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 …

Tumor Necrosis Factor Dynamically Regulates The Mrna Stabilome In Rheumatoid Arthritis Fibroblast-Like Synoviocytes, Konstantinos Loupasakis, David Kuo, Upneet K. Sokhi, Christopher Sohn, Bethany Syracuse, Eugenia G. Giannopoulou, Sung Ho Park, Hyelim Kang, Gunnar Rätsch, Lionel B. Ivashkiv, George D. Kalliolias

Publications and Research

During rheumatoid arthritis (RA), Tumor Necrosis Factor (TNF) activates fibroblast-like synoviocytes (FLS) inducing in a temporal order a constellation of genes, which perpetuate synovial inflammation. Although the molecular mechanisms regulating TNF-induced transcription are well characterized, little is known about the impact of mRNA stability on gene expression and the impact of TNF on decay rates of mRNA transcripts in FLS. To address these issues we performed RNA sequencing and genome-wide analysis of the mRNA stabilome in RA FLS. We found that TNF induces a biphasic gene expression program: initially, the inducible transcriptome consists primarily of unstable transcripts but progressively switches …

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 …

Dengue Virus Ns2b/Ns3 Protease Inhibitors Exploiting The Prime Side, Kuan-Hung Lin, Akbar Ali, Linah Rusere, Djade I. Soumana, Nese Kurt Yilmaz, Celia A. Schiffer

Celia A. Schiffer

The mosquito-transmitted dengue virus (DENV) infects millions of people in tropical and subtropical regions. Maturation of DENV particles requires proper cleavage of the viral polyprotein, including processing of 8 of the 13 substrate cleavage sites by dengue virus NS2B/NS3 protease. With no available direct-acting antiviral targeting DENV, NS2/NS3 protease is a promising target for inhibitor design. Current design efforts focus on the nonprime side of the DENV protease active site, resulting in highly hydrophilic and nonspecific scaffolds. However, the prime side also significantly modulates DENV protease binding affinity, as revealed by engineering the binding loop of aprotinin, a small protein …

Summary Report Of Enhanced Monitoring And Pollution Source Tracking Efforts In The Willard Beach Watershed, Maine, 2012-2016, M. Sims, K. Kaczor

Maine Sea Grant Publications

Willard Beach is a popular recreation area located in South Portland used primarily by families with young children. Routine monitoring at the beach revealed elevated bacteria levels, prompting the need for enhanced monitoring within the watershed to determine the nature and extent of potential bacteria inputs. Although the waste of domestic and wild animals can contribute to impaired water quality and pose a public health risk, efforts have focused primarily on identifying and removing human sources (e.g. malfunctioning septic systems, faulty sewer lines) of fecal pollution.

Maine Healthy Beaches Program 2016 Annual Report To U.S. Epa, K. Kaczor, M. Sims

Maine Sea Grant Publications

Maine Healthy Beaches (MHB) is managed by the Maine Department of Environmental Protection (ME DEP) and coordinated by the University of Maine Cooperative Extension (UMaine Extension). In 2016, this team worked with 28 local management entities to conduct routine monitoring, assessment, and public notification of water quality conditions for 60 beach management areas spanning Kittery to Mount Desert Island. MHB staff continued to build local capacity for well-informed beach management and to address pollution issues when they arose during the beach season.

Summary Report Of Enhanced Monitoring And Pollution Source Tracking Efforts In Goosefare Brook, Maine, 2012-2016, M. Sims, K. Kaczor

Maine Sea Grant Publications

The Goosefare Brook (GFB) forms the border between the City of Saco to the south and Town of Old Orchard Beach (OOB) to the north. In response to concerns over water quality in the mouth and adjacent beach water, the Maine Healthy Beaches (MHB) program has supported multi-year enhanced monitoring and pollution source tracking efforts, held Stakeholder Workshops, and more to address impaired water quality throughout the watershed. Over the past five years, the MHB program has focused primarily on paired enterococci and optical brightener samples in OOB’s New Salt Rd. Tributary (NSRT). This work identified widespread bacterial contamination throughout …

