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Leaf Optical And Indirect Lai Measurements In Wheat And Alfalfa At Maciv: Agmet Progress Report 89-4, E. A. Walter-Shea, B. L. Blad

School of Natural Resources: Documents and Reviews

No abstract provided.

Transcription Factor Expression Landscape In Drosophila Embryonic Cell Lines, Robert A. Drewell, Daniel Klonaros, Jacqueline Dresch

Biology

Background: Transcription factor (TF) proteins are a key component of the gene regulatory networks that control cellular fates and function. TFs bind DNA regulatory elements in a sequence-specific manner and modulate target gene expression through combinatorial interactions with each other, cofactors, and chromatin-modifying proteins. Large-scale studies over the last two decades have helped shed light on the complex network of TFs that regulate development in Drosophila melanogaster. Results: Here, we present a detailed characterization of expression of all known and predicted Drosophila TFs in two well-established embryonic cell lines, Kc167 and S2 cells. Using deep coverage RNA sequencing approaches we …

Effects Of Roadways On Seasonal Movement Strategies And Mate Location Success In An Imperiled Pit Viper (Crotalus Horridus), Elizabeth J. Noble

Graduate Research Showcase

A detailed understanding of animal movement behavior is fundamental to effective conservation and management. Within populations, a diversity of movement strategies can be displayed in search of critical resources, and these strategies are influenced by multiple interacting factors related to individuals and the environment. Mating partners are one critical resource that often serves as a prominent selective force shaping movement during mating seasons. For many large-bodied snakes, such as pit vipers (Viperidae: Crotalinae), male mate- searching movements are the primary determinant of mate location success. During this time, males incur significant risks associated with elevated movement. In an increasingly human- …

Oil Identification Of Harp Seal And Other Select Marine Mammals, Meghan Pinedo, Deborah A. Duffield, Dalin N. D’Alessandro, Erin R. Price, Edgard O. Espinoza

Biology Faculty Publications and Presentations

Because of the rich omega-3 fatty acids content, harp seal (Pagophilus groenlandicus) oil is a popular supplement that is packaged as pills in Canada and sold for medicinal purposes, although this practice is banned in the United States. Due to US regulations, it is important to be able to distinguish between fish oil and seal oil, but the taxonomic determination of oils provenance has been a difficult problem to solve. In this study, Direct Analysis in Real Time time-of-flight mass spectrometry (DART TOFMS) was used to analyze the chemotypes of blubber samples collected from seven species of …

The Effects Of Light Cycle Disruption On The Reactive Oxygen Species Production In Zebrafish, Talia Sanders

Honors College Theses

It has been proven that maintaining homeostasis is linked to regulation of circadian rhythms and the light cycles associated with them. Through investigation of zebrafish mitochondria subject to stress via unpredictable light cycle exposure, we previously studied the level of GSK3β protein as it relates to the health of the brain. The data has shown that when a brain undergoes stress, it results in the increased activation of GSK3β which leads to disruptions in circadian rhythm, inflammation, and cell death. Moreso, this overexpression results in reduced ATP production and lowered Complex 1 activity in the mitochondria. However, GSK3β activation is …

With Love, ; An Interdisciplinary And Intersectional Look At Why Creativity Is Essential, Theo Starr Gardner

Whittier Scholars Program

My Whittier Scholars Program self-designed major, Teaching Creativity, is a mixture of Art, Literature, and Education classes. My research and praxis classes have been focused on the ‘how?’s and 'why?’s of creativity, so it felt only right that my project should be a constructivist, generative project. The project I have been working on throughout my time at Whittier, and that has just fully come to fruition on April 11th, 2024, was a solo art gallery/open mic event entitled ‘With Love,’. With Love, was conceptually inspired by the research I’ve conducted on creativity and creative arts education over the past few …

The Interactions Of Centromeric Nucleosomes Elucidated By Atomic Force Microscopy, Shaun Filliaux

Theses & Dissertations

Nucleosomes are the fundamental unit of compaction for DNA in the genome. These positively charged proteins have two main types of nucleosomes: canonical (H3 containing) and centromere (CENP-A containing). The compacting of DNA allows for DNA to fit into the nucleus of cells, but creates a barrier for DNA accessibility for operations such as replication or transcription. Centromeric chromatin is a subset of chromatin structure and governs chromosome segregation. Compared to the bulk chromosome, centromeres are composed of H3 and CENP-A nucleosomes in which H3 histones is replaced by its homolog CENP-A histone. This results in nucleosomes with different structures, …

