Biology Commons^™

Effects Of Varying Biochar Concentrations On The Growth Of Lactuca Sativa (Newham Bibb Lettuce), Lauren Holler

Williams Honors College, Honors Research Projects

The objective of this research experiment was to investigate the effectiveness of using biochar in potting soil in terms of plant growth and soil quality. This experiment was carried out using varying amounts (0%, 5%, 10%, and 20%) of biochar in the soil to see its effect on seed germination, plant growth, and soil quality such as pH, water retention, and soil temperature. The aim of the experiment was to identify whether biochar can be used in soil to promote healthier and stronger plants. There were four treatments which included 0% (Control), 5% (Treatment 1), 10% (Treatment 2), and 20% …

Sexual Di(Et)Morphism: Using Experimental Evolution To Test Whether Resource Partitioning Promotes Divergence Of The Sexes In Drosophila Melanogaster, Owen A. Jamieson

Theses and Dissertations (Comprehensive)

Sexual dimorphism has been a long-studied phenomenon in the field of evolutionary biology. Usually, these differences in morphology, physiology and/or behaviour between the sexes are studied through the parsimonious lens of sexual selection. However, there are natural history cases where this lens does not seem applicable. Some species show sex specific morphological traits whose presence may not be due to a direct benefit to reproduction, but a difference in how each sex interacts with the environment and differing selective pressures from the environment on either sex. Darwin even brought up examples of this kind of dimorphism and pondered their existence, …

Sediment Redox-Driven Iron Flux And Phytoplankton Community Responses: Implications For Cyanobacterial Suppression And Functional Stability Across Boreal Lakes, Julia K. Kozak

Theses and Dissertations (Comprehensive)

Freshwater eutrophication contributes towards the development of cyanobacterial harmful algal blooms (cHABs), but nutrient availability alone does not fully explain variation in phytoplankton community composition or physiological performance. While phosphorus (P) availability has been known to regulate phytoplanktonic biomass, iron (Fe) is an important micronutrient supporting Fe-heavy processes within cyanobacteria (i.e., nitrogen fixation and photosynthetic electron transport). Sediment Fe availability in freshwater ecosystems is regulated by reduction oxidation (redox) conditions at the sediment-water interface (SWI), where nitrate (NO₃^-) has been found to maintain oxidizing conditions and prevent the reduction of Fe(III) to more readily bioavailable soluble Fe(II), …

Leveraging Mammal Mycophagy To Determine Environmental Drivers Of Truffle Diversity, Brittany Hartsock

Electronic Theses and Dissertations

Many mycorrhizal fungi are hypogeous (truffle-forming), producing underground fruiting bodies. Studying truffles is inherently challenging due to their hidden nature. However, mycophagous mammals provide a unique opportunity to study hypogeous fungi because they rely on truffles as a food source. Although several truffle species have recently been described in the southern Appalachian region, their fruiting patterns remain poorly understood. To address this, we quantified truffle richness and spore loads from 670 Peromyscus scat samples collected across 42 sites spanning an environmental gradient during 2024 in the Blue Ridge Mountains of East Tennessee. We found that truffle richness and spore abundance …

Comparative Analysis Of Bacterial Recbcd And Sbcc-Sbcd Systems And The Yeast Mre11-Rad50 Complex During Dna Replication, Tannos Seyedjavadi

Dissertations and Theses

Accurate completion of DNA replication when forks converge is essential for genome stability. In Escherichia coli, several proteins have been identified including RecG, ExoI, RecBCD, and SbcCD, that contribute to completing replication, and loss of these factors causes genetic instability. Eukaryotes encode proteins with homology to several E. coli completion enzymes. Mre11–Rad50 complex is structurally and functionally conserved with bacterial SbcCD, and Rrm3 shares homologous motifs with bacterial RecBCD. These proteins are often described as being involved in homologous double strand break repair. Whether they are also conserved and play a similar role as their E. coli counterparts in …

