Digital Commons Network^™

Applying Transcriptomics For Technology Development And Conservation In North American Marine Organisms, Cory Von Eiff

Dissertations

RNA biology is a rapidly expanding field, with many avenues of discovery among marine organisms. In this study, we analyze both mollusks and sawfish. First, we perform an evaluation of sRNA biogenesis pathways throughout Mollusca, with emphasis on the easter oyster, Crassostrea virginica. Understanding these molecules prescribes RNAi-based gene silencing approaches, benefiting genetic investigation and biotechnology. Similar to other animal groups, mollusks have conserved microRNAs (miRNAs), with some shared with ecdysozoans and deuterostomes; however, there is no evidence of an endogenous small interfering RNA (siRNA) pathway. These results suggest that long double-stranded RNA (dsRNA)-based RNAi is not appropriate for gene …

Perspectives On Water Policies And Alternative Land Uses Among Alfalfa Farmers In The Great Salt Lake Basin, Bryn Watkins, Stacia Ryder

Publications

Climate change threatens many resources necessary for life. In arid and semiarid regions like Utah, water represents one of the key climate-related conflicts (1,2). In Utah, a changing climate paired with human overconsumption has contributed to the drying of the Great Salt Lake. Rising temperatures will lead to greater evapotranspiration and decreasing headwater streamflow and groundwater storage, resulting in increasing dryness in the Great Salt Lake Basin regardless of human water consumption (3). This in turn threatens the ecosystems, economies, and cultures of the Great Salt Lake Basin, accelerating the local impacts of climate change (4).

Fisheries Research Report No. 353: Ecological Risk Assessment For The North Coast Demersal Scalefish Resource, Kimberley A. Smith, Brett Crisafulli, Gabby E. Mitsopoulos, Fabian I. Trinnie, Taylor Grosse, T Thompson, Stephen J. Newman

Fisheries Research Reports

On the 26 March 2025, the Department of Primary Industries and Regional Development (DPIRD) convened an ecological risk assessment (ERA) of the fisheries that access the North Coast Demersal Scalefish Resource (Resource). This Resource comprises a large number of tropical demersal scalefish species that occur in waters of the North Coast Bioregion, including tropical snappers, emperors and cods.

This document contains the results of the ERA along with the background information used to support the risk scoring process. This includes an overview of the Western Australian commercial fisheries that access the Resource, namely the Pilbara Fish Trawl Interim Managed Fishery, …

Using Published Undergraduate Biomechanics Research On Hydra Mouth Opening To Train Undergraduates, Stephen Hackler, T. Goel, Jonah Pacis , '25, Eva-Maria S. Collins

Biology Faculty Works

Biophysics research is exciting because physical approaches to biology can provide novel insights, and it is challenging because it requires knowledge and skills from multiple disciplines. We have developed an undergraduate biophysics laboratory module that teaches fundamental skills such as time-lapse microscopy, image analysis, programming, critical reading of scientific literature, and basics of scientific writing and peer review. The module is accessible to students who are familiar with introductory statistics, cell biology, and differential calculus. We used published research on the biomechanics of Hydra mouth opening as a framework because it describes a stunning biological phenomenon: Hydra, a freshwater …

Influence Of Exercise Opportunities On Bone Health In Laying Hens, Jaden Costner, Alexis Clark, Ahmed Ali

Publications

Laying hens are often housed in environments that restrict movement, which may contribute to bone fragility and decreased welfare. These confined environments, such as conventional cage systems, limit exercise and result in poor skeletal development. This study investigates the impact of exercise opportunities on bone health in laying hens by comparing the tibiotarsi and humeri bone characteristics in enriched and unenriched housing environments. A total of 200 hens were housed in pens (20 birds/pen) from 0 to 40 weeks of age. Five pens, which served as the experimental group, were equipped with multi-tier perches and ledges, providing exercise opportunities. In …

Fisheries Research Report No. 361: 2024 Assessment Of The Status Of The Elasmobranch Resource Of Western Australia, Matias Braccini, Alex Hesp

Fisheries Research Reports

This document provides the 2024 risk-based weight of evidence stock assessment for the elasmobranch (sharks and rays) resource of Western Australia (WA). Gummy (Mustelus antarcticus), dusky (Carcharhinus obscurus), whiskery (Furgaleus macki), and sandbar (C. plumbeus) sharks are the most commonly captured species (~80% of the elasmobranch catch) and have been selected as indicator species for the status of the temperate elasmobranch ‘suite’. However, over 100 elasmobranch species have been caught in commercial and/or recreational fisheries in WA and, with the increasing number of elasmobranch species being listed in national and international protection lists, species-specific scientific advice on stock status at …

