简介：AsthetopologicalpropertiesofeachspotinDNAmicroarrayimagesmayvaryfromoneanother,weemployedgranulometriestounderstandtheshape-sizecontentcontributedduetoasignificantintensityvaluewithinaspot.Analysiswasperformedonthemicroarrayimagethatconsistedof240spotsbyusingconceptsfrommathematicalmorphology.Inordertofindoutindicesforeachspotandtofurtherclassifythem,weadoptedmorphologicalmultiscaleopenings,whichprovidedmicroarraysatmultiplescales.Successiveopenedmicroarraysweresubtractedtoidentifytheprotrusionsthatweresmallerthanthesizeofstructuringelement.Spot-wisedetails,intermsofprobabilityoftheseobservedprotrusions,werecomputedbyplacingaregularlyspacedgridonmicroarraysuchthateachspotwascenteredineachgrid.Basedontheprobabilityofsizedistributionfunctionsoftheseprotrusionsisolatedateachlevel,weestimatedthemeansizeandtextureindexforeachspot.Withthesecharacteristics,weclassifiedthespotsinamicroarrayimageintobrightanddullcategoriesthroughpatternspectrumandshape-sizecomplexitymeasures.Thesesegregatedspotscanbecomparedwiththoseofhybridizationlevels.

简介：The2004SoutheastAsiaTsunamikillednearly5,400peopleinSouthernThailand,includingforeigntouristsandlocalresidents.TorecoverDNAevidenceasmuchaspossiblefromtheseriouslydecomposedbodies,weexploredproceduresofsamplepreparationfrombothboneandtoothsamplesaswellasbothmitochondrialandnuclearmarkers.DespitehavingfailedtorecoverenoughDNAfornuclearmarkertyping,wesucceededinobtainingfullyinformativeresultsformitochondrialmarkers(HV1andHV2)from258toothsampleswithasuccessrateof51%(258/507).UsinganorganicDNAextractionmethodcoupledwithanultrafiltrationstep,weobtained16STR(including13CODISloci,onesexdiscriminationlocus,andtwoIdentifilerloci)profilesfor834sampleswithasuccessrateof79%(834/1,062).Inaddition,bycomparingtheallelicfrequenciesbetweenthetypedsamplesasagroupandotherindexpopulations,weconcludethattheThaitsunamivictimsareacombinedgroupofseveralpopulations.Ourresultsprovidevaluableevidenceandprotocolsforthefutureforensicpractice.

简介：DNA聚合酶III是为DNA的复制负责的五eubacterialDNA聚合酶之一双。在DNA聚合酶III核心酶的十个子单元之中，高山哈子单元两个都为polymerizing催化反应DNA海滨。在这研究，我们提取了高山的genomic序列哈从159的子单元定序eubacterial染色体，并且执行了基于顺序的种系发生、结构的分析。我们发现所有eubacterial染色体有至少一座高山哈子单元，哪个形式homodimers或heterodimers。种系发生并且领域高山的结构的分析以及拷贝数字变化哈在每个细菌的子单元显示高山的分类哈子单元进四个基本的组：polC，dnaE1，dnaE2，和dnaE3。这个分类具有在染色体作文分析的本质。我们也巩固了命名惯例在基因注解避免进一步的混乱。

简介：DNAbarcodingisapowerfulapproachforcharacterizingspeciesoforganisms,especiallythosewithalmostidenticalmorphologicalfeatures,therebyhelpingtotoestablishphylogeneticrelationshipsandrevealevolutionaryhistories.Inthisstudy,wechosea648-bpsegmentofthemitochondrialgene,cytochromecoxidasesubunit1(COI),asastandardbarcoderegiontoestablishphylogeneticrelation-shipsamongbrineshrimp(Artemia)speciesfrommajorhabitatsaroundtheworldandfurtherfocusedonthebiodiversityofArtemiaspeciesinChina,especiallyintheTibetanPlateau.SamplesfromfivemajorsaltlakesoftheTibetanPlateaulocatedataltitudesover4,000mshowedcleardifferencesfromotherArtemiapop-ulationsinChina.Wealsoobservedtwoconsistentaminoacidchanges,153A/Vand183L/F,intheCOIgenebetweenthehighandlowaltitudespeciesinChina.Moreover,indelsintheCOIsequencewereidentifiedincystandadultsamplesuniquetotheCoQenpopulationfromtheTibetanPlateau,demonstratingtheneedforadditionalinvestigationsofthemitochondrialgenomeamongTibetanArtemiapopulations.

