Life Sciences Commons^™

Investigating Patterns Of (Mal)Adaptation In Two Dominant Cajun Prairie Grasses: Schizachyrium Scoparium And Panicum Virgatum, Braden Isaiah Doucet

Masters Theses

Local adaptation is assumed to be prevalent within natural populations, but anthropogenic climate change and habitat destruction have been demonstrated to cause maladaptation. This thesis examines patterns of adaptation within two dominant grass species of our local Cajun Prairie ecosystem, Panicum virgatum and Schizachyrium scoparium. Using a provenance common garden study, our results reveal how climate change and habitat destruction have altered the patterns of adaptation within local populations. Chapter 1 examines how source climate and geographic distance predicts population fitness. Chapter 2 examines the type, magnitude, and direction of selection acting on key ecological traits of both species, as …

City Farm Slo: A Case Study Of Nonprofit Regenerative Agriculture, Carver Tunnell

Master's Theses

The focus of this thesis is to create a case study on City Farm SLO, a nonprofit based in San Luis Obispo, California, that has engaged in education and regenerative agriculture on City owned land since 2013. This case study is intended for use in undergraduate agribusiness and natural resource management courses, to encourage thoughtful discussion surrounding nonprofit and regenerative agricultural systems. The case presents the nonprofit at a time of relative success, having recently secured a lease renewal, extending stewardship 40 years into the future. However, the reliance on grants and donations threatens the security of the operation going …

Independent And Combined Effects Of Early-Life Iron Deficiency And Antibiotic Exposure On Growth And Hematological Outcomes In A Piglet Model, Ginger M. Fitzpatrick

Master's Theses

Iron deficiency (ID) affects over 2 billion individuals globally. Children under 5 are at increased risk of ID due to rapid growth and are especially vulnerable to its negative consequences because of iron’s essential role in cognitive development and immune maturation. ID is the leading cause of iron deficiency anemia (IDA), with IDA affecting approximately 40% of children in this age group. Antibiotic (abx) exposure is also prevalent during early life and may disrupt growth and through gut dysbiosis, with increasing use posing additional risk in younger populations. Geographically, there is overlap in regions with high anemia prevalence and those …

Large Scale Kmer-Based Proteomic Analysis: An Application Towards Evolutionary Constraint Discovery, Matthew Chak

Master's Theses

Large protein databases now make it possible to study short peptides across natural protein sequence space at unprecedented scale, but exhaustively counting k-mers across billions of protein sequences remains computationally difficult. This thesis develops an exact amino-acid k-mer counting method based on direct addressing, in which fixed-length amino-acid strings are encoded as base-20 integers and updated with a sliding-window recurrence. By avoiding key storage and collision resolution, this approach removes overhead inherent to hash-map-based methods when the k-mer space is sufficiently dense. A memory analysis shows when direct addressing is preferable to open-addressing hash tables, and expected-saturation calculations motivate its …

Exploring Regenerative Vegetable Systems On The Central Coast Of California, Una S. O'Connell

Master's Theses

As climate change and current agricultural practices place pressure on the long term sustainability and resilience of food production systems, there is growing interest in whether existing agricultural systems can adapt to maintain productivity while improving environmental outcomes.

This study evaluated the effects of regenerative versus standard organic vegetable production systems on yield, insect communities, and weed suppression across three field trials conducted on California's Central Coast. In addition, I collected baseline soil health data for all trials. Trials 1 and 2 were carried out at the Cal Poly San Luis Obispo Organic Farm using cabbage and broccoli as cash …

The Effects Of Maceration And Enzymes On The Chemical Characteristics Of Hard Apple Cider, Manou De Pelsmaeker

Master's Theses

The purpose of this study was to analyze the effects of maceration and pectinase enzymes on the base chemical, polyphenolic, and volatile characteristics of cider. The apples (Fuji) were milled and macerated for 0, 4, 12, 24, or 36 hours, both with and without an enzymatic pectinase addition. While base chemical characteristics such as sugar content and ABV were unaffected, the acidity of cider was influenced maceration and enzymes. Extended maceration time resulted in lower concentrations of malic acid, and enzymes resulted in a lower pH compared to the control. Polyphenols were extracted during maceration time, resulting in higher concentrations …

Sustainable Management Of Soilborne Pathogens In Strawberry Production Through Host Resistance And Sanitation Practices, Maria G. Alvarez Arredondo

Master's Theses

Strawberry production in California is significantly impacted by soilborne pathogens that reduce plant productivity and increase management costs. This research addressed management of these pathogens through two independent approaches: evaluation of host resistance in strawberry cultivars and assessment of sanitation practices for reducing pathogen movement between fields.

