A procedure for the estimation over time of metabolic fluxes in scenarios where measurements are uncertain and/or insufficient

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Llaneras, Francisco ^a   Picó, Jesús ^a  

^a UNIVERSITAT POLITÈCNICA DE VALÈNCIA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL CONSTRAINTS; DYNAMIC BEHAVIOURS; ENVIRONMENTAL CONDITIONS; FLUX BALANCE ANALYSIS; INDUSTRIAL ENVIRONMENTS; INDUSTRIAL PROCESSS; METABOLIC FLUX ANALYSIS; OFF-LINE ANALYSIS;

DATA HANDLING; ESTIMATION; METABOLISM; OPTIMIZATION;

UNCERTAINTY ANALYSIS;

ANALYTIC METHOD; ANALYTICAL ERROR; ANIMAL CELL; ARTICLE; BIOMASS; CELL CULTURE; CELL METABOLISM; CHO CELL; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; FLUX SPECTRUM APPROACH; INTERMETHOD COMPARISON; MATHEMATICAL COMPUTING; MEASUREMENT; METABOLIC REGULATION; NONHUMAN; NONLINEAR SYSTEM; ONLINE MONITORING; RELIABILITY; TIME; ALGORITHM; ANIMAL; BIOLOGICAL MODEL; COMPUTER SIMULATION; CRICETULUS; HAMSTER; METABOLISM; PHYSIOLOGY; SIGNAL TRANSDUCTION; STATISTICAL ANALYSIS; STATISTICAL MODEL;

PROTEOME;

ALGORITHMS; ANIMALS; CHO CELLS; COMPUTER SIMULATION; CRICETINAE; CRICETULUS; DATA INTERPRETATION, STATISTICAL; MODELS, BIOLOGICAL; MODELS, STATISTICAL; PROTEOME; SIGNAL TRANSDUCTION;

EID: 38749117205     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-421     Document Type: Article

References (48)

