Biology Commons^™

Effects Of Common Herbicides On Organismal Interactions, Robert Chamberlin

All Theses

Pesticides are applied to agricultural lands to prevent undesirable weeds, animal pests, and fungi from harming crops and reducing crop yields. Pesticides are used in croplands at increasing rates around the world and have become an essential component of farming in recent decades. Often, rain, wind, and soil permeation move pesticides from farmlands to natural environments. Such contamination of natural environments by pesticides may threaten species by altering their behaviors, bodily functions, and the ways in which individuals interact. Atrazine and glyphosate are among the most widely used herbicides around the world and are useful in eliminating weeds, primarily in …

Engineering An In Vitro Hipsc-Derived Cardiac Tissue Construct For Regenerative Medicine Applications, Larry Mendoza

Electronic Theses, Projects, and Dissertations

Cardiovascular disease is the leading cause of mortality across the world with invasive surgeries and pharmaceutical intervention commonly associated with urgent care. Moreover, congenital, progressive, and hereditary heart diseases rely on many forms of medical prevention and intervention (pharmaceuticals, x-rays, bloodwork, etc.). Developing a three-dimensional (3D) cardiac tissue engineered in vitro model to study human cardiac physiology can revolutionize biomedical research. The purpose of this research is to optimize natural & synthetic biomaterials to fuse cardiac stem cells and synthesize a 3D-printed in vitro model for disease modeling, drug delivery, and regenerative medicine. Natural biopolymers needed for such innovations are …

Passive Electronic Cigarette Exposure Initiates Squamous Metaplasia In A Developing 3d Human Tracheobronchial Epithelial Tissue In-Vitro Model, Edgar Rolon

Electronic Theses, Projects, and Dissertations

The prevalence of vaping has rapidly increased. ECs are often perceived as less harmful than tobacco cigarettes. A recent meta-analysis showed electronic cigarette (EC) aerosols adversely affected the respiratory system, similar to cigarette smoke, with some effects specific to EC use. Failure to prevent these alterations could lead to life-long comorbidities, and predisposition to respiratory diseases, including COPD and squamous cell carcinoma. While these effects are the result of active vaping, EC aerosols can also settle on indoor surfaces, be absorbed passively through the skin or orally, enter the blood stream, and subsequently expose internal organs, including the airway basal …

Ghosts In Glass: Ghost Crabs As Judges Of Glass Sand For Coastal Restoration, Emily Parrish

Honors Theses

Over 60% of the Gulf of Mexico coastline is actively eroding, which has resulted in thousands of miles of lost coastline over the last 100 years. This drastic loss of coastal land highlights the dire need for coastal restoration across the entirety of the Gulf Coast. A vital aspect of restoring these eroded areas is replenishing eroded substrate, traditionally conducted through offshore dredging of substrates which comes with high economic and ecological costs. Recycled glass sand may be able to fill this role and reduce our reliance on dredging while lowering the amount of glass waste entering landfills each year. …

Antimicrobial Peptides Improve Antibiotic-Mediating Killing Of Methicillin-Resistant Staphylococcus Aureus (Mrsa) Biofilms, Alya R. Theriault

All Theses And Dissertations

Staphylococcus aureus can cause drug-resistant, biofilm-associated infections. These infections place methicillin-resistant S. aureus (MRSA) as one of the sixth leading bacterial pathogens associated with deaths due to antimicrobial resistance. Traditional antibiotics are no longer enough to treat these resistant infections and novel therapeutics are needed. Antimicrobial adjuvants are a potential strategy for improving efficacy of existing antibiotics, and antimicrobial peptides (AMPs) may have adjuvant activity. Recent reports showed that AMPs improve antibiotic activity against planktonic staphylococci, but whether AMPs might alter antibiotic efficacy against biofilm-resident staphylococcus is less clear. We tested the effect of nine AMPs on staphylococcal biofilm susceptibility …

The Impact Of Emdr Therapy On Past Suicidal Ideation: Lived Experiences Of Young Adults, Lindsey Faehnrich

Undergraduate Honors Theses

This study explores the effectiveness of Eye Movement Desensitization and Reprocessing (EMDR) therapy in reducing suicidal ideation and improving mental health outcomes among college-attending young adults (ages 18–24) with a history of trauma. EMDR is a body-based psychotherapy designed to alleviate distressing thoughts and trauma. It gained attention for its positive impact on PTSD and has more recently been applied to other mental health disorders. The literature review highlights risk factors including trauma, mental health disorders, suicidal ideation, and EMDR. The methods detail a phenomenological approach, interviewing four young adults who underwent EMDR and experienced past suicidal ideation. This provided …

