Microbiology Commons^™

A Metabolomics-Based Approach To The Screening Of Endometrial Cancer: Development Of A Gas Chromatography-Ion Trap Mass Spectrometry-Based Method, Allycia Lee

Honors Theses

Endometrial Cancer (EC) is the most common malignant tumor of the female reproductive tract. Currently there are no methods for effectively screening EC, but one method that is thought to be useful in screening EC is metabolomics. Metabolomics involves the analysis of metabolites which are low molecular weight inorganic and organic chemicals that are substrates, intermediates, and by-products of enzyme-mediated biochemical reactions in the cell. Previous research shows that the metabolic signature of EC patients are discernable from those of healthy patients. To aid in the development of an effective screening method for EC, blood serum, urine, and saliva samples …

Increasing Stress Tolerance In Saccharomyces Cerevisiae Using Lipocalin Genes, Ximena Leon

Honors Theses

Saccharomyces cerevisiae is a microorganism that is commonly used in industries, but its productivity is significantly hindered by its inability to resist high stress levels found in industrial processes. By increasing stress tolerance in S. cerevisiae, its role in industrial processes could be maximized. The objective of this study is to determine if complementation of lipocalin genes into the wildtype and knockout strains of S. cerevisiae can increase stress tolerance against a variety of stressors. We identified the knockout yeast strains, ALD3, ALD4, PDX3, and ILV1, as being sensitive to various stressors including salinity, heat, oxidative, and osmotic stresses. Arabidopsis …

Ecological, Evolutionary, And Molecular Mechanisms Driving Pyocin Diversity In Pseudomonas Aeruginosa., Aubrey A. Mojesky

Electronic Theses and Dissertations

Bacteriocins are narrow-spectrum antibiotics produced in nearly all lineages of bacteria, meaning that these antimicrobials target closely related individuals. The bacteriocins of Pseudomonas aeruginosa, called pyocins, are highly prevalent and diverse in populations of this species. Laboratory studies have shown that pyocins can function to mediate the outcome of interactions, often allowing for the coexistence of multiple strains, as no one pyocin genotype is competitively superior. Although this has been demonstrated under laboratory conditions, the function of pyocins in natural settings and the ecological, evolutionary, and genetic mechanisms underlying pyocin diversity remains unclear. As such, for my dissertation, I …

Determination Of The Biological Functions Of Undefined Domains Of Veev Nsp2., Andrew Michael Skidmore

Electronic Theses and Dissertations

Alphaviruses are positive sense, single strand, RNA viruses. These viruses occur on every populated continent. Alphaviruses are divided into two clades, the New-World and Old-World viruses. The New-World viruses include Eastern (EEEV), Western (WEEV), and Venezuelan equine encephalitis viruses (VEEV), and cause neuroinvasive disease. The Old-World viruses include Chikungunya (CHIKV) and Ross River viruses (RRV), and typically cause multijoint arthralgia. There are currently no approved antiviral therapeutics or vaccines for any alphavirus, making them a high priority for antiviral drug design and discovery. A benzamidine inhibitor (ML336) of VEEV was characterized, and determined to inhibit replication of VEEV RNA during …

Suppression Of Inflammation Of Cytokine Following Induced Francisella Tularensis Infection, Nicole Renee Setzu

Open Access Theses & Dissertations

Francisella tularensis is intracellular bacteria which is the causative agent of the disease Tularemia. Highly virulent in both humans and animals, it takes only as few as 10 microorganisms to cause a lethal infection. The bacteria can enter via direct or indirect routes causing the activations of the host innate inflammatory response to ensue. The bacteria invade host dendritic cells and neutrophils but predominately macrophages. This causes a mass inflammatory response resulting in the cytokine storm. Activation of Natural Killer T (NKT) cells has been shown to suppress inflammation in in vivo studies. Development and optimization of an in vitro …

Comparing The Incidence And Prevalence Of Oral Microbial Pathogens Selenomonas Noxia And Streptococcus Mitis Within The Unlv-Sdm Clinical Patient Population, Namgu Kim

UNLV Theses, Dissertations, Professional Papers, and Capstones

Introduction: Selenomonas noxia (SN) is a gram-negative, anaerobic bacteria, which contributes to development and progression of periodontal disease. Some evidence now suggests Streptococcus mitis (SM), a gram-positive, facultative bacterium contributing to the etiology of dental caries and periodontal disease, may also influence the prevalence of SN within subgingival complexes. Based upon the overall lack of prevalence data, the objective of this study was to evaluate presence of SN and SM using qPCR among saliva samples taken from pediatric, adult, and orthodontic dental school clinics.

