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Functional Analyses Of The Polycomb-Group Genes In Sea Lamprey Embryos Undergoing Programmed Dna Loss, Cody Saraceno

Theses and Dissertations--Biology

During early embryonic development, the sea lamprey (Petromyzon marinus) undergoes programmatic elimination of DNA from somatic progenitor cells in a process termed programmed genome rearrangement (PGR). Eliminated DNA eventually becomes condensed into micronuclei, which are then physically degraded and permanently lost from the cell. Previous studies indicated that many of the genes eliminated during PGR have mammalian homologs that are bound by polycomb repressive complex (PRC) in embryonic stem cells. To test whether PRC components play a role in the faithful elimination of germline-specific sequences, we used a combination of CRISPR/Cas9 and lightsheet microscopy to investigate the impact …

Understanding The Role Of Peroxiredoxin Iv In Colorectal Cancer Development, Pratik Thapa

Theses and Dissertations--Toxicology and Cancer Biology

Reactive oxygen species (ROS) are oxygen-containing free radicals and/or molecules that are more reactive than O₂. ROS such as hydroxyl radical (•OH) and hydrogen peroxide (H₂O₂) are produced naturally in the body as a result of reactions such as aerobic respiration and oxidative protein folding. ROS undergo reduction-oxidation (redox) reactions and mediate cell signaling. Accumulation of excessive ROS can damage DNA, RNA, protein and lipids. Antioxidants are enzymes and small molecules that react with ROS to modulate redox signaling and to prevent and repair oxidative damage. Examples of antioxidants include glutathione, thioredoxin, superoxide dismutase, …

Conserved Novel Interactions Between Post-Replicative Repair And Mismatch Repair Proteins Have Differential Effects On Dna Repair Pathways, Anna K. Miller

Theses and Dissertations--Toxicology and Cancer Biology

DNA mismatch repair (MMR) is the DNA repair mechanism that repairs base-base mispairs and small insertions and deletions remaining after replication. MMR is also required for apoptosis after certain types of exogenous DNA damage that result in damage-associated mispairs. The basic MMR mechanism is well understood; however, proteins associated with MMR continue to be identified. The roles of these interacting proteins in MMR are largely unknown. We have identified the yeast protein Rad5 as a novel interactor of the critical MMR proteins Msh2 and Mlh1. Rad5 is a DNA helicase and E3 ubiquitin ligase involved in post-replicative repair. However, to …

Beyond Mitosis, Plk1-Mediated Phosphorylation Re-Wires Cancer Metabolism And Promotes Cancer Progression, Qiongsi Zhang

Theses and Dissertations--Toxicology and Cancer Biology

Polo-like kinase 1 (PLK1) is a well- characterized regulator of cell division and is known to be highly expressed in certain types of tumors. It has been demonstrated the multifaceted roles of PLK1 in regulation of transcription, translation, epigenetics, DNA damage and cellular metabolism et al. Despite these findings, the precise mechanisms by which PLK1 regulates these processes beyond mitosis remain unclear. PLK1-mediated phosphorylation and misregulation of its substrates has been linked to tumorigenesis, cancer progression, drug resistance and worse prognosis. In this study, we investigated the non-canonical functions of PLK1 in cancer metabolism and drug resistance. We found that …

Targeting Ezh2 To Improve Outcomes Of Lung Squamous Cell Carcinoma, Tanner Ducote

Theses and Dissertations--Toxicology and Cancer Biology

Only 20% of patients diagnosed with lung squamous cell carcinoma (LSCC) respond to immunotherapy. Anti-PD1 immunotherapy is most commonly prescribed to these patients; however, most will become refractory. It is important to understand the mechanisms underlying this problem to increase durability and survival. Building upon the work of other groups, our lab has demonstrated that the inhibition of the histone methyltransferase, EZH2, is crucial to maintaining an immunologically responsive microenvironment. Based on our data, we hypothesize that combining EZH2 inhibitors with anti-PD1 therapy will increase response and durability. To study non-small cell lung cancers (NSLC) our lab uses a variety …

