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Theses/Dissertations

2013

Dissertations and Theses

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Full-Text Articles in Life Sciences

Novel Thermophilic Bacteria Isolated From Marine Hydrothermal Vents, Christine Demko Sislak Dec 2013

Novel Thermophilic Bacteria Isolated From Marine Hydrothermal Vents, Christine Demko Sislak

Dissertations and Theses

As part of a large study aimed at searching for patterns of diversity in the genus Persephonella along the north to south geochemical gradient of the ELSC, ten novel strains of Alphaproteobacteria were isolated unexpectedly. Using defined media under microaerophilic conditions to enrich for Persephonella from chimney samples collected at the seven vent fields on the ELSC and the dilution to extinction by serial dilution method to purify cultures, a total of ten strains belonging to the Alphaproteobacteria were isolated. Two of these isolates, designate MN-5 and TC-2 were chosen for further characterization and are proposed as two new species ...


Soil Development And Vegetation Response To Removal Of A Small Dam, Lassen Volcanic National Park, California, Stephanie Kay Rohdy Dec 2013

Soil Development And Vegetation Response To Removal Of A Small Dam, Lassen Volcanic National Park, California, Stephanie Kay Rohdy

Dissertations and Theses

Dam removal is increasing as dams age, yet little is understood about the pedogenic response to dam removal. This study reports on the edaphic changes of reservoir sediments and vegetation cover one year following removal of a small earthen dam in Northern California. In August 2012, I sampled surface sediments from the former Dream Lake reservoir in Lassen Volcanic National Park, and compared their physical and chemical properties with soil samples from two reference sites. I also estimated percent cover of vegetation in the former reservoir and reference sites. My results show that the reservoir was under reduced conditions, as ...


Investigation Of The Structure And Dynamics Of Regioisomeric Eu³⁺ And Gd³⁺ Chelates Of Nb-Dotma: Implications For Mri Contrast Agent Design, Benjamin Charles Webber Nov 2013

Investigation Of The Structure And Dynamics Of Regioisomeric Eu³⁺ And Gd³⁺ Chelates Of Nb-Dotma: Implications For Mri Contrast Agent Design, Benjamin Charles Webber

Dissertations and Theses

The detection of disease and abnormal pathology by magnetic resonance imaging (MRI) has been aided significantly by the use of gadolinium (Gd3+)-based contrast agents (CAs) over the past three decades. MRI and MRI CAs play a critical role in diagnosing tumors and diseases of the central nervous system. The agents used clinically have been shown to safely increase MRI contrast despite the toxicity of Gd3+, owing to the high kinetic and thermodynamic stability of these chelates. However, current CAs enhance contrast at a small fraction of what is theoretically possible. This leads to the necessity of introducing ...


Spatial Analysis Of Climate And Winegrape Production In Winegrape Growing Regions Of Oregon, United States Of America, Willow Devin Campbell Oct 2013

Spatial Analysis Of Climate And Winegrape Production In Winegrape Growing Regions Of Oregon, United States Of America, Willow Devin Campbell

Dissertations and Theses

American Viticultural Areas (AVAs) are susceptible to small variations in climate and microclimates and are found within a narrow latitudinal range of prime climate conditions. These AVAs are geographically determined based on the best soil, climate, precipitation and temperature combinations for specific winegrape regions. As climate change continues to alter the local weather and the greater climate region of the Western United States, winegrape growing regions in Oregon are being affected. In an effort to determine what the pattern of change is, and compare previous studies of climate change using climate indices, a comparative study based in part on prior ...


Gene Expression Life History Markers In A Hatchery And A Wild Population Of Young-Of-The-Year Oncorhynchus Mykiss, Ian D. F. Garrett Sep 2013

Gene Expression Life History Markers In A Hatchery And A Wild Population Of Young-Of-The-Year Oncorhynchus Mykiss, Ian D. F. Garrett

Dissertations and Theses

Life history within a single species can vary significantly. Many of these differences are associated with varying environmental conditions. Understanding what environmental conditions cue alternate life histories within a single species has been researched extensively. In salmonid fishes, more than almost any other group, varying environmental conditions give rise to individuals within species that take markedly different life history trajectories.