Mosquitoes: The 5 C’S Of Developing Disease- Commensals Changing To Consequential Pathogens, Alan L. Gillen, Caleb Mast, Robert Braden Somerville

Faculty Publications and Presentations

Hotter, longer summers and changing weather patterns in the United States are bringing more than just sweat and discomfort. In May 2025, a summer heat wave of 107⁰F hit Austin, Texas, and in humid Houston and San Antonio, Texas, temperatures felt over 100⁰ for several days. Normally, these temperatures don’t come until July and August. With temperatures reaching these marks early and heavy rains coming, mosquito activity and ranges expand. Many state and federal health officials report a rise in mosquito-borne illnesses across the US and globe in the last five years.

Cultivation Of Botryococcus Braunii For The Production Of Hydrocarbons Suitable For Fuel Use, Bryan C. Carroll

All Theses

Energy security, rural poverty, and climate change are pressing issues of our time. Biofuels provide a solution to these issues, with a focus on sustainable aviation fuel, SAF, due to compatibility with aircraft infrastructure and energy density. This research aims to review and produce knowledge about a specific microalga, Botryococcus braunii, for its potential for SAF. First a literature review on the process was conducted followed by an experimental study on the impact of aqueous media and inorganic carbon its growth and hydrocarbon content. The literature review found the process consists of cultivation followed by lipid extraction or hydrothermal …

Changing Globally, Acting Locally: Responses Of Coastal Plant Functional Traits To Global Change Are Mediated By Biotic And Abiotic Interactions., Shannon L. Walker

Electronic Theses and Dissertations

We live in a time of rapid global change with substantial consequences for planet-wide functioning. Local ecosystems reflect this change, yet we struggle to predict their responses. Coastal ecosystems, like dune and interdunal wetlands, have declined rapidly and predicting their responses to global change is essential for future management. Functional traits may be particularly informative as they drive species and ecosystem responses and can provide generalizable findings. This dissertation investigates how global change, especially anthropogenic nitrogen (N) enrichment, interacts with abiotic and biotic factors to affect coastal sand dune and interdunal wetland plant functional traits. First, I used a long-term …

Metabolic Regulation Of Cardiac Fibroblast Phenotype And Function., Collin Kleis Wells

Electronic Theses and Dissertations

Cardiac fibroblasts are central effectors of cardiac repair after myocardial infarction (MI). In response to signaling cues, they differentiate to a range of phenotypes with robust capacities to synthesize and secrete extracellular matrix (ECM) and signaling molecules. Although activated fibroblast phenotypes are associated with pronounced changes in metabolism, it remains unclear how the metabolic network upholds the effector functions of fibroblasts in the post-infarcted heart. Here, we identified that critical enzymes in the phosphoenolpyruvate (PEP) cycle, i.e. pyruvate kinase muscle-2 (PKM2) and phosphoenolpyruvate carboxykinase-2 (PCK2), are elevated in the heart after MI and examined their role in regulating post-MI remodeling …

Ecosystem Services Of Urban Green Spaces In Louisville, Ky., Julia Kachanova

Electronic Theses and Dissertations

Accelerating urbanization poses critical challenges to urban green spaces (UGS), vital for ecological balance and human health. Rapid development often results in fragmented habitats, biodiversity loss, and diminished ecosystem service delivery. There is an urgent need to explore and evaluate novel strategies capable of enhancing urban resilience, such as implementing urban orchards, and managing existing parks and gardens in sustainable ways. This dissertation explores how different forms of urban green spaces (UGS) contribute to the provision and maintenance of critical ecosystem services that support human well-being and urban biodiversity. By analyzing UGS impact on ecosystem service provisioning and long-term sustainability, …

Linked Lives In The Riverbed: Integrating Fish Host Dynamics, Community Structure, And Demography For Freshwater Mussel Conservation., Jonathan Patrick Frommeyer

Electronic Theses and Dissertations

Freshwater mussels are long-lived benthic invertebrates that play key roles in nutrient cycling, water filtration, and habitat stability in rivers and streams. Despite their ecological importance, they are among the most imperiled faunal groups in North America, with their persistence increasingly threatened by environmental degradation and disruptions to host–parasite dynamics. This dissertation integrates host ecology, community structure, and demographic modeling to assess population viability and guide conservation priorities for mussel species in Kentucky river systems. The first chapter introduces the ecological context and conservation urgency surrounding freshwater mussels. In particular, emphasizing the need for multi-scale approaches to understand how parasitic …

