Life Sciences Commons^™

Transcriptome-Wide Association Study Of The Plasma Proteme Reveals Cis And Trans Regulatory Mechanisms Underlying Complex Traits, Henry Wittich

Master's Theses

Most genetic variants associated with complex human traits exist in non-coding regions, and thus the mechanism by which they affect a trait can be unclear. Genetic regulation of transcription and translation are key mechanisms through which genetic variants impact traits. Quantitative trait locus (QTL) mapping studies leverage data produced by advanced sequencing and assay technology to identify variants associated with the abundance of a molecular trait like RNA expression (eQTL) or protein levels (pQTL). While proximal genetic variants (cis-acting), like those in promoter or enhancer regions of genes, tend to have the largest effect sizes on RNA transcript and protein …

Lactobacillus-Mediated Phage Induction And Inhibition Of Growth Of Escherichia Coli, Natalie Stegman

Master's Theses

Bacterial species inhabit both the “healthy” and symptomatic female urinary tract. Lactobacillus species are frequently dominant members of the healthy urinary tract microbiota (urobiome), and thus have been associated with the lack of lower urinary tract symptoms (LUTS). In contrast, colonization by Escherichia coli is the most common cause of urinary tract infections (UTIs). Prior research has found that strains of Lactobacillus can inhibit the growth of uropathogens such as E. coli as well as vaginosis-associated pathogens. Investigations into the means by which lactobacilli inhibit pathogenic growth have primarily focused on their production of hydrogen peroxide (H2O2) and lactic acid, …

The Skin Microbiome And Cutaneous T-Cell Lymphoma, Gail Hillary Lantaca Enriquez

Master's Theses

Skin microbiota is associated with disease activity in cutaneous T-cell lymphoma (CTCL). A common treatment for CTCL, narrowband ultraviolet B (nbUVB) phototherapy, has shown to shape the skin microbiome in association with disease improvement in other skin disorders such as atopic dermatitis. To assess the effect of nbUVB phototherapy on the skin microbiome, we performed a longitudinal analysis of skin samples of CTCL patients receiving nbUVB. We found that the treatment led to increased bacterial diversity and reduced abundances of Staphylococcus aureus and Staphylococcus lugdunensis, both bacteria known to be pathogenic. These findings imply that nbUVB treatment changes the skin …

Exploring Evolutionary Relationships Of New World Astragalus Through Phylogenomic Analyses, Victoria Martinez

Master's Theses

The legume Astragalus is the single most diverse genus of plants encompassing nearly 3,000 species. Not only is Astragalus remarkably diverse, but many species have considerable economic importance. For example, toxic Astragalus species also known as “locoweed” contain the chemical swainsonine which affects the reproductive and developmental traits of livestock and causes $100 million in annual losses in the United States alone. The genus is primarily distributed in temperate regions and is particularly diverse in southwest Asia (ca. 2,000 spp.), the Sino-Himalayas (ca. 400 spp.), western North America (ca. 400 spp.), and the Andes (ca.100 spp.; Wojciechowski, 2005; Podlech & …

Regulation Of Spermatogenesis By The Btb Transcription Factor Ribbon, Madeline Kyung Hee Hakala

Master's Theses

The transcription factor Ribbon (Rib) plays an essential role in Drosophila testis development and function. Increased expression of rib throughout development results in significant morphology defects in the adult testis. If overexpression is limited to germ cells and somatic cells in the adult, more mild defects are observed. To better understand how Rib regulates spermatogenesis, we are interested in identifying its transcriptional targets in this context. Through bulk RNA sequencing, differential expression analysis, and subsequent filtering of results, we identified 301 genes with significant changes in expression when rib was overexpressed. Given the previously described role of Rib in the …

Impacts Of Stormwater And Land Cover On The Abundance, Transport, And Composition Of Anthropogenic Litter In Urban Watersheds, Bailey Austin Schwenk

Master's Theses

Anthropogenic litter (AL; trash) is defined as any manufactured item that ends up in the environment. AL consists of many different materials including glass, metal, and plastic, the latter of which typically represents a dominant constituent and has been a major focus of research. Plastic litter and other AL types are pervasive to all types of ecosystems, are persistent in the environment, and are increasing. Rivers are a major conduit transporting AL to oceans. However, rivers also retain and transform AL. More research is needed to understand AL dynamics within rivers, which will improve global models of AL movement and …

Pattern, Process And The Evolution Of Sexual Dimorphism In Three-Spine Stickleback Fish Gasterosteus Aculeatus From Vancouver Island, British Columbia, Katie Van Dame

