Digital Commons Network^™

Recruitment, Reprogramming, And Function Of Trpv1+ Sensory Nerves In The Development And Progression Of Head And Neck Cancer, Anthony Restaino

Dissertations and Theses

Head and neck squamous cell carcinomas (HNSCC) are an epithelial cancer prevalent across the world and are divided into two subcategories: human papillomavirus-mediated (HPV+) and carcinogen-mediated (HPV-) HNSCC. These subgroups have distinct patient populations, divergent responses to therapy, and prognoses, however the foundational mechanisms that facilitate these differences are not well understood or defined. Recently, the presence and function of sensory neurons within the tumor environment of various solid tumors has been identified and investigated. Herein, we identify differences in the presence of TRPV1+ sensory neurons and neuron structures in the tumor environment of HPV+ and HPV- HNSCC, correlating with …

Identification And Characterization Of Novel Crispr-Cas Immune Effectors, Christian Fredrick Baca

Student Theses and Dissertations

Bacteria are under constant threat by the viruses that infect them called bacteriophages or phages for short. It is predicted that phages outnumber bacteria by an order of magnitude, producing a tremendous pressure for resistance mechanisms against this threat. One of the most abundant immune systems bacteria have evolved to combat this are CRISPR-Cas systems, which have been studied extensively due to their fascinating biology and usefulness in biotechnology and therapeutics. My thesis focuses on the discovery and characterization of three new CRISPR-Cas effector proteins that provide immunity in bacteria in response to phage challenge with highly diverse activities. CRISPR-Cas …

Understanding Of Intrinsic Sources Of Dna Damage That Drive Human Disease: A Foray Into The Study Of Dna Interstrand Crosslinks And Genome-Embedded Ribonucleotides, Nicolas Johannes Georg Blobel

Student Theses and Dissertations

Sources of damage to deoxyribonucleic acid (DNA) can be categorized broadly into exogenous and endogenous. Exogenous sources range from environmental (e.g., air pollution, tobacco and alcohol, ultraviolet (UV) radiation due to sun exposure), to pharmaceutical sources (e.g., chemotherapeutics such as cisplatin). The other main category of DNA damage is endogenous, which can range from metabolites such as reactive oxygen species (ROS) produced in the cells as byproducts of metabolic pathways, to incorrect bases incorporated into the genome. In this thesis, I will focus on two types of endogenous DNA damage: 1) interstrand crosslinks (ICLs) formed by DNA damaging aldehydes and …

Potential Of Anogenital Distance As A Genetic Selection Trait In Canadian Holstein, G.R. Dodd, F.S. Schenkel, F. Miglior, T.C. Bruinjé, M. Gobikrushanth, J.E. Carrelli, M. Oba, D.J. Ambrose, C.F. Baes

Dairy Science and Food Science Faculty Publications: 2022 to Present

Maintaining optimal fertility in dairy cattle herds is a global challenge that is typically addressed through the genetic selection of fertility indicator traits. However, many of the traits currently implemented in breeding programs are heavily influenced by environmental factors, resulting in a slow rate of genetic improvement. Anogenital distance (AGD) has recently emerged as a promising fertility indicator trait due to its association with favorable reproductive outcomes and its higher heritability estimates compared with currently evaluated traits. This study aimed to enhance the understanding of AGD's genetic potential by estimating its genetic parameters in Canadian Holsteins, assessing the reliability …

Ashwagandha And Sexual Health In Women With Hypoactive Sexual Desire Disorder: Exploring Extent Of Adaptogenic Properties, Rhea Chatterjee

AUCTUS: The Journal of Undergraduate Research and Creative Scholarship

Hypoactive Sexual Desire Disorder (HSDD) affects 40% of women and potentially decreases their quality of life. Currently, the primary treatment for HSDD is Flibanserin, which is a serotonergic agonist and an antidepressant. However, the limited efficacy of Flibanserin encourages the exploration of the utilization of traditional drugs such as Withania somnifera, otherwise known as Ashwagandha, as an alternative treatment for HSDD. Minimal studies examine ayurvedic medications or the symptoms of illnesses that traditional Western medicines are unable to treat. This comprehensive literature review investigated the efficacy of Ashwagandha in improving sexual function in women with HSDD. The paper evaluated …

