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Combination Of The Computational Methods: Molecular Dynamics, Homology Modeling And Docking To Design Novel Inhibitors And Study Structural Changes In Target Proteins For Current Diseases, Katherine Cristina Parra

USF Tampa Graduate Theses and Dissertations

In this thesis, molecular dynamics simulations, molecular docking, and homology modeling methods have been used in combination to design possible inhibitors as well as to study the structural changes and function of target proteins related to diseases that today are in the spotlight of drug discovery. The inwardly rectifying potassium (Kir) channels constitute the first target in this study; they are involved in cardiac problems. On the other hand, tensin, a promising target in cancer research, is the second target studied here.

The first chapter includes a brief update on computational methods and the current proposal of the combination of …

Regulatory Roles Of Facit Collagens Xii And Xiv In Cornea Stromal And Endothelial Development And Function, Chinda Hemmavanh

USF Tampa Graduate Theses and Dissertations

Purpose:

Corneal transparency depends upon the precise organization of corneal stromal extracellular matrix and corneal endothelial function. Stromal structure and extracellular matrix organization is responsible for proper refraction of light into the eye. The corneal endothelium is responsible for pumping excess fluid out of the cornea, effectively maintaining corneal hydration and thickness. Corneal transplantation is the current form of treatment for corneal endothelial and stromal dystrophies. The mechanisms controlling stromal collagen fibril packing and organization into orthogonal layers as well as maturation of the endothelium into a fully functioning cellular layer are unknown. Collagens XII and XIV, fibril associated collagens …

Host-Parasite Interactions In An Invasive Songbird, Courtney A.C. Coon

USF Tampa Graduate Theses and Dissertations

Introduced species are the greatest threat to biodiversity after habitat loss. Understanding the processes that permit organisms to become successful invaders may provide opportunities to prevent or limit their dispersal and establishment and thereby alleviate some of their harmful effects. The goal of my dissertation research has been to investigate whether invasive species have distinctive interactions with parasites, and some of the mechanisms that may underlie that variation. I used one of the world's most successful vertebrate invaders as a case study: the house sparrow (Passer domesticus; Introduction).

Previous research in the house sparrow suggested that loss of …

Balanced Artistry: Describing And Explaining Expert Teacher Practice As Adaptive Expertise, Nina Graham

USF Tampa Graduate Theses and Dissertations

This work was possible through the support of my personal and professional families. Personally, my husband Brad was my continual encourager through each phase of this journey. This accomplishment is as much his as mine. Also, through this process I feel I have matured at the hands of the Lord through His careful, peaceful leading within the many nuanced steps of completing the doctoral program. Professionally, the ladies forming my doctoral committee have been more than advisors, but mentors. Their thoughtful counsel helped me feel capable throughout the many phases of becoming a researcher and scholar, yet they offered insight …

Subversive Beauty - Victorian Bodies Of Expression, Lisa Michelle Hoffman-Reyes

USF Tampa Graduate Theses and Dissertations

Abstract

My dissertation seeks to bring aesthetics into conversation with the epistemological concerns of three Victorian texts, in response to the prevalence of beautiful feminine faces and bodies in Victorian texts, their presence amplified through the use of copious description. I examines the ways that Thomas Hardy, Oscar Wilde, and Robert Browning complicate traditional contemporary assumptions regarding behaviors and moralities through their constructions of feminine beauty. These writers challenge and dispute a variety of Victorian social norms imposed upon both men and women, most notably the mandate to adhere to prescribed behaviors that codify in order to regulate gender normativity. …

An Investigation Into The Habitat, Behavior And Opportunistic Feeding Strategies Of The Protected Goliath Grouper (Epinephelus Itajara), Angela Collins

USF Tampa Graduate Theses and Dissertations

Groupers (Epinephelidae: Epinephelinae) are apex predators within many reef communities worldwide. Grouper landings contribute significantly to global fisheries, and many populations are suffering from unsustainable levels of exploitation. The large size, site specificity and catchability of most groupers increase susceptibility to fishing pressure, and a large number of grouper species throughout the world are currently overfished. Multiple species are listed as endangered or threatened, and many have suffered local extirpations across their range. Removal of these upper level predators can significantly alter community structure and result in second order effects that may have critical ecological implications. The economic and ecological …

I Did That Wrong And It Sounded Good: An Ethnographic Study Of Vernacular Music Making In Higher Education, Victor Ezquerra

