Life Sciences Commons^™

The Role Of Agricultural Biomass In Supply Chain Decarbonization, Ruxia Lyu, Sobhan Arisian, Zhitang Li, Mohammad S. Taskhiri, Reza Kiani Mavi

Research outputs 2022 to 2026

To achieve supply chain decarbonization, environmentally conscious manufacturers are transforming their energy infrastructure. While certain manufacturers are adopting a pure bioenergy strategy in their production processes, others are opting for a hybrid energy approach that combines traditional energy with bioenergy. This choice is often influenced by limitations in land capacity and the developmental stage of biomass conversion technologies. This paper introduces a game-theoretic model that explores the optimal approach to achieving supply chain decarbonization by strategically selecting energy portfolios. Our findings reveal that in scenarios where the market size is small, manufacturers tend to adopt a hybrid energy strategy, particularly …

Corals, Creation, And Conservation: Evaluating Human-Marine Relations Through Coral Reef Biology And Artistic Practice, Emma Gray Garman

Scripps Senior Theses

This thesis investigates the relationship between humans and marine ecosystems through two complementary lenses: scientific research and artistic practice. The biology chapter proposes a five-year coral reef monitoring study across four Queensland, Australia islands — two heavily visited and inhabited (Fitzroy and Green Islands) and two minimally visited and uninhabited (High and Woody Islands) — to assess whether human activity correlates with bleaching severity over time. Grounded in preliminary survey data from Green Island in 2024, which revealed approximately 54% of coral bleached or dead, the study hypothesizes that reefs adjacent to inhabited islands will exhibit greater bleaching severity, consistent …

How Semiflightless Birds Adapt: A Survey From Barú, Costa Rica, Eli P. Laloudakis

Scripps Senior Theses

When we think of birds, we think of flight. Because of this, scientific research often focuses on how birds evolved flight and how their wings function during flight. However, not all birds can fly or fly well, as wings wax and wane on developmental, seasonal, and evolutionary time scales (Dial and Heers 2021). Consequently, rudimentary wings can be found in developing birds, secondarily flightless or semiflightless birds, birds that undergo simultaneous molts, and extinct theropods with “protowings” (structures that preceded fully functional wings). Secondarily flightless and semiflightless birds often evolve where there is no/low predation, abundant year-round food supply, and …

Lead Biosorption By Oceanobacillus Profundus Kbz 3-2: Strategies For Bioremediation Systems In Kabwe, Danielle S. Desmarteau

Scripps Senior Theses

Lead contamination remains a significant global public health concern, particularly in Kabwe, Zambia, the site of a former lead mining operation. Bioremediation, which utilizes biological materials and processes to remove environmental contaminants, represents a promising approach for addressing lead pollution. However, the development of effective bioremediation systems requires a detailed understanding of the mechanisms underlying metal removal and the feasibility of implementation in low-resource settings. Oceanobacillus profundus KBZ 3-2, a bacterium isolated from Kabwe mine waste, has demonstrated the ability to remove lead from aqueous environments. This study proposes to investigate the mechanism of lead biosorption by this organism, …

The Effect Of The Affordable Care Act Medicaid Expansion On The Risk Of Hospital Closure And Adolescent Hpv Immunization In Rural Counties, Juliette Des Rosiers

Scripps Senior Theses

From 2005 to 2025, over 200 rural hospitals shut their doors, often citing increased operational costs, staffing shortages, low patient volume, regulatory barriers, financial challenges exacerbated by the COVID-19 pandemic, and uncompensated care as common contributors to the closures. Rural patients are often referred by their primary care physician to a hospital for regular immunizations, since smaller clinics have less capacity to provide immunizations due to a shortage of pediatricians and limited vaccine stock. A crucial vaccine that is not required by schools and underutilized in rural areas is that against human papillomavirus (HPV), a virus that infects cutaneous and …

Assessing The Effect Of Wildfire-Specific Air Pollutants On Copd Hospitalizations In Los Angeles County, Kimberly Young

