Life Sciences Commons^™

A Study Of Inactive Enzyme-Homologues: The Biochemical And Biological Function Of Ecm14 In Saccharomyces Cerevisiae, Robert Christian Mcdonald

Master's Theses

Like most major enzyme families, the M14 family of metallocarboxypeptidases (MCPs) contains several pseudoenzymes predicted to lack enzyme activity and with unknown molecular function. The genome of the yeast Saccharomyces cerevisiae encodes only one member of the M14 MCP family, a pseudoenzyme named Ecm14 proposed to function in the extracellular matrix. Ecm14 is found throughout ascomycete fungi, with a group of related pseudoenzymes found in basidiomycetes. Although the prodomain of Ecm14 can be cleaved in vivo and in vitro by endopeptidases, suggesting an activation mechanism, no activity has been detected using standard carboxypeptidase substrates.

In order to examine the function …

Paleoenvironmental Implications Of Small-Animal Fossils From The Black Mountain Turtle Layer And Associated Layers, Eocene Of Wyoming, Jeremy Mclarty

Master's Theses

The Bridger Formation is an Early Middle Eocene deposit in southwestern Wyoming that preserves a rich record of life from North America. Some horizons within the Bridger Formation contain abundant fossil turtle shells, but turtle skulls are rarely found. Previous research focused on one of these fossil-rich horizons, the Black Mountain turtle layer, to develop a model for the abundance and taphonomic condition of the fossil turtles. The proposed model begins with a limestone layer deposited in a lake. Then, an influx of fine-grained volcanic ash (forming the Black Mountain turtle layer) was rapidly deposited into this lake likely causing …

The Use Of Multiple Sensory Modalities By The Antillean Manatee (Trichechus Manatus Manatus) To Locate Food In Their Natural Environments, Amanda Marie Moore

Master's Theses

Manatees are herbivorous aquatic mammals found in the coastal and inland waters of the Atlantic Ocean. All three manatee species are currently listed as vulnerable on the IUCN red list and there still remains much unknown about their ecology. It is currently unknown what sensory modalities manatees use to locate their food in the wild. A literature review of the Paenungulata clade (sirenians, proboscideans, and hyracoideans) was conducted in order to compare and contrast what is known about the sensory modalities of the clade, to better understand the sensory modalities of manatees, particularly the ones they use to locate their …

Effects Of Pharmaceutical Contamination On Sedment Microbial Communities In Streams, Benjamin Joseph Lorentz

Master's Theses

The objective of this study was to examine the interaction of pharmaceuticals and personal care products (PPCP) and microbial communities in freshwater ecosystems. This study included two components. The first component consisted of an artificial stream study in which sediment was exposed to environmentally relevant concentrations of three different pharmaceuticals (diphenhydramine, ciprofloxacin, and fluoxetine) individually and as a mixture. Pharmaceutical exposure had no effect on denitrification rates or respiration rates in the sediments, and sediment microbial community composition showed only slight differences between streams dosed with pharmaceuticals and control streams. The second component consisted of a field study in which …

Zika Virus Inactivates Polyamine Catabolism Via Alternative Splicing To Enhance Infection, Marion Lea Graham

Master's Theses

During viral infection, the virus and host must compete for resources inside the cell. One of these resources is polyamines. Polyamines are small, positively charged molecules that are found in all eukaryotic cells. They play a key role in several cellular functions including growth and proliferation, transcription and translation, and membrane stability. Viruses also rely polyamines for productive replication, utilizing them during DNA/RNa polymerization, nucleic acid packaging, and protein synthesis. in response to a virus infecting a host cell, the host cell will begin to regulate polyamine levels as a way to combat the infection. Polyamine levels are regulated by …

The Characterization Of Inflammatory Extracellular Vesicles, Barak Balva

Master's Theses

One of the driving factors behind innate immunity is the early response of inflammation. While beneficial in controlling infections, when uncontrolled it can lead to a plethora of disorders. Thus, it is essential to understand the driving factors behind inflammation. a cell's ability to recycle, discard, or transfer proteins is integral for survival and intercellular communication. It has been appreciated that inflammatory components, such as caspase-1, play a huge role in driving protein secretion. Thus, inflammation also plays a role in the distribution of proteins released from cells. These proteins are released via non-conventional secretory pathways, and our lab is …

Optimizing Gene Expression Prediction And Omics Integration In Populations Of African Ancestry, Paul Chukwuebuka Okoro

