Digital Commons Network^™

The Use Of Proteomic Techniques To Study The Physiology And Virulence Of Staphylococcus Aureus, Frances Rivera

USF Tampa Graduate Theses and Dissertations

Staphylococcus aureus

is a bacterial pathogen that is believed to be the most common agent of human infectious disease, causing conditions ranging from common skin lesions to life-threatening illnesses. S. aureus has also shown a remarkable ability to develop resistance to antimicrobial treatment, making infections difficult to treat. In the post-genomic era, proteomic studies analyzing the protein complement of a genome in a particular organism at any given time, have gained real significance. This result is largely due to dynamic changes in protein expression profiles which can lead wide alterations in physiology and behavior. For proteomics, it is necessary to …

Design And Fabrication Of A Membrane Integrated Microfluidic Cell Culture Device Suitable For High-Resolution Imaging, Alla A. Epshteyn

USF Tampa Graduate Theses and Dissertations

Malaria remains a serious concern for people living and traveling to warm climates in Africa, Asia, and some parts of America. Understanding the mechanism of the malaria parasite in the liver phase could lead to important discoveries for preventative and treatment therapeutics before the disease develops into the blood stage. While in vitro liver cell culture models have been explored, a device that mimics the liver cell architecture with the capability of high-resolution imaging has never been created. In this research, a cell culture microfluidic device was designed and fabricated with a membrane integrated design to mimic the architecture of …

Investigating The Mode Of Action Of A Novel N-Sec-Butylthiolated Beta-Lactam Against Staphylococcus Aureus, Katherine Rose Prosen

USF Tampa Graduate Theses and Dissertations

N-sec

-butylthioloated β-lactam (NsβL) is a novel beta-lactam antimicrobial with a mechanism of action proposed to inhibit 3-oxoacyl-acyl carrier protein synthase (ACP) III (FabH), resulting in the inhibition of fatty acid synthesis. It has been suggested that NsβL inhibits FabH indirectly by inactivating coenzyme-A (CoA). CoA is an essential cofactor for numerous proteins involved in glycolysis, the citric acid cycle (TCA), and pyruvate metabolism, in addition to fatty acid biosynthesis. This study aimed to determine the effects of NsβL on a diverse array of laboratory and clinical Staphylococcus aureus isolates by analyzing the mode of resistance in spontaneous and adaptive …

Phenotypic And Genotypic Analysis Of In Vitro Selected Artemisinin Resistant Plasmodium Falciparum, Matthew Scott Tucker

USF Tampa Graduate Theses and Dissertations

Artemisinin and its derivatives provide faster clearance of parasitemia than any other antimalarial drugs and these drugs are part of frontline combination therapies in areas where drug-resistant Plasmodium falciparum exists. Clinical resistance to artemisinins is emerging on the Thailand-Cambodia border, making it imperative to investigate mechanisms of artemisinin resistance. Previous work in our laboratory showed ring-stage parasites enter a dormant state after exposure to artemisinin. We hypothesize that this period of dormancy is directly related to recrudescence and prolonged parasite clearance times in patients, and possibly resistance. The target of artemisinin is currently unknown, and potential resistance mechanisms are not …

Gender And Cocaine Use Influence The Expression Of Urinary Markers Of Inflammation And Oxidative Stress, Marie Meagher Bourgeois

USF Tampa Graduate Theses and Dissertations

The purpose of this study was to investigate whether or not gender differences may be present in the expression of a number of urinary proteins which may serve as markers of inflammation and oxidative stress. Males and females have different patterns of illness and different life spans, suggesting basic biological traits exert significant control on the incidence of rhabdomyolysis, renal failure, atherosclerosis, myocardial ischemia, myocardial contraction band formation, autoimmune disorders and general inflammatory diseases. Men are at greater risk for cardiovascular disease; however women, particularly elderly women, have higher fatality rates due to heart failure. Renal diseases progress far more …