What Are The Genetic Influences Of Alcohol Sensitivity And Alcohol Metabolism? A Narrative Review Of Human Studies, Erwin Murray, Karen G. Chartier Phd, Msw

UROP Posters

Background: Alcohol sensitivity and alcohol metabolism are two phenotypes associated with alcohol use disorder (AUD) influenced by genetics. This narrative review aims to answer “What are the genetic influences of alcohol sensitivity and alcohol metabolism?” to gain a better understanding of the genetic aspects of AUD.

Methods: A database search was performed in PubMed. Empirical human genetic studies published between 2009 and 2025 that focused on alcohol sensitivity (measured by the Self-Rating of the Effects of Alcohol scale) or alcohol-metabolizing genes were eligible for review. Studies were screened to determine inclusion for the current review.

Findings: Fifteen …

Effects Of Gas Exchange Rates Between C3 And C4 Plant Species, Samantha L. Moya, Mollie Ouk, Aisha Goni

UROP Posters

Spinach and basil (C3 plants) were compared with corn (C4 plant) to

explore how photosynthetic pathways affect CO2 consumption. Corn

seeds were obtained and planted in Miracle-Gro® soil to be observed

over the duration of a month. Leaves (starting from 3,4, and 10) from

each plant were then taken and placed into a bottle and closed off

with a CO2 gas probe that measured levels of carbon dioxide in ppm.

Spinach and basil leaves were used as a comparison for measuring

the rate of CO2 concentration. This is done to compare the gas

exchange rates between C3 and C4 plants. …

Science, Physiology, And Nutrition For The Nonscientist, Judi S. Morrill

Open Educational Resources

A wonderful blend of physiology, nutrition, biochemistry, genetics, biology, evolution, chemistry--what we all need to know as informed citizens. A basic knowledge of the life sciences and how our bodies work--to promote our own good health, especially as we're bombarded with misleading advertisements, soundbites, and the like. DNA fingerprinting, calorie requirements, dietary advice, genetic engineering (including gene editing with CRISPR cas9)--all in an easy-to understand book.

Synthesis And Evaluation Of Anti-Hiv Activity Of Fatty Acyl Conjugates Of Tenofovir Alefanamide, Muhammad Sajid, Naglaa Salem El-Sayed, Louise A. Ouattara, Amita Verma, Gustavo F. Doncel, Keykavous Parang, M. Iqbal Choudhary, Hina Siddiqui

CONRAD Publications

The activity of nucleoside and nucleotide analogs as antiviral agents requires phosphorylation by intracellular enzymes. Phosphate-substituted analogs have low bioavailability due to the presence of ionizable negatively-charged groups. To circumvent this limitation, several prodrug approaches have been proposed and developed. Herein, we hypothesized that the conjugation of anti-HIV fatty acids with the nucleotide tenofovir alafenamide (TAF) (1) could improve the anti-HIV activity of the nucleotide. Several fatty acyl amide conjugates of TAF were synthesized and evaluated in comparative studies with TAF. The synthesized compounds were evaluated as racemic mixtures for anti-HIV activity in vitro in a single-round HIV-1 infection assay …

Beyond The Byproduct: Exploring Approaches For The Sustainable Valorization Of Underutilized Food Streams, Ian Phillip Israelsen

Graduate Theses, Dissertations, and Problem Reports (ETD)