Towards Identifying Fear And Safety Network States Across Sex, Rhonda Kolaric

Dissertations, Theses, and Capstone Projects

Post-traumatic stress disorder (PTSD) is a trauma- and stressor-related disorder with a lifetime prevalence of 5-6% in men, and 10-12% in women (National Center for PTSD). Generalized anxiety disorder (GAD) is a highly prevalent anxiety- and depression-related psychiatric disorder with a lifetime prevalence of 1-2% in men, and 3-4% in women (National Institutes of Health). Both of these disorders disproportionately affect women. A hallmark feature of both disorders is the maladaptive generalization of fear, in which defensive responses extend beyond the original traumatic or threatening stimulus to neutral or unrelated cues. This overgeneralization can become debilitating, disrupting cognitive, emotional, and …

Analysis Of Diterpenoid Alkaloids From American Aconitum Using Lc-Ms Metabolomic Methods, Yi Zhao

Dissertations, Theses, and Capstone Projects

Analysis of Diterpenoid Alkaloids from American Aconitum Using LC-MS Metabolomic Methods

by

Yi Zhao

Advisor: Edward J. Kennelly

Aconitum plants have been used as a traditional medicine in Asian countries for millennia to treat pain, rheumatism, syncope, fever, and other conditions. These therapeutic effects are mainly due to the bioactive diterpenoid alkaloids accumulated in the roots. Comparing with the large records and studies of Asian Aconitum and their medicinal use and the broad bioactive compounds, American Aconitum has been rarely investigated, not to mention how American Aconitum has been used medicinally. Based on previous phylogenetic and chemotaxonomic studies of Aconitum …

Data Curation And Integration For Cancer Cell Line Pharmacogenomics Analysis, Meric Kinali

Graduate Masters Theses

Cancer cell lines are essential resources for connecting genomic and molecular features with drug response and identifying biomarkers. Therefore, large-scale cancer cell line resources have been growing, but this introduces challenges such as data standardization, consistent annotation, matching identifiers, cross-database integration, and a reproducible computational framework. CellMiner Cross Database (CellMinerCDB) integrates pharmacogenomic datasets from multiple resources and provides a standardized analysis of cell lines across datasets. This thesis examines cancer cell line cross-databases and their importance in pharmacogenomics, with a particular focus on CellMinerCDB. As part of this work, I developed an R package for the gCSI (Genentech Cell Line …

Infrared Detectability Of Whale Species And Behaviors To Enhance Automatic Detection For Real-Time Vessel Strike Avoidance, Laura J. Howes

Graduate Masters Theses

Real-time detection of large whales at sea is critical for mitigating serious injury and mortality from ship strikes and other human activities such as seismic surveys, especially for endangered species such as the critically endangered North Atlantic Right Whale (Eubalaena glacialis). Traditional marine mammal observers are limited by environmental conditions and human factors, necessitating a robust, 24-hour solution. This study investigates the efficacy of a novel onboard detection tool infrared (IR) technology to detect whale blows and body parts. While IR is a promising advancement, its performance under varying sea conditions (e.g., fog, humidity) and its ability to …

Trophic Ecology Of A South Carolina Estuarine Predator Guild, Shane John Molander

Electronic Theses and Dissertations

Estuaries are among the world’s most productive ecosystems in the world and are characterized by the convergence of two distinct habitats, creating a mosaic of environmental conditions from inland rivers to the nearshore ocean. Many fishes occupy estuaries during various life stages for growth, reproduction, or foraging, and may reside in them seasonally. The co-occurrence of species, particularly upper-trophic level carnivores, can result in competitive interactions for prey resources within a shared environment. Identifying the degree of these interactions as well as understanding basal energy consumption can inform food web dynamics and how overlapping species use shared spaces. I used …

Exploring Foundations Of Animal Host-Microbe Interactions In A Freshwater Sponge, Jacob S. Pawley

