Homework

Weekly homework submissions:

  • Question 1 In the 1980’s, Keith Wood became the first to make a tobacco plant glow using firefly luciferase. However, he faced a critical limitation: they could not synthesize their own luciferin, requiring an external luciferin spray to emit light. 1 As Wood pivoted to fungal pathways, the firefly route has been largely abandoned despite its superior light efficiency. However, recent breakthrough have reopened this door, including the discovery of spontaneous benzoquinone + cysteine L-luciferin formation, and the identification of ACOT1 in D-luciferin transformation. My project aims to put these breakthroughs together, engineering plants capable of bioluminscence through firefly pathways.
  • Part 1: Benchling & In-silico Gel Art If ignoring ladder and lane 1, there is the design! I tried to recreate No Face from Spirited Away. link to benchling: https://benchling.com/s/seq-8pB9vY3uTYXRrqsIKJS6?m=slm-FP5NlW0BAaqfbSmaoUg0 DNA Design Challenge For my homework, I decided to pick the enzyme that is the strongest candidate for facilitating luciferin synthesis. I picked my enzyme from my independent research. First I downloaded Fallon’s paper data from Fallon et al. 2018, “Firefly genomes illuminate parallel origins of bioluminescence in beetles” in eLife (DOI: 10.7554/eLife.36495. This experiment compared gene expression between the fat body (a firefly’s liver) versus the lantern (the organ that makes light) to find which genes are highly expressed in the lantern. I ran a filter in the file PPYR_OGS1.1_fatbody-vs…_test.txt texts, keeping only the statistically significant genes of TPM ≥ 50 and sleuth b ≥ 3. The TPM measures how actively a gene is being expressed in the lantern tissue, a higher TMP signaling a higher likelihood of luciferin expression. The sleuth is the statistical software Fallon used, that estimates log2 fold change. The higher the b sleuth, the more expression a gene has specifically in the lantern than fat body. I also ran qval ≤ 1e-10 to adjust for random noise.
  • Python Script for Opentrons Artwork After designing in http://opentrons-art.rcdonovan.com/ (a pig with a heart in the centre), I chose to run the Collab notebook for simplicity. I used Claude Code to help generate my coordinates into proper code, before running all. After my first simulation I noticed “WASTING BIO-INK : more aspirated than dispensed” warnings, so I edited my code. The next simulation still seemed to be wasting ink, but Claude informed me it’s an issue with floating point rounding.