A Toi Rna Editing In Three Members Of The Microbotryum Violaceum Fungal Complext And Characterization Of Adar Genes Of Microbotryum Superbum., Shikhi Baruri

Electronic Theses and Dissertations

A-to-I RNA editing is a process that occurs post-transcriptionally. Through this process, adenosine (A) is replaced by inosine (I) in RNAs by adenosine deaminase enzymes that act on the single-stranded RNA. These enzymes, also known as ADARs, act on RNA. The translation and splicing mechanisms subsequently interpret inosine as guanosine (G), which effectively alters genetic information. This kind of RNA alteration can cause both nonsynonymous and synonymous changes in codon, which may have an impact on protein function. A group of over 89 basidiomycete fungal species known as the Microbotryum violaceum complex infects a similarly large group of plant host …

The Influence Of Psychological, Biological, And Social Determinants On Disordered Eating Behaviors Among U.S. Young Adults: Evidence From Nhanes 2015-2018., Samantha Kaye Gerbine

Electronic Theses and Dissertations

Disordered eating behaviors (DEBs) are influenced by biological, social, and psychological factors, yet research often narrowly focuses on White, college-aged women. This study assessed the predictors and prevalence of DEBs in a nationally representative sample of U.S. young adults using data from the 2015–2018 National Health and Nutrition Examination Survey (NHANES). Survey weights were applied to generate national estimates. Descriptive statistics characterized the sample, and logistic regressions tested biological, social, and psychological predictors of DEBs. A composite risk score was developed using variables retained in the final model. The unweighted sample (n = 1,062) represented 64 million U.S. young adults. …

Genes That Matter: Survival Modeling In Tcga-Brca With Treatment Interactions., David Pratt

Electronic Theses and Dissertations

High-dimensional genomic data offer both promise and challenges for identifying clinically relevant biomarkers. This study developed a parallelized survival modeling pipeline to identify genes associated with overall survival in breast cancer, with a focus on gene-by-treatment interactions and patient heterogeneity. RNA-Seq data from female patients in the TCGA-BRCA cohort were analyzed. Univariate Cox proportional hazards models were used to screen genes, adjusting for age, race/ethnicity, treatment status, and cancer stage. A LASSO-penalized Cox regression was fit across 2000 random seeds to assess feature stability. Genes were filtered by expression level, statistical significance, and hazard ratios (effect sizes) in either direction, …

Evaluating The Effectiveness Of Individual Cleaning Steps Of A Cip Protocol In Membrane Biofilm Removal Under Dynamic Conditions, Diwaker Singh, Sanjeev Anand

Dairy Science and Food Science Faculty Publications: 2022 to Present

This study evaluated the effectiveness of individual clean-in-place (CIP) steps in removing biofilms from reverse osmosis (RO) membranes under dynamic flow conditions using the Centers for Disease Control (CDC) biofilm reactor. Biofilms were developed in the laboratory under continuous flow, using mixed-species bacterial isolates obtained from 10-month-old RO membrane biofilms from a commercial facility. Individual CIP chemicals, representative of those used in commercial protocols, were tested against 24 h-old biofilms. Additionally, a complete six-step sequential CIP process was conducted under dynamic conditions, consisting of treatments with alkali, surfactant, acid, enzyme, a secondary surfactant, and sanitizer. All experiments were performed in …

Formosan Subterranean Termites Coptotermes Formosanus Shiraki (Blattodea: Heterotermitidae): An Underreported Threat To Commercial Shrimp Boats In The Midsouth, Usa, J. S. Portugal Iii

Midsouth Entomologist

No abstract provided.

Bioassay To Evaluate Resistance Levels In Tarnished Plant Bug (Hemiptera: Miridae) Populations In Alabama To Common Cotton Insecticides, T. J. Douglas, K. Kesheimer, A. Jacobson, S. Brown, F. R. Musser, L. S. Catchot, S. H. Graham

Midsouth Entomologist

The tarnished plant bug, Lygus lineolaris (Palisot de Beauvois), has emerged as the major insect pest of cotton in the mid-southern United States following the eradication of the boll weevil and the introduction of genetically modified Bt cotton for caterpillar pests. The objective of this study is to evaluate tarnished plant bug resistance to the five most common insecticides used for control across six distinct growing regions. Glass-vial bioassays were used to evaluate resistance of field populations in a laboratory setting. Elevated levels of resistance of tarnished plant bug to bifenthrin and, to a lesser degree, imidacloprid have been reported …

How Do Acoustic Indices Serve As Proxy Of Temperate Forests And In Relation To Presence Of Bobcat (Lynx Rufus) In Central Indiana Habitats, Faith Mcphee, Kristen Bellisario Dr.

