Life Sciences Commons^™

Development Of Software For Genetic Distances, Genotyping, And Phylogenetics Using Rna-Seq Data, Andrew C. Tapia

Theses and Dissertations--Computer Science

This dissertation concerns a new application of RNA-seq data—computation of pairwise genetic distance matrices. RNA-seq captures sequences of RNA molecules in some cells or tissues of interest. RNA-seq provides data are well-suited to studies examining gene expression, and its use for this purpose is currently widespread. A pairwise genetic distance matrix, the main topic of this dissertation, quantifies differences in the genomes of every pair of samples (e.g., individuals) in a given set. Genetic distance matrices are versatile; they can be used for various kinds of downstream analyses, including genotyping, phylogenetics, and genetic diversity measurement. Although DNA sequence data are …

Exploring The Role Of Transcription Factor Nrf1 In Autophagy And Inhibiting The Nrf1 Bounce-Back Response, Madison A. Ward

Theses and Dissertations

Cells exposed to proteotoxic stress invoke adaptive responses aimed at restoring proteostasis. Our previous studies have established a firm role for the transcription factor Nuclear factor-erythroid derived-2-related factor-1 (Nrf1) in responding to proteotoxic stress elicited by inhibition of cellular proteasome. Following proteasome inhibition, Nrf1 mediates the synthesis of new proteasomes, thus enabling cells to mitigate proteotoxic stress. Here, we report that under similar circumstances, multiple components of the autophagy-lysosomal pathway (ALP) were transcriptionally upregulated in an Nrf1-dependent fashion, thus providing the cells with an additional route to cope with proteasome insufficiency. In response to proteasome inhibitors, Nrf1-deficient cells exhibited profound …

Investigation Of Rna-Binding Protein Expression Changes In The Hippocampus Following Doxorubicin And Cyclophosphamide Treatment, Lijie Chen

Dissertations and Theses

This study investigated the molecular mechanisms underlying chemotherapy-induced cognitive impairment (CICI) following doxorubicin and cyclophosphamide treatment in a rat model, revealing three significant alterations in hippocampal tissue: selective downregulation of heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) (21% decrease, p=0.0298), compromised astrocytic network integrity evidenced by reduced GFAP-positive area in cornu ammonis 3 (CA3) (24%, pB=0.026) and dentate gyrus (DG) (19%, pB=0.027) regions, and elevated cellular senescence marker p19Arf specifically in DG (69%, pB=0.033) and CA3 (27%, pB=0.024). The inverse relationship between hnRNPA1 reduction and p19Arf elevation suggests a potential mechanistic link between RNA dysregulation and senescence induction, with pronounced vulnerability in …

Toxin-Like Proteins In The Venom Of Drosophila Parasitoids, Lady V. Cardenas

Dissertations and Theses

The figitid parasitoid wasps of Drosophila are gaining importance in agriculture due to their ability to kill the resilient soft-fruit pest Drosophila suzukii. Their success and infection strategies vary, and the mechanisms underlying these differences are largely unknown. Some of their venom proteins have been shown to be important in suppressing host defense. Here, we report that Ganaspis brasiliensis, a parasitoid of D. suzukii survives well on Drosophila yakuba, a host species with a strong cellular immunity, and infected flies are unable to mount a strong immune response. To predict possible toxin-like proteins in Ganaspis venoms that might suppress cellular …

Intracellular Survival Of Staphylococcus Aureus In Macrophages During Osteomyelitis, William A. Lathram, Christopher D. Radka

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Staphylococcus aureus, traditionally viewed as an extracellular pathogen, is increasingly recognized for its ability to persist intracellularly, particularly within macrophages. This intracellular lifestyle is central to osteomyelitis, a chronic bone infection characterized by persistent inflammation, bone destruction, and impaired repair. Within bone, S. aureus exploits macrophage plasticity by driving a shift from pro-inflammatory, bactericidal M1-like states to anti-inflammatory, tissue-reparative M2-like phenotypes. This polarization suppresses immune clearance and promotes an environment conducive to bacterial survival and dissemination. Additional strategies – including biofilm formation, small colony variants, and inhibition of phagolysosomal killing – further enhance persistence and immune evasion. While these …

