Microbiology Commons^™

A Portable Impedance Biosensing System Based On A Laptop With Labview For Rapid Detection Of Avian Influenza Virus, Yixiang Wang

Graduate Theses and Dissertations

Avian Influenza Virus (AIV) H5N1 is a highly pathogenic virus found not only in birds but also in human. Rapid and sensitive detection method is needed to help prevent the spread of AIV H5N1. In this study, a portable impedance biosensing system based on a laptop with LabVIEW software was developed for detection of AIV H5N1. First, a virtual instrument was programmed with LabVIEW software to form a platform for impedance measurement, data processing and control. The audio card of a laptop was used as a function generator while a data acquisition card was used with the signal channels for …

Enhancing Protein And Enzyme Stability Through Rationally Engineered Site-Specific Immobilization Utilizing Non-Canonical Amino Acids, Jeffrey Chun Wu

Theses and Dissertations

The demand for economical, efficient protein production, reuse, and recovery has never been greater due to their versatility in a large variety of applications ranging from industrial chemical manufacturing to pharmaceutical drug production. The applications for naturally and artificially produced proteins include protein drugs and other pharmaceutical products, as biocatalysts in environmentally friendly chemical manufacturing, as enzymes for food processing purposes, and as an essential component in many biomedical devices. However, protein production suffers from many challenges, which include the cost of production, protein stability especially under harsh conditions, and recoverability and reusability of the proteins. The combination of two …

Modulation Of Host Polyubiquitination By The Ankb F-Box Protein Of Legionella Pneumophila., William M. Bruckert

Electronic Theses and Dissertations

Legionella pneumophila is a facultative intracellular pathogen that infects a wide array of protozoan hosts and human alveolar macrophages. L. pneumophila is dependent on a functional Dot/Icm type IVB secretion system that translocates bacterial effector proteins into the host cell cytosol. L. pneumophila genomes encode more than 250 effector proteins, many of which inhibit host cellular processes to form a favorable niche termed the Legionella-containing vacuole (LCV). The eukaryotic-like Dot/Icm translocated effector AnkB contains two eukaryotic-like ankyrin protein-protein interacting domains, one eukaryotic-like F- box domain and an eukaryotic C-terminal CaaX motif. Immediately following attachment of extracellular bacteria, AnkB is translocated …

A Mechanism For Trif Adaptor-Biased Signaling By Toll-Like Receptor 4., Joseph Peterson Kolb

Electronic Theses and Dissertations

Host cells respond to bacterial lipid A through Toll-like receptor 4 (TLR4). Activation of TLR4 by lipid A triggers a response that involves two main adaptor proteins, MyD88 and TRIF. MyD88-dependent gene expression is associated with proinflammatory protein production, while TRIF-dependent gene expression is essential for optimal activation of adaptive immunity by antigen-presenting cells. Detoxified, monophosphoryl lipid A agonists (MPLA or synthetic MLA) were previously suggested to elicit TRIF-biased TLR4 signaling; that is, induction of weaker MyD88-associated gene expression but relatively intact TRIF-dependent gene expression when compared to fully active diphosphoryl lipid A (lipid A). In this work, we explored …

Quantitative Analysis And Imaging-Based Insights Into The Characteristics And Mechanisms Of Yeast Pattern Formation, Lin Chen

Dissertations and Theses (Open Access)

Biofilm formation is a common lifestyle adapted by bacteria and fungi in response to various environmental stresses. Bacterial and fungal biofilms adhering to medical devices convey resistance to antibiotics or biocides, causing high rates of clinical infections. Microorganisms are protected from harsh environmental conditions by reduced stress penetration through the complex biofilm architecture with distinct patterns. Although the molecular regulations of surface patterning have been well characterized in bacteria, the mechanisms underlying the complex pattern formation in eukaryotic biofilms remain unclear.

This dissertation aims to investigate the salient features of robust colony expansion in yeast biofilms and the processes driving …

Determining The Fate Of Non-O157 Shiga Toxin-Producing Escherichia Coli In Dairy Compost During Storage Using The Optimized Detection Method, Hongye Wang

All Theses

Shiga toxin-producing Escherichia coli (STEC), a member of Enterobacteriaceae family, has been recognized as emerging pathogens. Dairy compost is commonly applied to farmland as a soil amendment. Despite the agricultural benefit of manure-based soil amendment, the inadequately treated compost can contribute to fresh produce contamination on the farm. Moreover, the epidemiological results showed that the non-O157 STEC cases have surpassed those of E. coli O157. Therefore, it is critical to evaluate the behavior of non-O157 STEC strains in the dairy manure-based compost. The objectives of this study were to: 1) optimize a culturing method for detecting non-O157 STEC from dairy …

The Effects Of Probiotics Supplementation On Health Using Caenorhabditis Elegans As A Model System, Miranda Klees