Scripps Senior Theses

As the fourth leading cause of death in the world, chronic obstructive pulmonary disorder (COPD) is one of the most severe respiratory disorders characterized by airway inflammation.  For the past two decades, climate change has exacerbated the prevalence of wildfires in California due to rising temperatures and lower precipitation. With the influx of wildfires, poor atmospheric air quality continues to be a serious health problem in the Los Angeles area, especially after the recent Eaton fire in January of 2025. My study hopes to assess whether the air pollutants particulate matter 2.5 (PM_2.5), particulate matter 10 (PM_{10 …}

Antimicrobial Activity Of Violacein Extracted ​ From Janthinobacterium Lividum​, Catherine M. Brownhill-Slatore

Scripps Senior Theses

Abstract

Antibiotic-resistant bacteria have been a threat since the discovery of antibiotics. The increased rise of antibiotic-resistant bacteria has created an immediate need for new antibiotics. Violacein, a purple bisindole pigment produced by Janthinobacterium lividum, has been shown to be a promising new antibiotic. Its efficacy has not been completely demonstrated, and this project aims to further investigate the effectiveness of violacein as an antibiotic. To do this, a minimum inhibitory concentration (MIC) test was conducted. Violacein was grown, extracted, purified, and tested across concentrations ranging from 1.0 to 500.00 µg/mL to cover values well above and below previously cited …

Beyond Ssris: Omega-3 Fatty Acids And The Neurobiology Of Impulsivity In Borderline Personality Disorder, Sujean Doo

Scripps Senior Theses

Impulsivity is a central and clinically significant dimension of Borderline Personality Disorder (BPD), and is strongly associated with self-harm, aggression, and suicide risk. Despite its prognostic importance, pharmacologic management of impulsivity in BPD remains inconsistent. Selective serotonin reuptake inhibitors (SSRIs) are frequently prescribed; however, randomized controlled trials demonstrate limited efficacy for impulsive-aggression, and some patients experience a paradoxical behavioral activation. Meta-analytic and systematic reviews further suggest that mood stabilizers and second-generation antipsychotics may outperform antidepressants, yet no specific medication is indicated to target impulsive behavioral dyscontrol.

This thesis synthesizes findings from systematic reviews, randomized trials, and neuroimaging research to evaluate …

Indirect Effects Of Coral Bleaching On Tursiops Truncatus Diet And Foraging Behavior In Bocas Del Toro, Panama, Annabel Fiero

Scripps Senior Theses

Indirect effects, where another species or factor mediates the effects of a given species, are critical to ecosystem structure and resilience. Shifts in fish community structure, as a result of rapidly declining coral reefs in the Caribbean due to warming-induced bleaching, pose a threat to apex predators like Tursiops truncatus (bottlenose dolphins). Branching corals create habitat niches for numerous fish species. These fish rely on coral for food and habitat, and in turn provide food for upper trophic levels. Prior research has highlighted how coral bleaching will disrupt Acroporid reef building corals and fish community structure, but the effects of …

The Impact Of Heavy Resistance Training On Type Ii Muscle Fibers Throughout Female Reproductive Stages, Lily G. Colberg

Scripps Senior Theses

Type II muscle fibers, also known as fast-twitch muscle fibers, are reliant on aerobic glycolysis and are crucial for high-force contractions, mobility, and rapid movements, such as fast reflexes. Heavy resistance training has been found to increase type II muscle fiber concentration in young, middle-aged, and elderly individuals. However, there have been few studies conducted on female-only sample populations. In women, the impact of heavy resistance training on type II muscle fibers is affected by the progressive decline of estrogen that defines the transition throughout the four female reproductive stages: premenopause, perimenopause, late-transition menopause, and postmenopause. Menopausal estrogen depletion causes …

Seeing Through The Fuzz: Understanding Conformational Diversity In The Fuzzy Coat Of Amyloids Across Fibril Polymorphs Using Solid-State Nmr, Carah K. Allen

