Digital Commons Network^™

Plant-Microbe Interactions Across Scales: Diversity, Disease, And Stress In Herbaceous Plant Communities, Philippa Tanford

Arts & Sciences Graduate Student Theses and Dissertations

Plants interact consequentially with microbes spanning mutualism to pathogenicity, with broader effects on large-scale plant community structure. These plant communties, in turn, shape below and aboveground microbial communities through a variety of mechanisms. However, plant diversity-microbial diversity relationships remain broadly inconsistent across environments and among different plant and microbial assemblages. In my dissertation, I work to bridge some of these gaps in plant-microbial ecology in three experimental chapters assessing relationships between plant diversity and microbial diversity, including the influence of belowground-aboveground microbiome interactions, the influence of drought stress, and incorporating different spatial and experimental scales. First, I explore the microbial …

Early Detection Of Oak Wilt Using Unmanned Aerial Vehicles (Uav) & Computer Vision, Muttaki I. Bismoy

Masters Theses

Forests are critical ecosystems, delivering services such as biodiversity conservation, climate regulation, timber production, and recreation. However, they face increasing threats from pathogens like Bretziella fagacearum, which causes Oak Wilt, a lethal disease that disrupts water transport in oak trees, leading to canopy dieback and eventual death. Traditional detection methods rely on manual ground surveys, which are labor-intensive, time-consuming, and prone to error, particularly in early disease stages.

This research presents an automated, scalable, high-precision Oak Wilt detection system using Unmanned Aerial Vehicles (UAVs) combined with deep learning-based computer vision. Expanding on earlier work with a lightweight CNN achieving an …

Collaborative Research: Bocp-Implementation: Us-China: Multi-Scale, Multi- Proxy, Integrative Investigation Of Functional Biodiversity On A Changing Proterozoic Planet, Carol Dehler

Funded Research Records

No abstract provided.

Enhanced Meropenem Activity And Stability Following Load In Polyvinyl Alcohol Nanofiber Scaffolds With Sitagliptin As Quorum Sensing Inhibitor On Pseudomonas Aeruginosa, Samar A. Salim, Abdelrhman Mohsen, Mohamed Emara, Taghrid Elmahdy

Nanotechnology Research Centre

Background The increasing resistance of bacteria to conventional antibiotics poses a significant health challenge. Innovative strategies, such as combining antibiotics with agents like quorum sensing inhibitors (QSIs), have been developed to combat this issue. QSIs enhance antibiotic efficacy without inhibiting bacterial growth, minimizing the risk of resistance. Aims Evaluate the combined effect of Sitagliptin (STG) as a QSI with Meropenem (MER), fabricate drug-loaded Polyvinyl Alcohol (PVA) nanofibers, and investigate their antimicrobial activity against standard Pseudomonas aeruginosa (PAO1) and carbapenem-resistant P. aeruginosa (CRPA). Methods The combinatorial effect was assessed using a checkerboard assay. PVA/STG, PVA/MER, and PVA/STG/ MER nanofibers were fabricated …

Lipid-Laden Microglia: Characterization And Roles In Diseases, Jiani Xing, Takese Mckenzie, Jian Hu

Faculty, Staff and Student Publications

Microglia are resident phagocytes of the central nervous system that play an essential role in brain development and homeostasis. When the intracellular lipid content exceeds the metabolic capacity of microglia, lipid droplets accumulate, giving rise to a distinct population termed lipid-laden microglia (LLMs). LLMs have been implicated in various neuroinflammatory and neurodegenerative diseases, functioning as both regulators/indicators of inflammation and potential therapeutic targets. This review summarizes the current research on LLMs, focusing on disease-specific regulators and functions, protective roles, interactions with neighboring cells, and advances in diagnostic and analytical tools. We also discuss the blurred distinction between LLMs and macrophages, …

Trpc4 Regulates Limbic Behavior And Neuronal Development By Stabilizing Dendrite Branches Through Actomyosin-Driven Integrin Activation, Jaepyo Jeon, Travis I Moore, Insuk So, Marc Freichel, Veit Flockerzi, Lutz Birnbaumer, Michael X Zhu