Discovery Undergraduate Interdisciplinary Research Internship

Central Indiana is largely dominated by agriculture which has led to numerous historical extirpations of mammals. The bobcat (Lynx rufus) is slowly re-establishing across northern Indiana after near extirpation in the early 1900s and utilizes corridors similar to extirpated mammals. Bobcats as a focal species can serve as an indicator for habitat quality for future designated wildlife corridors. New metrics have emerged from species monitoring through remote sensing technologies such as eco-acoustic indices which summarize sound profiles, are a potential proxy for biodiversity, and could be utilized in monitoring large mammals. Here, we investigate the relationship between Lynx …

The Molecular And Behavioral Characterization Of The Murine Cre – Loxp Skeletal Muscle Synthesized Bdnf Knockout Model, Asha E. Rustad

All NMU Master's Theses

Brain derived neurotrophic factor (BDNF) is a neurotrophin essential for supporting the growth, differentiation, and health of neurons within the central and peripheral nervous systems. BDNF is also a member of the myokine family, where muscle synthesized-BDNF (msBDNF) is thought to facilitate the crucial bi-directional communication between the motor neuron and the muscle fibers it innervates. Since 2008, the Ottem Laboratory has investigated the role of msBDNF by employing Cre/LoxP recombinase technology to selectively delete the BDNF coding region within skeletal muscle of mice. This approach generates animals with either heterozygous or homozygous deletions of msBDNF, as well as BDNF …

Evaluating Quadrupedal Locomotion In Bats: A Geometric Morphometric Comparison Of Vertebral Adaptations Across Mammals, Jessica Upham

Electronic Theses and Dissertations

Flight is the primary locomotion of bats, while quadrupedal locomotion is not often observed and is widely variable among bats. Frugivorous bats in Pteropodidae are more efficient climbers than frugivorous bats in Phyllostomidae and insectivorous bats in Vespertilionidae, while phyllostomids and vespertilionids are better at walking on horizontal surfaces. The aim of this study is to investigate whether bats with differing modes of nonflight locomotion also exhibit disparity in thoracolumbar vertebral morphology. Using geometric morphometrics, we compared the thoracolumbar vertebral shapes of these bat families with other terrestrial and arboreal mammals. The results revealed distinct vertebral shapes among bat families …

Farm Management Practice For The Prevention Of Soil Erosion In The Carnarvon Horticultural Area, Kehinde O. Erinle

Horticulture research reports

The Carnarvon horticultural area has suffered considerable erosion damage following flooding of the Gascoyne River.

The purpose of this report is to describe the factors that contribute to soil erosion in the Carnarvon horticultural area (Section 1), provide guidelines for good soil management (Sections 2) and provide floodway hazard classes and associated soil management recommendations (Section 3).

This report:

• Provides detailed information on soil management for intensive irrigated cropping.
• Details cropping alternatives to better manage the soil erosion risk.
• Identifies appropriate plants for soil stabilisation in a range of situations.
• Promotes the concept of property management plans.
• Takes account of …

Raptors As Secondary Dispersers Of Mycorrhizal Fungal Spores, Joseph Anderson

Electronic Theses and Dissertations

Animals aid fungal dispersal by consuming fruiting bodies (e.g., truffles) and depositing spores elsewhere. Predators can act as secondary dispersers by preying on small mammals that eat truffles, although it is unclear how this dispersal may vary among species of raptors (hawks and owls) and fungal taxa. We experimentally fed four truffle taxa (with spores varying in size and wall thickness) to six raptor species (with differing gut morphology and acidity) to assess how spore viability and retention time may change between raptor casts and feces. Viability in smaller spores was more negatively affected by acidity compared to larger spores …

Hierarchy In Sensation: Exploring The 40 Hz Auditory Steady State Synchrony In The Primary Auditory And Prefrontal Association Cortices, Deepshila Gautam

Electronic Theses and Dissertations

Auditory processing begins in the cochlea and ascends through brainstem relays to the cortex, where sound features with increasing complexity are encoded. The 40 Hz auditory steady-state response (ASSR) reflects induced gamma synchrony shaped by local cortical circuit dynamics. Disrupted 40 Hz ASSR is a consistent finding in schizophrenia, linked to N-methyl-D-aspartate receptor (NMDAR) hypofunction in inhibitory interneurons, making it a promising translational biomarker. While multiple ASSR generators have been identified, it is not known if these are redundant or represent unique activity. This dissertation investigates regional differences in 40 Hz ASSR across two principal generators: the primary auditory cortex …

