Digital Commons Network^™

Removal Of Phenol From Oilfield Produced Water Using Non-Conventional Adsorbent Medium By An Eco-Friendly Approach, Salem Jawad Alhamd, Mohammed Nsaif Abbas, Hassan Jameel Jawad Al-Fatlawy, Thekra Atta Ibrahim, Zaid Nsaif Abbas

Karbala International Journal of Modern Science

Petroleum extraction generates substantial quantities of produced water, a challenge compounded by water scarcity in oil-producing regions, notably the Middle East. Leveraging produced water effectively, adhering to environmental standards, can offer a viable solution to the issue of water scarcity. This study explores the potential of mandarin peels as an available, cost-effective adsorbent for treating synthetic aqueous solution simulated to oil-field produced water, specifically targeting phenol, a dangerous pollutant. Employing a batch-mode adsorption unit, six operational factors—phenol concentration, acidity, agitation speed, contact time, adsorbent dose, and temperature—were investigated. Results revealed an inverse relationship between phenol removal and pH, concentration, and …

Vascular Electrophysiology And Pathogenic Consequences Of Cardiovascular Katp Channel Mutations, Alex Hanson

Arts & Sciences Graduate Student Theses and Dissertations

The complex cardiovascular disorder Cantú Syndrome (CS) arises from gain-of-function (GoF) mutations in either KCNJ8 or ABCC9, the genes encoding the Kir6.1 and SUR2 subunits of cardiovascular ATP-sensitive potassium (KATP) channels, respectively. CS involves an array of cardiovascular pathologies, including cardiac hypertrophy and hypercontractility, low systemic vascular resistance, and excessively compliant, dilated, and tortuous vessels. Together, the latter features exemplify the hypomyotonic and hyperelastic components of CS vasculopathy. It was recently established that CS vasculopathy drives the associated cardiac pathologies, which are observed even in the absence of cardiac KATP GoF. In this thesis, I carried out experiments to determine …

Inducible Crispr-Targeted ‘Knockdown’ Of Human Gut Bacteroides In Mice Reveals Glycan Utilization Strategies, Zachary Beller

Arts & Sciences Graduate Student Theses and Dissertations

Learning how members of the human gut microbiota compete and cooperate for dietary nutrients, such as fiber-associated glycans, should help facilitate development of more precise nutritional recommendations for improving health. To model how bacteria prioritize the utilization of different fiber glycans in the mammalian gut, germ-free mice were colonized with a 13-member consortium of cultured, genome-sequenced human bacterial strains, including seven Bacteroides species. Animals were fed a Western diet supplemented with pea fiber. Once the consortium had time to assemble, an inducible CRISPR-based system was used to deplete the absolute abundance of Bacteroides thetaiotaomicron or B. cellulosilyticus by 10- to …

Characterizing The Expression Of The Sphingosine 1-Phosphate Pathway In Injury And Post-Traumatic Fibrosis, Nicole Cubbage

Masters Theses, 2020-current

Following injury, tissue repair allows for the restoration of the architecture and function of the injured tissue, while tissue replacement is characterized by severely damaged or non-regenerable tissue that is repaired by the laying down of extensive connective tissue, also known as fibrosis. The fibrotic process should be arrested at its early stage to have the greatest impact on preventing or reversing associate sequelae and promoting the regeneration of normal tissue. Sphingosine 1-phosphate (S1P), a metabolic product of cell membrane sphingolipids, has emerged as a pathway that may be involved in fibrosis. Most of S1P’s actions are mediated through the …

Assessing Structural Variation In And Out Of The Classroom: Characterizing Structural Variation Within Campanula Americana And Effects Of Long Read Sequencing On Students Learning, Tyler Gandee

Masters Theses, 2020-current

Cytonuclear incompatibilities are proposed to be one of the first genetic barriers to arise during speciation, so understanding the underlying evolutionary forces that contribute to cytonuclear incompatibilities is important. Many studies have looked at SNP level variation in the plastid genome and its relationship with cytonuclear incompatibility, but no studies have examined structural variation and its relationship to cytonuclear incompatibility, particularly at the early stages of speciation, i.e. within species. Campanula americana is a great system for this because it exhibits cytonuclear incompatibility and the family in which it is found, the Campanulaceae, exhibits rapidly evolving plastid genomes, including …

