Microbiology Commons^™

Exploring Competitive Dynamics Between Pseudomonas Baetica And Salmonella In A Polymicrobial System, Braxton E.M. Stout

Electronic Theses and Dissertations

The global rise in antimicrobial resistance has catalyzed a greater focus on polymicrobial research aimed at characterizing microbial interactions and uncovering new therapeutic strategies. Though it has long been of interest, environmental soil-derived bacteria remain largely under-represented in research and thus uncharacterized in this field. This project aimed to identify soil microbes that display inhibitory mechanisms to potential nosocomial pathogens. Soil sample S1S3-2 displayed inhibitory phenotypes toward numerous bacteria and was identified as Pseudomonas baetica. In both planktonic and biofilm growth, P. baetica was able to inhibit Salmonella arizonae through a contact-dependent and temperature-dependent manner. Screening of a transposon insertion …

The Role Of Seed Mix Characteristics And Soil Amendments During Post-Agricultural Prairie Restoration, Valerie N. Thurston, Michaela J. Woods, Madelaine Gregory, Mary C. Lloyd, Ryan W. Mcewan

Biology Faculty Publications

Introduction: Prairie restoration on degraded lands may be influenced by seed mix characteristics, including species richness and legume establishment. Soil amendments may facilitate restoration; however, the practical usefulness of techniques such as applications of whole soil and leaf mulch remains relatively unclear.

Objectives: We assessed whether increasing species richness and legume content in seed mixes enhances prairie restoration success and examined how soil amendments interact with seed mix composition to influence cover, species richness, diversity, and legume establishment.

Methods: We conducted a field experiment on a 12-ha post-agricultural site in Ohio, U.S.A. Twenty 50 × 50 m plots received one …

Mutational Analysis Of Domain Functions In The Yeast Decapping Enzyme Dcp2, Jellisa Ewan, Ambro Van Hoof

Dissertations and Theses (Open Access)

In yeast, the major mRNA decay pathway involves deadenylation of the 3’ poly-A tail, followed by decapping of the 5’ m7Gppp cap and subsequent 5’ to 3’ degradation or 3’ to 5’ degradation. This is carried out by Pan2/Pan3 and Ccr4/Not deadenylases, the decapping enzyme Dcp2, and Xrn1 and  RNA exosome exoribonucleases, respectively. The eukaryotic mRNA decapping enzyme complex, Dcp1/Dcp2, is essential in yeast, and deletion of either gene is lethal. However, the deadenylases that act upstream and the 5’ exoribonuclease that act downstream of the decapping step are not, even though they are all highly conserved with no known …

Bridging The Gap In Science Research: Preparing Students For College- Level Research In The Sciences, Victoria Helwig, Yaoguang Li

UConn Library Presentations

Many first-year students enter college unprepared to fully engage with scientific literature and academic library resources. Drawing on experiences from academic librarians working with STEM students, this session explores common gaps in science research skills, including navigating databases, identifying scholarly sources, and understanding the structure of scientific literature. Participants will be introduced to practical strategies and classroom-ready activities to better prepare students for college-level research. Discussion questions: What science research skills do students struggle with most when entering college? How can high school instruction better support these skills? Where can librarians and educators collaborate to support student success?

Homocysteine Thiolactone From Translation Proofreading Is An Endogenous Ligand For Cell-Cell Signaling By The Receptor Sdia, Lorenzo Eugenio Leiva, Roberto A. Zúñiga, Gregory J. Phillips, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Several widespread mechanisms enable cellular communication and coordinate the behavior of bacterial populations. The modules responsible for cellular communication are often found in matching pairs: an enzyme that synthesizes a signal molecule and a specific receptor that decodes it. A notable exception is Escherichia coli SdiA, a homolog of known N-acyl-homoserine lactone (AHL) receptors, for which no corresponding AHL synthase exists. SdiA is an orphan receptor that enables cross-talk by sensing AHLs from other bacterial species. In this work, we investigated whether homocysteine thiolactone (HTL), an AHL-like molecule arising from a proofreading reaction of methionyl tRNA synthetase (MetRS) to correct …

Birds Of A Tether Flock Together: Examining Centromere Tethering And Chromosome Segregation In Caulobacter Crescentus, Jake Dwyer, Simon Kruczak, Rodrigo Arana-Garrido, Paola Mera

MICRO-CCS student projects

Introduction:

Chromosome segregation is essential for all domains of life. Caulobacter crescentus is a key model for studying this process. It divides asymmetrically into two morphologically distinct cells. Proteins can be seen directly with fluorescent tags.

