Microbiology Commons^™

Guano Among Bat Species From Two Regions Shows Influence Of Geography And Diet On Bacterial Community, Rahma Ahmed, Thomas Mcelroy, Shannon Whitney, Lydia Moore

Symposium of Student Scholars

Studies of bat guano have shown that the diversity and structure of associated microbial communities can be related to factors such as host phylogeny, life history and reproductive stage, geography, and diet. Many insectivorous bat species in the southeastern U.S. have generalist diets that may shift seasonally to take advantage of abundant prey species or maximize caloric intake. Seasonal shifts in prey availability or consumption should be reflected in a guano microbiome change. We also expected to detect distinct guano microbiomes within species. Within species, distinct microbial communities related to geography, and finally life history and reproductive stage. We compared …

Alternative Precautionary Measures Yielding Lower C. Diff Infection Rates In Healthcare Facilities, Matthew Kramer

Symposium of Student Scholars

Background: An international healthcare concern is the persistent spread of Clostridium difficile, a Gram-positive spore forming bacterium that is responsible for the most common hospital-acquired infection, amongst patients.

Objective: A systematic review was performed to summarize evidence that the interventions utilized in healthcare facilities which indicate a patient’s precautionary status are insufficient, outdated, and commonly lead to infection in neighboring patient rooms. Databases such as PubMed, NCBI, Google Scholar, and APHA’s Medical Care were searched, covering the period from 2017-2022. Studies were included if their focus concentrated on C. diff and the precautionary measures taken by employees at healthcare …

Detecting Bacterial Species From Ancient Human Skeletal Samples, Ariel Owens, Daisy Mcgrath, Tsai-Tien Tseng

Symposium of Student Scholars

Diagnosis of tuberculosis (TB) via morphological analysis is difficult and often inconsistent. With next-generation sequencing (NGS), ancient host microbiomes can be subjected to metagenomic analyses for the detection of TB in silico. Suitable bioinformatic workflows are needed for reliable ancient DNA (aDNA) analysis of causative agents. This study aims to enhance available bioinformatic screening methods to create more suitable bioinformatic processes and generate insights in relation to TB.

This research utilizes publicly available NGS data accessed through the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI). Initial quality control steps included adapter trimming with Trim …

Isolation And Characterization Of Chi-Like Salmonella Bacteriophages Infecting Two Salmonella Enterica Serovars, Typhimurium And Enteritidis, Addisu D. Teklemariam, Mona G. Alharbi, Rashad R. Al-Hindi, Ibrahim Alotibi, Abdullah A. Aljaddawi, Sheren A. Azhari, Ahmed Esmael

Nebraska Center for Virology: Faculty Publications

Salmonella enterica Serovar Typhimurium and Salmonella enterica Serovar Enteritidis are well-known pathogens that cause foodborne diseases in humans. The emergence of antibiotic-resistant Salmonella serovars has caused serious public health problems worldwide. In this study, two lysogenic phages, STP11 and SEP13, were isolated from a wastewater treatment plant in Jeddah, KSA. Transmission electron microscopic images revealed that both phages are new members of the genus “Chivirus” within the family Siphoviridae. Both STP11 and SEP13 had a lysis time of 90 min with burst sizes of 176 and 170 PFU/cell, respectively. The two phages were thermostable (0 ^◦C …

The Future Of Microbiome Research, Anna Vietmeier

D.U.Quark

No abstract provided.

