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An anonymous reader writes with this quote from Quanta Magazine:
Most genetic research to date has focused on just 1 percent of the genome — the areas that code for proteins. But new research, published today in Science, provides an initial map for the sections of the genome that orchestrate this protein-building process. "It's one thing to have the book — the big question is how you read the book," said Brendan Frey, a computational biologist at the University of Toronto who led the new research (abstract).
For example, researchers can use the model to predict what will happen to a protein when there’s a mistake in part of the regulatory code. Mutations in splicing instructions have already been linked to diseases such as spinal muscular atrophy, a leading cause of infant death, and some forms of colorectal cancer. In the new study, researchers used the trained model to analyze genetic data from people afflicted with some of those diseases. The scientists identified some known mutations linked to these maladies, verifying that the model works. They picked out some new candidate mutations as well, most notably for autism.
One of the benefits of the model, Frey said, is that it wasn’t trained using disease data, so it should work on any disease or trait of interest. The researchers plan to make the system publicly available, which means that scientists will be able to apply it to many more diseases.
10 comments | yesterday
BarbaraHudson sends this excerpt from The Province:
While exploring the effects of the protein-degrading enzyme Granzyme B on blood vessels during heart attacks, professor David Granville and other researchers at the University of British Columbia couldn't help noticing that mice engineered to lack the enzyme had beautiful skin at the end of the experiment, while normal mice showed signs of age. The discovery pushed Granville's research in an unexpected new direction.
The researchers built a mechanized rodent tanning salon and exposed mice engineered to lack the enzyme and normal mice to UV light three times a week for 20 weeks, enough to cause redness, but not to burn. At the end of the experiment, the engineered mice still had smooth, unblemished skin, while the normal mice were deeply wrinkled.
Granzyme B breaks down proteins and interferes with the organization and the integrity of collagen, dismantling the scaffolding — or extra-cellular matrix — that cells bind to. This causes structural weakness, leading to wrinkles. Sunlight appears to increase levels of the enzyme and accelerate its damaging effects.
174 comments | 3 days ago
An anonymous reader writes: Transcranial magnetic stimulation has been used for years to diagnose and treat neural disorders such as stroke, Alzheimer's, and depression. Soon the medical technique could be applied to virtual reality and entertainment. Neuroscientist Jeffrey Zacks writes, "it's quite likely that some kind of electromagnetic brain stimulation for entertainment will become practical in the not-too-distant future." Imagine an interactive movie where special effects are enhanced by zapping parts of the brain from outside to make the action more vivid. Before brain stimulation makes it to the masses, however, it has plenty of technical and safety hurdles to overcome.
88 comments | 3 days ago
Nerval's Lobster writes What if you could construct an unmanned aerial vehicle out of biological material, specifically a lightweight-but-strong one known as mycelium? The vegetative part of a fungus, mycelium is already under consideration as a building material; other materials would include cellulose sheets, layered together into "leather," as well as starches worked into a "bioplastic." While a mushroom-made drone is probably years away from takeoff, a proposal for the device caught some attention at this year's International Genetically Engineered Machine competition. Designed by a team of students from Brown, Spelman, and Stanford Universities in conjunction with researchers from NASA, such a drone would (theoretically) offer a cheap and lightweight way to get a camera and other tools airborne. 'If we want to fly it over wildfires to see where it's spreading, or if there's a nuclear meltdown and we want to fly in to see what's going on with the radioactivity, we can send in the drone and it can send back data without returning,' Ian Hull, a Stanford sophomore involved in the project, told Fast Company.
52 comments | about two weeks ago
Zothecula writes: A promising new study (abstract) suggests that a wireless, light-sensitive, and flexible film could potentially form part of a prosthetic device to replace damaged or defective retinas. The film both absorbs light and stimulates neurons without being connected to any wires or external power sources, setting it apart from silicon-based devices used for the same purpose. It has so far been tested only on light-insensitive retinas from embryonic chicks, but the researchers hope to see the pioneering work soon reach real-world human application.
24 comments | about two weeks ago
Jason Koebler writes: The shape of DNA is a double helix, right? That's what we are taught. Well, now the answer is "not always." Researchers at the Massachusetts Institute of Technology have discovered how to program DNA to be shaped like a bowl, or a spiral, or a ring, or other shapes that aren't found in nature.
It's the latest in a string of discoveries about the underlying structure of life and the building blocks by which it's made. Recently, scientists created new nucleotides that do not exist in nature and inserted them into a living organism. And now, this: DNA can look like just about anything and can be assembled into many shapes.
