Systems biology and food microbiology

Modelling Microorganisms in Food

Volumn , Issue , 2007, Pages 250-288

  Brul, S ^a,b   Westerhoff, H V ^c  

^a UNIVERSITY OF AMSTERDAM   (Netherlands)

^b UNILEVER RESEARCH VLAARDINGEN   (Netherlands)

^c VU UNIVERSITY AMSTERDAM   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84904148999     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1533/9781845692940.2.250     Document Type: Chapter

References (95)

1. Systems Biology: Perspectives and Definitions 2005, Springer, Berlin. L. Alberghina, H.V. Westerhoff (Eds.).
2. Almaas E., Kovacs B., Vicsek T., Oltvai Z.N., Barabasi A.L. Global organization of metabolic fluxes in the bacterium. Escherichia coli, Nature 2004, 427:839-843.
3. Almaas E., Oltvai Z.N., Barabasi A.L. The activity reaction core and plasticity of metabolic networks. PLoS Comput Biol 2005, 1:557-563.
4. Bakker B.M., Assmus H.E., Bruggeman F., Haanstra J.R., Klipp E., Westerhoff H.V. Network-based selectivity of antiparasitic inhibitors. Mol Biol Rep 2002, 29:1-5.
5. Balaban N.Q., Merrin J., Chait R., Kowalik L., Leibler S. Bacterial persistence as a phenotypic switch. Science 2004, 5690:1622-1625.
6. Barrett C.L., Herring C.D., Reed J.L., Palsson B.O. The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states. Proc Natl Acad Sci USA 2005, 102:19103-19108.
7. Bernhardt J., Buttner K., Scharf C., Hecker M. Dual imaging of two-dimensional electropherograms in. Bacillus subtilis, Electrophoresis 1999, 20:2225-2240.
8. Rutherford at Manchester 1962, Heywood and Co., London. J.B. Birks (Ed.).
9. Boorsma A., Foat B.C., Vis D., Klis F.M., Bussemaker H.J. T-profiler: scoring the activity of predefined groups of genes using gene expression data. Nucleic Acids Res 2005, 33:W592-595.
10. Brehm-Stecher B.F., Johnson E.A. Single-cell microbiology: tools, technologies, and applications. Microbiol Mol Biol Rev 2004, 68:538-559.
11. Bruin S., Jongen T. Food process engineering: The last 25 years and challenges ahead. Comprehen Revs Food Sci Food Saf 2003, 2:42-81.
12. Brul S., Montijn R., Schuren F., Oomes S., Klis F.M., Coote P., Hellingwerf K.J. Detailed process design based on genomics of survivors of food preservation processes. Trends Food Sci Technol 2002, 13:325-333.
13. Brul S., Coote P., Oomes S., Mensonides F., Hellingwerf K., Klis F.M. Physiological action of preservative agents: prospective of use of modern microbiological techniques in assessing microbial behaviour in food preservation. Int J Food Microbiol 2002, 79:55-64.
14. Brul S., Schuren F., Montijn R., Keijser B.J.F., Van Der Spek H., Oomes S.J.C.M. The impact of functional genomics on microbiological food quality and safety. Int J Food Micr 2006, (in press).
15. Brul S., van der Spek H., Keijser B.J.F., Schuren F., Oomes S.J.C.M., Montijn R. Functional genomics for optimal microbiological stability of processed food products 2006, IFT Press, Chicago, IL, (in press).
16. Bussemaker H.J., Li H., Siggia E.D. Regulatory element detection using correlation with expression. Nat Genet 2001, 27:167-171.
17. Cole M.B., Keenan M.H.J. A quantitative method for predicting shelf life of soft drinks using a model system. J Industr Microbiol Biotechnol 1987, 2:59-62.
18. Cooper R.A., Carucci D.J. Proteomic approaches to studying drug targets and resistance in Plasmodium. Curr Drug Targets Infect Disord 2004, 4:41-51.
19. Edwards J.S., Palsson B.O. The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc Natl Acad Sci 2000, 97:5528-5533.
20. Eisen M.B., Spellmann P.T., Brown P.O., Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998, 95:14863-14868.
21. Esty J.R., Meyer K.F. The heat resistance of the spores of B. botulinus and allied anaerobes. XI. J Infect Dis 1922, 31:650-663.