Faculty, Staff and Student Publications

Transient Receptor Potential Canonical 4 (TRPC4) channels have been implicated in multiple neurological functions, including anxiety and sociability. TRPC4 variants were also found in patients with autism. However, the contributions of TRPC4 to neurodevelopment remain undefined. Here, we show that neurobehavioral deficits appear early in young TRPC4 knockout (Trpc4^−/−) mice immediately after weaning, manifesting as alterations in multiple, limbic-related behaviors, such as nesting, marble burying, burrowing, self-grooming, and social interactions. Hippocampal neurons of Trpc4−/− mice exhibit reduced dendritic arborization both in vivo and in vitro. Mechanistically, we found that TRPC4 expression in dendrites surged at the …

Therapeutic Targeting Of Syndecan-1 Axis Overcomes Acquired Resistance To Kras-Targeted Therapy In Gastrointestinal Cancers, Madelaine S Theardy, Mitsunobu Takeda, Alexey Sorokin, Shuaitong Chen, Zecheng Yang, Xiaofei Wang, Preeti Kanikarla, Oluwadara Coker, Phuoc Nguyen, Yongkun Wei, Jun Yao, Liang Yan, Yanqing Jin, Yiming Cai, Masakatsu Paku, Ziheng Chen, Kara Z Li, Francesca Citron, Hideo Tomihara, Sisi Gao, Angela K Deem, Jun Zhao, Huamin Wang, Samir Hanash, Ronald A Depinho, Anirban Maitra, Giulio F Draetta, Haoqiang Ying, Scott Kopetz, Wantong Yao

Faculty, Staff and Student Publications

The therapeutic benefit of recently developed mutant KRAS (KRAS∗) inhibitors remains limited by the rapid onset of resistance. Here, we aim to delineate mechanisms underlying acquired resistance and identify actionable targets for overcoming this clinical challenge. Previously, we identified syndecan-1 (SDC1) as a key effector for pancreatic cancer progression whose surface expression is driven by KRAS∗. By leveraging both pancreatic and colorectal cancer models, we show that surface SDC1 expression initially diminishes upon KRAS∗ inhibition but recovers in tumor cells that bypass KRAS∗ dependency. Mechanistically, we reveal that YAP1 activation drives the recovery of SDC1 surface localization to enhance macropinocytosis-mediated …

Causes Of Symptoms And Symptom Persistence In Long Covid And Myalgic Encephalomyelitis/Chronic Fatigue Syndrome, Anthony L Komaroff, Robert Dantzer

Faculty, Staff and Student Publications

Debilitating symptoms for many years can follow acute COVID-19 ("long COVID"), myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), and various post-acute infection syndromes (PAISs). Together, long COVID and ME/CFS affect 60-400 million individuals, globally. Many similar underlying biological abnormalities have been identified in both conditions including autoantibodies against neural targets, endothelial dysfunction, acquired mitochondrial dysfunction, and a pro-inflammatory gut microbiome. Each of these abnormalities may directly cause some of the symptoms. In addition, the symptoms also may be caused by ancient, evolutionarily conserved symptomatic and metabolic responses to vital threats-sickness behavior and torpor-responses mediated by specific, recently discovered neural circuits. These neural …

Optimizing Motion Management And Baseline Shifts In Magnetic Resonance-Guided Spine Stereotactic Body Radiation Therapy, Yao Ding, Travis C Salzillo, Debra N Yeboa, Martin C Tom, Zhiheng Wang, Parmeswaran Diagaradjane, Ergys Subashi, Jinzhong Yang, Todd Swanson, Thomas Beckham, Chenyang Wang, Amol J Ghia, Tina Briere, Jihong Wang, Fabienne Lathuilière, Sneha Cloake, Eun Young Han

Faculty, Staff and Student Publications

BACKGROUND: Stereotactic body radiation therapy (SBRT) has proven effective in controlling spinal lesions with minimal toxicity, primarily due to its ability to limit spinal cord dose. Recent advances in MR-linac (MRL) technology offer superior spinal cord visualization and real-time gating, which can facilitate dose escalation in spinal tumor treatment while maintaining safety.

