Biology Commons^™

Impact Of Retinoic Acid Receptor Alpha Conditional Knockout On Ovarian Follicle Development In The Mouse, Zlata Bogin

College of Science and Health Theses and Dissertations

When there is abnormal endocrine signaling in the follicles, infertility, and ovarian diseases such as polycystic ovarian syndrome (PCOS), premature ovarian failure (POF), and different types of ovarian cancers may occur. Retinoic acid (RA), a biologically active derivative of vitamin A, is a critical signaling molecule that plays a vital role in various physiological processes, including embryonic development, tissue differentiation, and reproductive function. RA has been observed to influence granulosa cell proliferation through a cell signaling cascade involving Retinoic Acid Receptors (RARs), which have three isoforms alpha, beta, and gamma. We characterized a new retinoic acid receptor alpha (RARA) conditional …

Characterization Of The Immune Deficiency Pathway During Female Meiosis In Drosophila Melanogaster, Sarah Mashburn

College of Science and Health Theses and Dissertations

Organisms can defend against pathogens by significantly increasing the diversity of their progeny, so that some progeny are more likely to survive infection. This led to the prediction that infection should cause an increase in recombination rates which was seen in a previous study. However, the mechanism that regulates recombination rates in response to infection is not understood and in that study they did not provide a mechanism for how that can occur. In an RNAi screen, our lab found the gene mustard (mtd) is required for normal recombination rates. This gene was previously shown to be part of the …

Observations Of 25 Ghz Methanol Masers In W51a, Peter Wagstaff

College of Science and Health Theses and Dissertations

High mass stars are important because they alone are responsible for creating the heavy elements in the Universe. The observation of high mass star formation remains a challenging problem in astronomy because high mass stars form in densely clustered environments at large distances from us. Therefore, high angular resolution observations are required to unravel the action taking place in these dense environments. Masers can be used to observe distant regions with high angular resolution because masers are compact and bright sources. Class I methanol masers are believed to form in outflows from protostars where the shock generated by the outflowing …

Morphological Diversity Of Neurocrania In Sharks (Chondrichthyes: Elasmobranchii) And Its Ecological And Evolutionary Implications, Jake J. Wood

College of Science and Health Theses and Dissertations

Sharks occupy a wide range of ecological niches and lifestyle strategies attributed to their complex sensory system housed in their neurocranium. However, the diversity of neurocranial morphology in sharks and how the diversity may be related to their sensory capability have never been adequately surveyed. Therefore, the aims of this present study were: 1) to examine whether the relative sizes of rostral, olfactory, optic, and/or otic regions of neurocrania in sharks are related to their habitat, diet, and/or body form types; and 2) to investigate any possible patterns and insights into the ecology and evolution of sharks on the basis …

Targeting S. Maltophilia Biofilms With Phage Bfi2, Lydia Walther

College of Science and Health Theses and Dissertations

Stenotrophomonas maltophilia is a multidrug resistant bacterium which can cause severe infections of the respiratory tract, soft tissue, and bloodstream, and its ability to form biofilms on medical implants and devices contributes to its role as a hospital-acquired pathogen (Brooke, 2021; Flores-Treviño et al., 2019). The rise of antibiotic resistance has prompted the search for new treatments against bacteria. Bacteriophages, or phages, are a promising alternative to antibiotics because they infect and kill bacteria (Ling et al., 2022). Phage therapy has gained recent attention as a life-saving treatment for antibiotic resistant infections (Racenis et al., 2023; Schooley et al., 2017). …

Ultrasound Assisted Comparative Study Of Fucolam And So-Dium Alginate And Impact On Their Physiochemical Proper-Ties Using Box-Behnken Design, Uday Bagale, Ammar Kadi, Artem Malinin, Varisha Anjum, Irina Potoroko

