Digital Commons Network^™

Succession Of Microbial Populations And Nitrogen-Fixation Associated With The Biodegradation Of Sediment-Oil-Agglomerates Buried In A Florida Sandy Beach, Boryoung Shin, Ioana Bociu, Max Kolton, Markus Huettel, Joel E Kostka

C-IMAGE Publications

The Deepwater Horizon (DWH) oil spill contaminated coastlines from Louisiana to Florida, burying oil up to 70 cm depth in sandy beaches, posing a potential threat to environmental and human health. The dry and nutrient-poor beach sand presents a taxing environment for microbial growth, raising the question how the biodegradation of the buried oil would proceed. Here we report the results of an in-situ experiment that (i) characterized the dominant microbial communities contained in sediment oil agglomerates (SOAs) of DWH oil buried in a North Florida sandy beach, (ii) elucidated the long-term succession of the microbial populations that developed in …

Screening The Cultivable Cave Microbial Mats For The Production Of Antimicrobial Compounds And Antibiotic Resistance, Jerneja Ambrožič Avguštin, Patricia Petrič, Lejla Pašić

International Journal of Speleology

The current work extends the phenotypic characterization of a bacterial culture collection obtained from white, yellow, grey or pink microbial cave wall colonies that are common in the caves of Slovenian Karst. We have determined antibiotic resistance to 22 natural and synthetic antibiotics in 69 isolates from the microbial mats. Thirty-eight isolates (52%) were resistant to 1-5 antibiotics; another 27 isolates (37%) were resistant to 6-10 antibiotics; and 7 isolates (0.1%) were resistant to 11-17 antibiotics. We screened for production of antimicrobial compounds by growing cave isolates on five different media and overlaying individual cultures with ten Gram-positive and Gram …

Springs Of The Arabian Peninsula: Historical Trends, Current Status And Human Impact In Saudi Arabia, Oman And Jordan, Kamal M. Aljohani

USF Tampa Graduate Theses and Dissertations

This research was conducted to update previous studies of the springs of the Arabian Peninsula (Saudi Arabia, Oman and Jordan). Approach: 76 springs were surveyed in between March and July 2018: 15 Saudi Arabia, 41 Oman and 20 Jordan to ascertain the current status, water quality and zooplankton benthos and fish communities. Investigation of the changes of biota and chemical parameters downstream from the springs source in Saudi Arabia. Results: Mercury exceeded the WHO and USEPA maximum contaminant level (MCL) in 63 of 76 springs, Aluminum exceeded MCL in 8 of 76 springs, and both were the common dissolved heavy …

Physicochemical And Colligative Investigation Of Α (Shrimp Shell)-And Β (Squid Pen)-Chitosan Membranes: Concentration-Gradient-Driven Water Flux And Ion Transport For Salinity Gradient Power Andseparation Process Operations, Clifford R. Merz

Marine Science Faculty Publications

Chitin, and its derivative chitosan, is a naturally occurring biopolymer and an abundant polysaccharide containing acetylated units of N-acetyl-d-glucosamine. Chitosan membranes produced from shrimp shell (α) and squid pen (β) biowaste were prepared by solvent-casting, after which water flux and ionic transport diffusion experiments were conducted using a side-by-side concentration test cell under differing salinity concentration gradients. Physicochemical and experimental investigations were conducted, which confirmed that β-chitin possesses differing and enhanced performance characteristics than α-chitin with respect to diffusive water flux and ionic transport capabilities. In addition, novel colligative investigations through osmotic equilibrium were conducted to determine electrochemical characteristics …

Hepatobiliary Analyses Suggest Chronic Pah Exposure In Hakes (Urophycis Spp.) Following The Deepwater Horizon Oil Spill, Rachel E. Struch, Erin Pulster, Andrea D. Schreier, Steven A. Murawski

