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Exploring Mobility: Phylogenetic And Structural Analysis Of The Intein In The Helicase Of Mycobacteriophage Alice, Sandra Xu

Honors Scholar Theses

This paper investigates the intein insertion in the DNA helicase gene Alice_175 of the Mycobacterium phage Alice, exploring its evolutionary significance and potential propagation mechanisms. Using phylogenetic analysis, there is evidence for gene transfer as a driving force in intein dissemination in phage and bacterial genomes. Structural predictions of the Alice_175 intein that were generated through AlphaFold2 as well as a phylogeny generated using SeaView infer a timeline of the intein's invasion and reveal key features that may influence protein functionality and host adaptation. Additionally, protein database searches suggest that intein mobility in this gene may not rely on prophages, …

Marine Heat Waves Effects On Rocky Intertidal Ecosystem Functioning, Skyler Peterson, S. Schneider, C.L. Webb, A. Leighton

Undergraduate Research Symposium Posters

Severe heat waves may cause long-term changes in marine ecosystems and are expected to increase in magnitude and frequency. Here we use surveys from six localities across a six-year interval (2013-2019) to investigate the effects of heat waves on the functional diversity of rocky intertidal ecosystems (Vancouver Island, Canada).

Functional diversity, the number and types of functions performed by organisms, influences ecosystem stability and health. To assess changes in functional diversity we used analyses of biological traits. Biological traits are measurable properties of organisms that describe their morphology, physiology, and behavior. We quantitatively assessed changes in functional diversity in response …

Functional Morphology Of The Primate Knee And Its Implications For Hominin Bipedal Mechanics, Catherine K. Miller

Dartmouth College Ph.D Dissertations

Bipedal locomotion is central to the human condition, having shaped our evolutionary trajectory since its early emergence in the hominin lineage. Despite its importance, key questions remain about its origins and evolutionary trajectory. While many studies have focused on locomotor-related anatomies, comparatively less attention has been paid to the knee joint – a structure critical to the primate locomotor repertoire. This dissertation aims to clarify the form-function relationship of the knee in extant primates to better infer the locomotor behaviors of Miocene hominoids and Plio-Pleistocene hominins. To address these questions, this research employs a multifaceted analytical approach, integrating linear measurements, …

Longitudinal Profiling Of Circulating Tumor Dna Reveals The Evolutionary Dynamics Of Metastatic Prostate Cancer During Serial Therapy, Yuehui Zhao, Naveen Ramesh, Ping Xu, Emi Sei, Min Hu, Shanshan Bai, Patricia Troncoso, Ana M Aparicio, Christopher J Logothetis, Paul G Corn, Nicholas E Navin, Amado J Zurita

Faculty, Staff and Student Publications

Treatment decisions in metastatic castration-resistant prostate cancer are mostly guided by clinical variables, but efforts to molecularly monitor the disease remain hampered by challenges in acquiring tumor tissue repeatedly. In this study, we simultaneously profiled the genome copy number and exome in longitudinal plasma circulating tumor DNA (ctDNA) acquired before, during, and upon progression to serial treatments with androgen signaling inhibitors and taxane chemotherapy from 60 patients with metastatic castration-resistant prostate cancer (2-10 samples per patient). The genomic data were used to delineate the clonal substructure and evolutionary dynamics of each patient, and an evolutionary dynamic index was developed to …

A History Of Omics Discoveries Reveals The Correlates And Mechanisms Of Loading-Induced Hypertrophy In Adult Skeletal Muscle. 2024 Camps Young Investigator Award Invited Review, Toby L. Chambers, Kevin A. Murach

Health, Human Performance and Recreation Faculty Publications and Presentations

Since the early 2000s, omics approaches to study skeletal muscle hypertrophy consequent to loading (e.g., resistance exercise) have expanded dramatically. Beginning with genomics and transcriptomics, there are now omics datasets from hypertrophying skeletal muscle spanning methylomics, proteomics, and phosphoproteomics, with further integration of single cell/nucleus-specific omics, among others. The purpose of this review is to explore the history of leveraging omics to enable understanding and discovery with respect to loading-induced hypertrophy in adult skeletal muscle. We elaborate on key historical and contemporary studies and findings, highlight specific examples where omics discoveries led to a mechanistic understanding of skeletal muscle growth, …

