Microbiology Commons^™

Occurrence, Antibiotic Resistance, And Survival Of Fecal Enterococci In Turkey Litter, Steven Glynn Mcbride Ii

Masters Theses, 2010-2019

The United States Environmental Protection Agency’s National Water Quality Inventory and the Commonwealth of Virginia’s 305(b)/303(d) Water Quality Assessment Integrated Report show fecal bacteria to be the most common cause of impairment for both streams and estuaries. Human and animal sources have both been identified as significant contributors of pathogenic bacteria to surface waters. In this study, turkey litter from a farm in Shenandoah County, VA was surveyed for total culturable bacteria and total culturable enterococci before and after a transition to organic rearing practices. The enterococci were identified to species phenotypically using the Biolog Microbial Identification System and resistance …

Amino Acid Catabolism In Staphylococcus Aureus, Cortney Halsey

Theses & Dissertations

Staphylococcus aureus must rapidly adapt to a variety of carbon and nitrogen sources during invasion of a host. Within a staphylococcal abscess, preferred carbon sources such as glucose are limiting, suggesting S. aureus survives through the catabolism of secondary carbon sources. S. aureus encodes pathways to catabolize multiple amino acids including those that generate pyruvate, 2-oxoglutarate, and oxaloacetate. To assess amino acid catabolism, S. aureus JE2 and mutants were grown in complete defined medium containing 18 amino acids but lacking glucose (CDM). A mutation in glutamate dehydrogenase (gudB), which generates 2-oxoglutarate from glutamate, abrogated growth in CDM suggesting …

The Influence Of The Invasive Chinese Tallow (Triadica Sebifera) Leaf Litter On Aquatic Chemistry And Microbial Community Composition, Raymond D. Montez

Electronic Theses and Dissertations

Global climate change and anthropogenic activity have facilitated the movement and invasive potential of nonnative plants in native environments. These invasions can have negative effects on ecosystem diversity and function. The nonnative and invasive plant, Chinese Tallow (Triadica sebifera), has already invaded much of the south eastern US where it is outcompeting native tree species and changing ecosystem diversity in a variety of habitats. Leaf litter from the Chinese tallow has been shown cause changes in dissolved oxygen and pH in the aquatic environment. Turbidity is also affected when Chinese tallow litter is present in water. A series of …

Genomic Description And Annotation Of A New Colivirus; Kb1, Maggie Caswell

Honors Projects

KB1 is a bacteriophage with relatively few established characteristics. However, it is thought to be similar to the novel environmental isolate bacteriophage, JK5. The aim of this study was to describe and annotate the genome of this new colivirus, relative to the genome of JK5. This comparison confirms the hypothesis that these are similar, but distinct viruses, and provides a foundation for the further understanding of both of these novel environmental isolates.

Ecology Of Organohalide-Respiring Dehalococcoides Mccartyi: Corrinoid Cofactor-Related Community Interactions And Controls Over Strain Selection, Burcu Şimşir

Doctoral Dissertations

Organohalides such as tetrachloroethene (PCE) and trichloroethene (TCE) are among the most prevalent toxic groundwater contaminants. Remediation of organohalide-contaminated sites has high priority, and efficient and cost-effective remedies are needed to prevent environment and human exposure through contaminated water. Bacterial organohalide-respiration plays a major role in organohalide detoxification. Dehalococcoides mccartyi (Dhc) are key mediators in bioremediation, since only Dhc strains have been documented in complete detoxification of chlorinated ethenes to benign ethene. Dhc depends on other microorganisms in the environment for essential growth requirements (e.g., hydrogen and vitamins). For successful implementation of the reductive dechlorination to remediate contaminated …

Bioremediation Of Chlorinated Ethenes: Ph Effects, Novel Dechlorinators And Decision-Making Tools, Yi Yang

Doctoral Dissertations

Chlorinated solvents have been widely used in different areas of modern society. Usage of these chlorinated solvents was not necessarily accompanied with proper handling and disposal of these hazardous compounds, which caused a variety of environmental problems and continues to affect human health. Remediation of chlorinated ethenes contaminated sites has high priority for state regulators and site owners. Among the available treatment technologies, bioremediation shows great promise as a cost-effective corrective strategy for a variety of environmental pollutants. Prerequisites are that the microbiology involved in contaminant degradation and geochemical factors, such as pH, are understood, so that bioremediation technologies can …

Molecular And Ecological Aspects Of The Interactions Between Aureococcus Anophagefferens And Its Giant Virus, Mohammad Moniruzzaman