47 comments | about two weeks ago
Molly McHugh writes with this story about sensors that can be attached to temporary tattoos to monitor various medical information. "The Center for Wearable Sensors at the University of California San Diego has been experimenting with attaching sensors to temporary tattoos in order to extract data from the body. The tattoos are worn exactly as a regular temporary tattoo would be worn. The sensors simply sit atop the skin without penetrating it and interact with Bluetooth or other wireless devices with a signal in order to send the data....A biofuel battery applied as a temporary tattoo converts sweat into energy, and a startup within the center has developed a strip that extracts data from sweat to explain how your body is reacting to certain types of exercise. Amay Bandodkar, a fourth year PhD student at UCSD, explains that the sensors are programmed to react to the amount of lactate the body produces."
57 comments | about two weeks ago
MTorrice writes In the U.S. alone, consumers discard over 32 million tons of plastic each year, only 9% of which is recycled. Polyethylene is one of the most popular and, unfortunately, persistent types of plastics. Bags, bottles, and packaging made from the polymer accumulate in landfills and oceans across the globe. Scientists have lamented that the material isn't biodegradable because microbes can't chew up the plastic to render it harmless. However, a new study reports the first definitive molecular evidence that two species of bacteria, found in the guts of a common pantry pest, can thrive on polyethylene and break it apart.
45 comments | about two weeks ago
Anita Hunt (lissnup) writes: Iowa-based NewLink Genetics has secured a US$50million deal with pharmaceutical giant Merck for the experimental Ebola vaccine developed by Canadian government scientists. NewLink bought the exclusive commercial licensing rights to Canada's VSV-EBOV in 2010 with a milestone payment of just US$205,000. This is an interesting new twist in a story we've discussed previously, and which continues to draw media attention.
70 comments | about three weeks ago
rossgneumann writes: Pentagon officials are worried that the U.S. military is losing its edge compared to competitors like China, and are willing to explore almost anything to stay on top—including creating robots capable of becoming fighting machines. A 72-page document throws detailed light on the far-reaching implications of the Pentagon's plan to monopolize imminent "transformational advances" in biotechnology, robotics and artificial intelligence, information technology, nanotechnology, and energy.
117 comments | about three weeks ago
jenwike writes The Open Source Seed Initiative is a passionate group that wants to ensure their seeds are never patented, but making sure seeds are free for use and distribution by anyone isn't as easy as you might think. Part of the equation are plant characteristics, like an extended head on lettuce — is that an invention? Or, would you argue that it is the product of the collective sharing of material that improves the whole crop over time? In this report, one farmer says, "If you're not exchanging germplasm, you're cutting your own throat."
100 comments | about a month ago
sciencehabit writes If cells could talk, they'd have quite a story to tell: Their life history would include what molecules they'd seen passing by, which signals they'd sent to neighbors, and how they'd grown and changed. Researchers haven't quite given cells a voice, but they have now furnished them with a memory of sorts—one that's designed to record bits of their life history over the span of several weeks. The new method uses strands of DNA to store the data in a way that scientists can then read. Eventually, it could turn cells into environmental sensors, enabling them to report on their exposure to particular chemicals, among other applications.
48 comments | about a month ago
Lasrick writes 4H is in Africa, helping to distribute Big Ag products like DuPont's Pioneer seeds through ostensibly good works aimed at youth. In Africa, where the need to produce more food is especially urgent, DuPont Pioneer and other huge corporations have made major investments. But there are drawbacks: "DuPont's nutritious, high-yielding, and drought-tolerant hybrid seed costs 10 times as much. While Ghanaians typically save their own seeds to plant the next year, hybrid seeds get weaker by the generation; each planting requires another round of purchasing. What's more, says Devlin Kuyek, a researcher with the sustainable-farming nonprofit Genetic Resources Action International, because hybrid seeds are bred for intensive agriculture, they typically need chemicals to thrive."
377 comments | about a month ago
FirephoxRising writes Our genetic makeup influences whether we are fat or thin by shaping which types of microbes thrive in our body, according to a new study. Scientists identified a specific, little known bacterial family that is highly heritable and more common in individuals with low body weight. So we are what we eat, and what we got from out parents. From the article: "The study, funded by National Institutes of Health (NIH), researchers sequenced the genes of microbes found in more than 1,000 fecal samples from 416 pairs of twins. The abundances of specific types of microbes were found to be more similar in identical twins, who share 100 per cent of their genes, than in non-identical twins, who share on average only half of the genes that vary between people. These findings demonstrate that genes influence the composition of gut microbes."