Electronic Theses and Dissertations

The most ancient eukaryotic immune defense mechanisms evolved in unicellular species. Multicellular eukaryotes, however, expanded these mechanisms to meet challenges unique to multicellular life, including barrier formation, long-distance cell signaling, and coordinated responses that eliminate microbial threats while minimizing damage to the host. As such, animal immune signaling pathways are exceptionally intricate and diverse. Though, most of what is understood about animal host–microbe interactions stems from a small handful of model systems. Here, I evaluate host–microbe interactions and innate immunity in sponges using the highly tractable freshwater sponge, Ephydatia muelleri. I report the discovery of an external host-derived matrix …

Analysis Of Early Menopause And Endometriosis Genetics Merit In Use Of Polygenic Risk Assessments For Prediction, Emily Solomon

Graduate Student Dissertations, Theses, Capstones, and Portfolios

Endometriosis and Early Menopause are reproductive conditions that are under research in women's health. Both conditions impact a woman’s quality of life through severity of symptoms and associated risk factors and are influenced by genetic, hormonal and environmental elements. Both conditions have extensive and growing genetic knowledge that is being used to calculate either an increased or decreased risk of condition development. The array of genetic data shows promises in predicting risk for both conditions, as well as certain symptoms, to contribute to a personalized predictive tool to guide management of care. Endometriosis benefits from a potential polygenic risk assessment …

The Influence Of Circadian Rhythm Disruption And Apoe4 On The Prognosis And Progression Of Alzheimer’S Disease, Kayla Bradby

Graduate Student Dissertations, Theses, Capstones, and Portfolios

Alzheimer’s disease is characterized by cognitive decline and memory loss and is the most common form of dementia. Genetic factors such as apolipoprotein E have been significantly associated with AD development and progression, most specifically the APOE4 isoform. Emerging evidence has shown that when the body’s circadian rhythm, the 24-hour dark/light cycle, is disrupted, the potential to develop a neurodegenerative disease such as AD increases. The purpose of this literature review is to examine the relationship between AD, circadian rhythm, and the APOE isoforms. This review puts a particular emphasis on the APOE4 isoform, as it has been shown to …

Dissecting Tumor Evolution And Immune Composition In Prc2 Loss (H3k27me3 Loss) Vs Retained Mpnst, Kuangying Yang

Arts & Sciences Graduate Student Theses and Dissertations

Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive sarcomas that arise sporadically or in the setting of neurofibromatosis type 1 (NF1). Although benign plexiform neurofibromas (PNs) are common in NF1, only a subset undergo malignant transformation, and the molecular events that define high-risk progression remain incompletely understood. A major axis of biological heterogeneity in MPNST is loss of Polycomb Repressive Complex 2 (PRC2), commonly detected through loss of H3K27me3 and frequently mediated by alterations in SUZ12 or EED. This dissertation integrates three manuscript-based studies to define genomic resources, tumor-intrinsic vulnerabilities, and immune microenvironmental remodeling in NF1-associated peripheral nerve sheath tumors, …

Expression Profiling And Bioinformatic Characterization Of Depalmitoylation-Associated Genes During Sh-Sy5y Neuronal Differentiation, Ayesha Lodhi

Seton Hall University Dissertations and Theses (ETDs)

Palmitoylation is a reversible post-translational modification involving covalent attachment of palmitoyl groups to cysteine residues. Till date, 23 members of this family have been identified in mammals, located in Golgi apparatus and endoplasmic reticulum and nearly 40% of synaptic proteins are estimated undergo palmitoylation. These proteins include vesicle fusion proteins (SNARE), signaling molecules, ion channels and neurotransmitter receptors such as gamma-aminobutyric acidreceptors, kainate receptors and glutamate receptors. While its role in neuronal function has been widely recognized, comparatively little is known about how depalmitoylation-associated enzymes are regulated during neuronal differentiation. The present study aimed to characterize changes in depalmitoylation-associated gene …

