June 22, 2015

Vladimir Rogojin (Abo Akademi, Turku, Finland)

Intricate DNA manipulation during gene assembly in stichotrichous ciliates is an elegant example of a computational process which takes place in Nature. Ciliates form one of the most ancient and diverse groups of eukaryotes. Each ciliate has two types of nuclei where the same genetic information is organized in totally different ways. In macronuclei, DNA molecules contain contiguous sequences representing genes, while in micronuclei genes are broken into fragments that are shuffled, separated by non-coding sequences, and some of the gene fragments are even inverted. During gene assembly ciliates assemble micronulear gene fragments into macronuclear genes. Basically, during this process ciliates have to identify correctly gene fragments and assemble them in the correct order and orientation. In this way, one could say that ciliates are solving permutation sorting problem during gene assembly. We will discuss how computer scientists and mathematicians could reason about and analyze processes happening in living cells on an example of gene assembly in ciliates.