Digital Commons Network^™

Elucidating The Roles Of Eukaryotic Initiation Factors Involved In Dap5 Mediated Translation, Jacob Nk Quartey

Dissertations, Theses, and Capstone Projects

Translation initiation in eukaryotes is a highly regulated process essential for accurate protein synthesis. It is a dynamic process that involves a complex interplay between messenger RNAs (mRNAs), ribosomal subunits, and a host of initiation factors, ensuring precise start codon selection and the subsequent assembly of the translation machinery. This process has well been known to be mediated by the eukaryotic Initiation Factor (eIF4F), which consists of the cap binding protein eIF4E, the scaffolding protein eIF4GI, and the helicase factor eIF4A.The recognition and binding of eIF4E to the m⁷G cap structure of the mRNA is essential for the …

The Sub-Syllabic Symphonies Of Self-Learning: How Do Zebra Finches Sing Them?, Abiesha Abiola Budiman

Dissertations, Theses, and Capstone Projects

Learning is a lifelong journey, where the mind and muscle dance to a tune of memory and motion. It begins at infancy and continues throughout life, encompassing everything from singing to achieving peak performance in sports. Complex motor skills involve multiple components and require coordination of several muscles. Humans and animals are extremely adept at learning complex motor skills on their own. However, we do not completely understand how self-directed learning works. One group of animals used to observe self-directed learning are songbirds. Zebra finches, Taeniopygia guttata, are one of the most studied songbird species due to their well-defined …

Environmental Enrichment Reduces Cue-Induced Reinstatement Of Heroin-Seeking Following Prolonged Use And Reverses Region-Specific Heroin-Induced Neuroadaptations, Apoorva Vashisht

Dissertations, Theses, and Capstone Projects

Background: Relapse remains the greatest barrier to long-term recovery and the consequential rising overdose-related mortality in heroin use disorder (HUD). Currently available behavioral and pharmacological interventions fail to extend their benefits beyond the duration of the treatment. Additionally, opioid agonist-based medications accompany harmful neurobiological risks and propensity to promote further drug-seeking post-treatment. We have shown that environmental enrichment (EE), as a therapeutic strategy applied after drug intravenous-self administration (IVSA), can effectively facilitate abstinence and reduce reinstatement of drug-seeking in animal models of drug abuse. Moreover, dopamine receptors like D1 and D3, and mu-opioid (MO) receptors are well known for their …

When Avatars Go To School: The Effect Of Virtual Reality On Learning And Error Correction, Lauren Barack

Dissertations, Theses, and Capstone Projects

The pandemic in 2020 led to an increasing dependency on technology particularly in learning environments. National educational assessments in the proceeding years have indicated steep, measurable learning loss. While a fully virtual learning environment is not the norm today, we chose to investigate how virtual reality (VR) environments influence learning in college students.

Our primary research goal was to look at how students learn and remember information gathered in virtual spaces. In particular, we examined whether sensory inputs in the VR environment, including spatial audio and haptic feedback, such as vibrations felt in a handheld controller, would help to better …

Disturbance And Diversity: Lichens In Changing Landscapes, Laura Boggess

Dissertations, Theses, and Capstone Projects

Disturbance is a fundamental ecological force that shapes biodiversity, community composition, and ecosystem function. Human-driven disturbances—such as habitat fragmentation, deforestation, and air pollution—are increasing worldwide, altering ecosystems at unprecedented rates. While ecological research has illuminated many effects of disturbance, significant knowledge gaps remain for underappreciated but ecologically vital organisms, such as lichens. Lichens are obligate symbioses between at least one fungus and one alga or cyanobacterium. As such, they are sensitive bioindicators of environmental change, offering unique insights into ecosystem health due to their responses to stressors such as poor air quality, habitat fragmentation, and deforestation. Yet, their responses to …

Biophysical Analysis Of S100a12 And The Nucleosome Core Particle, Christopher Diforte Jr.