Whole-Genome Assembly And Annotation Of The Firecracker Penstemon (Penstemon Eatonii), David E. Jarvis, Mikel R. Stevens, Payton Carter, Ying Fei Lin, Kate E. Jaggi, Gabriela Jijon, Teal Kalt, Jouber Calixto, Samantha Standring, Kaitlin Torres, Kayla B. Stephensen, Hayley Mangelson, Noah H. Williams, Carolyn A. Wessinger, Peter J. Maughan, Paul B. Frandsen

Faculty Publications

The penstemons are ornamental annual flowering plants native to the Intermountain West and Rocky Mountains and commonly used for urban landscaping. Elite commercial penstemons are generally susceptible to abiotic stresses, including drought, root rot, cold, and high salinity. Firecracker penstemon (Penstemon eatonii), however, is much more tolerant to these stresses than most elite cultivars. Importantly, firecracker penstemon has been reported to hybridize with many other penstemons and therefore provides the opportunity to develop more tolerant elite cultivars through strategic crossing. To facilitate the study and utilization of firecracker penstemon, we sequenced and annotated the genome of a P. …

Unraveling Epigenetic Mechanisms That Regulate Breast Cancer Lung Metastatic Relapse By Rewiring The Immune Microenvironment, Jayanta Mondal

Dissertations and Theses (Open Access)

Metastasis accounts for >90% of cancer-related deaths and thwarting metastasis is widely considered to be the “Holy Grail” of cancer treatment. Breast cancer is the most common cause of cancer-related death among women and is characterized by its proclivity to spread to distant secondary organs like the lungs, and the brain. These disseminated tumor cells lie dormant at the secondary site and can undergo metastatic relapse. Epigenetic alterations are a predominant hallmark of cancer, however, its role in facilitating reawakening of dormant cancer cells and the subsequent metastatic relapse remains to be elucidated. To address this gap of knowledge, we …

Differential Progression Of Pancreatic Premalignancy In Geographically Distant Murine Transgenic Cohorts Uncovers Key Role Of Microbial Metabolites, Rian M. Howell

Dissertations and Theses (Open Access)

Cancer is a leading cause of death worldwide. Despite recent advances in diagnostic and therapeutic modalities, pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer that remains highly lethal. Efforts have been made to increase the understanding of the underlying mechanisms driving early stages of tumor development, when the cancer is most susceptible to intervention. To this end, genetically engineered mouse models (GEMMs) have been developed with the mutations most commonly seen in the patient population. Expression of these mutations in select cellular compartments has resulted in the ability to recapitulate characteristics of human pancreatic cancer such as the development of …

Physiological And Molecular Responses Of Diverse Rice Genotypes Under Drought Stress, Huda Mohmmed Alshaya

Graduate Theses and Dissertations

Climate change-induced drought stress is a significant constraint on global rice (Oryza sativa L.) production, threatening food security. This study evaluated the drought resilience of 15 diverse rice genotypes from the USDA mini-core collection under field, greenhouse, and osmotic stress conditions. Field trials assessed reproductive-stage drought tolerance based on panicle length (PL), number of spikelets per panicle (NSP), and spikelet sterility (SS). Greenhouse experiments examined moisture retention at the vegetative stage. Significant genotypic variation was observed, with genotypes 310724, 310779, 311181, 311603, 311793, and Vandana exhibiting drought tolerance through stable PL and SS. Additionally, genotypes 310100, 310428, 311255, N22, …

Impacts Of Reef Fish Length On Foraging Radius: Exploring Behavioral Patterns Within A Patch Reef Ecosystem, Kilia Brawand

Undergraduate Honors Capstone Projects

Reef fish exhibit various behaviors upon the Great Barrier Reef. One of these behaviors includes that of limiting their grazing distances from a patch reef refuge to a certain maximum distance in order to avoid predators. This is defined as a ‘foraging radius’ or ‘margin of safety’. This ‘foraging radius’ varies among fish due to many factors- including species, morphology, ontogenesis, habitat complexity, and importantly: speed. Quicker fish can outswim predators to safety more efficiently than slower fish, and can therefore afford to travel farther distances to forage. Speed varies among fish for a number of reasons, including fish size …

A Sex Comparison On The Effects Of Caveolin Scaffolding Domain On Fibrosis Formation After Chronic Sympathetic Stimulation, Crimsyn Price

