Microbiology Commons^™

In Situ Studies Of Limestone Dissolution In A Coastal Submarine Spring, Rachel Marie Schweers

USF Tampa Graduate Theses and Dissertations

Limestone dissolution in karst environments is likely due to geochemistry of the water, the actions of microbial communities, and the effect of water flow. We explored the rate of limestone dissolution and will examine here the microbial communities associated with the limestone. A conduit within the brackish cave, Double Keyhole Spring, on the coast of central west Florida was the site of the experiment. PVC pipes (5cm x 16cm) were filled with crushed limestone that was screened to a 1.9cm – 2.54cm size range. There were three treatments (5 replicates each): Control - sealed autoclaved controls with limestone and conduit …

Promoting Genome Stability Via Multiple Dna Repair Pathways, Scott Cukras

USF Tampa Graduate Theses and Dissertations

Maintaining genome integrity is indispensible for cells to prevent and limit accruement of deleterious mutations and to promote viable cell growth and proliferation. Cells possess a myriad of mechanisms to detect, prevent and repair incurred cellular damage. Here we discuss various proteins and their accompanying cellular pathways that promote genome stability. We first investigate the NEDD8 protein and its role in promoting homologous recombination repair via multiple Cullin E3 ubiquitin ligases. We provide specific mechanisms through which, UBE2M, an E2 conjugating enzyme, neddylates various Cullin ligases to render them catalytically active to degrade their substrates by the proteasome. We show …

Exploring The Pathogenic And Drug Resistance Mechanisms Of Staphylococcus Aureus, Whittney Burda

USF Tampa Graduate Theses and Dissertations

We have previously identified σS, an ECF sigma factor that is important in the virulence and stress response of S. aureus. Transcriptional profiling of sigS revealed that it is differentially regulated in a variety of laboratory and clinical strains of S. aureus, suggesting that there exists a regulatory network that modulates its expression. In order to identify direct regulators of sigS expression, we performed a biotin pull down assay in tandem with mass spectrometry. We identified CymR as a direct regulator and observed that sigS expression is increased in cells lacking cymR. In addition, transposon mutagenesis was performed to identify …

Investigation Of Post-Translational Modifications In Staphylococcus Aureus, Christina Nadia Krute

USF Tampa Graduate Theses and Dissertations

The work presented herein details post-translational modifications (PTMs) in Staphylococcus aureus that are involved in mediating the stress response and normal cellular processes. The first PTM that was investigated is regulated intramembrane proteolysis (RIP) for the activation of the ECF sigma factor σS. We achieved this by analyzing the role of the site-1 protease, which we termed “putative regulator of sigmaS” (PrsS), as it is predicted to be the first enzyme in the RIP cascade, leading to the activation of σS. It was determined that the putative site-1 protease, prsS, mimics transcriptional profiles of sigS; with expression low in all …

Exploring The Role Of Intracellular Aminopeptidases In Staphylococcus Aureus Pathogenesis, Devon Nicole Marking

USF Tampa Graduate Theses and Dissertations

Staphylococcus aureus is a remarkably pathogenic bacterium that is widely prevalent among the human population. It is the leading agent of skin and soft tissue infections, and is also responsible for causing an array of severe and life threatening diseases. The invasiveness of the pathogen, coupled with increasing antibiotic resistance seen for S. aureus infections, makes this bacterium a prominent public health concern. The extended pathogenicity of S. aureus is largely due to its repertoire of virulence factors, which are typically characterized by being bound to the cell wall, or secreted into the extracellular environment. Previously, our lab identified a …

A Functional Approach To Resolving The Biogeocomplexity Of Two Extreme Environments, Haydn Rubelmann Iii

USF Tampa Graduate Theses and Dissertations

The biodiversity of two distinct marine environments was observed to describe the biogeocomplexity of these extreme ecological systems. A shallow-water hydrothermal vent in Papua New Guinea served as a study of a thermophilic ecosystem influenced by arsenic rich vent fluids while a 60 m deep offshore primarily anoxic karst sink served as a study of an anaerobic sulfur-influenced habitat. Both environments support unique biological communities that are influenced by the physical and chemical pressures imposed on them by the harsh conditions of these systems. In Tutum Bay, Ambitle Isle, Papua New Guinea, a transect was created from a shallow hydrothermal …

Mechanisms And Molecular Biology Of Major Tumor Suppressors, Brienne E. Engel

USF Tampa Graduate Theses and Dissertations

This dissertation is devoted to the study of the molecular biology of major tumor suppressors, defined as those that prevent the cellular processes identified as the hallmarks of cancer. Specifically, the major tumor suppressors pRb and STK11 are explored in the context of osteosarcoma and lung cancer, respectively.

