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The In4mer Crispr/Cas12a Multiplex Knockout Platform And Its Applications, Nazanin Esmaeili Anvar

Dissertations and Theses (Open Access)

Discovering synthetic lethal interactions between genes holds the key to uncovering cancer vulnerabilities, enabling the development of more effective drugs for patients. However, identifying these vulnerabilities in the complex genome of human, which comprises thousands of genes, poses a significant challenge. One alternative approach to investigate these interactions involves exploring enriched sources of synthetic lethal interactions, such as paralog pairs. In recent years, a couple of studies have conducted dual-gene knockout experiments on paralog pairs using different approaches to identify synthetic lethal interactions. In this study, we conducted a meta-analysis of CRISPR genetic interaction screens. We identified a candidate set …

Mapping The Neural Circuits That Underlie Metabolic Vs. Emotional Regulation Of Food-Seeking Behavior, Xu Zhang

Dissertations and Theses (Open Access)

Flexibly adjusting food-seeking behaviors based on metabolic needs and environmental threats is crucial for animal survival. In humans, maladaptive food-seeking behaviors that contravene energy homeostasis, which is often driven by food-associated cues with hedonic reward values, lead to obesity and eating disorders. However, the neural mechanisms underlying the modulation of cued food-seeking behaviors by distinct metabolic and threat states remain elusive. Using an approach-food vs. avoid-predator threat conflict test in rats, we identified a subpopulation of neurons in the anterior portion of the paraventricular thalamic nucleus (aPVT) which express corticotrophin-releasing factor (CRF) and are preferentially recruited to respond to food …

Cord Blood-Derived Invariant Natural Killer T Cells As A Platform For Allogeneic Chimeric Antigen Receptor Cell Therapy, Maison Grefe

Dissertations and Theses (Open Access)

Chimeric antigen receptor (CAR) T cells have revolutionized the treatment of hematopoietic malignancies achieving >50% complete response rates in numerous refractory/relapsed B cell malignancies. However, there are challenges that hinder CAR-T efficacy and bar the broader use of this therapy in patients. One approach to address these challenges is to create a safe allogeneic CAR cell product by using cells that do not cause graft versus host disease (GvHD). Invariant natural killer T (iNKT) cells are an ideal candidate as they are restricted to the monomorphic CD1d protein in contrast to HLA restricted αβ-T cells and therefore are safe in …

Methods For The Prediction Of Osteoradionecrosis Resulting From Head And Neck Cancer Radiation Therapy, Brandon Reber

Dissertations and Theses (Open Access)

Head and neck cancer (HNC) is the sixth most diagnosed cancer worldwide with over 600,000 patients diagnosed every year. One of the primary methods to treat HNC is through radiation therapy (RT). While RT is effective at treating HNC, late toxicities resulting from treatment can occur months to years post-treatment and can cause debilitating quality of life changes for HNC survivors. One of these late toxicities is osteoradionecrosis (ORN), which is the death of bone due to radiation. For HNC, the mandible is commonly affected and can cause challenges chewing, swallowing, and physical appearance changes. Several factors indicate the pressing …

Retinoid X Receptor As A Mediator Of Post Stroke Recovery By Reversing Age-Associated Phenotypes Of Microglia/Macrophages, Shun-Ming Ting

Dissertations and Theses (Open Access)

After stroke, microglia (MG) and blood-derived macrophages, together (MF), clear dead cells and cellular debris in the infarcted brain through phagocytosis. However, the phagocytic capability of MF declines with age. Age-related changes in MF phenotype also include overactive inflammatory responses to stroke-induced brain injury, altogether resulting in poor recovery after stroke. Retinoid-X-receptor (RXR) is a pleiotropic transcription factor. Our studies suggest that RXRa enhances MF phagocytic functions, reduces inflammatory responses, and improves post-stroke recovery. To establish phenotypes of aging MF, MG were MACS-sorted from the brains of young adults (2-4 months old) and aged (18-20 months old) mice for transcriptomic …

Impact Of Genetic Counseling On Patient Empowerment After Diagnosis Of Fetal Anomaly, Carley Brueckner

Dissertations and Theses (Open Access)

Approximately 3-5% of pregnancies are affected by fetal anomalies, often leading to structural and functional differences that impact infant health and mortality. When anomalies are identified on prenatal ultrasound, genetic counseling (GC) and genetic testing may be offered to investigate the potential for a possible syndromic cause. Genetic counselors provide education on the chance for a genetic etiology, available testing options, potential changes in medical intervention related to an identified etiology, and psychosocial counseling and resources. Regardless of a patient’s testing decision, genetic counseling should include psychosocial counseling to support and empower patients in a time of prognostic uncertainty and …

