Ciliate Gene Unscrambling with Fewer Templates

One of the theoretical models proposed for the mechanism of gene unscrambling in some species of ciliates is the template-guided recombination (TGR) system by Prescott, Ehrenfeucht and Rozenberg which has been generalized by Daley and McQuillan from a formal language theory perspective. In this paper, we propose a refinement of this model that generates regular languages using the iterated TGR system with a finite initial language and a finite set of templates, using fewer templates and a smaller alphabet compared to that of the Daley-McQuillan model. To achieve Turing completeness using only finite components, i.e., a finite initial language and a finite set of templates, we also propose an extension of the contextual template-guided recombination system (CTGR system) by Daley and McQuillan, by adding an extra control called permitting contexts on the usage of templates.Comment: In Proceedings DCFS 2010, arXiv:1008.127

Two Refinements of the Template-Guided DNA Recombination Model of Ciliate Computing

To solve the mystery of the intricate gene unscrambling mechanism in ciliates, various theoretical models for this process have been proposed from the point of view of computation. Two main models are the reversible guided recombination system by Kari and Landweber and the template-guided recombination (TGR) system by Prescott, Ehrenfeucht and Rozenberg, based on two categories of DNA recombination: the pointer guided and the template directed recombination respectively. The latter model has been generalized by Daley and McQuillan. In this thesis, we propose a new approach to generate regular languages using the iterated TGR system with a finite initial language and a finite set of templates, that reduces the size of the template language and the alphabet compared to that of the Daley-McQuillan model. To achieve computational completeness using only finite components we also propose an extension of the contextual template-guided recombination system (CTGR system) by Daley and McQuillan, by adding an extra control called permitting contexts on the usage of templates. Then we prove that our proposed system, the CTGR system using permitting contexts, has the capability to characterize the family of recursively enumerable languages using a finite initial language and a finite set of templates. Lastly, we present a comparison and analysis of the computational power of the reversible guided recombination system and the TGR system. Keywords: ciliates, gene unscrambling, in vivo computing, DNA computing, cellular computing, reversible guided recombination, template-guided recombination

Genome Structure Drives Patterns of Gene Family Evolution in Ciliates, a Case Study Using \u3ci\u3eChilodonella uncinata\u3c/i\u3e (Protista, Ciliophora, Phyllopharyngea)

In most lineages, diversity among gene family members results from gene duplication followed by sequence divergence. Because of the genome rearrangements during the development of somatic nuclei, gene family evolution in ciliates involves more complex processes. Previous work on the ciliate Chilodonella uncinata revealed that macronuclear β-tubulin gene family members are generated by alternative processing, in which germline regions are alternatively used in multiple macronuclear chromosomes. To further study genome evolution in this ciliate, we analyzed its transcriptome and found that (1) alternative processing is extensive among gene families; and (2) such gene families are likely to be C. uncinata specific. We characterized additional macronuclear and micronuclear copies of one candidate alternatively processed gene family-a protein kinase domain containing protein (PKc)-from two C. uncinata strains. Analysis of the PKc sequences reveals that (1) multiple PKc gene family members in the macronucleus share some identical regions flanked by divergent regions; and (2) the shared identical regions are processed from a single micronuclear chromosome. We discuss analogous processes in lineages across the eukaryotic tree of life to provide further insights on the impact of genome structure on gene family evolution in eukaryotes

Further Open Problems in Membrane Computing

A series of open problems and research topics in membrane com- puting are pointed out, most of them suggested by recent developments in this area. Many of these problems have several facets and branchings, and further facets and branchings can surely be found after addressing them in a more careful manner

Small-scale biogeographic patterns of benthic bacterial and ciliate communities in the saline ponds of Lake MacLeod, North-Western Australia

This biogeographical thesis tests for the presence of taxa-area and distance-decay relationships, which are common among macrobionts, in prokaryotic (bacterial) and micro-eukaryotic (ciliate) communities. Microbial biogeographical patterns may be distinct because of the high abundances, diversity and dispersal capabilities of microbes, in comparison to macrobionts. The Northern Ponds of Lake MacLeod, north-western Australia, provide an ideal location to address this topic, because the ponds are effectively hydrogeomorphologically identical, other than in surface area, and biotic histories can be assumed to differ only according to distance of separation. This means that hypotheses concerning species-sorting and neutral processes on microbial assemblages can be tested in a natural setting. Characteristics of the physical environment were determined using bathymetric and hydrodynamic surveys in eight ponds. For each pond, evaporative outflow was determined using pan evaporation rates, and the hydrodynamic characteristics of each pond were described by measuring water flowing out of the ponds. Four pond morphotypes were distinguished on the basis of physical characteristics (surface area, volume and mean depth) and hydrodynamic properties (water residence time and percentage of evaporative loss). For ionic and nutrient variation within and between the ponds, concentrations were expected to vary based on residence time of the brine within the ponds, evapoconcentration and subsequent precipitation of mineral phases. The water chemistry was found to be similar to seawater, with major ionic ratios remaining rather constant throughout each pond. Cygnet Pond differed from the other ponds in that it was enriched in Mg and Ca and depleted in K. Sediment characteristics were also investigated by microscopy. Six sediment types were described based on the particles found in each sample. There were no clear relationships between sedimentology types and water chemistry, and between each of these and the pond morphotypes. The bacterial and ciliate biofilm communities were analysed using DNA community fingerprinting methods, and constrained to the above environmental parameters using redundancy analyses. Distance-decay relationships were found for the bacterial communities within the ponds, and occurred at relatively short distances ( The results therefore provide evidence that microbial bacteria and ciliate biofilm communities can conform to observed biogeographic patterns for macrobionts, although neither community displayed taxa-area relationships. The communities differed in that a distance-decay relationship was only found in the bacterial community, where ciliate taxa are distributed ‘patchily’, and not as a function of distance. An alternative model is proposed for the bacteria and ciliate communities of Lake MacLeod; each pond, because of their isolation from one another, is influenced by stochastic events which differentiate the ponds via ecological drift. This thesis demonstrates that these microbial communities are capable of having complex biogeographies, and that processes such as ecological drift may be important determinants of their structure

Models of natural computation : gene assembly and membrane systems

This thesis is concerned with two research areas in natural computing: the computational nature of gene assembly and membrane computing. Gene assembly is a process occurring in unicellular organisms called ciliates. During this process genes are transformed through cut-and-paste operations. We study this process from a theoretical point of view. More specifically, we relate the theory of gene assembly to sorting by reversal, which is another well-known theory of DNA transformation. In this way we obtain a novel graph-theoretical representation that provides new insights into the nature of gene assembly. Membrane computing is a computational model inspired by the functioning of membranes in cells. Membrane systems compute in a parallel fashion by moving objects, through membranes, between compartments. We study the computational power of various classes of membrane systems, and also relate them to other well-known models of computation.Netherlands Organisation for Scientific Research (NWO), Institute for Programming research and Algorithmics (IPA)UBL - phd migration 201