Multiobjective H2/H∞ synthetic gene network design based on promoter libraries

Mathematical Biosciences

Volumn 233, Issue 2, 2011, Pages 111-125

  Wu, Chih Hung ^a   Zhang, Weihei ^b   Chen, Bor Sen ^a  

^a NATIONAL TSING HUA UNIVERSITY   (Taiwan)

^b SHANDONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

LMIs; Multiobjective H2 H design; Nonlinear stochastic system; Reference tracking; Synthetic gene network

Indexed keywords

LMIS; MULTI-OBJECTIVE H; NON-LINEAR STOCHASTIC SYSTEMS; REFERENCE-TRACKING; SYNTHETIC GENE NETWORK;

APPROXIMATION THEORY; BIOLOGY; CONSTRAINED OPTIMIZATION; DESIGN; ENGINEERS; GENES; LIBRARIES; LINEAR MATRIX INEQUALITIES; MATHEMATICAL MODELS; SPURIOUS SIGNAL NOISE; STOCHASTIC SYSTEMS;

MULTIOBJECTIVE OPTIMIZATION;

SYNTHETIC DNA;

BIOLOGY; EXPERIMENTAL STUDY; FUZZY MATHEMATICS; GENETIC ANALYSIS; MATRIX; NETWORK ANALYSIS; NUMERICAL MODEL; OPTIMIZATION; PARAMETERIZATION; STOCHASTICITY;

ARTICLE; COMPUTER MODEL; ERROR; FUZZY SYSTEM; GENE ACTIVITY; GENE CONTROL; GENE LIBRARY; GENETIC ENGINEERING; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; NOISE REDUCTION; NONLINEAR SYSTEM; PROMOTER REGION; STOCHASTIC MODEL; BIOLOGICAL MODEL; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; METHODOLOGY; STATISTICS; SYNTHETIC BIOLOGY;

GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; GENES, SYNTHETIC; MODELS, GENETIC; PROMOTER REGIONS, GENETIC; STOCHASTIC PROCESSES; SYNTHETIC BIOLOGY;

EID: 80052544125     PISSN: 00255564     EISSN: 18793134     Source Type: Journal    
DOI: 10.1016/j.mbs.2011.07.001     Document Type: Article

References (72)

