Life Sciences Commons^™

Using Artificial Intelligence To Decipher Epigenetic Code Of Drug Resistance In The Deadliest Human Malaria Parasite, Samira Jahangiri

USF Tampa Graduate Theses and Dissertations

Malaria remains one of the immense global public health challenges, with an estimated ~200 million cases worldwide in 2019 despite the remarkable gains in reducing this deadly disease over the past decade. The recent emergence and spread of artemisinin resistance (ART-R) in Plasmodium falciparum will increasingly impede global efforts to control and eliminate malaria. Previous studies have observed broad transcriptional changes and identified several noncoding genetic variants strongly associated with ART-R. The broad transcriptional variations suggest that the malaria parasite uses sophisticated epigenetic regulation to survive under drug pressure. Therefore, evaluating the regulatory effects of noncoding-variants in malaria parasites is …

Effects Of Exogenous Ketone Therapy On Performance, Cardiorespiration, And Seizure Genesis During Exposure To Hbo2 In The Sprague Dawley Rat, Nicole M. Stavitzski

USF Tampa Graduate Theses and Dissertations

Hyperbaric oxygen (HBO2) is used for clinical HBO2 therapy and in undersea and aerospace medicine. HBO2 is a humanmade extreme environment and protracted exposures can cause several adverse physiological effects on the body. For example, HBO2 increases the partial pressure of oxygen (PO2) in the body leading to redox stress. Redox stress is, in part, a cause of oxygen toxicity that manifests as seizures in its most severe form (central nervous system oxygen toxicity, CNS-OT). This dissertation focuses on strategies to be employed specifically for the warfighter breathing HBO2. Currently, the only way to prevent CNS-OT is to lower the …

Multifaceted Approach To Understanding Acinetobacter Baumannii Biofilm Formation And Drug Resistance, Jessie L. Allen

USF Tampa Graduate Theses and Dissertations

Acinetobacter baumannii is a multi-drug resistant nosocomial pathogen known for causing wound related- and respiratory-infections. It is currently on the WHO’s list of critical pathogens due to its broadly drug resistant nature and the constant appearance of pan-resistant isolates. A majority of the infections caused by this organism are biofilm associated, however there is limited existing knowledge regarding the mechanisms used to engage in this multicellular lifestyle. As such, we set out to explore the factors influencing this behavior using an 10,000+ isolate transposon mutant library of A. baumannii strain AB5075. Of the strains tested, 6.45% demonstrated some level of …

The Ecological Role Of Cassiopea In Shallow Mangrove Habitats, David Marcel Durieux

USF Tampa Graduate Theses and Dissertations

Upside-down jellyfish, Cassiopea sp., can be locally abundant in shallow mangrove habitats throughout the tropics and subtropics. Unlike other jellyfish, Cassiopea sp. are epibenthic. Due to this unique lifestyle and their ability to achieve high population densities, an understanding is needed of their ecological impacts both individually and in aggregations, particularly given that Cassiopea sp. ranges are expanding poleward due to global climate change. We quantified the fluid flow produced by Cassiopea sp. feeding currents and found that an average-sized Cassiopea sp. can transport over 200 l/h of water in the vertical excurrent jet of their feeding current. Populations of …

Mechanistic Insight Into Β-Lactamase Catalysis, Inhibitor Design And Resistance, Michael Trent Kemp

USF Tampa Graduate Theses and Dissertations

The emergence of antibiotic resistance and spread of Gram negative bacteria poses a very real health threat to the public. The main mode of resistance within Gram negative bacteria is the production of β-lactamase enzymes that catalyze the breakdown of β-lactam antibiotics through a hydrolysis mechanism. Once the β-lactam ring is hydrolyzed and opened, the drug loses its efficacy, which allows for the bacteria to grow and proliferate uninhibited. These β-lactamase enzymes are organized into four categories based on the Ambler classification, with classes A, C and D being denoted as serine-based β-lactamase enzymes. Class B is composed of metalloenzymes …

Ubiquitous Yet Inconspicuous: Quantifying Trophic Impact Of A Widespread Oceanic Comb Jelly (Ctenophore), Elizabeth Potter

