Digital Commons Network^™

Circuit-Specific Vulnerability In A Mouse Model Of Alzheimer's Disease, Samuel Brunwasser

Arts & Sciences Graduate Student Theses and Dissertations

The relationship between brainwide functional decline and accumulation of pathological protein aggregates in Alzheimer’s disease (AD) is complex and not well understood. A set of highly interconnected cortical regions known as the Default Mode Network (DMN) exhibits selective vulnerability to both functional decline and amyloid beta (Aβ) plaques in early AD. One possibility is that early Aβ accumulation in the DMN drives vulnerability. However, it is unknown whether there is something intrinsic to neuronal projections within the DMN that biases these circuits towards dysfunction. In this dissertation, I describe the development of a multisite in vivo electrophysiology pipeline for chronic …

Induced Cd8a Identifies Enhanced Human Nk Cell Il-15-Induced Proliferation And Metabolism And Modulates Nk Cell Activation, Celia Cubitt

Arts & Sciences Graduate Student Theses and Dissertations

Natural Killer (NK) cells are cytotoxic innate lymphoid cells that play an important role in the surveillance and elimination of virally-infected and malignantly-transformed cells. These primary effector functions are achieved by producing cytokines and chemokines which activate and recruit additional immune effectors, as well as direct cytotoxic killing via perforin and granzymes. NK cell function is tightly regulated by a balance of germ-line encoded activating, inhibitory, co-stimulatory, and cytokine receptors expressed at the cell surface. Through these activating and inhibitory receptors, NK cells recognize and kill targets without prior sensitization through the loss of self-identifying molecules such as major histocompatibility …

Expanding The Druggable Proteome By Integrating Deep Learning With Molecular Simulations To Predict Cryptic Pockets, Artur Meller

Arts & Sciences Graduate Student Theses and Dissertations

Of the protein structures deposited in the Protein Data Bank, less than half have pockets suitable for the binding of drugs. Even when proteins contain pockets in their ground state structures (e.g., the nucleotide-binding active site in myosin motors), achieving specificity remains a central challenge in drug design as many protein families share common structural motifs. Cryptic pockets are cavities absent in ligand-free experimental structures that form due to protein fluctuations in solution. They provide a means to specifically target proteins currently considered undruggable. While cryptic pockets are alluring drug targets, it remains difficult to predict which proteins will form …

Parapinopsin: A Photoswitchable Inhibitory Gpcr For Two-Photon Optogenetics, Bobbie J. Brown

Arts & Sciences Graduate Student Theses and Dissertations

The development of optogenetic tools has greatly advanced the capability of researchers to understand the connection between neuronal activity and behavior. Optogenetics makes use of opsins, which are light activated ion-channels, ion pumps, or G-Protein coupled receptor (GPCR-based) proteins used to regulate cellular activity. Coupled with technological advances in genetics and optical physics/microscopy, optogenetics can be used to control specific populations of cells in a time-locked, spatially specific manner. The experiments possible with optogenetics depend largely on the capabilities and limitations of the opsin used; thus, there have been continuous efforts to design and employ new opsins with a variety …

Metabolic Reprogramming Driven By Ant2 Deficiency Augments T Cell Function And Anti-Tumor Immunity In Mice, Omri Yosef, Leonor Cohen-Daniel, Oded Shamriz, Zahala Bar-On, Wajeeh Salaymeh, Amijai Saragovi, Ifat Abramovich, Bella Agranovich, Veronika Lutz, Joseph Tam, Anna Permyakova, Eyal Gottlieb, Magdalena Huber, Michael Berger

Faculty, Staff and Student Publications

T cell activation requires a substantial increase in NAD+ production, often exceeding the capacity of oxidative phosphorylation (OXPHOS). To investigate how T cells adapt to this metabolic challenge, we generate T cell-specific ADP/ATP translocase-2 knockout (Ant2-/-) mice. Loss of Ant2, a crucial protein mediating ADP/ATP exchange between mitochondria and cytoplasm, induces OXPHOS restriction by limiting ATP synthase activity, thereby impeding NAD+ regeneration. Interestingly, Ant2-/- naïve T cells exhibit enhanced activation, proliferation and effector functions compared to wild-type controls. Metabolic profiling reveals that these T cells adopt an activated-like metabolic program with increased mitobiogenesis and anabolism. Lastly, pharmacological inhibition of ANT …