297 comments | about a month ago
KentuckyFC writes It's 20 years since the FDA approved the Flavr Savr tomato for human consumption, the first genetically engineered food to gain this status. Today, roughly 85 per cent of corn and 90 per cent of soybeans produced in the US are genetically modified. So it's easy to imagine that the scientific debate over the safety of genetically modified organisms has been largely settled. Not for Nassim Nicholas Taleb, author of The Black Swan and several academic colleagues who say that the risks have been vastly underestimated. They say that genetically modified organisms threaten harm on a global scale, both to ecosystems and to human health. That's different from many conventional risks that threaten harm on a local scale, like nuclear energy for example. They argue that this global threat means that the precautionary principle ought to be applied to severely limit the way genetically modified organisms can be used.
432 comments | about 2 months ago
First time accepted submitter Torontoman points out this story of a man with one of the rarest blood types in the world. Forty years ago, when ten-year-old Thomas went into the University Hospital of Geneva with a routine childhood infection, his blood test revealed something very curious: he appeared to be missing an entire blood group system. There are 35 blood group systems, organized according to the genes that carry the information to produce the antigens within each system. The majority of the 342 blood group antigens belong to one of these systems. The Rh system (formerly known as ‘Rhesus’) is the largest, containing 61 antigens. The most important of these Rh antigens, the D antigen, is quite often missing in Caucasians, of whom around 15 per cent are Rh D negative (more commonly, though inaccurately, known as Rh-negative blood). But Thomas seemed to be lacking all the Rh antigens. If this suspicion proved correct, it would make his blood type Rhnull – one of the rarest in the world, and a phenomenal discovery for the hospital hematologists.
75 comments | about 2 months ago
SternisheFan writes with news that medical researchers from Harvard Medical School and Massachusetts General Hospital have successfully cultivated stem cells that will kill brain cancer cells in mice without damaging healthy cells. "They used genetic engineering to make stem cells that spewed out cancer-killing toxins, but, crucially, were also able to resist the effects of the poison they were producing. ... In animal tests, the stem cells were surrounded in gel and placed at the site of the brain tumor after it had been removed. Their cancer cells then died as they had no defense against the toxins (abstract)." The next step in the research is to try the treatment on humans. Chris Mason, a professor of regenerative medicine, said, "This is a clever study, which signals the beginning of the next wave of therapies. It shows you can attack solid tumors by putting mini pharmacies inside the patient which deliver the toxic payload direct to the tumor. Cells can do so much. This is the way the future is going to be."
46 comments | about 2 months ago
BarbaraHudson writes: The Globe and Mail is reporting the success of a procedure to implant a replacement retina grown from cells from the patient's skin. Quoting: "Transplant doctors are stepping gingerly into a new world, one month after a Japanese woman received the first-ever tissue transplant using stem cells that came from her own skin, not an embryo. On Sept. 12, doctors in a Kobe hospital replaced the retina of a 70-year-old woman suffering from macular degeneration, the leading cause of blindness in the developed world. The otherwise routine surgery was radical because scientists had grown the replacement retina in a petri dish, using skin scraped from the patient's arm.
The Japanese woman is fine and her retinal implant remains in place. Researchers around the world are now hoping to test other stem-cell-derived tissues in therapy. Dr. Jeanne Loring from the Scripps Research Institute in La Jolla, Calif., expects to get approval within a few years to see whether neurons derived from stem cells can be used to treat Parkinson's disease."
56 comments | about 2 months ago
gthuang88 writes: Spider silk is touted for its strength and potential to be used in body armor, sports gear, and even artificial tendons and implants. Now several companies including EntoGenetics, Kraig Labs, and Araknitek have developed genetic approaches to producing commercial quantities of the stuff. One method is to implant spider genes into silkworms, which then act as spider-silk factories. Another is to place the gene that encodes spider web production into the DNA of goats; these "spidergoats" then produce milk containing spider-silk proteins that can be extracted. There's still a long way to go, however, and big companies like DuPont and BASF have tried and failed to commercialize similar materials.
82 comments | about 2 months ago
First time accepted submitter kwiecmmm writes A group of Harvard scientists reported that they have figured out how to turn embryonic stem cells into beta cells capable of producing insulin. This discovery could cure diabetes. From the article: "'It's a huge landmark paper. I would say it's bigger than the discovery of insulin,' says Jose Olberholzer, a professor of bioengineering at the University of Illinois. 'The discovery of insulin was important and certainly saved millions of people, but it just allowed patients to survive but not really to have a normal life. The finding of Doug Melton would really allow to offer them really something what I would call a functional cure. You know, they really wouldn't feel anymore being diabetic if they got a transplant with those kind of cells.'"
100 comments | about 2 months ago