A New Method of Genome-Scale Metabolic Model Validation for Biogeochemical Application

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dc.contributor.advisorJin, Qusheng
dc.contributor.authorShapiro, Benjamin
dc.date.accessioned2017-09-06T21:45:55Z
dc.date.issued2017-09-06
dc.description.abstractWe propose a new method to integrate genome-scale metabolic models into biogeochemical reaction modeling. This method predicts rates of microbial metabolisms by combining flux balance analysis (FBA) with microbial rate laws. We applied this new hybrid method to methanogenesis by Methanosarcina barkeri. Our results show that the new method predicts well the progress of acetoclastic, methanol, and diauxic metabolism by M. barkeri. The hybrid method represents an improvement over dynamic FBA. We validated genome-scale metabolic models of Methanosarcina barkeri, Methanosarcina acetivorans, Geobacter metallireducens, Shewanella oneidensis, Shewanella putrefaciens and Shewanella sp. MR4 for application to biogeochemical modeling. FBA was used to predict the response of cell metabolism, and ATP and biomass yield. Our analysis provides improvements to these models for the purpose of applications to natural environments.en_US
dc.description.embargo2019-07-28
dc.identifier.urihttps://hdl.handle.net/1794/22679
dc.language.isoen_US
dc.publisherUniversity of Oregon
dc.rightsAll Rights Reserved.
dc.subjectBiogeochemical reaction modelingen_US
dc.subjectFlux balance analysisen_US
dc.subjectGenome-scaleen_US
dc.subjectGeobacteren_US
dc.subjectMethanosarcinaen_US
dc.subjectShewanellaen_US
dc.titleA New Method of Genome-Scale Metabolic Model Validation for Biogeochemical Application
dc.typeElectronic Thesis or Dissertation
thesis.degree.disciplineDepartment of Geological Sciences
thesis.degree.grantorUniversity of Oregon
thesis.degree.levelmasters
thesis.degree.nameM.S.

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