Master's Theses

Popular transcriptome imputation methods such as PrediXcan and FUSIon use parametric linear assumptions, and thus are unable to flexibly model the complex genetic architecture of the transcriptome. Although non-linear modeling has been shown to improve imputation performance, replicability and potential cross-population differences have not been adequately studied. Therefore, to optimize imputation performance across global populations, we used the non-linear machine learning (ML) models random forest (RF), support vector regression (SVR), and K nearest neighbor (KNN) to build transcriptome imputation models, and evaluated their performance in comparison to elastic net (EN). We trained gene expression prediction models using genotype and blood …

Characterization Of Caspase 1 Substrate Specificity Utilizing Luminescent Reporter Constructs, Nicholas Rohlfes

Master's Theses

Inflammation is the bodies first response to defend itself against foreign pathogens and damage. Cellular sensors are constantly monitoring the body and checking for homeostatic disruption. Microbial pathogens and tissue damage are sensed by pattern recognition receptors (PRRs), which sense pathogen associated molecular patterns and damage associated molecular patterns, termed PAMPs and DAMPs respectively. Within the family of PRRs are sensors that can induce the formation of the multi-protein complex termed the inflammasome following activation. the inflammasome complex is a molecular platform for which caspase 1, a cysteine protease, is incorporated and is responsible for the maturation of pro-inflammatory cytokines …

Determining Interactions Between Bacteriophage And Urinary Microbiome Lysogens, Michael Bochert

Master's Theses

Bacteriophages (phages) are viruses that infect bacteria. They are the most abundant life forms on earth. It is estimated that there are approximately 10³⁰ phages on the planet (Chibani-Chennoufi et al. 2004). They outnumber their bacterial hosts approximately 10 to 1. Bacteria inhabit most niches on the planet including the human body, where they play critical roles in health and disease. Since phages shape bacterial populations the same way that viruses, such as smallpox and measles, shaped human populations, it is important to understand how they interact with their bacterial hosts. The majority of the phages that we know of …

Reducing Reperfusion Injury In An Adult Rat Stroke Model With St-115 Treatment, Morgan Rae Lenz

Master's Theses

The restoration of blood flow to ischemic cerebral tissue can result in reperfusion injury, and blocking reperfusion injury can significantly aid in recovery of ischemic tissue. Bradykinin has been shown to exhibit protective effects, but does not reach protective levels during reperfusion due to inactivation by aminopeptidase P2 (APP2). Therefore, inhibiting APP2 during reperfusion is a potential therapeutic strategy to aid in the reduction of reperfusion injury, leading to the development of ST-115, an APP2 inhibitor. It was hypothesized that administration of ST-115 during ischemic stroke, and just prior to reperfusion, will result in reduced neurological injury and increased functional …

Dna Methylation Patterns Of Repetitive Elements On Hc21, Navy Neang

Master's Theses

Cancer is one of the most prominent diseases resulting in death, thus the need for early detection remains essential to its treatments. It is usually associated with DNA methylation changes during tumorigenesis. While many studies focus on euchromatin, some studies have looked at the methylation changes in heterochromatin, since the methylation changes of repetitive elements is common and they contribute to karyotypic instability leading to enhanced chances for more mutations in tumor progression. Using bisulfite PCR and HC21 as a model, this study examines the DNA methylation changes of three repetitive elements in prostate cancer, NBL2, satellite I subfamilies, and …

Behavioral Ecology And Physiological Health Of Managed Populations Of Juvenile Blanding's Turtles (Emydoidea Blandingii) In Urban Wetlands, Armand Andre' Cann

Master's Theses

Substantial threats to reptile species biodiversity have become apparent in the last few decades. This is partly caused by significant losses in grasslands and their associate prairie-wetland ecosystems. One Midwestern prairie-wetland species, Blanding's Turtles (Emydoidea blandingii), are at risk of extirpation due to habitat loss, fragmentation, and increased predator populations. Consequently, significant head-starting efforts, a form of reintroduction conservation using captive-reared and then released turtles, have been conducted to recover populations of E. blandingii in northeastern Illinois. However, the success of these programs both locally and range-wide have not been fully quantified. Unfortunately, many approaches to guaging success involve long-term …

Investigating The Relationship Between Hormone Receptors Dax-1 And Estrogen Receptor Within Prostate Cancer Cell Lines, Meghana G. Vijayraghavan

