Digital Commons Network^™

Characterization Of The Effects Of The Pyrazolopyrimidine Inhibitor Grassofermata (Nav-2729) In The Eukaryotic Pathogen Trypanosoma Brucei, Kristina Marie Parman

All Dissertations

The protozoan pathogen, Trypanosoma brucei, is the causative agent of sleeping sickness in humans and nagana in livestock in sub-Saharan Africa. T. brucei cycles between tsetse fly and mammalian hosts, and it is adapted to survive in diverse host tissues. Variant Surface Glycoprotein (VSG) plays a key role in immune evasion in the mammalian host. The VSG membrane anchor requires two myristates, 14-carbon saturated fatty acids (FAs) that are scarce in the host. T. brucei can synthesize FAs de novo, but also readily takes up exogenous FAs, despite lacking homologs to fatty acid uptake proteins found in other …

Impact Of Copper-Containing Products And Irrigation On Hybrid Bermudagrass (Cynodon Dactylon (L.) Pers X C. Transvaalensis Burtt-Davy), Adam Gore

All Dissertations

Copper (Cu) is an often-seen component in various turf industry products including fungicides, algaecides, and colorants. Though an essential micronutrient in plants, excessive levels of Cu has been shown in various plant commodities to cause phytotoxicity and plant death. With the increasing use of pigments on hybrid bermudagrass [Cynodon dactylon (L.) Pers x. C. transvaalensis Burtt-Davy] putting greens to replace overseeding practices during traditional dormant periods combined with regular applications of fungicide, algaecide and spray additives containing Cu, the objective of this study was to investigate the potential impact of individual and combined copper-containing treatments on hybrid bermudagrass and …

Biochemical And Kinetic Analysis Of Phosphofructokinase In The Eukaryotic Human Pathogen Entamoeba Histolytica, Jin Cho

All Dissertations

Entamoeba histolytica is a water- and food-borne intestinal parasite that causes amoebiasis and liver abscess in ~100 million people each year leading to ~100,000 deaths. This amitochondriate parasite lacks many metabolic pathways including the tricarboxylic acid cycle and oxidative phosphorylation, and cannot synthesize purines, pyrimidines, or most amino acids. As a result, E. histolytica is presumed to rely on its modified pyrophosphate (PP_i)-dependent glycolytic pathway for ATP production during growth on glucose. This pathway relies on a PP_i-dependent rather than ATP-dependent phosphofructokinase (PFK) and thus has a net production of three ATP per glucose. However, in …

Interpretable Mechanistic And Machine Learning Models For Pre-Dicting Cardiac Remodeling From Biochemical And Biomechanical Features, Anamul Haque

All Dissertations

Biochemical and biomechanical signals drive cardiac remodeling, resulting in altered heart physiology and the precursor for several cardiac diseases, the leading cause of death for most racial groups in the USA. Reversing cardiac remodeling requires medication and device-assisted treatment such as Cardiac Resynchronization Therapy (CRT), but current interventions produce highly variable responses from patient to patient. Mechanistic modeling and Machine learning (ML) approaches have the functionality to aid diagnosis and therapy selection using various input features. Moreover, 'Interpretable' machine learning methods have helped make machine learning models fairer and more suited for clinical application. The overarching objective of this doctoral …

Biochemical Analyses Of Udgx-A Crosslinking Uracil-Dna Glycosylase, Chuan Liang

All Dissertations

DNA base damage is common due to exposure to various endogenous and exogenous factors. To repair the base lesions, such as uracil from cytosine deamination, enzymes from the uracil-DNA glycosylase (UDG) superfamily are critical, which can recognize the damaged base and initiate the base excision repair (BER) pathway. There used to be six families of proteins identified in the UDG superfamily until a new member, UDGX, was found in Mycobacterium smegmatis, which is a unique DNA-crosslinking UDG. In this dissertation work, a series of biochemical analyses of the newly found UDGX are performed, including the analyses of structures, functions, …

Cellular Mechanism Of Pentagalloyl Gucose-Mediated Prevention And Reversal Of Abdominal Aortic Aneurysms, Greg Halsey

All Dissertations

Abdominal aortic aneurysm (AAA) has been the 15th leading cause of death in persons older than 55 for the past ten years in several Western countries, with rupture resulting in an almost 100% mortality rate. AAA is a focal dilation of the aorta characterized by progressive loss of elastin and vascular smooth muscle cells (SMCs), as well as persistent inflammatory response [1]. The only treatment for AAA is surgery; however, the mortality post-procedure is still 1-4%, with a 15-30% chance of morbidity [2].

