Microbiology Commons^™

Understanding The Molecular Strategies Of Campylobacter Jejuni For Survival In Amoeba And Chicken., Deepti Pranay Samarth

Graduate Theses and Dissertations

Campylobacter jejuni endure to be major cause of gastroenteritis in humans worldwide. C. jejuni is fastidious in laboratory setup but can cause waterborne infection through contaminated water where none of these fastidious conditions are met. This dissertation presents an assortment of studies focused in reviewing three major factors which could present a helping hand to C. jejuni in its environmental survival viz. i) association with free-living amoebae (FLA) ii) horizontal gene transfer (HGT) contributing towards its genetic diversity iii). Viable but non-culturable (VBNC) state.

Acanthamoeba is a FLA linked to environmental survival of many intracellular pathogens, including C. jejuni. In …

Electrostatically Localized Proton Bioenergetics: Better Understanding Membrane Potential, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

In Mitchell's chemiosmotic theory, membrane potential Δψ was given as the electric potential difference across the membrane. However, its physical origin for membrane potential Δψ was not well explained. Using the Lee proton electrostatic localization model with a newly formulated equation for protonic motive force (pmf) that takes electrostatically localized protons into account, membrane potential has now been better understood as the voltage difference contributed by the localized surface charge density ([H-⁺_L] + ⁿΣ _i=1 [M⁽ⁱ⁺⁾_L]) at the liquid-membrane interface as in an electrostatically localized protons/cations-membrane-anions capacitor. That is, the origin of membrane …

A Rapid Viability And Drug‑Susceptibility Assay Utilizing Mycobacteriophage As An Indicator Of Drug Susceptibilities Of Anti‑Tb Drugs Against Mycobacterium Smegmatis Mc2 155, Gillian Catherine Crowley, Jim O'Mahony, Aidan Coffey, Riona G. Sayers, Paul D. Cotter

Department of Biological Sciences Publications

Background: A rapid in-house TM4 mycobacteriophage-based assay, to identify multidrug resistance against various anti-tuberculosis drugs, using the fast-growing Mycobacterium smegmatis mc² 155 in a microtiter plate format was evaluated, based on phage viability assays. Methods: A variety of parameters were optimized before the study including the minimum incubation time for the drugs, phage and M. smegmatis mc² 155 to be in contact. An increase in phage numbers over 2 h was indicative that M. smegmatis mc² 155 is resistant to the drugs under investigation, however when phage numbers remained static, M. smegmatis mc² 155 found to …

Fungi In A Hot, Dry, Changing World, Miriam I. Hutchinson

Biology ETDs

My doctoral work focused on understanding the reciprocal relationship between fungi and their environment, namely how fungi respond to environmental flux, as well as how fungi can modify and structure their habitats, especially in the context of climate change. As such, I aimed my research on fungi with distinct adaptations to their environmental niches: endophytic fungi that inhabit plant tissue and thermophilic fungi that are capable of growing at the upper temperature limit for eukaryotic life. My research consisted of three studies. First, I investigated the thermophilic species Myceliophthora heterothallica to demonstrate its use as a model organism for efficient …

Developing A Modern Microbiology Laboratory Manual To Enhance Student Learning, Alexander Yonchak

Senior Honors Projects

My project has been addressing the issue of incorporating recent developments in biosafety and pedagogical approaches for lab-courses into our existing educational curriculum by developing a new, modern lab manual aimed at improving experiential learning for introductory microbiology teaching labs. Through researching the most recent safety regulations, industry standards, & guidelines for such teaching labs, my manual clearly delineates learning outcomes to match the skills expected of undergraduates completing degrees within the life sciences. In addition, the lab manual that I have designed has been modernized to incorporate the most recent recommended safety precautions and is written in a user-friendly …

A Comparative Analysis Of The Fermentation Capabilities Of Various Bifidobacterium Strains, Ella Oney

Honors Program: Senior Projects (Public)

