Katie L. Burke
Proteins are involved in how our bodies develop and fight disease as well as how we behave and how we sense the world around us. Genes are instructions for making proteins, each of which is made up of some combination of building-block molecules called amino acids. Proteins can be hundreds of amino acids long, so they are complex and difficult to study. Although protein sequencing to find out the order of the amino acids in a particular protein is pretty easy for a biochemist, it is not simple for a biochemist to figure out all the possible shapes those amino acids can fold into. Foldit is a popular online citizen-science game, in which players are scored on the structure of proteins that they’ve folded. In Foldit puzzles, for example, players are rewarded for solving clashes and voids, places where the protein is not consistent with known biochemical patterns.
Seth Cooper is the lead designer of Foldit, and one of the original creators of the game. He is currently the creative director for the Center for Game Science at the University of Washington. In a recent Science Observer, American Scientist associate editor Katie Burke discussed Foldit and other citizen science games. The following is an extended version of her conversation with Cooper:
Compare playing Foldit to playing other games. What did you use as your inspiration, and what can a person who hasn’t played Foldit expect?
It’s most like a puzzle game. There’s not a lot of fast-paced action. There are no time-critical kinds of things, other than approaching the deadline for a particular puzzle closing. When we started, we often thought about it as a 3D Tetris. In Tetris you’re trying to fit all the blocks together to fill in all the empty space and remove the lines, and protein folding is a lot like that, except it’s in three dimensions. You want to remove all the empty space from the interior of the protein by packing everything in as tightly as possible. But there aren’t a lot of nonscientific games out there that are very similar to it that I know of. It definitely requires some kind of 3D spatial reasoning to follow.
You can also build your own protein, which could be a little bit like MineCraft, because there’s more creativity in the new design puzzles. You’re not just trying to solve a problem that already exists—it’s much more open-ended. You can build the protein up, more or less from scratch, starting with a scaffold that you can change to be whatever you want, building it with whatever little molecular subcomponents that you feel like. So there’s a lot of freedom and creativity.
What was it like to work on gamifying protein folding?
When we started out, we didn’t know what parts of the protein folding problem people would be good at, which parts people would find interesting, how much we would need to teach people about protein folding to allow them to be effective players, how we should make the protein look, what kinds of ways people should be able to interact with the protein. There were all these different variables and possibilities to consider. And it’s a double challenge when you’re making a game that has some kind of purpose, because you not only have to make a fun game, which just by itself is a pretty big challenge, but you’re also constrained by having to make a fun game that has some real scientific application. Before we released the game, we spent about a year coming up with prototypes. The game development team was going back and forth with the biochemists in the Baker Lab here at the University of Washington, seeing what they thought would be useful and watching people play the game to see where they got stuck, where they got confused, what kinds of things they liked to do and what kinds of problems they could solve. In a sense, we haven’t really stopped doing that.
We released Foldit about four years ago online, after a year of alpha testing. Instead of just a few people in the lab talking to people directly, we’re now using telemetry and analytics. The game records the structure and the moves that the players do, and we get data that we use to improve the game in every aspect, from the quality of the scientific results that are coming back to how long people play the introductory levels that are supposed to teach the game. The whole game is like an ongoing, continuous experiment. We release updates every couple of weeks with new features. Every week, we publish a different set of puzzles. So we’re adapting the game to the players to make it the most effective scientific problem-solving tool that we can.
What sort of people like playing this game, which requires quite a time investment to get to levels where they are working on a real-life protein?
A lot of different people are interested in playing the game. I think it’s much broader than what you might typically consider the core gamer demographic. There’s a pretty big international community. Most of the players are from the United States, but there are a large number from Europe, Australia, New Zealand and other countries. I think that a lot of the players are brought into the game or at least stick around for a number of reasons: They are motivated by the sense of purpose of contributing to science. It’s a game, but you’re not just playing a game. Something can come out of it, and we’ve shown that scientific results actually do come out of the game-play. A lot of the players, top players even, don’t have much background in biochemistry, and they’re still able to do well and solve interesting problems.
Do you get such a broad group because the game provides a variety of motivations, which in turn draw in a lot of different people?