Oncorhynchus mykissis a species of salmonid native to the Pacific Northwest region of North America. This species has two life history forms, anadromous and resident. The anadromous form spends a portion of its life in ocean while the resident life ...


Thinking Aloud In The Science Classroom: Can A Literacy Strategy Increase Student Learning In Science?, Lindsey Joan Mockel Aug 2013

Thinking Aloud In The Science Classroom: Can A Literacy Strategy Increase Student Learning In Science?, Lindsey Joan Mockel

Dissertations and Theses

This research study investigated the effect of using the think aloud protocol while reading informational text on students' ability to learn from text in a secondary science classroom. The participants in this study were high school students (n=47) in three classes of a mixed-grade Integrated Biology, Chemistry, and Physics course. The study tracked student achievement during a four-week curriculum unit on the theory of evolution and evidence for biological evolution. All students received instruction on using the think aloud protocol, and all students practiced the think aloud protocol when reading short articles related to scientific evidence for evolution. The ...


Tracking Fish And Human Response To Abrupt Environmental Change At Tse-Whit-Zen: A Large Native American Village On The Olympic Peninsula, Washington State, Kathryn Anne Mohlenhoff Aug 2013

Tracking Fish And Human Response To Abrupt Environmental Change At Tse-Whit-Zen: A Large Native American Village On The Olympic Peninsula, Washington State, Kathryn Anne Mohlenhoff

Dissertations and Theses

Evidence of large earthquakes occurring along the Pacific Northwest coast is reflected in coastal stratigraphy from Oregon to British Columbia, where there also exists an extensive archaeological record of Native American occupation. Tse-whit-zen, a large Native American village dating between 1824 and 54 cal B.P. located on the Olympic Peninsula of Washington State, was excavated with exceptionally fine stratigraphic control allowing for precise comparison of natural and cultural records. Here I report on the >10,000 fish remains from one 2x2 m excavation block; this assemblage spans one earthquake event, allowing study of changes in relative taxonomic abundance through ...


Modeling The Distribution Of Bobcats And Areas Of Reintroduction For Fisher In The Southern Washington Cascades, Shiloh Michael Halsey Aug 2013

Modeling The Distribution Of Bobcats And Areas Of Reintroduction For Fisher In The Southern Washington Cascades, Shiloh Michael Halsey

Dissertations and Theses

The fisher (Martes pennanti) is a medium sized member of the mustelid family that once roamed the forests of Washington and whose historic range in the western United States once spread throughout the northern Rocky Mountains, the Cascade and Coast Ranges, and the Sierra Nevada (Carroll, Zielinski, and Noss 1999; Powell 1993, Spencer et al. 2011). Due to pressures from trapping and habitat fragmentation, the abundance of the species in the western United States has decreased dramatically and is thought to be limited to several small, isolated populations. In 2008, fishers were reintroduced to the Olympic Peninsula; however, bobcat (Lynx ...


Exploring Tissue Engineering: Vitamin D3 Influences On The Proliferation And Differentiation Of An Engineered Osteoblast Precursor Cell Line During Early Bone Tissue Development, Shelley S. Mason Aug 2013

Exploring Tissue Engineering: Vitamin D3 Influences On The Proliferation And Differentiation Of An Engineered Osteoblast Precursor Cell Line During Early Bone Tissue Development, Shelley S. Mason

Dissertations and Theses

Most of the load-bearing demand placed on the human body is transduced by skeletal tissue, and the capacity of the skeleton to articulate in various opposing directions is essential for body movement and locomotion. Consequently, cartilage and bone defects due to trauma, disease, and developmental abnormalities result in disabling pain and immobility for millions of people worldwide. A novel way of promoting cartilage and bone regeneration is through the incorporation of either primary cells or multipotent progenitor cells in a three-dimensional (3D) biomaterial scaffold, and/or the addition of exogenous growth and differentiation factors. The first part of this study ...