22. Fischer E., Sauer U. Large-scale in vivo flux analysis shows rigidity and suboptimal performance of Bacillus subtilis metabolism. Nat Genet 2005, 37:636-640.
23. Geeraerd A.H., Valdramidis V.P., Van Impe J.F. GInaFiT, a freeware tool to assess non-log-linear microbial survivor curves. Int J Food Micr 2005, 102:95-105.
24. Getz W.M., Westerhoff H.V., Hofmeyr J.-H.S., Snoep J.L. Control analysis of trophic chains. Ecol Modell 2003, 168:153-171.
25. Grimm V., Revilla E., Berger U., Jeltsch F., Mooij W.M., Railsback S.F., Thulke H.H., Weiner J., Wiegand T., De Angelis D.L. Pattern oriented modelling of agent-based complex systems: lessons from ecology. Science 2005, 5750:987-991.
26. Hellingwerf K.J., Postma P.W., Tomasson J., Westerhoff H.V. Signal transduction in bacteria: phosphoneural networks in. Escherichia coli?, FEMS Microbiol Rev 1995, 16:309-321.
27. Hellmich W., Pelargus C., Leffhalm K., Ros A., Anselmetti D. Single cell manipulation, analytics, and label-free protein detection in microfluidic devices for systems nanobiology. Electrophoresis 2005, 26:3689-3696.
28. Hermann T. Using functional genomics to improve productivity in the manufacture of industrial biochemicals. Curr Opin Biotechnol 2004, 15:444-448.
29. Holyoak C.D., Stratford M., Mcmullin Z., Cole M.B., Crimmins K., Brown A.J., Coote P.J. Activity of the plasma membrane H(+)-ATPase and optimal glycolytic flux are required for rapid adaptation and growth of Saccharomyces cerevisiae in the presence of the weak acid preservative sorbic acid. Appl Environ Microbiol 1996, 62:3158-3364.
30. HÖPer D., Bernhardt J., Hecker M. Salt stress adaptation of Bacillus subtilis: a physiological proteomics approach. Proteomics 2006, 6:1550-1562.
31. Hutchison C.A., Peterson S.N., Gill S.R., Cline R.T., White O., Fraser C.M., Smith H.O., Venter J.C. Global transposon mutagenesis and a minimal Mycoplasma genome. Science 1999, 286:2165-2169.
32. Ibarra R.U., Edwards J.S., Palsson B.O. Evolution towards predicted optimal growth in Escherichia coli K-12. Nature 2002, 420:186-189.
33. Ikeda M., Nakagawa S. The Corynebacterium glutamicum genome: features and impacts on biotechnological processes. Appl Microbiol Biotechnol 2003, 30:129-132.
34. Kalinowski J., Bathe B., Bartels D., Bischoff N., Bott M., Burkovski A., Dusch N., Eggeling L., Eikmans B.J., Gaigalat L., Goesman A., Hartmann M., Huthmacher K., Kramer R., Linke B., Mchardy A.C., Meyer F., Mockel B., Pfefferle W., Puhler A., Rey D.A., Ruckert C., Rupp O., Sahm H., Wendisch V.F., Wiegrabe I., Tausch A. The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins. J. Biotechnol 2003, 104:5-25.
35. Keijser B.J.F. Control of preservation by biomarkers 2006, European patent application P73012PC00.
36. Kell D.B. Theodor Bucher Lecture. Metabolomics, modelling and machine learning in systems biology - towards an understanding of the languages of cells. FEBS J 2006, 273:873-894.
37. Kesseler I.M., Collado-Vides J., Gama-Castro S., Ingraham J., Paley S., Paulsen I.T., Peralta-Gil M., Karp P.D. EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res 2005, 33:D334-337.
38. Metabolic Engineering in the Post Genomic Era 2004, Horizon Bioscience, Wymondham. B.N. Kholodenko, H.V. Westerhoff (Eds.).
39. Kholodenko B.N., Westerhoff H.V. Metabolic Engineering in the Post Genomic Era. Metabolic engineering: What it was, and What it is; and What it should become 2004, 1-35. Horizon Bioscience, Wymondham, and 436-442. B.N. Kholodenko, H.V. Westerhoff (Eds.).