Exploring The Role Of Il-1Β/Il-1r In The Pathogenesis Of K-Ras Mutant Lung Cancer, Avantika Krishna

Dissertations and Theses (Open Access)

As the leading cause of cancer-related deaths worldwide, the development of targeted therapeutics to treat lung cancer remains crucial. Non-small cell lung cancer (NSCLC), the most common histological subtype predominantly comprises lung adenocarcinoma with driver mutations in the K-ras oncogene (KM-LUAD). KM-LUAD progression partly occurs through activation of the NF-κB pathway initiating an inflammatory response and creating a pro-tumor microenvironment. Notably, the pro-inflammatory cytokine IL-1β a potent activator and product of the NF-κB pathway is elevated in the lungs and sera of KM-LUAD patients. We have shown that IL-1β blockade promotes an anti-tumor immune phenotype in a mouse model of …

Histone Lysine Methyltransferase Nsd3 Governs Transcriptional Programs That Drive Pancreatic Neuroendocrine Tumors (Pannets), Mary Esmeralda Fuentes

Dissertations and Theses (Open Access)

Pancreatic Neuroendocrine Tumors (PanNETs) are the most common and lethal neuroendocrine malignancies where treatments used in advanced patients have limited efficacy, adverse side effects, and acquire resistance. Thus, there is a critical need to uncover novel precision therapeutics for PanNET patients. Additionally, pre-clinical models that more accurately represent disease are an urgent necessity for translational studies.

This dissertation directly addresses these challenges by identifying histone lysine methyltransferase (KMT) NSD3 as a critical oncogenic driver of PanNETs through di-methylation of histone H3K36 (H3K36me2).

The findings shown in this body of work indicate that H3K36 methylation by NSD3 functions as a transcriptional …

Motivations And Attitudes For Pursuing Anonymous Genetic Testing For Huntington’S Disease, Jordan Steffen

Dissertations and Theses (Open Access)

Huntington’s disease (HD) is a progressive neurodegenerative disorder for which predictive and confirmatory testing is available. However, only a small portion of at-risk individuals complete predictive testing. Concerns of privacy and genetic discrimination have been cited as reasons testing is declined. This leads some to seek anonymous testing, a process in which measures are taken to exclude identifying information, thereby preventing results from being linked to legal names, medical records, or health insurance. Previous research suggests anonymous testing is not widely favored amongst healthcare providers, but patient perspectives have not been described. These studies also precede the implementation of the …

Epiregulin As A Novel Target For Antibody-Drug Conjugate Development For The Treatment Of Colorectal Cancer, Joan Jacob

Dissertations and Theses (Open Access)

Antibody-drug conjugates (ADCs) are a fast-growing class of molecularly targeted therapies with 13 currently approved and over a 100 in clinical trials. ADCs consist of a monoclonal antibody (mAb) conjugated to a potent cytotoxic payload to selectively target tumor antigens highly expressed on the cell surface. ADC development has been limited in colorectal cancer (CRC) by the lack of novel and effective therapeutic targets. Epiregulin (EREG), is an epidermal growth factor receptor (EGFR) ligand that is highly expressed in CRCs of different subtypes and mutational statuses with low expression in normal tissues. Here, we have characterized the role of EREG …

Importance Of Specific Nk Cell Subsets For Antitumor Immunity In Hpv+ Cancers, Madison O'Hara

Dissertations and Theses (Open Access)

High-risk type human papillomaviruses (HPV) are associated with genital and oral cancers, and the incidence of HPV+ head and neck squamous cell cancers is fast increasing worldwide. Survival rates for patients with locally advanced disease are poor and variable after standard of care (SOC) treatment. Identifying the antitumor host immune mediators important for treatment response and designing strategies to promote them are essential for improving clinical outcome. The natural killer (NK) cells are a critical component for antitumor innate effector immunity. Among the multitude of activation and inhibitory receptors on immune cells, HLA-DR is recognized as an important activation marker …

Interrogating Therapeutic Resistance To Oncogenic Krasg12c-Based Therapies In Colorectal Cancer, Oluwadara Coker

Dissertations and Theses (Open Access)