Emotion Processing In Adolescents With Epilepsy And Healthy Controls Using Multi-Modal Neuroimaging, Frances Kathryn E. King

Bioengineering Dissertations - Archive

Epilepsy is increasingly recognized as a disorder not only of seizures but also of widespread network dysfunction, impacting cognitive and emotional processing. One critical cognitive process affected in epilepsy is emotional conflict processing, which relies on the interplay of multiple brain networks. However, the spatiotemporal dynamics of emotional conflict processing in epilepsy, particularly in adolescents, have remained poorly understood. This dissertation investigated the neural mechanisms underlying emotional conflict processing in typically developing adolescents and adolescents with epilepsy using magnetoencephalography (MEG). The first study elucidated the spatiotemporal profile of emotional conflict processing in 24 typically developing adolescents using magnetoencephalography (MEG). Cluster-based …

International Society Of Sports Nutrition Position Stand: Β-Hydroxy-Β-Methylbutyrate (Hmb), John A. Rathmacher, Lisa M. Pitchford, Jeffrey R. Stout, Jeremy R. Townsend, Ralf Jäger, Richard B. Kreider, Bill I. Campbell, Chad M. Kerksick, Patrick S. Harty, Darren G. Candow, Brandon M. Roberts, Shawn M. Arent Ph.D., Cscs*D, Fissn, Facsm, Fnak, Douglas S. Kalman, Jose Antonio

Faculty Publications

Position Statement: The International Society of Sports Nutrition (ISSN) bases the following position stand on an analysis of the literature regarding the effects of β-Hydroxy-β-Methylbutyrate (HMB). The following 12 points have been approved by the Research Committee of the Society: 1. HMB is a metabolite of the amino acid leucine that is naturally produced in both humans and other animals. Two forms of HMB have been studied: Calcium HMB (HMB-Ca) and a free acid form of HMB (HMB-FA). HMB-FA appears to lead to increased appearance of HMB in the bloodstream when compared to HMB-Ca, though recent results are mixed. 2. …

Comparative Dna Extraction Methods To Use For Lamp Assay As Molecular Diagnosis Of Human Schistosomes From Urine Samples, Brittany R. Pulkkila, Chummy Sikasunge, James Mwansa, Nilanjan Lodh

Clinical Lab Sciences Faculty Research and Publications

Background

Schistosomiasis in Africa is an ongoing public health problem that is caused by two major human species, Schistosoma mansoni and S. haematobium, which often cause concurrent infections. Due to the global goal of controlling or eliminating schistosomiasis as a public health problem, the issue of diagnostic sensitivity has become more critical in the assessment of program success. In that regard, the World Health Organization (WHO) has drawn attention to the need for field-applicable tests with high specificity and sensitivity.

Methods

To address this, we have evaluated the amplification of S. mansoni and S. haematobium cell-free repeat DNA by …

Effect Of Forage Allocation On Steer Performance When Grazing Cereal Rye, Shelby L. Davies-Jenkins, Abigail M. Sartin, Daren D. Redfearn, Mary E. Drewnoski

Nebraska Beef Cattle Reports

Summary with Implications

Cereal rye is the most common cover crop planted today. With its good winter tolerance and rapid spring growth during a gap in perennial pasture productivity, it is an attractive forage source in early spring. Unfortunately, optimum stocking rates and how they are related to forage biomass availability are unknown. The study objective was to understand the effect of forage allowance on steer performance when rotationally grazing fall-planted cereal rye in spring. Stocking rate was negatively correlated with pounds of forage offered. Surprisingly, amount of forage offered related to average daily gain. Growing steers grazing cereal rye …

Strategies Affecting Performance And Profitability Of May-Born Steers, Dempster M. Christenson, Jacki A. Musgrave, Richard N. Funston