Bioinformatic Analysis Of Proteomic And Genomic Data From Nsclc Tumors On Prognostic And Predictive Factors Of Immunotherapy Treatment, Mark Wuenschel

Theses and Dissertations--Pharmacy

Recent lung cancer research has led to advancements in molecular immunology, resulting in development of small molecule inhibitors, or immune checkpoint inhibitors, that propagate an anti-tumor T cell response. Despite increased overall and progression-free survival with reduced adverse effects compared to traditional chemotherapy, treating advanced stage lung adenocarcinoma patients remains non-curative, and evidence of non-responders or tumor recurrence to immune checkpoint inhibitor therapy is growing. Also, compared to traditional chemotherapy, there is a lower percentage of patients who respond to small molecule inhibitors. In this analysis of proteomic and genomic data from The Cancer Proteome Atlas and Global Data Commons …

Exploring The Molecular Basis Of Touch: A Comparative Analysis Of Gene Expression In Sensory Corpuscle-Rich And Corpuscle-Poor Skin Regions In The Duck, Thomas Hart

Theses and Dissertations--Biology

Cutaneous touch is facilitated by discrete cellular complexes composed of non-neuronal cells associated with mechanoreceptor neuron endings. The non-neuronal cells of these cutaneous end organ complexes (CEOCs) are believed to contribute to touch, but their role in touch sensation remains unclear. To better understand the function of CEOC cells, we sought to characterize the transcriptional profile of CEOC-rich tissue and identify genes expressed in CEOC cells. Bill skin of the tactile foraging Pekin duck (Anas platyrhynchos) is dense with CEOCs, specifically the avian analogs of mammalian Pacinian and Meissner corpuscles, while corpuscles in duck foot skin are scarce. Using RNA …

Development And Biological Evaluation Of Selective Small-Molecule Inhibitors Of The Human Cytochrome P450 1b1, Austin Hachey

Theses and Dissertations--Chemistry

The human cytochrome P450 1B1 (CYP1B1) is an emerging target for small- molecule therapeutics. Several solid tumors overexpress CYP1B1 to the degree that it has been referred to as a universal tumor antigen. Conversely, its expression is low in healthy tissues. CYP1B1 may drive tumorigenesis through promoting the formation of reactive toxins from environmental pollutants or from endogenous hormone substrates. Additionally, the expression of CYP1B1 in tumors is associated with resistance to several common chemotherapies and with poor prognoses in cancer patients. However, inhibiting CYP1B1 with small molecules has been demonstrated in cellular and murine model systems to reverse this …

Elucidating The Role Of Polycomb Repressive Complex 2 In Lung Stem Cell Fate And Lung Disease, Aria Byrd

Theses and Dissertations--Toxicology and Cancer Biology

The average human lungs take ~22,000 breaths and inhale ~2,000 gallons of air each day. This organ is the primary conduit for the transfer of oxygen to the internal organs, making it crucial for the sustainment of life. Consequently, mechanical malfunction of the lungs and/or pollution of inhaled air negatively impact internal organ function and ultimately put survival in jeopardy. Epigenetics, by nature, is a plastic phenomenon in which environmental stimuli influence short term, long term, and generational gene expression patterns. Chronic exposure of harmful stimuli to the lung epithelium has also been shown to alter epigenetic pathways, engender aberrant …

Understanding The Cellular And Physiological Mechanisms Of Fertilization And Early-Stage Seed Development, Mohammad Foteh Ali

Theses and Dissertations--Plant and Soil Sciences

Flowering plants have evolved a unique double-fertilization process. Two sperm cells fuse with two female gametophytic cells, the egg and central cells within the ovule, giving rise to the embryo and endosperm, respectively. Sperm cells in flowering plants are nonmotile and delivered in close proximity to the egg and central cells by the pollen tube. Flowering plants have established filamentous actin (F-actin) based sperm nuclear migration system for successful fertilization. Prior to fertilization, the female gamete forms a mesh-like structure of F-actin that shows constant inward movement from the plasma membrane periphery to the center of the cell where the …

