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

Unsteady feeding and optimal strokes of model ciliates

The flow field created by swimming microorganisms not only enables their locomotion but also leads to advective transport of nutrients. In this paper we address analytically and computationally the link between unsteady feeding and unsteady swimming on a model microorganism, the spherical squirmer, actuating the fluid in a time-periodic manner. We start by performing asymptotic calculations at low P\'eclet number (Pe) on the advection-diffusion problem for the nutrients. We show that the mean rate of feeding as well as its fluctuations in time depend only on the swimming modes of the squirmer up to order Pe^(3/2), even when no swimming occurs on average, while the influence of non-swimming modes comes in only at order Pe^2. We also show that generically we expect a phase delay between feeding and swimming of 1/8th of a period. Numerical computations for illustrative strokes at finite Pe confirm quantitatively our analytical results linking swimming and feeding. We finally derive, and use, an adjoint-based optimization algorithm to determine the optimal unsteady strokes maximizing feeding rate for a fixed energy budget. The overall optimal feeder is always the optimal steady swimmer. Within the set of time-periodic strokes, the optimal feeding strokes are found to be equivalent to those optimizing periodic swimming for all values of the P\'eclet number, and correspond to a regularization of the overall steady optimal.Comment: 26 pages, 11 figures, to appear in Journal of Fluid Mechanic

Computing with Metabolic Machines

If Turing were a first-year graduate student interested in computers, he would probably migrate into the field of computational biology. During his studies, he presented a work about a mathematical and computational model of the morphogenesis process, in which chemical substances react together. Moreover, a protein can be thought of as a computational element, i.e. a processing unit, able to transform an input into an output signal. Thus, in a biochemical pathway, an enzyme reads the amount of reactants (substrates) and converts them in products. In this work, we consider the biochemical pathway in unicellular organisms (e.g. bacteria) as a living computer, and we are able to program it in order to obtain desired outputs. The genome sequence is thought of as an executable code specified by a set of commands in a sort of ad-hoc low-level programming language. Each combination of genes is coded as a string of bits y ∈ {0, 1} L, each of which represents a gene set. By turning off a gene set, we turn off the chemical reaction associated with it. Through an optimal executable code stored in the “memory ” of bacteria, we are able to simultaneously maximise the concentration of two or more metabolites of interest. Finally, we use the Robustness Analysis and a new Sensitivity Analysis method to investigate both the fragility of the computation carried out by bacteria and the most important entities in the mathematical relations used to model them. 1 Introduction: From Turin

Osztott modellek a molekuláris számítástudományban = Distributed models of molecular computation

A vizsgálódások tárgyai olyan, biokémiai folyamatokat modellező vagy biokémiai folyamatok által inspirált működési elvű számítástudományi eszközök, számítási modellek voltak, melyek fő jellemzője az osztott és párhuzamos működés. A projekt célja volt a molekuláris számítások természetének, a modellek sajátosságainak jobban megfelelő szempontok figyelembe vétele, ezáltal esetleg a biokémiai folyamatok jobb megértése, illetve a formális nyelvek és automaták elméletének továbbfejlesztése, eszköztárának bővítése a biokémiai folyamatok és az osztott modellek által inspirált irányba. Vizsgálódásaink kiterjedtek a DNS rekombináció motiválta számítási eszközök mellett a membrán rendszerek területére, különös tekintettel a membrán automatákra. A kutatás során vizsgáltuk új működési módok tulajdonságait és az ezekből levonható következtetéseket, eredményeket értünk el bizonyos modellek méret-bonyolultságának vizsgálata illetve a formális nyelv fogalmának végtelen ábécére való kiterjesztése terén. | Our research concentrated on computational models which are not only based on or inspired by natural, mostly biochemical processes, but work in a distributed and parallel manner. The aim of the project was to investigate and identify those important aspects and special properties describing the nature of molecular computation which might not only help to better understand natural processes, but could also contribute to the extension of the theory of formal languages and automata by introducing new tools and techniques in a nature inspired, nature motivated way. Our investigations not only concerned computational models based on DNA recombination, but also membrane systems and membrane automata. We investigated new modes of operation of existing models, obtained results about the descriptional (size) complexity of certain devices, and about extending the notion of formal language to infinite alphabets

The hydrogenosomes of Psalteriomonas lanterna

Contains fulltext : 75716.pdf (publisher's version ) (Open Access) Contains fulltext : 75716.pdf (preprint version ) (Open Access

Trends in the use of protozoa in the assessment of wastewater treatment

Increasing environmental pollution and the continuous development of new chemicals and drugs has led to ever growing concern about the potential effects of these compounds directly or indirectly on human health. As concerns water pollution, protozoa seem to be an excellent tool to assess both toxicity and pollution: they are regarded as biological indicators of pollution when their presence or absence can be related to particular environmental conditions, and they are considered test organisms when a species or population is used to evaluate the toxicity of relevant toxic compounds. Thus, an integrated approach is being developed to assess how toxic compounds affect the different biological levels of organisation – from the community level to the species level – of ciliated protozoa. The present paper reports and discusses the current state of the art of this approach.Instituto de Biotecnologia e Química Fina (IBQF). Fundação para a Ciência e a Tecnologia - PRAXIS XXI-2/2.1/BIO/1118/95, PRAXIS XXI/BD/5080/95, PRAXIS XXI/BD/20328/99

Formal Model and Simulation of the Gene Assembly Process in Ciliates

The construction process of the functional macronucleus in certain types of ciliates is known as the ciliate gene assembly process. It consists of a massive amount of DNA excision from the micronucleus and the rearrangement of the rest of the DNA sequences (in the case of stichotrichous ciliates). While several computational models have tried to represent certain parts of the gene assembly process, the real process remains not completely understood. In this research, a new formal model called the Computational 2JLP model is introduced based on the recent biological 2JLP model. For justifying the formal model, a simulation is created and tested with real data. Several parameters are introduced in the model that are used to test ambiguities or edge cases of the biological model. Parameters are systematically tested from the simulation to try to find their optimal values. Interestingly, a negative correlation is found between a parameter (which is used to filter out scnRNAs that are similar to IES specific sequences from the macronucleus) and the outcome of the simulation. It indicates that if a scnRNA consists of both an MDS and IES, then from the perspective of maximizing the outcome of the simulation, it is desirable to filter out this scnRNA. The simulator successfully performs the gene assembly process whether the inputs are scrambled or unscrambled DNA sequences. It is desirable for this model to serve as a foundation for future computational and mathematical study, and to help inform and refine the biological model