Life Sciences Commons^™

A Comparative Analysis Of Small Nuclear Rna Sequences In Spinacia Oleracea, Arabidopsis Thaliana, And Homo Sapiens, Nhi T. Nguyen

2025 Spring Honors Capstone Projects - Archive

In eukaryotes, the structure and function of the Sm core and its associated small nuclear ribonucleoproteins (snRNPs) play a significant role in pre-mRNA splicing. These snRNPs exhibit a high degree of conservation. While plants also utilize alternative splicing, the conservation of plant snRNAs and other non-coding RNA such as snoRNA and scaRNA, which assemble the Sm core, remains largely unexplored. In this study, plant sequences were compared with human sequences using the multiple sequence alignment program Jalview to determine the conservation of snRNPs in other non-coding RNA. Sequences analysis showed that the Sm site in Spinacia oleracea and Arabidopsis thaliana …

Elucidating The Role Of Transposable Element Derived Gene, Dplg3, In Drosophila Melanogaster, Kaisy A. Martinez

2025 Spring Honors Capstone Projects - Archive

A big fraction of most eukaryotic genomes is comprised of transposable elements (TEs). TEs are mobile genetic sequences often causing deleterious effects as they increase in copy number. On rare occasions, TEs can undergo molecular domestication, where the TE proteins are co-opted by the host to serve cellular functions. In Drosophila melanogaster, domestication from PIF/Harbinger TEs has resulted in five Drosophila PIF-Like Genes (DPLG1-4 and 8). This study focuses on investigating the function of DPLG3. In DPLG3 knock out lines, DPLG3-KO, a fraction of the progeny shows an abnormal gonad phenotype. We sought to confirm …

Assessing The Prevalence Of Ehrlichia Spp. In Ticks Associated With Canids In Arkansas, Eva J. Berryhill

Animal Science Undergraduate Honors Theses

Canine ehrlichiosis is a disease that is commonly seen in dogs. In previous studies, the southeastern part of the United States has been identified as an area of high prevalence. Arkansas was included in the region where the prevalence is high. Changes in climate, household income, and tick population were identified as factors contributing to this high prevalence. Canine ehrlichiosis is caused by three Ehrlichia spp., which are E. canis, E. ewingii, and E. chaffeensis. Ticks are responsible for transmitting the disease, specifically R. sanguineus, D. variabilis, and A. americanum. For this study, the goal was to determine the prevalence …

Utilizing 16s Ribosomal Rna Sequencing To Identify Bacterial Species Colonizing Lame Birds With Bacterial Chondronecrosis With Osteomyelitis, Kara Hoover

Animal Science Undergraduate Honors Theses

Broiler chicken lameness has become prevalent in recent years due to high growth rates in broilerchickens. Bacterial chondronecrosis with osteomyelitis (BCO), the main cause of lameness, is characterized by necrosis of femoral and tibial heads in affected birds. Heavier birds are more susceptible to mechanical stress in these regions, which results in microfractures, leading to lameness. BCO lameness poses huge financial pressure to the poultry industry, as 14-50% of flocks can become affected during outbreaks. The purpose of this experiment was to identify bacterial species present in birds with BCO lameness. A total of 1,560 chicks were randomly distributed into …

The Effect Of 1,25-Dihydroxyvitamin D3 Supplementation On Humoral Immunity Against Bacterial Chondronecrosis With Osteomyelitis Lameness In Broiler Chickens, Bailey Herberger

Animal Science Undergraduate Honors Theses

Bacterial chondronecrosis with osteomyelitis (BCO) lameness, the most predominant locomotive illness in fast-growing broilers, causes substantial animal well-being issues and affects broiler production, leading to huge financial losses. Several strategies, including feed supplementations using organic trace minerals, vitamin D, probiotics, and prebiotics, have been utilized to alleviate BCO lameness incidences in broiler chickens. Previous studies have indicated that feeding an additive of Panbonis^®-G-1,25(OH)₂D₃ from Solanum glaucophyllum containing 1 µg/kg G-1,25(OH)₂D₃ to broilers for the first 28 days of their production cycle reduced BCO lameness by more than 50%. In this study, we …

