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    Novel Computational Methods that Facilitate Development of Cyanofactories for Free Fatty Acid Production

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    OlaaMotwalliThesis.pdf
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    Type
    Dissertation
    Authors
    Motwalli, Olaa Amin cc
    Advisors
    Bajic, Vladimir B. cc
    Committee members
    Moshkov, Mikhail cc
    Gojobori, Takashi cc
    Zhang, Zhang
    Program
    Computer Science
    KAUST Department
    Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division
    Date
    2017-05-28
    Embargo End Date
    2018-05-28
    Permanent link to this record
    http://hdl.handle.net/10754/623742
    
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    Access Restrictions
    At the time of archiving, the student author of this dissertation opted to temporarily restrict access to it. The full text of this dissertation became available to the public after the expiration of the embargo on 2018-05-28.
    Abstract
    Finding a source from which high-energy-density biofuels can be derived at an industrial scale has become an urgent challenge for renewable energy production. Some microorganisms can produce free fatty acids (FFA) as precursors towards such high-energy-density biofuels. In particular, photosynthetic cyanobacteria are capable of directly converting carbon dioxide into FFA. However, current engineered strains need several rounds of engineering to reach the level of FFA production for it to be commercially viable. Thus, new chassis strains that require less engineering are needed. Although more than 140 cyanobacterial genomes are sequenced, the natural potential of these strains for FFA production and excretion has not been systematically estimated. In relation to the above-mentioned problems, we developed the first in silico screening method (FFASC) that evaluates the cyanobacterial strains’ potential for FFA production based on the strains’ proteome, which for the first time allows non-experimental selection of the most promising chassis for cyanofactories. The solution is based on the original problem formulation, optimization and ranking. To provide developers and researchers easy means for evaluation and assessment of the cyanobacterial strains potential for production of FFA, we developed the BioPS platform. In addition to being able to compare capacity for FFA production of any novel strain against 140 pre-valuate strains, BioPS can be used to explore characteristics and assessment rules in play for an individual strain. This is the first tool of this type developed. Finally, we developed a novel generic in silico method (PathDES) for ranking and selection of the most suitable pathways / sets of metabolic reactions, which suggests genetic modifications for improved metabolic productivity. The method heavily relies on optimization and integration of disparate information in a novel manner. It has been successfully used in connection with FFASC for design of cyanofactories. In conclusion, this study has contributed novel and unique methods, and tools for the field of bioinformatics, with applications towards the metabolic design of cyanofactories. We believe that these will be of good use to researchers and technology developers in this field.
    Citation
    Motwalli, O. A. (2017). Novel Computational Methods that Facilitate Development of Cyanofactories for Free Fatty Acid Production. KAUST Research Repository. https://doi.org/10.25781/KAUST-X3B63
    DOI
    10.25781/KAUST-X3B63
    ae974a485f413a2113503eed53cd6c53
    10.25781/KAUST-X3B63
    Scopus Count
    Collections
    PhD Dissertations; Computer Science Program; Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division

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