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The Role Of Cis-Acting Super-Enhancer Long Noncoding Rnas In Triple Negative Breast Cancer Progression, Sakthi Muthukrishnan

Biological Sciences

Breast cancer encompasses a diverse range of diseases characterized by the uncontrolled proliferation of cells within the mammary gland. This condition results in an accumulation of a large number of genetic mutations within an individual, altering the complex internal signaling system of a cell. Millions of women are affected by breast cancer, which remains a significant threat despite medical advancements. Ductal carcinoma in situ (DCIS) acts as a precursor to invasive ductal carcinoma (IDC), however, not all cases progress to invasive cancer. Triple-negative breast cancer (TNBC) is identified to be one aggressive subtype of IDC, where the cells lack sufficient …

Non-Invasive Focused Ultrasound To Reduce Gut Inflammation In Parkinson’S Disease, Amal F. Siddiqui

Biological Sciences

Parkinson's Disease (PD) is a neurodegenerative motor disorder that affects millions of people worldwide, with projections suggesting the number of diagnosed cases could reach 15 million by 2040 (Dorsey et al., 2018). While PD is primarily recognized for its impact on movement, it also frequently causes non-motor symptoms, including gastrointestinal (GI) issues such as constipation, which affects 60-80% of patients. Chronic gut inflammation has been proposed as a key factor exacerbating these symptoms. Despite the prevalence of GI complications in PD, they are often overlooked, and existing treatments for constipation are limited in both efficacy and scope. Vagus Nerve Stimulation …

Genomic Diversity Of Salmonella Enterica Serotype Braenderup In New York State, Nicole Zac Soligno

Biological Sciences

The Gram-negative Salmonella enterica (family Enterobacteriaceae) is a common foodborne pathogen mainly isolated from foods of animal origin. Salmonella can be transmitted to humans, causing diverse symptoms, from self-limiting gastrointestinal diseases to more fatal typhoid fever. The young, elderly, and Individuals with weakened immune systems are especially at risk from salmonellosis. Salmonella is a concern to public health and the food industry throughout the world, and its severity depends largely on its serotype, a classification based on the unique combination of surface antigens. In this study, I aimed to elucidate the population structure and antimicrobial resistance determinants of S. enterica …

Cover Crop-Induced Improvements To Soil Hydraulic Properties And The Role Of Termination Time In Mitigating Negative Soil Moisture Impacts, Fabrizio Javier Pilco

Theses and Dissertations

In the Lower Rio Grande Valley of South Texas, water scarcity and drought pose ongoing challenges for farmers. Although cover crops are promoted for improving soil health and moisture, their effects on soil hydraulic properties in this region remain understudied. This thesis addresses both long-term (Chapter 2) and short-term (Chapter 3) impacts of cover crops on soil hydraulic properties and soil moisture. Long-term effects were evaluated through a three-year participatory field trial across four farms using a BACI design, while short terms were evaluated using a complete randomized block design. Soil hydraulic properties (residual water content θr, saturated water content …

Identification Of Cadmium As A Structural And Functional Modulator Of Psd-95 Regulating Nmdars At Postsynaptic Membranes, Claudia Garza

Theses and Dissertations

Postsynaptic density-95 (PSD-95) is an essential scaffolding protein in excitatory neurons. PSD-95’s N-terminal palmitoylation region elicits synaptic plasticity by targeting, anchoring, and trafficking glutamate receptors, such as N-methyl-d-aspartate receptors (NMDAR), to the postsynaptic membrane. The molecular interactions of PSD-95 and its dysregulation in excitatory synapses are currently being explored as primary causes of neurodegenerative diseases and disorders, such as Alzheimer’s disease, Schizophrenia, and Parkinson’s disease. Recent studies demonstrate an overaccumulation of zinc at two cysteines (C3 and C5) and two histidines (H24 and H28) of PSD-95 blocks palmitoylation, causing a loss of NMDAR at the postsynaptic membrane. In addition, exposure …

