Digital Commons Network^™

Multi-Omic Profiling Provides Insights Into The Heterogeneity, Microenvironmental Features, And Biomarker Landscape Of Small-Cell Lung Cancer, Mingchao Xie, Miljenka Vuko, Shashank Saran, Siyu Liu, Andrew G Chambers, Hana Baakza, Helen K Angell, Felicia Ng, Carl M Gay, Robert J Cardnell, Felix J Segerer, Alma Andoni, Jaime Rodriguez-Canales, Paul M Waring, Markus Schick, J Carl Barrett, Lauren A Byers, Giulia Fabbri

Faculty, Staff and Student Publications

Background: Greater understanding of differential therapeutic sensitivity, specifically to immunotherapy, in small-cell lung cancer (SCLC) is required.

Methods: We explored SCLC heterogeneity through integrated molecular characterization of tumor tissue samples from 159 treatment-naive patients, utilizing genetic, epigenetic, transcriptional, and proteomic profiling, immunohistochemistry staining for multiple biologically relevant markers including transcriptional subtype-defining proteins, and spatial immune profiling using multiplex immunofluorescence.

Results: Multi-omics analysis confirmed high heterogeneity across/within neuroendocrine and non-neuroendocrine subtypes. Methylomics analysis identified four methylome clusters that may enhance subtype prediction, prognosis, and longitudinal monitoring of subtype evolution. Immunohistochemistry analysis showed high MHC-I expression in non-neuroendocrine subtypes, which have greatest …

Inhibition Of Clostridioides Difficile-Specific Dna Adenine Methyltransferase Cama By Analogs Of S‑Adenosyl‑L‑Methionine, Jujun Zhou, Youchao Deng, Dan Yu, Taraneh Hajian, Masoud Vedadi, Xing Zhang, Robert M Blumenthal, Rong Huang, Xiaodong Cheng

Faculty, Staff and Student Publications

Epigenetically targeted therapies, especially those inhibiting S-adenosyl-l-methionine (SAM)-dependent methylations of DNA, mRNA, and histones, have advanced rapidly in cancer treatment. However, these therapies remain underexplored for antibiotic development, despite the growing threat of antimicrobial resistance. Here, we screened a focused library of SAM analogs against the DNA adenine methyltransferase CamA specific to the enteric pathogen Clostridioides difficile. At the same time, we examined six other adenine methyltransferases, including two bacterial DNA methyltransferases and four human RNA methyltransferases having distinct RNA substrates. Compound 113 selectively inhibited CamA (IC50 = 0.15 μM). In addition, compound 67 inhibited Caulobacter crescentus CcrM …

Hif-2-Dependent Regulation Of Pthrp And Paraneoplastic Hypercalcemia In Aggressive Clear-Cell Renal Cell Carcinoma, Arijit Mal, Bingqing Xie, Zane Gray, Charlotte Small, Susmita G Ramanand, Yunpeng Gao, Vanina Toffessi Tcheuyap, Sashi Debnath, Alana Christie, Jeffrey Miyata, Brooklyn Jackson, Hua Zhong, Boning Gao, Jay Lohrey, Naim M Maalouf, Sangeetha M Reddy, John D Minna, Ivan Pedrosa, Xiankai Sun, Ram S Mani, Payal Kapur, James Brugarolas

Faculty, Staff and Student Publications

Renal cell carcinoma (RCC) patients with hypercalcemia (HC) have worse outcomes. HC often involves PTHrP, and the role of HIF-2 is incompletely understood. Leveraging RCC tumorgraft (TG) models of HC, which were characterized by tumor cell autonomous inflamatory/immune signatures, we show that HIF-2 inhibition with PT2399 frequently normalized calcium, downregulated circulating PTHrP and reduced HIF-2 binding to the PTHLH (PTHrP) promoter. Likely contributing to the selective induction of PTHrP in a subset of HIF-2-dependent tumors, the PTHLH locus was generally more accessible in TG(HC). However, PTHLH chromatin accessibility was grossly unaffected by PT2399, unlike elsewhere (including EPO locus in a …

Single Compost Application Benefits For Organic Dryland Wheat Production, Shikha Sharma, Matt Yost, Earl Creech, Jennifer R. Reeve, Astrid R. Jacobson, Idowu Ademola Atoloye