North Central Extension Risk Management Education Center, Part I: Helps Producers Manage Risks, Christine Lockert, Sheila Aikanathan Johnson, Bradley D. Lubben

Cornhusker Economics

Educating producers to manage risk and position their farm or ranch for future growth and success is the fundamental purpose of the Extension Risk Management Education (ERME) program.

The ERME program, funded by United States Department of Aagriculture’s National Institute of Food and Agriculture, provides training to help producers learn new strategies to manage complex and growing agricultural risks.

Established in 2001 and located at the University of Nebraska-Lincoln Agricultural Economics Department, the North Central Extension Risk Management Education Center (NCERMEC) has a long history of supporting risk management education programs serving producers in the region. NCERMEC, in conjunction …

A Honduran Prevalence Study On Soil-Transmitted Helminths Highlights Serological Antibodies To Tm-Wap49 As A Diagnostic Marker For Exposure To Human Trichuriasis, Neima Briggs, Leroy Versteeg, Rojelio Mejia, Jeroen Pollet, Maria Jose Villar, Bin Zhan, Graeme Segal, Stephanie Novak, Patricia Lenihan, Paul Musgrave, Viviana Ellis, Carol Florencia Coello, K Jagannadha Sastry, Joe Craft, Peter J Hotez, Maria Elena Bottazzi

Faculty, Staff and Student Publications

Soil-transmitted helminth (STH) infections rank among the most prevalent communicable diseases of humans, yet detection of these parasites is mostly restricted to identifying active infection through fecal examinations. Currently, there are no commercial diagnostic tools to identify a prior whipworm or hookworm exposure, and the few serological assays for roundworm infection have not been well validated for crossreactivity or infections in humans. Such diagnostic restrictions limit the range of scientific and clinical questions that surround STH exposures and their implicated relationship to chronic diseases, such as autoimmunity, allergy, and cancer. The goal of this investigation was to evaluate the diagnostic …

Design, Implementation, And Reflection From An Interdisciplinary Course In Museum Studies, Brenna L. Decker

Journal on Empowering Teaching Excellence

Access the online Pressbooks version of this introduction here.

In Spring of 2023, I developed a special topics course titled Collection Material Handling to introduce students to museum management using Utah State University collections on the Logan, UT campus. The cross-listed upper-level course brought 16 USU students together from two disciplines: anthropology and natural sciences. The publication details how I used various learning theories to guide the creation of course content and how I structured and implemented activities in the classroom and in the collections. Examples of worksheets, activities, student feedback, and recommended improvements to assignments are provided. I encourage …

Physical Function In Young And Older Adult Active Pickleball Players – A Cross-Sectional Study, Leighanne T. Paulson, Eric Martin, Kent Adams, Marcus M. Lawrence

Topics in Exercise Science and Kinesiology

Topics in Exercise Science and Kinesiology Volume 6: Issue 1, Article 5, 2025. Limited information exists on pickleball’s impact on physical function in older adults (65+ years), despite reported health benefits. PURPOSE: This cross-sectional study evaluated the physical function of active older adult (OA) women and men recreational pickleball players via handgrip strength (HGS) and fatigue (HGF), 6-minute walk distance (6MWD) test, as well as the short physical performance battery (SPPB) compared to sex-matched young adult (YA) controls. METHODS: Thirty YA (18-26 years; n=15 women/men) and 27 OA (65-89 years; n=13 women, n=15 men) participants who played pickleball …

Investigating Genetic Regulators Of Crystal Cell Development In Drosophila Melanogaster, Anisa Turaeva, Nyla Walbrook, Andrea Feria, Rebecca Spokony