Bifidobacterium is a genus of anaerobic bacteria that are commonly found to inhabit the gastrointestinal tract of many members of the animal kingdom. These microorganisms are adapted to obtain their carbon from the breakdown of complex carbohydrates. Marmosets, a mammal whose gut microbiome is inhabited by high levels of Bifidobacteria, consume gum Arabic as a major part of their diet. The purpose of this experiment is to determine whether Bifidobacterium strains isolated from the guts of marmosets are able to degrade and ferment this complex carbohydrate or one of its main constituents, arabinose. This was accomplished by inoculating isolates of …

Genetic Study Of Checkpoint Defects Of The Mus81-1 Mutant In The Fission Yeast Schizosaccharomyces Pombe, Darlington Osei Abrefa

Browse all Theses and Dissertations

In response to various perturbations of DNA replication, the DNA replication checkpoint is activated in eukaryotes to stimulate a cascade of cellular responses that are crucial for maintaining genome stability and cell survival. Defects in the checkpoint pathway result in mutations and genome instability, which is a hallmark for cancers. This study used a genetic approach to identify a mutation in the MMS (methyl methanesulfonate) and UV-sensitive protein Mus81, a DNA repair enzyme that resolves aberrant DNA structures through the homologous recombination pathway. We show that a single missense mutation, identified in fission yeast mus81-1, causes moderate reduction in the …

Enhanced Expression Of Receptor Tyrosine Kinase Mer (Mertk) On Socs3-Treated Polarized Raw 264.7 Anti-Inflammatory M2c Macrophages, Sankhadip Bhadra

Browse all Theses and Dissertations

Macrophages are phagocytic cells located in tissues, organs and even circulated within our body as white blood cells. They are critical in detecting tissue damage and infection. Resident tissue macrophages initiate the signals for inflammation recruiting neutrophils and blood monocytes which mature into macrophages at sites of infection and in the resolution of inflammation. Based on the local cytokine milieu in tissue sites, macrophages may be polarized into pro-inflammatory M1 or anti-inflammatory M2 phenotypes. Receptor tyrosine kinase Mer (MERTK) helps in clearing dead neutrophils and other apoptotic cells from damaged tissue sites preventing chronic inflammation and autoimmune disorders. MERTK aids …

Six-Nine Months Long Term Culture Of Mouse Bone Marrow Cells Differentiated To Macrophages And Eosinophils, Olena B. Svitlova

Browse all Theses and Dissertations

Mouse models of eosinophil-associated diseases have been used to study the mechanisms of disease pathogenesis. In this study, mouse-derived bone marrow cells were used in long-term (6 and 9 months) cell cultures of differentiated eosinophils and macrophages. IL-5 was used to differentiate the stem cells to eosinophils and GM-CSF was used to propagate macrophages from the bone marrow stem cells. The maximum time period for observing the eosinophil cultures was 252 days which is censurably longer than the 18 days culture period observed by others. The results were assessed by describing the microscopic cell morphology by Wright staining, modified Giemsa …

A Full-Ocean-Depth Rated Modular Lander And Pressure-Retaining Sampler Capable Of Collecting Hadal-Endemic Microbes Under In Situ Conditions, Logan M. Peoples, Matthew Norenberg, David Price, Madeline Mcgoldrick, Mark Novotny, Alexander Bochdansky, Douglas H. Bartlett

OES Faculty Publications

The hadal zone remains one of the least studied environments because of its inaccessibility, in part because of hydrostatic pressures extending to 110 MPa. Few instruments are capable of sampling from such great depths. We have developed a full-ocean-depth-capable lander that can be fit with sampling packages for the collection of still images, video, motile megafauna, and hadal seawater. One payload includes a pressure-retaining sampler (PRS) able to maintain seawater samples under in situ pressure during recovery. We describe the technical specifications of the lander and the PRS and preliminary results from three deployments at depths in excess of 10,700 …

The Gut Microbiome: Is Fecal Matter Microbial Composition A Proxy For Intestinal Microbial Composition In Studies Of The Microbiome, Enique Reyes

