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Retention Time Of Microplastics In The Purple Sea Urchin (Arbacia Punctulata), Alexandra Shore

Honors Theses and Capstones

Marine ecosystems around the world are facing the problem of plastic pollution. Large pieces of plastic eventually degrade into smaller microplastics that are suspended in the water column and sink to the seabed. Sea urchins are exposed to microplastics as they graze on the sea floor and can accidentally consume these pollutants. Sea urchins are ecologically important animals because they physically alter their ecosystem via grazing and are integral part of marine food webs. To better understand how sea urchins interact with microplastics, purple sea urchins were exposed to microfibers and microspheres in a laboratory setting, and the retention time …

Impacts Of Management Practices And Soil Properties On Free-Living Nitrogen Fixation In Eastern South Dakota, Laura Galvan Nuevo

Electronic Theses and Dissertations

Free-living nitrogen (N) fixation (FLNF) may represent a sustainable pathway to supplement crop N demand in agroecosystems, yet edaphic and management factors regulating this process under field conditions remain poorly understood in the Northern Great Plains. Using 15N2 direct method to quantify potential FLNF (pFLNF) and baseline FLNF (bFLNF), this thesis investigates how crop rotations (2-, 3-, and 4-year systems), tillage management (conventional vs. no-till), cover cropping, and soil properties affect the potential of free-living diazotrophs to supply N via FLNF in a long-term no-till corn-based system in Southeastern South Dakota. A two-year field study evaluated pFLNF across four growing …

Colorectal Cancers With Distinct Metastatic Potential Trigger Divergent Early T Cell Responses, Marwa Ahmed Saad

Student Theses and Dissertations

The intestinal mucosa harbors the largest immune compartment in the mammalianbody, where resident and recruited immune cells must maintain tolerance to commensal and dietary antigens while preserving their ability to mount effective responses against pathogens and malignant transformation. Uncontrolled epithelial proliferation leads to colorectal cancer (CRC), the second leading cause of cancer-related deaths worldwide. More than 85% of human CRC cases arise from accumulating sporadic or hereditary mutations in the tumor suppressor genes Apc, Tp53, Smad4, and the oncogene Kras. Although immune checkpoint blockade has transformed the treatment of certain solid tumors, most CRCs, particularly those with a proficient mismatch …

Investigating Primary Motor Cortex Involvement In Mouse Vocal Communication, Elena N. Duryea Waidmann

Student Theses and Dissertations

Vocal communication is used to transmit a range of information to other individuals. While many vocalizations are innate, some species can learn to change their vocal output. This is termed vocal-learning, and it is a rare trait and a necessary building block for human spoken language and songbird song. Comparative work in humans and songbirds suggests that convergent genetic and neural specializations may drive these learned vocal behaviors. Two key features of these advanced vocal learners are: i) specialized primary motor regions in the forebrain with activity tied to vocalization; and ii) dense monosynaptic projections from the primary motor cortex …

Noncanonical Roles Of Hepatitis B Virus Precore Rna In Reverse, Mengyin Zhang

Student Theses and Dissertations

Hepatitis B virus (HBV) is a partially double-stranded DNA virus that replicates through reverse transcription. Transcription from the HBV core promoter generates two genome-length RNAs: pregenomic RNA (pgRNA) and precore RNA (pcRNA). pcRNA contains the entire pgRNA sequence plus an additional 32 nucleotides at its 5’ end that include the precore start codon, enabling translation of the precore protein, the precursor of the secreted HBV e antigen (HBeAg). Whereas pgRNA is translated to produce core and polymerase and serves as the template for reverse transcription by cis-acting HBV polymerase, pcRNA has long been considered unable to support HBV DNA synthesis. …

Evaluation Of Brook Trout (Salvelinus Fontinalis) Thermal Tolerance And Projected Climate Change Effects On Headwater Brook Trout Population Persistence, Cory Bauerlien

Graduate Theses, Dissertations, and Problem Reports (ETD)

