/Algorithms Can Bioengineer Cells for You

Algorithms Can Bioengineer Cells for You

Summary: Berkeley Lab scientists develop a tool that could drastically speed up the ability to design new biological systems

Original author and publication date: DOE Science News Source – September 24, 2020

Futurizonte Editor’s Note: If AI can bioengineer cells for you, it can also engineer you. The Borg collective is arriving.

Berkeley Lab scientists Tijana Radivojevic (left) and Hector Garcia Martin working on mechanistic and statistical modeling. Credit: Thor Swift/Berkeley Lab
Berkeley Lab scientists Tijana Radivojevic (left) and Hector Garcia Martin working on mechanistic and statistical modeling. Credit: Thor Swift/Berkeley Lab

From the article:

If you’ve eaten vegan burgers that taste like meat or used synthetic collagen in your beauty routine – both products that are “grown” in the lab – then you’ve benefited from synthetic biology. It’s a field rife with potential, as it allows scientists to design biological systems to specification, such as engineering a microbe to produce a cancer-fighting agent. Yet conventional methods of bioengineering are slow and laborious, with trial and error being the main approach.

Now scientists at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) have developed a new tool that adapts machine learning algorithms to the needs of synthetic biology to guide development systematically. The innovation means scientists will not have to spend years developing a meticulous understanding of each part of a cell and what it does in order to manipulate it; instead, with a limited set of training data, the algorithms are able to predict how changes in a cell’s DNA or biochemistry will affect its behavior, then make recommendations for the next engineering cycle along with probabilistic predictions for attaining the desired goal.

“The possibilities are revolutionary,” said Hector Garcia Martin, a researcher in Berkeley Lab’s Biological Systems and Engineering (BSE) Division who led the research. “Right now, bioengineering is a very slow process. It took 150 person-years to create the anti-malarial drug, artemisinin. If you’re able to create new cells to specification in a couple weeks or months instead of years, you could really revolutionize what you can do with bioengineering.”

Working with BSE data scientist Tijana Radivojevic and an international group of researchers, the team developed and demonstrated a patent-pending algorithm called the Automated Recommendation Tool (ART), described in a pair of papers recently published in the journal Nature Communications. Machine learning allows computers to make predictions after “learning” from substantial amounts of available “training” data.

In “ART: A machine learning Automated Recommendation Tool for synthetic biology,” led by Radivojevic, the researchers presented the algorithm, which is tailored to the particularities of the synthetic biology field: small training data sets, the need to quantify uncertainty, and recursive cycles. The tool’s capabilities were demonstrated with simulated and historical data from previous metabolic engineering projects, such as improving the production of renewable biofuels.

In “Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism,” the team used ART to guide the metabolic engineering process to increase the production of tryptophan, an amino acid with various uses, by a species of yeast called Saccharomyces cerevisiae, or baker’s yeast. The project was led by Jie Zhang and Soren Petersen of the Novo Nordisk Foundation Center for Biosustainability at the Technical University of Denmark, in collaboration with scientists at Berkeley Lab and Teselagen, a San Francisco-based startup company.

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