Extended repression mechanisms in modelling bistable genetic switches of adjustable characteristics within a variable cell volume modelling framework

Chemical and Biochemical Engineering Quarterly

Volumn 28, Issue 1, 2014, Pages 35-51

  Maria, G ^a  

^a UNIVERSITY POLITEHNICA OF BUCHAREST   (Romania)

Author keywords

Bistable genetic switch; Dynamic modelling; Hill kinetics; Repression complexes; Variable volume; Whole cell

Indexed keywords

COMPLEX NETWORKS; CYTOLOGY; DYNAMIC MODELS; ESCHERICHIA COLI; NUCLEIC ACIDS; TRANSCRIPTION FACTORS;

CONTINUOUS VARIABLES; ENVIRONMENTAL CHANGE; GENETIC REGULATORY CIRCUITS; GENETIC SWITCHES; MATHEMATICAL FORMULATION; REPRESSION COMPLEXES; VARIABLE VOLUME; WHOLE CELL;

CELLS;

EID: 84898950270     PISSN: 03529568     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (60)

1. Hlavacek, W. S., Savageau, M. A., J. Mol. Biol. 266 (1997) 538.
2. Atkinson, M. R., Savageau, M. A., Myers, J. T., Ninfa, A. J., Cell 113 (2003) 597.
3. Kaznessis, Y. N., Chem. Eng. Sci. 61 (2006) 940.
4. Alon, U., An introduction to system biology. Design princi-ples of biological circuits, Chapman & Hall /CRC, Boca Raton, 2007.
5. Maria, G., Asia-Pac. J. Chem. Eng. 4 (2009) 916.
6. Kholodenko, B. N., Kiyatkin, A., Bruggeman, F. J., Sontag, E., Westerhoff, H. V., Hoek, J. B., Proceedings of the Na-Tional Academy of Sciences of USA 99 (2002) 12841.
7. Hlavacek, W. S., Savageau, M. A., J. Mol. Biol. 255 (1996) 121.
8. Kobayashi, H., Kaern, M., Araki, M., Chung, K., Gardner, T. S., Cantor, C. R., Collins, J. J., Proc. Natl. Acad. Sci. U. S.A. 101 (2004) 8414.
9. Hasty, J., McMillen, D., Collins, J. J., Nature 420 (2002) 224.
10. Wall, M. E., Hlavacek, W. S., Savageau, M. A., J. Mol. Biol. 332 (2003) 861.
11. Benner, S. A., Sismour, A. M., Nat. Rev. Genet. 6 (2005) 533.
12. Heinemann, M., Panke, S., Bioinformatics 22 (2006) 2790.
13. Schümperli, M., Pellaux, R., Panke, S., Knoll, M., Pleiss, J., Calles, B., de Lorenzo, V., Davidescu, F. P., Jørgensen S. B., A modular platform for biosynthesis of complex molecules, Synthetic Biology 3.0 Conference, Zürich (CH), 24-27 June, 2007.
14. He, F., Balling, R., Zeng, A. P., Biotechnology 144 (2009) 190.
15. Polynikis, A., Hogan, S. J., di Bernardo, M., J. Theor. Biol. 261 (2009) 511.
16. Endy, D., Brent, R., Nature 409 (2001) 391.
17. De Jong, H., J. Comput. Biol. 9 (2002) 67.
18. Maria, G., Chem. Biochem. Eng. Q. 19 (2005) 213.
19. Roeva, O., Pencheva, T., Tzonkov, S., Arndt, M., Hitzmann, B., Kleist, S., Miksch, G., Friehs, K., J. Biotechnol. 10 (2007) 592.
20. Klipp, E., Liebermeister, W., Wierling, C., Kowald, A., Leh-rach, H., Herwig, R., Systems biology. A textbook, Wi-ley-VCH, Weinheim, 2009.
21. Chen, Z., Wilmanns, M., Zeng, A. P., Trends Biotechnol. 28 (2010) 534.
22. Buchholz, K., Hempel, D. C., Eng. Life Sci. 6 (2006) 437.
23. Hasty, J., Isaacs, F., Dolnik, M., McMillen, D., Collins, J. J., Chaos 11 (2001) 207.
24. Styczynski, M. P., Stephanopoulos, G., Comput. Chem. Eng. 29 (2005) 519.
25. Jacob, F., Monod, J., J. Mol. Biol. 3 (1961) 318.
26. Tyson, J. J., Albert, R., Goldbeter, A., Ruoff, P., Sible, J., J. R. Soc. Interface 5 (2008) S1.
