Digital Commons Network^™

Patterns Of Autonomous And Conditional Neural Specification For The Brain And Ventral Nerve Cord In Annelida, Nicole B. Webster, Johnny A. Davila-Sandoval, Allan M. Carrillo-Baltodano, Skyler Duda, B. Duygu Özpolat, Neva P. Meyer

Biology

Evolution of central nervous systems is a long-debated topic. Similar mechanisms of conditional neural specification linked to dorsal-ventral (D–V) axis formation have been used to support homology across several taxa. We tested for autonomous versus conditional neural specification in two distantly related annelids, Capitella teleta and Platynereis dumerilii, using blastomere isolations and ablations. Our results demonstrate autonomous specification of anterior neural tissue in isolated first-quartet (1q) micromeres for both annelids. In both annelids, partial larvae derived from isolation of the somatoblast, micromere 2d, also resulted in the formation of trunk neural tissue (ventral nerve cord or VNC), suggesting that this …

The Role Of External Factors In Shaping Carbohydrate Conformational Landscapes, Murat Yaman

Dissertations, Theses, and Capstone Projects

Carbohydrates (glycans) are among the most structurally diverse biomolecules and participate in a wide range of biological processes, including molecular recognition, cell adhesion, immune response, host-pathogen interactions, and cellular signaling. Their biological functions are governed by a complex interplay between sequence, stereochemistry, conformational flexibility, and environmental factors. However, the structural heterogeneity and dynamic nature of glycans present significant challenges for both experimental characterization and theoretical modeling. In particular, the relationships between glycan structure, conformational dynamics, and the resulting potential energy surfaces remain incomplete.

This dissertation investigates how external factors modulate the potential energy surfaces of carbohydrates through a combination of …

Architects Of Mrna Fate: Molecular And Cellular Control Of P-Body Organization In The Drosophilia Melanogaster Female Germline, Samantha Milano

Dissertations, Theses, and Capstone Projects

Processing bodies (P-bodies) are cytoplasmic ribonucleoprotein condensates that regulate mRNA storage, translational repression, and decay. While the biochemical principles governing condensate assembly have been extensively studied in vitro, how P-body organization is established and dynamically regulated in vivo to control specific mRNA populations remains poorly understood. This dissertation investigated the molecular and cellular mechanisms that govern P-body architecture and function in the Drosophila melanogaster female germline. First, I identified the conserved LSm protein Trailer Hitch (Tral) as a central organizer of P-body architecture. Using quantitative confocal and super-resolution microscopy combined with chemical perturbations, I showed that Tral coordinates the …

Killer Whales (Orcinus Orca) In The Indo-Pacific: A Review Of Their Distribution, Population Structure, And Ecology, Paola Lacetera, Paul Tixier, Isabella M. Reeves, Maeva Terrapon, Aaron Barnes, Christophe Guinet, Simon H. Elwen, John Totterdell, Jennah Tucker, Paul Cross, Georgia K. Bisset, John Dickie, John P.Y. Arnould

Research outputs 2022 to 2026

Aim: Killer whales, Orcinus orca, are cosmopolitan top predators showing highly variable ecology and behaviour across populations. In the Indo-Pacific, baseline knowledge in general remains scarce, limiting the assessment of their vulnerability to the accelerated environmental changes, including expanding fisheries this region is undergoing.

Methodology: This review synthesises 170 sources found between 2000–2025 to evaluate the current knowledge on distribution, population structure, and feeding ecology (including depredation) of killer whales in the Indo-Pacific, and to identify priorities for future research and management.

Results: Occurrence was highly variable, from sporadic sightings in most tropical sectors to seasonal and year-round presence at …

Organic Pesticides: A General Overview, Marion Murray, Ann Mull

All Current Publications

Organic pesticides are naturally occurring, nonsynthetic, or minimally processed substances that control unwanted organisms in the environment. Categories include insecticides, herbicides, fungicides, and miticides.

