Computer simulation of Escherichia coli metabolic pathways based on matabolome data
| Project/Area Number |
15013252
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| Research Category |
Grant-in-Aid for Scientific Research on Priority Areas
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| Allocation Type | Single-year Grants |
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| Review Section |
Biological Sciences
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| Research Institution | Keio University |
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Principal Investigator |
TOMITA Masaru Keio University, Faculty of Environmental Information, Professor, 環境情報学部, 教授 (60227626)
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| Co-Investigator(Kenkyū-buntansha) |
SOGA Tomoyoshi Keio University, Faculty of Environmental Information, Associate Professor, 環境情報学部, 助教授 (60338217)
KANAI Akio Keio University, Faculty of Environmental Information, Associate Professor, 環境情報学部, 助教授 (60260329)
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| Project Period (FY) |
2003 – 2004
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| Project Status |
Completed (Fiscal Year 2004)
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| Budget Amount *help |
¥32,000,000 (Direct Cost: ¥32,000,000)
Fiscal Year 2004: ¥16,000,000 (Direct Cost: ¥16,000,000)
Fiscal Year 2003: ¥16,000,000 (Direct Cost: ¥16,000,000)
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| Keywords | Computer Simulation / E-CELL / Metabolome / Bacteria / E. coli / Metabolites / CE-MS / Bioinformatics / バクテリア / CE / MS / 反応速度式 / モデリング / バイオインフォマティクス |
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| Research Abstract |
1. We constructed a computer model of the Escherichia coli metabolic pathways using E-CELL simulation system. The model contained 190 enzymatic reactions that are responsible for central metabolic pathways such as glycolysis, the TCA cycle, the pentose phosphate pathway and the nucleotide biosynthesis pathways.
2. For constructing this model, we initially developed a detection method for whole metabolites in E. coli by using capillary electrophoresis mass spectrometry (CE-MS) system. This method was applied to the comprehensive analysis of metabolic intermediates extracted from E. coli, hundreds of metabolites could be detected for collecting parameters in computer simulation.
3. We developed a computational technique to assist in the large-scale identification of charged metabolites. The electrophoretic mobility of metabolites in CE-MS was predicted from their structure, using an ensemble of artificial neural networks (ANNs).
4. We also developed a synthetic in vitro glycolysis system using ten purified E. coli enzymes to obtain kinetics for the computer simulation.
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Report
(3 results)
Research Products
(28 results)
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[Publications] Kikuchi, S., Fujimoto, K., Kitagawa, N., Fuchikawa, T., Abe, M., Oka, K., Takei, K., Tomita, M: "Kinetic simulation of signal transduction system in hippocampal long-term potentiation with dynamic modeling of protein phosphatase 2A"Neural Networks. 16. 1389-1398 (2003)
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[Publications] Soga, T., Ohashi, Y., Ueno, Y., Naraoka, H., Tomita, M., Nishioka, T: "Quantitative Metabolome Analysis Using CE-MS"Journal of Proteome Research. 2. 488-494 (2003)
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[Publications] Takahashi, K., Ishikawa, N., Sadamoto, Y., Sasamoto, H., Ohta, S., Shiozawa, A., Miyoshi, F., Naito, Y., Nakayama, Y., Tomita M: "E-CELL2 : Multi-platform E-CELL Simulation System"Bioinformatics. 19(13). 1727-1729 (2003)
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[Publications] Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Kobayashi, Y., Tomita, M: "G-language Genome Analysis Environment : a workbench for nucleotide sequence data mining"Bioinformatics. 19(2). 305-306 (2003)
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[Publications] M.Hucka, A.Finney, H.M.Sauro, H.Bolouri, J.C.Doyle, H.Kitano, A.P.Arkin, B.J.Bornstein, D.Bray, A.Cornish-Bowden, A.A.Cuellar, S.Dronov, E.D.Gilles, M.Ginkel, V.Gor, I.I.Goryanin, W.J.Hedley, T.C.Hodgman, J.-H.Hofmeyr, P.J.Hunter, N.S.Juty, J.L.Kasberger, A.Kremling, U.Kummer, N.Le Novere, L.M.Loew, D.Lucio, P.Mendes, E.D.Mjolsness, Y.Nakayama, M.R.Nelson, P.F.Nielsen, T.Sakurada, J.C.Schaff, B.E.Shapiro, T.S.Shimizu, H.D.Spence, J.Stelling, K.Takahashi, M.Tomita, J.Wagner, J.Wang: "The Systems Biology Markup Language (SBML) : A Medium for Representation and Exchange of Biochemical Network Models"Bioinformatics. 19(4). 524-531 (2003)
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