Dissertations, Theses, and Capstone Projects

Calcium signaling and chromatin remodeling are fundamental regulatory processes that control protein activity and gene expression, respectively. This thesis investigates the molecular mechanisms by which local ligand binding and structural perturbations propagate allosteric effects across larger protein systems, using two distinct yet mechanistically analogous models: the calcium binding protein S100A12 and the nucleosome core particle. These studies are unified by a shared emphasis on how physical forces govern biological function.

In the first part, we explore calcium mediated allostery in S100A12, focusing on the distinct roles of its two EF-hand calcium binding loops (EF-I and EF-II). Through a combination of …

Memory Interference In The Lateral Entorhinal Cortex, Omar Ghazy

Dissertations, Theses, and Capstone Projects

Memory interference occurs when previously formed memories disrupt the acquisition or retrieval of new information. A prominent example of proactive interference is latent inhibition (LI), defined as a reduced ability to form or express Pavlovian associations with a stimulus following non-reinforced exposure. The interference-based model suggests that LI arises because the memory that the pre-exposed stimulus is inconsequential interferes with the memory that it predicts a reinforcer.

Because interference increases with age, identifying its neural basis may help prevent or slow cognitive decline. Prior studies using the LI paradigm implicate the entorhinal cortex (EC) in retrieving the memory that a …

Individual, Social, And Environmental Factors Associated With Patterns Of Parasitic Infection In Capuchin Monkeys (Cebus Imitator), Megan C. Henriquez

Dissertations, Theses, and Capstone Projects

Parasites, and the infectious diseases they carry, are thought to have significantly impacted our evolutionary trajectory for millennia. Exploring how parasites are acquired and transmitted by their hosts in wild, natural populations is integral to understanding how similar processes may have shaped host-parasite co-evolutionary relationships over time. However, parasitological studies in humans and in non-human primates have produced inconsistent results, highlighting the dynamic, nuanced, and unique relationships individual parasites have with their hosts. These relationships are largely regulated by variation in factors at host, social, and environmental levels. Characteristics unique to the host (e.g., age and sex), factors pertaining to …

Structural Studies Towards The Mechanism Of Scanning And Initiator Trna Recruitment During Eukaryotic Translation Initiation, Da Cui

Dissertations, Theses, and Capstone Projects

The central dogma, proposed by Francis Crick in 1958, marks the direction of the flow of genetic information: from DNA to DNA (DNA replication), DNA to RNA (transcription), and RNA to protein (translation). Each of these is tightly regulated and important for cells and organisms to function correctly, grow, and reproduce.

In the eukaryotic system, the initiation stage of translation is the first, the rate-limiting, and the most regulated stage. It involves direct regulation of multiple eukaryotic initiation factors (eIFs), scanning factors such as DHX29, and other factors such as Poly-A binding protein (PABP). It starts with the small subunit …

Re-Evaluating The Host Specificity Of Thirteen Eimeria Species That Infect Galliform Birds: Cross-Infection Experiments In Chukar Partridges (Alectoris Chukar), Northern Bobwhites (Colinus Virginianus) And Turkeys (Meleagris Gallopavo), Jessica L. Rotolo, A. Leveille, Rachel K. Imai, Elizabeth G. Zeldenrust, Billy M. Hargis, Elijah G. Kiarie, John R. Barta

Poultry Science Faculty Publications and Presentations

The commercial poultry industry has expanded and profited from intensively rearing birds, but it is not without consequences. Coccidiosis is an intestinal disease caused by Eimeria species that is well recognized by poultry producers because of the resulting health implications that often contribute to reduced welfare of birds, meat production and profitability. Strict host specificity of these parasites (infection of one host species only) is often assumed; however, examples of Eimeria spp. capable of infecting multiple galliform hosts have been described. Despite the relevance of coccidiosis in commercial poultry production, the number and extent of such crossinfections remain poorly understood, …

Genetic Factors Of Campylobacter Jejuni Required For Its Interactions With Free-Living Amoeba, Deepti Pranay Samarth, Asim Z. Abbasi, Young Min Kwon

