Tuesday, November 30, 2010

ESRF REVEALS HUMAN CHILDREN OUTPACED NEANDERTHALS BY SLOWING DOWN

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Human childhood is considerably longer than chimpanzees, our closest-living ape relatives. A multinational team of specialists, led by researchers from Harvard University, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA) and the ESRF applied cutting-edge synchrotron X-ray imaging to resolve microscopic growth in 10 young Neanderthal and Homo sapiens fossils. They found that significant developmental differences exist despite some overlap, which is common in closely-related species. Modern humans are the slowest to the finish line, stretching out their maturation, which may have given them a unique evolutionary advantage.

Evolutionary biology has shown that small changes during early development may lead to differences that result in new species. These changes may take the form of modifications in the sequence or timing of developmental events; therefore, understanding developmental transformation is key to reconstructing evolutionary history. Anthropologists have documented many differences in adult characteristics among closely related species, such as humans and chimpanzees. Genomic data combined with fossil evidence indicate that these two lineages split six to seven million years ago, and have since been evolving separately. However, we know much less about which changes led to the separate lineages, how these changes arose, and when they occurred.

One poorly understood change is our unique life history, or the way in which we time growth, development, and reproductive efforts. Compared to humans, non-human primate life history is marked by a shorter gestation period, faster post-natal maturation rates, younger age at first reproduction, shorter post-reproductive period, and a shorter overall lifespan. For example, chimpanzees reach reproductive maturity several years before humans, bearing their first offspring by age 13, in contrast to the human average of 19.

It might seem that life history is invisible in the fossil record, but it turns out that many life history variables correlate strongly with dental development. “Teeth are remarkable time recorders, capturing each day of growth much like rings in trees reveal yearly progress. Even more impressive is the fact that our first molars contain a tiny ‘birth certificate,’ and finding this birth line allows us to calculate exactly how old a juvenile was when it died” says Tanya Smith, researcher at Harvard University and MPI-EVA.

This forensic approach to the past is possible with a ‘super-microscope:’ extremely powerful X-ray beams produced at the European Synchrotron Radiation Facility (ESRF) in Grenoble, France, which is one of the largest synchrotron in the world. Paul Tafforeau, from the ESRF, notes: “At the ESRF, we are able to look inside invaluable fossils without damaging them by using the special properties of high energy synchrotron X-rays. We can investigate fossils at different scales and in three-dimensions, ranging from studies of overall 3D shape down to microscopic daily growth lines. This is currently the only place where these studies of fossil humans are possible.” Scientists and curators have been quietly visiting the European synchrotron, often with some of the rarest hominin fossils in the world, for imaging with this state-of-the-art technique.

The study includes some of the most famous Neanderthal children, including the first hominin fossil ever discovered. This Belgian Neanderthal child, discovered in the winter of 1829-1830, was thought to be 4-5 years of age when it died. Powerful synchrotron X-rays and cutting-edge imaging software revealed that it actually died at a mere 3 years of age. Another invaluable Neanderthal discovered in Le Moustier, France in 1908, barely survived the shelling of its’ German repository during the Second World War.

A remarkable finding of this five-year study is that Neanderthals grow their teeth significantly faster than members of our own species, including some of the earliest groups of modern humans to leave Africa between 90-100,000 years ago. The Neanderthal pattern appears to be intermediate between early members of our genus (e.g., Homo erectus) and living people, suggesting that the characteristically slow development and long childhood is a recent condition unique to our own species. This extended period of maturation may facilitate additional learning and complex cognition, possibly giving early Homo sapiens a competitive advantage over their contemporaneous Neanderthal cousins.

These new results present a unique opportunity to assess the origins of a fundamentally human condition: the costly yet advantageous shift from a primitive “live fast and die young” strategy to the “live slow and grow old” strategy that has helped to make us one of the most successful organisms on the planet.

(Photo: Graham Chedd (PBS), Paul Tafforeau (ESRF), and Tanya Smith (Harvard University and MPI-EVA))

ESRF

NEW WAY OF PREDICTING DOMINANT SEASONAL FLU STRAIN

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Rice University scientists have found a way to predict rapidly whether a new strain of the influenza virus should be included in the annual seasonal flu vaccine. While it sometimes takes new flu strains up to three years to become dominant worldwide, the new method can predict whether they will become dominant as little as two weeks after the sequence first appears in the GenBank database, the National Institutes of Health's collection of all publicly available DNA sequences.

