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A Genetic And Biochemical Analysis Of Sulfolobus Spindle-Shaped Virus 1, Eric Alexander Iverson

Dissertations and Theses

Viruses infecting the Archaea exhibit a tremendous amount of morphological and genetic diversity. This is especially true for crenarchaeal viruses from the family Fuselloviridae, which possess spindle-shaped capsids and genomes that harbor a great number of uncharacterized genes. The functions of these unidentified gene products are of interest as they have the potential to provide valuable insights into the fusellovirus infection cycle and archaeal viruses in general. In an effort to better characterize the genetic requirements of the Fuselloviridae, we have performed genetic and biochemical experiments using the best studied fusellovirus, Sulfolobus spindle-shaped virus 1 (SSV1).

A comprehensive …

Mechanisms Of Adaptation In The Newly Invasive Species Brachypodium Sylvaticum (Hudson) Beauv., Gina Lola Marchini

Dissertations and Theses

It is common knowledge that invasive species cause worldwide ecological and economic damage, and are nearly impossible to eradicate. However, upon introduction to a novel environment, alien species should be the underdogs: They are present in small numbers, possess low genetic diversity, and have not adapted to the climate and competitors present in the new habitat. So, how are alien species able to invade an environment occupied by native species that have already adapted to the local environment? To discover some answers to this apparent paradox I conducted four ecological genetic studies that utilized the invasive species Brachypodium sylvaticum (Hudson) …

The Biology Of Eastern Kingbirds At Malheur National Wildlife Refuge: Survival, Reproduction, And Testosterone Secretion, Lucas J. Redmond

Dissertations and Theses

This dissertation presents the results of a study that I undertook to better understand the breeding biology of Eastern Kingbirds (hereafter, kingbirds) at Malheur National Wildlife Refuge in southeastern Oregon from 2003 to 2009. Kingbirds are long-distance migratory songbirds that breed across much of North America. This species is socially monogamous but, via frequent extra-pair copulations, is genetically polygamous. Kingbirds exhibit relatively high breeding site fidelity, often returning to the same tree to nest in subsequent years. Both members of a pair provide parental care, but there are often specific duties performed by both male and female kingbirds. For example, …

The Impeccable Timing Of The Apple Maggot Fly, Rhagoletis Pomonella (Dipetera: Tephritidae), And Its Implications For Ecological Speciation, Monte Arthur Mattsson

Dissertations and Theses

Speciation is the process by which life diversifies into discrete forms, and understanding its underlying mechanisms remains a primary focus for biologists. Increasingly, empirical studies are helping explain the role of ecology in generating biodiversity. Adaptive radiations are often propelled by selective fitness tradeoffs experienced by individuals that invade new habitats, resulting in reproductive isolation from ancestral conspecifics and potentially cladogenesis. Host specialist insects are among the most speciose organisms known and serve as highly useful models for studying adaptive radiations. We are just beginning to understand the pace and degree with which these insects diversify. The apple maggot, Rhagoletis …

Developmental Mechanisms That Support Genome Stability And Embryonic Survival In Stress-Tolerant Embryos Of The Annual Killifish Austrofundulus Limnaeus, Josiah Tad Wagner

Dissertations and Theses

In order to complete their life cycles, vertebrates require oxygen and water. However, environments are not always forgiving when it comes to constantly providing these basic needs for vertebrate life. The annual killifish Austrofundulus limnaeus is possibly the most well described extremophile vertebrate and its embryos have been shown to tolerate extremes in oxygen, salinity, and water availability. This phenotype is likely a result of the annual killifish life history, which includes periods of temporary habitat desiccation and oxygen deprivation, and requires the production of stress-tolerant embryos that depress metabolism in a state of suspended animation, known as diapause. Over …

The Role Of Pyrococcus Furiosus Transcription Factor E In Transcription Iniitiation, Robyn Lynn Eustis

Dissertations and Theses

All sequenced archaeal genomes encode a general transcription factor, TFE, which is highly conserved and homologous to the alpha subunit of the eukaryotic transcription factor TFIIE. TFE functions to increase promoter opening efficiency during transcription initiation, although the mechanism for this is unclear. The N-terminus of TFE contains a common DNA binding motif, a winged helix. At the tip of this winged helix is a highly conserved region of aromatic amino acids that is close to DNA during initiation. TFE activation can compensate for mutations in another transcription factor, TFB2, which is homologous to TFIIB. P. furiosus encodes two paralogs …