All Theses

The 'Western Diet,' prominent among developed nations, often refers to a diet rich in meat proteins and refined sugars. Western society may in part be plagued with obesity and obesity related diseases due to a diet enriched with glucose. With an increasing glycemic index observed in Western society, it comes to no surprise that obesity, diabetes, heart disease, and other obesity related diseases are on the rise. The Centers for Disease Control and Prevention describes obesity as an epidemic, affecting more than 35% of U.S. citizens. Shortened lifespan and increased susceptibility to pathogens are associated with these diseases and linked …

Inhibition Of Vibrio Cholerae Biofilm Formation By Water-Soluble Cranberry Extracts, Daniel Pederson

All Theses

Vibrio cholerae, a Gram-negative bacterium found in natural aquatic environments, is the causative agent of cholera, a severe diarrheal disease most commonly spread through drinking water. An essential component to this pathogen's success and persistence in the environment is its ability to attach to both biotic and abiotic surfaces via biofilm formation. Biofilms not only aid in surface attachment, but also provide a barrier that protects and enhances survival. Water-soluble extracts from the North American cranberry (Vaccinium macrocarpon) were found to dramatically inhibit V. cholerae biofilm formation at a low concentration of 2mg/ml. This inhibition was not due to acidification …

Antibacterial Activity Of Commercially Available Plant Extracts On Selected Campylobacter Jejuni Strains, Divya Oppath Sivasankaran

Graduate Theses and Dissertations

Campylobacter jejuni is recognized as a leading cause of foodborne illness worldwide with approximately 850,000 cases per year in the United Sates. A total of 18 species of Campylobacter have been identified worldwide to date. Foodborne transmission of C. jejuni is mainly through the consumption of unpasteurized milk, contaminated poultry meat and water. C. jejuni can survive in very diverse environments under stressful conditions in human and animals which is different from the specific conditions and media required in laboratory experiments. There has been increased research in recent years to identify naturally occurring antibacterial agents to control and eliminate C. …

Gut Bacteria And Their Influence On Metabolic Disorders, Stephanie Sorbara (Class Of 2015)

Biology Undergraduate Publications

The human gut microbial genome encodes for several metabolic processes that are not encoded for in the human genome. Through the study of metagenomics, mice, and human models, researchers have shown that changes in the gut bacterial composition can generate oxidative stress, release endotoxins, and induce lipogenesis. These pathways can disrupt normal metabolic function, resulting in obesity and other related metabolic disorders such as diabetes. Most of the health implications associated with obesity originate from the biological reactions carried out by the gut bacteria, which are strongly impacted by environmental factors. Probiotics, prebiotics and fecal transplantation are methods that can …

Studies Of Phou In Escherichia Coli: Metal Binding, Dimerization,Protein/Protein Interactions, And A Signaling Complex Model, Stewart G. Gardner

Theses and Dissertations

Phosphate is an essential nutrient for all forms of life. Escherichia coli has a PhoR/PhoB two component regulatory system that controls the expression of various genes whose products allow the cell to thrive in low phosphate environments. The signaling mechanism of the PhoR/PhoB system has been studied and the phosphorylation cascade that controls gene expression is well understood. What is still unknown is how PhoR senses the phosphate level of the environment. The PstS, PstC, PstA, PstB, and PhoU proteins play a role in this signal sensing. This work confirms the hypothesis that the PstSCAB complex senses the environmental phosphate …

Methane Production By A Packed-Bed Anaerobic Digester Fed Dairy Barn Flush Water, Sean Richard Thomson

Master's Theses

Packed-bed digesters are an alternative to covered lagoon digesters for methane production and anaerobic treatment of dilute wastewaters such as dairy barn flush water. The physical media of packed-beds retain biofilms, often allowing increased treatment rates. Previous studies have evaluated several types of media for digestion of dilute wastewaters, but cost and media fouling have setback commercial development. A major operational cost has been effluent recirculation pumping.

In the present effort, a novel approach to anaerobic digestion of flush dairy water was developed at pilot-scale: broken walnut shells were used as a low-cost packed-bed medium and effluent recirculation was replaced …

Ciliates Of Sagebrush-Steppe Soils Of Southwestern Idaho: Species Richness And Its Relationship To Changed Soil Variables After Wildfire Events, Laura G. Wendell

Boise State University Theses and Dissertations

I conducted a pilot study to examine species richness of terrestrial ciliates associated with big sagebrush habitat (Artemisia tridentata) in southwestern Idaho, USA. As wildland fires are a naturally occurring disturbance in this area, soil variables associated with these fires (% C, % N, pH, soil texture, and % clay) were measured at three sites, both in burned and unburned areas. These soil characteristics were compared to corresponding ciliate diversity and ratios of r-selected colpodeans to K-selected polyhymenophorans (C/P) in non-flooded Petri dish preparations. A total of 85 ciliate taxa were observed across the three sites, including …

