Life Sciences Commons^™

Virus Discovery In All Three Major Lineages Of Terrestrial Arthropods Highlights The Diversity Of Single-Stranded Dna Viruses Associated With Invertebrates, Karyna Rosario, Kaitlin Mettel, Bayleigh Benner, Ryan Johnson, Catherine Scott, Sohath Yusseff-Vanegas, Christopher Baker, Deby Cassill, Caroline Storer, Arvind Varsani, Mya Breitbart

Marine Science Faculty Publications

Viruses encoding a replication-associated protein (Rep) within a covalently closed, single-stranded (ss)DNA genome are among the smallest viruses known to infect eukaryotic organisms, including economically valuable agricultural crops and livestock. Although circular Rep-encoding ssDNA (CRESS DNA) viruses are a widespread group for which our knowledge is rapidly expanding, biased sampling toward vertebrates and land plants has limited our understanding of their diversity and evolution. Here, we screened terrestrial arthropods for CRESS DNA viruses and report the identification of 44 viral genomes and replicons associated with specimens representing all three major terrestrial arthropod lineages, namely Euchelicerata (spiders), Hexapoda (insects), and Myriapoda …

The Blurred Line Between Photic And Aphotic Environments: A Large Mexican Cave With Almost No Dark Zone, Luis M. Mejía-Ortíz, Tanja Pipan, David C. Culver, Peter Sprouse

International Journal of Speleology

Sistema Muévelo Rico is a 1.2 km long cave in Quintana Roo, less than 2 km from the Caribbean Sea. We measured illuminance to a level of 0.1 lux, organic matter (weight loss on ignition), temperature, and relative humidity. The last two were measured at hourly intervals for nearly one year. Approximately one-third of the cave has illuminance values greater than 0.01 lux, and most of the rest of the cave has light as well. Temperature and relative humidity were relatively constant, but they showed a daily cycle at all stations, albeit with different strengths. Organic matter averaged 8%, intermediate …

Assessing Preservation Priorities Of Caves And Karst Areas Using The Frequency Of Endemic Cave-Dwelling Species, Eugen Nitzu, Marius Vlaicu, Andrei Giurginca, Ioana N. Meleg, Ionut Popa, Augustin Nae, Ştefan Baba

International Journal of Speleology

Endemic and rare species as bioindicators of habitat vulnerability were used to develop protection and management plans for biotope prioritization (mainly islands habitats, lava tubes or groundwaters). Due to their narrow distribution, the endemic species (species confined to a restricted geographic area) are more susceptible to ecological disequilibrium and habitat loss than the widespread ones. Consequently, endemics become endangered in the context of ecological disturbance caused by anthropogenic pressure, making them suitable candidates to assess environmental preservation needs. Taking into consideration that most of the stygobitic and troglobitic species are endemic and confined to specific karst areas, based on their …

Automated Classification Of Dolphin Echolocation Click Types From The Gulf Of Mexico, Kaitlin E. Fraiser, Marie A. Roch, Melissa S. Soldevilla, Lance P. Garrison, John A. Hildebrand

C-IMAGE Publications

Delphinids produce large numbers of short duration, broadband echolocation clicks which may be useful for species classification in passive acoustic monitoring efforts. A challenge in echolocation click classification is to overcome the many sources of variability to recognize underlying patterns across many detections. An automated unsupervised network-based classification method was developed to simulate the approach a human analyst uses when categorizing click types: Clusters of similar clicks were identified by incorporating multiple click characteristics (spectral shape and inter-click interval distributions) to distinguish within-type from between-type variation, and identify distinct, persistent click types. Once click types were established, an algorithm for …

Role Of Heat Shock Transcription Factor 1 In Ovarian Cancer Epithelial-Mesenchymal Transition And Drug Sensitivity, Chase David Powell

USF Tampa Graduate Theses and Dissertations

The heat shock response (HSR) is a robust cellular reaction to mitigate protein damage from heat and other challenges to the proteome. This protective molecular program in humans is controlled by heat shock transcription factor 1 (HSF1). Activation of HSF1 leads to the induction of an array of cytoprotective genes, many of which code for chaperones. These chaperones, known as heat shock proteins (HSPs), are responsible for maintaining the functional integrity of the proteome. HSPs achieve this by promoting proper folding and assembly of nascent proteins, refolding denatured proteins, and processing for degradation proteins and aggregates which cannot be returned …