Macrophomina root rot, caused by Macrophomina phaseolina, was evaluated over two growing seasons (2024–2025 and 2025–2026) using field trials at California Polytechnic State University, San Luis Obispo. In Year 1, disease incidence varied widely among genotypes, with mortality ranging from 1.3% to 88.8% and an average mortality of 26.4%. Area under the …

Elucidating The Role Of The Rnf20 Histone Modifier In Pancreatic Beta Cells, Tanya Hans Pierre

ETDs from 2020-2029

Diabetes is defined as a loss of functional beta cell mass. It is classically categorized into Type 1 Diabetes (T1D), immune-mediated beta cell destruction and Type 2 Diabetes, which is characterized by whole body insulin resistance alongside beta cell dysregulation. The incidence of diabetes worldwide has risen annually. Despite the presence of therapeutic interventions, diabetes’ heterogeneity can prompt ineffective glycemic control and the development of diabetes-associated comorbidities. For that reason, new approaches to glycemic control for individuals with diabetes are required. One approach to restore glucose homeostasis is beta cell replacement therapy, in which stem cells are programmed into beta-like …

Protein Glycosylation In Natural And Synthetic Minimal Genome Mycoplasmas, John Sanford

ETDs from 2020-2029

Mycoplasmas are cell wall-less bacterial symbionts with remarkably streamlined genomes. Mycoplasmas offer two intriguing model organisms for studying concepts of minimal life. Mycoplasma genitalium has streamlined its genome to 580-kbp while maintaining virulence to suit its niche of parasitizing the human urogenital tract. The J. Craig Venter Institute has synthesized and transplanted a 543-kbp genome into a recipient cell, resulting in a non-pathogenic organism termed JCVI-syn3A. The conservation of a biological process in M. genitalium and JCVI-syn3A strongly implies an essential function in mycoplasmas, and potentially all life. Despite common thought of mycoplasmas being the simplest cells, much of their …

Dock7 Is A Novel Modifier Of Duchenne Muscular Dystrophy Pathology, Katherine English

ETDs from 2020-2029

Duchenne muscular dystrophy (DMD) is a progressive, x-linked neuromuscular disorder affecting 1/5000 male births every year. DMD results from mutations in DMD, a critical structural protein within the muscle. In the absence of Dystrophin, the muscle degrades, increasing inflammation, destabilizing the cell membrane and going through constant cycles of regeneration which depletes the stem cell population. Over time, muscle tissue is replaced by fibrosis and adipose tissue, leading to loss of ambulation, respiratory and cardiac failure leading to death by early 20s. The standard of care for DMD patients is corticosteroid treatment. However, gene therapies have recently emerged which present …

Aged 539 Internship Report: Cal Poly Rodeo Media And Marketing, Anna Grace Durham

Agricultural Education: Graduate Internship Reports

This internship report examines the role of media and marketing within the Cal Poly Rodeo Program and highlights the integration of leadership, athlete development, and strategic communications in a collegiate athletics setting. Serving as the Media Manager for Cal Poly Rodeo, the internship focused on strengthening the program's digital presence, enhancing brand identity, and increasing community engagement, particularly surrounding the 2026 Poly Royal Rodeo. Through collaboration with University Administrators, the Officer Team, sponsors, and external media partners, comprehensive marketing campaigns were developed and implemented, resulting in significant increases in social media reach, audience engagement, and ticket sales. The project included …

Chemical And Sensory Consequences Of Oxidative And Reductive Handling Of White Wines, Amelia Pargellis

Master's Theses

In the 2024 and 2025 vintage four experiments were performed each with a different varietal, namely Albariño, Grenache blanc, Loureiro, and Vermentino. These experiments investigated the effects of hyperoxygenation, reductive winemaking techniques, while monitoring the oxidation-reduction potential.