We built the game using many different rewards or motivations. It's designed to encourage competition, because everyone is trying to fold their version of the protein better than everyone else to get the highest score. But it’s not just every person competing against every other person. There’s a lot of social interaction that’s supported by the game—chat and forums and things like that. Players can form teams to work together. So individual players can fold the protein for a little while, and then they can share that with other members of their group, who can pick up where they left off. The whole group gets credit for what the members have done, and the groups are competing against each other as well.
The leaderboard system on the website is also meant to motivate people. We support different skill sets, rewarding and recognizing players for doing what they’re good at. There are leaderboards overall for everyone, but there are also leaderboards for different types of puzzles, for individuals working alone and for groups working collaboratively.
There are puzzles that are just protein structure prediction, where you’re trying to figure out the shape of a naturally occurring protein. And then there are puzzles where you’re trying to design an entirely new protein. There are extra tools in the game that allow you to change the amino acids and the atomic structure of the protein, rather than just fold up some existing one. And we actually have a fairly recent type of puzzle, called “Symmetry,” in which there are multiple subpieces of the protein that are all exactly the same; they’re symmetrical. You can only change one of those subpieces, and when you change that one, all the others change in that same way. So we reward all the different kinds of skills that people can bring to developing solutions to each type of game. The game also looks fun and approachable to make players feel more motivated than they might when opening up a science textbook and seeing a standard picture of a protein.
What is the outcome when you design a protein? Is it synthesized?
In Foldit’s design puzzles, the players are able to build a hypothetical protein and see how it works in the game. The game’s score is based on a proxy for how well the protein would work in the lab, whether that’s how well it catalyzes some reaction that the scientists are interested in, or how well this protein sticks to some part of a virus, or even in the case of the Symmetry puzzles, how well the protein sticks to itself. Then we take the solutions that players come up with and present those to scientists for analysis. Solutions that are promising are then synthesized in the lab. We’ve been doing this for a fair number of the puzzles that the players have completed now.
We published a paper several months ago about a structure that the scientists and the players codesigned. The scientists were interested in an enzyme that catalyzes the Diels-Alder reaction, which brings together two small molecules to form a particular kind of bond that the scientists were interested in making. This catalysis would be useful for building other kinds of small molecules, such as drugs and chemicals. We went back and forth between the scientists and the players with several rounds of puzzles. In the end, we designed an enzyme that was about 20 times more efficient in catalyzing the reaction than the one the scientists had started with. And the really cool part of the solution was that the players had inserted about 13 amino acids, a really big departure from the structure that we started with. When the scientists looked at it, they said it was such a drastic change that it was something they wouldn’t possibly have considered, because they wouldn’t have thought it would work at all. But the players didn’t know that, so they just tried something that they thought would work, and it turned out to work really well. So they ended up with an enzyme that was much more efficient than, and quite structurally different from, the initial enzyme.
What are some other major breakthroughs that should be highlighted?
One really exciting recent result was with something in the game called “The Cookbook,” which allows the players to script or code up their strategies in the game. You basically write up what we call a recipe, which is an automated tool that will run moves in Foldit that the players have written. Players can share and modify these recipes online. We had this tool in the game so that we could learn strategies from the players and then automate those strategies. When we looked at the data, we found that one recipe was beating pretty much the next couple recipes combined in terms of popularity. This recipe was called “Blue Fuse version 1.1.” It was pretty simple, only a few lines. When one of the biochemists we were working with looked at it, he said it looked pretty familiar to him because it was similar to an algorithm that they were developing in the biochemistry lab, but they hadn’t published it yet. Organically, the community of Foldit players had come up with the same algorithmic moves that the scientist in the biochemistry lab had come up with independently. So we wrote a joint paper on both of the algorithms.
Have educators used Foldit? How does Foldit help players understand proteins?
We’ve been contacted by a fair number of teachers who are using Foldit for their classes. We know that sometimes they assign playing a puzzle for homework, so the students can see what proteins are like and get a sense of what they are before they learn the scientific details. We designed the game not necessarily to teach biochemistry but to teach the mechanics of how you would go about folding a protein. The game is a good starting place to encourage excitement about science and proteins, before getting into details of how proteins work. But one of the things that we’re starting to work on now is a version of the game that’s tailored specifically toward use in the classroom. We're supporting as much of the scientific curriculum as we can through interaction with proteins and other biological molecules. We’d like this version to be an effective teaching tool, while also setting up a way for educators interested in using the game to connect more easily. That way, when someone comes up with a good way to integrate the game into the classroom, other teachers could learn from that.