Ccaat/Enhancer-Binding Protein Delta (C/Ebp-Delta) Expression In Antarctic Fishes: Implications For Cell Cycle And Apoptosis, Isaac Martin Sleadd Aug 2013

Ccaat/Enhancer-Binding Protein Delta (C/Ebp-Delta) Expression In Antarctic Fishes: Implications For Cell Cycle And Apoptosis, Isaac Martin Sleadd

Dissertations and Theses

Chapter 1: Antarctic fishes are extremely cold adapted. Despite their inability to upregulate heat shock proteins, recent studies have demonstrated a capacity for heat response in these animals. A cDNA microarray study looked at the Notothenioid fish Trematomus bernacchii and revealed heat sensitivities for hundreds of genes, two of which code for members of the CCAAT/Enhancer-binding protein (C/EBP) family of transcription factors. These molecular switches are best known for their roles in apoptosis, inflammation and cell cycle arrest. This dissertation further elucidates the role of C/EBP-delta in the Antarctic fishes T. bernacchii and Pagothenia borchgrevinki.

Chapter 2 ...


Ecomorphology And Mating Behavior Of Two Species Of Night-Stalking Tiger Beetles, Omus Audouini And O. Dejeanii, Robert Kent Richardson Aug 2013

Ecomorphology And Mating Behavior Of Two Species Of Night-Stalking Tiger Beetles, Omus Audouini And O. Dejeanii, Robert Kent Richardson

Dissertations and Theses

Night-stalking tiger beetles (Cicindelinae: Omus) are among the least studied members of the highly diverse Carabid sub-family Cicindelinae, the tiger beetles. Despite populations of Omus being common in the forest floor habitats of the west coast of North America and their conspicuous predatory role within terrestrial arthropod communities, little is known about the biology and ecology of Omus.

Field studies showed that two species of Omus existed in the forested areas of Powell Butte Nature Park, Portland, Oregon, USA: Omus audouiniand O. dejeanii. The co-occurrence of sympatric, and likely syntopic, species allowed for a comparative approach in examining and analyzing ...


The Role Of Wood Microsites At Timberline-Alpine Meadow Borders For Conifer Regeneration, Adelaide Chapman Johnson Aug 2013

The Role Of Wood Microsites At Timberline-Alpine Meadow Borders For Conifer Regeneration, Adelaide Chapman Johnson

Dissertations and Theses

This research aimed to determine whether wood microsites ("nurse logs"), which are regeneration sites in Pacific Northwest (PNW) subalpine forests, supported regeneration at timberline-alpine meadow borders. Upward advance of forests and conifer invasion into alpine meadows, which may be occurring in conjunction with climate warming, have gained worldwide attention. Successful alpine meadow seedling regeneration depends on suitable substrate availability, or microsites, for seedling establishment. To better understand factors associated with wood microsite occurrence, mechanisms of wood input were determined and four specific hypotheses were posed to assess: (1) seedling density and seedling survival; (2) growing season length, summer mean growing ...


An Evaluation Of The Nontarget Effects Of Transgenic Bacillus Thuringiensis Maize On Arbuscular Mycorrhizal Fungi In The Soil Ecosystem, Tanya Elizabeth Amy Cheeke Aug 2013

An Evaluation Of The Nontarget Effects Of Transgenic Bacillus Thuringiensis Maize On Arbuscular Mycorrhizal Fungi In The Soil Ecosystem, Tanya Elizabeth Amy Cheeke

Dissertations and Theses

My dissertation research examined the effect of the cultivation of insect-resistant Bacillus thuringiensis (Bt) maize on the soil environment with a goal of understanding how to obtain a balance between technological advancement and maintenance of a healthy soil ecosystem. Although Bt plants may help to reduce pesticide use, conferring benefits to farm workers and the environment, there are still unresolved questions about how the cultivation of Bt plants affects soil organisms. For this dissertation project, I used 14 different genotypes of Bt maize and non-Bt maize (Zea mays) to investigate the effects of transgenic Bt plants on the colonization ability ...


The View From The Table: An Analysis Of Participant Reactions To Community-Based Dialogues On Food And Justice, Jennifer Turner Jul 2013

The View From The Table: An Analysis Of Participant Reactions To Community-Based Dialogues On Food And Justice, Jennifer Turner

Dissertations and Theses

While Portland, Oregon's sustainable food movement wins accolades for explicitly situating itself in opposition to the industrialized global food system, it often fails to address systems of oppression that are reproduced within the alternative agri-food movement itself. This demonstrated aversion towards the messy, complex, contingent nature of the social world reflects larger processes of "de-politicization" of the overall sustainability agenda, which leads to the favoring of technological and/or spatial solutions that may undermine the social equity and justice dimensions of the "triple bottom line." This thesis focuses on an action research project involving a series of community dialogues ...