Karbala International Journal of Modern Science

The article discusses about the possibility of comparing the impact of ultrasonic treatment on fucolam and sodium algi-nate. The purpose was to study the effect of micronization on the sulfated heteropolysaccharide fucolam, analyzing its dispersed state and accessibility by reducing its molecular weight and increasing antioxidant activity. The optimization of the micronization process was carried out using the Box-Behnken Design (BBD) method, with a sonication time ranging from 15 to 45 min, power ranging from 50 to 100 W/cm2, and temperature between 30 °C and 40 °C. The fixed lower fucolam concentration was 0.1%. The results illustrated that sonochemical treatment …

Deep Learning-Based Cad System For Predicting The Covid-19 X-Ray Images, Aqeel R. Talib, Hana’ M. Ali

Karbala International Journal of Modern Science

According to World Health Organization data, Coronavirus (COVID-19) has infected about 660, 378, 145 patients around the world. It is nonetheless difficult for physicians to detect COVID-19 infections out of CT or X-ray radiographs. Thus, several computer-aided diagnosis (CAD) systems based on deep learning and radiographs were developed to detect COVID-19 infections. However, the majority of approaches considered small datasets, which is ineligible to provide diverse COVID-19 radiographs. This work utilizes a massive number of X-ray radiographs, and compared standard CNN, DenseNet-121, and GoogLeNet for isolating COVID-19 infections out from normal and other pneumonia radiographs. The dataset in this work …

Illegal Shooting Is Now A Leading Cause Of Death Of Birds Along Power Lines In The Western Usa, Eve C. Thomason, Natalie J. S. Turley, James R. Belthoff, Tara J. Conkling, Todd E. Katzner

Biology Faculty Publications and Presentations

Human actions, both legal and illegal, affect wildlife in many ways. Inaccurate diagnosis of cause of death undermines law enforcement, management, threat assessment, and mitigation. We found 410 dead birds collected along 196 km of power lines in four western USA states during 2019–2022. We necropsied these carcasses to test conventional wisdom suggesting that electrocution is the leading cause of death of birds at electrical infrastructure. Of 175 birds with a known cause of death, 66% died from gunshot. Both raptors and corvids were more likely to die from gunshot than from other causes, along both transmission and distribution lines. …

Recombination As An Enforcement Mechanism Of Prosocial Behavior In Cooperating Bacteria, Isaiah Paolo A. Lee, Omar Tonsi Eldakar, J. Peter Gogarten, Cheryl P. Andam

Biology Faculty Articles

Prosocial behavior is ubiquitous in nature despite the relative fitness costs carried by cooperative individuals. However, the stability of cooperation in populations is fragile and often maintained through enforcement. We propose that homologous recombination provides such a mechanism in bacteria. Using an agent-based model of recombination in bacteria playing a public goods game, we demonstrate how changes in recombination rates affect the proportion of cooperating cells. In our model, recombination converts cells to a different strategy, either freeloading (cheaters) or cooperation, based on the strategies of neighboring cells and recombination rate. Increasing the recombination rate expands the parameter space in …

Using Mesocosms To Model Optimal Levels Of Body Size Variation In Larval Spotted Salamanders (Ambystoma Maculatum), Ian Kratzer

Online Theses and Dissertations

Body size is a critical aspect of an organism’s biological identity mediated by various biotic and abiotic factors. Body size historically been approached through “single optima” approaches, but body size variation modifies both inter- and intraspecific interactions and impacts competition-driven fitness outcomes within populations. Understanding optimal levels of body size variation will help illuminate how variation influences competitive outcomes and reproductive fitness. Populations may be structured through resource partitioning or competitive hierarchies, yet these structures predict contradictory size variation optima. This study sought to determine optimal levels of intraspecific body size variation in populations of larval salamanders to evaluate these …

A Thesis On The Human Genetic Basis Of Severe Pneumococcal Infection In Papua New Guinea, Emma Catherine Walker

