Digital Commons Network^™

Beyond Autophagic Dysregulation: Vma21 Deficiency Reveals Altered Vesicle Trafficking And Broadens The Pathogenic Framework Of X-Linked Myopathy With Excessive Autophagy, Christian Suarez

Arts & Sciences Graduate Student Theses and Dissertations

Maintenance of protein homeostasis is essential for cellular function and depends on the coordinated regulation of protein synthesis and degradation. The major intracellular pathways responsible for protein degradation are the ubiquitin-proteasome system (UPS) and autophagy. Disruption of these processes has been implicated in a broad range of diseases, including neuromuscular disorders. X-linked myopathy with excessive autophagy (XMEA) is a rare vacuolar myopathy caused by mutations in VMA21, which encodes an assembly chaperone required for proper assembly of the vacuolar H⁺-ATPase (V-ATPase), the primary proton pump responsible for acidifying intracellular compartments, including lysosomes. Although impaired lysosomal acidification and autophagic dysregulation have …

The Gut-Bladder Axis: How Symbiont Microbes Alter Urinary Tract Infections, Benjamin S. Olson

Arts & Sciences Graduate Student Theses and Dissertations

Urinary tract infections (UTIs) are among the most common bacterial infections worldwide. Consequently, they are one of the leading indications for antibiotic prescription. Despite the typically successful treatment of an acute UTI, recurrent infections are exceedingly common, particularly among women. Nearly a quarter of otherwise healthy women will suffer recurrent UTIs (rUTI) after a primary UTI; why these select individuals are continually afflicted is unkown. There are no successful therapeutics to treat rUTI representing a gap not just in the medical toolkit but in our understanding of why rUTI is so prevalent. There are many hypotheses for the risk factors …

Integrative Evidence For Cryptic Diversity In The Thomomys Mazama Species Complex: Phylogenetics, Cranial Morphometrics, And Ecological Niche Modeling, Jessica Kate St. Michael

Dissertations and Theses

The population genetic structure and geographic distribution of the pocket gopher genus Thomomys Wied-Neuwied, 1839, lends itself to speciation events. Conserved morphology, ecological specialization, and high rates of molecular evolution may increase the probability of allopatric speciation, thereby contributing to the presence of morphologically cryptic taxa. In light of these patterns of evolution, we assessed genetic divergence and phylogenetic relationships, cranial morphometric differentiation, and ecological divergence among taxa in the Thomomys mazama species complex to test the hypothesis that T. mazama is a single species. Species delimitation analysis using Bayesian Poisson Tree Processes (bPTP) and data from the mitochondrial cytochrome …

Parental Thermal Environment Affects Offspring Resilience To Winter And Spring Weather Anomalies, Ruzhuo Chen, Mariel Dunn, Caroline A. Curtis, Mariana Abarca

Biological Sciences: Faculty Publications

Recent increases in the frequency and intensity of thermal anomalies can result in recurrent stressful weather events. Among annual insects, this phenomenon may expose parents and offspring to a succession of different weather anomalies (e.g. summer heatwaves and late spring frosts). Parental stress can alter offspring physiology and performance, potentially affecting their tolerance of environmental variation. We investigated the transgenerational effects of thermal anomalies on a univoltine wetland butterfly. We induced parental thermal stress by exposing pupae to a constant temperature, ranging from stressfully cold to stressfully hot (10 ◦C, 26 ◦C, 28 ◦C, 32 ◦C), for three days. Offspring …

Escherichia Coli Concentrations In Sand And Water At Tributary-Influenced Lake Michigan Beaches, Josie Elaine Kuhlman

Masters Theses

Contamination of public recreational water and sand is a human health concern, creating a management challenge for public health officials. Past research has shown that Escherichia coli can persist in sediment and can be washed into recreational water. Currently, beach monitoring practices only utilize E. coli concentrations in water samples to determine beach safety and do not consider potential exposure to sediment/sand concentrations. In this study, I investigated the relationship between E. coli concentrations in water and sand samples, which will aid public health officials in making more informed decisions about beach closures. I utilized culture-based measurements of E. coli …

Adaptive Phishing Url Detection Using Hybrid Fuzzy C-Means Clustering And Xgboost, Muntadher Mohammed Kareem, Rawaa I. Farhan

