Friday, October 2, 2009


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Denver released the largest amount of greenhouse gases (GHG) and Barcelona the smallest amount in a new study documenting how differences in climate, population density and other factors affect GHG emissions in global cities. The study, which could identify ways in which cities can reduce GHG emissions, is scheduled for October 1 issue of ACS' Environmental Science & Technology, a semi-monthly journal.

Christopher Kennedy and colleagues note in the new study that some cities are developing strategies to reduce releases of GHG, which include carbon dioxide, methane, and other gases that can contribute to global warming through the greenhouse effect. Not enough information was previously available on why emissions vary considerably among different cities. The authors asked, "How and why do emissions differ between cities?"

To help answer those questions, the scientists analyzed those variations and how climate, power generation, transportation, waste processing, and other factors contributed to the differences. Denver had the highest overall GHG emissions, with levels two to five times higher than other cities. Its high levels were due partly to its high use of electricity, heating and industrial fuels, and ground transportation, they note. Los Angeles was second on the list, followed by Toronto and Cape Town (tied for third), Bangkok, New York City, London, Prague, Geneva, and Barcelona.

(Photo: Wikimedia Commons)

American Chemical Society


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A University of Oregon research team has found that evolution can never go backwards, because the paths to the genes once present in our ancestors are forever blocked. The findings -- the result of the first rigorous study of reverse evolution at the molecular level -- appear in the Sept. 24 issue of Nature.

The team used computational reconstruction of ancestral gene sequences, DNA synthesis, protein engineering and X-ray crystallography to resurrect and manipulate the gene for a key hormone receptor as it existed in our earliest vertebrate ancestors more than 400 million years ago. They found that over a rapid period of time, five random mutations made subtle modifications in the protein's structure that were utterly incompatible with the receptor's primordial form.

The discovery of evolutionary bridge burning implies that today's versions of life on Earth may be neither ideal nor inevitable, said Joe Thornton, a professor in the UO's Center for Ecology and Evolutionary Biology and the Howard Hughes Medical Institute.

"Evolutionary biologists have long been fascinated by whether evolution can go backwards," Thornton said, "but the issue has remained unresolved because we seldom know exactly what features our ancestors had, or the mechanisms by which they evolved into their modern forms. We solved those problems by studying the problem at the molecular level, where we can resurrect ancestral proteins as they existed long ago and use molecular manipulations to dissect the evolutionary process in both forward and reverse directions."

Thornton's team, which included UO research scientist Jamie Bridgham and collaborator Eric A. Ortlund, a biochemist at Atlanta's Emory University, focused on the evolution of a protein called the glucocorticoid receptor (GR), which binds the hormone cortisol and regulates the stress response, immunity, metabolism and behavior in humans and other vertebrates.

"This fascinating study highlights the value of studying evolutionary processes," said Irene Eckstrand, who oversees evolution grants at the National Institutes of Health's National Institute of General Medical Sciences. "By showing how molecular structures are finely tuned by evolution, Dr. Thornton's research will have a broad impact on basic and applied sciences, including the design of drugs that target specific proteins."

In previous work, Thornton's group showed that the first GR evolved more than 400 millions ago from an ancestral protein that was also sensitive to the hormone aldosterone. They then identified seven ancient mutations that together caused the receptor to evolve its new specificity for cortisol.

Once Thornton's team knew how the GR's modern function evolved, they wondered if it could be returned to its ancestral function. So they resurrected the GR as it existed soon after cortisol specificity first evolved -- in the common ancestor of humans and all other vertebrates with bones -- and then reversed the seven key mutations by manipulating its DNA sequence.

'We expected to get a promiscuous receptor just like the GR's ancestor, but instead we got a completely dead, non-functional protein," Thornton said. "Apparently other mutations that occurred during early GR evolution acted as a sort of evolutionary ratchet, rendering the protein unable to tolerate the ancestral features that had existed just a short time earlier."

To identify the mutations, Thornton's team prepared crystals of resurrected ancient GR proteins and took them to the particle accelerator at the Advanced Photon Source outside Chicago, where they used powerful X-rays to determine the protein's atomic structure before and after the shift in function. By comparing the precise atomic maps of each protein, they identified five specific mutations in the later version of the GR that clashed with the architecture of the earlier protein.

"Suppose you're redecorating your bedroom -- first you move the bed, then you put the dresser where the bed used to be," Thornton said. "If you decide you want to move the bed back, you can't do it unless you get that dresser out of the way first. The restrictive mutations in the GR prevented evolutionary reversal in the same way."

