Microbiology Commons^™

Characterization Of The Function And Regulation Of The Hmpv Phosphoprotein, Rachel Thompson

Theses and Dissertations--Molecular and Cellular Biochemistry

Human metapneumovirus (HMPV) is a non-segmented, negative strand RNA virus (NNSV) that frequently causes respiratory tract infections in infants, the elderly, and the immunocompromised. Despite the initial identification of HMPV in 2001, there are currently no FDA approved antivirals or vaccines available. Therefore, understanding the mechanism of HMPV replication is critical for the identification of novel therapeutic targets. A key feature in the replication cycle of HMPV and other NNSVs is the formation of membrane-less, liquid-like replication and transcription centers in the cytosol termed inclusion bodies (IBs). Recent work on NNSV IBs suggests they display characteristics of biomolecular condensates formed …

Evaluating Innovative Methods Of Quantitatively Linking Microbial Community Structure To Ecosystem Function, Jeth Gv Walkup

Graduate Theses, Dissertations, and Problem Reports (ETD)

Microbial functional diversity is the product of community structure and intraspecific trait variation. Due to microbial diversity and limited availability of microbial trait measurements, it has been challenging to quantitatively link community structure to microbial function. Although community-level activity rates vary with community composition, issues in the scale of their measurement inhibit our understanding of their relationship. Quantitative stable isotope probing (qSIP) is a method for quantitatively measuring taxon-specific microbial traits, providing new opportunities to apply trait-based approaches for studying microbial ecology. Quantitative microbial trait data from these experiments enables the functional characterization of microbial communities, potentially enabling the extrapolation …

Confocal Analysis Of Sindbis Virus In Aedes Aegypti Unveils Novel Infection Site At Pyloric Armature, Katie Gillian Peters

UNF Graduate Theses and Dissertations

Arthropod-borne viruses (arboviruses), such as Sindbis virus (SINV), generate foci of infection within the midgut of viremic blood-fed mosquitoes. Arboviruses can disseminate out of the midgut into the surrounding musculature and hemolymph, eventually making it to the salivary glands where virus can be transmitted by saliva during a subsequent blood-feed. In this study, the virus SINV containing the reporter gene GFP, combined with immunohistochemistry, was imaged using confocal microscopy and used to evaluate the infection within the vector mosquito Aedes aegypti. The spatial distribution of SINV infection revealed two common characteristics of foci generated in the midgut. (1) There …

The Type Iv Pilus Secretin Bfpb: Structural Analysis And Binding Interactions, Janay I. Little

Theses and Dissertations

Enteropathogenic Escherichia coli (EPEC) causes severe diarrhea in young children. The type IV pilus (T4P) of EPEC, known as the bundle-forming pilus (BFP), plays an important role in EPEC pathogenesis. T4Ps are a family of surface appendages that are important for adhesion, colonization, biofilm formation, virulence, twitching motility and many other functions. One essential component of the BFP system is the secretin, BfpB. Secretins are a large family of integral outer membrane proteins found in T4Ps as well as type II and type III secretion systems, and filamentous phages. Details of the secretin structure have been limited to the overall …

Treponema Denticola Synthesizes C-Di-Amp And Encodes The Cdaa-Type Diadenylate Cyclase Cdaa, Claire R. O'Brien

Theses and Dissertations

Periodontitis is a form of oral disease characterized by dysbiosis of the oral microbiome, leading to inflammation, bone resorption, and in severe cases, entire tooth loss, affecting 42% of adults in the US. One of the bacteria most associated with periodontal disease progression is Treponema denticola (Td), an oral spirochete which inhabits the mouth in small quantities during health but which can dominate the biofilms that form during periodontal disease. The ability of Td to survive in a disease environment and contribute to the progression of disease requires the use of robust signaling networks. Analysis of Td cultures …

Probing The Porphyromonas Gingivalis Nitrosative Stress Response Network, Alexandra Galina

Theses and Dissertations

Objective: To persist in the oral cavity, the perio-pathogen Porphyromonas gingivalis must have an efficient nitrosative stress response mechanism. To better understand how P. gingivalis responds to nitrite (NO₂^-) we must determine what genes are involved in the nitrosative stress response network.

