Microbiology Commons^™

Impact Of Seasonal And Host-Related Factors On The Intestinal Microbiome And Cestode Community Of Sorex Cinereus And Sorex Monticola, Katelyn D. Cranmer

College of Graduate Studies: Theses & Dissertations

The intestinal microbiome of mammals plays a significant role in host health and response to environmental stimuli and can include both beneficial native bacteria as well as parasitic worms. In this study, I examined the intestinal cestode and bacterial communities of two closely related species of shrew, Sorex monticola and Sorex cinereus, over a six month period in 2016. Specimens were collected approximately every three weeks from May to October from the Sangre de Cristo Mountains in Cowles, New Mexico. A total of 79 shrews were prepared with the gastrointestinal tracts removed and flash-frozen in liquid nitrogen. An additional …

A Bioinfomatic Analysis Of Luminal And Mucosal Ileal Bacteria Colonizing Nursery Pigs Fed Different Protein Sources, Jamie L. Ortman

Electronic Theses and Dissertations

Weaning is a critical time in a young pig’s life that will greatly impact its adult growth and development. The objective of this research was to evaluate the effects of various protein sources on the bacterial composition within luminal and mucosal populations in simple and complex diets to gain a better understanding of factors influencing gut health. Weaned pigs were fed 1 of 3 simple experimental diets: 1) basic diet containing corn and soybean meal (Negative Control - NEG), 2) basic diet + fishmeal (FM; Positive Control - POS), and 3) basic diet + microbially-enhanced soybean meal (MSBM). Phase I …

Mapping The Effects Of 5’ Untranslated Region Deletions On Translation Of 3a In Bmv Rna3, Courtney Marie Bozman

Graduate Research Theses & Dissertations

Brome mosaic virus (BMV) is a positive sense, single-stranded RNA virus that infects a wide array of plant hosts globally including: wheat, oats, maize, barley, and rye. Since its discovery in the 1940s, BMV has served as a model organism in uncovering the modalities of viral infectivity, composition, translation, and replication. In many viruses, it is typically imperative to recruit cellular machinery to produce viral proteins as their coding capacity is limited. Therefore, there are sequences and structures within the leader sequences allow them to be competitive with the eukaryotic mRNAs. Although BMV has been thoroughly researched in these other …

Soil Microbial Succession Following Surface Mining Is Governed Primarily By Deterministic Factors, Jennifer Lynne Kane

Graduate Theses, Dissertations, and Problem Reports (ETD)

Understanding the successional dynamics governing soil microbial community assembly is a promising way to advance development of remediation strategies for lands disturbed by anthropogenic activities. The environmental and ecological influences shaping these communities following soil disturbance remain only partially understood. One example of a physical anthropogenic disturbance is extraction of minerals such as coal by surface mining. Surface mining removes natural soils and these soils may be replaced immediately on adjacent reclaimed areas or they may be stored in piles for later use. During reclamation, the soil is replaced on the landscape and the site is re-vegetated with grasses and …

Mine Reclamation Using Biofuel Crops: Insights Into The Microbial Ecology Of The Switchgrass (Panicum Virgatum) Microbiome, Brianna L. Mayfield

Graduate Theses, Dissertations, and Problem Reports (ETD)

Bioenergy crop production has steadily increased due to growing political support for renewable energy, thus initiating a demand to find alternative agricultural land. An innovative option is the use of marginal soils, such as reclaimed mine lands, to produce bioenergy crops. Switchgrass (Panicum virgatum) is a promising bioenergy crop that can be grown on marginal lands due to its robust growth in various soil types and climates. However, little is known regarding plant-microbe interactions among switchgrass systems within reclaimed mine lands. A study conducted in 2008 grew switchgrass on high- and low- quality reclaimed mine sites (Hampshire and …

Adaptation Of The Streptococcal Collagen-Like Protein 1, Scl1, Of Group A Streptococcus To Recognize Fibronectin Type Iii Repeats, Dudley H. Mcnitt

Graduate Theses, Dissertations, and Problem Reports (ETD)

Background: Group A Streptococcus (GAS) is responsible more than 700 million infections worldwide each year. Most of these infections start with initial colonization of the throat and skin, which is augmented by surface adhesins. The streptococcal collagen-like protein 1 (Scl1) is a major adhesin expressed by GAS that contains an N-terminal sequence-variable (V) domain, protruded away from the cell surface by the collagen domain. The Scl-V domain is comprised of three pairs of anti-parallel α-helices interconnected by surface-exposed loops. For attachment, GAS adhesins require a portal of entry, such as a wound or breach in the epithelium, to enter …

Modeling Disease Impact Of Vibrio-Phage Interactions, Christopher Botelho

Electronic Theses and Dissertations

Since the work of John Snow, scientists and medical professionals have understood that individuals develop cholera by means of consuming contaminated water. Despite the knowledge of cholera's route of infection, many countries have experienced and still experience endemic cholera. Cholera is caused by the Vibrio cholerae (V. cholerae) bacterium and presents with acute diarrhea and vomiting. If untreated, infected individuals may die due to dehydration. Cholera is a disease that most commonly affects countries with poor infrastructure and water sanitation. Despite efforts to control cholera in such countries, the disease persists. One such example is Haiti which has been experiencing …