Cost-Effectiveness Analysis Of Targeted Herpes Zoster Vaccination In Adults 50-59 At Increased Cardiovascular Risk, Kathleen M. Glassner

USF Tampa Graduate Theses and Dissertations

Background: Over the last twenty years the incidence of herpes zoster (HZ) infection, also known as shingles, has been increasing among adults for unknown reasons. The economic burden of HZ is currently estimated at over $1 billion per year in the United States (U.S.) and is expected to increase as the susceptible adult population ages. HZ is caused by a re-activation of the varicella zoster virus (VZV), chicken pox, and more than 95% of adults living today carry the virus with a lifetime risk of 1 in 3 for developing HZ. In 2006 the FDA approved a vaccine for the …

Glomerular Hyperfiltration And Hypertension In Diabetes, Jie Zhang

USF Tampa Graduate Theses and Dissertations

In the present study, we investigated the pathophysiological mechanisms of the hemodynamic alteration in diabetes. Glomerular hyperfiltration occurs in the early stage of diabetes mellitus and has been recognized to promote the pathogenesis of diabetic nephropathy. We determine the role of TGF response and the vascular tone of Af-Art in diabetic hyperfiltration and we found that 1) tubular high glucose directly activates NOS1 and increases NO generation in the macula densa, which inhibits TGF response and increases GFR; 2) high glucose dilates renal Af-Art through GLUT1 and mediated by NOS3-derived NO generation; 3) in diabetes, blunted TGF mediated by NOS1 …

18f-Fdg Pet/Ctct-Based Radiomics For The Prediction Of Radiochemotherapy Treatment Outcomes Of Cervical Cancer, Badereldeen Abdulmajeed Altazi

USF Tampa Graduate Theses and Dissertations

Cervical cancer remains the third most commonly diagnosed gynecological malignancy in the United States and throughout the world despite being potentially preventable. Patients diagnosed with cervical cancer may develop local recurrence in the cervix and surrounding structures (vaginal apex, parametrial, or paracervical), regional recurrence in pelvic lymph nodes, distant metastasis, or a combination of all. The management of such treatment outcomes has not been subject to rigorous investigation. Therefore, there is a need for studies and clinical trials that focus on decision making to support the choice of the best treatment modality that leads to the minimal number of adverse …

Investigations Into The Non-Mevalonate Isoprenoid Biosynthesis Pathway's First Two Enzymes Utilizing Hybrid Qm/Mm Techniques, Justin K. White

USF Tampa Graduate Theses and Dissertations

Molecular drug design begins with the identication of a problem to solve. This work identies the growing resistance among human pathogens to current treatments. Once the problem is identied and understood, solutions must be proposed. This one is straight forward, we need new antimicrobial drugs. More specically, we need to identify novel targets to inhibit. A large portion of antibiotics focus on disruption of macromolecular production while only a few target metabolic systems. Finally, you need to propose solutions based on the information gathered. In order to avoid existing resistance, it is important to avoid the macromolecular route and focus …

A Historical Assessment Of Asbestos Exposure, Abatement Methods And Containment Efficacy During Asbestos Containing Material Removal Activities At A Large Federal Facility, Daniel A. Newfang

USF Tampa Graduate Theses and Dissertations

Asbestos sampling and monitoring data, starting from 2003, located in a large federal facility’s Asbestos Air Database Management (AADM) repository will be queried and analyzed on airborne asbestos fiber concentrations generated from abatement activities of asbestos-containing materials (ACM) and asbestos-containing building materials (ACBM). Historically, concerns expressed by personnel outside of the containment areas, whether adjacent to or quite a distance from the asbestos abatement activities present operational challenges for the project manager, potential angst and uneasiness to personnel residing next to the abatement activity as well as programmatic concerns to the building/facility managers. The concerned individuals working outside the abatement …

Evaluation Of A Microsphere-Based Immunoassay (Mia) In Measuring Diagnostic And Prognostic Markers Of Dengue Virus Infection, Jason H. Ambrose

