Wednesday, 7 October 2009

Johnald's Fantastical Daily Link Splurge

Johnald's Fantastical Daily Link Splurge

Beyond the Genome

Posted: 07 Oct 2009 10:00 AM PDT


When scientists finished sequencing the human genome, the answers to diseases were supposed to follow. Six years later, that promise has gone unfulfilled. Genetics just isn't that useful for predicting who gets sick, and why. The blueprint of life turned out to be an intriguing parts list.

"It's much more complex than we had thought. There aren't going to be easy answers," said Teri Manolio, director of the National Human Genome Research Institute's Office of Population Genomics. "The genome is constantly surprising us. There's so much that we don't know about it."

Manolio is the lead author of a Nature article entitled "Finding the missing heritability of complex diseases." Published Wednesday, it's part of a major change in how scientists see the genome.

In April, several articles in the New England Journal of Medicine featured researchers arguing over why genome-wide association studies — in which thousands of genomes are compared in a hunt for disease-linked patterns — had found so little. Several months later, a massive hunt for schizophrenia genes was described as the field's "Pearl Harbor." At a conference this summer at the Jackson Laboratories, the shortcomings of gene-centered explanations were a starting point for talks by some of the world's most prominent geneticists.

It's not that genes are suddenly unimportant. Researchers are just acknowledging their variations as pieces of an extraordinarily complicated puzzle, along with how genes are turned on, how many copies are made of each, the shape of the genome itself, and how all of the genome's protein products mix and interact. talked to Manolio about the future of genomics research. What do you mean by "missing heritability"?

Teri Manolio: We know that diseases cluster in families. In some diseases, the risk might be two or three times higher than normal, or 30 times higher, for a relative of someone with a disease. But when we do these genomic studies, we find maybe a 50 percent increase in risk. That gap is what's missing. The numbers can get tricky. If you've found that someone with a certain genetic variant has double the risk of developing a disease, but the heritable risk is a hundred-fold, then we've only connected two percent of the heritability to genetics?

Manolio: That's a fair way of putting it. The gap varies. In some diseases, we're describing half of the genetic heritability. But that's unusual. Only macular degeneration has numbers that high. In many diseases, it's around five percent. How much of the gap is caused by our inability to link genetics to conditions, and how much has non-genetic causes?

Manolio: There's a lot of thought that this might be DNA and environment together. If you're not exposed to adverse environmental factors, then you may never develop a given disease. With a bad enough environmental exposure, you may get a disease regardless of your genetic makeup. What about aspects of our DNA that we're just starting to study, like variations in the number of copies we have of each gene, or how genes are activated or physically arranged inside a cell?

Manolio: All of those have been suggested. At least so far, it doesn't look like copy numbers explain a huge amount of this. But there are other places to look, and I suspect that the answer is going to be, "all of the above." How does all this fit with what the public expected of genomics? It seems we had different expectations than the scientific community.

Manolio: Well, to be honest, I think we were a bit naive about things, too. We'd hoped that when we identified where all the genes are, and all the coding regions and all the variations one could have, then that would explain everything. Those were the hopes, and then reality came crashing in. What about personalized genomics testing? That's been the big consumer application of genomics so far.

Manolio: Since we're not explaining a huge mount of the inherited tendencies between people, then the information you get from a genotyping company may not be very apparently useful for predicting your risk of disease in the future. That's what emerges from many of these studies: There are likely many other factors that increase your risks, and these factors are known and explain more than genomics does now. Genomics is a promising research tool, but right now it's really a research tool. How do we find the missing heritability?

Manolio: We'll follow multiple avenues of research. We have to be humble about how this works. Do we have the tools?

Manolio: Our sequencing is in good shape — the costs are coming down, we can get everyone's base pairs read — but interpreting them is a real challenge. Technologies for epigenetics research are still developing. And there will be other needs coming down the pipeline. Want to put a timetable on the research?

Manolio: I don't think we can. In the next few years, we'll see lots of variants associated with diseases. Many will be further investigated, and their functions determined. That's one of the missing links here: what's the function of all these things? We have over 400 variants identified in a whole variety of traits, but only in a few do we understand how they change a gene's function, and how that may change biology. But these are great clues to biology. Is that a better way of thinking about genetics — not in terms of answers, but clues?