Publications and Research

In Drosophila melanogaster, hematopoiesis produces three types of blood cells (hemocytes): plasmatocytes, lamellocytes, and crystal cells, all of which provide vital immunological activities. Crystal cells have an especially essential role in melanization, a wound reaction mediated by prophenoloxidase enzymes. This study investigates genetic regulators of crystal cell growth by RNAi-mediated knockdown of five potential genes: ACXA, ACXB, Gp210, CG4390, and Cyp4s3. We used the GAL4/UAS system to selectively silence each gene and quantify crystal cell counts in wandering third instar larvae after heat shock-induced melanization. Our findings indicate that knockdown of ACXA and ACXB resulted in higher crystal cell …

Meta-Kaolinite Metal Oxide Quaternary Composite For Layered Double Hydroxide Applied To A New Frontier In Adsorption Technology: Synthesis, Adsorption Performance And Kinetics Study, Samar A. Salim

Nanotechnology Research Centre

This study explores the synthesis and characterization of a quaternary composite based on meta-kaolinite and metal oxides (MgO, Al2O3, and Fe2O3) for the formation of layered double hydroxides (LDHs), aimed to the efficient removal of synthetic dyes from wastewater. The composite was synthesized using a co-precipitation method (Mg:Al:Fe molar ratio = 3:1:1) and thermally activated at 400 ◦C to enhance porosity and active site availability. Instrumental characterization through XRD, FTIR, SEM-EDX, and BET analyses confirmed the effective combination of metal oxides into the meta-kaolinite matrix, with BET results revealing a surface area of 540 m2/g (vs. 190 m2/g for raw …

Single-Cell Analysis Of Clonal And Transcriptional Dynamics During Direct Reprogramming, Brent Biddy

Arts & Sciences Graduate Student Theses and Dissertations

Direct lineage reprogramming converts one cell type into another, a process characterized by significant heterogeneity. Single-cell genomic techniques have been instrumental in dissecting this variability, yet they often fail to preserve lineage relationships. Here, I present CellTagging, a sequential, combinatorial indexing method that enables the reconstruction of clonal history and gene expression dynamics at single-cell resolution. This facilitates the construction of multi-level lineage trees, providing insights into cellular reprogramming trajectories. We applied CellTagging to investigate direct lineage reprogramming of mouse embryonic fibroblasts into induced endoderm progenitors. Our analysis revealed two distinct reprogramming trajectories: one leading to successful conversion and another …

Investigating The Roles Of Sox10 And Etv4 In Melanocyte And Melanoma Development, Catherine Marie Newsom-Stewart

Arts & Sciences Graduate Student Theses and Dissertations

The neural crest is a transient, multipotent cell population unique to vertebrates that gives rise to diverse lineages, including craniofacial cartilage, peripheral neurons, glia, and pigment-producing melanocytes. Proper specification and differentiation of neural crest derivatives are orchestrated by tightly regulated gene regulatory networks, and disruption of these developmental programs can lead to congenital disorders and malignancies. Melanocytes, derived from the neural crest, are best known for their role in skin pigmentation but also contribute to homeostasis and specialized functions in the eye, ear, and heart. These cells produce melanin to protect tissues from ultraviolet radiation and oxidative damage, and they …

Characterizing Piezo1 Mechanotransduction In Articular Chondrocytes, Jaquelin Marlen Garcia Castorena

Arts & Sciences Graduate Student Theses and Dissertations

Osteoarthritis (OA) is the most common degenerative joint disease, affecting more than 350 million people worldwide. Along with inflammation and pain, a hallmark of OA is the degradation of articular cartilage (AC), an avascular and aneural tissue that coats and facilitates the bending of diarthrodial joints. AC withstands millions of cyclic mechanical loads annually, and chondrocytes, the only resident cells in the tissue, sense these loads through mechanically gated ion channels, including Transient Receptor Potential Vanilloid 4 (TRPV4), PIEZO1 and PIEZO2. PIEZO1 is a highly expressed calcium ion channel in chondrocytes that can be activated through mechanical loading or chemically …

