New language lets researchers design novel biological circuits
MIT biological engineers have created a programming language that allows them to rapidly design complex, DNA-encoded circuits that give new functions to living cells.
Using this language, anyone can write a program for the function they want, such as detecting and responding to certain environmental conditions. They can then generate a DNA sequence that will achieve it.
“It is literally a programming language for bacteria,” says Christopher Voigt, an MIT professor of biological engineering. “You use a text-based language, just like you’re programming a computer. Then you take that text and you compile it and it turns it into a DNA sequence that you put into the cell, and the circuit runs inside the cell.”
Voigt and colleagues at Boston University and the National Institute of Standards and Technology have used this language, which they describe in the April 1 issue of Science, to build circuits that can detect up to three inputs and respond in different ways. Future applications for this kind of programming include designing bacterial cells that can produce a cancer drug when they detect a tumor, or creating yeast cells that can halt their own fermentation process if too many toxic byproducts build up.
The researchers plan to make the user design interface available on the Web.
No experience needed
Over the past 15 years, biologists and engineers have designed many genetic parts, such as sensors, memory switches, and biological clocks, that can be combined to modify existing cell functions and add new ones.
However, designing each circuit is a laborious process that requires great expertise and often a lot of trial and error. “You have to have this really intimate knowledge of how those pieces are going to work and how they’re going to come together,” Voigt says.
Users of the new programming language, however, need no special knowledge of genetic engineering.
“You could be completely naive as to how any of it works. That’s what’s really different about this,” Voigt says. “You could be a student in high school and go onto the Web-based server and type out the program you want, and it spits back the DNA sequence.”
The language is based on Verilog, which is commonly used to program computer chips. To create a version of the language that would work for cells, the researchers designed computing elements such as logic gates and sensors that can be encoded in a bacterial cell’s DNA. The sensors can detect different compounds, such as oxygen or glucose, as well as light, temperature, acidity, and other environmental conditions. Users can also add their own sensors. “It’s very customizable,” Voigt says.
The biggest challenge, he says, was designing the 14 logic gates used in the circuits so that they wouldn’t interfere with each other once placed in the complex environment of a living cell.
In the current version of the programming language, these genetic parts are optimized for E. coli, but the researchers are working on expanding the language for other strains of bacteria, including Bacteroides, commonly found in the human gut, and Pseudomonas, which often lives in plant roots, as well as the yeast Saccharomyces cerevisiae. This would allow users to write a single program and then compile it for different organisms to get the right DNA sequence for each one.
Using this language, the researchers programmed 60 circuits with different functions, and 45 of them worked correctly the first time they were tested. Many of the circuits were designed to measure one or more environmental conditions, such as oxygen level or glucose concentration, and respond accordingly. Another circuit was designed to rank three different inputs and then respond based on the priority of each one.
One of the new circuits is the largest biological circuit ever built, containing seven logic gates and about 12,000 base pairs of DNA.
Another advantage of this technique is its speed. Until now, “it would take years to build these types of circuits. Now you just hit the button and immediately get a DNA sequence to test,” Voigt says.
His team plans to work on several different applications using this approach: bacteria that can be swallowed to aid in digestion of lactose; bacteria that can live on plant roots and produce insecticide if they sense the plant is under attack; and yeast that can be engineered to shut off when they are producing too many toxic byproducts in a fermentation reactor.
Learn more: A programming language for living cells
The Latest on: Biological circuits
via Google News
The Latest on: Biological circuits
- Kaushik Roy - 2020 Arden L. Bement Jr. Awardon November 26, 2021 at 2:12 pm
Kaushik Roy is the Edward G. Tiedemann, Jr., Distinguished Professor of Electrical and Computer Engineering at Purdue University and Director of the Center for Brain-Inspired Computing (C-BRIC). He ...
- How to read a jellyfish's mindon November 26, 2021 at 8:00 am
The human brain has 100 billion neurons, making 100 trillion connections. Understanding the precise circuits of brain cells that orchestrate all of our day-to-day behaviors—such as moving our limbs, ...
- 4 families welcome new additions on Adoption Day in Oakland Countyon November 26, 2021 at 3:41 am
Three youngsters and one adult were officially welcomed into their “forever families” through Oakland County Circuit Court as part of Adoption Day, an annual event celebrated throughout the ...
- Tarsons Products locked in 20% upper circuit on debut despite market crash. What should investors do?on November 26, 2021 at 12:37 am
The rally indicates that the appetite for the stock is huge and that was seen when the offer was subscribed 77.49 times.
- Context-dependent, untangled persistency facilitates value signal coding across the brainon November 24, 2021 at 4:35 pm
University of California San Diego researchers discovered the area of the brain where "value decisions" are made.
- Biden nominates Alison Nathan to 2nd Circuit courton November 24, 2021 at 8:29 am
Keen News Service [email protected] President Biden on Wednesday, Nov. 17, nominated a second lesbian, Alison Nathan, to serve on the Second Circuit U.S. Court of Appeals. The U.S. Senate on Nov. 1 ...
- How Value Decisions Are Coded Into Our Brainson November 23, 2021 at 3:06 pm
Persistency allows value signals to be most efficiently coded across the brain, specifically in the retrosplenial cortex.
- How AI Is Deepening Our Understanding of the Brainon November 23, 2021 at 7:00 am
By studying how deep learning algorithms work, scientists can distill high-level theories about the brain and then go test them in the lab.
- Distributed E. Coli Biocomputer Solves Maze Problemson November 19, 2021 at 5:00 am
Engineered bacteria, which consisted of six different genetic logic circuits and distributed among six cell populations, processes the chemical information and solved the problems by expressing, or ...
- Governor Mills & DMR Commissioner Keliher Respond to First Circuit Court Decision Reinstating Lobster Fishery Closure in Gulf of Maineon November 17, 2021 at 10:44 am
Governor Mills and Department of Marine Resources Commissioner Patrick Keliher issued the following statements today on the U.S. Court of Appeals’ decision to reinstate a 967 square mile fisheries ...
via Bing News