Microbiology Commons^™

The Impact Of Processing Body Proteins On An Adenovirus Infection, La`Quita Randolph

Biology Theses

Adenovirus is a nonenveloped, double-stranded DNA virus that contains a 36 Kbp genome. The E4 ORF3 region of its genome consists of an E4 11k protein that can reorganize host cell components by relocalizing cellular proteins. One such cellular component is the cytoplasmic processing body, which consists of proteins involved in translational repression of mRNA and mRNA degradation. During an adenovirus infection, processing body proteins Ddx6 and Pat1b have been shown to colocalize and form aggresomes. Aggresomes induced by E4 11k are specific to the adenovirus serotype 5 (Ad 5). In this study, cytoplasmic Pat1b foci were observed and quantified …

Cdk8 Kinase Module Modifies Expression Of Specific Translation-Related Proteins Before And After Stress, Brittany Friedson, Katrina Cooper

Rowan-Virtua Research Day

Translation is tightly coupled to growth status. Efficient protein synthesis is necessary for cell growth in nutrient rich environments, while global translation inhibition combined with selective translation of stress-responsive mRNAs helps limit growth in times of stress. Environmental stress cues which inhibit the nutrient-sensing complex TORC1 are known to reduce general translation, but how does the cell alter protein synthesis machinery to adapt to these conditions? A few mechanisms to promote cell survival in nitrogen starvation include post-translational modification and selective degradation of specific mRNA-binding translation factors, as well as inhibition of activators of genes whose products are required for …

Comparative Transcriptomic Study Between Cyanobacteria That Contain Chlorophyll D And Those That Lack Chlorophyll D, Fernanda Montoya

Honors Capstones

All cyanobacteria, which perform oxygenic photosynthesis on Earth, contain the photosynthetic pigment chlorophyll a (Chl a) that absorbs light in the violet and red region of the visible spectrum. Cyanobacteria of the Acaryochloris species, however, contain the rare photosynthetic pigment chlorophyll d (Chl d) that absorbs light in the far-red region. Chl d’s ability to absorb light in this region allows it to avoid competing with other photosynthetic organisms for light. Creating a photosystem that uses Chl d in plants would be of great use for agricultural land optimization, but requires knowledge of the biosynthetic pathways of …

Effect Of Mycorrhizae Inoculation On The Growth And Success Of Three Taxodium Distichum Hybrids In Saline - Impacted Coastal Soils, Elif Ilhan

Electronic Theses and Dissertations

In 2008, Galveston Island was severely impacted by Hurricane Ike, resulting in high salt deposition in the soil and groundwater. This caused a loss of many native plant species. A study was initiated to determine effective ways to promote the growth conditions of three bald cypress genotypes (Taxodium distichum var distichum and Taxodium distichum var mexicanum crosses) in salt-affected soils. The treatments applied were mycorrhizae inoculation, fertilizer application, and a combination of mycorrhizae inoculation and fertilizer application. A total of sixty (60) trees planted in plots of three rows and divided into five randomized replication blocks of four treatments …

An Analysis Of The Effects Of Temperature And Other Environmental Factors On Microorganismal Productivity Within Aquatic Ecosystems Using Long-Term Data From Various Lter And Ilter Sites, Andrew Dorbu

Theses and Dissertations

Global climate change is a phenomenon resulting in more extreme weather patterns and species diversity loss. In this study, I explore the impacts of climate change on regional patterns of microbial productivity. Variation in microbial productivity was explained using temperature, salinity, and dissolved oxygen as predictors in regression models with data from the LTER and iLTER network of sites that ranged from the poles to the equator. I found a positive relationship between temperature and productivity. Antarctica and Arctic sites exhibited the strongest positive relationships supporting prior research demonstrating temperature as one of the driving forces of productivity change in …

Systems Biology Approach To Functionally Assess The Clostridioides Difficile Pangenome Reveals Genetic Diversity With Discriminatory Power, Charles J Norsigian, Heather A Danhof, Colleen K Brand, Firas S Midani, Jared T Broddrick, Tor C Savidge, Robert A Britton, Bernhard O Palsson, Jennifer K Spinler, Jonathan M Monk

Faculty, Staff and Students Publications

Combatting Clostridioides difficile infections, a dominant cause of hospital-associated infections with incidence and resulting deaths increasing worldwide, is complicated by the frequent emergence of new virulent strains. Here, we employ whole-genome sequencing, high-throughput phenotypic screenings, and genome-scale models of metabolism to evaluate the genetic diversity of 451 strains of C. difficile. Constructing the C. difficile pangenome based on this set revealed 9,924 distinct gene clusters, of which 2,899 (29%) are defined as core, 2,968 (30%) are defined as unique, and the remaining 4,057 (41%) are defined as accessory. We develop a strain typing method, sequence typing by accessory genome (STAG), …