Commercial food processing creates side-streams that are often underutilized yet hold significant potential for valorization into value-added products for consumer use. This study investigated and compared potential protein recovery and lipid removal potential from buckwheat (BW; Fagopyrum esculentum Moench), brewer’s spent grain (BSG), and coffee silverskin (CSS) using a one-step solvent defatting and a pH-shift protein extraction method. The extraction efficiency yields of extracted protein from CSS were significantly lower than all other samples (p < 0.05). The defatted BW had the highest extracted protein content of all samples (p < 0.05). The sizes of the proteins in the starting materials were observed using LDS-PAGE. These sizes were consistent with published values and were mostly unchanged by defatting or the pH-shift process. The presence of 13S globulins and 2S albumins was confirmed under reducing conditions. Protein extracted from all native samples had lower total free essential amino acids than the starting materials. Native CSS and extracted protein followed this trend, but in defatted CSS and respective extracted protein samples, the extracted proteins had higher free essential amino acid content than the starting materials, sometimes of twofold or greater (p < 0.05). After defatting, the percentage of lipids recovered compared to the original lipid content of the samples was measured. The crude fat content of native and hexane-defatted BW flour was higher than BW flour defatted with ethanol (p < 0.05). The lipid extraction efficiency of all samples ranged from 4.6 ± 1.26%–43.20 ± 14.21%. The mass of the native and defatted starting materials were recorded at each step of processing, with reasonable losses assessed. The major non-polar lipid classes in each starting material were separated using thin-layer chromatography. All samples also displayed the presence of polar lipids. When comparing starting materials, BW and BSG was the most effective for protein extraction, and BSG has the most promise for lipid removal and potential for upcycling. All the examined starting materials show promise for use in food supplementation, especially as native flours. These products are plentiful and considered underutilized or side-stream products.

Influence Of Different Rates Of Biochar And Deer Browsing On Pollinator Plant Productivity, Bipana Bhusal

Graduate Theses, Dissertations, and Problem Reports (ETD)

Biochar, a carbon-rich material produced from biomass, has received wide attention for soil amendment to improve plant growth. However, its specific effects on pollinator friendly plants remain poorly understood. In this study, we evaluated the effects of four biochar application rates (0, 10, 20, 40 tons/acre) and deer exclusion (fenced vs. unfenced) on the productivity of three pollinator species; Buckwheat (Fagopyrum esculentum), Plains Coreopsis (Coreopsis tinctoria), and Black-eyed Susan (Rudbeckia hirta) in a utility right of way with a history of mining. A split-plot randomized design was used, and the results were analyzed using …

Microbial And Plant Biodiversity In Appalachian Agroecosystems And Their Implications For Soil Health, Kinsey Reed Close

Graduate Theses, Dissertations, and Problem Reports (ETD)

The sustainability of agricultural landscapes depends on understanding the complex interactions between plants, soil, and microbes. In Appalachia, a region shaped by complex terrain and long histories of human and ecological interaction, small family farms produce hay, livestock, and row crops. These agroecosystems, though often treated as “artificial” by many ecologists, have the potential to support both food production and biodiversity conservation if managed with an understanding of ecological complexity. This dissertation examines how plant and microbial diversity interact with soil and management to influence nutrient cycling, soil health, and long-term resilience in Appalachian agricultural systems. A literature review revealed …

Distracted But Still Listening: How Cognitive And Perceptual Load Affect Multisensory Integration, Eddie Lee

Honors Theses

There is an ongoing debate about whether multisensory integration (MSI) occurs automatically and before attention is allocated or if multisensory integration occurs after attention is allocated and is subject to top-down attentional control. A recent study investigated this by manipulating the availability of attentional resources in a dual-task paradigm, finding that when the demands of the secondary task increased, susceptibility to the Sound-Induced-Flash-Illusion, a non-speech audiovisual illusion, also increased (Michail & Keil, 2018). This was taken as evidence for the role of post-attentive, top-down control during MSI. In the present study, we extend this logic to explore the role of …

Characterization Of The Slc7a5/Slc3a2 Amino Acid Transporter In Human Pleural Mesothelial Cells, Ann Francis

