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Evaluation Of The Global Durum Panel (Triticum Turgidum Ssp. Durum) For Wheat Streak Mosaic Virus Resistance, Winter Survival, And Seed Characteristics, Megan Engel

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

The majority of durum wheat (Triticum turgidum spp. durum; AABB; 2n=4x=28) is predominantly grown in the northern Great Plains of the United States, and is used in the production of semolina, a coarse flour that makes pasta and couscous. Durum has been widely regarded for being more tolerant to abiotic stress, due to its ability to withstand drought and high temperatures. In this thesis, we conducted greenhouse, field, and lab studies, for the traits wheat streak mosaic virus (WSMV), winter survival, and single kernel characteristics of the Global Durum Panel version 2 (GDPv2 n = 976), a panel …

Herbicide Management For Bromus Tectorum To Enhance Rangeland Productivity In Western Nebraska, Miranda Mueller

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Cheatgrass, Bromus tectorum (L.), has increased in the mixed-grass prairies of the Nebraska Panhandle. Limited research is available in these ecosystems on the ecological factors that influences its spread and options for management. This study focuses on the efficacy of herbicide treatments (indaziflam and imazapic) as a cheatgrass control method on the native rangelands of western Nebraska. In September of 2022, a mixture of indaziflam (73 g ai ha^-1, Rejuvra) and imazapic (70 g ai ha^-1, Plateau) was aerially applied at 6 unique upland ecological sites (1-3 ha) near Scottsbluff, Nebraska. Functional group plant biomass data …

Genetic And Soil Influences On The Grapevine Rhizosphere Microbiome, Lauren M. Quackenbush

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

In vineyard cropping systems, the rhizosphere microbiome arises through recruitment and filtering of the bulk soil microbiome shaped over time by soil carbon and nitrogen, climate, pH and historical legacies of vineyard management. The recruitment and filtering steps occur under the genetic influences of rootstock and scion that together drive variability in rhizosphere microbiome diversity and composition.

This study compares rhizosphere microbiomes of four Pinot Noir blocks under two rootstocks (101-14 and 420A) and four scions (777, 828, Calera, Mt. Eden). Core microbiomes were consistent across all replicates. The most abundant bacterial phyla were Actinobacteriota, Proteobacteria, and Acidobacteriota …

Soluble Cd13 Is A Potential Mediator Of Neutrophil-Induced Thrombogenic Inflammation In Sars-Cov-2 Infection, Pei-Suen Tsou, Ramadan A. Ali, Chenyang Lu, Gautam Sule, Carmelo Carmona-Rivera, Serena Lucotti, Yuzo Ikari, Qi Wu, Phillip L. Campbell, Mikel Gurrea-Rubio, Kohei Maeda, Sharon E. Fox, William D. Brodie, Megan N. Mattichak, Caroline Foster, Ajay Tambralli, Srilakshmi Yalavarthi, M Asif Amin, Katarina Kmetova, Bruna Mazetto Fonseca, Emily Chong, Yu Zuo, Michael D. Maile, Luisa Imberti, Arnaldo Caruso, Francesca Caccuri, Virginia Quaresima, Alessandra Sottini, Douglas B. Kuhns, Et Al

School of Medicine Faculty Publications

The soluble variant of the ectopeptidase CD13 (sCD13), released from the cell surface by matrix metalloproteinase 14 (MMP14), is a potent pro-inflammatory mediator, displaying chemotactic, angiogenic, and arthritogenic properties through bradykinin receptor B1 (B1R). We revealed a link between sCD13 and amplified neutrophil-mediated inflammatory responses in SARS-CoV-2 infection. sCD13 was markedly elevated in patients with COVID-19 and correlated with disease severity and variants, ethnicity, inflammation markers, and neutrophil extracellular trap formation (NETosis). Neutrophils treated with sCD13 showed heightened NETosis and chemotaxis, which were inhibited by sCD13 receptor blockade. Meanwhile sCD13 did not induce platelet aggregation. Single-cell analysis of COVID-19 lungs …

