Digital Commons Network^™

Can Carpobrotus Edulis Cause Significant Changes To The Soil Microbiome?, Samantha J. Cowan

Electronic Theses, Projects, and Dissertations

Invasive species cause significant damage to ecosystem biodiversity and can cost billions of dollars to restore native species (Van der Wal et al, 2008; Diagne et al., 2021).  In certain instances, even if the invasive species are removed, they can leave legacy effects on the environment that make restoration more challenging (Conser and Connor, 2008; Elgersma et al., 2011). Carpobrotus edulis is an invasive species of plant that is known to cause changes to its environment such as affecting the soil nitrogen cycle and the pH, potentially leading to persistent changes in the soil microbiome and causing native species to …

Assessing The Potential Of Taming Chicken Gut Commensal Bacteria Using Random Transposon Mutagenesis, Arjun Chapagain

Graduate Theses and Dissertations

The chicken gut microbiome comprises hundreds of bacterial species whose functional roles remain largely unknown, in part because the tools needed to experimentally manipulate these organisms in their native community context have not been systematically developed or validated. This dissertation addresses the gap through three connected research chapters that progressively build a framework for transposon-based genetic delivery in the chicken cecal microbiome, moving from community-wide accessibility mapping to vector optimization to library preparation refinement. In Chapter 2, we established the community-level insertion landscape in chicken cecal metagenome using Himar transposon delivery via RP4 conjugation and aligned Tn-seq reads to a …

Quantifying Macrophyte Ecosystem Services And Improving Environmental Nonprofit Messaging, Peyton R. Hughey

All Theses

Environmental nonprofits are essential to the management and restoration of our natural spaces. They are also tasked with engaging the public via outreach, education, and advocacy. As natural spaces are degraded, the ability of environmental nonprofits to deliver on their missions will become increasingly important. This study aimed to improve two approaches to environmental nonprofits’ missions: ecological restoration and social media communication.

Environmental nonprofits operate with limited resources, and ecological restoration can be an exhaustive task; therefore, we explore functional restoration as a tool. In this study, we focus on the use of functional, trait-based restoration to restore ecological function …

Mining The Usda Snap Bean Association Panel For Resilience: Genetic Dissection Of Heat And Disease Tolerance In Snap Bean, Atiya F. Khan

All Theses

Snap bean (Phaseolus vulgaris L.) is an economically and nutritionally important vegetable crop whose production is increasingly threatened by rising temperatures and emerging bacterial diseases, particularly in the southeastern United States. Heat stress during reproductive development can significantly reduce yield, while newly emerging pathogens such as Pseudomonas capsici present additional risks to crop productivity. This study leveraged the USDA Snap Bean Association Panel (SnAP) to investigate the genetic basis of heat tolerance and disease resistance and to identify germplasm and genomic regions useful for breeding resilient cultivars.

To evaluate heat tolerance, a subset of the SnAP panel was …

Forest Overstory Mortality & Recruitment Patterns Eight Years Following Wildfire In The Southern Appalachians, Ruth Cumberland

All Theses

In this study, we investigated patterns of forest overstory mortality and recruitment eight years after wildfire in a large wildfire site the Southern Appalachians, a topic that has not been thoroughly investigated to date. With evidence that pre-fire drought promotes post-fire mortality through impaired physiological function and increased fuel consumption, unknown patterns following wildfire are important to study under shifting climate and land-use conditions. In Chapter 1, three areas of interest were investigated: (a) functional group mortality response to wildfire effects, (b) temporal differences in early (1-3 years) and late (5-8 years) periods of delayed forest overstory mortality patterns following …

Modeling Repeated Evolution Of Polygenic Traits, Marshall N. Hoskins

All Theses

Understanding the genetic composition of adaptive evolution is a longstanding and primary goal of evolutionary genetics. Despite many advances in our knowledge of trait adaptation, it remains unclear how demographic changes and repeated selection might alter the expected genetic architecture of adaptation. We used forward-in-time genetic simulations to test and observe the effects of opposing, repeated selection regimes on a polygenic trait in populations with and without changes in demography to better understand the genetic alleles that underlie polygenic adaptation. To further illuminate how natural populations might evolve, we investigated the impact of mutation effect size, the role of dominant/recessive …

