Wednesday, April 7, 2010

EVEN SOIL FEELS THE HEAT

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Twenty years of field studies reveal that as the Earth has gotten warmer, plants and microbes in the soil have given off more carbon dioxide. So-called soil respiration has increased about one-tenth of 1 percent per year since 1989, according to an analysis of past studies in today's issue of Nature.

The scientists also calculated the total amount of carbon dioxide flowing from soils, which is about 10-15 percent higher than previous measurements. That number — about 98 petagrams of carbon a year (or 98 billion metric tons) — will help scientists build a better overall model of how carbon in its many forms cycles throughout the Earth. Understanding soil respiration is central to understanding how the global carbon cycle affects climate.

"There's a big pulse of carbon dioxide coming off of the surface of the soil everywhere in the world," said ecologist Ben Bond-Lamberty of the Department of Energy's Pacific Northwest National Laboratory. "We weren't sure if we'd be able to measure it going into this analysis, but we did find a response to temperature."

The increase in carbon dioxide given off by soils — about 0.1 petagram (100 million metric tons) per year since 1989 — won't contribute to the greenhouse effect unless it comes from carbon that had been locked away out of the system for a long time, such as in Arctic tundra. This analysis could not distinguish whether the carbon was coming from old stores or from vegetation growing faster due to a warmer climate. But other lines of evidence suggest warming is unlocking old carbon, said Bond-Lamberty, so it will be important to determine the sources of extra carbon.

Plants are famous for photosynthesis, the process that stores energy in sugars built from carbon dioxide and water. Photosynthesis produces the oxygen we breathe as a byproduct. But plants also use oxygen and release carbon dioxide in the same manner that people and animals do. Soil respiration includes carbon dioxide from both plants and soil microbes, and is a major component of the global carbon cycle.

Theoretically, the biochemical reactions that plants and soil microbes engage in to produce carbon dioxide suggest that higher temperatures should result in more carbon dioxide being released. But unlike the amount of sunlight reaching Earth, soil respiration can't be measured from space and can't yet be simulated effectively with computer models.

So, the researchers turned to previous studies to see if they could quantify changes in global soil respiration. PNNL's Bond-Lamberty and his colleague Allison Thomson, working at the Joint Global Change Research Institute in College Park, Md., examined 439 soil respiration studies published between 1989 and 2008.

They compiled data about how much carbon dioxide has leaked from plants and microbes in soil in an openly available database. To maintain consistency, they selected only data that scientists collected via the now-standard methods of gas chromatography and infrared gas analysis. The duo compared 1,434 soil carbon data points from the studies with temperature and precipitation data in the geographic regions from other climate research databases.

After subjecting their comparisons to statistical analysis, the researchers found that the total amount of carbon dioxide being emitted from soil in 2008 was more than in 1989. In addition, the rise in global temperatures correlated with the rise in global carbon flux. However, they did not find a similar relation between precipitation and carbon.

Previous climate change research shows that Arctic zones have a lot more carbon locked away than other regions. Using the complete set of data collected from the studies, the team estimated that the carbon released in northern — also called boreal — and Arctic regions rose by about 7 percent; in temperate regions by about 2 percent; and in tropical regions by about 3 percent, showing a trend consistent with other work.

The researchers wanted to know if their data could provide more detailed information about each region. So they broke down the complete data set by regional climates and re-examined the smaller groups of data using different statistical methods. The regional data from the temperate and tropical climates produced results consistent with other results, such as more carbon being released at higher temperatures, but the boreal-Arctic climate data did not. In addition, removing only 10 percent of the boreal-Arctic data points was enough to invalidate the statistical significance of the boreal-Arctic result. Together, the results support the idea that more boreal data on regional climates is needed to reach statistical relevance.

"We identified an area where we need to do more work," said Thomson.

(Photo: PNNL)

Pacific Northwest National Laboratory

EVIDENCE INDICATES HUMANS' EARLY TREE-DWELLING ANCESTORS WERE ALSO BIPEDAL

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Experiments by a UA anthropologist and his colleagues show that fossil footprints made 3.6 million years ago are the earliest direct evidence of early hominins using the kind of efficient, upright posture and gait now seen in modern humans.