Albariño grapes were made following two juice protocols, control/reductive (Reductive Control) and oxidative (HyOx). Reductive Control received antioxidants (50 ppm SO₂, 160 mg/L ascorbic acid) and CO₂ blanketing, and HyOx underwent hyperoxygenation at approximately 700 mL/L/h of air for two hours through a stainless-steel sparging stone with 10-µm pores. Juice was cold-settled and racked. Reductive Control juice was split into …

Viruses Causing Panleukopenia In Domestic Cats: A Review Of Feline And Canine Parvoviruses, Simon Colby

University Honors Theses

Parvoviruses remain among the most important viral pathogens in domestic cats today. Despite this, there is much confusion around which parvoviruses can infect cats, and what extent of disease they can cause. One of the two parvoviruses infecting cats, canine parvovirus type-2 (CPV-2), likely evolved from the other parvovirus infecting cats, feline parvovirus (FPV). These viruses differ at only a few places in their genomes, and share the method of cell entry via the transferrin receptor. The disease caused by FPV has been well characterized in cats, but disease caused by CPV-2 is more obscure. Additionally, current testing methods for …

Developing A High-Resolution Off-Axis Common-Mode Digital Holographic Microscope, Lucy Cook

University Honors Theses

Off-axis digital holographic microscopy (DHM) is a powerful tool for 3D, non-invasive live-cell tracking without moving parts. However, traditional setups face an inherent dilemma: split-path interferometers offer high spatial resolution but poor temporal stability, while more stable common-mode configurations are historically limited to lower numerical aperture (NA) regimes. This thesis bridges that gap by scaling a common-mode DHM architecture into a high-resolution benchtop instrument featuring NA = 0.65 objectives, paired with a high-power 520 nm laser source to combat transmission losses and sustain imaging frame rates across an expanded optical footprint. We map the multi-variable design space required to satisfy …

Shallow-Marine Crinoid Genera May Have Been More Resilient Across Permian Extinction Events In Terms Of Richness Than Deep-Marine Crinoid Genera, Amelia C. Kolstad

University Honors Theses

Throughout the Phanerozoic, one of the most successful phyla of marine invertebrates has been Echinodermata. Echinodermata was particularly successful throughout the Paleozoic, with class Crinoidea making up a majority of occurrences. The proportion of echinoderm occurrences that are crinoids declined massively at the end of the Permian and continued to decrease into modern day, never fully recovering. One of the factors thought to have been so important for crinoid success in the Paleozoic and their decreasing success throughout geologic time has been their propensity for success in shallow-marine environments, though crinoids also exist within deep-marine environments. This study seeks to …

Microbial Literacy, Equity, And Sustainability At Cal Poly: A Policy Framework With University Housing As A Pilot Case, Joseph B. Fewel

Biological Sciences

Microorganisms play a fundamental role in human health, environmental systems, and the functioning of built environments, yet they remain largely absent from sustainability and public policy discussions. This project proposes a framework for integrating microbial literacy, equity, and health into institutional decision-making, using California Polytechnic State University (Cal Poly) as a case study and university housing as a pilot site for implementation. Drawing on interdisciplinary literature in microbiology, public health, environmental justice, and sustainability, as well as policy analysis and stakeholder interviews, this project examines how campus systems, including housing, ventilation, sanitation, food systems, and waste management, shape microbial exposure …

Exploring The Durability Of Marine Picocyanobacterial Microcolonies, Erik Swanson

University Honors Theses

Picocyanobacteria of the genus Synechococcus are widespread aquatic photoautotrophs that play essential roles in primary production and carbon cycling. Some Synechococcus strains form multicellular microcolonies, but the mechanisms of cell-to-cell attachments and structural durability of these microcolonies remain poorly understood. This research investigated the physical durability of microcolonies in two marine Synechococcus strains (CC9605 and CC9311) using physical disruption treatments. Cultures were subjected to vortexing and sonication treatments, and populations of single cells and microcolonies were quantified using flow cytometry based on differences in measures of size. Results indicated that strain CC9605 showed no significant treatment effect, whereas CC9311 displayed …

Movement And Space Use Of Weaned Northern Elephant Seal (Mirounga Angustirostris) Pups During Their First At-Sea Foraging Migration, Katie Saenger

Master's Theses

The northern elephant seal (Mirounga angustirostris) is a marine mammal known for engaging in long foraging migrations at sea. Adult male northern elephant seals follow pathways along the western coast of North America towards Alaska and adult female northern elephant seals follow pathways to open ocean in the North Pacific. However, there is little information on weaned northern elephant seal pup foraging behavior during their first foraging migration. This lack of knowledge is significant because northern elephant seals have a mortality rate of >50% in the first year. This project aimed to better understand the at-sea migratory movement …

Effects Of Irrigation And Nitrogen Management On Yield And Leaching Risk In Organic And Conventional Broccoli Fields, Shane Egerstrom

