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A Tractable Nematode Model For The Emerging Fungal Pathogen, Candida Auris, Melissa Martinez

Dissertations and Theses (Open Access)

Candida auris is an emerging multidrug-resistant opportunistic fungal pathogen. It

poses a significant threat to immunocompromised patients and those with prolonged stays in

healthcare facilities. C. auris spreads rapidly in health care facilities through enhanced

colonization of skin and abiotic surfaces. The genetic factors contributing to this ability and to

the virulence, drug resistance, and stress-tolerant nature of C. auris are largely unknown.

Current animal models of C. auris infections are not well standardized and report conflicting

results. Additional animal models of virulence are needed, especially those amenable to high-

throughput analysis. The nematode Caenorhabditis elegans has been validated as …

Pattern Dynamics And Stochasticity Of Brain Rhythms And Spike Trains In A Tauopathy Mouse Model Of Alzheimer’S Disease, Clarissa M. Hoffman

Dissertations and Theses (Open Access)

Systems neuroscience posits that every aspect of perceived physical reality, every aspect of animal and human behavior, and every cognitive phenomenon emerges from patterns of neuronal activity. While most researchers embrace this idea, there are major difficulties in describing and analyzing these complex neuronal dynamics—spike flows produced by cells ensembles, synchronized extracellular field oscillations, and other patterns—which limits our understanding of how the activity of individual neurons and the whole-animal cognition and behavior might be connected. In particular, we lack the approaches and even the semantics for connecting the individual cell outputs and the integrated results of their activity. Current …

From Antigen Presentation To Tumor Control: Mechanisms Of Type I Conventional Dendritic Cell-Based Cancer Vaccines, Josue E. Pineda

Dissertations and Theses (Open Access)

Type 1 conventional dendritic cells (cDC1s) are important for generating and sustaining antitumor immunity. Accordingly, the abundance of cDC1s in human tumors correlates with improved outcomes in cancer. Capitalizing on this role, we previously demonstrated that vaccination with in vitro-derived murine cDC1s elicits durable tumor control in multiple preclinical models; however, the immunological mechanisms underlying the efficacy of cDC1 vaccination remain unclear. Here, we examined whether in vitro-derived cDC1s resemble tumor-infiltrating DC populations and whether MHC-I and MHC-II antigen presentation contribute to cDC1-mediated tumor control following vaccination in melanoma.

As expected, MHC-I- or MHC-II-deficiency had minimal impact on …

Membrane Organization Of Rheb And Rhoa: Roles In Function And Allosteric Druggability, Chase M. Hutchins

Dissertations and Theses (Open Access)

Small GTPases of the Ras superfamily are membrane-bound molecular switches that regulate nearly all major cellular processes, and their dysregulation drives cancers, neurological disorders, and metabolic diseases. While anchored to cellular membranes, the catalytic domains of small GTPases undergo orientation dynamics, adopting distinct configurations that can occlude or expose effector-binding surfaces and modulate signaling output. These dynamics have been characterized in the Ras oncoproteins, but whether they extend across the superfamily and influence allosteric druggability has remained unknown.

In this dissertation, I address these questions through Rheb and RhoA, two small GTPases with complementary differences in subfamily lineage, membrane localization, …

Desert Deep: The Great Salt Lake's Evanesce And The Gravity Of Recovery, Avery Truman

Undergraduate Honors Capstone Projects

The Great Salt Lake has been shrinking since the mid-19th century for several reasons, primarily due to a higher evaporation rate caused by climate change and water diversion from the Bear, Weber, and Jordan rivers. This problem will cause mass ecosystem destruction, release toxic chemicals into the air, and strand migrating birds. As an environmental studies and geography major, I’ve spent a lot of time learning about the Great Salt Lake in my courses. I decided to write Desert Deep, a series of essays, after I took my first creative nonfiction writing class. The goal was to tell the …

Diffuse Radiation Controls On Southern Pine Forest Ecosystem Functioning, Jeremy Forsythe

All Dissertations

Diffuse solar radiation, sunlight scattered by atmospheric aerosols and/or clouds, enhances plant photosynthesis through the diffuse fertilization effect (DFE), increasing ecosystem gross primary productivity (GPP) per unit of incoming radiation. Despite this known effect, pine forests of the southeastern United States remain comparatively understudied in the diffuse light literature. This is a critical knowledge gap, as the southeastern United States sequesters more carbon than any other region of the conterminous country (approximately 176 ± 26 Tg C yr⁻¹, or roughly 56% of national forest net carbon exchange), and the region experiences some of the highest biogenic aerosol loads in North …