When Thornton's group set the five mutations back to their ancestral state, the protein could now tolerate having the seven key changes reversed, which then transformed it into a promiscuous receptor just like the its ancestor.

Despite their powerful role as a ratchet preventing reversal, the five restrictive mutations had little or no direct effect on the protein's function when they occurred. And although they must be reversed before the protein can tolerate the ancestral state, reversing them first does absolutely nothing to enhance the ancestral function. "This means that even if the ancestral function were suddenly to become optimal again, there's no way natural selection could drive the protein directly back to its ancestral form," Thornton said.

GR's evolutionary irreversibility suggests that the molecules that drive our biology today may not be inevitable products of the evolutionary process. "In the GR's case, restrictive mutations erased the conditions that previously opened up the ancestral form as an evolutionary possibility. It's likely that throughout history other kinds of restrictive mutations have taken place, closing off innumerable trajectories that evolution might otherwise have taken," Thornton speculated.

"If we could wind back the clock and allow history to unfold again, different sets of mutations, apparently inconsequential at the time, would almost certainly occur, opening up some potential paths and blocking others -- including the one that leads to the present that actually evolved in our world," he said. "If what we observed in GR evolution is a general phenomenon, then the biology we have is just one of many possible rolls of the evolutionary dice."

(Photo: U. Oregon)

University of Oregon


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In a study published in the September 24th issue of Nature, an international team describes how they harnessed modern genomic technology to explore the ancient history of India, the world's second most populous nation.

The new research reveals that nearly all Indians carry genomic contributions from two distinct ancestral populations. Following this ancient mixture, many groups experienced periods of genetic isolation from each other for thousands of years. The study, which has medical implications for people of Indian descent, was led by scientists at the Centre for Cellular and Molecular Biology (CCMB) in Hyderabad, India together with US researchers at Harvard Medical School, the Harvard School of Public Health and the Broad Institute of Harvard and MIT.

"This work is an outstanding example of the power of international collaboration," said Lalji Singh, senior author of the Nature paper, who is a Bhatnagar Fellow and the former director of CCMB. "Scientists in India and the United States have together made discoveries that would have been impossible for either group working alone."

Although the genome sequences of any two unrelated people differ by just 0.1%, that tiny slice of genetic material is a rich source of information. It provides clues that can help reconstruct the historical origins of modern populations. It also points to genetic variations that heighten the risk of certain diseases. In recent years, maps of human genetic variation have opened a window onto the diversity of populations across the world, yet India has been largely unrepresented until now.

To shed light on genetic variability across the Indian subcontinent, the research team analyzed more than 500,000 genetic markers across the genomes of 132 individuals from 25 diverse groups, representing 13 states, all six language families, traditionally "upper" and "lower" castes, and tribal groups.

These genomic analyses revealed two ancestral populations. "Different Indian groups have inherited forty to eighty percent of their ancestry from a population that we call the Ancestral North Indians who are related to western Eurasians, and the rest from the Ancestral South Indians, who are not related to any group outside India," said co-author David Reich, an associate professor of genetics at Harvard Medical School and an associate member of the Broad Institute of Harvard and MIT.

The finding that nearly all Indian groups descend from mixtures of two ancestral populations applies to traditional "tribes" as well as "castes." Kumarasamy Thangaraj, a senior research scientist at CCMB in Hyderabad and a co-author said, "It is impossible to distinguish castes from tribes using the data. The genetics proves that they are not systematically different. This supports the view that castes grew directly out of tribal-like organizations during the formation of Indian society."

The one exception to the finding that all Indian groups are mixed is the indigenous people of the Andaman Islands, an archipelago in the Indian Ocean with a census of only a few hundred today. The Andamanese appear to be related exclusively to the Ancestral South Indian lineage and therefore lack Ancestral North Indian ancestry.

"The Andamanese are unique," said co-author Nick Patterson, a mathematician and researcher at the Broad Institute. "Understanding their origins provides a window onto the history of the Ancestral South Indians, and the period tens of thousands of years ago when they diverged from other Eurasians." Added Singh, "Our project to sample the disappearing tribes of the Andaman Islands has been more successful than we could have hoped, as the Andamanese are the only surviving remnant of the ancient colonizers of South Asia."

