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Analysis Of Alternative Oxidase In Non-Angiosperm Plants, Anissa M. Francis

Theses and Dissertations (Comprehensive)

Alternative oxidase (AOX) is a mitochondrial terminal oxidase that provides an alternative pathway for electron transport, allowing plants to maintain respiratory flexibility under environmental stress conditions. While AOX has been extensively studied in angiosperms (flowering plants), little is known about its distribution and conservation in non-angiosperms. Based on gaps identified in the literature, this thesis investigated the distribution of AOX across non-angiosperm plant lineages. Although AOX is present in many green algae and is therefore considered to be an ancient protein that originated before the existence of non-angiosperm plants, it remains unclear whether the protein is uniformly distributed across these …

Impact Of Cigarette Smoke On Immune And Stromal Cells, Justin Wong

Master's Projects

Cigarette smoke is a plight on human health, being a major contributor to lung diseases. The aryl hydrocarbon receptor (AHR) directs immune regulation and metabolic adaptation in response to environmental toxins. This study investigates transcriptomic changes between wild-type and AHR knockout mouse lung tissue under smoke and air conditions. Single-cell RNA sequencing data were generated by the Butcher Lab and analyzed in Seurat for differential gene expression (DGE) analysis. A two way ANOVA framework was used with DGE analysis to classify genes as smoke induced or suppressed in an AHR dependent or independent manner, and these gene sets were analyzed …

Searching For Cause Of Unexplained Protein Interaction With Multiple Assembly Methods, Gavin Anderson

Master's Projects

Research into colistin adjuvants has identified interactions between a host of proteins and proteins found within certain strains of bacteria. BLAST, a widely adopted local sequence alignment tool, was used to create a database containing the genomes of relevant bacterial strains, which would then be used to query against the previously identified proteins. Many of these strains do not have publicly available assemblies, which makes database construction difficult. CATwalk, a new naïve fragment extender, is first described in this paper and used to extend fragments of interest. BLAST results first identified short fragments with sufficient similarity, which can then be …

Detection And Characterization Of Cancer Using Cfdna Fragmentomic Analysis, Guneet Bhogal

Master's Projects

Cell-free DNA (cfDNA) fragmentomics has emerged as a promising non-invasive approach for detecting and characterizing cancer by analyzing DNA fragmentation patterns. These fragment patterns are unique and can be used to distinguish between tumor and healthy DNA. This paper uses machine learning models to detect cancer by evaluating Shannon entropy of fragment lengths at the first coding exon 1 regions and correlating them to targeted cancer genes. This approach was applied to two datasets consisting of samples with prostate, breast, and lung cancers. Our results indicated that exon 1 fragmentation entropy captures biologically relevant differences in cancer-specific chromatin organization and …

Combining Crispr And Nanoasv To Uncover The Rare Bacterial Communities Of The Human Oral Microbiome, Gilma Ruth Sevilla Alvarez

Master's Projects

Studying the oral microbiome is vital because its health implications are not contained to the mouth. Cariogenic bacteria cause tooth demineralization and oral microbes that translocate to extra-oral organ systems are linked to conditions like Alzheimer’s disease, heart disease, diabetes, and cancer. Some of these pathogens belong to the most abundant phyla in the oral cavity: Bacillota, Pseudomonadota, Bacteroidota, Actinomycetota, Spirochaetota, and Fusobacteriota, which together comprise 94% of the oral microbiome. This project uses CRISPR-Cas9 to deplete sequences from highly abundant phyla and the Eubacteria domain, enriching the remaining 6% of rarer taxa. Paired with NanoASV for single-nucleotide resolution, this …

The Coral Microbiome Under Climate Change: Shifting Symbiotic Interactions, Katherine E. Parker, Kate M. Quigley

Biological Sciences Faculty Publications

Host–microbe symbioses are central to organismal health, yet these complex partnerships are often strongly shaped by the environment. Climate change is increasingly altering environmental conditions, disrupting the balance of host–microbe interactions and pushing them along a continuum from mutualism (both partners benefit) toward parasitism (one partner gains at the other’s expense). Reef-building corals provide a clear example of this vulnerability, as the coral holobiont, an ecological unit comprising diverse photosynthetic algal symbionts (Symbiodiniaceae) and other microbial partners, depends largely on these mutualistic interactions for nutrition, immunity, and stress tolerance. Increasingly, evidence suggests that under heat stress, the algal symbionts retain …

Rapid Urbanization Reduces Genetic Diversity And Increases Genetic Differentiation Of A Lynx Spider Oxyopes Sertatus In Central Taiwan, Ying-Yuan Lo, Chi Wei, Wan-Jyun Chen, Chung-Ping Lin