Genomic Characterization Of High-Grade Serous Ovarian Carcinoma Reveals Distinct Somatic Features In Black Individuals, Katherine A Lawson-Michod, Jeffrey R Marks, Lindsay J Collin, David A Nix, Natalie R Davidson, Chad D Huff, Yao Yu, Aaron Atkinson, Courtney E Johnson, Lucas A Salas, Lauren C Peres, Casey S Greene, Joellen M Schildkraut, Jennifer A Doherty

Faculty, Staff and Student Publications

Black individuals experience worse survival after a diagnosis of high-grade serous ovarian carcinoma (HGSC) than White individuals and are underrepresented in ovarian cancer research. To date, the understanding of the molecular and genomic heterogeneity of HGSC is based primarily on the evaluation of tumors from White individuals. In the present study, we performed whole-exome sequencing on HGSC samples from 211 Black patients to identify significantly mutated genes and characterize mutational signatures, assessing their distributions by gene expression subtypes. The occurrence and frequency of somatic mutations and signatures by self-reported race were compared with historic data from The Cancer Genome Atlas …

Microbial Community And Water Quality Assessment Of Crassostrea Virginica Habitats In Southeast Florida, Stacy Brown

All HCAS Student Capstones, Theses, and Dissertations

Eastern oysters (Crassostrea virginica) are essential habitat-forming species that contribute significantly to coastal water quality due to their filter-feeding behavior. Unlike other coastal regions in the Gulf of Mexico and Northeastern United States, oysters are not commercially managed in Southeast Florida and as a result sparse data exists on locations of the Eastern oyster habitat. Similarly, the benefits of oyster reefs to water quality are also not fully documented in Southeast Florida. Although beneficial and often referred to as keystone habitat building species, populations of C. virginica are not currently listed as protected species so little work has …

Using Satellite Tracking And Stable Isotopes To Characterize The Movements, Core-Use Areas, And Distribution Of Loggerhead And Green Turtles Nesting In South Florida, Usa: Internesting, Foraging, And Migration, Glenn D. Goodwin

All HCAS Student Capstones, Theses, and Dissertations

The movements of animals in response to environmental variation influence the fitness of individuals and drive major ecological processes, while also varying their exposure level to anthropogenic risks. Understanding the movements and spatial distribution of imperiled species is critical for developing effective conservation strategies. This can be difficult for wide ranging and highly migratory species, such as sea turtles. Throughout their adult life stages, the females of most sea turtle species spend the majority of their time in their foraging areas for multiyear intervals between nesting periods. These foraging areas are typically widely dispersed and variable within nesting populations. To …

Table Of Contents And Front Matter, Bjur Staff

Butler Journal of Undergraduate Research

No abstract provided.

The Effect Of Boom Leveling On Spray Dispersion, Miguel Bustamante, Juan F. Vivanco, Travis A. Burgers

Mechanical Engineering Faculty Publications

Automatic boom height systems reduce the variability of agricultural sprayer boom height. When a boom is not at its target height, this can lead to uneven spray dispersion from the nozzles. Boom heights and sprayer position were previously measured in time for three commercially-available boom leveling systems for three test runs for at least three speeds over each of a mild, medium and rough terrain course. A computational model was created to use measured spray dispersion from a nozzle, measured boom heights in time, and measured sprayer position in time to calculate a spray coverage map. The model was used …

Autonomous Agricultural Equipment Evaluation For Broad-Acre Crop Production, Sofia Bahmutsky, Ashutosh Singh, Travis A. Burgers, Roy Maki

Mechanical Engineering Faculty Publications

No abstract provided.