Arts & Sciences Graduate Student Theses and Dissertations

Pneumonia remains a major cause of childhood mortality, especially in under-resourced communities. The profound morbidity of pediatric pneumonia in Papua New Guinea (PNG) compels innovative approaches to ameliorate disease. While the high incidence of pneumonia has been ascribed to environmental factors, we here identify a heritable allele increasing risk of severe pneumonia. In a pilot study, whole exome sequencing reveals a single nucleotide variant (SNV) in coenzyme Q6 (COQ6), a mitochondrial enzyme essential for ubiquinone biosynthesis. Significant association of SNV homozygosity with pneumonia replicates in an independently recruited cohort (p=0.036). Mice homozygous for the murine variant exhibit increased mortality after …

Investigating The Effects Of Opioid Exposure And Withdrawal On Endogenous Opioid Peptide Systems, Neuroimmune Interactions, And Striatal Neuron Activity, Marwa Mikati

Arts & Sciences Graduate Student Theses and Dissertations

Endogenous opioid peptides and their receptors perform critical roles in reward, aversion, and drug exposure processes. Both the peptides and the receptors perform distinct roles in modulating behavior depending on the brain region and stimulus in question. It has long been a challenge to study opioid peptides specifically because they are structurally similar to each other and occur at very low concentrations. Therefore, understanding their roles in stress, drug exposure, and drug withdrawal has presented difficulty for researchers over the years. To address this difficulty, I helped develop a method for the detection of enkephalins, a class of opioid peptides, …

Book Review: Elizabeth Wilson's Gut Feminism, İlkan C. İpekçi̇ Ph.D. Candidate

Feminist Pedagogy

No abstract provided.

Automated Processing Of Metabolomics Data For Population-Scale Studies, Ethan Stancliffe

Arts & Sciences Graduate Student Theses and Dissertations

The growth of untargeted metabolomic profiling technology has prompted the upstart of many large cohort studies. Metabolomics serves as an informative complement to other more established ‘omics (e.g., genomics, transcriptomics, proteomics). As a younger discipline, however, experimental and computational workflows are non-standardized and at times inadequate for large-scale studies. Two primary limitations in analysis of untargeted metabolomics data are 1) the poor performance and scalability of the algorithms applied to detect metabolite signals from the raw LC/MS data and 2) inefficient and arduous metabolite identification, which is the process of determining the biochemical structures that correspond to the detected LC/MS …

How Plants Cope With Stress, Nabila Riaz

Dartmouth College Ph.D Dissertations

Iron (Fe) is one of the essential micronutrients required by both plants and animals. In humans, Fe deficiency causes anemia, the most prevalent nutritional disorder in the world today. Most people rely on plant-based foods as their major Fe source, but plants are a poor source of dietary Fe.

Fe deficiency has many adverse effects on photosynthesis, which is not surprising given that 95% of foliar Fe is found in chloroplast. The Gueirnot lab had previously showed that the bHLH transcription factors ILR3 and PYE are required for photoprotection during Fe deficiency by preventing ROS damage to photosystem II (PSII). …

Function Of Deubiquitinase Mysm1 In Attenuation Of Dna Damage Responses, Brendan Mathias

Arts & Sciences Graduate Student Theses and Dissertations

MYSM1 deficiency has been identified in patients with B cell lymphopenia, hypogammaglobulinemia, primary immune deficiency and bone marrow failure. MYSM1 is a known deubiquitinase that acts on histone H2A to promote gene expression. MYSM1 also functions in cellular responses to DNA injury and patients with loss of MYSM1 have increased sensitivity to DNA damaging agents. The specific role and function of MYSM1 in DNA damage responses has yet to be determined. Here, I have shown that MYSM1 does not mediate generation or repair of DSBs, but rather acts to attenuate and terminate DNA damage signaling after repair. Loss of MYSM1 …

Using Μct Scans To Create 3d Skull Puzzles As Open-Access Pedagogical Tools For Anatomy And Comparative Osteology Classes., Alexis Slack