More than three million years ago, the ancestors of modern humans were still spending a considerable amount of their lives in trees, but something new was happening.

David Raichlen, an assistant professor in the University of Arizona School of Anthropology, and his colleagues at the University at Albany and City University of New York's Lehman College have developed new experimental evidence indicating that these early hominins were walking with a human-like striding gait as long as 3.6 million years ago.

The results of their research appear in PLoS ONE, a journal from the Public Library of Science.

A trackway of fossil footprints preserved in volcanic ash deposited 3.6 million years ago was uncovered in Laetoli, Tanzania, more than 30 years ago. The significance of those prints for human evolution has been debated ever since.

The most likely individuals to have produced these footprints, which show clear evidence of bipedalism, or walking on two legs, would have been members of the only bipedal species alive in the area at that time, Australopithecus afarensis. That species includes "Lucy," whose skeletal remains are the most complete of any individual A. afarensis found to date.

A number of features in the hips, legs and back of this group indicate that they would have walked on two legs while on the ground. But the curved fingers and toes as well as an upward-oriented shoulder blade provide solid evidence that Lucy and other members of her species also would have spent significant time climbing in trees.

This morphology differs distinctly from our own genus, Homo, who abandoned arboreal life around 2 million years ago and irrevocably committed to human-like bipedalism.

Since the Laetoli tracks were discovered, scientists have debated whether they indicate a modern human-like mode of striding bipedalism, or a less-efficient type of crouched bipedalism more characteristic of chimpanzees whose knees and hips are bent when walking on two legs.

To resolve this, Raichlen and his colleagues devised the first biomechanical experiment explicitly designed to address this question.

The team built a sand trackway in Raichlen's motion capture lab at the UA and filmed human subjects walking across the sand. The subjects walked both with normal, erect human gaits and then with crouched, chimpanzee-like gaits. Three-dimensional models of the footprints were collected by biological anthropologist Adam Gordon using equipment brought from his Primate Evolutionary Morphology Laboratory at the University at Albany.

The researchers examined the relative depth of footprints at the heel and toe, and found that depths are about equal when made by a person walking with an erect gait. In contrast, the toe print is much deeper than the heel print when produced by a crouched gait, a product of the timing of weight transfer over the length of the foot.

"Based on previous analyses of the skeletons of Australopithecus afarensis, we expected that the Laetoli footprints would resemble those of someone walking with a bent knee, bent hip gait typical of chimpanzees, and not the striding gait normally used by modern humans," Raichlen said. "But to our surprise, the Laetoli footprints fall completely within the range of normal human footprints."

The fossil footprints at Laetoli preserve a remarkably even depth at the toe and heel, just like those of modern humans. "This more human-like form of walking is incredibly energetically efficient, suggesting that reduced energy costs were very important in the evolution of bipedalism prior to the origins of our own genus, Homo," Raichlen said.

If the Laetoli footprints were made by Lucy's species, as most scientists agree to be the case, these experimental results have interesting implications for the timing of evolutionary events.

"What is fascinating about this study is that it suggests that, at a time when our ancestors had an anatomy well-suited to spending a significant amount of time in the trees, they had already developed a highly efficient, modern human-like mode of bipedalism," said Gordon.

"The fossil record indicates that our ancestors did not make a full-time commitment to leaving the trees and walking on the ground until well over a million years after these (Laetoli) prints were made. The fact that partially tree-dwelling animals, like Lucy, had such a remarkably modern gait is a testament to the importance of energetic efficiency in moving around on two legs," Gordon said.

(Photo: Randy Haas, University of Arizona)

University of Arizona

DINOSAURS MIGHT BE OLDER THAN PREVIOUSLY THOUGHT

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Paleontologists announced the discovery of a dinosaur-like animal that lived 240 million years ago — about10 million years earlier than the oldest known dinosaurs. This suggests that dinosaurs and close relatives such as pterosaurs (flying reptiles) originated much earlier than scientists previously thought. The research also suggests that at least three times in the evolution of dinosaurs and their closest relatives, meat-eating animals evolved into animals with diets that included plants. These shifts all occurred in less than 10 million years, a relatively short time by geological standards.