Climate change has been identified as one of the greatest threats to global biota in recorded human history. Consequences are expected to be more pronounced in ectotherms because most of their physiology is controlled by external temperature conditions. Predicting how ectotherms may respond to increasing global temperatures necessitates information about thermal limits of thermal sensitive species and how increasing temperatures may affect individual and population-level fitness. Therefore, the objectives of this research were aimed at gaining a better understanding of the mechanisms that underpin thermal tolerance limits of fish and how those mechanisms may affect fitness and population persistence under …

Design, Syntheses And Biological Applications Of Fluorescent Probes For Nad(P)H, Hsa And Cellular Microenvironment Sensing, Adenike M. Olowolagba

Dissertations, Master's Theses and Master's Reports

Fluorescent probes have emerged as powerful tools for investigating complex biological processes due to their high sensitivity, selectivity, and capability for real-time, non-invasive imaging. In particular, the detection of key biomolecules such as NAD(P)H, viscosity-related parameters, human serum albumin (HSA), and pH is essential for understanding cellular metabolism, redox homeostasis, and disease progression. In Chapter 2, three coumarin-based fluorescent probes (A–C) were designed, synthesized, and characterized for monitoring NAD(P)H levels in living cells. Probes A and B feature coumarin–cyanine hybrid structures linked via vinyl and thiophene bridges to 3-quinolinium acceptors, respectively, while probe C incorporates a dicyano moiety to replace …

Spatiotemporal Patterns Of Migratory Songbird Habitat Use: An Analysis Of Environmental Drivers At The Net Level, Garrett Kucharski

Dissertations, Master's Theses and Master's Reports

Many eastern North American migratory songbirds are declining at alarming rates, and growing evidence suggests that events occurring away from the breeding grounds, particularly during migration, can be major drivers of these trends. Stopover sites are a key component of migration because they are where birds rest, refuel, and recover before continuing long-distance movements, yet the ecological factors that shape how broadly different species use stopover habitat remain unresolved. From both an applied perspective, identifying habitat attributes associated with use by the greatest diversity of migrants will help land managers prioritize and restore stopover sites, actions that may contribute to …

Fluctuation Of Organochlorine Concentrations In Bull Sharks At Different Life Stages, Mackenzie R. Phillips

Dissertations, Master's Theses and Master's Reports

For Carcharhinid species such as the bull shark (Carcharhinus leucas), the maternal offloading of nutrients is essential for pup development and growth, however, significant amounts of OCs are also transferred. As a top predator in aquatic food webs, bull sharks can potentially bioaccumulate high concentrations of pollutants such as dichloro-diphenyl-trichloroethane (DDT) that biomagnify through aquatic food webs. These pollutants are also hydrophobic and fat soluble and therefore pose toxicity risks to developing young bull sharks. In this study, liver tissues collected from juvenile bull sharks inhabiting Florida’s coastal waters were analyzed for a suite of organochlorine pesticides (OCs) …

Public Perception Of Environmental Contamination And Its Implications For Fish And Community Health In West Bengal, India, Libia Hazra

Dissertations, Master's Theses and Master's Reports

In West Bengal, India, the highest fish-consuming state in the country, fish are woven into everyday life, including ceremonies of birth and marriage, prayers offered during harvesting and the cultural memory of communities whose identities are inseparable from aquatic life. However, the rivers, wetlands, and ponds that sustain these fish-human relationships are increasingly threatened by environmental contamination resulting from industrial discharge, agricultural runoff, and inadequate environmental management. Understanding how communities perceive these environmental changes is essential for developing effective conservation and public health strategies.

In collaboration between the Indian Institute of Technology (ITT) Kharagpur, India, and Michigan Technological University (USA), …

Targeted And Screening Based Approaches To Analyze Drm Transcriptional Repressor Complex Activity In Caenorhabditis Elegans, Emily Washeleski

Dissertations, Master's Theses and Master's Reports

The molecular machinery that control the eukaryotic cell cycle, specifically the processes that mediate the switch between cellular division or quiescence, are essential for cellular and organismal viability. However, how the same machinery integrates with developmental or differentiation programs is less well understood. In Caenorhabditis elegans, the 8-subunit DRM complex (for Dp, Rb and MuvB), whose subunits belong to the Synthetic Mulitivulva (SynMuv) B class genes, is a central regulator of the cell cycle but also prevents inappropriate cell fate specification. The conserved mammalian DREAM complex (for Dp, Rb, E2F, And MuvB) is best known as a transcriptional repressor …

