Modelling Genetic Gymnastics: The mathematics of gene scrambling in ciliates.

Dr. Mark Daley Assistant Professor Department of Computer Science

DEPARTMENT SEMINAR DATE: Friday, October 3, 2003 TIME: 3:30pm PLACE: Agriculture 2E25 *** Everyone is welcome ***

Abstract

The stichotrichous ciliates are a group of single-celled organisms which have generated a great deal of interest due to their unique genetic mechanisms. Most organisms store their genomic DNA in a linear sequence consisting of coding regions interspersed with non-coding regions. Several ciliate genes, however, are stored in a scrambled form. For example, if a functional copy of a gene consists of the coding regions arranged in the order 1-2-3-4-5, it may appear in the order 3-5-4-1-2 in the genome. This presents an interesting problem for the organism, who must somehow descramble these genes in order to generate functional proteins required for its continued existence.

Three major mathematical models of this descrambling process have been proposed in the literature. In this talk we will review each of these models and discuss both their mathematical properties and biological feasibility. Moreover, we will show how the abstract mathematical properties derived from these models can give us information about the underlying biological system.

Finally, we will address the possibility of true 'in vivo computing' by co-opting the gene descrambling mechanism to perform arbitrary computations.

About the speaker

Mark is an assistant professor here in the Deparment of Computer Science and has been with us since January 2003. His research interests are Natural Computing, Mathematical Modelling of Biological Systems, Formal Language Theory, Semigroups, High Performance Computer for Biology and Mathematics, and Molecular Evolution.

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