A Diatom Voucher Flora For The Pierce Ponds, Olivia Sandman

Honors Projects

Diatoms are a diverse group of microalgae with silica cell walls that produce ~ 25% of the Earth's oxygen. Due to their diversity and sensitivity to changes in water quality, diatoms are often used to monitor aquatic ecosystems. One such ecosystem is the Pierce Ponds, a series of small, constructed wetlands located southwest of the GVSU campus that were designed to limit erosion and remove contaminants from runoff and precipitation before entering the Lower Grand River Watershed. To explore the diatom populations of these ponds, we created a voucher flora to document the taxa present. In November, algal samples were …

Comparing Subjective Versus Objective Measures Of Sleep, Anusha Mukherjee, Katherine C. Ward, Justin Thomas

Expo Student Presentations

2025 Spring Expo Poster Presentation

• Biological & Life Sciences

Impact Of Diet Quality And Functional Food (Honey) On Gut Microbiota And Metabolic Health In Obesity, Sarah M. Eaton

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Understanding the impact of dietary patterns and functional foods on human health is crucial for the advancement of evidence-based nutrition choices. This dissertation investigates the effects of three a priori-defined healthful dietary patterns as well as a functional food, specifically Manuka honey, on gut health and metabolic markers in individuals with overweight and obesity. Two studies were conducted to explore these relationships. The first study, a post-hoc, cross-sectional analysis, compared the effects of three healthful dietary patterns: Healthy Eating Index-2010 (HEI-2010), Dietary Approaches to Stop Hypertension (DASH), and Mediterranean Dietary Pattern (MDP) on markers of intestinal permeability and gut microbiota …

Dental Disparities: An Analysis Of Dental Caries Risk Factors Promoting Disparities Between Rural And Urban Communities In Nebraska, Nick Lounsbery

Honors Program: Senior Projects (Public)

The prevalence of dental caries in the United States remains a public health concern, as it is one of the most common chronic conditions across people of all ages. Research shows that preventative measures including brushing, fluoridated water, and regular checkups are effective strategies to mitigate tooth decay. However, there appears to be a divide between rural and urban populations, as the presence of dental cavities is significantly greater in remote areas in the State of Nebraska. Research methods used in this analysis included analyzing accredited academic literature to illustrate how cavities form from a biochemical perspective. Research methods also …

Conservación Biológica Harakbut: Estudio De Caso Ori’Numba, Anya Held

Peru: Indigenous Peoples and Globalization

Through interviews, observations, and bibliographic research, this project investigates the Indigenous-based conservation project of Ori’Numba Garden. In 2018, the Tayori family moved to Ori’Numba and began transforming it from a former livestock farm into a holistic conservation project. The paper details the history of Ori’Numba and the process of its creation, the modern and traditional agricultural techniques used in the garden, a register of the pineapple and native bee species, and some of the relevant Harakbut mythology. Ori’Numba clearly demonstrates that there is Indigenous conservation biology, not just “indigenized” Western conservation biology.

Comparative Mechanical And Elastic Properties Of The Dorsal And Ventral Tendons In The Peduncle Of Harbor Porpoise (Phocoena Phocoena), Alexa R. Cesari, Jesse K. Placone, Nicole L. Ramo, Michael V. Rosario, Matthew Morris, Danielle S. Adams, Frank E. Fish

Biology Faculty Publications

Cetaceans swim via vertical movements of the tail. The tendons located in the caudal peduncle are attached to the caudal vertebrae to generate propulsive oscillations. Arguments have centered on whether the upstrokes and downstrokes of the tail and propulsive flukes are symmetrical or asymmetrical in time. Previous research from kinematics of swimming animals, muscle architecture and histology has supported both conditions. However, the composition and structure of the tendons suggest a potential mechanism to evaluate this disparity. In this study, the tendons of the caudal peduncle of the harbor porpoise (Phocoena phocoena) – specifically, the extensor caudae medialis …

Defective Sickle Cell Mutations, Elaine Vanterpool, Carroline Anderson

Student Posters

Sickle cell disease (SCD) is a group of inherited red blood cell disorders. It is an inherited hemoglobinopathy. Both alleles must be affected to manifest the disease. In sickle cell disease, the red blood cells become hard, sticky, and look like a sickle, making it difficult to pass through the blood vessels and carry oxygen. Sickle cell trait is more prevalent than sickle cell disease and affects 1 in 13 African American babies (According to the CDC). The clinical manifestation of sickle cell trait is not as aggressive and does not cause as much morbidity as sickle cell disease. This …