Functional Diversification Of Rice Ago1 Proteins, Rachel Elie Jouni

Arts & Sciences Graduate Student Theses and Dissertations

Global demand for food is outpacing gains from conventional plant breeding. Scientists have turned to molecular crop breeding techniques to increase crop output and mitigate global hunger; however, a common setback in this process is the pleiotropic effects of target genes. We need to develop strategies to specifically modulate desired traits without incurring undesired penalties. Natural evolution frequently balances such tradeoffs through extensive regulation, which we can leverage to produce more specific results. Reproductive development is an important target of breeding efforts due to its direct effect on yield. Rice, a major staple food crop for half the world’s population, …

Performative Biomechanics : Evolving Buildings Into Inhabitable Organisms, Josh Lopez

Bachelor of Architecture Theses - 5th Year

There has always been a connection between biology and architecture. Michael Pawlyn, in Biomimicry in Architecture, coined “biomechanical designs” to describe structural techniques derived from creatures. This study investigates chitin-based creatures. Crustaceans, insects, and microscopic organisms all have exoskeletons in nature. With a focus on crabs, other crustaceans and bugs, this study examines and evaluates the formal characteristics of chitin-based organisms. The architectural creations of OXMAN, NOX, which was founded by Lars Spuybroek; and Lebbeus Woods are among those that are analyzed and studied due to their inspiration from living things. They follow functional effectiveness in nature, which is why …

Language Mapping During Awake Brain Surgery In A Deaf Patient With A Brain Tumor: Illustrative Case, Ene Chibawanye I, Elizabeth Silva, Kyle Noll, Mariana Bradshaw, Katherine Connelly, Ho-Ling Liu, Ravi Tummala, David Ferson, Frederick F Lang, Vinodh A Kumar

Faculty, Staff and Student Publications

Background: Signed language integrates complex sensorimotor processes involving visual and motor networks. The contribution of language regions such as Broca's and Wernicke's areas during signing is not well established. Here, the authors report the case of a 45-year-old right-handed male with congenital deafness, who communicates using American Sign Language (ASL) and Signed English, presenting with focal seizures. Imaging showed a diffuse infiltrative glioma in the right cerebral hemisphere.

Observations: Remarkably, preoperative functional MRI language activations were bihemispheric and overlapped for both traditional language paradigms and sign paradigms, suggesting that the same cortical regions of the brain are used for language …

Mitochondrial Network Expansion And Loss During Oligodendrocyte Life And Death, Xhoela Bame

Dartmouth College Ph.D Dissertations

Oligodendrocytes are the myelinating cells of the central nervous system, known for modulating signal transmission, refining neural circuits, and providing metabolic support to axons. Oligodendrocytes are generated throughout life from oligodendrocyte precursor cells (OPCs) and are damaged or lost in demyelinating and neurodegenerative diseases and age-related pathologies. Thus, understanding the cellular checkpoints that occur during the generation and degeneration of oligodendrocytes is crucial for maintaining their population in health and recovering it in disease and aging.

Using high-resolution optical imaging, I have discovered a dynamic redistribution and subcellular partitioning of mitochondria during oligodendrogenesis. Mitochondria transiently expanded towards the differentiating OPC …

Examing The Role Of Complement Signaling In Viral Neuroinflammatory Responses, Marlene Kanmogne

Arts & Sciences Graduate Student Theses and Dissertations

The complement system is an ancient pathway that serves dual roles as a key regulator of neuroinflammation and a critical regulator of neural networks. Few studies have addressed how these two pathways may interact during infection of the central nervous system. While some components of complement are expressed in the healthy developing brain, complement component 3a receptor (C3aR) is a G protein coupled receptor that is expressed by astrocytes, microglia and infiltrating immune cells during inflammatory states. We previously found that C3aR is required for engulfment of synaptic material by activated microglia during neuroinvasive viral infection. Here, we used a …

Endemism Shapes Viral Ecology And Evolution In Globally Distributed Hydrothermal Vent Ecosystems, Marguerite V. Langwig, Faith Koester, Cody Martin, Zhichao Zhou, Samantha B. Joye, Anna-Louise Reysenbach, Karthik Anantharaman

