Microbiology Commons^™

Analysis Of The Chondroitinase Operon Of Flavobacterium Columnare, Erin L. Sorlien

Senior Honors Projects

Analysis of the chondroitinase operon of Flavobacterium columnare

Erin Sorlien

Major

Cell and Molecular Biology, Chemistry

Advisor

Dr. David R. Nelson

Date

May 2, 2013

Keywords

Flavobacterium columnare, columnaris disease, chondroitin AC lyase, complementation, csl operon

Abstract
Flavobacterium columnare, an opportunistic bacterial pathogen of fish, is the causative agent of columnaris disease (CD). The bacterium is a Gram-negative rod that exhibits gliding motility and avidly forms biofilms. CD affects both wild and cultured freshwater fish, and continues to cause large economic losses to the fish farming industry. According to an investigation conducted by the National Animal Health Monitoring System, CD …

Manipulating Aktivated Metabolism Via Mtorc1, Ivan Von Hack Prestinary

HIM 1990-2015

Although poorly understood, normal cells and cancerous cells of the same type exhibit different patterns of nutrient consumption, processing and utility of metabolic substrates. Differences in substrate uptake, preference, and alternately emphasized metabolic pathways offer opportunities for selective targeting of cancer versus stroma. This may be accomplished by using a sequential approach of nutrient deprivation and pharmaceutical perturbation of metabolic pathways to inhibit cellular proliferation. The purpose of this study was to investigate the effects of restricting glucose and glutamine concentrations, in vitro, to levels that resemble a potential human fasting state. The mammalian target of rapamycin (mTOR), a mediator …

Qcm Aptasensor For Rapid And Specific Detection Of Avian Influenza Virus, Luke Brockman

Graduate Theses and Dissertations

There has been a need for rapid detection of avian influenza virus (AIV) H5N1 due to it being a potential pandemic threat. Most of the current methods, including culture isolation and PCR, are very sensitive and specific but require specialized laboratories and trained personnel in order to complete the tests and are time-consuming. The goal of this study was to design a biosensor that would be able to rapidly detect AIV H5N1 using aptamers as biosensing material and a quartz crystal microbalance (QCM) for transducing method. Specific DNA aptamers against AIV H5N1 were immobilized, through biotin and streptavidin conjugation, onto …

Study Of Genes Relating To Degradation Of Aromatic Compounds And Carbon Metabolism In Mycobacterium Sp. Strain Kms, Chun Zhang

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Polycyclic aromatic hydrocarbons are produced from incomplete combustion of organic materials by human or natural activities. These polycyclic aromatic hydrocarbons are classified as pollutants because of their toxic, mutagenic, and carcinogenic characteristics. Mycobacterium sp. strain KMS, isolated from a contaminated soil, grows on the model polycyclic aromatic hydrocarbon, pyrene, with its degradation to water and carbon dioxide. This study locates genes on the chromosome and plasmids of isolate KMS relating to pyrene degradation, elucidates the influence of other carbon sources available in the habitats of isolate KMS on degradation of pyrene, and deduces possible metabolic pathways used by isolate …

Interaction Of Bacillus Anthracis Exosporium Protein Bcla With Complement Factor H And Spore Persistence In The Lung, Sarah A. Jenkins

Dissertations and Theses (Open Access)

Anthrax outbreaks in the United States and Europe and its potential use as a bioweapon have made Bacillus anthracis an interest of study. Anthrax infections are caused by the entry of B. anthracis spores into the host via the respiratory system, the gastrointestinal tract, cuts or wounds in the skin, and injection. Among these four forms, inhalational anthrax has the highest lethality rate and persistence of spores in the lungs of animals following pulmonary exposure has been noted for decades. However, details or mechanisms of spore persistence were not known. In this study, we investigated spore persistence in a mouse …

In Vitro Characterization Of Avian Influenza Virus Isolates With A Truncated Ns1 Gene Segment, Aaron Dick

Honors Scholar Theses

Avian Influenza Virus represents a significant threat to the world poultry population, and is a potential threat to humans due to the possibility of cross-species AIV infection. Our approach is to characterize a number of avian virus populations with respect to their content of biologically active particles that include hemagglutinating particles (HAP), plaque forming particles (PFP), interferon inducing particles (IFP), interferon induction-suppressing particles (ISP), defective-interfering particles (DIP), cell-killing particles (CKP) and non-infectious cell killing particles (niCKP) using unique in vitro assays developed for avian influenza virus in the Marcus-Sekellick Laboratory. Specifically, we will use a strain of Avian influenza virus, …