Karbala International Journal of Modern Science

Phishing attacks continue to evolve in sophistication, rendering static detection methods increasingly ineffective. Existing URL-based approaches suffer from limited adaptability to emerging phishing patterns, mislabeled training data, and insufficient validation protocols. This paper proposes a hybrid phishing URL detection system that integrates Fuzzy C-Means (FCM) clustering with XGBoost classification, enhanced by a novel Micro Adaptive Feature Extractor (MAFE). The system employs a multi-stage pipeline: feature engineering generating 36 statistical and interaction features, MAFE producing 15 adaptive features through class-aware dynamic weighting, micro-pattern detection, and entropy analysis, and FCM with K=2 clusters providing soft membership features to XGBoost. A two-pass confidence-based …

Ai-Enhanced Fluorescein Angiography Detection Of Diabetes-Induced Silent Retinal Capillary Dropout And Rna-Seq Identification Of Pre-Symptomatic Biomarkers, Yiyan Peng, Huishi Toh, Dennis Clegg, Peng Jiiang

Biological, Geological, and Environmental Faculty Publications

Objective: Retinal capillary dropout, characterized by acellular capillaries or "ghost vessels," is an early pathological sign of diabetic retinopathy (DR) that remains undetectable through standard clinical imaging techniques until visible morphological changes, such as microaneurysms or hemorrhages, occur. This study aims to develop a non-destructive artificial intelligence (AI)-based method using fluorescein angiography (FA) images to detect early-stage, silent retinal capillary dropout.

Methods: We utilized 94 FA images and corresponding destructive retinal capillary density measurements obtained through retinal trypsin digestion from 51 Nile rats. Early capillary dropout was defined as having an acellular capillary density of >= 18 counts per mm2. …

Phenological Plasticity Provides Limited Resilience To Climate Warming In A Sea Turtle Species With Temperature-Dependent Sex Determination, Blair P. Bentley, Lisa M. Komoroske, Cintia M. Santos, Armando J. B. Santos, Estefany Argueta, Vic Quennessen, Christina M. Coppenrath, Camille Kynoch, Vincent S. Saba, Claudio Bellini, Rafaely N. M. S. Ventura, J. Wilson White, Mariana M. P. B. Fuentes

Biological Sciences: Faculty Publications

Anthropogenic climate change is threatening global biodiversity, with sea turtles particularly vulnerable as offspring sex and developmental success are strongly influenced by incubation temperature. Behavioral plasticity, including the seasonal distribution of reproductive output, may provide short-term mechanisms for mitigating these impacts. Here, we investigated season-wide hatchling sex ratios and emergence success in a small population of green turtles (Chelonia mydas), tracking individual females across their nesting seasons. Sex ratios varied markedly through the nesting season, with later nests producing a greater proportion of male hatchlings. Moreover, sex ratios were relatively consistent among nests laid by individual females. Overall, females producing …

Enzymatic Synthesis Of Salicylate In Yersina Pestis Proceeds Via Intramolecular Hydroxyl Group Transfer., Clarke Miller

Georgia Journal of Science

The salicylate synthase (YbtS) of Yersinia pestis catalyzes the initial step in the biosynthesis of yersiniabactin, an iron-scavenging siderophore and critical virulence factor. While YbtS is proposed to share a  reaction mechanism with other anthranilate synthase homologs, the exact catalytic pathway has remained unresolved.  In this work, stable isotope (¹⁸O) labeling and mass spectrometry are utilized to clarify the catalytic mechanism of YbtS.  The results of the following set of experiments demonstrate that the salicylate hydroxyl group does not originate from solvent water, directly challenging previously proposed models. Instead, the lack of solvent-labeled oxygen incorporation and the absence …

Contributions Of Arginine And Nitrosative Stress To Huntington’S Disease Progression, Ian D. Gaudet

Electronic Theses and Dissertations

Neuroinflammation is a well-established component of Huntington's disease (HD) pathogenesis, yet the intricate molecular mechanisms that govern this process remain a topic of ongoing research and debate. This dissertation elucidates a novel pathway linking arginine metabolism and nitrosative stress to core HD pathology. We found that the arginine transporter SLC7A2 is selectively upregulated in various HD cellular models and patient samples. Our findings reveal that this upregulation drives an overactive inflammatory response, leading to abnormally high inducible nitric oxide synthase (iNOS) induction and subsequent nitric oxide (NO) production, which causes excessive protein nitrosylation and an increase in mitochondrial fragmentation.

