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

The Fibers and Range of Reduction Graphs in Ciliates

The biological process of gene assembly has been modeled based on three types of string rewriting rules, called string pointer rules, defined on so-called legal strings. It has been shown that reduction graphs, graphs that are based on the notion of breakpoint graph in the theory of sorting by reversal, for legal strings provide valuable insights into the gene assembly process. We characterize which legal strings obtain the same reduction graph (up to isomorphism), and moreover we characterize which graphs are (isomorphic to) reduction graphs.Comment: 24 pages, 13 figure

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

"Going back to our roots": second generation biocomputing

Researchers in the field of biocomputing have, for many years, successfully "harvested and exploited" the natural world for inspiration in developing systems that are robust, adaptable and capable of generating novel and even "creative" solutions to human-defined problems. However, in this position paper we argue that the time has now come for a reassessment of how we exploit biology to generate new computational systems. Previous solutions (the "first generation" of biocomputing techniques), whilst reasonably effective, are crude analogues of actual biological systems. We believe that a new, inherently inter-disciplinary approach is needed for the development of the emerging "second generation" of bio-inspired methods. This new modus operandi will require much closer interaction between the engineering and life sciences communities, as well as a bidirectional flow of concepts, applications and expertise. We support our argument by examining, in this new light, three existing areas of biocomputing (genetic programming, artificial immune systems and evolvable hardware), as well as an emerging area (natural genetic engineering) which may provide useful pointers as to the way forward.Comment: Submitted to the International Journal of Unconventional Computin

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

Future Marine Zooplankton Research- A Perspective

During the Second Marine Zooplankton Colloquium (MZC2) 3 issues were added to those developed 11 yr ago during the First Marine Zooplankton Colloquium (MZC1). First, we focused on hot spots, i.e., locations where zooplankton occur in higher than regular abundance and/or operate at higher rates. We should be able to determine the processes leading to such aggregations and rates, and quantify their persistence. Second, information on the level of individual species, even of highly abundant ones, is limited. Concerted efforts should be undertaken with highly abundant to dominant species or genera (e.g., Oithona spp., Calanus spp., Oikopleura spp., Euphausia superba) to determine what governs their abundance and its variability. Third, zooplankton clearly influence biogeochemical cycling in the ocean, but our knowledge of the underlying processes remains fragmentary. Therefore a thorough assessment of variables that still need to be quantified is required to obtain an understanding of zooplankton contributions to biogeochemical cycling. Combining studies on the 7 issues from MZC1 with the 3 from MZC2 should eventually lead to a comprehensive understanding of (1) the mechanisms governing the abundance and existence of dominant zooplankton taxa, and (2) the control of biodiversity and biocomplexity, for example, in the tropical ocean where diversity is high. These recommendations come from an assemblage of chemical, physical and biological oceanographers with experience in major interdisciplinary studies, including modeling. These recommendations are intended to stimulate efforts within the oceanographic community to facilitate the development of predictive capabilities for major biological processes in the ocean

A Convergence of Minds: Teilhard de Chardin and Conway Morris

While the work of Simon Conway Morris has garnered significant attention, very little has been paid to the overlap between his thought and the work of Pierre Teilhard de Chardin. Thus, I first detail the development of Conway Morris’s thought and note his “theological turn.” I then compare this with Teilhard’s evolutionary theology, establishing a broad conceptual overlap. Lastly, I demonstrate Conway Morris’s written engagement with and admiration for Teilhard’s work during his theological turn and conclude that Conway Morris’s later works have been impacted by Teilhardian thought. Consequently, this merits Teilhard’s inclusion in contemporary discussions of convergence and teleology

Explorations, Vol. 4, No. 3

Articles include: Cover: Trophy: MooseHorn, from the Trophy Series, by Caellaigh B. Desrosiers. Editorial Reflections, by Carole J. Bombard North Cascade Glacier Climate Project, by Mauri Pelto Stained Glass Molecules, by Anne P. Sherblom Lobsters Inside-Out: A Guide to the Maine Lobster Community Forestry: UMaine Cooperative Extension Service, by Nancy E. Coverstone and William D. Lilley Where Are They Now? — Robert F. LaPrade, M.D. ’81 Little Critters with a Big Job: Ciliated Protozoa and the Gulf of Maine Food Chain, by Marcia Gauvin from a paper by Charles Gregory The Innovation of Tradition: Low-Cost, Low-Input Alternatives for Maine Farmers, by Marcia Gauvin Just What IS An Animal? Preschoolers Investigate Merging Two Cultures: Our Cover Artist, by Caellaigh Bennett Derosiers Freezing and Photosynthesis, by Steven R. Dudgeon, Ian R. Davison, and Robert L. Vada