Biology Faculty Publications and Presentations

Viruses are ubiquitous in deep-sea hydrothermal vents, where they influence microbial communities and biogeochemistry. Yet, viral ecology and evolution remain understudied in these environments. Here, we identify 49,962 viruses from 52 globally distributed hydrothermal vent samples (10 plume, 40 deposit, and 2 diffuse flow metagenomes), and reconstruct 5708 viral metagenome-assembled genomes, the majority of which were bacteriophages. Hydrothermal viruses were largely endemic, however, some viruses were shared between geographically separated vents, predominantly between the Lau Basin and Brothers Volcano in the Pacific Ocean. Geographically distant viruses shared proteins related to core functions such as structural proteins, and rarely, proteins of …

The Impact Of Insufficient Sleep On The Serial Reproduction Of Information, David L. Dickinson, Sean P. A. Drummond

ESI Publications

Story retelling is an important form of communication, cultural practice, and message transmission. Insufficient sleep is known to affect relevant cognitive skill areas necessary for story retelling or transmission fidelity. We conducted a preregistered randomized cross-over study on n = 155 young adults with exogenously assigned nightly sleep levels experienced in their at-home environments. A serial story reproduction task was administered online, and chains of up to three retells of a given story involved varied numbers of sleep restricted (SR) versus well-rested (WR) retellers. While story content decayed with each retell, group-level analysis showed that additional SR retellers in a …

Effect Of The Multi-Elements On The Aerodynamic Performance Of Airfoil, Shereen Sibie, Tayeb Brahimi

Effat Undergraduate Research Journal

The design of an airfoil in the wind turbine and optimizing the blades is fundamental in a wind turbine aerodynamic performance. In this paper, the effect of the multiple multi-elements on the aerodynamic performance of airfoil is investigated. These multi-element configurations are expected to offer better performance of the wind turbine by maximizing the lift and drag coefficients. Based on the case studies analysis, the multi-elements have shown that the modified design results in high values of the power coefficient at low-speed ratios. This effect is attributed to the cancelation of the negative torque on the turbine rotor observed at …

Prognostic Value Of Serum And Bronchoalveolar Lavage Fluid Galactomannan Levels In Invasive Aspergillosis: An 8-Year Experience At A Tertiary Cancer Center, Saliba Wehbe, Anne-Marie Chaftari, Ray Hachem, Hiba Dagher, Andrea Haddad, Ann Philip, Ying Jiang, Ramia Zakhour, Peter Bakht, Jishna Shrestha, Peter Lamie, Robin Sherchan, Jennifer Makhoul, Patrick Chaftari, Issam I Raad

Faculty, Staff and Student Publications

Background: Invasive aspergillosis (IA) is a life-threatening fungal infection that primarily affects immunocompromised individuals and has high morbidity and mortality rates, necessitating timely diagnosis and treatment. This study aimed to evaluate the prognostic utility of serum and bronchoalveolar lavage (BAL) fluid galactomannan levels, as well as galactomannan kinetics, in patients with IA.

Methods: We retrospectively reviewed the medical records of patients who were diagnosed with proven or probable IA from March 2016 to April 2024 at a tertiary cancer center. The collected data included patient characteristics, baseline and peak galactomannan levels in serum and BAL fluid, galactomannan trends, and …

Evaluating Forage Quality As Animal Production Per Unit Of Forage And Land Area, D A. Rohweder, L Miller

IGC Proceedings (1977-2023)

The need to more adequately express feed value in forages and, that will communicate this value among agricultural scien­tists, agri-business clientele and producers has long been recognized world wide. Modern dairy, beef and sheep producers are becoming increasingly concerned about forage quality ; its translation into animal products per unit land area ; and its effect along with forage yield on enterprise profits. The Hay Marketing Task Force-Forage Analysis Subcom­mittee organized by the American Forage and Grassland Council in 1975 proposed hay standards based on in vivo digestible dry matter or energy availability (DDM) and dry matter intake (DMI) predicated …

Volume 11 Full Text, Bjur Staff

Butler Journal of Undergraduate Research

No abstract provided.

