Tuesday, 13 April 2010

Johnald's Fantastical Daily Link Splurge

Johnald's Fantastical Daily Link Splurge

Scrubbing IDs Out of Medical Records for Genetic Studies

Posted: 12 Apr 2010 03:18 PM PDT


A new technique allows medical records to be used for research on the genetics of disease while still protecting patients from prying eyes.

sciencenewsDatabases that link thousands of people's DNA profiles to their medical histories are a powerful tool for researchers who want to use genetics to individualize the diagnosis and treatment of disease. But this promise of personalized medicine comes with concerns about patient privacy. Now scientists have come up with a way to alter personal medical information so it's still meaningful for research, but meaningless to someone trying to ID an individual in a database.

"We're hoping that it's a game-changer," says Bradley Malin, a biomedical informatics specialist from Vanderbilt University in Nashville who helped develop the method.

The new method, published online April 12 in the Proceedings of the National Academy of Sciences, simply disguises parts of the medical history data that are not relevant to a geneticist's particular research question using an algorithm that combs through health records and makes some aspects of them more general.

For example, if scientists want to examine links between genes and asthma, parts of an individual's medical record that pertain to asthma are kept intact. But if that asthmatic patient also had a broken arm as a teenager, the algorithm changes the medical code for a broken left forearm to a code that indicates only a broken bone.

"What's really great about this is even though it anonymizes the data, it still allows you to go in and find an association with medical history," says Nils Homer of the University of California, Los Angeles, who was not involved with the research.

The researchers tested their algorithm against potential hackers using information from more than 2,600 patients. The team assumed a hacker might know a patient's identity, some of their medical history and maybe some of the medical codes associated with that history. The technique stymied efforts to ID an individual based on that information, the researchers report.

"There is definitely a need to de-identify individuals," says Homer, who was part of a team that demonstrated two years ago that it is possible to trace a genetic signature back to an individual even when that person's DNA profile was buried in a pool of thousands. The finding prompted the National Institutes of Health to restrict access to genetic databases that had previously been available to anyone with Internet access.

Genome-wide association studies, which comb through these giant databases looking for links between genetic and physical traits, have the potential to generate clinically valuable information. Establishing such links could help doctors understand, for example, why patients respond differently to certain drugs.

Image: alimander/flickr

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Lost Tribes Used Clever Tricks to Turn Amazon Wasteland to Farms

Posted: 12 Apr 2010 12:00 PM PDT


A vast series of earth mounds on the eastern coast of South America may be living landscape fossils of a forgotten civilization's agriculture.

People raised the mounds between 1,000 and 700 years ago in order to create cropland in terrain that is flooded for half the year, and parched for the other half. New insect ecosystems formed on the mounds, further enriching the soils and keeping them fertile for centuries, long after their human stewards had vanished. This lost agricultural system could be a model for modern farmers, according to a new study.

"Today these lands are used for cattle ranching or hunting. People think agriculture must not be possible in these areas," said ecologist Doyle McKey of the University of Montpellier in France, co-author of a study published April 12 in the Proceedings of the National Academy of Sciences. "The common conception is that these areas are wastelands."

guyanamapMcKey and a team of archaeologists, paleobiologists and soil scientists describe the earthworks, which run for 360 miles from the Berbice River to Cayenne, the modern-day capital of Guyana.

The study is part of a fast-growing body of research on the pre-Columbian world of the Amazon basin. Historians and anthropologists once thought it inhabited only by small bands of primitive hunters and gatherers, with interior jungles and coastal floodplains unable to support large-scale agriculture and complex societies. That picture no longer seems accurate.

Scientists have shown that now-vanished people transformed the Amazon, using biochar to nourish jungle soils, and moving floodplain soils to create irrigation channels and planting beds. McKey's findings expand the range of known coastal agriculture and take an in-depth look at the beneficial ecological changes it created.

amazonfarms_satellite"Human engineering, if we do it cleverly, can work together with natural ecosystem engineering," said McKey.

In addition to 100-foot-long, water-diverting berms, they identified expanses of mounds covering hundreds of acres. From the air, the mounds were too symmetrical to be natural. On the ground, soil samples returned fossilized evidence of maize, squash and manioc.

The mounds appear to have been constructed from layers of surrounding topsoil, which was shoveled out and layered like cakes. That formed the basis of the mounds, which put crops above the flood line but that was only one part of the agricultural trick.

