Biology Commons^™

Phenotypic And Transcriptomic Characterization Of Colonial Phase Variation In The Cholera Pathogen Reveals A Novel Smooth Biofilm-Defective Form, Bliss Nicole Lambert

LSU Doctoral Dissertations

Biofilm formation, through the production of Vibrio polysaccharide (VPS), greatly enhances the environmental fitness and pathogenic success of Vibrio cholerae. As a result of phase variation, V. cholerae can switch from a smooth form to rugose, whose cells produce excess VPS, resulting in highly structured biofilms and greater resistance to stress. To further characterize the reversible process of phase variation, we isolated three colonial lineages. Each lineage began with a smooth parent, N16961, and contained a rugose variant derived from the parent, N16961R, as well as a smooth revertant of the rugose, N16961SD. We found clear phenotypic and transcriptomic …

Prokaryotic Diversity And Aqueous Geochemistry Of Subsurface Environments Of The Death Valley Regional Flow System, Joshua David Sackett

UNLV Theses, Dissertations, Professional Papers, and Capstones

This dissertation summarizes over four years of effort towards the completion of a Ph.D. in Biological Sciences. The work presented in this document covers a broad range of topics, but a central unifying theme is prokaryotic life in the continental subsurface. The work presented in each chapter relied heavily on cultivation-independent methods for assessing prokaryotic communities, including prokaryotic community structure reconstruction from high-throughput sequencing of 16S rRNA gene libraries and single-cell genome analysis of novel uncultivated bacteria.

Chapter 2 examines the aqueous geochemistry and prokaryotic diversity of Devils Hole, a cavernous limnocrene and sole natural habitat for the critically endangered …

Methanogens, Plausible Extraterrestrial Life Forms On Mars, And Their Tolerance To Increasing Concentrations Of Illite Clay, Chandler Kern

Biological Sciences Undergraduate Honors Theses

Methanogens, some of Earth’s most primitive prokaryotic organisms, are candidates for possible life forms capable of inhabiting Mars. Specifically, four different species (Methanobacterium formicicum, Methanococcus maripaludis, Methanosarcina barkeri, Methanothermobacter wolfeii) were analyzed for their tolerance to the presence of illite clay. Illite is a crystalline mineral that has been identified from regions of Mars’s surface. Results indicated that all four species grew with some success in the illite at different concentrations. This experimentation with methanogens’ abilities to survive and reproduce in the presence of illite allows for a more accurate understanding of the potential capability of microbial …

Mastering Mycological Mysteries With Explorations Of Harpellales Associated With Culicidae And Other Dipterans In Idaho, Michael Mccormick

Boise State University Theses and Dissertations

Presented is the first field survey and laboratory-based study focused on Harpellales gut fungi found in Culicidae (mosquito) larvae collected from various parts of Idaho. Overall, 34 sites were sampled ranging from urban storm drains and irrigation puddles to pristine stream-side puddles. These sites yielded 17 different species of mosquitoes and three previously described species of gut fungi. Three species of mosquitoes were the first recorded observations as hosts of the following gut fungi: Culiseta alaskaensis was infested with Zancudomyces culisetae (from Renwyck Creek), Culex tarsalis with Smittium culicis (from Cottonwood Creek), and Ochleratus sp. with Smittium minutisporum (from Bear …

Evaluating Human-Associated Escherichia Coli Marker Genes For Microbial Source Tracking Applications In Florida, Jacob K. Senkbeil

USF Tampa Graduate Theses and Dissertations

Fecal pollution of surface water can lead to human health issues because waterborne transmission of pathogens is a common cause of gastroenteritis. Genetic markers developed for human-associated Escherichia coli (H8, H12, H14, and H24) are promising tools for microbial source tracking (MST) of sewage in environmental waterbodies but are untested in the US. H gene marker performance characteristics (specificity, sensitivity, and prevalence) were assessed, with the goal of developing a quantitative PCR assay for the markers with the best performance. Individual E. coli isolates from reference samples were tested to determine end-point PCR assay performance. Three hundred E. coli strains …

Identification And Characterisation Of Novel Phages Of Pectobacterium And Erwinia, Colin Buttimer

