Biology Commons^™

Methyl-Cpg-Binding Domain As A Protein Interaction Partner In Promoter Regulation And Neurodevelopment Through Evolutionary Expanded Entanglement, Stephanie M. Bilinovich, Surya B. Chhetri, Jackson T. Mitchell, Gage O. Leighton, Vladislav Jdanov, Jacob K. Zieba, Taylor W. Cook, Krysta L. Engel, Robert M. Vaughan, Humza Bhatti, Sadie L. Heeringa, Amy M. Wilstermann, Sophie Vanderweele, Akansha S. Das, Emily C. Sherry, Stephen A. Duncan, Katie L. Uhl, David C. Hinds, Mark Mackiewicz, Sarah K. Meadows, Kimberly M. Newberry, E. Christopher Partridge, Sara G. Cline, C. Joy Shepard, D. Casey Smith, Antonio Bradley, Daniel Vogt, Daniel B. Campbell, Lucas Pozzo-Miller, Caleb P. Bupp, Austin J. Goodyke, Surender Rajasekaran, Rebecca C. Knickmeyer, Benjie Blair

Research, Publications & Creative Work

There is increasing evidence that the methyl-binding domain (MBD) is a protein-protein interaction motif that can function independently of methylated DNA binding. The MBD proteins found throughout plants and invertebrates duplicated into multiple vertebrate DNA and non-DNA-binding members (MBD1, MBD2, MBD3, MBD4, MBD5, MBD6, MECP2, BAZ2A, BAZ2B, SETDB1, andSETDB2). Although many invertebrate species possess MBD proteins that can bind and recognize DNA methylation, the DNA-binding function has been independently lost multiple times, with only minor alterations to the protein interaction residues. The nucleosome remodeling and deacetylase (NuRD) complex, which interacts with MBD2/3 and is colocalized with MBD1/4 ChIP-Seq, is maintained …

Elucidating The Effects Of Environmental And Physiological Conditions On Stem Cell Regulation In Vivo, Nimmy John

Electronic Theses & Dissertations (2024 - present)

The Notch signaling pathway is a highly conserved intercellular signaling pathway that any dysregulation can lead to a variety of human diseases. These diseases are further exacerbated by various environmental, pathological and genetic conditions. Previous studies have shown that these conditions have been known to affect the Notch transcriptional response. However, the molecular mechanisms by which such conditions influence Notch signaling remained largely unknown. Moreover, most Notch studies have relied on in vitro systems and indirect reporters, which can miss the dynamic and contextual nature of Notch signaling. Here, we systematically analyzed the effects of these conditions with single molecule …

Phylogenetic Analysis Of Metabolic Enzymes In Hypoxic/Anoxic Conditions In Cetaceans And Cancer, Samerna A. Masih

Electronic Theses & Dissertations (2024 - present)

Cancer cells often exhibit a Warburg-like metabolism, which includes increased fatty acid synthesis and storage that help them survive in hypoxic conditions. This shift is marked by the heightened synthesis and accumulation of fatty acids, acting as a survival mechanism in low-oxygen environments (Baumann et al., 2016). Interestingly, deep-diving whales may utilize a similar metabolic pathway to produce wax esters during their prolonged dives.

Our study focused on exploring the genetic and metabolic similarities between breast cancer cells and deep-diving whales, using computational analyses to investigate lipid metabolism genes. We looked for evolutionarily conserved variations that might reveal adaptive mechanisms …

The Role Of The Nasal Migratory Mass In Olfactory Bulb Formation And Fertility, Charisse Martin

Electronic Theses & Dissertations (2024 - present)

The olfactory migratory mass plays an essential role in the development of the olfactory bulb by facilitating the migration of the gonadotropin-releasing hormone neurons from the olfactory placode to the pre-optic hypothalamic area in the brain. In mammals, the migration of GnRH neurons is critical for establishing the hypothalamic-pituitary-gonadal axis (HPG axis), which regulates reproductive function through the production and secretion of gonadotropins. Luteinizing hormone (LH) and Follicle-stimulating hormone (FSH) instruct the gonads to function appropriately, ensuring sexual maturation and fertility. Disruptions in this migratory pathway have been linked with Kallmann syndrome, a condition characterized by low levels of GnRH, …