Master's Theses

Males and females of a species often differ from one another in phenotype—a phenomenon known as sexual dimorphism. Sexual dimorphism is most often attributed to sexual selection. However, sexual dimorphism also derives from natural selection when resource competition generates disruptive selection favoring specialization on different resources, resulting in niche partitioning and the evolution of dimorphism in traits related to competition. Sexual dimorphism may be an important route to increased individual fitness (i.e., more resources, more survival). For example, ecologically driven divergent selection between sexes may derive from differences in their environments, resulting in the evolution of dimorphism in traits related …

Seal Counting On Our Plages (S.C.O.O.P.), Kaanan Kharwa

Master's Theses

The Vertebrate Integrative Physiology (VIP) lab monitors the population of northern elephant seals at the largest mainland breeding colony, located at Piedras Blancas (San Simeon, CA). As the population expands, more human-seal interactions and conflicts over land use occur. The VIP lab's work informs California State Parks and helps with the management of the rookery. Currently, members of the VIP lab fly a drone over the beaches, capture multiple images, and manually count the seals, which takes around 14 to 21 hours of analysis per survey. Machine learning methods such as Convolutional Neural Networks (CNN) and Region-based Convolutional Neural Networks …

Of Geese And Grass: Investigating Impacts Of Brant Grazing On Eeelgrass, Dakota L. Osborne

Master's Theses

Grazing pressure is important in structuring plant communities, particularly in aquatic environments. Eelgrass (Zostera marina), a keystone species in estuaries across North America, is experiencing widespread population declines. As a keystone species, eelgrass provides numerous important functions, including: 1) water filtration, 2) sediment stabilization, 3) providing refuge and nursery habitat for numerous species, and 4) carbon sequestration. Benefits which could be lost if eelgrass beds continue to diminish. California has experienced some of the greatest eelgrass declines, and Morro Bay, CA experienced a 96% decrease in eelgrass from 2007 to 2017. Most studies to date have examined bottom-up …

Development Of Extruded Puffed Snack Utilizing Carrot Pomace, Bean Flour, And Rice Starch As Primary Ingredients, Julia Zoe

Master's Theses

Every year, the carrot industry worldwide wastes up to 50% of carrots as raw material due to processing (Šeregelj et al., 2020). When carrots are juiced, the remaining fibrous pulp is often discarded as carrot pomace. In order to redirect this food waste, the first objective of this research was to optimize formulations for an extruded puffed snack that is most similar to commercially available puffed snacks, utilizing baby lima bean flour and carrot pomace

Hardness (kg), cross-sectional expansion ratio, bulk density (g/cm³), moisture content (%), water activity, specific mechanical energy (kJ/kg), carotenoid concentration (ppm), and total dietary …

Survey Of Soilborne Pathogens Infecting Strawberry In Oxnard, California & Effect Of Planting Date And Chill Treatment On Yield Of Strawberry, Samantha Z. Simard

Master's Theses

Survey to quantify the frequency of the five main pathogens (Macrophomina phaseolina, Fusarium oxysporum f. sp. fragariae races 1 and 2, Verticillium dahliae, and Phytophthora spp.) infecting strawberry in the Oxnard growing district of California. M. phaseolina was the most prevalent pathogen detected in diseased plants in the Oxnard growing district, present in 67.6% of samples positive for at least one pathogen. F. oxysporum f. sp. fragariae race 1 (35.3%), V. dahlia (8.8%), F. oxysporum f. sp. fragariae race 2 (5.9%) and Phytophthora spp. (2.9%) followed at lower prevalence. Associations were found between fewer drip irrigation lines …

Understanding The Mystery Of R-Loops And Their Relationship To Nucleolar Stress, Kevin Shane

Master's Theses

Genomic instability is an increase in the likelihood of DNA mutations and genetic changes during cell division, a common feature in cancer cells. One cause of genomic instability comes from the aberrant formation of three-stranded nucleic acid structures called R-loops. R-loop form when an RNA strand hybridizes to its complementary strand of DNA, forming a stable RNA:DNA hybrid and displacing one free strand of DNA 1. Accumulation of unscheduled R-loops can lead to replication stress, fork collision, gene expression changes, and double-strand breaks that are underlying causes of genome instability and the development of many diseases, including cancer 2. Many …

Terrestrial Salinization Impacts On Growth And Behavior Of A Common Detritivore Armadillidium Vulgare (Isopoda), Danielle Harmoney Orcutt