"We studied a new strain of the virus that evolved in British Columbia in the middle of March 2009," said Michael Deem, co-author of a new study featured on the cover of the Dec. 12 issue of Protein Engineering Design and Selection. "By the end of March, just about two weeks after it came out, we could detect that it would become the dominant strain of H3N2 in 2009. By contrast, it wasn't detectable as a novel strain by the standard methods that the World Health Organization uses until July or the middle of August."

It takes several months to produce the millions of doses of flu vaccine needed each year, and officials at the World Health Organization (WHO) use a combination of statistical methods and animal tests to choose the following year's formula.

Just a month before the British Columbia strain was first recorded in GenBank, the WHO had made its recommendations for the annual 2009-2010 vaccine. While the biggest flu story of 2009 was the H1N1 pandemic that began in Mexico and spread rapidly worldwide, the British Columbia strain went on to become the dominant variant of H3N2 the following year. Because it was significantly different from the H3N2 strain that had been included in the seasonal vaccine for that year, the vaccine's efficacy against British Columbia was estimated at about 20 percent.

"It's not that we could have predicted that British Columbia would have emerged out of thin air, but once it had emerged, our method could detect the signature of its eventual dominance with a very limited amount of sequence data," said Deem, the John W. Cox Professor in Biochemical and Genetic Engineering and professor of physics and astronomy at Rice.

Deem and study co-author Jiankui He, a graduate student in physics and astronomy, developed a mathematical method that used freely available genetic profiles of new flu strains to predict whether a strain will become dominant. Using the method, they examined the H3N2 flu strain for the past 14 years and made their own predictions based on the available data in GenBank, where public health officials post all the latest genetic sequences of new flu strains.

Deem and He compared their predictions with the WHO's predictions from 1996 to 2010. They found their new method correctly predicted the dominant strain of H3N2 for most years, including three years -- 2002, 2003 and 2009 -- when the WHO vaccine was formulated with an H3N2 strain that turned out not to be the dominant strain that year.

The new method involves a statistical technique called multidimensional scaling that is used to create graphical plots of complex data in fields as diverse as marketing and physics. In their study, He and Deem used multidimensional scaling to create a graphical plot of amino acid sequence data for all strains of H3N2. They limited their study to a 329-amino-acid region of the virus that mutates regularly to avoid detection by immune system.

"Using multidimensional scaling, we project from those 329 dimensions to the two dimensions that contain the most information," Deem said. "We just plot all of the points as a function of two variables instead of listing all 329, which is too much information to work with. With the two-dimensional scaling, we have a workable problem and we still have enough information to see clusters of new strains that will eventually become dominant."

Deem said the results of the study suggests that public health officials could benefit by using the new method, which is both fast and inexpensive, in addition to the well-accepted methods that are currently used to formulate vaccine strain recommendations.

Rice University

RESCUE MISSIONS UNDER WAY TO SAVE HAITI'S SPECIES FROM MASS EXTINCTION

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Haiti is on the brink of an era of mass extinctions similar to the time when dinosaurs and many other species suddenly disappeared from the Earth, reports a biologist at Penn State, who announced on Nov. 16 the establishment of a species-rescue program for Haiti's threatened frogs and other species, including captive-breeding and gene-preservation efforts.

"During the next few decades, many Haitian species of plants and animals will become extinct because the forests where they live, which originally covered the entire country, are nearly gone," said Blair Hedges, a professor of biology at Penn State and leader of the rescue missions in Haiti and other countries in the Caribbean. "The decline of frogs in particular, because they are especially vulnerable, is a biological early-warning signal of a dangerously deteriorating environment, just as a dying canary is an early-warning sign of dangerously deteriorating air in a coal mine," said Hedges, who is also one of the world's foremost authorities on amphibians and reptiles. "When frogs start disappearing, other species will follow and the Haitian people will suffer, as well, from this environmental catastrophe."

Hedges recently relocated 10 critically endangered species of frogs from Haiti to a captive-breeding program at the Philadelphia Zoo. One of these species already has begun breeding, laying eggs, and producing hatchlings in Philadelphia. Hedges has discovered at least five new frog species during three expeditions to Haiti this year, but he was not able to find two species that may now be extinct because they have not been seen there for 25 years. His scientific descriptions of the new species will be published in future issues of research journals.

The rescue mission led by Hedges is part of a new effort supported by the National Science Foundation to determine which species of amphibians and reptiles currently survive in Haiti, to pinpoint their locations, to discover any new species that previously were not documented scientifically, to relocate live populations of frogs for captive breeding, and to deep-freeze cells at Penn State. "Captive breeding and cryobanking are two efforts to preserve the species in case they become extinct in Haiti," said Hedges, who is one of the few scientists worldwide who have established cryobanking programs in their labs for endangered frogs and other species.

