Microbiology Commons^™

Stability Of Temperate Coral Astrangia Poculata Microbiome Is Reflected Across Different Sequencing Methodologies, Dawn B. Goldsmith, Zoe A. Pratte, Koty H. Sharp

Arts & Sciences Faculty Publications

The microbiome of the temperate coral Astrangia poculata was first described in 2017 using next-generation Illumina sequencing to examine the coral’s bacterial and archaeal associates across seasons and among hosts of differing symbiotic status. To assess the impact of methodology on the detectable diversity of the coral’s microbiome, we obtained near full-length Sanger sequences from clone libraries constructed from a subset of the same A. poculata samples. Eight samples were analyzed: two sets of paired symbiotic (brown) and aposymbiotic (white) colonies collected in the fall (September) and two sets collected in the spring (April). Analysis of the Sanger sequences revealed …

The Anaplasma Phagocytophilum Adhesin Asp14 Directs Pdi-Mediated Disulfide Reduction To Promote Infection, Ryan S. Green

Theses and Dissertations

Obligate intracellular pathogens must invade host cells to survive and pose a global health risk. As such, internalization is a critical life stage and represents an excellent therapeutic target. Oxidoreductase exploitation is a thematic invasion strategy among obligate intracellular pathogens. Delineating the mechanisms and proteins mediating this exploitation could identify novel therapeutic targets for many important pathogens. Anaplasma phagocytophilum infects neutrophils by an incompletely defined mechanism, resulting in the emerging potentially fatal disease, human granulocytic anaplasmosis. The bacterial adhesin, Asp14, contributes to invasion by virtue of its C-terminus engaging an unknown receptor. Yeast two-hybrid analysis identified protein disulfide isomerase (PDI) …

Linking Microbial Community Structure And Ecosystem Functions In Acidic Soil From Pennsylvania, Usa, Madison T. James, Sophia T. Farrisi, Shreya Shah, Vishal Shah

Sustainability Research & Creative Activities Grants Reports

Microorganisms play a critical role in the structure and functioning of soil ecosystems. Within acidic soil across the northeastern United States and Canada, we have little understanding of the microbial diversity present and its relationship to the biochemical cycles. The current study is aimed at understanding the taxonomical and functional diversities in the acidic soil obtained from near various types of trees, how the diversities change as a function of depth, and the linkage between taxonomical and functional diversities. From eight sampling locations, soil samples were collected from three horizons (depths). The three depths were 0-10 cm (A), 11-25 cm …

The Effect Of Proteolytic Queues On Antibiotic Tolerance And Persistence Cells Population In Escherichia Coli, Alawiah Abualrahi

Electronic Theses and Dissertations

A major contributing factor to the abundance of antibiotic-resistant microorganisms and failed antibiotic treatment is survival due to antibiotic tolerance and persistence. Antibiotic tolerance is a widespread phenomenon that enables cells to survive treatment without carrying a resistance gene. This phenomenon renders antibiotic treatments less effective and facilitates antibiotic resistance. We are particularly interested in proteases, responsible for degradation of proteins, because of their known relationship to tolerance and persistence. Here, we examine the effects of proteases and antibiotic survival using queueing theory, in which one type of customer competes for processing by servers, that has traditionally been applied to …

Genome Sequences Of Three Cruciviruses Found In The Willamette Valley (Oregon), Ignacio De La Higuera, Ellis L. Torrance, Alyssa A. Pratt, George Kasun, Amberlee Maluenda, Kenneth M. Stedman

Biology Faculty Publications and Presentations

Cruciviruses are single-stranded DNA (ssDNA) viruses whose genomes suggest the possibility of gene transfer between DNA and RNA viruses. Many crucivirus genome sequences have been found in metagenomic data sets, although no crucivirus has been isolated. Here, we present the complete genome sequences of three cruciviruses recovered from environmental samples from Oregon.

Functional Analyses Of The Dna- And Rna-Binding Protein Spovg In Borrelia Burgdorferi, Christina R. Savage

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

Borrelia burgdorferi, the causative agent of Lyme disease, exists in a defined enzootic cycle involving Ixodes scapularis ticks and various vertebrates. Humans can serve as an accidental host, if a tick colonized with B. burgdorferi happens to feed on a human. B. burgdorferi are also accidental pathogens: they do not make toxins, or destroy host tissue by other mechanisms. They merely transmit between vector and host to survive. In order to do this, they must effectively sense their current environment, and appropriately alter cellular processes. Understanding the regulatory mechanisms of how B. burgdorferi manages to do this has been …