USF Tampa Graduate Theses and Dissertations

The purpose of this ethnographic study was to examine vernacular music making in higher education. The participants, undergraduate music education majors (N=23 for Fall, N=10 for Spring), were investigated throughout the course of the 2012-2013 academic year. A constructivist philosophical framework was applied and data were collected using several methodologies including participant observation, journals, interviews, and audiovisual and multimedia methods. Results showed that students were able to successfully learn, create, and share music in a vernacular manner. Participants took a pragmatic approach to making music. Furthermore, students engaged several aspects of music making they had not encountered in traditional music …

Photocatalysis And Grazing-Ion Beam Surface Modifications Of Planar Tio2 Model Systems, Timothy Luttrell

USF Tampa Graduate Theses and Dissertations

This dissertation is related to the understanding of catalytic reactions of metal oxides. For several decades, the surfaces and bulk of materials have been probed to determine additional properties that relate to photocatalytic applications. This investigation furthers these efforts by the (a) modification of a metal oxide surface to isolate known influences of chemical properties and (b) proposing and utilizing a novel methodology for attribution of photocatalytic activity to a discernable influence. For the first effort, by effectively utilizing a known technique for a new application on a metal oxide, such isolations can be made despite unfavorable states. For the …

Solvent Dependent Molecular Mechanics: A Case Study Using Type I Collagen, Heather Harper

USF Tampa Graduate Theses and Dissertations

Being the most abundant protein in the body, by mass, type I collagen provides the building blocks for tissues such as bone, extra-cellular matrix, tendons, cornea, etc[1-3]. The ability of a single protein to create structures with such various mechanical properties is not fully understood. Before one can engineer and assemble a complex tissue, such as cornea, the mechanisms underlying the formation and assembly, mechanical properties, and structure must be investigated and quantified. The work presented herein contains an extensive study of Type I collagen from the molecular to the tissue level.

The engineering of collagenous tissues that mimic the …

Improving Spectrophotometric Carbon System Measurements, Mark Patsavas

USF Tampa Graduate Theses and Dissertations

This work provides improved procedures for spectrophotometric carbon system measurements. Indicator dyes used for routine spectrophotometric pH measurements in seawater suffer from impurity issues, which introduce vendor-specific systematic errors in pH determinations. The magnitude of these errors for several vendors was investigated for meta Cresol Purple (mCP) and Cresol Red (CR). Flash chromatography procedures were developed to obtain purified mCP and CR on a bulk scale in order to supply the oceanographic research community with the indicators. Easy access to the purified indicators ensures global intercomparability of spectrophotometric pH determinations.

Internal consistency of marine inorganic carbon system measurements was studied …

Design & Synthesis Of Peptidomimetics Adopting Secondary Structures For Inhibition Of P53/Mdm2 Protein-Protein Interaction And Multiple Myeloma Cell Adhesion, Hyun Joo Kil

USF Tampa Graduate Theses and Dissertations

The protein-protein interactions (PPIs) occur when two or more proteins are bound together. Also, this protein-protein interactions (PPIs) cause the various biological processes in the body. Due to this reason, abilities of controlling or inhibiting PPIs can give us promising advantages like (1) better understanding of biological systems, (2) development of new diagnostic approaches for health or disease, and (3) establishment of novel molecular therapeutics. Many proteins adopt the secondary structures, where most of protein-protein interactions take place. -Helices and -sheets are the prevalent secondary conformations, but there are extended secondary structures such as -hairpins, -turns, 310 helix, and so …

Pathogenic Mechanisms And Signaling Pathways In Plasmodium Falciparum, Jennifer L. Sedillo

USF Tampa Graduate Theses and Dissertations

Plasmodium falciparum is a human intracellular parasite that is the causative agent of a deadly form of malaria. This species alone is responsible for 200 million cases of malaria annually resulting in over 1 million deaths worldwide. The excessive mortality due to P. falciparum infection is due to its ability to cause severe pathogenesis through hyperparasitemia and cytoadherence defined as the ability of infected red blood cells to adhere to host vasculature. Cytoadherence is mediated through the export of parasite proteins to the surface of the infected red blood cell (RBC). Exported proteins have been identified but the pathway for …

Taken For Granted Or Taken With Gratitude? An Examination Of The Differential Effects Of Donations Of Time And Money On Consumers' Evaluation Of Corporate Philanthropy, Ryan Langan