Identification Of Genetic Elements Involved In Alcaligenes Faecalis’ Inhibitory Mechanism Against Polymicrobial Species, Abigail Mathis

Undergraduate Honors Theses

The rise of antibiotic resistance in common human pathogens and the lack of development of novel therapeutic treatments has created a threat to global health. A unique source for potential novel treatments are from microorganisms, particularly within the complex, antagonistic polymicrobial interactions that take place in microbial communities. These unique mechanisms utilized by microorganisms to fight each other could potentially identify novel therapeutic targets for use at a clinical level, however, there is a lack of research in this area to determine its applicability. Alcaligenes faecalis is a Gram-negative bacterium that seldom causes human disease and has been observed in …

Elevated Levels Of External Cysteine Inhibit Nitrogen Fixation By The Methanogenic Archaeon Methanosarcina Acetivorans, Regan Massey

Biological Sciences Undergraduate Honors Theses

Methanogens are nitrogen fixing and methane producing archaea that play a key role in the cycling of carbon and nitrogen on earth. The global carbon and nitrogen cycle is vital to all life which makes the methanogen a primary organism of study. Methanogens are the only archaea capable of fixing nitrogen, and in order to do so, methanogens use a vital enzyme called the nitrogenase which fixes dinitrogen (N2) to ammonia (NH3). Expanding our understanding on metabolic processes of methanogens allows us to understand their environmental impact and advance their use in biotechnological applications. Methanosarcina acetivorans is the model used …

Identification Of Critical Points For Bacterial Contamination In The Microbrewery Environment, Alex Ryan Thompson

All Theses

There are 8,884 craft breweries producing over 23 million barrels of beer in the United States as of 2020. These 23 million barrels of craft beer account for 12.3% of the United States beer consumption in 2020. The American craft beer industry is substantial and needs to protect its product from bacterial contamination.

Overall, beer is a microbially stable product. Beers pH, ethanol levels, CO₂ concentrations, the presence of hop-derived antimicrobial compounds, and low levels of O₂ make beer a highly unfavorable environment for most bacterial species. Furthermore, the brewing process, which involves heat treatments and chemical sanitizers …

Studying The Lysine Acetylation Of Aconitase Isozymes In E. Coli, Sara Ottinger

Chemistry & Biochemistry Undergraduate Honors Theses

The contents of this thesis have been modified from the publication “Araujo J, Ottinger S, Venkat S, Gan Q and Fan C (2022) Studying Acetylation of Aconitase Isozymes by Genetic Code Expansion. Front. Chem. 10:862483”. Though studies have found multiple lysine sites in which acetylation takes place in Escherichia Coli aconitase, acetylation’s effects on the enzyme’s activity have yet to be studied. Aconitase is the dehydratase-hydratase found in the citric acid and glyoxylate cycles responsible for the reversible isomerization of citrate to isocitrate via cis-aconitate intermediate. There are two isoforms of aconitase in E. coli: AcnA and AcnB. In …

Dynamics Of The Supragingival Dental Plaque Microbiome And Its Implications In Early Childhood Caries (Ecc), Lauren O'Connell

All Dissertations

Early childhood caries (ECC) is one of the most common chronic diseases worldwide and remains a serious public health crisis in developing countries and socioeconomically disadvantaged communities. Caries is a complex polymicrobial, sugar-driven disease caused by interactions between the biofilm and tooth surface. While there is a general understanding of the microbial processes driving dental caries development and progression, the microbiota associated with the initiation and progression of dental caries have yet to be fully characterized. The most-studied species associated with tooth health and disease are the oral streptococci. Nevertheless, there are still large gaps in our knowledge of the …

Mycobacteriosis Of Striped Bass (Morone Saxatilis) In Virginia Tributaries Of The Chesapeake Bay, Joshua S. Mcgilly

Biological Sciences Theses & Dissertations

Mycobacteriosis was first documented in Chesapeake Bay striped bass (Morone saxatilis) in 1997 after fish exhibited emaciation and skin lesions. Since it was first identified, studies of mycobacteriosis in the mainstem of the Chesapeake Bay (2003-2007) and the Rappahannock River (2005-2012) have shown high disease prevalence and disease-associated mortality. Until this study, no current prevalence data existed from the Rappahannock River, and no published prevalence data existed for the James River, leaving a gap in our understanding of this disease in major Chesapeake Bay tributaries. We began gathering mycobacteriosis prevalence data from an existing survey collecting striped bass …

