Document Type

Technical Report


Computer Science and Engineering

Publication Date






Technical Report Number



Shewanella bacteria are facultative anaerobes isolated from aquatic and sedimentary environments (Hau and Gralnick 2007) with a broad capacity for reduction of multiple electron receptors (Pinchuk et al. 2009; Serres and Riley 2006), including Fe(III), Mn(IV), sulfur, nitrate, and fumarate. With the accomplishment of complete genome sequencing of several Shewanella bacteria, the general pictures of the carbon metabolism have been revealed (Serres and Riley 2006). metabolism. One of the most physiological methods to decipher the time-variant metabolic regulation is to determine the dynamic distribution of intracellular metabolic fluxes since it reveals the final response of cellular metabolism to genomic, transcriptional and post-transcriptional regulations (Sauer 2006; Tang et al. 2009). In order to track the dynamic intracellular metabolic regulation, dynamic flux balance analysis (DFBA) was developed (Mahadevan et al. 2002), in which cell growth phase was divided into numerous stages, assuming that at each stage a new metabolic steady state was maintained. All the metabolic fluxes were then searched to satisfy the objective functions set for each stage. By solving this nonlinear optimization model using a cutting-edge nonlinear optimization solver (IPOPT), we confirmed the changing of carbon sources for the growth of Shewanella oneidensis MR-1 and deciphered the dynamic regulation of intracellular metabolism.


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