Microbiology Commons^™

Advancing Biological Applications Through Microfluidic-Based Tool Development, K.M. Taufiqur Rahman

Electronic Theses and Dissertations

This research undertook an interdisciplinary approach, integrating bioengineering, microbiology, molecular biology, and systems biology to investigate bacterial dynamics behavior. Specifically, it delved into the development of microfluidic devices for biological applications such as bacterial cell counts, real-time observation of plant roots (here, specialized lectin-coated microbeads are used that mimic root characteristics), and soil microbe interactions. Furthermore, Next-Generation Sequencing and systems biology methodologies were employed to explore the intricate, multifaceted survival mechanisms of Escherichia coli persister population. Studying and quantifying persisters or testing for the existence of VBNC (viable but nonculturable) is challenging. These experiments require precise counts. It has been …

Complete Genome Sequence Of Microbacterium Foliorum Phage Curie, A Podovirus Isolated From Soil In Spokane, Washington, Emma N. Horton, Kathryn T. Cook, Kyra G. Cronin, Avery T. Haag, Sierra M. Salter, Nicole A. Stojanovic, Zoe E. Fry, Brian M. Connolly, Rebekah F. Hare, Ann-Scott H. Ettinger, Marianne K. Poxleitner, Kirk Anders

Biology Faculty Scholarship

Bacteriophage Curie is a podovirus that infects Microbacterium foliorum. The Curie genome spans 16,810 bp, has 90 bp terminal inverted repeats, and includes 23 protein-coding genes. Its genome architecture resembles phage PineapplePizza and other phi29-like phages. Together, Curie and PineapplePizza form a new actinobacteriophage Cluster GI.

Persistence Of Wastewater-Associated Antibiotic Resistant Bacteria In River Microcosms, Aoife P. Mahaney

Theses and Dissertations

The spread of antibiotic-resistant bacteria (ARB) associated with wastewater is a significant environmental concern, but little is known about the persistence and proliferation of these organisms in receiving water bodies after discharge. To address this knowledge gap, we performed a series of microcosm experiments in which river water was amended with either untreated or treated wastewater, and the abundance of viable ciprofloxacin-, Bactrim-, and erythromycin-resistant bacteria was monitored for 72 hours.

Both types of wastewater amendments increased the initial abundance of ARB compared to microcosms containing only river water. The increase was greatest with untreated wastewater, but that effect decreased …

Do Duckweeds Adapt To Water And Microbes?, Ava M. Rose

Honors Theses and Capstones

Organisms in their home environment sometimes outperform transplanted individuals native to other areas, in a phenomenon termed local adaptation. While local adaptation is traditionally considered to be driven by the abiotic factors of an environment, scientists have recently increased consideration of biotic factors. Specifically, of interest to many is host-associated microbiomes, which can alter host trait expression. As the desire to commercialize microbiome treatments for agriculture and medicine grows, it is important to analyze the potential value of local microbiomes, which may be adapted to their hosts, or to which local hosts may have adapted. Using Lemna minor (duckweed) as …

Developing Methods For Analysis Of Chiral Small Molecules And D-Amino Acid Containing Peptides, Joshua I. Putman

Chemistry & Biochemistry Dissertations - Archive

This dissertation covers the development of methods to analyze chiral small molecules and d-amino acid containing peptides. The first section covers the development of liquid chromatographic chiral screening approaches for newly synthesized chiral molecules. The next part of the dissertation covers methodologies for the analysis of d-amino acid containing peptides. Lastly the bacterial degradation of three commonly used pesticides by bacteria harvested from Colorado potato beetles (Leptinotarsa decemliniata) is presented.

Twelve new azole compounds and eleven racemic ethanolamine derivatives were synthesized. These twenty-three compounds were evaluated using eight chiral columns, four macrocylic glycopeptides, a cyclodextrin derivative …

Sun Damages And Preventative Measures For Keratinocyte Carcinomas, Alex Kandolin

Biology and Microbiology Graduate Students Plan B Research Projects

UV rays from the sun cause damage to our genomic DNA and in turn have the ability to cause cancer. Protection methods such as sunscreen have been used for many years, however, the introduction of polyphenols and topical creams have brought new hope to skin protection. Polyphenols are a new method using an internal approach that directly targets the damaged DNA using different mechanisms through food. When used in addition to sunscreen, the chances of skin cancer are greatly reduced. Additionally, but using topical cream such as 5-fluorouracil can be an approach to already existing lesions caused from UV radiation. …

Regulation Of Inflammatory Signaling By The Gut Microbiome, Caden Johnson

Biology and Microbiology Graduate Students Plan B Research Projects

The human gut contains trillions of bacteria that play a key role in gastric homeostasis. Commensal bacteria play a critical role in the formation of the gastrointestinal barrier that prevents invasion of other pathogenic bacteria and also serves as a secondary metabolism system that aids in the synthesis of dietary fibers into many essential nutrients such as vitamins, sugars, and especially short chain fatty acids (SCFAs) in the anaerobic conditions in the large intestine. These SCFAs assist in regulating immune tolerance to commensal bacteria of the gut and promote an anti-inflammatory state important to lowering the incidence of inflammatory disorders …