Assessing Selective Export Of Fluorescent Ssa4 Reporters, Caroline Firmin, Rebecca Adams

Science University Research Symposium (SURS)

The process of creating proteins from mRNA is necessary for cell viability. Importantly, the proteins that are generated are differentially regulated so that the cell makes specific proteins in response to its environment. For example, mRNA is selectively exported during stress conditions to allow response to this stress. During heat shock at 42°C, in which proteins are denatured, the gene SSA4 encodes a selectively transported protein chaperone that allows refolding of denatured proteins. This study sought to explore the mechanisms of this selective export. To do this, I analyzed the expression of a fluorescent reporter wherein GFP is expressed with …

Functional Analysis Of Legionella Pneumophila Effector Protein, Shreya Neupane

Masters Theses & Specialist Projects

Legionella pneumophila is a gram-negative bacterium that causes Legionnaire’s disease (a severe form of pneumonia) in humans. L. pneumophila can cause infection by utilizing its Type IV secretion system, a protein secretion system that transports proteins from the bacterial cytosol into the infected macrophage. Effectors released from the Type Iv secretion system allow L. pneumophila to create a safe environment to survive, replicate and cause infection. One such effector, RavQ, inhibits cell proliferation of mammalian HEK 293T cells and localizes to the cell’s nucleus, leading us to hypothesize that RavQ interferes with cellular activity in the nucleus. To detect its …

Comparison Of Kanamycin-Resistant Bacteria In Earthworm Digestive Tracts And Soil From Compost Bins, Samantha Dooyema, Martin Dolan, Abigal Morse

Science University Research Symposium (SURS)

Antibiotic-resistant bacteria are becoming more prevalent in soil as humans have increased impacts on the environment. Previous research proposed that earthworms could affect bacteria distribution as soil is ingested and filtered through their bodies. This research aims to see if kanamycin-resistance bacteria is the same in earthworm digestive tracts as in the soil the earthworms inhabit. We expect that the gut contents and soil will vary in the occurrence of kanamycin-resistant bacteria. Earthworms and composted soil samples were collected from compost bins at a residential home in Nashville, Tennessee. Digestive tracts were dissected from the earthworms and homogenized. Kanamycin-resistant bacteria …

The Role Of The Filifactor Alocis Hypothetical Protein Fa1654 In Oxidative Stress Resistance, Malissa Makaylia Mangar

Loma Linda University Electronic Theses, Dissertations & Projects

The survival/adaptation of Fillifactor alocis, a fastidious gram positive asaccharolytic anaerobe in the inflammatory environment of the periodontal pocket, requires an ability to overcome oxidative stress. Moreover, emerging observations suggest its pathogenic characteristics are highlighted by its capacity to survive in the oxidative-stress microenvironment of the periodontal pocket and its likely ability to modulate the microbial community dynamics. There is still a significant gap in our understanding of F. alocis mechanism of oxidative stress resistance and its impact on the virulence and pathogenicity of the microbial biofilm. The pathogenicity of F. alocis may be impacted by its response to oxidative …

Characterizing The Cutaneous Microbiome Of Eurycea Lucifuga As A Potential Defense Against Chytridiomycosis, Madeline Key

Senior Honors Theses

Chytridiomycosis is an emerging infectious disease that is significantly reducing global amphibian populations. The disease is caused by Batrachochytrium dendrobatidis (Bd), a fungus that lethally modifies amphibian skin. Recent research has suggested that the cutaneous microbiome of individual amphibians may play a role in susceptibility to the pathogen. In this study, twelve cave salamanders (Eurycea lucifuga) were collected. Cutaneous bacteria from each salamander were isolated and identified using Sanger Sequencing. Additionally, a Bd-challenge assay was performed to determine each isolate’s antifungal activity. Results indicated many microbial isolates possessed inhibitory capabilities against Bd, which may …

Vircy-Seq : A Protocol For Characterizing Viral Activity, Tyler James Dion

Legacy Theses & Dissertations (2009 - 2024)

The main purpose of pharmaceutical production is to produce safe effective medicine for patient use. In an effort to ensure patient safety constant surveillance for viruses takes place. The detection of a viral nucleic acid in a pharmaceutical production setting results in investigations to assess its infectious potential. This is an intensive, expensive process that entails many tests such as the observation of hemadsorption, cytopathic effects (CPE), and more. These tests are typically specific and only capture certain viruses, as factors like CPE can only be observed in some viral species. A new investigational method that is effective on all …