Master's Theses

Prostate cancer (PCa) is estimated to be the second leading cause of cancer-related deaths among men in the United States in 2019. While most prostate tumors rely on androgens for growth signaling, there are subsets of tumors that become androgen-resistant, therefore resisting conventional androgen-depravation therapy. Consequently, research has focused on targeting different hormone receptors for novel therapeutics. One such receptor is Dosage-sensitive sex reversal, adrenal hypoplasia critical region, on chromosome X, gene 1 (DAX-1). DAX-1 is known to interact with other hormone receptors, such as androgen receptor (AR) and estrogen receptors (ERs) to suppress the proliferative effects …

Distribution, Abundance, And Trophic Ecology Of Anguilliform Leptocephali In The Northern Gulf Of Mexico, Lillian Collins

Master's Theses

All species of anguilliform eels have pelagic leptocephalus larval stages, which provides a means of monitoring the population dynamics of these otherwise cryptic and hard to study species. The goals of this study were to: 1) describe the distribution and abundance of anguilliform eel leptocephali across the northern Gulf of Mexico, and 2) examine the trophic ecology of leptocephali using stable isotope values of carbon and nitrogen (δ13C and δ15N). A 25-year (1990-2014) ichthyoplankton dataset provided by the National Oceanic and Atmospheric Administration (NOAA) Southeast Area Monitoring and Assessment Program (SEAMAP) was used to examine interannual variations in leptocephalus distribution, …

The Thiol Specific Antioxidant (Tsa1) Gene Is Required For Survival In Macrophages And Oxidative Stress Resistance In Histoplasma Capsulatum, Lauren Kennedy

Master's Theses

Histoplasma capsulatum(Hc) is a pathogenic fungus that causes one of the most common invasive fungal respiratory diseases, Histoplasmosis. Histoplasmaundergoes a dimorphic shift from mold to yeast which is crucial to pathogenesis of the organism.

The thiol specific antioxidant gene, Tsa1,is strongly upregulated in the yeast (pathogenic) morphotype. This data led to the hypothesis that this gene plays a role in protecting Hcfrom host mediated oxidative attack. To characterize Tsa1 function, a knockdown strain (tsa1-RNAi) was created by RNAi gene silencing. Expression of Tsa1in the tsa1-RNAistrain was reduced to 10% that …

Development And Employment Of Environmental Dna Methods For The Detection Of Bull Sharks (Carcharhinus Leucas) In A Freshwater And Estuarine Interface In The Mobile-Tensaw Delta And Mobile Bay, Alabama, Katherine Schweiss

Master's Theses

Species conservation and management is influenced by the quality of monitoring methods employed, especially when targeting elusive, but ecologically significant species, like elasmobranchs. Bull Sharks (Carcharhinus leucas) are highly mobile predators that rely on estuaries and freshwater rivers for maturation, resources, and refuge; their ability to withstand changing environmental conditions may mean they are linking ecosystems through their habitat usage and movements. Rather than setting nets or attaching acoustic monitoring devices, which can be expensive, time-consuming, and invasive, the analysis of environmental DNA (eDNA) for tracing species presence was used to target C. leucasDNA. The present research …

Early Recruitment Of Crassostrea Virginica To Restored And Natural Oyster Reefs In The Western Mississippi Sound: Larval Supply And Post-Settlement Success, Leah Morgan

Master's Theses

The eastern oyster (C. virginica) is a foundation species that improves water quality, protects shorelines, provides refuge for other organisms, and contributes to commercial fisheries. Successful early recruitment of eastern oyster is vital for resupplying adult populations in the face of habitat loss. Coastal oyster populations are challenged by freshwater input, hypoxia, predation and overfishing. Consequently, substantial efforts have been dedicated toward oyster restoration within the northern Gulf of Mexico. The overall objective of this study was to consider the role and importance of early recruitment to oyster restoration in western Mississippi Sound. During the summer 2018 recruitment period, we …

Effects Of Water Table Depth And Edaphic Characteristics On Plant Diversity In A Southern Mississippi Pitcher Plant Bog, Patrick Kirby

Master's Theses

This study examined the effects that water table depth and soil characteristics have on plant species richness and species composition within pitcher plant bogs across seasons. Eight piezometers were installed at random distances to monitor long-term water table depth and pressure fluctuations along a ~710-meter line transect traversing upland and bog habitats. Vegetation sampling quadrats (n=128) were set up near each piezometer. Cover data and water table depths were collected in spring and late summer. Soil samples collected from each treatment group were used to obtain soil texture and nutrient data. The summer collection period yielded a total gdiversity of …

