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：在染色体为特定的DNA目标设计锌手指蛋白质主题在染色体工程的领域里是批评的。我们为为绑在特定的目标DNA地点的C2H2锌手指预言识别helices开发了一个计算方法。这预言用锌手指蛋白质和他们的目标DNA三位字节的彻底的数据集基于人工的神经网络。用户们能为也要预言在的二或三根锌手指选择选择一模块化或为输入DNA顺序的synergistic时尚。这个方法将为对为几个生物、生物医学的应用程序设计特定的锌手指抄写因素和锌手指核酸酶感兴趣的研究人员是珍贵的。网工具ZiF预言在http://web.iitd.ac.in/sundar/zifpredict/在网上是可得到的。

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：Humantumornecrosisfactorα(hTNFα),apleiotropiccytokinewithactivitiesrangingfromhostdefensemechanismsininfectionandinjurytoseveretoxicityinsepticshockorotherrelateddiseases,isapromisingtargetfordrugscreening.UsingtheSELEX(systematicevolutionofligandsbyexponentialenrichment)process,weisolatedoligonucleotideligands(aptamers)withhighaffinitiesforhTNFα.Aptamerswereselectedfromastartingpoolof40randomizedsequencescomposedofabout1015RNAmolecules.RepresentativeaptamersweretruncatedtotheminimallengthwithhighaffinityforhTNFαandwerefurthermodifiedbyreplacementof2'-OHwith2'-Fand2'-NH2atallribopurinepositions.ThesemodifiedRNAaptamerswereresistanttonuclease.ThespecificityoftheseaptamersforhTNFαwasconfirmed,andtheiractivitytoinhibitthecytotoxicityofhTNFαonmouseL929cellswasdetermined.Resultsdemonstratedthatfour2'-NH2-modifiedaptamersboundtohTNFαwithhighaffinityandblockedthebindingofhTNFαtoitsreceptor,thusprotectingtheL929cellsfromthecytotoxicityofhTNFα.OligonucleotideaptamersdescribedherearepotentialtherapeuticsanddiagnosticsforhTNFc-relateddiseases.

简介：Domaindatabaseisessentialfordomainpropertyresearch.Eliminatingredundantinformationindatabasequeryisveryimportantfordatabasequality.Herewereportthemanualconstructionofanon-redundanthumanSH2domaindatabase.Thereare119humanSH2domainsin110SH2-containingproteins.HumanSH2swerealignedwithClustalX,andahomologoustreewasgenerated.Inthistree,proteinswithsimilarknownfunctionwereclassifiedintothesamegroup.Someproteinsinthesamegrouphavebeenreportedtohavesimilarbindingmotifsexperimentally.Thetreemightprovidecluesaboutpossiblefunctionsofhypotheticalproteinsforfurtherexperimentalverification.

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：以便获得米饭幼仔圆锥花序proteome的高分辨率的electrophorogram，我们评估了通常使用在的各种各样的协议二维(2D)蛋白质的polyacrylamide胶化电气泳动(页)包括染色协议的胶化，使不能调动的pH坡度(IPG)的pH范围脱衣并且样品装载数量。结果证明染色协议使用的银敏化包含冰川的醋酸，钠醋酸盐和钠thiosulfate的答案(在1988由Heukeshoven和Dernick报导了)并且染色方法使用答案包含的Coomassie灿烂的蓝色G-250，铵硫酸盐和磷的酸(在2010由粉红色的等报导了)表明了优异染色效果。另外，当有5-8的pH范围的IPG胶化长带被使用时，我们也与4-7的pH范围证明更高的分辨率被完成，与那相比。最后，最佳的装载数量作为与染色协议的银硝酸盐在联合与pH5-8使用17厘米长的非线性的IPG长带的130g被决定。评估结果将在年轻米饭颖果的proteome分析是有用的。

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：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。

