Week 3 HW: Lab Automation

Part 01: Python Script for Opentrons Artwork

In order to create my art, I use the Automation Art Interface, and uploaded my art into the required form.

Part 02: Post-Lab Questions

Question one: I belive a perfect example of a paper with automated lab use would be one that is also focused on it. Therefore, I found and read the 2019 research paper “Towards a fully automated algorithm driven platform for biosystems design” by Mohammad HamediRad (https://www.nature.com/articles/s41467-019-13189-z). This paper demonstrates a fully automated laboratory platform called BioAutomata that integrates robotics with machine learning to close the entire Design-Build-Test-Learn (DBTL) cycle in synthetic biology with minimal human intervention after initial setup.

Figure from the article showing the overall workflow of the BioAutomata.

As a proof-of-concept, the authors applied it to optimize the lycopene biosynthetic pathway in E. coli by fine-tuning expression levels of three genes (crtE, crtB, and crtI), exploring a combinatorial space of ~13,824 possible variants while evaluating fewer than 1% of them.

Question two: As for the integration of lab automation in my own final project, I belive the optimal choice would be the Ginkgo Nebula in biofoundries. Ginkgo Nebula is designed for exactly this: outsourcing the high-throughput “Build” phase. Instead of cloning one gene at a time, you submit a library of designs. I intend to use this automation in creation of a killswitch in my “Yeast Biosheild”.

Part 03: Final Project Ideas

For my final project ideas, I decided to build upon the projects I came up with for the first homework which seemed to hold great potential: 1. The use of yeast as a biosheild against bacteria, specially those with antibiotic resistence. 2. The use of moquitoes as a form of vaccination. While this idea was originally pushed aside because it has already been done before, I have recently decided to combine it with the use of gene editing to have antibodies be sprayed onto the blood the mosquito drinks as a way of stopping parasitic diseases being transferred into the saliva gland, and also improving the modified mosquitoes’ chance of reprodction through improvements such as more thirst for blood, better fly patterns and more keep sense of sight. 3. My final idea was the use of artficaial cells to replace damaged nerves and, eventually, the automation of their repair.