Characterizing And Epitope Mapping Single-Domain Antibodies On Borrelia Burgdorferi Protein Ospa, Saiful Basir

Legacy Theses & Dissertations (2009 - 2024)

Epitope mapping a protein that enables pathogenesis is crucial for the development of therapies and prophylactics that can inhibit the pathogen’s function and its transmission of disease. The lipoprotein OspA enables Lyme Disease etiologic pathogen, Borrelia burgdorferi, to inhabit the tick midgut until transmission occurs. Anti-OspA mAbs and their smaller VHH counterparts are highly specific and tailored to bind proteins such as OspA, reproducibly, at established binding sites or epitopes. Previous studies found an array of mAbs that successfully bound OspA and have already been used in epitope mapping. To our knowledge, this is the first use of VHHs in …

Understanding The Molecular Mechanism Of Ilv1 Stress Sensitivity In Yeast By Examination Of Differential Patterns Of Gene Expression Between Wild-Type And Ilv1 Knockout Strains Of Saccharomyces Cerevisiae, Emily Schuster

Honors Theses

As arguably the most widely used industrial eukaryote, Saccharomyces cerevisiae has become one of the many model organisms used to study molecular genetics. A recent unpublished study at the University of Tennessee - Chattanooga showed that yeast cells that had the ILV1 gene knocked out had reduced survivability under stress conditions. This study then focused on the role of ILV1 in the stress response of cells by measuring the expression levels of 11 candidate genes that are all involved in some critical pathway in the yeast to see how gene expression was influenced as a result of the loss of …

Single-Cell Approach Reveals Intercellular Heterogeneity In Phage-Producing Capacities, Sherin Kannoly, Gabriella Oken, Jonathan Shadan, David Musheyev, Kevin Singh, Abhyudai Singh, John J. Dennehy

Publications and Research

Bacteriophage burst size is the average number of phage virions released from infected bacterial cells, and its magnitude depends on the duration of an intracellular progeny accumulation phase. Burst size is often measured at the population level, not the single-cell level, and consequently, statistical moments are not commonly available. In this study, we estimated the bacteriophage lambda (ƛ) single-cell burst size mean and variance following different intracellular accumulation period durations by employing Escherichia coli lysogens bearing lysis-deficient ƛ prophages. Single lysogens can be isolated and chemically lysed at desired times following prophage induction to quantify progeny intracellular accumulation within individual …

The Mechanisms Of Mitochondrial Dysfunction In T Cell Aging During Chronic Viral Infection, Madison B. Schank

Electronic Theses and Dissertations

Human immunodeficiency virus (HIV) and hepatitis C virus (HCV) infections induce a myriad of disturbances to CD4 T cell functions, including mitochondrial compromise, excessive inflammation, increased telomeric DNA damage and attrition, cellular exhaustion and senescence, and accelerated aging. In this dissertation, the mechanisms underlying metabolic failure, accelerated aging, and cellular dysfunctions were evaluated in CD4 T cells from healthy subjects (HS) treated with a telomere-targeting drug (KML001) or HCV-infected individuals or people living with HIV (PLHIV) compared to HS. We observed that KML001-induced telomere injury resulted in mitochondrial swelling and decreased mitochondrial membrane potential, cellular respiration, mitochondrial DNA (mtDNA) copy …

The Antimicrobial Resistance Plasmid Mobilome Of Salmonella Enterica And Related Enteric Species And Factors That Influence The Transfer Efficiency., Suad Algarni

Graduate Theses and Dissertations

The dynamic distribution of antimicrobial resistance genes in Salmonella enterica is considered a public health risk. S. enterica is one of the most important etiological agents of foodborne illness and has a critical impact on global human health. In S. enterica and related species, mobile genetic elements (MGEs) serve as primary vehicles for the dissemination of antibiotic resistance genes in the bacterial evolution. This dissemination can be impacted by different selective pressures that leads to diverse antibiotic response phenotypes. This project focusses on the dynamics of antimicrobial resistance genes, particularly exploring the transfer efficiency of multidrug resistance plasmids in S. …