USF Tampa Graduate Theses and Dissertations

The oceanic lobate ctenophore Ocyropsis spp. has a widespread distribution throughout the world’s tropical and sub-tropical oceans. While patchy, Ocyropsis spp. population densities are known to exceed one individual per m3. Studies of coastal ctenophores have shown that some species are capable of exerting strong predatory impacts on their ecosystems, but little is known about the potential trophic impacts of their oceanic relatives. Many oceanic genera such as Ocyropsis, Bolinopsis, and Eurhamphaea exhibit morphologies and prey capture mechanisms that are different from the more well-studied coastal species. Thus, existing data on coastal taxa may not apply to oceanic species due …

Moving In Fluid: Exploring How Fishes Manipulate Water To Swim Efficiently, Nils B. Tack

USF Tampa Graduate Theses and Dissertations

Moving through a dense fluid such as water presents some unique challenges to minimizing energy use and maximizing performance (i.e., speed). Due to animal-fluid interactions during swimming (drag and thrust production) fish have evolved a variety of morphological structures and locomotor mechanisms. For instance, fish rely on body bending and/or fins to interact with the surrounding water such that energy can be transferred to generate thrust. Typically, this synergy promotes morphologies and behaviors aimed at enhancing propulsive efficiency and/or minimizing metabolic activity to lessen the cost of transport (COT). This work focuses on quantifying the energetic and hydromechanical benefits of …

Unraveling The Role Of Novel G5 Peptidase Family Proteins In Virulence And Cell Envelope Biogenesis Of Staphylococcus Aureus, Stephanie M. Marroquin

USF Tampa Graduate Theses and Dissertations

Virulence factors and the bacterial cell envelope are two important components in S. aureus pathogenesis and survival. More importantly, understanding the regulation of these cellular processes is crucial to further understanding and combating this successful pathogen. To date, numerous factors have been identified as playing a role in the regulation of Agr activity in S. aureus, including transcription factors, antisense RNAs, and host elements. Herein we investigate the product of SAUSA300_1984 (termed MroQ), a transmembrane G5 peptidase family protein, as a novel effector of this system. Using a USA300 mroQ mutant we observed a drastic reduction in proteolysis, hemolysis, and …

The Role Of Cpeb2 Alternative Splicing In Tnbc Metastasis, Shaun C. Stevens

USF Tampa Graduate Theses and Dissertations

Breast cancer is the second leading cause of cancer-related deaths for women in the U.S. Although the overall 5-year survival rate for breast cancer is 90%, this rate drops substantially for triple-negative breast cancer (TNBC) due to its high metastatic potential. Furthermore, there is a lack of targeted therapeutics for TNBC, and clinical trials have been largely unsuccessful. These characteristics validate the need for identifying novel therapeutic targets for the treatment of TNBC. The study of alternative splicing (AS) has emerged as a powerful tool to elucidate the molecular underpinnings driving cancer.

Our lab has identified cytoplasmic polyadenylation element-binding protein …

Ecological Genomics Of Two Coastal Foundation Plant Species, Jeannie Mounger

USF Tampa Graduate Theses and Dissertations

I was born and raised in rural Florida on a tributary of the Withlacoochee River. “Withlacoochee” comes from a series of Muscogee Creek words that together mean “big little water,” possibly owing to the seasonal fluctuations in the breadth and flow of the river or to the chain of lakes that in part form it. The name contains within it an understanding of the capacity of land and water to undergo great shifts. It conjures images of mutable boundaries, of water covering and receding across the landscape over and over again. Many of my clearest memories from childhood are related …

Exercise Prescription Practices In University Counseling Centers: Testing The Information-Motivation-Behavioral Skills Model, A'Naja M. Newsome

USF Tampa Graduate Theses and Dissertations

The co-occurence of physical inactivity and poor mental health in the college student population can lead to chronic health issues that have negative short-term (e.g., academic success and weight gain) and long-term (e.g., obesity, serious mental illness, and premature mortality) impacts. Integrating exercise prescription into the mental health treatment plan of college students could enhance the holistic care model described by The American College Health Association (ACHA) and Healthy Campus task force. Understanding the knowledge, attitudes, and skills that mental health professionals (MHPs) hold regarding exercise prescription is important for policy formation and program development for college student health. The …