Biology, Ecology And Control Of Eye Gnats In An Open Pine Ecosystem, Leela Hospach

All Theses

Eye gnats of the genus Liohippelates are bothersome flies of the family Chloropidae. They breed in moist, disturbed, sandy soils that contain organic matter, and have been implicated as vectors of conjunctivitis, bovine mastitis, and yaws. We conducted research into some basic biological and ecological characteristics. Using wild-caught gnats in a temperature-controlled incubator, we found that their activity peaks between 27°C and 41°C. Trapping at different heights above the forest floor in an open-pine savannah, we captured most gnats at 7.5 m off the ground. This may have to do with the attractiveness of the rotten egg lures we used, …

Characterizing The Molecular Response Of Embryonic Zebra Finch To Acute Sound Playback, Saidat O. Adeniran-Obey Miss

All Theses

Auditory stimuli are important cues that influence developmental plasticity in animals and are important for development and adaptation to an ever-changing environment. In the zebra finch (Taeniopygia guttata), there is evidence of adaptive developmental reprogramming in response to a prenatal ‘heat call’. Embryos exposed to this heat call exhibit changes in growth rate post-hatch, increased heat resistance, and enhanced reproductive success at maturity. However, it has long been assumed that embryonic zebra finches cannot respond to sound due to the immaturity of their auditory system. These findings raise the critical question of whether late-stage zebra finch embryos can, …

Comparative Biomechanics: Blattodea Antennal Morphology And Physiology, Lucas W. Marsh

All Theses

Equipped with muscle-free antennae, many insects can twist and bend their antennae on demand. We hypothesized that hemolymph circulating through the antennae provides pressure that facilitates twisting and bending and provides a feedback control channel for tactile sensing in insects. To test this hypothesis, we conducted a thorough morphological and physiological analysis of antennae in three Clades of Blattodea. We studied morphology by evaluating the distinguishable features of the body and antenna, as well as the internal structure of the antennal lumen. Then, in a series of experiments on live cockroaches, we measured blood pressure along the antenna. This was …

Ontogeny And The Effects Of Perinatal Stress In The First Immature Skeleton Of Teleoceras Aepysoma (Perissodactyla, Rhinocerotidae), Joe Gajewski

Electronic Theses and Dissertations

Recovery of an immature fossil rhinoceros (Teleoceras aepysoma) skeleton (ETMNH 32999) from the Gray Fossil Site in Tennessee offers the first insights into the ontogeny of the species. ETMNH 32999 is interpreted to be a subadult male in an age class equivalent to ~17-20% of potential lifespan. Comparative analyses support the hypothesis that subadults of related taxa are typically ~91% of average adult size in most dimensions. However, certain cranial dimensions are substantially lower than expected in ETMNH 32999, averaging only ~74% of the average conspecific adult. Such departure from typical growth rates is suggested to be attributable …

Assessment Of Super Absorbent Polymer In Soybean Cultivation Under Variable Irrigation Conditions In Nebraska, Ankit Chandra, Abia Katimbo, Ronaldo Marchezan, Martha Nabaggala

Department of Agricultural and Biological Systems Engineering: Presentations and White Papers

Water limitation is a primary constraint to soybean productivity in both irrigated and rainfed systems. Soil-applied superabsorbent polymers (SAPs) have been proposed as a strategy to buffer crops against episodic drought stress; however, their physiological and agronomic performance under varying irrigation regimes remains insufficiently quantified. Here, we evaluate three biodegradable polymer formulations: broader granules (BB), original granules (OG), and powder (PWR) applied at low (17.7 lb/ac) and high (120 lb/ac) rates under full (100% ET), reduced (50% ET), and no irrigation conditions in western Nebraska. Polymer application had negligible effects under full irrigation, with yields comparable to untreated controls. Under …

