Abdulrazzak N, Pollet B, Ehlting J, Larsen K, Asnaghi C, Ronseau S, Proux C, Erhardt M, Seltzer V, Renou JP, Ullmann P, Pauly M, Lapierre C, Werck-Reichhart D 2006 A coumaroyl-ester-3-hydroxylase insertion mutant reveals the existence of nonredundant meta-hydroxylation pathways and essential roles for phenolic precursors in cell expansion and plant growth. Plant Physiol. 140: 30-48.

Abee T, van Schaik W, Siezen RJ 2004 Impact of genomics on microbial food safety. Trends Biotechnol. 22: 653-660.

Abee T, Wouters JA 1999 Microbial stress response in minimal processing Int. J. Food Microbiol. 50: 65-91.

Acerenza L 1993 Metabolic control design. J. Theor. Biol. 165: 63-85.

Acerenza L, Cornish-Bowden A 1997 Generalization of the double-modulation method for in situ determination of elasticities. Biochem. J. 327: 217-224.

Acerenza L, Ortega F 2006 Metabolic control analysis for large changes: extension to variable elasticity coefficients. Syst. Biol. (Stevenage) 153: 323-326.

Achnine L, Blancaflor EB, Rasmussen S, Dixon RA 2004 Colocalization of L-phenylalanine ammonia-lyase and cinnamate 4-hydroxylase for metabolic channeling in phenylpropanoid biosynthesis. Plant Cell 16: 3098-3109.

Adachi T, Matoba N, Kurata H 2001 BIOCAD project for constructing a biological system in silico. Genome Informatics 12: 284-285.

Agrawal GK, Hajduch M, Graham K, Thelen JJ 2008 In-depth investigation of soybean seed-filling proteome and comparison with a parallel study of rapeseed. Plant Physiol. Jul 3 [Epub ahead of print].

Aharoni A, Jongsma MA, Bouwmeester HJ 2005 Volatile science? Metabolic engineering of terpenoids in plants. Trends Plant Sci. 10: 594-602.

Aharoni A, Ric de Vos CH, Verhoeven HA, Maliepaard CA, Kruppa G, Bino R, Goodenowe DB 2002 Nontargeted metabolome analysis by use of Fourier Transform Ion Cyclotron Mass Spectrometry. OMICS 6: 217-234.

Aharoni A, Vorst O 2002 DNA microarrays for functional plant genomics. Plant Mol. Biol. 48: 99-118.

Ahn J, Daidou T, Tsuneda S, Hirata A 2002 Transformation of phosphorus and relevant intracellular compounds by a phosphorus-accumulating enrichment culture in the presence of both the electron acceptor and electron donor. Biotechnol. Bioeng. 79: 83-93.

Ahrens K, Menzel K, Zeng A, Deckwer W 1998 Kinetic, dynamic, and pathway studies of glycerol metabolism by Klebsiella pneumoniae in anaerobic continuous culture: III. Enzymes and fluxes of glycerol dissimilation and 1,3-propanediol formation. Biotechnol. Bioeng. 59: 544-552.

Ainscow EK, Brand MD 1998 Errors associated with metabolic control analysis. Application of Monte-Carlo simulation of experimental data. J. Theor. Biol. 194: 223-233.

Ainscow EK, Brand MD 1998 Control analysis of systems with reaction blocks that 'cross-talk'. Biochim. Biophys. Acta 1366: 284-290.

Ainscow EK, Brand MD 1995 Top-down control analysis of systems with more than one common intermediate. Eur. J. Biochem. 231: 579-586.

Ainscow EK, Brand MD 1999 Top-down control analysis of ATP turnover, glycolysis and oxidative phosphorylation in rat hepatocytes. Eur. J. Biochem. 263: 671-685.

Ainscow EK, Brand MD 1999 Quantifying elasticity analysis: how external effectors cause changes to metabolic systems. Biosystems 49: 151-159.

Ajikumar PK, Tyo K, Carlsen S, Mucha O, Phon TH, Stephanopoulos G 2008 Terpenoids: opportunities for biosynthesis of natural product drugs using engineered microorganisms. Mol. Pharm. 5: 167-190.

Akesson M, Forster J, Nielsen J 2004 Integration of gene expression data into genome-scale metabolic models. Metab. Eng. 6: 285-293.

Akhtar MS, Oki Y, Adachi T 2008 Intraspecific variations of phosphorus absorption and remobilization, P forms, and their internal buffering in Brassica cultivars exposed to a P-stressed environment. J. Integr. Plant Biol. 50: 703-716.

Aki T, Shigyo M, Nakano R, Yoneyama T, Yanagisawa S 2008 Nano scale proteomics revealed the presence of regulatory proteins including three FT-Like proteins in phloem and xylem saps from rice. Plant Cell Physiol. 49: 767-790.

Akutsu T, Miyano S, Kuhara S 2000 Inferring qualitative relations in genetic networks and metabolic pathways. Bioinformatics 16: 727-734.

Alawady A, Reski R, Yaronskaya E, Grimm B 2005 Cloning and expression of the tobacco CHLM sequence encoding Mg protoporphyrin IX methyltransferase and its interaction with Mg chelatase. Plant Mol. Biol. 57: 679-691.

Alawady AE, Grimm B 2005 Tobacco Mg protoporphyrin IX methyltransferase is involved in inverse activation of Mg porphyrin and protoheme synthesis. Plant J. 41: 282-290.

Albe KR, Wright BE 1992 Systems analysis of the tricarboxylic acid cycle in Dictyostelium discoideum. II. Control analysis. J. Biol. Chem. 267: 3106-3114.

Albrecht G, Mustroph A, Fox TC 2004 Sugar and fructan accumulation during metabolic adjustment between respiration and fermentation under low oxygen conditions in wheat roots. Physiol. Plant. 120: 93-105.

Alder NN, Theg SM 2003 Energy use by biological protein transport pathways. Trends Biochem. Sci. 28: 442-451.

Aldor I, Keasling JD 2001 Metabolic engineering of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) composition in recombinant Salmonella enterica serovar typhimurium. Biotechnol. Bioeng. 76: 108-114.

Aldor IS, Keasling JD 2003 Process design for microbial plastic factories: metabolic engineering of polyhydroxyalkanoates. Curr. Opin. Biotechnol. 14: 475-483.

Aldridge C, Maple J, Moller SG 2005 The molecular biology of plastid division in higher plants. J. Exp. Bot. 56: 1061-1077.

Allen AE, Vardi A, Bowler C 2006 An ecological and evolutionary context for integrated nitrogen metabolism and related signaling pathways in marine diatoms. Curr. Opin. Plant Biol. 9: 264-273.

Allen DK, Shachar-Hill Y, Ohlrogge JB 2007 Compartment-specific labeling information in (13)C metabolic flux analysis of plants. Phytochemistry 68: 2197-2210.

Allen TE, Palsson BO 2003 Sequence-based analysis of metabolic demands for protein synthesis in prokaryotes. J. Theor. Biol. 220: 1-18.

Allwood JW, Ellis DI, Heald JK, Goodacre R, Mur LA 2006 Metabolomic approaches reveal that phosphatidic and phosphatidyl glycerol phospholipids are major discriminatory non-polar metabolites in responses by Brachypodium distachyon to challenge by Magnaporthe grisea. Plant J. 46: 351-368.

Alm EJ, Huang KH, Price MN, Koche RP, Keller K, Dubchak IL, Arkin AP 2005 The MicrobesOnline Web site for comparative genomics. Genome Res. 15: 1015-1022.

Almaas E, Kovacs B, Vicsek T, Oltvai ZN, Barabasi AL 2004 Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature 427: 839-843.

Almaas E, Oltvai ZN, Barabasi AL 2005 The activity reaction core and plasticity of metabolic networks. PLoS Comput. Biol. 1: e68.

Alonso AP, Goffman FD, Ohlrogge JB, Shachar-Hill Y 2007 Carbon conversion efficiency and central metabolic fluxes in developing sunflower (Helianthus annuus L.) embryos. Plant J. 52: 296-308.

Alonso AP, Raymond P, Hernould M, Rondeau-Mouro C, de Graaf A, Chourey P, Lahaye M, Shachar-Hill Y, Rolin D, Dieuaide-Noubhani M 2007 A metabolic flux analysis to study the role of sucrose synthase in the regulation of the carbon partitioning in central metabolism in maize root tips. Metab. Eng. 9: 419-432.

Alonso AP, Raymond P, Rolin D, Dieuaide-Noubhani M 2007 Substrate cycles in the central metabolism of maize root tips under hypoxia. Phytochemistry 68: 2222-2231.

Alper H, Jin YS, Moxley JF, Stephanopoulos G 2005 Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli. Metab. Eng. 7: 155-164.

Alper H, Stephanopoulos G 2008 Uncovering the gene knockout landscape for improved lycopene production in E. coli. Appl. Microbiol. Biotechnol. 78: 801-810.

Altintas MM, Eddy CK, Zhang M, McMillan JD, Kompala DS 2006 Kinetic modeling to optimize pentose fermentation in Zymomonas mobilis. Biotechnol. Bioeng. 94: 273-295.

Alvarez-Vasquez F, Gonzalez-Alcon C, Torres NV 2000 Metabolism of citric acid production by Aspergillus niger: model definition, steady-state analysis and constrained optimization of citric acid production rate. Biotechnol. Bioeng. 70: 82-108.

Alvarez-Vasquez F, Sims KJ, Cowart LA, Okamoto Y, Voit EO, Hannun YA 2005 Simulation and validation of modelled sphingolipid metabolism in Saccharomyces cerevisiae. Nature 433: 425-430.

Alves R, Savageau MA 2000 Systemic properties of ensembles of metabolic networks: application of graphical and statistical methods to simple unbranched pathways. Bioinformatics 16: 534-547.

Alves R, Savageau MA 2000 Effect of overall feedback inhibition in unbranched biosynthetic pathways. Biophys. J. 79: 2290-2304.

An S, Kumar R, Sheets ED, Benkovic SJ 2008 Reversible compartmentalization of de novo purine biosynthetic complexes in living cells. Science 320: 103-106.

Ananieva K, Malbeck J, Kaminek M, van Staden J 2004 Methyl jasmonate down-regulates endogenous cytokinin levels in cotyledons of Cucurbita pepo (zucchini) seedlings. Physiol. Plant. 122: 496-503.

Ananieva K, Malbeck J, Kaminek M, van Staden J 2004 Changes in endogenous cytokinin levels in cotyledons of Cucurbita pepo (zucchini) during natural and dark-induced senescence. Physiol. Plant. 122: 133-142.

Ander M, Beltrao P, Di Ventura B, Ferkinghoff-Borg J, Foglierini M, Kaplan A, Lemerle C, Toma's-Oliveira I, Serrano L 2004 SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks. Syst. Biol. 1: 129-138.

Andersen DC, Swartz J, Ryll T, Lin N, Snedecor B 2001 Metabolic oscillations in an E. coli fermentation. Biotechnol. Bioeng. 75: 212-218.

Andersen MR, Nielsen J 2008 Current status of systems biology in Aspergilli. Fungal Genet. Biol. Jul 19 [Epub ahead of print].

Anderson KJ, Allen AP, Gillooly JF, Brown JH 2006 Temperature-dependence of biomass accumulation rates during secondary succession. Ecol. Lett. 9: 673-682.

Anderson MD, Che P, Song J, Nikolau BJ, Wurtele ES 1998 3-Methylcrotonyl-coenzyme A carboxylase is a component of the mitochondrial leucine catabolic pathway in plants. Plant Physiol. 118: 1127-1138.

Andria G, Parenti G, Melis D, Sebastio G 2000 Genetic testing of metabolic disorders. Minerva Biotecnologica 12: 65-69.

Anesiadis N, Cluett WR, Mahadevan R 2008 Dynamic metabolic engineering for increasing bioprocess productivity. Metab. Eng. Jun 17 [Epub ahead of print].

Angelaccio S, Chiaraluce R, Consalvi V, Buchenau B, Giangiacomo L, Bossa F, Contestabile R 2003 Catalytic and thermodynamic properties of tetrahydromethanopterin-dependent serine hydroxymethyltransferase from Methanococcus jannaschii. J. Biol. Chem. 278: 41789-41797.

Aniya Y, Anders MW 1989 Activation of rat liver microsomal glutathione S-transferase by reduced oxygen species. J. Biol. Chem. 264: 1998-2002.

Ankri S, Serebrijski I, Reyes O, Leblon G 1996 Mutations in the Corynebacterium glutamicum proline biosynthetic pathway: a natural bypass of th proA step. J. Bacteriol. 178: 4412-4419.

Antachopoulos C, Meletiadis J, Roilides E, Sein T, Sutton DA, Wickes BL, Rinaldi MG, Merz WG, Shea YR, Walsh TJ 2006 Relationship between metabolism and biomass of medically important zygomycetes. Med. Mycol. 44: 429-438.

Anterola AM, Lewis NG 2002 Trends in lignin modification: a comprehensive analysis of the effects of genetic manipulations/mutations on lignification and vascular integrity. Phytochemistry 61: 221-294.

Antoniewicz MR, Kelleher JK, Stephanopoulos G 2006 Determination of confidence intervals of metabolic fluxes estimated from stable isotope measurements. Metab. Eng. 8: 324-337.

Antoniewicz MR, Kelleher JK, Stephanopoulos G 2007 Elementary metabolite units (EMU): a novel framework for modeling isotopic distributions. Metab. Eng. 9: 68-86.

Antoniewicz MR, Kraynie DF, Laffend LA, González-Lergier J, Kelleher JK, Stephanopoulos G 2007 Metabolic flux analysis in a nonstationary system: fed-batch fermentation of a high yielding strain of E. coli producing 1,3-propanediol. Metab. Eng. 9: 277-292.

Antoniewicz MR, Stephanopoulos G, Kelleher JK 2006 Evaluation of regression models in metabolic physiology: predicting fluxes from isotopic data without knowledge of the pathway. Metabolomics 2: 41-52.

Aoki K, Ogata Y, Shibata D 2007 Approaches for extracting practical information from gene co-expression networks in plant biology. Plant Cell Physiol. 48: 381-390.

Aon JC, Cortassa S 2001 Involvement of nitrogen metabolism in the triggering of ethanol fermentation in aerobic chemostat cultures of Saccharomyces cerevisiae. Metab. Eng. 3: 250-264.

Appeldoorn NJG, de Bruijn SM, Koot-Gronsveld EAM, Visser RGF, Vreugdenhil D, van der Plas LHW 1997 Developmental changes of enzymes involved in conversion of sucrose to hexose-phosphate during early tuberisation of potato. Planta 202: 220-226.

Arai K, Lee K, Berthiaume F, Tompkins RG, Yarmush ML 2001 Intrahepatic amino acid and glucose metabolism in a D-galactosamine-induced rat liver failure model. Hepatology 34: 360-371.

Arakawa K, Suzuki H, Fujishima K, Fujimoto K, Ueda S, Matsui M, Tomita M 2005 A comprehensive software suite for the analysis of cDNAs. Genomics Proteomics Bioinformatics 3: 179-188.

Arakawa K, Yamada Y, Shinoda K, Nakayama Y, Tomita M 2006 GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes. BMC Bioinformatics 7: 168.

Aranibar N, Singh BK, Stockton GW, Ott KH 2001 Automated mode-of-action detection by metabolic profiling. Biochem. Biophys. Res. Commun. 286: 150-155.

Arauzo-Bravo MJ, Shimizu K 2001 Estimation of bidirectional metabolic fluxes from MS and NMR data using positional representations. Genome Inform. Ser. Workshop Genome Inform. 12: 63-72.

Arcak M, Sontag ED 2008 A passivity-based stability criterion for a class of biochemical reaction networks. Math. Biosci. Eng. 5: 1-19.

Aristidou A, Penttila M 2000 Metabolic engineering applications to renewable resource utilization. Curr. Opin. Biotechnol. 11: 187-198.

Aristidou AA, San KY, Bennett GN 1995 Metabolic engineering of Escherichia coli to enhance recombinant protein production through acetate reduction. Biotechnol. Prog. 11: 475-478.

Aristidou AA, San KY, Bennett GN 1999 Metabolic flux analysis of Escherichia coli expressing the Bacillus subtilis acetolactate synthase in batch and continuous cultures. Biotechnol. Bioeng. 63: 737-749.

Arita M 2003 In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism. Genome Res. 13: 2455-2466.

Arnholdt-Schmitt B, Costa JH, de Melo DF 2006 AOX - a functional marker for efficient cell reprogramming under stress? Trends Plant Sci. 11: 281-287.

Arpat AB, Waugh M, Sullivan JP, Gonzales M, Frisch D, Main D, Wood T, Leslie A, Wing RA, Wilkins TA 2004 Functional genomics of cell elongation in developing cotton fibers. Plant Mol. Biol. 54: 911-929.

Arrigoni O 1994 Ascorbate system in plant development. J. Bioenerg. Biomembr. 26: 407-419.

Arruda P, Kemper EL, Papes F, Leite A 2000 Regulation of lysine catabolism in higher plants. Trends Plant Sci. 5: 324-330.

Artzy-Randrup Y, Fleishman SJ, Ben-Tal N, Stone L 2004 Comment on “Network Motifs: Simple Building Blocks of Complex Networks” and “Superfamilies of Evolved and Designed Networks” Science 305: 1107c.

Asai T, Stone JM, Heard JE, Kovtun Y, Yorgey P, Sheen J, Ausubel FM 2000 Fumonisin B1-induced cell death in Arabidopsis protoplasts requires jasmonate-, ethylene-, and salicylate-dependent signaling pathways. Plant Cell 12: 1823-1836.

Asakura Y, Kimura E, Usuda Y, Kawahara Y, Matsui K, Osumi T, Nakamatsu T 2007 Altered metabolic flux due to deletion of odhA causes L-glutamate overproduction in Corynebacterium glutamicum. Appl. Environ. Microbiol. 73: 1308-1319.

Ashihara H, Sano H, Crozier A 2008 Caffeine and related purine alkaloids: biosynthesis, catabolism, function and genetic engineering. Phytochemistry 69: 841-856.

Ashihara H, Zheng XQ, Katahira R, Morimoto M, Ogita S, Sano H 2006 Caffeine biosynthesis and adenine metabolism in transgenic Coffea canephora plants with reduced expression of N-methyltransferase genes. Phytochemistry 67: 882-886.

Ashley MK, Grant M, Grabov A 2006 Plant responses to potassium deficiencies: a role for potassium transport proteins. J. Exp. Bot. 57: 425-436.

Asur S, Ucar D, Parthasarathy S 2007 An ensemble framework for clustering protein-protein interaction networks. Bioinformatics 23: i29-i40.

Athwal GS, Lombardo CR, Huber JL, Masters SC, Fu H, Huber SC 2000 Modulation of 14-3-3 protein interactions with target polypeptides by physical and metabolic effectors. Plant Cell Physiol. 41: 523-533.

Aubert S, Bligny R, Douce R, Gout E, Ratcliffe RG, Roberts JK 2001 Contribution of glutamate dehydrogenase to mitochondrial glutamate metabolism studied by 13C and 31P nuclear magnetic resonance. J. Exp. Bot. 52: 37-45.

Aubert S, Gout E, Bligny R, MartyMazars D, Barrieu F, Alabouvette J, Marty F, Douce R 1996 Ultrastructural and biochemical characterization of autophagy in higher plant cells subjected to carbon deprivation: control by the supply of mitochondria with respiratory substrates. J. Cell Biol. 133: 1251-1263.

Augoustides-Savvopoulou P, Luka Z, Karyda S, Stabler SP, Allen RH, Patsiaoura K, Wagner C, Mudd SH 2003 Glycine N-methyltransferase deficiency: a new patient with a novel mutation. J. Inherit. Metab. Dis. 26: 745-759.

Avila MA, Corrales FJ, Ruiz F, Sanchez-Gongora E, Mingorance J, Carretero MV, Mato IM 1998 Specific interaction of methionine adenosyltransferase with free radicals. Biofactors 8: 27-32.

Azevedo RA, Lancien M, Lea PJ 2006 The aspartic acid metabolic pathway, an exciting and essential pathway in plants. Amino Acids 30: 143-162.

Babb VM, Haigler CH 2001 Sucrose phosphate synthase activity rises in correlation with high-rate cellulose synthesis in three heterotrophic systems. Plant Physiol. 127: 1234-1242.

Bachelard H, Badar-Goffer R, Ben-Yoseph O, Morris P, Thatcher N 1993 Studies on metabolic regulation using NMR spectroscopy. Dev. Neurosci. 15: 207-215.

Bachmann M, McMichael RW Jr, Huber JL, Kaiser WM, Huber SC 1995 Partial purification and characterization of a calcium-dependent protein kinase and an inhibitor protein required for inactivation of spinach leaf nitrate reductase. Plant Physiol. 108: 1083-1091.

Backhausen JE, Klein M, Klocke M, Jung S, Scheibe R 2005 Salt tolerance of potato (Solanum tuberosum L. var. Desire'e) plants depends on light intensity and air humidity. Plant Sci. 169: 229-237.

Badger MR, Bek EJ 2008 Multiple Rubisco forms in proteobacteria: their functional significance in relation to CO2 acquisition by the CBB cycle. J. Exp. Bot. 59: 1525-1541.

Baginsky S, Gruissem W 2004 Chloroplast proteomics: potentials and challenges. J. Exp. Bot. 55: 1213-1220.

Bago B, Pfeffer PE, Douds Jr DD, Brouillette J, Becard G, Shachar-Hill Y 1999 Carbon metabolism in spores of the arbuscular mycorrhizal fungus Glomus intraradices as revealed by nuclear magnetic resonance spectroscopy. Plant Physiol. 121: 263-272.

Bahar I, Jernigan RL 1999 Cooperative fluctuations and subunit communication in tryptophan synthase. Biochemistry 38: 3478-3490.

Bai C, Reilly CC, Wood BW 2006 Nickel deficiency disrupts metabolism of ureides, amino acids, and organic acids of young pecan foliage. Plant Physiol. 140: 433-443.

Baier M, Dietz KJ 2005 Chloroplasts as source and target of cellular redox regulation: a discussion on chloroplast redox signals in the context of plant physiology. J. Exp. Bot. 56: 1449-1462.

Bailey JE 1991 Toward a science of metabolic engineering. Science 252: 1668-1675.

Bailey JE 2001 Reflections on the scope and the future of metabolic engineering and its connections to functional genomics and drug discovery. Metab. Eng. 3: 111-114.

Bailey JE 1999 Lessons from metabolic engineering for functional genomics and drug discovery. Nat. Biotechnol. 17: 616-618.

Bailly J, Debaud JC, Verner MC, Plassard C, Chalot M, Marmeisse R, Fraissinet-Tachet L 2007 How does a symbiotic fungus modulate expression of its host-plant nitrite reductase? New Phytol. 175: 155-165.

Bajic VB, Veronika M, Veladandi PS, Meka A, Heng MW, Rajaraman K, Pan H, Swarup S 2005 Dragon Plant Biology Explorer. A text-mining tool for integrating associations between genetic and biochemical entities with genome annotation and biochemical terms lists. Plant Physiol. 138: 1914-1925.

Bak S, Olsen CE, Petersen BL, Moller BL, Halkier BA 1999 Metabolic engineering of p-hydroxybenzylglucosinolate in Arabidopsis by expression of the cyanogenic CYP79A1 from Sorghum bicolor. Plant J. 20: 663-671.

Bak S, Tax FE, Feldmann KA, Galbraith DW, Feyereisen R 2001 CYP83B1, a cytochrome P450 at the metabolic branch point in auxin and indole glucosinolate biosynthesis in Arabidopsis. Plant Cell 13: 101-111.

Baker DH 2005 Comparative nutrition and metabolism: explication of open questions with emphasis on protein and amino acids. Proc. Natl. Acad. Sci. U.S.A. 102: 17897-1902.

Balaban RS 2006 Modeling mitochondrial function. Am. J. Physiol. Cell Physiol. 291: C1107-C1113.

Baldet P, Devaux C, Chevalier C, Brouquisse R, Just D, Raymond P 2002 Contrasted responses to carbohydrate limitation in tomato fruit at two stages of development. Plant Cell Environ. 25: 1639-1649.

Bali M, Thomas SR 2001 A modelling study of feedforward activation in human erythrocyte glycolysis. C. R. Acad. Sci. III 324: 185-199.

Balibrea Lara ME, Gonzalez Garcia MC, Fatima T, Ehness R, Lee TK, Proels R, Tanner W, Roitsch T 2004 Extracellular invertase is an essential component of cytokinin-mediated delay of senescence. Plant Cell 16: 1276-1287.

Balmer Y, Vensel WH, DuPont FM, Buchanan BB, Hurkman WJ 2006 Proteome of amyloplasts isolated from developing wheat endosperm presents evidence of broad metabolic capability. J. Exp. Bot. 57: 1591-1602.

Balsa-Canto E, Alonso AA, Banga JR 2008 Computational procedures for optimal experimental design in biological systems. IET Syst. Biol. 2: 163.

Balsa-Canto E, Peifer M, Banga JR, Timmer J, Fleck C 2008 Hybrid optimization method with general switching strategy for parameter estimation. BMC Syst. Biol. 2: 26.

Baltz RH 2001 Genetic methods and strategies for secondary metabolite yield improvement in actinomycetes. Antonie Van Leewenhoek 79: 251-259.

Banerjee R, Vitvitsky V, Garg SK 2008 The undertow of sulfur metabolism on glutamatergic neurotransmission. Trends Biochem. Sci. Aug 12 [Epub ahead of print].

Bang JW, Crockford DJ, Holmes E, Pazos F, Sternberg MJ, Muggleton SH, Nicholson JK 2008 Integrative top-down system metabolic modeling in experimental disease states via data-driven Bayesian methods. J. Proteome Res. 7: 497-503.

Banga JR. 2008 Optimization in computational systems biology BMC Syst. Biol. 2: 47.

Banta S, Vemula M, Yokoyama T, Jayaraman A, Berthiaume F, Yarmush ML 2007 Contribution of gene expression to metabolic fluxes in hypermetabolic livers induced through burn injury and cecal ligation and puncture in rats. Biotechnol. Bioeng. 97: 118-137.

Baptista T, Costa E 2008 Evolution of a multi-agent system in a cyclical environment. Theory Biosci. 127: 141-148.

Barakat A, Wall K, Leebens-Mack J, Wang YJ, Carlson JE, Depamphilis CW 2007 Large-scale identification of microRNAs from a basal eudicot (Eschscholzia californica) and conservation in flowering plants. Plant J. 51: 991-1003.

Barbier G, Oesterhelt C, Larson MD, Halgren RG, Wilkerson C, Garavito RM, Benning C, Weber AP 2005 Comparative genomics of two closely related unicellular thermo-acidophilic red algae, Galdieria sulphuraria and Cyanidioschyzon merolae, reveals the molecular basis of the metabolic flexibility of Galdieria sulphuraria and significant differences… Plant Physiol. 137: 460-474.

Barcala M, García A, Cubas P, Almoguera C, Jordano J, Fenoll C, Escobar C 2008 Distinct heat-shock element arrangements that mediate the heat shock, but not the late-embryogenesis induction of small heat-shock proteins, correlate with promoter activation in root-knot nematode feeding cells. Plant Mol. Biol. 66: 151-164.

Bardey V, Vallet C, Robas N, Charpentier B, Thouvenot B, Mougin A, Hajnsdorf E, Regnier P, Springer M, Branlant C 2005 Characterization of the molecular mechanisms involved in the differential production of erythrose-4-phosphate dehydrogenase, 3-phosphoglycerate kinase and class II fructose-1,6-bisphosphate aldolase in Escherichia coli. Mol. Microbiol. 57: 1265-1287.

Baroja-Fernandez E, Munoz FJ, Akazawa T, Pozueta-Romero J 2001 Reappraisal of the currently prevailing model of starch biosynthesis in photosynthetic tissues: a proposal involving the cytosolic production of ADP-glucose by sucrose synthase and occurrence of cyclic turnover of starch in the chloroplast. Plant Cell Physiol. 42: 1311-1320.

Baroux C, Fransz P, Grossniklaus U 2004 Nuclear fusions contribute to polyploidization of the gigantic nuclei in the chalazal endosperm of Arabidopsis. Planta 220: 38-46.

Barr J, White WS, Chen L, Bae H, Rodermel S 2004 The GHOST terminal oxidase regulates developmental programming in tomato fruit. Plant Cell Environ. 27: 840-852.

Barrett PH, Bell BM, Cobelli C, Golde H, Schumitzky A, Vicini P, Foster DM 1998 SAAM II: Simulation, Analysis, and Modeling Software for tracer and pharmacokinetic studies. Metabolism 47: 484-492.

Barrett PH, Chan DC, Watts GF 2006 Thematic review series: patient-oriented research. Design and analysis of lipoprotein tracer kinetics studies in humans. J. Lipid Res. 47: 1607-1619.

Barrick JE, Breaker RR 2007 The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biol. 8: R239.

Barry RC, Young MJ, Stedman KM, Dratz EA 2006 Proteomic mapping of the hyperthermophilic and acidophilic archaeon Sulfolobus solfataricus P2. Electrophoresis 27: 2970-2983.

Barsch A, Carvalho HG, Cullimore JV, Niehaus K 2006 GC-MS based metabolite profiling implies three interdependent ways of ammonium assimilation in Medicago truncatula root nodules. J. Biotechnol. 127: 79-83.

Bassingthwaighte JB 2001 The modelling of a primitive 'sustainable' conservative cell. Phil. Trans. Roy. Soc. Lond. B. Math. Eng. Sci. 359: 1055-1072.

Batista D, Fonseca S, Serrazina S, Figueiredo A, Pais MS 2008 Efficient and stable transformation of hop (Humulus lupulus L.) var. Eroica by particle bombardment. Plant Cell Rep. 27: 1185-1196.

Batistic O, Kudla J 2004 Integration and channeling of calcium signaling through the CBL calcium sensor/CIPK protein kinase network. Planta 219: 915-924.

Baud S, Mendoza MS, To A, Harscoet E, Lepiniec L, Dubreucq B 2007 WRINKLED1 specifies the regulatory action of LEAFY COTYLEDON2 towards fatty acid metabolism during seed maturation in Arabidopsis. Plant J. 50: 825-838.

Baud S, Wuilleme S, Dubreucq B, de Almeida A, Vuagnat C, Lepiniec L, Miquel M, Rochat C 2007 Function of plastidial pyruvate kinases in seeds of Arabidopsis thaliana. Plant J. 52: 405-419.

Baudouin E, Pieuchot L, Engler G, Pauly N, Puppo A 2006 Nitric oxide is formed in Medicago truncatula-Sinorhizobium meliloti functional nodules. Mol. Plant Microbe Interact. 19: 970-975.

Bauer M, Hamm AC, Bonaus M, Jacob A, Jaekel J, Schorle H, Pankratz MJ, Katzenberger JD 2004 Starvation response in mouse liver shows strong correlation with life-span-prolonging processes. Physiol. Genomics 17: 230-244.

Baxter CJ, Carrari F, Bauke A, Overy S, Hill SA, Quick PW, Fernie AR, Sweetlove LJ 2005 Fruit carbohydrate metabolism in an introgression line of tomato with increased fruit soluble solids. Plant Cell Physiol. 46: 425-437.

Baxter CJ, Liu JL, Fernie AR, Sweetlove LJ 2007 Determination of metabolic fluxes in a non-steady-state system. Phytochemistry 68: 2313-2319.

Baxter CJ, Redestig H, Schauer N, Repsilber D, Patil KR, Nielsen J, Selbig J, Liu J, Fernie AR, Sweetlove LJ 2007 The metabolic response of heterotrophic Arabidopsis cells to oxidative stress. Plant Physiol. 143: 312-325.

Baxter CJ, Sabar M, Quick WP, Sweetlove LJ 2005 Comparison of changes in fruit gene expression in tomato introgression lines provides evidence of genome-wide transcriptional changes and reveals links to mapped QTLs and described traits. J. Exp. Bot. 56: 1591-1604.

Bayram M 1996 Automatic analysis of the control of metabolic networks. Comput. Biol. Med. 26: 401-408.

Beard DA, Liang SD, Qian H 2002 Energy balance for analysis of complex metabolic networks. Biophys. J. 83: 79-86.

Beck EH, Fettig S, Knake C, Hartig K, Bhattarai T 2007 Specific and unspecific responses of plants to cold and drought stress. J. Biosci. 32: 501-510.

Beck F, Blasius B, Luttge U, Neff R, Rascher U 2001 Stochastic noise interferes coherently with a model biological clock and produces specific dynamic behaviour. Proc. R. Soc. Lond. B. Biol. Sci. 268: 1307-1313.

Becker J, Klopprogge C, Wittmann C 2008 Metabolic responses to pyruvate kinase deletion in lysine producing Corynebacterium glutamicum. Microb. Cell Fact. 7: 8.

Becker J, Klopprogge C, Zelder O, Heinzle E, Wittmann C 2005 Amplified expression of fructose 1,6-bisphosphatase in Corynebacterium glutamicum increases in vivo flux through the pentose phosphate pathway and lysine production on different carbon sources. Appl. Environ. Microbiol. 71: 8587-8596.

Becker SA, Feist AM, Mo ML, Hannum G, Palsson BO, Herrgard MJ 2007 Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat. Protoc. 2: 727-738.

Becker SA, Palsson BO 2005 Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation. BMC Microbiol. 5: 8.

Becker SA, Palsson BO 2008 Context-specific metabolic networks are consistent with experiments. PLoS Comput. Biol. 4: e1000082.

Becker SA, Palsson BO 2008 Three factors underlying incorrect in silico predictions of essential metabolic genes. BMC Syst. Biol. 2: 14.

Becker SA, Price ND, Palsson BO 2006 Metabolite coupling in genome-scale metabolic networks. BMC Bioinformatics 7: 111.

Beckett RP, Minibayeva FV, Luthje S, Bottger M 2004 Reactive oxygen species metabolism in desiccation-stressed thalli of the liverwort Dumortiera hirsuta. Physiol. Plant. 122: 3-10.

Beckett RP, Minibayeva FV, Vylegzhanina NN, Tolpysheva T 2003 High rates of extracellular superoxide production by lichens in the suborder Peltigerineae correlate with indices of high metabolic activity. Plant Cell Environ. 26: 1827-1837.

Beckman KB, Ames BN 1998 The free radical theory of aging matures. Physiol. Rev. 78: 547-581.

Bede JC, Musser RO, Felton GW, Korth KL 2006 Caterpillar herbivory and salivary enzymes decrease transcript levels of Medicago truncatula genes encoding early enzymes in terpenoid biosynthesis. Plant Mol. Biol. 60: 519-531.

Bednarek P, Schneider B, Svatos A, Oldham NJ, Hahlbrock K 2005 Structural complexity, differential response to infection, and tissue specificity of indolic and phenylpropanoid secondary metabolism in Arabidopsis roots. Plant Physiol. 138: 1058-1070.

Beekwilder J, Alvarez-Huerta M, Neef E, Verstappen FW, Bouwmeester HJ, Aharoni A 2004 Functional characterization of enzymes forming volatile esters from strawberry and banana. Plant Physiol. 135: 1865-1878.

Beerling DJ, Rundgren M 2000 Leaf metabolic and morphological responses of dwarf willow (Salix herbacea) in the sub-arctic to the past 9000 years of global environmental change. New Phytol. 145: 257-269.

Behrenfeld MJ, Prasil O, Babin M, Bruyant F 2004 In search of a physiological basis for covariations in light-limited and light-saturated photosynthesis. J. Phycol. 40: 4-25.

Bekaert S, Storozhenko S, Mehrshahi P, Bennett MJ, Lambert W, Gregory JF 3rd, Schubert K, Hugenholtz J, Van Der Straeten D, Hanson AD 2008 Folate biofortification in food plants. Trends Plant Sci. 13: 28-35.

Bell KS, Sebaihia M, Pritchard L, Holden MT, Hyman LJ, Holeva MC, Thomson NR, Bentley SD, Churcher LJ, Mungall K, Atkin R, Bason N, Brooks K, Chillingworth T, Clark K, Doggett J, Fraser A, Hance Z, Hauser H, Jagels K, Moule S, Norbertczak H, et al 2004 Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors. Proc. Natl. Acad. Sci. U.S.A. 101: 11105-11110.

Bellazzi R, Guglielmann R, Ironi L, Patrini C 2001 A hybrid input-output approach to model metabolic systems: an application to intracellular thiamine kinetics. J. Biomed. Inform. 34: 221-248.

Belles JM, Garro R, Pallas V, Fayos J, Rodrigo I, Conejero V 2006 Accumulation of gentisic acid as associated with systemic infections but not with the hypersensitive response in plant-pathogen interactions. Planta 223: 500-511.

Bellin D, Schulz B, Soerensen TR, Salamini F, Schneider K 2007 Transcript profiles at different growth stages and tap-root zones identify correlated developmental and metabolic pathways of sugar beet. J. Exp. Bot. 58: 699-715.

Ben Zvi MM, Negre-Zakharov F, Masci T, Ovadis M, Shklarman E, Ben-Meir H, Tzfira T, Dudareva N, Vainstein A 2008 Interlinking showy traits: co-engineering of scent and colour biosynthesis in flowers. Plant Biotechnol. J. 6: 403-415.

Bender-Machado L, Bauerlein M, Carrari F, Schauer N, Lytovchenko A, Gibon Y, Kelly AA, Loureiro M, Muller-Rober B, Willmitzer L, Fernie AR 2004 Expression of a yeast acetyl CoA hydrolase in the mitochondrion of tobacco plants inhibits growth and restricts photosynthesis. Plant Mol. Biol. 55: 645-662.

Benderoth M, Textor S, Windsor AJ, Mitchell-Olds T, Gershenzon J, Kroymann J 2006 Positive selection driving diversification in plant secondary metabolism. Proc. Natl. Acad. Sci. U.S.A. 103: 9118-9123.

Bennett MR, Pang WL, Ostroff NA, Baumgartner BL, Nayak S, Tsimring LS, Hasty J 2008 Metabolic gene regulation in a dynamically changing environment. Nature Jul 30 [Epub ahead of print].

Benning C, Stitt M 2004 Physiology and metabolism; reacting to the full complexity of metabolic pathways in a postgenomic era. Curr. Opin. Plant Biol. 7: 231-234.

Berger F, Ramirez-Hernandez MH, Ziegler M 2004 The new life of a centenarian: signalling functions of NAD(P). Trends Biochem. Sci. 29: 111-118.

Bergman RN 1988 Modeling in nutrition and metabolism. Prog. Food Nutr. Sci. 12: 211-225.

Berlett BS, Levine RL, Stadtman ER 1998 Carbon dioxide stimulates peroxynitrite-mediated nitration of tyrosine residues and inhibits oxidation of methionine residues of glutamine synthetase: both modifications mimic effects of adenylylation. Proc. Natl. Acad. Sci. U.S.A. 95: 2784-2789.

Berlin J, Fecker LF 2000 Chapter 10. Genetic Engineering of Enzymes Diverting Amino Acids into Secondary Metabolism. In "Metabolic Engineering of Plant Secondary Metabolism" (Verpoorte R, Alfermann AW, eds), Kluwer Academic Publishers, Dortrecht, The Netherlands, pp. 195-216.

Bermudez L, Urias U, Milstein D, Kamenetzky L, Asis R, Fernie AR, Van Sluys MA, Carrari F, Rossi M 2008 A candidate gene survey of quantitative trait loci affecting chemical composition in tomato fruit. J. Exp. Bot. 59: 2875-2890.

Berrios-Rivera SJ, Bennett GN, San KY 2002 Metabolic engineering of Escherichia coli: increase of NADH availability by overexpressing an NAD(+)-dependent formate dehydrogenase. Metab. Eng. 4: 217-229.

Berrios-Rivera SJ, Bennett GN, San KY 2002 The effect of increasing NADH availability on the redistribution of metabolic fluxes in Escherichia coli chemostat cultures. Metab. Eng. 4: 230-237.

Berrios-Rivera SJ, San KY, Bennett GN 2002 The effect of NAPRTase overexpression on the total levels of NAD, the NADH/NAD+ ratio, and the distribution of metabolites in Escherichia coli. Metab. Eng. 4: 238-247.

Berrios-Rivera SJ, Yang YT, Bennett GN, San KY 2000 Effect of glucose analog supplementation on metabolic flux distribution in anaerobic chemostat cultures of Escherichia coli. Metab. Eng. 2: 149-154.

Berry A, Bhatnagar RK, Jensen RA 1987 Enzymic basis for leakiness of auxotrophs for phenylalanine in Pseudomonas aeruginosa. J. Gen. Microbiol. 133: 3257-3263.

Bertail P, Clemencon S, Tressou J 2008 A storage model with random release rate for modeling exposure to food contaminants. Math. Biosci. Eng. 5: 35-60.

Berthiaume F, MacDonald AD, Kang YH, Yarmush ML 2003 Control analysis of mitochondrial metabolism in intact hepatocytes: effect of interleukin-1beta and interleukin-6. Metab. Eng. 5: 108-123.

Berthon HA, Bubb WA, Kuchel PW 1993 13C NMR isotopomer and computer-simulation studies of the nonoxidative pentose-phosphate pathway of human erythrocytes. Biochem. J. 296: 379-387.

Berthoud H 2002 Multiple neural systems controlling food intake and body weight. Neurosci. Biobehav. Rev. 26: 393.

Bertram R, Wunsche A, Sprehe M, Hillen W 2006 Regulated expression of HPrK/P does not affect carbon catabolite repression of the xyn operon and of rocG in Bacillus subtilis. FEMS Microbiol. Lett. 259: 147-152.

Betenbaugh M, Bentley W 2008 Metabolic engineering in the 21st century: meeting global challenges of sustainability and health. Curr. Opin. Biotechnol. Aug 18 [Epub ahead of print].

Beun JJ, Dircks K, Van Loosdrecht MC, Heijnen JJ 2002 Poly-beta-hydroxybutyrate metabolism in dynamically fed mixed microbial cultures. Water Res. 36: 1167-1180.

Bevins MA, Madhavan S, Markwell J 1993 Two sweetclover (Melilotus alba Desr.) mutants temperature sensitive for chlorophyll expression. Plant Physiol. 103: 1123-1131.

Beylot M 1996 Regulation of in vivo ketogenesis: role of free fatty acids and control by epinephrine, thyroid hormones, insulin and glucagon. Diabetes Metab. 22: 299-304.

Bhadury P, Wright PC 2004 Exploitation of marine algae: biogenic compounds for potential antifouling applications. Planta 219: 561-578.

Bharali B, Bates JW 2006 Detoxification of dissolved SO2 (bisulfite) by terricolous mosses. Ann. Bot. (Lond.) 97: 257-263.

Bhattacharya S, Chakrabarti S, Nayak A, Bhattacharya SK 2003 Metabolic networks of microbial systems. Microbial Cell Factories 2: 3.

Bibiano Melo JF, Lundstedt LM, Meton I, Baanante IV, Moraes G 2006 Effects of dietary levels of protein on nitrogenous metabolism of Rhamdia quelen (Teleostei: Pimelodidae). Comp. Biochem. Physiol. A. Mol. Integr. Physiol. 145: 181-187.

Bicknell LS, Pitt J, Aftimos S, Ramadas R, Maw MA, Robertson SP 2008 A missense mutation in ALDH18A1, encoding Delta(1)-pyrroline-5-carboxylate synthase (P5CS), causes an autosomal recessive neurocutaneous syndrome. Eur. J. Hum. Genet. May 14 [Epub ahead of print].

Biemelt S, Hajirezaei MR, Melzer M, Albrecht G, Sonnewald U 1999 Sucrose synthase activity does not restrict glycolysis in roots of transgenic potato plants under hypoxic conditions. Planta 210: 41-49.

Bier DM 1997 Stable isotopes in biosciences, their measurement and models for amino acid metabolism. Eur. J. Pediatr. 156: S2-S8.

Bilu Y, Shlomi T, Barkai N, Ruppin E 2006 Conservation of expression and sequence of metabolic genes is reflected by activity across metabolic states. PLoS Comput. Biol. 2: e106.

Bindschedler LV, Palmblad M, Cramer R 2008 Hydroponic isotope labelling of entire plants (HILEP) for quantitative plant proteomics; an oxidative stress case study. Phytochemistry 69: 1962-1972.

Bishop L, Kanoff R, Charnas L, Krenzel C, Berry SA, Schimmenti LA 2008 Severe methylenetetrahydrofolate reductase (MTHFR) deficiency: a case report of nonclassical homocystinuria. J, Child. Neurol. 23: 823-828.

Biswas D, Das SK, Roy S 2008 Importance of scaling exponents and other parameters in growth mechanism: an analytical approach. Theory Biosci. 127: 271-276.

Blank LM, Ebert BE, Buhler B, Schmid A 2008 Metabolic capacity estimation of Escherichia coli as a platform for redox biocatalysis: constraint-based modeling and experimental verification. Biotechnol. Bioeng. 100: 1050-1065.

Blank LM, Kuepfer L, Sauer U 2005 Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast. Genome Biol. 6: R49.

Blank LM, Lehmbeck F, Sauer U 2005 Metabolic-flux and network analysis in fourteen hemiascomycetous yeasts. FEMS Yeast Res. 5: 545-558.

Blankenship RE 1992 Origin and early evolution of photosynthesis. Photosynth. Res. 33: 91-111.

Blaschke L, Legrand M, Mai C, Polle A 2004 Lignification and structural biomass production in tobacco with suppressed caffeic/5-hydroxy ferulic acid-O-methyl transferase activity under ambient and elevated CO concentrations. Physiol. Plant. 121: 75-83.

Blasing OE, Gibon Y, Gunther M, Hohne M, Morcuende R, Osuna D, Thimm O, Usadel B, Scheible WR, Stitt M 2005 Sugars and circadian regulation make major contributions to the global regulation of diurnal gene expression in Arabidopsis. Plant Cell 17: 3257-3281.

Blatt MR, Maurousset L, Meharg AA 1997 High-affinity NO(3-)-H+ cotransport in the fungus Neurospora: induction and control by pH and membrane voltage. J. Membr. Biol. 160: 59-76.

Bleakley K, Biau G, Vert JP 2007 Supervised reconstruction of biological networks with local models. Bioinformatics 23: i57-i65.

Bligny R, Douce R 2001 NMR and plant metabolism. Curr. Opin. Plant Biol. 4: 191-196.

Blom J, De Mattos MJ, Grivell LA 2000 Redirection of the respiro-fermentative flux distribution in Saccharomyces cerevisiae by overexpression of the transcription factor Hap4p. Appl. Environ. Microbiol. 66: 1970-1973.

Boatright J, Negre F, Chen X, Kish CM, Wood B, Peel G, Orlova I, Gang D, Rhodes D, Dudareva N 2004 Understanding in vivo benzenoid metabolism in petunia petal tissue. Plant Physiol. 135: 1993-2011.

Bodei C, Bracciali A, Chiarugi D 2008 On deducing causality in metabolic networks. BMC Bioinformatics 9 Suppl. 4: S8.

Bogdan JA, Nazario-Larrieu J, Sarwar J, Alexander P, Blake MS 2001 Bordetella pertussis autoregulates pertussis toxin production through the metabolism of cysteine. Infect. Immun. 69: 6823-6830.

Bogdanova N, Hell R 1997 Cysteine synthesis in plants: protein-protein interactions of serine acetyltransferase from Arabidopsis thaliana. Plant J. 11: 251-262.

Boghigian BA, Pfeifer BA 2008 Current status, strategies, and potential for the metabolic engineering of heterologous polyketides in Escherichia coli. Biotechnol. Lett. 30: 1323-1330.

Bohlmann J, Keeling CI 2008 Terpenoid biomaterials. Plant J. 54: 656-669.

Bohnensack R 1985 Theory of steady-state control in complex metabolic networks. Biomed. Biochim. Acta 44: 1567-1578.

Bohnert HJ, Sheveleva E 1998 Plant stress adaptations--making metabolism move. Curr. Opin. Plant Biol. 1: 267-274.

Boldt R, Edner C, Kolukisaoglu U, Hagemann M, Weckwerth W, Wienkoop S, Morgenthal K, Bauwe H 2005 D-GLYCERATE 3-KINASE, the last unknown enzyme in the photorespiratory cycle in Arabidopsis, belongs to a novel kinase family. Plant Cell 17: 2413-2420.

Bollard ME, Xu J, Purcell W, Griffin JL, Quirk C, Holmes E, Nicholson JK 2002 Metabolic profiling of the effects of D-galactosamine in liver spheroids using (1)H NMR and MAS-NMR spectroscopy. Chem. Res. Toxicol. 15: 1351-1359.

Bolling C, Fiehn O 2005 Metabolite profiling of Chlamydomonas reinhardtii under nutrient deprivation. Plant Physiol. 139: 1995-2005.

Bolotin A, Mauger S, Malarme K, Ehrlich SD, Sorokin A 1999 Low-redundancy sequencing of the entire Lactococcus lactis IL1403 genome. Antonie Van Leeuwenhoek 76: 27-76.

Bonarius HP, Houtman JH, de Gooijer CD, Tramper J, Schmid G 1998 Activity of glutamate dehydrogenase is increased in ammonia-stressed hybridoma cells. Biotechnol. Bioeng. 57: 447-453.

Bonarius HP, Timmerarends B, de Gooijer CD, Tramper J 1998 Metabolite-balancing techniques vs. 13C tracer experiments to determine metabolic fluxes in hybridoma cells. Biotechnol. Bioeng. 58: 258-262.

Bonarius HPJ, Schmid G, Tramper J 1997 Flux analysis of underdetermined metabolic networks: the quest for the missing constraints. Trends Biotechnol. 15: 308-314.

Bonaventure G, Bao X, Ohlrogge J, Pollard M 2004 Metabolic responses to the reduction in palmitate caused by disruption of the FATB gene in Arabidopsis. Plant Physiol. 135: 1269-1279.

Boneh A, Korman SH, Sato K, Kanno J, Matsubara Y, Lerer I, Ben-Neriah Z, Kure S 2005 A single nucleotide substitution that abolishes the initiator methionine codon of the GLDC gene is prevalent among patients with glycine encephalopathy in Jerusalem. J. Hum. Genet. 50: 230-234.

Bongaerts J, Kramer M, Muller U, Raeven L, Wubbolts M 2001 Metabolic engineering for microbial production of aromatic amino acids and derived compounds. Metab. Eng. 3: 289-300.

Bonner ER, Cahoon RE, Knapke SM, Jez JM 2005 Molecular basis of cysteine biosynthesis in plants: structural and functional analysis of O-acetylserine sulfhydrylase from Arabidopsis thaliana. J. Biol. Chem. 280: 38803-38013.

Bono H, Ogata H, Goto S, Kanehisa M 1998 Reconstruction of amino acid biosynthesis pathways from the complete genome sequence. Genome Res. 8: 203-210.

Bonomo J, Warnecke T, Hume P, Marizcurrena A, Gill RT 2006 A comparative study of metabolic engineering anti-metabolite tolerance in Escherichia coli. Metab. Eng. 8: 227-239.

Booth G 1997 Gecko: a continuous 2D world for ecological modeling. Artif Life 3: 147-163.

Bork P, Dandekar T, Diaz-Lazcoz Y, Eisenhaber F, Huynen M, Yuan YP 1998 Predicting function: from genes to genomes and back. J. Mol. Biol. 283: 707-725.

Borland A, Elliott S, Patterson S, Taybi T, Cushman J, Pater B, Barnes J 2006 Are the metabolic components of Crassulacean acid metabolism up-regulated in response to an increase in oxidative burden? J. Exp. Bot. 57: 319-328.

Borland AM, Taybi T 2004 Synchronization of metabolic processes in plants with Crassulacean acid metabolism. J. Exp. Bot. 55: 1255-1265.

Borodina I, Krabben P, Nielsen J 2005 Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism. Genome Res. 15: 820-829.

Borodina I, Scholler C, Eliasson A, Nielsen J 2005 Metabolic network analysis of Streptomyces tenebrarius, a Streptomyces species with an active Entner-Doudoroff pathway. Appl. Environ. Microbiol. 71: 2294-2302.

Borodina I, Siebring J, Zhang J, Smith CP, van Keulen G, Dijkhuizen L, Nielsen J 2008 Antibiotic overproduction in Streptomyces coelicolor A3(2) mediated by phosphofructokinase deletion. J. Biol. Chem. Jul 7 [Epub ahead of print].

Bost B, Dillmann C, de Vienne D 1999 Fluxes and metabolic pools as model traits for quantitative genetics. I. The L-shaped distribution of gene effects. Genetics 153: 2001-2012.

Botella-Pavia P, Besumbes O, Phillips MA, Carretero-Paulet L, Boronat A, Rodriguez-Concepcion M 2004 Regulation of carotenoid biosynthesis in plants: evidence for a key role of hydroxymethylbutenyl diphosphate reductase in controlling the supply of plastidial isoprenoid precursors. Plant J. 40: 188-199.

Both M, Csukai M, Stumpf MP, Spanu PD 2005 Gene expression profiles of Blumeria graminis indicate dynamic changes to primary metabolism during development of an obligate biotrophic pathogen. Plant Cell 17: 2107-2122.

Bottcher C, Roepenack-Lahaye EV, Schmidt J, Schmotz C, Neumann S, Scheel D, Clemens S 2008 Metabolome analysis of biosynthetic mutants reveals diversity of metabolic changes and allows identification of a large number of new compounds in Arabidopsis thaliana. Plant Physiol. 147: 2107-2120.

Bottiglieri T, Hyland K, Reynolds EH 1994 The clinical potential of ademetionine (S-adenosylmethionine) in neurological disorders. Drugs 48: 137-152.

Bouche N, Fait A, Bouchez D, Moller SG, Fromm H 2003 Mitochondrial succinic-semialdehyde dehydrogenase of the gamma-aminobutyrate shunt is required to restrict levels of reactive oxygen intermediates in plants. Proc. Natl. Acad. Sci. U.S.A. 100: 6843-6848.

Boudet AM 2007 Evolution and current status of research in phenolic compounds. Phytochemistry 68: 2722-2735.

Bowling FG, Morgan TJ 2005 Krebs cycle anions in metabolic acidosis. Crit. Care 9: E23.

Boxer AL, Kramer JH, Johnston K, Goldman J, Finley R, Miller BL 2005 Executive dysfunction in hyperhomocystinemia responds to homocysteine-lowering treatment. Neurology 64: 1431-1434.

Boyer JS, Westgate ME 2004 Grain yields with limited water. J. Exp. Bot. 55: 2385-2394.

Brana MF, Sanchez-Migallon A 2006 Anticancer drug discovery and pharmaceutical chemistry: a history. Clin. Transl. Oncol. 8: 717-728.

Branco-Price C, Kaiser KA, Jang CJ, Larive CK, Bailey-Serres J 2008 Selective mRNA translation coordinates energetic and metabolic adjustments to cellular oxygen deprivation and reoxygenation in Arabidopsis thaliana. Plant J. Jul 28 [Epub ahead of print].

Brand MD 1996 Top down metabolic control analysis. J. Theor. Biol. 182: 351-360.

Brand MD 1998 Top-down elasticity analysis and its application to energy metabolism in isolated mitochondria and intact cells. Mol. Cell Biochem. 184: 13-20.

Brand MD, Curtis RK 2002 Simplifying metabolic complexity. Biochem. Soc. Trans. 30: 25-30.

Branduardi P, Smeraldi C, Porro D 2008 Metabolically engineered yeasts: 'potential' industrial applications. J. Mol. Microbiol. Biotechnol. 15: 31-40.

Braus GH 1991 Aromatic amino acid biosynthesis in the yeast Saccharomyces cerevisiae: a model system for the regulation of a eukaryotic biosynthetic pathway. Microbiol. Rev. 55: 349-370.

Brautigam A, Hofmann-Benning S, Weber AP 2008 Comparative proteomics of chloroplasts envelopes from C3 and C4 plants reveals specific adaptations of the plastid envelope to C4 photosynthesis and candidate proteins required for maintaining C4 metabolite fluxes. Plant Physiol. Jul 3 [Epub ahead of print].

Breitling R, Gilbert D, Heiner M, Orton R 2008 A structured approach for the engineering of biochemical network models, illustrated for signalling pathways. Brief. Bioinform. 9: 404-421.

Brenner WG, Romanov GA, Kollmer I, Burkle L, Schmulling T 2005 Immediate-early and delayed cytokinin response genes of Arabidopsis thaliana identified by genome-wide expression profiling reveal novel cytokinin-sensitive processes and suggest cytokinin action through transcriptional cascades. Plant J. 44: 314-333.

Brigham LA, Woo HH, Nicoll SM, Hawes MC 1995 Differential expression of proteins and mRNAs from border cells and root tips of pea. Plant Physiol. 109: 457-463.

Brilli F, Barta C, Fortunati A, Lerdau M, Loreto F, Centritto M 2007 Response of isoprene emission and carbon metabolism to drought in white poplar (Populus alba) saplings. New Phytol. 175: 244-254.

Brindle KM 1996 Analysis of metabolic control in vivo using molecular genetics. Cell Biochem. Funct. 14: 269-276.

Bro C, Knudsen S, Regenberg B, Olsson L, Nielsen J 2005 Improvement of galactose uptake in Saccharomyces cerevisiae through overexpression of phosphoglucomutase: example of transcript analysis as a tool in inverse metabolic engineering. Appl. Environ. Microbiol. 71: 6465-6472.

Bro C, Nielsen J 2004 Impact of 'ome' analyses on inverse metabolic engineering. Metab. Eng. 6: 204-211.

Bro C, Regenberg B, Forster J, Nielsen J 2006 In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production. Metab. Eng. 8: 102-111.

Broeckling CD, Huhman DV, Farag MA, Smith JT, May GD, Mendes P, Dixon RA, Sumner LW 2005 Metabolic profiling of Medicago truncatula cell cultures reveals the effects of biotic and abiotic elicitors on metabolism. J. Exp. Bot. 56: 323-336.

Brosnan JT, Brosnan ME, Nissim I 2004 A window into cellular metabolism: hepatic metabolism of (15)N-labelled substrates. Metab. Eng. 6: 6-11.

Broun P 2004 Transcription factors as tools for metabolic engineering in plants. Curr. Opin. Plant Biol. 7: 202-209.

Brouquisse R, Rolin D, Cortes S, Gaudillere M, Evrard A, Roby C 2007 A metabolic study of the regulation of proteolysis by sugars in maize root tips: effects of glycerol and dihydroxyacetone. Planta 225: 693-709.

Brown CS, Piastuch WC 1994 Starch metabolism in germinating soybean cotyledons is sensitive to clinorotation and centrifugation. Plant Cell Environ. 17: 341-344.

Brown LA, Baker A 2003 Peroxisome biogenesis and the role of protein import. J. Cell. Mol. Med. 7: 388-400.

Brown MS, Segal A, Stadtman ER 1971 Modulation of glutamine synthetase adenylylation and deadenylylation is mediated by metabolic transformation of the P II -regulatory protein. Proc. Natl. Acad. Sci. U.S.A. 68: 2949-2953.

Brown PH, Bellaloui N, Wimmer MA, Bassil ES, Ruiz J, Hu H, Pfeffer H, Dannel F, Romheld V 2002 Boron in plant biology. Plant Biol. 4: 205-223.

Bruce TJ, Pickett JA 2007 Plant defence signalling induced by biotic attacks. Curr. Opin. Plant Biol. 10: 387-392.

Bruggeman FJ, Boogerd FC, Westerhoff HV 2005 The multifarious short-term regulation of ammonium assimilation of Escherichia coli: dissection using an in silico replica. FEBS J. 272: 1965-1985.

Bruggeman FJ, Kholodenko BN 2002 Modular interaction strengths in regulatory networks; an example. Mol. Biol. Rep. 29: 57-61.

Bruggeman FJ, Westerhoff HV, Hoek JB, Kholodenko BN 2002 Modular response analysis of cellular regulatory networks. J. Theor. Biol. 218: 507-520.

Bruneau L, Chapman R, Marsolais F 2006 Co-occurrence of both L-asparaginase subtypes in Arabidopsis: At3g16150 encodes a K(+)-dependent L-asparaginase. Planta 224: 668-679.

Buchanan-Wollaston V, Page T, Harrison E, Breeze E, Lim PO, Nam HG, Lin JF, Wu SH, Swidzinski J, Ishizaki K, Leaver CJ 2005 Comparative transcriptome analysis reveals significant differences in gene expression and signalling pathways between developmental and dark/starvation-induced senescence in Arabidopsis. Plant J. 42: 567-585.

Buckland BC, Robinson DK, Chartrain M 2000 Biocatalysis for pharmaceuticals--status and prospects for a key technology. Metab. Eng. 2: 42-48.

Buitink J, Leger JJ, Guisle I, Vu BL, Wuilleme S, Lamirault G, Bars AL, Meur NL, Becker A, Kuster H, Leprince O 2006 Transcriptome profiling uncovers metabolic and regulatory processes occurring during the transition from desiccation-sensitive to desiccation-tolerant stages in Medicago truncatula seeds. Plant J. 47: 735-750.

Buitink J, Thomas M, Gissot L, Leprince O 2004 Starvation, osmotic stress and desiccation tolerance lead to expression of different genes of the regulatory beta and gamma subunits of the SnRK1 complex in germinating seeds of Medicago truncatula. Plant Cell Environ. 27: 55-67.

Bum Kim H, Smith CP, Micklefield J, Mavituna F 2004 Metabolic flux analysis for calcium dependent antibiotic (CDA) production in Streptomyces coelicolor. Metab. Eng. 6: 313-325.

Bunik VI 2003 2-Oxo acid dehydrogenase complexes in redox regulation. Eur. J. Biochem. 270: 1036-1042.

Burbulis IE, Winkel-Shirley B 1999 Interactions among enzymes of the Arabidopsis flavonoid biosynthetic pathway. Proc. Natl. Acad. Sci. U.S.A. 96: 12929-12934.

Burgal J, Shockey J, Lu C, Dyer J, Larson T, Graham I, Browse J 2008 Metabolic engineering of hydroxy fatty acid production in plants: RcDGAT2 drives dramatic increases in ricinoleate levels in seed oil. Plant Biotechnol. J. Jul 17 [Epub ahead of print].

Burgard AP, Maranas CD 2003 Optimization-based framework for inferring and testing hypothesized metabolic objective functions. Biotechnol. Bioeng. 82: 670-677.

Burgard AP, Maranas CD 2001 Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions. Biotechnol. Bioeng. 74: 364-375.

Burger C, Buck A 1996 Tracer kinetic modelling of receptor data with mathematical metabolite correction. Eur. J. Nucl. Med. 23: 539-545.

Burgess SC, Jeffrey FM, Storey C, Milde A, Hausler N, Merritt ME, Mulder H, Holm C, Sherry AD, Malloy CR 2005 Effect of murine strain on metabolic pathways of glucose production after brief or prolonged fasting. Am. J. Physiol. Endocrinol. Metab. 289: E53-E61.

Burke JJ, Oliver MJ 1993 Optimal thermal environments for plant metabolic processes (Cucumis sativus L.). Light-harvesting chlorophyll a/b pigment-protein complex of photosystem II and seedling establishment in cucumber. Plant Physiol. 102: 295-302.

Burstenbinder K, Rzewuski G, Wirtz M, Hell R, Sauter M 2007 The role of methionine recycling for ethylene synthesis in Arabidopsis. Plant J. 49: 238-249.

Burtin D, Michael AJ 1997 Overexpression of arginine decarboxylase in transgenic plants. Biochem. J. 325: 331-337.

Busch R, Kim YK, Neese RA, Schade-Serin V, Collins M, Awada M, Gardner JL, Beysen C, Marino ME, Misell LM, Hellerstein MK 2006 Measurement of protein turnover rates by heavy water labeling of nonessential amino acids. Biochim. Biophys. Acta 1760: 730-744.

Busov V, Meilan R, Pearce DW, Rood SB, Ma C, Tschaplinski TJ, Strauss SH 2006 Transgenic modification of gai or rgl1 causes dwarfing and alters gibberellins, root growth, and metabolite profiles in Populus. Planta 224: 288-299.

Bytof G, Knopp SE, Kramer D, Breitenstein B, Bergervoet JH, Groot SP, Selmar D 2007 Transient occurrence of seed germination processes during coffee post-harvest treatment. Ann. Bot. (Lond.) 100: 61-66.

Cabrera ME, Saidel GM, Kalhan SC 1998 Role of O2 in regulation of lactate dynamics during hypoxia: mathematical model and analysis. Ann. Biomed. Eng. 26: 1-27.

Cabrera ME, Saidel GM, Kalhan SC 1999 Lactate metabolism during exercise: analysis by an integrative systems model. Am. J. Physiol. 277: R1522-R1536.

Cacas JL, Vailleau F, Devoine C, Ennar N, Agnel JP, Tronchet M, Ponchet M, Blein JP, Roby D, Triantaphylides C, Montillet JL 2005 The combined action of 9 lipoxygenase and galactolipase is sufficient to bring about programmed cell death during tobacco hypersensitive response. Plant Cell Environ. 28: 1367-1378.

Cahoon EB, Dietrich CR, Meyer K, Damude HG, Dyer JM, Kinney AJ 2006 Conjugated fatty acids accumulate to high levels in phospholipids of metabolically engineered soybean and Arabidopsis seeds. Phytochemistry 67: 1166-1176.

Cahoon EB, Shockey JM, Dietrich CR, Gidda SK, Mullen RT, Dyer JM 2007 Engineering oilseeds for sustainable production of industrial and nutritional feedstocks: solving bottlenecks in fatty acid flux. Curr. Opin. Plant Biol. 10: 236-244.

Cairns AJ, Gallagher JA 2004 Absence of turnover and futile cycling of sucrose in leaves of Lolium temulentum L.: implications for metabolic compartmentation. Planta 219: 836-846.

Cakir T, Kirdar B, Ulgen KO 2004 Metabolic pathway analysis of yeast strengthens the bridge between transcriptomics and metabolic networks. Biotechnol. Bioeng. 86: 251-260.

Cakir T, Tacer CS, Ulgen KO 2004 Metabolic pathway analysis of enzyme-deficient human red blood cells. Biosystems 78: 49-67.

Calas AG, Richard O, Meme S, Beloeil JC, Doan BT, Gefflaut T, Meme W, Crusio WE, Pichon J, Montecot C 2008 Chronic exposure to glufosinate-ammonium induces spatial memory impairments, hippocampal MRI modifications and glutamine synthetase activation in mice. Neurotoxicology 29: 740-747.

Caldara M, Dupont G, Leroy F, Goldbeter A, De Vuyst L, Cunin R 2008 Arginine biosynthesis in Escherichia coli: experimental perturbation and mathematical modeling. J. Biol. Chem. 283: 6347-6358.

Calderon-Vazquez C, Ibarra-Laclette E, Caballero-Perez J, Herrera-Estrella L 2008 Transcript profiling of Zea mays roots reveals gene responses to phosphate deficiency at the plant- and species-specific levels. J. Exp. Bot. 59: 2479-2497.

Calenge F, Saliba-Colombani V, Mahieu S, Loudet O, Daniel-Vedele F, Krapp A 2006 Natural variation for carbohydrate content in Arabidopsis thaliana. Interaction with complex traits dissected by quantitative genetics. Plant Physiol. 141: 1630-1643.

Calik P, Calik G, Taka S, Ozdamar TH 1999 Metabolic flux analysis for serine alkaline protease fermentation by Bacillus licheniformis in a defined medium: effects of the oxygen transfer rate. Biotechnol. Bioeng. 64: 151-167.

Cameron DC, Chaplen FW 1997 Developments in metabolic engineering. Curr. Opin. Biotechnol. 8: 175-80.

Cameroni E, De Virgilio C, Deloche O 2006 Phosphatidylinositol 4-phosphate is required for translation initiation in Saccharomyces cerevisiae. J. Biol. Chem. 281: 38139-38149.

Campos N, Rodriguez-Concepcion M, Sauret-Gueto S, Gallego F, Lois LM, Boronat A 2001 Escherichia coli engineered to synthesize isopentenyl diphosphate and dimethylallyl diphosphate from mevalonate: a novel system for the genetic analysis of the 2-C-methyl-D-erythritol 4-phosphate pathway for isoprenoid biosynthesis. Biochem. J. 353: 59-67.

Canas RA, Villalobos DP, Diaz-Moreno SM, Canovas FM, Canton FR 2008 Molecular and functional analyses support a role of ornithine-delta-aminotransferase in the provision of glutamate for glutamine biosynthesis during pine germination. Plant Physiol. Jul 11 [Epub ahead of print].

Canelas AB, van Gulik WM, Heijnen JJ 2008 Determination of the cytosolic free NAD/NADH ratio in Saccharomyces cerevisiae under steady-state and highly dynamic conditions. Biotechnol. Bioeng. 100: 734-743.

Cannizzaro C, Christensen B, Nielsen J, Stockar U 2004 Metabolic network analysis on Phaffia rhodozyma yeast using (13)C-labeled glucose and gas chromatography-mass spectrometry. Metab. Eng. 6: 340-351.

Cannons AC, Pendleton LC 1994 Possible role for mRNA stability in the ammonium-controlled regulation of nitrate reductase expression. Biochem. J. 297: 561-565.

Canovas M, Bernal V, Sevilla A, Iborra JL 2007 Salt stress effects on the central and carnitine metabolisms of Escherichia coli. Biotechnol. Bioeng. 96: 722-737.

Canovas M, Bernal V, Torroglosa T, Ramirez JL, Iborra JL 2003 Link between primary and secondary metabolism in the biotransformation of trimethylammonium compounds by Escherichia coli. Biotechnol. Bioeng. 84: 686-699.

Canovas M, Maiquez JR, Obon JM, Iborra JL 2002 Modeling of the biotransformation of crotonobetaine into L-(-)-carnitine by Escherichia coli strains. Biotechnol. Bioeng. 77: 764-775.

Canton FR, Suarez MF, Canovas FM 2005 Molecular aspects of nitrogen mobilization and recycling in trees. Photosynth. Res. 83: 265-278.

Cao A, Jain A, Baldwin JC, Raghothama KG 2007 Phosphate differentially regulates 14-3-3 family members and GRF9 plays a role in Pi-starvation induced responses. Planta 226: 1219-1230.

Capell T, Christou P 2004 Progress in plant metabolic engineering. Curr. Opin. Biotechnol. 15: 148-154.

Capote-Mainez N, Sanchez F 1997 Characterization of the common bean uricase II and its expression in organs other than nodules. Plant Physiol. 115: 1307-1317.

Carling D 2004 The AMP-activated protein kinase cascade--a unifying system for energy control. Trends Biochem. Sci. 29: 18-24.

Carlson R, Srienc F 2004 Fundamental Escherichia coli biochemical pathways for biomass and energy production: creation of overall flux states. Biotechnol. Bioeng. 86: 149-162.

Carlson RP 2007 Metabolic systems cost-benefit analysis for interpreting network structure and regulation. Bioinformatics 23: 1258-1264.

Carrari F, Baxter C, Usadel B, Urbanczyk-Wochniak E, Zanor MI, Nunes-Nesi A, Nikiforova V, Centero D, Ratzka A, Pauly M, Sweetlove L, Fernie AR 2006 Integrated analysis of metabolite and transcript levels reveals the metabolic shifts that underlie tomato fruit development and highlight regulatory aspects of metabolic network behavior. Plant Physiol. 142: 1380-1396.

Carrari F, Fernie AR 2006 Metabolic regulation underlying tomato fruit development. J. Exp. Bot. 57: 1883-1897.

Carrari F, Urbanczyk-Wochniak E, Willmitzer L, Fernie AR 2003 Engineering central metabolism in crop species: learning the system. Metab. Eng. 5: 191-200.

Carrau FM, Medina K, Farina L, Boido E, Henschke PA, Dellacassa E 2008 Production of fermentation aroma compounds by Saccharomyces cerevisiae wine yeasts: effects of yeast assimilable nitrogen on two model strains. FEMS Yeast Res. Jul 9 [Epub ahead of print].

Carretero-Paulet L, Cairo A, Botella-Pavia P, Besumbes O, Campos N, Boronat A, Rodriguez-Concepcion M 2006 Enhanced flux through the methylerythritol 4-phosphate pathway in Arabidopsis plants overexpressing deoxyxylulose 5-phosphate reductoisomerase. Plant Mol. Biol. 62: 683-695.

Carrier P, Baryla A, Havaux M 2003 Cadmium distribution and microlocalization in oilseed rape (Brassica napus) after long-term growth on cadmium-contaminated soil. Planta 216: 939-950.

Carroll AD, Fox GG, Laurie S, Phillips R, Ratcliffe RG, Stewart GR 1994 Ammonium assimilation and the role of gamma-aminobutyric-acid in pH homeostasis in carrot cell suspensions. Plant Physiol. 106: 513-520.