Elucidating The Role Of Polycomb Repressive Complex 2 In Lung Stem Cell Fate And Lung Disease, Aria Byrd

Theses and Dissertations--Toxicology and Cancer Biology

The average human lungs take ~22,000 breaths and inhale ~2,000 gallons of air each day. This organ is the primary conduit for the transfer of oxygen to the internal organs, making it crucial for the sustainment of life. Consequently, mechanical malfunction of the lungs and/or pollution of inhaled air negatively impact internal organ function and ultimately put survival in jeopardy. Epigenetics, by nature, is a plastic phenomenon in which environmental stimuli influence short term, long term, and generational gene expression patterns. Chronic exposure of harmful stimuli to the lung epithelium has also been shown to alter epigenetic pathways, engender aberrant …

Extracellular Vesicles And Cancer Therapy: An Insight Into The Role Of Oxidative Stress, Jenni Ho

Theses and Dissertations--Toxicology and Cancer Biology

As a result of improvements in cancer detection and treatment methods, a growing population of cancer survivors are living with side effects associated with their cancer therapy. Oxidative stress plays a significant role in the development of cancer and as a mechanism for cancer therapy to exert its therapeutic effects, resulting in off-target tissue damage. Radiation has been long established as a means to utilize the generation of reactive oxygen species to kill cancer cells, and 50% of chemotherapy agents currently used are associated with inducing oxidative stress. One major side effect observed in cancer survivors is a decline in …

A Multidisciplinary Characterization Of The Enzymology And Biology Of Reversible Glucan Phosphorylation In Toxoplasma Gondii , Robert Murphy

Theses and Dissertations--Molecular and Cellular Biochemistry

Toxoplasma gondii is an opportunistic, protozoan parasite of all warm-blooded animals, infecting roughly one-third of humans worldwide. Humans acquire infections by consuming T. gondii tissue cysts in undercooked meat or from oocysts shed in cat feces. Encysted parasites convert into rapidly growing tachyzoites that disseminate throughout the body, defining the acute phase of infection. Under host immune pressure, tachyzoites convert into bradyzoites that populate tissue cysts found in CNS or muscle tissue and persist for the lifetime of the host, defining the chronic phase of infection. Tissue cysts are responsible for transmission via carnivory, but also possess the ability to …

Investigating The Role Of Chd7 And Sox11 In Retinal Cell Development And The Ocular Complications Of Charge Syndrome, Laura Krueger

Theses and Dissertations--Biology

Proper formation of the visual system requires the precise interaction of several embryonic cell lineages, including the neuroectoderm (forms the retina and retinal pigment epithelium), surface ectoderm (forms the lens), mesoderm and cranial neural crest cells (form the ocular blood vessels and anterior ocular structures). When this process is disrupted structural birth defects such as coloboma result, leading to pediatric visual deficits. Ocular developmental defects are often present in larger syndromic disorders. One example is CHARGE syndrome, a genetic disorder characterized by coloboma, heart defects, choanal atresia, growth retardation, genital abnormalities, and ear abnormalities. Pathogenic variants in CHD7 have been …

Novel Mechanism Of Endogenous Pancreatic Cancer Cell Expression Of Immune Checkpoint Programmed Cell-Death 1 Protein (Pd-1) Inducing Epithelial-To-Mesenchymal Transition (Emt) Through The Met Pathway And Promoting Cancer Progression In An Immune-Independent Process, Megan M. Harper