Methods: This study involved a retrospective analysis of previously collected saliva samples from an existing biologic …

Genomic Analysis Of Paenibacillus Larvae Bacteriophages, Casey Stamereilers

UNLV Theses, Dissertations, Professional Papers, and Capstones

American Foulbrood is the most destructive bacterial infection of the honeybee (Apis mellifera) and is caused by the Gram-positive, spore forming bacterium Paenibacillus larvae. Current treatment methods rely on antibiotics, but antibiotics treatments are experiencing a reduction in efficacy due to the recent rise in antibiotic resistant strains of P. larvae. This has been a major catalyst for exploration of alternative treatment methods. Phage therapy is an alternative treatment method that uses viruses that exclusively infect bacteria, known as bacteriophages (phages), to combat bacterial infections. Several experimental studies have shown that phages P. larvae phages are effective at lysing P. …

Antibacterial Activity Of Pogostemon Cablin, Elizabeth Wong

Seton Hall University Dissertations and Theses (ETDs)

Patchouli (Pogostemon cablin Benth. of the mint family Lamiaceae) is a traditional Chinese medicine (TCM) plant valued for its aromatherapy, antifungal, and anti-inflammatory properties. This study examined the antibacterial effect of patchouli extract (PCE) on Grampositive Staphylococcus epidermidis (S. epidermidis) and Gram-negative Escherichia coli (E. coli) with microplate assays, CFU assays, fluorescent microscopy, molecular docking, and Omics data analysis. Microplate assay of E. coli and S. epidermidis showed that Pogostemon cablin extract (PCE) is bacteriostatic in E. coli with a MIC of 1.66 mg/ml PCE and in S. epidermidis with an MIC greater than 1.66 mg/ml PCE. Fluorescent microscopy and …

The Effect Of Egcg-P Containing Formulations On Bacillus Spp., Sabrina A. Lopez

Seton Hall University Dissertations and Theses (ETDs)

The Gram-positive Bacillus species is known for their spore-forming abilities. These spores are highly resistant to a multitude of factors such as heat, UV radiation, and chemical solvents, which can be attributed to the location of its DNA, and other components that make up the spore as a whole. Bacillus spp. can be detrimental to the food & beverage industry and the medical field due to their production of enterotoxins, which can manifest as bacterial infections. Antibiotic-resistant bacteria towards current treatments are of major concern, and thus the need for alternative therapeutic agents is urgent. The beneficial health properties of …

Sodium Pyruvate Ameliorates Influenza A Virus Infection In Vitro And In Vivo, Jessica M. Reel

Graduate Theses/Dissertations

Pyruvate is produced in duplicate at the end of glycolysis in addition to ATP and NADH. Pyruvate is the metabolite of choice in most cells, whether obtained exogenously or endogenously. Recently we found that the addition of pyruvate’s conjugate base, sodium pyruvate, to cell culture media dampened the immune response to influenza A virus (IAV) infection in cultured innate immune cells. Thus, I decided to investigate the mechanism and potential for treatment of IAV. In vitro using bone marrow derived macrophages that were infected with IAV we found that adding sodium pyruvate to the media decreased immune signaling pathways through …

Resistance Of The Freshwater Microbiome To A Combination Of Pesticides, Gabriel Hooper