Characterization Of Mettl3/14-Mediated M6a Modification In Human Transcriptome Using Nanopore Direct Rna Sequencing, Emily Kurtyan, Andrew J. Stein, Kelly J. Abdalla, Zhangerjiao Yuan, Miten Jain, Fadia Ibrahim

Department of Biochemistry and Molecular Biology Faculty Papers

Post-transcriptional RNA modifications modulate diverse aspects of RNA metabolism. N6-methyladenosine (m6A), one of the most abundant internal RNA modifications, is deposited by the core methyltransferase complex, METTL3 and METTL14. Oxford Nanopore Technologies (ONT) platform permits direct, single RNA molecule sequencing while preserving native modifications. However, without rigorous benchmarking, the accuracy and reproducibility of modification detection remain uncertain. Here, we leveraged ONT to comprehensively profile bona fide m6A modifications in cellular RNAs at single-nucleotide resolution by integrating two direct RNA sequencing chemistries (RNA002 and RNA004) with the m6Anet and Dorado modification-detection models. We independently depleted METTL3 and METTL14 in human cells …

New Wisconsin State Records For Predatory Fungus Gnats (Diptera: Bibionomorpha: Keroplatidae), Daniel K. Young

The Great Lakes Entomologist

In Wisconsin, no published literature species records for the keroplatid genera Keroplatus and Proceroplatus exist (Diptera: Bibionomorpha: Keroplatidae). New state records are presented for Keroplatus carbonarius Bosc, Keroplatus clausus Coquillett, Keroplatus militaris Johannsen and Proceroplatus elegans (Coquillett). The new records are associated largely with Malaise trap samples from Hemlock Draw (The Nature Conservancy), in the Baraboo Hills of Sauk County, and a Malaise trap at Kemp Natural Resources Station, in Oneida County, Wisconsin. Two specimens of K. clausus and a single specimen of K. militaris discovered within the research collection at the University of Wisconsin-Madison are also reported. The specimens …

Long-Term Monitoring And Response Of Papaipema Sciata Bird (Lepidoptera: Noctuidae) To Prescribed Fire In Michigan (Usa), Gregory J. Norwood, Logan M. Rowe, Brett A. Degregorio, David L. Cuthrell, Aaron D. Meredith, Steven M. Gray

The Great Lakes Entomologist

The Culver’s root borer moth (Papaipema sciata) (Lepidoptera: Noctuidae) is a rare Noctuid that requires Culver’s root (Veronicastrum virginicum) to complete its lifecycle within remnant native grasslands and open woodlands in the midwest and northeast United States. We report on 26 years of monitoring this species’ colonization of Culver’s root stems at Algonac State Park (ASP) in Michigan, where prairies have been maintained by prescribed fire since 1990. P. sciata is considered fire sensitive because eggs spend the dormant season in the combustible prairie litter and duff near host plants. The objectives were to determine the …

Could The European Thanasimus Formicarius Outcompete The North American Thanasimus Dubius (Coleoptera: Cleridae) If Introduced To North America?, Robert A. Haack, Robert K. Lawrence

The Great Lakes Entomologist

A federal quarantine was enacted in the United States (US) in the fall of 1992 in response to discovery of the Eurasian pine shoot beetle, Tomicus piniperda (L.) (Coleoptera: Scolytinae), in July 1992 in Ohio. The quarantine regulated movement of pine products (e.g., Christmas trees, nursery stock, and logs) at the county level from infested to uninfested US states. A classical biological program was considered for T. piniperda starting in 1995, focusing on the Eurasian clerid beetle Thanasimus formicarius (L.), an important predator of T. piniperda. Concerns were raised in 1996 that if T. formicarius were released in the …

Fecundity Of Thanasimus Dubius (Coleoptera: Cleridae) Rebounds After A Period Of Prey Scarcity, Robert A. Haack, Robert K. Lawrence