Colorectal cancer is the second leading cause of cancer-related deaths and the third most common cancer in the United States. Although KRAS is mutated in 50% of patients with metastatic CRC (mCRC), it has historically been a challenging therapeutic target. The recent approval of novel covalent inhibitors selective for KRASG12C mutation have entered the clinic, which has not only marked a major milestone in cancer drug discovery but has also intensified efforts to directly target other KRAS mutations that have also successfully entered the clinic. However, treatment-associated resistance mechanisms have long threatened to attenuate clinical benefit through either adaptive or …

Biophysical Model Of Retraction Motor Neurons And Their Modification By Operant Conditioning, Maria Rasheed

Dissertations and Theses (Open Access)

Operant conditioning (OC) is a form of associative learning in which an animal modifies its behavior based on the consequences that follow that behavior. Despite its ubiquity, the underlying mechanisms of OC are poorly understood. Insights into the mechanisms of OC can be obtained by studying Aplysia feeding behavior as it can be modified by OC. This behavior is mediated by a central pattern generator (CPG) network in the buccal ganglia that contains a relatively small number of neurons. This CPG generates rhythmic motor patterns (BMPs) that move food into the gut by closing a tongue-like structure (i.e., radula) during …

Syntaxin-3 Mediates Baseline And Stimulated Mucin Secretion, Brianne Wharton

Dissertations and Theses (Open Access)

There are two rates at which airway epithelial cells secrete mucin. The low baseline rate accounts for ciliary clearance, and the high stimulated rate obstructs airways in protection from helminths or in obstructive pulmonary diseases. The exocytosis of mucins occurs via the four-helix SNARE complex. The SNARE proteins contributing helices are the vesicle-SNARE VAMP, and the target-SNAREs SNAP and Syntaxin. Coiling of the complex fuses the granule and plasma membranes to release mucins into the extracellular space. The VAMP and SNAP isoforms mediating baseline and stimulated secretion are known, but the Syntaxin (Stx) isoform remains unknown.

Three candidate exocytic Stx, …

Structural And Functional Studies Of Ascc1 In Dna And Rna Alkylation Damage Response, Naga Babu Chinnam

Dissertations and Theses (Open Access)

Alkylating agents from environmental, endogenous, and certain chemotherapeutic sources constantly challenge cellular nucleic acids. Repairing the damage caused by alkylation is necessary for maintaining genomic stability. ALKB family Human Homolog ALKBH3 plays a key in repairing alkylated damages in DNA and RNA molecules. Activating signal co-integrator complex 1 (ASCC1) acts with ASCC-ALKBH3 complex in alkylation damage responses. ASCC1 uniquely combines two evolutionarily ancient domains: nucleotide-binding K-Homology (KH) (associated with splicing, transcriptional regulation, and translational control) and two-histidine phosphodiesterase (PDE) (associated with hydrolysis of cyclic nucleotide phosphate bonds). Germline mutations link ASCC1 loss of function to spinal muscular atrophy with congenital …

Dissecting The Relationship Between Mucin 5ac And The Lung/Gut Microbiome In The Pathogenesis Of K-Ras Mutant Lung Cancer, Maria T. Grimaldo

Dissertations and Theses (Open Access)

Non-small cell lung cancer, including its most common subtype, lung adenocarcinoma (LUAD), is the leading cause of cancer-related deaths worldwide. In LUAD patients, KRAS mutations are the most common oncogenic driver alteration. Given KRAS is upstream to many signaling pathways involved in cell survival and cytokine production, interventions against KRAS-mutant lung cancers are prone to develop acquired resistance. Thus, there is a need to develop alternate targeting strategies and test combination therapies for improved intervention. Previously, we have found that KRAS-mutant LUAD (KM-LUAD) patients whose tumors harbor high expression of Mucin 5 AC (MUC5AC), a main airway secretory mucin, have …

Chemical-Mediated Mate Attraction In Clover Root Curculio (Sitona Hispidulus F.), A Belowground Pest Of Forage Crops, Kristin Leutgeb

Undergraduate Honors Capstone Projects

Curculionid beetles are well known for their production of semiochemicals, including contact (e.g. cuticular hydrocarbons) and volatile pheromones that mediate conspecific attraction and mating. Clover root curculio (CRC; Sitona hispidulus) in particular is an emergent, soil-borne pest of significant concern to producers of alfalfa and other leguminous crops in the United States. Producers have few control options for CRC and a greater understanding of chemical-mediated attraction in this species can potentially improve the sustainability of its management. To examine which chemical cues are important for affecting the behavior of CRC and whether there are sex-based differences in response, I …

