The week's pick
Reseach Article
Large-Scale of Metabolic Network of E. Coli using MATLAB
| Majan College International Conference |
| Foundation of Computer Science USA |
| MIC - Number 1 |
| December 2014 |
| Authors: Kunna Mohamed, Tuty Kadir, Elrasheed I. Sultan |
| 367657cb-a1f3-47a0-9e95-bd68d5e5b62a |
Kunna Mohamed, Tuty Kadir, Elrasheed I. Sultan . Large-Scale of Metabolic Network of E. Coli using MATLAB. Majan College International Conference. MIC, 1 (December 2014), 22-26.
Abstract
In this study, we performed local sensitivity analysis on a large-scale kinetic dynamic metabolic network. Time profile for sensitivity indices has been calculated for each kinetic parameters based on highest variance. The dynamic model of E. coli used in this study contain Glycolysis, Pentose Phosphate, TCA cycle, Gluconeogenesis and Glycoxylate pathways in addition to Acetate formation PTS system. The model implicates twenty-four dynamic mass balance for extracellular glucose and intracellular, thirty kinetic rate expressions. We test all the kinetics in 10% and 20 % increasing one by one at steady state condition. The former analysis in 20%, has allowed identification of eight kinetic parameters as the most effective on this model.
References
- VassilyHatzimanikatis . , 1999 Nonlinear Metabolic Control Analysis. , metabolicengineering 1, 75-87. articleno. MT980108.
- TutyAsmawaty Abdul Kadir, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden, Kazuyuki Shimizu . , 2010, modeling and simulation of the main metabolism in Eshercichia coli and its several single-gene knockout mutants with experimental verification.
- Theobald U, Mailinger W, Baltes M, Rizzi M, Reuss M 1997 . , In vivo analysis of metabolic dynamic in Saccharomyces cerevisiae: I. Experimental observations. BiotechnolBioeng, 55:305-316.
- Vaseghi S, Baumeister A, Rizzi M, ReussM . , 1999 In vivo dynamics of the pentose phosphate pathway in Saccharomyces cerevisiae. MetabEng, 1:128-140. Debugging for Interactive User Interfaces. Doctoral Thesis. UMI Order Number: UMI Order No. GAX95-09398. , University of Washington.
- Eberhard Voit, Ana RuteNeves, and Helena Santos 2006. The intricate side of systems biology. Proceedings of the National Academy of Sciences of the United States of America 103 (25), 9452–9457.
- RadhakrishnanMahadevan, Jeremy S. Edwards, and Francis J. Doyle, 2002) (Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli) Biophysical Journal Volume 83 1331–1340.
- Chassagnole C, Noisommit-Rizzi N, SchmidJW, Mauch K, Reuss M2002 . , Dynamic modelling of the central carbon metabolism ofEscherichia coli. Biotech and Bioeng 79:53-73.
- K. Mauch, S. Arnold and M. Reuss . , 1997 Dynamic sensitivity analysis for metabolic systems, Chemical Enyineering Science, Vol. 52. No. 15, pp. 2589-2598.
- S. Noacka,A. Wahla, M. Haunschildb, E. Qelic, B. Freislebenc, W. Wiechert . , 2008, Visualizing regulatory interdependencies and parameter sensitivities in biochemical network models, pp. 991–998. doi:10. 1016/j. matcom. 2008. 02. 008.
- J. Di Maggioa, J. C. Diaz Riccib, M. S. Diaz. , 2010 Global sensitivity analysis in dynamic metabolic networks, pp. 770–781.
- Rafael S. Costa, Daniel Machado, Isabel Rocha, Eugénio C. Ferreira. , 2010. , Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis–Menten and approximate kinetic equations. R. S. Costa et al. / BioSystems100 (2010) 150–157.
- YukakoTohsato, Kunihiko Ikuta, AkitakaShionoya, YusakuMazaki, Masahiro Ito. , 2013 Parameter optimization and sensitivity analysis for large kinetic models using areal-coded genetic algorithm, pp. 84–90.
Index Terms
Keywords