To …

Attraction Of Nocturnal Scarab Beetles By Unusual Floral Volatiles In A Banksia (Proteaceae) With Functionally Diverse Pollinators, S. K. Wawrzyczek, B. Bohman, S. L. Krauss, I. M. Butler, G. R. Flematti, K. Farnier, S. E. Hoebee, R. A. Davis, R. D. Phillips

Research outputs 2022 to 2026

Pollination by beetles has evolved multiple times in flowering plants but with relatively few plant species adapted specifically to pollination by scarab beetles (Coleoptera: Scarabaeidae). However, some plant species may produce floral scents and offer floral rewards that attract scarabs alongside other pollinator functional groups. In Banksia attenuata (Proteaceae), nocturnal observations led to the discovery of extensive floral visitation by beetles, alongside birds, mammals and diurnal insects. Given the distinctive melon-like floral scent of B. attenuata, we predicted long-distance attraction of beetles by chemical cues. We undertook floral visitor surveys aided by camera traps and video recordings, and quantified insect …

Asm And A Culture Of Sharing, Caring, And Fun In Education, David J. Westenberg

Biological Sciences Faculty Research & Creative Works

One doesn't always equate a professional scientific society with sharing, caring, and fun, but in this age of public distrust, public engagement with science and active student learning are ways to regain trust. ASM holds a leadership position in promoting and recognizing the value of education in the future of our profession and is there to support your educational journey. From K12 outreach and public engagement, to professional development, to presenting and publishing scholarship of teaching and learning, ASM has been at the forefront of biology education. Under the leadership of visionary directors such as Amy Chang and now Irene …

Validating The Expression Of Genes Potentially Involved In The Development Of Aggressive Melanoma Tumor In The Zebrafish Melanoma Model, Mayra Matos Diaz

Theses, Dissertations and Culminating Projects

Melanoma is an aggressive form of skin cancer characterized by rapid progression, metastatic potential, and the frequent development of resistance to targeted therapies. Although the Inducible cAMP Early Repressor (ICER) has been identified as a potential tumor suppressor in melanoma, the molecular mechanisms underlying its role in tumor progression remain poorly understood. Building upon the transcriptomic findings of Wheelan et al. (2025), this study investigates the relationship between ICER and ten candidate genes (gdf6a, pdgfra, col4a4, fgfr2, pdgfrb, cdkn1a, fgf5, akt1, met, and notch3) associated with BMP signaling. Quantitative polymerase chain reaction (qPCR) was used to compare gene expression between …

Temperature And Salinity Effects On The Physiology Of Bullfrog Tadpoles (Lithobates Catesbeianus) From A Suburban Temperate Wetland, Angela Brown

Theses, Dissertations and Culminating Projects

One of the most robust amphibians is the American Bullfrog, Lithobates catesbeianus, which is a widespread species that is invasive worldwide, and is broadly tolerant of a range of environmental conditions. Despite this tolerance, survival and performance of adult L. catesbeianus can be negatively affected by increasing temperatures and salinity resulting from anthropogenic impacts, such as climate change and road salts. This study focuses on the effects of acute salinity exposure (mimicking road salt influx into a pond) on L. catesbeianus tadpoles at different larval stages. Increased salinity was predicted to negatively affect two physiological performance measures. Critical maximum temperature …

Effect Of Food Resource, Preservation Method, And Preservation Duration On Larval Size Of Forensically Important Fly Species (Order: Diptera), John Zukowski

Student Theses

Forensic entomology is a vital discipline that can aid in the proceedings of criminal cases. Larval age and development are important aspects to consider when utilizing blow flies (Family: Calliphoridae) for estimates pertaining to the initial time of colonization (TOC), which contributes to postmortem interval (PMI) estimations. Thus, it is important to understand the factors that influence larval size and development, since larval size is commonly used as a proxy for age. Larvae of three species of flies, Lucilia sericata (Meigen), Calliphora vicina (Robineau-Desvoidy), and Phormia regina (Meigen), were reared on five different food resources. Specimens of L. sericata and …

Land Condition Standards For The Western Australian Nullarbor Pastoral Region, Peter-Jon A. Waddell, Wayne J. Fletcher

Natural resources published reports

This report outlines the quantitative land condition standards that define acceptable pastoral land condition for the Western Australian part of the Nullarbor, to meet the regulatory requirements of the Land Administration Act 1997 and the Soil and Land Conservation Act 1945.

The Department of Primary Industries and Regional Development is developing regional-level pastoral land condition standards for Western Australia as a critical component of the Framework for sustainable pastoral management – revised edition (Fletcher 2022), the purpose of which is to address the Office of the Auditor General’s recommendations to improve the management of pastoral lands in WA …

Nh Dfl - 25 Years Of Hwa - Peterborough_2026_Aug_11, Ryan Crandall

UNH Cooperative Extension

No abstract provided.

