Nutritional systems biology modeling: From molecular mechanisms to physiology

PLoS Computational Biology

Volumn 5, Issue 11, 2009, Pages

  De Graaf, Albert A ^a   Freidig, Andreas P ^a,b   De Roos, Baukje ^c   Jamshidi, Neema ^d   Heinemann, Matthias ^e   Rullmann, Johan A C ^f   Hall, Kevin D ^g   Adiels, Martin ^h   Van Ommen, Ben ^a  

^a TNO   (Netherlands)

^b Amsterdam Molecular Therapeutics   (Netherlands)

^c ROWETT RESEARCH INSTITUTE   (United Kingdom)

^d UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^e ETH ZURICH   (Switzerland)

^f NV ORGANON   (Netherlands)

^g NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

^h UNIVERSITY OF GOTHENBURG   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; COMPUTATION THEORY; PHYSIOLOGY; TIME DOMAIN ANALYSIS;

BIOLOGICAL FIELDS; CELLULARS; COMPUTATIONAL MODELING AND SIMULATION; MODEL APPLICATION; MODELING APPROACH; MOLECULAR MECHANISM; PHYSIOLOGICAL LEVELS; RESEARCH QUESTIONS; SPACE AND TIME; SYSTEMS BIOLOGY;

NUTRITION;

APOLIPOPROTEIN B100; HYDROXYMETHYLGLUTARYL COENZYME A REDUCTASE INHIBITOR; INTERMEDIATE DENSITY LIPOPROTEIN; LOW DENSITY LIPOPROTEIN; OMEGA 3 FATTY ACID; VERY LOW DENSITY LIPOPROTEIN;

ABDOMINAL FAT; ADVANCED CANCER; AMINO ACID TRANSPORT; BIOLOGICAL MODEL; BODY FAT; BODY WEIGHT; CACHEXIA; CANCER PATIENT; COMPUTER MODEL; ENERGY EXPENDITURE; HUMAN; IN VIVO STUDY; LIFESTYLE MODIFICATION; LIPID TRANSPORT; LIPOLYSIS; LIPOPROTEIN METABOLISM; MACRONUTRIENT; MATHEMATICAL MODEL; MOLECULAR MECHANICS; MOLECULAR MODEL; NONHUMAN; NUTRITION; PATIENT PARTICIPATION; PHENOTYPE; PHYSIOLOGY; PROTEIN TRANSPORT; REVIEW; SYSTEMS BIOLOGY; VIRTUAL REALITY; WEIGHT CHANGE; WEIGHT REDUCTION; ANIMAL; COMPUTER SIMULATION; METHODOLOGY; NUTRITIONAL STATUS;

ANIMALS; COMPUTER SIMULATION; HUMANS; MODELS, BIOLOGICAL; NUTRITIONAL STATUS; SYSTEMS BIOLOGY;

EID: 73449130181     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000554     Document Type: Review

References (90)