Neurobiological Mechanisms Of Attention In Adolescents, Virginia Clark

All Dissertations

Adolescence is a transformative developmental period characterized by profound biological, neurological, and behavioral changes. This dissertation investigates the neurobiological underpinnings of attention in adolescents, emphasizing how internal mechanisms influence and individually shape cognitive development through the endosystem. Rooted in the intersection of human development, learning sciences, and cognitive neuroscience, this work argues for a more integrated understanding of attention as a fundamental cognitive function for learning, one that is behaviorally seen but also biologically and neurologically driven. While developmental science has often emphasized external influences such as family, culture, and environment, this work centers on the adolescent’s internal biological systems …

Developing An Independent Shallow-Water Survey For The Western Rock Lobster Fishery: Tracking Pre-Recruitment Abundance And Habitat Change, Lucy Rudd, Simon De Lestang, Owen Young, Benjamin Hebiton

Fisheries Research Reports

Background

Puerulus settlement has proven to be a good forecaster of legal recruitment of Western Rock Lobster entering into the commercial and recreational fisheries. However, in 2011, this relationship broke down, with average puerulus settlement levels not being reflected in commercial catch rates four years later. Some northern areas showed unexpectedly low catch rates, while other southern areas showed unexpectedly high catch rates. Since this change followed the 2011 marine heatwave, it was assumed that this event changed some component(s) which were important to the growth and survival of juvenile lobsters. It was determined that a better understanding of this …

Feeding Ecology In Coastal Systems, Randi L. Cannon

Graduate Theses and Dissertations (2019 - present)

Oysters (Crassostrea virginica) are critical foundation species in estuaries, providing numerous ecological and economic benefits. However, oyster populations have diminished worldwide. Effective oyster restoration and aquaculture require a mechanistic understanding of the physiological and environmental factors that govern oyster feeding, growth, and resilience under changing coastal conditions. We investigated how oyster ploidy and environmental conditions influenced oyster feeding and investigated how changes in abiotic conditions affected behavioral performance of oyster drills (Stramonita spp.), a key oyster predator. To better understand feeding responses and behaviors of both predator and prey we 1) used in-situ filter feeding assays to determine if feeding …

A Novel Method Of Protein Purification Using Hedgehog Proteins As An Inducible, Self-Cleaving Tag, Antonia Kladias

Undergraduate Honors Theses

Because removing extraneous purification tag sequences from native proteins can be challenging and costly, there is demand for simple all-in-one techniques that directly furnish a tagless, functional protein-of-interest (POI). Current tagless purification systems are based on intein biochemistry; however, intein-based purification requires expensive, specialized resins and the POI often must be fused to the intein’s C-terminus. In this thesis, I present a novel approach for tagless POI purification in which the Drosophila melanogaster hedgehog protein catalytic domain (HhC) is repurposed as a small-molecule inducible, self-cleaving element dubbed Gtag. With Gtag, the POI is fused to the N-terminus of HhC/Gtag with …

Comparing Awssi And Traditional Winter Metrics For Predicting Overwinter Survival Of Juvenile Walleye (Sander Vitreus), Camille N. Shifrin

Honors Program: Senior Projects (Public)

Winter conditions are an important driver of recruitment variability in freshwater fishes, yet winter severity is often characterized using single climate metrics. These simplified approaches may not capture the cumulative stress experienced by fishes during winter. The Accumulated Winter Season Severity Index (AWSSI) integrates multiple components of winter climate and may therefore provide a more biologically relevant indicator of overwinter survival. In this study, we compared AWSSI with traditional winter severity metrics to explain interannual variation in overwinter survival of juvenile Walleye (Sander vitreus) in Harlan County Reservoir, Nebraska. Model comparisons using Akaike’s Information Criterion (AIC) indicated that …

The Influence Of Additional Zinc Supplementation During Gestation On The Trace Mineral Concentrations Of Tissues, Milk, And Calf Serum At Birth, Hunter Miller

Animal Science Undergraduate Honors Theses

Minerals are known to play a key role in the immune system, growth, and development of animals. An important part of a calf's life is receiving colostrum immediately after birth, which provides the calf with immunoglobulins and necessary nutrients that are required. Furthermore, the gestation period is another very important aspect of the calf's life where they can take in the necessary nutrition. This study compared how two different supplements fed during the gestation period ultimately affected the mineral concentrations of the colostrum, placenta, calf plasma, and cow liver. The supplements that were provided were a 1) control that provided …

