Biology Commons^™

Building Genetic And Culturing Tools For The Understudied Soil Bacterium E. Flagellatus, Aaron Butler, Brenda Pratte, Lon Chubiz

Undergraduate Research Symposium

Soil bacteria play essential roles in nutrient cycling, yet many abundant groups remain poorly characterized due to challenges in cultivation and genetic manipulation. One such organism is Edaphobacter flagellatus, a member of the Acidobacteriota frequently detected in soil environments but lacking well-developed experimental tools. To address this limitation, our laboratory has generated a genome-wide mutant library using the Tn5 transposon, enabling random disruption of genes across the population.

This project aims to establish culture conditions necessary to support the use of this library for functional genomic studies. In particular, defined minimal media can impose selective pressures that reveal …

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 …

Hydrogels For Local Drug Delivery In Biofilm-Associated Periprosthetic Joint Infection: Current Progress And Future Directions, Karolina Kraus, Pawel Mikziński, Bindu Subhadra, Emil Paluch

Faculty Publications - Biological Sciences

Periprosthetic joint infection (PJI) remains one of the most serious complications of arthroplasty, largely due to the formation of microbial biofilms on implant surfaces. Biofilm-associated infections exhibit increased tolerance to antimicrobial therapy and host immune responses, making eradication difficult and often requiring repeated surgical interventions. Consequently, there is a growing need for effective local therapeutic strategies capable of delivering high concentrations of antimicrobial agents directly to the site of infection while minimizing systemic toxicity. Hydrogels have emerged as promising drug delivery platforms for the management of biofilm-associated PJI. Their biocompatibility, injectability, high water content, and tunable physicochemical properties enable controlled …

Host-Pathogen Dynamics Underpinning Staphylococcus Aureus Growth During Intracellular Osteoclast Infection, Luke D. O'Connor

WUSM Theses and Dissertations – All Programs

Bone infection is most commonly caused by the gram-positive bacterium Staphylococcus aureus. It has myriad ways in which it can circumvent or subvert killing by the host or antibiotics. Intracellular infection is one such niche that is protective from immune and antibiotic attack. In 2019, Krauss and colleagues discovered that infected osteoclasts (OCs) allow S. aureus to replicate intracellularly. There they found that the ability of S. aureus to grow inside the cell was tied to OC differentiation. The magnitude of overnight bacterial expansion positively correlated with OC maturity and duration cultured with the osteoclastogenic factor RANK ligand (RANKL). Bacterial …

Escherichia Coli Concentrations In Sand And Water At Tributary-Influenced Lake Michigan Beaches, Josie Elaine Kuhlman

Masters Theses

Contamination of public recreational water and sand is a human health concern, creating a management challenge for public health officials. Past research has shown that Escherichia coli can persist in sediment and can be washed into recreational water. Currently, beach monitoring practices only utilize E. coli concentrations in water samples to determine beach safety and do not consider potential exposure to sediment/sand concentrations. In this study, I investigated the relationship between E. coli concentrations in water and sand samples, which will aid public health officials in making more informed decisions about beach closures. I utilized culture-based measurements of E. coli …

Asm And A Culture Of Sharing, Caring, And Fun In Education, David J. Westenberg

Biological Sciences Faculty Research & Creative Works

One doesn't always equate a professional scientific society with sharing, caring, and fun, but in this age of public distrust, public engagement with science and active student learning are ways to regain trust. ASM holds a leadership position in promoting and recognizing the value of education in the future of our profession and is there to support your educational journey. From K12 outreach and public engagement, to professional development, to presenting and publishing scholarship of teaching and learning, ASM has been at the forefront of biology education. Under the leadership of visionary directors such as Amy Chang and now Irene …

Evaluating Pfas And Marine Microbial Interactions In Estuarine Sediments With Varying Urbanization And Assessments Of Microbial Responses To Pfos, Zachary J. Padgett

All Theses

Per- and polyfluoroalkyl substances (PFAS) are a diverse class of synthetic chemicals that have become globally distributed due to their extensive use in industrial and consumer products and their extraordinary resistance to environmental degradation. Their persistence and documented toxicity have made them a growing concern in coastal environments, particularly in estuaries where urban runoff, wastewater, and industrial discharges concentrate these compounds. Estuaries are unique in that tidal mixing and interactions with fine-grained sediments and organic matter promote PFAS retention, while the microbial communities living directly within estuarine sediments are positioned where PFAS preferentially accumulate, creating conditions for prolonged exposure and …

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?