All Current Publications

This research highlights the long-term value of compost in dryland wheat systems, where water scarcity and declining soil fertility limit productivity. A single, high-rate compost application (22 tons per acre) can improve soil moisture content, organic carbon content, aggregate stability, and microbial activity. All these benefits contributed to higher and more stable wheat yields, even more than two decades after application. These changes help to make the compost-treated wheat more resilient during dry years. While composting incurs a high upfront cost, its long-term benefits can significantly reduce the need for repeated fertilizer or soil amendments, offering cost and labor savings …

Using Insecticidal Compounds To Elucidate The Potential Role Of Neurotransmitters In Lepidoptera Pupal Ecdysis, Niranjana Krishnan, Cassandra Gorman, Jillian Stewart, Steven Bradbury, Russell Jurenka

Biological Sciences Faculty Research & Creative Works

Previously, we reported final-instar lepidopteran larvae exposed to low doses of imidacloprid, clothianidin, and thiamethoxam had arrest in pupal ecdysis, which is a novel adverse outcome for neonicotinoid insecticides. Since neonicotinoids disrupt acetylcholine signaling, we hypothesized that the excitatory neurotransmitter acetylcholine plays a critical role in regulation of pupal ecdysis, likely by modulating the release of peptides from crustacean cardioactive peptide (CCAP) neurons. In this paper, using two lepidopteran species, we undertook studies with five additional nicotinic acetylcholine receptor (nAChR) agonists and three muscarinic acetylcholine receptor (mAChR) agonists to hypothesize the putative nAChR subunits that mediate pupal ecdysis. We also …

Applicability Of Syntropic Agriculture To A Semi-Arid Continental Climate: Alentejo To New Mexico, Arielle Nathan, Joana Dionisio Msc, João Serra, Joseph Lanning, Cátia Magro Dr.

Journal of Critical Global Issues

Conventional industrial agriculture has detrimental effects on the environment including pollution and overconsumption of water, soil degradation, and biodiversity reduction. An environmentally sustainable future of food production requires alternative methods that limit negative environmental consequences. Syntropic Agriculture (SA) is a promising farming alternative especially for arid systems at risk of desertification. New Mexico, USA, is a semi-arid continental climate in a prolonged period of drought and predicted to experience worsening agricultural conditions including desertification, wildfire intensification, and exacerbated water scarcity. The Alentejo region of Portugal has a Mediterranean climate with similar agricultural challenges. The agroecological transition project, Terra Sintrópica, located …

Generating Predictive Gene Expression Signatures For Alzheimer's Disease Using Postmortem Brain Tissue, Ashley Duche

Pharmaceutical Sciences (PhD) Dissertations

Background: Alzheimer’s Disease (AD) is a progressive neurodegenerative disorder characterized by the accumulation of amyloid-beta (Aβ) plaques and tau protein aggregates. These pathological features develop in specific brain regions, but why some areas are more vulnerable to early AD-related changes remains unclear. To address this, predictive gene expression signatures were developed to explore the molecular mechanisms underlying regional susceptibility to AD pathology.

Methods: This was performed using postmortem brain (PMB) tissue from participants in the Religious Orders Study and Memory and Aging Project (ROSMAP), Mayo Clinic, and Mount Sinai Brain Bank (MSBB) to generate gene expression signatures from six brain …

Fisheries Research Report No. 362: Characterising Essential Benthic Habitats And Environmental Drivers Of Fishery Recruitment In The Exmouth Gulf Prawn Managed Fishery, Scott Evans, Nick Konzewitsch, Rachel Marks, Renae Hovey, Gary A. Kendrick, Lynda M. Bellchambers

Fisheries Research Reports

Fisheries management relies on the development and evolution of effective assessment and monitoring techniques that are applicable in a range of fishery contexts (Fletcher et al., 2016; L. M. Robinson et al., 2021). The assessment of fish habitats and environmental drivers that influence recruitment is central to sustainable fisheries management (de Lestang et al., 2010; Galindo-Cortes et al., 2010; Gao & Wang, 2021). Western Australia conducts robust fishery-specific monitoring and assessment programs to ensure the sustainable use of its aquatic resources (Newman et al., 2023). However, few long-term datasets exist that directly monitor critical fish habitats and environmental conditions that …

