Ting Lu, PhD
Associate Professor of Bioengineering
University of Illinois at Urbana-Champaign
Bacterial metabolism is a means by which a bacterium obtains energy and nutrients t live and reproduce. It is often implemented through the coordination of metabolic reactions and gene regulation, as well as their interactions with environmental cues. Current modeling schemes offer valuable strategies to describe underlying processes; however, under-appreciation of the complexity and systems nature of metabolism has rendered challenges in quantitatively understanding and predicting cellular behaviors. We recently developed a coarse-grained but systems modeling scheme that explicitly integrates metabolic kinetics with gene regulation through a systematic examination of their interactions. One such example is the acetone-butanol-ethanol (ABE) fermentation by Clostridium acetobutylicum, a prominent species for industrial biofuel production. Using a modular concept, we constructed an integrated description that successfully reproduced the fermentation of the wild type and its mutants, and further conferred predictions on various network perturbations. In another case, we investigated engineered gene circuits that operate in bacterial hosts. By combining circuit behaviors with host physiology, we were able to capture and predict a large set of experimental data concerning the host and its foreign gene overexpression. Furthermore, we elucidated the enriched behaviors of a growth-modulating feedback circuit and a toggle switch across scales.
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