Variable Drought Impacts On Stream Habitat Across The Northwestern United States, Sophia Withers

Undergraduate Honors Capstone Projects

The Western United States has been in an extended drought since 2002 which can drive negative impacts on stream habitats supporting native fish and aquatic species. Stream quality, specifically in the context of fish habitat, depends on many variables, including vegetation quality. Drought conditions affect vegetation conditions; however it is unclear how drought conditions impact stream habitat quality for fish. This study examines how stream habitat quality relates to drought across the National Forests of the Northwestern US, as well as exploring whether drought increases have had a significant impact on riparian vegetation over the past 20 years. Using a …

Testing Resilience Of Microalgae Biofilms When Exposed To Hydrothermal Liquefaction Aqueous Phase, Davis Riley Haag

Undergraduate Honors Capstone Projects

There are a multitude of experimental and processing techniques in the bioenergy field that produce sustainable and carbon negative to carbon neutral methods of converting renewable resources into biologically based hydrocarbons. One example of a process is hydrothermal liquefaction (HTL) which specializes in converting wet biomass into biocrude oil. One reason that these processes are not used outside experimental testing is due to the high cost of performing these processes. There is potential to move these processes to larger scale testing and eventually industrial adaptation if breakthroughs are made to offset the process expenses. There is a waste product produced …

An In Vitro Investigation Of Urothelial Cell Function In Response To Hypoxia And Pressure In Relation To Bladder Outlet Obstruction, Britney Hudson

All Dissertations

Bladder outlet obstruction (BOO) is a prevalent urological condition and can be characterized by the presence of lower urinary tract symptoms (LUTS), such as hesitancy, weak stream, and nocturia. The main cause of BOO is a partial blockage of the urethra, which results in elevated voiding pressure, high storage pressure, and tissue ischemia, which are thought to be the triggers of bladder inflammation and subsequent fibrosis. Often patients do not seek treatment until the conditions get severe. Thus, it would be ideal to have an early diagnostic tool to detect changes in the bladder due to BOO. Extracellular vesicles (EVs) …

Optical Wavelength Measurement Based On Microwave-Photonics And Fiber Dispersion, Yongji Wu

All Dissertations

In modern photonics, combining microwave techniques with optical measurements has introduced a novel research direction. This study introduces a novel Microwave Photonics Wavelength Measurement System (MP-WMS), integrating microwave photonics with fiber chromatic dispersion to achieve direct wavelength measurement. Utilizing cost effective single mode optical fibers as dispersion devices, this system employs chromatic dispersion to convert optical frequency domain measurements into microwave time domain measurements. We established a mathematical model to describe how different wavelengths are detected, enhancing the system's effectiveness. The MP-WMS system offers an affordable solution with high resolution. In the experiment, we used a 35km long SM-28 single-mode …

Phylogenetics And Biogeography Of Appalachian Trechus (Coleoptera: Carabidae), Patricia Wooden

All Dissertations

Insects have long been used as tools for understanding the health of the natural world and how changes to climate, landscape, and human interaction have affected the communities those environments support. The Appalachian Mountains, located in eastern North America, is the oldest mountain range on the continent, and during its lifespan it has supported an abundance of microhabitats and endemic species to fill them. Conservationists must balance the need to preserve the diversity that is known and continue to explore the region for new taxa, often with limited budget and expertise. A genus of small carabids, Trechus Clairville, may aid …

Single Cell Pharmacodynamic Modeling Of Cancer Cell Lines, Arnab Mutsuddy

All Dissertations

Cancer is one of the leading causes of disease related death worldwide. Since the discovery of the genomic origins of cancer, targeted therapy has been developed towards specific mutations implicated for oncogenic transformation. However, current standard-of-care for mapping cancer patients to efficacious drug combination is often inadequate. The pathophysiology of tumor progression relies on the dysregulation of biomolecular pathways of which the topology and the dynamics challenge prognosis. Moreover, the overall genomic instability involved in disease states and the resulting inter-patient as well as intra-tumoral heterogeneity challenge rationalization of therapy and clinical decision-making. It highlights the need for the use …

Ecology And Integrated Pest Management Of Major Insect Pests Of Field Corn, Tim Bryant

All Dissertations

In the southeastern United States, the brown stink bug, Euschistus servus (Say), and the southern green stink bug, Nezara viridula (L.) (Hemiptera: Pentatomidae), are common economic pests of corn, Zea mays L. (Poaceae: Poales). Although commonly found, the corn earworm, Helicoverpa zea (Boddie) (Lepidoptera: Noctuidae), is generally not an economic pest and is managed with transgenic corn hybrids expressing toxins produced by the Bacillus thuringiensis (Bt). Resistance to Bt toxins is a major thread to the sustainability of Bt crops. Understanding the ecology of stink bugs and corn earworms in field corn can help to effectively implement integrated pest management …

