Week 11 HW: Bioproduction
Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork
- what you contributed to the community bioart project
- what you liked about the project, and
- what about this collaborative art experiment could be made better for next year.
R/: I contributed one pixel in the upper right area of the collaborative canvas. It was a small but meaningful contribution to a collective bioart piece created by students from around the world.
What I liked most about this project was the idea of collaborating with people globally to build something together watching how individual contributions, as minimal as a single pixel, come together to form a unified artwork is a beautiful reflection of what collective science and art can achieve.
For next year, I think the project could be improved by giving contributors a way to see a live update of the canvas as it fills in, along with a small profile of who added each pixel making the human connection behind each contribution more visible.
Part B: Cell-Free Protein Synthesis | Cell-Free Reagents
Referencing the cell-free protein synthesis reaction composition (the middle box outlined in yellow on the image above, also listed below), provide a 1-2 sentence description of what each component’s role is in the cell-free reaction.
E. coli Lysate
- BL21 (DE3) Star Lysate (includes T7 RNA Polymerase) R/: The BL21 (DE3) Star lysate provides all the cellular machinery required for transcription and translation including ribosomes, tRNAs, and enzymes as well as T7 RNA Polymerase, which specifically transcribes genes under a T7 promoter.
Salts/Buffer
Potassium Glutamate HEPES-KOH pH 7.5 Magnesium Glutamate Potassium phosphate monobasic Potassium phosphate dibasic Energy / Nucleotide System
Ribose Glucose AMP CMP GMP UMP Guanine Translation Mix (Amino Acids)
17 Amino Acid Mix Tyrosine Cysteine Additives
Nicotinamide Backfill
Nuclease Free Water Describe the main differences between the 1-hour optimized PEP-NTP master mix and the 20-hour NMP-Ribose-Glucose master mix shown in the Google Slide above. (2-3 sentences)
Bonus question: How can transcription occur if GMP is not included but Guanine is?
Part C: Planning the Global Experiment | Cell-Free Master Mix Design
Assignees for this section MIT/Harvard students Required Committed Listeners Required Given the 6 fluorescent proteins we used for our collaborative painting, identify and explain at least one biophysical or functional property of each protein that affects expression or readout in cell-free systems. (Hint: options include maturation time, acid sensitivity, folding, oxygen dependence, etc) (1-2 sentences each)
sfGFP mRFP1 mKO2 mTurquoise2 mScarlet_I Electra2 The amino acid sequences are shown in the HTGAA Cell-Free Benchling folder.
Create a hypothesis for how adjusting one or more reagents in the cell-free mastermix could improve a specific biophysical or functional property you identified above, in order to maximize fluorescence over a 36-hour incubation. Clearly state the protein, the reagent(s), and the expected effect.
The second phase of this lab will be to define the precise reagent concentrations for your cell-free experiment. You will be assigned artwork wells with specific fluorescent proteins and receive an email with instructions this week (by April 24). You can begin composing master mix compositions here.
Important In order to be eligible for this, make sure that your final project slide is in the “2026 Committed Listener ONE FINAL PROJECT IDEA” slide deck. The final phase of this lab will be analyzing the fluorescence data we collect to determine whether we can draw any conclusions about favorable reagent compositions for our fluorescent proteins. This will be due a week after the data is returned (date TBD!). The reaction composition for each well will be as follows:
6 μL of Lysate 10 μL of 2X Optimized Master Mix from above 2 μL of assigned fluorescent protein DNA template 2 μL of your custom reagent supplements Total: 20 μL reaction
Part D: Build-A-Cloud-Lab | (optional) Bonus Assignment
Assignees for this section MIT/Harvard students Optional Committed Listeners Optional Ginkgo Nebula Cloud Laboratory Rendering, 2025 Ginkgo Nebula Cloud Laboratory Rendering, 2025
Use this simulation tool to create an interesting looking cloud lab out of the Ginkgo Reconfigurable Automation Carts. This is just a minimal implementation so far, but I would love to see some fun designs!