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Computational Processes in Living Cells (COMPROC)

Academy of Finland, 2004-2007, within the research program for Systems Biology and Bioinformatics.

Ciliates are an ancient group of organisms (about 2.5 billion years old), often classified as the most complex unicellular organisms on Earth. This family includes the fastest living form on Earth (Strombidium), as well as some unicellular organisms with digestive systems almost as complex as ours (Paramecium). A phenomenon unique to ciliates is the presence of two kinds of functional nuclei in the same cell: a micronucleus and a macronucleus. The macronucleus is the household nucleus that provides the RNA transcripts for producing proteins, while the micronucleus is activated only in the process of sexual reproduction, where at some stage the genome of the micronucleus gets transformed into the genome of the macronucleus in the process called gene assembly – this is the most involved process of DNA manipulation known in Nature !

The process of gene assembly has the attention of the Biocomputing community for several years already. It is by now clear that the process of gene assembly in ciliates is highly computational: it turns out that ciliates “know” one of the basic data structures of Computer Science – the linked list – and use it in a very elegant pattern matching manner in the process of gene assembly! We are investigating a set of three molecular operations that accomplishes the gene assembly through the “fold and recombine” paradigm. We introduced the mathematical model of pointer reduction systems to formalize the micronuclear gene patterns (through permutations, strings and graphs) and the gene assembly process. Our investigation of these systems resulted in a uniform explanation of all known experimental results concerning gene assembly in ciliates.