1. Purnick P.E., Weiss R. The second wave of synthetic biology: from modules to systems. Nat. Rev. Mol. Cell. Biol. 2009, 10:410.
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.
3. Gardner T.S., Cantor C.R., Collins J.J. Construction of a genetic toggle switch in Escherichia coli. Nature 2000, 403:339.
4. Ham T.S., Lee S.K., Keasling J.D., Arkin A.P. Design and construction of a double inversion recombination switch for heritable sequential genetic memory. PLoS One 2008, 3:e2815.
5. Kramer B.P., Viretta A.U., Daoud-El-Baba M., Aubel D., Weber W., Fussenegger M. An engineered epigenetic transgene switch in mammalian cells. Nat. Biotechnol. 2004, 22:867.
6. Hooshangi S., Thiberge S., Weiss R. Ultrasensitivity and noise propagation in a synthetic transcriptional cascade. Proc. Natl. Acad. Sci. USA 2005, 102:3581.
7. Basu S., Mehreja R., Thiberge S., Chen M.T., Weiss R. Spatiotemporal control of gene expression with pulse-generating networks. Proc. Natl. Acad. Sci. USA 2004, 101:6355.
8. Weber W., Stelling J., Rimann M., Keller B., Daoud-El Baba M., Weber C.C., Aubel D., Fussenegger M. A synthetic time-delay circuit in mammalian cells and mice. Proc. Natl. Acad. Sci. USA 2007, 104:2643.
9. Weber W., Kramer B.P., Fussenegger M. A genetic time-delay circuitry in mammalian cells. Biotechnol. Bioeng. 2007, 98:894.
10. Goh K.I., Kahng B., Cho K.H. Sustained oscillations in extended genetic oscillatory systems. Biophys. J. 2008, 94:4270.
11. Stricker J., Cookson S., Bennett M.R., Mather W.H., Tsimring L.S., Hasty J., fast A. robust and tunable synthetic gene oscillator. Nature 2008, 456:516.
12. Tigges M., Marquez-Lago T.T., Stelling J., Fussenegger M. A tunable synthetic mammalian oscillator. Nature 2009, 457:309.
13. Win M.N., Smolke C.D. Higher-order cellular information processing with synthetic RNA devices. Science 2008, 322:456.
14. Rinaudo K., Bleris L., Maddamsetti R., Subramanian S., Weiss R., Benenson Y. A universal RNAi-based logic evaluator that operates in mammalian cells. Nat. Biotechnol. 2007, 25:795.
15. Withers S.T., Keasling J.D. Biosynthesis and engineering of isoprenoid small molecules. Appl. Microbiol. Biotechnol. 2007, 73:980.
16. Weber W., Schoenmakers R., Keller B., Gitzinger M., Grau T., Daoud-El Baba M., Sander P., Fussenegger M. A synthetic mammalian gene circuit reveals antituberculosis compounds. Proc. Natl. Acad. Sci. 2008, 105:9994.
17. Basu S., Gerchman Y., Collins C.H., Arnold F.H., Weiss R. A synthetic multicellular system for programmed pattern formation. Nature 2005, 434:1130.
18. Lu T.K., Collins J.J. Dispersing biofilms with engineered enzymatic bacteriophage. Proc. Natl. Acad. Sci. 2007, 104:11197.
19. Lu T.K., Collins J.J. Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy. Proc. Natl. Acad. Sci. 2009, 106:4629.
20. Steen E.J., Chan R., Prasad N., Myers S., Petzold C.J., Redding A., Ouellet M., Keasling J.D. Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol. Microb. Cell Fact 2008, 7:36.
21. Lee S.K., Chou H., Ham T.S., Lee T.S., Keasling J.D. Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels. Curr. Opin. Biotechnol. 2008, 19:556.
22. Waks Z., Silver P.A. Engineering a synthetic dual-organism system for hydrogen production. Appl. Environ. Microbiol. 2009, 75:1867.
23. Guido N.J., Wang X., Adalsteinsson D., McMillen D., Hasty J., Cantor C.R., Elston T.C., Collins J.J. A bottom-up approach to gene regulation. Nature 2006, 439:856.
24. Kobayashi H., Kaern M., Araki M., Chung K., Gardner T.S., Cantor C.R., Collins J.J. Programmable cells: interfacing natural and engineered gene networks. Proc. Natl. Acad. Sci. USA 2004, 101:8414.
25. Kuepfer L., Sauer U., Parrilo P.A. Efficient classification of complete parameter regions based on semidefinite programming. BMC Bioinformat. 2007, 8:12.
26. Rosenfeld N., Young J.W., Alon U., Swain P.S., Elowitz M.B. Accurate prediction of gene feedback circuit behavior from component properties. Mol. Syst. Biol. 2007, 3:143.
27. Chen B.S., Chang Y.T., Wang Y.C. Robust H infinity-stabilization design in gene networks under stochastic molecular noises: fuzzy-interpolation approach. IEEE Trans. Syst. Man Cybern. B Cybern. 2008, 38:25.
28. Chen B.S., Chen P.W. Robust engineered circuit design principles for stochastic biochemical networks with parameter uncertainties and disturbances. IEEE Trans. Biomed. Circ. Syst. 2008, 2:114.
29. Lou C., Liu X., Ni M., Huang Y., Huang Q., Huang L., Jiang L., Lu D., Wang M., Liu C., Chen D., Chen C., Chen X., Yang L., Ma H., Chen J., Ouyang Q. Synthesizing a novel genetic sequential logic circuit: a push-on push-off switch. Mol. Syst. Biol. 2010, 6:350.
30. Friedland A.E., Lu T.K., Wang X., Shi D., Church G., Collins J.J. Synthetic gene networks that count. Science 2009, 324:1199.
31. Lu T.K., Khalil A.S., Collins J.J. Next-generation synthetic gene networks. Nat. Biotechnol. 2009, 27:1139.
32. Chen B.S., Chang C.H., Lee H.C. Robust synthetic biology design: stochastic game theory approach. Bioinformatics 2009, 25:1822.
33. Chen B.S., Wu C.H. A systematic design method for robust synthetic biology to satisfy design specifications. BMC Syst. Biol. 2009, 3:66.
34. Chen B.S., Wu C.H. Robust optimal reference-tracking design method for stochastic synthetic biology systems: T-S fuzzy approach. IEEE Trans. Fuzzy Syst. 2010, 18:1144.