Carsten LD, Watts T, Markow TA 2005 Gene expression patterns accompanying a dietary shift in Drosophila melanogaster. Mol. Ecol. 14: 3203-3208.

Carvalho RA, Jeffrey FMH, Sherry AD, Malloy CR 1998 C-13 isotopomer analysis of glutamate by heteronuclear multiple quantum coherence total correlation spectroscopy (HMQC-TOCSY). FEBS Lett. 440: 382-386.

Casazza AP, Basner A, Hofgen R, Hesse H 2000 Expression of threonine synthase from Solanum tuberosum L. is not metabolically regulated by photosynthesis-related signals or by nitrogenous compounds. Plant Sci. 157: 43-50.

Cascante M, Boros LG, Comin-Anduix B, de Atauri P, Centelles JJ, Lee PW 2002 Metabolic control analysis in drug discovery and disease. Nat. Biotechnol. 20: 243-249.

Cascante M, Curto R, Sorribas A 1995 Comparative characterization of the fermentation pathway of Saccharomyces cerevisiae using biochemical systems theory and metabolic control analysis: steady-state analysis. Math. Biosci. 130: 51-69.

Castrillo JI, Hayes A, Mohammed S, Gaskell SJ, Oliver SG 2003 An optimized protocol for metabolome analysis in yeast using direct infusion electrospray mass spectrometry. Phytochemistry 62: 929-937.

Casu RE, Grof CP, Rae AL, McIntyre CL, Dimmock CM, Manners JM 2003 Identification of a novel sugar transporter homologue strongly expressed in maturing stem vascular tissues of sugarcane by expressed sequence tag and microarray analysis. Plant Mol. Biol. 52: 371-386.

Catusse J, Strub JM, Job C, Van Dorsselaer A, Job D 2008 Proteome-wide characterization of sugarbeet seed vigor and its tissue specific expression. Proc. Natl. Acad. Sci. U.S.A. 105: 10262-10267.

Cave M, Deaciuc I, Mendez C, Song Z, Joshi-Barve S, Barve S, McClain C 2007 Nonalcoholic fatty liver disease: predisposing factors and the role of nutrition. J. Nutr. Biochem. 18: 184-195.

Cedergreen N, Madsen TV 2004 Light regulation of root and leaf NO3- uptake and reduction in the floating macrophyte Lemna minor. New Phytol. 161: 449-457.

Cefalu WT, Ye J, Zuberi A, Ribnicky DM, Raskin I, Liu Z, Wang ZQ, Brantley PJ, Howard L, Lefevre M 2008 Botanicals and the metabolic syndrome. Am. J. Clin. Nutr. 87: 481S-487S.

Cen YP, Layzell DB 2004 Does oxygen limit nitrogenase activity in soybean exposed to elevated CO2?. Plant Cell Environ. 27: 1229-1238.

Cerami EG, Bader GD, Gross B, Sander C 2006 cPath: open source software for collecting, storing, and querying biological pathways. BMC Bioinformatics 7: 497.

Cercos M, Soler G, Iglesias DJ, Gadea J, Forment J, Talon M 2006 Global analysis of gene expression during development and ripening of citrus fruit flesh. A proposed mechanism for citric acid utilization. Plant Mol. Biol. 62: 513-527.

Cerezo M, Flors V V, Legaz F, Garcia-Agustin P 2000 Characterization of the low affinity transport system for NO(3)(-) uptake by Citrus roots. Plant Sci. 160: 95-104.

Cerezo M, Tillard P, Gojon A, Primo-Millo E, Garcia-Agustin P 2001 Characterization and regulation of ammonium transport systems in Citrus plants. Planta 214: 97-105.

Cervantes-Cervantes M, Gallagher CE, Zhu C, Wurtzel ET 2006 Maize cDNAs expressed in endosperm encode functional farnesyl diphosphate synthase with geranylgeranyl diphosphate synthase activity. Plant Physiol. 141: 220-231.

Chaffei C, Pageau K, Suzuki A, Gouia H, Ghorbel MH, Masclaux-Daubresse C 2004 Cadmium toxicity induced changes in nitrogen management in Lycopersicon esculentum leading to a metabolic safeguard through an amino acid storage strategy. Plant Cell Physiol. 45: 1681-1693.

Chan C, Berthiaume F, Lee K, Yarmush ML 2003 Metabolic flux analysis of hepatocyte function in hormone- and amino acid-supplemented plasma. Metab. Eng. 5: 1-15.

Chan C, Berthiaume F, Washizu J, Toner M, Yarmush ML 2002 Metabolic pre-conditioning of cultured cells in physiological levels of insulin: generating resistance to the lipid-accumulating effects of plasma in hepatocytes. Biotechnol. Bioeng. 78: 753-760.

Chanda B, Venugopal SC, Kulshrestha S, Navarre DA, Downie B, Vaillancourt L, Kachroo A, Kachroo P 2008 Glycerol-3-phosphate levels are associated with basal resistance to the hemibiotrophic fungus Colletotrichum higginsianum in Arabidopsis. Plant Physiol. 147: 2017-2029.

Chandler RJ, Aswani V, Tsai MS, Falk M, Wehrli N, Stabler S, Allen R, Sedensky M, Kazazian HH, Venditti CP 2006 Propionyl-CoA and adenosylcobalamin metabolism in Caenorhabditis elegans: evidence for a role of methylmalonyl-CoA epimerase in intermediary metabolism. Mol. Genet. Metab. 89: 64-73.

Chang DE, Shin S, Rhee JS, Pan JG 1999 Acetate metabolism in a pta mutant of Escherichia coli W3110: importance of maintaining acetyl coenzyme A flux for growth and survival. J. Bacteriol. 181: 6656-6663.

Chang Y, Suthers PF, Maranas CD 2008 Identification of optimal measurement sets for complete flux elucidation in metabolic flux analysis experiments. Biotechnol. Bioeng. 100: 1039-1049.

Chang YJ, Kim BR, Kim SU 2005 Metabolic flux analysis of diterpene biosynthesis pathway in rice. Biotechnol. Lett. 27: 1375-1380.

Chao G, Shen J, Tseng CP, Park SJ, Gunsalus RP 1997 Aerobic regulation of isocitrate dehydrogenase gene (icd) expression in Escherichia coli by the arcA and fnr gene products. J. Bacteriol. 179: 4299-4304.

Chapple C 1998 Molecular-genetic analysis of plant cytochrome P450-dependent monooxygenases. Annu. Rev. Plant Physiol. Plant Mol. Biol. 49: 311-343.

Chartrain M, Salmon PM, Robinson DK, Buckland BC 2000 Metabolic engineering and directed evolution for the production of pharmaceuticals. Curr. Opin. Biotechnol. 11: 209-214.

Chassagnole C, Diano A, Letisse F, Lindley ND 2003 Metabolic network analysis during fed-batch cultivation of Corynebacterium glutamicum for pantothenic acid production: first quantitative data and analysis of by-product formation. J. Biotechnol. 104: 261-272.

Chassagnole C, Noisommit-Rizzi N, Schmid JW, Mauch K, Reuss M 2002 Dynamic modeling of the central carbon metabolism of Escherichia coli. Biotechnol. Bioeng. 79: 53-73.

Chastain CJ, Xu W, Parsley K, Sarath G, Hibberd JM, Chollet R 2008 The pyruvate, orthophosphate dikinase regulatory proteins of Arabidopsis possess a novel, unprecedented Ser/Thr protein kinase primary structure. Plant J. 53: 854-863.

Chatham JC, Forder JR, Glickson JD, Chance EM 1995 Calculation of absolute metabolic flux and the elucidation of the pathways of glutamate labeling in perfused rat heart by 13C NMR spectroscopy and nonlinear least squares analysis. J. Biol. Chem. 270: 7999-8008.

Chatziioannou A, Palaiologos G, Kolisis FN 2003 Metabolic flux analysis as a tool for the elucidation of the metabolism of neurotransmitter glutamate. Metab. Eng. 5: 201-210.

Chaui-Berlinck JG, Monteiro LH, Navas CA, Bicudo JE 2002 Temperature effects on energy metabolism: a dynamic system analysis. Proc. R. Soc. Lond. B. Biol. Sci. 269: 15-19.

Chaves MM, Oliveira MM 2004 Mechanisms underlying plant resilience to water deficits: prospects for water-saving agriculture. J. Exp. Bot. 55: 2365-2384.

Chavez-Bejar MI, Lara AR, Lopez H, Hernandez-Chavez G, Martinez A, Ramirez OT, Bolívar F, Gosset G 2008 Metabolic engineering of Escherichia coli for L-tyrosine production by expression of genes coding for the chorismate mutase domain of the native chorismate mutase-prephenate dehydratase and a cyclohexadienyl dehydrogenase from Zymomonas mobilis. Appl. Environ. Microbiol. 74: 3284-3290.

Chen DH, Ye GY, Yang CQ, Chen Y, Wu YK 2004 Effect after introducing Bacillus thuringiensis gene on nitrogen metabolism in cotton. Field Crop. Res. 87: 235-244.

Chen J, Kyte C, Valcin M, Chan W, Wetmur JG, Selhub J, Hunter DJ, Ma J 2004 Polymorphisms in the one-carbon metabolic pathway, plasma folate levels and colorectal cancer in a prospective study. Int. J. Cancer 110: 617-620.

Chen LM, Li KZ, Miwa T, Izui K 2004 Overexpression of a cyanobacterial phosphoenolpyruvate carboxylase with diminished sensitivity to feedback inhibition in Arabidopsis changes amino acid metabolism. Planta 219: 440-449.

Chen LR, Markhart AH, Shanmugasundaram S, Lin TY 2008 Early developmental and stress responsive ESTs from mungbean, Vigna radiata (L.) Wilczek, seedlings. Plant Cell Rep. 27: 535-552.

Chen NH, Reith MEA, Quick MW 2004 Synaptic uptake and beyond: the sodium- and chloride-dependent neurotransmitter transporter family SLC6. Pflugers Arch. 447: 519-531.

Chen NY, Paulus H 1988 Mechanism of expression of the overlapping genes of Bacillus subtilis aspartokinase II. J. Biol. Chem. 263: 9526-9532.

Chen R, Hatzimanikatis V, Yap WM, Postma PW, Bailey JE 1997 Metabolic consequences of phosphotransferase (PTS) mutation in a phenylalanine-producing recombinant Escherichia coli. Biotechnol. Prog. 13: 768-775.

Chen R, Yap WM, Postma PW, Bailey JE 1997 Comparative studies of Escherichia coli strains using different glucose uptake systems: metabolism and energetics. Biotechnol. Bioeng. 56: 583-590.

Chen S, Feng D 2006 Novel parameter estimation methods for 11C-acetate dual-input liver model with dynamic PET. IEEE Trans. Biomed. Eng. 53: 967-973.

Chen S, Glawischnig E, Jorgensen K, Naur P, Jorgensen B, Olsen CE, Hansen CH, Rasmussen H, Pickett JA, Halkier BA 2003 CYP79F1 and CYP79F2 have distinct functions in the biosynthesis of aliphatic glucosinolates in Arabidopsis. Plant J. 33: 923-937.

Chen S, Ho C, Feng D, Chi Z 2004 Tracer kinetic modeling of 11C-acetate applied in the liver with positron emission tomography. IEEE Trans. Med. Imaging 23: 426-432.

Chen TH, Murata N 2002 Enhancement of tolerance of abiotic stress by metabolic engineering of betaines and other compatible solutes. Curr. Opin. Plant Biol. 5: 250-257.

Chen WH, Tseng YC, Liu YC, Chuo CM, Chen PT, Tseng KM, Yeh YC, Ger MJ, Wang HL 2008 Cool-night temperature induces spike emergence and affects photosynthetic efficiency and metabolizable carbohydrate and organic acid pools in Phalaenopsis aphrodite. Plant Cell Rep. Aug 6 [Epub ahead of print].

Chen XJ, Wang X, Kaufman BA, Butow RA 2005 Aconitase couples metabolic regulation to mitochondrial DNA maintenance. Science 307: 714-717.

Cheng Y, Chen X 2004 Posttranscriptional control of plant development. Curr. Opin. Plant Biol. 7: 20-25.

Cheung AY, Wu HM 2007 Structural and functional compartmentalization in pollen tubes. J. Exp. Bot. 58: 75-82.

Chia T, Thorneycroft D, Chapple A, Messerli G, Chen J, Zeeman SC, Smith SM, Smith AM 2004 A cytosolic glucosyltransferase is required for conversion of starch to sucrose in Arabidopsis leaves at night. Plant J. 37: 853-863.

Chia TY, Pike MJ, Rawsthorne S 2005 Storage oil breakdown during embryo development of Brassica napus (L.). J. Exp. Bot. 56: 1285-1296.

Chiang YJ, Stushnoff C, McSay AE 2005 Overexpression of mannitol-1-phosphate dehydrogenase increases mannitol accumulation and adds protection against chilling injury in petunia. J. Am. Soc. Hortic. Sci. 130: 605-610.

Chibani K, Ali-Rachedi S, Job C, Job D, Jullien M, Grappin P 2006 Proteomic analysis of seed dormancy in Arabidopsis. Plant Physiol. 142: 1493-1510.

Chin JW, Khankal R, Monroe CA, Maranas CD, Cirino PC 2008 Analysis of NADPH supply during xylitol production by engineered Escherichia coli. Biotechnol. Bioeng. Jul 22 [Epub ahead of print].

Chintapakorn Y, Hamill JD 2003 Antisense-mediated down-regulation of putrescine N-methyltransferase activity in transgenic Nicotiana tabacum L. can lead to elevated levels of anatabine at the expense of nicotine. Plant Mol. Biol. 53: 87-105.

Chitnis PR 2001 Photosystem I: function and physiology. Annu. Rev. Plant Physiol. Plant Mol. Biol. 52: 593-626.

Chiu TL, Wen Z, Rupasinghe SG, Schuler MA 2008 Comparative molecular modeling of Anopheles gambiae CYP6Z1, a mosquito P450 capable of metabolizing DDT. Proc. Natl. Acad. Sci. U.S.A. 105: 8855-8860.

Chivasa S, Hamilton JM, Pringle RS, Ndimba BK, Simon WJ, Lindsey K, Slabas AR 2006 Proteomic analysis of differentially expressed proteins in fungal elicitor-treated Arabidopsis cell cultures. J. Exp. Bot. 57: 1553-1562.

Chiwocha SD, Cutler AJ, Abrams SR, Ambrose SJ, Yang J, Ross AR, Kermode AR 2005 The etr1-2 mutation in Arabidopsis thaliana affects the abscisic acid, auxin, cytokinin and gibberellin metabolic pathways during maintenance of seed dormancy, moist-chilling and germination. Plant J. 42: 35-48.

Choi HK, Choi YH, Verberne M, Lefeber AW, Erkelens C, Verpoorte R 2004 Metabolic fingerprinting of wild type and transgenic tobacco plants by 1H NMR and multivariate analysis technique. Phytochemistry 65: 857-864.

Choi YH, Tapias EC, Kim HK, Lefeber AW, Erkelens C, Verhoeven JT, Brzin J, Zel J, Verpoorte R 2004 Metabolic discrimination of Catharanthus roseus leaves infected by phytoplasma using 1H-NMR spectroscopy and multivariate data analysis. Plant Physiol. 135: 2398-2410.

Chong BF, Bonnett GD, Glassop D, O'Shea MG, Brumbley SM 2007 Growth and metabolism in sugarcane are altered by the creation of a new hexose-phosphate sink. Plant Biotechnol. J. 5: 240-253.

Chong J, Pierrel MA, Atanassova R, Werck-Reichhart D, Fritig B, Saindrenan P 2001 Free and conjugated benzoic acid in tobacco plants and cell cultures. Induced accumulation upon elicitation of defense responses and role as salicylic acid precursors. Plant Physiol. 125: 318-328.

Chou CJ, Jenney FJ Jr, Adams MW, Kelly RM 2008 Hydrogenesis in hyperthermophilic microorganisms: implications for biofuels. Metab. Eng. Jun 28 [Epub ahead of print].

Chourey PS, Jain M, Li QB, Carlson SJ 2006 Genetic control of cell wall invertases in developing endosperm of maize. Planta 223: 159-167.

Chrikishvili D, Sadunishvili T, Zaalishvili G 2006 Benzoic acid transformation via conjugation with peptides and final fate of conjugates in higher plants. Ecotoxicol. Environ. Saf. 64: 390-399.

Christensen B, Nielsen J 2000 Metabolic network analysis of Penicillium chrysogenum using 13C-labeled glucose. Biotechnol. Bioeng. 68: 652-659.

Christensen B, Nielsen J 2000 Metabolic network analysis. A powerful tool in metabolic engineering. Adv. Biochem. Eng. Biotechnol. 66: 209-231.

Christensen C, Thakar J, Albert R 2007 Systems-level insights into cellular regulation: inferring, analysing, and modelling intracellular networks. IET Syst. Biol. 1: 61-77.

Christensen KE, MacKenzie RE 2006 Mitochondrial one-carbon metabolism is adapted to the specific needs of yeast, plants and mammals. Bioessays 28: 595-605.

Christiansen T, Christensen B, Nielsen J 2002 Metabolic network analysis of Bacillus clausii on minimal and semirich medium using 13C-labeled glucose. Metab. Eng. 4: 159-169.

Chung H-J, Sehnke PC, Ferl RJ 1999 The 14-3-3 proteins: cellular regulators of plant metabolism. Trends Plant Sci. 4: 367-371.

Chung IM, Hong SB, Peebles CA, Kim JA, San KY 2007 Effect of the engineered indole pathway on accumulation of phenolic compounds in Catharanthus roseus hairy roots. Biotechnol. Prog. 23: 327-332.

Church GM 2005 From systems biology to synthetic biology. Mol. Syst. Biol. 1: 2005.0032.

Chwals WJ 2004 Regulation of the cellular and physiological effects of glutamine. Mini. Rev. Med. Chem. 4: 833-838.

Ciapaite J, Bakker SJ, Diamant M, van Eikenhorst G, Heine RJ, Westerhoff HV, Krab K 2006 Metabolic control of mitochondrial properties by adenine nucleotide translocator determines palmitoyl-CoA effects. FEBS J. 273: 5288-5302.

Clark AG 1991 Mutation-selection balance and metabolic control theory. Genetics 129: 909-923.

Clarke A, Gaston KJ 2006 Climate, energy and diversity. Proc. Biol. Sci. 273: 2257-2266.

Cle C, Hill LM, Niggeweg R, Martin CR, Guisez Y, Prinsen E, Jansen MA 2008 Modulation of chlorogenic acid biosynthesis in Solanum lycopersicum; consequences for phenolic accumulation and UV-tolerance. Phytochemistry 69: 2149-2156.

Cloutier M, Bouchard-Marchand E, Perrier M, Jolicoeur M 2008 A predictive nutritional model for plant cells and hairy roots. Biotechnol. Bioeng. 99: 189-200.

Cloutier M, Perrier M, Jolicoeur M 2007 Dynamic flux cartography of hairy roots primary metabolism. Phytochemistry 68: 2393-2404.

Cobelli C, Caumo A 1998 Using what is accessible to measure that which is not: necessity of model of system. Metabolism 47: 1009-1035.

Cobelli C, Foster DM 1998 Compartmental models: theory and practice using the SAAM II software system. Adv. Exp. Med. Biol. 445: 79-101.

Cochrane FC, Davin LB, Lewis NG 2004 The Arabidopsis phenylalanine ammonia lyase gene family: kinetic characterization of the four PAL isoforms. Phytochemistry 65: 1557-1564.

Coelho D, Suormala T, Stucki M, Lerner-Ellis JP, Rosenblatt DS, Newbold RF, Baumgartner MR, Fowler B 2008 Gene identification for the cblD defect of vitamin B12 metabolism. N. Engl. J. Med. 358: 1454-1464.

Cohen DM, Bergman RN 1994 SYNTAX: A rule-based stochastic simulation of the time-varying concentrations of positional isotopomers of metabolic intermediates. Computers and Biomedical Research 27: 130-147.

Cohen DM, Bergman RN 2004 Estimation of metabolic flux from dominant rate constants in vivo: application to brain and heart. Metab. Eng. 6: 59-74.

Colebatch G, Desbrosses G, Ott T, Krusell L, Montanari O, Kloska S, Kopka J, Udvardi MK 2004 Global changes in transcription orchestrate metabolic differentiation during symbiotic nitrogen fixation in Lotus japonicus. Plant J. 39: 487-512.

Coleman JO, Haslam RP, Downie AL 2005 Transcriptomics and proteomics: tools for optimising phytoremediation activities. Z. Naturforsch. [C] 60: 544-548.

Collado-Vides J, Hofestadt R, Mavrovouniotis M, Michal G 1999 Modeling and simulation of gene regulation and metabolic pathways. Biosystems 49: 79-82.

Comar KM, Sterling RK 2006 Review article: drug therapy for non-alcoholic fatty liver disease. Aliment. Pharmacol. Ther. 23: 207-215.

Conjard A, Komaty O, Delage H, Boghossian M, Martin M, Ferrier B, Baverel G 2003 Inhibition of glutamine synthetase in the mouse kidney - A novel mechanism of adaptation to metabolic acidosis. J. Biol. Chem. 278: 38159-38166.

Connelly HM, Pelletier DA, Lu TY, Lankford PK, Hettich RL 2006 Characterization of pII family (GlnK1, GlnK2, and GlnB) protein uridylylation in response to nitrogen availability for Rhodopseudomonas palustris. Anal. Biochem. 357: 93-104.

Conradie R, Westerhoff HV, Rohwer JM, Hofmeyr JH, Snoep JL 2006 Summation theorems for flux and concentration control coefficients of dynamic systems. Syst. Biol. (Stevenage) 153: 314-317.

Conrado RJ, Mansell TJ, Varner JD, Delisa MP 2007 Stochastic reaction-diffusion simulation of enzyme compartmentalization reveals improved catalytic efficiency for a synthetic metabolic pathway. Metab. Eng. 9: 355-363.

Conrath U, Linke C, Jeblick W, Geigenberger P, Quick WP, Neuhaus HE 2003 Enhanced resistance to Phytophthora infestans and Alternaria solani in leaves and tubers, respectively, of potato plants with decreased activity of the plastidic ATP/ADP transporter. Planta 217: 75-83.

Contento AL, Kim SJ, Bassham DC 2004 Transcriptome profiling of the response of Arabidopsis suspension culture cells to Suc starvation. Plant Physiol. 135: 2330-2347.

Converti A, Perego P 2002 Use of carbon and energy balances in the study of the anaerobic metabolism of Enterobacter aerogenes at variable starting glucose concentrations. Appl. Microbiol. Biotechnol. 59: 303-309.

Cooke JEK, Brown KA, Wu R, Davis JM 2003 Gene expression associated with N-induced shifts in resource allocation in poplar. Plant Cell Environ. 26: 757-770.

Cookson SJ, Williams LE, Miller AJ 2005 Light-dark changes in cytosolic nitrate pools depend on nitrate reductase activity in Arabidopsis leaf cells. Plant Physiol. 138: 1097-1105.

Cooper AJL 2004 The role of glutamine transaminase K (GTK) in sulfur and alpha-keto acid metabolism in the brain, and in the possible bioactivation of neurotoxicants. Neurochem. Int. 44: 557-577.

Corbineau F, Berjak P, Pammenter N, Vinel D, Picard MA, Come D 2004 Reversible cellular and metabolic changes induced by dehydration in desiccation-tolerant wheat seedling shoots. Physiol. Plant. 122: 28-38.

Cordier H, Mendes F, Vasconcelos I, Francois JM 2007 A metabolic and genomic study of engineered Saccharomyces cerevisiae strains for high glycerol production. Metab. Eng. 9: 364-378.

Cordoba-Pedregosa Mdel C, Villalba JM, Cordoba F, Gonzalez-Reyes JA 2005 Changes in intracellular and apoplastic peroxidase activity, ascorbate redox status, and root elongation induced by enhanced ascorbate content in Allium cepa L. J. Exp. Bot. 56: 685-694.

Cornish-Bowden A 1999 Enzyme kinetics from a metabolic perspective. Biochem. Soc. Trans. 27: 281-284.

Cornish-Bowden A 2008 Reinhart Heinrich (1946-2006): an annotated bibliography. J. Theor. Biol. 252: 379-387.

Cornish-Bowden A, Hofmeyr JH 1991 MetaModel: a program for modelling and control analysis of metabolic pathways on the IBM PC and compatibles. Comput. Appl. Biosci. 7: 89-93.

Cornish-Bowden A, Hofmeyr JH 1994 Determination of control coefficients in intact metabolic systems. Biochem. J. 298: 367-375.

Cornish-Bowden A, Hofmeyr JHS, Cardenas ML 1995 Strategies for manipulating metabolic fluxes in biotechnology. Bioorg. Chem. 23: 439-449.

Cornish-Bowden A, Hofmeyr JHS, Cardenas ML 2002 Stoicheiometric analysis in studies of metabolism. Biochem. Soc. Trans. 30: 43-46.

Cornish-Bowden A, Luz Cardenas M 2000 From genome to cellular phenotype-a role for metabolic flux analysis? Nat. Biotechnol. 18: 267-268.

Coruzzi GM, Zhou L 2001 Carbon and nitrogen sensing and signaling in plants: emerging ‘matrix effects’. Curr. Opin. Plant Biol. 4: 247-253.

Cosio C, DeSantis L, Frey B, Diallo S, Keller C 2005 Distribution of cadmium in leaves of Thlaspi caerulescens. J. Exp. Bot. 56: 765-775.

Costanzo JP, Lee RE Jr 2005 Cryoprotection by urea in a terrestrially hibernating frog. J. Exp. Biol. 208: 4079-4089.

Cota-Sanchez JH, Abreu DD 2007 Vivipary and offspring survival in the epiphytic cactus Epiphyllum phyllanthus (Cactaceae). J. Exp. Bot. 58: 3865-3873.

Couee I, Sulmon C, Gouesbet G, El Amrani A 2006 Involvement of soluble sugars in reactive oxygen species balance and responses to oxidative stress in plants. J. Exp. Bot. 57: 449-459.

Cove D, Bezanilla M, Harries P, Quatrano R 2006 Mosses as model systems for the study of metabolism and development. Annu. Rev. Plant Biol. 57: 497-520.

Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO 2004 Integrating high-throughput and computational data elucidates bacterial networks. Nature 429: 92-96.

Covert MW, Palsson BO 2003 Constraints-based models: regulation of gene expression reduces the steady-state solution space. J. Theor. Biol. 221: 309-325.

Covert MW, Schilling CH, Famili I, Edwards JS, Goryanin II, Selkov E, Palsson BO 2001 Metabolic modeling of microbial strains in silico. Trends Biochem. Sci. 26: 179-186.

Covert MW, Schilling CH, Palsson B 2001 Regulation of gene expression in flux balance models of metabolism. J. Theor. Biol. 213: 73-88.

Covert MW, Xiao N, Chen TJ, Karr JR 2008 Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli. Bioinformatics Jul 10 [Epub ahead of print].

Covi JA, Hand SC 2005 V-ATPase expression during development of Artemia franciscana embryos: potential role for proton gradients in anoxia signaling. J. Exp. Biol. 208: 2783-2798.

Cox SJ, Shalel Levanon S, Bennett GN, San KY 2005 Genetically constrained metabolic flux analysis. Metab. Eng. 7: 445-456.

Cox SJ, Shalel Levanon S, Sanchez A, Lin H, Peercy B, Bennett GN, San KY 2006 Development of a metabolic network design and optimization framework incorporating implementation constraints: a succinate production case study. Metab. Eng. 8: 46-57.

Crabtree B, Newsholme EA 1991 A method for testing the stability of a steady-state system during the calculation of a response to large changes in regulator concentrations. FEBS Lett. 280: 329-331.

Crabtree B, Newsholme EA 1987 A systematic approach to describing and analyzing metabolic control systems. Trends Biochem. Sci. 12: 4-8.

Cramer GR, Ergul A, Grimplet J, Tillett RL, Tattersall EA, Bohlman MC, Vincent D, Sonderegger J, Evans J, Osborne C, Quilici D, Schlauch KA, Schooley DA, Cushman JC 2007 Water and salinity stress in grapevines: early and late changes in transcript and metabolite profiles. Funct. Integr. Genomics 7: 111-134.

Crivori P, Poggesi I 2006 Computational approaches for predicting CYP-related metabolism properties in the screening of new drugs. Eur. J. Med. Chem. 41: 795-808.

Cross JM, von Korff M, Altmann T, Bartzetko L, Sulpice R, Gibon Y, Palacios N, Stitt M 2006 Variation of enzyme activities and metabolite levels in 24 Arabidopsis accessions growing in carbon-limited conditions. Plant Physiol. 142: 1574-1588.

Crowther GJ, Kosaly G, Lidstrom ME 2008 Formate as the main branch point for methylotrophic metabolism in Methylobacterium extorquens AM1. J. Bacteriol. 190: 5057-5062.

Cui S, Huang F, Wang J, Ma X, Cheng Y, Liu J 2005 A proteomic analysis of cold stress responses in rice seedlings. Proteomics 5: 3162-3172.

Cunningham FX Jr, Gantt E 1998 Genes and enzymes of carotenoid biosynthesis in plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 49: 557-583.

Curien G, Ravanel S, Dumas R 2003 A kinetic model of the branch-point between the methionine and threonine biosynthesis pathways in Arabidopsis thaliana. Eur. J. Biochem. 270: 4615-4627.

Curto R, Sorribas A, Cascante M 1995 Comparative characterization of the fermentation pathway of Saccharomyces cerevisiae using biochemical systems theory and metabolic control analysis: model definition and nomenclature. Math. Biosci. 130: 25-50.

Cushman JC, Bohnert HJ 1999 Crassulacean acid metabolism: molecular genetics. Annu. Rev. Plant Physiol. Plant Mol. Biol. 50: 305-332.

Cybulski RL, Fisher RR 1976 Intramitochondrial localization and proposed metabolic significance of serine transhydroxymethylase. Biochemistry 15: 3183-3187.

da Silva JM, Arrabaca MC 2004 Photosynthesis in the water-stressed C-4 grass Setaria sphacelata is mainly limited by stomata with both rapidly and slowly imposed water deficits. Physiol. Plant. 121: 409-420.

da Silveira NJ, Bonalumi CE, Uchoa HB, Pereira JH, Canduri F, de Azevedo WF 2006 DBMODELING: a database applied to the study of protein targets from genome projects. Cell. Biochem. Biophys. 44: 366-374.

Daae EB, Dunnill P, Mitsky TA, Padgette SR, Taylor NB, Valentin HE, Gruys KJ 1999 Metabolic modeling as a tool for evaluating polyhydroxyalkanoate copolymer production in plants. Metab. Eng. 1: 243-254.

Daae EB, Ison AP 1999 Classification and sensitivity analysis of a proposed primary metabolic reaction network for Streptomyces lividans. Metab. Eng. 1: 153-165.

Dahl C 1996 Insertional gene inactivation in a phototrophic sulphur bacterium: APS-reductase-deficient mutants of Chromatium vinosum. Microbiology 142: 3363-3372.

Dai N, Petreikov M, Portnoy V, Katzir N, Pharr DM, Schaffer AA 2006 Cloning and expression analysis of a UDP-galactose/glucose pyrophosphorylase from melon fruit provides evidence for the major metabolic pathway of galactose metabolism in raffinose oligosaccharide metabolizing plants. Plant Physiol. 142: 294-304.

Dalle-Donne I, Rossi R, Giustarini D, Colombo R, Milzani A 2007 S-Glutathionylation in protein redox regulation. Free Radic. Biol. Med. 43: 883-898.

Damiani I, Morreel K, Danoun S, Goeminne G, Yahiaoui N, Marque C, Kopka J, Messens E, Goffner D, Boerjan W, Boudet AM, Rochange S 2005 Metabolite profiling reveals a role for atypical cinnamyl alcohol dehydrogenase CAD1 in the synthesis of coniferyl alcohol in tobacco xylem. Plant Mol. Biol. 59: 753-769.

Dan M, Su M, Gao X, Zhao T, Zhao A, Xie G, Qiu Y, Zhou M, Liu Z, Jia W 2008 Metabolite profiling of Panax notoginseng using UPLC-ESI-MS. Phytochemistry 69: 2237-2244.

Dano S, Madsen MF, Schmidt H, Cedersund G 2006 Reduction of a biochemical model with preservation of its basic dynamic properties. FEBS J. 273: 4862-4877.

Darveau CA, Hochachka PW, Roubik DW, Suarez RK 2005 Allometric scaling of flight energetics in orchid bees: evolution of flux capacities and flux rates. J. Exp. Biol. 208: 3593-3602.

Darwent MJ, Paterson E, McDonald AJ, Tomos AD 2003 Biosensor reporting of root exudation from Hordeum vulgare in relation to shoot nitrate concentration. J. Exp. Bot. 54: 325-334.

Dash RK, Li Y, Kim J, Saidel GM, Cabrera ME 2008 Modeling cellular metabolism and energetics in skeletal muscle: large-scale parameter estimation and sensitivity analysis. IEEE Trans. Biomed. Eng. 55: 1298-1318.

Datta R, Chamusco KC, Chourey PS 2002 Starch biosynthesis during pollen maturation is associated with altered patterns of gene expression in maize. Plant Physiol. 130: 1645-1656.

Dauner M, Sauer U 2000 GC-MS analysis of amino acids rapidly provides rich information for isotopomer balancing. Biotechnol. Prog. 16: 642-649.

Dauner M, Sauer U 2001 Stoichiometric growth model for riboflavin-producing Bacillus subtilis. Biotechnol. Bioeng. 76: 132-143.

Dauwe R, Morreel K, Goeminne G, Gielen B, Rohde A, Van Beeumen J, Ralph J, Boudet AM, Kopka J, Rochange SF, Halpin C, Messens E, Boerjan W 2007 Molecular phenotyping of lignin-modified tobacco reveals associated changes in cell-wall metabolism, primary metabolism, stress metabolism and photorespiration. Plant J. 52: 263-285.

David H, Krogh AM, Roca C, Akesson M, Nielsen J 2005 CreA influences the metabolic fluxes of Aspergillus nidulans during growth on glucose and xylose. Microbiology 151: 2209-2221.

David H, Ozcelik IS, Hofmann G, Nielsen J 2008 Analysis of Aspergillus nidulans metabolism at the genome-scale. BMC Genomics 9: 163.

Davies KM 2000 Chapter 7. Plant Colour and Fragrance. In "Metabolic Engineering of Plant Secondary Metabolism" (Verpoorte R, Alfermann AW, eds), Kluwer Academic Publishers, Dortrecht, The Netherlands, pp. 127-163.

Dawson HN, Pendleton LC, Solomonson LP, Cannons AC 1996 Cloning and characterization of the nitrate reductase-encoding gene from Chlorella vulgaris: structure and identification of transcription start points and initiator sequences. Gene 171: 139-145.

Dawson KM, Baltz JM 1997 Organic osmolytes and embryos: substrates of the Gly and beta transport systems protect mouse zygotes against the effects of raised osmolarity. Biol. Reprod. 56: 1550-1558.

Dayan FE, Watson SB, Nanayakkara NP 2007 Biosynthesis of lipid resorcinols and benzoquinones in isolated secretory plant root hairs. J. Exp. Bot. 58: 3263-3272.

De Atauri P, Curto R, Puigjaner J, Cornish-Bowden A, Cascante M 1999 Advantages and disadvantages of aggregating fluxes into synthetic and degradative fluxes when modelling metabolic pathways. Eur. J. Biochem. 265: 671-679.

De Atauri P, Fell DA, Chassagnole C, Magret D, Mazat JP, Cascante M 2002 Dependence of control coefficient distribution on the boundaries of a metabolic system: a generalized analysis of theeffects of additional input and output reactions to a linear pathway. J. Theor. Biol. 215: 239-251.

de Atauri P, Orrell D, Ramsey S, Bolouri H 2004 Evolution of ‘design’ principles in biochemical networks. Syst. Biol. 1: 28-40.

de Atauri P, Sorribas A, Cascante M 2000 Analysis and prediction of the effect of uncertain boundary values in modeling a metabolic pathway. Biotechnol. Bioeng. 68: 18-30.

De Carolis E, De Luca V 1994 2-Oxoglutarate-dependent dioxygenase and related enzymes: biochemical characterization. Phytochemistry 36: 1093-1107.

de Crecy-Lagard V, El Yacoubi B, Diaz de la Garza R, Noiriel A, Hanson AD 2007 Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations. BMC Genomics 8: 245.

de Crecy-Lagard V, Hanson AD 2007 Finding novel metabolic genes through plant-prokaryote phylogenomics. Trends Microbiol. 15: 563-570.

de Graaf AA, Striegel K, Wittig RM, Laufer B, Schmitz G, Wiechert W, Sprenger GA, Sahm H 1999 Metabolic state of Zymomonas mobilis in glucose-, fructose-, and xylose-fed continuous cultures as analysed by 13C- and 31P-NMR spectroscopy. Arch. Microbiol. 171: 371-385.

de Groot MJ, Prathumpai W, Visser J, Ruijter GJ 2005 Metabolic control analysis of Aspergillus niger l-arabinose catabolism. Biotechnol. Prog. 21: 1610-1616.

de Jong CF, Laxalt AM, Bargmann BO, De Wit PJ, Joosten MH, Munnik T 2004 Phosphatidic acid accumulation is an early response in the Cf-4/Avr4 interaction. Plant J. 39: 1-12.

de Koning TJ, Klomp LWJ 2004 Serine-deficiency syndromes. Curr. Opin. Neurol. 17: 197-204.

de la Fuente A, Snoep JL, Westerhoff HV, Mendes P 2002 Metabolic control in integrated biochemical systems. Eur. J. Biochem. 269: 4399-4408.

De Luca V 2000 Chapter 9. Metabolic Engineering of Crops with the Tryptophan Decarboxylase of Catharanthus roseus. In "Metabolic Engineering of Plant Secondary Metabolism" (Verpoorte R, Alfermann AW, eds), Kluwer Academic Publishers, Dortrecht, The Netherlands, pp. 179-194.

De Luca V, St Pierre B 2000 The cell and developmental biology of alkaloid biosynthesis. Trends Plant Sci. 5: 168-173.

De Maria C, Grassini D, Vozzi F, Vinci B, Landi A, Ahluwalia A, Vozzi G 2008 HEMET: mathematical model of biochemical pathways for simulation and prediction of HEpatocyte METabolism. Comput. Methods Programs Biomed. Jul 18 [Epub ahead of print].

de Meer K, Roef MJ, Kulik W, Jakobs C 1999 In vivo research with stable isotopes in biochemistry, nutrition and clinical medicine: an overview. Isotopes in Environ. & Health Studies 35: 19-37.

de Mel VS, Kamberov ES, Martin PD, Zhang J, Ninfa AJ, Edwards BF 1994 Preliminary X-ray diffraction analysis of crystals of the PII protein from Escherichia coli. J. Mol. Biol. 243: 796-798.

De Mey M, Lequeux G, Maertens J, De Maeseneire S, Soetaert W, Vandamme E 2006 Comparison of DNA and RNA quantification methods suitable for parameter estimation in metabolic modeling of microorganisms. Anal. Biochem. 353: 198-203.

De Meyer T, Sinnaeve D, Van Gasse B, Tsiporkova E, Rietzschel ER, De Buyzere ML, Gillebert TC, Bekaert S, Martins JC, Van Criekinge W 2008 NMR-based characterization of metabolic alterations in hypertension using an adaptive, intelligent binning algorithm. Anal. Chem. 80: 3783-3790.

de Pinto MC, Paradiso A, Leonetti P, De Gara L 2006 Hydrogen peroxide, nitric oxide and cytosolic ascorbate peroxidase at the crossroad between defence and cell death. Plant J. 48: 784-795.

De RK, Das M, Mukhopadhyay S 2008 Incorporation of enzyme concentrations into FBA and identification of optimal metabolic pathways. BMC Syst. Biol. 2: 65.

De Vos D, Xu Y, Aerts T, Van Petegem F, Van Beeumen JJ 2008 Crystal structure of Sulfolobus acidocaldarius aspartate carbamoyltransferase in complex with its allosteric activator CTP. Biochem. Biophys. Res. Commun. 372: 40-44.

de Vos WM, Hugenholtz J 2004 Engineering metabolic highways in Lactococci and other lactic acid bacteria. Trends Biotechnol. 22: 72-79.

Dean JP, Dervakos GA 1998 Redesigning metabolic networks using mathematical programming. Biotechnol. Bioeng. 58: 267-271.

Deavours BE, Dixon RA 2005 Metabolic engineering of isoflavonoid biosynthesis in alfalfa. Plant Physiol. 138: 2245-2259.

Debreceni B, Farkas V, Fischer GM, Sandor A 2005 Effect of aromatic ring-containing drugs on carnitine biosynthesis in rats with special regard to p-aminomethylbenzoic acid. Metabolism 54: 1582-1586.

Degen T, Dillmann C, Marion-Poll F, Turlings TC 2004 High genetic variability of herbivore-induced volatile emission within a broad range of maize inbred lines. Plant Physiol. 135: 1928-1938.

Degenhardt J, Gershenzon J 2000 Demonstration and characterization of (E)-nerolidol synthase from maize: a herbivore-inducible terpene synthase participating in (3E)-4,8-dimethyl-1,3,7-nonatriene biosynthesis. Planta 210: 815-822.

Degenring D, Rohl M, Uhrmacher AM 2004 Discrete event, multi-level simulation of metabolite channeling. Biosystems 75: 29-41.

Deguchi M, Bennett AB, Yamaki S, Yamada K, Kanahama K, Kanayama Y 2006 An engineered sorbitol cycle alters sugar composition, not growth, in transformed tobacco. Plant Cell Environ. 29: 1980-1988.

Del Monte U 2005 Swelling of hepatocytes injured by oxidative stress suggests pathological changes related to macromolecular crowding. Med. Hypotheses 64: 818-825.

del Rio LA, Sandalio LM, Palma JM, Bueno P, Corpas FJ 1992 Metabolism of oxygen radicals in peroxisomes and cellular implications. Free Radic. Biol. Med. 13: 557-580.

Delgado J, Liao JC 1995 Control of metabolic pathways by time-scale separation. Biosystems 36: 55-70.

Delgado J, Liao JC 1992 Determination of Flux Control Coefficients from transient metabolite concentrations. Biochem. J. 282: 919-927.

Delgado J, Liao JC 1992 Metabolic control analysis using transient metabolite concentrations. Determination of metabolite concentration control coefficients. Biochem. J. 285: 965-972.

DellaPenna D 2001 Plant metabolic engineering. Plant Physiol. 125: 160-163.

Deluc L, Barrieu F, Marchive C, Lauvergeat V, Decendit A, Richard T, Carde JP, Merillon JM, Hamdi S 2006 Characterization of a grapevine R2R3-MYB transcription factor that regulates the phenylpropanoid pathway. Plant Physiol. 140: 499-511.

DeLuna A, Quezada H, Gomez-Puyou A, Gonzalez A 2005 Asparaginyl deamidation in two glutamate dehydrogenase isoenzymes from Saccharomyces cerevisiae. Biochem. Biophys. Res. Commun. 328: 1083-1090.

Demant T, Seeberg K, Bedynek A, Seidel D 2001 The metabolism of lipoprotein(a) and other apolipoprotein B-containing lipoproteins: a kinetic study in humans. Atherosclerosis 157: 325-339.

Deng MD, Severson DK, Grund AD, Wassink SL, Burlingame RP, Berry A, Running JA, Kunesh CA, Song L, Jerrell TA, Rosson RA 2005 Metabolic engineering of Escherichia coli for industrial production of glucosamine and N-acetylglucosamine. Metab. Eng. 7: 201-214.

Denu JM 2003 Linking chromatin function with metabolic networks: Sir2 family of NAD(+)-dependent deacetylases. Trends Biochem. Sci. 28: 41-48.

DePass AL, Crain RC, Hepler PK 2001 Inositol 1,4,5 trisphosphate is inactivated by a 5-phosphatase in stamen hair cells of Tradescantia. Planta 213: 518-524.

Depeint F, Bruce WR, Shangari N, Mehta R, O'brien PJ 2006 Mitochondrial function and toxicity: role of B vitamins on the one-carbon transfer pathways. Chem. Biol. Interact. 163: 113-132.

Des Rosiers C, Lloyd S, Comte B, Chatham JC 2004 A critical perspective of the use of (13)C-isotopomer analysis by GCMS and NMR as applied to cardiac metabolism. Metab. Eng. 6: 44-58.

Desai RP, Nielsen LK, Papoutsakis ET 1999 Stoichiometric modeling of Clostridium acetobutylicum fermentations with non-linear constraints. J. Biotechnol. 71: 191-205.

Desbrosses GG, Kopka J, Udvardi MK 2005 Lotus japonicus metabolic profiling. Development of gas chromatography-mass spectrometry resources for the study of plant-microbe interactions. Plant Physiol. 137: 1302-1318.

Desgagne-Penix I, Sponsel VM 2008 Expression of gibberellin 20-oxidase1 (AtGA20ox1) in Arabidopsis seedlings with altered auxin status is regulated at multiple levels. J. Exp. Bot. 59: 2057-2070.

Desvaux M 2005 Clostridium cellulolyticum: model organism of mesophilic cellulolytic clostridia. FEMS Microbiol. Rev. 29: 741-764.

Detarsio E, Maurino VG, Alvarez CE, Müller GL, Andreo CS, Drincovich MF 2008 Maize cytosolic NADP-malic enzyme (ZmCytNADP-ME): a phylogenetically distant isoform specifically expressed in embryo and emerging roots. Plant Mol. Biol. Jul 13 [Epub ahead of print].

Deutch CE, Hasler JM, Houston RM, Sharma M, Stone VJ 1989 Nonspecific inhibition of proline dehydrogenase synthesis in Escherichia coli during osmotic stress. Can. J. Microbiol. 35: 779-785.

Deutscher D, Meilijson I, Kupiec M, Ruppin E 2006 Multiple knockout analysis of genetic robustness in the yeast metabolic network. Nat. Genet. 38: 993-998.

Devaiah SP, Roth MR, Baughman E, Li M, Tamura P, Jeannotte R, Welti R, Wang X 2006 Quantitative profiling of polar glycerolipid species from organs of wild-type Arabidopsis and a phospholipase Dalpha1 knockout mutant. Phytochemistry 67: 1907-1924.

Devoto A, Turner JG 2003 Regulation of jasmonate-mediated plant responses in Arabidopsis. Ann. Bot. (Lond.) 92: 329-337.

Dewey TG, Galas DJ 2001 Dynamic models of gene expression and classification. Funct. Integr. Genomics 1: 269-278.

Deytieux C, Geny L, Lapaillerie D, Claverol S, Bonneu M, Doneche B 2007 Proteome analysis of grape skins during ripening. J. Exp. Bot. 58: 1851-1862.

di Salvo ML, Hunt S, Schirch V 2004 Expression, purification, and kinetic constants for human and Escherichia coli pyridoxal kinases. Protein Expr. Purif. 36: 300-306.

Diamond SG, Huppert TJ, Kolehmainen V, Franceschini MA, Kaipio JP, Arridge SR, Boas DA 2006 Dynamic physiological modeling for functional diffuse optical tomography. Neuroimage 30: 88-101.

Dias JM, Oehmen A, Serafim LS, Lemos PC, Reis MA, Oliveira R 2008 Metabolic modelling of polyhydroxyalkanoate copolymers production by mixed microbial cultures. BMC Syst. Biol. 2: 59.

Diaz C, Lemaitre T, Christ A, Azzopardi M, Kato Y, Sato F, Morot-Gaudry JF, Le Dily F, Masclaux-Daubresse C 2008 Nitrogen recycling and remobilisation are differentially controlled by leaf senescence and development stage in Arabidopsis thaliana under low nitrogen nutrition. Plant Physiol. 147: 1437-1449.

Diaz C, Purdy S, Christ A, Morot-Gaudry JF, Wingler A, Masclaux-Daubresse C 2005 Characterization of markers to determine the extent and variability of leaf senescence in Arabidopsis. A metabolic profiling approach. Plant Physiol. 138: 898-908.

Dichio B, Xiloyannis C, Sofo A, Montanaro G 2005 Osmotic regulation in leaves and roots of olive trees during a water deficit and rewatering. Tree Physiol. 26: 179-185.

Dietz KJ, Horling F, Konig J, Baier M 2002 The function of the chloroplast 2-cysteine peroxiredoxin in peroxide detoxification and its regulation. J. Exp. Bot. 53: 1321-1329.

Dietz KJ, Jacob S, Oelze ML, Laxa M, Tognetti V, de Miranda SM, Baier M, Finkemeier I 2006 The function of peroxiredoxins in plant organelle redox metabolism. J. Exp. Bot. 57: 1697-1709.

Dieuaide-Noubhani M, Alonso AP, Rolin D, Eisenreich W, Raymond P 2007 Metabolic flux analysis: recent advances in carbon metabolism in plants. EXS 97: 213-243.

Dieuaide-Noubhani M, Canioni P, Raymond P 1997 Sugar starvation induced changes of carbon metabolism in excised maize root tips. Plant Physiol. 115: 1505-1513.

Dieuaide-Noubhani M, Raffard G, Canioni P, Pradet A, Raymond P 1995 Quantification of compartmented metabolic fluxes in maize root tips using isotope distribution from 13C- or 14C-labeled glucose. J. Biol. Chem. 270: 13147-13159.

Dijken AJ, Schluepmann H, Smeekens SC 2004 Arabidopsis trehalose-6-phosphate synthase 1 is essential for normal vegetative growth and transition to flowering. Plant Physiol. 135: 969-977.

Dikicioglu D, Pir P, Onsan ZI, Ulgen KO, Kirdar B, Oliver SG 2008 Integration of metabolic modeling and phenotypic data in the evaluation and improvement of ethanol production using respiratory deficient mutants of Saccharomyces cerevisiae. Appl. Environ. Microbiol. Jun 27 [Epub ahead of print].

Diksic M, Young SN 2001 Study of the brain serotonergic system with labeled alpha-methyl-L-tryptophan. J. Neurochem. 78: 1185-1200.

Ding D, Ding Y, Cai Y, Chen S, Xu W 2008 Exploring poly-beta-hydroxy-butyrate metabolism through network-based extreme pathway analysis. Riv. Biol. 101: 67-80.

Dinkel RE, Barrett PH, Demant T, Parhofer KG 2006 In-vivo metabolism of VLDL-apolipoprotein-B, -CIII and -E in normolipidemic subjects. Nutr. Metab. Cardiovasc. Dis. 16: 215-221.

Diop NN, Kidric M, Repellin A, Gareil M, d'Arcy-Lameta A, Pham Thi AT, Zuily-Fodil Y 2004 A multicystatin is induced by drought-stress in cowpea (Vigna unguiculata (L.) Walp.) leaves. FEBS Lett. 577: 545-550.

Diretto G, Welsch R, Tavazza R, Mourgues F, Pizzichini D, Beyer P, Giuliano G 2007 Silencing of beta-carotene hydroxylase increases total carotenoid and beta-carotene levels in potato tubers. BMC Plant Biol. 7: 11.

Divol F, Vilaine F, Thibivilliers S, Amselem J, Palauqui JC, Kusiak C, Dinant S 2005 Systemic response to aphid infestation by Myzus persicae in the phloem of Apium graveolens. Plant Mol. Biol. 57: 517-540.

Dixon MH, Hill SA, Jackson MB, Ratcliffe RG, Sweetlove LJ 2006 Physiological and metabolic adaptations of Potamogeton pectinatus L. tubers support rapid elongation of stem tissue in the absence of oxygen. Plant Cell Physiol. 47: 128-140.

Dixon RA 2004 Phytoestrogens. Annu. Rev. Plant Biol. 55: 225-261.

Dixon RA, Howles PA, Lamb C, He XZ, Reddy JT 1998 Prospects for the metabolic engineering of bioactive flavonoids and related phenylpropanoid compounds. Adv. Exp. Med. Biol. 439: 55-66.

Dixon RA, Steele CL 1999 Flavonoids and isoflavonoids - a gold mine for metabolic engineering. Trends Plant Sci. 4: 394-400.

Djajanegara I, Finnegan PM, Mathieu C, McCabe T, Whelan J, Day DA 2002 Regulation of alternative oxidase gene expression in soybean. Plant Mol. Biol. 50: 735-742.

Dluzniewska P, Gessler A, Dietrich H, Schnitzler JP, Teuber M, Rennenberg H 2007 Nitrogen uptake and metabolism in Populus x canescens as affected by salinity. New Phytol. 173: 279-293.

Dobson CM, Gradinger A, Longo N, Wu X, Leclerc D, Lerner-Ellis J, Lemieux M, Belair C, Watkins D, Rosenblatt DS, Gravel RA 2006 Homozygous nonsense mutation in the MCEE gene and siRNA suppression of methylmalonyl-CoA epimerase expression: a novel cause of mild methylmalonic aciduria. Mol. Genet. Metab. 88: 327-333.

Doehlemann G, Wahl R, Horst RJ, Voll LM, Usadel B, Poree F, Stitt M, Pons-Kühnemann J, Sonnewald U, Kahmann R, Kämper J 2008 Reprogramming a maize plant: Transcriptional and metabolic changes induced by the fungal biotroph Ustilago maydis. Plant J. Jun 18 [Epub ahead of print].

Doering CB, Williams IR, Danner DJ 2000 Controlled overexpression of BCKD kinase expression: metabolic engineering applied to BCAA metabolism in a mammalian system. Metab. Eng. 2: 349-356.

Doi A, Fujita S, Matsuno H, Nagasaki M, Miyano S 2004 Constructing biological pathway models with hybrid functional Petri nets. In Silico Biol. 4: 0023.

Dojcinovic D, Krosting J, Harris AJ, Wagner DJ, Rhoads DM 2005 Identification of a region of the Arabidopsis AtAOX1a promoter necessary for mitochondrial retrograde regulation of expression. Plant Mol. Biol. 58: 159-175.

Doke N, Miura Y, Sanchez LM, Park HJ, Noritake T, Yoshioka H, Kawakita K 1996 The oxidative burst protects plants against pathogen attack: mechanism and role as an emergency signal for plant bio-defence--a review. Gene 179: 45-51.

Domach MM 1999 Summary of recent developments in analytical methods. J. Biotechnol. 71: 229-232.

Dominguez H, Rollin C, Guyonvarch A, Guerquin-Kern JL, Cocaign-Bousquet M, Lindley ND 1998 Carbon-flux distribution in the central metabolic pathways of Corynebacterium glutamicum during growth on fructose. Eur. J. Biochem. 254: 96-102.

Dong B, Sang WL, Jiang X, Zhou JM, Kong FX, Hu W, Wang LS 2002 Effects of aluminum on physiological metabolism and antioxidant system of wheat (Triticum aestivum L.). Chemosphere 47: 87-92.

Dong J, Keller WA, Yan W, Georges F 2004 Gene expression at early stages of Brassica napus seed development as revealed by transcript profiling of seed-abundant cDNAs. Planta 218: 483-491.

Dong QL, Zhao XM, Ma HW, Xing XY, Sun NX 2006 Metabolic flux analysis of the two astaxanthin-producing microorganisms Haematococcus pluvialis and Phaffia rhodozyma in the pure and mixed cultures. Biotechnol. J. 1: 1283-1292.

Dorka P, Fischer C, Budman H, Scharer JM 2008 Metabolic flux-based modeling of mAb production during batch and fed-batch operations. Bioprocess. Biosyst. Eng. Jun 17 [Epub ahead of print].

Douce R, Bourguignon J, Neuburger M, Rebeille F 2001 The glycine decarboxylase system: a fascinating complex. Trends Plant Sci. 6: 167-176.

Doverskog M, Jacobsson U, Chapman BE, Kuchel PW, Haggstrom L 2000 Determination of NADH-dependent glutamate synthase (GOGAT) in Spodoptera frugiperda (sf9) insect cells by a selective 1H/15N NMR in vitro assay. J. Biotechnol. 79: 87-97.

Downer J, Sevinsky JR, Ahn NG, Resing KA, Betterton MD 2006 Incorporating expression data in metabolic modeling: a case study of lactate dehydrogenase. J. Theor. Biol. 240: 464-474.

Drager A, Hassis N, Supper J, Schroder A, Zell A 2008 SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks. BMC Syst. Biol. 2: 39.

Drake TA, Schadt EE, Lusis AJ 2006 Integrating genetic and gene expression data: application to cardiovascular and metabolic traits in mice. Mamm. Genome 17: 466-479.

Drews M, Doverskog M, Ohman L, Chapman BE, Jacobsson U, Kuchel PW, Haggstrom L 2000 Pathways of glutamine metabolism in Spodoptera frugiperda (Sf9) insect cells: evidence for the presence of the nitrogen assimilation system, and a metabolic switch by 1H/15N NMR. J. Biotechnol. 78: 23-37.

Droge-Laser W, Siemeling U, Puhler A, Broer I 1994 The metabolites of the herbicide L-phosphinothricin (glufosinate): identification, stability, and mobility in transgenic, herbicide-resistant, and untransformed plants. Plant Physiol. 105: 159-166.

Droste P, Weitzel M, Wiechert W 2008 Visual exploration of isotope labeling networks in 3D. Bioprocess. Biosyst. Eng. 31: 227-239.

Druart N, Johansson A, Baba K, Schrader J, Sjodin A, Bhalerao RR, Resman L, Trygg J, Moritz T, Bhalerao RP 2007 Environmental and hormonal regulation of the activity-dormancy cycle in the cambial meristem involves stage-specific modulation of transcriptional and metabolic networks. Plant J. 50: 557-573.

Du C, Yan H, Zhang Y, Li Y, Cao Z 2006 Use of oxidoreduction potential as an indicator to regulate 1,3-propanediol fermentation by Klebsiella pneumoniae. Appl. Microbiol. Biotechnol. 69: 554-563.

Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD, Srivas R, Palsson BO 2007 Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc. Natl. Acad. Sci. U.S.A. 104: 1777-1782.

Dubouzet JG, Ishihara A, Matsuda F, Miyagawa H, Iwata H, Wakasa K 2007 Integrated metabolomic and transcriptomic analyses of high-tryptophan rice expressing a mutant anthranilate synthase alpha subunit. J. Exp. Bot. 58: 3309-3321.

Ducreux LJ, Morris WL, Hedley PE, Shepherd T, Davies HV, Millam S, Taylor MA 2005 Metabolic engineering of high carotenoid potato tubers containing enhanced levels of beta-carotene and lutein. J. Exp. Bot. 56: 81-89.

Dudareva N, Negre F 2005 Practical applications of research into the regulation of plant volatile emission. Curr. Opin. Plant Biol. 8: 113-118.

Dudareva N, Pichersky E 2008 Metabolic engineering of plant volatiles. Curr. Opin. Biotechnol. 19: 181-189.

Dudman NP, Guo XW, Gordon RB, Dawson PA, Wilcken DE 1996 Human homocysteine catabolism: three major pathways and their relevance to development of arterial occlusive disease. J. Nutr. 126: 1295S-1300S.

Dumas ME, Barton RH, Toye A, Cloarec O, Blancher C, Rothwell A, Fearnside J, Tatoud R, Blanc V, Lindon JC, Mitchell SC, Holmes E, McCarthy MI, Scott J, Gauguier D, Nicholson JK 2006 Metabolic profiling reveals a contribution of gut microbiota to fatty liver phenotype in insulin-resistant mice. Proc. Natl. Acad. Sci. U.S.A. 103: 12511-1256.

Dupuy DL, Rial DV, Ceccarelli EA 2004 Inhibition of pea ferredoxin-NADP(H) reductase by Zn-ferrocyanide. Eur. J. Biochem. 271: 4582-4593.

Durmus Tekir S, Cakir T, O Ulgen K 2006 Analysis of enzymopathies in the human red blood cells by constraint-based stoichiometric modeling approaches. Comput. Biol. Chem. 30: 327-338.

Durre P, Bohringer M, Nakotte S, Schaffer S, Thormann K, Zickner B 2002 Transcriptional regulation of solventogenesis in Clostridium acetobutylicum. J. Mol. Microbiol. Biotechnol. 4: 295-300.

Duwat P, Cesselin B, Sourice S, Gruss A 2000 Lactococcus lactis, a bacterial model for stress responses and survival. Int. J. Food Microbiol. 55: 83-86.

Dyckmans J, Flessa H, Brinkmann K, Mai C, Polle A 2002 Carbon and nitrogen dynamics in acid detergent fibre lignins of beech (Fagus sylvatica L.) during the growth phase. Plant Cell Environ. 25: 469-478.

Ebenhoh O, Heinrich R 2001 Evolutionary optimization of metabolic pathways. Theoretical reconstruction of the stoichiometry of ATP and NADH producing systems. Bull. Math. Biol. 63: 21-55.

Ebenhoh O, Liebermeister W 2006 Structural analysis of expressed metabolic subnetworks. Genome Inform. 17: 163-172.

Eckardt NA 2005 Temperature entrainment of the Arabidopsis circadian clock. Plant Cell 17: 645-647.

Edahiro J, Seki M 2006 Phenylpropanoid metabolite supports cell aggregate formation in strawberry cell suspension culture. J. Biosci. Bioeng. 102: 8-13.

Edwards JS, Ibarra RU, Palsson BO 2001 In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat. Biotechnol. 19: 125-130.

Edwards JS, Palsson BO 2000 Robustness analysis of the Escherichia coli metabolic network. Biotechnol. Prog. 16: 927-939.

Edwards JS, Palsson BO 1998 How will bioinformatics influence metabolic engineering? Biotechnol. Bioeng. 58: 162-169.

Edwards JS, Palsson BO 1999 Systems properties of the Haemophilus influenzae Rd metabolic genotype. J. Biol. Chem. 274: 17410-17416.

Edwards JS, Palsson BO 2000 Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions. BMC Bioinformatics 1: 1-10.

Edwards JS, Palsson BO 2000 The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities. Proc. Natl. Acad. Sci. U.S.A. 97: 5528-5533.

Edwards JS, Ramakrishna R, Palsson BO 2002 Characterizing the metabolic phenotype: a phenotype phase plane analysis. Biotechnol. Bioeng. 77: 27-36.

Edwards JW, Walker EL, Coruzzi GM 1990 Cell-specific expression in transgenic plants reveals nonoverlapping roles for chloroplast and cytosolic glutamine synthetase. Proc. Natl. Acad. Sci. U.S.A. 87: 3459-3463.

Ehlde M, Zacchi G 1995 MIST - a user-friendly metabolic simulator. Comp. Appl. Biosci. 11: 201-207.

Ehlting J, Mattheus N, Aeschliman DS, Li E, Hamberger B, Cullis IF, Zhuang J, Kaneda M, Mansfield SD, Samuels L, Ritland K, Ellis BE, Bohlmann J, Douglas CJ 2005 Global transcript profiling of primary stems from Arabidopsis thaliana identifies candidate genes for missing links in lignin biosynthesis and transcriptional regulators of fiber differentiation. Plant J. 42: 618-640.

Eisenreich W, Bacher A 2007 Advances of high-resolution NMR techniques in the structural and metabolic analysis of plant biochemistry. Phytochemistry 68: 2799-2815.

Eisenreich W, Slaghuis J, Laupitz R, Bussemer J, Stritzker J, Schwarz C, Schwarz R, Dandekar T, Goebel W, Bacher A 2006 13C Isotopologue perturbation studies of Listeria monocytogenes carbon metabolism and its modulation by the virulence regulator PrfA. Proc. Natl. Acad. Sci. U.S.A. 103: 2040-2045.

Ekman M, Tollback P, Bergman B 2007 Proteomic analysis of the cyanobacterium of the Azolla symbiosis: identity, adaptation, and NifH modification. J. Exp. Bot. 59: 1023-1034.

Eksittikul T, Chulavatnatol M, Limpaseni T 2001 Characterization of sucrose uptake system in cassava (Manihot esculenta Crantz). Plant Sci. 160: 733-737.

El Amrani A, Barakate A, Askari BM, Li X, Roberts AG, Ryan MD, Halpin C 2004 Coordinate expression and independent subcellular targeting of multiple proteins from a single transgene. Plant Physiol. 135: 16-24.

El Massaoudi M, Spelthahn J, Drysch A, de Graaf A, Takors R 2003 Production process monitoring by serial mapping of microbial carbon flux distributions using a novel sensor reactor approach: I--Sensor reactor system. Metab. Eng. 5: 86-95.

Elias CB, Carpentier E, Durocher Y, Bisson L, Wagner R, Kamen A 2003 Improving glucose and glutamine metabolism of human HEK 293 and Trichoplusia ni insect cells engineered to express a cytosolic pyruvate carboxylase enzyme. Biotechnol. Prog. 19: 90-97.

Eliopoulos E, Goulielmos GN, Loukas M 2004 Functional constraints of alcohol dehydrogenase (ADH) of tephritidae and relationships with other dipteran species. J. Mol. Evol. 58: 493-505.

Eliot AC, Kirsch JF 2004 Pyridoxal phosphate enzymes: mechanistic, structural, and evolutionary considerations. Annu. Rev. Biochem. 73: 383-415.

Else MA, Taylor JM, Atkinson CJ 2006 Anti-transpirant activity in xylem sap from flooded tomato (Lycopersicon esculentum Mill.) plants is not due to pH-mediated redistributions of root- or shoot-sourced ABA. J. Exp. Bot. 57: 3349-3357.

Elsner L, Giersch C 1998 Metabolic control analysis: separable matrices and interdependence of control coefficients. J. Theor. Biol. 193: 649-661.

Emmerling M, Bailey JE, Sauer U 2000 Altered regulation of pyruvate kinase or co-overexpression of phosphofructokinase increases glycolytic fluxes in resting Escherichia coli. Biotechnol. Bioeng. 67: 623-627.

Emmerling M, Dauner M, Ponti A, Fiaux J, Hochuli M, Szyperski T, Wuthrich K, Bailey JE, Sauer U 2002 Metabolic flux responses to pyruvate kinase knockout in Escherichia coli. J. Bacteriol. 184: 152-164.

Encarnacion S, Calderon J, Gelbard AS, Cooper AJ, Mora J 1998 Glutamine biosynthesis and the utilization of succinate and glutamine by Rhizobium etli and Sinorhizobium meliloti. Microbiology 144: 2629-2638.

Engel JM, Muhling J, Weiss S, Karcher B, Lohr T, Menges T, Little S, Hempelmann G 2006 Relationship of taurine and other amino acids in plasma and in neutrophils of septic trauma patients. Amino Acids 30: 87-94.

Engel N, van den Daele K, Kolukisaoglu U, Morgenthal K, Weckwerth W, Parnik T, Keerberg O, Bauwe H 2007 Deletion of glycine decarboxylase in Arabidopsis is lethal under nonphotorespiratory conditions. Plant Physiol. 144: 1328-1335.

Engels B, Dahm P, Jennewein S 2008 Metabolic engineering of taxadiene biosynthesis in yeast as a first step towards Taxol (Paclitaxel) production. Metab. Eng. 10: 201-206.

Ensminger I, Busch F, Huner NPA 2006 Photostasis and cold acclimation: sensing low temperature through photosynthesis. Physiol. Plant. 126: 28-44.

Epimashko S, Meckel T, Fischer-Schliebs E, Luttge U, Thiel G 2004 Two functionally different vacuoles for static and dynamic purposes in one plant mesophyll leaf cell. Plant J. 37: 294-300.

Escher CL, Widmer F 1997 Lipid mobilization and gluconeogenesis in plants: do glyoxylate cycle enzyme activities constitute a real cycle? A hypothesis. Biol. Chem. 378: 803-813.

Espen L, Dell'Orto M, De Nisi P, Zocchi G 2000 Metabolic responses in cucumber (Cucumis sativus L.) roots under Fe-deficiency: a 31P-nuclear magnetic resonance in-vivo study. Planta 210: 985-992.

Ettenhuber C, Radykewicz T, Kofer W, Koop HU, Bacher A, Eisenreich W 2005 Metabolic flux analysis in complex isotopolog space. Recycling of glucose in tobacco plants. Phytochemistry 66: 323-335.

Ewering C, Heuser F, Benolken JK, Bramer CO, Steinbuchel A 2006 Metabolic engineering of strains of Ralstonia eutropha and Pseudomonas putida for biotechnological production of 2-methylcitric acid. Metab. Eng. 8: 587-602.

Facchini PJ, De Luca V 2008 Opium poppy and Madagascar periwinkle: model non-model systems to investigate alkaloid biosynthesis in plants. Plant J. 54: 763-784.

Facchini PJ, DiCosmo F 1991 Secondary metabolite biosynthesis in cultured cells of Catharanthus roseus (L.) G. Don immobilized by adhesion to glass fibres. Appl. Microbiol. Biotechnol. 35: 382-392.

Fahmy AS, Mohamed SA, Girgis RB, Abdel-Ghaffar FA 1997 Enzymes of delta 1-pyrroline-5-carboxylate metabolism in the camel tick Hyalomma dromedarii during embryogenesis. Purification and characterization of delta 1-pyrroline-5-carboxylate dehydrogenases. Comp. Biochem. Physiol. [B.] 118: 229-237.

Fait A, Angelovici R, Less H, Ohad I, Urbanczyk-Wochniak E, Fernie AR, Galili G 2006 Arabidopsis seed development and germination is associated with temporally distinct metabolic switches. Plant Physiol. 142: 839-854.

Fait A, Fromm H, Walter D, Galili G, Fernie AR 2008 Highway or byway: the metabolic role of the GABA shunt in plants. Trends Plant Sci. 13: 14-19.

Fait A, Hanhineva K, Beleggia R, Dai N, Rogachev I, Nikiforova VJ, Fernie AR, Aharoni A 2008 Reconfiguration of the achene and receptacle metabolic networks during strawberry fruit development. Plant Physiol. Aug 20 [Epub ahead of print].

Falk KL, Behal RH, Xiang C, Oliver DJ 1998 Metabolic bypass of the tricarboxylic acid cycle during lipid mobilization in germinating oilseeds. Regulation of NAD+-dependent isocitrate dehydrogenase versus fumarase. Plant Physiol. 117: 473-481.

Falk KL, Tokuhisa JG, Gershenzon J 2007 The effect of sulfur nutrition on plant glucosinolate content: physiology and molecular mechanisms. Plant Biol. (Stuttg.) 9: 573-581.

Falkenberg B, Witt I, Zanor MI, Steinhauser D, Mueller-Roeber B, Hesse H, Hoefgen R 2008 Transcription factors relevant to auxin signalling coordinate broad-spectrum metabolic shifts including sulphur metabolism. J. Exp. Bot. 59: 2831-2846.

Falkenberg M, Larsson NG, Gustafsson CM 2007 DNA replication and transcription in mammalian mitochondria. Annu. Rev. Biochem. 76: 679-699.

Fall CP, Keizer JE 2001 Mitochondrial modulation of intracellular Ca(2+) signaling. J. Theor. Biol. 210: 151-165.

Famili I, Forster J, Nielsen J, Palsson BO 2003 Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network. Proc. Natl. Acad. Sci. U.S.A. 100: 13134-13139.

Famili I, Mahadevan R, Palsson BO 2005 k-Cone analysis: determining all candidate values for kinetic parameters on a network scale. Biophys. J. 88: 1616-1625.

Fan J, Quan S, Orth T, Awai C, Chory J, Hu J 2005 The Arabidopsis PEX12 gene is required for peroxisome biogenesis and is essential for development. Plant Physiol. 139: 231-239.

Fani R, Brilli M, Fondi M, Lio P 2007 The role of gene fusions in the evolution of metabolic pathways: the histidine biosynthesis case. BMC Evol. Biol. 7 Suppl. 2: S4.

Farmer WR, Liao JC 2000 Improving lycopene production in Escherichia coli by engineering metabolic control. Nat. Biotechnol. 18: 533-537.

Farre EM, Bachmann A, Willmitzer L, Trethewey RN 2001 Acceleration of potato tuber sprouting by the expression of a bacterial pyrophosphatase. Nat. Biotechnol. 19: 268-272.

Farre EM, Geigenberger P, Willmitzer L, Trethewey RN 2000 A possible role for pyrophosphate in the coordination of cytosolic and plastidial carbon metabolism within the potato tuber. Plant Physiol. 123: 681-688.

Farre EM, Tech S, Trethewey RN, Fernie AR, Willmitzer L 2006 Subcellular pyrophosphate metabolism in developing tubers of potato (Solanum tuberosum). Plant Mol. Biol. 62: 165-179.

Fasia L, Karava V, Siafaka-Kapadai A 2003 Uptake and metabolism of [3H]anandamide by rabbit platelets. Eur. J. Biochem. 270: 3498-3506.

