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The Hope College Department Of Biology: The First 50+ Years, Christopher C. Barney

Faculty Publications

The Hope College Department of Biology was founded in 1899 with the appointment of the first Professor of Biology at Hope, Samuel Mast. During the first 50+ years of the Biology Department, there were eight total faculty members in the department, including Frances Koeman, the first female faculty member in the natural sciences. Four faculty members, Mast, Frank Patterson, Oscar Thompson, and Teunis Vergeer were primarily responsible for developing the department’s curriculum and programs, with Mast and Vergeer also carrying out published research. The department was housed primarily in Van Raalte Hall and the Science Building (now Lubbers Hall) for …

A Computational Micropatterning Approach To Study Caveolae And Protein Localization In Vascular Biology, Andrew B. Grespin

Electronic Theses and Dissertations

Caveolae are specialized, flask-shaped membrane invaginations highly expressed in endothelium and dysregulated in atherosclerosis. Caveolae play a central role in buffering membrane tension, yet the principles governing their spatial organization remain elusive. Thus, we sought to generate the most comprehensive and systematic analysis of blood vessel caveolar spatial organization. However, cell culturing, the backbone of human-focused biological research, does not standardly do well to model physiologically relevant cell behaviors such as migration or polarity-based tissue formation, particularly for punctate proteins and structures like caveolae. Micropatterns are cell-adhesive shapes that biophysically confine cell(s) to a user defined geometry which stereotype organelle …

A Review Of Video Game Effects And Uses, David Corso

Caravel Undergraduate Research Journal

Video games are versatile in their form and function. Whether they’re training doctors or offsetting Alzheimer’s disease, video games can exercise both mental and physical features, train specific skills for a number of jobs, educate players about events and phenomenon in our world, research and understand natural human processes, and they can be designed for a number of other purposes. Multiple studies have demonstrated the effects of video games on physiological and cognitive levels—positive, negative, and everything in between. This paper identifies various physical and psychological effects that video games produce, and it suggests ways in which video games can …

Effects Of Tourist Feeding On The Gut Microbiome And Ecophysiology Of Endangered Northern Bahamian Rock Iguana (Cyclura Cychlura), Erin Lucy Lewis

All Graduate Theses and Dissertations, Fall 2023 to Present

The lifespan and reproduction of an animal depends on maintaining a healthy physiology. The proportion of individuals that survive to an age at which procreation can occur is important to long-term stability of populations and contributes to species survival. Health in an animal is measured in a variety of ways, including through monitoring of the body’s physiological systems, as well as its ability to respond to invading pathogens, and through the different types of bacteria present in the gut. Relationships among those different health metrics have been discovered in recent years and have been found to play important roles in …

Biol 210: Nutrition (Syllabus), Sam Newberry Ph.D.

School of Arts & Sciences

This syllabus was developed by SUNY Geneseo Professor Sam Newberry during the spring 2026 semester.

Course Learning Objectives:

Students who are active participants and complete course requirements will be able to: 

1. Demonstrate familiarity with nutrients, their food sources, their functions, and signs and symptoms of deficiency or excess.
2. Demonstrate familiarity with biological, psychological, social and cultural factors that influence human diet and nutrition.
3. Describe and explain in class discussion and on exams the relationship between diet and health, particularly for selected public health issues.
4. Demonstrate familiarity with nutritional guidelines used in the United States, and the challenges of establishing such …

Mitochondrial Calcium Uniporter Regulates Itam-Dependent Platelet Activation, Jehiel Abigail Ajanel Gomez

Arts & Sciences Graduate Student Theses and Dissertations

Thromboembolic conditions are the leading cause of disability and death in the United States. Platelets play an important role in the pathophysiology of thrombus formation by aiding in the formation and stabilization of the clot. Central to platelet activation is cytoplasmic calcium, which increases after platelet activation through ITAM (Immunoreceptor tyrosine-based activation motif) or GPCR (G-protein-coupled receptor) receptors. Platelet mitochondria rely on cytoplasmic calcium for mitochondrial calcium influx, which is critical for ATP formation and regulation of mitochondrial reactive oxygen species. In other cells, mitochondrial calcium entry is regulated by the multimeric protein complex, mitochondrial calcium uniporter (MCU). Deletion of …