Scripps Senior Theses

The aggregation of α-synuclein (α-syn) into amyloid fibrils is a central pathological hallmark of Parkinson’s disease and other related synucleinopathies. Although monomeric α-syn is intrinsically disordered, the protein assembles into multiple fibril polymorphs that differ in their β-sheet core structures. Surrounding each polymorph is the “fuzzy coat,” which is a highly dynamic, intrinsically disordered region (IDR) that is not resolved by high-resolution structural techniques, such as Cryo-EM, but is thought to influence fibril interactions, propagation, and toxicity. Understanding whether different polymorphs maintain distinct fuzzy-coat conformational ensembles is therefore essential for connecting amyloid structure to biological function. To address this question, …

Food Stamp Participation And Health Outcomes In Ca Immigrants, Esther Kang

Scripps Senior Theses

The U.S. social welfare system includes programs aiming to increase access to nutritious food to reduce nutrition insecurity. However, studies suggest that immigrants continue to face disproportionate risks of nutrition insecurity and may face barriers to enrollment due to legal status. This study, using secondary data from the 2023 California Health Interview Survey, examines the associations between food stamp participation, food insecurity, and clinical diagnosis of diabetes among adult U.S.-born, naturalized, and non-citizen adults in California. The findings suggest that those enrolled in food stamps are more likely to report food insecurity than those who are not enrolled, and that …

Evaluating Soil And Plant Health In A Wide-Row Maize (Zea Mays L.) Production System Integrated With Perennial Cover Crops And Turkey (Meleagris Gallopavo), Sovika Bhattarai

All Graduate Theses, Dissertations, and Other Capstone Projects

In regions dominated by intensive maize (Zea mays L.) production systems, such as the US Midwest, sustainable agricultural practices such as cover crops and livestock integration are gaining interest for their potential to improve soil, plant, and environmental health. Traditionally, annual cover cropping systems (ACCs) have been used to maintain soil quality and crop performance without compromising ecosystem services. However, the high establishment and management costs of ACCs highlight the need for alternative approaches, such as perennial cover crops (PCCs). Grown as companion crops with maize, PCCs provide extended soil cover and can improve soil biochemical properties (e.g., total C …

Impacts Of Management Practices And Soil Properties On Free-Living Nitrogen Fixation In Eastern South Dakota, Laura Galvan Nuevo

Electronic Theses and Dissertations

Free-living nitrogen (N) fixation (FLNF) may represent a sustainable pathway to supplement crop N demand in agroecosystems, yet edaphic and management factors regulating this process under field conditions remain poorly understood in the Northern Great Plains. Using 15N2 direct method to quantify potential FLNF (pFLNF) and baseline FLNF (bFLNF), this thesis investigates how crop rotations (2-, 3-, and 4-year systems), tillage management (conventional vs. no-till), cover cropping, and soil properties affect the potential of free-living diazotrophs to supply N via FLNF in a long-term no-till corn-based system in Southeastern South Dakota. A two-year field study evaluated pFLNF across four growing …

Colorectal Cancers With Distinct Metastatic Potential Trigger Divergent Early T Cell Responses, Marwa Ahmed Saad

Student Theses and Dissertations

The intestinal mucosa harbors the largest immune compartment in the mammalianbody, where resident and recruited immune cells must maintain tolerance to commensal and dietary antigens while preserving their ability to mount effective responses against pathogens and malignant transformation. Uncontrolled epithelial proliferation leads to colorectal cancer (CRC), the second leading cause of cancer-related deaths worldwide. More than 85% of human CRC cases arise from accumulating sporadic or hereditary mutations in the tumor suppressor genes Apc, Tp53, Smad4, and the oncogene Kras. Although immune checkpoint blockade has transformed the treatment of certain solid tumors, most CRCs, particularly those with a proficient mismatch …

Investigating Primary Motor Cortex Involvement In Mouse Vocal Communication, Elena N. Duryea Waidmann

Student Theses and Dissertations

Vocal communication is used to transmit a range of information to other individuals. While many vocalizations are innate, some species can learn to change their vocal output. This is termed vocal-learning, and it is a rare trait and a necessary building block for human spoken language and songbird song. Comparative work in humans and songbirds suggests that convergent genetic and neural specializations may drive these learned vocal behaviors. Two key features of these advanced vocal learners are: i) specialized primary motor regions in the forebrain with activity tied to vocalization; and ii) dense monosynaptic projections from the primary motor cortex …

