Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical
Reexamination Certificate
2004-08-26
2010-11-02
Clow, Lori A (Department: 1631)
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Biological or biochemical
Reexamination Certificate
active
07826975
ABSTRACT:
A computer-assisted method for identifying functionalities to add to an organism-specific metabolic network to enable a desired biotransformation in a host includes accessing reactions from a universal database to provide stoichiometric balance, identifying at least one stoichiometrically balanced pathway at least partially based on the reactions and a substrate to minimize a number of non-native functionalities in the production host, and incorporating the at least one stoichiometrically balanced pathway into the host to provide the desired biotransformation. A representation of the metabolic network as modified can be stored.
REFERENCES:
patent: 4520103 (1985-05-01), Ensley, Jr.
patent: 6117108 (2000-09-01), Woehr et al.
patent: 2002/0012939 (2002-01-01), Palsson
patent: 2002/0142321 (2002-10-01), Palsson et al.
patent: 2002/0168654 (2002-11-01), Maranas et al.
patent: 2003/0073092 (2003-04-01), Maranas et al.
patent: 2004/0009466 (2004-01-01), Maranas et al.
patent: 2005/0079482 (2005-04-01), Maranas et al.
patent: 00/268018 (1999-03-01), None
patent: WO 98/18814 (1998-05-01), None
patent: WO 00/18906 (2000-04-01), None
patent: WO 00/42559 (2000-07-01), None
patent: WO 01/90346 (2001-11-01), None
patent: WO 02/055995 (2002-07-01), None
patent: PCT/US03/21598 (2003-07-01), None
Biebl, H., et al. “Microbial production of 1,3-propanediol”, Appl Microbiol Biotechnol (1999) 52: 289-297 Mini-Review.
Bogarad, Leonard D., et al. “A hierarchical approach to protein molecular evolution”, Proc. Natl. Acad. Sci. USA, vol. 96, pp. 2591-2595, Mar. 1999.
Burgard, Anthony P., “Optimization-Based Framework for Inferring and Testing Hypothesized Metabolic Objecive Functions” 2003 Wiley Periodicals, Inc.
Burgard, Anthony P., “Probing the Performance Limits of theEscherichia coliMetabolic Network Subject to Gene Additions or Deletions” 2001 John Wiley & Sons, Inc. Biotechnology & Bioengineering (Sep. 5, 2001), vol. 74, No. 5, p. 364-375.
Burgard, Anthony P., et al., “Minimal Reaction Sets forEscherichia coliMetabolism under Different Growth Requirements and Uptake Environments” 2001 American Chemical Society and American Institute of Chemical Engineers, Published on Web Sep. 14, 2001.
Burgard, Anthony P., et al., AIChE XP-002216514—[309d]—“Tightening Flux Balance Models Through Boolean Relations” 2001 American Institute of Chemical Engineers.
Cameron, D.C., et al. “Metabolic Engineering of Propanediol Pathways” Biotechnol. Prog. 1998, 14, 116-125, Published on Web Jan. 16, 1998.
Chen, Haoyuan, et al. BioComputiung XP-002250110 “Computer Program for DCalculating the Melting Temperature of Degenerate Oligonucleotides Used in PCR or Hybridization” BioTechniques 22:1158-1160 (Jun. 1997).
Compagno, Concetta, et al. “Glycerol Production in a Triose Phosphate Isomerase Deficient Mutant ofSaccharomyces cerevisiae” Biotechnol. Prog. 1996, 12, 591-595.
Covert, Markus W., et al. XP-002216513 “Regulation of Gene Expression in Flux Balance Models of Metabolism”J. theor. Biol.(2001) 213, 73-88.
Edwards, Jeremy S., et al. “In silico predictions ofEscherichia colimetabolic capabilities are consistent with experimental data” 2001 Nature Publishing Group; Nature Biotechnology, vol. 19, Feb. 2001.
Edwards, Jeremy S., et al. XP-002153942 “How Will Bioinformatics Influence Metabolic Engineering?” 1998 John Wiley & Sons, Inc.
Edwards, J. S., et al. “TheEscherichia coliMG1655 in silico metabolic genotype: Its defin8ition, characteristics, and capabilities” PNAS, May 9, 2000, vol. 97, No. 10.
Gupta, Shashi, et al. “Escherichia coliDerivatives Lacking Both Alcohol Dehydrogenase and Phosphotransacetylase Grow Anaerobically by Lactate Fermentation” Journal of Bacteriology, Jul. 1989, p. 3650-3655.
Hartlep, M., et al. “Study of two-stage processes for the microbial production of 1,3-propanediol from glucose” Appl Microbiol Biotechnol (2002) 60:60-66.
