Tag: DNA

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Scientists double down on DNA data storage

DNA data storage experiment
The University of Washington’s Luis Ceze and Lee Organick prepare DNA containing digital data for sequencing. (UW Photo / Tara Brown Photography)

Twist Bioscience says it’s extending its collaboration with Microsoft and the University of Washington on a project aimed at perfecting a process for encoding digital data in DNA molecules.

In a news release issued today, San Francisco-based Twist said Microsoft will purchase 10 million strands of synthetic DNA from the company for use in future experiments. The deal comes more a year after an initial purchase of the same number of strands for data storage.

Last July, researchers at Microsoft and UW announced that they were able to store and read out a record 200 megabytes of DNA-encoded data with 100 percent accuracy.

“After working together for over a year, the organizations have improved storage density, thereby reducing the cost of DNA digital data storage by encoding more data per strand and increasing the throughput of DNA production,” Twist said.

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DNA sequenced in space for the first time

Image: Kate Rubins with DNA experiment
NASA astronaut Kate Rubins sequenced DNA using the MiniON device at lower right. (Credit: NASA)

NASA biologist-astronaut Kate Rubins performed the first DNA sequencing experiment in space over the weekend, using a miniaturized device that was delivered to the International Space Station just last month.

The palm-sized MiniON DNA sequencer, built by Oxford Nanopore Technologies, could eventually open the way for full-fledged experiments studying how space radiation might scramble the genes of earthly organisms. This time around, the experiment was aimed merely at finding out whether the device worked.

Rubins used the MiniON sequencer to analyze prepared DNA samples from a mouse, bacteria and a virus. The same analysis was done with equipment down on the ground, with the aim of reading out and matching up the chemical letters of genetic code – that is, adenine, guanine, cytosine and thymine.

The outcome? In today’s status update, NASA reported that the experiment demonstrated for the first time that DNA sequencing could indeed be done in an orbiting spacecraft. That wasn’t a sure thing. Some researchers worried that air bubbles could have gummed up the works in zero-G.

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Microsoft, UW raise the bar on DNA data storage

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The pink smear of DNA at the end of this test tube can store incredible amounts of encoded digital data. (Credit: Tara Brown Photography / University of Washington)

Computer scientists from Microsoft and the University of Washington say they’ve set a new standard for DNA storage of digital data – but they acknowledge that the standard won’t last long.

For now, the bar is set at 200 megabytes. That’s how much data the researchers were able to encode in synthetic DNA pairings, and then correctly read out again. The encoded files included a high-definition music video by the band OK Go, titled “This Too Shall Pass”… the Universal Declaration of Human Rights in more than 100 languages … the top 100 books from Project Gutenberg … and the Crop Trust’s global seed database.

But Karin Strauss, the principal Microsoft researcher on the project, acknowledges that so much more is theoretically possible.

“You could pack an exabyte of data in an inch cubed,” she told GeekWire. An exabyte is equal to 8 quintillion bits of information, which is much more information than is contained in the Library of Congress. (Exactly how much more? That’s a matter of debate.)

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LOL! Cat photo data stored in DNA molecules

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All the movies, images and other data from more than 600 basic smartphones (10 terabytes) can be stored in the pink smear of DNA at the end of this test tube. (Credit: Tara Brown Photography / UW)

Researchers at the University of Washington and Microsoft are developing a digital storage system that can archive data in DNA molecules, with the random-access readability and error correction protocols that’d be required for real-world applications.

Once they’ve overcome those hurdles, they just have to figure out how to make the technology affordable. Eventually, such research could help open the way for data storage devices that can pack information millions of times more tightly than current silicon-based methods.

“Life has produced this fantastic molecule called DNA that efficiently stores all kinds of information about your genes and how a living system works — it’s very, very compact and very durable,” Luis Ceze, UW associate professor of computer science and engineering, said in a news release. “We’re essentially repurposing it to store digital data — pictures, videos, documents — in a manageable way for hundreds or thousands of years.”

Ceze and his colleagues describe their work in a paper presented this week in Atlanta at the ACM International Conference on Architectural Support for Programming Languages and Operating Systems, or ASPLOS.

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DNA dragnet widens for elephants and pangolins

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The black-market trade in ivory drives elephant poaching. (Credit: Gary M. Stoltz / USFWS)

WASHINGTON, D.C. – DNA tests conducted by researchers from the University of Washington helped bring down one of Africa’s biggest kingpins in the illegal elephant ivory trade, but the scientists say they’re just getting started. Now they’re ramping up their efforts to go after more of the smugglers, and extending their efforts to protect other endangered species as well.