The Effect Of The Markle Mill Dam Removal On The Habitat And Riverine Food Web Of Otter Creek, Jenna Blanton

All-Inclusive List of Electronic Theses and Dissertations

Across the United States, dam removals are increasing in frequency. Despite this, the effects of dam removal on freshwater food webs are under-studied. Most existing studies investigate the impacts on fish assemblages, and very few investigate the impact on diatom, crayfish, and turtle communities. Furthermore, low-head dams are more abundant than large hydropower dams, yet the impacts of their removal are less studied than their larger counterparts. I used a Before After Control Impact (BACI) study design to survey populations of benthic diatoms, riffle-dwelling crayfish, and aquatic turtles. Species richness, species evenness, and Shannon Diversity Index values were used to …

Fouling Community Assessment On Anthropogenic Structures In Barnegat Bay, Nj: Who's Fouling With Our Lagoons?, Jesi Herterich

Theses, Dissertations and Culminating Projects

Biofouling communities consist of both mobile and non-mobile species which settle and attach themselves to both natural and artificial substrata. With increased construction of lagoon communities and marinas in Barnegat Bay, NJ utilizing PVC material, it allows space for invasive and generalist species to recruit. This study examines the impacts of man-made structures and abiotic factors on the distribution of recruiting fouling organisms in coastal lagoon communities in Barnegat Bay, NJ. Polyvinyl chloride settling plates were deployed in late May of 2024. Settling plates were retrieved and replaced at one month intervals to assess monthly settlement patterns, while a second …

Advanced Interactions Of Directed Energy With Retinal Pigment Epithelial Cells And Their Photochemical And Photothermal Responses, Jin B. Ha

Theses & Dissertations

Excess optical radiation can injure the retina through either rapid heat deposition (photothermal damage) or cumulative photo‑oxidative stress (photochemical damage), yet current laser‑safety limits treat these mechanisms as independent. To test that assumption, this dissertation integrated systematic wavelength, duration and temperature‑controlled laser exposures with live/dead fluorescence imaging in a melanin‑loaded hTERT‑RPE1 monolayer model. First, concurrent 447 nm (blue) and 2 µm (infra‑red) beams delivered for 200 s demonstrated a strong thermal–photochemical synergy: each beam alone was sub‑threshold (≤25 % lethality) but together produced 100 % RPE death without exceeding 50 °C, proving that modest heating markedly lowers the photon dose …

The Effect Of An Invasive Species (Lantana Camara) And A Fast-Growing Herb (Acanthus Pubescens) On The Plant And Animal Communities In Kibale National Park, Uganda, Kathleen Bufka

Theses and Dissertations

Fast-growing plant species, like Lantana camara and Acanthus pubescens, could threaten biodiversity in Kibale National Park, Uganda. I surveyed plants and wildlife in areas where these plants were frequently encountered compared to those areas where they are infrequent. I found mixed results based on plant traits and the animals considered. My findings support management efforts on these two species to prevent forest degradation.

Commodity Diversification, Technological Innovation, And Market Dynamics: Insights Into Beef Cattle Production And Feeder Cattle Basis In The United States, Nik Berg

All Theses

The beef cattle industry plays an important role in the agricultural economy, contributing to both domestic food supply and global trade. The United States is one of the world's largest producers of beef, with production systems varying widely across regions largely due to differences in available resources and market structures. Market conditions, technological advancements, and policy interventions shape the way producers operate, making research into these factors essential for both industry stakeholders and policymakers.

Producers are continuously adapting to changing economic conditions, environmental challenges, and evolving consumer preferences. By analyzing these factors, researchers can provide insights to support informed decision-making …

Two Essays On Index-Based Risk Management In U.S. Rangeland And Livestock Production, Wajdi Belgacem

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

This dissertation investigates two distinct but complementary dimensions of risk management in United States rangeland agriculture. Essay 1 measures spatial variation in basis risk within the Pasture, Rangeland, and Forage (PRF) rainfall-index program for 176 Nebraska grid cells (1988–2023). By linking official NOAA rainfall indices with 30-m Rangeland Analysis Platform biomass estimates, we find rainfall–forage correlations that peak at 0.45 but display pronounced heterogeneity. The probability that neither insured interval triggers during an actual forage loss averages 12%, rising to nearly 30% in several Sandhills cells, whereas optimally pairing late-spring and summer intervals reduces complete misses below 10%. These results …