Honors Thesis

As access to affordable 3D printing technologies increases, the use of Computed Tomography (CT) technologies is well positioned to contribute to the advancement of pedagogical experiences through the creation of physical models for teaching. Such complementary efforts may enhance broader impacts by simultaneously boosting the education system with a unique hands-on experience for students and providing an alternative to expensive osteological and other artificial models. Two 3D printed skull puzzles were created to aid in teaching human and vertebrate anatomy, and comparative osteology courses. After segmenting all the bones from each respective skull, the individual skeletal elements were 3D printed, …

Investigation Of Metabolic And Molecular Pathways That Promote Gastric Parietal Cell Regeneration, Mahliyah Lenore Adkins-Threats

Arts & Sciences Graduate Student Theses and Dissertations

The stomach contains gastric epithelial cells, including acid-pumping parietal cells (PCs), that are constantly renewed throughout life from a multipotent stem cell to maintain a balance between producing and protecting from the acid and enzymes needed to kill pathogens and initiate digestion. Despite this dynamic renewal, disorders of the gastric epithelium occur and are one of the most common etiologies of human diseases ranging from simple heartburn to reflux, peptic ulcers and gastric cancer. PCs are characterized by elaborate plasma membrane foldings and vesicles that house their proton pumps and an abundance of mitochondria needed to power secretion of that …

Investigating Novel Neoantigen Sources For Personalized Cancer Vaccines, Megan Richters

Arts & Sciences Graduate Student Theses and Dissertations

The adaptive immune system has inherent antitumor properties that are capable of inducing tumor-specific cell death. CD8+ and CD4+ T cells, two immune cell types critical to this process, recognize antigens bound by class I and II major histocompatibility complexes on the cell surface, respectively. After antigen recognition, T cells can signal growth arrest and cell death to tumor cells displaying the antigen. Neoantigens, or tumor-specific peptides, are targeted by cancer immunotherapies to induce T cell-mediated degradation. Treatments such as personalized vaccines and immune checkpoint blockade thus provide a unique avenue to selectively recognize and destroy tumor cells while keeping …

Mass Spectrometry-Based Discovery Of Tumor Antigens For Cancer Immunotherapy, Wei Meng

Arts & Sciences Graduate Student Theses and Dissertations

The immune system plays an essential role in cancer evolution and cancer treatment. One of the major mechanisms of immune-mediated tumor rejection is the recognition of tumor antigens by T cells. Upon recognition of tumor antigens, naïve T cells become activated and subsequently infiltrate inside the tumor. Since the early discovery of tumor-specific T cells, many efforts have elucidated the molecular nature of their cognate antigens. It is now established that MHC-I and MHC-II restricted peptides are critical to generate CD8+ and CD4+ antigen-specific T cells that can recognize tumor-derived antigens. Two main categories of these antigens are those originating …

Exploiting Vulnerabilities In The Ras-Rac Signaling Pathway For The Selective Targeting Of Pancreatic Cancer Cells, Neha Chaudhary

Theses & Dissertations

Deregulation of the KRas (Kirsten rat sarcoma virus) GTPase is one of the early hallmarks of Pancreatic Cancer (PC). The most common genetic alteration found in PC are mutations in the KRas protein that block its ability to hydrolyze GTP to GDP and resulting in higher levels of GTP-bound KRas, its active form. Pancreatic tumors driven by oncogenic mutants of KRas tend to be addicted to the oncogene, to the extent that its repression leads to the induction of cell death. This addiction to the KRAS oncogene makes the KRas protein an ideal target for cancer therapy. However, the globular …

The Co-Oncogenic Function Of Ecdysoneless Protein With Erbb2 In Mammary Epithelial Cells, Benjamin B. Kennedy

