Designer chromosome synthesis with the help of PIXL
Patrick Cai, Daniel Schindler. Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street Manchester, M1 7DN
The Synthetic Yeast Genome Project: Sc2.0
The Cai lab is at the forefront of synthetic genomics, DNA synthesis automation, and applying synthetic biology approaches to antimicrobial drug discovery and designer chromosome synthesis. Most notably, they are one of the teams tackling the Synthetic Yeast Genome Project (Sc2.0), an ambitious, global effort to re-design and synthesise an entire yeast genome. Professor Patrick Cai and his team will contribute to the design and synthesis of at least one constituent neochromosome.
Professor Patrick Cai
The Cai Lab
Manchester Institute of Biotechnology
University of Manchester
Application
Dr. Daniel Schindler, who has been a member of Patrick’s team since 2017 uses the PIXL colony picker as a part of his usual workflows. He explains the lab’s requirements for colony picking:
“We do a lot of combinatorial DNA assemblies and molecular cloning in E. coli which constantly results in the need to pick many candidate colonies, for example, for plasmid extractions.”
“Our lab is also building synthetic chromosomes and large pathways in yeast, so we have to pick and characterise multiple isolates of 96 or more candidates. For this example, I used PIXL to do a stability assay to see if the neochromosome is lost between multiple rounds of growth without selection pressure.”
Dr. Daniel Schindler
The Cai Lab
Manchester Institute of Biotechnology
University of Manchester
Key benefits
1) More time and throughput
PIXL automates imaging, colony recognition, and selection, as well as picking and pinning. This allows Daniel to achieve the level of throughput necessary for confirming genetic stability in thousands of colonies per day.
“The most valuable part of PIXL is picking to high-density arrays. When we do high-throughput assays, it’s really important to get an accurate array. which we can use on other machines or with imaging software,” Daniel explained. “That’s the most important feature besides, maybe, the re-arraying function: if I have a certain pattern, and I want to re-array them into a new format, that’s helpful.”
When asked why manual colony picking wasn’t an option for this type of work, Daniel laughed, “That’s obvious, right? It’s challenging to generate arrayed plates of 384 colonies manually, even 96. I picked in one experimental setup up to, in total, 12 x 384 colonies per day over a time course of multiple days, so manual picking is impossible at this stage. No one would be able to pick colonies for eight hours every day, but PIXL can.”
Aside from producing the high-density arrays required for these PIXL testimonial experiments, PIXL frees up more time for Daniel to focus on other areas of his research. This is chiefly due to PIXL’s picking accuracy and it not requiring supervision. “PIXL saves time by being able to perform other experiments while PIXL does its job, so I am more productive. It also reduces the potential error rate, which reduces a lot of downstream troubleshooting time,” he says.
2) Reduced errors and costs
Through the adoption of PIXL, the Cai lab has also benefited from a reduction in expenditure on consumables. “The exclusion of manual errors saves a lot on downstream reagents and consumables,” Daniel commented. “The filament is even cheaper than using pipette tips.”
Daniel is referring to PickupLine, a reel of sterile polymer extrusion used for picking microbial colonies. The PickupLine is cut and extended between picks, eliminating the need for washing cycles, which can be a common source of microbial or ethanol contamination.
“PIXL uses a sterilised filament to pick individual colonies. For each step, the filament is cut so you have a fresh tip. That means you always transfer a colony with a sterile tip. For us, this is a good concept.”
