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Saturday, 10 October 2009

Johnald's Fantastical Daily Link Splurge

35 Years of the World’s Best Microscope Photography

Posted: 09 Oct 2009 04:21 PM PDT

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This image of the male sex organ of a flowering plant took first place in Nikon's annual Small World photomicrography competition this year.

Chosen for both its scientific and artistic qualities from among a record 2,000 entries, this image was captured by Estonian scientist Heiti Paves.

"As part of my work as a research scientist, I have been taking photographs through the microscope for almost 30 years to observe the processes in living cells," Paves said Thursday in a press release.

Nikon honored 20 images including an anglerfish ovary,cotton fibersand fish scales.

Winning the popular vote online out of 137 finalists was the image below of a bundle of fluorescent actin protein filaments captured by Dennis Breitsprecher of the Institute of Biophysical Chemistry at Germany's Hannover Medical School.

See the winners of the competition over the last 35 years on the following pages.

Images: Above: Arabidopsis thaliana (thale cress) anther (20x) Confocal / Heiti Paves, Tallinn University of Technology, courtesy of Nikon Small World.

Below: Fluorescent actin protein filaments. / Dennis Breitsprecher, Institute of Biophysical Chemistry at Germany's Hannover Medical School. Courtesy of Nikon Small World.

nikon2009popular

Can Life Survive Deep Space? Let’s Send It There!

Posted: 09 Oct 2009 10:45 AM PDT

LIFE on Earth was all neatly packed up inside a pucklike container and ready to blast off on an unmanned Russian mission to a Martian moon this month.

After more than 10 months traveling through deep space, the Planetary Society's Living Interplanetary Flight Experiment would land on the surface of the Martian moon Phobos with its cargo of voyagers from all three kingdoms of life, including tiny, extremely hardy animals called tardigrades.

Then, after a couple of weeks on the surface, the first Earthly life to have lived on another solar body would return to Earth. A tiny, robotic, interplanetary lander was going to spring off the base craft, fire off its rocket, and hurtle through space before crash landing in Kazakhstan.

Now, though, Russian space officials have delayed the mission due to safety and technical problems that typically plague ambitious trips beyond low-Earth orbit. And because of the nature of Earth's orbit in relation to Mars, the Planetary Society-backed researchers will have to wait two long years before their next launch window to determine if life could have originated outside Earth and hitched a ride here.

Despite the delay, LIFE will eventually get a chance to fly, assuming the funding will remain in place.

"LIFE is a test of part of the so-called transpermian theory to see whether life can travel through space between planets," said Bruce Betts, the experiment's manager at the Planetary Society, which was co-founded by Carl Sagan. "If we send a bunch of microorganisms out to space for three years, will they still be alive?"

shake_table_with_life_dsc05102

We already know that plenty of life forms can survive in low-Earth orbit. In fact, we've sent up all kinds of living things, including dozens of animals and various kinds of nasty bacteria.

But deep space is different. At the International Space Station, say, the Earth's magnetosphere protects life from radiation. We're not really sure what will happen when life is exposed to the depths of space for years. The Biostack 1 and 2 experiments, flown during the Apollo 16 and 17 missions to the moon proved organisms could survive during a two-week journey through space. But that's not long enough to simulate the hypothetical journey of bacteria from Mars to Earth.

"It's a see-what-happens experiment, which you don't get a lot of anymore," Betts said.

If the living things in the LIFE experiment survive the 34-month journey aboard thespacecraft Phobos Grunt, it would provide support for the idea that living things could travel between planets aboard rocks ejected by cosmic collisions.

On the other hand, Betts said, "If you find everything is dead and confirm it's not some fluky other thing, then it casts more doubt on whether life can travel between the planets."

They fought through months of bureaucracy, both in the United States and Russia, to make the mission happen.

"Because this launch is on a spacecraft, we are subject to [International Traffic in Arms Regulations], so the Planetary Society is registered as what you might call an arms tracker," Betts said.

If the governments were a hassle, the engineering assignment was much worse. Completing the packaging of 30 living specimens into a tiny 100-gram "BioModule" consumed the team as they raced to send off their part of the mission to Russia.

"You need to understand the constraints for the Phobos mission," Betts said. "We had 100 grams. We had to be passive. We had to not interfere with anything else. And, by the way, you have to survive a 4,000-g impact."

