Phenotypic deconstruction of gene circuitry

Chaos

Volumn 23, Issue 2, 2013, Pages

  Lomnitz, Jason G ^a   Savageau, Michael A ^a,b  

^a University of California Davis   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; FEEDBACK SYSTEM; GENE REGULATORY NETWORK; NONLINEAR SYSTEM; PHENOTYPE;

FEEDBACK, PHYSIOLOGICAL; GENE REGULATORY NETWORKS; NONLINEAR DYNAMICS; PHENOTYPE;

EID: 84880352483     PISSN: 10541500     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4809776     Document Type: Article

References (35)

1. Alberty R.A. Enzyme Kinetics 2011, (Wiley & Sons, Hoboken, N.J., ).
2. Atkinson M.R. Savageau M.A. Myers J.T. Ninfa A.J. Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell 2003, 113:597-607. 10.1016/S0092-8674(03)00346-5, and ",".
3. Bisswanger H. Enzyme Kinetics 2008, (Wiley-VCH, Weinheim, Germany, ).
4. Blundell M. Kennell D. Evidence for endonucleolytic attack in decay of lac messenger RNA in Escherichia coli. J. Mol. Biol. 1974, 83:143-161. 10.1016/0022-2836(74)90385-4, and ",".
5. Blattner F.R. Plunkett G. Bloch C.A. Perna N.T. Burland V. Riley M. Collado-Vides J. Glasner J.D. Rode C.K. Mayhew G.F. Gregor J. Davis N.W. Kirkpatrick H.A. Goeden M.A. Rose D.J. Mau B. Shao Y. The complete genome sequence of Escherichia coli K-12. Science 1997, 277:1453-1462. 10.1126/science.277.5331.1453, and ",".
6. Brenner S. Genomics: The end of the beginning. Science 2000, 287:2173-2174. 10.1126/science.287.5461.2173, ",".
7. Capellas C. Bielski B.H. J. Kinetic Systems 1972, and (Wiley-Interscience, New York, ).
8. Coelho P.M. B. M. Salvador A. Savageau M.A. Global tolerance of biochemical systems and the design of moiety-transfer cycles. PLOS Comput. Biol. 2009, 5(3):e1000319. 10.1371/journal.pcbi.1000319, and ",".
9. Dantzig G.B. Linear Programming and Extensions 1963, (Princeton University Press, Princeton, NJ, ).
10. Erdi P. Toth J. Mathematical Models of Chemical Reactions: Theory and Applications of Deterministic and Stochastic Models 1989, and (Manchester University Press, Manchester, UK, ).
11. Fasani R.A. Savageau M.A. Automated construction and analysis of the design space for biochemical systems. Bioinformatics 2010, 26:2601-2609. 10.1093/bioinformatics/btq479, and ",".
12. Fasani R.A. Savageau M.A. Molecular mechanisms of multiple toxin-antitoxin systems are coordinated to govern the persister phenotype. Proc. Natl. Acad. Sci. U.S.A. and "," (to be published).
13. Gantmacher F.R. Applications of the Theory of Matrices 1959, (Interscience Publishers, N.Y., ).
14. Gunawardena J. A linear framework for time-scale separation in nonlinear biochemical systems. PLoS One 2012, 7(5):e36321. 10.1371/journal.pone.0036321, ",".
15. Hartwell L.H. Hopfield J.J. Leibler S. Murray A.W. From molecular to modular cell biology. Nature 1999, 402:C47-C52. 10.1038/35011540, and ",".
16. Hintze A. Adami C. Evolution of complex modular biological networks. PLoS Comput. Biol. 2008, 4(2):e23. 10.1371/journal.pcbi.0040023, and ",".
17. Leive L. Kollin V. Synthesis, utilization and degradation of lactose operon mRNA in Escherichia coli. J. Mol. Biol. 1967, 24:247-259. 10.1016/0022-2836(67)90330-0, and ",".
18. Oehler S. Alberti S. Müller-Hill B. Induction of the lac promoter in the absence of DNA loops and the stoichiometry of induction. Nucl. Acids Res. 2006, 34:606-612. 10.1093/nar/gkj453, and ",".
19. Sadler J.R. Novick A. The properties of repressor and the kinetics of its action. J. Mol. Biol. 1965, 12:305-327. 10.1016/S0022-2836(65)80255-8, and ",".
20. Savageau M.A. Concepts relating the behavior of biochemical systems to their underlying molecular properties. Arch. Biochem. Biophys. 1971, 145:612-621. 10.1016/S0003-9861(71)80021-8, ",".
21. Savageau M.A. Optimal design of feedback control by inhibition: Dynamic considerations. J. Mol. Evol. 1975, 5:199-222. 10.1007/BF01741242, ",".
22. Savageau M.A. Design principles for elementary gene circuits: Elements, methods, and examples. Chaos 2001, 11:142-159. 10.1063/1.1349892, ",".
23. Savageau M.A. Biochemical Systems Analysis: A Study of Function and Design in Molecular Biology 1976, 40th Anniversary Edition (Amazon, ) [a reprinting of the original edition published by Addison-Wesley, Reading, MA ,)].
24. Savageau M.A. Design of the lac gene circuit revisited. Math. Biosci. 2011, 231:19-38. 10.1016/j.mbs.2011.03.008, ",".
25. Savageau M.A. Phenotypes and design principles in system design space. Handbook of Systems Biology 2013, 287-310. A. J. M. Walhout, M. Vidal, J. Dekker, "," in edited by and (Elsevier, San Diego, CA, )
26. Savageau M.A. Voit E.O. Recasting nonlinear differential equations as S-systems: A canonical nonlinear form. Math. Biosci. 1987, 87:83-115. 10.1016/0025-5564(87)90035-6, and ",".
27. Savageau M.A. Coelho P.M. B. M. Fasani R. Tolla D. Salvador A. Phenotypes and tolerances in the design space of biochemical systems. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:6435-6440. 10.1073/pnas.0809869106, and ",".
28. Srere P.A. Mosbach K. Metabolic compartmentation: Symbiotic, organellar, multienzymic, and microenvironmental. Ann. Rev. Microbiol. 1974, 28:61-83. 10.1146/annurev.mi.28.100174.000425, and ",".
29. Stricker J. Cookson S. Bennett M.R. Mather W.H. Tsimring L.S. Hasty J. A fast, robust and tunable synthetic gene oscillator. Nature 2008, 456:516-520. 10.1038/nature07389, and ",".
30. Strogatz S.H. Nonlinear Dynamics and Chaos 1994, (Westview Press, Cambridge, MA, ).
31. Taniguchi Y. Choi P.J. Li G.-W. Chen H. Babu M. Hearn J. Emili A. Xie X.S. Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 2010, 329:533-538. 10.1126/science.1188308, and ",".
32. Vanderbei R.J. Linear Programming: Foundations and Extensions 2008, (Springer, New York, NY, ).
33. Waddington C.H. The Strategy of the Genes 1957, (Macmillan, New York, ).
34. Williams K. Savageau M.A. Blumenthal R.M. A bistable hysteretic switch in an activator-repressor regulated restriction-modification system. Nucl. Acid Res. 10.1093/nar/gkt324, and "," (to be published).
35. Yarchuk O. Jacques N. Guillerez J. Dreyfus M. Inter-dependence of translation, transcription and mRNA degradation in the lacZ gene. J. Mol. Biol. 1992, 226:581-596. 10.1016/0022-2836(92)90617-S, and ",".