Digital Commons Network^™

Protein Glycosylation In Natural And Synthetic Minimal Genome Mycoplasmas, John Sanford

ETDs from 2020-2029

Mycoplasmas are cell wall-less bacterial symbionts with remarkably streamlined genomes. Mycoplasmas offer two intriguing model organisms for studying concepts of minimal life. Mycoplasma genitalium has streamlined its genome to 580-kbp while maintaining virulence to suit its niche of parasitizing the human urogenital tract. The J. Craig Venter Institute has synthesized and transplanted a 543-kbp genome into a recipient cell, resulting in a non-pathogenic organism termed JCVI-syn3A. The conservation of a biological process in M. genitalium and JCVI-syn3A strongly implies an essential function in mycoplasmas, and potentially all life. Despite common thought of mycoplasmas being the simplest cells, much of their …

Effects Of Hot Water Dipping And Sub-Zero Saline Chilling On The Microbial Safety Of Broiler Carcasses And Recycled Chilling Water, Elen Zhu

Master's Theses

Broiler meat became the most widely consumed meat within the United States and across the world in 2019. The trend of increasing broiler consumption is expected to continue due to affordability, health benefits, and production efficiency. To meet the growing demand of broilers, a substantial number of birds need to be produced and processed while minimizing bacteria contamination, water consumption and wastewater generation.

In this study, the microbial safety (mesophilic aerobic bacteria, coliforms, and Escherichia coli) of broiler carcasses and post-chill water (red water) was assessed, using innovative processing techniques and red water recycling. A total of 144 broilers …

Independent And Combined Effects Of Early-Life Iron Deficiency And Antibiotic Exposure On Growth And Hematological Outcomes In A Piglet Model, Ginger M. Fitzpatrick

Master's Theses

Iron deficiency (ID) affects over 2 billion individuals globally. Children under 5 are at increased risk of ID due to rapid growth and are especially vulnerable to its negative consequences because of iron’s essential role in cognitive development and immune maturation. ID is the leading cause of iron deficiency anemia (IDA), with IDA affecting approximately 40% of children in this age group. Antibiotic (abx) exposure is also prevalent during early life and may disrupt growth and through gut dysbiosis, with increasing use posing additional risk in younger populations. Geographically, there is overlap in regions with high anemia prevalence and those …

Evaluation Of Ultraviolet-C Light For Control Of Mites And Western Tarnished Plant Bug In Strawberry & Interactive Lethal Effects Of Common Strawberry Fungicides And Adjuvants On Phytoseiulus Persimilis, Colin T. Koubek

Master's Theses

California strawberry production relies heavily on chemical pesticides to manage arthropod pests and diseases, but pesticide resistance, regulatory pressure, and the need to conserve biological control agents have increased interest in alternative pest management tools. This thesis evaluated ultraviolet-C (UV-C) light as a nonchemical management tool for key strawberry arthropod pests and assessed the compatibility of common strawberry fungicides and adjuvants with the predatory mite Phytoseiulus persimilis Athias-Henriot. The first objective was to determine the ovicidal and lethal effects of UV-C light on Lygus hesperus Knight eggs and nymphs. Laboratory and field ovicide assays were conducted using UV-C doses relevant …

Effects Of Irrigation And Nitrogen Management On Yield And Leaching Risk In Organic And Conventional Broccoli Fields, Shane Egerstrom

Master's Theses

Under regulatory pressures to reduce groundwater contamination by nitrate from fertilizer, such as those posed by the Central Coast Regional Water Quality Control Board’s Agricultural Order 4.0, a need exists to better understand interactions between irrigation and nitrogen (N) management. To increase N use efficiency (NUE), growers are encouraged to account for additional sources of N in their management plans, such as irrigation water N and preplant soil N. The availability of these N sources for plant uptake and how it is affected by other management conditions is not yet well documented. We conducted 6 field trials, 3 organic and …

Assessing Nitrogen Leaching Risk In Organic Vegetable Production, Megan Widle

Master's Theses

Nitrogen (N) leaching is the primary driver of groundwater contamination in agricultural regions. On California’s Central Coast, Agricultural Order 4.0 regulates this risk by constraining field-level N balances (N applied minus N removed). However, the assumption that unrecovered N is lost via leaching may not hold in organic and regenerative systems that promote soil organic matter accumulation. This study evaluated whether measured N leaching aligns with estimates derived from partial N budgets in organic systems, and whether management practices (intercrops, cover crops, and reduced tillage) can mitigate leaching risk. Four field trials were conducted to investigate N dynamics in organic …