Integrative Taxonomic Analysis Of Cryptic Species Diversity In The Spiny Witch-Hazel Gall Aphid, Hamamelistes Spinosus (Hemiptera: Aphididae: Hormaphidini) In Eastern North America, Gavin Andrew Powell Munson

All Graduate Theses and Dissertations, Fall 2023 to Present

Taxonomy is the practice of identifying, classifying and categorizing species, providing structure for the vast diversity of life. Aphids are an ecologically important group of soft-bodied insects, but they can be difficult to identify because of their tiny anatomical size, reduced or simplified morphological features, and morphological variation within a single species across different generations. In this study, the taxonomy of the spiny witch-hazel gall aphid, Hamamelistes spinosus, is revised. The complex multi-generational life cycle of the aphids, which alternates between witch-hazel and birch trees, has led to confusion regarding past descriptions. Scientists in the late 1800s who were …

From Genes To Streams: Mitochondrial Approaches To Population Monitoring Of The Santa Ana Sucker Catostomus Santaanae, Mariana Antonio

Electronic Theses, Projects, and Dissertations

This study was developed to use aquatic environmental DNA (eDNA) as a tool to detect the presence of the Santa Ana sucker (Catostomus santaanae), a federally threatened fish species, across the Santa Ana River in Southern California. Environmental DNA is any genetic material that an organism sheds into the environment. We can get an idea of what aquatic species are present when sampling water at a given site. We sequenced the complete mitochondrial genome (mitogenome) of the Santa Ana sucker and designed custom DNA primers to improve eDNA detection accuracy. These primers were selected based on high genetic …

Comparative Assessment Of Developmental Fidelity In Hpsc-Derived Neural Crest Cells, Michael H. Zepeda

Electronic Theses, Projects, and Dissertations

Neural crest cells (NCCs) are a transient, multipotent cell population that contributes to craniofacial structures, peripheral neurons, melanocytes, and smooth muscle. Defects in NCC development underlie a broad range of congenital disorders known as neurocristopathies. Human pluripotent stem cell (hPSC)-derived NCCs provide an evaluable model for studying early human development; however, existing differentiation protocols produce variable outcomes, and no standardized method consistently generates high-fidelity NCC populations. To address this challenge, we compared five published hPSC-to-NCC differentiation protocols using the H9 human embryonic stem cell line. We hypothesized that specific protocols more faithfully recapitulate neural crest development through coordinated regulation of …

A Geometric Morphometric Analysis Of Acetabular Shape Variation Across Bat Families, Jordan L. Huff

Electronic Theses and Dissertations

Bats are the only mammals capable of powered flight, and research is concentrated on this adaptation. Their non-flight locomotion has received comparatively little attention. Previous studies show that non-flight locomotor behaviors vary across families. Members of Pteropodidae are efficient climbers but cannot effectively walk, whereas Phyllostomidae and Vespertilionidae are better at terrestrial locomotion but show reduced arboreal capabilities. The non-flight locomotion of Hipposideridae and Rhinolophidae is less understood, although rhinolophids exhibit limited terrestrial locomotion. This study examined whether differences in locomotor behavior are associated with variation in acetabular morphology. A geometric morphometric analysis of acetabular shape was conducted across multiple …

Transcriptional Regulation In The Uterine Luminal Epithelium, Evelyn A. Carrion

Dissertations and Theses (Open Access)

Transcriptional Regulation in the Uterine Luminal Epithelium

Evelyn A. Carrion

Advisor: Richard R. Behringer, PhD

Abstract

The uterus is an organ comprised of multiple tissues that are essential for women’s health and reproduction. The uterus is composed of multiple tissue layers, including the perimetrium, myometrium, and the endometrium. The endometrium is the inner lining of the uterus, and contains the luminal epithelium, glandular epithelium, and stroma. The luminal epithelium is a simple columnar layer of cells that is necessary for embryo implantation. The uterus is derived in part from the embryonic precursor tissue called the Müllerian duct. There are no …

Alfred Russel Wallace Notes 42: How Accurate Are The Transcriptions Presented At The Alfred Russel Wallace Page Website?, Charles H. Smith

Faculty/Staff Personal Papers

A look is taken at the level of accuracy displayed by the transcriptions of Wallace writings offered at the Alfred Russel Wallace Page website, as determined by a ChatGPT analysis.