Senior Honors Theses

Pesticides are used prevalently throughout the United States and can negatively affect non-target organisms. Rain run-off can move multiple pesticides into freshwater ecosystems and bring them in contact with non-target organisms that have variable tolerances to pollution. This study seeks to improve our understanding of how an acute exposure to a combination of pesticides may restructure microbial communities by examining the microbiome before and after a 48-hour exposure to 2000 ppb of herbicides (glyphosate, atrazine, and 2,4-D). Pesticide exposure did not significantly alter the alpha or beta diversity of the sample types, which demonstrates the ability of freshwater microbiomes to …

Unraveling Host-Gut Microbiota Dialogue And Its Impact On Response To Immune Checkpoint Blockade, Alexandria Cogdill

Dissertations and Theses (Open Access)

Cancer is a disease with only one degree of separation, affecting one in two men and one in three women in their lifetimes; accounting for 1 of every 6 deaths. While cancer mortality rates continue to improve, incidence rates are expected to rise and shift through 2050 due to epidemiological and demographic transitions worldwide. As such, it is imperative to continue to investigate and improve our understanding of both disease etiology and hallmarks of response to treatment. Currently, conventional therapies include, but are not limited to, surgery, chemotherapy, and radiotherapy. However, within the past decade, major advances have been made …

Implications Of The Evolutionary Past On The Activities Of Virb: A Key Transcriptional Regulator Of Virulence Genes In Shigella Flexneri, Jillian Nicole Socea

UNLV Theses, Dissertations, Professional Papers, and Capstones

Shigella species are bacterial agents that are the leading cause of diarrheal diseases, the second leading cause of child mortality worldwide. One key protein in Shigella is VirB, a transcriptional regulator of virulence genes that is essential for pathogenicity. VirB functions to antagonize H-NS, a histone-like nucleoid structuring protein that silences many genes found on the large virulence plasmid (pINV). The interplay between H-NS, the silencer, and VirB, the anti-silencer, is fundamental for Shigella virulence. Furthermore, this mechanism of gene regulation appears widespread in many bacteria including other enteric pathogens.

The goal of my dissertation was to explore the activities …

Pathogenicity Of Staphylococcus Agnetis Associated With Lame Broilers With Osteomyelitis, Sura Faris Salih Zaki

Graduate Theses and Dissertations

We developed High Resolution Melt Analysis (HERMA) as a rapid and reliable molecular diagnostic assay for the detection and identification of the main bacterial species recovered from the blood and lesions of bacterial chondronecrosis with osteomyelitis (BCO) from the lame broilers at the University of Arkansas poultry research farm. Also, the present study confirms that raising young birds on suspended wire flooring has been proved to successfully induce lameness attributable to BCO with birds being more susceptible to bacteraemia than those that were raised on litter flooring. The newly described pathogen, Staphylococcus agnetis, has been reported to be overrepresented in …

Effects On The Human Microbiome: Antibiotics And Other Chemicals, Katherine Moulton

Thinking Matters Symposium

With skin being the largest organ of the human body, there is a very large surface area for a microbiome to form and live. The human microbiome is composed of different types of bacteria, fungi, and archaea, in different locations of the body. This layer can be greatly affected by daily practices including, hygiene habits, exercise, and antibiotic uses. The major objective of this study is to identify species of the human microbiome from various body sites and test their resistance to major chemicals. To achieve this objective, the mouth, ear, axillary area, hand, belly button, and foot of several …

Bioremediation: Breaking Down The Regulations Of Genetically Modified Microorganisms, Lora Katharine Naismith

Texas A&M Law Review

Environmental bioremediation is the use of biological activity to reduce the concentration or toxicity of a pollutant. A rapidly increasing population leads to a consequential increase in industrial waste and pollution, and innovators are researching numerous techniques to degrade these pollutants and prevent their spread into the environment. These techniques are expensive and often result in secondary pollutants, which limits their widespread application. Bioremediation, however, presents a cost-friendly and more efficient way to degrade pollutants with little or no secondary pollutants. This Article explores how scientists can use genetically modified microorganisms (“GMMs”) to target specific hazardous wastes that are otherwise …