Do you think that humans will always be better than computers at folding proteins?
Once the players have the ability to automate some of the things that they do, some of the game becomes strategizing when you would run particular algorithms. If the players came up with an algorithm that solves protein folding, that would be really amazing. Proteins are very complex. It would take a long time, I think, for computers to catch up with people in many of these spatial reasoning and visual processing problems, because there are just so many variables. But even beyond that, players can be creative and come up with new things, which is even more challenging for computers to do. I think that thinking in nonintuitive and novel ways puts people even that much further beyond what computers are able to do.
What are the major changes that you’ve seen as the game has developed?
We started the game in 2007 and released it in 2008. The first Nature paper that we published compared the players’ protein folding with the biochemists’ state-of-the-art protein-folding algorithm. The game teaches some high-level rules, and one of them is that hydrophobic regions of the protein should be on the interior of the protein and away from water. In the game, hydrophobic and hydrophilic regions are color-coded. The players fixed incorrectly exposed hydrophobic areas better than the computational algorithm could. Soon after that paper, we discovered the shape of a retroviral protease enzyme that is associated with AIDS in monkeys. Then we added support for the recipes and the scripts, and we had the “Blue Fuse” result. We’ve added support for protein design, which resulted in the design of the Diels-Alder enzyme. Recently, we added support for the different leaderboards for the different puzzle categories. Since then, we’ve added a lot of new features, such as the “Symmetry” puzzles. We also added puzzles based on electron density, where, from some experiments, you can get a little information about where the mass of the protein is, and you can visualize that as a cloud that you want to fit the protein into. We just released a version of the game that supports Kinect. Rather than just using the mouse and keyboard, you can use Kinect to grab parts of the protein and push pieces with your hands. We wanted to try to support more natural 3D interactions and movements with the proteins.
What can we expect from Foldit in the future?
In
addition to novel protein designs, new symmetry games, the latest
interactions using Kinect, and innovative educational interfaces, we’re
also looking into new kinds of games beyond Foldit. One idea is based on
DNA and DNA nanomachines. You can use DNA as a building material and,
based on the preferences of the nucleotide-base pairings, you can cause
DNA to self-assemble into little shapes, machines and devices that move
and interact with other molecules. We want to build something inspired
by Foldit through which players build little pieces of DNA from scratch
or from some initial scaffold. These DNA pieces can be designed to do
things such as move around in the body, help to actively build up
structures or fight a disease. We want it to be really open-ended, so
that players can come up with things that we haven’t even thought of.
There’s really no telling what people will be able to do if you give
them the tools and the power to do it.
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from the New York Times (Registration Required)
For years, bacteria have had a bad name. They are the cause of infections, of diseases. They are something to be scrubbed away, things to be avoided.
But now researchers have taken a detailed look at another set of bacteria that may play even bigger roles in health and disease: the 100 trillion good bacteria that live in or on the human body. No one really knew much about them. They are essential for human life, needed to digest food, to synthesize certain vitamins, to form a barricade against disease-causing bacteria. But what do they look like in healthy people, and how much do they vary from person to person?
In a new five-year federal endeavor, the Human Microbiome Project, which has been compared to the Human Genome Project, 200 scientists at 80 institutions sequenced the genetic material of bacteria taken from nearly 250 healthy people. They discovered more strains than they had ever imagined -- as many as a thousand bacterial strains on each person. And each person's collection of microbes, the microbiome, was different from the next person's. To the scientists' surprise, they also found genetic signatures of disease-causing bacteria lurking in everyone's microbiome. But instead of making people ill, or even infectious, these disease-causing microbes simply live peacefully among their neighbors.
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from the Los Angeles Times (Registration Required)
UC Davis faculty leaders have declared that medical school administrators there violated the academic freedom of a professor who published a 2010 opinion article criticizing a campus event promoting prostate cancer screening.
In a unanimous vote, the faculty Senate's Representative Assembly admonished administrators for threatening cuts in title and funding and possible legal action against medical professor Michael Wilkes after his piece appeared in the San Francisco Chronicle. The faculty governing panel last week also called for medical school leaders to apologize and "take concrete steps to prevent future violations of rights of academic freedom."
Although disciplinary action was not carried out against Wilkes, raising that possibility violated his rights, according to microbiologist Linda Bisson, who chairs the UC Davis faculty Senate. "It's not a gray area or even a little cloudy. This is a textbook example of what is protected in academic freedom," Bisson said Wednesday.