Nat10 Stabilizes Immune Response Factors Aiding With Cellular Immune Response To Zika Virus Infection, Shawn Gianola

Electronic Theses & Dissertations (2024 - present)

Zika virus (ZIKV) remains a significant public health concern due to major gaps in our understanding of its infection mechanisms and immune evasion strategies. Despite its link to severe complications such as microcephaly and Guillain-Barré Syndrome (GBS), no vaccine or targeted antiviral therapies exist. Compounding this concern is the expanding habitat of ZIKV-carrying mosquito vectors, driven by climate change, which increases the risk of future outbreaks in previously unaffected regions.

One promising area of investigation involves post-transcriptional modifications (PTMs) chemical alterations to RNA that influence its stability, translation, and function. Although over 170 PTMs have been identified, their roles remain …

Transcriptome-Wide Gene Expression Analysis Of Skeletal Muscles Of Duchenne Muscular Dystrophy Mouse Models And Patients, Olivia N. Ransiear

Electronic Theses & Dissertations (2024 - present)

Duchenne Muscular Dystrophy (DMD) is an X-linked recessive muscle degenerative disease that frequently proves fatal by age 30. It primarily affects adolescent males with symptoms appearing as early as age 6. Patients quickly lose their ability to walk due to muscle weakness and are confined to wheelchairs for the remainder of their lives. DMD is caused by a mutation in the dystrophin gene. Without dystrophin, mechanical stress, injury, or shock takes a drastic toll on muscle tissue and muscle stem cells, rendering them unable to regenerate or be repaired. This results in a rapid loss of muscular strength and muscle …

Blattella Germanica As A Vector Of Salmonella Typhimurium, Matthew Turner

Dissertations and Theses

The following investigates the role of the German cockroach (Blattella germanica) as a vector of the bacterium Salmonella enterica subspecies enterica serovar Typhimurium (S. Typhimurium). As such, this work examines various host-pathogen-microbiome interactions that define the vectorial capacity of the German cockroach for Salmonella. To date, the majority of literature focuses on the general association of the German cockroach with various human pathogens, claiming any dissemination to be carried out via passive mechanical transmission. This project recognizes those claims, while expanding to include the possibility of biological transmission, involving active and complex host-pathogen interactions, including mechanisms like replication within the …

Understanding Trends In Zostera Research, Stressors, And Response Variables, Hannah R. Lyford, Emma Guerrini Romano, Shayna A. Sura, Sarah Joy Bittick

Biology Faculty Works

Background. Seagrass meadows are ecologically significant habitats that are globally threatened. Thus, there is increased interest in conservation of seagrasses as they face widespread decline. Biotic and abiotic factors that influence seagrass can be classified as stressors, such as rising temperature and eutrophication. Our study met an imminent need to consolidate data from previous studies to discern knowledge gaps and identify trends in studies, stressors, species, and geographic origination of research for the genus Zostera. For our systematic review, the objectives were to (A) qualitatively assess and summarize the current state of literature focused on seagrass species within the Zostera …

A Comprehensive Embryonic Staging Series Of The Turtle Trachemys Scripta, Christina M. Noravian, Perla G. Rand, Amira Mahomed, Maxellende Ezin, Annie Rickard, Oscar D. Juvera, Maria Elena De Bellard

Biology Faculty Works

Background: Turtles hold a unique place in vertebrate evolutionary history, making them critical assets in embryology research. Yet, they remain understudied as potential model organisms in the field. Here, to support experimental manipulations with turtle embryos, we have created a complete normal table of development for comprehensive embryonic staging of Trachemys scripta, one of the most common invasive turtle species worldwide.

