Digital Commons Network^™

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 …

Divergent Belowground Strategies Of Savanna Grasses Under Varying Fire Regimes, Abigail C. Schmidt

All Graduate Theses and Dissertations, Fall 2023 to Present

Savannas are unique ecosystems, where trees and grasses live together across the landscape, not quite forming full forests or open grasslands. The ability for trees and grass to coexist is largely the result of widespread disturbances, such as fire. Fire in savannas is largely thought of in how it maintains plants above ground, however, fire also plays a key role in ecosystem and plant processes belowground. First, fire can change how soil nutrients, namely phosphorus, are cycled. Phosphorus is a key nutrient that plants need to function, and plants acquire phosphorus through their roots. Frequent fire can enhance phosphorus availability, …

Secure Agricultural Futures: Re-Defining And -Imagining Agricultural Water Landscapes In The Us West, Britta L. Schumacher

All Graduate Theses and Dissertations, Fall 2023 to Present

Aridity is swiftly becoming the US West’s new normal. As agricultural communities adjust to persistent growing-season scarcity, they find their livelihoods under increasing threat. This points to the urgency of finding paths toward more secure water futures. A piece of this future puzzle includes water (re-)distribution – taking excess from one place and delivering it to another in need. To begin thinking about (re-)distribution, this dissertation engages with three mixed-methods and multiscale studies. The first study pairs county-level data across the 11 westernmost US states with survey data collected from individual producers in Utah to assess past and current trends …

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 …

Agronomic And Economic Evaluation Of Alternative Forage Crops Under Irrigation Technologies And Deficit Irrigation, Shikha Sharma

All Graduate Theses and Dissertations, Fall 2023 to Present

Water is becoming more limited in the western United States, including Utah, so farmers need forage crops that can produce well while using less irrigation water. This study examined how different forage crops respond to reduced irrigation and different irrigation application methods, and whether some crops can provide better economic returns under limited water conditions.

Field studies were conducted at three Utah locations, Cedar City, Logan, and Vernal, from 2020 to 2024. The alternative forage crops included teff, sorghum-sudangrass (sudex), and forage rye. For economic comparison, conventional forage crops included alfalfa, corn, and three-way small grains. Four to five irrigation …

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 …

Integrating Space Use And Demography To Support Management Of An Endangered Alpine Ungulate, Danielle J. Berger

All Graduate Theses and Dissertations, Fall 2023 to Present

The places animals choose to live affect the food they find, the dangers they face, and the weather conditions they experience. These experiences influence whether individual animals survive and reproduce, which in turn affects the size and health of animal populations. Although scientists have long believed that animal movements play an important role in population trends, there has been limited real-world evidence showing this connection. Advances in GPS tracking technology now allow researchers to follow animals over long periods and better understand how movement influences survival. Using 20 years of GPS tracking data from the endangered Sierra Nevada bighorn sheep …

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 …

Integrated Soil-Water Processes And Irrigation Management For Agricultural Water Optimization In Semi-Arid Regions, Tejinder Singh

All Graduate Theses and Dissertations, Fall 2023 to Present

Water is one of the most important resources for agriculture in the western United States. In semi-arid regions, farmers depend on irrigation to grow crops, but water supplies are becoming less reliable because of drought, declining snowpack, groundwater depletion, and increasing competition for limited water. Improving agricultural water use is therefore not simply about applying less water. It also requires understanding where water goes after it enters a field, how long it remains available to crops, and how farmers can use that information to make better irrigation decisions. This dissertation follows water through irrigated agricultural systems to better understand how …

Understanding And Predicting Precipitation Characteristics In The United States Through Machine Learning, Numerical Modeling And Measurements, Cody Luther Ratterman

All Graduate Theses and Dissertations, Fall 2023 to Present

Precipitation is one of the most important yet uncertain variables in the climate system. It varies dramatically in terms of timing, accumulation, rate, and phase, depending on location, season, circulation patterns, and atmospheric conditions. Precipitation forecasts, especially snowfall, are essential to supporting drought mitigation and water management in the Intermountain West. Because rainfall and snowfall lead to opposite effects on snowpack, accurately partitioning rain and snow is important to estimate snowpack levels, winter recreation, mountain ecosystems and runoff. The research findings in this dissertation have advanced the understanding and prediction of precipitation and snowpack in the U.S. by addressing the …