C-IMAGE Publications

Prior to the Deepwater Horizon oil spill, we lacked a comprehensive baseline of oil contamination in the Gulf of Mexico's sediments, water column, and biota. Gaps in prespill knowledge limit our ability to determine the aftereffects of the Deepwater Horizon blowout or prepare to mitigate similar impacts during future oil spill disasters. We examined spatiotemporal differences in exposure to and metabolism of polycyclic aromatic hydrocarbons (PAHs) in 2 hake species (Urophycis spp.) to establish a current baseline for these ecologically important, abundant, and at-risk demersal fishes. Gulf hake (Urophycis cirrata) and southern hake (Urophycis floridana) were collected throughout the Gulf …

Drivers Of Ant Composition, Richness, And Trophic Guilds In Neotropical Iron Ore Cavities, Rodrigo A. Castro-Souza, Thais G. Pellegrini, Marconi Souza-Silva, Rodrigo L. Ferreira

International Journal of Speleology

Subterranean habitats may be considered limiting for animal colonization, especially for ants, due to permanent darkness and mainly because of oligotrophic conditions. While not as deep as limestone caves, iron ore caves and other subterranean habitats may be more available for colonization because of their shallower depth. We use the richness and composition of ants to assess how differences in habitat structure affect the biodiversity and ecosystem function between cavities and surrounding epigean landscapes. We predicted that the distribution of ants would be different because of the variation in habitat structure and cavity conditions may act as a filter for …

The Peculiar Nature Of Florida’S Sandhill Wetlands, Ponds & Lakes— Their Ecohydrology, Relationship With The Regional Aquifer & Importance Within The Landscape., Renae Starr Nowicki

USF Tampa Graduate Theses and Dissertations

This dissertation explores the ecohydrology of Florida’s peculiar and poorly studied sandhill wetland and water features, particularly those located in west-central Florida. The primary research goals include: compilation and summarization of the available ecohydrologic information for features across Florida; comparison of water level and water geochemistry data between sandhill wetlands and waters and the regional aquifer to provide evidence of regional hydrologic control; and use of geophysical applications to examine the hydraulic connections between sandhill wetlands and waters and the regional aquifer.

From this research, a natural history of sandhill wetland and water ecohydrology is presented, highlighting: the differences between …

Lung Cancer Cells Survive Egfr Tki Exposure Through Upregulation Of Cholesterol Synthesis, Mark Howell

USF Tampa Graduate Theses and Dissertations

Lung cancer is the number one cause of cancer related death in both males and females. About 20% of all non-small cell lung cancer (NSCLC) patients are expected to harbor an epidermal growth factor receptor (EGFR) activating mutation. EGFR inhibitors have been shown to provide clinical benefits over chemotherapy for lung cancer patients with EGFR activating mutations. However, despite the initial clinical responses to these EGFR targeted therapies, long-term efficacy is not possible because acquired drug resistance hampers the effectiveness of these therapies. We found that a fiber inspired smart scaffold (FiSS) platform established in our laboratory allows growth of …

Constituent Partitioning Consensus Docking Models And Application In Drug Discovery, Rainer Metcalf

USF Tampa Graduate Theses and Dissertations

This work expounds on some of the current computational tools and programs available and the best practices associated with their use. A high-level introduction, intended for both novices and the semi-experienced, focusing on the more common programs used in scientific literature is the scope of this topic. Both classical and quantum techniques are described. Classical methodologies include Molecular Dynamics, Monte Carlo, energy minimization methods, molecular docking, low-mode, and homology modeling. Quantum chemistry techniques are also discussed encompassing Hartree-Fock, Post-Hartree-Fock theories, and Density Functional Theory along with associated basis sets.