Nebraska Beef Cattle Reports

Summary with Implications

This study compared the performance and economic outcomes of differing backgrounding and feedlot systems in May-born yearling steers. We hypothesized reduced supplementation with adequate forage availability while backgrounding weaned steers will yield a similar carcass with greater profitability. It was hypothesized yearling steers backgrounded on pasture before finishing in feedlot would have a more valuable carcass that is more profitable than steers that enter the feedlot immediately. Weaned steer calves were backgrounded with ad libitum hay and 4 lb/d supplement in drylot or on pasture with 1 lb/d supplement. As yearlings, half of each backgrounding group immediately …

Impact Of Feeding Distillers Grains Compared To New Fractionated Distillers Grains (Solbran) On Feedlot Cattle Performance And Enteric Methane, Debora G. Sousa, Rebecca L. Mcdermott, Mitchell M. Norman, James C. Macdonald, Rick Stock, Ryan A. Mass, Galen E. Erickson

Nebraska Beef Cattle Reports

Summary with Implications

This study evaluated feeding wet or dry traditional distillers grains with wet and dry fractionated distillers (Solbran) fed at 40% of diet DM compared to a corn control diet on enteric methane emissions and performance. Compared to the control, there was no difference in carbon dioxide production, but there was an increase in methane production in the steers fed fractionated distillers compared to conventional distillers. Feeding steers traditional or fractionated distillers grains increased consumption, increased gain, but improved conversions only for steers fed WDGS, while steers fed the other distillers grains had worse or the same feed …

Spatial Analysis Of Heavy Metal Enrichment In A Historic Appalachian Mining Stream, Eric M. Torres

Research and Creativity Symposium

This study examined the spatial distribution of heavy metals along the Levisa Fork and primary tributaries in Buchanan County, VA and Pike County, KY. Buchanan and Pike Counties have a long history of coal mining, a process known to release heavy metals into surrounding waterways. Exposure to certain heavy metals, such as arsenic and lead, has been known to cause health problems, such as cancer and organ damage. The study looked at concentrations in riverine sediments, surface water and groundwater for As, Al, Cr, Cu, Fe, Li, Mg, Mn, Ni, Pb and Zn. Sediment samples were collected, dried and digested …

How To Approach Medical Education Research, Stefanie Attardi, Jeff Cross, Sarah Lerchenfeldt

Books and Book Chapters

Medical education research blends two of the core functions of academic medicine: teaching and scholarship. Its value is increasingly recognized in promotion and tenure decisions, and in the number of funding sources available. Similar to other types of research, it starts with a well-crafted question and a thorough review of the literature. For a successful project, it is critical to select the research design that can best answer the research question, keeping in mind its advantages and limitations. Because the research design must also adhere to ethical principles, working closely with the local Institutional Review Board prior to starting the …

Aspen Stands Enrich Bird Communities Following A Wildfire In A Montane, Mixed Conifer Forest, Cody Q. Lane

Graduate Student Theses, Dissertations, & Professional Papers

Fire is a major ecological force in most terrestrial systems, but the responses of animal communities to fire vary markedly across ecosystems due to variability in fire regimes and vegetation communities. Quaking aspen (Populus tremuloides) is unique within coniferous forests of western North America for its ability to regenerate following wildfire via vegetative resprouting. As managers employ techniques to restore fire regimes and conserve declining aspen forests, it becomes important to understand how aspen alters postfire communities. Our objectives were to (1) assess how aspen interacted with fire severity and years since fire to influence avian species and …