Post-Translational Modifications And Functional Studies Of Dksa In Escherichia Coli, Andrew Charles Isidoridy

Legacy Theses & Dissertations (2009 - 2024)

DksA is a bacterial gene regulator that functions synergistically with the stress alarmone ppGpp to mediate the stringent response. DksA also functions independently of ppGpp to regulate transcription of a number of genes. DksA function is dependent on its binding affinity to RNA polymerase and requires specific interactions between RNAP and catalytic amino acids located on the coiled coil tip, D74 and A76. While much of the previous work on DksA has focused on understanding the mechanisms of action and the numerous gene targets for transcriptional regulation, little is known about the mechanisms by which DksA expression and function may …

Transcriptional Regulation Of Dksa In E. Coli, Daniel Thomas Woods

Legacy Theses & Dissertations (2009 - 2024)

DksA is a global transcription factor that binds RNAP directly to regulate the expression of many genes and operons, including ribosomal RNA, in a ppGpp-dependent or ppGpp–independent manner. It is also involved in facilitating the process of DNA replication by removing stalled transcription elongation complexes that could block the progress of the replication fork. In addition, DksA is important for colonization, establishment of biofilms, and pathogenesis. In order to sustain these various functions, an adequate level of cellular DksA is required. This work tested the hypothesis that the E. coli dksA is substantially regulated at the level of transcription. Using …

Premature Rho-Dependent Transcription Termination In Escherichia Coli : Link To Translation And Gene Regulation, Gabriele Baniulyte

Legacy Theses & Dissertations (2009 - 2024)

Transcription termination factor Rho is an essential protein in Escherichia coli and related bacteria. The primary function of Rho is to clear unproductive RNA polymerases from the DNA template to minimize negative effects associated with uncontrolled transcription. Although most of the Rho termination events are constitutive, premature Rho-mediated termination was observed at 3% of all affected transcripts indicating active regulation of Rho activity. In this work, we investigated the regulatory mechanism behind premature Rho-dependent transcription termination in two unrelated genes: suhB and topAI. We show that in both cases transcription is terminated inside the coding gene as a consequence of …

Contrasting Roles Rna Binding Proteins G3bp1 And Hur Influence Zika Virus And A Proposed Mechanism By Which Zika Virus Induces Neurological Complications, Gaston Bonenfant

Legacy Theses & Dissertations (2009 - 2024)

Globalization and climate change have contributed to the rampant spread of mosquitos from tropical and subtropical climates into more moderate climates, and thus also the spread of a number of vector-borne viruses. As of 2016, the World Health Organization (WHO) estimates that of all human infections world-wide, 16% result from vectors such as flies, ticks, and mosquitos. The spread of such viruses has encouraged expedient evolutionary pressures resulting in more pathogenic viruses that continually pose a serious threat to public health. First discovered in 1947, Zika virus (ZIKV) has only recently presented as a detriment to public health. The importance …

Comparative Characteristics Of Antibacterial Activity Of Plants Growing In The Central Part Of The Republic Of Tajikistan., Saidbeg Satorov, F. Mirzoeva, Sh. Satorov, M. Vakhidova, Vyacheslav Dushenkov

Publications and Research

Objective: To evaluate the spectrum of antibacterial activity of plants growing in the central part of the Republic of Tajikistan.
Methods: The antibacterial properties of 18 plant species from the 14 families were studied. The extract samples on dry filter discs were prepared according to the method developed at Rutgers University. Screens-to-Nature (STN) and disc diffusion (DD) methods were used to assess antimicrobial properties of the extracts. The antimicrobial activity of plant extracts was determined against four types of pathogenic standard museum strains of Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, as well as …

Development Of A Biosafety Level-2 Facility For Irradiation Of Biological Cells Using Mev Ions, Jay D. Diaz, Naresh T. Deoli, Deborah Rogers, Armin De Vera, Karen M. Smith, Robin Schmeider-Broussard, Harry J. Whitlow

Louisiana Accelerator Center

The development of a facility for irradiation of murice and primate tissue presents several challenges. First, extremely low fluences (10⁶-10¹¹ ions cm⁻²) are required to deliver doses of 1 mGy - 50 Gy using MeV proton. Second,the tissues, particularly from non-human primate, may be infectious to humans. Third, protection of irradiated tissue samples from contamination by mold and bacteria is critical. Here we present an ultra-low flux irradiation facility and associated fluence control for biological cell and tissue irradiation under sterile biosafety level 2 (BSL-2) conditions suitable for use with low energy (1-3.4 MeV) protons. The operation is demonstrated using …