PURPOSE: This study aimed to optimize motion management for spine SBRT on an MRL by analyzing patient-specific motion dynamics and evaluating the most effective registration structures. We hypothesized that baseline shifts (BLS) would improve delivery efficiency while maintaining spinal cord dose constraints. The goal was to establish displacement …

A Brief History Of Circadian Time In The Heart, Martin E Young, Vanya Khanna, Mallory Metcalfe, Niruththaan Rameshkumar, Sarah Harington, Leo H Li, Janan Shoja Doost, Heinrich Taegtmeyer, Tami A Martino

Faculty, Staff and Student Publications

This review tracks the discovery of circadian biology in cardiovascular science, starting with early clinical observations of daily changes in heart rate, blood pressure, and cardiovascular events. These patterns suggested that time of day matters, but it was not until the past two decades that the mechanisms and knowledge translation of these rhythms were uncovered. We describe the heart's intrinsic circadian properties and importantly how this leads to regulation of cardiac gene and protein expression, neuroendocrine and vascular rhythms, metabolism, cellular electrophysiology, and cell signaling pathways. Next, we explore emerging themes, including the impact of circadian timing on ischemic injury, …

Mechanism Of Unconventional Il-33 Release In Airway Disease, Omar Osorio

Arts & Sciences Graduate Student Theses and Dissertations

The alarmin cytokine IL-33 is a strong inducer of type two inflammation and has been implicated in various chronic lung diseases. Although much work has been done to understand the inflammatory effects of extracellular IL-33, there is still a knowledge gap in understanding how this cytokine is secreted by airway epithelial cells in steady-state conditions. In the work laid out in this document, a COPD-disease associated isoform of IL-33, that has exons 3 and 4 (IL-3334) spliced out and is tonically secreted at baseline conditions. This IL-33 isoform is secreted from airway epithelial cells alongside, or as part of, extracellular …

Three New Species Of Androctonus From Morocco (Arachnida: Scorpiones: Buthidae), František Kovařík, Graeme Lowe, František Šťáhlavský

Euscorpius

New data are presented on the taxonomy and distribution of the dark species of the genus Androctonus Ehrenberg, 1828 in Morocco and Western Sahara. Three new species, A. argoubi sp. n., A. stockmanni sp. n., and A. vaneki sp. n. from Morocco are described, characterized by having metasoma I–IV ventrally punctate, a character that is well developed in A. stockmanni sp. n., and A. vaneki sp. n., and weakly developed in A. argoubi sp. n. Dark species from Morocco are compared with A. sergenti Vachon, 1948, and A. bourdoni Vachon, 1948. We describe and compare their …

Validity And Reliability Of The 'Feelfit®' Accelerometer In Evaluating Physical Activity And Sedentary Time In Children: A Comparative Study With Two Different Accelerometers, Songdhasn Chinapong, Korntawat Klinchan, Hanif Abdul Rahman, Michael Chia, Waris Wongpipit, Jetsada Arnin, Areekul Amornsriwatanakul

International Journal of Exercise Science

International Journal of Exercise Science 18(2): 794-810, 2025. Accurate physical activity (PA) measurement is crucial for public health surveillance. While self-report questionnaires are commonly used, they have limitations, especially in young children. An affordable and user-friendly device like Feelfit® offers a promising alternative particularly for countries with limited research resources. This study aimed to evaluate Feelfit®’s performance against the widely used ActiGraph® accelerometer in measuring PA among children. A quasi-experimental design was applied. Thirty-nine children (19 boys; 20 girls; aged 11.4 ± 0.5 years) wore both Feelfit® and ActiGraph® during sequentially specified activities of varying intensity ranging from sedentary to …

Evaluating The Toxicity Of Electronic Cigarette Aerosols For Firsthand And Secondhand Exposure Under Different Device Operating Conditions, Kashala Fabrice Kapiamba, Hsin Yin Chuang, Weixing Hao, Ta Chun Lin, Lung Chi Chen, Yue-Wern Huang, Yang Wang