A Stella Model For Integrated Algal Biofuel Production And Wastewater Treatment, Ivy Cormier

USF Tampa Graduate Theses and Dissertations

Based on a municipal wastewater treatment plant (WWTP) in Tampa, FL, a dynamic multiple-systems model was developed on the STELLA software platform to explore algae biomass production in wastewater by incorporating two photobioreactors into the WWTP‟s treatment train. Using a mass balance approach, the model examined the synergy through algal growth and substrate removal kinetics, as well as macroeconomic-level analyses of algal biomass conversion to biodiesel, biogas, or fertilizer. A sensitivity analysis showed that biomass production is highly dependent on Monod variables and harvesting regime, and profitability was sensitive to processing costs, market prices of products, and energy environment. The …

A Contingent Valuation Of Tampa’S Urban Forest Resource, Alec Foster

USF Tampa Graduate Theses and Dissertations

Urban forests provide environmental, social, and economic benefits to urban residents. These benefits are often overlooked when making spatial and financial distributive decisions in urban areas. The City of Tampa has demonstrated interest in its urban forest resource and estimated its extent and some of the benefits provided. Estimating economic values for benefits that have not been quantified can help to ensure that resources are distributed more efficiently. Five methods to estimate urban forest benefits in the City of Tampa are reviewed, with contingent valuation being the method chosen out of this review process. A mailed, dichotomous choice contingent valuation …

Molecular Mechanism Of Agc Kinases In Human Malignant, Shaokun Shu

USF Tampa Graduate Theses and Dissertations

The maintenance of normal cell function and tissue homeostasis is dependent on the precise regulation of multiple signaling pathways that control cellular decisions to either proliferate, differentiate, arrest cell growth, or initiate programmed cell death (apoptosis). Cancer arises when clones of mutated cells escape this balance and proliferate inappropriately without compensatory apoptosis. Deregulated cell growth occurs as a result of perturbed signal transduction that modulates or alters cellular behavior or function to keep the critical balance between the rate of cell-cycle progression (cell division) and cell growth (cell mass) on one hand, and programmed cell death (apoptosis, autophagy) on the …

Molecular Detection Of The Toxic Marine Diatom Pseudo-Nitzschia Multiseries, Jennifer A. Delaney

USF Tampa Graduate Theses and Dissertations

The marine diatom genus Pseudo-nitzschia includes species that produce domoic acid, a neurotoxin responsible for illness and mortality in both humans and marine wildlife. Because of the expertise and time required for the microscopic discrimination of species, molecular methods that monitor environmental concentrations of Pseudo-nitzschia provide a rapid alternative for the early detection of blooms and prediction of toxin accumulation. We have developed a nucleic acid sequence-based amplification with internal control RNA (IC-NASBA) assay and a quantitative reverse transcription PCR (qRT-PCR) assay for the detection of the toxic species P. multiseries targeting the ribulose- 1,5-biphosphate carboxylase/oxygenase small subunit (rbcS) gene. …

The Biocomplexity Of Benthic Communities Associated With A Shallow-Water Hydrothermal System In Papua New Guinea, David J. Karlen

USF Tampa Graduate Theses and Dissertations

Shallow-water hydrothermal vents occur world-wide in regions of volcanic activity. The vents located at Tutum Bay, Ambitle Island, Papua New Guinea are unique in that the vent fluids and surrounding sediments contain some of the highest concentrations of arsenic in a natural system. This study addresses the effects of the vent system on the benthic communities, focusing on the eukaryotes, macrofauna, meiofauna and bacteria.

