Microbiology Commons^™

Characterization Of Sars-Cov-2 Replication And Transcription Complexes Via Structural And Evolutionary Approaches, Amelie Ghirardo, Ben Shabatian, Avishai Aghelian, Kyle Tau, Eleonora Gianti

Undergraduate Research

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused around 700M cases and over 7M COVID-19-related deaths recorded worldwide (World Health Organization, March 2025). Aiming to effectively combat this and other disease-causing Coronaviruses (CoV), unprecedented research efforts led to the development of new vaccines and antiviral therapies. Due to emergence of variants of concern (VOCs) with increased transmissibility, immune evasion from vaccination, and potential to resist the available treatments, SARS-CoV-2 continues to represent a major threat to global health. Hence, there is a pressing need to discover new antivirals with broad-spectrum efficacy against multiple SARS-CoV-2 variants and related CoVs. This project …

A Complete Transfer Learning-Based Pipeline For Discriminating Between Select Pathogenic Yeasts From Microscopy Photographs, Ryan A. Parker, Danielle S. Hannagan, Jan H. Strydom, Christopher J. Boon, Jessica Fussell, Chelbie A. Mitchell, Katie L. Moerschel, Aura G. Valter-Franco, Christopher Cornelison

Faculty Articles

Pathogenic yeasts are an increasing concern in healthcare, with species like Candida auris often displaying drug resistance and causing high mortality in immunocompromised patients. The need for rapid and accessible diagnostic methods for accurate yeast identification is critical, especially in resource-limited settings. This study presents a convolutional neural network (CNN)-based approach for classifying pathogenic yeast species from microscopy images. Using transfer learning, we trained the model to identify six yeast species from simple micrographs, achieving high classification accuracy (93.91% at the patch level, 99.09% at the whole image level) and low misclassification rates across species, with the best performing model. …

Impacts Of Land Development On Soil Microdiversity And Antibiotic Production, Dennis Guillen Castro, Robert Garcia, Jonathan Castro, Davida Smyth

Masters Theses (Archived)

The impact of land development on soil microbial diversity and antibiotic production is critical due to industrial expansion and the scarcity of effective antibiotics. Low Impact Development (LID) aims to preserve ecosystems, but its effectiveness in maintaining microbial diversity is uncertain. This study compares soil samples from nine sites: undisturbed (UD), residential (RD), and Madla Greenway (GW) within the VIDA development area and Texas A&M University-San Antonio campus. Isolated microbes were screened for antibiotic production and genetically characterized. Preliminary findings indicate that UD sites harbor greater microbial abundance, and a higher proportion of antibiotic-producing microbes compared to GW and RD …

Assessing The Efficiency Of Methotrexate (Mtx) As An Antiviral Drug Against Gammaherpes Virus Replication, Yennifer A. Gaspar Garcia

Honors Projects

It is estimated that ~15% of all cancers are caused by oncogenic virus infections. Two of the top seven cancer-causing human viruses are members of the gammaherpesvirus family: Epstein Barr Virus (EBV) and Kaposi’s Sarcoma Herpesvirus (KSHV). Our lab uses Murine Herpesvirus 68 (MHV-68), a mouse gammaherpesvirus with shares significant genetic homology to KSHV and EBV, as a model system to understand how gammaherpesviruses alter the metabolism of their host during lytic infection to promote their replication. We recently metabolically profiled MHV-68 infected host cells at various time points during the lytic infectious cycle. Our data showed nucleotide metabolism is …

Viral Detection In Anterior Nasal Swabs Versus Nasopharyngeal Swabs In Children, Nicole Neeley, Abby Kietzman, Rangaraj Selvarangan, Dithi Banerjee, Jennifer Goldman, Jennifer Schuster

Research Days

Background: Respiratory viruses are a significant cause of pediatric illness and healthcare utilization. Diagnostic testing for respiratory viruses is generally performed using nasopharyngeal (NP) specimens obtained by trained staff, limiting testing to medical settings. Evaluating additional sampling methods in children that are easier to collect and can be performed outside of medical settings, such as anterior nasal swab (NS) specimens may expand access to diagnostic testing and aid public health surveillance.