Poultry Science Faculty Publications and Presentations

Acanthamoeba, a free-living amoeba ubiquitous in environmental water, has been considered as the environmental reservoir of certain bacterial pathogens, including Campylobacter jejuni, an intracellular human pathogen causing self-limiting gastroenteritis. Acanthamoeba-C. jejuni interaction mechanisms may help clarify how the otherwise fastidious bacterium C. jejuni survives in environmental waters. In this study, we constructed single deletion mutants of C. jejuni strain 81-176 for the 10 selected genes (motAB, ciaB, kpsE, virB11, cheY, flaAB, cstII, docB, sodB, and cadF) previously shown to be important for the interaction (invasion and intracellular survival) of C. jejuni with mammalian hosts. We used a modified gentamicin protection …

The Influence Of Geographic Ranges, Climatic Niches And Temperature Fluctuations On Population Variability, Cleber Ten Canten, Lauren Holian, Tad Dallas

Faculty Publications

The existence of patterns in population dynamics across species geographic ranges and climatic niches is a pervasive idea in ecology. Population variability (i.e. temporal variability in population density) should hypothetically increase near range edges or niche limits because of less suitable environments in these areas, but the occurrence of such patterns remains largely unexplored. Further, fluctuations in temperature could pose demographic constraints on populations and also influence their variability. We used Breeding Bird Survey data to show that the population variability of 97 resident North American birds consistently increases towards their niche limits and in areas with more variable temperatures, …

Identification Of Loci And Candidate Genes Associated With Arginine Content In Soybean, Jiahao Ma, Qing Yang, Cuihong Cu, Zhi Liu, Xiaolei Shi, Xintong Wu, Rongqing Xu, Pengshuo Shen, Yuechen Zhang, Ainong Shi, Long Yan

Horticulture Faculty Publications and Presentations

Soybean (Glycine max) seeds are rich in amino acids, offering key nutritional and physiological benefits. In this study, 290 soybean accessions from the USDA Germplasm Collection based in Urbana, IL Information Network (GRIN) were analyzed. Four Genome-Wide Association Study (GWAS) models-Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK), Mixed Linear Model (MLM), Fixed and Random Model Circulating Probability Unification (FarmCPU), and Multi-Locus Mixed Model (MLMM)-identified two significant Single Nucleotide Polymorphisms (SNPs) associated with arginine content: Gm06_19014194_ss715593808 (LOD = 9.91, 3.91% variation) at 19,014,194 bp on chromosome 6 and Gm11_2054710_ss715609614 (LOD = 9.05, 19% variation) at 2,054,710 bp on chromosome 11. Two …

Neovascular Pruning By Ido1 Inhibitors Can Potentiate Immunogenic Cytotoxicity Of Ischemia-Targeted Agents To Synergistically Enhance Anti-Pd-1 Responsiveness, Shih-Chun Shen, Souvik Dey, James B. Duhadaway, Erika Sutanto-Ward, Maurice T. Hampton, Serguei V. Kozlov, George C. Prendergast, Alexander J. Muller

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

BACKGROUND: Strategies for deploying indoleamine 2,3-dioxygenase 1 (IDO1)-targeted therapies for use against cancer have focused on IDO1's role in promoting peripheral immune tolerance that shields tumors from effector T cells. However, preclinical investigation of both primary and metastatic tumor development in the lungs has uncovered a previously unappreciated role for IDO1 in directing a counterregulatory response to interferon (IFN)-γ that realigns the local inflammatory environment to promote tumor neovascularization. Understanding how to therapeutically leverage the ability of IDO1 inhibitors to subvert inflammatory neovascularization within the tumor microenvironment has potential ramifications for future clinical development of these compounds.

METHODS: Pulmonary metastases …

The Tweak/Fn14 Signaling Mediates Skeletal Muscle Wasting During Cancer Cachexia, Meiricris Tomaz Da Silva, Anirban Roy, Anh Tuan Vuong, Aniket S Joshi, Cristeena Josphien, Meghana V Trivedi, Sajedah M Hindi, Vihang A Narkar, Ashok Kumar

