Life Sciences Commons^™

A Rho5-Cnc1-Dnm1 Signalling Module Coordinates Multi-Organelle Execution Of Regulated Cell Death In Yeast, Justin Bauer

Theses and Dissertations

Regulated cell death is a conserved process with major implications for health and disease, yet how yeast cells integrate stress signals to determine survival versus death remains unclear. This thesis investigates Cyclin C (Cnc1), a conserved Mediator kinase module component with both transcriptional and mitochondrial roles. Together with Cdk8 Cnc1 primarily represses stress response genes, while upon stress it translocates to the mitochondria to induce mitochondrial fragmentation with the dynamin-related GTPase Dnm1. Using structure-guided separation-of-function mutants, I demonstrate that Cnc1-dependent death requires its mitochondrial function rather than its transcriptional role, and that its effector Dnm1 acts as a signaling node …

Quantitative Determination Of Nano Delivered Kras Sirna, Axel S. Deraspe

USF Tampa Graduate Theses and Dissertations

This study focuses on the development and validation of analytical methods for the detection of therapeutic KRAS-targeting siRNA in biological systems. Physicochemical characterization showed that p5RHH-formulated siRNA nanoparticles exhibit a controlled nanoscale size distribution, moderate polydispersity, and a negative zeta potential, suggesting colloidal stability and potential suitability for cellular uptake. Scanning electron microscopy confirmed a predominantly spherical morphology with a relatively uniform size distribution, consistent with dynamic light scattering measurements.

To enable accurate siRNA quantification, stem–loop reverse transcription (SL-RT) coupled with SYBR Green–based quantitative Polymerase Chain Reaction (qPCR) was optimized. Key parameters, including a primer concentration of 100 nM and …

(Re)Claiming Homeplace: Dance As Embodied Resistance & Healing For Health & Spatial Justice, Preeya G. Kannan

University Honors Theses

This thesis argues that dance functions as both an upstream public health intervention and a form of radical spatial resistance; creating healing, agency, and belonging among historically marginalized communities. Drawing on bell hooks' concept of homeplace, Jasbir Puar's assemblage theory, Nancy Krieger's eco-social theory, and Katherine McKittrick's Black geographies, I position the body as both an ecological and political landscape shaped by histories of colonialism, racial capitalism, displacement, and resilience.

Through this community-based participatory research study, Homeplace, I explore dance as a form of social prescription that centers liberation rather than pathology. Movement is often reduced in public health discourse …

Elucidating The Function Of Yedk In Response To Dna Damage, Hank Munro

University Honors Theses

Apurinic/Apyrimidinic (AP) sites are one of the most prevalent forms of DNA damage. These lesions arise spontaneously or during base excision repair of modified DNA bases and are potentially mutagenic in both mammalian and bacterial cells. 5-hydroxymethylcytosine binding, ES cell specific (HMCES), a protein found in eukaryotic cells, has been shown to form a stable DNA-protein crosslink with AP sites in single stranded DNA and to reduce the number of AP sites occurring either spontaneously or after alkylative DNA damage, resulting in increased genome stability. YedK, the Escherichia coli ortholog of HMCES exhibits some of the same biochemical properties as …

The Neuroprotective Effect Of Cdc42 Inhibition In The G93a Mutant Hsod1 Mouse Model Of Als, Andrea Koly

Undergraduate Theses, Capstones, and Recitals

Amyotrophic lateral sclerosis (ALS) is a progressive and fatal neurodegenerative disease characterized by the selective loss of upper and lower motor neurons, leading to muscle weakness, neuromuscular junction (NMJ) degeneration, paralysis, and eventual death due to respiratory failure. Despite extensive research, effective disease-modifying therapies remain limited, underscoring the need to identify novel molecular targets involved in ALS pathogenesis. Dysregulation of Rho family GTPases has been implicated in neurodegeneration, with Rac and Rho exerting opposing effects on neuronal survival; however, the role of the closely related GTPase Cdc42 remains poorly understood in ALS. In this study, the therapeutic potential of inhibiting …

Differential Roles Of Moesin And Vasp In Β-Catenin-Associated Networks During Zebrafish Heart Regeneration, Allen Rutman

Undergraduate Theses, Capstones, and Recitals

With cardiovascular disease remaining as the leading cause of mortality worldwide, it is largely due to the limited regenerative capacity of the human heart. However, zebrafish (Danio rerio) can fully regenerate cardiac tissue following injury, providing a valuable model for studying the mechanisms of heart repair. To investigate these mechanisms, we used proteomics methods in the past. Proximity labeling is a technique that identifies proteins based on their physical proximity to a protein of interest. It can be applied in organisms and in living cells (Roux et al., 2012; Cho et al., 2020). We used proximity labeling to characterize protein …

A Computational Micropatterning Approach To Study Caveolae And Protein Localization In Vascular Biology, Andrew B. Grespin

Electronic Theses and Dissertations

Caveolae are specialized, flask-shaped membrane invaginations highly expressed in endothelium and dysregulated in atherosclerosis. Caveolae play a central role in buffering membrane tension, yet the principles governing their spatial organization remain elusive. Thus, we sought to generate the most comprehensive and systematic analysis of blood vessel caveolar spatial organization. However, cell culturing, the backbone of human-focused biological research, does not standardly do well to model physiologically relevant cell behaviors such as migration or polarity-based tissue formation, particularly for punctate proteins and structures like caveolae. Micropatterns are cell-adhesive shapes that biophysically confine cell(s) to a user defined geometry which stereotype organelle …

The Palm Farm Next-Door: Land Concessions, Livelihoods, And Nutrition In Plantation-Adjacent Communities, Julia Entwistle

Electronic Theses and Dissertations

Large-scale land concessions have reshaped agrarian landscapes globally, yet their implications for community land tenure, livelihoods, and nutrition remain unevenly understood. This dissertation examines how plantation agriculture and foreign investment have transformed land access, labor relations, and food systems in Liberia, a country with one of the highest proportions of land under concession globally. Guided by a political ecology framework, the study employs a mixed-methods design integrating policy analysis, in-depth interviews, and household surveys across two palm oil concession sites. The findings show that ambiguous land policies historically facilitated dispossession, while recent legal reforms have enabled communities to strategically mobilize …

Defining Replication-Driven Vulnerabilities In High Grade Serous Ovarian Cancers, Natasha Maya Ramakrishnan

Arts & Sciences Graduate Student Theses and Dissertations

High grade serous ovarian carcinoma (HGSOC) is an aggressive, highly lethal subtype of ovarian cancer. These cancers are typically diagnosed in later stages and are associated with poor patient prognosis. Additionally, HGSOC is characterized by numerous markers of genomic instability and defects in DNA repair pathways, vulnerabilities which have been exploited by the advancement of chemotherapy. Despite these clinical advancements, HGSOC remains a significant therapeutic challenge due to emergence of chemoresistance and limited targeted treatment options. Taken together, these factors highlight an ongoing need to study the development of HGSOC and its progression to identify more effective treatment opportunities. We …

The Gut Microbiome, The Gut-Brain Axis, And College Student Well-Being, Idi Mckay

University Honors Theses

This literature review examines how diet, stress, environmental exposure, and food accessibility may influence college students' mental health and academic performance through the gut microbiome and the Gut-Brain Axis (GBA). Current microbiome research often focuses on early childhood development, clinical disease populations, or older adults, while overlooking college-age students who experience significant social, environmental, and biological transitions. College students frequently face food insecurity, irregular eating patterns, chronic stress, inconsistent sleep schedules, and reduced access to nutrient-dense foods, all of which may influence microbial diversity and overall gut health.