Neurobiology Of Seasonal Life-History Transitions, Ashley Rae Lucas

Dissertations and Theses

Many animals exhibit seasonal changes in life-history stages, and these seasonal transitions are often accompanied by dramatic switches in behavior. While the neuroendocrine mechanisms that regulate such behavioral transitions are poorly understood, arginine vasotocin (AVT) and neuropeptide Y (NPY) are excellent candidates because they regulate reproductive and feeding behavior, respectively. In this study, I asked if seasonal changes in AVT and/or NPY are concomitant with spring migration away from the breeding grounds, as male and female red-sided garter snakes (Thamnophis sirtalis parietalis) are transitioning from reproductive to non-reproductive behavior during this time. To address this question, I collected …

Defining The Terroir Of The Columbia Gorge Wine Region, Oregon And Washington, Usa Using Geographic Information Systems (Gis), Hilary Whitney

Dissertations and Theses

The Columbia Gorge Wine Region (CGWR) is an emerging wine producing area that extends for about 100km along the Columbia River in Oregon and Washington State in which the number of vineyards, wineries and physical terroir conditions have yet to be defined. To better understand the physical factors affecting Oregon and Washington wine, this project analyzes climate, topography, geology and soil at vineyards in the CGWR. This was accomplished using Geographic Information Systems, existing earth science databases and field work. The region, which includes the Columbia Gorge American Viticulture Area (AVA) and the southwest portion of the Columbia Valley AVA, …

Investigations Of Larval Pacific Lamprey Entosphenus Tridentatus Osmotic Stress Tolerance And Occurrence In A Tidally-Influenced Estuarine Stream, Gregory Shell Silver

Dissertations and Theses

Pacific lamprey is a culturally valuable species to indigenous people, and has significant ecological importance in freshwater and marine ecosystems. Over the past several decades, constrictions in range and reductions in Pacific lamprey abundance have been observed in Western North America, and may be indicators of range-wide declines. In the face of declining populations, the U.S. Fish and Wildlife Service has partnered with tribal, state, federal, and local entities to implement a regional Pacific lamprey conservation agreement aimed at reducing threats to Pacific lamprey and improving their habitats and population status. Research needs identified in the conservation agreement include assessing …

The Erosion Of Coastal Sediment And Regeneration Of Rhizophora Mangle Following Anthropogenic Disturbance On Turneffe Atoll, Belize, Heather Lyn Hayden

Dissertations and Theses

As communities and managers become aware of the long-term impacts of mangrove loss, estimated at 1-2% per year, interest in sediment erosion and mangrove rehabilitation has increased substantially. In this thesis project I 1) examine erosion rates within coastal fringing Rhizophora mangle ecosystems following mangrove clearing and compare these rates to accretion rates in intact mangroves; and 2) investigate the abiotic factors influencing mangrove seedling survival and regeneration of naturally colonizing R. mangle, in historic mangrove habitat after anthropogenic clearing.

Differences in erosion were compared between patches of open-coast intact and anthropogenically cleared R. mangle to quantify the sediment trapping …

The Response Of Zooplankton Communities In Montane Lakes Of Different Fish Stocking Histories To Atmospheric Nitrogen Deposition Simulations, Jeffrey Thomas Brittain

Dissertations and Theses

Freshwater ecosystems are subject to a wide variety of stressors, which can have complex interactions and result in ecological surprises. Non-native fish introductions have drastically reduced the number of naturally fishless lakes and have resulted in cascading food web repercussions in aquatic and terrestrial habitats. Additional anthropogenic influences that result from increases in global airborne emissions also threaten wildlife habitat. Atmospheric nitrogen deposition has been recognized as an anthropogenic contributor to acidification and eutrophication of wilderness ecosystems. Planktonic communities have shown declines in response to predation and shifts in composition as a result of nutrient inputs and acidification, both of …

Effects Of Selective Logging And Roads On Instream Fine Sediments And Macroinvertebrate Assemblages In The Clackamas Basin, Oregon, Paula Elizabeth Hood

Dissertations and Theses

Logging and associated skid trails, haul routes, and roads can have significant impacts on the magnitude and timing of sediments in streams in forested watersheds. Loss of vegetation, soil compaction, use of heavy logging equipment, and alteration of natural hydrologic patterns within the watershed can increase landslide rates, create erosion, and generate fine sediments. Selective logging, also called thinning, is a logging practice that leaves some trees within sale units unharvested. The ecological impacts of thinning on stream ecosystems are not fully understood and need further study. My hypothesis was that macroinvertebrate assemblages would be different in streams in non-reference …

Combining Systems Methodologies To Reduce Allergen-Related Food Recalls, Jill Marie Sweney