Automated Plant Morphological Assessment And Microbial Community Monitoring In Simulated Lunar Regolith, Collin R. Topolski

Doctoral Dissertations and Master's Theses

Upcoming lunar bases will need to leverage in-situ resources to ensure long-term sustainability and reduce mission costs. One key challenge is food production, which could be addressed by growing crops in lunar regolith-based substrates. However, lunar regolith lacks essential nutrients, requiring organic amendments to support continuous plant cultivation. This study examined the impact of manure-amended lunar regolith simulant on Mizuna mustard growth while assessing microbial community diversity and functionality. To support this effort, a custom software pipeline utilizing an open-source library, PlantCV, was developed to automatically track plant leaf area and height via image analysis. Results indicated that amended rhizosphere …

“Seeing Someone Like Me Succeed Made Me Believe I Could Too!”: Evaluating The Big-Sib & Little-Sib Mentorship Program At Swarthmore College, Lina Verghese , '25

Senior Theses, Projects, and Awards

This thesis evaluates the Bio Big Sib & Little Sib Mentorship Program in Swarthmore College’s Biology Department, a student-led initiative supporting racial/ethnic minority and first-generation, low-income (FLI) students. Launched in 2021, the program pairs upperclassmen with underclassmen to offer guidance, build community, and affirm student identity within a predominantly white, elite academic environment. Using a mixed-methods approach, combining qualitative interviews and survey data, this study examines the program’s effectiveness and long-term impact on student belonging, academic navigation, and identity development. Findings reveal that the program has become a vital support structure, helping participants access the “hidden curriculum” and fostering emotional …

Host Range And Efficiency Of Plating Determination Of Phages Infecting Caulobacter And Non-Caulobacter Species, Christopher Scott

Senior Theses

Seven bacteriophages were studied to determine their host range among Caulobacter and non-Caulobacter bacteria. Recently, Caulobacter-associated phages have been shown to have broader host ranges than previously believed. Thus, it is crucial to thoroughly verify the range of bacteria strains that these phages can infect. To understand the extent of each phage’s host range, phage lysates were spotted on bacterial lawns to determine whether lysis could occur. Host-range analyses in this project conclude that these Dolichocephalovirinae phages were able to infect multiple genera and species of host bacteria. Plating efficiency experiments were also conducted to compare the phage’s …

Neutrophil Inflammatory Death Regulation By Bacterial Type Iii Secreted Effectors, Arianna D. Reuven

Dartmouth College Ph.D Dissertations

Yersinia and Pseudomonas use a T3SS to secrete effectors into host cells that inhibit phagocytosis and modulate immune responses, such as inflammasome activation. Inflammasomes promote the activation of the proinflammatory protease caspase-1. The activation of an inflammasome sensor in response to a signal or ligand initiates the assembly of the inflammasome leading to activation of caspase-1 which cleaves GSDMD and pro-inflammatory cytokines IL-1β and IL-18 into their mature forms. As neutrophils are recruited in large quantities to sites of infection, they are excellent candidates to drive inflammasome dependent responses. Neutrophils have been shown to produce multiple inflammasomes, like pyrin and …

Llm-Ie: A Python Package For Biomedical Generative Information Extraction With Large Language Models, Enshuo Hsu, Kirk Roberts

Faculty, Staff and Student Publications

Objectives: Despite the recent adoption of large language models (LLMs) for biomedical information extraction (IE), challenges in prompt engineering and algorithms persist, with no dedicated software available. To address this, we developed LLM-IE: a Python package for building complete IE pipelines.

Materials and methods: The LLM-IE supports named entity recognition, entity attribute extraction, and relation extraction tasks. We benchmarked it on the i2b2 clinical datasets.

Results: The sentence-based prompting algorithm resulted in the best 8-shot performance of over 70% strict F1 for entity extraction and about 60% F1 for entity attribute extraction.