简介：Shigellaflexneriisaninfectiouspathogenthatcausesdysenterytohuman,whichremainsaseriousthreattopublichealth,particularlyindevelopingcountries.Inthisstudy,theglobalproteinexpressionpatternsofS.flexneriduringtransitionfromexponentialgrowthtostationaryphaseinvitrowereanalyzedbyusing2-DPAGEcombinedwithMALDI-TOFMS.Inatime-courseexperimentwithfivetimepoints,therelativeabundanceof49proteinspotsvariedsignificantly.In-terestingly,aputativeoutermembraneproteinYciD(OmpW)wasalmostnotdetectedintheexponentialgrowthphasebutbecameoneofthemostabundantproteinsinthewholestationary-phaseproteome.SomeproteinsregulatedbytheglobalregulatorFNRwerealsosignificantlyinduced(suchasAnsB,AspA,FrdAB,andKatG)orrepressed(suchasAceEF,OmpX,SodA,andSucAB)duringthegrowthphasetransition.Theseproteinsmaybethekeyeffectorsofthebacterialcellcycleorplayimportantrolesinthecellularmaintenanceandstressresponses.Ourexpressionprofiledataprovidevaluableinformationforthestudyofbacterialphysiologyandformthebasisforfutureproteomicanalysesofthispathogen.

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简介：我们分析了表示的基因(transcriptomes)和翻译的蛋白质(专业版--teomes)在肌肉纸巾和激活的CD4+和五种类型的CD8+T淋巴细胞(T房间)，2糖尿病(T2DM)用Affymetrix微数组和集体spectrometry使遭到，并且把他们与匹配的非糖尿病的控制作比较。胰岛素受体(INSR)的基因表达，维生素D受体，胰岛素降级酶，Akt，胰岛素受体substrate-1(IRS-1)，IRS-2，葡萄糖transporter4(GLUT4)，并且glycolytic小径的酶被减少至少50%在T2DM比在控制。然而，有比在血浆房间glycoprotein-1的规定上面的双重的基因大，肿瘤坏死因素(在T2DM的TNF，和gluconeogenic酶比在控制。为INSR或TNF的基因silencing分别地导致了GLUT4的抑制或刺激。相应于上述翻译transcriptomes的分子的重量的Proteome侧面显示出在T2DM和控制之间的变化的不同模式。同时，在在肌肉和T2DM的激活的T房间之间的transcriptomes和proteomes的变化是可比较的。激活的T房间，类似于肌肉房间，表示胰岛素发信号和葡萄糖新陈代谢基因和基因产品。在结论，在T2DM的T房间和肌肉相对非糖尿病的控制在某些基因和基因产品的表示展出了差别。在transcriptomes的这些改变和在T2DM的proteomes可以涉及胰岛素抵抗。

简介：细螺旋体病是螺旋体种类引起的传染细菌的疾病。在这研究，我们克隆并且定序从L编码immunodominant蛋白质GroEL的基因。interrogansserovarAutumnalis种类N2，在Chennai在细螺旋体病的爆发期间从一个病人的尿被孤立，印度。这groEL基因另外的leptospiralserovars与相同(99%类似)的高度编码60kDa的蛋白质到那些。RecombinantGroEL是在Escherichiacoli的overexpressed。当没有反应从seronegative控制病人与sera被观察时，Immunoblot分析显示从证实的细螺旋体病病人的sera与recombinantGroEL显示出强壮的反应。另外，GroEL的3D结构作为模板从Thermusthermophilus用chaperonin建筑群cpn60被构造并且验证。结果显示了8.35的Z分数，它在对为蛋白质的期望的价值的好同意。cpn60结构的Ca踪迹和leptospiralGroEL的预言的结构的重叠与1.5的RMSD价值显示第二等的结构元素的好同意?。进一步的学习是必要的作为一个疫苗的部件为细螺旋体病的血清学的诊断并且为它的潜力评估GroEL。

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