A Comparative Study Of Urban And Natural Nesting Gray Hawks In The Lower Rio Grande Valley Of South Texas, Evan Farese

Theses and Dissertations

Urbanization can negatively impact birds of prey, which occupy higher trophic levels. The Gray Hawk (Buteo plagiatus) is a neotropical raptor inhabiting the Lower Rio Grande Valley (LRGV) of Texas, where it is threatened. The species’ ecology has been little studied and it is unclear how urbanization may affect population viability. I studied Gray Hawk reproductive success, diet, and thermal ecology at nests in urban and natural habitats in the LRGV. Camera trap data showed adults at urban nests delivered mostly avian prey, while mammalian prey was most frequently brought to natural nests. Data from temperature loggers showed …

Simulating Chill: Exploring The Cognitive And Therapeutic Potential Of Cold Vr Environments, Jessica Turner, Piper Hutson, James Hutson

Faculty Scholarship

This study investigates the cognitive and therapeutic potential of immersive virtual reality (VR) environments designed to simulate cold conditions. Through the engagement of participants through multisensory stimuli—including vivid visual representations of the Athabasca Glacier, auditory effects of icy winds, and corresponding haptic feedback—the research evaluates neurological and physiological responses associated with attention, emotional regulation, and stress modulation. Participants experienced virtual scenarios featuring icy winds and snow, activating specific neurological pathways involving the occipital lobe, primary visual cortex, superior colliculus, and insula, thus reinforcing sensory integration. Through predictive coding, the anterior insula and hypothalamus were engaged, prompting thermoregulatory simulations and subconscious …

Impact Of Shear Flow On Marine Biofilms Using Hyperspectral Imaging, Shantanu Mahesh Kore

All Theses

Various microbial communities in marine biofilms cause biofouling on submerged surfaces, posing challenges to marine industries. Despite their ecological and economic importance, biofilms' biomechanical and biochemical responses to hydrodynamic shear stress are insufficiently understood, particularly in dynamic flow conditions. To fill this gap, our study uses an innovative fiber-optic hyperspectral imaging (HSI) system and a supercontinuum laser source to examine marine biofilms' structure, composition, and detachment behavior at different shear stress levels.

To detect spectral and spatial heterogeneity in live biofilms without labeling, we created a custom imaging pipeline that captures reflectance spectra in the 600-850 nm range, targeting microbial …

Berm-Leveling Machine For Peach Orchards: Incorporation Of Tree-Sensing Feature And Profitability Study, Shubham Singh

All Theses

Root collar excavation extends the productive life of peach trees in Armillaria root rot-infested soil, but the process requires trees to be planted on berms. Berm-planted peach orchards restrict the mobility of workers and machinery and can lead to increased erosion in furrows on either side of the berms. The current inter-tree berm-leveling machine depends on the driver's command to dodge the peach trees. The objectives of this thesis were to (1) integrate the feeler, infrared, and LiDAR-based tree sensing systems in the berm-leveling machine to make the soil excavating head's movement independent, (2) measure the impact of finger weeder-based …

Behavior Change: Actions To Restore Piedmont Prairie And Adopt Sustainable Behavior, Kacey Marie Kaibery

All Theses

Restoration of an ecosystem or adoption of sustainable behavior could benefit the environment. Valuable ecosystem services, like water filtration and habitat for pollinators, inspire investigation into the restoration of grasslands, like Piedmont prairies. This research endeavors to determine the impact of disturbance type (tilling, herbicide, mowing, fire, control with seed or no seed). The second-year aboveground biomass was harvested, identified, counted, and weighed to understand plant species’ response after the application of the disturbance. Target species and plant community diversity did not significantly vary between disturbance types. Planting methods (hand dispersal, drill, one-month and six-month transplanting) on Asclepias tuberosa establishment …

Ghosts In Glass: Ghost Crabs As Judges Of Glass Sand For Coastal Restoration, Emily Parrish

