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Post-Fire Tree Mortality And Regeneration Patterns As Proxies Of Conifer Forest Resilience, Sebastian Upton Busby

Dissertations and Theses

Shifting wildfire patterns and climate conditions, magnified by anthropogenic climate change, are threatening the resilience of conifer forests in North America and more specifically, the western US. If native conifer species are functionally maladapted to novel fire patterns and post-fire climate conditions, large-scale shifts in conifer forest structure, composition, and extent may occur as warming intensifies. Forest resilience in the context of fire and climate can be understood and quantified by the survival of trees through fire events and success of trees to regenerate post-fire and maintain population levels. In this dissertation, I use field observations and remote sensing to …

Modeling Environmental Factors Related To Drought-Induced Tree Mortality Based On Lidar And Hyperspectral Imagery, Lauren Nicole Sharwood

Dissertations and Theses

Climate change is projected to bring more frequent and prolonged droughts, causing widespread forest die-off. Identifying tree mortality over large spatial extents in response to the most recent California drought will help forest managers and conservationists understand where there may be a greater likelihood of future die-offs. In order to find more at-risk areas, this study evaluated how interacting site-specific topographic, climate, substrate, and stand characteristics mediated tree mortality in the Central Sierra Nevada during the 2012-2016 drought. The author used lidar and hyperspectral imagery provided by the National Ecological Observatory Network to identify individual dead trees using the Random …

A Bioinformatic And Biochemical Analysis Of Cruciviruses, George William Kasun

Dissertations and Theses

Cruciviruses are novel ssDNA viruses discovered through metagenomics and direct environmental DNA amplification and cloning. The genomes of cruciviruses suggest that gene transfer between RNA and DNA viruses occurred due to the presence of putative protein-encoding genes that are homologous to both ssRNA and ssDNA viruses. In order to gain a better understanding of this group of viruses both bioinformatic analyses and in vitro biochemical experiments were employed. The results of the bioinformatic analyses show that cruciviruses are a highly diverse group of ssDNA viruses. Their placement within established ssDNA phylogenies is difficult due to heterogeneity in their putative replication-associated …

Selenium Probes For The Detection Of Thioredoxin Reductase Activity, Tendai Joseph Mafireyi

Dissertations and Theses

The identification and quantification of proteins and enzymatic activity in living tissues frequently requires the use of invasive procedures such as biopsy. These techniques can inhibit measurements of protein levels in real-time, and the disruption of tissue can lead to the loss of important information concerning the spatial distribution and differential activities in various cell types. The use of small organic fluorescent probes that rely on activation or accumulation within a tissue embody robust methods of detection that address these issues. This dissertation describes the design, synthesis and evaluation of fluorescent probes that can detect the enzyme thioredoxin reductase (TrxR). …

Mitonuclear Mismatch Is Associated With Increased Male Frequency, Outcrossing, And Male Sperm Size In Experimentally-Evolved C. Elegans, Brent William Bever

Dissertations and Theses

We provide the first controlled study of how male frequencies and rates of outcrossing evolve in response to mitonuclear mismatch by allowing replicate lineages of C. elegans nematodes containing either mitochondrial or nuclear mutations of electron transport chain (ETC) genes to evolve under three sexual systems: facultatively outcrossing (wildtype), obligately selfing, and obligately outcrossing. In partial support of a tenet of the mitonuclear sex hypothesis, which predicts that outcrossing will be favored in cases of mitonuclear mismatch, we found evolution of increased male frequency in at least one replicate line of all four ETC mutant backgrounds tested--nuclear isp-1, mitochondrial …

Mechanisms Of Substrate Recognition By The Cul3-Based E3 Ligase, Katia Graziella De Oliveira Rebola

Dissertations and Theses

Cul3-based E3 ligase is responsible for regulating a variety of cellular pathways, many of which are known to have profound effects on the proper function of multicellular organisms. Although progress over the past years has been truly impressive, our understanding of the mechanisms of E2 recruitment and selection by the BCR complex and all the roles that Cul3 plays on kidneys remains in its infancy. To explore these aspects, this dissertation aims to analyze the Cul3 complex using two different approaches: (1) We used the powerful tool of chimeric analysis to map the essential domain binding characteristics of Cul3 taking …