Dynamics Of Skin-Based Gene Expression In Red-Sided Garter Snakes (Thamnophis Sirtalis Parietalis): Sex And Seasonal Influences, Emily C. Plant

Masters Theses, 2020-current

The skin is the key organ regulating the animal-environment interface and is particularly sensitive to the abiotic factors of temperate environments, such as extreme cold and aridity during winter. Previous research found that, in the skin, temperate birds and reptiles upregulate expression of lipid synthesis genes to prevent tissue freezing and evaporative water loss in winter. My study species, the red-sided garter snake (Thamnophis sirtalis parietalis), has seasonally variable skin lipid composition, and females produce a modified set of these lipids that function as a sex pheromone. The pheromone is maximally produced in the spring breeding season following …

The Ecology And Genetic Diversity Of Buckleya Distichophylla (Santalaceae), Montana Hill

Masters Theses, 2020-current

Piratebush (Buckleya distichophylla) is a native, rare, shrub found along the Blue Ridge mountains in North Carolina, Virginia, and Tennessee. Research on its ecology and genetic diversity is limited due to its rarity; only one population on Poor Mountain has been studied extensively in the past. To determine if there are ecological differences between populations of B. distichophylla, research on sex distribution, floral visitors, individual length, leaf area, and amount of light that reached each specimen were conducted and then compared between a population located on Dragon’s Tooth Trail and a population on Poor Mountain, both located …

Greening The Edge: Investigating Riparian Buffer Restorations In A Pastoral Setting And Their Effects On Soil Carbon And Microbial Community Composition., Seth Mccullough

Masters Theses, 2020-current

Riparian buffer restoration represents a critical strategy for enhancing ecosystem health and resilience in agricultural landscapes. This study investigates the effects of riparian buffer restoration on soil properties, microbial communities, and carbon dynamics in Rockingham County, VA. Through a comprehensive field study, we assessed the physicochemical properties of soil, microbial biomass, community composition, and soil carbon storage in restored and unrestored riparian buffers. Our findings reveal significant improvements in soil physical properties in restored buffers, including increased soil moisture (p < 0.05) and decreased bulk density (p < 0.01), indicating enhanced soil structure and water retention capacity. While no significant differences were detected in soil pH or cation exchange capacity, restored buffers exhibited higher soil carbon stocks (p < 0.05) and carbon-to-nitrogen ratios, suggesting potential differences in nutrient cycling processes and organic matter decomposition rates. Moreover, restored buffers showed increased microbial biomass (p < 0.01), potentially driven by improved habitat conditions and shifts towards a fungal-dominated microbial community.

Although no significant differences were found in overall microbial community composition between restored and unrestored sites, specific shifts in bacterial …

Locating Vitamin D Receptors (Vdrs) In Annual Killifish, Austrofundulus Limnaeus, Rosalia N. Tanori, Amie L. Romney, Jason E. Podrabsky

Student Research Symposium

Austrofundulus limnaeus, a species of annual killifish found in unpredictable temporary habitats in South America, has a profound ability to survive long periods without water and oxygen. This tolerance is associated with the ability to enter metabolic dormancy associated with diapause. Entrance into diapause and tolerance of environmental stress is governed by an interplay of genetic and environmental factors. The vitamin D receptor (VDR) is among these factors and plays a crucial role in determining if an embryo will enter diapause or actively develop. My work aims to identify the genomic locations of VDR proteins in the A. limnaeus genome …

Dragon Pseudoscorpions Shed Light On Ancient Climate History In The Pacific Northwest, Joshua W. Hootman