Exploring Csf Microrna Signatures As Diagnostic Biomarkers In Adult-Type Diffuse Gliomas, Maryam Pirhoushiaran, Kamilah Walker-Charles, Tsung-Hung Yao, Satwikreddy Putluri, Nehal Patel, Daniel H Wang, Isabel Wang, Srividya Arjuna, Antonio Dono, Angel Bueno, Sophia Nguyen, Ashish P Balar, Jason T Huse, Suprateek Kundu, Yoshua Esquenazi, Chirag B Patel, Sujit S Prabhu, Frederick F Lang, Leomar Y Ballester

Faculty, Staff and Student Publications

Mutations in isocitrate dehydrogenase (IDH) genes, specifically IDH1 and IDH2, are frequently observed in diffuse gliomas (DG) and define distinct molecular subtypes, namely IDH-wildtype and IDH-mutant. Abnormal expression of extracellular vesicle-derived microRNAs (EV-miRNAs) in the cerebrospinal fluid (CSF) of DG patients may serve as minimally invasive diagnostic and prognostic biomarkers. To investigate this potential, we employed miRNA-sequencing (miRNA-seq), quantitative real-time PCR (qRT-PCR), and multivariable logistic regression (MLR) to identify differentially expressed microRNAs (DE-miRNAs) in CSF samples from DG patients. qRT-PCR analysis demonstrated that EV-miR-21-5p effectively differentiated CSF from glioblastoma (GBM) patients versus controls (p = 0.012, AUC = 0.84) and …

Nlrp3 Inflammasome: A Link Between Systemic Infection And Alzheimer’S Disease, Tatiana Barichello, Felipe Dal-Pizzol

Faculty, Staff and Student Publications

No abstract provided.

Exploring Csf Microrna Signatures As Diagnostic Biomarkers In Adult-Type Diffuse Gliomas, Maryam Pirhoushiaran, Kamilah Walker-Charles, Tsung-Hung Yao, Satwikreddy Putluri, Nehal Patel, Daniel H Wang, Isabel Wang, Srividya Arjuna, Antonio Dono, Angel Bueno, Sophia Nguyen, Ashish P Balar, Jason T Huse, Suprateek Kundu, Yoshua Esquenazi, Chirag B Patel, Sujit S Prabhu, Frederick F Lang, Leomar Y Ballester

Faculty, Staff and Student Publications

Mutations in isocitrate dehydrogenase (IDH) genes, specifically IDH1 and IDH2, are frequently observed in diffuse gliomas (DG) and define distinct molecular subtypes, namely IDH-wildtype and IDH-mutant. Abnormal expression of extracellular vesicle-derived microRNAs (EV-miRNAs) in the cerebrospinal fluid (CSF) of DG patients may serve as minimally invasive diagnostic and prognostic biomarkers. To investigate this potential, we employed miRNA-sequencing (miRNA-seq), quantitative real-time PCR (qRT-PCR), and multivariable logistic regression (MLR) to identify differentially expressed microRNAs (DE-miRNAs) in CSF samples from DG patients. qRT-PCR analysis demonstrated that EV-miR-21-5p effectively differentiated CSF from glioblastoma (GBM) patients versus controls (p = 0.012, AUC = 0.84) and …

Ldm-Morph: Latent Diffusion Model Guided Deformable Image Registration, Jiong Wu, Tinsu Pan, Kuang Gong

Faculty, Staff and Student Publications

Deformable image registration plays an essential role in various medical image tasks. Existing deep learning-based deformable registration frameworks primarily utilize convolutional neural networks (CNNs) or Transformers to learn features to predict the deformations. However, the lack of semantic information in the learned features limits the registration performance. Furthermore, the similarity metric of the loss function is often evaluated only in the pixel space, which ignores the matching of high-level anatomical features and can lead to deformation folding. To address these issues, in this work, we proposed LDM-Morph, an unsupervised deformable registration algorithm for medical image registration. LDM-Morph integrated features extracted …