Bovine Cellular And Innate Immune Response To Hemostatic Polysaccharides, Brian Kobylkevich

Electronic Theses and Dissertations

Chronic wounds are longstanding dermal wounds that do not heal in a normal amount of time and can commonly last for over a year. These wounds plague humans and farm animals alike. Wounds are characterized by chronic inflammation and are often painful, difficult to heal, have a high recurrence rate, and are potentially debilitating. Long term wounds that do not fully heal are distressing for both humans and animals, but understandably more resources have been directed towards humans. Some treatment options for humans may be suitable for adaptation into the field of animal care. Chronic lesions such as bovine digital …

Interactions Of Arbuscular Mychorrhizal Fungi And Bacterial Endophytes On Disease Resistance Of Common Root Pathogens In Wheat, Janice L. Eibensteiner

Electronic Theses and Dissertations

Arbuscular mycorrhiza, a symbiosis between plants and fungi, help plants to capture nutrients such as phosphorus (P), nitrogen (N) and other micronutrients from the aggre in exchange for up to 20% of the fixed carbon (C) from the plant. In addition, arbuscular mycorrhizal (AM) fungi can improve the resistance against abiotic (drought, salinity), and also biotic (pathogen) stresses. Bacterial endophytes promote plant growth and yield by fixing N2 from the atmosphere, assimilating N and transfer it to the plant. Bacterial endophytes can also solubilize phosphate and stimulate plant defense responses, suppressing pathogens. The host plant provides sucrose and a favorable …

Development Of Computational Techniques For Identification Of Regulatory Dna Motif, Cankun Wang

Electronic Theses and Dissertations

Identifying precise transcription factor binding sites (TFBS) or regulatory DNA motif (motif) plays a fundamental role in researching transcriptional regulatory mechanism in cells and helping construct regulatory networks for biological investigation. Chromatin immunoprecipitation combined with sequencing (ChIP-seq) and lambda exonuclease digestion followed by high-throughput sequencing (ChIP-exo) enables researchers to identify TFBS on a genome-scale with improved resolution. Several algorithms have been developed to perform motif identification, employing widely different methods and often giving divergent results. In addition, these existing methods still suffer from prediction accuracy. Thesis focuses on the development of improved regulatory DNA motif identification techniques. We designed an …

Increasing Accumulation Of Glyceollins In Soybeans Via Optimization Of The Fungal Incubation Process, Stephanie Wootton

Electronic Theses and Dissertations

Continual use of antibiotics in the feed of food animals was viewed a solution to the problem of disease outbreaks in livestock produced in confinement operations. This practice also improved animal performance, likely due to the reduction in sub-clinical infections. Unfortunately, this practice led to a new problem, the development of antibiotic resistant microbes. This increase in antibiotic resistance reduced the direct benefits of antibiotics in animal production. Moreover, as antibiotic resistance spread from animal to human pathogens, this practice created a major public health concern. This led the FDA to enact the Veterinary Feed Directive in 2017 that greatly …

Comparative Optic Nerve Head Physiology: Glaucoma Induced Retinal Ganglion Cell Apoptosis By Disruption Of The Translaminar Pressure Gradient And Reduced Neurotrophic Signaling, Cassidy Christopherson

Biology and Microbiology Graduate Students Plan B Research Projects

Glaucoma is the leading cause of irreversible blindness, and the second leading vision loss neurodegenerative disease affecting millions worldwide. Glaucoma is characterized as a group of eye disorders which are initially asymptomatic but may progress to significant optic nerve head damage and vision loss with time. Early stages of glaucoma often go undetected, leading to irreversible damage to the optic nerve head prior to patients seeking medical care. Glaucoma leads to vision loss via death of retinal ganglion cells. Retinal ganglion cell apoptosis is thought to begin due to interference with the normal transmission of neurotrophic signals that arrive by …

Irritable Bowel Syndrome With Constipation (Ibs-C) Treatment Efficacy And The Emerging Importance Of Serotonin, Meghan Schenk

Biology and Microbiology Graduate Students Plan B Research Projects

Irritable bowel syndrome with constipation (IBS-C) affects a large proportion of the population. It decreases quality of life for the patient both physically and mentally. Patients report higher levels of mental health issues and other gastrointestinal maladies compared to the normal population, in addition to an IBS diagnosis. Patients have increased healthcare visits and costs, raising insurance rates for all, and also results in more missed time from work. There are limited treatments available for IBS-C, and medicinal and non-medicinal modalities are differentially prescribed to patients throughout the country. Recently, serotonin has emerged as a key mediator of normal gut …

