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Computational Complexity pp 228–237Cite as

Bacterial Computing

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Article Outline

Glossary

Definition of the Subject

Introduction

Motivation for Bacterial Computing

The Logic of Life

Rewiring Genetic Circuitry

Successful Implementations

Future Directions

Bibliography

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Abbreviations

DNA:

Deoxyribonucleic acid. Molecule that encodes the genetic information of cellular organisms.

Operon:

Set of functionally related genes with a common promoter (“on switch”).

Plasmid:

Small circular DNA molecule used to transfer genes from one organism to another.

RNA:

Ribonucleic acid. Molecule similar to DNA, which helps in the conversion of genetic information to proteins.

Transcription:

Conversion of a genetic sequence into RNA.

Translation:

Conversion of an RNA sequence into an amino acid sequence (and, ultimately, a protein).

Bibliography

Primary Literature

  1. Anon (2004) Roger Brent and the alpha project. ACM Ubiquity, 5(3)

    Google Scholar 

  2. Arkin A, Ross J (1994) Computational functions in biochemical reaction networks.Biophysical J 67:560–578

    Article  Google Scholar 

  3. Barkai N, Leibler S (2000) Circadian clocks limited by noise. Nature 403:267–268

    Google Scholar 

  4. Basu S, Gerchman Y, Collins CH, Arnold FH, Weiss R (2005) A synthetic multicellular system for programmed pattern formation. Nature 434:1130–1134

    Article  Google Scholar 

  5. Benner SA, Sismour M (2005) Synthetic biology. Nature Rev Genet 6:533–543

    Article  Google Scholar 

  6. Brown C (2004) BioBricks to help reverse‐engineer life. EE Times, June 11

    Google Scholar 

  7. Brown S (2005) Command performances. San Diego Union-Tribune, December 14

    Google Scholar 

  8. Brown TA (1990) Gene cloning: an introduction, 2nd edn. Chapman and Hall, London

    Google Scholar 

  9. Crick F (1970) Central dogma of molecular biology. Nature 227:561–563

    Article  Google Scholar 

  10. Eisenberg A (2000) Unlike viruses, bacteria find a welcome in the world of computing. New York Times, June 1

    Google Scholar 

  11. Elowitz M, Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403:335–338

    Article  Google Scholar 

  12. Ferber D (2004) Synthetic biology: microbes made to order. Science 303(5655):158–161

    Article  Google Scholar 

  13. Gardner T, Cantor R, Collins J (2000) Construction of a genetic toggle switch in Escherichia coli. Nature 403:339–342

    Article  Google Scholar 

  14. Geyer CR, Battersby TR, Benner SA (2003) Nucleobase pairing in expanded Watson-Crick-like genetic information systems.Structure 11:1485–1498

    Article  Google Scholar 

  15. Gibbs WW (2004) Synthetic life. Scientific Am April 26

    Google Scholar 

  16. Gravitz L (2004) 10 emerging technologies that will change your world. MIT Technol Rev February

    Google Scholar 

  17. Hasty J (2002) Design then mutate. Proc Natl Acad Sci 99(26):16516–16518

    Article  Google Scholar 

  18. Hopkin K (2004) Life: the next generation. The Scientist 18(19):56

    Google Scholar 

  19. Jackson DA, Symons RH, Berg P (1972) Biochemical method for inserting new genetic information into DNA of simian virus 40: circular SV40 DNA molecules containing lambda phage genes and the galactose operon of Escherichia coli. Proc Natl Acad Sci 69:2904–2909

    Article  Google Scholar 

  20. Jacob F, Monod J (1961) Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 3:318–356

    Article  Google Scholar 

  21. Jha A (2005) From the cells up. The Guardian, March 10

    Google Scholar 

  22. Kauffman S (1993) Gene regulation networks: a theory for their global structure and behaviors.Current topics in developmental biology 6:145–182

    Google Scholar 

  23. Kauffman SA (1993) The origins of order: Self‐organization and selection in evolution. Oxford University Press, New York

    Google Scholar 

  24. Levskaya A, Chevalier AA, Tabor JJ, Simpson ZB, Lavery LA, Levy M, Davidson EA, Scouras A, Ellington AD, Marcotte EM, Voight CA (2005) Engineering Escherichia coli to see light.Nature 438:441–442