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from the New York Times (Registration Required)
BRADLEY, Me. -- Under a bright sky here, a convoy of heavy equipment rolled onto the bed of the Penobscot River on Monday to smash the Great Works Dam, a barrier that has blocked the river for nearly two centuries.
Before the destruction began, a tribal elder from the Penobscot Indian Nation used an eagle wing to fan smoke from a smoldering smudge of sage, tobacco and sweet grass over the crowd that had gathered to watch."Today signifies the most important conservation project in our 10,000-year history on this great river that we share a name with, and that has provided for our very existence," said the tribal chief, Kirk Francis.
The Penobscot River's once-abundant runs of salmon, shad, sturgeon, alewives, eels and smelt were nearly wiped out because for years the dams -- there are three in the river's first 10 miles alone -- impeded migrations to their spawning grounds. "Returning these species of fish to their historic habitat, we will see the river continue to come back to life in a major way," Mr. Francis said.
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from the Los Angeles Times (Registration Required)
Swedish researchers have, for the first time, implanted a tissue-engineered vein made from her own stem cells into a 10-year-old girl. The implant of the portal vein had to be repeated after a year, but the team reported that the new vein dramatically improved the young girl's quality of life, allowing her to grow taller, gain weight and begin exercising.
The portal vein drains blood from the intestines and spleen to the liver, and blockages, which are usually genetic in origin, can cause serious medical complications such as enlarging the spleen and stunting growth. It can even be fatal. Normal treatment is to transplant a vein taken from the leg or the deep neck, but surgery to remove the vein can cause limb problems. The transplanted vein can also lead to loss of the liver and the need for an organ transplant.
Researchers have also been working with artificial veins made of Dacron or polytetrafluoroethylene, but have encountered problems with those as well. The synthetic grafts often fail, particularly if the vein is small.
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from the BBC News Online
Scientists working on Voyager 1 are receiving further data suggesting the probe is close to crossing into interstellar space. The NASA mission, which launched from Earth in 1977, could leave our Solar System at any time.
It is now detecting a sharp rise in the number of high-energy particles hitting it from distant exploded stars.
The observation was predicted, and is another indication that Voyager will soon reach its historic goal.
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from BBC News Online
One unusual aspect of the doping case brought against Lance Armstrong is that three doctors have been charged in addition to the champion cyclist. The United States anti-doping agency (USADA) says that Armstrong and the doctors were involved in a "pervasive pattern of doping." The seven-time Tour de France winner vehemently denies the charges.
But experts say that if proven the case would signal that responsibility for doping no longer stops at the athlete. Respected anti-doping scientist Dr Michael Ashenden told BBC News that the case marked a significant change.
"It is no longer enough to stop at the athlete, but instead authorities are now seeking to investigate further and root out the doctors, support staff and drug dealers who make doping possible." USADA has sent a 15-page letter to Lance Armstrong and five others detailing the range of the charges and some of the evidence against them.
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from Nature News
The Italian research minister, Francesco Profumo, has bowed to pressure from Italian and international scientists and agreed to take a closer look at a proposed nuclear research programme at one of the country's leading institutes. He has also withdrawn his nomination of a proponent of the controversial research for the institute's scientific council.
The research -- on piezonuclear fission, the theory that compressing solids can provoke nucleus-splitting reactions without emitting γ-rays or producing nuclear waste -- was being led by Alberto Carpinteri, a structural engineer and president of the Italian National Institute of Metrological Research (INRIM) in Turin. Carpinteri and his collaborators have published a series of papers on the theme, mostly in Strain, a journal for which Carpinteri is on the editorial board.
But the theory is widely disputed. "The experiments are badly described and no other groups have been able to reproduce them so far," says Ezio Puppin, a nuclear engineer at Milan Polytechnic.
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from ScienceNOW Daily News
In dense fields of seagrass that carpet coastal waters around the world, there's a three-way interaction keeping the ecosystem thriving. Two-shelled mollusks called bivalves, bacteria inhabiting the bivalves' gills, and seagrasses themselves all live symbiotically, new research reveals. The finding helps explain the long-standing puzzle of how seagrasses can survive in murky shoreline waters and offers insight into how scientists can better restore seagrass ecosystems, which are declining worldwide.