The Great Lakes Entomologist

We field-collected Thanasimus dubius (Fabricius) (Coleoptera: Cleridae) adults during spring, maintained them separately in the laboratory, and initially gave them four bark beetle adults [Ips grandicollis (Eichhoff) or Tomicus piniperda (L.) (Coleoptera: Curculionidae: Scolytinae)] daily as prey. Using a subset of the female clerids (N = 41), we assigned them to one of four feeding groups that varied in the number of prey provided daily. For the first four weeks of a 12–week study, the four diets were: four prey daily, two prey daily, one prey daily, and one prey every 2 days. After four weeks, all females were …

Volume 9 (2026) Climate And Responsibility

International Journal on Responsibility

This issue focuses on the various ways responsibility affects environmental justice. Specifically, this volume urges us to think about how societal and individual (in)action influences ecological crises and what informs this behavior, with a specific focus on religious and Indigenous beliefs and values.

Evaluation Of Mdm2 Mrna Expression According To Clinicopathological Characteristics In Oral Squamous Cell Carcinoma (Oscc) Patients, Tirta Wardana

Chulalongkorn Medical Journal

Background: The murine double minute 2 (MDM2) gene encodes an E3 ubiquitin ligase that targets p53 for degradation, thereby influencing the pathogenesis of oral squamous cell carcinoma (OSCC).

Objective. The present study investigates MDM2 mRNA expression and its association with clinical and pathological characteristics in OSCC patients.

Methods: We conducted an observational-analytical study using a cross-sectional design. The study involved 39 OSCC patients. RNA extraction, cDNA synthesis, and quantitative PCR (qPCR) were performed. We quantified relative MDM2 mRNA expression using the Livak method (2-ΔΔCT) and GenEX MultiD software version 6.0. Statistical significance was assessed using independent t-tests.

Results: Although no …

Erratum: Genetic Variations In Extracellular Matrix Degradation Pathways Linking To Major Depressive Disorder: Evidence From A Large-Scale Genetic Association Study, Halliru Zailani, Daniel Tzu-Li Chen, Sheng-Che Lin, Jia-Hau Lee, Mei-Ling Li, Bing-Fang Huang, Jane Pei-Chen Chang, Kuan-Pin Su

BioMedicine

No abstract provided.

Design And Development Of Novel Peptidomimetic Compounds For Cancer Therapeutics: Focus On Hsp90–Cdc37 Interaction, Sarath Perumal, Ramanathan Karuppasamy

BioMedicine

Background: The HSP90 and CDC37 molecular chaperone complex governs the

stability and function of numerous client protein kinases, making it a crucial cancer target. Given their central role, disrupting this interaction induces proteotoxic stress and inhibits tumor progression. Therapeutic peptides are the mainstay of treatment for disruption of key interactions, yet they face limitations such as toxicity, resistance, and poor stability. Aim: This study aims to leverage peptidomimetics as novel disruptors of the HSP90–CDC37 interaction. Methods: Two peptides, a 9-mer and a 7-mer, were rationally designed by analyzing key regions facilitating HSP90–CDC37 complex formation. In silico mutational analysis identified …

Traditional Chinese Medicine And Healthcare Utilization In Bipolar Disorder: A Population-Based Study With Propensity-Matched And Mirror-Image Analyses, Shu-Ping Chen, Su-Tso Yang, Kai-Chieh Hu, Hui-Chih Chang, Jane Pei-Chen Chang, Kuan-Pin Su

BioMedicine

Background: Bipolar disorder (BD) is a chronic relapsing illness associated with high rates of acute psychiatric hospitalizations (APH) and emergency services (ES) use, placing burdens on healthcare systems. Many patients seek complementary modalities, including traditional Chinese medicine (TCM), alongside standard pharmacotherapy. However, population-based evidence regarding TCM’s effect on acute healthcare utilization in BD is lacking.