Research done on Caulobacter can apply to many different bacteria. The ParABS system is integral to chromosome segregation in Caulobacter.

ParS – DNA sequence on the chromosome

ParB – CTP-binding protein that specifically recognizes parS

ParA – ATP-binding protein that non-specifically binds DNA and provides the force for segregation.

PopZ – Polar tethering protein via interactions with ParB.

TipN - Polar protein that …

Mobile Genetic Elements Shape Microbial Diversity And Functions In Thawing Permafrost Soils, Jiarong Guo, Samuel T. N. Aroney, Guillermo Domínguez-Huerta, Derek Smith, Dean Vik, Carlos Owusu-Ansah, Akbar Adjie Pratama, Sergei Solonenko, Funing Tian, Cristina Howard-Varona, Zhi-Ping Zhong, Aminata Fofana, Garrett J. Smith, Suzanne B. Hodgkins, Dylan Cronin, Isogenie Field Teams 2010–2017, 2019, Emerge Coordinators, Ben J. Woodcroft, Gene W. Tyson, Virginia I. Rich, Matthew B. Sullivan, Simon Roux, Sarah C. Bagby, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Ecosystems are shaped by communities of microorganisms whose niches and impacts depend on functional profiles influenced by gene gains and losses. Culture-based experiments demonstrate that mobile genetic elements (MGEs) can mediate gene flux, but quantitative understanding of these dynamics in natural systems remains limited. Here we develop and apply a systematic, meta-omic framework to investigate MGEs in a complex natural system using an 8-year soil time series collected at Stordalen Mire, in Sweden’s thawing permafrost margin. In this climate-critical peatland, we identify ~2.1 million MGE recombinases across 89 microbial phyla and assess ecological distributions, affected functions, past mobility and current …

Marine Heatwaves And Fish Reproduction: Endocrine Responses In The Eurythermal Sheepshead Minnow (Cyprinodon Variegatus), Isabel Villafuerte

Master's Theses

Marine heatwaves associated with climate change are increasing in frequency and severity, posing significant threats to fish populations in shallow habitats such as estuaries and salt marshes. Because temperature is a primary regulator of fish reproduction, understanding how heatwaves affect reproductive physiology is critical for anticipating the biological consequences of ongoing climate change for coastal fishes. Here we examined how simulated heatwave conditions affect the reproductive hypothalamic-pituitary-gonadal (HPG) endocrine axis in the estuarine sheepshead minnow (Cyprinodon variegatus), a eurythermal fish well suited to studying thermal stress responses in estuarine environments. Adult sheepshead minnows acclimated to a daily oscillating …

The Influence Of Prosthetic Obturators On Quality Of Life In Individuals With Maxillectomy Defects, Minseok Kim

Oral Health

Abstract

Introduction: In recent years, there has been a growing focus on understanding the impact of oral cancer on patients' quality of life. Prosthetic rehabilitation techniques, such as maxillary obturators, often in conjunction with reconstructive surgery, have emerged as interventions to address the challenges posed by post-maxillectomy abnormalities.

Objective: This study aims to systematically review and evaluate the effectiveness of maxillofacial prosthetic rehabilitation using obturators in enhancing the quality of life of patients following maxillectomy.

Methodology: Systematic review of identified literature spanning the timeframe from 2000 to 2020 was used. The comprehensive search encompassed widely recognized databases including PubMed, …

An Investigation Of Entamoeba Histolytica Chitin Synthases And Other Encystation Factors In Early Encystation, John N. Talledo

All Theses

Entamoeba histolytica is a food-and-water-borne human protozoan pathogen that relies on a two-stage life cycle for successful proliferation outside of the host. E. histolytica exists in its dormant cyst form while outside of its host and converts to the motile trophozoite (amoeba) form in the small intestine. The trophozoites colonize the large intestine to cause symptomatic disease in ~10% of infections, resulting in ~100 million cases of amoebic dysentery each year. Trophozoites can convert back to the cyst form, which is shed in feces to continue the infection cycle.