USF Tampa Graduate Theses and Dissertations

This dissertation examines the potential for two forms of corporate philanthropy, donations of time and money, to have differential effects on consumers' response to corporate giving. Drawing upon indirect-reciprocity theory I show that corporate donations of time compared to money elicit a greater desire to reciprocate on the part of consumers. It is found that the influence of corporate donations on consumers' desire to reciprocate occurs through serial mediation, whereby donations of time are perceived as being more effortful than monetary donations. This in turn leads to more altruistic motive attributions, and ultimately greater admiration towards the firm and a …

Overwintering And Early Season Amplification Of Eastern Equine Encephalitis Virus In The Southeastern United States, Andrea Bingham

USF Tampa Graduate Theses and Dissertations

Eastern equine encephalitis virus (EEEV) is a highly pathogenic arbovirus that causes severe disease, with a mortality rate of approximately 30-35% in humans and 80-90% in horses. Studies dating back to the 1930's have identified many of the epidemiological and ecological aspects of the virus. However, there are several aspects of EEEV's transmission cycle that remain unclear. In the northeastern states, transmission is seasonal, peaking in the late summer months, while in Florida there is year-round transmission of EEEV. Recent phylogenetic studies have also suggested that Florida may serve as a reservoir for EEEV; the virus may periodically be introduced …

Obesity And Dining Out: An Exploration Of Dietary Trends In Urban Malaysia, Sylvia S. Lim

USF Tampa Graduate Theses and Dissertations

Economic growth has spurred rapid urbanization in Malaysia and triggered changes in diet, lifestyle, and disease trends. National studies show that a third of Malaysia's population is overweight/obese while household expenditures on dining out grow. In metropolitan Kuala Lumpur (KL), residents navigate concepts of nutrition, body weight, and health as they dine out. Using the biocultural framework, this study examined links between body weight, diet, income, street food consumption, and nutritional knowledge through the perspectives of consumers and vendors. Altogether, 77 participants were recruited for this three-phase research. In the first phase, a survey was administered to 60 participants recruited …

Synthesis And Evaluation Of 3-Aryl-4(1h)-Quinolones As Orally Active Antimalarials: Overcoming Challenges In Solubility, Metabolism, And Bioavailability, Andrii Monastyrskyi

USF Tampa Graduate Theses and Dissertations

Infectious diseases are the second leading cause of deaths in the world with malaria being responsible for approximately the same amount of deaths as cancer in 2012. Despite the success in malaria prevention and control measures decreasing the disease mortality rate by 45% since 2000, the development of single-dose therapeutics with radical cure potential is required to completely eradicate this deadly disease. Targeting multiple stages of the malaria parasite is becoming a primary requirement for new candidates in antimalarial drug discovery and development. Recently, 4(1H)-pyridone, 4(1H)-quinolone, 1,2,3,4-tetrahydroacridone, and phenoxyethoxy-4(1H)-quinolone chemotypes have been shown to be antimalarials with blood stage activity, …

Molecular Evidence For Vector Implication Of Onchocerca Lupi In Los Angeles County, Ca, Shanna June Bolcen

USF Tampa Graduate Theses and Dissertations

Onchocerca is a genus of roundworm most commonly associated with the human infection onchocerciasis, or river blindness. While typically a zoonotic infection of ungulate populations, canine cases (Onchocerca lupi) have been identified in the United States and Greece. In 2012, Los Angeles County, Veterinary Public Health Program identified 3 cases of Onchocerca spp. infections in domestic canines. Samples from the ensuing blackfly collections were sent to the Global Health Infectious Disease Research Unnasch Laboratory for parasite isolation and vector species identification. Species-specific primers were designed and optimized for O. lupi using a non- specific cytochrome oxidase (COI) gene target (689bp) …

Water Availability As The Driving Factor Of Growth And Physiological Function Of Co-Occurring Scrub Species In Central Florida, Tammy Foster

USF Tampa Graduate Theses and Dissertations

Florida scrub is a xeromorphic upland shrub community dominated by evergreen oaks that resprout after fire, occurring on moderately to excessively well-drained nutrient-poor sand. Scrub is home to several threatened and endangered animal species (e.g., Florida scrub-jay, gopher tortoise, and indigo snake) and rare and endemic plants. Urban development and agriculture has greatly reduced and fragmented scrub habitat, and because of this Florida scrub is considered one of the most endangered ecosystems in the United States. Climate change is a further threat to Florida scrub. Under a warmer and drier climate, scrub species will be exposed to more frequent and …