简介：Arraycomparativegenomichybridization(CGH)hasbeenpopularlyusedforanalyzingDNAcopynumbervariationsindiseaseslikecancer.Inthisstudy,weinvestigated82sporadicsamplesfrom49breastcancerpatientsusing1-MbresolutionbacterialartificialchromosomeCGHarrays.Anumberofhighlyfrequentgenomicaberrationswerediscovered,whichmayactas'drivers'oftumorprogression.Meanwhile,thegenomicprofilesoffour'normal'breasttissuesamplestakenatleast2cmawayfromtheprimarytumorsiteswerealsofoundtohavesomegenomicaberrationsthatrecurredwithhighfrequencyintheprimarytumors,whichmayhaveimportantimplicationsforclinicaltherapy.Additionally,weperformedclasscomparisonandclasspredictionforvariousclinicopathologicalparameters,andalistofcharacteristicgenomicaberrationsassociatedwithdifferentclinicopathologicalphenotypeswascompiled.Ourstudyprovidescluesforfurtherinvestigationsoftheunderlyingmechanismsofbreastcarcinogenesis.

简介：DNAsequencescanbetreatedasfinite-lengthsymbolstringsoverafour-letteralphabet(A,C,T,G).Asauniversalandcomputablecomplexitymeasure,LZcomplexityisvalidtodescribethecomplexityofDNAsequences.Inthisstudy,aconceptofconditionalLZcomplexitybetweentwosequencesisproposedaccordingtotheprincipleofLZcomplexitymeasure.AnLZcomplexitydistancemetricbetweentwononnullsequencesisdefinedbyutilizingconditionalLZcomplexity.BasedonLZcomplexitydistance,aphylogenetictreeof26speciesofplacentalmammals(Eutheria)withthreeoutgroupspecieswasreconstructedfromtheircompletemitochondrialgenomes.Onthedebatethatwhichtwoofthethreemaingroupsofplacentalmammals,namelyPrimates,Ferungulates,andRodents,aremorecloselyrelated,thephylogenetictreereconstructedbasedonLZcomplexitydistancesupportsthesuggestionthatPrimatesandFerungulatesaremorecloselyrelated.

简介：AninteractivetooltovisualizetheK-stringcompositionoflongDNAsequencesincludingbacterialcompletegenomesisdescribed.Itisespeciallyusefulforexploringshortpalindromicstructuresinthesequences.TheSeeDNAprogramrunsonRedHatLinuxwithGTK+support.Itdisplaystwo-dimensional(2D)orone-dimensional(1D)histogramsoftheK-stringdistributionofagivensequenceand/oritsrandomizedcounterpart.ItisalsocapableofshowingthedifferenceofK-stringdistributionsbetweentwosequences.TheCsourcecodeusingtheGTK+packageisfreelyavailable.

简介：Accurateidentificationofprotein-codingregions(exons)inDNAsequenceshasbeenachallengingtaskinbioinformatics.Particularlythecodingregionshavea3-baseperiodicity,whichformsthebasisofallexonidentificationmethods.Manysignalprocessingtoolsandtechniqueshavebeenappliedsuccessfullyfortheidentificationtaskbutstillimprovementinthisdirectionisneeded.Inthispaper,wehaveintroducedanewpromisingmodel-independenttime-frequencyfilteringtechniquebasedonS-transformforaccurateidentificationofthecodingregions.TheS-transformisapowerfullineartime-frequencyrepresentationusefulforfilteringintime-frequencydomain.Thepotentialoftheproposedtechniquehasbeenassessedthroughsimulationstudyandtheresultsobtainedhavebeencomparedwiththeexistingmethodsusingstandarddatasets.Thecomparativestudydemonstratesthattheproposedmethodoutperformsitscounterpartsinidentifyingthecodingregions.