Currently, there is a lack of understanding of the exact molecular …

Genetic Screen For Regulators Of Pol4, A Dna Repair Polymerase In Saccharomyces Cerevisiae, Pasang Dolma Sherpa

Theses and Dissertations

In Saccharomyces cerevisiae, DNA polymerase 4 (POL4) is the beta repair polymerase, the product of the POL4 gene, and is involved in base excision repair (BER) and microhomology-mediated end joining (MMEJ). Despite its involvement in these repair pathways and its conservation across eukaryotes, deletion of POL4 shows no detectable phenotype under standard laboratory conditions. I hypothesized that unknown genes act as backup systems, providing redundant activities that allow pol4Δ cells to survive. To test this, a genetic screen for mutants showing synthetic lethality with pol4Δ was implemented. I constructed a strain lacking the POL4 gene and carrying …

Validation Of A Real-Time Pcr Laboratory Developed Test For The Detection Of Pneumocystis Jirovecii In Bronchoalveolar Lavage Samples, Caitlyn Moon

Honors Scholar Theses

Pneumocystis jirovecii is an opportunistic, host-obligate fungal pathogen responsible for causing P. jirovecii pneumonia (PJP) in humans. PJP is treated with trimethoprim-sulfamethoxazole (TMP-SMX), a strong broad-spectrum antibiotic that carries risk of renal and hepatotoxicity. Therefore, rapid diagnosis or exclusion of PJP is crucial to ensure PJP-positive patients receive effective treatment and PJP-negative patients avoid unnecessary antibiotics. Unlike most microorganisms, P. jirovecii cannot be cultured, presenting complications for the typical methods of diagnosing fungal pathogens. Historically, the gold standard for diagnosis was direct microscopic examination with stains such as methenamine silver and calcofluor white, but this diagnostic technique requires highly skilled …

The Role Of The Virb Ligand Ctp In The Molecular Mechanism Of Transcriptional Anti-Silencing In Shigella Flexneri, Taylor M. Gerson, Monika M A Karney, Helen Wing

Life Sciences Faculty Research

In bacteria, nucleoid-structuring proteins bind and constrain DNA, often leading to transcriptional silencing. In Shigella spp., the histone-like nucleoid-structuring protein H-NS silences many genes on the large virulence plasmid. Upon a shift to human body temperature, VirB, a DNA-binding protein and key transcriptional regulator of the Shigella virulence cascade, is produced. VirB counteracts H-NS-mediated transcriptional silencing and belongs to a fast-evolving clade of the ParB superfamily. Like other ParB proteins, VirB binds the ligand CTP. While CTP is essential for the anti-silencing activity of VirB, the role of CTP in the mechanism of VirB-dependent anti-silencing has yet to be …

Metagenomic Profiling Of Gut Microbiome Signatures Across Liver Disease Stages And Hcv-Related Hepatocellular Carcinoma In Egyptian Patients, Marwa A. Zahra

Theses and Dissertations

Dysbiosis in the gut microbiome, particularly concerning the synchronous crosstalk between the gut and the liver, has been associated with various diseases. This study profiles the gut microbiome in liver diseases among Egyptian patients, with a focus on the hepatitis C virus (HCV) and hepatocellular carcinoma (HCC), both of which are highly prevalent in Egypt. Utilizing shotgun metagenomic sequencing, we analyzed microbial gene catalogs and taxonomic profiles from 46 Egyptian patients categorized into five groups: healthy individuals, liver disease patients of different etiologies, post-HCV, treated HCV, and HCV-HCC patients. Healthy and treated HCV patients exhibited distinct microbial profiles characterized by …

Humanity Is Evolving Its Consciousness: The Role Of Archetypal Energies As Guides During An Unfolding Weeding Out And Alignment Process, Carroy U. Ferguson

Psychology Faculty Publication Series

Humanity is evolving its consciousness at individual and collective levels.  Given these seemingly tumultuous times, as of this writing (January 2026), to make such a statement may sound like a strange thing to say.  However, I suggest that if you are alive today and if you are reading these words, these are the very times for which you were born—to assist Humanity as it evolves its consciousness with your unique gifts, whatever they may be.  That is, this period of our individual and collective human being-ness may be characterized as an unfolding period of weeding out and alignment with the …

