Week 3 - Lab Automation

This week we get hands-on (or at least code-on) with pipetting robots

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1. Python Script for Opentrons Artwork

LifeFab node at London only have 3 colors : Purple, Pink and Blue. Therefore I try making imaging working with just those ones.

Here is my first attempt: a reproduction of The Great Wave of Kanagawa from Hokusai. link : opentrons-art.rcdonovan.com/?id=faftr8467659586

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My second attemps is a spirale: link : opentrons-art.rcdonovan.com/?id=d3599rykx19y474

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I got and adapted the code to operate the opentrons to produce my image. I’ll stay listening to my node to know what are the possibilities, adapt my work and maybe make it.

2. Post-Lab Questions

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

Slowpoke: An Automated Golden Gate Cloning Workflow for Opentrons OT-2 and Flex, Malcı Koray Malcı et al. American Chemical Society, https://doi.org/10.1021/acssynbio.5c00629

This paper presents Slowpoke, an open-source, automated workflow for Golden Gate DNA assembly in synthetic biology. It is designed to run on affordable liquid-handling robots such as the Opentrons OT-2 and Opentrons Flex, making high-throughput cloning accessible to standard laboratories rather than only large biofoundries.

Slowpoke automates the full cloning pipeline: Golden Gate assembly of modular DNA parts, transformation into Escherichia coli, plating, and colony PCR screening. By precisely pipetting and handling dozens of DNA combinations in parallel, the robot enables rapid construction of large combinatorial genetic libraries with high accuracy and minimal human intervention. This automation allows researchers to quickly build and test multi-gene pathways, regulatory circuits, and standardized toolkit constructs, accelerating the design–build–test cycle.

  1. Write a description about what you intend to do with automation tools for your final project.

I’m not really sure yet but I think I might be able to run experiment from a cloud lab.

3. Final Project Ideas

Synthetic Biology Based Solution for Caffeine Production

Caffeine has become one of the most widely consumed psychoactive substances in the world. The estimated global coffee consumption in 2023/2024 was 10.6 million tonnes (ICO). This level of production generates significant impacts on human labor, land use, water consumption, transportation, and other environmental and socio-economic factors.

Caffeine naturally occurs in plants such as coffee, tea, and guarana, and it can be chemically extracted from these sources or produced synthetically through chemical processes starting from compounds such as ammonia. It could be interesting to explore synthetic biology approaches to develop alternative production solutions that could be deployed closer to areas of consumption and scaled to reduce these environmental impacts.

Some research has already been conducted in this area and could be starting points:

ref :

Could Synth Bio Improve Concrete: Reduce C02 FootPrint and/or Self repairability ?

No need to present concret its usages and impacts. Quite self explanatory title. Exploration of the actual possibilities, research on the strain of bacteria used, how and what are key limitations. Could lead into trying to improve them and doing concrete experiments

Some research has already been conducted in this area and could be starting points:

Synthetic Biology for Fermentation and Probiotics Improvements

Fermentation as been a technique to keep for for longer and even get more nutrients out of them though almost symbiotic relationship with bacterias and yeast. It could be interesting to take a closer looks on it and maybe try to characterise best levain colony and evaluate the value they brings.

It could also be done around other type of fermentation processes, we could optimize the good nutrients and probiotics creation of lactic acid based fermentation or pickling of different vegetables and seed as: cabbage, peppers, mustard and many more

Some research has already been conducted in this area and could be starting points: