Physical Sciences and Mathematics Commons^™

Investigating High Speed Localization Microscopy Through Experimental Methods, Data Processing Methods, And Applications Of Localization Microscopy To Biological Questions, Andrew J. Nelson

Electronic Theses and Dissertations

Fluorescence Photoactivation Localization Microscopy(FPALM) and other super resolution localization microscopy techniques can resolve structures with nanoscale resolution. Unlike techniques of electron microscopy, they are also compatible with live cell and live animal studies, making FPALM and related techniques ideal for answering questions about the dynamic nature of molecular biology in living systems. Many processes in biology occur on rapid sub second time scales requiring the imaging technique to be capable of resolving these processes not just with a high enough spatial resolution, but with an appropriate temporal resolution. To that end, this Dissertation in part investigates high speed FPALM as …

Pepper Mild Mottle Virus As A Surrogate For Enteric Viruses: Implications For Assessing Water Quality, Erin Michelle Symonds

USF Tampa Graduate Theses and Dissertations

Less than 10% of the world’s domestic wastewater is disinfected prior to discharge into surface waters; therefore, human exposure to diverse wastewater-related pathogens results in millions of cases of illness each year. Among the enteric pathogens, viruses represent an important group of emerging pathogens and are frequently the cause of food- and water-borne outbreaks of illness. Although the World Health Organization and many government agencies mandate the use of bacterial indicators to identify poor microbial water quality, it is well known that these indicators poorly correlate with fecal pollution contamination events and risk of disease. The field of public health-related …

Specific Binding Affinity Of The Non-Catalytic Domain Of Eukaryotic Like Type Ib Topoisomerase Of Vaccinia Virus, Benjamin R. Reed

Dissertations, Theses, and Capstone Projects

Topoisomerases are ubiquitous proteins that alter supercoiling in double stranded DNA (dsDNA) during transcription and replication and. vaccinia and the closely related poxvirus variola virus, at 314 amino acids in length, encode the smallest of the type I topoisomerases(TopIB). TopIB is a two domain protein that recognizes the sequence 5’-T/CCCTT, cleaves at the 3’-end and relaxes supercoiling through rotation. The C-terminal domain (CTD) alone contains the catalytic activity and specificity. Deletion of the N-terminal domain results in a greatly reduced rate of relaxation and rapid dissociation. Biochemical data suggests that the N-terminal domain (NTD) is important for pre-cleavage binding and …

Do Novel Weapons That Degrade Mycorrhizal Mutualisms Explain Invasive Species Success?, Philip L. Pinzone Mr.

Biology Theses

Invasive plants often dominate novel habitats where they did not co-evolve with local species. Several hypotheses suggest mechanisms that explain increased exotic plant success, including 'novel weapons' and 'degraded mutualisms'. Japanese knotweed (Fallopia japonica) and European buckthorn (Rhamnus cathartica) are widespread plant invaders in North America that can dominate ecosystems. The goal of this study is to test whether these impacts are more consistent with novel weapons or degraded mutualism hypotheses. I examine tree seedling recruitment, (germination and initial survival) growth, (biomass) and mycorrhizal invasion (AMF content) as a function of F. japonica and R. cathartica …

Metabolomics Approaches To Decipher The Antibacterial Mechanisms Of Yerba Mate (Ilex Paraguariensis) Against Staphylococcus Aureus And Salmonella Enterica Serovar Typhimurium, Caroline Sue Rempe

Doctoral Dissertations

The increasing prevalence of drug-resistant pathogens is an urgent problem that requires novel methods of bacterial control. Plant extracts inhibit bacterial pathogens and could contain antibacterial compounds with novel mechanisms of action. Yerba mate, a common South American beverage made from Ilex paraguariensis, has antibiotic activity against a broad range of bacterial pathogens. In this work, an attempt was first made to characterize the antibacterial source of an aqueous yerba mate extract by generating a series of extract fractions, collecting GC-MS and antibacterial activity profiles, and then ranking the hundreds of compounds by their presence in fractions with high antibacterial …