Undergraduate Honors Theses

Cardiovascular disease (CVD) is the leading cause of mortality worldwide. There are various trends that influence the rates of cardiovascular disease in each country. Factors that create these trends involve diet, exercise, genetics, socioeconomic status, and geographical location. Additionally, CVD is typically higher in middle-income and lower-income classes. Hospital routes, rates of poverty, insurance policies, and lifestyle culture are all factors that can impact the time of treatment which in turn affect the rate of CVD. However, we explored in this study the shift in CVD women experience after menopause. Women were excluded from clinical trials until 1986, and the …

Investigating Self-Healing Mechanisms In Host-Pathogen Interactions: A Literature Review Of Macrophage Functions In Tuberculosis, Blessing Savusa

Open Access Theses & Dissertations

Tuberculosis (TB) remains a leading cause of mortality, particularly in underdeveloped regions. Mycobacterium tuberculosis (Mtb) is regarded as one of the most successful pathogens due to its ability to evade host immunity and persist within granulomas. Macrophages are the first-line host defenders that engulf Mtb into phagosomes, which initiates lysosomal activity for degradation. However, the virulence factor of Mtb is able to inhibit phagolysosome fusion. The host immune system forms granulomas to contain the mycobacterium at the site of inflammation. This, in turn, causes a necrotic state and causes tissue damage from the prolonged inflammation. Studies suggest that the host's …

Regulation Of Ccr7 Signaling Events By G-Protein-Coupled Receptor Kinases 2 And 3, Anahi Sanchez

Open Access Theses & Dissertations

G protein-coupled receptors (GPCR) can bind multiple ligands, leading to differential signaling events termed biased signaling. C-C chemokine receptor 7 (CCR7) is a GPCR known to have biased signaling between the two ligands it binds to, CCL19 and CCL21. Binding of C-C Chemokine Ligand 19 (CCL19) promotes a high level of CCR7 phosphorylation, while CCL21 leads to a much lower level of CCR7 phosphorylation; findings observed in HEK and dendritic cells. GPCR kinases (GRKs), which can control the phosphorylation patterns of a GPCR, are hypothesized to regulate biased signaling of a receptor. GRK expression differs between cell lines and cell …

Ghrelin And Decision-Making: Exploring Its Role In Food Reward, Novelty-Seeking, And Cost Valuation, Serina A. Batson

Open Access Theses & Dissertations

When low energy levels are detected, Ghrelin, a peptide hormone, is produced in the fundus of the stomach. Referred to as the "hunger hormone", Ghrelin is traditionally associated with increased food intake and blood sugar levels. A key modulator in the gut-brain interaction, Ghrelin's growth hormone secretagogue receptor can be found widely across the cortico-striosomal circuit. Critical for decision-making, Ghrelin-based manipulation of this circuit can directly affect reward and cost valuation. While Ghrelin is uniformly considered to increase the valuation of food-based rewards, little research has explored its impact on non-food-based rewards or its effects on cost valuation. Therefore, to …

Variation In Stress Response Regulation Across Natural Isolates Of Saccharomyces Cerevisiae, Crystal Christine Crook

Graduate Theses and Dissertations

The stress response of Saccharomyces cerevisiae is a valuable area of study for understanding cellular adaptation mechanisms that govern survival in fluctuating environments. This dissertation investigates stress response regulation in yeast through the roles of Hog1 mitogen-activated protein kinase (MAPK) and the post-transcriptional regulator Mkt1, a key post-transcriptional regulator, in diverse wild yeast isolates. Hog1 is traditionally known for its central role in osmotic stress regulation in the high-osmolarity glycerol (HOG) pathway. This study expands the functional scope of Hog1 to include oxidative and ethanol-induced stress responses.

In parallel, we investigate post-transcriptional regulation of stress responses by the Mkt1 interactome, …

Parasitic Effects Of Amoebidium Appalachense On Daphnia Magna Heart Rate, Hopping Frequency, And Metabolic Rate, Vanessa Wise

Honors Program: Senior Projects (Public)

Daphnia magna are a crustacean that inhabits multiple different types of freshwater ecosystems and thus is plays a part in many different types of interspecies interactions, one of which is parasitism. Amoebidium appalachense is a Mesomycetozoean parasite of aquatic arthropods that colonizes the antenna of D. magna. Previous research has shown that A. appalachense infection will reduce the fecundity and increase mortality rate of D. magna but how it causes these effects is unknown. To determine if A. appalachense causes these effects on D. magna by either stealing nutrients inside the D. magna like a tick or by compromising …

Gene Promoters Are Genomically Encoded To Facilitate Histone Exchange/Incorporation, Blaine Bartholomew

Faculty, Staff and Student Publications

Gene promoters are intrinsically hardwired not only to facilitate transcription preinitiation complex formation but also the release of paused RNA polymerase by H2A.Z. A new PLOS Biology study reveals poly (dA) tracts at promoters positively stimulate H2A.Z incorporation by the SWR complex in yeast.