Bees In The Trap: Leveraging Bumble Bee (Hymenoptera: Apidae: Bombus) Bycatch For Ecological And Genetic Insights, Tori L. Strausser

All Graduate Theses and Dissertations, Fall 2023 to Present

Managers rely on insect monitoring traps to detect insect pests that harm crops and protect food and other agricultural production. However, these traps also capture non-target insects, including bumble bees, raising concerns about whether repeated trapping could harm pollinator populations. This thesis explores whether bees caught as non-targets, also called bycatch, in routine pest monitoring traps can be used to better understand bumble bee populations, and whether traps pose risks to their long-term persistence. Using bumble bees collected from pest surveillance traps placed in crop fields across Utah, this research examined seasonal patterns in body size, timing of capture, and …

Advancing Management Strategies For Two Promising Mason Bee Species (Osmia Ribifloris And Osmia Bruneri) For Berry Pollination, Miranda L. Jones

All Graduate Theses and Dissertations, Fall 2023 to Present

Bee management can broadly refer to human manipulation of one or multiple parts of a bee’s lifecycle. Managing honey bees, commonly referred to as beekeeping, is responsible for providing most pollination for global food crops. However, using more than one bee species for crop pollination can have many benefits. Benefits include better crop pollination and insurance in case one bee species underperforms or its population collapses. Some bees within the genus Osmia are already widely managed for crop pollination because their developmental lifecycle allows bee managers to readily deploy pollinating bees in sync with varying crop blooms, and for certain …

Carbon Cycling, Salinization, And Long-Term Water Quality Trends In Rocky Mountain Streams, Allyson J. Marrs

All Graduate Theses and Dissertations, Fall 2023 to Present

Humans have greatly affected streams and rivers worldwide through urbanization, agriculture, and water use. The purpose of my dissertation is to increase our understanding of various human impacts on rivers. In chapter two, I aim to determine whether there are differences in greenhouse gas (GHG) emissions between a natural river and manmade canals. I did this by measuring the emissions and dissolved concentrations of three of the most prevalent GHGs, carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O). I found that most of the sites I studied were emitting CO₂ and CH …

Regional Occurrence And Spatiotemporal Habitat Partitioning Of The Culex Genus Mosquitoes In Salt Lake City And Uintah Basin, Utah, Katelyn Graybeal

All Graduate Theses and Dissertations, Fall 2023 to Present

West Nile virus is the most common mosquito-borne disease in North America and can cause serious illness, including inflammation of the brain and nervous system. Because there is currently no widely available vaccine for humans, preventing mosquito bites and monitoring mosquito populations remain the most effective ways to reduce disease risk. Understanding which mosquito species are present, where they occur, and how they respond to environmental change is critical for protecting public health.

This research examined the mosquito species responsible for spreading West Nile virus in Utah through two complementary studies. The first study focused on the Uinta Basin in …

Drought And Diet Breadth: Does Insect Specialization Influence Herbivory When Plants Are Under Stress?, Jakob Palmer

All Graduate Theses and Dissertations, Fall 2023 to Present

Climate change will alter precipitation worldwide, causing more frequent and severe drought events worldwide. Drought affects many ecological processes, including plant-herbivore interactions, which are critical to biodiversity and ecosystem health. A variety of plant characteristics can influence herbivory – such as how hairy, nutritious, or toxic a leaf is – and drought has been shown to alter many of these traits. Unique characteristics of herbivore species are also important: herbivores can either feed on a variety of plants (generalists) or a group of closely related plants (specialists). Specialists can cope with traits of the plants they eat, while generalists are …

Microbes In Pollination Systems: Effects On Pollinator Health, Floral Traits, Nectar Robbing, And Plant Fitness, Valerie Nicole Martin

All Graduate Theses and Dissertations, Fall 2023 to Present

Flowers produce nectar to attract pollinators, but nectar is also a habitat for yeasts and bacteria that arrive via pollinators, robbers, and other visitors. These microbes consume nectar sugars and release byproducts that change the smell and taste of nectar. Whether these changes affect how pollinators find and choose flowers, and whether they ultimately affect how many seeds a plant produces, is not well understood. In this dissertation, I studied how a common nectar yeast and a plant-associated bacterium affect the scent of wildflowers, the behavior of bumble bees and hummingbirds, and plant reproduction in montane meadows in central Colorado. …

The Evolution Of Hymenopteran Recombination Rates, Timothy John Delory

All Graduate Theses and Dissertations, Fall 2023 to Present

Individuals of some species mix their DNA frequently when producing sex cells, while others do so much less. Hymenopterans (ants bees and wasps) are especially useful for understanding this variation for several reasons. They show large differences in this frequency of shuffling, or rate of recombination, have well-studied genomes, and vary widely in how they live and reproduce. I capitalized on these features examines how recombination rates have evolved in this group at the trait, and gene level.

First, I revisited long-standing ideas about why recombination rates differ among these species, incorporating more than a decade of new research. This …