classes of motor neurons,...

  • [Article] A Direct Interaction between the RAG2 C Terminus and the Core Histones Is Required for Efficient V(D)J Recombination - By Kelly L. West, Netai C. Singha, Pablo De Ioannes, Lynne Lacomis, Hediye Erdjument-Bromage, Paul Tempst, and Patricia Cortes. V(D)J recombination is a tightly controlled process of somatic recombination whose regulation is mediated in part by chromatin structure. Here, we report that RAG2 binds...

  • [Article] A Dual Inhibitory Mechanism Restricts msl-2 mRNA Translation for Dosage Compensation in Drosophila - By Karsten Beckmann, Marica Grskovic, Fátima Gebauer, and Matthias W. Hentze. Drosophila MSL-2 is the limiting component of the dosage compensation complex. Female flies must inhibit msl-2 mRNA translation for survival, and this inhibition is mediated...

  • [Article] A Genetic Screen for Candidate Tumor Suppressors Identifies REST - By Thomas F. Westbrook, Eric S. Martin, Michael R. Schlabach, Yumei Leng, Anthony C. Liang, Bin Feng, Jean J. Zhao, Thomas M. Roberts, Gail Mandel, Gregory J. Hannon, Ronald A. DePinho, Lynda Chin, and Stephen J. Elledge. Tumorigenesis is a multistep process characterized by a myriad of genetic and epigenetic alterations. Identifying the causal perturbations that confer malignant transformation is a central...

  • [Article] A Genetic Screen Identifies PITX1 as a Suppressor of RAS Activity and Tumorigenicity - By Ingrid G.M. Kolfschoten, Bart van Leeuwen, Katrien Berns, Jasper Mullenders, Roderick L. Beijersbergen, Rene Bernards, P. Mathijs Voorhoeve, and Reuven Agami. Activating mutations of RAS frequently occur in subsets of human cancers, indicating that RAS activation is important for tumorigenesis. However, a large proportion of these...

  • [Article] A Gradient of Template Dependence Defines Distinct Biological Roles for Family X Polymerases in Nonhomologous End Joining - By Stephanie A. Nick McElhinny, Jody M. Havener, Miguel Garcia-Diaz, Raquel Juárez, Katarzyna Bebenek, Barbara L. Kee, Luis Blanco, Thomas A. Kunkel, and Dale A. Ramsden. Three Pol X family members have been linked to nonhomologous end joining (NHEJ) in mammals. Template-independent TdT promotes diversity during NHEJ-dependent repair of V(D)J recombination...

  • [Article] A Membrane Binding Domain in the Ste5 Scaffold Synergizes with Gβγ Binding to Control Localization and Signaling in Pheromone Response - By Matthew J. Winters, Rachel E. Lamson, Hideki Nakanishi, Aaron M. Neiman, and Peter M. Pryciak. Activation of mitogen-activated protein (MAP) kinase cascade signaling by yeast mating pheromones involves recruitment of the Ste5 scaffold protein to the plasma membrane by the...

  • [Article] A Methylation-Dependent Electrostatic Switch Controls DNA Repair and Transcriptional Activation by E. coli Ada - By Chuan He, Jean-Christophe Hus, Li Jing Sun, Pei Zhou, Derek P.G. Norman, Volker Dötsch, Hua Wei, John D. Gross, William S. Lane, Gerhard Wagner, and Gregory L. Verdine. The transcriptional activity of many sequence-specific DNA binding proteins is directly regulated by posttranslational covalent modification. Although this form of regulation was first described nearly...

  • [Article] A mouse model for cyclin E-dependent genetic instability and tumorigenesis - By Keith R. Loeb, Heather Kostner, Eduardo Firpo, Thomas Norwood, Karen D. Tsuchiya, Bruce E. Clurman, and James M. Roberts. Ubiquitination of murine cyclin E is triggered by phosphorylation on threonine 393. Cyclin ET393A knockin mice exhibited increased cyclin E stability, but no phenotypic abnormalities....

  • [Article] A Network of PDZ-Containing Proteins Regulates T Cell Polarity and Morphology during Migration and Immunological Synapse Formation - By Mandy J. Ludford-Menting, Jane Oliaro, Faruk Sacirbegovic, Eric T.-Y. Cheah, Natalie Pedersen, Suzanne J. Thomas, Anupama Pasam, Rosa Iazzolino, Lukas E. Dow, Nigel J. Waterhouse, Amanda Murphy, Sarah Ellis, Mark J. Smyth, Michael H. Kershaw, Phillip K. Darcy, Patrick O. Humbert, and Sarah M. Russell. T cell shape is dictated by the selective recruitment of molecules to different regions of the cell (polarity) and is integral to every aspect of...

  • [Article] A Polar Mechanism Coordinates Different Regions of Alternative Splicing within a Single Gene - By Juan P. Fededa, Ezequiel Petrillo, Mikhail S. Gelfand, Alexei D. Neverov, Sebastián Kadener, Guadalupe Nogués, Federico Pelisch, Francisco E. Baralle, Andrés F. Muro, and Alberto R. Kornblihtt. Alternative splicing plays a key role in generating protein diversity. Transfections with minigenes revealed coordination between two distant, alternatively spliced exons in the same gene....

  • [Article] A Role for Proapoptotic BID in the DNA-Damage Response - By Sandra S. Zinkel, Kristen E. Hurov, Christy Ong, Farvardean M. Abtahi, Atan Gross, and Stanley J. Korsmeyer. The BCL-2 family of apoptotic proteins encompasses key regulators proximal to irreversible cell damage. The BH3-only members of this family act as sentinels, interconnecting specific...

  • [Article] A Sliding-Clamp Toolbelt Binds High- and Low-Fidelity DNA Polymerases Simultaneously - By Chiara Indiani, Peter McInerney, Roxana Georgescu, Myron F. Goodman, and Mike O’Donnell. This report demonstrates that the β sliding clamp of E. coli binds two different DNA polymerases at the same time. One is the high-fidelity Pol...

  • [Article] A Stress-Induced, Superoxide-Mediated Caspase-1 Activation Pathway Causes Plasma IL-18 Upregulation - By Atsuo Sekiyama, Haruyasu Ueda, Shin-ichiro Kashiwamura, Ryuji Sekiyama, Masatoshi Takeda, Kazuhito Rokutan, and Haruki Okamura. Psychological/physical stresses are known to cause relapses of autoimmune and inflammatory diseases. To reveal a mechanism by which noninflammatory stresses affect host defenses, responses to...

  • [Article] A Switch from High-Fidelity to Error-Prone DNA Double-Strand Break Repair Underlies Stress-Induced Mutation - By Rebecca G. Ponder, Natalie C. Fonville, and Susan M. Rosenberg. Special mechanisms of mutation are induced in microbes under growth-limiting stress causing genetic instability, including occasional adaptive mutations that may speed evolution. Both the mutation...

  • [Article] A Topological Interaction between Cohesin Rings and a Circular Minichromosome - By Dmitri Ivanov, and Kim Nasmyth. Sister chromatid cohesion depends on a multiprotein cohesin complex containing two SMC subunits, Smc1 and Smc3, that dimerize to form V-shaped molecules with ABC-like ATPase...

  • [Article] A Transient Luminal Chitinous Matrix Is Required to Model Epithelial Tube Diameter in the Drosophila Trachea - By Anna Tonning, Johanna Hemphälä, Erika TÃ¥ng, Ulf Nannmark, Christos Samakovlis, and Anne Uv. Epithelial tubes are found in many vital organs and require uniform and correct tube diameters for optimal function. Tube size depends on apical membrane growth...

  • [Article] A Two-Step Process for Cytokine Production Revealed by IL-4 Dual-Reporter Mice - By Katja Mohrs, Adil E. Wakil, Nigel Killeen, Richard M. Locksley, and Markus Mohrs. To monitor IL-4 expression at the single-cell level, we generated mice with insertions of different reporter genes into both copies of the Il4 gene that...

  • [Article] A Vertebrate Homolog of the Cell Cycle Regulator Dbf4 Is an Inhibitor of Wnt Signaling Required for Heart Development - By Barbara K. Brott, and Sergei Y. Sokol. Early stages of vertebrate heart development have been linked to Wnt signaling. Here we show in both gain- and loss-of-function experiments that XDbf4, a known...

  • [Article] Activation-Loop Autophosphorylation Is Mediated by a Novel Transitional Intermediate Form of DYRKs - By Pamela A. Lochhead, Gary Sibbet, Nick Morrice, and Vaughn Cleghon. Autophosphorylation of a critical residue in the activation loop of several protein kinases is an essential maturation event required for full enzyme activity. However, the...

  • [Article] Active Site Sharing and Subterminal Hairpin Recognition in a New Class of DNA Transposases - By Donald R. Ronning, Catherine Guynet, Bao Ton-Hoang, Zhanita N. Perez, Rodolfo Ghirlando, Michael Chandler, and Fred Dyda. Many bacteria harbor simple transposable elements termed insertion sequences (IS). In Helicobacter pylori, the chimeric IS605 family elements are particularly interesting due to their proximity...

  • [Article] Adaptation to Synaptic Inactivity in Hippocampal Neurons - By Tara C. Thiagarajan, Maria Lindskog, and Richard W. Tsien. In response to activity deprivation, CNS neurons undergo slow adaptive modification of unitary synaptic transmission. The changes are comparable in degree to those induced by...

  • [Article] Aβ42 Is Essential for Parenchymal and Vascular Amyloid Deposition in Mice - By Eileen McGowan, Fiona Pickford, Jungsu Kim, Luisa Onstead, Jason Eriksen, Cindy Yu, Lisa Skipper, M. Paul Murphy, Jenny Beard, Pritam Das, Karen Jansen, Michael DeLucia, Wen-Lang Lin, Georgia Dolios, Rong Wang, Christopher B. Eckman, Dennis W. Dickson, Mike Hutton, John Hardy, and Todd Golde. Considerable circumstantial evidence suggests that Aβ42 is the initiating molecule in Alzheimer’s disease (AD) pathogenesis. However, the absolute requirement for Aβ42 for amyloid deposition has...

  • [Article] Akt/PKB Regulates Actin Organization and Cell Motility via Girdin/APE - By Atsushi Enomoto, Hideki Murakami, Naoya Asai, Nobuhiro Morone, Takashi Watanabe, Kumi Kawai, Yoshiki Murakumo, Jiro Usukura, Kozo Kaibuchi, and Masahide Takahashi. The serine/threonine kinase Akt (also called protein kinase B) is well known as an important regulator of cell survival and growth and has also been...

  • [Article] Allosteric Modulation of the RNA Polymerase Catalytic Reaction Is an Essential Component of Transcription Control by Rifamycins - By Irina Artsimovitch, Marina N. Vassylyeva, Dmitri Svetlov, Vladimir Svetlov, Anna Perederina, Noriyuki Igarashi, Naohiro Matsugaki, Soichi Wakatsuki, Tahir H. Tahirov, and Dmitry G. Vassylyev. Rifamycins, the clinically important antibiotics, target bacterial RNA polymerase (RNAP). A proposed mechanism in which rifamycins sterically block the extension of nascent RNA beyond three...

  • [Article] An Alternate Pathway for CD4 T Cell Development: Thymocyte-Expressed MHC Class II Selects a Distinct T Cell Population - By Wei Li, Moon-Gyo Kim, Tania S. Gourley, Brian P. McCarthy, Derek B. Sant’Angelo, and Cheong-Hee Chang. Conventional understanding of CD4 T cell development is that the MHC class II molecules on cortical thymic epithelial cell are necessary for positive selection, as...

  • [Article] An Essential Cytoplasmic Function for the Nuclear Poly(A) Binding Protein, PABP2, in Poly(A) Tail Length Control and Early Development in Drosophila - By Béatrice Benoit, Géraldine Mitou, Aymeric Chartier, Claudia Temme, Sophie Zaessinger, Elmar Wahle, Isabelle Busseau, and Martine Simonelig. Translational control of maternal mRNA through regulation of poly(A) tail length is crucial during early development. The nuclear poly(A) binding protein, PABP2, was identified biochemically...

  • [Article] An Essential Function of the C. elegans Ortholog of TPX2 Is to Localize Activated Aurora A Kinase to Mitotic Spindles - By Nurhan Özlü, Martin Srayko, Kazuhisa Kinoshita, Bianca Habermann, Eileen T. O’Toole, Thomas Müller-Reichert, Natalie Schmalz, Arshad Desai, and Anthony A. Hyman. In vertebrates, the microtubule binding protein TPX2 is required for meiotic and mitotic spindle assembly. TPX2 is also known to bind to and activate Aurora...

  • [Article] Analysis of Notch Function in Presomitic Mesoderm Suggests a γ-Secretase-Independent Role for Presenilins in Somite Differentiation - By Stacey S. Huppert, Ma. Xenia G. Ilagan, Bart De Strooper, and Raphael Kopan. The role of Notch signaling in general and presenilin in particular was analyzed during mouse somitogenesis. We visualize cyclical production of activated Notch (NICD) and...

  • [Article] Assembly of Trigeminal Sensory Ganglia by Chemokine Signaling - By Holger Knaut, Patrick Blader, Uwe Strähle, and Alexander F. Schier. Sensory neurons with related functions form ganglia, but how these precisely positioned clusters are assembled has been unclear. Here, we use the zebrafish trigeminal sensory...

  • [Article] ATP citrate lyase inhibition can suppress tumor cell growth - By Georgia Hatzivassiliou, Fangping Zhao, Daniel E. Bauer, Charalambos Andreadis, Anthony N. Shaw, Dashyant Dhanak, Sunil R. Hingorani, David A. Tuveson, and Craig B. Thompson. Many tumors display a high rate of glucose utilization, as evidenced by 18-F-2-deoxyglucose PET imaging. One potential advantage of catabolizing glucose through glycolysis at a...

  • [Article] Auditory Hair Cell-Afferent Fiber Synapses Are Specialized to Operate at Their Best Frequencies - By M.E. Schnee, D.M. Lawton, D.N. Furness, T.A. Benke, and A.J. Ricci. Auditory afferent fiber activity is driven by high-fidelity information transfer from the sensory hair cell. Presynaptic specializations, posited to maintain fidelity, are investigated at synapses...

  • [Article] B-1a and B-1b Cells Exhibit Distinct Developmental Requirements and Have Unique Functional Roles in Innate and Adaptive Immunity to S. pneumoniae - By Karen M. Haas, Jonathan C. Poe, Douglas A. Steeber, and Thomas F. Tedder. B-1a and B-1b lymphocytes were found to exhibit specialized roles in providing immunity to Streptococcus pneumoniae and differ dramatically in their developmental requirements. Transgenic mice...

  • [Article] BACH1 is critical for homologous recombination and appears to be the Fanconi anemia gene product FANCJ - By Rachel Litman, Min Peng, Zhe Jin, Fan Zhang, Junran Zhang, Simon Powell, Paul R. Andreassen, and Sharon B. Cantor. We showed in this study that cells deficient of the BRCA1-associated BACH1 helicase, also known as BRIP1, failed to elicit homologous recombination (HR) after DNA...

  • [Article] Bacterial Infections Promote T Cell Recognition of Self-Glycolipids - By Gennaro De Libero, Anthony P. Moran, Hans-Jürgen Gober, Emmanuel Rossy, Abdijapar Shamshiev, Olga Chelnokova, Zaima Mazorra, Silvia Vendetti, Alessandra Sacchi, Martina M. Prendergast, Sebastiano Sansano, Alexander Tonevitsky, Regine Landmann, and Lucia Mori. Recognition of self is essential for repertoire selection, immune regulation, and autoimmunity and may be a consequence of infection. Self-induced recognition may represent the escape...

  • [Article] Basophils Play a Critical Role in the Development of IgE-Mediated Chronic Allergic Inflammation Independently of T Cells and Mast Cells - By Kaori Mukai, Kunie Matsuoka, Choji Taya, Hidenori Suzuki, Hiroo Yokozeki, Kiyoshi Nishioka, Katsuiku Hirokawa, Maki Etori, Makoto Yamashita, Toshiyuki Kubota, Yoshiyuki Minegishi, Hiromichi Yonekawa, and Hajime Karasuyama. The recruitment of basophils into the sites of allergic inflammation is often observed. However, no definitive evidence has been provided that basophils are crucially involved...

  • [Article] Bcl-2 Antiapoptotic Proteins Inhibit Beclin 1-Dependent Autophagy - By Sophie Pattingre, Amina Tassa, Xueping Qu, Rita Garuti, Xiao Huan Liang, Noboru Mizushima, Milton Packer, Michael D. Schneider, and Beth Levine. Apoptosis and autophagy are both tightly regulated biological processes that play a central role in tissue homeostasis, development, and disease. The anti-apoptotic protein, Bcl-2, interacts...

  • [Article] Binding and Phosphorylation of Par-4 by Akt Is Essential for Cancer Cell Survival - By Anindya Goswami, Ravshan Burikhanov, Aurelie de Thonel, Naoya Fujita, Mamta Goswami, Yanming Zhao, John E. Eriksson, Takashi Tsuruo, and Vivek M. Rangnekar. Activation of the PI3K-Akt pathway by loss of tumor suppressor PTEN (phosphatase and tensin homolog deleted on chromosome 10) function, increased growth factor signaling, or...

  • [Article] Binding of GEF-H1 to the Tight Junction-Associated Adaptor Cingulin Results in Inhibition of Rho Signaling and G1/S Phase Transition - By Saima Aijaz, Fabio D’Atri, Sandra Citi, Maria S. Balda, and Karl Matter. The activity of Rho GTPases is carefully timed to control epithelial proliferation and differentiation. RhoA is downregulated when epithelial cells reach confluence, resulting in inhibition...

  • [Article] Breaking the Covalent Bond—A Pigment Property that Contributes to Desensitization in Cones - By Vladimir J. Kefalov, Maureen E. Estevez, Massahiro Kono, Patrice W. Goletz, Rosalie K. Crouch, M. Carter Cornwall, and King-Wai Yau. Retinal rod and cone pigments consist of an apoprotein, opsin, covalently linked to a chromophore, 11-cis retinal. Here we demonstrate that the formation of the...

  • [Article] c-Myb Is Critical for B Cell Development and Maintenance of Follicular B Cells - By Matthew D. Thomas, Christopher S. Kremer, Kodi S. Ravichandran, Klaus Rajewsky, and Timothy P. Bender. The c-Myb transcription factor is crucial during definitive hematopoiesis. However, the embryonic lethality of Myb traditional null mutations has precluded analysis of c-Myb function in...

  • [Article] c-Rel-Dependent Priming of Naive T Cells by Inflammatory Cytokines - By Daliya Banerjee, Hsiou-Chi Liou, and Ranjan Sen. The intrinsic refractoriness of naive T cells for cytokine production is counteracted by cells of the innate immune system. Upon sensing danger via Toll-like receptors,...

  • [Article] CAML Is a p56Lck-Interacting Protein that Is Required for Thymocyte Development - By David D. Tran, Contessa E. Edgar, Karin L. Heckman, Shari L. Sutor, Catherine J. Huntoon, Jan van Deursen, David L. McKean, and Richard J. Bram. Calcium modulating cyclophilin ligand (CAML) is a ubiquitously expressed protein implicated in T cell signaling, although its mechanism and physiologic role in the immune system...

  • [Article] Canonical Wnt Signaling in Differentiated Osteoblasts Controls Osteoclast Differentiation - By Donald A. Glass, Peter Bialek, Jong Deok Ahn, Michael Starbuck, Millan S. Patel, Hans Clevers, Mark M. Taketo, Fanxin Long, Andrew P. McMahon, Richard A. Lang, and Gerard Karsenty. Inactivation of β-catenin in mesenchymal progenitors prevents osteoblast differentiation; inactivation of Lrp5, a gene encoding a likely Wnt coreceptor, results in low bone mass (osteopenia)...

  • [Article] Canonical Wnt/β-Catenin Signaling Prevents Osteoblasts from Differentiating into Chondrocytes - By Theo P. Hill, Daniela Später, Makoto M. Taketo, Walter Birchmeier, and Christine Hartmann. Osteoblasts and chondrocytes are involved in building up the vertebrate skeleton and are thought to differentiate from a common mesenchymal precursor, the osteo-chondroprogenitor. Although numerous...

  • [Article] CD19 Regulates B Cell Maturation, Proliferation, and Positive Selection in the FDC Zone of Murine Splenic Germinal Centers - By Yue Wang, and Robert H. Carter. Mice with mutations in CD19 Y482/Y513 form germinal centers (GC) but fail to produce high-affinity antibodies. In these mice, GC B cell differentiation, proliferation, and...

  • [Article] Cdk1-Dependent Regulation of the Mitotic Inhibitor Wee1 - By Stacy L. Harvey, Alyson Charlet, Wilhelm Haas, Steven P. Gygi, and Douglas R. Kellogg. The Wee1 kinase phosphorylates and inhibits cyclin-dependent kinase 1 (Cdk1), thereby delaying entry into mitosis until appropriate conditions have been met. An understanding of the...

  • [Article] Cdk1/Erk2- and Plk1-Dependent Phosphorylation of a Centrosome Protein, Cep55, Is Required for Its Recruitment to Midbody and Cytokinesis - By Megan Fabbro, Bin-Bing Zhou, Mikiko Takahashi, Boris Sarcevic, Preeti Lal, Mark E. Graham, Brian G. Gabrielli, Phillip J. Robinson, Erich A. Nigg, Yoshitaka Ono, and Kum Kum Khanna. Centrosomes in mammalian cells have recently been implicated in cytokinesis; however, their role in this process is poorly defined. Here, we describe a human coiled-coil...

  • [Article] CDKs Promote DNA Replication Origin Licensing in Human Cells by Protecting Cdc6 from APC/C-Dependent Proteolysis - By Niels Mailand, and John F.X. Diffley. Cyclin-dependent kinases (CDKs) restrict DNA replication origin firing to once per cell cycle by preventing the assembly of prereplicative complexes (pre-RCs; licensing) outside of G1...

  • [Article] Cell Type-Specific Involvement of RIG-I in Antiviral Response - By Hiroki Kato, Shintaro Sato, Mitsutoshi Yoneyama, Masahiro Yamamoto, Satoshi Uematsu, Kosuke Matsui, Tohru Tsujimura, Kiyoshi Takeda, Takashi Fujita, Osamu Takeuchi, and Shizuo Akira. Toll-like receptors (TLRs) play an important role in antiviral response by recognizing viral components. Recently, a RNA helicase, RIG-I, was also suggested to recognize viral...

  • [Article] Centriolin Anchoring of Exocyst and SNARE Complexes at the Midbody Is Required for Secretory-Vesicle-Mediated Abscission - By Adam Gromley, Charles Yeaman, Jack Rosa, Sambra Redick, Chun-Ting Chen, Stephanie Mirabelle, Minakshi Guha, James Sillibourne, and Stephen J. Doxsey. The terminal step in cytokinesis, called abscission, requires resolution of the membrane connection between two prospective daughter cells. Our previous studies demonstrated that the coiled-coil...

  • [Article] Chlamydomonas Shortens Its Flagella by Activating Axonemal Disassembly, Stimulating IFT Particle Trafficking, and Blocking Anterograde Cargo Loading - By Junmin Pan, and William J. Snell. Almost all eukaryotic cells form cilia/flagella, maintain them at their genetically specified lengths, and shorten them. Here, we define the cellular mechanisms that bring about...

  • [Article] Chromosome and Replisome Dynamics in E. coli: Loss of Sister Cohesion Triggers Global Chromosome Movement and Mediates Chromosome Segregation - By David Bates, and Nancy Kleckner. Chromosome and replisome dynamics were examined in synchronized E. coli cells undergoing a eukaryotic-like cell cycle. Sister chromosomes remain tightly colocalized for much of S...

  • [Article] Clathrin-Dependent and Clathrin-Independent Retrieval of Synaptic Vesicles in Retinal Bipolar Cells - By Wolf J. Jockusch, Gerrit J.K. Praefcke, Harvey T. McMahon, and Leon Lagnado. Synaptic vesicles can be retrieved rapidly or slowly, but the molecular basis of these kinetic differences has not been defined. We now show that substantially...

  • [Article] Common Molecular Pathways Mediate Long-Term Potentiation of Synaptic Excitation and Slow Synaptic Inhibition - By Cindy Shen Huang, Song-Hai Shi, Jernej Ule, Matteo Ruggiu, Laura A. Barker, Robert B. Darnell, Yuh Nung Jan, and Lily Yeh Jan. Synaptic plasticity, the cellular correlate for learning and memory, involves signaling cascades in the dendritic spine. Extensive studies have shown that long-term potentiation (LTP) of...

  • [Article] Computer Simulations and Image Processing Reveal Length-Dependent Pulling Force as the Primary Mechanism for C. elegans Male Pronuclear Migration - By Akatsuki Kimura, and Shuichi Onami. A male pronucleus migrates toward the center of an egg to reach the female pronucleus for zygote formation. This migration depends on microtubules growing from...

  • [Article] Constitutive NF-κB activation by the t(11;18)(q21;q21) product in MALT lymphoma is linked to deregulated ubiquitin ligase activity - By Honglin Zhou, Ming-Qing Du, and Vishva M. Dixit. Mucosa-associated lymphoid tissue (MALT) lymphoma is a common type of lymphoma in extranodal sites. The most frequent chromosome translocation associated with MALT lymphoma is t(11;18)(q21;q21),...

  • [Article] Core Transcriptional Regulatory Circuitry in Human Embryonic Stem Cells - By Laurie A. Boyer, Tong Ihn Lee, Megan F. Cole, Sarah E. Johnstone, Stuart S. Levine, Jacob P. Zucker, Matthew G. Guenther, Roshan M. Kumar, Heather L. Murray, Richard G. Jenner, David K. Gifford, Douglas A. Melton, Rudolf Jaenisch, and Richard A. Young. The transcription factors OCT4, SOX2, and NANOG have essential roles in early development and are required for the propagation of undifferentiated embryonic stem (ES) cells...

  • [Article] Crosstalk between tumor and endothelial cells promotes tumor angiogenesis by MAPK activation of Notch signaling - By Qinghua Zeng, Shenglin Li, Douglas B. Chepeha, Thomas J. Giordano, Jong Li, Honglai Zhang, Peter J. Polverini, Jacques Nor, Jan Kitajewski, and Cun-Yu Wang. While significant progress has been made in understanding the induction of tumor vasculature by secreted angiogenic factors, little is known regarding contact-dependent signals that promote...

  • [Article] Crystal Structure of A. aeolicus Argonaute, a Site-Specific DNA-Guided Endoribonuclease, Provides Insights into RISC-Mediated mRNA Cleavage - By Yu-Ren Yuan, Yi Pei, Jin-Biao Ma, Vitaly Kuryavyi, Maria Zhadina, Gunter Meister, Hong-Ying Chen, Zbigniew Dauter, Thomas Tuschl, and Dinshaw J. Patel. Argonaute (Ago) proteins constitute a key component of the RNA-induced silencing complex (RISC). We report the crystal structure of Aquifex aeolicus Ago (Aa-Ago) together with...

  • [Article] Cutaneous CXCL14 Targets Blood Precursors to Epidermal Niches for Langerhans Cell Differentiation - By Patrick Schaerli, Katharina Willimann, Lisa M. Ebert, Alfred Walz, and Bernhard Moser. Dendritic cells (DCs) are major constituents of peripheral tissues, where they control immunity to foreign and self-antigens. The process of continuous DC renewal under homeostatic...

  • [Article] Cyclin D Regulation of a Sexually Dimorphic Asymmetric Cell Division - By Christopher Tilmann, and Judith Kimble. The C. elegans somatic gonadal precursor cell (SGP) divides asymmetrically to establish gonad-specific coordinates in both sexes. In addition, the SGP division is sexually dimorphic...

