Biology Commons^™

Assessing Knowledge, Attitudes, And Practices Regarding Refractive Errors And Spectacle Wear Among Children In Sana’A: A Cross-Sectional Study, Tariek Aldoais, Zakarya Rageh, Khaled Al-Hemyari, Saleh Altheeb, Abdulmogni Al-Barrag, Mahfouth Bamashmus

AUIQ Complementary Biological System

Background: Understanding the knowledge, attitudes, and practices (KAP) regarding refractive errors and spectacle use is essential for promoting eye health and effective vision correction, especially in children.

Objective: This study assessed the demographic characteristics, knowledge, attitudes, and practices of participants concerning refractive errors and spectacle use, focusing on correlations influencing these factors.

Methods: A cross-sectional study of 228 participants analyzed demographic data, duration of glasses use, and responses to a structured questionnaire on KAP related to refractive errors and spectacles.

Results: Among participants, 53.1% were female, and 45.2% were aged 8–13 years. Glasses use for 1–3 years was reported by …

Achievement Goals And Burnout In Pre-Health Profession Undergraduate Students, Jamie Jensen, Hunter Nelson, Grant Rousseau, Kenneth Harrington, Isaiah Aduse-Poku, Alexis Call, Tanner Brown

ScholarsArchive Data

These are survey results of BYU undergraduates who are enrolled in pre-health programs. We assessed their Achievement Goal Orientations and their feelings of Burnout.

The Investigation Of Lateral Foraging Patterns In Fin And Sei Whales, Alex Eschmann

Theses - ALL

Lateralization is the specialization that enhances an organism’s survival by dedicating specific tasks to the hemispheres of the brain, strengthening neural pathways to enhance speed and dexterity of task performance. First described in humans in 1861, lateralization has also been observed in non-human organisms where it often plays a critical role in predator-prey dynamics. Lateralized behaviors for prey foraging, social interactions, and communication have been described in some species of marine mammals from across all three distinct taxonomic orders. In the Order Cetacea, toothed and baleen whale species exhibit lateralized foraging behaviors for prey capture. In this study, I investigated …

Temporal Assessment Of Fish Communities In A South Central Plains Ecoregion Watershed, Tara L. Schnelting

ATU Theses and Dissertations 2021 - Present

Among South Central Plains ecoregion fish communities, there is limited knowledge of the importance of headwaters yet this information is needed to understand their role in fish communities. I addressed this gap by assessing seasonal changes in fish communities in headwater streams of the Moro Creek watershed, Arkansas. I conducted two studies pertaining to temporal fish community assessments: (i) utilize multi-season, community occupancy models to estimate μ (species probability), Ω (community occupancy mean), and p (detection probability) and (ii) utilize beta diversity (β) analyses to address the diversity across different scales in the headwaters of the Moro Creek …

Impacts Of Polyploidization On Endocrine Regulation And Vocalization In The Gray Treefrog Complex, Avery Thigpen

Honors Theses

Comparative genomics data suggest that vertebrates are descendants of ancestral polyploids and that historical polyploidization events fueled evolutionary innovations. For example, polyploidization can modify gene expression patterns and/or increase gene mutation rates to alter the phenotype. While considerable emphasis has been placed on the evolutionary impact of ancient polyploidization events, less is known regarding phenotypic modifications in extant polyploids. I examined circulating levels of adrenal glucocorticoids and gonadal steroids in the diploid-tetraploid gray treefrog complex to understand how polyploidization has impacted hormonal regulation. Furthermore, I examined the relationships between levels of these hormones and acoustic signals to examine if and …

Academic Burnout In Human Anatomy & Physiology I Students, Shivani Shukla

Honors Theses

Human Anatomy and Physiology I is the study of the function and structure of the human body. It is a challenging class that many students have to take for their undergraduate degree. Due to the vast information that is given in this complex class, students can struggle with understanding the material and knowing how to study thus leading to burnout in the course. Understanding why students undergo burnout in their courses could uncover ways that professors and institutions could help the students to prevent burnout. The goal of this study was to determine the level of burnout in Human Anatomy …

Understanding Temporal Changes In Leaf Traits Of Native Smilax Rotundifolia And Invasive Lonicera Japonica Using Long-Term Herbarium Records From Kentucky, Claudia Ebbecke, Claudia Ebbecke