Noncanonical Roles Of Hepatitis B Virus Precore Rna In Reverse, Mengyin Zhang

Student Theses and Dissertations

Hepatitis B virus (HBV) is a partially double-stranded DNA virus that replicates through reverse transcription. Transcription from the HBV core promoter generates two genome-length RNAs: pregenomic RNA (pgRNA) and precore RNA (pcRNA). pcRNA contains the entire pgRNA sequence plus an additional 32 nucleotides at its 5’ end that include the precore start codon, enabling translation of the precore protein, the precursor of the secreted HBV e antigen (HBeAg). Whereas pgRNA is translated to produce core and polymerase and serves as the template for reverse transcription by cis-acting HBV polymerase, pcRNA has long been considered unable to support HBV DNA synthesis. …

Astrocyte Identity And Function Acquisition During Nervous System Development In C. Elegans, Simin Liu

Student Theses and Dissertations

Astrocytes are essential regulators of nervous system development, homeostasis, and function. Beyond their well-established roles in synapse formation, metabolic support, and neural circuit modulation, astrocytes are increasingly recognized as dynamic participants in behavior regulation and neurological disease. Despite their importance, the developmental logic by which astrocytes acquire their identity and functional properties remains incompletely understood. In particular, how distinct developmental programs coordinate to establish astrocyte identity, and how immature glial cells transition into fully functional astrocytes, are central unresolved questions in neurobiology. In this thesis, I investigate the developmental mechanisms that establish astrocyte identity and function using the astrocyte-like Caenorhabditis …

Spatiotemporal Patterns Of Migratory Songbird Habitat Use: An Analysis Of Environmental Drivers At The Net Level, Garrett Kucharski

Dissertations, Master's Theses and Master's Reports

Many eastern North American migratory songbirds are declining at alarming rates, and growing evidence suggests that events occurring away from the breeding grounds, particularly during migration, can be major drivers of these trends. Stopover sites are a key component of migration because they are where birds rest, refuel, and recover before continuing long-distance movements, yet the ecological factors that shape how broadly different species use stopover habitat remain unresolved. From both an applied perspective, identifying habitat attributes associated with use by the greatest diversity of migrants will help land managers prioritize and restore stopover sites, actions that may contribute to …

Fluctuation Of Organochlorine Concentrations In Bull Sharks At Different Life Stages, Mackenzie R. Phillips

Dissertations, Master's Theses and Master's Reports

For Carcharhinid species such as the bull shark (Carcharhinus leucas), the maternal offloading of nutrients is essential for pup development and growth, however, significant amounts of OCs are also transferred. As a top predator in aquatic food webs, bull sharks can potentially bioaccumulate high concentrations of pollutants such as dichloro-diphenyl-trichloroethane (DDT) that biomagnify through aquatic food webs. These pollutants are also hydrophobic and fat soluble and therefore pose toxicity risks to developing young bull sharks. In this study, liver tissues collected from juvenile bull sharks inhabiting Florida’s coastal waters were analyzed for a suite of organochlorine pesticides (OCs) …

Exploring Fructose Mimetics As Chemotherapeutic Potentiators: Impact On Glut5-Mediated Cancer Cell Vulnerability, Vedant Buwa

Dissertations, Master's Theses and Master's Reports

Metabolic reprogramming toward increased sugar uptake is a hallmark of cancer, and fructose-specific uptake through the facilitative transporter GLUT5 is selectively upregulated in several adenocarcinomas, including breast and lung cancer. This dissertation develops and characterizes a panel of fluorescent fructose mimetics – the coumarin-based ManCou probes and the quinolinone-based ManQuin probes – as GLUT5-targeted reporters, cytotoxic effectors, and chemosensitization adjuvants, and establishes the boundaries within which each role holds.