Positive Allosteric Modulation Of Glun1/Glun3 Nmda Receptors, Mia Ruth Johns

Graduate Student Theses, Dissertations, & Professional Papers

N-methyl-D-aspartate (NMDA) receptors are ionotropic glutamate receptors that mediate excitatory neurotransmission in the central nervous system (CNS) where they play critical roles in normal and pathological brain functions and neurodevelopment. While the glutamate/glycineactivated GluN2-containing NMDA receptors (GluN1/GluN2) have been extensively studied, the physiological roles and pharmacology of glycine-activated GluN3-containing receptors (GluN1/GluN3) remain less understood. Although GluN1/GluN3 receptors exhibit unique functional properties and play distinct roles in neuronal development and synapse maturation, studies of their precise roles in neurophysiology and circuit function are impeded by limited availability of GluN3-selective pharmacological tools. This study describes UCM-A86, a novel GluN3-selective positive allosteric …

Small Mammal Population Dynamics And Torpor Use In A Changing Subnivean Environment, Derik Butts

Graduate Student Theses, Dissertations, & Professional Papers

Despite global temperature increases, winter soil surface temperatures in some northern regions might actually be getting colder due to diminishing snowpacks exposing the soil surface to ambient winter conditions. Small mammal species in northern temperate areas often utilize a microclimate beneath the snow, known as the subnivium, to escape harsh winter conditions. Exposure to winter conditions without the subnivium as a buffer could cause small mammals to experience physiological stress and population declines. In this thesis, I explore the impacts of a declining subnivium from two complementary perspectives. In chapter 1, we used a structural equation model (SEM) to test …

Investigating Mono-Driver Versus Multi-Driver Oncogenesis Via Alterations To Cell Signaling Pathways, Abygail Chapdelaine

Open Access Dissertations

The latest edition of Global Cancer Statistics released by the American Cancer Society reported approximately 20 million newly diagnosed cancer cases worldwide in 2022 with 9.7 million deaths. This ranks cancer as the second leading cause of death worldwide. For the majority of cancer patients, the standard treatment approach is chemotherapy and/or radiation therapy, and while this has been successful in some patients, a lack of specificity to cancer cells causes severe side-effects when these agents damage healthy cells. Despite extensive efforts that have gone into developing targeted cancer therapeutics that block functions specific to cancer, they have not been …

Light, Symbiosis, And The Biology Of Corals, Taylor R. Lindsay

Open Access Dissertations

Light is critical for the survival of most shallow water scleractinian corals. Corals are mixotrophs, acquiring energy via both feeding on water column plankton and photosynthesis via a symbiotic relationship with dinoflagellates living within their tissues. Corals rely heavily on photosynthetically derived metabolites through this symbiotic relationship, intrinsically linking their biology to light availability. Corals are known to modulate their biology to maximize light capture. However, there is a limited understanding of the interaction between morphology, physiology, and energetic strategy, as well as how light may affect these relationships. In Chapter 1, we quantified the morphology, physiology and energetic …

Impacts Of Multiple Coastal Stressors Across Life-History Stages In The Eastern Oyster, Amaelia Zyck

Open Access Dissertations

Urbanized estuaries are characterized as a complex of biotic and abiotic stressors, which currently challenge marine life and are expected to intensify and become increasingly unpredictable under the ongoing impacts of climate change. The persistence of coastal species that inhabit these stressful environments will ultimately depend on their ability to adapt. Many of these species have complex life cycles, featuring distinct morphological and physiological developmental stages that can exhibit unique responses to environmental pressures. However, since all stages share the same genome, selective pressures acting on one stage can have cascading effects throughout the life cycle. The larval stage, being …

Novel Methodology And Proof-Of-Concept For Proton Ct Using Spot Profile Rather Than Bragg Peak Location, Brett Albert Ruben

Open Access Dissertations

Proton radiation therapy offers a highly precise method for cancer treatment, theoretically providing superior dose deposition characteristics compared to conventional X-ray radiation therapy. Its steep and finite dose fall-off region allows for superior tumor coverage while reducing, though not eliminating, dose to surrounding healthy tissue. However, its full potential is limited by range uncertainties, particularly those arising from the reliance on X-ray-based imaging methods called computed tomography (CT) for proton-based treatment. CT image Hounsfield Units (HU) must be converted to stopping power ratios (SPR) as these ratios are the clinically relevant value for accurately planning particle interactions during proton therapy. …

“What’S Supp” Developing An In Vitro Model For Healthy Oral Biofilms, Alex Labossiere

Open Access Dissertations

The study of oral plaque has largely been influenced by the study of pathogens. Here in Chapter 1, I will discuss how this pathogenic focus has been dominant until the onset of microbiome research and begin to explain microbiomes in the context of supragingival plaque in homeostatic communities. From there we will then discuss the possible roots where dysbiosis may arise from plaque to cause disease and ways in which we can study healthy supragingival plaque by in vitro models.