Analyzing The Effects Of Message Testing On The Public's Opinion About Gene Editing In Agriculture And Medicine, Luke Sanford Wimpy

Graduate Theses and Dissertations

This paper will present results from the final survey of a multi-stage project examining factors that influence opinions about gene editing in agriculture and medicine. In this final survey, 3,200 U.S. respondents were recruited and randomized to view one of eight videos that communicated the safety of gene editing to determine which factors are most influential in changing opinions. The eight videos were designed based on data collected from focus groups and three previous surveys in this multi-stage project. The eight videos varied by three attributes: messenger, message, and application. The messenger in the videos was either a researcher or …

Which Energy Expenditure Equation Is Most Accurate In A Field-Based Setting?, Merrill C. Ward

All Graduate Reports and Creative Projects, Fall 2023 to Present

Several energy expenditure prediction equations for walking on varied terrain exist; however, these predictions are often theoretical and have not undergone rigorous field testing for accuracy. Field research on this topic is sparse. The aim of this study was to determine if any existing energy expenditure prediction equations are accurate in a field-based setting with load and gradient being taken into account (i.e., under conditions that are most applicable to day hiking). This was done by directly measuring relative VO₂ (ml/kg/min) of study participants and comparing these direct measurements to the values generated from the existing prediction equations. Fifteen …

Long Term Changes In Elk Group Size And Composition (2002-2023) In Relation To Wolf Hunting Sucess, Kennedy Price

Undergraduate Honors Capstone Projects

Elk (Cervus elaphus) in Yellowstone National Park exist within a predator-prey system shaped by long-term interactions with wolves (Canis lupus). This predator-prey system represents an important model for understanding how predation influences ungulate behavior and social organization. Predators affect prey behavior through direct and indirect interactions and may cause long-term changes. What this study strives to answer is if predator success can have long term effects on prey grouping behavior and age-sex structure. In a previous study, wolves were found to be most successful hunting medium sized group of elk (20-49 individuals) in Yellowstone National Park. …

Understanding Vaccine Hesitancy In Veterinary Medicine: A Review Of Client Attitudes, Grace Moore

Undergraduate Honors Capstone Projects

Uncertainty toward vaccination, long recognized as a public health concern in human medicine, is increasingly recognized within veterinary contexts, posing risks to both animal and community health. This literature review examines the development, causes, and implications of reduced vaccine confidence in veterinary medicine, with emphasis on small animal and some large animal practices. The review combines historical and current research to explore how vaccination perceptions have evolved among veterinarians and clients, and how factors such as the COVID-19 pandemic have shaped current attitudes.

The literature highlights recurring themes surrounding vaccine reluctance in veterinary settings. Client perceptions of safety, efficacy, and …

Behind The Smile: A Qualitative Study On Dentist Burnout And Workplace Satisfaction In Cache Valley, Luke Thomas Hatch

Undergraduate Honors Capstone Projects

This qualitative research study examined satisfaction, stressors, and burnout among dental professionals in Cache Valley, Utah. Eight practitioners at various points in their careers were interviewed with a range of specialties including general dentistry (n = 3), pedodontics (n = 3), oral and facial surgery (n = 1), and orthodontics (n = 1). Analysis of the interviews showed that level of clinical autonomy was a primary factor influencing burnout levels. Stress levels in more experienced practitioners and owners tended to be lower than those who worked in multiple practices (multi-doctor) or with corporations. Individuals in these environments reported higher levels …

Design And Optimization Of Peptide Inhibitors Targeting Kinesin: Molecular Modeling Studies And Virtual Screening For Therapeutic Candidate Development, Maraf Mbah Bake

Open Access Theses & Dissertations

Kinesins are ATP-driven molecular motors essential for intracellular transport and mitotic spindle assembly, and their mechanochemical behavior has been extensively characterized through computational tools. The first project reviews decades of advances in molecular dynamic simulations, including all-atom and coarse-grained molecular dynamics, Markov state models, Brownian dynamics, and free-energy approaches, which have collectively deepened our understanding of conformational transitions, microtubule-binding interfaces, and ligand interactions, especially for the mitotic motor Eg5. The second review examines the rapid emergence of quantum computing as a transformative technology for drug discovery, highlighting key historical milestones, recent progress in hybrid quantum-classical algorithms, quantum-enhanced docking, and quantum …