A Review: The Association Of Asthma And The Microbiome, Kathleen Olson

Biology and Microbiology Graduate Students Plan B Research Projects

The microbiome gut-lung axis has been associated with asthma. Asthma is a respiratory disease that presents itself in many different ways. The microbiome is the bacteria, fungi, protozoa, and viruses found in a particular environment. The association of the microbiome gutlung axis in an asthmatic individual compared to a healthy individual has shown that different types and/or concentrations of bacterial genera are present in an asthmatic individual compared to a healthy individual. A causal relationship between the microbiome and asthma has not yet been identified. The aim of this review is to present the association of asthma and the microbiome …

Pathogenesis Of Cte: A Review Of Ptau, Lewy Bodies, And Cytokine Involvement In Cte, Karter Keefer

Biology and Microbiology Graduate Students Plan B Research Projects

Chronic Traumatic Encephalopathy (CTE) is a neuropathological disease that develops years after experiencing repetitive traumatic brain injuries. In recent years, this disease has been gaining recognition from professional, college, and high school teams that participate in contact sports. The purpose of this paper is to review available information about this neurodegenerative disease. Only limited published experiments are available on this disease. Research on CTE has been limited by the fact that patients can only be diagnosed with the disease by a post mortem autopsy. Many experiments were analyzed regarding different CTE pathologies, symptoms, and treatments. Articles used in this paper …

Serosurvey For Evidence Of Dengue And West Nile Virus Human Infections In El Paso, Texas, Veronica Suarez

Open Access Theses & Dissertations

Dengue viruses (DENV), including the 4 serotypes are the cause of dengue fever and dengue hemorrhagic fever. The viruses are transmitted by Aedes aegypti mosquitoes in urban communities in tropical, sub-tropical, and temperate regions and are the cause of the highest rate of infection and death of all known Flaviviruses. DENV are endemic in United States (US) -Mexico (MX) border communities in the Rio Grande Valley and suspected of being endemic in Ciudad Juarez, a sister city to El Paso, TX. To determine if DENV were endemic in the El Paso community, cord-blood samples from mothers were tested for antibody …

Nurse Practitioner Attitudes, Perceptions And Knowledge About Antimicrobial Stewardship, Evelyn C. Fabian

Walden Dissertations and Doctoral Studies

Resistance to antibiotics has increased dramatically in the United States, with serious associated medical, social, and economic consequences. The purpose of this project was to assess nurse practitioners' attitudes, perceptions, and knowledge about antimicrobial stewardship and knowledge in the management of anaerobic infections as well as resistant gram-negative bacteremia. Data were collected using a web-based survey in a hospital facility. The practice question explored whether nurse practitioners' attitudes, perceptions, and knowledge about antimicrobial stewardship significantly increased after an education program on antimicrobial stewardship. The project was framed by Knowles's adult learning theory. A 16-item survey was administered before and after …

Pyocyanin, A Virulence Factor Produced By Sepsis-Causing Pseudomonas Aeruginosa, Promotes Adipose Wasting And Cachexia, Nika Larian

Theses and Dissertations--Pharmacology and Nutritional Sciences

Sepsis is a leading cause of death among critically ill patients that results in metabolic alterations including hypercatabolism, lipoatrophy, and muscle wasting, contributing to the development of cachexia. Septic cachexia is associated with loss of body weight, fat mass, and lean mass and dysregulated immune function. There are currently no efficacious treatment strategies for septic cachexia, and nutritional interventions have limited success in preventing hypercatabolic wasting. Pyocyanin is a virulence factor produced by sepsis-causing Pseudomonas aeruginosa that has been shown to activate the aryl hydrocarbon receptor (AhR), increase inflammation, and produce reactive oxygen species. Thus, pyocyanin represents a novel mechanistic …

Development And Evaluation Of Nonradioactive Methods For Monitoring T Lymphocyte Response To Equine Arteritis Virus (Eav) In Horses, Annet Kyomuhangi

Theses and Dissertations--Veterinary Science

Target cell lysis is the hallmark of immune effector responses of cytotoxic T lymphocytes (CTL), natural killer (NK) cells, and monocytes. The most commonly used assay to measure target cell lysis is the 51Cr release assay and is considered the ‘gold standard’. However, this assay has many disadvantages that limit its use by most laboratories. Thus, several alternative assays have been developed. Some of these alternative assays are more sensitive, easy to perform and do not use radioactive elements.