Student Research Symposium

Pseudoscorpions are an ancient and diverse group of understudied arachnids, and there is much to be learned about their relationships to each other. Pseudoscorpions are one of many leaf-litter dwelling and low dispersing invertebrates that inhabit the forests of the Pacific Northwest. Previous phylogeographic studies of Pacific Northwest taxa have shed light on some of the climatic and geologic events that have shaped the area's flora and fauna. One purpose of this study is to determine if there is similar genetic structuring within the pseudoscorpion populations present in the study area, or if there is even more structure likely influenced …

Crossing The Ocean: The Importance Of Gene Flow In Island Evolution, Ethan F. Gyllenhaal

Biology ETDs

Islands have long been a critical arena for the development of ecological and evolutionary theory, particular due to persistent open-water gaps between them. In this dissertation I demonstrates how these caps are permeable, which can be leveraged to understand evolution on islands and more broadly. The first chapter develops this connection between ongoing, overwater gene flow and island biogeographic theory, and tests it on an archipelago species. The second take a three-pronged approach in demonstrating how over-water gene flow can bias phylogenetic inference, and how many phylogeographic metrics in islands are likely shaped by long-term gene flow. The final two …

Microbial Community Composition And Assembly In Diverse Environmental Systems, Rhiannon Celeste Vargas

Arts & Sciences Graduate Student Theses and Dissertations

Analyzing microbial community responses across systems, particularly in coordinated ways, is critical to informing meaningful community ecology patterns. In Chapter 1, I provide historical contexts to the field of microbial community ecology. In Chapter 2 I have investigated a specific opportunistic pathogen, Staphyloccocus pseudintermedius, by utilizing whole genome sequencing to understand the genomic architecture that contributes to the community structures of S. pseudintermedius found in different environmental niches. We found that unlike other Staphylococcal pathogens, S. pseudintermedius niches are indistinguishable by core and accessory gene architecture. Rather, niches are resolved through the encoding of antimicrobial resistances such as those isolates …

Autism Risk Gene Cul3 Alters Neuronal Morphology Via Caspase-3 Activity In Mouse Hippocampal Neurons, Qiang-Qiang Xia, Anju Singh, Jing Wang, Zhong Xin Xuan, Jeffrey D. Singer, Craig M. Powell

Biology Faculty Publications and Presentations

Autism Spectrum Disorders (ASDs) are neurodevelopmental disorders (NDDs) in which children display differences in social interaction/communication and repetitive stereotyped behaviors along with variable associated features. Cul3, a gene linked to ASD, encodes CUL3 (CULLIN-3), a protein that serves as a key component of a ubiquitin ligase complex with unclear function in neurons. Cul3 homozygous deletion in mice is embryonic lethal; thus, we examine the role of Cul3 deletion in early synapse development and neuronal morphology in hippocampal primary neuronal cultures. Homozygous deletion of Cul3 significantly decreased dendritic complexity and dendritic length, as well as axon formation. Synaptic spine density significantly …

Identification And Characterization Of Ube3a Gain Of Function Variants As A Driver Of Neurodevelopmental Disease, Kellan Phoebe Weston

Arts & Sciences Graduate Student Theses and Dissertations

UBE3A is a HECT (homologous to E6AP-Terminus) domain E3 ubiquitin ligase that targets substrate proteins for polyubiquitination and subsequent degradation through the ubiquitin-proteasome pathway. The UBE3A gene is of unique interest for its gene dosage-dependent effect in the developing brain: deletion of the maternal copy of UBE3A causes a severe intellectual disability known as Angelman syndrome; meanwhile, duplication or triplication of the genomic region containing UBE3A is linked to a prevalent syndromic form of autism known as Dup15q syndrome. However, little is known about the effects of missense variants which cause a single amino acid change in the resulting UBE3A …

Regulation Of Neuronal Cell-Type-Specific Transcription By Non-Cg Methylation And Mecp2, James Russell Moore