The Relationship Between Food Allergies And Intolerances And The Development Of Disordered Eating Patterns, Lucy M. Scholma

Human Nutrition and Hospitality Management Undergraduate Honors Theses

Food allergies and food intolerances are becoming an increasingly more prevalent issue in the Unites States. To mitigate adverse reactions, these individuals often eliminate food or food groups from their diets and the ramifications of these lifestyle changes may result in disordered eating patterns. In regard to food allergies and intolerances and eating disorders, it is reasonable to suggest that the overlapping lifestyle choices and physical, social, and emotional ramifications may lead to a correlation between the two phenomena. This study explores the relationship between food allergic and food intolerant individuals and disordered eating habits among college students. Survey results …

Excess Fructose In High-Fructose Corn Syrup Reduces Cell Viability & Promotes Nitric Oxide Release In Raw 264.7 Macrophages, Renzo F. Galarza, Edward L. Villegas

Research and Creativity Symposium

High-fructose corn syrup (HFCS) is an artificial sweetener that contains slightly higher concentrations of fructose compared to standard sucrose. It has been linked to an increased risk of obesity, type 2 diabetes, cardiovascular disease, and fatty liver disease. While both HFCS and sucrose are widely used sweeteners, growing evidence suggests they may differ in their inflammatory potential. We sought to understand the effects of elevated fructose on RAW 264.7 macrophages. To investigate these effects, we treated the cells with either a sucrose solution or a
solution designed to mimic high-fructose corn syrup. Lipopolysaccharide (LPS) stimulation was used to model innate …

Impacts Of German Yellowjacket (Vespula Germanica) Removal On Pollinator Communities In Western New York, Jonathan M. Promowicz

Biology Theses

Invasive social insects can restructure native arthropod communities through predation and competition. Vespula germanica (German yellowjacket) is a globally invasive wasp species that dominates vespid assemblages across urban and suburban landscapes. This study tested the hypothesis that reducing V. germanica using protein-based fipronil baits would increase native pollinator abundance, species richness and native vespid abundance. Vespula germanica was experimentally suppressed at suburban and urban sites. Pollinator abundance and richness increased with V. germanica baiting. Native vespids had mixed results from baiting with suburban sites increasing in overall abundance and urban sites decreasing. These results indicate that suppressing dominant invasive wasps …

Evaluating The Health Of The Latah Creek Tributary And Its Impact On The Health Of The Spokane River By Aquatic Macroinvertebrate Analysis, Andee West, Ian Townley

CURCI Student Research

Research question: How does the Latah Creek tributary impact water quality of the Spokane River, monitoring the riverbanks and macroinvertebrate families?

The Anorexigenic Peptide Nesfatin-1 Dampens The B Cell Response To Receptor-Mediated Stimulation Through Inhibition Of Nf-Jb Signaling, Tara L. Steffen, Joshua D. Stafford, Colleen R. Bocke, Willis K. Samson, Gina L.C. Yosten

Biological Sciences Faculty Research & Creative Works

Nesfatin-1, a posttranslational product of the protein encoded by the nucleobindin 2 gene (NUCB2), was functionally identified as an appetite regulatory molecule in rat hypothalamic nuclei. In the years following the discovery, those findings have been corroborated and expanded upon, and we now know that nesfatin-1 is expressed throughout peripheral tissues and exerts physiological effects beyond feeding control. Literature indicates that adipose tissue is one of the peripheral sources of NUCB2/nesfatin-1, and in this setting, it has anti-inflammatory effects that have recently been implicated in regulating chronic inflammation associated with diet-induced obesity. Currently, there are gaps in our understanding of …

Large Mammal Herbivores As Gardeners Of Tropical Forest Ecosystems, Kathryn Garner

Student Scholarship

Ecosystems worldwide are experiencing changes in structure and function as populations of fauna decline and experience local extinctions (Torres-Romero et al. 2020). Due primarily to their body size, large mammal herbivores (LMHs) are disproportionately prone to extinction from human activities such as agricultural expansion, deforestation, and anthropogenic climate change (Pringle et al. 2023). Additionally, as the number of domesticated LMHs (i.e. cattle, pigs, etc.) continue to increase in both density and distribution, their wild counterparts are continually displaced, resulting in increased competition for resources and an increased risk of disease transmission between domestic to wild species (Pringle et al. 2023; …

Examining Sustainable And Regenerative Viticultural Practices In The Rheinhessen Wine Region Of Germany, Claire Hoffmann

CISLA Senior Integrative Projects

No abstract provided.