Fatland BL, Nikolau BJ, Wurtele ES 2005 Reverse genetic characterization of cytosolic acetyl-CoA generation by ATP-citrate lyase in Arabidopsis. Plant Cell 17: 182-203.

Faure JD, Jullien M, Caboche M 1994 Zea3: a pleiotropic mutation affecting cotyledon development, cytokinin resistance and carbon-nitrogen metabolism. Plant J. 5: 481-491.

Featherstone DE, Broadie K 2002 Wrestling with pleiotropy: genomic and topological analysis of the yeast gene expression network. Bioessays 24: 267-274.

Feist AM, Palsson BO 2008 The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat. Biotechnol. 26: 659-667.

Feist AM, Scholten JC, Palsson BO, Brockman FJ, Ideker T 2006 Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Mol. Syst. Biol. 2: 2006.0004.

Fell DA 2005 Enzymes, metabolites and fluxes. J. Exp. Bot. 56: 267-272.

Fell DA 1997 Systems properties of metabolic networks. Proceedings of the International Conference on Complex Systems, Nashua, NH, 21-26 Sept, 1997.

Fell DA 1992 Metabolic Control Analysis - a survey of its theoretical and experimental development. Biochem. J. 286: 313-330.

Fell DA 1998 Increasing the flux in metabolic pathways: a metabolic control analysis perspective. Biotechnol. Bioeng. 58: 121-124.

Fell DA, Thomas S 1995 Physiological control of metabolic flux: the requirement for multisite modulation. Biochem. J. 311: 35-39.

Fell DA, Wagner A 2000 The small world of metabolism. Nat. Biotechnol. 18: 1121-1122.

Fell DA, Wagner A 2000 Structural properties of metabolic networks: implications for evolution and modelling of metabolism. In: "Animating the cellular map" (Hofmeyr J-HS, Rohwer JM, Snoep JL eds) Stellenbosch Press, Stellenbosch, pp. 79-85.

Feng D, Ho D, Lau KK, Siu WC 1999 GLLS for optimally sampled continuous dynamic system modeling: theory and algorithm. Comput. Methods Programs Biomed. 59: 31-43.

Feng J, Atkinson MR, McCleary W, Stock JB, Wanner BL, Ninfa AJ 1992 Role of phosphorylated metabolic intermediates in the regulation of glutamine synthetase synthesis in Escherichia coli. J. Bacteriol. 174: 6061-6070.

Fernandez AP, Strand A 2008 Retrograde signaling and plant stress: plastid signals initiate cellular stress responses. Curr. Opin. Plant Biol. Jul 16 [Epub ahead of print].

Fernandez-Murray JP, McMaster CR 2005 Glycerophosphocholine catabolism as a new route for choline formation for phosphatidylcholine synthesis by the Kennedy pathway. J. Biol. Chem. 280: 38290-38296.

Fernie AR, Geigenberger P, Stitt M 2005 Flux an important, but neglected, component of functional genomics. Curr. Opin. Plant Biol. 8: 174-182.

Fernie AR, Roessner U, Trethewey RN, Willmitzer L 2001 The contribution of plastidial phosphoglucomutase to the control of starch synthesis within the potato tuber. Planta 213: 418-426.

Fernie AR, Tadmor Y, Zamir D 2006 Natural genetic variation for improving crop quality. Curr. Opin. Plant Biol. 9: 196-202.

Ferreira C, Lucas C 2007 Glucose repression over Saccharomyces cerevisiae glycerol/H+ symporter gene STL1 is overcome by high temperature. FEBS Lett. 581: 1923-1927.

Ferrer JL, Austin MB, Stewart C Jr, Noel JP 2008 Structure and function of enzymes involved in the biosynthesis of phenylpropanoids. Plant Physiol. Biochem. 46: 356-370.

Feussner I, Wasternack C 2002 The lipoxygenase pathway. Annu. Rev. Plant Biol. 53: 275-297.

Fiegel HC, Kaufmann PM, Bruns H, Kluth D, Horch RE, Vacanti JP, Kneser U 2008 Hepatic tissue engineering: from transplantation to customized cell-based liver directed therapies from the laboratory. J. Cell. Mol. Med. 12: 56-66.

Fiehn O 2002 Metabolomics--the link between genotypes and phenotypes. Plant Mol. Biol. 48: 155-171.

Fiehn O 2001 Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks. Comparative & Functional Genomics 2: 155-168.

Fiehn O 2003 Metabolic networks of Cucurbita maxima phloem. Phytochemistry 62: 875-886.

Fiehn O 2001 Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks. Comp. Funct. Genomics 2: 155-168.

Fiehn O, Kopka J, Dormann P, Altmann T, Trethewey RN, Willmitzer L 2000 Metabolite profiling for plant functional genomics. Nat. Biotechnol. 18: 1157-1161.

Fiehn O, Weckwerth W 2003 Deciphering metabolic networks. Eur. J. Biochem. 270: 579-588.

Field B, Cardon G, Traka M, Botterman J, Vancanneyt G, Mithen R 2004 Glucosinolate and amino acid biosynthesis in Arabidopsis. Plant Physiol. 135: 828-839.

Figueiredo A, Fortes AM, Ferreira S, Sebastiana M, Choi YH, Sousa L, Acioli-Santos B, Pessoa F, Verpoorte R, Pais MS 2008 Transcriptional and metabolic profiling of grape (Vitis vinifera L.) leaves unravel possible innate resistance against pathogenic fungi. J. Exp. Bot. Jul 22 [Epub ahead of print].

Filipe CD, Daigger GT, Grady CP Jr 2001 A metabolic model for acetate uptake under anaerobic conditions by glycogen accumulating organisms: Stoichiometry, kinetics, and the effect of pH. Biotechnol. Bioeng. 76: 17-31.

Finkelstein JD 2006 Inborn errors of sulfur-containing amino acid metabolism. J. Nutr. 136: 1750S-1754S.

Fischer CR, Klein-Marcuschamer D, Stephanopoulos G 2008 Selection and optimization of microbial hosts for biofuels production. Metab. Eng. Jul 3 [Epub ahead of print].

Fischer E, Sauer U 2005 Large-scale in vivo flux analysis shows rigidity and suboptimal performance of Bacillus subtilis metabolism. Nat. Genet. 37: 636-640.

Fischer E, Sauer U 2003 Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism using GC-MS. Eur. J. Biochem. 270: 880-891.

Fischer HP 2005 Towards quantitative biology: integration of biological information to elucidate disease pathways and to guide drug discovery. Biotechnol. Annu. Rev. 11: 1-68.

Fischer R, Drossard J, Schillberg S, Artsaenko O, Emans N, Naehring JM 2000 Chapter 5. Modulation of Plant Function and Plant Pathogens by Antibody Expression. In "Metabolic Engineering of Plant Secondary Metabolism" (Verpoorte R, Alfermann AW, eds), Kluwer Academic Publishers, Dortrecht, The Netherlands, pp. 87-109.

Fisher SH, Wray LV Jr 1989 Regulation of glutamine synthetase in Streptomyces coelicolor. J. Bacteriol. 171: 2378-2383.

Fleming A 2006 Metabolic aspects of organogenesis in the shoot apical meristem. J. Exp. Bot. 57: 1863-1870.

Flexas J, Bota J, Loreto F, Cornic G, Sharkey TD 2004 Diffusive and metabolic limitations to photosynthesis under drought and salinity in C(3) plants. Plant Biol. (Stuttg.) 6: 269-279.

Flores N, Xiao J, Berry A, Bolivar F, Valle F 1996 Pathway engineering for the production of aromatic compounds in Escherichia coli. Nat. Biotechnol. 14: 620-623.

Floryszak-Wieczorek J, Milczarek G, Arasimowicz M, Ciszewski A 2006 Do nitric oxide donors mimic endogenous NO-related response in plants? Planta 224: 1363-1372.

Fojtova M, Kovarik A, Votruba I, Holy A 1998 Evaluation of the impact of S-adenosylhomocysteine metabolic pools on cytosine methylation of the tobacco genome. Eur. J. Biochem. 252: 347-352.

Follstad BD, Stephanopoulos G 1998 Effect of reversible reactions on isotope label redistribution--analysis of the pentose phosphate pathway. Eur. J. Biochem. 252: 360-371.

Fondi M, Brilli M, Emiliani G, Paffetti D, Fani R 2007 The primordial metabolism: an ancestral interconnection between leucine, arginine, and lysine biosynthesis. BMC Evol. Biol. 7 Suppl. 2: S3.

Fondi M, Brilli M, Fani R 2007 On the origin and evolution of biosynthetic pathways: integrating microarray data with structure and organization of the Common Pathway genes. BMC Bioinformatics 8 Suppl. 1: S12.

Fong SS, Marciniak JY, Palsson BO 2003 Description and interpretation of adaptive evolution of Escherichia coli K-12 MG1655 by using a genome-scale in silico metabolic model. J. Bacteriol. 185: 6400-6408.

Fong SS, Nanchen A, Palsson BO, Sauer U 2006 Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes. J. Biol. Chem. 281: 8024-8033.

Fong SS, Palsson BO 2004 Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes. Nat. Genet. 36: 1056-1058.

Fonseca CP, Jones JG, Carvalho RA, Jeffrey FM, Montezinho LP, Geraldes CF, Castro MM 2005 Tricarboxylic acid cycle inhibition by Li+ in the human neuroblastoma SH-SY5Y cell line: a 13C NMR isotopomer analysis. Neurochem. Int. 47: 385-393.

Fonseca LL, Monteiro MA, Alves PM, Carrondo MJ, Santos H 2005 Cultures of rat astrocytes challenged with a steady supply of glutamate: new model to study flux distribution in the glutamate-glutamine cycle. Glia 51: 286-296.

Fontecave M, Atta M, Mulliez E 2004 S-Adenosylmethionine: nothing goes to waste. Trends Biochem. Sci. 29: 243-249.

Forbes NS, Clark DS, Blanch HW 2001 Using isotopomer path tracing to quantify metabolic fluxes in pathway models containing reversible reactions. Biotechnol. Bioeng. 74: 196-211.

Forlani G, Obojska A, Berlicki L, Kafarski P 2006 Phosphinothricin analogues as inhibitors of plant glutamine synthetases. J. Agric. Food Chem. 54: 796-802.

Forsberg H, Gilstring CF, Zargari A, Martinez P, Ljungdahl PO 2001 The role of the yeast plasma membrane SPS nutrient sensor in the metabolic response to extracellular amino acids. Mol. Microbiol. 42: 215-228.

Forst CV, Schulten K 1999 Evolution of metabolisms: a new method for the comparison of metabolic pathways using genomics information. J. Comput. Biol. 6: 343-360.

Forster J, Famili I, Fu P, Palsson BO, Nielsen J 2003 Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res. 13: 244-253.

Forster J, Famili I, Palsson BO, Nielsen J 2003 Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae. OMICS 7: 193-202.

Forster ME 1988 Citric acid cycle as a "one-step" reaction. J. Theor. Biol. 133: 1-11.

Fouchard S, Pruvost J, Degrenne B, Titica M, Legrand J 2008 Kinetic modeling of light limitation and sulfur deprivation effects in the induction of hydrogen production with Chlamydomonas reinhardtii: Part I. Model development and parameter identification. Biotechnol. Bioeng. Jul 18 [Epub ahead of print].

Fowler B 2005 Homocysteine: overview of biochemistry, molecular biology, and role in disease processes. Semin. Vasc. Med. 5: 77-86.

Fowler S, Zhang H 2008 In vitro evaluation of reversible and irreversible cytochrome P450 inhibition: current status on methodologies and their utility for predicting drug-drug interactions. AAPS J. Aug 7 [Epub ahead of print].

Foyer CH, Noctor G 2005 Redox homeostasis and antioxidant signaling: a metabolic interface between stress perception and physiological responses. Plant Cell 17: 1866-1875.

Franceschetti M, Perry B, Thompson B, Hanfrey C, Michael AJ 2004 Expression proteomics identifies biochemical adaptations and defense responses in transgenic plants with perturbed polyamine metabolism. FEBS Lett. 576: 477-480.

Francis D, Halford NG 2006 Nutrient sensing in plant meristems. Plant Mol. Biol. 60: 981-993.

Franke R, McMichael CM, Meyer K, Shirley AM, Cusumano JC, Chapple C 2000 Modified lignin in tobacco and poplar plants over-expressing the Arabidopsis gene encoding ferulate 5-hydroxylase. Plant J. 22: 223-234.

Frederich M, Choi YH, Angenot L, Harnischfeger G, Lefeber AW, Verpoorte R 2004 Metabolomic analysis of Strychnos nux-vomica, Strychnos icaja and Strychnos ignatii extracts by (1)H nuclear magnetic resonance spectrometry and multivariate analysis techniques. Phytochemistry 65: 1993-2001.

Fredlund E, Beerlage C, Melin P, Schnurer J, Passoth V 2006 Oxygen and carbon source-regulated expression of PDC and ADH genes in the respiratory yeast Pichia anomala. Yeast 23: 1137-1149.

Freitag A, Mendez C, Salas JA, Kammerer B, Li SM, Heide L 2006 Metabolic engineering of the heterologous production of clorobiocin derivatives and elloramycin in Streptomyces coelicolor M512. Metab. Eng. 8: 653-661.

Frelet-Barrand A, Kolukisaoglu HU, Plaza S, Ruffer M, Azevedo L, Hortensteiner S, Marinova K, Weder B, Schulz B, Klein M 2008 Comparative mutant analysis of Arabidopsis ABCC-type ABC transporters: AtMRP2 contributes to detoxification, vacuolar organic anion transport and chlorophyll degradation. Plant Cell Physiol. 49: 557-569.

Frick O, Wittmann C 2005 Characterization of the metabolic shift between oxidative and fermentative growth in Saccharomyces cerevisiae by comparative 13C flux analysis. Microb. Cell. Fact. 4: 30.

Fricke W, Pahlich E 1992 Malate: a possible source of error in the NAD glutamate dehydrogenase assay. J. Exp. Bot. 43: 1515-1518.

Fridlyand LE, Backhausen JE, Scheibe R 1999 Homeostatic regulation upon changes of enzyme activities in the Calvin cycle as an example for general mechanisms of flux control. What can we expect from transgenic plants? Photosynth. Res. 61: 227-239.

Fridlyand LE, Scheibe R 2000 Regulation in metabolic systems under homeostatic flux control. Arch. Biochem. Biophys 374: 198-206..

Fridlyand LE, Scheibe R 1999 Regulation of the Calvin cycle for CO2 fixation as an example for general control mechanisms in metabolic cycles. Biosystems 51: 79-93.

Fridman E, Pichersky E 2005 Metabolomics, genomics, proteomics, and the identification of enzymes and their substrates and products. Curr. Opin. Plant Biol. 8: 242-248.

Fridman E, Wang J, Iijima Y, Froehlich JE, Gang DR, Ohlrogge J, Pichersky E 2005 Metabolic, genomic, and biochemical analyses of glandular trichomes from the wild tomato species Lycopersicon hirsutum identify a key enzyme in the biosynthesis of methylketones. Plant Cell 17: 1252-1267.

Frizzi A, Huang S, Gilbertson LA, Armstrong TA, Luethy MH, Malvar TM 2008 Modifying lysine biosynthesis and catabolism in corn with a single bifunctional expression/silencing transgene cassette. Plant Biotechnol. J. 6: 13-21.

Fu J, Momcilovic I, Clemente TE, Nersesian N, Trick HN, Ristic Z 2008 Heterologous expression of a plastid EF-Tu reduces protein thermal aggregation and enhances CO(2) fixation in wheat (Triticum aestivum) following heat stress. Plant Mol. Biol. Jul 13 [Epub ahead of print].

Fu J, Peterson K, Guttieri M, Souza E, Raboy V 2008 Barley (Hordeum vulgare L.) inositol monophosphatase: gene structure and enzyme characteristics. Plant Mol. Biol. 67: 629-642.

Fu J, Sampalo R, Gallardo F, Canovas FM, Kirby EG 2003 Assembly of a cytosolic pine glutamine synthetase holoenzyme in leaves of transgenic poplar leads to enhanced vegetative growth in young plants. Plant Cell Environ. 26: 411-418.

Fu J, Swertz MA, Keurentjes JJ, Jansen RC 2007 MetaNetwork: a computational protocol for the genetic study of metabolic networks. Nat. Protoc. 2: 685-694.

Fu J, Wenzel SC, Perlova O, Wang J, Gross F, Tang Z, Yin Y, Stewart AF, Muller R, Zhang Y 2008 Efficient transfer of two large secondary metabolite pathway gene clusters into heterologous hosts by transposition. Nucleic Acids Res. Aug 13 [Epub ahead of print].

Fu L, Miseta A, Hunton D, Marchase RB, Bedwell DM 2000 Loss of the major isoform of phosphoglucomutase results in altered calcium homeostasis in Saccharomyces cerevisiae. J. Biol. Chem. 275: 5431-5440.

Fu RY, Bongers RS, van Swam II, Chen J, Molenaar D, Kleerebezem M, Hugenholtz J, Li Y 2006 Introducing glutathione biosynthetic capability into Lactococcus lactis subsp. cremoris NZ9000 improves the oxidative-stress resistance of the host. Metab. Eng. 8: 662-671.

Fu YH, Marzluf GA 1990 nit-2, the major nitrogen regulatory gene of Neurospora crassa, encodes a protein with a putative zinc finger DNA-binding domain. Mol. Cell Biol. 10: 1056-1065.

Fujii N, Inui T, Iwasa K, Morishige T, Sato F 2007 Knockdown of berberine bridge enzyme by RNAi accumulates (S)-reticuline and activates a silent pathway in cultured California poppy cells. Transgenic Res. 16: 363-375.

Fujioka S, Yokota T 2003 Biosynthesis and metabolism of brassinosteroids. Annu. Rev. Plant Biol. 54: 137-164.

Fujisawa M, Watanabe M, Choi SK, Teramoto M, Ohyama K, Misawa N 2008 Enrichment of carotenoids in flaxseed (Linum usitatissimum) by metabolic engineering with introduction of bacterial phytoene synthase gene crtB. J. Biosci. Bioeng. 105: 636-641.

Fujiwara M, Umemura K, Kawasaki T, Shimamoto K 2006 Proteomics of Rac GTPase signaling reveals its predominant role in elicitor-induced defense response of cultured rice cells. Plant Physiol. 140: 734-745.

Fukao T, Xu K, Ronald PC, Bailey-Serres J 2006 A variable cluster of ethylene response factor-like genes regulates metabolic and developmental acclimation responses to submergence in rice. Plant Cell 18: 2021-2034.

Fulton TM, Van Der Hoeven R, Eannetta NT, Tanksley SD 2002 Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell 14: 1457-1467.

Fung E, Wong WW, Suen JK, Bulter T, Lee SG, Liao JC 2005 A synthetic gene-metabolic oscillator. Nature 435: 118-122.

Fussenegger M 2001 The impact of mammalian gene regulation concepts on functional genomic research, metabolic engineering, and advanced gene therapies. Biotechnol. Prog. 17: 1-51.

Fux C, Fussenegger M 2003 Toward higher order control modalities in mammalian cells-independent adjustment of two different gene activities. Biotechnol. Prog. 19: 109-120.

Gachon CM, Langlois-Meurinne M, Henry Y, Saindrenan P 2005 Transcriptional co-regulation of secondary metabolism enzymes in Arabidopsis: functional and evolutionary implications. Plant Mol. Biol. 58: 229-245.

Gagneul D, Ainouche A, Duhaze C, Lugan R, Larher FR, Bouchereau A 2007 A reassessment of the function of the so-called compatible solutes in the halophytic plumbaginaceae Limonium latifolium. Plant Physiol. 144: 1598-1611.

Gagneur J, Klamt S 2004 Computation of elementary modes: a unifying framework and the new binary approach. BMC Bioinformatics 5: 175.

Galban CJ, Locke BR 1997 Analysis of cell growth in a polymer scaffold using a moving boundary approach. Biotechnol. Bioeng. 56: 422-432.

Galili G, Hofgen R 2002 Metabolic engineering of amino acids and storage proteins in plants. Metab. Eng. 4: 3-11.

Galili G, Tang G, Zhu X, Gakiere B 2001 Lysine catabolism: a stress and development super-regulated metabolic pathway. Curr. Opin. Plant Biol. 4: 261-266.

Galili G, Tang GL, Zhu XH, Amir R, Levanony H, Shy G, Herman EM 2000 Plant seeds: An exciting model system for dissecting molecular and cellular regulation of metabolic processes. Isr. J. Plant Sci. 48: 181-187.

Galis I, Simek P, Narisawa T, Sasaki M, Horiguchi T, Fukuda H, Matsuoka K 2006 A novel R2R3 MYB transcription factor NtMYBJS1 is a methyl jasmonate-dependent regulator of phenylpropanoid-conjugate biosynthesis in tobacco. Plant J. 46: 573-592.

Gallagher CE, Matthews PD, Li F, Wurtzel ET 2004 Gene duplication in the carotenoid biosynthetic pathway preceded evolution of the grasses. Plant Physiol. 135: 1776-1783.

Gallagher DT, Gilliland GL, Xiao G, Zondlo J, Fisher KE, Chinchilla D, Eisenstein E 1998 Structure and control of pyridoxal phosphate dependent allosteric threonine deaminase. Structure 6: 465-475.

Gallardo K, Job C, Groot SP, Puype M, Demol H, Vandekerckhove J, Job D 2002 Proteomics of Arabidopsis seed germination. A comparative study of wild-type and gibberellin-deficient seeds. Plant Physiol. 129: 823-837.

Galpaz N, Ronen G, Khalfa Z, Zamir D, Hirschberg J 2006 A chromoplast-specific carotenoid biosynthesis pathway is revealed by cloning of the tomato white-flower locus. Plant Cell 18: 1947-1960.

Galvez S, Lancien M, Hodges M 1999 Are isocitrate dehydrogenases and 2-oxoglutarate involved in the regulation of glutamate synthesis? Trends Plant Sci. 4: 484-490.

Gambhir A, Korke R, Lee J, Fu PC, Europa A, Hu WS 2003 Analysis of cellular metabolism of hybridoma cells at distinct physiological states. J. Biosci. Bioeng. 95: 317-327.

Gandre S, Bercovich Z, Kahana C 2002 Ornithine decarboxylase-antizyme is rapidly degraded through a mechanism that requires functional ubiquitin-dependent proteolytic activity. Eur. J. Biochem. 269: 1316-1322.

Gang DR 2005 Evolution of flavors and scents. Annu. Rev. Plant Biol. 56: 301-325.

Gangl IC, Weigand WA, Keller FA 1991 Metabolic modeling of fumaric acid production by Rhizopus arrhizus. Appl. Biochem. Biotechnol. 29: 471-486.

Gao C, Wang Y, Liu G, Yang C, Jiang J, Li H 2008 Expression profiling of salinity-alkali stress responses by large-scale expressed sequence tag analysis in Tamarix hispid. Plant Mol. Biol. 66: 245-258.

Garabagi F, Duns G, Strommer J 2005 Selective recruitment of Adh genes for distinct enzymatic functions in Petunia hybrida. Plant Mol. Biol. 58: 283-294.

Garcia J, Shea J, Alvarez-Vasquez F, Qureshi A, Luberto C, Voit EO, Del Poeta M 2008 Mathematical modeling of pathogenicity of Cryptococcus neoformans. Mol. Syst. Biol. 4: 183.

Garcia-Espinosa MA, Rodrigues TB, Sierra A, Benito M, Fonseca C, Gray HL, Bartnik BL, Garcia-Martin ML, Ballesteros P, Cerdan S 2004 Cerebral glucose metabolism and the glutamine cycle as detected by in vivo and in vitro NMR spectroscopy. Neurochem. Int. 45: 297-303.

Garcia-Maurino S, Jimenez ET, Monreal JA, Morillo-Velarde R, Echevarria C 2005 Adenylate patterns of autumn-sown sugar beet differ from spring-sown sugar beet. Implications for root quality. Physiol. Plant. 124: 200-207.

Garfinkel D, Achs MJ, Kohn MC, Menten LE 1979 Analysis of metabolic modeling in terms of engineering and computer science techniques. Fed. Proc. 38: 991-991.

Garg AK, Sawers RJ, Wang H, Kim JK, Walker JM, Brutnell TP, Parthasarathy MV, Vierstra RD, Wu RJ 2006 Light-regulated overexpression of an Arabidopsis phytochrome A gene in rice alters plant architecture and increases grain yield. Planta 223: 627-636.

Gavaghan McKee CL, Wilson ID, Nicholson JK 2006 Metabolic phenotyping of nude and normal (Alpk:ApfCD, C57BL10J) mice. J. Proteome Res. 5: 378-384.

Gavilano LB, Coleman NP, Burnley LE, Bowman ML, Kalengamaliro NE, Hayes A, Bush L, Siminszky B 2006 Genetic engineering of Nicotiana tabacum for reduced nornicotine content. J. Agric. Food Chem. 54: 9071-9078.

Gaxiola RA, Palmgren MG, Schumacher K 2007 Plant proton pumps. FEBS Lett. 581: 2204-2214.

Gayen K, Venkatesh KV 2006 Analysis of optimal phenotypic space using elementary modes as applied to Corynebacterium glutamicum. BMC Bioinformatics 7: 445.

Geck MK, Kirsch JF 1999 A novel, definitive test for substrate channeling illustrated with the aspartate aminotransferase/malate dehydrogenase system. Biochemistry 38: 8032-8037.

Gegelashvili M, Rodriguez-Kern A, Pirozhkova I, Zhang J, Sung L, Gegelashvili G 2006 High-affinity glutamate transporter GLAST/EAAT1 regulates cell surface expression of glutamine/neutral amino acid transporter ASCT2 in human fetal astrocytes. Neurochem. Int. 48: 611-615.

Geigenberger P 2003 Regulation of sucrose to starch conversion in growing potato tubers. J. Exp. Bot. 54: 457-465.

Geigenberger P, Fernie AR, Gibon Y, Christ M, Stitt M 2000 Metabolic activity decreases as an adaptive response to low internal oxygen in growing potato tubers. Biol. Chem. 381: 723-740.

Geigenberger P, Kolbe A, Tiessen A 2005 Redox regulation of carbon storage and partitioning in response to light and sugars. J. Exp. Bot. 56: 1469-1479.

Geigenberger P, Regierer B, Lytovchenko A, Leisse A, Schauer N, Springer F, Kossmann J, Fernie AR 2004 Heterologous expression of a ketohexokinase in potato plants leads to inhibited rates of photosynthesis, severe growth retardation and abnormal leaf development. Planta 218: 569-578.

Geigenberger P, Stitt M, Fernie AR 2004 Metabolic control analysis and regulation of the conversion of sucrose to starch in growing potato tubers. Plant Cell Environ. 27: 655-673.

Genard M, Bertin N, Borel C, Bussieres P, Gautier H, Habib R, Lechaudel M, Lecomte A, Lescourret F, Lobit P, Quilot B 2007 Towards a virtual fruit focusing on quality: modelling features and potential uses. J. Exp. Bot. 58: 917-928.

Gerdes S, Edwards R, Kubal M, Fonstein M, Stevens R, Osterman A 2006 Essential genes on metabolic maps. Curr. Opin. Biotechnol. 17: 448-456.

Gerdes SY, Kurnasov OV, Shatalin K, Polanuyer B, Sloutsky R, Vonstein V, Overbeek R, Osterman AL 2006 Comparative genomics of NAD biosynthesis in cyanobacteria. J. Bacteriol. 188: 3012-3023.

Gerdtzen ZP, Daoutidis P, Hu WS 2004 Non-linear reduction for kinetic models of metabolic reaction networks. Metab. Eng. 6: 140-154.

Gerlach JC, Zeilinger K, Patzer II JF 2008 Bioartificial liver systems: why, what, whither? Regen. Med. 3: 575-595.

Gershenzon J, McConkey ME, Croteau RB 2000 Regulation of monoterpene accumulation in leaves of peppermint. Plant Physiol. 122: 205-214.

Gessler A, Tcherkez G, Peuke AD, Ghashghaie J, Farquhar GD 2008 Experimental evidence for diel variations of the carbon isotope composition in leaf, stem and phloem sap organic matter in Ricinus communis. Plant Cell Environ. 31: 941-953.

Gevorgyan A, Poolman MG, Fell DA 2008 Detection of stoichiometric inconsistencies in biomolecular models. Bioinformatics Aug 12 [Epub ahead of print].

Gharbi I, Ricard B, Rolin D, Maucourt M, Andrieu MH, Bizid E, Smiti S, Brouquisse R 2007 Effect of hexokinase activity on tomato root metabolism during prolonged hypoxia. Plant Cell Environ. 30: 508-517.

Gharieb MM, Gadd GM 2004 The kinetics of 75[Se]-selenite uptake by Saccharomyces cerevisiae and the vacuolization response to high concentrations. Mycol. Res. 108: 1415-1422.

Ghim CM, Goh KI, Kahng B 2005 Lethality and synthetic lethality in the genome-wide metabolic network of Escherichia coli. J. Theor. Biol. 237: 401-411.

Ghosh S, Grant DF, Dey DK, Hill DW 2008 A semiparametric modeling framework for potential biomarker discovery and the development of metabonomic profiles. BMC Bioinformatics 9: 38.

Ghosh S, Grossmann IE, Ataai MM, Domach MM 2006 A three-level problem-centric strategy for selecting NMR precursor labeling and analytes. Metab. Eng. 8: 491-507.

Gianchandani EP, Oberhardt MA, Burgard AP, Maranas CD, Papin JA 2008 Predicting biological system objectives de novo from internal state measurements. BMC Bioinformatics 9: 43.

Gibson SI 2004 Sugar and phytohormone response pathways: navigating a signalling network. J. Exp. Bot. 55: 253-264.

Giddings G, Allison G, Brooks D, Carter A 2000 Transgenic plants as factories for biopharmaceuticals. Nat. Biotechnol. 18: 1151-1155.

Giersch C 1997 Co-response coefficients, monovalent units, and combinatorial rules: unification of concepts in Metabolic Control Analysis. J. Theor. Biol. 189: 1-9.

Giersch C 2000 Mathematical modelling of metabolism. Curr. Opin. Plant Biol. 3: 249-253.

Giersch C, Cornish-Bowden A 1996 Extending double modulation: Combinatorial rules for identifying the modulations necessary for determining elasticities in metabolic pathways. J. Theor. Biol. 182: 361-369.

Gil MJ, Coego A, Mauch-Mani B, Jorda L, Vera P 2005 The Arabidopsis csb3 mutant reveals a regulatory link between salicylic acid-mediated disease resistance and the methyl-erythritol 4-phosphate pathway. Plant J. 44: 155-166.

Gill RT 2003 Enabling inverse metabolic engineering through genomics. Curr. Opin. Biotechnol. 14: 484-490.

Gill RT, Dodge T 2004 Special issue on inverse metabolic engineering. Metab. Eng. 6: 175-176.

Gille C, Hoffmann S, Holzhutter HG 2005 Combining bioinformatics resources for the structural modelling of eukaryotic metabolic networks. Genome Inform. Ser. Workshop Genome Inform. 16: 223-232.

Gilliland A, Singh DP, Hayward JM, Moore CA, Murphy AM, York CJ, Slator J, Carr JP 2003 Genetic modification of alternative respiration has differential effects on antimycin A-induced versus salicylic acid-induced resistance to tobacco mosaic virus. Plant Physiol. 132: 1518-1528.

Gilliland LU, Magallanes-Lundback M, Hemming C, Supplee A, Koornneef M, Bentsink L, DellaPenna D 2006 Genetic basis for natural variation in seed vitamin E levels in Arabidopsis thaliana. Proc. Natl. Acad. Sci. U.S.A. 103: 18834-18841.

Giovannoni JJ 2007 Fruit ripening mutants yield insights into ripening control. Curr. Opin. Plant Biol. 10: 283-289.

Gissot L, Polge C, Jossier M, Girin T, Bouly JP, Kreis M, Thomas M 2006 AKINbetagamma contributes to SnRK1 heterotrimeric complexes and interacts with two proteins implicated in plant pathogen resistance through its KIS/GBD sequence. Plant Physiol. 142: 931-944.

Giuliano G, Tavazza R, Diretto G, Beyer P, Taylor MA 2008 Metabolic engineering of carotenoid biosynthesis in plants. Trends Biotechnol. 26: 139-145.

Giuseppin ML, van Riel NA 2000 Metabolic modeling of Saccharomyces cerevisiae using the optimal control of homeostasis: a cybernetic model definition. Metab. Eng. 2: 14-33.

Givan CV 1999 Evolving concepts in plant glycolysis: two centuries of progress. Biol. Rev. Camb. Phil. Soc. 74: 277-309.

Glaasker E, Konings WN, Poolman B 1996 Glycine betaine fluxes in Lactobacillus plantarum during osmostasis and hyper- and hypo-osmotic shock. J. Biol. Chem. 271: 10060-10065.

Glassbrook G, Beecher C, Ryals J 2000 Metabolic profiling on the right path. Nat. Biotechnol. 18: 1142-1143.

Glassbrook N, Ryals J 2001 A systematic approach to biochemical profiling. Curr. Opin. Plant Biol. 4: 186-190.

Glawischnig E, Gierl A, Tomas A, Bacher A, Eisenreich W 2001 Retrobiosynthetic nuclear magnetic resonance analysis of amino acid biosynthesis and intermediary metabolism. metabolic flux in developing maize kernels. Plant Physiol. 125: 1178-1186.

Glawischnig E, Gierl A, Tomas A, Bacher A, Eisenreich W 2002 Starch biosynthesis and intermediary metabolism in maize kernels. Quantitative analysis of metabolite flux by nuclear magnetic resonance. Plant Physiol. 130: 1717-1727.

Gnanasambandam A, Polkinghorne IG, Birch RG 2007 Heterologous signals allow efficient targeting of a nuclear-encoded fusion protein to plastids and endoplasmic reticulum in diverse plant species. Plant Biotechnol. J. 5: 290-296.

Go VL, Nguyen CT, Harris DM, Paul Lee WN 2005 Nutrient-gene interaction: metabolic genotype-phenotype relationship. J. Nutr. 135: 3016S-3020S.

Goddijn OJ, Lohman FP, de Kam RJ, Schilperoort RA, Hoge JH 1994 Nucleotide sequence of the tryptophan decarboxylase gene of Catharanthus roseus and expression of tdc-gusA gene fusions in Nicotiana tabacum. Mol. Gen. Genet. 242: 217-225.

Goel A, Lee J, Domach MM, Ataai MM 1999 Metabolic fluxes, pools, and enzyme measurements suggest a tighter coupling of energetics and biosynthetic reactions associated with reduced pyruvate kinase flux. Biotechnol. Bioeng. 64: 129-134.

Goerke AR, Loening AM, Gambhir SS, Swartz JR 2008 Cell-free metabolic engineering promotes high-level production of bioactive Gaussia princeps luciferase. Metab. Eng. 10: 187-200.

Goes da Silva F, Iandolino A, Al-Kayal F, Bohlmann MC, Cushman MA, Lim H, Ergul A, Figueroa R, Kabuloglu EK, Osborne C, Rowe J, Tattersall E, Leslie A, Xu J, Baek J, Cramer GR, Cushman JC, Cook DR 2005 Characterizing the grape transcriptome. Analysis of expressed sequence tags from multiple Vitis species and development of a compendium of gene expression during berry development. Plant Physiol. 139: 574-597.

Goffman FD, Alonso AP, Schwender J, Shachar-Hill Y, Ohlrogge JB 2005 Light enables a very high efficiency of carbon storage in developing embryos of rapeseed. Plant Physiol. 138: 2269-2279.

Gokarn RR, Eiteman MA, Altman E 2000 Metabolic analysis of Escherichia coli in the presence and absence of the carboxylating enzymes phosphoenolpyruvate carboxylase and pyruvate carboxylase. Appl. Environ. Microbiol. 66: 1844-1850.

Goldstein BN, Selivanov VA 1990 Graph-theoretic approach to metabolic pathways. Biomed. Biochim. Acta 49: 645-650.

Golovleva L, Golovlev E 2000 Microbial cellular biology and current problems of metabolic engineering. J. Molecular Catalysis B-Enzymatic 10: 5-21.

Gombert AK, Moreira dos Santos M, Christensen B, Nielsen J 2001 Network identification and flux quantification in the central metabolism of Saccharomyces cerevisiae under different conditions of glucose repression. J. Bacteriol. 183: 1441-1451.

Gombert AK, Nielsen J 2000 Mathematical modelling of metabolism. Curr. Opin. Biotechnol. 11: 180-186.

Gomes RA, Miranda HV, Silva MS, Graca G, Coelho AV, Ferreira AE, Cordeiro C, Freire AP 2006 Yeast protein glycation in vivo by methylglyoxal. FEBS J. 273: 5273-5287.

Gong HJ, Zhu XY, Chen KM, Wang SM, Zhang CL 2005 Silicon alleviates oxidative damage of wheat plants in pots under drought. Plant Sci. 169: 313-321.

Gonzalez A, Tenorio M, Vaca G, Mora J 1983 Neurospora crassa mutant impaired in glutamine regulation. J. Bacteriol. 155: 1-7.

Gonzalez O, Gronau S, Falb M, Pfeiffer F, Mendoza E, Zimmer R, Oesterhelt D 2008 Reconstruction, modeling & analysis of Halobacterium salinarum R-1 metabolism. Mol. Biosyst. 4: 148-159.

Gonzalez R, Andrews BA, Molitor J, Asenjo JA 2003 Metabolic analysis of the synthesis of high levels of intracellular human SOD in Saccharomyces cerevisiae rhSOD 2060 411 SGA122. Biotechnol. Bioeng. 82: 152-169.

Gonzalez R, Tao H, Shanmugam KT, York SW, Ingram LO 2002 Global gene expression differences associated with changes in glycolytic flux and growth rate in Escherichia coli during the fermentation of glucose and xylose. Biotechnol. Prog. 18: 6-20.

Gonzalez-Lergier J, Broadbelt LJ, Hatzimanikatis V 2006 Anlysis of the maximum theoretical yield for the synthesis of erythromycin precursors in Escherichia coli. Biotechnol. Bioeng. 95: 638-644.

Gonzalez-Pajuelo M, Meynial-Salles I, Mendes F, Andrade JC, Vasconcelos I, Soucaille P 2005 Metabolic engineering of Clostridium acetobutylicum for the industrial production of 1,3-propanediol from glycerol. Metab. Eng. 7: 329-336.

Goodacre R 2005 Making sense of the metabolome using evolutionary computation: seeing the wood with the trees. J. Exp. Bot. 56: 245-254.

Goodacre R, Vaidyanathan S, Dunn WB, Harrigan GG, Kell DB 2004 Metabolomics by numbers: acquiring and understanding global metabolite data. Trends Biotechnol. 22: 245-252.

Goodacre R, York EV, Heald JK, Scott IM 2003 Chemometric discrimination of unfractionated plant extracts analyzed by electrospray mass spectrometry. Phytochemistry 62: 859-863.

Goryanin I, Hodgman TC, Selkov E 1999 Mathematical simulation and analysis of cellular metabolism and regulation. Bioinformatics 15: 749-758.

Goslings D, Meskauskiene R, Kim C, Lee KP, Nater M, Apel K 2004 Concurrent interactions of heme and FLU with Glu tRNA reductase (HEMA1), the target of metabolic feedback inhibition of tetrapyrrole biosynthesis, in dark- and light-grown Arabidopsis plants. Plant J. 40: 957-967.

Goto S, Bono H, Ogata H, Fujibuchi W, Nishioka T, Sato K, Kanehisa M 1997 Organizing and computing metabolic pathway data in terms of binary relations. Pac. Symp. Biocomput. 1997: 175-186.

Gottlieb OR, Borin MR 2000 Biodiversity: modelling angiosperms as networks. Phytochemistry 55: 559-565.

Goudar C, Biener R, Zhang C, Michaels J, Piret J, Konstantinov K 2006 Towards industrial application of quasi real-time metabolic flux analysis for mammalian cell culture. Adv. Biochem. Eng. Biotechnol. 101: 99-118.

Gouesbet G, Abaibou H, Wu LF, Mandrand-Berthelot MA, Blanco C 1993 Osmotic repression of anaerobic metabolic systems in Escherichia coli. J. Bacteriol. 175: 214-221.

Goulas E, Schubert M, Kieselbach T, Kleczkowski LA, Gardestrom P, Schroder W, Hurry V 2006 The chloroplast lumen and stromal proteomes of Arabidopsis thaliana show differential sensitivity to short- and long-term exposure to low temperature. Plant J. 47: 720-734.

Goupry S, Croguennec T, Gentil E, Robins RJ 2000 Metabolic flux in glucose/citrate co-fermentation by lactic acid bacteria as measured by isotopic ratio analysis. FEMS Microbiol. Lett. 182: 207-211.

Goutsias J, Kim S 2004 A nonlinear discrete dynamical model for transcriptional regulation: construction and properties. Biophys. J. 86: 1922-1945.

Goyer A, Johnson TL, Olsen LJ, Collakova E, Shachar-Hill Y, Rhodes D, Hanson AD 2004 Characterization and metabolic function of a peroxisomal sarcosine and pipecolate oxidase from Arabidopsis. J. Biol. Chem. 279: 16947-16953.

Grace SC, Logan BA 2000 Energy dissipation and radical scavenging by the plant phenylpropanoid pathway. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 355: 1499-1510.

Graciet E, Lebreton S, Gontero B 2004 Emergence of new regulatory mechanisms in the Benson-Calvin pathway via protein-protein interactions: a glyceraldehyde-3-phosphate dehydrogenase/CP12/phosphoribulokinase complex. J. Exp. Bot. 55: 1245-1254.

Graham IA, Larson T, Napier JA 2007 Rational metabolic engineering of transgenic plants for biosynthesis of omega-3 polyunsaturates. Curr. Opin. Biotechnol. 18: 142-147.

Granstrom TB, Aristidou AA, Jokela J, Leisola M 2000 Growth characteristics and metabolic flux analysis of Candida milleri. Biotechnol. Bioeng. 70: 197-207.

Grattapaglia D 2004 Integrating genomics into Eucalyptus breeding. Genet. Mol. Res. 3: 369-379.

Gray GR, Heath D 2005 A global reorganization of the metabolome in Arabidopsis during cold acclimation is revealed by metabolic fingerprinting. Physiol. Plant. 124: 236-248.

Green MA, Fry SC 2005 Vitamin C degradation in plant cells via enzymatic hydrolysis of 4-O-oxalyl-L-threonate. Nature 433: 83-87.

Green ML, Karp PD 2007 Using genome-context data to identify specific types of functional associations in pathway/genome databases. Bioinformatics 23: i205-i211.

Green R 2008 Indicators for assessing folate and vitamin B12 status and for monitoring the efficacy of intervention strategies. Food Nutr. Bull. 29: S52-S63.

Grenville-Briggs LJ, Avrova AO, Bruce CR, Williams A, Whisson SC, Birch PR, van West P 2005 Elevated amino acid biosynthesis in Phytophthora infestans during appressorium formation and potato infection. Fungal Genet. Biol. 42: 244-256.

Griffin JL, Bollard ME 2004 Metabonomics: its potential as a tool in toxicology for safety assessment and data integration. Curr. Drug Metab. 5: 389-398.

Griffiths WJ, Wang Y, Alvelius G, Liu S, Bodin K, Sjovall J 2006 Analysis of oxysterols by electrospray tandem mass spectrometry. J. Am. Soc. Mass Spectrom. 17: 341-362.

Grimaud F, Rogniaux H, James MG, Myers AM, Planchot V 2008 Proteome and phosphoproteome analysis of starch granule-associated proteins from normal maize and mutants affected in starch biosynthesis. J. Exp. Bot. Jul 24 [Epub ahead of print].

Grimm B 1998 Novel insights in the control of tetrapyrrole metabolism of higher plants. Curr. Opin. Plant Biol. 1: 245-250.

Gross GG 2007 From lignins to tannins: forty years of enzyme studies on the biosynthesis of phenolic compounds. Phytochemistry Jun 7 [Epub ahead of print].

Grossman A, Takahashi H 2001 Macronutrient utilization by photosynthetic eukaryotes and the fabric of interactions. Annu. Rev. Plant Physiol. Plant Mol. Biol. 52: 163-210.

Grossniklaus U, Madhusudhan MS, Nanjundiah V 1996 Nonlinear enzyme kinetics can lead to high metabolic flux control coefficients: implications for the evolution of dominance. J. Theor. Biol. 182: 299-302.

Grosu P, Townsend JP, Hartl DL, Cavalieri D 2002 Pathway Processor: a tool for integrating whole-genome expression results into metabolic networks. Genome Res. 12: 1121-1216.

Grote EM, Ejeta G, Rhodes D 1994 Inheritance of glycinebetaine deficiency in sorghum. Crop Sci. 34: 1217-1220.

Grotewold E 2005 Plant metabolic diversity: a regulatory perspective. Trends Plant Sci. 10: 57-62.

Grotewold E 2008 Transcription factors for predictive plant metabolic engineering: are we there yet? Curr. Opin. Biotechnol. 19: 138-144.

Grotkjaer T, Christakopoulos P, Nielsen J, Olsson L 2005 Comparative metabolic network analysis of two xylose fermenting recombinant Saccharomyces cerevisiae strains. Metab. Eng. 7: 437-444.

Grubb CD, Abel S 2006 Glucosinolate metabolism and its control. Trends Plant Sci. 11: 89-100.

Gu M, Lim HK 2001 An intelligent data acquisition system for simultaneous screening of microsomal stability and metabolite profiling by liquid chromatography/mass spectrometry. J. Mass Spectrom. 36: 1053-1061.

Guan L, Scandalios JG 1998 Two structurally similar maize cytosolic superoxide dismutase genes, Sod4 and Sod4A, respond differentially to abscisic acid and high osmoticum. Plant Physiol. 117: 217-224.

Guebel DV 2004 Canonical sensitivities: a useful tool to deal with large perturbations in metabolic network modeling. In Silico Biol. 4: 0015.

Guerrero CA, Aranda C, Deluna A, Filetici P, Riego L, Anaya VH, Gonzalez A 2005 Salt-dependent expression of ammonium assimilation genes in the halotolerant yeast, Debaryomyces hansenii. Curr. Genet. 47: 163-171.

Guevara-Garcia A, San Roman C, Arroyo A, Cortes ME, de la Luz Gutierrez-Nava M, Leon P 2005 Characterization of the Arabidopsis clb6 mutant illustrates the importance of posttranscriptional regulation of the methyl-D-erythritol 4-phosphate pathway. Plant Cell 17: 628-643.

Guillon S, Tremouillaux-Guiller J, Pati PK, Rideau M, Gantet P 2006 Harnessing the potential of hairy roots: dawn of a new era. Trends Biotechnol. 24: 403-409.

Guillon S, Tremouillaux-Guiller J, Pati PK, Rideau M, Gantet P 2006 Hairy root research: recent scenario and exciting prospects. Curr. Opin. Plant Biol. 9: 341-346.

Guimera R, Sales-Pardo M, Amaral LA 2007 A network-based method for target selection in metabolic networks. Bioinformatics 23: 1616-22.

Guimera R, Sales-Pardo M, Amaral LA 2007 Classes of complex networks defined by role-to-role connectivity profiles. Nat. Phys. 3: 63-69.

Gummadova JO, Fletcher GJ, Moolna A, Hanke GT, Hase T, Bowsher CG 2007 Expression of multiple forms of ferredoxin NADP+ oxidoreductase in wheat leaves. J. Exp. Bot. 58: 3971-3985.

Guo X, Shriver CD, Hu H, Liebman MN 2005 Analysis of metabolic and regulatory pathways through Gene Ontology-derived semantic similarity measures. AMIA Annu. Symp. Proc. 2005: 972.

Guthrie TA, Apgar GA, Griswold KE, Lindemann MD, Radcliffe JS, Jacobson BN 2004 Nutritional value of a corn containing a glutamate dehydrogenase gene for growing pigs. J. Anim. Sci. 82: 1693-1698.

Guttal V, Jayaprakash C 2007 Self-organization and productivity in semi-arid ecosystems: implications of seasonality in rainfall. J. Theor. Biol. 248: 490-500.

Guy C, Kaplan F, Kopka J, Selbig J, Hincha DK 2008 Metabolomics of temperature stress. Physiol. Plant. 132: 220-235.

Guy RD, Vanlerberghe GC 2005 Partitioning of respiratory electrons in the dark in leaves of transgenic tobacco with modified levels of alternative oxidase. Physiol. Plant. 125: 171-180.

Guyer D, Patton D, Ward E 1995 Evidence for cross-pathway regulation of metabolic gene expression in plants. Proc. Natl. Acad. Sci. U.S.A. 92: 4997-5000.

Haberle J, Gorg B, Toutain A, Rutsch F, Benoist JF, Gelot A, Suc AL, Koch HG, Schliess F, Haussinger D 2006 Inborn error of amino acid synthesis: human glutamine synthetase deficiency. J. Inherit. Metab. Dis. 29: 352-358.

Hack R, Ebert E, Ehling G, Leist KH 1994 Glufosinate ammonium--some aspects of its mode of action in mammals. Food Chem. Toxicol. 32: 461-470.

Hagedorn CH, Phang JM 1986 Catalytic transfer of hydride ions from NADPH to oxygen by the interconversions of proline and delta 1-pyrroline-5-carboxylate. Arch. Biochem. Biophys. 248: 166-174.

Hagel JM, Weljie AM, Vogel HJ, Facchini PJ 2008 Quantitative 1H NMR metabolite profiling as a functional genomics platform to investigate alkaloid biosynthesis in opium poppy. Plant Physiol. 147: 1805-1821.

Hagemann M, Vinnemeier J, Oberpichler I, Boldt R, Bauwe H 2005 The glycine decarboxylase complex is not essential for the cyanobacterium Synechocystis sp. strain PCC 6803. Plant Biol. (Stuttg.) 7: 15-22.

Haigler CH, Zhang DH, Wilkerson CG 2005 Biotechnological improvement of cotton fibre maturity. Physiol. Plant. 124: 285-294.

Hain R, Grimmig B 2000 Chapter 11. Modification of Plant Secondary Metabolism by Genetic Engineering. In "Metabolic Engineering of Plant Secondary Metabolism" (Verpoorte R, Alfermann AW, eds), Kluwer Academic Publishers, Dortrecht, The Netherlands, pp. 217-231.

Hajduch M, Casteel JE, Hurrelmeyer KE, Song Z, Agrawal GK, Thelen JJ 2006 Proteomic analysis of seed filling in Brassica napus. Developmental characterization of metabolic isozymes using high-resolution two-dimensional gel electrophoresis. Plant Physiol. 141: 32-46.

Hakemian AS, Rosenzweig AC 2007 The biochemistry of methane oxidation. Annu. Rev. Biochem. 76: 223-241.

Hakkinen ST, Tilleman S, Swiatek A, De Sutter V, Rischer H, Vanhoutte I, Van Onckelen H, Hilson P, Inze D, Oksman-Caldentey KM, Goossens A 2007 Functional characterisation of genes involved in pyridine alkaloid biosynthesis in tobacco. Phytochemistry 68: 2773-2785.

Halford NG, Paul MJ 2003 Carbon metabolite sensing and signalling. Plant Biotechnol. J. 1: 381-398.

Halford NG, Paul MJ 2003 Carbon metabolite sensing and signalling. Plant Biotechnol. J. 1: 381-398.

Halket JM, Waterman D, Przyborowska AM, Patel RK, Fraser PD, Bramley PM 2005 Chemical derivatization and mass spectral libraries in metabolic profiling by GC/MS and LC/MS/MS. J. Exp. Bot. 56: 219-243.

Halkier BA, Gershenzon J 2006 Biology and biochemistry of glucosinolates. Annu. Rev. Plant Biol. 57: 303-333.

Hall A, Bastow RM, Davis SJ, Hanano S, McWatters HG, Hibberd V, Doyle MR, Sung S, Halliday KJ, Amasino RM, Millar AJ 2003 The TIME FOR COFFEE gene maintains the amplitude and timing of Arabidopsis circadian clocks. Plant Cell 15: 2719-2729.

Hall DA, Zhu H, Zhu X, Royce T, Gerstein M, Snyder M 2004 Regulation of gene expression by a metabolic enzyme. Science 306: 482-484.

Hallam SJ, Putnam N, Preston CM, Detter JC, Rokhsar D, Richardson PM, DeLong EF 2004 Reverse methanogenesis: testing the hypothesis with environmental genomics. Science 305: 1457-1462.

Halls C, Yu O 2008 Potential for metabolic engineering of resveratrol biosynthesis. Trends Biotechnol. 26: 77-81.

Hammond ET, Andrews TJ, Mott KA, Woodrow IE 1998 Regulation of Rubisco activation in antisense plants of tobacco containing reduced levels of Rubisco activase. Plant J. 14: 101-110.

Hampp R, Hoffmann E, Schonherr K, Johann P, De Filippis L 1997 Fusion and metabolism of plant cells as affected by microgravity. Planta 203 Suppl.: 42S-53S.

Han SJ, Chang HN, Lee J 2001 Characterization of an oxygen-dependent inducible promoter, the nar promoter of Escherichia coli, to utilize in metabolic engineering. Biotechnol. Bioeng. 72: 573-576.

Hancock J, Desikan R, Harrison J, Bright J, Hooley R, Neill S 2006 Doing the unexpected: proteins involved in hydrogen peroxide perception. J. Exp. Bot. 57: 1711-1718.

Hanigan MD, Bateman HG, Fadel JG, McNamara JP 2006 Metabolic models of ruminant metabolism: recent improvements and current status. J. Dairy Sci. 89 Suppl. 1: E52-E64.

Hanisch D, Zien A, Zimmer R, Lengauer T 2002 Co-clustering of biological networks and gene expression data. Bioinformatics 18 Suppl. 1: S145-S154.

Hanke GT, Okutani S, Satomi Y, Takao T, Suzuki A, Hase T 2005 Multiple iso-proteins of FNR in Arabidopsis: evidence for different contributions to chloroplast function and nitrogen assimilation. Plant Cell Environ. 28: 1146-1157.

Hansch R, Lang C, Riebeseel E, Lindigkeit R, Gessler A, Rennenberg H, Mendel RR 2006 Plant sulfite oxidase as novel producer of H2O2: combination of enzyme catalysis with a subsequent non-enzymatic reaction step. J. Biol. Chem. 281: 6884-6888.

Hanson AD, Rathinasabapathi B, Rivoal J, Burnet M, Dillon MO, Gage DA 1994 Osmoprotective compounds in the Plumbaginaceae: a natural experiment in metabolic engineering of stress tolerance. Proc. Natl. Acad. Sci. U.S.A. 91: 306-310.

Hanson KR 1984 Stereochemical determination of carbon partitioning between photosynthesis and photorespiration in C3 plants: use of (3R)-D-[3-3H1, 3-14C]glyceric acid. Arch. Biochem. Biophys. 232: 58-75.

Hanson KR, Peterson RB 1985 The stoichiometry of photorespiration during C3-photosynthesis is not fixed: evidence from combined physical and stereochemical methods. Arch. Biochem. Biophys. 237: 300-313.

Hansson O, Donsmark M, Ling C, Nevsten P, Danfelter M, Andersen JL, Galbo H, Holm C 2005 Transcriptome and proteome analysis of soleus muscle of hormone-sensitive lipase-null mice. J. Lipid Res. 46: 2614-2623.

Hare PD, Cress WA 1997 Metabolic implications of stress-induced proline accumulation in plants. Plant Growth Regulation 21: 79-102.

Harms K, von Ballmoos P, Brunold C, Hofgen R, Hesse H 2000 Expression of a bacterial serine acetyltransferase in transgenic potato plants leads to increased levels of cysteine and glutathione. Plant J. 22: 335-343.

Harndahl L, Schmoll D, Herling AW, Agius L 2006 The role of glucose 6-phosphate in mediating the effects of glucokinase overexpression on hepatic glucose metabolism. FEBS J. 273: 336-346.

Harris DM, Diderich JA, van der Krogt ZA, Luttik MA, Raamsdonk LM, Bovenberg RA, van Gulik WM, van Dijken JP, Pronk JT 2006 Enzymic analysis of NADPH metabolism in beta-lactam-producing Penicillium chrysogenum: presence of a mitochondrial NADPH dehydrogenase. Metab. Eng. 8: 91-101.

Harris LM, Blank L, Desai RP, Welker NE, Papoutsakis ET 2001 Fermentation characterization and flux analysis of recombinant strains of Clostridium acetobutylicum with an inactivated solR gene. J. Ind. Microbiol. Biotechnol. 27: 322-328.

Harrison-Lowe N, Olsen LJ 2006 Isolation of glyoxysomes from pumpkin cotyledons. Curr. Protoc. Cell Biol. Chapter 3: Unit 3.19.

Hartman JL 4th 2007 Buffering of deoxyribonucleotide pool homeostasis by threonine metabolism. Proc. Natl. Acad. Sci. U.S.A. 104: 11700-11705.

Hartwell J 2005 The co-ordination of central plant metabolism by the circadian clock. Biochem. Soc. Trans. 33: 945-948.

Hashida SN, Takahashi H, Kawai-Yamada M, Uchimiya H 2007 Arabidopsis thaliana nicotinate/nicotinamide mononucleotide adenyltransferase (AtNMNAT) is required for pollen tube growth. Plant J. 49: 694-703.

Hashimoto T, Yamada Y 2003 New genes in alkaloid metabolism and transport. Curr. Opin. Biotechnol. 14: 163-168.

Hasunuma T, Takeno S, Hayashi S, Sendai M, Bamba T, Yoshimura S, Tomizawa K, Fukusaki E, Miyake C 2008 Overexpression of 1-deoxy-d-xylulose-5-phosphate reductoisomerase gene in chloroplast contributes to increment of isoprenoid production. J. Biosci. Bioeng. 105: 518-526.

Hattrup E, Neilson KA, Breci L, Haynes PA 2007 Proteomic analysis of shade-avoidance response in tomato leaves. J. Agric. Food Chem. 55: 8310-8318.

Hatzimanikatis V 1999 Nonlinear metabolic control analysis. Metab. Eng. 1: 75-87.

Hatzimanikatis V, Bailey JE 1996 MCA has more to say. J. Theor. Biol. 182: 233-242.

Hatzimanikatis V, Emmerling M, Sauer U, Bailey JE 1998 Application of mathematical tools for metabolic design of microbial ethanol production. Biotechnol. Bioeng. 58: 154-161.

Haugen AC, Kelley R, Collins JB, Tucker CJ, Deng C, Afshari CA, Brown JM, Ideker T, Van Houten B 2004 Integrating phenotypic and expression profiles to map arsenic-response networks. Genome Biol. 5: R95.

Hausler N, Browning J, Merritt M, Storey C, Milde A, Jeffrey FM, Sherry AD, Malloy CR, Burgess SC 2006 Effects of insulin and cytosolic redox state on glucose production pathways in the isolated perfused mouse liver by integrated 2H and 13C NMR. Biochem. J. 394: 465-473.

Hausler RE, Schlieben NH, Flugge UI 2000 Control of carbon partitioning and photosynthesis by the triose phosphate/phosphate translocator in transgenic tobacco plants (Nicotiana tabacum). II. Assessment of control coefficients of the triose phosphate/phosphate translocator. Planta 210: 383-390.

Hausler RE, Schlieben NH, Nicolay P, Fischer K, Fischer KL, Flugge UI 2000 Control of carbon partitioning and photosynthesis by the triose phosphate/phosphate translocator in transgenic tobacco plants (Nicotiana tabacumL.). I. Comparative … Planta 210: 371-382.

Hayashi M, Nishimura M 2003 Entering a new era of research on plant peroxisomes. Curr. Opin. Plant Biol. 6: 577-582.

Hayes JE, Reid RJ 2004 Boron tolerance in barley is mediated by efflux of boron from the roots. Plant Physiol. 136: 3376-3382.

He XZ, Dixon RA 2000 Genetic manipulation of isoflavone 7-O-methyltransferase enhances biosynthesis of 4'-O-methylated isoflavonoid phytoalexins and disease resistance in alfalfa. Plant Cell 12: 1689-1702.

Heazlewood JL, Tonti-Filippini JS, Gout AM, Day DA, Whelan J, Millar AH 2004 Experimental analysis of the Arabidopsis mitochondrial proteome highlights signaling and regulatory components, provides assessment of targeting prediction programs, and indicates plant-specific mitochondrial proteins. Plant Cell 16: 241-256.

Hecker M, Volker U 2004 Towards a comprehensive understanding of Bacillus subtilis cell physiology by physiological proteomics. Proteomics 4: 3727-3750.

Heide L 2000 Chapter 12. Expression of the Bacterial ubiC Gene Opens a New Biosynthetic Pathway in Plants. In "Metabolic Engineering of Plant Secondary Metabolism" (Verpoorte R, Alfermann AW, eds), Kluwer Academic Publishers, Dortrecht, The Netherlands, pp. 233-251.

Heijnen JJ 2001 New experimental and theoretical tools for metabolic engineering of micro-organisms. Meded. Rijksuniv. Gent. Fak. Landbouwkd.Toegep. Biol. Wet. 66: 11-30.

Heijnen JJ, van Gulik WM, Shimizu H, Stephanopoulos G 2004 Metabolic flux control analysis of branch points: an improved approach to obtain flux control coefficients from large perturbation data. Metab. Eng. 6: 391-400.

Heilmann I, Pidkowich MS, Girke T, Shanklin J 2004 Switching desaturase enzyme specificity by alternate subcellular targeting. Proc. Natl. Acad. Sci. U.S.A. 101: 10266-10271.

Heim WG, Jelesko JG 2004 Association of diamine oxidase and S-adenosylhomocysteine hydrolase in Nicotiana tabacum extracts. Plant Mol. Biol. 56: 299-308.

Heineke D, Bykova N, Gardestrom P, Bauwe H 2001 Metabolic response of potato plants to an antisense reduction of the P-protein of glycine decarboxylase. Planta 212: 880-887.

Heino J, Tunyan K, Calvetti D, Somersalo E 2007 Bayesian flux balance analysis applied to a skeletal muscle metabolic model. J. Theor. Biol. 248: 91-110.

Heinrich R 1985 Mathematical models of metabolic systems: general principles and control of glycolysis and membrane transport in erythrocytes. Biomed. Biochim. Acta 44: 913-927.

Heinrich R, Holzhutter HG 1985 Efficiency and design of simple metabolic systems. Biomed. Biochim. Acta 44: 959-969.

Heinrich R, Reder C 1991 Metabolic control analysis of relaxation processes. J. Theor. Biol. 151: 343-350.

Heinrich R, Schuster S 1998 The modelling of metabolic systems. Structure, control and optimality. Biosystems 47: 61-77.

Heinzle E, Matsuda F, Miyagawa H, Wakasa K, Nishioka T 2007 Estimation of metabolic fluxes, expression levels and metabolite dynamics of a secondary metabolic pathway in potato using label pulse-feeding experiments combined with kinetic network modelling and simulation. Plant J. 50: 176-187.

Heinzle E, Yuan Y, Kumar S, Wittmann C, Gehre M, Richnow HH, Wehrung P, Adam P, Albrecht P 2008 Analysis of (13)C labeling enrichment in microbial culture applying metabolic tracer experiments using gas chromatography-combustion-isotope ratio mass spectrometry. Anal. Biochem. 380: 202-210.

Hellerstein MK 2003 In vivo measurement of fluxes through metabolic pathways: the missing link in functional genomics and pharmaceutical research. Annu. Rev. Nutr. 23: 379-402.

Hellerstein MK 2004 New stable isotope-mass spectrometric techniques for measuring fluxes through intact metabolic pathways in mammalian systems: introduction of moving pictures into functional genomics and biochemical phenotyping. Metab. Eng. 6: 85-100.

Hellmann H, Barker L, Funck D, Frommer WB 2000 The regulation of assimilate allocation and transport. Aust. J. Plant Physiol. 27: 583-594.

Hemmler R, Becker T, Schleiff E, Bolter B, Stahl T, Soll J, Gotze TA, Braams S, Wagner R 2006 Molecular properties of Oep21, an ATP-regulated anion-selective solute channel from the outer chloroplast membrane. J. Biol. Chem. 281: 12020-12029.

Henry O, Perrier M, Kamen A 2005 Metabolic flux analysis of HEK-293 cells in perfusion cultures for the production of adenoviral vectors. Metab. Eng. 7: 467-476.

Henry PG, Adriany G, Deelchand D, Gruetter R, Marjanska M, Oz G, Seaquist ER, Shestov A, Ugurbil K 2006 In vivo 13C NMR spectroscopy and metabolic modeling in the brain: a practical perspective. Magn. Reson. Imaging 24: 527-539.

Henry SA, Patton-Vogt JL 1998 Genetic regulation of phospholipid metabolism: yeast as a model eukaryote. Prog. Nuc. Acid Res. Mol. Biol. 61: 133-179.

Herd S, Christensen MJ, Saunders K, Scott DB, Schmid J 1997 Quantitative assessment of in planta distribution of metabolic activity and gene expression of an endophytic fungus. Microbiology 143: 267-275.

Hermans C, Hammond JP, White PJ, Verbruggen N 2006 How do plants respond to nutrient shortage by biomass allocation? Trends Plant Sci. 11: 610-617.

Hernandez G, Ramirez M, Valdes-Lopez O, Tesfaye M, Graham MA, Czechowski T, Schlereth A, Wandrey M, Erban A, Cheung F, Wu HC, Lara M, Town CD, Kopka J, Udvardi MK, Vance CP 2007 Phosphorus stress in common bean: root transcript and metabolic responses. Plant Physiol. 144: 752-767.

Hernandez-Sebastia C, Marsolais F, Saravitz C, Israel D, Dewey RE, Huber SC 2005 Free amino acid profiles suggest a possible role for asparagine in the control of storage-product accumulation in developing seeds of low- and high-protein soybean lines. J. Exp. Bot. 56: 1951-1963.

Herrero O, Ramón D, Orejas M 2008 Engineering the Saccharomyces cerevisiae isoprenoid pathway for de novo production of aromatic monoterpenes in wine. Metab. Eng. 10: 78-86.

Herrgard MJ, Covert MW, Palsson BO 2004 Reconstruction of microbial transcriptional regulatory networks. Curr. Opin. Biotechnol. 15: 70-77.

Herrmann KM, Weaver LM 1999 The shikimate pathway. Annu. Rev. Plant Physiol. Plant Mol. Biol. 50: 473-503.

Hertz L 2006 Glutamate, a neurotransmitter--and so much more. A synopsis of Wierzba III. Neurochem. Int. 48: 416-425.

Hertz L 2004 Intercellular metabolic compartmentation in the brain: past, present and future. Neurochem. Int. 45: 285-296.

Hervieu F, Vaucheret H 1996 A single amino acid change in acetolactate synthase confers resistance to valine in tobacco. Mol. Gen. Genet. 251: 220-224.

Hesse F, Ebel M, Konisch N, Sterlinski R, Kessler W, Wagner R 2003 Comparison of a production process in a membrane-aerated stirred tank and up to 1000-L airlift bioreactors using BHK-21 cells and chemically defined protein-free medium. Biotechnol. Prog. 19: 833-843.

Hesse H, Kreft O, Maimann S, Zeh M, Hoefgen R 2004 Current understanding of the regulation of methionine biosynthesis in plants. J. Exp. Bot. 55: 1799-1808.

Heuett WJ, Beard DA, Qian H 2008 Linear analysis near a steady-state of biochemical networks: control analysis, correlation metrics and circuit theory. BMC Syst. Biol. 2: 44.

Heux S, Cachon R, Dequin S 2006 Cofactor engineering in Saccharomyces cerevisiae: expression of a H(2)O-forming NADH oxidase and impact on redox metabolism. Metab. Eng. 8: 303-314.

Heux S, Sablayrolles JM, Cachon R, Dequin S 2006 Engineering a Saccharomyces cerevisiae wine yeast that exhibits reduced ethanol production during fermentation under controlled microoxygenation conditions. Appl. Environ. Microbiol. 72: 5822-5828.

Hevia H, Varela-Rey M, Corrales FJ, Berasain C, Martinez-Chantar ML, Latasa MU, Lu SC, Mato JM, Garcia-Trevijano ER, Avila MA 2004 5'-Methylthioadenosine modulates the inflammatory response to endotoxin in mice and in rat hepatocytes. Hepatology 39: 1088-1098.

Hewezi T, Petitprez M, Gentzbittel L 2006 Primary metabolic pathways and signal transduction in sunflower (Helianthus annuus L.): comparison of transcriptional profiling in leaves and immature embryos using cDNA microarrays. Planta 223: 948-964.

Hill KL, Hassett R, Kosman D, Merchant S 1996 Regulated copper uptake in Chlamydomonas reinhardtii in response to copper availability. Plant Physiol. 112: 697-704.

Hills MJ 2004 Control of storage-product synthesis in seeds. Curr. Opin. Plant Biol. 7: 302-308.

Hintze A, Adami C 2008 Evolution of complex modular biological networks. PLoS Comput. Biol. 4: e23.

Hiraga K, Koyata H 1992 Abnormal metabolism of substances related to glycine and beta-alanine. Nippon Rinsho 50: 1575-1580.

Hirai MY, Saito K 2004 Post-genomics approaches for the elucidation of plant adaptive mechanisms to sulphur deficiency. J. Exp. Bot. 55: 1871-1879.

Hirel B, Andrieu B, Valadier MH, Renard S, Quillere I, Chelle M, Pommel B, Fournier C, Drouet JL 2005 Physiology of maize II: Identification of physiological markers representative of the nitrogen status of maize (Zea mays) leaves during grain filling. Physiol. Plant. 124: 178-188.

Hirel B, Marsolier MC, Hoarau A, Hoarau J, Brangeon J, Schafer R, Verma DP 1992 Forcing expression of a soybean root glutamine synthetase gene in tobacco leaves induces a native gene encoding cytosolic enzyme. Plant Mol. Biol. 20: 207-218.

Hirel B, Martin A, Terce-Laforgue T, Gonzalez-Moro MB, Estavillo JM 2005 Physiology of maize I: A comprehensive and integrated view of nitrogen metabolism in a C4 plant. Physiol. Plant. 124: 167-177.

Hirose N, Takei K, Kuroha T, Kamada-Nobusada T, Hayashi H, Sakakibara H 2008 Regulation of cytokinin biosynthesis, compartmentalization and translocation. J. Exp. Bot. 59: 75-83.

Hjersted JL, Henson MA, Mahadevan R 2007 Genome-scale analysis of Saccharomyces cerevisiae metabolism and ethanol production in fed-batch culture. Biotechnol. Bioeng. 97: 1190-1204.

Ho NW, Chen Z, Brainard AP, Sedlak M 1999 Successful design and development of genetically engineered Saccharomyces yeasts for effective cofermentation of glucose and xylose from cellulosic biomass to fuel ethanol. Adv. Biochem. Eng. Biotechnol. 65: 163-192.

Ho QT, Verboven P, Verlinden BE, Lammertyn J, Vandewalle S, Nicolai BM 2008 A continuum model for metabolic gas exchange in pear fruit. PLoS Comput. Biol. 4: e1000023.

Hochachka PW 1999 Cross-species studies of glycolytic function. Adv. Exp. Med. Biol. 474: 219-229.

Hochgrafe F, Wolf C, Fuchs S, Liebeke M, Lalk M, Engelmann S, Hecker M 2008 Nitric oxide stress induces different responses but mediates comparable protein thiol protection in Bacillus subtilis and Staphylococcus aureus. J. Bacteriol. 190: 4997-5008.

Hofer T, Heinrich R 1993 A second-order approach to metabolic control analysis. J. Theor. Biol. 164: 85-102.

Hofestadt R, Meineke F 1995 Interactive modelling and simulation of biochemical networks. Comput. Biol. Med. 25: 321-334.

Hofestadt R, Thelen S 1998 Quantitative modeling of biochemical networks. In Silico Biol. 1: 39-53.

Hoffmann M, Wagner M, Abbadi A, Fulda M, Feussner I 2008 Metabolic engineering of omega 3-very long chain polyunsaturated fatty acid production by an exclusively acyl-CoA-dependent pathway. J. Biol. Chem. 283: 22352-22362.

Hofmeyr JH 1986 Steady-state modelling of metabolic pathways: a guide for the prospective simulator. Comput. Appl. Biosci. 2: 5-11.

Hofmeyr JH 1995 Metabolic regulation: a control analytic perspective. J. Bioenerg. Biomembr. 27: 479-490.

Hofmeyr JH 1989 Control-pattern analysis of metabolic pathways. Flux and concentration control in linear pathways. Eur. J. Biochem. 186: 343-354.

Hofmeyr JH, Cornish-Bowden A 1991 Quantitative assessment of regulation in metabolic systems. Eur. J. Biochem. 200: 223-236.