Hatzimanikatis, Vassily et al. “Analysis and Design of Metabolic Reaction Networks via Mixed-Integer Linear Optimization” AIChE Journal, May 1996, vol. 42, No. 5.
Hugler, Michael, et al. “Malonyl-Coenzyme A Reductase fromChloroflexus aurantiacus, a Key Enzyme of the 3-Hydroxypropionate Cycle for Autotrophic CO2Fixation” Journal for Bacteriology, May 2002, p. 2404-2410.
Ibarra, Rafael U., et al. “Escherichia coliK-12 undergoes adaptive evolution to achieve in silico predicted optimal growth” 2004 Nature Publishing, vol. 420, Nov. 14, 2002.
Lutz, Stefan et al. “Creating multiple-crossover DNA libraries independent of sequence identity” XP-002250112 PNAS Sep. 25, 2001 vol. 98, No. 20.
Menendez, Castor et al. “Presence of Acetyl Coenzyme A (CoA) Carboxylase and Propionyl-CaA Carboxylase in AutotrophicCrenarchaeotaand Indication for Operation of a 3-Hydroxypropionate Cycle in Autotrophic Carbon Fixation” Journal of Bacteriology, Feb. 1999, p. 1088-1098.
Moore, Gregory L., et al. “Modeling DNA Mutation and Recombination for Directed Evolution Experiments” XP-002250109J. theor. Biol.(2000) 205, 483-503.
Moore, Gregory L., et al. “Predicting crossover generation in DNA shuffling” XP-002250111, PNAS Mar. 13, 2001, vol. 98, No. 6.
Palsson, Bernhard, “The challenges of in silico biology” XP-002216516; Nature Biotechnology, vol. 18, Nov. 18, 2000.
Pramanik, J., et al. “Stoichiometric Model ofEscherichia coliMetabolism: Incorporation of Growth-Rate Dependent Biomass Composition and Mechanistic Energy Requirements” 1997 John Wiley & Sons, Inc.
SantaLucia, Jr., John “A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics”Proc. Natl. Acad. Sci. USAvol. 95, pp. 1460-1465 Feb. 1998.
Schilling, Christophe H., et al. “Combining Pathway Analysis with Flux Balance Analysis for the Comprehensive Study of Metabolic Systems” XP-002216515; 2001 John Wiley & Sons, Inc.
Schilling, Christophe H., et al. “The underlying pathway structure of biochemical reaction networks” XP-002216518 Proc. Natl. Acad. Sci. USA, vol. 95, pp. 4193-4198, Apr. 1998.
Segre, Daniel, et al. “Analysis of optimality in nature and perturbed metabolic networks” PNAS Nov. 12, 2002, vol. 99, No. 23.
Stols, Lucy, “Production of Succinic Acid through Overexpression of NAD+-Dependent Malic Enzyme in anEscherichia coliMutant” Applied and Environmental Microbiology, Jul. 1997, p. 2695-2701.
Sun, Fengzhu “Modeling DNA Shuffling” XP-002145606; GO6G19/00A2; p. 251-257, Dept of Genetics RECOMB 1998.
Varma, Amit, et al. “Metabolic Capabilities ofEscherichia coli: I. Synthesis of Biosynthetic Precursors and Cofactors” J. theor. Biol. (1993) 165, 477-502.
Yang, Yea-Tyng et al. “Genetic and metabolic engineering” EJB Electronic Journal of Biotechnology ISSN: 0717-3458 vol. 1, No. 3, Jan. 4, 2002.
Zeikus, J. G., et al. “Biotechnology of succinic acid production and markets for derived industrial products” Appl Microbiol Biotechnol (1999) 51: 545-552.
Zeng, An-Ping et al. “Bulk Chemical from Biotechnology:The Case of 1,3-Propanediol Proudction and the New Trends” Advances in Biochemical Engineering/Biotechnology, vol. 74, 2002.
Zhu, Marie M., et al. “Improving 1,3-Propanediol Production from Blycerol in a Metabolically EngineeredEscherich8ia coliby Reducing Accumulation of sn-Glycerol-3-phosphate” Biotechnol. Prog. 2002, 18, 694-699.
“Appendix 1: Flux balance analysis primer” www.che.udel.edu/edwardsgroup/LAB/NBT—ExpPhPP/FBAprimer/FBAC Jan. 4, 2002.
Supplemental European Search Report, The Penn State Research Foundation, EP 04 78 2168, dated Jul. 8, 2009, 2 pages.
Kauffman, Kenneth J., et al., “Advances in flux balance analysis”, Current Opinion in Biology,
Burgard Anthony P.
Maranas Costas D.
Pharkya Priti
Clow Lori A
McKee Voorhees & Sease, P.L.C.
The Penn State Research Foundation
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