Week 3 HW: Lab Automation

Part 1

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

The paper I’ll be analyzing is titled “Development of a high-throughput minimum inhibitory concentration (HT-MIC) testing workflow” published in Frontiers in Microbiology.

In summary, the researchers used an Opentrons OT-2 robot to automate an assay used to test the safety-efficacy profile of an antibiotic. They accomplished this by programmatically preparing a serial dilution of the antibiotic candidate across multiple 96-well plates with replicates, innoculating the wells with the test bacteria, then measuring the optical density of each well with a plate reader to determine bacterial viability after the antibiotic challenge.

The method outlined in the paper minimizes human error, standardizes the innoculation pattern used for each plate well and allows for a massive range of antibiotic concentrations, as well as antibiotics to be tested in parallel. This allows for massive improvements in thoroughput, accuracy and replicability of results.

Part 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.

Considering my main plan, SoilBuddy, lab automation serves primarily to augment the speed at which my experiments may be run, and allow for overlapping scheduling to optimize lab time.

There are a few key steps where lab automation will come in handy:

  • Building: plasmid digestion, transformation, and selection of bacteria
  • Testing: Testing the performance of the reporter system against multiplexed stimulus conditions

Building

Roughly, here are the steps I’ll be following along with the corresponding pieces of lab equipment required for each:

  • (if the plasmid isn’t ordered with gene construct and genetic switch incorporated) ATC Thermal cycler for PCR amplification of casette, Plate incubator for plasmid digestion
  • Plate incubator for heat shock transformation
  • Plate incubator for bacterial recovery, expansion and selection

Testing

Roughly, here are the steps I’ll be following along with the corresponding pieces of lab equipment required for each:

  • Opentrons OT-2 for preparing serial dilutions of N2 agent and pH
  • Opentrons OT-2 for preparing different innoculations of culture and replicate plates
  • Spark plate reader for reading out reporter results