Biology Commons^™

Du Undergraduate Showcase: Research, Scholarship, And Creative Works: Abstracts, Emma Aggeler, Elena Arroway, Daisy T. Booker, Justin Bravo, Kyle Bucholtz, Megan Burnham, Nicole Choi, Spencer Cockerell, Rosie Contino, Jackson Garske, Kaitlyn Glover, Caroline Hamilton, Haley Hartmann, Madalyne Heiken, Colin Holter, Leah Huzjak, Alyssa Jeng, Cole Jernigan, Chad Kashiwa, Adelaide Kerenick, Emily King, Abigail Langeberg, Maddie Leake, Meredith Lemons, Alec Mackay, Greer Mckinley, Ori Miller, Guy Milliman, Katherine Miromonti, Audrey Mitchell, Lauren Moak, Megan Morrell, Gelella Nebiyu, Zdenek Otruba, Toni V. Panzera, Kassidy Patarino, Sneha Patil, Alexandra Penney, Kevin Persky, Caitlin Pham, Gabriela Recinos, Mary Ringgenberg, Chase Routt, Olivia Schneider, Roman Shrestha, Arlo Simmerman, Alec Smith, Tessa Smith, Nhi-Lac Thai, Kyle Thurmann, Casey Tindall, Amelia Trembath, Maria Trubetskaya, Zachary Vangelisti, Peter Vo, Abby Walker, David Winter, Grayden Wolfe, Leah York

DU Undergraduate Research Journal Archive

Abstracts from the DU Undergraduate Showcase.

The Nature Of Phenotypes: Provoking And Measuring The Dynamic Processes Of Swarm Expansion, Predation, And Antibiotic Resistance In Myxococcus Xanthus, Linnea Judith Ritchie

Dissertations - ALL

The question of how genotype affects phenotype has fascinated and puzzled scientists for generations. Regardless of organism, the correlation between observation and underlying condition is necessary for scientists to understand the world around us. Myxococcus xanthus, a fascinating organism with a large genome (7,314 genes), is known for complex social behaviors and is an excellent model system for the study of this relationship. Upon starvation, M. xanthus cells condense into large multicellular aggregates to await renewed nutrient availability. M. xanthus cells swarm together on surfaces as a predatory biofilm, lysing and killing prey as a singular unit. During predation, swarms …

A Review Of Current Methods In Avian Dietary Analysis And Their Integrated Application To Characterize The Trophic Niche Of Louisiana Waterthrush (Parkesia Motacilla)., Brandon Hoenig

Electronic Theses and Dissertations

Characterizing a species’ dietary composition presents an avenue to understand many facets of its ecological niche and can provide essential information for the species’ long-term conservation. To date, the vast majority of diet studies have relied on direct identification of prey during foraging observations or from diet samples to characterize the dietary habits of birds. However, advancements in laboratory-based approaches have revolutionized the field of trophic ecology by allowing researchers to indirectly infer dietary habits with higher resolution across greater time scales. Here, I apply two of these laboratory-based techniques, namely DNA metabarcoding and stable isotope analysis, to characterize the …

Evaluating Threats To The Water Quality Of Little Buffalo Creek And Sarver Run Through Water Quality Analysis And Backpack Electrofishing Surveys, Riley Williams

Electronic Theses and Dissertations

Currently, 64.8% and 52.2% of Little Buffalo Creek and Sarver Run stream kilometers are impaired, respectively. Impairment sources to Little Buffalo Creek include agriculture, riparian deforestation, on-site wastewater, and urban runoff. Impairment sources to Sarver Run are unknown. Our goal was to understand sources of impairment through water quality analysis and fish surveys. Water samples were collected monthly and analyzed for cation and anion concentrations. Mass ratio analysis comparing Br/SO₄ and Mg/Li, Ca/Mg and Ca/Sr, Mg/Na and SO₄/Cl, and SO_4/Cl and Mg/Li suggests that mine drainage and conventional oil and gas may be impacting water …

Developing A Novel Place Preference Assay To Compare Drosophila Species Over Time, Martha M. Brinson

