Tag: dna

Researchers encode a movie onto living bacteria

Forget USB drives and the cloud — what if you could carry every bit of data you’ve ever used on your skin? That’s the long-term goal of researchers at Harvard Medical School, who have stored a video in the DNA of bacteria. It’s the first time a video has been recorded into living cells, as opposed to synthetic material. The team inserted a short animated image of ‘The Horse in Motion’ (one of the earliest moving images ever created) into E. coli, using gene-editing system CRISPR. The movie was split into five frames, and each frame chopped into single-colored pixels. They then created DNA codes corresponding to each color and strung them together. Each bacterium carried snippets of the video stored in their DNA, and when taken together, the scientists were able to retrieve and reconstruct the pieces to play the video. It’s not the first time we’ve seen data stored in this fashion. Back in 2003 a small message was encoded into DNA, and more recently we’ve seen a full operating system written into DNA strands. One team is even trying to store poetry in DNA. But this is the first time it’s been attempted with living bacteria, rather than synthetic material, which presents a unique set of challenges. Live cells are constantly moving and changing, and are liable to interpret the addition of data to their DNA as an invading virus, and subsequently destroy it. That’s why, shaky and blurred as it is, this movie breaks new ground. The world is generating huge amounts of digital data, and scientists see DNA as an effective way of not only dealing with the volumes produced, but as a secure method of preservation. In the face of nuclear explosions, radiation exposure or extreme temperature fluctuation some bacteria can continue to exist — data centers will not. It’ll be some time before you can use this technology to upload data into your body, but in the meantime it has valuable research applications. The scientists behind the study hope the breakthrough will eventually lead to the creation of “living sensors” that can record what is happening inside a cell or in its environment. Via: Stat News Source: Nature (PDF)

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Researchers encode a movie onto living bacteria

Scientists revive an extinct virus using off-the-shelf DNA

It’s no longer far-fetched to synthesize a basic organism . However, a team of researchers has taken that work one step further. They recently reconstituted and reanimated an extinct virus, horsepox, using DNA they’d ordered via mail. The team stitched together multiple gene fragments (each with about 30, 000 base pairs) into the complete 212, 000-pair horsepox genome and inserted it into cells already infected with a different pox, bringing the inanimate virus to life. It’s clever work, especially given the relative complexity of a pox virus compared to earlier efforts, but it’s also a double-edged sword — it could at once provide a breakthrough in medical research and pose a potential threat. As odd as it sounds, reviving the virus would most likely be helpful. The pharmaceutical company Tonix funded the work in hopes of using the relatively benign horsepox as a transport method for a more effective smallpox vaccine. It would also let scientists use other viruses for fighting diseases, such as introducing cancer-fighting systems using the vaccinia virus. If you could generate the necessary viruses on demand, it’d be that much easier to prevent or defeat illnesses that might otherwise have free rein. The threat, as you might guess, comes from the ease of synthesizing a virus. The horsepox strain in question isn’t a threat to humans or even horses, but it might only take the right genetic know-how, several months’ work and a relatively modest shopping budget (this group spent $100, 000) to do the same for a dangerous virus. A hostile nation or extremist group could theoretically engineer a virus and spark an outbreak in a rival country. It’s not extremely likely — they’d need access to both the DNA and corrupt scientists, and would have to take the risk that they might accidentally infect their own people. It’s not impossible, though, and it’s that risk which might prevent further work. Nature and Science have refused to publish the relevant research paper because they’re worried about the “dual-use” potential for the findings. They don’t want to help create a bioweapon , after all. The researchers say their paper deliberately avoids providing so much information that newcomers could create their own viruses, though, and there are concerns that denying the paper might be stifling crucial progress. For better or for worse, this discovery may end up sitting in limbo for a long time. Via: STAT , Reddit Source: Science

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Scientists revive an extinct virus using off-the-shelf DNA

Atomic ‘photos’ help make gene editing safer

Believe it or not, scientists haven’t had a close-up look at CRISPR gene editing . They’ve understood its general processes, but not the minutiae of what’s going on — and that raises the risk of unintended effects. They’ll have a much better understanding going forward. Cornell and Harvard researchers have produced snapshots of the CRISPR-Cas3 gene editing subtype (not the Cas9 you normally hear about) at near atom-level resolution. They used a mix of cryo-electron microscopy and biochemistry to watch as a riboprotein complex captured DNA, priming the genes so the namesake Cas3 enzyme can start cutting. The team combined hundreds of thousands of particles into 2D averages of CRISPR’s functional states (many of which haven’t been seen before) and turned them into 3D projections you can see at the source link. As for what the researchers learned? Quite a bit, actually. They found that the riboprotein forces a small piece of DNA to unwind, allowing an RNA strand to bind and create a “seed bubble” that serves as a sort of fail-safe — if the targeted DNA matches the RNA, the bubble gets bigger and the rest of the RNA continues binding until it forms a loop structure. The riboprotein then locks down the DNA and lets the enzyme get to work. The whole process is surprisingly precise and accident-proof, so it shouldn’t cut the wrong genes. The Cas3 technique isn’t what you’d call delicate. The team likens it to a “shredder” that eats DNA past the point of no return where Cas9 is more of a surgical tool. The discoveries made here could improve gene editing across the board, however. They could modify CRISPR to improve its accuracy and avoid any inadvertent effects, and methods that have only a limited use right now (like Cas3) could be used for other purposes. Ultimately, this could give scientists the confidence they need to use gene editing to eliminate diseases and harmful bacteria — they can go forward knowing their genetic tweaking should be safe. Via: Reddit Source: Harvard , Cell