The Phobos lander won't have a parachute, so it's possible the landing will bring intense forces to bear on the scientific instruments. It's imperative, too, that the organisms remain sealed in their container for the duration of the journey, so they won't contaminate Phobos.

To test the BioModule's durability, they first filled the inside with fluorescent liquid, so that any leakage would be apparent. Then, the scientists strapped it to a shake table and violently vibrated it. Then, they shot it out of an air cannon onto a target. The first iteration of the BioModule leaked a bit of its fluorescent liquid, but held tough in the second round.

Sitting tight now, though, has become the scientists' main task.

More photos of the assembly and testing of the LIFE experiment can be found on the following page.

Images: 1) The LIFE BioModule. 2) The BioModule strapped to the shake table.
Bruce Betts

Friday, 9 October 2009

Johnald's Fantastical Daily Link Splurge

Crash Into the Moon With LCROSS Friday Morning
Your Bug-Coated Windshield Is Lousy With Genomes
The Direction of NASA’s Future at an Impasse
The Human Genome in Three Dimensions
Pigs Use Mirrors to Find Hidden Food

Crash Into the Moon With LCROSS Friday Morning

Posted: 08 Oct 2009 04:36 PM PDT

lcross_impact

Tomorrow morning you'll have a rare opportunity to experience a live moon crash. At 7:31 a.m. EDT, NASA's LCROSS satellite will send a rocket hurtling toward the moon at a whopping 1.55 miles per second, and a camera mounted on the spacecraft will send live footage back to Earth. Four minutes later, the entire satellite will smack into the moon, generating a giant plume of debris that should be visible from our planet with an amateur telescope.

To find out how and where to watch the carnage, check out the posts by our friends at GeekDad:

Ways to See LCROSS Crash on Friday Morning

Moon Shot Part Deux: Even More Ways of Observing the LCROSS Impact …

Image: Northrup Grumman

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Your Bug-Coated Windshield Is Lousy With Genomes

Posted: 08 Oct 2009 02:53 PM PDT

That disgusting layer of bug guts plastered across your bumper after a road trip could also be a great way to analyze the biodiversity of where you've been.

After a long-distance drive to a conference yielded a tremendous number of squashed bugs on his bumper, genomics researcher Anton Nekrutenko of Pennsylvania State University decided to try an experiment: Why not apply the tools of metagenomics, which is the study of DNA taken directly from an environmental sample, to the collection of insects decorating his car?

"How many species inhabit our immediate surroundings?" wrote Nekrutenko and colleagues in a paper published Thursday in Genome Research. "A straightforward collection technique suitable for answering this question is known to anyone who has ever driven a car at highway speeds."

By sequencing DNA taken from the bug splatter generated by two different car trips, one from Pennsylvania to Connecticut and the other from Maine to New Brunswick, Canada, the researchers discovered significant differences in insect diversity between the two regions.

In addition to proving that bug carnage can provide valuable information about biodiversity, the experiment served as proof-of-principle for a new kind of metagenomic analsyis. Until now, metagenomics had been used primarily to study mixed samples of bacteria, such as the microbes that inhabit the human gut or live on the surface of our skin. But scientists are increasingly interested in applying the same shotgun analysis of genetic material to answer questions about higher organisms.

For instance, researchers have debated for decades just how many different kinds of insects are out there, with estimates ranging from 10 million to 30 million. Of those, only a few hundred thousand have been cataloged by biologists. But analysis of insect diversity from environmental DNA samples is incredibly complex, and the researchers say our current computational tools aren't quite up to the task.

"It's somewhat easier with bacteria because normally bacteria have small genomes, and their genomes are packed with genes that produce proteins," Nekrutenko said. Higher organisms are more complicated because they tend to have larger genomes and more "junk" DNA that doesn't code for proteins. To handle analysis of the massive amounts of data necessary to screen even a simple collection, like bugs scraped from a car, the group had to create new tools.

"One of our main goals was technology development," Nekrutenko said. "In general, life sciences are becoming kind of like physics, very data-driven, but most biologists are not trained in data-driven research." Along with colleagues from the University of California, San Diego and Emory University, Nekrutenko's group developed a straightforward, web-based program called Galaxy that walks scientists through the steps of metagenomic analysis, from obtaining raw sequencing data to drawing up an evolutionary tree.