Samples were collected in November 2003 and May/June 2005. Analysis of the 2003 macrofaunal samples indicated that pH, rather than arsenic was influencing the benthic community, and that the hydrothermal influence occurred at a greater distance …

The Virtual Hip: An Anatomically Accurate Finite Element Model Based On The Visible Human Dataset, Jonathan M. Ford

USF Tampa Graduate Theses and Dissertations

The purpose of this study is to determine if element decimation of a 3-D anatomical model affects the results of Finite Element Analysis (FEA). FEA has been increasingly applied to the biological and medical sciences. In order for an anatomical model to successfully run in FEA, the 3-D model’s complex geometry must be simplified, resulting in a loss of anatomical detail. The process of decimation reduces the number of elements within the structure and creates a simpler approximation of the model. Using the National Library of Medicine’s Visible Human Male dataset, a virtual 3-D representation of several structures of the …

The Biogeochemistry Of Submerged Coastal Karst Features In West Central Florida, Keith Michael Garman

USF Tampa Graduate Theses and Dissertations

West Central Florida is a complex karst environment with numerous sinkholes, springs, and submerged cave systems. Many of these karst features are anchialine, located within the subterranean estuary where freshwater and saltwater mix. Water quality data and/or fauna data were obtained from twenty-one karst features and their associated cave systems. The anchialine karst environment of the study area has a wide range of habitats with measured salinities ranging from freshwater at <0.2 ppt to sulfidic, hypersaline water at 38.5 ppt and measured pH readings ranging from 6.39 in water impacted by sulfur oxidizing bacteria to 10.3 in an isolated room of a cave. Stygobitic crustaceans were identified in conduits extending beneath the Gulf of Mexico supporting the hypotheses that freshwater crustaceans could survive higher sea levels in freshwater conduits beneath saltwater. The fauna associated with the anchialine cave systems included Sabellidae and Polychaeta worms, hydroids, cnidarians and hydrobiid snails. Jewfish Sink, like other anaerobic marine basins that were submarine springs, has four zones: oxic zone, transition zone, upper anoxic zone and anoxic bottom water. The upper zones have seasonal water quality variations from winter cooling and sinking of surface water and changes in the microbial communities. Activity of sulfate reducing bacteria is carbon limited in the anoxic zones, where sulfate reduction is the major metabolic process, and primary production is phosphate limited in the oxic zones. Organic input from the Gulf of Mexico drives the bacterial anaerobic ecosystem, resulting in a “sulfide pump”, in which sulfide percolates upward removing oxygen from the overlying sediment.

Design Of A New Suturing And Knot Tying Device For Laparoscopic Surgery, Sinan Onal

USF Tampa Graduate Theses and Dissertations

Minimally invasive or laparoscopic surgery has completely changed the focus of surgery becoming an alternative to various types of open surgery. Minimally invasive surgery avoids invasive open surgery as the operation is performed through one or more small incisions in the abdomen and using a small camera called laparoscope. Through these incisions, surgeons insert specialized surgical instruments to perform the operation resulting in less postoperative pain, shorter hospital stay, and faster recovery. However, the main problems during minimally-invasive surgery are the limited space for operating instruments and the reduced visibility and range of motion inside the patient’s body. During minimally-invasive …

Design And Combinatorial Synthesis Approach Of Non-Peptidic Trimeric Small Molecules Mimicking I, I + 4(3), I + 7 Positions Of Alpha-Helices, Mingzhou Zhou

USF Tampa Graduate Theses and Dissertations

Protein-protein interactions are key to several biological processes that facilitate signal transduction and many other processes. These interactions are involved in pathways that are critical to many human diseases. Targeting specific protein-protein interactions is a challenging goal because protein-protein interactions are predominately through hydrophobic interactions. Antagonists of the protein-protein interactions need to be perfectly fit into the binding pockets to ensure the activity. The -helical domain of the proteins behaves as the recognition motifs for numerous protein-protein, and protein-nucleic acid interactions. Research has shown that pathways of many diseases contain protein-protein interactions involving -helical domains, e.g. neurological disorders, bacterial infections, …

