Friday, 5 March 2010

Johnald's Fantastical Daily Link Splurge

Johnald's Fantastical Daily Link Splurge

First Microbes Colonized Land by Using Fat For Protection

Posted: 05 Mar 2010 02:30 AM PST


The earliest microbes thatsurvived on landmay have synthesized fat molecules to prevent their death from dehydration.

Themolecules, called wax esters,could have helped the microbescolonize land byprotecting them against the harsh environments that probably characterized the lifeless continents, scientists hypothesizes in the March issue of Geology .

"Production of [wax esters] may represent an adaptation to cross a critical evolutionary threshold, i.e. surviving dehydration and/or dessication cycles," wrote David Finkelstein, a biogeochemist at the University of Tennessee-Knoxville, and his co-authors. "This adaptation could have facilitated bacterial migration into the earliest lakes, and aided survival in terrestrial environments."

Little is known about early terrestrial microbial life, which probably colonized land sometime before 500 million years ago. Unlike animals, they don't leave behind much that scientists can find. But these organisms prepared the way for more complex life by seeding the land with organic compounds that became soil.

Finkelstein's team has been investigating the behavior of modern communities of microbes called "microbial mats" in seasonal lakes near Warner Valley, Oregon. They found that dessicated mats have nearly double the amount of wax esters as their hydrated brethren, implying that the microbes start producing the molecules when times get tough.

When a microbe makes a wax ester from the molecules available to it, it also generates a water molecule. So, making esters could be a way of helping cells survive in environments with varying levels of moisture.

"It's a really cool idea if it actually turns out in a concrete way that this is a way of waterproofing yourself and forestalling the loss of cellular water," Finkelstein told "The first microbial mass that colonized land sure would have needed some kind of adaptation like this to make it successful."

Beyond the ability to survive drying out, microbes would have also needed a way to spread across the land. Finkelstein believes that the dessicated mats could have been transported long distances by wind. The idea came to his team when they were at one of the lakes in Oregon.

"You could see mats blown out of the water and up the hills," Finkelstein said. "Once the mat makes it to the top of the hill, you could blow into the next lake basin. If you could survive the drying, you could rehydrate yourself and live on."

The next step in their research will be to look for telltale microbial wax esters deeper in the geological record. In doing so, they'll be looking back through time, and it's possible they'll find them or other molecules that suggest they once existed. If they do, it will go a long way towards indicating that these fatty molecules were key to the evolution of terrestrial life as we know it.

Citation: "Microbial biosynthesis of wax esters during desiccation: Adaptation for colonization of the earliest terrestrial environments?" in Geology, March 2010 by David Finkelstein, Simon Brassell, and Lisa Pratt.

Image: Microbial mats in Yellowstone. flickr/paleoligo

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

Fears of Undersea Methane Leaks Already Coming True

Posted: 04 Mar 2010 01:51 PM PST


Prodigious plumes of planet-warming methane are bubbling from sediments across a broad region of Arctic seafloor previously thought to be sealed by permafrost, new analyses indicate. The resulting increase of methane gas in the atmosphere may accelerate climate warming, scientists say.

sciencenewsThough immense amounts of carbon are known to be trapped in the peatlands of Siberia, a larger, often unrecognized carbon reservoir lies hidden just north of that frigid region, says Natalia Shakhova, a biogeochemist at the University of Alaska in Fairbanks. The East Siberian Arctic Shelf — a 2.1-million-square-kilometer patch of Arctic seafloor that was exposed during the most recent ice age, when sea levels were lower — is three times larger than all of today's land-based Siberian wetlands. When the region was above sea level, tundra vegetation pulled carbon dioxide from the air as plants grew. That organic material, much of which didn't decompose in the frigid Arctic, accumulated in the soil and is the source of modern methane.

Now, field studies by Shakhova and her colleagues, reported in the March 4 Science, suggest that the submarine reservoir of carbon has begun to leak.

During six cruises in the region from 2003 to 2008, the researchers gathered data at more than 1,000 spots in the Greenland-sized stretch of shallow ocean. The team also took atmospheric readings of methane concentration during one helicopter survey and a wintertime excursion from shore onto the ice-covered sea, says Shakhova.

methane_graphs_2The researchers found unexpectedly high amounts of methane dissolved in seafloor waters across 80 percent of the area they studied. In some spots, methane concentrations during those six years averaged more than 80 times normal. Because the water over the shelf is relatively shallow — average depth in the region is about 45 meters, Shakhova notes — much of the methane reaches the ocean surface and then wafts into the atmosphere.