Faculty, Staff and Student Publications

Cancer cachexia is a multifactorial syndrome characterized by progressive skeletal muscle wasting. The TWEAK-Fn14 system regulates muscle mass in diverse conditions. However, its role in the regulation of muscle mass during cancer cachexia remains less understood. Here, we demonstrate that the levels of Fn14 are induced in skeletal muscle of multiple mouse models of cancer cachexia. Muscle-specific deletion of Fn14 reduces myofiber atrophy in mouse models of pancreatic and lung cancer cachexia. Silencing of Fn14 in KPC pancreatic cancer cells prior to their implantation in mice attenuates tumor growth without affecting myofiber size. Muscle-specific deletion of Fn14 reduces the gene …

Neurenteric Cysts: A Neurosurgical Case Series And Treatment Perspectives, Defran Ercan, Walter Stummer, Maryam Khaleghi Ghadiri

BioMedicine

Neurenteric cysts (NC) are rare lesions of endodermal origin lined by mucin-secreting cuboidal or columnar epithelium of an intestinal or respiratory type. They occur more frequently spinally than cranially. From the radiological view, NC may be confused with other lesions of the central nervous system, like arachnoid or epidermoid cysts. However, due to advances in neuroimaging, there is an increasing trend in preoperative diagnosis of NC. We are reporting three cases of NC, each exhibiting markedly distinct symptoms and postoperative courses. The first patient, a 45year-old woman, had NC in the fourth ventricle. Although she underwent surgery, the lesion recurred …

Integrating Radiogenomics And Machine Learning In Musculoskeletal Oncology Care, Rahul Kumar, Kyle Sporn, Akshay Khanna, Phani Paladugu, Chirag Gowda, Alex Ngo, Ram Jagadeesan, Nasif Zaman, Alireza Tavakkoli

Department of Medicine Faculty Papers

Musculoskeletal tumors present a diagnostic challenge due to their rarity, histological diversity, and overlapping imaging features. Accurate characterization is essential for effective treatment planning and prognosis, yet current diagnostic workflows rely heavily on invasive biopsy and subjective radiologic interpretation. This review explores the evolving role of radiogenomics and machine learning in improving diagnostic accuracy for bone and soft tissue tumors. We examine integrating quantitative imaging features from MRI, CT, and PET with genomic and transcriptomic data to enable non-invasive tumor profiling. AI-powered platforms employing convolutional neural networks (CNNs) and radiomic texture analysis show promising results in tumor grading, subtype differentiation …

The Effects Of Morphine, Thc, And Lsd On Synaptic Plasticity Of The Ventral Tegmental Area, Michael Von Gunten

Theses and Dissertations

The brain is an intricate network of neurons that communicate via synapses. Synaptic plasticity, which is the ability to strengthen or weaken synaptic connections, plays a key role in learning, memory, and reward learning. Disruptions to synaptic plasticity play a central role in addiction, particularly in brain circuits involved in reward and motivation. The mesolimbic reward system, which includes the ventral tegmental area (VTA) and its dopaminergic projections, is a primary target of drugs of abuse, including opioids and cannabinoids. However, the physiological consequences of combined exposure to opioids and cannabinoids and the potential for psychedelics to reverse drug-induced neuroadaptations …

Integrating Cover Crops And Targeted Herbicide Applications In Cotton Production, Tristen H. Avent, Jason K. Norsworthy, Gerson L. Drescher

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

Cover crops are part of integrated weed control management to help mitigate herbicide resistance evolution. Targeted sprays from the John Deere See & Spray are currently not recommended in cover crops. Experiments were conducted yearly from 2022 to 2024 in Keiser, AR, to evaluate targeted applications (TAs) with cover crops in cotton (Gossypium hirsutum L.). Treatments assessed the main effect of winter cover crop (fallow, cereal rye [Secale cereale L.], or hairy vetch [Vicia villosa Roth]), herbicide application methods (nontreated, broadcast [BC], TA + BC residuals [TA + BCRs], or TA only), and the interaction on cotton tolerance, weed control, …

Protein Word Detection Using Text Segmentation Techniques, Ashish V. Tendulkar, Sutanu Chakraborti, Ganesh Devi