Unpaired Virtual Histological Staining Of Tissue From Autofluorescence Using Regularized Cycle-Consistent Adversarial Networks, Zhesi Wen

Theses and Dissertations

We present a regularized CycleGAN with a Dense Residual U-Net to virtually stain autofluorescence images of tissue into H&E-like images. Our method outperforms standard architectures, reduces artifacts, and achieves superior FID scores, enabling efficient, label-free, and accurate digital pathology for unpaired datasets using multi-channel fluorescence inputs.

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

All HCAS Student Capstones, Theses, and Dissertations

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

Know Thyself: A History Of Ancient Neuroscience, Alex Delano

Departmental Honors & Graduate Capstone Projects

Neuroscience is often described as one of the youngest bodies of science, but documented study of the brain begins as early as the Neolithic period. The ancient Mediterranean was a hub for science, mathematics, philosophy, and literature, all disciplines necessary for the study of the brain. Evidence of neurosurgical procedures like trepanation and craniotomy began in the Neolithic period and were practiced and improved upon throughout the ancient Mediterranean. The first detailed studies on brain anatomy were carried out in the 3^rd century BCE in Greece which created a necessary structure for future scientists to build on. While many …

The Role Of Elongin B In Drosophila Melanogaster Muscle Development, Madelyne Dayan

Student Theses and Dissertations

Muscle atrophy is a result of a number of muscle diseases, as well as aging, disuse, and infections. Muscles weakened in these ways exhibit a characteristic decrease in size, strength, and mobility. The similarities between muscle in humans and Drosophila allow for direct comparisons to be made in vertebrates from studying muscle in Drosophila. Differential gene expression has been shown to play an important role in embryonic muscle development in Drosophila melanogaster. A previous study identified Elongin B (EloB) to be involved in somatic muscle morphogenesis in Drosophila, with mutant embryos displaying severe muscle defects, including thin, mis-attached, and missing …

Role Of The Small Intestinal Microbiota In The Pathogenesis Of Environmental Enteric Dysfunction In Undernourished Children And Mothers, Clara Kao

Arts & Sciences Graduate Student Theses and Dissertations

Undernutrition in women and its propagation in their children remains a major global health challenge. Worldwide, one in five children under five years of age manifests undernutrition as impaired linear growth, or stunting. Stunting, defined as having a length-for-age z-score (LAZ) <-2, is associated with poor developmental outcomes, including impaired neurodevelopment and immune responses. Furthermore, stunting and its long-term sequelae persist across generations, contributing to an intergenerational cycle of undernutrition. Existing nutritional interventions fail to substantially improve stunting, highlighting the need to (i) better understand other factors contributing to stunting and (ii) focus clinical efforts towards treating maternal undernutrition. Environmental enteric dysfunction (EED) is a subclinical inflammatory enteropathy of the small intestine proposed to contribute to stunting. EED is diagnosed histologically by blunted intestinal villi, epithelial barrier disruption and an immunoinflammatory infiltrate in the lamina propria. However, the pathophysiology of EED remains poorly defined. Furthermore, the small intestinal microbiota remains understudied due to difficulties in sampling. Evidence that the small intestinal microbiota contributes to EED pathogenesis comes in part from our collaborative work with colleagues at icddr,b (the International Centre for Diarrhoeal Disease Research, Bangladesh) who oversaw the Bangladesh EED (BEED) study. In this study children, aged 12-18 months residing in an urban slum in the Mirpur district of Dhaka who failed a nutritional intervention for their stunting, underwent esophago-gastroduodenoscopy (EGD) to obtain duodenal mucosal biopsies, aspirates of duodenal luminal fluid and plasma samples. A set of 14 bacteria taxa (defined by 16S rRNA amplicon sequencing) were identified in the duodenal microbiota of >80% of children with EED. Moreover, the absolute abundances of these ‘core taxa’ were positively correlated with duodenal mucosal and systemic inflammation in study participants and negatively correlated with linear growth. Our lab showed that introduction of a consortium of bacteria cultured from these duodenal aspirates, including these core taxa, produced small intestinal inflammation in young adult gnotobiotic, providing …