Arts & Sciences Graduate Student Theses and Dissertations

Modulation of gene expression is fundamental to the exceptional complexity and diversity of cells in the nervous system. Within that last decade, evidence has emerged that neurons utilize unique forms of DNA methylation to regulate transcriptional programs, with multiple types of neurons displaying high levels of cytosine methylation in a non-CG context compared to non-neural cells. This non-CG methylation primarily occurs at CA dinucleotides (mCA) and is read out by methyl-CpG binding protein 2 (MeCP2). Inactivation of MeCP2 results in Rett Syndrome (RTT), a severe neurodevelopmental disorder, while overexpression of MeCP2 results in MeCP2 duplication syndrome, an autism spectrum disorder. …

Identification Of Potent Pan-Ephrin Receptor Kinase Inhibitors Using Dna-Encoded Chemistry Technology, Chandrashekhar Madasu, Zian Liao, Sydney E Parks, Kiran L Sharma, Kurt M Bohren, Qiuji Ye, Feng Li, Murugesan Palaniappan, Zhi Tan, Fei Yuan, Chad J Creighton, Suni Tang, Ramya P Masand, Xiaoming Guan, Damian W Young, Diana Monsivais, Martin M Matzuk

Faculty, Staff and Students Publications

EPH receptors (EPHs) are highly sought-after drug targets owing to their essential roles in maintaining appropriate cellular functions in both physiological and disease conditions. However, limited potency and specificity pose significant obstacles to the development of small-molecule inhibitors for EPHs. Here, using high-throughput DNA-encoded chemical library screenings, we developed potent and selective inhibitors of the EPH receptor kinase family. Our results also emphasize the therapeutic potential of our EPH inhibitors in cancer and endometriosis, a global health concern that causes chronic pain and often leads to infertility in women. This study showcases the robust pipeline of using DNA-encoded chemistry technology …

Investigating The Involvement Of Gabaergic Interneurons And A Gene Therapy Strategy For Epilepsy In Cln2 Disease, Keigo Takahashi

Arts & Sciences Graduate Student Theses and Dissertations

The neuronal ceroid lipofuscinoses (NCLs) are a group of neurodegenerative lysosomal storage disorders affecting children and young adults. CLN2 disease, or classic late infantile neuronal ceroid lipofuscinosis, is one of the most common forms of NCL and is caused by a deficiency of tripeptidyl peptidase 1 (TPP1). Although an FDA-approved enzyme replacement therapy for CLN2 disease now exists, a poor understanding of pathophysiology has hampered the development of more effective and persistent therapy. While Cln2R207X/R207X knock-in mice which carry one of the most common pathogenic mutations in human patients were developed in 2017, this genetically accurate mouse model for CLN2 …

Measuring The Effects Of Selenium Exposure On Batrachochytrium Dendrobatidis (Bd) Growth In Vivo In Larval American Bullfrogs (Rana Catesbeiana)., Taylor Morrison

Honors Thesis

Most amphibians in today’s world are exposed to a variety of environmental stressors. This project’s main objective was to determine any effects of selenium on Batrachochytrium dendrobatidis (Bd) and infection levels in South Dakota amphibians. I selected American bullfrogs (Rana catesbeiana) as they are susceptible to Bd and are found throughout eastern South Dakota. The secondary objective of this project was to measure any impact of Bd and selenium, combined, on growth measures of the frogs. The third objective was to see if survival rates were reduced when amphibians were exposed to Bd and selenium. Tadpoles were collected (n=225) from …

Lmpact Of Salmonella Enterica Effector Proteins On Plant Physiology And Immunity, Sara Qader

Honors Theses

Salmonella enterica serovar Typhimurium are primarily recognized as pathogens associated with foodborne illnesses in humans. Salmonella also can colonize plant tissue effectively. The pathogen relies on type III secretion systems (T3SS) to infect mammals and plants successfully and counteract the immune response. Understanding the molecular mechanisms underlying Salmonella’s interactions with plants is essential for developing effective strategies to reduce its impact on human health and agriculture. Effector proteins, known for their role in modulating host-pathogen interactions, have been implicated in the virulence and pathogenicity of Salmonella. However, their specific functions and contributions to Salmonella’s interactions with plants remain largely unknown. …

Investigating The Electrostatics Of Mucins As Key Contributors To Mucus Stasis In Cystic Fibrosis, Elex Skylar Rose

