Physical Sciences and Mathematics Commons^™

Design And Synthesis Of Analogs Of Myo-Inositol, Serine, And Cysteine To Enable Chemical Biology Studies, Tanei J. Ricks

Doctoral Dissertations

Phosphorylated myo-inositol compounds including inositol phosphates (InsPs) as well as the phosphatidylinositol polyphosphate lipids (PIP_ns) are critical biomolecules that regulate many of the most important biological processes and pathways. They are aberrant in many disease states due to their regulatory function. The same is true of the phospholipid phosphatidylserine (PS) which can serve as a marker to begin apoptosis. However, the full scope of activities of these structures is not clear, particularly since techniques that enable global detection and analysis of the production of these compounds spatially and temporally are lacking. With all of these obstacles in …

Fungi Of Forests: Examining The Diversity Of Root-Associated Fungi And Their Responses To Acid Deposition, Donald Jay Nelsen

Graduate Theses and Dissertations

Global importance of forests is difficult to overestimate, given their role in oxygen production, ecological roles in nutrient cycling and supporting numerous living species, and economic value for industry and as recreational zones. Fitness of the forest-forming trees strongly depends on microbial communities associated with tree roots. In particular, fungi impact tree fitness: mycorrhizal species provide water and nutrients for the trees in exchange for C, endophytic fungi play key roles in host defense against pathogenic organisms, and saprotrophic fungi decompose dead organic matter and facilitate nutrient cycling. In addition, pathogenic fungal species strongly affect forest fitness. Despite their importance, …

The Ecology Of Antibiotic Resistance: Sources And Persistence Of Vancomycin-Resistant Enterococci And Antibiotic Resistant Genes In Aquatic Environments, Suzanne M. Young

USF Tampa Graduate Theses and Dissertations

The growing crisis of antibiotic resistance is a major threat to ecosystems and human health. Infections caused by known and emerging antibiotic resistant pathogens are on the rise globally, with approximately 700,000 deaths per year caused by antibiotic resistant bacteria (1). In the United States, infections from antibiotic resistant bacteria cause more than 2 million illnesses and 23,000 deaths (2). Antibiotic resistant bacteria and antibiotic resistance genes are released into aquatic ecosystems through hospital waste, residential sewer lines and animal agricultural waste streams. Animal agriculture accounts for approximately 70% of antibiotic use in the United States (3). In agricultural ecosystems, …

Packaging Of Genetic Material By Gene Transfer Agents (Gtas) Produced By Marine Roseobacter Species And Their Effect On Stimulating Bacterial Growth, Shahd Bader Aljandal

USF Tampa Graduate Theses and Dissertations

Horizontal gene transfer is one of the most important mechanisms for prokaryotic genome innovation and evolution. Gene Transfer Agents (GTAs) are phage-like particles that package small fragments of the genome of a GTA-producing bacterial cell. GTA chromosomal gene clusters usually contain 15-conserved open reading frames (ORFs) and are present in most of the sequenced marine alpha-proteobacteria genomes. Some marine strains have been shown to produce GTA particles that were biologically active in marine environment.

GTA particles range in size, morphology and the amount of host DNA they package. To date, the characteristics of GTAs are largely based on observations of …

Role Of Viruses Within Metaorganisms: Ciona Intestinalis As A Model System, Brittany A. Leigh

USF Tampa Graduate Theses and Dissertations

Marine animals live and thrive in a literal sea of microorganisms, yet are often able to maintain specific associations that are largely dictated by the environment, host immunity and microbial interactions. Animal-associated microbiomes include bacteria and viruses that vastly outnumber host cells, especially in the gut environment, and are considered to be integral parts of healthy, functioning animals that act as a metaorganism. However, the processes underlying the initial establishment of these microbial communities are not very well understood. This dissertation focuses on the establishment of a well-known developmental animal model, Ciona intestinalis (sea squirt), to study the establishment and …

Assessing A Fluorescence Spectroscopy Method For In-Situ Microbial Drinking Water Quality, Taylor Jeffery Sharpe

Dissertations and Theses

Waterborne disease is a significant contributor to the global burden of disease, in particular among high-risk populations in developing nations. State-of-the-art methods for the enumeration of microbial pathogens in drinking water sources have important limitations, including high initial cost, 24-48 hour delays in results, high staffing and facility requirements, and training requirements which all become especially problematic in the developing nation context.

A number of alternative approaches to microbial water quality testing have been proposed, with the goal of decreasing the required testing time, decreasing overall costs, leveraging appropriate technology approaches, or improving sensitivity or specificity of the water quality …

Growth And Survivability Of Microorganisms At Martian Temperatures And Pressures, Rebecca Lynne Mickol

Graduate Theses and Dissertations

The discovery of methane in the martian atmosphere via numerous ground- and space-based sources has prompted the study of methanogens as models for life on Mars. Methanogens are microorganisms within the domain Archaea, many of which utilize carbon dioxide (CO2) and hydrogen to produce methane. The non-photosynthetic nature of methanogens indicates that they could exist in sub-surface environments, protected from harmful UV and ionizing radiation on the surface of Mars. These organisms also do not require organics, which are sparse on the planet.

