DNA
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Oxford makes big push into Bigfoot research, enlists Swiss zoologists for DNA study
The search for Bigfoot continues and, no, that's not a nod to a very special episode of Unsolved Mysteries. Though Harry and the Hendersons did its best to humanize that monster of myth, a group of well-heeled European scientists are seeking to go beyond the Hollyweird fantasy to actually prove the creature's existence using advanced genetic techniques on Yeti remains. Part of a collaborative effort between Oxford University and the Lausanne Museum of Zoology, the Collateral Hominid project aims to gather material from public and private cryptozoological collections for analysis to determine whether that elusive species branched off from bears or our neanderthal forebears. Project head Prof. Bryan Sykes hopes the research, the results of which will eventually make the rounds of peer-reviewed journals, will dispel skepticism that has surrounded this controversial creature by providing " a mechanism for... identification that is unbiased, unambiguous and impervious to falsification." Basically, these real-life Mulder & Scullys want incontrovertible DNA proof that these fantastic ape-like beings are simply the stuff of evolution. Whatever the case, the truth is most certainly out there, folks -- it's just likely encased in fossilized dung. [Image courtesy Worch.com]
Scientists develop rewritable digital storage built into DNA; biological binary exists
We've seen DNA flirt with computing and storage before, but a biological system that can record digital data? That's something different. Stanford researchers used natural enzymes to create rewritable data storage built directly into living cells' DNA. The enzymes can flip DNA sequences back and forth, enabling a programmable, binary-like system where the DNA section is a zero if it points in a particular direction and a one if it points the other way. (Color coding indicates which way a section of genetic code is facing.) The so-called recombinase addressable data (RAD) module can store one bit of information without consuming any power, and in addition to letting scientists switch DNA sequences, it allows them to count how many times a given cell has doubled. That capability could come in handy for studying how cancer spreads, and could even give scientists the ability to "turn off" affected cells. The next step for the scientists will be upping the storage capacity to a byte, which will reportedly take a good ten years. That gives you plenty of time to study up on that science -- for a start, check out a more detailed account of the research in the source link.
Amazon stores 1,700 human genomes in the cloud
Not content with speeding up web browsing and hosting federal data, Amazon Web Services are now helping in the fight against disease. Bezos' crew is donating a chunk of free cloud storage to the 1000 Genomes project, which aims to make it easier for scientists to search for genetic variations linked to diseases. These gene-hunters can also use Amazon's Elastic Cloud Compute service to analyze data and discover patterns, although those functions won't come gratis. The DNA sequences of 1,700 mostly anonymous Homo sapiens from around the world have already been logged, but the project has to upload another 1,000 samples before it meets statistical requirements. If it ever needs fresh volunteers, perhaps a free USB gene sequencer and a Prime subscription might do the trick?
MinION USB stick decodes DNA in a matter of seconds
If you happen to be "special," then this $900 USB device is just about the worst thing ever. The aptly named MINion serves its masters by interrogating the cells of living organisms and rooting out their genetic secrets. We won't pretend to know exactly how it works, but it starts by pulling a strand of DNA through a razor-like nanotube that unzips the double helix. The nucleotide bases are then electrocuted one by one until they give up their code. The resulting sequence is stored like a ticker-tape readout, for the whole world to see. The MinION can complete its task in seconds and, unlike most other DNA sequencers, it's portable and simply plugs into a laptop. Luckily, it has so far only been shown to work on very short genomes, like those belonging viruses and bacteria, so for now you're probably safe.
Biological computer can decode images stored in DNA chips, applications remain unclear
Scientists from the Scripps Research Institute and Technion–Israel Institute of Technology have taken biological computing one step further, with a new molecular machine capable of decoding images stored on a DNA chip. Though it's referred to as a "biological computer," the researchers' machine isn't much like a CPU at all -- unless your CPU was manufactured in a test tube filled with a smoothie of DNA molecules, enzymes and ATP. Once they found the right mix, the team proceeded to encrypt images on a DNA chip and used their Turing machine-like creation to decode them, with fluorescent stains helping to track its progress. The above image, read from left to right, gives a more literal idea of what the system can do -- basically, it takes a hidden image and extracts a given sequence. Storing data on DNA isn't anything new, but decrypting said data in this fashion apparently is. The applications for this kind of organic computing remain a bit fuzzy, but it's pretty clear that whatever follows probably won't look anything like a typical computer. The team's findings were recently published in a paper for the journal Angewandte Chemie, the abstract for which is linked below. For a slightly more readable explanation, check out the full press release after the break.