The central experimental strategy pairs each GLUT5-targeted glycoconjugate with its sugar-free aglycone control, isolating transporter-mediated cytotoxicity from cytotoxicity intrinsic to the fluorophore itself. In luminal (MCF7) and triple-negative (MDA-MB-231) breast carcinoma, …

Public Perception Of Environmental Contamination And Its Implications For Fish And Community Health In West Bengal, India, Libia Hazra

Dissertations, Master's Theses and Master's Reports

In West Bengal, India, the highest fish-consuming state in the country, fish are woven into everyday life, including ceremonies of birth and marriage, prayers offered during harvesting and the cultural memory of communities whose identities are inseparable from aquatic life. However, the rivers, wetlands, and ponds that sustain these fish-human relationships are increasingly threatened by environmental contamination resulting from industrial discharge, agricultural runoff, and inadequate environmental management. Understanding how communities perceive these environmental changes is essential for developing effective conservation and public health strategies.

In collaboration between the Indian Institute of Technology (ITT) Kharagpur, India, and Michigan Technological University (USA), …

Systematics Of Disk-Winged Bats (Thyroptera), Courtney L. Klumpp

Capstone Showcase

This thesis investigates the evolutionary relationships among disk-winged bats in the genus Thyroptera, a small group of Neotropical bats known for the adhesive suction disks on their wings and feet that allow them to roost inside tightly rolled leaves. The distinctive morphology and behavior of these bats have not been extensively documented, and their phylogenetic relationships remain only partially resolved. The goal of this research is to better understand how these species are related to one another and to determine whether the five recognized species of Thyroptera form a single monophyletic group. To address this question, morphological and genetic …

Mitochondrial Efficiency: Bridging Early-Life Environment And Organismal Performance, Kayla E. Lichtner

Master’s Theses

Mitochondria operate at the forefront of organismal-environmental interactions. Despite remarkable diversity in mitochondrial function both within and among species, all mitochondria serve a universal role in facilitating the flow of energy between organisms and their environment. Energetic efficiency, the way in which organisms assimilate and transform environmental substrate into physiological currency, is a major determinant of organismal performance. Although previous studies have shown that early-life environment can have lasting effects on metabolism, the underlying mechanisms driving the emergence of mitochondrial phenotypic variation remain poorly understood. Leach’s storm-petrels (Hydrobates leucorhous) provide a valuable opportunity to investigate longitudinal hypotheses of …

Rate Response Of Curlyleaf Pondweed And Native Plants To Flumioxazin In Minnesota Lakes, Pearl J. Jensen

All Graduate Theses, Dissertations, and Other Capstone Projects

Curlyleaf pondweed (Potamogeton crispus L.) is an invasive aquatic plant present across the United States that causes significant recreational issues, outcompetes native plant species, and depletes water quality. Before senescing in mid-summer, curlyleaf pondweed forms a large number of turions that can lay dormant in the sediment for several years. Typical herbicide management of this species occurs in early spring to target the plant before turion production occurs and while native plants are dormant. Flumioxazin has shown potential in curlyleaf pondweed management in small scale studies, but its effects have not been assessed in operational management. In this study, treatments …

Ethanol And Iron Absorption Interactions Within Crayfish Invertebrate Models, James Rollman, Andrew Wissmar

Williams Honors College, Honors Research Projects

Analysis of the effects of alcohol consumption (ethyl-alcohol) on iron absorption within crayfish model. The use of tube-feeding provides a novel, more precise output, and less invasive procedure compared to the traditional approach of dissolving the target substance in tank water and measuring hemolymph changes. The project aims to determine the extent to which alcohol influences iron absorption. Ultimately, the choice of iron reflect the future potential to aid in research with genetic hemochromatosis and or Iron overload.