Dissertations and Theses

The risk of poor food safety is a major focus for managers in the food manufacturing industry. Despite industry-led and regulatory efforts to improve the overall food safety of US packaged consumer foods, product recalls and market withdrawals are increasing. This is especially true for the most frequent cause for food recall: the undeclared allergen. With industry trends leaning toward adoption of third-party food safety management certifications, a popular food safety code from the Safe Quality Foods Institute is evaluated using Systems Analysis. Three changes to the food safety code are proposed to address three of the top causes for …

Age Determination Of Modern And Archaeological Chinook Salmon (Oncorhynchus Tshawytcha) Using Vertebrae, Anthony Raymond Hofkamp

Dissertations and Theses

Incremental growth rings in X-rays of salmon vertebrae have been used since the 1980s to age Pacific salmon (Oncorhynchus spp.) remains from archaeological sites in the Pacific Northwest. These age estimates, paired with generalized life history patterns, have been used to determine salmon species, season of capture and in turn season of site occupation. This approach relies on a variety of assumptions, the most fundamental of which is that rings represent true years. Archaeologists using vertebral age determination techniques have failed to adequately test this assumption and present their methodologies. This thesis assesses the validity of using incremental …

Phenotypic And Mutational Consequences Of Mitochondrial Etc Genetic Damage, Michael James Lue

Dissertations and Theses

Genetic mutation is the ultimate source of new phenotypic variation in populations. The importance of mutation cannot be understated, and constitutes a significant evolutionary force. Although single mutations may have little to no impact on organismal performance or fitness, when multiplied across the total number of potential sites within the genome, mutation can have a large impact. Accurate measurement of the rates, molecular mechanisms, and distributions of effects of mutations are critical for many applications of evolutionary theory. Despite the importance of both deleterious and beneficial mutations, their genome-wide patterns and phenotypic consequences are poorly understood when considering the mitochondrial …

Genes Affecting The Repair And Survival Of Escherichia Coli Following Psoralen-Induced Damage: A Dna Interstrand Crosslinking Agent, Anthonige Vidya Perera

Dissertations and Theses

Photoactivated psoralens and other agents that form DNA interstrand crosslinks are highly cytotoxic and are useful in treating a range of diseases, including vitiligo, psoriasis, and some forms of cancer. Unlike many lesions that damage only one strand of the duplex DNA, DNA interstrand crosslinks form covalent bonds with both strands. Thus, repairing these lesions is complicated both by the lack of an undamaged strand to serve as a template for resynthesis following excision, as well as the potential to form double strand breaks if both strands are incised. A number of models have proposed that repair is likely to …

Applying Gps And Accelerometers To The Study Of African Savanna (Loxodonta Africana) And Asian Elephant (Elephas Maximus) Welfare In Zoos, Matthew Robert Holdgate

Dissertations and Theses

African savanna elephants (Loxodonta africana) and Asian elephants (Elephas maximus) are a focus of welfare research in zoos due to their high intelligence, complex social structure, and sheer size. Due to these challenges, some argue that zoos are inherently incapable of providing appropriate care for elephants, while others believe that zoos can fulfill the needs of these species with improved husbandry. There is a general consensus from both within and outside of zoos, however, that zoos must improve their elephant programs or cease exhibiting these animals altogether. Now more than ever, applied research on zoo elephant welfare is needed to …

Paleological And Ecological Impacts Of Virus Silicification, James Robert Laidler

Dissertations and Theses

Silicification of organisms in silica-depositing environments can impact both their ecology and their presence in the fossil record. Although microbes have been silicified under laboratory and environmental conditions, viruses had not been, prior to this work. Bacteriophage T4 was successfully silicified under laboratory conditions that closely simulated those found in silica-depositing hot springs. Virus morphology was maintained during the short period of silicification (48 hours), and a clear elemental signature of silicon and phosphorus was detected by energy-dispersive X-ray spectrophotometry (EDX). However, the EDX signature of silicified virus was not sufficiently distinct from that of cell membrane or phosphate minerals …

Sex Dependent Efficacy Of Taurine As A Treatment For Cocaine Drug Use: A Study Of Reward, Kevin Uribe

Dissertations and Theses

No abstract provided.

Effects Of Acetyl Salicyclic Acid On Drosophila Models Of Cancer-Inflammation, Roma Rajwani

Dissertations and Theses

Chronic inflammation is a fundamental condition underlying many human disease pathologies including diabetes, cancer, and neurodegeneration. Indeed, one of the most commonly-used anti-inflammatory drugs, aspirin, has been shown to be effective in the treatment of many cancers. To understand the mechanistic linkages between inflammation and cancer, we used Drosophila models in which hyperactive immune signaling causes overproliferation of the hematopoietic system leading to the production of inflammatory blood tumors. In mutant animals, hematopoietic cells divide uncontrollably and exhibit pre-mature differentiation giving rise to large sticky cells. Some mutant cells infiltrate and adhere to cells of the fat body. The fat …

The Widespread Skink Mabuya Dorsivittata Reveals Complex Patterns Of Genetic Diversity In South America, Danielle Rivera

Dissertations and Theses

No abstract provided.

