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Modeled Changes in Foredune Morphology Influenced by Storm Intensity, Sea-level Rise, and Mitigation Strategies
No full textCoastal foredunes can mitigate the impacts of hurricanes and extratropical storms on vulnerable, low-lying communities. However, the degree of foredune resilience to climatic changes remains largely unquantified. Here, we use AeoLiS, a numerical model that simulates sediment transport in supply limited conditions. We first project annual-scale patterns of accretion and erosion within coastal foredunes for a range of beach and dune morphologies representative of those along the Outer Banks, North Carolina, USA. The model is subsequently used to explore how sea-level rise and changes in storminess may modify future dune volumes across beach morphologies. Model outcomes suggest that even modest rates of sea-level rise may greatly exacerbate dune erosion. In contrast, increased storminess may either lead to dune accretion, due to increased wind speeds, or exacerbate erosion due to increased total water levels. The precise nature of these future impacts on coupled dune-beach systems is highly dependent on how climate change and the pre-existing beach morphology. Maintenance of the protective benefits of foredunes with increased sea-level and storminess will require management implementation such as vegetation plantings, sand fences and beach nourishment. To test vegetation planting mitigation capabilities against elevated coastal hazards, we also varied the plant coverage within the model domain to reflect the distribution observed within the Outer Banks. Model runs indicate dune vegetation can mitigate impacts of future environmental forcings, though spatial distribution can change dune accretion patterns. We found that climate change is unlikely to impact coastal foredunes uniformly, posing a challenge for communities relying on these features for protective services into the future in the context of both increasing sea level and changing storm properties.GeologyBachelors of Science (BS
Cutting Translation out of the Equation: Exploring the P4 CI RNA as the Basis for a Novel Family of Translation-Independent Genetic Parts
No full textSynthetic biology (SynBio) aims to engineer living organisms for applications in industry, medicine, and environmental health. Central to SynBio is the concept of genetic circuits, DNA sequences fabricated from standardized biological parts to perform specific functions. Traditionally, these circuits rely on translation, the biochemical process of synthesizing proteins from mRNA. However, translation-independent logic presents a promising alternative paradigm for engineering genetic circuits that are less burdensome to their hosts, function with less latency, and have a number of other potential advantages. One relevant approach uses antisense RNA-mediated transcriptional attenuation, a molecular mechanism through which small antisense RNAs halt transcription by binding to attenuation sites on nascent RNA transcripts. Engineered orthogonal (mutually non-interfering) antisense-attenuator pairs have enabled RNA-only genetic circuits. However, RNA-based inhibitors of transcription remain scarce compared to their protein counterparts, in part because very few naturally existing antisense-attenuator pairings have been thoroughly investigated for this purpose. This project aims to expand translation-independent genetic parts by characterizing and working towards a genetic parts library derived from an alternative antisense RNA, designated CI, and derived from the bacteriophage satellite P4.Computational & Applied Mathematics & StatisticsBachelors of Science (BS
An Analysis of the Tweety Gene Family Members 1 and 3 and Their Role During Neural Development in Xenopus laevis
No full textNeural development is a complex process regulated by numerous cell signaling pathways. The Notch signaling pathway plays an essential role in guiding development and regulating stem cell potency. One gene linked to the Notch pathway is tweety 1 (ttyh1), a member of the highly conserved tweety gene family. In vertebrates, the tweety gene family has 3 paralogous members: tweety 1 (ttyh1), tweety 2 (ttyh2), and tweety 3 (ttyh3). These genes are thought to encode calcium-dependent and independent, volume-sensitive chloride channels. Previous research has shown ttyh1 and ttyh3 to be highly expressed in the nervous system during development and adulthood, with ttyh3 showing broader expression in maturity. These genes have been further shown to have clinical relevance, with ttyh1 being associated with numerous diseases and cancers, and ttyh3 found to drive the proliferation and metastasis of tumor cells. This thesis will investigate the role of tweety genes 1 and 3 during neural development in Xenopus laevis by knocking them out using a CRISPR/Cas9 system and overexpressing them through the injection of synthetic tweety mRNA. Analysis of mutation efficiency following knockout injection showed significant induction of INDEL mutations at the target site, indicating the ability of this system to induce gene knockout in Xenopus laevis. Following tweety 1 overexpression, chromogenic in situ hybridization revealed changes in the expression of tubb2b and sox2 consistent with a function in maintaining neural progenitor cell potency. Tweety 3 overexpression induced less obvious and, in comparison, somewhat contrasting changes in sox2 and tubb2b expression. Overexpression of both genes induced distinct, prominent changes in embryo morphology. Together, these results indicate tweety 1 and tweety 3 as proteins that play a significant role in development.NeuroscienceBachelors of Science (BS