Oral Streptococcus And Vitamin B12 Deficiency In E-Cigarette Users: A Microbial–Nutrient–Neurotransmitter Axis Linking To Mood Disturbances, Maryam Sabah Naser, Ali Jabbar Abd Al-Hussain Alkawaz, Ali Abbas Hashim Almusawi, Ali Jalil Obaid, Hasanain Ayed Mohammed Al-Khafaji, Reihaneh Sabbaghzadeh

Karbala International Journal of Modern Science

Background: With the rising popularity of e-cigarettes, questions have emerged regarding their broader influence on oral ecology, nutrient absorption, and psychological health. Disruptions in the oral microbiome may alter vitamin B12 dynamics. This, in turn, may indirectly influence serotonin biosynthesis and mood regulation.

Methods: An observational cross-sectional study involved 150 young adults segregated into groups of 50 each as vapers, smokers, or non-users. Streptococcus sanguinis and vitamin B12 metabolism-related variable statuses methylmalonic acid and holotranscobalamin were quantified in samples, along with inflammatory markers interleukin-6, kynurenine/tryptophan ratio, and serotonin. Statistical techniques, including ANOVA and the Kruskal-Walli’s test, correlation, and serial mediation …

Effects Of Volatile Organic Compounds Produced By Temperature-Adapted Microbes On Duckweed Growth, Phaedra Yael Stemp

Honors Theses and Capstones

As host-associated microbes adapt to their abiotic environment, these adaptations can affect their host species as well. Previous research showed that varying temperatures and volatile organic compound (VOC) production can affect microbial benefits to hosts. This experiment analyzed how 27 microbes pre-adapted to different temperature conditions affected growth of their host, common duckweed plants, comparing effects of direct contact with microbes, effects of microbe VOCs alone, or both. Each microbe was pre-adapted to one of three temperature regimes: “Northern” at 28 °C, “Southern” at 33 °C, and “Extreme” at 36 °C. We then grew duckweeds in I-plates with each microbe …

Microbial Community Structure In Global Soils, Matthew Jabro

CMC Senior Theses

Soil harbors the most diverse microbial communities on Earth, yet whether predictable community types exist across biomes and whether taxonomic composition encodes habitat of origin remain open questions at global scale. This thesis addresses both questions by applying unsupervised clustering and supervised classification to transformed 16S ribosomal RNA (rRNA) amplicon profiles from two independent datasets: the global topsoil survey of Bahram et al. (193 samples) and the Earth Microbiome Project (EMP) soil subset of Thompson et al. (2,209 samples). Application of a sample clustering method based on a mixture of Gaussian Graphical Models (MixGGM) identified 19 clusters in the topsoil …

The Rna-Binding Protein Pumilio Limits Polymodal Noiception In Drosophila Larvae, Sara Palega, Hannah Davenport, Rebeccah K. Stewart, Jessica Horton, Andrew Bellemer

Microbiology & Molecular Cell Biology Faculty Publications

Nociception is the process by which the nervous system detects and processes information about potentially harmful environmental stimuli to generate behavioral and physiological responses. The process of nociception undergoes plasticity in response to injury, inflammation, and infection to shape the sensitivity of nociceptive circuits and the behavioral responses they control. We are increasingly aware that post-transcriptional regulation of gene expression shapes the sensitivity and plasticity of nociceptive sensory neurons and nociceptive behavior. In Drosophila, the Pumilio RNA-binding protein interacts with diverse target mRNAs to regulate their abundance and translation in a wide range of contexts including the establishment of …

Coordinating The Layers: Regulation Of Peptidoglycan Synthesis And Cell Wall Assembly In Mycobacterium Smegmatis By Murj And Pgfa, Karen Emmanuella Samaga-De-Tembiwa

Biology Dissertations

The mycobacterial cell envelope consists of three covalently linked layers whose synthesis must be coordinated to maintain structural integrity during polar growth. While the biosynthetic enzymes for each layer are well characterized, the molecular mechanisms that coordinate synthesis across layers have remained poorly understood. This thesis investigates two essential transmembrane proteins, PgfA and MurJ, that regulate peptidoglycan metabolism in Mycobacterium smegmatis and provide new insight into how mycobacteria synchronize cell wall assembly.