All ETDs from UAB

Cystic fibrosis (CF) is a genetic disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which encodes a channel responsible for the transport of chloride and bicarbonate ions across the apical cell surface. In the respiratory tract, defective CFTR results in viscous and adherent mucus that becomes static within the airway, which leads to chronic infections, progressive lung damage, and early mortality. Historically, CF mucus stasis has been attributed to significant airway dehydration; however, growing evidence has demonstrated that aberrant electrostatic properties of mucins also contribute to mucus stasis in CF. Mucins are large, polymeric glycoproteins …

Mammalian Roadkill Trends In Central Georgia, Lucy Beck

Biology Theses

Wildlife-vehicle collisions are a global concern for both wildlife conservation and driver safety, and knowledge of spatiotemporal trends are required in order to effectively mitigate these consequences. This study documents species composition and spatiotemporal trends in terrestrial mammalian roadkill using ten-years of data recorded along a 12.8 mile stretch of State Route 212 in Baldwin and Putnam Counties, Georgia. From January 1 2012 to December 31 2021, 2,263 roadkilled vertebrates were observed on the survey route, and terrestrial mammals accounted for 84% of the observations. Two methods of hotspot identification indicated a non-random spatial distribution of roadkill associated with physical …

Comparing Oxidative Balance Of Summer And Winter Acclimatized Birds, Olivia R. Gulseth

Honors Thesis

The oxidative stress system allows air-breathing animals to deal with the potentially harmful byproducts of metabolism. How this system reacts to the increasing thermoregulatory demands in winter for birds from cold winter climates is poorly understood. The purpose of this project was to compare the oxidative balance of summer (warm acclimatized) and winter (cold acclimatized) phenotypes of overwintering songbirds in South Dakota to determine if there is a significant difference between the seasonal phenotypes and among species. Seasonal differences in oxidative balance were expected due to the increased metabolic costs of elevating metabolism to maintain body temperature during winter. Blood …

Beating The Heat: The Use Of Coral-Benefitting Bacteria For Heat-Stressed Anemones And Inspiring Future Biologists, Navah Eshraghi

Undergraduate Honors Theses

The warming of ocean temperatures has caused mass coral-bleaching events characterized by the expulsion of vital algal symbionts from coral tissues. However, the possibility of algal reuptake and existence of bacteria that support coral-algal symbiosis are two avenues of potential restoration efforts. Using the sea anemone Exaiptasia diaphana as a model for corals, I tested whether the coral-benefitting bacterium Endozoicomonas montiporae could enhance algal uptake under ambient (27°C) and heat-stressed (32°C) conditions. I then turned acquired results into an article modeled after National Geographic Kids to introduce the experiment to younger ages. While temperature was a larger determinant of algal-uptake …

Assessing The Effects Of Cold Storage Regimes Of North American Bombus Gynes, Thuy Tien T. Lindsay, Marcia M. Hagen, Joyce N. Knoblett, Joseph P. Rinehart, Karen M. Kapheim, James P. Strange

Biology Faculty Publications

Bumble bees are the primary commercial pollinators for greenhouse-grown crops and managing them requires insight into the Bombus life cycle. However, some aspects of the life cycle are not fully understood. Once mated, adult Bombus gynes can be stored for a short term at a constant low temperature (CLT). However, survival rates for some species are low during CLT, particularly when storage periods exceed a month. To address this, we tested the hypothesis that Bombus gynes stored in a fluctuating thermal regime (FTR) have increased survival compared to gynes stored in CLT. Specifically, the FTR had a baseline temperature of …

Dual Modes Of Dopamine Underly Distinct Facets Of Impulsive Actions, Tzvia Pinkhasov

Arts & Sciences Graduate Student Theses and Dissertations

During the pursuit of basic needs, animals sometimes fail to suppress actions that are maladaptive and counterproductive to their survival. In humans, these actions are often called impulsive because they can incur negative consequences. Impulsivity is ubiquitous across psychiatric disorders and related to debilitating outcomes such as substance abuse, crime and suicidality. Despite its risks, a lack of a neural mechanism understanding of impulsive actions impedes the development of effective treatments.In this dissertation, I set out to bridge the knowledge gained from the parallel fields of neuropsychopharmacology, experimental psychology, and systems neuroscience to uncover neural mechanisms of impulsive actions. Clinicians …