Methods: Eligible children hospitalized at Children’s Mercy Hospital who had a standard of care NP specimen collected for respiratory viral testing were enrolled. Research NS specimens were obtained through …

The Roles Of Oprf In Pseudomonas Aeruginosa Biofilms, Erin K. Cassin

UNLV Theses, Dissertations, Professional Papers, and Capstones

Many bacteria form multicellular communities known as biofilms. Biofilms contain bacterial cells and a protective extracellular biofilm matrix. This matrix contains exopolysaccharides, extracellular DNA (eDNA), membrane vesicles, and proteins. The matrix proteins are far less characterized than other extracellular biofilm components. In biofilms formed by the model organism Pseudomonas aeruginosa, the protein OprF is abundant in the cellular outer membrane and the extracellular matrix. In my dissertation research, I have presented data supporting the hypothesis that the OprF protein significantly affects P. aeruginosa biofilms. By examining various strain backgrounds and the nutrient-dependent effects of glucose and sodium chloride, I demonstrate …

Oral Prevalence Of Selenomonas Noxia Differs Among Orthodontic Patients Compared To Non-Orthodontic Controls: A Retrospective Biorepository Analysis, Kyle Hodges

UNLV Theses, Dissertations, Professional Papers, and Capstones

Introduction: The introduction of fixed orthodontic brackets in orthodontic therapy has the potential to significantly alter the oral microbial flora. Most orthodontic research has focused on cariogenic pathogens, while some evidence has demonstrated an increase in many known periodontal pathogens. However, little is known about the prevalence of the gram-negative periodontal pathogen, Selenomonas noxia (SN) among these patients.Methods: Using an existing saliva biorepository, n=208 samples from adult and pediatric orthodontic and non-orthodontic patients were identified and screened for the presence of SN using qPCR and validated primers. Results: In the pediatric study sample (n=89) 36% tested positive for the presence …

Investigating The Influence Of Environmental Stressors To Exopolysaccharide Production In Soil Cyanobacteria: Genomic And Physiological Perspectives, Benjy Sedano-Herrera

UNLV Theses, Dissertations, Professional Papers, and Capstones

Cyanobacteria are photosynthetic microbes with essential roles in Earth’s ecosystems. The secretion of long–chain polysaccharides, known as exopolysaccharides (EPS), is a key trait facilitating cyanobacterial adaptation to diverse ecosystems. Genomics studies have shown that aquatic cyanobacteria harbor multiple gene copies encoding EPS export proteins, likely conferring a selective advantage in lakes or oceans. In addition, physiological experiments showed that nutrient limitation in aquatic habitats influences EPS production, affecting cyanobacterial fitness. However, whether terrestrial cyanobacteria also harbor multiple EPS-related genes and how nutrient limitation impacts their EPS production is not well understood.In the first chapter of my thesis, we investigated the …

Microbial Biodiversity Of The James River Rock Pool Ecosystem., Jordan C. Heydt

Masters Theses, 2020-current

Rock pools are ephemeral aquatic environments that offer a unique opportunity to study complex communities and their responses to environmental changes. The urban James River rock pool system consists of over 700 individual rock pools varying in size and depth. This unique urban freshwater ecosystem has been studied for its invertebrate, plant, and zooplankton populations but not for its microbial community composition. To fill that gap, the microbial community of this system was characterized using 16S rRNA gene sequencing, and the influence of environmental variables on the community composition was analyzed. Our findings show variation in microbial community composition across …

Microbial Community Contribution To Oxidative Stress Defense In High-Biomass Forming Cyanobacteria Harmful Algal Blooms (Chabs), Chelsea Donovan