Pentagalloyl glucose (PGG) treatment is effective in the reversal of AAA. While its stabilizing interactions with extracellular …

An Integrative Approach To Managing A Species Of Conservation Concern: Resource Selection, Spatial Ecology, And Population Genetics Of The Green Salamander (Aneides Aeneus), Megan Novak

All Dissertations

The relationship between wildlife and the environment they inhabit is dependent on both spatial and temporal scales. It is therefore crucial that biological investigations account for ecological scale when analyzing patterns and processes established, particularly when such investigations inform conservation management plans. This dissertation provides extensive insight into the conservation biology of the green salamander (Aneides aeneus), a critically imperiled species in South Carolina. The green salamander is a species that exists in a patchy network of rock outcrops within mountainous forest landscapes, and most studies on habitat suitability for green salamanders have been conducted on the macrohabitat, …

Developing Disinfection Strategies For Controlling Human Norovirus, Sars-Cov-2, And Clostridioides Difficile Endospores In Long-Term Care Facilities, Jinge Huang

All Dissertations

Long-term care facilities (LTCFs) provide an environment favorable for the transmission of three critical human pathogens: human norovirus (HuNoV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and Clostridioides difficile. Given residents in LTCFs are susceptible to infections due to their advanced ages and compromised immune systems, effective environmental surface disinfection plays a crucial role in controlling the spread of human pathogens within these settings and, therefore, mitigates the risk of infections caused by these pathogens. This dissertation aimed to assess the efficacy of various types of disinfectants against two HuNoV surrogates [feline calicivirus (FCV) and Tulane virus (TuV)], two …

Biology And Herbicide Resistance Characteristics Of Various Annual Bluegrass (Poa Annua L.) Biotypes From Across The United States, Jacob William Taylor

All Dissertations

Annual bluegrass (Poa annua L.) is one of the most problematic winter annual weeds in managed turfgrass systems, having rapidly adapted to different climates and management practices. Characteristics such as prolific seedhead production, clumped bunch-type growth habit, and lack of stress tolerance negatively impact turfgrass quality. Achieving adequate control can be difficult because annual bluegrass exhibits high levels of genetic diversity, the ability to germinate year-round, and has a high tendency for evolving herbicide resistance, currently resistant to at least nine different herbicide sites of action. Current management programs rely heavily on herbicides for control; however, frequent use without implementing …

Effect Of Authentic Kefir And Nigella Sativa On Broilers Challenged By Coccidia And Clostridium Perfringens, Julian E. Nixon

All Dissertations

Black seed oil concentrations of 0%, 0.1%, 1% and 5% were added to milk inoculated with kefir grains and incubated at 25°C for 22 h. The pH and microbial count indicated 1% black seed oil caused low inhibition (P > 0.05) of fermentation, but 5% black seed oil caused significant inhibition of the kefir microorganisms (P < 0.05).

Cobb 500 male chicks (n = 256) were distributed in a randomized block design and received one of four treatments: CTRL1 (Non-medicated, no kefir, no Clostridium perfringens), CTRL2 (Non-medicated, no kefir, C. perfringens inoculated), CTRL3 (BMD medicated, no kefir, C. perfringens inoculated), KTRT (Non-medicated, …

Evaluation Of Bone And Muscle Quality In Laying Hens Using Quantitative, Radiographic, Computed Tomographic, Biomechanical, And Tissue Level Measures, Cerano Harrison

All Dissertations

Bone quality is an important measure of welfare in laying hens for researchers, veterinarians, and commercial producers who bear the responsibility of providing them with care. Breeding practices that have resulted in high egg productivity of laying hen strains have resulted in an increased susceptibility to developing osteoporosis. Osteoporosis, a decrease in mineralized bone, is accompanied by increased bone fragility that can lead to potentially painful bone fractures that can inhibit some aspects of the birds natural living, respiration and flight being two examples. Current methods of examining laying hen bone quality involve the implementation of diagnostic imaging and biomechanical …

Fatty Acids And Parasitism: Towards A Better Understanding Of Lipid Metabolism In Trypanosoma Brucei, Joshua Saliutama

