简介：TheE(envelope)proteinisthesmalleststructuralproteininallcoronavirusesandistheonlyviralstructuralproteininwhichnovariationhasbeendetected.WeconductedgenomesequencingandphylogeneticanalysesofSARS-CoV.Basedongenomesequencing,wepredictedtheEproteinisatransmembrane(TM)pro-teincharacterizedbyaTMregionwithstronghydrophobicityandα-helixcon-formation.Weidentifiedasegment(NH2-_L-Cys-A-Y-Cys-Cys-N_-COOH)inthecarboxyl-terminalregionoftheEproteinthatappearstoformthreedisulfidebondswithanothersegmentofcorrespondingcysteinesinthecarboxyl-terminusoftheS(spike)protein.ThesebondspointtoapossiblestructuralassociationbetweentheEandSproteins.OurphylogeneticanalysesoftheEproteinsequencesinallpub-lishedcoronavirusesplaceSARS-CoVinanindependentgroupinCoronaviridaeandsuggestanon-humananimalorigin.

简介：U7smallnuclearRNA(snRNA)sequenceshavebeendescribedonlyforahandfulofanimalspeciesinthepast.Herewedescribeacomputationalsearchforfunc-tionalU7snRNAgenesthroughoutvertebratesincludingtheupstreamsequenceelementscharacteristicforsnRNAstranscribedbypolymeraseⅡ.Basedontheresultsofthissearch,wediscussthehighvariabilityofU7snRNAsinbothse-quenceandstructure,andreportonanattempttofindU7snRNAsequencesinbasaldeuterostomesandnon-drosophilidsinsectgenomesbasedonacombinationofsequence,structure,andpromoterfeatures.Duetotheextremelyshortse-quenceandthehighvariabilityinbothsequenceandstructure,nounambiguouscandidateswerefound.TheseresultscastdoubtonputativeU7homologsinevenmoredistantorganismsthatarereportedinthemostrecentreleaseoftheRfamdatabase.

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简介：Thesurfaceglycoproteinhemagglutinin(HA)helpstheinfluenzaAvirustoevadethehostimmunesystembyantigenicvariationandisamajordrivingforceforviralevolution.Inthisstudy,theselectionpressureonHAofH5N1influenzaAviruswasanalyzedusingbioinformaticsalgorithms.Mostoftheidentifiedpositiveselection(PS)siteswerefoundtobewithinoradjacenttoepitopesites.SomeoftheidentifiedPSsitesareconsistentwithpreviousexperimentalstudies,providingfurthersupporttothebiologicalsignificanceofourfindings.ThehighestfrequencyofPSsiteswasobservedinrecentstrainsisolatedduring2005–2007.PhylogeneticanalysiswasalsoconductedonHAsequencesfromvarioushosts.Viraldriftisalmostsimilarinbothavianandhumanspecieswithaprogressivetrendovertheyears.OurstudyreportsnewmutationsinfunctionalregionsofHAthatmightprovidemarkersforvaccinedesignorcanbeusedtopredictisolatesofpandemicpotential.

简介：骨头导出髓的间充质的干细胞(MSC)是为房间移植在临床的应用程序显示出一个重要潜力的pluripotent干细胞。在现在的论文，proteomic技术被用来接近与猪的骨头髓MSC联系的蛋白质侧面并且在5-azacytidine(5-aza)的效果上调查MSC蛋白质的规定。超过1,700蛋白质种类根据胶化分析与MSC被分开。与控制MSC介绍的表达式相比，有起来调整的11个蛋白质点并且26在5-aza-treated房间的蛋白质模式下面调整。21蛋白质的一个总数被MALDI-TOF-MS分析成功地识别，在哪个之中一些有趣的蛋白质，例如高山哈B-crystallin，在A2的附属建筑，和stathmin1，被报导了通过不同发信号的小径在房间增长和区别包含。我们的数据应该为MSC区别和apoptosis的未来学习是有用的。

