Biology Commons^™

Cultivating Curiosity Across Academic Audiences: Biology And Evidence-Based Science Communication, Nathan D. Forbes

Whittier Scholars Program

Effective Science Communicators must speak to a variety of audiences, with varying quantities of prior interest and qualities of background knowledge. The purpose of this paper was to engage differing audiences in scientific learning. This was done through a hypothetical newsletter made up for four different segments exploring a variety of topics in biology. Each segment intends to speak to a different audience with a different level of interest and/or educational level. Simplifying or analogizing without sacrificing the statistical basis of this project was of paramount importance. In the two segments targeted towards younger audiences, the primary focus was on …

Pepper Spray Exposure And The Effect On Dna Profiling Of Blood, Brandon Schmakel

Honors Projects

Pepper spray is a common self defense tool used in both law enforcement and civilian settings, with the goal of incapacitating the sprayed individual. In real casework where pepper spray was used, a red-brown stain which tested positive presumptively for blood provided no DNA profile after further testing six months later. A previous graduate student, Emma Crawn, attempted to emulate these casework conditions and instead achieved a DNA profile with slight indications of inhibition or degradation. Further analysis of active pepper spray ingredients such as Oleoresin Capsicum (OC) and Chloroacetophenone (CN) reveals that there are observed reactions, such as oxidation, …

High Performance Ae-Cnn Model Enhanced Via Gaussian Augmentation For Rssi-Dependent Indoor Positioning In Wireless Sensor Networks, Kahlaa K. Al-Nassrawy, Ghaidaa A Al-Sultany

Karbala International Journal of Modern Science

Precise indoor positioning system remains a significant challenge within Wireless Sensor Networks (WSNs) due to the instability and noise sensitivity of Received Signal Strength Indicator (RSSI) data. This paper proposes an advanced hybrid deep learning framework designed for 2D indoor localization, utilizing RSSI measurements to predict human or object position. Furthermore, to enhance the robustness of the model against signal variance and promote its generalization capability under this uncertainty, a data augmentation strategy is applied using three methods: Gaussian Noise Injection (GNI), Gaussian Mixture Model (GMM), and Bayesian Gaussian Mixture Model (BGMM). The purpose of data augmentation is to simulate …

Parasite Prevalence In Local Grasshopper Populations, Lucia B. Freund, Ali Gronquist

Research & Creative Achievement Day

Spur-throated grasshoppers (genus Melanoplus) are a common agricultural pest in North America. Spur-throated grasshoppers are also a common host to several parasitic organisms. Horsehair worms (phylum Nematomorpha) are parasitic organisms known for their ability to manipulate the behavior of its insect host, particularly grasshoppers and crickets, by urging the host to enter water so it can complete its life cycle. Along with being a host to parasitic worms, they are a frequent target of grasshopper mites. Grasshopper mites (Eutrombidium locustarum) is a short-lived parasite that can negatively influence the reproductive ability of their host. Because grasshoppers are a major agricultural …

Characterization Of Bacteria In Cattle Specimens, Jacob D. Hanson, Josie M. Tieskoetter

Research & Creative Achievement Day

Cattle nasal cavities provide a favorable environment for microbial colonization and can habit a wide population of bacteria, including opportunistic and pathogenic species. The objective of this research was to isolate, characterize, and identify bacteria present is nasal swap specimen collected from multiple calves. Samples were cultured and analyzed using selective and differential media, Gram staining, spore staining, and a range of biochemical assays. Several bacterial species were identified including the genus Corynebacterium and Streptococcus while some isolates could not be identified using classical biochemical methods alone. These results demonstrate that calf nasal specimens commonly contain diverse bacterial populations, some …

The Effects Of Oleuropein In Olive Leaf Extract Alone Or Combined With Calcitriol On The Viability And Migration Of Human Endometrial Cells In Vitro, Katelyn Devereaux

Electronic Theses and Dissertations 2020 - Present

Endometriosis is a chronic inflammatory disease affecting approximately 10% of reproductive-aged women worldwide and is commonly associated with pelvic pain, infertility, and reduced quality of life. Current management strategies, including hormonal therapies and surgical intervention, often provide only temporary relief and are associated with recurrence and adverse effects. These limitations highlight the need for alternative, non-hormonal therapeutic approaches that target underlying inflammatory and cellular mechanisms of disease progression.