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Atomic ‘photos’ help make gene editing safer

Amazon is buying the ‘Amazon of the Middle East’

Amazon wants to be a one-stop shop for the entire world, but has struggled to get a foothold in the Middle East. After months of deliberations , the company has finally purchased Souq.com, the “Amazon of the Middle East.” Russ Grandinetti, Amazon VP, says that the deal is a no-brainer, since both sites “share the same DNA, ” adding that the pair will now “work hard to provide the best possible service” in the region. The price hasn’t been disclosed, but rumors from the back-end of 2016 claimed that Souq’s founders were looking for a cool $1 billion. TechCrunch believes that the price was haggled down during negotiations, and thinks that the final fee was closer to $650 million. For that chunk of change, Amazon will now have a strong presence in Egypt, Saudi Arabia and the UAE with plenty of the knotty issues of doing business in the Middle East already fixed. For example, credit cards aren’t ubiquitous in the area, so Souq developed a prepayment card where users top up in retail stores before ordering goods online. There’s also no unified logistics platform in many locations, or addresses, so Souq had to build a network of local couriers who knows where people live. There’s no word on if Amazon will look to rebrand Souq with its own logo, although it’s not that likely given its normal procedure. After all, Zappos, Twitch, and IMDb aren’t called Amazon Shoes, Amazon Game Videos or Amazon Movie Database for nothing. Then again, the fact that the site is gaining a foothold in a new region, there may be a temptation to bring everything under the classic brand. Source: Amazon (BusinessWire)

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Amazon is buying the ‘Amazon of the Middle East’

Entire operating system written into DNA at 215 Pbytes/gram

Enlarge / Genetics background. 3D render. (credit: NIH ) With humanity’s seemingly insatiable desire for data, archiving it safely has become a bit of a problem. The various means we’ve been using all have tradeoffs in terms of energy and space efficiency, many of which change as the technologies mature. And, as new tech moves in, many earlier storage media become obsolete—to the point where it’s essentially impossible to read some old formats. What if there were a storage medium that would be guaranteed to be readable for as long as humanity’s around and didn’t need any energy to maintain? It’s called DNA, and we’ve become very good at both making and decoding it. Now, two researchers have pushed the limits of DNA storage close to its theoretical maximum using a coding scheme that was originally designed for noisy communication channels. The result: an operating system and some movies were stuffed into genetic code at a density of 215 Petabytes per gram. The new work comes courtesy of Yaniv Erlich and Dina Zielinski, who work at the New York Genome Center. They have built on a variety of earlier work. Not much challenge is involved in putting data into DNA: each place in the sequence can hold one of four bases: A, T, C, or G. That lets us write two bits per position. The trick is getting things back out reliably. Read 10 remaining paragraphs | Comments

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Entire operating system written into DNA at 215 Pbytes/gram

DNA ‘computers’ could lead to self-activated smart pills

Imagine a pill that knew if you were ill enough to need drugs, and wouldn’t release chemicals if it thought you didn’t need it. That’s the breakthrough that’s been made at Eindhoven University in the Netherlands by a team of researchers ld by Maarten Merkx. The team has harnessed the power of DNA itself to form an organic computer that performs crude calculations on the state of your health. When you get ill, or suffer from a chronic condition, doctors normally prescribe drugs to help you get better, but this is based on a set of generic guidelines. The idea is that a smart pill will be able to offer specific doses, tailored to your needs, reducing the risk of side effects and waste. The computation comes in the form of the DNA, which looks for molecules that it can react with as a form of data-gathering. Put simply, the pill will journey inside your body and sniff the local environment to decide if you need more medicine. Of course, like so many things at the bleeding edge of technology, it’s still early days for this form of treatment, but the potential is exciting. Source: TUE , Nature

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DNA ‘computers’ could lead to self-activated smart pills