Neuroepigenetic Mechanisms Of Brain Development: From Technology To Biological Insights, Allen Yen

Arts & Sciences Graduate Student Theses and Dissertations

Each cell in the brain has the same genomic sequence, yet they can have vastly different phenotypes and function. This diversity is a result of complex genetic and signaling pathways, and knowing how these are regulated is key to understanding physiological development and how pathogenic dysfunctions arise. Genomic methods such as chromatin immunoprecipitation followed by sequencing (ChIP-seq) and assay for transposase-accessible chromatin with sequencing (ATAC-seq) have played pivotal roles in dissecting these processes. However, a key limitation is that the cells are destroyed upon observation of their molecular states, which preclude our ability to correlate historical epigenetic information with future …

The First Draft Genome Of Cold-Water Octocoral Anthothela Grandiflora, The Great Flowerbud Coral, Laurel Humphrey

Honors Scholar Theses

Cold-water corals are important sources of ocean biodiversity, yet populations are increasingly threatened by human activity and climate change. Soft octocorals may endure higher ocean acidification levels in comparison to stony hexacorals, although the mechanisms of octocoral biomineralization are less understood. Building genomic resources for cold-water octocorals could help to close information gaps by elucidating the evolutionary history of octocoral calcification and provide a reference for future studies of adaptation to acidified waters. This report describes the first reference genome for the cold-water octocoral species Anthothela grandiflora found throughout the Atlantic Ocean. Sequencing using Oxford Nanopore Technologies generated 43.6 Gb …

The Effect Of Population Density On Harmful Algal Blooms In Southwest Florida, Emma Barry '25

Biology Student Scholarship

Karenia brevis is a species of algae native to the Gulf of Mexico. Times when its growth becomes uncontrollable are called harmful algal blooms (formerly called “red tide events”), and they are often caused by increased nutrients in the water. These excessive nutrients come from watersheds and runoff that contain anthropogenic materials like fertilizer, and the phosphate and nitrogen in fertilizers catalyze the growth of algae. As population density in Florida increases, fertilizer runoff increases as well. Harmful algal bloom events are dangerous to both humans and the environment. Thick layers of algal growth on the water’s surface create “dead …

Alcohol Reward Memory In Drosophila: Investigating Changes In Neural Activity In Response To Cues Alcohol Associations And Their Role In Regulating Other Alcohol-Related Behaviors., Marieke Guitink

Honors Projects in Biological and Biomedical Sciences

With more than 200 health conditions associated with Alcohol Use Disorder, excessive drinking can take a serious toll on an individual's health, mental health, and relationships. Despite significant disruptions, there are a few treatments for Alcohol Use Disorder that support long-term abstinence. To develop effective long-term treatments for Alcohol Use Disorder, it is essential to obtain an understanding of the underlying complex changes that alcohol has on the brain, however, the complexity of the mammalian nervous system has precluded researchers from achieving this. Drosophila melanogaster is a powerful model organism for investigating how alcohol hijacks neural circuits within the brain …

Ultraconserved Elements Based Phylogeny Of The New Zealand Mite Harvester Genus Rakaia, Zade Alafranji

Biology Honors Projects

New Zealand is home to a remarkable number of endemic taxa, some of which existed on the archipelago before the breakup of Gondwana. The mite harvesters (suborder Cyphophthalmi), tiny arachnids which dwell in forest leaf litter and caves, are one such group. The mite harvester family Pettalidae exhibits a classic Gondwanan distribution, informative for describing ancient patterns of diversification. Within New Zealand, there are three genera of pettalids; our research focuses on the phylogeny of the most widespread and diverse of these: Rakaia. Through phylogenetic analysis, we provide a window into patterns of ancient diversification and infer historical biogeographic trends. …