This study evaluated the effects of oleuropein, contained within an olive leaf extract, and calcitriol, the active form of vitamin D, on cellular viability and migration in immortalized human endometriotic epithelial (12Z) …

Cognition In Pair-Living Owl Monkeys: The Role Of Partner Affiliation In The Willingness To Cooperate To Solve A Cognitive Task, Aaron J. Mencia

Electronic Theses and Dissertations 2020 - Present

Cooperative problem-solving tasks, including the loose-string paradigm, require individuals to coordinate their actions simultaneously to obtain a shared reward. These paradigms have been used extensively to assess social cognition, behavioral coordination, and partner preferences across taxa. Although the loose-string paradigm has been widely tested, it has not been applied to pair-bonded, monogamous primates such as owl monkeys (Aotus nancymaae), which exhibit affiliative behaviors including food sharing and bi-parental care. Investigating cooperation in this species may offer some clarification on whether more stable social bonds are associated with cooperative and cognitive task success as compared to those observed in …

Modulating Acute Stress Reactivity: Behavioral Interventions And Caffeine-Linked Stress Physiology In College Students, Kaitlyn Smith

Honors Theses

College students frequently rely on caffeine to manage academic demands, yet its physiological and psychological effects on acute stress remain poorly understood. Although caffeine is known to increase cardiovascular arousal and self‑reported anxiety, little research has compared different caffeine sources within the same individuals or examined whether brief behavioral interventions can buffer these effects. Self‑affirmation, a short writing exercise centered on personal values, has been shown to reduce stress reactivity, but its interaction with caffeine‑induced arousal has not been tested. This within‑subjects study examines how coffee, energy drinks, and a no‑caffeine control influence acute cardiovascular and self‑reported stress responses, and …

Tree Resin Effects On Environmental Microbial Growth In Tetramorium Ant Colonies, Abigail Peralta, Emma Crisman

Biology Student Scholarship

No abstract provided.

Trial Of Vaginal Microbiome Transplant To Prevent Recurrent Bacterial Vaginosis, Grace Pierson

Biology Student Scholarship

Comparative Inhibition Testing for Personalized Microbiota Selection

This case report evaluates a strategy for selecting optimal donor material for Cervicovaginal Secretion (CVS) transplantation. To identify a suitable match, CVS from four healthy, Lactobacillus-dominated donors was tested against a patient’s sample to observe microbial inhibition. Theoretically, effective donor material should produce a visible inhibition zone (halo), indicating suppressed growth of pathogenic bacteria. However, initial testing yielded unreadable results with no conclusive evidence of inhibition. Consequently, my study pivoted to analyze the direct effects of donor samples on the growth of specific pathogens, Gardnerella vaginalis and Prevotella bivia.

Altered Clock Genes Affect Fly Circadian Rhythms And Rhythms Of Cell Respiration In The Brain, Connor Enestvedt, Campbell Bridges, Anna Costello, Brenda Rodrigues, Jake Antosca

Biology Student Scholarship

Drosophila have circadian rhythms which are daily biological rhythms synchronized by an internal clock. These rhythms regulate behavioral and physiological systems within their bodies. The endogenous fly clock—made of an oscillating gene-protein feedback loop found in central pacemaker cells in the brain— sets endocrine, locomotor, and metabolic rhythms to the 24-hour Earth day The central clock signals to peripheral clocks, setting measurable rhythms. Mutations to these clock genes disrupts the oscillator, resulting in rhythm changes. In this project, we will study how flies’ circadian rhythms and cell respiration in the brain changes with mutations to clock genes. By measuring oxygen …

Wheel-Running As A Window Into The Pten-Ko Neurological Clock, Jake Antosca, Campbell Bridges, Elizabeth Burke, Chris Sama

Biology Student Scholarship

The phosphatase and tensin homolog protein (PTEN) is a critical regulator of the PI3K/AKT/mTOR signaling pathway, which governs cellular growth and metabolic balance. Mutations in the PTEN gene are strongly linked to macrocephaly and Autism Spectrum Disorder (ASD) in humans. While PTEN deficiency is known to cause neuronal hypertrophy and metabolic stress, its impact on the< endogenous circadian clock, the internal timing system that regulates daily physiological cycles, remains poorly understood. Proper circadian function is vital for metabolic homeostasis, which may be dysregulated in PTEN-deficient models.