Methods: Through genomic screening, a list of genes was generated that were hypothesized to be part of the nitrosative stress response network and believed to be involved in nitrate/nitrite metabolism or redox state of the cells. Protein coding regions were replaced with the ermF sequence by allelic exchange mutagenesis. 15 mutants were created …

Triclosan Degrading Bacteria From Wastewater Treatment Plants In Central Illinois, Mohammed Alsulami

Masters Theses

Triclosan is an antimicrobial agent that has been used in personal care products and has been identified to cause malformation on cartilage and bone development in zebrafish and influence on thyroid hormone system in humans. Due to its widespread usage and insufficient removal from wastewater treatment plants, triclosan has emerged as a pervasive contaminant that poses a potential threat to the environment and human health. The goal of the study was to isolate and characterize triclosan-degrading bacteria from WWTPs in central Illinois. Using enrichment culture with NMS media containing triclosan as sole carbon source, eighteen bacterial strains were isolated. The …

Comparing The Microbiomes Of Dental Plaques In 19th Century Ancestral Remains, Ananya Udyaver

UROP Posters

During the construction of VCU’s Hermes A. Kontos Medical Sciences Building in April 1994, nineteenth century ancestral remains were found in an abandoned well on the Medical College of Virginia (MCV) campus. This well, now known as the East Marshall Street Well (EMSW), is thought to have been used as a disposal location for cadaver dissection for surgical and other medical waste in the past. VCU is now seeking to use DNA sequencing technology to match and assemble bones from each individual for a proper burial, uncover the cultural and historical context in which these people lived, and bring a …

Bioprospecting For And The Applications Of Halophilic Acidophiles In Bioleaching Operations, Melissa K. Corbett, Elizabeth L. J. Watkin

Research outputs 2022 to 2026

The economic recovery of metals from sulfide ores has become a topic of increasing interest due to the escalating demand for critical minerals and the reducing grade of available ores. Bioleaching is the use of acidophilic iron and sulfur-oxidising microorganisms to facilitate the extraction of base metals from primary sulfide ores and tailings. One significant issue limiting the use of bioleaching is the availability of freshwater due to the sensitivity of these microbes to chloride. The use of saline tolerant acidophilic iron- and-sulfur oxidising microorganisms will go a long way to addressing this issue. There are three possible means of …

Elucidating The Role Of A Staphylococcal Glucosaminidase In Host Innate Immune Responses, Zachary Resko

Dissertations

The peptidoglycan of Staphylococcus aureus is a critical cell envelope constituent and virulence factor that subverts host immune defenses and provides protection against environmental stressors. Peptidoglycan chains of the S. aureus cell wall are processed to characteristically short lengths by the glucosaminidase, SagB. It is well established that peptidoglycan is an important pathogen-associated molecular pattern (PAMP) that is recognized by the host innate immune system and promotes production of pro-inflammatory cytokines, including IL-1β. However, how bacterial processing of peptidoglycan drives IL-1β production is comparatively unexplored. Here, we tested the involvement of staphylococcal glucosaminidases in shaping innate immune responses and identified …

Identification Of Conditions That Promote Biofilm Formation By Vibrio Fischeri And Elucidation Of The Underlying Signal Transduction Pathway, Courtney Noelle Dial

Dissertations

Biofilms are communities of microorganisms that have intrinsically antimicrobial properties and are difficult to treat in the clinical setting. The marine bacterium Vibrio fischeri efficiently colonizes its symbiotic squid host, Euprymna scolopes, by producing a transient biofilm dependent on the symbiosis polysaccharide (SYP), making it the perfect model system to study biofilm dynamics. In vitro, however, wild-type (WT) strain ES114 fails to form SYP – dependent biofilms. Instead, genetically engineered strains, such as those lacking the negative regulator BinK, have been developed to study SYP biofilms. Historically, V. fischeri has been grown using LBS, a complex medium containing tryptone and …

Characterization Of Mroq-Dependent Regulation Of Staphylococcus Aureus Quorum Sensing, Madison Ruth Stock

Dissertations

Gram-positive bacteria produce small autoinducing peptides (AIPs), which act to regulate expression of genes that promote adaptive traits including virulence. The Gram-positive pathogen Staphylococcus aureus generates a cyclic AIP that controls expression of virulence factors via the accessory gene regulatory (Agr) system. S. aureus strains belong to one of four Agr groups (I, II, III, and IV), and each group harbors allelic variants of AgrD, the precursor of AIP. In a prior screen for S. aureus virulence factors, the Alonzo lab identified MroQ, a putative peptidase. A ΔmroQ mutant closely resembled a Δagr mutant and had significant defects in AIP …