Master's Theses

Climate change and human activities are changing the nutritional landscape by increasing the availability of some essential elements and decreasing others. Sodium (Na) is an essential element in heterotrophs, which is required for water regulation, nerve function, and muscle function. Heterotrophs can acquire Na through diet and environment, often experiencing limited availability of Na due to plants concentrating Na 10-100 times less than heterotrophs need. The Sodium Subsidy-Stress (SSS) hypothesis posits that organismal performance follows a hump-shaped curve of a physiological response, where Na acts as a subsidy, increasing organismal performance such as growth until an optimal threshold is reached, …

Assessment Of Mediterranean Diet Adherence Using The Kidmed Diet 2.0 Tool: College Student Questionnaire, Nakia Cyrice Hilton

Master's Theses

The Mediterranean Diet has garnered increasing popularity due to its multifaceted health benefits. The MedDiet enhances well-being across all age groups, emphasizing high consumption of fruits, vegetables, legumes, nuts, olive oil, and whole grains and moderate fish, poultry, and dairy intake. Recent research underscores the significant impact of Mediterranean diet adherence on college students' physical and mental health. The diet's emphasis on nutrient-dense foods rich in vitamins, minerals, and antioxidants supports cognitive function, which is pivotal for academic performance. Moreover, the abundant presence of healthy fats, particularly from olive oil and fatty fish, may contribute to improved mood regulation, potentially …

Division I Collegiate Baseball Pitching Performance In Relation To Forearm Kinematics And Kinetics, Christopher W. Watson

Master's Theses

This thesis investigates physical and anthropometric factors influenced by forearm rotation biases associated with supination and pronation on pitch characteristics among Division I college baseball pitchers. The study involved twenty-two participants who underwent comprehensive physical assessments, including measures of forearm strength, range of motion, and grip strength, as well as finger and hand length measurements. Ball flight metrics were collected during intrasquad scrimmages using advanced radar tracking technology. Results revealed significant relationships between distinct physical biases of strength in pronation and supination, pinch strength, anthropometrics such as middle finger length, and specific pitch characteristics. This study lays the groundwork for …

Oral Nutritional Supplement Prescription And Adherence Perspectives, Kristyn Bordelon Hood

Master's Theses

Oral nutritional supplements (ONS) are nutrient-dense beverages that aid in meeting the nutrient needs of patients. Recent research has indicated that patient adherence to prescribed nutritional supplements may depend on palatability, tolerance, and taste fatigue. Registered Dietitian Nutritionists (RDNs) are healthcare professionals who may prescribe these supplements directly or make recommendations to the patient’s physician for a prescription, thereby influencing patient adherence. Little research has been documented regarding taste fatigue and the influences of the RDN’s decisions on patient adherence to nutritional supplement adherence. The purpose of this study was to gain an understanding of the perspectives of nutrition professionals …

Development Of A Urothelial Cell Line Expressing A Caspase-1 Biosensor To Measure Cellular Inflammatory Responses To Potential Uropathogens, Nikita Riya Kesav

Master's Theses

Urinary tract infections are one of the most common bacterial infections, historically implicating Escherichia coli as the causative pathogen. However, it is now known that there are a variety of bacteria that exist within the urinary tract, acting as either beneficial uroprotectives or opportunistic uropathogens. Furthermore, there are significant gaps in our understanding as to how these bacteria interact with the urothelium and what role each plays in maintaining or disrupting homeostasis. Research has shown that Toll-like receptor 4 (TLR4) signaling and Nod-like Receptor Protein 3 play a role in inflammasome activation during infection, triggering caspase-1 activation and inducing release …

Evolutionary Patterns Of Anolis Lizard Skulls: An Investigation In Geometric Morphometrics And An Educational Exploration Of Structure And Function, Katherine Beyer Starr

Master's Theses

This study explores the evolutionary patterns of Anolis lizard skulls and integrates findings into a curriculum focused on elucidating the structure and function of a lizard's head. The first objective was to develop an understanding of how the evolutionary patterns, of an extraordinary group of lizards (Anolis) compares to their relatives. Most of the prior research on Anolis morphology has focused on the post-cranium because of its significance towards subdivision of the arboreal habitat. But the group’s remarkable diversity in head shape has been seriously under-investigated. By performing geometric morphometric analysis of skull shape across a large sample of anoles …

Regulation Of Sterile Inflammatory Responses By Mitochondria-Associated Proteins, Meghana Venkatesan

