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Scientists create 'semi-synthetic' living cells with extra DNA letters
It turns out that your biology teacher (and a certain 1997 sci-fi flick) got something wrong -- DNA isn't necessarily limited to four letters. Scripps Research Institute scientists tell Wired that they've created living cells which include two artificial letters (that is, nucleotides) in their genetic code in addition to the naturally occurring A, C, G and T. The researchers' primary obstacle was making sure these nucleotides cooperated with the enzymes that copy and transcribe DNA; after that, it was just a matter of getting some E. coli bacteria to accept and propagate the newly augmented sequences.
Engadget Daily: #AmazonCart, Oculus VR denies IP theft, and more!
You might say the day is never really done in consumer technology news. Your workday, however, hopefully draws to a close at some point. This is the Daily Roundup on Engadget, a quick peek back at the top headlines for the past 24 hours -- all handpicked by the editors here at the site. Click on through the break, and enjoy.
Scientists can trace your ancestors to within 30 miles using DNA
You might know where your forebears lived a few generations prior, but how about the exact village they came from -- 1,000 years ago? Thanks to DNA sequencing, it's now possible to find that out in many cases according to researchers from the University of Sheffield in the UK. The aptly-named GPS or Geographic Population Structure tool was modeled using more than 100,000 DNA signatures called AIMs (ancestry-informative markers). Since those are often typical to geographic regions, the researchers were able to pinpoint where subjects came from, even if they moved around later (see the video below). During a Sardinian study, for instance, a quarter of the test subject were located to their exact villages and the remainder to within 31 miles. You can even try it for yourself by getting a simple DNA test from 23andme or ancestry.com (for $100-200), then uploading the results to the GPS tool.
Hand-held malaria tester sequences DNA, suggests meds quickly
Despite how far we've come with technology, malaria is still a serious threat for huge chunks of the developing world. A prototype tool from UK-outfit QuantuMDx, however, could help stave off mosquito-related deaths by giving health-workers the power to diagnose the disease in 10 - 15 minutes. As the team tells it, typical DNA sequencing can take days, weeks or even months, but its "lab on a chip" can rapidly diagnose a disease and accurately predict which drug and what dosage to administer -- all based on the parasite's genetic code. That last bit is key because malaria has a nasty habit of being resistant to medications.
This machine can sequence your DNA for just $1,000
Even a decade ago, sequencing a genetic code would set you back around $250,000. The target, of course, has been to crunch that figure down to a more reasonable sum, and now a company believes that it can do it for just $1,000 a go. Illumina Inc. has announced that the $10 million HiSeq X Ten kit will crank out tens of thousands of genomes per year. Even better, is that the $1,000 figure includes the hefty price for the hardware -- which is hoped will kickstart a new era of genetic research. Naturally, the first customers include the Harvard-MIT Broad institute and Regeneron, with the latter planning to use the tech to develop cheap new drugs to heal our ailing bodies.
FDA orders 23andMe to stop selling DNA-testing kits pending approval
For more than five years, 23andMe has sent out personalized DNA test kits, offering consumers hundreds of clinical reports on their genetic risk for everything from diabetes to prostate cancer. Its mission to educate customers about their health and ancestry appears to have been dealt a blow, however, after the US Food and Drug Administration (FDA) said the company needs its approval. It's told 23andMe to stop advertising its DNA-testing product until it gets the medical device classification it needs, which involves conducting studies of the kits to gain documented proof of their accuracy. The agency is also worried that customers might take action, or not, based on test results that may or may not be correct. 23andMe has attempted to gain clearance in the past, but hasn't done everything it needs to get the green light. Make no mistake, a run-in with the FDA is not to be taken lightly: satisfying the agency's requirements is going to be a long and expensive process. 23andMe now has to tell the agency exactly how it intends to gain marketing authorization for the device, or it could face regulatory action (which includes injunctions, seizures and hefty fines). Update: 23andMe has issued a statement on the matter, and sent a letter to its customers: We have received the warning letter from the Food and Drug Administration. We recognize that we have not met the FDA's expectations regarding timeline and communication regarding our submission. Our relationship with the FDA is extremely important to us and we are committed to fully engaging with them to address their concerns.