Along with established methodologies, novel theoretical methods are introduced for furthering …

Ecological Responses Of Seascape Heterogeneity, Dinorah H. Chacin

USF Tampa Graduate Theses and Dissertations

A core aim of landscape ecologists as well as conservation and management practices has been to understand how processes that structure communities vary as a function of landscape context. Landscape heterogeneity (i.e. landscape composition, configuration) and fine-scale habitat characteristics can influence ecological interactions across habitat patches at a range of scales. Therefore, the main objective of this work is to apply a landscape ecology perspective to understand how seascape heterogeneity can influence demographic rates, community patterns, and ecological processes. To accomplish this overall goal, I conducted a literature review on oyster reefs from a seascape ecology perspective (Chapter 1) and …

Untapped Potential Of Gorgonian Octocorals For Detecting Environmental Change In Biscayne National Park, Florida, Usa, Selena A. Kupfner Johnson

USF Tampa Graduate Theses and Dissertations

One consequence of dramatic stony-coral loss has been recognition that gorgonian octocorals (Anthozoa: Octocorallia) have emerged among the dominant reef fauna. However, gorgonians are notoriously difficult to field-identify and consequently have been underrepresented in most monitoring efforts resulting in a lack of long-term data. The rich diversity of habitats, close proximity to the urban center of Miami, and connectivity to other areas of Florida have made Biscayne National Park an active location for reef research since its establishment in 1968. As such, a plethora of data (e.g., museum specimen and species abundance data) has been collected and stored in archives …

Amyloid Protein Aggregation And Associated Toxicity, Chamani A. Niyangoda

USF Tampa Graduate Theses and Dissertations

Amyloidosis is a group of diseases in which amyloid fibrils accumulate and deposit into plaques and intracellular inclusions which lead to disruption of the tissue architecture and function. Most of the amyloid diseases are incurable due to a lack of understanding of the amyloid formation, as well as associated toxicity. My research work is focused on three different aspects of amyloid aggregation.

The aim of the first project is to investigate the potential use of deep-blue autofluorescence (dbAF) as an intrinsic optical probe to study amyloid self-assembly. This novel fluorescence signal is excited at the long wavelength edge of the …

The Role Of Atypical Protein Kinase C In Colorectal Cancer Cells Carcinogenesis, S M Anisul Islam

USF Tampa Graduate Theses and Dissertations

Colorectal cancer (CRC) is the third most common malignancy and the fourth most common cause of cancer-related death worldwide. CRC is a life-threatening disease due to therapy-resistant cancerous cells. The exact mechanisms of cell growth, survival, metastasis and inter & intracellular signaling pathways involved in CRC are still a significant challenge. Moreover, the treatment of metastatic CRC considered palliative for many years aimed for an improved life, with little hope of a cure, highlighting the need for developing novel targeted therapy for CRC. Hence, investigating new molecular mechanism(s) that lead to colorectal carcinogenesis may give insight into the therapeutic target. …

The Role Of Secreted Proteases In Regulating Disease Progression In Staphylococcus Aureus, Brittney D. Gimza

USF Tampa Graduate Theses and Dissertations

Staphylococcus aureus is a highly successful pathogen capable of producing a wealth of virulence factors in the human host. Of note, ten extracellular proteases are produced alongside these virulence factors and play a multifaceted role during infection. They not only cleave host proteins to promote bacterial invasion, immune evasion and survival, but also control disease progression by modulating the stability of self-derived pathogenic determinants. The importance of the secreted proteases modulating virulence factor stability is evidenced by our groups previous finding that a protease-null strain has a substantially increased infectious capacity in a murine model of sepsis; resulting from the …

Investigating Among-Individual Growth Heterogeneity In Longleaf Pine: Advancing Dendrochronological Approaches, Jamie E. Munn

USF Tampa Graduate Theses and Dissertations

Within a population, individuals frequently differ in the rate at which they grow, and this rate can be impacted by both genetic differences and abiotic factors. Often, dendrochronology is used to elucidate growth trends based on climate or other factors. This dissertation explores new statistical approaches to dendrochronological research.

