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PhD Talk: Gene Assembly in Ciliates Robert Brijder Fundamental Computer Science Ciliates • • Ciliates form a large group of unicellular organisms. Ciliates have a property that is interesting from a computational point of view. Preliminaries • • • All organisms (except ciliates) have one kind of nuclei. This nuclei consists of a number of chromosomes. A chromosome is a enormously long DNA molecule. A gene is a specific sequence in a DNA molecule. A gene is a `building plan’ for a protein. Gene 1 Gene 2 Gene 3 Micronucleus • • • • Ciliates have two kinds of nuclei: the micronucleus and the macronucleus. The micronucleus consist of chromosomes. The genes are silent in the micronucleus: the gene is divided into parts, which are dispersed along one or more chromosomes. Gene parts for the actin protein of Sterkiella nova: 3 4 6 5 7 9 2 1 8 Macronucleus • The macronucleus consist of a large number of short DNA molecules. Each DNA molecule contains a single gene in the appropriate order. 1 2 3 4 5 6 7 8 9 Gene • During cell mating, a daughter micronucleus is formed. A copy is transformed into the macronucleus. This is called gene assembly. Example of Sterkiella nova Micronucleus 3 4 6 5 7 9 2 Gene Assembly Macronucleus 1 2 3 4 5 Gene 6 7 8 9 1 8 Nuclear Dualism and Gene Assembly Gene Assembly • • The gene assembly process is done using molecular operations. How do these operations know how these parts need to be glued together? Answer: pointers. 3 1 2 4 Actually Double linked list! 3 4 b 2 3 2 4 e Gene Assembly The gene assembly process is accomplished using three molecular operations: • Loop recombination • Hairpin recombination • Double-loop recombination Gene Assembly • Loop recombination • Hairpin recombination Gene Assembly • Double-loop recombination Modeling Gene Assembly • • • • • • Allows us to gain more insight and to prove facts. State results in terms of the model. Translation back to real world is possible. Different models used: MDS-PRS, S-PRS, GPRS. All models are equivalent, and are assumed to be a correct model of the reality. Model the layout of the gene parts. Model the molecular operations. Modeling Gene Assembly 3 4 b 2 3 2 SPRS legal string Loop recombination: Hairpin recombination: Double-loop recombination: where 4 e Modeling Gene Assembly Legal string or • corresponds to a successful assembled gene. • Non-deterministic process. b • No deadlocks. • Finite process. Pointers are removed in every step. e What can we prove? • • • Given a legal string, is it possible to reduce this string without using snr operations (=loop recombination)? Already proved. Given a legal string, how many parallel steps are needed to reduce this string? Open question! .. Questions?