Point Of Use Biosand Filters Of The Rural Dominican Republic, Kurtis Quamme

Theses and Dissertations

The point of use biosand filter (BSF) is used globally as a drinking water treatment solution. In this research, point of use BSFs were inoculated with active biosand from the Linnwood Drinking Water Treatment plant slow sand filter beds (Milwaukee, Wisconsin) and with sands collected from point of use filters operating in the Dominican Republic. These filters were maintained with varying source waters (surface water, groundwater, or tap water to simulate chlorination encountered in the field). The microbial community of filters with varied influents and biosand inoculum were analyzed quantitatively by sequencing and qPCR. Filter efficacy and microbial community were …

Microbial Extracellular Enzymes In Marine Sediments: Methods Development And Potential Activities In The Baltic Sea Deep Biosphere, Jenna Marie Schmidt

Masters Theses

The deep biosphere is defined as the subsurface ecosystem in which little energy is available to microorganisms and microorganisms can live for thousands of years. Heterotrophic microbes survive in the deep biosphere even though organic matter is limited and highly recalcitrant in nature. Measuring microbial extracellular enzyme activity provides a potential means to evaluate the rate at which microorganisms are performing carbon remineralization in the energy limited sediment beneath the seafloor. Extracellular enzymes breakdown organic compounds so that the nutrients can move inside the cell and be used for energy. This study explored the role extracellular enzymes play in the …

Incomplete Denitrification In Thermus Species, Chrisabelle Mefferd

UNLV Theses, Dissertations, Professional Papers, and Capstones

Members the bacterial genus Thermus have been shown to be incomplete denitrifiers, terminating with nitrite or nitrous oxide (N2O). However, the ability to carry out denitrification and the evolution of nitrogen oxide reductase genes in Thermus remains poorly understood. This study tests the hypothesis that incomplete denitrification is common in Thermus and seeks to uncover patterns in the evolution of denitrification pathways in Thermus. Denitrification capacity was determined in a collection of 25 strains representing ten species of Thermus and phylogenetic analysis was performed to determine whether denitrification genes evolved horizontally in Thermus. No strains in this study reduced nitrate …

Biogeochemistry Of A Saline, Alkaline, Terminal Lake Ecosystem In Transition; Walker Lake, Nevada, Katherine Lynn Willever

UNLV Theses, Dissertations, Professional Papers, and Capstones

Walker Lake is a saline, alkaline, terminal lake ecosystem located in west-central Nevada. For over one hundred years, anthropogenic streamflow diversions within the Walker River Basin have ultimately led to little or no water reaching Walker Lake, the basin’s terminus for water flow. These diversions have resulted in a >46 meter decrease in the lake surface altitude and increases in salinity and dissolved salt constituents that have caused the elimination of native fish species. This study examines how the lack of freshwater inflow has altered the physical, chemical, and microbiological structure of Walker Lake during the lake’s ongoing desiccation.

Between …

Monitoring And Mitigation Of Elevated Co2 Impacts Using Microalgae, Terry-Rene Wiesner Brown

USF Tampa Graduate Theses and Dissertations

Climate change is arguably the greatest environmental and economic challenge of our time. There are considerable documented and projected impacts to both human and natural systems as a result of climate change. These impacts include changes in temperature, sea level, precipitation patterns, and biogeography of ecologically and economically relevant species, including pathogens. One of the main drivers of climate change is elevated levels of atmospheric carbon dioxide (CO₂), a greenhouse gas. Since pre-industrial times, atmospheric CO₂ levels have increased from approximately 280 ppm to over 400 ppm, as a result of fossil fuel combustion, cement production and …

Synthesis And Biological Activity Of Novel Quorum Sensing Compounds, Joseph Nicholas Capilato