Colonization Density Of The Upper Respiratory Tract As A Predictor Of Pneumonia-Haemophilus Influenzae, Moraxella Catarrhalis, Staphylococcus Aureus, And Pneumocystis Jirovecii., Daniel E Park, Henry C Baggett, Stephen R C Howie, Qiyuan Shi, Nora L Watson, W Abdullah Brooks, Perch Study Group

Epidemiology Faculty Publications

Background.

There is limited information on the association between colonization density of upper respiratory tract colonizers and pathogen-specific pneumonia. We assessed this association for Haemophilus influenzae, Moraxella catarrhalis, Staphylococcus aureus, and Pneumocystis jirovecii. Methods.

In 7 low- and middle-income countries, nasopharyngeal/oropharyngeal swabs from children with severe pneumonia and age-frequency matched community controls were tested using quantitative polymerase chain reaction (PCR). Differences in median colonization density were evaluated using the Wilcoxon rank-sum test. Density cutoffs were determined using receiver operating characteristic curves. Cases with a pathogen identified from lung aspirate culture or PCR, pleural fluid culture or …

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 …

Simplified Reversed Chloroquines To Overcome Malaria Resistance To Quinoline-Based Drugs, Bornface Gunsaru, Steven J. Burgess, Westin Morrill, Jane X. Kelly, Shawheen Shomloo, Martin J. Smilkstein, Katherine May Liebman, David H. Peyton

Chemistry Faculty Publications and Presentations

Building on our earlier work of attaching a chemosensitizer (reversal agent) to a known drug pharmacophore, we have now expanded the structure-activity relationship study to include simplified versions of the chemosensitizer. The change from two aromatic rings in this head group to a single ring does not appear to detrimentally affect the antimalarial activity of the compounds. Data from in vitro heme binding and beta-hematin inhibition assays suggest that the single aromatic RCQ compounds retain activities against Plasmodium falciparum similar to those of CQ, although other mechanisms of action may be relevant to their activities.

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.

Draft Nuclear Genome Sequence Of The Liquid Hydrocarbon–Accumulating Green Microalga Botryococcus Braunii Race B (Showa), Daniel R. Browne, Jerry Jenkins, Jeremy Schmutz, Shengqiang Shu, Kerrie Barry, Jane Grimwood, Jennifer Chiniquy, Aditi Sharma, Thomas Daniel Niehaus, Taylor L. Weiss, Andrew T. Koppisch, David T. Fox, Suraj Dhungana, Shigeru Okada, Joe Chappell, Timothy P. Devarenne

Plant and Soil Sciences Faculty Publications

Botryococcus braunii has long been known as a prodigious producer of liquid hydrocarbon oils that can be converted into combustion engine fuels. This draft genome for the B race of B. braunii will allow researchers to unravel important hydrocarbon biosynthetic pathways and identify possible regulatory networks controlling this unusual metabolism.

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 …

Detection And Quantitation Of Tetracycline Antibiotics In Agricultural Swine Wastes, Ali Jamal Abdulrheem

Masters Theses & Specialist Projects

The spread of tetracyclines through agricultural systems is causing the present bacteria to develop antibiotic resistance. The spread of this bacteria, as well as the tetracycline antibiotics in the environment is dangerous because these antibiotics pose health hazards for humans. The overuse of antibiotics, which are added to livestock feed, results in the antibiotics being released into the environment via animal feces. In this research, we have attempted to design an analytical method to isolate antibiotics from agricultural wastes with subsequent detection using liquid chromatography and mass spectrometry (LC-MS). The antibiotics investigated in this study were tetracycline, chlortetracycline, and oxytetracycline. …