Uncovering The Evolutionary Origins Of Neo-Sex Chromosomes In The Insect Family Membracidae, Mary Kumah

2025 Spring Honors Capstone Projects - Archive

This research explores the evolution of the neo-XX/XY sex chromosome system of Amblyophallus exaltatus, a treehopper insect in the family Membracidae. Neo-XX/XY sex chromosome systems can evolve from an XX/X0 sex chromosome system via fusion events between the X chromosome and an autosome. Although cytological work has indicated the presence of a neo-XX/XY system within A.exaltatus, the chromosomal identity of the fused autosome and the molecular drivers behind this chromosomal fusion remain poorly understood. By performing a coverage analysis with whole genome sequence data, the parts of the A.exaltatus genome that fused with the X chromosome will be better …

Establishing Methods For In Vitro Static Culture Of Gut Microbiomes For Nutritional Intervention Studies, Jeremy Mathew Case

Undergraduate Honors Capstone Projects

Lipid oxidation products (LOPs), which form during high-heat processing of oils common in Western diets, are known to cause inflammation and cellular damage. While LOPs have been implicated in exacerbating colitis and promoting colon tumorigenesis in mouse models, their direct impact on the gut microbiome remains poorly understood. This capstone project aimed to develop a low-cost in vitro protocol to culture the mouse gut microbiome under anaerobic conditions, enabling future investigations into the direct effects of bioactive dietary compounds such as LOPs. The study also assessed whether viable microbial communities could be recovered from fecal samples stored at -80°C. Fecal …

Phylogeny And Historical Biogeography Of Uroleucon Aphids, Audrey Michelle Mullen

Undergraduate Honors Capstone Projects

The aphid genus Uroleucon (Aphididae: Aphidinae: Macrosiphini) is a diverse group of about 230 species found globally in most temperate regions, principally in the northern hemisphere. Only 23 species are described from the southern hemisphere, in South American temperate regions such as Chile, Argentina, and Peru. However, the origins of the South American species are unknown, as are the relationships of these taxa to northern hemisphere Uroleucon species. This study seeks to establish the relationships between Uroleucon aphids native to South America and their North American and Eurasian counterparts using genetic data. We use phylogenetic analysis of cytochrome c oxidase …

Adaptation Of Influenza A Virus Strains A/Anhui/1/2013 (H7n9) And A/Shanghai/1/2013 (H7n9) For Development Of Effective Mouse Models, Spencer T. Mullen

Undergraduate Honors Capstone Projects

The emergence of avian Influenza A (H7N9) virus strains in humans poses a significant threat to human health globally due to their pandemic potential, limited human immunity, and lack of virus-specific interventions. This capstone aims to address some of the limitations in antiviral research regarding Influenza A H7N9 virus by adapting two low-pathogenic virus strains A/Anhui/1/2013 (H7N9) and A/Shanghai/1/2013 (H7N9) to BALB/c mice through sequential passaging through lung tissue. Following 12 serial passages, increased virulence was observed as evidenced by increased virus replication, increased weight loss, and increased mortality in infected mice. Titration of the initial non-adapted virus isolates were …

Creating A Stat2 Knock-Out Rat With Crispr/Cas9 Using I-Gonad, Isabella Dejesus

Undergraduate Honors Capstone Projects

Through the use of genetically modified animals, a more holistic understanding of physiologic responses to various diseases and pathologies can be obtained^7,19. The STAT2 gene encodes a protein called Signal Transducer and Activator of Transcription 2 and is an excellent target for genetic manipulation due to its essential role in type I and III interferon signaling pathways¹¹. A member of the STAT family of transcription factors, this protein is directly involved in mediating cellular responses to various cytokines and growth factors, particularly those related to the innate immune response¹¹. While the STAT2 signaling pathway …

Investigation Of Immune/Performance Trade-Offs In Neonate Children's Pythons (Antaresia Childreni), Ellie Hartman