Identification Of A Chlorovirus Pbcv-1 Protein Involved In Degrading The Host Cell Wall During Virus Infection, Irina V. Agarkova, Leslie C. Lane, David D. Dunigan, Cristian F. Quispe, Garry A. Duncan, Elad Milrot, Abraham Minsky, Ahmed Esmael, Jayadri S. Ghosh, James L. Van Etten

Nebraska Center for Virology: Faculty Publications

Chloroviruses are unusual among viruses infecting eukaryotic organisms in that they must, like bacteriophages, penetrate a rigid cell wall to initiate infection. Chlorovirus PBCV-1 infects its host, Chlorella variabilis NC64A by specifically binding to and degrading the cell wall of the host at the point of contact by a virus-packaged enzyme(s). However, PBCV-1 does not use any of the five previously characterized virus-encoded polysaccharide degrading enzymes to digest the Chlorella host cell wall during virus entry because none of the enzymes are packaged in the virion. A search for another PBCV-1-encoded and virion-associated protein identified protein A561L. The fourth domain …

Increasing The Frequency Of Periodic Spatial Disturbance Decreases Surface Attachment Protein Expression In Staphylococcus Aureus, Ivana M. Barraza

All HCAS Student Capstones, Theses, and Dissertations

Staphylococcus aureus is an opportunistic pathogen that can cause a variety of acute and chronic illnesses. The severity of these illnesses such as sepsis, necrotizing pneumonia, and toxic shock syndrome is measured through the virulence that S. aureus inflicts on its host. Methicillin-resistant S. aureus (MRSA) is commonly associated with secondary infections and is challenging to treat given the limited selection of antibiotics that are effective against it. Accordingly, novel approaches to reduce S. aureus pathogenicity are required. S. aureus regulates pathogenesis through a cell-to-cell communication system referred to as quorum sensing. Effective communication determines the production of two broad …

The Anti-Sigma Factor Muca Is Required For Viability In Pseudomonas Aeruginosa, Melissa C. Schofield, Daniela Q. Rodriguez, Amanda A. Kidman, Erin K. Cassin, Lia A. Michaels, Elizabeth A. Campbell, Peter A. Jorth, Boo Shan Tseng

Teaching and Learning Faculty Research

During decades-long infections in the cystic fibrosis (CF) airway, Pseudomonas aeruginosa undergoes selection. One bacterial genetic adaptation often observed in CF isolates is mucA mutations. MucA inhibits the sigma factor AlgU. Mutations in mucA lead to AlgU misregulation, resulting in a mucoid phenotype that is associated with poor CF disease outcomes. Due to its ability to be mutated, mucA is assumed to be dispensable for bacterial viability. Here we show that, paradoxically, a portion of mucA is essential in P. aeruginosa. We demonstrate that mucA is no longer required in a strain lacking algU, that mucA alleles encoding for proteins …

Process Interventions For Improving The Microbiological Safety Of Low Moisture Food Ingredients, Tushar Verma

Department of Food Science and Technology: Dissertations, Theses, and Student Research

The recurrence of Salmonella in low moisture foods and the implementation of the FSMA rule requires a need to validate legacy and novel processing technologies. In this dissertation, a legacy thermal (extrusion), a novel thermal (radiofrequency (RF) heating), and a non-thermal (chlorine dioxide) technology, were evaluated as intervention technologies for Salmonella in low moisture foods. The twin-screw extruder was performed at different levels of screw speeds, temperatures, moisture contents, and fat contents to understand the impact of processing conditions on Salmonella inactivation in oat flour. At temperature >65°C, the Salmonella population was below the detection limit. At 55°C, Salmonella reduction …

Respiratory Pathogens In Patients With Acute Exacerbation Of Non-Cystic Fibrosis Bronchiectasis From A Developing Country, Shayan Shahid, Kausar Jabeen, Nousheen Iqbal, Joveria Farooqi, Muhammad Irfan

