Robotic Platforms Accelerate Directed Evolution of Molecules


Are you familiar with directed evolution? Normally evolution is a very slow process that requires millennia, not decades, to show for significant changes and genetic mutations. Can robotics have a place in this kind of science? However, there have been scientific breakthroughs that allow researchers to speed up this process heavily, giving them the option to create new proteins and other molecules in their lab rapidly.

This new but already widely adapted practice is known as directed evolution or DE in short. It helps scientists in various fields such as yielding new antibodies to treat diseases such as cancer or others. It could help to create enzymes as they are used in the production of biofuel or help with imaging agents that are part of magnetic resonance imaging (MRI).

Faster than nature

Researchers led by Kevin Esvelt have developed a new robotic platform that allows them to monitor hundreds of microbial populations at once and keep an eye on how proteins and other molecules evolve. The robot can also help save populations from extinction if they struggle to survive.

As background knowledge for understanding this study, Robotic Platforms are used in many research areas, including the genetic engineering of cells. Directed evolution is a method that speeds up the accumulation and selection of novel mutations. Understanding evolution is vital in developing new drugs and vaccines and engineering cells for other purposes.

Example cycle of directed evolution
An example of directed evolution with comparison to natural evolution. (Image: Thomas Shafee, Evolvability of a viral protease: experimental evolution of catalysis, robustness, and specificity)

The research technique described in this article, which the researchers have named phage and robotics-assisted near-continuous evolution (PRANCE), allows for many more evolutionary trajectories to coincide, increasing the chances of success. Robotic platforms help to automate experiments that would otherwise be difficult, time-consuming, or impossible to achieve.

Molecules and proteins on the fast lane

Under Professor Martin A. Nowak, the Robotic Evolution Laboratory is developing new technologies for tracking the evolution of cellular populations over long periods. One challenge that this group deals with is how to observe what happens during an evolutionary process without interfering with it. For example, they have thought about tackling the problem by running the experiments in virtual reality without knowing about having done so.

Directed evolution - Landscape graphic
Performing multiple rounds of directed evolution is useful not only because a new library of mutants is created in each round but also because each new library uses better mutants as templates. The experiment is analogous to climbing a hill on a ‘fitness landscape’ where elevation represents the desired property. (Image: Thomas Shafee, Evolvability of a viral protease: experimental evolution of catalysis, robustness, and specificity)

The Robotic Evolution Laboratory affixed its high-resolution microscope to a robot whose movements are controlled by a computer. This enables simultaneous imaging of hundreds of microbial colonies. By allowing them to simultaneously track hundreds of microbial populations as they evolve new proteins or other molecules, it can be used for drug development or to better understand how evolution works.

Comments and conclusion

“Traditionally, directed evolution has been much more of an art than a science, let alone an engineering discipline. And that remains true until you can systematically explore different permutations and observe the results,” says Kevin Esvelt, an assistant professor in MIT’s Media Lab and the senior author of the new study.

“The robot can babysit this population of viruses by measuring this readout, which allows it to see whether the viruses are performing well, or whether they’re really struggling and something needs to be done to help them,” Erika A. DeBenedictis says.

Also interesting: Gramener Uses AI For Counting Penguins To Study and Save Them

“We can tune these evolutions in real-time, in direct response to how well these evolutions are occurring,” Emma J. Chory says. “We can tell when an experiment is succeeding, and we can change the environment, which gives us many more shots on goal, which is great from both a bioengineering perspective and a basic science perspective.”

“Our system allows us to actually perform these evolutions with substantially more understanding of what’s happening in the system,” Chory adds. “We can learn about the history of the evolution, not just the end point.”

Robotic platforms are becoming more widely used by researchers around the world. Using different conditions, PRANCE can evolve 100 times as many populations in parallel. PRANCE can help save populations from extinction if they are struggling to survive. Robotic Platforms significantly reduce the time and effort required to observe an evolutionary process without actually experimenting on it.

For more information, you can also review the MIT news report or the paper “Systematic molecular evolution enables robust biomolecule discovery” by Erika A. DeBenedictis, Emma J. Chory, Dana W. Gretton, Brian Wang, Stefan Golas, and Kevin M. Esvelt, which was published on December 30, 2021.

YouTube: The 2018 Nobel Prize in Chemistry: Directed evolution & phage display — Speaking of Chemistry

Photo credit: The feature image is symbolic and has been done by DC Studio. The graphics in the body of the article have been done by Thomas Shafee.

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Christopher Isak
Christopher Isak
Hi there and thanks for reading my article! I'm Chris the founder of TechAcute. I write about technology news and share experiences from my life in the enterprise world. Drop by on Twitter and say 'hi' sometime. ;)
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