  • [Article] De novo carcinogenesis promoted by chronic inflammation is B lymphocyte dependent - By Karin E. de Visser, Lidiya V. Korets, and Lisa M. Coussens. Chronic inflammation predisposes tissue to cancer development; however, regulatory mechanisms underlying recruitment of innate leukocytes toward developing neoplasms are obscure. We report that genetic elimination...

  • [Article] Deregulated BCL6 expression recapitulates the pathogenesis of human diffuse large B cell lymphomas in mice - By Giorgio Cattoretti, Laura Pasqualucci, Gianna Ballon, Wayne Tam, Subhadra V. Nandula, Qiong Shen, Tongwei Mo, Vundavalli V. Murty, and Riccardo Dalla-Favera. Diffuse large B cell lymphomas (DLBCL) derive from germinal center (GC) B cells and display chromosomal alterations deregulating the expression of BCL6, a transcriptional repressor...

  • [Article] Differential Regulation of AMPA Receptor Subunit Trafficking by Palmitoylation of Two Distinct Sites - By Takashi Hayashi, Gavin Rumbaugh, and Richard L. Huganir. Modification of AMPA receptor function is a major mechanism for the regulation of synaptic transmission and underlies several forms of synaptic plasticity. Post-translational palmitoylation is...

  • [Article] Direction-Selective Dendritic Action Potentials in Rabbit Retina - By Nicholas Oesch, Thomas Euler, and W. Rowland Taylor. Dendritic spikes that propagate toward the soma are well documented, but their physiological role remains uncertain. Our in vitro patch-clamp recordings and two-photon calcium imaging...

  • [Article] Dissociable Controlled Retrieval and Generalized Selection Mechanisms in Ventrolateral Prefrontal Cortex - By David Badre, Russell A. Poldrack, E. Juliana Paré-Blagoev, Rachel Z. Insler, and Anthony D. Wagner. How does ventrolateral prefrontal cortex (VLPFC) control mnemonic processing? Alternative models propose that VLPFC guides top-down (controlled) retrieval of knowledge from long-term stores or selects...

  • [Article] DNA Binding Selectivity of MeCP2 Due to a Requirement for A/T Sequences Adjacent to Methyl-CpG - By Robert J. Klose, Shireen A. Sarraf, Lars Schmiedeberg, Suzanne M. McDermott, Irina Stancheva, and Adrian P. Bird. DNA methylation is interpreted by a family of methyl-CpG binding domain (MBD) proteins that repress transcription through recruitment of corepressors that modify chromatin. To compare...

  • [Article] Do Motoneurons Encode the Noncommutativity of Ocular Rotations? - By Fatema F. Ghasia, and Dora E. Angelaki. As we look around, the orientation of our eyes depends on the order of the rotations that are carried out, a mathematical feature of rotatory...

  • [Article] Dopamine-Dependent Interactions between Limbic and Prefrontal Cortical Plasticity in the Nucleus Accumbens: Disruption by Cocaine Sensitization - By Yukiori Goto, and Anthony A. Grace. The prefrontal cortex and the hippocampus exhibit converging projections to the nucleus accumbens and have functional reciprocal connections via indirect pathways. As a result, information...

  • [Article] Downregulated REST Transcription Factor Is a Switch Enabling Critical Potassium Channel Expression and Cell Proliferation - By Alex Cheong, Andrew J. Bingham, Jing Li, Bhaskar Kumar, Piruthivi Sukumar, Christopher Munsch, Noel J. Buckley, Craig B. Neylon, Karen E. Porter, David J. Beech, and Ian C. Wood. Induction of KCa3.1 (IKCa) potassium channel plays an important role in vascular smooth muscle cell proliferation. Here, we report that the gene encoding KCa3.1 (KCNN4)...

  • [Article] Drosophila E2F1 Has Context-Specific Pro- and Antiapoptotic Properties during Development - By Nam-Sung Moon, Maxim V. Frolov, Eun-Jeong Kwon, Luisa Di Stefano, Dessislava K. Dimova, Erick J. Morris, Barbie Taylor-Harding, Kristin White, and Nicholas J. Dyson. E2F transcription factors are generally believed to be positive regulators of apoptosis. In this study, we show that dE2F1 and dDP are important for the...

  • [Article] Drosophila Exocyst Components Sec5, Sec6, and Sec15 Regulate DE-Cadherin Trafficking from Recycling Endosomes to the Plasma Membrane - By Johanna Langevin, Matthew J. Morgan, Carine Rossé, Victor Racine, Jean-Baptiste Sibarita, Sandra Aresta, Mala Murthy, Thomas Schwarz, Jacques Camonis, and Yohanns Bellaïche. The E-Cadherin-catenin complex plays a critical role in epithelial cell-cell adhesion, polarization, and morphogenesis. Here, we have analyzed the mechanism of Drosophila E-Cadherin (DE-Cad) localization....

  • [Article] Drosophila Melted Modulates FOXO and TOR Activity - By Aurelio A. Teleman, Ya-Wen Chen, and Stephen M. Cohen. The insulin/PI3K signaling pathway controls both tissue growth and metabolism. Here, we identify Melted as a new modulator of this pathway in Drosophila. Melted interacts...

  • [Article] Drug resistance by evasion of antiangiogenic targeting of VEGF signaling in late-stage pancreatic islet tumors - By Oriol Casanovas, Daniel J. Hicklin, Gabriele Bergers, and Douglas Hanahan. Function-blocking antibodies to VEGF receptors R1 and R2 were used to probe their roles in controlling angiogenesis in a mouse model of pancreatic islet carcinogenesis....

  • [Article] Dual Functional Activity of Semaphorin 3B Is Required for Positioning the Anterior Commissure - By Falk Julien, Ahmad Bechara, Roberto Fiore, Homaira Nawabi, Heather Zhou, Carolina Hoyo-Becerra, Muriel Bozon, Geneviève Rougon, Martin Grumet, Andreas W. Püschel, Joshua R. Sanes, and Valérie Castellani. Chemorepulsion by semaphorins plays a critical role during the development of neuronal projections. Although semaphorin-induced chemoattraction has been reported in vitro, the contribution of this...

  • [Article] Dynamic Error Correction and Regulation of Downstream Bubble Opening by Human RNA Polymerase II - By Xue Q. Gong, Chunfen Zhang, Michael Feig, and Zachary F. Burton. The nucleotide triphosphate (NTP)-driven translocation hypothesis posits that NTP substrates bind to templated DNA sites prior to translocation into the active site. By using millisecond...

  • [Article] Dynamics of Parietal Neural Activity during Spatial Cognitive Processing - By David A. Crowe, Bruno B. Averbeck, Matthew V. Chafee, and Apostolos P. Georgopoulos. Dynamic neural processing unrelated to changes in sensory input or motor output is likely to be a hallmark of cognitive operations. Here we show that...

  • [Article] Early inactivation of p53 tumor suppressor gene cooperating with NF1 loss induces malignant astrocytoma - By Yuan Zhu, Frantz Guignard, Dawen Zhao, Li Liu, Dennis K. Burns, Ralph P. Mason, Albee Messing, and Luis F. Parada. Malignant astrocytoma, the most prevalent primary brain tumor, is resistant to all known therapies and frequently harbors mutations that inactivate p53 and activate Ras signaling....

  • [Article] Effects of α-Synuclein Immunization in a Mouse Model of Parkinson’s Disease - By Eliezer Masliah, Edward Rockenstein, Anthony Adame, Michael Alford, Leslie Crews, Makoto Hashimoto, Peter Seubert, Michael Lee, Jason Goldstein, Tamie Chilcote, Dora Games, and Dale Schenk. Abnormal folding of α-synuclein (α-syn) is thought to lead to neurodegeneration and the characteristic symptoms of Lewy body disease (LBD). Since previous studies suggest that...

  • [Article] Eomesodermin Is a Localized Maternal Determinant Required for Endoderm Induction in Zebrafish - By Christopher R.R. Bjornson, Kevin J.P. Griffin, Gist H. Farr, Akira Terashima, Charis Himeda, Yutaka Kikuchi, and David Kimelman. In zebrafish, endoderm induction occurs in marginal blastomeres and requires Casanova (Cas), the first endoderm-specific factor expressed in the embryo. Whereas the transcription factors Gata5...

  • [Article] Escaping the Nuclear Confines: Signal-Dependent Pre-mRNA Splicing in Anucleate Platelets - By Melvin M. Denis, Neal D. Tolley, Michaeline Bunting, Hansjörg Schwertz, Huimiao Jiang, Stephan Lindemann, Christian C. Yost, Frederick J. Rubner, Kurt H. Albertine, Kathryn J. Swoboda, Carolyn M. Fratto, Emilysa Tolley, Larry W. Kraiss, Thomas M. McIntyre, Guy A. Zimmerman, and Andrew S. Weyrich. Platelets are specialized hemostatic cells that circulate in the blood as anucleate cytoplasts. We report that platelets unexpectedly possess a functional spliceosome, a complex that...

  • [Article] Essential Role for the PKC Target MARCKS in Maintaining Dendritic Spine Morphology - By Barbara Calabrese, and Shelley Halpain. Spine morphology is regulated by intracellular signals, like PKC, that affect cytoskeletal and membrane dynamics. We investigated the role of MARCKS (myristoylated, alanine-rich C-kinase substrate)...

  • [Article] Evidence of Marginal-Zone B Cell-Positive Selection in Spleen - By Lijun Wen, Joni Brill-Dashoff, Susan A. Shinton, Masanao Asano, Richard R. Hardy, and Kyoko Hayakawa. Antigen receptor-mediated signaling is critical for the development and survival of B cells. However, it has not been established whether B cell development requires a...

  • [Article] Exon-Junction Complex Components Specify Distinct Routes of Nonsense-Mediated mRNA Decay with Differential Cofactor Requirements - By Niels H. Gehring, Joachim B. Kunz, Gabriele Neu-Yilik, Stephen Breit, Marcelo H. Viegas, Matthias W. Hentze, and Andreas E. Kulozik. Messenger RNAs (mRNAs) bearing premature translation termination codons (PTCs) are degraded by nonsense-mediated mRNA decay (NMD). For mammalian NMD, current models propose a linear pathway...

  • [Article] Exploration of the Topological Requirements of ERAD Identifies Yos9p as a Lectin Sensor of Misfolded Glycoproteins in the ER Lumen - By Arunashree Bhamidipati, Vladimir Denic, Erin M. Quan, and Jonathan S. Weissman. ER-associated degradation (ERAD) of glycoproteins depends on dual recognition of protein misfolding and remodeling of the substrate’s N-linked glycans. After recognition, substrates are retrotranslocated to...

  • [Article] FAK-Mediated Src Phosphorylation of Endophilin A2 Inhibits Endocytosis of MT1-MMP and Promotes ECM Degradation - By Xiaoyang Wu, Boyi Gan, Youngdong Yoo, and Jun-Lin Guan. Focal adhesion kinase (FAK) is an important mediator of integrin signaling in the regulation of cell proliferation, survival, migration, and invasion. To understand how FAK...

  • [Article] FcγRIV: A Novel FcR with Distinct IgG Subclass Specificity - By Falk Nimmerjahn, Pierre Bruhns, Ken Horiuchi, and Jeffrey V. Ravetch. Mouse IgG subclasses display a hierarchy of in vivo activities, with IgG2a and IgG2b showing the greatest protective and pathogenic properties. These enhanced activities result,...

  • [Article] Features of Ribosome-Peptidyl-tRNA Interactions Essential for Tryptophan Induction of tna Operon Expression - By Luis Rogelio Cruz-Vera, Soumitra Rajagopal, Catherine Squires, and Charles Yanofsky. Certain nascent peptide sequences, when within the ribosomal exit tunnel, can inhibit translation termination and/or peptide elongation. The 24 residue leader peptidyl-tRNA of the tna...

  • [Article] Fezl Is Required for the Birth and Specification of Corticospinal Motor Neurons - By Bradley J. Molyneaux, Paola Arlotta, Tustomu Hirata, Masahiko Hibi, and Jeffrey D. Macklis. The molecular mechanisms controlling the differentiation of neural progenitors into distinct subtypes of neurons during neocortical development are unknown. Here, we report that Fezl is...

  • [Article] FGF Signal Interpretation Is Directed by Sprouty and Spred Proteins during Mesoderm Formation - By Jeremy M. Sivak, Lars F. Petersen, and Enrique Amaya. Vertebrate gastrulation requires coordination of mesoderm specification with morphogenetic movements. While both of these processes require FGF signaling, it is not known how mesoderm specification...

  • [Article] Formal Learning Theory Dissociates Brain Regions with Different Temporal Integration - By Jan Gläscher, and Christian Büchel. Learning can be characterized as the extraction of reliable predictions about stimulus occurrences from past experience. In two experiments, we investigated the interval of temporal...

  • [Article] FOS-1 Promotes Basement-Membrane Removal during Anchor-Cell Invasion in C. elegans - By David R. Sherwood, James A. Butler, James M. Kramer, and Paul W. Sternberg. Cell invasion through basement membranes is crucial during morphogenesis and cancer metastasis. Here, we genetically dissect this process during anchor-cell invasion into the vulval epithelium...

  • [Article] Functional Characterization of Core Promoter Elements: DPE-Specific Transcription Requires the Protein Kinase CK2 and the PC4 Coactivator - By Brian A. Lewis, Robert J. Sims, III, William S. Lane, and Danny Reinberg. Downstream core promoter elements are an expanding class of regulatory sequences that add considerable diversity to the promoter architecture of RNA polymerase II-transcribed genes. We...

  • [Article] Functional Connectivity between Immune Cells Mediated by Tunneling Nanotubules - By Simon C. Watkins, and Russell D. Salter. Intercellular signals can be transmitted through neuronal synapses or through gap junctions, with the latter mediating transmission of calcium fluxes and small molecules between cells....

  • [Article] G Protein-Gated Inhibitory Module of N-Type (CaV2.2) Ca2+ Channels - By Heather L. Agler, Jenafer Evans, Lai Hock Tay, Molly J. Anderson, Henry M. Colecraft, and David T. Yue. Voltage-dependent G protein (Gβγ) inhibition of N-type (CaV2.2) channels supports presynaptic inhibition and represents a central paradigm of channel modulation. Still controversial are the proposed...

  • [Article] GABAergic Excitation Promotes Neuronal Differentiation in Adult Hippocampal Progenitor Cells - By Yusuke Tozuka, Satoshi Fukuda, Takashi Namba, Tatsunori Seki, and Tatsuhiro Hisatsune. Hippocampal activity influences neurogenesis in the adult dentate gyrus; however, little is known about the involvement of the hippocampal circuitry in this process. In the...

  • [Article] Gene Expression Profiling of Facilitated L-LTP in VP16-CREB Mice Reveals that BDNF Is Critical for the Maintenance of LTP and Its Synaptic Capture - By Angel Barco, Susan Patterson, Juan M. Alarcon, Petra Gromova, Manuel Mata-Roig, Alexei Morozov, and Eric R. Kandel. Expression of VP16-CREB, a constitutively active form of CREB, in hippocampal neurons of the CA1 region lowers the threshold for eliciting the late, persistent phase...

  • [Article] General Translational Repression by Activators of mRNA Decapping - By Jeff Coller, and Roy Parker. Translation and mRNA degradation are affected by a key transition where eukaryotic mRNAs exit translation and assemble an mRNP state that accumulates into processing bodies...

  • [Article] Genetic evidence for a tumor suppressor role of HIF-2α - By Till Acker, Antonio Diez-Juan, Julian Aragones, Marc Tjwa, Koen Brusselmans, Lieve Moons, Dai Fukumura, Maria Paz Moreno-Murciano, Jean-Marc Herbert, Angelika Burger, Johanna Riedel, Gerd Elvert, Ingo Flamme, Patrick H. Maxwell, Désiré Collen, Mieke Dewerchin, Rakesh K. Jain, Karl H. Plate, and Peter Carmeliet. The hypoxia-inducible transcription factors HIF-1α and HIF-2α are activated in hypoxic tumor regions. However, their role in tumorigenesis remains controversial, as tumor growth promoter and...

  • [Article] Genetic Evidence Supporting Selection of the Vα14i NKT Cell Lineage from Double-Positive Thymocyte Precursors - By Takeshi Egawa, Gerard Eberl, Ichiro Taniuchi, Kamel Benlagha, Frederic Geissmann, Lothar Hennighausen, Albert Bendelac, and Dan R. Littman. Invariant Vα14i NKT (iNKT) cells are a specialized subset of T lymphocytes with regulatory functions. They coexpress TCRαβ and natural killer cell markers. They differentiate...

  • [Article] Genome-wide Map of Nucleosome Acetylation and Methylation in Yeast - By Dmitry K. Pokholok, Christopher T. Harbison, Stuart Levine, Megan Cole, Nancy M. Hannett, Tong Ihn Lee, George W. Bell, Kimberly Walker, P. Alex Rolfe, Elizabeth Herbolsheimer, Julia Zeitlinger, Fran Lewitter, David K. Gifford, and Richard A. Young. Eukaryotic genomes are packaged into nucleosomes whose position and chemical modification state can profoundly influence regulation of gene expression. We profiled nucleosome modifications across the...

  • [Article] Genome-Wide Transcriptional Changes Associated with Enhanced Activity in the Drosophila Nervous System - By Zhuo Guan, Sudipta Saraswati, Bill Adolfsen, and J. Troy Littleton. Neuronal plasticity is an important feature of the developing brain and requires neuronal circuits to reconfigure their functional connectivity depending upon activity patterns. To explore...

  • [Article] Genomic analysis of single cytokeratin-positive cells from bone marrow reveals early mutational events in breast cancer - By Julian A. Schardt, Manfred Meyer, Claudia H. Hartmann, Falk Schubert, Oleg Schmidt-Kittler, Christine Fuhrmann, Bernhard Polzer, Marco Petronio, Roland Eils, and Christoph A. Klein. Chromosomal instability in human breast cancer is known to take place before mammary neoplasias display morphological signs of invasion. We describe here the unexpected finding...

  • [Article] Genotoxic Stress Targets Human Chk1 for Degradation by the Ubiquitin-Proteasome Pathway - By You-Wei Zhang, Diane M. Otterness, Gary G. Chiang, Weilin Xie, Yun-Cai Liu, Frank Mercurio, and Robert T. Abraham. The Chk1 kinase is a major effector of S phase checkpoint signaling during the cellular response to genotoxic stress. Here, we report that replicative stress...

  • [Article] Gliomedin Mediates Schwann Cell-Axon Interaction and the Molecular Assembly of the Nodes of Ranvier - By Yael Eshed, Konstantin Feinberg, Sebastian Poliak, Helena Sabanay, Offra Sarig-Nadir, Ivo Spiegel, John R. Bermingham, and Elior Peles. Accumulation of Na+ channels at the nodes of Ranvier is a prerequisite for saltatory conduction. In peripheral nerves, clustering of these channels along the axolemma...

  • [Article] Global loss of imprinting leads to widespread tumorigenesis in adult mice - By Teresa M. Holm, Laurie Jackson-Grusby, Tobias Brambrink, Yasuhiro Yamada, William M. Rideout, and Rudolf Jaenisch. Loss of imprinting (LOI), commonly observed in human tumors, refers to loss of monoallelic gene regulation normally conferred by parent-of-origin-specific DNA methylation. To test the...

  • [Article] Gp78, a Membrane-Anchored Ubiquitin Ligase, Associates with Insig-1 and Couples Sterol-Regulated Ubiquitination to Degradation of HMG CoA Reductase - By Bao-Liang Song, Navdar Sever, and Russell A. DeBose-Boyd. Sterol-regulated ubiquitination is an obligatory step in ER-associated degradation (ERAD) of HMG CoA reductase, a rate-limiting enzyme in cholesterol synthesis. Accelerated degradation of reductase, one...

  • [Article] GPCR Signaling Is Required for Blood-Brain Barrier Formation in Drosophila - By Tina Schwabe, Roland J. Bainton, Richard D. Fetter, Ulrike Heberlein, and Ulrike Gaul. The blood-brain barrier of Drosophila is established by surface glia, which ensheath the nerve cord and insulate it against the potassium-rich hemolymph by forming intercellular...

  • [Article] Heat shock phenocopies E1B-55K late functions and selectively sensitizes refractory tumor cells to ONYX-015 oncolytic viral therapy - By Clodagh C. O’Shea, Conrado Soria, Bridget Bagus, and Frank McCormick. ONYX-015 is an E1B-55K-deleted adenovirus that has promising clinical activity as a cancer therapy. However, many tumor cells fail to support ONYX-015 oncolytic replication. E1B-55K...

  • [Article] Hierarchical and Ontogenic Positions Serve to Define the Molecular Basis of Human Hematopoietic Stem Cell Behavior - By Farbod Shojaei, Jennifer Trowbridge, Lisa Gallacher, Lou Yuefei, David Goodale, Francis Karanu, Krysta Levac, and Mickie Bhatia. The molecular basis governing functional behavior of human hematopoietic stem cells (HSCs) is largely unknown. Here, using in vitro and in vivo assays, we isolate...

  • [Article] HIF overexpression correlates with biallelic loss of fumarate hydratase in renal cancer: Novel role of fumarate in regulation of HIF stability - By Jennifer S. Isaacs, Yun Jin Jung, David R. Mole, Sunmin Lee, Carlos Torres-Cabala, Yuen-Li Chung, Maria Merino, Jane Trepel, Berton Zbar, Jorge Toro, Peter J. Ratcliffe, W. Marston Linehan, and Len Neckers. Individuals with hemizygous germline fumarate hydratase (FH) mutations are predisposed to renal cancer. These tumors predominantly exhibit functional inactivation of the remaining wild-type allele, implicating...

  • [Article] High Binaural Coherence Determines Successful Sound Localization and Increased Activity in Posterior Auditory Areas - By U. Zimmer, and E. Macaluso. Our brain continuously receives complex combinations of sounds originating from different sources and relating to different events in the external world. Timing differences between the...

  • [Article] Higher-Order Substrate Recognition of eIF2α by the RNA-Dependent Protein Kinase PKR - By Arvin C. Dar, Thomas E. Dever, and Frank Sicheri. In response to binding viral double-stranded RNA byproducts within a cell, the RNA-dependent protein kinase PKR phosphorylates the α subunit of the translation initiation factor...

  • [Article] Histone H3 Lysine 9 Methylation and HP1γ Are Associated with Transcription Elongation through Mammalian Chromatin - By Christopher R. Vakoc, Sean A. Mandat, Benjamin A. Olenchock, and Gerd A. Blobel. Methylation of histones modulates chromatin structure and function. Whereas methylation of histone H3 on lysines 4, 36, and 79 has been linked with gene activation,...

  • [Article] Histone Modifications Associated with Somatic Hypermutation - By Valerie H. Odegard, Sean T. Kim, Shannon M. Anderson, Mark J. Shlomchik, and David G. Schatz. A number of modified histones, including acetylated H3 and H4 and phosphorylated H2AX (γH2AX), are associated with V(D)J recombination and class switch recombination (CSR). In...

  • [Article] HuR as a Negative Posttranscriptional Modulator in Inflammation - By Vicky Katsanou, Olympia Papadaki, Stavros Milatos, Perry J. Blackshear, Paul Anderson, George Kollias, and Dimitris L. Kontoyiannis. HuR is an RNA binding protein with an alleged role in the posttranscriptional activation of inflammatory mRNAs bearing AU-rich elements (AREs). Here, we show that...

  • [Article] Identification and Characterization of Factors Required for Microtubule Growth and Nucleation in the Early C. elegans Embryo - By Martin Srayko, Aynur Kaya, Joanne Stamford, and Anthony A. Hyman. Microtubules (MTs) are dynamic polymers that undergo cell cycle and position-sensitive regulation of polymerization and depolymerization. Although many different factors that regulate MT dynamics have...

  • [Article] Identification of Bronchioalveolar Stem Cells in Normal Lung and Lung Cancer - By Carla F. Bender Kim, Erica L. Jackson, Amber E. Woolfenden, Sharon Lawrence, Imran Babar, Sinae Vogel, Denise Crowley, Roderick T. Bronson, and Tyler Jacks. Injury models have suggested that the lung contains anatomically and functionally distinct epithelial stem cell populations. We have isolated such a regional pulmonary stem cell...

  • [Article] Identification of FBL2 As a Geranylgeranylated Cellular Protein Required for Hepatitis C Virus RNA Replication - By Chunfu Wang, Michael Gale, Jr., Brian C. Keller, Hua Huang, Michael S. Brown, Joseph L. Goldstein, and Jin Ye. We recently reported that Hepatitis C virus (HCV) RNA replication requires one or more geranylgeranylated host proteins. Using a combination of [3H]mevalonate labeling, coimmunoprecipitation, and...

  • [Article] Identification of Genes Needed for Regeneration, Stem Cell Function, and Tissue Homeostasis by Systematic Gene Perturbation in Planaria - By Peter W. Reddien, Adam L. Bermange, Kenneth J. Murfitt, Joya R. Jennings, and Alejandro Sánchez Alvarado. Planarians have been a classic model system for the study of regeneration, tissue homeostasis, and stem cell biology for over a century, but they have...

  • [Article] In Vivo Identification of Novel Regulators and Conserved Pathways of Phagocytosis in A. gambiae - By Luís F. Moita, Rui Wang-Sattler, Kristin Michel, Timo Zimmermann, Stephanie Blandin, Elena A. Levashina, and Fotis C. Kafatos. Anopheles gambiae uses effective immune responses, including phagocytosis, to fight microbial infection. We have developed a semiquantitative phagocytosis test and used it in conjunction with...

  • [Article] Inactivation of the SR Protein Splicing Factor ASF/SF2 Results in Genomic Instability - By Xialu Li, and James L. Manley. SR proteins constitute a family of pre-mRNA splicing factors now thought to play several roles in mRNA metabolism in metazoan cells. Here we provide evidence...

  • [Article] Induction of apoptosis by an inhibitor of the mitotic kinesin KSP requires both activation of the spindle assembly checkpoint and mitotic slippage - By Weikang Tao, Victoria J. South, Yun Zhang, Joseph P. Davide, Linda Farrell, Nancy E. Kohl, Laura Sepp-Lorenzino, and Robert B. Lobell. The inhibition of KSP causes mitotic arrest by activating the spindle assembly checkpoint. While transient inhibition of KSP leads to reversible mitotic arrest, prolonged exposure...

  • [Article] Inhibition of Bacterial RNA Polymerase by Streptolydigin: Stabilization of a Straight-Bridge-Helix Active-Center Conformation - By Steven Tuske, Stefan G. Sarafianos, Xinyue Wang, Brian Hudson, Elena Sineva, Jayanta Mukhopadhyay, Jens J. Birktoft, Olivier Leroy, Sajida Ismail, Arthur D. Clark, Chhaya Dharia, Andrew Napoli, Oleg Laptenko, Jookyung Lee, Sergei Borukhov, Richard H. Ebright, and Eddy Arnold. We define the target, mechanism, and structural basis of inhibition of bacterial RNA polymerase (RNAP) by the tetramic acid antibiotic streptolydigin (Stl). Stl binds to...

  • [Article] Initiation of DNA Replication Requires the RECQL4 Protein Mutated in Rothmund-Thomson Syndrome - By Mahesh N. Sangrithi, Juan A. Bernal, Mark Madine, Anna Philpott, Joon Lee, William G. Dunphy, and Ashok R. Venkitaraman. How the replication machinery is loaded at origins of DNA replication is poorly understood. Here, we implicate in this process the Xenopus laevis homolog (xRTS)...

  • [Article] Integration of Notch 1 and Calcineurin/NFAT Signaling Pathways in Keratinocyte Growth and Differentiation Control - By Cristina Mammucari, Alice Tommasi di Vignano, Andrey A. Sharov, Joel Neilson, Matthew C. Havrda, Dennis R. Roop, Vladimir A. Botchkarev, Gerald R. Crabtree, and G. Paolo Dotto. The Notch and Calcineurin/NFAT pathways have both been implicated in control of keratinocyte differentiation. Induction of the p21WAF1/Cip1 gene by Notch 1 activation in differentiating...