The Role Of Individual Specialization In Migration Phenology And How Restored Habits Are Used By Native And Nonnative Fishes, Austin Garner

All Graduate Theses and Dissertations, Fall 2023 to Present

Native fish species around the world have declined due to habitat loss, habitat fragmentation, and the spread of non-native species. Because these problems often happen at the same time and interact, recovery efforts can stall unless they address all of the factors limiting a species' comeback. The June sucker (Chasmistes liorus), native only to Utah Lake, UT, has declined for many of these reasons, though its recovery effort has made significant progress due in large part to a successful hatchery program. Yet, the recovery efforts have not yet been able to establish a self-sustaining population in Utah Lake, …

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. …

Time-Frequency Analysis Of Arterial Pulse Signals Of Cardiovascular Disease Patients Measured By A Microfluidic-Based Tactile Sensor, Md Mahfuzur Rahman

Mechanical & Aerospace Engineering Theses & Dissertations

This dissertation presents a single-degree-of-freedom (SDOF) based time–frequency analysis framework that can simultaneously extract a comprehensive set of cardiovascular autonomic indices from arterial pulse wave recordings obtained at rest and post-exercise, supporting non-invasive monitoring of autonomic recovery during cardiac rehabilitation. The framework rests on three technical contributions.

First, an SDOF analytical model of motion artefacts quantifies two physically distinct distortion mechanisms: additive baseline drift and Time-Varying System Parameter (TVSP) generated distortion of the Tissue-Contact-Sensor (TCS) stack. Baseline drift is slowly varying and removable by filtering; TVSP distortion rides on all harmonics of the true pulse signal and cannot be removed …

Silviculture For Coastal Forest Resilience: Promoting Forest Regeneration And Managing Invasive Plant Species, Ryan Bohannon

All Dissertations

Coastal forests of the southern United States and the ecosystem services they provide are threatened by an intensifying and interacting suite of disturbances associated with global change. Silvicultural strategies such as enrichment planting, invasive plant management, and browse mitigation treatments can enhance the resilience and adaptive capacity of forests to these threats by promoting sustainable regeneration and recruitment dynamics. To improve our understanding of coastal forest disturbance regimes and their impacts on forest stand dynamics, I conducted a systematic literature review of maritime forest disturbance ecology and identified coastal storms, ungulate browsing pressure, and invasive plants as primary disturbances shaping …

Regional Forecasting Of Southern Pine Beetle Outbreaks In The Southeastern Usa Using Spbom1 With Artificial Intelligence-Based Modeling, Ebere L. Anozie

All Dissertations

Southern pine beetle (SPB; Dendroctonus frontalis) outbreaks are among the most damaging biological disturbances affecting pine forests of the southeastern United States, capable of causing extensive tree mortality, economic losses, and reduced ecosystem resilience. This dissertation evaluated and advanced predictive approaches for SPB outbreak forecasting by integrating systematic review, geospatial modeling, comparative model evaluation, and artificial intelligence-based prediction. First, a systematic review of SPB predictive tools from 1978 to 2024 showed that modeling has evolved from statistical, climatic, and mechanistic approaches to remote sensing, GIS, machine learning, hybrid modeling, and decision-support systems, although many tools remain limited by scale …

Lizards In The Trees: Structural, Functional, And Behavioral Specializations To A High-Risk Environment, Victor D. Munteanu

All Dissertations

Animals must contend with unexpected changes in their habitat and environment to thrive. Arboreal habitats can consist of a wide variety of environmental features, and failure to adequately contend with these features can result in high risk of injury or death upon falling. Despite these strong selective pressures, many vertebrate lineages have successfully invaded arboreal habitats. Using lizard taxa as a model system, I investigated how morphology and behavior have evolved within this specific habitat transition. I pursued these investigations through complementary analyses including: 1) evaluating the effect of stance height and tail prehensility on perturbation recovery, 2) assessing behavior …