(R2135) System Dynamical Analysis For Ann-Based Numerical Solutions Of A Compartmental Model: A Bio-Mathematical Model Of Drug Diffusion Through The Compartments Of Blood And Tissue, Rakesh Kumar, Sudarshan Dhua

Applications and Applied Mathematics: An International Journal (AAM)

This paper provides a considerably efficient numerical approach to acquire the solutions of a biomathematical model administrating oral and intravenous distribution of pharmaceuticals in the human body. The proposed numerical approach based on an artificial neural network is employed to extract numerical solutions for a detailed set of ordinary differential equations and analyze the change in concentration of drug diffusion via the compartments of blood and tissue medium. We primarily focus on analyzing three different models established on the diffusion process, exercising laws of mass action and Fick’s principle. In this work, the existing model is reformulated as an optimization …

The Science Of Sound: Studying The Cognitive, Emotional, And Physiological Effects Of Frequency, Genre, And Music, Jett Yarborough

Senior Honors Theses

Music influences emotion, physiology, and cognition, yet little is known about how the frequency it is tuned to affects these influences. Prior research has shown that music tuned to 432 Hz can reduce stress, lower blood pressure, and improve sleep. My colleagues and I conducted two studies to investigate this. Our research found that music tuned to 432 Hz promotes a significant increase in memory retention and induces a state of focus and relaxation. These results suggest that shifting from the standard tuning frequency of 440 Hz to 432 Hz could have a profoundly positive impact on our daily lives. …

Examining Light-Circadian Interactions In Regulation Of Amyloid Plaque Pathology, Melvin William King

Arts & Sciences Graduate Student Theses and Dissertations

Circadian disruption has long been appreciated as a downstream consequence of Alzheimer’s Disease in humans. However, an upstream role for circadian disruption in regulating AD pathology remains an open question. The mammalian circadian system is hierarchical, with cellular clocks – driven largely by BMAL1 – synchronized by the hypothalamic SCN (suprachiasmatic nucleus) via a combination of hormonal and synaptic cues. To assess the relative contributions of each component to Alzheimer’s Disease pathology, we crossed mice harboring either microglial (Cx3cr1/Lyz2-Cre) or GABAergic (VGAT-iCre, expressed in more than 95% of the SCN) BMAL1-knockout to mouse models of Aβ aggregation (5xFAD; APP/PS1-21), which …

Psilostachyin B As Potential Immune Checkpoint Inhibitor Targeting Ctla-4 And Pd-L1 In The Development Of Cancer Immunotherapy: A Computational Investigation, Moh Dliyauddin, Nabila Shafa Yumna Salsabila, Noviana Dwi Lestari, Sapti Puspitarini, Mansur Ibrahim, Sri Rahayu, Muhammad Sasmito Djati, Muhaimin Rifa’I

Karbala International Journal of Modern Science

Immunotherapy is a promising treatment approach by targeting immune checkpoints such as CTLA-4 and PD-L1 to overcome cancer progression. The utilization of Curcuma longa and Phyllanthus niruri as potential immune checkpoint inhibitors offers an alternative cancer therapy. Computational analyses including molecular docking and molecular dynamics with validation using Molecular Mechanics/Poisson-Boltzmann Surface Area (MM-PBSA), Dynamic Cross-Correlation Matrix (DCCM), and Principal Component Analysis (PCA), were performed in this study. Results show that Psilostachyin B is the most promising inhibitor candidate against CTLA-4 and PD-L1, with binding affinity values of -6.9 and -6.8 kcal/mol, respectively. Molecular dynamics simulation results indicated that Psilostachyin B …

Neurophysiology And Endocrine Responses To Hunger And Satiety Mechanisms: The Brain-Gut Crosstalk, Nour Shakir Rezaieg, Muthanna M. Awad