  • [Article] Interaction with Vesicle Luminal Protachykinin Regulates Surface Expression of δ-Opioid Receptors and Opioid Analgesia - By Ji-Song Guan, Zhen-Zhong Xu, Hua Gao, Shao-Qiu He, Guo-Qiang Ma, Tao Sun, Li-Hua Wang, Zhen-Ning Zhang, Isabelle Lena, Ian Kitchen, Robert Elde, Andreas Zimmer, Cheng He, Gang Pei, Lan Bao, and Xu Zhang. Opioid and tachykinin systems are involved in modulation of pain transmission in the spinal cord. Regulation of surface opioid receptors on nociceptive afferents is critical...

  • [Article] Interplay between SRPK and Clk/Sty Kinases in Phosphorylation of the Splicing Factor ASF/SF2 Is Regulated by a Docking Motif in ASF/SF2 - By Jacky Chi Ki Ngo, Sutapa Chakrabarti, Jian-Hua Ding, Adolfo Velazquez-Dones, Brad Nolen, Brandon E. Aubol, Joseph A. Adams, Xiang-Dong Fu, and Gourisankar Ghosh. The arginine-serine (RS)-rich domain of the SR protein ASF/SF2 is phosphorylated by SR protein kinases (SRPKs) and Clk/Sty kinases. However, the mode of phosphorylation by...

  • [Article] μ-Opioid Receptor and CREB Activation Are Required for Nicotine Reward - By Carrie L. Walters, Jessica N. Cleck, Yuo-chen Kuo, and Julie A. Blendy. Environmental cues associated with nicotine delivery are an important part of the stimulus that sustains smoking behavior and is often coupled with craving and relapse;...

  • [Article] Knockdown of Cone-Specific Kinase GRK7 in Larval Zebrafish Leads to Impaired Cone Response Recovery and Delayed Dark Adaptation - By Oliver Rinner, Yuri V. Makhankov, Oliver Biehlmaier, and Stephan C.F. Neuhauss. Phosphorylation of rhodopsin by rhodopsin kinase GRK1 is an important desensitization mechanism in scotopic vision. For cone vision GRK1 is not essential. However, cone opsin...

  • [Article] LIM Kinase1 Controls Synaptic Stability Downstream of the Type II BMP Receptor - By Benjamin A. Eaton, and Graeme W. Davis. Here, we demonstrate that the BMP receptor Wishful Thinking (Wit) is required for synapse stabilization. In the absence of BMP signaling, synapse disassembly and retraction...

  • [Article] Lineage-Specific Requirement for the PH Domain of Vav1 in the Activation of CD4+ but Not CD8+ T Cells - By Antonella Prisco, Lesley Vanes, Sandra Ruf, Cesar Trigueros, and Victor L.J. Tybulewicz. Vav1 is a guanine nucleotide exchange factor (GEF) for Rho-family GTPases, which is activated by tyrosine phosphorylation following TCR stimulation. Vav1-deficient mice have defects in...

  • [Article] Loss of ARNT/HIF1β Mediates Altered Gene Expression and Pancreatic-Islet Dysfunction in Human Type 2 Diabetes - By Jenny E. Gunton, Rohit N. Kulkarni, SunHee Yim, Terumasa Okada, Wayne J. Hawthorne, Yu-Hua Tseng, Russell S. Roberson, Camillo Ricordi, Philip J. O’Connell, Frank J. Gonzalez, and C. Ronald Kahn. β cell dysfunction is a central component of the pathogenesis of type 2 diabetes. Using oligonucleotide microarrays and real-time PCR of pancreatic islets isolated from...

  • [Article] Mammalian CARMIL Inhibits Actin Filament Capping by Capping Protein - By Changsong Yang, Martin Pring, Martin A. Wear, Minzhou Huang, John A. Cooper, Tatyana M. Svitkina, and Sally H. Zigmond. Actin polymerization in cells occurs via filament elongation at the barbed end. Proteins that cap the barbed end terminate this elongation. Heterodimeric capping protein (CP)...

  • [Article] Math1 Expression Redefines the Rhombic Lip Derivatives and Reveals Novel Lineages within the Brainstem and Cerebellum - By Vincent Y. Wang, Matthew F. Rose, and Huda Y. Zoghbi. The rhombic lip (RL) is an embryonic proliferative neuroepithelium that generates several groups of hindbrain neurons. However, the precise boundaries and derivatives of the RL...

  • [Article] Mathematical Modeling of Nucleotide Excision Repair Reveals Efficiency of Sequential Assembly Strategies - By Antonio Politi, Martijn J. Moné, Adriaan B. Houtsmuller, Deborah Hoogstraten, Wim Vermeulen, Reinhart Heinrich, and Roel van Driel. Nucleotide excision repair (NER) requires the concerted action of many different proteins that assemble at sites of damaged DNA in a sequential fashion. We have...

  • [Article] Mechanistic Link between PKR Dimerization, Autophosphorylation, and eIF2α Substrate Recognition - By Madhusudan Dey, Chune Cao, Arvin C. Dar, Tomohiko Tamura, Keiko Ozato, Frank Sicheri, and Thomas E. Dever. The antiviral protein kinase PKR inhibits protein synthesis by phosphorylating the translation initiation factor eIF2α on Ser51. Binding of double-stranded RNA to the regulatory domains...

  • [Article] Memory Strength and Repetition Suppression: Multimodal Imaging of Medial Temporal Cortical Contributions to Recognition - By Brian D. Gonsalves, Itamar Kahn, Tim Curran, Kenneth A. Norman, and Anthony D. Wagner. Declarative memory permits an organism to recognize stimuli that have been previously encountered, discriminating them from those that are novel. One basis for recognition is...

  • [Article] Metabolic Regulation of Oocyte Cell Death through the CaMKII-Mediated Phosphorylation of Caspase-2 - By Leta K. Nutt, Seth S. Margolis, Mette Jensen, Catherine E. Herman, William G. Dunphy, Jeffrey C. Rathmell, and Sally Kornbluth. Vertebrate female reproduction is limited by the oocyte stockpiles acquired during embryonic development. These are gradually depleted over the organism’s lifetime through the process of...

  • [Article] MMP-7 promotes prostate cancer-induced osteolysis via the solubilization of RANKL - By Conor C. Lynch, Atsuya Hikosaka, Heath B. Acuff, Michelle D. Martin, Noriyasu Kawai, Rakesh K. Singh, Tracy C. Vargo-Gogola, Jennifer L. Begtrup, Todd E. Peterson, Barbara Fingleton, Tomoyuki Shirai, Lynn M. Matrisian, and Mitsuru Futakuchi. We developed a rodent model that mimics the osteoblastic and osteolytic changes associated with human metastatic prostate cancer. Microarray analysis identified MMP-7, cathepsin-K, and apolipoprotein...

  • [Article] Modulation of Coreceptor Transcription during Positive Selection Dictates Lineage Fate Independently of TCR/Coreceptor Specificity - By Sophia D. Sarafova, Batu Erman, Qing Yu, François Van Laethem, Terry Guinter, Susan O. Sharrow, Lionel Feigenbaum, Kathryn F. Wildt, Wilfried Ellmeier, and Alfred Singer. For developing T cells, coreceptor choice is matched to T cell antigen receptor (TCR) MHC specificity during positive selection in the thymus, but the mechanism...

  • [Article] Modulation of Transmitter Release by Presynaptic Resting Potential and Background Calcium Levels - By Gautam B. Awatramani, Gareth D. Price, and Laurence O. Trussell. Activation of presynaptic ion channels alters the membrane potential of nerve terminals, leading to changes in transmitter release. To study the relationship between resting potential...

  • [Article] Molecular Substrates for Retrieval and Reconsolidation of Cocaine-Associated Contextual Memory - By Courtney A. Miller, and John F. Marshall. Relapse into drug taking among addicts often depends on learned associations between drug-paired cues and the rewarding effects of these drugs, such as cocaine (COC)....

  • [Article] moody Encodes Two GPCRs that Regulate Cocaine Behaviors and Blood-Brain Barrier Permeability in Drosophila - By Roland J. Bainton, Linus T.-Y. Tsai, Tina Schwabe, Michael DeSalvo, Ulrike Gaul, and Ulrike Heberlein. We identified moody in a genetic screen for Drosophila mutants with altered cocaine sensitivity. Hypomorphic mutations in moody cause an increased sensitivity to cocaine and...

  • [Article] Motions of the Fingers Subdomain of Klentaq1 Are Fast and Not Rate Limiting: Implications for the Molecular Basis of Fidelity in DNA Polymerases - By Paul J. Rothwell, Vesselin Mitaksov, and Gabriel Waksman. Various kinetic studies on nucleotide incorporation by DNA polymerases have established that a rate-limiting step occurs that is crucial in the mechanism of discrimination between...

  • [Article] Multiple Mechanisms Confining RNA Polymerase II Ubiquitylation to Polymerases Undergoing Transcriptional Arrest - By Baggavalli P. Somesh, James Reid, Wei-Feng Liu, T. Max M. Søgaard, Hediye Erdjument-Bromage, Paul Tempst, and Jesper Q. Svejstrup. In order to study mechanisms and regulation of RNA polymerase II (RNAPII) ubiquitylation and degradation, highly purified factors were used to reconstitute RNAPII ubiquitylation in...

  • [Article] Mutation of Smooth Muscle Myosin Causes Epithelial Invasion and Cystic Expansion of the Zebrafish Intestine - By Kenneth N. Wallace, Amy C. Dolan, Christoph Seiler, Erin M. Smith, Shamila Yusuff, Linda Chaille-Arnold, Ben Judson, Rachel Sierk, Christopher Yengo, H. Lee Sweeney, and Michael Pack. Zebrafish meltdown (mlt) mutants develop cystic expansion of the posterior intestine as a result of stromal invasion of nontransformed epithelial cells. Positional cloning identified zebrafish...

  • [Article] MutH Complexed with Hemi- and Unmethylated DNAs: Coupling Base Recognition and DNA Cleavage - By Jae Young Lee, Judy Chang, Nimesh Joseph, Rodolfo Ghirlando, Desirazu N. Rao, and Wei Yang. MutH initiates mismatch repair by nicking the transiently unmethylated daughter strand 5′ to a GATC sequence. Here, we report crystal structures of MutH complexed with...

  • [Article] Mutually Exclusive Splicing of the Insect Dscam Pre-mRNA Directed by Competing Intronic RNA Secondary Structures - By Brenton R. Graveley. Drosophila Dscam encodes 38,016 distinct axon guidance receptors through the mutually exclusive alternative splicing of 95 variable exons. Importantly, known mechanisms that ensure the mutually...

  • [Article] NCAM 180 Acting via a Conserved C-Terminal Domain and MLCK Is Essential for Effective Transmission with Repetitive Stimulation - By Luis Polo-Parada, Florian Plattner, Christian Bose, and Lynn T. Landmesser. NCAM 180 isoform null neuromuscular junctions are unable to effectively mobilize and exocytose synaptic vesicles and thus exhibit periods of total transmission failure during high-frequency...

  • [Article] Neuregulin-1 Type III Determines the Ensheathment Fate of Axons - By Carla Taveggia, George Zanazzi, Ashley Petrylak, Hiroko Yano, Jack Rosenbluth, Steven Einheber, Xiaorong Xu, Raymond M. Esper, Jeffrey A. Loeb, Peter Shrager, Moses V. Chao, Douglas L. Falls, Lorna Role, and James L. Salzer. The signals that determine whether axons are ensheathed or myelinated by Schwann cells have long been elusive. We now report that threshold levels of neuregulin-1...

  • [Article] Neuronal apoptosis linked to EglN3 prolyl hydroxylase and familial pheochromocytoma genes: Developmental culling and cancer - By Sungwoo Lee, Eijiro Nakamura, Haifeng Yang, Wenyi Wei, Michelle S. Linggi, Mini P. Sajan, Robert V. Farese, Robert S. Freeman, Bruce D. Carter, William G. Kaelin, and Susanne Schlisio. Germline NF1, c-RET, SDH, and VHL mutations cause familial pheochromocytoma. Pheochromocytomas derive from sympathetic neuronal precursor cells. Many of these cells undergo c-Jun-dependent apoptosis during...

  • [Article] Nicastrin Functions as a γ-Secretase-Substrate Receptor - By Sanjiv Shah, Sheu-Fen Lee, Katsuhiko Tabuchi, Yi-Heng Hao, Cong Yu, Quincey LaPlant, Haydn Ball, Charles E. Dann, Thomas Südhof, and Gang Yu. γ-secretase catalyzes the intramembrane cleavage of amyloid precursor protein (APP) and Notch after their extracellular domains are shed by site-specific proteolysis. Nicastrin is an essential...

  • [Article] Novel Role of the Ras Cascade in Memory B Cell Response - By Yoshimasa Takahashi, Ayako Inamine, Shu-ichi Hashimoto, Sachiko Haraguchi, Emi Yoshioka, Naoya Kojima, Ryo Abe, and Toshitada Takemori. Engagement of the B cell antigen receptor (BCR) triggers the Ras cascade, but the biological role of the latter in B cell response is unknown....

  • [Article] Nucleophosmin/B23, a Nuclear PI(3,4,5)P3 Receptor, Mediates the Antiapoptotic Actions of NGF by Inhibiting CAD - By Jee-Yin Ahn, Xia Liu, Dongmei Cheng, Junmin Peng, Pui-Kwang Chan, Paul A. Wade, and Keqiang Ye. Phosphatidylinositol 3,4,5-triphosphate [PI(3,4,5)P3] is an essential second messenger implicated in various cellular processes. Cytoplasmic PI(3,4,5)P3 has been well characterized, but little is known about the...

  • [Article] Nutritional Regulation of Hepatic Heme Biosynthesis and Porphyria through PGC-1α - By Christoph Handschin, Jiandie Lin, James Rhee, Anne-Kathrin Peyer, Sherry Chin, Pei-Hsuan Wu, Urs A. Meyer, and Bruce M. Spiegelman. Inducible hepatic porphyrias are inherited genetic disorders of enzymes of heme biosynthesis. The main clinical manifestations are acute attacks of neuropsychiatric symptoms frequently precipitated by...

  • [Article] Oscillating CD8+ T Cell Effector Functions after Antigen Recognition in the Liver - By Masanori Isogawa, Yoshihiro Furuichi, and Francis V. Chisari. When hepatitis B virus (HBV)-specific CD8+ cytotoxic T lymphocytes (CTLs) are adoptively transferred into HBV transgenic mice, they enter the liver, recognize antigen, secrete interferon...

  • [Article] Perceptual Organization of Tone Sequences in the Auditory Cortex of Awake Macaques - By Christophe Micheyl, Biao Tian, Robert P. Carlyon, and Josef P. Rauschecker. Acoustic sequences such as speech and music are generally perceived as coherent auditory “streams,†which can be individually attended to and followed over time. Although...

  • [Article] Perforin Triggers a Plasma Membrane-Repair Response that Facilitates CTL Induction of Apoptosis - By Dennis Keefe, Lianfa Shi, Stefan Feske, Ramiro Massol, Francisco Navarro, Tomas Kirchhausen, and Judy Lieberman. Perforin delivers granzymes to induce target-cell apoptosis. At high concentrations, perforin multimerizes in the plasma membrane to form pores. However, whether granzymes enter target cells...

  • [Article] Perisinusoidal B Cells in the Bone Marrow Participate in T-Independent Responses to Blood-Borne Microbes - By Annaiah Cariappa, Irina B. Mazo, Catharine Chase, Hai Ning Shi, Haoyuan Liu, Qian Li, Harris Rose, Harry Leung, Bobby J. Cherayil, Paul Russell, Ulrich von Andrian, and Shiv Pillai. Mature recirculating B cells are generally assumed to exist in follicular niches in secondary lymphoid organs, and these cells mediate T-dependent humoral immune responses. We...

  • [Article] Phagosome Maturation Proceeds Independently of Stimulation of Toll-like Receptors 2 and 4 - By Robin M. Yates, and David G. Russell. Toll-like receptors modulate many aspects of the innate immune response. Recent reports suggest that the maturation of phagosomes following particle uptake is modulated through signaling...

  • [Article] Phenotypic Modulation of Smooth Muscle Cells through Interaction of Foxo4 and Myocardin - By Zhi-Ping Liu, Zhigao Wang, Hiromi Yanagisawa, and Eric N. Olson. Smooth muscle cells (SMCs) modulate their phenotype between proliferative and differentiated states in response to physiological and pathological cues. Insulin-like growth factor-I stimulates differentiation of...

  • [Article] Phosphodiesterase 4D Deficiency in the Ryanodine-Receptor Complex Promotes Heart Failure and Arrhythmias - By Stephan E. Lehnart, Xander H.T. Wehrens, Steven Reiken, Sunita Warrier, Andriy E. Belevych, Robert D. Harvey, Wito Richter, S.-L. Catherine Jin, Marco Conti, and Andrew R. Marks. Phosphodiesterases (PDEs) regulate the local concentration of 3′,5′ cyclic adenosine monophosphate (cAMP) within cells. cAMP activates the cAMP-dependent protein kinase (PKA). In patients, PDE inhibitors...

  • [Article] Phosphorylation of FADD at Serine 194 by CKIα Regulates Its Nonapoptotic Activities - By Elizabeth C. Alappat, Christine Feig, Benjamin Boyerinas, Jörg Volkland, Martin Samuels, Andrea E. Murmann, Andrew Thorburn, Vincent J. Kidd, Clive A. Slaughter, Stephanie L. Osborn, Astar Winoto, Wei-Jen Tang, and Marcus E. Peter. FADD is essential for death receptor (DR)-induced apoptosis. However, it is also critical for cell cycle progression and proliferation, activities that are regulated by phosphorylation...

  • [Article] Phosphorylation of Neurogenin2 Specifies the Migration Properties and the Dendritic Morphology of Pyramidal Neurons in the Neocortex - By Randal Hand, Dante Bortone, Pierre Mattar, Laurent Nguyen, Julian Ik-Tsen Heng, Sabrice Guerrier, Elizabeth Boutt, Eldon Peters, Anthony P. Barnes, Carlos Parras, Carol Schuurmans, François Guillemot, and Franck Polleux. The molecular mechanisms specifying the dendritic morphology of different neuronal subtypes are poorly understood. Here we demonstrate that the bHLH transcription factor Neurogenin2 (Ngn2) is...

  • [Article] Physical Association and Coordinate Function of the H3 K4 Methyltransferase MLL1 and the H4 K16 Acetyltransferase MOF - By Yali Dou, Thomas A. Milne, Alan J. Tackett, Edwin R. Smith, Aya Fukuda, Joanna Wysocka, C. David Allis, Brian T. Chait, Jay L. Hess, and Robert G. Roeder. A stable complex containing MLL1 and MOF has been immunoaffinity purified from a human cell line that stably expresses an epitope-tagged WDR5 subunit. Stable interactions...

  • [Article] Placebo in Emotional Processing— Induced Expectations of Anxiety Relief Activate a Generalized Modulatory Network - By Predrag Petrovic, Thomas Dietrich, Peter Fransson, Jesper Andersson, Katrina Carlsson, and Martin Ingvar. Placebo analgesia and reward processing share several features. For instance, expectations have a strong influence on the subsequent emotional experience of both. Recent imaging data...

  • [Article] Pleiotropic effects of HIF-1 blockade on tumor radiosensitivity - By Benjamin J. Moeller, Matthew R. Dreher, Zahid N. Rabbani, Thies Schroeder, Yiting Cao, Chuan Y. Li, and Mark W. Dewhirst. We have previously shown that radiation increases HIF-1 activity in tumors, causing significant radioprotection of the tumor vasculature. The impact that HIF-1 activation has on...

  • [Article] Prefrontal Cortex Activity Related to Abstract Response Strategies - By Aldo Genovesio, Peter J. Brasted, Andrew R. Mitz, and Steven P. Wise. Many monkeys adopt abstract response strategies as they learn to map visual symbols to responses by trial and error. According to the repeat-stay strategy, if...

  • [Article] Proapoptotic BID Is an ATM Effector in the DNA-Damage Response - By Iris Kamer, Rachel Sarig, Yehudit Zaltsman, Hagit Niv, Galia Oberkovitz, Limor Regev, Gal Haimovich, Yaniv Lerenthal, Richard C. Marcellus, and Atan Gross. The “BH3-only†proapoptotic BCL-2 family members are sentinels of intracellular damage. Here, we demonstrated that the BH3-only BID protein partially localizes to the nucleus in...

  • [Article] Probabilistic Regulation in TH2 Cells Accounts for Monoallelic Expression of IL-4 and IL-13 - By Liying Guo, Jane Hu-Li, and William E. Paul. Il4 and Il13, closely linked genes, are expressed monoallelically in TH2 cells. Four different approaches (RNA FISH, cultures from Il13T-Il4/Il13-G4 mice, cultures from heterozygous Il13-Il4...

  • [Article] Protein Kinase D1 and the β1 Integrin Cytoplasmic Domain Control β1 Integrin Function via Regulation of Rap1 Activation - By Ricardo B. Medeiros, Deborah M. Dickey, Heekyoung Chung, Angie C. Quale, Lakshmi R. Nagarajan, Daniel D. Billadeau, and Yoji Shimizu. The functional activity of integrins is dynamically regulated by T cell receptor stimulation and by protein kinase C (PKC). We report a novel function for...

  • [Article] Pten constrains centroacinar cell expansion and malignant transformation in the pancreas - By Ben Z. Stanger, Bangyan Stiles, Gregory Y. Lauwers, Nabeel Bardeesy, Michael Mendoza, Ying Wang, Amy Greenwood, Kuang-hung Cheng, Margaret McLaughlin, Dennis Brown, Ronald A. DePinho, Hong Wu, Douglas A. Melton, and Yuval Dor. To determine the role of the phosphatidylinositol 3-kinase (PI3-K) pathway in pancreas development, we generated a pancreas-specific knockout of Pten, a negative regulator of PI3-K...

  • [Article] Ptf1a, a bHLH Transcriptional Gene, Defines GABAergic Neuronal Fates in Cerebellum - By Mikio Hoshino, Shoko Nakamura, Kiyoshi Mori, Takeshi Kawauchi, Mami Terao, Yoshiaki V. Nishimura, Akihisa Fukuda, Toshimitsu Fuse, Naoki Matsuo, Masaki Sone, Masahiko Watanabe, Haruhiko Bito, Toshio Terashima, Christopher V.E. Wright, Yoshiya Kawaguchi, Kazuwa Nakao, and Yo-ichi Nabeshima. The molecular machinery governing glutamatergic-GABAergic neuronal subtype specification is unclear. Here we describe a cerebellar mutant, cerebelless, which lacks the entire cerebellar cortex in adults....

  • [Article] PU.1 Expression Delineates Heterogeneity in Primary Th2 Cells - By Hua-Chen Chang, Shangming Zhang, Vivian T. Thieu, Roger B. Slee, Heather A. Bruns, R. Nicholas Laribee, Michael J. Klemsz, and Mark H. Kaplan. Primary T helper 2 cells are heterogeneous, expressing subsets of cytokines at varying levels. Mechanisms controlling this spectrum of phenotypes are still unclear. The ETS...

  • [Article] Radial glia cells are candidate stem cells of ependymoma - By Michael D. Taylor, Helen Poppleton, Christine Fuller, Xiaoping Su, Yongxing Liu, Patricia Jensen, Susan Magdaleno, James Dalton, Christopher Calabrese, Julian Board, Tobey MacDonald, Jim Rutka, Abhijit Guha, Amar Gajjar, Tom Curran, and Richard J. Gilbertson. Tumors of the same histologic type often comprise clinically and molecularly distinct subgroups; however, the etiology of these subgroups is unknown. Here, we report that...

  • [Article] Rap2-JNK Removes Synaptic AMPA Receptors during Depotentiation - By Yinghua Zhu, Daniel Pak, Yi Qin, Stefanie G. McCormack, Myung J. Kim, Joel P. Baumgart, Vanisree Velamoor, Yves P. Auberson, Pavel Osten, Linda van Aelst, Morgan Sheng, and J. Julius Zhu. The related small GTPases Ras and Rap1 are important for signaling synaptic AMPA receptor (-R) trafficking during long-term potentiation (LTP) and long-term depression (LTD), respectively....

  • [Article] Rational design of shepherdin, a novel anticancer agent - By Janet Plescia, Whitney Salz, Fang Xia, Marzia Pennati, Nadia Zaffaroni, Maria Grazia Daidone, Massimiliano Meli, Takehiko Dohi, Paola Fortugno, Yulia Nefedova, Dmitry I. Gabrilovich, Giorgio Colombo, and Dario C. Altieri. Anticancer agents that selectively kill tumor cells and spare normal tissues are urgently needed. Here, we engineered a cell-permeable peptidomimetic, shepherdin, modeled on the binding...

  • [Article] Receptor for RACK1 Mediates Activation of JNK by Protein Kinase C - By Pablo López-Bergami, Hasem Habelhah, Anindita Bhoumik, Weizhou Zhang, Lu-Hai Wang, and Ze’ev Ronai. Activation of the Jun-N-terminal kinase (JNK) signaling cascade by phorbol esters (TPA) or protein kinase C (PKC) is well documented, although the underlying mechanism is...

  • [Article] Recognition of Antimicrobial Peptides by a Bacterial Sensor Kinase - By Martin W. Bader, Sarah Sanowar, Margaret E. Daley, Anna R. Schneider, Uhnsoo Cho, Wenqing Xu, Rachel E. Klevit, Hervé Le Moual, and Samuel I. Miller. PhoQ is a membrane bound sensor kinase important for the pathogenesis of a number of Gram-negative bacterial species. PhoQ and its cognate response regulator PhoP...

  • [Article] Regulation by let-7 and lin-4 miRNAs Results in Target mRNA Degradation - By Shveta Bagga, John Bracht, Shaun Hunter, Katlin Massirer, Janette Holtz, Rachel Eachus, and Amy E. Pasquinelli. MicroRNAs (miRNAs) are ∼22 nucleotide RNAs that negatively regulate the expression of protein-coding genes. In a present model of miRNA function in animals, miRNAs that...

  • [Article] Regulation of Nuclear Proteasome by Rhp6/Ubc2 through Ubiquitination and Destruction of the Sensor and Anchor Cut8 - By Kojiro Takeda, and Mitsuhiro Yanagida. While proteasome is central to the degradation of cellular ubiquitinated proteins, the control of its nuclear function is barely understood. Here we show that the...

  • [Article] Regulation of p53 Translation and Induction after DNA Damage by Ribosomal Protein L26 and Nucleolin - By Masatoshi Takagi, Michael J. Absalon, Kevin G. McLure, and Michael B. Kastan. Increases in p53 protein levels after DNA damage have largely been attributed to an increase in the half-life of p53 protein. Here we demonstrate that...

  • [Article] Regulation of Protein Compartmentalization Expands the Diversity of Protein Function - By Kelly L. Shaffer, Ajay Sharma, Erik L. Snapp, and Ramanujan S. Hegde. Proteins destined for the secretory pathway are translocated into the endoplasmic reticulum (ER) by signal sequences that vary widely in their functional properties. We have...

  • [Article] Regulation of Smurf2 Ubiquitin Ligase Activity by Anchoring the E2 to the HECT Domain - By Abiodun A. Ogunjimi, Douglas J. Briant, Nadia Pece-Barbara, Christine Le Roy, Gianni M. Di Guglielmo, Peter Kavsak, Richele K. Rasmussen, Bruce T. Seet, Frank Sicheri, and Jeffrey L. Wrana. The conjugation of ubiquitin to proteins involves a cascade of activating (E1), conjugating (E2), and ubiquitin-ligating (E3) type enzymes that commonly signal protein destruction. In...

  • [Article] Regulation of Yeast mRNA 3′ End Processing by Phosphorylation - By Xiaoyuan He, and Claire Moore. Recent studies have found that the phosphatase Glc7 associates with the yeast cleavage/polyadenylation factor (CPF), but the role of Glc7 in 3′ end processing has...