We present evidence that PgfA functions as a bifunctional regulator that links peptidoglycan metabolism to the availability of trehalose monomycolate (TMM), a key mycolic acid precursor. Through epistasis …

Regulation And Localization Of Urease In Sporosarcina Pasteurii: Implications For Coastal Protection, Amar Kosovac

UNF Graduate Theses and Dissertations

Coastal erosion is a persistent problem exacerbated by global warming. As the climate changes, the southeastern coast is likely to experience an increased frequency and intensity of storms, which can significantly damage the coastline. The coast is crucial as it serves as a habitat for numerous animals, supports tourism, and underpins infrastructure. Microbially induced calcite precipitation (MICP) is a novel method to enhance erosion resistance in sandy soils using the non-pathogenic bacterium Sporosarcina pasteurii. S. pasteurii produces urease to catalyze urea into bicarbonate, which drives the precipitation of calcium carbonate. Maximal expression of urease is a limiting factor for …

Assessing The Impact Of Storing Water Samples At Ambient Temperature On Plankton Metabarcoding, Stephanie N. Lievano

Honors Undergraduate Theses

Increasing incidence of Harmful Algal Blooms (HABs) has led to fish kills, air quality hazards, and economic impacts. One economic impact is on tourism, one of the main sources of Florida’s income, where billions of dollars are lost to such events. The Florida Fish and Wildlife Conservation Commission Fish and Wildlife Research Institute (FWC-FWRI), with the help of collaborators, collects water samples from across the state for HAB monitoring. These samples are stored at ambient temperature for up to 24 hours which could directly affect data analyses. Here, in collaboration with FWRI-FWC, I investigated whether this storage technique affects plankton …

Targeted And Screening Based Approaches To Analyze Drm Transcriptional Repressor Complex Activity In Caenorhabditis Elegans, Emily Washeleski

Dissertations, Master's Theses and Master's Reports

The molecular machinery that control the eukaryotic cell cycle, specifically the processes that mediate the switch between cellular division or quiescence, are essential for cellular and organismal viability. However, how the same machinery integrates with developmental or differentiation programs is less well understood. In Caenorhabditis elegans, the 8-subunit DRM complex (for Dp, Rb and MuvB), whose subunits belong to the Synthetic Mulitivulva (SynMuv) B class genes, is a central regulator of the cell cycle but also prevents inappropriate cell fate specification. The conserved mammalian DREAM complex (for Dp, Rb, E2F, And MuvB) is best known as a transcriptional repressor …

Structure And Function Studies On Trna Splicing Endonuclease, Justin G. Underwood

Dissertations and Theses (Open Access)

A subset of eukaryotic pre-tRNAs have introns that must be spliced out to become mature molecules capable of functioning in translation. This essential processing step is performed by tRNA splicing endonuclease (TSEN), a highly conserved heterotetramer with two catalytic and two structural subunits. In addition to this conserved function, archaeal TSEN also processes pre-rRNA and yeast TSEN cleaves some mRNAs that encode mitochondrial proteins to initiate mRNA degradation. Interestingly, single amino acid mutations in TSEN cause the human Mendelian disease pontocerebellar hypoplasia (PCH) by an unknown mechanism. Recently, several groups have determined the structure of human TSEN, revealing similarities and …

Fostering Entrepreneurial Thinking And Practice Through Teaching And Learning Integration, Mohammad G. Sabbir

Learning and Educational Center Virtual Teaching and Learning Conference

This session explores an innovative, evidence-based approach to integrating entrepreneurial thinking into undergraduate neuroscience education through hands-on gene editing experiences. Using the commercially available Bio-Rad CRISPR/Cas9-based “Out of the Blue” kit for bacterial LacZ gene editing, students are guided not only through the scientific principles underlying modern gene editing technologies but also through the entrepreneurial challenge of replicating and manufacturing the kit using existing lab resources. This model empowers students to extend their learning beyond the classroom by engaging in cost-effective, scalable biotechnology practices—particularly valuable for institutions with limited funding. Classroom-based research demonstrates increased student engagement, deeper conceptual understanding, and …