All Dissertations

Trypanosoma brucei is an extracellular eukaryotic parasite that causes sleeping sickness in humans and cattle. As an extracellular parasite, T. brucei relies on the host’s nutrients to satisfy its growth requirements. The parasite is unusual because it does not uptake most of the host’s lipid species. Instead, T. brucei prefers to perform de novo synthesis of most lipid species. One of the lipid species that T. brucei can both uptake and synthesize is fatty acids. In my thesis work, I investigated the dynamics of fatty acid uptake, metabolism, and utilization of T. brucei. My work starts by determining the …

The Functional Implications Of Anuran Metamorphosis For Survival, Locomotor Performance, And Limb Bone Mechanical Properties, Chase Kinsey

All Dissertations

Many organisms must contend with navigating their environments from birth. An organism could be classified as – and is often studied – in the context of locomotion through a single habitat type. However, many organisms must contend with a wide variety of environmental obstacles and substrates. What’s more, a large group of animals, Lissamphibia, do so while undergoing drastic transformation of their morphology and locomotor appendages. This transformation, term metamorphosis, typically coincides with a movement from water as a tadpole, to land as a frog or salamander. Many studies have associated this transitionary period with decreased locomotor performance and worse …

A Systems Genetics Approach To Drosophila Melanogaster Models Of Rare And Common Neurodevelopmental Disorders, Rebecca Macpherson

All Dissertations

Fetal Alcohol Spectrum Disorders are a group of disorders resulting from prenatal alcohol exposure, presenting with neurodevelopmental and facial abnormalities of varying severity. SSRIDDs and CdLS are rare disorders of chromatin modification, resulting in patients with a wide range of craniofacial, digit and/or neurodevelopmental abnormalities. All of these disorders have a wide range of clinical phenotypes and disease severity, yet the role of potential genetic modifiers and gene-gene or gene-environment interactions in disease pathogenesis is largely unknown and cannot be studied in humans. Insufficient numbers of patients with a single rare disorder prevent investigation of genetic factors beyond the focal …

Investigating The Potential Of A Cell-Based Gene Editing Therapy For Inherited Metabolic Liver Disease, Ilayda Ates

All Dissertations

Inherited metabolic diseases (IMDs) affecting the liver are relatively rare but collectively have a prevalence of 1 in 800 live births. These diseases result from autosomal recessive single-gene mutations, leading to organ dysfunction and potentially fatal consequences if left untreated. One potential therapeutic strategy for IMDs of the liver involves using CRISPR-Cas9-induced loss of function mutations. However, translating this approach into the clinic is limited by the need for safe and effective CRISPR delivery methods. Adeno-associated viral vectors (AAVs), commonly used for CRISPR delivery, are associated with significant safety and efficacy concerns, including risks for immunogenicity, off-target mutagenesis, and genotoxicity …

Filth Flies As A Vector For Some Pathogenic Bacteria Transfer, Ahmet Buyukyavuz

All Dissertations

Two separate sets of experiments were conducted to determine the transfer of bacteria by flies. An Escherichia coli ampicillin-resistant strain with a fluorescent gene was used during the experiments. The first set of experiments were divided into two trials to measure the transfer of E. coli by fruit flies to apple slices and bologna during short term exposure. Short time exposure (1, 5 and 15 min) of flies to inoculated apple slices were tested in the first trial to determine the transfer of E. coli to flies. No difference (P>0.05) in the number of bacteria transferred to flies were …

Developing A Cultural Management Approach To Bermudagrass Mite (Acari: Eriophyidae) Infestation, Matthew Brown

All Dissertations

Bermudagrass mite (Aceria cynodoniensis Sayed) (Acari: Eriophyidae) infestation stunts bermudagrass growth, leading to thinned turf and lower aesthetic and recreational value. Cultural management practices may impact bermudagrass mite infestation and turfgrass recovery from mite damage. Scalping or mowing shorter may physically remove mites, while drought stress may increase grass susceptibility to mites. Fertilizer application may promote mite infestation by improving plant nutrition. I conducted greenhouse, nursery, and field experiments to evaluate the impact of nitrogen fertility, irrigation rate, mowing height, and scalping on turf health and bermudagrass mite infestation in terms of the densities of witch’s brooms (i.e., stunted …

New Dna Repair And Demethylation Functions In Uracil Dna Glycosylase Superfamily, Chenyan Chang

All Dissertations

Uracil-DNA glycosylase (UDG) superfamily, which consists of several groups of enzymes that recognize the damaged DNA bases and initiate the base excision repair (BER) pathway, is most important in dealing with DNA deamination and other base modifications. Thymine DNA glycosylase (TDG), which belongs to family 2 in the UDG superfamily, is able to specifically recognize and cleave the 5-methylcytosine (mC) oxidative derivatives including 5-formylcytosine (fC), 5-carboxylcytosine (caC), 5-hydromethyluracil (hmU) caused by active demethylation or DNA damage. My dissertation work is mainly focused on the fC and caC glycosylase activity within UDG superfamily. Chapter 1 is a general introduction to the …

