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

Scrambling analysis of ciliates

Ciliates are a class of organisms which undergo a genetic process called gene descrambling after mating. In order to better understand the problem, a literature review of past works has been presented in this thesis. This includes a brief summary of both the relevant biology and bioinformatics literature. Then, a formal definition of scrambling systems is developed which attempts to model the problem of sequence alignment between scrambled and descrambled genes. With this system, sequences can be classified into relevant functional segments. It also provides a framework whereby we can compare various ciliate sequence alignment algorithms. After that, a new method of predicting the various functional segments is studied. This method shows better coverage, and usually a better labelling score with certain parameters. Then we discuss several recent hypotheses as to how ciliates naturally descramble genes. An algorithm suite is developed to test these hypotheses. With the tests, we are able to computationally check which factors are potentially the most important. According to the current results with 247 pointer sequences of 13 micronuclear genes, examining repeats which are the same distance together with either the sequence or the size, as the real pointers, is almost always enough information to guide descrambling. Indeed, the real pointer sequence is the unique repeat 92.7% and 94.3% of the time within the 247 pointers, from the left and right respectively, using only the pointer distance and the pointer sequence information

Computational Power of Gene Rearrangement

In [8] we proposed a model to describe the homologous recombinations that take place during massive gene rearrangements in hypotrichous ciliates. Here we develop the model by introducing the dependency of homologous recombinations on the presence of certain contexts. We then prove that such a model has the computational power of a Turing machine. This indicates that, in principle, some unicellular organisms may have the capacity to perform any computation carried out by an electronic computer