Department of Applied Mathematics, University of Leeds, UK

A Stochastic Model of T cell Repertoire Maintenance

IGC - Computational Genomics Group

Mini-size me! From free-living to parasite

We tend to think of intracellular parasites as a distorted version of Aesop's fable "The Ant and the Cicada" or like a son in his thirties who still lives in his mother's house - does the minimum necessary and takes everything they have to give. This view stems in part from the extensive gene loss displayed by parasite's genomes. But which genes are lost? In order to answer this question, we built a neutral model of evolution simulating a random loss scenario. Deviations from neutrality identify possible signs of selection. We study the distribution of structural domains in free-living and parasites, as these represent units of protein evolution. Interestingly our preliminary results show a preferential loss of duplicates rather than single copies. We interpret this as maintenance of diversity at the expense of loss in redundancy. In this tale the cicada tends to look more like a minimized version of the ant. It may be that it needs a minimal set of genes/proteins for parasitic lifestyle that does not deviate from free-living. Can this imply a physical endpoint? In this seminar we'll try to address the implications of this and future steps in the search of understanding the mechanisms of genome compaction.