简介：Inthepost-genomicera,variouscomputationalmethodsthatpredictprotein-proteininteractionsatthegenomelevelareavailable;however,eachmethodhasitsownadvantagesanddisadvantages,resultinginfalsepredictions.Herewedevel-opedauniqueintegratedapproachtoidentifyinteractingpartner(s)ofSemaphorin5A(SEMA5A),beginningwithsevenproteinssharingsimilarligandinteractingresiduesasputativebindingpartners.ThemethodsincludeDwyerandRoot-Bernstein/Dillontheoriesofproteinevolution,hydropathiccomplementarityofproteinstructure,patternofproteinfunctionsamongmolecules,informationondomain-domaininteractions,co-expressionofgenesandproteinevolution.AmongthesetofsevenproteinsselectedasputativeSEMA5Ainteractingpartners,wefoundthefunctionsofPlexinB3andNeuropilin-2tobeassociatedwithSEMA5A.WemodeledthesemaphorindomainstructureofPlexinB3andfoundthatitsharessimilaritywithSEMA5A.Moreover,avirtualexpressiondatabasesearchandRT-PCRanalysisshowedco-expressionofSEMA5AandPlexinB3andtheseproteinswerefoundtohaveco-evolved.Inaddition,weconfirmedtheinterac-tionofSEMA5AwithPlexinB3inco-immunoprecipitationstudies.Overall,thesestudiesdemonstratethatanintegratedmethodofpredictioncanbeusedatthegenomelevelfordiscoveringmanyunknownproteinbindingpartnerswithknownligandbindingdomains.

简介：InFebruary2006,twooutbreaksofhighlypathogenicavianinfluenzaAvirussubtypeH5N1occurredinchickensintwoneighboringdistricts(firstinNandurbarandsecondinJalgaon)ofMaharashtra,India,inaspanof12days.Inthepresentstudy,theneuraminidase(NA)geneofthetwoIndianH5N1isolateswastakenintoconsiderationtofindifthetwostrainsaregeneticallysimilar.PhylogeneticanalysisoftheNAgeneshowedthattheH5N1strainsisolatedfromthetwooutbreakswerenotoriginatedfromthesamesource.ThefirstIndianisolate(Nandubar/7972/06)wasclusteredclosesttoanisolatefromchickeninVietnamin2004,whereasthesecondIndianisolate(Jalgaon/8824/06)showedresemblancetostrainsisolatedfromswaninItalyandIranin2006.Moreover,aminoacidsequenceanalysisshowedvaryinghotspotsforsubstitutionsbetweenthesetwoIndianisolates,andthreesubstitutionswerefoundatfunctionaldomainsites.Secondarystructurechangesduetothesesubstitutionswerealsoreported.ThisstudyrevealsthattheH5N1strainsisolatedfromchickensduring2006birdfluoutbreaksintwoneighboringdistrictsofMaharashtra,Indiaaregeneticallydifferent.

简介：ExpressedSequenceTag(EST)analysishaspioneeredgenome-widegenediscoveryandexpressionprofiling.Inordertoestablishageneexpressionindexinthericecultivarindica,wesequencedandanalyzed86,136ESTsfromninericecDNAlibrariesfromthesuperhybridcultivarLYP9anditsparentalcultivars.WeassembledtheseESTsinto13,232contigsandleave8,976singletons.Overall,7,497sequenceswerefoundsimilartotheexistingsequencesinGenBankand14,711arenovel.Thesesequencesareclassifiedbymolecularfunction,biologicalprocessandpathwaysaccordingtotheGeneOntology.WecomparedoursequencedESTswiththepubliclyavailable95,000ESTsfromjaponica,andfoundlittlesequencevariation,despitethelargedifferencebetweengenomesequences,Wethenassembledthecombined173,000riceESTsforfurtheranalysis.UsingthepooledESTs,wecomparedgeneexpressioninmetabolismpathwaybetweenriceandArabidopsisaccordingtoKEGG.Wefurtherprofiledgeneexpressionpatternsindifferenttissues,developmentalstages,andinaconditionalsterilemutant,aftercheckingthelibrariesarecomparablebymeansofsequencecoverage.Wealsoidentifiedsomepossiblelibraryspecificgenesandanumberofenzymesandtranscriptionfactorsthatcontributetoricedevelopment.

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简介：Circulargenomes,beingthelargestproportionofsequencedgenomes,playanimportantroleingenomeanalysis.However,traditional2Dcircularmaponlyprovidesanoverviewandannotationsofgenomebutdoesnotofferfeature-basedcomparison.Forremedyingtheseshortcomings,wedeveloped3DGenomeTuner,ahybridofcircularmapandcomparativemaptools.Itscapabilityofviewingcomparisonsbetweenmultiplecircularmapsina3Dspaceoffersgreatbenefitstothestudyofcomparativegenomics.Theprogramisfreelyavailable(underanLGPLlicence)athttp://sourceforge.net/projects/dgenometuner.