Core Promoter Function In Brugia Malayi, Michelle Bailey

USF Tampa Graduate Theses and Dissertations

Previous studies have indicated that the promoters of the human filarial parasite Brugia malayi are unusual in that they do not exhibit the CAAT or TATAA sequences usually found in the core domains of promoters of most eukaryotic organisms. Analysis of the promoters of the ribosomal proteins showed that the region flanking the splice leader (SL) addition site plays an important role in transcription and may function as the core promoter domain in B. malayi. To test the hypothesis that the SL addition domain is the most important essential region of the ribosomal protein promoters, the SL addition site of …

Discrimination Of Human And Non-Human Sources Of Pollution In Gulf Of Mexico Waters By Microbial Source Tracking Methods And The Investigation Of The Influence Of Environmental Factors On Escherichia Coli Survival, Asja Korajkic

USF Tampa Graduate Theses and Dissertations

Water quality worldwide is assessed by enumeration of fecal indicator bacteria (FIB) (fecal coliforms, Escherichia coli, and enterococci) intended to act as surrogates for human enteric pathogens. In environmental waters, this predictive relationship is confounded by many possible sources of FIB with varying implications for human health. Many physico-chemical and biological factors influence the fate of enteric pathogens and FIB in aquatic habitats, but are poorly understood, thus limiting our understanding of the usefulness of FIB as fecal pollution indicators.

These studies explored the field application of a “toolbox” approach to microbial source tracking (MST) intended to discriminate between human …

Evolution Of The Hammerhead Cephalofoil: Shape Change, Space Utilization, And Feeding Biomechanics In Hammerhead Sharks (Sphyrnidae), Kyle Reid Mara

USF Tampa Graduate Theses and Dissertations

The relationship between form and function is often used to elucidate the biological role of a structure. Hammerhead sharks offer a unique opportunity to study form and function through phylogeny. Because sphyrnid sharks display a range of cranial morphologies this group can be used to address questions about the evolution of cranial design and investigate the effects of changes in head morphology on feeding structures and bite force. Geometric morphometrics, volumetric analyses, morphological dissections, and phylogenetic analyses of the cephalofoil were used to gain insight into changes in cranial design through evolutionary history. External morphometrics and internal volumetric analyses indicated …

Preservice Teachers’ Developing Understandings About Culturally Responsive Teaching In A Field-Based Writing Methods Course, Susan V. Bennett

USF Tampa Graduate Theses and Dissertations

I investigated eight preservice teachers’ understandings about culturally responsive pedagogy as they participated in a writing methods course in which they tutored children from different ethnic, socioeconomic, cultural, and linguistic backgrounds in an afterschool program at a local community center. I also investigated how these preservice teachers demonstrated culturally responsive teaching within the writing curriculum. I recognized the need for research relevant to my own personal beliefs and how to strive for more equitable schools. I want to contribute further to the understandings and insights related to culturally responsive pedagogy. According to the literature, it appears teachers remain unprepared to …

Geographic Variation In Life History Tactics, Adaptive Growth Rates, And Habitatspecific Adaptations In Phylogenetically Similar Species: The Eastern Fence Lizard, Sceloporus Undulatus Undulatus, And The Florida Scrub Lizard, Sceloporus Woodi, Travis R. Robbins

USF Tampa Graduate Theses and Dissertations

To understand the evolutionary and ecological significance of geographic variation in life

history traits, we must understand whether the patterns are induced through plastic or adaptive

responses. The Eastern Fence Lizard,

Sceloporus undulatus

, exhibits countergradient variation

(larger body sizes, et cetera, in northern, cooler environments; presumed adaptive) in life history

traits across its large geographic range. However, cogradient variation (the expected result from

a plastic response, although not necessarily inconsistent with adaptation) has been suggested as

a null hypothesis, especially on fine geographic scales because of relatively small environmental

changes. Here we focus on life history variation on a …

“Some Marvelous Thing”: Leonardo, Caterina, And The Madonna Of The Rocks, Michael Thomas Jahosky