Ecology And Diversity Of Boletes Of The Southeastern United States, Arian Farid

USF Tampa Graduate Theses and Dissertations

The boletes are conspicuous stipito-pileate macrofungi that are generally defined by their tubulose hymenophores. Molecular phylogenetic analyses have informed extensive taxonomic revisions across the boletes. Despite this, the boletes in the southeastern USA have been largely absent from the literature. This dissertation seeks to understand the microbiome inhabiting the tuberculate ectomycorrhizae of the bolete Hemileccinum rubropunctum, and addresses taxonomic revisions of boletes found in the Boletaceae and Suillaceae. The introduction provides a brief background on boletes, as well as our understanding of tuberculate ectomycorrhizae. The second chapter seeks to understand the composition of the microbiome tuberculate ectomycorrhizae of H. rubropunctum …

Metastatic Mat Phenotype Driven By Noncanonical Epha2 Signaling In Melanoma, Chao Zhang

USF Tampa Graduate Theses and Dissertations

Acquired BRAF/MAPK/extracellular signal‒regulated kinase inhibitor resistance in melanoma results in a new transcriptional state associated with an increased risk of metastasis. In this study, we identified noncanonical ephrin receptor (Eph) EphA2 signaling as a driver of the resistance-associated metastatic state. We used mass spectrometry‒based proteomic and phenotypic assays to demonstrate that the expression of active noncanonical EphA2-S897E in melanoma cells led to a mesenchymal-to-amoeboid transition driven by Cdc42 activation. The induction of mesenchymal-to-amoeboid transition promoted melanoma cell invasion, survival under shear stress, adhesion to endothelial cells under continuous-flow conditions, increased permeability of endothelial cell monolayers, and stimulated melanoma transendothelial cell …

Machine Learning For Species Habitat Analysis, Abigail Lavallin

USF Tampa Graduate Theses and Dissertations

Management and conservation initiatives will always be controlled by finite resources, whether financialor temporal. Understanding a species’ spatial ecology, and how its requirements vary across habitats and locations is key to a successful species management plan. During recent decades, it has been noted how many species populations have declined, despite conservation practices working to increase their numbers. The most prevalent impacts affecting fauna populations have come from anthropogenic change in the form of habitat loss and destruction, along with fragmentation, and global climate change. There is a clear need for management practices to now operate on an entire landscape instead …

Evolutionary Mechanisms For Host Resistance To Tumor Growth And Subsequent Cancer Cell Counter-Adaptations, Arig Ibrahim Hashim

USF Tampa Graduate Theses and Dissertations

Cancer is well-recognized as an evolutionary system, as first proposed by Cairns and Nowell more than 60 years ago. In an evolutionary context, cancers growing in vivo typically consist of heterogeneous subpopulations of cells that interact with each other and with host cells through selection forces operating at many temporal and spatial scales. Moreover, the tumor environment comprises more than just cancer cells; it includes a rich cancer stroma and cancer-driving molecules such as cytokines and metabolites. The tumor’s environment comprises intratumoral heterogeneity that often leads to therapy resistance attributed to the essential roles of many genetic and nongenetic mechanisms. …

Investigation Of Immobilized Enzymes In Confined Environment Of Mesoporous Host Matrices, Xiaoliang Wang

USF Tampa Graduate Theses and Dissertations

Enzyme immobilization in metal-organic frameworks (MOFs) as a promising strategy, is attracting the interest of scientists from different disciplines with the expansion of MOF’s development. Different from other traditional host materials, their unique strengths of high surface areas, large yet adjustable pore sizes, functionalizable pore walls, and diverse architectures make MOFs an ideal platform to investigate hosted enzymes, which is critical to the industrial and commercial process. In addition to the protective function of MOFs, the extensive roles of MOFs in the enzyme immobilization are being well-explored by making full use of their remarkable properties like well-defined structure, high porosity, …

Microbial Dark Matter: Culturing The Uncultured In Search Of Novel Chemotaxonomy, Sarah J. Kennedy