Unraveling The Antiviral Mechanisms Of Bat Cells: Processing Of Genomic Rnas By Dicer In Bat Cells Limits Sars-Cov-2 Replication, Iyanuoluwani Owolabi

Dissertations

Bats are reservoirs for numerous viruses that cause serious diseases in other animals and humans. Several mechanisms are proposed to contribute to the tolerance of bats to these pathogens. This study investigates the response of bat cells to double-stranded RNA generated by SARS-CoV-2 replication. Here, we found the involvement of Dicer in the processing of viral genomic RNAs during SARS-CoV-2 infection. Examining RNA sequencing of infected cells, small-interfering RNA (siRNA)-like fragments were found derived from viral RNAs. Depletion of Dicer showed a reduction in these RNAs and an increase in viral loads suggesting unlike other mammals, bats may use Dicer …

The Effect Of Implementing A Development Program Using Mental Imagery On The Time To Master Psychomotor Skills, Randal Agee

Dissertations

Psychomotor skills development programs that use mental imagery have been demonstrated to help individuals acquire psychomotor skills (Anu et al., 2020; Seymore-Walsh et al., 2020; Toth et al., 2020). The commercial trucking industry is presently experiencing a global shortage of qualified truck drivers (American Trucking Association, 2019; Staats et al., 2017). One reason individuals are avoiding or leaving careers as commercial truck drivers is the time spent away from home (Staats et al., 2017). A couple logistical strategies have been developed to improve the situation (Mittal et al., 2018; Prime Inc, 2024); however, for the solutions to be sustainable, the …

Joe Rogan And The Manosphere In The Age Of Modern Misogyny, Alexandra Klocker

CSB and SJU Distinguished Thesis

Much scholarly research analyzes extreme misogynistic language in “manosphere” forums, due to their connections to radicalization and violence. However, less attention has been given to the prevalence of such content in mainstream media, such as podcasts. The Joe Rogan Experience (JRE) podcast, a prominent and influential platform, has been praised for its wide-ranging discussions but critiqued for fostering and amplifying harmful ideologies, including misogyny. Despite its controversy, limited research has explored how pre-existing misogynistic rhetoric in online communities might shape or influence the content of JRE episodes. This study examines how misogynistic language and themes proliferate in JRE episodes through …

Correlation Between Maximal Strength And Standing Power Position In Shot Put Throwers, Ryan E. Joule

Honors Theses

This study determined the correlation between maximal strength to performance in a standing power shot put throw. Collegiate athletes (N = 7, 1 female, 6 males) conducted a one-repetition maximum for the bench press, back squat, and hang power clean, and executed three shot put throws at two different time points (three months apart). For the first time point, there were positive, moderate correlations of shot put distance to bench press (r = 0.41) and back squat (r = 0.45). A positive, strong correlation between distance thrown to hang power clean (r = 0.66) was present. For the second time …

Pseudomonas Aeruginosa Exoy Enzymatic Activity Inhibits Exos-Induced Caspase-3/7 Activation But Not Cytotoxicity In Pmvecs, Connor Holm

Poster Presentations

Pseudomonas aeruginosa (P. aer.) is the most common cause of ventilator associated pneumonia (VAP) in ICU patients. Different combinations of exoenzymes (S, T, Y, and U) are found in P. aer. strains. ExoY is most often associated with VAP in ICU patients. ExoY infection of pulmonary microvascular endothelial cells (PMVECs) induces cell rounding but does not activate intracellular caspase-3/7 or cause cell death. ExoS and ExoT infection of epithelial cells leads to caspase-3/7 dependent cell death. Previous studies using epithelial cells show that ExoY alleviates the cytotoxic effects of ExoS and ExoT. Here, we sought to determine whether ExoY inhibits …

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

Poster Presentations

Coastal erosion is heavily impacting coastal ecosystems across the Gulf. For instance, the state of Louisiana loses a football field worth of land every 100 minutes (Couvillion, 2017). The drastic loss of coastline highlights the dire need for restoration in the Northern Gulf Coast. An unexpected solution to this sediment loss may solve two major environmental issues at once by diverting millions of tons of glass waste from entering America’s landfills each year. By crushing glass to create sand and gravel for coastal restoration, we may generate a consistent and sustainable source of substrate. Our goal is to determine the …