Karenia Brevis Harmful Algal Blooms: Their Role In Structuring The Organismal Community On The West Florida Shelf, Alisha Marie Gray

USF Tampa Graduate Theses and Dissertations

Karenia brevis dinoflagellate blooms off the west coast of Florida can create devastating effects on marine communities when they release a neurotoxin known as a brevetoxin. These blooms, informally referred to as red tides, can cause massive fish kills, necessitate closures of shellfish fisheries, and can even leave lingering toxins that impact shelf communities long after the bloom has dissipated. As a result, much effort has been put into studying K. brevis bloom initiation and dynamics. However, how K. brevis blooms impact Florida's fisheries is not fully understood because the relationship between K. brevis cell counts and fish mortality is …

The Black Experience In The United States: An Examination Of Lynching And Segregation As Instruments Of Genocide, Brandy Marie Langley

USF Tampa Graduate Theses and Dissertations

Abstract

This thesis analyzes lynching and segregation in the American South between the years 1877 and 1951. It argues that these crimes of physical and social violence constitute genocide against black Americans, according to the definitions of genocide proposed by Raphael Lemkin and then the later legal definition adopted by the United Nations. American law and prevailing white American social beliefs sanctioned these crimes. Lynching and segregation were used as tools of persecution intended to keep black people in their designated places in a racial hierarchy in the United States at this time period. These crimes were two of many …

Sigma Factor N: A Novel Regulator Of Acid Resistance And Locus Of Enterocyte Effacement In Escherichia Coli O157:H7, Avishek Mitra

USF Tampa Graduate Theses and Dissertations

In enterohemorrhagic E. coli (EHEC) sigma factor N (σ^N) regulates glutamate-dependent acid resistance (GDAR) and the locus of enterocyte effacement (LEE), discrete genetic systems required for transmission and virulence of this intestinal pathogen. Regulation of these systems requires nitrogen regulatory protein C, NtrC, and is a consequence of NtrC/σ^N-dependent reduction in the activity of sigma factor S (σ^S). This study elucidates pathway components and stimuli for σ^N-directed regulation of GDAR and the LEE in EHEC. Deletion of fliZ, the product of which reduces σ^S activity, phenocopies rpoN (σ^N) …

Elective Early Term Delivery And Adverse Infant Outcomes In A Population-Based Multiethnic Cohort, Jason Lee Salemi

USF Tampa Graduate Theses and Dissertations

The length of human pregnancy, arguably the most natural of physiological processes, is undergoing subtle but consequential modification in order to adapt to modern societal demands. The gestational age distribution of births in the United States has been shifting to lower gestational ages over the past two decades, parallel to a concomitant rise in obstetrical intervention in pregnancy. The result has been an increase in elective deliveries at 37-38 weeks (early term).

A population-based retrospective cohort study of over 616,000 live-born full-term singleton infants was conducted to investigate the association between elective early term delivery and subsequent infant morbidity, mortality, …

Influence Of Diet On Element Incorporation In The Shells Of Two Bivalve Molluscs: Argopecten Irradians Concentricus And Mercenaria Mercenaria, William Noland Elsaesser

USF Tampa Graduate Theses and Dissertations

Recently, biogenic carbonates have received much attention as potential proxies of environmental change; however, a major pathway of elemental incorporation is often overlooked when making interpretations or designing experiments. This research experimentally examines the influence of diet on elemental composition in juvenile shells of the bay scallop, Argopecten irradians concentricus, and the northern quahog, Mercenaria mercenaria.

Exploratory trials were conducted using Argopecten irradians concentricus juveniles fed different algal diets: Isochrysis, Chaetoceros, Pavlova, Tetraselmis, or a mix of all four in a 2:1:2:2 ratio. No differences between the left and right valves were revealed, thus, subsequent analysis of the dietary influence …

Beyond Performance: Rhetoric, Collective Memory, And The Motive Of Imprinting Identity, Brenda M. Grau

USF Tampa Graduate Theses and Dissertations

This thesis reconsiders Maurice Halbwachs' theory of collective memory in terms of rhetoric. My purpose is to examine specifically how fading generations conform the present to the past as they fight to maintain and defend their collective identities. Although rhetoric and memory studies have often focused on the complex matters of national collectives, Halbwachs was also concerned with the individual and his or her interaction among those groups that matter in everyday living and memory's role in generational shifts that slowly transform culture. Halbwachs' theory helps determine exactly how attempts at conflict resolution are sometimes guarded defenses against threats to …

