Microbiology Commons^™

Seasonal Detection Of Coliphages In Freshwater Bodies At Coastal Carolina University, Ella Caldwell

Honors Theses

Bacteriophages, commonly referred to as phages, are non-living viruses that only infect bacteria. As the most abundant biological entities on Earth, understanding their role in regulating microbial populations is essential. This ongoing research aims to identify naturally occurring bacteriophages that could effectively control bacteria blooms. The primary objective of this study is to detect coliphages on Coastal Carolina University's campus and determine their viral families. Coliphages are a subgroup of bacteriophages that specifically infect coliform bacteria. Water samples were collected across multiple sites on campus, and polymerase chain reaction (PCR) was employed to amplify the viral DNA from the potential …

Can Chaperones Promote Protein Splicing?, Hazel Thomas

Honors College Theses

Inteins are a mobile genetic element hypothesized to function as regulatory molecules in microbes. They bear a homing endonuclease domain for genome traversal, as well as specific residues allowing for protein splicing. In the protein splicing reaction, the intein is removed and the flanking residues, termed exteins, are ligated together with a peptide bond to form a functional host protein. Due to their interruption prior to splicing, inteins prevent a host protein from functioning until the intein ligates the two exteins. To measure factors that regulate protein splicing in vivo, an intein-based biosensor based on kanamycin resistance (K …

Bibliometric Analysis Of Research Trends Related To Human Immunodeficiency Virus., Madyson E. Johnson, Kaitlyn R. Coffman, Valerie Rivas, Elizabeth Barrett

ATU Scholars Symposium

Human immunodeficiency virus poses major health burden across the globe including the United States of America and has its zoonotic origin from the Simian Immunodeficiency viruses of sooty mangabey monkey and chimpanzee in Africa. Epidemiological trends indicate that even though the mortality rates for HIV are falling globally, the rates of new cases have been rising since 2010 in several countries including the USA. An estimated 0.5% of the human population is currently infected with the virus with countries like USA, India, Nigeria and South Africa carrying the highest burden of the disease. Host receptors such as CD4 and coreceptors …

Bacterial Microbiomes In Different Depths Of Sand At The Mississippi Gulf Coast, Hays S. Roth

Honors Theses

Microbial communities in sand play essential roles in their ecosystems, yet little is known about how bacterial diversity and function vary across different sand depths. This study investigated bacterial microbiomes at varying depths (0, 10, 20, 30, and 40 cm) on Biloxi East Beach, on the Mississippi Gulf Coast, using 16S rRNA gene sequencing and assays of extracellular enzyme activity. 11,161 amplicon sequence variants (ASVs) were identified across all samples, with the most abundant bacterial phyla being Planctomycetota, Gammaproteobacteria, and Bacteroidota. Depth had a significant impact on bacterial community composition, with surface layers having more diverse bacterial communities. Microbial diversity …

Expression, Characterization, And Comparative Analysis Of Bacillus Bacteriophage Endolysins, Stephen D. Zdgiebloski

Research and Creativity Symposium

Bacteriophages present a promising alternative for combating antibiotic-resistant bacteria without disrupting the normal microbiome or harming human cells. The antibacterial properties of lytic bacteriophages are largely attributed to endolysins, enzymes active in the lytic cycle. Endolysins recognize bacterial cell walls and cleave the peptidoglycan matrix, leading to cell wall disruption. Their specificity and effectiveness against bacterial hosts are determined by two functional domains, including the cell wall binding domain. Our research focuses on characterizing Bacillus phage endolysins. We analyzed the protein sequences of endolysins from six Bacillus phages isolated at the University of Mary Washington. Although these phages were isolated …

From Dysbiosis To Dysfunction: Investigating The Effects Of Chronic Cocaine Use On Oral Microbial Shifts And Neuropathogenesis, Douglas E. Johnson

MUSC Theses and Dissertations

Cocaine use disorder remains a significant public health challenge. However, the mechanisms by which chronic cocaine use contributes to neuroinflammation and cognitive decline are still not fully understood. Chronic non-intravenous cocaine use is associated with oral microbial dysbiosis. Although the gut-brain axis has been widely studied, the impact of cocaine-mediated shifts on the oral microbiome on systemic and neuroinflammation remains a significant yet largely unexplored gap. This dissertation investigates the hypothesis that cocaine-specifically enriched oral Streptococcus parasanguinis triggers neuroinflammation, neuropathology, and cognitive deficits. In a human study, the saliva microbiomes from chronic cocaine users exhibited reduced α-diversity, enriched Streptococcus genus, …