Honors College Theses

Herbarium specimens are the most valuable, verifiable, and sustainable records to study the impacts of climate change on natural ecosystems. Temporal herbarium data can provide critical information on how species respond to changes in habitat conditions by tracking changes in species’ morphological and phenological traits. This study aims to use Japanese honeysuckle (Lonicera japonica) and common greenbrier (Smilax rotundifolia) to assess the impact of climate change on invasive and native plants. Leaf traits, such as leaf size and stomatal density are good indicators of plant’s adaptation to the changing environment. By examining changes in leaf traits …

Student Perceptions Of Supports And Barriers For Transferring Quantitative Reasoning In Introductory Biology Lab Courses, Joelle Prate, Jeremy L. Hsu

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Quantitative reasoning is a critical skill in biology and has been highlighted as a core competency by Vision and Change. Despite its importance, students often struggle to apply mathematical skills in new contexts in biology, a process called transfer of knowledge. However, the supports and barriers that students perceive for this process remain unclear. To explore this further, we interviewed undergraduate students in an introductory biology lab course about how they understand and report the transfer of quantitative skills in these courses. We then applied these themes to the Step Back, Translate, and Extend (SBTE) framework to examine student …

Depalmitoylation Regulates Metabolism And Mitochondrial Function, Sarah Lilly Speck

Arts & Sciences Graduate Student Theses and Dissertations

Tens of millions of Americans suffer from metabolic disorders, predisposing patients to cardiovascular disease, kidney disease, liver disease, infertility, and cancer. Unfortunately, the etiology of many of these diseases remains a mystery, limiting our ability to identify targets for pharmacologic therapies. Due to the relationship between altered lipid dynamics and metabolic dysfunction, we decided to study the effect of the posttranslational lipid modification, S-palmitoylation, on metabolism. S-palmitoylation is the only known reversible lipid modification for proteins, and this depalmitoylation process is catalyzed by acyl-protein thioesterases including APT1 and APT2. We hypothesized that APT deficiency in various tissues would predispose mammals …

Parental Guidance Suggested: Genetic, Epigenetic, And Environmental Factors Shape Allele-Specific Gene Regulation In Metabolic Traits, Celine Louise St. Pierre

Arts & Sciences Graduate Student Theses and Dissertations

Deciphering the “genotype to phenotype” map is a crucial goal of biology. We will not improve our ability to predict phenotypes from DNA sequences until we better incorporate epigenetic and environmental variation into our models of human health and disease. Genes are typically presumed to express both parental alleles equally, but genetic and epigenetic factors can cause one allele to function differently than the other (e.g. expressed or silenced more). These allele-specific imbalances can alter the final composition of a gene’s transcriptional product and ultimately shape phenotypes. Allele-specific effects have widespread impacts on complex traits, but how environmental signals contribute …

Pan-Cancer Universal Targets For Immunotherapy Resulted From Transposable Elements Activation, Yonghao Liang

Arts & Sciences Graduate Student Theses and Dissertations

Transposable elements (TEs) contribute to nearly half of the human genome yet have been overlooked in genomic medicines due to the stereotypic impression as “junk DNA” and technical challenges. However, studies in the last two decades demonstrated that dysregulation of the epigenome in cancer cells resurrects the cis-regulatory functions of TEs, including the promoter activities. The tumor-specific TE activation events along with the resulting tumor-specific RNA and protein molecules, provide a potential “gold mine” for identifying tumor-specific therapeutic targets for cancer treatments, including immunotherapy. Here, I present a series of works to investigate the potential of providing actionable, pan-cancer, and …

A Subset Of Senescent Myofibroblasts Orchestrates Immunosuppression In Pancreatic Cancer., Jad Belle

Arts & Sciences Graduate Student Theses and Dissertations

Pancreatic Ductal Adenocarcinoma (PDAC) is the most lethal solid malignancy with a 12% 5-year survival rate. Most tumors are detected at metastatic stages that are extremely resistant to therapy. PDAC recalcitrance is driven by a unique tumor microenvironment (TME) comprising dense collagenous fibrosis embedded with an abundance of cancer associated fibroblasts (CAFs) and infiltrating leukocytes. Preclinical studies have indicated that PDAC CAFs can have both pro- and anti-tumorigenic effects. This is likely owed to CAF phenotypic heterogeneity which was recently uncovered by single cell transcriptomics. Three major CAF subpopulations have been identified in mouse and human PDAC thus far: myofibroblastic …

Circuit-Specific Vulnerability In A Mouse Model Of Alzheimer's Disease, Samuel Brunwasser