“We are now hot on the trail of probably the largest ivory dealer in Africa,” Samuel Wasser, head of UW’s Center for Conservation Biology, said here at the American Association for the Advancement of Science’s annual meeting.

Wasser declined to comment further on that investigation – but it’s worth noting that authorities in Tanzania have arrested several high-profile figures in the ivory trade, including the so-called “the Queen of Ivory” and “The Devil.” DNA evidence could well play a part in the prosecutions, just as it did in the conviction of Togo’s Emile N’Bouke in 2014. Wasser’s DNA data provided the key for cracking the case.

For 15 years, Wasser and his colleagues have been building a DNA database that links elephant populations across Africa to the tons of illegally exported ivory that are being seized every year.

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Neanderthal DNA linked to modern maladies

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Researchers say Neanderthal DNA influences modern traits. (Credit: Michael Smeltzer / Vanderbilt)

A comparison of Neanderthal DNA with the genomes of present-day patients has pointed up connections between our now-extinct cousins and modern traits ranging from addiction and depression to blood clotting and skin problems.

“Our main finding is that Neanderthal DNA does influence clinical traits in modern humans,” Vanderbilt University geneticist John Capra, the senior author of a paper published Feb. 11 by the journal Science, said in a news release.

The comparison drew upon a database that links biological samples from 28,000 patients with anonymized versions of their electronic health records. The Electronic Medical Records and Genomics Network, also known as eMERGE, is funded by the National Human Genome Research Institute.

The network collects records from nine hospital systems across the country, including Vanderbilt University Medical Center as well as Group Health Cooperative / University of Washington Medical Center / Fred Hutchinson Cancer Research Center in Seattle.

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Gates and Bezos invest in cancer testing venture

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Illumina’s gene sequencers are already being used to study cancer cells, and the new venture known as Grail is expected to take the field to the next level. (Credit: Illumina)

One of the giants of gene sequencing, Illumina, has spun off a new $100 million company called Grail to create an all-in-one blood test for cancer – and its investors include Microsoft co-founder Bill Gates and Amazon’s Jeff Bezos.

The name reflects the view that such a blood test is a “holy grail” for cancer diagnosis. Grail would use ultra-deep gene sequencing to look for the characteristic nucleic acids that are shed into the blood by tumors. Those traces are known as circulating tumor DNA, or ctDNA.

If the technology is perfected, it could offer a non-invasive way to find out if a patient has cancer well before symptoms appear. That would better the chances for treatment.

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Scientists set up systems for DNA data storage

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A 3-D animation shows how DNA can be used in computational devices. (Credit: Microsoft Research)

Data storage is getting better and better, but the final frontier for the long-term preservation of digital bits may well be DNA molecules – and the University of Washington and Microsoft Research are trying to make it so.

The work on DNA data storage architecture is one of the angles in Friday’s New York Times story on the subject. In a paper prepared for an international conference on software architecture, researchers propose an error-tolerant encoding scheme for reading out the data in a DNA-based storage system.

Such a system would take advantage of DNA’s amazing information storage capability – the kind of capability that’s able to hold all the genetic code for any organism in a single cell. The Times notes that all of the world’s digital information could be stored in about 2.4 gallons (9 liters) of solution, which would fit inside a typical water cooler bottle.

The benefits of such a system not only include being able to put a lot of data in a small space, but also being able to preserve the data for millennia under the right conditions.

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DNA art honors genetic pioneer Francis Crick

Image: Kindra Crick
Portland artist Kindra Crick shows off “What Mad Pursuit,” a sculpture inspired by the work of her grandfather, DNA pioneer Francis Crick. (Credit: Alex Crick / @crickontour)

The granddaughter of genetic pioneer Francis Crick joined 20 other artists to create a series of 7-foot-high sculptures inspired by DNA’s double helix – and now those sculptures are going on the auction block to benefit cancer research.

Portland artist Kindra Crick told GeekWire she took on the project for several reasons: She’s trained as a molecular biologist as well as a painter, and her grandparents include the late Nobel-winning biologist and his artist wife, Odile Crick. What’s more, proceeds from the auction will go to the Francis Crick Institute, a London facility that’s due to open next year with backing from Cancer Research UK and five other leading medical research organizations. The two-week online sale begins on Wednesday.

Francis Crick, who won the Nobel Prize with colleague James Watson for revealing the double-helix structure of DNA, died in 2004 at the age of 88 after battling colon cancer.

“This seemed like the perfect project, not only to bring awareness to the institute, but also to use my skills and my background to present this beautiful union of art and science,” Kindra Crick said.

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