In Vivo Expression Profiling Of Listeria Monocytogenes Internalins (Inlf, Inlp, Inlj) And Their Corresponding Host Receptors (Vim, Afdn, Muc2) Using A Rabbit Ligated Intestinal Loop Model, Nawar Al-Janabi, Nadhim Mushtaq Hashim Al-Bderee, Zahraa M. Madania, Mohanad Jawad Kadhim

Karbala International Journal of Modern Science

Listeria monocytogenes is a Gram-positive pathogen that causes severe infections, particularly in immunocompromised individuals. Internalin genes are important virulence factors that facilitate the bacterium's invasion of host cells. This research aimed to quantify in vivo expression of selected internalin genes (inlF, inlP, and inlJ) and their corresponding host receptors (VIM, AFDN, and MUC2) during L. monocytogenes infection. To achieve this aim, a rabbit ligated intestinal loop model was constructed comprising two intestinal loops. The first loop was injected with 1 mL of L. monocytogenes (1 × 10⁷ CFU/mL), while the second loop was injected with 1 mL of PBS as …

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 …

Promiscuous Mutualisms: John Dupré And The Centrality Of Symbiosis In The Living World, Thomas Pradeu

Presidential Fellows Articles and Research

My goal in this chapter is to show that symbiosis, especially symbiotic interactions between ‘macrobes’ (non-microbial organisms) and microbes, is a central topic in John Dupré’s work. This topic is undeniably one of the topics by which Dupré has gained wide recognition among practicing scientists, in addition to his recognition within the philosophical community. I spell out why symbiosis has turned out to be a sort of ideal trope for Dupré, as it encapsulates many of his main personal themes—from promiscuous realism to process ontology. I then show that immunology offers one interesting and complementary entry point into microbial symbiosis …

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, …

Impacts Of Salinity On Microbial Enzyme Activity In Coastal Waters, Natali Ariyoshi

Honors Theses

Microbial extracellular enzymes are critical for the breakdown of organic matter and nutrient cycling in aquatic ecosystems. Extracellular enzyme activity serves as an indicator of nutrient turnover rates, metabolic states, and nutrient limitations within an ecosystem. Coastal ecosystems are especially dynamic as the influx of freshwater from inland runoff or seawater intrusion from storm surges can lead to fluctuations in salinity which can restructure microbial communities and alter enzymatic activity. Despite the ecological significance of these changes, few studies have explored the effects of short-term salinity shifts on microbial extracellular enzyme activity in coastal waters. This study investigated the effects …

Antibiotic Resistance Patterns In Bacterial Isolates From Mississippi Gulf Coastal Environments, Lawler F. Horn

Honors Theses

Coastal environments host diverse microbial communities that play essential ecological roles but may also serve as reservoirs for antibiotic-resistant bacteria. This study investigated patterns of antibiotic resistance in microbial isolates collected from public beaches along the Mississippi Gulf Coast. A total of 143 bacterial isolates exhibited growth and were included in antibiotic susceptibility screening. High levels of antibiotic resistance were observed, with 137 of 143 isolates showing growth on vancomycin, 124 on amoxicillin, and 102 on erythromycin. Resistance to kanamycin (19/143 isolates) and tetracycline (33/143) was less common. Multidrug resistance was widespread, with 101 isolates (70.6%) resistant to three or …

Acquisition Behavior Response: Investigating The Ability Of Leptoglossus Phyllopus To Choose Between A “Good” Versus “Sub-Optimal” Strain Of Caballeronia, Irene L. Pham

2026 Spring Honors Capstones Projects

Leptoglossus phyllopus is a polyphagous pest that primarily feasts on citrus, tomatoes, and legumes. They must form a mutualistic symbiosis with Caballeronia every generation by ingesting the bacterium from their environment. However, not all species of Caballeronia confer the same fitness on the L. phyllopus host, raising the question of whether L. phyllopus possesses a partner choice mechanism that would allow it to distinguish between a good (GAOX1) and a suboptimal (Lep1P3) symbiosis partner. This was examined by conducting a choice experiment in which the two symbionts (GAOX1 vs. Lep1P3) were placed in a plastic box, and the bug’s roaming …

Ai×Life 2026: Advances In Computational Biology Across Scales For Life & Health Sciences, Suma Mohan S., Devika N. T., Pranavathiyani G.

Conference Proceedings

Book of Abstracts of the International Conference, AIxLife 2026: Advances in Computational Biology Across Scales for Life & Health Sciences, held on 17–18 April 2026, SASTRA Deemed to be University, Thanjavur, Tamil Nadu, INDIA 

About the Conference

Conventional computational biology laid the foundation for biological data analysis through statistical models, algorithms, and curated databases, enabling insights into genes, proteins, and pathways. Today, the integration of artificial intelligence, spanning machine learning, deep learning, and large language models (LLMs) is driving a transformative shift across biological scales, from atomic and molecular interactions to pathways, cellular systems, organisms, and populations.