RB1 was the first tumor suppressor gene discovered. Over four decades of work have revealed that the Rb protein (pRb) is a master regulator of biological pathways influencing virtually every aspect of intrinsic cell fate including cell growth, cell-cycle checkpoints, differentiation, senescence, self-renewal, replication, genomic stability and apoptosis. While these many processes …

Role And Regulation Of Snon/Skil And Plscr1 Located At 3q26.2 And 3q23, Respectively, In Ovarian Cancer Pathophysiology, Madhav Karthik Kodigepalli

USF Tampa Graduate Theses and Dissertations

Ovarian cancer is one of the most common causes of gynecological cancer related deaths in women. In 2014, the estimated number of deaths due to ovarian cancer is 14,270 with occurrence of over 22, 240 new cases (National Cancer Institute, http://seer.cancer.gov/statfacts/html/ovary.html). Despite improvement in treatment strategies, the 5-year survival rate is still below 50% mainly due to chemoresistance and relapse. Amplification of chromosomal region 3q26 is a common characteristic in various epithelial cancers including ovarian cancer. This region harbors various oncogenes including the TGFβ signaling mediators EVI1 and SnoN/SkiL, PKCι and PIK3CA amplified at 3q26.2 and 3q26.3, respectively, in ovarian …

Karst Estuaries: A Newly Described Ecosystem Governed By Aquifer Hydrology, Damian M. Menning

USF Tampa Graduate Theses and Dissertations

The overall goal of this dissertation is to define the hydrological, geochemical, and biological characteristics of a Karst Estuary. These types of estuaries represent a unique ecosystem created by freshwater inputs from direct flow through karst conduits and/or diffuse flow through a karst matrix. In order to determine the characteristics of a Karst Estuary we monitored short-term tidal fluctuations, long-term rainfall patterns, aquifer levels, spring discharge, multiple geochemical parameters, microbial communities in the water column and sediment, and macrofaunal communities in the sediment along a transect from a submarine spring through the Gulf of Mexico. Four sites were selected along …

Bartonella Henselae Infection And Host Response In The Zebrafish Embryo Model, Amorce Lima

USF Tampa Graduate Theses and Dissertations

The Gram-negative bacterium Bartonella henselae (Bh) is an emerging zoonotic pathogen that has been associated with a variety of human diseases including bacillary angiomatosis which is characterized by vasoproliferative tumor-like lesions on the skin and internal organs of some immunosuppressed individuals. Several virulence factors associated with Bartonella-induced pathogenesis have been characterized. However, the study of those virulence factors has been limited to in vitro cell culture systems due to the lack of a practical animal model. Therefore, we wanted to investigate whether the zebrafish embryo (Danio rerio) could be used to model human infection with Bh. We investigated …

Cancer And Infection, Kathleen Hope Plummer

USF Tampa Graduate Theses and Dissertations

E. coli is the most frequently isolated Gram negative pathogen from bacteremia in cancer patients and is repeatedly recovered from many other extraintestinal illnesses. These infections are commonly endogenous in nature and interfere with the treatment of cancer resulting in increased healthcare costs, morbidity, and mortality rates. Cancer and the treatments related to cancer cause alterations in the microbiome of the gut and other organs. Despite this point, there is a serious lack of knowledge about the genetic types of E. coli infecting cancer patients. This gap results in vague prevention strategies and limited treatment options for cancer patients. Multi …

Topological Data Analysis Of Properties Of Four-Regular Rigid Vertex Graphs, Grant Mcneil Conine

USF Tampa Graduate Theses and Dissertations

Homologous DNA recombination and rearrangement has been modeled with a class of four-regular rigid vertex graphs called assembly graphs which can also be represented by double occurrence words. Various invariants have been suggested for these graphs, some based on the structure of the graphs, and some biologically motivated.

In this thesis we use a novel method of data analysis based on a technique known as partial-clustering analysis and an algorithm known as Mapper to examine the relationships between these invariants. We introduce some of the basic machinery of topological data analysis, including the construction of simplicial complexes on a data …

From Co2 To Cell: Energetic Expense Of Creating Biomass Using The Calvin-Benson-Bassham And Reductive Citric Acid Cycles Based On Genomic Data, Mary Ann Mangiapia

USF Tampa Graduate Theses and Dissertations

Abstract

The ubiquity of the Calvin-Benson-Bassham cycle (CBB) amongst autotrophic organisms suggests that it provides an advantage over a wide range of environmental conditions. However, in some habitats, such as hydrothermal vents, the reductive citric acid cycle (rCAC) is an equally predominant carbon fixation pathway. It has been suggested that the CBB cycle poses a disadvantage under certain circumstances due to being more energetically demanding compared to other carbon fixation pathways. The purpose of this study was to compare the relative metabolic cost of cell biosynthesis by an autotrophic cell using either the CBB cycle or the rCAC. For both …

Investigating The Diversity Of Single-Stranded Dna Bacteriophages In Marine Environments, Max Stephen Hopkins

USF Tampa Graduate Theses and Dissertations

There are estimated to be 1030 virus-like particles in the world's oceans. Most are viruses that infect bacteria, called `bacteriophages' or simply `phages'. Phages exert tremendous influence on marine biogeochemical cycling because they are responsible for about half of all bacterial death in the oceans, causing nutrient release into the dissolved and particulate organic matter pools. Traditional paradigms of phage biology held that most of these ocean phages belonged to the Caudovirales group: phages that contain a double-stranded DNA genome within a geometric capsid `head' to which a `tail' is joined, in one of several morphological variants, that is the …

Marine Viral Diversity And Spatiotemporal Variability, Dawn Goldsmith

USF Tampa Graduate Theses and Dissertations

Marine viruses are the most numerous biological entities in the ocean, with an estimated abundance of 4 x 10³⁰. They merit study not only because of their sheer abundance, but also because of the role they play in the Earth's biogeochemical cycles. Viral lysis of bacteria redirects the flow of nutrients among marine microbes, which ultimately affects the efficiency of the biological pump. Viral diversity is important because most viruses are host-specific. In preying on a certain type of bacteria, viruses affect the diversity and structure of the bacterial community, leading to changes in carbon and nutrient flows. …

Genetic Basis For The Virulence Of Enterohemorrhagic Escherichia Coli Strain Tw14359, Jason Kyle Morgan

USF Tampa Graduate Theses and Dissertations

Enterohemorrhagic Escherichia coli (EHEC) is a virulent pathotype of E. coli that is associated with major outbreaks of hemorrhagic colitis and the life-threatening kidney disease hemolytic uremic syndrome. For successful host colonization and attachment to the intestinal mucosa, EHEC requires the locus of enterocyte effacement (LEE) pathogenicity island, which encodes a type III secretion system (TTSS) responsible for secreting and translocating effector proteins into host colonocytes. Regulation of the LEE is primarily directed through the first operon, LEE1, encoding the locus encoded regulator (Ler), and occurs through the direct and indirect action of several regulators. The 2006 U.S. spinach outbreak …

Structure-Based Design Of Novel Inhibitors And Ultra High Resolution Analysis Of Ctx-M Beta-Lactamase, Derek Allen Nichols

USF Tampa Graduate Theses and Dissertations

The emergence of CTX-M class-A extended-spectrum β-lactamases, which confer resistance to second and third-generation cephalosporins, poses a serious health threat to the public. CTX-M β-lactamases use a catalytic serine to hydrolyze the β-lactam ring. Specifically, the hydrolysis reaction catalyzed by CTX-M β-lactamase proceeds through a pre-covalent complex, a high-energy tetrahedral acylation intermediate, a low-energy acyl-enzyme complex, a high-energy tetrahedral deacylation intermediate after attack via a catalytic water, and lastly, the hydrolyzed β-lactam ring product which is released from the enzyme complex. The crystallographic structure of CTX-M at sub-angstrom resolution has enabled us to study enzyme catalysis as well as perform …

Assessment Of A Modified Double Agar Layer Method To Detect Bacteriophage For Assessing The Potential Of Wastewater Reuse In Rural Bolivia, Sakira N. Hadley

USF Tampa Graduate Theses and Dissertations

Water scarcity is a global concern that impacts many developing countries, forcing people to depend on unclean water sources for domestic, agricultural, and industrial needs. Wastewater is an alternative water source that contains nutrients needed for crop growth. Wastewater reuse for agriculture can cause public health problems because of human exposure to pathogens. Pathogen monitoring is essential to evaluate the compliance of wastewater with established World Health Organization (WHO) and U.S. Environmental Protection Agency (EPA) wastewater reuse guidelines. Indicator organisms are commonly used to detect pathogens in water and wastewater because they are quick and easy to measure, non-pathogenic, and …

Direct And Indirect Effects Of Agrochemicals On Bacterial Pathogens And Fecal Indicator Bacteria, Zachery Staley