Impact Of Industrial Biocides On Bacterial Isolates From Hydraulic Fracturing Produced Water, Waad Ahmed Aljohani

Dissertations, Master's Theses and Master's Reports

Biocides are antimicrobial compounds that are designed to kill diverse groups of microbes in an untargeted fashion. Glutaraldehyde and DBNPA are commonly used to manage microbial growth in different industries. It is possible that biocide use may result in the development of bacterial resistance. However, resistance to DBNPA is believed to be limited under normal use conditions. We isolated a number of bacteria from produced water from a hydraulically fractured site in West Texas. We then tested the ability of these isolates to resist Glutaraldehyde and DBNPA. In this study, we found that these isolates have varying resistance to these …

The Infectivity Of Naegleria Fowleri Cysts In Vivo And In Vitro, And Mediation Of Encystment By Camp, Anna L. Evdokiou

Theses and Dissertations

The free-living amoeba and causative agent of Primary Amoebic Meningoencephalitis, Naegleria fowleri, has three life stages: the trophozoite, the flagellate, and the cyst. This study examined the ability of the cyst to attach to, excyst upon, and destroy cell cultures grown to confluent monolayers, and to cause Primary Amoebic Meningoencephalitis in a murine animal model. The co-culture of cysts with P388D.1, CHME3, Vero, human nasal epithelial, and rat primary mixed glial cells resulted in destruction of the monolayer of all cell types once the cysts attached and excysted. One day post exposure to cysts, the mixed glial cells exhibited …

The Role Of Rmta In The Opportunistic Pathaogen Aspergillus Fumigatus, Roshan Dahal

Graduate Research Theses & Dissertations

The fungus Aspergillus fumigatus is an opportunistic human pathogen capable of causing

a life-threatening systemic lung infection known as invasive aspergillosis among immune compromised

patients. This group includes individuals infected with HIV, people with hematological

malignancies, solid organ transplant patients, persons with genetic immunodeficiency and cancer

patient undergoing chemotherapy. Due to the medical relevance of this organism, it is imperative

to discover novel genetic elements to design antifungal drugs against A. fumigatus dissemination,

virulence and survival during human infection. Previously, the putative arginine methyltransferase

gene rmtA was characterized in the model organism Aspergillus nidulans and the opportunistic

plant pathogen Aspergillus …

Practical Bioinformatics Applications In Microbes, Sarah Anne Entwistle

Graduate Research Theses & Dissertations

This thesis examines three methodologies for applying bioinformatics techniques to microbial data. A computational analysis of RNA sequencing data showed that hbx1 is a global regulator in Aspergillus flavus. A particular focus of this analysis is the characterization of hbx1 in regard to regulation of secondary metabolite gene clusters and their production of aflatoxins. An analysis of bacterial genomes identified ORFans in both pathogenic and non-pathogenic genomes, along with their presence in sequence features. This investigation demonstrated that ORFan genes shared by pathogenic genomes were more related to bacterial pathogenicity. Evaluation of multiple types of recombination events in RNA sequencing …

The Link Between Antibiotic Resistance Used For Recombinant Dna Selection And Cellular Phenotype In Rat Liver Epithelial Cells, Doaa Alshammari

Graduate Research Theses & Dissertations

Recombinant DNA plasmids are often used to mediate forced gene overexpression or suppression in mammalian cells, to address questions regarding the role of specific proteins in cell behavior and function. To select for cells harboring such recombinant plasmids, lethal antibiotics such as Puromycin, Geneticin (Neomycin) and Zeocin are frequently used, as plasmids contain selective antibiotic resistance genes that biochemically disarm them. Antibiotic resistance, induced by plasmid-borne genes and chronic exposure to lethal antibiotics can likewise potentially change the phenotype of cells, confounding the conclusions drawn from experiments on gene overexpression or suppression. Yet, little is known about the effects of …

Microbiome And Metagenome Of An Anthropogenic Hyperalkaline Slag-Fill Waterway In South Chicago, Illinois, Usa, Jan Ingemar Ohlsson

Graduate Research Theses & Dissertations

The aquifers and waterways around the Lake Calumet area of south Chicago, IL, USA have been affected by a century of intensive industrial waste dumping. Steel slag in particular was used as infilling to claim most of the Calumet Wetlands for industrial and residential development. Since the prohibition and cessation of these disposal activities, a growing body of research has recorded the environmental and health effects of the infill, particularly where interactions between slag minerals and rainwater produces extremely alkaline groundwater (pH ≥13). Atmospheric carbon dioxide interacting with these calcium hydroxide-rich slag fluids produces massive precipitation of a loose, white …

Detection Of Beta-Lactamase Variants In Municipal Wastewater And Fresh Water, Sunil Pandey