Theses and Dissertations--Clinical and Translational Science

Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest cancers with few treatment options, necessitating an urgent need for novel therapeutics. Immuno-oncologic (IO) therapies have revolutionized anti-cancer regimens in the past decade but typically involve reactivation of adaptive immune responses. In particular, immune checkpoint PD-1 is traditionally expressed only on immune cells while PD-L1 (PD-1 ligand) is overexpressed on cancer cells. When tumor-endogenous PD-L1 binds the PD-1 receptor on T-cells, the immune cells undergo anergy resulting in self-tolerance and cancer cell immune evasion. However, contrary to standard dogma, we previously demonstrated tumor-endogenous PD-1 expression in PDAC. Our data indicated that …

The Role Of Sox4 In Ocular Morphogenesis And Retinal Differentiation, Rebecca Petersen

Theses and Dissertations--Biology

Visual impairment ranges from mild forms that can be corrected with glasses to more severe cases that result in permanent loss of vision. Microphthalmia, anophthalmia, and coloboma (collectively referred to as MAC) account for 11% of cases of pediatric blindness and are a result of improper ocular morphogenesis. Retinitis Pigmentosa (RP) is a retinal degenerative disease that affects 1 in 3000 people worldwide. It is a progressive disorder that initially begins with loss of vision in low light settings due to rod photoreceptor degeneration but progresses to complete blindness upon loss of cone photoreceptors. Currently, there is no cure for …

Cell-Engineered Vesicles For Therapeutic Delivery And Immunomodulatory Applications, Khaga Neupane

Theses and Dissertations--Chemistry

Development of a new kind of drug delivery system (DDS) that could efficiently deliver therapeutics to the cell of interest would allow us to accomplish cell-specific drug delivery while eliminating systemic toxicity. Although nanocarriers including endogenously released extracellular vesicles (EEVs), liposomes, and small molecules seem to be promising drug delivery systems, biological challenges persist for their use in clinical applications. Here, we demonstrate nanovesicles engineered by fragmenting cellular membranes can be exploited as versatile DDSs for therapeutics delivery as well as immunomodulatory functions. Cell-engineered vesicles were produced by cavitating cells using nitrogen gas at high pressure followed by serial centrifugation. …

Metabolic Diversity Among Fibroblasts From Regenerating And Non-Regenerating Mammals, Ebenezer Aryee

Theses and Dissertations--Biology

Regeneration is a wound repair process that terminates in the restoration of tissue function and structure. Fibroblasts play pivotal roles in regenerative and fibrotic wound repair. Reports of extensive regenerative ability in mammals have been historically rare, but more recently spiny mice (Acomys) have emerged as a bona fide model of complex tissue regeneration. Recent work has indicated that fibroblasts from regenerators (Acomys and Oryctolagus) are more resistant to reactive oxygen species (ROS)-induced senescence compared to non-regenerating species, suggesting the influence of intrinsic cellular states on the fate of wound repair. Determining the basal metabolic signature …

Understanding The Effects Of Embryonic Hyperglycemia On Retinal Development And Maintenance, Kayla Titialii-Torres

Theses and Dissertations--Biology

Hundreds of millions of people are affected by diabetes worldwide. Whether they are diagnosed with prediabetes or Type I or II diabetes, there are a variety of mechanisms in the pathogenesis of diabetes. Diabetes is a disease which consists of recurring states of hyperglycemia that can be difficult to manage due to either lack of insulin production or improper utilization of insulin. While these mechanisms of action differ, complications induced by diabetes occur in both poorly regulated Type I and II. Common complications of diabetes include nerve damage, kidney damage, and eye damage. Eye damage specifically is called diabetic retinopathy …

Identifying Epidermal Enriched Genes Required For Planarian Regeneration- Sp. Schmidtea Mediterranea, Pallob Barai

Theses and Dissertations--Biology

The outer epithelial layer covering an organism, commonly known as the epidermis, is crucial for maintaining homeostasis and for the wound healing processes after injury. The planarian epidermis allows flatworms to heal their wounds and virtually restore any missing tissues. Immediately after amputation, planarians contract their muscle and stretch their epidermis to heal the wound area. However, how the planarian epidermis coordinates with other tissues and mechanisms after the initial wound healing processes begins is not understood in detail. I hypothesized that epidermal cell stretching upon wound healing induces transcriptional changes that are required for effective regeneration. To test this …