All Master's Theses

As many health phenomena seem to be affected directly and indirectly by the microbiome, gut microbiome research has increased in the last decade. Issues such as allergies, cancer, obesity, and other health complications have been shown to be influenced by the microbiome. Most of gut microbiome research is done by collecting and sequencing the DNA of the microbiome of the fecal matter from model organisms or human subjects. Studies that use this method of sample collection and analysis assume that fecal matter microbiomes are similar to intestinal microbiomes, and that it can be used as a proxy. At present, no …

Bacterioplankton Biogeography Of The Mississippi River Basin, Jason Taylor Payne

Electronic Theses and Dissertations

Bacterioplankton are important structural and functional components of river networks yet their biogeographical patterns in these systems are largely unknown. Using Illumina sequencing of the 16S rRNA gene we characterized variation in bacterioplankton community alpha diversity (within-sample richness of operational taxonomic units OTUs) and beta diversity (between-sample differences in composition) (1) along a 1 300-km downstream reach of the Mississippi River (2) over a range of temporal scales in the Lower Mississippi River (LMR) and (3) along cross-sectional transects repeated monthly for six months across the LMR floodplain. Particle-associated assemblages were richer in bacterial OTUs and more productive than free-living …

The Role Of Cody In Hydrogen Peroxide Tolerance And Biofilm Formation Of Streptococcus Mutans, Kaitlin M. Rioux, Brandaliz Santiago-Narvaez

Honors Program Theses

Streptococcus mutans is the major cariogenic bacterium in the oral cavity. S. mutans causes disease by three main virulence factors: acid production, acid tolerance, and biofilm formation. S. mutans outcompetes various other species in the oral cavity, however it is affected by hydrogen peroxide production by these species. Based on previous findings and this research, hydrogen peroxide is shown to extend the lag phase of S. mutans but does not kill it unless present in extremely high amounts that are generally not produced by commensal species like S. sanguinis and S. gordonii in the oral cavity. CodY is a global …

The Effects Of Socs1 And Socs3 Peptide Mimetics On Macrophage Phagocytosis Of Malignant Cells, Tahirah M. Madkhali

Browse all Theses and Dissertations

Macrophages are essential phagocytic cells involved in both innate and adaptive immune systems and play vital roles in the host defense and inflammation. Macrophages have a remarkably high capacity to clear unnecessary cellular materials in interstitial environment through a process called “phagocytosis”, which is affected by many factors including suppressors of cytokine signaling (SOCS). SOCSs are a group of intracellular proteins that downregulate the cytokine signals involved in various JAK/STAT pathways through a negative feedback loop. This study focuses on investigating the effects of SOCS1 and SOCS3 on the phagocytic ability of RAW 264.7 macrophages polarized into M2a with IL-4/IL-13 …

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 …

Riparian Zone Soil Microbial Community Dynamics: Interactions With Nutrient Loadings, James Bannister

Theses and Dissertations (Comprehensive)

Riparian zones are a type of wetland described as the interface between land and a body of water such as a river or stream. Riparian zones are effective buffers against anthropogenic pollutants and nutrient loads from non-point sources that can greatly diminish water quality. Riparian zones can host a variety of plant species and associated microbial communities. The combined biological processes of plants, bacteria, and arbuscular mycorrhizal fungi (AMF) are key to nutrient cycling and nutrient removal in riparian zones. As such, understanding the factors that influence them is critical for watershed management. This research is targeted at obtaining a …

Structural Investigation Of Bcsc: Insight Into Periplasmic Transport During Cellulose Export, William Scott, Joel T. Weadge

Theses and Dissertations (Comprehensive)

A biofilm can be defined by a community of microbes coexisting within a self-produced protective polymeric matrix. Exopolysaccharide (EPS) is a key component in biofilms and a contributor to their virulence and pathogenicity. The cellulose bacterial synthesis complex is one such EPS system that is found in many Enterobacteriaceae,including Escherichia coli and Salmonella spp., and is responsible for the production and secretion of the EPS cellulose. BcsC is the periplasmic protein responsible for the export of the exopolysaccharide cellulose and was the focus of this research. Sequence homology comparisons and structural predictions between BcsC, and the previously characterized alginate …