1. Palsson B The challenges of in silico biology Nat Biotechnol 2000, 18:1147-1150. 10.1038/81125 11062431
2. Kitano H Computational systems biology Nature 2002, 420:206-210. 10.1038/ nature01254 12432404
3. Papin JA Price ND Wiback SJ Fell DA Palsson BO Metabolic pathways in the post-genome era Trends Biochem Sci 2003, 28:250-258. 10.1016/ S0968-0004(03)00064-1 12765837
4. Cornish-Bowden A Cardenas ML From genome to cellular phenotype - a role for metabolic flux analysis? Nat Biotechnol 2000, 18:267-268. 10.1038/ 73696 10700136
5. Stephanopoulos GN Aristidou AA Nielsen J Metabolic Engineering: Principles and Methodologies San Diego: Academic Press 1998.
6. Bonarius HPJ Schmid G Tramper J Flux Analysis of underdetermined metabolic networks: The quest for the missing constraints Tibtech 1997, 15(308):309-314.
7. Wiback SJ Famili I Greenberg HJ Palsson BO Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space J Theor Biol 2004, 228:437-447. 10.1016/j.jtbi.2004.02.006 15178193
8. Edwards JS Covert M Palsson B Metabolic modelling of microbes: The flux-balance approach Environ Microbiol 2002, 4:133-140. 10.1046/ j.1462-2920.2002.00282.x 12000313
9. Duarte NC Palsson BØ Fu P Integrated analysis of metabolic phenotypes in Saccharomyces cerevisiae BMC Genomics 2004, 5:63. 520746 15355549 10.1186/1471-2164-5-63
10. Bonarius HPJ Hatzimanikatis V Meesters KPH de Gooijer CD Schmid G Tramper J Metabolic flux analysis of hybridoma cells in different culture media using mass balances Biotechnol Bioeng 1996, 50:299-318. 10.1002/(SICI)1097-0290(19960505)50:3<299::AID-BIT9>3.0.CO;2-B
11. Follstad BD Balcarcel RR Stephanopoulos G Wang DI Metabolic flux analysis of hybridoma continuous culture steady state multiplicity Biotechnol Bioeng 1999, 63:675-683. 10.1002/ (SICI)1097-0290(19990620)63:6<675::AID-BIT5>3.0.CO;2-R 10397824
12. Nyberg GB Balcarcel RR Follstad BD Stephanopoulos G Wang DI Metabolism of peptide amino acids by Chinese hamster ovary cells grown in a complex medium Biotechnol Bioeng 1999, 62:324-335. 10.1002/ (SICI)1097-0290(19990205)62:3<324::AID-BIT9>3.0.CO;2-C 10099544
13. Fischer E Zamboni N Sauer U High-throughput metabolic flux analysis based on gas chromatography-mass spectrometry derived 13C constraints Anal Biochem 2004, 325:308-316. 10.1016/j.ab.2003.10.036 14751266
14. Klamt S Schuster S Gilles ED Calculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteria Biotechnol Bioeng 2002, 77:734-751. 10.1002/ bit.10153 11835134
15. Kauffman KJ Prakash P Edwards JS Advances in flux balance analysis Curr Opin Biotechnol 2003, 14:491-496. 10.1016/j.copbio.2003.08.001 14580578
16. Price ND Papin JA Schilling CH Palsson BO Genome-scale microbial in silico models: The constraints-based approach Trends Biotechnol 2003, 21:162-169. 10.1016/S0167-7799(03)00030-1 12679064
17. Edwards JS Ibarra RU Palsson BO In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data Nat Biotechnol 2001, 19:125-130. 10.1038/84379 11175725
18. Price ND Papin JA Palsson BO Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis Genome Res 2002, 12:760-769. 186586 11997342 10.1101/gr.218002. Article published online before print in April 2002.
19. Schilling CH Covert MW Famili I Church GM Edwards JS Palsson BO Genome-Scale Metabolic Model of Helicobacter pylori 26695 J Bacteriol 2002, 184:4582-4593. 135230 12142428 10.1128/JB.184.16.4582-4593.2002
20. Mahadevan R Burgard A Famili I Van Dien S Schilling C Applications of Metabolic Modeling to Drive Bioprocess Development for the Production of Value-added Chemicals BIOTECHNOLOGY AND BIOPROCESS ENGINEERING 2005, 10:408.
21. Mahadevan R Edwards JS Doyle FJ Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli Biophys J 2002, 83:1331-1340. 1302231 12202358
22. Gayen K Venkatesh K Analysis of optimal phenotypic space using elementary modes as applied to Corynebacterium glutamicum BMC Bioinformatics 2006, 7:445. 1617123 17038164 10.1186/1471-2105-7-445
23. Provost A Metabolic design of dynamic bioreaction models Faculté des Sciences Appliquées, Université catholique de Louvain, Louvain-la-Neuve, Louvain-la-Neuve 2006.
24. Herwig C von Stockar U A small metabolic flux model to identify transient metabolic regulations in Saccharomyces cerevisiae Bioprocess and Biosystems Engineering 2002, 24:395-403. 10.1007/s00449-001-0277-2