Elucidating The Role Of The Tyrosine Phosphatase, Shp-2, In Regulation Of Pd-L1 Expression In Non-Small Lung Cancer Using Both Biochemical Analyses And Real-World Genomic Information, Keller Toral

Theses and Dissertations--Pharmacy

Immune checkpoint inhibitors (ICIs), especially those that target programmed cell death protein 1 (PD-1) and programmed cell death ligand-1 (PD-L1), have been shown to provide substantial clinical benefit in many patients with non-small cell lung cancer (NSCLC). While these therapeutic agents can be highly effective in the correct context, the biological systems that malignant cells draft from normal activities of the cell are poorly characterized. Tumor cell-specific expression of PD-L1 is likely important for clinical benefit from PD-1 and PD-L1 inhibitors. It is known that PD-L1 is inappropriately expressed in many cancers harboring mutations in the RAS family of genes. …

Therapeutic Targeting Of Leukemia Stem Cells To Prevent T-Cell Acute Lymphoblastic Leukemia Relapse, Meghan G. Haney

Theses and Dissertations--Molecular and Cellular Biochemistry

The survival rate of T-cell Acute Lymphoblastic Leukemia (T-ALL) relapse is a dismal 10% of affected adults and 30% of children, largely due to the relapsed disease being more aggressive and treatment resistant than the initial disease. Relapse is thought to occur because conventional chemotherapies are unable to reliably eliminate a unique cell type known as leukemia stem (or propagating) cells (LSCs). LSCs are the only cells within the leukemia with the ability to self-renew and remake or replenish the ALL from a single cell. Currently, the pathways governing self-renewal in LSCs are largely unknown, precluding our ability to successfully …

Reversible Glucan Phosphorylation In The Red Alga, Cyanidioschyzon Merolae, Corey Owen Brizzee

Theses and Dissertations--Molecular and Cellular Biochemistry

Starch and glycogen are an essential component for the majority of species and have been developed to maintain homeostasis in response to environmental changes. Water-soluble glycogen is an excellent source of quick, short-term energy in response to energy demands. In contrast, plants and algae have developed the macromolecule starch that is elegantly suitable for their dependence on external circumstances. Semi-crystalline starch is water-insoluble and inaccessible to most amylolytic enzymes, thus plants and algae have developed a coordinated system so that these enzymes can gain access to the denser starch energy cache. Starch-like semi-crystalline polysaccharides are also found in red algae, …

Entry And Replication Of Negative-Strand Rna Viruses, Kerri Boggs

Theses and Dissertations--Molecular and Cellular Biochemistry

Hendra virus (HeV) and human metapneumovirus (HMPV) are negative-sense, singled-stranded RNA viruses. The paramyxovirus HeV is classified as a biosafety level 4 pathogen due to its high fatality rate and the lack of a human vaccine or antiviral treatment. HMPV is a widespread pneumovirus that causes respiratory tract infections which are particularly dangerous for young children, immunocompromised individuals, and the elderly. Like HeV, no vaccines or therapies are available to combat HMPV infections. These viruses fuse their lipid envelopes with a cell to initiate infection. Blocking cell entry is a promising approach for antiviral development, and many vaccines are designed …

Human Regulatory T Cells Control Inflammation From Effector T Cells In Prediabetes, Rui Liu

Theses and Dissertations--Pharmacy

Type 2 diabetes (T2D) is a chronic low-grade inflammatory disease. A T cell cytokine profile (Th17) from PBMCs can distinguish obese T2D from obese non-diabetes subjects. Individual T cell subsets interact with each other and the diverse subsets jointly determine overall inflammation. Cellular metabolism drives cytokine production of CD4⁺ T cells, and therefore contributes to inflammation in T2D. However, specific changes in metabolism and function of CD4⁺ T cells during the progression from lean healthy to obese and diabetic stages in people have not been clarified.