The description of the new species Asilisaurus kongwe (a-SEE-lee- SOAR-us KONG-way) appears in the March 4, 2010 issue of the journal Nature in a paper lead-authored by Sterling Nesbitt, a postdoctoral researcher at The University of Texas at Austin's Jackson School of Geosciences. A co-author of the paper was Kenneth D. Angielczyk, assistant curator of paleomammology at Chicago's Field Museum.

Asilisaurus is part of a sister group to dinosaurs known as silesaurs. Silesaurs are considered dinosaur-like because they share many dinosaur characteristics but still lack key characteristics all dinosaurs share. The relationship between silesaurs and dinosaurs is analogous to the close relationship of humans and chimps. Even though the oldest dinosaurs discovered so far are only 230 million years old, the presence of their closest relatives 10 million years earlier implies that dinosaurs and silesaurs had already diverged from their common ancestor by 240 million years ago. Silesaurs continued to live side by side with early dinosaurs throughout much of the Triassic (between about 250 and 200 million years ago).

This is the first dinosaur-like animal recovered from the Triassic of Africa. Fossil bones of at least 14 individuals were recovered from a single bone bed in southern Tanzania making it possible to reconstruct a nearly entire skeleton, except portions of the skull and hand.

Kenneth D. Angielczyk, of The Field Museum, helped discover and excavate specimens found in Tanzania. "We brought many of the specimens back to Chicago where Field Museum paleontologists cleaned and conserved them in the Museum's fossil preparation labs," explained Angielczyk.

Asilisaurus walked on four legs and most likely ate plants or a combination of plants and meat. They stood about 0.5 to 1 meter (1.5 to 3 feet) tall at the hips and were 1 to 3 meters (3 to 10 feet) long. They weighed about 10 to 30 kilograms (22 to 66 pounds).

Silesaurs have triangular teeth and a lower jaw with a beak like tip which suggest that they were specialized for an omnivorous and/or herbivorous diet. These same traits evolved independently in at least two dinosaur lineages. In all three cases, the features evolved in animals that were originally meat-eaters. Although difficult to prove, it's possible that this shift conferred an evolutionary advantage. An ecosystem can support far more plant eaters than meat eaters. So being able to eat plants might have opened up a broader range of habitats. Not counting modern birds, dinosaurs survived for about 180 million years.

This new species is found along with a number of primitive crocodilian relatives in the same fossil bed in southern Tanzania. The presence of these animals together at the same time and place suggests that the diversification of the relatives of crocodilians and birds was rapid and happened earlier than previously suggested. It sheds light on a group of animals that later came to dominate the terrestrial ecosystem throughout the Mesozoic (250 to 65 million years ago).

"Everyone loves dinosaurs," said Nesbitt. "But this new evidence suggests that they were really only one of several large and distinct groups of animals that exploded in diversity in the Triassic, including silesaurs, pterosaurs, and several groups of crocodilian relatives."

Silesaurus, the first known member of the silesaur group was discovered in 2003. In just 7 short years, specimens of 8 other members have been unearthed from Triassic rocks across the globe.

"This goes to show that there are whole groups of animals out there that we've never even found evidence of that were very abundant during the Triassic," said Nesbitt. "It's exciting because it means there is still so much chance for discovery."

The name Asilisaurus kongwe is derived from asili (Swahili for ancestor or foundation), sauros (Greek for lizard), and kongwe (Swahili for ancient).

(Photo: M.H. Donnelly/Field Museum)

Field Museum

YALE RESEARCHERS FIND GENETIC HOME OF SOME OF LIFE’S DIVERSITY

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Almost a decade after the first draft of the human genome was published, scientists now know that many differences among individuals arise not only from the content of their genes but where and when those genes are expressed.

Now a Yale-led team of scientists, using advanced DNA sequencing technology, has for the first time pinpointed individual variations of where, along the chain of 3 billion letters that make up the human genome, important gene regulatory elements do their jobs.

The findings — both in humans, as reported online March 18 in the journal Science Express, and in yeast, detailed in a complementary paper by Yale scientists published March 17 in the journal Nature — shed new light on the mechanisms that contribute to life’s diversity.

