Network analysis of intermediary metabolism using linear optimization. I. Development of mathematical formalism

Alberts, 1983 Ardawi, 1982, Maximum activities of some enzymes of glycolysis, the tricarboxylic acid cycle and ketone-body and glutamine utilization pathways in lymphocytes of the rat, Biochem. J., 208, 743, 10.1042/bj2080743 Bailey, 1972, Control of lipid metabolism in cultured cells, Lipids, 7, 125, 10.1007/BF02532600 Beavis, 1986, The upper and lower limits of the mechanistic stoichiometry of mitochondrial oxidative phosphorylation, Eur. J. Biochem., 158, 315, 10.1111/j.1432-1033.1986.tb09753.x Blum, 1982, On the analysis of metabolic networks, Vol. 3A, 99 Brand, 1989, Metabolism of glutamine in lymphocytes, Metabolism, 38, 29, 10.1016/0026-0495(89)90136-4 Crawford, 1983, Quantitative analysis of flux along the gluconeogenic, glycolytic and pentose phosphate pathways under reducing conditions in hepatocytes isolated from fed rats, Biochem. J., 212, 595, 10.1042/bj2120585 Creighton, 1984 Darnell, 1976, mRNA structure and function, Prog. Nucl. Acad Res. Molec. Biol., 19, 493, 10.1016/S0079-6603(08)60941-1 Eagle, 1965, Amino acid and protein metabolism. I. The metabolic characteristics of serially propagated cells, Vol. I, 277 Eigenbrodt, 1985, New perspectives on carbohydrate metabolism in tumor cells, Vol. II, 141 Fell, 1986, Fat synthesis in adipose tissue: an examination of stoichiometric constraints, Biochem. J., 238, 781, 10.1042/bj2380781 Fleischaker, 1986, Practical matters in instrumentation for mammalian cell cultures, 199 Glazer, 1974, Glutamate dehydrogenase activity related to histopathological grade of hepatocellular carcinoma in man, Cancer Res., 34, 2975 Greenhouse, 1976, Occurrence of the malate-aspartate shuttle in various tumor types, Cancer Res., 36, 1392 Holms, 1986, The central metabolic pathways of Escherichia coli: relationship between flux and control at a branch point, efficiency of conversion to biomass, and excretion of acetate, Curr. Top. Cell. Regul., 28, 69, 10.1016/B978-0-12-152828-7.50004-4 Ingraham, 1983 Kilburn, 1969, The energetics of mammalian cell growth, J. Cell Sci., 4, 645, 10.1242/jcs.4.3.645 Kovacevic, 1971, The pathways of glutamine and glutamate oxidation in isolated mitochondria from mammalian cells, Biochem. J., 125, 757, 10.1042/bj1250757 Lemasters, 1984, The ATP-to-oxygen stoichiometries of oxidative phosphorylation by rat liver mitochondria. An analysis of ADP-induced oxygen jumps by linear nonequilibrium thermodynamics, J. biol. Chem., 259, 13123, 10.1016/S0021-9258(18)90666-6 Lopez-Alarcon, 1979, Evidence for the oxidation of glycolytic NADH by the malate-aspartate shuttle in Ehrlich ascites tumor cells, Arch. Biochem. Biophys., 192, 391, 10.1016/0003-9861(79)90107-3 Luenberger, 1984 Majewski, 1990, Simple constrained-optimization view of acetate overflow in E. coli, Biotechnol. Bioengng., 35, 732, 10.1002/bit.260350711 McKeehan, 1986, Glutaminolysis in animal cells, 111 Miller, 1988, Transient and steady-state responses in continuous hybridoma culture Miller, 1988, Transient responses of hybridoma metabolism to changes in the oxygen supply rate in continuous culture, Bioprocess Engng., 3, 1 Miller, 1986, Hybridoma responses to nutrient pulse and step changes in continuous culture. Implications for metabolic regulation Moreadith, 1984, The pathways of glutamate and glutamine oxidation by tumor cell mitochondria. Role of mitochondrial NAD(P)+-dependent malic enzyme, J. biol. Chem., 259, 6215, 10.1016/S0021-9258(20)82128-0 Niranjan, 1989, Analysis of a framework using material balances in metabolic pathways to elucidate cellular metabolism, Biotechnol. Bioengng., 34, 496, 10.1002/bit.260340409 Ozturk, 1990, Effects of dissolved oxygen on hybridoma cell growth, metabolism, and antibody production kinetics in continuous culture, Biotech. Prog., 6, 437, 10.1021/bp00006a006 Ozturk, 1991, Growth metabolic, and antibody production kinetics of hybridoma cell culture: II effects of serum concentration, dissolved oxygen concentration, and medium pH in a batch reactor, Biotech. Prog., 7, 481, 10.1021/bp00012a002 Papoutsakis, 1985, Equations and calculations of product yields and preferred pathways for butanediol and mixed-acid fermentations, Biotechnol. Bioengng., 27, 50, 10.1002/bit.260270108 Perez-Rodriguez, 1987, Malate-citrate cycle during glycolysis and glutaminolysis in Ehrlich ascites tumor cells, Biochimie, 69, 469, 10.1016/0300-9084(87)90084-8 Pirt, 1982, Maintenance energy: a general model for energy-limited and energy-sufficient growth, Arch. Microbiol., 133, 300, 10.1007/BF00521294 Rabkin, 1985, Quantitative analysis of intermediary metabolism in hepatocytes incubated in the presence and absence of glucagon with a substrate mixture containing glucose, ribose, fructose, alanine and acetate, Biochem. J., 225, 761, 10.1042/bj2250761 Rudland, 1975, Changes in RNA metabolism and accumulation of presumptive messenger RNA during transition from the growing to the quiescent state of cultured mouse fibroblasts, J. molec. Biol., 96, 745, 10.1016/0022-2836(75)90150-3 Safer, 1973, Mitochondrial and cytosolic interactions in perfused rat heart. Role of coupled transamination in repletion of citric acid cycle intermediates, J. biol. Chem., 248, 2570, 10.1016/S0021-9258(19)44146-X Sauer, 1970, Turnover rates and intracellular pool size distribution of citrate cycle intermediates in normal, diabetic and fat-fed rats estimated by computer analysis from specific activity decay data of 14C-labeled citrate cycle acids, Eur. J. Biochem., 17, 350, 10.1111/j.1432-1033.1970.tb01173.x Savinell, 1991, Network analysis of intermediary metabolism using linear optimization. II. Interpretation of hybridoma cell metabolism, J. theor. Biol., 154, 455, 10.1016/S0022-5193(05)80162-6 Stucki, 1972, Pyruvate metabolism in mitochondria from rat liver: measured and computer-simulated fluxes, Eur. J. Biochem., 30, 60, 10.1111/j.1432-1033.1972.tb02072.x Thomas, 1986, Nutrients, oxygen, and pH, 109 Tsai, 1988, Application of Gibbs' rule and a simple pathway method to microbial stoichiometry, Biotechnol. Prog., 4, 82, 10.1002/btpr.5420040206 Walsh, 1985, Branch point control by the phosphorylation state of isocitrate dehydrogenase, J. biol. Chem., 260, 8430, 10.1016/S0021-9258(17)39492-9