This thesis explores how modern campus environments and lifestyle factors may contribute …

Bap1 Loss Links Myc Activation, Stress Response Vulnerability, And Disease Progression In Kidney Cancer, Ilya Strunilin

Arts & Sciences Graduate Student Theses and Dissertations

BAP1, a chromatin modifier, is a frequently mutated tumor suppressor in clear cell renal cell carcinoma (ccRCC). Mutations in BAP1 are associated with a more aggressive and lethal disease. However, the downstream mediators of BAP1 loss in ccRCC oncogenesis are not well understood. To better understand mechanisms of BAP1-mediated tumor suppression, I have extensively characterized the very early transcriptional mediators of BAP1 loss in a postnatal kidney-specific genetic knockout model. Because VHL loss is the initiating event in ccRCC, we modeled Bap1 loss in a Vhl-deficient background. I have found that Vhl/Bap1 double-knockout cells of PT segment S2 strongly activate …

Mapping The Neuroexposome: Integrative Analysis Of Dementia Risk Factors Through Multi-Omics And Environmental Profiling In The Egyptian Population., Mai Ahmed Saadzaghloul Othman

Theses and Dissertations

Background: Dementia represents one of the most pressing public health challenges of the twenty-first century, with the global burden projected to reach 153 million cases by 2050. Egypt, as the most populous Arab nation, faces a corresponding rise in age-related diseases, yet comprehensive data from low- and middle-income countries remain severely limited. The neuroexposome framework, integrating genetic susceptibility, environmental exposures, and metabolic alterations, offers a powerful strategy to characterize the complex interplay between internal and external risk factors for Alzheimer's disease (AD) and Alzheimer's disease Related Dementias (ADRD).

Objectives: This thesis aimed to: (1) examine the distribution of APOE alleles …

Determinants Of Corporal Punishment And Severe Physical Punishment In Egypt: A Mixed-Methods Analysis For Child Protection Policy, Marwa Moustafa Nassef

Theses and Dissertations

Corporal punishment (CP) and severe physical punishment (SPP) remain a major public health, child rights, and child protection policy concern. In Egypt, despite legislative reforms, survey-weighted analysis of the 2021 Egypt Family Health Survey (EFHS) 2021 (CAPMAS, 2022) reveals prevalence rates of 60.5% for CP and 27.4% for SPP among children aged 1–14 (author’s calculations using EFHS-2021, n=7623), yet evidence distinguishing the determinants of routine corporal punishment from escalation to severe physical punishment remains limited in low- and middle-income contexts. Guided by Bronfenbrenner’s ecological framework, this mixed-methods study identifies key drivers of CP and its escalation to SPP among Egyptian …

Sequencing Of Chenopodium A-Genome Diploids To Identify Potential Mechanisms Of Speciation: A Preliminary Study, Riley Roser

Theses and Dissertations

The genus Chenopodium is of increasing significance, mainly due to allotetraploid quinoa (C. quinoa Willd.,2x = 4x =36, AABB genome) becoming globally recognized for its high nutritional value and tolerance for stress. Diploid A-genome relatives of quinoa in the Western Hemisphere have shown speciation patterns congruent to adaptive radiation, particularly in the North American continent, where a number inhabit ecological niches while others form mixed populations where they are sympatric. Characterization of the genetic mechanism(s) underlying this rapid speciation, could clarify their potential usefulness for improving quinoa . Previous whole-genome assemblies of AA diploids C. watsonii A. Watson and C. …

Exploring The Effects Of Pest-Induced Hemlock Mortality On Growth In Neighboring Trees, Sidney L. Booher

McNair Culminating Research Projects

Trees provide many important products and services to humans. In particular, tree growth is critical to carbon storage, air and water quality, and helps determine demographic processes like population growth and reproductive success. Importantly, tree growth is sensitive to both abiotic (environmental) and biotic factors and is vulnerable to ecological disturbances. Understanding how tree populations respond to disturbances, like invasive pests, is therefore crucial to formulating timely and effective forest management practices.

