Digital Commons Network^™

Patterns And Potential Mechanisms Of Phenotypic Changes In Urban Small Mammals, Leslie Lopez

Master's Theses

Urbanization is an example of human induced rapid environmental change that can have wide-reaching ecological effects, including habitat destruction, fragmentation, and alteration of local climates. Effects of urbanization have been shown to impact wildlife, as disturbances resulting from urbanization can create novel environments and selective pressures that could lead to changes in morphology, physiology, or both. Small mammals such as rodents are an ecologically important set of wildlife species because they are a key prey item for several predators, hold strong influence over plants as a primary consumer, and some species carry and transmit major human and animal diseases. Previous …

Clonal Plants' Traits And Responses Following Fire Disturbance In Ponderosa Pine Ecosystems In The Colorado Front Range, Raymond Erskine

Master's Theses

Mountain ecosystems are currently experiencing increasing impacts of disturbances (e.g., wildfire) due to global changes in climate and land use, leading to significant changes in vegetation composition and landscape dynamics. Clonal plants, characterized by their vegetative reproduction strategies, offer a range of ecologically important traits to cope with disturbances. However, clonality is often excluded in studies of post-fire vegetation dynamics in mountain ecosystems, and our knowledge of the ability of clonal plants to respond to differing disturbance regimes is limited. Therefore, I examined the response of understory vegetation following fire disturbance in burned and unburned ponderosa pine stands of the …

Role Of Atp-Binding Cassette (Abc) Transporters As A Protector Of Testis Stem Cell Niche From Chemotherapy Drugs In Drosophila Melanogaster, Swagata Maity

Master's Theses

In chemotherapy treatments most tumor cells are destroyed by drugs, but some tumor cells are drug resistant, and these are known as cancer stem cells (CSCs). Normal adult stem cells are also chemo resistant. Therefore, investigation of normal stem cells can be useful to provide further knowledge of CSCs. One of the primary ways that CSCs achieve drug resistance is by drug efflux through transmembrane pumps called ATP-binding cassette (ABC) transporters. Many studies on ABC transporters have been performed in vitro using cultured cell lines, but very few studies have been performed on normal stem cell populations in vivo. Drosophila …

Molecular Characterization Of Stress Response In Western Honey Bee (Apis Mellifera), Faizan Tahir

Master's Theses

Honey bees are incredibly important for the reproduction of flowering plants and the sustainability of agricultural ecosystems. However, they face various stressors such as pesticides, pathogens, habitat loss, and climate change. Extensive research has been conducted to understand how bees respond to these stressors. Scientists have discovered that honey bees exhibit complex physiological and behavioral responses to stress at individual and colony levels. Stress can have a significant impact on their immune function, foraging behavior, and reproductive success (Decourtye et al., 2010). Understanding bee responses to stress is crucial for several reasons. Firstly, honey bees are vital for the pollination …

The Assessment Of Autonomic Function In Young Adults With An Elevated Risk Of Metabolic Syndrome, Ta'quoris Newsome

Master's Theses

Metabolic syndrome (MetS) is a complex medical condition defined by the co-occurrence of multiple cardiometabolic risk factors. Despite the well-defined profile of autonomic function in individuals with MetS, autonomic function in those with an elevated risk of developing MetS remains unclear. Our study aimed to shed light on the progression of cardiometabolic disease and its impact on autonomic function. To investigate, twenty participants, ten of whom were classified as having an elevated risk of developing MetS based on identification of risk factors using NCEP ATP III criteria, completed a two-visit study protocol. In the second visit, spontaneous cardiovagal baroreflex sensitivity …

Salinity Tolerance Of Flowering Rush, Butomus Umbellatus, Andrew Coomes

Master's Theses

Flowering rush is an invasive aquatic plant in North America that causes deleterious effects to native ecosystems. There are two cytotypes, a triploid and diploid, and multiple genotypes contained within the diploid cytotype currently established in the U.S. Despite its presence in river drainages connected to estuarine areas, documentation on the salinity tolerance of flowering rush is scarce. Currently, information is limited to anecdotal reports suggesting intolerance to saline conditions. A better understanding of the osmotic tolerance of this species is essential to providing insight into its’ invasive range and better inform management efforts. These studies investigated vegetative propagule germination …