First, I created a chronology for a population of longleaf pine (Pinus palustris P. Mill.) individuals in a southwest Florida sandhill community. I then used generalized linear mixed models to investigate the effects of fire frequency, year, tree age and size, and elevation on variation in radial growth heterogeneity. I then …

A Novel Cytokine Response Modulatory Function Of Mek Inhibitors Mediates Therapeutic Efficacy, Mengyu Xie

USF Tampa Graduate Theses and Dissertations

Despite the recent success of immune-checkpoint blockade therapy for late-stage non-small cell lung cancer (NSCLC), lung cancer is still the leading cause of cancer deaths worldwide. One of the most important characteristics of lung cancer in therapeutic decision-making are the targetable molecules, including EGFR, ALK, BRAF, and MEK. The excitement of immune-checkpoint blockade therapy has triggered concerted efforts that focus on exploring combinations of immune checkpoint therapy with other approved therapeutic regimens aiming at further augmenting positive outcomes and survival. However, the lack of understanding of underlying mechanisms and evidence-based clinical testing has hindered the progress to a cure. Hence, …

The Adaptations Of The Sulfur-Oxidizing, Gammaproteobacterium "Candidatus Endoriftia Persephone", Endosymbiont Of The Giant Tubeworm Riftia Pachyptila, To Hydrothermal Vent Habitat Heterogeneity, Juliana M. Leonard

USF Tampa Graduate Theses and Dissertations

The siboglinid tubeworm Riftia pachyptila is a dominant member of the deep-sea megafauna where seawater and hydrothermal vent (HTV) effluent interface and mix. It is one of the fastest growing invertebrates on land or in the sea. It does not have a digestive tract (e.g. mouth, gut, or anus), and is completely dependent on its sulfur-oxidizing endosymbiont, the Gammaproteobacterium “Candidatus Endoriftia persephone” for its nutritional requirements. This association was the first and is the most well studied among chemolithoautotrophic symbioses. “Ca. E. persephone” is a chemolithoautotrophic bacterium that oxidizes sulfide as an electron donor for energy, reduces oxygen as a …

Targeting Bacterial Resistance And Cancer Metastasis: A Structure Based Approach, Kyle Galen Kroeck

USF Tampa Graduate Theses and Dissertations

Current research in pharmaceutical development commonly utilizes a profusion of methods in molecular modeling in order to probe intricate biological problems. Many original and promising compounds have been identified and developed by integrating experimental and computational methods. Structural biology utilizes many different research techniques including x-ray crystallography, NMR, and electron microscopy in order to develop molecular models of macromolecules that are of biological interest. Such techniques can be used in conjunction with molecular docking, which utilizes those molecular models in order to target macromolecules of therapeutic interest by computationally analyzing the conformations adopted by ligands upon interaction with a desired …

An Investigation Into The Heterogeneity Of Insect Arylalkylamine N-Acyltransferases, Brian G. O'Flynn

USF Tampa Graduate Theses and Dissertations

Arylalkylamine N-acyltransferases (AANATs) have in recent years been suggested as potential new insecticide targets. These promiscuous enzymes are involved in the N-acylation of biogenic amines to form N-acylamides. Mammalian AANAT is predominantly associated with circadian rhythm regulation, as it catalyzes the formation of N-acetylserotonin, the precursor of melatonin, from serotonin. In insects, this process is a key step in melanism, as well as hardening of the cuticle, removal of biogenic amines, and in the biosynthesis of fatty acid amides. The unique nature of each insect AANAT (iAANAT) isoform characterized indicates that while catalyzing similar reactions, each insect accommodates …

Understanding The Influence Of The Cancer Microenvironment On Metabolism And Metastasis, Shonagh Russell

USF Tampa Graduate Theses and Dissertations

Cancer is a complex and heterogeneous disease. Not only is there considerable variability between different cancer types, but there is enormous variability between and within patients who have the same type of cancer. Within tumors, there are multiple cell types, including cancer cells, stromal cells, and immune cells. The tumor microenvironment often induces the healthy cells to become pro-tumorigenic. Cell metabolism is exquisitely sensitive to changes in the tumor microenvironment and can be measured to infer the aggressiveness of cancer and predict response to therapy. In this dissertation, we aim to understand how the microenvironment, specifically low pH, affects the …