Biology And Epidemiology Of Dengue Viruses In The El Paso And The Surrounding Usa And Mexico Border Communities, Pedro Miguel Palermo Infante

Open Access Theses & Dissertations

Dengue is considered one of the most important human arboviral diseases worldwide. Dengue cases have increased in the last three decades in the Americas, especially along the United States (US)- Mexico (MX) border region, where the main vector of dengue, Aedes aegypti mosquito, is widely distributed. Explosive outbreaks of dengue in northern Mexico have been associated with imported and local transmission of dengue in the US border communities, especially in the Southeast Texas area, also known as Rio Grande Valley. Due to the unknown if dengue virus (DENV) is present in other areas in the US border located west of …

Biology And Ecology Of Aedes (Stegomyia) Aegypti In The Northern Chihuahuan Desert, Adam Joseph Vera

Open Access Theses & Dissertations

Aedes aegypti is a medically important mosquito species that transmits multiple arboviruses, including dengue, chikungunya, Zika, and yellow fever. This mosquito species has expanded its geographical range into expanded into the Northern Chihuahuan Desert to further increase the risk of infection by these viruses in naïve human populations. Although Ae. aegypti is abundant along the U.S.â??Mexico border, the biology and ecology of this mosquito species in this temperate/arid climate region is not understood. The objective of this study was to understand the environmental factors that influence the invasive species of Ae. aegypti abundance, breeding habitat selection, host feeding behavior, and …

Optimization Of Clostridium Septicum Antigen Production And Evaluation Of Vaccine Administration Parameters For A Candidate Bacterin-Toxoid To Prevent Dermatitis In Commercial Turkeys, Aaron Forga

Graduate Theses and Dissertations

The objective of this thesis was to optimize the hemolytic activity of two isolates of Clostridium septicum to evaluate if hemolytic titer of C. septicum antigen at time of formalin inactivation corresponded to increased serum antibody titer to the C. septicum alpha-toxin of turkeys immunized with an experimental formalin inactivated bacterin-toxoid vaccine. Chapter 1 provides a brief overview of the thesis. Chapter 2 consists of a literature review focused on clostridial dermatitis, specifically C. septicum-associated dermatitis (cellulitis) that affects commercial turkeys. Chapter 3 outlines our attempts to optimize an experimental autogenous bacterin-toxoid vaccine as a potential strategy to mitigate clostridial …

Death Of A Bacterium: Exploring The Inhibition Of Staphylococcus Aureus By Burkholderia Cenocepacia., Tiffany Brandt

Electronic Theses and Dissertations

Antimicrobial resistance is a phenomenon of increasing concern as antimicrobial overuse and misuse eliminate current therapeutic options, ushering society into a post-antimicrobial era. Antibiotic discovery and synthesis efforts are urgently needed to counter the increasing burden of antimicrobial resistance. Staphylococcus aureus is a causative agent of a variety of clinical manifestations including bacteremia, endocarditis, soft tissue infection, osteomyelitis, and device-related infections. S. aureus infection presents additional treatment challenges due to its capacity for biofilm formation, which is a mode of growth that confers protection from antibiotics and physical elimination, and the emergence of antibiotic resistant strains, including methicillin-resistant S. aureus …

The Role Of Microbiota-Biotransformed Bile Acid Metabolites On Campylobacter Jejuni- And Clostridium Perfringens-Infection, Ying Fu