The Role Of B Cell Activation State And Sex In Aryl Hydrocarbon Receptor Mediated Induction Of Chemokine Receptor 9 And Alpha4beta7 Expression In Vitro, Logan Bauerle

Master's Theses

Defense of mucosal tissues from microbial infection and allergy is reliant on continual production of antibodies. The aryl hydrocarbon receptor (AhR) is known to regulate B cell development and is associated with suppression of systemic humoral immunity. Recent attention has been paid to the role of the AhR in altering expression of cell adhesion molecules (CAMs). B cells express CAMs and chemokine receptors to migrate around the body for localized secretion of antibodies. AhR agonists promote B cell migration to the small intestine through upregulation of chemokine receptor 9 (CCR9) and integrin α₄β₇. Both the AhR …

Clonal Growth And Trait Variation In The Colorado Front Range: The Influence Of Elevation And Ecosystem, Jordan Conley

Master's Theses

Amid global climate change, exploring adaptive strategies among alpine flora, particularly through clonal growth, becomes critical for biodiversity conservation. This study aims to explore the patterns of dominance and distributions among clonal species across environmental gradients in the Colorado Front Range, employing a trait-based comparative analysis to understand the adaptive strategies of alpine flora and their implications for conservation amid rapid climate change. We focused on two species, studying traits like lateral spread, bud count, and bulbil numbers. Advanced statistical methods such as Permutational Multivariate Analysis of Variance (PerMANOVA) and Multi-Response Permutation Procedures (MRPP) were used to evaluate community compositions …

Role Of Toll-Like Receptor 2 In Macrophage Recognition And Response To Borrelia Burgdorferi, Yukiye A. Koide

Master's Theses

Lyme disease is the most common vector-borne disease in the US and will experience an uptick as the insect host, the ixodid tick, gains habitat with climate change. The causative agent of Lyme disease, Borrelia burgdorferi, is recognized by Toll-like receptor 2 (TLR2), which initiates the innate immune response. Here, I used ELISA and SEAP detection assays to determine that knocking out TLR2 in THP-1 macrophages reduces the amount of NFkB activation, as well as IL-10 and IL-1β secretion. Then, I used fluorescence microscopy and Incucyte assays to quantify the amount of phagocytosis performed by wild-type and knock-out THP-1 cells. …

Species Delimitation Of Slimy Salamanders, Plethodon Kisatchie And Plethodon Mississippi, Across The Lower Mississippi River, Brock Hunter Stevenson

Master's Theses

Species are fundamental units of biodiversity yet delimiting species can be challenging. Slimy Salamanders of the Plethodon glutinosus species complex are a classic example of cryptic species for which species boundaries and relationships have proved difficult to determine. Once thought to be a single species ranging across the eastern United States, protein analysis revealed high genetic divergences among geographically distinct groups of populations, leading to 16 species being recognized within the group. Two of these species, the Louisiana Slimy Salamander (Plethodon kisatchie) and the Mississippi Slimy Salamander (Plethodon mississippi), are closely related but occur on opposite sides of the Mississippi …

Coralai: Emergent Ecosystems Of Neural Cellular Automata, Aidan A. Barbieux, Aidan A. Barbieux

Master's Theses

Artificial intelligence has traditionally been approached through centralized architectures and optimization of specific metrics on large datasets. However, the frontiers of fields spanning cognitive science, biology, physics, and computer science suggest that intelligence is better understood as a multi-scale, decentralized, emergent phenomenon. As such, scaling up approaches that mirror the natural world may be one of the next big advances in AI. This thesis presents Coralai, a framework for efficiently simulating the emergence of diverse artificial life ecosystems integrated with modular physics. The key innovations of Coralai include: 1) Hosting diverse Neural Cellular Automata organisms in the same simulation that …

Effects Of Anthropogenic Noise On The Provisioning Behavior Of Western Bluebirds And Artificial Light At Night On Nestling Development, Kerstin H. Ozkan

Master's Theses

Sensory environments are rapidly changing due to increased human activity in urban and non-urban areas alike. For instance, background sounds can interfere with parent-offspring communication and mask cues reflective of predation risk, resulting in elevated vigilance at the cost of provisioning. In chapter 1, we studied nestling provisioning behavior among Western Bluebirds (Sialia mexicana) in response to short-term (1 hr) and long-term (continuous exposure throughout nesting period) noise exposure. Provisioning rates were lower at nests exposed to short-term experimental traffic noise compared to exposure to ambient background sounds. Trial order strongly influenced provisioning behavior, with the decline in …