Fauna Of The Kemp Caldera And Its Upper Bathyal Hydrothermal Vents (South Sandwich Arc, Antarctica), Katrin Linse, Jonathan T. Copley, Douglas P. Connelly, Robert D. Larter, David A. Pearce, Nick V. C. Polunin, Alex D. Rogers, Chong Chen, Andrew Clarke, Adrian G. Glover, Alastair G. C. Graham, Veerle A. I. Huvenne, Leigh Marsh, William D. K. Reid, C. Nicolai Roterman, Christopher J. Sweeting, Katrin Zwirglmaier, Paul A. Tyler

Marine Science Faculty Publications

Faunal assemblages at hydrothermal vents associated with island-arc volcanism are less well known than those at vents on mid-ocean ridges and back-arc spreading centres. This study characterizes chemosynthetic biotopes at active hydrothermal vents discovered at the Kemp Caldera in the South Sandwich Arc. The caldera hosts sulfur and anhydrite vent chimneys in 1375–1487 m depth, which emit sulfide-rich fluids with temperatures up to 212°C, and the microbial community of water samples in the buoyant plume rising from the vents was dominated by sulfur-oxidizing Gammaproteobacteria. A total of 12 macro- and megafaunal taxa depending on hydrothermal activity were collected in these …

Submesoscale And Mesoscale Eddies In The Florida Straits: Observations From Satellite Ocean Color Measurements, Yingjun Zhang, Chuanmin Hu, Yonggang Liu, Robert H. Weisberg, Vassiliki H. Kourafalou

Marine Science Faculty Publications

Despite their well-recognized importance in driving ocean physics and biology, submesoscale (diameter < Rossby radius of deformation) eddies have been extremely difficult to observe due to technical difficulties from both field and remote platforms. Here using novel satellite ocean color data products and modified algorithms, we address this challenge for the Florida Straits (22–28°N, 78–85°W). Between 2002 and 2018, while mesoscale eddies (radius >15 km) show strong seasonality with occurrence frequency decreasing from Lower Keys to Upper Keys, submesoscale eddies show little or no seasonality with high occurrence frequency restricted to 30–200-m isobaths. The number of mesoscale eddies decreases exponentially in size, but submesoscale eddies show a normal distribution in size. These findings are significant in filling our knowledge gap in submesoscale eddies in this physically and ecologically important region as it encompasses world-renowned coral reefs, seagrasses, and fisheries.

Improving The Integration Of Restoration And Conservation In Marine And Coastal Ecosystems: Lessons From The Deepwater Horizon Disaster, Richard L. Wallace, Gilbert Gilbert, John E. Reynolds Iii

C-IMAGE Publications

In the wake of the Deepwater Horizon disaster, much has been learned about the biological, ecological, physical, and chemical conditions of the Gulf of Mexico. In parallel, the research community has also gained insight about the social and organizational structures and processes necessary for oil spill response and subsequent marine and coastal restoration. However, even with these lessons from both the Deepwater Horizon and previous spills, including 1989’s Exxon Valdez and the Ixtoc 1 in 1979, our understanding of how to avoid future crises has not advanced at the same pace as offshore oil and gas development. We argue that …

Evaluating The Effect Of Temperature On A Human Parasite And Its Intermediate Snail Host: Implications For A Changing Climate, Karena H. Nguyen

USF Tampa Graduate Theses and Dissertations

Global climate change is impacting the emergence, re-emergence, prevalence, and incidence of infectious diseases worldwide, including parasitic diseases of humans (Blum and Hotez 2018). Neglected tropical diseases, defined as a group of parasitic diseases affecting developing countries in the tropics (Hotez et al. 2007), are of particular concern because these diseases occur in areas that are also expected to experience rapid population growth and agricultural development in the coming decades. As human population and food demand increase, the greater the likelihood of humans encountering intermediate hosts that either inhabit agricultural areas or are impacted by agricultural development, which will influence …

Modeling Of Interaction Of Ions With Ether- And Ester-Linked Phospholipids, Matthew W. Saunders