USF Tampa Graduate Theses and Dissertations

Although <1% of environmental isolates can be cultured, insights into the culturable fraction refine future techniques to unlock the cryptic biodiversity. This cryptic biodiversity is omnipresent within culture-independent surveys of environmental bacterial populations. Subsequently, these elusive organisms are termed “microbial dark matter” due to the intrigue surrounding their potential taxonomic and biosynthetic impacts. To this end of investigating bacterial-specific dark matter, we employed high-throughput culturing techniques to examine Gulf of Mexico sediments and sponges for chemotaxonomically important bacteria. Through stepwise implementation of permissive and selective recovery techniques, we succeeded in recovering over 150 unique bacterial isolates. We observed several isolates that pose as chemotaxonomically interesting, including several strains that belong to critical bioremediation taxa. In addition to these biotechnological-amenable isolates, we have also succeeded in culturing taxa historically attributed with antibacterial discoveries. One such isolate was a previously sponge-associated organism belonging to the rarely cultured Verrucosispora genus. Through extensive comparative genomics, we identified it as a novel species and subsequently named it Verrucosispora sioxanthis sp. nov. with the published genome serving as a resource for continued microbial dark matter investigations. Following continued passaging of the organism, we observed improved growth, biomass, and liquid growth dispersal within each increasingly sub-passaged generation of the isolate. As such, the laboratory attenuation, or domestication, of the organism warranted in-depth whole genomic analyses to generate insight into the increased laboratory sustainability. Through phenotypically-guided bioinformatics, we determined that the domestication was mediated through genome-wide selective pseudo- or non-pseudogenization of genes. As the previously sponge-associated organism evolved with the selection pressures of the static laboratory, we demonstrate that isolate effectively underwent genomic atrophy to resolve into a largely stable, sustainable laboratory-domesticated strain. Collectively, our chemotaxonomic discovery pipeline expands on the culturable bacterial biodiversity and ultimately provides a previously uncultured model organism for initial forays into resolving the microbial dark matter knowledge gap.

Application Of Gold Nanoshells For Photothermal Therapy In Lung Cancer Cells, Yva K. Luc

USF Tampa Graduate Theses and Dissertations

Lung cancer is the leading cause of cancer deaths in the world. For the year 2020, it was estimated 1.8 million deaths were due to lung cancer alone, making it more lethal than breast cancer and prostate cancer combined. For the year 2021, it is estimated 235,760 new cases of lung cancer and 50% will lead to death. The primary cause of lung cancer is due to cigarette smoking, which accounts for 80% of all lung cancer deaths. Lung cancer screening relies on only different methods, biopsy, bronchoscopy, ultrasound, chest x-ray film, and sputum cytology. These techniques are used to …

Investigation Of An Alternative Protocol For The Production Of Sars-Cov-2 Antigenic Proteins, Nichole Ninaltowski

USF Tampa Graduate Theses and Dissertations

With the COVID-19 pandemic showing no signs of slowing down, large-scale antigenic protein production is still needed for surveillance using serologic assays. From screening to vaccines to biotherapeutics, being able to produce the proteins for these assays is essential; however, the current gold standard method for producing SARS-CoV-2 spike proteins is prohibitively expensive for most research groups.

Alternative methods of transfecting mammalian cells to produce recombinant proteins that are relatively inexpensive have been used for years. Unlike the expensive, commercially available lipid-based methods, other established methods such as polyethyleneimine (PEI), are considerably easier, and cheaper to meet the needs of …

A Functional Characterization Of The Omega (Ω) Subunit Of Rna Polymerase In Staphylococcus Aureus, Shrushti B. Patil

USF Tampa Graduate Theses and Dissertations

In bacteria, RNA polymerase (RNAP) is a well-characterized and highly conserved multi-subunit enzyme complex responsible for transcription of DNA into RNA. The ω subunit (rpoZ/RpoZ), one of the smaller accessory subunits of RNAP, is often overlooked and under-studied, however, particularly in Gram-positive species. We have previously shown that deleting ω impacts the integrity of RNA polymerase in S. aureus, especially the β' subunit, and alters preference of the core enzyme for sigma factors, skewing heavily towards σB instead of the housekeeping σ factor. Consequently, this causes deregulation of myriad transcriptional processes, strongly rewiring gene expression circuits, and ultimately impairing the …

Evaluating Daily Systemic Betaine Delivery In Alleviating Dry-Amd Pathophysiology, Dawin Khiev