Host-Microbe Interactions In Non-Native Estuarine Anemones: Biogeography And Temperature, Parker K. Lund

Cal Poly Humboldt theses and projects

Non-native species are increasing in prevalence around the world, resulting in negative economic and ecological impacts. However, the broad distributions of non-native species also offer a system for investigating the response of host-associated microbial communities to environmental factors across a range of ecological scales. At the broadest scale, I investigated the geography of microbial communities in the non-native estuarine anemone Diadumene lineata on the west coast of the United States of America. Across latitudes, microbial community composition was very similar and displayed a high percentage of Klebsiella spp. at all sites. However, the communities in California tended to exhibit higher …

Changes And Relationships Of Soil Aluminum, Organic Matter, And Hydrogen Ion Concentration With Rye Cover Crop, Arron Wilder

Cal Poly Humboldt theses and projects

Soil acidity is a common agricultural problem worldwide, as approximately 50% of all potentially arable soils are affected by pH limitations. At soil pH 3+) is considered to be the chemical form of aluminum in acid soil that hinders plant growth the most. Potentially, soil organic matter (SOM) can ameliorate the toxic effects of Al³⁺ on plants and microbes by binding with Al³⁺, thus preventing Al³⁺ (and other species of aluminum) from interacting in the rhizosphere. Increasing SOM also increases soil health indicators (i.e., microbial activity, soil water holding capacity, aggregate stability, porosity, etc.) while the …

Marineepi: A Gui-Based Matlab Toolbox To Simulate Marine Pathogen Transmission, Gorka Bidegain, Tal Ben-Horin, Eric N. Powell, John M. Klinck, Eileen E. Hofmann

CCPO Publications

The Graphical User Interface (GUI) MarineEpi is presented as a Matlab toolbox for easily (i) constructing disease transmission models for different marine host-pathogen systems, (ii) running simulations by specifying initial conditions and model parameters, and (iii) interpreting the resulting time series of the host and pathogen population dynamics. MarineEpi users can generate models for systems in which pathogen transmission occurs through contact with infected individuals (SI), contact with dead infected individuals (SID), contact with environmental pathogens released by infected individuals (SIP), and contact with environmental pathogens released by dead infected individuals (SIPD). MarineEpi is a freely available GUI that provides …

Identification Of Novel Biosynthetic Gene Clusters Encoding For Polyketide/Nrps-Producing Chemotherapeutic Compounds From Marine-Derived Streptomyces Hygroscopicus From A Marine Sanctuary, Hannah Ruth Flaherty

Honors Theses and Capstones

Nearly one out of six deaths in 2020, around ten million people, were caused by cancer, making it a leading cause of death worldwide (WHO, 2022). This major public health issue, in addition to the rise of multidrug-resistant (MDR) pathogens, provides a high demand for the discovery of new pharmaceutical drugs to be used clinically to treat these conditions. The Streptomyces genus accounts to produce 39% of all microbial metabolites currently approved for human health, indicating its potential as an important species to study for antimicrobial and anticancer agents. The long linear genome of Streptomyces contains specialized sequences known as …

Odd Bedfellows & Marriage Of Necessity: Public Health And Politics In American Federalism, Gabriella Victoria Chianese

Honors Theses and Capstones

In the wake of the coronavirus disease 2019 (COVID-19) pandemic, while the public disagrees over mask mandates, required vaccinations, and social distancing, it seems like one common sentiment exists – a distaste for the odd bedfellows of politics and public health. There are those who cry for the compartmentalization of the science of public health and the art of politics to rectify this situation. In the wake of so much confusion and chaos, it is not unjustified to demand the depoliticization of public health; however, this response is unrealistic given the modern political climate, demonstrates a narrow understanding of the …

Effects Of Altering Physiologically Relevant Cholesterol Levels And Media Types On Porin Gene Expression In Klebsiella Pneumoniae And The Resulting Impact On Antibiotic Resistance, Megan R. Camden

UNF Graduate Theses and Dissertations

Klebsiella pneumoniae is a Gram-negative, non-motile bacterium belonging to the Enterobacteriaceae family. K. pneumoniae is a rising threat in the clinical setting, as there has been a large increase in the presence of antibiotic resistant isolates. While much research is conducted on laboratory and clinical strains of bacteria, not much is known regarding the impact that human physiology can have on bacterial gene expression, and in response, to antibiotic susceptibility. The goal of this study is to determine if physiologically relevant cholesterol levels and media types impact porin gene expression and antibiotic resistance in K. pneumoniae. To accomplish this, …