Additionally, the wide variety of environments we find life in on Earth, as well as evidence for …

Microbial Community Richness Distinguishes Shark Species Microbiomes In South Florida, Rachael Cassandra Karns

HCNSO Student Theses and Dissertations

The microbiome (microbial community) of individuals is crucial when characterizing and understanding processes that are required for organism function and survival. Microbial organisms, which make up an individual’s microbiome, can be linked to disease or function of the host organism. In humans, individuals differ substantially in their microbiome compositions in various areas of the body. The cause of much of the composition diversity is yet unexplained, however, it is speculated that habitat, diet, and early exposure to microbes could be altering the microbiomes of individuals (Human Microbiome Project Consortium, 2012b, 2012a). To date, only one study has reported on microbiome …

Bacterial Communities Associated With Healthy And Diseased Acropora Cervicornis (Staghorn Coral) Using High-Throughput Sequencing, Charles Walton

HCNSO Student Theses and Dissertations

Coral diseases were first noted in the 1960s and 1970s and have had major impacts globally on coral reef community structures. In the Caribbean, a major outbreak of white band disease has been considered responsible for the drastic decline of Caribbean Acroporids since the 1970s. In addition to white band disease, another more recently described condition known as rapid tissue loss (RTL) has had major impacts on Acropora cervicornis populations, specifically offshore Broward County Southeast Florida. While these diseases have contributed to the population decline, determining their etiologies has been elusive.

Coral diseases have been characterized by shifts in their …

An Integrated Bioinformatic/Experimental Approach For Discovering Novel Type Ii Polyketides Encoded In Actinobacterial Genomes, Wubin Gao

Chemistry and Chemical Biology ETDs

Discovery of new natural products (NPs) is critical both for diseases treatment and crops protection. Numerous NP biosynthetic gene clusters (BGCs) in sequenced microbial genomes allow identification of new NPs through genome mining. Developing an integrated bioinformatic/experimental approach for discovering novel type II polyketides (PK-IIs) facilitates investigation of this family of NPs in an efficient, systematic way. Here, we developed an approach to analyze ketosynthase α/β (KSα/β) gene sequences to predict PK-II core structures, allowing us to target novel PK-II BGCs either from isolated genomic DNA or genomes from the NCBI databank, and to isolate novel PK-IIs produced by these …

Towards Autonomous Microcystin Detection: Investigating Methods For Automation, Maureen Anne Schneider

Theses and Dissertations

Due to increased anthropogenic activity, severe eutrophication is occurring in bodies of water around the world. Effects include decreased water quality, decreased value of surrounding land and recreational use (estimated loss in revenue of 0.67 and 3.96 U.S. billion dollars per year), and increased occurrence of toxin producing Harmful Algal Blooms (HABs). Microcystins are cyclic peptides made up of 7 amino acids and 800-1100 Daltons in size. They are one of the most predominantly produced of these toxins, and therefore was the focus of this study. Numerous structural variants of microcystin (referred to as congeners) exist, but microcystin-LR is one …

Range-Wide Prevalence And Impacts Of Pseudocercosporella Inconspicua On Lilium Grayi And An Assessment Of L. Superbum And L. Michauxii As Reservoirs, Cindy L. Barrett

Electronic Theses and Dissertations

Lilium grayi (Gray’s Lily), a southern Appalachian endemic species, is threatened by a Lilium-specific fungal pathogen, Pseudocercosporella inconspicua. The disease is characterized by tan lesions that can cause early senescence, while also lowering seed production and viability. This project tested for P. inconspicua conidia and accessed health at nine locations. The disease was present and ubiquitous across the range of L. grayi. Through identification of P. inconspicua conidia in the field, L. superbum (Turk’s Cap Lily) was identified as an additional host, while L. michauxii (Michaux’s Lily) was disease-free. However, infection was inducible in both species. With …

Evaluation Of A Fluorescence Method For Quantifying Bioaerosol Concentrations On Air Quality Filter Samples, Rachel Kolberg