Some biologists who have already started using Galaxy give it rave reviews. "My lab would be lost without it," said biologist Ross Hardison of Pennsylvania State University, who has collaborated with Nekrutenko but was not involved in this research. "We are dependent on Galaxy for a very large fraction of the analyses we do."

Even more importantly, Nekrutenko said, Galaxy allows researchers to publish their entire dataset and methods so that other researchers can reproduce their results. "Metagenomics is kind of a parameter-dependent science," Nekrutenko said. "You run certain tools, and they have dials, and depending how you set these dials you can get completely different results. Through our system, you can see exactly how we set these dials."

That means other researchers can repeat Nekrutenko's analysis and see if they get the same results. For instance, someone might want to double-check a particularly bizarre feature of the data: In addition to finding plenty of insect and bacterial DNA, the group uncovered genetic material from the genus Homo.

Nekrutenko said the unexpected result probably represents an artifact: Because current databases of eukaryotic DNA sequences are dominated by the human genome, spurious human results are likely to pop up. "Precise species ID from mixed samples like this is very, very challenging," he said. "We have sequences that map to human DNA, even though I'm pretty sure we didn't kill anybody."

Image 1: Flickr/John Beales. Image 2: A photograph of Nekrutenko's bumper after one of the bug collection trials/Anton Nekrutenko.

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The Direction of NASA’s Future at an Impasse

Posted: 08 Oct 2009 02:25 PM PDT

The committee charged with rethinking American human spaceflight is done thinking, but it's still unclear what the future of NASA's astronaut corps might be, and some nagging issues have yet to be resolved.

The U.S. Human Space Flight Plans Committee — known informally as the Augustine commission, after its head Norm Augustine, former CEO of Lockheed Martin — held its last teleconference today. The ball, or hot potato, will soon be in the Obama administration's court when the group formally presents its alternatives to the Office for Science and Technology Policy.

"We did not rate the overall options because, first of all, we were not asked to do that — and doing it would have required that we apply some sort of judgment as to what the relative weighting of those factors should be," Augustine said.

Even in its waning days, though, some controversies remain. The final meeting revealed some internal disputes within the group on how to "score" the alternative plans. A particularly sticky issue is the safety of the Ares I rocket, a key component of the current Constellation program.

The safety risk the panel assigned to the various human spaceflight options was based largely on the destination of the missions — to low-Earth orbit, the moon, or elsewhere.

The specific vehicles and systems involved in the missions were not a significant factor, said Ed Crawley, an MIT professor and committee member, in introducing the meeting.

Still, some members, notably Bohdan Bejmuk, chair of the Constellation program Standing Review Board, argued that the Ares I should get a higher safety rating than its competitors.

"I completely disagree with that assessment," shot back Jeff Greason, CEO of XCOR Aerospace and vice-chair of Personal Spaceflight Federation.

Other committee members, notably Augustine himself, tried to find common ground between the panel members, but the dispute clearly remains.

"Different partisans of different systems have arguments for why their systems should be exempt from the lessons of history," Greason said, before noting that probabilistic risk assessments based on the architecture of a particular space machine don't capture 90 percent of the accidents that have actually occurred.

Still, Bejmuk stuck to his guns, arguing multiple times that the Ares I was intrinsically safer than the alternatives.

"The program of record has a simpler rocket and we're not giving it credit," he contended.

Disagreement among these experts won't make decision-making any easier for John Holdren, Obama's top science adviser, who created the panel. The panel's summary report, released in September, a few weeks later than scheduled, seemed to raise as many question as it answered. During Congressional hearings, Augustine faced heated questions from several House members who attacked the meaning and methodology of the committee's work.

"Instead of focusing on how to strengthen the exploration program in which we have invested so much time and treasure," Gabrielle Giffords, Democrat chair of the space subcommittee a Democrat from Arizona, railed, "they gave only glancing attention to Constellation—even referring to it in the past tense in their summary report and instead spent the bulk of their time crafting alternative options that do little to illuminate the choices confronting Congress and the White House."

Many questioned whether the Augustine commission had given enough attention to the safety of astronauts. Several others questioned the emphasis that the Augustine committee placed on working with commercial entities.

Augustine got a kinder, almost bored reception in the Senate, but it seems clear that any plan the Obama administration may entertain to scrap the Bush-era Constellation program will face fierce criticism.

Image: NASA/Ares I test firing.

