Week 3: Automation Research & Project Proposal

1. Published Automation Research

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

The Paper

Description

This research utilizes the Opentrons OT-2 to automate the setup of cell-free protein synthesis (CFPS) reactions. The authors focused on characterizing genetic parts like promoters and riboswitches. By using automation, they were able to test over 1,000 different conditions in a fraction of the time it would take a human, with much higher reproducibility across plates.

This is highly relevant to my interest in carbon fixation. To improve the efficiency of an enzyme like Rubisco, you have to test many different genetic combinations. This paper proves that the OT-2 can handle the tiny volumes and viscosity of cell-free lysates to build those testing libraries accurately.

2. Final Project Proposal: The Carbon Optimizer

Question: Write a description about what you intend to do with automation tools for your final project. Include core details of what you would automate.

Project Vision

My project involves engineering Rubisco variants to improve carbon fixation rates. Rubisco is a major bottleneck in plant growth because it is slow and often reacts with oxygen instead of CO2. I want to build an automated screening platform to find mutations that improve its carboxylation speed.

Automation Strategy

I plan to use the Opentrons OT-2 as the core of my workflow, potentially integrating with Ginkgo Nebula for large-scale synthesis.

  1. Library Preparation: The robot will be responsible for mixing DNA templates of various Rubisco mutants with cell-free protein synthesis master mix in 384-well plates.
  2. Biosensor Integration: I will include a fluorescent pH-responsive dye in the mixture. When Rubisco fixes CO2, it changes the pH of the well. The automated system will dispense this dye at precise intervals to ensure the readings are consistent across all variants.
  3. Environmental Control: I will use a custom 3D printed plate holder to secure the wells during CO2 gas injection. Automation ensures that every well is treated with the same concentration of CO2 for the same amount of time.