Previously, scientists presumed that the carbon trapped in sediments on the East Siberian Arctic Shelf was sealed by permafrost, as nearby deposits on land are. But there's a big difference between the two, Shakhova says: Much of the permafrost on land remains intact because it's exposed to bitter winter cold, whereas the seafloor permafrost is bathed in cold, yet definitely not freezing, salt water. The annual average temperature of seafloor permafrost is between 12 and 17 degrees warmer than that of nearby land-based permafrost, she notes.

The warmth of the seawater, as well as heat flowing up from within the Earth, has thawed the seafloor permafrost, releasing the methane, the researchers speculate. "We don't know how long it's been bubbling like this," Shakhova adds.

Sonar images show plumes of methane bubbling from the seafloor, indicating that the gas originates in sediments there. Other measurements show that the methane isn't generated in the water by microbes or brought to the seas by rivers, Shakhova says.

Each year, the researchers estimate, nearly 8 million metric tons of methane make their way to the atmosphere over the East Siberian Arctic Shelf. That's more than previous estimates for all of the world's oceans, Shakhova notes.

Siberian seafloor sediments are spewing much more methane than previously thought, but they're providing only a small fraction of the estimated 440 million tons of that planet-warming gas emitted to the atmosphere each year, Martin Heimann, a biogeochemist at the Max Planck Institute for Biogeochemistry in Jena, Germany, comments in Science. Nevertheless, he notes, release of a sizeable fraction of the carbon trapped in these sediments would lead to warmer atmospheric temperatures, which would in turn cause more methane to be released.

Images: 1) Igor Semiletov, University of Alaska Fairbanks. 2) Science/AAAS.

Senator Proposes Shuttle-Extension Hail Mary

Posted: 04 Mar 2010 11:10 AM PST


The turmoil and political maneuvering over the future of NASA continues in the wake of the Obama administration's cancellation of the Constellation program.

Sen. Kay Bailey Hutchinson (R-Texas) proposed adding $3.4 billion to the agency's budget between 2010 and 2012 to extend operation of the shuttle until NASA is confident that a replacement vehicle is available.

When NASA scoped out a similar Shuttle extension plan (.pdf) in April 2009, they determined that a shuttle extension through fiscal year 2012 would require at least $4.6 billion.

The new bill, S. 3068, which was read in the Senate Wednesday, has not been added to the publicly available database of legislation (THOMAS).

Its introduction comes as NASA itself gropes around for a politically viable path. While the Constellation program was widely seen as unable to meet the goals laid out for it by President Bush in the Vision for Space Exploration, it had been providing the direction for the agency since 2004.

An internal NASA e-mail obtained by laid out Administrator Charles Bolden's call for a compromise "Plan B" that could garner support in Congress.

The proposed set of new ideas would include the "development of a manned spacecraft, heavy-lift launch vehicle and launch-vehicle test program."

It's not clear if such moves will satisfy pro-Constellation congressional leaders, who have reacted negatively to the Obama plan, which would place low-Earth orbit human spaceflight in the hands of commercial space companies.

See Also:

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

Gut Bacteria Cause Overeating in Mice

Posted: 04 Mar 2010 11:04 AM PST


The connection between gut bacteria and obesity has gained some weight, with new findings demonstrating links in mice among immune-system malfunction, bacterial imbalance and increased appetite.

Mice with altered immune systems developed metabolic disorders and were prone to overeating. When microbes from their stomachs were transplanted into other mice, they also become obese.

"This supports the notion that some of the increase in obesity may be because of changes to gut bacteria," said Andrew Gewirtz, an Emory University immunologist and co-author of the study, published March 4 in Science.

The findings are the latest in a growing body of research about the long-unappreciated role of bacteria in our bodies. Bacterial cells actually outnumber human cells in the body: From an outside perspective, people are not so much individual organisms as symbiotic human-bacteria collectives.

Disturbances to internal bacteria have been linked to asthma, cancer and many autoimmune diseases. Gut flora have also been linked to obesity. In 2006, researchers led by Washington University microbiologist Jeffrey Gordon documented bacterial changes in the stomachs of mice who became obese on high-fat diets.

When transplanted, their gut bugs turned other mice obese, suggesting that altered bacteria were not only an effect of weight gain, but a cause. The Science findings complement those, but also emphasize the immune system's role and the possibility of appetite change.

"The reason why people are eating too much may not simply be because unhealthy food is cheap and available, but that their appetites may be driven by changes in gut bacteria," said Gewirtz,

In the Science study, Gewirtz and Emery microbiologist Matam Vijay-Kumar studied a strain of mice deficient in TLR-5, a gene that's required for immune systems to recognize many types of bacteria.

They found that TLR-5–deficient mice are about 20 percent heavier than regular mice. They overeat, have high blood pressure and high cholesterol, and are insulin-resistant. In humans, that constellation of conditions is known as metabolic syndrome, and in both people and mice leads to obesity and diabetes.

