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The smallest recorder in the world is built from microbes

Audio signals can be stored in a medium of magnetic tape; similarly, the microscopic data recorder stores biological signals on a CRISPR tape in bacteria. Credit: Wang Lab / Columbia University Medical Center

Through some clever molecular tricks, researchers at Columbia University Medical Center have turned a natural bacterial immune system into a microscopic data logger, laying the groundwork for a new class of technologies that use bacterial cells for all , from the diagnosis of diseases to environmental monitoring.

Researchers modified a common laboratory strain of the ubiquitous human gut microbe Escherichia coli which allows bacteria to not only record their interactions with the environment but also mark the time of events.

The bacteria, swallowed by a patient, could record the changes they experience throughout the digestive tract, producing an unprecedented view of previously inaccessible phenomena, "says Harris Wang, assistant professor in the Department of Pathology and Cell Biology and Systems Biology at CUMC and lead author of the new work, described in today's issue of Science Other applications could include environmental sensors and basic studies in ecology and microbiology, where bacteria could monitor changes that otherwise they would be invisible without disturbing their environment.

Wang and members of his laboratory created the microscopic data logger by taking advantage of CRISPR-Cas, an immune system system in many species of bacteria CRISPR-Cas copies DNA fragments of viruses invaders so that the following generations of bacteria can repel these pathogens more effectively. As a result, the CRISPR locus of the bacterial genome accumulates a chronological record of bacterial viruses that he and his ancestors have survived. When those same viruses try to infect again, the CRISPR-Cas system can recognize them and eliminate them.

The microscopic data logger takes advantage of CRISPR to monitor the biological environment. Credit: Columbia University Medical Center

"The CRISPR-Cas system is a natural biological memory device," says Wang. "From an engineering perspective that is really nice, because it is already a system perfected through the evolution that It's really excellent for storing information. "

CRISPR-Cas normally uses its recorded sequences to detect and cut the DNA of the incoming phages. The specificity of this DNA-cutting activity has made CRISPR-Cas the favorite of gene therapy researchers, who have modified it to make precise changes in the genomes of cultured cells, laboratory animals and even humans. In fact, more than a dozen clinical trials are underway to treat various diseases through CRISPR-Cas gene therapy.

But Ravi Sheth, a graduate student in Wang's laboratory, saw unrealized potential in the CRISPR-Cas recording function. "When you think about recording signals that change temporarily with electronics, or an audio recording … that's a very powerful technology, but we were thinking how you can scale this to living cells." says Sheth.

Conceptual interpretation of the CRISPR tape recording system. Credit: Wang lab / Columbia University Medical Center

To build his microscopic recorder, Sheth and other members of Wang's lab modified a fragment of DNA called a plasmid, which gave him the ability to create more copies of himself in the bacterial cell in response to an external signal. A separate recording plasmid, which controls the recorder and marks the time, expresses the components of the CRISPR-Cas system. In the absence of an external signal, only the recording plasmid is active, and the cell adds copies of a spacer sequence to the CRISPR locus in its genome. When the cell detects an external signal, the other plasmid is also activated, which leads to the insertion of its sequences. The result is a mixture of background sequences that record time and signal sequences that change according to the cell environment. Researchers can then examine the bacterial CRISPR locus and use computational tools to read the recording and its synchronization.

The current document shows that the system can handle at least three simultaneous signals and record for days.

"We are now planning to see several markers that could be altered under changes in natural or disease states, in the gastrointestinal system or elsewhere," says Dr. Wang.

The TRACE system can be used to record signals chemical and biological changes in the environment in CRISPR tape in bacteria. Credit: Ravi Sheth

Synthetic biologists have previously used CRISPR to store poems, books and images in DNA, but this is the first time that CRISPR has been used to record cellular activity and the timing of those events.

The document Science is entitled, "Multiplex recording of cellular events more than 1 time in a biological CRISPR tape".

Explore more:
The alternative CRISPR system is less specific, more robust

More information:
R.U. Sheth et al., "Multiplex recording of cellular events over time in a CRISPR biological tape", Science (2017). science.sciencemag.org/lookup/ … 1126 / science.aao0958

Journal reference:

Provided by:
Medical Center of Columbia University

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