“Differences in how our genes are regulated may provide a better understanding of disease, advance the cause of personalized medicine and even help explain how species evolved,” said Maya Kasowski, an M.D./Ph.D. candidate in Yale’s Department of Molecular, Cellular and Developmental Biology. Kasowski is co-lead author of the paper with Fabian Grubert, formerly a postdoctoral researcher at Yale now a post-doc at Stanford.

Michael Snyder, formerly the Lewis B. Cullman Professor of Molecular, Cellular and Developmental Biology launched both studies at Yale. Snyder is now professor and chair of genetics at Stanford University.

In the Science paper, the researchers analyzed genomes of several individuals and a chimpanzee to look for variations in areas along the genome where proteins called transcription factors bind to specific sites of DNA. Transcription factors are crucial for life because they control the activity of multiple genes by regulating the transfer, or transcription, of information from DNA into RNA molecules, which in turn carry the information to the cell’s protein-making machinery. The location of these binding sites is crucial to determining the function of genes that are regulated.

Researchers found individuals differed in 25 percent of binding sites that regulate RNA polymerases II, one of the molecules crucial in the transcriptions of genes to proteins. The differences between humans and chimps were also pronounced, suggesting they may play a key role in creating variation between the species. When researchers looked at a well-known immune system pathway, only 7.5 percent of the binding sites were found to differ among individual humans.

In the Nature paper, a Yale team led by Wei Zheng, now a biostatistician in the University’s Keck Laboratory, analyzed a big family of yeast cells, including a sample from the lung of an AIDS patient.

“We now can do molecular analysis that was unimaginable a couple of years ago,” Zheng said. “The analysis of sequencing data revealed two previously unknown regulatory genes that help govern mating and other functions in yeast.”

She said the work may also help explain why usually harmless yeast becomes a pathogen in AIDS patients whose immune system has been compromised.

“We believe it will be essential to monitor differences in regulatory information in order to understand both how we are different from one another as well as the underlying basis of many diseases,” Snyder said.

(Photo: Yale U.)

Yale University

HUBBLE CONFIRMS COSMIC ACCELERATION WITH WEAK LENSING

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A group of astronomers, led by Tim Schrabback of the Leiden Observatory, conducted an intensive study of over 446 000 galaxies within the COSMOS field, the result of the largest survey ever conducted with Hubble. In making the COSMOS survey, Hubble photographed 575 slightly overlapping views of the same part of the Universe using the Advanced Camera for Surveys (ACS) onboard Hubble. It took nearly 1000 hours of observations.

In addition to the Hubble data, researchers used redshift data from ground-based telescopes to assign distances to 194 000 of the galaxies surveyed (out to a redshift of 5). "The sheer number of galaxies included in this type of analysis is unprecedented, but more important is the wealth of information we could obtain about the invisible structures in the Universe from this exceptional dataset," says co-author Patrick Simon from Edinburgh University.

In particular, the astronomers could "weigh" the large-scale matter distribution in space over large distances. To do this, they made use of the fact that this information is encoded in the distorted shapes of distant galaxies, a phenomenon referred to as weak gravitational lensing. Using complex algorithms, the team led by Schrabback has improved the standard method and obtained galaxy shape measurements to an unprecedented precision. The results of the study will be published in an upcoming issue of Astronomy and Astrophysics.

The meticulousness and scale of this study enables an independent confirmation that the expansion of the Universe is accelerated by an additional, mysterious component named dark energy. A handful of other such independent confirmations exist. Scientists need to know how the formation of clumps of matter evolved in the history of the Universe to determine how the gravitational force, which holds matter together, and dark energy, which pulls it apart by accelerating the expansion of the Universe, have affected them. "Dark energy affects our measurements for two reasons. First, when it is present, galaxy clusters grow more slowly, and secondly, it changes the way the Universe expands, leading to more distant — and more efficiently lensed — galaxies. Our analysis is sensitive to both effects," says co-author Benjamin Joachimi from the University of Bonn. "Our study also provides an additional confirmation for Einstein's theory of general relativity, which predicts how the lensing signal depends on redshift," adds co-investigator Martin Kilbinger from the Institut d'Astrophysique de Paris and the Excellence Cluster Universe.