Graduate Theses and Dissertations

Campylobacter jejuni (C. jejuni) and Clostridium perfringens (C. perfringens) are two leading pathogenic bacteria responsible for both human and animal diseases. In chapters Ⅱ to Ⅳ, I presented an overview of current knowledge on the role of immune response, microbiota, bile acids and their microbial metabolites on campylobacteriosis, and C. perfringens induced necrotic diseases.In chapter Ⅴ, I investigated effects of deoxycholic acid-modulated anaerobes (DCA-Anaero) on attenuating chicken transmission-exacerbated campylobacteriosis. SPF Il10-/- mice were gavaged with clindamycin for 7 days followed by infected with three C. jejuni strains, Cj-P0 (C. jejuni AR101), Cj-P1 (from chicken pre-infected with C. jejuni AR101), and …

Molecular Characterization Of Nitrogenase Regulation In Methanosarcina Acetivorans, Melissa Chanderban

Graduate Theses and Dissertations

Nitrogenase is the metalloenzyme only found in bacteria and archaea that is essential for biological nitrogen fixation (diazotrophy), but it can also serve as a catalyst in biofuel production. All diazotrophs contain a molybdenum (Mo) nitrogenase, while some species contain additional alternative nitrogenases where either vanadium (V) or iron (Fe) replace Mo in the active site cofactor. Nitrogen fixation by bacteria has been extensively studied. The limited investigation of nitrogen fixation in methanogenic archaea (methanogens) indicates production of nitrogenase is simpler than in bacteria and methanogen nitrogenase has different biochemical properties. Thus, methanogen nitrogenases provide a promising alternative for genetic …

Taxonomic And Physiological Insights Into Novel Bacterial Class Fervidibacteria, Nancy Nou

UNLV Theses, Dissertations, Professional Papers, and Capstones

Recent studies incorporating cultivation-independent techniques to assess microbial communities, namely metagenomics and single-cell genomics, have pushed the proposed number of bacterial phyla from less than 50 to over 100. One such lineage is the candidate bacterial phylum Fervidibacteria, a strictly thermophilic group that has been identified in terrestrial geothermal springs in North America, Asia, and Antarctica through DNA sequencing. By analyzing 62 medium- and high-quality genomes and through cultivation-dependent experiments, this study serves to set up taxonomy and describe physiology within the taxon. Over the course of this study, we propose Candidatus Fervidibacteria should be reclassified as novel class Fervidibacteria …

Calcite Spherulite Formations And Their Controls In Halophilic Bacterial Cultures, Zakaria Jibrin

UNLV Theses, Dissertations, Professional Papers, and Capstones

This study arose from an accidental discovery of calcite spherulites forming on colonies of various halophilic bacteria grown on solid Luria-Bertani medium made containing water from a brine pool in Death Valley, their natural habitat. Further studies with a large spherulite forming bacteria, Pseudoalteromonas haloplanktis, showed that calcite precipitation conditions were the consequence of bacteria using amino acids as a source of carbon and energy, a metabolism that produces NH3 and CO2 waste products. NH3 raises the pH of the medium, turning CO2 into CO32-. Calcium in the natural brine combines with CO32-. The resulting spherulitic calcite precipitation is nano-acicular …

T-Cell Antigen Receptors In Multiple Sclerosis, Lisa Lanée Keyes Jones

Biomedical Sciences Theses & Dissertations

Multiple Sclerosis (MS) is T-cell mediated autoimmune disease characterized by inflammation, demyelination, and degeneration of axons in the brain and spinal cord. A T cell-mediated immune response in MS is directed against myelin components and possibly other antigens in genetically susceptible individuals and is triggered by a viral infection. The T-cell antigen receptor (TCR) on T cells is responsible for antigen recognition and determines specificity. Our overall hypothesis is to determine whether clonally expanded T cells in patients with MS recognize viral or self-antigens and to determine whether molecular mimicry is involved in the development of the disease. To study …

Investigating The Pi3k/Akt/Atm Pathway, Telomeric Dna Damage, T Cell Death, And Crispr/Cas9-Mediated Gene Editing During Acute And Chronic Hiv Infection, Sushant Khanal

