Localization of choline acetyltransferase in rat peripheral sympathetic neurons and its coexistence with nitric oxide synthase and neuropeptides.

Indirect immunofluorescence methods using a mouse monoclonal antibody raised to rat choline acetyltransferase (ChAT) revealed dense networks of ChAT-immunoreactive fibers in the superior cervical ganglion, the stellate ganglion, and the celiac superior mesenteric ganglion of the rat. Numerous and single ChAT-immunoreactive cell bodies were observed in the stellate and superior cervical ganglia, respectively. The majority of ChAT-immunoreactive fibers in the stellate and superior cervical ganglia were nitric oxide synthase (NOS) positive. Some ChAT-immunoreactive fibers contained enkephalin-like immunoreactivity. Virtually all ChAT-positive cell bodies in the stellate ganglion were vasoactive intestinal polypeptide (VIP)-positive, and some were calcitonin gene-related peptide (CGRP)-positive. After transection of the cervical sympathetic trunk almost all ChAT- and NOS-positive fibers and most enkephalin- and CGRP-positive fibers disappeared in the superior cervical ganglion. The results suggest that most preganglionic fibers are cholinergic and that the majority of these in addition can release nitric oxide, some enkephalin, and a few CGRP. Acetylcholine, VIP, and CGRP are coexisting messenger molecules in some postganglionic sympathetic neurons.

Grouping genetic operators for the delineation of functional areas based on spatial interaction

The delineation of functional economic areas, or market areas, is a problem of high practical relevance, since the delineation of functional sets such as economic areas in the US, Travel-to-Work Areas in the United Kingdom, and their counterparts in other OECD countries are the basis of many statistical operations and policy making decisions at local level. This is a combinatorial optimisation problem defined as the partition of a given set of indivisible spatial units (covering a territory) into regions characterised by being (a) self-contained and (b) cohesive, in terms of spatial interaction data (flows, relationships). Usually, each region must reach a minimum size and self-containment level, and must be continuous. Although these optimisation problems have been typically solved through greedy methods, a recent strand of the literature in this field has been concerned with the use of evolutionary algorithms with ad hoc operators. Although these algorithms have proved to be successful in improving the results of some of the more widely applied official procedures, they are so time consuming that cannot be applied directly to solve real-world problems. In this paper we propose a new set of group-based mutation operators, featuring general operations over disjoint groups, tailored to ensure that all the constraints are respected during the operation to improve efficiency. A comparative analysis of our results with those from previous approaches shows that the proposed algorithm systematically improves them in terms of both quality and processing time, something of crucial relevance since it allows dealing with most large, real-world problems in reasonable time.

Beta diversity at multiple hierarchical levels: explaining the high diversity of scarab beetles in tropical montane forests

Aim: High gamma diversity in tropical montane forests may be ascribed to high geographical turnover of community composition, resulting from population isolation that leads to speciation. We studied the evolutionary processes responsible for diversity and turnover in assemblages of tropical scarab beetles (Scarabaeidae) by assessing DNA sequence variation at multiple hierarchical levels. Location: A 300-km transect across six montane forests (900–1100 m) in Costa Rica. Methods: Assemblages of Scarabaeidae (subfamilies Dynastinae, Rutelinae, Melolonthinae) including 118 morphospecies and > 500 individuals were sequenced for the cox1 gene to establish species limits with a mixed Yule–coalescent method. A species-level phylogenetic tree was constructed from cox1 and rrnL genes. Total diversity and turnover among assemblages were then assessed at three hierarchical levels: haplotypes, species and higher clades. Results: DNA-based analyses showed high turnover among communities at all hierarchical levels. Turnover was highest at the haplotype level (community similarity 0.02–0.12) and decreased with each step of the hierarchy (species: 0.21–0.46; clades: 0.41–0.43). Both compositional and phylogenetic similarities of communities were geographically structured, but turnover was not correlated with distance among forests. When three major clades were investigated separately, communities of Dynastinae showed consistently higher alpha diversity, larger species ranges and lower turnover than Rutelinae and Melolonthinae. Main conclusions: Scarab communities of montane forests show evidence of evolutionary persistence of communities in relative isolation, presumably tracking suitable habitats elevationally to accommodate climatic changes. Patterns of diversity on all hierarchical levels seem to be determined by restricted dispersal, and differences in Dynastinae could be explained by their greater dispersal ability. Community-wide DNA sequencing across multiple lineages and hierarchical levels reveals the evolutionary processes that led to high beta diversity in tropical montane forests through time.

