Storing computer files– in bacteria. Wow. 

This mind-bending work from Seth Shipman and coworkers published in Nature via The Verge. It again shows off the magic and future application of CRISPR-Cas-9


Scientists have inserted a GIF into the DNA of living bacteria, bringing us one step closer to one day embedding information in our own skin.

Using DNA to store data isn’t new, but until now the data was stored in synthetic — not living — DNA. Storing information in living DNA is more difficult because the cells are always changing. In a paper published today in the journal Nature, scientists took advantage of bacteria’s natural defense system to embed a picture of a hand and a five-frame clip from Eadweard Muybridge’s Human and Animal Locomotion into E. coli bacteria. They reconstructed the image perfectly, and the video with 90 percent accuracy.

The technique takes advantage of the gene-editing system CRISPR. When viruses attack bacteria, the bacteria use this defense mechanism to cut parts of the virus’s DNA and paste them inside its own DNA. This essentially makes the virus DNA part of the bacteria cell. Those sequences serve as a memory of the viral invasion, so that the cell can go out and cut up future versions of that virus if it’s attacked again.

To the left is an image of a human hand, which was encoded into nucleotides and captured by the CRISPR-Cas adaptation system in living bacteria. To the right is the image after multiple generations of bacterial growth, recovered by sequencing bacterial genomes.
 Image by Seth Shipman

These virus attacks are “recorded” in the reverse chronology of how they occurred, so that, over time, the sequences become a living, physical record of all the different viruses that invaded. The team decided to hack this system for their own purposes, says study co-author Seth Shipman, a neuroscience researcher at Harvard University.

The images and videos the researchers pasted inside E. Coli are composed of black-and-white pixels. First, the scientists encoded the pixels into DNA. Then, they put their DNA into the E. coli cells using electricity. Running an electrical current across cells opens small channels in the cell wall, and then the DNA can flow inside. From here, the E. Coli’s CRISPR system grabbed the DNA and incorporated it into its own genome. “We found that if we made the sequences we supplied look like what the system usually grabs from viruses, it would take what we give,” Shipman says.

Once the information was inside, the next step was to retrieve it. So, the team sequenced the E. coli DNA and ran the sequence through a computer program, which successfully reproduced the original images. So the running horse you see at the top of the page is really just the computer’s representation of the sequenced DNA, since we can’t see DNA with the naked eye.

The choice of image and video weren’t random. Shipman says that the team wanted to “reference some of the original images that humankind ever put in the natural world,” like the cave drawings of hands. Similarly, the five frames of the Muybridge movie, showing a horse galloping, was one of the first moving images ever recorded, using technology that was new in the 1870s. “We figured that we were also encoding information onto the natural world in a new way and should go with something that was tried and tested,” says Shipman.

So far, this method can’t handle a lot of information. The video is only 36 by 26 pixels, which isn’t a lot considering we can encode books and longer movies in synthetic DNA. But the new method of using live bacteria opens the door to exciting possibilities. For instance, we could make cells that record information about what’s happening in the nearby environment. Shipman, as a neuroscientist, hopes that one day the system can be used to record events that happen over time, such as how neurons form in the brain. And yes, maybe one day you could embed all of Game of Thrones in your skin.

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