Undergraduate Honors Capstone Projects

Energetic costs and constraints are key considerations when analyzing an organism’s life history and may require trade-offs to be made between different life history traits. One of these trade-offs occurs between investment in immunity and performance. The purpose of this study is to discover if this trade-off influences behavior in neonate Children’s pythons (Antaresia childreni). We hypothesize that snakes undergoing an immune response will have reduced behaviors promoting survival. To test this hypothesis, neonate Children’s pythons were randomly assigned to receive an immune challenge of keyhole limpet hemocyanin (KLH) or a vehicle injection as a control. Two days …

Ethical Concerns And Implications Of Expanded Carrier Screening, Emily Andres

Undergraduate Honors Capstone Projects

The rapid evolution in the field of genetics is often met with uncertainty and skepticism. With the advancements in genetic technologies, expanded carrier screening (ECS) has emerged as a powerful tool in reproductive medicine. Traditionally, carrier screening was provided less broadly, often relying on ethnic-based approaches. However, further advancements have deemed this practice no longer equitable or widely accepted. While ECS provides prospective parents with insight into their genetic risk and may prevent severe genetic conditions, it also raises serious ethical questions for many. These concerns span medical, political, and societal facets including medicalization, defining severity, abortion, legislation, insurability, the …

Survey Of Insect Pests On Cut Flowers In Utah, Elliot Roberts

Undergraduate Honors Capstone Projects

Cut flower production is a relatively new industry in the state of Utah, gaining momentum by 2020. However, little research concerning management of the crops and their pests has been conducted. One issue producers face are insects that harm the plants in ways such as feeding damage and transmission of diseases. Currently, it is unknown which insects target different species of cut flowers in Utah. Morphological identification of genera and species is often difficult or impossible because of the small size of many of the insects and minute differences between species. This project uses PCR and DNA sequencing to identify …

Evaluating The Economic Viability Of Feeding Hydroponic Barley Fodder To Growing Wethers, Fallon Johnson

All Graduate Reports and Creative Projects, Fall 2023 to Present

As the livestock industry combats challenges including rising feed costs and ensuring sustainable production practices, some attention is being given to hydroponic fodder as a feed source. Hydroponic fodder offers a potential alternative to traditional feed sources. Research has demonstrated hydroponic fodder production has increased water efficiency while providing a sustainable green feed source throughout the year. This study seeks to understand how using hydroponically produced barley fodder in a total mixed ration for growing wethers compares economically to feeding traditional feed sources. A stochastic simulation model is used to determine the expected total feed costs, costs of gain, and …

Mechanisms Of Particulate Hexavalent Chromium-Induced Inhibition Of Homologous Recombination Repair: Targeting The Bcdx2 Complex Considered Through A One Health Perspective., Aggie W. Brownell

Electronic Theses and Dissertations

Lung cancer remains the leading cause of cancer death, often linked to smoking. However, smoking alone does not account for all cases. Exposure to environmental metals like hexavalent chromium [Cr(VI)] also contributes to lung cancer. Cr(VI) causes lung cancer by inducing chromosome instability (CIN), an early hallmark of its carcinogenic mechanism. While it has been established that Cr(VI) induces chromosome instability, the precise mechanisms underlying the chromosome instability are poorly understood. This dissertation investigates the mechanisms of carcinogenesis associated with zinc chromate, a particularly potent particulate form of hexavalent chromium. Studies show Cr(VI) induces DNA double-strand breaks and impairs the …

Genetic Influence Of Allelic Variation On The Phenotypic Variability Of Cognitive Outcomes In Individuals With Williams Syndrome., Marinie P. Joseph

Electronic Theses and Dissertations

Williams syndrome (WS) is caused by a rare microdeletion of 25 – 27 genes on chromosome 7q11.23, characterized by a distinctive cognitive profile with considerable phenotypic heterogeneity. However, the genetic factors underlying this phenotypic variability remain unclear. I explored two genetic mechanisms—parent-of-origin (PoO) effects and genome-wide polygenic variation, as measured by polygenic scores (PGSs)—to elucidate possible influences on cognitive variability in WS. The first study examined PoO effects on cognitive abilities in two overlapping samples of children with WS (N = 211, N = 251). PoO refers to which parental homolog of chromosome 7 contains the WS deletion. Despite …