Hofmeyr JH, Cornish-Bowden A 1996 Co-response analysis: a new experimental strategy for metabolic control analysis. J. Theor. Biol. 182: 371-380.

Hofmeyr JH, Cornish-Bowden A, Rohwer JM 1993 Taking enzyme kinetics out of control; putting control into regulation. Eur. J. Biochem. 212: 833-837.

Hofmeyr JH, Kacser H, van der Merwe KJ 1986 Metabolic control analysis of moiety-conserved cycles. Eur. J. Biochem. 155: 631-641.

Hofmeyr JH, van der Merwe KJ 1986 METAMOD: software for steady-state modelling and control analysis of metabolic pathways on the BBC microcomputer. Comput. Appl. Biosci. 2: 243-249.

Hogenhout SA, Loria R 2008 Virulence mechanisms of Gram-positive plant pathogenic bacteria. Curr. Opin. Plant Biol. 11: 449-456.

Holmes E, Nicholson JK, Tranter G 2001 Metabonomic characterization of genetic variations in toxicological and metabolic responses using probabilistic neural networks. Chem. Res. Toxicol. 14: 182-191.

Holms H 1996 Flux analysis and control of the central metabolic pathways in Escherichia coli. FEMS Microbiol. Rev. 19: 85-116.

Holtgrawe D, Scholz A, Altmann B, Scheibe R 2005 Cytoskeleton-associated, carbohydrate-metabolizing enzymes in maize identified by yeast two-hybrid screening. Physiol. Plant. 125: 141-156.

Holzhutter HG 1985 Compartmental analysis: theoretical aspects and application. Biomed. Biochim. Acta 44: 863-873.

Holzhutter HG 2006 The generalized flux-minimization method and its application to metabolic networks affected by enzyme deficiencies. Biosystems 83: 98-107.

Holzhutter HG, Heinrich R 1990 The structure of metabolic systems: a theoretical approach. Biomed. Biochim. Acta 49: S154-S159.

Holzhutter HG, Schuster R, Buckwitz D, Jacobasch G 1990 Mathematical modelling of metabolic pathways affected by an enzyme deficiency. Biomed. Biochim. Acta 49: 791-800.

Holzhutter HG, Schwendel A, Grune T, Quedenau J, Siems W 1993 Estimation of steady-state flux rates in metabolic systems by computer simulations of radioactive tracer experiments. Comput. Appl. Biosci. 9: 573-580.

Hong HT, Nose A, Agarie S, Yoshida T 2008 Malate metabolism in Hoya carnosa mitochondria and its role in photosynthesis during CAM phase III. J. Exp. Bot. 59: 1819-1827.

Hong SB, Peebles CA, Shanks JV, San KY, Gibson SI 2006 Expression of the Arabidopsis feedback-insensitive anthranilate synthase holoenzyme and tryptophan decarboxylase genes in Catharanthus roseus hairy roots. J. Biotechnol. 122: 28-38.

Hong SH, Lee SY 2001 Metabolic flux analysis for succinic acid production by recombinant Escherichia coli with amplified malic enzyme activity. Biotechnol. Bioeng. 74: 89-95.

Hong SH, Park SJ, Moon SY, Park JP, Lee SY 2003 In silico prediction and validation of the importance of the Entner-Doudoroff pathway in poly(3-hydroxybutyrate) production by metabolically engineered Escherichia coli. Biotechnol. Bioeng. 83: 854-863.

Hoon Yang T, Wittmann C, Heinzle E 2006 Respirometric (13)C flux analysis. Part II: in vivo flux estimation of lysine-producing Corynebacterium glutamicum. Metab. Eng. 8: 432-446.

Hoon Yang T, Wittmann C, Heinzle EE 2004 Metabolic network simulation using logical loop algorithm and Jacobian matrix. Metab. Eng. 6: 256-267.

Hooykaas PJ 2000 Chapter 3. Agrobacterium, a Natural Metabolic Engineer of Plants. In "Metabolic Engineering of Plant Secondary Metabolism" (Verpoorte R, Alfermann AW, eds), Kluwer Academic Publishers, Dortrecht, The Netherlands, pp. 51-67.

Hopkins S, Schirch V 1984 5,10-Methenyltetrahydrofolate synthetase. Purification and properties of the enzyme from rabbit liver. J. Biol. Chem. 259: 5618-5622.

Horst I, Welham T, Kelly S, Kaneko T, Sato S, Tabata S, Parniske M, Wang TL 2007 TILLING mutants of Lotus japonicus reveal that nitrogen assimilation and fixation can occur in the absence of nodule-enhanced sucrose synthase. Plant Physiol. 144: 806-820.

Hosp J, Tashpulatov A, Roessner U, Barsova E, Katholnigg H, Steinborn R, Melikant B, Lukyanov S, Heberle-Bors E, Touraev A 2007 Transcriptional and metabolic profiles of stress-induced, embryogenic tobacco microspores. Plant Mol. Biol. 63: 137-149.

Hoth S, Schneidereit A, Lauterbach C, Scholz-Starke J, Sauer N 2005 Nematode infection triggers the de novo formation of unloading phloem that allows macromolecular trafficking of green fluorescent protein into syncytia. Plant Physiol. 138: 383-392.

Hou CX, Pursiheimo S, Rintamaki E, Aro EM 2002 Environmental and metabolic control of LHCII protein phosphorylation: revealing the mechanisms for dual regulation of the LHCII kinase. Plant Cell Environ. 25: 1515-1525.

Howe GA, Schilmiller AL 2002 Oxylipin metabolism in response to stress. Curr. Opin. Plant Biol. 5: 230-236.

Hsieh MH, Lam HM, van de Loo FJ, Coruzzi G 1998 A PII-like protein in Arabidopsis: putative role in nitrogen sensing. Proc. Natl. Acad. Sci. U.S.A. 95: 13965-13970.

Hu CA, Bart Williams D, Zhaorigetu S, Khalil S, Wan G, Valle D 2008 Functional genomics and SNP analysis of human genes encoding proline metabolic enzymes. Amino Acids May 28 [Epub ahead of print].

Hu CA, Delauney AJ, Verma DP 1992 A bifunctional enzyme (delta 1-pyrroline-5-carboxylate synthetase) catalyzes the first two steps in proline biosynthesis in plants. Proc. Natl. Acad. Sci. U.S.A. 89: 9354-9358.

Hua Q, Joyce AR, Fong SS, Palsson BO 2006 Metabolic analysis of adaptive evolution for in silico designed lactate-producing strains. Biotechnol. Bioeng. 95: 992-1002.

Hua Q, Yang C, Oshima T, Mori H, Shimizu K 2004 Analysis of gene expression in Escherichia coli in response to changes of growth-limiting nutrient in chemostat cultures. Appl. Environ. Microbiol. 70: 2354-2366.

Hua Q, Yang C, Shimizu K 1999 Metabolic flux analysis for efficient pyruvate fermentation using vitamin-auxotrophic yeast of Torulopsis glabrata. J. Biosci. Bioeng. 87: 206-213.

Hua Q, Yang C, Shimizu K 2000 Metabolic control analysis for lysine synthesis using Corynebacterium glutamicum and experimental verification. J. Biosci. Bioeng. 90: 184-192.

Huang CY, Roessner U, Eickmeier I, Genc Y, Callahan DL, Shirley N, Langridge P, Bacic A 2008 Metabolite profiling reveals distinct changes in carbon and nitrogen metabolism in phosphate-deficient barley plants (Hordeum vulgare L.). Plant Cell Physiol. 49: 691-703.

Huang J, Hirji R, Adam L, Rozwadowski KL, Hammerlindl JK, Keller WA, Selvaraj G 2000 Genetic engineering of glycinebetaine production toward enhancing stress tolerance in plants: metabolic limitations. Plant Physiol. 122: 747-756.

Huber SC, Hardin SC 2004 Numerous posttranslational modifications provide opportunities for the intricate regulation of metabolic enzymes at multiple levels. Curr. Opin. Plant Biol. 7: 318-322.

Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, et al 2003 The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19: 524-531.

Huege J, Sulpice R, Gibon Y, Lisec J, Koehl K, Kopka J 2007 GC-EI-TOF-MS analysis of in vivo carbon-partitioning into soluble metabolite pools of higher plants by monitoring isotope dilution after (13)CO(2) labelling. Phytochemistry 68: 2258-2272.

Huemer M, Simma B, Fowler B, Suormala T, Bodamer OA, Sass JO 2005 Prenatal and postnatal treatment in cobalamin C defect. J. Pediatr. 147: 469-472.

Huerta-Saquero A, Calderon-Flores A, Diaz-Villasenor A, Du Pont G, Duran S 2004 Regulation of transcription and activity of Rhizobium etli glutaminase A. Biochim. Biophys. Acta 1673: 201-207.

Hughes EH, Hong SB, Gibson SI, Shanks JV, San KY 2004 Metabolic engineering of the indole pathway in Catharanthus roseus hairy roots and increased accumulation of tryptamine and serpentine. Metab. Eng. 6: 268-276.

Hughes EH, Hong SB, Gibson SI, Shanks JV, San KY 2004 Expression of a feedback-resistant anthranilate synthase in Catharanthus roseus hairy roots provides evidence for tight regulation of terpenoid indole alkaloid levels. Biotechnol. Bioeng. 86: 718-727.

Hughes EH, Shanks JV 2002 Metabolic engineering of plants for alkaloid production. Metab. Eng. 4: 41-48.

Humphrey TV, Richman AS, Menassa R, Brandle JE 2006 Spatial organisation of four enzymes from Stevia rebaudiana that are involved in steviol glycoside synthesis. Plant Mol. Biol. 61: 47-62.

Hurth MA, Suh SJ, Kretzschmar T, Geis T, Bregante M, Gambale F, Martinoia E, Neuhaus HE 2005 Impaired pH homeostasis in Arabidopsis lacking the vacuolar dicarboxylate transporter and analysis of carboxylic acid transport across the tonoplast. Plant Physiol. 137: 901-910.

Huser AT, Chassagnole C, Lindley ND, Merkamm M, Guyonvarch A, Elisakova V, Patek M, Kalinowski J, Brune I, Puhler A, Tauch A 2005 Rational design of a Corynebacterium glutamicum pantothenate production strain and its characterization by metabolic flux analysis and genome-wide transcriptional profiling. Appl. Environ. Microbiol. 71: 3255-3268.

Husnik JI, Volschenk H, Bauer J, Colavizza D, Luo Z, van Vuuren HJ 2006 Metabolic engineering of malolactic wine yeast. Metab. Eng. 8: 315-323.

Hwang D, Stephanopoulos G, Chan C 2004 Inverse modeling using multi-block PLS to determine the environmental conditions that provide optimal cellular function. Bioinformatics 20: 487-499.

Ibarra RU, Edwards JS, Palsson BO 2002 Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420: 186-189.

Ideker T, Lauffenburger D 2003 Building with a scaffold: emerging strategies for high- to low-level cellular modeling. Trends Biotechnol. 21: 255-262.

Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L 2001 Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292: 929-934.

Ihekwaba AEC, Broomhead DS, Grimley RL, Benson N, Kell DB 2004 Sensitivity analysis of parameters controlling oscillatory signalling in the NF-kB pathway: the roles of IKK and IkBa. Syst. Biol. 1: 93-103.

Iijima Y, Nakamura Y, Ogata Y, Tanaka K, Sakurai N, Suda K, Suzuki T, Suzuki H, Okazaki K, Kitayama M, Kanaya S, Aoki K, Shibata D 2008 Metabolite annotations based on the integration of mass spectral information. Plant J. 54: 949-962.

Iles RA 2008 Nuclear magnetic resonance spectroscopy and genetic disorders. Curr. Med. Chem. 15: 15-36.

Imielinski M, Belta C, Rubin H, Halasz A 2006 Systematic analysis of conservation relations in Escherichia coli genome-scale metabolic network reveals novel growth media. Biophys. J. 90: 2659-2672.

Imsande J 1999 Iron-sulfur clusters: Formation, perturbation, and physiological functions. Plant Physiol. Biochem. 37: 87-97.

Inaba Y, Brotherton JE, Ulanov A, Widholm JM 2007 Expression of a feedback insensitive anthranilate synthase gene from tobacco increases free tryptophan in soybean plants. Plant Cell Rep. 26: 1763-1771.

Inagaki E, Ohshima N, Takahashi H, Kuroishi C, Yokoyama S, Tahirov T 2006 Crystal structure of Thermus thermophilus Delta(1)-pyrroline-5-carboxylate dehydrogenase. J. Mol. Biol. 362: 490-501.

Ingalls BP 2004 Autonomously oscillating biochemical systems: parametric sensitivity of extrema and period. Syst. Biol. 1: 62-70.

Ingalls BP, Sauro HM 2003 Sensitivity analysis of stoichiometric networks: an extension of metabolic control analysis to non-steady state trajectories. J. Theor. Biol. 222: 23-36.

Ingram LO, Gomez PF, Lai X, Moniruzzaman M, Wood BE, Yomano LP, York SW 1998 Metabolic engineering of bacteria for ethanol production. Biotechnol. Bioeng. 58: 204-214.

Iragne F, Nikolski M, Sherman D 2008 Extrapolation of metabolic pathways as an aid to modelling completely sequenced nonSaccharomyces yeasts. FEMS Yeast Res. 8: 132-139.

Ishida N, Saitoh S, Ohnishi T, Tokuhiro K, Nagamori E, Kitamoto K, Takahashi H 2006 Metabolic engineering of Saccharomyces cerevisiae for efficient production of pure L: -(+)-lactic acid. Appl. Biochem. Biotechnol. 131: 795-807.

Ishihara A, Asada Y, Takahashi Y, Yabe N, Komeda Y, Nishioka T, Miyagawa H, Wakasa K 2006 Metabolic changes in Arabidopsis thaliana expressing the feedback-resistant anthranilate synthase alpha subunit gene OASA1D. Phytochemistry 67: 2349-2362.

Ishihara A, Hashimoto Y, Tanaka C, Dubouzet JG, Nakao T, Matsuda F, Nishioka T, Miyagawa H, Wakasa K 2008 The tryptophan pathway is involved in the defense responses of rice against pathogenic infection via serotonin production. Plant J. 54: 481-495.

Ishii K, Nakamura S, Morohashi M, Sugimoto M, Ohashi Y, Kikuchi S, Tomita M 2008 Comparison of metabolite production capability indices generated by network analysis methods. Biosystems 91: 166-170.

Ishikawa T, Morimoto Y, Madhusudhan R, Sawa Y, Shibata H, Yabuta Y, Nishizawa A, Shigeoka S 2005 Acclimation to diverse environmental stresses caused by a suppression of cytosolic ascorbate peroxidase in tobacco BY-2 cells. Plant Cell Physiol. 46: 1264-1271.

Ivanov AG, Sane PV, Zeinalov Y, Malmberg G, Gardestrom P, Huner NP, Oquist G 2001 Photosynthetic electron transport adjustments in overwintering Scots pine (Pinus sylvestris L.). Planta 213: 575-585.

Ivleva NB, Gao T, Liwang AC, Golden SS 2006 Quinone sensing by the circadian input kinase of the cyanobacterial circadian clock. Proc. Natl. Acad. Sci. U.S.A. 103: 17468-17473.

Iwatani S, Van Dien S, Shimbo K, Kubota K, Kageyama N, Iwahata D, Miyano H, Hirayama K, Usuda Y, Shimizu K, Matsui K 2007 Determination of metabolic flux changes during fed-batch cultivation from measurements of intracellular amino acids by LC-MS/MS. J. Biotechnol. 128: 93-111.

Iwatani S, Yamada Y, Usuda Y 2008 Metabolic flux analysis in biotechnology processes. Biotechnol. Lett. 30: 791-799.

Iyer VV, Sriram G, Fulton DB, Zhou R, Westgate ME, Shanks JV 2008 Metabolic flux maps comparing the effect of temperature on protein and oil biosynthesis in developing soybean cotyledons. Plant Cell Environ. 31: 506-517.

Izallalen M, Mahadevan R, Burgard A, Postier B, Didonato R Jr, Sun J, Schilling CH, Lovley DR 2008 Geobacter sulfurreducens strain engineered for increased rates of respiration. Metab. Eng. Jun 27 [Epub ahead of print].

Izmailov SF 2004 Saturation and utilization of nitrate pools in pea and sugar beet leaves. Russ. J. Plant Physiol. 51: 189-193.

Jackowski S, Rock CO 1984 Metabolism of 4'-phosphopantetheine in Escherichia coli. J. Bacteriol. 158: 115-120.

Jackson RC 1995 Toxicity prediction from metabolic pathway modelling. Toxicology 102: 197-205.

Jacobsen JR, Khosla C 1998 New directions in metabolic engineering. Curr. Opin. Chem. Biol. 2: 133-137.

Jakob T, Wagner H, Stehfest K, Wilhelm C 2007 A complete energy balance from photons to new biomass reveals a light- and nutrient-dependent variability in the metabolic costs of carbon assimilation. J. Exp. Bot. 58: 2101-2112.

Jakobs C, Jaeken J, Gibson KM 1993 Inherited disorders of GABA metabolism. J. Inherit. Metab. Dis. 16: 704-715.

Jalanko A, Tyynela J, Peltonen L 2006 From genes to systems: new global strategies for the characterization of NCL biology. Biochim. Biophys. Acta 1762: 934-944.

James SJ, Cutler P, Melnyk S, Jernigan S, Janak L, Gaylor DW, Neubrander JA 2004 Metabolic biomarkers of increased oxidative stress and impaired methylation capacity in children with autism. Am. J. Clin. Nutr. 80: 1611-1617.

James SJ, Melnyk S, Pogribna M, Pogribny IP, Caudill MA 2002 Elevation in S-adenosylhomocysteine and DNA hypomethylation: potential epigenetic mechanism for homocysteine-related pathology. J. Nutr. 132: 2361S-2366S.

Jamshidi N, Edwards JS, Fahland T, Church GM, Palsson BO 2001 Dynamic simulation of the human red blood cell metabolic network. Bioinformatics 17: 286-287.

Jannaschk D, Burgos M, Centerlles JJ, Ovadi J, Cascante M 1999 Application of metabolic control analysis to the study of toxic effects of copper in muscle glycolysis. FEBS Lett. 445: 144-148.

Janosikova B, Pavlikova M, Kocmanova D, Vitova A, Vesela K, Krupkova L, Kahleova R, Krijt J, Kraml P, Hyanek J, Zvarova J, Andel M, Kozich V 2003 Genetic variants of homocysteine metabolizing enzymes and the risk of coronary artery disease. Mol. Genet. Metab. 79: 167-175.

Jansen MAK, Hill LM, Thorneley RNF 2004 A novel stress-acclimation response in Spirodela punctata (Lemnaceae): 2,4,6-trichlorophenol triggers an increase in the level of an extracellular peroxidase, capable of the oxidative dechlorination of this xenobiotic pollutant. Plant Cell Environ. 27: 603-613.

Jarvis AP, Schaaf O, Oldham NJ 2000 3-Hydroxy-3-phenylpropanoic acid is an intermediate in the biosynthesis of benzoic acid and salicylic acid but benzaldehyde is not. Planta 212: 119-126.

Javelle A, Thomas G, Marini AM, Kramer R, Merrick M 2005 In vivo functional characterisation of the Escherichia coli ammonium channel AmtB: evidence for metabolic coupling of AmtB to glutamine synthetase. Biochem. J. 390: 215-222.

Jayakumar AR, Rao KVR, Schousboe A, Norenberg MD 2004 Glutamine-induced free radical production in cultured astrocytes. Glia 46: 296-301.

Jeffries TW 2006 Engineering yeasts for xylose metabolism. Curr. Opin. Biotechnol. 17: 320-326.

Jensen PR, Hammer K 1998 Artificial promoters for metabolic optimization. Biotechnol. Bioeng. 58: 191-195.

Jeong E, Nagasaki M, Saito A, Miyano S 2007 Cell system ontology: representation for modeling, visualizing, and simulating biological pathways. In Silico Biol. 7: 623-638.

Jeong H, Tombor B, Albert R, Oltvai ZN, Barabasi AL 2000 The large-scale organization of metabolic networks. Nature 407: 651-654.

Jeong ML, Jiang H, Chen HS, Tsai CJ, Harding SA 2004 Metabolic profiling of the sink-to-source transition in developing leaves of quaking aspen. Plant Physiol. 136: 3364-3375.

Jesch SA, Liu P, Zhao X, Wells MT, Henry SA 2006 Multiple endoplasmic reticulum-to-nucleus signaling pathways coordinate phospholipid metabolism with gene expression by distinct mechanisms. J. Biol. Chem. 281: 24070-24083.

Jetter R, Kunst L 2008 Plant surface lipid biosynthetic pathways and their utility for metabolic engineering of waxes and hydrocarbon biofuels. Plant J. 54: 670-683.

Jeuffroy MH, Ney B, Ourry A 2002 Integrated physiological and agronomic modelling of N capture and use within the plant. J. Exp. Bot. 53: 809-823.

Jiang K, Zhang S, Lee S, Tsai G, Kim K, Huang H, Chilcott C, Zhu T, Feldman LJ 2006 Transcription profile analyses identify genes and pathways central to root cap functions in maize. Plant Mol. Biol. 60: 343-363.

Jiang P, Ninfa AJ 2007 Escherichia coli PII signal transduction protein controlling nitrogen assimilation acts as a sensor of adenylate energy charge in vitro. Biochemistry 46: 12979-12996.

Jiao Y, Ma L, Strickland E, Deng XW 2005 Conservation and divergence of light-regulated genome expression patterns during seedling development in rice and Arabidopsis. Plant Cell 17: 3239-3256.

Jin YS, Jeffries TW 2004 Stoichiometric network constraints on xylose metabolism by recombinant Saccharomyces cerevisiae. Metab. Eng. 6: 229-238.

Jin YS, Stephanopoulos G 2007 Multi-dimensional gene target search for improving lycopene biosynthesis in Escherichia coli. Metab. Eng. 9: 337-347.

Job C, Rajjou L, Lovigny Y, Belghazi M, Job D 2005 Patterns of protein oxidation in Arabidopsis seeds and during germination. Plant Physiol. 138: 790-802.

Jobe AM, Herwig C, Surzyn M, Walker B, Marison I, Von Stockar U 2003 Generally applicable fed-batch culture concept based on the detection of metabolic state by on-line balancing. Biotechnol. Bioeng. 82: 627-639.

Johansson M, Nordlund S 1997 Uridylylation of the P(II) protein in the photosynthetic bacterium Rhodospirillum rubrum. J. Bacteriol. 179: 4190-4194.

Jones AM, Thomas V, Bennett MH, Mansfield J, Grant M 2006 Modifications to the Arabidopsis defense proteome occur prior to significant transcriptional change in response to inoculation with Pseudomonas syringae. Plant Physiol. 142: 1603-1620.

Jones KD, Kompala DS 1999 Cybernetic model of the growth dynamics of Saccharomyces cerevisiae in batch and continuous cultures. J. Biotechnol. 71: 105-131.

Jonsson A, Teixeira PF, Nordlund S 2007 The activity of adenylyltransferase in Rhodospirillum rubrum is only affected by alpha-ketoglutarate and unmodified PII proteins, but not by glutamine, in vitro. FEBS J. 274: 2449-2460.

Jorgensen K, Rasmussen AV, Morant M, Nielsen AH, Bjarnholt N, Zagrobelny M, Bak S, Moller BL 2005 Metabolon formation and metabolic channeling in the biosynthesis of plant natural products. Curr. Opin. Plant Biol. 8: 280-291.

Joseph G, Kelsey RG 2004 Ethanol synthesis and aerobic respiration in the laboratory by leader segments of Douglas-fir seedlings from winter and spring. J. Exp. Bot. 55: 1095-1103.

Joshi S, Singh AR, Kumar A, Misra PC, Siddiqi MI, Saxena JK 2008 Molecular cloning and characterization of Plasmodium falciparum transketolase. Mol. Biochem. Parasitol. 160: 32-41.

Joshi V, Laubengayer KM, Schauer N, Fernie AR, Jander G 2006 Two Arabidopsis threonine aldolases are nonredundant and compete with threonine deaminase for a common substrate pool. Plant Cell 18: 3564-3575.

Jost R, Altschmied L, Bloem E, Bogs J, Gershenzon J, Hahnel U, Hansch R, Hartmann T, Kopriva S, Kruse C, Mendel RR, Papenbrock J, Reichelt M, Rennenberg H, Schnug E, Schmidt A, Textor S, Tokuhisa J, Wachter A, Wirtz M, Rausch T, Hell R 2005 Expression profiling of metabolic genes in response to methyl jasmonate reveals regulation of genes of primary and secondary sulfur-related pathways in Arabidopsis thaliana. Photosynth Res. 86: 491-508.

Joyce AR, Palsson BO 2008 Predicting gene essentiality using genome-scale in silico models. Methods Mol. Biol. 416: 433-457.

Julsing MK, Koulman A, Woerdenbag HJ, Quax WJ, Kayser O 2006 Combinatorial biosynthesis of medicinal plant secondary metabolites. Biomol. Eng. 23: 265-279.

Jumtee K, Bamba T, Okazawa A, Fukusaki E, Kobayashi A 2008 Integrated metabolite and gene expression profiling revealing phytochrome A regulation of polyamine biosynthesis of Arabidopsis thaliana. J. Exp. Bot. 59: 1187-1200.

Jung H, Buchholz M, Clausen J, Nietschke M, Revermann A, Schmid R, Jung K 2002 CaiT of Escherichia coli: a new transporter catalyzing L-carnitine/gamma-butyrobetaine exchange. J. Biol. Chem. 277: 39251-39258.

Junker BH, Wuttke R, Tiessen A, Geigenberger P, Sonnewald U, Willmitzer L, Fernie AR 2004 Temporally regulated expression of a yeast invertase in potato tubers allows dissection of the complex metabolic phenotype obtained following its constitutive expression. Plant Mol. Biol. 56: 91-110.

Juty NS, Spence HD, Hotz HR, Tang H, Goryanin I, Hodgman TC 2001 Simultaneous modelling of metabolic, genetic and product-interaction networks. Brief Bioinform. 2: 223-232.

Juvvadi PR, Seshime Y, Kitamoto K 2005 Genomics reveals traces of fungal phenylpropanoid-flavonoid metabolic pathway in the filamentous fungus Aspergillus oryzae. J. Microbiol. 43 :475-486.

Kadirkamanathan V, Yang J, Billings SA, Wright PC 2006 Markov Chain Monte Carlo algorithm based metabolic flux distribution analysis on Corynebacterium glutamicum. Bioinformatics 22: 2681-2687.

Kai K, Horita J, Wakasa K, Miyagawa H 2007 Three oxidative metabolites of indole-3-acetic acid from Arabidopsis thaliana. Phytochemistry 68: 1651-1663.

Kai K, Shimizu B, Mizutani M, Watanabe K, Sakata K 2006 Accumulation of coumarins in Arabidopsis thaliana. Phytochemistry 67: 379-386.

Kai K, Wakasa K, Miyagawa H 2007 Metabolism of indole-3-acetic acid in rice: identification and characterization of N-beta-d-glucopyranosyl indole-3-acetic acid and its conjugates. Phytochemistry 68: 2512-2522.

Kameya M, Ikeda T, Nakamura M, Arai H, Ishii M, Igarashi Y 2007 A novel ferredoxin-dependent glutamate synthase from the hydrogen-oxidizing chemoautotrophic bacterium Hydrogenobacter thermophilus TK-6. J. Bacteriol. 189: 2805-2812.

Kamiya A, Inoue Y, Kodama T, Gonzalez FJ 2004 Hepatocyte nuclear factors 1alpha and 4alpha control expression of proline oxidase in adult liver. FEBS Lett. 578: 63-68.

Kanani H, Chrysanthopoulos PK, Klapa MI 2008 Standardizing GC-MS metabolomics. J. Chromatogr. B. Analyt. Technol. Biomed. Life Sci. 871: 191-201.

Kanno T, Komatsu A, Kasai K, Dubouzet JG, Sakurai M, Ikejiri-Kanno Y, Wakasa K, Tozawa Y 2005 Structure-based in vitro engineering of the anthranilate synthase, a metabolic key enzyme in the plant tryptophan pathway. Plant Physiol. 138: 2260-2268.

Kao KC, Tran LM, Liao JC 2005 A global regulatory role of gluconeogenic genes in Escherichia coli revealed by transcriptome network analysis. J. Biol. Chem. 280: 36079-36087.

Kaplan F, Kopka J, Haskell DW, Zhao W, Schiller KC, Gatzke N, Sung DY, Guy CL 2004 Exploring the temperature-stress metabolome of Arabidopsis. Plant Physiol. 136: 4159-4168.

Kaplan F, Kopka J, Sung DY, Zhao W, Popp M, Porat R, Guy CL 2007 Transcript and metabolite profiling during cold acclimation of Arabidopsis reveals an intricate relationship of cold-regulated gene expression with modifications in metabolite content. Plant J. 50: 967-981.

Kaplun A, Binshtein E, Vyazmensky M, Steinmetz A, Barak Z, Chipman DM, Tittmann K, Shaanan B 2008 Glyoxylate carboligase lacks the canonical active site glutamate of thiamine-dependent enzymes. Nat. Chem. Biol. 4: 113-118.

Karim Z, Szutkowska M, Vernimmen C, Bichara M 2005 Renal handling of NH(3)/NH(4): recent concepts. Nephron Physiol. 101: p77-p81.

Karl T, Curtis AJ, Rosenstiel TN, Monson RK, Fall R 2002 Transient releases of acetaldehyde from tree leaves - products of a pyruvate overflow mechanism?. Plant Cell Environ. 25: 1121-1131.

Karp PD 2001 Pathway databases: a case study in computational symbolic theories. Science 293: 2040-2044.

Karp PD 1998 Metabolic databases. Trends Biochem. Sci. 23: 114-116.

Karp PD, Krummenacker M, Paley S, Wagg J 1999 Integrated pathway-genome databases and their role in drug discovery. Trends Biotechnol. 17: 275-281.

Karp PD, Ouzounis CA, Moore-Kochlacs C, Goldovsky L, Kaipa P, Ahren D, Tsoka S, Darzentas N, Kunin V, Lopez-Bigas N 2005 Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res. 33: 6083-6089.

Karp PD, Paley S, Krieger CJ, Zhang P 2004 An evidence ontology for use in pathway/genome databases. Pac. Symp. Biocomput. 2004: 190-201.

Karunanandaa B, Qi Q, Hao M, Baszis SR, Jensen PK, Wong YH, Jiang J, Venkatramesh M, Gruys KJ, Moshiri F, Post-Beittenmiller D, Weiss JD, Valentin HE 2005 Metabolically engineered oilseed crops with enhanced seed tocopherol. Metab. Eng. 7: 384-400.

Kasimova MR, Grigiene J, Krab K, Hagedorn PH, Flyvbjerg H, Andersen PE, Moller IM 2006 The free NADH concentration is kept constant in plant mitochondria under different metabolic conditions. Plant Cell 18: 688-698.

Katagiri M, Nakamura M 2002 Animals are dependent on preformed alpha-amino nitrogen as an essential nutrient. IUBMB Life 53: 125-129.

Katagiri M, Nakamura M 2003 Reappraisal of the 20th-century version of amino acid metabolism. Biochem. Biophys. Res. Commun. 312: 205-208.

Katahira R, Ashihara H 2006 Profiles of purine biosynthesis, salvage and degradation in disks of potato (Solanum tuberosum L.) tubers. Planta 225: 115-126.

Katoh T, Yuguchi D, Yoshii H, Shi H, Shimizu K 1999 Dynamics and modeling on fermentative production of poly (beta-hydroxybutyric acid) from sugars via lactate by a mixed culture of Lactobacillus delbrueckii and Alcaligenes eutrophus. J. Biotechnol. 67: 113-134.

Kauffman KJ, Pajerowski JD, Jamshidi N, Palsson BO, Edwards JS 2002 Description and analysis of metabolic connectivity and dynamics in the human red blood cell. Biophys. J. 83: 646-662.

Kauffman KJ, Prakash P, Edwards JS 2003 Advances in flux balance analysis. Curr. Opin. Biotechnol. 14: 491-496.

Kaufmann H, Mazur X, Fussenegger M, Bailey JE 1999 Influence of low temperature on productivity, proteome and protein phosphorylation of CHO cells. Biotechnol. Bioeng. 63: 573-582.

Kawalleck P, Plesch G, Hahlbrock K, Somssich IE 1992 Induction by fungal elicitor of S-adenosyl-L-methionine synthetase and S-adenosyl-L-homocysteine hydrolase mRNAs in cultured cells and leaves of Petroselinum crispum. Proc. Natl. Acad. Sci. U.S.A. 89: 4713-4717.

Kayser A, Weber J, Hecht V, Rinas U 2005 Metabolic flux analysis of Escherichia coli in glucose-limited continuous culture. I. Growth-rate-dependent metabolic efficiency at steady state. Microbiology 151: 693-706.

Keasling JD, Chou H 2008 Metabolic engineering delivers next-generation biofuels. Nat. Biotechnol. 26: 298-299.

Kell DB, Mendes P 1999 Snapshots of systems - metabolic control analysis and biotechnology in the post-genomic era. NATO ARW on Technological and Medical Implications of Metabolic Control Analysis, Visegrad 10-16 April, 1999.

Kelleher JK 2004 Probing metabolic pathways with isotopic tracers: insights from mammalian metabolic physiology. Metab. Eng. 6: 1-5.

Kelleher JK 2001 Flux estimation using isotopic tracers: common ground for metabolic physiology and metabolic engineering. Metab. Eng. 3: 100-110.

Kemp GJ, Manners DN, Clark JF, Bastin ME, Radda GK 1998 Theoretical modelling of some spatial and temporal aspects of the mitochondrion/creatine kinase/myofibril system in muscle. Mol. Cell Biochem. 184: 249-289.

Kempa S, Rozhon W, Samaj J, Erban A, Baluska F, Becker T, Haselmayer J, Schleiff E, Kopka J, Hirt H, Jonak C 2007 A plastid-localized glycogen synthase kinase 3 modulates stress tolerance and carbohydrate metabolism. Plant J. 49: 1076-1090.

Kempf B, Gade J, Bremer E 1997 Lipoprotein from the osmoregulated ABC transport system OpuA of Bacillus subtilis: purification of the glycine betaine binding protein and characterization of a functional lipidless mutant. J. Bacteriol. 179: 6213-6220.

Kertesz MA, Mirleau P 2004 The role of soil microbes in plant sulphur nutrition. J. Exp. Bot. 55: 1939-1945.

Keskitalo J, Bergquist G, Gardestrom P, Jansson S 2005 A cellular timetable of autumn senescence. Plant Physiol. 139: 1635-1648.

Keusch GT 2006 What do -omics mean for the science and policy of the nutritional sciences? Am. J. Clin. Nutr. 83: 520S-522S.

Khannapho C, Zhao H, Bonde BK, Kierzek AM, Avignone-Rossa CA, Bushell ME 2008 Selection of objective function in genome scale flux balance analysis for process feed development in antibiotic production. Metab. Eng. Jun 17 [Epub ahead of print].

Kharade SV, Mittal N, Das SP, Sinha P, Roy N 2005 Mrg19 depletion increases S. cerevisiae lifespan by augmenting ROS defence. FEBS Lett. 579: 6809-6813.

Kharbanda KK, Rogers DD 2nd, Mailliard ME, Siford GL, Barak AJ, Beckenhauer HC, Sorrell MF, Tuma DJ 2005 Role of elevated S-adenosylhomocysteine in rat hepatocyte apoptosis: protection by betaine. Biochem. Pharmacol. 70: 1883-1890.

Kholodenko BN, Cascante M, Westerhoff HV 1995 Control theory of metabolic channelling. Mol. Cell Biochem. 143: 151-168.

Kholodenko BN, Rohwer JM, Cascante M, Westerhoff HV 1998 Subtleties in control by metabolic channelling and enzyme organization. Mol. Cell Biochem. 184: 311-320.

Kholodenko BN, Schuster S, Rohwer JM, Cascante M, Westerhoff HV 1995 Composite control of cell function: metabolic pathways behaving as single control units. FEBS Lett. 368: 1-4.

Kichey T, Heumez E, Pocholle D, Pageau K, Vanacker H, Dubois F, Gouis J, Hirel B 2006 Combined agronomic and physiological aspects of nitrogen management in wheat highlight a central role for glutamine synthetase. New. Phytol. 169: 265-278.

Kichey T, Le Gouis J, Sangwan B, Hirel B, Dubois F 2005 Changes in the cellular and subcellular localization of glutamine synthetase and glutamate dehydrogenase during flag leaf senescence in wheat (Triticum aestivum L.). Plant Cell Physiol. 46: 964-974.

Kiefer P, Nicolas C, Letisse F, Portais JC 2007 Determination of carbon labeling distribution of intracellular metabolites from single fragment ions by ion chromatography tandem mass spectrometry. Anal. Biochem. 360: 182-188.

Kilberg MS, Hutson RG, Laine RO 1994 Amino acid-regulated gene expression in eukaryotic cells. FASEB J. 8: 13-19.

Kim BJ, Forbes NS 2007 Flux analysis shows that hypoxia-inducible-factor-1-alpha minimally affects intracellular metabolism in tumor spheroids. Biotechnol. Bioeng. 96: 1167-1182.

Kim HJ, Chen F, Wang X, Choi JH 2006 Effect of methyl jasmonate on phenolics, isothiocyanate, and metabolic enzymes in radish sprout (Raphanus sativus L.). J. Agric. Food Chem. 54: 7263-7269.

Kim HU, Kim TY, Lee SY 2008 Metabolic flux analysis and metabolic engineering of microorganisms. Mol. Biosyst. 4: 113-120.

Kim HU, Li Y, Huang AH 2005 Ubiquitous and endoplasmic reticulum-located lysophosphatidyl acyltransferase, LPAT2, is essential for female but not male gametophyte development in Arabidopsis. Plant Cell 17: 1073-1089.

Kim J, Saidel GM, Kalhan SC 2008 A computational model of adipose tissue metabolism: evidence for intracellular compartmentation and differential activation of lipases. J. Theor. Biol. 251: 523-540.

Kim JH, Jander G 2007 Myzus persicae (green peach aphid) feeding on Arabidopsis induces the formation of a deterrent indole glucosinolate. Plant J. 49: 1008-1019.

Kim JH, Lee YJ, Kim BG, Lim Y, Ahn JH 2008 Flavanone 3beta-hydroxylases from rice: key enzymes for favonol and anthocyanin biosynthesis. Mol. Cells 25: 312-316.

Kim JK, Bamba T, Harada K, Fukusaki E, Kobayashi A 2007 Time-course metabolic profiling in Arabidopsis thaliana cell cultures after salt stress treatment. J. Exp. Bot. 58: 415-424.

Kim KJ, Park CJ, An JM, Ham BK, Lee BJ, Paek KH 2005 CaAlaAT1 catalyzes the alanine: 2-oxoglutarate aminotransferase reaction during the resistance response against tobacco mosaic virus in hot pepper. Planta 221: 857-867.

Kim PJ, Lee DY, Kim TY, Lee KH, Jeong H, Lee SY, Park S 2007 Metabolite essentiality elucidates robustness of Escherichia coli metabolism. Proc. Natl. Acad. Sci. U.S.A. 104: 13638-13642.

Kim TY, Sohn SB, Kim HU, Lee SY 2008 Strategies for systems-level metabolic engineering. Biotechnol. J. 3: 612-623.

Kim YS, Sano H 2008 Pathogen resistance of transgenic tobacco plants producing caffeine. Phytochemistry 69: 882-888.

Kinnersley AM, Turano FJ 2000 Gamma aminobutyric acid (GABA) and plant responses to stress. Crit. Rev. Plant Sci. 19: 479-509.

Kinney AJ 2006 Metabolic engineering in plants for human health and nutrition. Curr. Opin. Biotechnol. 17: 130-138.

Kinney AJ 1998 Manipulating flux through plant metabolic pathways. Curr. Opin. Plant Biol. 1: 173-178.

Kinoshita A, Nakayama Y, Tomita M 2001 Towards simulation of whole metabolic pathways in human erythrocyte. Genome Informatics 12: 312-313.

Kinraide TB, Parker DR, Zobel RW 2005 Organic acid secretion as a mechanism of aluminium resistance: a model incorporating the root cortex, epidermis, and the external unstirred layer. J. Exp. Bot. 56: 1853-1865.

Kirby J, Keasling JD 2008 Metabolic engineering of microorganisms for isoprenoid production. Nat. Prod. Rep. 25: 656-661.

Kirchberger S, Tjaden J, Ekkehard Neuhaus H 2008 Characterization of the Arabidopsis Brittle1 transport protein and impact of reduced activity on plant metabolism. Plant J. Jun 18 [Epub ahead of print].

Kirst M, Myburg AA, De Leon JP, Kirst ME, Scott J, Sederoff R 2004 Coordinated genetic regulation of growth and lignin revealed by quantitative trait locus analysis of cDNA microarray data in an interspecific backcross of Eucalyptus. Plant Physiol. 135: 2368-2378.

Kitami T, Rubio R, O'Brien W, Quackenbush J, Nadeau JH 2008 Gene-environment interactions reveal a homeostatic role for cholesterol metabolism during dietary folate perturbation in mice. Physiol. Genomics Aug 12 [Epub ahead of print].

Kiviharju K, Moilanen U, Leisola M, Eerikainen T 2007 A chemostat study of Streptomyces peucetius var. caesius N47. Appl. Microbiol. Biotechnol. 73: 1267-1274.

Kizer L, Pitera DJ, Pfleger BF, Keasling JD 2008 Application of functional genomics to pathway optimization for increased isoprenoid production. Appl. Environ. Microbiol. 74: 3229-3241.

Klamt S, Schuster S 2002 Calculating as many fluxes as possible in underdetermined metabolic networks. Mol. Biol. Rep. 29: 243-248.

Klamt S, Schuster S, Gilles ED 2002 Calculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteria. Biotechnol. Bioeng. 77: 734-751.

Klamt S, Stelling J 2002 Combinatorial complexity of pathway analysis in metabolic networks. Mol. Biol. Rep. 29: 233-236.

Klamt S, Stelling J 2003 Two approaches for metabolic pathway analysis? Trends Biotechnol. 21: 64-69.

Klamt S, Stelling J, Ginkel M, Gilles ED 2003 FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. Bioinformatics 19: 261-269.

Klapa MI, Aon JC, Stephanopoulos G 2003 Systematic quantification of complex metabolic flux networks using stable isotopes and mass spectrometry. Eur. J. Biochem. 270: 3525-3542.

Klapa MI, Park SM, Sinskey AJ, Stephanopoulos G 1999 Metabolite and isotopomer balancing in the analysis of metabolic cycles: I. Theory. Biotechnol. Bioeng. 62: 375-391.

Kleerebezem R, Stams AJ 2000 Kinetics of syntrophic cultures: a theoretical treatise on butyrate fermentation. Biotechnol. Bioeng. 67: 529-543.

Kleijn RJ, Geertman JM, Nfor BK, Ras C, Schipper D, Pronk JT, Heijnen JJ, van Maris AJ, van Winden WA 2007 Metabolic flux analysis of a glycerol-overproducing Saccharomyces cerevisiae strain based on GC-MS, LC-MS and NMR-derived (13)C-labelling data. FEMS Yeast Res. 7: 216-231.

Kleijn RJ, Liu F, van Winden WA, van Gulik WM, Ras C, Heijnen JJ 2007 Cytosolic NADPH metabolism in penicillin-G producing and non-producing chemostat cultures of Penicillium chrysogenum. Metab. Eng. 9: 112-123.

Kleijn RJ, van Winden WA, Ras C, van Gulik WM, Schipper D, Heijnen JJ 2006 13C-Labeled gluconate tracing as a direct and accurate method for determining the pentose phosphate pathway split ratio in Penicillium chrysogenum. Appl. Environ. Microbiol. 72: 4743-4754.

Kleijn RJ, van Winden WA, van Gulik WM, Heijnen JJ 2005 Revisiting the 13C-label distribution of the non-oxidative branch of the pentose phosphate pathway based upon kinetic and genetic evidence. FEBS J. 272: 4970-4982.

Klein CT, Mayer B 1999 Sources for structure formation and switches in metabolic pathways. Biosystems 51: 41-52.

Klein W, Horlacher R, Boos W 1995 Molecular analysis of treB encoding the Escherichia coli enzyme II specific for trehalose. J. Bacteriol. 177: 4043-4052.

Kliebenstein DJ, Rowe HC, Denby KJ 2005 Secondary metabolites influence Arabidopsis/Botrytis interactions: variation in host production and pathogen sensitivity. Plant J. 44: 25-36.

Klipp E, Heinrich R 1999 Competition for enzymes in metabolic pathways: implications for optimal distributions of enzyme concentrations and for the distribution of flux control. Biosystems 54: 1-14.

Klipp E, Liebermeister W, Wierling C 2004 Inferring dynamic properties of biochemical reaction networks from structural knowledge. Genome Inform. 15: 125-137.

Klotke J, Kopka J, Gatzke N, Heyer AG 2004 Impact of soluble sugar concentrations on the acquisition of freezing tolerance in accessions of Arabidopsis thaliana with contrasting cold adaptation - evidence for a role of raffinose in cold acclimation. Plant Cell Environ. 27: 1395-1404.

Knappe J, Sawers G 1990 A radical-chemical route to acetyl-CoA: the anaerobically induced pyruvate formate-lyase system of Escherichia coli. FEMS Microbiol. Rev. 6: 383-398.

Kobayashi K, Masuda T, Takamiya K, Ohta H 2006 Membrane lipid alteration during phosphate starvation is regulated by phosphate signaling and auxin/cytokinin cross-talk. Plant J. 47: 238-248.

Koch KE 1996 Carbohydrate-modulated gene expression in plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 47: 509-540.

Koebmann B, Solem C, Jensen PR 2005 Control analysis as a tool to understand the formation of the las operon in Lactococcus lactis. FEBS J. 272: 2292-2303.

Koebmann B, Solem C, Jensen PR 2006 Control analysis of the importance of phosphoglycerate enolase for metabolic fluxes in Lactococcus lactis subsp. lactis IL1403. Syst. Biol. (Stevenage) 153: 346-349.

Koffas M, Roberge C, Lee K, Stephanopoulos G 1999 Metabolic engineering. Annu. Rev. Biomed. Eng. 1: 535-557.

Koffas M, Stephanopoulos G 2005 Strain improvement by metabolic engineering: lysine production as a case study for systems biology. Curr. Opin. Biotechnol. 16: 361-366.

Kohler A, Delaruelle C, Martin D, Encelot N, Martin F 2003 The poplar root transcriptome: analysis of 7000 expressed sequence tags. FEBS Lett. 542: 37-41.

Kohn MC 1992 Propagation of information in MetaNet graph models. J. Theor. Biol. 154: 505-517.

Kolbe A, Oliver SN, Fernie AR, Stitt M, van Dongen JT, Geigenberger P 2006 Combined transcript and metabolite profiling of Arabidopsis leaves reveals fundamental effects of the thiol-disulfide status on plant metabolism. Plant Physiol. 141: 412-422.

Kolker E, Purvine S, Picone A, Cherny T, Akerley BJ, Munson RS Jr, Palsson BO, Daines DA, Smith AL 2002 H. influenzae consortium: integrative study of H. influenzae-human interactions. OMICS 6: 341-348.

Koller M, Horvat P, Hesse P, Bona R, Kutschera C, Atlic A, Braunegg G 2006 Assessment of formal and low structured kinetic modeling of polyhydroxyalkanoate synthesis from complex substrates. Bioprocess. Biosyst. Eng. 29: 367-377.

Komives C, Parker RS 2003 Bioreactor state estimation and control. Curr. Opin. Biotechnol. 14: 468-474.

Kompala DS 1999 Cybernetic modeling of spontaneous oscillations in continuous cultures of Saccharomyces cerevisiae. J. Biotechnol. 71: 267-274.

Kondo M, Oyama-Okubo N, Sagae M, Ando T, Marchesi E, Nakayama M 2007 Metabolic regulation of floral scent in Petunia axillaris lines: biosynthetic relationship between dihydroconiferyl acetate and iso-eugenol. Biosci. Biotechnol. Biochem. 71: 458-463.

Konishi T, Ohmiya Y, Hayashi T 2004 Evidence that sucrose loaded into the phloem of a poplar leaf is used directly by sucrose synthase associated with various beta-glucan synthases in the stem. Plant Physiol. 134: 1146-1152.

Kooijman SA 2001 Quantitative aspects of metabolic organization: a discussion of concepts. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 356: 331-349.

Kooijman SA, Kooi BW, Hallam TG 1999 The application of mass and energy conservation laws in physiologically structured population models of heterotrophic organisms. J. Theor. Biol. 197: 371-392.

Koonin EV, Mushegian AR, Galperin MY, Walker DR 1997 Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea. Mol. Microbiol. 25: 619-637.

Koonin EV, Mushegian AR, Rudd KE 1996 Sequencing and analysis of bacterial genomes. Curr. Biol. 6: 404-416.

Kore-eda S, Cushman MA, Akselrod I, Bufford D, Fredrickson M, Clark E, Cushman JC 2004 Transcript profiling of salinity stress responses by large-scale expressed sequence tag analysis in Mesembryanthemum crystallinum. Gene 341: 83-92.

Korendyaseva TK, Kuvatov DN, Volkov VA, Martinov MV, Vitvitsky VM, Banerjee R, Ataullakhanov FI 2008 An allosteric mechanism for switching between parallel tracks in mammalian sulfur metabolism. PLoS Comput. Biol. 4: e1000076.

Korzeniewski B 1998 Is it possible to predict any properties of oxidative phosphorylation in a theoretical way? Mol. Cell Biochem. 184: 345-358.

Koschutzki D, Schwobbermeyer H, Schreiber F 2007 Ranking of network elements based on functional substructures. J. Theor. Biol. 248: 471-479.

Kose F, Weckwerth W, Linke T, Fiehn O 2001 Visualizing plant metabolomic correlation networks using clique-metabolite matrices. Bioinformatics 17: 1198-1208.

Kota P, Guo D, Zubieta C, Noel J, Dixon RA 2004 O-Methylation of benzaldehyde derivatives by "lignin specific" caffeic acid 3-O-methyltransferase. Phytochemistry 65: 837-846.

Kowaluk EA, Jarvis MF 2000 Therapeutic potential of adenosine kinase inhibitors. Expert Opin. Investig. Drugs 9: 551-564.

Krab K 1995 Kinetic and regulatory aspects of the function of the alternative oxidase in plant respiration. J. Bioenerg. Biomembr. 27: 387-396.

Kramer DL, Diegelman P, Jell J, Vujcic S, Merali S, Porter CW 2008 Polyamine acetylation modulates polyamine metabolic flux, a prelude to broader metabolic consequences. J. Biol. Chem. 283: 4241-4251.

Kramer M, Bongaerts J, Bovenberg R, Kremer S, Muller U, Orf S, Wubbolts M, Raeven L 2003 Metabolic engineering for microbial production of shikimic acid. Metab. Eng. 5: 277-283.

Kramer SF, Bentley WE 2003 RNA interference as a metabolic engineering tool: potential for in vivo control of protein expression in an insect larval model. Metab. Eng. 5: 183-190.

Krappmann S, Lipscomb WN, Braus GH 2000 Coevolution of transcriptional and allosteric regulation at the chorismate metabolic branch point of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A. 97: 13585-13590.

Krauss S, Quant PA 1996 Regulation and control in complex, dynamic metabolic systems: experimental application of the top-down approaches of metabolic control analysis to fatty acid oxidation and ketogenesis. J. Theor. Biol. 182: 381-388.

Kremling A, Bettenbrock K, Laube B, Jahreis K, Lengeler JW, Gilles ED 2001 The organization of metabolic reaction networks. Metab. Eng. 3: 362-379.

Kremling A, Gilles ED 2001 The organization of metabolic reaction networks II. Signal processing in hierarchical structured functional units. Metab. Eng. 3: 138-150.

Kremling A, Jahreis K, Lengeler JW, Gilles ED 2000 The organization of metabolic reaction networks: a signal-oriented approach to cellular models. Metab. Eng. 2: 190-200.

Krens FA, Keizer LCP, Capel IEM 1997 Transgenic caraway, Carum carvi L.: a model species for metabolic engineering. Plant Cell Rep. 17: 39-43.

Kresnowati MT, van Winden WA, Heijnen JJ 2005 Determination of elasticities, concentration and flux control coefficients from transient metabolite data using linlog kinetics. Metab. Eng. 7: 142-153.

Krinke O, Ruelland E, Valentova O, Vergnolle C, Renou JP, Taconnat L, Flemr M, Burketova L, Zachowski A 2007 Phosphatidylinositol 4-kinase activation is an early response to salicylic acid in Arabidopsis suspension cells. Plant Physiol. 144: 1347-1359.

Krishnan N, Dickman MB, Becker DF 2008 Proline modulates the intracellular redox environment and protects mammalian cells against oxidative stress. Free Radic. Biol. Med. 44: 671-681.

Krishnan P, Kruger NJ, Ratcliffe RG 2005 Metabolite fingerprinting and profiling in plants using NMR. J. Exp. Bot. 56: 255-265.

Kristensen C, Morant M, Olsen CE, Ekstrom CT, Galbraith DW, Moller BL, Bak S 2005 Metabolic engineering of dhurrin in transgenic Arabidopsis plants with marginal inadvertent effects on the metabolome and transcriptome. Proc. Natl. Acad. Sci. U.S.A. 102: 1779-1784.

Kromer JO, Heinzle E, Schroder H, Wittmann C 2006 Accumulation of homolanthionine and activation of a novel pathway for isoleucine biosynthesis in Corynebacterium glutamicum McbR deletion strains. J. Bacteriol. 188: 609-618.

Kromer JO, Sorgenfrei O, Klopprogge K, Heinzle E, Wittmann C 2004 In-depth profiling of lysine-producing Corynebacterium glutamicum by combined analysis of the transcriptome, metabolome, and fluxome. J. Bacteriol. 186: 1769-1784.

Kromer JO, Wittmann C, Schroder H, Heinzle E 2006 Metabolic pathway analysis for rational design of L-methionine production by Escherichia coli and Corynebacterium glutamicum. Metab. Eng. 8: 353-369.

Kroth PG, Chiovitti A, Gruber A, Martin-Jezequel V, Mock T, Parker MS, Stanley MS, Kaplan A, Caron L, Weber T, Maheswari U, Armbrust EV, Bowler C 2008 A model for carbohydrate metabolism in the diatom Phaeodactylum tricornutum deduced from comparative whole genome analysis. PLoS ONE 3: e1426.

Kruger NJ, Huddleston JE, Le Lay P, Brown ND, Ratcliffe RG 2007 Network flux analysis: impact of 13C-substrates on metabolism in Arabidopsis thaliana cell suspension cultures. Phytochemistry 68: 2176-2188.

Kruger NJ, Le Lay P, Ratcliffe RG 2007 Vacuolar compartmentation complicates the steady-state analysis of glucose metabolism and forces reappraisal of sucrose cycling in plants. Phytochemistry 68: 2189-2196.

Kruger NJ, Ratcliffe RG 2007 Dynamic metabolic networks: going with the flow. Phytochemistry 68: 2136-2138.

Kruger NJ, Troncoso-Ponce MA, Ratcliffe RG 2008 1H NMR metabolite fingerprinting and metabolomic analysis of perchloric acid extracts from plant tissues. Nat. Protoc. 3: 1001-1012.

Kruger NJ, von Schaewen A 2003 The oxidative pentose phosphate pathway: structure and organisation. Curr. Opin. Plant Biol. 6: 236-246.

Kruschwitz HL, McDonald D, Cossins EA, Schirch V 1994 5-Formyltetrahydropteroylpolyglutamates are the major folate derivatives in Neurospora crassa conidiospores. J. Biol. Chem. 269: 28757-28763.

Kruse E, Mock HP, Grimm B 1995 Coproporphyrinogen III oxidase from barley and tobacco--sequence analysis and initial expression studies. Planta 196: 796-803.

Krusell L, Krause K, Ott T, Desbrosses G, Kramer U, Sato S, Nakamura Y, Tabata S, James EK, Sandal N, Stougaard J, Kawaguchi M, Miyamoto A, Suganuma N, Udvardi MK 2005 The sulfate transporter SST1 is crucial for symbiotic nitrogen fixation in Lotus japonicus root nodules. Plant Cell 17: 1625-1636.

Kubis SE, Pike MJ, Everett CJ, Hill LM, Rawsthorne S 2004 The import of phosphoenolpyruvate by plastids from developing embryos of oilseed rape, Brassica napus (L.), and its potential as a substrate for fatty acid synthesis. J. Exp. Bot. 55: 1455-1462.

Kuchel PW, Philp DJ 2008 Isotopomer subspaces as indicators of metabolic-pathway structure. J. Theor. Biol. 252: 391-401.

Kucho K, Okamoto K, Tabata S, Fukuzawa H, Ishiura M 2005 Identification of novel clock-controlled genes by cDNA macroarray analysis in Chlamydomonas reinhardtii. Plant Mol. Biol. 57: 889-906.

Kuepfer L, Sauer U, Blank LM 2005 Metabolic functions of duplicate genes in Saccharomyces cerevisiae. Genome Res. 15: 1421-1430.

Kuipers OP 1999 Genomics for food biotechnology: prospects of the use of high-throughput technologies for the improvement of food microorganisms. Curr. Opin. Biotechnol. 10: 511-516.

Kumar N, Kumar S, Vats SK, Ahuja PS 2006 Effect of altitude on the primary products of photosynthesis and the associated enzymes in barley and wheat. Photosynth. Res. 88: 63-71.

Kumar P, Kumar A, Verma SS, Dwivedi N, Singh N, Siddiqi MI, Tripathi RP, Dube A, Singh N 2008 Leishmania donovani pteridine reductase 1: Biochemical properties and structure-modeling studies. Exp. Parasitol. 120: 73-79.

Kumar S, Punekar NS, SatyaNarayan V, Venkatesh KV 2000 Metabolic fate of glutamate and evaluation of flux through the 4-aminobutyrate (GABA) shunt in Aspergillus niger. Biotechnol. Bioeng. 67: 575-584.

Kummel A, Panke S, Heinemann M 2006 Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data. Mol. Syst. Biol. 2: 2006.0034.

Kure S, Takayanagi M, Narisawa K, Tada K, Leisti J 1992 Identification of a common mutation in Finnish patients with nonketotic hyperglycinemia. J. Clin. Invest. 90: 160-164.

Kuznetsova E, Proudfoot M, Gonzalez CF, Brown G, Omelchenko MV, Borozan I, Carmel L, Wolf YI, Mori H, Savchenko AV, Arrowsmith CH, Koonin EV, Edwards AM, Yakunin AF 2006 Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family. J. Biol. Chem. 281: 36149-36161.

La S, Yoo HH, Kim DH 2005 Liquid chromatography-mass spectrometric analysis of urinary metabolites and their pattern recognition for the prediction of drug-induced hepatotoxicity. Chem. Res. Toxicol. 18: 1887-1896.

Lahoz-Beltra R 2001 Evolving hardware as model of enzyme evolution. Biosystems 61: 15-25.

Lai K, Klapa MI 2004 Alternative pathways of galactose assimilation: could inverse metabolic engineering provide an alternative to galactosemic patients? Metab. Eng. 6: 239-244.

Lai LC, Kosorukoff AL, Burke PV, Kwast KE 2005 Dynamical remodeling of the transcriptome during short-term anaerobiosis in Saccharomyces cerevisiae: differential response and role of Msn2 and/or Msn4 and other factors in galactose and glucose media. Mol. Cell. Biol. 25: 4075-4091.

Lalonde S, Ehrhardt DW, Frommer WB 2005 Shining light on signaling and metabolic networks by genetically encoded biosensors. Curr. Opin. Plant Biol. 8: 574-581.

Lam HM, Coschigano KT, Oliveira IC, Melo-Oliveira R, Coruzzi GM 1996 The molecular-genetics of nitrogen assimilation into amino acids in higher plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 47: 569-593.

Lam HM, Peng SS, Coruzzi GM 1994 Metabolic regulation of the gene encoding glutamine-dependent asparagine synthetase in Arabidopsis thaliana. Plant Physiol. 106: 1347-1357.

Lamkemeyer P, Laxa M, Collin V, Li W, Finkemeier I, Schottler MA, Holtkamp V, Tognetti VB, Issakidis-Bourguet E, Kandlbinder A, Weis E, Miginiac-Maslow M, Dietz KJ 2006 Peroxiredoxin Q of Arabidopsis thaliana is attached to the thylakoids and functions in context of photosynthesis. Plant J. 45: 968-981.

Lancien M, Martin M, Hsieh MH, Leustek T, Goodman H, Coruzzi GM 2002 Arabidopsis glt1-T mutant defines a role for NADH-GOGAT in the non-photorespiratory ammonium assimilatory pathway. Plant J. 29: 347-358.

Lang D, Eisinger J, Reski R, Rensing SA 2005 Representation and high-quality annotation of the Physcomitrella patens transcriptome demonstrates a high proportion of proteins involved in metabolism in mosses. Plant Biol. (Stuttg.) 7: 238-250.

Lange BM 2006 Integrative analysis of metabolic networks: from peaks to flux models? Curr. Opin. Plant Biol. 9: 220-226.

Lange HC, Heijnen JJ 2001 Statistical reconciliation of the elemental and molecular biomass composition of Saccharomyces cerevisiae. Biotechnol. Bioeng. 75: 334-344.

Lapadatescu C, Ginies C, Le Quere JL, Bonnarme P 2000 Novel scheme for biosynthesis of aryl metabolites from L-phenylalanine in the fungus Bjerkandera adusta. Appl. Environ. Microbiol. 66: 1517-1522.

Lapcík O 2007 Isoflavonoids in non-leguminous taxa: a rarity or a rule? Phytochemistry 68: 2909-2916.

Laposky AD, Bass J, Kohsaka A, Turek FW 2008 Sleep and circadian rhythms: key components in the regulation of energy metabolism. FEBS Lett. 582: 142-151.

Lapujade P, Cocaign-Bousquet M, Loubiere P 1998 Glutamate biosynthesis in Lactococcus lactis subsp. lactis NCDO 2118. Appl. Environ. Microbiol. 64: 2485-2489.

Larsen M, Trapp S, Pirandello A 2004 Removal of cyanide by woody plants. Chemosphere 54: 325-333.

Laryea MD, Steinhagen F, Pawliczek S, Wendel U 1998 Simple method for the routine determination of betaine and N,N-dimethylglycine in blood and urine. Clin. Chem. 44: 1937-1941.

Last R, Willmitzer L 2001 Physiology and metabolism: Editorial overview. Curr. Opin. Plant Biol. 4: 179-180.

Last RL, Jones AD, Shachar-Hill Y 2007 Towards the plant metabolome and beyond. Nat. Rev. Mol. Cell. Biol. 8: 167-174.

Latino DA, Zhang QY, Aires-de-Sousa J 2008 Genome-scale classification of metabolic reactions and assignment of EC numbers with self-organizing maps. Bioinformatics Aug 1 [Epub ahead of print].

Latté KP, Kaloga M, Schäfer A, Kolodziej H 2008 An ellagitannin, n-butyl gallate, two aryltetralin lignans, and an unprecedented diterpene ester from Pelargonium reniforme. Phytochemistry 69: 820-826.

Latz A, Becker D, Hekman M, Müller T, Beyhl D, Marten I, Eing C, Fischer A, Dunkel M, Bertl A, Rapp UR, Hedrich R 2007 TPK1, a Ca(2+)-regulated Arabidopsis vacuole two-pore K(+) channel is activated by 14-3-3 proteins. Plant J. 52: 449-459.

Lawlor DW 2002 Carbon and nitrogen assimilation in relation to yield: mechanisms are the key to understanding production systems. J. Exp. Bot. 53: 773-787.

Lawlor DW, Cornic G 2002 Photosynthetic carbon assimilation and associated metabolism in relation to water deficits in higher plants. Plant Cell Environ. 25: 275-294.

Le Lay P, Isaure MP, Sarry JE, Kuhn L, Fayard B, Le Bail JL, Bastien O, Garin J, Roby C, Bourguignon J 2006 Metabolomic, proteomic and biophysical analyses of Arabidopsis thaliana cells exposed to a caesium stress. Influence of potassium supply. Biochimie 88: 1533-1547.

Leaf TA, Srienc F 1998 Metabolic modeling of polyhydroxybutyrate biosynthesis. Biotechnol. Bioeng. 57: 557-570.

Leakey AD, Uribelarrea M, Ainsworth EA, Naidu SL, Rogers A, Ort DR, Long SP 2006 Photosynthesis, productivity, and yield of maize are not affected by open-air elevation of CO2 concentration in the absence of drought. Plant Physiol. 140: 779-790.

Lee B, Yen J, Yang L, Liao JC 1999 Incorporating qualitative knowledge in enzyme kinetic models using fuzzy logic. Biotechnol. Bioeng. 62: 722-729.

Lee CJ, Lee JH, Seok JH, Hur GM, Park Js J, Bae S, Lim JH, Park YC 2004 Effects of betaine, coumarin and flavonoids on mucin release from cultured hamster tracheal surface epithelial cells. Phytother. Res. 18: 301-305.

Lee DY, Fan LT, Park S, Lee SY, Shafie S, Bertok B, Friedler F 2005 Complementary identification of multiple flux distributions and multiple metabolic pathways. Metab. Eng. 7: 182-200.

Lee DY, Yun C, Cho A, Hou BK, Park S, Lee SY 2006 WebCell: a web-based environment for kinetic modeling and dynamic simulation of cellular networks. Bioinformatics 22: 1150-1151.

Lee DY, Zimmer R, Lee SY, Park S 2006 Colored Petri net modeling and simulation of signal transduction pathways. Metab. Eng. 8: 112-122.

Lee K, Berthiaume F, Stephanopoulos GN, Yarmush DM, Yarmush ML 2000 Metabolic flux analysis of postburn hepatic hypermetabolism. Metab. Eng. 2: 312-327.

Lee K, Berthiaume F, Stephanopoulos GN, Yarmush ML 1999 Metabolic flux analysis: a powerful tool for monitoring tissue function. Tissue Eng. 5: 347-368.

Lee K, Berthiaume F, Stephanopoulos GN, Yarmush ML 2003 Profiling of dynamic changes in hypermetabolic livers. Biotechnol. Bioeng. 83: 400-415.

Lee K, Berthiaume F, Stephanopoulos GN, Yarmush ML 2003 Induction of a hypermetabolic state in cultured hepatocytes by glucagon and H2O2. Metab. Eng. 5: 221-229.

Lee KM, Rhee CH, Kang CK, Kim JH 2006 Statistical medium formulation and process modeling by mixture design of experiment for peptide overexpression in recombinant Escherichia coli. Appl. Biochem. Biotechnol. 135: 81-110.

Lee LK, Roth CM 2003 Antisense technology in molecular and cellular bioengineering. Curr. Opin. Biotechnol. 14: 505-511.

Lee MB, Storer MK, Blunt JW, Lever M 2006 Validation of (1)H NMR spectroscopy as an analytical tool for methylamine metabolites in urine. Clin. Chim. Acta 365: 264-269.

Lee SG, Liao JC 2008 Control of acetate production rate in Escherichia coli by regulating expression of single-copy pta using lacI(Q) in multicopy plasmid. J. Microbiol. Biotechnol. 18: 334-337.

Lee SJ, Lee DY, Kim TY, Kim BH, Lee J, Lee SY 2005 Metabolic engineering of Escherichia coli for enhanced production of succinic acid, based on genome comparison and in silico gene knockout simulation. Appl. Environ. Microbiol. 71: 7880-7887.

Lee SY, Lee DY, Hong SH, Kim TY, Yun H, Oh YG, Park S 2003 MetaFluxNet, a program package for metabolic pathway construction and analysis, and its use in large-scale metabolic flux analysis of Escherichia coli. Genome Inform. Ser. Workshop Genome Inform. 14: 23-33.

Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA 2002 Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298: 799-804.

Lee W, Dasilva NA 2006 Application of sequential integration for metabolic engineering of 1,2-propanediol production in yeast. Metab. Eng. 8: 58-65.

Lee WN, Go VL 2005 Nutrient-gene interaction: tracer-based metabolomics. J. Nutr. 135: 3027S-3032S.

Lee YY, Wong KT, Nissom PM, Wong DC, Yap MG 2007 Transcriptional profiling of batch and fed-batch protein-free 293-HEK cultures. Metab. Eng. 9: 52-67.

Leech MJ, Burtin D, Hallard D, Hilliou F, Kemp B, Palacios N, Rocha P, O'Callaghan D, Verpoote R, Christou P 2000 Chapter 4. Particle Gun Methodology as a Tool in Metabolic Engineering. In "Metabolic Engineering of Plant Secondary Metabolism" (Verpoorte R, Alfermann AW, eds), Kluwer Academic Publishers, Dortrecht, The Netherlands, pp. 69-86.

Leegood RC 2008 Roles of the bundle sheath cells in leaves of C3 plants. J. Exp. Bot. 59: 1663-1673.

Leegood RC, von Caemmerer S 1994 Regulation of photosynthetic carbon assimilation in leaves of C3-C4 intermediate species of Moricandia and Flaveria. Planta 192: 232-238.

Leggat W, Buck BH, Grice A, Yellowlees D 2003 The impact of bleaching on the metabolic contribution of dinoflagellate symbionts to their giant clam host. Plant Cell Environ. 26: 1951-1961.

Lehfeldt C, Shirley AM, Meyer K, Ruegger MO, Cusumano JC, Viitanen PV, Strack D, Chapple C 2000 Cloning of the SNG1 gene of Arabidopsis reveals a role for a serine carboxypeptidase-like protein as an acyltransferase in secondary metabolism. Plant Cell 12: 1295-1306.

Leienbach KW, Heeger V, Barz W 1976 Metabolism of nicotinic acid in plant cell suspension cultures. IV: Occurrence and metabolism of nicotinic acid N-alpha-arabinoside. Hoppe Seylers Z. Physiol. Chem. 357: 1089-1095.

Leiser J, Blum JJ 1987 On the analysis of substrate cycles in large metabolic systems. Cell Biophys. 11: 123-138.

Lemaire-Chamley M, Petit J, Garcia V, Just D, Baldet P, Germain V, Fagard M, Mouassite M, Cheniclet C, Rothan C 2005 Changes in transcriptional profiles are associated with early fruit tissue specialization in tomato. Plant Physiol. 139: 750-769.

Lemaitre T, Gaufichon L, Boutet-Mercey S, Christ A, Masclaux-Daubresse C 2008 Enzymatic and metabolic diagnostic of nitrogen deficiency in Arabidopsis thaliana Wassileskija accession. Plant Cell Physiol. 49: 1056-1065.

Lemaitre T, Urbanczyk-Wochniak E, Flesch V, Bismuth E, Fernie AR, Hodges M 2007 NAD-dependent isocitrate dehydrogenase mutants of Arabidopsis suggest the enzyme is not limiting for nitrogen assimilation. Plant Physiol. 144: 1546-1558.

Lemeshko SV, Lemeshko VV 2000 Metabolically derived potential on the outer membrane of mitochondria: a computational model. Biophys. J. 79: 2785-2800.

Lengeler JW 2000 Metabolic networks: a signal-oriented approach to cellular models. Biol. Chem. 381: 911-920.

Leonard E, Yan Y, Fowler ZL, Li Z, Lim CG, Lim KH, Koffas MA 2008 Strain improvement of recombinant Escherichia coli for efficient production of plant flavonoids. Mol. Pharm. 5: 257-265.

Leonard E, Yan Y, Koffas MA 2006 Functional expression of a P450 flavonoid hydroxylase for the biosynthesis of plant-specific hydroxylated flavonols in Escherichia coli. Metab. Eng. 8: 172-181.

Leonhartsberger S, Korsa I, Bock A 2002 The molecular biology of formate metabolism in enterobacteria. J. Mol. Microbiol. Biotechnol. 4: 269-276.

Lepiniec L, Debeaujon I, Routaboul JM, Baudry A, Pourcel L, Nesi N, Caboche M 2006 Genetics and biochemistry of seed flavonoids. Annu. Rev. Plant Biol. 57: 405-430.

Leprince O, Harren FJ, Buitink J, Alberda M, Hoekstra FA 2000 Metabolic dysfunction and unabated respiration precede the loss of membrane integrity during dehydration of germinating radicles. Plant Physiol. 122: 597-608.

Lerma C, Rich PJ, Ju GC, Yang WJ, Hanson AD, Rhodes D 1991 Betaine deficiency in maize: complementation tests and metabolic basis. Plant Physiol. 95: 1113-1119.