Arts & Sciences Graduate Student Theses and Dissertations

The relationship between brainwide functional decline and accumulation of pathological protein aggregates in Alzheimer’s disease (AD) is complex and not well understood. A set of highly interconnected cortical regions known as the Default Mode Network (DMN) exhibits selective vulnerability to both functional decline and amyloid beta (Aβ) plaques in early AD. One possibility is that early Aβ accumulation in the DMN drives vulnerability. However, it is unknown whether there is something intrinsic to neuronal projections within the DMN that biases these circuits towards dysfunction. In this dissertation, I describe the development of a multisite in vivo electrophysiology pipeline for chronic …

Disrupting Nrf2-Driven Cancer Biology Through One-Carbon Metabolism Inhibition, Julius Chembo

Arts & Sciences Graduate Student Theses and Dissertations

Cancer remains a leading cause of mortality worldwide, with treatment resistance and recurrence posing major barriers to long-term survival. Despite advancements in targeted therapies, many cancers develop resistance to chemotherapy, radiation, and immunotherapy, significantly limiting their effectiveness. One key driver of therapeutic resistance is nuclear factor erythroid 2-related factor 2 (NFE2L2/NRF2), a transcription factor that regulates antioxidant responses and drug detoxification. While NRF2 protects normal cells from oxidative stress, its aberrant activation in cancer promotes tumor progression, metabolic reprogramming, and resistance to standard treatments. Alarmingly, NRF2 hyperactivation is implicated in some of the most aggressive and refractory malignancies, yet no …

Induced Cd8a Identifies Enhanced Human Nk Cell Il-15-Induced Proliferation And Metabolism And Modulates Nk Cell Activation, Celia Cubitt

Arts & Sciences Graduate Student Theses and Dissertations

Natural Killer (NK) cells are cytotoxic innate lymphoid cells that play an important role in the surveillance and elimination of virally-infected and malignantly-transformed cells. These primary effector functions are achieved by producing cytokines and chemokines which activate and recruit additional immune effectors, as well as direct cytotoxic killing via perforin and granzymes. NK cell function is tightly regulated by a balance of germ-line encoded activating, inhibitory, co-stimulatory, and cytokine receptors expressed at the cell surface. Through these activating and inhibitory receptors, NK cells recognize and kill targets without prior sensitization through the loss of self-identifying molecules such as major histocompatibility …

Mechanisms Of Mll-Rearranged Infant Leukemogenesis, Jonny Mendoza-Castrejon

Arts & Sciences Graduate Student Theses and Dissertations

Infant leukemias arise as either B cell acute lymphoblastic leukemia (B-ALL) or acute myeloid leukemia (AML) and are primarily driven by MLL/KMT2A-rearrangements (MLLr). Prior work has shown that MLLr transform fetal/neonatal hematopoietic progenitors more efficiently than adult progenitors. However, the genetics and epidemiology of MLLr leukemias present an important paradox. MLLr arise during late gestation under conditions that would seemingly favor leukemic transformation (i.e., fetal/neonatal progenitors have high proliferation rates and self-renewal). Furthermore, MLLr infant leukemias require very few cooperating mutations for transformation. Yet congenital leukemias are 10-fold less common than infant leukemias and >100-fold less common than childhood leukemias …

Expanding The Druggable Proteome By Integrating Deep Learning With Molecular Simulations To Predict Cryptic Pockets, Artur Meller

Arts & Sciences Graduate Student Theses and Dissertations

Of the protein structures deposited in the Protein Data Bank, less than half have pockets suitable for the binding of drugs. Even when proteins contain pockets in their ground state structures (e.g., the nucleotide-binding active site in myosin motors), achieving specificity remains a central challenge in drug design as many protein families share common structural motifs. Cryptic pockets are cavities absent in ligand-free experimental structures that form due to protein fluctuations in solution. They provide a means to specifically target proteins currently considered undruggable. While cryptic pockets are alluring drug targets, it remains difficult to predict which proteins will form …

Oxycodone Self-Administration Modulates Ventral Pallidal Neuron Activity And Plasticity, Jessica Tooley

Arts & Sciences Graduate Student Theses and Dissertations

Opioid use disorder is an urgent public health crisis in the United States. Over 800,000 Americans have died from opioid-related overdoses since 2000. Nearly 30% of people who misuse opioids begin with prescription oral opioids, such as oxycodone, and continue misusing to avoid the immediate aversive state of withdrawal and the persistent dysphoria associated with protracted abstinence from opioids. The persistency of these dysphoric symptoms increases the risk of relapse even after long periods of abstinence. Treatment for opioid use disorder currently consists of pharmacological opioid treatment to reduce withdrawal symptoms and behavioral counseling. However, these strategies have significant real-world …