Detection Method For Escherichia Coli Using Real-Time Polymerase Chain Reaction Targeting The Yhav Gene, Muktiningsih Nurjayadi, Anisa Fitriyanti, Royna Rahma Musie, Gusti Angieta Putri, Puan Aqila Azizah, Helzi Angelina, Grace Grace, Ananda Indah Putri Sihombing, Agus Setiawan, Jefferson Lynford Declan, Gladys Indira Putri, Dandy Akbar Juliansyah, Siti Fatimah, Ayu Berkahingrum, Irma Ratna Kartika, Fera Kurniadewi, Vira Saamia, Shyi-Tien Chen, Bassam Aboemolak, Hesham Ali El Enshasy

Makara Journal of Science

Escherichia coli is a foodborne pathogenic bacterium that can cause diarrhea, while yhaV is a virulence-associated gene linked to the toxin–antitoxin system in E. coli. This study was aimed at evaluating the confirmation, specificity, and sensitivity of a yhaV gene primer using real-time polymerase chain reaction. The yhaV-targeting PCR successfully amplified a DNA fragment with an amplicon length of 207 bp (base pairs) under an annealing temperature optimized to a range of 54 °C to 62 °C via gradient PCR. The PCR using the primer pair produced a consistent Ct (cycle threshold) of 14.14 ± 0.05 and showed …

Enhancing Preparedness: A Genetic Study Of Sar-Cov-2 And Other Microbial Public Health Threats In Wastewater From A College Town, Christian N. Hutchinson

Master's Theses

Problem

The SARS-CoV-2 (COVID-19) pandemic revealed both the systemic vulnerabilities of our healthcare system as well as the importance of timely, localized data for informing public health responses. Traditional testing approaches were essential but often failed to capture the full extent of viral spread, especially in those with mild or asymptomatic conditions that relied on at home testing. This underreporting hindered effective allocation of resources and made developing effective intervention strategies difficult. We also realized the potential for wastewater surveillance to be applied to tracking antimicrobial resistance gene markers. Taken together, this approach should have important implications for improving public …

Enhancing Cataract Surgery Outcomes: Optimal Use Of Pre- And Post-Operative Eye Drops, Keith Skolnick M.D., Anu Valiaveedu

Mako: NSU Undergraduate Student Journal

Many preoperative and postoperative cataract patients struggle with comprehending the use of prescription medication as directed. Language barriers and low health literacy levels are major factors contributing to improper use of prescriptions. To increase patients comprehension, the Fort Lauderdale Eye Institute employed an educational intervention consisting of a live presentation and an instructional video. Results found that 44% of patients were hesitant to ask questions to clinical staff, 32% felt overwhelmed, and nearly 70% lacked confidence in using their prescribed eye drops. Following the intervention, 91% of patients reported increased confidence in their medications, and most indicated that the video …

A Toi Rna Editing In Three Members Of The Microbotryum Violaceum Fungal Complext And Characterization Of Adar Genes Of Microbotryum Superbum., Shikhi Baruri

Electronic Theses and Dissertations

A-to-I RNA editing is a process that occurs post-transcriptionally. Through this process, adenosine (A) is replaced by inosine (I) in RNAs by adenosine deaminase enzymes that act on the single-stranded RNA. These enzymes, also known as ADARs, act on RNA. The translation and splicing mechanisms subsequently interpret inosine as guanosine (G), which effectively alters genetic information. This kind of RNA alteration can cause both nonsynonymous and synonymous changes in codon, which may have an impact on protein function. A group of over 89 basidiomycete fungal species known as the Microbotryum violaceum complex infects a similarly large group of plant host …

Phylogenetic Analysis Of Ftsz In Wolbachia: Implications For Host Specificity, Anwar Rovik, Ayu Rahayu

Makara Journal of Science

Wolbachia are the most prevalent and successful endosymbiont in invertebrates and are categorized into 21 supergroups based on genetic phylogeny. The filamenting temperature-sensitive Z (FtsZ) protein is essential for bacterial cell division and is hypothesized to play a role in Wolbachia's control of host reproduction. However, despite FtsZ's importance, little is known about its diversity and function within Wolbachia. This study investigated the variability of the FtsZ-encoding gene among Wolbachia strains and their hosts. FtsZ gene sequences were retrieved from the National Center for Biotechnology Information database, and representative sequences were randomly selected from each host species and analyzed …