The Effect Of Historic Shipwrecks On Sediment Microbiomes In The Northern Gulf Of Mexico, Melissa Brock

Master's Theses

Microorganisms are ubiquitously distributed across all aquatic habitats, but it is the environmental conditions of a habitat that determine which microorganisms can thrive in terms of abundance or metabolic activity. Habitats that experience consistent physical and chemical environmental conditions repeatedly favor specific taxonomic groups which may result in a microbial assemblage that is commonly associated with that habitat (i.e., a core microbiome). Core microbiomes have been identified for a variety of natural marine habitats including methane seeps, wood falls, octocoral, and deep-sea sediments. However, it was unknown if the presence of man-made structures on the seafloor, including historic shipwrecks, also …

The Water Table, Soil Moisture And Evapotranspiration Conditions Following The Removal Of Conifers From Two Encroached Meadows, Tyler J. Davis

Master's Theses

Montane meadows provide essential habitat for a variety of unique species and important ecosystem services in the western United States. Although important, meadows have experienced increased rates of conifer encroachment due to climate change, fire suppression and grazing. To combat meadow degradation from conifer encroachment, land managers have employed various restoration strategies one of which is conifer removal. Multiple studies have investigated the relationship between meadow hydrology and vegetation; however, few have assessed the effect of conifer removal on meadow groundwater. The goal of this study is to determine if the removal of conifers from an encroached meadow has an …

Evaluation Of Pheromone Mating Disruption For California Red Scale Control In Commercial California Citrus, Joel Timothy Leonard

Master's Theses

California red scale (CRS), Aonidella aurantii, is an increasingly injurious insect pest for the California citrus industry due to insecticide resistance, changing weather patterns, and shifting trade regulations. The presence of the insect on fruit, damages the rind of the fruit and high populations can cause dieback of branches as well as lower yields. Pheromone mating disruption of CRS has the potential to alleviate population control concerns and reduce insecticide use. The efficacy of the pheromone mating disruption technique for pest management of CRS was determined using the products CheckMate® CRS and Semios CRS Plus. CheckMate® CRS was evaluated …

The Democratization And Development Of Cell-Free Protein Synthesis, Max Z. Levine

Master's Theses

Cell-free protein synthesis (CFPS) using crude lysates has developed into a robust platform technology over the last 60 years to express numerous types of recombinant proteins. The open-nature, elimination of reliance on cell viability, and focus of all energy towards production of the protein of interest represent substantial advantages of CFPS over in vivo protein expression methods. CFPS has provided new opportunities across a series of research fields that include metabolic engineering, therapeutic and vaccine development, education, biosensors, and many more. In recent years, optimizations of CFPS have even allowed the platform to reach the industrial level of protein production. …

Effects Of Intertidal Position On Metabolism And Behavior In The Acorn Barnacle, Balanus Glandula, Kali Horn

Master's Theses

The intertidal zone is characterized by persistent, tidally-driven fluctuations in both abiotic (e.g., temperature, [O₂], salinity) and biotic (e.g., food availability, predation) conditions, which makes this a very physiologically challenging habitat for resident organisms. The magnitude and degree of variability of these environmental stressors differs between intertidal zones, with the most extreme physiological stress often being experienced by organisms in the high intertidal. Given that many of the fluctuating conditions in this environment are primary drivers of metabolic rate (e.g., temperature, [O₂], food availability), we hypothesized that sessile conspecifics residing in different tidal zones would exhibit …

Diet Quality And Micronutrient Intake In Long-Term Weight Loss Maintainers, Rebecca W. Pascual

Master's Theses

Objective: This study’s purpose was to examine dietary quality, macronutrient intake, and micronutrient adequacy among long term weight loss maintainers (WLM) in a commercial weight management program.

Methods: Participants were 1,207 WLM in WW (formerly Weight Watchers) who had maintained a 9.1 kg or greater weight loss (29.7 kg on average) for 3.4 years, and had an average BMI of 28.3 kg/m². A control group of weight stable adults with obesity (Controls; N=102) had a BMI of 41.1 kg/m² and 2.3 kg or less weight change over the previous five years.