Doctoral Dissertations

Viruses are increasingly being recognized as an important biotic component of all ecosystems including agents that control the rapid ecological events that are harmful algal blooms (HABS). Aureococcus anophagefferens is a pelagophyte which causes recurrent ecosystem devastating brown tide blooms along the east coast of the USA and has recently spread to China and South Africa. It has been suggested that a large virus (AaV) is possibly an important agent for demise of brown tide blooms. This observation is consistent with the recognition of a number of other giant viruses modulating algal blooms in marine systems. In this dissertation, we …

Regulatory Mechanisms In Borrelia Burgdorferi-Induced Arthritis, Emily Siebers Hansen

Theses and Dissertations

Lyme arthritis is a common symptom of Lyme borreliosis that involves inflammation of the synovial joints. Elucidating the immune events involved in Lyme arthritis is complicated by the fact that not all individuals infected with B. burgdorferi develop arthritis. Additionally, Lyme arthritis manifests in different severities between affected individuals. It is known that an inflammatory response is initiated by B. burgdorferi infection and that inflammatory T cells contribute to the development of arthritis. However, the anti-inflammatory mechanisms that regulate the pathogenic T cells’ response are not entirely understood. Here, the hypothesis that a dysregulated immune response results in an excessive …

Utilization Of Ferrioxamine Microarrays For The Rapid Detection Of Pathogenic Bacteria, Nigam Bir Arora

Open Access Dissertations

Siderophores are low-molecular weight species utilized by bacteria for the sequestration of iron, an essential nutrient. Siderophores and their cognate receptors are considered to be virulence factors, due to their prominent role in pathogenicity. The work presented here focuses on ferrioxamine (FOx) as an “immutable” ligand for pathogen detection. A number of bacterial strains expressing high-affinity FOx receptors were identified by a proteomic BLAST search, and screened against microarrays patterned with FOx conjugates for detection using label-free optical imaging. Aspects such as inkjet printing and surface chemistry, iron-limiting conditions and bacterial selection protocols, and linker conjugate design were addressed and …

Investigating The Effects Of Ph On Alphaviral E3-E2 Glycoprotein Association, Organization, And Cellular Tropism, Jason Michael Sequra

Open Access Dissertations

In alphaviruses the role of E3 is required in protecting the fusion peptide region of E1 during intracellular transport. Throughout viral processing, the association of E2 and E3 is required for the successful trafficking and incorporation of E1 into the mature virion. This E3-E2 association has been observed to extend to mature virions in the solved structure for the envelope of Semliki Forest virus (SFV) and supported by the solved structure for the entire Venezuelan equine encephalitis virion (VEEV) with exclusive contacts being made between E3-E2. Immunization with monoclonal antibodies against VEEV E3 provided protection for mice challenged by lethal …

Complex Glycan Utilization Preferences Of Human Gut Bacteria, Yunus Emre Tuncil

Open Access Dissertations

Complex glycans, making up dietary fiber, have gained significance in recent years as they are the main energy source for the colonic microbiota which are physiologically important for the host health. Understanding glycan utilization strategies of the members of this community is essential to maximize beneficial health outcomes obtained from them. In order to investigate how the members of our gut microbiota utilize glycans and activate their respective polysaccharide utilization loci (PULs), we performed a series of time-course assays in which two model organisms, Bacteroides thetaiotamicron (Bt) and B. ovatus (Bo), were individually grown in a medium containing carbohydrates utilized …

Genomic And Transcriptomic Analysis Of Biofilm Formation In Persistent And Transient L. Monocytogenes, Clara Assisi

Open Access Theses

The Next Generation Sequencing (NGS) has been popularized and aid in the advancement of many fields of science. The other field of science that is being revolutionized is food science and technology, especially food safety. NGS application in food safety, especially the whole genome sequencing analysis (WGS), has been widely used for tracing back the source of outbreaks. The other application of NGS that is also being developed is the analysis of global transcriptomic or RNA-sequencing (RNA-Seq). In this research, we utilize NGS (Ilumina MiSeq Sequencing platform) to perform sequence comparison and identify single nucleotide polymorphisms (SNPs) and observe the …

The Role Of Streptococcus Gallolyticus Subspecies Gallolyticus In Colon Cancer Development, Jennifer L. Herold

Dissertations & Theses (Open Access)