Kinasefusiondb: An Integrative Knowledge Of Kinase Fusion Proteins In Multi-Scales, Himansu Kumar, Zikang Chen, Abayomi Adegunlehin, Loren Trowbridge, Leonardo Aguilar, Pora Kim

Faculty, Staff and Student Publications

Kinase fusion genes were the most targeted fusion gene group among multiple major cellular gene groups. Kinase inhibitors disrupt aberrant signaling cascades and inhibit tumor progression, yet the specific mechanisms of action of the U.S. Food and Drug Administration (FDA)-approved inhibitors in the context of kinase fusion oncoproteins remain largely unknown. This gap limits our ability to develop personalized therapies and next-generation kinase inhibitors. To address this, we developed a novel in silico pipeline for predicting 3D structures of kinase fusion proteins and performing structure-based virtual screening. This approach enables large-scale structural annotation and drug screening across pan-cancer kinase fusions. …

Ai Model For Predicting Asthma Prognosis In Children, Elham Sagheb, Chung-Il Wi, Katherine S King, Bhavani Singh Agnikula Kshatriya, Euijung Ryu, Hongfang Liu, Miguel A Park, Hee Yun Seol, Shauna M Overgaard, Deepak K Sharma, Young J Juhn, Sunghwan Sohn

Faculty, Staff and Student Publications

BACKGROUND: Childhood asthma often continues into adulthood, but some children experience remission. Utilizing electronic health records (EHRs) to predict asthma prognosis can aid health care providers and patients in developing effective prioritized care plans.

OBJECTIVE: We aimed to develop artificial intelligence (AI) models using various clinical variables extracted from EHRs to predict childhood asthma prognosis (remission vs no remission) in different age groups.

METHODS: We developed AI models utilizing patients' EHRs during the first 6, 9, or 12 years of their lives to predict their asthma prognosis status at ages 6 to 9, 9 to 12, or 12 to 15 …

Bmal1-Hif2a Heterodimer Modulates Circadian Variations Of Myocardial Injury, Wei Ruan, Tao Li, In Hyuk Bang, Jaewoong Lee, Wankun Deng, Xinxin Ma, Cong Luo, Fang Du, Seung-Hee Yoo, Boyun Kim, Jiwen Li, Xiaoyi Yuan, Katherine Figarella, Yu A An, Yin-Ying Wang, Yafen Liang, Matthew Deberge, Dongze Zhang, Zhen Zhou, Yanyu Wang, Joshua M Gorham, Jonathan G Seidman, Christine E Seidman, Sary F Aranki, Ragini Nair, Lei Li, Jagat Narula, Zhongming Zhao, Alemayehu A Gorfe, Jochen D Muehlschlegel, Kuang-Lei Tsai, Holger K Eltzschig

Faculty, Staff and Student Publications

Acute myocardial infarction is a leading cause of morbidity and mortality worldwide1. Clinical studies have shown that the severity of cardiac injury after myocardial infarction exhibits a circadian pattern, with larger infarcts and poorer outcomes in patients experiencing morning-onset events2–7. However, the molecular mechanisms underlying these diurnal variations remain unclear. Here we show that the core circadian transcription factor BMAL17–11 regulates circadian-dependent myocardial injury by forming a transcriptionally active heterodimer with a non-canonical partner—hypoxia-inducible factor 2 alpha (HIF2A)12–16—in a diurnal manner. To substantiate this finding, we determined …

Strategies For Increasing Methane Removal In Methanotroph Bench-Scale Systems For The Production Of Ectoine, Jaden Storrer

All Graduate Theses and Dissertations, Fall 2023 to Present

Anthropogenic methane emissions contribute to the greenhouse gas profile which is the chief cause of climate change. One significant source of methane emissions is biogas produced from bacteria in wastewater facilities and landfills. Methane rich biogas has the potential to be valorized into high value bioproducts by using methanotrophs (microbes that use methane as their primary carbon source). Methylotuvimicrobium alcaliphilum 20Z was selected for this study as it can generate ectoine when grown in highly saline environments. Ectoine has been proven to have many benefits such as it prevents protein denaturation, it has hydration properties, and is a UV protectant. …