27. Elowitz, M. B., Leibler, S., Nature 403 (2000) 335.
28. Hua, S. S., Markovitz, A., J. Bacteriol. 110 (1972) 1089.
29. Ponnambalam, S., Spassky, A., Busby, S., FEBS Letters 219 (1987) 189.
30. Tabaka, M., Regulation of trp operon in E. coli, PhD The-sis, Institute of Physical Chemistry of the Polish Academy of Sciences, Warsaw, 2009.
31. Zak, D. E., Vadigepalli, R., Gonye, G. E., Doyle III, F. J., Schwaber, J. S., Ogunnaike, B. A., Comput. Chem. Eng. 29 (2005) 547.
32. Maria, G., Chem. Biochem. Eng. Q. 20 (2006) 353.
33. Smolen, P., Baxter, D. A., Byrne, J. H., Bull. Math. Biol. 62 (2000) 247.
34. Maria, G., Chem. Biochem. Eng. Q. 21 (2007) 417.
35. EcoCyc, Encyclopedia of Escherichia coli K-12 genes and metabolism, SRI Intl., The Institute for Genomic Research, Univ. of California at San Diego, 2005. (http://ecocyc.org/).
36. Salis, H., Kaznessis, Y., Comput. Chem. Eng. 29 (2005) 577.
37. Dondo, R., Marques, D., Lat. Am. Appl. Res. 32 (2002) 195.
38. Roubos, J. A., Bioprocess modelling and optimization-Fed-batch clavulanic acid production by Steptomyces clavuligerus, PhD Thesis, TU Delft, 2002.
39. Laurent, M., Charvin, G., Guespin-Michel, J., Cell. Mol. Biol. 51 (2005) 583.
40. Cherry, J. L., Adler, F. R., J. Theor. Biol. 203 (2000) 117.
41. Kaern, M., Blake, W. J., Collins, J. J., Annu. Rev. Biomed. Eng. 5 (2003) 179.
42. Gonze, D., BioSystems 99 (2010) 60.
43. Goodwin, B. C., Temporal organization in cells, Academic Press, New York, 1963.
44. Tyson, J. J., Othmer, H. G., Prog. Theor. Biol. 5 (1978) 1.
45. Del Vecchio, D., Design and analysis of an activator-repres-sor clock in E. Coli, Proc. American Control Conference, July 2007, New York. pp. 1589-1594.
46. Voit, E. O., IEE Proc.-Systems Biology 152 (2005) 207.
47. Widder, S., Schicho, J., Schuster, P., J. Theor. Biol. 246 (2007) 395.
48. Savageau, M. A., Math. Biosci. 180 (2002) 237.
49. Grognard, F., de Jong, H., Gouzé, J. L., Piecewise-linear models of genetic regulatory networks: Theory and exam-ple, In: Queinnec, I., Tarbouriech, S., Garcia, G., Nicules-cu, S. (Eds.), Biology and control theory: current challeng-es, Lecture Notes in Control and Information Sciences 357, 137-159, Springer-Verlag, Berlin, 2007.
50. Casey, R., de Jong, H., Gouze, J. L., J. Math. Biol. 52 (2006) 27.
51. Grainger, J. N. R., Gaffney, P. E., West, T. T., J. Theor. Biol. 21 (1968) 123.
52. Kinoshita, A., Nakayama, Y., Tomita, M., In silico analysis of human erythrocyte using E-Cell system, 2nd Intl. Con-ference on Systems Biology, California Institute of Tech-nology, Pasadena (USA), November 4-7, 2001.
53. Yang, Q., Lindahl, P., Morgan, J., J. Theor. Biol. 222 (2003) 407.
54. Maria, G., Chem. Biochem. Eng. Q. 17 (2003) 99.
55. Savageau, M. A., Chaos 11 (2001) 142.
56. Morgan, J. J., Surovtsev, I. V., Lindahl, P. A., J. Theor. Biol. 231 (2004) 581.
57. Rosenfeld, N., Elowitz, M. B., Alon, U., J. Mol. Biol. 323 (2002) 785.
58. Wang, X., Li, Y., Xu, X., Wang, Y., Biosystems 100 (2010) 31.
59. Volkmer, B., Heinemann, M., PLoS One 6 (2011) 1.
60. Trun, N. J., Gottesman, S., Gene. Dev. 4 (1990) 2036.