FPGA implementation of a multi-population PBIL algorithm

Evolutionary-based algorithms play an important role in finding solutions to many problems that are not solved by classical methods, and particularly so for those cases where solutions lie within extreme non-convex multidimensional spaces. The intrinsic parallel structure of evolutionary algorithms are amenable to the simultaneous testing of multiple solutions; this has proved essential to the circumvention of local optima, and such robustness comes with high computational overhead, though custom digital processor use may reduce this cost. This paper presents a new implementation of an old, and almost forgotten, evolutionary algorithm: the population-based incremental learning method. We show that the structure of this algorithm is well suited to implementation within programmable logic, as compared with contemporary genetic algorithms. Further, the inherent concurrency of our FPGA implementation facilitates the integration and testing of micro-populations.

Ecosystem size matters: The dimensionality of intralacustrine diversification in Icelandic stickleback is predicted by lake size

Cases of evolutionary diversification can be characterized along a continuum from weak to strong genetic and phenotypic differentiation. Several factors may facilitate or constrain the differentiation process. Comparative analyses of replicates of the same taxon at different stages of differentiation can be useful to identify these factors. We estimated the number of distinct phenotypic groups in threespine stickleback populations from nine lakes in Iceland and in one marine population. Using the inferred number of phenotypic groups in each lake, genetic divergence from the marine population, and physical lake and landscape variables, we tested if ecosystem size, approximated by lake size and depth, or isolation from the ancestral marine gene pool predict the occurrence and the extent of phenotypic and genetic diversification within lakes. We find intralacustrine phenotypic diversification to be the rule rather than the exception, occurring in all but the youngest lake population and being manifest in ecologically important phenotypic traits. Neutral genetic data further indicates non-random mating in four out of nine studied lakes, and restricted gene flow between sympatric phenotypic groups in two. Although neither the phenotypic variation nor the number of intralacustrine phenotypic groups were associated with any of our environmental variables, the number of phenotypic traits that were differentiated was significantly positively related to lake size, and evidence for restricted gene flow between sympatric phenotypic groups was only found in the largest lakes where trait specific phenotypic differentiation was highest.

The association of feeding behavior with the resistance and tolerance to parasites in recently diverged sticklebacks

Divergent natural selection regimes can contribute to adaptive population divergence, but can be sensitive to human-mediated environmental change. Nutrient loading of aquatic ecosystems, for example, might modify selection pressures by altering the abundance and distribution of resources and the prevalence and infectivity of parasites. Here, we used a mesocosm experiment to test for interactive effects of nutrient loading and parasitism on host condition and feeding ecology. Specifically, we investigated whether the common fish parasite Gyrodactylus sp. differentially affected recently diverged lake and stream ecotypes of three-spined stickleback (Gasterosteus aculeatus). We found that the stream ecotype had a higher resistance to Gyrodactylus sp. infections than the lake ecotype, and that both ecotypes experienced a cost of parasitism, indicated by negative relationships between parasite load and both stomach fullness and body condition. Overall, our results suggest that in the early stages of adaptive population divergence of hosts, parasites can affect host resistance, body condition, and diet.