Manolio: Absolutely. And if you're a glass half-full person, then four years ago, we had practically no associations that we could replicate in multiple populations. Now there are hundreds. All of these are clues, and that's wonderful. We just need to be patient in figuring out what they mean.

Image: From "Circos: an Information Aesthetic for Comparative Genomics."

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Citation: "Finding the missing heritability of complex diseases." By Teri A. Manolio, Francis S. Collins, Nancy J. Cox, David B. Goldstein, Lucia A. Hindorff, David J. Hunter, Mark I. McCarthy, Erin M. Ramos, Lon R. Cardon, Aravinda Chakravarti, Judy H. Cho, Alan E. Guttmacher, Augustine Kong, Leonid Kruglyak, Elaine Mardis, Charles N. Rotimi, Montgomery Slatkin, David Valle, Alice S. Whittemore, Michael Boehnke, Andrew G. Clark, Evan E. Eichler, Greg Gibson, Jonathan L. Haines, Trudy F. C. Mackay, Steven A. McCarroll & Peter M. Visscher. Nature, Vol. 461, No. 7265. October 8, 2009.

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

Supermassive Black Holes Collide to Become Even More Super and Massive

Posted: 07 Oct 2009 07:01 AM PDT


New X-ray data from NASA's Chandra X-ray Observatory added to an imagepreviously captured by the Hubble Space Telescope created this amazing composite image of two black holes on the verge of colliding.

The two supermassive black holes, which show up as two points of light in the center of the galaxy NGC 6240, are only 3,000 light-years apart. Astronomers think the two will eventually combine into a single, larger black hole.

Also combining to make a whole greater than the sum of its parts are the two pieces of this image, shown below. Space photos are often a combination of multiple images and sets of data, designed to bring out the details and beauty of the subject. In this case, Chandra's X-ray data and Hubble's optical data come together to create an image so stunning that it looks like it must be an artist's rendering.


Images: X-ray: NASA/CXC/MIT/C.Canizares, M.Nowak. Optical: NASA/STScI.

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Bird Cam Captures Albatross, Killer Whale Rendezvous

Posted: 06 Oct 2009 05:00 PM PDT


Tiny cameras attached to the backs of four Antarctic albatrosses have revealed a clever feeding strategy: Instead of randomly scanning the open ocean for prey, some birds appear to fly alongside killer whales and scavenge for scraps left by the mammalian predators.

Albatrosses often have to fly hundreds of miles in just a few days in order to find their prey, and scientists have long wondered how the birds navigate over a largely featureless ocean. Previous studies suggested the birds might use a combination of scent and vision to guide them, but until now, no one had been able to directly record the behavior of the foraging seabirds.

To track the birds, scientists attached lipstick-sized digital cameras, equipped with depth and temperature sensors, to the backs of four albatrosses from Bird Island off the coast of South Georgia in the Antarctic Ocean. After three foraging trips, the bird-borne cameras had captured more than 28,725 images. Although many photos were too dark to be useful — and 6,600 were obscured by feathers fluttering in front of the camera lens — the remaining images yielded a startling result.

albatross-with-killer-whale"One surprising finding was that one of the study birds encountered a killer whale, Ornicus orca, during the course of the trip," wrote the researchers in a paper published this week in the journal PLoS ONE. "This image showed that the killer whale broke the surface and that three other albatrosses were also apparently following the whale."

Unfortunately, several subsequent images were blocked by feathers. But based on a rapid temperature drop recorded by the camera, it appears the albatross landed on the sea surface after spotting the killer whale, and likely spent the next 30 minutes diving for prey alongside the whale.

The researchers say it's difficult to quantify how often black-browed albatrosses associate with killer whales in the open ocean, but they say their findings suggest that shared meals may be quite common.

"When killer whales feed on fish, fragments of prey are often left near the sea surface," the scientists wrote. "These prey fragments could be an important food resource for albatrosses. Scavenging on such prey fragments may be more energetically advantageous than the pursuit and capture of live prey, as such activities can require frequent take-off, landing and prey handling, which may all be energetically costly."

Similar behavior has been recorded in tropical birds, who scavenge alongside tuna, but this is the first time the behavior has been seen among albatrosses in the deep ocean.