Results: The development of T. scripta embryos from 0 days post-oviposition (DPO) to hatching (~60 DPO) was described from approximately 300 viable eggs collected at California State University, Northridge during the 2021–2024 nesting seasons. Thirty-one stages between oviposition and …

Investigating Mitochondrial Stress Response Mechanisms In Aging, Aileigh E. Daniel

Theses and Dissertations

Mitochondrial dysfunction is widely recognized as a key contributor to aging and age-related diseases. The concept of mitohormesis suggests that low levels of ROS can activate stress-responsive transcription factors, promoting adaptive mechanisms that enhance longevity. We hypothesized that changes in protein abundance under conditions of mild mitochondrial stress reflect an adaptive response, and that commonly altered proteins across diverse genetic backgrounds of mitochondrial stress can help identify key regulators of stress resilience and aging. Our study identified conserved mitochondrial stress response pathways and highlighted candidate regulators for further investigation. These regulators appear to impair mitochondrial energy production by downregulating ATP …

Climate Change-Induced Shifts In Mediterranean Fungal Fruiting Phenology And Productivity, Rachel Demay

Theses and Dissertations

We used a 29-year dataset of mushroom fruiting from the Pinar Grande forest in northern Spain to investigate the effects of climate change on the phenology, productivity, and diversity of mycorrhizal and saprotrophic mushrooms. We investigated the long-term trends in fruiting season length, yield (by count, total weight, and average weight), and genus richness. Additionally, we identified associations between monthly temperature and monthly precipitation with these fungal responses across functional groups: mycorrhizal, saprotrophic, litter-decaying saprotrophic, and wood-decaying saprotrophic mushrooms, and the economically-important edible genera Boletus and Lactarius. We found that autumnal season length in the Pinar Grande has shortened over …

Molecular Mechanisms Of Kynurenine-Mediated Lifespan Regulation In Yeast, Ryan E. Counterman Jobb

Theses and Dissertations

The kynurenine pathway is a highly conserved pathway that acts as the primary pathway for tryptophan catabolism and has been found to be involved in lifespan regulation across many diverse organisms. Caloric restriction (CR) is the only known dietary intervention to date that both increases the mean lifespan and the health span of multiple organisms, although the molecular mechanisms of these effects are not fully understood. There are known and sometimes contradictory relationships between the kynurenine pathway activity and the life- extending effect of CR but the crosstalk between the two is not well characterized. Understanding these relationships could lead …

Soils From Different Solidago Altissima Clones Mediate Intraspecific Interactions In Schizachyrium Scoparium, Sarah Alharbi

Masters Theses

While previous studies have examined plant intraspecific competition and soil microbial effects separately, fewer studies have investigated how these factors interact, particularly in the context of genotype-specific soil conditioning effects. Plant-soil feedbacks can significantly alter interspecific competitive outcomes, yet few studies have examined how local variation in soil conditioning influences plant responses to density-dependent competition. I investigated how soil inocula derived from four Solidago altissima clones that were previously shown to differ in their soil conditioning effects (Foster et al., 2022) affected the growth and root traits of Schizachyrium scoparium across a gradient of intraspecific competition (1, 2, or 4 …

Gustatory Behaviors Of House Flies: Body Parts Used And Response To Bitter, R M Panchalie Bhagya Gunathunga

Graduate Research Theses & Dissertations

Insects use multiple body parts, not just their mouth, to taste. Whether a particular body part has a taste function can be determined indirectly by examining the morphology or electrophysiological response of its sensilla (sense organs) or directly by the insects’ behavioral response. Understanding the taste system of insects allows development of better management strategies against pest insects and strategies to protect beneficial insects.House flies, Musca domestica L., are pests at livestock facilities. House fly numbers are controlled mainly by manure management and chemical controls. Toxic granular fly baits remain one of the most popular and effective forms of chemical …

Geology, Paleoecology And Vertebrate Biostratigraphy Of The Hell Creek Formation, Carter County, Montana, Usa, Joshua Collin Mathews