Partial Insect-Based Meal Inclusion In The Diets Of Ross® 308 Broilers Upregulates Growth And Immune Related Genes, Victor K. Rotich, Isaac M. Osuga, Mathew G. Gicheha, Shaphan Y. Chia, Jandouwe Villinger, Anderson N. Maina, Jinhua Xiao, Dennis Beesigamukama, Chrysantus M. Tanga

All Peer-Reviewed Publications

This work investigated the effects of black soldier fly ( Hermetia illucens L.) larvae meal (BSFLM) on growth- and immune-related gene expression in Ross 308 broilers. Birds were fed diets containing soybean meal (SBM), fishmeal (FM), combinations with BSFLM, or BSFLM alone. Growth, organ weights, immune genes [interleukin-2 (IL-2), interleukin-6 (IL-6), tumor necrotic factor alpha (TNF-α), interferon-gamma (IFN-γ)] and growth-related genes [chicken growth hormone (cGH), insulin growth factor 1 (IGF-1)] expression were measured. Our results demonstrate that birds fed FM+BSFLM had significantly higher final liveweight, average daily weight gain (ADG), and low feed conversion ratio. Birds fed FM+BSFLM showed highest …

Decentralizing Dementia Research To The Us–Mexico Border: The Rio Grande Valley Ad-Rcmar As A Model For Translational Equity, Gladys E. Maestre, John Blangero, Eron Manusov, Gabriel A. De Erausquin, Francisco Fernandez, Silvia Mejia-Arango, Vincent P. Diego, Juan C. Lopez-Alvarenga, Claudia Alaniz, Neyra García, Rosa V. Pirela, Andrew Tsin, Michael Mahaney

School of Medicine Publications

Translational equity means ensuring that diagnostics, treatments, care models, and prevention strategies are developed and implemented so they work for populations with the greatest burden and least access to care. In Alzheimer's disease and related dementias (ADRD), where most evidence derives from highly educated, non-Hispanic White participants at large academic centers, translational equity is critical to prevent misclassification, limited access, and widening disparities and to ensure that underrepresented communities shape how new knowledge moves into practice. Hispanic and other populations in the United States are disproportionately affected by ADRD yet remain underrepresented in research, with gaps especially pronounced in high-poverty …

Invasion Patterns And Niche Dynamics Of The Pollinivorous Florida Calligrapher, Toxomerus Floralis (Diptera: Syrphidae) In The Afrotropical Region, Burgert Muller, John Midgley, Georg Goergen, Ali Al Jahdhami, Michelson Azo'o Ela, Terence Bellingan, Simon Cavaillès, Robert Copeland, Marc De Meyer, Martin Hauser, Allen Holmes, Ximo Mengual, Gabriel Nève, Menno Reemer, Jeff Skevington, Gunilla Ståhls, Eugène Sinzinkayo, John Smit, Axel Ssymank, Genevieve Theron, Kurt Jordaens

All Peer-Reviewed Publications

The rapid spread of Toxomerus floralis (Fabricius, 1798) (Diptera: Syrphidae) within the Afrotropical region is described. We characterise and compare the climatic niches of T. floralis in its native (Southern North America, Central America and South America) and invaded (Afrotropical Region) range to assess the potential for further expansion across Africa and beyond, and included future global climate models and socioeconomic pathways as projections. Occurrence data for native and invaded ranges were obtained from field sampling by authors, major collections of Afrotropical Syrphidae, collections records and occurrence data from the Global Biodiversity Information Facility (GBIF), including iNaturalist data. Single and …

Climate-Driven Stochastic Modelling Of Crimean-Congo Haemorrhagic Fever Transmission In Uganda, P. G. Kpatchana, J. Aduda, K. M. Agboka

All Peer-Reviewed Publications

Crimean-Congo haemorrhagic fever (CCHF) is a climate-sensitive tick-borne zoonosis that remains a significant public health concern in Uganda, where temperature and vapour pressure deficit influence tick ecology and consequently disease transmission. This study aimed to develop and analyse a climate-driven stochastic model for CCHF transmission among ticks, livestock, and humans under environmental variability in Uganda. A compartmental transmission model was formulated and extended into a stochastic differential equation framework by incorporating multiplicative environmental noise. Climate-dependent tick recruitment, development, and mortality were parameterized using district-level temperature and vapour pressure deficit data to capture spatial heterogeneity in transmission risk. Theoretical analyses based …