  • [Article] Regulators of Endocytosis Maintain Localized Receptor Tyrosine Kinase Signaling in Guided Migration - By Gáspár Jékely, Hsin-Ho Sung, Carlos M. Luque, and Pernille Rørth. Guidance receptors detect extracellular cues and instruct migrating cells how to orient in space. Border cells perform a directional invasive migration during Drosophila oogenesis and...

  • [Article] Regulatory Mutations of mir-48, a C. elegans let-7 Family MicroRNA, Cause Developmental Timing Defects - By Ming Li, Matthew W. Jones-Rhoades, Nelson C. Lau, David P. Bartel, and Ann E. Rougvie. The C. elegans heterochronic genes program stage-specific temporal identities in multiple tissues during larval development. These genes include the first two miRNA-encoding genes discovered, lin-4...

  • [Article] Roles of NMDA NR2B Subtype Receptor in Prefrontal Long-Term Potentiation and Contextual Fear Memory - By Ming-Gao Zhao, Hiroki Toyoda, Yong-Seok Lee, Long-Jun Wu, Shanelle W. Ko, Xue-Han Zhang, Yongheng Jia, Fanny Shum, Hui Xu, Bao-Ming Li, Bong-Kiun Kaang, and Min Zhuo. Cortical plasticity is thought to be important for the establishment, consolidation, and retrieval of permanent memory. Hippocampal long-term potentiation (LTP), a cellular mechanism of learning...

  • [Article] Rpe65 Is the Retinoid Isomerase in Bovine Retinal Pigment Epithelium - By Minghao Jin, Songhua Li, Walid N. Moghrabi, Hui Sun, and Gabriel H. Travis. The first event in light perception is absorption of a photon by an opsin pigment, which induces isomerization of its 11-cis-retinaldehyde chromophore. Restoration of light...

  • [Article] Rules of Recruitment for Th1 and Th2 Lymphocytes in Inflamed Liver: A Role for Alpha-4 Integrin and Vascular Adhesion Protein-1 - By Claudine S. Bonder, M. Ursula Norman, Mark G. Swain, Lori D. Zbytnuik, Jun Yamanouchi, Pere Santamaria, Maureen Ajuebor, Marko Salmi, Sirpa Jalkanen, and Paul Kubes. The mechanisms that mediate the recruitment of Th1 and Th2 lymphocytes in vivo are poorly understood. We demonstrate that the mechanisms by which exogenously produced...

  • [Article] Sar1p N-Terminal Helix Initiates Membrane Curvature and Completes the Fission of a COPII Vesicle - By Marcus C.S. Lee, Lelio Orci, Susan Hamamoto, Eugene Futai, Mariella Ravazzola, and Randy Schekman. Secretory proteins traffic from the ER to the Golgi via COPII-coated transport vesicles. The five core COPII proteins (Sar1p, Sec23/24p, and Sec13/31p) act in concert...

  • [Article] Sec15, a Component of the Exocyst, Promotes Notch Signaling during the Asymmetric Division of Drosophila Sensory Organ Precursors - By Hamed Jafar-Nejad, Hillary K. Andrews, Melih Acar, Vafa Bayat, Frederik Wirtz-Peitz, Sunil Q. Mehta, Juergen A. Knoblich, and Hugo J. Bellen. Asymmetric division of sensory organ precursors (SOPs) in Drosophila generates different cell types of the mature sensory organ. In a genetic screen designed to identify...

  • [Article] Sequence of Steps in Ribosome Recycling as Defined by Kinetic Analysis - By Frank Peske, Marina V. Rodnina, and Wolfgang Wintermeyer. After termination of protein synthesis in bacteria, ribosomes are recycled from posttermination complexes by the combined action of elongation factor G (EF-G), ribosome recycling factor...

  • [Article] Serine Protease Cathepsin G Regulates Adhesion-Dependent Neutrophil Effector Functions by Modulating Integrin Clustering - By Sofia Z. Raptis, Steven D. Shapiro, Pamela M. Simmons, Alec M. Cheng, and Christine T.N. Pham. The polymorphonuclear leukocyte (PMN)-derived serine proteases play a key role in immune complex (IC)-mediated inflammation. However, the mechanisms by which these proteases regulate inflammatory response...

  • [Article] Shh Controls Epithelial Proliferation via Independent Pathways that Converge on N-Myc - By Pleasantine Mill, Rong Mo, Ming Chang Hu, Lina Dagnino, Norman D. Rosenblum, and Chi-chung Hui. Shh signaling induces proliferation of many cell types during development and disease, but how Gli transcription factors regulate these mitogenic responses remains unclear. By genetically...

  • [Article] SHIP Represses the Generation of Alternatively Activated Macrophages - By Michael J. Rauh, Victor Ho, Carla Pereira, Anita Sham, Laura M. Sly, Vivian Lam, Lynsey Huxham, Andrew I. Minchinton, Alice Mui, and Gerald Krystal. We recently reported that SHIP restrains LPS-induced classical (M1) activation of in vitro differentiated, bone marrow-derived macrophages (BMMΦs) and that SHIP upregulation is essential for...

  • [Article] Signaling Pathways and Genes that Inhibit Pathogen-Induced Macrophage Apoptosis—CREB and NF-κB as Key Regulators - By Jin Mo Park, Florian R. Greten, Athena Wong, Randal J. Westrick, J. Simon C. Arthur, Kinya Otsu, Alexander Hoffmann, Marc Montminy, and Michael Karin. Certain microbes evade host innate immunity by killing activated macrophages with the help of virulence factors that target prosurvival pathways. For instance, infection of macrophages...

  • [Article] Single-Molecule Microscopy Reveals Plasma Membrane Microdomains Created by Protein-Protein Networks that Exclude or Trap Signaling Molecules in T Cells - By Adam D. Douglass, and Ronald D. Vale. Membrane subdomains have been implicated in T cell signaling, although their properties and mechanisms of formation remain controversial. Here, we have used single-molecule and scanning...

  • [Article] SLIM Is a Nuclear Ubiquitin E3 Ligase that Negatively Regulates STAT Signaling - By Takashi Tanaka, Michelle A. Soriano, and Michael J. Grusby. STAT proteins are a family of latent cytoplasmic transcription factors that are activated by tyrosine phosphorylation in response to a variety of cytokines, growth factors,...

  • [Article] Spatial and Temporal Recruitment of Androgen Receptor and Its Coactivators Involves Chromosomal Looping and Polymerase Tracking - By Qianben Wang, Jason S. Carroll, and Myles Brown. Androgen receptor (AR) plays a critical role in the development and progression of prostate cancer, where it is a key therapeutic target. Here we report...

  • [Article] Spatiotemporal Elements of Macaque V1 Receptive Fields - By Nicole C. Rust, Odelia Schwartz, J. Anthony Movshon, and Eero P. Simoncelli. Neurons in primary visual cortex are classically divided into two groups. Simple cells respond precisely to the location and contrast polarity of features in the...

  • [Article] Spiroplasma Swim by a Processive Change in Body Helicity - By Joshua W. Shaevitz, Joanna Y. Lee, and Daniel A. Fletcher. Microscopic organisms must rely on very different strategies than their macroscopic counterparts to swim through liquid. To date, the best understood method for prokaryotic swimming...

  • [Article] Structural and Biochemical Mechanisms for the Specificity of Hormone Binding and Coactivator Assembly by Mineralocorticoid Receptor - By Yong Li, Kelly Suino, Jennifer Daugherty, and H. Eric Xu. Mineralocorticoid receptor (MR) controls sodium homeostasis and blood pressure through hormone binding and coactivator recruitment. Here, we report a 1.95 Ã… crystal structure of the...

  • [Article] Structural Basis for an Unexpected Mode of SERM-Mediated ER Antagonism - By Ya-Ling Wu, Xiaojing Yang, Zhong Ren, Donald P. McDonnell, John D. Norris, Timothy M. Willson, and Geoffrey L. Greene. Tamoxifen is effective for the prevention and treatment of estrogen-dependent breast cancers, but is associated with an increased incidence of endometrial tumors. We report the...

  • [Article] Structural Basis of the Cks1-Dependent Recognition of p27Kip1 by the SCFSkp2 Ubiquitin Ligase - By Bing Hao, Ning Zheng, Brenda A. Schulman, Geng Wu, Julie J. Miller, Michele Pagano, and Nikola P. Pavletich. The ubiquitin-mediated proteolysis of the Cdk2 inhibitor p27Kip1 plays a central role in cell cycle progression, and enhanced degradation of p27Kip1 is associated with many...

  • [Article] Structural Basis of Transcription Inhibition by Antibiotic Streptolydigin - By Dmitry Temiakov, Nikolay Zenkin, Marina N. Vassylyeva, Anna Perederina, Tahir H. Tahirov, Ekaterina Kashkina, Maria Savkina, Savva Zorov, Vadim Nikiforov, Noriyuki Igarashi, Naohiro Matsugaki, Soichi Wakatsuki, Konstantin Severinov, and Dmitry G. Vassylyev. Streptolydigin (Stl) is a potent inhibitor of bacterial RNA polymerases (RNAPs). The 2.4 Ã… resolution structure of the Thermus thermophilus RNAP-Stl complex showed that, in...

  • [Article] Structure of an OhrR-ohrA Operator Complex Reveals the DNA Binding Mechanism of the MarR Family - By Minsun Hong, Mayuree Fuangthong, John D. Helmann, and Richard G. Brennan. The mechanisms by which Bacillus subtilis OhrR, a member of the MarR family of transcription regulators, binds the ohrA operator and is induced by oxidation...

  • [Article] SUMO Modification Is Involved in the Maintenance of Heterochromatin Stability in Fission Yeast - By Jin A Shin, Eun Shik Choi, Hyun Soo Kim, Jenny C.Y. Ho, Felicity Z. Watts, Sang Dai Park, and Yeun Kyu Jang. Several studies have suggested that SUMO may participate in the regulation of heterochromatin, but direct evidence is lacking. Here, we present a direct link between...

  • [Article] Suppression of RNA Recognition by Toll-like Receptors: The Impact of Nucleoside Modification and the Evolutionary Origin of RNA - By Katalin Karikó, Michael Buckstein, Houping Ni, and Drew Weissman. DNA and RNA stimulate the mammalian innate immune system through activation of Toll-like receptors (TLRs). DNA containing methylated CpG motifs, however, is not stimulatory. Selected...

  • [Article] Syndecan Recyling Is Controlled by Syntenin-PIP2 Interaction and Arf6 - By Pascale Zimmermann, Zhe Zhang, Gisèle Degeest, Eva Mortier, Iris Leenaerts, Christien Coomans, Joachim Schulz, Francisca N’Kuli, Pierre J. Courtoy, and Guido David. Syndecans are heparan sulfate proteoglycans that modulate the activity of several growth factors and cell adhesion molecules. PDZ domains in the adaptor protein syntenin interact...

  • [Article] Systems-Level Dissection of the Cell-Cycle Oscillator: Bypassing Positive Feedback Produces Damped Oscillations - By Joseph R. Pomerening, Sun Young Kim, and James E. Ferrell. The cell-cycle oscillator includes an essential negative-feedback loop: Cdc2 activates the anaphase-promoting complex (APC), which leads to cyclin destruction and Cdc2 inactivation. Under some circumstances,...

  • [Article] Targeting ornithine decarboxylase in Myc-induced lymphomagenesis prevents tumor formation - By Jonas A. Nilsson, Ulrich B. Keller, Troy A. Baudino, Chunying Yang, Sara Norton, Jennifer A. Old, Lisa M. Nilsson, Geoffrey Neale, Debora L. Kramer, Carl W. Porter, and John L. Cleveland. Checkpoints that control Myc-mediated proliferation and apoptosis are bypassed during tumorigenesis. Genes encoding polyamine biosynthetic enzymes are overexpressed in B cells from Eμ-Myc transgenic mice....

  • [Article] Tensional homeostasis and the malignant phenotype - By Matthew J. Paszek, Nastaran Zahir, Kandice R. Johnson, Johnathon N. Lakins, Gabriela I. Rozenberg, Amit Gefen, Cynthia A. Reinhart-King, Susan S. Margulies, Micah Dembo, David Boettiger, Daniel A. Hammer, and Valerie M. Weaver. Tumors are stiffer than normal tissue, and tumors have altered integrins. Because integrins are mechanotransducers that regulate cell fate, we asked whether tissue stiffness could...

  • [Article] The AXH Domain of Ataxin-1 Mediates Neurodegeneration through Its Interaction with Gfi-1/Senseless Proteins - By Hiroshi Tsuda, Hamed Jafar-Nejad, Akash J. Patel, Yaling Sun, Hung-Kai Chen, Matthew F. Rose, Koen J.T. Venken, Juan Botas, Harry T. Orr, Hugo J. Bellen, and Huda Y. Zoghbi. Spinocerebellar ataxia type 1 (SCA1) is a neurodegenerative disease caused by an expanded glutamine tract in human Ataxin-1 (hAtx-1). The expansion stabilizes hAtx-1, leading to...

  • [Article] The “Soluble†Adenylyl Cyclase in Sperm Mediates Multiple Signaling Events Required for Fertilization - By Kenneth C. Hess, Brian H. Jones, Becky Marquez, Yanqiu Chen, Teri S. Ord, Margarita Kamenetsky, Catarina Miyamoto, Jonathan H. Zippin, Gregory S. Kopf, Susan S. Suarez, Lonny R. Levin, Carmen J. Williams, Jochen Buck, and Stuart B. Moss. Mammalian fertilization is dependent upon a series of bicarbonate-induced, cAMP-dependent processes sperm undergo as they “capacitate,†i.e., acquire the ability to fertilize eggs. Male mice...

  • [Article] The BAD protein integrates survival signaling by EGFR/MAPK and PI3K/Akt kinase pathways in PTEN-deficient tumor cells - By Qing-Bai She, David B. Solit, Qing Ye, Kathryn E. O’Reilly, Jose Lobo, and Neal Rosen. Tumor cells with mutated PTEN proliferate in an EGFR-independent manner. Induction of PTEN sensitizes cells to EGFR inhibition, and the combination causes synergistic apoptosis. Synergy...

  • [Article] The Cdk1 Complex Plays a Prime Role in Regulating N-Myc Phosphorylation and Turnover in Neural Precursors - By Sarah K. Sjostrom, Greg Finn, William C. Hahn, David H. Rowitch, and Anna Marie Kenney. Myc family transcription factors are destabilized by phosphorylation of a conserved amino-terminal GSK-3β motif. In proliferating cerebellar granule neuron precursors (CGNPs), Sonic hedgehog signaling induces...

  • [Article] The Cellular Mechanism of Aire Control of T Cell Tolerance - By Mark S. Anderson, Emily S. Venanzi, Zhibin Chen, Stuart P. Berzins, Christophe Benoist, and Diane Mathis. Aire promotes the tolerization of thymocytes by inducing the expression of a battery of peripheral-tissue antigens in thymic medullary epithelial cells. We demonstrate that the...

  • [Article] The Coordinated Mapping of Visual Space and Response Features in Visual Cortex - By Hongbo Yu, Brandon J. Farley, Dezhe Z. Jin, and Mriganka Sur. Whether general principles can explain the layouts of cortical maps remains unresolved. In primary visual cortex of ferret, the relationships between the maps of visual...

  • [Article] The Drosophila Ovarian and Testis Stem Cell Niches: Similar Somatic Stem Cells and Signals - By Eva Decotto, and Allan C. Spradling. The stem cell niches at the apex of Drosophila ovaries and testes have been viewed as distinct in two major respects. While both contain germline...

  • [Article] The FK506 Binding Protein Fpr3 Counteracts Protein Phosphatase 1 to Maintain Meiotic Recombination Checkpoint Activity - By Andreas Hochwagen, Wai-Hong Tham, Gloria A. Brar, and Angelika Amon. The meiotic recombination checkpoint delays gamete precursors in G2 until DNA breaks created during recombination are repaired and chromosome structure has been restored. Here, we...

  • [Article] The Hippo Signaling Pathway Coordinately Regulates Cell Proliferation and Apoptosis by Inactivating Yorkie, the Drosophila Homolog of YAP - By Jianbin Huang, Shian Wu, Jose Barrera, Krista Matthews, and Duojia Pan. Coordination between cell proliferation and cell death is essential to maintain homeostasis in multicellular organisms. In Drosophila, these two processes are regulated by a pathway...

  • [Article] The Human Tumor Antigen PRAME Is a Dominant Repressor of Retinoic Acid Receptor Signaling - By Mirjam T. Epping, Liming Wang, Michael J. Edel, Leone Carlée, Maria Hernandez, and René Bernards. Retinoic acid (RA) induces proliferation arrest, differentiation, and apoptosis, and defects in retinoic acid receptor (RAR) signaling have been implicated in cancer. The human tumor...

  • [Article] The Kinetic Stability of MHC Class II:Peptide Complexes Is a Key Parameter that Dictates Immunodominance - By Christopher A. Lazarski, Francisco A. Chaves, Scott A. Jenks, Shenhong Wu, Katherine A. Richards, J.M. Weaver, and Andrea J. Sant. T cell priming to exogenous antigens reflects regulated antigen processing in dendritic cells, subsequent homing to lymph nodes, sustained interactions between T cells and antigen-bearing...

  • [Article] The let-7 MicroRNA Family Members mir-48, mir-84, and mir-241 Function Together to Regulate Developmental Timing in Caenorhabditis elegans - By Allison L. Abbott, Ezequiel Alvarez-Saavedra, Eric A. Miska, Nelson C. Lau, David P. Bartel, H. Robert Horvitz, and Victor Ambros. The microRNA let-7 is a critical regulator of developmental timing events at the larval-to-adult transition in C. elegans. Recently, microRNAs with sequence similarity to let-7...

  • [Article] The Mammalian RNA Polymerase II C-Terminal Domain Interacts with RNA to Suppress Transcription-Coupled 3′ End Formation - By Syuzo Kaneko, and James L. Manley. RNA polymerase II plays a critical role not only in transcription of mRNA precursors but also in their subsequent processing. This later function is mediated...

  • [Article] The Mnks Are Novel Components in the Control of TNFα Biosynthesis and Phosphorylate and Regulate hnRNP A1 - By Maria Buxadé, Josep L. Parra, Simon Rousseau, Natalia Shpiro, Rodolfo Marquez, Nick Morrice, Jenny Bain, Enric Espel, and Christopher G. Proud. Posttranscriptional regulatory mechanisms control TNFα expression through AU-rich elements in the 3′UTR of its mRNA. This is mediated through Erk and p38 MAP kinase signaling,...

  • [Article] The Neural Basis of Financial Risk Taking - By Camelia M. Kuhnen, and Brian Knutson. Investors systematically deviate from rationality when making financial decisions, yet the mechanisms responsible for these deviations have not been identified. Using event-related fMRI, we examined...

  • [Article] The oncoprotein gankyrin binds to MDM2/HDM2, enhancing ubiquitylation and degradation of p53 - By Hiroaki Higashitsuji, Hisako Higashitsuji, Katsuhiko Itoh, Toshiharu Sakurai, Toshikazu Nagao, Haruhiko Sumitomo, Tomoko Masuda, Simon Dawson, Yutaka Shimada, R. John Mayer, and Jun Fujita. Gankyrin is an ankyrin repeat oncoprotein commonly overexpressed in hepatocellular carcinomas. Gankyrin interacts with the S6 proteasomal ATPase and accelerates the degradation of the tumor...

  • [Article] The Polyadenylation Factor CPSF-73 Is Involved in Histone-Pre-mRNA Processing - By Zbigniew Dominski, Xiao-cui Yang, and William F. Marzluff. During 3′ end processing, histone pre-mRNAs are cleaved 5 nucleotides after a conserved stem loop by an endonuclease dependent on the U7 small nuclear ribonucleoprotein...

  • [Article] The Pore Helix Dipole Has a Minor Role in Inward Rectifier Channel Function - By Franck C. Chatelain, Noga Alagem, Qiang Xu, Raika Pancaroglu, Eitan Reuveny, and Daniel L. Minor. Ion channels lower the energetic barrier for ion passage across cell membranes and enable the generation of bioelectricity. Electrostatic interactions between permeant ions and channel pore...

  • [Article] The Putative RNA Helicase Dbp4p Is Required for Release of the U14 snoRNA from Preribosomes in Saccharomyces cerevisiae - By Martin KoÅ¡, and David Tollervey. Around 70 yeast snoRNAs guide rRNA modification, frequently forming base-paired interactions predicted to be very stable at physiological temperatures. Eighteen putative RNA helicases are required...

  • [Article] The Rho/Rac-Family Guanine Nucleotide Exchange Factor VAV-1 Regulates Rhythmic Behaviors in C. elegans - By Kenneth R. Norman, Robert T. Fazzio, Jerry E. Mellem, Maria V. Espelt, Kevin Strange, Mary C. Beckerle, and Andres V. Maricq. Rhythmic behaviors are a fundamental feature of all organisms. Pharyngeal pumping, the defecation cycle, and gonadal-sheath-cell contractions are three well-characterized rhythmic behaviors in the nematode...

  • [Article] The Role of Erk1 and Erk2 in Multiple Stages of T Cell Development - By April M. Fischer, Carol D. Katayama, Giles Pagès, Jacques Pouysségur, and Stephen M. Hedrick. Activation of extracellular-signal-regulated protein kinase (Erk) is central to growth-factor-receptor-mediated signaling including that originating from the T cell antigen receptor. It integrates cytoplasmic signals to...

  • [Article] The Structural Basis of Myosin V Processive Movement as Revealed by Electron Cryomicroscopy - By Niels Volkmann, HongJun Liu, Larnele Hazelwood, Elena B. Krementsova, Susan Lowey, Kathleen M. Trybus, and Dorit Hanein. The processive motor myosin V has a relatively high affinity for actin in the presence of ATP and, thus, offers the unique opportunity to visualize...

  • [Article] The Structure of the Follistatin:Activin Complex Reveals Antagonism of Both Type I and Type II Receptor Binding - By Thomas B. Thompson, Thomas F. Lerch, Robert W. Cook, Teresa K. Woodruff, and Theodore S. Jardetzky. TGF-β ligands stimulate diverse cellular differentiation and growth responses by signaling through type I and II receptors. Ligand antagonists, such as follistatin, block signaling and...

  • [Article] The Synaptic Localization of NR2B-Containing NMDA Receptors Is Controlled by Interactions with PDZ Proteins and AP-2 - By Kate Prybylowski, Kai Chang, Nathalie Sans, Lilly Kan, Stefano Vicini, and Robert J. Wenthold. The NMDA receptor (NMDAR) is a component of excitatory synapses and a key participant in synaptic plasticity. We investigated the role of two domains in...

  • [Article] The T-Box Transcription Factor SEA-1 Is an Autosomal Element of the X:A Signal that Determines C. elegans Sex - By Jennifer R. Powell, Margaret M. Jow, and Barbara J. Meyer. Sex is determined in C. elegans by a chromosome-counting mechanism that tallies X chromosome dose relative to the sets of autosomes, the X:A ratio. A...

  • [Article] The Transcriptional Coactivator Yes-Associated Protein Drives p73 Gene-Target Specificity in Response to DNA Damage - By Sabrina Strano, Olimpia Monti, Natalia Pediconi, Alessia Baccarini, Giulia Fontemaggi, Eleonora Lapi, Fiamma Mantovani, Alexander Damalas, Gennaro Citro, Ada Sacchi, Giannino Del Sal, Massimo Levrero, and Giovanni Blandino. The transcriptional coactivator Yes-associated protein (YAP) has been shown to interact with and to enhance p73-dependent apoptosis in response to DNA damage. Here, we show...

  • [Article] The Transcriptional Repressor Gfi1 Controls STAT3-Dependent Dendritic Cell Development and Function - By Chozhavendan Rathinam, Robert Geffers, Raif Yücel, Jan Buer, Karl Welte, Tarik Möröy, and Christoph Klein. The mechanisms controlling the differentiation of dendritic cells (DCs) remain largely unknown. Using a transcriptional profiling approach, we identified Gfi1 as a novel critical transcription...

  • [Article] The transcriptional repressor Snail promotes mammary tumor recurrence - By Susan E. Moody, Denise Perez, Tien-chi Pan, Christopher J. Sarkisian, Carla P. Portocarrero, Christopher J. Sterner, Kathleen L. Notorfrancesco, Robert D. Cardiff, and Lewis A. Chodosh. Breast cancer recurrence is a fundamental clinical manifestation of tumor progression and represents the principal cause of death from this disease. Using a conditional transgenic...

  • [Article] The Ubiquitin Ligase dTopors Directs the Nuclear Organization of a Chromatin Insulator - By Maya Capelson, and Victor G. Corces. Chromatin insulators are gene regulatory elements implicated in the establishment of independent chromatin domains. The gypsy insulator of D. melanogaster confers its activity through a...

  • [Article] The v-Jun point mutation allows c-Jun to escape GSK3-dependent recognition and destruction by the Fbw7 ubiquitin ligase - By Wenyi Wei, Jianping Jin, Susanne Schlisio, J. Wade Harper, and William G. Kaelin. The c-Jun and c-Myc oncogenic transcription factors are highly unstable proteins due to polyubiquitination. Similar to c-Myc, we report here that phosphorylation of c-Jun by...

  • [Article] Therapy-induced malignant neoplasms in Nf1 mutant mice - By Richard C. Chao, Urszula Pyzel, Jane Fridlyand, Yien-Ming Kuo, Lewis Teel, Jennifer Haaga, Alexander Borowsky, Andrew Horvai, Scott C. Kogan, Jeannette Bonifas, Bing Huey, Tyler E. Jacks, Donna G. Albertson, and Kevin M. Shannon. Therapy-induced cancers are a severe complication of genotoxic therapies. We used heterozygous Nf1 mutant mice as a sensitized genetic background to investigate tumor induction by...

  • [Article] Thymocyte-Thymocyte Interaction for Efficient Positive Selection and Maturation of CD4 T Cells - By Eun Young Choi, Kyeong Cheon Jung, Hyo Jin Park, Doo Hyun Chung, Jin Sook Song, Seung Don Yang, Elizabeth Simpson, and Seong Hoe Park. Despite numerous reports on MHC class II expression by T cells from a wide spectrum of mammalian species including humans, the biological relevance of this...

  • [Article] Thyroid Hormone-Induced Juxtaposition of Regulatory Elements/Factors and Chromatin Remodeling of Crabp1 Dependent on MED1/TRAP220 - By Sung Wook Park, Guangjin Li, Ya-Ping Lin, Maria J. Barrero, Kai Ge, Robert G. Roeder, and Li-Na Wei. The cellular retinoic acid binding protein I gene is induced by thyroid hormone (T3) through a T3 response element (TRE) approximately 1 kb upstream of...

  • [Article] Tie2 identifies a hematopoietic lineage of proangiogenic monocytes required for tumor vessel formation and a mesenchymal population of pericyte progenitors - By Michele De Palma, Mary Anna Venneri, Rossella Galli, Lucia Sergi Sergi, Letterio S. Politi, Maurilio Sampaolesi, and Luigi Naldini. Bone marrow-derived cells contribute to tumor angiogenesis. Here, we demonstrate that monocytes expressing the Tie2 receptor (Tie2-expressing monocytes [TEMs]) (1) are a distinct hematopoietic lineage...

  • [Article] Trp53R172H and KrasG12D cooperate to promote chromosomal instability and widely metastatic pancreatic ductal adenocarcinoma in mice - By Sunil R. Hingorani, Lifu Wang, Asha S. Multani, Chelsea Combs, Therese B. Deramaudt, Ralph H. Hruban, Anil K. Rustgi, Sandy Chang, and David A. Tuveson. To define the genetic requirements for pancreatic ductal adenocarcinoma (PDA), we have targeted concomitant endogenous expression of Trp53R172H and KrasG12D to the mouse pancreas, revealing...