Archon Genomics X Prize offers up $10 million for sequencing 100 human genomes
Sure, we've come to love the X Prize for all of its crazy futuristic car building and moon racing contests, but the latest competition is decidedly smaller -- at least in one sense. For the Archon Genomics X Prize, the foundation is asking teams to sequence "medical grade" human genomes -- 100 of them, in fact -- using the DNA of 100 centenarians (folks who've made it to the ripe old age of 100), referred to pithily as the "Medco 100 Over 100." The centenarian DNA may contain secrets to overcoming disease -- after all, they made it to 100 for a reason. The competition opens to teams on January 3rd of next year -- once completed, the data gathered will be opened up to researchers. Press info can be unlocked after the break.
NASA finds DNA components in meteorites, says they originated in space (video)
So, this is kinda wild: scientists at NASA have uncovered new evidence that DNA components found in meteorites can originate in space, lending new credence to the theory that life on Earth may have arisen from a pre-existing "kit" of materials delivered via asteroid. The discovery is outlined in a new paper from Dr. Michael Callahan, whose team of researchers closely analyzed samples from 12 different meteorites, using a mass spectrometer and liquid chromatography. In their samples, they found traces of adenine, guanine, and a variety of molecules known as nucleobase analogs -- including three that are rarely found on Earth. Scientists have long known that meteorites can contain DNA elements, but were unsure whether these materials actually originate in space. The presence of these three molecules, however, suggest that they do, potentially raising new questions about the dawn of life on Earth, and beyond. It's all quite heady, but steam ahead for a NASA video that might help clarify things, after the break.
Portable device can sniff out anthrax in an hour, won't bring the noise
Got some mysterious white powder sitting on your coffee table? A new, suitcase-sized device can tell you whether you've got dandruff, or anthrax. Developed by researchers at Cornell and the University of Albany, the detector uses a microfluidic chip (pictured on the left) to collect and purify the DNA on a given sample, before conducting a series of polymerase chain reactions -- processes that can quickly identify biological materials. The machine, which has been in the works for seven years, is powerful enough to deliver test results in just one hour (requiring a sample of only 40 microscopic spores), but is slim enough to fit in an airline's overhead luggage bin. Scientists say their creation could also be catered to pick up on other pathogens, including salmonella, and may even pay dividends for crime scene investigators handling forensic evidence. No word yet on when the device could hit the market, but we won't touch an ounce of sugar until it does.
DNA-based artificial neural network is a primitive brain in a test tube (video)
Many simpler forms of life on this planet, including some of our earliest ancestors, don't have proper brains. Instead they have networks of neurons that fire in response to stimuli, triggering reactions. Scientists from Caltech have actually figured out how to create such a primitive pre-brain using strands of DNA. Researchers, led by Lulu Qian, strung together DNA molecules to create bio-mechanical circuits. By sequencing the four bases of our genetic code in a particular way, they were able to program it to respond differently to various inputs. To prove their success the team quizzed the organic circuit, essentially playing 20 questions, feeding it clues to the identity of a particular scientist using more DNA strands. The artificial neural network nailed answer every time. Check out the PR and pair of videos that dig a little deeper into the experiment after the break.
Seven free iOS apps to help you out in the lab
There are apps for converting between weights, volumes and areas, for converting currency and even to calculate your split of the tip at a bar; but what about apps for scientists? An iOS device, like an iPhone, is almost constantly on your person, so why not get some apps for helping you out in the lab? Here are some of the best free apps for your perusal.