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

The Human Genome in Three Dimensions

Posted: 08 Oct 2009 12:16 PM PDT

By breaking the human genome into millions of pieces and reverse-engineering their arrangement, researchers have produced the highest-resolution picture ever of the genome's three-dimensional structure.

The picture is one of mind-blowing fractal glory, and the technique could help scientists investigate how the very shape of the genome, and not just its DNA content, affects human development and disease.

"It's become clear that the spatial organization of chromosomes is critical for regulating the genome," said study co-author Job Dekker, a molecular biologist at the University of Massachusetts Medical School. "This opens up new aspects of gene regulation that weren't open to investigation before. It's going to lead to a lot of new questions."

As depicted in basic biology textbooks and the public imagination, the human genome is packaged in bundles of DNA and protein on 23 chromosomes, arrayed in a neatly X-shaped form inside each cell nucleus. But that's only true during the fleeting few moments when cells are poised to divide. The rest of the time, those chromosomes exist in a dense and ever-shifting clump. Of course their constituent DNA strings are clumped, too: If the genome could be laid out end-to-end, it'd be six feet long.

For decades, some cell biologists suspected that the genome's compression wasn't just an efficient storage mechanism, but linked to the very function and interaction of its genes. But this wasn't easy to study: Sequencing the genome destroys its shape, and electron microscopes can barely penetrate its active surface. Though its constituent parts are known, the genome's true shape has been a mystery.

In April, a paper published in the Proceedings of the National Academy of Sciences linked patterns of gene activation to their physical proximity on chromosomes. It still provided the most persuasive evidence to date that genome shape matters, even though the researchers' chromosome map was relatively low-resolution. The topography described in the latest research, published Thursday in Science, is far more detailed.

"It's going to change the way that people study chromosomes. It will open up the black box. We didn't know the internal organization. Now we can look at it in high resolution, try to link that structure to the activity of genes, and see how that structure changes in cells and over time," said Dekker.

To determine genome structure without being able to directly see it, the researchers first soaked cell nuclei in formaldehyde, which interacts with DNA like glue. The formaldehyde stuck together genes that are distant from each other in linear genomic sequences, but adjacent to each other in actual three-dimensional genomic space.

The researchers then added a chemical that dissolved the gene-by-gene linear sequence bonds, but left the formaldehyde links intact. The result was a pool of paired genes, something like a frozen ball of noodles that had been sliced into a million fragmentary layers and mixed.

By studying the pairs, the researchers could tell which genes had been near each other in the original genome. With the aid of software that cross-referenced the gene pairs with their known sequences on the genome, they assembled a digital sculpture of the genome. And what a marvelous sculpture it is.

"There's no knots. It's totally unentangled. It's like an incredibly dense noodle ball, but you can pull out some of the noodles and put them back in, without disturbing the structure at all," said Harvard University computational biologist Erez Lieberman-Aiden, also a study co-author.

In mathematical terms, the pieces of the genome are folded into something similar to a Hilbert curve, one of a family of shapes that can fill a two-dimensional space without ever overlapping — and then do the same trick in three dimensions.

How evolution arrived at this solution to the challenge of genome storage is unknown. It might be an intrinsic property of chromatin, the DNA-and-protein mix from which chromosomes are made. But whatever the origin, it's more than mathematically elegant. The researchers also found that chromosomes have two regions, one one for active genes and another for inactive genes, and the unentangled curvatures allow genes to be moved easily between them.

Lieberman-Aden likened the configuration to the compressed rows of mechanized bookshelves found in large libraries. "They're like stacks, side-by-side and on top of each other, with no space between them. And when the genome wants to use a bunch of genes, it opens up the stack. But not only does it open the stack: it moves it to a new section of the library," he said.

The segregation of active and inactive genes adds to evidence that genome structure affects gene function.

"It's a great description of the structure of the nucleus, and if you put that on top of what we did, it forms the big picture," said Steven Kosak, a Northwestern University cell biologist and co-author of the April PNAS paper that linked rough outlines of chromosome arrangement to gene activation. Whereas that study only looked at a few chromosomes, the Science paper "looks at fine resolution over the whole genome," said Kosak.

"Now you can produce these genome maps, and superimpose them with genome-wide analyses of gene expression. You can really start asking how changes in spatial organization relate to changes in genes turning on and off," said Tom Misteli, a National Cancer Institute cell biologist who studies how glitches in chromosome structure may turn cells cancerous. Neither Misteli nor Kosak were involved in the Science study.

