Dr. Laurence Yang, Assistant Professor, Queen's University Toward precision whole-cell simulators Manufacturing industries find computer simulations to be indispensable: they speed up design, increase product quality, and reduce R&D costs while helping to find alternatives to traditional design methods. Likewise, the bio-manufacturing industry has relied on simulators to model reactors and processes. Increasingly, companies are finding value in simulating the living cell factories themselves (microbes, mammalian cell lines, etc.). We will demonstrate cell modeling with examples from multiple organisms (Pseudomonas, Escherichia coli, algae), and for varying applications (drug discovery, bioproducts, discovery). We discuss modeling of microbial stress responses in the context of antimicrobial resistance. With recent advances in integrated genome-scale models of metabolism and protein expression, we developed a framework to predict microbial response to thermal, oxidative, and acid stresses. The models accurately compute how E. coli changes gene expression and metabolic states in response to these stresses, together with variations in nutrient availability. Furthermore, these models explain the molecular mechanisms underlying improved fitness observed for several microbes that were adaptively evolved under oxidative stress. We then show how the modeling method extends to eukaryotes, using algae as an example.
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