Theses & Dissertations

The Ecdysoneless (ECD) protein is highly evolutionarily conserved and ubiquitously expressed across human tissues. ECD has established roles in cell cycle regulation, embryogenesis, cell survival, and RNA biogenesis. ECD mRNA and protein are overexpressed in breast cancer, and its overexpression correlates with poor patient survival, especially in ErbB2/HER2-positive breast cancer. This thesis work investigates the co-oncogenic role of ECD in ErbB2-driven oncogenesis using immortalized mammary epithelial cells. Here, we show that ECD and ErbB2 overexpression in immortalized human mammary epithelial cells increases cancer traits, such as invasion, migration, and anchorage independent growth. Significantly, ECD+ErbB2 co-overexpression further enhanced all oncogenic traits. …

Hedgehog Signaling As An Underlying Mechanism For Midline Modification During Asexual Reproduction In Convolutriloba Longifissura Acoels, James M. Sikes Ph.D., Jaclyn Cherry

Master's Theses

The mechanisms that control midline specification and modification during post-embryonic development are some of the least understood in developmental biology.  Because acoel flatworms have varied modes of asexual reproduction which can involve the dramatic modification of their orthogonal axes and midline, we have chosen the acoel species Convolutriloba longifissura as a model to study the mechanisms behind midline modification.  C. longifissura asexually reproduces through a double fission process where novel midlines arise within laterally located tissues while the adult midline is destroyed prior to an initial transverse fission event, which is then followed by a second longitudinal fission.  Previous work …

A Review With Updated Perspectives On In Vitro And In Vivo Wound Healing Models, Murni Nazira Sarian, Nabilah Zulkefli, Shazeli Zain, Sandra Maniam, Sharida Fakurazi

Turkish Journal of Biology

A skin wound or perforation triggers a series of homeostatic reactions to safeguard internal organs from invasion by pathogens or other substances that could damage body tissues. An injury may occasionally heal quickly, leading to the closure of the skin's structure. Healing from chronic wounds takes a long time. Although many treatment options are available to manage wound healing, an unmet therapy need remains because of the complexity of the processes and the other factors involved. It is crucial to conduct consistent research on novel therapeutic approaches to find an effective healing agent. Therefore, this work aims to cover various …

Aquatic Insect Communities Remain Impaired Following Large-Scale River Restoration, Jared Meek, Jackson Birrell, Teagan Mulford, Dennis K. Shiozawa, C. Riley Nelson

Western North American Naturalist

River manipulation and degradation can cause detrimental impacts on aquatic insect communities. River restoration projects seek to mitigate these human disturbances. Assessing the efficacy of river restoration remains an important goal for river managers and conservation biologists so that improved restoration methods can be used in the future. From 1999 to 2008, the Utah Reclamation Mitigation and Conservation Commission restored a 15-km channelized portion of the Provo River (Wasatch County, Utah, USA). Before (1999) and during (2002) the restoration project, macroinvertebrate samples were collected using modified kick nets from 3 sites within the restored area and 1 site outside the …

Antioxidant Potential Of Nanomaterials, David Gonzalez Flores, Javier Espino, Jose A. Pariente

Turkish Journal of Biology

Background/aim: The novel field of nanomaterials allows infinite possibilities in order to create antioxidant therapies. The present review is aimed to describe the state of art concerning on nanomaterials and their effects on reactive oxygen species (ROS) production. A wide range of nanoparticles has been designed for this purpose, and each one possesses some particular characteristics which allow these significant antioxidant results. Several in vivo and in vitro works state the ability of these nanoparticles to mimic the redox systems of the cells, and thus, the potential role of nanoparticles as antioxidant treatment for several diseases. Materials and methods: This …

Targeting Of Notch, Il-1, And Leptin Has Therapeutic Potential In Xenograft Colorectal Cancer, Rumeysa Özyurt, Ni̇lüfer Erkasap, Mete Özkurt, Serdar Mustafa Erkasap, Konstanti̇nos Di̇mas, Ayşe Çakir Gündoğdu, Engi̇n Ulukaya