Connecting genome shape to gene function could also help explain the connection between genes and disease, which remain largely unexplained by traditional, sequence-focused genomics.

"It's perfectly reasonable and almost inevitable that the 3-D structure of DNA is going to influence how it functions," said Teri Manolio, director of the National Human Genome Research Institute's Office of Population Genomics.

Researchers also want to study how genome shape is altered. That appears to happen constantly during the transition from stem cell to adult cell, and then during cell function.

"How much variation is there in structure across cell types? What controls it? Exactly how important is it? We don't know," said Dekker. "This is a new area of science."

Image: From Science, a two-dimensional Hilbert curve, and the three-dimensional shape of a genome.

See Also:

Citation: "Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome." Erez Lieberman-Aiden, Nynke L. van Berkum, Louise Williams, Maxim Imakaev, Tobias Ragoczy, Agnes Telling, Ido Amit, Bryan R. Lajoie, Peter J. Sabo, Michael O. Dorschner, Richard Sandstrom, Bradley Bernstein, M. A. Bender, MarkGroudine, Andreas Gnirke, John Stamatoyannopoulos, Leonid A. Mirny, Eric S. Lander, Job Dekker. Science, Vol. 326 No. 5950, October 9, 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.

Pigs Use Mirrors to Find Hidden Food

Posted: 08 Oct 2009 09:48 AM PDT

In just five hours, an average farm pig can learn how to interpret an image in the mirror and use it to find hidden food.

Scientists consider the ability to use a mirror a sign of complex cognitive processing and an indication of a certain level of awareness. In addition to humans and some primates, dolphins, elephants, magpies and a famous African grey parrot named Alex have all been known to retrieve objects or remove marks on their body using a mirror. Now it looks like pigs should be added to the list of clever critters that can master a mirror: After spending five hours with a mirror in their pen, seven out of eight pigs could use the reflection to find a hidden bowl of grub.

"This is the first demonstration of the ability of pigs to use mirrors," animal behavior expert Donald Broom of the University of Cambridge wrote in an email. "Finding sophisticated learning and awareness in animals can alter the way that people think about the species and may result in better welfare in the long run." Broom co-authored the paper published this month in Animal Behaviour.

Like most animals, pigs were immediately curious when researchers placed the shiny, reflective object in their pen. They approached the mirror until they bumped into it with their snout, and then checked to see what was behind the mirror. The pigs spent an average of 20 minutes gazing at their reflection, often turning in different directions to inspect themselves from several angles.

"These kind of movements suggest that the pigs were correlating the movements of their body with the visual stimulus they were receiving from the mirror, and so learning the contingency between the two," biologist Louise Barrett of the University of Liverpool wrote in a commentary about the paper, also published this month in Animal Behaviour.

After five hours with a mirror, the pigs were placed into a new test area that contained a food bowl hidden behind a barrier. Although the pigs could see the reflection of the bowl in the mirror, they couldn't see the food directly. A fan above the bowl circulated the scent of food around the room, prohibiting the pigs from smelling their way to the treat.

Seven out of eight of the pigs with previous mirror experience spotted the reflection of the food bowl and correctly interpreted its location: Instead of searching for the food in its apparent position behind the mirror, the pigs headed around the barrier and straight for the true location of the bowl. When the researchers tested pigs with no prior mirror exposure, however, nine out of 11 of them became confused, searching behind the mirror for the food.

"These results suggest not only that pigs learn the contingency between their own movements and their image in the mirror," Barrett wrote, "but that their knowledge incorporates the layout of the environment as well, so that they can locate objects in space."

The researchers say their experiment is more than a nifty trick: The fact that pigs can learn to use a mirror means they are capable of a type of awareness called assessment awareness, which means they can understand the significance of a situation in relation to themselves, over a short period of time. In this case, the pigs remembered how their own movements appeared in the mirror, and were able to apply that knowledge to a separate situation involving a hidden food bowl.

"Having a sense of self and using it is a form of assessment awareness," Broom wrote. Although the mirror experiment doesn't directly prove that pigs have a sense of self, the researchers suggest that given how quickly the pigs learn to recognize their own movements in a mirror, they may have some degree of self-awareness. "We have no conclusive evidence of a sense of self," Broom wrote, "but you might well conclude that it is likely from our results."