Microbial Interactions In The Phyllosphere Increase Plant Performance Under Herbivore Biotic Stress, Muhammad Saleem, Nicole Meckes, Zahida H. Pervaiz, Milton B. Traw

Plant and Soil Sciences Faculty Publications

The phyllosphere supports a tremendous diversity of microbes and other organisms. However, little is known about the colonization and survival of pathogenic and beneficial bacteria alone or together in the phyllosphere across the whole plant life-cycle under herbivory, which hinders our ability to understand the role of phyllosphere bacteria on plant performance. We addressed these questions in experiments using four genetically and biogeographically diverse accessions of Arabidopsis thaliana, three ecologically important bacterial strains (Pseudomonas syringae DC3000, Xanthomonas campestris, both pathogens, and Bacillus cereus, plant beneficial) under common garden conditions that included fungus gnats (Bradysia spp.). …

2016 Goosefare Brook Mst Summary And Next Steps, M. Sims, K. Kaczor

Maine Sea Grant Publications

No abstract provided.

Jordan River Monitoring Report, Ashley Taylor, Anna Farrell

Maine Sea Grant Publications

In congruence with the Maine Department of Marine Resources’ (DMR) efforts to monitor declining water quality in the Jordan River, Frenchman Bay, Maine, the Community Lab at MDI Biological Laboratory implemented regular water quality monitoring at additional sites in the watershed to supplement the work of the DMR. Water samples were collected weekly between June and August of 2017 by staff and students from the Community Lab. Samples were collected via boat and foot to reach additional intermittent streams and smaller tributaries that feed into the Jordan River. Samples were analyzed for Enterococcus bacteria, optical brighteners, and salinity. A goal …

Eukaryotic Microbes, Principally Fungi And Labyrinthulomycetes, Dominate Biomass On Bathypelagic Marine Snow, Alexander B. Bochdansky, Melissa A. Clouse, Gerhard J. Herndl

OES Faculty Publications

In the bathypelagic realm of the ocean, the role of marine snow as a carbon and energy source for the deep-sea biota and as a potential hotspot of microbial diversity and activity has not received adequate attention. Here, we collected bathypelagic marine snow by gentle gravity filtration of sea water onto μm filters from similar to 1000 to 3900 m to investigate the relative distribution of eukaryotic microbes. Compared with sediment traps that select for fast-sinking particles, this method collects particles unbiased by settling velocity. While prokaryotes numerically exceeded eukaryotes on marine snow, eukaryotic microbes belonging to two very distant …

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 …

Modeling Beta-Traces For Beta-Barrels From Cryo-Em Density Maps, Dong Si, Jing He

Computer Science Faculty Publications

Cryo-electron microscopy (cryo-EM) has produced density maps of various resolutions. Although ά-helices can be detected from density maps at 5-8 angstrom resolutions, β-strands are challenging to detect at such density maps due to close-spacing of β-strands. The variety of shapes of β-sheets adds the complexity of β-strands detection from density maps. We propose a new approach to model traces of β-strands for β-barrel density regions that are extracted from cryo-EM density maps. In the test containing eight β-barrels extracted from experimental cryo-EM density maps at 5.5 angstrom-8.25 angstrom resolution, StrandRoller detected about 74.26% of the amino acids in the β-strands …

Comparing An Atomic Model Or Structure To A Corresponding Cryo-Electron Microscopy Image At The Central Axis Of A Helix, Stephanie Zeil, Julio Kovacs, Willy Wriggers, Jing He

Computer Science Faculty Publications

Three-dimensional density maps of biological specimens from cryo-electron microscopy (cryo-EM) can be interpreted in the form of atomic models that are modeled into the density, or they can be compared to known atomic structures. When the central axis of a helix is detectable in a cryo-EM density map, it is possible to quantify the agreement between this central axis and a central axis calculated from the atomic model or structure. We propose a novel arc-length association method to compare the two axes reliably. This method was applied to 79 helices in simulated density maps and six case studies using cryo-EM …