In Vivo Identification Of Eugenol-Responsive And Muscone-Responsive Mouse Odorant Receptors, Timothy S. Mcclintock, Kaylin Adipietro, William B. Titlow, Patrick Breheny, Andreas Walz, Peter Mombaerts, Hiroaki Matsunami

Physiology Faculty Publications

Our understanding of mammalian olfactory coding has been impeded by the paucity of information about the odorant receptors (ORs) that respond to a given odorant ligand in awake, freely behaving animals. Identifying the ORs that respond in vivo to a given odorant ligand from among the ∼1100 ORs in mice is intrinsically challenging but critical for our understanding of olfactory coding at the periphery. Here, we report an in vivo assay that is based on a novel gene-targeted mouse strain, S100a5-tauGFP, in which a fluorescent reporter selectively marks olfactory sensory neurons that have been activated recently in vivo. Because each …

A Comparison Of The Caulobacter Na1000 And K31 Genomes Reveals Extensive Genome Rearrangements And Differences In Metabolic Potential, Craig Stephens, Kurt Ash, Theta Brown, Tynetta Watford, Latia E. Scott, Bert Ely

Biology

The genus Caulobacter is found in a variety of habitats and is known for its abilityto thrive in low-nutrient conditions. K31 is a novel Caulobacter isolate that has the ability to tolerate copper and chlorophenols, and can grow at 48Cwith a doubling time of 40 h. K31 contains a 5.5 Mb chromosome that codes for more than 5500 proteins and two large plasmids (234 and 178 kb) thatcode for 438 additional proteins. A comparison of the K31 and the Caulobactercrescentus NA1000 genomes revealed extensive rearrangements of gene order,suggesting that the genomes had been randomly scrambled. However, a careful analysis revealed …

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 …

Genetic Susceptibility, Colony Size, And Water Temperature Drive White-Pox Disease On The Coral Acropora Palmata, Erinn M. Muller, Robert Van Woesik

Ocean Engineering and Marine Sciences Faculty Publications

Outbreaks of coral diseases are one of the greatest threats to reef corals in the Caribbean, yet the mechanisms that lead to coral diseases are still largely unknown. Here we examined the spatial-temporal dynamics of white-pox disease on Acropora palmata coral colonies of known genotypes. We took a Bayesian approach, using Integrated Nested Laplace Approximation algorithms, to examine which covariates influenced the presence of white-pox disease over seven years. We showed that colony size, genetic susceptibility of the coral host, and high-water temperatures were the primary tested variables that were positively associated with the presence of white-pox disease on A. …

Two Distinct Microbial Communities Revealed In The Sponge Cinachyrella, Marie L. Cuvelier, Emily Blake, Rebecca Mulheron, Peter J. Mccarthy, Patricia Blackwelder, Rebecca Vega-Thurber, Jose V. Lopez

Marine & Environmental Sciences Faculty Articles

Marine sponges are vital components of benthic and coral reef ecosystems, providing shelter and nutrition for many organisms. In addition, sponges act as an essential carbon and nutrient link between the pelagic and benthic environment by filtering large quantities of seawater. Many sponge species harbor a diverse microbial community (including Archaea, Bacteria and Eukaryotes), which can constitute up to 50% of the sponge biomass. Sponges of the genus Cinachyrella are common in Caribbean and Floridian reefs and their archaeal and bacterial microbiomes were explored here using 16S rRNA gene tag pyrosequencing. Cinachyrella specimens and seawater samples were collected from the …

Role Of Type Iv Pili In Predation By Bdellovibrio Bacteriovorus, Ryan M Chanyi, Susan F Koval

Microbiology & Immunology Publications

Bdellovibrio bacteriovorus, as an obligate predator of Gram-negative bacteria, requires contact with the surface of a prey cell in order to initiate the life cycle. After attachment, the predator penetrates the prey cell outer membrane and enters the periplasmic space. Attack phase cells of B. bacteriovorus have polar Type IV pili that are required for predation. In other bacteria, these pili have the ability to extend and retract via the PilT protein. B. bacteriovorus has two pilT genes, pilT1 and pilT2, that have been implicated in the invasion process. Markerless in-frame deletion mutants were constructed in a prey-independent mutant to …

Draft Genome Sequences Of Antibiotic-Resistant Commensal Escherichia Coli, Meghan Garrett, Jennifer Parker, Craig M. Stephens

Biology

Antimicrobial resistance is a significant public health issue. We report here the draft genome sequences of three drug-resistant strains of commensal Escherichia coli isolated from a single healthy college student. Each strain has a distinct genome, but two of the three contain an identical large plasmid with multiple resistance genes.