  • [Article] Updating Visual Space during Motion in Depth - By Nuo Li, and Dora E. Angelaki. Whether we are riding in a car or walking, our internal map of the environment must be continuously updated to maintain spatial constancy. Using a...

  • [Article] Upregulation of TGF-β, FOXP3, and CD4+CD25+ Regulatory T Cells Correlates with More Rapid Parasite Growth in Human Malaria Infection - By Michael Walther, Jon Eric Tongren, Laura Andrews, Daniel Korbel, Elizabeth King, Helen Fletcher, Rikke F. Andersen, Philip Bejon, Fiona Thompson, Susanna J. Dunachie, Fanny Edele, J. Brian de Souza, Robert E. Sinden, Sarah C. Gilbert, Eleanor M. Riley, and Adrian V.S. Hill. Understanding the regulation of immune responses is central for control of autoimmune and infectious disease. In murine models of autoimmunity and chronic inflammatory disease, potent...

  • [Article] VISA Is an Adapter Protein Required for Virus-Triggered IFN-β Signaling - By Liang-Guo Xu, Yan-Yi Wang, Ke-Jun Han, Lian-Yun Li, Zhonghe Zhai, and Hong-Bing Shu. Viral infection or stimulation of TLR3 triggers signaling cascades, leading to activation of the transcription factors IRF-3 and NF-κB, which collaborate to induce transcription of...

  • [Article] WDR5 Associates with Histone H3 Methylated at K4 and Is Essential for H3 K4 Methylation and Vertebrate Development - By Joanna Wysocka, Tomek Swigut, Thomas A. Milne, Yali Dou, Xin Zhang, Alma L. Burlingame, Robert G. Roeder, Ali H. Brivanlou, and C. David Allis. Histone H3 lysine 4 (K4) methylation has been linked to the transcriptional activation in a variety of eukaryotic species. Here we show that a common...

  • [Article] Wnt/β-Catenin Signaling in Mesenchymal Progenitors Controls Osteoblast and Chondrocyte Differentiation during Vertebrate Skeletogenesis - By Timothy F. Day, Xizhi Guo, Lisa Garrett-Beal, and Yingzi Yang. Chondrocytes and osteoblasts are two primary cell types in the skeletal system that are differentiated from common mesenchymal progenitors. It is believed that osteoblast differentiation...

  • [Article] Wnt11 Functions in Gastrulation by Controlling Cell Cohesion through Rab5c and E-Cadherin - By Florian Ulrich, Michael Krieg, Eva-Maria Schötz, Vinzenz Link, Irinka Castanon, Viktor Schnabel, Anna Taubenberger, Daniel Mueller, Pierre-Henri Puech, and Carl-Philipp Heisenberg. Wnt11 plays a central role in tissue morphogenesis during vertebrate gastrulation, but the molecular and cellular mechanisms by which Wnt11 exerts its effects remain poorly...

  • [Article] Wnt9b Plays a Central Role in the Regulation of Mesenchymal to Epithelial Transitions Underlying Organogenesis of the Mammalian Urogenital System - By Thomas J. Carroll, Joo-Seop Park, Shigemi Hayashi, Arindam Majumdar, and Andrew P. McMahon. The vertebrate urogenital system forms due to inductive interactions between the Wolffian duct, its derivative the ureteric bud, and their adjacent mesenchymes. These establish epithelial...

  • [Article] Yos9 Protein Is Essential for Degradation of Misfolded Glycoproteins and May Function as Lectin in ERAD - By Reka Szathmary, Regula Bielmann, Mihai Nita-Lazar, Patricie Burda, and Claude A. Jakob. The Htm1/EDEM protein has been proposed to act as a “degradation lectin†for endoplasmic reticulum-associated degradation (ERAD) of misfolded glycoproteins. In this study, we provide...

  • [Article] Yos9p Detects and Targets Misfolded Glycoproteins for ER-Associated Degradation - By Woong Kim, Eric D. Spear, and Davis T.W. Ng. Endoplasmic reticulum (ER) quality control mechanisms monitor the folding of nascent secretory and membrane polypeptides. Immature molecules are actively retained in the folding compartment whereas...

  • [Book reviews] A Handbook of Anatomical Pathology - (No abstract is available for this citation)

  • [Book reviews] Biology and Management of Multiple Myeloma - (No abstract is available for this citation)

  • [Book reviews] Bloody Easy: Blood Transfusions, Blood Alternatives and Transfusion Reactions: a Guide to Transfusion Medicine - (No abstract is available for this citation)

  • [Book reviews] Colour Atlas of Anatomical Pathology, 3rd Edition - (No abstract is available for this citation)

  • [Book reviews] Forensic Pathology Reviews: Volume 1 - (No abstract is available for this citation)

  • [Book reviews] Infection and Immunity - (No abstract is available for this citation)

  • [Book reviews] Molecular Microbiology - (No abstract is available for this citation)

  • [Book reviews] WHO Classification of Tumours: Pathology and Genetics of Tumours of the Breast and Female Genital Organs - (No abstract is available for this citation)

  • [Book review] Cells, Tissues, and Disease; 2nd edition - (No abstract is available for this citation)

  • [Book review] Embryo and Fetal Pathology. Color Atlas with Ultrasound Correlation - (No abstract is available for this citation)

  • [Case reports] A rare presentation of zygomycosis (mucormycosis) and review of the literature -

    Zygomycosis (mucormycosis) is a rare fungal infection seen most often in association with prolonged neutropenia. Intestinal zygomycosis is extremely rare and difficult to diagnose, but it is important not to miss, because early medical and surgical treatment can improve survival. This report describes a 56 year old woman who developed this infection while receiving chemotherapy for acute lymphoblastic leukaemia. Medical and surgical measures proved unsuccessful because there was a delay in diagnosis and institution of appropriate treatment.


  • [Case reports] A teratoid cyst containing nephrogenic tissue in a woman with a horseshoe kidney -

    A 21 year old woman presenting with flank pain and vomiting was found to have a cystic lesion associated with a horseshoe kidney. The inner aspect of the cyst wall consisted of connective tissue intermingled with colonic-type epithelium. Within the cyst wall there were multiple foci of immature and incompletely differentiated renal elements, together with fragments of urothelium, smooth muscle, bone, and neuroendocrine tissue. No immature renal blastema were found. This lesion is unique and labelled as a teratoid cyst containing nephrogenic tissue.


  • [Case reports] Adenosquamous carcinoma of the pancreas with an acantholytic pattern together with osteoclast-like and pleomorphic giant cells -

    A 45 year old man presented with abdominal pain, loss of appetite, and significant weight loss over a period of about four weeks. Imaging of the abdomen showed a mass in the region of the head of the pancreas. In view of the size of the mass and the clinical picture, a Whipple’s procedure was performed. Histological evaluation of the pancreatic tumour showed an adenosquamous carcinoma (predominantly composed of squamous carcinoma), which was extensively infiltrative with perineural invasion and involvement of peripancreatic lymph nodes. Areas of pancreatic intraepithelial neoplasia grade III and merging of the squamous and adenocarcinoma components were evident. Unusual histological features that characterised this case included a pronounced acantholytic pattern within the squamous carcinoma component, and the presence of both osteoclastic and pleomorphic giant cells. Giant cells have not been documented previously in association with an adenosquamous carcinoma. Although an acantholytic pattern has been noted in squamous carcinomas in other sites, this is the first report of such a pattern in an adenosquamous carcinoma of the pancreas.


  • [Case reports] ALK positive inflammatory myofibroblastic tumour of the pineal region -

    Inflammatory myofibroblastic tumours (IMTs) are an uncommon spindle cell neoplasm with a dense inflammatory infiltrate, usually encountered in children. IMTs of the central nervous system are extremely rare. This report describes the case of an IMT in a 61 year old man, in the pineal region. The tumour was completely excised, and immunohistochemistry demonstrated anaplastic lymphoma kinase 1 expression. There was no tumour recurrence during 18 months of follow up. Our case extends both the age range and sites of occurrence of this rare tumour.


  • [Case reports] Colonic angiomyolipoma with a monotypic expression and a predominant epithelioid component -

    Angiomyolipomas are rare lesions, often arising in the kidney, and are part of a group of tumours with a diverse appearance and evidence of dual melanocytic and smooth muscle differentiation known as PEComas (tumours of perivascular epithelioid cell origin). This report describes an unusual case of a colonic PEComa in a 40 year old woman. Unlike most of the previous colonic angiomyolipomas/PEComas reported in the literature, this case formed a large, mainly extrinsic mass and was monotypic, and composed entirely of the myomatous component with no adipose tissue or typical vasculature.


  • [Case reports] Combined fibrolamellar carcinoma and cholangiocarcinoma exhibiting biphenotypic antigen expression: a case report -

    Fibrolamellar carcinoma (FLC), a variant of hepatocellular carcinoma (HCC), very rarely occurs in association with cholangiocarcinoma (CC). This report describes the first case of FLC coexisting with CC (FLC-CC) from Japan. Although the major part of the tumour located in the right lobe of the liver showed the typical features of FLC, CC was admixed with the FLC, not only in the primary hepatic tumour, but also in the lymph node metastases. Immunohistochemical analysis revealed that, although carcinoembryonic antigen (CEA), which can be detected with monoclonal antibodies in the cytoplasm and the cell surface of CC cells but not HCC cells, was expressed in only the CC cells in the primary tumour, it was expressed extensively in the cytoplasm of both CC and FLC cells in the metastatic and recurrent tumours. Furthermore, Hep Par 1, a hepatocyte specific antigen, was also expressed in both the FLC and CC cells. These findings suggest that, in this case, both FLC and CC were possibly derived from the same cancer stem cell with the capacity to differentiate into both hepatocytes and bile duct epithelium, and that both the cellular components, therefore, exhibited biphenotypic antigen expression.


  • [Case reports] Congenital dermatofibrosarcoma protuberans with fibrosarcomatous and myxoid change -

    This report describes a case of congenital dermatofibrosarcoma protuberans (DFSP) with fibrosarcomatous (FS) and myxoid areas. Immunohistochemical results showed that tumour cells in ordinary DFSP areas were diffusely positive for CD34, whereas in the FS and myxoid areas, few tumour cells were positive for this antigen. Ki-67 positive tumour cell numbers were greater in the FS (11.8%) and myxoid areas (19.8%) relative to ordinary DFSP areas (2.2%). Reverse transcription polymerase chain reaction and sequence analysis showed the presence of an identical COL1A1–PDGFB fusion transcript in ordinary DFSP (plaque-like area), FS, and myxoid areas of DFSP. These results indicate that the three components of DFSP have a common histogenesis. This study documents the first application of gene analysis involving the myxoid area of DFSP.


  • [Case reports] Di-George syndrome presenting with hypocalcaemia in adulthood: two case reports and a review -

    This report describes two cases of Di-George syndrome presenting with hypoparathyroidism in adulthood. The first patient presented with profound hypocalcaemia that resulted in a generalised seizure. Routine investigations revealed hypoparathyroidism. The clue to her underlying condition was the postnatal death of her young child. This case shows that Di-George syndrome can present in adulthood with hypocalcaemia in the absence of other classic features of this condition. This has enormous implications for future family planning and may also have important health implications. The second patient, diagnosed on routine blood testing, had previously suffered with a congenital heart condition, but the syndrome was not revealed until she was of postmenopausal age. These two patients show that Di-George syndrome can present in adulthood with hypocalcaemia. This is an important observation because the condition has profound implications for health and family planning.


  • [Case reports] Epidural angiolipoma is histologically distinct from its cutaneous counterpart in the calibre and density of its vascular component; a case report with review of the literature -

    Angiolipoma of the spine is a rare tumour and no studies have investigated a sufficient number of cases to reach general conclusions. Therefore, as yet, the pathological definition of this entity is not well established. The case of epidural angiolipoma reported here and a review of the literature revealed that this entity is distinct from cutaneous angiolipoma in that the calibre of its predominant vascular component is far greater than that of the fat cells. Therefore, epidural angiolipoma can be regarded as not only topographically, but also histologically, distinct from its subcutaneous counterpart.


  • [Case reports] Gastrointestinal stromal tumour treated with neoadjuvant imatinib -

    This report describes a case of unresectable primary gastrointestinal stromal tumour (GIST) treated with imatinib on a neoadjuvant basis, before subsequent successful surgical resection. After six months of imatinib, computed tomography and positron emission tomography imaging demonstrated a significant size reduction and complete metabolic response to treatment, rendering the tumour resectable. Mutational analysis showed an activating KIT mutation in exon 11. The pathological appearance of the resected tumour was heterogeneous with extensive necrosis, cystic and myxoid change, extensive hypocellularity, and patchy foci of residual viable tumour. The implications for this management option of radiological, pathological, and molecular assessment are discussed.


  • [Case reports] Guillain Barre syndrome precipitated by the use of antilymphocyte globulin in the treatment of severe aplastic anaemia -

    This report describes the case of a 54 year old woman with very severe aplastic anaemia who was treated with antilymphocyte globulin (ALG) and developed Guillain Barré syndrome (GBS). No antecedent infective aetiology was identified. Although there are numerous reports of autoimmune disease after treatment with ALG in aplastic anaemia, and GBS after immunosuppressive treatment, there are none reporting GBS after the use of ALG for severe aplastic anaemia. The occurrence of autoimmune disease after immunosuppressive treatment, in particular ALG, is discussed, together with the possible mechanisms that result from T cell depression.


  • [Case reports] Idiopathic pure red cell aplasia: first report on CD8 positive lymphocytosis in bone marrow biopsy sections -

    There is no information in the literature regarding the lymphocyte content or type in bone marrow biopsies from patients with "idiopathic" pure red cell aplasia (PRCA). This report describes the bone marrow biopsy sections of a patient with PRCA. A diffuse CD3 positive (CD8 positive, granzyme B negative) lymphocytosis of approximately 1500/mm3 was revealed by immunohistochemical staining. The extent of the T cell increase was not evident from morphological examination of the bone marrow aspirate or biopsy, from flow cytometric analysis of the aspirate, or from the peripheral blood lymphocyte count. Therefore, immunohistochemical analysis should be performed routinely in this rare disease and the data acquired may help to inform the choice of treatment.


  • [Case reports] Large cell neuroendocrine carcinoma of the larynx: a case report and a review of the classification of this neoplasm -

    This report describes a case of large cell neuroendocrine carcinoma (LCNEC) of the larynx. A 74 year old man who presented with otalgia underwent direct laryngoscopy with biopsy, which revealed an invasive poorly differentiated carcinoma. Laryngectomy with bilateral neck dissections revealed invasion of the pre-epiglottic space by the tumour, with metastases to bilateral lymph nodes (AJCC T3N2c). The tumour was characterised by large cells with vesicular chromatin and prominent nucleoli. The cells were arranged in organoid and trabecular patterns with a background of extensive necrosis and numerous mitotic figures. Immunohistochemical and ultrastructural analyses confirmed the neuroendocrine nature of the tumour. Metastatic disease was present in the liver, and the patient died within weeks of surgery. LCNEC carcinoma is a rare tumour of the larynx. Recognition at this site is essential so that proper patient management can be initiated.


  • [Case reports] Myeloid metaplasia in the gall bladder: a case report -

    Idiopathic myelofibrosis is often associated with myeloid metaplasia (extramedullary haemopoiesis) in the spleen and liver. However, the gall bladder is an extremely unusual site for it to occur. A 59 year old man with myelofibrosis, who underwent cholecystectomy for chronic cholecystitis, showed myeloid metaplasia in his gall bladder. Pathologically, this may lead to diagnostic difficulties.


  • [Case reports] Parvovirus B19 infection associated with unilateral cervical lymphadenopathy, apoptotic sinus histiocytosis, and prolonged fatigue -

    This report describes the case of a 16 year old girl with a history of high fever, prolonged fatigue, and cervical lymphadenopathy of the right side. In addition, the patient showed neutropenia, thrombopenia, and pronounced reticulopenia. Cervical ultrasound showed unilateral hypoechoic lymph nodes up to 23 mm in diameter suspicious for malignant lymphoma. Histology of a cervical lymph node specimen revealed massive nodular histiocytic proliferation and prominent apoptosis without necrosis. Parvovirus B19 was detected by polymerase chain reaction and immunohistochemistry in the lymph node. In summary, this case is an unusual presentation of parvovirus B19 infection. The virus was identified as the potential causative agent of unilateral cervical lymphoma and apoptotic sinus histocytosis, thus broadening the clinicopathological spectrum of parvovirus B19 induced diseases.


  • [Case reports] Sarcoidosis and HTLV-1 infection -

    An asymptomatic, homosexual, white man was found to have an abnormal chest x ray. A presumptive diagnosis of sarcoidosis was made, but pulmonary function tests and a transbronchial biopsy were normal. He then remained asymptomatic for 10 years until he developed a progressive spastic paraparesis. At this point, antibodies to human T cell lymphotropic virus type 1 (HTLV-1) were identified in the serum and cerebrospinal fluid, and the diagnosis of HTLV-1 associated myelopathy was made, the history suggesting sexual exposure to HTLV-1 many years previously. HTLV-1 is associated with a spectrum of immune related disorders, including a pulmonary sarcoid-like syndrome. Infection with this chronic proinflammatory retrovirus should be considered in the differential diagnosis of all immune disorders in at risk individuals.


  • [Case reports] Small cell neuroendocrine carcinoma of the breast: a report of three cases and review of the literature -

    Small cell neuroendocrine carcinoma of the breast is a rare tumour with less than 30 cases reported in the literature. The clinicopathological findings of three cases of primary neuroendocrine carcinoma of the breast and a review of the pertinent literature are presented. The morphological and immunohistochemical patterns of this tumour are similar to its pulmonary counterpart. Expression of neuroendocrine markers is inconsistent, so morphology is the mainstay of diagnosis. Size is a very important prognostic factor in this tumour, as in breast carcinomas of the usual type.


  • [Case reports] Squamous cell carcinoma arising in a tall cell papillary carcinoma of the thyroid -

    Transformation of differentiated thyroid cancer into poorly differentiated carcinoma is rare. This report describes a case in which preoperative fine needle aspiration suggested a squamous cell carcinoma whereas needle core biopsy favoured an undifferentiated carcinoma of probable thyroid origin. Histology of the subsequent total thyroidectomy specimen revealed a biphasic tumour comprising areas of tall cell papillary carcinoma merging with moderately to poorly differentiated squamous cell carcinoma. The immunohistochemical findings are discussed in detail.


  • [Case reports] The value of c-kit mutational analysis in a cytokeratin positive gastrointestinal stromal tumour -

    The expression of cytokeratins in gastrointestinal stromal tumours (GISTs) is rare and may lead to diagnostic confusion when it occurs. This report describes a metastatic GIST that stained strongly for cytokeratins, CD117, and CD34 in a patient who was previously diagnosed with gastric epithelioid angiosarcoma. A review of both tumours showed the same histological and immunohistochemical profiles, and c-kit molecular analysis revealed an insertional mutation at codon 558 of exon 11 in both tumours. Thus, pathologists should be aware that GISTs can occasionally express cytokeratins, and that c-kit mutational investigations may have a key diagnostic role and may prevent diagnostic mistakes that could have important clinical implications.


  • [Case reports] Uterine tumour resembling an ovarian sex cord tumour -

    Endometrial stromal sarcomas account for 0.25% of all uterine malignancies. These tumours were originally divided into low grade and high grade stromal sarcomas, but the recent World Health Organisation classification (2003) recognises low grade stromal sarcoma and undifferentiated endometrial sarcoma. Low grade sarcomas may exhibit other forms of differentiation, including smooth muscle and sex cord differentiation. In the latter form, the tumour contains epithelial-like or sex cord-like elements often with epithelioid appearance, arranged in nests, cords, trabeculae, solid, or tubular structures. If this element predominates, the tumour is considered to be a uterine tumour resembling ovarian sex cord tumour, and may cause diagnostic difficulties. This case report describes the histological and immunohistochemical features of a uterine stromal sarcoma showing exclusively a pattern reminiscent of ovarian sex cord tumour.


  • [Central neurocytoma: a study of five cases] -
    Related Articles

    [Central neurocytoma: a study of five cases]

    Tunis Med. 2005 Aug;83(8):484-7

    Authors: Lobna A, Abdelmajid K, Najib BY, Saloua M, Ahmed S, Abdelfattah Z, Ben Mansour H, Rachid J, Tahya B

    Central neurocytoma is a very rare brain tumour recently described. The diagnosis rests on the data provided by anatomopathological examination and immunohistochemestry. We report a retrospective study of five cases of neurocytoma diagnosed in the Pathological laboratories of Anatomy and Cytology of Habib Bourguiba and Fattouma Bourguiba Hospitals over a period of two years (1999/2000); this study was based on clinical, radiological and anatomopathological data. It was about three women and two men with an average age of 29 years (17 to 49 years) The tumor was located in the side ventricles in three cases. Two differential diagnoses were often discussed: oligodendroglioma and ependymoma. Immunohistochemistry showed an expression of the synaptophysine in every case. The treatment was exclusively surgical and the course was favourable with an average follow up of 48 months; only one case of relapse was noted of 36 months after the diagnosis.

    PMID: 16238277 [PubMed - in process]


  • [Chemistry] The sacrificial role of easily oxidizable sites in the protection of DNA from damage -

    It has been suggested that DNA contains sacrificial nucleobase sequences that protect sensitive regions of the genome from oxidative damage. Oxidation of DNA by loss of an electron generates a radical cation that can migrate long distances by hopping. The radical cation can be trapped irreversibly at certain sites (GG steps) by reaction with H2O or O2 leading to the formation of lesions (oxidative damage). A series of DNA oligomers that contain regularly spaced GG steps and an 8-oxo-7,8-dihydroguanine (8-oxoG), which serves as a proxy for possibly sacrificial protective low oxidation potential sites, was prepared and analyzed. We find that in certain special sequences of DNA nucleobases that 8-oxoG protects remote GG steps from oxidative damage but that this is not a general phenomenon extending to normal mixed sequence DNA. This is a consequence of the change in the relative rate of charge hopping compared with trapping of the radical cation. When hopping is relatively slow, 8-oxoG exerts no protective effect. Thus, it seems unlikely that low oxidation potential sequences play a meaningful part in protecting mixed sequence DNA from damage.


  • [Commentary] Chemokines in inflammatory bowel disease - (No abstract is available for this citation)

  • [Computational Biology] Constraining ribosomal RNA conformational space -

    Despite the potential for many possible secondary-structure conformations, the native sequence of ribosomal RNA (rRNA) is able to find the correct and universally conserved core fold. This study reports a computational analysis investigating two mechanisms that appear to constrain rRNA secondary-structure conformational space: ribosomal proteins and rRNA sequence composition. The analysis was carried out by using rRNA–ribosomal protein interaction data for the Escherichia coli 16S rRNA and free energy minimization software for secondary-structure prediction. The results indicate that selection pressures on rRNA sequence composition and ribosomal protein–rRNA interaction play a key role in constraining the rRNA secondary structure to a single stable form.


  • [Corrections] CORRECTION - (No abstract is available for this citation)

  • [Corrections] CORRECTION - (No abstract is available for this citation)

  • [Corrections] RETRACTION - (No abstract is available for this citation)

  • [Correspondence] A case of Aspergillus fumigatus peritonitis in a patient undergoing continuous ambulatory peritoneal dialysis (CAPD): diagnostic and therapeutic challenges - (No abstract is available for this citation)

  • [Correspondence] Audit of the histological definition of cervical transformation zone - (No abstract is available for this citation)

  • [Correspondence] Bilateral breast lumps in a patient after sex mismatched allogeneic transplantation for aplastic anaemia - (No abstract is available for this citation)

  • [Correspondence] Establishing a contract for bench training of specialist registrars in medical microbiology - (No abstract is available for this citation)

  • [Correspondence] Fibrocartilagenous mesenchymoma of bone: the youngest reported case in a patient aged 1 year and 7 months - (No abstract is available for this citation)

  • [Correspondence] Know the whole history - (No abstract is available for this citation)

  • [Correspondence] Large vessel arteritis: a diagnostic challenge in the elderly - (No abstract is available for this citation)

  • [Correspondence] On Regenerating the Ovary and Generating Controversy - By Evelyn E. Telfer, Roger G. Gosden, Anne Grete Byskov, Norah Spears, David Albertini, Claus Yding Andersen, Richard Anderson, Ruth Braw-Tal, Hugh Clarke, Alain Gougeon, Eileen McLaughlin, Anne McLaren, Kenneth McNatty, Gerald Schatten, Sherman Silber, and Alex Tsafriri. For more than a half a century, biologists have upheld the theory that in most mammalian species, oocytes are formed before or shortly after birth,...

  • [Correspondence] Simplified semiquantitative culture using washed sputum from children with lower respiratory tract infections - (No abstract is available for this citation)

  • [Correspondence] Thoracic invasion in gastric carcinoma - (No abstract is available for this citation)

  • [Correspondence] {gamma}-Glutamyltransferase decreases in patients with the chronic form of schistosomiasis mansoni treated with ursodeoxycholic acid - (No abstract is available for this citation)

  • [Corrigenda] Both CAG repeats and inverted DNA repeats stimulate spontaneous unequal sister-chromatid exchange in Saccharomyces cerevisiae - (No abstract is available for this citation)

  • [Corrigenda] Empirical evaluation of data transformations and ranking statistics for microarray analysis - (No abstract is available for this citation)

  • [Corrigenda] Statistical analysis of over-represented words in human promoter sequences - (No abstract is available for this citation)

  • [Corrigendum] CisMols Analyzer: identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes - (No abstract is available for this citation)

  • [Corrigendum] Conservation versus parallel gains in intron evolution - (No abstract is available for this citation)

  • [Corrigendum] Human POL II promoter prediction: time series descriptors and machine learning - (No abstract is available for this citation)

  • [Corrigendum] Identification of regulatory targets of tissue-specific transcription factors: application to retina-specific gene regulation - (No abstract is available for this citation)

  • [Echoes] CA IV may be target antigen in autoimmune pancreatitis - (No abstract is available for this citation)

  • [Echoes] Molecular method simplifies diagnosis of infective endocarditis - (No abstract is available for this citation)

  • [Echoes] PCR assay to the rescue in neurobrucellosis - (No abstract is available for this citation)

  • [Echoes] Postmortems on very preterm infants are valuable - (No abstract is available for this citation)

  • [Echoes] Study clarifies PCR results for viral CNS infections - (No abstract is available for this citation)

  • [Echo] Rules on organ donation are coherent - (No abstract is available for this citation)

  • [Editorials] Antibiotic treatment and susceptibility testing - (No abstract is available for this citation)

  • [Editorials] CCN workshop - (No abstract is available for this citation)

  • [Editorials] Chemical pathology and Krapp's last tape - (No abstract is available for this citation)

  • [Editorials] Immunology - (No abstract is available for this citation)

  • [Editorials] Interpretive comments on clinical biochemistry reports - (No abstract is available for this citation)

  • [Editorials] Sixty years of haematology - (No abstract is available for this citation)

  • [Editorials] The Journal of Clinical Pathology - (No abstract is available for this citation)

  • [Editorials] Translating research into cancer molecular diagnostics and patents - (No abstract is available for this citation)

  • [Errata] Structural Basis for the EBA-175 Erythrocyte Invasion Pathway of the Malaria Parasite Plasmodium falciparum - By Niraj H. Tolia, Eric J. Enemark, B. Kim Lee Sim, and Leemor Joshua-Tor. (Cell 122, 183–193; July 29, 2005)

  • [Erratum] A Dual Inhibitory Mechanism Restricts msl-2 mRNA Translation for Dosage Compensation in Drosophila - By Karsten Beckmann, Marica Grskovic, Fátima Gebauer, and Matthias W. Hentze. (Cell 122, 529–540; August 26, 2005)

  • [Erratum] A Mitochondrial Protein, Bit1, Mediates Apoptosis Regulated by Integrins and Groucho/TLE Corepressors - By Yiwen Jan, Michelle Matter, Jih-tung Pai, Yen-Liang Chen, Jan Pilch, Masanobu Komatsu, Edgar Ong, Minoru Fukuda, and Erkki Ruoslahti. (Cell 116, 751–762; March 5, 2004)

  • [Erratum] Evidence that HIV-1 Encodes an siRNA and a Suppressor of RNA Silencing - By Yamina Bennasser, Shu-Yun Le, Monsef Benkirane, and Kuan-Teh Jeang. (Immunity 22, 607–619; May 2005)

  • [Erratum] Kaiso/p120-Catenin and TCF/β-Catenin Complexes Coordinately Regulate Canonical Wnt Gene Targets - By Jae-il Park, Si Wan Kim, Jon P. Lyons, Hong Ji, Thi T. Nguyen, Kyucheol Cho, Michelle C. Barton, Tom Deroo, Kris Vleminckx, Randall T. Moon, and Pierre D. McCrea. (Developmental Cell 8, 843–854; June 2005)

  • [Erratum] ON01910, a non-ATP-competitive small molecule inhibitor of Plk1, is a potent anticancer agent - By Kiranmai Gumireddy, M.V. Ramana Reddy, Stephen C. Cosenza, R. Boominathan, Stacey J. Baker, Nabisa Papathi, Jiandong Jiang, James Holland, and E. Premkumar Reddy. In this article (Cancer Cell 7, pp. 275–286), the name of one of the authors was listed incorrectly. The author incorrectly listed as “R. Boomi...