Molecular Pathway Dysregulation In Chronic Liver Disease: Metabolic And Mechanotransductive Drivers Of Hepatic Pathophysiology, Samantha Harvat

Department of Chemical and Biomolecular Engineering: Dissertations, Theses, and Student Research

Metabolic dysfunction–associated steatotic liver disease (MASLD) represents a rapidly growing cause of chronic liver injury, yet the molecular interactions linking metabolic stress, inflammation, fibrosis, and hepatocellular carcinoma (HCC) remain incompletely defined. This thesis integrates transcriptomic analyses across multiple GEO datasets to identify coordinated metabolic, inflammatory, and mechanotransductive pathways that collectively drive disease progression.

Analysis of human liver biopsy datasets (GSE126848 and GSE89632) revealed consistent suppression of glycolysis, β-oxidation, and oxidative phosphorylation across MASLD and MASH samples, accompanied by modest compensatory TCA cycle activation. These alterations reflect impaired metabolic flexibility, mitochondrial stress, and increased ROS susceptibility. Concurrently, cytokine-network enrichment demonstrated activation …

Teaching Leadership In The Context Of Crisis: Connecting Organizational Leadership And Crisis Competencies In A Faculty Leadership Education Program, Caitlin Lunzmann, Nicole Lamee Perez Stedman, Matthew Sowcik

Journal of Human Sciences and Extension

This research focused on enhancing leadership instruction in colleges of agriculture. A multi-institutional research team initiated a program to teach agricultural and natural resource faculty how to create leadership-oriented case studies for undergraduates. Forty faculty members participated in an online training academy centered on Bolman and Deal’s Organizational Frames and case study writing. Following the academy, these faculty members participated in field experiences in the southeastern U.S. to gather data on natural disasters, which they used to write case studies about leadership in agriculture. Though the program focused on organizational leadership, it also discussed leadership in the context of natural …

The Price Of Priorities: How Human Choices Fuel Climate And Ecological Decline, Keisha Hickman

Biological Sciences Undergraduate Honors Theses

This thesis examines the ways in which human priorities and behaviors contribute to the escalating climate crisis and ecological systems. We will first analyze the role of social media in shaping public discourse on climate change and critically evaluate the priorities of institutions that have the means to assist in wildlife conservation. Both speak to the current behaviors of humankind prioritizing their own entertainment over meaningful efforts to mitigate climate change and preserve biodiversity. We will then shift to exploring the profound impact of human population growth and its associated activities on other species and ecosystems. Finally, the thesis will …

A Persistent Homology Framework For Scrna-Seq: Assessing Clustering Robustness And Quantifying Preprocessing And Integration Effects On Topological Features., Jonah Daneshmand

Electronic Theses and Dissertations

As single-cell RNA sequencing (scRNA-seq) data expands, robust methods for integrating diverse datasets are critical. This dissertation applies Persistent Homology (PH), a technique from Topological Data Analysis (TDA), to a collection of scRNA-seq datasets spanning eight tissue types to quantify how data integration affects topological features and biological interpretability. We assessed global topological structure using Betti curves, Euler characteristics, and persistence landscapes across raw, normalized, and integrated data representations. Our analysis revealed a performance inversion: while conventional methods excelled on unintegrated data, high-granularity topological methods, particularly those sensitive to global data structure, became superior after integration. This suggests a synergy …

Characterizing Hexavalent Chromium Neurotoxicity Across Laboratory Models., Samuel Thomas Vielee

Electronic Theses and Dissertations

Hexavalent chromium [Cr(VI)] is a ubiquitous environmental pollutant and potent toxicant. Exposure to Cr(VI) in drinking water is primarily associated with cancers, inflammation, and hepatotoxicity; however, recent studies have identified Cr(VI) as a neurotoxicant in rodent and cell culture models. The literature suggest chromium accumulates in the brain, induces widespread neurodegeneration, and alters rodent behaviors. Despite these data, we lack a detailed and consistent assessments of Cr(VI) neurotoxicity across models, and interactions between aging and Cr(VI) neurotoxicity are not reported in the literature. In this dissertation, we characterize Cr(VI) neurotoxicity across 3 laboratory models: Sprague-Dawley rats, Caenorhabditis elegans, and …