PhDs

Losses in crop yields due to disease need to be reduced to meet increasing global food demands associated with growth in the human population. There is a well-recognised need to develop new environmentally-friendly control strategies to combat bacterial crop diseases. There are several crop diseases for which no effective bactericidal agents are currently available, such as potato blackleg and soft rot disease caused by Pectobacterium atrosepticum and other members of soft rot Enterobacteriaceae (Czajkowski et al., 2011). Furthermore, current control measures involving the use of traditional chemicals or antibiotics are losing their efficacy due to the natural development of bacterial …

Viral Mhc Class I Evasion Affects Anti-Viral T Cell Development And Responses, Elvin James Lauron

Arts & Sciences Electronic Theses and Dissertations

Cytotoxic CD8+ T cells (CTLs) play a critical role in protective immunity against viruses, a fact underscored by the evolution of viral CTL evasion mechanisms. For instance, many viruses commonly target the major histocompatibility complex class I (MHCI) antigen presentation pathway to prevent CTLs from recognizing infected cells. A striking example of this is cowpox virus (CPXV), which interferes with MHCI antigen presentation through two distinct mechanisms. One mechanism of CPXV-mediated MHCI inhibition is to retain MHCI molecules in the endoplasmic reticulum (ER). The second mechanism is to prevent antigen peptide loading onto MHCI molecules. When combined these mechanisms result …

Microbial Ecology Of South Florida Surface Waters: Examining The Potential For Anthropogenic Influences, Chase P. Donnelly

HCNSO Student Theses and Dissertations

South Florida contains one of the largest subtropical wetlands in the world, and yet not much is known about the microbes that live in these surface waters. These microbes play an important role in chemical cycling and maintaining good water quality for both human and ecosystem health. The hydrology of Florida’s surface waters is tightly regulated with the use of canal and levee systems run by the US Army Corps of Engineers and The South Florida Water Management District. These canals run through the Everglades, agriculture, and urban environments to control water levels in Lake Okeechobee, the Water Conservation Areas, …

Sodium Pyruvate Alters The Immune Response To Influenza A Virus Infection In Macrophages, Hazzar Abysalamah

MSU Graduate Theses

ABSTRACT

Pyruvate is the end product of glycolysis. It can either be transported into the mitochondria for use in the TCA cycle or be used to regenerate NAD⁺ during fermentation or aerobic glycolysis (also called the Warburg Effect). I recently discovered that addition of sodium pyruvate to the culture medium during infection of macrophages with influenza A virus affects the production of cytokines involved in immune signaling. While infection of macrophages with influenza A virus resulted in high levels of cytokines (IL-6, IL-1β, and TNF-α) in the absence of sodium pyruvate, the addition of sodium pyruvate significantly impaired cytokine …

Post-Transcriptional Regulation Of Rsma In Pseudomonas Aeruginosa, Ian Miller

Electronic Theses and Dissertations

Pseudomonas aeruginosa is a Gram-negative bacillus found in numerous environments. Gene regulatory mechanisms such as; Two-Component Systems, transcriptional and post-transcriptional regulators, and small non-coding RNAs control the expression of virulence factors that allow P. aeruginosa to initiate acute infections and persist as a chronic infection. A significant post-transcriptional regulator involved in these regulatory networks is the Regulator of Secondary Metabolites (RsmA). In this study, we investigated the contribution of a putative stem-loop on expression of RsmA. We constructed rsmA leader fusions to measure translation with and without the stem-loop present. Secondly, we introduced point mutations to disrupt the formation …

Comparative Genetic And Genomic Analysis Of The Novel Fusellovirus Sulfolobus Spindle-Shaped Virus 10, David Andrew Goodman

Dissertations and Theses

Viruses that infect thermophilic Archaea are unique in both their structure and genetic makeup. The lemon-shaped fuselloviruses - which infect members of the order Sulfolobales, growing optimally at 80º C and pH 3 - are some of the most ubiquitous and best studied viruses of the thermoacidophilic Archaea. They provide a malleable and useful genetic tool for probing into the functions of their host, as well as the host responses to infection. Nonetheless, much about these viruses remains to be learned to further understand their morphological, genetic, and life cycle characteristics.

