Mar 4, 2017

Microbiome diversity is influenced by chance encounters

After feeding C. elegans worms an equal mix of bacteria that express either red or green fluorescent protein, MIT researchers found that the microbial populations in the worms’ digestive tracts tend to become dominated by one or the other.
Within the human digestive tract, there are trillions of bacteria, and these communities contain hundreds or even thousands of species. The makeup of those populations can vary greatly from one person to another, depending on factors such as diet, environmental exposure, and health history.

A new study of the microbe populations of worms offers another factor that may contribute to this variation: chance.

MIT researchers found that when they put genetically identical worms into identical environments and fed them the same diet, the worms developed very different populations of bacteria in their gut, depending on which bacteria happened to make it there first.

"This study shows that you can have heterogeneity that's driven by the randomness of the initial colonization event. That's not to say the heterogeneity between any two individuals has to be driven by that, but it's a potential source that is often neglected when thinking about this variation," says Jeff Gore, the Latham Family Career Development Associate Professor of Physics at MIT.

Gore is the senior author of the study, which appears in the March 3 issue of the journal PLOS Biology. The paper's lead author is MIT postdoc Nicole Vega.

A simple model

Variations in the human gut microbiome have been shown to contribute to gastrointestinal disorders such as colitis and Crohn's disease, and studies suggest that microbiome composition can also influence diabetes, heart disease, and cancer.

"We know that gut communities are different within different individuals, and that this could have really important implications for health and disease, but it's often difficult to figure out the origin of this diversity between different individuals," Gore says.

The researchers chose to study the worm C. elegans because it is among the simplest animals with a digestive tract colonized by bacteria, offering a way to model what might be happening in the human gut.

"What you would like to do is take a bunch of identical individuals, place them in identical environments, and then look to see whether the microbial communities are the same or different. That's a very difficult experiment to do with people, but with model organisms it's feasible," Gore says.

C. elegans consume bacteria as part of their normal diet, so the researchers first fed a group of genetically identical worms a mix of six different species of bacteria. When the experiment began, the worms had no bacteria in their digestive tracts, but after being exposed to the identical bacterial diet, the worms each generated very different microbe populations in their guts.

The researchers explored this further by feeding the worms a mix of only two types of bacteria, making it easier to study their interactions. In this scenario, all of the bacteria were E. coli, but half were engineered to produce a green fluorescent protein and the other half produced a red fluorescent protein.

After a week of this diet, each worm had about 30,000 bacteria in its digestive tract. However, these populations were not evenly divided between red and green. Instead, each population was dominated by one or the other. This happens, Gore says, because the initial colonization of the gut is a rare event, so whichever microbe makes it there first tends to dominate the entire population.

"Whichever color bacteria is lucky and happens to survive getting eaten and sticks to the gut, this bacterium starts growing, and it can grow to dominate the gut community," he says.

This randomness tends to prevail when the colonization rate is low. When the researchers fed the worms larger amounts of bacteria, the colonization rate went up and the researchers found much less variation among individuals' microbe populations.

An overlooked source

The researchers also found the same effect when they fed the worms two different species of bacteria: Enterobacter aerogenes and Serratia marcescens.

Gore says that this random variability may contribute to the differences in microbe populations seen in the human gut as well, since usually only a small fraction of bacteria consumed by humans and other animals survives the digestion process. However, many other factors such as environmental exposure also play roles, he says.

"I don't believe that stochastic colonization is the only or dominant source of heterogeneity between individuals, but I think it's a source of heterogeneity that is often overlooked," Gore says.

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Most complex nanoparticle crystal ever made by design

The most complex crystal designed and built from nanoparticles. Left: An electron microscope image of a slice of the structure (Northwestern University). Right: A matching slice from a simulation of the structure (University of Michigan).
The most complex crystal designed and built from nanoparticles has been reported by researchers at Northwestern University and the University of Michigan. The work demonstrates that some of nature's most complicated structures can be deliberately assembled if researchers can control the shapes of the particles and the way they connect using DNA.

"This is a tour de force demonstration of what is possible when one harnesses the chemistry of DNA and combines it with nanoparticles whose shapes encourage a particular crystal structure," said Chad A. Mirkin, the George B. Rathmann Professor of Chemistry in the Weinberg College of Arts and Sciences at Northwestern.

Nanotechnology promises to bring materials together in new ways, forging new capabilities by design. One potential application for crystals built of nanoparticles, such as these newly reported ones, is the control of light -- nanoparticles interact well with light waves because they are similar in size. This could lead to materials that can change colors or patterns on command or block certain wavelengths of light, while transmitting or amplifying others. New types of lenses, lasers and even Star Trek-like cloaking materials are possible.