Exposure To Pm2.5 And Aging., Daniel Chris Gomes

Electronic Theses and Dissertations

Inhalation of fine airborne particulate matter (PM_2.5) is an environmental risk factor for numerous health disorders, including cardiovascular diseases (CVD). While several studies have shown that PM_2.5 exposure can induce oxidative stress, DNA damage, and inflammation, the underlying mechanisms that translate these effects into systemic pathology remain poorly understood. Some recent studies have shown that PM_2.5 exposure can lead to telomere shortening in leukocytes, but the generality of this outcome and contribution to endothelial dysfunction has not yet been fully explored. We hypothesized that PM_2.5inhalation accelerates cellular aging and senescence in both circulating peripheral …

A Ralgef Inhibitor Suppresses Lung Cancer Stem Cell Development And Tumorigenesis., Raphael Ngozichi Suarez Jigo

Electronic Theses and Dissertations

The RALGEF family of proteins are direct downstream effectors of the RAS oncoprotein. RALGEFs act as guanine nucleotide exchange factors (GEFs) for downstream RAL proteins, thus tying RAS to the regulation of RAL. Genetic studies have demonstrated RAL proteins to be key drivers of RAS-driven transformation and metastasis. Furthermore, this pathway has been implicated in chemoresistance, exocyst-mediated transport, and the modulation of cancer stem cells. Previous work in our lab reported the activity of a novel pan-RALGEF inhibitor (C4-180) against RAS-driven pancreatic cancer models. Here we show the agent to be active against in vitro and in vivo models of …

Further Characterization Of The Fungal Effector Mvlg-01732 In Planta And Heterologous Expression Of Fungal Effectors In Different Smut Fungi., Joseph Paul Ham

Electronic Theses and Dissertations

Host-pathogen interactions in smut fungi are characterized by effector proteins and their role in infection. The goal of this work is to better understand these interactions by further characterizing an effector from Microbotryum lychnidis-dioicae and heterologously expressing this and other effectors in heterologous species to see if the range of these effectors can play a role in pathogenicity when expressed in distantly and closely related fungal species. These effectors have been attuned over time to their host plant but have homologous interactors in other plant species. In this study, Microbotryum lychnidis-dioicae, Sporisorium reilianum, and Ustilago maydis, were all used …

The Autonomic And Arrhythmogenic Effects Of Gestational E-Cigarette Exposure., Brittany Rachelle Reynolds

Electronic Theses and Dissertations

Introduction. E-cigarettes (e-cigs) have been shown to be pro-arrhythmic in both human and male rodent studies; however, little is known about how e-cig use impacts patients with a predisposed heightened risk for arrhythmias, including pregnant women. Both pregnancy and e-cig use have independently been shown to increase heart rate, diminish heart rate variability, and increase ventricular premature beats, which is suspected to be due to sympathetic dominance. Importantly, β-blockers have been shown to reduce sympathetic activity, reduce heart rate, increase HRV, and reduce arrhythmias. Thus, the use of β-blockers may help prevent adverse health effects driven by sympathetic dominance from …

Tumor Infiltrating Lymphocytes: From Discovery To Clinical Application., Lewis Clayton Chew

Electronic Theses and Dissertations

This thesis explores the evolution of TIL therapy from its discovery to clinical application, focusing on its use in treating metastatic cancer. Adoptive cell therapy (ACT), particularly TIL therapy, has emerged as a promising alternative to traditional treatments like chemotherapy. This review article traces the historical development of TILs, highlighting key experiments and clinical trials that have shaped its understanding and application as a therapeutic strategy for patients with metastatic and difficult to treat cancers including melanoma. Importantly, this article highlights recent advancements, including the FDA approval of Lifileucel, and explores emerging strategies to enhance therapeutic efficacy of TILs through …

El Poder Del Bilingüismo Y La Ciencia, Isabella Winslow

World Languages and Cultures

This project is an explanation of the importance of bilingualism, science, and our responsibility as humans within this environment. As living beings on this planet, we have a responsibility to respect and protect it. Over the course of the last several hundred years, we humans have made countless advancements. We have created unimaginable technology and discovered incredible resources produced by the land. However, in the process of doing so, we have damaged and continue to damage our environment. Reefs in the ocean have been bleached by increases in acidity, thousand year old glaciers have melted, forests have been destroyed by …

