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Exploring Eukaryotic Genome Evolution Through Phylogenomics and Microscopy
No full textMeiosis is a process in which a cell replicates its genetic material and undergoes two reductive divisions to form haploid nuclei. Meiosis is a critical part of many eukaryotic life cycles, as it controls ploidy levels and generates genetic diversity through recombination. The distribution of meiosis in diverse lineages across the eukaryotic tree of life indicates that this process was present in the last eukaryotic common ancestor (LECA), thus, truly asexual eukaryotes are thought to be scarce and derived from sexual ancestors. With the advent of high-throughput genomic sequencing, putatively asexual genomes can now be probed for constituents from a conserved set of genes with known involvement in meiosis, together called the “meiosis toolkit.” However, this gene set is underexplored in many microbial lineages and the designation of some genes as “meiosis-specific” is controversial as some have been found to be active in other processes. Here, I extend a taxon-rich, gene-rich phylogenomic pipeline to explore the evolution of meiosis genes. I develop robust data curation methods to identify gene families of interest, which include multiple rounds of homology assessment. I create a user-friendly pipeline that combines gene tree topology and sequence composition to further curate gene families of interest by removing contaminant sequences. With robustly curated data, I build 67 trees for gene families involved in meiosis across more than 400 taxa from all major clades. I find that while many meiosis genes seem to be eukaryotic innovations, others likely predate LECA. Eukaryotic parasites from multiple major clades lack meiosis genes to the greatest extent, in concordance with the known gene loss and genome reduction in parasite evolution. Overall, the “meiosis toolkit” shows a bias towards metazoans, fungi, and plants, reflecting the intensity of study on these lineages and demonstrating the need for in-depth exploration of microbial genomes
The Structural and Kinetic NMR Studies of the Spiroiminodihydantoin (Sp) Lesion Mismatched to Guanine in a 11-mer DNA Duplex
No full textErrors are often introduced to deoxyribonucleic acid (DNA), whether the nucleobases are incorrectly paired during replication or the nucleobase itself becomes oxidized by damaging agents. These errors are detected by the repair mechanisms of the human cell. However, when damaged DNA isn\u27t successfully repaired, it can lead to many health problems, such as cancer. There have been prior studies on the structural and dynamic effects of DNA lesions and dynamic properties of mismatched bases, but much less is known about mismatch bases. Therefore, it is helpful to characterize the structure and dynamic of DNA duplex containing one pair of DNA mismatched bases to determine how they affect the double helix structure. As the base with the lowest reduction potential, guanine (G) is easily oxidized to produce 8-oxoguanine (8-oxoG) which leads to G → T transversion mutations, where a purine is being substituted by a pyrimidine. Further oxidation produces hyperoxidized guanine lesions, such as the (R/S) spirominodiydantoin (Sp) lesion. The presence of Sp lesion in normal DNA can lead to further transverse mutations resulting in DNA containing mismatch base pairs. Mismatched DNA, such as G-G instead of G-C in a DNA duplex, generally destabilizes the double helical structure by weakening the hydrogen bonding. This project focuses on the mismatched GG base pair effect on DNA through base pair opening studies using 1H Nuclear Magnetic Resonance (NMR) spectroscopy. The overarching goal of the lab is to combine mismatched base pair studies with lesion to further grasp the damage of both mutations effect on DNA. This would be done by an investigation of the Sp lesion’s effect on an 11-mer G-G mismatched DNA duplex compared to a control G-C 11-mer DNA duplex. This thesis will focus on a comparative study of the mismatched GG DNA and GC control DNA
Episode 9: Dresser-Rand DC1213
Get PDFEpisode 9: This episode features three alums from the Class of 2013: Zin Min Aye, Phoebe DeGroot, and Celeste To. Their Design Clinic project with Dresser-Rand was on the design of an impeller labyrinth seal for centrifugal compressors
Racism as a Source of Pain
No full textThe epidemic of chronic pain, affecting approximately20% of Americans and estimated to cost $600 billion per year, exacts a tremendous personal, economic, and societal toll. Though various social groups experience heightened rates of trauma, discrimination, and pain, here we focus onBlack Americans, given their unique history of anti-Black racism in the United States (US) context. We propose that racism is an overlooked but preventable source of, or exacerbating factor for, chronic pain and its consequences, and we advance a framework offering innovative pathways for re-search, treatment, advocacy, and policy
Episode 5: NDPW DC0910
Get PDFEpisode 5
This episode features three alums from the class of 2010, Margaret Akofio-Sowah, Mallori Harrell, and Lindsey Nguyen. Their Design Clinic project with the Northampton Department of Public Works was on the design for nitrogen reduction at the Northampton Wastewater treatment plant
“A Plague Broke Out among Them”: Reflections on the Bible and the Pandemic