Evaluating Efficacy Of Anti-Batrachochytrium Dendrobatidis Probiotic Treatment On Pacific Chorus Frogs (Pseudacris Regilla) At Current And Modeled Climate Change Temperatures, Autumn N. Holley

EWU Masters Thesis Collection

Amphibian populations are declining due to a variety of threats, including the chytrid fungal pathogen, Batrachochytrium dendrobatidis (Bd), the causative agent of the disease chytridiomycosis. Climate change and other stressors can have complicated interactions with amphibian disease. Some amphibian populations are less susceptible to chytridiomycosis due to factors such as symbiotic skin microbes that may inhibit Bd through secondary metabolites. There have been several attempts to develop probiotics from these symbiotic, antifungal bacteria to provide protection against Bd infection, but these studies have had mixed success. Our study evaluated anti-Bd bacteria isolated from the skin of Pacific chorus frogs (Pseudacris …

Surveillance And Monitoring Of Amphibian Pathogens And Evaluating The Impacts Of An Associated Course-Based Undergraduate Research Experience (Cure), Jennifer Perez

EWU Masters Thesis Collection

Amphibians are a highly diverse class of vertebrates and crucial for natural ecosystems, inhabiting both aquatic and terrestrial environments at different life stages. However, amphibians are facing devastating declines largely due to the disease chytridiomycosis, caused by the fungal pathogens Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal). This disease can lead to population declines, biodiversity loss, and species extinction. However, resources to study and mitigate this disease are limited and an opportunity to assist in these efforts has been created in the form of a course-based undergraduate research experience (CURE). Chapter 1 of my thesis used Roger's Diffusion of Innovations …

Monitoring Archaeal Persistence In Cultivation, Payton Hall

Honors Program Theses

It was previously thought that microbes in the domain Archaea were only found in extreme environments such as hot thermal vents at the bottom of the ocean and hypersaline environments, but as scientists began to use environmental DNA to survey soil, they detected archaea from the phylum Thaumarchaeota in relatively benign environments including farm fields, forests, and prairies. In spite of their widespread global distribution, relatively few of these species have been grown in laboratory culture. It is now known that Thaumarchaeota play an important role in the nitrogen cycle because they can generate energy through ammonia-oxidation. To increase the …

Evaluation Of Methods To Analyze Microbial Composition In Soils, Joseph Correa

Honors Program Theses

DNA testing has become a vital tool for studying microbes in their natural environments, but there is a lack of standardization in the protocols for extracting environmental DNA. Cave systems provide a special and unique area to research how life thrives in extreme environments. Many parts of caves receive no sunlight and very little nutrients yet harbor microbial communities. Previous work in our lab developed a DNA extraction protocol that works with a wide range of microbial species and with different soil types. I updated this protocol by adding a pre-lysis rinse step and tested whether it performed better with …

Structural Impact Of Epstein-Barr Virus- Encoded Small Rna -1 On Its Transport And Function, Zubaida Hassan

Dissertations

Epstein-Barr Virus (EBV)-Encoded RNAs (EBERs) are two small, noncoding, structurally conserved transcripts that are expressed in millions of copies in all stages of EBV infection. Despite their abundant expression, the role of EBERs in EBV biology or pathogenesis is not well defined. However, they are associated with driving cell proliferation and improving intercellular communication via their secretion in exosomes. In spite of the pathogenic potentials of EBERs, the mechanisms involved in their transport and function remain to be elucidated. The aim of this PhD dissertation was to investigate the structural impact of EBER1 in its transport and function. The conserved …

The Persistence And Stabilization Of Auxiliary Genes In The Human Skin Virome, Ema H. Graham, Wesley A. Tom, Alison C. Neujahr, Michael Adamowicz, Jennifer Clarke, Joshua R. Herr, Samodha C. Fernando

Nebraska Center for Virology: Faculty Publications

Background The human skin contains a diverse microbiome that provides protective functions against environmental pathogens. Studies have demonstrated that bacteriophages modulate bacterial community composition and facilitate the transfer of host-specific genes, potentially influencing host cellular functions. However, little is known about the human skin virome and its role in human health. Especially, how viral-host relationships influence skin microbiome structure and function is poorly understood.