Characterization Of Free Oxylipins In Extracellular Vesicles From Bovine Milk, Kai Filio

Food Science (MS) Theses

Background. Extracellular vesicles (EVs) are membrane-bound nanostructures released by human and bovine mammary epithelial cells that carry bioactive lipids and oxidized lipid metabolites. Found in bovine milk, EVs contribute to immune modulation, gut health, and cellular signaling. However, gaps remain in understanding the full composition of milk-derived EVs and how processing alters EV content. This research aimed to characterize the free oxylipin content of EVs from bovine milk treated by pasteurization and homogenization. The hypothesis was that EVs from raw bovine milk would retain higher oxylipin levels than processed milk. Methods. Raw milk was treated by high-temperature short time (HTST), …

The Nebraska Bird Review (December 2025) 93(4), Whole Issue

Nebraska Bird Review

Changes to The Nebraska Bird Review, by Janis Paseka

Fall Field Report, August–November 2025, by W. Ross Silcock

First definitive records of Hermit Thrush and Wilson’s Warbler subspecies for Nebraska, by Stephen J. Brenner and Joel G. Jorgensen

Ogallala Fall Field Days, Sept. 26–28, 2025

Index to Volume 93

Subscription and Organization Information

Index To Volume 93

Nebraska Bird Review

Adams, Morgan
Aguiar: Maritza, Stephanie
Albright, Don
Alexander: Jeff, Jan
Aliferis, Taylor
Allard, Savannah
Allen, Edward
Allison, Betty
Altman, Dakota
Alvarado, A. H.
Ammon, E. M.
Anandan, Sampath Kumar
Andersen, Brett
Anderson: Ann, Chris, Will
Andrews, Ryan
Anhinga
Ani, Groove-billed
Annunziata, Laura
Armstrong, Nancy
Augustine, Jackie
Aurilio, James
Avocet, American

. . .

Zagst: Fred, Kay
Zeillemaker, Fred
Zemaitis, William
Zicafoose, Kirby
Zonotrichia leucophrys: gambelii, leucophrys, oriantha

First Definitive Records Of Hermit Thrush And Wilson’S Warbler Subspecies For Nebraska, Stephen J. Brenner, Joel G. Jorgensen

Nebraska Bird Review

During the fall of 2025, we initiated a pilot migratory bird-banding project in the Nebraska Panhandle. While the project’s goals included examining species composition, volume, and body condition of migratory birds at the western edge of the state compared to the eastern edge of the state, we also used this project to document the occurrence of subspecies and species which are very challenging or impossible to identify through field observation. Here, we report on the first definitive records of two subspecies in Nebraska.

On 16 September 2025, SJB banded an adult male Wilson’s Warbler (Cardellina pusilla) that was …

Fall Field Report, August–November 2025, W. Ross Silcock

Nebraska Bird Review

As in previous fall seasons, by far the most modifications to BONO came from late departure dates; around 87 species were included, no fewer than 13 of these setting record late dates, notably Eastern Whip-poor-will, Mountain Plover, Brown Thrasher (north), Henslow’s Sparrow (flight call only), and Orchard Oriole.

Although this is a Fall Seasonal Report, noted or suggested breeding activity is of interest. Exciting were the 2nd and 3rd presumed breeding records of Black-chinned Hummingbird and, in Dodge Co, the 5th record of breeding by Black-bellied Whistling-Duck. Perhaps the strangest west to east occurrence was a Golden Eagle adventure in …

Changes To The Nebraska Bird Review, Janis Paseka

Nebraska Bird Review

As of this issue, The Nebraska Bird Review has been in existence for 93 years, looking very much now as it did when it began in 1933. However, due to the increasing costs of printing and postage, there will be some changes in its future. Our newsletter, The Burrowing Owl, is already provided online to our members, in a user-friendly and informative form. Future issues of The Nebraska Bird Review will also utilize a digital format to offer a more timely and colorful publication.