Biological Sciences Faculty Research & Creative Works

The rapid proliferation of electronic cigarettes (ECs) has raised significant concerns about their potential health effects on both users and bystanders. This study systematically investigates the impact of EC aerosol exposure on human alveolar epithelial cells (A549), considering variations in device parameters, nicotine concentration, and exposure type. Using a gravity-based air–liquid interface exposure system, we assessed cytotoxicity and epithelial barrier integrity by measuring cell viability and transepithelial electrical resistance (TEER). Our results indicate that EC aerosol exposure significantly reduces cell viability and disrupts monolayer integrity in a dose- and device-dependent manner. Notably, VUSE (pod-type) exposure led to a 16% decrease …

Simulated Emergency Room Sign-Outs: What They Tell Us About Diagnostic Accuracy And Opportunities For Improvement, Roni Matin, Brent R King, Amit M Mehta, Susan H Fenton, Nathan R Hoot, David J Robinson, Charles L Maddow, Amy Franklin

Faculty, Staff and Student Publications

Objective: Emergency department (ED) sign-outs provide continuity of care for patients at shift changes. However, these periods have been associated with communication breakdowns and medical errors. We explored information factors (stage-of-the-case and the explicitness of the sign-out narrative) to determine their impact on clinicians' diagnostic accuracy and confidence.

Methods: Clinicians from 2 academic ED sites reviewed patient vignettes sign-out narratives (N=69). Using a within-subjects experiment, the explicitness of the sign-out information (i.e., broad statement about labs versus stating each test) and the patient's stage in the diagnostic process (e.g., labs pending, treatment occurring, etc.) at the time of sign-out varied. …

Two Decapod Crustaceans, Panopeus Herbstii And Petrolisthes Armatus, Stabilize Their Gaze Using Achromatic Visual Cues, But Not The Angle Of Linearly Polarized Light, M. Janakis, S. Guirges, A. C. Grant, I. Paris, E. F. Lopresti, Daniel Isaac Speiser

Faculty Publications

No abstract provided.

08.18.2025 Ored Connect, Liz Williamson

ORED Newsletter

ORED on-demand training, Tableau training, Research Reception 2025

Dominant Tree Species As A Driver Of Forest Herb Community Assembly: The Peculiar Case Of Pawpaw (Asimina Triloba), Anna Wassel

Arts & Sciences Graduate Student Theses and Dissertations

Understanding the drivers of community assembly is a key goal in ecology and conservation. One way to better understand community assembly is to understand how the presence or absence of dominant species– highly abundant species with a proportionally large effect on the ecosystem–affects assembly. This approach allows for a more generalized understanding of community assembly based on the presence or abundance of one species rather than pairwise interactions among all species in a community. In forests, studies on dominant tree species have focused on how they affect patterns of species diversity. In contrast, surprisingly little is known about how dominant …

Mechanisms Of Ssdna Gap Resection In Brca1-Proficient And -Deficient Cells, Isabelle Seppa

Arts & Sciences Graduate Student Theses and Dissertations

Single-stranded (ss) DNA gaps are potentially genome-destabilizing structures that require prompt repair (or filling) to prevent DNA breakage and genome instability. We previously showed that gap repair is defective in cancer cells with deficiencies in the breast cancer susceptibility gene BRCA1. These findings explain why ssDNA gaps accumulate in BRCA1-deficient cells in response to therapies that target DNA, such as platinum-based compounds, or therapies that inhibit specific repair pathways, such as PARP inhibitors (PARPi). We also discovered that gap repair can be restored in BRCA1-deficient cells by inhibiting MRE11 nuclease activity, indicating that nuclease processing plays a central role in …

Cardiac And Coronary Hemodynamics: Using An Integrated Ex-Vivo Beating Heart Experiments And Computational Modeling, Chenghan Cai

Master's Theses (2009 -)

Cardiovascular function arises from the complex interactions among the heart, the arterial system, and the coronary circulation. Questions such as how variations in left ventricular (LV) loading conditions affect LV and aortic functions through LV–aorta interactions; and how coronary artery diseases, such as stenosis, impact cardiac function and myocardial perfusion including left and right coronary perfusion via LV–coronary interactions, remain understudied. To answer these questions, this thesis focuses on two core objectives: (1) investigate the effects of LV loading conditions on LV and aortic functions through LV–aortic interactions by performing ex-vivo beating rat heart experiments, and (2) elucidate the impact …

