Hong Kong researchers store data in bacteria

Jan 09, 2011 by Judith Evans
Biochemistry students from the School of Life Sciences at The Chinese University of Hong Kong (CUHK) show bacteria growing in a petri dish in Hong Kong. The group is making strides towards storing such vast amounts of information in an unexpected home: the E.coli bacterium better known as a potential source of serious food poisoning.

The US' national archives occupy more than 500 miles (800 kilometres) of shelving; France's archives stretch for more than 100 miles of shelves, as do Britain's.

Yet a group of students at Hong Kong's Chinese University are making strides towards storing such vast amounts of information in an unexpected home: the E.coli bacterium better known as a potential source of serious food poisoning.

"This means you will be able to keep large datasets for the long term in a box of bacteria in the refrigerator," said Aldrin Yim, a student instructor on the university's biostorage project, a 2010 gold medallist in the Massachusetts Institute of Technology (MIT)'s prestigious iGEM competition.

Biostorage -- the art of storing and encrypting information in -- is a young field, having existed for about a decade.

In 2007, a team at Japan's Keio University said they had successfully encoded the equation that represents Einstein's , E=MC2, in the DNA of a common .

They pointed out that because bacteria constantly reproduce, a group of the single-celled organisms could store a piece of information for thousands of years.

But the Hong Kong researchers have leapt beyond this early step, developing methods to store more complex data and starting to overcome practical problems which have lent weight to sceptics who see the method as science fiction.

The group has developed a method of compressing data, splitting it into chunks and distributing it between different , which helps to overcome limits on . They are also able to "map" the DNA so information can be easily located.

This opens up the way to storing not only text, but images, music, and even video within cells.

As a storage method it is extremely compact -- because each cell is minuscule, the group says that one gram of bacteria could store the same amount of information as 450 2,000 gigabyte hard disks.

They have also developed a three-tier security fence to encode the data, which may come as welcome news to US diplomats who have seen their thoughts splashed over the Internet thanks to WikiLeaks.

"Bacteria can't be hacked," points out Allen Yu, another student instructor.

"All kinds of computers are vulnerable to electrical failures or data theft. But bacteria are immune from cyber attacks. You can safeguard the information."

The team have even coined a word for this field -- biocryptography -- and the encoding mechanism contains built-in checks to ensure that mutations in some bacterial cells do not corrupt the data as a whole.

Professor Chan Ting Fung, who supervised the student team, told AFP that practical work in the field -- fostered by MIT, who have helped develop standards enabling researchers to collaborate -- was in its early stages.

Biochemistry students from the School of Life Sciences at the Chinese University of Hong Kong (CUHK), seen here posing for a picture. The group is making strides towards storing vast amounts of information in an unexpected home: the E.coli bacterium better known as a potential source of serious food poisoning.

But he said: "What the students did was to try it out and make sure some of the fundamental principles are actually achievable."

The Hong Kong group's work may have a more immediate application.

The techniques they use -- removing DNA from bacterial cells, manipulating them using enzymes and returning them to a new cell -- are similar to those used to create genetically modified foods.

But rather than changing the building blocks of an organism, the Hong Kong group allows extra information to piggyback on the DNA of the cell, after checking their changes against a master database to make sure they do not have accidental toxic effects.

Their work could enable extra information to be added to a genetically modified crop in the form of a "bio barcode", Chan said.

"For example, a company that makes a GM tomato that grows extra large with a gene that promotes growth -- on top of that we can actually encode additional information like safety protocols, things that are not directly related to the biological system."

Other types of information, like copyright and design history, could help to monitor the spread of GM crops, he said.

"It's kind of a safety net for synthetic organisms," said Wong Kit Ying, from the student team.

Beyond this, Chan and the students are evangelical about the future possibilities of synthetic biology.

"The field is getting popular because of the energy crisis, environmental pollution, climate change. They are thinking that a biological system will be a future solution to those -- as alternative energy sources, as a remedy for pollution. For these, micro-organisms are the obvious choice," Chan said.

One type of bacterium, Deinococcus radiodurans, can even survive nuclear radiation.

"Bacteria are everywhere: they can survive on things that are unthinkable to humans. So we can make use of this," Chan said.

So is it possible that a home computer could one day consist of a dish filled with micro-organisms?

The group dismisses concerns that this could be dangerous, pointing out that despite E.coli's poor reputation, they use an altered form that cannot exist outside a rich synthetic medium.

In fact, says Chan, while safety rules are strict, more measures are taken to protect the bacteria from contamination than to protect the researchers from the bacteria.

However, Yim admitted that while the group's work is a "foundational advance", a petri dish PC is not likely to be on the market in the coming years, not least because the method of retrieving the data requires experts in a laboratory.

"It's possible," he said, "but there's a long way to go."

Explore further: Elucidating extremophilic 'microbial dark matter'

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User comments : 15

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cmn
not rated yet Jan 09, 2011
It would be cool to see a secret message encoded in the gut bacteria of a foreign diplomat or spy. Just a swab of the mouth and the message is yours.
nanotech_republika_pl
1 / 5 (1) Jan 09, 2011
how is that a news? Venter wrote web page address and other information in the genome of the first synthetic bacteria last year.
plasma_guy
not rated yet Jan 09, 2011
It seems readout is inconveniently biological as expected.
Mercury_01
3 / 5 (2) Jan 09, 2011
how is that a news? Venter wrote web page address and other information in the genome of the first synthetic bacteria last year.