Viruses Causing Panleukopenia In Domestic Cats: A Review Of Feline And Canine Parvoviruses, Simon Colby

University Honors Theses

Parvoviruses remain among the most important viral pathogens in domestic cats today. Despite this, there is much confusion around which parvoviruses can infect cats, and what extent of disease they can cause. One of the two parvoviruses infecting cats, canine parvovirus type-2 (CPV-2), likely evolved from the other parvovirus infecting cats, feline parvovirus (FPV). These viruses differ at only a few places in their genomes, and share the method of cell entry via the transferrin receptor. The disease caused by FPV has been well characterized in cats, but disease caused by CPV-2 is more obscure. Additionally, current testing methods for …

Exploring The Durability Of Marine Picocyanobacterial Microcolonies, Erik Swanson

University Honors Theses

Picocyanobacteria of the genus Synechococcus are widespread aquatic photoautotrophs that play essential roles in primary production and carbon cycling. Some Synechococcus strains form multicellular microcolonies, but the mechanisms of cell-to-cell attachments and structural durability of these microcolonies remain poorly understood. This research investigated the physical durability of microcolonies in two marine Synechococcus strains (CC9605 and CC9311) using physical disruption treatments. Cultures were subjected to vortexing and sonication treatments, and populations of single cells and microcolonies were quantified using flow cytometry based on differences in measures of size. Results indicated that strain CC9605 showed no significant treatment effect, whereas CC9311 displayed …

Routine Transfusion Of Rh(D)-Positive Rbcs To Rh(D)-Negative Patients Designated As Do Not Resuscitate Conserves Rh(D)-Negative Red Blood Cell Inventory, Julie Katz Karp, Jovanna Everetts, Juliana Guarente, Angelica Vivero, Tiffany Bohr, Mary Harach

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

Background: A minority of blood donors are Rh(D)-negative, and Rh(D)-negative red blood cell (RBC) products are often overutilized. As such, Rh(D)-negative RBCs may be difficult to maintain in blood bank inventory.

Study design and methods: We changed our blood bank laboratory policy to approve non-alloimmunized Rh(D)-negative patients to receive Rh(D)-positive RBCs for routine transfusion under defined criteria. Those criteria included Rh(D)-negative males (all ages) and females (aged >50 years) who were designated as do not resuscitate (DNR), either with or without intubation, in the electronic medical record.

Results: From August 15, 2024 through August 15, 2025, a total of 204 …

Exercise Therapy For Mood Disorders In Retiring/Former Athletes, Christian Antos

Dissertations

This dissertation examined the potential integration of exercise therapy and psychotherapy as a treatment approach for mood-related difficulties experienced by former elite athletes during the transition out of competitive sport. Retirement from athletics is often associated with significant biopsychosocial challenges, including disruptions in identity, healthy routines, social support, and emotional well-being. Existing literature suggests that exercise may serve as an effective adjunctive intervention for improving mood and overall psychological functioning, though limited research has explored its application among retiring athletes within psychotherapeutic contexts. This literature review synthesized current research related to athletic retirement, neurobiological mechanisms associated with physical activity, and …

Synergies Of Microecology And Macroecology Elicit Insights For Creation Care, David Warners, John T. Wertz

University Faculty Publications and Creative Works

This article reports on a collection of microecological and macroecological insights that emerged from extended conversations between Calvin University professors David Warners, a botanist concentrating in restoration ecology, and John Wertz, a micro-biologist specializing in microbial ecology. Classic descriptions of ecology identify biological interactions as happening at the ecosystem, community, or population level. And yet, ecological interactions are very much occurring at the microbial level as well. Furthermore, microbial-level interactions frequently influence the quality and character of macroecological relationships and vice versa. Allowing ecological principles to be applied across all life forms broadens our comprehension of interactions that are happening …

Climate Change Reduces Pollination Services And Sunflower Yields Across Europe And Northern Africa, Stella Gachoki, Clémence Riva, Danilo Bevk, Yamina Haider, Noureddine Adjlane, Ioannis Manthos, Bojan Stipešević, Zlatko Puškadija, Marin Kovačić, Leonidas Charistos, Fani Hatjina, Fabrice Requier