USF Tampa Graduate Theses and Dissertations

The presence of agrochemical residues in both urban and agricultural water bodies has become ubiquitous, often producing deleterious effects in the impacted watershed including reductions in biodiversity, alterations in species interactions, and toxicity to non-target organisms. While these effects have been studied on metazoan consumers, the consequences of agrochemical contamination on microorganisms, such as bacteria, protozoa, and viruses, are poorly understood. Agrochemicals could act directly on microorganisms, including pathogens, by either facilitating their survival or decreasing their abundance. Further, a multitude of indirect effects of agrochemicals on microorganisms are possible, whereby agrochemicals alter predation, competition, or parasitism on or available …

Prenatal Stress, Depression, And Herpes Viral Titers, Pao-Chu Hsu

USF Tampa Graduate Theses and Dissertations

Recent studies suggest that some cases of prenatal depression may be associated with reactivation of latent infections of the herpesvirus family. The possible relationships among stress, prenatal depression, and herpes viral reactivation in pregnancy are understudied and the molecular pathways such as the neuroimmune biogenic amine pathway are unidentified. Chronic stress shifts the T helper-1 cell (Th1) cytokine profile to a Th2 profile, which favors virus induced pathogenesis and survival. Pregnancy is also associated with a similar Th2 dominance. In non-pregnant individuals, exposure to psychological or physical stress may be associated with latent herpes viral reactivation and could result in …

Innate Immune Responses To Respiratory Syncytial Virus: Age-Associated Changes, Terianne Maiko Wong

USF Tampa Graduate Theses and Dissertations

Respiratory syncytial virus (RSV) infection causes ~64 million cases of respiratory disease and 200,000 deaths annually worldwide, yet there is no broadly effective prophylactic or treatment regimen. RSV can produce acute respiratory illness in patients of all ages but strikes the age extremes, infants and the elderly, with highest frequency presumably due to innate immune deficiencies. A higher morbidity and mortality has been reported for the elderly above 65 years of age, which has been attributed to immune senescence. Efforts to generate an effective vaccine have thus far been unsuccessful.

The innate immune system provides the first line of defense …

Persistent Infection With Human Herpesvirus-6 In Patients With An Inherited Form Of The Virus: A Newly Described Disease, Shara Pantry

USF Tampa Graduate Theses and Dissertations

Human Herpesvirus 6A (HHV-6A) and 6B (HHV-6B) are ubiquitous betaherpesviruses. Both viruses are associated with a variety of adult disorders including neurological disorder, such as multiple sclerosis and chronic fatigue syndrome. HHV-6 viruses are capable of establishing latency by integration into the telomeres of the host chromosome and are transmitted in a Mendelian manner in approximately one percent of the population. To date little is known about the immunological and neurological consequences of HHV-6 inheritance. This study focused on a unique population of individuals that inherited HHV-6 and present with chronic fatigue-like symptoms, including hypersomnia, generalized fatigue, headache, and short …

Complete Genome Sequences And Phylogeny Of West Nile Virus Isolates From Southeastern United States, 2003-2012, Crystal Wedin

USF Tampa Graduate Theses and Dissertations

The study of the evolution and phylogeny of West Nile virus (WNV) has been an important area of research since the introduction of WNV in 1999. However, genome sequencing of isolates from the Southeastern part of the United States has been somewhat limited. To determine how WNV has evolved at a more localized level, ten isolates from Florida and Georgia from 2003-2012 were completely sequenced using Illumina's next-generation technology. In addition, a phylogenetic comparison of both the complete genome and select partial genomes was completed to ensure consistency among the results. This study further demonstrated the dominance of the North …

The Role And Regulation Of Nsars: A Cell-Envelope Stress Sensing Two-Component System In Staphylococcus Aureus, Stacey Lynn Kolar

USF Tampa Graduate Theses and Dissertations

Abstract

S. aureus has 16 predicted two-component systems (TCS) that respond to a range of environmental stimuli, and allow for adaptation to stresses. Of these 16, three have no known function, and are not homologous to any other TCS found in closely related organisms. NsaRS is one such element, and belongs to the intramembrane-sensing histidine kinase (IM-HK) family, which is conserved within the Firmicutes. The regulators are defined by a small sensing domain within their histidine kinase, suggesting that they do not sense external signals, but stress in or at the membrane. Our characterization of NsaRS in this work reveals …

Sigma Factor N (Σn): A Novel Regulator Of Extreme Acid Resistance In Enterohemorrhagic E. Coli O157:H7, Pamela Ann Fay