USF Tampa Graduate Theses and Dissertations

Infections with dengue viruses (DENV) constitute both a global problem as well as locally in Florida. DENV comprise four distinct serotypes of single-stranded RNA viruses and belong to the family Flaviviridae. DENV are among the most medically important arboviruses in the world and cases may currently exceed 400 million per annum. Additionally, dengue established its first recorded endemic transmission cycle in the state of Florida in over a half century, first within the Florida Keys during 2009-10 followed by an unrelated outbreak in Martin County in 2013. The clinical profile of DENV infections ranges from a mild febrile illness …

Ecological Epigenetics Of Avian Range Expansions, Holly J. Kilvitis

USF Tampa Graduate Theses and Dissertations

In light of human-mediated environmental change, a fundamental goal for biologists is to determine which phenotypic characteristics enable some individuals, populations or species to be more adept at coping with such change, while rendering others more vulnerable. Studying ongoing range expansions provide a unique opportunity to address this question by allowing documentation of how novel environments shape phenotypic variation on ecological timescales. At range-edges, individuals are exposed to strong selective pressures and population genetic challenges (e.g. bottlenecks and/or founder effects), which make genetic adaptation difficult. Nevertheless, certain species, such as the house sparrow (Passer domesticus), seem to thrive in their …

Design And Synthesis Of Cpg-Lytic Peptide Conjugate, Brachytherapy Beads And A Combinatorial Library Of Primary Amines Used As Potential Therapeutics In The Treatment Of Cancers, Josanne-Dee Woodroffe

USF Tampa Graduate Theses and Dissertations

Cancer remains one of the most feared diseases affecting the modern world. Second to heart disease, it is the largest cause of deaths, affecting one in three persons. Cancer cells are formed when normal, healthy cells become damage, losing their normal regulatory mechanism that control cell growth. There are many different types and progression of these cancer cells that determine the type of treatment a patient receives. The primary focus of this dissertation is to propose three studies of anticancer agents. In Chapter one, a CpG-lytic peptide conjugate was designed to target receptors on the cell membrane to concentrate the …

The Role Of Sgs1 And Exo1 In The Maintenance Of Genome Stability., Lillian Campos-Doerfler

USF Tampa Graduate Theses and Dissertations

Genome instability is a hallmark of human cancers. Patients with Bloom’s syndrome, a rare chromosome breakage syndrome caused by inactivation of the RecQ helicase BLM, result in phenotypes associated with accelerated aging and develop cancer at a very young age. Patients with Bloom’s syndrome exhibit hyper-recombination, but the role of BLM and increased genomic instability is not fully characterized. Sgs1, the only member of the RecQ family of DNA helicases in Saccharomyces cerevisiae, is known to act both in early and late stages of homology-dependent repair of DNA damage. Exo1, a 5′–3′ exonuclease, first discovered to play a role …

Rehabilitating Asymmetric Gait Using Asymmetry, Tyagi Ramakrishnan

USF Tampa Graduate Theses and Dissertations

Human gait is a complex process that involves the coordination of the central nervous and muscular systems. A disruption to the either system results in the impairment of a person’s ability to walk. Impairments can be caused by neurological disorders such as stroke and physical conditions like amputation. There is not a standardized method to quantitatively assess the gait asymmetry of affected subjects. The purpose of this research is to understand the fundamental aspects of asymmetrical effects on the human body and improve rehabilitation techniques and devices. This research takes an interdisciplinary approach to address the limitations with current rehabilitation …

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, …

Disorder Levels Of C-Myb Transactivation Domain Regulate Its Binding Affinity To The Kix Domain Of Creb Binding Protein, Anusha Poosapati

USF Tampa Graduate Theses and Dissertations

Intrinsically disordered proteins (IDPs) do not form stable tertiary structures like their ordered partners. They exist as heterogeneous ensembles that fluctuate over a time scale. Intrinsically disordered regions and proteins are found across different phyla and exert crucial biological functions. They exhibit transient secondary structures in their free state and become folded upon binding to their protein partners via a mechanism called coupled folding and binding. Some IDPs form alpha helices when bound to their protein partners. We observed a set of cancer associated IDPs where the helical binding segments of IDPs are flanked by prolines on both the sides. …

Mechanism Elucidation And Inhibitor Discovery Against Serine And Metallo-Beta-Lactamases Involved In Bacterial Antibiotic Resistance, Orville A. Pemberton