Optimization Of Tyrosine Hydroxylase Antibody For Immunohistochemistry Fluorescence Detection In Zebrafish (Danio Rerio), Madison Thurber

Theses/Capstones/Creative Projects

Dopamine is an important neurotransmitter produced through the catecholamine synthesis pathway that affects brain activity. Unregulated dopamine levels can lead to various diseases such as Parkinson’s Disease or attention deficit hyperactivity disorder (ADHD). Optimization of an immunohistochemistry protocol will allow for the quantification of tyrosine hydroxylase antibody, which indirectly allows for dopamine quantification in dopaminergic regions within the brain. However, the antibody concentration to give the optimal signal-to-noise ratio in IHC varies across studies. Through this experiment, I determined the concentration of tyrosine hydroxylase (TyrH) antibody for immunohistochemistry that gave the best signal-to-background noise ratio within several known dopaminergic regions …

Molecular Mechanisms Of Opioid Use Disorder In Human Brain Models, Emily Mendez

Dissertations & Theses (Open Access)

Opioid use disorder (OUD) is a national and global public health crisis with no end in sight. While studies from animal models hint at widespread epigenetic and transcriptomic alterations of opioid drugs, the molecular consequences of long-term exposure to opioid drugs in human brain is still unclear, and human-centered translational models are necessary to discern the human cell type-specific effects of OUD.

Using postmortem brain Brodmann area 9 (BA9) from the UTHealth Brain Collection for Research on Psychiatric Disorders, I identified angiogenic gene networks perturbed in the RNA and protein of OUD subjects, as well as downregulation of many neuron-correlated …

Characterizing The Role Of Pa5189 Of Pseudomonas Aeruginosa In Deletion And Overexpression Mutants, Seh Na Mellick

Theses/Capstones/Creative Projects

In the context of rising multidrug resistance in biofilm-forming pathogens like Pseudomonas aeruginosa, this study investigates the role of the understudied transcription factor PA5189 in antibiotic resistance and biofilm formation. PA5189 deletion and overexpression mutants were created in a parent P. aeruginosa strain using pEX18Tc-based recombinant suicide vectors, with genotypic verification of putative triparental conjugants achieved through restriction digestion and PCR. The study revealed that PA5189 overexpression significantly increases resistance to commonly used broad spectrum antibiotics such as ciprofloxacin and imipenem. Additionally, differential expression of PA5189 was found to notably affect biofilm formation, with variations contingent on the nutrient …

P300 Event-Related Potential Responses To Self-Relevant Stimuli, Jordan Razzak

Electronic Theses and Dissertations

Previous literature has suggested an apparent P300 sensitivity to self-relevant stimuli. To further explore this relationship, we asked participants to submit 10 photos, each of a particular category (e.g. footwear, plants), to be used as either targets or distractors in a given condition of an oddball task. Furthermore, we attempted to see whether the effect of self-relevance on the P300 could be induced in a participant by allowing them to study a set of unique photos which would then be used as targets. Our analysis suggested that P300 amplitude elicited in response to self-relevant stimuli used as targets was statistically …

Proposing Urban Agroforestry Designs For Lincoln, Nebraska: A Model From Berlin, Germany, Noah Johnson

Honors Theses

Given the threat of a worsening climate crisis, there is a strong need for community and ecosystem resilience. Diverse urban agroforestry systems have the potential to accomplish both and meet many of the objectives outlined in the city of Lincoln, Nebraska’s climate action plan. Additionally, Berlin, Germany could provide an effective model for Lincoln in this regard given the city’s extensive history of established urban agroforestry systems. The objective of this study then is to develop a design for an urban agroforestry site modeled on Berlin’s allotment gardens and tailored to Lincoln’s needs. The methods for creating this design included …

Determining The Impacts Of Corn Silage Mixing Ratios On Hydrogen Production From Beef Cattle Manure, Katya Faber-Quimby

Honors Theses

With global warming becoming an increasingly serious threat and a growing population requiring additional energy resources, interest in the production of clean energy from the agricultural sector has surged in popularity. Biohydrogen, also known as green hydrogen, is H₂ that has been produced using renewable energy, such as from agricultural byproducts or waste materials. It presents a promising alternative to nonrenewable resources due to its high potential for energy storage and lack of carbon emissions when used. Cattle manure has been explored as a resource for the production of biohydrogen. Selecting for hydrogen-producing microbes in the manure serves the …