First Jolla phone will launch November 27th on Finnish carrier DNA: available unlocked, on or off contract
We knew Finnish carrier DNA would be the first to launch the Sailfish-powered Jolla phone, and thanks to a tweet from Jolla HQ we now know that it will launch in Helsinki on November 27th. Unfortunately, that's about all we have to work with in terms of availability info -- the company hasn't said when the device will make its way to other markets. It has, however, shared that the first Jolla phone will be available both on and off contract and with "no SIM lock." Judging by Jolla's responses to fans on Twitter, it looks like those who placed pre-orders could also be getting the handset soon. Any other questions? The Finnish company is dutifully responding to tweets at the moment, so have at it.
Supreme Court rules that naturally occurring DNA cannot be patented
In a plot twist straight out of Orphan Black, the Supreme Court has ruled that naturally occurring DNA cannot be patented, but synthetic biological material is fair game. The case involved Myriad Genetics, a company specializing in molecular testing, after it tried to patent two genes -- BRCA1 and BRCA2 -- that are often linked to breast and ovarian cancer. The Association for Molecular Pathology filed the suit, arguing that the patent would place undue restrictions on research since only Myriad would be allowed to tinker with those genes. The ruling established that isolating naturally occurring genetic material -- as Myriad did -- wasn't enough to justify legal ownership, but so-called complementary DNA (meaning it's man-made) would be eligible for patenting. Myriad had no comment at the time of this writing, but Sandra Park, an attorney with the ACLU Women's Rights Project said, "Myriad did not invent the BRCA genes and should not control them. Because of this ruling, patients will have greater access to genetic testing and scientists can engage in research on these genes without fear of being sued."
Finnish carrier DNA confirms it will be the first to launch Jolla phones running Sailfish
Jolla recently revealed its first phone, and now Finland-based carrier DNA has confirmed it will be the first operator in the world to offer the self-titled handset. Running the Sailfish operating system, these devices continue on a path blazed by Meego while also promising Android app compatibility out of the box. The Jolla phone features 4.5-inch "HD" display, dual-core CPU, 16GB storage with microSD expansion slot, LTE and an 8MP rear camera. Our hands-on demo should reveal a bit more about what it's bringing to the table (including an interesting split design that could allow future hardware augmentation), interested local residents can hit the source link to pre-order one now.
Stanford researchers create genetic transistors, make biologic computing possible
When constructing computer circuits, most folks start with silicon and metal, but not the researchers at Stanford. The boffins in Palo Alto want to build computers out of living tissue, and to that end they've created a biological transistor, called the transcriptor. Transcriptors substitute DNA for semiconductors and RNA for the electrons in traditional transistors -- essentially, the transcriptor controls the flow of a specific RNA protein along a DNA strand using tailored combinations of enzymes. Using these transcriptors, researchers built logic gates to derive true/false answers to biochemical questions posed within living cells. Using these bio-transistors, researchers gain access to data not previously available (like whether an individual cell has been exposed to certain external stimuli), in addition to allowing them to control basic functions like cellular reproduction. This new breakthrough -- when combined with the DNA-based data storage and a method to transmit DNA between cells the school's already working on -- means that Stanford has created all the necessary components of a biologic computer. Such computers would allow man to actually reprogram how living systems operate. Of course, they haven't built a living genetic PC just yet, but to speed up its development, the team has contributed all the transcriptor-based logic gates to the public domain. Looking to build your own biologic computer? A full explanation of the transcriptor awaits below.
MIT crafts genetic circuits that remember their work through DNA
It's easy to find work on gene-based storage; finding genes that will do any of the heavy lifting is another matter. MIT believes it has a genetic circuit that will finally get to work, and then some. In using recombinase enzymes to alter DNA sequences serving as logic gates, researchers have developed a cellular circuit that not only mimics its silicon cousins, but has its own built-in memory. As the gate activation makes permanent changes to a given DNA sequence, any gate actions stay in memory for up to 90 generations -- and will hang around even if the cell's life is cut short. MIT sees its technique as having ultimate uses for areas where longer-term memory is important, such as environmental sensors, but could also see varying output values helping with digital-to-analog converters and other devices where there's a need for more precision. While there's no word on imminent plans for real-world use, the development raises the possibility of processors that could skip the traditional memory cache as they pass info down the family tree.