Biological Sciences Faculty Publications

Urbanization is a dominant force driving destructive and irreversible changes of natural habitats in modern times. While the effects of urbanization on community composition and phenotypic responses are well-documented, its influence on genetic diversity and population structure remains understudied, particularly for invertebrates in subtropical regions. This study tested the hypothesis that urbanization reduces genetic diversity and increases population differentiation in the lynx spider Oxyopes sertatus, a common foliage-dwelling spider in Taiwan. We sampled 245 individuals from 17 sites distributed along an urban-rural gradient and quantified urbanization intensity using land-use composition at both landscape (4 km²) and local (0.25 km²) …

Ovarian Cancer Immunology And Immunotherapy: Editorial Note, Chris D. Platsoucas

Biological Sciences Faculty Publications

[Introduction] As the guest editor of the Special Issue on Ovarian Cancer Immunology Immunotherapy, I would like to include certain brief comments on the current state of the field and to introduce the Special Issue. Ovarian carcinoma and malignant melanoma are the first human tumors where immune responses, primarily restricted to autologous tumor cells, were first demonstrated. T-cell lines and clones developed in recombinant interleukin-2 (rIL-2) from tumor-infiltrating lymphocytes (TIL) from these tumors exhibited cytotoxicity and/or cytokine production, primarily restricted to autologous tumor cells. The T-cell receptor (TCR) and the CD3 differentiation antigen on effector T cells and HLA on …

Microarray Analysis Of Human Abdominal Aortic Aneurysm With Emphasis On Cardiovascular Genes Revealed Differentially Expressed Genes, Song Lu, Li Ping Li, John V. White, Xiaoying Zhang, Ifeyinwa Nwaneshiudu, Adaobi Nwaneshiudu, Nectaria Ntaoula, John Gaughan, Dimitri S. Monos, Wan-Lu Lin, Charalambos C. Solomides, Emilia L. Oleszak, Chris D. Platsoucas

Biological Sciences Faculty Publications

Background/Aim: We examined gene expression profiles in abdominal aortic aneurysm (AAA) lesions vs. normal aortas by cDNA microarray and real-time quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR).

Materials and Methods: Phosphorus (32P)-labeled cDNA from AAA specimens (mean AAA size 6.65 cm) and normal aortas were hybridized with a 588-gene microarray primarily of the cardiovascular system. The results were validated by qRT-PCR.

Results: A total of 35 out of the 588 genes were differentially expressed, with either log2 ratio of AAAs/controls ≥1 (upregulated; 20 genes) or ≤−1 (downregulated; 15 genes) in AAA lesions vs. normal aorta, and 25 of these were significantly …

Evaluating Species At Risk In Data-Limited Fisheries: A Productivity-Susceptibility Analysis For Marine Aquarium Fish, Gabrielle A. Baillargeon, Alice A. Wynn, Jemelyn Grace P. Baldisimo, Michael F. Tlusty, Andrew L. Rhyne

Biological Sciences Faculty Publications

The marine aquarium trade (MAT) is a significant global industry harvesting millions of wild-caught, live coral reef fishes for public and private aquaria markets in the United States and Europe annually, while supporting fisher livelihoods in the Indo-Pacific. This diverse and species-rich trade is considered data-limited, creating barriers to quantifying the current and future socio-ecological sustainability of the fishery. We present a revised and expanded productivity–susceptibility analysis (PSA) that serves as a holistic risk assessment to estimate the vulnerability of marine aquarium fish to overfishing. Our global analysis includes 306 species that are actively in trade. Improvements to the PSA …

Challenging And Diagnosing Structured Population Models By Testing Predictions From Stochastic Demography, Stephen P. Ellner, Robin E. Snyder, Daniel T. Blumstein, Dylan Z. Childs, Joshua C. Fowler, Christina M. Hernández, Julien G. A. Martin, María Paniw, Yngvild Vindenes

Biological Sciences Faculty Publications

1. Structured population models are parameterized to accurately project expected population sizes, stage/state distributions and population growth rates, but they also predict the variation in outcomes among individuals, such as the variance and skewness of lifetime reproductive output (LRO) and lifespan, the probability of never reproducing, and many other life-history metrics.