Post-Activation Potentiation Following Maximal Effort, Multi-Joint, Isokinetic Eccentric Contractions, Tom Dickey

All Graduate Reports and Creative Projects, Fall 2023 to Present

Post-activation potentiation (PAP) is a phenomenon that can enhance muscle performance following maximal or near-maximal muscle contractions. While the effects of concentric and isometric conditioning contractions on PAP have been studied, less is known about the influence of eccentric muscle actions. This study investigated the effects of a multi-joint eccentric overload (EOL) protocol on PAP expressed through countermovement jump (CMJ) height and isokinetic peak force (PF) outcome measures. Twenty-eight recreationally trained participants (18-30 years) completed three visits in a randomized, counterbalanced design. Following familiarization, participants performed either an EOL protocol involving 2 sets of 6 maximal isokinetic eccentric contractions or …

Utilizing Biomimicry To Design Sustainable Architecture, Virginia Hammond

Architecture Undergraduate Honors Theses

Nature has an integral relationship with architecture and serves as a sustainable role model and inspiration for designers. The process of biomimicry in architecture has the potential to produce more sustainable design solutions and foster a connection between humans and nature. Existing biomimetic design projects have varying strengths and weaknesses as examples of the process. Utilizing guidelines and references from key leaders in biomimetic design consultancy (Biomimicry 3.8), selected case studies are assessed for their ability to demonstrate the benefits of this design strategy. Using these evaluations, the case studies are diagrammed and critiqued to determine how new projects could …

Revegetation Strategies For Native Wetland Plant Restoration In The Face Of Phragmites Australis Reinvasion And Hydrologic Extremes, Maddie Houde

All Graduate Theses and Dissertations, Fall 2023 to Present

Reestablishing native plant communities in degraded habitats through seeding or planting ("revegetation") is a necessary step to restore ecosystems and their functions (e.g., supporting biodiversity, nutrient cycling, etc.). Globally, wetlands have suffered high rates of degradation and also experience numerous invasions. Invasive species are those that cause environmental, economic, or societal harm. Phragmites australis is a widespread invasive species that outcompetes native plants and reduces habitat diversity. Reestablishing native plant communities can limit P. australis invasion, yet effective methods to do so remain somewhat untested in wetlands. Additionally, stressful environmental conditions can increase plant mortality in revegetation efforts. In semi-arid …

Gaseous Ozone To Improve The Microbial Safety Of Spices, Seeds, And Nuts, Arshpreet Kaur Khattra

Graduate Theses and Dissertations

Due to the increasing number of reported outbreaks of pathogens in low-moisture foods (LMFs), there is a need to investigate novel non-thermal gaseous technologies to increase the microbiological safety of spices, nuts, and seeds without compromising the product quality. The objective of this study was to inactivate Salmonella spp. in different spices, seeds, and nuts using gaseous ozone treatment and evaluate the suitability of Enterococcus faecium as a potential surrogate for Salmonella. Each food product (dried basil leaves, black peppercorn, chia seeds, and walnuts) was separately inoculated with a 5-strain Salmonella and E. faecium cocktail and equilibrated to water activity …

Synthesis Of Gold Nanoparticles Via Pulsed Liquid Ablation For Use In The Photodynamic Therapy Of Bacteria, Justice Ben Yosef

Masters Theses & Specialist Projects

With the ever-increasing threat of antibiotic resistant bacteria, alternative treatment methods have been developed including photodynamic therapy (PDT). Within the PDT process, photosensitizers are used to generate reactive oxygen species (ROS) and facilitate the cell termination process. This work lays the conceptual foundation for the functionalization of the photosensitizer methylene blue (MB) with gold nanoparticles (AuNPs) and INF-55 as a potential inhibitor of the AcrAB-TolC efflux pump to enhance the effectivity of the PDT process.