  • [Erratum] Rap2-JNK Removes Synaptic AMPA Receptors during Depotentiation - By Yinghua Zhu, Daniel Pak, Yi Qin, Stefanie G. McCormack, Myung J. Kim, Joel P. Baumgart, Vanisree Velamoor, Yves P. Auberson, Pavel Osten, Linda van Aelst, Morgan Sheng, and J. Julius Zhu. (Neuron 46, 905–916; June 16, 2005)

  • [Erratum] Syk-Dependent Cytokine Induction by Dectin-1 Reveals a Novel Pattern Recognition Pathway for C Type Lectins - By Neil C. Rogers, Emma C. Slack, Alexander D. Edwards, Martijn A. Nolte, Oliver Schulz, Edina Schweighoffer, David L. Williams, Siamon Gordon, Victor L. Tybulewicz, Gordon D. Brown, and Caetano Reis e Sousa. (Immunity 22, 507–517; April 2005)

  • [Erratum] The Fission Yeast Homolog of the Human Transcription Factor EAP30 Blocks Meiotic Spindle Pole Body Amplification - By Ye Jin, Joel J. Mancuso, Satoru Uzawa, Daniela Cronembold, and W. Zacheus Cande. (Developmental Cell 9, 63–73; July 2005)

  • [Erratum] The oncoprotein gankyrin binds to MDM2/HDM2, enhancing ubiquitylation and degradation of p53 - By Hiroaki Higashitsuji, Hisako Higashitsuji, Katsuhiko Itoh, Toshiharu Sakurai, Toshikazu Nagao, Yasuhiko Sumitomo, Tomoko Masuda, Simon Dawson, Yutaka Shimada, R. John Mayer, and Jun Fujita. In this article (Cancer Cell 8, pp. 75–86), the name of one of the authors was listed incorrectly. The author incorrectly listed as “Haruhiko Sumitomoâ€...

  • [Erratum] The Transcriptional Coactivator Yes-Associated Protein Drives p73 Gene-Target Specificity in Response to DNA Damage - By Sabrina Strano, Olimpia Monti, Natalia Pediconi, Alessia Baccarini, Giulia Fontemaggi, Eleonora Lapi, Fiamma Mantovani, Alexander Damalas, Gennaro Citro, Ada Sacchi, Giannino Del Sal, Massimo Levrero, and Giovanni Blandino. (Molecular Cell 18, 447–459; May 13, 2005)

  • [Essay] Canadian Stem Cell Scientists Take the Prize - By Saul J. Sharkis. This year, the recipients of the Lasker Award for Basic Medical Research are Ernest A. McCulloch and James E. Till. The landmark studies of McCulloch...

  • [Genomics] Comparative genomics analysis of NtcA regulons in cyanobacteria: regulation of nitrogen assimilation and its coupling to photosynthesis -

    We have developed a new method for prediction of cis-regulatory binding sites and applied it to predicting NtcA regulated genes in cyanobacteria. The algorithm rigorously utilizes concurrence information of multiple binding sites in the upstream region of a gene and that in the upstream regions of its orthologues in related genomes. A probabilistic model was developed for the evaluation of prediction reliability so that the prediction false positive rate could be well controlled. Using this method, we have predicted multiple new members of the NtcA regulons in nine sequenced cyanobacterial genomes, and showed that the false positive rates of the predictions have been reduced on an average of 40-fold compared to the conventional methods. A detailed analysis of the predictions in each genome showed that a significant portion of our predictions are consistent with previously published results about individual genes. Intriguingly, NtcA promoters are found for many genes involved in various stages of photosynthesis. Although photosynthesis is known to be tightly coordinated with nitrogen assimilation, very little is known about the underlying mechanism. We postulate for the fist time that these genes serve as the regulatory points to orchestrate these two important processes in a cyanobacterial cell.


  • [Matters Arising] Quantitative and Dynamic Assessment of the Contribution of the ER to Phagosome Formation - By Nicolas Touret, Paul Paroutis, Mauricio Terebiznik, Rene E. Harrison, Sergio Trombetta, Marc Pypaert, Amy Chow, Aimin Jiang, James Shaw, Christopher Yip, Hsiao-Ping Moore, Nicole van der Wel, Diane Houben, Peter J. Peters, Chantal de Chastellier, Ira Mellman, and Sergio Grinstein. Phagosomes were traditionally thought to originate from an invagination and scission of the plasma membrane to form a distinct intracellular vacuole. An alternative model implicating...

  • [Meeting Report] Developmental Biology Takes on a Latin American Rhythm - By José Xavier-Neto, and Richard R. Behringer. At a recent meeting in Latin America, developmental biologists discussed both traditional and not so traditional organisms that are valuable models for dissecting the intricate...

  • [Meeting Report] RNA Reigns in Neurons - By Henri Tiedge. A workshop entitled “RNA Control of Neuronal Function†was recently held in Kfar Blum, Israel. The main topics discussed at the meeting included neuronal RNA...

  • [Meeting Report] Stem Cells: A Plant Biology Perspective - By Ben Scheres. A recent meeting at the Juan March Foundation in Madrid, Spain brought together plant biologists to discuss the characteristics of plant stem cells that are...

  • [Meeting Review] At the Heart of Cell Polarity and the Cytoskeleton - By Monica Gotta. Researchers working on cell polarity and cytoskeletal processes met at a Keystone meeting in Coeur d’Alene, Idaho in March to present and discuss the newest...

  • [Methods Online] A complementation method for functional analysis of mammalian genes -

    Our progress in understanding mammalian gene function has lagged behind that of gene identification. New methods for mammalian gene functional analysis are needed to accelerate the process. In yeast, the powerful genetic shuffle system allows deletion of any chromosomal gene by homologous recombination and episomal expression of a mutant allele in the same cell. Here, we report a method for mammalian cells, which employs a helper-dependent adenoviral (HD-Ad) vector to synthesize small hairpin (sh) RNAs to knock-down the expression of an endogenous gene by targeting untranslated regions (UTRs). The vector simultaneously expresses an exogenous version of the same gene (wild-type or mutant allele) lacking the UTRs for functional analysis. We demonstrated the utility of the method by using PRPF3, which encodes the human RNA splicing factor Hprp3p. Recently, missense mutations in PRPF3 were found to cause autosomal-dominant Retinitis Pigmentosa, a form of genetic eye diseases affecting the retina. We knocked-down endogenous PRPF3 in multiple cell lines and rescued the phenotype (cell death) with exogenous PRPF3 cDNA, thereby creating a genetic complementation method. Because Ad vectors can efficiently transduce a wide variety of cell types, and many tissues in vivo, this method could have a wide application for gene function studies.


  • [Methods Online] A FRET-based analysis of SNPs without fluorescent probes -

    Fluorescence resonance energy transfer (FRET) is a simple procedure for detecting specific DNA sequences, and is therefore used in many fields. However, the cost is relatively high, because FRET-based methods usually require fluorescent probes. We have designed a cost-effective way of using FRET, and developed a novel approach for the genotyping of single nucleotide polymorphisms (SNPs) and allele frequency estimation. The key feature of this method is that it uses a DNA-binding fluorogenic molecule, SYBR Green I, as an energy donor for FRET. In this method, single base extension is performed with dideoxynucleotides labeled with an orange dye and a red dye in the presence of SYBR Green I. The dyes incorporated into the extended products accept energy from SYBR Green I and emit fluorescence. We have validated the method with ten SNPs, which were successfully discriminated by end-point measurements of orange and red fluorescence intensity in a microplate fluorescence reader. Using a mixture of homozygous samples, we also confirmed the potential of this method for estimation of allele frequency. Application of this strategy to large-scale studies will reduce the time and cost of genotyping a vast number of SNPs.


  • [Methods Online] A gene truncation strategy generating N- and C-terminal deletion variants of proteins for functional studies: mapping of the Sec1p binding domain in yeast Mso1p by a Mu in vitro transposition-based approach -

    Bacteriophage Mu in vitro transposition constitutes a versatile tool in molecular biology, with applications ranging from engineering of single genes or proteins to modification of genome segments or entire genomes. A new strategy was devised on the basis of Mu transposition that via a few manipulation steps simultaneously generates a nested set of gene constructions encoding deletion variants of proteins. C-terminal deletions are produced using a mini-Mu transposon that carries translation stop signals close to each transposon end. Similarly, N-terminal deletions are generated using a transposon with appropriate restriction sites, which allows deletion of the 5'-distal part of the gene. As a proof of principle, we produced a set of plasmid constructions encoding both C- and N-terminally truncated variants of yeast Mso1p and mapped its Sec1p-interacting region. The most important amino acids for the interaction in Mso1p are located between residues T46 and N78, with some weaker interactions possibly within the region E79–N105. This general-purpose gene truncation strategy is highly efficient and produces, in a single reaction series, a comprehensive repertoire of gene constructions encoding protein deletion variants, valuable in many types of functional studies. Importantly, the methodology is applicable to any protein-encoding gene cloned in an appropriate vector.


  • [Methods Online] A method for cloning and sequencing long palindromic DNA junctions -

    DNA sequences containing long adjacent inverted repeats (palindromes) are inherently unstable and are associated with many types of chromosomal rearrangements. The instability associated with palindromic sequences also creates difficulties in their molecular analysis: long palindromes (>250 bp/arm) are highly unstable in Escherichia coli, and cannot be directly PCR amplified or sequenced due to their propensity to form intra-strand hairpins. Here, we show that DNA molecules containing long palindromes (>900 bp/arm) can be transformed and stably maintained in Saccharomyces cerevisiae cells lacking a functional SAE2 gene. Treatment of the palindrome-containing DNA with sodium bisulfite at high temperature results in deamination of cytosine, converting it to uracil and thus reducing the propensity to form intra-strand hairpins. The bisulfite-treated DNA can then be PCR amplified, cloned and sequenced, allowing determination of the nucleotide sequence of the junctions. Our data demonstrates that long palindromes with either no spacer (perfect) or a 2 bp spacer can be stably maintained, recovered and sequenced from sae2 yeast cells. Since DNA sequences from mammalian cells can be gap repaired by their co-transformation into yeast cells with an appropriate vector, the methods described in this manuscript should provide some of the necessary tools to isolate and characterize palindromic junctions from mammalian cells.


  • [Methods Online] A novel high-throughput (HTP) cloning strategy for site-directed designed chimeragenesis and mutation using the Gateway cloning system -

    There is an increasing demand for easy, high-throughput (HTP) methods for protein engineering to support advances in the development of structural biology, bioinformatics and drug design. Here, we describe an N- and C-terminal cloning method utilizing Gateway cloning technology that we have adopted for chimeric and mutant genes production as well as domain shuffling. This method involves only three steps: PCR, in vitro recombination and transformation. All three processes consist of simple handling, mixing and incubation steps. We have characterized this novel HTP method on 96 targets with >90% success. Here, we also discuss an N- and C-terminal cloning method for domain shuffling and a combination of mutation and chimeragenesis with two types of plasmid vectors.


  • [Methods Online] A novel mammalian expression system derived from components coordinating nicotine degradation in arthrobacter nicotinovorans pAO1 -

    We describe the design and detailed characterization of 6-hydroxy-nicotine (6HNic)-adjustable transgene expression (NICE) systems engineered for lentiviral transduction and in vivo modulation of angiogenic responses. Arthrobacter nicotinovorans pAO1 encodes a unique catabolic machinery on its plasmid pAO1, which enables this Gram-positive soil bacterium to use the tobacco alkaloid nicotine as the exclusive carbon source. The 6HNic-responsive repressor-operator (HdnoR-ONIC) interaction, controlling 6HNic oxidase production in A.nicotinovorans pAO1, was engineered for generic 6HNic-adjustable transgene expression in mammalian cells. HdnoR fused to different transactivation domains retained its ONIC-binding capacity in mammalian cells and reversibly adjusted transgene transcription from chimeric ONIC-containing promoters (PNIC; ONIC fused to a minimal eukaryotic promoter [Pmin]) in a 6HNic-responsive manner. The combination of transactivators containing various transactivation domains with promoters differing in the number of operator modules as well as in their relative inter-ONIC and/or ONIC-Pmin spacing revealed steric constraints influencing overall NICE regulation performance in mammalian cells. Mice implanted with microencapsulated cells engineered for NICE-controlled expression of the human glycoprotein secreted placental alkaline phosphatase (SEAP) showed high SEAP serum levels in the absence of regulating 6HNic. 6HNic was unable to modulate SEAP expression, suggesting that this nicotine derivative exhibits control-incompatible pharmacokinetics in mice. However, chicken embryos transduced with HIV-1-derived self-inactivating lentiviral particles transgenic for NICE-adjustable expression of the human vascular endothelial growth factor 121 (VEGF121) showed graded 6HNic response following administration of different 6HNic concentrations. Owing to the clinically inert and highly water-soluble compound 6HNic, NICE-adjustable transgene control systems may become a welcome alternative to available drug-responsive homologs in basic research, therapeutic cell engineering and biopharmaceutical manufacturing.


  • [Methods Online] A novel method of screening thrombin-inhibiting DNA aptamers using an evolution-mimicking algorithm -

    Thrombin-inhibiting DNA aptamers have already been obtained through the systematic evolution of ligands by exponential enrichment (SELEX). However, SELEX is a method that screens DNA aptamers that bind to their target molecules, and it sometimes fails to screen good inhibitors. Therefore, it is necessary to develop a method of screening DNA aptamers based on their inhibitory effects on the target molecules. We developed a novel method of detecting aptamers using an evolution-mimicking algorithm, and we applied it to the search of new aptamers which inhibit thrombin. First, we randomly designed and synthesized ten 15mer oligonucleotides presumed to form G-quartet structures, and then measured their thrombin-inhibiting activities. The aptamers showing high inhibitory activity were selected, and we shuffled and mutated those sequences in silico to generate 10 new sequences of next-generation aptamers. After repeating the cycle five times, we successfully obtained the same aptamers reported previously, and they showed high inhibitory activity. In addition, we added 8mer oligonucleotides to both the 5' and the 3' end of the selected 15mer aptamers, and then repeated the evolution in silico. After two cycles, we were able to obtain aptamers with higher inhibitory activity than that of the 15mer aptamers.


  • [Methods Online] A novel PCR strategy for high-efficiency, automated site-directed mutagenesis -

    We have developed a novel three-primer, one-step PCR-based method for site-directed mutagenesis. This method takes advantage of the fact that template plasmid DNA cannot be efficiently denatured at its reannealing temperature (Tra), which is otherwise a troublesome problem in regular PCR. Two flanking primers and one mutagenic primer with different melting temperatures (Tm) are used together in a single PCR tube continuously without any intervention. A single-stranded mutagenic DNA (smDNA) is synthesized utilizing the high Tm mutagenic primer at a high annealing temperature, which prevents the priming of the low Tm primers (i.e. the two flanking primers). A megaprimer is then produced using this smDNA as the template at a denaturing temperature that prevents wild-type template DNA activity. The desired mutant DNA is then obtained by cycling again through these first two steps, resulting in a mutagenic efficiency of 100% in all tested cases. This highly automated method not only eliminates the necessity of any intermediate manipulation and accomplishes the mutagenesis process in a single round of PCR but, most notably, enables complete success of mutagenesis. This novel method is also both cost and time efficient and fully automated.


  • [Methods Online] A novel transcriptome subtraction method for the detection of differentially expressed genes in highly complex eukaryotes -

    We have designed a novel transcriptome subtraction method for the genome-scale analysis of differential gene expression in highly complex eukaryotes, in which suppression subtractive hybridization (SSH) is performed first to enrich the target and, after exchange of adapters, negative subtraction chain (NSC) is then used to eliminate the remaining background. NSC evolved from differential subtraction chain (DSC). We designed novel adapters which make the subtraction system more robust. SSH and NSC were then combined to successfully detect differentially expressed genes in Solanum. The combined technique improves qualitatively upon SSH, the only commercially available transcriptome subtraction system, by detecting target genes in the middle abundance class, to which most differentially expressed genes in highly complex eukaryotes are expected to belong. The main advantage of the combined technique with SSH/NSC is its ability to isolate differentially expressed genes quickly and cost-efficiently from non-standard models, for those microarrays are unavailable.


  • [Methods Online] A novel transgenic chimaeric mouse system for the rapid functional evaluation of genes encoding secreted proteins -

    A major challenge of the post-genomic era is the functional characterization of anonymous open reading frames (ORFs) identified by the Human Genome Project. In this context, there is a strong requirement for the development of technologies that enhance our ability to analyze gene functions at the level of the whole organism. Here, we describe a rapid and efficient procedure to generate transgenic chimaeric mice that continuously secrete a foreign protein into the systemic circulation. The transgene units were inserted into the genomic site adjacent to the endogenous immunoglobulin (Ig) locus by homologous recombination, using a modified mouse embryonic stem (ES) cell line that exhibits a high frequency of homologous recombination at the Ig region. The resultant ES clones were injected into embryos derived from a B-cell-deficient host strain, thus producing chimaerism-independent, B-cell-specific transgene expression. This feature of the system eliminates the time-consuming breeding typically implemented in standard transgenic strategies and allows for evaluating the effect of ectopic transgene expression directly in the resulting chimaeric mice. To demonstrate the utility of this system we showed high-level protein expression in the sera and severe phenotypes in human EPO (hEPO) and murine thrombopoietin (mTPO) transgenic chimaeras.


  • [Methods Online] A post-processing method for optimizing synthesis strategy for oligonucleotide microarrays -

    The broad applicability of gene expression profiling to genomic analyses has generated huge demand for mass production of microarrays and hence for improving the cost effectiveness of microarray fabrication. We developed a post-processing method for deriving a good synthesis strategy. In this paper, we assessed all the known efficient methods and our post-processing method for reducing the number of synthesis cycles for manufacturing a DNA-chip of a given set of oligos. Our experimental results on both simulated and 52 real datasets show that no single method consistently gives the best synthesis strategy, and post-processing an existing strategy is necessary as it often reduces the number of synthesis cycles further.


  • [Methods Online] A rapid and efficient method to generate multiple gene disruptions in Dictyostelium discoideum using a single selectable marker and the Cre-loxP system -

    Dictyostelium discoideum has proven an exceptionally powerful system for studying numerous aspects of cellular and developmental functions. The relatively small (~34 Mb) chromosomal genome of Dictyostelium and high efficiency of targeted gene disruption have enabled researchers to characterize many specific gene functions. However, the number of selectable markers in Dictyostelium is restricted, as is the ability to perform effective genetic crosses between strains. Thus, it has been difficult to create multiple mutations within an individual cell to study epistatic relationships among genes or potential redundancies between various pathways. We now describe a robust system for the production of multiple gene mutations in Dictyostelium by recycling a single selectable marker, Blasticidin S resistance, using the Cre-loxP system. We confirm the effectiveness of the system by generating a single cell carrying four separate gene disruptions. Furthermore, the cells remain sensitive to transformation for additional targeted or random mutagenesis requiring Blasticidin selection and for functional expression studies of mutated or tagged proteins using other selectable markers.


  • [Methods Online] A universal BMV-based RNA recombination system--how to search for general rules in RNA recombination -

    At present, there is no doubt that RNA recombination is one of the major factors responsible for the generation of new RNA viruses and retroviruses. Numerous experimental systems have been created to investigate this complex phenomenon. Consequently, specific RNA structural motifs mediating recombination have been identified in several viruses. Unfortunately, up till now a unified model of genetic RNA recombination has not been formulated, mainly due to difficulties with the direct comparison of data obtained for different RNA-based viruses. To solve this problem, we have attempted to construct a universal system in which the recombination activity of various RNA sequences could be tested. To this end, we have used brome mosaic virus, a model (+)RNA virus of plants, for which the structural requirements of RNA recombination are well defined. The effectiveness of the new homomolecular system has been proven in an experiment involving two RNA sequences derived from the hepatitis C virus genome. In addition, comparison of the data obtained with the homomolecular system with those generated earlier using the heteromolecular one has provided new evidence that the mechanisms of homologous and non-homologous recombination are different and depend on the virus' mode of replication.


  • [Methods Online] A versatile reducible polycation-based system for efficient delivery of a broad range of nucleic acids -

    Synthetic vectors based on reducible polycations consisting of histidine and polylysine residues (HIS RPCs) were evaluated for their ability to deliver nucleic acids. Initial experiments showed that RPC-based vectors with at least 70% histidine content mediated efficient levels of gene transfer without requirement for the endosomolytic agent chloroquine. Significant gene transfer was observed in a range of cell types achieving up to a 5-fold increase in the percentage of transfected cells compared to 25 kDa PEI, a gold standard synthetic vector. In contrast to 25 kDa PEI, HIS RPCs also mediated efficient transfer of other nucleic acids, including mRNA encoding green fluorescent protein in PC-3 cells and siRNA directed against the neurotrophin receptor p75NTR in post-mitotic cultures of rat dorsal root ganglion cell neurons. Experiments to elevate intracellular glutathione and linear profiling of cell images captured by multiphoton fluorescent microscopy highlighted that parameters such as the molecular weight and rate of cleavage of HIS RPCs were important factors in determining transfection activity. Altogether, these results demonstrate that HIS RPCs represent a novel and versatile type of vector that can be used for efficient cytoplasmic delivery of a broad range of nucleic acids. This should enable different or a combination of therapeutic strategies to be evaluated using a single type of polycation-based vector.


  • [Methods Online] An ultrasensitive photoelectrochemical nucleic acid biosensor -

    A simple and ultrasensitive procedure for non-labeling detection of nucleic acids is described in this study. It is based on the photoelectrochemical detection of target nucleic acids by forming a nucleic acid/photoreporter adduct layer on an ITO electrode. The target nucleic acids were hybridized with immobilized oligonucleotide capture probes on the ITO electrode. A subsequent binding of a photoreporter—a photoactive threading bis-intercalator consisting of two N,N'-bis(3-propyl-imidazole)-1,4,5,8-naphthalene diimides (PIND) linked by a $${\hbox{ Ru }\left(\hbox{ bpy }\right)}_{2}^{2+}$$ (bpy = 2,2'-bipyridine) complex (PIND–Ru–PIND)—allowed for photoelectrochemical detection of the target nucleic acids. The extremely low dissociation rate of the adduct and the highly reversible photoelectrochemical response under visible light illumination (490 nm) make it possible to conduct nucleic acid detection, with a sensitivity enhancement of four orders of magnitude over voltammetry. These results demonstrate for the first time the potential of photoelectrochemical biosensors for PCR-free ultrasensitive detection of nucleic acids.


  • [Methods Online] Cancer siRNA therapy by tumor selective delivery with ligand-targeted sterically stabilized nanoparticle -

    Potent sequence selective gene inhibition by siRNA ‘targeted’ therapeutics promises the ultimate level of specificity, but siRNA therapeutics is hindered by poor intracellular uptake, limited blood stability and non-specific immune stimulation. To address these problems, ligand-targeted, sterically stabilized nanoparticles have been adapted for siRNA. Self-assembling nanoparticles with siRNA were constructed with polyethyleneimine (PEI) that is PEGylated with an Arg-Gly-Asp (RGD) peptide ligand attached at the distal end of the polyethylene glycol (PEG), as a means to target tumor neovasculature expressing integrins and used to deliver siRNA inhibiting vascular endothelial growth factor receptor-2 (VEGF R2) expression and thereby tumor angiogenesis. Cell delivery and activity of PEGylated PEI was found to be siRNA sequence specific and depend on the presence of peptide ligand and could be competed by free peptide. Intravenous administration into tumor-bearing mice gave selective tumor uptake, siRNA sequence-specific inhibition of protein expression within the tumor and inhibition of both tumor angiogenesis and growth rate. The results suggest achievement of two levels of targeting: tumor tissue selective delivery via the nanoparticle ligand and gene pathway selectivity via the siRNA oligonucleotide. This opens the door for better targeted therapeutics with both tissue and gene selectivity, also to improve targeted therapies with less than ideal therapeutic targets.


  • [Methods Online] Cell-type-specific transcriptomics in chimeric models using transcriptome-based masks -

    Regulatory networks involving different cell types control inflammation, morphogenesis and tissue homeostasis. Cell-type-specific transcriptional profiling offers a powerful tool for analyzing such cross-talk but is often hampered by mingling of cells within a tissue. Here, we present a novel method that performs cell-type-specific expression measurements without prior cell separation. This involves inter-species transplantation or chimeric co-culture models among which the human mouse system is frequently used. Here, we exploit the sufficiently divergent transcriptomes of human and mouse in conjunction with high-density oligonucleotide arrays. This required a masking procedure based on transcriptome databases and exhaustive fuzzy mapping of oligonucleotide probes onto these data. The approach was tested in a human–mouse experiment, demonstrating that we can efficiently measure species-specific transcriptional profiles in chimeric RNA samples without physically separating cells. Our results stress the importance of transcriptome databases with accurate 3' mRNA termination for computational prediction of accurate probe masks. We find that most human and mouse 3'-untranslated region contain unique stretches to allow for an effective control of cross-hybridization between the two species. This approach can be applied to xenograft models studying tumor–host interactions, morphogenesis or immune responses.


  • [Methods Online] Characterization of zebrafish Rad52 and replication protein A for oligonucleotide-mediated mutagenesis -

    Zebrafish has become a favorite model organism not only in genetics and developmental biology, but also for the study of cancer, neuroscience and metabolism. However, strategies for reverse genetics in zebrafish are mostly limited to the use of antisense oligonucleotides, and therefore the development of other targeting methods is highly desirable. Here, we report an approach to gene targeting in this system in which single-stranded oligonucleotides and zebrafish Rad52 protein are employed. It has been proposed that a single-stranded oligonucleotide containing a mutation can be incorporated into the genome by annealing to the single-stranded region of the lagging strand of the replication fork. Rad52 is expected to accelerate the annealing step. In vitro experiments using purified truncated Rad52 proteins and replication protein A (RPA) showed that annealing of oligonucleotides is accelerated by Rad52 in the presence of RPA. We developed a simple and sensitive PCR-based method to detect point mutations in the genome. In exploratory experiments, we found that microinjection of single-stranded oligonucleotide targeted to a specific gene together with truncated Rad52 into zebrafish embryos resulted in a low level of recombinant copies in 3 of the 80 embryos tested under these conditions.