Other mirror tests have been used to more directly examine an animal's sense of self — if researchers apply a yellow mark to the black feathers of a magpie, for instance, the bird will use a mirror to clean itself off. Unfortunately, Broom says the mark experiments just don't work on pigs: Pigs are so accustomed to being streaked with mud, they don't much care if researchers apply extra marks on their bodies. "We have put marks on pigs," Broom wrote. "They take little notice of them."

Combined with a host of other research studies demonstrating the keen intelligence of pigs, the researchers hope their study will lead to better treatment of the farm animals. "If an animal is clever," Broom wrote, "it is less likely to be treated as if it is an object or a machine to produce food, and more likely to be considered as an individual of value in itself."

Image: Flickr/The Pug Father

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Thursday, 8 October 2009

Johnald's Fantastical Daily Link Splurge

Counting Elephants by Voice
Nobel Prize for the Chemistry of Protein Production
Alligator Swamps Are Lousy With Monogamy
More Than Meets the Eye: How the CCD Transformed Science

Counting Elephants by Voice

Posted: 08 Oct 2009 08:34 AM PDT

By putting microphones in the jungle, researchers are better able to perform the surprisingly tricky task of counting elephants.

Sure, pachyderm polling doesn't seem difficult. They're not exactly hard to see. But covering hundreds of square miles, day after day, requires time, money and personnel — all of which are in short supply in the developing countries where elephants live.

Enter the Elephant Listening Project at Cornell University. Using acoustic monitoring and analysis techniques originally developed for counting birds by song, they track elephants in the jungles of Central Africa.

In a paper published in the September African Journal of Ecology, project researchers describe the calibration of their model at a Central African Republic site. First they personally observed forest clearings where elephants were known to gather, counting the animals they saw and the noises they made. The researchers then turned these observations into a framework for interpreting recordings made by microphones installed throughout the forest.

The same approach "provides an opportunity to improve management and conservation of many acoustically active taxa whose populations are currently under-monitored," wrote the researchers.

In addition to being relatively inexpensive and geographically comprehensive, bioacoustic monitoring offers other advantages over traditional animal counts. It can give detailed ecological snapshots, counting anything that makes a noise.

For the elephant counts, each monitor covered a square mile of ground, "a dramatic increase in coverage over dung survey transects." In other words, it's a lot easier to listen to elephants than gather their poop.

Image: Elephant Listening Project

Via the Conservation Maven.

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Citation: "Acoustic estimation of wildlife abundance: methodology for vocal mammals in forested habitats." By Mya E. Thompson , Steven J. Schwager, Katharine B. Payne and Andrea K. Turkalo. African Journal of Ecology, Vol. 47 No. 3, September, 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.

Nobel Prize for the Chemistry of Protein Production

Posted: 07 Oct 2009 01:48 PM PDT

This year's Nobel Prize in Chemistry went to three molecular biologists who study ribosomes, the protein factories within cells.

Ribosomes were discovered in the 1950's by George Palade, who went on to win the Nobel Prize in Physiology or Medicine for his work on the makeup of cells, but scientists weren't able to take a close look at those organelles till the end of the century. Thomas Steitz, Venkatraman Ramakrishnan, and Ada Yonath developed tricks for examining the tiny structures with x-rays and electron beams. The high-resolution 3D images they acquired will help chemists develop a host of better medications.

"Scientists around the world are using the winners' research to develop new antibiotics that can be used in the ongoing battle against antibiotic-resistant microbes that cause so much illness, suffering and death." said Thomas Lane, president of the American Chemical Society, in a press release.

Dozens of antibiotics — including tetracycline and clindamycin — work by gumming up the ribosomes inside bacteria. Each of those medications is made up of relatively small molecules that can wedge themselves into crevices in the ribosome, destroying the microbes' ability to make protein, and thus rendering them helpless.

Armed with 3D images of antibiotic molecules wedged into ribosomes, medicinal chemists can refine their strategy for fighting bacteria. They can find new weak spots in bacterial ribosomes.

That approach is a lot like the way that the Rebel Alliance destroyed the first Death Star: by looking at its blueprint and finding a weak spot. Except, in this case the researchers are looking for vulnerable nooks and crannies in a blob of RNA and protein, rather than a thermal exhaust port.

Dozens of 3D images that show antibiotics sticking to ribosomes are available in the Protein DataBank, and you can look at them yourself with a tool called First Glance.