1. McLester JS (1927) Nutrition and diet in health and disease. Philadelphia: W.B. Saunders Company.
2. Kooijman SA (2001) Quantitative aspects of metabolic organization: a discussion of concepts. Philos Trans R Soc Lond B Biol Sci 356: 331-349.
3. Coburn SP, Townsend DW (1988) A multicompartment model of vitamin B6 metabolism. Prog Food Nutr Sci 12: 227-242.
4. Foster DM, Aamodt RL, Henkin RI, Berman M (1979) Zinc metabolism in humans: a kinetic model. Am J Physiol 237: R340-R349.
5. Green MH, Green JB (1990) The application of compartmental analysis to research in nutrition. Annu Rev Nutr 10: 41-61.
6. Patterson BH, Zech LA (1992) Development of a model for selenite metabolism in humans. J Nutr 122: 709-714.
7. de Graaf AA, Venema K (2008) Gaining insight into microbial physiology in the large intestine: a special role for stable isotopes. Adv Microb Physiol 53: 73-168.
8. Di Ventura B, Lemerle C, Michalodimitrakis K, Serrano L (2006) From in vivo to in silico biology and back. Nature 443: 527-533.
9. 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.
10. Klipp E, Nordlander B, Kruger R, Gennemark P, Hohmann S (2005) Integrative model of the response of yeast to osmotic shock. Nat Biotechnol 23: 975-982.
11. Reed MC, Nijhout HF, Neuhouser ML, Gregory JF, III, Shane B, et al. (2006) A mathematical model gives insights into nutritional and genetic aspects of folatemediated one-carbon metabolism. J Nutr 136: 2653-2661.
12. Fell DA (1992) Metabolic control analysis: a survey of its theoretical and experimental development. Biochem J 286 ( Pt 2): 313-330.
13. Kuepfer L, Peter M, Sauer U, Stelling J (2007) Ensemble modeling for analysis of cell signaling dynamics. Nat Biotechnol 25: 1001-1006.
14. Oda K, Matsuoka Y, Funahashi A, Kitano H (2005) A comprehensive pathway map of epidermal growth factor receptor signaling. Mol Syst Biol 1: 2005.0010.
15. Oda K, Kitano H (2006) A comprehensive map of the toll-like receptor signaling network. Mol Syst Biol 2: 2006.0015.
16. MaH, SorokinA,MazeinA, SelkovA, Selkov E, et al. (2007)The Edinburgh human metabolic network reconstruction and its functional analysis. Mol Syst Biol 3: 135.
17. Reed JL, Famili I, Thiele I, Palsson BO (2006) Towards multidimensional genome annotation. Nat Rev Genet 7: 130-141.
18. 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.
19. Sheikh K, Forster J, Nielsen LK (2005) Modeling hybridoma cell metabolism using a generic genome-scale metabolic model of Mus musculus. Biotechnol Prog 21: 112-121.
20. Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, et al. (2007) Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci U S A 104: 1777-1782.
21. Chaves M, Sontag ED, Albert R (2006) Methods of robustness analysis for Boolean models of gene control networks. Syst Biol (Stevenage) 153: 154-167.
22. Bornholdt S (2008) Boolean network models of cellular regulation: prospects and limitations. J R Soc Interface 5 Suppl 1: S85-S94.
23. Ma HW, Zhao XM, Yuan YJ, Zeng AP (2004) Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph. Bioinformatics 20: 1870-1876.
24. 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.
25. Kummel A, Panke S, Heinemann M (2006) Systematic assignment of thermodynamic constraints in metabolic network models. BMC Bioinformatics 7: 512.
26. 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.
27. Price ND, Reed JL, Palsson BO (2004) Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol 2: 886-897.
28. Beard DA, Liang SD, Qian H (2002) Energy balance for analysis of complex metabolic networks. Biophys J 83: 79-86.
29. Beg QK, Vazquez A, Ernst J, de Menezes MA, Bar-Joseph Z, et al. (2007) Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity. Proc Natl Acad Sci U S A 104: 12663-12668.
30. Petersen S, van Lieres E, de Graaf AA, Sahm H, WiechertW(2004) A multi-scale approach for the predictive modeling of metabolic regulation. Kholodenko BN, Westerhoff HV, eds. Metabolic engineering in the post genomic era. Norwich (United Kingdom): Horizon Scientific Press.
31. Smallbone K, Simeonidis E, Broomhead DS, Kell DB (2007) Something from nothing: bridging the gap between constraint-based and kinetic modelling. FEBS J 274: 5576-5585.
32. Brown KS, Hill CC, Calero GA, Myers CR, Lee KH, Sethna JP, et al. (2004) The statistical mechanics of complex signaling networks: nerve growth factor signaling. Phys Biol 1: 184-195.
33. Gutenkunst RN, Waterfall JJ, Casey FP, Brown KS, Myers CR, et al. (2007) Universally sloppy parameter sensitivities in systems biology models. PLoS Comput Biol 3: 1871-1878. doi:10.1371/journal.pcbi.0030189.
34. Jamshidi N, Palsson BO (2008) Formulating genome-scale kinetic models in the post-genome era. Mol Syst Biol 4: 171.
35. Stephanopoulos G, Vallino JJ (1991) Network rigidity and metabolic engineering in metabolite overproduction. Science 252: 1675-1681.