Honors Theses

Across phylogeny, integration of external factors, memory, and internal states of the organism dictate organismal behavior and mechanisms. The underlying genetic components can affect these behaviors such as in genomic changes arising from speciation. In this thesis, a new place preference assay was evaluated in the analysis and investigation of two species of Drosophila flies (D. melanogaster and D. simulans) to measure similarities and differences and their attraction to two different food substrates. Sleep and circadian measurements were also recorded during experimentation. The Drosophila Activity Monitor 5M (DAM5M) System and Sleep Circadian Analysis MATLAB Program (SCAMP) analysis were …

Invasion Of The Northeastern United States By The Southern Pine Beetle, Dendroctonus Frontalis, And The Impacts On Signatures Of Isolation By Distance Assessed Using Mitochondrial Dna, Lora Grace Holman

Honors Theses

The southern pine beetle (SPB) is a small, black beetle that parasitizes pine trees across the United States and Central America. Recently it has been recognized that the range of SPB is not limited to the southern United States, but rather extends northward across the eastern United States, which raises concerns for pine trees that have never encountered the pest before. Using mitochondrial DNA sequences from a section of the cytochrome oxidase I gene and four different measures of genetic distance compared to geographic distance, we tested for evidence of isolation by distance (IBD) among sampled SPB to see whether …

Isolation Of Arabidopsis Thaliana Plants Homozygous For An Insertional Inactivation Mutation Within Atprp4., Sydney Raitz, Timothy D. Trott

Faculty Works

The AtPRP4 gene in Arabidopsis thaliana has been shown to function in several specific parts of the plant’s cell wall. It is shown to be expressed in the seeds, radicles, roots, leaves, inflorescences, and embryos of Arabidopsis thaliana. These patterns have suggested unique functions for ATPRP4 in determining cell-type-specific wall structure during the development of a plant as well as contributing to defense reactions against physical damage to the plant and pathogen infection within the plant. In this study, a simple DNA prep was performed on the true leaves of Arabidopsis thaliana. Subsequent PCR reactions were performed using …

Functional Role Of Ppal And Potential For Moss In Industrial Applications., Susana Perez Martinez

Electronic Theses and Dissertations

This dissertation is an examination and characterization of the functional roles of PPAL. PROTEIN PRENYLTRANSFERASE ALPHA SUBUNIT-LIKE (PPAL) is a recently discovered gene. PPAL homologs are present in all plants and many animals, where its function is largely unknown. It is possible that PPAL could participate in prenylation processes since it shares similarity to the α subunits of known prenylation enzymes. Prenylation is a post-translational modification of proteins that involves the addition of a lipid moiety to proteins to facilitate membrane targeting and association and promote protein-protein interactions. Prenylation has important roles in plant growth and development, including …

Identifying Genetic Differences Among African American And Caucasian Triple Negative Breast Cancer Genotypes, Christopher Jordan Dixon

Theses (2016-Present)

Triple negative breast cancers (TNBC) are closely related to basal-like cancers and classified based on their molecular signatures and their progenitor cell type. TNBCs lack the presence of three common types of receptors known to fuel breast cancer growth: estrogen receptors (ER), progesterone receptors (PR), and human epidermal growth factor receptors 2 (HER2neu). TNBC represent 10-20% of all molecular breast cancer subtypes. Even though genomic and transcriptome analyses show that many of the molecular signatures associated with TNBC are not related to ethnicity, clinicians and researchers find that African American (AA) TNBC women have higher mortality rates compared to Caucasian …

Temporal And Spatial Comparison Of Pseudo-Nitzschia Species Composition And Domoic Acid In Narragansett Bay, Rhode Island And The Northeast U.S. Shelf, Isabella Church, Bethany D. Jenkins

Senior Honors Projects

Diatoms are unicellular algae that make up a significant portion of phytoplankton biomass at the base of marine food webs. Narragansett Bay (NB), RI is home to several species of the diatom genus Pseudo-nitzschia (P-n), some of which are known to cause harmful algal blooms through the production of the potent neurotoxin domoic acid (DA). This toxin can lead to Amnesic Shellfish Poisoning in humans through the consumption of affected shellfish. Although the presence of P-n has been well established in NB for over 50 years, DA levels have only recently become a problem, with shellfish harvest closures …

Through The Leaves: Understanding Population Genetic Structure Of Clematis Morefieldii, Keith Andrew Greenway

Honors Capstone Projects and Theses

No abstract provided.