Multi-Scale Environmental Conditions Associated With Shade-Tolerant Conifer Regeneration In Forest Park, Portland, Oregon, Matthew Cook

Dissertations and Theses

Forest Park is a 5,100-acre urban forest located in Portland, Oregon, that has been impacted by various anthropogenic stressors including logging, fragmentation, invasive species, air pollution and recreation use due to its proximity to the urban environment. This legacy of land use coupled with natural disturbances has resulted in changes to forest structure, composition, and function--threatening the long-term sustainability of the park. Past research in Forest Park has identified a lack of regenerating shade-tolerant conifers, particularly western hemlock and western red cedar species, in the section of the park closest to the city. Typically, western hemlock and western red cedar …

Exploring Mirna Function And Host Response To Coxiella Burnetii Infection, Madhur Sachan

Dissertations and Theses

Alveolar macrophages attempt to control bacterial infection through a spectrum of defense processes, including induction of apoptosis, autophagy, inflammatory response, and nutrient sequestration. MicroRNAs (miRNAs), a class of small non-coding RNAs, are involved in a spectrum of physiological processes, including immune response to intracellular infections. However, whether microRNAs have any functions in host response to Coxiella burnetii infection is unknown. Coxiella burnetii is a highly infectious intracellular pathogen that causes Q fever, a zoonosis with a worldwide occurrence. In this work, I investigated the functions of miRNAs in host response to C. burnetii infection and found that miRNAs are an …

Microbes On The Mountain: Plant-Microbe Associations And Interactions On Mount St. Helens, Emily Rose Wolfe

Dissertations and Theses

Plant-microbe associations and interactions provide critical context to studies in both community and ecosystem ecology, especially in systems that are relatively new and still undergoing early successional processes. Microbes can colonize the surfaces and interiors of all plant tissues, and these assemblages vary in composition both spatially and temporally, even within the same plant. Endophytes are bacteria or fungi that spend most of their lifecycles living within plant tissues asymptomatically--typically, "endophyte" refers specifically to aboveground tissues such as leaves and stems, and therefore may have direct influences on defenses against herbivory, pathogen or pest tolerance, and even afterlife effects on …

Experiences Of Undergraduates And Graduate Teaching Assistants In Biology Course-Based Undergraduate Research Experiences, Emma Crystal Goodwin

Dissertations and Theses

Evidence of positive student outcomes from course-based undergraduate research experiences (CUREs) has sparked implementation of CUREs in introductory biology laboratory courses, as one approach to boosting student engagement in research. In a CURE, students collaborate with other students and instructors on a research project, where they conduct novel scientific research that has relevance to a local or scientific community. However, previous research rarely considers that graduate teaching assistants (GTAs) often teach introductory labs. The classroom role of GTAs expands in a CURE--they no longer need to simply teach a lab class, but also to serve as research mentors. GTAs, who …

Opportunities And Challenges In The Collection And Use Of Socio-Spatial Data In National Forest Planning, Diane Trechsel Besser

Dissertations and Theses

Understanding human-environment connections to places is an important component of land-use management. Tools for collecting geographically referenced public values-based data (defined as socio-spatial data) for use in natural resource planning have been reported in academic journals for decades. The utility of socio-spatial data is in making public values tangible and potentially actionable in land-use analyses and decision processes. However, there is a lack of comprehensive documentation on the ways in which socio-spatial data is perceived, collected, interpreted and applied at a practical level. A better understanding of these factors allows planners to mitigate barriers and leverage opportunities to more …

Mechanisms Of Connexin-46 And -50 Intercellular Channel Function And Stability By Molecular Dynamics Simulations, Bassam George Haddad

