Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical
Reexamination Certificate
2005-04-01
2009-06-30
Zeman, Mary K (Department: 1631)
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Biological or biochemical
C702S020000, C703S011000, C707S793000
Reexamination Certificate
active
07555392
ABSTRACT:
A method for determining metabolic flux distribution of a cell, which comprises the steps of:1) creating a stoichiometric matrix based on formulas of biochemical reactions from a substrate to a product,2) computing a set of vectors of solutions existing in a solution space which the stoichiometric matrix may have,3) selecting, from the computed set of vectors of solutions, maximum vectors whose vector elements corresponding to respective substances for which input values can be obtained are maximum, and4) performing linear combination for the selected vectors in accordance with the following equations to obtain a vector representing metabolic flux distribution:Sflux=∑i=1nai·pi·S(i)+∑i=1nbi·qi·A(i)(I)∑i=1nai+∑i=1nbi=1(II)Sflux: Vector representing metabolic flux distribution to be determined,S(i): Vector selected for substance for which inputted value can be obtained,A(i): Adjustment vector,a, b: Coefficients for linear combination (b may be 0),p: Coefficient for obtaining consistency with input value as numerical value,q: Coefficient of adjustment vector.
REFERENCES:
patent: 2003/0228567 (2003-12-01), Famili et al.
patent: 2004/0033975 (2004-02-01), Fu et al.
patent: WO 00/46405 (2000-08-01), None
patent: WO 02/055995 (2002-07-01), None
patent: WO 02/061115 (2002-08-01), None
patent: WO03/029425 (2003-04-01), None
patent: 2005/010794 (2005-02-01), None
Arauzo-Bravo et al. Journal of Biotechnology 105 (2003) 117-133.
Ross Carlson, “FundamentalEscherichia coliBiochemical Pathways for Biomass and Energy Production: Identification of Reactions.” Biotechnology and Bioengineering, vol. 85, No. 1, Jan. 5, 2004, pp. 1-19.
Ross Carlson, “FundamentalEscherichia coliBiochemical Pathways for Biomass and Energy Production: Creation of Overall Flux States.” Biotechnoloy and Bioengineering, vol. 86, No. 2, Apr. 20, 2004, pp. 149-162.
Steffen Klamt, “Flux Analyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps.” Bioinformatics (Oxford), vol. 19, No. 2, Jan. 22, 2003, pp. 261-269.
Steffen Klamt, “Calculability Analysis in Undetermined Metabolic Networks Illustrated by a Model of the Central Metabolism in Purple Nonsulfer Bacteria,” Biotechnology and Bioengineering, vol. 77, No. 7, Mar. 30, 2002, pp. 734-751.
Varma, A. et al. “Stoichiometric Flux Balance Models Quantitatively Predict Growth and Metabolic By-Product Secretion in Wild-TypeEscherichia coliW3110”,Applied Environmental Microbiology,vol. 60 (10) pp. 3724-3731, 1994.
Schilling, C.H. et al. “Toward Metabolic Phenomics: Analysis of Genomic Data Using Flux Balances”,Biotechnol. Prog.,vol. 15 pp. 288-295, 1999.
Schilling, C.H. et al. “Metabolic Pathway Analysis: Basic Concepts and Scientific Applications in the Post-genomic Era”,Biotechnol. Prog.,vol. 15 pp. 296-303, 1999.
Pramanik, J. et al. “Stoichiometric Model ofEscherichia coliMetabolism: Incorporation of Growth-Rate Dependant Biomass Composition and Mechanistic Energy Requirements”,Biotechnology and Bioengineering,vol. 56 (4) pp. 398-421, 1997.
Ibarra, R.U. et al. “Escherichia coliK-12 undergoes adaptive evolution to achievein silicopredicted optimal growth”,Nature,vol. 420 pp. 186-189, 2002.
Vallino, J.J. et al. “Metabolic Flux Distributions inCorynebacterium glutamicumDuring Growth and Lysine Overproduction”,Biotechnology and Bioengineering,vol. 41 pp. 633-646, 1993.
Wiechert , W. “Modeling and simulation: tools for metabolic engineering”,Journal of Biotechnology,vol. 94 pp. 37-63, 2002.
Wiechert, W. “Minireview-1 3C Metabolic Flux Analysis”,Metabolic Engineering,vol. 3 pp. 195-206, 2001.
Dien Stephen Van
Iwatani Shintaro
Matsui Kazuhiko
Usuda Yoshihiro
Ajinomoto Co. Inc.
Hopkins Susanne M.
The Nath Law Group
Zeman Mary K
Zytcer Ari G.
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