Karbala International Journal of Modern Science

Background: Obesity is a main public health problem which substantially increases the risk of many diseases. The complex neural circuitry controls energy homeostasis and food consumption by the incorporation of hormonal and neural signals. Circulating hormones, in specific the gut hormones, have been found to be very important in appetite regulation. These hormones transfer energy situation signs to the brain throughout three principle paths: the circulation system, activation of the vagus nerve, and direct modification of main brain regions such as the hypothalamus and brainstem. The control of food eating is not exclusively dependent on the homeostatic processes, rather it …

The Impact Of Growth Hormone-Releasing Hormone Antagonist On Human Adipose-Derived Stem Cells, Jeanne Michelle Dugas

Master's Theses

Obesity is a condition that affects over 40% of American adults and contributes to numerous preventable health issues. This condition is caused by increased adipose tissue, which forms when stem cells transform into adipocytes. Mesenchymal stem cells, including human adipose-derived stem cells (hASC), are multipotent with the ability to differentiate into adipocytes, osteocytes, or chondrocytes. Many factors affect this transformation, including the peptide growth hormone-releasing hormone (GHRH). The main role of GHRH is to trigger the release of growth hormone, but it has also been found to play an important role in adipocyte metabolism. We expect that if the differentiation …

Computational Design Of Potent Sirna For Braf Oncogene Silencing For Enhancing Cancer Therapy, Muhammad Hermawan Widyananda, Ricadonna Raissa

Karbala International Journal of Modern Science

The discovery of oncogenic BRAF mutations has prompted the development of inhibitors, yet resistance remains widespread. A more effective strategy involves targeting BRAF mRNA with siRNA to overcome resistance to BRAF inhibitors. This study aims to design potent siRNA for BRAF oncogene silencing using a computational approach. The full coding sequence of BRAF was retrieved from the NCBI database and potential siRNAs were predicted using the Ui-Tei, Reynolds, and Amarzguioui rules. Identified siRNAs were further analyzed using various prediction systems and parameters, including their interaction with the hAgo2 protein. The results identified that seven siRNAs (siRNA 23, siRNA 24, siRNA …

The Effects Of Pfos Exposure On Zebrafish Dopaminergic Neurodevelopment, Allison G. Fletcher

Departmental Honors & Graduate Capstone Projects

Per- and polyfluoroalkyl substances (PFAS) are a group of environmental contaminants that cause disruptions to the nervous and endocrine systems. Perfluorooctanesulfonate (PFOS) is considered one of the most disruptive PFAS to the nervous system, and may disrupt neurodevelopment of the dopaminergic system, which has been linked to neurodevelopmental disorders like Attention Deficit/Hyperactivity Disorder (ADHD) in humans. I hypothesized that early life PFOS exposure disrupts the development of the dopaminergic system. To test this hypothesis, I exposed zebrafish to 0.05, 0.5, and 5.0 mg/L PFOS through 5 days of embryonic and larval development. To assess acute effects of PFOS on the …

Engineering An In Vitro Hipsc-Derived Cardiac Tissue Construct For Regenerative Medicine Applications, Larry Mendoza

Electronic Theses, Projects, and Dissertations

Cardiovascular disease is the leading cause of mortality across the world with invasive surgeries and pharmaceutical intervention commonly associated with urgent care. Moreover, congenital, progressive, and hereditary heart diseases rely on many forms of medical prevention and intervention (pharmaceuticals, x-rays, bloodwork, etc.). Developing a three-dimensional (3D) cardiac tissue engineered in vitro model to study human cardiac physiology can revolutionize biomedical research. The purpose of this research is to optimize natural & synthetic biomaterials to fuse cardiac stem cells and synthesize a 3D-printed in vitro model for disease modeling, drug delivery, and regenerative medicine. Natural biopolymers needed for such innovations are …