A Rapid And Sensitive System For Recovery Of Nucleic Acids From Mycobacteria Sp. On Archived Glass Slides, Balkis A. Talip, William J. Snelling, Roy D. Sleator, Colm Lowery, James S.G. Dooley

Department of Biological Sciences Publications

The field of diagnostics continues to advance rapidly with a variety of novel approaches, mainly dependent upon high technology platforms. Nonetheless much diagnosis, particularly in developing countries, still relies upon traditional methods such as microscopy. Biological material, particularly nucleic acids, on archived glass slides is a potential source of useful information both for diagnostic and epidemiological purposes. There are significant challenges faced when examining archived samples in order that an adequate amount of amplifiable DNA can be obtained. Herein, we describe a model system to detect low numbers of bacterial cells isolated from glass slides using (laser capture microscopy) LCM …

Effects Of Evolution On Laboratory Sublines Of Myxococcus Xanthus Dk1622, Mackenzie Ryan, Francesca Scribano, Kimberly Murphy

Celebration of Learning

Microbes have served as effective models for studying evolution because of their ability to be easily replicated, stored, and manipulated. Myxococcus xanthus is a soil bacterium that has served as a model organism in many laboratories. The unique social and motile behaviors exhibited by this bacterium make it ideal for phenotypic assays. A wild-type strain of M. xanthus, DK1622, has been distributed to laboratories across the United States and therefore we now have DK1622 sublines. The genomes of a number of these sublines have been sequenced and their social and motile phenotypes have been analyzed. When nine of these sublines …

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, …

General Microbiology (Dalton State), April Kay, Susan Burran, Leah Howell

Biological Sciences Grants Collections

This Grants Collection for General Microbiology was created under a Round Nine ALG Textbook Transformation Grant.

Affordable Learning Georgia Grants Collections are intended to provide faculty with the frameworks to quickly implement or revise the same materials as a Textbook Transformation Grants team, along with the aims and lessons learned from project teams during the implementation process.

Documents are in .pdf format, with a separate .docx (Word) version available for download. Each collection contains the following materials:

• Linked Syllabus
• Initial Proposal
• Final Report

Inhibition Of Listeria Monocytogenes By Human Gut Bacteria, Patrycja Sylvia Olesky

Masters

Listeria monocytogenes is a foodborne pathogen, which continues to be problematic to the food industry due to its ability survive within food products and persist within food processing environments. The growing trend towards natural food preservatives and antimicrobial agents increases the need for the development of novel, natural anti-Listeria agents. Evidence presented in the literature suggests that the human gut microbiota is a reservoir of novel antimicrobial agents. It was therefore hypothesized that novel anti-Listeria agents are produced by human gut-derived bacteria. The objective of this study was to isolate and characterize gut bacteria with anti-Listeria monocytogenes activity. A total …

Characterizing Cultivable Bacteria From Trachymyrmex Septentrionalis Fungus Gardens, Hannah Beatty

Honors Scholar Theses

The relationship between the fungus-growing ant Trachymyrmex septentrionalis, its symbiotic cultivar fungus, and the transient and residential community of microorganisms is a diverse and complex symbiosis that has evolved over space and time. The fungus garden, comprised primarily of the cultivar fungus belonging to the family Leucocoprineae,provides an environment that hosts many bacteria, which may also play an important role in this symbiosis. Although it is known that Pseudonocardia bacteria defend the ant host against fungal pathogens, other species of bacteria that are present in these fungus gardens also likely contribute to this symbiosis. Previous studies of this …

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 …

Functional Similarity Of Prd-Containing Virulence Regulators In Bacillus Anthracis, Malik Raynor

Dissertations and Theses (Open Access)

Bacillus anthracis produces three regulators, AtxA, AcpA, and AcpB, that control virulence gene expression and are members of an emerging class of regulators termed “PCVRs” (Phosphoenolpyruvate-dependent phosphotransferase regulation Domain-Containing Virulence Regulators). AtxA controls expression of the toxin genes; lef, cya, and pag, and is the master virulence regulator and archetype PCVR. AcpA and AcpB are less well studied. AcpA and AcpB independently positively control transcription of the capsule biosynthetic operon capBCADE, and culture conditions that enhance AtxA activity result in capBCADE transcription in strains lacking acpA and acpB. RNA-Seq was used to assess the regulons of the …