In order to investigate these aspects of these …

Zika Modulates Arthropod Histone Methylation In Mosquito Cells, Telvin Lee Harrell

Biological Sciences Theses & Dissertations

Epigenetics is the heritable series of covalent modifications that affect chromatin structure, gene expression, and protein function. Methylation is one such epigenetic modification that involves the addition of chemical modifying entities, such as methyl groups, on nucleic acids or proteins. Recent studies have reported that Zika virus (ZIKV) modulates methylation of human and viral RNA important for its replication in vertebrate cells. However, little is known whether ZIKV exerts methylation in arthropod vectors. In this study, I show that ZIKV modulates S-adenosyl methionine (SAMe) synthase, an enzyme involved in the production of SAMe, and histone methylation for its survival in …

Screening For The Novel Cariogenic Pathogen Scardovia Wiggsiae Among Orthodontic Patients, Adam Whiteley

UNLV Theses, Dissertations, Professional Papers, and Capstones

Screening for the Novel Cariogenic Pathogen Scardovia wiggsiae among Orthodontic Patients

by

Adam Whiteley

Dr. Karl Kingsley, Examination Committee Chair Professor of Biomedical Sciences University of Nevada, Las Vegas School of Dental Medicine

The recent discovery of a novel cariogenic pathogen Scardovia wiggsiae has led many scientists and oral health researchers to re-evaluate and re-examine existing saliva repositories to determine the prevalence among patient populations. Recent efforts at this institution have used existing saliva samples to determine the prevalence among both adults and pediatric patients. These studies have revealed this organism may be found in approximately one-quarter of all samples …

The Role And Contribution Of Saprotrophic Fungi During Standing Litter Decomposition Of Two Perennial Grass Species, Schizachyrium Scoparium And Schizachyrium Tenerum, Matthew Lodato

Master's Theses

In terrestrial ecosystems, most of the plant biomass produced enters the detrital pool, where microbial decomposers colonize, enzymatically degrade, and assimilate plant litter carbon and nutrients in amounts sufficient to bring about the decomposition of plant litter. Here, I estimated the biomass and production of fungi and microbial respiration associated with decaying Schizachyrium scoparium and Schizachyrium tenerum leaf litter, and constructed a partial organic matter budget estimating C flow into and through fungal decomposers. Significant losses in S. scoparium (57%) and S. tenerum (68%) leaf mass was observed during litter decomposition along with concomitant increases in fungal biomass, which reached …

Regulation Of The Tubulin Homolog Ftsz In Escherichia Coli, Monika S. Buczek

Dissertations, Theses, and Capstone Projects

Escherichia coli is a well-known pathogen, and importantly, a widely used model organism in all fields of biological sciences for cloning, protein purification, and as a model for Gram-negative bacterial species. And yet, researchers do not fully understand how this bacterium replicates and divides. Every year additional division proteins are discovered, which adds complexity to how we understand E. coli undergoes cell division. Due to their specific roles in cytokinesis, some of these proteins may be potential targets for development of antibacterials or bacteriostatics, which are much needed for fighting the current global antibacterial deficit. My thesis work focuses on …

Identification Of “Fhua” Like Genes In Rhizobium Leguminosarum Atcc 14479 And Its Role In Vicibactin Transport And Investigation Of Heme Bound Iron Uptake System, Sushant Khanal

Electronic Theses and Dissertations

Siderophores are low molecular weight, iron chelating compounds produced by many bacteria for uptake of iron in case of iron scarcity. Vicibactin is a trihydroxamate type siderophore produced by Rhizobium leguminosarum bv. trifolii ATCC 14479. This work focuses on identifying an outer membrane receptor involved in the transport of vicibactin. We have confirmed the presence of the putative fhuA gene in R. leguminosarum bv. trifolii ATCC 14479. This bacteria shows mutualistic symbiosis with the red clover plant Trifoliium prantense. Leghemoglobin, with its cofactor heme is present in the plant root nodules that surrounds the infecting organism present in the nodules. …

Changes In The Microbial Community Of Lubomirskia Baicalensis Affected By Red Sponge Disease, Colin Rorex

Electronic Theses and Dissertations

Lake Baikal is the oldest known lake and a unique ecosystem, home to several species of fresh water sponge. A disease outbreak affecting the dominant species, Lubormirskia baialensis, was recently reported. The cause of the disease has not been determined but one of the current hypothesis is that the increase in methane concentration is correlated to the disease outbreak. This pilot study characterized the microbiomes of sick and healthy sponges through the use of 16S rRNA sequencing. Sick sponge microbiomes shared a conserved group of taxa while the healthy sponge microbiomes had greater diversity. Indicator species analysis identified two significant …

Specimen Accountability Process Change In A Non-Automated Consolidated Microbiology Laboratory, Michael Monh

