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Metabolic network properties help assign weights to elementary modes to understand physiological flux distributions

By Sherry Evans,2014-12-15 03:15
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Metabolic network properties help assign weights to elementary modes to understand physiological flux distributions

    Metabolic network properties help assign weights to elementary modes to understand

    physiological flux distributions Keywords:CL0STRIDIJM

    BUTyRjCUM:ESCHERICHIACOLI;ENTEROBACTERAGGLOMERANS:GL

    EILFERMEN?I,ION:CITROBACTERFREUNDII:MICROBIAL

    PRODUCrrION:REACTI,TINGFACTOR;

    CONTINUOUSCUEFURE;DEHYDROGENASE;GROWTH

    /4lEDANDENVIRONMENTALMICROBIOL0GY2007,73(14):4515-4521

    Metabolicnetworkpropertieshelpassignweightstoelementarymodesto understandphysiologicalfluxdistributions

    Wang,QZYang,YDMa,HWZhao,XM

    FianjinUniv,MetabEngnLab,DeptBiochemEngn,SchChemEngn&Technol,Tianjin300072,PeoplesRChina

    Wang,Qz,TianjinUniv,MetabEngnLab,DeptBiocheraEngn,SchChemEngn&Technol,Tianjin300072,PeoplesRChina

    Wangqingzhao@eyou.corn

    Abstract:Motivation:Elementarymodes(EMs1analysishasbeenwel1established.Theexistingmethodologiesfor

    assigningweightstoEMscannotbedirectlyappliedfor1arge

    scalelnetabolicnetworks.sincethetremendous

    numberofmodeswouldmakethecomputationatilne

    COllsumingorevenanimpossiblemission.Fherefore.deve1

    oPing1110reefficie11t111ethodstodealwithlargesetofEMsisurgent. Result"Wedevelopamethodtoevaluatetheperformanceofemployingasubsetoftheelementarymodestorecon

    structarea1fluxdistributionbyusingtherelativeerrorbetweentherea1fluxvectorandthereconstructedoneasan

    indicator.Wehavefoundapowerfimctionrelationshipbetweenthedecreaseofrelativeerrorandtheincreaseofthe

    numberoftheselectingEMs.anda1ogarithmicrelationshipbetweentheincreasesofthenumberofnonzero

    weightedEMsandthatofthenumberoftheselectingEMs.0urdiscoveriesshowthatitispossibletoreconstruct

    agivenfluxdistributiOllbyaselectedsubsetofEMsfromalargemetabolicnetworkandrthernlore.theyhelpus

    identifythe'governingmodes'torepresentthecelMarmetabolismforsuchacondition. KeINGULARVALUEDECOION:P=fTH,^YANARECONSTRUCTION.

    ~vords:SMP0SITSIS;

    BIOINFORMATICS2007,23(9):10491052

    SimulationoffluxdistributionincentralmetabolismofSaccharomyces

    cerevisiaebyhybridizedgeneticalgorithm

    Zhang,HMYao,SJ

    ZhejiangUniv,DeptChem&BiochemEngn,Hangzhou310027,PeoplesRChina JiaxingUniv,DeptChemEngn,Jiaxing3I4000,PeoplesRChina

    Yao,SJ,Zh~iangUnivDeptChem&BiochemEngn,Hangzhou310027,PeoplesRChina.yaosj@zjueducn

    Abstract:Asche111eofinvestigatingtheintracellularmetabolicfluxesincentralmetabolismofSaccharomyces

    cerevisiaebasedOllisotopemodelandtracerexperimentwasdeveloped.Themetabolicmodelappliedinthisstudy

    includestheEmbden

    Meyerhof-Pamaspathway,thepentosephosphatepathway,thetricarboxylicacidcycle,C02

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