Wrky Transcription Factors: Integral Regulators Of Defence Responses To Biotic Stress In Crops, Dongjiao Wang, Ruize Zhang, Wenhui Zou, Yuanyuan Zhang, Wanying Zhao, Tingting Sun, Qibin Wu, Zheng Qing Fu, Youxiong Que

Faculty Publications

Crops are continually challenged by biotic stresses, including fungal, bacterial and viral pathogens and insect pests, which cause substantial yield and quality losses worldwide. WRKY transcription factors constitute a plant-specific and functionally diverse family that is central to immune regulation. Recent advances in genomic resources and multi-omics approaches have accelerated the identification and functional characterisation of WRKYs in crops. This review summarises the structural features and classification of WRKY genes and their genome-wide distribution across crop species. It also synthesises WRKY-centred regulatory modules that mediate resistance to major classes of biotic stress. In antifungal defence, WRKYs reinforce pattern- and effector-triggered …

Vitaltitration Predicts Fermentation Performance Of Phylogenetically Distinct Saccharomyces Cerevisiae Yeast Strains, Samantha White Ms

All Student Scholarship

Accurate assessment of yeast physiological health is essential for achieving consistent, efficient, and predictable beer fermentations. Although yeast vitality is more predictive of fermentation performance than viability alone, no universally adopted vitality assay currently exists in the brewing industry. This thesis investigates vitaltitration (VT) as a rapid, robust, and brewery-feasible method for quantifying yeast vitality and predicting fermentation performance. We hypothesize that VT provides a reliable measure of metabolic competence that correlates with fermentation kinetics across brewery-relevant yeast strains. To test this hypothesis, VT was evaluated alongside Acidification Power (AP) in structured serial-fermentation experiments in two phylogenetically distinct brewing yeasts: …

Diacylglycerol Kinase Eta As A Novel Target In Nras Mutant Melanoma, Haley P. Wilson, Casey D. Stefanski, Signe Caksa, Glenn L. Mersky, Scott D. Varney, Jelan I. Haj, Dan A. Erkes, Timothy J. Purwin, Vivian Chua, Andrew E. Aplin

Department of Pharmacology, Physiology, and Cancer Biology Faculty Papers

NRAS mutations occur in 10%-30% of cutaneous melanomas and are associated with high tumor mutational burden. Mutant NRAS signaling drives aberrant cell growth and proliferation, in part, through activation of the RAF-MEK-ERK1/2 kinase pathway; however, targeted therapies to this pathway have limited effectiveness in patients with NRAS mutant melanoma. The role of other targetable signaling pathways in NRAS mutant melanoma is poorly characterized. Here, we demonstrated that one isoform of diacylglycerol kinase, diacylglycerol kinase eta (DGKη), a lipid signaling regulator, was highly expressed in NRAS mutant melanoma patient samples. Knockdown of DGKH in NRAS mutant melanoma cell lines resulted in …

Conventional Vs. Regenerative Apple Orchard Management In Michigan, Anthony Poynter

Masters Theses

This study compares the variables and outcomes of a conventional apple orchard and a regenerative apple orchard production system in Kent County, Michigan. The premise is that conventional agriculture relies on high-input systems characterized by synthetic fertilizers, pesticides, herbicides, and fungicides, while regenerative agriculture focuses on long-term soil health, biodiversity, and ecological processes. These differences are important as soil degradation, nutrient loss, and environmental impacts are becoming too significant to ignore. Most research on alternative ways to farm, such as regenerative practices, is focused on annual crops, while perennial orchard systems, especially in the Great Lakes region, have gained limited …

Changing Dynamics Of Microbial Communities At A Hydrocarbon Contaminated Site And Methanogenic Interactions With Iron Minerals, Jakob Sell