Comparison Of Staphylococcus Phage K With Close Phage Relatives Commonly Employed In Phage Therapeutics, Jude Ajuebor, Colin Buttimer, Sara Arroyo-Moreno, Nina Chanishvili, Emma M. Gabriel, Jim O'Mahony, Olivia Mcauliffe, Horst Neve, Charles Franz, Aidan Coffey

Department of Biological Sciences Publications

The increase in antibiotic resistance in pathogenic bacteria is a public health danger requiring alternative treatment options, and this has led to renewed interest in phage therapy. In this respect, we describe the distinct host ranges of Staphylococcus phage K, and two other K-like phages against 23 isolates, including 21 methicillin-resistant S. aureus (MRSA) representative sequence types representing the Irish National MRSA Reference Laboratory collection. The two K-like phages were isolated from the Fersisi therapeutic phage mix from the Tbilisi Eliava Institute, and were designated B1 (vB_SauM_B1) and JA1 (vB_SauM_JA1). The sequence relatedness of B1 and JA1 to phage K …

Investigation Of Bacteria From The Trachymyrmex Septentrionalis Fungus Garden For Potential Antibacterial Drug Leads, Brendan Stewart

University Scholar Projects

Bacterial and fungal strains are growing resistance to antibiotics and antifungal agents at an alarming rate. According to the Centers for Disease Control and Prevention, over two million people in the United States in 2016 were diagnosed with an infection resistant to antibiotics. As such, there has been increased interest in natural products as sources of novel compounds that are essential to the development of new drugs and treatment methods. Within the environment, there are various host-microbe symbioses, one of which is the Trachymyrmex septentrionalis leaf-cutter ant community. The microbes in symbioses like the T. septentrionalis community are hypothesized to …

Investigation Of Bacteria From The Trachymyrmex Septentrionalis Fungus Garden For Potential Antibacterial Drug Leads, Brendan Stewart

Honors Scholar Theses

Bacterial and fungal strains are growing resistance to antibiotics and antifungal agents at an alarming rate. According to the Centers for Disease Control and Prevention, over two million people in the United States in 2016 were diagnosed with an infection resistant to antibiotics. As such, there has been increased interest in natural products as sources of novel compounds that are essential to the development of new drugs and treatment methods. Within the environment, there are various host-microbe symbioses, one of which is the Trachymyrmex septentrionalis leaf-cutter ant community. The microbes in symbioses like the T. septentrionalis community are hypothesized to …

Microbiology (Sgsc), Molly Smith, Sara Selby

Biological Sciences Grants Collections

This Grants Collection for Microbiology was created under a Round Six ALG Textbook Transformation Grant.

Affordable Learning Georgia Grants Collections are intended to provide faculty with the frameworks to quickly implement or revise the same materials as a Textbook Transformation Grants team, along with the aims and lessons learned from project teams during the implementation process.

Documents are in .pdf format, with a separate .docx (Word) version available for download. Each collection contains the following materials:

• Linked Syllabus
• Initial Proposal
• Final Report

A Cultured Learning Environment: Implementing A Problem- And Service-Based Microbiology Capstone Course To Assess Process- And Skill-Based Learning Objectives, Rachel M. Watson, John D. Willford, Mariel A. Pfeifer

Interdisciplinary Journal of Problem-Based Learning

In this study, a problem-based capstone course was designed to assess the University of Wyoming Microbiology Program’s skill-based and process-based student learning objectives. Students partnered with a local farm, a community garden, and a free downtown clinic in order to conceptualize, propose, perform, and present studies addressing problems experienced by these partners. Instructor assessments enabled understanding of student competencies, and according to external subject matter experts students demonstrated mastery of all learning objectives on the final research presentation. Community partners were completely satisfied with the students’ solutions, professionalism, and communication. Instructional diagnosis and student course evaluations showed satisfaction, engagement, and …