genetics
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Google wants to define a healthy human with its new baseline genetic study
Google's got a big new project and it's you. Well, not just you, but a genetic and molecular study of humanity that aims to grasp at what a healthy human should be. It's in its early days, collecting anonymous data from 175 people, but it plans to expand to thousands later. The project is headed up by molecular biologist Andrew Conrad, who pioneered cheap HIV tests for blood-plasma donations. According to the WSJ, the team at Google X current numbers between 70 and 100, encompassing experts in physiology, biochemistry, optics, imaging and molecular biology. The Baseline project will apparently take in hundreds of different samples, with Google using its information processing talents to expose biomarkers and other patterns - the optimistic result hopefully being faster ways of diagnosing diseases. Biomarkers has typically been used with late-stage diseases, as these studies have typically used already-sick patients. "He gets that this is not a software project that will be done in one or two years," said Dr. Sam Gambhir, who is working with Dr. Conrad on the project. "We used to talk about curing cancer and doing this in a few years. We've learned to not say those things anymore."
Future pacemakers might be completely biological
It's pretty amazing that humanity has invented a small electrical device that can be used to ensure a heart keeps a steady beat, but pacemakers have to be maintained, replaced -- sometimes they can even become infected. Researchers say they're working on a less invasive solution: a "biological pacemaker." It's a form of gene therapy that implants the heart with a gene-carrying virus that creates a "sino-atrail node," a collection of neurons that acts as a natural metronome for the body's most important muscle.
Sorry, folks: Study says musical talent mostly comes from your genes
We like to imagine that musical talent is just a matter of putting in enough hours. The Beatles became superstars because they spent years honing their craft in Hamburg, right? Well, maybe not. A recently published study from the Karolinska Institute's Miriam Mosing suggests that you need the right genes to become a true maestro. The research compared thousands of identical and fraternal twins to see whether lots of practice improves a person's ability to detect changes in melody, pitch and rhythm. Unfortunately, it didn't make a lick of difference for the identical twins; they had the same level of appreciation, regardless of how much time a given twin spent performing.
Researchers teach a computer to predict teen binge drinkers
Intervention during someone's teenage years is frequently the key to preventing alcohol abuse in adult life. It's good to know, then, that a group of scientists has found a way to predict that abuse at an early age using computer modeling. The approach teaches the computer how to spot a likely teen binge drinker by weighing 40-plus biological and social factors that include brain structure, any enabling genes, past events and personality traits. If a 13-year-old is already smoking because of an addictive personality or family influences, for instance, it's more likely that this child will pick up a dangerous drinking habit a few years later.
Artist stuffs Wikipedia into apple DNA to create real trees of knowledge
If DNA is code, and code can be art, then DNA can be art... right? Harvard artist in residence Joe Davis certainly thinks so. He's working on a project, Malus Ecclesia, that will insert Wikipedia entries into the non-essential genetic strands of apples. The effort will translate English Wikipedia articles to DNA's four nucleotide letters (A, C, G and T) and use bacteria to insert the resulting text into saplings. When the saplings are grafted on to apple stock and grow up, they'll bear fruit with that genetic data (and therefore the articles) intact, producing very real trees of knowledge.
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.
IBM sends Watson on a genetic quest to find the best cancer treatments
Sure, IBM's Watson crunches data for mobile apps and powers food trucks, but its owners are constantly looking for important studies that can put its cognitive computing expertise to the test. With the recent announcement of a clinical trial studying ways to deliver personalized care to brain cancer patients, the Jeopardy-conquering supercomputer appears to have found that next major challenge. In collaboration with New York Genome Center, Watson will be tasked with trawling archives of medical literature and clinical data, using its patten recognition skills to identify the best cancer treatments based on a patient's genetic make-up. Teams of scientists had manually undertaken the process before, but it's exactly the kind of problem Watson was designed to help solve. IBM says it will begin a trial later this year and hopes to open its findings to doctors across the world.
23andMe's Anne Wojcicki envisions the future of preventative medicine
Anne Wojcicki and her genetic sequencing company 23andMe are locked in a battle with the FDA. Even though it can't report results to customers right now, Wojcicki isn't letting herself get bogged down in the present. At SXSW 2014 she laid out her vision of the future of preventative medicine -- one where affordable genome sequencing comes together with "big data." In addition to simply harvesting your genetic code, the company is doing research into how particular genes effect your susceptibility to disease or your reaction to treatments. And 23andMe isn't keeping this information locked down. It has been building APIs that allow it to share the results of its research as well as the results your genetic tests, should you wish to.
Sony gets into genetic analysis with aim of helping docs pick better treatments
We tend to forget that many companies celebrated for their shiny things also have significant interest in health care; everyone gets sick, after all. Sony is one of this gang, producing medical-grade equipment and the like under its own name, as well as buying up and investing in outfits that have other, specific expertise. Starting February 2014, Sony will also become part owner of P5, a new venture that'll provide human genome analysis in Japan, which just happens to be one of the world's largest pharmaceutical/biotechnology markets. With help from M3, which Sony's invested in, and DNA specialists Illumina, P5's quest is also to marry genetic data with other info, like medical histories, to make headway in the area of personalized medicine (where therapies are selected for the individual, not just the affliction). We doubt Kaz Hirai will be heavily involved, aside from his efforts to find the "Xbox fanboy gene" and any way to silence it, of course. Dan Cooper contributed his image manipulations skills to this report.
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.