Get PDFThis essay seeks to utilize ideas and texts found in the Hebrew Bible in order to historically contextualize the COVID-19 pandemic and to illuminate various existential, religious, political, and ethical issues raised by the current pandemic and our responses to it
STEM Outreach Activities in Academic Libraries: Planning Strategies, COVID’s Impact, and Future Considerations
Get PDFOutreach in academic libraries is an important aspect of their mission to support campus communities, but the nature of these activities, and the steps taken to plan them, is not fully understood at the profession-wide level. This study aimed to start the process of gathering data on outreach, especially among those who serve STEM-related constituents, and to begin recording the effects of COVID on library programming and events. In the summer of 2022, surveys were sent to representative librarians from Association of Academic Universities (AAU) members asking about their current outreach offerings and whether they utilized a formal outreach document to help plan and evaluate their efforts. Though all reported engaging in some sort of outreach, most shared that they had an informal approach to outreach planning. A majority reported that COVID required a shift in outreach, with staffing continuing to be a concern. Survey results are offered, along with a discussion of the findings and thoughts on the next steps towards a clearer understanding of the effects outreach has, as well as its role in academic libraries post COVID
Cranial Neural Crest Cells: Breaking Convention to Build the Forebrain
No full textNeural crest cells (NCCs) are a multipotent, neural progenitor cell type that migrate from the neural tube following its closure. This cell type can differentiate into multiple subtypes, one of which includes cranial neural crest cells (CNCCs). CNCCs have been shown to contribute to the craniofacial skeleton, sensory structures and the meninges of the forebrain. Previously we showed using live cell tracking of a UV photoconvertible line Tg(sox10:nls-eos) with confocal microscopy that some CNCCs migrate anteriorly toward and potentially into the embryonic forebrain. By 19 hpf, CNCCs can be seen reaching the dorsal and ventral rostral clusters of the forebrain, and prefigure commissures. By 22 hpf, the majority of expression of the marker used to track NCCs, sox10, is lost, raising questions about the contribution of CNCCs in forebrain development, and what other cell types CNCCs may be differentiating into. In combination with live-cell tracing, we previously utilized the tfap2a/2c double mutant, which demonstrates a total loss of NCCs, and observed decreased intracommisural distance at 28 hpf and infiltration of neuronal cells into the preoptic space. In order to further interrogate the migratory patterns of NCCs and their role in commissure development, we utilized the Tg(sox10:nls-eos) line on the Multi-View lightsheet, which offers increased visualization capabilities to previous microscopy techniques and the potential to track this cell type past 28 hpf. Attempts to capture NCC migration with this method have led to consistent death of the embryo during the time course, illustrating the need to troubleshoot issues in survivability within the constraints of the necessary mounting conditions. We have also employed a complementary approach to the tfap2a/2c double mutant through targeted ablation of NCCs prior to their migration using the combined GAL4/UAS nitroreductase system. Following ablation, we have demonstrated a decreased presence of NCCs at the midline at 22 hpf. At 24 hpf, we observed a qualitative reduction to the expression of one of the first genes expressed in the forebrain, family zinc finger family 2 (fezf2). By 28 hpf, we observed significant changes to gross morphology, including decreased presence of melanophores and alterations to transgene presentation. Moreover, we observed mispatterning of the anterior commissure and a decreased presence of neuronal cells within the forebrain. Taken together, these findings suggest that NCC loss may impact proper commissure formation as well as patterning of neuronal cell types and the genetic marker fezf2 within the forebrain. Funded by the Nancy Kershaw Tomlinson Memorial Fund
Conceptual Analysis of Scientific Process Paragraphs
No full textThis project translates the fundamental principles of Micro ELI, a computer program that analyzes natural language sentences and paragraphs to create nonlinguistic representations, from the Lisp programming language to Python, improving the compatibility and maintainability of the program. In addition to that, this project improves the Analyzer to make it capable of parsing expressions with more complicated English grammar structures. To better track changes of objects in a process, the project proposes a new conceptual representation system called Mental Motion Pictures (MMP). MMP records events in Frames in chronological order, keeping track of CD primitive ACTs—a conceptual structure that represents events coined by Roger C. Schank—and spatial relationships between objects. The project also implements a Converter that converts an MMP to a Dependency Graph (DG) similar to DGs from ProPara. The DG converted from MMP is found to be more informative and accurate than the corresponding ProPara DG, demonstrating the effectiveness of the MMP system in analyzing complex scientific processes