Robust Design of Biological Circuits: Evolutionary Systems Biology Approach
作者： Bor-Sen Chen , Chih-Yuan Hsu , Jing-Jia Liou
DOI: 10.1155/2011/304236
关键词:
摘要: Artificial gene circuits have been proposed to be embedded into microbial cells that function as switches, timers, oscillators, and the Boolean logic gates. Building more complex systems from these basic circuit components is one key advance for biologic design synthetic biology. However, behavior of bioengineered remains unstable uncertain. In this study, a nonlinear stochastic system model biological with intrinsic parameter fluctuations environmental molecular noise cellular context in host cell. Based on evolutionary biology algorithm, parameters target can evolve specific values order robustly track desired spite noise. The fitness selected inversely proportional tracking error so achieve optimal mimicking process circuit. Finally, several examples are given silico Monte Carlo simulation illustrate procedure confirm robust performance method. result shows designed behaviors minimal errors even nontrivial external
hindawi.com参考文章(36)
Stanislaw H. Zak, Systems and control ,(2002)
Bor Sen Chen, Wei Sheng Wu, Underlying Principles of Natural Selection in Network Evolution: Systems Biology Approach Evolutionary Bioinformatics. ,vol. 3, pp. 245- 262 ,(2007) , 10.4137/EBO.S0
Uri Alon, An Introduction to Systems Biology Chapman and Hall/CRC. ,(2006) , 10.1201/9781420011432
Michael B. Elowitz, Stanislas Leibler, A synthetic oscillatory network of transcriptional regulators Nature. ,vol. 403, pp. 335- 338 ,(2000) , 10.1038/35002125
Bor-Sen Chen, Yu-Chao Wang, On the attenuation and amplification of molecular noise in genetic regulatory networks. BMC Bioinformatics. ,vol. 7, pp. 52- 52 ,(2006) , 10.1186/1471-2105-7-52
Mads Kærn, William J. Blake, J.J. Collins, The engineering of gene regulatory networks. Annual Review of Biomedical Engineering. ,vol. 5, pp. 179- 206 ,(2003) , 10.1146/ANNUREV.BIOENG.5.040202.121553
Subhayu Basu, Yoram Gerchman, Cynthia H. Collins, Frances H. Arnold, Ron Weiss, A synthetic multicellular system for programmed pattern formation Nature. ,vol. 434, pp. 1130- 1134 ,(2005) , 10.1038/NATURE03461
Bor-Sen Chen, Chih-Hung Wu, A systematic design method for robust synthetic biology to satisfy design specifications. BMC Systems Biology. ,vol. 3, pp. 66- 66 ,(2009) , 10.1186/1752-0509-3-66
K. F. Murphy, G. Balazsi, J. J. Collins, Combinatorial promoter design for engineering noisy gene expression. Proceedings of the National Academy of Sciences of the United States of America. ,vol. 104, pp. 12726- 12731 ,(2007) , 10.1073/PNAS.0608451104
Jeff Hasty, David McMillen, J. J. Collins, Engineered gene circuits Nature. ,vol. 420, pp. 224- 230 ,(2002) , 10.1038/NATURE01257