Graduate Research Theses & Dissertations

The Hell Creek Formation of the Northern Great Plains records one of the greatest mass extinction events in Earth’s history, bringing to a close the reign of the dinosaurs at the end of the Cretaceous period. This rock unit comprises one of the most studied geological formations in the world and is one of the few locations on the planet that preserve terrestrial deposits containing ejecta from the bolide impact that slammed into the Yucatan Peninsula 66 million years ago. This profound event in the geologic record has led to numerous studies of paleobiotas, climate change, ecosystem recovery dynamics, and …

Establishing A Microfiber Recovery Rate In Human Lung Tissue, Kylie Nicole Babin-Howard

Graduate Research Theses & Dissertations

Microplastics (plastic particles smaller than 5mm) are of increasing concern to environmental and human health as they have persistently been found in all areas of study—becoming a ubiquitous part of the planet. Microplastics have been found in a variety of human tissues (lungs, blood, brain matter, etc.) yet their health effects are poorly understood, with experimental exposure model studies indicating adverse health effects. Microfibers have been found to be more toxic when compared to other microplastic shapes and are also shed from a majority of everyday items, with environmental reports showing that fibers are more than twice as prevalent than …

Effect Of Six-Day Germination On Chemical Composition, Functional, And Nutritional Properties Of Pea Varieties, Hojjat Abdollahikhamene

Electronic Theses and Dissertations

Pulses, particularly peas, have long been a crucial source of protein in vegetarian and cost-effective diets worldwide. They have gained popularity in Western diets as more people turn to plant-based proteins as alternatives to animal products. Peas are known for their high protein content; however, their use in food products has been limited due to factors like poor solubility and digestibility. Germination improves the nutritional profile of peas by enhancing protein content and digestibility. The objective of this study was to determine the effects of six days of germination on the nutritional composition and functional properties of different varieties of …

Using Fungal Dna Barcoding To Identify Fungal Species In A James River Park System Soil Microbiome, Erwin Murray, D Jennings

UROP Posters

Fungi in the soil have the ability to form mutualistic relationships with plant roots and improve the way they resist a variety of plant diseases and abiotic stressors, influencing the survivability of the plants. The James River Park System (JRPS) is home to a variety of ecosystems that support diverse plant and fungal populations, including native plants and invasive plants. Therefore, it is important to identify what is present in the soil microbiome. The purpose of this project is to isolate fungal sequences from soil samples collected in the JRPS to identify what fungal species are present in the JRPS …

Effects Of Single-Cell Dietary Protein Sources On Feeding, Growth, And Resource Allocation In The Juvenile Sea Urchin Lytechinus Variegatus, Darrien Jamila De Jesus

All ETDs from UAB

An understanding of nutrition can improve culture of sea urchins, whether as a research model or in the production of seafood products. Macronutrients, including dietary protein sources, can affect growth and reproductive profiles and alter resource allocation to somatic and gametic tissues. Although sea urchins in culture can be fed natural products, diet formulations using various ingredients can be developed to reliably produce desired outcomes. Single-cell protein sources represent a potential alternative to current industry standards of animal-derived protein sources such as fish and squid meal, which are becoming increasingly overfished and expensive. In the present study, we evaluated the …

Endothelial Cell Cd36 In Alzheimer’S Disease And Breast Cancer Progression, Atul Kumar

All ETDs from UAB

Vascular endothelial cells (ECs) are increasingly recognized as a distinct class of innate immune cells, with CD36, an innate immunity receptor, playing a pivotal role in regulating immune function and its regulation, angiogenesis, cancer progression, brain related disorder as well as the exchange of nutrients and waste. To investigate this further, we developed EC-specific CD36 knockout mice using the translating ribosome affinity purification (TRAP) technique. By isolating ribosome-bound mRNA directly from vascular endothelial cells in vivo in these knockout and control mice, we conducted deep RNA sequencing and transcriptional profiling. Our findings revealed that CD36 deficiency in brain endothelia led …