Automated Tree Mortality Detection Using Ubiquitously Available Public Data, Michael T. Huggins

Master's Theses

Understanding the dynamic interplay between fire severity, topography, and tree mortality, is crucial for predicting future forest dynamics and enhancing resilience against climate change-induced wildfire regimes. This thesis develops a multi-sensor approach for automated estimation of tree mortality, then applies it to examine trends in tree mortality over a six-year period across a fire affected study site in the Trinity River basin in Northern California. The Random Forest model uses publicly available USGS 3D Elevation Program Lidar (3DEP) and NAIP imagery as inputs and is likely to be easily adaptable to other landscapes. The model had a Receiver Operating Characteristic …

Descriptive Study Of Adult Male Acheta Domesticus Phonotaxis, Dana Husana

Master's Theses

The phonotactic behavior of male Acheta domesticus has not been described at length. The present study evaluates the phonotactic responses of male A. domesticus in relation to age. Male crickets of different ages (young and old) were exposed to calls with attractive and non-attractive syllable periods for this species. Both age groups exhibited phonotaxis but did not show a preference towards the attractive call over the non-attractive ones. No significant relationship was found between age and phonotactic response. Additionally, no significant differences were observed between age and preferred syllable period. Acoustic responses were also observed in some of the older …

Covalent Inhibition Of Enzyme Sortase A As A New Pathway Against Bacterial Resistance Of Staphylococcus Aureus, Umyeena Bashir

Master's Theses

The continued rise of antibiotic-resistant bacteria, such as MRSA (methicillin-resistant Staphylococcus aureus), has made the discovery of novel antibiotics critical. While bacteriostatic and bactericidal antibiotics inevitably exert evolutionary pressure on bacteria to develop resistance, small molecules that target mechanisms of bacterial virulence present a promising alternative for treatment. Sortase A (Srt A), a cysteine protease of S. aureus, promotes bacterial virulence by covalently attaching proteins such as pilin to the bacterial surface, enabling bacterial adhesion to mammalian cells. Inhibitory studies of this enzyme have gained prominent interest as a new pathway for drug development since blocking this enzyme's ability to …

Evaluating Habitat Use By Nekton In Widgeon Grass (Ruppia Maritima), Shoal Grass (Halodule Wrightii), And Unvegetated Bottom Habitats In The Grand Bay National Estuarine Research Reserve, Jessica Woodall

Master's Theses

Seagrass beds support high biodiversity and animal abundance, serve as feeding grounds for a variety of animals, offer shelter from predation, and act as a nursery habitat for juveniles. The species composition of seagrass beds can impact their use as habitat by animals. Two common species of seagrass in the Gulf of Mexico are Ruppia maritima (widgeon grass) and Halodule wrightii (shoal grass). The shallow coastal waters of the Grand Bay National Estuarine Research Reserve (NERR) support both species, but the use of each seagrass as habitat by nekton is poorly understood, which can limit management decision-making. Nekton communities were …

How Sewage Pollution Affects Distribution And Life History Traits Of The Southern House Mosquito, Culex Quinquefasciatus, Catherine Dean Bermond

Master's Theses

Eutrophication from wastewater can cause fluxes of nutrients like and carbon and nitrogen in urban waters. One source of nitrogen in freshwater is from untreated sewage discharging from septic tanks. This causes a variety of environmental issues including harmful algal blooms, harming natural predators, and increased production of mosquitoes. Culex quinquefasciatus is the vector of West Nile Virus in St. Tammany Parish, Louisiana. St. Tammany Parish has over 600 miles of septic ditches, which receive effluent directly from aerated treatment units. Culex quinquefasciatus oviposit in polluted waters, and larvae perform well in water with high levels of decomposing organic matter. …

Deep Ocean Vehicle Applications And Modifications, Nichole "Nikki" T. Arm

Master's Theses

This project had two primary goals: (1) to explore opportunities to further a deep-ocean vehicle’s reach using alternative pressure spheres, and (2) to implement an existing deep-ocean vehicle (lander) in active scientific research.