  • [Methods Online] Combining SELEX with quantitative assays to rapidly obtain accurate models of protein-DNA interactions -

    Models for the specificity of DNA-binding transcription factors are often based on small amounts of qualitative data and therefore have limited accuracy. In this study we demonstrate a simple and efficient method of affinity chromatography-SELEX followed by a quantitative binding (QuMFRA) assay to rapidly collect the data necessary for more accurate models. Using the zinc finger protein EGR as an e.g. we show that many bindings sites can be obtained efficiently with affinity chromatography-SELEX, but those sequences alone provide a weight matrix model with limited accuracy. Using a QuMFRA assay to determine the quantitative relative affinity for only a subset of the sequences obtained by SELEX leads to a much more accurate model. Application of this method to variants of a transcription factor would allow us to generate a large collection of quantitative data for modeling protein–DNA interactions that could facilitate the determination of recognition codes for different transcription factor families.


  • [Methods Online] Detection of ApoE E2, E3 and E4 alleles using MALDI-TOF mass spectrometry and the homogeneous mass-extend technology -

    Apolipoprotein (Apo) E is one of the five main types of blood lipoproteins (A–E). It is synthesized primarily in the liver and brain and helps in transporting lipids from one place to another as well as facilitates the clearing of dietary fats, such as triglycerides, from the blood. The ApoE gene exists in three different forms: E2, E3 and E4. E3 is considered to be the normal form. Variants of the ApoE gene have been associated with various diseases. Developing an assay for the genotyping of ApoE variants for use both in clinical and large cohort based association settings would be extremely valuable and would require the use of a platform that has high-throughput capabilities and is highly accurate. Here we describe an assay for the simultaneous genotyping of the ApoE variants in a single bi-plex reaction and a single well using the matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry and the homogeneous mass-extend (hME) technology. The assay is robust, highly accurate and suitable for both clinical applications and for the genotyping of large disease cohorts. Moreover, the prevalence of ApoE variants in a cohort of Caucasians from the central Wisconsin area is outlined.


  • [Methods Online] Direct detection of methylation in genomic DNA -

    The identification of methylated sites on bacterial genomic DNA would be a useful tool to study the major roles of DNA methylation in prokaryotes: distinction of self and nonself DNA, direction of post-replicative mismatch repair, control of DNA replication and cell cycle, and regulation of gene expression. Three types of methylated nucleobases are known: N6-methyladenine, 5-methylcytosine and N4-methylcytosine. The aim of this study was to develop a method to detect all three types of DNA methylation in complete genomic DNA. It was previously shown that N6-methyladenine and 5-methylcytosine in plasmid and viral DNA can be detected by intersequence trace comparison of methylated and unmethylated DNA. We extended this method to include N4-methylcytosine detection in both in vitro and in vivo methylated DNA. Furthermore, application of intersequence trace comparison was extended to bacterial genomic DNA. Finally, we present evidence that intrasequence comparison suffices to detect methylated sites in genomic DNA. In conclusion, we present a method to detect all three natural types of DNA methylation in bacterial genomic DNA. This provides the possibility to define the complete methylome of any prokaryote.


  • [Methods Online] Direct molecular haplotyping by melting curve analysis of hybridization probes: beta 2-adrenergic receptor haplotypes as an example -

    Direct determination of the association of multiple genetic polymorphisms, or haplotyping, in individual samples is challenging because of chromosome diploidy. Here, we describe the ability of hybridization probes, commonly used as genotyping tools, to establish single nucleotide polymorphism (SNP) haplotypes in a single step. Three haplotypes found in the beta 2-adrenergic receptor (ßbeta;2AR) gene and characterized by three different SNPs combinations are presented as examples. Each combination of SNPs has a unique stability, recorded by its melting temperature, even when intervening sequences from the template must loop out during probe hybridization. In the course of this study, two haplotypes in ßbeta;2AR not described previously were discovered. This approach provides a tool for molecular haplotyping that should prove useful in clinical molecular genetics diagnostics and pharmacogenetic research where methods for direct haplotyping are needed.


  • [Methods Online] Discovery of a novel restriction endonuclease by genome comparison and application of a wheat-germ-based cell-free translation assay: PabI (5'-GTA/C) from the hyperthermophilic archaeon Pyrococcus abyssi -

    To search for restriction endonucleases, we used a novel plant-based cell-free translation procedure that bypasses the toxicity of these enzymes. To identify candidate genes, the related genomes of the hyperthermophilic archaea Pyrococcus abyssi and Pyrococcus horikoshii were compared. In line with the selfish mobile gene hypothesis for restriction–modification systems, apparent genome rearrangement around putative restriction genes served as a selecting criterion. Several candidate restriction genes were identified and then amplified in such a way that they were removed from their own translation signal. During their cloning into a plasmid, the genes became connected with a plant translation signal. After in vitro transcription by T7 RNA polymerase, the mRNAs were separated from the template DNA and translated in a wheat-germ-based cell-free protein synthesis system. The resulting solution could be directly assayed for restriction activity. We identified two deoxyribonucleases. The novel enzyme was denoted as PabI, purified and found to recognize 5'-GTAC and leave a 3'-TA overhang (5'-GTA/C), a novel restriction enzyme-generated terminus. PabI is active up to 90°C and optimally active at a pH of around 6 and in NaCl concentrations ranging from 100 to 200 mM. We predict that it has a novel 3D structure.


  • [Methods Online] DNA microarrays on a dendron-modified surface improve significantly the detection of single nucleotide variations in the p53 gene -

    Selectivity and sensitivity in the detection of single nucleotide polymorphisms (SNPs) are among most important attributes to determine the performance of DNA microarrays. We previously reported the generation of a novel mesospaced surface prepared by applying dendron molecules on the solid surface. DNA microarrays that were fabricated on the dendron-modified surface exhibited outstanding performance for the detection of single nucleotide variation in the synthetic oligonucleotide DNA. DNA microarrays on the dendron-modified surface were subjected to the detection of single nucleotide variations in the exons 5–8 of the p53 gene in genomic DNAs from cancer cell lines. DNA microarrays on the dendron-modified surface clearly discriminated single nucleotide variations in hotspot codons with high selectivity and sensitivity. The ratio between the fluorescence intensity of perfectly matched duplexes and that of single nucleotide mismatched duplexes was >5–100 without sacrificing signal intensity. Our results showed that the outstanding performance of DNA microarrays fabricated on the dendron-modified surface is strongly related to novel properties of the dendron molecule, which has the conical structure allowing mesospacing between the capture probes. Our microarrays on the dendron-modified surface can reduce the steric hindrance not only between the solid surface and target DNA, but also among immobilized capture probes enabling the hybridization process on the surface to be very effective. Our DNA microarrays on the dendron-modified surface could be applied to various analyses that require accurate detection of SNPs.


  • [Methods Online] DNA microarrays on nanoscale-controlled surface -

    We have developed new surface to ensure a proper spacing between immobilized biomolecules. While DNA microarray on this surface provided each probe DNA with ample space for hybridization with incoming target DNAs, the microarray showed enhanced discrimination efficiency for various types of single nucleotide polymorphism. The high discrimination efficiency holds for all tested cases (100:<1 for internal mismatched cases; 100:<28 for terminal mismatched ones). In addition, by investigating influence of hybridization temperature and washing condition on the fluorescence intensity and the discrimination efficiency with and without controlled mesospacing, it was observed that the nanoscale-controlled surface showed good discrimination efficiency in a wide range of temperature (37–50°C), and hybridization behavior on the surface was in agreement with the solution one. Intriguingly, it was found that washing process after the hybridization was critical for the high discrimination efficiency. For the particular case, washing process was so efficient that only 30 s washing was sufficient to reach the optimal discrimination ratio.


  • [Methods Online] Electrochemically directed synthesis of oligonucleotides for DNA microarray fabrication -

    We demonstrate a new method for making oligonucleotide microarrays by synthesis in situ. The method uses conventional DNA synthesis chemistry with an electrochemical deblocking step. Acid is delivered to specific regions on a glass slide, thus allowing nucleotide addition only at chosen sites. The acid is produced by electrochemical oxidation controlled by an array of independent microelectrodes. Deblocking is complete in a few seconds, when competing side-product reactions are minimal. We demonstrate the successful synthesis of 17mers and discrimination of single base pair mismatched hybrids. Features generated in this study are 40 µm wide, with sharply defined edges. The synthetic technique may be applicable to fabrication of other molecular arrays.


  • [Methods Online] End invasion of peptide nucleic acids (PNAs) with mixed-base composition into linear DNA duplexes -

    Peptide nucleic acid (PNA) is a synthetic DNA mimic with valuable properties and a rapidly growing scope of applications. With the exception of recently introduced pseudocomplementary PNAs, binding of common PNA oligomers to target sites located inside linear double-stranded DNAs (dsDNAs) is essentially restricted to homopurine–homopyrimidine sequence motifs, which significantly hampers some of the PNA applications. Here, we suggest an approach to bypass this limitation of common PNAs. We demonstrate that PNA with mixed composition of ordinary nucleobases is capable of sequence-specific targeting of complementary dsDNA sites if they are located at the very termini of DNA duplex. We then show that such targeting makes it possible to perform capturing of designated dsDNA fragments via the DNA-bound biotinylated PNA as well as to signal the presence of a specific dsDNA sequence, in the case a PNA beacon is employed. We also examine the PNA–DNA conjugate and prove that it can initiate the primer-extension reaction starting from the duplex DNA termini when a DNA polymerase with the strand-displacement ability is used. We thus conclude that recognition of duplex DNA by mixed-base PNAs via the end invasion has a promising potential for site-specific and sequence-unrestricted DNA manipulation and detection.


  • [Methods Online] Evaluation of multiple displacement amplification in a 5 cM STR genome-wide scan -

    Multiple displacement amplification (MDA) has emerged as a promising new method of whole genome amplification (WGA) with the potential to generate virtually unlimited genome-equivalent DNA from only a small amount of seed DNA. To date, genome-wide high marker density assessments of MDA–DNA have focussed mainly upon suitability for single nucleotide polymorphism (SNP) genotyping applications. Suitability for short tandem repeat (STR) genotyping has not been investigated in great detail, despite their inherent instability during DNA replication, and the obvious challenge that this presents to WGA techniques. Here, we aimed to assess the applicability of MDA in STR genotyping by conducting a genome-wide scan of 768 STR markers for MDAs of 15 high quality genomic DNAs. We found that MDA genotyping call and accuracy rates were only marginally lower than for genomic DNA. Pooling of three replicate MDAs resulted in a small increase in both call rate and genotyping accuracy. We identified 34 STRs (4.4% of total markers) of which five essentially failed with MDA samples, and 29 of which showed elevated genotyping failures/discrepancies in the MDAs. We emphasise the importance of DNA and MDA quality checks, and the use of appropriate controls to identify problematic STR markers.


  • [Methods Online] Expressible molecular colonies -

    Carrying out polymerase chain reaction in a gel layer generates a 2-D pattern of DNA colonies comprising pure genetic clones. Here we demonstrate that transcription, translation and protein folding can be performed in the same gel. The resulting nucleoprotein colonies mimic living cells by serving as compartments in which the synthesized RNAs and proteins co-localize with their templates. Yet, due to the absence of penetration barriers, such a molecular colony display allows cloned genes to be directly tested for the encoded functions. Now, the results imply that virtually any manipulations with genes and their expression products can be accomplished in vitro.


  • [Methods Online] Four new type I restriction enzymes identified in Escherichia coli clinical isolates -

    Using a plasmid transformation method and the RM search computer program, four type I restriction enzymes with new recognition sites and two isoschizomers (EcoBI and Eco377I) were identified in a collection of clinical Escherichia coli isolates. These new enzymes were designated Eco394I, Eco826I, Eco851I and Eco912I. Their recognition sequences were determined to be GAC(5N)RTAAY, GCA(6N)CTGA, GTCA(6N)TGAY and CAC(5N)TGGC, respectively. A methylation sensitivity assay, using various synthetic oligonucleotides, was used to identify the adenines that prevent cleavage when methylated (underlined). These results suggest that type I enzymes are abundant in E.coli and many other bacteria, as has been inferred from bacterial genome sequencing projects.


  • [Methods Online] Generation of subspecies level-specific microbial diagnostic microarrays using genes amplified from subtractive suppression hybridization as microarray probes -

    The generation of microarray probes with specificity below the species level is an ongoing challenge, not least because the high-throughput detection of microorganisms would be an efficient means of identifying environmentally relevant microbes. Here, we describe how suppression subtractive hybridization (SSH) can be applied to the production of microarray probes that are useful for microbial differentiation at the subspecies level. SSH was used to initially isolate unique genomic sequences of nine Salmonella strains, and these were validated in quadruplicate by microarray analysis. The results obtained indicate that a large group of genes subtracted by SSH could serve together, as one probe, for detecting a microbial subspecies. Similarly, the whole microbial genome (not subjected to SSH) can be used as a species-specific probe. The detailed methods described herein could be used and adapted for the estimation of any cultivable bacteria from different environments.


  • [Methods Online] Genome amplification of single sperm using multiple displacement amplification -

    Sperm typing is an effective way to study recombination rate on a fine scale in regions of interest. There are two strategies for the amplification of single meiotic recombinants: repulsion-phase allele-specific PCR and whole genome amplification (WGA). The former can selectively amplify single recombinant molecules from a batch of sperm but is not scalable for high-throughput operation. Currently, primer extension pre-amplification is the only method used in WGA of single sperm, whereas it has limited capacity to produce high-coverage products enough for the analysis of local recombination rate in multiple large regions. Here, we applied for the first time a recently developed WGA method, multiple displacement amplification (MDA), to amplify single sperm DNA, and demonstrated its great potential for producing high-yield and high-coverage products. In a 50 µl reaction, 76 or 93% of loci can be amplified at least 2500- or 250-fold, respectively, from single sperm DNA, and second-round MDA can further offer >200-fold amplification. The MDA products are usable for a variety of genetic applications, including sequencing and microsatellite marker and single nucleotide polymorphism (SNP) analysis. The use of MDA in single sperm amplification may open a new era for studies on local recombination rates.


  • [Methods Online] Genome-wide estimation of transcript concentrations from spotted cDNA microarray data -

    A method providing absolute transcript concentrations from spotted microarray intensity data is presented. Number of transcripts per µg total RNA, mRNA or per cell, are obtained for each gene, enabling comparisons of transcript levels within and between tissues. The method is based on Bayesian statistical modelling incorporating available information about the experiment from target preparation to image analysis, leading to realistically large confidence intervals for estimated concentrations. The method was validated in experiments using transcripts at known concentrations, showing accuracy and reproducibility of estimated concentrations, which were also in excellent agreement with results from quantitative real-time PCR. We determined the concentration for 10 157 genes in cervix cancers and a pool of cancer cell lines and found values in the range of 105–1010 transcripts per µg total RNA. The precision of our estimates was sufficiently high to detect significant concentration differences between two tumours and between different genes within the same tumour, comparisons that are not possible with standard intensity ratios. Our method can be used to explore the regulation of pathways and to develop individualized therapies, based on absolute transcript concentrations. It can be applied broadly, facilitating the construction of the transcriptome, continuously updating it by integrating future data.


  • [Methods Online] Genome-wide selection of unique and valid oligonucleotides -

    Functional genomics methods are used to investigate the huge amount of information contained in genomes. Numerous experimental methods rely on the use of oligo- or polynucleotides. Nucleotide strand hybridization forms the underlying principle for these methods. For all these techniques, the probes should be unique for analyzed genes. In addition to being unique for the studied genes, the probes should fulfill a large number of criteria to be usable and valid. The criteria include for example, avoidance of self-annealing, suitable melting temperature and nucleotide composition. We developed a method for searching unique and valid oligonucleotides or probes for genes so that there is not even a similar (approximate) occurrence in any other location of the whole genome. By using probe size 25, we analyzed 17 complete genomes representing a wide range of both prokaryotic and eukaryotic organisms. More than 92% of all the genes in the investigated genomes contained valid oligonucleotides. Extensive statistical tests were performed to characterize the properties of unique and valid oligonucleotides. Unique and valid oligonucleotides were relatively evenly distributed in genes except for the beginning and end, which were somewhat overrepresented. The flanking regions in eukaryotes were clearly underrepresented among suitable oligonucleotides. In addition to distributions within genes, the effects on codon and amino acid usage were also studied.


  • [Methods Online] Genomic profiling by DNA amplification of laser capture microdissected tissues and array CGH -

    Comparative genomic hybridization by means of BAC microarrays (array CGH) allows high-resolution profiling of copy-number aberrations in tumor DNA. However, specific genetic lesions associated with small but clinically relevant tumor areas may pass undetected due to intra-tumor heterogeneity and/or the presence of contaminating normal cells. Here, we show that the combination of laser capture microdissection, 29 DNA polymerase-mediated isothermal genomic DNA amplification, and array CGH allows genomic profiling of very limited numbers of cells. Moreover, by means of simple statistical models, we were able to bypass the exclusion of amplification distortions and variability prone areas, and to detect tumor-specific chromosomal gains and losses. We applied this new combined experimental and analytical approach to the genomic profiling of colorectal adenomatous polyps and demonstrated our ability to accurately detect single copy gains and losses affecting either whole chromosomes or small genomic regions from as little as 2 ng of DNA or 1000 microdissected cells.


  • [Methods Online] Headloop suppression PCR and its application to selective amplification of methylated DNA sequences -

    Selective amplification in PCR is principally determined by the sequence of the primers and the temperature of the annealing step. We have developed a new PCR technique for distinguishing related sequences in which additional selectivity is dependent on sequences within the amplicon. A 5' extension is included in one (or both) primer(s) that corresponds to sequences within one of the related amplicons. After copying and incorporation into the PCR product this sequence is then able to loop back, anneal to the internal sequences and prime to form a hairpin structure—this structure is then refractory to further amplification. Thus, amplification of sequences containing a perfect match to the 5' extension is suppressed while amplification of sequences containing mismatches or lacking the sequence is unaffected. We have applied Headloop PCR to DNA that had been bisulphite-treated for the selective amplification of methylated sequences of the human GSTP1 gene in the presence of up to a 105-fold excess of unmethylated sequences. Headloop PCR has a potential for clinical application in the detection of differently methylated DNAs following bisulphite treatment as well as for selective amplification of sequence variants or mutants in the presence of an excess of closely related DNA sequences.


  • [Methods Online] High sensitivity EndoV mutation scanning through real-time ligase proofreading -

    The ability to associate mutations in cancer genes with the disease and its subtypes is critical for understanding oncogenesis and identifying biomarkers for clinical diagnosis. A two-step mutation scanning method that sequentially used endonuclease V (EndoV) to nick at mismatches and DNA ligase to reseal incorrectly or nonspecifically nicked sites was previously developed in our laboratory. Herein we report an optimized single-step assay that enables ligase to proofread EndoV cleavage in real-time under a compromise between buffer conditions. Real-time proofreading results in a dramatic reduction of background cleavage. A universal PCR strategy that employs both unlabeled gene-specific primers and labeled universal primers, allows for multiplexed gene amplification and precludes amplification of primer dimers. Internally labeled PCR primers eliminate EndoV cleavage at the 5' terminus, enabling high-throughput capillary electrophoresis readout. Furthermore, signal intensity is increased and artifacts are reduced by generating heteroduplexes containing only one of the two possible mismatches (e.g. either A/C or G/T). The single-step assay improves sensitivity to 1:50 and 1:100 (mutant:wild type) for unknown mutations in the p53 and K-ras genes, respectively, opening prospects as an early detection tool.


  • [Methods Online] Hypervariable genes--experimental error or hidden dynamics -

    In a homogeneous group of samples, not all genes of high variability stem from experimental errors in microarray experiments. These expression variations can be attributed to many factors including natural biological oscillations or metabolic processes. The behavior of these genes can tease out important clues about naturally occurring dynamic processes in the organism or experimental system under study. We developed a statistical procedure for the selection of genes with high variability denoted hypervariable (HV) genes. After the exclusion of low expressed genes and a stabilizing log-transformation, the majority of genes have comparable residual variability. Based on an F-test, HV genes are selected as having a statistically significant difference from the majority of variability stabilized genes measured by the ‘reference group’. A novel F-test clustering technique, further noted as ‘F-means clustering’, groups HV genes with similar variability patterns, presumably from their participation in a common dynamic biological process. F-means clustering establishes, for the first time, groups of co-expressed HV genes and is illustrated with microarray data from patients with juvenile rheumatoid arthritis and healthy controls.


  • [Methods Online] I-ApeI: a novel intron-encoded LAGLIDADG homing endonuclease from the archaeon, Aeropyrum pernix K1 -

    Over 50 introns have been reported in archaeal rRNA genes (rDNAs), a subset of which nests putative homing endonuclease (HEase) genes. Here, we report the identification and characterization of a novel archaeal LAGLIDADG-type HEase, I-ApeI, encoded by the ApeK1.S908 intron within the 16S rDNA of Aeropyrum pernix K1. I-ApeI consists of 222 amino acids and harbors two LAGLIDADG-like sequences. It recognizes the 20 bp non-palindromic sequence 5'-GCAAGGCTGAAACTTAAAGG and cleaves target DNA to produce protruding tetranucleotide 3' ends. Either Mn2+ or Co2+ can be substituted for Mg2+ as a cofactor in the cleavage reaction. Of the 20 bases within the minimal recognition site, 7 are essential for cleavage and are located at positions proximal to the cleavage sites.


  • [Methods Online] Improved microarray methods for profiling the yeast knockout strain collection -

    A remarkable feature of the Yeast Knockout strain collection is the presence of two unique 20mer TAG sequences in almost every strain. In principle, the relative abundances of strains in a complex mixture can be profiled swiftly and quantitatively by amplifying these sequences and hybridizing them to microarrays, but TAG microarrays have not been widely used. Here, we introduce a TAG microarray design with sophisticated controls and describe a robust method for hybridizing high concentrations of dye-labeled TAGs in single-stranded form. We also highlight the importance of avoiding PCR contamination and provide procedures for detection and eradication. Validation experiments using these methods yielded false positive (FP) and false negative (FN) rates for individual TAG detection of 3–6% and 15–18%, respectively. Analysis demonstrated that cross-hybridization was the chief source of FPs, while TAG amplification defects were the main cause of FNs. The materials, protocols, data and associated software described here comprise a suite of experimental resources that should facilitate the use of TAG microarrays for a wide variety of genetic screens.


  • [Methods Online] Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools -

    Saccharomyces cerevisiae knockout collection TAG microarrays are an emergent platform for rapid, genome-wide functional characterization of yeast genes. TAG arrays report abundance of unique oligonucleotide ‘TAG’ sequences incorporated into each deletion mutation of the yeast knockout collection, allowing measurement of relative strain representation across experimental conditions for all knockout mutants simultaneously. One application of TAG arrays is to perform genome-wide synthetic lethality screens, known as synthetic lethality analyzed by microarray (SLAM). We designed a fully defined spike-in pool to resemble typical SLAM experiments and performed TAG microarray hybridizations. We describe a method for analyzing two-color array data to efficiently measure the differential knockout strain representation across two experimental conditions, and use the spike-in pool to show that the sensitivity and specificity of this method exceed typical current approaches.


  • [Methods Online] Isolation of mRNA from specific tissues of Drosophila by mRNA tagging -

    To study the function of specific cells or tissues using genomic tools like microarray analyses, it is highly desirable to obtain mRNA from a homogeneous source. However, this is particularly challenging for small organisms, like Caenorhabditis elegans and Drosophila melanogaster. We have optimized and applied a new technique, mRNA tagging, to isolate mRNA from specific tissues of D.melanogaster. A FLAG-tagged poly(A)-binding protein (PABP) is expressed in a specific tissue and mRNA from that tissue is thus tagged by the recombinant PABP and separated from mRNA in other tissues by co-immunoprecipitation with a FLAG-tag specific antibody. The fractionated mRNA is then amplified and used as probe in microarray experiments. As a test system, we employed the procedures to identify genes expressed in Drosophila photoreceptor cells. We found that most known photoreceptor cell-specific mRNAs were identified by mRNA tagging. Furthermore, at least 11 novel genes have been identified as enriched in photoreceptor cells. mRNA tagging is a powerful general method for profiling gene expression in specific tissues and for identifying tissue-specific genes.


  • [Methods Online] Magnetically assisted DNA assays: high selectivity using conjugated polymers for amplified fluorescent transduction -

    We report a strategy for conjugated polymer (CP)-based optical DNA detection with improved selectivity. The high sensitivity of CP-based biosensors arises from light harvesting by the CP and the related amplified fluorescent signal transduction. We demonstrate that the use of magnetic microparticles significantly improves the selectivity of this class of DNA sensors. Compared with previously reported DNA sensors with CP amplification, this novel sensing strategy displays excellent discrimination against non-cognate DNA in the presence of a protein mixture or even human serum. We also demonstrate that the magnetically assisted DNA sensor can conveniently identify even a single-nucleotide mismatch in the target sequence.


  • [Methods Online] Methylation-Specific MLPA (MS-MLPA): simultaneous detection of CpG methylation and copy number changes of up to 40 sequences -

    Copy number changes and CpG methylation of various genes are hallmarks of tumor development but are not yet widely used in diagnostic settings. The recently developed multiplex ligation-dependent probe amplification (MLPA) method has increased the possibilities for multiplex detection of gene copy number aberrations in a routine laboratory. Here we describe a novel robust method: the methylation-specific MLPA (MS-MLPA) that can detect changes in both CpG methylation as well as copy number of up to 40 chromosomal sequences in a simple reaction. In MS-MLPA, the ligation of MLPA probe oligonucleotides is combined with digestion of the genomic DNA–probe hybrid complexes with methylation-sensitive endonucleases. Digestion of the genomic DNA–probe complex, rather than double-stranded genomic DNA, allowed the use of DNA derived from the formalin treated paraffin-embedded tissue samples, enabling retrospective studies. To validate this novel method, we used MS-MLPA to detect aberrant methylation in DNA samples of patients with Prader–Willy syndrome, Angelman syndrome or acute myeloid leukemia.


  • [Methods Online] Minimal cross-recombination between wild-type and loxP511 sites in vivo facilitates truncating both ends of large DNA inserts in pBACe3.6 and related vectors -

    Contrary to several earlier reports, we find that cross-recombination between wild-type and the mutant loxP511 sites is <0.5% of that between two wild-type sites if Cre protein is expressed by phage P1 during an infection. The finding enabled us to develop a procedure to truncate DNA progressively from both ends of large genomic inserts flanked by these two loxP sites in pBACe3.6 and related vectors with transposons carrying either a wild-type or a loxP511 sequence. Newly constructed loxP511 transposons contained either a kanamycin resistance gene or no marker. Insert DNA ends in deletions were sequenced with primers unique to each transposon-end remaining after the respective recombination. End-sequencing 223 deletions confirmed that the low level of cross-recombination, observed between those sites during the P1 transductions, does not complicate the procedure: truncations from the unintended end of genomic inserts did not occur. Multiple BACs pooled together could also be processed in a single tube to make end-deletions. This deletion technology, utilizing the very minimal cross-recombination between the mutant and wild-type loxP sites of most BAC clones in the public domain and a heterologous one inserted as a transposon, should facilitate functionally mapping long-range gene regulatory sequences and help to isolate genes with defined functional boundaries in numerous projects including those of therapeutic interest.


  • [Methods Online] MSRE-PCR for analysis of gene-specific DNA methylation -

    Abnormal DNA methylation is observed in certain promoters of neoplastic cells, although the likelihood of methylation for each individual promoter varies. Simultaneous analysis of many promoters in the same sample can allow use of statistical methods for identification of neoplasia. Here we describe an assay for such analysis, based on digestion of genomic DNA with methylation-sensitive restriction enzyme and multiplexed PCR with gene-specific primers (MSRE-PCR). MSRE-PCR includes extensive digestion of genomic DNA (uncut fragments cannot be identified by PCR), can be applied to dilute samples (<1 pg/µl), requires limited amount of starting material (42 pg or genomic equivalent of seven cells) and can identify methylation in a heterogeneous mix containing <2% of cells with methylated fragments. When applied to 53 promoters of breast cancer cell lines MCF-7, MDA-MB-231 and T47D, MSRE-PCR correctly identified the methylation status of genes analyzed by other techniques. For selected genes results of MSRE-PCR were confirmed by methylation-specific PCR and bisulfite sequencing. The assay can be configured for any number of desired targets in any user-defined set of genes.


