Computational Processes in Living Cells
Project leader: ION PETRE
Department of Computer Science, Abo Akademi University
Doctoral students of the project:
Chang Li, Dept. of Computer Science, Abo Akademi
Other researchers of the project:
Vladimir Rogojin, Dept. of Computer Science, Åbo Akademi,
Jose Ignacio Castaner Alocen, Dep. of Computer Science, University of Valencia
Zuhair Iftikhar, Dept. of Computer Science, University of Turku
Andreas Pada, Dep. Of Computer Science, Abo Akademi
Dr. Tero Harju, Dep. of Mathematics, University of Turku
Prof. Grzegorz Rozenberg, Dep. Of Computer Science, University of Leiden, Holland
Key words: Bioinformatics, biocomputing, DNA computing, computational processes, ciliates, gene assembly, pointer reduction systems, invariants, universality.
Project desciption and main results:
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 suctures of Computer Science - the linked list - and use it in a very elegant pattern matching manner in the process of gene assembly! We have been investigating for a few years now a set of 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. The fact that we could provide a theory for this process that is consistent with the experimental results carries a positive promise for the continuation of this research, which should cover at least the following topics:
- Simple operations. Our results suggest it possible that ciliates use only simple operations for gene assembly. To postulate this, one has to investigate properties of simple operations - this research could culminate in the description of a deterministic simple gene assembly process, thus explaining the amazing reliability (more than 99%) of gene assembly in ciliates.
- Parallel assembly. It is likely that the gene assembly in ciliates involves parallel manipulations of DNA: theoretical investigations of parallel assembly strategies are thus needed.
- Micronuclear gene patterns. Deeper understanding of the micronuclear patterns that can be assembled using only a given subset of our operations is needed to analyze experimental data to integrate in our computer-based tools - the simple operations must also be considered.
- Intermolecular assembly. Some efforts to compare the two competing models (our intramolecular model and the Princeton-Western Ontario intermolecular model) for gene assembly are needed.
Publications: