Digital Commons Network^™

Robustness Of Network Inference Algorithms Under Network Class Misspecification, Roberto Ceja

Electronic Theses, Projects, and Dissertations

Inferring phylogenies in the presence of hybridization remains a difficult problem. As a result, many current methods for reconstructing phylogenetic networks are restricted to a simple class of networks known as level-1. This restriction arises from theoretical considerations rather than empirical evidence, with real data possibly arising from complex networks. In this work, we evaluate the robustness of two level-1 network inference methods, SNaQ and NANUQ+, through a simulation study, when the input data originates from a more complex network. Specifically, we investigate whether these methods can accurately recover important features of the true species network, such as the circular …

Requirement Of Prepiilin Peptidase Activity For Variovorax Paradoxus Eps Flp/Fap Pilus Assembly, Jenny L. Lanthripp

Electronic Theses, Projects, and Dissertations

Variovorax paradoxus is a Gram-negative aerobic bacterium present in both soil and the human oral microbiome. This species contributes to biotransformation of xenobiotics and promotes plant growth. Interestingly, although the genome of strain EPS lacks the flagellum operon annotated in strain S110, the microbe remains motile, and flagella can be observed microscopically. To investigate this unexpected phenotype, motility mutants were enriched from a Tn5 mutant library using a liquid culture settling strategy. A total of 122 isolates were screened for motility defects, and 57 exhibited significantly reduced motility compared to the wild type. Rescue cloning revealed that over 60% of …

Characterization Of A New Domestic Feline Macrophage Cell Line To Study Molecular Mechanisms Of Feline Coronavirus, Adam Espinoza

Electronic Theses, Projects, and Dissertations

Feline Coronavirus (FCoV) is a veterinary pathogen common in domestic cats. FCoV is transmitted via the fecal-oral route, results in mild enteric symptoms, and is considered feline enteric coronavirus (FECV). During infection the virus may transition from infecting host enteric epithelial cells to infecting host macrophages, resulting in a lethal systemic disease, and the virus is now considered feline infectious peritonitis virus (FIPV). FIPV arises in an infected individual, is not shed in the feces, and is not transmitted from cat to cat. There is limited research defining the host molecular mechanisms driving FCoV lethal outcomes, with few feline cell …

Factors Affecting Diet Selection In Sheep Fed Endophyte-Infected Toxic Fescue, Jordan Thomas

Animal Science Undergraduate Honors Theses

Tall fescue infected with endophyte‑producing fungi can induce fescue toxicosis in grazing ruminants, reducing performance and altering forage intake. Isoflavones—such as biochanin A, a major compound in red clover (Trifolium pratense)—have been proposed to mitigate these effects through improved palatability and vascular relaxation. This study examined whether inclusion of ground red clover (GRC)—either directly or combined with hydroxypropyl methylcellulose (HPMC) and polyethylene glycol (PEG)—affected voluntary diet selection in lambs offered toxic fescue.

Thirty‑two lambs were housed individually and assigned randomly to one of four diets: (1) toxic fescue silage (CONT), (2) silage + 5% GRC (RC5), (3) silage + 10% …

Engineered An Ultrasmall Curcumin Oral Nanoformulation Restores Intestinal Integrity And Gut Microbiota Dysbiosis, Vivek Sharma, Prateeksha Prateeksha, Balwant Paliya, Sateesh Gupta, Sarvendra Singh, Anand Anunay, Sushil Agrahari, Shailendra Singh, Chandana Rao, Saroj Barik, Brahma Singh

Department of Biochemistry and Molecular Biology Faculty Papers

Antibiotic therapy for bacterial infections often disrupts gut microbiota (GM) and intestinal integrity, inducing chronic inflammation and inflammatory bowel diseases. An effective therapeutic intervention is urgently needed to alleviate the aforementioned adverse effects of antibiotics. Curcumin (CUR) reveals great potential to restore intestinal integrity and GM dysbiosis due to its strong antiinflammatory and prebiotic effects. However, the weak solubility and stability of CUR result in limited bioavailability and a short half-life, which restricts its clinical uses. An ultra-small CUR oral nanoformulation was created using a carboxylated galactomannan (cGM), facilitated by hydrogen bonding between the phenolic hydroxyl groups of CUR and …

Modeling And Analysis Of Electric Signal In Neurons, Kevin J. Roberts

All Graduate Reports and Creative Projects, Fall 2023 to Present

Neurons in humans and other species transmit information by sending electric signals via axons. This process relies on the generation and propagation of action potentials—rapid changes in the membrane potential of the axon. Understanding the mechanisms of action potentials, including how they are generated and influenced by the axon geometry and material parameters, is crucial for gaining insight into neurological diseases such as Alzheimer’s and Multiple Sclerosis (diseases highly correlated to demyelination). In this work, we review and summarize mathematical models for signal transmission–including the classical Hodgkin-Huxley model, the Single Cable (SC) model, and the Double Cable (DC) model. We …

Assessing Response Diversity Of Spawning Conditions For Native Trout Among Streams To Interannual Changes In Snowpack, Autumn Kaye Zierenberg

Undergraduate Honors Capstone Projects

Stream habitat suitability for fish is controlled by physical, chemical and biological conditions impacted by interannual changes in climate. Intermittent streams are particularly sensitive to climatic variation and have long been overlooked as potential spawning habitats for fish and other riverine species. Spawning suitability in stream habitats is strongly influenced by connectivity to perennial habitats, the duration of surface flows and water temperatures, each of which are driven by annual snowpack and discharge conditions. Here, we examine how the spawning habitat suitability in different tributaries within a single river basin respond to changes in annual snowpack conditions. Specifically, we examined …

From Morphology To Machine Learning And Genomics: Understanding Phenotypic Variation In Wild Ducks, Sara Gonzalez

Open Access Theses & Dissertations

Understanding the genetic underpinning and distribution of phenotypic variation within and between divergent groups is core towards shedding light into how populations diverge and adapt, as well as how hybridization breaks or builds on these scenarios; and thus, central to evolutionary biology. In wild organisms, however, quantifying and linking phenotypic traits to underlying genetic processes, like mutation, gene expression, epigenetics and allele interactions, remains challenging. This difficulty arises from the complex interplay between morphology, environment, and gene regulation, as well as the logistical barriers of collecting and standardizing large-scale data across individuals and populations. As a result, researchers are increasingly …

What Limits Dryland Ecosystems? Patterns Of Soil Fertility And Resource Limitation In The Chihuahuan Desert, Dylan Stover

Open Access Theses & Dissertations

Human activities are substantially altering global resource cycles with widespread implications for biogeochemistry and ecosystem functioning globally. Drylands, regions where precipitation is outweighed by water losses, are especially sensitive to these large shifts in resource cycles due to their inherently low and variable resource availability. In these regions, resource availability and biological activity are often concentrated around plants – or fertile islands – and predominantly driven by pulses of water. However, our knowledge of the processes influencing biological productivity in drylands – patterns of soil fertility and resource limitation – remains lacking, and their unique biogeochemical and biological processes create …

Analyzing The Impact Of Diet On Dusky Gopher Frog (Lithobates Sevosus) Development In Head Start Programs, Mckalyn Nelson

Honors Theses

Species are constantly impacted by human activity, directly or indirectly. One critically endangered species under investigation is the dusky gopher frog (Lithobates sevosus), which is an endemic species of frog found in the southeastern United States. Historically found from Louisiana to Alabama, a drought in 2002 narrowed the dusky gopher frog range even further. Head start programs have been shown to be effective in increasing population numbers; however, there is not much published data on the effectiveness of captive rearing diets for these programs. The dusky gopher frog head start program at the University of Southern Mississippi’s Lake …

Exploring Life History Trade-Offs In The Facultative Eusocial Bee Megalopta Genalis, Ana Gutiérrez Zuluaga

All Graduate Theses and Dissertations, Fall 2023 to Present

Organisms face many trade-offs in how to invest in these traits. One example is the trade-off between reproduction and longevity. Queens of social insects seem to escape this trade-off, producing thousands of eggs daily, despite having a longer lifespan than their workers. Some hypotheses have been proposed to explain this phenomenon, such as an evolutionary change in the molecular pathways that regulate queen investment in maintenance, growth, and reproduction. An alternative hypothesis suggests that the tradeoffs are rarely observed in queens due to the extensive resources provided by the help of workers. While these hypotheses have supporting evidence, they have …

Integrating Manager Perspectives Into The Evaluation Of Wetland Revegetation Strategies, Loren F. Taylor

All Graduate Theses and Dissertations, Fall 2023 to Present

Ecological restoration is the process of assisting the recovery of an ecosystem that has been degraded and is dependent on complex and context-specific decisions. The decision-making process influencing restoration is rarely examined alongside ecological processes. There is a need for research that incorporates the social, economic, institutional, and logistical considerations that shape real-world practices, as well as ecological processes. Decisions made by restoration practitioners and land managers (hereon “manager”) are challenged by the lack of information shared regarding the practical constraints (e.g., cost, labor, specialized equipment) they face. Revegetation, particularly in wetlands, poses challenges due to site conditions and degradation …

Golden Eagle Predation Of Greater Sage-Grouse On Diamond Mountain Plateau, Victoria E. Thorpe

All Graduate Theses and Dissertations, Fall 2023 to Present

Predation and the perceived risk of predation can have major impacts on prey populations. Golden Eagles are considered one of the main predators of adult greater sage-grouse. Sage-grouse populations have been declining for decades throughout the West and wildlife managers are concerned about the impacts of golden eagles on sage-grouse. We investigated the nonconsumptive effects of golden eagles on sage-grouse by conducting observational surveys for golden eagles, sage-grouse, and other predators at sage-grouse lek sites near Vernal, Utah during the sage-grouse breeding season from 2022–2024. Additionally, we examined the prevalence of sage-grouse in golden eagle diet using DNA metabarcoding of …

From Mechanisms To Management: Implications Of Biogeochemical Controllers And Land Management For Soil Carbon Cycling And Storage, Savannah R. Adkins

All Graduate Theses and Dissertations, Fall 2023 to Present

Climate change and its cascading effects are driven by increases in atmospheric carbon dioxide (CO₂). Many climate solutions exists to remove this excess carbon (C) from the atmosphere, and soils, in particular, represent one of the few win-win solutions. Soils play a vital role in the global C cycle because they store more C than plants and the atmosphere combined, however, they also release more CO₂ annually than fossil fuel combustion (a major contributor to accelerating climate change). Therefore, preventing CO₂ loss from soil could help slow the progression of climate change, and increasing overall soil …

Heating Methods To Advance Primocane Emergence And Yields In Red Raspberries, Alyssa Palmer

All Graduate Theses and Dissertations, Fall 2023 to Present

Raspberries are an important high value crop for local markets in Utah and throughout the Intermountain West. However, Utah’s harsh winter and short growing seasons present challenging growing conditions. New primocane-bearing cultivars are becoming available, but many of these produce fruit later than what is needed for local markets. Protected cultivation offers the opportunity to give more consistent production under Utah’s difficult growing conditions for berry crops. Protected cultivation methods include high tunnels, low tunnels and row covers. In addition to protecting against damaging temperatures, protected cultivation also advances crop growth through warming the soil and plants. Combinations of heating …

Lagomorphs, Ungulates, And Predation: Exploring Interactions And Quantifying The Effect Of Lagomorph Herbivory In Rangelands, Shantell Marie Garrett

All Graduate Theses and Dissertations, Fall 2023 to Present

Rangelands are expansive ecosystems that make up more than 30% of the total surface land area in the contiguous United States. In the west, they are typically categorized as shrublands, grasslands or deserts with low precipitation. The vegetation communities consist largely of grasses and forbs and are thus widely used for livestock grazing. Despite their barren appearance, rangelands are diverse ecosystems that are home to a wide breadth of species.

The Henry Mountains, located in south central Utah, is one example of this system type. With their inspiring red-rock mesas and towering plateaus, this public land, managed by the Bureau …

Impacts Of Including Sprouted Barley In The Diet Of Beef Cattle On Production, Ruminal Health, And Meat Quality, Zachary C. Crump

All Graduate Theses and Dissertations, Fall 2023 to Present

Beef producers in the United States are working to meet rising global demand for animal protein while facing major challenges such as drought, climate uncertainty, and rapid urbanization. These issues make it difficult to produce consistent and dependable feed, pushing producers to explore new ways to grow feed using fewer natural resources. Vertical farming systems are one option that can grow sprouted cereal grains indoors throughout the year while using decreased land and water than traditional agriculture. Sprouted barley grows within six to seven days and may serve as a nutrient dense alternative feed source for cattle at several stages …

Biocontrol Of Canada Thistle (Cirsium Arvense) With The Rust Fungus, Puccinia Punctiformis In The Intermountain West: Integrated Weed Management Compatibility And Characterization Of Microbiome Associations, Caitlin Henderson

All Graduate Theses and Dissertations, Fall 2023 to Present

Canada thistle (Cirsium arvense) is an invasive weed of major concern in both agricultural and native areas. It competes against native plants, reduces crop production and quality, and causes significant costs in management and damages. Canada thistle can survive and spread through seeds, but primarily does so through its extensive root system, which causes the greatest management difficulties. There are several control methods for this invasive weed, herbicides are perhaps the most common and effective, however, they have limitations and negative consequences. Herbicide use near waterways is restricted and there are growing concerns of the development of herbicide …

Investigating Pyrethroid Insecticide Resistance In The Alfalfa Pest Insects Hypera Postica (Alfalfa Weevil) And Lygus Spp. (Lygus Bugs) In Utah Alfalfa Fields, Rosalie Sepesy

All Graduate Theses and Dissertations, Fall 2023 to Present

Chemical insecticides are commonly used to manage the damage to crops caused by agricultural pest insects. Reliance on insecticides for pest management has resulted in insecticide resistance in many insect species worldwide. Alfalfa weevils (Hypera postica) and lygus bugs (species within the genus, Lygus), are major pests to alfalfa hay and seed respectively and cause significant economic damage. The goal of this dissertation was screen Utah alfalfa fields for resistant alfalfa weevil and lygus bug populations, investigate genetic mutations that can influence resistance in alfalfa weevils, and establish which species of lygus bugs are present in Utah …

The Effects Of Lactoferrin And Iron-Enriched Whey On Iron Status Of Collegiate Females, Connor Kemp

All Graduate Theses and Dissertations, Fall 2023 to Present

Iron deficiency has remained a global issue even in developed countries despite food fortification and increased nutritional literacy, biological women of child baring age are at particular risk due to menstruation and reduced dietary intake of iron containing foods compared to men. This issue is of particular concern in athletics due to the critical role of iron in oxygen transport and energy metabolism. With nearly half of female athletes presenting low iron status iron supplementation is often necessary. With iron supplementation often resulting in gastrointestinal symptoms that could negatively impact sport performance itself there is a need to explore other …

Understanding Impact Of Starter Culture Blends On The Ph Variation In Cheddar Cheese During Early Aging, Samuel J. Clarke

All Graduate Theses and Dissertations, Fall 2023 to Present

Consumer expectations govern what is acceptable when it comes to the flavor, texture, and color of the cheese. These quality attributes of cheese are all influenced by the pH of the cheese which is in turn controlled by the acid production of the starter lactic acid bacteria (SLAB) used to make cheese. Whatever the final pH of the cheese is, is what determines the quality of the cheese. Unfortunately, there are some Cheddar cheese manufacturers that have observed pH variation during the early aging of their cheeses. We hypothesize that the addition of thermophilic, fast-acid producing bacteria, like Streptococcus thermophilus …

