简介：ApoptosisplaysanessentialroleinTcellbiology.ThymocytesexpressingnonfunctionalorautoreactiveTCRsareeliminatedbyapoptosisduringdevelopment.ApoptosisalsoleadstothedeletionofexpandedeffectorTcellsduringimmuneresponses.Thedysregulationofapoptosisintheimmunesystemresultsinautoimmunity,tumorogenesisandimmunodeficiency.Twomajorpathwaysleadtoapoptosis:theintrinsiccelldeathpathwaycontrolledbyBcl-2familymembersandtheextrinsiccelldeathpathwaycontrolledbydeathreceptorsignaling.Thesetwopathwaysworktogethertoregu

简介：HELcells,ahumanerythroleukemiacellline,mainlyexpressthefetal(γ)globingeneandtraceamountoftheembryonic(ε)globingene,butnotadult(β)globingene.Hereweshowthathydroxyurea(HU)caninduceHELcellstoexpressadult(β)globingeneandleadthesecellstoterminaldifferentiation.ResultsshowedinGelmobilityshiftassaysthatGATAfactorscouldspecificallybindtotheregulatoryelementsofhumanβ-globingene,includingtheproximalregulatoryelement(theβ-promoter)andthedistalregulatoryelements(theDNaseIhypersensitivesitesintheLCR,HS2-HS4coresequences).However,theDNAbindingpatternsofGATAfactorswerequitedifferentbetweenHU-inducedanduninducedHELcells.Western-blotanalysisofnuclearextractsfromboththeuninducedandHU-inducedHELcellsrevealedthatthelevelofGATA-2transcriptionfactordecreased,whereasthelevelofGATA-1transcriptionfactorincreasedfollowingthetimeofhydroxyureainduction.Furthermore,usingRT-PCRanalysistheexpressionofhumanβ-globingeneinHU-inducedHELcellscouldbeblockedagainwhenHELcellswereincubatedinthepresenceofantisenseoligonucleotidesforhGATA-1,suggestingthattheupregulationofhGATA-1transcriptionfactormightbecriticalfortheexpressionofhumanβ-globingeneinHU-inducedHELcells.

简介：Thethree-dimensional(3D)structurepredictionofproteinsisanimportanttaskinbioinformatics.Findingenergyfunctionsthatcanbetterrepresentresidue-residueandresidue-solventinteractionsisacrucialwaytoimprovethepredictionaccuracy.Thewidelyusedcontactenergyfunctionsmostlyonlyconsiderthecontactfrequencybetweendifferenttypesofresidues;however,wefindthatthecontactfrequencyalsorelatestotheresiduehydrophobicenvironment.Accordingly,wepresentanimprovedcontactenergyfunctiontointegratethetwofactors,whichcanreflecttheinfluenceofhydrophobicinteractiononthestabilizationofprotein3Dstructuremoreeffectively.Furthermore,afoldrecognition(threading)approachbasedonthisenergyfunctionisdeveloped.Thetestingresultsobtainedwith20randomlyselectedproteinsdemonstratethat,comparedwithcommoncontactenergyfunctions,theproposedenergyfunctioncanimprovetheaccuracyofthefoldtemplatepredictionfrom20%to50%,andcanalsoimprovetheaccuracyofthesequence-templatealignmentfrom35%to65%.

简介：Itisstandardpractice,wheneveraresearcherfindsanewgene,tosearchdatabasesforgenesthathaveasimilarsequence.Itisnotstandardpractice,wheneveraresearcherfindsanewgene,tosearchforgenesthathavesimilarexpression(coexpression).Failuretoperformco-expressionsearcheshasleadtoincorrectconclusionsaboutthelikelyfunctionofnewgenes,andhasleadtowastedlaboratoryattemptstoconfirmfunctionsincorrectlypredicted.WepresentheretheexampleofGliaMaturationFactorgamma(GMF-gamma).Despiteitsname,ithasnotbeenshowntoparticipateingliamaturation.ItisageneofunknownfunctionthatissimilarinsequencetoGMF-beta.ThesequencehomologyandchromosomallocationledtoanunsuccessfulsearchforGMF-gammamutationsinglioma.WeexaminedGMF-gammaexpressionin1432humancDNAlibraries.Highestexpressionoccursinphagocytic,antigen-presentingandotherhematopoieticcells.WefoundGMF-gammamRNAinalmosteverytissueexamined,withexpressioninnervoustissuenohigherthaninanyothertissue.OurevidenceindicatesthatGMF-gammaparticipatesinphagocytosisinantigenpresentingcells.Searchesforgeneswithsimilarsequencesshouldbesupplementedwithsearchesforgeneswithsimilarexpressiontoavoidincorrectpredictions.