Risky Genes: The Impact Of Social Determinants Of Health On Dna Methylation In Indigenous Communities, Ella Martin

Celebrating Scholarship and Creativity Day (2018-)

Epigenetics is the study of molecular modifications to DNA structure that do not impact the sequence of the DNA itself. This biological study works to link health outcomes later in life with environmental interactions that affect our genetic predispositions. These complex factors can greatly impact longevity and quality of life. DNA methylation is one type of epigenetic mark that happens through natural biological processes. However, this marking has been shown to be detrimental to the process of aging and can be accelerated by harmful exposures such as stress, substance-use, or chemicals in the environment. Exposure to these compounds is exasperated …

Passive Dna Transfer To Fidget Blasters Stored In Cars, Rachel Chan

Student Theses

This study evaluated the amount of detectable DNA accumulated on clean plastic fidget blasters, used to simulate firearms, over a seven-day storage period inside a vehicle. Twelve volunteers were asked to place one fidget blaster each in the glove box and underneath the driver’s seat from behind. After the seven-day period, the volunteers returned the fidget blasters, donated a reference sample, and filled out a questionnaire. The grip, slide, and trigger were swabbed for DNA and extracted. The extracts were quantified to determine the concentration of human DNA, and if the samples met the PCR threshold to be genotyped. The …

Spatial Variaiton In Host-Associated Microbiota, Daniel Malagon

All Dissertations

Many organisms rely upon the internal and/or external microbial communities they harbor. Microbial communities which depend upon other organisms for survival are known as host-associated (HA) microbial communities. HA microbial communities differ in diversity and composition from surrounding environmental microbiota and are generally less diverse than surrounding soil microbiomes. Although distinct bacterial profiles exist between host and environment, microbial scale dispersal often links the two. For this reason, host and environmental microbial communities can be correlated (e.g., dominant taxa in HA microbiota are dominant in the host microenvironment or vice versa). Eukaryotic hosts act as islands for HA microbiota. Unlike …

Synthetic Modification Of Agrobacterium To Inhibit Plant Pathogenesis, Rosemala Agarwala

Honors Theses

Crown Gall disease caused by Agrobacterium is a leading cause of plant damage and current solutions used to prevent the disease are not as effective. This research aims to use a synthetic biology approach to design a plasmid that upregulates Curdlan, a molecule that activates plant defenses, when the bacteria senses a wounded plant. Thus this research uses a synthetic biology approach to develop a biocontrol agent for Crown Gall disease. This research also looks at the transferability of the sugar phenol sensing mechanism in Agrobacterium, which is needed for plant pathogenesis.

A Cross-Taxa Comparison Of Avian Telomere Dynamics, Age, And Lifespan, Benjamin Konigsberg

Honors Theses

When eukaryotes replicate cells throughout their life, the end regions of chromosomes naturally degrade as a result of the 5' to 3' directionality of DNA polymerase. There is a point when the chromosome is too damaged to provide normal cellular functions, so the cell will die. Telomeres act as a buffer by providing repetitive sequences of non-coding nucleotides. While telomeres do shorten during replication events, the enzyme telomerase can extend telomeres to prevent senescence. Telomere lengths vary between individuals based on different stressor and stress mitigation. Telomeric rate of change is a metric that can capture telomerase activity by measuring …

Genomic Analysis Of The Lyme Disease Vector Across Virginia’S Spatial Expansion Front, Amy Jablonski

Honors Theses

Lyme disease is the most common vector-borne disease in the United States and is expanding with rising incidence in Virginia . This study investigates populations of lxodes scapularis across Virginia using RAD-seq to analyze SNPs from ticks collected in seven Virginia counties and four U.S. states as references . Results show a clear genetic split between western and eastern Virginia ticks . These results follow previously noted patterns in regional differences in Lyme disease risk.