A Mathematical Model For Antibiotic Resistance In A Hospital Setting With A Varying Population, Edward H. Snyder

Electronic Theses and Dissertations

Antibiotic-resistant bacteria(ARB) is causing increased health risk and cost to society. Mathematical models have been developed to study the transmission of resistant bacteria and the efficacy of preventive measures to slow its spread within a hospital setting. The majority of these models have assumed a constant total hospital population with the admission and discharge rates being equal throughout the duration. But a typical hospital population varies from day to day and season to season. In this thesis, we apply variable admission and discharge daily rates to existing deterministic and stochastic models which examine the transmission of single and dual resistant …

Molecular And Genomic Based Insights Into The Evolution Of Enterococcus Faecium From Commensal To Hospital-Adapted Pathogen, Jessica R. Galloway-Pena

Dissertations and Theses (Open Access)

The basis for the recent transition of Enterococcus faecium from a primarily commensal organism to one of the leading causes of hospital-acquired infections in the United States is not yet understood. To address this, the first part of my project assessed isolates from early outbreaks in the USA and South America using sequence analysis, colony hybridizations, and minimal inhibitory concentrations (MICs) which showed clinical isolates possess virulence and antibiotic resistance determinants that are less abundant or lacking in community isolates. I also revealed that the level of ampicillin resistance increased over time in clinical strains. By sequencing the pbp5 gene, …

The Presence Of Methicillin Resistant Staphylococcus Aureus (Mrsa) On Environmental Surfaces In Healthcare Facilities Pre- And Post-Cleaning, Aaron Thomas Hunt

UNLV Theses, Dissertations, Professional Papers, and Capstones

The emergence of antibiotic resistant bacteria is a serious public health issue affecting millions of people. Methicillin-resistant Staphylococcus aureus(MRSA) is a leading cause of healthcare acquired infections today. Research has shown that patients infected or colonized with MRSA shed the bacteria into the environment, where the bacteria can survive for long periods of time and become potential sources of infection. Currently, infection prevention efforts focus on active surveillance, hand hygiene, personal protective equipment use and antimicrobial stewardship, with less attention given to environmental cleaning. Nevertheless, environmental cleaning is essential to remove infectious agents from environmental surfaces and prevent transmission. The …

Bioelectrochemical Reduction Of Carbon Dioxide To Acetate Using A Microbial Consortium Derived From The Cow Rumen, Ryan Hammonds

All Theses

Pure cultures of chemoautotrophic microorganisms have previously been reported to produce acetate from carbon dioxide using reductive electric current. We hypothesized that electrofuel precursors could be produced in a similar manner from a consortium consisting of microbial populations acting as a stable community. This approach might offer improved efficiency and selectivity, greater sustainability, a more diverse group of end products, and more opportunities for community optimization in electrofuel production than is possible with pure cultures. To evaluate this concept, bovine rumen contents were enriched for autotrophic, anaerobic microbes for several generations using hydrogen and carbon dioxide for growth and energy. …

Analysis Of The Interaction Of Francisella Tularensis Lvs And Legionella Pneumophila Biofilms With Components Of The Aquatic Environment, Uma Mahajan

All Dissertations

Biofilms are complex communities of organisms enclosed in a matrix (EPS) composed of polysaccharides, proteins and DNA. Biofilms are the base of the aquatic ecosystem and interact with the biotic as well as the abiotic components in the environment. Biofilms interact with biotic components of the environment such as protozoa and aquatic invertebrates. In this project, the biotic interactions of Francisella tularensis LVS biofilms are studied in relation to the mosquito larvae of Culex quinquefasciatus. F. tularensis is the causative agent of tularemia and is transmitted by ticks, deer flies, and mosquitoes. Mosquitoes are believed to play a role in …

Evolution Of Human Immunodeficiency Virus Type 1 Clade C Envelope V1–V5 Region During Disease Progression In Non-Human Primate Model, For Yue Tso

School of Biological Sciences: Dissertations, Theses, and Student Research

Human immunodeficiency virus type 1 (HIV-1) clade C strain is the fastest spreading HIV-1 strain globally, especially in Africa. It has been decades since the acquired immune deficiency syndrome (AIDS) pandemic first started. However, an effective anti-HIV-1 vaccine is not yet available, which is partly due to the highly variable nature of HIV-1 envelope gene and the absence of a suitable animal model. Strengthening of the understanding of envelope evolution during disease progression will contribute significantly towards future anti-HIV-1 treatment and preventions.