36. Marx A, de Graaf AA, Wiechert W, Eggeling L, Sahm H (1996) Determination of the fluxes in the central metabolism of Corynebacterium glutamicum by nuclear magnetic resonance spectroscopy combined with metabolite balancing. Biotechnol Bioeng 49: 111-129.
37. Wiechert W, de Graaf AA (1997) Bidirectional reaction steps in metabolic networks: I. Modeling and simulation of carbon isotope labeling experiments. Biotechnol Bioeng 55: 101-117.
38. 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.
39. Noh K, Wahl A, Wiechert W (2006) Computational tools for isotopically instationary 13C labeling experiments under metabolic steady state conditions. Metab Eng 8: 554-577.
40. 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.
41. Wittmann C, de Graaf AA (2005) Metabolic flux analysis in Corynebacterium glutamicum. Eggeling L, Bott M, eds. Handbook of Corynebacterium glutamicum. Boca Raton (Florida): CRC Press/Taylor and Francis. pp 277-304.
42. Simha V, Garg A (2006) Lipodystrophy: lessons in lipid and energy metabolism. Curr Opin Lipidol 17: 162-169.
43. Adiels M, Olofsson SO, Taskinen MR, Boren J (2006) Diabetic dyslipidaemia. Curr Opin Lipidol 17: 238-246.
44. Parhofer KG, Barrett PH (2006) Thematic review series: patient-oriented research. What we have learned about VLDL and LDL metabolism from human kinetics studies. J Lipid Res 47: 1620-1630.
45. Patterson BW, Mittendorfer B, Elias N, Satyanarayana R, Klein S (2002) Use of stable isotopically labeled tracers to measure very low density lipoproteintriglyceride turnover. J Lipid Res 43: 223-233.
46. Adiels M, Packard C, Caslake MJ, Stewart P, Soro A, et al. (2005) A new combined multicompartmental model for apolipoprotein B-100 and triglyceride metabolism in VLDL subfractions. J Lipid Res 46: 58-67.
47. Hubner K, Schwager T, Winkler K, Reich JG, Holzhutter HG (2008) Computational lipidology: predicting lipoprotein density profiles in human blood plasma. PLoS Comput Biol 4: e1000079. doi:10.1371/journal. pcbi.1000079.
48. van Schalkwijk DB, de Graaf AA, van Ommen B, van Bochove K, Rensen PC, et al. (2009) Improved cholesterol phenotype analysis by a model relating lipoprotein lifecycle processes to particle size. J Lipid Res. In press.
49. Pearson T, Wattis JA, O'Malley B, Pickersgill L, Blackburn H, et al. (2009) Mathematical modelling of competitive LDL/VLDL binding and uptake by hepatocytes. J Math Biol 58: 845-880.
50. Chan DC, Barrett PH, Watts GF (2004) Lipoprotein transport in the metabolic syndrome: pathophysiological and interventional studies employing stable isotopy and modelling methods. Clin Sci (Lond) 107: 233-249.
51. Adiels M, Boren J, Caslake MJ, Stewart P, Soro A, et al. (2005) Overproduction of VLDL1 driven by hyperglycemia is a dominant feature of diabetic dyslipidemia. Arterioscler Thromb Vasc Biol 25: 1697-1703.
52. Kissebah AH, Alfarsi S, Evans DJ, Adams PW (1982) Integrated regulation of very low density lipoprotein triglyceride and apolipoprotein-B kinetics in noninsulin-dependent diabetes mellitus. Diabetes 31: 217-225.
53. Duvillard L, Pont F, Florentin E, Galland-Jos C, Gambert P, Verges B (2000) Metabolic abnormalities of apolipoprotein B-containing lipoproteins in noninsulin-dependent diabetes: a stable isotope kinetic study. Eur J Clin Invest 30:685-694.
54. Adiels M, Taskinen MR, Packard C, Caslake MJ, Soro-Paavonen A, et al. (2006) Overproduction of large VLDL particles is driven by increased liver fat content in man. Diabetologia 49: 755-765.
55. Adiels M, Westerbacka J, Soro-Paavonen A, Hakkinen AM, Vehkavaara S, et al. (2007) Acute suppression of VLDL1 secretion rate by insulin is associated with hepatic fat content and insulin resistance. Diabetologia 50: 2356-2365.
56. Riches FM, Watts GF, Hua J, Stewart GR, Naoumova RP, et al. (1999) Reduction in visceral adipose tissue is associated with improvement in apolipoprotein B-100 metabolism in obese men. J Clin Endocrinol Metab 84: 2854-2861.
57. James AP, Slivkoff-Clark K, Mamo JC (2003) New insights into cardiovascular disease risk in subjects with visceral obesity. Asia Pac J Public Health 15 Suppl: 37-40.
58. Bordin P, Bodamer OA, Venkatesan S, Gray RM, Bannister PA, et al. (1998) Effects of fish oil supplementation on apolipoprotein B100 production and lipoprotein metabolism in normolipidaemic males. Eur J Clin Nutr 52: 104-109.
59. Chan DC, Watts GF, Barrett PH, Beilin LJ, Redgrave TG, et al. (2002) Regulatory effects of HMG CoA reductase inhibitor and fish oils on apolipoprotein B-100 kinetics in insulin-resistant obese male subjects with dyslipidemia. Diabetes 51: 2377-2386.
60. Chan DC, Watts GF, Barrett PH, Beilin LJ, Mori TA (2002) Effect of atorvastatin and fish oil on plasma high-sensitivity C-reactive protein concentrations in individuals with visceral obesity. Clin Chem 48: 877-883.