"This work shows that nanoparticle crystals of extraordinary complexity are possible with DNA technology, once one begins to exploit particle shape," said Sharon C. Glotzer, the John W. Cahn Distinguished University Professor of Engineering and the Stuart W. Churchill Collegiate Professor of Chemical Engineering at U-M. "And, it's a great example of what can be achieved by experimentalists and simulators teaming up."

The study, titled "Clathrate Colloidal Crystals," will be published March 3 in the journal Science. Mirkin and Glotzer are co-corresponding authors of the paper.

In chemistry, clathrates are known for their chambers that can house small molecules. They have been used for capturing pollutants from the environment, for example. The nanoparticle clusters also leave room for cargo, which the authors suggest could be useful for storing, delivering and sensing materials for environmental, medical diagnostic and therapeutic applications.

While natural materials exhibit a dizzying array of crystal structures, most nanotechnology labs struggle to get past simple designs. The structures produced by Haixin Lin, now a postdoctoral fellow in Mirkin's lab, are far more interesting. The new structures are composed of clusters of up to 42 particles, forming larger polyhedral, such as the great dodecahedron. These clusters connect into cage-like crystal structures called clathrates.

Still, the story isn't the crystal itself: it's how the crystal came to be. Mirkin's group has pioneered many structures through the use of DNA strands as a sort of smart glue, linking nanoparticles together in a particular way. The particle is both a building block and a template that directs bonding interactions. Meanwhile, Glotzer's group has championed the role of nanoparticle shape in guiding the assembly of crystal structures through computer simulation.

"Chad's group got the idea of exploring new phases by looking at predictions we had made," Glotzer said. "One day, I got a phone call from him. 'We just got these incredible structures!' he said. And he texted me micrograph after micrograph -- they just kept popping up. He said, we need to figure out a way to definitively assign their structures."

The electron microscope images, or micrographs, showed complex crystalline structures that formed in large part thanks to the shape of the gold nanoparticles. The triangular bipyramidal shape, like two flattened tetrahedrons stuck together at their bases, was similar to a shape Glotzer's group predicted would form a quasicrystal. Quasicrystals are prized in the field of nanoassembly because they are as complex as crystals get.

Lin's shape had just the right angles to make clathrate structures, which often turn up in molecular systems that form quasicrystals. But to do so, they needed strands of DNA attached to their sides at just the right length.

Lin systematically made the gold bipyramids of consistent size and shape, with edge lengths of 250 nanometers -- half the wavelength of blue light. He then modified them with different length sequences of DNA. When the DNA strands were too short, the nanoparticles made disordered, ill-defined structures.

When longer strands produced exotic patterns in the electron microscope images, Lin brought the results to Mirkin, who was both thrilled and intrigued.

"These are stunning -- no one has made such structures before," said Mirkin, director of Northwestern's International Institute for Nanotechnology.

It was clear they had made phases never observed before, but getting the structure accurately identified was essential. After Mirkin alerted Glotzer at U-M, Sangmin Lee and Michael Engel 3-D printed Lin's bipyramids and glued them together to explore how they might make the structures in the electron micrographs. Lee is a doctoral student in chemical engineering, and Engel was then an assistant research scientist, both in Glotzer's group.

Once they saw how the shapes fit together, they hypothesized the clathrate structures. To confirm their suspicions, they built a computer model of the hypothesized clathrates from bipyramids and compared it to the Northwestern micrographs. It was a perfect match.

As a definitive test, Lee and Matthew Spellings, also a doctoral student in chemical engineering at U-M, developed a molecular model of the DNA-linked nanoparticles. Lee carried out simulations to confirm that the particles would indeed form clathrate structures.

"To really know for sure, we had to run simulations that mimicked the conditions Haixin used in the lab to see if a disordered fluid of DNA-linked bipyramids would assemble into the Northwestern crystals," Glotzer said. "Once we saw the computer crystals, I knew we had nailed it."

Mirkin is director of the research group that invented the chemistry for conjugating DNA and nanoparticles and a pioneer of the concept of programmable colloidal crystallization with nucleic acids. In 1996, he introduced the concept of using nanoparticles as atoms and synthetic DNA -- the blueprint of life -- as a chemically programmable bond to make designer materials based upon the ability of the particles to recognize one another through sequences immobilized on their surfaces. Mirkin has been experimentally studying the role of particle shape in colloidal crystal formation for the past two decades. He is also a professor of medicine, chemical and biological engineering, biomedical engineering, and materials science and engineering.