  • [Methods Online] Multiplex PCR: use of heat-stable Thermus thermophilus RecA protein to minimize non-specific PCR products -

    In this paper we report that the inclusion of heat-resistant RecA protein from a thermophilic bacteria, Thermus thermophilus, and its cofactor (ATP) in PCR effectively eliminates non-specific PCR products. The effect of RecA protein, which catalyzes pairing between homologous DNA molecules with great fidelity in genetic recombination, is due to its promotion of precise priming in PCR (i.e. priming at sites where the primer sequence is completely complementary to that of the target sequence). In addition, the RecA protein substantially reduces the primer concentration required for PCR. These experimental results have led to the realization of multiplex PCR, which involves PCR for multiple sites in the same reaction mixture. We were able to successfully perform multiplex PCR with over a dozen reactions without affecting the amplification pattern of the PCR products.


  • [Methods Online] Natural and synthetic tetracycline-inducible promoters for use in the antibiotic-producing bacteria Streptomyces -

    Bacteria in the genus Streptomyces are major producers of antibiotics and other pharmacologically active compounds. Genetic and physiological manipulations of these bacteria are important for new drug discovery and production development. An essential part of any ‘genetic toolkit’ is the availability of regulatable promoters. We have adapted the tetracycline (Tc) repressor/operator (TetR/tetO) regulatable system from transposon Tn10 for use in Streptomyces. The synthetic Tc controllable promoter (tcp), tcp830, was active in a wide range of Streptomyces species, and varying levels of induction were observed after the addition of 1–100 ng/ml of anhydrotetracycline (aTc). Streptomyces coelicolor contained an innate Tc-controllable promoter regulated by a TetR homologue (SCO0253). Both natural and synthetic promoters were active and inducible throughout growth. Using the luxAB genes expressing luciferase as a reporter system, we showed that induction factors of up to 270 could be obtained for tcp830. The effect of inducers on the growth of S.coelicolor was determined; addition of aTc at concentrations where induction is optimal, i.e. 0.1–1 µg/ml, ranged from no effect on growth rate to a small increase in the lag period compared with cultures with no inducer.


  • [Methods Online] Nucleotide exchange and excision technology (NExT) DNA shuffling: a robust method for DNA fragmentation and directed evolution -

    DNA shuffling is widely used for optimizing complex properties contained within DNA and proteins. Demonstrated here is the amplification of a gene library by PCR using uridine triphosphate (dUTP) as a fragmentation defining exchange nucleotide with thymidine, together with the three other nucleotides. The incorporated uracil bases were excised using uracil-DNA-glycosylase and the DNA backbone subsequently cleaved with piperidine. These end-point reactions required no adjustments. Polyacrylamide urea gels demonstrated adjustable fragmentation size over a wide range. The oligonucleotide pool was reassembled by internal primer extension to full length with a proofreading polymerase to improve yield over Taq. We present a computer program that accurately predicts the fragmentation pattern and yields all possible fragment sequences with their respective likelihood of occurrence, taking the guesswork out of the fragmentation. The technique has been demonstrated by shuffling chloramphenicol acetyltransferase gene libraries. A 33% dUTP PCR resulted in shuffled clones with an average parental fragment size of 86 bases even without employment of a fragment size separation, and revealed a low mutation rate (0.1%). NExT DNA fragmentation is rational, easily executed and reproducible, making it superior to other techniques. Additionally, NExT could feasibly be applied to several other nucleotide analogs.


  • [Methods Online] Offset recombinant PCR: a simple but effective method for shuffling compact heterologous domains -

    DNA shuffling and other in vitro recombination strategies have proven highly effective at generating complex libraries for mutagenesis studies. While most recombination techniques employ DNA polymerases in part of a multi-step process, few seek to exploit the natural recombinogenic tendencies and exponential amplification rates of PCR. Here, we characterize a simple but effective method for using standard PCR to promote high recombination frequencies among compact heterologous domains by locating the domains near one end of the template. In a typical amplification reaction, Pfu polymerase generated chimeric crossover events in 13% of the population when markers were separated by only 70 nt. The fraction of recombinant sequences reached 42% after six consecutive rounds of PCR, a value close to the 50% expected from a fully shuffled population. When homology within the recombinant region was reduced to 82%, the recombination frequency dropped by nearly half for a single amplification reaction and crossover events were clustered toward one end of the domain. Surprisingly, recombination frequencies for template populations with high and low sequence homologies converged after just four rounds of PCR, suggesting that the exponential accumulation of chimeric molecules in the PCR mixture serves to promote recombination within heterologous domains.


  • [Methods Online] Oligonucleotide-assisted cleavage and ligation: a novel directional DNA cloning technology to capture cDNAs. Application in the construction of a human immune antibody phage-display library -

    The use of oligonucleotide-assisted cleavage and ligation (ONCL), a novel approach to the capture of gene repertoires, in the construction of a phage-display immune antibody library is described. ONCL begins with rapid amplification of cDNA ends to amplify all members equally. A single, specific cut near 5' and/or 3' end of each gene fragment (in single stranded form) is facilitated by hybridization with an appropriate oligonucleotide adapter. Directional cloning of targeted DNA is accomplished by ligation of a partially duplex DNA molecule (containing suitable restriction sites) and amplification with primers in constant regions. To demonstrate utility and reliability of ONCL, a human antibody repertoire was cloned from IgG mRNA extracted from human B-lymphocytes engrafted in Trimera mice. These mice were transplanted with peripheral blood lymphocytes from Candida albicans infected individuals and subsequently immunized with C.albicans glyceraldehyde-3-phosphate dehydrogenase (GAPDH). DNA sequencing showed that ONCL resulted in efficient capture of gene repertoires. Indeed, full representation of all VH families/segments was observed showing that ONCL did not introduce cloning biases for or against any VH family. We validated the efficiency of ONCL by creating a functional Fab phage-display library with a size of 3.3 x 1010 and by selecting five unique Fabs against GAPDH antigen.


  • [Methods Online] One-step random mutagenesis by error-prone rolling circle amplification -

    In vitro random mutagenesis is a powerful tool for altering properties of enzymes. We describe here a novel random mutagenesis method using rolling circle amplification, named error-prone RCA. This method consists of only one DNA amplification step followed by transformation of the host strain, without treatment with any restriction enzymes or DNA ligases, and results in a randomly mutated plasmid library with 3–4 mutations per kilobase. Specific primers or special equipment, such as a thermal-cycler, are not required. This method permits rapid preparation of randomly mutated plasmid libraries, enabling random mutagenesis to become a more commonly used technique.


  • [Methods Online] Optical absorption assay for strand-exchange reactions in unlabeled nucleic acids -

    The nucleic acid exchange reaction is a common feature for genetic recombination, DNA replication and transcription. Due to the fact that in the strand-exchange reactions the reactant and product molecules have similar or identical nucleotide sequences, the reaction is undetectable. As a rule, the nucleic acids with radioactive or fluorescence labels are used in such studies. Besides the fact that the labels can perturb the reaction and pose a health risk to the investigators, the assays usually involve extra experimental steps: quenching the reaction, separation, visualization and quantification of the products. Here, we describe a straightforward, direct and precise method to study strand-exchange reaction of unlabeled nucleic acids by real-time measurements of optical absorption. The method takes advantage of the property of some guanine-rich oligonucleotides to adopt monomolecular quadruplex conformation in the presence of certain cations. The conformation is characterized by significant absorption in long-wavelength range of the ultraviolet region where usually other secondary structures are transparent. The ‘signal’ oligonucleotide is incorporated into reactant duplex by annealing with target sequence. Adding the replacement sequence initiates the release of the ‘signal’ oligonucleotide into solution, which is accompanied by ultraviolet absorption in long-wavelength range.


  • [Methods Online] Pattern of genes influenced by conditional expression of the transcription factors HNF6, HNF4{alpha} and HNF1{beta} in a pancreatic {beta}-cell line -

    Using the rat insulinoma cell line INS-1 we generated ßbeta;-cell clones that are most efficient for gene transfer, as they contain an FRT site for Flp recombinase-mediated, site-directed integration of a single copy transgene. Therefore, the gene-of-interest can be introduced by DNA transfection without the need to select individual cell clones. Additionally, the clones contain the tetracycline repressor allowing tetracycline induction of the transgene. By oligonucleotide microarray we define the ßbeta;-cell specific phenotype of the Flp-In T-REx cell clones. Using a clone expressing the HNF6, HNF4 and HNF1ßbeta; transcription factors at a limited level, we introduced the expression vectors encoding these factors. We show efficient tetracycline induction of these transcription factors by western blots and immunocytochemistry. Microarrays reveal that these three factors affect a similar number of genes with only few genes regulated in common. Statistical analysis reveals that the three transcription factors affect genes categorized to different biological processes. Furthermore, we document the usefulness of these Flp-In T-REx cells for the functional analysis of mutated HNF1ßbeta; transcription factors found in human MODY5 patients. We show that the expression of the mutant P328L329del and A263insGG affects only very few transcripts and these are predominantly distinct from those induced by wild-type HNF1ßbeta;.


  • [Methods Online] PCR amplification from single DNA molecules on magnetic beads in emulsion: application for high-throughput screening of transcription factor targets -

    We have developed a novel method of genetic library construction on magnetic microbeads based on solid-phase single-molecule PCR in a fine and robust water-phase compartment formed in water-in-oil (w/o) emulsions. In this method, critically diluted DNA fragments were distributed over the emulsion as templates, where beads crosslinked with multiple primers and other PCR components were encapsulated to form multiple reaction compartments. The delivered DNA was then amplified and covalently immobilized on the beads in parallel, within individual compartments, to construct a genetic library on beads (GLOBE), which was readily applicable to a genomewide global scanning of genetic elements recognized by a defined DNA-binding protein. We constructed a GLOBE of Paracoccus denitrificans and selected gene beads that were bound to the His-tagged transcription factor PhaR by flow cytometry. As a result of flow cytometry screening with an anti-His fluorescent antibody, the PhaR target fragments were enriched 1200-fold from this library with this system. Therefore, this system is a powerful tool for analyzing the transcription network on a genomewide scale.


  • [Methods Online] PPC: an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays -

    Robust estimation of allele frequencies in pools of DNA has the potential to reduce genotyping costs and/or increase the number of individuals contributing to a study where hundreds of thousands of genetic markers need to be genotyped in very large populations sample sets, such as genome wide association studies. In order to make accurate allele frequency estimations from pooled samples a correction for unequal allele representation must be applied. We have developed the polynomial based probe specific correction (PPC) which is a novel correction algorithm for accurate estimation of allele frequencies in data from high-density microarrays. This algorithm was validated through comparison of allele frequencies from a set of 10 individually genotyped DNA's and frequencies estimated from pools of these 10 DNAs using GeneChip 10K Mapping Xba 131 arrays. Our results demonstrate that when using the PPC to correct for allelic biases the accuracy of the allele frequency estimates increases dramatically.


  • [Methods Online] Quantitative sequential chromatin immunoprecipitation, a method for analyzing co-occupancy of proteins at genomic regions in vivo -

    Sequential chromatin immunoprecipitation (SeqChIP) is a procedure in which formaldehyde-crosslinked, protein–DNA complexes from living cells are subjected to two sequential immunoprecipitations with antibodies of different specificity. SeqChIP has been used to address, in a qualitative manner, whether two proteins can simultaneously co-occupy a stretch of DNA in vivo. Here, we expand on our earlier work and describe theoretical and practical considerations for performing and interpreting SeqChIP experiments in a quantitative manner. We provide a detailed experimental procedure for designing and performing SeqChIP experiments as well as experimental examples of the three possible outcomes: full co-occupancy, no co-occupancy and partial co-occupancy. In some cases of partial co-occupancy, the order of immunoprecipitations in SeqChIP can strongly influence the outcome. We experimentally confirm a quantitative parameter that provides a measure of co-occupancy of two proteins on a given region of DNA and provide information on how to interpret the results of SeqChIP experiments. Our quantitative treatment of SeqChIP data substantially expands the usefulness of the technique for elucidating molecular mechanisms in vivo.


  • [Methods Online] Real-time monitoring of enzymatic DNA hydrolysis by electrospray ionization mass spectrometry -

    A fast and direct method for the monitoring of enzymatic DNA hydrolysis was developed using electrospray ionization mass spectrometry. We incorporated the use of a robotic chip-based electrospray ionization source for increased reproducibility and throughput. The mass spectrometry method allows the detection of DNA fragments and intact non-covalent protein–DNA complexes in a single experiment. We used the method to monitor in real-time single-stranded (ss) DNA hydrolysis by colicin E9 DNase and to characterize transient non-covalent E9 DNase–DNA complexes present during the hydrolysis reaction. The mass spectra showed that E9 DNase interacts with ssDNA in the absence of a divalent metal ion, but is strictly dependent on Ni2+ or Co2+ for ssDNA hydrolysis. We demonstrated that the sequence selectivity of E9 DNase is dependent on the ratio protein:ssDNA or the ssDNA concentration and that only 3'-hydroxy and 5'-phosphate termini are produced. It was also shown that the homologous E7 DNase is reactive with Zn2+ as transition metal ion and that this DNase displays a different sequence selectivity. The method described is of general use to analyze the reactivity and specificity of nucleases.


  • [Methods Online] Reproducible doxycycline-inducible transgene expression at specific loci generated by Cre-recombinase mediated cassette exchange -

    Comparative analysis of mutants using transfection is complicated by clones exhibiting variable levels of gene expression due to copy number differences and genomic position effects. Recombinase-mediated cassette exchange (RMCE) can overcome these problems by introducing the target gene into pre-determined chromosomal loci, but recombination between the available recombinase targeting sites can reduce the efficiency of targeted integration. We developed a new LoxP site (designated L3), which when used with the original LoxP site (designated L2), allows highly efficient and directional replacement of chromosomal DNA with incoming DNA. A total of six independent LoxP integration sites introduced either by homologous recombination or retroviral delivery were analyzed; 70–80% of the clones analyzed in hamster and human cells were correct recombinants. We combined the RMCE strategy with a new, tightly regulated tetracycline induction system to produce a robust, highly reliable system for inducible transgene expression. We observed stable inducible expression for over 1 month, with uniform expression in the cell population and between clones derived from the same integration site. This system described should find significant applications for studies requiring high level and regulated transgene expression and for determining the effects of various stresses or oncogenic conditions in vivo and in vitro.


  • [Methods Online] Reversibly switchable DNA nanocompartment on surfaces -

    Biological macromolecules have been used to fabricate many nanostructures, biodevices and biomimetics because of their physical and chemical properties. But dynamic nanostructure and biomachinery that depend on collective behavior of biomolecules have not been demonstrated. Here, we report the design of DNA nanocompartments on surfaces that exhibit reversible changes in molecular mechanical properties. Such molecular nanocompartments are used to encage molecules, switched by the collective effect of Watson–Crick base-pairing interactions. This effect is used to perform molecular recognition. Furthermore, we found that ‘fuel’ strands with single-base variation cannot afford an efficient closing of nanocompartments, which allows highly sensitive label-free DNA array detection. Our results suggest that DNA nanocompartments can be used as building blocks for complex biomaterials because its core functions are independent of substrates and mediators.


  • [Methods Online] RNA interference by mixtures of siRNAs prepared using custom oligonucleotide arrays -

    RNA interference (RNAi) is a process in which double-strand RNA (dsRNA) directs the specific degradation of a corresponding target mRNA. The mediators of this process are small dsRNAs, of ~21 bp in length, called small interfering RNAs (siRNAs). siRNAs, which can be prepared in vitro in a number of ways and then transfected into cells, can direct the degradation of corresponding mRNAs inside these cells. Hence, siRNAs represent a powerful tool for studying gene functions, as well as having the potential of being highly specific pharmaceutical agents. Some limitations in using this technology exist because the preparation of siRNA in vitro and screening for siRNAs efficient in RNAi can be expensive and time-consuming processes. Here, we demonstrate that custom oligonucleotide arrays can be efficiently used for the preparation of defined mixtures of siRNAs for the silencing of exogenous and endogenous genes. The method is fast, inexpensive, does not require siRNA optimization and has a number of advantages over methods utilizing enzymatic preparation of siRNAs by digestion of longer dsRNAs, as well as methods based on chemical synthesis of individual siRNAs or their DNA templates.


  • [Methods Online] Sequence dependence of cross-hybridization on short oligo microarrays -

    One of the critical problems in the short oligo microarray technology is how to deal with cross-hybridization that produces spurious data. Little is known about the details of cross-hybridization effect at molecular level. Here, we report a free energy analysis of cross-hybridization on short oligo microarrays using data from a spike-in study. Our analysis revealed that cross-hybridization on the arrays is mostly caused by oligo fragments with a run of 10–16 nt complementary to the probes. Mismatches were estimated to be energetically much more costly in cross-hybridization than that in gene-specific hybridization, implying that the sources of cross-hybridization must be very different between a PM–MM probe pair. Consequently, it is unreliable to use MM probe signal to track cross-hybridizing signal on a corresponding PM probe. Our results also showed that the oligo fragments tend to bind to the 5' ends of the probes, and are rarely seen at the 3' ends. These results are useful for microarray design and data analysis.


  • [Methods Online] Simultaneous detection of microsatellite repeats and SNPs in the macrophage migration inhibitory factor (MIF) gene by thin-film biosensor chips and application to rural field studies -

    Microsatellite repeat and single nucleotide polymorphisms (SNPs) are abundant sources of genetic variation, but existing methodologies cannot simultaneously detect these variants in a facile or inexpensive way. We describe herein a thin-film biosensor chip based on an allele-discriminating oligonucleotide array that enables genotyping for both microsatellite repeats and SNPs in a single analysis. We validated this methodology for the functionally polymorphic –794 CATT5–8 repeat and –173 G/C SNP present in the promoter of the human gene for macrophage migration inhibitory factor (MIF). In a comparison of 30 samples collected at a rural hospital in Zambia, we observed a 100% concordance for both the CATT repeat and G/C SNP between the biosensor methodology and the conventional capillary electrophoresis. The biosensor chips are low in cost and once printed, they are robust and require no instrumentation for analysis. When combined with multiple displacement amplification, this methodology can be utilized in primitive settings for the genotyping of nanogram quantities of DNA present in blood, dried and stored on filter paper samples. We applied this methodology to a field study of MIF genotype in children with malaria, and provide first evidence for a potential association between MIF alleles and malaria infection. We also present data supporting significant population stratification of the low- versus high-expression forms of MIF that may bear on the role of this gene in infectious diseases.


  • [Methods Online] Single nucleotide extension technology for quantitative site-specific evaluation of metC/C in GC-rich regions -

    The development and use of high throughput technologies for detailed mapping of methylated cytosines (metC) is becoming of increasing importance for the expanding field of epigenetics. The single nucleotide primer extension reaction used for genotyping of single nucleotide polymorphisms has been recently adapted to interrogate the bisulfite modification induced ‘quantitative’ C/T polymorphism that corresponds to metC/C in the native DNA. In this study, we explored the opportunity to investigate C/T (and G/A) ratios using the Applied Biosystems (ABI) SNaPshot technology. The main effort of this study was dedicated to addressing the complexities in the analysis of DNA methylation in GC-rich regions where interrogation of the target cytosine can be confounded by variable degrees of methylation in other cytosines (resulting in variable C/T or G/A ratios after treatment with bisulfite) in the annealing site of the interrogating primer. In our studies, the mismatches of the SNaPshot primer with the target DNA sequence resulted in a biasing effect of up to 70% while these effects decreased as the location of the polymorphic site moved upstream of the target cytosine. We demonstrated that the biasing effect can be corrected with the SNaPshot primers containing degenerative C/T and G/A nucleotides. A series of experiments using various permutations of quantitative C/T and G/A polymorphisms at various positions of the target DNA sequence demonstrated that SNaPshot is able to accurately report cytosine methylation levels with <5% average SD from the true values. Given the relative simplicity of the method and the possibility to multiplex C/T and G/A interrogations, the SNaPshot approach may become a useful tool for large-scale mapping of metC.


  • [Methods Online] Site-selective and hydrolytic two-strand scission of double-stranded DNA using Ce(IV)/EDTA and pseudo-complementary PNA -

    By combining Ce(IV)/EDTA with two pseudo-complementary peptide nucleic acids (pcPNAs), both strands in double-stranded DNA were site-selectively hydrolyzed at the target site. Either plasmid DNA (4361 bp) or its linearized form was used as the substrate. When two pcPNAs invaded into the double-stranded DNA, only the designated portion in each of the two strands was free from Watson–Crick base pairing with the counterpart DNA or the pcPNA. Upon the treatment of this invasion complex with Ce(IV)/EDTA at 37°C and pH 7.0, both of these single-stranded portions were selectively hydrolyzed at the designated site, resulting in the site-selective two-strand scission of the double-stranded DNA. Furthermore, the hydrolytic scission products were successfully connected with foreign double-stranded DNA by using ligase. The potential of these artificial systems for manipulation of huge DNA has been indicated.


  • [Methods Online] SiteFinding-PCR: a simple and efficient PCR method for chromosome walking -

    In this paper, we present a novel PCR method, termed SiteFinding-PCR, for gene or chromosome walking. The PCR was primed by a SiteFinder at a low temperature, and then the target molecules were amplified exponentially with gene-specific and SiteFinder primers, and screened out by another gene-specific primer and a vector primer. However, non-target molecules could not be amplified exponentially owing to the suppression effect of stem–loop structure and could not be screened out. This simple method proved to be efficient, reliable, inexpensive and time-saving, and may be suitable for the molecules for which gene-specific primers are available. More importantly, large DNA fragments can be obtained easily using this method. To demonstrate the feasibility and efficiency of SiteFinding-PCR, we employed this method to do chromosome walking and obtained 16 positive results from 17 samples.


  • [Methods Online] Small circular DNAs for synthesis of the human telomere repeat: varied sizes, structures and telomere-encoding activities -

    We describe the construction, structural properties and enzymatic substrate abilities of a series of circular DNA oligonucleotides that are entirely composed of the C-rich human telomere repeat, (CCCTAA)n. The nanometer-sized circles range in length from 36 to 60 nt, and act as templates for synthesis of human telomere repeats in vitro. The circles were constructed successfully by the application of a recently developed adenine-protection strategy, which allows for cyclization/ligation with T4 DNA ligase. Thermal denaturation studies showed that at pH 5.0, all five circles form folded structures with similar stability, while at pH 7.0 no melting transitions were seen. Circular dichroism spectra at the two pH conditions showed evidence for i-motif structures at the lower pH value. The series was tested as rolling circle templates for a number of DNA polymerases at pH = 7.3–8.5, using 18mer telomeric primers. Results showed that surprisingly small circles were active, although the optimum size varied from enzyme to enzyme. Telomeric repeats >>1000 nt in length could be synthesized in 1 h by the Klenow (exo-) DNA polymerase. The results establish a convenient way to make long human telomeric repeats for in vitro study of their folding and interactions, and establish optimum molecules for carrying this out.


  • [Methods Online] Stringent doxycycline-dependent control of gene activities using an episomal one-vector system -

    Conditional expression systems are of pivotal importance for the dissection of complex biological phenomena. Here, we describe a novel EBV-derived episomally replicating plasmid (pRTS-1) that carries all the elements for conditional expression of a gene of interest via Tet regulation. The vector is characterized by (i) low background activity, (ii) high inducibility in the presence of doxycycline (Dox) and (iii) graded response to increasing concentrations of the inducer. The chicken beta actin promoter and an element of the murine immunoglobin heavy chain intron enhancer drive constitutive expression of a bicistronic expression cassette that encodes the highly Dox-sensitive reverse tetracycline controlled transactivator rtTA2S-M2 and a Tet repressor-KRAB fusion protein (tTSKRAB) (silencer) placed downstream of an internal ribosomal entry site. The gene of interest is expressed from the bidirectional promoter Ptetbi-1 that allows simultaneous expression of two genes, of which one may be used as surrogate marker for the expression of the gene of interest. Tight down regulation is achieved through binding of the silencer tTSKRAB to Ptetbi-1 in the absence of Dox. Addition of Dox releases repression and via binding of rtTA2S-M2 activates Ptetbi-1.


  • [Methods Online] Subcellular localization as a limiting factor for utilization of decoy oligonucleotides -

    Transfection of cells with short double-stranded synthetic DNA molecules that contain a transcription factor binding site, known as decoy oligodeoxynucleotides (ODNs), has been proposed as a novel approach in vitro and in vivo for the study of gene regulation and for gene therapy. Once delivered into cells, decoy ODNs are predicted to bind to nuclear transcription factors, preventing their binding to consensus sequences in target genes. Using a fluorescein-labeled decoy ODN containing a consensus sequence for the AP-1 transcription factor, we show that lipid-complexed decoys were readily transfectable into cells, but were consistently detectable in the cytoplasm and not in the nucleus. The same phenomenon was observed in three different cell lines including KB-3, CHO and MDA-MB-231. The AP-1 decoy ODNs failed to inhibit the transcriptional activity of an AP-1-dependent luciferase reporter. The effect of cytoplasmic AP-1 decoy ODNs on the subcellular localization and function of c-Jun induced by the microtubule inhibitor vinblastine, which strongly induced c-Jun expression, was assessed. No difference in protein level or nuclear localization of vinblastine-induced c-Jun, or of one of its target genes, p53, was noted when cells were transfected with wild-type or mutated forms of the decoy ODNs. We suggest that subcellular localization is an unappreciated and key limiting factor for the use of transcription factor decoy ODNs that must be addressed before meaningful data interpretation can be made.


  • [Methods Online] Targeted disruption of transcriptional regulatory function of p53 by a novel efficient method for introducing a decoy oligonucleotide into nuclei -

    Decoy oligonucleotides have been used for functional sequestering of transcription factors. Efficient introduction into cells is a prerequisite for the oligonucleotides to exert their blocking function. Lipofection is the most widely used technique for that purpose because of its convenience and relatively high efficiency. However, the transduction efficiency of lipofection largely depends on cell types and experimental conditions and the introduced nucleotides are not specifically directed to nuclei where they exert their major function. In the present study, we designed a new system for transporting oligonucleotides into cell nuclei. The vehicle is composed of glutathione-S-transferase, 7 arginine residues, the DNA-binding domain of GAL4 and a nuclear localization signal, which are linked with flexible glycine stretches. The p53-responsive element linked to the GAL4 upstream activating sequence was efficiently transferred by the vehicle protein into nuclei of primary cultures of neuronal cells, embryonic stem cells and various human normal cells. Transcriptional activation of p21WAF1/CIP1 and Bax by p53 on exposure to cisplatin was completely blocked by introducing the p53 decoy oligonucleotide. Thus, the system developed in the present study can be a convenient and powerful tool for specifically disrupting the function of DNA-binding proteins in culture.


  • [Methods Online] Thermal difference spectra: a specific signature for nucleic acid structures -

    We show that nucleic acid structures may be conveniently and inexpensively characterized by their UV thermal difference spectra. A thermal difference spectrum (TDS) is obtained for a nucleic acid by simply recording the ultraviolet absorbance spectra of the unfolded and folded states at temperatures above and below its melting temperature (Tm). The difference between these two spectra is the TDS. The TDS has a specific shape that is unique for each type of nucleic acid structure, a conclusion that is based on a comparison of >900 spectra from 200 different sequences. The shape of the TDS reflects the subtleties of base stacking interactions that occur uniquely within each type of nucleic acid structure. TDS provides a simple, inexpensive and rapid method to obtain structural insight into nucleic acid structures, which is applicable to both DNA and RNA from short oligomers to polynucleotides. TDS complements circular dichroism as a tool for the structural characterization of nucleic acids in solution.


  • [Methods Online] Transformation of isolated mammalian mitochondria by bacterial conjugation -

    We have developed a method for transferring exogenous DNA molecules into isolated mammalian mitochondria using bacterial conjugation. In general, we accompl