Here, I used tree ring analysis to investigate how competition for water between neighboring trees changes following the decline of Eastern and Carolina Hemlock(ECH) trees due to the …

Uncovering Dkk1 As A Therapeutically Relevant Target In Aggressive Er+ Breast Cancer Using A Novel Antiestrogen, Kristen Young

Dissertations

Over 70 percent of breast cancers are estrogen receptor-positive (ERα+), meaning that the hormone estrogen drives tumor growth. Although first-line targeted therapies that directly block ERα from hormone-dependent pathologies are initially effective, almost half of patients ultimately progress. These patients show high mutational rates to the ESR1 gene that encodes for ERα. A hotspot missense tyrosine to serine mutation at position 537 (Y537S) initiates hormone-independent, allele-specific transcriptional programs that increase metastasis. While next-generation ERα-targeted therapies show promise, benefits are often limited compared to standard-of-care. Understanding the mechanisms of action used by the Y537S ESR1 breast cancer cells to evade therapeutic …

Polygenic Risk Scores, Sex, And Socioeconomic Factors As Predictors Of Age Of Onset For Major Depressive Disorder, Kaitlyn M. Nowak

USF Tampa Graduate Theses and Dissertations

Major Depressive Disorder (MDD) is a heterogeneous psychiatric condition influenced by genetic, sociodemographic, and environmental factors, yet the extent to which these factors jointly shape the timing of disease onset remains unclear. This study evaluated the effects of polygenic risk scores (PRS), sex, and socioeconomic status (SES) on age of onset for MDD across two independent cohorts: the Pharmacogenomics Research Network Antidepressant Medication Pharmacogenomics Study (PGRN-AMPS) (N = 486) and the All of Us Research Program (N = 8,014). Analyses were restricted to individuals of European genetic ancestry, and PRS were constructed using both European-ancestry (EA) and multi-ancestry (MA) genome-wide …

Synthesis And Characterization Of Synergistic Bioactive– Organometallic Condensation Polymers, Francesca Isabel Mosca

Electronic Theses and Dissertations 2020 - Present

This research focuses on the synthesis and structural characterization of polymers with anticipated anticancer and antiviral properties by combining metal-containing Lewis acids, organotin dichlorides (R2SnCl2), Group 4 metallocene dichlorides (Cp2TiCl2, Cp2ZrCl2 and Cp2HfCl2), and triphenyl Group 15 metal dichlorides (Ph3AsCl2, Ph3SbCl2 and Ph3BiCl2), with biologically active Lewis bases, lamivudine, a synthetic nucleoside, and camphoric acid, a dicarboxylic acid, to achieve synergistic effect.

Five classes of polymers were synthesized using interfacial polymerization: lamivudine and organotin dichlorides, lamivudine and Group 4 metallocene dichlorides, camphoric acid and triphenyl Group 15 metal dichlorides, camphoric acid and organotin dichlorides, and camphoric acid and Group 4 …

Synthesis And Characterization Of Organometallic Polymers And Their Cytotoxicity Towards Human Cancer Cell Lines, Paul Peter Slawek

Electronic Theses and Dissertations 2020 - Present

This research aimed to synthesize organometallic polymers from dialkyl (methyl, ethyl, butyl, cyclohexyl, and octyl) and diaryl (phenyl) tin dichlorides and three organic monomers, dipicolinic acid (DPA), chloramphenicol (CH), and isomannide (IS), using interfacial polymerization. Structure-activity relationships were investigated through physicochemical characterization (light-scattering photometry, proton NMR, and IR spectroscopy) and cytotoxicity was evaluated against six human cancer cell lines (AsPC-1, PANC-1, MCF-7, MDA-MB-231, HT-29, PC-3), with cisplatin serving as the reference standard.

Five DPA/tin polymers were synthesized, with IC₅₀ values in the range of 0.60–0.71 μg/mL. Their cytotoxicity was significantly lower than that of cisplatin (0.0023-0.044 μg/mL), suggesting that …

Discovery Of Bmi-Associated Gut Microbiome Signatures In The Awi-Gen 2 Cohort, Meriem Yagoubi

Theses and Dissertations

Obesity is increasing across sub-Saharan Africa amid rapid dietary, environmental, and urbanization transitions, yet the gut microbiome features associated with adiposity in African populations remain under-characterized. This study investigated whether species-level gut microbiome composition is associated with body mass index (BMI) in the AWI-Gen 2 cohort, and whether BMI-associated microbial signals remain detectable after accounting for the dominant geographic structure of the microbiome. Gut microbiome community structure and diversity were characterized across 1,665 participants, and differential abundance analysis was used to identify taxa associated with BMI after controlling for study site. Machine learning models were then trained to assess how …