Read more at Science Daily

Mar 3, 2017

What global climate change may mean for leaf litter in streams and rivers

Leaf skeleton with invertebrates, location unknown.
Carbon emissions to the atmosphere from streams and rivers are expected to increase as warmer water temperatures stimulate faster rates of organic matter breakdown.

But a new study led by University of Utah researcher Jennifer J. Follstad Shah, in collaboration with a team of 15 scientists in the U.S. and Europe, suggests these decay rates may not increase as much as expected. In fact, the study indicates average breakdown rates may increase 5 percent to 21 percent with a 1 degree to 4-degree Celsius rise in water temperature -- half as much as the 10 percent to 45 percent increase predicted by metabolic theory. Mean annual water temperature for some streams and rivers is currently rising at an annual rate of about 0.01 degrees to 0.1 degrees Celsius due to changes in climate and land use.

The study "Global synthesis of the temperature sensitivity of leaf litter breakdown in streams and rivers" was published Feb. 28 in Global Change Biology.

Streams and rivers cover about 3 percent of Earth's land surface but are an important contributor to the global carbon cycle. These waterways constitute a major habitat where organic matter such as leaf litter is transformed through physical processes and consumption by microbes and invertebrates. Some of the organic matter consumed contributes to the growth of these organisms, but a portion is 'lost' downstream as invertebrates tear litter into smaller pieces and some is emitted to the atmosphere as carbon dioxide through respiration.

Carbon dioxide is a greenhouse gas that contributes to global warming and ocean acidification.

Warmer water enhances the breakdown of organic matter, but it is unclear if climate change will result in more carbon emitted to the atmosphere relative to carbon transported downstream to the ocean.

"This process is not as obvious as the melting of ice caps and impacts on a charismatic creature like the polar bear, but it is an important indicator of global climate change," Follstad Shah said, and one that has implications for values used in climate change models.

"There is still a lot about the carbon cycle we don't understand," she said. "Understanding the temperature sensitivity of ecosystem processes that govern carbon cycling is imperative as global temperatures rise."

The new study reviewed data from more than 1,000 reports representing 41 countries and 85 different plant genera to quantify the sensitivity of litter breakdown in streams and rivers to changes in temperature. It took into account invertebrate density, global position and litter quality as factors controlling temperature sensitivity of litter breakdown.

The study found that rising temperatures will likely increase the rate of litter decay but not quite as fast as expected based on metabolic theory, Follstad Shah said. Metabolic theory posits that organisms' metabolic rate, which depends in part on temperature, governs ecological processes. In this case, according to metabolic theory, the rate of litter breakdown would depend on the metabolic rate of stream organisms -- which is stimulated by elevated temperatures.

Follstad Shah and colleagues found that temperature sensitivity of litter breakdown was greater in tropical than temperate biomes. The study estimates that a roughly 10 percent increase in litter breakdown rate requires only a 1-degree Celsius rise in the tropics but a 4-degree Celsius rise in temperate biomes.

Temperature sensitivity varied among the different plant types, which the data suggest may be due to differences in leaf chemistry. The study also found temperature sensitivity of leaf litter breakdown was similar whether mediated by microbes alone or by microbes and invertebrates.

That suggests the balance between the amount of carbon dioxide released versus the amount of carbon remaining in solid form -- leaf litter moving downstream as smaller particles to an ocean -- should remain relatively consistent even if temperatures rise, Follstad Shah said. It also suggests that it is possible to make an initial, broad-scale forecast of breakdown rate response to altered stream temperatures.

"Our study is applicable to efforts using standardized measures to gauge the health of streams and rivers," she said.

Many streams and rivers around the world are impaired. Sometimes impairment is due to shifts in water temperature or other forms of pollution.

Read more at Science Daily

Study sheds new light on how species extinction affects complex ecosystems

At present, predictions assume that any contribution is completely lost at the point of extinction -- leading to a decline in ecosystem performance.
Research by the University of Southampton (UK) has found that methods used to predict the effect of species extinction on ecosystems could be producing inaccurate results. This is because current thinking assumes that when a species vanishes, its role within an environment is lost too.

However, scientists working on a new study have found that when a species, (for example a group of sea creatures), is wiped out by a catastrophic event, other species can change their behaviour to compensate, exploiting the vacant role left behind. This leads to positive or negative effects on ecosystems, and in turn, either better or worse outcomes than current estimates would suggest.

At present, predictions assume that any contribution is completely lost at the point of extinction -- leading to a decline in ecosystem performance.

The findings are published in the journal Scientific Reports. Lead author Matthias Schmidt Thomsen, of Ocean and Earth Science at the University of Southampton, says: "We have known for some time that a reduction in biodiversity has negative ecological consequences, but predictions of what happens to an ecosystem have not accounted for the occurrence of compensatory responses."