Honors Theses

Over 60% of the Gulf of Mexico coastline is actively eroding, which has resulted in thousands of miles of lost coastline over the last 100 years. This drastic loss of coastal land highlights the dire need for coastal restoration across the entirety of the Gulf Coast. A vital aspect of restoring these eroded areas is replenishing eroded substrate, traditionally conducted through offshore dredging of substrates which comes with high economic and ecological costs. Recycled glass sand may be able to fill this role and reduce our reliance on dredging while lowering the amount of glass waste entering landfills each year. …

Interventions Of Eating Habits And Healthy Behaviors, Diego Armando Mazariegos Espinosa

Undergraduate Honors Theses

About thirty to fifty percent of college students report having negative emotions such as anxiety, depression, sadness, anger, hopelessness, shame, fear, and more. And over seventy percent feel exhausted or overwhelmed by schoolwork. According to scholarly research, these emotions pose obstacles during college life impacting the eating habits and healthy behaviors of college students. These habits can have a possibility of bringing lifelong issues in social, educational, and self-esteem aspects. Technology has revolutionized the world in a spectacular way in a short period of time. As students today have access to all sorts of technology like phones and computers, the …

Whole-Genome Assembly And Annotation Of The Firecracker Penstemon (Penstemon Eatonii), David E. Jarvis, Mikel R. Stevens, Payton Carter, Ying Fei Lin, Kate E. Jaggi, Gabriela Jijon, Teal Kalt, Jouber Calixto, Samantha Standring, Kaitlin Torres, Kayla B. Stephensen, Hayley Mangelson, Noah H. Williams, Carolyn A. Wessinger, Peter J. Maughan, Paul B. Frandsen

Faculty Publications

The penstemons are ornamental annual flowering plants native to the Intermountain West and Rocky Mountains and commonly used for urban landscaping. Elite commercial penstemons are generally susceptible to abiotic stresses, including drought, root rot, cold, and high salinity. Firecracker penstemon (Penstemon eatonii), however, is much more tolerant to these stresses than most elite cultivars. Importantly, firecracker penstemon has been reported to hybridize with many other penstemons and therefore provides the opportunity to develop more tolerant elite cultivars through strategic crossing. To facilitate the study and utilization of firecracker penstemon, we sequenced and annotated the genome of a P. …

Network-Based Attacks In Cloud Computing In 2020-2024, Yaswanth Sai Manikanta Anguluri

Electronic Theses, Projects, and Dissertations

As the use of cloud technologies has increased in the past five years, the number of network attacks is also increasing. During 2020 to 2024, there are lot of changes in cloud technologies which led to various network attacks in the cloud computing environments from 2020 to 2024. This study investigates the evolution of network-based attacks in cloud environments from 2020 to 2024. Data was collected from Kaggle website to analyze the trends of the evolution of network-based attacks. The research questions are: (Q1) How do the trends change in network-based attack from 2020 to 2024 and why? (Q2) Which …

Unraveling Epigenetic Mechanisms That Regulate Breast Cancer Lung Metastatic Relapse By Rewiring The Immune Microenvironment, Jayanta Mondal

Dissertations and Theses (Open Access)

Metastasis accounts for >90% of cancer-related deaths and thwarting metastasis is widely considered to be the “Holy Grail” of cancer treatment. Breast cancer is the most common cause of cancer-related death among women and is characterized by its proclivity to spread to distant secondary organs like the lungs, and the brain. These disseminated tumor cells lie dormant at the secondary site and can undergo metastatic relapse. Epigenetic alterations are a predominant hallmark of cancer, however, its role in facilitating reawakening of dormant cancer cells and the subsequent metastatic relapse remains to be elucidated. To address this gap of knowledge, we …

Developing Novel Therapies Targeting The Tumor Microenvironment Of Aggressive Breast Cancer, Lan T H Phi

Dissertations and Theses (Open Access)

Triple-negative breast cancer (TNBC) and inflammatory breast cancer (IBC) are the most aggressive breast cancer subtypes. The tumor microenvironment (TME) is critical in driving these aggressive breast cancers' clinical phenotype and aggressiveness. Therefore, we explored novel actionable targets and complementary therapies targeting the TME to improve the outcomes of patients with these cancers.

