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    Flux Balance Analysis of Escherichia coli under Temperature and pH Stress Conditions

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    Thesis-XiaopengXU copy.pdf
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    Description:
    Thesis
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    Type
    Thesis
    Authors
    Xu, Xiaopeng cc
    Advisors
    Gao, Xin cc
    Committee members
    Solovyev, Victor cc
    Bajic, Vladimir B. cc
    Program
    Computer Science
    KAUST Department
    Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division
    Date
    2015-05-12
    Embargo End Date
    2016-05-12
    Permanent link to this record
    http://hdl.handle.net/10754/552665
    
    Metadata
    Show full item record
    Access Restrictions
    At the time of archiving, the student author of this thesis opted to temporarily restrict access to it. The full text of this thesis became available to the public after the expiration of the embargo on 2016-05-12.
    Abstract
    An interesting discovery in biology is that most genes in an organism are dispensable. That means these genes have minor effects on survival of the organism in standard laboratory conditions. One explanation of this discovery is that some genes play important roles in specific conditions and are essential genes under those conditions. E. coli is a model organism, which is widely used. It can adapt to many stress conditions, including temperature, pH, osmotic, antibiotic, etc. Underlying mechanisms and associated genes of each stress condition responses are usually different. In our analysis, we combined protein abundance data and mutant conditional fitness data into E. coli constraint-based metabolic models to study conditionally essential metabolic genes under temperature and pH stress conditions. Flux Balance Analysis was employed as the modeling method to analysis these data. We discovered lists of metabolic genes, which are E. coli dispensable genes, but conditionally essential under some stress conditions. Among these conditionally essential genes, atpA in low pH stress and nhaA in high pH stress found experimental evidences from previous studies. Our study provides new conditionally essential gene candidates for biologists to explore stress condition mechanisms.
    Citation
    Xu, X. (2015). Flux Balance Analysis of Escherichia coli under Temperature and pH Stress Conditions. KAUST Research Repository. https://doi.org/10.25781/KAUST-A4IY4
    DOI
    10.25781/KAUST-A4IY4
    ae974a485f413a2113503eed53cd6c53
    10.25781/KAUST-A4IY4
    Scopus Count
    Collections
    MS Theses; Computer Science Program; Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division

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