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Development of an In Vivo Computer Based on Escherichia coli

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Part of the Lecture Notes in Computer Science book series (LNTCS,volume 3892)

Abstract

We present a novel framework to develop a programmable and autonomous in vivo computer using E. coli, and implement in vivo finite-state automata based on the framework by employing the protein-synthesis mechanism of E. coli. Our fundamental idea to develop a programmable and autonomous finite-state automata on E. coli is that we first encode an input string into one plasmid, encode state-transition functions into the other plasmid, and introduce those two plasmids into an E. coli cell by electroporation. Second, we execute a protein-synthesis process in E. coli combined with four-base codon techniques to simulate a computation (accepting) process of finite automata, which has been proposed for in vitro translation-based computations in [8]. This approach enables us to develop a programmable in vivo computer by simply replacing a plasmid encoding a state-transition function with others. Further, our in vivo finite automata are autonomous because the protein-synthesis process is autonomously executed in the living E. coli cell. We show some successful experiments to run an in vivo finite-state automaton on E. coli.

Keywords

  • Finite Automaton
  • Input String
  • Input Symbol
  • lacZ Reporter Gene
  • Blue Signal

These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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© 2006 Springer-Verlag Berlin Heidelberg

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Nakagawa, H., Sakamoto, K., Sakakibara, Y. (2006). Development of an In Vivo Computer Based on Escherichia coli . In: Carbone, A., Pierce, N.A. (eds) DNA Computing. DNA 2005. Lecture Notes in Computer Science, vol 3892. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11753681_16

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  • DOI: https://doi.org/10.1007/11753681_16

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-34161-1

  • Online ISBN: 978-3-540-34165-9

  • eBook Packages: Computer ScienceComputer Science (R0)