35. Kelly J.R., Rubin A.J., Davis J.H., Ajo-Franklin C.M., Cumbers J., Czar M.J., de Mora K., Glieberman A.L., Monie D.D., Endy D. Measuring the activity of BioBrick promoters using an in vivo reference standard. J. Biol. Eng. 2009, 3:4.
36. Marchisio M.A., Stelling J. Computational design of synthetic gene circuits with composable parts. Bioinformatics 2008, 24:1903.
37. Ellis T., Wang X., Collins J.J. Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nat. Biotechnol. 2009, 27:465.
38. Cantone I., Marucci L., Iorio F., Ricci M.A., Belcastro V., Bansal M., Santini S., di Bernardo M., di Bernardo D., Cosma M.P. A yeast synthetic network for in vivo assessment of reverse-engineering and modeling approaches. Cell 2009, 137:172.
39. Lu T.K., Khalil A.S., Collins J.J. Next-generation synthetic gene networks. Nat. Biotechnol. 2009, 27:1139.
40. Chesi G. LMI techniques for optimization over polynomials in control: a survey. IEEE Trans. Automat. Control 2010, 55:2500.
41. Chen X., Zhou K. Multiobjective H2/H8 control design. SIAM J. Control Optim. 2002, 40:33.
42. Chen B.S., Tseng C.S., Uang H.J. Mixed H2/H8 fuzzy output feedback control design for nonlinear dynamic systems: an LMI approach. IEEE Trans. Fuzzy Syst. 2000, 8:249.
43. Chen B.S., Zhang W. Stochastic H2/H8 control with state-dependent noise. IEEE Trans. Automat. Control 2004, 49:45.
44. Bambang R.T., Shimemura E., Uchida K. Mixed H2/H8 control with pole placement in a class of regions. Optim. Control Appl. Methods 1994, 15:151.
45. Hammer K., Mijakovic I., Jensen P.R. Synthetic promoter libraries - tuning of gene expression. Trends Biotechnol. 2006, 24:53.
46. Alper H., Fischer C., Nevoigt E., Stephanopoulos G. Tuning genetic control through promoter engineering. Proc. Natl. Acad. Sci. USA 2005, 102:12678.
47. Cox R.S., Surette M.G., Elowitz M.B. Programming gene expression with combinatorial promoters. Mol. Syst. Biol. 2007, 3:145.
48. Murphy K.F., Balazsi G., Collins J.J. Combinatorial promoter design for engineering noisy gene expression. Proc. Natl. Acad. Sci. USA 2007, 104:12726.
49. Canton B., Labno A., Endy D. Refinement and standardization of synthetic biological parts and devices. Nat. Biotechnol. 2008, 26:787.
50. Leveau J.H., Lindow S.E. Predictive and interpretive simulation of green fluorescent protein expression in reporter bacteria. J. Bacteriol. 2001, 183:6752.
51. Alon U. An Introduction to Systems Biology: Design Principles of Biological Circuits 2007, Chapman & Hall/CRC.
52. Kobayashi T., Chen L., Aihara K. Modeling genetic switches with positive feedback loops. J. Theor. Biol. 2003, 221:379.
53. Chen G., Hsu S.H. Linear Stochastic Control Systems 1995, CRC.
54. Zhang W., Chen B.S. State feedback H8 control for a class of nonlinear stochastic systems. SIAM J. Control Optim. 2006, 44:1973.
55. Fujita M., Uchida K., Matsumura F. Gain perturbation tolerance in H8 state feedback control. Int. J. Control 1990, 51:315.
56. Takagi T., Sugeno M. Fuzzy identification of systems and its applications to modeling and control. IEEE Trans. Syst. Man Cybern. 1985, 15:116.
57. Elowitz M.B., Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature 2000, 403:335.
58. Mukherji S., van Oudenaarden A. Synthetic biology: understanding biological design from synthetic circuits. Nat. Rev. Genet. 2009, 10:859.
59. Wang R., Chen L., Aihara K. Construction of genetic oscillators with interlocked feedback networks. J. Theor. Biol. 2006, 242:454.
60. Wang R., Jing Z., Chen L. Modelling periodic oscillation in gene regulatory networks by cyclic feedback systems. Bull. Math. Biol. 2005, 67:339.
61. Chen L., Aihara K. A model of periodic oscillation for genetic regulatory systems. IEEE Trans. Circ. Syst. I: Fund. Theor. Appl. 2002, 49:1429.
62. Basu S., Gerchman Y., Collins C.H., Arnold F.H., Weiss R. A synthetic multicellular system for programmed pattern formation. Nature 2005, 434:1130.
63. Gertz J., Siggia E.D., Cohen B.A. Analysis of combinatorial cis-regulation in synthetic and genomic promoters. Nature 2009, 457:215.
64. Segal E., Widom J. From DNA sequence to transcriptional behaviour: a quantitative approach. Nat. Rev. Genet. 2009, 10:443.
65. Yokobayashi Y., Weiss R., Arnold F.H. Directed evolution of a genetic circuit. Proc. Natl. Acad. Sci. USA 2002, 99:16587.
66. Jensen P.R., Hammer K. Artificial promoters for metabolic optimization. Biotechnol. Bioeng. 1998, 58:191.
67. Wu C.H., Lee H.C., Chen B.S. Robust synthetic gene network design via library-based search method. Bioinformatics 2011, (in revision).
68. Boyd S., El Ghaoui L., Feron E., Balakrishnan V. Linear Matrix Inequalities in System and Control Theory 1994, Society for Industrial Mathematics.
69. Braun D., Basu S., Weiss R. Parameter estimation for two synthetic gene networks: a case study. IEEE International Conference on Acoustics, Speech, and Signal Processing 2005, IEEE.
70. Iadevaia S., Mantzaris N.V. Genetic network driven control of PHBV copolymer composition. J. Biotechnol. 2006, 122:99.
71. Tuttle L.M., Salis H., Tomshine J., Kaznessis Y.N. Model-driven designs of an oscillating gene network. Biophys. J. 2005, 89:3873.
72. Arkin A., Ross J., McAdams H.H. Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. Genetics 1998, 149:1633.