40. Kilsby D.C. Food microbiology: the challenges for the future. Int J Food Microbiol 1999, 50:59-63.
41. Klipp E., Herwig R., Kowald A., Wierling Ch, Lehrach H. Systems Biology in Practice: Concepts, Implementation and Application 2005, Wiley-VCH, Weinheim.
42. Koebmann B.J., Westerhoff H.V., Snoep J.L., Nilsson D., Jensen P.R. The glycolytic flux in E. coli is controlled by the demand for ATP. J Bacteriol 2002, 184:3909-3916.
43. Koffas M., Stephanopoulos G. Strain improvement by metabolic engineering: lysine production as a case study for systems biology. Curr Opin Biotechnol 2005, 16:361-366.
44. Kort R., O'brien A.C., Van Stokkum I.H., Oomes S.J., Crielaard W., Hellingwerf K.J., Brul S. Assessment of heat resistance of bacterial spores from food product isolates by fluorescence monitoring by dipicolinic acid release. Appl Env Microbiol 2005, 71:3556-3564.
45. Levin B.R. Microbiology. Noninherited resistance to antibiotics. Science 2004, 5690:1578-1579.
46. Lin B. Composition and functioning of iron-reducing communities in two contrasting environments, i.e. a landfill leachate-polluted aquifer and estuarine sediments 2006, PhD thesis, Free University Amsterdam. http://www.dare.ubvu.vu.nl/bitstream/1871/9250/1/Bin_thesis_VUlibrary.pdf.
47. Margulies M., Egholm M., Altman W.E., Attiya S., Bader J.S., Bemben L.A., Berka J., Braverman M.S., Chen Y.J., Chen Z., Dewell S.B., Du L., Fierro J.M., Gomes X.V., Godwin B.C., He W., Helgesen S., Ho C.H., Irzyk G.P., Jando S.C., Alenquer M.L., Jarvie T.P., Jirage K.B., Kim J.B., Knight J.R., Lanza J.R., Leamon J.H., Lefkowitz S.M., Lei M., Li J., Lohman K.L., Lu H., Makhijani V.B., Mcdade K.E., Mckenna M.P., Myers E., Nickerson E., Nobile J.R., Plant R., Puc B.P., Ronan M.T., Roth G.T., Sarkis G.J., Simons J.F., Simpson J.W., Srinivasan M., Tartaro K.R., Tomasz A., Vogt K.A., Volkmer G.A., Wang S.H., Wang Y., Weiner M.P., Yu P., Begley R.F., Rothberg J.M. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437:376-380.
48. Marthi B., Vaughan E.V., Brul S. Functional genomics and food safety. New Food 2004, 7:14-18.
49. Mcmeekin T.A., Ross T. Predictive Microbiology: providing a knowledge-based framework for change management. Int J Food Microbiol 2002, 78:133-153.
50. Mensonides F.I., Schuurmans J.M., Teixeira De Mattos M.J., Hellingwerf K.J., Brul S. The metabolic response of Saccharomyces cerevisiae to continuous heat stress. Mol Biol Rep 2002, 29:103-106.
51. Mensonides F.I., Brul S., Klis F.M., Hellingwerf K.J., Teixeira De Mattos M.J. Activation of the protein kinase C1 pathway upon continuous heat stress in Saccharomyces cerevisiae is triggered by an intracellular increase in osmolarity due to trehalose accumulation. Appl Env Microbiol 2005, 71:4531-4538.
52. Miller C., Thomsen L.E., Gaggero C., Mosseri R., Ingmer H., Cohen S.N. SOS response induction by beta-lactams and bacterial defense against antibiotic lethality. Science 2004, 5690:1629-1631.
53. Mitchell P. Chemiosmotic Coupling and Energy Transduction 1968, Glynn Research Ltd., Bodmin.
54. Mollapour M., Fong D., Balakrishnam K., Harris N., Thompson S., Schuller C., Kuchler K., Piper P.W. Screening the yeast deletant mutant collection for hypersensitivity and hyperresistance to sorbate, a weak organic acid food preservative. Yeast 2004, 21:927-946.
55. Moreira Dos Santos M., Akesson M., Nielsen J. Metabolic Engineering in the Post Genomic Era. Metabolic flux analysis in the post genomic era 2004, 89-106. Horizon Bioscience, Wymondham. B.N. Kholodenko, H.V. Westerhoff (Eds.).