The researchers' work also has surprising and important medical implications. They discovered that many groups in modern India descend from a small number of founding individuals, and have since been genetically isolated from other groups. In scientific parlance this is called a "founder event."

"The finding that a large proportion of modern Indians descend from founder events means that India is genetically not a single large population, but instead is best described as many smaller isolated populations," said Singh. Thangaraj continued, "The widespread history of founder events helps explain why the incidence of genetic diseases among Indians is different from the rest of the world."

Founder events in other groups, such as Finns and Ashkenazi Jews, are well known to increase the incidence of recessive genetic diseases, and the new study predicts that the same will be true for many groups in India. "It is important to carry out a systematic survey of Indian groups to identify which ones descend from the strongest founder events," said Reich. "Further studies of these groups should lead to the rapid discovery of genes that cause devastating diseases, and will help in the clinical care of individuals and their families who are at risk."

"Just as important as these findings are the statistical approaches that led to them," said Alkes Price, an assistant professor of epidemiology at the Harvard School of Public Health and a co-author of the Nature study. "In studying Indian genetic variation we also developed a novel toolkit for understanding the relationships among groups and the history of mixture. We believe that these tools can drive future studies not only of Indian history but of groups worldwide."

(Photo: D. Reich, K. Thangaraj, N. Patterson, A. Price and L. Singh)

Broad Institute


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A fossil supervolcano has been discovered in the Italian Alps' Sesia Valley by a team led by James E. Quick, a geology professor at Southern Methodist University. The discovery will advance scientific understanding of active supervolcanoes, like Yellowstone, which is the second-largest supervolcano in the world and which last erupted 630,000 years ago.

A rare uplift of the Earth's crust in the Sesia Valley reveals for the first time the actual "plumbing" of a supervolcano from the surface to the source of the magma deep within the Earth, according to a new research article reporting the discovery. The uplift reveals to an unprecedented depth of 25 kilometers the tracks and trails of the magma as it moved through the Earth's crust.

Supervolcanoes, historically called calderas, are enormous craters tens of kilometers in diameter. Their eruptions are sparked by the explosive release of gas from molten rock or "magma" as it pushes its way to the Earth's surface.

Calderas erupt hundreds to thousands of cubic kilometers of volcanic ash. Explosive events occur every few hundred thousand years. Supervolcanoes have spread lava and ash vast distances and scientists believe they may have set off catastrophic global cooling events at different periods in the Earth's past.

Sesia Valley's caldera erupted during the "Permian" geologic time period, say the discovery scientists. It is more than 13 kilometers in diameter.

"What's new is to see the magmatic plumbing system all the way through the Earth's crust," says Quick, who previously served as program coordinator for the Volcano Hazards Program of the U.S. Geological Survey. "Now we want to start to use this discovery. We want to understand the fundamental processes that influence eruptions: Where are magmas stored prior to these giant eruptions? From what depth do the eruptions emanate?"

Sesia Valley's unprecedented exposure of magmatic plumbing provides a model for interpreting geophysical profiles and magmatic processes beneath active calderas. The exposure also serves as direct confirmation of the cause-and-effect link between molten rock moving through the Earth's crust and explosive volcanism.

"It might lead to a better interpretation of monitoring data and improved prediction of eruptions," says Quick, lead author of the research article reporting the discovery. The article, "Magmatic plumbing of a large Permian caldera exposed to a depth of 25 km.," appears in the July issue of the peer-reviewed journal "Geology."

Calderas, which typically exhibit high levels of seismic and hydrothermal activity, often swell, suggesting movement of fluids beneath the surface.

"We want to better understand the tell-tale signs that a caldera is advancing to eruption so that we can improve warnings and avoid false alerts," Quick says.

To date, scientists have been able to study exposed caldera "plumbing" from the surface of the Earth to a depth of only 5 kilometers. Because of that, scientific understanding has been limited to geophysical data and analysis of erupted volcanic rocks. Quick likens the relevance of Sesia Valley to seeing bones and muscle inside the human body for the first time after previously envisioning human anatomy on the basis of a sonogram only.

"We think of the Sesia Valley find as the 'Rosetta Stone' for supervolcanoes because the depth to which rocks are exposed will help us to link the geologic and geophysical data," Quick says. "This is a very rare spot. The base of the Earth's crust is turned up on edge. It was created when Africa and Europe began colliding about 30 million years ago and the crust of Italy was turned on end."