61. Forbes GB (1987) Lean body mass-body fat interrelationships in humans. Nutr Rev 45: 225-231.
62. Hall KD (2007) Body fat and fat-free mass inter-relationships: Forbes's theory revisited. Br J Nutr 97: 1059-1063.
63. Hall KD (2008) What is the required energy deficit per unit weight loss? Int J Obes (Lond) 32: 573-576.
64. Hall KD, Jordan PN (2008) Modeling weight-loss maintenance to help prevent body weight regain. Am J Clin Nutr 88: 1495-1503.
65. Hallgreen CE, Hall KD (2008) Allometric relationship between changes of visceral fat and total fat mass. Int J Obes (Lond) 32: 845-852.
66. Hall KD, Hallgreen CE (2008) Increasing weight loss attenuates the preferential loss of visceral compared with subcutaneous fat: a predicted result of an allometric model. Int J Obes (Lond) 32: 722.
67. Chow CC, Hall KD (2008) The dynamics of human body weight change. PLoS Comput Biol 4: e1000045. doi:10.1371/journal.pcbi.1000045.
68. Hall KD, Bain HL, Chow CC (2007) How adaptations of substrate utilization regulate body composition. Int J Obes (Lond) 31: 1378-1383.
69. Jordan PN, Hall KD (2008) Dynamic coordination of macronutrient balance during infant growth: insights from a mathematical model. Am J Clin Nutr 87: 692-703.
70. Hall KD (2006) Computational model of in vivo human energy metabolism during semistarvation and refeeding. Am J Physiol Endocrinol Metab 291: 23-37.
71. Hall KD, Baracos VE (2008) Computational modeling of cancer cachexia. Curr Opin Clin Nutr Metab Care 11: 214-221.
72. Lieffers JR, Mourtzakis M, Hall KD, McCargar LJ, Prado CM, et al. (2009) A viscerally driven cachexia syndrome in patients with advanced colorectal cancer: contributions of organ and tumor mass to whole-body energy demands. Am J Clin Nutr 89: 1173-1179.
73. Southern J, Pitt-Francis J, Whiteley J, Stokeley D, Kobashi H, et al. (2008) Multi-scale computational modelling in biology and physiology. Prog Biophys Mol Biol 96: 60-89.
74. Hunter PJ, Crampin EJ, Nielsen PM (2008) Bioinformatics, multiscale modeling and the IUPS Physiome Project. Brief Bioinform 9: 333-343.
75. Noble D (2008) Computational models of the heart and their use in assessing the actions of drugs. J Pharmacol Sci 107: 107-117.
76. Hall K, Baillie R, Michelson S (2002) Biosimulation: dynamic modelling of biological systems. Annu Rep Med Chem 37: 279-288.
77. Kansal AR, Trimmer J (2005) Application of predictive biosimulation within pharmaceutical clinical development: examples of significance for translational medicine and clinical trial design. Syst Biol (Stevenage ) 152: 214-220.
78. Hall KD (2006) Computational model of in vivo human energy metabolism during semistarvation and refeeding. Am J Physiol Endocrinol Metab 291: E23-E37.
79. Bergman RN, Phillips LS, Cobelli C (1981) Physiologic evaluation of factors controlling glucose tolerance in man: measurement of insulin sensitivity and beta-cell glucose sensitivity from the response to intravenous glucose. J Clin Invest 68: 1456-1467.
80. Sedaghat AR, Sherman A, Quon MJ (2002) A mathematical model of metabolic insulin signaling pathways. Am J Physiol Endocrinol Metab 283: E1084-E1101.
81. Hall KD, Bain HL, Chow CC (2007) How adaptations of substrate utilization regulate body composition. Int J Obes (Lond) 31: 1378-1383.
82. Pattaranit R, van den Berg H A (2008) Mathematical models of energy homeostasis. J R Soc Interface 5: 1119-1135.
83. Handschin C, Spiegelman BM (2008) The role of exercise and PGC1alpha in inflammation and chronic disease. Nature 454: 463-469.
84. Wang H, Zhang Y, Yehuda-Shnaidman E, Medvedev AV, Kumar N, et al. (2008) Liver X receptor alpha is a transcriptional repressor of the uncoupling protein 1 gene and the brown fat phenotype. Mol Cell Biol 28: 2187-2200.
85. Guerra C, Navarro P, Valverde AM, Arribas M, Bruning J, et al. (2001) Brown adipose tissue-specific insulin receptor knockout shows diabetic phenotype without insulin resistance. J Clin Invest 108: 1205-1213.
86. Leroith D, Accili D (2008) Mechanisms of disease: using genetically altered mice to study concepts of type 2 diabetes. Nat Clin Pract Endocrinol Metab 4: 164-172.
87. Yang E, Almon RR, Dubois DC, Jusko WJ, Androulakis IP (2008) Extracting global system dynamics of corticosteroid genomic effects in rat liver. J Pharmacol Exp Ther 324: 1243-1254.
88. Lamb J, Crawford ED, Peck D, Modell JW, Blat IC, et al. (2006) The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science 313: 1929-1935.
89. Bild AH, Yao G, Chang JT, Wang Q, Potti A, et al. (2006) Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature 439: 353-357.
90. Berg EL, Hytopoulos E, Plavec I, Kunkel EJ (2005) Approaches to the analysis of cell signaling networks and their application in drug discovery. Curr Opin Drug Discov Devel 8: 107-114.