56. Mori H. From the sequence to cell modeling: comprehensive functional genomics in Escherichia coli. J Biochem Mol Biol 2004, 37:83-92.
57. Nobel-De H., Lawrie L., Brul S., Klis F., Davis M., Alloush H., Coote P. Parallel and comparative analysis of the proteome and transcriptome of sorbic acid-stressed. Saccharomyces cerevisiae, Yeast 2001, 18:1413-1428.
58. Orij R., Brul S., Smits G. Online intracellular pH measurements upon sorbic acid stress in yeast. Proceedings of the International Specialised Symposium on Yeasts ISSY 25; Systems Biology of Yeasts - from Models to Applications 2006, Hanasaari, Espoo, Finland, 18-21 June, 151. A. Kuokka, M. Penttilä (Eds.).
59. Pal C., Papp B., Lercher M.J., Csermely P., Oliver S.G., Hurst L.D. Chance and necessity in the evolution of minimal metabolic networks. Nature 2006, 440:667-670.
60. Systems Biology, Properties of Reconstructed Networks 2006, Cambridge University Press, Cambridge. B.O. Palsson (Ed.).
61. Papadimitriou M.N.B., Resende C., Kuchler K., Brul S. High Pdr12 levels in spoilage yeast (Saccharomyces cerevisiae) correlate directly with sorbic acid levels in the culture medium but are not sufficient to provide cells with acquired resistance to the food preservative. Int J Food Microbiol 2006, (in press).
62. Papin J.A., Palsson B.O. Hierarchical thinking in network biology: The unbiased modularization of biochemical network-based pathway analysis methods. Trends Biotechnol 2004, 22:400-405.
63. Papin J.A., Stelling J., Price N.D., Klamt S., Schuster S., Palsson B.O. Comparison of network-based pathway analysis methods. Trends Biotechnol 2004, 22(8):400-405.
64. Picon A., Teixeira De Mattos M.J., Postma P.W. Reducing the glucose uptake rate in Escherichia coli affects growth rate but not protein production. Biotechnol Bioeng 2005, 90:191-200.
65. Piper P., Mahe Y., Thompson S., Pandjaitan R., Holyoak C., Egner R., Muhlbauer M., Coote P., Kuchler K. The Pdr12 ABC transporter is required for the development of weak organic acid resistance in yeast. EMBO J 1998, 17:4257-4265.
66. Pirt S.J. Maintenance energy: a general model for energy-limited and energy-sufficient growth. Arch Microbiol 1982, 133:300-302.
67. Popper K.R. Conjectures and Refutations 1963, Routledge and Kegan Paul, London.
68. Railsback S.F. Getting 'results': the pattern-oriented approach to analyzing natural systems with individual-based models. Nat Res Modell 2001, 14:465-474.
69. Reed J.L., Palsson B.O. Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction substets that comprise network states. Genome Res 2004, 14:1797-1805.
70. Rossell S., Van Der Weijden C.C., Lindenbergh A., Van Tuijl A., Francke C., Bakker B.M., Westerhoff H.V. Unraveling the complexity of flux regulation: a new method demonstrated for nutrient starvation in. Saccharomyces cerevisiae, Proc Natl Acad Sci USA 2006, 103:2166-2171.
71. Roven C., Bussemaker H.J. REDUCE: an online tool for inferring cis-regulatory elements and transcriptional module ectivities from microarray data. Nucleic Acids Res 2003, 31:3487-3490.
72. Schilling C.H., Edwards J.S., Letscher D., Palsson B.O. Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems. Biotechnol Bioeng 2000, 71:286-306.
73. Schilling C.H., Letscher D., Palsson B.O. Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. J Theor Biol 2000, 203:229-248.
74. Schuster S., Hilgetag C. On elementary flux modes in biochemical reaction systems at steady state. J Biol Syst 1994, 2:165-182.
75. Schuster S., Fell D.A., Dandekar T. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat Biotechnol 2000, 18:326-332.
76. Senn H., Lendenmann U., Snozzi M., Hamer G., Egli T. The growth of Escherichia coli in glucose-limited chemostat cultures: a re-examination of the kinetics. Biochim Biophys Acta 1994, 1201:424-436.