Asymmetric Fgf Receptor Dimerization: Implications For Fgf23 Biology And Drug Discovery, Mohammed S. Razzaque, Moosa Mohammadi

School of Medicine Publications

Fibroblast growth factor 23 (FGF23) requires both αKlotho and heparan sulfate proteoglycans (HSPGs) as obligatory coreceptors to bind, dimerize, and activate its FGF receptors (FGFRs) in the kidney, thereby regulating mineral ion and vitamin D homeostasis. Cryogenic electron microscopy studies reveal that FGF23 signaling proceeds through an asymmetric 1:2:1:1 FGF23–FGFR–αKlotho–HS assembly. According to this structural model, αKlotho simultaneously anchors FGF23 and one FGFR chain, referred to as the primary receptor (FGFRP), to form a 1:1:1 FGF23-FGFRP-αKlotho triplex, which boosts FGF23-FGFRP interaction. Subsequently, the HS coreceptor aids the triplex in recruiting a second FGFR chain, or secondary receptor (FGFRS), leading to …

Meta-Analytic Insights On Cover Crop Weed Suppression In The Midsouthern United States, Amar S. Godar, Jason K. Nprsworthy

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

Herbicide resistance poses an escalating challenge to successful weed management in contemporary cropping systems, prompting growing interest in integrated strategies to reduce reliance on herbicides. Although cover cropping has long been recognized for its potential to suppress weeds, it has recently gained renewed attention as a weed management tool and for its ability to help producers achieve broader goals of soil health and environmental sustainability. Although research on its efficacy in the midsouthern United States has accumulated, a meta-analytic synthesis has been lacking. This meta-analysis synthesized 746 effect sizes from 27 peer-reviewed studies (selected based on explicit reporting of weed …

In Silico Investigations Of Class Ii Trans Activator (Ciita): Its Plausible Implications In Neuroinflammation And Neurological Disorders, Kishore N

Theses and Dissertations

Inflammation plays a significant role in maintaining homeostasis. Neuroinflammation is a chronic inflammatory response in the central nervous system (CNS), leading to brain or spinal cord dysfunction. To promote mental health, it is crucial to understand the regulation of neuroinflammation. Class II transactivator (CIITA) is a master-regulator of the major histocompatibility complex II (MHCII).

Modulation of CIITA has been suggested as a promising intervention for inflammatory conditions, including neurological disorders. However, there is limited knowledge about the role of CIITA and its interactors in inflammation. This study aimed to understand the role of CIITA in neuroinflammation and neurological disorders using …

3d Bioprinting On Electrospun Nanofibrous Scaffolds To Fabricate Myocardial Patches, Muthu Parkkavi S

Theses and Dissertations

Tissue-engineered three-dimensional (3D) myocardial patches offer superior and innovative treatment strategy for myocardial infarction (MI). Among the various scaffold fabrication techniques, electrospinning and 3D bioprinting have received great attention due to their ability to recreate native cardiac tissue mimetic characteristics. Despite several advantages, electrospun nanofibers have limitations in cell delivery due to random cell seeding, while bioprinting faces challenges in creating hydrogel constructs with ideal mechanical properties capable of supporting cardiac contraction/relaxation cycle. Hence in this work, hybrid myocardial patches were developed by converging electrospinning and bioprinting techniques.

Electrospinning of PLCL:PEOz (B73, 7:3 blend of poly-L-lactide-co-ε-caprolactone (PLCL) and polyethyl oxazoline …

Effect Of Osmolytes On The Interplay Of Water Protein And Dna In Ecori Dna Recognition Using Molecular Dynamics Simulations, Aathithya D

Theses and Dissertations

EcoRI is a type II restriction endonuclease that has been widely used as a model system to study protein-DNA interaction owing to its high degree of specificity. This enzyme does not recognize even a single basepair change in its recognition sequence, (GAATTC)2, under normal conditions. However, in the presence of osmolytes, such as glycerol and DMSO, the specificity of EcoRI is slightly relaxed and recognizes sequences that differ from its cognate sequence in the first basepair position. This relaxed specificity has been attributed to the dehydration of the EcoRI-DNA which presumably results in tighter complex formation and subsequent catalysis. However, …