Host-Pathogen Dynamics Underpinning Staphylococcus Aureus Growth During Intracellular Osteoclast Infection, Luke D. O'Connor

WUSM Theses and Dissertations – All Programs

Bone infection is most commonly caused by the gram-positive bacterium Staphylococcus aureus. It has myriad ways in which it can circumvent or subvert killing by the host or antibiotics. Intracellular infection is one such niche that is protective from immune and antibiotic attack. In 2019, Krauss and colleagues discovered that infected osteoclasts (OCs) allow S. aureus to replicate intracellularly. There they found that the ability of S. aureus to grow inside the cell was tied to OC differentiation. The magnitude of overnight bacterial expansion positively correlated with OC maturity and duration cultured with the osteoclastogenic factor RANK ligand (RANKL). Bacterial …

Beyond Autophagic Dysregulation: Vma21 Deficiency Reveals Altered Vesicle Trafficking And Broadens The Pathogenic Framework Of X-Linked Myopathy With Excessive Autophagy, Christian Suarez

Arts & Sciences Graduate Student Theses and Dissertations

Maintenance of protein homeostasis is essential for cellular function and depends on the coordinated regulation of protein synthesis and degradation. The major intracellular pathways responsible for protein degradation are the ubiquitin-proteasome system (UPS) and autophagy. Disruption of these processes has been implicated in a broad range of diseases, including neuromuscular disorders. X-linked myopathy with excessive autophagy (XMEA) is a rare vacuolar myopathy caused by mutations in VMA21, which encodes an assembly chaperone required for proper assembly of the vacuolar H⁺-ATPase (V-ATPase), the primary proton pump responsible for acidifying intracellular compartments, including lysosomes. Although impaired lysosomal acidification and autophagic dysregulation have …

The Gut-Bladder Axis: How Symbiont Microbes Alter Urinary Tract Infections, Benjamin S. Olson

Arts & Sciences Graduate Student Theses and Dissertations

Urinary tract infections (UTIs) are among the most common bacterial infections worldwide. Consequently, they are one of the leading indications for antibiotic prescription. Despite the typically successful treatment of an acute UTI, recurrent infections are exceedingly common, particularly among women. Nearly a quarter of otherwise healthy women will suffer recurrent UTIs (rUTI) after a primary UTI; why these select individuals are continually afflicted is unkown. There are no successful therapeutics to treat rUTI representing a gap not just in the medical toolkit but in our understanding of why rUTI is so prevalent. There are many hypotheses for the risk factors …

Integrative Evidence For Cryptic Diversity In The Thomomys Mazama Species Complex: Phylogenetics, Cranial Morphometrics, And Ecological Niche Modeling, Jessica Kate St. Michael

Dissertations and Theses

The population genetic structure and geographic distribution of the pocket gopher genus Thomomys Wied-Neuwied, 1839, lends itself to speciation events. Conserved morphology, ecological specialization, and high rates of molecular evolution may increase the probability of allopatric speciation, thereby contributing to the presence of morphologically cryptic taxa. In light of these patterns of evolution, we assessed genetic divergence and phylogenetic relationships, cranial morphometric differentiation, and ecological divergence among taxa in the Thomomys mazama species complex to test the hypothesis that T. mazama is a single species. Species delimitation analysis using Bayesian Poisson Tree Processes (bPTP) and data from the mitochondrial cytochrome …

Escherichia Coli Concentrations In Sand And Water At Tributary-Influenced Lake Michigan Beaches, Josie Elaine Kuhlman

Masters Theses

Contamination of public recreational water and sand is a human health concern, creating a management challenge for public health officials. Past research has shown that Escherichia coli can persist in sediment and can be washed into recreational water. Currently, beach monitoring practices only utilize E. coli concentrations in water samples to determine beach safety and do not consider potential exposure to sediment/sand concentrations. In this study, I investigated the relationship between E. coli concentrations in water and sand samples, which will aid public health officials in making more informed decisions about beach closures. I utilized culture-based measurements of E. coli …