Methods: Using data from Taiwan’s Longitudinal Health Insurance Database 2000 (LHID 2000), this population-based study employed propensity score matching (PSM) based on age, gender, the index year (defined as the calendar year of the index date for TCM users and their matched nonTCM counterparts), and …

The Association Between Rapid Growth In Children Under The Age Of Five And Adolescent Obesity, Ratu Ayu Dewi Sartika, Fadila Wirawan, Iche Andriyani Liberty, Nurul Husna Mohd Shukri, Siti Arifah Pujonarti, Edy Purwanto, Munaya Fauziah

Kesmas

Early-life nutrition is a critical predictor of long-term health, yet the association between rapid early-childhood growth and adolescent obesity, particularly in relation to the “double burden of malnutrition,” remains under-researched in Indonesia. This study aimed to analyze the association between rapid growth and adolescent obesity. Data were obtained from the 1997, 2000, and 2014 waves of the Indonesian Family Life Survey (IFLS). This study included 641 children (aged 0–23 months at baseline) with complete anthropometric measurements across all three waves. Rapid growth was defined as an increase in z-scores of >0.67 in weight-for-age (WAZ), height-for-age (HAZ), or weight-for-height (WHZ) between …

Modeling Kinetics Of 5-Aminolevulinic Acid-Induced Protoporphyrin Ix Accumulation For Optimal Photodynamic Therapy, Priscilla Melebor

Graduate Masters Theses

Photodynamic therapy (PDT) is a minimally invasive treatment that uses light-activated photosensitizers to selectively destroy diseased tissue through the generation of reactive oxygen species. However, conventional in vitro models often fail to accurately reproduce the pharmacokinetics of photosensitizer accumulation and clearance observed in vivo. This study investigated protoporphyrin IX (PpIX) accumulation following 5-aminolevulinic acid (ALA) exposure under physiologically relevant conditions using two-dimensional (2D) monolayers and three-dimensional (3D) spheroids. By comparing continuous ALA exposure with transient exposure followed by ALA washout, this work provides a more biologically relevant framework for studying PpIX kinetics and optimizing photodynamic therapy.

Effect Of Partial Ablation Of Skeletal Dynamin Related Protein 1 On Mitochondrial Health, Inflammation, And Fibrosis In A Mouse Model Of Duchenne Muscular Dystrophy, Tessa L. Duzz

Graduate Masters Theses

Duchenne muscular dystrophy (DMD) is a progressive neuromuscular disorder characterized by muscle weakness, degeneration, fibrosis, and impaired muscle regeneration. Mitochondrial dysfunction is an early pathological feature of DMD and has been linked to excessive mitochondrial fission. Dynamin-related protein 1 (Drp1) is a central regulator of mitochondrial fission, a key process in regulating mitochondrial quality and function. Inhibition of Drp1-mediated mitochondrial fission has shown promise as a potential therapeutic target for alleviating pathology and dysfunction in dystrophic muscle. The objective of this study was to determine whether partial skeletal muscle-specific ablation of Drp1 could improve muscle pathology and mitochondrial health in …

Spider Biodiversity And Insecticide Sensitivity Across Active And Restored Cranberry Bogs On Nantucket, Tyler J. Kulak

Graduate Masters Theses

Spiders are one of the most diverse groups of organisms on the planet with over 53,000 species described as of 2026. They provide a suite of ecosystem services including their regulation of problematic pests in agricultural systems, appearing in high biomasses across a breadth of ecological niches. While beneficial as pest regulators, they are also susceptible to the same management techniques as pest organisms and are especially vulnerable to chemical control. Cranberry production in Massachusetts likely benefits from spider ecosystem services, but diversity research on spiders in these systems is limited. This study compares the diversity of spider populations from …

Crosstalk Between Upr And Mitochondria: The Triad Of Er-Mitochondria Contacts, Ca²⁺, And Ros, Ester Zito, György Hajnóczky

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

Endoplasmic reticulum (ER) stress is triggered by several cellular perturbations causing protein misfolding, and activates the unfolded protein response (UPR), an initially adaptive signaling network that aims to restore ER and cellular homeostasis. Growing evidence indicates that UPR signaling extends beyond ER proteostasis, influencing mitochondrial function and bioenergetics through ER-mitochondria contact sites (ERMCs). The CHOP-ERO1A-IP3R axis has a primary role in recruiting mitochondria to adaptive UPR. However, its sustained activation renders UPR signaling maladaptive, leading to mitochondrial dysfunction through both outer mitochondrial membrane permeabilization (OMMP) and mitochondrial permeability transition pore (mPTP) opening, ultimately contributing to irreversible cell injury and disease …

