简介：Althoughvariousgenomeprojectshaveprovidedusenormousstaticsequenceinformation,understandingofthesophisticatedbiologycontinuestorequireintegratingthecomputationalmodeling,systemanalysis,technologydevelopmentforexperiments,andquantitativeexperimentsalltogethertoanalyzethebiologyarchitectureonvariouslevels,whichisjusttheoriginofsystemsbiologysubject.Thisreviewdiscussestheobject,itscharacteristics,andresearchattentionsinsystemsbiology,andsummarizestheanalysismethods,experimentaltechnologies,researchdevelopments,andsooninthefourkeyfieldsofsystemsbiology-systemicstructures,dynamics,controlmethods,anddesignprinciples.

简介：Theaimofthisstudyistodesignabiologicalinformationretrievalandanalysissystem(BIRAS)basedontheInternet.Usingthespecificnetworkprotocol,BIRASsystemcouldsendandreceiveinformationfromtheEntrezsearchandretrievalsystemmaintainedbyNationalCenterforBiotechnologyInformation(NCBI)inUSA.Theliteratures,nucleotidesequence,proteinsequences,andotherresourcesaccordingtotheuser-definedtermcouldthenberetrievedandsenttotheuserbypopupmessageorbyE-mailinformingautomaticallyusingBIRASsystem.Alltheinformationretrievingandanalyzingprocessesaredoneinreal-time.Asarobustsystemforintelligentlyanddynamicallyretrievingandanalyzingontheuser-definedinformation,itisbelievedthatBIRASwouldbeextensivelyusedtoretrievespecificinformationfromlargeamountofbiologicaldatabasesinnowdays.Theprogramisavailableonrequestfromthecorrespondingauthor.

简介：Expressedsequencetags(ESTs)arewidelyusedingenesurveyresearchtheseyears.TheESTPipelineSystem,softwaredevelopedbyHangzhouGenomicsInstitute(HGI),canautomaticallyanalyzedifferentscalarESTsequencesbysuitablemethods.Alltheanalysisreports,includingthoseofvectormasking,sequenceassembly,geneannotation,GeneOntologyclassification,andsomeotheranalyses,canbebrowsedandsearchedaswellasdownloadedintheExcelformatfromthewebinterface,savingresearcheffortsfromroutinedataprocessingforbiologicalrulesembeddedinthedata.

简介：赤霉素(GA)一起被指一组diterpenoid酸，其中一些充当植物荷尔蒙并且为正常植物生长和开发是必要的。DNA微数组技术为大量送信人RNA抄本的平行数量化离子成为了标准工具。这条途径的力量在把被表明了植物生理学和开发，并且在解开内在的细胞的发信号小径。理解GA由调整植物的生长和发展的分子的机制与单音的简易窄床模型植物大米的参考，在被GA调整的抄写和翻译层次识别并且分析更多的基因和他们的产品是必要的。与二种主要米饭类型，indica和装饰用的梨树米饭的草稿序列的可获得性，在染色体规模上分析基因的全球表示侧面变得可能。在这评论，进步在用微数组系统在米饭叶鞘发现新基因做了，他们的描述被讨论。调查结果做了在这方面，这被相信为理解GA由调整米饭的生长和发展的机制有重要含意。

简介：Annotationsofcompletegenomesequencessubmitteddirectlyfromsequencingprojectsarediverseintermsofannotationstrategiesandupdatefrequencies.Theseinconsistenciesmakecomparativestudiesdifficult.Toallowrapiddataprepara-tionofalargenumberofcompletegenomes,automationandspeedareimpor-tantforgenomere-annotation.Hereweintroduceanopen-sourcerapidgenomere-annotationsoftwaresystem,Restauro-G,specializedforbacterialgenomes.Restauro-Gre-annotatesagenomebysimilaritysearchesutilizingtheBLAST-LikeAlignmentTool,referringtoproteindatabasessuchasUniProtKB,NCBInr,NCBICOGs,Pfam,andPSORTb.Re-annotationbyRestauro-Gachievedover98%accuracyformostbacterialchromosomesincomparisonwiththeoriginalmanuallycuratedannotationofEMBLreleases.Restauro-GwasdevelopedinthegenericbioinformaticsworkbenchG-languageGenomeAnalysisEnvironmentandisdistributedathttp://restauro-g.iab.keio.ac.jp/undertheGNUGeneralPublicLicense.

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

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：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.