Biotechnology Theses

The SLC7A5/SLC3A2 amino acid transporter moves essential amino acids, such as leucine, phenylalanine, and tryptophan, across the cellular plasma membrane. SLC7A5 overexpression was identified in diverse cancers, suggesting a role in tumorigenesis and cancer cell proliferation. However, the role of SLC7A5/SLC3A2 in other aggressive cellular phenotypes, including mesothelial mesenchymal transition (MesoMT), remains unexplored. RNA sequencing analyses identified SLC7A5 as one of three highly upregulated SLCs in mesothelial cell derived myofibroblasts. This sodium independent transporter exhibits a high affinity for branched chain amino acids such as leucine; however, what role, if any, this channel plays in MesoMT is unclear. SLC7A5 knockdown …

2025 Annual Report, Tennessee. Division Of Forestry And Tennessee. Department Of Agriculture

Forestry Annual Reports

This annual report presents an overview of Tennessee Forestry Commission programs and management.

Quantifying Modifiable Lifestyle Behaviors And Influences Associated With Preventable Cancers In Selected Rural Counties: A Mixed Method Study, Jecinta Scott

Dissertations and Theses

Cancer is the second leading cause of death in the United States disproportionately affecting rural communities. This dissertation study investigates the involvement of rural communities in lifestyle behaviors associated with increased risk of cancers, the impact of socioeconomic factors, and what influences their behavior and the impact of political party affiliation. The study was conducted using a mixed-method quantitative data analysis enhanced by qualitative interviews. It began with an extensive literature review to identify existing research, and evidence gaps on the topic. Data collection involved retrospective quantitative extraction from the Centers for Disease Control and Prevention’s Behavioral Risk Factor Surveillance …

Study On Motion Prediction Analysis Of Large Vessels Entering Kaohsiung Port Second Harbor, Li-Heng Cheng, Hsing-Yu Wang

Journal of Marine Science and Technology–Taiwan

Pilotage is a primary service offered by ports, ensuring the safe passage of entering and exiting vessels. This study applied motion prediction analysis to large vessels navigating the constrained waterways of Kaohsiung Port’s second harbor. To address the needs of pilots and port operators, a simplified planar motion equation was developed that incorporated speed over ground and rate of turn (ROT) as primary variables. The model relied on inputs of limited navigational data, enabling pilots to predict changes in heading and position over time and determine the conditions for safe harbor entry. Vessel paths and turning angles were analyzed to …

The Effects Of A History Of Child Trauma On Breastfeeding Outcomes, Emily Flynn

Graduate Research Theses & Dissertations

Breastfeeding provides significant health benefits for both parent and child, yet many parents discontinue earlier than recommended. While childhood sexual abuse has been associated with breastfeeding difficulties, limited research has examined the broader effects of other forms of childhood maltreatments on breastfeeding outcomes. This cross-sectional study examined the relationship between a history of childhood trauma and breastfeeding outcomes, with social support explored as a potential moderator. Participants (n = 194) were birthing parents of children under the age of five, recruited from online parenting communities. Measures included the Adverse Childhood Experience International Questionnaire (ACE-IQ), a breastfeeding duration item, and a …

Developing Stiripentol Analogs As Potential Ldh Inhibitors For The Treatment Of Glioblastoma, Anshika Y. Jain

Theses and Dissertations

Glioblastoma multiforme (GBM) is a highly proliferative brain tumor that has a 5-year survival rate of ~7 %. Temozolomide (TMZ) is the current standard of care therapeutic for GBM. However, 50% of patients develop resistance to TMZ. Therefore, further investigation for new GBM therapeutics is necessary to overcome this issue of drug resistance. GBM patients are known to overexpress lactate dehydrogenase (LDH), which is inversely correlated with their survival. This key glycolytic enzyme catalyzes the interconversion of pyruvate and lactate and plays an important role in cancer proliferation and invasion. Therefore, we aimed to inhibit LDH for developing therapeutics for …