He added: "Our study provides evidence that the response of surviving species to novel circumstances can, at least partially, offset, or indeed exacerbate, changes in an ecosystem that are associated with species removal."

The researchers based their findings on the interaction of species in a community of invertebrates (such as clams, shrimps and worms) obtained from marine seabed samples collected in Galway Bay, Ireland. Bottom dwelling marine organisms are particularly vulnerable to extinction because they are often unable to avoid disturbance. These organisms are important because they churn up sediments from the bottom of the ocean, a process known as 'bioturbation', playing a vital role in returning nutrients to surrounding water as food for other creatures.

Using mathematical simulations, the team were able to explore what happens to the bioturbation process as species are removed from the system under different extinction scenarios. The simulations also accounted for the nuances of how other creatures would react as circumstances change. The direction and strength of response depends on the type of compensation and the extinction scenario.

Co-author, Dr Clement Garcia, an ecologist from the Centre for Environment, Fisheries and Aquaculture Science in Lowestoft said: "There have been concerns over the gradual erosion of our natural habitat for some time. These findings will help resolve some of the detail that has previously been unavailable, allowing us to better identify both vulnerabilities and opportunities that coincide with environmental change and human endeavour."

Read more at Science Daily

100,000-year-old human skulls from east Asia reveal complex mix of trends in time, space

Virtual reconstructions of the Xuchang 1 and 2 human crania are superimposed on the archeological site where they were discovered.
Two partial archaic human skulls, from the Lingjing site, Xuchang, central China, provide a new window into the biology and populations patterns of the immediate predecessors of modern humans in eastern Eurasia.

Securely dated to about 100,000 years ago, the Xuchang fossils present a mosaic of features.

  • With late archaic (and early modern) humans across the Old World, they share a large brain size and lightly built cranial vaults with modest brow ridges.
  • With earlier (Middle Pleistocene) eastern Eurasian humans, they share a low and broad braincase, one that rounds onto the inferior skull.
  • With western Eurasian Neandertals, they share two distinct features -- the configuration of their semicircular canals and the detailed arrangement of the rear of the skull.

"The biological nature of the immediate predecessors of modern humans in eastern Eurasia has been poorly known from the human fossil record," said Erik Trinkaus, a corresponding author for the study and professor of anthropology at Washington University in St. Louis. "The discovery of these skulls of late archaic humans, from Xuchang, substantially increases our knowledge of these people."

More importantly, he noted: "The features of these fossils reinforce a pattern of regional population continuity in eastern Eurasia, combined with shared long-terms trends in human biology and populational connections across Eurasia. They reinforce the unity and dynamic nature of human evolution leading up to modern human emergence."

From Science Daily

Why pandas are black and white

The black and white markings of the giant panda serve them as both camouflage and communication, scientists learned.
The scientists who uncovered why zebras have black and white stripes (to repel biting flies), took the coloration question to giant pandas in a study published this week in the journal Behavioral Ecology.

The study, a collaboration between the University of California, Davis, and California State University, Long Beach, determined that the giant panda's distinct black-and-white markings have two functions: camouflage and communication.

Deconstructing a Giant Panda 

"Understanding why the giant panda has such striking coloration has been a long-standing problem in biology that has been difficult to tackle because virtually no other mammal has this appearance, making analogies difficult," said lead author Tim Caro, a professor in the UC Davis Department of Wildlife, Fish and Conservation Biology. "The breakthrough in the study was treating each part of the body as an independent area."

This enabled the team to compare different regions of fur across the giant panda's body to the dark and light coloring of 195 other carnivore species and 39 bear subspecies, to which it is related. Then they tried to match the darkness of these regions to various ecological and behavioral variables to determine their function.

Hiding in Snow or Forest

Through these comparisons, the study found that most of the panda -- its face, neck, belly, rump -- is white to help it hide in snowy habitats. The arms and legs are black, helping it to hide in shade.

The scientists suggest that this dual coloration stems from its poor diet of bamboo and inability to digest a broader variety of plants. This means it can never store enough fat to go dormant during the winter, as do some bears. So it has to be active year-round, traveling across long distances and habitat types that range from snowy mountains to tropical forests.

The markings on its head, however, are not used to hide from predators, but rather to communicate. Dark ears may help convey a sense of ferocity, a warning to predators. Their dark eye patches may help them recognize each other or signal aggression toward panda competitors.