Dissertations, Masters Theses, Capstones, and Culminating Projects

The pre-analytical phase contributes 60-70% of total error of the total testing process (TTP) (Plebani 2006). The pre-analytical phase can be further divided into two phases; the ‘pre-preanalytical’ and ‘preanalytical’ phases, which commonly includes tasks performed outside of the laboratory walls, and tasks perform within the laboratory’s walls and control, respectively. Additionally, medical care reimbursement policies in the U.S. along with the need to efficiently produce quality results and reduce the costs to clients, has caused the microbiology lab to move from on-site to more resourcefully abundant consolidate labs (Sautter 2014). Serving many satellite facilities, it is of interest to …

Isolation And Identification Of A Chloromethane-Degrading Bacterium From A Strictly Anaerobic Mixed Culture, Samiha Sadruddin

Chancellor’s Honors Program Projects

No abstract provided.

Characterization Of The Interaction Between R. Conorii And Human Host Vitronectin In Rickettsial Pathogenesis, Abigail Inez Fish

LSU Doctoral Dissertations

Spotted Fever Group Rickettsia are inoculated into the mammalian host during hematophagous arthropod feeding. Once in the bloodstream and during dissemination, the survival of these pathogens is dependent upon their ability to evade innate host defenses until a proper cellular target is reached. The establishment of a successful infection also relies on the ability of the bacteria to attach and invade target cells, as failure to do so results in destruction of the bacterium. Rickettsia conorii expresses an outer membrane protein, Adr1, which binds the multifunctional human glycoprotein, vitronectin, to promote resistance to complement mediated killing. Homologs of Adr1 are …

Immunization By Radiotherapy: Enhancing An Immune-Mediated Abscopal Effect, Amy Steffen

Biology and Microbiology Graduate Students Plan B Research Projects

Radiotherapy aims to destroy tumors by inducing DNA damage in their cells at the local irradiation site. Its immune-mediated systemic effects, called abscopal effect, has shown to enhance anti-tumor immunity when combined with immune therapies and thus, have gained attention by researchers and clinicians to investigate. Below is a summary of the fundamentals of cancer and the immune system’s response to it, as well as the changes in the phenotype and microenvironment of tumor cells after exposure to radiation. Impacts of the abscopal effect and the induction of effective antitumor immunity with various immune therapy strategies will be outlined. The …

Increasing The Clinical Efficacy Of Radiotherapeutics For Solid Tumors By Inhibition Of Hypoxia Inducible Factor-1a, Austin Levi Walz

Biology and Microbiology Graduate Students Plan B Research Projects

Radiotherapy is commonly used in a variety of tumor types and is effective in control of long term progression and may be curative under certain circumstances. Radiotherapeutics have been shown to be the single most effective therapeutic for cancer and only account for 5% of the total cost. However, treatment of cells with radiation causes the tumor microenvironment to undergo changes and leads to cycles of hypoxia inside the tumor which allows for the cell to undergo angiogenesis, metastasize and may lead to repopulation of the tumor. Current systemic chemotherapeutics typically have an additive toxicity due to the unintended targeting …

A Biological Review Of Mental Illness: An Overview Of Genetics And Pathophysiology Of Schizophrenia, Major Depression, And Addiction, Christopher R. Angerhofer

Biology and Microbiology Graduate Students Plan B Research Projects

Novel approaches in understanding mental illness present solutions to current issues in treatment and diagnosis. With advancements in genetics and neurology, the etiology and pathophysiology of mental illness is slowly unwrapping. In discovering biomarkers for depression, addiction, and schizophrenia, the precision for preventing, diagnosing, and treating these disorders increases. The aim of this paper is to review current research for addiction, major depression, and schizophrenia in genetics and physiology, while also clarifying the need for reclassifying mental illness as diseases with a pathophysiological basis, not syndromal, idiopathic disorders. Mental illness is dynamic in that it encompasses both environmental and biological …

Transcranial Magnetic Stimulaton: In-Depth Review Of Methods, Efficacy And Future Applications, Matthew Carpenter

Biology and Microbiology Graduate Students Plan B Research Projects

Transcranial magnetic stimulation (TMS) has been regarded as a novel technique of neuromodulation with applications that span from the treatment of depression or depression related symptoms to the mapping of cerebral regions. This review takes an in depth look into the different forms of magnetic stimulation including repetitive TMS, theta-burst stimulation, and navigated TMS. The efficacy of these different forms of stimulation is addressed as well as comparisons made to current standards being used. Potential clinically relevant future applications of TMS are also discussed from the treatment of obsessive compulsive disorder to improving motor function after stroke. The purpose of …