AuNPs were synthesized using pulsed laser ablation in an aqueous citrate solution. Both nanosecond and picosecond pulse durations, as well as both 532 nm and …

Assessing Impact Of Food Structure On Oral Tribology And In-Vitro Digestion Of Dairy Products, Lamis Ali

All Graduate Theses and Dissertations, Fall 2023 to Present

In this research, we focused on understanding the critical elements impacting consumer experience and the nutritional value of dairy products, specifically their texture, mouthfeel, and protein breakdown in the gastrointestinal tract. Our study aimed to accomplish two main goals. First, we performed analysis of the tribological attributes of various commercially dairy products. The second objective was to investigate the process of disintegration and protein release in selected dairy products.

The study included an assessment of eight dairy products of varied consistencies: solid like cheddar, cheese curd, and parmesan; semi-solid such as cottage cheese, ricotta cheese, and yogurt; and liquid represented …

Grey Relational Analysis And Canonical Correlation Analysis Of Air Pollution In Three Kentucky Counties, Sarah Hartman

Masters Theses & Specialist Projects

Air pollution is a crucial factor that affects both the environment and public health. Various methods are available for assessing air quality and pollution levels, such as regression models, principal component analysis, and factor analysis tools. However, some of these methods present issues in multicollinearity and the nature of collected data. It is important to recognize that air pollution data is often uncertain, incomplete, and contains limited valid data points. Weather conditions and economic activities are also factors that can affect air pollution. With growing communities in Kentucky (KY), it is essential to address these factors as the state has …

Experimental Nonnative Wood Addition Enhances Instream Habitat For Native Fishes And Investigating Dryland River Alterations, Benjamin J. Miller

All Graduate Theses and Dissertations, Fall 2023 to Present

The rivers of the Colorado River Basin (CRB) have been degraded by human activities such flow regulation, water overallocation, and the introduction of invasive riparian vegetation (primarily tamarisk tamarix spp. and Russian olive Elaeagnus angustifolia). These stressors have resulted in widespread habitat loss and simplification, which is a major contributor to the endangerment of native fishes in the CRB.

The objectives of this study were to 1) assess the effectiveness of enhancing native fish habitat by experimentally adding cut wood from nonnative Russian olive to the San Juan River, a highly degraded dryland river, and 2) determine the …

The Role Of Extracellular Vesicles In Immunomodulation During Bovine Pregnancy, Amber E. Thornton

All Graduate Theses and Dissertations, Fall 2023 to Present

During pregnancy, the maternal immune system must be altered to protect the partially non-self fetus from attack. Our previous studies show an inflammatory response in the uterus of cows carrying somatic cell nuclear transfer (SCNT), commonly known as cloned, pregnancies due to abnormalities in proteins expressed by placental trophoblast cells. Between 30 and 90 days the rate of pregnancy loss is 50-100% for SCNT compared to 2-10% for artificial insemination (AI) pregnancies. Abnormal communication between the maternal and fetal systems during placentation is a major cause of this loss. The trafficking of extracellular vesicles (EVs), membrane-bound cargo carriers, potentially represents …

Reinforcements Of A Greater Sage-Grouse Population In Utah: Applications For Range-Wide And Local Conservation Translocation Efforts, Melissa S. Chelak

All Graduate Theses and Dissertations, Fall 2023 to Present

In a small, isolated greater sage-grouse (Centrocercus urophasianus) population in the Sheeprock Mountain Sage-Grouse Management Area (SGMA) located in Utah's West Desert, peak male lek counts declined from 190 males in 2006 to 23 males in 2015. A collaborative effort across all federal, state, and local partners yielded 146 (40 male, 106 female) sage-grouse captured, marked with either a very-high frequency or global positioning systems (GPS) transmitter, and translocated into the Sheeprock sage-grouse management area between 2016 and 2019, complete with radiotelemetry monitoring during the spring and summers of 2016-2020 translocated individuals in addition to radiotelemetry monitoring of …

Analyzing Phototaxis And Related Visual Behaviors Among Diverse Species Of Drosophila, Madeline M. Hill

Honors Theses

Phototaxis and related visual behaviors can vary between species, and thus members of the genus Drosophila make an excellent study system to examine the evolution of vision. While some existing research points to these phototactic behaviors arising due to mating requirements or due to their species-specific ecology or environmental factors, there exists a lack of understanding as to why striking behavioral differences can exist between closely related species, or between members belonging to the same genus. The present research seeks to uncover the specifics regarding these discrepancies in visual evolution and aims to provide a foundation of knowledge about visual …

Toxicological Effects And Treatment Of Accidental Ingestion Of Simparica Trio® In Felis Catus: An Investigative Review, Aussia Stander

Honors Theses

Simparica TRIO^®, a canine endectocide manufactured by Zoetis, contains sarolaner, moxidectin, and pyrantel pamoate salt in an orally administered chewable tablet. These compounds are all toxic to both cats and dogs in sufficient amounts. As Simparica TRIO^® rises in popularity among pet owners, Felis catus (felines, cats) in multi-pet households (households with both cats and dogs) are at increased risk of overdosage and toxicosis from accidental ingestion of Simparica TRIO^® due to their smaller weight.