"I think it's a really exciting and interesting idea," says ecologist Jay Stachowicz of the University of California, Davis, who was not involved in the new study. "This is a type of interaction that people really hadn't considered before as being critical to seagrasses."
Often called marine nurseries, seagrass meadows harbor juvenile fish that spend their adult lives in coral reefs. Because of their shoreline locations and lush grasses, the meadows have dense layers of sediment and decaying organic material, a rich feeding ground for most ocean life. But the muddy deposits present a conundrum for the seagrasses: the bacteria responsible for breaking down the decaying matter emit high levels of sulfide, which should be toxic to the plants.
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from the Christian Science Monitor
Responding to a lawsuit from 11 states, the Environmental Protection Agency is proposing new air quality standards to lower the amount of soot that can be released into the air
The Obama administration, facing strong resistance from congressional Republicans and industry officials, had sought to delay the politically fraught rule until after the election, but was forced to act by a court order. Critics, including officials representing the oil and gas industry, refineries and manufacturers, complained that overly strict rules could hurt economic growth and lead to job losses.
Soot, made up of microscopic particles released from smokestacks, diesel trucks, wood-burning stoves and other sources, contributes to haze and can burrow into lungs. Breathing in soot can cause lung and heart problems.
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from Science News
Red disks, hand stencils and club-shaped drawings lining the walls of several Stone Age caves in Spain were painted so long ago that Neandertals might have been their makers, say researchers armed with a high-powered method for dating ancient stone.
Scientists have struggled for more than a century to determine the ages of Europe's striking Stone Age cave paintings. A new rock-dating technique, which uses bits of mineralized stone to estimate minimum and maximum ages of ancient paintings, finds that European cave art started earlier than researchers have assumed -- at least 40,800 years ago, say archaeologist Alistair Pike of the University of Bristol in England and his colleagues.
Pike's team presents its findings in the June 15 Science.Previous age estimates were based on stylistic comparisons of drawings in different caves and radiocarbon dates for ancient pigments containing charcoal or other organic material. That research indicated that people began creating cave paintings in Europe possibly 36,000 years ago. Some researchers suspect that Homo sapiens made rapid advances in symbolic thinking around that time.
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from the New York Times (Registration Required)
Young adults from broken homes in which a parent had had a same-sex relationship reported modestly more psychological and social problems in their current lives than peers from other families that had experienced divorce and other disruptions, a new study has found, stirring bitter debate among partisans on gay marriage.
The study counted parents as gay or lesbian by asking participants whether their parents had ever had a same-sex relationship; the parents may not have identified themselves as gay or lesbian. Gay-rights groups attacked the study, financed by conservative foundations, as biased and poorly done even before its publication on Sunday in the journal Social Science Research.
But outside experts, by and large, said the research was rigorous, providing some of the best data yet comparing outcomes for adult children with a gay parent with those with heterosexual parents. But they also said the findings were not particularly relevant to the current debate over gay marriage or gay parenting.
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from the Washington Post (Registration Required)
When I was a baby, my mother gazed down at me in her hospital bed and did something that would permanently change the way my brain developed. Something that would make me better at learning, multi-tasking and solving problems. Eventually, it might even protect my brain against the ravages of old age. Her trick? She started speaking to me in French.
At the time, my mother had no idea that her actions would give me a cognitive boost. She is French and my father English, and they simply felt it made sense to raise me and my brothers as bilingual. Yet a mass of research has emerged to suggest that speaking two languages while growing up may profoundly affect the way I think.
Cognitive enhancement is just the start. According to some studies, my memories, my values, even my personality may change depending on which language I happen to be speaking. It is almost as though the bilingual brain houses two separate minds. All of which highlights the fundamental role of language in human thought. "Bilingualism is quite an extraordinary microscope into the human brain," says cognitive neuroscientist Laura Ann Petitto of Gallaudet University.
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from the New York Times (Registration Required)
A report from a new institute at the State University at Buffalo asserting that state oversight has made natural gas drilling safer is causing tumult on campus and beyond, with critics arguing that the institute is biased toward industry and could undercut the university's reputation.
The study, issued on May 15, said that state regulation in Pennsylvania had made drilling there far safer and that New York rules were even more likely to ensure safety once drilling gets under way in the state.
But a government watchdog group quickly raised questions about the study's data and the authors' ties to the oil and gas industry. And a newly formed group of professors and students is calling for a broader inquiry into the genesis of the institute, which issued the report only weeks after its creation was announced in April.