USF Tampa Graduate Theses and Dissertations

MnSod (Sod2) deletion in the retinal pigment epithelium (RPE) of Sod2flox/floxVMD2-cre mice leads to oxidative stress-induced apoptosis of the RPE and photoreceptor cells that show salient features of dry-AMD. The purpose of this study was to investigate the potential antioxidant effect of betaine in protecting retinal health in Sod2flox/floxVMD2-cre mice. Betaine low dose (50mg/Kg Body Weight) and high dose (500mg/kg Body Weight, n=9) were administered intraperitoneally to 8-weeks old male and female Sod2flox/floxVMD2-cre mice daily for four months, while the control group (Sod2flox/floxVMD2-cre mice; n=9) received saline. We used spectral-domain optical coherence tomography (SD-OCT), retinal outer nuclear layer (ONL) thickness …

Quercetin Loaded Nanoparticles For The Treatment Of Dry Eye Disease, Bassma Sami Nashaat Hamed Eltanameli

USF Tampa Graduate Theses and Dissertations

Dry eye disease (DED) is a common condition that affects the eye's anterior surface due to tear deficiency or excessive evaporation. The lack of tears leads to dryness and initiation of an inflammatory response which can irritate the eye and interfere with daily activities. Current treatment depends mainly on artificial tears eye drops which offer temporary relief and require repetitive administration due to frequent blinking. Prescription medications are also available but need around three months to relieve dry eye symptoms. Quercetin is a flavonoid that has an anti-inflammatory and antioxidant effect. However, it suffers from low water solubility and low …

The Multifaceted Role Of Ccar-1 In The Alternative Splicing And Germline Regulation In Caenorhabditis Elegans, Doreen Ikhuva Lugano

USF Tampa Graduate Theses and Dissertations

The Cell Division Cycle and Apoptosis Regulator (CCAR) family members are an enigmatic family of proteins regulating metabolism, cancer, apoptosis, DNA damage, and stress. Mammals have CCAR family members, CCAR1 and CCAR2/DBC1, which evolved from the founding family member CCAR-1/LST-3 expressed in Caenorhabditis elegans. Several studies have shown the importance of understanding these proteins' function in standard and altered physiological processes. Our studies aim to understand the genome-wide alternative splicing and germline regulation of Caenorhabditis elegans CCAR-1 in normal and heat shock conditions. Recently, mammalian CCAR family member CCAR2/DBC1 regulates the alternative splicing by forming a complex with ZNF326. This …

Synthesis Of A Multimodal Ecological Model For Scalable, High-Resolution Arboviral Risk Prediction In Florida, Sean P. Beeman

USF Tampa Graduate Theses and Dissertations

West Nile virus (WNV) and Eastern Equine Encephalitis virus (EEEV) represent the two greatest endemic arboviral risks to the state of Florida. Currently, no approved human vaccine exists for the prevention of either virus. In the absence of a vaccine, effective disease surveillance is paramount for public health. In Florida, WNV and EEEV sentinel chicken surveillance is conducted by mosquito control programs operated at the county, municipality, or special taxing district level. This program was implemented in 1978 following human outbreaks of St. Louis Encephalitis virus (SLEV) that occurred between 1959 and 1977, with initial sentinel coops placed in proximity …

Mitigation Strategies For Central Nervous System Oxygen Toxicity In Rodents: Ketone Metabolic Therapy And Mitochondrial Antioxidant Therapy, Christopher Manuel Hinojo

USF Tampa Graduate Theses and Dissertations

Hyperbaric oxygen (HBO2) is a frequently encountered condition in undersea medicine and hyperbaric oxygen therapy (HBOT). The risk of CNS oxygen toxicity (CNS-OT) seizures limits its use in hyperbaric medicine and limits bottom time for diving operations. In this study, we sought to understand the role of reactive oxygen species (ROS) in two mitigation strategies for CNS-OT; ketone metabolic therapy (KMT), which is known to delay onset of CNS-OT seizures, and mitochondria targeted antioxidant therapy (MitoTAT), which has never been tested under HBO2 conditions. We specifically focused on superoxide anions, one of the early reduction products of molecular oxygen, and …

Cellular And Molecular Alterations Associated With Ovarian And Renal Cancer Pathophysiology, Ravneet Kaur Chhabra

USF Tampa Graduate Theses and Dissertations

Elucidating molecular alterations underlying tumor development and chemoresistance are critical to expand our understanding of the disease pathophysiology. This dissertation is focused on analyzing the cellular and molecular alterations associated with LPA-induced chemoresistance in clear cell renal cell carcinoma (ccRCC) cells and chronic iron-induced deregulation of miRNA expression in fallopian tube secretory epithelial cells (FTSECs).