Journal of Global Awareness

Literature in Molecular Biology is abundant with linguistic metaphors. There has been works in the past that attempt to draw parallels between linguistics and biology, driven by the fundamental premise that proteins have a language of their own. Since word detection is crucial to the decipherment of any unknown language, we attempt to establish a problem mapping from natural language text to protein sequences at the level of words. Towards this end, we explore the use of an unsupervised text segmentation algorithm for the task of extracting "biological words” from protein sequences. We demonstrate the effectiveness of using domain knowledge …

The Aquatic Symbiosis Genomics Project: Probing The Evolution Of Symbiosis Across The Tree Of Life, Matthew Berriman, Victoria Mckenna, Roxanne Beinart, John M. Archibald, Ute Hentschel, Michael N. Dawson, Jose V. Lopez, Patrick J. Keeling, Jillian M. Petersen, Anne W. Thompson, Multiple Addiional Authors

Biology Faculty Publications and Presentations

We present the Aquatic Symbiosis Genomics Project, a global collaboration to generate high quality genome sequences for a wide range of eukaryotes and their microbial symbionts. Launched under the Symbiosis in Aquatic Systems Initiative of the Gordon and Betty Moore Foundation, the ASG Project brings together researchers from across the globe who hope to use these reference genomes to augment and extend their analyses of the dynamics, mechanisms and environmental importance of symbioses. Applying large-scale, high-throughput sequencing and assembly technologies, the ASG collaboration will assemble and annotate the genomes of 500 symbiotic organisms – both the “hosts” and the microbial …

Cytogenetic Annotation Automation In Myelodysplastic Syndrome Research Databases, Samuel Urrutia, Kelly S Chien, Ziyi Li, Alexandre Bazinet, Guilin Tang, Guillermo Garcia-Manero

Faculty, Staff and Student Publications

No abstract provided.

Tickborne Colpodella Species Infections: Time For A New Integrated Approach To Understand Transmission And Pathogenicity, T. Y. Sam-Yellowe, Trinity Nims, Sona Qaderi, Mary M. Asraf

Biological, Geological, and Environmental Faculty Publications

Colpodella species are free-living predatory protists that prey on algae, ciliates and bodonids using myzocytosis. Colpodella species have been reported in human and animal infections. Polymerase chain reaction (PCR) using primers targeting 18S rRNA genes of Cryptosporidium and piroplasms have identified Colpodella species in arthropods, host blood and feces, demonstrating the phylogenetic closeness of Colpodella species to the apicomplexa. However, in human, animal and arthropod hosts, the life cycle stages of Colpodella are unknown. In this literature review, we provide an overview of the widespread occurrence of Colpodella species in ticks, and pathogenicity in humans and animals. We discuss methods …

The Impact Of Narratives And Active Video Games Among Black And Hispanic Children With Overweight And Obesity: A Randomized Controlled Trial, Amy S Lu, Tom Baranowski, Tiago V Barreira, Amy Fleischman, Melanie C Green, Shirley Y Huang, I-Min Lee, Lynne L Levitsky, Farzad Noubary, Debbe Thompson

Children’s Nutrition Research Center Staff Publications

Background: Overweight and obesity disproportionately affect Black and Hispanic children who also play more video games. Narratives, coupled with home-based active video games (AVGs), may enhance PA and mitigate these disparities. This study tested the effect of narrative-enhanced home-based AVGs among predominantly Black and Hispanic children with overweight and obesity.

Methods: This 6-month three-group RCT recruited 135 children aged 7-14 from pediatric clinics in Boston, MA (January 2020 - May 2022) during the COVID-19 pandemic. Participants were randomized into: [Narrative + AVG], receiving an Xbox/Kinect with six AVGs interspersed with a narrative animation Ataraxia (72 episodes over six months), which …

Correction: Complement Activity And Autophagy Are Dysregulated In The Lungs Of Patients With Nonresolvable Covid-19 Requiring Lung Transplantation, Pooja Shivshankar, Stacey L Mueller-Ortiz, Aleksey Y Domozhirov, Weizhen Bi, Scott D Collum, Marie-Francoise Doursout, Manish Patel, Isabella N Lefebvre, Bindu Akkanti, Simon Yau, Howard J Huang, Rahat Hussain, Harry Karmouty-Quintana

Faculty, Staff and Student Publications

No abstract provided.