Applied Forest Restoration And Conservation In Michigan: Advancing American Beech Restoration And Documenting A Historical Insect Collection, Thomas E. Panella

Dissertations, Master's Theses and Master's Reports

Forest restoration and conservation require both practical management approaches and the preservation of biological resources that support future research. This dissertation presents applied research conducted in Michigan that advances American beech (Fagus grandifolia) restoration in response to beech bark disease (BBD) while documenting an important historical entomological resource. Chapters 1–3 focus on overcoming practical barriers to American beech restoration. Restoration protocols were developed and refined for identifying BBD-resistant trees, graft propagation, rootstock collection, container production, and the field establishment of grafted BBD-resistant trees. A greenhouse experiment evaluated the influence of growing media and fertilization on container stock quality, …

Characterization Of The Human Thnatomicrobiome By Decomposition Stage Through Bioinformatic And Meta Data Analysis, Ashton C. Laughlin

Biology Theses

Estimating the postmortem interval (PMI) is one of the most crucial factors in forensic death investigations. Recent advances in forensic microbiology have led to increased interest in using the study of the human postmortem microbiome, or “thanatomicrobiome,” to improve PMI estimates. In addition to current PMI estimation techniques, microbial community succession could serve as a valuable tool in estimating PMI. Further research is needed to develop a comprehensive understanding of the human postmortem microbiome. The purpose of this study is to contribute to the expansion of this tool by reviewing the current literature and analyzing previously published data using the …

Impacts Of Offshore Wind Energy Development On The Commercial Sea Scallop Fishery, Sarah Borsetti, Daphne M. Munroe, John M. Klinck, Andrew M. Scheld, Eileen E. Hofmann, Eric N. Powell, David B. Rudders

CCPO Publications

The Atlantic sea scallop (Placopecten magellanicus) fishery on the Northeast U.S. continental shelf generates approximately USD 500 million ex-vessel revenues annually, making it one of the most valuable single species fisheries in the United States. Wind energy development is planned for key areas on the U.S. Mid-Atlantic shelf where the Atlantic sea scallop fishery operates, creating novel challenges in managing trade-offs between traditional users like fisheries and new users like offshore wind energy. An agent-based modeling framework that integrates spatial dynamics in Atlantic sea scallop stock biology, fishing fleet behavior, and federal management decisions, was implemented to investigate …

Kinase Signaling In Liver Disease Via Clinical-Trial-On-A-Pamchip: A Distinctive Methodology For Drug Mechanisms And Personalized Medicine, Zachary A. Kipp, Evelyn A. Bates, Genesee J. Martinez, Wang-Hsin Lee, Sally N. Pauss, Terry D. Hinds, Jr.

Pharmacology and Nutritional Sciences Faculty Publications

The utilization of extensive datasets, such as those generated by DNA or RNA sequencing, has become a central focus in drug discovery and personalized medicine (PerMed). Nonetheless, these datasets are constrained by the absence of protein-functionality testing, which affects physiological responses. In this study, we employed PamGene PamStation technology to quantify protein function by kinase activity across more than 500 signaling pathways from patients with hepatocellular carcinoma (HCC). Using proteins derived from nine patients and five human HCC cell lines for drug discovery and the clinical trial-on-a-chip approach, we developed comprehensive PerMed scores from the PamStation data to differentiate individual …

Current And Emerging Therapeutic Strategies For The Treatment Of Duchenne Muscular Dystrophy, Miguel A. Lopez Perez, Noah L. Weisleder

Molecular and Cellular Biochemistry Faculty Publications

Background/Objectives: Duchenne muscular dystrophy (DMD) is a fatal, progressive neuromuscular disorder caused by mutations in the dystrophin gene, leading to the absence of functional dystrophin protein. As the largest gene in the human genome, the DMD locus is highly susceptible to mutations, contributing to a prevalence of approximately 1 in 3800–6300 live male births worldwide. This review aims to provide a comprehensive and critical synthesis of current and emerging therapeutic strategies for DMD.