Lermontova I, Grimm B 2006 Reduced activity of plastid protoporphyrinogen oxidase causes attenuated photodynamic damage during high-light compared to low-light exposure. Plant J. 48: 499-510.

Lerner-Ellis JP, Tirone JC, Pawelek PD, Dore C, Atkinson JL, Watkins D, Morel CF, Fujiwara TM, Moras E, Hosack AR, Dunbar GV, Antonicka H, Forgetta V, Dobson CM, Leclerc D, Gravel RA, Shoubridge EA, Coulton JW, Lepage P, Rommens JM, Morgan K, Rosenblatt D 2006 Identification of the gene responsible for methylmalonic aciduria and homocystinuria, cblC type. Nat. Genet. 38: 93-100.

Lerondel G, Doan T, Zamboni N, Sauer U, Aymerich S 2006 YtsJ has the major physiological role of the four paralogous malic enzyme isoforms in Bacillus subtilis. J. Bacteriol. 188: 4727-4736.

Lessard PA, Kulaveerasingam H, York GM, Strong A, Sinskey AJ 2002 Manipulating gene expression for the metabolic engineering of plants. Metab. Eng. 4: 67-79.

Letellier T, Reder C, Mazat JP 1991 CONTROL: software for the analysis of the control of metabolic networks. Comput. Appl. Biosci. 7: 383-390.

Lever M, Sizeland PCM, Frampton CM, Chambers ST 2004 Short and long-term variation of plasma glycine betaine concentrations in humans. Clin. Biochem. 37: 184-190.

Levillain O, Hus-Citharel A, Garvi S, Peyrol S, Reymond I, Mutin M, Morel F 2004 Ornithine metabolism in male and female rat kidney: mitochondrial expression of ornithine aminotransferase and arginase II. Am. J. Physiol. Renal Physiol. 286: F727-F738.

Levy HL 2005 Metabolic disorders in the center of genetic medicine. N. Engl. J Med. 353: 1968-1970.

Lezon TR, Banavar JR, Cieplak M, Maritan A, Fedoroff NV 2006 Using the principle of entropy maximization to infer genetic interaction networks from gene expression patterns. Proc. Natl. Acad. Sci. U.S.A. 103: 19033-19038.

Li C, Allen A, Kwagh J, Doliba NM, Qin W, Najafi H, Collins HW, Matschinsky FM, Stanley CA, Smith TJ 2006 Green tea polyphenols modulate insulin secretion by inhibiting glutamate dehydrogenase. J. Biol. Chem. 281: 10214-1021.

Li F, Vallabhaneni R, Yu J, Rocheford T, Wurtzel ET 2008 The maize phytoene synthase gene family: overlapping roles for carotenogenesis in endosperm, photomorphogenesis, and thermal stress-tolerance. Plant Physiol. 147: 1334-1346.

Li FX, Jin ZP, Zhao DX, Cheng LQ, Fu CX, Ma F 2006 Overexpression of the Saussurea medusa chalcone isomerase gene in S. involucrata hairy root cultures enhances their biosynthesis of apigenin. Phytochemistry 67: 553-560.

Li H, Flachowsky H, Fischer TC, Hanke MV, Forkmann G, Treutter D, Schwab W, Hoffmann T, Szankowski I 2007 Maize Lc transcription factor enhances biosynthesis of anthocyanins, distinct proanthocyanidins and phenylpropanoids in apple (Malus domestica Borkh.). Planta 226: 1243-1254.

Li H, Sun J, Fan X, Sui X, Zhang L, Wang Y, He Z 2008 Considerations and recent advances in QSAR models for cytochrome P450-mediated drug metabolism prediction. J. Comput. Aided Mol. Des. Jun 24 [Epub ahead of print].

Li J, Kuang Y, Mason CC 2006 Modeling the glucose-insulin regulatory system and ultradian insulin secretory oscillations with two explicit time delays. J. Theor. Biol. 242: 722-735.

Li J, Wu XD, Hao ST, Wang XJ, Ling HQ 2008 Proteomic response to iron deficiency in tomato root. Proteomics 8: 2299-2311.

Li K, Xu C, Li Z, Zhang K, Yang A, Zhang J 2008 Comparative proteome analyses of phosphorus responses in maize (Zea mays L.) roots of wild-type and low-P tolerant mutant reveal root characteristics associated with P-efficiency. Plant J. May 19 [Epub ahead of print].

Li L, Ilarslan H, James MG, Myers AM, Wurtele ES 2007 Genome wide co-expression among the starch debranching enzyme genes AtISA1, AtISA2, and AtISA3 in Arabidopsis thaliana. J. Exp. Bot. 58: 3323-3342.

Li M, Ho PY, Yao S, Shimizu K 2006 Effect of lpdA gene knockout on the metabolism in Escherichia coli based on enzyme activities, intracellular metabolite concentrations and metabolic flux analysis by (13)C-labeling experiments. J. Biotechnol. 122: 254-266.

Li TH, Li SH 2005 Leaf responses of micropropagated apple plants to water stress: nonstructural carbohydrate composition and regulatory role of metabolic enzymes. Tree Physiol. 25: 495-504.

Li WD, Duan W, Fan PG, Yan ST, Li SH 2007 Photosynthesis in response to sink-source activity and in relation to end products and activities of metabolic enzymes in peach trees. Tree Physiol. 27: 1307-1318.

Li XM, Li NQ, Yang Y, Jiang XL, Qiu YJ, Zhang XY 2004 Metabolic flux analysis of L-valine fermentation in Corynebacterium glutamicum. Sheng Wu Gong Cheng Xue Bao 20: 403-407.

Li Y, Beisson F, Ohlrogge J, Pollard M 2007 Monoacylglycerols are components of root waxes and can be produced in the aerial cuticle by ectopic expression of a suberin-associated acyltransferase. Plant Physiol. 144: 1267-1277.

Li Z, Chan C 2004 Inferring pathways and networks with a Bayesian framework. FASEB J. 18: 746-748.

Li Z, Chan C 2004 Integrating gene expression and metabolic profiles. J. Biol. Chem. 279: 27124-27137.

Liang CR, Leow CK, Neo JC, Tan GS, Lo SL, Lim JW, Seow TK, Lai PB, Chung MC 2005 Proteome analysis of human hepatocellular carcinoma tissues by two-dimensional difference gel electrophoresis and mass spectrometry. Proteomics 5: 2258-2271.

Liang Y, Sun WQ 2002 Rate of dehydration and cumulative desiccation stress interacted to modulate desiccation tolerance of recalcitrant cocoa and ginkgo embryonic tissues. Plant Physiol. 128: 1323-1331.

Liang Y, Zhao S 2008 Progress in understanding of ginsenoside biosynthesis. Plant Biol. (Stuttg.) 10: 415-421.

Liao JC 1999 Inverse flux analysis. J. Biotechnol. 71: 259-262.

Liao JC, Delgado J 1998 Flux calculation using metabolic control constraints. Biotechnol. Prog. 14: 554-560.

Liao JC, Delgado J 1992 Dynamic metabolic control theory. A methodology for investigating metabolic regulation using transient metabolic data. Ann. N.Y. Acad. Sci. 665: 27-38.

Liao JC, Hou SY, Chao YP 1996 Pathway analysis, engineering, and physiological considerations for redirecting central metabolism. Biotechnol. Bioeng. 52: 129-140.

Liao JC, Lightfoot EN Jr 1987 Extending the quasi-steady state concept to analysis of metabolic networks. J. Theor. Biol. 126: 253-273.

Liao JC, Oh MK 1999 Toward predicting metabolic fluxes in metabolically engineered strains. Metab. Eng. 1: 214-223.

Liapi C, Feskou I, Zarros A, Carageorgiou H, Galanopoulou P, Tsakiris S 2008 Equilibrated diet restores the effects of early age choline-deficient feeding on rat brain antioxidant status and enzyme activities: the role of homocysteine, L-phenylalanine and L-alanine. Metab. Brain Dis. 23: 289-301.

Libourel IG, Gehan JP, Shachar-Hill Y 2007 Design of substrate label for steady state flux measurements in plant systems using the metabolic network of Brassica napus embryos Phytochemistry 68: 2211-2221.

Libourel IG, Shachar-Hill Y 2008 Metabolic flux analysis in plants: from intelligent design to rational engineering. Annu. Rev. Plant Biol. 59: 625-650.

Liebermeister W 2005 Response to temporal parameter fluctuations in biochemical networks. J. Theor. Biol. 234: 423-438.

Liebermeister W, Baur U, Klipp E 2005 Biochemical network models simplified by balanced truncation. FEBS J. 272: 4034-4043.

Liebermeister W, Klipp E 2005 Biochemical networks with uncertain parameters. Syst. Biol. (Stevenage) 152: 97-107.

Liebermeister W, Klipp E 2006 Bringing metabolic networks to life: convenience rate law and thermodynamic constraints. Theor. Biol. Med. Model. 3: 41.

Liebermeister W, Klipp E 2006 Bringing metabolic networks to life: integration of kinetic, metabolic, and proteomic data. Theor. Biol. Med. Model. 3: 42.

Liebermeister W, Klipp E, Schuster S, Heinrich R 2004 A theory of optimal differential gene expression. Biosystems 76: 261-278.

Liepman AH, Nairn CJ, Willats WG, Sørensen I, Roberts AW, Keegstra K 2007 Functional genomic analysis supports conservation of function among cellulose synthase-like a gene family members and suggests diverse roles of mannans in plants. Plant Physiol. 143: 1881-1893.

Liguzinski P, Korzeniewski B 2006 Metabolic control over the oxygen consumption flux in intact skeletal muscle: in silico studies. Am. J. Physiol. Cell. Physiol. 291: C1213-C1224.

Lillo C, Meyer C, Lea US, Provan F, Oltedal S 2004 Mechanism and importance of post-translational regulation of nitrate reductase. J. Exp. Bot. 55: 1275-1282.

Lima L, Seabra A, Melo P, Cullimore J, Carvalho H 2006 Post-translational regulation of cytosolic glutamine synthetase of Medicago truncatula. J. Exp. Bot. 57: 2751-2761.

Lin H, Bennett GN, San KY 2005 Metabolic engineering of aerobic succinate production systems in Escherichia coli to improve process productivity and achieve the maximum theoretical succinate yield. Metab. Eng. 7: 116-127.

Lin H, Bennett GN, San KY 2005 Chemostat culture characterization of Escherichia coli mutant strains metabolically engineered for aerobic succinate production: a study of the modified metabolic network based on metabolite profile, enzyme activity, and gene expression profile. Metab. Eng. 7: 337-352.

Lin J, Qian J, Greenbaum D, Bertone P, Das R, Echols N, Senes A, Stenger B, Gerstein M 2002 GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing. Nucleic Acids Res. 30: 4574-4582.

Lin SJ, Kaeberlein M, Andalis AA, Sturtz LA, Defossez PA, Culotta VC, Fink GR, Guarente L 2002 Calorie restriction extends Saccharomyces cerevisiae lifespan by increasing respiration. Nature 418: 344-348.

Lin Y, Ulanov AV, Lozovaya V, Widholm J, Zhang G, Guo J, Goodman HM 2006 Genetic and transgenic perturbations of carbon reserve production in Arabidopsis seeds reveal metabolic interactions of biochemical pathways. Planta 225: 153-164.

Lindahl M, Florencio FJ 2003 Thioredoxin-linked processes in cyanobacteria are as numerous as in chloroplasts, but targets are different. Proc. Natl. Acad. Sci. U.S.A. 100: 16107-16112.

Lindberg S, Landberg T, Greger M 2004 A new method to detect cadmium uptake in protoplasts. Planta 219: 526-532.

Lindermayr C, Saalbach G, Durner J 2005 Proteomic identification of S-nitrosylated proteins in Arabidopsis. Plant Physiol. 137: 921-930.

Lion S, Gabriel F, Bost B, Fievet J, Dillmann C, de Vienne D 2004 An extension to the metabolic control theory taking into account correlations between enzyme concentrations. Eur. J. Biochem. 271: 4375-4391.

Liscombe DK, Facchini PJ 2008 Evolutionary and cellular webs in benzylisoquinoline alkaloid biosynthesis. Curr. Opin. Biotechnol. 19: 173-180.

Lisec J, Meyer RC, Steinfath M, Redestig H, Becher M, Witucka-Wall H, Fiehn O, Torjek O, Selbig J, Altmann T, Willmitzer L 2008 Identification of metabolic and biomass QTL in Arabidopsis thaliana in a parallel analysis of RIL and IL populations. Plant J. 53: 960-972.

Liska AJ, Shevchenko A, Pick U, Katz A 2004 Enhanced photosynthesis and redox energy production contribute to salinity tolerance in Dunaliella as revealed by homology-based proteomics. Plant Physiol. 136: 2806-2817.

Lisso J, Altmann T, Mussig C 2006 Metabolic changes in fruits of the tomato d(x) mutant. Phytochemistry 67: 2232-2238.

Little R, Colombo V, Leech A, Dixon R 2002 Direct interaction of the NifL regulatory protein with the GlnK signal transducer enables the Azotobacter vinelandii NifL-NifA regulatory system to respond to conditions replete for nitrogen. J. Biol. Chem. 277: 15472-15481.

Little R, Reyes-Ramirez F, Zhang Y, van Heeswijk WC, Dixon R 2000 Signal transduction to the Azotobacter vinelandii NIFL-NIFA regulatory system is influenced directly by interaction with 2-oxoglutarate and the PII regulatory protein. EMBO J. 19: 6041-6050.

Liu CZ, Cheng XY 2008 Enhancement of phenylethanoid glycosides biosynthesis in cell cultures of Cistanche deserticola by osmotic stress. Plant Cell Rep. 27: 357-362.

Liu J, Crawford JW, Viola R, Goodman B 1997 Prospects for advancing the understanding of complex biochemical systems. Plant Mol. Biol. 33: 573-581.

Liu L, Li Y, Zhu Y, Du G, Chen J 2007 Redistribution of carbon flux in Torulopsis glabrata by altering vitamin and calcium level. Metab. Eng. 9: 21-29.

Liu L, Zhou Y, Zhou G, Ye R, Zhao L, Li X, Lin Y 2008 Identification of early senescence-associated genes in rice flag leaves. Plant Mol. Biol. 67: 37-55.

Liu PK, Wang FS 2008 Inference of biochemical network models in S-system using multiobjective optimization approach. Bioinformatics 24: 1085-1092.

Liu R, Hu Y, Li J, Lin Z 2007 Production of soybean isoflavone genistein in non-legume plants via genetically modified secondary metabolism pathway. Metab. Eng. 9: 1-7.

Liu W, Wang J, Mitsui K, Shen H, Tsurugi K 2002 Interaction of the GTS1 gene product with glyceraldehyde- 3-phosphate dehydrogenase 1 required for the maintenance of the metabolic oscillations of the yeast Saccharomyces cerevisiae. Eur. J. Biochem. 269: 3560-3569.

Liu Y, Ren D, Pike S, Pallardy S, Gassmann W, Zhang S 2007 Chloroplast-generated reactive oxygen species are involved in hypersensitive response-like cell death mediated by a mitogen-activated protein kinase cascade. Plant J. 51: 941-954.

Llamas I, Moral AD, Martinez-Checa F, Arco Y, Arias S, Quesada E 2006 Halomonas maura is a physiologically versatile bacterium of both ecological and biotechnological interest. Antonie. Van. Leeuwenhoek. 89: 395-403.

Llaneras F, Pico J 2008 Stoichiometric modelling of cell metabolism. J. Biosci. Bioeng. 105: 1-11.

Llaneras F, Pico J 2007 An interval approach for dealing with flux distributions and elementary modes activity patterns. J. Theor. Biol. 246: 290-308.

Lobachevska O, Kyjak N, Khorkavtsiv O, Dovgalyuk A, Kit N, Klyuchivska O, Stoika R, Ripetsky R, Cove D 2005 Influence of metabolic stress on the inheritance of cell determination in the moss, Pottia intermedia. Cell Biol. Int. 29: 181-186.

Loew LM, Schaff JC 2001 The Virtual Cell: a software environment for computational cell biology. Trends Biotechnol. 19: 401-406.

Logemann E, Tavernaro A, Schulz W, Somssich IE, Hahlbrock K 2000 UV light selectively coinduces supply pathways from primary metabolism and flavonoid secondary product formation in parsley. Proc. Natl. Acad. Sci. U.S.A. 97: 1903-1907.

Lohse S, Schliemann W, Ammer C, Kopka J, Strack D, Fester T 2005 Organization and metabolism of plastids and mitochondria in arbuscular mycorrhizal roots of Medicago truncatula. Plant Physiol. 139: 329-340.

Loizeau K, Gambonnet B, Zhang GF, Curien G, Jabrin S, Van Der Straeten D, Lambert WE, Rebeille F, Ravanel S 2007 Regulation of one-carbon metabolism in Arabidopsis: the N-terminal regulatory domain of cystathionine gamma-synthase is cleaved in response to folate starvation. Plant Physiol. 145: 491-503.

Lopez AB, Van Eck J, Conlin BJ, Paolillo DJ, O'Neill J, Li L 2008 Effect of the cauliflower Or transgene on carotenoid accumulation and chromoplast formation in transgenic potato tubers. J. Exp. Bot. 59: 213-223.

Lopez de Felipe F, Kleerebezem M, de Vos WM, Hugenholtz J 1998 Cofactor engineering: a novel approach to metabolic engineering in Lactococcus lactis by controlled expression of NADH oxidase. J. Bacteriol. 180: 3804-3808.

Loreto F, Barta C, Brilli F, Nogues I 2006 On the induction of volatile organic compound emissions by plants as consequence of wounding or fluctuations of light and temperature. Plant Cell Environ. 29: 1820-1828.

Loreto F, Centritto M, Barta C, Calfapietra C, Fares S, Monson RK 2007 The relationship between isoprene emission rate and dark respiration rate in white poplar (Populus alba L.) leaves. Plant Cell Environ. 30: 662-669.

Loudet O, Chaillou S, Merigout P, Talbotec J, Daniel-Vedele F 2003 Quantitative trait loci analysis of nitrogen use efficiency in Arabidopsis. Plant Physiol. 131: 345-358.

Loudet O, Saliba-Colombani V, Camilleri C, Calenge F, Gaudon V, Koprivova A, North KA, Kopriva S, Daniel-Vedele F 2007 Natural variation for sulfate content in Arabidopsis thaliana is highly controlled by APR2. Nat. Genet. 39: 896-900.

Lozovaya V, Ulanov A, Lygin A, Duncan D, Widholm J 2006 Biochemical features of maize tissues with different capacities to regenerate plants. Planta 224: 1385-1399.

Lu BB, Yuan YZ, Zhang CF, Ou JQ, Zhou W, Lin QH 2005 Modulation of key enzymes involved in ammonium assimilation and carbon metabolism by low temperature in rice (Oryza sativa L.) roots. Plant Sci. 169: 295-302.

Lu C, Mansoorabadi K, Jeffries T 2007 Comparison of multiple gene assembly methods for metabolic engineering. Appl. Biochem. Biotechnol. 137-140: 703-10.

Lu LL, Tian SK, Yang XE, Wang XC, Brown P, Li TQ, He ZL 2008 Enhanced root-to-shoot translocation of cadmium in the hyperaccumulating ecotype of Sedum alfredii. J. Exp. Bot. 59: 3203-3213.

Lu M, Zhou L, Stanley WC, Cabrera ME, Saidel GM, Yu X 2008 Role of the malate-aspartate shuttle on the metabolic response to myocardial ischemia. J. Theor. Biol. Jul 4 [Epub ahead of print].

Lu P, Rangan A, Chan SY, Appling DR, Hoffman DW, Marcotte EM 2007 Global metabolic changes following loss of a feedback loop reveal dynamic steady states of the yeast metabolome. Metab. Eng. 9: 8-20.

Lu S, Li L 2008 Carotenoid metabolism: biosynthesis, regulation, and beyond. J. Integr. Plant Biol. 50: 778-785.

Lucas KA, Filley JR, Erb JM, Graybill ER, Hawes JW 2007 Peroxisomal metabolism of propionic acid and isobutyric acid in plants. J. Biol. Chem. 282: 24980-24989.

Lucker J, Schwab W, Franssen MC, Van Der Plas LH, Bouwmeester HJ, Verhoeven HA 2004 Metabolic engineering of monoterpene biosynthesis: two-step production of (+)-trans-isopiperitenol by tobacco. Plant J. 39: 135-145.

Lugli J, Campbell A, Gaziola SA, Smith RJ, Lea PJ, Azevedo RA 2002 Enzymes of lysine metabolism from Coix lacryma-jobi seeds. Plant Physiol. Biochem. 40: 25-32.

Lukashin AV, Lukashev ME, Fuchs R 2003 Topology of gene expression networks as revealed by data mining and modeling. Bioinformatics 19: 1909-1916.

Lundberg P, Lundquist PO 2004 Primary metabolism in N2-fixing Alnus incana-Frankia symbiotic root nodules studied with (15)N and (31)P nuclear magnetic resonance spectroscopy. Planta 219: 661-672.

Lundstrom K 2006 Latest development in drug discovery on G protein-coupled receptors. Curr. Protein Pept. Sci. 7: 465-470.

Lunn JE 2007 Compartmentation in plant metabolism. J. Exp. Bot. 58: 35-47.

Luo RY, Liao S, Tao GY, Li YY, Zeng S, Li YX, Luo Q 2006 Dynamic analysis of optimality in myocardial energy metabolism under normal and ischemic conditions. Mol. Syst. Biol. 2: 2006.0031.

Luo YE, Fan DD, Shang LA, Shi HJ, Ma XX, Mi Y, Zhao GF 2008 Analysis of metabolic flux in Escherichia coli expressing human-like collagen in fed-batch culture. Biotechnol. Lett. 30: 637-643.

Luque I, Vazquez-Bermudez MF, Paz-Yepes J, Flores E, Herrero A 2004 In vivo activity of the nitrogen control transcription factor NtcA is subjected to metabolic regulation in Synechococcus sp. strain PCC 7942. FEMS Microbiol. Lett. 236: 47-52.

Luttik MA, Vuralhan Z, Suir E, Braus GH, Pronk JT, Daran JM 2008 Alleviation of feedback inhibition in Saccharomyces cerevisiae aromatic amino acid biosynthesis: quantification of metabolic impact. Metab. Eng. 10: 141-153.

Lynch MD, Gill RT, Stephanopoulos G 2004 Mapping phenotypic landscapes using DNA micro-arrays. Metab. Eng. 6: 177-185.

Lynd LR, Wyman CE, Gerngross TU 1999 Biocommodity engineering. Biotechnol. Prog. 15: 777-793.

Lytovchenko A, Sonnewald U, Fernie AR 2007 The complex network of non-cellulosic carbohydrate metabolism. Curr. Opin. Plant Biol. 10: 227-235.

Ma H, Xu SP, Luo D, Xu ZH, Xue HW 2004 OsPIPK 1, a rice phosphatidylinositol monophosphate kinase, regulates rice heading by modifying the expression of floral induction genes. Plant Mol. Biol. 54: 295-310.

Ma JF, Tamai K, Ichii M, Wu GF 2002 A rice mutant defective in Si uptake. Plant Physiol. 130: 2111-2117.

Ma QH, Tian B 2005 Biochemical characterization of a cinnamoyl-CoA reductase from wheat. Biol. Chem. 386: 553-560.

Ma S, Gong Q, Bohnert HJ 2006 Dissecting salt stress pathways. J. Exp. Bot. 57: 1097-1107.

Ma X, Gang DR 2006 Metabolic profiling of in vitro micropropagated and conventionally greenhouse grown ginger (Zingiber officinale). Phytochemistry 67: 2239-2255.

Maaheimo H, Fiaux J, Cakar ZP, Bailey JE, Sauer U, Szyperski T 2001 Central carbon metabolism of Saccharomyces cerevisiae explored by biosynthetic fractional C-13 labeling of common amino acids. Eur. J. Biochem. 268: 2464-2479.

Maayan I, Shaya F, Ratner K, Mani Y, Lavee S, Avidan B, Shahak Y, Ostersetzer-Biran O 2008 Photosynthetic activity during olive (Olea europaea) leaf development correlates with plastid biogenesis and Rubisco levels. Physiol. Plant. Jul 8 [Epub ahead of print].

Macfarlane AJ, Liu X, Perry CA, Flodby P, Allen RH, Stabler SP, Stover PJ 2008 Cytoplasmic serine hydroxymethyltransferase regulates themetabolic partitioning of methylenetetrahydrofolate but is not essential in mice. J. Biol. Chem. Jul 21 [Epub ahead of print].

Macfarlane C, White DA, Adams MA 2004 The apparent feed-forward response to vapour pressure deficit of stomata in droughted, field-grown Eucalyptus globulus Labill. Plant Cell Environ. 27: 1268-1280.

Maczek J, Junne S, Nowak P, Goetz P 2006 Metabolic flux analysis of the sterol pathway in the yeast Saccharomyces cerevisiae. Bioprocess. Biosyst. Eng. 29: 241-252.

Madison LL, Huisman GW 1999 Metabolic engineering of Poly(3-Hydroxyalkanoates): from DNA to plastic. Microbiol. Mol. Biol. Rev. 63: 21-53.

Maechler P, Carobbio S, Rubi B 2006 In beta-cells, mitochondria integrate and generate metabolic signals controlling insulin secretion. Int. J. Biochem. Cell. Biol. 38: 696-709.

Maggio A, De Pascale S, Ruggiero C, Barbieri G 2005 Physiological response of field-grown cabbage to salinity and drought stress. Eur. J. Agron. 23: 57-67.

Mahadevan R, Bond DR, Butler JE, Esteve-Nunez A, Coppi MV, Palsson BO, Schilling CH, Lovley DR 2006 Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling. Appl. Environ. Microbiol. 72: 1558-1568.

Mahadevan R, Edwards JS, Doyle FJ 3rd 2002 Dynamic flux balance analysis of diauxic growth in Escherichia coli. Biophys. J. 83: 1331-1340.

Mahadevan R, Schilling CH 2003 The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab. Eng. 5: 264-276.

Mahmoud SS, Williams M, Croteau R 2004 Cosuppression of limonene-3-hydroxylase in peppermint promotes accumulation of limonene in the essential oil. Phytochemistry 65: 547-554.

Mahroug S, Courdavault V, Thiersault M, St-Pierre B, Burlat V 2006 Epidermis is a pivotal site of at least four secondary metabolic pathways in Catharanthus roseus aerial organs. Planta 223: 1191-1200.

Maier K, Hofmann U, Reuss M, Mauch K 2008 Identification of metabolic fluxes in hepatic cells from transient 13C-labeling experiments: Part II. Flux estimation. Biotechnol. Bioeng. 100: 355-370.

Maimann S, Hoefgen R, Hesse H 2001 Enhanced cystathionine beta-lyase activity in transgenic potato plants does not force metabolite flow towards methionine. Planta 214: 163-170.

Maiwald T, Timmer J 2008 Dynamical modeling and multi-experiment fitting with PottersWheel. Bioinformatics Jul 9 [Epub ahead of print].

Majeran W, Zybailov B, Ytterberg AJ, Dunsmore J, Sun Q, van Wijk KJ 2008 Consequences of C4 differentiation for chloroplast membrane proteomes in maize mesophyll and bundle sheath cells. Mol. Cell. Proteomics May 2 [Epub ahead of print].

Majewski RA, Domach MM 1985 Consideration of the gain, enzymatic capacity utilization, and response time properties of metabolic networks as a function of operating point and structure. Biosystems 18: 15-22.

Majoul T, Bancel E, Triboi E, Ben Hamida J, Branlard G 2004 Proteomic analysis of the effect of heat stress on hexaploid wheat grain: characterization of heat-responsive proteins from non-prolamins fraction. Proteomics 4: 505-513.

Malakar D, Dey A, Basu A, Ghosh AK 2008 Antiapoptotic role of S-adenosyl-L-methionine against hydrochloric acid induced cell death in Saccharomyces cerevisiae. Biochim. Biophys. Acta 1780: 937-947.

Malanovic N, Streith I, Wolinski H, Rechberger G, Kohlwein SD, Tehlivets O 2008 S-Adenosyl-L-homocysteine hydrolase, key enzyme of methylation metabolism, regulates phosphatidylcholine synthesis and triacylglycerol homeostasis in yeast: implications for homocysteine as a risk factor of atherosclerosis. J. Biol. Chem. Jun 30 [Epub ahead of print].

Maliga P 2002 Engineering the plastid genome of higher plants. Curr. Opin. Plant Biol. 5: 164-172.

Maliga P, Graham I 2004 Molecular farming and metabolic engineering promise a new generation of high-tech crops. Curr. Opin. Plant Biol. 7: 149-151.

Malthankar-Phatak GH, de Lanerolle N, Eid T, Spencer DD, Behar KL, Spencer SS, Kim JH, Lai JC 2006 Differential glutamate dehydrogenase (GDH) activity profile in patients with temporal lobe epilepsy. Epilepsia 47: 1292-1299.

Mamun AN 2007 Reversible male sterility in transgenic tobacco carrying a dominant-negative mutated glutamine synthetase gene under the control of microspore-specific promoter. Indian J. Exp. Biol. 45: 1022-1030.

Mancuso A, Sharfstein ST, Tucker SN, Clark DS, Blanch HW 1994 Examination of primary metabolic pathways in a murine hybridoma with C-13 nuclear magnetic resonance spectroscopy. Biotechnol. Bioeng. 44: 563-585.

Mandaokar A, Thines B, Shin B, Markus Lange B, Choi G, Koo YJ, Yoo YJ, Choi YD, Choi G, Browse J 2006 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling. Plant J. 46: 984-1008.

Manetti C, Bianchetti C, Casciani L, Castro C, Di Cocco ME, Miccheli A, Motto M, Conti F 2006 A metabonomic study of transgenic maize (Zea mays) seeds revealed variations in osmolytes and branched amino acids. J. Exp. Bot. 57: 2613-2625.

Mansoor S, Amin I, Hussain M, Zafar Y, Briddon RW 2006 Engineering novel traits in plants through RNA interference. Trends Plant Sci. 11: 559-565.

Manzano D, Fernandez-Busquets X, Schaller H, Gonzalez V, Boronat A, Arro M, Ferrer A 2004 The metabolic imbalance underlying lesion formation in Arabidopsis thaliana overexpressing farnesyl diphosphate synthase (isoform 1S) leads to oxidative stress and is triggered by the developmental decline of endogenous HMGR activity. Planta 219: 982-992.

Mapelli V, Olsson L, Nielsen J 2008 Metabolic footprinting in microbiology: methods and applications in functional genomics and biotechnology. Trends Biotechnol. 26: 490-497.

Maranas CD, Burgard AP 2001 Web site review: review of EcoCyc and MetaCyc databases. Metab. Eng. 3: 98-99.

Maris AJ, Konings WN, Dijken JP, Pronk JT 2004 Microbial export of lactic and 3-hydroxypropanoic acid: implications for industrial fermentation processes. Metab. Eng. 6: 245-255.

Maroco JP, Ku MSB, Edwards GE 2000 Utilization of O2 in the metabolic optimization of C4 photosynthesis. Plant Cell Environ. 23: 115-121.

Marsh KJ, Wallis IR, Andrew RL, Foley WJ 2006 The detoxification limitation hypothesis: where did it come from and where is it going? J. Chem. Ecol. 32: 1247-1266.

Marsolais F, Boyd J, Paredes Y, Schinas AM, Garcia M, Elzein S, Varin L 2007 Molecular and biochemical characterization of two brassinosteroid sulfotransferases from Arabidopsis, AtST4a (At2g14920) and AtST1 (At2g03760). Planta 225: 1233-1244.

Martens S, Mithofer A 2005 Flavones and flavone synthases. Phytochemistry 66: 2399-2407.

Martin DE, Reinhold-Hurek B 2002 Distinct roles of PII-like signal transmitter proteins and amtB in regulation of nif gene expression, nitrogenase activity, and posttranslational modification of NifH in Azoarcus sp strain BH72. J. Bacteriol. 184: 2251-2259.

Martin F, Ramstedt M, Soderhall K 1987 Carbon and nitrogen metabolism in ectomycorrhizal fungi and ectomycorrhizas. Biochimie 69: 569-581.

Martin FP, Wang Y, Sprenger N, Yap IK, Rezzi S, Ramadan Z, Pere-Trepat E, Rochat F, Cherbut C, van Bladeren P, Fay LB, Kochhar S, Lindon JC, Holmes E, Nicholson JK 2008 Top-down systems biology integration of conditional prebiotic modulated transgenomic interactions in a humanized microbiome mouse model. Mol. Syst. Biol. 4: 205.

Martinoia E, Maeshima M, Neuhaus HE 2007 Vacuolar transporters and their essential role in plant metabolism. J. Exp. Bot. 58: 83-102.

Martinov MV, Vitvitsky VM, Mosharov EV, Banerjee R, Ataullakhanov FI 2000 A substrate switch: a new mode of regulation in the methionine metabolic pathway. J. Theor. Biol. 204: 521-532.

Martz F, Kiviniemi S, Palva TE, Sutinen ML 2006 Contribution of omega-3 fatty acid desaturase and 3-ketoacyl-ACP synthase II (KASII) genes in the modulation of glycerolipid fatty acid composition during cold acclimation in birch leaves. J. Exp. Bot. 57: 897-909.

Marx CJ, Van Dien SJ, Lidstrom ME 2005 Flux analysis uncovers key role of functional redundancy in formaldehyde metabolism. PLoS Biol. 3: e16.

Masclaux C, Valadier MH, Brugiere N, Morot-Gaudry JF, Hirel B 2000 Characterization of the sink/source transition in tobacco (Nicotiana tabacum L.) shoots in relation to nitrogen management and leaf senescence. Planta 211: 510-518.

Masclaux-Daubresse C, Purdy S, Lemaitre T, Pourtau N, Taconnat L, Renou JP, Wingler A 2007 Genetic variation suggests interaction between cold acclimation and metabolic regulation of leaf senescence. Plant Physiol. 143: 434-446.

Maskow T, von Stockar U 2005 How reliable are thermodynamic feasibility statements of biochemical pathways? Biotechnol. Bioeng. 92: 223-230.

Mason GF, Petersen KF, de Graaf RA, Shulman GI, Rothman DL 2007 Measurements of the anaplerotic rate in the human cerebral cortex using (13)C magnetic resonance spectroscopy and [1-(13)C] and [2-(13)C] glucose. J. Neurochem. 100: 73-86.

Mason GF, Rothman DL 2004 Basic principles of metabolic modeling of NMR (13)C isotopic turnover to determine rates of brain metabolism in vivo. Metab. Eng. 6: 75-84.

Mason JB, Choi SW 2005 Effects of alcohol on folate metabolism: implications for carcinogenesis. Alcohol 35: 235-241.

Massiah A 2000 Physiology and metabolism - web alert. Curr. Opin. Plant Biol. 3: 177-178.

Masuda S, Mizusawa K, Narisawa T, Tozawa Y, Ohta H, Takamiya K 2008 The bacterial stringent response, conserved in chloroplasts, controls plant fertilization. Plant Cell Physiol. 49: 135-141.

Matsuda F, Morino K, Ano R, Kuzawa M, Wakasa K, Miyagawa H 2005 Metabolic flux analysis of the phenylpropanoid pathway in elicitor-treated potato tuber tissue. Plant Cell Physiol. 46: 454-466.

Matsuda F, Wakasa K, Miyagawa H 2007 Metabolic flux analysis in plants using dynamic labeling technique: application to tryptophan biosynthesis in cultured rice cells. Phytochemistry 68: 2290-2301.

Matsuda F, Yamada T, Miyazawa H, Miyagawa H, Wakasa K 2005 Characterization of tryptophan-overproducing potato transgenic for a mutant rice anthranilate synthase alpha-subunit gene (OASA1D). Planta 222: 535-545.

Matsumoto F, Obayashi T, Sasaki-Sekimoto Y, Ohta H, Takamiya K, Masuda T 2004 Gene expression profiling of the tetrapyrrole metabolic pathway in Arabidopsis with a mini-array system. Plant Physiol. 135: 2379-2391.

Mattana M, Biazzi E, Consonni R, Locatelli F, Vannini C, Provera S, Coraggio I 2005 Overexpression of Osmyb4 enhances compatible solute accumulation and increases stress tolerance of Arabidopsis thaliana. Physiol. Plant. 125: 212-223.

Matthews PD, Wurtzel ET 2000 Metabolic engineering of carotenoid accumulation in Escherichia coli by modulation of the isoprenoid precursor pool with expression of deoxyxylulose phosphate synthase. Appl. Microbiol. Biotechnol. 53: 396-400.

Mattoo AK, Sobolev AP, Neelam A, Goyal RK, Handa AK, Segre AL 2006 NMR spectroscopy based metabolite profiling of transgenic tomato fruit engineered to accumulate spermidine and spermine reveals enhanced anabolic and nitrogen-carbon interactions. Plant Physiol. 142: 1759-1770.

Matz C, Webb JS, Schupp PJ, Phang SY, Penesyan A, Egan S, Steinberg P, Kjelleberg S 2008 Marine biofilm bacteria evade eukaryotic predation by targeted chemical defense. PLoS ONE 3: e2744.

Mavrovouniotis ML 1993 Identification of localized and distributed bottlenecks in metabolic pathways. Ismb 1: 275-283.

May P, Wienkoop S, Kempa S, Usadel B, Christian N, Rupprecht J, Weiss J, Recuenco-Munoz L, Ebenhoh O, Weckwerth W, Walther D 2008 Metabolomics- and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii. Genetics 179: 157-166.

Mayrhofer S, Teuber M, Zimmer I, Louis S, Fischbach RJ, Schnitzler JP 2005 Diurnal and seasonal variation of isoprene biosynthesis-related genes in grey poplar leaves. Plant Physiol. 139: 474-484.

Mazat JP, Letellier T, Reder C 1990 Metabolic control theory: the geometry of the triangle. Biomed. Biochim. Acta 49: 801-810.

Mazumdar J, Banerjee M, Teng LY 1991 A mathematical study of simple exponential modelling in biochemical processes. Australas. Phys. Eng. Sci. Med. 14: 226-233.

Mazzella MA, Zanor MI, Fernie AR, Casal JJ 2008 Metabolic responses to red/far-red ratio and ontogeny show poor correlation with the growth rate of sunflower stems. J. Exp. Bot. 59: 2469-2477.

McCaskill D, Croteau R 1999 Strategies for bioengineering the development and metabolism of glandular tissues in plants. Nat. Biotechnol. 17: 31-36.

McClung CR 2008 Comes a time. Curr. Opin. Plant Biol. Aug 3 [Epub ahead of print].

McConnell MD, Koop R, Vasil'ev S, Bruce D 2002 Regulation of the distribution of chlorophyll and phycobilin-absorbed excitation energy in cyanobacteria. A structure-based model for the light state transition. Plant Physiol. 130: 1201-1212.

McCully KS 2007 Homocysteine, vitamins, and vascular disease prevention. Am. J. Clin. Nutr. 86: 1563S-1568S.

McIntyre M, Muller C, Dynesen J, Nielsen J 2001 Metabolic engineering of the morphology of Aspergillus. Adv. Biochem. Eng. Biotechnol. 73: 103-128.

McKinlay JB, Shachar-Hill Y, Zeikus JG, Vieille C 2007 Determining Actinobacillus succinogenes metabolic pathways and fluxes by NMR and GC-MS analyses of 13C-labeled metabolic product isotopomers. Metab. Eng. 9: 177-192.

McLean S, Duncan AJ 2006 Pharmacological perspectives on the detoxification of plant secondary metabolites: implications for ingestive behavior of herbivores. J. Chem. Ecol. 32: 1213-1228.

McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes S, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman A, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, et al 2007 The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. Nucleic Acids Res. 35: D347-D353.

McNeil SD, Nuccio ML, Hanson AD 1999 Betaines and related osmoprotectants. Targets for metabolic engineering of stress resistance. Plant Physiol. 120: 945-950.

McNeil SD, Nuccio ML, Rhodes D, Shachar-Hill Y, Hanson AD 2000 Radiotracer and computer modeling evidence that phospho-base methylation is the main route of choline synthesis in tobacco. Plant Physiol. 123: 371-380.

McNeil SD, Nuccio ML, Ziemak MJ, Hanson AD 2001 Enhanced synthesis of choline and glycine betaine in transgenic tobacco plants that overexpress phosphoethanolamine N-methyltransferase. Proc. Natl. Acad. Sci. U.S.A. 98: 10001-10005.

McNeil SD, Rhodes D, Russell BL, Nuccio ML, Shachar-Hill Y, Hanson AD 2000 Metabolic modeling identifies key constraints on an engineered glycine betaine synthesis pathway in tobacco. Plant Physiol. 124: 153-162.

McShan DC, Updadhayaya M, Shah I 2004 Symbolic inference of xenobiotic metabolism. Pac. Symp. Biocomput. 2004: 545-556.

Meadows AL, Roy S, Clark DS, Blanch HW 2007 Optimal design of metabolic flux analysis experiments for anchorage-dependent mammalian cells using a cellular automaton model. Biotechnol. Bioeng. 98: 221-229.

Mechin V, Balliau T, Chateau-Joubert S, Davanture M, Langella O, Negroni L, Prioul JL, Thevenot C, Zivy M, Damerval C 2004 A two-dimensional proteome map of maize endosperm. Phytochemistry 65: 1609-1618.

Meehan TD 2006 Mass and temperature dependence of metabolic rate in litter and soil invertebrates. Physiol. Biochem. Zool. 79: 878-884.

MeiBner D, Albert A, Bottcher C, Strack D, Milkowski C 2008 The role of UDP-glucose:hydroxycinnamate glucosyltransferases in phenylpropanoid metabolism and the response to UV-B radiation in Arabidopsis thaliana. Planta 228: 663-674.

Meijer SC, Van Loosdrecht MC, Heijnen JJ 2001 Metabolic modelling of full-scale biological nitrogen and phosphorus removing wwtp's. Water Res. 35: 2711-2723..

Melendezhevia E, Waddell TG, Montero F 1994 Optimization of metabolism: the evolution of metabolic pathways toward simplicity through the game of the pentose-phosphate cycle. J. Theor. Biol. 166: 201-219.

Melnyk S, Pogribna M, Pogribny IP, Yi P, James SJ 2000 Measurement of plasma and intracellular S-adenosylmethionine and S-adenosylhomocysteine utilizing coulometric electrochemical detection: alterations with plasma homocysteine and pyridoxal 5'-phosphate concentrations. Clin. Chem. 46: 265-272.

Memelink J 2005 The use of genetics to dissect plant secondary pathways. Curr. Opin. Plant Biol. 8: 230-235.

Memelink J 2005 Tailoring the plant metabolome without a loose stitch. Trends Plant Sci. 10: 305-307.

Memelink J, Menkw FL, van der Fits L, Kijne JW 2000 Chapter 6. Transcriptional Regulators to Modify Secondary Metabolism. In "Metabolic Engineering of Plant Secondary Metabolism" (Verpoorte R, Alfermann AW, eds), Kluwer Academic Publishers, Dortrecht, The Netherlands, pp. 111-125.

Mendes P 1993 GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems. Comput. Appl. Biosci. 9: 563-571.

Mendes P, Camacho D, de la Fuente A 2005 Modelling and simulation for metabolomics data analysis. Biochem. Soc. Trans. 33: 1427-1429.

Mendes P, Kell D 1998 Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation. Bioinformatics 14: 869-883.

Mendes P, Kell DB 1996 On the analysis of the inverse problem of metabolic pathways using artificial neural networks. Biosystems 38: 15-28.

Mendes P, Kell DB 2001 MEG (Model Extender for Gepasi): a program for the modelling of complex, heterogeneous, cellular systems. Bioinformatics 17: 288-289.

Mendes P, Kell DB 1998 Numerical optimization and simulation for rational metabolic engineering. In (C Larsson, IL Pahlman, L Gustaffson eds) "BioThermoKinetics in the Post Genomic Era", Chalmers Reproservice, Goteborg, pp. 345-349.

Mendes P, Kell DB, Welch GR 1995 Metabolic channelling in organized enzyme systems: experiments and models. Adv. Mol. Cell. Biol. 11: 1-19.

Mendes P, Kell DB, Westerhoff HV 1992 Channelling can decrease pool size. Eur. J. Biochem. 204: 257-266.

Mendes P, Kell DB, Westerhoff HV 1996 Why and when channelling can decrease pool size at constant net flux in a simple dynamic channel. Biochim. Biophys. Acta 1289: 175-186.

Mendoza-Cozatl DG, Moreno-Sanchez R 2006 Control of glutathione and phytochelatin synthesis under cadmium stress. Pathway modeling for plants. J. Theor. Biol. 238: 919-936.

Meng TC, Somani S, Dhar P 2004 Modeling and simulation of biological systems with stochasticity. In Silico Biol. 4: 0024.

Menu T, Saglio P, Granot D, Dai N, Raymond P, Ricard B 2004 High hexokinase activity in tomato fruit perturbs carbon and energy metabolism and reduces fruit and seed size. Plant Cell Environ. 27: 89-98.

Menzel K, Ahrens K, Zeng A, Deckwer W 1998 Kinetic, dynamic, and pathway studies of glycerol metabolism by Klebsiella pneumoniae in anaerobic continuous culture: IV. Enzymes and fluxes of pyruvate metabolism. Biotechnol. Bioeng. 60: 617-626.

Merali Z, Mayer MJ, Parker ML, Michael AJ, Smith AC, Waldron KW 2007 Metabolic diversion of the phenylpropanoid pathway causes cell wall and morphological changes in transgenic tobacco stems. Planta 225: 1165-1178.

Mercade M, Cocaign-Bousquet M, Loubiere P 2006 Glyceraldehyde-3-phosphate dehydrogenase regulation in Lactococcus lactis ssp. cremoris MG1363 or relA mutant at low pH. J. Appl. Microbiol. 100: 1364-1372.

Meric PA, Wise MJ 1999 Quantitative, scalable discrete-event simulation of metabolic pathways. Ismb 7: 187-194.

Merighi M, Majerczak DR, Stover EH, Coplin DL 2003 The HrpX/HrpY two-component system activates hrpS expression, the first step in the regulatory cascade controlling the Hrp regulon in Pantoea stewartii subsp. stewartii. Mol. Plant Microbe Interact. 16: 238-248.

Meskauskas A, Novak Frazer L, Moore D 1999 Mathematical modelling of morphogenesis in fungi: a key role for curvature compensation ('autotropism') in the local curvature distribution model. New Phytol. 143: 387-399.

Mesnard F, Ratcliffe RG 2005 NMR analysis of plant nitrogen metabolism. Photosynth. Res. 83: 163-180.

Messana I, Misiti F, el-Sherbini S, Giardina B, Castagnola M 1999 Quantitative determination of the main glucose metabolic fluxes in human erythrocytes by 13C- and 1H-MR spectroscopy. J. Biochem. Biophys. Methods 39: 63-84.

Messerli G, Partovi Nia V, Trevisan M, Kolbe A, Schauer N, Geigenberger P, Chen J, Davison AC, Fernie AR, Zeeman SC 2007 Rapid classification of phenotypic mutants of Arabidopsis via metabolite fingerprinting. Plant Physiol. 143: 1484-1492.

Metwally A, Safronova VI, Belimov AA, Dietz KJ 2005 Genotypic variation of the response to cadmium toxicity in Pisum sativum L. J. Exp. Bot. 56: 167-178.

Meurice G, Bondon A, Deborde C, Boyaval P 2001 Determination of metabolic fluxes during glucose catabolism in Propionibacterium freudenreichii subsp. shermanii. Meded. Rijksuniv. Gent. Fak. Landbouwkd. Toegep. Biol. Wet. 66: 219-225.

Meyer RC, Steinfath M, Lisec J, Becher M, Witucka-Wall H, Torjek O, Fiehn O, Eckardt A, Willmitzer L, Selbig J, Altmann T 2007 The metabolic signature related to high plant growth rate in Arabidopsis thaliana. Proc. Natl. Acad. Sci. U.S.A. 104: 4759-4764.

Meynial Salles I, Forchhammer N, Croux C, Girbal L, Soucaille P 2007 Evolution of a Saccharomyces cerevisiae metabolic pathway in Escherichia coli. Metab. Eng. 9: 152-159.

Miccheli A, Tomassini A, Puccetti C, Valerio M, Peluso G, Tuccillo F, Calvani M, Manetti C, Conti F 2006 Metabolic profiling by 13C-NMR spectroscopy: [1,2-13C2]glucose reveals a heterogeneous metabolism in human leukemia T cells. Biochimie 88: 437-448.

Michalecka AM, Agius SC, Moller IM, Rasmusson AG 2004 Identification of a mitochondrial external NADPH dehydrogenase by overexpression in transgenic Nicotiana sylvestris. Plant J. 37: 415-425.

Michel KP, Pistorius EK 2004 Adaptation of the photosynthetic electron transport chain in cyanobacteria to iron deficiency: The function of IdiA and IsiA. Physiol. Plant. 120: 36-50.

Michel-Reydellet N, Calhoun K, Swartz J 2004 Amino acid stabilization for cell-free protein synthesis by modification of the Escherichia coli genome. Metab. Eng. 6: 197-203.

Michels AK, Wedel N, Kroth PG 2005 Diatom plastids possess a phosphoribulokinase with an altered regulation and no oxidative pentose phosphate pathway. Plant Physiol. 137: 911-920.

Mijts BN, Schmidt-Dannert C 2003 Engineering of secondary metabolite pathways. Curr. Opin. Biotechnol. 14: 597-602.

Miki R, Kadota K, Bono H, Mizuno Y, Tomaru Y, Carninci P, Itoh M, Shibata K, Kawai J, Konno H, Watanabe S, Sato K, Tokusumi Y, Kikuchi N, Ishii Y, Hamaguchi et al 2001 Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays. Proc. Natl. Acad. Sci. U.S.A. 98: 2199-2204.

Miller GP 2008 Advances in the interpretation and prediction of CYP2E1 metabolism from a biochemical perspective. Expert Opin. Drug Metab. Toxicol. 4: 1053-1064.

Milton SL, Prentice HM 2007 Beyond anoxia: the physiology of metabolic downregulation and recovery in the anoxia-tolerant turtle. Comp. Biochem. Physiol. A. Mol. Integr. Physiol. 147: 277-290.

Min Lee J, Gianchandani EP, Eddy JA, Papin JA 2008 Dynamic analysis of integrated signaling, metabolic, and regulatory networks. PLoS Comput. Biol. 4: e1000086.

Minguet EG, Vera F, Marina A, Carbonell J, Blazquez MA 2008 Evolutionary diversification in polyamine biosynthesis. Mol. Biol. Evol. Jul 24 [Epub ahead of print].

Misawa N, Shimada H 1997 Metabolic engineering for the production of carotenoids in non-carotenogenic bacteria and yeasts. J. Biotechnol. 59: 169-181.

Mishra A, Mandoli A, Jha B 2008 Physiological characterization and stress-induced metabolic responses of Dunaliella salina isolated from salt pan. J. Ind. Microbiol. Biotechnol. Jul 5 [Epub ahead of print].

Misson J, Raghothama KG, Jain A, Jouhet J, Block MA, Bligny R, Ortet P, Creff A, Somerville S, Rolland N, Doumas P, Nacry P, Herrerra-Estrella L, Nussaume L, Thibaud MC 2005 A genome-wide transcriptional analysis using Arabidopsis thaliana Affymetrix gene chips determined plant responses to phosphate deprivation. Proc. Natl. Acad. Sci. U.S.A. 102: 11934-11939.

Mitani N, Ma JF 2005 Uptake system of silicon in different plant species. J. Exp. Bot. 56: 1255-1261.

Mixson AJ, Phang JM 1988 The uptake of pyrroline 5-carboxylate. Group translocation mediating the transfer of reducing-oxidizing potential. J. Biol. Chem. 263: 10720-10724.

Miyama M, Tada Y 2008 Transcriptional and physiological study of the response of Burma mangrove (Bruguiera gymnorhiza) to salt and osmotic stress. Plant Mol. Biol. 68: 119-129.

Miyashita Y, Dolferus R, Ismond KP, Good AG 2007 Alanine aminotransferase catalyses the breakdown of alanine after hypoxia in Arabidopsis thaliana. Plant J. 49: 1108-1121.

Mizuno S, Osakabe Y, Maruyama K, Ito T, Osakabe K, Sato T, Shinozaki K, Yamaguchi-Shinozaki K 2007 Receptor-like protein kinase 2 (RPK 2) is a novel factor controlling anther development in Arabidopsis thaliana. Plant J. 50: 751-766.

Mizusawa K, Masuda S, Ohta H 2008 Expression profiling of four RelA/SpoT-like proteins, homologues of bacterial stringent factors, in Arabidopsis thaliana. Planta 228: 553-562.

Moco S, Bino RJ, Vorst O, Verhoeven HA, de Groot J, van Beek TA, Vervoort J, de Vos CH 2006 A liquid chromatography-mass spectrometry-based metabolome database for tomato. Plant Physiol. 141: 1205-1218.

Mohamed SA, Mohamed TM, Fahmy AS, El-Badry MO, Abdel-Gany SS 2008 Fasciola gigantica: enzymes of the ornithine-proline-glutamate pathway - characterization of delta1-pyrroline-5-carboxylate dehydrogenase. Exp. Parasitol. 118: 47-53.

Moller K, Christensen B, Forster J, Piskur J, Nielsen J, Olsson L 2002 Aerobic glucose metabolism of Saccharomyces kluyveri: growth, metabolite production, and quantification of metabolic fluxes. Biotechnol. Bioeng. 77: 186-193.

Mollney M, Wiechert W, Kownatzki D, de Graaf AA 1999 Bidirectional reaction steps in metabolic networks: IV. Optimal design of isotopomer labeling experiments. Biotechnol. Bioeng. 66: 86-103.

Montie DB, Montie TC 1975 Methionine transport in Yersinia pestis. J. Bacteriol. 124: 296-306.

Monzani PS, Moraes G 2008 Urea cycle enzymes through the development of pacu (Piaractus mesopotamicus): the role of ornithine carbamoyl transferase. Fish Physiol. Biochem. 34: 139-149.

Moore Bd B 2004 Bifunctional and moonlighting enzymes: lighting the way to regulatory control. Trends Plant Sci. 9: 221-228.

Moorhead KT, Chase JG, David T, Arnold J 2006 Metabolic model of autoregulation in the Circle of Willis. J. Biomech. Eng. 128: 462-466.

Morbiducci U, Andrea Tura, Grigioni M 2005 Genetic algorithms for parameter estimation in mathematical modeling of glucose metabolism. Comput. Biol. Med. 35: 862-874.

Moreno MC, Sande P, Marcos HA, de Zavalia N, Keller Sarmiento MI, Rosenstein RE 2005 Effect of glaucoma on the retinal glutamate/glutamine cycle activity. FASEB J. 19: 1161-1162.

Moreno-Sanchez R, Encalada R, Marin-Hernandez A, Saavedra E 2008 Experimental validation of metabolic pathway modeling. An illustration with glycotic segments from Entamoeba histolytica. FEBS J. 275: 3454-3469.

Moreno-Sanchez R, Saavedra E, Rodriguez-Enríquez S, Olín-Sandoval V 2008 Metabolic control analysis: a tool for designing strategies to manipulate metabolic pathways. J. Biomed. Biotechnol. 2008: 597913.

Morey KJ, Ortega JL, Sengupta-Gopalan C 2002 Cytosolic glutamine synthetase in soybean is encoded by a multigene family, and the members are regulated in an organ-specific and developmental manner. Plant Physiol. 128: 182-193.

Morgan JA, Rhodes D 2002 Mathematical modeling of plant metabolic pathways. Metab. Eng. 4: 80-89.

Morgan JA, Shanks JV 2000 Determination of metabolic rate-limitations by precursor feeding in Catharanthus roseus hairy root cultures. J. Biotechnol. 79: 137-145.

Morikawa H, Takahashi M, Sakamoto A, Ueda-Hashimoto M, Matsubara T, Miyawaki K, Kawamura Y, Hirata T, Suzuki H 2005 Novel metabolism of nitrogen in plants. Z. Naturforsch. [C] 60: 265-271.

Morino K, Matsuda F, Miyazawa H, Sukegawa A, Miyagawa H, Wakasa K 2005 Metabolic profiling of tryptophan-overproducing rice calli that express a feedback-insensitive alpha subunit of anthranilate synthase. Plant Cell Physiol. 46: 514-521.

Morley-Smith ER, Pike MJ, Findlay K, Kockenberger W, Hill LM, Smith AM, Rawsthorne S 2008 The transport of sugars to developing embryos is not via the bulk endosperm in Brassica napus seeds. Plant Physiol. 147: 2121-2130.

Morreel K, Goeminne G, Storme V, Sterck L, Ralph J, Coppieters W, Breyne P, Steenackers M, Georges M, Messens E, Boerjan W 2006 Genetical metabolomics of flavonoid biosynthesis in Populus: a case study. Plant J. 47: 224-237.

Morris JG 1985 Nutritional and metabolic responses to arginine deficiency in carnivores. J. Nutr. 115: 524-531.

Morris WL, Ducreux LJ, Hedden P, Millam S, Taylor MA 2006 Overexpression of a bacterial 1-deoxy-D-xylulose 5-phosphate synthase gene in potato tubers perturbs the isoprenoid metabolic network: implications for the control of the tuber life cycle. J. Exp. Bot. 57: 3007-3018.

Moscatelli A, Scali M, Prescianotto-Baschong C, Ferro M, Garin J, Vignani R, Ciampolini F, Cresti M 2005 A methionine synthase homolog is associated with secretory vesicles in tobacco pollen tubes. Planta 221: 776-789.

Moulin M, Deleu C, Larher F, Bouchereau A 2006 The lysine-ketoglutarate reductase-saccharopine dehydrogenase is involved in the osmo-induced synthesis of pipecolic acid in rapeseed leaf tissues. Plant Physiol. Biochem. 44: 474-482.

Mrazek J, Spormann AM, Karlin S 2006 Genomic comparisons among gamma-proteobacteria. Environ. Microbiol. 8: 273-288.

Mudd SH, Cerone R, Schiaffino MC, Fantasia AR, Minniti G, Caruso U, Lorini R, Watkins D, Matiaszuk N, Rosenblatt DS, Schwahn B, Rozen R, LeGros L, Kotb M, Capdevila A, Luka Z, Finkelstein JD, Tangerman A, Stabler SP, Allen RH, Wagner C 2001 Glycine N-methyltransferase deficiency: a novel inborn error causing persistent isolated hypermethioninaemia. J. Inherit. Metab. Dis. 24: 448-464.

Mukhopadhyay A, Redding AM, Rutherford BJ, Keasling JD 2008 Importance of systems biology in engineering microbes for biofuel production. Curr. Opin. Biotechnol. 19: 228-234.

Müller GL, Drincovich MF, Andreo CS, Lara MV 2008 Nicotiana tabacum NADP-malic enzyme: cloning, characterization and analysis of biological role. Plant Cell Physiol. 49: 469-480.

Muller U, van Assema F, Gunsior M, Orf S, Kremer S, Schipper D, Wagemans A, Townsend CA, Sonke T, Bovenberg R, Wubbolts M 2006 Metabolic engineering of the E. coli L-phenylalanine pathway for the production of D-phenylglycine (D-Phg). Metab. Eng. 8: 196-208.

Mulquiney PJ, Kuchel PW 1999 Model of 2,3-bisphosphoglycerate metabolism in the human erythrocyte based on detailed enzyme kinetic equations: equations and parameter refinement. Biochem. J. 342: 581-596.

Mulquiney PJ, Kuchel PW 1999 Model of 2,3-bisphosphoglycerate metabolism in the human erythrocyte based on detailed enzyme kinetic equations: computer simulation and Metabolic Control Analysis. Biochem. J. 342: 597-604.

Munier-Jolain NG, Salon C 2005 Are the carbon costs of seed production related to the quantitative and qualitative performance? An appraisal for legumes and other crops. Plant Cell Environ. 28: 1388-1395.

Munns R 2002 Comparative physiology of salt and water stress. Plant Cell Environ. 25: 239-250.

Munns R 2002 Comparative physiology of salt and water stress. Plant Cell Environ. 25: 239-250.

Munoz-Bertomeu J, Arrillaga I, Ros R, Segura J 2006 Up-regulation of 1-deoxy-D-xylulose-5-phosphate synthase enhances production of essential oils in transgenic spike lavender. Plant Physiol. 142: 890-900.

Mur LA, Kenton P, Lloyd AJ, Ougham H, Prats E 2008 The hypersensitive response; the centenary is upon us but how much do we know? J. Exp. Bot. 59: 501-520.

Muralidharan V, Rinker KD, Hirsh IS, Bouwer EJ, Kelly RM 1997 Hydrogen transfer between methanogens and fermentative heterotrophs in hyperthermophilic cocultures. Biotechnol. Bioeng. 56: 268-278.

Naeimpoor F, Mavituna F 2000 Metabolic flux analysis in Streptomyces coelicolor under various nutrient limitations. Metab. Eng. 2: 140-148.

Nagarajan L, Storms RK 1997 Molecular characterization of GCV3, the Saccharomyces cerevisiae gene coding for the glycine cleavage system hydrogen carrier protein. J. Biol. Chem. 272: 4444-4450.

Nagasaki M, Saito A, Li C, Jeong E, Miyano S 2008 Systematic reconstruction of TRANSPATH data into Cell System Markup Language. BMC Syst. Biol. 2: 53.

Nagegowda DA, Ramalingam S, Hemmerlin A, Bach TJ, Chye ML 2005 Brassica juncea HMG-CoA synthase: localization of mRNA and protein. Planta 221: 844-856.

Naito Y, Ohno H, Seno S, Oguchi Y, Sano A, Nakajima H, Tomita M 2001 A simulation model of diabetes using E-Cell system. Genome Informatics 12: 310-311.

Najdi TS, Yang CR, Shapiro BE, Hatfield GW, Mjolsness ED 2005 Application of a generalized MWC model for the mathematical simulation of metabolic pathways regulated by allosteric enzymes. Proc. IEEE Comput. Syst. Bioinform. Conf. 2005: 279-288.

Najdi TS, Yang CR, Shapiro BE, Hatfield GW, Mjolsness ED 2006 Application of a generalized MWC model for the mathematical simulation of metabolic pathways regulated by allosteric enzymes. J. Bioinform. Comput. Biol. 4: 335-355.

Nakamura CE, Whited GM 2003 Metabolic engineering for the microbial production of 1,3-propanediol. Curr. Opin. Biotechnol. 14: 454-459.

Nakano MM, Hulett FM 1997 Adaptation of Bacillus subtilis to oxygen limitation. FEMS Microbiol. Lett. 157: 1-7.

Nakano MM, Zuber P 1998 Anaerobic growth of a "strict aerobe". Annu. Rev. Microbiol. 52: 165-190.

Nakayama Y, Matsushima R, Tomita M 1999 Computer simulation of human erythrocyte using the E-cell system. Genome Informatics 10: 364-365.

Nambara E, Marion-Poll A 2005 Abscisic acid biosynthesis and catabolism. Annu. Rev. Plant Biol. 56: 165-185.

Nambara E, Marion-Poll A 2003 ABA action and interactions in seeds. Trends Plant Sci. 8: 213-217.

Namjoshi AA, Hu WS, Ramkrishna D 2003 Unveiling steady-state multiplicity in hybridoma cultures: The cybernetic approach. Biotechnol. Bioeng. 81: 80-91.

Namjoshi AA, Ramkrishna D 2001 Multiplicity and stability of steady states in continuous bioreactors: dissection of cybernetic models. Chem. Eng. Sci. 56: 5593-5607.

Nanchen A, Fuhrer T, Sauer U 2006 Determination of metabolic flux ratios from 13C-experiments and gas chromatography-mass spectrometry data: protocol and principles. Methods Mol. Biol. 358: 177-198.

Nau-Wagner G, Boch J, Le Good JA, Bremer E 1999 High-affinity transport of choline-O-sulfate and its use as a compatible solute in Bacillus subtilis. Appl. Environ. Microbiol. 65: 560-568.

Navratil T, Petr M, Senholdova Z, Pristoupilova K, Pristoupil TI, Heyrovsky M, Pelclova D, Kohlikova E 2007 Diagnostic significance of urinary thiodiglycolic acid as a possible tool for studying the role of vitamins B12 and folates in the metabolism of thiolic substances. Physiol. Res. 56: 113-122.

Naya L, Ladrera R, Ramos J, Gonzalez EM, Arrese-Igor C, Minchin FR, Becana M 2007 The response of carbon metabolism and antioxidant defenses of alfalfa nodules to drought stress and to the subsequent recovery of plants. Plant Physiol. 144: 1104-1114.

Neelam A, Cassol T, Mehta RA, Abdul-Baki AA, Sobolev AP, Goyal RK, Abbott J, Segre AL, Handa AK, Mattoo AK 2008 A field-grown transgenic tomato line expressing higher levels of polyamines reveals legume cover crop mulch-specific perturbations in fruit phenotype at the levels of metabolite profiles, gene expression, and agronomic characteristics. J. Exp. Bot. 59: 2337-2346.

Neelon K, Schreier HJ, Meekins H, Robinson PM, Roberts MF 2005 Compatible solute effects on thermostability of glutamine synthetase and aspartate transcarbamoylase from Methanococcus jannaschii. Biochim. Biophys. Acta 1753: 164-173.

Nelson DE, Shen B, Bohnert HJ 1998 Salinity tolerance--mechanisms, models and the metabolic engineering of complex traits. Genet. Eng. (N.Y.) 20: 153-176.

Neuhaus HE, Hausler RE, Sonnewald U 2005 No need to shift the paradigm on the metabolic pathway to transitory starch in leaves. Trends Plant Sci. 10: 154-156.

Neves AR, Ramos A, Nunes MC, Kleerebezem M, Hugenholtz J, de Vos WM, Almeida J, Santos H 1999 In vivo nuclear magnetic resonance studies of glycolytic kinetics in Lactococcus lactis. Biotechnol. Bioeng. 64: 200-212.

Newton RP, Brenton AG, Smith CJ, Dudley E 2004 Plant proteome analysis by mass spectrometry: principles, problems, pitfalls and recent developments. Phytochemistry 65: 1449-1485.

Nguyen HT, Dieterich A, Athenstaedt K, Truong NH, Stahl U, Nevoigt E 2004 Engineering of Saccharomyces cerevisiae for the production of l-glycerol 3-phosphate. Metab. Eng. 6: 155-163.

Ni TC, Savageau MA 1996 Application of biochemical systems theory to metabolism in human red blood cells. Signal propagation and accuracy of representation. J. Biol. Chem. 271: 7927-7941.

Nicholson JK, Holmes E, Lindon JC, Wilson ID 2004 The challenges of modeling mammalian biocomplexity. Nat. Biotechnol. 22: 1268-1274.

Nicolai M, Roncato MA, Canoy AS, Rouquie D, Sarda X, Freyssinet G, Robaglia C 2006 Large-scale analysis of mRNA translation states during sucrose starvation in Arabidopsis cells identifies cell proliferation and chromatin structure as targets of translational control. Plant Physiol. 141: 663-673.

Niederberger P, Prasad R, Miozzari G, Kacser H 1992 A strategy for increasing an in vivo flux by genetic manipulations. The tryptophan system of yeast. Biochem. J. 287: 473-479.

Nielsen J 1998 Metabolic engineering: techniques for analysis of targets for genetic manipulations. Biotechnol. Bioeng. 58: 125-132.

Nielsen J 1998 The role of metabolic engineering in the production of secondary metabolites. Curr. Opin. Microbiol. 1: 330-336.

Nielsen J 2001 Metabolic engineering. Appl. Microbiol. Biotechnol. 55: 263-283.

Niemeyer H, Cardenas ML 1985 Concurrence of multiple and integrated mechanisms in the modulation of enzyme activities: significance for the regulation of metabolic fluxes. Arch. Biol. Med. Exp. (Santiago) 18: 331-358.

Nierop Groot MN, de Bont JAM 1998 Conversion of phenylalanine to benzaldehyde initiated by an aminotransferase in Lactobacillus plantarum. Appl. Environ. Microbiol. 64: 3009-3013.

Niittyla T, Comparot-Moss S, Lue WL, Messerli G, Trevisan M, Seymour MD, Gatehouse JA, Villadsen D, Smith SM, Chen J, Zeeman SC, Smith AM 2006 Similar protein phosphatases control starch metabolism in plants and glycogen metabolism in mammals. J. Biol. Chem. 281: 11815-11818.

Niittyla T, Messerli G, Trevisan M, Chen J, Smith AM, Zeeman SC 2004 A previously unknown maltose transporter essential for starch degradation in leaves. Science 303: 87-89.

Nikerel IE, van Winden WA, Verheijen PJ, Heijnen JJ 2008 Model reduction and a priori kinetic parameter identifiability analysis using metabolome time series for metabolic reaction networks with linlog kinetics. Metab. Eng. Aug 5 [Epub ahead of print].

Nikiforova VJ, Bielecka M, Gakiere B, Krueger S, Rinder J, Kempa S, Morcuende R, Scheible WR, Hesse H, Hoefgen R 2006 Effect of sulfur availability on the integrity of amino acid biosynthesis in plants. Amino Acids 30: 173-183.

Nikiforova VJ, Daub CO, Hesse H, Willmitzer L, Hoefgen R 2005 Integrative gene-metabolite network with implemented causality deciphers informational fluxes of sulphur stress response. J. Exp. Bot. 56: 1887-1896.

Nikiforova VJ, Kopka J, Tolstikov V, Fiehn O, Hopkins L, Hawkesford MJ, Hesse H, Hoefgen R 2005 Systems rebalancing of metabolism in response to sulfur deprivation, as revealed by metabolome analysis of Arabidopsis plants. Plant Physiol. 138: 304-318.

Niklas KJ 2006 Plant allometry, leaf nitrogen and phosphorus stoichiometry, and interspecific trends in annual growth rates. Ann. Bot. (Lond.) 97: 155-163.

Nikolau BJ, Perera MA, Brachova L, Shanks B 2008 Platform biochemicals for a biorenewable chemical industry. Plant J. 54: 536-545.

Nikolic M, Nikolic N, Liang Y, Kirkby EA, Romheld V 2007 Germanium-68 as an adequate tracer for silicon transport in plants. Characterization of silicon uptake in different crop species. Plant Physiol. 143: 495-503.

Nims E, Dubois CP, Roberts SC, Walker EL 2006 Expression profiling of genes involved in paclitaxel biosynthesis for targeted metabolic engineering. Metab. Eng. 8: 385-394.

Ninfa AJ, Jiang P 2005 PII signal transduction proteins: sensors of alpha-ketoglutarate that regulate nitrogen metabolism. Curr. Opin. Microbiol. 8: 168-173.

Nissen TL, Kielland-Brandt MC, Nielsen J, Villadsen J 2000 Optimization of ethanol production in Saccharomyces cerevisiae by metabolic engineering of the ammonium assimilation. Metab. Eng. 2: 69-77.

Nissim I, Daikhin Y, Nissim I, Luhovyy B, Horyn O, Wehrli SL, Yudkoff M 2006 Agmatine stimulates hepatic fatty acid oxidation: a possible mechanism for up-regulation of ureagenesis. J. Biol. Chem. 281: 8486-8496.

No authors listed 2008 Metabolic engineering of the initial stages of xylose catabolism in yeasts for construction of efficient producers of ethanol from lignocelluloses. Tsitol. Genet. 42: 70-84.

Noctor G, Dutilleul C, De Paepe R, Foyer CH 2004 Use of mitochondrial electron transport mutants to evaluate the effects of redox state on photosynthesis, stress tolerance and the integration of carbon/nitrogen metabolism. J. Exp. Bot. 55: 49-57.

Noel JP, Austin MB, Bomati EK 2005 Structure-function relationships in plant phenylpropanoid biosynthesis. Curr. Opin. Plant Biol. 8: 249-253.

Nogales J, Guijo MI, Quesada A, Merchan F 2004 Functional analysis and regulation of the malate synthase from Chlamydomonas reinhardtii. Planta 219: 325-331.

Nogues S, Tcherkez G, Streb P, Pardo A, Baptist F, Bligny R, Ghashghaie J, Cornic G 2006 Respiratory carbon metabolism in the high mountain plant species Ranunculus glacialis. J. Exp. Bot. 57: 3837-3845.

Noh K, Gronke K, Luo B, Takors R, Oldiges M, Wiechert W 2007 Metabolic flux analysis at ultra short time scale: isotopically non-stationary 13C labeling experiments. J. Biotechnol. 129: 249-267.

Noh K, Wiechert W 2006 Experimental design principles for isotopically in stationary 13C labeling experiments. Biotechnol. Bioeng. 94: 234-251.

Nohl H, Staniek K, Kozlov AV 2005 The existence and significance of a mitochondrial nitrite reductase. Redox Rep. 10: 281-286.