Effects Of Urbanization On Barrier Island Bobcats, Meghan P. Keating

All Dissertations

Urbanization is a leading driver of ecological change and presents unique challenges for carnivores by altering habitat availability, prey communities, and exposure to anthropogenic threats. Although many carnivore species persist in developed landscapes, the ecological and demographic consequences of urbanization often remain poorly understood, particularly over long timescales. Using one of the longest-running studies of a free-ranging carnivore population, I evaluated the effects of urbanization on the behavior, resource use, exposure risk, and population dynamics of bobcats (Lynx rufus) inhabiting a residentially developed barrier island in coastal South Carolina, USA. I first examined temporal and spatial responses to …

Towards Improved Stress Resilience, Optimal Growth And Enhanced Biosafety In Transgenic Plants, Xiaotong Chen

All Dissertations

This dissertation investigates biotechnology strategies to improve plant stress resilience, growth, and biosafety in transgenic perennial grasses using creeping bentgrass as a model system. Functional analyses of non-coding RNAs such as miR164 and miR169 showed that regulatory non-coding RNAs influence plant architecture and abiotic stress responses through broad developmental and transcriptional networks, supporting them as valuable engineering targets for complex trait improvement. The dissertation also developed a dual recombinase platform for transgene containment and removal, linking trait engineering with biosafety control. Additionally, the recombinases themselves were examined for their potential impact on heterologous host and were found to reshape plant …

The Past, Present, And Future Of Climate Adaptation In A Widespread Lizard Species, Matthew R. Mcternan

All Dissertations

Climate, as a selective force, shapes patterns of biodiversity globally. However, how species adapt to climate remains a central question of biology. The need to understand climate adaptation is paramount, as global climate change threatens a large portion of global diversity. Climate can impose selection on life by either controlling rates of energy intake and expenditure through effects on body temperature and activity, or by exposing organisms to conditions beyond their physiological limits. Studies of climate adaptation have identified a wide-range of putatively adaptive phenotypic patterns, but genomic evidence is increasingly being used to investigate these patterns and better understand …

Quaking Aspen On Cedar Mountain, Utah: Status And Update, Jaycee Cappaert, Larissa L. Yocom, Paul C. Rogers, Darren J. Mcavoy, R. Justin Derose

Wildland Resources Student Research

Quaking aspen forests are important communities in the western United States where they provide preferential food and habitat for animals, limit wildfires from spreading, and have favorable aesthetics, among other things. Their putative decline is an issue for ecology and management. We remeasured the aspen population on Cedar Mountain, Utah, to assess changes to its condition since it was originally measured in 2008 and laid the groundwork for continued aspen monitoring on Cedar Mountain. Our objectives were to compare current metrics of stand structure and composition, mortality, crown dieback, bole damage, regeneration, and recruitment, to those of the original inventory. …

Oxidative Stress Mediated Glutamate Release And Nmda Receptor-Dependent Synaptic Remodeling In Radiation-Induced Cognitive Dysfunction, Thanh Lam

Dissertations and Theses (Open Access)

In children younger than 14 years old, the brain and other parts of the central nervous system are the most common sites for solid tumors. Radiotherapy is an effective treatment for central nervous system (CNS) tumors. However, it often causes a progressive decline in cognitive functions, which is especially devastating for pediatric patients. Although post-mitotic neurons are generally considered resistant to radiation-induced immediate cell death, ionizing radiation causes complex neurochemical and structural changes that damage synaptic integrity. In this study, we examined the molecular cascades following a 10 Gy radiation dose applied to mouse cortical neurons. We found that radiation-induced …

Antigen Discovery In Multiple Myeloma Using Integrated Long-Read Transcriptomics And Immunopeptidomics, Aya Albittar

Dissertations and Theses (Open Access)

Multiple myeloma (MM) remains an incurable plasma cell malignancy, with relapse driven by persistent chemotherapy-resistant cells and residual disease following treatment. Although immunotherapies have transformed MM care, their success depends on identifying tumor-specific antigens that can be safely targeted. While aberrant genomic structural variation and transcriptional dysregulation are increasingly recognized as sources of novel antigens in MM, the HLA-presented antigenic landscape of MM remains incompletely characterized, particularly for non-canonical, structurally-derived peptides, and long-read transcriptome-informed immunopeptidomic data specific to MM remain scarce.