Determining Zap-70 Signaling Pathways Mediated By Ccr7 In Tcr T Cell Activation, Vivian Torres

Open Access Theses & Dissertations

Activation of T lymphocytes is the main event that occurs in the adaptive immune response after engagement of the T cell receptor (TCR) with the peptide of the major histocompatibility complex (pMHC) molecules that are demonstrated by antigen presenting cells [1]. A key step in this process is the recruitment and activation of the zeta chain associated protein of 70 kDa (ZAP-70). ZAP-70 couples TCR engagement to downstream intracellular signaling pathways through phosphorylation of tyrosine residues within intracellular tyrosine activation motifs (ITAMs) [2]. Although there have been extensive studies on the signaling response through TCR activation, the regulatory influence of …

Molecular Mechanisms Of Pfas Induced Protein Dysfunction: Implications For Neurodegenerative Risk, Daisy Lee Wilson

Open Access Theses & Dissertations

Per- and polyfluoroalkyl substances (PFAS) are persistent environmental contaminants with widespread human exposure and well-established links to adverse health outcomes. However, despite increasing epidemiological and experimental evidence, the molecular mechanisms underlying PFAS-induced neurotoxicity remain incompletely defined. This dissertation investigates PFAS toxicity across biological scales, integrating protein biophysics with neuronal cell models to elucidate pathways relevant to neurodegeneration. At the molecular level, we demonstrate that PFAS disrupts the structure and function of globular proteins, including the impairment of α-lactalbumin's calcium-binding capacity and of β-lactoglobulin's retinol binding, through concentration-dependent conformational destabilization. By applying these findings to a neuronal model, we show that …

Sequential Products Of Anaerobic Denitrification In Calcareous And Noncalcareous Soils By Use Of The Gas Chromatograph, Grant S. Cooper

All Graduate Theses and Dissertations, Fall 2023 to Present

The sequential products of anaerobic denitrification were determined on seven Western soils (four alkaline, two acid, and one neutral) by soil and gas analysis. The soils with 1% alfalfa and added KNO3 were incubated at moistures slightly greater than field capacity and with an atmosphere of He. The soils and gases were periodically analyzed and balance sheets prepared. The sequence of NO3-->NO2-->N2O-->N2 operated in all soils. The rates of nitrogen interchanges and maximal amounts of nitrate, N2O2 and N2 were determined. From this data it was postulated that the rate-limiting process for denitrification in acid soils is …

Evaluation Of Fertilizer Recommendation And Soil Amendment Impacts On Crop Production In The Intermountain West, Megan Baker

All Graduate Theses and Dissertations, Fall 2023 to Present

Fertilizers improve crop yield and quality by supplying crops with essential nutrients, but can also be a significant input cost. Determining what nutrients and rates to apply for optimal crop growth can be difficult, leading many growers to use external sources for these decisions. Land-grant universities are a common source for fertilizer recommendations, but often based on decades-old research and should be evaluated periodically to verify effectiveness and calibrated to current soil analysis methods. Current Utah State University (USU) guidelines for sulfur (S) and zinc (Zn) were tested across Utah in on-farm trials in 2021-2025. Zinc applications of 5 or …

Forage Responses To Biological Inoculant And Seed Rates In The Intermountain West, Roy Reid

All Graduate Theses and Dissertations, Fall 2023 to Present

Improving the efficiency of fertilizer and seed use is increasingly important for forage producers in the Intermountain West, where alfalfa and silage corn form the foundation of dairy and livestock feed. This thesis evaluates two strategies designed to boost crop productivity: microbial fertilizer coatings and variable-rate seeding.

The first study examined whether Powercoat®, a fertilizer-applied microbial inoculant, could enhance yield, forage quality, or soil phosphorus availability in alfalfa grown on four commercial fields in northern Utah. Across all locations, fertilizer increased yield at only two sites, and Powercoat did not provide additional improvements in yield, forage quality, or soil nutrient …

Post-Wildfire Erosion And Biogeochemistry: Integrating Aerial Imagery And Soil Testing To Assess Landscape Recovery, Justin A. Allred

All Graduate Theses and Dissertations, Fall 2023 to Present

After a wildfire, land managers are required to monitor large tracts of land with limited time and budgets. Traditionally, tracking landscape recovery is a time intensive process. This research explored the effectiveness of using drones (UAVs), strategic soil sampling, and computer modeling as additional tools for land managers in order to monitor the recovery more efficiently.