USF Tampa Graduate Theses and Dissertations

The emergence and proliferation of Gram-negative bacteria expressing β-lactamases is a significant threat to human health. β-Lactamases are enzymes that degrade the β-lactam antibiotics (e.g., penicillins, cephalosporins, monobactams, and carbapenems) that we use to treat a diverse range of bacterial infections. Specifically, β-lactamases catalyze a hydrolysis reaction where the β-lactam ring common to all β-lactam antibiotics and responsible for their antibacterial activity, is opened, leaving an inactive drug. There are two groups of β-lactamases: serine enzymes that use an active site serine residue for β-lactam hydrolysis and metalloenzymes that use either one or two zinc ions for catalysis. Serine enzymes …

Bioleaching Potential Of Filamentous Fungi To Mobilize Lithium And Cobalt From Spent Rechargeable Li-Ion Batteries, Aldo Lobos

USF Tampa Graduate Theses and Dissertations

Demand for lithium (Li) and cobalt (Co) is on the rise, due in part to their increased use in rechargeable Li-ion batteries (RLIB). Current recycling processes that utilize chemical leaching efficiently recover in Li and Co from the cathode material in spent batteries; however, these processes are costly and emit hazardous waste into the environment. Therefore, a more sustainable process for recycling Li and Co is needed, and bioleaching may provide a solution. Fungal bioleaching has been shown in previous studies to effectively mobilize metals (Pb, Al, Mn, Cu, and Zn) from mine tailings, electronic scrap, and spent batteries with …

Validation Of The Electronic Kids Dietary Index (E-Kindex) Screening Tool For Early Identification Of Risk For Overweight/Obesity (Ow/Ob) In A Pediatric Population: Associations With Quality Of Life Perceptions, Patricia A. Hall

USF Tampa Graduate Theses and Dissertations

Despite a worsening obesity epidemic and despite the American Medical Association (AMA) declaring Obesity a disease (2013), few assessment tools exist that assist practitioners who are charged with identifying risk for development of OW/OB in children. The Center for Health Statistics (2017) reported a 40% rate in obesity in the adult population and 18.5% in children in the U.S. Successful weight loss maintenance after 1 to 2 years of non-invasive treatment is less than 1%, indicating obesity is nearly incurable, making prevention imperative. Assessing risk for OW/OB in children has proven difficult given the lack of validated tools. The purposes …

Perceptions Affecting Tree Valuation: An Analysis Of Recently Sold And Leased Properties In Tampa, Florida, Cody R. Winter

USF Tampa Graduate Theses and Dissertations

The urban forest is a structure that is fluid in both species composition and how it is integrated in our cities and suburban areas. Much like the fluidity in its structure, the urban forest provides ecosystem services and disservices in many forms. These services and disservices can often come in the form of temperature regulation, lower crime rates, and even higher property values. The latter, which is associated with the economic value of trees, is a part of the hedonic pricing literature which suggests that there is a disparity in the value associated with trees to house prices. With the …

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 …

Reef Fish Biodiversity In The Florida Keys National Marine Sanctuary, Megan E. Hepner

USF Tampa Graduate Theses and Dissertations

The biological diversity of reef-fish in the Florida Keys National Marine Sanctuary (FKNMS) from 1999 – 2016 was evaluated in terms of abundance, biomass, species richness, evenness, Shannon diversity, Simpson diversity, and functional diversity, using observations collected by multiple agencies and institutions under the Reef Visual Census (RVC) program. To compare the different diversity indices species richness, Shannon diversity, Simpson diversity, and functional diversity were converted into effective number of species. I examined the seven indices by no-take marine zones, in seven benthic habitat strata, and across the three-distinct geographic subregions in the Florida Keys domain (Upper, Middle, and Lower …

Dataset For: Toxicity And Mutagenicity Of The Gulf Of Mexico Waters During And After The Deepwater Horizon Oil Spill, July 2010-August 2013, Lauren Mcdaniel

C-IMAGE data

The dataset is representative of 20 research cruises spanning from July 2010 to August 2013 in the North and West Florida Shelf regions of the Gulf of Mexico. This dataset reports microtoxicity data from each site and is an extension and revision of C-IMAGE I dataset R1.x135.119:0005. The North Florida Self data also contains PAH measurements for three cruises (12/6/2010, 12/15/2011, 8/6/2013).