Assesment Of Structure, Function, And Microevolutionary Dynamics Of Extrachromosomal Circular Dna In Chinese Hamster Ovary Cells, Dylan Chitwood

All Dissertations

Chinese hamster ovary (CHO) cell lines are among the most popular expression hosts used in biopharmaceutical manufacturing due to relative ease of culture, capacity to perform human-like post-translational modifications, and non-susceptibility to viruses. However, the intrinsic plasticity of the CHO genome can lead to undesired genetic rearrangements, phenotypic shifts, reduced product quality, and early culture termination that prevents continuous biomanufacturing. A characteristic of plastic and unstable genomes that is poorly understood in CHO cells is extrachromosomal circular DNA (eccDNA). EccDNAs are focal amplifications of the genome that reside in the extranuclear space. These plasmid-like entities are structurally complex and are …

Revision, Description, And Diagnosis Of Adult And Larval Pycnopsyche Spp. (Trichoptera: Limnephilidae) Using Morphological And Molecular Methods, Matthew Green

All Dissertations

The genus Pycnopsyche Banks, 1905 (Trichoptera: Limnephilidae) is the 2nd most species-rich genus of Nearctic Limnephilidae. Larvae and adults are ecologically diverse and widespread throughout eastern North America. Larvae construct cases from mineral or plant material and are frequently used by biomonitoring professionals at the species level to monitor trends in water quality. However, only two species of Pycnopsyche are currently separable as larvae, with diagnosis limited by the number of unknown larvae associated with known adults. Using morphological and molecular data, the phylogenetic relationships among Pycnopsyche species and species groups were inferred with Bayesian and Maximum Likelihood analyses to …

Methyltransferase, Glucose Adaptation, And Import Complex In Trypanosoma Brucei, Emily Knight

All Dissertations

Trypanosoma brucei is a kinetoplastid parasite responsible for human African trypanosomiasis (HAT) and nagana, a livestock wasting disease, which both endemic to sub-Saharan Africa. Unique to kinetoplastids are the specialized peroxisomes, named glycosomes, which compartmentalize the first several steps of glycolysis and gluconeogenesis, nucleotide sugar biosynthesis, and many other metabolic processes. Kinetoplastids are unique in that they have a single mitochondrion. In this work, I present the first study into SET domain proteins in any kinetoplastid parasites. We have characterized a predicted SET domain protein, TbSETD3, that localizes to the mitochondrion and a depletion of the protein results in growth …

Influence Of Cover Cropping And Nitrogen Fertilization On Soil Properties And Cotton Productivity, Christianah Oladoye

All Dissertations

Conservation practices with cover crops have proven to be effective in nutrient enrichment, increased yield, and environmental stability. Field studies were conducted from 2019 to 2022 to evaluate the short-term effect of No cover crop [NC], RYE, a mix of rye + vetch [R+V], and mix of five species (radish, rye, vetch, clover, and lupin) [5W] on short term soil physical, chemical properties, cotton growth, and lint yield. Cover crops were planted in November and terminated in May of each year. Soil dry and wet aggregate fractions (0-0.05 m) and soil compaction (0-0.4 m depth) were measured at termination. The …

An Integrative Approach To Modelling Human-Wildlife Coexistence Landscapes In The Northern Great Plains, Keifer Titus

All Dissertations

Restoring wildlife populations in a human dominated world requires a deep understanding of the ecological conditions required for species persistence as well as the human social factors that influence restoration outcomes. Until recently, the majority of prior research has focused on understanding the ecological conditions and human social processes that contribution to wildlife restoration success separately, and often assign a higher value to ecological factors. I studied the human dimensions surrounding ongoing wildlife restoration efforts in the Northern Great Plains (NGP) of Montana to better understand how human social factors can affect and inform restoration efforts for a variety of …

Drivers Of White-Tailed Deer (Odocoileus Virginianus) Behavior, Survival, And Population Growth In The Piedmont Of South Carolina, Michael Muthersbaugh