    Article  Google Scholar 

  25. Lobban PE, Sutton CA (1973) Enzymatic end-to-end joining of DNA molecules. J Mol Biol 78(3):453–471

    Article  Google Scholar 

  26. Marks P (2005) For ultrasharp pictures, use a living camera. New Scientist, November 26, p 28

    Google Scholar 

  27. McAdams HH, Shapiro L (1995) Circuit simulation of genetic networks. Science 269(5224):650–656

    Article  Google Scholar 

  28. McAdams HH, Arkin A (2000) Genetic regulatory circuits: Advances toward a genetic circuit engineering discipline.Current Biol 10:318–320

    Article  Google Scholar 

  29. Monod J (1970) Chance and Necessity. Penguin, London

    Google Scholar 

  30. Monod J, Changeux JP, Jacob F (1963) Allosteric proteins and cellular control systems. J Mol Biol 6:306–329

    Article  Google Scholar 

  31. Morton O (2005) Life, Reinvented. Wired 13(1), January

    Google Scholar 

  32. Registry of Standard Biological Parts. http://parts.mit.edu/

  33. Old R, Primrose S (1994) Principles of Gene Manipulation, an Introduction to Genetic Engineering, 5th edn. Blackwell, Boston

    Google Scholar 

  34. Ptashne M (2004) A Genetic Switch, 3rd edn. Phage Lambda Revisited. Cold Spring Harbor Laboratory Press, Woodbury

    Google Scholar 

  35. Roberts L, Murrell C (eds) (1998) An introduction to genetic engineering. Department of Biological Sciences, University of Warwick

    Google Scholar 

  36. Strogatz S (2003) Sync: The Emerging Science of Spontaneous Order. Penguin, London

    Google Scholar 

  37. Turing AM (1952) The chemical basis of morphogenesis.Phil Trans Roy Soc B 237:37–72

    Article  Google Scholar 

  38. von Neumann J (1941) The general and logical theory of automata. In: Cerebral Mechanisms in Behavior. Wiley, New York

    Google Scholar 

  39. Yokobayashi Y, Weiss R, Arnold FH (2002) Directed evolution of a genetic circuit. Proc Natl Acad Sci 99(26):16587–16591

    Article  Google Scholar 

  40. You L, Cox III RS, Weiss R, Arnold FH (2004) Programmed population control by cell-cell communication and regulated killing. Nature 428:868–871

    Article  Google Scholar 

Books and Reviews

  1. Alon U (2006) An Introduction to Systems Biology: Design Principles of Biological Circuits. Chapman and Hall/CRC

    Google Scholar 

  2. Amos M (ed) (2004) Cellular Computing.Series in Systems Biology Oxford University Press

    MATH  Google Scholar 

  3. Amos M (2006) Genesis Machines: The New Science of Biocomputing. Atlantic Books, London

    Google Scholar 

  4. Benner SA (2003) Synthetic biology: Act natural.Nature 421:118

    Article  Google Scholar 

  5. Endy D (2005) Foundations for engineering biology.Nature 436:449–453

    Article  Google Scholar 

  6. Kobayashi H, Kaern M, Araki M, Chung K, Gardner TS, Cantor CR, Collins JJ (2004) Programmable cells: interfacing natural and engineered gene networks.Proc Natl Acad Sci 101(22):8414–8419

    Article  Google Scholar 

  7. Sayler GS, Simpson ML, Cox CD (2004) Emerging foundations: nano‐engineering and bio‐microelectronics for environmental biotechnology.Curr Opin Microbiol 7:267–273

    Article  Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Computing and Mathematics, Manchester Metropolitan University, Manchester, UK

    Martyn Amos

Authors
  1. Martyn Amos
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Editor information

Editors and Affiliations

  1. RAMTECH LIMITED, 122 Escalle Lane, Larkspur, CA, 94939, USA

    Robert A. Meyers Ph. D. (Editor-in-Chief) (Editor-in-Chief)

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© 2012 Springer-Verlag

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Amos, M. (2012). Bacterial Computing. In: Meyers, R. (eds) Computational Complexity. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-1800-9_15

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