Masters Theses, 2020-current

Cyanobacterial harmful algal blooms (cHABs) occur globally, excluding Antarctica, and often involve toxin-producing species such as Microcystis aeruginosa. These blooms threaten both ecosystems and public health, making it essential to understand their underlying drivers. Cyanobacteria generate reactive oxygen species (ROS) during photosynthesis, which can cause cellular damage unless neutralized. Some, like M. aeruginosa, lack the genetic capacity to detoxify ROS and rely on associated bacterioplankton for protection. To investigate the role of phycosphere bacteria in mitigating ROS stress, we conducted an incubation experiment using samples collected throughout the 2023 Lake Erie bloom season. Samples were treated with 10 …

Theta Oscillons In Behaving Rats, M S Zobaer, Nastaran Lotfi, Carli M Domenico, Clarissa Hoffman, Luca Perotti, Daoyun Ji, Yuri Dabaghian

Faculty, Staff and Students Publications

Recently discovered constituents of the brain waves—the oscillons—provide a high-resolution representation of the extracellular field dynamics. Here, we study the most robust, highest-amplitude oscillons recorded in actively behaving male rats, which underlie the traditional θ-waves. The resemblances between θ-oscillons and the conventional θ-waves are manifested primarily at the ballpark level—mean frequencies, mean amplitudes, and bandwidths. In addition, both hippocampal and cortical oscillons exhibit a number of intricate, behavior-attuned, transient properties that suggest a new vantage point for understanding the θ-rhythms’ structure, origins and functions. In particular, we demonstrate that oscillons are frequency-modulated waves, with speed-controlled …

In The Quest For New Horizons: Evaluating Novel Therapeutic Approaches For Tuberculosis Treatment, Selassie Mawuko, Aminata Traore, Bibi-Sakeena Khemraj, Anna Steto, Richa Gupta

Publications and Research

Tuberculosis (TB) in humans, caused by Mycobacterium tuberculosis, is a significant global health concern, resulting in high disease burden and mortality each year which together make it the world’s topmost infectious killer. The emergence of multidrug-resistant tuberculosis (MDR-TB) in recent decades has further exacerbated the present situation and warrants an urgent need to develop and investigate innovative treatment regimes. This study aims to assess the therapeutic potential of newly identified drug candidates, namely Bedaquiline, Delamanid, and Linezolid, in treating MDR-TB. We adopted a consolidated and integrated approach encompassing a thorough literature review, empirical experimental studies, multiple sequence alignments, and …

Relationship Between Prodigiosin Production And Batrachochytrium Dendrobatidis Metabolite Concentration, Nautica Ek Hagg

Honors Thesis

Batrachochytrium dendrobatidis (Bd) is a pathogenic fungus that has been causing extirpations of amphibian species across the globe. The microbiome on the skin of amphibians is known to be a key factor in infection dynamics. It has been established that one species of cutaneous bacteria, Serratia marcescens, and a secondary metabolite with antifungal properties it produces, prodigiosin, has shown a promising ability to decrease the growth of Bd. However, when Serratia marcescens is grown in the same media with added metabolites produced by Bd, there is an observed decrease in the production of the bacteria’s protective metabolite, prodigiosin. This experiment …

Fine-Scale Spatial Patterns In Microbial Activity And Community Composition In Shoreline Marine Sediments, Elizabeth Basha

Honors Theses

Coastal environments of the Gulf of Mexico host diverse and dynamic microbial communities essential for biogeochemical cycling, yet the fine-scale environmental drivers of microbial function and community structure in these systems remain underexplored. This study investigated the relationships between sand moisture content, microbial extracellular enzyme activity, and bacterial community composition along beach transects on Biloxi East Beach, Mississippi. Sand was sampled at five points along four transects spanning a gradient from submerged intertidal zones to dry upper beach sands. Extracellular enzyme activities linked to carbon, nitrogen, and phosphorus cycling (β-glucosidase, N-acetylglucosaminidase, phosphatase, phenol oxidase, and peroxidase) were measured, and bacterial …

Intrinsic And Extrinsic Drivers Of Bioaerosol Decay: Investigating Pathogen Stability Of Bacteriophage Ms2, Sin Nombre Virus, And Sars-Cov-2 In Simulated Environments, Elizabeth A. Klug