2. Testing such predictions about individual outcomes can be very useful model 'stress tests', because they depend on how components of the model (e.g. submodels for survival and fecundity) interact over multiple time steps, not just on the accuracy of the submodels. Because data on among-individual variation is rarely …

Leveraging Cross-Reactivity For Dual Serological Detection Of Closely Related Schistosoma Species, Oyetunde T. Oyeyemi, Lisa M. Shollenberger

Biological Sciences Faculty Publications

Schistosomiasis is a disease of poverty that is highly prevalent in Sub-Saharan African countries. Cross-reacting proteins in Schistosoma mansoni (Sm) and S. haematobium (Sh) have been reported to pose diagnostic challenges. Proteins from these two parasites may help overcome diagnostic limitations caused by cross-reactivity and poor species discrimination in serological assays. The study aims to identify cross-reacting protein markers from S. mansoni and S. haematobium for possible concurrent diagnosis of the two parasites. High-quality protein extracts were prepared from the eggs (soluble egg antigen, SEA) and adult worms (Schistosoma worm antigens preparation, SWAP) of S. haematobium and S. mansoni …

Dual Language Learner Status In Relation To Cortisol For Children In Head Start Preschool, Keala Bratsch

West Chester University Graduate Theses, Dissertations, and Final Projects

Early childhood education (ECE) has well documented school readiness benefits, especially for children facing economic hardship. Yet preschool context poses challenges that are associated with elevated stress levels and potential long-term tax on physiological systems that respond to stress. The present study examined dual language learner (DLL) status in relation to levels of the stress hormone cortisol among low-income children attending Head Start Preschool programs. Participants included 207 children ages 3- 5 years who attended preschool in 2021-22 (60.9% attending a dual-language learning school, 39.1% attending an English-instruction-only preschool; all participants meeting the criteria for low-income), and their parents or …

Using Genetic Analysis To Infer Familial Relationships Of Westslope Cutthroat Trout In The Lower Priest River, Idaho, Kolby Emtman

EWU Masters Thesis Collection

The Westslope Cutthroat Trout (Oncorhynchus lewisi) is a native species of salmonid that holds both cultural and ecological significance in the Idaho Panhandle region of the United States. Within this region, the Priest River is a major contributor of migrant Westslope Cutthroat Trout to the Clark Fork Pend Oreille basin. This study aimed to estimate the proportion of juveniles that have at least one migrant parent, illustrate gene flow using juvenile half sibling relationships, and showcase varying levels of spawning success using juvenile full sibling relationships. Sampling of juvenile individuals occurred in 11 tributaries of the Priest River over …

Assessing Forest Health And Small Mammals After A Limited Suppression Wildfire In Colville National Forest, Samantha J. Kennel

EWU Masters Thesis Collection

In the face of a wildfire crisis, there is a growing need to expand the pace and scale of forest treatments, including the strategic use of wildfire as a management tool. However, ecological outcomes remain uncertain in forests shaped by more than a century of fire suppression. The 2022 Thor Fire, a managed wildfire in the Colville National Forest, Washington, provides an opportunity to evaluate forest health in a relatively understudied system. Using a control–impact design, I established 100 monitoring plots in burned and adjacent unburned forests to assess how wildfire and fire severity influence forest structure, fuels, and tree …

Molecular Detection Of Campylobacter Spp. In Filth Flies Associated With Broiler Breeder Facilities In Oklahoma And Arkansas, Allen Szalanski

Entomology and Plant Pathology Faculty Publications and Presentations

Adult filth flies (Diptera: Muscidae) (non-biting flies that develop in decaying organic matter) are abundant in poultry facilities and may contribute to the dissemination of pathogenic Campylobacter spp. among flocks. We sampled adult house flies, Musca domestica L., and black dump flies, Hydrotaea aenescens (Wiedemann), at five broiler-breeder farms in Oklahoma and Arkansas to determine the prevalence of Campylobacter spp. vectored by filth flies and the effects of farm, fly species, and location (inside vs outside houses) on the rates of Campylobacter spp. occurrence. A total of 1,076 house flies and 1,008 black dump flies were collected inside and outside …

Predicting Oil Contamination In Water Using Machine Learning On Microbial Compositions, Tong Gao, Isaac Bigcraft, Stephen Techtmann, Issei Nakamura

Michigan Tech Publications

We present a compact and generative machine-learning framework that predicts oil contamination based on microbial community compositions from experimental samples. Our method combines dimensionality reduction with data augmentation and generative modeling to address high-dimensional, non-linear, and sparse microbial data. To reduce the 503-dimensional bacterial composition dataset, we compared three dimensionality reduction techniques: feature importance from random forest, principal component analysis (PCA), and t-distributed stochastic neighbor embedding (t-SNE). Feature importance outperformed PCA and t-SNE, improving predictive performance and identifying microbial species most strongly correlated with oil contamination. To mitigate data scarcity, we augmented the training data using an augmented data neural …

Modeling Inherited Retinal Disease In Zebrafish, Meet Patel

Theses and Dissertations--Biology

Inherited retinal diseases (IRDs) affect millions of people worldwide. Majority of IRDs are caused by degeneration of rod and cone photoreceptor cells (PRCs) due to gene mutations. The overarching goal of my dissertation is to model and evaluate the molecular role of various gene candidates involved in IRDs such as cone rod dystrophy (CRD) and retinitis pigmentosa (RP).