Diversification Of Ghost Electric Fishes (Gymnotiformes, Apteronotidae) In Tropical South America: How Traits And Environmental Factors Constrain Macroevolutionary Diversification, Jonathan Gifford Allen

Doctoral Dissertations

Neotropical electric fishes (Apteronotidae) display remarkable phenotypic and ecological diversity, offering an exceptional system for studying macroevolutionary processes in freshwater environments. Here I investigate the morphological, ecological, and historical factors shaping diversification in the clade Navajini, with a focus on craniofacial evolution, species delimitation, and biogeographic patterns. First, using high-resolution micro-CT scans, 3D geometric morphometrics, and phylogenetic comparative methods, I analyze skull shape variation across Navajini. Key traits resulting from heterocephaly exhibit strong phylogenetic signal and reflect functional differentiation among genera. Sexual dimorphism contributes significantly to cranial disparity in some lineages, while others show conserved, modular patterns likely tied to …

Growing Pains: The Loss Of Plasticity To Extreme Anoxia In Developing Embryos Of Austrofundulus Limnaeus, Patrick Ryan Clouser

Dissertations and Theses

Oxygen plays a pivotal role for most animal life on Earth, so much so that even short exposures to no oxygen, anoxia, can have severe effects on the animal's wellbeing. Conversely, aerobic recovery after anoxic insult can be just as detrimental. Some animals are the exception to this rule and demonstrate survival through anoxia and recovery. There has been a great deal of research around anoxia tolerant animals, but what remains unclear are the genetic underpinnings that determine the anoxia tolerant phenotype. RNA sequencing allows for the quantification of RNA transcripts within a sample, which can indicate if a gene …

Targeting Inflammatory And Growth Signaling Pathways In Breast Cancer Through Diet, Microbiome, And Metabolite Interactions, Brittany Lorraine Witt

ETDs from 2020-2029

Breast cancer (BC) accounts for 1 in 3 (or 30%) of all new female cancers each year and is the most common malignant cancer in women in the United States. Since the 1990s, there has been a 44% decrease in BC, but there is still a significant gap between certain groups in terms of mortality rates. Black women have a higher mortality rate and risk for triple-negative breast cancer (TNBC). This may be due to social (inadequate access to health care facilities, insurance, or completion of therapy) and biological (genetic mutations, tumor characteristics, or comorbidity) factors between races and other …

The Relationship Between The Environment And Pollution With Surgical Outcomes And Disparities, Wendelyn Marie Oslock

ETDs from 2020-2029

Air pollution exposure has been linked to many surgically managed diseases and adverse health events that occur in the postoperative period. Despite this, the impact of air pollution on postoperative recovery is poorly understood. This knowledge gap may be one of the underlying mechanisms for persistent disparities in surgical outcomes. Previous studies have found racial and economic disparities in air pollution exposure. These same communities have been shown to experience worse surgical outcomes. The goal of this thesis is to explore if exposure to air pollution impacts surgical outcomes and determine if disparities in socioeconomic factors impact this relationship. The …

Biologically Informed Negative Samplingfor Antibody Chain Pairing Classification, Ishita Singh

Computer Science Senior Theses

Antibody heavy and light chain (H/L) pairing is fundamental to antigen recognition and stability. While single-cell sequencing preserves native pairing information, widely used bulk repertoire and spatial transcriptomics platforms do not, motivating the need for efficient ML methods to infer H/L pairing. Training a binary classifier for this task faces the methodological challenge of a lack of true biological negatives, since natural selection eliminates B cells with incompatible H/L pairs.