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简介：在cis的第二上的一个部件的transcriptional活动的直接否定的影响被叫作transcriptional干扰(TI)。U6是通常使用在基于向量的RNAi驾驶小发卡RNA(shRNA)表示的一个类型IIIRNA聚合酶III倡导者。在病毒的向量的设计和构造，多重抄写单位可以在空间有限向量在靠近的最近被安排。决定U6倡导者活动是否能被TI影响为在基因治疗的目标shRNA的表示是批评的或loss-of-function学习。在这研究，我们设计了并且实现shRNA和外长的基因表情由二个独立transcriptional单位被驾驶的一个修改retroviral系统。我们安排了在二倡导者安排驾驶shRNA表示和UbiC倡导者的U6倡导者。在主要巨噬细胞，我们发现U6倡导者活动被UbiC倡导者禁止什么时候在分叉的安排然而并非在双人脚踏车。相反，PKG倡导者没有如此的否定影响。而不是提高U6倡导者活动，CMVenhancer面对UbiC倡导者在U6倡导者活动有重要否定影响。我们的结果显示那项U6倡导者活动能被TI影响在一近似倡导者特定并且安排依赖者举止。

简介：Ithasbeenshownthattheprogressinthedeterminationofmembraneproteinstructuregrowsexponentially,withapproximatelythesamegrowthrateasthatofthewater-solubleproteins.Inordertoinvestigatetheeffectofthis,ontheperformanceofpredictionalgorithmsforbothα-helicalandβ-barrelmembraneproteins,weconductedaprospectivestudybasedonhistoricalrecords.WetrainedseparatehiddenMarkovmodelswithdifferentsizedtrainingsetsandevaluatedtheirperformanceontopologypredictionforthetwoclassesoftransmembraneproteins.Weshowthattheexistingtop-scoringalgorithmsforpredictingthetransmembranesegmentsofα-helicalmembraneproteinsperformslightlybetterthanthatofβ-barreloutermembraneproteinsinallmeasuresofaccuracy.Withthesamerationale,ameta-analysisoftheperformanceofthesecondarystructurepredictionalgorithmsindicatesthatexistingalgorithmictechniquescannotbefurtherimprovedbyjustaddingmorenon-homologoussequencestothetrainingsets.Theupperlimitforsecondarystructurepredictionisestimatedtobenomorethan70%and80%ofcorrectlypredictedresiduesforsinglesequencebasedmethodsandmultiplesequencebasedones,respectively.Therefore,weshouldconcentrateoureffortsonutilizingnewtechniquesforthedevelopmentofevenbetterscoringpredictors.

简介：Werecentlyreportedtheuseofagene-trappingapproachtoisolatecellclonesinwhichareportergenehadintegratedintogenesmodulatedbyT-cellactivation.WehavenowtestedapanelofclonesfromthatreportandidentifiedtheonethatrespondstoavarietyofG-proteincoupledreceptors(GPCR).TheβlactamasetaggedEGR-3JurkatcellwasusedtodissectspecificGPCRsignalinginvivo.ThreeGPCRswerestudied,includingthechemokinereceptorCXCR4(Gicoupled)thatwasendogenouslyexpressed,theplateletactivationfactor(PAF)receptor(Gq-coupled),andβ2adrenergicreceptor(Gs-coupled)thatwasbothstablytransfected.Agonistsforeachreceptoractivatedtranscriptionoftheβ-lactamasetaggedEGR-3gene.InductionofEGR-3throughCXCR4wasblockedbypertussistoxinandPD58059,aspecificinhibitorofMEK(MAPK/ERKkinase).NeitheroftheseinhibitorsblockedisoproterenolorPAF-mediatedactivationofEGR-3.Conversely,β2-andPAF-mediatedEGR-3activationwasblockedbythep38,specificinhibitorSB580.Inaddition,bothβ2-andPAF-mediatedEGR-3activationcouldbesynergisticallyactivatedbyCXCR4activation.ThiscombinedresultindicatesthatEGR-3canbeactivatedthroughdistinctsignaltransductionpathwaysbydifferentGPCRsandthatsignalscanbeintegratedandamplifiedtoefficientlytunethelevelofactivation.