Cryobanking involves the preservation of cells and DNA in liquid nitrogen that will permit whole-animal cloning, if necessary, in the future. "These are time-consuming and costly backup plans to save species, normally reserved for those species closest to extinction, as in Haiti," Hedges said. "The goal is to release offspring of rescued frogs in Haiti if and when their forest habitat improves." Hedges and the Philadelphia Zoo also are working with the Haitian government and non-governmental agencies to train Haitians in this conservation research so that they can develop the capacity to breed these species in Haiti.

Frog species have been disappearing worldwide during the last 10 to 20 years, and one-third of the 6,000 frog species on Earth now are threatened with extinction. But 92 percent of Haiti's 50 frog species are threatened -- the highest percentage of any country in the world. Even worse, most Haitian frog species are officially designated as "endangered" or "critically endangered," the two highest levels of concern. "We found that as many as 26 species occur together in the isolated mountain forests of southwest Haiti, greatly increasing the threat of mass extinctions when the forests there are cut down," Hedges said. Of the 50 frog species in Haiti, two-thirds -- 30 species -- live only in Haiti and do not occur in the neighboring Dominican Republic.

"Less than one percent of the original forest is left in Haiti, which is a lower percentage than in any other country that I know of," Hedges said. "There definitely is no other place in the western half of the world -- and some scientists would argue in the entire world -- where the extinction threat is greater than in Haiti."

Hedges explained that the forests of Haiti are disappearing because the trees are being cut down to produce charcoal for the 10 million Haitian people who have few other sources of cooking fuel. "When you have a species that lives only in one mountain-top forest, and that forest suddenly disappears because you start harvesting all the trees for charcoal, then that species is guaranteed to become extinct along with all other species of animals and plants living only in that forest," Hedges said. "Virtually every truck you see on the rural roads is loaded down with bags of charcoal coming from the mountains, where people are cutting down the trees and making charcoal to be sold in the city of Port au Prince. The forests from some entire mountains now have been removed completely. In places, it looks like a lunar landscape, with nearly all the soil washed away and only the rocks and some weeds left behind."

Hedges has found that trees are not being protected even in the national parks of Haiti. "The commander of the park guards in the largest national park told us that only 10 unarmed guards are working at any one time in the park but typically 200 teams of tree cutters are at work there, armed with machetes and other weapons."

Recently a park guard in Haiti was killed by tree cutters.

"The pressure for cutting down the forests is coming from a whole island nation of people needing cooking fuel -- a problem requiring economic and possibly engineering solutions and needing the help of major international conservation organizations and government agencies," said Philippe Bayard, president of the Audubon Society of Haiti and collaborator with Hedges in efforts to save Haiti's biodiversity. "Unless effective help arrives soon, it is inevitable that there will be mass extinctions, and I think they are in progress."

Robin Moore, amphibian conservation officer for Conservation International, agrees. He joined Hedges and Martinez on the latest rescue mission. He points out, optimistically, that "despite the massive deforestation, the fact that the frogs are still hanging on, though barely, means that it is not too late to protect their habitat."

The scientists emphasize that the loss of forests also is a catastrophe for the Haitian people because forests are their major source of energy and they are critical for their economy, agriculture and drinking water.

Hedges, who has studied the genomes of diverse species worldwide in his laboratory research, is focusing his efforts in Haiti on preserving the cells and genomes of the endangered species there. Besides rescuing 10 frog species for captive breeding at the Philadelphia Zoo, he has cryobanked frogs and other species in his lab. One of the rescued frog species is the smallest one known on the island -- a species whose adults are the size of a small human fingernail.

"A captive-breeding program is a huge responsibility. You have to feed the animals, breed them, and keep them going for years and years, possibly indefinitely," said Carlos Martinez, Amphibian Conservation Biologist for the Philadelphia Zoo, who accompanied Hedges on the recent frog rescue mission. "But the survival of these species may depend on this work, so it is well worth the effort." Hedges was impressed with the zoo's willingness to take on this challenge. "I am absolutely delighted that the Philadelphia Zoo generously agreed to accept all 10 species, and I consider it a huge success that so many critically endangered frog species are being captive bred and cryobanked."

Ideally, a population should have at least 30 males and females to begin successful captive breeding, but some of these 10 species at the Philadelphia Zoo have fewer individuals. Hedges explains, "we were up on the top of a mountain that we might never get to again anytime soon, and we feared that this could be the last chance for the survival of this species, so we decided to at least try to breed them in captivity." He points out that, despite their limited habitat, these small animals occur in sufficient numbers to be unaffected by collecting efforts of the rescue team. Hedges now is looking for more zoos with the capability and willingness to host captive-breeding programs for endangered Haitian species, including reptiles, which he hopes to rescue during future expeditions.