We established an integrated antigen discovery platform combining long-read RNA sequencing (Iso-Seq) with mass spectrometry-based HLA immunoprecipitation and immunopeptidomics …

Optimizing Urban Forestry Through Green Infrastructure: Tree Health And Water Retention In Ciudad Juarez Rain Gardens, Tomas Rogelio Lizarraga Ruiz

Open Access Theses & Dissertations

Urban green spaces (UGS) in arid regions face significant challenges due to water scarcity and extreme thermal demand. This study evaluates the efficacy of Nature Based Solutions (NBS), rain gardens and median strips, in enhancing the physiological resilience of urban trees in Ciudad Juárez, Mexico. Using a comparative framework, the research monitored a native evergreen (Dermatophyllum secundiflorum) and an introduced deciduous species (Morus sp.) across six planting treatments. Statistical analysis reveals that green infrastructure (GI) acts as a critical physiological accelerant. Trees situated within rain gardens and medians significantly outperformed those in restricted pot and sidewalk settings, maintaining higher stomatal …

Visual Cues Attract Adult Tunga Penetrans (Siphonaptera: Tungidae), Ayako Hyuga, Paul Ouma, Lynne Elson, Kazuchiyo Miyamichi, Satoshi Kaneko, Kensuke Goto, Tullu Bukhari, Jürgen Krücken, Ulrike Fillinger

All Peer-Reviewed Publications

Tunga penetrans (Linnaeus, 1758) (Siphonaptera: Tungidae) is an ectoparasitic flea whose adult females cause tungiasis by embedding into the host’s skin. Environmental, social and financial challenges in tungiasis endemic areas have left this disease neglected and lacking locally available control measures. One possible approach for controlling T. penetrans targets its off-host stages; however, surveillance tools for adult fleas are still lacking. Moreover, host-seeking cues and behaviour of adult T. penetrans remain largely unknown. In this study, we show that visual cues are attractive to adult T. penetrans. Newly emerged T.penetrans responded to light stimuli across a broad spectrum, ranging from …

Machine Learning In Flow Cytometry For Acute Myeloid Leukemia Diagnosis: A Scoping Review, Katrina Jezzela M. Dela Pena Md, Mls (Ascp)

Other Specialties

Manuscript version:

Introduction: Flow cytometry is essential for the diagnosis of acute myeloid leukemia (AML), but conventional analysis is labor-intensive, operator-dependent, and increasingly complex. Machine learning (ML) may support automated analysis; however, its readiness for clinical implementation remains unclear. This scoping review mapped ML approaches applied to flow cytometry for AML-related diagnosis.

Methods: PubMed was searched for English-language primary studies applying artificial intelligence, ML, or deep learning to human flow cytometry data for AML diagnosis or classification. Eligible studies reported diagnostic performance metrics. Study characteristics, preprocessing, data representation, model architecture, validation strategy, performance metrics, interpretability, and implementation considerations were descriptively …

The Massbank Contributions Of The Mfam Collaboration, Anusha Ahlendorf, Asaph Aharoni, Khabat Vahabi, Tillmann G. Fischer, Pierre Marie Allard, Megan Augustin, Ulschan Bathe, David Broadhurst, Corey Broeckling, Joerg Buescher, Adrian Covaci, Katyeny Manuela Da Silva, Ric C.H. De Vos, Micha Gracianna Devi, Stefanie Döll, Maximilian Frey, Andrej Frolov, Emmanuel Gaquerel, Vasuk Gautam, Esteban Charria-Girón, Alain Goossens, Jeremy Grosjean, Maria Halabalaki, Elias Iturrospe, Kim Kultima, Stephanie Herman, Toni M. Kutchan, Romain Larbat, René Meier, Eleni V. Mikropoulou, Gregory Mouille, Luca Nicolotti, Nir Shahaf, François Perreau, Pierre Pétriacq, Michael Reichelt, Stacey N. Reinke, Rani Robeyns, Alena Soboleva, Otmar Spring, Akshai Parakkal Sreenivasan, Alain Tissier, Jean Chrisologue Totozafy, Hiroshi Tsugawa, Josep Valls-Fonayet, Maria Van De Lavoir, Justin J.J. Van Der Hooft, Fredd Vergara, David Wishart, Ludger A. Wessjohann, Jean-Luc Wolfender, Jörg Ziegler, Gerd Ulrich Balcke, Steffen Neumann