Mew-Genics will let you influence, mutate cats using furniture
Lots of people feel that cats have some of the strongest personalities in the animal kingdom; but what if instead of just animal personalities, a cat could be a hipster, a VHS lover or Super Meat Boy fan? What if you could control and selectively breed cat personalities so that you could, as Mew-Genics creator Edmund McMillen puts it in the latest update on the Team Meat blog, "storm the cat fights with your epic army of thugged out pussy?" McMillen explains that in Mew-Genics, cats will have varying personalities when they're born, "from lazy to sexy, from passive to psychotic." Personalities are influenced by items and furniture, which McMillen detailed the function of earlier this month. If a piece of home decor is rare, it's also possible the cat will identify with it so strongly that the cat will mutate and an element or design of the item will become part of the cat. In one screen, a cat that identifies with a Super Meat Boy doll has the same black eye and missing tooth as the hamburger hero. In another, a cat that identifies with gangster rap has a tattoo of a knife on his cheek and a bandana on his head. Again: there is a cat thug with a bandana and knife tattoo on his face. I ... I don't know how to end this post.
23andMe stops selling DNA health tests following FDA crackdown (updated)
If you've been mulling over getting screened by 23andMe for genetic risks like cancer, we're afraid you'll have to look elsewhere. The company has just announced that it's suspending sales of its health-related personalized DNA kits its health-related genetic tests to comply with the FDA's order, as the agency has yet to conduct tests to prove its accuracy. In a blog post on the company website, co-founder Anne Wojcicki says she's "committed to making sure that 23andMe is a trusted consumer product." For now, the company is focusing on research and ensuring those who purchased a kit before November 22nd still get their results. Folks who bought one after that date will, unfortunately, have to make do with a refund. Oh, and it's worth adding that the company will still offer paternity testing and will happily send you your raw genetic data -- there just won't be any color commentary provided alongside. Update (12/7/13): Well, it looks like 23andMe will continue selling test kits, just not returning health reports to anyone who bought after November 22nd, while the company continues its dialogue with the FDA. A spokesperson told us anyone who buys a kit can still get the firm's Personal Genome Service, which includes genetic ancestry information and raw genetic data.
Mew-Genics wants you to hoard attribute-boosting furniture
Team Meat recently unveiled another aspect of Mew-Genics' gameplay: furniture collecting. Super Meat Boy creator Edmund McMillen discussed the game's furniture system in a blog post on the game's site, drawing comparisons to Nintendo's Animal Crossing series. In Mew-Genics, players acquire furniture through Baby Jack's store then place it in a room in their house. Each piece of furniture, which belongs to one of five "types," influences a variety of stats in the game, from disease rates to each cat's life span. The five types of furniture are large, medium, small, wall furniture and those belonging to item sets. Team Meat says Mew-Genics will include 750 pieces of furniture in total, not including rare alternates for each one. The cat genetics and breeding game will launch in 2014 for Steam, iOS and Android.
Push two cats together to create a new one in Mew-Genics
Team Meat's Edmund McMillen recently attempted to explain how the Super Meat Boy developer's next game, Mew-Genics, operates. Naturally, McMillen opted to describe the game in webcomic form, noting that it is about "cat genetics and the forced evolution of the most adaptive species on this whole planet." The comic illustrates players' ability in the breeding game to mash two cats together in order to create a new kitten, care for them as well as enter them into battles and pageant-style contests. Team Meat previously referred to Mew-Genics as a "cat lady sim" that blends elements of "The Sims and Pokemon with a sprinkling of Animal Crossing and a dash of Tamagotchi." McMillen likened Mew-Genics to an unreleased Nintendo game called Cabbage that was in development by Earthbound creator Shigesato Itoi and Mario creator Shigeru Miyamoto for the canceled Nintendo 64DD system. Cabbage was a multiplayer breeding game that was expected to allow players to take their creature on the go with their Game Boy systems. Mew-Genics is in development for Steam, iOS and Android, and will launch in 2014.
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."
MIT crafts analog circuits from living bacteria
Previous work on using organisms as circuitry has usually involved shoehorning parts of the digital world into a very analog environment. MIT has just found an approach that uses the subtlety of the natural world to its advantage: the circuits themselves are analog. By combining genes that produce similar molecules in response to different inputs, the school's scientists have created bacterial cells that perform basic math -- the exact quantity or ratio of a given molecule is the answer. The approach offers a much wider range of results than a binary circuit (10,000 versus 2), and it exploits the cell enzymes' inherent ratio awareness to do some of the hard work. MIT wants more variety in genetic ingredients before it can produce a truly universal system, but its work could lead to organic sensors that are much simpler and more precise than their digital peers.
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.
Allen Institute completes gene expression map of the human brain in high-resolution 3D
As a species, we've spent a lot of time learning how the human brain works, but we've had to go without a true, thorough map of how genes manifest themselves in our craniums; previous maps have been limited to the simpler minds of mice. The Allen Institute for Brain Science is now known to have solved that mystery by recently finishing an extensive, detailed 3D atlas of genetic expression within our own brain tissue. Accomplishing the feat required no small amount of resources, including the definition of 900 subdivisions, conducting over 62,000 gene expression probes and producing the MRI scans of two and a half brains, but the result is a potentially vital tool for neuroscience and education. Curious web users can see a visual map of gene expression based on virtually any criteria they need, whether it's a physical region of the brain, a disease type or the exact gene they'd like to track down. For many, the best news about the map may simply be that it's free and public: anyone with enough experience in genetics can learn more about what makes the mind tick through their browsers, and what they find might just lead to new discoveries.
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.