Thermodynamic And Kinetic Aspects Of Hen Egg White Lysozyme Amyloid Assembly, Tatiana Miti

USF Tampa Graduate Theses and Dissertations

Deposition of protein fibers with a characteristic cross-β sheet structure is the molecular marker associated with human disorders ranging from Alzheimer's disease to type II diabetes and spongiform encephalopathy. Given the large number of non-disease related proteins and peptides that have been shown to form amyloid fibrils in vitro, it has been suggested that amyloid fibril formation represents a generic protein phase transition. In the last two decades it has become clear that the same protein/peptide can assemble into distinct morphologically and structurally amyloid aggregates depending on the solution conditions. Moreover, recent studies have shown that the early stage, oligomeric …

Species-Specific Metabolism Of Naphthalene And Phenanthrene In 3 Species Of Marine Teleosts Exposed To Deepwater Horizon Crude Oil, Erin Pulster, Kevan Main, Dana Wetzel, Steven Murawski

C-IMAGE Publications

The 2 most abundant polycyclic aromatic hydrocarbons (PAHs) measured in Deepwater Horizon crude oil, naphthalene and phenanthrene, and their associated homologs have both been shown to be acutely toxic in fish. Although fish have a relatively high metabolic capacity for PAHs, hydroxylated PAH (OH-PAH) derivatives formed during the initial metabolic response can negatively impact the health of fish. Species-specific metabolism of naphthalene and phenanthrene was evaluated in 3 marine teleosts, red drum (Scianops ocellatus), Florida pompano (Trachinotus carolinus), and southern flounder (Paralichthys lethostigma). Fish were exposed to Deepwater Horizon crude oil by intraperitoneal injections at time 0 and 48 h, …

Response To Nitrogen And Salinity Conditions In Rhizophora Mangle Seedlings Varies By Site Of Origin, Kristen L. Langanke

USF Tampa Graduate Theses and Dissertations

Many coastal plant species thrive across a range of environmental conditions, often displaying dramatic phenotypic variation in response to environmental variation. We characterized the response of the critical foundation species Rhizophora mangle L. to full factorial combinations of salt and nitrogen (N). We used seedlings collected from five populations and measured traits related to salt tolerance and N amendment. The response to increasing salt included significant plasticity in succulence, leaf mass area (LMA), and root to shoot ratio (R:S). Seedlings also showed overall reduced maximum photosynthetic rate in response to N amendment, but this response depended on the level of …

Identifying New Treatment Options And Risk Factors For Type 2 Diabetes: The Potential Role Of Thymoquinone And Persistent Organic Pollutants, Shpetim Karandrea

USF Tampa Graduate Theses and Dissertations

Type 2 Diabetes Mellitus (T2DM) is a metabolic disorder characterized by chronic hyperglycemia, which develops as a consequence of peripheral insulin resistance and defective insulin secretion from pancreatic β-cells. A high calorie diet coupled with physical inactivity are known risk factors for the development of T2DM; however, these alone fail to account for the rapid rise of the disease. Recent attention has turned to the role of environmental pollutants in the development of metabolic diseases. PBDEs (polybrominated diphenyl ethers) are environmental pollutants that have been linked to the development of type 2 diabetes (T2D), however, the precise mechanisms are not …

Sun Glint Critical Angle Oil Detection, Shaojie Sun

C-IMAGE data

This dataset includes two MODIS L1B images and the generated sun glint reflectance (LGN) data after atmospheric correction. LGN was also modeled for the two images according to the sun/view geometry, oil and water fresnel reflection. This dataset introduced atmospheric correction and different oil fresnel reflection with water in the calculation of sun glint reflectance from MODIS imagery. By doing this, the calculated sun glint reflectance results are more accurate and the original concept of sun glint critical angle is refined.

Development Of A Marine Compatible Biological Assay For Mutagenic Compounds, Lauren Mcdaniel

C-IMAGE data

One of the primary negative effects of environmental oil exposure is the potential for mutagenic, or DNA damaging effects. This can lead to heritable genetic damage in higher organisms with long-term environmental impact. The biological effect of contamination is difficult to estimate on the basis of chemical profiles due to the complexity of environmental samples. Thus, biologically based assays give a closer approximation of the actual ecological impacts of contamination. To measure the mutagenic or DNA damaging potential of samples we currently utilize the Microscreen Assay, which is based upon a strain of Escherichia coli that is sensitive to mutagenic …