Survey And Analysis Of Rumen Microbiota In Yaks At Different Growth Stages, Shengwei Jin, Xinyue Liu, Yin-Cang Han, Yong-Gang Sun, Wei-Qin Ding, Ya-Qian Liu, Fa-Jie Gou, Jian-Yu Chen

The Thai Journal of Veterinary Medicine

This study investigated changes in the richness and composition of the rumen microbiome in yaks at various developmental stages. Eighteen healthy male yaks at the ages of 5 months (M5), 12 months (M12), and 24 months (M24) had samples of their rumen digesta taken for 16S rRNA gene sequencing. The 11087 amplicon sequence variations (ASVs) in total were found; the M5, M12, and M24 groups had 3585, 1146 and 5545 distinct ASVs, respectively. Alpha diversity indices Chao, Shannon, Sobs, and ace indicated significant differences among the groups. The principal coordinate analysis (PCoA) indicated significant changes in microbial community composition across …

Emergence Of Heterogeneity In Bacteria During Antibiotic Exposures, Mirjana Stevanovic

Dartmouth College Ph.D Dissertations

Bacterial populations exposed to antibiotics often exhibit phenotypic heterogeneity, with individual cells displaying distinct responses with fates ranging from survival to arrest or death. The emergence of this heterogeneity is largely driven by feedback mechanisms mediated by the interactions between antibiotic action, gene regulation, and cellular metabolism. These responses unfold in dynamic environments where conditions such as nutrient availability and drug concentration fluctuate over time and space. Yet, these complex interactions and their role in shaping population-level outcomes during drug responses remain poorly understood. Using tetracycline resistance in E. coli as a model system, this thesis focuses on how these …

Progesterone Signaling In Oviductal Epithelial Cells Modulates The Immune Response To Support Preimplantation Embryonic Development, Emily A Mcglade, Jiude Mao, Kalli K Stephens, Ryan M Marquardt, Feyza Nur Arguc, Peter F Lais, San-Pin Wu, Sarayut Winuthayanon, Haval Shirwan, Esma S Yolcu, Mark I Hunter, James K Pru, John P Lydon, Francesco J Demayo, Wipawee Winuthayanon

Faculty, Staff and Students Publications

More than 60% of pregnancy losses occur during the first trimester, highlighting the need to understand the role of the oviduct in early pregnancy. In this study, we conditionally ablated the classical progesterone receptor (Pgr) in oviductal epithelial cells, called the Pgrd/d mouse model. We found that 40% of embryos collected from Pgrd/d females were nonviable or developmentally delayed, indicating that epithelial PGR expression is crucial for embryonic development. Single-cell RNA sequencing revealed up-regulation of proinflammatory genes, including interleukin-22 (IL-22), in the epithelial cells of Pgrd/d females. Pharmacological inhibition of inflammation using nonsteroidal anti-inflammatory drugs …

Antibiotic Resistance Testing And Enumeration Of E. Coli, Coliforms, And Salmonella In Canada Geese Feces Based On Natural Water Sources And Retention Ponds, Ceejay Ritzke

Research Days

Canada Geese (Branta canadensis) are migrating birds. They can transmit antibiotic resistant bacteria when they are traveling. They do this by ingesting antibiotic resistant bacteria that is on the food they eat in one area, and then excrete some of it at the next place they travel to. Retention ponds have increased amounts of antibiotic-resistant bacteria that Canada geese can pick up if they stop there while migrating. Canada geese that land at a retention pond should have an increased amount of antibiotic resistance compared to landing at a natural water source. Their feces were tested in eight different areas …

Investigating The Effect Of Soil Origin On Antibiotic Production In Streptomyces, Emu Suzuki

Undergraduate Research Symposium 2025

Streptomyces bacteria produce antibiotics that inhibit competing microorganisms. We hypothesized that Streptomyces from the rhizosphere (around plant roots) would be more likely to produce antibiotics than those from bulk soil (further away from roots). Soil samples were collected from rhizosphere and bulk soils in transitional and long-term organic fields of corn and alfalfa. Streptomyces from these soils were cultured on glucose-asparagine agar media. Their antibiotic production was evaluated by testing whether they could inhibit the growth of two target Streptomyces strains. No significant effects of soil type (rhizosphere vs. bulk), crop, or management on antibiotic production were observed for one …