In this poster, we compare PTEN conditional knockout mice with CRE controls to test whether PTEN-related cerebellar dysfunction alters entrainment to a light-dark cycle, free-running period in constant conditions, and food-anticipatory activity in age-matched animals between approximately 130 and …

Characterizing The Functional Diversity Of Rocky Intertidal Environments Of Southern New England, Hailey Arman

Biology Student Scholarship

Tidal pools are a diverse ecosystem that are home to a wide range of important species that support our environment and marine habitats. Tidal pools along the New England coastline have been greatly affected by human activity, through direct contact with humans, as well as the increasing effects of climate change. Adapting the protocols from UC Santa Cruz Multi-Agency Rocky Intertidal Network (MARINe) and the National Park Service Northeast Temperate Network’s (NETN), we set up multi-year plots to track abundances intertidal species throughout Rhode Island. Ultimately, by gaining a better understanding of how these systems change over time, we can …

Advancing Early Detection Of Diabetic Retinopathy At Clínica Esperanza/Hope Clinic, Rachel Burke

Biology Student Scholarship

No abstract provided.

Clec7a Deficiency Affects Cerebellar Microglia Development And Purkinje Cell Axon Myelination, Olivia Barbarini, Grace Belt, Lauren Bedford, Julia Carson, Kayla Fordyce, Michael Martinez, Lindsay Walsh

Neuroscience Program Student Scholarship

No abstract provided.

Exploring How Light Source Influences Bluegill Positioning And Behavior, Anthony Aldana Mendez

Biology Student Scholarship

No abstract provided.

Image Analysis Of Pupal Sex Ratio In Honey Bee Hives, Anna R. Tattelman, Grace E. O’Brien

Biology Student Scholarship

No abstract provided.

Wild Bee Foraging And Movement Behavior In Urban Gardens, Claire Crowther, Maggie Ritchie

Biology Student Scholarship

No abstract provided.

Studies On The Contribution Of Osh6 To The Functions Of Late Endosomes, William King

Theses and Dissertations

The late endosome (LE) is a hub organelle connecting endocytic, biosynthetic, exocytotic, and autophagic vesicle traffic pathways. Malfunctions of LEs are associated with multiple age dependent diseases such as Parkinson’s disease (PD). Despite this significance, how cells refurbish lipids and proteins to LEs to maintain their sustained activities are not clear. Previous studies in the model organism budding yeast show that up-regulation of a lipid transporter Osh6 (PERG6-OSH6) accumulates phosphatidylinositol-4-phosphate (PI4P) on the trans-Golgi network. It also promotes vacuole fusion and maintains the robustness of vacuoles in aged cells. Since LEs are the organelle between the TGN and vacuoles in …

Single-Walled Carbon Nanotube-Mediated Plasmid Dna Delivery In The Model Monocot Brachypodium Distachyon, Kaya İşleyen Bi̇lge, Bahar Soğutmaz Özdemi̇r

Turkish Journal of Biology

Background/aim: Plant genetic engineering is a valuable approach for improving stress tolerance, crop productivity, and quality traits. However, its progress is limited by the drawbacks of traditional transformation methods. Commonly used techniques, such as Agrobacterium-mediated transformation and biolistics, are restricted by genotype dependency, lengthy tissue culture steps, and low efficiency, particularly in monocot species. Therefore, the development of alternative gene delivery strategies remains an ongoing research focus in plant biotechnology. Nanoparticle-based delivery systems have recently gained attention due to their physiochemical properties, biocompatibility, and potential for alternative gene delivery approaches in plant systems.Materials and methods: We investigated the use of …

Combinatorial Effect Of Epirubicin And 5-Fluorouracil In The Treatment Of Temozolomide-Resistant Glioblastoma Cells, Mehrsa Bayat, Muhli̇s Akman, Türker Kiliç, Ti̇muçi̇n Avşar

Turkish Journal of Biology

Background: Glioblastoma (GBM) is a highly aggressive form of brain tumor characterized by rapid proliferation and invasiveness. It is associated with a poor prognosis due to acquired resistance to temozolomide (TMZ). In this study, we investigated whether a combination of epirubicin, 5-fluorouracil (5-FU), and TMZ could improve TMZ sensitivity in resistant GBM cells and help overcome resistance.Materials and methods: TMZ resistance was established in the U87MG cell line. The MTT assay was used to measure cell viability. Reactive oxygen species (ROS) and apoptosis were measured using flow cytometry. RNA-seq was used to evaluate genomic changes based on treatment with drugs …

