Week 3 HW: Lab Automation

Opentrons Artwork

For this activity, I decided to do Majora’s Mask from The Legend of Zelda:

To view the design in the Opentrons page, follow this link: https://opentrons-art.rcdonovan.com/?id=7f6p4e5817h6ar0

To view the full code in Google Colab, follow this link: https://colab.research.google.com/drive/1FpWo3znYjL6Z7uWbc_opzQbmgbDo33rL?usp=sharing

Post Lab Questions

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

Fedorec et al. (2024) developed a biocomputer where bacterial colonies perform logic operations, eliminating the need for complex genetic engineering of individual cells: instead of building circuits inside the bacteria, they engineered “receiver” strains that respond to chemical concentration thresholds, then located the engineered strains at specific distances from some chemical input sources. The chemical gradients that overlap create concentrations at each colony location, and by changing the bacteria colony’s locations, they are programming them to perform AND and OR logic gates. The researchers used Opentrons OT2 handling robot to dispense the cultures onto agar plates and then add the chemical gradients. This approach is very interesting, because it treats physical space as the programmable medium.

Reference:

• Fedorec, A. J., Treloar, N. J., Wen, K. Y., Dekker, L., Ong, Q. H., Jurkeviciute, G., … & Barnes, C. P. (2024). Emergent digital bio-computation through spatial diffusion and engineered bacteria. Nature Communications, 15(1), 4896.

2. 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.

Since we had to think about two other final project ideas to add to the slide deck, here are my three final project ideas and how I could use automation tools as methodology:

1. Biofilm Filters for Amphibian Pathogens

For the automation tools, a handling robot can inoculate wells with different bacterial communities on small carrier materials; and add standardised Bd zoospore suspensions, incubate, and sample over time.

2. Bacterial Pattern Recognition

For the automation tools, a handling robot (such as the OT2) could be used to dispense the E.coli cultures and to then add the chemical gradients.

3. Beneficial Biofilm Coats for Corals

In terms of automation, an automated handling robot can assemble different combinations of candidate strains in wells with CaCO₃ chips or shell fragments to act as the coral.