The evolution of cellular computing: Nature's solution to a computational problem

BioSystems

Volumn 52, Issue 1-3, 1999, Pages 3-13

  Landweber, Laura F ^a   Kari, Lila ^b  

^a PRINCETON UNIVERSITY   (United States)

^b UNIVERSITY OF WESTERN ONTARIO   (Canada)

Author keywords

Ciliate; DNA computing; Hypotrich; Molecular evolution; Scrambled gene

Indexed keywords

DNA;

ARTICLE; CALCULATION; CILIATE; DNA DETERMINATION; GENETICS; GENOME; MOLECULAR EVOLUTION; NONHUMAN; PROTOZOON;

EID: 0032725008     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0303-2647(99)00027-1     Document Type: Article

References (27)

1. Adleman L.M. Molecular computation of solutions to combinatorial problems. Science. 266:1994;1021-1024.
2. Bartel D.P., Szostak J.W. Isolation of new ribozymes from a large pool of random sequences. Science. 261:1993;1411-1418.
3. Beaver D. A universal molecular computer. Lipton R.J., Baum E.B. DNA Based Computers. DIMACS Series in Discrete Mathematics and Theoretical Computer Science. 27:1996;29-36 AMS.
4. Blum B., Bakalara N., Simpson L. A model for RNA editing in kinetoplastid mitochondria: 'Guide' RNA molecules transcribed from maxicircle DNA provide the edited information. Cell. 60:1990;189-198.
5. Csuhaj-Varju E., Freund R., Kari L., Paun G. DNA computing based on splicing: universality results. Hunter L., Klein T. Proceedings of 1st Pacific Symposium on Biocomputing. 1996;179-190 World Scientific, Singapore.
6. Dubois M., Prescott D.M. Scrambling of the actin I gene in two Oxytricha species. Proc. Natl. Acad. Sci. USA. 92:1995;3888-3892.
7. Feagin J.E., Abraham J.M., Stuart K. Extensive editing of the cytochrome c oxidase III transcript in Trypanosoma brucei. Cell. 53:1988;413-422.
8. Head T. Formal language theory and DNA: an analysis of the generative capacity of specific recombinant behaviors. Bull. Math. Biol. 49:1987;737-759.
9. Hoffman D.C., Prescott D.M. Evolution of internal eliminated segments and scrambling in the micronuclear gene encoding DNA polymerase α in two Oxytricha species. Nucl. Acids Res. 25:1997;1883-1889.
10. Kari L., Thierrin G. Contextual insertion/deletions and computability. Inform. Comput. 131:1996;47-61.
11. Klobutcher L.A., Turner L.R., LaPlante J. Circular forms of developmentally excised DNA in Euplotes crassus have a heteroduplex junction. Genes Dev. 7:1993;84-94.
12. Landweber, L.F., 1997. RNA based computing. DIMACS Technical Report 97-83.
13. Landweber L.F., Gilbert W. RNA editing as a novel source of genetic variation. Nature. 363:1993;179-182.
14. Landweber L.F., Gilbert W. Phylogenetic analysis of RNA editing: a primitive genetic phenomenon. Proc. Natl. Acad. Sci. USA. 91:1994;918-921.
15. Landweber L.F., Fiks A.G., Gilbert W. The boundaries of partially edited cytochrome c oxidase III transcripts are not conserved in kinetoplastids: implications for the guide RNA model of editing. Proc. Natl. Acad. Sci. USA. 90:1993;9242-9246.
16. Lynn D.H., Corliss J.O. Ciliophora. Microscopic Anatomy of Invertebrates. Volume 1. Protozoa. 1991;333-467 Wiley-Liss, New York.
17. Maslov D.A., Simpson L. The polarity of editing within a multiple gRNA-mediated domain is due to formation of anchors for upstream gRNAs by downstream editing. Cell. 70:1992;459-467.
18. Mitcham J.L., Lynn A.J., Prescott D.M. Analysis of a scrambled gene: the gene encoding α-telomere-binding protein in Oxytricha nova. Genes Dev. 6:1992;788-800.
19. Paun G. On the power of the splicing operation. Int. J. Comp. Math. 59:1995;27-35.
20. Pixton D. Linear and circular splicing systems. Proceedings of the First International Symposium on Intelligence in Neural and Biological Systems. 1995;181-188 IEEE Computer Society Press, Los Alamos.
21. Prescott D.M., Dubois M.L. Internal eliminated segments (IESs) of oxytrichidae. J. Euk. Microbiol. 43:1996;432-441.
22. Siromoney R., Subramanian K.G., Rajkumar Dare V. Circular DNA and splicing systems. Parallel Image Analysis. Lecture Notes in Computer Science 654. 1992;260-273 Springer, Berlin.
23. Smith W.D. DNA computers in vitro and vivo. DIMACS Series in Discrete Mathematics and Theoretical Computer Science. 27:1996;121-185.
24. Sommer B., Kohler M., Sprengel R., Seeburg P.H. RNA editing in brain controls a determinant of ion flow in glutamate-gated channels. Cell. 67:1991;11-19.
25. Sullenger B.A., Cech T.R. Ribozyme-mediated repair of defective mRNA by targeted, trans-splicing. Nature. 371:1994;619-622.
26. Tausta S.L., Klobutcher L.A. Detection of circular forms of eliminated DNA during macronuclear development in E. crassus. Cell. 59:1989;1019-1026.
27. Wen J., Maercker C., Lipps H.J. Sequential excision of internal eliminated DNA sequences in the differentiating macronucleus of the hypotrichous ciliate Stylonychia lemnae. Nucl. Acids Res. 24:1996;4415-4419.