(Table 1) Number of invertebrate species per bottom trawl haul in the Kapp Norvegia to Halley Bay area on cruise EASIZ I (ANT-XIII/3) and in the Kapp Norvegia - Austasen area on cruise EASIZ III (ANT-XVII/3)

Ecological work carried out on the Antarctic and Magellan shelves since the first IBMANT conference held at the UMAG, Punta Arenas in 1997 is summarized to identify areas where progress has been made and others, where impor- tant gaps have remained in understanding past and present interaction between the Antarctic and the southern tip of South America. This information is complementary to a review on shallow-water work along the Scotia Arc (Barnes, 2005) and recent work done in the deep sea (Brandt and Hilbig, 2004). While principally referring to shipboard work in deeper water, above all during the recent international EASIZ and LAMPOS campaigns, relevant work from shore stations is also included. Six years after the first IBMANT symposium, significant progress has been made along the latitudinal gradient from the Magellan region to the high Antarctic in the fields of biodiversity, biogeography and community structure, life strategies and adaptations, the role of disturbance and its significance for biodiversity, and trophic coupling of the benthic realm with the water column and sea ice. A better understanding has developed of the role of evolutionary and ecological factors in shaping past and present-day environmental conditions, species composition and distribution, and ecosystem functioning. Furthermore, the science community engaged in unravelling Antarctic-Magellan interactions has advanced in methodological aspects such as new analytical approaches for comparing biodiversity derived from visual methods, growth and age determination, trophic modelling using stable isotope ratios, and molecular approaches for taxonomic and phylogenetic purposes. At the same time, much effort has been invested to complement the species inventory of the two adjacent regions. However, much work remains to be done to fill the numerous gaps. Some perspectives are outlined in this review, and sug- gestions are made where particular emphasis should be placed in future work, much of which will be developed in the frame of SCAR's EBA (Evolution and Biodiversity in the Antarctic) programme.

Stable oxygen isotope ratios of benthic and planktonic foraminifera from early Miocene sediments of DSDP Site 90-593 on the Challenger Plateau, Pacific Ocean (Table 1)

Oxygen isotope data are compared with relative abundances of selected planktic foraminifera through a ca. 15 m interval at DSDP Site 593 (Tasman Sea, southwest Pacific, 40°S) in which there are prominent changes in population sizes, as well as several evolutionary events. We focus on the relation between faunal and climatic histories. The base of early Miocene oxygen isotope Zone Mi1b (uppermost planktic foraminiferal Zone N.6) is identified from closesampled (c. 14 kyr) isotope records of Globigerina woodi and Cibicides kullenbergi. Chronostratigraphic interpolations, using the first occurrences of Globorotalia praescitula, G. mimea and Praeorbulina curva give an age estimate of ca. 18.4 Ma (cf. 18.1 -18.3 Ma for the base of the zone at DSDP Site 608 (type level, north Atlantic, 43°N) ). Another significant benthic delta18O enrichment event, informally designated as the base of zone "Mi1c", is identified 10 m higher in the sequence at ca. 17.8 Ma. Populations of Globoquadriau dehiscens and Globigerinoides trilobus (inferred to be near the southern margin of their distributions) either reduced considerably or withdrew, particularly in the vicinity of zone "Mi1c". A bioseries linking Globorotalia incognita with G. zealandica developed following the benthic delta18O enrichment spike at the base of Zone Mi1b; the latter species became extinct (at least regionally) just above the base of zone "Mi1c". In contrast, the apparently opportunistic Globorotlia praescitula increased dramatically in abundance at this time; there were also transformations in its architecture, leading to the evolutionary appearance of G. miozea. While planktic foraminifera abundances often do not closely covary with the detailed isotope records and tend to be more stable through time, the near coincidence of evolutionary and biogeographic events with isotopic events suggests at least indirect adaptive responses to climatic changes. Early Miocene middle-latitude planktic foraminiferal evolution, biogeography, and biostratigraphy, may be intimately connected with climatic history.

Teaching College Writing in a High School Setting: The Impact of Concurrent Enrollment on Teacher Learning and Practice

Thesis (Ph.D.)--University of Washington, 2016-06

High throughput determination of sequence-function relationships in protein and RNA

Thesis (Ph.D.)--University of Washington, 2016-06

Functionality, Robustness and Control of Nonlinear Network Dynamics: Modeling and Understanding the C. elegans Connectome

Thesis (Ph.D.)--University of Washington, 2016-06

Targeting genetic resource conservation in widespread species: a case study of Cedrela odorata L.