简介：Computationalanalysisisessentialfortransformingthemassesofmicroarraydataintoamechanisticunderstandingofcancer.Herewepresentamethodforfindinggenefunctionalmodulesofcancerfrommicroarraydataandhaveappliedittocoloncancer.First,acoloncancergenenetworkandanormalcolontissuegenenetworkwereconstructedusingcorrelationsbetweenthegenes.Thenthemodulesthattendedtohaveahomogeneousfunctionalcompositionwereidentifiedbysplit-tingupthenetwork.Analysisofbothnetworksrevealedthattheyarescale-free.Comparisonofthegenefunctionalmodulesforcoloncancerandnormaltissuesshowedthatthemodules’functionschangedwiththeirstructures.

简介：陷阱，SLD5的heterotetramer，PSF1，PSF2，和PSF3蛋白质，一个新兴的染色质因素被认出涉及开始和DNA复制的延伸步。尽管酵母和Xenopus陷阱基因很好被记录，他们在更高的优核质的orthologous基因充分没被描绘。在这研究，我们报导genomic结构和哺乳动物的陷阱基因的transcriptional规定。浆液刺激在人的房间增加了GINSmRNA层次。用通常认为的陷阱倡导者序列的记者基因试金表明哺乳动物的陷阱的表示被17beta-Estradiol-stimulated雌激素受体高山调整哈，并且人的PSF3充当对抄写因素E2F1应答的基因。这研究的目标是介绍当前的数据以便在哺乳动物的房间在陷阱基因规定和函数的领域里鼓励进一步的工作。

简介：流行性感冒A病毒(H1N1)2009，一个新猪起源流行性感冒A病毒，世界范围地被散布了并且引起了大公共害怕。高产量的transcriptomics和proteomics方法现在正在被使用识别H1N1和H1N1主人相互作用。这篇文章在H1N1诊断，处理，和H1N1病毒主人相互作用考察最近的transcriptomics和proteomics研究，到为进一步理解感染机制并且控制H1N1传播提供一些帮助。

简介：流行性感冒A病毒(H1N1)，人的地方性的紧张的一个基因分类，鸟并且猪流感，穿过种类障碍到人并且显然获得了人的能力到人的传播。因为NS1蛋白质禁止抗病毒的干扰素/生产，H5N1子类型的一些紧张是高度剧毒的。另一蛋白质NS2调停到通过出口的细胞质的从原子核的病毒的ribonucleoprotein的出口信号。在这份报纸，我们学习了H1N1子类型的这些蛋白质的结构功能关系并且决定了他们的致病力的原因。我们的结果证明非保守的变化稍微稳定了或使动摇NS1或NS1-dsRNA建筑群的结构的域，稍微因此增加了或减少NS1蛋白质并且因而的函数提高了或减少H1N1病毒的致病力。不同紧张的NS2蛋白质在不同领域带了非保守的变化，导致功能的细微损失。这些变化稍微减少了病毒的致病力。因此，结果证实这些病毒的蛋白质的结构功能关系。

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

简介：在这研究，L1蛋白质定序的人的乳头状瘤病毒(HPV)的107种类型从可得到的数据库，和这些HPVL1蛋白质的原子本地化信号(NLS)被获得被生物信息的分析分析并且预言。从107种类型，39种类型的NLS被PredictNLS软件(由两部组成的NLS的35种类型和单音的深裂的NLS的4种类型)预言。留下的HPV类型的NLS象NLS的一般规则一样根据特征和已经预言的NLS的相同被预言。根据结果，HPVL1蛋白质的107种类型的NLS被分类进15个范畴。在一样的NLS范畴的HPVL1蛋白质的不同类型能分享类似或一样的nucleocytoplasmic运输小径。他们可能被用作一样的目标阻止并且对待HPV感染的不同类型。结果也证明生物信息的技术能被用来分析并且预言蛋白质的NLS。