Masters Theses

Microbial life is not only ubiquitous but also plays a critical role in the geochemical makeup of our planet. While researchers have long studied easily culturable aerobic microbes, the influence of anaerobic life on soils and mineral cycling is less understood. Notably, knowledge about interactions between anaerobic microbes and inorganic elements such as iron has progressed with the discovery that magnetite influences how anaerobic archaea carry out methanogenesis. To better understand anaerobic bacterial metabolisms and how they interact with minerals and subsurface hydrocarbons, we extracted 16S rRNA genes from two adjacent subsurface petroleum plumes, sequenced the DNA, and analyzed it …

Degradation And Metabolic Analysis Of Synthesized Quorum-Sensing Signals By The Model Eukaryote Chlamydomonas Reinhardtii, Adam Josef Bach

Theses and Dissertations

Bacterial organisms can “talk” with one another on a colony-wide scale using a communication system known as quorum-sensing (QS) via chemical signals. These signals are produced at a basal rate throughout the life of the bacteria and are classified as autoinducers, which diffuse across the cell membrane. Once the critical concentration is reached, they begin to diffuse back into the cell and initiate a phenotypic change. As these signals exist outside the membrane of their producer, they are also accessible to other organisms. It has already been noted that some plant species uptake these compounds through their roots and break …

Ecological Responses To Living Shoreline Restoration, Aaron S. Bland

Graduate Theses and Dissertations (2019 - present)

Coastal built communities and natural coastal ecosystems face similar and interrelated hazards: shoreline sediment erosion, shoreline retreat, and worsening storms, each of which is exacerbated by relative sea level rise. Living shorelines are coastal defense projects that incorporate natural habitats to provide more sustainable shoreline defense and improve the coastal ecosystem. Living shorelines have been widely adopted, but their performance has been highly variable, and the mechanisms of project success and failure are unclear. The overarching goal of this dissertation was to better understand the ecosystem responses to coastal restoration, focusing on the primary habitats of coastal salt marsh and …

2nd Place Research Paper: Shaping The Ape: Storytelling, Cultural Reflection, And Boundary Negotiation In Human-Ape Zoo Encounters, Abigail Bond Halling

Kevin and Tam Ross Undergraduate Research Prize

The typical Western zoo functions as a unique environment in which animals are frequently positioned as subjects of education and entertainment through the medium of storytelling. In this sense, the zoological institution can also be read as an extension of popular Western constructions surrounding nonhuman animals, particularly those who are symbolically charged characters in our collective imaginary– the great apes. Given the morphological, behavioral, and psychological similarities between humans and other great apes (chimpanzees, gorillas, and orangutans), nonhuman great ape enclosures at the Western zoo become spaces where humans are most radically confronted with navigating the boundaries of the “human-animal …

Awe As Signpost: An Argument For The Consistency Of Lewis’S “Joy” And Psychological Awe, Audrey Hendricks

Senior Honors Theses

C.S. Lewis’s Surprised by Joy details Lewis’s autobiographical apologetic for the existence of God through his experiences of “Joy,” a technical term invented by Lewis. Upon close study, his experiences of Joy contain many similarities to psychological awe. This investigation compares Lewis’s Joy with psychological awe using the Awe Experience Scale (AWE-S) to determine consistency. Lewis’s Joy was found to be consistent with all six criteria of the AWE-S in addition to other recognized psychological characteristics of awe. In addition to qualitative consistency, this review also argues for the teleological consistency of the two concepts, contending for a Christian teleological …

Volume 17, Christian O’Neill, Kyara Greene, Savva Sidorov, Laura Bisaillon, Luke Clemmer, Hannah Gordon, Kitt Benson, Taylor Blount, Rachel Danzitz, Nicholas Duellman, Chase Gionis, Hima Fernando, Seth Franzyshen, Onyx Gonzalez, Bryan Lin, Samantha Start, Ysabel Wells, Maggie Duncan

Incite: The Journal of Undergraduate Scholarship

Introduction Dr. Amorette Barber, Director, Office of Student Research

From the Editor Dr. Hannah Dudley-Shotwell

Cover Artist’s Statement Maggie Duncan

On Mentoring Dr. Yulia Uryadova

Ukrainian Resistance in the Face of Russification: Nestor Makhno and Anarchism

by Christian O’Neill

Life Vest by Kyara Greene

Isolation and 16S rRNA Identification of Bacteria from Fire Department Connection Pipe by Savva Sidorov