77. Snoep J.L., Van Der Weijden C.C., Andersen H.W., Westerhoff H.V., Jensen P.R. DNA supercoiling in Escherichia coli is under tight and subtle homeostatic control, involving gene-expression and metabolic regulation of both topoisomerase I and DNA gyrase. Eur J Biochem 2002, 269:1662-1669.
78. Snoep J.L., Hoefnagel M.H.N., Westerhoff H.V. Metabolic Engineering in the Post Genomic Era. Metabolic flux analysis in the post genomic era 2004, 357-375. Horizon Bioscience, Wymondham. B.N. Kholodenko, H.V. Westerhoff (Eds.).
79. Snoep J.L., Bruggeman F., Olivier B.G., Westerhoff H.V. Towards building the silicon cell: a modular approach. Biosystems 2006, 83:207-216.
80. Stouthamer A.H. The search for correlation between theoretical and experimental growth yields. Int Rev Biochem 1979, 21:1-47.
81. Ter Beek A., Keijser B.J.F., Boorsma A., Brul S. Mild treatment of Bacillus subtilis with the food preservative sorbic acid induces a stringent-type response, but not the general stress response or sporulation. Proceedings of the 20th International ICFMH symposium, Food Micro 2006; food safety and food biotechnology: diversity and global impact 2006, Bologna, Italy, 29 Aug-2 Sept 92. E. Parente, L. Cocolin, D. Ercolini, L. Vannini (Eds.).
82. Teusink B., Smid E.J. Modelling strategies for the industrial exploitation of lactic acid bacteria. Nat Rev Microbiol 2006, 4:46-56.
83. Veening J.W., Kuipers O.P., Brul S., Hellingwerf K.J., Kort R. Effects of phosphorelay perturbations on architecture, sporulation and spore resistance in biofilms of. Bacillus subtilis, J Bacteriol 2006, 188:3099-3109.
84. Volker V., Hecker M. From genomics via proteomics to cellular physiology of the Gram-positive model organism. Bacillus subtilis, Cell Microbiol 2005, 7:1077-1085.
85. Vos De W. Advances in genomics for microbial food fermentations and safety. Curr Opin Biotechnol 2001, 12:493-498.
86. Waharte F., Spriet C., Heliot L. Setup and characterization of a multiphoton FLIM instrument for protein-protein interaction measurements in living cells. Cytometry 2006, 69:299-306.
87. Ward D.E., Van Der Weijden C.C., Van Der Merwe M.J., Westerhoff H.V., Claiborne A., Snoep J. Branched-chain α-keto acid catabolism via the gene products of the bdk operon in Enterococcus faecalis: a new, secreted metabolite serving as a temporary redox sink. J Bacteriol 2000, 182:3239-3246.
88. Watson J.D., Crick F.H. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 1953, 171:737-738.
89. Westerhoff H.V. Systems biology ... in action. Curr Opin Biotechnol 2005, 16:326-328.
90. Westerhoff H.V., Palsson B.O. The evolution of molecular biology. Nat Biotechnol 2004, 22:1249-1252.
91. Thermodynamics and Control of Biological Free-energy Transduction 1987, Elsevier, Amsterdam. H.V. Westerhoff, K. Van Dam (Eds.).
92. Westerhoff H.V., Lolkema J.S., Otto R., Hellingwerf K.J. Thermodynamics of growth. Non-equilibrium thermodynamics of bacterial growth. The phenomenological and the mosaic approach. Biochim Biophys Acta 1982, 683:181-220.
93. Westerhoff H.V., Hellingwerf K.J., Van Dam K. Thermodynamic efficiency of microbial growth is low, but optimal for maximal growth rate. Proc Natl Acad Sci USA 1983, 80:305-309.
94. Wu L., Wang W., Van Winden W.A., Van Gulik W.M., Heijnen J.J. A new framework for the estimation of control parameters in metabolic pathways using lin-log kinetics. Eur J Biochem 2004, 271:3348-3359.
95. Zakrzewska A., Boorsma A., Brul S., Hellingwerf K.J., Klis F.M. Transcriptional response of Saccharomyces cerevisiae to the plasma membrane-perturbing compound chitosan. Eukaryot Cell 2005, 4:703-715.