Dissertations and Theses

Gap junctions make up a class of intercellular channels that characteristically connect the cytoplasm of directly apposed cells through large assemblies, or plaques, constituted by a multitude of intercellular channels. Gap junction mediated intercellular communication is critical for a variety of physiological functions, from coordinating electrical impulses in the heart and brain to maintaining homeostasis in most tissues. There are 21 isoforms of connexins, the constituent subunit of the gap junction, expressed in a tissue dependent manner. Gap junctions formed from different isoforms exhibit distinct biophysical properties, such as gating kinetics and sensitivity, as well as unique permeability and selectivity …

Exploring Linkages Between Landscape Patterns And Freshwater And Estuarine Bivalves In The Coast Range Of Oregon, Kaegan Michael Scully-Engelmeyer

Dissertations and Theses

Spatial configurations of landscape variables (biotic, abiotic, and socio-ecological) affect and are affected by ecological processes and species in watersheds. This dissertation explores relationships among landscape patterns, ecosystem processes and bivalve species dynamics in coastal watersheds in Oregon, USA. I approached this broad topic through two primary avenues of research: investigating cross-ecosystem threats from pesticide use in forestland management to downstream aquatic environments, and the landscape ecology of an at-risk freshwater mussel species.

Terrestrial land use activities present cross-ecosystem threats to riverine and marine species and processes. Specifically, pesticide runoff can disrupt hormonal, reproductive, and developmental processes in aquatic organisms, …

Nesting Habits Of Cavity Nesting Bees And Wasps In Portland, Oregon, Stefanie Kay Steele

Dissertations and Theses

Native bees are threatened by habitat loss through urbanization, however, there is increasing interest in creating bee nesting habitat in urban areas. Few studies have determined what species are present in the region, or examined the role of nest height or cavity size in attracting the approximate one-third of native bees that nest in cavities. To determine what species were present, and whether they showed preferences for nesting at a certain height or cavity width, we set up artificial wooden cavity nest blocks across fourteen locations in the greater Portland, OR area. Wooden posts were erected with nest blocks at …

Temperature-Induced Activation Of The Reproductive Axis Through Melatonin-Mediated Changes In Thyrotropin, Treven J. Winters

Dissertations and Theses

An animal's ability to synchronize life-history events or stages with optimal environmental conditions is paramount to successfully reproducing and maximizing fitness. Additional events including migration, foraging, rearing of young, and emergence from hibernation are all examples of processes under environmental control in one species or another. An exciting new mechanism involving neural thyroid hormone metabolism has been elucidated that links environmental control to the neuroendocrine reproductive axis. In birds and mammals with seasonal breeding cycles, this neuroendocrine pathway is activated by photoperiod-induced changes in thyroid stimulating hormone (TSH, also known as thyrotropin) production within the pars tuberalis region of the …

Testing Functional Variation In Thermal Properties For Antarctic Mosses, Andrew Forrest Clements

Dissertations and Theses

As the maritime Antarctic ecosystem continues to warm, glacial retreat will further expose subterranean permafrost to warmer conditions. One of the most visible changes in the ecosystem is the colonization of the new ice-free areas by bryophytes, particularly mosses. These bryophytes are having important effects on terrestrial thermal properties, but little is known about differences among Antarctic moss species in their thermal properties. Here, I measured the thermal conductivity, specific heat capacity, and the water content of moss species on King George Island to understand the insulation ability of Antarctic mosses, Polytrichastrum alpinum, Sanionia georgicouncinata, Chorisodontium aciphyllum, …

Elucidating The Evolution And Function Of Srnas That Facilitate Bacterial Stress Tolerance, Madeline Claire Krieger

Dissertations and Theses

Non-coding small RNAs (sRNAs) are ubiquitous post-transcriptional regulators found in both gram-negative and gram-positive bacteria. Despite their integral role in many regulatory pathways, including those that facilitate stress-tolerance, little is known about the evolutionary forces that drive the emergence of novel sRNAs, how prevalent sRNAs are within bacterial species, or the functions of a majority of these transcripts. In this work, I first describe the evolution of OxyS, a well-characterized sRNA in gram-negative Enterobacteriaceae that is involved in coordinating the bacterial response to oxidative stress. Next, I identify novel sRNAs differentially produced by the gram-positive oral pathogen Streptococcus mutans in …

