FRANCE CENTURI AIX MARSEILLE UNIVERSITY Niles Huang, Brasenose College, Final year undergraduate, Master of Biochemistry and Molecular Biology, In-person internship Work Projects I worked in a lab investigating the physical mechanisms of embryogenesis. My specific project sought to correlate patterns of gene expression to patterns of tissue deformations in a synthetic organoid model of mammalian development. My project employed a diverse set of approaches that can be grouped as follows. I helped optimize experiments to analyze the effect of extracellular matrix proteins on organoid development, requiring skills in cell culture, micromanipulation and live microscopy imaging. For analysis, I used deep learning to precisely detect the boundaries of organoids in microscopy data. These boundaries could then be used for detailed image analysis, including quantification of morphology and coarse-grained inference of tissue flows and deformations. I implemented a pipeline for these analyses conducive for high throughput analyses. The lab hopes to use these tools to produce accurate mechanogenetic models of embryonic development and to understand variability in development. My supervisor helped me by providing me lab training, codes and research papers. She also gave advice for how to improve my codes and lab protocols. Daily Life The internship was held in person in the Aix Marseille University campus at Luminy. On suite dorms were provided on campus, so the lab was a five-minute walk away. As well as my main supervisor, I had two additional mentors who taught me cell culture and preparation
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