Theory Inspired by Gene Assembly in Ciliates
Ciliates (ciliated protozoa) are unicellular organisms with an evolutionary history that extends back perhaps two billion (2 x 109) years. The unique extraordinary feature of ciliates is that they posses two kinds of nuclei within the same cell: macronucleus containing genes that provide the genetic information needed to maintain the structure and function of the cell, and micronucleus that does not contribute to the maintainance, growth and proliferation of the cell – it is reserved for the sexual exchange of DNA between two mating cells.
When ciliates are starved they may mate. At some stage during sexual reproduction a micronucleus develops into a new macronucleus. This process of transformation of the micronuclear genome into the macronuclear genome, called gene assembly, is perhaps the most involved process of DNA manipulation yet known in living organisms. It is fascinating from both the biological and computational point of view.
The computational nature of gene assembly has attracted much attention in recent years and considerable body of theory has been developed. This theory involves, among others, novel kinds of string and graph rewriting systems, novel sorts of graphs as well as new questions about various known graph families, and novel topics in the combinatorics of words. In our talk we will survey some of the main developments of this theory.