Progression Of Electrophysiological Impairments In Diabetic Cardiomyopathy And Intervention Using Enicostemma Axillare, Victor Arokia Doss, Dharaniyambigai Kuberapandian

Turkish Journal of Biology

Earlier studies widely reported advanced ventricular impairments only at the later stages of diabetic cardiomyopathy (DCM). The present study aimed to understand the duration-based early to late stages of cardiac electrophysiological impairments using electrocardiography (ECG) and intervention using Enicostema axillare subsp. littorale. The experimental rats were streptozotocin (SZ)-induced diabetic rats that were administered E. axillare formulations as follows: (1) normal; (2) SZ - 40 mg/kg, single, i.p.); (3) SZ + insulin (2 U/day) + losartan (10 mg/kg); (4) SZ + insulin + losartan + E. axillare decoction (2 mL/day); (5) SZ + E. axillare decoction; (6) SZ + E. axillare …

Effects Of Hyperglycemia In Cognition And Sex, Erin E. Mcdonald

Senior Honors Theses

An empirical study tested the effects of Type 1 Diabetes (T1D) on cognitive function in a hyperglycemic mouse model. Strong correlations between mental illnesses, such as major depressive disorder, neuropathologies like Alzheimer’s disease, and diabetes suggest comorbid pathology. Considering the prevalence of both T1D and cognitive decline within the general population, the findings were relevant and aimed to identify early signs of cognitive decline in diabetic patients. Behavioral tests and immunohistochemical staining were utilized to determine the cognitive function of the mice, revealing decline or deterioration caused by hyperglycemia. Data gathered from the hyperglycemic or control mice were analyzed based …

Understanding Strain-Level Dynamics In Gut Commensal-Pathogen-Host Interactions, Anna Louise Deveaux

Arts & Sciences Graduate Student Theses and Dissertations

The human gut microbiome is a consortium of trillions of bacteria, archaea, fungi, and viruses that colonizes the gastrointestinal tract and promotes health under homeostatic conditions. This microbial community trains the immune system, modulates inflammation and anticancer immunity, promotes cardiometabolic health, enables nutrient extraction, and prevents pathogen overgrowth. The latter function manifests through colonization resistance, in which microbes occupy spatial and nutritional niches thereby excluding pathogens from the community entirely, and through limiting pathogen population growth if colonization occurs. These roles are facilitated by complex host-microbe and microbe-microbe interactions that underlie differences in susceptibility to microbiome-mediated infectious diseases. The strain-level …

Therapeutic Role Of Bioactive Peptides Derived From Hemoglobin, Priya Antony Pereppadan

Dissertations

Bioactive peptides are peptide fragments derived from the proteolytic cleavage or maturation of functional proteins that have shown promising therapeutic potential in addressing major health challenges, including type 2 diabetes, hypertension, and pain management. Diabetes is characterized by high blood glucose levels due to insufficient insulin production or utilization. There are several therapeutic targets for managing diabetes, and one key target is dipeptidyl peptidase IV (DPP IV) due to its role in glucose metabolism. In hypertension, angiotensin-converting enzyme 1 (ACE1) is critical for regulating blood pressure by forming angiotensin II, and its inhibition represents an established treatment strategy. Additionally, the …

Analysis Of Kcnj2 Variants Associated With Wolff-Parkinson-White Syndrome, Elaine Vanterpool, Kerenlaime Bautista

Student Posters

Wolff-Parkinson-White (WPW) syndrome is a cardiac disorder characterized by an accessory electrical pathway, leading to tachycardia and arrhythmias. It is diagnosed via electrocardiogram (ECG), showing a shortened PR interval and delta wave. WPW is typically managed with medications, catheter ablation, or surgery. Although primarily caused by anatomical anomalies, emerging research suggests genetic factors, including ion channel mutations, may contribute to the condition. The KCNJ2 gene encodes an inward-rectifier potassium channel critical for cardiac excitability. Mutations in KCNJ2 are linked to Andersen-Tawil syndrome, a disorder featuring arrhythmias and muscle weakness, raising questions about its role in WPW. This study investigates whether …

Ai-Infused Discussion Boards: Enhancing Engagement, Reflection, And Academic Integrity In Anatomy And Physiology Education, Wade Dauberman

Teaching Repository of AI-Infused Learning

This paper presents the design, implementation, and evaluation of an AI-infused discussion board assignment that promotes ethical AI engagement, enhances student learning in anatomy and physiology, and addresses academic integrity concerns in higher education.