Results: WLM vs. …

The Effects Of Cluster Thinning On Vine Performance, Fruit, And Wine Composition Of Pinot Noir (Clone 115) In The Edna Valley Of California, Paul F W Mawdsley

Master's Theses

A three-year study was conducted at a commercial vineyard site in California’s Edna Valley AVA to evaluate the physiological and agronomical effects of the timing of cluster thinning on Pinot noir (clone 115) grapevines. Vines were thinned to one cluster per shoot at three selected time-points during the growing season (bloom, bloom + 4 weeks, bloom + 8 weeks), and fruit from each treatment was harvested and made into wine. Across all growing seasons, yield decreased 43% in thinned vines relative to un-thinned control vines. No effect of cluster thinning or interaction with growing season was found in vine shoot …

Evaluation Of Chilling Efficiency, Meat Tenderness, And Microbial Analysis Of Broiler Carcasses Using Sub-Zero Saline Solutions, Samira Viliani

Master's Theses

The poultry industry is seeking an advanced chilling system that can improve chilling efficiency, microbial safety, and water consumption without compromising meat quality. The objective of this study was to evaluate the effects of sub-zero saline chilling methods on chilling efficiency, breast fillet tenderness and microbial reduction of broiler carcasses. Following evisceration and rinsing, broiler carcasses were randomly assigned to one of three chilling solutions: 1) 0% salt or ice water control (0% NaCl/0.5^oC), 2) 3% salt (3% NaCl/-1.8^oC), and 3) 4% salt (4% NaCl/-2.41^oC) solutions. Broiler carcasses in sub-zero saline solutions reached the …

Heat Activation Of Bacillus Anthracis Persists Over A Seven Day Period, Nathan T. Ross

Master's Theses

Bacteria of the Bacillus genera are capable of forming dormant and resilient cells called spores in response to starvation. Spores can break dormancy in the presence of nutrients in a process called germination. Historically, spores are exposed to sublethal heat treatments to increase the extent and rate of germination. This process is known as heat activation (HA). Previous studies on Bacillus species indicate the effects of HA are reversible after 72 hours. After this time period, the spores must be reactivated. However, spores of Bacillus anthracis, a member of the Bacillus family, have not been tested to see how long …

Effects Of Sudangrass Cover Crop And Soil Solarization On Weed And Pathogen Management In Organic Strawberry Production, Timothy Jacobs

Master's Theses

Field and lab experiments were conducted to determine the efficacy of sudangrass (Sorghum X drumondii (Nees ex Steud.) Millsp. & Chase) cover crop management techniques and soil solarization on important agricultural weeds and pathogens in organic strawberry production in Central California. Lab experiments assessed the time needed to kill weed seeds at temperatures typically achieved during soil solarization (40°C, 45°C, 50°C, 55°C, and 60°C) in California. Seeds tested included little mallow, redstem filaree, bristly oxtongue, annual sowthistle, common purslane, nettleleaf goosefoot, and redroot pigweed. Efficacy of simulated …

The Evolutionary Diversity And Biological Function Of Phenazine Metabolite Biosynthesis In Burkholderia Spp, Samuel Hendry

Master's Theses

Burkholderia encompass a group of ubiquitous Gram-negative bacteria that include numerous saprophytes, as well as several species that cause infections in animals, immunocompromised patients, and plants. Some species of Burkholderia produce colored redox-active secondary metabolites called phenazines (Phz). In the model opportunistic pathogen Pseudomonas aeruginosa, phenazines strongly contribute to the competitiveness, formation of biofilms, and virulence in multiple models of infection. Similar depth of knowledge on the diversity, biosynthesis, and biological functions of phenazines in Burkholderiais missing. This project aimed to bridge this gap in knowledge by focusing on phenazine pathways of B. lata and closely related …

The Effects Of Aqueous Atorvastatin On Steroidogenesis Of Xenopus Laevis At Environmentally Relevant Concentrations, Jeremy Johnson

Master's Theses

Statin drugs are a class of drug that work to reduce endogenous production of cholesterol by competitively inhibiting 3-hydroxy-3-methyl-glutaryl-CoA reductase (Hmgcr) thus inhibiting production of mevalonic acid in the mevalonate pathway. Atorvastatin (Lipitor) is one of the most widely prescribed statin drugs and contamination of wastewater effluent is a growing environmental concern because of the potential to interfere with steroidogenesis in wildlife. Amphibians may be particularly susceptible to the effects of atorvastatin contamination because of their highly permeable integument. I used an amphibian model, Xenopus laevis to test the hypothesis that chronic exposure to low concentrations of atorvastatin …