Interspecific Variation In Leaf-Level Biogenic Emissions Of The Bambuseae, Andrea Natalie Melnychenko Jun 2013

Interspecific Variation In Leaf-Level Biogenic Emissions Of The Bambuseae, Andrea Natalie Melnychenko

Dissertations and Theses

Plants emit a diverse range of biogenic volatile organic compounds (BVOCs) into the atmosphere, of which isoprene is the most abundantly emitted. Isoprene significantly affects biological and atmospheric processes, but the range of isoprene and BVOCs present in bamboos has not been well characterized. In this thesis I explore the range of isoprene emission found in bamboos and relate it to plant morphological and physiological characteristics. In addition, I measure and relate the entire suite of BVOCs present in the bamboos to their fundamental isoprene emission rate.

Interspecific variation in isoprene emission documented in a comprehensive survey of bamboos. Two ...


Understory Diversity And Succession On Coarse Woody Debris In A Coastal, Old-Growth Forest, Oregon, Shannon Lee Mcdonald Jun 2013

Understory Diversity And Succession On Coarse Woody Debris In A Coastal, Old-Growth Forest, Oregon, Shannon Lee Mcdonald

Dissertations and Theses

This research examines the relationship between understory plant diversity and logs in a Pacific Northwest (PNW) Sitka spruce (Picea sitchensis)-western hemlock (Tsuga heterophylla) old-growth, coastal forest. These forests are renowned for their high forest productivity, frequent wind storms, and slow log decomposition rates that produce unmatched accumulations of coarse woody debris (CWD) yet few studies have examined the relationship between CWD and understory vegetation ecology. My research addressed this topic by comparing understory plant census data between paired fallen log and forest floor sites (n=20 pairs). My objectives were to: 1) determine the influence of substrate type on ...


Preserving Nature Through Film: Wilderness Alps Of Stehekin And The North Cascades, 1956-1968, Nicolas Timothy Bergmann Jun 2013

Preserving Nature Through Film: Wilderness Alps Of Stehekin And The North Cascades, 1956-1968, Nicolas Timothy Bergmann

Dissertations and Theses

On March 22, 1958 David Brower's film Wilderness Alps of Stehekin premiered to an audience of conservationists in Seattle, Washington. Almost two years in the making, the thirty-one minute film advocated the preservation of nature in Washington's North Cascades through the creation of a national park. Over the next decade, Wilderness Alps of Stehekin became the most influential publicity tool in the struggle to preserve the North Cascades. Because of the region's geographic isolation, the film was the first time many people throughout the nation were exposed to the scenic grandeur of the area. Images of craggy ...


The Effect Of Temperature On Phenotypes Of The Invasive European Green Crab: Physiologic Mechanisms That Facilitate Invasion Success, Amanda Kelley May 2013

The Effect Of Temperature On Phenotypes Of The Invasive European Green Crab: Physiologic Mechanisms That Facilitate Invasion Success, Amanda Kelley

Dissertations and Theses

Invasion physiology is an emerging field that endeavors to understand the influence of physiological traits on the establishment of non-native species in novel environments. The invasive European green crab,Carcinus maenas, is one of the world's most successful aquatic invaders, and is currently distributed across temperate marine ecosystems globally. The work presented here explored the thermal physiology of this species, and has highlighted several physiological traits that have likely influenced establishment success.

Intraspecific comparisons of crabs sampled from the northern and southern edges of their recipient, or invaded range on the west coast of North America have identified both ...


Application Of Gis And Spatial Analysis Of Golden Eagle Fatalities Caused By Wind Turbines At The Altamont Pass Wind Resource, Andrew James Pinger Apr 2013

Application Of Gis And Spatial Analysis Of Golden Eagle Fatalities Caused By Wind Turbines At The Altamont Pass Wind Resource, Andrew James Pinger

Dissertations and Theses

The Altamont Pass Wind Resource Area (Altamont) near Livermore, California is the oldest and largest wind farm in the United States. It is known as a location of high avian mortality, especially for diurnal raptors such as the Golden Eagle (Aquila chrysaetos). Using the avian monitoring data collected at Altamont for over thirteen years (1998-2003, 2005- 2011), records were analyzed of 134 golden eagle deaths caused by wind turbine collisions. All wind turbines present during the same temporal range were characterized according to turbine variables, and geographic placement characteristics. Values of turbines that killed golden eagles were compared to values ...