USF Tampa Graduate Theses and Dissertations

Leonardo's Virgin of the Rocks (or Madonna of the Rocks, c.1486) is a masterpiece. Scholars have been unclear, however, about the unconventional cave setting and where Leonardo's inspiration came from. The Song of Songs mentions a beautiful bride being invited to come "into the wall of rocks," and the apocryphal Gospel of James (written around 150 A.D.) tells the story of Jesus being born in a cave outside of Bethlehem. But Leonardo's own personal cave experience in 1481 spurred his desire to find literature that placed Jesus' birth in a cave, or a "wall of rocks." This …

Characterization Of Unidentified Viruses From Florida, Jessie L. Dyer

USF Tampa Graduate Theses and Dissertations

Public Health and clinical laboratories occasionally obtain viral isolates that cannot be typed by routine methods. Therefore, the sequence-independent, single primer amplification (SISPA) technique was adapted to rapidly identify and characterize viral isolates of unknown etiology. A panel of known (West Nile virus and St. Louis encephalitis virus) and unknown viral isolates (environmental samples collected in Florida) were used to develop and refine the SISPA technique. Selectivity for viral genomic sequences was obtained through enriching viral particles by centrifugation, removal of cellular debris by filtration and removal of host genomic material by benzonase application. The SISPA method successfully amplified the …

Fluorescence Molecular Tomography: A New Volume Reconstruction Method, Stephen Joseph Shamp

USF Tampa Graduate Theses and Dissertations

Medical imaging is critical for the detection and diagnosis of disease, guided biopsies, assessment of therapies, and administration of treatment. While computerized tomography (CT), magnetic resonance imaging (MRI), positron emission tomography (PET), and ultra-sound (US) are the more familiar modalities, interest in yet other modalities continues to grow. Among the motivations are reduction of cost, avoidance of ionizing radiation, and the search for new information, including biochemical and molecular processes. Fluorescence Molecular Tomography (FMT) is one such emerging technique and, like other techniques, has its advantages and limitations. FMT can reconstruct the distribution of fluorescent molecules in vivo using near-infrared …

The Novel Use Of Recombinant Granulocyte-Macrophage Colony-Stimulating Factor (Gm-Csf) To Reverse Cerebral Amyloidosis And Cognitive Impairment In Alzheimer’S Disease Mouse Models: Insights From The Investigation Of Rheumatoid Arthritis As A Negative Risk Factor For Alzheimer’S Disease, Timothy David Boyd

USF Tampa Graduate Theses and Dissertations

For many years, it has been known that Rheumatoid arthritis (RA) is a negative risk factor for the development of Alzheimer’s disease (AD). It has been commonly assumed that RA patients’ usage of non-steroidal anti-inflammatory drugs (NSAIDs) have helped prevent the onset and progression of AD pathogenesis. Furthermore, experiments in animal models of Alzheimer’s disease have looked to inhibit inflammation, and have demonstrated some efficacy against AD-like pathology in these models. Thus many NSAID clinical trials have been performed over the years, but all have proven unsuccessful in AD patients. This suggests that intrinsic factors within RA pathogenesis itself may …

Teaching Social Skills To Children With Asperger’S And High Functioning Autism: An Evaluation Of Video Self-Modeling And Behavior Skills Training, Krystal M. Mcfee

USF Tampa Graduate Theses and Dissertations

The purpose of this study was to evaluate the effects of video self-modeling and behavior skills training to teach social skills to children with Asperger’s and high functioning autism. The targeted social skills were social initiations and social responses. The video self-modeling alone condition was implemented first using a video feedforward approach. A behavior skills training (BST) procedure was implemented following the video self-modeling alone condition for each participant. BST consisted of instructions, modeling, rehearsal, and feedback. The frequency of each target behavior was scored from videotapes using 10-second frequency within interval recording. After the video self-modeling was introduced, a …