Noirel J, Ow SY, Sanguinetti G, Jaramillo A, Wright PC 2008 Automated extraction of meaningful pathways from quantitative proteomics data. Brief. Funct. Genomic. Proteomic. 7: 136-146.

Noiriel A, Naponelli V, Gregory JF 3rd, Hanson AD 2007 Pterin and folate salvage. Plants and Escherichia coli lack capacity to reduce oxidized pterins. Plant Physiol. 143: 1101-1109.

Nolan RP, Fenley AP, Lee K 2006 Identification of distributed metabolic objectives in the hypermetabolic liver by flux and energy balance analysis. Metab. Eng. 8: 30-45.

Nomura M, Mai HT, Fujii M, Hata S, Izui K, Tajima S 2006 Phosphoenolpyruvate carboxylase plays a crucial role in limiting nitrogen fixation in Lotus japonicus nodules. Plant Cell Physiol. 47: 613-621.

Nomura T, Jager CE, Kitasaka Y, Takeuchi K, Fukami M, Yoneyama K, Matsushita Y, Nyunoya H, Takatsuto S, Fujioka S, Smith JJ, Kerckhoffs LH, Reid JB, Yokota T 2004 Brassinosteroid deficiency due to truncated steroid 5{alpha}-reductase causes dwarfism in the lk mutant of pea. Plant Physiol. 135: 2220-2229.

Nookaew I, Meechai A, Thammarongtham C, Laoteng K, Ruanglek V, Cheevadhanarak S, Nielsen J, Bhumiratana S 2007 Identification of flux regulation coefficients from elementary flux modes: a systems biology tool for analysis of metabolic networks. Biotechnol. Bioeng. 97: 1535-1549.

Noor S, Punekar NS 2005 Allosteric NADP-glutamate dehydrogenase from aspergilli: purification, characterization and implications for metabolic regulation at the carbon-nitrogen interface. Microbiology 151: 1409-1419.

Noren A, Soliman A, Nordlund S 1997 The role of NAD+ as a signal during nitrogenase switch-off in Rhodospirillum rubrum. Biochem. J. 322: 829-832.

North GB, Martre P, Nobel PS 2004 Aquaporins account for variations in hydraulic conductance for metabolically active root regions of Agave deserti in wet, dry, and rewetted soil. Plant Cell Environ. 27: 219-228.

Novak L, Loubiere P 2000 The metabolic network of Lactococcus lactis: distribution of 14C-labeled substrates between catabolic and anabolic pathways. J. Bacteriol. 182: 1136-1143.

Novak M, Modha A, Blackburn BJ 1993 Metabolic alterations in organs of Meriones unguiculatus infected with Echincoccus multilocularis. Comp. Biochem. Physiol. [B] 105: 517-521.

Novakova M, Motyka V, Dobrev PI, Malbeck J, Gaudinova A, Vankova R 2005 Diurnal variation of cytokinin, auxin and abscisic acid levels in tobacco leaves. J. Exp. Bot. 56: 2877-2883.

Nuccio ML, McNeil SD, Ziemak MJ, Hanson AD, Jain RK, Selvaraj G 2000 Choline import into chloroplasts limits glycine betaine synthesis in tobacco: analysis of plants engineered with a chloroplastic or a cytosolic pathway. Metab. Eng. 2: 300-311.

Nuccio ML, Rhodes D, McNeil SD, Hanson AD 1999 Metabolic engineering of plants for osmotic stress resistance. Curr. Opin. Plant Biol. 2: 128-134.

Nudler E, Mironov AS 2004 The riboswitch control of bacterial metabolism. Trends Biochem. Sci. 29: 11-17.

Nuno JC, Sanchez-Valdenebro I, Perez-Iratxeta C, Melendez-Hevia E, Montero F 1997 Network organization of cell metabolism: monosaccharide interconversion. Biochem. J. 324: 103-111.

O'Callaghan PM, James DC 2008 Systems biotechnology of mammalian cell factories. Brief. Funct. Genomic. Proteomic. 7: 95-110.

O'Neill MA, Hilgetag CC 2001 The portable UNIX programming system (PUPS) and CANTOR: a computational environment for dynamical representation and analysis of complex neurobiological data. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 356: 1259-1276.

Obara M, Szeliga M, Albrecht J 2008 Regulation of pH in the mammalian central nervous system under normal and pathological conditions: facts and hypotheses. Neurochem. Int. 52: 905-919.

Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M 1999 KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 27: 29-34.

Oh E, Yamaguchi S, Hu J, Yusuke J, Jung B, Paik I, Lee HS, Sun TP, Kamiya Y, Choi G 2007 PIL5, a phytochrome-interacting bHLH protein, regulates gibberellin responsiveness by binding directly to the GAI and RGA promoters in Arabidopsis seeds. Plant Cell 19: 1192-1208.

Oh IJ, Lee HW, Park CH, Lee SY, Lee J 2008 Succinic acid production from continuous fermentation process using Mannheimia succiniciproducens LPK7. J. Microbiol. Biotechnol. 18: 908-912.

Oh JE, Fountoulakis M, Juranville JF, Rosner M, Hengstschlaeger M, Lubec G 2004 Proteomic determination of metabolic enzymes of the amnion cell: Basis for a possible diagnostic tool?. Proteomics 4: 1145-1158.

Oh MK, Liao JC 2000 DNA microarray detection of metabolic responses to protein overproduction in Escherichia coli. Metab. Eng. 2: 201-209.

Oh YK, Palsson BO, Park SM, Schilling CH, Mahadevan R 2007 Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data. J. Biol. Chem. 282: 28791-28799.

Ohlrogge J 1999 Plant metabolic engineering: are we ready for phase two? Curr. Opin. Plant Biol. 2: 121-122.

Ohlrogge JB, Jaworski JG 1997 Regulation of fatty acid synthesis. Annu. Rev. Plant Physiol. Plant Mol. Biol. 48: 109-136.

Ohno H, Naito Y, Nakajima H, Tomita M 2008 Construction of a biological tissue model based on a single-cell model: a computer simulation of metabolic heterogeneity in the liver lobule. Artif. Life 14: 3-28.

Ohta D, Mori I, Ward E 1997 Inhibitors of imidazoleglycerolphosphate dehydratase as herbicides. Weed Sci. 45: 610-620.

Oikawa A, Nakamura Y, Ogura T, Kimura A, Suzuki H, Sakurai N, Shinbo Y, Shibata D, Kanaya S, Ohta D 2006 Clarification of pathway-specific inhibition by Fourier transform ion cyclotron resonance/mass spectrometry-based metabolic phenotyping studies. Plant Physiol. 142: 398-413.

Okamoto M, Morita Y, Tominaga D, Tanaka K, Kinoshita N, Ueno JI, Miura Y, Maki Y, Eguchi Y 1997 Toward a virtual-labo-system for metabolic engineering: development of biochemical engineering system analyzing tool-kit (BEST-KIT). Pac. Symp. Biocomput. 1997: 304-315.

Okar DA, Lange AJ 1999 Fructose-2,6-bisphosphate and control of carbohydrate metabolism in eukaryotes. Biofactors 10: 1-14.

Okazaki K, Oka N, Shinano T, Osaki M, Takebe M 2008 Differences in the metabolite profiles of spinach (Spinacia oleracea L.) leaf in different concentrations of nitrate in the culture solution. Plant Cell Physiol. 49: 170-177.

Oksman-Caldentey KM, Arroo R 2000 Chapter 13. Regulation of Tropane Alkaloid Metabolism in Plants an Plant Cell Cultures. In "Metabolic Engineering of Plant Secondary Metabolism" (Verpoorte R, Alfermann AW, eds), Kluwer Academic Publishers, Dortrecht, The Netherlands, pp. 253-281.

Oksman-Caldentey KM, Saito K 2005 Integrating genomics and metabolomics for engineering plant metabolic pathways. Curr. Opin. Biotechnol. 16: 174-179.

Olah J, Orosz F, Puskas LG, Hackler L Jr, Horanyi M, Polgar L, Hollan S, Ovadi J 2005 Triosephosphate isomerase deficiency: consequences of an inherited mutation at mRNA, protein and metabolic levels. Biochem J. 392: 675-683.

Olano C, Lombo F, Mendez C, Salas JA 2008 Improving production of bioactive secondary metabolites in actinomycetes by metabolic engineering. Metab Eng. Jul 15 [Epub ahead of print].

Oldiges M, Kunze M, Degenring D, Sprenger GA, Takors R 2004 Stimulation, monitoring, and analysis of pathway dynamics by metabolic profiling in the aromatic amino acid pathway. Biotechnol. Prog. 20: 1623-1633.

Oliveira AP, Nielsen J, Forster J 2005 Modeling Lactococcus lactis using a genome-scale flux model. BMC Microbiol. 5: 39.

Oliveira IC, Brenner E, Chiu J, Hsieh MH, Kouranov A, Lam HM, Shin MJ, Coruzzi G 2001 Metabolite and light regulation of metabolism in plants: lessons from the study of a single biochemical pathway. Braz. J. Med. Biol. Res. 34: 567-575.

Oliveira IC, Coruzzi GM 1999 Carbon and amino acids reciprocally modulate the expression of glutamine synthetase in Arabidopsis. Plant Physiol. 121: 301-310.

Oliveira JS, Bailey CG, Jones-Oliveira JB, Dixon DA 2001 An algebraic-combinatorial model for the identification and mapping of biochemical pathways. Bull. Math. Biol. 63: 1163-1196.

Oliver DJ, Nikolau B, Wurtele ES 2002 Functional genomics: high-throughput mRNA, protein, and metabolite analyses. Metab. Eng. 4: 98-106.

Oliver MJ, Dowd SE, Zaragoza J, Mauget SA, Payton PR 2004 The rehydration transcriptome of the desiccation-tolerant bryophyte Tortula ruralis: transcript classification and analysis. BMC Genomics. 5: 89.

Oliver SG 2006 From genomes to systems: the path with yeast. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 361: 477-482.

Oliver SN, Tiessen A, Fernie AR, Geigenberger P 2008 Decreased expression of plastidial adenylate kinase in potato tubers results in an enhanced rate of respiration and a stimulation of starch synthesis that is attributable to post-translational redox-activation of ADP-glucose pyrophosphorylase. J. Exp. Bot. 59: 315-325.

Olry A, Schneider-Belhaddad F, Heintz D, Werck-Reichhart D 2007 A medium-throughput screening assay to determine catalytic activities of oxygen-consuming enzymes: a new tool for functional characterization of cytochrome P450 and other oxygenases. Plant J. 51: 331-340.

Olsson PA, Van Aarle IM, Allaway WG, Ashford AE, Rouhier H 2002 Phosphorus effects on metabolic processes in monoxenic arbuscular mycorrhiza cultures. Plant Physiol. 130: 1162-1171.

Ono E, Hatayama M, Isono Y, Sato T, Watanabe R, Yonekura-Sakakibara K, Fukuchi-Mizutani M, Tanaka Y, Kusumi T, Nishino T, Nakayama T 2006 Localization of a flavonoid biosynthetic polyphenol oxidase in vacuoles. Plant J. 45: 133-143.

Oren A 1999 Bioenergetic aspects of halophilism. Microbiol. Mol. Biol. Rev. 63: 334.

Oren A 2008 Microbial life at high salt concentrations: phylogenetic and metabolic diversity. Saline Systems 4: 2.

Orlova I, Marshall-Colon A, Schnepp J, Wood B, Varbanova M, Fridman E, Blakeslee JJ, Peer WA, Murphy AS, Rhodes D, Pichersky E, Dudareva N 2006 Reduction of benzenoid synthesis in petunia flowers reveals multiple pathways to benzoic acid and enhancement in auxin transport. Plant Cell 18: 3458-3475.

Ortega F, Acerenza L 2002 Elasticity analysis and design for large metabolic responses produced by changes in enzyme activities. Biochem. J. 367: 41-48.

Ortega F, Acerenza L 1998 Optimal metabolic control design. J. Theor. Biol. 191: 439-449.

Ortega F, Acerenza L, Westerhoff HV, Mas F, Cascante M 2002 Product dependence and bifunctionality compromise the ultrasensitivity of signal transduction cascades. Proc. Natl. Acad. Sci. U.S.A. 99: 1170-1175.

Osbourn A, He SY 2006 Biotic interactions. Towards a unifying and balanced view. Curr. Opin. Plant Biol. 9: 347-350.

Ostergaard S, Olsson L, Johnston M, Nielsen J 2000 Increasing galactose consumption by Saccharomyces cerevisiae through metabolic engineering of the GAL gene regulatory network. Nat. Biotechnol. 18: 1283-1286.

Ostergaard S, Olsson L, Nielsen J 2000 Metabolic engineering of Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 64: 34-50.

Ostin A, Kowalyczk M, Bhalerao RP, Sandberg G 1998 Metabolism of indole-3-acetic acid in Arabidopsis. Plant Physiol. 118: 285-296.

Osuna D, Usadel B, Morcuende R, Gibon Y, Blasing OE, Hohne M, Gunter M, Kamlage B, Trethewey R, Scheible WR, Stitt M 2007 Temporal responses of transcripts, enzyme activities and metabolites after adding sucrose to carbon-deprived Arabidopsis seedlings. Plant J. 49: 463-491.

Ovadi J, Srere PA 1996 Metabolic consequences of enzyme interactions. Cell Biochem. Funct. 14: 249-258.

Overbeek R, Larsen N, Pusch GD, D'Souza M, Selkov E Jr, Kyrpides N, Fonstein M, Maltsev N, Selkov E 2000 WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction. Nucleic Acids Res. 28: 123-125.

Overy SA, Walker HJ, Malone S, Howard TP, Baxter CJ, Sweetlove LJ, Hill SA, Quick WP 2005 Application of metabolite profiling to the identification of traits in a population of tomato introgression lines. J. Exp. Bot. 56: 287-296.

Oyama-Okubo N, Ando T, Watanabe N, Marchesi E, Uchida K, Nakayama M 2005 Emission mechanism of floral scent in Petunia axillaris. Biosci. Biotechnol. Biochem. 69: 773-777.

Padilla L, Agosin E 2005 Heterologous expression of Escherichia coli ppsA (phosphoenolpyruvate synthetase) and galU (UDP-glucose pyrophosphorylase) genes in Corynebacterium glutamicum, and its impact on trehalose synthesis. Metab. Eng. 7: 260-268.

Pageau K, Reisdorf-Cren M, Morot-Gaudry JF, Masclaux-Daubresse C 2006 The two senescence-related markers, GS1 (cytosolic glutamine synthetase) and GDH (glutamate dehydrogenase), involved in nitrogen mobilization, are differentially regulated during pathogen attack and by stress hormones and reactive oxygen species … J. Exp. Bot. 57: 547-557.

Pail M, Peterbauer T, Seiboth B, Hametner C, Druzhinina I, Kubicek CP 2004 The metabolic role and evolution of L-arabinitol 4-dehydrogenase of Hypocrea jecorina. Eur. J. Biochem. 271: 1864-1872.

Pal C, Papp B, Lercher MJ 2005 Horizontal gene transfer depends on gene content of the host. Bioinformatics 21 Suppl. 2: ii222-ii223.

Pal C, Papp B, Lercher MJ 2005 Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat. Genet. 37: 1372-1375.

Palauqui JC, Elmayan T, Pollien JM, Vaucheret H 1997 Systemic acquired silencing: transgene-specific post-transcriptional silencing is transmitted by grafting from silenced stocks to non-silenced scions. EMBO J. 16: 4738-4745.

Palsson BO, Joshi A, Ozturk SS 1987 Reducing complexity in metabolic networks: making metabolic meshes manageable. Fed. Proc. 46: 2485-2489.

Palsson BO, Lee ID 1993 Model complexity has a significant effect on the numerical value and interpretation of metabolic sensitivity coefficients. J. Theor. Biol. 161: 299-315.

Palsson BO, Lightfoot EN 1985 Mathematical modelling of dynamics and control in metabolic networks. V. Static bifurcations in single biochemical control loops. J. Theor. Biol. 113: 279-298.

Palsson BO, Palsson H, Lightfoot EN 1985 Mathematical modelling of dynamics and control in metabolic networks. III. Linear reaction sequences. J. Theor. Biol. 113: 231-259.

Palsson BO, Price ND, Papin JA 2003 Development of network-based pathway definitions: the need to analyze real metabolic networks. Trends Biotechnol. 21: 195-198.

Palumbo MC, Colosimo A, Giuliani A, Farina L 2005 Functional essentiality from topology features in metabolic networks: a case study in yeast. FEBS Lett. 579: 4642-4646.

Palumbo MC, Colosimo A, Giuliani A, Farina L 2007 Essentiality is an emergent property of metabolic network wiring. FEBS Lett. 581: 2485-2489.

Palva ET, Thtiharju S, Tamminen I, Puhakainen T, Laitinen R, Svensson J, Helenius E, Heino P 2002 Biological mechanisms of low temperature stress response: cold acclimation and development of freezing tolerance in plants. JIRCAS Working Report No.23, "Genetic Engineering of Crop Plants for Abiotic Stress" (Iwanaga M, ed.) p. 9-15.

Panagiotou G, Christakopoulos P, Grotkjaer T, Olsson L 2006 Engineering of the redox imbalance of Fusarium oxysporum enables anaerobic growth on xylose. Metab. Eng. 8: 474-482.

Pandey A, Chakraborty S, Datta A, Chakraborty N 2008 Proteomics approach to identify dehydration responsive nuclear proteins from chickpea (Cicer arietinum L.). Mol. Cell. Proteomics 7: 88-107.

Pandey KD, Shukla SP, Shukla PN, Giri DD, Singh JS, Singh P, Kashyap AK 2004 Cyanobacteria in Antarctica: ecology, physiology and cold adaptation. Cell. Mol. Biol. (Noisy-le-grand) 50: 575-584.

Pandey R, Guru RK, Mount DW 2004 Pathway Miner: extracting gene association networks from molecular pathways for predicting the biological significance of gene expression microarray data. Bioinformatics 20: 2156-2158.

Pandey SP, Baldwin IT 2007 RNA-directed RNA polymerase 1 (RdR1) mediates the resistance of Nicotiana attenuata to herbivore attack in nature. Plant J. 50: 40-53.

Pandhal J, Snijders AP, Wright PC, Biggs CA 2008 A cross-species quantitative proteomic study of salt adaptation in a halotolerant environmental isolate using (15)N metabolic labelling. Proteomics 8: 2266-2284.

Pandhal J, Wright PC, Biggs CA 2008 Proteomics with a pinch of salt: a cyanobacterial perspective. Saline Systems 4: 1.

Papenbrock J, Grimm B 2001 Regulatory network of tetrapyrrole biosynthesis--studies of intracellular signalling involved in metabolic and developmental control of plastids. Planta 213: 667-681.

Papin JA, Price ND, Edwards JS, Palsson BO 2002 The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy. J. Theor. Biol. 215: 67-82.

Papin JA, Price ND, Palsson BO 2002 Extreme pathway lengths and reaction participation in genome-scale metabolic networks. Genome Res. 12: 1889-1900.

Papin JA, Price ND, Wiback SJ, Fell DA, Palsson BO 2003 Metabolic pathways in the post-genome era. Trends Biochem. Sci. 28: 250-258.

Papp B, Pal C, Hurst LD 2004 Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast. Nature 429: 661-664.

Paradise EM, Kirby J, Chan R, Keasling JD 2008 Redirection of flux through the FPP branch-point in Saccharomyces cerevisiae by down-regulating squalene synthase. Biotechnol. Bioeng. 100: 371-378.

Park EJ, Jeknic Z, Sakamoto A, Denoma J, Yuwansiri R, Murata N, Chen TH 2004 Genetic engineering of glycinebetaine synthesis in tomato protects seeds, plants, and flowers from chilling damage. Plant J. 40: 474-487.

Park JH, Lee SY, Kim TY, Kim HU 2008 Application of systems biology for bioprocess development. Trends Biotechnol. 26: 404-412.

Park JS, Kim JB, Cho KJ, Cheon CI, Sung MK, Choung MG, Roh KH 2008 Arabidopsis R2R3-MYB transcription factor AtMYB60 functions as a transcriptional repressor of anthocyanin biosynthesis in lettuce (Lactuca sativa). Plant Cell Rep. 27: 985-994.

Park SJ, Huang Y, Ayoubi P 2006 Identification of expression profiles of sorghum genes in response to greenbug phloem-feeding using cDNA subtraction and microarray analysis. Planta 223: 932-947.

Park SM, Klapa MI, Sinskey AJ, Stephanopoulos G 1999 Metabolite and isotopomer balancing in the analysis of metabolic cycles: II. Applications. Biotechnol. Bioeng. 62: 392-401.

Park SM, Sinskey AJ, Stephanopoulos G 1997 Metabolic and physiological studies of Corynebacterium glutamicum mutants. Biotechnol. Bioeng. 55: 864-879.

Parsot C 1986 Evolution of biosynthetic pathways: a common ancestor for threonine synthase, threonine dehydratase and D-serine dehydratase. EMBO J. 5: 3013-3019.

Pasini E, Aquilani R, Dioguardi FS 2004 Amino acids: chemistry and metabolism in normal and hypercatabolic states. Am. J. Cardiol. 93: 3A-5A.

Pastenes C, Horton P 1996 Effect of high temperature on photosynthesis in beans. II. CO2 assimilation and metabolite contents. Plant Physiol. 112: 1253-1260.

Pasternack LB, Laude DA Jr, Appling DR 1994 Whole-cell detection by 13C NMR of metabolic flux through the C1-tetrahydrofolate synthase/serine hydroxymethyltransferase enzyme system and effect of antifolate exposure in Saccharomyces cerevisiae. Biochemistry 33: 7166-7173.

Pasternack LB, Laude DA Jr, Appling DR 1992 13C NMR detection of folate-mediated serine and glycine synthesis in vivo in Saccharomyces cerevisiae. Biochemistry 31: 8713-8719.

Pastor-Satorras R, Smith E, Sole RV 2003 Evolving protein interaction networks through gene duplication. J. Theor. Biol. 222: 199-210.

Patil KR, Akesson M, Nielsen J 2004 Use of genome-scale microbial models for metabolic engineering. Curr. Opin. Biotechnol. 15: 64-69.

Patil KR, Nielsen J 2005 Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proc. Natl. Acad. Sci. U.S.A. 102: 2685-2689.

Patnaik PR 2000 Are microbes intelligent beings?: An assessment of cybernetic modeling. Biotechnol. Adv. 18: 267-288.

Paul MJ, Foyer CH 2001 Sink regulation of photosynthesis. J. Exp. Bot. 52: 1383-1400.

Pavan A, Thomaseth K, Valerio A 2003 Modeling population kinetics of free fatty acids in isolated rat hepatocytes using Markov Chain Monte Carlo. Ann. Biomed. Eng. 31: 854-866.

Pavillard V, Drbal AAA, Swaine DJ, Phillips RM, Double JA, Nicolaou A 2004 Analysis of cell-cycle kinetics and sulfur amino acid metabolism in methionine-dependent tumor cell lines; the effect of homocysteine supplementation. Biochem. Pharmacol. 67: 1587-1599.

Pe'er D, Regev A, Elidan G, Friedman N 2001 Inferring subnetworks from perturbed expression profiles. Bioinformatics 17 Suppl. 1: S215-S224.

Pears MR, Cooper JD, Mitchison HM, Mortishire-Smith RJ, Pearce DA, Griffin JL 2005 High resolution 1H NMR based metabolomics indicates a neurotransmitter cycling deficit in cerebral tissue from a mouse model of batten disease. J. Biol. Chem. 280: 42508-42814.

Pedersen H, Carlsen M, Nielsen J 1999 Identification of enzymes and quantification of metabolic fluxes in the wild type and in a recombinant Aspergillus oryzae strain. Appl. Environ. Microbiol. 65: 11-19.

Pedras MS, Zheng QA, Gadagi RS, Rimmer SR 2008 Phytoalexins and polar metabolites from the oilseeds canola and rapeseed: differential metabolic responses to the biotroph Albugo candida and to abiotic stress. Phytochemistry 69: 894-910.

Peebles CA, Hong SB, Gibson SI, Shanks JV, San KY 2006 Effects of terpenoid precursor feeding on Catharanthus roseus hairy roots over-expressing the alpha or the alpha and beta subunits of anthranilate synthase. Biotechnol. Bioeng. 93: 534-540.

Peebles CA, Hong SB, Gibson SI, Shanks JV, San KY 2005 Transient effects of overexpressing anthranilate synthase alpha and beta subunits in Catharanthus roseus hairy roots. Biotechnol. Prog. 21: 1572-1576.

Peletier MA, Westerhoff HV, Kholodenko BN 2003 Control of spatially heterogeneous and time-varying cellular reaction networks: a new summation law. J. Theor. Biol. 225: 477-487.

Peng M, Hudson D, Schofield A, Tsao R, Yang R, Gu H, Bi YM, Rothstein SJ 2008 Adaptation of Arabidopsis to nitrogen limitation involves induction of anthocyanin synthesis which is controlled by the NLA gene. J. Exp. Bot. 59: 2933-2944.

Perales M, Portoles S, Mas P 2006 The proteasome-dependent degradation of CKB4 is regulated by the Arabidopsis biological clock. Plant J. 46: 849-860.

Peres S, Beurton-Aimar M, Mazat JP 2006 Pathway classification of TCA cycle. Syst. Biol. (Stevenage) 153: 369-371.

Periappuram C, Steinhauer L, Barton DL, Taylor DC, Chatson B, Zou J 2000 The plastidic phosphoglucomutase from Arabidopsis. A reversible enzyme reaction with an important role in metabolic control. Plant Physiol. 122: 1193-1200.

Perrin RM, Wigge PA 2001 Physiology and metabolism: Web alert. Curr. Opin. Plant Biol. 4: 177-178.

Perrin RM, Wigge PA 2002 Physiology and metabolism: Web alert. Curr. Opin. Plant Biol. 5: 189-190.

Pesquet E, Barbier O, Ranocha P, Jauneau A, Goffner D 2004 Multiple gene detection by in situ RT-PCR in isolated plant cells and tissues. Plant J. 39: 947-959.

Peters RJ 2006 Uncovering the complex metabolic network underlying diterpenoid phytoalexin biosynthesis in rice and other cereal crop plants. Phytochemistry 67: 2307-2317.

Petersen BL, Andreasson E, Bak S, Agerbirk N, Halkier BA 2001 Characterization of transgenic Arabidopsis thaliana with metabolically engineered high levels of p-hydroxybenzylglucosinolate. Planta 212: 612-618.

Petersen M 2007 Current status of metabolic phytochemistry. Phytochemistry 68: 2847-2860.

Petersen S, Mack C, De Graaf AA, Riedel C, Eikmanns BJ, Sahm H 2001 Metabolic consequences of altered phosphoenolpyruvate carboxykinase activity in Corynebacterium glutamicum reveal anaplerotic regulation mechanisms in vivo. Metab. Eng. 3: 344-361.

Peterson JD, Ingram LO 2008 Anaerobic respiration in engineered Escherichia coli with an internal electron acceptor to produce fuel ethanol. Ann. N. Y. Acad. Sci. 1125: 363-372.

Petkov SB, Maranas CD 1997 Quantitative assessment of uncertainty in the optimization of metabolic pathways. Biotechnol. Bioeng. 56: 145-161.

Petschacher B, Nidetzky B 2008 Altering the coenzyme preference of xylose reductase to favor utilization of NADH enhances ethanol yield from xylose in a metabolically engineered strain of Saccharomyces cerevisiae. Microb. Cell Fact. 7: 9.

Pettersson G 1996 Error associated with experimental flux control coefficient determinations in the Calvin cycle. Biochim. Biophys. Acta 1289: 169-174.

Pettersson G 1996 Errors associated with experimental determinations of enzyme flux control coefficients. J. Theor. Biol. 179: 191-197.

Pfefferle W, Mockel B, Bathe B, Marx A 2003 Biotechnological manufacture of lysine. Adv. Biochem. Eng. Biotechnol. 79: 59-112.

Pfeiffer T, Sanchez-Valdenebro I, Nuno JC, Montero F, Schuster S 1999 METATOOL: for studying metabolic networks. Bioinformatics 15: 251-257.

Pfleger BF, Pitera DJ, Newman JD, Martin VJ, Keasling JD 2007 Microbial sensors for small molecules: development of a mevalonate biosensor. Metab. Eng. 9: 30-38.

Phair RD 1997 Development of kinetic models in the nonlinear world of molecular cell biology. Metabolism 46: 1489-1495.

Phalakornkule C, Lee S, Zhu T, Koepsel R, Ataai MM, Grossmann IE, Domach MM 2001 A MILP-based flux alternative generation and NMR experimental design strategy for metabolic engineering. Metab. Eng. 3: 124-137.

Phelps TJ, Palumbo AV, Beliaev AS 2002 Metabolomics and microarrays for improved understanding of phenotypic characteristics controlled by both genomics and environmental constraints. Curr. Opin. Biotechnol. 13: 20-24.

Phue JN, Noronha SB, Hattacharyya R, Wolfe AJ, Shiloach J. 2005 Glucose metabolism at high density growth of E. coli B and E. coli K: differences in metabolic pathways are responsible for efficient glucose utilization in E. coli B as determined by microarrays and Northern blot analyses. Biotechnol. Bioeng. 90: 805-820.

Piazza M, Feng XJ, Rabinowitz JD, Rabitz H 2008 Diverse metabolic model parameters generate similar methionine cycle dynamics. J. Theor. Biol. 251: 628-639.

Picchini U, Ditlevsen S, De Gaetano A 2006 Modeling the euglycemic hyperinsulinemic clamp by stochastic differential equations. J. Math. Biol. 53: 771-796.

Piccoli C, Scrima R, Boffoli D, Capitanio N 2006 Control by cytochrome c oxidase of the cellular oxidative phosphorylation system depends on the mitochondrial energy state. Biochem. J. 396: 573-583.

Pichereau V, Pocard JA, Hamelin J, Blanco C, Bernard T 1998 Differential effects of dimethylsulfoniopropionate, dimethylsulfonioacetate, and other S-methylated compounds on the growth of Sinorhizobium meliloti at low and high osmolarities. Appl. Environ. Microbiol. 64: 1420-1429.

Pichersky E, Dudareva N 2007 Scent engineering: toward the goal of controlling how flowers smell. Trends Biotechnol. 25: 105-110.

Pickard WF 2003 The role of cytoplasmic streaming in symplastic transport. Plant Cell Environ. 26: 1-15.

Pierard C, Peres M, Satabin P, Guezennec CY, Lagarde D 1999 Effects of GABA-transaminase inhibition on brain metabolism and amino-acid compartmentation: an in vivo study by 2D 1H-NMR spectroscopy coupled with microdialysis. Exp. Brain Res. 127: 321-327.

Pierce S, Winter K, Griffiths H 2002 The role of CAM in high rainfall cloud forests: an in situ comparison of photosynthetic pathways in Bromeliaceae. Plant Cell Environ. 25: 1181-1189.

Pines O, Shemesh S, Battat E, Goldberg I 1997 Overexpression of cytosolic malate dehydrogenase (MDH2) causes overproduction of specific organic acids in Saccharomyces cerevisiae. Appl. Microbiol. Biotechnol. 48: 248-255.

Pinheiro C, Rodrigues AP, de Carvalho IS, Chaves MM, Ricardo CP 2005 Sugar metabolism in developing lupin seeds is affected by a short-term water deficit. J. Exp. Bot. 56: 2705-2712.

Pirkov I, Albers E, Norbeck J, Larsson C 2008 Ethylene production by metabolic engineering of the yeast Saccharomyces cerevisiae. Metab. Eng. Jun 27 [Epub ahead of print].

Pitula JS, Deck KM, Clarke SL, Anderson SA, Vasanthakumar A, Eisenstein RS 2004 Selective inhibition of the citrate-to-isocitrate reaction of cytosolic aconitase by phosphomimetic mutation of serine-711. Proc. Natl. Acad. Sci. U.S.A. 101: 10907-10912.

Platta HW, Erdmann R 2007 The peroxisomal protein import machinery. FEBS Lett. 581: 2811-2819.

Plaxton WC 1996 The organization and regulation of plant glycolysis. Annu. Rev. Plant Physiol. Plant Mol. Biol. 47: 185-214.

Pleite R, Pike MJ, Garces R, Martinez-Force E, Rawsthorne S 2005 The sources of carbon and reducing power for fatty acid synthesis in the heterotrophic plastids of developing sunflower (Helianthus annuus L.) embryos. J. Exp. Bot. 56: 1297-1303.

Poirier Y 2002 Polyhydroxyalknoate synthesis in plants as a tool for biotechnology and basic studies of lipid metabolism. Prog. Lipid Res. 41: 131-155.

Poirier Y, Antonenkov VD, Glumoff T, Hiltunen JK 2006 Peroxisomal beta-oxidation. A metabolic pathway with multiple functions. Biochim. Biophys. Acta 1763: 1413-1426.

Polakof S, Ceinos RM, Fernandez-Duran B, Miguez JM, Soengas JL 2007 Daily changes in parameters of energy metabolism in brain of rainbow trout: dependence on feeding. Comp. Biochem. Physiol. A. Mol. Integr. Physiol. 146: 265-273.

Polisetty PK, Voit EO, Gatzke EP 2006 Identification of metabolic system parameters using global optimization methods. Theor. Biol. Med. Model. 3: 4.

Polle A 2001 Dissecting the superoxide dismutase-ascorbate-glutathione-pathway in chloroplasts by metabolic modeling. Computer simulations as a step towards flux analysis. Plant Physiol. 126: 445-462.

Pommerrenig B, Barth I, Niedermeier M, Kopp S, Schmid J, Dwyer RA, McNair RJ, Klebl F, Sauer N 2006 Common plantain. A collection of expressed sequence tags from vascular tissue and a simple and efficient transformation method. Plant Physiol. 142: 1427-1441.

Pomposiello PJ, Bennik MH, Demple B 2001 Genome-wide transcriptional profiling of the Escherichia coli responses to superoxide stress and sodium salicylate. J. Bacteriol. 183: 3890-3902.

Pongrac J, Middleton FA, Lewis DA, Levitt P, Mirnics K 2002 Gene expression profiling with DNA microarrays: advancing our understanding of psychiatric disorders. Neurochem. Res. 27: 1049-1063.

Pool WA, Neves AR, Kok J, Santos H, Kuipers OP 2006 Natural sweetening of food products by engineering Lactococcus lactis for glucose production. Metab. Eng. 8: 456-464.

Poolman MG, Assmus HE, Fell DA 2004 Applications of metabolic modelling to plant metabolism. J. Exp. Bot. 55: 1177-1186.

Poolman MG, Fell DA, Thomas S 2000 Modelling photosynthesis and its control. J. Exp. Bot. 51: 319-328.

Poolman MG, Venkatesh KV, Pidcock MK, Fell DA 2004 A method for the determination of flux in elementary modes, and its application to Lactobacillus rhamnosus. Biotechnol. Bioeng. 88: 601-612.

Porro D, Bianchi MM, Brambilla L, Menghini R, Bolzani D, Carrera V, Lievense J, Liu CL, Ranzi BM, Frontali L, Alberghina L 1999 Replacement of a metabolic pathway for large-scale production of lactic acid from engineered yeasts. Appl. Environ. Microbiol. 65: 4211-4215.

Portillo F, Mulet JM, Serrano R 2005 A role for the non-phosphorylated form of yeast Snf1: tolerance to toxic cations and activation of potassium transport. FEBS Lett. 579: 512-516.

Potrykus J, White RL, Bearne SL 2008 Proteomic investigation of amino acid catabolism in the indigenous gut anaerobe Fusobacterium varium. Proteomics 8: 2691-2703.

Poughon L, Dussap CG, Gros JB 2001 Energy model and metabolic flux analysis for autotrophic nitrifiers. Biotechnol. Bioeng. 72: 416-433.

Poyck PP, Hoekstra R, Vermeulen JL, van Wijk AC, Chamuleau RA, Hakvoort TB, van Gulik TM, Lamers WH 2008 Expression of glutamine synthetase and carbamoylphosphate synthetase I in a bioartificial liver: markers for the development of zonation in vitro. Cells Tissues Organs Mar 20 [Epub ahead of print].

Pramanik J, Keasling JD 1997 Stoichiometric model of Escherichia coli metabolism: incorporation of growth-rate dependent biomass composition and mechanistic energy requirements. Biotechnol. Bioeng. 56: 398-421.

Prati EG, Matasci M, Suter TB, Dinter A, Sburlati AR, Bailey JE 2000 Engineering of coordinated up- and down-regulation of two glycosyltransferases of the O-glycosylation pathway in Chinese hamster ovary (CHO) cells. Biotechnol. Bioeng. 68: 239-244.

Previs SF, Hallowell PT, Neimanis KD, David F, Brunengraber H 1998 Limitations of the mass isotopomer distribution analysis of glucose to study gluconeogenesis. Heterogeneity of glucose labeling in incubated hepatocytes. J. Biol. Chem. 273: 16853-16859.

Price J, Laxmi A, St Martin SK, Jang JC 2004 Global transcription profiling reveals multiple sugar signal transduction mechanisms in Arabidopsis. Plant Cell 16: 2128-2150.

Price ND, Papin JA, Palsson BO 2002 Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis. Genome Res. 12: 760-769.

Price ND, Papin JA, Schilling CH, Palsson BO 2003 Genome-scale microbial in silico models: the constraints-based approach. Trends Biotechnol. 21: 162-169.

Price ND, Reed JL, Papin JA, Famili I, Palsson BO 2003 Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices. Biophys. J. 84: 794-804.

Price ND, Reed JL, Papin JA, Wiback SJ, Palsson BO 2003 Network-based analysis of metabolic regulation in the human red blood cell. J. Theor. Biol. 225: 185-194.

Price ND, Schellenberger J, Palsson BO 2004 Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies. Biophys. J. 87: 2172-2186.

Price ND, Thiele I, Palsson BO 2006 Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints. Biophys. J. 90: 3919-3928.

Prieto R, Dubus A, Galvan A, Fernandez E 1996 Isolation and characterization of two new negative regulatory mutants for nitrate assimilation in Chlamydomonas reinhardtii obtained by insertional mutagenesis. Mol. Gen. Genet. 251: 461-471.

Prisic S, Peters RJ 2007 Synergistic substrate inhibition of ent-copalyl diphosphate synthase: a potential feed-forward inhibition mechanism limiting gibberellin metabolism. Plant Physiol. 144: 445-454.

Prisic S, Xu M, Wilderman PR, Peters RJ 2004 Rice contains two disparate ent-copalyl diphosphate synthases with distinct metabolic functions. Plant Physiol. 136: 4228-4236.

Proctor MC, Ligrone R, Duckett JG 2007 Desiccation tolerance in the moss Polytrichum formosum: physiological and fine-structural changes during desiccation and recovery. Ann. Bot. (Lond.) 99: 75-93.

Pross A 2003 The driving force for life's emergence: kinetic and thermodynamic considerations. J. Theor. Biol. 220: 393-406.

Przybyla D, Gobel C, Imboden A, Hamberg M, Feussner I, Apel K 2008 Enzymatic, but not non-enzymatic, 1O2-mediated peroxidation of polyunsaturated fatty acids forms part of the EXECUTER1-dependent stress response program in the flu mutant of Arabidopsis thaliana. Plant J. 54: 236-248.

Pscheidt B, Glieder A 2008 Yeast cell factories for fine chemical and API production. Microb. Cell Fact. 7: 25.

Puccetti C, Aureli T, Manetti C, Conti F 2002 13C-NMR isotopomer distribution analysis: a method for measuring metabolic fluxes in condensation biosynthesis. NMR Biomed. 15: 404-415.

Puglisi JL, Wang F, Bers DM 2004 Modeling the isolated cardiac myocyte. Prog. Biophys. Mol. Biol. 85: 163-178.

Puig S, Andres-Colas N, Garcia-Molina A, Penarrubia L 2007 Copper and iron homeostasis in Arabidopsis: responses to metal deficiencies, interactions and biotechnological applications. Plant Cell Environ. 30: 271-290.

Puigjaner J, Rais B, Burgos M, Comin B, Ovadi J, Cascante M 1997 Comparison of control analysis data using different approaches: modelling and experiments with muscle extract. FEBS Lett. 418: 47-52.

Punekar NS 2000 A simple setup to illustrate metabolic pathway dynamics. Biochem. & Mol. Biol. Education 28: 248-250.

Purcarea C, Evans DR, Herve G 1999 Channeling of carbamoyl phosphate to the pyrimidine and arginine biosynthetic pathways in the deep sea hyperthermophilic archaeon Pyrococcus abyssi. J. Biol. Chem. 274: 6122-6129.

Qi X, Bakht S, Qin B, Leggett M, Hemmings A, Mellon F, Eagles J, Werck-Reichhart D, Schaller H, Lesot A, Melton R, Osbourn A 2006 A different function for a member of an ancient and highly conserved cytochrome P450 family: from essential sterols to plant defense. Proc. Natl. Acad. Sci. U.S.A. 103: 18848-18853.

Qian H, Beard DA 2006 Metabolic futile cycles and their functions: a systems analysis of energy and control. Syst. Biol. (Stevenage) 153: 192-200.

Qiu QS, Hardin SC, Mace J, Brutnell TP, Huber SC 2007 Light and metabolic signals control the selective degradation of sucrose synthase in maize leaves during deetiolation. Plant Physiol. 144: 468-478.

Quant PA 1993 Experimental application of top-down control analysis to metabolic systems. Trends Biochem. Sci. 18: 26-30.

Quesada-Vargas T, Ruiz ON, Daniell H 2005 Characterization of heterologous multigene operons in transgenic chloroplasts. Transcription, processing, and translation. Plant Physiol. 138: 1746-1762.

Quigg A, Beardall J 2003 Protein turnover in relation to maintenance metabolism at low photon flux in two marine microalgae. Plant Cell Environ. 26: 693-703.

Quinlivan EP, Hanson AD, Gregory JF 2006 The analysis of folate and its metabolic precursors in biological samples. Anal. Biochem. 348: 163-184.

Qureshi MI, Qadir S, Zolla L 2007 Proteomics-based dissection of stress-responsive pathways in plants. J. Plant Physiol. 164: 1239-1260.

R Poulsen B, Nohr J, Douthwaite S, Hansen LV, Iversen JJ, Visser J, Ruijter GJ 2005 Increased NADPH concentration obtained by metabolic engineering of the pentose phosphate pathway in Aspergillus niger. FEBS J. 272: 1313-1325.

Raamsdonk LM, Teusink B, Broadhurst D, Zhang N, Hayes A, Walsh MC, Berden JA, Brindle KM, Kell DB, Rowland JJ, Westerhoff HV, van Dam K, Oliver SG 2001 A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations. Nat. Biotechnol. 19: 45-50.

Radajewski S, McDonald IR, Murrell JC 2003 Stable-isotope probing of nucleic acids: a window to the function of uncultured microorganisms. Curr. Opin. Biotechnol. 14: 296-302.

Radchuk R, Radchuk V, Gotz KP, Weichert H, Richter A, Emery RJ, Weschke W, Weber H 2007 Ectopic expression of phosphoenolpyruvate carboxylase in Vicia narbonensis seeds: effects of improved nutrient status on seed maturation and transcriptional regulatory networks. Plant J. 51: 819-839.

Radchuk R, Radchuk V, Weschke W, Borisjuk L, Weber H 2006 Repressing the expression of the SUCROSE NONFERMENTING-1-RELATED PROTEIN KINASE gene in pea embryo causes pleiotropic defects of maturation similar to an abscisic acid-insensitive phenotype. Plant Physiol. 140: 263-278.

Radzio JA, Lorence A, Chevone BI, Nessler CL 2003 L-Gulono-1,4-lactone oxidase expression rescues vitamin C-deficient Arabidopsis (vtc) mutants. Plant Mol. Biol. 53: 837-844.

Rae C, Moussa Cel-H, Griffin JL, Bubb WA, Wallis T, Balcar VJ 2005 Group I and II metabotropic glutamate receptors alter brain cortical metabolic and glutamate/glutamine cycle activity: a 13C NMR spectroscopy and metabolomic study. J. Neurochem. 92: 405-416.

Raghavendra AS, Padmasree K 2003 Beneficial interactions of mitochondrial metabolism with photosynthetic carbon assimilation. Trends Plant Sci. 8: 546-553.

Raghunathan A, Price ND, Galperin MY, Makarova KS, Purvine S, Picone AF, Cherny T, Xie T, Reilly TJ, Munson R Jr, Tyler RE, Akerley BJ, Smith AL, Palsson BO, Kolker E 2004 In silico metabolic model and protein expression of Haemophilus influenzae strain Rd KW20 in rich medium. OMICS 8: 25-41.

Rahman M, Hasan MR, Shimizu K 2008 Growth phase-dependent changes in the expression of global regulatory genes and associated metabolic pathways in Escherichia coli. Biotechnol. Lett. 30: 853-860.

Rai PK, Mallick N, Rai LC 1994 Effect of Cu and Ni on growth, mineral uptake, photosynthesis and enzyme activities of Chlorella vulgaris at different pH values. Biomed. Environ. Sci. 7: 56-67.

Rais B, Chassagnole C, Mazat JP 1995 Control of threonine pathway in E. coli. Application to biotechnologies. Acta Biotheor. 43: 285-297.

Rais B, Mazat JP 1995 Control of the metabolic pathway of threonine in E coli. Application of biotechnology. Acta Biotheor. 43: 143-153.

Raisner RM, Madhani HD 2008 Genome-wide screen for negative regulators of sirtuin activity in S. cerevisiae reveals 40 loci and links to metabolism. Genetics 179: 1933-1944.

Ralley L, Enfissi EM, Misawa N, Schuch W, Bramley PM, Fraser PD 2004 Metabolic engineering of ketocarotenoid formation in higher plants. Plant J. 39: 477-486.

Ralph SG, Yueh H, Friedmann M, Aeschliman D, Zeznik JA, Nelson CC, Butterfield YS, Kirkpatrick R, Liu J, Jones SJ, Marra MA, Douglas CJ, Ritland K, Bohlmann J 2006 Conifer defence against insects: microarray gene expression profiling of Sitka spruce (Picea sitchensis) induced by mechanical wounding or feeding by spruce budworms (Choristoneura occidentalis) or white pine weevils (Pissodes strobi) reveals large… Plant Cell Environ. 29: 1545-1570.

Ralston L, Subramanian S, Matsuno M, Yu O 2005 Partial reconstruction of flavonoid and isoflavonoid biosynthesis in yeast using soybean type I and type II chalcone isomerases. Plant Physiol. 137: 1375-1388.

Ramakrishna R, Edwards JS, McCulloch A, Palsson BO 2001 Flux-balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraints. Am. J. Physiol. Regul. Integr. Comp. Physiol. 280: R695-R704.

Raman K, Rajagopalan P, Chandra N 2005 Flux balance analysis of mycolic acid pathway: targets for anti-tubercular drugs. PLoS Comput. Biol. 1: e46.

Ramli US, Baker DS, Quant PA, Harwood JL 2002 Control analysis of lipid biosynthesis in tissue cultures from oil crops shows that flux control is shared between fatty acid synthesis and lipid assembly. Biochem. J. 364: 393-401.

Ramli US, Baker DS, Quant PA, Harwood JL 2001 Use of control analysis to study the regulation of plant lipid biosynthesis. Biochem. Soc. Trans. 30: 1043-1046.

Ramli US, Salas JJ, Quant PA, Harwood JL 2005 Metabolic control analysis reveals an important role for diacylglycerol acyltransferase in olive but not in oil palm lipid accumulation. FEBS J. 272: 5764-5770.

Ramos I, Downs DM 2003 Anthranilate synthase can generate sufficient phosphoribosyl amine for thiamine synthesis in Salmonella enterica. J. Bacteriol. 185: 5125-5132.

Ramos I, Vivas EI, Downs DM 2008 Mutations in the tryptophan operon allow PurF-independent thiamine synthesis by altering flux in vivo. J. Bacteriol. 190: 815-822.

Ramos RLB, Tovar FJ, Junqueira RM, Lino FB, Sachetto-Martins G 2001 Sugarcane expressed sequences tags (ESTs) encoding enzymes involved in lignin biosynthesis pathways. Genet. Mol. Biol. 24: 235-241.

Ramsay RR, Naismith JH 2003 A snapshot of carnitine acetyltransferase. Trends Biochem. Sci. 28: 343-346.

Rantalainen M, Cloarec O, Ebbels TM, Lundstedt T, Nicholson JK, Holmes E, Trygg J 2008 Piecewise multivariate modelling of sequential metabolic profiling data. BMC Bioinformatics 9: 105.

Rantanen A, Mielikainen T, Rousu J, Maaheimo H, Ukkonen E 2006 Planning optimal measurements of isotopomer distributions for estimation of metabolic fluxes. Bioinformatics 22: 1198-1206.

Rantanen A, Rousu J, Kokkonen JT, Tarkiainen V, Ketola RA 2002 Computing positional isotopomer distributions from tandem mass spectrometric data. Metab. Eng. 4: 285-294.

Rapheal SV, Swaminathan KR, Lalitha K 2003 Metabolic characteristics of an aerobe isolated from a methylotrophic methanogenic enrichment culture. J. Biosci. 28: 235-242.

Raschle T, Amrhein N, Fitzpatrick TB 2005 On the two components of pyridoxal 5'-phosphate synthase from Bacillus subtilis. J. Biol. Chem. 280: 32291-32300.

Raskin I, Turner IM, Melander WR 1989 Regulation of heat production in the inflorescences of an Arum lily by endogenous salicylic acid. Proc. Natl. Acad. Sci. U.S.A. 86: 2214-2218.

Rasmussen S, Dixon RA 1999 Transgene-mediated and elicitor-induced perturbation of metabolic channeling at the entry point into the phenylpropanoid pathway. Plant Cell 11: 1537-1552.

Ratcliffe RG, Shachar-Hill Y 2001 Probing plant metabolism with NMR. Annu. Rev. Plant Physiol. Plant Mol. Biol. 52: 499-526.

Ratcliffe RG, Shachar-Hill Y 2006 Measuring multiple fluxes through plant metabolic networks. Plant J. 45: 490-511.

Ratcliffe RG, Shachar-Hill Y 2005 Revealing metabolic phenotypes in plants: inputs from NMR analysis. Biol. Rev. Camb. Philos. Soc. 80: 27-43.

Rathinasabapathi B 2000 Metabolic engineering for stress tolerance: Installing osmoprotectant synthesis pathways. Ann. Bot. (Lond.) 86: 709-716.

Rathinasabapathi B, Fouad WM, Sigua CA 2001 beta-Alanine betaine synthesis in the Plumbaginaceae. Purification and characterization of a trifunctional, S-adenosyl-L-methionine-dependent N-methyltransferase from Limonium latifolium leaves. Plant Physiol. 126: 1241-1249.

Rathinasabapathi B, McCue KF, Gage DA, Hanson AD 1994 Metabolic engineering of glycine betaine synthesis: plant betaine aldehyde dehydrogenases lacking typical transit peptides are targeted to tobacco chloroplasts where they confer betaine aldehyde resistance. Planta 193: 155-162.

Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabasi AL 2002 Hierarchical organization of modularity in metabolic networks. Science 297: 1551-1555.

Raymond J, Segre D 2006 The effect of oxygen on biochemical networks and the evolution of complex life. Science 311: 1764-1767.

Raynaud S, Perrin R, Cocaign-Bousquet M, Loubiere P 2005 Metabolic and transcriptomic adaptation of Lactococcus lactis subsp. lactis Biovar diacetylactis in response to autoacidification and temperature downshift in skim milk. Appl. Environ. Microbiol. 71: 8016-8023.

Reddy VN, Mavrovouniotis ML, Liebman MN 1993 Petri net representations in metabolic pathways. Ismb 1: 328-336.

Reder C 1988 Metabolic control theory: a structural approach. J. Theor. Biol. 135: 175-201.

Redig P, Schmulling T, Van Onckelen H 1996 Analysis of cytokinin metabolism in ipt transgenic tobacco by liquid chromatography-tandem mass spectrometry. Plant Physiol. 112: 141-148.

Reed JL, Patel TR, Chen KH, Joyce AR, Applebee MK, Herring CD, Bui OT, Knight EM, Fong SS, Palsson BO 2006 Systems approach to refining genome annotation. Proc. Natl. Acad. Sci. U.S.A. 103: 17480-17484.

Reeves AR, Cernota WH, Brikun IA, Wesley RK, Mark Weber J 2004 Engineering precursor flow for increased erythromycin production in Aeromicrobium erythreum. Metab. Eng. 6: 300-312.

Regan L, Gregory M 1995 Flux analysis of microbial metabolic pathways using a visual programming environment. J. Biotechnol. 42: 151-161.

Reich JG, Sel'kov EE 1975 Time hierarchy, equilibrium and non-equilibrium in metabolic systems. Biosystems 7: 39-50.

Reid RJ, Hayes JE, Post A, Stangoulis JCR, Graham RD 2004 A critical analysis of the causes of boron toxicity in plants. Plant Cell Environ. 27: 1405-1414.

Reijenga KA, Westerhoff HV, Kholodenko BN, Snoep JL 2002 Control analysis for autonomously oscillating biochemical networks. Biophys. J. 82: 99-108.

Reiter WD 2008 Biochemical genetics of nucleotide sugar interconversion reactions. Curr. Opin. Plant Biol. 11: 236-243.

Reiter WD, Vanzin GF 2001 Molecular genetics of nucleotide sugar interconversion pathways in plants. Plant Mol. Biol. 47: 95-113.

Reitzer L 2003 Nitrogen assimilation and global regulation in Escherichia coli. Annu. Rev. Microbiol. 57: 155-176.

Rennenberg H, Loreto F, Polle A, Brilli F, Fares S, Beniwal RS, Gessler A 2006 Physiological responses of forest trees to heat and drought. Plant Biol. (Stuttg.) 8: 556-571.

Reumann S 2000 The structural properties of plant peroxisomes and their metabolic significance. Biol. Chem. 381: 639-648.

Reumann S, Ma C, Lemke S, Babujee L 2004 AraPerox. A database of putative Arabidopsis proteins from plant peroxisomes. Plant Physiol. 136: 2587-2608.

Reumann S, Weber AP 2006 Plant peroxisomes respire in the light: some gaps of the photorespiratory C2 cycle have become filled - others remain. Biochim. Biophys. Acta 1763: 1496-1510.

Reyes JC, Florencio FJ 1994 A mutant lacking the glutamine synthetase gene (glnA) is impaired in the regulation of the nitrate assimilation system in the cyanobacterium Synechocystis sp. strain PCC 6803. J. Bacteriol. 176: 7516-7523.

Rhee SG, Park SC, Koo JH 1985 The role of adenylyltransferase and uridylyltransferase in the regulation of glutamine synthetase in Escherichia coli. Curr. Top. Cell Regul. 27: 221-232.

Rhodes D, Handa S, Bressan RA 1986 Metabolic changes associated with adaptation of plant cells to water stress. Plant Physiol. 82: 890-903.

Rhodes D, McNeil SD, Nuccio ML, Hanson AD 2004 Metabolic engineering and flux analysis of glycine betaine synthesis in plants: progress and prospects. In (BN Kholodenko, HV Westerhoff, eds.) "Metabolic Engineering in the Post Genomic Era", Horizon Bioscience, Wymondham, Norfolk, U.K., pp. 409-434.

Rhodes D, Peel GJ, Dudareva N 2004 Metabolism, secondary: engineering pathways of. In (RM Goodman, ed) Encyclopedia of Plant and Crop Science, Marcell Dekker, N.Y., pp. 720-723.

Riano-Pachon DM, Ruzicic S, Dreyer I, Mueller-Roeber B 2007 PlnTFDB: an integrative plant transcription factor database. BMC Bioinformatics 8: 42.

Ribarits A, Mamun AN, Li S, Resch T, Fiers M, Heberle-Bors E, Liu CM, Touraev A 2007 Combination of reversible male sterility and doubled haploid production by targeted inactivation of cytoplasmic glutamine synthetase in developing anthers and pollen. Plant Biotechnol. J. 5: 483-494.

Rider SD Jr, Hemm MR, Hostetler HA, Li HC, Chapple C, Ogas J 2004 Metabolic profiling of the Arabidopsis pkl mutant reveals selective derepression of embryonic traits. Planta 219: 489-499.

Ridley CP, Lee HY, Khosla C 2008 Evolution of polyketide synthases in bacteria. Proc. Natl. Acad. Sci. U.S.A. 105: 4595-4600.

Rijhwani SK, Ho CH, Shanks JV 1999 In vivo 31P and multilabel 13C NMR measurements for evaluation of plant metabolic pathways. Metab. Eng. 1: 12-25.

Riley M, Staley JT, Danchin A, Wang TZ, Brettin TS, Hauser LJ, Land ML, Thompson LS 2008 Genomics of an extreme psychrophile, Psychromonas ingrahamii. BMC Genomics 9: 210.

Rimmele M, Boos W 1994 Trehalose-6-phosphate hydrolase of Escherichia coli. J. Bacteriol. 176: 5654-5664.

Ringemann C, Ebenhoh O, Heinrich R, Ginsburg H 2006 Can biochemical properties serve as selective pressure for gene selection during inter-species and endosymbiotic lateral gene transfer? Syst. Biol. (Stevenage) 153: 212-222.

Ringenberg M, Lichtensteiger C, Vimr E 2001 Redirection of sialic acid metabolism in genetically engineered Escherichia coli. Glycobiology 11: 533-539.

Rios-Estepa R, Turner GW, Lee JM, Croteau RB, Lange BM 2008 A systems biology approach identifies the biochemical mechanisms regulating monoterpenoid essential oil composition in peppermint. Proc. Natl. Acad. Sci. U.S.A. 105: 2818-2823.

Ripley BS, Gilbert ME, Ibrahim DG, Osborne CP 2007 Drought constraints on C4 photosynthesis: stomatal and metabolic limitations in C3 and C4 subspecies of Alloteropsis semialata. J. Exp. Bot. 58: 1351-1363.

Rischer H, Oresic M, Seppanen-Laakso T, Katajamaa M, Lammertyn F, Ardiles-Diaz W, Van Montagu MC, Inze D, Oksman-Caldentey KM, Goossens A 2006 Gene-to-metabolite networks for terpenoid indole alkaloid biosynthesis in Catharanthus roseus cells. Proc. Natl. Acad. Sci. U.S.A. 103: 5614-5619.

Rius SP, Casati P, Iglesias AA, Gomez-Casati DF 2006 Characterization of an Arabidopsis thaliana mutant lacking a cytosolic non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase. Plant Mol. Biol. 61: 945-957.

Rivett AJ, Roseman JE, Oliver CN, Levine RL, Stadtman ER 1985 Covalent modification of proteins by mixed-function oxidation: recognition by intracellular proteases. Prog. Clin. Biol. Res. 180: 317-328.

Rivoal J, Hanson AD 1994 Metabolic control of anaerobic glycolysis. Overexpression of lactate dehydrogenase in transgenic tomato roots supports the Davies-Roberts hypothesis and points to a critical role for lactate secretion. Plant Physiol. 106: 1179-1185.

Rizzi M, Baltes M, Theobald U, Reuss M 1997 In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae. 2. Mathematical model. Biotechnol. Bioeng. 55: 592-608.

Robbins MP, Morris P 2000 Chapter 8. Metabolic Engineering of Condensed Tannins and Other Phenolic Pathways in Forage and Fodder Crops. In "Metabolic Engineering of Plant Secondary Metabolism" (Verpoorte R, Alfermann AW, eds), Kluwer Academic Publishers, Dortrecht, The Netherlands, pp. 165-177.

Robert L 1999 Management of time by the cell and by the organism. J. Soc. Biol. 193: 401-410.

Roberts JK, Hooks MA, Miaullis AP, Edwards S, Webster C 1992 Contribution of malate and amino acid metabolism to cytoplasmic pH regulation in hypoxic maize root tips studied using nuclear magnetic resonance spectroscopy. Plant Physiol. 98: 480-487.

Roberts JKM 2000 NMR adventures in the metabolic labyrinth within plants. Trends Plant Sci. 5: 30-34.

Roberts K, Granum E, Leegood RC, Raven JA 2007 C3 and C4 pathways of photosynthetic carbon assimilation in marine diatoms are under genetic, not environmental, control. Plant Physiol. 145: 230-235.

Robinson AR, Gheneim R, Kozak RA, Ellis DD, Mansfield SD 2005 The potential of metabolite profiling as a selection tool for genotype discrimination in Populus. J. Exp. Bot. 56: 2807-2819.

Roby C, Martin JB, Bligny R, Douce R 1987 Biochemical changes during sucrose deprivation in higher plant cells. Phosphorus-31 nuclear magnetic resonance studies. J. Biol. Chem. 262: 5000-5007.

Roca M, James C, Pruzinska A, Hortensteiner S, Thomas H, Ougham H 2004 Analysis of the chlorophyll catabolism pathway in leaves of an introgression senescence mutant of Lolium temulentum. Phytochemistry 65: 1231-1238.

Roche J, Hewezi T, Bouniols A, Gentzbittel L 2007 Transcriptional profiles of primary metabolism and signal transduction-related genes in response to water stress in field-grown sunflower genotypes using a thematic cDNA microarray. Planta 226: 601-617.

Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS 2004 Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems. Nucleic Acids Res. 32: 3340-3353.

Rodriguez J, Kleerebezem R, Lema JM, van Loosdrecht MC 2006 Modeling product formation in anaerobic mixed culture fermentations. Biotechnol. Bioeng. 93: 592-606.

Rodriguez-Caso C, Montanez R, Cascante M, Sanchez-Jimenez F, Medina MA 2006 Mathematical modeling of polyamine metabolism in mammals. J. Biol. Chem. 281: 21799-21812.

Roenneberg T, Merrow M 1999 Circadian systems and metabolism. J. Biol. Rhythms 14: 449-459.

Roessner U, Luedemann A, Brust D, Fiehn O, Linke T, Willmitzer L, Fernie A 2001 Metabolic profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems. Plant Cell 13: 11-29.

Roessner U, Patterson JH, Forbes MG, Fincher GB, Langridge P, Bacic A 2006 An investigation of boron toxicity in barley using metabolomics. Plant Physiol. 142: 1087-1101.

Roessner U, Willmitzer L, Fernie AR 2001 High-resolution metabolic phenotyping of genetically and environmentally diverse potato tuber systems. Identification of phenocopies. Plant Physiol. 127: 749-764.

Roessner-Tunali U, Liu J, Leisse A, Balbo I, Perez-Melis A, Willmitzer L, Fernie AR 2004 Kinetics of labelling of organic and amino acids in potato tubers by gas chromatography-mass spectrometry following incubation in C labelled isotopes. Plant J. 39: 668-679.

Rognes SE, Lea PJ, Miflin BJ 1980 S-Adenosylmethionine - a novel regulator of aspartate kinase. Nature 287: 357-359.

Rohwer JM, Botha FC 2001 Analysis of sucrose accumulation in the sugar cane culm on the basis of in vitro kinetic data. Biochem. J. 358: 437-445.

Rohwer JM, Postma PW, Kholodenko BN, Westerhoff HV 1998 Implications of macromolecular crowding for signal transduction and metabolite channeling. Proc. Natl. Acad. Sci. U.S.A. 95: 10547-10552.

Rohwer JM, Schuster S, Westerhoff HV 1996 How to recognize monofunctional units in a metabolic system. J. Theor. Biol. 179: 213-328.

Roitsch T, Balibrea ME, Hofmann M, Proels R, Sinha AK 2003 Extracellular invertase: key metabolic enzyme and PR protein. J. Exp. Bot. 54: 513-524.

Roitsch T, Bittner M, Godt DE 1995 Induction of apoplastic invertase of Chenopodium rubrum by D-glucose and a glucose analog and tissue-specific expression suggest a role in sink-source regulation. Plant Physiol. 108: 285-294.

Roitsch T, Gonzalez MC 2004 Function and regulation of plant invertases: sweet sensations. Trends Plant Sci. 9: 606-613.

Rokhlenko O, Shlomi T, Sharan R, Ruppin E, Pinter RY 2007 Constraint-based functional similarity of metabolic genes: going beyond network topology. Bioinformatics 23: 2139-2146.

Rommens CM, Yan H, Swords K, Richael C, Ye J 2008 Low-acrylamide French fries and potato chips. Plant Biotechnol. J. Jul 23 [Epub ahead of print].

Rontein D, Basset G, Hanson AD 2002 Metabolic engineering of osmoprotectant accumulation in plants. Metab. Eng. 4: 49-56.

Rontein D, Rhodes D, Hanson AD 2003 Evidence from engineering that decarboxylation of free serine is the major source of ethanolamine moieties in plants. Plant Cell Physiol. 44: 1185-1191.

Rosati C, Aquilani R, Dharmapuri S, Pallara P, Marusic C, Tavazza R, Bouvier F, Camara B, Giuliano G 2000 Metabolic engineering of beta-carotene and lycopene content in tomato fruit. Plant J. 24: 413-420.

Roscher A, Kruger NJ, Ratcliffe RG 2000 Strategies for metabolic flux analysis in plants using isotope labelling. J. Biotechnol. 77: 81-102.

Roseman JE, Levine RL 1987 Purification of a protease from Escherichia coli with specificity for oxidized glutamine synthetase. J. Biol. Chem. 262: 2101-2110.

Rosnoblet C, Aubry C, Leprince O, Vu BL, Rogniaux H, Buitink J 2007 The regulatory gamma subunit SNF4b of the sucrose non-fermenting-related kinase complex is involved in longevity and stachyose accumulation during maturation of Medicago truncatula seeds. Plant J. 51: 47-59.

Ross BM, Moszczynska A, Erlich J, Kish SJ 1998 Phospholipid-metabolizing enzymes in Alzheimer's disease: increased lysophospholipid acyltransferase activity and decreased phospholipase A2 activity. J. Neurochem. 70: 786-793.

Rossard S, Luini E, Perault JM, Bonmort J, Roblin G 2006 Early changes in membrane permeability, production of oxidative burst and modification of PAL activity induced by ergosterol in cotyledons of Mimosa pudica. J. Exp. Bot. 57: 1245-1252.

Rossell S, van der Weijden CC, Kruckeberg A, Bakker BM, Westerhoff HV 2002 Loss of fermentative capacity in baker's yeast can partly be explained by reduced glucose uptake capacity. Mol. Biol. Rep. 29: 255-257.

Rossell S, van der Weijden CC, Lindenbergh A, van Tuijl A, Francke C, Bakker BM, Westerhoff HV 2006 Unraveling the complexity of flux regulation: a new method demonstrated for nutrient starvation in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A. 103: 2166-2171.

Rossini L, Bernardi M, Concettoni C, De Florio L, Deslauriers R, Moretti V, Piantelli F, Pigini P, Re L, Rossini P, et al 1994 Some approaches to the pharmacology of multisubstrate enzyme systems. Pharmacol. Res. 29: 313-335.

Rost U, Kummer U 2004 Visualisation of biochemical network simulations with SimWiz. Syst. Biol. 1: 184-189.

Roth U, von Roepenack-Lahaye E, Clemens S 2006 Proteome changes in Arabidopsis thaliana roots upon exposure to Cd2+. J. Exp. Bot. 57: 4003-4013.

Rother M, Krauss GJ, Grass G, Wesenberg D 2006 Sulphate assimilation under Cd stress in Physcomitrella patens - combined transcript, enzyme and metabolite profiling. Plant Cell Environ. 29: 1801-1811.

Rotoli BM, Uggeri J, Dall'Asta V, Visigalli R, Barilli A, Gatti R, Orlandini G, Gazzola GC, Bussolati O 2005 Inhibition of glutamine synthetase triggers apoptosis in asparaginase-resistant cells. Cell. Physiol. Biochem. 15: 281-292.

Rotter A, Usadel B, Baebler S, Stitt M, Gruden K 2007 Adaptation of the MapMan ontology to biotic stress responses: application in solanaceous species. Plant Methods 3: 10.

Routaboul JM, Kerhoas L, Debeaujon I, Pourcel L, Caboche M, Einhorn J, Lepiniec L 2006 Flavonoid diversity and biosynthesis in seed of Arabidopsis thaliana. Planta 224: 96-107.

Roy A, Parker RS 2006 Dynamic modeling of free fatty acid, glucose, and insulin: an extended "minimal model". Diabetes Technol. Ther. 8: 617-626.

Rozwadowski KL, Khachatourians GG, Selvaraj G 1991 Choline oxidase, a catabolic enzyme in Arthrobacter pascens, facilitates adaptation to osmotic stress in Escherichia coli. J. Bacteriol. 173: 472-478.

Rubio V, Bustos R, Irigoyen ML, Cardona-Lopez X, Rojas-Triana M, Paz-Ares J 2008 Plant hormones and nutrient signaling. Plant Mol. Biol. Aug 9 [Epub ahead of print].

Rud I, Solem C, Jensen PR, Axelsson L, Naterstad K 2008 Co-factor engineering in lactobacilli: effects of uncoupled ATPase activity on metabolic fluxes in Lactobacillus (L.) plantarum and L. sakei. Metab. Eng. Jun 5 [Epub ahead of print].

Rudolph MC, McManaman J, Phang T, Russell T, Kominsky DJ, Serkova NJ, Stein T, Anderson SM, Neville MC 2007 Metabolic regulation in the lactating mammary gland: a lipid synthesizing machine. Physiol. Genomics 28: 323-336.

Ruelland E, Miginiac-Maslow M 1999 Regulation of chloroplast enzyme activities by thioredoxins: activation or relief from inhibition? Trends Plant Sci. 4: 136-141.

Runquist M, Kruger NJ 1999 Control of gluconeogenesis by isocitrate lyase in endosperm of germinating castor bean seedlings. Plant J. 19: 423-431.

Ryde-Pettersson U 1992 Oscillations in coupled enzymatic reactions at high concentration of enzyme. Biochim. Biophys. Acta 1119: 118-122.

Ryde-Pettersson U 1991 Identification of possible two-reactant sources of oscillations in the Calvin photosynthesis cycle and ancillary pathways. Eur. J. Biochem. 198: 613-619.

Ryde-Pettersson U 1990 On the mechanistic origin of damped oscillations in biochemical reaction systems. Eur. J. Biochem. 194: 431-436.

Ryu DD, Nam DH 2000 Recent progress in biomolecular engineering. Biotechnol. Prog. 16: 2-16.

Rzhetsky A, Gomez SM 2001 Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome. Bioinformatics 17: 988-996.

Sabina RL, Paul AL, Ferl RJ, Laber B, Lindell SD 2007 Adenine nucleotide pool perturbation is a metabolic trigger for AMP deaminase inhibitor-based herbicide toxicity. Plant Physiol. 143: 1752-1760.

Sabra W, Zeng A-P, Sabry S, Omar S, Deckwer W-D 1999 Effect of phosphate and oxygen concentrations on alginate production and stoichiometry of metabolism of Azotobacter vinelandiiunder microaerobic conditions. Appl. Microbiol. Biotechnol. 52: 773-780.

Saenz DA, Goldin AP, Minces L, Chianelli M, Sarmiento MI, Rosenstein RE 2004 Effect of melatonin on the retinal glutamate/glutamine cycle in the golden hamster retina. FASEB J. 18: 1912-1913.

Saerens SM, Verstrepen KJ, Van Laere SD, Voet AR, Van Dijck P, Delvaux FR, Thevelein JM 2006 The Saccharomyces cerevisiae EHT1 and EEB1 genes encode novel enzymes with medium-chain fatty acid ethyl ester synthesis and hydrolysis capacity. J. Biol. Chem. 281: 4446-4456.

Sagae M, Oyama-Okubo N, Ando T, Marchesi E, Nakayama M 2008 Effect of temperature on the floral scent emission and endogenous volatile profile of Petunia axillaris. Biosci. Biotechnol. Biochem. 72: 110-115.

Sage RF, McKown AD 2006 Is C4 photosynthesis less phenotypically plastic than C3 photosynthesis? J. Exp. Bot. 57: 303-317.

Saha SK, Uma L, Subramanian G 2003 Nitrogen stress induced changes in the marine cyanobacterium Oscillatoria willei BDU 130511. FEMS Microbiol. Ecol. 45: 263-272.

Sahle S, Mendes P, Hoops S, Kummer U 2008 A new strategy for assessing sensitivities in biochemical models. Philos. Transact. A. Math. Phys. Eng. Sci. Jul 16 [Epub ahead of print].

Sahm H, Eggeling L, de Graaf AA 2000 Pathway analysis and metabolic engineering in Corynebacterium glutamicum. Biol. Chem. 381: 899-910.