Non-human primates have been an essential animal model for many biomedical research areas. Using simian-human immunodeficiency virus (SHIV) …

Telomere-Related Factors And Human Papillomavirus Genome Maintenance, Adam J. Rogers

School of Biological Sciences: Dissertations, Theses, and Student Research

Human papillomaviruses (HPVs) are small DNA tumor viruses identified by their characteristic ability to replicate as a nuclear plasmid in mitotically active basal keratinocytes. A key characteristic of the HPV life cycle is the establishment of a stable maintenance phase wherein the virus replicates at low copy number, which likely occurs in cells expressing little to no E1 and E2. It is thought that HPV16 replicates in a once-per-cell-cycle manner during this portion of its life cycle and presumably interacts with host chromosome replication and maintenance factors to facilitate this replication. The adaptive radiation of papillomaviruses in response to changing …

Small Interfering Rna-Mediated Translation Repression Alters Ribosome Sensitivity To Inhibition By Cycloheximide In Chlamydomonas Reinhardtii, Xinrong Ma

School of Biological Sciences: Dissertations, Theses, and Student Research

RNA interference (RNAi) is an evolutionarily conserved gene silencing mechanism in eukaryotes, with regulatory roles in a variety of biological processes, including cell cycle, cell differentiation, physiological and metabolic pathways, and stress responses. RNAi can function by transcriptional silencing, mRNA target cleavage, translation repression and/or DNA elimination. In this study, we used the unicellular green alga Chlamydomonas reinhardtii as a model system to study RNAi-mediated translation repression. We demonstrated that small RNAs (sRNAs) generated from exogenously introduced inverted repeat transgenes, with perfect complementarity to the 3’UTR of a target transcript, can inhibit protein synthesis, without or with only minimal mRNA …

Development Of A Predictive Modeling System For Validation Of The Cumulative Mirobial Inactivation Of The Salmonellae In Pepperoni Utilizing A Non-Pathogenic Surrogate Microorganism (Enterococcus Faecalis), Scott Donald Stillwell

Graduate Theses and Dissertations

Salmonellosis is the most frequently occurring bacterial foodborne illness in the United States and the human case rate has not improved for the past two decades. The federal agency responsible for oversight of meat and poultry processors has announced the intent to extend existing pathogen reduction performance standards for Salmonella spp. to cover all classes of products including fermented sausages that are currently produced under HACCP plans that are validated for control of Escherichia coli O157:H7. The proposed regulatory modifications will require processors to revalidate HACCP plan controls to achieve either a 6.5 or a 7.0 log10 inactivation of the …

Proteomic Studies Of The Influenza Virus-Human Cell Interactions: The Responses Of Host Cell Protein Expression To Viral Infection And The Novel Host Proteins That Interact With Virus Protein Ns1, Yimeng Wang

Graduate Theses and Dissertations

Influenza A viruses (IAVs) continue to be a threat to human health. Despite extensive studies, the mechanisms underlying the IAVs-host interactions during IAV infection remain elusive. We employed quantitative proteomic methods to systematically explore the host cell protein expression responses to IAV infection and examine the function of a critical IAV protein called NS1 by identifying its host binding partners. Specifically, we used a 2-dimentional gel electrophoresis (2-DE) based proteomic method to screen host proteins whose expression was substantially altered by IAV. One critical protein named IκB kinase-gamma (IKKγ) was found to be significantly down-regulated during IAV infection. Functional studies …

Litter Conditioning Is Differentially Affected By Leaf Species, Phosphorus Enrichment, And Light Availability, Erin E. Scott

Graduate Theses and Dissertations

Anthropogenic enrichment of nitrogen and phosphorus is one of the most pervasive and detrimental threats to aquatic ecosystems worldwide. In streams that rely on allochthonous basal food resources, such as leaves, nutrient pollution can result in altered food quality and decreased carbon (C) standing stocks. However, the magnitude and mechanisms of this change in quality are poorly understood. Laboratory microcosm studies were conducted to 1) quantify the response of litter C:P to a gradient of phosphorus (P) enrichment (0, 0.05, and 0.5 mg SRP/L) across leaf species with variable levels of degradability (sugar maple and oak), and 2) quantify the …

Malignant Vascular Tumours Associatedwith The Breast: A Study Of 7 Cases, Azizun-Nisa, Zeeshanuddin, Naila Kayani

Department of Pathology and Laboratory Medicine

Angiosarcomas account for less than 0.05% of the malignant neoplasms of the breast. We present here 7 cases of malignant vascular neoplasms of the breast, including 2 cases of postmastectomy Stewart-Treves syndrome. In this case series, most of the patients were young. Tumour was bilateral at presentation in one case. The size of the tumours ranged from 1.6 cm to 11 cm. Although breast angiosarcomas are rare neoplasms, with the increasing use of radiation therapy for breast cancer patients, post-radiation skin lesions should not be ignored.