Master's Theses

Under regulatory pressures to reduce groundwater contamination by nitrate from fertilizer, such as those posed by the Central Coast Regional Water Quality Control Board’s Agricultural Order 4.0, a need exists to better understand interactions between irrigation and nitrogen (N) management. To increase N use efficiency (NUE), growers are encouraged to account for additional sources of N in their management plans, such as irrigation water N and preplant soil N. The availability of these N sources for plant uptake and how it is affected by other management conditions is not yet well documented. We conducted 6 field trials, 3 organic and …

Assessing Nitrogen Leaching Risk In Organic Vegetable Production, Megan Widle

Master's Theses

Nitrogen (N) leaching is the primary driver of groundwater contamination in agricultural regions. On California’s Central Coast, Agricultural Order 4.0 regulates this risk by constraining field-level N balances (N applied minus N removed). However, the assumption that unrecovered N is lost via leaching may not hold in organic and regenerative systems that promote soil organic matter accumulation. This study evaluated whether measured N leaching aligns with estimates derived from partial N budgets in organic systems, and whether management practices (intercrops, cover crops, and reduced tillage) can mitigate leaching risk. Four field trials were conducted to investigate N dynamics in organic …

Evaluating The Commercial Aquaculture Potential Of The Native Pacific Littleneck Clam (Leukoma Staminea) As A Climate Resilient Alternative To The Non-Native Manila Littleneck Clam (Ruditapes Philippinarum)., Skylar M. Wuelfing

Master's Theses

The California shellfish industry’s near-exclusive reliance on the non-native Manila littleneck clam (Ruditapes philippinarum) creates an economic vulnerability to climate-driven disturbances, which can cause mortality events that eradicate up to 80% of stocks. This singular reliance on an introduced species highlights a need for the evaluation of native alternatives like the Pacific littleneck clam (Leukoma staminea). Our goal was to assess the feasibility of using the native Pacific littleneck in commercial aquaculture by comparing their performance to the non-native Manila littlenecks across the following conditions: 1) a five-month field outplant trial at high and low intertidal …

Marine Heatwaves And Fish Reproduction: Endocrine Responses In The Eurythermal Sheepshead Minnow (Cyprinodon Variegatus), Isabel Villafuerte

Master's Theses

Marine heatwaves associated with climate change are increasing in frequency and severity, posing significant threats to fish populations in shallow habitats such as estuaries and salt marshes. Because temperature is a primary regulator of fish reproduction, understanding how heatwaves affect reproductive physiology is critical for anticipating the biological consequences of ongoing climate change for coastal fishes. Here we examined how simulated heatwave conditions affect the reproductive hypothalamic-pituitary-gonadal (HPG) endocrine axis in the estuarine sheepshead minnow (Cyprinodon variegatus), a eurythermal fish well suited to studying thermal stress responses in estuarine environments. Adult sheepshead minnows acclimated to a daily oscillating …

Effects Of Hot Water Dipping And Sub-Zero Saline Chilling On The Microbial Safety Of Broiler Carcasses And Recycled Chilling Water, Elen Zhu

Master's Theses

Broiler meat became the most widely consumed meat within the United States and across the world in 2019. The trend of increasing broiler consumption is expected to continue due to affordability, health benefits, and production efficiency. To meet the growing demand of broilers, a substantial number of birds need to be produced and processed while minimizing bacteria contamination, water consumption and wastewater generation.

In this study, the microbial safety (mesophilic aerobic bacteria, coliforms, and Escherichia coli) of broiler carcasses and post-chill water (red water) was assessed, using innovative processing techniques and red water recycling. A total of 144 broilers …

Evaluation Of Ultraviolet-C Light For Control Of Mites And Western Tarnished Plant Bug In Strawberry & Interactive Lethal Effects Of Common Strawberry Fungicides And Adjuvants On Phytoseiulus Persimilis, Colin T. Koubek

Master's Theses

California strawberry production relies heavily on chemical pesticides to manage arthropod pests and diseases, but pesticide resistance, regulatory pressure, and the need to conserve biological control agents have increased interest in alternative pest management tools. This thesis evaluated ultraviolet-C (UV-C) light as a nonchemical management tool for key strawberry arthropod pests and assessed the compatibility of common strawberry fungicides and adjuvants with the predatory mite Phytoseiulus persimilis Athias-Henriot. The first objective was to determine the ovicidal and lethal effects of UV-C light on Lygus hesperus Knight eggs and nymphs. Laboratory and field ovicide assays were conducted using UV-C doses relevant …

Title Page And Abstract: Diet Quality And Sustainability Based On Nut Intake Among Free-Living Adults, Raquel Aurora Martínez

Loma Linda University Electronic Theses, Dissertations & Projects

Background: There is increasing interest in dietary patterns that support both human and planetary health. Plant-forward dietary patterns commonly promoted within sustainability frameworks frequently include nuts. Despite concerns regarding resource use, particularly water demands, nuts may contribute to improved diet quality and sustainable dietary behaviors.

