Week 3 HW: Opentrons and automation tools

Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications.

Semiautomated Production of Cell-Free Biosensors
https://www.sciencedirect.com/org/science/article/abs/pii/S2161506325000725

Cell-free biosensors combine the gene expression machinery of cells with engineered genetic circuits, enabling detection of molecules through measurable outputs like fluorescence (GFP) or color change (LacZ). These systems have unique advantages - they can be freeze-dried, distributed cheaply, and used at the point of need without living cells, making them promising platforms for environmental and health diagnostics. However, traditional workflows rely on manual pipetting to assemble reactions, which is slow and introduces variability in performance.

To overcome this bottleneck, the authors developed and evaluated a semiautomated manufacturing protocol using the Opentrons OT-2 liquid handling robot. They compared traditional manual assembly of reactions with an automated protocol and demonstrated the approach by constructing a full 384-well plate of fluoride-sensing cell-free biosensors. The reactions assembled by Opentrons performed comparably to expectations from manual assembly, supporting the idea that liquid-handling automation can improve scalability, reproducibility, and quality control in biosensor production.

Write a description about what you intend to do with automation tools for your final project. You may include example pseudocode, Python scripts, 3D printed holders, a plan for how to use Ginkgo Nebula, and more. You may reference this week’s recitation slide deck for lab automation details.

One of my ideas is to build a Programmable Regenerative Biofilter for Selective VOC Destruction
I would use the cloud lab to answer:

• Which detector design is most sensitive? Test 30-100 versions the promoter (the “on switch” strength), the regulator amount, the reporter (GFP glow vs luciferase glow)
• Which enzyme destroys formaldehyde fastest?
• Which setup lasts the longest before it wears out?

Find the best formaldehyde detector (it glows only when formaldehyde is present). Then find the best enzyme that destroys formaldehyde. Then test how to glue that enzyme onto a filter material so it works in a cartridge. Finally, combine detection and cleanup into a system that turns itself on only when formaldehyde is in the air.

Automated Build/Test Pipeline (Formaldehyde Focused):

1. Design & DNA Assembly (Build)
Upload formaldehyde sensor variants and enzyme gene sequences to the cloud lab → automated DNA synthesis, Gibson assembly, transformation, and sequence verification.

2. High-Throughput Sensor Screening (Test)
Express sensor constructs in 96-well cell-free reactions → expose to a formaldehyde concentration gradient → measure fluorescence to identify lowest detection threshold and highest signal-to-noise ratio.

3. Enzyme Activity Optimization (Test)
Express candidate formaldehyde-degrading enzymes in cell-free → add formaldehyde substrate → quantify degradation rate via colorimetric or absorbance assay → rank by turnover and stability.

4. Immobilization & Stability Assay (Build/Test)
Attach top enzyme candidates to bead or hydrogel matrices → wash and stress-test (heat, humidity simulation) → measure retained catalytic activity over time.

5. Closed-Loop Integration Test (Build/Test)
Combine best sensor + enzyme modules in automated plate workflow → confirm: formaldehyde detection triggers enzyme expression → formaldehyde concentration decreases over time → quantify response dynamics and regeneration capacity.