Describing The Effect Of Thin Layer Sediment Placement On Coastal Microbial Communities Using Foraminifera Diversity, Elizabeth B. Billings

Senior Honors Projects

Salt marshes are rich ecosystems that play an important role in aquatic food systems and prevent erosion while also providing essential habitats for wildlife. Climate change has resulted in rising sea levels and erosion of these coastal wetlands. Thin Layer Sediment Placement (TLP) is a restoration effort being implemented to mitigate the effects of climate change on coastal ecosystems. The TLP process raises elevation of the marsh and provides substrates for vegetative growth by spraying dredged sediment over existing marsh. The impacts of TLP on microbial populations is not widely understood, therefore metrics are required to study the effects of …

Characterization Of The Role Of The Replicase And Quasispecies Diversity In Flaviviral Evolution And Host Adaptation, Haley Caldwell

Legacy Theses & Dissertations (2009 - 2024)

Flaviviruses include several emerging and re-emerging arboviruses that cause millions of infections each year. Although relatively well-studied, much remains unknown regarding the mechanisms and means by which these viruses adapt to different hosts and rapidly alternate between hosts. Different aspects of flaviviral biology impact host switching, viral fitness, and the generation of viral diversity during genome replication by the NS3 and NS5 proteins. Together these factors may impact host plasticity.

Temporal And Spatial Comparison Of Pseudo-Nitzschia Species Composition And Domoic Acid In Narragansett Bay, Rhode Island And The Northeast U.S. Shelf, Isabella Church, Bethany D. Jenkins

Senior Honors Projects

Diatoms are unicellular algae that make up a significant portion of phytoplankton biomass at the base of marine food webs. Narragansett Bay (NB), RI is home to several species of the diatom genus Pseudo-nitzschia (P-n), some of which are known to cause harmful algal blooms through the production of the potent neurotoxin domoic acid (DA). This toxin can lead to Amnesic Shellfish Poisoning in humans through the consumption of affected shellfish. Although the presence of P-n has been well established in NB for over 50 years, DA levels have only recently become a problem, with shellfish harvest closures …

Native And Non-Native Ant Impacts On Soil Microbes, Hannah A. Stewart

Biology Theses

Organisms produce chemical weapons for defense, but target organisms can develop resistance. In their introduced range, non-native species may bring “novel weapons” against which native organisms have not co-evolved resistance. The invasive European fire ant (Myrmica rubra) may have brought antimicrobial secretions to the Northeastern United States that are novel weapons against native fungal and bacterial soil organisms. I hypothesized that M. rubra would better inhibit seed pathogens resulting in greater emergence of native myrmecochorous Viola sororia seeds and, as a side effect, more strongly inhibit arbuscular mycorrhizal fungi than a native seed dispersing ant (Aphaenogaster picea …

Nitrogen Availability In Dune Systems And Its Effect On Root Fungal Endophyte Communities., Haley E. Sage

College of Arts & Sciences Senior Theses

As global change persists, changes in resource availability can influence plant-microbe interactions. To understand how resource availability can influence these interactions and species diversity, I focused this research on how varying nitrogen (N) levels affect root endophyte communities in the plant species Ammophila breviligulata, an ecosystem engineer in the dune system. I analyzed the relationship between nitrogen addition and microbial community composition across 60 plots treated with three nitrogen addition levels (control, low, and high) in a long-term experimental field site in the Lake Michigan dunes. I identified Ammophila breviligulata's root endophyte community after creating a culture collection and …

Functional Characterization Of A Putative Alternative Oxidase In Sporisorium Reilianum F. Sp. Zeae., Emma A Lamb

College of Arts & Sciences Senior Theses

Sporisorium reilianum is a pathogenic basidiomycete fungus with two formae speciales, each capable of infecting corn (SRZ) or sorghum (SRS), respectively. This fungus is also a dimorphic variety, meaning it can switch between its haploid, yeast-like sporidia and diploid teliospore stages over the course of its life cycle (Schirawski). When S. reilianum is found in a haploid state and conditions are favorable, it will mate with a compatible non-self mating type to begin filamentous growth and proliferation in the plant host (Zhao). S. relianum, like most fungi, utilizes the four classical components of the electron transport chain to produce …