Differential Microrna Profiling Of Blood L1cam And Bulk Extracellular Vesicles In Bipolar Disorder, Gabriel R Fries, Salahudeen Mirza, Jun Wang, Camila N C Lima, Wei Zhang, Marcela Carbajal Tamez, Giselli Scaini, Jair C Soares, Joao Quevedo

Faculty, Staff and Student Publications

Objective: This preliminary study aimed to identify microRNA (miRNA) signatures associated with bipolar disorder (BD) by profiling blood-derived extracellular vesicles (EVs) of both putative neuronal origin and from all sources.

Method: In two parallel studies of individuals with BD and controls (CON), we characterized miRNA expression profiles of blood EVs selected for L1CAM, a putative marker of neuronal origin (n = 20 BD/20 CON), as well as bulk EVs (n = 21 BD/20 CON). For each study, analyses identified miRNAs differentially expressed between groups, followed by functional interrogation and testing for associations with clinical features.

Results: Results of …

Sleep-Disordered Breathing Subtypes And Future Diet Quality In The Multi-Ethnic Study Of Atherosclerosis, Kaitlin S Potts, Cecilia Castro-Diehl, Tianyi Huang, Alexis C Wood, Jerome I Rotter, Stephen S Rich, Tamar Sofer, Susan Redline, Heming Wang

Children’s Nutrition Research Center Staff Publications

Objectives: Sleep-disordered breathing (SDB) and diet quality impact cardiometabolic disease, but few studies have examined if SDB influences diet quality. This study estimated the association between SDB subtypes (with and without sleepiness) and future diet quality in the Multi-Ethnic Study of Atherosclerosis.

Methods: Probable SDB was characterized by self-reported physician-diagnosed sleep apnea (PDSA) or habitual snoring and subtyped by presence or absence of sleepiness. A food frequency questionnaire measured diet 1.6 years before, and 7.8 years after SDB assessment. Diet quality was measured with the Alternate Healthy Eating Index-2010 (AHEI). Mean differences in AHEI at follow-up by SDB subtypes were …

Hyperspectral Indicators And Characterization Of Glyphosate-Induced Stress In Common Lambsquarters (Chenopodium Album L.), Mario Andrés Soto Valencia

Graduate Theses and Dissertations

Hyperspectral sensing enables detection of herbicide stress in weeds, but practical use requires strategies for redundancy control, rating variability management, and evaluator bias mitigation. This thesis evaluates common lambsquarters (Chenopodium album) under glyphosate exposure, aiming to identify key wavelengths, construct vegetation indices, and improve injury modeling. Greenhouse experiments used dimensionality reduction methods (principal component analysis, Relief F, Bayesian discriminant analysis) to isolate 34 unique wavelengths from about 3,200 bands. Calibration data were collected 14 days after treatment (DAT) to support wavelength selection and model development, while data from 27 DAT were used for independent validation. Class comparisons across six statistically …

Transcriptomic And Contractile Adaptations In Skeletal Muscle In A Rodent Model Of Anorexia Nervosa, Oscar Armando Vicen

Graduate Theses and Dissertations

BACKGROUND: Anorexia Nervosa (AN) is a psychiatric disorder marked by severe chronic caloric restriction and is primarily diagnosed through psychological and behavioral symptoms. AN has the highest mortality of any psychiatric disorder with an increased risk of all-cause mortality. Many individuals with a history of AN experience incomplete recovery despite intervention treatment. Skeletal muscle molecular mechanisms under chronic energy deprivation remain poorly understood. PURPOSE: To investigate transcriptomic profiles of the gastrocnemius muscle following one month of a rodent model of AN. This study analyzed whether the molecular changes correlate with collected muscular force data to provide a comprehensive understanding of …