"Haiti has suffered a terrible earthquake and it is enduring a cholera outbreak and so many other environmental and human disasters, and now it is clear that Haiti also is suffering the beginning of a mass-extinction event that likely will affect many more species in addition to its frogs," Hedges said. "I would like to have hope that the destruction is going to stop and the forests are going to come back, but I have fears about what will happen to the animals and the people of Haiti unless something major is done very soon to resolve the life-threatening problems there."

Hedges has set up a website, at http://www.CaribNature.org/ online, where he is posting multimedia information as well as links to conservation organizations that are working to solve the problems that are causing the species extinctions in Haiti and other areas of the Caribbean.

(Photo: Claudio Contreras)

Penn State

NEW ANALYSIS EXPLAINS FORMATION OF BULGE ON FARSIDE OF MOON

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A bulge of elevated topography on the farside of the moon--known as the lunar farside highlands--has defied explanation for decades. But a new study led by researchers at the University of California, Santa Cruz, shows that the highlands may be the result of tidal forces acting early in the moon's history when its solid outer crust floated on an ocean of liquid rock.

Ian Garrick-Bethell, an assistant professor of Earth and planetary sciences at UC Santa Cruz, found that the shape of the moon's bulge can be described by a surprisingly simple mathematical function. "What's interesting is that the form of the mathematical function implies that tides had something to do with the formation of that terrain," said Garrick-Bethell, who is the first author of a paper on the new findings published in the November 11 issue of Science.

The paper describes a process for formation of the lunar highlands that involves tidal heating of the moon's crust about 4.4 billion years ago. At that time, not long after the moon's formation, the crust was decoupled from the mantle below it by an intervening ocean of magma. As a result, the gravitational pull of the Earth caused tidal flexing and heating of the crust. At the polar regions, where the flexing and heating was greatest, the crust became thinner, while the thickest crust would have formed in the regions in line with the Earth.

This process still does not explain why the bulge is now found only on the farside of the moon. "You would expect to see a bulge on both sides, because tides have a symmetrical effect," Garrick-Bethell said. "It may be that volcanic activity or other geological processes over the past 4.4 billion years have changed the expression of the bulge on the nearside."

The paper's coauthors include Francis Nimmo, associate professor of Earth and planetary sciences at UCSC, and Mark Wieczorek, a planetary geophysicist at the Institut de Physique du Globe in Paris. The researchers analyzed topographical data from NASA's Lunar Reconnaissance Orbiter and gravitational data from Japan's Kaguya orbiter.

A map of crustal thickness based on the gravity data showed that an especially thick region of the moon's crust underlies the lunar farside highlands. The variations in crustal thickness on the moon are similar to effects seen on Jupiter's moon Europa, which has a shell of ice over an ocean of liquid water. Nimmo has studied the effects of tidal heating on the structure of Europa, and the researchers applied the same analytical approach to the moon.

"Europa is a completely different satellite from our moon, but it gave us the idea to look at the process of tidal flexing of the crust over a liquid ocean," Garrick-Bethell said.

The mathematical function that describes the shape of the moon's bulge can account for about one-fourth of the moon's shape, he said. Although mysteries still remain, such as what made the nearside so different, the new study provides a mathematical framework for further investigations into the shape of the moon.

"It's still not completely clear yet, but we're starting to chip away at the problem," Garrick-Bethell said.

(Photo: NASA/Goddard)

University of California, Santa Cruz

ASTRONOMERS DISCOVER MERGING STAR SYSTEMS THAT MIGHT EXPLODE

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Sometimes when you're looking for one thing, you find something completely different and unexpected. In the scientific endeavor, such serendipity can lead to new discoveries. Today, researchers who found the first hypervelocity stars escaping the Milky Way announced that their search also turned up a dozen double-star systems. Half of those are merging and might explode as supernovae in the astronomically near future.

All of the newfound binary stars consist of two white dwarfs. A white dwarf is the hot, dead core left over when a sun-like star gently puffs off its outer layers as it dies. A white dwarf is incredibly dense, packing as much as a sun's worth of material into a sphere the size of Earth. A teaspoon of it would weigh more than a ton.

"These are weird systems - objects the size of the Earth orbiting each other at a distance less than the radius of the Sun," said Smithsonian astronomer Warren Brown, lead author of the two papers reporting the find.

The white dwarfs found in this survey are lightweight among white dwarfs, holding only about one-fifth as much mass as the Sun. They are made almost entirely of helium, unlike normal white dwarfs made of carbon and oxygen.

