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University of Saskatchewan, Department of Computer Science

2001-2002 Seminar Series

At the Intersection of Bioinformatics and Biocomputing: Models and Applications of Gene Descrambling in Hypotrichous Ciliates

Mark Daley
Department of Computer Science
University of Western Ontario
London, Ontario

DEPARTMENT SEMINAR
DATE: Friday, June 7, 2002
TIME: 3:30pm
PLACE: Anthropology 132
*** Everyone is welcome ***

Abstract

Advances in the techniques and tools available to molecular biologists have made it possible to examine the genetic processes of a wide variety of organisms with a level of detail hitherto impossible. One such area of active research is the gene-descrambling process of the hypotrichous ciliates. These tiny unicellular organisms store their genome in an encrypted form and possess mechanisms capable of descrambling their genes to create functional copies.

The research presented will begin with a formal mathematical model of the gene descrambling process. From there we will investigate abstract properties of the model and present a deterministic algorithm for descrambling an arbitrary gene. In addition to providing a hypothesis for the true in vivo descrambling mechanism, the algorithm can be treated as a method for generating a complexity measure of a given gene. We will show the results of applying this technique to genes from the ciliates Sterkiella Nova (formerly Oxytricha Nova) and Stylonychia Lemnae.

The ultimate goal of this research is not only a better model of ciliate genetics, but also the ability to make use of this unique genetic mechanism for performing an arbitrary in vivo computation. We will end the presentation with a discussion of current efforts towards making this a reality.

About the speaker

Mark Daley is currently a Ph.D. candidate at the University of Western Ontario. His research focusses on the application of mathematical modelling to biological problems and unconventional methods of computing. He received his honours Bachelor's degree in Computer Science and Mathematics from the University of Western Ontario in 1999. [an error occurred while processing this directive]