Microexpression Spotting In Video Using Optical Strain, Sridhar Godavarthy

USF Tampa Graduate Theses and Dissertations

Microexpression detection plays a vital role in applications such as lie detection and psychological consultations. Current research is progressing in the direction of automating microexpression recognition by aiming at classifying the microexpressions in terms of FACS Action Units. Although high detection rates are being achieved, the datasets used for evaluation of these systems are highly restricted. They are limited in size - usually still pictures or extremely short videos; motion constrained; containing only a single microexpression and do not contain negative cases where microexpressions are absent. Only a few of these systems run in real time and even fewer have …

The Accidental Practitioner: Principles Of Rational Emotive Behavior Therapy In The Works Of Kurt Vonnegut, Joseph J. Ward

USF Tampa Graduate Theses and Dissertations

Just as psychology and philosophy have influenced the field of literary studies, literature provides insight about the theories and practices of its sister disciplines. The purpose of this thesis is to demonstrate how literary works of Kurt Vonnegut illuminate principles of the influential branch of psychotherapy known as Rational Emotive Behavior Therapy (REBT).

This thesis traces the similar philosophies and shared beliefs of Vonnegut and REBT's founder, Albert Ellis, and details how Ellis's REBT is illustrated in selected works of Vonnegut, specifically, Slaughterhouse-Five, Breakfast of Champions, Galapagos, and Timequake. The thesis concludes by suggesting that Vonnegut's …

Malaria In Prehistoric Sardinia (Italy): An Examination Of Skeletal Remains From The Middle Bronze Age, Teddi J. Setzer

USF Tampa Graduate Theses and Dissertations

Sardinia was an island with a history of a malarious environment until eradication efforts were conducted from 1946 to 1950. While historic documents suggest the disease was introduced from North Africa around 500 BC, no study has been conducted to test for the presence of malaria in prehistoric native populations, such as the Nuragic people of the Bronze Age. However, it has been suggested that aspects of the Nuragic culture, for example the stone structures found throughout the island, are adaptations to a malarious environment. The purpose of this dissertation is to test the hypothesis that malaria was present in …

Bastards, Brains, Boobs And Performance: A Retrospective Account, Joanna Bartell

USF Tampa Graduate Theses and Dissertations

The two essays that comprise this thesis use personal narrative to discuss various aspects of illness, resistance and the body. The first essay uses performance theory to explore the social structures, mandates and restrictions concerning illness. I use the cancer experience to explore the co-creation of self, identity, and modes of being between "performer" and "audience." "Performer," in this case, is the "breast cancer patient," and the "audience" is comprised of the "social others.” The second essay explores cyborgization of the body, its painful effects, and associated social and moral values. It also discusses how we create theory and understanding …

An Ecology Of Performance: Gregory Bateson's Cybernetic Performance, Daniel Matthew Blaeuer

USF Tampa Graduate Theses and Dissertations

This dissertation is a case study of the public performances of Gregory Bateson at The Esalen Institute. The case study is a reconsideration of the work of Gregory Bateson from the perspective of performance studies. The author brings together performativity, cybernetics, and the sacred to argue that Gregory Bateson, in his public performances, was striving for grace in encounters with others. The author has conducted archival research into Bateson’s presentations and has spoken with several close to Bateson to get a sense of how his process of public presentation paralleled his ideas—a process of continually working through ideas in conversation …

An Integrated Building Water Management Model For Green Building, Caryssa Joustra

USF Tampa Graduate Theses and Dissertations

The U.S. Green Building Council (USGBC) is the developer of the Leadership in Energy and Environmental Design (LEED™) green building scoring system. On first inspection of LEED points, few address water efficiency. However, water management encompasses other points beyond the Water Efficiency (WE) category. In general, the industry is apt to take a somewhat compartmentalized approach to water management. The use of alternative water sources or the reuse of wastewater significantly complicates the water budget picture. A total water management systems approach, taking into consideration water from various sources, both inside and outside the building, should be implemented in order …