Discussion: We developed a Python package, LLM-IE, …

Barriers In Receiving A Diagnosis Of Sanfilippo Syndrome: Perceptions From Healthcare Providers And Caregivers, Cassidy Lena

Theses and Dissertations

Sanfilippo syndrome (MPS III) is a rare, degenerative condition characterized by symptoms impacting neurological functioning, behavior, and quality of life. Diagnosis is often not made until three to six years of age, but comprehensive and effective symptom management have been reported to optimize patient longevity. The aim of this study was to identify barriers to diagnosis and the corresponding impact on patients. This study surveyed healthcare providers and caregivers of individuals with Sanfilippo syndrome. Both quantitative and qualitative methods were employed to assess provider knowledge and comfortability in managing Sanfilippo syndrome. Additionally, it explored caregiver perspectives on healthcare system navigation, …

Investigation Of The Effects Of The Peptidylarginine Deiminase Inhibitor Cl-Amidine On Apoptosis And Gene Expression In Ovarian Cancer, Victoria Walden

Longwood Senior Thesis Proposal

Peptidylarginine deiminases (PADs) are a family of enzymatic proteins responsible for the conversion of arginine and methylarginine residues to citrulline. This conversion is important for several key cellular processes including transcriptional gene regulation. Recently, a link has been established between overexpression of a particular PAD, PAD4, and the accelerated progression of both autoimmune diseases and cancers. Ovarian cancer exhibits heightened levels of PAD4 in affected cells. High levels of PAD4 are associated with the formation of neutrophil extracellular traps (NETs) that promote cancer metastasis, and downregulation of the p53 apoptotic pathway. Thus, it is important to explore inhibitors of PAD4. …

Eating The Fat Of The Land: The Work Of Coxiella Burnetii To Traverse Intracellular Lipid Landscapes, Charlie Porto

Theses & Dissertations

Coxiella burnetii is an obligate intracellular pathogen and the causative agent of Q fever in humans. With primary hosts in livestock ruminants, C. burnetii is endemic globally, presenting significant health risks to agricultural workers and herd health at large. Numerous wild animal reservoirs exist, increasingly threatened by expanding livestock ranges. Furthermore, with a low infectious dose through aerosol transmission, the CDC considers C. burnetii a potential bioweapon, though in humans a large amount of infections persist subclinically, occasionally progressing to pneumonia and hepatitis with chronic infections leading to endocarditis.

The parasitic life cycle of C. burnetii is biphasic, a small …

College Of Natural Sciences Newsletter, Spring 2025, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Page 1 Dean's Message from Dr. Sen Subramanian
Page 2 Student Spotlights
Page 3 Kaushik honored, Three-Minute Thesis, & Ice Cores revealed
Page 4 Alumni Spotlight
Page 5 Day of Scholars
Page 6 Cyanide research, Record Research Expenditures, Adhikari awarded Miller Research Award
Page 8 Hanson Receives NSF Grant
Page 9 Snow Lab Research Team
Page 10 Faculty Awards
Page 11 Drone Day
Page 13 Khalaf Awarded Presidential Award

Playful Paws: Are There Sex Differences In Playfulness With Freshwater Otters?, Julianne Pena

Posters - 2025

Personality is crucial for understanding the lives of species because it affects how they survive, the way they move, reactions to diseases, and much more (Merrick & Koprowski, 2017; Wolf & Weissing, 2012). The importance of this research is to understand how biological sex may interact with otter personalities through social interactions amongst other otters, the physical world, and humans. Female and male otters vary in the way that they play, with males playing more rough than females (Green, 2000). Play, which is associated with rock juggling, decreases as otters mature (Alliston et al., 2020). Females used object play more …

Seasonal Changes In Gene Expression Of The Three Estrogen Receptor Subtypes In The Atlantic Croaker, Micropogonias Undulatus, Elena Mares

Posters - 2025

Vertebrates have multiple estrogen receptor (ER) subtypes which facilitate transcriptional activity of genes when activated by estrogenic ligands. Teleost fish have 3 distinct estrogen receptor subtypes, including ERα, ERβ, and a unique type, ERγ. Each subtype has a different binding affinities to many estrogenic compounds, but their subsequent transcriptional regulatory mechanisms are not wellknown1. The focused species of the project is Micropogonias undulatus, the Atlantic Croaker.

Offering Alternatives To Biblical Literalism May Be The Key To Increasing The Public’S Acceptance Of Evolution, Jamie Jensen, Dalton Bourne, Kenneth Harrington, Grant Rousseau, Jessica Abele, Daniel Ferguson

ScholarsArchive Data

These are data from two cohorts: a nationwide dataset, and a BYU-specific student dataset. We gathered information on evolution acceptance (using the I-SEA), biblical literalism (using the EALS) and religiosity (using the Sethi and Seligman instrument).