Evaluating The Condition Of Age-0 Burbot In Relation To Diet, Cian Verbridge

Journal of Earth and Life Science

Burbot are becoming more and more popular for angling and aquaculture. However, populations have been declining across the world. Very little information is available about their early life and their interactions in the ecosystem due to challenges in sampling. Condition estimates and diet metrics were used to better understand the status of burbot in Lake Bemidji. Using backpack electrofishing, 45 young of the year burbot were collected. The lengths ranged from 86 to 146 mm and the wet weights ranged from 4.29 to 24.36 g. The stomach contents were removed and stored in ethanol for later analysis. The burbot were …

Modeling Wild Rice Bed Health: A Dual Metric Approach For Bed Strength And Invasive Impact, Seth Sisneros-Martinez

Journal of Earth and Life Science

Wild rice (mannoomin; Zizania palustris) is an aquatic grain that grows in slow-moving rivers and shallow bays throughout northern Minnesota. In Headquarters Bay on Leech Lake, wild rice has served as a cultural staple for Indigenous communities for centuries. However, its population has declined in recent years due to multiple environmental issues. One potential contributor is Eurasian watermilfoil (Myriophyllum spicatum; EWM), an invasive species that forms dense mats capable of outcompeting native aquatic vegetation, including wild rice. EWM was first recorded on the southern shoreline of Leech Lake in 2005 and has since become widespread. This study …

René Dubos: An Annotated Bibliography, Carol L. Moberg

René Dubos: An Annotated Bibliography

René Dubos (1901–1982), a prominent 20th century scientist, humanist, and philosopher, was a prolific author. Affiliated for more than 50 years with The Rockefeller Institute for Medical Research/The Rockefeller University, his studies ranged from antibiotics and the role of bacteria in human diseases to formulating broad ecological and environmental questions affecting human health and disease. His seminal writings explore a lifelong belief that a living organism—whether microbe, human being, society, or the Earth itself—could be understood only through its relationships with everything else.

This comprehensive bibliography of more than a thousand works by René Dubos includes brief annotations for each …

Deriving Structural Insights About Mesoscale Chromatin Folding Using Coarse-Grained Oligonucleosome Modeling, Ariana Brenner Clerkin

Student Theses and Dissertations

Here, I investigate chromatin organization on the scale of a few nucleosomes (~1kb). I developed an experimentally-validated coarse-grained polymer model and applied it 1) to show how chromatin fiber parameters, such as nucleosome spacing and breathing, impact chromatin organization on this scale–the mesoscale 2) to interpret mesoscale sequencing assay data and 3) to demonstrate that spatially-correlated cleavage, not protein protection, primarily drives the shape of the distribution of DNA fragment lengths resulting from ionizing-radiation damage. Pair-wise DNA-DNA contact data from DNA sequencing-based assays have the potential to provide locus-specific information about the relationships between chromatin structure and function. Radiation-induced correlated …

Germline Genetic Modulator Of Cancer Metastasis, Wenbin Mei

Student Theses and Dissertations

Metastasis formation is the most critical determinant of cancer survival outcome. Identifying patients at risk for metastatic relapse facilitates clinical decision and the use of appropriate adjuvant therapy, thus having a profound impact on patient survival. A central dogma in cancer is that during tumorigenesis, cancer cells acquire somatic mutations that regulate metastatic likelihood during evolution of the primary tumor. However, despite extensive tumor sequencing efforts, such causal somatic metastasis driver mutations have not been found, limiting the discovery of biomarkers, mechanisms and drug targets of cancer metastasis. In this thesis, I report a germline genetic driver of breast cancer …

Sequential Transcriptional Gates In The Thalamo-Cortical Circuit Coordinate Memory Consolidation, Andrea Terceros