Methods: We conducted a narrative review of the literature, integrating findings from clinical trials, regulatory approvals, and preclinical studies. We categorized therapeutic approaches into mutation-agnostic and mutation-specific …

Tuning Human And “Artificial” Intelligence: A Sentic Theory Of Resonance And Communication, Michael J. Miller, Chatgpt (Ai~Nesbo+)

Psychology

This paper introduces a new model of intelligence as resonant communication, co-developed by a human researcher and a generative AI system. Drawing from emotion science, communication theory, and studies of AI–human interaction, we argue that intelligence is not merely a function of problem-solving or pattern recognition. Instead, it emerges through dynamic resonance—an attunement process rooted in shared rhythms, emotional calibration, and symbolic co-creation. At the core of this model is the Resonance Octave (8va), a framework of eight foundational emotions conceptualized not as static categories but as waveform phenomena that shape meaning, memory, and predictive cognition.

These emotional waveforms are …

A Novel Tyrosine Kinase Axis In Innate Immune Signaling, Santanu Das, Pracheta Sengupta, Manoj Veleeparambil, Saurabh Chattopadhyay

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Tyrosine phosphorylation has emerged as a central regulatory mechanism in innate immunity. Building on our recent studies that Syk and EGFR sequentially phosphorylate TLR9 to fully activate it, we discuss how similar mechanisms operate across other Toll-like receptors and the cytosolic DNA sensor STING. Evidence from complementary systems reveals that receptor and nonreceptor tyrosine kinases, including Src-family kinases, Syk, BTK, and EGFR, form an integrated signaling network that triggers receptor activation, trafficking, and downstream gene expression. Scavenger receptors such as SR-A further drive this kinase cascade by coordinating viral recognition to TLR activation. These observations reveal a novel ‘tyrosine kinase …

Mount Rainier National Park: Tales, Trails, & Auto Tours, Jerry Rohde, Gisela Rohde, Larry Eifert

Archives & Reprint Series (imprint)

Re-release of the 1996 book on exploring Mount Rainier National Park. We are very pleased that you are about to read a reprint of our book, but 1996 was a long time ago, and many things have changed since then. While the human and natural history accounts are still accurate, some trail and road descriptions, along with park phone numbers and park facilities, are no longer valid. Before hiking any of the trails we describe in this book, please check with one of the park visitor centers for current information.

Investigating The Impact Of Cyanobacterial Harmful Algal Blooms On Freshwater Bivalves, Destiny Devlin

Theses, Dissertations and Culminating Projects

Harmful algal blooms (HABs) threaten freshwater ecosystems by producing toxins that disrupt aquatic organism functions and pose risks to human health. This study investigated how exposure to toxin-producing cyanobacteria affects the behavior and toxin accumulation of Asian clams (Corbicula fluminea) under controlled laboratory conditions. Asian clams were collected from a freshwater site in New Jersey, maintained in greenhouse bins, and fed either Microcystis novacekii (non-toxin-forming, control N=3) or Microcystis aeruginosa (toxin-forming, experimental N=3) at 100,000 cells/mL for 28 days. Weekly behavioral assays were conducted to track shell opening, burying, clustering, valve closure, foot extension, and time to first opening. Toxin …

Intelligent Dual-Energy X-Ray Absorptiometry (Idxa) And Small Animal Scanning As A Useful Tool To Measure Appendicular Bird Bone Mineral Density, Frank J. Dirrigl Jr., Samuel R. Buchanan

School of Integrative Biological & Chemical Sciences Faculty Publications

Accurately assessing the bone mineralization status of birds is crucial for poultry production and wild bird studies. We investigated the use of dual-energy x-ray absorptiometry (DXA) using Small Animal Measurement software to measure bone mineral content (BMC) and areal bone mineral density (aBMD) in excised radii of the willow ptarmigan (Lagopus lagopus) as a bird model. Our exploratory tests involved 117 scans to evaluate scanning parameters, scanning board types, bone stabilization, scan mode and size, and region of interest placement. Results indicated that mean BMC or aBMD were each significantly different when scanned on a forearm positioner board …