In this thesis, I introduce a biologically informed negative sampling strategy for H/L pairing classification, drawing on known V-gene biases in heavy and light chain pairing. Pseudo-negatives are constructed by …

Life Without Oxygen: Cellular Mechanisms Enabling Genome Maintenance And Proliferation In Cells From An Anoxia-Tolerant Vertebrate, Riley Asa Roth-Carter

Dissertations and Theses

When exposed to the complete loss of oxygen (anoxia) most organisms undergo rapid cellular deterioration driven by a range of metabolic dysfunctions associated with the loss of the terminal electron acceptor for aerobic respiration. This loss of ability to create and maintain necessary levels of cellular ATP through oxidative phosphorylation contributes to loss of membrane potentials, increase in the accumulation of acidic by-products of anaerobic metabolism, and a decrease in the ability to support other molecular processes that rely on a steady supply of ATP. While this extreme oxygen stress is lethal to a majority of vertebrate organisms there are …

An Integrative Approach To The Evolution Of Neotropical Whale Catfishes (Family: Cetopsidae), Daniel Akin

Doctoral Dissertations

The catfishes (order Siluriformes) represent over five percent of world’s vertebrate diversity. The story of vertebrate evolution remains incomplete without a thorough evaluation of catfishes, and the ichthyological community is yet to reach consensus on some of the deeper evolutionary patterns within this fascinating group. Our complete macro-evolutionary understanding of catfishes is inhibited by a paucity of information on the taxonomies, phylogenetics, ecologies, and life histories of many understudied groups of catfishes. One such group is the Neotropical whale catfishes of the family Cetopsidae. This dissertation provides an integrated approach to studying the family Cetopsidae. I use genomics to determine …

The Evolutionary Response Of HawaiʻI ʻAmakihi (Chlorodrepanis Virens) To The Introduction Of Avian Malaria (Plasmodium Relictum), Gabrielle Atkinson

Doctoral Dissertations

The emergence of novel pathogens can impose intense selective pressures on natural populations, driving rapid evolutionary change or precipitating population collapse. In Hawaiʻi, the introduction of avian malaria (Plasmodium relictum) and its mosquito vector (Culex quinquefasciatus) have caused severe declines and extinctions among native forest birds. Yet some populations of Hawaiʻi ʻamakihi (Chlorodrepanis virens) persist across a broad elevational and disease gradient, providing a powerful natural system for examining the genomic basis of rapid adaptation, the role of gene flow in adaptive response, and the potential for parallel evolutionary responses. This dissertation integrates genomic, population genetic, and transcriptomic approaches to …

Diversity, Systematics, And Phylogenomics Of The Neotropical Glass And Longtail Knifefishes (Gymnotiformes: Sternopygidae), Kevin Thomas Torgersen

Doctoral Dissertations

This dissertation provides a comprehensive systematic and phylogenetic study of the electric knifefish family Sternopygidae, integrating morphological, molecular, osteological, and phylogenomic data to clarify species diversity, evolutionary relationships, and biogeographic patterns in this Neotropical group. Across six studies, the work reveals that Sternopygidae diversity has been significantly underestimated due to morphological conservatism that obscures species boundaries. Chapter 1 revises the genus Sternopygus in the Guiana Shield, identifying nine species (five new) using osteology, morphometrics, and µCT imaging. Distinct anatomical traits and distribution patterns show strong regional structuring, highlighting the Guiana Shield as a diversification center. Chapter 2 describes a new …

Severity Of Deficit In Skeletal Muscle Lipid Metabolism Invokes Unique Adaptive Responses In Dietary Lipid Intake And Absorption, Victoria Datta

Masters Theses

Skeletal muscle plays a central role in whole-body lipid metabolism through mitochondrial and peroxisomal fatty acid oxidation (FAO). When skeletal muscle lipid metabolism is impaired, whole-body adaptations occur to maintain metabolic homeostasis. We hypothesized that limiting skeletal muscle lipid metabolism through mitochondria and/or peroxisomes would trigger adaptive responses to reduce dietary lipid intake and/or absorption with the most robust changes coinciding with deficit severity. Mice were generated with skeletal muscle-specific deletion of 1) carnitine palmitoyltransferase 1b (Cpt1bM-/-) to limit mitochondrial FAO, 2) peroxin 5 (Pex5M-/-) to impair peroxisomal FAO, and 3) both Cpt1b and Pex5 (DKO). Results were compared to …