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Synthetic biologists dream of reproducing life's basic processes from the ground up. Borrowing concepts from physics and engineering, some of them want to start by designing tiny genetic circuits inside cells so the cells behave like the switches and amplifiers in your radio or car.
So far, they've made bits and pieces like cellular toggle switches, counters and edge detectors. But until recently, their circuit-building toolbox lacked a basic instrument: an oscillator.
Oscillators switch back and forth between two states. You've seen simple oscillators if you've ever encountered a swinging pendulum, a weight on a spring or alternating current in a power outlet. Your body is filled with natural oscillators, too, such as the daily light/dark cycling of circadian rhythms.
Synthetic biologists made their first primitive cellular oscillator in 2000. Building one that was more stable and strong seemed just around the corner.
However, "it's been harder than we thought," says Jeff Hasty, a bioengineer at the University of California, San Diego.
A Decade in the Making
Nine years later, Hasty and his team transformed cells—in this case, pill-shaped E. coli bacteria—into the robust oscillators biologists had envisioned. He did it by inserting two genes that take turns switching on and off. When there's too much of the "on" gene, the "off" gene activates and shuts it down. As the genes continue to switch on and off at intervals, they also turn a fluorescent protein called GFP on and off so the researchers can see what's happening.
Hasty still had work to do, though. Each cell oscillated on its own. The cells behaved like "a bunch of guys doing their own thing" with no coordination, he says.
Now, Hasty's team has tweaked the oscillator to work in synchrony. One of the two circuit genes now sends out small signaling molecules that tell cells when other cells are nearby. As the cells sense a big enough community, they start to oscillate together. Researchers call this coordinated behavior "quorum sensing."
Hasty's synchronized oscillator represents the first big step toward developing a blink-based sensor that could detect pollutants or release drugs into the body when they're needed. That's because the engineered bacteria react to subtle environmental changes by blinking faster or slower, or dimming or brightening.
While ten years may seem like a long time to develop an oscillator that shows bacterial sensors are possible, it would have taken even longer without the help of computer modeling.
"We use computers to see if we're in the right ballpark," says Hasty. "We're not at a point where we can make precise predictions, but we can get a sense of what we might want to change to get the circuit to work."
For instance, computer models showed his team that they needed to continually flush away some of the signaling molecule in their experiment. Otherwise, the bacteria would stay on instead of blinking.
Although modeling let Hasty and others work through complex questions ahead of time, it didn't reveal everything. Hasty says the bacteria behaved in ways he hadn't expected.
"Every time we build something and it surprises us, we're reminded that we don't understand [these phenomena] all that well," he adds. "By designing circuits with parts whose properties we think we understand, we find out what we don't understand. Then we adjust what we know. So synthetic biology both requires and contributes to fundamental knowledge."