Evaluation Of Antibiotic Use Using The Gyssens Method On Clinical Outcomes In Ischemic Stroke Patients, Juniarto Mende, Graciano A. Maturbongs, Yohana K. A. Mbulang

Pharmacology and Clinical Pharmacy Research

Ischemic stroke is a health problem that causes death and neurovascular disability worldwide. The inflammatory response due to infection can increase ischemic stroke and increase brain damage through changes in blood pressure, coagulation, immune response, and endothelial function. This study aims to evaluate the rationality of antibiotic use on clinical outcomes in ischemic stroke patients. This study used a cross-sectional design. Retrospective data were taken from the medical records of Jayapura Regional Hospital for the period January 1, 2023, to May 31, 2025. The study subjects were all patients who suffered ischemic stroke and received antibiotics. Evaluation of the rationality …

Development Of Ultrafast Protein Digestion And Standards Free Quantitation Methods For Mass Spectrometric Analysis, Praneeth Ivan Joel Fnu

Dissertations

A wide variety of biologically important molecules, such as enzymes, antibodies, hormones, transporters and receptors are proteins by composition and they play key roles in biological functions such as cellular regulation, communication, metabolism and physiological function. Protein dysfunctions and abnormalities are associated with numerous diseases, making proteins critical targets for understanding disease mechanisms and developing therapeutic interventions. Protein-based therapeutics such as monoclonal antibodies, hormones and vaccines gained popularity due to their high specificity, efficacy, and ability to treat complex diseases that are often difficult to address with small-molecule drugs.

Given the important role of proteins in a variety of biological …

Geographic And Environmnetal Influences On Color Pattern Similarity Between Coral Snakes (Genus: Micrurus) And Their Lookalikes, Anthony Sena

Dissertations

Venomous coral snakes and their lookalikes are often regarded as a classic example of Batesian mimicry, whereby a harmless species imitates a harmful species. The existing literature regarding coral snake resemblance presents a divisive stance on whether Batesian mimicry is the primary driver of shared color patterns or if alternative factors are responsible. While recent literature largely favors the Batesian hypothesis, empirical support remains inconsistent, and the specific geographic and interpretation of the conditions required for mimicry lacks consensus within the scientific community.

To evaluate the mechanisms maintaining these phenotypes, a quantitative, multivariate framework was utilized to analyze 400 museum …

Infrared Detectability Of Whale Species And Behaviors To Enhance Automatic Detection For Real-Time Vessel Strike Avoidance, Laura J. Howes

Graduate Masters Theses

Real-time detection of large whales at sea is critical for mitigating serious injury and mortality from ship strikes and other human activities such as seismic surveys, especially for endangered species such as the critically endangered North Atlantic Right Whale (Eubalaena glacialis). Traditional marine mammal observers are limited by environmental conditions and human factors, necessitating a robust, 24-hour solution. This study investigates the efficacy of a novel onboard detection tool infrared (IR) technology to detect whale blows and body parts. While IR is a promising advancement, its performance under varying sea conditions (e.g., fog, humidity) and its ability to …

Innovating A Crustacean Embryo Toxicity (Cet) Assay For Screening Environmental Contaminants, Irina A. Polunina-Proulx

Graduate Doctoral Dissertations

Environmental pollutants can disrupt normal developmental processes, leading to neurobehavioral and developmental abnormalities. Toxicity tests are important for evaluating environmental contaminants; however, standard assays are often time- and cost-intensive and typically require large numbers of vertebrate animals. These limitations highlight the need to reduce reliance on vertebrate testing and to develop New Approach Methodologies that provide comparable results while improving efficiency and cost-effectiveness. This research utilizes a novel screening assay to evaluate developmental toxicity using Hyalella azteca. H. azteca is a freshwater amphipod widely used as a model organism for sediment toxicity in ecotoxicology, yet its embryos have been minimally …