Electromagnetic Sensor Sampling Volumes And Water Content Calibration In Coarse-Textured Porous Media Using Layered Mixing Theories, Chieh Yun Chang

All Graduate Theses and Dissertations, Fall 2023 to Present

Measuring soil water content is crucial for various applications, such as agriculture and environmental monitoring. Scientists use sensors that rely on electromagnetic waves to estimate soil water content by measuring the dielectric of media. However, factors, including the frequency of the sensor's measurements, soil particle size and distribution, and the soil's electrical conductivity, can affect the dielectric measurements and, consequently, the accuracy of the water content estimation. To improve the accuracy of electromagnetic-based sensors, it is important to calibrate them properly and understand their sensing volume to ensure the use of an appropriately sized calibration container. In this study, we …

Analyzing Microalgae-Bacteria Population Changes In Response To Environmental Parameters For Improved Wastewater Treatment, Amanda M. Moravek

All Graduate Theses and Dissertations, Fall 2023 to Present

Microalgae are incredible organisms that have a variety of uses such as wastewater treatment, fertilizer, livestock feed, and bio-compound production. Microalgae require a light source and minimal nutrients space to proliferate, making them an environmentally friendly and sustainable option for such processes. The Sustainable Wastes-to-Bioproducts Engineering Center at Utah State University is developing and implementing a Rotating Algae Biofilm Reactor (RABR) to remove total nitrogen and phosphorous from the Central Valley Wastewater Reclamation Facility wastewater effluent. Harmful compounds such as nitrates and phosphates are metabolized by the microalgae and converted into useful bioproducts, resulting in a circular economy. These RABRs …

Seeding Rate, Planting Date, And Herbicides For Dormant Seeded Safflower In Utah, Rodney Daniel Nelson

All Graduate Theses and Dissertations, Fall 2023 to Present

Dryland crop production in the Intermountain West is largely limited by the amount of precipitation received. Increasing dryland safflower (Carthamus tinctorius L.) production yields in a semi-arid climate is possible with a dormant planting but is not well understood. A two-year (2020-22) project was designed to gain an understanding of the effects of variety, seeding rate, and planting date, on dormant seeded safflower. Chemical weed control options for safflower were also evaluated. One study, conducted at three Utah State University research farms near Blue Creek, Clarkston, and Kaysville, UT, evaluated four varieties, S-208, S-333, 7325 and Hybrid-446, seeded at …

Uv-A Light And Heat-Activated Antimicrobial And Biodegradable Materials For Food Packaging And Preservation, Michael J. Bodily

All Graduate Theses and Dissertations, Fall 2023 to Present

Current food packaging materials are often non-biodegradable and harmful for ingestion, which poses a threat to the environment and public health. Thus far, the dangers of microbial contamination of food on human health have outweighed the risks associated with using these conventional packaging plastics. A possible solution to these issues is to use a combination of innovative materials and microbial inactivation methods that can potentially both reduce plastic waste and combat harmful microorganisms. In this study, two antimicrobial, biodegradable composites were developed and tested for their ability to inactivate two types of bacterium, Escherichia coli K12 and Listeria innocua, …

Screening Of A Diversity Of Legumes And Non-Legumes Forb Species At Five Strategic Locations Across Utah For The Development Of Smart Foodscapes, Surbhi Verma

All Graduate Theses and Dissertations, Fall 2023 to Present

Grass-dominated rangelands in the Western United States often lack sufficient protein for pregnant cows after grasses mature in mid- summer, leading ranchers to rely on expensive feed supplements such as protein cubes or alfalfa hay. The goal of this study was to screen 27 perennial legume and forb species with the potential to remain green into late summer and provide sufficient protein to supplement cows on grass-dominated rangeland. Three experiments were carried out to understand germination of species, plant establishment and persistence at five Utah locations, and agronomic characteristics. The seed of five hard-to-germinate species were studied for the ability …

Gone With The Flow: Flow Reduction Coincides With Reduced Metabolism And Standing Stock Of Benthic Algae And Macroinvertebrates In Desert Rivers, Chloe E. Lyles