UNLV Theses, Dissertations, Professional Papers, and Capstones

Airborne particulate matter (PM) in outdoor environments contains many components that cause adverse human health effects. The size of the particulates determine in what manner the particles would bypass the body’s defense mechanisms to enter the respiratory system and is directly related to their health impacts. Currently the United States Environmental Protection Agency is enforcing the National Ambient Air Quality Standards (NAAQS) to regulate the annual and 24-hour average concentrations of PM2.5 and PM10 in the air. PM2.5 are fine particles with aerodynamic diameter <2.5μm, small enough to reach the deepest parts of the bronchi and lungs. PM10 include PM2.5 and larger particles with aerodynamic diameter of 2.5-10μm. Both PM2.5 and PM10 contain multiple components from multiple sources. Bioaerosols are an important component of PM, but there is limited knowledge about how bioaerosols contribute to PM2.5 and PM10 concentrations. There is also a lack of research about the incidence and prevalence of disease caused by bioaerosols and about the limits of exposure to bioaerosol particulates. The main barrier to assess bioaerosol concentrations and health-related effects is the absence of quick and inexpensive methodology for quantifying bioaerosols. This study explored the feasibility of using fluorescence microscopy to quickly quantify bioaerosols in PM2.5 and PM10 collected on polycarbonate filters. Bioaerosols were stained with a DNA marker directly on a filter, followed by fixation, microscopic imaging, and automatic counting. The method was first validated using reference samples prepared by depositing different known concentrations of E. coli onto blank polycarbonate filters. The results indicated a linear response over two orders of magnitude (R2 = 0.9) and an accuracy within ±25%. E. coli were also deposited onto selected ambient PM10 and PM2.5 filter samples to determine if pre-loaded particles would interfere with bioaerosol imaging and counting. It was found that despite an increase in uncertainty (variability), the calibration slope remained within ±10% of unity for both PM2.5 and PM10 samples. Bioaerosol concentrations in ambient samples, as quantified by this method, were on average 14% higher for PM10 than for PM2.5 acquired concurrently in a desert environment of Las Vegas, Nevada. The application of this method to other types of compliance filters, such as Teflon filters and tapes of a Beta Attenuation Monitor (BAM) were also explored in this study. By means of a high-yield approach this method is expected to facilitate bioaerosol research, support exposure and health assessments, and help refine NAAQS for PM2.5 and PM10.

Mutagenic And Spectroscopic Investigation Of Ph Dependent Cooa Dna Binding, Brian R. Weaver

Chemistry Honors Papers

The carbon monoxide (CO) sensing heme protein, CooA, is a transcription factor which exists in several bacteria that utilize CO as an energy source. CooA positively regulates the expression of coo genes in the presence of CO such that the corresponding proteins may metabolize CO. The present studies have yielded the unexpected result that Fe(III) CooA binds DNA tightly at pH < 7, deviating from all previously reported work which indicate that CooA DNA binding is initiated only when the exogenous CO effector reacts with the Fe(II) CooA heme. This observation suggests that the disruption of one or more salt bridges upon effector binding may be a critical feature of the normal CooA activation mechanism. To test this possibility, several protein variants that eliminated a selected salt bridge for the CooA homolog from Rhodospirillum rubrum were prepared via site-directed mutagenesis. Samples of these variant proteins, which were overexpressed in Escherichia coli, were then characterized by spectroscopic methods and functional assays to investigate the impact these mutations had on CooA heme coordination …

Investigating The Role Of Epitranscriptomics In Viral Immunity, Kaycie S. Lawson

Legacy Theses & Dissertations (2009 - 2024)

The characterization of host-virus relationships is essential for understanding the process of viral replication and driving the development of effective viral targeting strategies. In this work, I tested the hypothesis that ribonucleic acid (RNA) post-transcriptional modifications (PTMs) may play a significant role in defining host-virus interactions. The model system consisted of a yeast strain capable of harboring the endogenous L-A virus, which allowed me to evaluate the possible involvement of PTMs in the process of cellular immunity to virus-borne toxicity. A mass spectrometry-based platform was utilized to compare the global PTM profile of wild-type yeast with those of the same …

Antimicrobial Activity Of Fractionated Borohydride-Capped And Electrochemical Colloidal Silver, Marjorie M. Markopoulos

Browse all Theses and Dissertations

Silver nanoparticles (AgNPs) and ionic silver (Ag+) are known to be broad-spectrum antimicrobial agents. Recent studies show these agents may be an alternative to the most widely used drinking water disinfectant, chlorine. Chlorine is a toxic industrial chemical with a lethal concentration of 430 ppm after 30 minutes. Additionally, chlorine can react with naturally occurring materials to produce a number of disinfection byproducts such as chloroform and trihalomethanes. Some of these byproducts pose cancer risks in addition to other negative impacts to human health. These would be eliminated with the use of Ag+ or AgNPs. The main goal of this …

Analysis Of Microbial Diversity In Disturbed Soil, Tyler G. Sanda

Williams Honors College, Honors Research Projects

This paper uses the composition and abundance of microbial species to analyze soil recovery in disturbed land. Surface mining disturbs ecological communities throughout the world. As organizations seek to reclaim these disturbed lands, a proper analysis of recovery is needed. In previous studies, recovery of disturbed land was limited to surface examinations, which do not characterize the possible unseen devastating effects of the subsoil. Soil microorganisms are extremely sensitive to environmental changes such as strip mining. It is proposed that these microorganisms may serve as better indicators of recovery post disturbance. Our analysis indicates microbial recovery, however it may not …