Just type the Protein DataBank ID number for the ribosome that you want to look at, and then start exploring.

Here are some of the best structures:

Ribosome with Clindamycin: 1YJN
Ribosome with Azithromycin: 1NWY
Ribosome with Erythromycin: 1JZY

Image: A ribosome reads an mRNA sequence and produces protein according to its genetic code. Credit: Lawrence Berkeley National Laboratory

Posted: 07 Oct 2009 01:25 PM PDT

Alligators don't seem to be the promiscuous, indiscriminate reptiles scientists once though they were. A new 10-year study of alligator mating habits shows that most female crocodilians prefer to mate over and over with the same male, despite encountering a vast array of eligible alligator bachelors each year.

As the only surviving members of a class of reptiles called archosaurs, which included dinosaurs and the ancient ancestors of birds, alligators are in a unique position to help scientists understand the mating patterns of dinosaurs and birds. For the past 10 years, ecologists have been tracking female alligators at the Rockefeller Wildlife Refuge in Louisiana and recording their mate preferences by looking at the DNA of their young. The data, published today in Molecular Ecology, reveals that up to 70 percent of female alligators choose the same partner year after year.

"Given how incredibly open and dense the alligator population is at RWR, we didn't expect to find fidelity," biologist Stacey Lance of the Savannah River Ecology Laboratory in South Carolina said in a press release. "To actually find that 70 percent of our re-trapped females showed mate fidelity was really incredible. I don't think any of us expected that the same pair of alligators that bred together in 1997 would still be breeding together in 2005 and may still be producing nests together to this day."

Finding mate fidelity in alligators is surprising because most reptiles are polygamous, often mating with multiple partners during the same breeding year and producing young from multiple fathers. Alligators do exhibit multiple paternity — in this study, roughly 50 percent of nests contained eggs from more than one father — but surprisingly, females appeared to pick the same male (or males) year after year.

Because of the dense population of alligators at the wildlife refuge, the researchers don't think the repeat pairings were a result of chance. Instead, it appears that female alligators are actively choosing specific males that they've mated with in the past. Only a few other reptilian species exhibit this type of mate preference, and this is the first time anyone has shown fidelity in alligators.

The researchers are still trying to understand what drives alligator mate choice, and how picking the same mate might benefit future generations. Unlike most other reptiles, female alligators spend significant energy nurturing their young, both by sitting on their nests and defending their babies once they're born. It's possible that a successful pairing in the past means a higher chance of successful breeding in the future, but the scientists say further study is necessary to prove what makes an alligator stay faithful.

"In this study, by combining molecular techniques with field studies we were able to figure something out about a species that we never would have known otherwise," Lance said. "Hopefully future studies will also lead to some unexpected and equally fascinating results."

Images: Phillip "Scooter" Trosclair

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More Than Meets the Eye: How the CCD Transformed Science

Posted: 07 Oct 2009 12:45 PM PDT

The 2009 Nobel Prize for Physics went, in part, to the inventors of the charge-coupled device George Smith and Willard Boyle this week. Their innovation, sketched out in 1969, is now the imager in millions of digital cameras and telescopes.

The very first prototype, pieced together months after Smith and Boyle laid out its working principles, is pictured above.

A charge-coupled device, in most applications, translates light into an electronic signal. Photons of light striking an array of capacitors create an electrical charge proportional to their intensity, which the charge-coupler transforms into voltage. That signal can be digitized and transformed by the dull magic of high-performance computing into Hubble's images.

Millions of CCDs are made each year for mass market cameras, but they also proved a transformational technology in science by providing a much more sensitive light sensor than previously existed. After being overlooked for decades, the Nobel win was a mild surprise but well deserved.

"There wasn't anything that could compete in scientific imaging," said Tony Tyson, an astronomer at the University of California, Davis, who built the first CCD camera for scientific applications in the late 1970s. "You're interested in getting very high signal-to-noise ratios. There's nothing that really competes with CCDs."

For the really dim things astronomers look at, the number of photons of light coming from a source is so small that each one counts. Out of every 100 photons, a CCD can record more than 90 of them. Photographic plates can barely reach 10 percent. And your eyes? Their quantum efficiency is in the 1 to 4 percent range.