Theses and Dissertations

Bacteria communicate with chemical signals in a process known as quorum sensing. This population density-dependent process involves the bacterial production, release and detection of structurally specific small molecules and enables the bacterial pathogen to regulate its virulence on a population-wide level. Using a variety of chemical and biological techniques, I have studied various quorum sensing systems in several bacteria, including Vibrio cholera and Pseudomonas aeruginosa. A key principle of this research involves the design, synthesis and testing of novel compounds for their biological activity. These molecules are typically based off of an initial lead target, which is often identified …

The Influence Of Juncus-Rhizosphere Dissolved Organic Matter On Coastal Plankton Communities, Brittany Zepernick, Robert Michael Mckay, George S. Bullerjahn, Jeffrey W. Krause, Behzad Mortazavi

Honors Projects

Many aquatic plants produce copious amounts of dissolved organic matter (DOM) which enters surrounding waters and potentially stimulates planktonic activity. In the northern Gulf of Mexico, Juncus roemarianus (i.e. black needlerush) is a dominant marsh grass species residing in coastal zones and barrier islands. The below-ground biomass i.e. rhizosphere, can be consistently submerged, serving as a potential source of DOM to the surrounding waters. The lability and possible stimulatory effect of J. roemarianus DOM was examined for three plankton communities collected within the discharge region of Mobile Bay and adjacent waters of Gulf Shores, Alabama (less affected by Mobile Bay). …

Characterization Of The Marine Sponge Amphimedon Compressa Microbiome Across A Spatial Gradient, Renee Michelle Potens

HCNSO Student Theses and Dissertations

Diverse and ecologically important microbial communities (microbiomes) are symbiotic within marine sponges. In this study, the microbiome of Amphimedon compressa from three sample locations (Broward and Dade Counties, Southeast Florida, USA and the Southern Caribbean, Bocas del Toro, Panama) is characterized using 16S rRNA Illumina sequencing. The predominant taxa are Proteobacteria and Cyanobacteria, as expected for Low Microbial Abundance sponges, accounting for over 53% of the total microbiome community. The numbers of Operational Taxonomic Units (OTUs) decrease from Broward County (2,900) to Dade County (2,300) and then Bocas del Toro (1,200). The correlates to a decreasing north-south gradient of …

Biophysical Studies Of Cell Division Protein Localization Mechanisms In Escherichia Coli, Matthew Wayne Bailey

Doctoral Dissertations

How nanometer-scale proteins position accurately within micron-scale bacteria has intrigued both biologists and physicists alike. A critical process requiring precise protein localization is cell division. In most bacteria, cell division starts with the self-assembly of the FtsZ proteins into filaments that form a ring-like structure encircling the cell at its middle, the Z-ring. The Z-ring is a scaffold for additional proteins that synthesize the lateral cell wall which separates the two daughter cells. If division planes are misplaced relative to bacterial chromosomes, also called nucleoids, daughter cells with incomplete genetic material can be produced. In Escherichia coli, research carried out …

The Selective Survival Of Escherichia Coli In Freshwater Beach Sand, Natalie Ann Rumball

Theses and Dissertations

The quantification of Escherichia coli or E. coli is the most common method used to detect recent fecal pollution in recreational water, as this species is known for its high abundance in fecal matter and assumed host-associated nature. However, it has been determined that some strains are capable of long-term survival and potential propagation in non-host environments, such as the beach sand. These long-term environmental survivors are host-independent and are not associated with the same health risks as those E. coli from recent fecal pollution. However, they have been shown to impact how water quality is perceived as they are …

Dissemination And Persistence Of Plasmid Located, Integron Associated Antibiotic Resistant Genes In Wastewater Treatment Plant Effluent And Stream Water Bacteria, _ Suhartono

Graduate Theses and Dissertations

Transmissible plasmid-mediated integrons play important role in the persistence and dissemination of antibiotic resistance throughout the environment. Plasmids from 139 multi-antibiotic resistant Escherichia coli recovered from wastewater treatment plant effluent and upstream and downstream receiving stream water in Northwest Arkansas were extracted and profiled. Genes of class 1 and class 2 integrase (intI), mobilization (mob), sulfamethoxazole resistance (sul), and trimethoprim resistance (dfr) were detected using PCR and confirmed through DNA sequencing. Plasmids from almost half of the isolates (47%) were transmissible with mobF12 gene as the most frequently detected mobilization gene. Plasmid-borne class 1 with and without class 2 integrons …