Elements Of Social Capital And Counterspace Processes Contribute To Undergraduate Stem Student Development Of A Sense Of Belonging, Mackenzie J. Gray, Jasmine N. Yacobian, Erin Shortlidge

Biology Faculty Publications and Presentations

Having a sense of belonging can promote persistence in the STEM fields, but less is known about what it means to develop that sense of belonging. To investigate this phenomenon, we conducted semi‐structured interviews with a cohort of STEM students (n = 10) nearing graduation at an urban university regarding their sense of belonging and qualitatively coded the interviews using thematic analysis. Results revealed that all interviewed students clearly articulated feelings of belonging, making them an ideal population from which to learn more. We applied two frameworks to guide our understanding of what factors promoted the development of a sense …

Analysis Of Mapt On Alzheimer’S Disease, Elaine Vanterpool, Marc Morgan Jr.

Student Posters

Alzheimer’s is the 7 th most common cause for death in humans and unfortunately has no cure. Coincidentally the gene MAPT (microtubule-associated protein tau) increases chances of obtaining Alzheimer's. The purpose of this study is to discover the mutation that resides within this gene. A website database called Simple Clinvar was used to generate information concerning Alzheimer’s disease and the different genetic variants associated with the disease. The SIFT algorithm was used to show whether the changes in amino acid sequences of the MAPT gene can affect protein function. PolyPhen was another prediction algorithm used to predict the influence that …

Exploring The Ecological Relevance Of Biotic And Abiotic Stressors In Structuring Legume Microbial Communities, Cian Dotson

Dissertations

Heavy metal hyperaccumulation is prevalent throughout plant evolution, particularly in the legume family (Fabaceae), and acts as a presumed chemical defense against herbivory. However, heavy metal hyperaccumulation can have non-target impacts on other biological interactors including plant-microbe interactions. This information is important given the interest in utilizing hyperaccumulating plants for phytoremediation of anthropogenically contaminated soils. Here we employ a greenhouse experiment manipulating selenium level along with 16S rRNA gene amplicon sequencing methods to explore the effect of selenium on the prokaryotic microbiome of the selenium hyperaccumulator Astragalus crotalariae and non-accumulator Astragalus lentiginosus var. borreganus. Regardless of hyperaccumulator status, both plant …

Evaluation Of Bacteriophage Infection Of Enterococcus Faecalis In A Monolayer, Alexandria Osborn

Dissertations

Enterococcus faecalis is one of the first colonizers of the human gastrointestinal tract, and it plays a role in the intestinal immune development at the very early stages of life. However, it is also an opportunistic pathogen, capable of translocating across the mucosal barrier to cause systemic infections. E. faecalis is also linked to infections including endocarditis, recurrent urinary tract infections (rUTIs), bacteremia, wound infections, meningitis, root canal infections, intra-abdominal and pelvic infections, and septicemia. Persistent enterococcal opportunistic infections have been associated with the production of virulence factors and sharing of antibiotic resistance genes, thus making E. faecalis difficult to …

Effects Of Nitrogen, Phosphorus And The Fungicide Azoxystrobin Additions On Larval And Post-Metamorphic Fitness Of American Toads (Anaxyrus Americanus), Michael Vosburgh

Dissertations

Since European settlement, vast areas of U.S. land have been modified by humans. In the Midwest, an estimated 99% of native grasslands have been replaced by agriculture and urban development. Such alternations have replaced native habitat, redefined hydrology and introduced a wide array of chemicals into aquatic ecosystems. Modern agricultural practices utilize fertilizers and pesticides to maximize crop production. These chemicals frequently runoff into surrounding waters, potentially effecting aquatic organisms. One group of organism thought to be susceptible to agricultural contaminants are amphibians. Amphibians are vulnerable to pollution due, in part, to their permeable skin and biphasic life history. Global …

Food Finding Ability Does Not Predict Annual Survival In Winter Resident Birds, Aidan Hand

Honors Program: Senior Projects (Public)