The Effectiveness of Planned Exercise in Reducing ADHD Symptoms in Children by Laura Bisaillon & Luke Clemmer

Linguistic Analysis on Confidence and Communication Strategies with Disparities Between Sign Fluency and Hearing Impairment by Hannah Gordon

Freedmen in Indian Territory by Kitt …

Effects Of M6a Dna Methylation By Bacterial Methyltransferase In Colorectal Cancer, Fabian Alejandro Mendoza Galvan

Dissertations and Theses (Open Access)

Effects of m6A DNA methylation by bacterial methyltransferase in colorectal cancer Fabian Alejandro Mendoza Galvan Advisory Professor: Angela H. Ting, Ph.D. Fusobacterium nucleatum animalis (Fna) is found in the human oral cavity and gut. A distinct clade of Fna is primarily enriched in the tumor microenvironment (TME) and within colorectal cancer (CRC) cells. This clade DNA methylation pattern is primarily catalyzed by a cell-cycle regulated methyltransferase (CcrM) ortholog, M.FnI, that targets the GANTC sequence motif through methyl-6-Adenine (m6A) DNA methylation. We hypothesized that M.FnI enzyme can induce m6A methylation abnormalities in CRC cells to promote cancer progression. Evidence for endogenous …

Targeting Breast Cancer Brain Metastasis Through Novel Combination Of Fda-Approved Orally Active Blood-Brain Barrier Permeable Ret And Tgli1 Inhibitors, Joshua Cha

Dissertations and Theses (Open Access)

Breast cancer is the most diagnosed cancer in American women, and breast cancer brain metastasis (BCBM) exhibits the worst prognoses with a life-expectancy averaging at 6 months. This short life expectancy is largely attributed to the lack of effective treatment. Many challenges remain unsolved, including the limited number of actionable targets for targeted therapy and effective blood-brain barrier (BBB) permeable drugs that are safe without promoting drug resistance. Therefore, there is an urgent call for identification of novel therapeutic targets and development of BBB-permeable drugs. One of the potential targets identified by our lab for BCBM targeted therapy is the …

Pattern Dynamics And Stochasticity Of Brain Rhythms And Spike Trains In A Tauopathy Mouse Model Of Alzheimer’S Disease, Clarissa M. Hoffman

Dissertations and Theses (Open Access)

Systems neuroscience posits that every aspect of perceived physical reality, every aspect of animal and human behavior, and every cognitive phenomenon emerges from patterns of neuronal activity. While most researchers embrace this idea, there are major difficulties in describing and analyzing these complex neuronal dynamics—spike flows produced by cells ensembles, synchronized extracellular field oscillations, and other patterns—which limits our understanding of how the activity of individual neurons and the whole-animal cognition and behavior might be connected. In particular, we lack the approaches and even the semantics for connecting the individual cell outputs and the integrated results of their activity. Current …

Characterization Of Staphylococcus Aureus Clinical Isolates From Deep Musculoskeletal Infections For An In Vitro Biofilm Model For Phage Therapy, Raquel C. Luna

Dissertations and Theses (Open Access)

The rise of multidrug-resistant (MDR) infections is a growing concern in the treatment of deep musculoskeletal infections (MSKIs) and orthopaedic device-related infections (ODRIs). Staphylococcus aureus is responsible for about one third of these infections due to its strong biofilm forming capacity, presence on human skin, and the large number of antibiotic-resistant variants. Bacteriophage (phage) therapy is now being considered as a treatment for MDR MSKIs/ODRIs. We are investigating the use of phage encapsulated into or adsorbed onto biodegradable microspheres for local delivery to the site of these MDR infections. We determined that the anti-staphylococcal phage K effectively lyses the S. …