Predictive Modeling Of Listeria Monocytogenes Growth In Ready-To-Eat Meat Products, Manjari Singh

Graduate Theses and Dissertations

Listeria monocytogenes remains a significant food safety concern in ready-to-eat (RTE) meat and poultry products due to its persistence under refrigerated and stressed conditions. Predictive models play a vital role in risk assessment and food safety management; broth models are highly conservation & results in overprocessing. This thesis focuses on developing and validating meat-specific predictive models for Listeria monocytogenes growth and lag for RTE beef, pork, and poultry products. Matrix-specific secondary models were built to predict the maximum specific growth rate (μmax) of Listeria monocytogenes under varying environmental conditions, including temperature, pH, water activity, salt, organic acids, and nitrites. Growth …

Broiler Responsiveness To Dietary Amino Acid Density In A Commercial Setting, Virginia Slick

Graduate Theses and Dissertations

The majority of research assessing the amino acid responsiveness in broilers has been conducted in experimental designs utilizing pens that contain 12 to 25 birds with high replication. While this trial design is beneficial as a way to perform high replications with multiple treatments in a way that is both economically and spatially feasible, it may not accurately translate to a rearing environment more similar to that of commercial open floor housing. This research was conducted to determine if the effects of lysine driven amino acid density diets that have been found in the traditional floor pen setting correlate to …

Impact Of Polystyrene Nanoplastics On Oncogenic Signaling Pathways In Prostate Cells, Luis Alfonso Adel-Alvarez

Open Access Theses & Dissertations

Prostate cancer (PC) remains the most prevalent malignant disease among the male population worldwide, with a dramatic increase observed in the European Union from the 1980s to the 2000s. The etiology of PC is attributed to both hereditary factors and environmental pollutants. Among these, endocrine disruptors and polystyrene nanoparticles (PSNPs) interact with the prostate gland via the circulatory system, inducing intense oxidative stress. This study aims to characterize, for the first time, the pathobiological effects of PSNPs in both non-malignant (RWPE1) and malignant (22RV1) prostate cell lines. The objective was to elucidate the mechanisms by which environmental pollutants, such as …

Enduring Efffects Of Juvenile Fluoxetine Exposure On Serotonin Transporter Expression Within The Hippocampus And Prefrontal Cortex Of Male C57bl/6 Mice, Daniel Eduardo Calvo

Open Access Theses & Dissertations

Prescription rates of fluoxetine, the most dispensed selective serotonin reuptake inhibitor, have been rising among the juvenile population. Since adolescence is a critical developmental period in which the brain undergoes pruning, chronic increases in serotonin levels may lead to long-term neurobiological changes in brain regions responsible for emotional regulation. Thus, using mice as a model system, this thesis evaluated how adolescent fluoxetine exposure (AFE) influences the expression of serotonin transporters (SERT) in the adult hippocampus and prefrontal cortex. To do this, postnatal day (PD)-35 male C57BL/6 mice were administered with fluoxetine (250 mg/l in their drinking water) for 15 consecutive …

Advancing Trypanosoma Cruzi N-Myristoyltransferase As A Drug Target For Chagas Disease Through In Silico Discovery And Biochemical Evaluation, Diana Citlali González García

Open Access Theses & Dissertations

Chagas disease remains one of the most persistent and neglected parasitic infections in the Americas, advancing silently through the intracellular replication of Trypanosoma cruzi amastigotes and the invasive spread of trypomastigotes. The survival of the parasite is critically reliant on protein N-myristoylation, a lipid modification catalyzed by N-myristoyltransferase (NMT). This dissertation aims to advance beyond prior studies by systematically investigating NMT inhibition across multiple biological levels, spanning from the characterization of the purified enzyme, through cellular infection models, to the global proteomic remodeling induced within the parasite, thereby evaluating TcNMT as a potential therapeutic vulnerability in T.cruzi.Recombinant TcNMT was expressed, …