Group 12 coordination complexes of a tridentate imidazolyl ligand
No full textHistidine is an essential amino acid with crucial involvement in antioxidant activity, metal-ion chelation, and toxic metal scavenging, and has demonstrated utility in Zn(II) coordination of many fundamental human proteins, like carbonic anhydrases. This prevalence of histidine in Zn(II) metalloprotein coordination sites has prompted group 12 coordination studies of a similar imidazole bis[2-(1-methylimidazolyl)methyl] amine ligand, nicknamed BMIMA. Here, we present the synthesis, characterization, crystallographic data, and crystal analysis of a suite of five- and six-coordinate divalent group 12 metal ions in complex with BMIMA in 1:1 and 1:2 metal ligand ratios. The compounds are characterized using X-ray crystallography, 1H NMR, IR, and elemental analysis. Bond angles around the central metal atom have elucidated a preferred square pyramidal orientation with heavier group 12 [M(BMIMA)Cl2] compounds and a particular trend of cis-facial geometry maintained by the [M(BMIMA)2](ClO4)2 complexes. Offset face-to-face (OFF) and edge-to-face (EF) intermolecular aromatic interactions are visualized for the complexes, providing synthetic parallels to crucial interactions stabilizing biomacromolecules. Furthermore, Hirshfeld surfaces generated for select complexes qualitatively detail relevant close contacts and possible hydrogen donor and acceptor roles, and deconstructed 2D fingerprint plots and various surface properties applied to the Hirshfeld surface glean additional information on these intermolecular contacts. A highly unusual triangular, non-bridging Hg34+ complex is also presented due to its inadvertent synthesis during crystallization trials of [Hg(BMIMA)Cl2]. Its distinct structure was found to be novel and lacking comparable analogs, facilitating discussion on its unique molecular geometry.ChemistryBachelors of Science (BS
Novel Phage Discovery and Phagelet Functional Analysis
No full textBacteriophage, viruses that infect bacteria, are a subject of intense scientific interest for their diverse clinical, ecological, and synthetic applications. There have been numerous large-scale efforts to capture the genetic diversity of phage and to describe novel phage systems. This thesis explores a novel phage satellite system, wherein a group of satellites, mobile genetic elements that cannot replicate and infect independently, called “phagelets” are hypothesized to parasitize the helper phage, HerbertWM. Genome annotation and comparison reveals that these 13 phagelet genomes, each approximately 11 kbp in length, fall into three distinct clusters with high homology within and across clusters. Genes shared across clusters include a terminase, a serine integrase, a tape measure protein, and a major capsid protein. Putative partial antirepressor genes were uncovered and investigated further as a set of candidate genes which might be responsible for the induction and subsequent parasitization of HerbertWM. Plasmids were created to express these genes and measure for prophage induction. It was found that the putative partial antidepressants were not sufficient to induce the prophage HerbertWM. Further, a novel phage in Cupriavidus gilardii was discovered from environmental samples. This phage’s genome is approximately 38 kbp in length. It shares similarities to Mu-like phages, and may be packaging host DNA into its capsid due to its transposase gene.BiologyBachelors of Science (BS
Transcriptomic Analysis of Xenopus laevis embryo response to Anterior-Posterior Axis Rotation
No full textThis study investigates the molecular basis of developmental plasticity in Xenopus laevis embryos during a critical window between mid-gastrula (stage 11.5) and late-gastrula (stage 12.5) stages. Using comprehensive RNA-seq analysis following 180° rotation of the presumptive neural tissue, we examined transcriptional changes in embryos with differential recovery capacity. Mid-gastrula rotated embryos (70% recovery rate) exhibited more extensive transcriptional responses (923 differentially expressed genes) compared to late-gastrula rotated embryos (30% recovery rate, 559 DEGs), indicating a more robust compensatory capacity at the earlier stage. Key pathways affected included Wnt signaling, FGF signaling, and chromatin remodeling regulators, with mid-gastrula embryos showing significant upregulation of epigenetic modifiers (hdac9.L, kat2a.S) and redox-related genes (nmral1.S, gstp1.L). By developmental stage 30, mid-gastrula rotated embryos uniquely upregulated genes involved in synaptic function (syp.L, cplx1.L) and neuronal connectivity, suggesting successful reestablishment of neural circuitry. Our findings reveal that coordinated regulation of chromatin remodeling, morphogen signaling, and neuronal differentiation pathways underlies successful developmental compensation following axial perturbations, with implications for understanding neural regeneration and plasticity mechanisms in vertebrates.Computational & Applied Mathematics & StatisticsBachelors of Science (BS
The role of NRF2 antioxidant genes in the embryonic development of Xenopus laevis