Scientists encode Shakespeare sonnets, MP3 and more into glitch-free DNA
We've seen scientists experiment with DNA as a storage medium -- most recently with a Harvard team fitting 704TB of data onto a single gram of the genetic material -- and it looks like that research trend is only picking up. Scientists at the European Bioinformatics Institute in the UK have encoded an MP3 file -- along with a digital photo and all 154 of Shakespeare's sonnets -- into DNA, with a hulking storage density of 2.2 petabytes per gram. The information was written using the language of DNA's four bases (A, T, C and G, if you remember high-school bio), and to provide error correction the scientists reserved one of the letters to break up long runs of any of the other three bases. In practice, this system allowed for 100-percent accuracy in sequencing and retrieving the encoded files. Though DNA storage is still quite expensive, the researchers say this method could eventually provide a viable option for archiving information, especially considering DNA's high capacity and long life span. Still, you won't be ditching that hard drive just yet.
NEC shows 2014-era portable DNA analyzer that could outpace your favorite crime drama
NEC gave us promises of truly on-the-spot forensics when it unveiled its first portable DNA analyzer back in 2007, although the reality hasn't been quite in line with the dream: its current system takes an hour to get a result and won't win any awards for sleekness. From what we're seeing of a next-generation analyzer due in 2014, those expectations are more likely to be met. The new version puts the full DNA extraction, amplification and separation processes on a newer chip that meets NEC's original goal of producing output in 25 minutes -- faster than a short cop drama, if you include the commercial breaks. Few beyond the police will be casually tossing the analyzer around given its 70.5-pound weight and $120,000 price, but a much slicker design at least gives it the profile of a small, rolling suitcase. The upgrade could be vital for identifying suspects and victims in record time; if our only worry is that NEC takes all the mystery out of our favorite TV shows, we'll be more than satisfied.
Jolla's Sailfish OS promises multitasking, personalization and 'effortless interaction' (updated)
The date we were promised an introduction to Sailfish is here, and it turns out Jolla's not just targeting smartphones with its MeeGo-based OS, but tablets, smart TVs and other devices, too. Jolla has kept its OS under wraps until now, but it wants Sailfish to be an open-source affair which "will be built through community involvement and participation." The SDK will be available soon, and we should get a look at the UI during a presentation occurring shortly. We're assured superb multitasking capabilities, as well as deep personalization and "fast and effortless interaction." Jolla has said Sailfish will be available for use with "multiple chipset technologies," and is already supported on ST-Ericsson's NovaThor platforms. It's also reported that it's partnering with Finnish carrier DNA to promote and sell Sailfish smartphones on home turf. The full reveal is coming shortly, so we'll let you know more as soon as we do. Update: The Jolla team took to the stage with touchscreen hardware in hand (we also spotted a Raspberry Pi), keen to express how they've been working all hours to boot Sailfish on anything they can find. The company called its creation the first truly "open ecosystem," and said that development will be fully transparent from the outset. While there will be Jolla-branded phones launching, Sailfish is also being offered to handset manufacturers to use on their own hardware. The UI tour wasn't as in depth as we'd have liked, but "true multitasking" was the main focus. Active programs can be pinned to the homescreen as tiles (in a layout that looks something like BlackBerry 10), which offer some control of the app without it hogging the screen. They also showed off a feature called "Ambiance," which uses colors from a picture you select to tint the UI. We wish we had more info to share, but right now, we're all just left wanting more.
HTC Droid DNA review
Guanine, adenine, thymine, cytosine... Android? The Droid DNA -- the latest addition to Verizon's Droid series -- may not contain any actual nucleotides (that we know of), but that doesn't make this HTC-made superphone any less of a powerhouse. On the contrary, we've been eyeballing this handset with eager anticipation ever since it first launched in Japan as the J Butterfly; much like its counterpart from the Land of the Rising Sun, the DNA boasts a jaw-dropping 5-inch, 1080p display. But while that may be the headliner-worthy feature, you certainly can't go wrong with a quad-core Snapdragon S4 Pro processor and 2GB of RAM taking charge behind the scenes, along with an ImageSense camera and other top-notch specs. In certain respects, the Droid DNA is a sneak preview of what's to come in 2013: a wave of high-performance "superphones" that take advantage of this improved resolution, and offer a long list of other top-notch features. Indeed, that's a future we could all definitely live with, but let's not get too ahead of ourselves; we've got a phone to review, after all. Is the display as tantalizing as it sounds? Will its size be a selling point or a major distraction? Should you waltz into a Verizon store on Black Friday and demand they take your hard-earned $200? Follow us after the break as we focus on the here and now.