In chapter 2, I will discuss molecular commensalism and how it can be viewed as a tool to further understand …

Ischemia-Induced Cytoskeletal And Nuclear Disruptions Drive Neuronal Death And Dysfunction: Insights Into The Connection Between Stroke And Dementia From In Vitro And In Vivo Models Of Stroke, Emily Potts

Open Access Dissertations

Stroke and Alzheimer’s disease and related dementias (ADRD) represent two of the leading causes of neurological disability worldwide, and their prevalence is expected to rise as the global population ages. Although stroke is traditionally viewed as an acute vascular event, a growing body of evidence suggests that transient ischemic injury can trigger lasting cellular disturbances that increase neuronal vulnerability to later neurodegeneration. Understanding how ischemic stress alters neuronal structure and function, and how these changes may overlap with pathways implicated in ADRD, is an emerging focus for stroke and neurodegenerative researchers. This dissertation addresses these questions through an integrated combination …

Non-Coding Rnas As Regulators Of Coral Biology, Jill Ashey

Open Access Dissertations

Coral reef ecosystems face increasing threats from climate change, yet knowledge of the molecular mechanisms that underlie coral acclimatization, resilience, and development remains incomplete. Among these mechanisms, non-coding RNAs (ncRNAs), specifically microRNAs (miRNAs), are emerging as key regulators of gene expression in response to environmental and developmental cues. This dissertation explores the diversity, function, and dynamics of ncRNAs in scleractinian corals across ecological, physiological, and developmental contexts. In Chapter 1, I present the first comprehensive analysis of ncRNAs - specifically long ncRNAs (lncRNAs), miRNAs, and piwi-RNAs (piRNAs) - in three reef-building coral species from Mo’orea, French Polynesia: Acropora pulchra, …

Nanotube Spectral Fingerprinting And Machine Learning For Optimized Bioimaging/Sensing And Disease Detection Applications In Als, Rodrigo Monroy Lopez

Open Access Master's Theses

Single-walled carbon nanotubes (SWCNTs) possess unique physicochemical and optical properties that make them ideal candidates for biomedical imaging, biosensing, and disease diagnostics. This thesis explores the potential of SWCNT-based spectral fingerprinting combined with ML (Machine Learning) algorithms to optimize bioimaging, disease detection and prediction, with a specific focus on differentiating between healthy and amyotrophic lateral sclerosis (ALS) lymphoblastic patient samples. By functionalizing SWCNTs with single-stranded DNA, we enhance their stability and target specificity, enabling their application in serum patient samples.

A comprehensive spectral analysis of DNA-SWCNTs was conducted using near-infrared fluorescence spectroscopy and other characterization techniques, including UV-Vis-absorption spectroscopy. The …

The P3 Event-Related Potential (Erp) In Visual And Auditory Tasks: Implications For Executive Functioning In Adhd Preadolescent Children, Alex Visal Seng

Open Access Master's Theses

Attention-Deficit/Hyperactivity Disorder (ADHD) is a widespread psychological disorder in children, poorly impacting executive functioning domains of inhibitory control and working memory. Event-related potentials (ERPs) provide neuroelectric insight into these cognitive processes. However, most ERP research focuses on one task type, limiting direct comparisons of cognitive demands across different task paradigms. This study examined P3 amplitude and latency in ADHD children using a visual NoGo task (response inhibition) and an auditory oddball task (working memory), and associations between the P3 ERP and behavioral measures of executive functions.