Medical College Documents

Bronchiectasis unrelated to cystic fibrosis (non-CF bronchiectasis) has become a major respiratory disease in developing nations. The dilated mucus filled airways promote bacterial overgrowth followed by chronic infection, bronchial inflammation, lung injury and re-infection Accurate pathogen identification and antimicrobial susceptibility allowing appropriate treatment, in turn, may break this vicious cycle. To study the spectrum and antimicrobial spectrum of pathogen yielded from respiratory specimens in adult patients with acute exacerbation of non-cystic fibrosis (CF) bronchiectasis. This cross-sectional study was performed at the pulmonology clinics of the Aga Khan University, Karachi, Pakistan from 2016-2019. Respiratory specimens were collected from adult patients with …

A Novel Jumbo Phage Phima05 Inhibits Harmful Microcystis Sp., Ampapan Naknaen, Oramas Suttinun, Komwit Surachat, Eakalak Khan, Rattanaruji Pomwised

Civil and Environmental Engineering and Construction Faculty Research

Microcystis poses a concern because of its potential contribution to eutrophication and production of microcystins (MCs). Phage treatment has been proposed as a novel biocontrol method for Microcystis. Here, we isolated a lytic cyanophage named PhiMa05 with high efficiency against MCs-producing Microcystis strains. Its burst size was large, with approximately 127 phage particles/infected cell, a short latent period (1 day), and high stability to broad salinity, pH and temperature ranges. The PhiMa05 structure was composed of an icosahedral capsid (100 nm) and tail (120 nm), suggesting that the PhiMa05 belongs to the Myoviridae family. PhiMa05 inhibited both planktonic and aggregated …

Microbially-Mediated Carbonate Dissolution And Precipitation; Towards A Protocol For Ex-Situ, Cave-Analogue Cultivation Experiments, Vanessa E. Johnston, Andrea Martín-Pérez, Sara Skok, Janez Mulec

International Journal of Speleology

Subterranean calcite dissolution and precipitation are often considered as strictly geochemical processes. The active involvement of microbes in these processes is commonly underestimated in the literature due to general oligotrophic conditions in caves, except in particular cave conditions, such as sulfidic caves and moonmilk deposits, where the presence of microbes likely plays a key role in mineral deposition. Here, we study the possible involvement of microbes from Postojna Cave, Slovenia, in carbonate dissolution (litholysis) and precipitation (lithogenesis). Microbes were sampled from small pools below hydrologically diverse drip sites and incubated on polished limestone tablets at 10 and 20°C for 2 …

Project Alien, Rebecca Mccallin, Madelyn Hoying, Alex Evans, Matthew Nestler, Karli Rae Sutton, Garett Craig, Lucia Secaia Del Cid, Alexander Guy, Rachel Fernandez, Amanda Trusiak, Paige Aley, Ingabire Gakwerere, Nina Dorfner, Maria Mosbacher, Mary Flavin, Selvin Hernandez, Audrey Steen, Benjamin Kazimer

Undergraduate Research and Scholarship Symposium

Project ALIEN is a comprehensive plan to send humans to Mars to look for life on the Martian surface while exploring the viability and adaptability of terrestrial microbes in Martian atmospheric conditions. ALIEN will use a ballistic capture trajectory to get to Mars and stay in aerostationary orbit for a 30-day surface mission, during which two surface crewmembers will perform a variety of experiments to achieve the mission’s goals of Martian microbial discovery within brines of the Gale Crater and terrestrial microbe adaptability and viability to Martian conditions. Experimentation is based on the presumption that Martian microbes are metabolically similar …

Root Exudates Alter The Expression Of Diverse Metabolic, Transport, Regulatory, And Stress Response Genes In Rhizosphere Pseudomonas, Olga V. Mavrodi, Janiece R. Mcwilliams, Jacob O. Peter, Anna Berim, Karl A. Hassan, Liam D.H. Elbourne, Melissa K. Letourneau, David R. Gang, Ian T. Paulsen, David M. Weller, Linda S. Thomashow, Alex S. Flynt, Dmitri V. Mavrodi

Faculty Publications

Plants live in association with microorganisms that positively influence plant development, vigor, and fitness in response to pathogens and abiotic stressors. The bulk of the plant microbiome is concentrated belowground at the plant root-soil interface. Plant roots secrete carbon-rich rhizodeposits containing primary and secondary low molecular weight metabolites, lysates, and mucilages. These exudates provide nutrients for soil microorganisms and modulate their affinity to host plants, but molecular details of this process are largely unresolved. We addressed this gap by focusing on the molecular dialog between eight well-characterized beneficial strains of the Pseudomonas fluorescens group and Brachypodium distachyon, a model …