A Review Of Multiple Sclerosis Treatments: Interferon Beta, Glatiramer Acetate, Fingolimod, And Natalizumab, Ryan Golden

Biology and Microbiology Graduate Students Plan B Research Projects

Multiple Sclerosis (MS) is an autoimmune disease in which the body’s own immune system works to demyelinate the myelin sheaths in the central nervous system. The beginning of the review will concentrate on the history of MS while also describing how MS, the disease, differs from that of normal immune responses. The review then shifts to the four different stages of MS and how to differentiate between the stages, since the treatment options are often dependent on the stage of MS that the patient is in. The main focus of this review is to take an in depth look on …

The Rtfa Gene Regulates Plant And Animal Pathogenesis And Secondary Metabolism In Aspergillus Flavus, Jessica Michelle Lohmar

Graduate Research Theses & Dissertations

Aspergillus flavus is an opportunistic fungal plant and human pathogen and producer of mycotoxins including aflatoxin B1 (AFB1). As part of our ongoing studies to elucidate biological functions of the A. flavus rtfA gene, we examined its role in pathogenicity of both plant and animal model systems. rtfA encodes a putative RNA-Pol II transcription elongation factor, previously characterized in Saccharomycese cerevisiae, Aspergillus nidulans, Aspergillus fumigatus, where it was shown to regulate several important cellular processes, including morphogenesis, secondary metabolism. In addition, an initial study in A. flavus indicated that rtfA also influences development and production of AFB1, however its effect …

Microbial Community Response To Light And Heavy Crude Oil In Freshwater Systems, Timothy M. Butler

Dissertations, Master's Theses and Master's Reports

With increased demand for oil, there is an increased risk for oil spills in many environments. A number of pipelines transport oil near or across freshwater systems including the Great Lakes. Microbes are capable of breaking down oil and have thus been proposed as tools for oil spill response through bioremediation. There is a need to understand the microbial response to diverse oil types in freshwater environments due to the lack of research into this topic. This study’s main objectives are to understand how the freshwater microbial communities respond to oil, and how the bacterial communities may respond to different …

Mild Traumatic Brain Injuries And Cte: A Review Highlighting The Connection Between The Two, Leandre Kennedy

Biology and Microbiology Graduate Students Plan B Research Projects

Chronic Traumatic Encephalopathy (CTE) is a traumatic brain injury based disease that is garnering a lot of attention in the United States. The purpose of this paper is to conduct an extensive review of the information available about the condition. Recently there has been a limited amount of published information and treatment opportunities are rare since the only way of diagnosing has come post mortem. Various literary reviews and experiments were analyzed for appropriate information regarding CTE’s pathology and treatments and only peer reviewed published works were allowed in this paper. This resulted in promising information about the disease and …

Characterization Of Two Cyclic Di-Gmp Phosphodiesterases Hypothesized To Regulate Virulence In Streptomyces Scabies, Madison Flasco

Undergraduate Honors Thesis Projects

Common scab is a devastating disease that affects the marketability of potatoes. The disease results in raised and pitted lesions seen on the surface of the potato and is caused by the soil pathogen, Streptomyces scabies. The S. scabies genome has two cyclic-di-GMP phosphodiesterases, RmdA and RmdB, both regulators of morphology and development. These proteins break down the ubiquitous second messenger molecule cyclic di-GMP, a molecule in charge of cell cycle progression and virulence. Both proteins contain diguanylate cyclase domains and phosphodiesterase domains, GGDEF and EAL, respectively, while RmdA contains an additional PAS_4 domain. Despite similar domain configurations, the two …

Marine Bioactives From Saccharina Latissima, Orlaith O'Connell

Masters

Due to rapid global urbanization and therefore increased adoption of a 'Westernized' lifestyle, including decreased physical activity and increased consumption of highly processed and refined foods with a high sugar, fat and salt content, prevalence of gastrointestinal disorders are on the rise. Inflammatory bowel disease (IBD) in particular is closely associated with this type of lifestyle. IBD is a term used to describe chronic inflammatory conditions which affects all or parts of the gastrointestinal tract. It includes conditions such as Crohn's Disease, which affects all the gastrointestinal tract and Ulcerative Colitis which mainly affects the colan. Due to the role …