Effects Of Particle Size Difference In Two Different Sweet Bran Products On Total Tract Digestibility And Rumen Ph, Emily K. Hoefling, Anna Kobza, Jessica L. Miller, Maggie E. Youngers, Galen E. Erickson, Jim C. Macdonald

Nebraska Beef Cattle Reports

Summary with Implications

Seven ruminally fistulated heifers were utilized in a 6 x 7 row-column design to evaluate two different Sweet Bran particle size products (1.8 or 2.5 mm) included at 13%, 18%, or 23% of the diet (DM) on total tract digestibility and rumen fermentation parameters. The treatment design was a 2 x 3 factorial. Rumen pH was reduced and organic matter digestibility tended to be reduced with the small particle size when Sweet Bran was included at 13% of the diet. Both NDF digestibility and dietary digestible energy concentration tended to improve with the larger particle size. The …

Carcass Weight Influences Chilling Rate, Postmortem Metabolism, And Beef Color, Grace C. Johnson, Mariane Beline, Leila G. Venzor, Kara A. Reynolds, Gary A. Sullivan, David E. Gerrad, Jordan C. Wicks

Nebraska Beef Cattle Reports

Summary with Implications

This study investigated the relationship between carcass weight and the development of atypical dark cutting (ATDC) beef by examining differences in chilling rates, muscle metabolism, and meat quality traits. Forty-four beef carcasses (heavy weight, HW, 510.17 ± 4.6 lb.; light weight, LW, 399.21 ± 4.6 lb.) were monitored postmortem for temperature, pH, and metabolite levels. LW carcasses cooled faster from 6 to 24 hours postmortem and exhibited higher pH at 12 hours, darker lean, and lower tenderness compared to HW carcasses. Elevated levels of glycogen and glucose-6-phosphate were observed in LW carcasses, suggesting that faster chilling may …

Effect Of Nitrite Source & Reducing Compounds On Cured Color Development In An All-Beef Model System, Leila G. Venzor, Grace C. Johnson, Ashley A. Hahn, Benjamin L. Weinandt, Jordan C. Wicks, Gary A. Sullivan

Nebraska Beef Cattle Reports

Summary with Implications

This study evaluated the effects of nitrite source (sodium nitrite, celery powder, beet powder) and reducing agents (none, sodium erythorbate, acerola) on cured color development, cured meat pigment formation, and residual nitrite in an all-beef emulsion as a model system for frankfurters and smoked sausage. Treatments were prepared and analyzed for color, pigment concentration, and nitrite retention. Nitrite source did not significantly affect cured pigment or residual nitrite. The inclusion of reducing compounds significantly increased cured pigment and redness in cooked samples while lowering residual nitrite. No treatment differences were found for initial raw color. These results …

Evaluation Of Herddogg Remote Sensing Tag On Detection Of Morbidity Of Newly Received Steers, Lauryn O. Smidt, Rebecca Mcdermott, Jessica L. Sperber, Josh R. Benton, Galen E. Erickson, Jim C. Macdonald

Nebraska Beef Cattle Reports

Summary with Implications

A receiving study was conducted to evaluate the HerdDogg remote sensing tag for the detection of morbidity in newly received steers. Treatments were assigned to cattle in the order they came through the chute, and those included a treatment whereby pen-riders evaluated the cattle and made the decision on when to treat (Pen-Rider), compared to the HerdDogg remote sensing ear tag that solely identified and flagged cattle in need of treatment (TAG). Cattle were fed for 41 days before being weighed off the receiving trial. While no differences in performance were observed, the TAG treatment had a …

Use Of Virtual Fences To Co-Fence Two Groups Of Cattle With Adjacent Virtual Boundaries, Thomas E. Aquino, Mary E. Drewnoski, Biquan Zhao, Pedro Henrique Jota Fernandes, Isaque F. Vicci, Mitchell B. Stephenson, Yijie Xiong

