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：Nineshorttandemrepeat(STR)markersontheXchromosome(DXS101,DXS6789,DXS6799,DXS6804,DXS7132,DXS7133,DXS7423,DXS8378,andHPRTB)wereanalyzedinfourpopulationgroups(Mongol,Ewenki,Oroqen,andDaur)fromInnerMongolia,China,inordertolearnaboutthegeneticdiversity,forensicsuitability,andpossiblegeneticaffinitiesofthepopulations.Frequencyestimates,Hardy-Weinbergequilibrium,andotherparametersofforensicinterestwerecomputed.Theresultsrevealedthattheninemarkershaveamoderatede-greeofvariabilityinthepopulationgroups.Mostheterozygosityvaluesfortheninelocirangefrom0.480to0.891,andthereareevidentdifferencesofgeneticvariabilityamongthepopulations.AUPGMAtreeconstructedonthebasisofthegenerateddatashowsverylowgeneticdistancebetweentMongolandHan(Xi’an)populations.Ourresultsbasedongeneticdistanceanalysisareconsistentwiththeresultsofearlierstudiesbasedonlinguisticsandtheimmigrationhistoryandoriginofthesepopulations.TheminisatellitelociontheXchromosomestudiedherearenotonlyusefulinshowingsignificantgeneticvariationbetweenthepop-ulations,butalsoaresuitableforhumanidentitytestingamongInnerMongolianpopulations.

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

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：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：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.

简介：一个新奇高产量的系统，为分离和反应(4SR)叫了叠的片胶化系统，为DNA/RNA和蛋白质/肽的分析被开发。系统提供利用叠的片胶化的性质的一条新奇三维的胶化电气泳动途径。它同时允许多重样品反应以及被分开，出现一二维(mxn)样品装载系统。为这个目的，包含井(在这篇论文的100口井)的可变数字的高产量的多微的容器(MMV)被使用了，它用25公里做的是方形尺寸的polyacrylamide胶化。在electrophoretic分离以后，而且，包含一件需要的样品的片胶化能容易被移开并且继续到下一步。不同生物反应以及产品的连续分离有效地被执行处理DNA/RNA和蛋白质/肽。它证明这个系统有多种潜力被发展。

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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.