Life After Death: Investigating The Resistance And Recovery Of Fungal Communities To Foundation Tree Mortality, Jessie F. Marlenee

Biology ETDs

Tree mortality can have cascading effects on the composition and resilience of interacting fungal communities. Yet, little is known about the impact tree mortality, distinct from abiotic drivers (i.e., drought), has on these communities. This dissertation focuses on the resilience of fungal communities to experimental tree mortality in a piñon-juniper woodland. In chapter one, I found that piñon mortality reduced piñon fine root biomass and piñon mycorrhizal fungal diversity, whereas juniper mycorrhizal fungi were unaffected by juniper mortality. In chapter two, I revealed that piñon mortality altered the composition and spatial structure of mycorrhizal and saprotrophic fungi in the soil, …

Lineage Tracing And Single-Cell Rna Sequencing Reveal A Common Transcriptional State In Breast Cancer Tumor-Initiating Cells Characterized By Ifn/Stat1 Activity, Eric P Souto, Ping Gong, John D Landua, Ramakrishnan Rajaram Srinivasan, Abhinaya Ganesan, Lacey E Dobrolecki, Stephen C Purdy, Xingxin Pan, Michael Zeosky, Anna Chung, S Stephen Yi, Heide L Ford, Michael T Lewis

Faculty, Staff and Students Publications

A tumor cell subpopulation of tumor-initiating cells (TIC) or "cancer stem cells" is associated with therapeutic resistance, as well as both local and distant recurrences. Signal transducer and activator of transcription (STAT) activity is elevated in TICs in claudin-low models of human triple-negative breast cancer, which enables enrichment of TICs using a STAT-responsive reporter. Lineage tracing of TICs as they undergo cell state changes could enable a better understanding of the molecular phenotypes of TIC and uncover strategies to selectively target TICs. In this study, we developed a STAT-responsive lineage-tracing system and used it in conjunction with the original reporter …

From Microplastic Impacts To Biodegradation Solutions: Investigating Microplastic Contamination, Microbial Responses, And Efficacy Of Synthetic Microbial Consortia In Plastic Degradation, Rener Sahot De Jesus

Thesis/ Dissertation Defenses

Plastics, including microplastics, pose significant environmental threats due to their widespread presence and harmful ecological effects. This dissertation present three distinct, yet interconnected studies. First, a study on microplastic contamination in urban recreational parks was conducted in Al Ain, UAE. Results showed that low-density microplastics were present in 87% of soil samples, with FTIR analysis identifying synthetic polymers such as PE and PP. Additionally, these microplastics were found to negatively affect soil pH and moisture levels, emphasizing the need for enhanced monitoring and management strategies. Second, the effects of ground microplastics on Photobacterium leiognathi spp., a marine luminous bacterium, were …

Biology Department Publications: 2024, Sam Lindgren

Biology Department Bibliographies

This document is a non-comprehensive list of publications made by graduate students, post-doctoral researchers, and faculty members in the Biology Department in 2024. It indexes those publications available through PubMed, and serves as an archival record of the Department's robust scholarly contributions.

Genome Analysis Of Aeromonas Hydrophila Strain S14-452, Zarin Tasnim Raya

Undergraduate Research Conference

The Aeromonas hydrophila are gram-negative, opportunistic bacteria that can infect many groups of organisms, mainly fish and amphibians. In channel catfish, A. hydrophila causes fatal bacterial septicemia, leading to massive economic losses for catfish farmers. Therefore, an understanding of its genome will aid in identifying its virulence factors, metabolic pathways and survival mechanisms within the host. This study details the draft genome sequence of A. hydrophila strain S14-452, isolated from channel catfish exhibiting bacterial septicemia during a disease outbreak at a catfish farm.

