Developing a Model of Synthesis Logic Circuits Based on Gene with Genetic Algorithm

Main Article Content

Chakkrit Preuksakarn

Abstract

This article mentions about applying the engineering method for studying and developing more complex gene expression by defining the terms of protein expression. Using the idea of transcription process of lac operon which is similar to the electronic circuit due to the process that we can assume as the state ON and OFF by the inputs of one or two inducers to the circuit. By using the genetic algorithm for searching the most optimal parameter to calculate the amount of protein product of the transcription process in various concentration of inducers. The resulting optimal design of these biological logic gates can be extended to synthesis advanced sequential logic circuits.

Article Details

Section
Engineering Research Articles

References

[1] E. Andrianantoandro, S. Basu, D. K. Karig, and R. Weiss, “Synthetic biology: New engineering rules for an emerging discipline,” Molecular Systems Biology, vol. 2, pp. 1–14, 2006.

[2] G. Cuccato, G. D. Gatta, and D. di Bernardo, “Systems and synthetic biology: Tackling genetic networks and complex diseases,” Heredity, vol. 102, no. 6, pp. 527–532, 2009.

[3] A. S. Khalil and J. J. Collins, “Synthetic biology: Applications come of age,” Nature Reviews Genetics, vol. 11, no. 5, pp. 367–379, 2010.

[4] Y. Naasse, H. Charoute, B. E. Houate, C. Elbekkay, L. Razoki, A. Malki, A. Barakat, and H. Rouba, “Chromosomal abnormalities and Y chromosome microdeletions in infertile men from Morocco,” BMC Urology, vol. 95, no. 15, pp. 2–6, 2015.

[5] L. Bintu, N. E. Buchler, H. G. Garcia, U. Gerland, T. Hwa, J. Kondev, T. Kuhlman, and R. Phillips, “Transcriptional regulation by the numbers: Applications,” Current Opinion in Genetics & Development, vol. 15, no. 2, pp. 125–135, 2005.

[6] M. N. Win and C. D. Smolke, “Higher-order cellular information processing with synthetic RNA devices,” Science, vol. 322, no. 5900, pp. 456–460, 2008.

[7] S. Ausländer, D. Ausländer, M. Müller, M. Wieland, and M. Fussenegger, “Programmable single-cell mammalian biocomputers,” Nature, vol. 487, pp. 123–127, 2012.

[8] K. Hattori, “Advanced biological computer developed,” ScienceDaily, American Technion Society, Rockville, MD, May 2013.

[9] S. Konur and M. Gheorghe, “Design and analysis of genetically constructed logic gates,” in Proceedings of The University of Sheffield Engineering Symposium Conference, 2014, pp. 31–32.

[10] A. Wong, H. Wang, C. L. Poh, and R. I. Kitney, “Layering genetic circuits to build a single cell, bacterial half adder,” BMC Biology, vol. 13, no. 1, pp. 40, 2015.

[11] A. E. Mayo, Y. Setty, S. Shavit, A. Zaslaver, and U. Alon, “Plasticity of the cis-regulatory input function of a gene,” PLoS Biology, vol. 4, no. 4, 2006.

[12] C. H. Yuh, H. Bolouri, and E. H. Davidson, “Genomic cis-regulatory logic: Experimental and computational analysis of a sea urchin gene,” Science, vol. 279, no. 5358, pp. 1896–1902, 1998.

[13] N. E. Buchler, U. Gerland, and T. Hwa, “On schemes of combinatorial transcription logic,” PNAS, vol. 100, no. 9, pp. 5136–5141, 2003.

[14] N. Ichinose, T. Yada, O. Gotoh, and K. Aihara, “Reconstruction of transcription–translation dynamics with a model of gene networks,” Journal of Theoretical Biology, vol. 255, no. 4, pp. 378–386, 2008.

[15] Y. Maki, Y. Takahashi, Y. Arikawa, S. Watanabe, K. Aoshima, Y. Eguchi, T. Ueda, S. Aburatani, S. Kuhara, and S. Okamoto, “An integrated comprehensive workbench for inferring genetic networks: Voyagene,” Journal of Bioinformatics and Computational Biology, vol. 2, no. 3, pp. 533, 2004.

[16] R. S. Cox, M. G. Surette, and M. B. Elowitz, “Programming gene expression with combinatorial promoters,” Molecular Systems Biology, vol. 3, pp. 145, 2007.

[17] C. H. Chuang, C. L. Lin, Y. C. Chang, T. Jennawasin, and P. K. Chen, “Design of synthetic biological logic circuits based on evolutionary algorithm,” IET Systems Biology, vol. 7, no. 4, pp. 89–105, 2013.

[18] T. Pencheva, K. Atanassov, and A. Shannon, “Modelling of a roulette wheel selection operator in genetic algorithms using generalized nets,” International Journal Bioautomation, vol. 13, no. 4, pp. 257–264, 2009.

[19] J. M. Mendes, “A comparative study of crossover operators for genetic algorithms to solve the job shop scheduling problem,” WSEAS Transactions on Computers, vol. 12, no. 4, pp. 164–173, 2013.