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Elementary mode analysis

Copasi (http //www.copasi.org) offers stochastic and deterministic time course simulation (the latter with LSODA, a stiff solver), steady state analysis (including stability), metabolic control analysis, elementary mode analysis, mass conservation analysis, parameter scans, and sliders for interactive parameter changes. It is platform-independent and offers a user-friendly GUI. [Pg.75]

Diniz, C.S., Voss, I., and Steinbuchel, A. (2006) Optimization of cyanophycin production in recombinant strains of Pseudomonas putida and Ralstonia eutropha employing elementary mode analysis and statistical experimental design. Biotechnol. Bioeng., 93,... [Pg.276]

Trinh, C.T. and Thompson, R.A. (2012) Elementary mode analysis a useful metabolic pathway analysis tool for reprograming microbial metabolic pathways, in Reprogramming Microbial Metabolic Pathways, Vol. 64 (eds X. Wang, J. Chen, and P. Quinn), Springer Netherlands, Dordrecht, pp. 21 -42. [Pg.796]

Li S, Huang D, Li Y, Wen J, Jia X. (2012b). Rational improvement of the engineered isobutanol-producing Bacillus subtilis by elementary mode analysis. Microb Cell Fact, 11, 101. [Pg.351]

Elementary Mode Analysis A Useful Metabolic Pathway Analysis Tool for Reprograming Microbial Metabolic Pathways... [Pg.21]

Keywords Elementary mode analysis Engineering Genetic knockout analysis Metabohc minimal metabolic functionality Rational strain design... [Pg.21]

Flynn CM, Hunt KA, Gralnick JA, Srienc F (2012) Construction and elementary mode analysis of a metabolic model for shewanella oneidensis Mr-1. Biosystems 107 120-128 Fong SS, Burgard AP, Herring CD, Knight EM, Blattner FR, Maranas CD, Palsson BO (2005) In silica design and adaptive evolution of Escherichia coli for production of lactic acid. Biotechnol Bioeng 91 643-648... [Pg.38]

Kurata H, Zhao Q, Okuda R, Shimizu K (2007) Integration of enzyme activities into metabolic flux distributions by elementary mode analysis. BMC Syst Biol 1 31 Larhlimi A, Bockmayr A (2009) A New constraint-based description of the steady-state flux cone of metabolic networks. Discret Appl Math 157 2257-2266 Larhlimi A, Blachon S, Selbig J, Nikoloski Z (2011) Robustness of metabolic networks a review of existing definitions. Biosystems 106 1-8... [Pg.39]

Trinh CT, Wlaschin A, Srienc F (2009) Elementary mode analysis a useful metabolic pathway analysis tool for characterizing cellular metabolism. Appl Microbiol Biotechnol 81 813-826 Trinh CT, 14 J, Blanch H W, Clark DS (2011) Redesigning Escherichia coli metabolism for anaerobic production of isobutanol. Appl Environ Microbiol 77 4894-4904 Unrean P, Srienc F (2011) Metabolic networks evolve towards states of maximum entropy production. Metab Eng 13 666-673... [Pg.42]

Unrean P, Trinh CT, Srienc F (2010) Rational design and construction of an efficient E. coli for production of diapolycopendioic acid. Metab Eng 12 112-122 Vijayasankaran N, Carlson R, Srienc E (2005) Metabolic pathway structures for recombinant protein synthesis in Escherichia coli. Appl Microbiol Biotechnol 68 737-746 von Kamp A, Schuster S (2006) Metatool 5.0 fast and flexible elementary modes analysis. Bioinformatics 22 1930-1931... [Pg.42]

Extreme pathway analysis and elementary mode analysis... [Pg.226]

In order to extract more information from the steady-state flux model, extreme pathway analysis (EPA) and elementary mode analysis (EMA) have been developed [14,15]. In these approaches, the metaboHc reaction network is decomposed into a collection of small irreversible functional pathways. When these pathways are weighted and superimposed back together, they are able to form the original metaboHc flux network. By examining the elementary pathways, and using Hnear optimization tools, it is possible to better explore the metaboHc capabilities of a network, and this can also be used to suggest useful metaboHc pathway alterations. [Pg.228]

Elementary mode analysis is one such computational tool that aids in the selection of genes and pathways for deletion in order to improve the production of the target metabolite. While it was first demonstrated in S. cerevisiae for the improvement of poly-/)-hydroxybutyrate production [74], one of the most highly cited applications deals with the improvement of mixed-sugar utilization by E. coli for ethanol production [55]. The challenge of mixed-sugar utilization and the solution implemented by Trinh et al. are described below. [Pg.554]

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