I gained a greater understanding of the limitations and design choices made for existing pressure spheres using Finite Element Analysis (FEA). My simplified FEA model predicted sphere failure for the existing 30% Fiber Glass 70% Nylon injection molded spheres at an external pressure of 3,954psi or 2,690m ocean-depth (only a 7.38% error compared to the tested minimum failure depth), so I determined it a valid model. I …

Evaluation Of Facilitation On Translocation Outcomes For San Joaquin Antelope Squirrel In The Carrizo Plain, California, Patrick R. Anderson

Master's Theses

In arid and semi-arid environments, burrowing mammals play a key role in increasing landscape heterogeneity through facilitative species interactions. The loss of burrowing mammal populations can consequently lead to negative effects cascading through the ecosystem. It is critical to understand these facilitative interactions for conservation and management. Understanding facilitative interactions may improve wildlife management tools, like translocation, which is often not very successful. To investigate the importance of burrow facilitation on San Joaquin antelope squirrel (Ammospermophilus nelsoni; SJAS) translocation success, I designed a natural experiment with a burrowing facilitator, the giant kangaroo rat (Dipodomys ingens; GKR). I …

Using Noninvasive Calibrated Cuff Plethysmography To Observe The Effects Of Cold-Water Immersion On Arterial Compliance, Rita M. Grigorian

Master's Theses

As the prevalence of cardiovascular diseases continues to exponentially grow in populations across the globe, the necessity of determining underlying factors, effective methods of diagnoses, and universally available preventive measures also grows. Early detection of endothelial dysfunction, a proven precursor of cardiovascular diseases, can be extremely impactful in encouraging preventative measures and early intervention before medical conditions become chronic. In recent years, ice plunging, a form of cryotherapy involving full body immersion in cold water, has gained popularity within circles of fitness and health practitioners, gaining the interest of people of all backgrounds. Certain parallels observed between the human physiological …

Physical Treatments To Modify The Functionality Of Carrot Pomace And The Development Of An Enhanced Beef Patty, Jordan O.A Richards

Master's Theses

Approximately one-third of the global food produced for human consumption is lost or wasted somewhere along the food chain. Carrots are one of the most important and widely produced root vegetables grown worldwide; they are rich in many beneficial bioactive compounds such as dietary fiber and carotenoids. Every year, an estimated 29% of processed carrots are lost as waste. The U.S. is the 3^rd largest producer of carrots worldwide, 85% of which come from California. During carrot juice processing, up to 50% of the raw material remains as carrot pomace. Carrot pomace may contain up to 55% total dietary …

Nanodiscs: A Novel Approach To The Study Of The Methionine Abc Transporter System, Michael T. Winslow

Master's Theses

Membrane transporter proteins play the vital role of moving compounds in and out of the cell and are essential for all living organisms. ATP Binding Cassette (ABC) family transporters function both as importers and exporters in prokaryotes. MetNI is an E. coli Type I ABC transporter responsible for the uptake of methionine into the cytosol from the cell periplasmic space through the cell membrane to maintain intracellular methionine pools. ABC transporters, like other membrane proteins, are most often mechanistically and structurally studied in vitro, solubilized by detergents. However, detergent micelles may affect the conformational changes of membrane proteins relative to …

Biomarkers In Borrelia Burgdorferi Infected Triple-Negative Breast Cancer Cells, Sambuddha Paul

Master's Theses

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with limited treatment options and a poor prognosis. Although some studies have attempted to identify new biomarkers and therapies, only a few have shown promise in clinical trials. In the context of cancer development, infectious agents rank as the third major risk factor, contributing to approximately 15-20% of cancer cases, according to the American Cancer Society. Hence, the identification of biomarkers associated with infection-originated cancer is crucial for enhancing cancer prevention, early detection, diagnosis, and treatment. Borrelia burgdorferi, the causative agent of Lyme disease, has been linked to TNBC …

Mountain Lion Resource Selection In The California Central Coast: Modeling Habitat Suitability For A Large Carnivore In A Rapidly Changing Environment, Megan Elizabeth O'Connor

Master's Theses

Land use conversion toward agriculture such as orchards and vineyards can have severe negative impacts on habitat and wildlife, particularly large carnivores, globally through habitat fragmentation and loss. The mountain lion (Puma concolor) population in the California Central Coast is thought to provide “stepping-stone” connectivity between several severely genetically compromised coastal populations throughout the Santa Cruz Mountains and several mountain ranges in Southern California; however, the California Central Coast is one of the fastest-developing regions of California with little protection against future land use conversion. Conserving areas of and corridors between high-quality mountain lion habitat through conservation easements …