Characterization Of Bacterial Diversity In Cold-Water Anthothelidae Corals, Stephanie Nichole Lawler

USF Tampa Graduate Theses and Dissertations

Cold-water corals, similar to tropical corals, contain a diverse and complex microbial landscape. Comprised of vital microscopic organisms (i.e. bacteria, viruses, archaea), the coral microbiome is a driving factor in the proliferation and survival of the coral host. Bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic …

Effects Of Epichloë Coenophiala−Tall Fescue Symbiosis On Plant-Microbe-Soil Interactions In A Temperate Pasture, Lindsey C. Slaughter

Theses and Dissertations--Plant and Soil Sciences

Plants interact in myriad ways with microorganisms to influence ecosystem processes such as nutrient cycling, which can regulate ecosystem response to global change. One important plant-microbe symbiosis occurs between cool-season grasses and asexual fungal Epichloë endophytes, such as tall fescue (Schedonorus arundinaceus) and Epichloë coenophiala. Because the common toxic strain of the endophyte (CTE) harms grazing livestock, non-livestock toxic endophyte (NTE) strains have been developed and are increasingly deployed in pastures. Little is known about how these symbioses impact other plant-microbe interactions and microbe-mediated soil processes in grassland ecosystems. I conducted three studies to determine how E. …

Ecological Dynamics In Compost-Amended Soils And The Resulting Effects On Escherichia Coli Survival, Anya Cutler

Graduate College Dissertations and Theses

Escherichia coli (E. coli) are common and typically innocuous copiotrophic bacteria found in the mammalian gut microbiome. However, over the past 30 years, pathogenic E. coli have been responsible for several outbreaks of foodborne illness linked to contaminated produce. The introduction of Escherichia coli to an agricultural soil, via contaminated water, compost, or raw manure, exposes the bacterium to a medley of ecological forces not found in a mammalian gut environment. This study assesses a variety of abiotic and biotic soil factors that influence the ability of an "invasive" copiotrophic coliform bacterium to survive in compost-amended agricultural soil. The study …

The Characterization Of A Recombinant Virophage Integrase, Martin Christopher Chacon

Open Access Theses & Dissertations

Virophages are satellite-like dsDNA viruses that parasitize giant viruses of the family Mimiviridae. Mavirus is the second virophage discovered that associates with its host virus Cafeteria roenbergensis Virus (CroV). When co-infecting their common host cell Cafeteria roenbergensis, a marine zooplankton that is widely spread throughout the oceans, mavirus will inhibit CroV's replication. In addition, mavirus was shown to share high similarities to the Maverick/Polinton eukaryotic DNA transposons. A coding sequence in mavirus genome (MV02) reveals high homology to retroviral integrases such as those found in HIVs. The putative integrase MV02 is predicted to integrate mavirus DNA into the host genome. …

Toxicity Of Engineered Nanomaterials To Plant Growth Promoting Rhizobacteria, Ricky W. Lewis

Theses and Dissertations--Plant and Soil Sciences

Engineered nanomaterials (ENMs) have become ubiquitous in consumer products and industrial applications, and consequently the environment. Much of the environmentally released ENMs are expected to enter terrestrial ecosystems via land application of nano-enriched biosolids to agricultural fields. Among the organisms most likely to encounter nano-enriched biosolids are the key soil bacteria known as plant growth promoting rhizobacteria (PGPR). I reviewed what is known concerning the toxicological effects of ENMs to PGPR and observed the need for high-throughput methods to evaluate lethal and sublethal toxic responses of aerobic microbes. I addressed this issue by developing high-throughput microplate assays which allowed me …