Colorectal cancer (CRC) is the third most common cancer in men and women and is also the third most common cause of cancer death. A large body of evidence points towards the possibility that bacteria can have a significant impact on the development of cancer. It has been suggested that Streptococcus gallolyticus subsp. gallolyticus, a group D streptococci, may play a role in the development of CRC. Sg, formerly S. bovis biotype I, has been shown to be highly associated with CRC. In observing patients with either Sg bacteremia or endocarditis it was found that 25-80% of …

Repurposing Non-Antimicrobial Drugs To Treat Multi-Drug Resistant Bacterial And Fungal Infections, Shankar Thangamani

Open Access Dissertations

Bacterial and fungal resistance to conventional antimicrobials is a burgeoning global health epidemic that necessitates urgent action. Even more alarming, the development of new antimicrobials to treat these multidrug-resistant pathogens has not kept pace with the rapid emergence of resistance to current antimicrobials. Antimicrobial drug development through the traditional de novo process is a risky venture given the significant financial and time investment required by researchers and limited success rate of translating these compounds to the clinical setting. This has led researchers to mine existing libraries of clinical molecules in order to repurpose old drugs for new applications (as antimicrobials). …

Antibacterial Activity Of Essential Oil Encapsulated Sodium Iota-Carrageenan Fibers, Carlos D. Carter

Open Access Theses

Spoilage microorganisms cause food waste and loss of quality. While the foodborne pathogen outbreaks lead to thousands of hospitalizations and deaths. Essential oils (EOs), plant extracts, possess the required antimicrobial activities and thus their usage stands out as a feasible approach for controlling the undesirable bacterial growth in food systems. However, EOs are highly volatile and lose their activity upon exposure to environmental conditions. In this regard, their encapsulation in Generally Recognized As Safe (GRAS) matrices such as food grade polysaccharides especially iota-carrageenan could be one of the viable alternatives. Iota-carrageenan, sulfated polysaccharide from marine algae, is being used in …

Recombinant Listeria Adhesion Protein Expressing Probiotics Protect Against Listeria Monocytogenes Infection In Animal Models, Valerie E. Ryan

Open Access Theses

Listeria monocytogenes (Lm) is a foodborne pathogen, found ubiquitously in nature, and has a high morbidity rate among immunocompromised individuals, the elderly, and especially pregnant women and their fetuses resulting in abortion, stillbirth, and neonatal infection. There are currently no preventative medical interventions against Lm infection. The Listeria adhesion protein (LAP) is present in both pathogenic and non-pathogenic Listeria (i.e., L. innocua) and has shown to interact with host epithelial proteins causing tight junction dysregulation aiding in pathogen attachment and paracellular translocation across the host intestinal epithelium. Our lab has demonstrated that recombinant probiotics, Lactobacillus casei (LbcWT) expressing LAP …

Whole Genome Sequencing As A Tool For Identifying Phenotypic Properties And Underlying Genetic Mechanisms In Staphylococcus Pseudintermedius, Matthew C. Riley

Doctoral Dissertations

Staphylococcus pseudintermedius is a Gram-positive bacterial opportunistic pathogen commonly associated with dermal infections in canines, but capable of causing serious disease in other species. Reports of human infections caused by S. pseudintermedius along with an increase in resistance to multiple antibiotics highlights the importance of this organism. Whole genome sequencing can allow large scale investigation of genetic mechanisms underlying phenotypic properties that contribute to the expansion of successful S. pseudintermedius clonal lineages.

The increase in multidrug and methicillin-resistant S. pseudintermedius (MRSP) may result from horizontal transfer of genetic material between bacterial isolates, yet is thought to be rare in Staphylococci …

Tetrameric Photosystem I: From Initial Discovery And Characterization In Chroococcidiopsis Sp. Ts-821 To Exploration Of Its Distribution And Understanding Of Its Significance In Cyanobacteria, Meng Li

Doctoral Dissertations

Photosystem I (PSI) forms trimeric complexes in most characterized cyanobacteria. We had reported the tetrameric form of PSI in the unicellular cyanobacterium, Chroococcidiopsis sp. TS-821 (TS-821). Using Cryo-EM, a 3D model of the PSI tetramer structure at 11.5 [Angstrom] resolution was obtained and a 2D map within the membrane plane of at 6.1 [Angstrom]. In contrast to the three-fold symmetry in trimeric PSI crystal structure from T. elongatus, two different inter-monomer interactions involving PsaLs are found in the PSI tetramer. Phylogenetic analysis based on PsaL protein sequences shows that TS-821 is closely related to heterocyst-forming cyanobacteria. Additionally, this tetrameric …

Microbial Respiration And Community Response To Crude Oil In Deep Eastern Mediterranean And The Great Australian Bight, Jiang Liu

Doctoral Dissertations

The Deep Water Horizon (DWH) oil spill in 2010 was the largest deep ocean oil spill in world history. Very limited information about oil biodegradation is available in deep oceans other than GOM since DWH. In this study, we investigate the microbial communities’ response to crude oil contamination in the deep Eastern Mediterranean sea (E.Med) and Great Australian Bight (GAB). In addition, we will assess feasible methods for oil bioremediation in those locations.