All Graduate Theses and Dissertations, Fall 2023 to Present

River metabolism, the measure of energy flow in a river, is driven by hydrological and physicochemical regimes (e.g., temperature, turbidity, and nutrients). However, these regimes are increasingly altered by human water demand and climate change-driven drought. These stressors alter the magnitude, timing, and duration of critical spring-snowmelt floods with poorly understood consequences on ecosystem function, particularly in desert rivers. To investigate the linkages between flow reduction, river metabolism, and basal food resource productivity (i.e., algae and aquatic invertebrates), we measured metabolism and basal resource availability in seven desert tributaries with varying degrees of flow reduction during low-flow conditions in 2023 …

Understanding The Impact Of Colloidal Calcium Phosphate On The Ph Variation In Cheddar Cheese During Early Stages Of Aging, Rachel Lindstrom

All Graduate Theses and Dissertations, Fall 2023 to Present

The Cheddar cheese industry has recently observed variation in the pH of their cheese during the early stage of storage. This variation may be due to the addition of the faster acid producing thermophilic starter culture Streptococcus thermophilus which was recently introduced into the Cheddar cheese making process. This starter culture may impact the calcium buffering properties of the cheese due to more retention of the insoluble calcium (INSOL Ca) within the cheese. To investigate this problem, we studied how insoluble calcium affects cheeses with pH ranging from 4.8 to 6.6 and found that INSOL Ca was positively correlated with …

Maximizing Dryland Seed-Based Restoration Success Via Retrospective Analyses Of Species-Use Patterns And Field Testing Of Seed Mix Composition, Spencer J. Good

All Graduate Theses and Dissertations, Fall 2023 to Present

Due to harsh and variable environmental conditions, successful plant establishment in "dryland" ecosystems – areas with scarce precipitation – is a major challenge for restoration. One of the most important decisions influencing restoration outcomes is choosing which species to plant (i.e., species selection). Here I explored two opportunities to improve restoration success related to species selection. First, I examined recent restoration projects across Utah, USA to understand species selection patterns by site conditions (e.g., precipitation, elevation) and seed costs, and to identify tools for matching species to sites. Second, I tested how commonly used non-native species – those not originally …

First Specimen-Based Record Of Barbonymus Schwanefeldii (Bleeker, 1854) (Teleostei: Cyprinidae) From Laguna De Bay, Philippines, Kent Elson S. Sorgon, Marjorie Juliana L. Martinez, Andrei Justin F. So, Mariko Franccesca R. Aboganda, Jazreen Nicole G. Parungo, Aeris Johanne G. Poricallan, Keona Tiffany B. Prieto, Mellissa Jewel S. Magday, Alexa Charlize Dc Geronimo, Ma. Vianca Julia E. Anupol, Derreck O. De Leon

Biology Faculty Publications

The introduction of non-native fish species in the freshwater ecosystems of the Philippines presents a clear threat to native ichthyofauna, making verified reports of such introductions all the more critical. Through the examination of a collected specimen and anecdotes from fisherfolk and social media, we present here the first records of the occurrence of the tinfoil barb, Barbonymus schwanefeldii (Bleeker, 1854), in Laguna de Bay, Luzon Island, Philippines. This represents the addition of another non-native fish species in this lake, which is increasingly becoming dominated by non-native and invasive fishes that have been intentionally or accidentally introduced. Monitoring landed fish …

Volatile Organic Compounds And Their Relation To Sympathetic Activation And Autonomic Balance In Humans., Cameron Kyle Stopforth

Electronic Theses and Dissertations

Cardiovascular disease (CVD) is a multifaceted pathology that affects almost half of Americans ≥20 years old. One modifiable risk factor associated with CVD is air pollution exposure. The intricacy of air pollution exposure and CVD can make it difficult to elucidate on the multitude of mechanisms underpinning these associations. In this dissertation, we selected a relevant exposure (i.e., volatile organic compounds (VOC)) and an intermediate outcome (i.e., autonomic balance) that may represent one of these pertinent mechanisms. We tested the central hypothesis that higher VOC exposures would lead to increased sympathetic activation and autonomic imbalance. Aim 1 (Chapter III …