简介：Inourpreviousstudies,DAZAP2geneexpressionwasdown-regulatedinuntreatedpatientsofmultiplemyeloma(MM).ForbetterstudyingthestructureandfunctionofDAZAP2,afull-lengthCdnawasisolatedfrommononuclearcellsofanormalhumanbonemarrow,sequencedanddepositedtoGenbank(AY430097).ThissequencehasanidenticalORF(openreadingframe)astheNM_014764fromhumantestisandtheD31767fromhumancelllineKG-1.PhylogeneticanalysisandstructurepredictionrevealthatDAZAP2homologuesarehighlyconservedthroughoutevolutionandshareapolyprolineregionandseveralpotentialSH2/SH3bindingsites.DAZAP2occursasasingle-copygenewithafour-exonorganization.WefurthernoticedthatthefunctionalDAZAP2geneislocatedonChromosome12anditspseudogenegeneisonChromosome2withelectroniclocationofhumanchromosomeinGenbank,thoughnogeneticabnormalitiesofMMhavebeenreportedonChromosome12.TheORFofhumanDAZAP2encodesa17-kDaprotein,whichishighlysimilartomousePrtb.TheDAZAP2proteinismainlylocalizedincytoplasmwithadiscretepatternofpunctuateddistribution.DAZAP2mayassociatewithcarcinogenesisofMMandparticipateinyet-to-beidentifiedsignalingpathwaystoregulateproliferationanddifferentiationofplasmacells.

简介：Wntsignalingplaysanimportantroleinembryogenesisandtumorgenesis.AlthoughthemechanismabouthowWntstransducetheirsignalingfromreceptorfrizzled(Fz)tocytosolhasnotbeenunderstood,dishevelled(Dvl)proteinwasconsideredastheintersectionofWntsignaltraffic.Inthisstudy,wecharacterizedthefunctionofthreedomains(DIX,PDZandDEP)ofDvl-1incanonicalWntsignaltransductionandDvl-1membranetranslocation.ItwasfoundbothDIXandDEPdomainweresufficienttoblockWnt-3a-inducedLEF-1transcriptionalactivityandfreecytosolβ-cateninaccumulation;whereasPDZdomainandafunctionalmutantformofDEPdomain(DEP-KM)hadnoeffectoncanonicalWntsignaling.Inaddition,whencotransfectedwithFz-7,DEPdomain,butnotDIX,PDZorDEP-KM,translocatedandco-localizedwithFz-7totheplasmamembrane,whichwassimilartoDvl-1.Furthermore,itwasDEPdomainthatcouldblockFz-7-inducedmembranetranslocationofDvl-1viaapossiblecompetitivemechanism.TheseresultsstronglysuggestthatDEPdomainisresponsibleforthemembranetranslocationofDvl-1proteinuponWntsignalstimulation.

简介：Thenorepinephrinetransporter(NET)isamemberoftheNa^+/Cl^-dependentneurotransmittertransporterfamilyandconstitutesthetargetofseveralclinicallyimportantantidepressants.TodelineatethecriticalaminoacidresiduesandthefunctionofC-terminalinregulatingtransportactivityofNET,hereweconstructedtwositemutants(V70F,F72V;V70I,F72V)andoneC-terminaltruncatedmutant(Δ611-617).ThewildtypeandmutantsofNETwereexpressedinXenopusoocytesbyinjectionoftheircRNA.Wefoundthatallofthesemutantslosttheirtransportactivity.TheseresultsindicatethattheaminoacidresiduesofV70andF72,andthelastsevenaminoacidsofC-terminalareessentialtothetransportactivityofNET.

简介：TheR(replicase)proteinistheuniquelydefinednon-structuralprotein(NSP)responsibleforRNAreplication,mutationrateorfidelity,regulationoftranscrip-tionincoronavirusesandmanyotherssRNAviruses.Basedonourcompletegenomesequencesoffourisolates(BJ01-BJ04)ofSARS-CoVfromBeijing,China,weanalyzedthestructureandpredictedfunctionsoftheRproteinincomparisonwith13otherisolatesofSARS-CoVand6othercoronaviruses.TheentireORF(open-readingframe)encodesfortwomajorenzymeactivities,RNA-dependentRNApolymerase(RdRp)andproteinaseactivities.TheRpolyproteinunder-goesacomplexproteolyticprocesstoproduce15function-relatedpeptides.Ahydrophobicdomain(HOD)andahydrophilicdomain(HID)arenewlyidentifiedwithinNSP1.ThesubstitutionrateoftheRproteinisclosetotheaverageoftheSARS-CoVgenome.ThefunctionaldomainsinallNSPsoftheRproteingivedifferentphylogeneticresultsthatsuggesttheirdifferentmutationrateunderselectivepressure.ElevenhighlyconservedregionsinRdRpandtwelvecleavagesitesby3CLP(chymotrypsin-likeprotein)havebeenidentifiedaspotentialdrugtargets.Findingssuggestthatitispossibletoobtaininformationaboutthephy-logenyofSARS-CoV,aswellaspotentialtoolsfordrugdesign,genotypinganddiagnosticsofSARS.