Treatment-Related Adverse Effects In African Cancer Patients: A Systematic Review, Gabriel T. Fagbenro

Biology and Microbiology Graduate Students Plan B Research Projects

Treatment associated with cancer comes with serious adverse effects which affect patients’ physiological functioning, worsen financial toxicity, reduce quality of life, and increased risk of treatment discontinuation. There is dearth of evidence on prevalence and pattern of side effects among African patients receiving cancer-directed therapies. Primary research studies reporting side effects of non-surgical interventions among patients in African countries were selected for review. The most prevalent side effects included nausea, vomiting, and loss of appetite (chemotherapy); radiation dermatitis and mucositis (radiation therapy); anaemia, neutropenia/febrile neutropenia, and thrombocytopenia (chemoradiation), and cardiotoxicity (immunotherapy). Oncologists need to pre-empt and provide necessary prophylactic and …

Fungal Activity In Fusarium Keratoplasticum Isolates With And Without Endohyphal Bacteria On Various Carbon Sources, Maya Brown

Honors College Theses

In recent years, the fungus Fusarium keratoplastic has been associated with failed sea turtle eggs. One fungal isolate collected from a failed egg collected on Wassaw Island, GA in 2020 contained endohyphal bacteria, bacteria living within the hyphae of the fungus. The type of endohyphal bacteria (EHB), as well as the relationship between the bacteria and fungal hosts, are currently unknown. Previous research on the same fungus and EHB, specifically Chitinophaga sp., discovered that EHB influenced the ability of the fungus to utilize carbon sources. Our research goal was to examine the metabolic relationship of Fusarium isolated from failed sea …

Investigating Antimicrobial Producing Bacteria Within The Soil, Adam Zwawi

A with Honors Projects

Genetic sequencing techniques used to identify soil antibiotic bacteria

Effect Of Dietary Flavonoids On Growth In Saccharomyces Cerevisiae, Vivian Rivera

Mahurin Honors College Capstone Experience/Thesis Projects

Plant foods contain a diversity of biologically active compounds called phytochemicals, produced by plant species as secondary metabolites. A phytochemical group known as flavonoids has received much scientific attention in recent times with respect to their antioxidative and anti-inflammatory roles. This investigation examined how quercetin and naringenin, the most common dietary flavonoids, affect growth potential of yeast under optimal and stress conditions (temperature, glucose, and oxidative stress). Using Saccharomyces cerevisiae as a model, a dose dependency effect of quercetin and naringenin was observed under optimal conditions when liquid cultures were treated with three different concentrations (75 μM, 150 μM, and …

Contributions Of The Replication Initiator Protein Dnaa To Physiology And Virulence Of The Lyme Disease Spirochete, Andrew Krusenstjerna

Theses and Dissertations--Microbiology, Immunology, and Molecular Genetics

Borrelia burgdorferi, the etiological agent of Lyme disease, is the most prevalent vector-borne disease in the United States. The spirochetal population is naturally maintained by consistently cycling between Ixodid ticks and small vertebrates. To survive within these diverse niches, B. burgdorferi has evolved a unique physiology and regulatory network to sense and respond to environmental fluxes. Replication is a hallmark of the Lyme spirochete’s enzootic life cycle, specifically at the nymphal tick-to-vertebrate interface. The mechanisms and regulatory schema for the basic cellular processes in B. burgdorferi, or indeed any member of the phylum spirochaetota, are largely unknown. The central hypothesis …

Role Of Autophagy-Related Genes In Lipid Transport For Efficient Replication Of Tombusviruses, Yuanrong Kang

Theses and Dissertations--Plant Pathology

Tombusviruses are positive-strand RNA viruses, which utilize numerous co-opted host factors and massive de-novo synthesized membrane resources to modify host membranes and form large viral replication organelles (VROs). Among plenty of host cellular processes, autophagy emerges as a potential membrane resource for VROs formation due to its ability to de-novo generate the double membrane structures, known as autophagosomes. Besides, as an important host defense pathway, autophagy is also a target for tombusviruses to prevent its antiviral activities. In this study, I identify the role of key autophagy related genes, Atg11, Atg8, and Atg2, which are involved in autophagosome formation, and …

Role Of Ph And Plant Age On The Selection Of Rhizobial Endophytes In Soybean Root Nodules, Cole Alexander Roman

Graduate Theses/Dissertations

Soybeans form symbiotic relationships with nitrogen-fixing bacteria in their root nodules to acquire most of their nitrogen requirement; nitrogen is often one of the limiting nutrients in the soil. Members of the Bradyrhizobium, Sinorhizobium, Mesorhizobium, and Rhizobium genera can nodulate soybeans. Bradyrhizobium is preferentially selected over other types of rhizobia in varying environmental conditions and is often found in acidic soils. Sinorhizobium is often identified in the root nodules of soybeans in neutral and alkaline soil. So far, the potential role of soil pH on the selection of rhizobial endophytes with soybean root nodules is unknown. Likewise, …