Characterization Of Human Gut Microbiota Dynamics Using Model Communities In Gnotobiotic Mice, Nathaniel Patrick Mcnulty

All Theses and Dissertations (ETDs)

The human gut is colonized by a diverse array of microbes, collectively referred to as the microbiota. The microbiota's complexity poses significant challenges in characterizing the rules dictating its assembly, inferring the functional roles of its component species, and understanding how communities sense and respond to changes in their habitat. We developed defined, representative model communities comprised of sequenced human gut bacteria that could be characterized in a highly controlled manner in gnotobiotic mice, plus a suite of scalable molecular tools for assaying community properties. These tools were first used to evaluate how the microbiota is impacted by probiotic bacterial …

Validation Of Microwave Heating Instructions For The Destruction Of Salmonella Spp. In Microwaveable Foods, Carol J. Valenzuela

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Microwave heating instructions for three products (chicken nuggets, turkey pot-pies and mashed potato) were developed and validated based on end point temperatures using two microwave ovens (2,459 MHz; 700 W and 1,350 W). Heating instructions for chicken nuggets were validated using different configuration of product placement (edge or center of the carousel) and number of units (4, 6 and 8). Salmonella spp. reductions of 6.56 log CFU/g (700 W) were observed in chicken nuggets heated in groups of 4 and placed at the center of the carousel with 1 min 26 s of heating time with a target end point …

The Influence Of Diet On The Mammalian Gut Microbiome, Brian David Muegge

All Theses and Dissertations (ETDs)

The mammalian gut is residence to a large microbial community whose collective set of millions of genes: microbiome) encodes a vast array of functions, including many that process dietary components. Few tools are available to change the microbiome's properties to promote host health because the factors governing community assembly and operation are poorly understood. My thesis focused on the impact of one factor, host diet.

I used a variety of experimental and computational methods to perform a comparative metagenomic study of the fecal communities of 39 diverse mammals to assess microbiome variation. These animals included herbivores, omnivores and carnivores representing …

Enrollment In Yfv Vaccine Trial: An Evaluation Of Recruitment Outcomes Associated With A Randomized Controlled Double-Blind Trial Of A Live Attenuated Yellow Fever Vaccine, Paula M. Frew, Eve T. Shapiro, Lu Lu, Srilatha Edupuganti, Harry L. Keyserling, Mark J. Mulligan

Environmental & Global Health Faculty Research

This investigation evaluated several factors associated with diverse participant enrollment of a clinical trial assessing safety, immunogenicity, and comparative viremia associated with administration of 17-D live, attenuated yellow fever vaccine given alone or in combination with human immune globulin. We obtained baseline participant information (e.g., sociodemographic, medical) and followed recruitment outcomes from 2005 to 2007. Of 355 potential Yellow Fever vaccine study participants, 231 cases were analyzed. Strong interest in study participation was observed among racial and ethnically diverse persons with 36.34% eligible following initial study screening, resulting in 18.75% enrollment. The percentage of white participants increased from 63.66% (prescreened …

Molecular Mechanisms Of Lupus Risk Conferred By Allele In The Gene For Interferon Response Factor 5, Dr. Brian Poole

Journal of Undergraduate Research

The academic objectives of this proposal were met. Using the funding provided by the MEG, we generated data that was used to publish four peer-reviewed journal articles and one peer-reviewed book chapter. These are:

Transcriptional Activity Of The Novel Nuclear Protein Nbmp-2, Dr. Laura Bridgewater

Journal of Undergraduate Research

The goal of this project was to follow up on preliminary data suggesting that nBmp2 directly activated transcription. A few months of follow-up experiments, however, showed that the original transcription data was not reproducible. At that point we turned our attention to two different questions about nBmp2 function: 1) Does nBMP-2 affect the cell cycle? 2) Is nBMP-2 involved in the immune response? These questions have each yielded interesting and important results that are leading toward publications and grant proposals.