All Peer-Reviewed Publications

Sunflower (Helianthus annuus) productivity is highly dependent on pollinators, yet the effects of climate on pollination services and crop yield remain poorly understood. In this study, we investigate how temperature gradients influence flower-visiting communities, pollination services, and sunflower productivity across Europe and Northern Africa. We conducted standardized two-year (2022 and 2023) pollination exclusion experiments across 36 sunflower fields spanning a broad climatic gradient, from temperate regions in Slovenia to arid conditions in Algeria. We found that sunflower production (seed set, seed number, and oil content) relied heavily on insect pollination. However, this benefit declined with rising temperatures, likely due to …

Why Smallholders (Do Not) Adopt Productivity-Increasing Technologies? Developing A Smallholder Adoption-Process Model Through An In-Depth Qualitative Study In Ethiopia, Tamiru Amanu Abetu, Paul T.M. Ingenbleek, K. E. Giller, Endalkachew Wolde-Meskel, Edward Baars

All Peer-Reviewed Publications

Research and innovation have developed an impressive number of technologies that can increase the agricultural productivity of African smallholders. The impact of technology is nevertheless hindered by the heterogenous and unpredictable adoption patterns of smallholders. Most current studies examine farm-level constraints and environmental barriers (e.g., distance to market and access to financial capital) as the main explanation for variations in adoption. We take a complementary approach that draws on adoption theories from consumer psychology, thus considering the interplay between contextual barriers and the micro-level decision making processes of smallholders with regard to the adoption of technology. Qualitative data on the …

Gc-Ms-Based Comparative Analysis Of Compounds In Host Plants And Insect Gut Extracts, Rita Dill, Kimberly Smith, Shelia Okoth, Xavier Cheseto, Anne Osano

All Peer-Reviewed Publications

Background/Objectives: Herbivorous insects feed on plant tissues to obtain nutrients necessary for growth and development while simultaneously ingesting diverse plant secondary metabolites. Understanding the fate of these compounds during digestion is important for advancing knowledge of insect nutritional physiology and diet-associated biochemical processes. This study aimed to comparatively profile metabolites in host plants and corresponding insect gut extracts to generate insights into compound transfer and compositional changes within these systems. Methods: Gas Chromatography-Mass Spectrometry (GC-MS) metabolomics was combined with Ultraviolet-Visible (UV–Vis) quantification of total phenols and flavonoids to compare host plant tissues and insect gut extracts in three systems: fall …

The Cultivation Of Public Perception: Cultivated Meat Narratives And Misinformation On Tiktok, Anna M. Balkus

Graduate Masters Theses

Cultivated meat is an emerging tissue engineering technology that has the potential to address major issues threatening food systems, including climate change, rapid population growth, and the spread of disease. Among technical challenges, public perception remains a significant barrier for the widespread adoption of cultivated meat. While social media has transformed communication globally, it has simultaneously contributed to corrupt online environments infected with misinformation—unintentional inaccuracies that differ from disinformation, which is spread with the intent to mislead. The way the public receives and digests information regarding new food technologies, like cultivated meat, will be shaped by their social media environment. …

Intervention Levers For Stunting Reduction In Indonesia: Evidence From The 2023 Indonesian Health Survey Data, Iwan Ariawan, Hafizah Jusril, Zahra Izza Afifa, Azka Fitri, Elmarizha Sekar Utami, Mikail Hasan, Dwi Puspasari

Kesmas

Stunting remains the largest public health challenge among macro-nutrition problems in Indonesia, affecting almost a quarter of children under five in 2023. The prevalence is considered high according to the World Health Organization standard. This study analyzed 15 aggregated provincial variables from the 2023 Indonesian Health Survey using Structural Equation Modeling (SEM), focusing on determinants of stunting among children under two to identify primary intervention levers. Findings indicated that intervention urgency should focus on the first 1,000 days, particularly the steep increase in stunting prevalence observed in the 12–24-month age range. While the highest prevalence is in Eastern provinces (e.g., …

Vergence Task-Based Neural Pathways With Binocularly Normal Vision And Comorbid Persistent Post-Concussive Symptoms -Convergence Insufficiency, Ayushi Sangoi