Theses & Dissertations

The threat posed by a virus as a bioaerosol depends largely on its stability under various environmental conditions (relative humidity (RH), sunlight, ozone, etc.). This stability is typically studied through aerosol decay—how the virus' viability changes over time when exposed environmental conditions. The Goldberg rotating drum, a widely used tool for studying bioaerosols, has been the basis of such research (Goldberg et al., 1958). However, it has significant limitations, including an inability to measure initial pathogen infectivity loss and the use of small sample volumes. Additionally, it does not answer the question of what intrinsic factors (lipids, proteins, nucleic acids) …

Coxiella Burnetii Manipulation Of Membrane Contact Sites In The Intracellular Niche, Margaret F. Sladek

Theses & Dissertations

Coxiella burnetii is a highly infectious and environmentally persistent bacterium that causes the disease Q Fever. Its intracellular home, the Coxiella-Containing Vacuole (CVV), is formed from fusion of host-derived vesicles and is rich in sterols - yet cholesterol accumulation in the CCV is bacteriolytic. Our lab’s goal is to understand how Coxiella manages intracellular cholesterol levels and survives within the host. One way Coxiella may modulate CCV cholesterol is through membrane contact sites (MCS), areas where molecular complexes bridge two organelles and exchange lipids. This thesis explores how Coxiella uses both a mammalian lipid transfer protein and bacterially-encoded effector …

Evaluation Of Phenotypic Antimicrobial Resistance From Bacterial Pathogen Isolates In Bison, Aleena M. Kallan

Honors Capstones

Bison, the American buffalo, are increasingly utilized for food consumption due to their high protein content. Shiga toxin-producing Escherichia coli (STEC) is an important food-borne pathogen that leads to severe clinical infections and becomes antimicrobial-resistant (AMR). Specifically, fluoroquinolone antibiotics can complicate human treatment when infected with resistant STEC. This study aims to determine the presence of STEC in bison reservoirs and their antimicrobial resistance. Fecal samples (n=320) from bison herds were collected, followed by specific culture-based isolation for STEC. Polymerase chain reaction (PCR) was employed for pathogen confirmation, with 25.6% prevalence. PCR targeting gene, gyrA (resistant to fluoroquinolone), was tested …

Microbial Community And Water Quality Assessment Of Crassostrea Virginica Habitats In Southeast Florida, Stacy Brown

All HCAS Student Capstones, Theses, and Dissertations

Eastern oysters (Crassostrea virginica) are essential habitat-forming species that contribute significantly to coastal water quality due to their filter-feeding behavior. Unlike other coastal regions in the Gulf of Mexico and Northeastern United States, oysters are not commercially managed in Southeast Florida and as a result sparse data exists on locations of the Eastern oyster habitat. Similarly, the benefits of oyster reefs to water quality are also not fully documented in Southeast Florida. Although beneficial and often referred to as keystone habitat building species, populations of C. virginica are not currently listed as protected species so little work has …

Enhancing Food Safety: Detecting Pathogens In Bison, Vrinda Brahmbhatt

Honors Capstones

Bison herds are being reintroduced across Illinois for prairie conservation efforts and as an important food source, with bison meat gaining popularity as a healthier alternative to beef. However, bison can act as reservoirs of pathogens such as Shiga toxin-producing Escherichia coli (STEC) and antimicrobial resistance (AMR) genes, posing food safety and public health risks. Conservational and commercial herds are managed differently, which may influence the prevalence of STEC and associated AMR genes. To address concerns about potential AMR transmission from bison to humans via fecal-oral routes, we examined the prevalence of AMR in STEC isolates from both herd types. …

Competence Protein Comea And Oxidative Stress In Bacillus Subtilis Stationary Phase Mutagenesis, Angeline Roldan, Sam Schauf

Undergraduate Research Symposium Posters

Stationary Phase Mutagenesis is a process where a bacterium can accumulate mutations in the absence of cell division. This may occur via competent DNA uptake and oxidant DNA damage and repair. ComEA is a transmembrane protein in B. subtilis that is required for the transport of exogenous DNA into the cell. (Figure 1)