Alt-week 10.13.12: is the Universe a simulation, cloning dinosaurs and singing mice
Alt-week peels back the covers on some of the more curious sci-tech stories from the last seven days. Are you reading this? Seriously, are you? Sure, we know you think you are, but what if you're just a sub-feature of a complex computer program. A sprite, nothing more than the creation of software. The problem with this question is, how would you ever know? You wouldn't, right? Well, not so fast there. Turns out, maybe there is a way to unravel the matrix (if there is one). It'll come as no surprise, that this is one of the topics in this week's collection of alternative stories. Think that's all we got? Not even close. We'll explore the truth behind cloning dinosaurs, as well a rare performance by singing mice -- all before dinner. Or is it really dinner? This is alt-week.
Max Planck Institute sequences genome of Siberian girl from 80,000 years ago, smashes DNA barriers
We've known little of the genetic sequences of our precursors, despite having found many examples of their remains: the requirement for two strands in traditional DNA sequencing isn't much help when we're usually thankful to get just one. The Max Planck Institute has devised a new, single-strand technique that may very well fill in the complete picture. Binding specific molecules to a strand, so enzymes can copy the sequence, has let researchers make at least one pass over 99.9 percent of the genome of a Siberian girl from roughly 80,000 years ago -- giving science the most complete genetic picture of any human ancestor to date, all from the one bone you see above. The gene map tells us that the brown-skinned, brown-eyed, brown-haired girl was part of a splinter population known as the Denisovans that sat in between Neanderthals and ourselves, having forked the family tree hundreds of thousands of years before today. It also shows that there's a small trace of Denisovans and their Neanderthal roots in modern East Asia, which we would never have known just by staring at fossils. Future discoveries could take years to leave an impact, but MPI may have just opened the floodgates of knowledge for our collective history.
Harvard stores 704TB in a gram of DNA, may have us shopping for organically-grown storage (video)
Early research has had DNA making circuits and little factories. We haven't really seen DNA used as a storage medium, however, and it's evident we've been missing out. A Harvard team led by George Church, Sriram Kosuri and Yuan Gao can stuff 96 bits into a DNA strand by treating each base (A, C, G, T) as though it's a binary value. The genetic sequence is then synthesized by a microfluidic chip that matches up that sequence with its position in a relevant data set, even when all the DNA strands are out of order. The technique doesn't sound like much on its own, but the microscopic size amounts to a gigantic amount of information at a scale we can see: about 704TB of data fits into a cubic millimeter, or more than you'd get out of a few hundred hard drives. Caveats? The processing time is currently too slow for time-sensitive content, and cells with living DNA would destroy the strands too quickly to make them viable for anything more than just transfers. All the same, such density and a lifespan of eons could have us turning to DNA storage not just for personal backups, but for backing up humanity's collective knowledge. We're less ambitious -- we'd most like to know if we'll be buying organic hard drives alongside the fair trade coffee and locally-sourced fruit.
Alt-week 7.8.2012: Solar flares, trapping dark matter, and life-sized Lego trees
Alt-week peels back the covers on some of the more curious sci-tech stories from the last seven days. This week we swing by some superhero news, look at how solar panels might shape up in the future, explore a Lego forest and see how to grab dark matter just using some household gold and strands of DNA. Not only that, we discover how the sun likes to celebrate the fourth of July with its own firework display. This is alt-week
UCSB engineers proteins that make silicon, leads hipsters to insist on organically-grown computers
Organic circuits have been in development for awhile, but it's still rare that the organics are producing the circuitry themselves. Researchers at the University of California, Santa Barbara plan to break that silence with genetically engineered proteins that can make silicon dioxide or titanium dioxide structures like those used in the computer chips and solar cells that we hold dear. The trick, the university's Daniel Morse found, is to attach silica-forming DNA to plastic beads that are in turn soaked in the silicon or titanium molecules they're looking for: after some not-so-natural selection for the best genes, the thriving proteins can produce not only substantial minerals, but whole fiber sheets. Much work is left to get the proteins producing the kind of silicon or titanium dioxides that could run a computer or power your house, but the dream is to have synthetic creations that organically produce what would normally need a mining expedition -- imagine something akin to the glass-like Venus' Flower Basket sponge (pictured above) sitting in an Intel factory. We're half-expecting organically-grown smartphones at Whole Foods, right next to the kale chips and fair trade coffee. [Image credit: Ryan Somma, Flickr]