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from Time
Despite the widely touted benefits of omega-3 fatty acids for preserving cognitive function and memory, a new review by the Cochrane Library finds that those effects may be overstated: healthy elderly people taking omega-3 supplements did no better on tests of thinking and verbal skills than those taking placebo.
A number of previous studies have associated omega-3 consumption with better brain health and a lower risk of Alzheimer's disease. One recent study by Columbia University researchers found that people who ate diets higher in omega-3s had lower blood levels of beta amyloid, the telltale protein that gums up brains in Alzheimer's patients. In another study published in the journal Neurology in February, researchers showed that people with the highest levels of omega-3s in their blood had bigger brain volumes and performed better on tests of visual memory and abstract reasoning, compared with those with the lowest levels.
Much of this previous data has been observational, however. So, for the Cochrane review, researchers looked specifically at so-called "gold standard" studies, those that randomly assigned people to take either omega-3s or a placebo and then tracked the participants over time. The authors of the review, from the London School of Hygiene & Tropical Medicine, included three studies involving a total of 3,536 people over the age of 60, which lasted between six and 40 months. All the participants started the studies in good cognitive health.
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from BBC News Online
The US space agency (NASA) has launched its latest orbiting X-ray observatory. The Nuclear Spectroscopic Telescope Array (Nustar) was sent into space on a Pegasus rocket operated out of the Kwajalein Atol in the central Pacific.
Nustar will study high-energy X-rays coming from exotic sources such as black holes, exploded stars and the hot gas in galaxy clusters. The observatory will capture its target X-rays using a novel optics system held on the end of a 10m-long extension.
"Nustar will open up a whole new window on the Universe by being the very first telescope to focus high-energy X-rays," explained Fiona Harrison, Nustar's principal investigator from the California Institute of Technology in Pasadena, California. "As such it will make images that are 10 times crisper and 100 times more sensitive than any telescope that has operated in this region of the spectrum."
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from Nature News
Monkeys infected with Ebola have been cured by a cocktail of three antibodies first administered 24 hours or more after exposure. The result raises hopes that a future treatment could improve the chances of humans surviving the disease caused by the deadly virus, which kills up to 90% of infected people and could potentially be used as a biological weapon. Most treatment regimes tested to date only improve chances of survival if administered within one hour of infection. There are no approved treatments for people infected with Ebola.
Researchers based at the National Microbiology Laboratory in Winnipeg, Canada, administered an antibody cocktail named ZMAb to cynomolgus monkeys (Macaca fascicularis) infected with the Zaire virus -- the deadliest strain of Ebola, prevalent in African countries including the Democratic Republic of Congo and Gabon. All four of the monkeys that began the three-dose treatment regime within 24 hours of being infected survived. Two of four monkeys given the cocktail from 48 hours of infection also lived. A monkey that was not treated died within five days of infection.
"The antibodies slowed replication until the animals' own immune systems kicked in and completely cleared the virus," says Gary Kobinger, a medical microbiologist at the University of Manitoba who led the study. The results are published today in Science Translational Medicine.
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from the Guardian (UK)
Crops genetically modified to poison pests can deliver major environmental benefits, according to a landmark study spanning two decades and 1.5 million square kilometres. The benefits extended to non-GM crops grown in neighbouring fields, researchers found.
Plants engineered to produce a bacterial toxin lethal to some insects but harmless to people were grown in over 66 million hectares around the world in 2011. So-called Bt cotton is one type and now makes up 95% of the vast plantations in China. Since its introduction there in 1997, pesticide use has halved and the new study showed this led to a doubling of natural insect predators such as ladybirds, lacewings and spiders. These decimated pests not targeted by the Bt cotton, not only in the cotton fields, but also in conventional corn, soybean and peanut fields in the region.
"Insecticide use usually kills the natural enemies of pests and weakens the biocontrol services that they provide," said Professor Kongming Wu at the Chinese Academy of Agricultural Sciences in Beijing, who led the research team. "Transgenic crops reduce insecticide use and promote the population increase of natural enemies. Therefore, we think that this is a general principle."
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from the San Francisco Chronicle
A gene that's been known for two decades as the largest inheritable risk for developing Alzheimer's disease mostly affects the brains of women, not men, according to a team of researchers from Stanford and UCSF.
