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UBC Theses and Dissertations

Identification of essential metabolites in metabolite networks Long, Cai


Metabolite essentiality is an important topic in systems biology and as such there has been increased focus on their prediction in metabolic networks. Specifically, two related questions have become the focus of this field: how do we decrease the amount of gene knock-out workloads and is it possible to predict essential metabolites in different growth conditions? Two different approaches to these questions: interaction-based method and constraints-based method, are conducted in this study to gain in depth understanding of metabolite essentiality in complex metabolic networks. In the interaction-based approach, the correlations between metabolite essentiality and the metabolite network topology are studied. With the idea of predicting essential metabolites, the topological properties of the metabolite network are studied for the Mycobacterium tuberculosis model. It is found that there is strong correlation between metabolite essentiality and the degree and the number of shortest paths through the metabolite. Welch’s two sample T-test is performed to help identify the statistical significance of the differences between groups of essential metabolites and non-essential metabolites. In the constraint-based approach, essential metabolites are identified in-silico. Flux Balance Analysis (known as FBA), is implemented with the most advanced in-silico model of Chlamydomonas Reinhardtii, which contains light usage information in 3 different growth environments: autotrophic, mixotrophic, and heterotrophic. Essential metabolites are predicted by metabolite knock out analysis, which is to set the flux of a certain metabolite to zero, and categorized into 3 types through Flux Sum Analysis. The basal flux-sum for metabolites is found to follow a exponential distribution, it is also found that essential metabolites tend to have larger basal flux-sum.

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