The Msaabcr Operon Regulates Persister Formation By Modulating Energy Metabolism In Staphylococcus Aureus, Shanti Pandey, Gyan S. Sahukhal, Mohamed O. Elasri

Faculty Publications

Staphylococcus aureus is a major human pathogen that causes chronic, systemic infections, and the recalcitrance of these infections is mainly due to the presence of persister cells, which are a bacterial subpopulation that exhibits extreme, yet transient, antibiotic tolerance accompanied by a transient halt in growth. However, upon cessation of antibiotic treatment, a resumption in growth of persister cells causes recurrence of infections and treatment failure. Previously, we reported the involvement of msaABCR in several important staphylococcal phenotypes, including the formation of persister cells. Additionally, observations of the regulation of several metabolic genes by the msaABCR operon in transcriptomics and …

Microplastics: Nacogdoches County’S Hidden Threat, Jordan Stanford, Sydney Matlock, Courtney Sims, Samantha Montes

Undergraduate Research Conference

Microplastics and their threat to marine environments are well known, but studies in freshwater environments are few and far between. Microplastics can be created by the breaking down of plastics or in the process of making plastics. They affect biological lifeforms in a multitude of ways, water temperature, permeability of the sediment. Pollution in Texas waterways have motivated groups like the Environmental Protection Agency, Trash Free Texas, and Environment Texas to get involved. The objectives of this study are two analyze Bonita and La Nana Bayou for microplastic presence and to educate and create awareness for Nacogdoches County on microplastics. …

Human Ace2‑Functionalized Gold “Virus‑Trap” Nanostructures For Accurate Capture Of Sars‑Cov‑2 And Single‑Virus Sers Detection, Yong Yang, Yusi Peng, Chenglong Lin, Li Long, Jingying Hu, Jun He, Hui Zeng, Zhengren Huang, Zhi-Yuan Li, Masaki Tanemura, Jianlin Shi, John R. Lombardi, Xiaoying Luo

Publications and Research

The current COVID-19 pandemic urges the extremely sensitive and prompt detection of SARS-CoV-2 virus. Here, we present a Human Angiotensin-converting-enzyme 2 (ACE2)-functionalized gold “virus traps” nanostructure as an extremely sensitive SERS biosensor, to selectively capture and rapidly detect S-protein expressed coronavirus, such as the current SARS-CoV-2 in the contaminated water, down to the single-virus level. Such a SERS sensor features extraordinary 106- fold virus enrichment originating from high-affinity of ACE2 with S protein as well as “virus-traps” composed of oblique gold nanoneedles, and 109- fold enhancement of Raman signals originating from multicomponent SERS effects. Furthermore, the identification standard of virus …

B25: Generation And Characterization Of Sars-Cov-2 Spike Protein-Pseudotyped Lentivirus Particles For Use In Neutralizing Antibody Titer Testing Of Human Serum, Luis Sanchez

Annual Research Symposium

No abstract provided.

B16: Chikungunya Virus Time Course Infection Of Human Macrophages, Madison Gray, Israel Guerrero-Arguero, Antonio Solis Leal, Richard Robison, Brad Burges, Brett Pickett

Annual Research Symposium

Chikungunya virus (CHIKV) is an Alphavirus spread by Aedes spp. mosquitoes and is responsible for infecting 1.1 million people per year worldwide, including a large epidemic in the western hemisphere in 2014-2015. During the body’s immune response to CHIKV, human macrophages become infected after phagocytosis of CHIKV and undergo induced apoptosis, catalyzing the virus spread in the body. It is presently unclear what macrophage genes, functions, and intracellular signaling pathways are impacted during the early, intermediate, and late stages of CHIKV infection. Therefore we quantified the transcriptional response of human macrophage cells infected with CHIKV at two different timepoints.