AI-powered approaches …

Identifying The Role Of Human Dna Polymerase Delta During Human Cytomegalovirus Genome Synthesis, Rachel Laree Dansereau

Dartmouth College Master’s Theses

Human cytomegalovirus (HCMV) is a large double stranded DNA virus and member of the Herpesviridae family. Like all herpesviruses, HCMV presents with characteristics of persistent, lifelong infections that transition between lytic and latent states. The replication of the viral genome is traditionally thought to occur by a rolling circle mechanism, but this model is supported by little evidence. It is known that HCMV actively recruits several host proteins to viral replication compartments (RCs), including proteins involved in the DNA damage response (DDR). The exact mechanisms of how these proteins are used and in what ways they help the virus remain …

College Of Natural Sciences Spring Newsletter, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

[Page 1] Dean's Message
[Page] 2 Awards & Recognitions // Student Spotlights
[Page] 3 Zhang Named to Landsat Science Team // The Power of Teaching
[Page] 4 “Science as Art” Competition Welcomes High School Artists
[Page] 5 Testing for “Forever Chemicals” in Surface Water // New Faculty Spotlight
[Page] 6 Ambassador Initiated Outreach
[Page] 7 57th Annual Geography Convention
[Page] 8 Twice the Impact on On Call with the Prairie Doc
[Page] 9 Making Staple Foods Healthier // Halaweish & Cole-Dai Retire
[Page] 10 Drone Day 2026
[Page] 11 Student Research, Scholarship, and Creative Activity Day (SRSCAD)
[Page] 12 Ceremony …

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 …

Characterization Of The Antiviral Activity Of Mouse Schlafen Proteins, Wendy Paola Alvarez Leal

Open Access Theses & Dissertations

The goal of this work was to characterize the anti-viral role of mouse Schlafen8 and Schlafen9. Expression of these proteins is induced by type I interferon in response to viral infections. Importantly, their human functional orthologs exhibit anti-viral functions, and the structural element required for these activities are conserved in Schlafen8 and Schlafen9. Therefore, it is expected that these proteins will also impair viral replication. An important limitation in this field is that the anti-viral function of human SLFNs has been evidenced only in in vitro cellular models. No informative mutations have been described in human populations so far. Thus, …

Elasmobranchii Oral Microbiome Diversity Within Southeast Florida: Implications Of Shark Zoonotic And Antibiotic Resistant Pathogens Associated With Human Interactions, Amanda Finnefrock

All HCAS Student Capstones, Theses, and Dissertations

Sharks are incredibly common in the Atlantic and Gulf waters surrounding Florida. Despite the prevalent nature of these animals, little research exists on the composition of their microbial communities (or “microbiomes”). Here we aim to determine the microbial makeup of the oral environment of sharks so that we can determine if there are any bacteria of clinical significance to humans, such as being antibiotic-resistant or having elevated capability for pathogenicity. A total of 41 samples were collected from the mouths and teeth of bull, Caribbean reef, great hammerhead, lemon, nurse, and sandbar sharks caught in Southeast Florida using sterile swabs …

Geographical And Anatomical Microbiome Variation In Invasive Green Iguanas (Iguana Iguana), Amanda A. Diaz

All HCAS Student Capstones, Theses, and Dissertations

The common green iguana (Iguana iguana) was introduced to South Florida in 1965 and has since been an especially pernicious threat both environmentally and economically. This highly invasive species is also expanding in range and populations at an astonishing rate. Understanding how this reptile is able to adapt and thrive in novel environments is of imperative need in order to begin managing their disruptive populations. Notwithstanding their negative impacts and significance, the microbiome of wild populations has not yet been characterized. Here, using 16S ribosomal RNA gene sequencing, this study is the first to characterize the microbiome composition …

Harnessing The Gut-Diet Axis To Enhance Chemotherapy And Immunotherapy, Jill Carline

Bryant REDay (Research and Engagement Day)

The human microbiome, a complex ecosystem of trillions of microorganisms including bacteria, fungi, and viruses, represents a critical "gut-diet axis" that significantly influences cancer progression and therapeutic efficacy. While a state of homeostasis supports systemic immunity, dysbiosis is linked to chronic inflammation and can actively promote resistance to standard cytotoxic chemotherapies and modern immune checkpoint inhibitors. Specifically, research indicates that Bacteroides fragilis (ETBF) promotes resistance to 5-Fluorouracil and Oxaliplatin in colorectal cancer by activating Notch1 receptors to inhibit apoptosis and push cancer cells into a resilient, stem-cell-like state. Conversely, the introduction of fiber-rich and fermented foods can cultivate beneficial bacteria …

Site-Directed Mutagenesis Of The He1Α Subunit Of Human Branched Chain Α-Ketoacid Dehydrogenase Complex, Riley B. Corcoran, Isabel Wilson, Bálint Csuka-Nagy, Stephen Baron

ASPIRE 2026

No abstract provided.