Kidney cancer is one of the ten most common cancers worldwide with <15% survival rate at advanced stage (American Cancer Society). ccRCC is the most common type of kidney cancer and is described as a metabolic disease characterized by deregulated lipid metabolism leading to increased intracellular lipid droplets [9, 10]. The current molecular-targeted treatment strategies involve VEGF/VEGFR and mTOR inhibition [9, 12]. However, there are limitations to these approaches leading to the reduced efficacy and/or increased resistance in ccRCC cells [13, 14]. Therefore, it is important to decipher the factors involved in compromising the chemosensitivity in these cells.

Lysophosphatidic acid (LPA), a bioactive phospholipid, was previously reported to increase resistance against Sunitinib (VEGFR/PDGFR inhibitor) in ccRCC cells and to increase migration and invasion in various tumors [15-17]. In Chapter 3 of …

Screening Next-Generation Fluorine-19 Probe And Preparation Of Yeast-Derived G Proteins For Gpcr Conformation And Dynamics Study, Wenjie Zhao

USF Tampa Graduate Theses and Dissertations

GPCR regulates numerous diverse physiological processes relevant to diabetes, obesity, Alzheimer's diseases, and several central nervous system disorders and targets proteins in signaling pathways. It has created nearly 200 billion profits from its derivative drugs in 2018. There are near 400 structures of over 70 GPCRs have been resolved by X-ray crystallography, cryo-electron microscopy, and NMR spectroscopy. One of the current challenges that remain in the conformational transition and dynamics study using NMR spectroscopy is to obtain sufficient quantities of the G proteins and GPCRs. Pichia pastoris has shown its tremendous promise in expressing the GPCRs in a high yield, …

Role Of Nhe3 In The Intestine And Thick Ascending Limb Of The Kidneys, Jianxiang Xue

USF Tampa Graduate Theses and Dissertations

The sodium-hydrogen exchanger isoform 3 (NHE3, SLC9A3) mediates most Na+/H+ exchange in the gastrointestinal tract and the kidney, where it plays crucial roles in Na+ and fluid absorption as well as acid-base homeostasis. Whole body NHE3 knockout (NHE3-/-) mice show overt absorptive defects in both the intestine and kidneys. Genetic mutations of NHE3 gene in humans are associated with congenital sodium diarrhea (CSD). In the kidneys, NHE3 is expressed in the proximal tubule (PT) and the thick ascending limb (TAL). Whole kidney-specific (PT and TAL) NHE3 knockout (NHE3Pax8cre) mice and PT-specific NHE3 knockout (PT-NHE3-/-) mice have shown the importance of …

Evolution Of Targeted Therapy Resistance In Eml4-Alk Positive Non-Small Cell Lung Cancer, Robert Vander Velde

USF Tampa Graduate Theses and Dissertations

Targeted therapies have emerged as potent treatments that lead to the remission of many tumors. However, they rarely cure cancers in advanced, metastatic settings. This is due to the evolution of resistance, which in turn can be ascribed to the survival of small subpopulations of tolerant and/or resistant cells. Here we investigated the evolution of resistance to EML4-ALK inhibitors in non-small cell lung cancer (NSCLC) and demonstrated that resistance evolves gradually, from unique pre-treatment sub-populations, as multiple resistance mechanisms accumulate in a Darwinian fashion. Despite accumulating multiple changes, cells evolved, in parallel, toward similar inhibitor specific phenotypes. Evolving cells have …

Transcriptomic And Functional Investigation Of Bacterial Biofilm Formation, Brooke R. Nemec

USF Tampa Graduate Theses and Dissertations

Staphylococcus aureus and Acinetobacter baumannii are two highly successful human pathogens, which have adopted very different, but effective survival strategies. The success of S. aureus is attributed to the tight regulation of an arsenal of virulence factors. Conversely, A. baumannii lacks what would be considered traditional virulence factors and, instead, has developed a high tolerance for environmental stress, which allows it to persist in unforgiving environments, including nosocomial settings and the human body. One common characteristic of these two organisms is their proclivity for biofilm formation. Herein, we discuss the diverse mechanisms governing biofilm formation for A. baumannii and S. …