Ultrasound-Assisted Enzymatic Extraction Improves The Antiinflammatory Activity Of Red Dragon Fruit Peel Pectin, Bao Le, Seung Hwan Yang, Hoang Dang Khoa Ta

Turkish Journal of Biology

Background/aim: Inflammatory bowel disease is a chronic inflammatory disorder characterized by excessive immune activation, primarily mediated by nitric oxide and proinflammatory cytokines. This condition encompasses ulcerative colitis and Crohn’s disease, both of which significantly impair patients’ quality of life and pose persistent challenges in clinical management. Pectin, a complex carbohydrate found in plant cell walls, has shown promise in reducing inflammation. Materials and methods: In this study, pectin was extracted from red dragon fruit peel using two methods: ultrasound-assisted extraction and ultrasound-assisted enzymatic extraction. The structural characteristics and antiinflammatory effects of the extracted pectin were evaluated in lipopolysaccharide-stimulated RAW 264.7 …

Modulating Microtubule Stability Via Α-Tubulin Acetylation Partially Restores Golgi Fragmentation In Spinal Muscular Atrophy, Peli̇n Zobaroğlu Özer, Memet Gözüböyük, Özge Çeti̇n, Niko Hensel, Güzi̇n Emecen, Adam Malik, Melissa Bowerman, Peter Claus, Hayat Erdem Yurter, Gamze Bora Akoğlu

Turkish Journal of Biology

Background/aim: Spinal muscular atrophy (SMA) is a neurodegenerative disease caused by the loss of survival of motor neuron (SMN) protein. SMN deficiency leads to perturbations of the cytoskeleton, including microtubules, which are mainly involved in motilityrelated cellular processes. However, the molecular mechanisms of microtubule dysregulation in SMA remain elusive. Alpha (α)-tubulin is a structural component of microtubules, and its posttranslational modifications affect microtubule dynamics. Here, we aimed to investigate α-tubulin acetylation and related molecular mechanisms in SMA. Materials and methods: Two different SMA mouse models, the Drosophila melanogaster model and patient-derived fibroblasts, were used in the study. Western blot and …

Ankrd2 May Alleviate Denervation-Induced Skeletal Muscle Atrophy By Inhibiting Inflammation, Yalin Zhang, Lin Zhang, Li Li, Liqin Zhang, Li Zeng, Jiaying Qiu, Zhengrong Xi, Wenwen Wang

Turkish Journal of Biology

Background/aim: Sciatic nerve injury causes a loss of skeletal muscle innervation, reduced motor function, and eventual muscle atrophy. Inflammation and increased protein degradation are key factors contributing to muscle atrophy. Inflammation is activated early during muscle atrophy and can be modulated by various factors. However, the precise role of inflammation in denervation-induced muscle atrophy remains unclear. Materials and methods: Transcriptome sequencing was used to determine that the inflammatory response occurs early during denervation-induced muscle atrophy. RT-qPCR validation of several inflammatory factors showed rapid upregulation at early stages, followed by gradual downregulation. Weighted gene coexpression network analysis of differentially expressed genes …

Unusual Rna Polymerase Ii Patterns In Meiotic Prophase I In Nannospalax Xanthodon: Insights Into Chromatin, Telomeres, And Sex Chromosomes, Sergey N. Matveevsky, Ferhat Matur, Faruk Çolak, Andrei Kandaurov, Mustafa Sözen, Svetlana V. Pavlova, Oxana Kolomiets

Turkish Journal of Biology

Background: Meiotic transcription is a highly regulated process involving stage-specific chromatin remodeling and dynamic RNA polymerase II (RNAPII) activity. Nevertheless, our current understanding is largely based on classical model organisms, while many nonmodel mammals remain unexplored. This study investigates the transcriptional dynamics and chromatin features during meiotic prophase I in Nannospalax xanthodon, a subterranean blind mole rat species with extensive intraspecific karyotype variation.Materials and methods: Using immunofluorescence, we analyzed synapsis and transcriptional activity in spermatocyte nuclei of two geographically distant N. xanthodon males, detecting SYCP3, CREST, γH2AFX, and phosphorylated RNAPII (Ser5, Ser2). Telomereassociated proteins RAP1 and TERT were also examined …