Read more at Science Daily

Evolution of bipedalism in ancient dinosaur ancestors

Skeleton of the proto-dinosaur Marasuchus -- a squirrel-sized carnivore that likely walked on all fours but ran on two legs.
Paleontologists at the University of Alberta have developed a new theory to explain why the ancient ancestors of dinosaurs stopped moving about on all fours and rose up on just their two hind legs.

Bipedalism in dinosaurs was inherited from ancient and much smaller proto-dinosaurs. The trick to this evolution is in their tails explains Scott Persons, postdoctoral fellow and lead author on the paper.

"The tails of proto-dinosaurs had big, leg-powering muscles," says Persons. "Having this muscle mass provided the strength and power required for early dinosaurs to stand on and move with their two back feet. We see a similar effect in many modern lizards that rise up and run bipedally."

Over time, proto-dinosaurs evolved to run faster and for longer distances. Adaptations like hind limb elongation allowed ancient dinosaurs to run faster, while smaller forelimbs helped to reduce body weight and improve balance. Eventually, some proto-dinosaurs gave up quadrupedal walking altogether.

The research, conducted by Persons and Phil Currie, paleontologist and Canada Research Chair, also debunks theories that early proto-dinosaurs stood on two legs for the sole purpose of free their hands for use in catching prey.

"Those explanations don't stand up," says Persons. "Many ancient bipedal dinosaurs were herbivores, and even early carnivorous dinosaurs evolved small forearms. Rather than using their hands to grapple with prey, it is more likely they seized their meals with their powerful jaws."

But, if it is true that bipedalism can evolve to help animals run fast, why aren't mammals like horses and cheetahs bipedal?

"Largely because mammals don't have those big tail-based leg muscles," Persons explains. "Looking across the fossil record, we can trace when our proto-mammal ancestors actually lost those muscles. It seems to have happened back in the Permian period, over 252 million years ago."

At that time the mammalian lineage was adapting to dig and to live in burrows. In order to dig, mammals had strong front limbs. Muscular back legs and tails likely made it more difficult to maneuver in the narrow confines of a burrow.

"It also makes the distance a predator has to reach in to grab you that much shorter," says persons. "That's why modern burrowers tend to have particularly short tails. Think rabbits, badgers, and moles."

Read more at Science Daily

Mar 2, 2017

Mollusk graveyards are time machines to oceans' pristine past

Florida Museum of Natural History researchers found that mollusk graveyards accurately recorded patterns of biodiversity across a range of marine habitats.
A University of Florida study shows that mollusk fossils provide a reliable measure of human-driven changes in marine ecosystems and shifts in ocean biodiversity across time and space.

Collecting data from the shells of dead mollusks is a low-cost, low-impact way of glimpsing how oceans looked before pollution, habitat loss, acidification and explosive algae growth threatened marine life worldwide. Mollusk fossils can inform current and future conservation and restoration efforts, said Michal Kowalewski, the Jon L. and Beverly A. Thompson Chair of Invertebrate Paleontology at the Florida Museum of Natural History on the UF campus and the study's principal investigator.

"These fossils are like marine time machines that can unveil bygone habitats that existed before humans altered them," he said. "Shells can help us understand past marine life and more precisely gauge recent changes in marine ecosystems. Fossils are the only direct way of learning what these ecosystems looked like before human activities altered them."

Because mollusks, such as conchs, oysters and mussels, are abundant and often have sturdy shells, their remains litter much of Earth's sea floor. These mollusk graveyards offer a treasure trove of information about the state of oceans over thousands of years, recording patterns in the diversity and distribution of marine animals across and within habitats with surprising accuracy, said Carrie Tyler, who conducted the work as a postdoctoral researcher at the museum and is now an assistant professor of invertebrate paleontology at the Miami University of Ohio.

Many scientists have questioned whether mollusks alone can provide insights into entire ecosystems. Currents and storms can carry organisms' remains away, while others are fragmented, destroyed or -- in the case of soft-bodied animals such as jellyfish and worms -- completely absent from the fossil record. Also, shell graveyards are often a mix of specimens from many centuries, which can muddle ecological interpretations.

"The remains that do accumulate only represent part of the whole ecosystem," said Tyler, the study's lead author. "These and other factors can create bias in the fossil record, making comparisons between modern and fossil ecosystems suspect."

To test mollusks' ability to faithfully record biodiversity, Tyler and Kowalewski surveyed living and dead marine animals at 51 sites off the coast of North Carolina, selecting spots that differed in environmental conditions and the kinds of species they hosted. Aiming to capture a range of habitats, the researchers surveyed inlets, estuaries and open ocean, from the coast to miles offshore. They tested whether changes in diversity from place to place were accurately recorded by the newly-forming fossil record. They also assessed whether mollusks could reflect these ecosystem-wide changes.