British researchers introduced the term "supervolcano" in the last 10 years. Scientists have documented fewer than two dozen caldera eruptions in the last 1 million years.

Besides Yellowstone, other monumental explosions have included Lake Toba on Indonesia's Sumatra island 74,000 years ago, which is believed to be the largest volcanic eruption on Earth in the past 25 million years.

Described as a massive climate-changing event, the Lake Toba eruption is thought to have killed an estimated 60% of humans alive at the time.

Another caldera, and one that remains active, Long Valley in California erupted about 760,000 years ago and spread volcanic ash for 600 cubic kilometers. The ash blanketed the southwestern United States, extending from California to as far west as Nebraska.

"There will be another supervolcano explosion," Quick says. "We don't know where. Sesia Valley could help us to predict the next event."

(Photo: USGS, Smith and Siegel)


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Black holes are invading stars, providing a radical explanation to bright flashes in the universe that are one of the biggest mysteries in astronomy today.

The flashes, known as gamma ray bursts, are beams of high energy radiation – similar to the radiation emitted by explosions of nuclear weapons – produced by jets of plasma from massive dying stars.

The orthodox model for this cosmic jet engine involves plasma being heated by neutrinos in a disk of matter that forms around a black hole, which is created when a star collapses.

But mathematicians at the University of Leeds have come up with a different explanation: the jets come directly from black holes, which can dive into nearby massive stars and devour them.

Their theory is based on recent observations by the Swift satellite which indicates that the central jet engine operates for up to 10,000 seconds - much longer than the neutrino model can explain.

Mathematicians believe that this is evidence for an electromagnetic origin of the jets, i.e. that the jets come directly from a rotating black hole, and that it is the magnetic stresses caused by the rotation that focus and accelerate the jet's flow.

For the mechanism to operate the collapsing star has to be rotating extremely rapidly. This increases the duration of the star's collapse as the gravity is opposed by strong centrifugal forces.

One particularly peculiar way of creating the right conditions involves not a collapsing star but a star invaded by its black hole companion in a binary system. The black hole acts like a parasite, diving into the normal star, spinning it with gravitational forces on its way to the star's centre, and finally eating it from the inside.

"The neutrino model cannot explain very long gamma ray bursts and the Swift observations, as the rate at which the black hole swallows the star becomes rather low quite quickly, rendering the neutrino mechanism inefficient, but the magnetic mechanism can," says Professor Komissarov from the School of Mathematics at the University of Leeds.

"Our knowledge of the amount of the matter that collects around the black hole and the rotation speed of the star allow us to calculate how long these long flashes will be – and the results correlate very well with observations from satellites," he adds.

(Photo: U. Leeds)


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After decades of debate and four years of investigation an international body of earth scientists has formally agreed to move the boundary dates for the prehistoric Quaternary age by 800,000 years, reports the Journal of Quaternary Science.

The decision has been made by the International Commission on Stratigraphy (ICS), the authority for geological science which has acted to end decades of controversy by formally declaring when the Quaternary Period, which covers both the ice age and moment early man first started to use tools, began.

In the 18th Century the earth's history was split into four epochs, Primary, Secondary, Tertiary, and Quaternary. Although the first two have been renamed Palaeozoic and Mesozoic respectively, the second two have remained in use by scientists for more than 150 years. There has been a protracted debate over the position and status of Quaternary in the geological time scale and the intervals of time it represents.

"It has long been agreed that the boundary of the Quaternary Period should be placed at the first sign of global climate cooling," said Professor Philip Gibbard. "What we have achieved is the definition of the boundary of the Quaternary to an internationally recognised and fixed point that represents a natural event, the beginning of the ice ages on a global scale."

Controversy over when exactly the Quaternary Period began has raged for decades, with attempts in 1948 and 1983 to define the era. In 1983 the boundary was fixed at 1.8 million years, a decision which sparked argument within the earth science community as this point was not a 'natural boundary' and had no particular geological significance.

Up to now it has been widely felt within the scientific community that the boundary should be located earlier, at a time of greater change in the earth-climate system.

"For practical reasons such boundaries should ideally be made as easy as possible to identify all around the world. The new boundary of 2.6 million years is just that," concluded Gibbard, "hence we are delighted at finally achieving our goal of removing the boundary to this earlier point."

"The decision is a very important one for the scientific community working in the field," said Journal Editor Professor Chris Caseldine. "It provides us with a point in geological time when we effectively did move into a climatic era recognisably similar to the geological present."





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