Is Less More, Or More Better? Behavioral Insights From Bottlenose Dolphins During Dolphin Interaction Programs, Megan E. Davis, Alicia Virthe, Heather Manitzas Hill, Kathleen Dudzinski, Michelle Samm, Buck Lyman, Kelly Flaherty Clark, Todd Robeck

Posters - 2025

This poster was created for the 5th annual Research Showcase. From the poster:

Using video recordings collected during randomly selected human-dolphin interaction programs (2022-2023), 19 target dolphins were assessed for their behavioral repertoire, correct and incorrect responses to trainer/guest-given cues, and the total number of unique requested behaviors.

Obstacles And Opportunities In Marine Mammals Care And Welfare: Insights From Trainers, Alicia Virthe, Heather Manitzas Hill, Sabrina Brando

Posters - 2025

This poster was created for the 5th annual Research Showcase. From the poster:

The aims of the study included:

Identifying obstacles faced by caregivers

Exploring beliefs hindering the promotion of animal care and welfare

Highlighting the opportunities that caregivers perceive to maintain and enhance animal welfare and care

Do Otters Remember What They Solved? Manyotters - Collaborative Science, Manyotters, Heather Manitzas Hill, Deirdre Yeater, Caroline M. Delong, Catina Wright, Emily Langdon, Lisa Halstead

Posters - 2025

This poster was created for the 5th annual Research Showcase. From the Poster:

The ManyOtters group seeks to promote studies with larger sample sizes and a variety of species of otters, while developing a collaborative network of scientists. ...

Our initial project focuses on long term memory in otters.

For more information about ManyOtters please visit

https://manyotters.github.io/

Many Otters Project - Coding Analysis Of Otter Behavior With Foraged Puzzles, Isaiah Charles, Andres Vega

Posters - 2025

The study of long-term memory and the cognitive abilities of otters is not extensively documented. This research consisted of the use of foraging puzzles, which are different containers with food inside such as fish, squid, and oysters. This research project, named ManyOtters, takes inspiration from the foraging puzzle techniques exhibited in separate studies (e.g., Saliveros et al., 2022; Ladds et al. 2017). Based on the studies, foraging puzzles have shown to draw engagement for several otter species. The species focused on in this study were Asian small-clawed otters (Aonyx cinereus) and African spotted-necked otters (Hydrictis maculicollis) housed at SeaWorld San …

Market Structure Evolution In The U.S. Automobile Industry: A Review Of Diversity And Concentration Metrics, P.V. (Sundar) Balakrishnan

AMTP Proceedings 2025

I examine the evolution of market structure in the U.S. automobile industry from 1937 to the present, focusing on the application of both traditional and novel diversity and concentration metrics. I use the Herfindahl-Hirschman Index (HHI), Comprehensive Concentration Index (CCI), and newer metrics from fields such as ecology and genetics to uncover insights into the shifting dynamics of market power, firm turnover, and industry stability. The U.S. automobile industry, characterized by consolidation and technological advancement, provides a unique case study for analyzing long-term market evolution. I contribute to the literature by synthesizing a broad range of diversity metrics and offering …

Understanding How Chaperones Influence Protein Aggregation, Hannah Buchholz

Dissertations (1934 -)

Cells depend on properly folded proteins to function and remain healthy. If proteins adopt a nonnative conformation, they may have an increased propensity to clump together or aggregate, which can compromise cell viability. Unwanted aggregates are linked to a class of diseases called proteinopathies, which include fatal disorders such as Alzheimer’s disease and amyotrophic lateral sclerosis (ALS). Fortunately, cellular factors, known as molecular chaperones, help maintain protein homeostasis by limiting and disassembling protein aggregates. However, the mechanisms that underlie how chaperones modify protein aggregation are poorly understood. The goal of this dissertation is to explore the molecular mechanisms used by …

Ecological Studies Of Wolves On Isle Royale, Sarah R. Hoy, John A. Vucetich, Rolf O. Peterson

Ecological Studies of Wolves on Isle Royale

Annual Report 2024-2025