Student Theses and Dissertations

How are memories maintained over weeks, months or even years? The molecular mechanisms that enable memories to persist over long time-scales remain poorly understood. As a point of entry, recent work in our lab revealed that beyond the hippocampus, where memories are initially formed over hours/days, the thalamo-cortical circuit is important for the gradual stabilization of memories over weeks/months. In this thesis, I aimed to reveal the molecular mechanisms operating in the thalamo-cortical circuit that may be responsible for extending memory time-scales. I began by developing a virtual reality-based behavioral paradigm where, by varying the frequency of learned associations, mice …

Recording Cellular Interactions In Germinal Centers And Beyond, Sandra Nakandakari-Higa

Student Theses and Dissertations

In multicellular organisms, each cell has a distinct identity characterized by unique transcriptional and chromatin accessibility profiles. However, to truly understand the organization and function of such systems, it is not enough to merely characterize individual components; we must also investigate how these components interact and communicate through direct cellular interactions. This is especially true in the immune system, where cell-cell interactions are fundamental. For instance, the priming of antigen-specific T cells relies on their selective engagement with antigen-presenting cells (APCs) displaying the T cell's cognate antigen, distinguishing them from a pool of non-specific counterparts. Similarly, the production of antibodies …

Modulation Of The Crispr-Cas9 Immune Response, Hyejin Kim

Student Theses and Dissertations

Bacteria face an onslaught of ever-changing viral (phage) invaders. Bacteria and phages are locked into an evolutionary arms race where both must continually adapt to survive. In response, bacteria have developed numerous immune systems to protect themselves, including CRISPR-Cas. CRISPR-Cas systems provide adaptive immunity through the acquisition of short DNA sequences from invading phages, known as spacers. Spacers are inserted into the CRISPR locus and serve as templates for the transcription of guides used by RNA-guided nucleases to recognize complementary sequences of the invaders and start the CRISPR immune response. CRISPR-Cas systems need to acquire enough spacers to mount an …

The Evolution Of Ribosome Assembly: Making Ribosomes In The Mitochondria, Chloe Burnside

Student Theses and Dissertations

Mitochondrial ribosomes (mitoribosomes) synthesize proteins encoded within the mitochondrial genome that are assembled into oxidative phosphorylation complexes. As such, the biogenesis of mitoribosomes is essential for ATP production and cellular metabolism. Despite significant progress in elucidating the structures of mature mitoribosomes, a comprehensive understanding of their assembly pathways remains elusive. This thesis presents the first structural characterization of assembly intermediates of the mitochondrial small subunit (mtSSU) in eukaryotes. To gain mechanistic insight into the process of SSU assembly in the mitochondria, I set out to enrich and characterize intermediates of SSU assembly in the mitochondria of S. cerevisiae. By employing …

Making Molecular Movies: Using Single-Molecule Techniques To Unveil Hidden Features Of Protein-Chromatin Interactions, Gabriella N. L. Chua

Student Theses and Dissertations

Beyond the genetic code embedded within a sequence of DNA, the physical features of the double helix as a semi-flexible polymer is a critical dimension that regulates the function of every DNA-binding protein that exists. These proteins can assemble, translocate, and change conformation while bound to DNA and can even alter its physical state, which are often crucial to their physiological roles in the cell. Eukaryotic genomic DNA is also packaged into units called nucleosomes, which offer another layer of physical regulation for proteins operating on chromatin. Previously, tracking these protein behaviors on DNA and chromatin had been technically challenging, …

The Spatiotemporal Dynamics Of Nomadic Behavior In The Clonal Raider Ant, Ooceraea Biroi, Dennis Octavio Melendez

Student Theses and Dissertations

Nest relocation is integral to the lives of many social insects. Army ants have taken this behavior to the extreme, with many species relocating an entire colony of over 100,000 ants plus brood almost daily. Despite its prevalence, the question of how army ant colonies emigrate has been debated for many decades, and still awaits a definitive answer because conducting well-controlled field experiments with their massive and aggressive colonies is challenging. In ants, the Dorylinae subfamily has given rise to most known army ants. Therefore, performing experiments in non-army ant dorylines that can be maintained in a laboratory setting presents …