SCRIBE Enables Distributed Genomically Encoded Memory
MIT engineers have transformed the genome of the bacterium E. coli into a long-term storage device for memory. SCRIBE (Synthetic Cellular Recorders Integrating Biological Events ) is a scalable platform that uses genomic DNA for analog, rewritable, and flexible memory distributed across living cell populations. They envision that this stable, erasable, and easy-to-retrieve memory will be well suited for applications such as sensors for environmental and medical monitoring.
“You can store very long-term information,” says Timothy Lu, an associate professor of electrical engineering and computer science and biological engineering. “You could imagine having this system in a bacterium that lives in your gut, or environmental bacteria. You could put this out for days or months, and then come back later and see what happened at a quantitative level.”The new strategy, described in the Nov. 13, 2014 issue of the journal Science ("Genomically encoded analog memory with precise in vivo DNA writing in living cell populations"), overcomes several limitations of existing methods for storing memory in bacterial genomes, says Lu, the paper’s senior author. Those methods require a large number of genetic regulatory elements, limiting the amount of information that can be stored.The earlier efforts are also limited to digital memory, meaning that they can record only all-or-nothing memories, such as whether a particular event occurred. Lu and graduate student Fahim Farzadfard, the paper’s lead author, set out to create a system for storing analog memory, which can reveal how much exposure there was, or how long it lasted. To achieve that, they designed a “genomic tape recorder” that lets researchers write new information into any bacterial DNA sequence.
The researchers showed that SCRIBE enables the recording of arbitrary transcriptional inputs into DNA storage registers in living cells by translating regulatory signals into ssDNAs. In E. coli, they expressed ssDNAs from engineered retrons that use a reverse transcriptase protein to produce hybrid RNA-ssDNA molecules. These intracellularly expressed ssDNAs are targeted into specific genomic loci where they are recombined and converted into permanent memory. The team could show that genomically stored information can be readily reprogrammed by changing the ssDNA template and controlled via both chemical and light inputs. This demonstrates that genomically encoded memory can be read with a variety of techniques, including reporter genes, functional assays, and high-throughput DNA sequencing.
SCRIBE enables the recording of analog information such as the magnitude and time span of exposure to an input. This convenient feature is facilitated by the intermediate recombination rate of our current system (~10–4 recombination events per generation), which we validated via a mathematical model and computer simulations. For example, the scientists stored the overall exposure time to chemical inducers in the DNA memory of bacterial populations for 12 days (~120 generations), independently of the induction pattern. The frequency of mutants in these populations was linearly related to the total exposure time.
The idea that DNA could be used to store information is an idea that is long familiar to sf readers. Fantasy writer Barbara Hambly uses a similar idea in her 1982 Darwath trilogy. She describes how wizards succeeded in tying information to the DNA of selected individuals.
In the story, several people from 1980's California find themselves transported across the Void to another planet and the Realm of Darwath. They face a deadly species of queerly magical beings - the Dark - who destroyed civilization thousands of years ago. Everything that was made of paper (like books and records) were burned to stave off attacks by the Dark. Tying memories to a few suitable bloodlines was the only way to preserve a record of that period that would endure.
Update 15-Apr-2017: See the Heritable Memories Bloodline from The Time of the Dark (1982) by Barbara Hambly. End update.
Scroll down for more stories in the same category. (Story submitted 11/18/2014)
Follow this kind of news @Technovelgy.
| Email | RSS | Blog It | Stumble | del.icio.us | Digg | Reddit |
you like to contribute a story tip?
Get the URL of the story, and the related sf author, and add
Comment/Join discussion ( 0 )
Related News Stories -
Twist Bioscience High Density Digital Data On DNA
'They tied the memory to the bloodline and that was their record!' - Barbara Humbly, 1982.
Store One Bit On One Atom
'...each individual molecule has a meaning.' - Robert Heinlein, 1951.
DataTraveler Ultimate Generation 2 Terabyte Flashdrive
'A man or woman could carry AIs or complete planetary data spheres...' - Dan Simmons, 1989.
Sandisk 1 Terabyte SD Memory Card Surfaces
'They should be Welton Fine-Grains, or they would be too bulky to ship...' - Robert Heinlein, 1973.
Technovelgy (that's tech-novel-gee!)
is devoted to the creative science inventions and ideas of sf authors. Look for
the Invention Category that interests
you, the Glossary, the Invention
Timeline, or see what's New.
China Melts Tibetan Permafrost To Plant Forest
'Can you give us a microwave spotlight?'
iFlytek Doctor Robot First To Pass Medical Exams
Doctor shortage? No problem, we'll just use the autodoc.
Slaughterbot AI KIller Quadcopter Drones
'The real border was defended by... a swarm of quasi-independent aerostats.'
Do We Really Want Backflipping Robots?
Also includes wonderful blooper reel.
RNA-Based Biocomputing Device
Living things can sense and analyze complex signals in living cells.
Seasteading Floating Cities
'It was a remarkable island, circular, about half a kilometer in diameter.'
Tesla Semi 'Electrotruck' Unveiled
Elon Musk unveils yet another technological marvel.
Watch What People Are Seeing Via Brain Scanning
'had managed to see through the other man's eyes as the other man, all unaware, washed their Zis limousine sixteen hundred meters away...'
Integrated Circuits Printed Right Onto Fabric!
'...a shirt that displayed email on its sleeve.
Interstellar Asteroid Visits Our Solar System
'This asteroid had whirled in from the cold of the interplanetary space...'
PRIMA Bionic Vision Restoration
'The VISOR... was a medical device used in the Federation to aid patients who have suffered loss of eyesight...'
Audi Traffic Jam Pilot Knows If You're Sleeping
'Even here, riding a garbage truck to eternity, the machine watched him...'
UM Hall Thruster Breaks Records
Someday, we'll see an ion drive used to get to Mars.
Ionity Ultra-fast Charging Station Network
'Recharge the batteries... in almost every town and village...'
VAuth Voice Security Wearable From University of Michigan
'Siri, I gave you a voice command...' 'Yes, but do I know you?'
Ubiquiti FrontRow Camera Records Your Life
Why be choosy? Just upload your whole life to the Internet, and be done with it.
More SF in the News Stories
More Beyond Technovelgy science news stories