Species of ants and termites settled in the mounds, where their colonies wouldn't flood. Their burrowing aerated the soil, and plant matter foraged from surrounding areas enriched it further. As a result, the mounds acted like sponges for rainfall, and outsourced insect labor made them rich in key fertilizer nutrients of nitrogen, potassium and calcium. The root systems of perennial plants kept the mound structures intact, and likely did so when mounds were rotated out of production.

McKey is reluctant to speculate on how many people were supported by mound agriculture. A conservative guess based on crop yields from modern raised-bed farming experiments put the figure at one person for every two acres of farmland. That's a very rough estimate, but enough to suggest that the farmers were not just small, family-based tribes.

More important than exact numbers is the evidence of agricultural success in a region that's not considered suitable for modern agriculture. McKey thinks today's farmers could learn from ancient tricks, and supplement them with modern tools.

As for the original inhabitants, little is known. They belonged to so-called Arauquinoid cultures, which emerged 1,500 years ago and vanished shortly before the arrival of Europeans. Whether they left descendants is unknown. They're known only from a single wooden shove, some ceramic fragments and their farms.

"When people modified these ecosystems long ago, they changed the way the ecosystems work. We can use that knowledge," said McKey.

Images: 1) Farm mounds from above and the ground./PNAS. 2) A map of northeastern Amazon coastal earthworks./PNAS. 3) Satellite and interpretive imagery of a site near Kourou, Frency Guiana/PNAS.

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Citation: "Pre-Columbian agricultural landscapes, ecosystem engineers, and self-organized patchiness in Amazonia." By Doyle McKey, Stéphen Rostain, José Iriarte, Bruno Glaser, Jago Jonathan Birk, Irene Holst, Delphine Renard. Proceedings of the National Academy of Sciences, Vol. 107 No. 15, April 12, 2010.

Brandon Keim's Twitter stream and reportorial outtakes; Wired Science on Twitter. Brandon is currently working on a book about ecological tipping points.

Gigantic Baby Stars Discovered in Cloud of Space Dust

Posted: 12 Apr 2010 11:24 AM PDT


Huge new baby stars shine bright in this image of the Rosette Molecular Cloud.

The previously undiscovered protostars are the small points of orangey light in the center of the image. They are up to 10 times more massive than the sun.

The Herschel Space Observatory, operated by the European Space Agency, obtained the new image, which is a composite of three different wavelengths of light all in the infrared part of the spectrum. Infrared light waves are longer and scatter less than visible light, allowing scientists to probe dust-shrouded areas of space. In this image, the shortest wavelength is blue, the medium green, and the longest red.

The intense star-forming region of the Milky Way is about 5,000 light-years away in the direction of the constellationMonoceros, the Unicorn.This image shows only part of the massive cloud of dust. If the whole thing, seen below, were visible to the naked eye, it would be large in the sky, appearing around five times the size of a full moon.


Images: 1.ESA/PACS & SPIRE Consortium/HOBYS Key Programme Consortia. High-resolution TIFF image.
2. Oliver Stein.

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WiSci 2.0: Alexis Madrigal's Twitter, Tumblr, and green tech history research site; Wired Science on Twitter and Facebook.

Mapping the Fly Brain, Neuron by Neuron

Posted: 12 Apr 2010 10:22 AM PDT


WASHINGTON — A new computer-based technique is exploring uncharted territory in the fruit fly brain with cell-by-cell detail that can be built into networks for a detailed look at how neurons work together. The research may ultimately lead to a complete master plan of the entire fly brain. Mapping the estimated 100,000 neurons in a fly brain, and seeing how they interact to control behavior, will be a powerful tool for figuring out how the billions of neurons in the human brain work.

sciencenewsThe program has already found some new features of the fruit fly brain, said study coauthor Hanchuan Peng of the Howard Hughes Medical Institute's Janelia Farm Research Campus in Ashburn, Va. "We can see very beautiful and very complicated patterns," said Peng, who presented the results April 9 at the 51st Annual Drosophila Research Conference. "If you look at neurons at a better resolution, or look at regions you've never looked at before, you'll find something new."

Peng and his colleagues developed a method, also described in the April Nature Biotechnology, which incorporates many different images of fruit fly brains. The brains come from flies that were genetically programmed so that select neurons glow when struck with a particular type of laser light. By combining thousands of these digital images from different flies, the researchers can create maps of how these different neuronal populations fit together. The full map of the fly brain isn't yet complete, but it will grow as more images are added.