Master's Theses

Inflammation is an important defense mechanism through which cells respond to pathogenic insults and damage/stress signals. Immune cells mediate extracellular inflammatory responses by synthesizing and releasing small proteins called cytokines, which play critical roles in modulating these responses. Specifically, key pro-inflammatory cytokines such as IL-1beta are released upon the assembly and activation of a multi-protein intracellular complex called the inflammasome, the most well-studied of which is the NLRP3 inflammasome. Several proteins have been identified as important regulators of cellular stress responses, including vacuole membrane protein 1 (VMP1). The present research shows that VMP1-depleted cells exhibit exacerbated cellular inflammation and are …

Development Of Targeted, Statin Loaded Nanoparticle Delivery Systems, Stephanie Judkins

Master's Theses

Statins lower endogenous production of cholesterol through their inhibition of the mevalonate pathway. Lipophilic statins in particular exhibit anti-inflammatory effects at supraphysiological doses by preventing downstream signaling through small molecule GTPases. Interest lies in development of statins as anti-inflammatory therapeutics, however, achieving effective doses locally incurs serious off-target effects. Our goal was to develop and optimize a targeted delivery system to traffic these drugs to inflamed sites and unload the drug at effective concentrations while avoiding systemic exposure. Lipophilic statins (lovastatin, simvastatin, and atorvastatin) were incorporated into polymeric nanoparticles (NPs) due to their hydrophobicity. We have shown that statins released …

Investigating The Roles Of Sirtuins During Cvb3 Infection And Innate Immunity, Bridget M. Hulsebosch

Master's Theses

Coxsackievirus B3 (CVB3) is an enterovirus that chronically infects heart tissue, leading to dilated cardiomyopathy. However, no vaccines or antivirals exist for CVB3 infection or to treat CVB3-induced dilated cardiomyopathy, except for a heart transplant. Sirtuins (SIRTs), class III lysine deacetylases, have diverse and complex roles in cellular functions, contributing to energy production, NF-κB signaling, cell cycle regulation, and inflammation. Previous studies showed that SIRTs are essential for hepatitis B and A viral replication and regulate the IFN response during viral infection. However, the role of SIRT1 and 2 during CVB3 infection is entirely unknown. CVB3-infected SIRT1 and SIRT2 knockout …

Investigating The Oncogenic Role Of Nkx3.1 In Prostate Cancer, Audris Budreika

Master's Theses

Prostate cancer is a unique disease in that it is fueled by androgen receptor (AR) signaling. In the clinic, AR signaling is disrupted by removing androgens via chemical castration and employing AR-antagonists such as enzalutamide. Unfortunately, these therapies are short-lived, resistance sets in, and tumors evolve to a form of the disease called castration-resistant prostate cancer (CRPC). At this stage, therapeutic options are virtually exhausted and palliative care is pursued. There is a growing need to characterize other molecular players that cooperate with AR or play a unique role in CRPC on their own. One such potential candidate is the …

Characterization Of Cd11c-Expressing Gut-Associated T Cells, Ana Cvetkovic

Master's Theses

Our immune system is a remarkable defense network that protects our bodies from a range of threats. Its’ intricate machinery comprises of messenger and effector cells that work together to coordinate an effective immune response. Traditionally, T lymphocytes have been considered effectors: they receive instructions from messengers, known as Antigen Presenting Cells (APCs), that alter T-cell activation state and behavior. In the gut, Dendritic Cells (DCs) are the APCs that most often instruct T cells. To accomplish their messenger role, DCs express CD11c at high levels, a surface marker involved in cell-to-cell signaling and phagocytosis. As such, CD11c expression has …

The Effects Of Conditional Loss Of Myosin Binding Protein H-Like On Cardiac Function, Hope Victoria Burnham

Master's Theses

Dilated cardiomyopathy (DCM) is a common cause of heart failure with a strong hereditary component. Mutations in the myosin-binding protein H-like (MYBPHL) gene are linked to hereditary DCM, atrial fibrillation, and atrioventricular arrhythmias. MyBP-HL is a sarcomeric protein that is highly expressed in the atria with only scarce, distinct clusters of MyBP-HL positive cells in the ventricles, mostly in or surrounding the ventricular conduction system (VCS). Constitutive knock-out of MyBP-HL in mice causes atrial dilation, ventricular dysfunction, arrhythmia, and DCM. Whether MyBP-HL plays a developmental role, or if knock-down in adulthood will recapitulate a similar phenotype has yet to be …

