New device could make large biological circuits practical

Innovation from MIT could allow many biological components to be connected to produce predictable effects.

Researchers have made great progress in recent years in the design and creation of biological circuits — systems that, like electronic circuits, can take a number of different inputs and deliver a particular kind of output. But while individual components of such biological circuits can have precise and predictable responses, those outcomes become less predictable as more such elements are combined.

Freedawn Scientia - MI New device could make large biological circuits practical  Innovation from MIT could allow many biological components to be connected to produce predictable effects. T-Biological-Circuit-01_1

Left to right: Ron Weiss, professor of biological engineering; Domitilla Del Vecchio, associate professor of mechanical engineering; and Deepak Mishra, MIT graduate student in biological engineering.
Photo: Brian Teague

A team of researchers at MIT has now come up with a way of greatly reducing that unpredictability, introducing a device that could ultimately allow such circuits to behave nearly as predictably as their electronic counterparts. The findings are published this week in the journal Nature Biotechnology, in a paper by associate professor of mechanical engineering Domitilla Del Vecchio and professor of biological engineering Ron Weiss.

The lead author of the paper is Deepak Mishra, an MIT graduate student in biological engineering. Other authors include recent master’s students Phillip Rivera in mechanical engineering and Allen Lin in electrical engineering and computer science.

There are many potential uses for such synthetic biological circuits, Del Vecchio and Weiss explain. “One specific one we’re working on is biosensing — cells that can detect specific molecules in the environment and produce a specific output in response,” Del Vecchio says. One example: cells that could detect markers that indicate the presence of cancer cells, and then trigger the release of molecules targeted to kill those cells.

It is important for such circuits to be able to discriminate accurately between cancerous and noncancerous cells, so they don’t unleash their killing power in the wrong places, Weiss says. To do that, robust information-processing circuits created from biological elements within a cell become “highly critical,” Weiss says.

To date, that kind of robust predictability has not been feasible, in part because of feedback effects when multiple stages of biological circuitry are introduced. The problem arises because unlike in electronic circuits, where one component is physically connected to the next by wires that ensure information is always flowing in a particular direction, biological circuits are made up of components that are all floating around together in the complex fluid environment of a cell’s interior.

Freedawn Scientia - MI New device could make large biological circuits practical Innovation from MIT could allow many biological components to be connected to produce predictable effects. T-Biological-Circuit-01_1

Information flow is driven by the chemical interactions of the individual components, which ideally should affect only other specific components. But in practice, attempts to create such biological linkages have often produced results that differed from expectations.

“If you put the circuit together and you expect answer ‘X,’ and instead you get answer ‘Y,’ that could be highly problematical,” Del Vecchio says.

The device the team produced to address that problem is called a load driver, and its effect is similar to that of load drivers used in electronic circuits: It provides a kind of buffer between the signal and the output, preventing the effects of the signaling from backing up through the system and causing delays in outputs.

While this is relatively early-stage research that could take years to reach commercial application, the concept could have a wide variety of applications, the researchers say. For example, it could lead to synthetic biological circuits that constantly measure glucose levels in the blood of diabetic patients, automatically triggering the release of insulin when it is needed.

The addition of this load driver to the arsenal of components available to those designing biological circuits, Del Vecchio says, “could escalate the complexity of circuits you could design,” opening up new possible applications while ensuring that their operation is “robust and predictable.”

James Collins, a professor of biomedical engineering at Boston University who was not associated with this research, says, “Efforts in synthetic biology to create complex gene circuits are often hindered by unanticipated or uncharacterized interactions between submodules of the circuits. These interactions alter the input-output characteristics of the submodules, leading to undesirable circuit behavior.”

But now, Collins says, “Del Vecchio and Weiss have made a major advance for the field by creating a genetic device that can account for and correct for such interactions, leading to more predictable circuit behavior.”

The research was supported by an Eni-MIT Energy Research Fellowship, the National Science Foundation, the U.S. Army Research Office, the U.S. Air Force Office of Scientific Research, and the National Institutes of Health.

This follows on from – MIT team builds most complex synthetic biology circuit yet

New sensor can detect four different molecules, could be used to program cells to precisely monitor their environments.

Anne Trafton, MIT News Office
October 7, 2012

Freedawn Scientia -  MIT team builds most complex synthetic biology circuit yet  New sensor can detect four different molecules, could be used to program cells to precisely monitor their environments.