Parapinopsin: A Photoswitchable Inhibitory Gpcr For Two-Photon Optogenetics, Bobbie J. Brown

Arts & Sciences Graduate Student Theses and Dissertations

The development of optogenetic tools has greatly advanced the capability of researchers to understand the connection between neuronal activity and behavior. Optogenetics makes use of opsins, which are light activated ion-channels, ion pumps, or G-Protein coupled receptor (GPCR-based) proteins used to regulate cellular activity. Coupled with technological advances in genetics and optical physics/microscopy, optogenetics can be used to control specific populations of cells in a time-locked, spatially specific manner. The experiments possible with optogenetics depend largely on the capabilities and limitations of the opsin used; thus, there have been continuous efforts to design and employ new opsins with a variety …

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 Role Of The Cgas-Sting Sensing Pathway In Hiv-1 And Sars-Cov-2 Infections, Jenna Eve Eschbach

Arts & Sciences Graduate Student Theses and Dissertations

Human immunodeficiency virus type I (HIV-1) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are the causative agents of two unique pandemics. For a successful replication cycle to occur, viruses need to strategically outmaneuver host cell defenses. The innate immune system is the first line of defense against viruses and other pathogens. Host pattern recognition receptors detect viral nucleic acids and initiate signaling cascades that culminate in the expression of interferon (IFN) and transcriptional upregulation of antiviral interferon-stimulated genes (ISGs). This dissertation examines the involvement of the innate immune response during early, post-entry steps of HIV-1 and SARS-CoV-2 infection. During …

Investigating Genetic Regulators Of Crystal Cell Development In Drosophila Melanogaster, Anisa Turaeva, Nyla Walbrook, Andrea Feria, Rebecca Spokony

Publications and Research

In Drosophila melanogaster, hematopoiesis produces three types of blood cells (hemocytes): plasmatocytes, lamellocytes, and crystal cells, all of which provide vital immunological activities. Crystal cells have an especially essential role in melanization, a wound reaction mediated by prophenoloxidase enzymes. This study investigates genetic regulators of crystal cell growth by RNAi-mediated knockdown of five potential genes: ACXA, ACXB, Gp210, CG4390, and Cyp4s3. We used the GAL4/UAS system to selectively silence each gene and quantify crystal cell counts in wandering third instar larvae after heat shock-induced melanization. Our findings indicate that knockdown of ACXA and ACXB resulted in higher crystal cell …

The Role Of Il-33 In Itch, Anna M. Trier

Arts & Sciences Graduate Student Theses and Dissertations

Chronic itch is associated with a broad range of medical conditions, from inflammatory skin diseases to cancer and organ dysfunction, and has a lifetime prevalence of up to 20%. Despite being common and debilitating, the cellular and molecular mechanisms that drive chronic itch are just beginning to be elucidated. Thus, therapeutic options are limited. Recent studies have identified that various pro-inflammatory cytokines can directly activate sensory neurons. This has resulted in mounting interest in the therapeutic potential of inhibiting these neuro-immune interactions. IL-33 is constitutively expressed by epithelial cells, which allows for its rapid release upon tissue damage or stress. …

Understanding Loss Of Beta-Cell Identity And Progression Of Diabetes In Polygenic Mouse Models Of T2dm, Sumitkumar Patel

Arts & Sciences Graduate Student Theses and Dissertations

Type 2 diabetes (T2DM) is caused by the complex interaction of multiple genes and environmental factors. T2DM is characterized by hyperglycemia, insulin resistance in peripheral tissues and impaired insulin secretion by the pancreas. While the decline in insulin production and secretion was previously attributed to apoptosis of insulin-producing β-cells, recent studies indicate that β cell apoptosis rates are relatively low in diabetes. In this dissertation, I investigated β-cell failure in diabetes using KK and KKAy mouse models of polygenic T2DM, which spontaneously develop hyperglycemia, glucose intolerance, glucosuria, impaired insulin secretion and insulin resistance. I found that β-cell failure in KK …

Single-Cell Analysis Of Clonal And Transcriptional Dynamics During Direct Reprogramming, Brent Biddy