Small non-migratory birds in temperate locations face many challenges to survive the winter. They must be able to find enough food, which is in decreased supply, to fuel the energetic demands of staying warm. Prior work has demonstrated that birds show individual variation in their foraging behaviors that could contribute to the discovery of new foraging patches, such as novel environment exploration. A better ability to discover new food sources could increase a bird’s chance of surviving the winter by increasing its access to new food patches. To test this hypothesis, we used radio frequency identification (RFID)-enabled bird feeders to …

Squid Paralarvae Turn With High Agility Using Jets Near The Reynolds Number Threshold For Viscous Domination, Ian K. Bartol, Alissa M. Ganley, Paul S. Krueger, Joseph T. Thompson

Biological Sciences Faculty Publications

Turning is critical for survival in the ocean, as marine animals need to maneuver to capture prey, elude predators, and navigate complex environments. While prior research has focused on turning performance of adult swimmers, less is known about early ontogenetic stages that locomote within lower Reynolds number (Re) regimes, especially young jetters. To evaluate squid paralarval turning proficiency and the role of the pulsed jet in maneuvers, recently hatched longfin squid Doryteuthis pealeii swimming in a viewing chamber were studied using digital particle image velocimetry and kinematic motion analyses. Paralarvae exhibited a wide repertoire of turning behaviors, including those performed …

Genome-Wide Snp Analyses Reveal High Gene Flow Of Endemic Smallscale Croaker (Boesemania Microlepsis) In The Lower Mekong Basin, Quyen Dang Ha Vu, Christopher E. Bird, Oanh Thi Truong, Sang Quang Tran, Ellen E. Biesack, Amanda S. Ackiss, Kent E. Carpenter, Binh Truy Dang

Biological Sciences Faculty Publications

The Smallscale Croaker, Boesemania microlepis, is a valuable fishery resource in the Mekong River basin that lacks clear biological data to understand its basic ecology and conservation management priorities. This species is common in the southernmost floodplain of the Mekong which extends from Tonlé Sap in Cambodia to the Mekong Delta in Vietnam. This floodplain is of particular biodiversity conservation concern because of the many upstream dams that restrict water flow in an ecology that relies heavily on a flood-pulse cycle. The literature regarding the biology B. microlepis in this region contains conflicting ideas that populations are both highly …

Intraspecific Variation In Plant–Fungal Interactions Across Tidal Elevation In A Salt Marsh, Torrie Hanley, Catherine Gehring, Ron Deckert, Behzad Mortazavi, Christina Richards, A. Randall Hughes

Biology Faculty Publications

Interspecific interactions vary depending on environmental and genetic factors, with intraspecific variation potentially altering these relationships. Specifically, intraspecific variation within host plants and their endosymbionts may affect above- and belowground interactions depending on environmental conditions. We examined how intraspecific variation within the salt marsh foundation species Spartina alterniflora and a common fungal root endosymbiont (Lulworthia sp.) affected their interactions. We conducted a glasshouse experiment comparing interactions between Spartina growth forms (tall-form from low marsh and short-form from high marsh) and Lulworthia isolates from different marsh locations, and a laboratory experiment exposing Lulworthia isolates from both endpoints of a tidal elevation …

Comparing The Development And Viability Of Horseshoe Crab Eggs Laid In Beach And Salt Marsh Habitats, Daniel A. Sasson, Christopher C. Chabot, Jo-Marie Kasinak, Jennifer Mattei Ph.D., Elizabeth U. Scott, Fletcher K. Hall, Michael R. Kendrick

Biology Faculty Publications

The horseshoe crab, Limulus polyphemus, has recently been found to spawn regularly in salt marshes, despite the long-held assumption that salt marsh sediments are not conducive for embryonic development. Here, we tested the prediction that eggs laid in the salt marsh would develop more slowly and be less viable than eggs laid on beaches. We flagged the nests of spawning horseshoe crabs in the marshes and beaches of three states—South Carolina, Connecticut, and New Hampshire—and then excavated those nests one or three weeks later. We staged the excavated embryos to compare developmental progress between marshes and beaches. We found …