In this study, four of these assays were evaluated for their ability to detect antigen- specific CTL responses in equine blood. …

Modulation Of Inflammatory Cytokine, Chemokine, And Toll-Like Receptor Genes And Transcriptome Analysis Of Equine Endothelial Cells Following Infection With Equid Herpesvirus-1, And Equine Arteritis Virus., Saranajith Wangisa Dunuwille

Theses and Dissertations--Veterinary Science

EHV-1 is a double-stranded DNA virus whereas EAV is a positive sense, single-stranded RNA virus. Therefore, genetically, they are very different from one another. However, both these viruses are endotheliotropic and thus, infect and replicates in equine endothelial cells resulting in vasculitis. Vasculitis is central to the pathogenesis of these two viruses. Thus, the main objective of this thesis was to investigate the inflammatory and innate immune responses of EECs that contribute towards the development of vasculitis following infection with EHV-1 and EAV in-vitro. Since proinflammatory cytokines and chemokines produced by endothelial cells play a significant role in the …

Mechanisms Of Type-I Ifn Inhibition: Equine Herpesvirus-1 Escape From The Antiviral Effect Of Type-1 Interferon Response In Host Cell, Fatai S. Oladunni

Theses and Dissertations--Veterinary Science

Equine herpesvirus-1 (EHV-1) is one of the most important and prevalent viral pathogens of horses causing a major threat to the equine industry throughout most of the world. EHV-1 primarily causes respiratory disease but viral spread to distant organs enables the development of more severe sequelae; abortion and neurologic disease. In order to produce disease, EHV-1 has to overcome the innate barrier of the type-I interferon (IFN) system in host cells. However, the underlying mechanisms employed by EHV-1 to circumvent the type-I IFN response in host cells are not well understood. In this project study, using molecular techniques, we explored …

The Abundance Of Akkermansia Muciniphila And Its Relationship With Sulphated Colonic Mucins In Health And Ulcerative Colitis, Helen Earley, Grainne Earley, Aine Balfe, J. Calvin Coffey, Desmond C. Winter, Ronan O'Connell

Articles

Akkermansia muciniphila utilises colonic mucin as its substrate. Abundance is reduced in ulcerative colitis (UC), as is the relative proportion of sulphated mucin in the mucus gel layer (MGL). It is unknown if these phenomena are related, however reduced sulphated mucins could contribute to reduced abundance, owing to a lack of substrate. The aim of this study was to quantify A. muciniphila within the MGL and to relate these findings with markers of inflammation and the relative proportion of sulphomucin present. Colonic biopsies and mucus brushings were obtained from 20 patients with active UC (AC), 14 with quiescent UC (QUC) …

The Role Of Polyamines In Enteroviral Attachment, Thomas Mckenzie Kicmal

Master's Theses

Polyamines are small polycationic molecules with flexible carbon chains that are found in all eukaryotic cells. Polyamines are involved in the regulation of many host processes and have been shown to be implicated in viral replication. Depletion of polyamine pools in cells with FDA approved drugs restricts replication of diverse RNA viruses. Viruses can exploit host polyamines to facilitate packaging, transcription, translation, and protease activity but other mechanisms remain largely unknown. Picornaviruses, including Coxsackievirus B3 (CVB3), are sensitive to depletion of polyamines and remain a significant public health threat. We employed CVB3 as a model system to investigate a potential …

Dissecting A Role For Polyamines In Rift Valley Fever Virus Infection, Vincent Mastrodomenico

Master's Theses

Bunyaviruses are emerging viral pathogens that cause encephalitis, hemorrhagic fevers, and meningitis. Rift Valley fever virus is a particularly devastating bunyavirus, infecting both humans and livestock with significant morbidity and mortality. By coordinating several host and viral processes Rift Valley fever virus is able to produce infectious virions. Polyamines are small, positively-charged host-derived molecules that play diverse roles in human cells and in infection. We previously demonstrated that polyamines are crucial for RNA viruses; however, the mechanisms by which polyamines function remain unknown. Here, we investigated polyamines' role in the replication of the Rift Valley fever virus (vaccine strain MP-12). …

A Possible Role Of Clostridium Difficile Association With The Gi Tract In Relapsing Clostridium Difficile Infection, Asiyya Ashraf

Master's Theses

Clostridium difficile infection (CDI), caused by the anaerobic spore-former C. difficile, is a major cause of health-care associated morbidity. CDI occurs in individuals that have a disrupted GI tract microbiota, typically in patients who are on antibiotic therapy. After recovery from an episode of CDI, approximately, 15-30% of patients experience relapse of disease. The mechanism of relapse is not well understood. It is plausible for relapse to occur if C. difficile cells and spores associate with the GI tract mucosa during infection and persist after infection. However, little is known about the association of cells and spores with the GI …