From Antigen Presentation To Tumor Control: Mechanisms Of Type I Conventional Dendritic Cell-Based Cancer Vaccines, Josue E. Pineda

Dissertations and Theses (Open Access)

Type 1 conventional dendritic cells (cDC1s) are important for generating and sustaining antitumor immunity. Accordingly, the abundance of cDC1s in human tumors correlates with improved outcomes in cancer. Capitalizing on this role, we previously demonstrated that vaccination with in vitro-derived murine cDC1s elicits durable tumor control in multiple preclinical models; however, the immunological mechanisms underlying the efficacy of cDC1 vaccination remain unclear. Here, we examined whether in vitro-derived cDC1s resemble tumor-infiltrating DC populations and whether MHC-I and MHC-II antigen presentation contribute to cDC1-mediated tumor control following vaccination in melanoma.

As expected, MHC-I- or MHC-II-deficiency had minimal impact on …

Membrane Organization Of Rheb And Rhoa: Roles In Function And Allosteric Druggability, Chase M. Hutchins

Dissertations and Theses (Open Access)

Small GTPases of the Ras superfamily are membrane-bound molecular switches that regulate nearly all major cellular processes, and their dysregulation drives cancers, neurological disorders, and metabolic diseases. While anchored to cellular membranes, the catalytic domains of small GTPases undergo orientation dynamics, adopting distinct configurations that can occlude or expose effector-binding surfaces and modulate signaling output. These dynamics have been characterized in the Ras oncoproteins, but whether they extend across the superfamily and influence allosteric druggability has remained unknown.

In this dissertation, I address these questions through Rheb and RhoA, two small GTPases with complementary differences in subfamily lineage, membrane localization, …

Understanding Epigenomic Landscapes In Cancer Progression And Immunotherapy Response, Jonathan Schulz

Dissertations and Theses (Open Access)

Nonmutational epigenomic reprogramming has emerged as a key hallmark of cancer that plays crucial roles in tumor evolution during its progression and response to therapy. However, the extent and nature of epigenomic reprogramming remains poorly understood. This dissertation examines how epigenetic regulation shapes cancer progression and response to immunotherapy. Working at the intersection of cancer biology and computational genomics, it develops analytical frameworks for characterizing chromatin structure and DNA methylation across diverse tumor contexts and uses these frameworks to address two complementary biological questions: how promoter-associated chromatin organization varies across cancer types, and how epigenetic perturbation modulates tumor immunogenicity in …

Understanding Vaccine Hesitancy In Veterinary Medicine: A Review Of Client Attitudes, Grace Moore

Undergraduate Honors Capstone Projects

Uncertainty toward vaccination, long recognized as a public health concern in human medicine, is increasingly recognized within veterinary contexts, posing risks to both animal and community health. This literature review examines the development, causes, and implications of reduced vaccine confidence in veterinary medicine, with emphasis on small animal and some large animal practices. The review combines historical and current research to explore how vaccination perceptions have evolved among veterinarians and clients, and how factors such as the COVID-19 pandemic have shaped current attitudes.

The literature highlights recurring themes surrounding vaccine reluctance in veterinary settings. Client perceptions of safety, efficacy, and …

Donor And Recipient Microbiome Interactions Determine Functional Outcomes Of Fecal Microbiota Transplantation For Clostridioides Difficile Infection, Sophie A. Millard

All Dissertations

Clostridioides difficile is a major cause of healthcare-associated diarrhea. Infection typically occurs after antibiotic treatment disrupts the gut microbiome, allowing C. difficile to colonize and produce toxins leading to disease (CDI). Standard antibiotic treatments can resolve acute infection but frequently lead to recurrence, highlighting the need for alternative strategies that restore the gut ecosystem. Fecal microbiota transplantation (FMT), the transfer of stool from a healthy donor, has emerged as an effective therapy for recurrent C. difficile infection (rCDI). Understanding the mechanisms underlying the success of FMT for treatment of rCDI could lead to safer, more defined microbial mixtures.

This dissertation …