Strategies of Loop Recombination in Ciliates

Gene assembly in ciliates is an extremely involved DNA transformation process, which transforms a nucleus, the micronucleus, to another functionally different nucleus, the macronucleus. In this paper we characterize which loop recombination operations (one of the three types of molecular operations that accomplish gene assembly) can possibly be applied in the transformation of a given gene from its micronuclear form to its macronuclear form. We also characterize in which order these loop recombination operations are applicable. This is done in the abstract and more general setting of so-called legal strings.Comment: 22 pages, 14 figure

Reducibility of Gene Patterns in Ciliates using the Breakpoint Graph

Gene assembly in ciliates is one of the most involved DNA processings going on in any organism. This process transforms one nucleus (the micronucleus) into another functionally different nucleus (the macronucleus). We continue the development of the theoretical models of gene assembly, and in particular we demonstrate the use of the concept of the breakpoint graph, known from another branch of DNA transformation research. More specifically: (1) we characterize the intermediate gene patterns that can occur during the transformation of a given micronuclear gene pattern to its macronuclear form; (2) we determine the number of applications of the loop recombination operation (the most basic of the three molecular operations that accomplish gene assembly) needed in this transformation; (3) we generalize previous results (and give elegant alternatives for some proofs) concerning characterizations of the micronuclear gene patterns that can be assembled using a specific subset of the three molecular operations.Comment: 30 pages, 13 figure

Local properties of graphs with large chromatic number

This thesis deals with problems concerning the local properties of graphs with large chromatic number in hereditary classes of graphs. We construct intersection graphs of axis-aligned boxes and of lines in $\mathbb{R}^3$ that have arbitrarily large girth and chromatic number. We also prove that the maximum chromatic number of a circle graph with clique number at most $\omega$ is equal to $\Theta(\omega \log \omega)$. Lastly, extending the $\chi$-boundedness of circle graphs, we prove a conjecture of Geelen that every proper vertex-minor-closed class of graphs is $\chi$-bounded

Chemical programming to eploit chemical Reaction systems for computation

This thesis is on programming approaches to exploit the computational capabilities of chemical systems, consisting of two parts. In the first part, constructive design, research activities on theoretical development of chemical programming are reported. As results of the investigations, general programming principles, named organization-oriented programming, are derived. The idea is to design reaction networks such that the desired computational outputs correspond to the organizational structures within the networks. The second part, autonomous design, discusses on programming strategies without human interactions, namely evolution and exploration. Motivations for this programming approach include possibilities to discover novelty without rationalization. Regarding first the evolutionary strategies, we rather focused on how to track the evolutionary processes. Our approach is to analyze these dynamical processes on a higher level of abstraction, and usefulness of distinguishing organizational evolution in space of organizations from actual evolution in state space is emphasized. As second strategy of autonomous chemical programming, we suggest an explorative approach, in which an automated system is utilized to explore the behavior of the chemical reaction system as a preliminary step. A specific aspect of the system's behavior becomes ready for a programmer to be chosen for a particular computational purpose. In this thesis, developments of autonomous exploration techniques are reported. Finally, we discuss combining those two approaches, constructive design and autonomous design, titled as a hybrid approach. From our perspective, hybrid approaches are ideal, and cooperation of constructive design and autonomous design is fruitful

Formal systems for gene assembly in ciliates

AbstractDNA processing in ciliates, a very ancient group of organisms, is among the most sophisticated DNA processing in living organisms. It has a quite clear computational structure and even uses explicitly the linked list data structure! Particularly interesting from the computational point of view is the process of gene assembly from its micronuclear to its macronuclear form. We investigate here the string rewriting and the graph rewriting models of this process, involving three molecular operations, which together form a universal set of operations in the sense that they can assembly any macronuclear gene from its micronuclear form. In particular we prove that although the graph rewriting system is more “abstract” than the string rewriting system, no “essential information” is lost, in the sense that one can translate assembly strategies from one system into the other