The Effects Of Deletion Of The Cytoplasmic Domain Of Robo3 On Drosophila, Jessie Agcaoili

Biological Sciences Undergraduate Honors Theses

My research project examines how the deletion of the cytoplasmic domain affects the function of Robo3. If Robo3 is signaling repulsion in response to SLIT this activity should require the cytoplasmic domain. I investigated the functional importance of Robo3 by deleting the cytoplasmic domain of Robo3 using a CRISPR-based technique. This modified gene was then injected into Drosophila embryos where it replaced the normal copy of the gene. Embryos expressing the modified version of robo3 in place of normal robo3 were dissected and examined.

Alterations Of The Gut Mycobiome In Patients With Ms - A Bioinformatic Approach, Saumya Shah

Honors Scholar Theses

The mycobiome is the fungal component of the gut microbiome and is implicated in several autoimmune diseases. However, its role in multiple sclerosis (MS) has not been studied. We performed descriptive and formal statistical tests using the R language to characterize the gut mycobiome in people with MS (pwMS) and healthy controls. We found that the microbiome composition of multiple sclerosis patients is different from healthy people. The mycobiome had significantly higher alpha diversity and inter-subject variation in pwMS than controls. Additionally, Saccharomyces and Aspergillus were over-represented in pwMS. Different mycobiome profiles, defined as mycotypes, were associated with different bacterial …

Invisible Disabilities, Academic Capital And Competitiveness Of Genetic Counseling Applicants, Natalie E. Stoner, Meagan Choates, Carla Mcgruder, Debra Murray, Theresa Wittman, Sara Wofford, Claire N. Singletary

Dissertations and Theses (Open Access)

The field of genetic counseling has historically lacked diversity. Recent research has begun to explore how visible diversity may present barriers to a genetic counseling applicant becoming competitive, but has not yet characterized potential barriers with invisible diversities, such as being a first-generation college student, or a part of the LBGTQ+ community. Therefore, this study aimed to address this gap among those with invisible diversities, as well as explore their academic capital (AC), a theoretical framework used to identify factors that make students more likely to succeed in post-secondary work including supportive networks, trustworthy information, family uplift, college knowledge, overcoming …

Computational Approaches To Understand Chemoresistance & Tumor Evolution Using Longitudinal Clinical Data And Lineage Tracing, Sahil Seth

Dissertations and Theses (Open Access)

Tumors are highly heterogeneous and dynamic, continually adapting and evolving in response to their microenvironment as well as external perturbations. Multi-region (spatial) and single cell sequencing has enabled us to anatomize the heterogeneity further and provide evidence of its association with chemo and drug resistance. To investigate this further we took two different approaches to understand the chemo-resistance, and functional heterogeneity in Triple negative breast cancer (TNBC) and Pancreatic ductal carcinoma in situ (PDAC) from an evolutionary perspective.

The first approach was to leverage tumor profiling from an ongoing randomized clinical trial in triple-negative breast cancer (ARTEMIS) to assess mechanisms …

Impact Of Genetic Variation And Timescale On Diatom Salinity Stress Response, Kala M. Downey

Graduate Theses and Dissertations

Natural environments are dynamic, and organisms must sense and respond to changing conditions. One common way organisms deal with stressful environments is through gene expression changes, allowing for stress acclimation and resistance which occurs over varying time spans in different species. The recent evolutionary history of populations could greatly influence their ability to respond successfully. An evolutionary history in disturbed or fluctuating conditions could promote increased resistance or a more rapid response to these environmental stressors. To understand the impact of genotypic variation and timescales on response and acclimation to salinity changes, we have been exploiting the abilities of euryhaline …

Comparative Analysis Of Rna Tran-Scriptomes In Ptsd Patients, Tyler Forrest Chan

Honors Capstone Projects and Theses

No abstract provided.