Next Generation Sequencing Identifies Population Structure And Signatures Of Local Adaptation In Red Alder (Alnus Rubra Bong.), Jacob Brent Loveless

Dissertations and Theses

Red alder (Alnus rubra Bong.) is the dominant hardwood tree species in the Pacific Northwest. Red alders are only found in western North America, generally within 200 km of the coast and below 1000 m in elevation--although there are several disjunct populations in the northern Rocky Mountains in Idaho. Commonly a riparian species, the shade intolerant red alder generates most of the leaf litter in the streams and rivers it occupies which has been shown to greatly influence the decomposer communities. This, in turn, has a cascading effect throughout the entire riparian ecosystem greatly influencing multiple levels of the …

Steady-State Transmembrane Water Exchange In Proliferating Cultures Of Saccharomyces Cerevisiae, Joseph O'Malley Armstrong

Dissertations and Theses

Cellular water exchange is often considered in terms of a change in volume, where a net flux of water moves across the cell membrane due to a change in osmotic pressure. Osmotic pressure can cause a cell to shrink or swell, however, rapid water exchange persists across the membrane even when the volume of the cell is constant. Steady-state transmembrane water exchange describes the exchange of water across the cell membranes which results in no net change in cell volume. This exchange is astonishingly rapid; the entire pool of intracellular water of a Saccharomyces cerevisiae cell may exchange 2-5 times …

Chemical Characterization Of Toxicologically Relevant Molecules In Cannabis Concentrates And Vaporizer Aerosols, Jiries Meehan-Atrash

Dissertations and Theses

Consumption of cannabis concentrates using the relatively novel non-combustion methods dabbing and vaping has steadily grown in popularity as cannabis legalization in North America has allowed increased access to sophisticated cannabis products and technology. In order to assess the safety of these products, it is necessary to gain a chemical understanding of the decomposition reactions that occur when the active ingredients are heated in the conditions seen when dabbing or vaping. This dissertation contains a manuscript that details efforts to structurally characterize a toxic cannabis concentrate adulterant, and three manuscripts that studied the chemical decomposition of the two primary cannabis …

Connecting Environment And Phenotype: Deciphering Mechanisms Of Diapause Entry And Exit In The Annual Killifish Austrofundulus Limnaeus, Erin Monica Davis

Dissertations and Theses

Embryonic development is complex, dynamic, and dependent on environmental factors. Mechanisms of sensing and integrating environmental stimuli are diverse, and understanding these mechanisms in extant species can elucidate how complex phenotypes emerge from genomic information expressed in an environmental context. In Austrofundulus limnaeus, an annual killifish with alternative developmental trajectories, light and temperature are vital factors that determine if an embryo will enter a state of diapause. We hypothesize that embryos of A. limnaeus use the vitamin D₃ signaling pathway as a vehicle to incorporate these ecological signals into their developmental programing. Here we provide evidence of …

Public Perception Of Air Quality Risks In Portland, Oregon, Dawn Nolan

Dissertations and Theses

The availability and demand for localized air quality information from communities are on the rise. However, not all information and not all communities are the same. Effective engagement and communication strategies will depend on a community's existing knowledge, opinion about air quality, individual experiences with inequities, and more. This study aims to understand how people living in Portland, Oregon understand and experience air pollution as an environmental risk and examine the extent to which those risk perceptions relate to confidence in science and technology. This gap is critical because of the complex interaction between air pollution and the risk perception …

Thermodynamics Of Ligand Binding And Global Structural Stability Of Human Serum Albumin, Matthew Walter Eskew

Dissertations and Theses

Protein structure is integral to its function. For the past 70 years differential scanning calorimetry has been used to measure protein structural stability. More recently it has been used to study macromolecular interactions. Interactions between proteins and ligands can manifest on differential scanning calorimetry melting curves or thermograms. Utilizing differential scanning calorimetry thermograms to detect or diagnose diseases has been a major goal in disease diagnostics. However, correlating specific ligand-protein interactions, as manifested in a thermogram, with a disease-specific plasma thermogram, has proven elusive.

Modified human serum albumin was utilized to develop a process to capture and retrieve ligands from …