"Biostorage -- the art of storing and encrypting information in living organisms -- is a young field, having existed for about a decade."

You're not special.

Quantum_Conundrum
2 / 5 (4) Jan 09, 2011
As a storage method it is extremely compact -- because each cell is minuscule, the group says that one gram of bacteria could store the same amount of information as 450 2,000 gigabyte hard disks.


We've already seen demonstrations of 4nm transistors, racetrack memory, and other non-volatile spintronic memory which works on scales that are already as small or smaller than the bases of DNA.

There's nothing special about this. WE don't need a disease causing bacteria as a storage medium.

Using spintronics it will eventually be possible to store something like 19 petabytes in one gram of matter, roughly 1 cubic centimeter or so, even if you have 99% space wasted on circuitry, scaffolding, cooling, etc.

Biostorage is a complete waste of time.
gwrede
1 / 5 (1) Jan 09, 2011
At the very least, this means that from now on, every GM crop by Monsanto will carry a copyright message.

I'm waiting for the day when some text inadvertently encodes an unexpected "feature", which yields the organism pandemic.
trekgeek1
not rated yet Jan 09, 2011


We've already seen demonstrations of 4nm transistors, racetrack memory, and other non-volatile spintronic memory which works on scales that are already as small or smaller than the bases of DNA.

There's nothing special about this. WE don't need a disease causing bacteria as a storage medium.

Using spintronics it will eventually be possible to store something like 19 petabytes in one gram of matter, roughly 1 cubic centimeter or so, even if you have 99% space wasted on circuitry, scaffolding, cooling, etc.

Biostorage is a complete waste of time.


I agree with you. I think we're close to besting natures best biological attempts.
DamienS
5 / 5 (1) Jan 09, 2011
I know they've said this:
the encoding mechanism contains built-in checks to ensure that mutations in some bacterial cells do not corrupt the data as a whole

but I would still think that would be a big problem given the rates of mutation in bacteria and their rate of reproduction. Even error correcting codes fail if there is sufficient corruption.

But the most disturbing quote in the who article was this:
Chan and the students are EVANGELICAL about the future possibilities of synthetic biology.

WTF? Did the reporter add this or was it a direct quote from the researchers? Either way, it made me sick to my stomach!
PS3
1 / 5 (1) Jan 10, 2011
As a storage method it is extremely compact -- because each cell is minuscule, the group says that one gram of bacteria could store the same amount of information as 450 2,000 gigabyte hard disks.


We've already seen demonstrations of 4nm transistors, racetrack memory, and other non-volatile spintronic memory which works on scales that are already as small or smaller than the bases of DNA.

There's nothing special about this. WE don't need a disease causing bacteria as a storage medium.

Using spintronics it will eventually be possible to store something like 19 petabytes in one gram of matter, roughly 1 cubic centimeter or so, even if you have 99% space wasted on circuitry, scaffolding, cooling, etc.

Biostorage is a complete waste of time.


I think reproduction would be the main thing and not size.The ability for certain bacteria to reach trillions in under 15 hours is INSANE!!
mfritz0
3 / 5 (2) Jan 10, 2011
Wouldn't it be interesting to find data stored in the naturally occurring bacteria that has supposedly evolved from the primordial soup of evolution. Imagine if there were cures for the diseases written in their DNA. It would be interesting to find a bacterial culture with all the knowledge of the universe encoded in it. Who would have put it there?
mfritz0
1 / 5 (1) Jan 10, 2011
On a further note, perhaps this is the method for organic memory in the brain tissue of animals. Perhaps our brains are the computer they are talking about here. Perhaps the memory is stored in the mucus cells that flow around the folds of our cerebellum.
gwrede
1 / 5 (3) Jan 11, 2011
The ability for certain bacteria to reach trillions in under 15 hours is INSANE!!
What is INSANE is the lack of basic math skills on this forum.

If each bacterium becomes two every half hour, then that is what you get. Hardly an insane rate of growth.
mfritz0
3 / 5 (2) Jan 12, 2011
Assuming the food supply didn't run out and conditions remained stable. The rate of one becoming 2 every half hour is really incredible. It describes geometric progression that would produce 2^30 bacterium in 15 hours. That's 1,073,741,824 bacterium in 15 hours, and that is just from a single bacteria.
crackerhead
not rated yet Jan 15, 2011
WOW, did anyone check if there was any message already there ?
Quantum_Conundrum
1 / 5 (1) Jan 15, 2011
Assuming the food supply didn't run out and conditions remained stable. The rate of one becoming 2 every half hour is really incredible. It describes geometric progression that would produce 2^30 bacterium in 15 hours. That's 1,073,741,824 bacterium in 15 hours, and that is just from a single bacteria.


Pointless.

We'll be making self-replicating nano-bots in a few decades anyway.