Arts & Sciences Graduate Student Theses and Dissertations

Direct lineage reprogramming converts one cell type into another, a process characterized by significant heterogeneity. Single-cell genomic techniques have been instrumental in dissecting this variability, yet they often fail to preserve lineage relationships. Here, I present CellTagging, a sequential, combinatorial indexing method that enables the reconstruction of clonal history and gene expression dynamics at single-cell resolution. This facilitates the construction of multi-level lineage trees, providing insights into cellular reprogramming trajectories. We applied CellTagging to investigate direct lineage reprogramming of mouse embryonic fibroblasts into induced endoderm progenitors. Our analysis revealed two distinct reprogramming trajectories: one leading to successful conversion and another …

Investigating The Roles Of Sox10 And Etv4 In Melanocyte And Melanoma Development, Catherine Marie Newsom-Stewart

Arts & Sciences Graduate Student Theses and Dissertations

The neural crest is a transient, multipotent cell population unique to vertebrates that gives rise to diverse lineages, including craniofacial cartilage, peripheral neurons, glia, and pigment-producing melanocytes. Proper specification and differentiation of neural crest derivatives are orchestrated by tightly regulated gene regulatory networks, and disruption of these developmental programs can lead to congenital disorders and malignancies. Melanocytes, derived from the neural crest, are best known for their role in skin pigmentation but also contribute to homeostasis and specialized functions in the eye, ear, and heart. These cells produce melanin to protect tissues from ultraviolet radiation and oxidative damage, and they …

Characterizing Piezo1 Mechanotransduction In Articular Chondrocytes, Jaquelin Marlen Garcia Castorena

Arts & Sciences Graduate Student Theses and Dissertations

Osteoarthritis (OA) is the most common degenerative joint disease, affecting more than 350 million people worldwide. Along with inflammation and pain, a hallmark of OA is the degradation of articular cartilage (AC), an avascular and aneural tissue that coats and facilitates the bending of diarthrodial joints. AC withstands millions of cyclic mechanical loads annually, and chondrocytes, the only resident cells in the tissue, sense these loads through mechanically gated ion channels, including Transient Receptor Potential Vanilloid 4 (TRPV4), PIEZO1 and PIEZO2. PIEZO1 is a highly expressed calcium ion channel in chondrocytes that can be activated through mechanical loading or chemically …

Effects Of Angptl3 Deficiency On The Regulation Of Hepatic Lipoprotein Production And Lipid Metabolism, Kendall Helene Burks

Arts & Sciences Graduate Student Theses and Dissertations

Cardiovascular disease is the leading cause of death worldwide. A major treatment goal is to lower plasma lipids, especially low-density lipoprotein cholesterol (LDL), the cardinal risk factor for coronary artery disease (CAD). Patients with familial hypercholesterolemia (FH) experience early-onset CAD due to extremely high LDL. Underdiagnosis and undertreatment of FH are exacerbated by limited therapeutic options. However, one strategy has successfully lowered LDL in FH patients: Inhibition of the hepatically secreted protein Angiopoietin-like protein 3 (ANGPTL3). Despite promising clinical data, the mechanism by which ANGPTL3 inhibition lowers LDL has not been fully described. Although ANGPTL3 has been shown to modulate …

Jarid2-Mediated Reprogramming Of Human Hematopoietic Progenitors For Stem Cell Transplantation, Wentao Han

Arts & Sciences Graduate Student Theses and Dissertations

Hematopoietic stem cell transplantation (HSCT) is a well-established treatment for various hematological disorders. Umbilical cord blood (UCB) has emerged as an alternative source of hematopoietic stem and progenitor cells (HSPCs). However, the limited number of functional repopulating cells in UCB units has encouraged researchers to develop methods to expand them ex vivo. Hematopoiesis is strictly regulated by epigenetic modifiers. JARID2 is a co-factor of the Polycomb Repressive Complex 2 (PRC2), which recruits the complex to specific genomic loci and promotes the deposition of Histone 3 lysine 27 trimethylation (H3K27me3), a repressive epigenetic mark that mediates condensed chromatin packing to silence …

Functional Diversification Of Rice Ago1 Proteins, Rachel Elie Jouni

Arts & Sciences Graduate Student Theses and Dissertations

Global demand for food is outpacing gains from conventional plant breeding. Scientists have turned to molecular crop breeding techniques to increase crop output and mitigate global hunger; however, a common setback in this process is the pleiotropic effects of target genes. We need to develop strategies to specifically modulate desired traits without incurring undesired penalties. Natural evolution frequently balances such tradeoffs through extensive regulation, which we can leverage to produce more specific results. Reproductive development is an important target of breeding efforts due to its direct effect on yield. Rice, a major staple food crop for half the world’s population, …