By using drones to collect aerial imagery and using machine learning, plant regrowth was monitored in back-to-back years. The machine learning model performed well at telling broad groups apart (trees vs grass) but it struggled to identify differences between plant species. Because many plants …

Mapping Spatial Variability For Precision Management In Utah’S Tart Cherry Orchards, Kurt T. Wedegaertner

All Graduate Theses and Dissertations, Fall 2023 to Present

Tart cherry orchards are a major part of the agricultural landscape in Utah, but producing cherries is becoming increasingly difficult and expensive. Orchard land is not uniform. Some parts of a field grow strong, healthy trees, while other parts struggle because of differences in soil, water, and landscape. Even though these differences exist, orchards are usually managed the same way everywhere. Over many years, this causes some trees to become much larger than others, making orchards harder to manage, less efficient to harvest and prune, and more costly to maintain.

This research focused on finding practical ways to measure these …

Influence Of Predation Risk On Elk Feeding Behavior In A Multi-Predator Environment, Rosemarie C. Pugh

All Graduate Theses and Dissertations, Fall 2023 to Present

Sometimes predators don’t just affect prey by killing them, they can also change how prey behave. For example, animals may spend more time watching for danger and less time eating, which could affect their health and survival. In Yellowstone National Park, past research has suggested that elk may reduce feeding because they are trying to avoid predators like wolves and cougars. However, most previous studies have only looked at elk behavior during the daytime and have often looked at responses from single predators rather than multiple.

In this study, I used high-resolution tracking collars equipped with motion sensors to directly …

Understanding Impact Of Redox Potential On Microbial Community Of Cheddar Cheese During Aging, Abrianna Y. Paez

All Graduate Theses and Dissertations, Fall 2023 to Present

Cheese ripening is a complex process that shapes the flavor, texture, and overall quality of cheese, yet many of the factors that control how these changes occur are still not fully understood. One factor that may play an important role is redox potential, which describes the balance between oxidation and reduction reactions happening inside the cheese. These reactions can influence both the activity of bacteria and the chemical processes that create flavor. Past efforts to control redox using chemical additives often harmed beneficial bacteria, limiting their usefulness.

In this study, we tested the use of mechanical disruption and gas exposure …

Food-Form Delivery Of Spore-Forming Probiotics As An Alternative To Gavage In Animal Models, Aubreyona Faith Migliori Skalka

All Graduate Theses and Dissertations, Fall 2023 to Present

Western dietary patterns are characterized by nutrient-poor, calorie-rich diets and have been linked to poor health outcomes and gut inflammation phenotypes. Probiotics are often taken to support gut health, but many beneficial bacteria do not survive transport through the digestive system to produce any effect. Spore-forming bacteria, such as Bacillus coagulans, are more resilient due to their hardy outer coat which aids in survival through many obstacles encountered in the gastrointestinal tract, including acidic stomach conditions. In research studies, probiotics are usually given to mice through a procedure called oral gavage, where a tube is used to deliver the …

Cannabis: A Model Plant To Study Light-Mediated Reproductive Development, Madigan J.H. Eckels

All Graduate Theses and Dissertations, Fall 2023 to Present

Cannabis (Cannabis sativa) is a plant of increasing importance for research, medical, recreational, industrial, and agricultural purposes, but a strict legal landscape means that it was chronically understudied. Now that research institutions can utilize this plant for study, we require updated terminology to describe various cannabis flowering types that occur under ideal and non-ideal growing conditions. We introduce new flowering terminology and describe them in text and with photographs.

Plants use light as a resource to power photosynthesis, and a greater total sum of photons generally increases yield. In controlled environment agriculture where growers utilize light fixtures instead …

Salience Network Circuit Dynamics In Distress Tolerance And Drug-Seeking Vulnerability, Marina Alicia Smoak

Open Access Theses & Dissertations

The psychological distress experienced during drug withdrawal can lead individuals with substance use disorder to abandon their goal of abstinence. Numerous human studies demonstrate that an inability to persist in challenging, goal-directed behavior while experiencing psychological distress is associated with multiple stages of substance use, including relapse. This behavioral construct is referred to as low distress tolerance (DT). Rodent models of DT similarly show that low DT predicts elevated cocaine relapse, particularly when DT is assessed following extended abstinence. This abstinence period corresponds with the incubation of craving, a phenomenon characterized by progressively increased cocaine-seeking over time. Importantly, relapse vulnerability …