Sahr T, Ravanel S, Basset G, Nichols BP, Hanson AD, Rebeille F 2006 Folate synthesis in plants: purification, kinetic properties, and inhibition of aminodeoxychorismate synthase. Biochem. J. 396: 157-162.

Saigo M, Bologna FP, Maurino VG, Detarsio E, Andreo CS, Drincovich MF 2004 Maize recombinant non-C4 NADP-malic enzyme: a novel dimeric malic enzyme with high specific activity. Plant Mol. Biol. 55: 97-107.

Sakamoto A, Murata N 2000 Genetic engineering of glycinebetaine synthesis in plants: current status and implications for enhancement of stress tolerance. J. Exp. Bot. 51: 81-88.

Sakamoto N 1987 A transfer-function representation for regulatory responses of a controlled metabolic pathway. Biosystems 20: 317-327.

Saks V, Dos Santos P, Gellerich FN, Diolez P 1998 Quantitative studies of enzyme-substrate compartmentation, functional coupling and metabolic channelling in muscle cells. Mol. Cell Biochem. 184: 291-307.

Saks VA, Ventura-Clapier R, Aliev MK 1996 Metabolic control and metabolic capacity: two aspects of creatine kinase functioning in the cells. Biochim. Biophys. Acta 1274: 81-88.

Saleet Jafri M, Kotulska M 2006 Modeling the mechanism of metabolic oscillations in ischemic cardiac myocytes. J. Theor. Biol. 242: 801-817.

Salmona J, Dussert S, Descroix F, de Kochko A, Bertrand B, Joet T 2008 Deciphering transcriptional networks that govern Coffea arabica seed development using combined cDNA array and real-time RT-PCR approaches. Plant Mol. Biol. 66: 105-124.

Saltveit ME, Choi YJ, Tomas-Barberan FA 2005 Involvement of components of the phospholipid-signaling pathway in wound-induced phenylpropanoid metabolism in lettuce (Lactuca sativa) leaf tissue. Physiol. Plant. 125: 345-355.

Salusjarvi L, Kankainen M, Soliymani R, Pitkanen JP, Penttila M, Ruohonen L 2008 Regulation of xylose metabolism in recombinant Saccharomyces cerevisiae. Microb. Cell Fact. 7: 18.

Salvador A 2000 Synergism analysis of biochemical systems. II. Tensor formulation and treatment of stoichiometric constraints. Math. Biosci. 163: 131-158.

Salvador A 2000 Synergism analysis of biochemical systems. I. Conceptual framework. Math. Biosci. 163: 105-129.

Samal A, Singh S, Giri V, Krishna S, Raghuram N, Jain S 2006 Low degree metabolites explain essential reactions and enhance modularity in biological networks. BMC Bioinformatics 7: 118.

Samanani N, Liscombe DK, Facchini PJ 2004 Molecular cloning and characterization of norcoclaurine synthase, an enzyme catalyzing the first committed step in benzylisoquinoline alkaloid biosynthesis. Plant J. 40: 302-313.

San KY, Bennett GN, Berrios-Rivera SJ, Vadali RV, Yang YT, Horton E, Rudolph FB, Sariyar B, Blackwood K 2002 Metabolic engineering through cofactor manipulation and its effects on metabolic flux redistribution in Escherichia coli. Metab. Eng. 4: 182-192.

Sanchez AM, Bennett GN, San KY 2006 Batch culture characterization and metabolic flux analysis of succinate-producing Escherichia coli strains. Metab. Eng. 8: 209-226.

Sanchez AM, Bennett GN, San KY 2005 Novel pathway engineering design of the anaerobic central metabolic pathway in Escherichia coli to increase succinate yield and productivity. Metab. Eng. 7: 229-239.

Sanchez DH, Lippold F, Redestig H, Hannah MA, Erban A, Kramer U, Kopka J, Udvardi MK 2008 Integrative functional genomics of salt acclimatization in the model legume Lotus japonicus. Plant J. 53: 973-987.

Sanchez DH, Siahpoosh MR, Roessner U, Udvardi M, Kopka J 2008 Plant metabolomics reveals conserved and divergent metabolic responses to salinity. Physiol. Plant. 132: 209-219.

Sandermann H 2006 Plant biotechnology: ecological case studies on herbicide resistance. Trends Plant Sci. 11: 324-328.

Sandhu JS, Fraser DR 1981 The metabolic origin of trigonelline in the rat. Biochem. J. 200: 495-500.

Sandmann G, Romer S, Fraser PD 2006 Understanding carotenoid metabolism as a necessity for genetic engineering of crop plants. Metab. Eng. 8: 291-302.

Sanguinetti G, Noirel J, Wright PC 2008 MMG: a probabilistic tool to identify submodules of metabolic pathways. Bioinformatics 24: 1078-1084.

Santos-Mendoza M, Dubreucq B, Baud S, Parcy F, Caboche M, Lepiniec L 2008 Deciphering gene regulatory networks that control seed development and maturation in Arabidopsis. Plant J. 54: 608-520.

Santucci DM, Haas B, Smarrelli J Jr 1995 Regulation of the inducible soybean nitrate reductase isoform in mutants lacking constitutive isoform(s). Biochim. Biophys. Acta 1247: 46-50.

Sariyar B, Perk S, Akman U, Hortacsu A 2006 Monte Carlo sampling and principal component analysis of flux distributions yield topological and modular information on metabolic networks. J. Theor. Biol. 242: 389-400.

Sariyar-Akbulut B, Salman-Dilgimen A, Ceylan S, Perk S, Denizci AA, Kazan D 2008 Preliminary phenotypic characterization of newly isolated halophilic microorganisms by footprinting: a rapid metabolome analysis. Arch. Microbiol. 189: 19-26.

Sarup A, Larsson OM, Schousboe A 2003 GABA transporters and GABA-transaminase as drug targets. Curr. Drug Target CNS Neurol. Disord. 2: 269-277.

Sasaki K, Hiraga S, Ito H, Seo S, Matsui H, Ohashi Y 2002 A wound-inducible tobacco peroxidase gene expresses preferentially in the vascular system. Plant Cell Physiol. 43: 108-117.

Sasaki-Sekimoto Y, Taki N, Obayashi T, Aono M, Matsumoto F, Sakurai N, Suzuki H, Hirai MY, Noji M, Saito K, Masuda T, Takamiya K, Shibata D, Ohta H 2005 Coordinated activation of metabolic pathways for antioxidants and defence compounds by jasmonates and their roles in stress tolerance in Arabidopsis. Plant J. 44: 653-668.

Sauer N 2007 Molecular physiology of higher plant sucrose transporters. FEBS Lett. 581: 2309-2317.

Sauer U 2004 High-throughput phenomics: experimental methods for mapping fluxomes. Curr. Opin. Biotechnol. 15: 58-63.

Sauer U 2001 Evolutionary engineering of industrially important microbial phenotypes. Adv. Biochem. Eng. Biotechnol. 73: 129-169.

Sauer U 2006 Metabolic networks in motion: 13C-based flux analysis. Mol. Syst. Biol. 2: 62.

Sauer U, Hatzimanikatis V, Bailey JE, Hochuli M, Szyperski T, Wuthrich K 1997 Metabolic fluxes in riboflavin-producing Bacillus subtilis. Nat. Biotechnol. 15: 448-452.

Sauer U, Lasko DR, Fiaux J, Hochuli M, Glaser R, Szyperski T, Wuthrich K, Bailey JE 1999 Metabolic flux ratio analysis of genetic and environmental modulations of Escherichia coli central carbon metabolism. J. Bacteriol. 181: 6679-6688.

Sauer U, Schlattner U 2004 Inverse metabolic engineering with phosphagen kinase systems improves the cellular energy state. Metab. Eng. 6: 220-228.

Saul ZM, Filkov V 2007 Exploring biological network structure using exponential random graph models. Bioinformatics 23: 2604-2611.

Sauret-Gueto S, Botella-Pavia P, Flores-Perez U, Martinez-Garcia JF, San Roman C, Leon P, Boronat A, Rodriguez-Concepcion M 2006 Plastid cues posttranscriptionally regulate the accumulation of key enzymes of the methylerythritol phosphate pathway in Arabidopsis. Plant Physiol. 141: 75-84.

Sauro HM 1993 SCAMP: a general-purpose simulator and metabolic control analysis program. Comput. Appl. Biosci. 9: 441-450.

Sauro HM 1994 Moiety-conserved cycles and metabolic control analysis: problems in sequestration and metabolic channelling. Biosystems 33: 55-67.

Sauro HM, Small JR, Fell DA 1987 Metabolic control and its analysis. Extensions to the theory and matrix method. Eur. J. Biochem. 165: 215-221.

Sauter M, Cornell KA, Beszteri S, Rzewuski G 2004 Functional analysis of methylthioribose kinase genes in plants. Plant Physiol. 136: 4061-4071.

Savinell JM, Palsson BO 1992 Network analysis of intermediary metabolism using linear optimization. I. Development of mathematical formalism. J. Theor. Biol. 154: 421-454.

Scaraffia PY, Zhang Q, Wysocki VH, Isoe J, Wells MA 2006 Analysis of whole body ammonia metabolism in Aedes aegypti using [(15)N]-labeled compounds and mass spectrometry. Insect Biochem. Mol. Biol. 36: 614-622.

Schaff JE, Mbeunkui F, Blackburn K, Bird DM, Goshe MB 2008 SILIP: a novel stable isotope labeling method for in planta quantitative proteomic analysis. Plant J. Jul 28 [Epub ahead of print].

Scharte J, SchonH, Weis E 2005 Photosynthesis and carbohydrate metabolism in tobacco leaves during an incompatible interaction with Phytophthora nicotianae. Plant Cell Environ. 28: 1421-1435.

Schatz G 2007 The magic garden. Annu. Rev. Biochem. 76: 673-678.

Schauer N, Zamir D, Fernie AR 2005 Metabolic profiling of leaves and fruit of wild species tomato: a survey of the Solanum lycopersicum complex. J. Exp. Bot. 56: 297-307.

Scheibe R 2004 Malate valves to balance cellular energy supply. Physiol. Plant. 120: 21-26.

Scheibe R, Backhausen JE, Emmerlich V, Holtgrefe S 2005 Strategies to maintain redox homeostasis during photosynthesis under changing conditions. J. Exp. Bot. 56: 1481-1489.

Schijlen EG, Ric de Vos CH, van Tunen AJ, Bovy AG 2004 Modification of flavonoid biosynthesis in crop plants. Phytochemistry 65: 2631-2648.

Schilling CH, Covert MW, Famili I, Church GM, Edwards JS, Palsson BO 2002 Genome-scale metabolic model of Helicobacter pylori 26695. J. Bacteriol. 184: 4582-4593.

Schilling CH, Edwards JS, Letscher D, Palsson BO 2000 Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems. Biotechnol. Bioeng. 71: 286-306.

Schilling CH, Edwards JS, Palsson BO 1999 Toward metabolic phenomics: analysis of genomic data using flux balances. Biotechnol. Prog. 15: 288-295.

Schilling CH, Letscher D, Palsson BO 2000 Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. J. Theor. Biol. 203: 229-248.

Schilling CH, Palsson BO 2000 Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis. J. Theor. Biol. 203: 249-283.

Schilling CH, Schuster S, Palsson BO, Heinrich R 1999 Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic Era. Biotechnol. Prog. 15: 296-303.

Schilmiller AL, Last RL, Pichersky E 2008 Harnessing plant trichome biochemistry for the production of useful compounds. Plant J. 54: 702-711.

Schinnerl J, Brem B, But PP, Vajrodaya S, Hofer O, Greger H 2007 Pyrrolo- and pyridoazepine alkaloids as chemical markers in Stemona species. Phytochemistry 68: 1417-1427.

Schlosser PM, Bailey JE 1990 An integrated modeling-experimental strategy for the analysis of metabolic pathways. Math. Biosci. 100: 87-114.

Schluter U, Kopke D, Altmann T, Mussig C 2002 Analysis of carbohydrate metabolism of CPD antisense plants and the brassinosteroid-deficient cbb1 mutant. Plant Cell Environ. 25: 783-791.

Schmelz EA, Engelberth J, Tumlinson JH, Block A, Alborn HT 2004 The use of vapor phase extraction in metabolic profiling of phytohormones and other metabolites. Plant J. 39: 790-808.

Schmelz EA, LeClere S, Carroll MJ, Alborn HT, Teal PE 2007 Cowpea chloroplastic ATP synthase is the source of multiple plant defense elicitors during insect herbivory. Plant Physiol. 144: 793-805.

Schmid JW, Mauch K, Reuss M, Gilles ED, Kremling A 2004 Metabolic design based on a coupled gene expression-metabolic network model of tryptophan production in Escherichia coli. Metab. Eng. 6: 364-377.

Schmidt B, Joussen N, Bode M, Schuphan I 2006 Oxidative metabolic profiling of xenobiotics by human P450s expressed in tobacco cell suspension cultures. Biochem. Soc. Trans. 34: 1241-1245.

Schmidt I, van Spanning RJ, Jetten MS 2004 Denitrification and ammonia oxidation by Nitrosomonas europaea wild-type, and NirK- and NorB-deficient mutants. Microbiology 150: 4107-4114.

Schmidt K, Carlsen M, Nielsen J, Villadsen J 1997 Modeling isotopomer distributions in biochemical networks using isotopomer mapping matrices. Biotechnol. Bioeng. 55: 831-840.

Schmidt K, Carlsen M, Nielsen J, Villadsen J 1997 Modeling isotopomer distributions in biochemical networks using isotopomer mapping matrices. Biotechnol. Bioeng. 55: 831-840.

Schmidt K, Marx A, de Graaf AA, Wiechert W, Sahm H, Nielsen J, Villadsen J 1998 13C tracer experiments and metabolite balancing for metabolic flux analysis: comparing two approaches. Biotechnol. Bioeng. 58: 254-257.

Schmidt K, Nielsen J, Villadsen J 1999 Quantitative analysis of metabolic fluxes in Escherichia coli, using two-dimensional NMR spectroscopy and complete isotopomer models. J. Biotechnol. 71: 175-189.

Schmidt M, Gessner G, Luff M, Heiland I, Wagner V, Kaminski M, Geimer S, Eitzinger N, Reissenweber T, Voytsekh O, Fiedler M, Mittag M, Kreimer G 2006 Proteomic analysis of the eyespot of Chlamydomonas reinhardtii provides novel insights into its components and tactic movements. Plant Cell 18: 1908-1930.

Schmidt S, Sunyaev S, Bork P, Dandekar T 2003 Metabolites: a helping hand for pathway evolution? Trends Biochem. Sci. 28: 336-341.

Schmitt B, Schneider B 2001 Phenylpropanoid interconversion in Anigozanthos preissii observed by high-performance liquid chromatography-nuclear magnetic resonance spectroscopy. Phytochem. Anal. 12: 43-47.

Schneider A, Kirch T, Gigolashvili T, Mock HP, Sonnewald U, Simon R, Flugge UI, Werr W 2005 A transposon-based activation-tagging population in Arabidopsis thaliana (TAMARA) and its application in the identification of dominant developmental and metabolic mutations. FEBS Lett. 579: 4622-4628.

Schneider BL, Ruback S, Kiupakis AK, Kasbarian H, Pybus C, Reitzer L 2002 The Escherichia coli gabDTPC operon: specific gamma-aminobutyrate catabolism and nonspecific induction. J. Bacteriol. 184: 6976-6986.

Schoder H, Knight RJ, Kofoed KF, Schelbert HR, Buxton DB 1998 Regulation of pyruvate dehydrogenase activity and glucose metabolism in post-ischaemic myocardium. Biochim. Biophys. Acta 1406: 62-72.

Schoolnik GK 2002 Microarray analysis of bacterial pathogenicity. Adv. Microb. Physiol. 46: 1-45.

Schoolnik GK 2002 Functional and comparative genomics of pathogenic bacteria. Curr. Opin. Microbiol. 5: 20-26.

Schrader J, Moyle R, Bhalerao R, Hertzberg M, Lundeberg J, Nilsson P, Bhalerao RP 2004 Cambial meristem dormancy in trees involves extensive remodelling of the transcriptome. Plant J. 40: 173-187.

Schroder M, Giermann N, Zrenner R 2005 Functional analysis of the pyrimidine de novo synthesis pathway in Solanaceous species. Plant Physiol. 138: 1926-1938.

Schroder P, Abele C, Gohr P, Stuhlfauth-Roisch U, Grosse W 1999 Latest on enzymology of serotonin biosynthesis in walnut seeds. Adv. Exp. Med. Biol. 467: 637-644.

Schugerl K 2001 Progress in monitoring, modeling and control of bioprocesses during the last 20 years. J. Biotechnol. 85: 149-173.

Schuler MA, Werck-Reichhart D 2003 Functional genomics of P450s. Annu. Rev. Plant Biol. 54: 629-667.

Schulte M, Von Ballmoos P, Rennenberg H, Herschbach C 2002 Life-long growth of Quercus ilex L. at natural CO2 springs acclimates sulphur, nitrogen and carbohydrate metabolism of the progeny to elevated pCO(2). Plant Cell Environ. 25: 1715-1727.

Schulte-Hermann R, Wogan GN, Berry C, Brown NA, Czeizel A, Giavini E, Holmes LB, Kroes R, Nau H, Neubert D, Oesch F, Ott T, Pelkonen O, Robert-Gnansia E, Sullivan FM 2006 Analysis of reproductive toxicity and classification of glufosinate-ammonium. Regul. Toxicol. Pharmacol. 44: S1-S76.

Schulz AR 1998 Control analysis of muscle glycogen metabolism. Arch. Biochem. Biophys. 353: 172-180.

Schumann U, Prestele J, O'Geen H, Brueggeman R, Wanner G, Gietl C 2007 Requirement of the C3HC4 zinc RING finger of the Arabidopsis PEX10 for photorespiration and leaf peroxisome contact with chloroplasts. Proc. Natl. Acad. Sci. U.S.A. 104: 1069-1074.

Schuster S 1999 Studies on the stoichiometric structure of enzymatic reaction systems. Theor. Biosci. 118: 125-139.

Schuster S 1999 Use and limitations of modular metabolic control analysis in medicine and biotechnology. Metab. Eng. 1: 232-242.

Schuster S 2001 Flux determination by isotopomer balancing - a successful application of theory to experiment. Trends Biotechnol. 19: 85.

Schuster S 1996 Control analysis in terms of generalized variables characterizing metabolic systems. J. Theor. Biol. 182: 259-268.

Schuster S, Dandekar T, Fell DA 1999 Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. Trends Biotechnol. 17: 53-60.

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: 326-332.

Schuster S, Kahn D, Westerhoff HV 1993 Modular analysis of the control of complex metabolic pathways. Biophys. Chem. 48: 1-17.

Schuster S, Kenanov D 2005 Adenine and adenosine salvage pathways in erythrocytes and the role of S-adenosylhomocysteine hydrolase - A theoretical study using elementary flux modes. FEBS J. 272: 5278-5290.

Schuster S, Kholodenko BN, Westerhoff HV 2000 Cellular information transfer regarded from a stoichiometry and control analysis perspective Biosystems 55: 73-81.

Schuster S, von Kamp A, Pachkov M 2006 Understanding the roadmap of metabolism by pathway analysis. Methods Mol. Biol. 358: 199-226.

Schuster S, Westerhoff HV 1999 Modular control analysis of slipping enzymes. Biosystems 49: 1-15.

Schuster S, Zevedei-Oancea I 2002 Treatment of multifunctional enzymes in metabolic pathway analysis. Biophys. Chem. 99: 63.

Schutzendubel A, Polle A 2002 Plant responses to abiotic stresses: heavy metal-induced oxidative stress and protection by mycorrhization. J. Exp. Bot. 53: 1351-1365.

Schwaighofer A, Schroeter T, Mika S, Hansen K, Ter Laak A, Lienau P, Reichel A, Heinrich N, Muller KR 2008 A probabilistic approach to classifying metabolic stability. J. Chem. Inf. Model. 48: 785-796.

Schwalm K, Aloni R, Langhans M, Heller W, Stich S, Ullrich CI 2003 Flavonoid-related regulation of auxin accumulation in Agrobacterium tumefaciens-induced plant tumors. Planta 218: 163-178.

Schwartz JM, Kanehisa M 2006 Quantitative elementary mode analysis of metabolic pathways: the example of yeast glycolysis. BMC Bioinformatics 7: 186.

Schwarz R, Musch P, von Kamp A, Engels B, Schirmer H, Schuster S, Dandekar T 2005 YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities. BMC Bioinformatics 6: 135.

Schwender J 2008 Metabolic flux analysis as a tool in metabolic engineering of plants. Curr. Opin. Biotechnol. 19: 131-137.

Schwender J, Goffman F, Ohlrogge JB, Shachar-Hill Y 2004 Rubisco without the Calvin cycle improves the carbon efficiency of developing green seeds. Nature 432: 779-782.

Schwender J, Ohlrogge J, Shachar-Hill Y 2004 Understanding flux in plant metabolic networks. Curr. Opin. Plant Biol. 7: 309-317.

Schwender J, Ohlrogge JB, Shachar-Hill Y 2003 A flux model of glycolysis and the oxidative pentosephosphate pathway in developing Brassica napus embryos. J. Biol. Chem. 278: 29442-29453.

Schwender J, Shachar-Hill Y, Ohlrogge JB 2006 Mitochondrial metabolism in developing embryos of Brassica napus. J. Biol. Chem. 281: 34040-34047.

Seagle C, Christie MA, Winnike JH, McClelland RE, Ludlow JW, O'Connell TM, Gamcsik MP, Macdonald JM 2008 High-throughput nuclear magnetic resonance metabolomic footprinting for tissue engineering. Tissue Eng. Part C. Methods 14: 107-118.

Seginer I, Bleyaert P, Breugelmans M 2004 Modelling ontogenetic changes of nitrogen and water content in lettuce. Ann. Bot. (Lond.) 94: 393-404.

Segre D, Deluna A, Church GM, Kishony R 2005 Modular epistasis in yeast metabolism. Nat. Genet. 37: 77-83.

Segre D, Vitkup D, Church GM 2002 Analysis of optimality in natural and perturbed metabolic networks. Proc. Natl. Acad. Sci. U.S.A. 99: 15112-15117.

Sehnke PC, Henry R, Cline K, Ferl RJ 2000 Interaction of a plant 14-3-3 protein with the signal peptide of a thylakoid-targeted chloroplast precursor protein and the presence of 14-3-3 isoforms in the chloroplast stroma. Plant Physiol. 122: 235-242.

Seifert GJ 2004 Nucleotide sugar interconversions and cell wall biosynthesis: how to bring the inside to the outside. Curr. Opin. Plant Biol. 7: 277-284.

Seki H, Nishizawa T, Tanaka N, Niwa Y, Yoshida S, Muranaka T 2005 Hairy root-activation tagging: a high-throughput system for activation tagging in transformed hairy roots. Plant Mol. Biol. 59: 793-807.

Seki M, Umezawa T, Urano K, Shinozaki K 2007 Regulatory metabolic networks in drought stress responses. Curr. Opin. Plant Biol. 10: 296-302.

Sekiyama Y, Kikuchi J 2007 Towards dynamic metabolic network measurements by multi-dimensional NMR-based fluxomics. Phytochemistry 68: 2320-2329.

Sekowska A, Denervaud V, Ashida H, Michoud K, Haas D, Yokota A, Danchin A 2004 Bacterial variations on the methionine salvage pathway. BMC Microbiol. 4: 9.

Selivanov VA, Marin S, Lee PW, Cascante M 2006 Software for dynamic analysis of tracer-based metabolomic data: estimation of metabolic fluxes and their statistical analysis. Bioinformatics 22: 2806-2812.

Selivanov VA, Meshalkina LE, Solovjeva ON, Kuchel PW, Ramos-Montoya A, Kochetov GA, Lee PW, Cascante M 2005 Rapid simulation and analysis of isotopomer distributions using constraints based on enzyme mechanisms: an example from HT29 cancer cells. Bioinformatics 21: 3558-3564.

Selivanov VA, Sukhomlin T, Centelles JJ, Lee PW, Cascante M 2006 Integration of enzyme kinetic models and isotopomer distribution analysis for studies of in situ cell operation. BMC Neurosci. 7 Suppl. 1: S7.

Selmar D, Bytof G, Knopp SE 2008 The storage of green coffee (Coffea arabica): decrease of viability and changes of potential aroma precursors. Ann. Bot. (Lond.) 101: 31-38.

Sen AK 1990 Application of electrical analogues for control analysis of simple metabolic pathways. Biochem. J. 272: 65-70.

Sen AK 1991 Quantitative analysis of metabolic regulation. A graph-theoretic approach using spanning trees. Biochem. J. 275: 253-258.

Senecoff JF, McKinney EC, Meagher RB 1996 De novo purine synthesis in Arabidopsis thaliana. II. The PUR7 gene encoding 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole synthetase is expressed in rapidly dividing tissues. Plant Physiol. 112: 905-917.

Senoo K, Solaiman Z, Tanaka S, Kawaguchi M, Imaizumi-Anraku H, Akao S, Tanaka A, Obata H 2007 Isolation and characterization of arbuscules from roots of an increased-arbuscule-forming mutant of Lotus japonicus. Ann. Bot. (Lond.) 100: 1599-1603.

Seressiotis A, Bailey JE 1988 MPS - an artificially intelligent software system for the analysis and synthesis of metabolic pathways. Biotechnol. Bioeng. 31: 587-602.

Serkova NJ, Jackman M, Brown JL, Liu T, Hirose R, Roberts JP, Maher JJ, Niemann CU 2006 Metabolic profiling of livers and blood from obese Zucker rats. J. Hepatol. 44: 956-962.

Seshime Y, Juvvadi PR, Fujii I, Kitamoto K 2005 Genomic evidences for the existence of a phenylpropanoid metabolic pathway in Aspergillus oryzae. Biochem. Biophys. Res. Commun. 337: 747-751.

Sevilla A, Schmid JW, Mauch K, Iborra JL, Reuss M, Canovas M 2005 Model of central and trimethylammonium metabolism for optimizing l-carnitine production by E. coli. Metab. Eng. 7: 401-425.

Sgherri C, Stevanovic B, Navari-Izzo F 2004 Role of phenolics in the antioxidative status of the resurrection plant Ramonda serbica during dehydration and rehydration. Physiol. Plant. 122: 478-485.

Shachar-Hill Y 2007 Quantifying flows through metabolic networks and the prospects for fluxomic studies of mycorrhizas. New Phytol. 174: 235-240.

Shakoury-Elizeh M, Tiedeman J, Rashford J, Ferea T, Demeter J, Garcia E, Rolfes R, Brown PO, Botstein D, Philpott CC 2004 Transcriptional remodeling in response to iron deprivation in Saccharomyces cerevisiae. Mol. Biol. Cell 15: 1233-1243.

Shane B 1989 Folylpolyglutamate synthesis and role in the regulation of one-carbon metabolism. Vitam. Horm. 45: 263-335.

Shanks JV 2001 In situ NMR systems. Curr. Issues Mol. Biol. 3: 15-26.

Shanks JV, Bhadra R, Morgan J, Rijhwani S, Vani S 1998 Quantification of metabolites in the indole alkaloid pathways of Catharanthus roseus: implications for metabolic engineering. Biotechnol. Bioeng. 58: 333-338.

Shanks JV, Morgan J 1999 Plant 'hairy root' culture. Curr. Opin. Biotechnol. 10: 151-155.

Shanks JV, Stephanopoulos G 2000 Biochemical engineering. Bridging the gap between gene and product. Curr. Opin. Biotechnol. 11: 169-170.

Shao HB, Chu LY, Lu ZH, Kang CM 2007 Primary antioxidant free radical scavenging and redox signaling pathways in higher plant cells. Int. J. Biol. Sci. 4: 8-14.

Shao HB, Chu LY, Shao MA, Jaleel CA, Hong-Mei M 2008 Higher plant antioxidants and redox signaling under environmental stresses. C. R. Biol. 331: 433-441.

Sharma SB, Dixon RA 2005 Metabolic engineering of proanthocyanidins by ectopic expression of transcription factors in Arabidopsis thaliana. Plant J. 44: 62-75.

Sharma SS, Dietz KJ 2006 The significance of amino acids and amino acid-derived molecules in plant responses and adaptation to heavy metal stress. J. Exp. Bot. 57: 711-726.

Sharon-Asa L, Shalit M, Frydman A, Bar E, Holland D, Or E, Lavi U, Lewinsohn E, Eyal Y 2003 Citrus fruit flavor and aroma biosynthesis: isolation, functional characterization, and developmental regulation of Cstps1, a key gene in the production of the sesquiterpene aroma compound valencene. Plant J. 36: 664-674.

Sharples SC, Fry SC 2007 Radioisotope ratios discriminate between competing pathways of cell wall polysaccharide and RNA biosynthesis in living plant cells. Plant J. 52: 252-262.

Shastri AA, Morgan JA 2005 Flux balance analysis of photoautotrophic metabolism. Biotechnol. Prog. 21: 1617-1626.

Shayan AJ, Brodin L, Ottersen OP, Birinyi A, Hill CE, Govind CK, Atwood HL, Shupliakov O 2000 Neurotransmitter levels and synaptic strength at the Drosophila larval neuromuscular junction are not altered by mutation in the sluggish-A gene, which encodes proline oxidase and affects adult locomotion. J. Neurogenet. 14: 165-192.

Shen H, Ligaba A, Yamaguchi M, Osawa H, Shibata K, Yan X, Matsumoto H 2004 Effect of K-252a and abscisic acid on the efflux of citrate from soybean roots. J. Exp. Bot. 55: 663-671.

Shen YG, Du BX, Zhang WK, Zhang JS, Chen SY 2002 AhCMO, regulated by stresses in Atriplex hortensis, can improve drought tolerance in transgenic tobacco. Theor. Appl. Genet. 105: 815-821.

Sheoran IS, Ross AR, Olson DJ, Sawhney VK 2007 Proteomic analysis of tomato (Lycopersicon esculentum) pollen. J. Exp. Bot. 58: 3525-3535.

Sheridan R, Jackson GA, LR, Ward J, Dunnill P 1998 Rational engineering of the TOL meta-cleavage pathway. Biotechnol. Bioeng. 58: 240-249.

Sherry AD, Jeffrey FM, Malloy CR 2004 Analytical solutions for (13)C isotopomer analysis of complex metabolic conditions: substrate oxidation, multiple pyruvate cycles, and gluconeogenesis. Metab. Eng. 6: 12-24.

Shewmaker CK, Sheehy JA, Daley M, Colburn S, Ke DY 1999 Seed-specific overexpression of phytoene synthase: increase in carotenoids and other metabolic effects. Plant J. 20: 401-412.

Shi C, Koch G, Ouzunova M, Wenzel G, Zein I, Lubberstedt T 2006 Comparison of maize brown-midrib isogenic lines by cellular UV-microspectrophotometry and comparative transcript profiling. Plant Mol. Biol. 62: 697-714.

Shi H, Nikawa J, Shimizu K 1999 Effect of modifying metabolic network on poly-3-hydroxybutyrate biosynthesis in recombinant Escherichia coli. J. Biosci. Bioeng. 87: 666-677.

Shi H, Shimizu K 1998 On-line metabolic pathway analysis based on metabolic signal flow diagram. Biotechnol. Bioeng. 58: 139-148.

Shi M, Larrondo LF, Loros JJ, Dunlap JC 2007 A developmental cycle masks output from the circadian oscillator under conditions of choline deficiency in Neurospora. Proc. Natl. Acad. Sci. U.S.A. 104: 20102-20107.

Shiga M, Takigawa I, Mamitsuka H 2007 Annotating gene function by combining expression data with a modular gene network. Bioinformatics 23: i468-i478.

Shigeoka S, Ishikawa T, Tamoi M, Miyagawa Y, Takeda T, Yabuta Y, Yoshimura K 2002 Regulation and function of ascorbate peroxidase isoenzymes. J. Exp. Bot. 53: 1305-1319.

Shimazaki K, Doi M, Assmann SM, Kinoshita T 2007 Light regulation of stomatal movement. Annu. Rev. Plant Biol. 58: 219-247.

Shimizu H 2002 Metabolic engineering--integrating methodologies of molecular breeding and bioprocess systems engineering. J. Biosci. Bioeng. 94: 563-573.

Shimizu H, Takiguchi N, Tanaka H, Shioya S 1999 A maximum production strategy of lysine based on a simplified model derived from a metabolic reaction network. Metab. Eng. 1: 299-308.

Shimizu K 2000 An overview on metabolic systems engineering approach and its future perspectives for efficient microbial fermentation. J. Chin. Inst. Chem. Eng. 31: 429-442.

Shin M, Sano K, Umezawa C 1991 Metabolism of tryptophan to niacin in Saccharomyces uvarum. J. Nutr. Sci. Vitaminol. (Tokyo) 37: 269-283.

Shinmyo A, Shoji T, Bando E, Nagaya S, Nakai Y, Kato K, Sekine M, Yoshida K 1998 Metabolic engineering of cultured tobacco cells. Biotechnol. Bioeng. 58: 329-332.

Shintani D, DellaPenna D 1998 Elevating the vitamin E content of plants through metabolic engineering. Science 282: 2098-2100.

Shinya T, Galis I, Narisawa T, Sasaki M, Fukuda H, Matsuoka H, Saito M, Matsuoka K 2007 Comprehensive analysis of glucan elicitor-regulated gene expression in tobacco BY-2 cells reveals a novel MYB transcription factor involved in the regulation of phenylpropanoid metabolism. Plant Cell Physiol. 48: 1404-1413.

Shirai T, Fujimura K, Furusawa C, Nagahisa K, Shioya S, Shimizu H 2007 Study on roles of anaplerotic pathways in glutamate overproduction of Corynebacterium glutamicum by metabolic flux analysis. Microb. Cell Fact. 6: 19.

Shirai T, Nakato A, Izutani N, Nagahisa K, Shioya S, Kimura E, Kawarabayasi Y, Yamagishi A, Gojobori T, Shimizu H 2005 Comparative study of flux redistribution of metabolic pathway in glutamate production by two coryneform bacteria. Metab. Eng. 7: 59-69.

Shirke PA, Pathre UV 2004 Influence of leaf-to-air vapour pressure deficit (VPD) on the biochemistry and physiology of photosynthesis in Prosopis juliflora. J. Exp. Bot. 55: 2111-2120.

Shlomi T, Berkman O, Ruppin E 2005 Regulatory on/off minimization of metabolic flux changes after genetic perturbations. Proc. Natl. Acad. Sci. U.S.A. 102: 7695-7700.

Shono M, Liu J, Sanmiya K, Singh I, ud Din J, Suzuki K, Tsukaguchi T, Egawa Y 2002 Functional analysis of mitochondrial small heat shock protein. JIRCAS Working Report No.23, "Genetic Engineering of Crop Plants for Abiotic Stress" (Iwanaga M, ed.) p. 17-23.

Shou M, Hayashi M, Pan Y, Xu Y, Morrissey K, Xu L, Skiles GL 2008 Modeling, prediction, and in vitro in vivo correlation of CYP3A4 induction. Drug Metab. Dispos. Jul 31 [Epub ahead of print].

Shrestha R, Kim SC, Dyer JM, Dixon RA, Chapman KD 2006 Plant fatty acid (ethanol) amide hydrolases. Biochim. Biophys. Acta 1761: 324-334.

Shrestha R, Noordermeer MA, Van Der Stelt M, Veldink GA, Chapman KD 2002 N-acylethanolamines are metabolized by lipoxygenase and amidohydrolase in competing pathways during cottonseed imbibition. Plant Physiol. 130: 391-401.

Shulaev V, Cortes D, Miller G, Mittler R 2008 Metabolomics for plant stress response. Physiol. Plant. 132: 199-208.

Shulaev V, Oliver DJ 2006 Metabolic and proteomic markers for oxidative stress. New tools for reactive oxygen species research. Plant Physiol. 141: 367-372.

Shulman RG, Rothman DL 2001 13C NMR of intermediary metabolism: implications for systemic physiology. Annu. Rev. Physiol. 63: 15-48.

Shvaleva AL, Costa E Silva F, Breia E, Jouve J, Hausman JF, Almeida MH, Maroco JP, Rodrigues ML, Pereira JS, Chaves MM 2005 Metabolic responses to water deficit in two Eucalyptus globulus clones with contrasting drought sensitivity. Tree Physiol. 26: 239-248.

Sibson NR, Mason GF, Shen J, Cline GW, Herskovits AZ, Wall JE, Behar KL, Rothman DL, Shulman RG 2001 In vivo 13C NMR measurement of neurotransmitter glutamate cycling, anaplerosis and TCA cycle flux in rat brain during. J. Neurochem. 76: 975-989.

Sidari M, Panuccio MR, Muscolo A 2004 Influence of acidity on growth and biochemistry of Pennisetum clandestinum. Biol. Plant. 48: 133-136.

Siddique MA, Grossmann J, Gruissem W, Baginsky S 2006 Proteome analysis of bell pepper (Capsicum annum L.) chromoplasts. Plant Cell Physiol. 47: 1663-1673.

Siedow JN, Stitt M 1998 Plant metabolism: where are all those pathways leading us? Curr. Opin. Plant Biol. 1: 197-200.

Siezen RJ, van Enckevort FH, Kleerebezem M, Teusink B 2004 Genome data mining of lactic acid bacteria: the impact of bioinformatics. Curr. Opin. Biotechnol. 15: 105-115.

Silpi U, Lacointe A, Kasempsap P, Thanysawanyangkura S, Chantuma P, Gohet E, Musigamart N, Clement A, Ameglio T, Thaler P 2007 Carbohydrate reserves as a competing sink: evidence from tapping rubber trees. Tree Physiol. 27: 881-889.

Simeonidis E, Rison SC, Thornton JM, Bogle ID, Papageorgiou LG 2003 Analysis of metabolic networks using a pathway distance metric through linear programming. Metab. Eng. 5: 211-219.

Simier P, Delavault P, Demarsy E, Pouvreau JB, Pageau K, Le Bizec B, Fer A, Thalouarn P 2005 Characterization of an unusually regulated gene encoding asparagine synthetase in the parasitic plant Striga hermonthica (Scrophulariaceae). Physiol. Plant. 123: 9-20.

Simpson NE, Han Z, Berendzen KM, Sweeney CA, Oca-Cossio JA, Constantinidis I, Stacpoole PW 2006 Magnetic resonance spectroscopic investigation of mitochondrial fuel metabolism and energetics in cultured human fibroblasts: effects of pyruvate dehydrogenase complex deficiency and dichloroacetate. Mol. Genet. Metab. 89: 97-105.

Simpson TW, Follstad BD, Stephanopoulos G 1999 Analysis of the pathway structure of metabolic networks. J. Biotechnol. 71: 207-23.

Simpson TW, Shimizu H, Stephanopoulos G 1998 Experimental determination of group flux control coefficients in metabolic networks. Biotechnol. Bioeng. 58: 149-153.

Singer SW, Chan CS, Zemla A, VerBerkmoes NC, Hwang M, Hettich RL, Banfield JF, Thelen MP 2008 Characterization of cytochrome 579, an unusual cytochrome isolated from an iron-oxidizing microbial community. Appl. Environ. Microbiol. 74: 4454-4462.

Singh AK, Elvitigala T, Bhattacharyya-Pakrasi M, Aurora R, Ghosh B, Pakrasi HB 2008 Integration of carbon and nitrogen metabolism with energy production is crucial to light acclimation in the cyanobacterium Synechocystis. Plant Physiol. Jul 3 [Epub ahead of print].

Singh SA, Christendat D 2006 Structure of Arabidopsis dehydroquinate dehydratase-shikimate dehydrogenase and implications for metabolic channeling in the shikimate pathway. Biochemistry 45: 7787-7796.

Singh SP, Zhou XR, Liu Q, Stymne S, Green AG 2005 Metabolic engineering of new fatty acids in plants. Curr. Opin. Plant Biol. 8: 197-203.

Singh VK, Ghosh I 2006 Kinetic modeling of tricarboxylic acid cycle and glyoxylate bypass in Mycobacterium tuberculosis, and its application to assessment of drug targets. Theor. Biol. Med. Model. 3: 27.

Sitbon F, Astot C, Edlund A, Crozier A, Sandberg G 2000 The relative importance of tryptophan-dependent and tryptophan-independent biosynthesis of indole-3-acetic acid in tobacco during vegetative growth. Planta 211: 715-721.

Siu KK, Lee JE, Smith GD, Horvatin-Mrakovcic C, Howell PL 2008 Structure of Staphylococcus aureus 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase. Acta Crystallogr. Sect. F. Struct. Biol. Cryst. Commun. 64: 343-350.

Sivaprakasam S, Mahadevan S, Rajakumar S 2008 Biocalorimetric studies of the metabolic activity of Pseudomonas aeruginosa aerobically grown in a glucose-limited complex growth medium. Biosci. Biotechnol. Biochem. 72: 936-942.

Siverio J 2002 Assimilation of nitrate by yeasts. FEMS Microbiol. Rev. 26: 277.

Sjogren LL, Stanne TM, Zheng B, Sutinen S, Clarke AK 2006 Structural and functional insights into the chloroplast ATP-dependent Clp protease in Arabidopsis. Plant Cell 18: 2635-2649.

Skipsey M, Cummins I, Andrews CJ, Jepson I, Edwards R 2005 Manipulation of plant tolerance to herbicides through co-ordinated metabolic engineering of a detoxifying glutathione transferase and thiol cosubstrate. Plant Biotechnol. J. 3: 409-420.

Skopelitis DS, Paranychianakis NV, Kouvarakis A, Spyros A, Stephanou EG, Roubelakis-Angelakis KA 2007 The isoenzyme 7 of tobacco NAD(H)-dependent glutamate dehydrogenase exhibits high deaminating and low aminating activities in vivo. Plant Physiol. 145: 1726-1734.

Slater S, Mitsky TA, Houmiel KL, Hao M, Reiser SE, Taylor NB, Tran M, Valentin HE, Rodriguez DJ, Stone DA, Padgette SR, Kishore G, Gruys KJ 1999 Metabolic engineering of Arabidopsis and Brassica for poly(3-hydroxybutyrate-co-3-hydroxyvalerate) copolymer production. Nat. Biotechnol. 17: 1011-1016.

Small JR, Fell DA 1990 Covalent modification and metabolic control analysis. Modification to the theorems and their application to metabolic systems containing covalently modifiable enzymes. Eur. J. Biochem. 191: 405-411.

Small JR, Fell DA 1989 The matrix method of metabolic control analysis: its validity for complex pathway structures. J. Theor. Biol. 136: 181-197.

Small JR, Kacser H 1993 Responses of metabolic systems to large changes in enzyme activities and effectors. 1. The linear treatment of unbranched chains. Eur. J. Biochem. 213: 613-624.

Small JR, Kacser H 1993 Responses of metabolic systems to large changes in enzyme activities and effectors. 2. The linear treatment of branched pathways and metabolite concentrations. Assessment of the general non-linear case. Eur. J. Biochem. 213: 625-640.

Smedsgaard J, Nielsen J 2005 Metabolite profiling of fungi and yeast: from phenotype to metabolome by MS and informatics. J. Exp. Bot. 56: 273-286.

Smigielski AJ, Muir ME, Wallace BJ 1985 Studies on the accumulation of putrescine and spermidine in Escherichia coli. Aust. J. Biol. Sci. 38: 383-392.

Smirnoff N 1998 Plant resistance to environmental stress. Curr. Opin. Biotechnol. 9: 214-219.

Smith AM 2008 Prospects for increasing starch and sucrose yields for bioethanol production. Plant J. 54: 546-558.

Smith AM, Zeeman SC 2006 Quantification of starch in plant tissues. Nat. Protoc. 1: 1342-1345.

Smith AM, Zeeman SC, Smith SM 2005 Starch degradation. Annu. Rev. Plant Biol. 56: 73-98.

Smith E, Morowitz HJ 2004 Universality in intermediary metabolism. Proc. Natl. Acad. Sci. U.S.A. 101: 13168-13173.

Smith JL 1998 Glutamine PRPP amidotransferase: snapshots of an enzyme in action. Curr. Opin. Struct. Biol. 8: 686-694.

Soeda Y, Konings MC, Vorst O, van Houwelingen AM, Stoopen GM, Maliepaard CA, Kodde J, Bino RJ, Groot SP, van der Geest AH 2005 Gene expression programs during Brassica oleracea seed maturation, osmopriming, and germination are indicators of progression of the germination process and the stress tolerance level. Plant Physiol. 137: 354-368.

Soga T, Ueno Y, Naraoka H, Ohashi Y, Tomita M, Nishioka T 2002 Simultaneous determination of anionic intermediates for Bacillus subtilis metabolic pathways by capillary electrophoresis electrospray ionization mass spectrometry. Anal. Chem. 74: 2233-2239.

Soitamo AJ, Sippola K, Aro EM 1998 Expression of psbA genes produces prominent 5' psbA mRNA fragments in Synechococcus sp. PCC 7942. Plant Mol. Biol. 37: 1023-1033.

Solanky KS, Bailey NJ, Beckwith-Hall BM, Bingham S, Davis A, Holmes E, Nicholson JK, Cassidy A 2005 Biofluid 1H NMR-based metabonomic techniques in nutrition research - metabolic effects of dietary isoflavones in humans. J. Nutr. Biochem. 16: 236-244.

Solanky KS, Burton IW, MacKinnon SL, Walter JA, Dacanay A 2005 Metabolic changes in Atlantic salmon exposed to Aeromonas salmonicida detected by 1H-nuclear magnetic resonance spectroscopy of plasma. Dis. Aquat. Organ. 65: 107-114.

Somleva MN, Snell KD, Beaulieu JJ, Peoples OP, Garrison BR, Patterson NA 2008 Production of polyhydroxybutyrate in switchgrass, a value-added co-product in an important lignocellulosic biomass crop. Plant Biotechnol. J. May 19 [Epub ahead of print].

Sonderegger M, Schumperli M, Sauer U 2005 Selection of quiescent Escherichia coli with high metabolic activity. Metab. Eng. 7: 4-9.

Sontag E, Kiyatkin A, Kholodenko BN 2004 Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data. Bioinformatics 20: 1877-1886.

Sontag ED 2004 Some new directions in control theory inspired by systems biology. Syst. Biol. 1: 9-18.

Sorin C, Negroni L, Balliau T, Corti H, Jacquemot MP, Davanture M, Sandberg G, Zivy M, Bellini C 2006 Proteomic analysis of different mutant genotypes of Arabidopsis led to the identification of 11 proteins correlating with adventitious root development. Plant Physiol. 140: 349-364.

Sorribas A, Curto R, Cascante M 1995 Comparative characterization of the fermentation pathway of Saccharomyces cerevisiae using biochemical systems theory and metabolic control analysis: model validation and dynamic behavior. Math. Biosci. 130: 71-84.

Sorribas A, Samitier S, Canela EI, Cascante M 1993 Metabolic pathway characterization from transient response data obtained in situ: parameter estimation in S-system models. J. Theor. Biol. 162: 81-102.

Sorribas A, Savageau MA 1989 A comparison of variant theories of intact biochemical systems. II. Flux-oriented and metabolic control theories. Math. Biosci. 94: 195-238.

Sorribas A, Savageau MA 1989 Strategies for representing metabolic pathways within biochemical systems theory: reversible pathways. Math. Biosci. 94: 239-269.

Sorribas A, Savageau MA 1989 A comparison of variant theories of intact biochemical systems. I. Enzyme-enzyme interactions and biochemical systems theory. Math. Biosci. 94: 161-193.

Sparks JD, Collins HL, Chirieac DV, Cianci J, Jokinen J, Sowden MP, Galloway CA, Sparks CE 2006 Hepatic very-low-density lipoprotein and apolipoprotein B production are increased following in vivo induction of betaine-homocysteine S-methyltransferase. Biochem. J. 395: 363-371.

Spicer R, Holbrook NM 2007 Effects of carbon dioxide and oxygen on sapwood respiration in five temperate tree species. J. Exp. Bot. 58: 1313-1320.

Spicer R, Holbrook NM 2007 Parenchyma cell respiration and survival in secondary xylem: does metabolic activity decline with cell age? Plant Cell Environ. 30: 934-943.

Spijkerman E 2007 Phosphorus acquisition by Chlamydomonas acidophila under autotrophic and osmo-mixotrophic growth conditions. J. Exp. Bot. 58: 4195-4202.

Sprunck S, Baumann U, Edwards K, Langridge P, Dresselhaus T 2005 The transcript composition of egg cells changes significantly following fertilization in wheat (Triticum aestivum L.). Plant J. 41: 660-672.

Sreenivasulu N, Altschmied L, Radchuk V, Gubatz S, Wobus U, Weschke W 2004 Transcript profiles and deduced changes of metabolic pathways in maternal and filial tissues of developing barley grains. Plant J. 37: 539-553.

Sreevidya V, Srinivasa Rao C, Sullia S, Ladha JK, Reddy PM 2006 Metabolic engineering of rice with soybean isoflavone synthase for promoting nodulation gene expression in rhizobia. J. Exp. Bot. 57: 1957-1969.

Srinivasan A, Giri AP, Harsulkar AM, Gatehouse JA, Gupta VS 2005 A Kunitz trypsin inhibitor from chickpea (Cicer arietinum L.) that exerts anti-metabolic effect on podborer (Helicoverpa armigera) larvae. Plant Mol. Biol. 57: 359-374.

Sriram G, Fulton DB, Iyer VV, Peterson JM, Zhou R, Westgate ME, Spalding MH, Shanks JV 2004 Quantification of compartmented metabolic fluxes in developing soybean embryos by employing biosynthetically directed fractional 13C labeling, two-dimensional [13C, 1H] nuclear magnetic resonance, and comprehensive isotopomer balancing. Plant Physiol. 136: 3043-3057.

Sriram G, Fulton DB, Shanks JV 2007 Flux quantification in central carbon metabolism of Catharanthus roseus hairy roots by (13)C labeling and comprehensive bondomer balancing. Phytochemistry 68: 2243-2257.

Sriram G, Gonzalez-Rivera O, Shanks JV 2006 Determination of biomass composition of Catharanthus roseus hairy roots for metabolic flux analysis. Biotechnol. Prog. 22: 1659-1663.

Sriram G, Shanks JV 2004 Improvements in metabolic flux analysis using carbon bond labeling experiments: bondomer balancing and Boolean function mapping. Metab. Eng. 6: 116-132.

Srivastava R, Varner J 2007 Emerging technologies: systems biology. Biotechnol. Prog. 23: 24-27.

Srivastava S, Chan C 2007 Application of metabolic flux analysis to identify the mechanisms of free fatty acid toxicity to human hepatoma cell line. Biotechnol. Bioeng. 99: 399-410.

St Maurice M, Reinhardt L, Surinya KH, Attwood PV, Wallace JC, Cleland WW, Rayment I 2007 Domain architecture of pyruvate carboxylase, a biotin-dependent multifunctional enzyme. Science 317: 1076-1079.

Stadtman ER, Hohman RJ, Davis JN, Wittenberger M, Chock PB, Rhee SG 1980 Subunit interaction of adenylylated glutamine synthetase. Mol. Biol. Biochem. Biophys. 32: 144-156.

Stafford DE, Yanagimachi KS, Lessard PA, Rijhwani SK, Sinskey AJ, Stephanopoulos G 2002 Optimizing bioconversion pathways through systems analysis and metabolic engineering. Proc. Natl. Acad. Sci. U.S.A. 99: 1801-1806.

Stafford DE, Yanagimachi KS, Stephanopoulos G 2001 Metabolic engineering of indene bioconversion in Rhodococcus sp. Adv. Biochem. Eng. Biotechnol. 73: 85-101.

Stam F, Smulders YM, van Guldener C, Jakobs C, Stehouwer CD, de Meer K 2005 Folic acid treatment increases homocysteine remethylation and methionine transmethylation in healthy subjects. Clin. Sci. (Lond.) 108: 449-456.

Stasolla C, Loukanina N, Yeung EC, Thorpe TA 2005 Progression of programmed cell death in tobacco BY-2 cells is delineated by specific changes in de novo and salvage synthesis of purine nucleotides. Physiol. Plant. 123: 254-261.

Stasolla C, Loukanina N, Yeung EC, Thorpe TA 2004 Alterations in pyrimidine nucleotide metabolism as an early signal during the execution of programmed cell death in tobacco BY-2 cells. J. Exp. Bot. 55: 2513-2522.

Stenzel I, Hause B, Miersch O, Kurz T, Maucher H, Weichert H, Ziegler J, Feussner I, Wasternack C 2003 Jasmonate biosynthesis and the allene oxide cyclase family of Arabidopsis thaliana. Plant Mol. Biol. 51: 895-911.

Stepanova AN, Alonso JM 2005 Ethylene signalling and response pathway: a unique signalling cascade with a multitude of inputs and outputs. Physiol. Plant. 123: 195-206.

Stepansky A, Yao Y, Tang G, Galili G 2005 Regulation of lysine catabolism in Arabidopsis through concertedly regulated synthesis of the two distinct gene products of the composite AtLKR/SDH locus. J. Exp. Bot. 56: 525-536.

Stephani A, Heinrich R 1998 Kinetic and thermodynamic principles determining the structural design of ATP-producing systems. Bull. Math. Biol. 60: 505-543.

Stephani A, Nuno JC, Heinrich R 1999 Optimal stoichiometric designs of ATP-producing systems as determined by an evolutionary algorithm. J. Theor. Biol. 199: 45-61.

Stephanopoulos G 1998 Metabolic engineering. Biotechnol. Bioeng. 58: 119-120.

Stephanopoulos G 2001 Editorial. Metab. Eng. 3: 97.

Stephanopoulos G 1999 Metabolic fluxes and metabolic engineering. Metab. Eng. 1: 1-11.

Stephanopoulos G 1994 Metabolic engineering. Curr. Opin. Biotechnol. 5: 196-200.

Stephanopoulos G, Gill RT 2001 After a decade of progress, an expanded role for metabolic engineering. Adv. Biochem. Eng. Biotechnol. 73: 1-8.

Stephanopoulos G, Simpson TW 1997 Flux amplification in complex metabolic networks. Chem. Eng. Sci. 52: 2607-2627.

Stephanopoulos G, Sinskey AJ 1993 Metabolic engineering--methodologies and future prospects. Trends Biotechnol. 11: 392-396.

Stephanopoulos G, Vallino JJ 1991 Network rigidity and metabolic engineering in metabolite overproduction. Science 252: 1675-1681.

Steuer R, Gross T, Selbig J, Blasius B 2006 Structural kinetic modeling of metabolic networks. Proc. Natl. Acad. Sci. U.S.A. 103: 11868-11873.

Steuer R, Nesi AN, Fernie AR, Gross T, Blasius B, Selbig J 2007 From structure to dynamics of metabolic pathways: application to the plant mitochondrial TCA cycle. Bioinformatics 23: 1378-1385.

Steunou AS, Bhaya D, Bateson MM, Melendrez MC, Ward DM, Brecht E, Peters JW, Kuhl M, Grossman AR 2006 In situ analysis of nitrogen fixation and metabolic switching in unicellular thermophilic cyanobacteria inhabiting hot spring microbial mats. Proc. Natl. Acad. Sci. U.S.A. 103: 2398-2403.

Stipanuk MH, Dominy JE Jr 2006 Surprising insights that aren't so surprising in the modeling of sulfur amino acid metabolism. Amino Acids 30: 251-256.

Stitt M, Fernie AR 2003 From measurements of metabolites to metabolomics: an 'on the fly' perspective illustrated by recent studies of carbon-nitrogen interactions. Curr. Opin. Biotechnol. 14: 136-144.

Stitt M, Schulze E-D 1994 Plant growth, storage, and resource allocation: From flux control in a metabolic chain to the whole-plant level. In (E-D Schulze ed) "Flux Control in Biological Systems: From Enzymes to Populations and Ecosystems." Academic Press, New York, pp. 57-118.

Stoffers HJ, Sonnhammer EL, Blommestijn GJ, Raat NJ, Westerhoff HV 1992 METASIM: object-oriented modelling of cell regulation. Comput. Appl. Biosci. 8: 443-449.

Stouthamer AH 1992 Metabolic pathways in Paracoccus denitrificans and closely related bacteria in relation to the phylogeny of prokaryotes. Antonie Van Leeuwenhoek 61: 1-33.

Streaker ED, Beckett D 2006 The biotin regulatory system: kinetic control of a transcriptional switch. Biochemistry 45: 6417-6425.

Strohl WR 2001 Biochemical engineering of natural product biosynthesis pathways. Metab. Eng. 3: 4-14.

Struik PC, Yin X, de Visser P 2005 Complex quality traits: now time to model. Trends Plant Sci. 10: 513-516.

Struis RP, Ludwig C, Barrelet T, Krahenbuhl U, Rennenberg H 2008 Studying sulfur functional groups in Norway spruce year rings using S L-edge total electron yield spectroscopy. Sci. Total Environ. 403: 196-206.

Stuckrath I, Lange HC, Kotter P, van Gulik WM, Entian KD, Heijnen JJ 2002 Characterization of null mutants of the glyoxylate cycle and gluconeogenic enzymes in S. cerevisiae through metabolic network modeling verified by chemostat cultivation. Biotechnol. Bioeng. 77: 61-72.

Su N, He K, Jiao Y, Chen C, Zhou J, Li L, Bai S, Li X, Deng XW 2007 Distinct reorganization of the genome transcription associates with organogenesis of somatic embryo, shoots, and roots in rice. Plant Mol. Biol. 63: 337-349.

Suarez RK, Darveau CA 2005 Multi-level regulation and metabolic scaling. J. Exp. Biol. 208: 1627-1634.

Suh MC, Kim MJ, Hur CG, Bae JM, Park YI, Chung CH, Kang CW, Ohlrogge JB 2003 Comparative analysis of expressed sequence tags from Sesamum indicum and Arabidopsis thaliana developing seeds. Plant Mol. Biol. 52: 1107-1123.

Sun Q, Yoda K, Suzuki H 2005 Internal axial light conduction in the stems and roots of herbaceous plants. J. Exp. Bot. 56: 191-203.

Suormala T, Baumgartner MR, Coelho D, Zavadakova P, Koich V, Koch HG, Berghauser M, Wraith JE, Burlina A, Sewell A, Herwig J, Fowler B 2004 The cblD defect causes either isolated or combined deficiency of methylcobalamin and adenosylcobalamin synthesis. J. Biol. Chem. 279: 42742-42749.

Suthers PF, Burgard AP, Dasika MS, Nowroozi F, Van Dien S, Keasling JD, Maranas CD 2007 Metabolic flux elucidation for large-scale models using (13)C labeled isotopes. Metab. Eng. 9: 387-405.

Suzuki A, Knaff DB 2005 Glutamate synthase: structural, mechanistic and regulatory properties, and role in the amino acid metabolism. Photosynth. Res. 83: 191-217.

Suzuki H, Reddy MS, Naoumkina M, Aziz N, May GD, Huhman DV, Sumner LW, Blount JW, Mendes P, Dixon RA 2005 Methyl jasmonate and yeast elicitor induce differential transcriptional and metabolic re-programming in cell suspension cultures of the model legume Medicago truncatula. Planta 220: 696-707.

Suzuki M, Hashioka A, Mimura T, Ashihara H 2005 Salt stress and glycolytic regulation in suspension-cultured cells of the mangrove tree, Bruguiera sexangula. Physiol. Plant. 123: 246-253.

Svetic RE, MacCluer CR, Buckley CO, Smythe KL, Jackson JH 2004 A metabolic force for gene clustering. Bull. Math Biol. 66: 559-581.

Swaraj K, Sheokand S, Fernandez-Pascual MM, de Felipe MR 2001 Dark-induced changes in legume nodule functioning. Aust. J. Plant Physiol. 28: 429-438.

Swarbrick PJ, Schulze-Lefert P, Scholes JD 2006 Metabolic consequences of susceptibility and resistance (race-specific and broad-spectrum) in barley leaves challenged with powdery mildew. Plant Cell Environ. 29: 1061-1076.

Sweetlove LJ, Fernie AR 2005 Regulation of metabolic networks: understanding metabolic complexity in the systems biology era. New Phytol. 168: 9-24.

Sweetlove LJ, Last RL, Fernie AR 2003 Predictive metabolic engineering: a goal for systems biology. Plant Physiol. 132: 420-425.

Sweetlove LJ, Mowday B, Hebestreit HF, Leaver CJ, Millar AH 2001 Nucleoside diphosphate kinase III is localized to the inter-membrane space in plant mitochondria. FEBS Lett. 508: 272-276.

Swiderek H, Logan A, Al-Rubeai M 2008 Cellular and transcriptomic analysis of NS0 cell response during exposure to hypoxia. J. Biotechnol. 134: 103-111.

Sybesma W, Burgess C, Starrenburg M, Sinderen Dv D, Hugenholtz J 2004 Multivitamin production in Lactococcus lactis using metabolic engineering. Metab. Eng. 6: 109-115.

Syriopoulos C, Panayotarou A, Lai K, Klapa MI 2008 Transcriptomic analysis of Saccharomyces cerevisiae physiology in the context of galactose assimilation perturbations. Mol. Biosyst. 4: 937-949.

Syu M-J, Hou C-L 1997 A neural network study on the dynamic identification of a fermentation system. Bioprocess Engineering 17: 203-213.

Szczesiul M, Wampler DE 1976 Regulation of a metabolic system in vitro: synthesis of threonine from aspartic acid. Biochemistry 15: 2236-2244.

Sze JY, Remboutsika E, Kohlhaw GB 1993 Transcriptional regulator Leu3 of Saccharomyces cerevisiae: separation of activator and repressor functions. Mol. Cell Biol. 13: 5702-5709.

Szymanski J, Bielecka M, Carrari F, Fernie AR, Hoefgen R, Nikiforova VJ 2007 On the processing of metabolic information through metabolite-gene communication networks: an approach for modelling causality. Phytochemistry 68: 2163-2175.

Szyperski T 1995 Biosynthetically directed fractional 13C-labeling of proteinogenic amino acids. An efficient analytical tool to investigate intermediary metabolism. Eur. J. Biochem. 232: 433-448.

Szyperski T, Glaser RW, Hochuli M, Fiaux J, Sauer U, Bailey JE, Wuthrich K 1999 Bioreaction network topology and metabolic flux ratio analysis by biosynthetic fractional 13C labeling and two-dimensional NMR spectroscopy. Metab. Eng. 1: 189-197.

Tada K, Kishimoto M, Omasa T, Katakura Y, Suga K 2000 L-Lysine production by exponential feeding of L-threonine. J. Biosci. Bioeng. 90: 669-674.

Tadege M, Dupuis I, Kuhlemeier C 1999 Ethanolic fermentation: new functions for an old pathway. Trends Plant Sci. 4: 320-325.

Takahashi H, Hayashi M, Goto F, Sato S, Soga T, Nishioka T, Tomita M, Kawai-Yamada M, Uchimiya H 2006 Evaluation of metabolic alteration in transgenic rice overexpressing dihydroflavonol-4-reductase. Ann. Bot. (Lond.) 98: 819-825.

Takahashi H, Uchimiya H, Hihara Y 2008 Difference in metabolite levels between photoautotrophic and photomixotrophic cultures of Synechocystis sp. PCC 6803 examined by capillary electrophoresis electrospray ionization mass spectrometry. J. Exp. Bot. 59: 3009-3018.

Takata N, Kasuga J, Takezawa D, Arakawa K, Fujikawa S 2007 Gene expression associated with increased supercooling capability in xylem parenchyma cells of larch (Larix kaempferi). J. Exp. Bot. 58: 3731-3742.

Takaya N 2002 Dissimilatory nitrate reduction metabolisms and their control in fungi. J. Biosci. Bioeng. 94: 506-510.

Takubo K, Morikawa T, Nonaka Y, Mizutani M, Takenaka S, Takabe K, Takahashi MA, Ohta D 2003 Identification and molecular characterization of mitochondrial ferredoxins and ferredoxin reductase from Arabidopsis. Plant Mol. Biol. 52: 817-830.

Tambasco-Studart M, Titiz O, Raschle T, Forster G, Amrhein N, Fitzpatrick TB 2005 Vitamin B6 biosynthesis in higher plants. Proc. Natl. Acad. Sci. U.S.A. 102: 13687-13692.

Tanaka K, Asami T, Yoshida S, Nakamura Y, Matsuo T, Okamoto S 2005 Brassinosteroid homeostasis in Arabidopsis is ensured by feedback expressions of multiple genes involved in its metabolism. Plant Physiol. 138: 1117-1125.

Tanaka Y, Ohmiya A 2008 Seeing is believing: engineering anthocyanin and carotenoid biosynthetic pathways. Curr. Opin. Biotechnol. 19: 190-197.

Tanaka Y, Tsuda S, Kusumi T 1998 Metabolic engineering to modify flower color. Plant Cell Physiol. 39: 1119-1126.

Tang AC, Boyer JS 2003 Root pressurization affects growth-induced water potentials and growth in dehydrated maize leaves. J. Exp. Bot. 54: 2479-2488.

Tang Y, Pingitore F, Mukhopadhyay A, Phan R, Hazen TC, Keasling JD 2007 Pathway confirmation and flux analysis of central metabolic pathways in Desulfovibrio vulgaris Hildenborough using GC-MS and FT-ICR mass spectrometry. J. Bacteriol. 189: 940-949.

Tang YJ, Hwang JS, Wemmer DE, Keasling JD 2007 The Shewanella oneidensis MR-1 fluxome under various oxygen conditions. Appl. Environ. Microbiol. 73: 718-729.

Tanizawa Y, Matsuda K, Matsuo M, Ohta Y, Ochi N, Adachi M, Koga M, Mizuno S, Kajita M, Tanaka Y, Tachibana K, Inoue H, Furukawa S, Amachi T, Ueda K, Oka Y 2000 Genetic analysis of Japanese patients with persistent hyperinsulinemic hypoglycemia of infancy: nucleotide-binding fold-2 mutation impairs cooperative binding of adenine nucleotides to sulfonylurea receptor 1. Diabetes 49: 114-120.

Tannler S, Zamboni N, Kiraly C, Aymerich S, Sauer U 2008 Screening of Bacillus subtilis transposon mutants with altered riboflavin production. Metab. Eng. Jun 5 [Epub ahead of print].

Tao L, Jackson RE, Cheng Q 2005 Directed evolution of copy number of a broad host range plasmid for metabolic engineering. Metab. Eng. 7: 10-17.

Tarachiwin L, Masako O, Fukusaki E 2008 Quality evaluation and prediction of Citrullus lanatus by (1)H NMR-based metabolomics and multivariate analysis. J. Agric. Food Chem. 56: 5827-5835.

Tarczynski MC, Jensen RG, Bohnert HJ 1992 Expression of a bacterial mtlD gene in transgenic tobacco leads to production and accumulation of mannitol. Proc. Natl. Acad. Sci. U.S.A. 89: 2600-2604.

Tartakovsky B, Sheintuch M, Hilmer J-M, Scheper T 1997 Modelling of E. coli fermentations: comparison of multicompartment and variable structure models. Bioprocess Engineering 16: 323-329.

Tatarko M, Romeo T 2001 Disruption of a global regulatory gene to enhance central carbon flux into phenylalanine biosynthesis in Escherichia coli. Curr. Microbiol. 43: 26-32.

Tavernier P, Besson I, Portais JC, Courtois J, Courtois B, Barbotin JN 1998 In vivo 13C-NMR studies of polymer synthesis in Rhizobium meliloti M5N1 strain. Biotechnol. Bioeng. 58: 250-253.

Taylor DK, Rank DR, Keiser DR, Smith BN, Criddle RS, Hansen LD 1998 Modelling temperature effects on growth-respiration relations of maize. Plant Cell Environ. 21: 1143-1151.

Taylor NJ, Cowan AK 2004 Xanthine dehydrogenase and aldehyde oxidase impact plant hormone homeostasis and affect fruit size in 'Hass' avocado. J. Plant Res. 117: 121-130.

Tcherkez G, Bligny R, Gout E, Mahe A, Hodges M, Cornic G 2008 Respiratory metabolism of illuminated leaves depends on CO2 and O2 conditions. Proc. Natl. Acad. Sci. U.S.A. 105: 797-802.

Tcherkez G, Cornic G, Bligny R, Gout E, Ghashghaie J 2005 In vivo respiratory metabolism of illuminated leaves. Plant Physiol. 138: 1596-1606.

Tcherkez G, Hodges M 2008 How stable isotopes may help to elucidate primary nitrogen metabolism and its interaction with (photo)respiration in C3 leaves. J. Exp. Bot. 59: 1685-1693.

Tegner J, Skogsberg J, Bjorkegren J 2007 Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Multi-organ whole-genome measurements and reverse engineering to uncover gene networks underlying complex traits. J. Lipid Res. 48: 267-277.

Teixeira AP, Santos SS, Carinhas N, Oliveira R, Alves PM 2008 Combining metabolic flux analysis tools and 13C NMR to estimate intracellular fluxes of cultured astrocytes. Neurochem. Int. 52: 478-486.

Telef N, Stammitti-Bert L, Mortain-Bertrand A, Maucourt M, Carde JP, Rolin D, Gallusci P 2006 Sucrose deficiency delays lycopene accumulation in tomato fruit pericarp discs. Plant Mol. Biol. 62: 453-469.

ter Schure EG, van Riel NA, Verrips CT 2000 The role of ammonia metabolism in nitrogen catabolite repression in Saccharomyces cerevisiae. FEMS Microbiol. Rev. 24: 67-83.

Terce-Laforgue T, Mack G, Hirel B 2004 New insights towards the function of glutamate dehydrogenase revealed during source-sink transition of tobacco (Nicotiana tabacum) plants grown under different nitrogen regimes. Physiol. Plant. 120: 220-228.

Tesniere C, Torregrosa L, Pradal M, Souquet JM, Gilles C, Dos Santos K, Chatelet P, Gunata Z 2006 Effects of genetic manipulation of alcohol dehydrogenase levels on the response to stress and the synthesis of secondary metabolites in grapevine leaves. J. Exp. Bot. 57: 91-99.

Tessem MB, Bathen TF, Cejkova J, Midelfart A 2005 Effect of UV-A and UV-B irradiation on the metabolic profile of aqueous humor in rabbits analyzed by 1H NMR spectroscopy. Invest. Ophthalmol. Vis. Sci. 46: 776-781.

Teusink B, Baganz F, Westerhoff HV, Oliver SG 1998 Metabolic control analysis as a tool in the elucidation of the function of novel genes Yeast Gene Anal. 26: 297-336.

Teusink B, Westerhoff HV 2000 'Slave' metabolites and enzymes. A rapid way of delineating metabolic control. Eur. J. Biochem. 267: 1889-1893.

Teusink B, Wiersma A, Molenaar D, Francke C, de Vos WM, Siezen RJ, Smid EJ 2006 Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model. J. Biol. Chem. 281: 40041-40048.

Textor S, Bartram S, Kroymann J, Falk KL, Hick A, Pickett JA, Gershenzon J 2004 Biosynthesis of methionine-derived glucosinolates in Arabidopsis thaliana: recombinant expression and characterization of methylthioalkylmalate synthase, the condensing enzyme of the chain-elongation cycle. Planta 218: 1026-1035.

Thelander M, Nilsson A, Olsson T, Johansson M, Girod PA, Schaefer DG, Zrÿd JP, Ronne H 2007 The moss genes PpSKI1 and PpSKI2 encode nuclear SnRK1 interacting proteins with homologues in vascular plants. Plant Mol. Biol. 64: 559-573.

Theobald U, Mailinger W, Baltes M, Rizzi M, Reuss M 1997 In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae. 1. Experimental observations. Biotechnol. Bioeng. 55: 305-316.

Thiele I, Price ND, Vo TD, Palsson BO 2005 Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet. J. Biol. Chem. 280: 11683-11695.

Thimm O, Blasing O, Gibon Y, Nagel A, Meyer S, Kruger P, Selbig J, Muller LA, Rhee SY, Stitt M 2004 MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. 37: 914-939.

Thom E, Mohlmann T, Quick WP, Camara B, Neuhaus H-E 1998 Sweet pepper plastids: enzymic equipment, characterisation of the plastidic oxidative pentose-phosphate pathway, and transport of phosphorylated intermediates across the envelope membrane. Planta 204: 226-233.

Thomas GH 2001 Metabolomics breaks the silence. Trends Biotechnol. 19: 126-127.

Thomas S, Fell DA 1998 A control analysis exploration of the role of ATP utilisation in glycolytic-flux control and glycolytic-metabolite-concentration regulation. Eur. J. Biochem. 258: 956-967.

Thomas S, Mooney PFJ, Burrell MM, Fell DA 1997 Metabolic Control Analysis of glycolysis in tuber tissue of potato (Solanum tuberosum): Explanation for the low control coefficient of phosphofructokinase over respiratory flux. Biochem. J. 322: 119-127.