First, we discovered the fast adaption of the E.Med deep water microbial community to oil contamination in terms of phylogeny and functional genes. Based on the 16S …

Investigating High Speed Localization Microscopy Through Experimental Methods, Data Processing Methods, And Applications Of Localization Microscopy To Biological Questions, Andrew J. Nelson

Electronic Theses and Dissertations

Fluorescence Photoactivation Localization Microscopy(FPALM) and other super resolution localization microscopy techniques can resolve structures with nanoscale resolution. Unlike techniques of electron microscopy, they are also compatible with live cell and live animal studies, making FPALM and related techniques ideal for answering questions about the dynamic nature of molecular biology in living systems. Many processes in biology occur on rapid sub second time scales requiring the imaging technique to be capable of resolving these processes not just with a high enough spatial resolution, but with an appropriate temporal resolution. To that end, this Dissertation in part investigates high speed FPALM as …

The Elasmobranch-Microbe Relationship: Trimethylamine N-Oxide Synthesis, Urea Hydrolysis, And Microbe-Osmolyte Interactions In The Atlantic Stingray, Dasyatis Sabina, Kaitlin Kelly Doucette

Master's Theses

The elasmobranch osmoregulatory strategy is predicated on the accumulation of nitrogenous compounds, primarily urea and trimethylamine n¬-oxide (TMAO). Despite the abundance of these plasma osmolytes, it is notable that elasmobranchs appear to lack urease and TMA oxidase (Tmase), enzymes that scavenge urea-nitrogen and synthesize TMAO, respectively. However, urease and Tmase are found in many species of bacteria. Therefore, I hypothesized that intestinal bacteria are responsible for urease and Tmase activity in elasmobranchs. Absent dietary nitrogen sources, I evaluated the effects of reduced intestinal microbiota on osmoregulation in Atlantic stingray (Dasyatis sabina) in vivo. D. sabina were given …

Fecal Bacterial Communities As An Indicator Of Trophic Interactions Among Anuran Larvae, Steven Jacob Everman

Master's Theses

Anurans are mass spawners, often with multiple females spawning together, resulting in thousands of tadpoles sharing a habitat. Such large numbers of tadpoles with limited dispersal can lead to intense competition for resources. Inter and intra-specific competition for food could have negative impacts on the growth and survival of smaller tadpoles. Fecal bacterial communities have the potential to be used as indicators of changes in diet making it possible to determine if tadpoles in the wild are eating the same food or not. After feeding on two prepared diets that differed in the percentage of complex carbohydrates, the fecal bacterial …

Effects Of Acute Heat And Oxidative Stress On The Hepatic Expression Of Orexin And Its Related Receptors, Stephanie Khaldi

Graduate Theses and Dissertations

It is widely known that orexin A and B peptides as well as their receptors are expressed in the hypothalamus and distributed throughout the central nervous system, but there have been few studies regarding its presences in other parts of the body. There is now evidence that orexin (ORX) and its receptors (ORXR1/2) are present in the avian liver; however, their regulation under different environmental conditions is still unknown. In the current study, we sought to determine the effects of heat and oxidative stress using hydrogen peroxide (H2O2) and 4-hydroxynonenal (4-HNE) on the hepatic expression of ORX and ORXR1/2 in …

A Portable And Automatic Biosensing Instrument For Detection Of Foodborne Pathogenic Bacteria In Food Samples, Zhuo Zhao

Graduate Theses and Dissertations

Foodborne diseases are a growing public health problem. In recent years, many rapid detection methods have been reported, but most of them are still in lab research and not practical for use in the field. In this study, a portable and automatic biosensing instrument was designed and constructed for separation and detection of target pathogens in food samples using nanobead-based magnetic separation and quantum dots (QDs)-labeled fluorescence measurement. The instrument consisted of a laptop with LabVIEW software, a data acquisition card (DAQ), a fluorescent detector, micro-pumps, stepper motors, and 3D printed tube holders. First, a sample in a syringe was …

Genetic Determinants Of Salmonella And Campylobacter Required For In Vitro Fitness, Rabindra Kumar Mandal