Earlier research had found unusual patterns of bacteria in the guts of those mice. When the researchers transferred bacteria from the stomachs of TLR-5–deficient mice to mice without gut bacteria, the recipients started to eat more, and soon developed metabolic syndrome.

"It's a really exciting paper. It confirms and supports a lot of the findings we've had, and adds in the interaction between gut bacteria and the immune system," said Peter Turnbaugh, a systems biologist who moved from Jeffrey Gordon's lab to Harvard University. "It's been thought for a long time that maybe the immune system is an important regulator of what's in the gut."

How gut bacteria produce metabolic changes isn't known. They may process nutrients directly, or alter the activity of metabolism-regulating genes.

Mice used in the research are not considered exact models of bacteria and obesity in humans. Instead they're models of these sorts of relationships likely to exist in people. Gewirtz's team is now investigating whether people with metabolic syndrome have unusual gut bacteria.

The findings don't suggest obesity is literally contagious, said Turnbaugh. But they do raise the possibility of altering the composition of gut bacteria, either directly or — more realistically — by learning what sort of environmental and lifestyle factors produce obesity-causing bugs.

One possible culprit is the ubiquitous presence of antibiotics, both prescribed and in the environment, said Gewirtz.

"It may be that an unintended consequence of this has been the upset of bacterial populations that are promoting obesity and metabolic syndrome," he said.

Image: Left, regular and TLR-5–knockout mice. Right, a comparison of their insulin-producing islet cells./Andrew Gewirtz

See Also:

Citation: "Metabolic Syndrome and Altered Gut Microbiota in Mice Lacking Toll-Like Receptor-5." By Matam Vijay-Kumar, Jesse D. Aitken, Frederic A. Carvalho, Tyler C. Cullender, Simon Mwangi, Shanthi Srinivasan, Shanthi V. Sitaraman, Rob Knight, Ruth E. Ley, Andrew T. Gewirtz. Science, Vol. 327, No. 5970, March 4, 2010.

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

Pharma Watchdog Needs Your Help With Incriminating Documents

Posted: 04 Mar 2010 09:54 AM PST


Overwhelmed by thousands of documents describing the inner workings of pharmaceutical companies, the Drug Industry Document Archive wants to enlist the help of crowds.

Documents uncovered during lawsuits against drug companies could be made searchable to the public, just like documents from tobacco company lawsuits. The problem is that there are more files than DIDA's own workers can handle. Until they're processed, they can't be properly searched. Crowdsourcing the project could speed the database's growth.

"In the long run, it's not feasible to get grants to add the documents, and we want to do it sooner rather than later," said Kim Klausner, the Archive's manager.

DIDA is an offshoot of the University of California, San Francisco's Legacy Tobacco Documents Archive, which was born from the 1998 legal settlement between tobacco companies and 46 states that sued them. As a condition of the settlement, all industry documents uncovered during the trial had to be made readily available to the public. It now contains 11 million documents numbering some 60 million pages.

In 2006, two UCSF professors who had served as expert witnesses in a lawsuit against pharmaceutical company Parke-Davis, accused of illegally promoting their anticonvulsant drug Neurontin for unapproved uses, approached the Tobacco Documents Archive about setting up a similar project for drug industry information. Thus began DIDA, which has since gathered thousands of documents from attorneys and journalists involved in drug company lawsuits, and plans to gather millions more.

But whereas tobacco companies had to hire people to enter document metadata — document type, authorship and other information that makes an archive usefully searchable — the drug company records still need to be indexed, evaluated and entered. Until then, they're of limited use.

Klausner envisions an internet army of students, journalists and concerned citizens helping, in much the same way as the Guardian newspaper invited the public to catalogue records of government-expense violations and the National Library of Australia enlisted crowds to correct errors made by automated scanners.

Data entry can be tedious, but it's a chance to get a first-hand look at potentially revealing information, said Klausner.

In a batch of internal AstraZeneca communications uploaded in February, for instance, a company researcher says the antipsychotic drug Seroquel is "now the responsibility of sales and marketing." In other documents, marketing strategists give instructions on massaging unfavorable data, researchers talk about how to "spin" and "de-emphasize" weight gain caused by the drug,

Astrazeneca is currently being sued for hiding the diabetes risk posed by Seroquel, which has been used by 19 million people worldwide.

Before DIDA is ready for the crowds, however, its interface needs work. Programmers are welcome to help; those with experience with J2EE and Spring MVC are welcome to contact Klausner.

"There are thousands, if not millions of documents that could be added as a result of these lawsuits," she said.

Image: DIDA

See Also:

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