Using An Ecological And Cultural Lens To Examine The 1st Year Persistence And Science Identity Development Of At-Risk Biology Students Experiencing Multiple Equity-Minded High Impact Practices, Aura Fajardo Grandidge

Open Access Dissertations

In this study, I used an ecological and a cultural perspective to examine the first-year experiences of two cohorts of biology students exposed to multiple equity-minded High Impact Practices (HIPs) designed to promote their persistence and science identity development.

In chapter 1, I applied Graham et al.’s Persistence Framework (2013) and Bronfenbrenner’s Ecological Systems Theory (1977) to investigate the bridges and barriers to persistence that biology students face while experiencing either an equity minded learning community, a first-year seminar, a course-based research experience, and/or an active learning introductory biology course. Using a mixed methods approach that focused on phenomenology, I …

Investigation Into The Effect Of Aspartame On The Expression Of P53 And Bax In Mouse Stomach Tissue, Angelique Cheryl, Aoife Mac Cooey

SURE Journal: Science Undergraduate Research Experience Journal

Introduction: The recent reclassification of aspartame as a Group 2B hazard by the International Agency for Research on Cancer, along with studies suggesting links to cancer, has raised concerns and prompted further investigation. Evidence suggests that aspartame exposure may alter p53 and BAX gene expression, affecting apoptosis in cancer cells. This study aims to examine how aspartame exposure affects p53 and BAX gene expression in normal mouse stomach tissue, shedding light on cellular stress and apoptosis mechanisms.

Methods: Mice were sacrificed, and stomach tissue was excised and divided into control and treatment groups. RNA extraction was carried out in the …

Evaluating Uv-Protective Low-Emissivity Window Films: Implications For Thermal And Visual Comfort In Luminous Office Buildings, Lina M. Shaker

AUIQ Complementary Biological System

This review article explores the integration of thin window films and solar energy systems to enhance thermal comfort in luminous office buildings. Luminous office buildings, which prioritize natural lighting, often face challenges in maintaining thermal comfort for occupants. By integrating solar energy systems, such as photovoltaic (PV) and solar thermal systems, with thin window films, it is possible to optimize thermal comfort while harnessing sustainable energy sources. Thin window films act as a barrier against solar radiation, reducing heat gain while allowing therapeutic blue light (400-520nm) transmission. The advantages of thin window films include improved thermal insulation, glare reduction, and …

Ophidiomyces Ophidiicola And Texas Snakes: A Field To Bench Study Of Ophidiomycosis, Kenlynn L. Volz

Biology Theses

Ophidiomyces ophidiicola (Oo), the primary cause of Ophidiomycosis, is a fungal pathogen recently detected in Texas snakes. Prior to this study, there were major knowledge gaps regarding Oo growth, spread, and suitable environmental conditions. This study filled those gaps using a field to bench approach involving sampling snakes across Texas, in vitro fungal growth, and ecological niche modeling. 103 snakes were sampled across Texas in 2023 and 2024 and six cases of Oo infection were detected. Results of the growth experiment suggest that Oo prefers more stable temperatures and high humidity to a point and that there is a …

The Effects Of High Fat Diet On Lipid Deposition In Skeletal Muscle, Alexander Huss

Theses and Dissertations

By the year 2030, almost 50% of adults in the United States are expected to be obese. Obesity has been shown to increase the risk of several chronic metabolic diseases, several cancers, and is associated with impaired skeletal muscle function and metabolism. Despite this, little it is known about the role of altered muscle lipid homeostasis, lipid droplet dynamics, and lipid droplet-mitochondrial interactions in contributing to muscle dysfunction in obesity. Therefore, we sought to investigate the impact of high-fat diet induced obesity on overall skeletal muscle lipid deposition, intramyocellular lipid droplet content and morphology, and lipid droplet-mitochondrial contact. Male C57/BL6 …