This is the final issue for which Ross Silcock will be compiler of the seasonal …

Ogallala Fall Field Days, Janis Paseka

Nebraska Bird Review

The 2025 NOU Fall Field Days were held in Ogallala on September 26–28, with about 80 in attendance. The programs were held at the Quality Inn, and the meeting was planned by Boni Edwards, Dave Cunningham, and Paul Pearson. Field trips were led by Tobin and Keegan Brown, Jacob Cooper and UNK ornithology students, Joel Jorgensen and Stephen Brenner, T. J. Walker, and Thane Dinsdale. Destinations included various sites around Lake McConaughy, Lake Ogallala, Cedar Point Biological Station, Sutherland Reservoir SRA, Ash Hollow State Historical Park, Crescent Lake NWR, Arthur Co and various Sandhills lakes. The total species count was …

Wacsaw: An Adaptive, Statistical Method To Classify Movement Into Sleep And Wakefulness States, Austin Vandegriffe, V. A. Samaranayake, Matthew S. Thimgan

Mathematics and Statistics Faculty Research & Creative Works

Wearable actimeters can improve our understanding of sleep in the natural environments. Current algorithms may produce inaccuracies in specific individuals and circumstances, such as quiet wakefulness. New hardware allows data collection at higher frequencies enabling sophisticated analytical methods. We have developed a novel statistical algorithm, the Wasserstein Algorithm for Classifying Sleep and Wakefulness (WACSAW), to identify behavioral states from recordings of everyday movement. WACSAW employs optimal transport techniques to identify segments with differing activity variability. Functions characterizing the segments' movement distributions were clustered into two groups using a k-nearest neighbors and labeled as sleep or wake based on their proximity …

Draft Genome Sequences Of Four Phosphate-Solubilizing Microbes Of The Family Burkholderiaceae Isolated From Tailings From The Former Pea Ridge Mine In Washington County, Mo, Usa, Prince Oppong Amoh, Abiodun E. Idowu, Elizabeth R. Grube, Melanie R. Mormile, Hunter W. Schroer

Biological Sciences Faculty Research & Creative Works

We present draft genome sequences of four Gram-negative phosphate-solubilizing microbes isolated from Pea Ridge Mine tailings in Missouri, USA. Belonging to the family Burkholderiaceae, these isolates exhibit a phosphate-mineral-dissolving phenotype in liquid and solid cultures. Genome sizes span 5.6–9.7 Mb, with GC contents of 61.6%–67.0%.

Effect Of Successive Subculturing On Virulence, Growth, And Germination Of Fungus Metarhizium Rileyi For Biological Control Of Fall Armyworm, Joanna Marie E. Valeros, Trisha Anne P. Garcia, Noel G. Sabino, Marcela M. Navasero, Melissa P. Montecalvo

The Philippine Agricultural Scientist

This study explored the impact of successive subcultures of Metarhizium rileyi (Farl.) Kepler, S.A. Rehner & Humber on its cultural traits, spore germination, and virulence against fall armyworm, Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae), a key pest in agricultural systems. The mass production of infective propagules is essential for effective biological control. Notable changes were observed in the texture and mycelial appearance of the fungus across subcultures. Initially, the fungus exhibited a powdery texture up to the 6th subculture. However, the fungal growth became fluffy and cottony by the 8th and 10th subcultures. Additionally, sporulation rates (7.05 × 10^{8 …}

Dendrimer Gel Nanoparticles With Dual-Targeting Of Upar And Ribonucleotide Reductase R2 Influence Necrosis, Apoptosis, And Cell Cycle Arrest In Triple-Negative Breast Cancer, Hsin Yin Chuang, Yue-Wern Huang, Hu Yang

Biological Sciences Faculty Research & Creative Works

Triple-negative breast cancer (TNBC) is an aggressive breast cancer subtype with limited treatment options due to the absence of estrogen (ER), progesterone (PR), and human epidermal growth factor receptor 2 (HER2) receptors. We previously developed highly adaptable polyamidoamine (PAMAM) dendrimer-based gel nanoparticles (GDP-uPA/GTI) with dual-targeting capabilities against urokinase-type plasminogen activator receptor (uPAR) and ribonucleotide reductase R2 (R2) to achieve selective antitumor effects. In this study, we investigated the underlying mechanisms of GDP-uPA/GTI-induced tumor inhibition. In vivo, GDP-uPA/GTI significantly downregulated R2 expression and activated caspase 8 and caspase 3, indicating caspase-dependent apoptosis. Histological evaluation of major organs revealed no observable toxicity. …