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OpenBU is Boston University’s digital institutional repository for scholarly articles, theses and dissertations, preprints, and grey literature. This repository enables BU researchers to share, disseminate, and preserve their scholarship, and makes their research more accessible
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Recent Submissions

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Dissecting the airway field of injury and immune microenvironment in lung squamous premalignancy at a single cell resolution
(2025) Conrad, Regan D.; Beane-Ebel, Jennifer E.
Lung cancer is the leading cause of cancer deaths globally, but early detection significantly improves survival, as evidenced by the success of low-dose computed tomography (LDCT) in reducing mortality rates. While LDCT identifies lung cancer at earlier stages, further improvements to survival may be achieved by detecting and treating premalignant lesions (PMLs), the abnormal airway changes that precede lung cancer. Not all PMLs progress to invasive cancer; some remain stable or regress, emphasizing the need to understand the mechanisms behind these outcomes. Beyond localized lesions, molecular alterations in the airway field reflect processes occurring throughout the lung, providing a potential avenue for noninvasive biomarker opportunities. Studies show gene expression in bronchial and nasal brushings can distinguish between benign and malignant lung nodules, suggesting airway profiling can aid lung cancer risk assessments. This thesis employs single-cell RNA sequencing (scRNA-seq) and bulk transcriptomic analysis to examine immune and epithelial changes linked to PML severity and to identify molecular shifts in the airway field that may serve as early detection biomarkers and inform prevention strategies. Previous studies identified immune changes associated with PML progression but lacked the resolution needed to determine the contributions of specific immune populations. I analyzed immune cells from endobronchial biopsies across histological grades, identifying 14 subpopulations that differed in abundance between low-grade (LGB) and high-grade (HGB) samples. A cluster of CD4+ T regulatory cells and a subset of plasma cells were enriched in HGB, while multiple CD8+ T cell subpopulations and a neutrophil subpopulation were more abundant in LGB. To examine airway-wide molecular alterations, I analyzed scRNA-seq data from bronchial and nasal brushes along with the biopsies. Nasal brush cells were enriched in gene modules associated with detoxification and mucous production, indicating upper airway specialization. Smoking-related transcriptional changes exhibited a gradient, being most pronounced in bronchial biopsies, followed by bronchial brushes, and least evident in nasal brushes. Notably, some cells from bronchial brush sample clustered with high-grade basal cells and an upregulated gene module in those cells correlated with the most severe lesion histology from bronchial brushes analyzed via bulk RNA-seq. Together, these findings highlight how both immune and epithelial cell populations are altered in PMLs and illustrate how molecular changes throughout the airway reflect the biology of nearby lesions. By leveraging profiling of the immune microenvironment in PMLs and samples collected using noninvasive brush techniques, this work offers new insights into the early stages of lung carcinogenesis and the potential for developing biomarkers to improve PML detection and risk stratification.
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Characterizing Y224 conformational flexibility in FtmOx1-catalysis using 19F NMR spectroscopy
(Royal Society of Chemistry (RSC), 2025-01-20) Wang, Xinye; Yang, Lingyun; Wang, Shenlin; Wang, Jun; Li, Kelin; Naowarojna, Nathchar; Ju, Yi; Ye, Ke; Han, Yuchen; Yan, Wupeng; Liu, Xueting; Zhang, Lixin; Liu, Pinghua
α-Ketoglutarate-dependent non-haem iron (αKG-NHFe) enzymes play a crucial role in natural product biosynthesis, and in some cases exhibiting multifunctional catalysis capability. This study focuses on αKG-NHFe enzyme FtmOx1, which catalyzes endoperoxidation, dealkylation, and alcohol oxidation reactions in verruculogen biosynthesis. We explore the hypothesis that the conformational dynamics of the active site Y224 confer the multifunctional activities of FtmOx1-catalysis. Utilizing Y224-to-3,5-difluorotyrosine-substituted FtmOx1, produced via the amber codon suppression method, we conducted 19F NMR characterization to investigate FtmOx1's structural flexibility. Subsequent biochemical and X-ray crystallographic analyses provided insights into how specific conformations of FtmOx1-substrate complexes influence their catalytic activities. These findings underscore the utility of 19F NMR as a powerful tool for elucidating the complex mechanisms of multifunctional enzymes, offering potential avenues for developing biocatalytic processes to produce novel therapeutic agents harnessing their unique catalytic properties.
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Mapping the dynamics of aquatic vegetation in Lake Kyoga and its linkages to satellite lakes
(Elsevier BV, 2024-12) Ma, Yaxiong; Gopal, Sucharita; Koch, Magaly; Kaufman, Les
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Connecting the dots: information visualization and text analysis of the Searchlight Project newsletters
(Boston University Frederick S. Pardee Center for the Study of the Longer �, 2012) Gopal, Sucharita; Najam, Adil
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La Experiencia Emocional en Estudiantes Transnacionales. Un estudio entre Texas y Jalisco
(2024-12-02) Gueta Solis, L.M.; Jimenez Ramirez, M.G.; Castro Burgos, D.C.; Castro, Dina
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Teachers’ noticing of proportional reasoning
(Springer Science and Business Media LLC, 2024-02-27) Amador, Julie M.; Glassmeyer, David; Brakoniecki, Aaron
The importance of understanding what and how mathematics teachers notice is well documented, but more research is needed on content-specific noticing. In particular, knowing how teachers notice proportional reasoning, a vital topic spanning all grades of mathematics, could inform measures that support students’ proportional reasoning. We examined how teachers noticed when responding to two prompts (one student-focused and one teacher–student-interaction-focused) after watching a video of a middle grades proportional reasoning lesson. We analyzed the proportional reasoning reported from 13 elementary and 20 secondary prospective teachers and used cooccurrences along with noticing practices to describe how teachers noticed proportional reasoning and what aspects of proportional reasoning they noticed. Results indicate: (a) the two prompts resulted in differences in what and how participants noticed proportional reasoning, (b) participants were primarily descriptive and not interpretative when describing the proportional reasoning they noticed, and (c) the elementary and secondary prospective teachers both noticed similar aspects of proportional reasoning but showed differences in how the proportional reasoning cooccurred with the noticing practices. These findings reiterate the importance of the prompts used with teachers, the potential of using video to advance teachers’ noticing of proportional reasoning, and the methodological potential of using cooccurrences to examine teachers’ content-specific noticing.
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