Cross-sectional data of symptomatic ADHD children (N=13; F=5; aged 9.15 ± 1.86 years) were …

Best Methods For Establishment And Maintenance Of Pollinator Plantings In Highway Rights-Of-Way, Sophia Lopardo

Open Access Master's Theses

This study explores the potential of highway rights-of-way (ROWs) to serve as habitats for native New England grasses and flowering plants, while also enhancing resources essential for native pollinator communities. This project emphasizes the adaptability of regionally native and insect-pollinated wildflowers and grasses to periodically mowed ROWs; the research assesses various establishment methods that are commonly used in new roadside construction. The study aims to evaluate the effectiveness of different establishment methods for developing roadside pollinator meadows within ROW settings, using species richness (separated into forbs, grasses, insect pollinated functional groups), bare ground percentage, and seed mix germination and persistence …

Micro- And Nano-Plastics Preparation And Their Impact On Cobetia Marina, Lauren Lamothe

Open Access Master's Theses

Plastic pollution has become an increasing threat to marine and coastal environments. Macroplastics derived from consumer waste are broken down by chemical and physical degradation processes, resulting in micro- and nano-plastics (MPs and NPs). This thesis presents an investigation into the MP and NP pollution in the sea surface microlayer (SSML). The SSML contains surface active compounds and natural and anthropogenic matter. This study provides insight into the deeper impacts on the transport and fate of MPs and NPs and on marine bacteria. The first chapter works through the breakdown of plastic particles with the use of a top-down approach …

Plastics And Their Interactions With Bacterial Biofilms Of Synechococcus Sp. Pcc 7002 And Escherichia Coli Nissle 1917, Jackson Zmich

Open Access Master's Theses

Plastic waste is a leading global pollutant with increasing concerns, as recent studies have shown that these wastes are not only concentrated on a macro scale but on a micro and nano scale. These micro- and nano- sized plastic particles, denoted as MPs and NPs, have been measured in marine and freshwater sources, air, food products, and within biosolids expelled from organisms, including humans. Due to their small size, MNPs are entering organisms through inhalation, ingestion, or dermal absorption. [1] Humans are ingesting MNPs daily, with median rates of approximately 200 ng/capita/day for children and 600 ng/capita/day for adults. [2] …

Alterations Of Serotonin Receptor 7 Expression In The Spinal Cord In A Model Of Cerebral Palsy, Tracy Santos

Open Access Master's Theses

Cerebral palsy often results from perinatal hypoxia-ischemia and is characterized by motor and sensory dysfunction associated with altered serotonergic signaling in the spinal cord. The 5-HT₇ receptor, a G-protein-coupled receptor implicated in both motor control and nociceptive modulation, may thus play a critical role in these post-injury changes. However, the regional and developmental patterns of expression of 5-HT₇ following HI injury are not well understood.

In this study, we investigated the expression of spinal 5-HTR₇ in a neonatal rabbit model of HI injury at P1, P5, and P8 using Western blot analyses normalized to total protein. Tissue was …

On! Original Flavor Oral Nicotine Pouch Characterization: Biorelevant In Vitro Nicotine Release Apparatus Assessment, Jason C. Funderburk, Melissa Morgan, Maria Lasaosa Garcia, Andreas S. L. Mendez, Matthew S. Halquist

Graduate Research Posters

Background: Oral nicotine pouch (ONP) use is rising. The sales of ONPs in 2019 were 126 million units, increasing to 808 million units in 2022. Understanding ONP in vitro release is critical for assessing exposure to ONP products.

Methods: The commercial brand ON! ONPs with nicotine label claims of 2, 4, and 8 mg, were evaluated in vitro for cumulative nicotine release using the bidirectional transmucosal apparatus (BTA) for 90 minutes. Nicotine quantification was performed by HPLC-PDA. For pH determination, ONP samples were prepared in water or artificial saliva (pH 6.8) with measurements for 30 minutes. BTA results were compared …