Objectives: To examine whether diets characterized by higher nut intake are associated with dietary quality, adherence to sustainable dietary patterns, and food-related sustainability behaviors among free-living adults.

Methods: Cross-sectional analyses were conducted using data from an online validated semi-quantitative food frequency questionnaire integrated with sustainability-related survey items. Energy-adjusted nut intake was categorized …

Effects Of Led Light Spectra And 1-Mcp On Postharvest Quality And Bioactive Compounds Of Cucumber (Cucumis Sativus L.) During Cold Storage, Imad Eldin Abbas Yousif

Theses

Extending postharvest quality and maintaining the nutritional value of cucumber fruit requires specific storage conditions to postpone senescence and enhance marketability. The postharvest lighting environment is a main factor that influences quality preservation for harvested biomass. The objective of this study was to investigate the effects of different light emitting diodes (LED) spectra (green, red, blue, and white LED) alone or in combination with 1-Methylcyclopropene (1-MCP) on postharvest quality and bioactive compounds of cucumber fruit during cold storage for 16 days at 5°C, the control fruit were left in the dark. For combined treatment, the fruits were exposed to 1-MCP …

The Impact Of Elevated Co2, Uv-B Irradiation, And Rising Temperature On Quinoa, Mohamed Yousif

Theses

Climate change is driving simultaneous increases in atmospheric CO₂, surface UV-B radiation, and temperature, yet most crop research has examined these stressors in isolation, leaving their combined effect on nutritional quality poorly understood. Quinoa (Chenopodium Quinoa Wild.), a stress-tolerant C3 pseudocereal, has been promoted as a climate-resilient forage and food crop for arid regions, but its performance under realistic multi-stress conditions remains uncertain. This study therefore asked whether quinoa can maintain biomass, yield, and mineral quality when exposed to elevated CO₂, enhanced UV-B, and rising temperature individually and in combination, and whether their interaction is additive or non-additive.

To …

Exercise Therapy For Mood Disorders In Retiring/Former Athletes, Christian Antos

Dissertations

This dissertation examined the potential integration of exercise therapy and psychotherapy as a treatment approach for mood-related difficulties experienced by former elite athletes during the transition out of competitive sport. Retirement from athletics is often associated with significant biopsychosocial challenges, including disruptions in identity, healthy routines, social support, and emotional well-being. Existing literature suggests that exercise may serve as an effective adjunctive intervention for improving mood and overall psychological functioning, though limited research has explored its application among retiring athletes within psychotherapeutic contexts. This literature review synthesized current research related to athletic retirement, neurobiological mechanisms associated with physical activity, and …

Supramolecular Assembly In Short Peptide Systems For Selective Metabolite Recognition And Drug Nanoencapsulation, Maithreyi Ramakrishnan

Dissertations, Theses, and Capstone Projects

Short peptides can form adaptive supramolecular assemblies, and understanding how minimal sequences organize around neurometabolites or hydrophobic cancer drugs enables the rational design of functional materials. This thesis combines molecular dynamics with experimental validation to establish design rules linking peptide sequence to emergent structure and function. Chapter 1 outlines the molecular determinants governing peptide assembly. Chapter 2 reviews computational workflows that reveal sequence-dependent conformations and supramolecular organization. Chapter 3 applies these principles to Dynamic Peptide Libraries which identify tetrapeptides that selectively interact with neurometabolites. Chapter 4 extends the same interaction-driven framework to design tryptophan-rich pentapeptides that co-assemble with kinase inhibitors …

Neural Correlates Of Recognition Memory And Metamemory In Breast Cancer Survivors: An Event-Related Potential Study, Dishari Zaman Azad

Dissertations, Theses, and Capstone Projects

Breast cancer survivors (BCS) often report noticeable cognitive difficulties despite showing limited impairment on standardized neuropsychological tests. Some have theorized that this is simply an insensitivity of standardized testing to subtle cognitive changes (test-insensitivity hypothesis), whereas others have suggested there are early neural changes that are detected by patients but precede detection by these tests (early signal hypothesis) or that when they achieve normal performance, it is through saliently effortful compensatory processes (compensation hypothesis). The present study tested these theories by assessing metamemory and recognition memory retrieval in BCS and non-cancer controls (NCC) using both behavioral and event-related potential (ERP) …