Effects Of Temperature Stress On Coral Fluorescence And Reflectance, Andrea Gomez

Dissertations and Theses

Around the world, climate change, land-based pollution and fishing impacts are recognized as principal threats to coral reef ecosystems. Sea surface temperatures, in particular, are expected to change dramatically over the next decades and result in high coral mortality in some regions. Through controlled experiments, I examined changes in coral fluorescence and reflectance in response to water temperature alterations to assess the potential of employing these signatures as a diagnostic tool to measure coral health. At the NOAA Coral Culture and Collaborative Research Facility, I conducted controlled laboratory-based heat stress experiments on three Caribbean species of coral: Acropora cervicornis, Orbicella …

"Model Complexity And Variable Selection In Maxent Niche Models: Analyses For Rodents In Madagascar", Peter Galante

Dissertations and Theses

Ecological niche models (ENMs) characterize the relationship between localities where a species is known to occur and the abiotic characteristics of these regions. While widely used, ENMs remain subject to several outstanding issues, including those related to model complexity and violation of modeling assumptions (e.g., representative sampling). Critical in resolving these issues is a better understanding of the effectiveness of model selection techniques. Here, I compare two strategies for optimizing ENMs: an information-criterion approach (AICc) and a sequential approach that assesses model performance on withheld data. I do so for a single species using two datasets, one with all available …

Characterization Of The Interaction Between Ftsz-Ring Stabilizer Zapc And The Conserved Protease Clpxp In E. Coli Cytokinesis, Andrea Cardenas Arevalo

Dissertations and Theses

Cell division in bacteria requires the assembly of a macromolecular protein machinery at midcell that is spatiotemporally regulated during the bacterial cell cycle. Central to the process of division is the assembly of a cytokinetic ring-like structure, termed the Z-ring, formed by polymers of the essential tubulin-homolog FtsZ. Polymerization of FtsZ is regulated by a number of proteins that bind FtsZ and regulate its assembly/disassembly mechanisms. Despite being extensively studied, the molecular nature of the diverse protein-protein interactions that regulate the assembly of FtsZ during early stages of division is not well understood. Here, I focus on an FtsZ-ring stabilizer …

Development And Maintenance Of Thymic Epithelial Microenvironment, Varan J. Singh

Dissertations and Theses

Thymus is a primary lymphoid organ responsible for proper development and selection Of T-­‐cells. The thymic microenvironment, however, undergoes age related involution, Resulting in a reduction of the repertoire of T-­‐cells that are produced, and a decreased Capacity to respond to new antigen. Even though significant thymic epithelial turnover occurs, it is unclear if postnatal thymic progenitors/stem cell are responsible for the maintenance of the TEC microenvironment. Here we use the K5rtTA:TetO-­‐H2BGFP transgenic model to identify a slow cycling potential stem cells/progenitor population in the postnatal thymus. These cells were isolated, expanded in culture, and successfully differentiated into adipocytes, chondrocytes …

The Impact Of Forest Successional Status On Community Structure Of Neotropical Cerambycid Beetles, Lin Li

Dissertations and Theses

Due to anthropogenic activities, tropical rain forests face many challenges in sustaining biodiversity and maintaining global climates. This project examines how forest successional status affects community composition of saproxylic cerambycids, which, as early colonists of moribund trees, have an important role in nutrient cycling. In the lowland rain forest of Costa Rica, thirty-nine trees in five plant families (Fabaceae, Lecythidaceae, Malvaceae, Moraceae, and Sapotaceae) were sampled in a mosaic of old growth and secondary forest. They yielded 3545 cerambycid individuals in 49 species. Species richness was almost identical in old growth and secondary forest; but abundance was higher in old-growth. …

Refinement Of Feedforward Projections, Neuronal Density, And Characterization Of Synapsesin Layer 4 Of Ferret Primary Visual Cortex, Violeta Contreras Ramirez

Dissertations and Theses

No abstract provided.

The Drosophila Dynamin, Shibire, Contributes To Blood Cell Division And Differentiation, But May Not Be Required For Host Defence Against Parasitic Wasps, Adam D. Hudgins

Dissertations and Theses

No abstract provided.