All Dissertations

Prey species adjust behaviors in response to various stimuli, responding to both top-down and bottom-up pressures. Large herbivores must attempt to avoid predation either through adjusting behaviors or seeking spatial or temporal refugia, which can scale up to influence individual fitness and ultimately population dynamics. Specifically, predation risk has a great potential to influence ungulate populations by impacting behaviors and survival. Our objective was to quantify ungulate behavioral and population response to a regionally important predator through a case study – white-tailed deer (Odocoileus virginianus) responses to coyotes (Canis latrans) on private lands in the Piedmont …

Top Down Effects And Resource Selection By Coyotes In South Carolina, Alex Jensen

All Dissertations

Top predators play important roles in functioning ecosystems, including regulating the populations of prey species and competing with other predators. However, in the face of global change, many top terrestrial predators have declined in both range and abundance, making room for some smaller predators to expand into new niches. Coyotes (Canis latrans) in North America are a prime example of this – they have rapidly expanded their range in the last 120 years, raising concerns about their impacts on both domestic and wild species. In eastern North America, research has centered around their effects on white-tailed deer ( …

Acetate Metabolism In The Fungal Pathogen Cryptococcus Neoformans, Oly Ahmed

All Dissertations

Cryptococcus neoformans is an environmental basidiomycetous fungus with a worldwide distribution and a wide range of habitats. Inhalation of the desiccated yeasts or spores of C. neoformans often leads to opportunistic pulmonary infections in immunocompromised individuals, and in severe cases causes lethal meningitis following hematogenous dissemination. During infection, depending on the tissue and disease state, the invading fungi experience a range of nutrient microenvironments within the host body. As a result, rapid metabolic adaptations geared towards efficient utilization of carbon sources alternative to glucose become one of the prime determinants of survival and growth for the pathogen. Incidentally, cryptococcal infection …

Diagnosis Of Urinary Tract Infections And Rapid Molecular Characterization Of Antibiotic Resistance, Mohammed Harris

All Dissertations

Urinary tract infections (UTIs) are one of the most common infectious clinical entities in both community and hospital settings. They have a broad range of clinical severity yet inflict large epidemiological burden of morbidity and mortality on patients and the healthcare system with billions of dollars in cost of treatment. Understanding what methods are optimal for diagnosing UTIs are critical to mitigate the marked impact and cost of these infections.

Chapter 1 and 2 in this work surveys the broad array of diagnostic modalities for UTIs and highlights their advantages and limitations in the context of the current standard of …

A Multi-Pronged Investigation To Identify Genes Affecting The Autoregulation Of Nodulation: Lasercapture Microdissection And The Barely Any Meristem Gene Family In Medicago Truncatula, Jacklyn Thomas

All Dissertations

The unique evolutionary adaptation of legumes for nitrogen-fixing symbiosis leading to nodulation is tightly regulated by the host plant. One pathway negatively regulates the number of nodules formed in response to the metabolic status of the shoot (carbon) and root (nitrogen); this long-distance systemic regulation is the autoregulation of nodulation (AON) pathway. AON is a root to shoot pathway that allows the plant to limit the number of nodules formed on roots. Central to the receptor complex in the shoots is a leucine-rich-repeat receptor-like kinase (LRR-RLK) called MtSUNN mutation of which results in plants with too many nodules. SUNN …

Epidemiological Approaches For Practical Solutions To Pertinent Peanut Problems, Hope Becton

All Dissertations

Peanut is an important food crop grown in the southeastern region of the United States. Diseases are the most yield-limiting component in peanut production with one of the most important being late leaf spot (LLS), caused by Nothopassalora personata (Np). The disease initially appears in the lower canopy as dark brown to black lesions and conidiophores bearing conidia are produced on the abaxial side of the lesion. Np is passively dispersed primarily by wind and rain events. Spore traps were used to detect and quantify conidia captured up to 70 m from an inoculum source and to further assess …

Glycolytic Inhibitors As Leads For Drug Discovery In The Pathogenic Free-Living Amoebae, Jillian Milanes

All Dissertations

The free-living amoeba, Naegleria fowleri, can cause a rare yet usually lethal infection of the brain called primary amebic meningoencephalitis. Because of poor diagnostics and limited treatment options, the mortality rate associated with the disease is >97%. Due to our finding that glucose is critical for trophozoite growth in culture, we have been interested in exploiting amoebae glucose metabolism to identify new potential drug targets. We have characterized the first enzyme of the glycolytic pathway, glucokinase (Glck), from N. fowleri and two other pathogenic free-living amoeba, Acanthamoeba castellanii and Balamuthia mandrillaris. We have assessed their biochemical properties and …