In this thesis, we identified AXL as a potential therapeutic target in IBC due to its role in generating an immunosuppressive TME. Indeed, inhibiting the AXL pathway suppresses IBC tumor growth and reduces M2 macrophage populations in various mouse models. Mechanistically, AXL facilitates the polarization of M2 …

The Extracellular Domains Of The Ampa, Kainate, And Orphan Delta Receptor Regulate Channel Gating In Distinct Ways, Cuauhtemoc Ulises Gonzalez

Dissertations and Theses (Open Access)

The ionotropic glutamate receptors are ligand-gated cationic channels essential for neuroplasticity and neurological functions such as learning, memory, behavior, cognition, and motor coordination. Mutations in these channels are linked to various disorders including autism, ataxia, and epilepsy, making them compelling pharmacological targets. Within this family, the α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) and kainate receptor mediate their function through fast glutamate-gated ionotropic activity, which needs precise structural changes to perform properly. While Cryo-EM structures have provided snap shots of these proteins, questions remain regarding the dynamics across conformations and individual roles of the extracellular amino-terminal and agonist binding domain in dictating function. …

Relationship Between Processing Body Formation, Epithelial-To-Mesenchymal Transition, And Invasion In Lung Adenocarcinoma, Amanda Warner

Dissertations and Theses (Open Access)

Lung cancer is the leading cause of cancer-related deaths in the United States, largely due to its ability to metastasize. Epithelial-to-mesenchymal transition (EMT) is a process that enhances the ability of cells to lose their cell-cell contacts, invade, and enter the blood stream which are essential during metastasis. Many transcriptional gene programs are altered during EMT such as activation of mesenchymal transcription factors, like ZEB1, and enhanced response to the TGFβ1 cytokine. In oncogenic contexts, TGFβ1 enhances the formation of processing-bodies (P-bodies) where P-body proteins are required for invasion in multiple cancerous cell lines. P-bodies are a type of ribonucleoprotein …

Rod Photoreceptor Regeneration In A Zebrafish Model With Retinitis Pigmentosa, Eyad Shihabeddin

Dissertations and Theses (Open Access)

A cellular hallmark of inherited retinal degenerative diseases is progressive loss of photoreceptors until one is completely blind. Unlike mammalian models, Zebrafish have the ability to naturally regenerate their neurons after injury or disease is detected. We have generated a zebrafish model with the most common autosomal dominant form of the inherited retinal degenerative disease known as Retinitis Pigmentosa. We utilize immunohistochemistry, single-cell RNA sequencing, several analysis tools, behavioral assays and oligonucleotides to characterize our zebrafish model and identify the transcription factors necessary for rod photoreceptor regeneration. We show that our zebrafish model has continuous degeneration and regeneration of rod …

The Gut Microbiome As A Novel Approach For Reversing Long-Term Inflammation And Accelerated Aging Across The Lifespan, Janelle M. Korf

Dissertations and Theses (Open Access)

Introduction: Neonatal hypoxic-ischemic encephalopathy (HIE) arises from disrupted perinatal cerebral oxygenation and perfusion. It is a leading global cause of infant death and disability which disproportionally affects males. Like adult stroke, HIE initiates a rapid influx of inflammatory cells across the blood brain barrier and a loss of microglial homeostasis. Persistent peripheral inflammation in children with a history of HIE is recognized but its ramifications, including accelerated aging, are poorly understood. As this coincides with critical stages of brain development, interventions started months or years post-injury may still improve survivors’ quality of life. One promising intervention is to manipulate the …

Impact Of Personal And Family History Of Huntington's Disease On The Decision And Ability To Obtain Life, Long-Term Care, And Disability Insurance, Karli Livingston

Dissertations and Theses (Open Access)