Masters Theses

The occurrence and spread of antibiotic-resistant genes (ARGs) are pressing public health problems worldwide. A key factor contributing to the spread of ARGs is lateral gene transfer. Wastewater treatment plants (WWTPs) are measured hot spots of microbial diversity and resistance because they receive polluted wastewater from diverse sources and contain a variety of different environments with dense bacterial loads. Due to the overuse of antibiotics the genetic capacities of microbes have profited. This helps every source of resistance gene and every means of horizontal gene transmission to develop the multiple mechanism of resistance to each antibiotic used clinically, agriculturally, or …

Study Of Genetic Regulators That Control Development And Secondary Metabolism In The Genus Aspergillus, Timothy Satterlee

Graduate Research Theses & Dissertations

In this study, I investigated the role of two different regulatory genes in two different species of pathogenic fungi from the genus Aspergillus. The first study involves a transcriptome analysis of the epigenetic regulator rmtA in the plant pathogen Aspergillus flavus. A. flavus colonizes numerous oil seed crops such as corn, peanuts, treenuts and cotton worldwide, contaminating them with aflatoxins and other harmful potent toxins. Previously our lab characterized the gene rmtA, which encodes an arginine methyltransferase in A. flavus, and demonstrated its role as regulator of the expression of the aflatoxin gene cluster and concomitant synthesis of toxin. Furthermore, …

Impacts Of Plant-Microbe Interactions On Seedling Performance In A Riparian Forest Invaded By Lonicera Maackii, Taylor E. K. Strehl

Masters Theses

Soil microbes have profound impacts on plant growth and survival and can either promote or inhibit plant dominance. Exotic plants are often strongly invasive because they have escaped their natural enemies, potentially including antagonistic soil microbes. I examined how the invasive shrub Lonicera maackii and a common native tree, Acer negundo, responded to soil microbial communities to determine the role of soil microbes in regulating invasion success. This was done by growing both species with microbes from invaded (L. maackii) and uninvaded (A. negundo) soils collected from three locations within a riparian forest. Seedlings were …

Evaluation Of Intra-Species Diversity Of Oxalobacter Formigenes Strains Using Pulsed-Field Gel Electrophoresis (Pfge) And Multiplex Pcr, Nivedita Pareek

Masters Theses

Oxalobacter formigenes is a beneficial, strict anaerobic gut bacterium that plays an important role in the prevention of kidney stone disease with a unique characteristic of using only oxalate as a carbon and energy source. To date, twenty-one strains of O. formigenes have been isolated which are further divided into two groups based on differences in the patterns of cell membrane lipids, cellular proteins, and nucleic acid fragments. The objective of the study was to evaluate intra-species diversity of O. formigenes strains using pulsed-field gel electrophoresis (PFGE) and multiplex PCR.

Nine pure cultures of O. formigenes strains (5 strains group …

Xylan Metabolism By Caulobacter Crescentus, Viet Bui

Masters Theses

Bacteria present unique opportunities to explore the molecular mechanisms of nutrient acquisition processes at single cell level under various experimental conditions. Caulobacter crescentus is a gram-negative oligotrophic environmental bacterium with adaptive physiological responses, such as slow growth or complete arrest of cell cycle, presence of sessile and motile progenies with the sessile cells growing stalk to enhance nutrient uptake for growth in low-nutrient conditions. Details of plant polysaccharide-derived carbon compound, such as cellobiose, maltose, and xylose utilization by C. crescentus can be found but molecular details or mechanisms of polysaccharide utilization, such as xylan, has not been reported. Database analyses …

Efficacy Of Cold Plasma For Direct Deposition Of Antibiotics As A Novel Approach For Localized Delivery And Retention Of Effect, Agatha Los, Dana Ziuzina, Daniela Boehm, Lu Han, Denis O'Sullivan, Liam O'Neill, Paula Bourke

Articles

Antimicrobial coating of medical devices has emerged as a potentially effective tool to prevent or ameliorate device-related infections. In this study the plasma deposition process for direct deposition of pharmaceutical drugs on to a range of surfaces and the retention of structure function relationship and antimicrobial efficacy against mono-species biofilms were investigated. Two selected sample antibiotics—ampicillin and gentamicin, were deposited onto two types of surfaces—polystyrene microtiter plates and stainless steel coupons. The antimicrobial efficacy of the antibiotic-coated surfaces was tested against challenge populations of both planktonic and sessile Escherichia coli and Pseudomonas aeruginosa, with responses monitored for up to …

Best Practices In Patellar Tendinopathy Management: An Evidence To Practice Review, Christopher J. Burcal, Adam B. Rosen, Tony Taylor, Mike Nicola

Clinical Practice in Athletic Training

Patellar tendinopathy (PT) is a degenerative condition that is common in sporting populations due to the loads placed on the tendon during dynamic activity. PT often occurs in overtraining situations; however, it may also occur in conjunction with and/or worsen through poor biomechanics, persistent inflammation, and altered movement patterns. Although sports medicine practitioners have evidence to support the prevalence of this injury, we do not have a strong base of evidence surrounding the contributing factors and pathophysiology that lead the pain and disability reported in patients with PT. The purpose of this evidence to practice review was to summarize a …