Increased Risk Of Mental Illness Due To Epigenetic Alteration Of The Nr3c1 Gene After Early Life Adversity., Erin Mccue

Thinking Matters Symposium

Early life adversity (ELA), such as malnutrition, abuse, and economic disparity, is an issue commonly seen in adolescents, a group already facing increased risk for stress-related disorders. This review of current literature reveals that gestational stress exposure, as well as variations in maternal care during postnatal development, cause latent effects on the epigenome, specifically impacting the glucocorticoid receptors (GRs) encoded by the NR3C1 gene. GRs bind to glucocorticoids to regulate the body’s neuroendocrine stress response. However, in those with a history of ELA, the number of GRs is reduced, generating dysregulation within the hypothalamic-pituitary-adrenal (HPA) axis. Rodent studies are utilized …

The Central Dogma: Gene Expression, Ayisha Sookdeo

Open Educational Resources

In this lesson plan, students will learn the basic structure and function of DNA and RNA. They will also learn the process of gene expression. Finally, students will learn about the scientific contributor, Ernest Everest Just, and his contributions to the field of Biology.

Metabolism, Cognition, And Male Coloration In Eastern Mosquitofish, Katelyn Ashleigh Giltner

Honors Capstone Projects and Theses

No abstract provided.

Annual Faculty Research Symposium 2022, Oakwood University

Proceedings

No abstract provided.

Microbial Diversity And Community Structure In Sediments Associated With The Seagrass (Thallassia Testudinum) In Apalachicola Bay, Florida, Rahma Ahmed, Thomas Mcelroy, Troy Mutchler

Symposium of Student Scholars

Seagrass is an angiosperm which provides many ecosystem services in coastal areas, such as providing food, shelter and nurseries for many species, and decreasing the impact of waves on shorelines. A global assessment reported that 29% of known seagrass meadows are in a state of decline due to the effects of human activity. Seagrass is commonly found in shallow marine waters where they form meadows containing a microbiome that plays an important role in providing nutrients for seagrass growth, though little is known about the microorganisms within the seagrass meadow sediments. Our project collected sediments from seagrass meadows and adjacent …

Improving Photosynthetic Efficiency In Microalgae Through The Genetic Engineering Of Energy Sensors And Photoreceptors, Taylor L. Britton

Biology ETDs

Through photosynthesis microalgae can convert sunlight, water, and CO₂ into chemical energy that can be used to generate carbon neutral biofuels and biomass. With an ever-increasing demand and need for petroleum substitutes it is imperative that we improve the output of industrial-relevant crops such as microalgae. One important way of improving output in algae is by understanding the roles that stress and energy conversion is regulated in these organisms. Photosynthetic organisms fundamentally depend on light- and sugar-driven metabolic and signaling networks, which integrate environmental cues to govern and sustain growth and survival. SnRKs (SNF1-related protein kinases) and the photoreceptor …

Sex And Starvation Influences Latrotoxin Expression In The Brown Widow Spider, Mattie Harris

Honors College Theses

Widow spiders (genus Latrodectus) are well-known for their potent venom. Seven latrotoxin proteins constitute the main components of widow spider venom. The vertebrate specific (α-latrotoxin) and insect specific (α-latroinsectotoxin) latrotoxins have been well-characterized with respect to structure and function. Regulation of latrotoxin gene expression is not well understood but sex and feeding could be factors influencing production. In this study, I used quantitative qPCR to (1) characterize the expression patterns of both the insect and vertebrate specific latrotoxins in male and female brown widow spiders (Latrodectus geometricus) to characterize sex-biased expression and to (2) study expression patterns …

Host-Pathogen Coevolution Between Tasmanian Devils (Sarcophilus Harrisii) And Devil Facial Tumor Disease, Dylan Garret Gallinson

USF Tampa Graduate Theses and Dissertations

Coevolution is a driving force of rapid evolution, yet the complexity of coevolutionary interactions has made it difficult to characterize the genomic basis of traits mediating such relationships. Coevolutionary dynamics are especially important in host-pathogen systems where the host and pathogen must constantly adapt to one another. The Tasmanian devil and its species-specific transmissible cancer, devil facial tumor disease (DFTD), provide the rare opportunity to study host-pathogen coevolution in a complex natural system. Extensive spatiotemporal devil sampling, high linkage disequilibrium in devils, and a large selective pressure imposed by DFTD facilitate a system tractable for study. Here, we characterized devil …