简介：Asystematicphylogeneticfootprintingapproachwasperformedtoidentifycon-servedtranscriptionfactorbindingsites(TFBSs)inmammalianpromoterregionsusinghuman,mouseandratsequencealignments.Wefoundthatthescoredis-tributionsofmostbindingsitemodelsdidnotfollowtheGaussiandistributionrequiredbymanystatisticalmethods.Therefore,weperformedanempiricaltesttoestablishtheoptimalthresholdforeachmodel.WegaugedourcomputationalpredictionsbycomparingwithpreviouslyknownTFBSsinthePCK1genepro-moterofthecytosolicisoformofphosphoenolpyruvatecarboxykinase,andachievedasensitivityof75%andaspecificityofapproximately32%.Almostallknownsitesoverlappedwithpredictedsites,andseveralnewputativeTFBSswerealsoidentified.WevalidatedapredictedSP1bindingsiteinthecontrolofPCK1tran-scriptionusinggelshiftandreporterassays.Finally,weappliedourcomputationalapproachtothepredictionofputativeTFBSswithinthepromoterregionsofallavailableRefSeqgenes.OurfullsetofTFBSpredictionsisfreelyavailableathttp://bfgl.anri.barc.usda.gov/tfbsConsSites.

简介：Leishmaniaisassociatedwithabroadspectrumofdiseases,rangingfromsimplecutaneoustoinvasivevisceralleishmaniasis.Here,thesequencesoftencysteineproteasesoftypesA,BandCofLeishmaniamajorwereobtainedfromGeneDBdatabase.PredictionofMHCclassIepitopesofthesecysteineproteaseswasperformedbyNetCTLprogramversion1.2.Inaddition,byusingBcePredserver,differentstructuralpropertiesoftheproteinswerepredictedtofindouttheirpotentialBcellepitopes.Accordingtothiscomputationalanalysis,nineregionswerepredictedasBcellepitopes.Theresultsprovideusefulinformationfordesigningpeptide-basedvaccines.

简介：

简介：染色体17q21.31倒置是普通结构的多型性首先在欧洲人口发现了的900-kb。尽管在倒置区域以内的基因流动被假定可观压制，它关于在H1(非转换的顺序)和H2(转换顺序)之间的基因交换的细节仍然是不清楚的这倒置的haplotypes。这里，我们在17q21.31区域以内描述在一些基因安排之间的基因交换的一张精制地图。用1,546单个核苷酸多型性的HapMap阶段II数据，我们成功地由加入邻居的树重建在欧洲样品推出了96H1和24H2haplotypes。而且，我们分别地与相互、非相互的基因交换识别了15和26条候选人道。在怀有相互的交换的所有15个区域，haplotypes由克隆定序重建了没支持这些交换事件，建议这在某些异质接合的个人在二个姐妹染色体之间的交换发信号被分阶段执行错误区域引起。在另一方面，与非相互的基因流动越过26条道中的4个定序的完成的克隆证实这种基因交换被基因变换引起。在摘要，更加作为在一些基因安排之间的转线路被压制了，基因变换可能是为在17q21.31的基因交换的最重要的机制。

简介：Leptospirosisisrecognizedasthemostwidespreadzoonosiswithaglobaldistribution.Inthisstudy,theantigenicvariationinLeptospirainterrogansandLeptospiraborgpeterseniiisolatedfromhumanurineandfieldratkidneywaspreliminarilyconfirmedbymicroscopicagglutinationtestusingmonoclonalantibodies,andwasfurthersubjectedtoamplificationandidentificationofoutermembranelipoproteinswithstructuralgenevariation.Sequencesimilarityanalysisrevealedthattheseproteinsequences,namelyOmpL1,LipL32andLipL41,showednomorehomologiestooutermembranelipoproteinsofnon-pathogenicLeptospiraandothercloselyrelatedSpirochetes,butshowedastrongidentitywithinL.interrogans,suggestingintra-specificphylogeneticlineagesthatmightbeoriginatedfromacommonpathogenicleptospiralorigin.Moreover,theompL1geneshowedmoreantigenicvariationthanlipL32andlipL41duetolessconservationinsecondarystructuralevolutionwithincloselyrelatedspecies.Phylogenetically,ompL1andlipL41ofthesestrainsgaveaconsiderableproximitytoL.weiliiandL.santarosai.TheompL1geneofL.interrogansclustereddistinctlyfromotherpathogenicandnon-pathogenicleptospiralspecies.ThediversityofompLgeneshasbeenanalyzedanditenvisagedthatsequence-specificvariationsatantigenicdeterminantsiteswouldresultinslowevolutionarychangesalongwithnewserovaroriginationwithincloselyrelatedspecies.Thus,acrucialworkoneffectiverecombinantvaccinedevelopmentandengineeredantibodieswillhopefullymeettosolvethetherapeuticchallenges.