Research outputs 2022 to 2026

Introduction: The analysis of metabolic profiles using high resolution mass spectrometry (MS) data provides deep insights into biological processes. In metabolomics, MS analysis generates a large number of features that represent metabolites. However, identifying specific metabolites from these features can be challenging. One of the major bottlenecks in the metabolomics field is the identification of MS features, which is a prerequisite for any biochemical interpretation. By identifying similarities and differences within a metabolite family (mFam), evaluating MS features at the metabolite family level can help assigning functional roles to individual MS features. These data can help interpreting metabolic pathways and …

The Feeding Ecology, Habitat Use, And Monitoring Of Juvenile Alosines: Alewife (Alosa Pseudoharengus), Blueback Herring (A. Aestivalis), And American Shad (A. Sapidissima) In The Kennebec River, Maine, Brian Determan

All Student Scholarship

The Kennebec River, Maine is home to three species of anadromous fish of the genus Alosa: alewife (A. pseudoharengus) and blueback herring (A. aestivalis), jointly referred to and managed as river herring, as well as American shad (A. sapidissima). These ecologically, economically, and culturally important fish populations are depressed compared to historic levels and have been subject to extensive restoration efforts. While spawning adults have been well-studied, much less is known about the juveniles including whether they engage in resource partitioning to minimize competition and facilitate coexistence. In Chapter 1, I use stomach contents to compare diets as well as …

Temporal Dynamics Of Sensorimotor Integration For Auditory And Proprioceptive Target Information During Movement Preparation And Execution, Ivan Camponogara

All Works

Actions toward non-visual targets exhibit modality-specific patterns of endpoint variability, with movements toward auditory targets being more variable than those toward proprioceptive or multisensory targets. However, whether such modality-specific effects emerge already during movement preparation and how they evolve across movement execution remains unclear. The present study addressed this question by asking participants to perform reaching movements toward auditory, proprioceptive, or audio-proprioceptive targets while electromyography and movement kinematics were recorded. Movement preparation and initiation was assessed by analyzing two temporal components of reaction time, premotor and motor, together with movement kinematics at peak acceleration. Movement execution was investigated by analyzing …

Membrane Progestin Receptors Α And Β (Paqr7 And 8) Are Necessary For Oogenesis In Zebrafish, Md. Almamun Farid, Md. Razain Tanvir, Takumi Mouri, Eisei Tsutsumi, Md. Sohanur Rahman Sohan, Md. Ekramul Hasan, Md Saydur Rahman, Chihiro Yamamoto, Akiteru Maeno, Toshinobu Tokumoto

School of Integrative Biological & Chemical Sciences Faculty Publications

Paqr7 and paqr8 are genes encoding membrane progestin receptor αand β (mPRα and mPRβ, respectively), which are currently classified as members of the progestin and adipoQ receptor (PAQR) family. For mPRα, the first identified mPR gene, there are two paralogs in zebrafish, paqr7a and paqr7b. In order to elucidate the physiological functions of the mPR subtypes, we created gene knockout (KO) fish by editing seven paqr genes in zebrafish and analyzing their phenotypes. The null-mutant strains of paqr7a, paqr7b, and paqr8 presented no significant abnormalities in reproductive functions. Thus, we generated a triple-gene knockout (TKO) strain of …

Harnessing Kenyan Aquaculture Through Social Media: Impacts, Challenges And Strategic Directions, Domitila Kyule, Jonathan Munguti, Mavindu Muthoka, Esther Magondu, Menaga Meenakshisundaram, Chrysantus M. Tanga, Kevin Obiero, Cecilia Githukia

All Peer-Reviewed Publications

Aquaculture is increasingly important for food, nutrition and livelihoods in Kenya, but the sector still faces persistent constraints in extension delivery, farmer learning, input access, market coordination and information reliability. This review examines how social media and related digital communication tools are shaping aquaculture development in Kenya, with attention to impacts, challenges, governance needs and strategic directions. A systematic literature review of studies and institutional sources published between 2015 and 2025 was conducted. The search identified 388 records, of which 45 sources were included in the final synthesis after screening, eligibility assessment and quality appraisal. Because the evidence was heterogeneous, …