Graduate Theses and Dissertations

Non-typhoidal Salmonella (NTS) and Campylobacter play a major role in foodborne illness caused by the consumption of food contaminated by pathogens worldwide. A comprehensive understanding of the genetic factors that increase the survival fitness of these foodborne pathogens will effectively help us formulate mitigation strategies without affecting the nutrition ecology. The objective of this study was to identify the genetic determinants of Salmonella and Campylobacter that are required for fitness under various in vitro conditions. For the purpose, we used a high throughput Transposon sequencing (Tn-seq) that utilizes next generation sequencing (NGS) to screen hundreds of thousands of mutants simultaneously. …

Analysis Of Nucleosome Isolation And Recovery: From In Silico Invitrosomes To In Vivo Nucleosomes, Collin Brendan Skousen

Theses and Dissertations

There are a vast number of factors that influence nucleosome formation, and consequently gene regulation. These factors include histone modifications, nucleotide composition, transcriptional region elements, and specific nucleotide motifs, among others. Although the amount we know now is limited, we are creating new techniques and discoveries to assist us in continued understanding of chromatin. To make a significant contribution to the field of chromatin, I conducted two hypothesis driven sets of experiments that address the topic of chromatin structure. First, I created a technique for tissue specific nucleosome isolation with the goal of observing the effect of single nucleotide polymorphisms …

The Role Of Viral Interleukin-6 In Tumor Development Of Kaposi's Sarcoma-Associated Herpesvirus Lymphomas, Rebecca A. Fullwood

Theses and Dissertations

Kaposi's sarcoma herpesvirus (KSHV) is a cancer-causing virus, primarily affecting AIDS patients. KSHV is found in 3-10% of the U.S. population and can cause a range of cancers in the highly immunosuppressed; these cancers include Kaposi's sarcoma, pleural effusion lymphoma (PEL) and multicentric Castleman's disease (MCD). The current techniques for treating these cancers are relatively ineffective, largely due to their inefficiency at targeting tumors formed by the infection. One protein produced by KSHV, the viral homolog of interleukin-6 (vIL-6), is thought to play a major role in tumor development post-infection. Here a novel animal model is implemented to study the …

Switchgrass Extractives Have Potential As A Value-Added Antimicrobial Against Plant Pathogens And Foodborne Pathogens, Alexander Ian Bruce

Masters Theses

Panicum virgatum (switchgrass), a perennial grass native to North America, is a leading biomass feedstock candidate for the manufacture of cellulosic ethanol. Switchgrass is considered a viable option for biofuel production due to its cheap production cost and ability to grow on marginal land. Biofuel derived from switchgrass has been shown to be very energy efficient, producing 540% more renewable energy versus nonrenewable energy expended. Switchgrass-derived biofuel is also estimated to have greenhouse gas emissions that are 94% lower than emissions from gasoline (Schmer et al 2008). Biofuels are created through biochemical processes that utilize various enzymes and microorganisms for …

Epidemiology Of White Spot Syndrome Virus In The Daggerblade Grass Shrimp (Palaemonetes Pugio) And The Gulf Sand Fiddler Crab (Uca Panacea), Muhammad

Dissertations

Ever since the first outbreaks of White spot syndrome virus (WSSV), which causes White Spot Disease (WSD), in Asia in the early 1990s, the pathogen has been a major constraint to the profitability of the shrimp aquaculture industry across the globe. WSSV has a broad host range and is routinely detected in wild decapod crustaceans. In the present study, two common species in the tidal salt marsh along the northern coast of the Gulf of Mexico, the daggerblade grass shrimp (Palaemonetes pugio) and the Gulf sand fiddler crab (Uca panacea), were investigated for their role as …

A Microbiomic Approach To The Characterization Of The Impacts And Influences Of Viral, Bacterial, And Harmful Algal Bloom Toxins On The Bottlenose Dolphin, Corey David Russo

Dissertations

As apex predators that display high site fidelity Tursiops truncatus (bottlenose dolphin) are indicators of marine ecosystem health. Bottlenose dolphins, additionally, display pathogenesis and immune response similar to that of humans. Humans and coastal bottlenose dolphins, in particular, are constantly exposed to the same industrial, agricultural and domestic toxins and pathogens, contaminants and pollutants. Thus, studies on the bottlenose dolphin are also valuable in bridging the gap between ocean and human health. Bottlenose dolphins are susceptible to viral bacterial and toxin infection. Infection in the bottlenose dolphin manifests itself in the form of mass stranding events, unusual mortality events, chronic …