Biosensors For Biomedicine, Drake O'Leary

Miners Solving for Tomorrow Research Conference

This project investigated the use of engineered bacterial reporter systems to detect cellular stress responses associated with antibiotic activity. While constructs were successfully introduced and tested against known antibiotics, the reporter consistently produced a blue signal across conditions, limiting the ability to distinguish specific stress responses. This suggests issues such as leaky expression, insufficient regulatory control, or lack of specificity in the reporter design. Although results were inconclusive, this work highlights key challenges in developing reliable biosensors and provides a foundation for future optimization. Improving signal specificity and reducing background expression will be critical for enabling accurate characterization of antibiotic …

Life Line Spring 2026, Jonathan Atwood

Life Line - The Biology Department Newsletter

In This Issue:

Greetings and Farewell: Part Deux; Signs for Trees; Passing of Dr. Mary Gahbauer: a Beloved Friend and Colleague; Dr. Lisa Marr Retires; The Department Welcomes Dr. Ann Feke; Dr. Kevin Svitana Retires; Ms. Donna Rhodeback Retires; Tucker Adds Swan Specimen to Otterbein's Collection; An UnbeLEAFable Year for the Otterbein Chapter of Botanical Society of America; Field Geology Course Visits Death Valley and Beyond; Agar Art: An Unexpected Canvas; Dr. Kevin Svitana Wins the Anderson Award for Outstanding Contribution to Groundwater Research; Introducing Opi: A New Face for Zoo and Conservation Ambassador Work; Michael Hoggarth, Professor Emeritus, Wins …

Imidacloprid Effects On The Survival And Cutaneous Microbiome Of Northern Leopard Frogs, Evelyn Margaret Osterloo

Honors Thesis

Amphibians are experiencing population declines due to habitat loss, climate change, and diseases, particularly chytridiomycosis caused by the fungus Batrachochytrium dendrobatidis. Protection from this fungal infection stems from the cutaneous microbiome. Pesticides have been shown to affect amphibians in a variety of ways, including reducing survival, locomotor performance, and accumulation in body tissues. Pesticides may also lead to changes in the cutaneous microbiome affecting amphibians who rely on these organisms as an anti-Bd defense mechanism. To investigate the effect of imidacloprid, a neonicotinoid insecticide, Northern Leopard frogs (Lithobates pipiens) were subjected to sublethal concentrations (control = …

Role Of Listeria Adhesion Protein In Monocyte-Associated And Extracellular Translocation Of Listeria Monocytogenes Across The In Vitro Placental Barrier Co-Culture Model, Ayesha Atique

Biological Sciences Theses & Dissertations

Listeria monocytogenes is a facultative intracellular foodborne pathogen capable of crossing the placental barrier, leading to miscarriage, stillbirth, and neonatal sepsis, and has a fetal/neonatal fatality rate of ~20–30%. Although the importance of canonical virulence factors such as Internalin A (InlA) and Internalin B (InlB) in L. monocytogenes crossing of the placental barrier has been demonstrated, clinical strains lacking functional canonical internalins have been reported to cause severe neonatal disease, suggesting additional mechanisms of placental translocation.

To investigate these virulence mechanisms, we adapted a physiologically relevant co-culture human placental barrier Transwell model composed of BeWo trophoblasts and primary human placental …

Bio 230 - Microbiology, Sarah Moroianu

Open Educational Resources

This open educational resource (OER) syllabus is designed for BIO 230: Microbiology at Lehman College, City University of New York (CUNY), a single-semester introductory microbiology course for non-biology majors such as Nursing, Dietetics, Health Education, and Physical Education. The course reviews microbial structure, metabolism, genetics, and microbial ecology, with applied emphasis on infectious disease, antimicrobial drugs, host immune defenses, and microbial diseases. The syllabus aligns course content with the freely available OpenStax Microbiology textbook (Parker et al., CC BY 4.0) and reflects accessibility best practices consistent with CUNY guidelines.