"These white dwarfs have gone through a dramatic weight loss program," said Carlos Allende Prieto, an astronomer at the Instituto de Astrofisica de Canarias in Spain and a co-author of the study. "These stars are in such close orbits that tidal forces, like those swaying the oceans on Earth, led to huge mass losses."

Remarkably, because they whirl around so close to each other, the white dwarfs stir the space-time continuum, creating expanding ripples known as gravitational waves. Those waves carry away orbital energy, causing the stars to spiral closer together. Half of the systems are expected to merge eventually. The tightest binary, orbiting once every hour, will merge in about 100 million years.

"We have tripled the number of known, merging white-dwarf systems," said Smithsonian astronomer and co-author Mukremin Kilic. "Now, we can begin to understand how these systems form and what they may become in the near future."

When two white dwarfs merge, their combined mass can exceed a tipping point, causing them to detonate and explode as a Type Ia supernova. Brown and his colleagues suggest that the merging binaries they have discovered might be one source of underluminous supernovae -- a rare type of supernova explosion 100 times fainter than a normal Type Ia supernova, which ejects only one-fifth as much matter.

"The rate at which our white dwarfs are merging is the same as the rate of underluminous supernovae - about one every 2,000 years," explained Brown. "While we can't know for sure whether our merging white dwarfs will explode as underluminous supernovae, the fact that the rates are the same is highly suggestive."

(Photo: Clayton Ellis (CfA))

CfA

STUDY REWRITES THE EVOLUTIONARY HISTORY OF C4 GRASSES

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According to a popular hypothesis, grasses such as maize, sugar cane, millet and sorghum got their evolutionary start as a result of a steep drop in atmospheric carbon dioxide levels during the Oligocene epoch, more than 23 million years ago. A new study overturns that hypothesis, presenting the first geological evidence that the ancestors of these and other C4 grasses emerged millions of years earlier than previously established.

The findings are published in the journal Geology.

C4 plants are more efficient than C3 plants at taking up atmospheric carbon dioxide and converting it into the starches and sugars vital to plant growth. (C3 and C4 refer to the number of carbon atoms in the first molecular product of photosynthesis.) Having evolved relatively recently, C4 plants make up 3 percent of all living species of flowering plants. But they account for about 25 percent of global plant productivity on land. They dominate grasslands in tropical, subtropical and warm temperate areas. They also are a vital food source and an important feedstock for the production of biofuels.

"C4 plants are very successful, they're economically very important, but we actually don't know when they originated in the geological history," said University of Illinois plant biology professor Feng Sheng Hu, who led the new analysis. "To me, it's one of the most profound geological and ecological questions as a paleoecologist I can tackle."

A previous study dated the oldest C4 plant remnant found, a tiny fragment called a phytolith, to about 19 million years ago. Other studies analyzed the ratios of carbon isotopes in bulk soil samples to determine the ratio of C3 to C4 plant remains at different soil horizons, which correspond to different geological time periods. (C3 and C4 plants differ in their proportions of two carbon isotopes, C-12 and C-13.) Those studies indicated that C4 grasses were present as early as the Early Micocene, about 18 million years ago.

Rather than analyzing plant matter in bulk sediment samples, David Nelson, a postdoctoral researcher in Hu's lab at the time of the study (now a professor at the University of Maryland), analyzed the carbon isotope ratios of individual grains of grass pollen, a technique he pioneered while working with Hu in the lab of biogeochemistry professor Ann Pearson at Harvard University.

Using a spooling-wire micro-combustion device to combust the grains, and an isotope mass spectrometer to determine the relative ratio of C-12 and C-13 in the sample, Nelson and Illinois graduate student Michael Urban analyzed hundreds of individual grains of grass pollen collected from study sites in Spain and France.

"Because we analyze carbon isotopes in a material unique to grasses (pollen) we were able to detect C4 grasses at lower abundances than previous studies," Nelson said.

This analysis found "unequivocal evidence for C4 grasses in southwestern Europe by the Early Oligocene," the authors wrote. This means these grasses were present 32 to 34 million years ago, well before studies indicate atmospheric carbon dioxide levels made their precipitous decline.

"The evidence refutes the idea that low (atmospheric) CO2 was an important driver and/or precondition for the development of C4 photosynthesis," the authors wrote.

"This study challenges that hypothesis and basically says that something else was responsible for the evolution of C4 plants, probably higher temperature or drier conditions," Hu said. With atmospheric carbon dioxide levels now on the increase, he said, "there are also implications about how C3 and C4 plants will fare in the future."

(Photo: L. Brian Stauffer, U. of I. News Bureau)

University of Illinois at Urbana-Champaign

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