Week 10: Bio Production
Context
Focus this week: lycopene/β-carotene production in E. coli, automation mindset, and design–build–test–learn iteration.
Timetable
| Date | Duration | Section |
|---|---|---|
| 2025/04/13 | 00:21 | Part A |
| 2025/04/13 | 01:30 | Part B |
| 2025/04/2 | 01:45 | Draw some figures for questions |
Lecture
- Class recording: https://mit.zoom.us/rec/share/ZBjjJ9UrX3prdOvgh0GKoVAFAJ9hRo_dVgyURNpLdrNGHEZ3ka5jJeF_LLzgnkNp.xWS9f4VWmWl4EBcx
- Slides (Lycopene/β-carotene bioproduction): https://docs.google.com/presentation/d/1RW-sN_T8bYeFN6toOoF_j2fi5sIgFyiDmez04OKoupg/edit
Recitation
- Slides: https://docs.google.com/presentation/d/1RW-sN_T8bYeFN6toOoF_j2fi5sIgFyiDmez04OKoupg/edit
- Recording: https://mit.zoom.us/rec/share/hRB2UHTiD6jTUMVIjN0URbJVH72vJAud_y4SItB_0jMtvsAy2k9BiQXvgGynyjxq.l631zyVPNKJGG_Lz
Homework — Part A (lecture questions)
Info
Prompt source: Patrick Boyle’s lecture questions (automation + scale; “metric tons” thought experiment).
Q1 — If all the molecular biology could be automated, what new questions would you ask or what new products would you make?
My notes (summary):
- Automation would unlock scale (more variants, conditions, and replicates) and tighten iteration loops from in silico → in vitro → in vivo, reducing the gap between lab and real-world tests.
- I’d target areas where iteration speed matters (e.g., monoclonal antibodies for oncology), using closed-loop optimization to refine binders and assays.
Q2 — If you could make metric tons of any protein, what would you make and why?
My notes (summary):
- Environmental: enzymes for plastic degradation in marine settings (stability/half-life crucial).
- Health: high-demand proteins (e.g., therapeutic proteins or vaccine antigens) for global access and outbreak response.
Sketches from my notes
Homework — Part B (lab questions)
Key link (protocol):
- HTGAA 2025 Bio Production Lab Protocol (Google Doc): https://docs.google.com/document/d/15-tlrejgbbr4FMpA6rKogTjlv6qXJhFqQm7o_Ppfh-I/edit?tab=t.0
Key papers mentioned:
- E. coli on fructose improves biomass yield and recombinant expression (classic result). DOI: https://doi.org/10.1021/bp980115v
- Lycopene/β-carotene pathway genes (crtE, crtI, crtB, + crtY for β-carotene) background and implementations: Addgene pAC-LYC / pAC-BETA pages (see references).
Representative question: Which genes, when moved into E. coli, induce lycopene vs β-carotene production?
Answer (concise):
- Lycopene: crtE, crtI, crtB (e.g., pAC-LYC).
- β-carotene: crtE, crtI, crtB, crtY (e.g., pAC-BETA).
What to turn in
- Short responses to Part A questions (+ your diagrams or screenshots).
- Part B answers with 1–2 supporting citations (protocol or papers).
- Any images/plots from your experiments or calculations.
References / resources
- Lecture recording (Zoom). :contentReference[oaicite:0]{index=0}
- Recitation recording (Zoom). :contentReference[oaicite:1]{index=1}
- Slides — Lycopene/β-carotene bioproduction (Google Slides). :contentReference[oaicite:2]{index=2}
- Bio Production Lab Protocol (Google Doc). :contentReference[oaicite:3]{index=3}
- Fructose vs glucose (classic bioproduction result, DOI). :contentReference[oaicite:4]{index=4}
- pAC-LYC / pAC-BETA plasmids (crtE/I/B/[Y]) — Addgene. :contentReference[oaicite:5]{index=5}