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dc.contributor.advisor Moustafa, Ahmed Sharaf, Hazem 2014-06-07T22:59:00Z 2014-06-08T03:00:08Z 2014 Spring en 2014-06-08
dc.description.abstract With the advent of high-throughput genome sequencing, metabolic network reconstructions gained prominence as the de facto standard of attaining a holistic approach towards the understanding of an organism's metabolism. A reconstructed network supplemented with genome annotations and literature mining is turned into a knowledgebase on the organism. Such a network serves as powerful predictive tool for the state of metabolism by applying flux balance analysis (FBA) which is based on a mathematical linear optimization approach. The advantages of FBA are to derive insights about the metabolic phenotype of an organism and to direct metabolic engineering for further capabilities. This has been demonstrated through numerous experiments with several organisms and has led to expanding biotechnological applications such as advanced strain design and discovery of drug targets. Diatoms are photosynthetic eukaryotic algae that inhabit aquatic environments worldwide. They are responsible for more than one fifth of the global organic carbon production and half of the photosynthetic activity in the world oceans. In addition, they have a cell wall made of silica, which sends them to the bottom of the ocean floor upon their death, stressing their critical role in geochemical cycles of the oceans. They also accumulate up to half of their dry weight in lipids when under stress, making them a potential source for biofuels. The pennate Phaeodactylum tricornutum is one of only two diatoms with a complete genome sequenced and published until now, and whose genome has revealed novel metabolic pathways in nitrogen and carbon assimilation. This work presents the first thorough genome-scale metabolic reconstruction for a diatom, which incorporates 947 reactions catalyzed by 869 genes. In-silico simulations of the model through FBA have revealed the first insights into the carbon fixation pathways and the metazoan-like urea cycle. It also includes the first pathway reconstructions of diatom-specific metabolites such as the carbohydrate chrysolaminarin and carotenoid fucoxanthin. This model serves as a platform for the design of future biotechnological applications in diatoms. en
dc.format.extent 67 p. en
dc.format.medium theses en
dc.language.iso en en
dc.rights Author retains all rights with regard to copyright. en
dc.subject Diatoms en
dc.subject Metabolism en
dc.subject Modelling en
dc.subject Systems biology en
dc.subject.lcsh Thesis (M.S.)--American University in Cairo en
dc.subject.lcsh Diatoms.
dc.subject.lcsh Metabolism.
dc.subject.lcsh Systems biology.
dc.title Genome-wide reconstruction of the metabolic network of Phaeodactylum tricornutum en
dc.type Dataset en
dc.type Text en
dc.subject.discipline Biotechnology en
dc.rights.access This item is available en
dc.contributor.department American University in Cairo. Dept. of Biology en
dc.description.irb American University in Cairo Institutional Review Board approval is not necessary for this item, since the research is not concerned with living human beings or bodily tissue samples. en
dc.contributor.committeeMember Valentin, Klaus
dc.contributor.committeeMember Bos, Arthur
dc.contributor.committeeMember El Gogary, Sawsan

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  • Theses and Dissertations [1827]
    This collection includes theses and dissertations authored by American University in Cairo graduate students.

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