Transcriptional Control Of Toxoplasma Development, Joshua Byran Radke

USF Tampa Graduate Theses and Dissertations

Toxoplasma gondii is an obligate intracellular protozoan parasite of animals and man. The asexual life cycle of Toxoplasma involves three very distinct, but tightly coordinated developmental stages. In nature, the sporozoite (contained within an oocyst) and bradyzoite (contained within a tissue cyst) initiate infection of the intermediate host, followed by rapid differentiation into the actively replicating tachyzoite. When countered by an effective host response, the tachyzoite differentiates back into the latent bradyzoite and this unique ability of Toxoplasma to interconvert between the replicating tachyzoite and the latent bradyzoite within a single host is the cause of life long infection. The …

Lead (Pb) Contamination Of Water Drawn From Pitcher Pumps In Eastern Madagascar, David Bradlee Akers

USF Tampa Graduate Theses and Dissertations

Access to safe water supply--a major determinant of public health--is less than 50% in Madagascar, and access to piped, treated water remains out of reach financially for many in the urban and peri-urban areas where available. The Self-supply option of the Pitcher Pump has been meeting the need for household water in coastal areas of Madagascar since the early 1960s and has proven a sustainable option for many. These pumps make use of leaded components in the construction, however, which may pose a health risk for heavy metal intoxication and therefore cause the water to be unsafe for drinking and …

Characterization Of Iron Response In Gynecological Cell Lines, Kyle A. Bauckman

USF Tampa Graduate Theses and Dissertations

Ovarian carcinoma afflicts over 22,000 women each year with a 5 year survival rate of only 18% for stage IV patients [23]. Current treatment options are limited due to high rates of drug resistance and recurrence. Further, the identity of "precursor lesions" which give rise to various subclasses of epithelial ovarian cancer has been evasive. This is due to discovery of the cancer at already an advanced stage. Interestingly, endometriosis a benign but invasive gynecological disease has been described as a "precursor lesion" in the development of specific subtypes of ovarian cancer. Endometriotic cyst development involves the accumulation of "old …

Insights Into [Aacute]-Aa Peptides And Ã-Aa Peptides As Broad Spectrum Antimicrobial Peptidomimetics And As Anti-Biofilm Agents, Shruti Padhee

USF Tampa Graduate Theses and Dissertations

The emergent resistance of bacteria against the conventional antibiotics has motivated the search for novel antimicrobial agents. Nature abounds with a number of antimicrobial peptides that are a part of our innate immune system and protect us against a variety of pathogenic bacteria. While they are broad-spectrum in their activity and show less drug-resistance induction, their intrinsic metabolic stability limits their potential therapeutic applications. Herein we describe the development of novel broad-spectrum bioactive antimicrobial peptidomimetics AA-peptides. AApeptides were designed based on chiral PNA backbone. Substitution of nucleobases yields AApeptides that are resistant to proteolysis and capable of mimicking peptides. Two …

Sustainable Energy And Nutrient Recovery From Swine Waste, Adib Amini

USF Tampa Graduate Theses and Dissertations

Swine production represents approximately 40% of the world's meat production, and swine wastes contain high concentrations of organic matter, nitrogen (N) and phosphorus (P). Swine production is intensifying as meat demand increases and concentrated animal feeding operations (CAFOs) are becoming increasingly common, making it difficult to treat the waste generated. A system for holistic treatment of swine waste produced in CAFOs was investigated in this study that sustainably generates energy and recovers N and P as saleable fertilizers. The system uses anaerobic digestion (AD) for methane production and solids stabilization, followed by precipitation of struvite (MgNH4PO4*6H2O) and recovery of N …

Pathways Of Embodiment: Drug Use Among Adolescents In Popay[Aacute]N Colombia, Sarah Louise Fishleder

USF Tampa Graduate Theses and Dissertations

This research examines the interrelated biological and cultural factors that determine pathways by which recreational drug use is manifest to addiction in the lives of youth aged 12-18 in Popay[aacute]n, Colombia. It utilizes existing data from mixed methods research conducted between 2004-2005 examining epidemiological risk factors, drug use, perceptions about drugs, and a biological phenomenon of the brain known as incentive salience. Perceptions and experiences related to drugs were gathered using structured methods. MDS and hierarchical plots of drug perceptions are presented in order to demonstrate the power of culture and expectation on perception and choice. Structural equation modeling was …