Huntington’s disease (HD) is an inherited, neurodegenerative condition characterized by a clinical triad of motor, cognitive, and psychiatric symptoms. Individuals diagnosed with HD manifest characteristic symptoms of the disease including motor and cognitive changes, and they may or may not have undergone genetic testing to confirm the diagnosis. Individuals at-risk for HD are those who have not yet undergone genetic testing for HD, but have a first- or second- degree relative diagnosed with the disease. Genetic testing for HD is categorized into two forms: predictive and confirmatory. However, many individuals choose not to pursue testing due to a fear of …

The Influence Of Scientific, Genetic, And Health Literacy On Carrier Screening Decision-Making, Brenna D. Albracht

Dissertations and Theses (Open Access)

For those wishing to assess their reproductive risks and make informed decisions in their reproductive planning, carrier screening for autosomal recessive and X-linked conditions, as well as cell-free DNA (cfDNA) screening for aneuploidy, are recommended during pregnancy. Despite similarities in purpose, sample requirements, insurance coverage, and safety, a lower percentage of individuals elect carrier screening than cfDNA screening, suggesting there may be a disconnect in what patients perceive as valuable information for their pregnancy. Previous studies have attempted to explain the factors associated with carrier screening uptake or decline; however, no models have yet accounted for a patient’s literacy level …

Role Of Mir-4732-3p In Breast Cancer Brain Metastasis And Brain Metastatic Tumor Microenvironment, Munazza Samar Khan

Dissertations and Theses (Open Access)

In this study, we aimed to identify microRNAs (miRNAs) that may play important roles in breast cancer brain metastasis (BCBM). To this end, we conducted miRNA-sequencing of extracellular vesicles isolated from the serum samples of 6 BCBM patients and 8 Stage I/II/III breast cancer patients, and identified 49 circulating miRNAs that were upregulated in BCBM patients compared to Stage I/II/III breast cancer. Upon further analysis, we identified miR-4732-3p to be upregulated in brain-tropic triple-negative breast cancer (TNBC) cell lines, compared to parental lines. MiR-4732-3p overexpression increased metastatic properties of TNBC cells, including proliferation, migration, invasion, and maintenance of a mesenchymal …

Uncovering A Fundamental Mechanism Underlying Female Oocyte Quality And Rasopathies Using C. Elegans As A Model System, Han Bit Baek

Dissertations and Theses (Open Access)

Signaling pathways are molecular networks that allow cells to communicate between and within themselves. They are crucial for the coordination of diverse cellular processes and are the molecular mechanism in which cells sense and respond to their environment. RAS (Rat Sarcoma) is a small GTPase that transmits extracellular growth factor signals through a downstream kinase cascade and ERK (Extracellular-signal regulated kinase) is the terminal kinase, and it controls cellular processes such as proliferation, differentiation, and survival by phosphorylating its downstream effectors. This post translational modification regulates the effector by modulating its activity, levels, and/or interaction with other molecules. Given the …

Mhc Class I Tyrosine Phosphorylation Site Y320 Augments Cd8+ T Cell Priming, Effector Function, And Memory Response, Yimo Sun, Gregory A Lizee, Yitao Tang, Priscilla Ortiz, R Eric Davis

Dissertations and Theses (Open Access)

The cytoplasmic domain of MHC class I (MHC-I) molecules contains a single, highly conserved tyrosine residue (Y320). In previous work, we found that mice expressing a Y320F-mutated form of H-2K^b had reduced capacity to generate K^b-restricted cytotoxic T lymphocyte (CTL) responses following viral infection, due (at least in part) to defects in endolysosomal trafficking of H-2K^b and antigen cross-presentation by dendritic cells (DCs). In this study, we investigated whether there are additional, post-presentation dependencies on Y320 for T-cell priming. We engineered both human- and mouse-derived antigen-presenting cells (APCs) to express either wild-type MHC-I or variants of …

Neural Activity Within And Between Visual And Executive Areas Is Modulated Post-Locomotion In Rhesus Macaques, Sergey Egranov

Dissertations and Theses (Open Access)

Physical activity has been shown to benefit cognitive and mental health by improving cerebrovascular perfusion and regulating hormone-mediated processes on a systemic level. However, the acute effects of physical activity, such as locomotion, on the neuronal circuits underlying cognitive processes have yet to be fully characterized. This body of work seeks to rectify this gap in knowledge through analysis of how both behavioral performance and neuronal activity signatures in visual and executive brain regions are modulated post-locomotion in rhesus macaques.