Results Population dynamics and genetic diversity of bacteriophage communities in viral metagenomic data collected from three anatomical skin locations from 60 subjects at five different time points revealed that cutaneous bacteriophage populations are mainly composed of …

Soil And Compost Tea: A New Restoration Technique?, Carol E. Day

Master's Theses and Doctoral Dissertations

Historically, prairie restorations have lacked the plant diversity seen in remnant prairies. Most restoration practices focus on reestablishing the plant community but overlook the soil microbial community even though microbes are critical to habitat functioning. Developing techniques that increase soil microbes in prairie restorations is critical to ensuring diverse restored habitats. We compared how microbial communities differed between remnant and restored prairie sites. We also investigated if soil and compost teas could be used to reintroduce microbes to restored prairie soil and if the teas affected native plant establishment. We found significant differences in the levels of bacterial taxa between …

Community Ecology And Disease Dynamics In Pacific Oysters: Unraveling Microbiome-Pathogen Interactions In The Wild, Victoria E. Cifelli

Cal Poly Humboldt theses and projects

In the context of multispecies microbial assemblages, disruptions can occur when there are alterations in host conditions, such as the onset of a disease. Notably, viruses have the potential to reshape a host's microbial community. However, the role of the host's habitat and environment, which could be pivotal in communities with shifting niche space and habitat filters, is often overlooked in host-microbe-pathogen interactions. Recognizing the importance of these factors, I employed a field-based approach to understand microbial community dynamics in the presence of disease. To address the influence of geographical location, I conducted an analysis involving healthy and infected oysters …

Investigating The Effectiveness Of Microplastic Removal And The Relationship Between Microplastics, Bacterial Communities, And Nitrogen Cycling In The Natural Treatment Systems At The Arcata Wastewater Treatment Facility, Fiona Connor

Cal Poly Humboldt theses and projects

This thesis addressed two challenging aspects of microplastic research, including the quantification of microplastics in organic-rich water, and the investigation of how microplastics impact microorganisms and related nutrient-cycling. Two projects were designed and executed to address specific research objectives relating to these broad topics. The first objective was to develop and implement methods to determine the effectiveness of microplastic removal across the natural treatment systems at the Arcata Wastewater Treatment Facility (AWTF). The second objective was to observe how microplastics found in domestic wastewater impact the bacterial communities and nitrogen cycling in freshwater treatment wetland sediment through a bench-scale experiment, …

Fine-Scale Genetic Structure In Rhizosphere Microbial Communities Associated With Chamaecrista Fasciculata (Fabaceae), Mahboubeh Hosseinalizadeh Nobarinezhad, Lisa E. Wallace

Biological Sciences Faculty Publications

Soil microbiota of the rhizosphere are an important extension of the plant phenotype because they impact the health and fitness of host plants. The composition of these communities is expected to differ among host plants due to influence by host genotype. Given that many plant populations exhibit fine-scale genetic structure (SGS), associated microbial communities may also exhibit SGS. In this study, we tested this hypothesis using Chamaecrista fasciculata, a legume species that has previously been determined to have significant SGS. We collected genetic data from prokaryotic and fungal rhizosphere communities in association with 70 plants in an area of …

Understanding Human Gut Bacterial Interactions And Their Role In Colonization Resistance Against Clostridioides Difficile Using Mini-Bioreactor Array And Caenorhabditis Elegans As Model Systems, Achuthan Ambat

Electronic Theses and Dissertations

No abstract provided.

Indigenous Toxin Affects Cell Viability, While An Artificial Proteolytic Queueing Causes The Upregulation Of Specific Genes, Mohammed Salahuddin

Electronic Theses and Dissertations

Studying bacterial physiology is crucial to understand the fundamental mechanisms that govern bacterial growth, survival, and adaptation. This thesis combines two chapters investigating bacterial physiology by studying important cellular processes like bacterial toxin-antitoxin systems and proteolytic pathways. The first chapter involves studying bacterial toxin-antitoxin systems to understand the regulation and function of hypothetical toxin-antitoxin (TA) systems of bacteria and the effects of these TA systems on bacterial growth and survival. The emergence of these genetic modules in bacterial research and the unrevealing of some of their important roles in cell physiology in recent years has drawn much attention in scientific …