DNA GRA-TRA 2004
ICGT 2004 Tutorial on
One day tutorial on graph transformation in gene assembly
This is a full day (6 lectures) tutorial on formal methods in DNA computing.
Natural Computing is a research area concerned with computing taking place in nature and with human-designed computing inspired by nature. It is a fast growing, genuinely interdisciplinary field involving, among others, biology and computer science.
We shall discuss the computational model of a very intricate DNA processing taking place in single cell organisms called ciliates, in the process of gene assembly.
We emphasize the role of graph transformations in modelling and studying gene assembly process. In particular, we demonstrate that graph transformations provide the good level of abstraction, and useful technical tools for studying gene assembly. On the other hand, the gene assembly process inspires a new computing paradigm; computing by folding and recombination, which induces novel questions and challenges for research on graph transformation.
Ciliates (ciliated protozoa) are single-celled eukaryotic organisms. It is an ancient group of organisms which originated around two billion years ago, and it is a very diverse group - some 8,000 different species are currently known. Two characteristics hold ciliates together as a single group: the possession of hair-like cilia used for motility and food capture, and the presence of two kinds of functionally different nuclei in the same cell - a micronucleus and a macronucleus.
The macronucleus is the ''household nucleus'' that provides RNA transcripts for producing proteins, while the micronucleus is a dormant nucleus, where no production of RNA transcripts is attempted at all. 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 - it is the most involved DNA processing known in living organisms. Gene assembly is so involved because the form of the micronuclear genome is drastically different from the form of the macronuclear genome.
Preliminary Program (Tuesday September 2, 2004)