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Boffins make bio-chip breakthrough

Cancer-detecting yogurt now possible

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MIT boffins have made a breakthrough in biological computing that paves the way for cancer-detecting yogurts and other gloopy marvels.

The advance, which saw the researchers combine logic and memory within a single living cell, was published in the "Synthetic circuits integrating logic and memory in living cells" paper in Nature Biotechnology on Sunday.

The MIT researchers were able to create a biological circuit that could perform all 16 two-input Boolean logic functions in e-coli cells and store the output in DNA.

"We have created an efficient system for integrated logic and memory within single cells," the researchers wrote in the Nature paper. "Our modular DNA assembly strategy enables straightforward plug-and-play encoding of logic functions with concomitant memory arising from the ability of recombinases to 'write' information in DNA."

The circuits work by using recombinases - genetic recombination enzymes - to invert targeted stretches of DNA, letting the researches encode a single bit of memory into the DNA's orientation. When the e-coli divides (roughly every 30 minutes), the information is copied over to a new generation of bacteria, adding redundancy to stored data over time.

Potential applications of the technology include diagnosis of diseases, drug delivery and toxin detection.

"It's bringing computation to another realm, to the realm of biology," professor of MIT's Synthetic Biology Group and a senior author of the paper Timothy Lu told The Register.

"The goal here is not to replace silicon-based computers - most forms of biocomputing are probably too slow to compete with electronics," he said. What the technology does do is open up "a whole new class of applications," he said.

Previously boffins around the world have managed to create synthetic datastores in DNA and implement Boolean logic in living cells, but Lu believes this is the first time researchers have been able to cram both together within a single cell (or, for you semi-buffs out there, onto the same biological die).

This is a major advance because it allows the technology to work better within the "resource-constrained" environments of biological systems. "Direct and efficient encoding of complex logic functions without the need to cascade multiple universal gates together is desirable."

Want a cancer diagnosis with your morning yogurt, sir?

A future application of the technology could be diagnosis of early stage cancers.

"People eat yoghurt all the time, perhaps you could put this type of circuit into a harmless bacteria you'd already eat anyway, it could go in and sense some kind of early stage colon cancer and at the other end you could see these cells and collect them," Lu mused.

Messy collection of data aside, the example demonstrates one of the ways in which organic computing is more attractive than digital computing in a medical diagnosis setting: tell a person that you're going to feed them a fleet of microscopic nanomachines and they might get a bit nervy, offer them some fermented cow-juice and they'll probably open wide.

There are also opportunities for drug delivery, as the technology would make it possible to make a cellular circuit that could instruct cells to grow, produce recombinant proteins, and then self-destruct.

Bomb detection is a possibility as well, as this technology could be used to make biosensors that would sit around not doing much until they detected toxins or explosive, at which point they could turn a different colour.

Now that the scientists know how to mush logic and memory into the same circuit - a kind of biological memristor, if you will - the next area of development is creating biological devices with reversible memory.

This would let them "build circuits that can be reused over and over again for more complex computations," Lu says. By example, he noted that to count in binary you need to be able to reverse memory bits as counting from 0 to 7 is 0, 1, 10, 11, 100, 101, 110, 111.

Having this capability would let the scientists build sequential logic systems that could be reset or tied to a kind of system clock.

"I'm excited about extending this platform to higher organisms to tackle applications in biotechnology and basic science," Lu said. "We're also interested in expanding the complexity of computations that can be achieved with this approach." ®

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