Decoding Bacterial Resilience: Srnas And Sigma Factors In Stress Adaptation And Persistence Of Salmonella, Anita Nguyen

Poster Presentations

Small RNAs (sRNAs) are noncoding RNA molecules in bacteria that function primarily to regulate gene expression, including those associated with stress. The Borchert Lab has identified 173 sRNAs and > 500 sRNAs that are responsive to desiccation and carbon starvation (c-starvation), respectively. Prokaryotic transcription involves an RNA Polymerase (RNAP) that transcribes DNA into RNA. RNAP involves sigma factors, which recognize promoters for the initial steps of RNA synthesis. The Borchert Lab has determined that there are significant overlaps between sRNAs expressed in cells subjected to both short-term durations and long-term durations of carbon starvation. Salmonella enterica serovars can have outbreaks associated …

The Effects Of Incubation Humidity On Broiler Chicks, Claire Caples

Animal Science Undergraduate Honors Theses

Leg health issues are a welfare problem in commercial broiler chickens and an economic issue for the broiler industry. Broilers exhibiting leg abnormalities show altered gait, reduced ability to access resources, and increased lameness incidence. These leg health issues can result from many animal and environmental factors during incubation and post-hatch. Incubation strategies may contribute to the development of leg health issues, and recent research has increased focus on incubation factors affecting embryonic development and health and welfare post-hatch. Thus, the objective of this study was to evaluate the effect of high (80%), low (55%), and ideal (65%) humidity on …

Fisheries Occasional Publication No.148 - Aquaculture Of Seaweed In Western Australia: Policy Principles Relating To Licences And Exemptions For The Aquaculture Of Seaweed In Western Australia, Department Of Primary Industries And Regional Development, Western Australia

Fisheries Occasional Publications

of aquaculture, and clarifies the process and information required to assess applications for aquaculture licences, leases and exemptions for seaweed aquaculture in WA.

Development of principles will support decision-making for the take of wild seaweed and for the grant or variation of aquaculture licences for seaweed aquaculture.

Effect Of Soil Amended With Biochar On Growth Dynamics Of Radishes, Colin Brennan, Jake Werner, Ian Townley

CURCI Student Research

How do different percentages (15%, 10%, 5%, 0%) of biochar in soil affect the initial growth rate and final mass of radish plants (Raphanus sativus). We used 15%, 10%, 5% biochar, and using pure soil as our control group. For each soil type, we prepared 12 samples, totaling 48 samples across all conditions. After germination and initial plant growth, the number of leaves and the plant’s height from the top of the plant to the soil (in centimeters) were recorded every school day. The purpose of this study is to better understand if biochar is an effective way to stimulate …

Western Australia’S Marine Heatwave Update - 9th May 2025, Department Of Primary Industries And Regional Development, Western Australia

Marine Heatwave Notification Reports

Category 1 – Moderate marine heatwave (MHW) conditions continue for the Gascoyne and South Coast Bioregions. Marine heatwave conditions in the North Coast Bioregion have abated and the West Coast Bioregion remains warm but neither are categorised as experiencing MHW conditions.

Investigating Regulation Of Neutrophil-Mediated Inflammation In Mycoplasma Pneumoniae Infection, Nathan D. Velazquez

University Scholar Projects

No vaccine exists for Mycoplasma pneumoniae (Mp) infections, largely due to the

gap in understanding in the virulence and immunopathogenesis of this bacterium.

We have recently demonstrated that neutrophils are maladaptive in the context of

Mp infection, and drive disease severity while also impairing bacterial clearance.

Furthermore, we observed that B cells play a regulatory role in limiting disease

severity by modulating neutrophilic inflammation. We investigated this

phenomenon further to elucidate the mechanisms by which B cells regulate

neutrophilic inflammation. We utilized a monoclonal antibody to deplete B cells

during Mp infection and found that B-cell-depleted mice had elevated neutrophil …