Mate Choice And Sexual Conflict In A Livebearing Fish, Julia C. Kasper

Master's Theses

Eavesdropping occurs when a receiver extracts information from an interaction without directly engaging with the signaler. Eavesdropping has been shown to be an effective way of evaluating the quality of potential mates and their abilities in male-male competition, without having to directly interact with them, thereby reducing energy costs and mating harassment. Girardinus metallicus is a livebearing poeciliid fish endemic to Cuba whose mating system is dominated by mating harassment in the form of sneak copulations, persistent displaying, and male-male aggression. G. metallicus has a male specific polymorphism in both melanin coloration and behavior. Males with melanin coloration are known …

Annotation Of Non-Model Species’ Genomes, Taiya Jarva

Master's Theses

The innovations in high throughput sequencing technologies in recent decades has allowed unprecedented examination and characterization of the genetic make-up of both model and non-model species, which has led to a surge in the use of genomics in fields which were previously considered unfeasible. These advances have greatly expanded the realm of possibilities in the fields of ecology and conservation. It is now possible to the identification of large cohorts of genetic markers, including single nucleotide polymorphisms (SNPs) and larger structural variants, as well as signatures of selection and local adaptation. Markers can be used to identify species, define population …

Solving The Cable Equation, A Second-Order Time Dependent Pde For Non-Ideal Cables With Action Potentials In The Mammalian Brain Using Kss Methods, Nirmohi Charbe

Master's Theses

In this thesis we shall perform the comparisons of a Krylov Subspace Spectral method with Forward Euler, Backward Euler and Crank-Nicolson to solve the Cable Equation. The Cable Equation measures action potentials in axons in a mammalian brain treated as an ideal cable in the first part of the study. We shall subject this problem to the further assumption of a non-ideal cable. Assume a non-uniform cross section area along the longitudinal axis. At the present time, the effects of torsion, curvature and material capacitance are ignored. There is particular interest to generalize the application of the PDEs including and …

Genetic Population Structure And Effective Number Of Breeders In Systems Across The Range Of The Gulf Sturgeon, Jacob Zona

Master's Theses

Gulf sturgeon (Acipenser oxyicnhus desotoi) are a large, anadromous fish belonging to an ancient lineage that diverged as early as 400 MYA. Overfishing for meat and caviar during the early 1900’s reduced their range and abundance and continued habitat destruction and mortality have limited their ability to recover, leading to their listing under the Endangered Species Act. This study uses genetic techniques to determine the effective number of breeders for multiple spawning groups of Gulf sturgeon in river systems across their range to set a baseline for tracking reproductive success of the species. Accompanying genetic information relevant to …

Predictive Ability Of A 3d Body Scanning Mobile Application For Metabolic Health Risk, Caleb Brandner

Master's Theses

There is an increasing prevalence of obesity within the US and rising rates of metabolic syndrome among those aged 20-39 concurrent with a decrease in the reception of primary care. Limitations to healthcare including access, cost, and availability, highlighting the need for simple, efficient, and accessible cardiometabolic health risk screening. Given the surge in smartphone ownership over the last decade, this study sought to determine the predictive ability of a mobile 3D-optical (3DO) body composition assessment application in determining metabolic health risk. A total of 62 participants (female: 36) underwent traditional anthropometric measurements, 3DO body scanning using a smartphone application, …

Development Of Wiskott-Aldrich Syndrome Knock Out Protocol For Drug Substance Assay Development, Julia C. Hanna

Master's Theses

Wiskott-Aldrich Syndrome (WAS) is a rare X-linked primary immunodeficiency affecting approximately 1 in 100,000 live XY births in North America and is caused by a mutation to the WAS gene which is expressed across hematopoietic lineages. The WAS protein (WASp) plays a role in regulating actin polymerization. On a cellular level, there are a variety of effects of a lack of WASp or expression of a dysfunctional WASp protein for patients including issues with migration, adhesion, chemotactic response, phagocytosis, activation, and proliferation across different cell types in addition to reduced platelet size and output. This can lead to several systematic …