USF Tampa Graduate Theses and Dissertations

Phospholipids are present in all parts of cells and are used in many signalling and struc- tural roles. As structural molecules they act as the main component of cellular membranes. Bilayer properties are heavily influenced by the structure of their component polar lipids, and different lipids are found in different organisms. A distinguishing feature of Archaeal plasma membranes is that their phospholipids contain ether-links, as opposed to bacterial and eukaryotic plasma membranes where phospholipids primarily contain ester-links. In our work we examine the effects of salt on bilayer structure in the case of both ester- and ether-linked lipid bilayers. We …

Design And Delivery Of Synthetic Mrna By A Peptide Nanoparticle, John H. Lockhart

USF Tampa Graduate Theses and Dissertations

The field of synthetic mRNA therapeutics is a rapidly expanding arm of gene therapies. The use of mRNA provides multiple benefits over viral or DNA vectors. synthetic mRNA vectors are immediately translated into protein after entering the cytoplasm of cells in contrast to DNA vectors that must first be transcribed to mRNA in the nucleus. This allows synthetic mRNA to produce a therapeutic protein in any cell type, including non-dividing cells. In addition, the non-replicative nature of mRNA means that insertional mutagenesis or generation of escape mutants is not a concern. However, the stimulation of innate immune responses by unmodified …

Development And Validation Of Wireless Sensors For Applications To Human Head Angular And Mechanical Motions, Karthick Natesan

USF Tampa Graduate Theses and Dissertations

In this project, we programmed a 9 degree of freedom Razor sensor, which incorporates an accelerometer and gyroscope to measure the head linear and angular motions produced by activities of daily living (ADL). The majority of studies concentrate on linear accelerations, so the purpose of this study is to determine the importance of both linear and angular components of acceleration in everyday activities and find interlinked relation between them. The sensor was validated using another calibrated and validated system. The general size and wireless nature make this sensor very suitable for use with human subjects. After obtaining informed consent, we …

Mechanisms Of Organic Matter Export In Estuaries With Contrasting Carbon Sources, A. R. Arellano, T. S. Bianchi, C. L. Osburn, E. J. D'Sa, N. D. Ward, D. Oviedo-Vargas, I. D. Joshi, D. S. Ko, M. R. Shields, G. Kurian, J. Green

Marine Science Faculty Publications

Modifications in land use and climate will result in shifts in the magnitude and composition of organic matter (OM) transported from wetlands to coastal waters, but differentiation between riverine and wetland OM sources in coastal areas remains a challenge. Here, we evaluate particulate and dissolved OM export dynamics in two representative estuary geomorphologies—Apalachicola Bay (AP) and Barataria Bay (BB), characterized primarily by blackwater river inputs and high particle abundance, respectively. The magnitude and composition of OM exported from each estuary was evaluated based on seasonal measurements of surface water dissolved organic carbon (DOC), particulate organic carbon (POC), particulate nitrogen, the …

Mechanisms Of Organic Matter Export In Estuaries With Contrasting Carbon Sources, A. R. Arellano, T. S. Bianchi, C. L. Osburn, E. J. D'Sa, N. D. Ward, D. Oviedo-Vargas, I. D. Joshi, D. S. Ko, M. R. Shields, G. Kurian, J. Green

Marine Science Faculty Publications

Modifications in land use and climate will result in shifts in the magnitude and composition of organic matter (OM) transported from wetlands to coastal waters, but differentiation between riverine and wetland OM sources in coastal areas remains a challenge. Here, we evaluate particulate and dissolved OM export dynamics in two representative estuary geomorphologies—Apalachicola Bay (AP) and Barataria Bay (BB), characterized primarily by blackwater river inputs and high particle abundance, respectively. The magnitude and composition of OM exported from each estuary was evaluated based on seasonal measurements of surface water dissolved organic carbon (DOC), particulate organic carbon (POC), particulate nitrogen, the …

Resolving The Dilemma Of Dispersant Use For Deep Oil Spill Response, Steven Murawski, Michael Schlüter, Claire B. Paris-Limouzy, Zachary M. Aman

C-IMAGE Publications

No abstract provided.