4 research outputs found
Yeast Systems Biotechnology for Production of Value-Added Biochemicals
Ph.DDOCTOR OF PHILOSOPH
Flux-sum analysis: a metabolite-centric approach for understanding the metabolic network
<p>Abstract</p> <p>Background</p> <p>Constraint-based flux analysis of metabolic network model quantifies the reaction flux distribution to characterize the state of cellular metabolism. However, metabolites are key players in the metabolic network and the current reaction-centric approach may not account for the effect of metabolite perturbation on the cellular physiology due to the inherent limitation in model formulation. Thus, it would be practical to incorporate the metabolite states into the model for the analysis of the network.</p> <p>Results</p> <p>Presented herein is a metabolite-centric approach of analyzing the metabolic network by including the turnover rate of metabolite, known as flux-sum, as key descriptive variable within the model formulation. By doing so, the effect of varying metabolite flux-sum on physiological change can be simulated by resorting to mixed integer linear programming. From the results, we could classify various metabolite types based on the flux-sum profile. Using the <it>i</it>AF1260 <it>in silico </it>metabolic model of <it>Escherichia coli</it>, we demonstrated that this novel concept complements the conventional reaction-centric analysis.</p> <p>Conclusions</p> <p>Metabolite flux-sum analysis elucidates the roles of metabolites in the network. In addition, this metabolite perturbation analysis identifies the key metabolites, implicating practical application which is achievable through metabolite flux-sum manipulation in the areas of biotechnology and biomedical research.</p
Cofactor modification analysis: A computational framework to identify cofactor specificity engineering targets for strain improvement
10.1142/S0219720013430063Journal of Bioinformatics and Computational Biology116-JBCB
Metabolic reconstruction and flux analysis of industrial Pichia yeasts
10.1007/s00253-013-4702-7Applied Microbiology and Biotechnology9751865-1873AMBI