BMW’s all-new 2017 5 series stirs up a technology tsunami

Jim Resnick Pleasing widely diverse masters can be a death sentence. For BMW’s newest 2017 5 series sedan, competing interests tug on it in a multitude of different directions. The traditional BMW enthusiast who factors fun first needs all the best of BMW’s driving machine DNA—and needs it close to the skin. Those needy for general luxury prefer isolation rather than inclusion in the driving process. The tech-focused need digital entertainment. So this is a veritable three-ring circus of sport sedan requirements. BMW’s last-generation 5 series garnered mixed feelings, so with the all-new G30 platform 5 series, BMW hopes to reboot impressions, and we’ve driven it. Launching globally on February 11, the new 5 is actually a bit lighter than the last iteration, BMW quoting a weight loss of as much as 137lb (62kg) from the outgoing model, depending on exact model compared. The new 5 also comes out of the starting gate with several engine configurations. The bottom of the range here in the US is the 2.0L turbocharged four-cylinder, issuing 248hp (185kW) and 258lb-ft (350Nm) in the 530i, netting acceleration to 60 mph in 6.0 seconds or 5.8 when equipped with BMW’s “xDrive” all-wheel-drive. A 3.0L, 335hp (265kW) inline six, which also generates 332lb-ft (450Nm) of torque, powers the 540i to 60mph in just 4.9 seconds or 4.7 seconds with xDrive. Later this spring, the M550i with all-wheel drive will debut, powered by a 456hp (347kW) turbocharged V8 packing 480lb-ft (650Nm) of torque, promising even quicker, 3.9-second 0 to 60 blasts, quicker than the outgoing M5. Read 12 remaining paragraphs | Comments

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BMW’s all-new 2017 5 series stirs up a technology tsunami

Scientists design the next-gen CRISPR for gene editing

CRISPR is already effective enough to be used in experimental therapies for leukemia, cystic fibrosis, sickle cell disease and other conditions. But a team of scientists from Western University have created an even more effective version of CRISPR by adding an engineered enzyme called TevCas9. The current version of CRISPR uses an enzyme known as Cas9 to cut DNA segments, such as the specific parts that cause genetic disorders. Western’s scientists created TevCas9 by combining Cas9 with another enzyme called I-Tevl. According to the team, the next-gen CRISPR is more precise and more efficient. Plus, it has the potential to prevent genes from repairing themselves. Lead scientist David Edgell explains: “The problem with CRISPR is that it will cut DNA, but then DNA-repair will take that cut and stick it back together. That means it is regenerating the site that the CRISPR is trying to target, creating a futile cycle. The novelty of our addition, is that it stops that regeneration from happening.” See, the upgraded CRISPR cuts genes in two places instead of just one to make it tougher for self-repair to kick in. The team still has to confirm that through further testing, but as the team says, that “is the hope and the expectation.” If you want to read the study’s technical details, check out the team’s paper in the Proceedings of the National Academy of Sciences . Source: PNAS , Western University

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Scientists design the next-gen CRISPR for gene editing

Every Year of Smoking Causes About 150 New DNA Mutations That Can Make Cancer More Likely, Says Study

An anonymous reader quotes a report from Los Angeles Times: For every year that you continue your pack-a-day habit, the DNA in every cell in your lungs acquires about 150 new mutations. Some of those mutations may be harmless, but the more there are, the greater the risk that one or more of them will wind up causing cancer. The threat doesn’t stop there, according to a study in Friday’s edition of the journal Science. After a year of smoking a pack of cigarettes each day, the cells in the larynx pick up roughly 97 new mutations, those in the pharynx accumulate 39 new mutations, and cells in the oral cavity gain 23 new mutations. Even organs with no direct exposure to tobacco smoke appear to be affected. The researchers counted about 18 new mutations in every bladder cell and six new mutations in every liver cell for each “pack-year” that smokers smoked. The findings are based on a genetic analysis of 5, 243 cancers, including 2, 490 from smokers and 1, 063 from patients who said they had never smoked tobacco cigarettes. The researchers used powerful supercomputers to compare thousands of cancer genome sequences. The computers grouped the sequences into about 20 distinct categories, or “mutational signatures.” Mutations tied to five of these signatures were more common in tumors from smokers than in tumors from nonsmokers. One of the signatures involves a specific DNA nucleobase change — instead of a C for cytosine, there was an A for adenine — that “is very similar” to the change that occurs in the lab when cells are exposed to benzo[a]pyrene, a compound that the International Agency for Research on Cancer says is carcinogenic to humans. Most of the lung and larynx cancers obtained from smokers had this type of mutation, the researchers reported. They also found that the signature was more common among smokers than nonsmokers. Another mutational signature was characterized by Cs that should have been Ts (thymine) and vice versa. Although these changes can be found in all kinds of cancers, the signature was 1.3 to 5.1 times more common in tumors from smokers than in tumors from nonsmokers, according to the study. Read more of this story at Slashdot.

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Every Year of Smoking Causes About 150 New DNA Mutations That Can Make Cancer More Likely, Says Study