Microbiology Commons^™

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 …

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, …

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

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

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.

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. …

Clinical Characteristics And Outcomes Of Pediatric Staphylococcal Scalded Skin Syndrome (Ssss) At An Inner-City Tertiary Care Center, Nina Kb Gust Md, Ashley Frei Bs, Rebecca M. Adams Bs, Elika Ridelman Phd, Christina Shanti Md, Ronald Thomas Phd, Jocelyn Y. Ang Md

Medical Student Research Symposium

Introduction

Staphylococcal Scalded Skin Syndrome (SSSS) is a blistering skin condition caused by a toxin-producing staphylococcus species. Epidemiologic studies on pediatric SSSS in the United States are limited, with a reported incidence of 7.67 cases per million children and 45.1 per million infants. Immature renal function, lack of protective antibodies, and increased exotoxin target desmoglein-1 are hypothesized to increase incidence in younger children. We aimed to determine clinical and microbiological characteristics of pediatric SSSS and factors that could help predict disease severity.

Methods

A retrospective chart review was performed for admitted patients under 18 years old diagnosed with SSSS from …