Tyler and Kowalewski found that live and dead mollusks accurately recorded spatial diversity patterns in both living and fossil communities of marine bottom-dwelling organisms. By comparing present-day communities of marine animals to dead remains, they discovered that mollusk shells alone accurately reconstructed differences in ecosystems across habitats and correctly tracked changes in the distribution of animals from shallow to deeper waters.

A unique aspect of the study, Kowalewski said, was investigating whether mollusks reliably recorded shifts in entire communities of bottom-dwelling animals across habitats and space.

"If we look at many spots on the sea floor and evaluate how living bottom-dwelling animals vary in space, do we recover the same information by analyzing shell remains of only one type of organism, such as mollusks? Our data indicate that we can," he said. "The good match between dead and living organisms suggests that we can use historical data to look at not just which species existed in the past, but also whether the spatial structure of these ecosystems changed."

Understanding how the diversity of species changes within habitats and from site to site across the sea floor is crucial for effectively planning protected marine areas and coastal resource management, Kowalewski said. It is also a part of an increased effort to approach ecosystem conservation more broadly, focusing not only on the vulnerability of individual species but also on how species congregate within and across habitats.

Whether mollusks can provide insights into an ecosystem's more mobile animals, such as fish, remains unclear. But regardless of how much mollusks can tell us about fish, turtles or mammals, understanding marine invertebrate biodiversity is critical to restoring and protecting ocean health, Tyler said.

Read more at Science Daily

Rapid changes point to origin of ultra-fast black hole 'burp'

This is an artist impression illustrating a supermassive black hole with X-ray emission emanating from its inner region (pink) and ultrafast winds streaming from the surrounding disk (purple).
Gas outflows are common features of active supermassive black holes that reside in the center of large galaxies. Millions to billions of times the mass of the Sun, these black holes feed on the large disks of gas that swirl around them. Occasionally the black holes eat too much and burp out an ultra-fast wind, or outflow. These winds may have a strong influence on regulating the growth of the host galaxy by clearing the surrounding gas away and suppressing star formation.

Scientists have now made the most detailed observation yet of such an outflow, coming from an active galaxy named IRAS 13224-3809. The outflow's temperature changed on time scales of less than an hour, which is hundreds of times faster than ever seen before. The rapid fluctuations in the outflow's temperature indicated that the outflow was responding to X-ray emissions from the accretion disk, a dense zone of gas and other materials that surrounds the black hole.

The new observations are published in the journal Nature on March 2, 2017.

"Although we have seen these outflows before, this observation was the first time we were able to see the launching of the gases being connected with changes in the luminosity of black holes," said Erin Kara, a postdoctoral researcher in astronomy at the University of Maryland and a co-author of the study.

Scientists made these measurements using two space telescopes, NASA's NuSTAR (Nuclear Spectroscopic Telescope Array) telescope and the European Space Agency's (ESA) XMM-Newton. To capture the variability of these signals, scientists focused the XMM-Newton on the black hole for 17 days in a row, and observed the black hole with NuSTAR for six days.

To measure the temperatures of these winds, scientists studied X-rays coming from the edge of the black hole. As they travel towards Earth, these X-rays pass through the outflows. Elements such as iron or magnesium present in the outflows can absorb specific parts of the X-ray spectrum, creating signature "dips" in the X-ray signal. By observing these dips, called absorption features, astronomers can learn what elements exist in the wind.

The team noticed that the absorption features disappeared and reappeared in the span of a few hours. The researchers concluded that the X-rays were heating up the winds to millions of degrees Celsius, at which point the winds became incapable of absorbing any more X-rays.

The observations that the outflows appear to be linked with X-rays, and that both are so highly variable, provide possible clues for locating where exactly the X-rays and outflows originate.

"The radiating gas flows into black holes are most variable at their centers," Kara said. "Because we saw such rapid variability in the winds, we know that the emission is coming from very close to the black hole itself, and because we observed that the wind was also changing on rapid time scales, it must also be coming from very close to the black hole."

To further study galaxy formation and black holes, Chris Reynolds, a professor of astronomy at UMD and a co-PI on the project, noted the need for more detailed data and observations.

Read more at Science Daily

Biochemical 'fossil' shows how life may have emerged without phosphate

This is a schematic depiction of how an early metabolism could have expanded from an initial set of prebiotic molecules, with thioester (S) vs. phosphate (P) as the main driving force.
One major mystery about life's origin is how phosphate became an essential building block of genetic and metabolic machinery in cells, given its poor accessibility on early Earth. In a study published on March 9 in the journal Cell, researchers used systems biology approaches to tackle this long-standing conundrum, providing compelling, data-driven evidence that primitive life forms may not have relied on phosphate at all. Instead, a few simple, abundant molecules could have supported the emergence of a sulfur-based, phosphate-free metabolism, which expanded to form a rich network of biochemical reactions capable of supporting the synthesis of a broad category of key biomolecules.