25. Takiguchi N Shimizu H Shioya S An on-line physiological state recognition system for the lysine fermentation process based on a metabolic reaction model Biotechnol Bioeng 1997, 55:170-181. 10.1002/ (SICI)1097-0290(19970705)55:1<170::AID-BIT18>3.0.CO;2-Q
26. Henry O Kamen A Perrier M Monitoring the physiological state of mammalian cell perfusion processes by on-line estimation of intracellular fluxes Journal of Process Control 2007, 17:241-251. 10.1016/j.jprocont.2006.10.006
27. Ren HT Yuan JQ Bellgardt KH Macrokinetic model for methylotrophic Pichia pastoris based on stoichiometric balance J Biotechnol 2003, 106:53-68. 10.1016/j.jbiotec.2003.08.003 14636710
28. Provost A Bastin G Agathos SN Schneider YJ Metabolic Design of Macroscopic Models: Application to CHO cells Decision and Control, 2005 and 2005 European Control Conference. CDC-ECC'05.44th IEEE Conference on 2005:2982-2989.
29. d'Anjou MC Daugulis AJ A rational approach to improving productivity in recombinant Pichia pastoris fermentation Biotechnol Bioeng 2001, 72:1-11. 10.1002/1097-0290(20010105)72:1<1::AID-BIT1>3.0.CO;2-T 11084587
30. Lei F Rotbøll M Jørgensen SB A biochemically structured model for Saccharomyces cerevisiae J Biotechnol 2001, 88:205-221. 10.1016/S0168-1656(01)00269-3 11434967
31. Teixeira AP Alves C Alves PM Carrondo MJ Oliveira R Hybrid elementary flux analysis/nonparametric modeling: Application for bioprocess control BMC Bioinformatics 2007, 8:30. 1800868 17261182 10.1186/1471-2105-8-30
32. Sainz J Pizarro F Perez-Correa JR Agosin E Modeling of yeast metabolism and process dynamics in batch fermentation Biotechnol Bioeng 2003, 81:818-828. 10.1002/bit.10535 12557315
33. Llaneras F Pico J An interval approach for dealing with flux distributions and elementary modes activity patterns J Theor Biol 2007, 246:290-308. 10.1016/j.jtbi.2006.12.029 17292923
34. Henry CS Jankowski MD Broadbelt LJ Hatzimanikatis V Genome-Scale Thermodynamic Analysis of Escherichia coli Metabolism Biophys J 2006, 90:1453-1461. 1367295 16299075 10.1529/biophysj.105.071720
35. Kummel A Panke S Heinemann M Systematic assignment of thermodynamic constraints in metabolic network models BMC Bioinformatics 2006, 7:512. 1664590 17123434 10.1186/1471-2105-7-512
36. Hoppe A Hoffmann S Holzhutter HG Including metabolite concentrations into flux balance analysis: Thermodynamic realizability as a constraint on flux distributions in metabolic networks BMC Syst Biol 2007, 1:23. 1903363 17543097 10.1186/1752-0509-1-23
37. Henry CS Broadbelt LJ Hatzimanikatis V Thermodynamics-based metabolic flux analysis Biophys J 2007, 92:1792-1805. 10.1529/biophysj.106.093138 17172310
38. Van der Heijden RTJM Romein B Heijnen JJ Hellinga C Luyben K Ch AM Linear Constraint Relations in Biochemical Reaction Systems: I. Classification of the Calculability and the Balanceability of Conversion Rates Biotechnol Bioeng 1994, 43:3-10. 10.1002/bit.260430103
39. Van der Heijden RTJM Romein B Heijnen JJ Hellinga C Luyben K Ch AM Linear Constraint Relations in Biochemical Reaction Systems: II. Diagnosis and Estimation of Gross Errors Biotechnol Bioeng 1994, 43:11-20. 10.1002/bit.260430104
40. Bastin G Dochain D On-line Estimation and Adaptative Control of Bioreactors Amsterdam: Elsevier 1990.
41. Schügerl K Bellgardt KH Bioreaction Engineering: Modeling and Control Springer 2000.
42. Herwig C Marison I von Stockar U On-line stoichiometry and identification of metabolic state under dynamic process conditions Biotechnol Bioeng 2001, 75:345-354. 10.1002/bit.10058 11590607
43. Pei SC Shyu JJ Eigenfilter design of higher-order digital differentiators Acoustics, Speech, and Signal Processing [see also IEEE Transactions on Signal Processing], IEEE Transactions on 1989, 37:505-511.
44. Luenberger D An introduction to observers Automatic Control, IEEE Transactions on 1971, 16:596-602. 10.1109/TAC.1971.1099826
45. Levant A Robust exact differentiation via sliding mode technique Automatica 1998, 34:379-384. 10.1016/S0005-1098(97)00209-4
46. Dochain D Pauss A On-line Estimation of Microbial Specific Growth-Rates: An Illustrative Case Study The Can J Chem Eng 1988, 66:626. 10.1139/ v88-107
47. Farza M Busawon K Hammouri H Simple nonlinear observers for on-line estimation of kinetic rates in bioreactors Automatica 1998, 34:301-318. 10.1016/S0005-1098(97)00166-0
48. Provost A Bastin G Dynamic metabolic modelling under the balanced growth condition Journal of Process Control 2004, 14:717-728. 10.1016/ j.jprocont.2003.12.004