Mitochondrial Trna-Derived Fragments As Candidate Metastasis-Modifying Rna, Katy L. Swancutt, R. Mckinnon Walsh, Sydney Quijano, Emily Schueddig, Devin C. Koestler, Adam D. Scheid, Tony Vanden Bush, Yi Jing, Isidore Rigoutsos, Danny R. Welch

Computational Medicine Center Faculty Papers

UNLABELLED: How mitochondrial DNA (mtDNA) polymorphisms influence complex phenotypes remains poorly understood. Using mitochondrial-nuclear exchange mice, we previously showed that mtDNA single-nucleotide polymorphisms (SNP) modify metastasis, cardiovascular disease, and epigenetic marks independently of metabolic differences. The only mtDNA SNP correlating with these phenotypes resides in the gene encoding mitochondrial transfer RNA (tRNA)-arginine [mt-tRNAArg (UCG), mt-TR], suggesting a role for non-protein-coding loci. In this study, we identify and preliminarily characterize previously undescribed tRNA-derived fragments (tRF) generated from mt-TRs. Northern blotting revealed distinct tRF that are differentially expressed among mtDNA SNPs, between lung and liver, and between sexes. Surprisingly, small RNA sequencing …

Visualizing 25 Years Of Change In The Glades Oak Savanna, Zoe Fieberg

Summer Research Showcase

Oak savannas represent one of the most threatened ecosystems in Minnesota due to changing land use management, particularly absence of fire (Davis, 2001). Frequent burns kill fire-sensitive mesophytic tree species, reducing the dominance of woody understory and allowing for restoration of the oak savanna environment. The GLADES (Grid for Landscape Analysis and Demographic Study) site was established in 1988 in East Bethel, Minnesota to study the effect of frequent burning on oak savanna restoration. Through the use of standardized methods of photography, we compared canopy differences across GLADES between 2001 and 2026. Preliminary observations revealed increased canopy density and reduced …

Utah Vegetable Production Guide (5th Edition), Nick Volesky, Marion Murray, Amelia Olds, Bridger Carey

All Current Publications

This guide, written by a collection of Utah State University (USU) Extension faculty and specialists, provides information on general Utah vegetable production, soil, nutrient, and water management, integrated pest management practices, and pesticides. The included chapters cover various vegetable crops, including brassicas, cucurbits, leafy greens, potatoes, legumes, onions, root crops, sweet corn, and solanaceous crops.

Trophic Ecology Of A South Carolina Estuarine Predator Guild, Shane John Molander

Electronic Theses and Dissertations

Estuaries are among the world’s most productive ecosystems in the world and are characterized by the convergence of two distinct habitats, creating a mosaic of environmental conditions from inland rivers to the nearshore ocean. Many fishes occupy estuaries during various life stages for growth, reproduction, or foraging, and may reside in them seasonally. The co-occurrence of species, particularly upper-trophic level carnivores, can result in competitive interactions for prey resources within a shared environment. Identifying the degree of these interactions as well as understanding basal energy consumption can inform food web dynamics and how overlapping species use shared spaces. I used …

Nasa’S Ecostress Satellite Reveals Widespread Midday Depression In Ecosystem Evapotranspiration, Jingyi Bu, Jingfeng Xiao, Joshua B. Fisher, Yiqi Luo

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Plants often exhibit a midday depression in water use (i.e., transpiration), reflecting a constraint on their ability to sustain maximum water transport, which may occur at the cost of reduced photosynthesis. Eddy covariance observations and geostationary satellites cannot quantify this widespread phenomenon globally while resolving fine-scale spatial variability. Using evapotranspiration measurements from the ECOsystem Spaceborne Thermal Radiometer Experiment on Space Station (ECOSTRESS) and machine learning, we quantify the global distribution of midday depression in evapotranspiration. Midday depression primarily occurs during peak-growing seasons in temperate zones and dry periods in the tropics, with a morning shift of the peak evapotranspiration time …