"The significance of this work is that future efforts to understand life's origin should take into account the concrete possibility that phosphate-based processes, which are essential today, may not have been around when the first life-like processes started emerging," says senior study author Daniel Segrè (@dsegre) of Boston University. "An early phosphate-independent metabolism capable of producing several key building blocks of living systems is in principle viable."

Phosphate is essential for all living systems and is present in a large proportion of known biomolecules. A sugar-phosphate backbone forms the structural framework of nucleic acids, including DNA and RNA. Moreover, phosphate is a critical component of adenosine triphosphate (ATP), which transports chemical energy within cells, and a compound called NADH, which has several essential roles in metabolism. But it is unclear how phosphate could have assumed these central roles on primordial Earth, given its scarcity and poor accessibility.

In light of this puzzle, some have proposed that early metabolic pathways did not rely on phosphate. In many of these scenarios, sulfur and iron found on mineral surfaces are thought to have fulfilled major catalytic and energetic functions prior to the appearance of phosphate. One notable origin-of-life scenario suggests that the role of ATP was originally assumed by sulfur-containing compounds called thioesters, which are widely involved in protein, carbohydrate, and lipid metabolism. Despite the availability of iron and sulfur on early Earth, concrete evidence supporting these scenarios has been lacking.

To test the feasibility of the "iron-sulfur world hypothesis" and the "thioester world scenario," Segrè and his team used computational systems biology approaches originally developed for large-scale analyses of complex metabolic networks. The researchers used a large database to assemble the complete set of all known biochemical reactions. After exploring this so-called "biosphere-level metabolism," the researchers identified a set of eight phosphate-free compounds thought to have been available in prebiotic environments. They then used an algorithm that simulated the emergence of primitive metabolic networks by compiling all possible reactions that could have taken place in the presence of these eight compounds, which included formate, acetate, hydrogen sulfide, ammonium, carbon dioxide, water, bicarbonate, and nitrogen gas.

This analysis revealed that a few simple prebiotic compounds could support the emergence of a rich, phosphate-independent metabolic network. This core network, consisting of 315 reactions and 260 metabolites, was capable of supporting the biosynthesis of a broad category of key biomolecules such as amino acids and carboxylic acids. Notably, the network was enriched for enzymes containing iron-sulfur clusters, bolstering the idea that modern biochemistry emerged from mineral geochemistry. Moreover, thioesters rather than phosphate could have enabled this core metabolism to overcome energetic bottlenecks and expand under physiologically realistic conditions.

"Before our study, other researchers had proposed a sulfur-based early biochemistry, with hints that phosphate may not have been necessary until later," Segrè says. "What was missing until now was data-driven evidence that these early processes, rather than scattered reactions, could have constituted a highly connected and relatively rich primitive metabolic network."

Although this non-experimental evidence does not definitively prove that life started without phosphate, it provides compelling support for the iron-sulfur world hypothesis and the thioester world scenario. At the same time, the study calls into question the "RNA world hypothesis," which proposes that self-replicating RNA molecules were the precursors to all current life on Earth. Instead, the results support the "metabolism-first hypothesis," which posits that a self-sustaining phosphate-free metabolic network predated the emergence of nucleic acids. In other words, nucleic acids could have been an outcome of early evolutionary processes rather than a prerequisite for them.

"Evidence that an early metabolism could have functioned without phosphate indicates that phosphate may have not been an essential ingredient for the onset of cellular life," says first author Joshua Goldford of Boston University. "This proto-metabolic system would have required an energy source and may have emerged either on the Earth's surface, with solar energy as the main driving force, or in the depth of the oceans near hydrothermal vents, where geochemical gradients could have driven the first life-like processes."

Read more at Science Daily

Woolly mammoths experienced a genomic meltdown just before extinction

Mammoth skeleton
Dwindling populations created a "mutational meltdown" in the genomes of the last wooly mammoths, which had survived on an isolated island until a few thousand years ago. Rebekah Rogers and Montgomery Slatkin of the University of California, Berkeley, report these findings in a study published March 2nd, 2017 in PLOS Genetics.