Red Clover Isoflavones And Establishment In The Context Of Tall Fescue Toxicosis Mitigation In The Mid-South, Jonathan L. Stephens

Theses and Dissertations--Plant and Soil Sciences

Low levels of red clover (Trifolium pratense L.) have been shown to mitigate tall fescue (Lolium arundinaceum (Schreb.) toxicosis symptoms. This is because of the presence of plant-produced compounds known as isoflavones. Production of a red clover supplement on a commercial scale would require industrial-level processing of raw plant material into granules or pellets. The first study of this thesis evaluated the impact of drying temperature on bioavailability of isoflavones. Drying temperatures up to 104°C had minimal impact on isoflavone concentrations. Additionally, varietal differences in isoflavone concentrations were documented. The second study of this thesis evaluated optimal establishment …

Characterizing The Role Off The Sp1/Klf Transcription Factor Huckebein In The Drosophila Melanogaster Ventral Nerve Cord, Benjamin Almond

Distinguished Undergraduate Researcher Program

Over the course of embryonic development, the ectodermal cell layer gives rise to a vast array of neurons and glia patterned across the central nervous system (CNS). Neurulation and specification is achieved in the ectoderm through temporospatial patterns of transcription factor (TF) expression, many of which are conserved across evolutionary history. These conserved regulatory motifs allow the use of Drosophila melanogaster to study the mechanisms of neurodevelopment across the animal kingdom. The huckebein (hkb) gene encodes a conserved SP1/KLF TF known to play important roles in cell cycle regulation, tissue morphogenesis during tubular organ development, and gut specification in Drosophila. …

Measuring The Rise And Fall Of Plasma 25-Hydroxyvitamin D Concentrations In Blue-Tongued Skinks (Tiliqua Scincoides) Following Ultraviolet B Exposure And Withdrawal, Ashleigh Godke, Haerin Rhim, M. Graciela Aguilar, Keishla Marrero-Acosta, Mark Mitchell

Distinguished Undergraduate Researcher Program

Species-specific husbandry guidelines remain limited for blue-tongued skinks (Tiliqua scincoides), especially in relation to ultraviolet B (UVB) lighting and vitamin D requirements. This study aimed to determine whether UVB exposure is necessary for these skinks and how long 25-hydroxyvitamin D (25-OHD) concentrations persist after UVB withdrawal. Eleven adult skinks who had been fed with wet cat food were exposed to 12 or 2 h of UVB per day for four weeks. Plasma 25-OHD concentrations were very low at the baseline, and significantly increased post-UVB in both groups (p < 0.01), with the 12-hour group increasing from baseline concentrations of 18.5 [12.8–20.5] nmol/L to 820 [730–1251.3] nmol/L and the 2-hour group increasing from baseline concentrations of 22 [15.5–22] nmol/L to 635 [401–892.5] nmol/L. Following the discontinuation of UVB exposure, 25-OHD gradually declined and was not significantly different from baseline concentrations at 7 and 4 months for the 12-hour and 2-hour groups, respectively. Dietary vitamin D3 (2.5 IU/g as dry matter basis), provided through wet cat food alone, appeared insufficient to support sustained plasma 25-OHD concentrations. These findings strongly suggest that blue-tongued skinks rely on UVB exposure to increase their 25-OHD concentrations. Moreover, the shorter 2-hour exposure provided a significant rise in 25-OHD concentrations and remained above baseline for 4 months, suggesting the shorter exposure can benefit these animals, while potentially reducing secondary risks associated with UVB exposure.

Structural Determination And Regulatory Mechanisms Of Rice Lipoxygenase-1, Lillie Ballanco, Nathaniel Gilbert, Adam Offenbacher

Distinguished Undergraduate Researcher Program

Lipoxygenases (LOXs) are non-heme iron containing enzymes that catalyze the oxygenation of polyunsaturated fatty acids (PUFAs) such as linoleic acid (LA). These lipoxygenase enzymes are found in both plants and animals. In humans, LOXs have been linked to inflammatory diseases such as asthma, atheroscelerosis, and allergic rhinitis. Plant LOXs have been primarily linked to the growth, development, and stress response of the plant. This paper focuses on Oryza sativa lipoxygenase-1 (OsLOX1), an enzyme found in rice (Oryza sativa). OsLOX1 has been associated with enhanced drought tolerance in rice and may play a role in regulating growth under water-limited conditions. Understanding …