Development Of Real-Time Polymerase Chain Reaction (Q-Pcr) Assays For The Specific Detection And Characterization Of Select Bacterial Pathogens, Dr. Richard Robison

Journal of Undergraduate Research

Primer generation software will be used to design primer and probe sequences that will theoretically perform optimally in PCR reactions. All sequences will be subjected to BLAST searches to confirm their specificity for a particular organism. Once primer sequences have been obtained, they will be synthesized by Integrated DNA Technologies, Inc. (IDT). These primers will be evaluated in q-PCR reactions using target DNA from multiple isolates and SyberGreen to detect nucleic acid amplification. Parameters for each reaction will be optimized using these same tools. Once a reaction has been optimized, a specific labeled probe will be synthesized which contains both …

Cytokine Signaling In The Microenvironment May Aid In Tumor Development And Progression, Dr. Kim O'Neill

Journal of Undergraduate Research

Studies have indicated that in breast tumors a high number of tumor associated macrophages (TAM’s) is indicative of a poor prognosis. TAM’s in the breast tumor microenvironment generally have a compromised immune response and focus their energy toward tissue repair which leads to angiogenesis, tumor growth, and metastasis. These macrophages have been termed M2 macrophages. Conversely, studies also indicate that in the microenvironment of some colon cancers, M1 phenotypic macrophages are present and that a high number of TAM’s is associated with a good prognosis.

A Novel Nuclear Variant Of Nbmp-2: Role In Ca2+ Transport, Dr. Laura Bridgewater

Journal of Undergraduate Research

The goal of this project was to elucidate the role that nBMP-2 plays in Ca2+ transport. In the previous year, we demonstrated that mice that have no nBMP-2 in the nuclei of their cells exhibit delays in the transport of Ca2+ back into the sarcoplasmic reticulum after each muscle contraction. During the period of this award we have extended our focus on nBMP-2 and Ca2+ transport to its effects on neurological function, since learning and memory are also dependent on intracellular Ca2+ transport. To do so, we collaborated with Dr. Jeff Edwards, a neuroscientist in the Department of Physiology and …

Interferon Alpha In Systemic Lupus Erythematosus, Dr. Brian Poole

Journal of Undergraduate Research

We presented data from this project at two meetings, 2 presentations at the American society for Microbiology Branch Meeting, Provo UT 2010 and one at the Intermountain Research Symposium, Logan Utah 2010. At the ASM meeting one of my undergraduates was selected to give an oral presentation, and all presentations were done by students. We also published a paper with student authorship that was supported by the MEG. The paper is “Neiwold, Timothy; Clark, Daniel; Salloum, Rafeh; Poole Brian D. Interferon alpha in systemic lupus erythematosus. J Biomed Biotechnol. 2010;2010:948364” We also have three manuscripts in preparation that include data …

Secretion Of Tcpf By The Vibrio Cholerae Toxin-Coregulated Pilus Biogenesis Apparatus Requires An N-Terminal Determinant, Christina J. Megli, Ronald K. Taylor

Dartmouth Scholarship

Type IV pili are important for microcolony formation, biofilm formation, twitching motility, and attachment. We and others have shown that type IV pili are important for protein secretion across the outer membrane, similar to type II secretion systems. This study explored the relationship between protein secretion and pilus formation in Vibrio cholerae. The toxin-coregulated pilus (TCP), a type IV pilus required for V. cholerae pathogenesis, is necessary for the secretion of the colonization factor TcpF (T. J. Kirn, N. Bose, and R. K. Taylor, Mol. Microbiol. 49:81–92, 2003). This phenomenon is not unique to V. cholerae; secreted …

Novel Neutralizing Antibody Assays For Recombinant Human Hookworm Na-Gst-1 Vaccine, Xi Chen, Brian Keegan, Peter J. Hotez, Jeffrey M. Bethony, Amar R. Jariwala

GW Research Days 2013

BACKGROUND

Necator Americanus, a human hookworm causes approximately 85% of the global hookworm infections. Hookworm ingest hemoglobin containing erythrocytes. Hemoglobin is further digested to Heme and Globin by hookworm's gut enzymes. Iron-containing Heme is a potent enzyme inhibitor and generates toxic reactive oxygen species which is toxic to hookworms. Hookworm's gut enzyme Na-GST-1 (Necator Americanus Glutathione S-Transferase-1) has been hypothesized to detoxify Heme. Na-GST-1 adjuvanted with Alhydrogel® is a new vaccine which is currently under clinical development. Na-GST-1 has two active sites, the ligand binding or Heme detoxification site (H-site) and the catalytic active glutathione binding …