These kinds of large-scale studies that focus on how neurons are connected are "very important for the future," commented geneticist Wei Xie of Southeast University in Nanjing, China. Understanding how all of the neurons work together is much more meaningful than studying how a single brain cell connects to another cell, Xie said. "Just a neuron is not enough."

"What we want to do in the next few years is to add more and more neuron reconstructions into this map," Peng said. He likened the process to a Google Earth resource. "If you think about the fruit fly brain as the Earth, the little neurons will be the streets. We want to map a lot of neuron streets onto the Earth," he said.

Peng and his colleagues have started combing their preliminary brain map for interesting features and comparing different flies' brains to one another. For the most part, patterns of neuron-connecting pathways don't vary much from brain to brain, the researchers found.

On the other hand, the shapes of cells in the same brain structure can differ dramatically. For example, the variety of shapes found in the neurons of a wheel-shaped brain structure called the ellipsoid body "are just amazing," Peng says. In the same fly, some of the cells spread inside the ring, while others point outward in a complex lock-and-key arrangement.

The results are preliminary, but finding such unexpected variation could mean that these neurons — which were thought to be nearly carbon copies of each other — have important functional differences.

Image: Hanchuan Peng

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Floating Nanosheets Could Be the Plywood of Nanotechnology

Posted: 12 Apr 2010 03:00 AM PDT


A synthetic, free-floating nanosheetjust two molecules thick may provide the perfect substrate for creating future electronic devices.

The biologically inspired sheet is made of polymers, or long molecules with repeating units, that mimic the precision and order seen in proteins and crystal structures. But these synthetic sheets are made of molecular building blocks that are more durable than their natural counterparts.

"We're making molecular plywood — a flat piece of building material that you can build nanoscale structures with," said chemist Ronald Zuckermann of Lawrence Berkeley National Laboratory, coauthor of a study April 11 in Nature Materials. "This study will open people's eyes and make them talk about proteins and plastics in the same sentence."

Zuckermann's team made the discovery by stumbling upon a particular sequence of repeating units that formed perfectly aligned two-dimensional crystals. "Ours is the largest and thinnest two-dimensional self-assembled organic crystal known,"he said.

Proteins are made of a chain of amino acids that fold up into three-dimensional structures, such as alpha-helices and beta-sheets. Zuckermann had previously developed polymers that mimic alpha-helices, and here for the first time he has developed a material that mimics beta-sheets.

"This study is a great advancement," said materials scientist Yi Cui of Stanford University. "The fact that they can produce a really large sheet on a nanometer-scale is really surprising."

By using only two types of molecular building blocks, the team dramatically reduced the number of possible sequences and simplified the self-assembly of the polymers into larger structures, such as sheets. They created 3-nanometer-thick sheets with hydrophobic, or water-fearing, chemical groups facing the inside and hydrophilic, or water-loving, molecular units on the surface.

The team systematically adjusted the hydrophilic and hydrophobic groups until they discovered a pattern of molecular sequences that self-assemble into layered sheets. The sheets resemble a plasma membrane, the bilayered structure made of lipids and proteins that surrounds cells.

When Zuckermann looked at the polymer chains directly under the most powerful electron microscope in the world, he observed them wiggling around like little worms as they slid against each other. The idea of using high-resolution electron microscopy to visualize the shape of individual polymer chains was previously unheard of, he said

"It completely blew us away that these crystallizine sheets are so well-ordered and have very straight edges, even though their component polymer chains are flexible and spaghetti-like," Zuckermann said. "It was a real thrill to figure out how to really order material in a precise way at the atomic level." His team knows exactly where each atom is located in the structure, so it's possible to chemically engineer the material to serve specific functions.

A smooth, layered surface may be ideal for building flat electrical components, such as photovoltaic devices, batteries and fuel cells, Zuckermann said. Decorating the hydrophilic surface of the sheet with molecules that specifically bind to proteins may be useful for biosensing applications, such as developing catalysts and recognizing molecules, he added.

What's more, the sheets form layers that can separate and selectively transport different materials. He foresees developing more complicated three-dimensional structures using the same technology. Scientists may also one day use the technology for biological applications, such as drug delivery or tissue engineering.

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