Exploring The Role Of The Id2 And Rab11fip3 Pathway In X-Linked Chronic Granulomatous Disease (Xcgd) Through Comparative Gene Expression Analysis, Kaili Coenen

Honors Theses

X-linked chronic granulomatous disease (XCGD) is a debilitating immunodeficiency disorder primarily affecting men. The disease results from mutations in the CYBB gene on the X chromosome, which encodes the GP91^PHOX protein responsible for electron transfer from NADPH to molecular oxygen. Despite the identification of the CYBB mutation, the pathological mechanism underlying the reduction in reactive oxygen species (ROS) generation in XCGD remains unclear. We hypothesized that comparative gene expression analysis, combined with pathway analysis, could identify genes and signaling pathways contributing to reduced reactive oxygen species (ROS) levels in XCGD. In this study, we analyzed gene expression data from four …

Investigating Evolution Through The Lens Of Ai-Driven Protein Exploration And Phylogenetic Modeling, Mataya Duncan

Graduate Theses and Dissertations

Recent advances in computational biology, artificial intelligence, and sequencing technologies have enabled new perspectives for addressing longstanding questions in evolutionary biology. Increased computational power has made large-scale simulations feasible for investigating diverse aspects of evolutionary and phylogenetic modeling. Similarly, deep learning algorithms now allow for the prediction of reasonably accurate tertiary protein structures, unlocking the potential for investigating diversity and evolution of protein structure across a broad range of organisms. This thesis presents two studies that target different aspects of evolutionary inference from unique perspectives. Yet, the share an overarching goal of presenting new perspectives on the evolutionary basis of …

Population Dynamics, Life History Characteristics, And Environmental Drivers Of Neomysis Americana In The Damariscotta River Estuary, Allison Fogg Ms '25

All Student Scholarship

Mysid shrimp (Neomysis americana) play a pivotal role in estuarine food webs by linking primary producers to higher trophic levels and serving as an important food source for commercially valuable fish. Despite their ecological significance, mysids are often under sampled, leading to gaps in our understanding of their population dynamics and life history traits. My study investigated N. americana over a full year (June 2023 to May 2024) in the temperate Damariscotta River Estuary in Maine. My research focused on how environmental factors such as temperature, turbidity, salinity, chlorophyll-a, and zooplankton biomass affect mysid density and reproduction. Temperature emerged as …

A Qualitative Nmr And Histological Analysis Of Adipocere Formation In Different Aqueous Environments Using Sus Scrofa Models, Mia M. Sorrentino

Student Theses

Adipocere is a wax-like crust that has the potential to form over corpses in moist, humid, and anaerobic environments, preserving them in a process similar to that of mummification. The substance can be identified within 3-6 months postmortem and is characterized by the ratio of saturated fatty acids to unsaturated fatty acids. Palmitic acid and stearic acid are the most abundant in comparison to myristic and oleic acids. The goal of this study was to investigate factors affecting adipocere formation in different aqueous environments. Pork belly samples were submerged in water samples collected from different places around New York City …

Interferon Regulatory Factor 3 In Interferon Gamma Receptor Signaling And Cancer Immunology, Zachary P. Guinn

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

Every year millions of people die from cancer throughout the world, and tens of millions of people are diagnosed with cancer worldwide. When surgery is not an option, treatment options commonly rely on the host immune system for optimal treatment efficacy. The expression of Interferon gamma (IFN-γ) by host immune cells is often associated with favorable antitumor immune responses. How IFN-γ is optimally induced in immune cells, and how IFN-γ promotes the transcription of genes downstream of the Interferon gamma receptor (IFNGR) is incompletely understood. Understanding how to induce immune cells to express optimal IFN-γ …

Analyzing Microalgae-Bacteria Population Changes In Response To Environmental Parameters For Improved Wastewater Treatment, Amanda M. Moravek

All Graduate Theses and Dissertations, Fall 2023 to Present

Microalgae are incredible organisms that have a variety of uses such as wastewater treatment, fertilizer, livestock feed, and bio-compound production. Microalgae require a light source and minimal nutrients space to proliferate, making them an environmentally friendly and sustainable option for such processes. The Sustainable Wastes-to-Bioproducts Engineering Center at Utah State University is developing and implementing a Rotating Algae Biofilm Reactor (RABR) to remove total nitrogen and phosphorous from the Central Valley Wastewater Reclamation Facility wastewater effluent. Harmful compounds such as nitrates and phosphates are metabolized by the microalgae and converted into useful bioproducts, resulting in a circular economy. These RABRs …