No full textEmbryonic development is a complex process through which a single cell gives rise to a fully formed organism, relying on tightly regulated cellular events such as proliferation, differentiation, and programmed cell death. Proper regulation of these processes depends on maintaining physiological levels of reactive oxygen species (ROS). ROS levels are controlled by antioxidant genes, many of which are regulated by the Nrf2 antioxidant pathway, a conserved defense mechanism against oxidative stress in both invertebrates and vertebrates. Although the Nrf2 pathway has been widely studied in cancer biology, its role in embryonic development remains less understood. Nrf2 is negatively regulated by Kelch-like ECH-associated protein 1 (keap1), which targets Nrf2 for degradation under normal conditions. Upon oxidative stress, Nrf2 is stabilized and induces the expression of various antioxidant genes, including oxidative stress-induced growth inhibitor 1 (Osgin1). To explore the role of the Nrf2 pathway during development, we performed whole mount in situ hybridization to examine the spatiotemporal expression of keap1 and Osgin1 in Xenopus laevis embryos. We found that Osgin1 is expressed in the notochord and prechordal plate during neurulation, and in the brain and spinal cord during tailbud stages, suggesting it may link oxidative stress regulation to neural tissue induction and differentiation. Previous studies also implicate Osgin1 in apoptosis and autophagy, indicating that it may influence these processes in the notochord and prechordal plate. Keap1 was ubiquitously expressed from neurulation through later development, supporting its essential role in sensing ROS and regulating Nrf2 activity throughout the embryo. These findings offer new insights into the expression of Nrf2 pathway genes and provide a foundation for further research into their roles in embryonic development.NeuroscienceBachelors of Science (BS
The Age and Origin of Nelsonite in the Central Virginia Blue Ridge
No full textA diverse suite of Grenvillian basement rocks are exposed in the central Virginia Blue Ridge province. In Nelson and Amherst counties, the basement complex includes the Roseland Anorthosite, a 5 x 15 km pluton that intrudes older ortho- and para-gneisses. Nelsonite, a distinctive apatite and ilmenite rich igneous rock, occurs as a minor, but important rock in this district. In the early 20th century nelsonite was extensively quarried as a source of both Ti and P; more recently (2016) nelsonite was designated Virginia’s state rock. We combine new geological mapping, petrology, geochemistry, and geochronology to better understand the age and origin of nelsonite as well as the thermochronology of the Blue Ridge basement complex in central Virginia. Nelsonite is inferred to form because of the liquid immiscibility between a Ti- and P-rich magma with a silicate melt which leads to density-driven settling to the bottom of a magma chamber. In the Roseland district, previous researchers posit that the nelsonite developed at the base of the ~1,010 Ma charnokitic Roses Mill Pluton, interpreted to be a sheet-like body that intruded into/above the Roseland Anorthosite. Nelsonite occurs as irregular dike-like and sill-like bodies, the largest of which is ~1 km in length and ~20 m thick. In addition to ilmenite and apatite, the nelsonite contains accessory titanite, magnetite, rutile, ± zircon. Geochemically, nelsonite samples range from 40 - 48% Fe2O3, 30 - 48% TiO2, 8 - 18% CaO, and 5 - 12% P2 O5 with 200 – 600 ppm Zr and ~0.3 ppm U. LA-ICP-MS U-Pb zircon analyses yield a concordia age of 949 ± 7 Ma for the nelsonite. Our new ages are 80 to 100 Ma younger than the inferred age for the nelsonite by previous workers. These data indicate that nelsonite is 1) not co-magmatic with the youngest Grenvillian rocks in the Roseland district and 2) significantly post-dates Grenvillian magmatism in the region. We hypothesis that nelsonite in the Roseland district was generated by post-Grenvillian orogenic collapse and crustal decompression of a Ti and P-rich source region.GeologyBachelors of Science (BS
Application and Characterization of a Novel Biocomposite Derived from Invasive Didymosphenia geminata
No full textDidymosphenia geminata is a species of diatom, a clade of algae so abundant that it is responsible for 20% of photosynthetic activity worldwide. D. geminata has also been classified as an invasive species on multiple continents due to their extracellular stalks creating thick mats, which can destroy benthic ecosystems in rivers, lakes, and streams. This research outlines methodology and preliminary applications of a biocomposite derived from the extracellular stalks of D. geminata. Biocomposite alternatives are becoming more necessary due to the rampant carbon emissions generated by materials in the construction industry. We specifically focus on creating an alternative to expanded polystyrene packing materials, as well as fiberglass and polystyrene insulators. We propose a fast, single-step chemical treatment process that allows the bulk composite to be molded depending on its application, and find results comparable to our target materials. Notably, the bulk material can be recycled between mechanical and thermal applications without loss of strength or insulating capabilities, provided the thermal breakdown point of 300°C is not reached. For another application of our composite, we investigate the use of powdered D. geminata material in the adsorption of small-scale oil spills. We find that the cleaned, unaltered material acts as an average adsorber, but has the ability to be enhanced through the binding of silica nanoparticles. Future avenues of work involve improving the mechanical strength of the material, or increasing its porosity to lower thermal conductivity. We also outline potential processes to make the nanoparticle binding process more environmentally friendly, with optimized chemical usage and less harmful byproducts.Applied ScienceBachelors of Science (BS