USF Tampa Graduate Theses and Dissertations

Extreme acid resistance contributes to the successful transmission of enterohemorrhagic E. coli (EHEC) through acidic food matrices and the stomach, allowing it to gain access to the intestine and elicit disease in humans. Alternative sigma factor N (σ^N, encoded by rpoN) was previously identified as a novel regulator of extreme acid resistance in EHEC. This study investigated the role for σ^N and co-expressed products of the rpoN operon in the acid resistance phenotype of EHEC. The results revealed that σ^N primarily controls acid resistance through repression of the glutamate-dependent acid resistance (GDAR) system through control …

Investigation Into The Mechanism Of Salicylate-Associated Genotypic Antibiotic Resistance In Staphylococcus Aureus, Nada Salah Helal

USF Tampa Graduate Theses and Dissertations

Growth of Staphylococcus aureus with the NSAID salicylate increases phenotypic resistance (SAPAR), and the frequency at which heritable resistance occurs to various antibiotics (SAGAR). This study describes the effect of salicylate on heritable and phenotypic resistance to a set of antibiotics for laboratory and multi-drug resistant strains of S. aureus and investigates the link between resistance and SAGAR. Drug gradient plates were used to determine phenotypic resistance to antibiotics targeting DNA replication, transcription, translation and the cell wall in the presence or absence of salicylate. To measure heritable resistance, mutation frequencies were determined for each antibiotic in the presence and …

Assessing The Microbial Consequences Of Remediation: Surrogate Microbial Screening And Native Metabolic Signatures In Tc(Vii) Contaminated Sediments, Kathryn Lafaye Bailey

USF Tampa Graduate Theses and Dissertations

The chemical and physical processes controlling contaminant fate and transport in the vadose zone limit the options for application of many remedial technologies. Foam delivery technology (FDT) has been developed as a potential solution to overcome these limitations for remediating subsurface and deep vadose zone environments using reactive amendments. Although there are many advantages to utilizing FDT for treatment in the deep vadose zone, little information is available on how the addition of these surfactants and remedial amendments affect the indigenous microbial communities in the deep vadose zone as well as the impact of biological transformations of surfactant-based foams on …

Evidence For Viral Infection In The Copepods Labidocera Aestiva And Acartia Tonsa In Tampa Bay, Florida, Darren Stephenson Dunlap

USF Tampa Graduate Theses and Dissertations

Mesozooplankton are of critical importance to marine food webs by transferring energy from the microbial food web to higher trophic levels and depositing energy to the deeper ocean layers through fecal deposition. While decades of research have shown that viruses have significant impacts in the oceans, and infect a wide range of organisms from bacteria to whales, there is still little known about the impacts of viruses on the mesozooplankton community. As copepods are the most abundant mesozooplankton group, this study sought to characterize the viruses present in natural populations of the calanoid copepods Acartia tonsa and Labidocera aestiva in …

Characterization Of The Lone Extracytoplasmic Function Sigma Factor, Ós, And Its Role In The Staphylococcus Aureus Virulence And Stress Responses, Halie Kay Miller

USF Tampa Graduate Theses and Dissertations

Previously our laboratory had identified a novel component of the Staphylococcus aureus regulatory network, an extracytoplasmic function ó factor, óS, involved in stress response and disease causation. Here we present additional characterization of óS, demonstrating a role for it in protection against DNA damage, cell wall disruption and interaction with components of the innate immune system. Promoter mapping reveals the existence of four unique sigS start sites, one of which appears to be subject to auto-regulation. Transcriptional profiling revealed that sigS expression remains low in a number of S. aureus wild-types, but is upregulated in the highly mutated strain RN4220. …

Investigation Of Reservoirs Of Fecal Indicator Bacteria And Water Quality On The Presence Of Allochthonous Pathogens And The Ecology And Virulence Of Vibrio Vulnificus, Christopher Staley

USF Tampa Graduate Theses and Dissertations

The quality of recreational and shellfishing waters has historically been monitored using commensal, allochthonous bacteria shed in feces (fecal indicator bacteria, FIB). The fate of FIB in the environment should mimic that of bacterial, protozoan, and viral human pathogens, which may also be allochthonous (e.g. Salmonella, Cryptosporidium, or enteric viruses) or autochthonous (e.g. Vibrio spp.) to aquatic environments. FIB are contributed to water from human and animal sources; however, pollution source cannot be determined by conventional FIB measurements. Because fecal source determination is important for pollution remediation and assessment of human health risks, microbial source tracking (MST) methods are …