We hypothesize that human regulatory T cells (Treg) impact metabolism of effector …

Delineating The Role Of Fatty Acid Metabolism To Improve Therapeutic Strategies For Colorectal Cancer, James Drury

Theses and Dissertations--Toxicology and Cancer Biology

Colorectal cancer (CRC) remains a leading cause of cancer-related deaths in the world, comprising over 1 million new cases each year and over 500,000 deaths. CRC, when detected at an early stage of disease development, can be effectively treated, with a 5-year survival rate of over 90%. Such standard treatments include surgical resection of the primary tumor in combination with adjuvant chemotherapy. However, even with advancements in surgical procedures and chemotherapeutic targets, when CRC progresses to a more advance stage, the 5-year survival rate decreases significantly to just under 14%. This stark decrease in patient survival rate can be directly …

Developing Synthetic Strategies For Multifaceted Applications Of Stable Gold-Based Complexes, Randall Tyler Mertens

Theses and Dissertations--Chemistry

Development of stable gold-based complexes has been a rapidly advancing field due to the popularity of gold complexes, particularly for use in biomedical research and catalytic transformations. Given that auranofin, a gold(I) complex with FDA approval for the treatment of rheumatoid arthritis is used in the clinic, the development of stable gold-based molecules of clinical relevance is urgently needed. Herein are reported, synthetic strategies used for the development of new classes of gold(I) and gold(III) complexes for advancement in mitochondrial modulation for use as chemotherapeutics as well as application to gold catalysis due to the unique geometry of complexes presented …

Molecular Mechanisms Regulating Optic Fissure Fusion During Zebrafish Eye Development, Megan Weaver

Theses and Dissertations--Biology

Vertebrate retinal development requires timely and precise fusion of the optic fissure. Failure of this event leads to congenital vision impairment in the form of coloboma. Recent studies have suggested hyaloid vasculature to be involved in OF fusion. In order to examine this link, we analyzed optic fissure fusion and hyaloid vasculogenesis in the zebrafish pax2a noi mutant line. We first determined that pax2a^-/- embryos fail to accumulate F-actin in the optic fissure prior to basement membrane (BM) degradation. Furthermore, using 3D and live imaging we observed reduced OF hyaloid vascularization in pax2a^-/- embryos. When examining the connection …

Investigation Of Multidrug Efflux Transporter Acrb In Escherichia Coli: Assembly, Degradation And Dynamics, Prasangi Irosha Rajapaksha

Theses and Dissertations--Chemistry

The Resistant Nodulation Division (RND) super family member, tripartite AcrA-AcrB-TolC efflux pump, is a major contributor in conferring multidrug-resistance in Escherichia coli. The structure of the pump complex, and drug translocation by functional rotation mechanism have been widely studied. Despite of all these data, the dynamics of the assembly process of the pump and AcrB during functional rotation in the process of drug efflux remains poorly understood. My thesis focuses on understanding the pump assembly process, dynamics of AcrB in functional rotation mechanism, and also investigate the mechanism of degradation of AcrB facilitated by a C-terminal ssrA tag.

In the …

Periocular Mesenchyme Heterogeneity During Morphogenesis Of The Vertebrate Ocular Anterior Segment, Kristyn L. Van Der Meulen

Theses and Dissertations--Biology

The vertebrate eye is a complex organ, responsible for the primary sense with which we interact with our environment: vision. Development of the eye is a tightly regulated process, controlled by a vast network of genes. This process begins with eye morphogenesis, when the eye structure is formed through a series of morphogenetic movements and culminates in the creation of the optic cup, lens, and presumptive optic stalk. Next, retinal differentiation creates the critical cell layers of the retina needed to process light waves that enter the eye, including rod and cone photoreceptors, interneurons, and support cells. Failure in either …