Advertisement

Solutions to Computational Problems Through Gene Assembly

  • Artiom Alhazov
  • Ion Petre
  • Vladimir Rogojin
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4848)

Abstract

Gene assembly in ciliates is an impressive computational process. Ciliates have a unique way of storing their genetic information in two fundamentally different forms within their two types of nuclei. Micronuclear genes are broken into blocks (called MDSs), with MDSs shuffled and separated by non-coding material; some of the MDSs may even be inverted. During gene assembly, all MDSs are sorted in the correct order to yield the transcription-able macronuclear gene. Based on the intramolecular model for gene assembly, we prove in this paper that gene assembly may be used in principle to solve computational problems. We prove that any given instance of the hamiltonian path problem may be encoded in a suitable way in the form of an ‘artificial’ gene so that gene assembly is successful on that gene-like pattern if and only if the given problem has an affirmative answer.

Keywords

Directed Graph Turing Machine Computational Problem Hamiltonian Path Gene Assembly 
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.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Adleman, L.M.: Molecular computation of solutions to combinatorial problems. Science 226, 1021–1024 (1994)CrossRefGoogle Scholar
  2. 2.
    Angeleska, A., Jonoska, N., Saito, M., Landweber, L.F.: RNA-Template Guided DNA Assembly. In: Garzon, M., Yan, H. (eds.) Preliminary Proceedings on DNA13 meeting, University of Memphis, Memphis, p. 364 (2007)Google Scholar
  3. 3.
    Ehrenfeucht, A., Harju, T., Petre, I., Prescott, D.M., Rozenberg, G.: Computation in Living Cells: Gene Assembly in Ciliates. Springer, Heidelberg (2003)Google Scholar
  4. 4.
    Ehrenfeucht, A., Harju, T., Petre, I., Prescott, D.M., Rozenberg, G.: Formal systems for gene assembly in ciliates. Theoret. Comput. Sci. 292, 199–219 (2003)zbMATHCrossRefMathSciNetGoogle Scholar
  5. 5.
    Ehrenfeucht, A., Harju, T., Petre, I., Rozenberg, G.: Characterizing the micronuclear gene patterns in ciliates. Theory of Comput. Syst. 35, 501–519 (2002)zbMATHCrossRefMathSciNetGoogle Scholar
  6. 6.
    Ehrenfeucht, A., Petre, I., Prescott, D.M., Rozenberg, G.: String and graph reduction systems for gene assembly in ciliates. Math. Structures Comput. Sci. 12, 113–134 (2001)CrossRefMathSciNetGoogle Scholar
  7. 7.
    Ehrenfeucht, A., Petre, I., Prescott, D.M., Rozenberg, G.: Circularity and other invariants of gene assembly in ciliates. In: Ito, M., Păun, G., Yu, S. (eds.) Words, semigroups, and transductions, pp. 81–97. World Scientific, Singapore (2001)Google Scholar
  8. 8.
    Ehrenfeucht, A., Prescott, D.M., Rozenberg, G.: Computational aspects of gene (un)scrambling in ciliates. In: Landweber, L.F., Winfree, E. (eds.) Evolution as Computation, pp. 216–256. Springer, Heidelberg (2001)Google Scholar
  9. 9.
    Harju, T., Petre, I., Li, C., Rozenberg, G.: Parallelism in gene assembly. In: Ferretti, C., Mauri, G., Zandron, C. (eds.) DNA Computing. LNCS, vol. 3384, pp. 138–148. Springer, Heidelberg (2005)Google Scholar
  10. 10.
    Harju, T., Petre, I., Rozenberg, G.: Gene assembly in ciliates: Molecular operations. In: Păun, G., Rozenberg, G., Salomaa, A. (eds.) Current Trends in Theoretical Computer Science (2004)Google Scholar
  11. 11.
    Harju, T., Petre, I., Rozenberg, G.: Gene assembly in ciliates: formal frameworks. In: Păun, G., Rozenberg, G., Salomaa, A. (eds.) Current Trends in Theoretical Computer Science (2004)Google Scholar
  12. 12.
    Kari, L., Landweber, L.F.: Computational power of gene rearrangement. In: Winfree, E., Gifford, D.K. (eds.) Proceedings of DNA Bases Computers, V. American Mathematical Society, pp. 207–216 (1999)Google Scholar
  13. 13.
    Landweber, L.F., Kari, L.: The evolution of cellular computing: Nature’s solution to a computational problem. In: Proceedings of the 4th DIMACS Meeting on DNA-Based Computers, Philadelphia, PA, pp. 3–15 (1998)Google Scholar
  14. 14.
    Landweber, L.F., Kari, L.: Universal molecular computation in ciliates. In: Landweber, L.F., Winfree, E. (eds.) Evolution as Computation, Springer, New York (2002)Google Scholar
  15. 15.
    Onolt-Ishdorj, T., Petre, I., Rogojin, V.: Computational Power of Intramolecular Gene Assembly. Computability in Europe (submitted 2007)Google Scholar
  16. 16.
    Papadimitriou, C.H.: Computational Complexity. Addison-Wesley, Reading (1994)zbMATHGoogle Scholar
  17. 17.
    Prescott, D.M.: The DNA of ciliated protozoa. Microbiol. Rev. 58(2), 233–267 (1994)Google Scholar
  18. 18.
    Prescott, D.M., Ehrenfeucht, A., Rozenberg, G.: Molecular operations for DNA processing in hypotrichous ciliates. Europ. J. Protistology 37, 241–260 (2001)CrossRefGoogle Scholar
  19. 19.
    Petre, I.: Invariants of gene assembly in stichotrichous ciliates. IT, Oldenbourg Wissenschftsverlag 3, 161–167 (2006)Google Scholar
  20. 20.
    Prescott, D.M., Rozenberg, G.: How ciliates manipulate their own DNA – A splendid example of natural computing. Natural Computing 1, 165–183 (2002)zbMATHCrossRefMathSciNetGoogle Scholar
  21. 21.
    Prescott, D.M., Rozenberg, G.: Encrypted genes and their reassembly in ciliates. In: Amos, M. (ed.) Cellular Computing, Oxford University Press, Oxford (2003)Google Scholar
  22. 22.
    Vijayan, V., Nowacki, M., Zhou, Y., Doak, T., Landweber, L.: Programming a Ciliate Computer: Template-Guided In Vivo DNA Rearrangements in Oxytricha. In: Garzon, M., Yan, H. (eds.) Preliminary Proceedings on DNA13 meeting, University of Memphis, Memphis, p. 172 (2007)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Artiom Alhazov
    • 2
  • Ion Petre
    • 1
    • 2
  • Vladimir Rogojin
    • 2
  1. 1.Academy of Finland 
  2. 2.Computational Biomodelling LaboratoryTurku Center for Computer ScienceFinland

Personalised recommendations