Thomas S, Mooney PJF, Burrell MM, Fell DA 1997 Finite change analysis of glycolytic intermediates in tuber tissue of lines of transgenic potato (Solanum tuberosum) overexpressing phosphofructokinase. Biochem. J. 322: 111-117.

Thomaseth K 2001 A modeling tool for biomedical systems. Simulation Practice & Theory 9: 1-19.

Thomaseth K 1994 PANSYM: a symbolic equation generator for mathematical modelling, analysis and control of metabolic and pharmacokinetic systems. Comput. Methods Programs Biomed. 42: 99-112.

Thum KE, Shin MJ, Gutierrez RA, Mukherjee I, Katari MS, Nero D, Shasha D, Coruzzi GM 2008 An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis. BMC Syst. Biol. 2: 31.

Thykaer J, Christensen B, Nielsen J 2002 Metabolic network analysis of an adipoyl-7-ADCA-producing strain of Penicillium chrysogenum: elucidation of adipate degradation. Metab. Eng. 4: 151-158.

Tian L, Blount JW, Dixon RA 2006 Phenylpropanoid glycosyltransferases from osage orange (Maclura pomifera) fruit. FEBS Lett. 580: 6915-6920.

Tian L, Dixon RA 2006 Engineering isoflavone metabolism with an artificial bifunctional enzyme. Planta 224: 496-507.

Tian ZD, Liu J, Wang BL, Xie CH 2006 Screening and expression analysis of Phytophthora infestans induced genes in potato leaves with horizontal resistance. Plant Cell Rep. 25: 1094-1103.

Tianniam S, Tarachiwin L, Bamba T, Kobayashi A, Fukusaki E 2008 Metabolic profiling of Angelica acutiloba roots utilizing gas chromatography-time-of-flight-mass spectrometry for quality assessment based on cultivation area and cultivar via multivariate pattern recognition. J. Biosci. Bioeng. 105: 655-659.

Ticconi CA, Delatorre CA, Lahner B, Salt DE, Abel S 2004 Arabidopsis pdr2 reveals a phosphate-sensitive checkpoint in root development. Plant J. 37: 801-814.

Tikunov Y, Lommen A, de Vos CH, Verhoeven HA, Bino RJ, Hall RD, Bovy AG 2005 A novel approach for nontargeted data analysis for metabolomics. Large-scale profiling of tomato fruit volatiles. Plant Physiol. 139: 1125-1137.

Tjellstrom H, Andersson MX, Larsson KE, Sandelius AS 2008 Membrane phospholipids as a phosphate reserve: the dynamic nature of phospholipid-to-digalactosyl diacylglycerol (DGDG) exchange in higher plants. Plant Cell Environ. Jul 14 [Epub ahead of print].

Todd CD, Tipton PA, Blevins DG, Piedras P, Pineda M, Polacco JC 2006 Update on ureide degradation in legumes. J. Exp. Bot. 57: 5-12.

Tokimatsu T, Sakurai N, Suzuki H, Ohta H, Nishitani K, Koyama T, Umezawa T, Misawa N, Saito K, Shibata D 2005 KaPPA-View. A web-based analysis tool for integration of transcript and metabolite data on plant metabolic pathway maps. Plant Physiol. 138: 1289-1300.

Tomas-Pejo E, Oliva JM, Ballesteros M, Olsson L 2008 Comparison of SHF and SSF processes from steam-exploded wheat straw for ethanol production by xylose-fermenting and robust glucose-fermenting Saccharomyces cerevisiae strains. Biotechnol. Bioeng. 100: 1122-1131.

Tomb JF, White O, Kerlavage AR, Clayton RA, Sutton GG, Fleischmann RD, Ketchum KA, Klenk HP, Gill S, Dougherty BA, Nelson K, Quackenbush J, Zhou L, Kirkness EF, Peterson S, Loftus B, Richardson D, Dodson R et al 1997 The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 388: 539-547.

Tomita M 2001 Whole-cell simulation: a grand challenge of the 21st century. Trends Biotechnol. 19: 205-210.

Tonelli J, Kishore P, Lee DE, Hawkins M 2005 The regulation of glucose effectiveness: how glucose modulates its own production. Curr. Opin. Clin. Nutr. Metab. Care 8: 450-456.

Tonon T, Harvey D, Larson TR, Graham IA 2002 Long chain polyunsaturated fatty acid production and partitioning to triacylglycerols in four microalgae. Phytochemistry 61: 15-24.

Tonsor SJ, Alonso-Blanco C, Koornneef M 2005 Gene function beyond the single trait: natural variation, gene effects, and evolutionary ecology in Arabidopsis thaliana. Plant Cell Environ. 28: 2-20.

Toroser D, Plaut Z, Huber SC 2000 Regulation of a plant SNF1-related protein kinase by glucose-6-phosphate. Plant Physiol. 123: 403-412.

Torralba AS, Rodriguez Y, Montero F 2003 Phenomenological definition of response times with application to metabolic reactions. J. Theor. Biol. 221: 475-489.

Torrecilla A, Marques AF, Buscalioni RD, Oliveira JM, Teixeira NA, Atencia EA, Gunther Sillero MA, Sillero A 2001 Metabolic fate of AMP, IMP, GMP and XMP in the cytosol of rat brain: an experimental and theoretical analysis. J. Neurochem. 76: 1291-1307.

Torres NV 1996 Metabolic control analysis of inhibitory feedback interaction: application to biotechnological processes. J. Theor. Biol. 182: 405-410.

Torres NV, Mateo F, Sicilia J, Melendez-Hevia E 1988 Distribution of the flux control in convergent metabolic pathways: theory and application to experimental and simulated systems. Int. J. Biochem. 20: 161-165.

Touraine B, Boutin JP, Marion-Poll A, Briat JF, Peltier G, Lobreaux S 2004 Nfu2: a scaffold protein required for [4Fe-4S] and ferredoxin iron-sulphur cluster assembly in Arabidopsis chloroplasts. Plant J. 40: 101-111.

Traufeller K, Gellerich FN, Zierz S 2004 Different sensitivities of CPT I and CPT II for inhibition by L-aminocarnitine in human skeletal muscle. Biochim. Biophys. Acta 1608: 149-154.

Trawick JD, Schilling CH 2006 Use of constraint-based modeling for the prediction and validation of antimicrobial targets. Biochem. Pharmacol. 71: 1026-1035.

Tremouillaux-Guiller J, Huss VA 2007 A cryptic intracellular green alga in Ginkgo biloba: ribosomal DNA markers reveal worldwide distribution. Planta 226: 553-557.

Trethewey RN 2001 Gene discovery via metabolic profiling. Curr. Opin. Biotechnol. 12: 135-138.

Trethewey RN 2004 Metabolite profiling as an aid to metabolic engineering in plants. Curr. Opin. Plant Biol. 7: 196-201.

Trethewey RN, Fernie AR, Bachmann A, Fleischer-Notter H, Geigenberger P, Willmitzer L 2001 Expression of a bacterial sucrose phosphorylase in potato tubers results in a glucose-independent induction of glycolysis. Plant Cell Environ. 24: 357-365.

Trethewey RN, Krotzky AJ, Willmitzer L 1999 Metabolic profiling: a Rosetta Stone for genomics? Curr. Opin. Plant Biol. 2: 83-85.

Trethewey RN, Riesmeier JW, Willmitzer L, Stitt M, Geigenberger P 1999 Tuber-specific expression of a yeast invertase and a bacterial glucokinase in potato leads to an activation of sucrose phosphate synthase and the creation of a sucrose futile cycle. Planta 208: 227-238.

Tretyn A, Kendrick RE 1991 Acetylcholine in plants: presence, metabolism and mechanism of action. Bot. Rev. 57: 33-73.

Treutter D 2005 Significance of flavonoids in plant resistance and enhancement of their biosynthesis. Plant Biol. (Stuttg.) 7: 581-591.

Trinh CT, Carlson R, Wlaschin A, Srienc F 2006 Design, construction and performance of the most efficient biomass producing E. coli bacterium. Metab. Eng. 8: 628-638.

Trinh CT, Unrean P, Srienc F 2008 A minimal Escherichia coli cell for most efficient ethanol production from hexoses and pentoses. Appl. Environ. Microbiol. 74: 3634-3643.

Tripathi BN, Gaur JP 2006 Physiological behavior of Scenedesmus sp. during exposure to elevated levels of Cu and Zn and after withdrawal of metal stress. Protoplasma 229: 1-9.

Tritsch D, Mawlawi H, Biellmann JF 1993 Mechanism-based inhibition of proline dehydrogenase by proline analogues. Biochim. Biophys. Acta 1202: 77-81.

Troein C, Ahren D, Krogh M, Peterson C 2007 Is transcriptional regulation of metabolic pathways an optimal strategy for fitness? PLoS ONE 2: e855.

Troen AM, Shea-Budgell M, Shukitt-Hale B, Smith DE, Selhub J, Rosenberg IH 2008 B-vitamin deficiency causes hyperhomocysteinemia and vascular cognitive impairment in mice. Proc. Natl. Acad. Sci. U.S.A. Aug 18 [Epub ahead of print].

Trotter PJ 2001 The genetics of fatty acid metabolism in Saccharomyces cerevisiae. Annu. Rev. Nutr. 21: 97-119.

Trotter PJ, Adamson AL, Ghrist AC, Rowe L, Scott LR, Sherman MP, Stites NC, Sun Y, Tawiah-Boateng MA, Tibbetts AS, Wadington MC, West AC 2005 Mitochondrial transporters involved in oleic acid utilization and glutamate metabolism in yeast. Arch. Biochem. Biophys. 442: 21-32.

Troufflard S, Roscher A, Thomasset B, Barbotin JN, Rawsthorne S, Portais JC 2007 In vivo(13)C NMR determines metabolic fluxes and steady state in linseed embryos. Phytochemistry 68: 2341-2350.

Truesdale MR, Toldi O, Scott P 1999 The effect of elevated concentrations of fructose 2,6-bisphosphate on carbon metabolism during deacidification in the Crassulacean acid metabolism plant Kalanchoe daigremontiana. Plant Physiol. 121: 957-964.

Truksa M, Wu G, Vrinten P, Qiu X 2006 Metabolic engineering of plants to produce very long-chain polyunsaturated fatty acids. Transgenic Res. 15: 131-137.

Truman W, de Zabala MT, Grant M 2006 Type III effectors orchestrate a complex interplay between transcriptional networks to modify basal defence responses during pathogenesis and resistance. Plant J. 46: 14-33.

Trump S, Laudi S, Unruh N, Goelz R, Leibfritz D 2006 (1)H-NMR metabolic profiling of human neonatal urine. MAGMA 19: 305-312.

Tsagou V, Aggelis G 2006 Growth dynamics of Azospirillum lipoferum at steady and transitory states in the presence of NH4+. J. Appl. Microbiol. 100: 286-295.

Tsaneva-Atanasova K, Zimliki CL, Bertram R, Sherman A 2006 Diffusion of calcium and metabolites in pancreatic islets: killing oscillations with a pitchfork. Biophys. J. 90: 3434-3446.

Tu BP, Kudlicki A, Rowicka M, McKnight SL 2005 Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes. Science 310: 1152-1158.

Tukiainen T, Tynkkynen T, Makinen VP, Jylanki P, Kangas A, Hokkanen J, Vehtari A, Grohn O, Hallikainen M, Soininen H, Kivipelto M, Groop PH, Kaski K, Laatikainen R, Soininen P, Pirttila T, Ala-Korpela M 2008 A multi-metabolite analysis of serum by (1)H NMR spectroscopy: early systemic signs of Alzheimer's disease. Biochem. Biophys. Res. Commun. Aug 9 [Epub ahead of print].

Turner SM, Linfoot PA, Neese RA, Hellerstein MK 2005 Sources of plasma glucose and liver glycogen in fasted ob/ob mice. Acta Diabetol. 42: 187-193.

Tuteja N 2003 Plant DNA helicases: the long unwinding road. J. Exp. Bot. 54: 2201-2214.

Tzvetkova-Chevolleau T, Franck F, Alawady AE, Dall'Osto L, Carriere F, Bassi R, Grimm B, Nussaume L, Havaux M 2007 The light stress-induced protein ELIP2 is a regulator of chlorophyll synthesis in Arabidopsis thaliana. Plant J. 50: 795-809.

Ueda A, Kathiresan A, Inada M, Narita Y, Nakamura T, Shi W, Takabe T, Bennett J 2004 Osmotic stress in barley regulates expression of a different set of genes than salt stress does. J. Exp. Bot. 55: 2213-2218.

Uemura M, Steponkus PL 2003 Modification of the intracellular sugar content alters the incidence of freeze-induced membrane lesions of protoplasts isolated from Arabidopsis thaliana leaves. Plant Cell Environ. 26: 1083-1096.

Ueno D, Iwashita T, Zhao FJ, Ma JF 2008 Characterization of Cd translocation and identification of the Cd form in xylem sap of the Cd-hyperaccumulator Arabidopsis halleri. Plant Cell Physiol. 49: 540-548.

Ueyama Y, Suzuki K, Fukuchi-Mizutani M, Fukui Y, Miyazaki K, Ohkawa H, Kusumi T, Tanaka Y 2002 Molecular and biochemical characterization of torenia flavonoid 3'-hydroxylase and flavone synthase II and modification of flower color by modulating the expression of these genes. Plant Sci. 163: 253-263.

Ulanov A, Widholm JM 2007 Effect of the expression of cyanamide hydratase on metabolites in cyanamide-treated soybean plants kept in the light or dark. J. Exp. Bot. 58: 4319-4332.

Umana P, Bailey JE 1997 A mathematical model of N-linked glycoform biosynthesis. Biotechnol. Bioeng. 55: 890-908.

Unno H, Uchida T, Sugawara H, Kurisu G, Sugiyama T, Yamaya T, Sakakibara H, Hase T, Kusunoki M 2006 Atomic structure of plant glutamine synthetase: a key enzyme for plant productivity. J. Biol. Chem. 281: 29287-29296.

Urbanczik R 2006 SNA--a toolbox for the stoichiometric analysis of metabolic networks. BMC Bioinformatics 7: 129.

Urbanczik R, Wagner C 2005 Functional stoichiometric analysis of metabolic networks. Bioinformatics 21: 4176-4180.

Urbanczyk-Wochniak E, Baxter C, Kolbe A, Kopka J, Sweetlove LJ, Fernie AR 2005 Profiling of diurnal patterns of metabolite and transcript abundance in potato (Solanum tuberosum) leaves. Planta 221: 891-903.

Urbanczyk-Wochniak E, Fernie AR 2005 Metabolic profiling reveals altered nitrogen nutrient regimes have diverse effects on the metabolism of hydroponically-grown tomato (Solanum lycopersicum) plants. J. Exp. Bot. 56: 309-321.

Urbanczyk-Wochniak E, Sumner LW 2007 MedicCyc: a biochemical pathway database for Medicago truncatula. Bioinformatics 23: 1418-1423.

Urbanczyk-Wochniak E, Usadel B, Thimm O, Nunes-Nesi A, Carrari F, Davy M, Blasing O, Kowalczyk M, Weicht D, Polinceusz A, Meyer S, Stitt M, Fernie AR 2006 Conversion of MapMan to allow the analysis of transcript data from Solanaceous species: effects of genetic and environmental alterations in energy metabolism in the leaf. Plant Mol. Biol. 60: 773-792.

Usadel B, Nagel A, Thimm O, Redestig H, Blaesing OE, Palacios-Rojas N, Selbig J, Hannemann J, Piques MC, Steinhauser D, Scheible WR, Gibon Y, Morcuende R, Weicht D, Meyer S, Stitt M 2005 Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of coresponding genes, and comparison with known responses. Plant Physiol. 138: 1195-1204.

Uys L, Botha FC, Hofmeyr JH, Rohwer JM 2007 Kinetic model of sucrose accumulation in maturing sugarcane culm tissue. Phytochemistry 68: 2375-2392.

Vadali RV, Bennett GN, San KY 2004 Cofactor engineering of intracellular CoA/acetyl-CoA and its effect on metabolic flux redistribution in Escherichia coli. Metab. Eng. 6: 133-139.

Valette J, Chaumeil M, Guillermier M, Bloch G, Hantraye P, Lebon V 2008 Diffusion-weighted NMR spectroscopy allows probing of (13)C labeling of glutamate inside distinct metabolic compartments in the brain. Magn. Reson. Med. 60: 306-311.

Valle J, Da Re S, Schmid S, Skurnik D, D'Ari R, Ghigo JM 2008 The amino acid valine is secreted in continuous-flow bacterial biofilms. J. Bacteriol. 190: 264-274.

Vallino JJ, Stephanopoulos G 2000 Metabolic flux distributions in Corynebacterium glutamicum during growth and lysine overproduction. Biotechnol. Bioeng. 67: 872-885.

Valliyodan B, Nguyen HT 2006 Understanding regulatory networks and engineering for enhanced drought tolerance in plants. Curr. Opin. Plant Biol. 9: 189-195.

Valverde F, Losada M, Serrano A 1999 Engineering a central metabolic pathway: glycolysis with no net phosphorylation in an Escherichia coli gap mutant complemented with a plant GapN gene. FEBS Lett. 449: 153-158.

van Damme M, Huibers RP, Elberse J, Van den Ackerveken G 2008 Arabidopsis DMR6 encodes a putative 2OG-Fe(II) oxygenase that is defense-associated but required for susceptibility to downy mildew. Plant J. 54: 785-793.

van de Mortel JE, Almar Villanueva L, Schat H, Kwekkeboom J, Coughlan S, Moerland PD, Ver Loren van Themaat E, Koornneef M, Aarts MG 2006 Large expression differences in genes for iron and zinc homeostasis, stress response and lignin biosynthesis distinguish Arabidopsis thaliana and the related metal hyperaccumulator Thlaspi caerulescens. Plant Physiol. 142: 1127-1147.

van der Star WR, van de Graaf MJ, Kartal B, Picioreanu C, Jetten MS, van Loosdrecht MC 2008 Response of anaerobic ammonium-oxidizing bacteria to hydroxylamine. Appl. Environ. Microbiol. 74: 4417-4426.

Van Dien SJ, Iwatani S, Usuda Y, Matsui K 2006 Theoretical analysis of amino acid-producing Escherichia coli using a stoichiometric model and multivariate linear regression. J. Biosci. Bioeng. 102: 34-40.

Van Dien SJ, Lidstrom ME 2002 Stoichiometric model for evaluating the metabolic capabilities of the facultative methylotroph Methylobacterium extorquens AM1, with application to reconstruction of C(3) and C(4) metabolism. Biotechnol. Bioeng. 78: 296-312.

Van Dongen JT, Roeb GW, Dautzenberg M, Froehlich A, Vigeolas H, Minchin PE, Geigenberger P 2004 Phloem import and storage metabolism are highly coordinated by the low oxygen concentrations within developing wheat seeds. Plant Physiol. 135: 1809-1821.

Van Heerden PDR, Kruger GHJ, Loveland JE, Parry MAJ, Foyer CH 2003 Dark chilling imposes metabolic restrictions on photosynthesis in soybean. Plant Cell Environ. 26: 323-337.

van Helden J, Naim A, Mancuso R, Eldridge M, Wernisch L, Gilbert D, Wodak SJ 2000 Representing and analysing molecular and cellular function using the computer. Biol. Chem. 381: 921-935.

van Riel NA, Giuseppin ML, TerSchure EG, Verrips CT 1998 A structured, minimal parameter model of the central nitrogen metabolism in Saccharomyces cerevisiae: the prediction of the behavior of mutants. J. Theor. Biol. 191: 397-414.

van Riel NA, Giuseppin ML, Verrips CT 2000 Dynamic optimal control of homeostasis: an integrative system approach for modeling of the central nitrogen metabolism in Saccharomyces cerevisiae. Metab. Eng. 2: 49-68.

van Walsum GP, Lynd LR 1998 Allocation of ATP to synthesis of cells and hydrolytic enzymes in cellulolytic fermentative microorganisms: bioenergetics, kinetics, and bioprocessing. Biotechnol. Bioeng. 58: 316-320.

van Winden W, Schipper D, Verheijen P, Heijnen J 2001 Innovations in generation and analysis of 2D [13C,1H] COSY NMR spectra for metabolic flux analysis purposes. Metab. Eng. 3: 322-343.

van Winden W, Verheijen P, Heijnen S 2001 Possible pitfalls of flux calculations based on 13C-labeling. Metab. Eng. 3: 151-162.

Van Winden WA, Heijnen JJ, Verheijen PJ 2002 Cumulative bondomers: A new concept in flux analysis from 2D [13C,1H] COSY NMR data. Biotechnol. Bioeng. 80: 731-745.

van Winden WA, Heijnen JJ, Verheijen PJ, Grievink J 2001 A priori analysis of metabolic flux identifiability from 13C-labeling data. Biotechnol. Bioeng. 74: 505-516.

van Winden WA, van Dam JC, Ras C, Kleijn RJ, Vinke JL, van Gulik WM, Heijnen JJ 2005 Metabolic-flux analysis of Saccharomyces cerevisiae CEN.PK113-7D based on mass isotopomer measurements of (13)C-labeled primary metabolites. FEMS Yeast Res. 5: 559-568.

Van Winden WA, Van Gulik WM, Schipper D, Verheijen PJ, Krabben P, Vinke JL, Heijnen JJ 2003 Metabolic flux and metabolic network analysis of Penicillium chrysogenum using 2D [13C, 1H] COSY NMR measurements and cumulative bondomer simulation. Biotechnol. Bioeng. 83: 75-92.

Vanholme R, Morreel K, Ralph J, Boerjan W 2008 Lignin engineering. Curr. Opin. Plant Biol. 11: 278-285.

Vanlerberghe GC, Robson CA, Yip JY 2002 Induction of mitochondrial alternative oxidase in response to a cell signal pathway down-regulating the cytochrome pathway prevents programmed cell death. Plant Physiol. 129: 1829-1842.

Vanrolleghem PA, Heijnen JJ 1998 A structured approach for selection among candidate metabolic network models and estimation of unknown stoichiometric coefficients. Biotechnol. Bioeng. 58: 133-138.

Varma A, Boesch BW, Palsson BO 1993 Biochemical production capabilities of Escherichia coli. Biotechnol. Bioeng. 42: 59-73.

Varma A, Boesch BW, Palsson BO 1993 Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates. Appl. Environ. Microbiol. 59: 2465-2473.

Varma A, Palsson BO 1994 Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Appl. Environ. Microbiol. 60: 3724-3731.

Varma A, Palsson BO 1994 Metabolic flux balancing: basic concepts, scientific and practical use. Bio-Technol. 12: 994-998.

Varma R, Hector S, Greco WR, Clark K, Hawthorn L, Porter C, Pendyala L 2007 Platinum drug effects on the expression of genes in the polyamine pathway: time-course and concentration-effect analysis based on Affymetrix gene expression profiling of A2780 ovarian carcinoma cells. Cancer Chemother. Pharmacol. 59: 711-723.

Varner J, Ramkrishna D 1998 Application of cybernetic models to metabolic engineering: investigation of storage pathways. Biotechnol. Bioeng. 58: 282-291.

Varner J, Ramkrishna D 1999 Metabolic engineering from a cybernetic perspective. 1. Theoretical preliminaries. Biotechnol. Prog. 15: 407-425.

Varner J, Ramkrishna D 1999 Mathematical models of metabolic pathways. Curr. Opin. Biotechnol. 10: 146-150.

Varner J, Ramkrishna D 1999 Metabolic engineering from a cybernetic perspective. 2. Qualitative investigation of nodal architechtures and their response to genetic perturbation. Biotechnol. Prog. 15: 426-438.

Varner J, Ramkrishna D 1998 The non-linear analysis of cybernetic models. Guidelines for model formulation. J. Biotechnol. 71: 67-103.

Varner J, Ramkrishna D 1999 Metabolic engineering from a cybernetic perspective: aspartate family of amino acids. Metab. Eng. 1: 88-116.

Varner JD 2000 Large-scale prediction of phenotype: concept. Biotechnol. Bioeng. 69: 664-678.

Vaseghi S, Macherhammer F, Zibek S, Reuss M 2001 Signal transduction dynamics of the protein kinase-A/phosphofructokinase-2 system in Saccharomyces cerevisiae. Metab. Eng. 3: 163-172.

Vasquez-Robinet C, Mane SP, Ulanov AV, Watkinson JI, Stromberg VK, De Koeyer D, Schafleitner R, Willmot DB, Bonierbale M, Bohnert HJ, Grene R 2008 Physiological and molecular adaptations to drought in Andean potato genotypes. J. Exp. Bot. 59: 2109-2023.

Vaubourdolle M, Jardel A, Coudray-Lucas C, Ekindjian OG, Agneray J, Cynober L 1989 Fate of enterally administered ornithine in healthy animals: interactions with alpha-ketoglutarate. Nutrition 5: 183-187.

Veech RL, Fell DA 1996 Distribution control of metabolic flux. Cell Biochem. & Function 14: 229-236.

Veenhoff LM, Heuberger EH, Poolman B 2002 Quaternary structure and function of transport proteins. Trends Biochem. Sci. 27: 242-249.

Veflingstad SR, Almeida J, Voit EO 2004 Priming nonlinear searches for pathway identification. Theor. Biol. Med. Model. 1: 8.

Velasco I, Arevalo-Rodriguez M, Marina P, Calderon IL 2005 A new mutation in the yeast aspartate kinase induces threonine accumulation in a temperature-regulated way. Yeast 22: 99-110.

Velasco-Garcia R, Gonzalez-Segura L, Munoz-Clares RA 2000 Steady-state kinetic mechanism of the NADP+- and NAD+-dependent reactions catalysed by betaine aldehyde dehydrogenase from Pseudomonas aeruginosa. Biochem. J. 352: 675-683.

Venkatesh KV, Doshi P, Rengaswamy R 1997 An optimal strategy to model microbial growth in a multiple substrate environment. Biotechnol. Bioeng. 56: 635-644.

Vera J, de Atauri P, Cascante M, Torres NV 2003 Multicriteria optimization of biochemical systems by linear programming: application to production of ethanol by Saccharomyces cerevisiae. Biotechnol. Bioeng. 83: 335-343.

Vercoutere B, Durozard D, Baverel G, Martin G 2004 Complexity of glutamine metabolism in kidney tubules from fed and fasted rats. Biochem. J. 378: 485-495.

Vereecke D, Cornelis K, Temmerman W, Holsters M, Goethals K 2002 Versatile persistence pathways for pathogens of animals and plants. Trends Microbiol. 10: 485-488.

Verma K, Shekhawat GS, Sharma A, Mehta SK, Sharma V 2008 Cadmium induced oxidative stress and changes in soluble and ionically bound cell wall peroxidase activities in roots of seedling and 3-4 leaf stage plants of Brassica juncea (L.) czern. Plant Cell Rep. 27: 1261-1269.

Vermeulen T, Gorg B, Vogl T, Wolf M, Varga G, Toutain A, Paul R, Schliess F, Haussinger D, Haberle J 2008 Glutamine synthetase is essential for proliferation of fetal skin fibroblasts. Arch. Biochem. Biophys. Jul 17 [Epub ahead of print].

Verpoorte R 2000 Chapter 1. Secondary Metabolism. In "Metabolic Engineering of Plant Secondary Metabolism" (Verpoorte R, Alfermann AW eds), Kluwer Academic Publishers, Dortrecht, The Netherlands, pp. 1-29.

Verpoorte R, van der Heijden R, Memelink J 2000 Chapter 2. General Strategies. In "Metabolic Engineering of Plant Secondary Metabolism" (Verpoorte R, Alfermann AW, eds), Kluwer Academic Publishers, Dortrecht, The Netherlands, pp. 31-50.

Verslues PE, Kim YS, Zhu JK 2007 Altered ABA, proline and hydrogen peroxide in an Arabidopsis glutamate:glyoxylate aminotransferase mutant. Plant Mol. Biol. 64: 205-217.

Vert JP, Kanehisa M 2003 Extracting active pathways from gene expression data. Bioinformatics 19 Suppl. 2: II238-II244.

Veyres N, Danon A, Aono M, Galliot S, Karibasappa YB, Diet A, Grandmottet F, Tamaoki M, Lesur D, Pilard S, Boitel-Conti M, Sangwan-Norreel BS, Sangwan RS 2008 The Arabidopsis sweetie mutant is affected in carbohydrate metabolism and defective in the control of growth, development and senescence. Plant J. Apr 30 [Epub ahead of print].

Vicre M, Farrant JM, Driouich A 2004 Insights into the cellular mechanisms of desiccation tolerance among angiosperm resurrection plant species. Plant Cell Environ. 27: 1329-1340.

Vidal G, Ribas-Carbo M, Garmier M, Dubertret G, Rasmusson AG, Mathieu C, Foyer CH, De Paepe R 2007 Lack of respiratory chain complex I impairs alternative oxidase engagement and modulates redox signaling during elicitor-induced cell death in tobacco. Plant Cell 19: 640-655.

Vigeolas H, Mohlmann T, Martini N, Neuhaus HE, Geigenberger P 2004 Embryo-specific reduction of ADP-Glc pyrophosphorylase leads to an inhibition of starch synthesis and a delay in oil accumulation in developing seeds of oilseed rape. Plant Physiol. 136: 2676-2686.

Viitanen PV, Devine AL, Khan MS, Deuel DL, Van Dyk DE, Daniell H 2004 Metabolic engineering of the chloroplast genome using the Echerichia coli ubiC gene reveals that chorismate is a readily abundant plant precursor for p-hydroxybenzoic acid biosynthesis. Plant Physiol. 136: 4048-4060.

Vimr ER, Kalivoda KA, Deszo EL, Steenbergen SM 2004 Diversity of microbial sialic acid metabolism. Microbiol. Mol. Biol. Rev. 68: 132-153.

Vinnakota K, Kemp ML, Kushmerick MJ 2006 Dynamics of muscle glycogenolysis modeled with pH time course computation and pH-dependent reaction equilibria and enzyme kinetics. Biophys. J. 91: 1264-1287.

Viola R, Pelloux J, VAN DER Ploeg A, Gillespie T, Marquis N, Roberts AG, Hancock RD 2007 Symplastic connection is required for bud outgrowth following dormancy in potato (Solanum tuberosum L.) tubers. Plant Cell Environ. 30: 973-983.

Visser D, Heijnen JJ 2002 The mathematics of metabolic control analysis revisited. Metab. Eng. 4: 114-123.

Visser D, Schmid JW, Mauch K, Reuss M, Heijnen JJ 2004 Optimal re-design of primary metabolism in Escherichia coli using linlog kinetics. Metab. Eng. 6: 378-390.

Visser D, van der Heijden R, Mauch K, Reuss M, Heijnen S 2000 Tendency modeling: a new approach to obtain simplified kinetic models of metabolism applied to Saccharomyces cerevisiae. Metab. Eng. 2: 252-275.

Visser WF, van Roermund CW, Ijlst L, Hellingwerf KJ, Waterham HR, Wanders RJ 2006 First identification of a 2-ketoglutarate/isocitrate transport system in mammalian peroxisomes and its characterization. Biochem. Biophys. Res. Commun. 348: 1224-1231.

Viswanathan K, Lawrence S, Hinderlich S, Yarema KJ, Lee YC, Betenbaugh MJ 2003 Engineering sialic acid synthetic ability into insect cells: identifying metabolic bottlenecks and devising strategies to overcome them. Biochemistry 42: 15215-15225.

Vital-Lopez FG, Armaou A, Nikolaev EV, Maranas CD 2006 A computational procedure for optimal engineering interventions using kinetic models of metabolism. Biotechnol. Prog. 22: 1507-1517.

Vitkup D, Kharchenko P, Wagner A 2006 Influence of metabolic network structure and function on enzyme evolution. Genome Biol. 7: R39.

Vitvitsky V, Thomas M, Ghorpade A, Gendelman HE, Banerjee R 2006 A functional transsulfuration pathway in brain links to glutathione homeostasis. J. Biol. Chem. 281: 35785-35793.

Vladutiu GD 2001 Heterozygosity: An expanding role in proteomics. Mol. Gen. & Metab. 74: 51-63.

Vo TD, Greenberg HJ, Palsson BO 2004 Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data. J. Biol. Chem. 279: 39532-39540.

Vo TD, Palsson BO 2006 Isotopomer analysis of myocardial substrate metabolism: a systems biology approach. Biotechnol. Bioeng. 95: 972-983.

Vohradsky J, Thompson CJ 2006 Systems level analysis of protein synthesis patterns associated with bacterial growth and metabolic transitions. Proteomics 6: 785-793.

Voicu MC, Zwiazek JJ 2004 Cycloheximide inhibits root water flow and stomatal conductance in aspen (Populus tremuloides) seedlings. Plant Cell Environ. 27: 199-208.

Voit EO 2002 Metabolic modeling: a tool of drug discovery in the post-genomic era. Drug Discov. Today 7: 621-628.

Voit EO, Almeida J 2004 Decoupling dynamical systems for pathway identification from metabolic profiles. Bioinformatics 20: 1670-1681.

Voit EO, Alvarez-Vasquez F, Sims KJ 2004 Analysis of dynamic labeling data. Math. Biosci. 191: 83-99.

Voit EO, Del Signore M 2001 Assessment of effects of experimental imprecision on optimized biochemical systems. Biotechnol. Bioeng. 74: 443-448.

Voit EO, Radivoyevitch T 2000 Biochemical systems analysis of genome-wide expression data. Bioinformatics 16: 1023-1037.

Voit EO, Savageau MA 1987 Accuracy of alternative representations for integrated biochemical systems. Biochemistry 26: 6869-6880.

Volaire F, Norton M 2006 Summer dormancy in perennial temperate grasses. Ann. Bot. (Lond.) 98: 927-933.

von Kamp A, Schuster S 2006 Metatool 5.0: fast and flexible elementary modes analysis. Bioinformatics 22: 1930-1931.

von Roepenack-Lahaye E, Degenkolb T, Zerjeski M, Franz M, Roth U, Wessjohann L, Schmidt J, Scheel D, Clemens S 2004 Profiling of Arabidopsis secondary metabolites by capillary liquid chromatography coupled to electrospray ionization quadrupole time-of-flight mass spectrometry. Plant Physiol. 134: 548-559.

Von Sternberg R 2000 Genomes and form. The case for teleomorphic recursivity. Ann. N.Y. Acad. Sci. 901: 224-236.

von Wettstein D 2007 From analysis of mutants to genetic engineering. Annu. Rev. Plant Biol. 58: 1-19.

Vongsangnak W, Olsen P, Hansen K, Krogsgaard S, Nielsen J 2008 Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae. BMC Genomics 9: 245.

Wackett LP 1998 Directed evolution of new enzymes and pathways for environmental biocatalysis. Ann. N.Y. Acad. Sci. 864: 142-152.

Wackett LP 2004 Evolution of enzymes for the metabolism of new chemical inputs into the environment. J. Biol. Chem. 279: 41259-41262.

Waditee R, Bhuiyan MN, Hirata E, Hibino T, Tanaka Y, Shikata M, Takabe T 2007 Metabolic engineering for betaine accumulation in microbes and plants. J. Biol. Chem. 282: 34185-34193.

Wagner A 2000 Robustness against mutations in genetic networks of yeast. Nat. Genet. 24: 355-361.

Wagner A, Fell DA 2001 The small world inside large metabolic networks. Proc. Roy. Soc. Lond. B. Biol. Sci. 268: 1803-1810.

Wagner A, Ralph J, Akiyama T, Flint H, Phillips L, Torr K, Nanayakkara B, Te Kiri L 2007 Exploring lignification in conifers by silencing hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyltransferase in Pinus radiata. Proc. Natl. Acad. Sci. U.S.A. 104: 11856-11861.

Wagner C, Koury MJ 2007 S-Adenosylhomocysteine: a better indicator of vascular disease than homocysteine? Am. J. Clin. Nutr. 86: 1581-1585.

Wagner C, Urbanczik R 2005 The geometry of the flux cone of a metabolic network. Biophys. J. 89: 3837-3845.

Wagner WP, Helmig D, Fall R 2000 Isoprene biosynthesis in Bacillus subtilis via the methylerythritol phosphate pathway. J. Nat. Prod. 63: 37-40.

Wahl SA, Noh K, Wiechert W 2008 13C labeling experiments at metabolic nonstationary conditions: an exploratory study. BMC Bioinformatics 9: 152.

Wahl SA, Takors R, Wiechert W 2006 Interpretation of metabolic flux maps by limitation potentials and constrained limitation sensitivities. Biotechnol. Bioeng. 94: 263-272.

Wakasa K, Hasegawa H, Nemoto H, Matsuda F, Miyazawa H, Tozawa Y, Morino K, Komatsu A, Yamada T, Terakawa T, Miyagawa H 2006 High-level tryptophan accumulation in seeds of transgenic rice and its limited effects on agronomic traits and seed metabolite profile. J. Exp. Bot. 57: 3069-3078.

Walters RG, Ibrahim DG, Horton P, Kruger NJ 2004 A mutant of Arabidopsis lacking the triose-phosphate/phosphate translocator reveals metabolic regulation of starch breakdown in the light. Plant Physiol. 135: 891-906.

Walters RG, Rogers JJ, Shephard F, Horton P 1999 Acclimation of Arabidopsis thaliana to the light environment: the role of photoreceptors. Planta 209: 517-527.

Wan XY, Liu JY 2008 Comparative proteomic analysis reveals an intimate protein network provoked by hydrogen peroxide stress in rice seedling leaves. Mol. Cell. Proteomics 7: 1469-1488.

Wang F, Jiang JG, Chen Q 2007 Progress on molecular breeding and metabolic engineering of biosynthesis pathways of C(30), C(35), C(40), C(45), C(50) carotenoids. Biotechnol. Adv. 25: 211-222.

Wang F, Raab RM, Washabaugh MW, Buckland BC 2000 Gene therapy and metabolic engineering. Metab. Eng. 2: 126-139.

Wang H, Hao L, Shung CY, Sunter G, Bisaro DM 2003 Adenosine kinase is inactivated by geminivirus AL2 and L2 proteins. Plant Cell 15: 3020-3032.

Wang H, Zheng HQ, Sha W, Zeng R, Xia QC 2006 A proteomic approach to analysing responses of Arabidopsis thaliana callus cells to clinostat rotation. J. Exp. Bot. 57: 827-835.

Wang HJ, Wan AR, Hsu CM, Lee KW, Yu SM, Jauh GY 2007 Transcriptomic adaptations in rice suspension cells under sucrose starvation. Plant Mol. Biol. 63: 441-463.

Wang J, Chen N, Zhang B, Tan Q, Zhang K 2003 Metabolic flux analysis of L-tryptophan biosynthesis. Wei Sheng Wu Xue Bao 43: 473-480.

Wang JX, Breaker RR 2008 Riboswitches that sense S-adenosylmethionine and S-adenosylhomocysteine. Biochem. Cell Biol. 86: 157-168.

Wang L, Gamez A, Archer H, Abola EE, Sarkissian CN, Fitzpatrick P, Wendt D, Zhang Y, Vellard M, Bliesath J, Bell SM, Lemontt JF, Scriver CR, Stevens RC 2008 Structural and biochemical characterization of the therapeutic Anabaena variabilis phenylalanine ammonia lyase. J. Mol. Biol. 380: 623-635.

Wang L, Hatzimanikatis V 2006 Metabolic engineering under uncertainty. II: Analysis of yeast metabolism. Metab. Eng. 8: 142-159.

Wang L, Hatzimanikatis V 2006 Metabolic engineering under uncertainty. I: Framework development. Metab. Eng. 8: 133-141.

Wang MY, Siddiqi MY, Ruth TJ, Glass A 1993 Ammonium uptake by rice roots. II. Kinetics of 13NH4+ influx across the plasmalemma. Plant Physiol. 103: 1259-1267.

Wang Q, Chen X, Yang Y, Zhao X 2006 Genome-scale in silico aided metabolic analysis and flux comparisons of Escherichia coli to improve succinate production. Appl. Microbiol. Biotechnol. 73: 887-894.

Wang Q, Yang Y, Ma H, Zhao X 2007 Metabolic network properties help assign weights to elementary modes to understand physiological flux distributions. Bioinformatics 23: 1049-1052.

Wang S, Nagrath D, Chen PC, Berthiaume F, Yarmush ML 2008 Three-dimensional primary hepatocyte culture in synthetic self-assembling peptide hydrogel. Tissue Eng. Part A. 14: 227-236.

Wang W, Sun J, Hartlep M, Deckwer WD, Zeng AP 2003 Combined use of proteomic analysis and enzyme activity assays for metabolic pathway analysis of glycerol fermentation by Klebsiella pneumoniae. Biotechnol. Bioeng. 83: 525-536.

Wang X, Li W, Li M, Welti R 2006 Profiling lipid changes in plant response to low temperatures. Physiol. Plant. 126: 90-96.

Wang Y, Li Y, Li Y, Ma X, Yang S, Yang L 2006 Investigations into the analysis and modeling of the cytochrome P450 cycle. J. Phys. Chem. B. Condens. Matter Mater. Surf. Interfaces Biophys. 110: 10139-10143.

Wang YH, Garvin DF, Kochian LV 2001 Nitrate-induced genes in tomato roots. Array analysis reveals novel genes that may play a role in nitrogen nutrition. Plant Physiol. 127: 345-359.

Wang Z, Xiang L, Shao J, Wegrzyn A, Wegrzyn G 2006 Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism. Microb. Cell Fact. 5: 34.

Wasaki J, Yonetani R, Kuroda S, Shinano T, Yazaki J, Fujii F, Shimbo K, Yamamoto K, Sakata K, Sasaki T, Kishimoto N, Kikuchi S, Yamagishi M, Osaki M 2003 Transcriptomic analysis of metabolic changes by phosphorus stress in rice plant roots. Plant Cell Environ. 26: 1515-1523.

Waters MT, Fray RG, Pyke KA 2004 Stromule formation is dependent upon plastid size, plastid differentiation status and the density of plastids within the cell. Plant J. 39: 655-667.

Watford M, Chellaraj V, Ismat A, Brown P, Raman P 2002 Hepatic glutamine metabolism. Nutrition 18: 301-303.

Weber AP 2004 Solute transporters as connecting elements between cytosol and plastid stroma. Curr. Opin. Plant Biol. 7: 247-253.

Weber AP, Fischer K 2007 Making the connections - the crucial role of metabolite transporters at the interface between chloroplast and cytosol. FEBS Lett. 581: 2215-2222.

Weber AP, Horst RJ, Barbier GG, Oesterhelt C 2007 Metabolism and metabolomics of eukaryotes living under extreme conditions. Int. Rev. Cytol. 256: 1-34.

Weber AP, Oesterhelt C, Gross W, Brautigam A, Imboden LA, Krassovskaya I, Linka N, Truchina J, Schneidereit J, Voll H, Voll LM, Zimmermann M, Jamai A, Riekhof WR, Yu B, Garavito RM, Benning C 2004 EST-analysis of the thermo-acidophilic red microalga Galdieria sulphuraria reveals potential for lipid A biosynthesis and unveils the pathway of carbon export from rhodoplasts. Plant Mol. Biol. 55: 17-32.

Weber AP, Schwacke R, Flugge UI 2005 Solute transporters of the plastid envelope membrane. Annu. Rev. Plant Biol. 56: 133-164.

Weber H, Borisjuk L, Wobus U 2005 Molecular physiology of legume seed development. Annu. Rev. Plant Biol. 56: 253-279.

Weber H, Chetelat A, Reymond P, Farmer EE 2004 Selective and powerful stress gene expression in Arabidopsis in response to malondialdehyde. Plant J. 37: 877-888.

Weber J, Kayser A, Rinas U 2005 Metabolic flux analysis of Escherichia coli in glucose-limited continuous culture. II. Dynamic response to famine and feast, activation of the methylglyoxal pathway and oscillatory behaviour. Microbiology 151: 707-716.

Weber W, Link N, Fussenegger M 2006 A genetic redox sensor for mammalian cells. Metab. Eng. 8: 273-280.

Weber W, Rimann M, de Glutz FN, Weber E, Memmert K, Fussenegger M 2005 Gas-inducible product gene expression in bioreactors. Metab. Eng. 7: 174-181.

Weckwerth W, Morgenthal K 2005 Metabolomics: from pattern recognition to biological interpretation. Drug Discov. Today 10: 1551-1558.

Wei B, Shin S, LaPorte D, Wolfe AJ, Romeo T 2000 Global regulatory mutations in csrA and rpoS cause severe central carbon stress in Escherichia coli in the presence of acetate. J. Bacteriol. 182: 1632-1640.

Wei H, Persson S, Mehta T, Srinivasasainagendra V, Chen L, Page GP, Somerville C, Loraine A 2006 Transcriptional coordination of the metabolic network in Arabidopsis thaliana. Plant Physiol. 142: 762-774.

Weise SE, Kim KS, Stewart RP, Sharkey TD 2005 beta-Maltose is the metabolically active anomer of maltose during transitory starch degradation. Plant Physiol. 137: 756-761.

Weiss B 2006 Evidence for mutagenesis by nitric oxide during nitrate metabolism in Escherichia coli. J. Bacteriol. 188: 829-833.

Weissbach H, Brot N 1991 Regulation of methionine synthesis in Escherichia coli. Mol. Microbiol. 5: 1593-1597.

Weitzel M, Wiechert W, Noh K 2007 The topology of metabolic isotope labeling networks. BMC Bioinformatics 8: 315.

Welchen E, Chan RL, Gonzalez DH 2002 Metabolic regulation of genes encoding cytochrome c and cytochrome c oxidase subunit Vb in Arabidopsis. Plant Cell Environ. 25: 1605-1615.

Welti R, Wang X 2004 Lipid species profiling: a high-throughput approach to identify lipid compositional changes and determine the function of genes involved in lipid metabolism and signaling. Curr. Opin. Plant Biol. 7: 337-344.

Wendisch VF, Bott M, Kalinowski J, Oldiges M, Wiechert W 2006 Emerging Corynebacterium glutamicum systems biology. J. Biotechnol. 124: 74-92.

Wendisch VF, de Graaf AA, Sahm H, Eikmanns BJ 2000 Quantitative determination of metabolic fluxes during coutilization of two carbon sources: comparative analyses with Corynebacterium glutamicum during growth on acetate and/or glucose. J. Bacteriol. 182: 3088-3096.

Wenzler M, Holscher D, Oerther T, Schneider B 2008 Nectar formation and floral nectary anatomy of Anigozanthos flavidus: a combined magnetic resonance imaging and spectroscopy study. J. Exp. Bot. Jul 24 [Epub ahead of print].

Weretilnyk EA, Alexander KJ, Drebenstedt M, Snider JD, Summers PS, Moffatt BA 2001 Maintaining methylation activities during salt stress. The involvement of adenosine kinase. Plant Physiol. 125: 856-865.

Werle M, Kreuzer J, Hofele J, Elsasser A, Ackermann C, Katus HA, Vogt AM 2005 Metabolic control analysis of the Warburg-effect in proliferating vascular smooth muscle cells. J. Biomed. Sci. 12: 827-834.

Wernicke S, Rasche F 2007 Simple and fast alignment of metabolic pathways by exploiting local diversity. Bioinformatics 23: 1978-1985.

Weselake RJ, Shah S, Tang M, Quant PA, Snyder CL, Furukawa-Stoffer TL, Zhu W, Taylor DC, Zou J, Kumar A, Hall L, Laroche A, Rakow G, Raney P, Moloney MM, Harwood JL 2008 Metabolic control analysis is helpful for informed genetic manipulation of oilseed rape (Brassica napus) to increase seed oil content. J. Exp. Bot. Aug 13 [Epub ahead of print].

Westerhoff HV 1989 Control, regulation and thermodynamics of free-energy transduction. Biochimie 71: 877-886.

Westerhoff HV, Getz WM, Bruggeman F, Hofmeyr JH, Rohwer JM, Snoep JL 2002 ECA: control in ecosystems. Mol. Biol. Rep. 29: 113-117.

Westerhoff HV, Groen AK, Wanders RJ 1984 Modern theories of metabolic control and their applications (review). Biosci. Rep. 4: 1-22.

Westerhoff HV, Hofmeyr JH, Kholodenko BN 1994 Getting to the inside of cells using metabolic control analysis. Biophys. Chem. 50: 273-283.

Westerhoff HV, Kolodkin A, Conradie R, Wilkinson SJ, Bruggeman FJ, Krab K, van Schuppen JH, Hardin H, Bakker BM, Mone MJ, Rybakova KN, Eijken M, van Leeuwen HJ, Snoep JL 2008 Systems biology towards life in silico: mathematics of the control of living cells. J. Math. Biol. Feb 16 [Epub ahead of print].

Wheeler MC, Arias CL, Tronconi MA, Maurino VG, Andreo CS, Drincovitch MF 2008 Arabidopsis thaliana NADP-malic enzyme isoforms: high degree of identity but clearly distinct properties. Plant Mol. Biol. 67: 231-242.

White PJ, Bowen HC, Marshall B, Broadley MR 2007 Extraordinarily high leaf selenium to sulfur ratios define 'Se-accumulator' plants. Ann. Bot. (Lond.) 100: 111-118.

Whittaker A, Martinelli T, Bochicchio A, Vazzana C, Farrant J 2004 Comparison of sucrose metabolism during the rehydration of desiccation-tolerant and desiccation-sensitve leaf material of Sporobolus stapfianus. Physiol. Plant. 122: 11-20.

Whittaker A, Martinelli T, Farrant JM, Bochicchio A, Vazzana C 2007 Sucrose phosphate synthase activity and the co-ordination of carbon partitioning during sucrose and amino acid accumulation in desiccation-tolerant leaf material of the C4 resurrection plant Sporobolus stapfianus during dehydration. J. Exp. Bot. 58: 3775-3787.

Wiback SJ, Famili I, Greenberg HJ, Palsson BO 2004 Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space. J. Theor. Biol. 228: 437-447.

Wiback SJ, Mahadevan R, Palsson BO 2004 Using metabolic flux data to further constrain the metabolic solution space and predict internal flux patterns: the Escherichia coli spectrum. Biotechnol. Bioeng. 86: 317-331.

Wiback SJ, Palsson BO 2002 Extreme pathway analysis of human red blood cell metabolism. Biophys. J. 83: 808-818.

Wiechert W 2002 Modeling and simulation: tools for metabolic engineering. J. Biotechnol. 94: 37-63.

Wiechert W 2007 The thermodynamic meaning of metabolic exchange fluxes. Biophys. J. 93: 2255-2264.

Wiechert W 2001 13C metabolic flux analysis. Metab. Eng. 3: 195-206.

Wiechert W, de Graaf AA 1997 Bidirectional reaction steps in metabolic networks. 1. Modeling and simulation of carbon isotope labeling experiments. Biotechnol. Bioeng. 55: 101-117.

Wiechert W, de Graaf AA 1996 In vivo stationary flux analysis by 13C labeling experiments. Adv. Biochem. Eng. Biotechnol. 54: 109-154.

Wiechert W, Mollney M, Isermann N, Wurzel M, de Graaf AA 1999 Bidirectional reaction steps in metabolic networks: III. Explicit solution and analysis of isotopomer labeling systems. Biotechnol. Bioeng. 66: 69-85.

Wiechert W, Mollney M, Petersen S, de Graaf AA 2001 A universal framework for 13C metabolic flux analysis. Metab. Eng. 3: 265-283.

Wiechert W, Noh K 2005 From stationary to instationary metabolic flux analysis. Adv. Biochem. Eng. Biotechnol. 92: 145-172.

Wiechert W, Schweissgut O, Takanaga H, Frommer WB 2007 Fluxomics: mass spectrometry versus quantitative imaging. Curr. Opin. Plant Biol. 10: 323-330.

Wiechert W, Wurzel M 2001 Metabolic isotopomer labeling systems. Part I: global dynamic behavior. Math Biosci. 169: 173-205.

Wieczorek K, Hofmann J, Blochl A, Szakasits D, Bohlmann H, Grundler FM 2008 Arabidopsis endo-1,4-beta-glucanases are involved in the formation of root syncytia induced by Heterodera schachtii. Plant J. 53: 336-351.

Wienkoop S, Zoeller D, Ebert B, Simon-Rosin U, Fisahn J, Glinski M, Weckwerth W 2004 Cell-specific protein profiling in Arabidopsis thaliana trichomes: identification of trichome-located proteins involved in sulfur metabolism and detoxification. Phytochemistry 65: 1641-1649.

Wilderman PR, Xu M, Jin Y, Coates RM, Peters RJ 2004 Identification of syn-pimara-7,15-diene synthase reveals functional clustering of terpene synthases involved in rice phytoalexin/allelochemical biosynthesis. Plant Physiol. 135: 2098-2105.

Wilhelm C, Becker A, Toepel J, Vieler A, Rautenberger R 2004 Photophysiology and primary production of phytoplankton in freshwater. Physiol. Plant. 120: 347-357.

Wilhelm T, Behre J, Schuster S 2004 Analysis of structural robustness of metabolic networks. Syst. Biol. (Stevenage) 1: 114-120.

Wilkie MP, Claude JF, Cockshutt A, Holmes JA, Wang YS, Youson JH, Walsh PJ 2006 Shifting patterns of nitrogen excretion and amino acid catabolism capacity during the life cycle of the sea lamprey (Petromyzon marinus). Physiol. Biochem. Zool. 79: 885-898.

Williams AG, Withers SE, Brechany EY, Banks JM 2006 Glutamate dehydrogenase activity in lactobacilli and the use of glutamate dehydrogenase-producing adjunct Lactobacillus spp. cultures in the manufacture of cheddar cheese. J. Appl. Microbiol. 101: 1062-1075.

Williams KT, Schalinske KL 2007 New insights into the regulation of methyl group and homocysteine metabolism. J. Nutr. 137: 311-314.

Williams RE, Lenz EM, Evans JA, Wilson ID, Granger JH, Plumb RS, Stumpf CL 2005 A combined (1)H NMR and HPLC-MS-based metabonomic study of urine from obese (fa/fa) Zucker and normal Wistar-derived rats. J. Pharm. Biomed. Anal. 38: 465-471.

Williams TC, Miguet L, Masakapalli SK, Kruger NJ, Sweetlove LJ, Ratcliffe RG 2008 Metabolic network fluxes in heterotrophic Arabidopsis cells: stability of the flux distribution under different oxygenation conditions. Plant Physiol. Jul 30 [Epub ahead of print].

Wilson KE, Krol M, Huner NP 2003 Temperature-induced greening of Chlorella vulgaris. The role of the cellular energy balance and zeaxanthin-dependent nonphotochemical quenching. Planta 217: 616-627.

Winder WW, Hardie DG 1999 AMP-activated protein kinase, a metabolic master switch: possible roles in type 2 diabetes. Am. J. Physiol. 277: E1-E10.

Wingler A 2002 The function of trehalose biosynthesis in plants. Phytochemistry 60: 437-440.

Winkel BS 2004 Metabolic channeling in plants. Annu. Rev. Plant Biol. 55: 85-107.

Winkel-Shirley B 1999 Evidence for enzyme complexes in the phenylpropanoid and flavonoid pathways. Physiol. Plant. 107: 142-149.

Winkler HH, Daugherty RM 1984 Proline transport and metabolism in Rickettsia prowazekii. J. Bacteriol. 158: 460-463.

Wirtz M, Hell R 2007 Dominant-negative modification reveals the regulatory function of the multimeric cysteine synthase protein complex in transgenic tobacco. Plant Cell 19: 625-639.

Wishart DS 2005 Metabolomics: the principles and potential applications to transplantation. Am. J. Transplant. 5: 2814-2820.

Withers PC, Guppy M 1996 Do Australian desert frogs co-accumulate counteracting solutes with urea during aestivation? J. Exp. Biol. 199: 1809-1816.

Wittmann C 2002 Metabolic flux analysis using mass spectrometry. Adv. Biochem. Eng. Biotechnol. 74: 39-64.

Wittmann C, Heinzle E 1999 Mass spectrometry for metabolic flux analysis. Biotechnol. Bioeng. 62: 739-750.

Wittmann C, Heinzle E 2001 Application of MALDI-TOF MS to lysine-producing Corynebacterium glutamicum: a novel approach for metabolic flux analysis. Eur. J. Biochem. 268: 2441-2455.

Wittmann C, Heinzle E 2001 Modeling and experimental design for metabolic flux analysis of lysine-producing Corynebacteria by mass spectrometry. Metab. Eng. 3: 173-191.

Wittmann C, Heinzle E 2002 Genealogy profiling through strain improvement by using metabolic network analysis: metabolic flux genealogy of several generations of lysine-producing Corynebacteria. Appl. Environ. Microbiol. 68: 5843-59.

Wittmann C, Kiefer P, Zelder O 2004 Metabolic fluxes in Corynebacterium glutamicum during lysine production with sucrose as carbon source. Appl. Environ. Microbiol. 70: 7277-7287.

Wittmann C, Kromer JO, Kiefer P, Binz T, Heinzle E 2004 Impact of the cold shock phenomenon on quantification of intracellular metabolites in bacteria. Anal. Biochem. 327: 135-139.

Wlaschin AP, Trinh CT, Carlson R, Srienc F 2006 The fractional contributions of elementary modes to the metabolism of Escherichia coli and their estimation from reaction entropies. Metab. Eng. 8: 338-352.

Wojas S, Clemens S, Hennig J, Sklodowska A, Kopera E, Schat H, Bal W, Antosiewicz DM 2008 Overexpression of phytochelatin synthase in tobacco: distinctive effects of AtPCS1 and CePCS genes on plant response to cadmium. J. Exp. Bot. 59: 2205-2219.

Wolf J, Heinrich R 1997 Dynamics of two-component biochemical systems in interacting cells; synchronization and desynchronization of oscillations and multiple steady states. Biosystems 43: 1-24.

Wolf J, Sohn H, Heinrich R, Kuriyama H 2001 Mathematical analysis of a mechanism for autonomous metabolic oscillations in continuous culture of Saccharomyces cerevisiae. FEBS Lett. 499: 230-234.

Wolfertz M, Sharkey TD, Boland W, Kuhnemann F, Yeh S, Weise SE 2003 Biochemical regulation of isoprene emission. Plant Cell Environ. 26: 1357-1364.

Wong KT, Lee YY, Brusic V, Tan J, Yap MG, Nissom PM 2005 Elevation of gamma-glutamyltransferase activity in 293 HEK cells constitutively expressing antisense glutaminase mRNA. Metab. Eng. 7: 375-383.

Wong WW, Tran LM, Liao JC 2008 A hidden square-root boundary between growth rate and biomass yield. Biotechnol. Bioeng. Jul 15 [Epub ahead of print].

Wood NT 2001 Profiling modified metabolomes. Trends Plant Sci. 6: 191.

Wright BE, Field RJ 1994 The tricarboxylic acid cycle in Dictyostelium discoideum. Two methods of analysis using the same data. J. Biol. Chem. 269: 19931-19932.

Wright TC, Cant JP, Brenna JT, McBride BW 2006 Acetyl CoA carboxylase shares control of fatty acid synthesis with fatty acid synthase in bovine mammary homogenate. J. Dairy Sci. 89: 2552-2558.

Wu G, Truksa M, Datla N, Vrinten P, Bauer J, Zank T, Cirpus P, Heinz E, Qiu X 2005 Stepwise engineering to produce high yields of very long-chain polyunsaturated fatty acids in plants. Nature Biotechnol. 23: 1013-1017.

Wu L, Mashego MR, Proell AM, Vinke JL, Ras C, van Dam J, van Winden WA, van Gulik WM, Heijnen JJ 2006 In vivo kinetics of primary metabolism in Saccharomyces cerevisiae studied through prolonged chemostat cultivation. Metab. Eng. 8: 160-171.

Wu L, van Winden WA, van Gulik WM, Heijnen JJ 2005 Application of metabolome data in functional genomics: a conceptual strategy. Metab. Eng. 7: 302-310.

Wu S, Chappell J 2008 Metabolic engineering of natural products in plants; tools of the trade and challenges for the future. Curr. Opin. Biotechnol. 19: 145-152.

Wu X, Skog K, Jagerstad M 1997 Trigonelline, a naturally occurring constituent of green coffee beans behind the mutagenic activity of roasted coffee? Mutat. Res. 391: 171-177.

Wu ZF, Du GC, Chen J 2005 Effects of culture conditions on coenzyme Q10 production by Rhizobium radiobacter by metabolic flux analysis. Wei Sheng Wu Xue Bao 45: 231-235.

Wuchty S 2006 Topology and weights in a protein domain interaction network - a novel way to predict protein interactions. BMC Genomics 7: 122.

Wunderlich Z, Mirny LA 2006 Using the topology of metabolic networks to predict viability of mutant strains. Biophys. J. 91: 2304-2311.

Wunderling M, Paul HH, Lohmann W 1986 Evaluation of a direct spectrophotometric method for the rapid determination of ascorbate and dehydroascorbate in blood using ascorbate oxidase. Biol. Chem. Hoppe Seyler 367: 1047-1054.

Wurtele ES, Li J, Diao L, Zhang H, Foster CM, Fatland B, Dickerson J, Brown A, Cox Z, Cook D, Lee EK, Hofmann H 2003 MetNet: software to build and model the biogenetic lattice of Arabidopsis. Comp. Funct. Genomics 4: 239-245.

Wyka TP, Bohn A, Duarte HM, Kaiser F, Luttge UE 2004 Perturbations of malate accumulation and the endogenous rhythms of gas exchange in the Crassulacean acid metabolism plant Kalanchoe daigremontiana: testing the tonoplast-as-oscillator model. Planta 219: 705-713.

Xia XQ, Wise MJ 2003 DiMSim: a discrete-event simulator of metabolic networks. J. Chem. Inf. Compu. Sci. 43: 1011-1019.

Xia Y, Yu H, Jansen R, Seringhaus M, Baxter S, Greenbaum D, Zhao H, Gerstein M 2004 Analyzing cellular biochemistry in terms of molecular networks. Annu. Rev. Biochem. 73: 1051-1087.

Xiao J, Shi Z, Gao P, Feng H, Duan Z, Mao Z 2006 On-line optimization of glutamate production based on balanced metabolic control by RQ. Bioprocess. Biosyst. Eng. 29: 109-117.

Xie DY, Sharma SB, Wright E, Wang ZY, Dixon RA 2006 Metabolic engineering of proanthocyanidins through co-expression of anthocyanidin reductase and the PAP1 MYB transcription factor. Plant J. 45: 895-907.

Xie Z, Kapteyn J, Gang DR 2008 A systems biology investigation of the MEP/terpenoid and shikimate/phenylpropanoid pathways points to multiple levels of metabolic control in sweet basil glandular trichomes. Plant J. 54: 349-361.

Xiu ZL, Zeng AP, Deckwer WD 1998 Multiplicity and stability analysis of microorganisms in continuous culture: effects of metabolic overflow and growth inhibition. Biotechnol. Bioeng. 57: 251-261.

Xu M, Hillwig ML, Prisic S, Coates RM, Peters RJ 2004 Functional identification of rice syn-copalyl diphosphate synthase and its role in initiating biosynthesis of diterpenoid phytoalexin/allelopathic natural products. Plant J. 39: 309-318.

Xu W, Bak S, Decker A, Paquette SM, Feyereisen R, Galbraith DW 2001 Microarray-based analysis of gene expression in very large gene families: the cytochrome P450 gene superfamily of Arabidopsis thaliana. Gene 272: 61-74.

Xu W, Sato SJ, Clemente TE, Chollet R 2007 The PEP-carboxylase kinase gene family in Glycine max (GmPpcK1-4): an in-depth molecular analysis with nodulated, non-transgenic and transgenic plants. Plant J. 49: 910-923.

Xu YL, Li L, Gage DA, Zeevaart JA 1999 Feedback regulation of GA5 expression and metabolic engineering of gibberellin levels in Arabidopsis. Plant Cell 11: 927-936.

Xue GP, McIntyre CL, Glassop D, Shorter R 2008 Use of expression analysis to dissect alterations in carbohydrate metabolism in wheat leaves during drought stress. Plant Mol. Biol. 67: 197-214.

Xue HH, Fujie M, Sakaguchi T, Oda T, Ogawa H, Kneer NM, Lardy HA, Ichiyama A 1999 Flux of the L-serine metabolism in rat liver. The predominant contribution of serine dehydratase. J. Biol. Chem. 274: 16020-16027.

Xue Y, Zhao L, Liu HW, Sherman DH 1998 A gene cluster for macrolide antibiotic biosynthesis in Streptomyces venezuelae: architecture of metabolic diversity. Proc. Natl. Acad. Sci. U.S.A. 95: 12111-12116.

Yamakawa H, Hirose T, Kuroda M, Yamaguchi T 2007 Comprehensive expression profiling of rice grain filling-related genes under high temperature using DNA microarray. Plant Physiol. 144: 258-277.

Yamaki H, Yamaguchi M, Tsuruo T, Yamaguchi H 1992 Mechanism of action of an antifungal antibiotic, RI-331, (S) 2-amino-4-oxo-5-hydroxypentanoic acid; kinetics of inactivation of homoserine dehydrogenase from Saccharomyces cerevisiae. J. Antibiot. (Tokyo) 45: 750-755.

Yamamoto T, Kimura S, Mori Y, Oka M, Ishibashi T, Yanagawa Y, Nara T, Nakagawa H, Hashimoto J, Sakaguchi K 2004 Degradation of proliferating cell nuclear antigen by 26S proteasome in rice (Oryza sativa L.). Planta 218: 640-646.

Yamamoto YT, Zamski E, Williamson JD, Conkling MA, Pharr DM 1997 Subcellular localization of celery mannitol dehydrogenase. A cytosolic metabolic enzyme in nuclei. Plant Physiol. 115: 1397-1403.

Yamashita M 2003 Engineering of closed ecological system in space and inter-organismal interactions. Biol. Sci. Space 17: 51-53.

Yamazaki D, Motohashi K, Kasama T, Hara Y, Hisabori T 2004 Target proteins of the cytosolic thioredoxins in Arabidopsis thaliana. Plant Cell Physiol. 45: 18-27.

Yan D 2007 Protection of the glutamate pool concentration in enteric bacteria. Proc. Natl. Acad. Sci. U.S.A. 104: 9475-9480.

Yan J, He C, Wang J, Mao Z, Holaday SA, Allen RD, Zhang H 2004 Overexpression of the Arabidopsis 14-3-3 protein GF14 lambda in cotton leads to a "stay-green" phenotype and improves stress tolerance under moderate drought conditions. Plant Cell Physiol. 45: 1007-1014.

Yan L, Ropella GE, Park S, Roberts MS, Hunt CA 2008 Modeling and simulation of hepatic drug disposition using a physiologically based, multi-agent in silico liver. Pharm. Res. 25: 1023-1036.

Yanagimachi KS, Stafford DE, Dexter AF, Sinskey AJ, Drew S, Stephanopoulos G 2001 Application of radiolabeled tracers to biocatalytic flux analysis. Eur. J. Biochem. 268: 4950-4960.

Yancey PH 2005 Organic osmolytes as compatible, metabolic and counteracting cytoprotectants in high osmolarity and other stresses. J. Exp. Biol. 208: 2819-2830.

Yang C, Hua Q, Shimizu K 2002 Quantitative analysis of intracellular metabolic fluxes using GC-MS and two-dimensional NMR spectroscopy. J. Biosci. Bioeng. 93: 78-87.

Yang C, Hua Q, Shimizu K 1999 Development of a kinetic model for L-lysine biosynthesis in Corynebacterium glutamicum and its application to metabolic control analysis. J. Biosci. Bioeng. 88: 393-403.

Yang C, Hua Q, Shimizu K 2002 Integration of the information from gene expression and metabolic fluxes for the analysis of the regulatory mechanisms in Synechocystis. Appl. Microbiol. Biotechnol. 58: 813-822.

Yang CR 2008 An enzyme-centric approach for modelling non-linear biological complexity. BMC Syst. Biol. 2: 70.

Yang F, Qian H, Beard DA 2005 Ab initio prediction of thermodynamically feasible reaction directions from biochemical network stoichiometry. Metab. Eng. 7: 251-259.

Yang J, Park S, Kamdem DP, Keathley DE, Retzel E, Paule C, Kapur V, Han KH 2003 Novel gene expression profiles define the metabolic and physiological processes characteristic of wood and its extractive formation in a hardwood tree species, Robinia pseudoacacia. Plant Mol. Biol. 52: 935-956.

Yang J, Wongsa S, Kadirkamanathan V, Billings SA, Wright PC 2005 Metabolic flux distribution analysis by 13C-tracer experiments using the Markov chain-Monte Carlo method. Biochem. Soc. Trans. 33: 1421-1422.

Yang L, Kasumov T, Kombu RS, Zhu SH, Cendrowski AV, David F, Anderson VE, Kelleher JK, Brunengraber H 2008 Metabolomic and mass isotopomer analysis of liver gluconeogenesis and citric acid cycle: II. Heterogeneity of metabolite labeling pattern. J. Biol. Chem. 283: 21988-21996.

Yang L, Kombu RS, Kasumov T, Zhu SH, Cendrowski AV, David F, Anderson VE, Kelleher JK, Brunengraber H 2008 Metabolomic and mass isotopomer analysis of liver gluconeogenesis and citric acid cycle: I. Interrelation between gluconeogenesis and cataplerosis; formation of methoxamates from aminooxyacetate and ketoacids. J. Biol. Chem. 283: 21978-21987.

Yang Q, Wang Y, Zhang J, Shi W, Qian C, Peng X 2007 Identification of aluminum-responsive proteins in rice roots by a proteomic approach: cysteine synthase as a key player in Al response. Proteomics 7: 737-749.

Yang TH, Heinzle E, Wittmann C 2005 Theoretical aspects of 13C metabolic flux analysis with sole quantification of carbon dioxide labeling. Comput. Biol. Chem. 29: 121-133.

Yang TH, Wittmann C, Heinzle E 2006 Respirometric 13C flux analysis, part I: design, construction and validation of a novel multiple reactor system using on-line membrane inlet mass spectrometry. Metab. Eng. 8: 417-431.

Yang WJ, Rich PJ, Axtell JD, Wood KV, Bonham CC, Ejeta G, Mickelbart MV, Rhodes D 2003 Genotypic variation for glycinebetaine in sorghum. Crop Sci. 43: 162-169.

Yang YT, Aristidou AA, San KY, Bennett GN 1999 Metabolic flux analysis of Escherichia coli deficient in the acetate production pathway and expressing the Bacillus subtilis acetolactate synthase. Metab. Eng. 1: 26-34.

Yang YT, Bennett GN, San KY 1998 Genetic and metabolic engineering. EJB Electronic Journal of Biotechnology 1: 1-8.

Yang YT, Peredelchuk M, Bennett GN, San KY 2000 Effect of variation of Klebsiella pneumoniae acetolactate synthase expression on metabolic flux redistribution in Escherichia coli. Biotechnol. Bioeng. 69: 150-159.

Yang YT, San KY, Bennett GN 1999 Redistribution of metabolic fluxes in Escherichia coli with fermentative lactate dehydrogenase overexpression and deletion. Metab. Eng. 1: 141-152.

Yaniv Y, Stanley WC, Saidel GM, Cabrera ME, Landesberg A 2008 The role of Ca2+ in coupling cardiac metabolism with regulation of contraction: in silico modeling. Ann. N. Y. Acad. Sci. 1123: 69-78.

Yara A, Yaeno T, Hasegawa M, Seto H, Montillet JL, Kusumi K, Seo S, Iba K 2007 Disease resistance against Magnaporthe grisea is enhanced in transgenic rice with suppression of {omega}-3 fatty acid desaturases. Plant Cell Physiol. 48: 1263-1274.

Yaronskaya E, Vershilovskaya I, Poers Y, Alawady AE, Averina N, Grimm B 2006 Cytokinin effects on tetrapyrrole biosynthesis and photosynthetic activity in barley seedlings. Planta 224: 700-709.

Yaronskaya E, Ziemann V, Walter G, Averina N, Borner T, Grimm B 2003 Metabolic control of the tetrapyrrole biosynthetic pathway for porphyrin distribution in the barley mutant albostrians. Plant J. 35: 512-522.

Yazaki K 2005 Transporters of secondary metabolites. Curr. Opin. Plant Biol. 8: 301-307.

Yazdani SS, Gonzalez R 2007 Anaerobic fermentation of glycerol: a path to economic viability for the biofuels industry. Curr. Opin. Biotechnol. 18: 213-219.

Ye C, Wu S, Yang Q, Ma C, Yang G, Wang B 2005 Cloning, sequencing and salt induced expression of PEAMT and BADH in oilseed rape (Brassica napus). DNA Seq. 16: 364-371.

Yeang CH, Vingron M 2006 A joint model of regulatory and metabolic networks. BMC Bioinformatics 7: 332.

Yen J, Liao JC, Lee