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International Conference on Bio-Inspired Computing: Theories and Applications

BIC-TA 2019: Bio-inspired Computing: Theories and Applications pp 18–25Cite as

Using of Processed Data to Design Genetic Circuits in GenoCAD

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Part of the book series: Communications in Computer and Information Science ((CCIS,volume 1160))

Abstract

In recent years, synthetic biology develops rapidly, the purpose of which is to create beneficial products or organisms with special functions. Genetic circuits are dynamic regulating systems of organisms controlling their own life processes. According to specific rules and grammar, synthetic biologists try to design artificial genetic circuits to achieve their goals. In our research, we designed grammar rules on basis of the context-free grammar, imported a part library which we acquired from IGEM database and then we processed, and constructed a genetic circuit for expressing TetR in GenoCAD, which is a free web-based application for synthetic biology. Finally, we generated a plasmid map on the PlasMapper, and we can see the concrete information of the plasmid. We creatively designed the genetic circuit to express the TetR. The work provides a new dynamic regulating system for synthetic biology. We think the genetic circuit will help us predict the biological regulator process.

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References

  1. Dragosits, M., Nicklas, D., Tagkopoulos, I.: A synthetic biology approach to self-regulatory recombinant protein production in Escherichia coli. J. Biol. Eng. 6(1), 2 (2012)

    Article  Google Scholar 

  2. Kiessling, L.: Synthetic science: assembly required. ACS Chem. Biol. 3(1), 1–2 (2008)

    Article  Google Scholar 

  3. Hesselman, M.C., Koehorst, J.J., Slijkhuis, T., et al.: The constructor: a web application optimizing cloning strategies based on modules from the registry of standard biological parts. J. Biol. Eng. 6(1), 14 (2012)

    Article  Google Scholar 

  4. Wang, Z., Hou, Z., Xin, H.: Internal noise stochastic resonance in a synthetic gene network. Chem. Phys. Lett. 401(1–3), 307–311 (2005)

    Article  Google Scholar 

  5. Keller, A.D.: Model genetic circuits encoding autoregulatory transcription factors. J. Theor. Biol. 172(2), 169–185 (1995)

    Article  MathSciNet  Google Scholar 

  6. Judd, E.M., Laub, M.T., Mcadams, H.H.: Toggles and oscillators: new genetic circuit designs. BioEssays 22(6), 507–509 (2000)

    Article  Google Scholar 

  7. Silva-Rocha, R., de Lorenzo, V.: Mining logic gates in prokaryotic transcriptional regulation networks. FEBS Lett. 582(8), 1237–1244 (2008)

    Article  Google Scholar 

  8. Atkinson, M.R., Savageau, M.A., Myers, J.T., et al.: Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell 113(5), 597–607 (2003)

    Article  Google Scholar 

  9. Bene, D., Sosík, P., Rodríguez-Patón, A.: An Autonomous in vivo dual selection protocol for boolean genetic circuits. Artif. Life 21(2), 247–260 (2015)

    Article  Google Scholar 

  10. Liu, Q., Schumacher, J., Wan, X., Lou, C., Wang, B.: Orthogonality and burdens of heterologous AND gate gene circuits in E. coli. ACS Synth. Biol. 7(2), 553–564 (2018)

    Article  Google Scholar 

  11. Marchisio, M.A., Colaiacovo, M., Whitehead, E., et al.: Modular, rule-based modeling for the design of eukaryotic synthetic gene circuits. BMC Syst. Biol. 7, 42 (2013)

    Article  Google Scholar 

  12. Czar, M.J., Cai, Y., Peccoud, J.: Writing DNA with GenoCADTM. Nucleic Acids Res. 37(Web Server), W40–W47 (2009)

    Article  Google Scholar 

  13. Zeng, Y., Jones, A.M., Thomas, E.E., et al.: A split transcriptional repressor that links protein solubility to an orthogonal genetic circuit. ACS Synth. Biol. 7, 2126–2138 (2018). https://doi.org/10.1021/acssynbio.8b00129

    Article  Google Scholar 

  14. Shi, W., Taylor, K., Kull, J.: Characterization and crystallization of BreR, the TetR family member bile response repressor of vibrio cholerae. Biophys. J. 102(3), 72a–72a (2012)

    Article  Google Scholar 

  15. Yang, M., Gao, C., Cui, T., et al.: A TetR-like regulator broadly affects the expressions of diverse genes in Mycobacterium smegmatis. Nucleic Acids Res. 40(3), 1009–1020 (2012)

    Article  Google Scholar 

  16. Cai, Y., Hartnett, B., Gustafsson, C., et al.: A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts. Bioinformatics 23(20), 2760–2767 (2007)

    Article  Google Scholar 

  17. Coll, A., Wilson, L., Gruden, K., et al.: Rule-based design of plant expression vectors using GenoCAD. PLoS One 10(7), e0132502 (2015)

    Article  Google Scholar 

  18. Dong, Y., Shi, P., Lv, Q., et al.: Use of structured query language to simplify and analyze non-redundant data. J. Comput. Theor. Nanosci. 14, 3741–3746 (2017)

    Article  Google Scholar 

Download references

Acknowledgment

This research is supported by National Natural Science Foundation of China (Grant number Nos. 61572302 and 61272246). The authors acknowledge the anonymous referee’s suggestion to this paper.

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Authors and Affiliations

  1. School of Computer Science, Shaanxi Normal University, Xi’an, 710119, Shaanxi, China

    Mingzhu Li

  2. College of Life Science, Shaanxi Normal University, Xi’an, 710119, Shaanxi, China

    Yafei Dong

Authors
  1. Mingzhu Li
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  2. Yafei Dong
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Corresponding author

Correspondence to Yafei Dong .

Editor information

Editors and Affiliations

  1. Huazhong University of Science and Technology, Wuhan, China

    Linqiang Pan

  2. Zhengzhou University, Zhengzhou, China

    Jing Liang

  3. Zhongyuan University of Technology, Zhengzhou, China

    Boyang Qu

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© 2020 Springer Nature Singapore Pte Ltd.

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Li, M., Dong, Y. (2020). Using of Processed Data to Design Genetic Circuits in GenoCAD. In: Pan, L., Liang, J., Qu, B. (eds) Bio-inspired Computing: Theories and Applications. BIC-TA 2019. Communications in Computer and Information Science, vol 1160. Springer, Singapore. https://doi.org/10.1007/978-981-15-3415-7_2

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  • DOI: https://doi.org/10.1007/978-981-15-3415-7_2

  • Published:

  • Publisher Name: Springer, Singapore

  • Print ISBN: 978-981-15-3414-0

  • Online ISBN: 978-981-15-3415-7

  • eBook Packages: Computer ScienceComputer Science (R0)

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