Contributions Of Arginine And Nitrosative Stress To Huntington’S Disease Progression, Ian D. Gaudet

Electronic Theses and Dissertations 2020 - Present

Neuroinflammation is a well-established component of Huntington's disease (HD) pathogenesis, yet the intricate molecular mechanisms that govern this process remain a topic of ongoing research and debate. This dissertation elucidates a novel pathway linking arginine metabolism and nitrosative stress to core HD pathology. We found that the arginine transporter SLC7A2 is selectively upregulated in various HD cellular models and patient samples. Our findings reveal that this upregulation drives an overactive inflammatory response, leading to abnormally high inducible nitric oxide synthase (iNOS) induction and subsequent nitric oxide (NO) production, which causes excessive protein nitrosylation and an increase in mitochondrial fragmentation.

To …

Comparative Assessment Of Developmental Fidelity In Hpsc-Derived Neural Crest Cells, Michael H. Zepeda

Electronic Theses, Projects, and Dissertations

Neural crest cells (NCCs) are a transient, multipotent cell population that contributes to craniofacial structures, peripheral neurons, melanocytes, and smooth muscle. Defects in NCC development underlie a broad range of congenital disorders known as neurocristopathies. Human pluripotent stem cell (hPSC)-derived NCCs provide an evaluable model for studying early human development; however, existing differentiation protocols produce variable outcomes, and no standardized method consistently generates high-fidelity NCC populations. To address this challenge, we compared five published hPSC-to-NCC differentiation protocols using the H9 human embryonic stem cell line. We hypothesized that specific protocols more faithfully recapitulate neural crest development through coordinated regulation of …

From Genes To Streams: Mitochondrial Approaches To Population Monitoring Of The Santa Ana Sucker Catostomus Santaanae, Mariana Antonio

Electronic Theses, Projects, and Dissertations

This study was developed to use aquatic environmental DNA (eDNA) as a tool to detect the presence of the Santa Ana sucker (Catostomus santaanae), a federally threatened fish species, across the Santa Ana River in Southern California. Environmental DNA is any genetic material that an organism sheds into the environment. We can get an idea of what aquatic species are present when sampling water at a given site. We sequenced the complete mitochondrial genome (mitogenome) of the Santa Ana sucker and designed custom DNA primers to improve eDNA detection accuracy. These primers were selected based on high genetic …

Temperature And Salinity Effects On The Physiology Of Bullfrog Tadpoles (Lithobates Catesbeianus) From A Suburban Temperate Wetland, Angela Brown

Theses, Dissertations and Culminating Projects

One of the most robust amphibians is the American Bullfrog, Lithobates catesbeianus, which is a widespread species that is invasive worldwide, and is broadly tolerant of a range of environmental conditions. Despite this tolerance, survival and performance of adult L. catesbeianus can be negatively affected by increasing temperatures and salinity resulting from anthropogenic impacts, such as climate change and road salts. This study focuses on the effects of acute salinity exposure (mimicking road salt influx into a pond) on L. catesbeianus tadpoles at different larval stages. Increased salinity was predicted to negatively affect two physiological performance measures. Critical maximum temperature …

Bees In The Trap: Leveraging Bumble Bee (Hymenoptera: Apidae: Bombus) Bycatch For Ecological And Genetic Insights, Tori L. Strausser

All Graduate Theses and Dissertations, Fall 2023 to Present

Managers rely on insect monitoring traps to detect insect pests that harm crops and protect food and other agricultural production. However, these traps also capture non-target insects, including bumble bees, raising concerns about whether repeated trapping could harm pollinator populations. This thesis explores whether bees caught as non-targets, also called bycatch, in routine pest monitoring traps can be used to better understand bumble bee populations, and whether traps pose risks to their long-term persistence. Using bumble bees collected from pest surveillance traps placed in crop fields across Utah, this research examined seasonal patterns in body size, timing of capture, and …