In the video below, albatrosses fly around Bird Island, groom one another and care for their fuzzy gray chicks.

Image 1: Black-browed albatrosses fly over Bird Island, British Antarctic Survey. Image 2: Albatrosses interact with a killer whale on the open ocean. Photo taken with the bird-borne camera, National Institute of Polar Research, Japan.

Video: British Antarctic Survey.

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Anatomy of an Asteroid

Posted: 06 Oct 2009 02:15 PM PDT


FAJARDO, Puerto Rico — Planetary scientists have reported a slew of new findings about the first asteroid ever spotted before pieces of it fell to Earth. The space rock contained a number of amino acids, had a flattened shape and appears to have been blasted off the surface of a larger body, researchers reported October 5 at the annual meeting of the American Astronomical Society's Division for Planetary Sciences.

sciencenewsThe asteroid, 2008 TC3, first came into the limelight in 2008 when researchers spotted the body just 19 hours before it broke apart in Earth's atmosphere and crashed into northern Sudan. Planetary scientists tracked the intact asteroid as it fell to the ground as meteorites (SN: 4/25/09, p. 13).

As observed through a telescope during the last two hours of its journey to Earth, the small asteroid appeared only as a flickering point of light. But by analyzing the variations in brightness of the rock as it tumbled through space, along with information culled from fragments on the ground, Peter Scheirich of the Czech Academy of Sciences in Ondrejov and his colleagues have now reconstructed what the asteroid would have looked like up close. The space rock resembled a flattened loaf of bread, Scheirich reported.

Further analysis of the shape of the asteroid, along with estimates of the asteroid's mass and the reflectivity of the recovered meteorites, could reveal whether the rock is solid through and through or porous, like a loosely held rubble pile, he adds.

The rock entered Earth's atmosphere "like the Apollo space capsule, flat face forward," says Peter Jenniskens of the SETI Institute in Mountain View, Calif., who led an effort to recover some 300 meteorites in Sudan in October 2008.

Structures in the meteorites — pores lined with fine-grained crystals of a mineral called olivine — suggest that the asteroid was blasted off the surface of a larger rock, reported Michael Zolensky of NASA's Johnson Space Center in Houston. That means it should be relatively easy to use the properties of these meteorites to understand the properties of thousands of observed asteroids in space, which only reveal clues about their surfaces through telescope images and spectra, he says.

Other studies, also reported October 5, reveal that the meteorites contain amino acids, the building blocks of proteins, that must have come from 2008 TC3, reported Michael Callahan of NASA's Goddard Space Flight Center in Greenbelt, Md.

The meteorites belong to a rare type called ureilites, which contain microscopic diamonds. "To my knowledge this is the first report of amino acids in any ureilite-type meteorite," said Daniel Glavin of NASA-Goddard, who collaborated with Callahan and other colleagues on the analysis.

The researchers identified 18 amino acids, including alpha-aminoisobutyric acid and isovaline. Because they are uncommon on Earth, Glavin said, "it is highly likely that these two amino acids were formed in space."

"The discovery of amino acids in [2008 TC3] provides additional support for the idea that organic matter delivered by asteroids could have seeded the early Earth with the raw ingredients for life," he noted.At the same time, the presence of the amino acids is puzzling, Glavin added.

Evidence suggests that 2008 TC3 was heated to temperatures as high as 1,300˚ Celsius billions of years ago, yet amino acids are destroyed at temperatures above 500–600˚C, Glavin said.Other researchers, including Richard Zare, Amy Morrow and Hassan Sabbah of Stanford University in Palo Alto, Calif., reported that they had found common components of soot known as polycyclic aromatic hydrocarbons in the meteorites. This soot is interspersed with amino acids, Zare said.

"The big mystery now is how did these complex organic compounds survive such high temperatures?" notes Glavin.

One possibility is that the amino acids or their precursors were incorporated into the asteroid's parent rock during its formation and survived the heating and melting that would have occurred when the parent rock was blasted into pieces. Another possibility, he notes, is that amino acids formed inside 2008 TC3 itself much later on, after it cooled to temperatures below 500–600˚C.

To help settle these and other questions, Jenniskens plans to return to Sudan this December to pick up more specimens.

Image: The contrail left by the asteroid's passage through the atmosphere. / Muawia Shaddad.

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