Exploring Nitrogen Fixation In Methanosarcina Acetivorans, Rylee Cook

Biological Sciences Undergraduate Honors Theses

As of 2016, the genomes of over sixty species of methanogenic archaea have been sequenced.4 Research on the genomes of methanogens such as M. acetivorans led to the characterization of numerous genes with unknown functions. Genes similar to those of nitrogenase have been shown to possess functions unrelated to nitrogen fixation, such as F430 biosynthesis genes. 5,6,7 My research focused on the uncharacterized gene clusters ma2032-33 and ma1631-33 (Figure 1). These genes have conserved nitrogenase domains: ma2032 has fused nifH and nifD domains, while ma2033 has a nifD domain. The ma1631-33 gene cluster contains two nitrogenase homologs and one iron …

The Role Of Stm1987 And Arti In Arginine Response Of Salmonella Typhimurium, Deeba Mohseni

Undergraduate Honors Theses

Cyclic-di-GMP, a common bacterial second messenger, has been thought to help develop virulence and biofilms in bacteria, most specifically in Salmonella Typhimurium. By being able to dysregulate cyclic-di-GMP production, virulence may be better combatted. STM1987, an L-arginine-responsive diguanylate cyclase with a periplasmic sensory domain, dimerizes and generates the bacterial second messenger cyclic-di-GMP in response to the amino acid L-arginine in a pathway that also requires the periplasmic L-arginine-binding protein ArtI. Their biochemical responses to L-arginine and when they dimerize could help clarify this pathway, so I sought to develop a periplasmic dimerization sensor to better monitor these biochemical interactions. Similar …

Aggregatibacter Actinomycetemcomitans Exploits And Modulates The Immune Response By Human Neutrophils For Survival In The Anaerobic Environment., Hazel Ozuna

Electronic Theses and Dissertations

Aggregatibacter actinomycetemcomitans (Aa) is a Gram-negative facultative anaerobe and an opportunistic oral pathogen, strongly associated with localized periodontitis and other inflammatory diseases. Periodontitis is a chronic inflammation of the periodontium resulting from the inflammatory response of the host towards the dysbiotic microbial community present at the gingival crevice. The host immune response creates a hostile environment for microorganisms; therefore, it is important for Aa to be able to regulate the necessary genes to survive and thrive in such an environment. Aaexpresses several virulence factors such as a cytolethal distending toxin (Cdt), lipopolysaccharide (LPS) and leukotoxin A (LtxA), …

Lysosomal Evasion Of Legionella Pneumophilia The Effector., Bethany Vaughn

Electronic Theses and Dissertations

Legionella pneumophila is a Gram-negative facultative intracellular bacterium found in freshwater environments that has co-evolved to survive and proliferate in various amoeba and protozoan species, which serve as the natural host for the bacterium. Humans are an accidental host of L. pneumophila, where infection occurs upon inhalation of aerosolized water droplets that contain the bacteria. Intracellular proliferation of L. pneumophila in alveolar macrophages is essential for manifestation of pneumonia, designated as Legionnaires’ Disease. Biogenesis of the legionella containing vacuole (LCV) occurs via interception of ER-Golgi vesicle trafficking and avoids the default endosomal/lysosomal degradation pathway. Intracellular proliferation of L. pneumophila …

Mathematical Modeling Of Potassium Modulated Viral Infection, Zaira Elizabeth Mather

Open Access Theses & Dissertations

In recent years, there is a growing interest in the investigation of using potassium to treat virus infections. In the region of infection, there is a biological observation of extracel- lular potassium level being typically very low whereas the intracellular potassium levels are much higher. There are numerous biological studies showing that elevated potassium levels in the extracellular membrane tends to block virus infections. A recent effort in this direction is a collaborative research conducted by mathematicians and biologists from the University of Texas at El Paso, New Mexico State University, and the University of New Mexico, where we develop …

Alterations Of The Gut Mycobiome In Patients With Ms - A Bioinformatic Approach, Saumya Shah

Honors Scholar Theses

The mycobiome is the fungal component of the gut microbiome and is implicated in several autoimmune diseases. However, its role in multiple sclerosis (MS) has not been studied. We performed descriptive and formal statistical tests using the R language to characterize the gut mycobiome in people with MS (pwMS) and healthy controls. We found that the microbiome composition of multiple sclerosis patients is different from healthy people. The mycobiome had significantly higher alpha diversity and inter-subject variation in pwMS than controls. Additionally, Saccharomyces and Aspergillus were over-represented in pwMS. Different mycobiome profiles, defined as mycotypes, were associated with different bacterial …

Describing Bacterial Mutagenic Hotspots And Signatures Along With The Factors That Drive Them, Carmen Vallin

