Week 1 HW: Final Project Ideas

HTBAA Homework #1 Due: Tuesday September 22, by 2:30p ET

For your first homework, propose and describe one idea for something you would like to biomanufacture. This could be medicine, material, food, energy, an art, design, or architectural artifact, or beyond. Draw from your own background and interests for inspiration.

(1) What you would like to biomanufacture and why? Describe the target product or output you would like to make.

I want to create a Coffee Cherry Borer resistant tree.

Why are you interested in making it? Your motivation might be utilitarian—for example, addressing a problem in health, sustainability, food, energy, or manufacturing—but it does not need to be. Your project might instead have a social, cultural, artistic, or personal motivation.

I own a coffee farm in the Kona coffee belt on Hawaii. One of the bigger problems I face is the pest called coffee cherry borer

https://www.ctahr.hawaii.edu/site/cbbmanage.aspx

I would love to accelerate Mendal and create a cherry that does not taste good to the beatle.

(2) What living system would you use? Propose at least one living-system manufacturing chassis that could produce your target—for example, a microbial, mammalian, or cell-free system.

The chasis would be a tree itself

At a high level, describe how the system would make your target product. What goes into the system? What biological process or processes occur? What comes out?

I would edit the genome in tissue culture (CRISPER-CAS9?), regenerate one engineered plantlet, then clonally propagate that exact tree via grafting/cuttings.

(3) How would you use automation? Identify at least one automation technology that you would combine with your living system.

I would use liquid-handling robots preparing CRISPR reagents and applying them to many callus/explant samples in parallel, then automated PCR-based genotyping to screen which calli actually took up the edit correctly

I could use robotic arms with fine scalpels or laser dissection for explant transfer, automated subculturing systems (e.g. NuPlant’s SmartClone), and machine-vision quality control that sorts healthy vs. struggling plantlets

If available I could use a commercial robotic grafting system built specifically for woody plants: it 3D-scans the rootstock and scion, calculates the optimal cut, and assembles the graft with controlled pressure

(4) How much would you need to make, and how long would it take?

Perform a back-of-the-envelope calculation estimating what it would take to manufacture your target at a meaningful scale.

(a) How much?

I would create enough viables shoots to test in 1/4 acre of my farm - appx 200 trees

(b) How long?

No idea - I would need the TAs help in estimating that

What don’t you know yet? After completing your analysis, identify the 2–3 biggest technical unknowns, bottlenecks, or assumptions in your proposed biomanufacturing system.

If a viable DNA strand can be identified and created If the CRSPER-CAS9 technique will work when intorducing it into the tree If the social factors about bio-engineered crops will allow testing on my farm

AI Prompts (Claude Sonnet 5.0) I want to create a Cherry Beatle Borer resistant tree. what kind of living system would that be? create a seed whose DNA is altered?
how would I use automation to edit the genome in tissue culture, regenerate one engineered plantlet, then clonally propagate that exact tree via grafting/cuttings
Paused Start a new session Sonnet 5’s safeguards flagged this message. This sometimes happens with safe, normal conversations. Switching models won’t resume this session, so continue in a new one. Send feedback or learn more.

Papers https://www.nature.com/articles/s41597-025-05658-6
https://academic.oup.com/g3journal/article/15/1/jkae262/7900928
https://coffee-genome-hub.southgreen.fr
https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1215012/