Exploring The Functionality Of Putative Bop3 Post-Translational Modifications, Liliya Tkachuk

Honors Scholars Collaborative Projects

All eukaryotic cells require that transcribed mRNAs undergo export form the nucleus to the cytoplasm where they can be translated into proteins. This process requires a host of proteins which are conserved between the unicellular budding yeast, S. cerevisiae, and humans. During this process, Mex67 and other associated proteins facilitate the mRNA to travel across the nuclear pore complex (NPC), doorways embedded in the nuclear envelope. Upon the exit of mRNA, Mex67 is released and recycled back into the nucleus to facilitate the export of more mRNA. This occurs through the action of Dbp5, whose activity is regulated through …

Cryptic Hybridization In The Temperate Bamboos: Is Pleioblastus Simonii A Species Of Hybrid Origin?, Morgan Brown

Theses

Japanese river bamboo (Pleioblastus simonii, ‘medake,’‘kawadake’) is an ecologically important species of temperate bamboo native to Japan. This species is widely known and historically important in Japanese rural farm life. Based on morphological data, Japanese river bamboo is classified in Pleioblastus section Medakea (Poaceae: Bambusoideae) along with five other Japanese species, which are collectively considered to represent a phylogenetically distinct lineage. However, recent studies suggest that Japanese river bamboo may have arisen as a result of previously undetected hybridization (i.e., cryptic hybridization), while also calling into question the diversity of section Medakea. The role of hybridization in natural plant populations …

Forming Connections: The Cell-Autonomous Roles Of Gata3 And Neurod1 In Developing Auditory Neurons, Elizabeth Madison Ketchum

Dissertations

Hearing loss is the most prevalent sensory disorder, yet current treatment options are restricted to hearing aids and cochlear implants. Both treatment options require the presence and proper formation of inner ear auditory afferent neurons, known as spiral ganglion neurons (SGNs). In many patients with hearing loss, these neurons are either not present or are improperly organized, making current therapeutic options nonviable. Although it would be ideal to preserve functioning SGNs or to regenerate them, we are still learning how SGNs develop and form their projections to their peripheral and central targets. Therefore, a better understanding of the genes involved …

Characterization Of Hemocytes In Amblyomma Americanum And Investigation Of Traf6’S Role In Proliferation Of Hemocytes In Response To Infection, Jacquelyn T. May

Electronic Theses and Dissertations

Amblyomma americanum is a medically important vector in the southeast United States. Cellular and molecular aspects of the immune system of this species were examined. To investigate cellular processes, hemocytes produced in response to gram-negative infection were characterized according to their ultrastructure. Four hemocyte types were identified: prohemocytes, plasmatocytes, type-I granulocytes, and type-II granulocytes. To elucidate molecular processes, we investigated AamTRAF as an immune-related gene by silencing the gene using RNAi then quantifying the hemocytes after inoculation with gram-negative and positive bacteria. It was found that silencing AamTRAF caused a decrease in hemocyte proliferation in response to gram-positive but not …

Origin And Epigenetic Regulation Of Cutaneous T Cell Lymphoma, Carly M. Harro

USF Tampa Graduate Theses and Dissertations

The pathogenesis of Cutaneous T cell lymphoma (CTCL) remains unclear. Using conditional knockout mice, we found that ablation of the genomic organizer Special AT-rich sequence-binding protein-1 (Satb1) caused malignant transformation of mature, skin-homing, Notch-activated CD4+ and CD8+ T cells into progressively fatal lymphoma. Mechanistically, Satb1 restrained Stat5 phosphorylation and the expression of skin-homing chemokine receptors in mature T cells. H3K27 and H3K9 trimethylation occluded the SATB1 promoter in Sézary cells, while inhibition of SUV39H1/2 methyltransferases (unlike EZH2 inhibition), restored protective SATB1 expression and selectively abrogated the growth of primary Sézary cells more effectively than romidepsin. Additionally, using single-cell RNA/TCR sequencing …