A. hydrophila strain S14-452 was sequenced using the Illumina iSeq 100 System. Assembly was performed with SPAdes, …

Discovery And Identification Of Muwow Bacteriophage From Columbus, Ms, Olivia Reese Carlisle, Jess Holden Collins, Kaliyah J. Moore, Nykeria J. Pratt

Undergraduate Research Conference

Bacteriophages are an abundant type of virus with the ability to infect and kill bacteria while using them to replicate through lytic or lysogenic processes. Bacteriophages play a key role in the regulation of bacterial populations in various environments and are being explored as potential tools in phage therapy. The aim of this study was to isolate, characterize, and manually annotate the genome of the bacteriophage MUWow collected from the campus of the Mississippi University for Women in Columbus, MS at GPS coordinates 33.493021 N, 88.419611 W. MUWow was isolated from a soil sample on Arthrobacter globiformis B-2979. Plaque assays, …

Pseudomonas Parafulva Confirmed To Have Antifungal Properties When Grown In Conjunction With Botrytis Cinerea, Caden Dupee, Kylee Eldredge, Zachary Elmer, Joshua Hartvigsen

Student Research Symposium

Widespread antibiotic use has led to antibiotic resistance of infectious bacteria. (Young, 2017) As part of the TinyEarth Program, the lab group collected and tested local soil samples for bacteria with hopes of finding novel antibiotic properties. From the soil samples, a bacteria was isolated, subsequently sequenced, and determined to be Pseudomonas parafulva. P. parafulva is a Gram-negative bacterium that has been known to frequent rice paddies of eastern Asian countries and has been collected in select regions of North America, including that of Cache Valley. P. parafulva has been linked to anti-fungal activities on plants. (Lui et …

Internship As An In-Vivo Technician At The Institute For Antiviral Research, Ashlynn Clark

Student Research Symposium

The Institute for Antiviral Research (IAR), located at Utah State University, specializes in evaluating antiviral agents and vaccines against a wide array of human pathogenic viruses, such as influenza, enterovirus, West Nile virus, yellow fever, zika virus, polio, and SARS-CoV-2, utilizing in vivo and in vitro models.

Identifying Compensatory Mutations In The Envelope Protein Of Japanese Encephalitis Virus That Restore Neurovirulence, Nathan Taylor, Jiyoun Kim

Student Research Symposium

• Japanese Encephalitis Virus (JEV) is a positive sense, single stranded Enveloped virus

Vaccine Stabilization With Spider Silk, Mallory Wootton

Student Research Symposium

Most vaccines must be stored between 2 - 8°C to maintain their efficacy, with some vaccines requiring temperatures as low as -70°C for long-term storage. These temperature requirements pose issues for vaccine distribution, notably to remote/rural areas, in hotter climates, and low- and middle-income countries which are largely dependent on vaccine imports. [1]

Distributor-Specific Variability In Balb/C Mouse Mortality Following Sars-Cov-2-Ma10 Infection, Taylor Kerr

Student Research Symposium

In recent years SARS-COV-2 has become a rapidly expanding area of research. To model human infections, this virus was adapted to mice enabling valuable insight into these processes.² Mice are often an effective research model due to their low cost, short reproduction time, and ability to adapt to a wide variety of viruses. Research into these immunological responses is crucial in developing vaccines, treatments, and furthering our understanding of this virus' behavior.¹ However, genetic variability in mouse models may be confounding previous and on-going research.

Mdpk Cell Lines Can Be Used For In Vitro Antiviral Testing With Highly Pathogenic Avian Influenza (H5n1), Jada L. Westover

Student Research Symposium

• Outbreak in agricultural poultry starting in 2022
• In March 2024 first confirmed case in Dairy Cattle
• Tested drugs T705, Oseltamivir, Baloxivir, Ribavirin, EIDD-2947, and EIDD-2749 on three different cell lines
• Goal: See if MDBK cell lines could be used for in vitro studies

Gastric Survivability Of Streptomyces Narbonensis, Laramie Johnson, Laurel Hilterbrand, Ephraim Mohr, Eliza Lewis

Student Research Symposium

Human sciences and medicine have continually been advancing, and taken off in the last few centuries. This has included the development of many new medicines, antibiotics, and disinfectants. Antibiotics have to be able to survive and perform its duty within the human body, despite the changes in pH that occur naturally within the body in response to stimuli (Cotter, 2003). If a bacteria is unable to adapt to the pH environment of the human body in which it is placed, it will not be able to survive and continue to reproduce. The bacteria may be able to adapt via membrane …

Peribacillus Simplex Does Not Exhibit Antimicrobial Properties Against Staphylococcus, Dallin Thomas, Jordan Wheeler, Natalie Yoho