Nanopore DNA sequencing technique promises entire genome in minutes or your money back
Those vaguely affordable DNA tests that promise to tell you just how likely you are to be stricken by some horrible and unavoidable genetic affliction in the future? They only look at a tiny fraction of the bits and bobs and bases that make up your genetic code. There's a race on to develop a quick and inexpensive way to sequence a human's entire genome, a process that costs about a million thousands of dollars now and takes ages but, via the technique under development at Imperial College London, could be done in a few minutes for a couple of bucks in 10 years. The process relies on nanopores, which are the go-to tech for companies trying to pull this off. Basically, a DNA strand is pushed through a 2nm hole on a silicon chip and, as it moves through, that chip is able to use an electrical charge to read the strand's coding sequence. That is then spit out to a supercomputer to crunch the numbers at a speed of 10 million bases per second and, within minutes, you too can have some hard data to make you freak out about the future -- and maybe a place to put your iPod, too. Update: As many of you pointed out, there are multiple places to get your full genome scanned now for prices in the mere thousands of dollars. Pocket change, really.
Ion Personal Genome Machine: the DNA sequencer with an iPod dock
We're still struggling to find the speakers on this thing, but Life Technologies' new Ion Personal Genome Machine does at least have one big advantage over most other iPod docks: it's... a personal genome machine. Curiously, the company itself isn't doesn't seem to be talking up the iPod dock at all, but MedGadget reports that it can be used to explore a genome and check on the status of given sequencing run with either an iPhone or iPod touch. As for the device itself, while it's still only designed for research use and "not intended for animal or human therapeutic or diagnostic use," the company does have some pretty grand designs for the future. According to Ion Torrent founder Dr. Jonathan M. Rothberg, the company hopes to eventually do nothing short of doing for DNA sequencing what digital cameras did for photography. Head on past the break for the complete press release.
Scientists developing E.Coli bacteria that stores, encrypts data
Apparently it's not good enough for bacteria to cause leprosy and tuberculosis any more, as scientists have been hard at work adapting the microorganisms for use as everything from microbial fuel cells to really, really small gears. Now, researchers at the Chinese University of Hong Kong have developed a way to use a colony of E.Coli for data storage and encryption. The technique involved placing data (in this case, The Declaration of Independence) in the DNA of bacterial cells, and can even harness site specific genetic recombination to encrypt the data. That said, the technology is still in its infancy: retrieving the info is "tedious and expensive," according to Cambridge University's Tim Middleton, and there is still the possibility that as organisms mutate, so will the data. Currently the only application of all this is the storage of copyright info in genetically engineered organisms, although further research might yield a bacterial storage medium that could survive the electromagnetic pulses and radiation of nuclear fallout.
NC State gurus find 'Goldilocks' of DNA self-assembly, look to improve drug-delivery vehicles
We're guessing that most Wolfpackers in the greater Raleigh area are in full-on tailgate mode right now, but aside from laying a beating on the Seminoles this evening, NC State faithful are also trumpeting a new DNA discovery that could one day make it easy to get vital drugs to hard-to-reach places within you. Researchers from the university have purportedly discovered the 'Goldilocks' of DNA self-assembly, which holds promise for technologies ranging from drug delivery to molecular sensors. The concept, known as DNA-assisted self-assembly, has been vastly improved by using "computer simulations of DNA strands to identify the optimal length of a DNA strand for self-assembly." You see, perfection occurs when strands aren't long enough to intertwine with each other, yet not short enough to simply fold over on each other. We know, it's a lot to wrap your brain around with half a hot dog shoved in your mouth, but hit the video after the break for a... shall we say, more visual explanation.
Self-assembling nanodevices could advance medicine one tiny leap at a time
Seems like Harvard wasn't content with making robotic bees, and has taken its quest for miniaturization right down to the nanoscale level. One nanometer-wide, single-stranded DNA molecules are the topic of the university's latest research, which sets out a way they can be used to create "3D prestressed tensegrity structures." Should these theoretical scribblings ever pan out in the real world, we could see the resulting self-assembled nanodevices facilitating drug delivery targeted directly at the diseased cells, and even the reprogramming of human stem cells. Infusing a nanodevice with the relevant DNA data passes instructions on to your stem cells, which consequently turn into, for example, new bone tissue or neurons to augment your fleshy CPU. Yes, we're kinda freaked out, but what's cooler than being able to say you're going to the doctor for a shot of nanotransformers?