Thsd1 Is A Multifaceted Regulator In Health And Disease, Mengjun Dai, Kuizhi Qu, Sophie Liu, Zhen Xu, Yan-Ning Rui

Faculty, Staff and Student Publications

Thrombospondin Type 1 Domain-Containing Protein 1 (THSD1) is a transmembrane protein increasingly recognized for its critical roles in vascular biology and disease pathogenesis. Initially identified as a marker of hematopoietic stem and endothelial cells during embryogenesis, THSD1 has since been implicated in a wide spectrum of physiological and pathological processes. This paper consolidates current knowledge on THSD1, with a focus on its roles in vascular integrity, perinatal disorders, and tumorigenesis. In vascular systems, THSD1 promotes focal adhesion assembly and suppresses autophagy-mediated adhesion turnover, thereby stabilizing endothelial attachment and maintaining barrier function. Genetic and functional studies support its protective role against …

“Non-Markovian” And “Directional” Errors Inhibit Scientific Self-Correction And Can Lead Fields Of Study Astray: An Illustration Using Gardening And Obesity-Related Outcomes, Jon Agley, Sarah E Deemer, David B Allison

Children’s Nutrition Research Center Staff Publications

Herein we coin the terms non-Markovian error and biased Markovian error to describe categories of scientific errors for which general progress within a field of study may be unlikely to result in scientific self-correction. We provide examples of such errors and show their impact on studies about gardening and obesity.

Characterization Of Sars-Cov-2 Replication And Transcription Complexes Via Structural And Evolutionary Approaches, Amelie Ghirardo, Ben Shabatian, Avishai Aghelian, Kyle Tau, Eleonora Gianti

Undergraduate Research

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused around 700M cases and over 7M COVID-19-related deaths recorded worldwide (World Health Organization, March 2025). Aiming to effectively combat this and other disease-causing Coronaviruses (CoV), unprecedented research efforts led to the development of new vaccines and antiviral therapies. Due to emergence of variants of concern (VOCs) with increased transmissibility, immune evasion from vaccination, and potential to resist the available treatments, SARS-CoV-2 continues to represent a major threat to global health. Hence, there is a pressing need to discover new antivirals with broad-spectrum efficacy against multiple SARS-CoV-2 variants and related CoVs. This project …

Intergenerational Toxic Stress In Preschool Children, Cynthia R. Rovnaghi

Doctoral Dissertations and Projects

Worldwide there is an outcry for understanding, integrating, preventing, coordinating, and collaboratively treating the neuropsychosocial components of intergenerational transmission of trauma-induced toxic stress (ITTS). The purpose of this quasi-experimental, cross-sectional, secondary analysis of the Hair Biomarkers Study Phase I (HBS-I) was to obtain empirical evidence supporting the introduction of the Theory of Neurogenesis Abruption (ToNA) and to standardize the use of hair biomarkers and child developmental scales for early detection of central nervous system (CNS) dysregulation. Birth and developmental outcomes of children born to parents with a diagnosed serious mental health condition (DSMHC) and/or substance (ab)use (SA/SU) disorder (children, n …

Effectiveness Of Exercise-Based Rehabilitation In Chronic Fatigue Syndrome: A Systematic Review And Meta-Analysis, Antonio De Vera Martín, Alberto Díaz Salazar, Isidro Miguel Martín Pérez, Sebastián Eustaquio Martín Pérez

International Journal of Exercise Science

International Journal of Exercise Science 18(5): 495-530, 2025. Chronic Fatigue Syndrome is a complex and debilitating disorder characterized by persistent fatigue, musculoskeletal pain, sleep disturbances, and cognitive impairments. The global prevalence is estimated between 0.2% and 0.4%, affecting over 17 million individuals worldwide, with an estimated burden exceeding 40,000 cases in Spain. Despite the exploration of exercise-based rehabilitation as a therapeutic strategy, its clinical efficacy remains a subject of ongoing debate. This study aims to evaluate the effectiveness of exercise-based rehabilitation relative to conventional treatments in improving functional capacity and alleviating fatigue among adults with CFS A systematic review and …