To this end, we performed high-yield electrophysiological recordings simultaneously from area V4, a mid-tier visual cortical region, and the dorsolateral …

Investigating Metabolic And Mitochondrial Adaptations Triggered By Blood Flow During The Endothelial-To-Hematopoietic Transition, Paulina Horton

Dissertations and Theses (Open Access)

Hematopoietic stem cell (HSC) transplant is the standard of care for many hematologic diseases. However, many patients cannot benefit from this potentially curative treatment because they cannot find a suitable donor, contributing to a high level of unmet need. Recently, bona fide HSCs capable of robust engraftment and differentiation have been generated from iPSCs utilizing wall shear stress (WSS) to help promote HSC generation. However, the mechanisms through which WSS regulates hematopoiesis remain poorly understood. Scientists, therefore, continue to look for the mechanotransduction pathways that promote hematopoiesis, and key answers may lie in examining the role of extrinsic factors that …

The Evolving Changes In The Regionalization Of Export Bans On U.S. Poultry Trade From The 2015 And 2022 Highly Pathogenic Avian Influenza Events, Kylie A. Roesler

Graduate Theses and Dissertations

As food security becomes a growing concern worldwide in a trading system dominated by globalization, the safeguarding of a bio-secure food system is at risk. One of the greatest risks to this stability of the system is, highly pathogenic avian influenza or HPAI which is growing in frequency and impact. Therefore, the global response to disease events is evolving into a newfound understanding of disease prevalence across the animal protein industries. This study will analyze the 2022 HPAI event in the United States regarding the regionalization of restrictions imposed by trading partners accounting for trade agreements executed. The examination of …

Physiological And Molecular Responses Of Diverse Rice Genotypes Under Drought Stress, Huda Mohmmed Alshaya

Graduate Theses and Dissertations

Climate change-induced drought stress is a significant constraint on global rice (Oryza sativa L.) production, threatening food security. This study evaluated the drought resilience of 15 diverse rice genotypes from the USDA mini-core collection under field, greenhouse, and osmotic stress conditions. Field trials assessed reproductive-stage drought tolerance based on panicle length (PL), number of spikelets per panicle (NSP), and spikelet sterility (SS). Greenhouse experiments examined moisture retention at the vegetative stage. Significant genotypic variation was observed, with genotypes 310724, 310779, 311181, 311603, 311793, and Vandana exhibiting drought tolerance through stable PL and SS. Additionally, genotypes 310100, 310428, 311255, N22, …

Comparison Analyses Of Consumer Acceptance, Evoked Emotions, And Purchase Intent Between Gluten-Containing Versus Gluten-Free Chocolate Chip Cookie Products, Shaelyn Frauenhoffer, Eniola Ola, Suzanne Jervis, Susan E. Gauch, Han-Seok Seo

Food Science Faculty Publications and Presentations

The demand for gluten-free products has increased significantly over the past few decades. This study aimed to determine differences in consumer acceptance, emotional responses, and purchase intent between gluten-containing versus gluten-free chocolate chip cookies. Twelve commercially available chocolate chip cookie products from 11 brands were evaluated, including 7 gluten-free and 5 gluten-containing options. Eighty-nine participants without celiac disease took part in this 2-day study, evaluating six cookies per day. Participants rated sensory acceptance (appearance, flavor, texture, and overall liking) using a 9-point hedonic scale and evaluated specific sensory attributes (chocolate flavor, sweetness, chewiness, and hardness) using a 5-point just-about-right (JAR) …