Synthetic Microbial Communities For Plastic Upcycling, Isabel B. A. Valencia

Dissertations, Master's Theses and Master's Reports

Plastic waste and human hunger pose major threats to the health and wellbeing of populations world-wide. Using microbial methods to upcycle polyethylene terephthalate (PET) plastic into value-added compounds such as single cell protein (SCP) for human consumption is a unique solution to both these issues. Two monomers of chemically deconstructed PET (DCPET), terephthalate (TPA) and ethylene glycol (EG), have been previously shown to be biodegradable by enriched microbial communities. Using this top-down knowledge to inform the reconstruction of a minimal microbial community constructed from isolated members of these communities is a novel way to efficiently process these monomers via a …

Social Interactions And Spatial Structure Drive Community Assembly Of Bacterial Biofilm, Matthew C. Bond

Dartmouth College Ph.D Dissertations

Despite the critical nature which microbial communities play in the natural world and human civilization, the breadth of understanding remains shallow. Challenged by scale, high variability between environments, and extensive diversity, microbial ecologists strive to understand connections between a community’s structure and function, as well as the ecological and evolutionary mechanisms underlying observed natural patterning of communities. Biofilms are the predominate mode of growth for microbial communities—characterized by cellular attachment to a surface via a self-produced matrix and heterogeneous structure, often resulting in a primary growth front along the biofilm surface due to differential access to bulk nutrients (cite). This …

Batch Culture Models Of The Murine Gut Microbiome & The Impact Of Simple Dormancy On Dormancy-Capable Microorganisms Models, Ana C. Mendez

Mathematics Dissertations - Archive

The proposed mathematical biology research utilizes mathematical models to gain insight into biological systems. These systems of ordinary differential equations model diverse topics, ranging from gut microbiomes to harmful algal blooms. A complete stability analysis, supporting phase plane portraits, bifurcation diagrams, and numerical simulations will accompany the models presented. In Chapter 2, the murine gut microbiome is modeled to match laboratory experiments in the literature. In these experiments, mice eat plasmid-carrying “donor” bacteria and naturally carry plasmid-free “resident” bacteria in their gut. The models aim to capture the behavior of plasmids, donor bacteria, and resident bacteria. Chapter 3 explores dormancy …

Inflammation And Tumor Progression: The Differential Impact Of Saa In Breast Cancer Models, Daniel Wilhelm Olivier, Carla Eksteen, Manisha Du Plessis, Louis De Jager, Lize Engelbrecht, Nathaniel Wade Mcgregor, Preetha Shridas, Frederick C. De Beer, Willem J. S. De Villiers, Etheresia Pretorius, Anna-Mart Engelbrecht

Saha Cardiovascular Research Center Faculty Publications

Background: Previous research has shown that the Serum Amyloid A (SAA) protein family is intricately involved in inflammatory signaling and various disease pathologies. We have previously demonstrated that SAA is associated with increased colitis disease severity and the promotion of tumorigenesis. However, the specific role of SAA proteins in breast cancer pathology remains unclear. Therefore, we investigated the role of systemic SAA1 and SAA2 (SAA1/2) in a triple-negative breast cancer mouse model.

Methods: Syngeneic breast tumors were established in wild-type mice, and mice lacking the SAA1/2 (SAADKO). Subsequently, tumor volume was monitored, species survival determined, the inflammatory profiles of mice …

Investigating Birds As Dispersal Vectors Of Litylenchus Crenatae Subsp. Mccannii (Anguinidae), The Nematode Associated With Beech Leaf Disease, Spencer Rock Parkinson

Graduate Theses, Dissertations, and Problem Reports (ETD)

Beech leaf disease (BLD) is an emerging forest pathogen primarily affecting American beech (Fagus grandifolia, Ehrh.) in North America and has been attributed to tree mortality of sapling sized trees within five to seven years of infection. Symptoms typically occur in regenerating American beech thickets sprouting from roots of trees killed by beech bark disease. Scientists first observed BLD in Ohio in 2012 and currently has spread to 15 states in the USA and one Canadian province. The nematode Litylenchus crenatae subsp. mccannii (Lcm) is highly associated with BLD symptoms, interveinal chlorosis and defoliation of leaves, and is currently …

Characterization Of Host Cell Specific Interactions During Spotted Fever Group Rickettsiae Infection, Emerson Towey

Graduate Theses, Dissertations, and Problem Reports (ETD)

Vector-borne diseases have been increasing over the past few years due to changes in climate and disturbances in the vectors’ natural environment. To mitigate the risks of these diseases, it is necessary to understand pathogen biology and how it interacts with a host to cause disease. Here we focus our attention on the tick-borne pathogen, Rickettsia rickettsii. R. rickettsii is a member of the spotted fever group (SFG) Rickettsiae and is the etiological agent of Rocky Mountain spotted fever (RMSF), a fatal human disease that is lacking an effective vaccine. Members of the bacterial genus Rickettsia are obligate intracellular endoparasites …