Electronic Theses and Dissertations

Human Immunodeficiency Virus (HIV) infection initiates major metabolic and cell- survival complications. Anti-retroviral therapy (ART) is the current approach to suppress active HIV replication to a level of undetected viral load, but it is not a curative approach. Newer and sophisticated gene editing technologies could indeed be a potent antiviral therapy to achieve a clinical sterilization/cure of HIV infection. Chronic HIV patients, even under a successful ART regimen, exhibit a low-grade inflammation, immune senescence, premature aging, telomeric DNA attrition, T cell apoptosis, and cellular homeostasis. In this dissertation, we investigated CD4 T cell homeostasis, degree of T cell apoptosis, an …

The Effects Of Tubulin Post-Translational Modifications On The Flagellar Motility Of Trypanosoma Brucei, Katherine Wentworth

All Theses

Trypanosoma brucei is a parasitic kinetoplastid that causes African trypanosomiasis and is transmitted to a mammalian host by the tsetse fly (Glossina spp.). T. brucei relies on its flagellar motility to carry out its morphological changes from the procyclic form (predominant in the fly vector) to the bloodstream form (infectious form in mammals) and navigate the bloodstream of its host. The driving structure within the flagellum is the axoneme, which is composed of microtubules and dynein motor proteins. The tubulin code hypothesis suggests that cells regulate microtubule motor protein activity through post-translational modifications (PTMs) of alpha and beta …

A Common Mechanism Links Epstein‐Barr Virus Infections And Autoimmune Diseases, Luwen Zhang

Nebraska Center for Virology: Faculty Publications

Epstein‐Barr virus (EBV) infection is associated with a variety of the autoimmune diseases. There is apparently no unified model for the role of EBV in autoimmune diseases. In this article, the development of autoimmune diseases is proposed as a simple two‐step process: specific autoimmune initiators may cause irreversible changes to genetic materials that increase autoimmune risks, and autoimmune promoters promote autoimmune disease formation once cells are susceptible to autoimmunity. EBV has several types of latencies including type III latency with higher proliferation potential. EBV could serve as autoimmune initiators for some autoimmune diseases. At the same time, EBV may play …

Hematophagy And Tick-Borne Rickettsial Pathogen Shape The Microbial Community Structure And Predicted Functions Within The Tick Vector, Amblyomma Maculatum., Abdulsalam Adegoke, Deepak Kumar, Khemraj Budachetri, Shahid Karim

Faculty Publications

Background: Ticks are the primary vectors of emerging and resurging pathogens of public health significance worldwide. Analyzing tick bacterial composition, diversity, and functionality across developmental stages and tissues is crucial for designing new strategies to control ticks and prevent tick-borne diseases.

Materials and methods: Here, we explored the microbial communities across the developmental timeline and in different tissues of the Gulf-Coast ticks (Amblyomma maculatum). Using a high-throughput sequencing approach, the influence of blood meal and Rickettsia parkeri, a spotted fever group rickettsiae infection in driving changes in microbiome composition, diversity, and functionality was determined.

Results: This study …

Il-33 Promotes Increased Replication Of Theiler’S Murine Encephalomyelitis Virus In Raw264.7 Macrophage Cells With An Irf3-Dependent Response, Ahmed Esmael, Thomas M. Petro

Nebraska Center for Virology: Faculty Publications

Interleukin-33 (IL-33), which promotes M2 macrophage development, may influence the control of viruses, such as Theiler’s Murine Encephalomyelitis Virus (TMEV) that infect macrophages. Because Interferon Regulatory Factor-3 (IRF3) is also critical to control of TMEV infection in macrophages, information on the relationship between IL-33 and IRF3 is important. Thus, RAW264.7 Lucia murine macrophage lineage cells with an endogenous IRF3-ISRE promoter driving secreted luciferase and IRF3KO RAW Lucia, a subline deficient in IRF3, were challenged with TMEV. After the challenge, considerable TMEV RNA detected at 18 and 24 h in RAW cells was significantly elevated in IRF3KO RAW cells. TMEV induction …