MIT biological engineers created new genetic circuits using genes found in Salmonella (seen here) and other bacteria.

Using genes as interchangeable parts, synthetic biologists design cellular circuits that can perform new functions, such as sensing environmental conditions. However, the complexity that can be achieved in such circuits has been limited by a critical bottleneck: the difficulty in assembling genetic components that don’t interfere with each other.

Unlike electronic circuits on a silicon chip, biological circuits inside a cell cannot be physically isolated from one another. “The cell is sort of a burrito. It has everything mixed together,” says Christopher Voigt, an associate professor of biological engineering at MIT.

Because all the cellular machinery for reading genes and synthesizing proteins is jumbled together, researchers have to be careful that proteins that control one part of their synthetic circuit don’t hinder other parts of the circuit.

Voigt and his students have now developed circuit components that don’t interfere with one another, allowing them to produce the most complex synthetic circuit ever built. The circuit, described in the Oct. 7 issue of Nature, integrates four sensors for different molecules. Such circuits could be used in cells to precisely monitor their environments and respond appropriately.

“It’s incredibly complex, stitching together all these pieces,” says Voigt, who is co-director of the Synthetic Biology Center at MIT. Larger circuits would require computer programs that Voigt and his students are now developing, which should allow them to combine hundreds of circuits in new and useful ways.

Lead author of the paper is former MIT postdoc Tae Seok Moon, now an assistant professor of energy, environmental and chemical engineering at Washington University in St. Louis. Other authors are MIT postdocs Chunbo Lou and Brynne Stanton, and Alvin Tamsir, a graduate student at the University of California at San Francisco.

Expanding the possibilities

Previously, Voigt has designed bacteria that can respond to light and capture photographic images, and others that can detect low oxygen levels and high cell density — both conditions often found in tumors. However, no matter the end result, most of his projects, and those of other synthetic biologists, use a small handful of known genetic parts. “We were just repackaging the same circuits over and over again,” Voigt says.

To expand the number of possible circuits, the researchers needed components that would not interfere with each other. They started out by studying the bacterium that causes salmonella, which has a cellular pathway that controls the injection of proteins into human cells. “It’s a very tightly regulated circuit, which is what makes it a good synthetic circuit,” Voigt says.

The pathway consists of three components: an activator, a promoter and a chaperone. A promoter is a region of DNA where proteins bind to initiate transcription of a gene. An activator is one such protein. Some activators also require a chaperone protein before they can bind to DNA to initiate transcription.

The researchers found 60 different versions of this pathway in other species of bacteria, and found that most of the proteins involved in each were different enough that they did not interfere with one another. However, there was a small amount of crosstalk between a few of the circuit components, so the researchers used an approach called directed evolution to reduce it. Directed evolution is a trial-and-error process that involves mutating a gene to create thousands of similar variants, then testing them for the desired trait. The best candidates are mutated and screened again, until the optimal gene is created.

Aindrila Mukhopadhyay, a staff scientist at Lawrence Berkeley National Laboratory, says the amount of troubleshooting the researchers did to create each functional module is impressive. “A lot of people are charmed by the idea of creating complex genetic circuits. This study provides valuable examples of the types of optimizations that they may have to do in order to accomplish such goals,” says Mukhopadhyay, who was not part of the research team.

Layered circuits

To design synthetic circuits so they can be layered together, their inputs and outputs must mesh. With an electrical circuit, the inputs and outputs are always electricity. With these biological circuits, the inputs and outputs are proteins that control the next circuit (either activators or chaperones).

These components could be useful for creating circuits that can sense a variety of environmental conditions. “If a cell needs to find the right microenvironment — glucose, pH, temperature and osmolarity [solute concentration] — individually they’re not very specific, but getting all four of those things really narrows it down,” Voigt says.

The researchers are now applying this work to create a sensor that will allow yeast in an industrial fermenter to monitor their own environment and adjust their output accordingly.

The research was funded by the U.S. Office of Naval Research, the National Institutes of Health, Life Technologies, Defense Advanced Research Projects Agency and the National Science Foundation.

– Credit and Resources –

David L. Chandler | MIT News Office (Biological circuit)
Anne Trafton | MIT News Office (MIT Team Builds Bio Circuit)

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