The gene variant known as APOE4 is the most common genetic risk factor for Alzheimer's - only about 15 percent of people carry the gene, but it's found in more than half of all Alzheimer's patients.
The variant was first connected to Alzheimer's in 1993, but doctors and scientists for the most part have been unaware of any gender differences, despite early studies that showed an increased risk for women with the gene.
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from ScienceNOW Daily News
Chimpanzees now have to share the distinction of being our closest living relative in the animal kingdom. An international team of researchers has sequenced the genome of the bonobo for the first time, confirming that it shares the same percentage of its DNA with us as chimps do. The team also found some small but tantalizing differences in the genomes of the three species--differences that may explain how bonobos and chimpanzees don't look or act like us even though we share about 99% of our DNA.
"We're so closely related genetically, yet our behavior is so different," says team member and computational biologist Janet Kelso of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. "This will allow us to look for the genetic basis of what makes modern humans different from both bonobos and chimpanzees."
Ever since researchers sequenced the chimp genome in 2005, they have known that humans share about 99% of our DNA with chimpanzees, making them our closest living relatives. But there are actually two species of chimpanzees that are this closely related to humans: bonobos (Pan paniscus) and the common chimpanzee (Pan troglodytes). This has prompted researchers to speculate whether the ancestor of humans, chimpanzees, and bonobos looked and acted more like a bonobo, a chimpanzee, or something else--and how all three species have evolved differently since the ancestor of humans split with the common ancestor of bonobos and chimps between 5 million and 7 million years ago in Africa.
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from Nature News
Nestling among the dunes in the dry equatorial region of Saturn's moon Titan is what appears to be a hydrocarbon lake. The observation, by the Cassini spacecraft, suggests that oases of liquid methane -- which might be a crucible for life -- lie beneath the moon's surface. The work is published today in Nature.
Besides Earth, Titan is the only object in the Solar System to circulate liquids in a cycle of rain and evaporation, although on Titan the process is driven by methane rather than water.
This cycle is expected to form liquid bodies near the moon's poles, but not at its dune-covered equator, where Cassini measurements show that humidity levels are low and little rain falls to the surface. "The equatorial belt is like a desert on Earth, where evaporation trumps precipitation," says astrobiologist Jonathan Lunine of Cornell University in Ithaca, New York.
Any surface liquid there should evaporate and be transported to the cooler poles, where it should condense as rain. "Lakes at the poles are easy to explain, but lakes in the tropics are not," says Caitlin Griffith, a planetary scientist at the University of Arizona in Tucson. Indeed, Cassini has spotted hundreds of lakes and three seas in Titan's polar regions.
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from the New York Times (Registration Required)
In recent decades, there have been few new treatments for people with stubbornly high blood pressure. Exercise and a low-sodium diet, along with such stalwart drugs as diuretics, ACE inhibitors and beta-blockers, have made up the standard regimens. But these efforts fail in a surprising number of patients. On three or more medications, many still suffer from uncontrolled hypertension and with it a heightened risk of heart attack and stroke.
Now, doctors are experimenting with an innovative but drastic new approach that may help lessen the danger in patients for whom nothing else works. During the procedure, called renal denervation, a physician threads a catheter into the arteries leading to the kidney, then delivers pulses of radio-frequency energy that interrupt the signaling in nerves to and from that organ. The damage to the nerves is probably permanent, although no one is certain.
Small clinical trials, conducted mainly outside the United States, have suggested that in combination with drugs, renal denervation may help to reduce high blood pressure in patients with so-called treatment-resistant disease. The treatment is already available in Australia and Europe.
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from the San Francisco Chronicle
Space scientists at UC Berkeley are about to train their sights on a unique telescope that will fly into orbit Wednesday to explore the violent edges of black holes at the centers of countless galaxies like our own Milky Way.
The new NASA telescope, operated by the university's Space Sciences Laboratory, will also aim its X-ray eyes at the embers of burned-out exploding stars and at the sun's bursts of high-energy flares that send solar particles streaming to Earth at 2 million mph.
The telescope's instrument chief, astrophysicist William Craig of Berkeley's Space Sciences Laboratory, said Monday the mission, named NuSTAR, "will open a new window into the high-energy universe."