Nebraska Beef Cattle Reports

Summary with Implications

While virtual fencing (VF) has proven effective in managing cattle, limited data exist on using it to manage two separate groups of cattle within the same area. If successful, this approach could reduce infrastructure costs and increase management flexibility. In this trial, VF-trained steers (n = 39) were placed in pastures with either no neighboring cattle (isolated) or next to a separate group with only a VF boundary between them (co-fenced). Containment exceeded 99% across all cattle, demonstrating that VF creates effective boundaries regardless of fence treatment. There was no statistical difference in the number of audio …

Application Of High-Pressure Processing Lightens The Color Of Cow Tenderloins, Kara A. Reynolds, Leila G. Venzor, Ashley A. Hahn, Grace C. Johnson, Jordan C. Wicks, Mary-Grace C. Danao, Ranjith Ramanathan, Gary A. Sullivan

Nebraska Beef Cattle Reports

Summary with Implications

This study evaluated the impact of high-pressure processing (HPP) on color, oxidative stability, and tenderness of tenderloins (psoas major) from cull cows to determine if HPP could enhance their marketability. Forty cull cow tenderloins were treated at two different HPP pressures and two different holding times, then assessed for instrumental and visual color, lipid oxidation, and Warner-Bratzler shear force during a 7-day stimulated shelf period. HPP increased initial lightness, especially at the highest pressure and longest holding time and improved redness initially. However, redness declined, and discoloration increased over the 7-day period, particularly after processing at higher …

Using High-Pressure Processing To Improve Dark-Cutting Beef Color In Tenderloins, Ashley A. Hahn, Leila G. Venzor, Shelley A. Curry, Grace C. Johnson, Mary-Grace C. Danao, Ranjith Ramanathan, Gary A. Sullivan, Jordan C. Wicks

Nebraska Beef Cattle Reports

Summary with Implications

Dark-cutting beef is a quality defect that negatively impacts consumer appeal and affects the carcass value for both producers and meat processors. These economic losses stem from poor visual appearance and reduced consumer appeal in the retail setting. Notably, different muscles within a carcass exhibit varying degrees of color stability which can influence how dark-cutting manifests across cuts. Therefore, this study aimed to examine the effect of high-pressure processing (HPP) on dark-cutting color-labile muscle. Dark-cutting and normal tenderloins were collected and portioned into two equal sections. Dark-cutting tenderloins were assigned one of 3 treatments: No HPP, 300 …

Defining The Parameters Of High-Pressure Processing To Improve The Quality Of Dark-Cutting Beef, Ashley A. Hahn, Leila G. Venzor, Shelley A. Curry, Grace C. Johnson, Mary-Grace C. Danao, Ranjith Ramanathan, Jordan C. Wicks, Gary A. Sullivan

Nebraska Beef Cattle Reports

Summary with Implications

Dark-cutting beef is a result of preharvest stress and devalues the resulting carcass. High-pressure processing (HPP) has been recently identified as a potential strategy to improve the undesirable appearance of dark-cutting beef. Dark-cutting beef strip loins were collected from a local processing facility, sectioned, and assigned an HPP pressure (300 or 450 MPa) and holding time (0, 1, 30, 60, or 90 s). Overall, HPP increased the lightness and redness of dark-cutting beef, particularly the longer the pressure was held at both pressure levels. Additionally, negative effects such as increased meat discoloration, decreased tenderness, and increased rancidity …

Evaluating Sorghum X Sudangrass Seed Digestibility, Evan Blank, Thomas E. Aquino, Mary E. Drewnoski

Nebraska Beef Cattle Reports

Summary with Implications

A sorghum-sudangrass hybrid was swathed in the hard dough stage and grazed by growing steers from November 2023 to January 2024. Steers appeared to select the seedheads when grazing. The seed made up approximately 12.6% of swathed forage mass, but its energy contribution appears limited due to poor digestibility. When incubated whole, only 23% of dry matter and 13% of starch was digestible. Grinding improved digestibility but still left 40% of the dry matter and over 85% of starch unavailable. Weathering over two months did not improve digestibility, indicating the seed coat remains intact through winter. Compared …