Prediction of metabolic function from limited data: Lumped Hybrid Cybernetic Modeling (L-HCM)

Biotechnology and Bioengineering

Volumn 106, Issue 2, 2010, Pages 271-284

  Song, Hyun Seob ^a   Ramkrishna, Doraiswami ^a  

^a PURDUE UNIVERSITY   (United States)

Author keywords

Crabtree effect; Elementary mode; Lumped hybrid cybernetic model; Saccharomyces cerevisiae

Indexed keywords

BATCH GROWTH; CELLULAR REGULATION; CLASSICAL MODEL; CONTROL LAWS; CYBERNETIC MODELING; CYBERNETIC MODELS; DATA SETS; DETAILED MODELS; ELEMENTARY MODE; EMPIRICAL PARAMETERS; ENVIRONMENTAL CONDITIONS; FLUX DISTRIBUTIONS; LARGER NETWORKS; LIMITED DATA; METABOLIC ENGINEERING; METABOLIC FUNCTION; METABOLIC NETWORK; METABOLIC SHIFT; PARAMETER IDENTIFICATION; PARAMETER-TUNING; PRIMARY METABOLITE; QUANTITATIVE ASSESSMENTS; RELATIVE IMPORTANCE; RETURN ON INVESTMENTS; SACCHAROMYCES CEREVISIAE; SATISFACTORY PREDICTIONS; YIELD COEFFICIENT;

ENZYME ACTIVITY; FORECASTING; INVESTMENTS; LAWS AND LEGISLATION; MODELS; PHYSIOLOGY; STOICHIOMETRY; TUNING; YEAST;

METABOLISM;

AEROBIC FERMENTATION; ARTICLE; BREATHING; CELL METABOLISM; CHEMOSTAT; CYBERNETICS; ENZYME ACTIVITY; FUNGUS GROWTH; GENOTYPE; LUMPED HYBRID CYBERNETIC MODEL; METABOLIC ENGINEERING; METABOLITE; NONHUMAN; PREDICTION; SACCHAROMYCES CEREVISIAE; STOICHIOMETRY;

ALGORITHMS; COMPUTER SIMULATION; CYBERNETICS; MODELS, BIOLOGICAL; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

SACCHAROMYCES CEREVISIAE;

EID: 77953080992     PISSN: 00063592     EISSN: 10970290     Source Type: Journal    
DOI: 10.1002/bit.22692     Document Type: Article

References (22)

1. Baloo S, Ramkrishna D. 1991a. Metabolic-regulation in bacterial continuous cultures. 1. Biotechnol Bioeng 38(11):1337-1352.
2. Baloo S, Ramkrishna D. 1991b. Metabolic-regulation in bacterial continuous cultures. 2. Biotechnol Bioeng 38(11):1353-1363.
3. Bijkerk AHE, Hall RJ. 1977. Mechanistic model of aerobic growth of Saccharomyces cerevisiae. Biotechnol Bioeng 19(2):267-296. (Pubitemid 8051903)
4. Cakir T, Kirdar B, Ulgen KO. 2004. Metabolic pathway analysis of yeast strengthens the bridge between transcriptornics and metabolic networks. Biotechnol Bioeng 86(3):251-260. (Pubitemid 38560353)
5. Crabtree HG. 1929. Observations on the carbohydrate metabolism of tumours. Biochem J 23(3):536-545.
6. Di Serio M, Tesser R, Santacesaria E. 2001. A kinetic and mass transfer model to simulate the growth of baker's yeast in industrial bioreactors. Chem Eng J 82(1-3):347-354. (Pubitemid 32325096)
7. Jones KD, Kompala DS. 1999. Cybernetic model of the growth dynamics of Saccharomyces cerevisiae in batch and continuous cultures. J Biotechnol 71(1-3):105-131. (Pubitemid 29354244)
8. Kim JI, Varner JD, Ramkrishna D. 2008. A hybrid model of anaerobic E. coli GJT001: Combination of elementary flux modes and cybernetic variables. Biotechnol Prog 24(5):993-1006.
9. Kompala DS, Ramkrishna D, Jansen NB, Tsao GT. 1986. Investigation of bacterial-growth on mixed substrates - Experimental evaluation of cybernetic models. Biotechnol Bioeng 28(7):1044-1055. (Pubitemid 16588537)
10. Pham HTB, Larsson G, Enfors SO. 1998. Growth and energy metabolism in aerobic fed-batch cultures of Saccharomyces cerevisiae: Simulation and model verification. Biotechnol Bioeng 60(4):474-482. (Pubitemid 28489512)
11. Reed JL, Palsson BO. 2003. Thirteen years of building constraint-based in silico models of Escherichia coli. J Bacteriol 185(9):2692-2699.
12. Schuster S, Fell DA, Dandekar T. 2000. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat Biotechnol 18(3):326-332. (Pubitemid 30159487)
13. Schuster S, Hilgetag C, Woods JH, Fell DA. 2002. Reaction routes in biochemical reaction systems: Algebraic properties, validated calculation procedure and example from nucleotide metabolism. J Math Biol 45(2):153-181. (Pubitemid 44200164)
14. Song HS, Ramkrishna D. 2009. Reduction of a set of elementary modes using yield analysis. Biotechnol Bioeng 102(2):554-568.
15. Song HS, Morgan JA, Ramkrishna D. 2009. Systematic development of hybrid cybernetic models: Application to recombinant yeast co-consuming glucose and xylose. Biotechnol Bioeng 103(5):984-1002.
16. Turner BG, Ramkrishna D, Jansen NB. 1989. Cybernetic modeling of bacterial cultures at low growth-rates - Single-substrate systems. Biotechnol Bioeng 34(2):252-261. (Pubitemid 18621679)
17. Verduyn C. 1991. Physiology of yeasts in relation to biomass yields. Antonie Van Leeuwenhoek Int J Gen Mol Microbiol 60(3-4):325-353.
18. Verduyn C, Postma E, Scheffers WA, Vandijken JP. 1990. Energetics of Saccharomyces cerevisiae in anaerobic glucose-limited chemostat cultures. J Gen Microbiol 136:405-412. (Pubitemid 20109731)
19. von Kamp A, Schuster S. 2006. Metatool 5.0: Fast and flexible elementary modes analysis. Bioinformatics 22(15):1930-1931. (Pubitemid 44283044)
20. von Meyenburg HK. 1969. Katabolit-repsression under Sprossungszklus von Saccharomyces cerevisiae [Ph.D. Dissertation]. Zurich: Eidgenossischen Technischen Hoschshule.
21. Young JD, Ramkrishna D. 2007. On the matching and proportional laws of cybernetic models. Biotechnol Prog 23(1):83-99. (Pubitemid 46293491)
22. Young JD, Henne KL, Morgan JA, Konopka AE, Ramkrishna D. 2008. Integrating cybernetic modeling with pathway analysis provides a dynamic, systems-level description of metabolic control. Biotechnol Bioeng 100(3):542-559. (Pubitemid 351792930)