Conservation of genetic resources is a recognised necessity for the long term maintenance of evolutionary potential. Effective assessment and implementation Strategies are required to permit rapid evaluation and protection of resources. Here we use information from the chloroplast, total genome and quantitative characters assayed across wide-ranging populations to assess genetic resources in a Neotropical tree, Cedrela odorata. A major differentiation identified for organelle, total genomic and quantitative variation was found to coincide with an environmental gradient across Costa Rica. However, a major evolutionary divergence between the Yucatan region and Honduras/Nicaragua identified within the chloroplast genome was not differentiated using quantitative characters. Based on these and other results, a three-tiered conservation genetic prioritisation process is recommended. In order of importance, and where information is available, conservation units should be defined using quantitative (expressed genes), nuclear (genetic connectivity) and organellar (evolutionary) measures. Where possible, information from range wide and local scale studies should be combined and emphasis should be placed on coincidental disjunctions for two or more measures. However, if only rapid assessments of diversity are possible, then assessment of organelle variation provides the most cautious assessment of genetic resources, at least for C. odorata, and can be used to propose initial conservation units. When considering effective implementation of genetic resource management strategies a final tier should be considered, that of landuse/geopolitical divisions. (C) 2004 Elsevier B.V. All rights reserved.

Design and implementation of a windows-based parallel computing environment for large scale optimization

A parallel computing environment to support optimization of large-scale engineering systems is designed and implemented on Windows-based personal computer networks, using the master-worker model and the Parallel Virtual Machine (PVM). It is involved in decomposition of a large engineering system into a number of smaller subsystems optimized in parallel on worker nodes and coordination of subsystem optimization results on the master node. The environment consists of six functional modules, i.e. the master control, the optimization model generator, the optimizer, the data manager, the monitor, and the post processor. Object-oriented design of these modules is presented. The environment supports steps from the generation of optimization models to the solution and the visualization on networks of computers. User-friendly graphical interfaces make it easy to define the problem, and monitor and steer the optimization process. It has been verified by an example of a large space truss optimization. (C) 2004 Elsevier Ltd. All rights reserved.

Implications of social capital for the inclusion of people with disabilities and families in community life

This paper seeks to ascertain the usefulness of the theory of social capital as a framework for developing and sustaining the inclusion of people with disabilities and families in community life. We discuss the theoretical elements of social capital and assess its relevance when understanding both the experiences of people with disabilities and their families and the possible implications for policy and programme efforts to promote inclusion. Preliminary findings from two studies of the experiences and social networks of people with disabilities and their families in communities in regional and rural Australia are presented. It is argued that to date, people with disabilities and their families have largely been excluded from the broader social capital debate and that social capital thinking has had minimal influence on efforts to achieve the inclusion of people with disabilities into community life. It is further argued that new paradigms of support are needed that build capacity and social capital through working alongside individuals and families to influence not only outcomes for them, but also for the communities on which they live. The local area coordination model as it has developed in Australia since 1989 provides some instructive signposts for integrating individual, family and community approaches. It is concluded that social capital theory can make a contribution to inclusion theory and practice but we should use it with circumspection.

Gene duplication and hierarchical modularity in intracellular interaction networks

Networks of interactions evolve in many different domains. They tend to have topological characteristics in common, possibly due to common factors in the way the networks grow and develop. It has been recently suggested that one such common characteristic is the presence of a hierarchically modular organization. In this paper, we describe a new algorithm for the detection and quantification of hierarchical modularity, and demonstrate that the yeast protein-protein interaction network does have a hierarchically modular organization. We further show that such organization is evident in artificial networks produced by computational evolution using a gene duplication operator, but not in those developing via preferential attachment of new nodes to highly connected existing nodes. (C) 2004 Elsevier Ireland Ltd. All rights reserved.