Dissertations

Binocular dysfunctions are more prevalent in the persistent post-concussive symptoms (PPCS) population than in the general population. The most prevalent binocular disorder is convergence insufficiency (CI), affecting 3-17% of the general population and up to 10 times as many people with PPCS. CI makes it difficult to fuse or maintain fusion on targets at near, and its symptoms include double or blurry vision and headaches when performing close-range tasks such as reading, which can exacerbate PPCS symptoms. Given controversy over the subjectivity and effectiveness of diagnostic tools and symptom surveys for both PPCS and CI, understanding why CI has high …

Transcranial Ac Modulation Of Cerebellar Nuclear Activity In Awake Animals, Nuran Kavakli

Dissertations

Entrainment of cerebellar nuclear (CN) cells via cerebellar transcranial alternating current stimulation (ctACS) has been reported in animals under ketamine/xylazine anesthesia. Our main objective was to demonstrate modulation of CN activity in unanesthetized, freely moving animals using ctACS. Multi-channel carbon-fiber electrodes were implanted into the interpositus nucleus for recording multi-unit (MU) activity, and thin-film electrodes were implanted subcutaneously over the posterior cerebellum for stimulation. A frequency-domain-based metric was developed to quantify modulation from MU signals. The results demonstrated modulation in a wide range of frequencies (4 Hz-300 Hz) as in anesthetized animals. In contrast, the amplitude of the peak in …

Pickleweed In The Disappearing Marsh: Population Genetics & Metal Accumulation In Salicornia Depressa, Alice Kaisla

Graduate Doctoral Dissertations

Salicornia is a genus of succulent halophytes found in salt marshes around the world. Salicornia species have a remarkably high tolerance for heavy metal pollution and have been shown to accumulate high concentrations of heavy metals in their tissue under experimental conditions. As a result, they are both a useful system for studying evolution in polluted coastlines and a potential candidate for use in phytoremediation. My research focuses on Salicornia depressa, known as pickleweed, a species commonly found in marshes along the heavily urbanized and industrialized New England coast. I investigate genetic diversity and population structure in S. depressa populations …

Investigation Of Environmental Influences On Multiple Sclerosis: A Study For Egypt’S Health, Noha Ezzaldin Alziny Ali

Theses and Dissertations

Background: Multiple sclerosis (MS) is a complex, chronic neuroinflammatory disease influenced by both genetic and environmental factors. While global research has identified potential environmental influences, most evidence comes from Western populations, creating a significant knowledge gap for regions like Egypt, which has witnessed a dramatic rise in MS prevalence over recent decades. This study hypothesized that Egyptian MS patients exhibit a distinct biological signature in their blood, characterized by an imbalance in essential and toxic trace elements (the metallome) and alterations in stress-response biomarkers associated with neuroaxonal injury and cellular stress. Objective: This study aimed to comprehensively profile and compare …

Is Trimethylamine N-Oxide A Friend, Foe, Or Hormetic Agent In Patients With Parkinson’S Disease: A Focused Review Of One Microbial Metabolite, Abraham B. Alton

Student Works

This review synthesizes recent literature examining trimethylamine N-oxide (TMAO) synthesis and its potential role in Parkinson’s Disease (PD) pathology. An increase in TMAO plasma and CSF concentration is associated with PD progression and severity. TMAO biosynthesis is a two-step process. First, precursors including carnitine and choline are converted to trimethylamine (TMA) by gut microbes. Second, TMAO is oxidized to TMAO in the liver. Once absorbed into circulation TMAO crosses the blood brain barrier and may influence PD disease pathology by increasing neuroinflammation and astrocyte activation and damaging the cerebral lymphatic system. These mechanisms may contribute to the cognitive and motor …

Working Out Your Self-Image: Strength, Self-Esteem, And Human Flourishing, Kingston K. Christie

Honors Projects

This project integrates empirical research in exercise science with theological anthropology to examine the psychological effects of resistance training and the meaning of strength within a Christian framework of human dignity and flourishing. The empirical component investigated the effects of a four-week progressive resistance training intervention on global self-esteem and physical self-concept among undergraduate university students with moderate-to-low baseline self-esteem. Eleven participants (N = 11; 20.15 ± 1.52 yrs) completed the Rosenberg Self-Esteem Scale (RSES) and Physical Self-Description Questionnaire Short Form (PSDQ-S) before and after the intervention, with muscular strength assessed via submaximal testing across the squat, bench press, deadlift, …