Turkish Journal of Biology

Background/aim: Colorectal cancer (CRC) is a fatal malignancy type and its occurence still needs to be explored mechanistically. Notch, IL-1, and leptin crosstalk is reported to play a role in the proliferation, migration, and expression of proangiogenic molecules. In this study, we aimed to investigate the effect of inhibition of Notch, IL-1, and leptin on CRC. Materials and methods: To generate colorectal cancer tumor xenografts, 1 × 107 cells from exponentially growing cultures of HCT15 cells were injected subcutaneously, at the axillary region of the left and right rear flanks of forty NOD.CB17-Prkdcscid/J (NOD/SCID) female mice. The mice were then …

Soloxolone Methyl Induces Apoptosis And Oxidative/Er Stress In Breast Cancer Cells And Target Cancer Stem Cell Population, Eli̇f Ertürk, Oğuzhan Akgün, Yaren Yildiz, Pinar Kalkan, Oksana V. Salomatina, Nariman F. Salakhutdinov, Engi̇n Ulukaya, Ferda Ari

Turkish Journal of Biology

One of the most prevalent malignancies in women and one of the leading causes of cancer-related death is breast cancer. There is a need for new treatment approaches and drugs for breast cancer. Many studies show the high potential of triterpene compounds and their semisynthetic derivatives as anticancer agents due to their ability to induce apoptosis and suppress tumorigenesis. The effects of soloxolone methyl (SM), a semisynthetic derivative of 18-H-glycyrrhetinic acid, on the cytotoxicity and apoptosis of human breast cancer cell line (T-47D) and cancer stem cell (CSCs) population (mammospheres; CD44+/CD24-antigen) derived from breast cancer cells, were examined in this …

The Effects Of Anti-Pd-L1 Monoclonal Antibody On The Expression Of Angiogenesis And Invasion-Related Genes, Cansu Babahan, Samira Abdi Abgarmi, Fatma Gi̇zem Sonugür, Müge Öçal Demi̇rtaş, Hakan Akbulut

Turkish Journal of Biology

Background/aim: The role of PD-L1 in regulating the immunosuppressive tumor microenvironment via its binding on PD-1 receptors is extensively studied. The PD-1/PD-L1 axis is a significant way of cancer immune escape, and PD-L1 expression on tumor cells is suggested as a predictive marker for anti-PD-1/PD-L1 monoclonal antibodies (MoAbs). However, the tumor-intrinsic role of PDL1 is not known well. Therefore, we aimed to investigate the effects of anti-PD-L1 antibodies on the expression of angiogenesis and metastasis-related genes in tumor cells. Materials and methods: The experiments were done with prostate cancer and melanoma cells with low PD-L1 expression (<5%) and prostate and breast cancer cells with high PD-L1 expression (>50%). The gene …

Antileukemic Potential Of Nile Blue-Mediated Photodynamic Therapy On Hl60 Human Myeloid Leukemia Cells, Serçi̇n Özlem Çalişkan, Aynur Karadağ, Bariş Uzunok, Numan Taşpinar, Berna Akin, Meti̇n Çalişkan, Rahşan Ilikçi Sağkan

Turkish Journal of Biology

Background/aim: Photodynamic therapy (PDT) has received great attention over the past decade in the treatment of diseases such as leukemia which is a cancer of the blood and bone marrow cells that causes a significant number of deaths worldwide. In this study, it was aimed to investigate the effects of Nile blue-mediated PDT (NB-mediated PDT) on HL60 cells. Materials and methods: The effect of NB-mediated PDT on cell proliferation was evaluated with cell volume analysis using flow cytometry at 24 h. Cell apoptosis, ROS production, mitochondrial membrane potential, and cell cycle analysis were evaluated using annexin V-FITC, H2 DCFDA, JC-1, …