Advancing Management Strategies For Two Promising Mason Bee Species (Osmia Ribifloris And Osmia Bruneri) For Berry Pollination, Miranda L. Jones

All Graduate Theses and Dissertations, Fall 2023 to Present

Bee management can broadly refer to human manipulation of one or multiple parts of a bee’s lifecycle. Managing honey bees, commonly referred to as beekeeping, is responsible for providing most pollination for global food crops. However, using more than one bee species for crop pollination can have many benefits. Benefits include better crop pollination and insurance in case one bee species underperforms or its population collapses. Some bees within the genus Osmia are already widely managed for crop pollination because their developmental lifecycle allows bee managers to readily deploy pollinating bees in sync with varying crop blooms, and for certain …

Integrative Taxonomic Analysis Of Cryptic Species Diversity In The Spiny Witch-Hazel Gall Aphid, Hamamelistes Spinosus (Hemiptera: Aphididae: Hormaphidini) In Eastern North America, Gavin Andrew Powell Munson

All Graduate Theses and Dissertations, Fall 2023 to Present

Taxonomy is the practice of identifying, classifying and categorizing species, providing structure for the vast diversity of life. Aphids are an ecologically important group of soft-bodied insects, but they can be difficult to identify because of their tiny anatomical size, reduced or simplified morphological features, and morphological variation within a single species across different generations. In this study, the taxonomy of the spiny witch-hazel gall aphid, Hamamelistes spinosus, is revised. The complex multi-generational life cycle of the aphids, which alternates between witch-hazel and birch trees, has led to confusion regarding past descriptions. Scientists in the late 1800s who were …

Fibrous Protein Biomaterials: Characterization Of Solitary Bee Silk And Cocoons, And Development Of Recombinant Hagfish And Bee Silk Materials, Oran Wasserman

All Graduate Theses and Dissertations, Fall 2023 to Present

This dissertation explores two complementary aspects of fibrous protein biomaterials: the characterization of understudied naturally occurring solitary bee silk and cocoons; and recombinant expression and biomaterial formation of recombinant hagfish intermediate filaments (rHIF) and a single Osmia lignaria Say (Hymenoptera: Megachilidae) silk protein. Some solitary bee species, which make up about 75% of all bee species, spin silk to construct protective cocoons during development. Despite the importance of silk and cocoons to the solitary bees' life history, their properties remain largely unexplored. This dissertation presents a novel method for isolating and testing individual silk fibers without interfering with the development …

Carbon Cycling, Salinization, And Long-Term Water Quality Trends In Rocky Mountain Streams, Allyson J. Marrs

All Graduate Theses and Dissertations, Fall 2023 to Present

Humans have greatly affected streams and rivers worldwide through urbanization, agriculture, and water use. The purpose of my dissertation is to increase our understanding of various human impacts on rivers. In chapter two, I aim to determine whether there are differences in greenhouse gas (GHG) emissions between a natural river and manmade canals. I did this by measuring the emissions and dissolved concentrations of three of the most prevalent GHGs, carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O). I found that most of the sites I studied were emitting CO₂ and CH …

Regional Occurrence And Spatiotemporal Habitat Partitioning Of The Culex Genus Mosquitoes In Salt Lake City And Uintah Basin, Utah, Katelyn Graybeal

All Graduate Theses and Dissertations, Fall 2023 to Present

West Nile virus is the most common mosquito-borne disease in North America and can cause serious illness, including inflammation of the brain and nervous system. Because there is currently no widely available vaccine for humans, preventing mosquito bites and monitoring mosquito populations remain the most effective ways to reduce disease risk. Understanding which mosquito species are present, where they occur, and how they respond to environmental change is critical for protecting public health.

This research examined the mosquito species responsible for spreading West Nile virus in Utah through two complementary studies. The first study focused on the Uinta Basin in …