Biogenic Calcite Precipitation For Coastal Sand Stabilization: A Synergistic Approach Using Marine Bacteria And Natural Fibers, Aparna Gs

Theses and Dissertations

Coastal erosion, driven by natural forces such as waves, tides, winds, and currents and further intensified by anthropogenic activities like urbanization, climate change, and coastal infrastructure development, poses a significant threat to shoreline stability. Conventional erosion control methods, including jetties, embankments, and artificial reefs, often face limitations in sustainability and effectiveness. In this context, microbially induced calcite precipitation (MICP) has emerged as a promising ecofriendly solution for ground stabilization.

The present study investigates the potential of an indigenous ureolytic marine bacterium, Bacillus sp. N₉, isolated from the coastal sediments of Nagapattinam, Tamil Nadu, for coastal sand stabilization. The strain was …

Fabrication Of Protein-Based Nanomicelle Against Inflamed Synoviocytes In Rheumatoid Arthritis, Madhumithra Thangadurai

Theses and Dissertations

Rheumatoid arthritis (RA) is a chronic autoimmune disease marked by persistent synovial inflammation, progressive cartilage and bone destruction, and systemic complications. 1% of the global population are affected by RA, when their immune system targets synovial tissues, leading to joint pain, swelling, and functional disability. Standard treatments, such as disease-modifying antirheumatic drugs (DMARDs) like methotrexate (MTX), are limited by systemic toxicity and inconsistent patient responses, highlighting the need for improved therapies. This research work explores protein-glycosaminoglycan nanomicelles engineered using Zein with Chondroitin or carboxymethylated Dextran Sulfate as targeted drug delivery vehicles for RA.

MTX was encapsulated within these nanomicelles to …

Genomic Surveillance Of Indian Klebsiella Pneumoniae And Exploration Of Resistance Inhibitors, Abhirami Ks Ms

Theses and Dissertations

Klebsiella pneumoniae is an important ESKAPE pathogen that causes life threatening infections. The strains exhibiting multidrug-resistance (MDR) and hypervirulence are the priority pathogens for which immediate treatment and dissemination prevention strategies are required. To address this, genome profiling was performed to understand the AMR patterns, role of episomes, phages, virulence determinants and its association with sequence types.

The study includes 267 publicly available Indian K. pneumoniae genomes over a period of ten years and four sequenced isolates. Whole genome analysis revealed the widespread presence of diverse β-lactamase genes, with β-lactam resistance being predominant. Genes such as blaCTX-M-15, blaTEM-1B and blaOXA-232 …

Differences In Fitness Between Cadet And General Population Firefighter Academy Recruits, Scott D. Brau, David Cornell, Benjamin J. Mendelson, Rudi A. Marciniak, Kyle Ebersole

International Journal of Exercise Science

International Journal of Exercise Science 18(8): 774-793, 2025. This longitudinal study explored entry route- and age-related fitness differences between cadet (CR) and general population (GR) firefighter recruits. Fitness data were collected from eight separate firefighter recruit academy cohorts (N = 317; 122 CR, 195 GR; 27.17 ± 7.58 yrs, 177.30 ± 8.72 cm, 88.65 ± 17.78 kg). In the first week of the academy, recruits completed an assessment battery including: body composition via skinfold measures to estimate body fat (BF, %) and fat-free mass (FFM, kg); aerobic fitness (VO_2peak, mL· kg^-1· min^-1) and …

Periodic Evaluations Indicate Increased Effectiveness Of Oregon Master Woodland Manager Volunteer Program, Alicia Christiansen, Lauren Grand, Norma Kline, Tiffany Hopkins

Journal of Extension

The Oregon State University Extension Service Master Woodland Manager (MWM) volunteer program trains landowners in core forestry and natural resource topics. Landowners participate in the MWM program to increase their forest management knowledge, improve their own management practices, and prepare them to volunteer in their community (Bowers, 2000). We surveyed MWM volunteers to understand the effectiveness of the program and what barriers exist to volunteering. Volunteers find the program to be increasingly adequate for personal management and answering questions, but time continues to be the biggest barrier for completing required volunteer hours.