Researchers to map Ozzy Osbourne's genome
Ozzy Osbourne is about to join the ranks of a very fortunate (or unfortunate, depending on how you look at it) minority. DNA research lab Knome has announced that it is going to sequence the lead singer of Black Sabbath's entire genome. Knome, -- which focuses on DNA sequencing in the interest of disease research -- has said that Ozzy's "extreme" medical history (i.e., years of hard partying) makes him an ideal candidate for their purposes. Very few people have had their entire DNA mapped, and the sequencing will take about 3 months to complete, so we'll just have to make do by watching the video after the break until we get the results.
Latest Planet Calypso newsletter announces new developments in game
The newest edition of the Planet Calypso newsletter brings some pretty exciting news for longtime players: Jon "NEVERDIE" Jacobs is selling his rock. Yes, you heard that right. The guy who made the Guinness Book of World Records by paying $100,000 for the asteroid in Planet Calypso is taking offers for that same asteroid. You get everything except the name -- he understandably wants to keep that. If your pockets aren't deep enough to take him up on his offer, how about some Proteron DNA instead? Proteron DNA pieces are now dropping, leading hunters to roam around chasing after it in the hopes of spawning their very own Proteron. Hunters roaming into new lands means taxes, which means more money all around. In either case, the new happenings in Planet Calypso are sure to keep many players entertained!
DNA used to build nanoscale assembly line, Arto Lindsay unavailable for comment
This is what they call in the blog biz a "DNA Two-fer." Earlier today we heard about self-assembling DNA circuits, and now what do we have? NYU chemistry professor Nadrian Seeman and his colleagues have developed what they call "DNA robot factories." Featuring a DNA track (like an assembly line), molecular forklifts for delivering parts, and a DNA "walker" that CNET describes as moving "like a car on an assembly line," the invention is currently being used to construct various types of gold nanoparticle chemical species (whatever that means), although it could eventually be used in processors or for building on the cellular level. Hit up the source link to see the Nature article for all the in-depth details of this nanoscale assembly line.
Self-assembling DNA circuits could power your next computer
Sick of silicon? It is getting a bit played, so maybe it's time to shift some paradigms, and Duke University engineer Chris Dwyer thinks that pure proteins deoxyribonucleic acids are where it's at. He's demonstrated a way to force DNA to create shapes all by itself, a process he likens to a puzzle that puts itself together: It's like taking pieces of a puzzle, throwing them in a box and as you shake the box, the pieces gradually find their neighbors to form the puzzle. What we did was to take billions of these puzzle pieces, throwing them together, to form billions of copies of the same puzzle. Right now the waffle-shaped structures he can form aren't particularly useful, but going forward the hope is that nearly any type of circuitry could be made to build itself in massive quantities at next to no cost. It sounds exciting, promising, almost utopian -- exactly the kind of research that we usually never hear of again. Update: We've had a few people commenting on the inaccuracy of the word "proteins" above, so it's been fixed and we hereby invite all you armchair molecular biologists to get back to curing cancer already.
iPhone app ecosystem bigger than Facebook's app space
Last week at GDC, I joked that I really only heard about two things every day: Facebook and the iPhone. Of course, that's because I was mostly there to cover iPhone gaming (and certainly there were plenty of traditional game developers in the house), but those two platforms are definitely the hottest new frontier in gaming this year. Facebook offers a gigantic user base, and the iPhone offers unprecedented access (just $100 and a Mac), as well as a ready-made market place. But a new report says that there's a clear winner here: the App Store. The Flurry Smartphone Industry Pulse report says that both platforms are growing, but that the iPhone is growing faster, and they cite the App Store's "monetization possibilities" for the reason that Apple's store is now carrying twice as many applications as the Facebook platform. Facebook actually has more users (not surprising, considering it's been around longer and it's free, while you have to buy an iPhone to use its apps), but the iPhone has more developers and more apps available for sale. The report also looks at "iPhone developer DNA" -- where iPhone developers are coming from -- and it actually seems like iPhone devs are starting out from a good mix of places. Some iPhone developers have traditional development backgrounds, but up to 20% of the developer base is composed of individuals with no past experience. The iPad will probably be a big driver in application development going forward as well. Since its announcement, Flurry believes that the number of "in development" iPhone OS projects started per month has gone up 185%. The App Store is already one of the biggest platforms of the past few years, and it's only going to grow bigger. [via GigaOm]
