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：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.

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.