Corneal Epithelial Tissue Engineering Approaches To Treat Limbal Stem Cell Deficiency, Sasirekha K

Theses and Dissertations

A clear healthy cornea is essential for visual acuity. As a self-renewing and regenerating tissue, the corneal epithelium has a stem cell pool, the limbus that acts as its proliferative reservoir. When limbal epithelial stem cells are destroyed or become dysfunctional, a pathological state known as limbal stem cell deficiency (LSCD) manifests. Damaged corneas have been successfully reconstructed by transplanting the cultured limbal epithelial stem cells. Limbal stem cell transplantation (LSCT) is one of the applicable and most challenging procedures in clinical ophthalmology for the reconstruction of the stratified ocular surface epithelium in patients with LSCD. Given the above challenge, …

The Role Of An Ultraconserved Long Non-Coding Rna In B-Cell Lymphomagenesis, Swati Mohapatra

Dissertations and Theses (Open Access)

Ultraconserved regions (UCRs) are genomic segments with perfect (100%) conservation between the orthologous regions of human, rat, and mouse genomes. UCRs can be transcribed into mono-exonic long non-coding RNAs (lncRNAs) known as transcribed ultraconserved regions (T-UCRs). These regions, despite lacking protein-coding potential, are increasingly recognized for their regulatory roles in gene expression, including the modulation of non-coding RNA (ncRNA) transcripts. NcRNAs play crucial roles in cellular processes, including oncogenic transformation, with emerging evidence revealing their ability to encode small peptides known as ncRNA-encoded peptides (ncPEPs). These peptides, originating from small open reading frames (smORFs), contribute to diverse cellular functions and …

Effects Of Hypoxia On Monocyte Differentiation And Macrophage Specification During Ischemic Heart Injury, Farid Faridovich Kadyrov

Arts & Sciences Graduate Student Theses and Dissertations

Myocardial infarction (MI) occurs following cessation of blood flow to an area of the heart and leads to ischemia, cardiomyocyte death, and inflammation. Chronically, MI initiates a compensatory process referred to as left ventricular remodeling, which is characterized by cardiomyocyte hypertrophy, fibrosis, and a decline in heart function. Left ventricular remodeling is central to the pathogenesis of heart failure. During myocardial infarction, Ly6chigh CCR2+ monocytes enter the heart and differentiate into a variety of macrophage populations including inflammatory CCR2+ macrophages. Resident cardiac macrophages are also present within the heart at homeostasis. Previous research from several groups has shown that once …

Genetic Diversity Of 1,845 Rhesus Macaques Improves Genetic Variation Interpretation And Identifies Disease Models, Jun Wang, Meng Wang, Ala Moshiri, R Alan Harris, Muthuswamy Raveendran, Tracy Nguyen, Soohyun Kim, Laura Young, Keqing Wang, Roger Wiseman, David H O'Connor, Zach Johnson, Melween Martinez, Michael J Montague, Ken Sayers, Martha Lyke, Eric Vallender, Tim Stout, Yumei Li, Sara M Thomasy, Jeffrey Rogers, Rui Chen

Faculty, Staff and Students Publications

Understanding and treating human diseases require valid animal models. Leveraging the genetic diversity in rhesus macaque populations across eight primate centers in the United States, we conduct targeted-sequencing on 1845 individuals for 374 genes linked to inherited human retinal and neurodevelopmental diseases. We identify over 47,000 single nucleotide variants, a substantial proportion of which are shared with human populations. By combining rhesus and human allele frequencies with established variant prediction methods, we develop a machine learning-based score that outperforms established methods in predicting missense variant pathogenicity. Remarkably, we find a marked number of loss-of-function variants and putative deleterious variants, which …