Effects Of Increased Nitrogen Deposition On The Dominance Of Hedera Helix In The Pacific Northwest, Bianca Christine Dolan Mar 2013

Effects Of Increased Nitrogen Deposition On The Dominance Of Hedera Helix In The Pacific Northwest, Bianca Christine Dolan

Dissertations and Theses

Increased nitrogen deposition has been shown to promote the dominance of invasive species, and nitrogen deposition rates have steadily increased in most of the Western United States in recent years due to population increases. The purpose of this study was to determine if increased rates of nitrogen deposition are contributing to the success of Hedera helix in the Pacific Northwest. Plots were established in Lesser Park in Portland, Oregon and received monthly treatments of ammonium nitrate for one year. Growth, measured as change in percent cover, was compared between treated and untreated plots for both H. helix and native species ...


Expression Of Growth Arrest And Dna Damage Protein 45-Alpha (Gadd45-Alpha) And The Ccaat/Enhancer Binding Protein-Delta (C/Ebp-Delta) In Fishes Exposed To Heat And Hypoxia, Daniel Omar Hassumani Mar 2013

Expression Of Growth Arrest And Dna Damage Protein 45-Alpha (Gadd45-Alpha) And The Ccaat/Enhancer Binding Protein-Delta (C/Ebp-Delta) In Fishes Exposed To Heat And Hypoxia, Daniel Omar Hassumani

Dissertations and Theses

The cellular stress response (CSR) is one of the most highly conserved mechanisms among all organisms. Cellular stress can be defined as damage or the threat of damage to proteins, macromolecules and/or DNA. The response to damage can involve cell cycle regulation, protein chaperoning, DNA repair or, if macromolecular damage is too severe, apoptotic mechanisms can be initiated. This thesis details experiments that were designed to examine the cellular response to non-lethal environmental stressors at the protein level, using two fish species as study models. Two proteins that can cause cell cycle arrest and apoptosis mechanisms were examined. Expression ...


Evaluating The Effects Of Road Crossing Structures On Stream-Associated Amphibians In The Wilson River Watershed, Tillamook State Forest, Oregon, Sara Erin Twitchell Mar 2013

Evaluating The Effects Of Road Crossing Structures On Stream-Associated Amphibians In The Wilson River Watershed, Tillamook State Forest, Oregon, Sara Erin Twitchell

Dissertations and Theses

As replacement and removal of undersized culverts gains momentum as an effective technique for restoring natural stream flows and removing fish passage barriers, it is important to evaluate the benefits of these efforts on the in-stream and adjacent riparian habitat for other species of potential concern. This study compares stream-associated amphibian (SAA) occurrence in streams adjacent to different road crossing structures on unpaved forest roads in the Wilson River watershed located within the Tillamook State Forest, Oregon. Surveys were conducted at road crossing structures for three taxa of SAA; Pacific giant salamander (Dicamptodon tenebrosus), coastal tailed frog (Ascaphus truei), and ...


An Experimental Investigation Of Nest Reuse And Nest Site Selection In An Open-Cup Nesting Passerine, Sarah A. Cancellieri Mar 2013

An Experimental Investigation Of Nest Reuse And Nest Site Selection In An Open-Cup Nesting Passerine, Sarah A. Cancellieri

Dissertations and Theses

Eastern Kingbirds (Tyrannus tyrannus) breed from coast to coast in North America and build open-cup nests in trees. They have been extensively studied across most of their range and have only on occasion been documented to reuse a nest from a previous season. However, at Malheur National Wildlife Refuge (MNWR), located in southeastern Oregon, ~10 % of female Eastern Kingbirds reuse old nests of mainly American Robins (Turdus migratorius). In an attempt to address why nest reuse is so common at MNWR, I used artificial nests to evaluate two hypotheses as to why nest reuse is common in this breeding population ...