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from the Telegraph (UK)
Both nature (meaning our genes) and nurture (the environment we grow up in) are known to significantly affect traits like our height and weight, our IQ, and our chance of developing behavioural problems or autism. But how strong environmental factors are in determining each characteristic, compared with the influence of DNA, differs significantly across the country, scientists have found.
Researchers from King's College London studied 45 childhood characteristics in 6,759 pairs of identical and non-identical twins across the UK, to determine whether their genes or their environment was more important.
A new series of "nature-nurture" maps produced by the team revealed that some areas are "environmental hotspots" for particular traits, but in other places the same attribute is mainly governed by genetics.
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from BBC News Online
Exhaust fumes from diesel engines do cause cancer, a panel of experts working for the World Health Organization says. It concluded that the exhausts were definitely a cause of lung cancer and may also cause tumours in the bladder. It based the findings on research in high-risk workers such as miners, railway workers and truck drivers. However, the panel said everyone should try to reduce their exposure to diesel exhaust fumes.
The International Agency for Research on Cancer, a part of the World Health Organization, had previously labelled diesel exhausts as probably carcinogenic to humans.
IARC has now labelled exhausts as a definite cause of cancer, although it does not compare how risky different carcinogens are. Diesel exhausts are now in the same group as carcinogens ranging from wood chippings to plutonium and sunlight to alcohol. It is thought people working in at-risk industries have about a 40% increased risk of developing lung cancer.
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from the New York Times (Registration Required)
A hospital offers Zumba and cooking classes. Farmers markets dole out $2 coupons for cantaloupe and broccoli. An adopt-a-bodega program nudges store owners to stock low-fat milk. And one apartment building even slowed down its elevator, and lined its stairwells with artwork, to entice occupants into some daily exercise.
In the Bronx, where more than two-thirds of adults are overweight, the message has been unmistakably clear for a long time: Slim down now. But, if anything, this battery of efforts points to how intractable the obesity problem has become in New York's poorest borough. The number of the overweight and obese continue to grow faster in the Bronx than anywhere else in the city--nearly one in three Bronx adults is obese--leading the city's health commissioner to call it "ground zero for the obesity epidemic problem."
So it was to the weight-burdened Bronx that Mayor Michael R. Bloomberg went last week to make the case for his controversial proposal to ban supersized sodas and sugary drinks. Standing in the lobby of Montefiore Medical Center, the borough's largest hospital, he was flanked by doctors who spoke of treating more patients than ever with diabetes, hypertension and other obesity-related diseases.
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from Nature News
Science-publishing ventures continually battle for market space, yet most operate on one of only two basic business models. Either subscribers pay for access, or authors pay for each publication--often thousands of dollars--with access being free. But in what publishing experts say is a radical experiment, an open-access venture called PeerJ, which formally announced its launch on 12 June, is carving out a fresh niche. It is asking its authors for only a one-off fee to secure a lifetime membership that will allow them to publish free, peer-reviewed research papers.
Relying on a custom-built, open-source platform to streamline its publication process, PeerJ aims to drive down the costs of research publishing, say its founders: Peter Binfield, who until recently was publisher of the world's largest journal, PLoS ONE, and Jason Hoyt, who previously worked at the research-paper-sharing site Mendeley. Their involvement is a major reason for the buzz around PeerJ. "I thought--wow--if the people I'm hearing about are working there--that's the sign of something happening. It makes it less crazy," says John Wilbanks, an advocate of open access and a senior fellow at the Ewing Marion Kauffman Foundation in Kansas City, Missouri.
PeerJ is just one of a flurry of experiments, encouraged in part by the gathering momentum of open access, that might shape the future of research publishing. "We are seeing a Cambrian explosion of experiments with new publishing models. It's going to be an interesting period for the next few years," says Binfield.
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from BBC News Online
UK researchers have developed a porous material that can preferentially soak up CO2 from the atmosphere. NOTT-202 is a "metal-organic framework" that works like a sponge, absorbing a number of gases at high pressures.
But as the pressure is reduced, CO2 is retained as other gases are released. The development, reported in Nature Materials, holds promise for carbon capture and storage, or even for removing CO2 from the exhaust gases of power plants and factories.
Metal-organic frameworks have been considered promising structures to trap gases for a number of years. They are so named because they comprise atoms of a metallic element at their core, surrounded by scaffolds of longer, carbon-containing chains. These complex molecules can be made to join together in frameworks that leave gaps suitable for capturing gases.
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