Protective Effect Of Pinocembrin On Zearalenone-Induced Hepatotoxicity Via Pi3k/Akt And Nrf2 Signaling In Albino Mice, Sujatha Tejavat

Turkish Journal of Biology

Background/aim: Zearalenone (ZEA) is a Fusarium-derived mycotoxin that frequently contaminates food and feed and induces hepatotoxicity in humans and animals through oxidative stress and inflammation. Pinocembrin (PCM), a naturally occurring flavonoid, has potent antioxidant and antiinflammatory properties. This study investigated the hepatoprotective effects of PCM against ZEAinduced liver injury in albino mice, with a focus on the nuclear factor erythroid 2–related factor 2 (NRF2) and phosphoinositide 3-kinase/protein kinase B (PI3K/Akt) signaling pathways. Materials and methods: Twenty-four albino male mice were allocated into four groups: (1) control (vehicle 0.05% dimethyl sulfoxide), (2) ZEA-treated (40 mg/kg body weight), (3) PCM-treated (50 mg/kg …

Skin Pattern As A Potential Monitoring Tool For Frog Populations, Lídize Sagarnaga Rivera, Virginie Rolland Dr., Lorin Neuman-Lee Dr.

Create@State

Skin pattern as a potential monitoring tool for frog populations

Population monitoring, which requires identifying individuals, is crucial for species conservation. Common techniques involve marking, which can harm animals and alter their behaviors. Natural markings are an alternative not yet explored for amphibians. Yet, the traditional method with elastomers (fluorescent implants) is invasive and not completely reliable—the tag may become lost or hard to see. The American green tree frog (Dryophytes cinereus) possesses naturally occurring and distinct golden dots on their dorsal side.  Therefore, we aim to assess whether patterns of golden dots on the skin of green …

Amyloid Beta-42 Neurotoxicity In Drosophila Retinal Development, Shay O. Sims, Pierce Duncan, Malachi Abon, Jacob G. Smith

Create@State

Alzheimer's disease (AD) represents one of the most prevalent neurodegenerative disorders globally. Thus far, the underlying mechanisms associated with the pathogenesis of AD are innately elusive. Two hallmarks associated with the progression of AD exist, including Amyloid-Beta 42 (Aβ42) protein plaque formation and hyperphosphorylation of tau proteins in neurons. Amyloid-beta is known to concentrate with other neuronal proteins as complexes form, including the cytoskeletal protein actin. However, whether actin contributes to neuronal decline in AD is unknown. To further understand the cellular cascades associated with AD, we investigated the role of cytoskeleton dynamics in modulating oxidative stress and neuroinflammation within …

Variation In Infection Prevalence Of Splendidofilaria Pectoralis Across Alaskan Grouse Populations, Anahi Garcia Valdez, Diego Martinez

Create@State

In recent years, rapid climate change has altered species distributions worldwide and influenced parasite transmission dynamics in wildlife systems. Parasite infections play an important role in shaping patterns of disease distribution across species and populations. Understanding variation in infection prevalence across geographic regions and host demographic groups is essential for interpreting these patterns. Splendidofilaria pectoralis is a filarial nematode that infects the connective tissues of grouse (Aves: Tetraonini) in Alaska and has been moving northward as the climate warms. However, relatively little is known about the variation in prevalence of the nematode across geography and demography. This project examines variation …

Inc3vits Model: A Hybrid Architecture To Accelerate And Reduce Complexity For The Deepvariant Model For Variant Calling, Mustafa Al-Saffar, Sura Z. Al Rashid

Karbala International Journal of Modern Science

Deep learning has revolutionized genomic variant calling, yet the computational cost of current systems continues to limit scalability. We present a controlled efficiency study of DeepVariant-style pileup architectures under identical training and inference conditions, comparing architectural downsizing with a hybrid CNN–local attention design. Inc3ViTs pairs a streamlined InceptionV3 stem with a lightweight local attention head based on patch tokenization and windowed self-attention, enabling a direct comparison with a CNN-only reduced Inception baseline. Across whole-genome and whole-exome short-read datasets, Inc3ViTs reduces training time by ~40–50% and reduces inference runtime relative to the original DeepVariant. The CNN-only baseline indicates that most speedups …