Status Of Nutria (Myocastor Coypus) Populations In The Pacific Northwest And Development Of Associated Control And Management Strategies, With An Emphasis On Metropolitan Habitats, Trevor Robert Sheffels Mar 2013

Status Of Nutria (Myocastor Coypus) Populations In The Pacific Northwest And Development Of Associated Control And Management Strategies, With An Emphasis On Metropolitan Habitats, Trevor Robert Sheffels

Dissertations and Theses

The nutria (Myocastor coypus) is a semi-aquatic rodent native to South America that was introduced to the Pacific Northwest, USA, in the 1930s. Primary damage categories from this invasive species include burrowing and herbivory, resulting in habitat degradation. Nutria have become well-established in metropolitan habitats, and anecdotal information suggests the problem has increased in recent years. However, little regional research on the species has been conducted. The scope of this research, which emphasizes metropolitan habitats, includes three primary foci in relation to nutria populations in the Pacific Northwest: modeling habitat suitability, assessing activity and movement patterns, and identifying and managing ...


First Bacterial Endosymbionts Found In The Phylum Ascomycota, Eileen Elizabeth Fitzpatrick Mar 2013

First Bacterial Endosymbionts Found In The Phylum Ascomycota, Eileen Elizabeth Fitzpatrick

Dissertations and Theses

Organisms belonging to the Kingdom Fungi are known to occupy a wide variety of ecological niches and are found globally in virtually all environments. Two members of the smallest of the fungal phylum, the Zygomycota, have also been found to harbor intercellular bacteria initially described as being from or closely related to organisms from the Genus Burkholderia. In this study two microaerophilic members of the species Verticilium from the phyla Ascomycota were characterized. Both appear to carry two bacterial endosymbionts. This is the first evidence of bacterial endosymbionts found within a member of the Ascomycota. Through the use of fluorescent ...


Microbial Biomineralization Of Iron, Wen Fang Feb 2013

Microbial Biomineralization Of Iron, Wen Fang

Dissertations and Theses

Iron is a common cation in biomineral sand; it is present for example in magnetite produced by magnetotactic bacteria and in iron sulfides produced by sulfate reducing microorganisms. The work presented in this thesis focused on two types of microorganisms capable of forming iron biominerals. In the first project I have studied the effect of O2 on the respiratory physiology and the formation of magnetosomes by Magnetospirillum magneticum AMB-1. In the second project I have studied the relationship between olivine and the activity of dissimilatory sulfate reducing (DSR) microorganisms. For the first project, I grew cells of AMB-1 in cultures ...


Synthesis Of 4-Azidocoumarins And Their Use In Copper-Catalyzed Azide-Alkyne Cycloaddition Reactions, Anthony J. Netsuri Jan 2013

Synthesis Of 4-Azidocoumarins And Their Use In Copper-Catalyzed Azide-Alkyne Cycloaddition Reactions, Anthony J. Netsuri

Dissertations and Theses

Triazole-containing compounds have shown great biological activity ranging from antiviral, antibacterial, to anticancer, to name a few. Coumarin derivatives have also shown interesting biological activities. The combination of these bioactive compounds appears to have great promise for new and future medicines. In this work, various 4-azido-coumarins were synthesized via the transformation of the 4-hydroxy derivatives to 4-benzotriazolyloxy coumarins by reaction with the peptide coupling agent (benzotriazol-1-yloxy)tris-(dimethylamino)phosphonium hexafluorophosphate (BOP), and 1,8-diazabicycloundec-7-ene (DBU) as the base, in tetrahydrofuran (THF) solvent. The 4-benzotriazolyloxy coumarins were converted to the 4-azidocoumarins by reaction with sodium azide (NaN3), and the overall process ...


Carcass Feeding For Captive Vultures: Testing Assumptions About Zoos And Effects On Birds And Visitors, Hannah Gaengler Jan 2013

Carcass Feeding For Captive Vultures: Testing Assumptions About Zoos And Effects On Birds And Visitors, Hannah Gaengler

Dissertations and Theses

Carcass feeding is a potentially controversial feeding method for zoo animals. The common assumption is that many North American zoos refrain from feeding large carcasses to their carnivorous animals because zoo visitors might not approve of this feeding method. However, since there are several species of carnivores in zoos that feed from large carcasses in nature, this food type also has the potential to be beneficial to their welfare. In intelligent and usually inquisitive scavengers like vultures, a lack of activity and behavioral opportunities could be a welfare problem in captivity; providing them with a more complex food item might ...