360 research outputs found
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
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