Toxicokinetics And Toxicodynamics Of Radium-226 In An Estuarine Sentinel Species Geukensia Demissa, Sarah Donaher

All Dissertations

The historical use of radioluminescent objects, most notably those containing radium-226 (²²⁶Ra)-based paint, has contributed to contemporary environmental contamination of radioactive material, often near naval installations or other military-associated coastal sites. The risk to both human and environmental health from this small-scale, discrete radioactive material is challenging to predict due to large uncertainties in the source terms, bioavailability, and toxicity of these objects. The objective of this study was to provide information on the accumulation and toxicity of acute ²²⁶Ra exposure in a sentinel species to improve risk assessments for small-scale, coastal radiological contamination. The sentinel species …

Examining Context Dependency Of Invasion Hypotheses At The Continental Scale Using Riverine Fish Communities, Lily Thompson

All Dissertations

Many well-supported hypotheses seek to explain invasion dynamics, but evidence for common patterns among regions and taxa remains inconclusive and often contradictory. Invasion ecology is fundamentally linked to spatial scale, and discrepancies in results among invasion studies may be attributed, in part, to a failure to fully consider scale dependency. In this dissertation, I investigate the sources of inconsistencies across spatial scales and large geographic extents using riverine fish communities across the conterminous United States. To do so, I tested three main ideas. First, that cross-scale interactions contextualize estimated invasion mechanisms among regions. My results demonstrate that local empirical support …

A Rhetorical-Sociological Understanding Of Emotion, Amy Boone

All Dissertations

This project presents a rhetorical-sociological understanding of emotion while foregrounding the place and role of language. Born from Sara Ahmed’s work in The Cultural Politics of Emotion, it presents a simplified equation (contact + orientation = emotion) as both a prescriptive and descriptive formula for making sense of human emotional experience. Starting with an exploration of the difficult-to-understand affect system, this dissertation identifies both rhetoric and affect as energies which cannot be understood apart from their traces, the things they move, produce, and become. As a way to get at these often-invisible forces, two trace studies are conducted which explore …

Additive Manufacturing With Bioresorbable Polymers: Process-Structure-Property Relationships For Biomimetic Tissue Scaffolds, Clayton Joseph Culbreath

All Dissertations

Tissue engineering has a base requirement of scaffold structures to support cell growth, proliferation, and regeneration. However, attempts to use artificial scaffold structures have often fallen short of clinical needs to justify the change away from the established, biologic-based current standard of care. Based on the limited number of successful tissue scaffolds produced by material extrusion modes of additive manufacturing, fused filament 3d printing and electrospinning, critical design specifications for a tissue scaffold are six minimum requirements: 1) biocompatibility, 2) porosity, 3) mechanical properties, 4) bioresorbable medical grade materials, 5) bioactivity, and 6) appropriately scaled production methods compliant with medical …

Exploring Novel Nutrient Acquisition Mechanisms For Maintaining Energy Metabolism In Toxoplasma Gondii, Melanie Key

All Dissertations

Toxoplasma gondii is an infectious intracellular parasite that establishes infection within various mammalian hosts, including humans. Toxoplasma infects approximately one-third of the global population, making it an impactful pathogen of study. T. gondii is the causative agent of toxoplasmosis, an opportunistic infection that causes severe illness or fatality in immunocompromised individuals or pregnant women. The parasite possesses a very effective invasion strategy, allowing it to cross different tissue types to disseminate infection across the placental and blood-brain barrier. Although there are a few treatments for acute toxoplasmosis, these drugs can produce adverse side effects. These options are not effective against …

Can I Get A Witness? Employee Reactions To Witnessing Visible Self-Compassion At Work, Sara Krivacek

All Dissertations

Self-compassion is defined as a tripartite process whereby an individual notices their own suffering, feels empathetic concern for oneself, and responds to alleviate or address the suffering. Research on self-compassion has proliferated in the last decade, and a major theme in the literature posits that it is beneficial for the practicing individual. However, less attention is given to the impact of self-compassion expression on other individuals in the workplace – partly because one major assumption is that self-compassion is an internalized process. In this dissertation, I conceptualize self-compassion as a social process and draw from affective events theory to make …