UNLV Theses, Dissertations, Professional Papers, and Capstones

In my dissertation work, I investigated bacterial mutagenesis. I asked: where do mutations occur in the bacterial genome? What types of mutations occur? What factors promote or prevent mutations? And lastly, how do the answers to these questions change depending on the bacterial life cycle (When)? I used Bacillus subtilis, a Gram-positive bacterium belonging to the phylum Firmicutes, and Escherichia coli, a Gram-negative bacterium belonging to the phylum Proteobacteria, to answer these questions. B. subtilis and E. coli are model systems that have been used to gain insights into fundamental processes of mutations and evolution for nearly ~8 decades. Here, …

Roles Of Small Rnas And Paralogous Proteins In Bacillus Anthracis Virulence Gene Regulation, Ileana Corsi

Dissertations and Theses (Open Access)

Bacteria have evolved a myriad of regulatory mechanisms to control gene expression. One of the most common mechanisms is post-transcriptional control through the function of small regulatory RNAs (sRNAs). Small regulatory RNAs (sRNAs) are short transcripts that base-pair to mRNA targets or interact with regulatory proteins. sRNA function has been studied extensively in Gram-negative bacteria; comparatively less is known about sRNAs in Firmicutes. In this dissertation, I investigated two sRNAs encoded within the virulence plasmid pXO1 of Bacillus anthracis, the causative agent of anthrax. The sRNAs, named “XrrA and XrrB” (for p­XO1-encoded regulatory RNA) are abundant and highly stable …

Investigation Of Genomic Instability Induced By G-Quadruplexes In The Absence Of Functional To Poisomerase 1 In Yeast, Alexandra Berroyer

Dissertations and Theses (Open Access)

Topoisomerase 1 (Top1) is an enzyme that removes transcriptionally generated negative supercoils by binding and nicking DNA. Since transcription of guanine-rich DNA leads to the formation of G-quadruplex (G4) structures, Top1’s function likely suppresses G4-formation. In support of this, Top1 significantly reduces co-transcriptional G4 DNA-associated genomic instability at a model G4-motif in Saccharomyces cerevisiae. However, whether Top1 suppresses G4-formation on a genome-wide scale in yeast remains unexplored. Therefore, I aimed to uncover if deletion of Top1 enhances genome-wide G4-formation in S. cerevisiae. As an approach to quantify global G4-formation, I expressed the G4-specific antibody BG4 from a yeast …

The Effect Of Cognitive Status And Residency On Oral Health In Patients With Dementia, Nicole Stephens

Dissertations and Theses (Open Access)

Poor oral health is a predictor of cognitive decline in elderly populations and has been shown to precede dementia. As cognitive decline progresses, patients are likely to move from the community into nursing facilities. We hypothesize that severity of dementia and residency type will impact the oral health of patients with dementia. Fifty-two participants of two dementia levels were recruited from the UTHealth Neurocognitive Disorders Center and two Houston-area nursing homes. A standardized oral health assessment, plaque index, and oral bacteria analysis determined participants’ oral health status. Further, data was collected on participants’ medical history, oral hygiene habits, dietary habits, …

Effects Of Continuous In Situ Low-Dose Ionizing Radiation On Microorganisms, Molly E. Wintenberg

All Dissertations

Precise detection and monitoring of nuclear fuel cycle, enrichment, and weapon development activities are critical for supporting warfighter preparation in chemical, biological, radiological, nuclear, and explosives (CBRNE) operations, clandestine activities, and nuclear compliance. A biological sensing system could serve as an alternative to traditional detection methods by using organic material naturally present in the environment to discreetly detect residual trace nuclear material. Microorganisms provide an optimal platform for an alternative sensing system; however, their response to low levels of ionizing radiation is poorly characterized. Combining the power of next-generation sequencing and transcriptomic analysis, this dissertation takes an approach to obtain …

Diffusive Dynamics Of Biological Macromolecules In The Cytoplasm Of Live Bacteria, Asmaa Ali Sadoon

Graduate Theses and Dissertations

Bacteria are small organisms that play important roles in our bodies and in maintaining our surrounding environment. However, bacterial infections are considered as one of the health diseases that threatens the lives of humans. Resistance of bacteria to antibiotics has made treating bacterial infections more challenging. With the emergence of many developed optical techniques, it has become possible to study various biological mechanisms of molecules inside these small organisms with high resolution and precise localization. In this research, single particle tracking photoactivation localization microscopy (sptPALM) technique was used to investigate the dynamics of fluorescent histonelike nucleoid-structuring proteins (H-NS) in live …