Simparica TRIO^® is not for feline use and little literature exists on the symptoms of and treatment for accidental ingestion …

Sarcopenia And The Importance Of Resistance Training And Protein-Rich Diets For Prevention Of Muscle Loss In Older Adults: A Literature Review And Informational Pamphlet, Madison Steele

Honors Theses

The growing prevalence of sarcopenia among older adults as well as youths has prompted further research aimed at developing effective preventative measures and treatment plans. Sarcopenia is often thought to occur solely due to aging, but several other factors contribute to progressive muscle loss. Previous research studies have found an effect of physical activity and dietary protein levels on the risk of developing sarcopenia as well as its onset age. This study aims to review existing knowledge in the field to compile an extensive list of sarcopenia causes and methods of prevention. The main causes identified in this review are …

Investigating Large Repeats In The Arabidopsis Thaliana Mitochondrial Genome Using Mitotalens, Megan Gusso

Honors Theses

This lab project explores the complexity of the mitochondrial genome by investigating large genomic repeats and their effect on flowering plants’ reproduction and viability. Mitochondria are the site of cellular respiration to create energy and contain their own DNA. This is counterintuitive because the byproducts of cellular respiration impose a threat of mutation for the stored DNA. The mitochondrial genome differs in size between animals and plants. Plant mitochondrial DNA is larger due to the presence of large, noncoding repeated sequences, and a large amount of DNA of unknown function. These sequences undergo high levels of recombination and rearrangement. The …

Understanding Taf13 (Tata Box-Binding Protein-Associated Factor 13) Upregulation In Eukaryotic Cells, Selin Kaplanoglu

Honors Theses

TATA-binding protein (TBP) and TBP-associated factors (Tafs) comprise RNA Polymerase II (RNA Pol II) pre-initiation complex. This universal component carefully controls the transcriptional initiation process. One of the Tafs, Taf13, also plays an important role in the regulation of RNA Pol II transcription initiation which is evolutionarily conserved from yeast to humans. It is found that Taf13 is overexpressed in cancer cells, although the exact mechanism that is responsible for this overexpression is unclear. Our hypothesis suggests that targeted degradation by the 26S proteasome via ubiquitylation [Ubiquitin-Proteasome System (UPS)] may be the mechanism that regulates the stability of Taf13. To …

Contrasting Nitrogen Sources Impact Nitrogen Use Efficiency And Soil Health Under Silage Corn Production In A Semi-Arid Environment, Phearen Kit Miller

All Graduate Theses and Dissertations, Fall 2023 to Present

Silage corn production challenges sustainable intensification and soil health in semi-arid environments because the entire aboveground biomass is harvested and removed from the field. An irrigated silage corn field study was conducted over a decade comparing nitrogen fertility sources using a complete randomized block design with four treatments: control with no nitrogen fertilizer (control), low ammonium sulfate at 112 kg N ha⁻¹ (AS100), high ammonium sulfate at 224 kg N ha⁻¹ (AS200), and steer manure compost at 224 kg total N ha⁻¹ (compost). Research focused on the impact of these contrasting nitrogen sources on silage corn production, …

Spatial Ecology Of Mule Deer Migrations From Grand Teton National Park And The Teton Range, Justin K. Schwabedissen

All Graduate Theses and Dissertations, Fall 2023 to Present

The Greater Yellowstone Ecosystem hosts several of the longest, fully intact ungulate migrations remaining in the continental United States. However, expanding development and an increasing human footprint continue to truncate migratory routes. While the endpoints are often a seasonal range on protected lands, these migration corridors frequently cross other jurisdictional boundaries, including large tracts of private or multiple-use lands, with varying levels of protection. Thus, it is critical resource managers understand the dynamics of migratory movements to define population-level corridors and prioritize appropriate conservation strategies. Mule deer in Wyoming have been documented traveling long distances between summer and winter ranges; …