Student Research Symposium

Antibiotics are powerful drugs that combat previously fatal diseases. These miracle drugs have saved countless lives, but have the tendency to be misused. They are used incorrectly to treat patients who don't need them, and given to animals for non therapeutic use. Antibiotics are also known to pollute soils and groundwater all around the world (3). As antibiotics are found more readily in the environment, they encourage evolution, recombination, and dissemination of antibiotic resistant bacteria (5). According to the Centers for Disease Control and Prevention (6) antibiotic resistance kills at least 1.27 million people worldwide for diseases that used to …

Do Chaperones Promote Protein Splicing?, Christopher Powell, Christopher Lennon Dr

Scholars Week

Intervening proteins (inteins) are translated within host proteins and removed by protein splicing. Inteins are abundant in the microbial world and are often found within essential genes involved in DNA replications, recombination, and repair. Recent studies have made efforts to understand conditional proteins splicing, whereby intein removal and subsequent host protein activation is regulated by environmental factors. However, within the cellular context, factors influencing protein splicing are still largely unknown. In this work, we probe whether the chaperonin system GroEL/ES promotes protein splicing in vivo. Chaperonins, a family of chaperone proteins, help proteins fold under normal and stressed conditions. …

Metabolite Analysis To Understand Factors Limiting Microbial Fermentation At High Substrate Concentrations, Bishal D. Sharma

Dartmouth College Ph.D Dissertations

Clostridium thermocellum, a thermophilic anaerobic bacterium, holds promise as a biocatalyst for conversion of lignocellulosic biomass into biofuels. This microbe has been subjected to various metabolic engineering strategies, including the deletion of genes encoding secondary fermentation products such as H₂, formate, acetate, and lactate, as well as the expression of heterologous genes to redirect carbon flux toward ethanol production. Despite these efforts, achieving economically viable ethanol titers remains a challenge. We hypothesized that studying how intracellular metabolite concentrations change as fermentation stops could reveal metabolic bottlenecks or regulatory mechanisms limiting ethanol production at high titers. However, metabolomics studies at …

Improved Protein Splicing Through Viral Passaging, John Smetana

Scholars Week

Intervening proteins (inteins) are translated as subdomains within host proteins and removed through an intein-driven splicing reaction where the flanking sequences (exteins) are joined with a peptide bond. Previously, we developed a self-removing translation reporter for labeling Ebola virus (EBOV). In this reporter, an intein (RadA) containing the fluorescent protein ZsGreen (ZsG) is inserted within the EBOV protein VP30. Upon VP30-RadA-ZsG expression from the viral genome, RadA-ZsG is removed from VP30 through the protein splicing activity of RadA, generating functional, non-tagged VP30 and functional ZsGreen. While incorporation of our VP30-RadA-ZsG fusion reporter into recombinant EBOV (rEBOV- RadA-ZsG) resulted in an …

Biochemical And Structural Insights Into The Yersinia Effector Yopm And Its Negative Regulation Of The Pyrin Inflammasome, Bethany Wairimu Mwaura

Dartmouth College Ph.D Dissertations

Bacteria utilize sophisticated secretion systems to inject effectors into host cells in order to facilitate their survival and replication in the host. Some pathogenic species of Gram-negative bacteria use a conserved contact-dependent T3SS to inject a wide array of effectors. While the effectors diverge in their structures, functions and cell-localization, the T3SS is well conserved. Several effectors discussed in this thesis target key host inflammasome responses. The focus of this work is how the Yersinia effector YopM inhibits the pyrin inflammasome. During Yersinia infection, two effectors, YopE and YopT inadvertently activate the pyrin inflammasome while targeting RhoA to avoid phagocytosis. …

Resistant & Persistent Bacterial Cells, Jean-Louis Bru

Open Educational Resources

An activity on the difference between resistant & persistent bacterial cells. This activity aims to build on the pre-lecture materials about resistant bacterial cells, so that students can make a connection toward persistent cells. In both cases, they make antibiotics less effective.

Learning Objectives

Recognize the importance of antibiotics in fighting bacterial infections. Understand how bacterial species become antibiotic resistant. Determine the difference between resistant and persistent bacterial cells.

Social and Collaborative

Students work together on this in-class activity in groups of 2-4 (3, ideally). Each student will have one of the following roles: encourager, recorded, investigator, and time keeper. …