According to lore, Smith and Boyle sketched out the design for the ubiquitous imaging device in an hour, over lunch at Bell Labs in October 1969. Working under the intense pressure applied by their taskmaster of a boss, Jack Morton, the pair had the device fabricated within a couple of months. George Smith took a photo of it, which you can see at the top of the page.

The road, though, from the creation of the prototype to the development of an actual technology that could be used by scientists and photographers was long and hard. Though CCDs would come to dominate astronomy, the device, as invented, was nowhere near high enough resolution to be worthwhile. With its poor signal-to-noise ratio, it was not immediately clear that the CCD was destined for greatness.

"I joined the company in 1969, the very year that Dick Boyle and George Smith invented this thing," Tyson said. "I actually, frankly viewed it as a toy. It was so small and awfully noisy."

Historians Robert W. Smith and Joseph N. Tararewicz note that "astronomers could not simply procure a CCD 'off the shelf' soon after the device's invention at Bell Labs." In fact, a number of other imaging systems were suggested for what became the Hubble Space Telescope including a panoply of image tubes.

Some astronomers, though, saw the potential for CCDs down the road. They were in Smith and Tararewicz's terms, "counting on invention."

In the face of budget cuts in 1974 that threatened the installation of the still speculative, expensive CCD technology on the Large Space Telescope (Hubble), an astronomer delivered an impassioned plea for the technology.

"To decide now, eight years before the LST can possibly fly, on what is already an out-dated detector, less than state-of-the-art, will be regarded in the future, I think as a poor choice of the options which are conceivable in other directions for cutting the cost of the LST," Margaret Burbidge, a prominent astrophysicist, wrote. "It is like deciding to treat a sick patient by cutting out his heart on the grounds he would be saved the energy used by the heart muscles in pumping the blood around the body."

Hard work by hundreds of scientists and engineers pushed CCDs closer to reality over the next few years. Companies like Fairchild, Kodak and Tektronix, rather than Bell Labs, developed the technology into usable form. Military, scientific and consumer applications were all benefiting from the money being thrown at the CCD problems from different directions, but it was still tough.

"It was a very painful development," Tyson said. "There were all these problems making really large cameras and getting uniform CCDs out of companies that were already pushing the envelope."

Still, scientists like Tyson persevered. After nearly a decade, he put his latest camera on the 40-inch telescope at Mt. Palomar Observatory and was able to measure the distribution of the faint blue galaxies. That work became an important piece of evidence that dark energy — the mysterious force propelling the acceleration of the universe outward — actually exists.

Now, nearly every major astronomical observatory uses CCDs. They also remain the gold-standard for medical imaging, or really any type of science that needs to capture photons. Though CMOS imaging technology is making inroads in consumer technology, there's "still nothing like a huge CCD," Tyson said, for high-end science.

Tyson's latest project is the Large Synoptic Sky Survey, which will incorporate a 3,200-megapixel camera. Plotted against time, CCD performance, measured in pixels, has grown at close to the same dizzying logarithmic rate that computing power has (see below).

Clearly, that hour of lunch at Bell Labs opened up a technological development path that was as broad and deep as nearly any in the 20th century. And after decades of being overlooked for the biggest prize in science, the inventors of the CCD are finally getting their due.

"Back, say, 30 years ago when I was at Bell Labs, we thought that CCDs could very well be a Nobel Prize," said Cherry Murray, dean of engineering and physical science at Harvard University and a one-time colleague of Smith and Boyle at Bell Labs. "It had been overlooked for so long … It's nice to see."

Images: Sent by Tony Tyson to Wired.com. 1. George Smith. 2. Tony Tyson. 3. Tony Tyson.

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Wednesday, 7 October 2009

Johnald's Fantastical Daily Link Splurge

Beyond the Genome
Supermassive Black Holes Collide to Become Even More Super and Massive
Bird Cam Captures Albatross, Killer Whale Rendezvous
Anatomy of an Asteroid

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.

Wired.com talked to Manolio about the future of genomics research.

Wired.com: 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.

Wired.com: 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.

Wired.com: 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.

Wired.com: 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."

Wired.com: 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.

Wired.com: 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.

Wired.com: How do we find the missing heritability?

Manolio: We'll follow multiple avenues of research. We have to be humble about how this works.

Wired.com: 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.

Wired.com: 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.

Wired.com: 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

blackholecomposite

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.

blackholeoptical-copy

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.

"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

asteroidtracks

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.

The 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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