The large number of galaxies included in this study, along with information on their redshifts is leading to a clearer map of how, exactly, part of the Universe is laid out; it helps us see its galactic inhabitants and how they are distributed. "With more accurate information about the distances to the galaxies, we can measure the distribution of the matter between them and us more accurately," notes co-investigator Jan Hartlap from the University of Bonn. "Before, most of the studies were done in 2D, like taking a chest X-ray. Our study is more like a 3D reconstruction of the skeleton from a CT scan. On top of that, we are able to watch the skeleton of dark matter mature from the Universe's youth to the present," comments William High from Harvard University, another co-author.

The astronomers specifically chose the COSMOS survey because it is thought to be a representative sample of the Universe. With thorough studies such as the one led by Schrabback, astronomers will one day be able to apply their technique to wider areas of the sky, forming a clearer picture of what is truly out there.

(Photo: NASA, ESA, P. Simon (University of Bonn) and T. Schrabback (Leiden Observatory))

Hubble Information Centre

FLEXIBLE ELECTRONICS COULD HELP PUT OFF-BEAT HEARTS BACK ON RHYTHM

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Arrhythmic hearts soon may beat in time again, with minimal surgical invasion, thanks to flexible electronics technology developed by a team of University of Illinois researchers, in collaboration with the University of Pennsylvania School of Medicine and Northwestern University. These biocompatible silicon devices could mark the beginning of a new wave of surgical electronics.

Co-senior author John Rogers, the Lee J. Flory-Founder Chair in Engineering Innovation and a professor of materials science and engineering at Illinois, and his team will publish their breakthrough in the cover story of the March 24 issue of Science Translational Medicine.

Several treatments are available for hearts that dance to their own tempo, ranging from pacemaker implants to cardiac ablation therapy, a process that selectively targets and destroys clusters of arrhythmic cells. Current techniques require multiple electrodes placed on the tissue in a time-consuming, point-by-point process to construct a patchwork cardiac map. In addition, the difficulty of connecting rigid, flat sensors to soft, curved tissue impedes the electrodes' ability to monitor and stimulate the heart.

Rogers and his team have built a flexible sensor array that can wrap around the heart to map large areas of tissue at once. The array contains 2,016 silicon nanomembrane transistors, each monitoring electricity coursing through a beating heart.

The Pennsylvania team demonstrated the transistor array on the beating hearts of live pigs, a common model for human hearts. They witnessed a high-resolution, real-time display of the pigs' pulsing cardiac tissues – something never before possible.

"We believe that this technology may herald a new generation of devices for localizing and treating abnormal heart rhythms," said co-senior author Brian Litt, of the University of Pennsylvania.

"This allows us to apply the full power of silicon electronics directly to the tissue," said Rogers, a renowned researcher in the area of flexible, stretchable electronics. As the first class of flexible electronics that can directly integrate with bodily tissues, "these approaches might have the potential to redefine design strategies for advanced surgical devices, implants, prosthetics and more," he said.

The biocompatible circuits – the first ones unperturbed by immersion in the body's salty fluids – represent a culmination of seven years of flexible electronics study by Rogers' group. The researchers build circuits from ultrathin, single-crystal silicon on a flexible or stretchy substrate, like a sheet of plastic or rubber. The nanometer thinness of the silicon layer makes it possible to bend and fold the normally rigid semiconductor.

"If you can create a circuit that's compliant and bendable, you can integrate it very effectively with soft surfaces in the body," such as the irregular, constantly moving curves of the heart, Rogers said.

Collaborations with a theoretical mechanics group at Northwestern University, led by Younggang Huang, yielded important insights into the designs.

The patchwork grid of cardiac sensors adheres to the moist surfaces of the heart on its own, with no need for probes or adhesives, and lifts off easily. The array of hundreds of sensors gives cardiac surgeons a more complete picture of the heart's electrical activity so they can quickly find and fix any short circuits. In fact, the cardiac device boasts the highest transistor resolution of any class of flexible electronics for non-display applications.

The team's next step is to adapt the technology for use with non-invasive catheter procedures, Rogers said. The U. of I. and Pennsylvania teams also are exploring applications for the arrays in neuroscience, applying grids to brain surfaces to study conditions of unusual electrical activity, such as epilepsy.

"It sets out a new design paradigm for interfacing electronics to the human body, with a multitude of possible applications in human health," Rogers said.

(Photo: Thompson-McClellan)

University of Illinois

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