Testing Strategies To Develop A Mucosal T Cell Inducing Vaccine For Hiv-1, Reynolds Boone

Master's Theses

Despite numerous efforts, HIV vaccine is still not available. Because HIV Envelop protein varies among subtypes and isolates, it is impossible for one vaccine against HIV Env to induce neutralizing antibodies against all subtypes and isolates. Previous vaccine attempts inducing HIV-specific CD4+ T cells have even been shown to enhance the HIV infection because HIV preferentially infects activated CD4+ T cells. It is known that CD8+ cytotoxic T cells (CTLs) play an important role in controlling HIV infections. We hypothesize that a vaccine inducing only CD8+ CTLs but not CD4+ T cells will be effective in preventing HIV infections. Thus, …

The Anti-Inflammatory Properties Of Exopolysaccharide From Bacillus Subtilis, Nikolay Todorov

Master's Theses

Commensal microorganisms can be used therapeutically to ameliorate a variety of diseases. The laboratory of Dr. Katherine L. Knight studies these therapeutic properties in the commensal microorganism known as Bacillus subtilis. Previously, the Knight lab has demonstrated that B. subtilis can protect against colitis caused by Citrobacter rodentium suggesting that B. subtilis possesses anti-inflammatory properties. These properties are specific to the polysaccharide capsule of the microorganism known as exopolysaccharide or EPS. EPS can be produced and purified for study. EPS has been demonstrated to be protective in a variety of diseases such as allergic eosinophilia, sepsis, Graft versus Host disease, …

Absolute Quantification Of Human Myosin And Titin Isoforms In Disease By A Mass Spectrometry Approach, Nitha Aima Muntu

Master's Theses

Heart failure (HF) is the leading cause of death worldwide and produces an immense economic burden. Dilated cardiomyopathy (DCM), characterized by contractile weakness and chamber dilation, is a significant cause of HF. The sarcomeric proteins play a crucial role in regulating the contractile properties of the heart. As the primary motor protein, the expression of cardiac myosin isoforms (α-MHC and β-MHC) dictates the performance and cardiac energy utilization of the sarcomere. Titin is the giant spring protein in the sarcomere, and titin isoform expression impacts the passive stiffness of the myocardium. Small changes in the α-MHC/β-MHC and titin isoform ratios …

Sport And Environmental Issues: Ncaa Division I Student-Athletes’ Personal Experiences, Ivanna M. Anderson-Villela

Master's Theses

While sport ecology is a growing category in sport management literature, there is a lack of research exploring athletes’ experiences regarding environmental issues, and the impacts environmental issues have on student-athletes. The present study qualitatively explored the personal lived experiences of eight NCAA Division I student-athletes regarding environmental issues with the aim of identifying potential influences on values and beliefs through social norms and understanding the student-athlete perspective. Thematic analysis identified 152 raw data themes and 19 higher order themes, which were organized into four central themes: awareness, care and concern from athletic departments, implications, and advocacy. Generally, student-athletes perceived …

Observations Of Currents, Waves, And Turbulence Within A Giant Kelp Forest In Stillwater Cove, Carmel, California, Logan A. Grady

Master's Theses

Nutrient distribution and propagule dispersal within Giant kelp (Macrocystis pyrifera) forests are significantly influenced by turbulence. In-situ measurements of turbulence within giant kelp forests are limited and driving mechanisms are primarily informed by controlled-flume experiments. This study investigates relationships between currents, surface gravity waves, and turbulence within a kelp forest through deployment of moored instrumentation and kelp surveys in Stillwater Cove, California during summer of 2022. Oceanographic conditions were primarily driven by coastal upwelling and a semi-diurnal internal tide, which was associated with cooling events and enhanced onshore velocity within the kelp forest during rising tides. Estimates of gradient Richardson …

Overnight Rice Fermentation: An Analysis Of The Physicochemical Changes In White, Brown, And Enriched Rice Varieties, Kavin Sivakumar

Master's Theses

Fermentation refers to the activity of microorganisms breaking down substrates, resulting in changes to a food product. One fermented food practice from the Indian subcontinent is overnight fermented rice. The traditional preparation consists of covering cooled cooked rice in water and leaving it at room temperature to ferment overnight. The objective of this project was to investigate overnight rice fermentation through quantifying its physicochemical changes. The study utilized three types of rice: white, enriched white, and brown. Mixtures of cooked rice and water at a 1 gram: 2 milliliter ratio were fermented at 29 degrees Celsius and 60% humidity for …