Mutations in CDHR1, a photoreceptor specific cadherin have been associated with CRD and recapitulated in mouse CDHR1 knockouts. However, the molecular function of CDHR1 remains unknown. CDHR1 has been shown to localize at the leading edge of murine rod nascent outer segment …

Kentucky Bluegrass (Poa Pratensis L.) As A Perennial Groundcover: Establishment And Weed Management In Corn, Kiera S. Searcy

Theses and Dissertations--Plant and Soil Sciences

Perennial groundcover (PGC) systems offer a cost-effective alternative to annual cover crops, by providing continuous soil cover, reducing soil erosion, and contributing to integrated weed management (IWM) in corn (Zea mays L.) production systems. Kentucky bluegrass (Poa pratensis L.) has been proposed as a perennial groundcover for corn due to its low growth habit and seasonal dormancy; however, successful adoption is limited by challenges associated with establishment-phase weed competition and compatibility with weed management programs during corn production. The objectives of this research were to (1) evaluate weed management strategies that support Kentucky bluegrass establishment and (2) assess …

Integrated Crop Management For Hemp (Cannabis Sativa L.) Grain Production In Kentucky, Maria M. Ricciardi

Theses and Dissertations--Plant and Soil Sciences

Cannabis sativa L. is legally defined (U.S.) as hemp if the total tetrahydrocannabinol (THC) concentration remains less than 0.3% on a dry weight basis. Hemp can be produced for cannabinoid extraction, fiber, or grain. Hempseed meal and hempseed oil were approved as feed ingredients for chickens and performance horses in Kentucky. To leverage this opportunity, production requires improvement through an integrated crop management approach. This dissertation (1) reports the main arthropod and disease pests impacting hemp grain; (2) identifies grain yield components and their relationship with corn earworm, Helicoverpa zea (Boddie) (CEW); (3) evaluates Fusarium head blight (FHB) development across …

Breeding For Fhb Resistance And Post-Harvest Quality In Soft Red Winter Wheat, Margaret E. Gillum

Theses and Dissertations--Plant and Soil Sciences

Soft red winter wheat (Triticum aestivum L.) is both an economically and nutritionally important crop in the global food supply. Despite its global importance, wheat is continually threatened by fungal diseases. Fusarium head blight (FHB), caused by Fusarium graminearum, is a devastating fungal disease affecting wheat worldwide, resulting in low yields, reduced test weight and mycotoxin production. The mycotoxin deoxynivalenol (DON) is toxic to humans, results in feed rejection in livestock, and is heavily monitored in the food supply. Because of wheat’s importance in the food system, post-harvest quality (milling, baking, and flavor) has been a growing area of …

Evaluating Spatial Variability Of Corn Yield Response To Phosphorus Fertilizer For Improved Precision Phosphorus Management, Jennifer Fridgen

Theses and Dissertations--Plant and Soil Sciences

Soil scientists did not develop soil test-based fertilizer recommendations to support precision nutrient management. Knowledge of crop responses to applied essential nutrients, such as phosphorus (P), and the processes governing these responses at high spatial resolution are necessary to improve precision agronomic recommendations. This dissertation investigates the limitations of current soil sampling methodologies and recommendation frameworks for crop response to fertilizer, with particular emphasis on P fertility in Kentucky (KY) corn production. The first study examined the relationship between the resolution of systematic grid sampling and the spatial structure of soil test variables (Mehlich-3 P (M3P), Mehlich-3 potassium (M3K), and …

Table Of Contents

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

The Biology Of Soulmates: Are We Wired For Connection?, Christiane Betfarhad

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

Light At The Wrong Time, Alexis Murdock

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

Your Brain's Favorite Cheat Code: The Neuroscience Of Self-Affirmation, Maeve Mclaughlin

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

The Silent Architecture Of A Lifetime: How Early Endocrine-Disrupting Chemical Exposure Rewrites The Developing Brain, Becca Gwynne

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

Dancing To The Rhythm: How To Coordinate Parkinson's Movement, Denil Joseph

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

Think It, Believe It, Receive It, Angelia Nguyen

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

Robots Are Watching You Sleep: The Hidden World Of Sleep Trackers, Luke Latterman

Scientific Kenyon: The Neuroscience Edition

No abstract provided.