Woolly mammoths were one of the most common large herbivores in North America, Siberia, and Beringia until a warming climate and human hunters led to their extinction on the mainland about 10,000 years ago. Small island populations persisted until about 3,700 years ago before the species finally disappeared. Researchers compared existing genomes from a mainland mammoth that dates back to 45,000 years ago, when the animal was plentiful, to one that lived about 4,300 years ago. The recent genome came from a mammoth that had lived in a group of about 300 animals on Wrangel Island in the Arctic Ocean. The analysis showed that the island mammoth had accumulated multiple harmful mutations in its genome, which interfered with gene functions. The animals had lost many olfactory receptors, which detect odors, as well as urinary proteins, which can impact social status and mate choice. The genome also revealed that the island mammoth had specific mutations that likely created an unusual translucent satin coat.

The comparison gives researchers the rare opportunity to see what happens to the genome as a population declines, and supports existing theories of genome deterioration stemming from small population sizes. The study also offers a warning to conservationists: preserving a small group of isolated animals is not sufficient to stop negative effects of inbreeding and genomic meltdown. For those interested in wooly mammoth "de-extinction," the study demonstrates that some mammoth genomes carry an overabundance of negative mutations.

Rebekah Rogers adds: "When I first started this project, I was excited to be working with the new woolly mammoth sequences, published by Love Dalen's lab. It was even more exciting when we found an excess of what looked like bad mutations in the mammoth from Wrangel Island. There is a long history of theoretical work about how genomes might change in small populations. Here we got a rare chance to look at snapshots of genomes 'before' and 'after' a population decline in a single species. The results we found were consistent with this theory that had been discussed for decades.

The mammoth genome analysis was also a great project to do with Monty Slatkin. He has spent his career developing mathematical models of how genomes will look different when population conditions change. With only two specimens to look at, these mathematical models were important to show that the differences between the two mammoths are too extreme to be explained by other factors."

From Science Daily

Ancient peoples shaped the Amazon rainforest

Amazon rainforest in Tambopata reserve, Peru
We often think of the Amazon rainforest as a vast expanse of nature untouched by humans. But a new study in Science suggests that's not true -- in fact, today's rainforest is shaped by trees that were cultivated by indigenous peoples thousands of years ago.

"Some of the tree species that are abundant in Amazonian forests today, like cacao, açaí, and Brazil nut, are probably common because they were planted by people who lived there long before the arrival of European colonists," says Nigel Pitman, the Mellon Senior Conservation Ecologist at Chicago's Field Museum and a co-author of the study.

The team made the discovery by overlaying data from more than 1,000 forest surveys on a map of more than 3,000 archaeological sites across the Amazon. By comparing forest composition at varying distances from archaeological sites, the analysis generated the first Amazon-wide picture of how pre-Columbian peoples influenced Amazonian biodiversity. The study focused on 85 tree species known to have been domesticated by Amazonian peoples for food, shelter, or other uses over the last several thousand years. The researchers found that throughout the Amazon basin, these species were five times more likely to be common in mature upland forests than non-domesticated species. In some parts of the basin, domesticated species were found to be both more common and more diverse in forests closer to archaeological sites.

"That's even the case for some really remote, mature forests that we'd typically assumed to be pristine and undisturbed," says Pitman.

The finding promises to heat up a long-simmering debate among scientists about how thousands of years of human settlement in the Amazon basin have influenced modern-day patterns of Amazonian biodiversity. The immense size of Amazonian forests has historically hampered archaeological research and given the impression of an untouched landscape, but a large number of new archaeological sites have been discovered in recent years.

The team, made up by hundreds of ecologists and social scientists worldwide, was led by Carolina Levis, a PhD student at Brazil's National Institute for Amazonian Research and Wagenigen University and Research in the Netherlands. "For many years, ecological studies ignored the influence of pre-Columbian peoples on the forests we see today. We found that a quarter of these domesticated tree species are widely distributed in the basin and dominate large expanses of forest. These species are vital for the livelihood and economy of Amazonian peoples and indicate that the Amazonian flora is in part a surviving heritage of its former inhabitants," says Levis.

The study also pinpointed regions of the Amazon that today concentrate especially high diversities and large populations of domesticated species. Southwestern Amazonia, where large stands of Brazil nut trees remain a foundation of local residents' livelihoods, is one such example. Other regions showed fewer domesticated species, or a weaker relationship between domesticated species and archeological sites, highlighting the need for more research on the history of Amazonian settlement. The degree to which the recent history of Amazonian settlement has affected the distribution and abundance of domesticated species in the Amazon also remains to be studied.

While the small number of domesticated species used in the study was sufficient to reveal a strong human signal in modern forests, the authors point out that the signal may be even stronger than they documented, since hundreds of other Amazonian tree species were used by pre-Colombian peoples and also deserve study. Untangling the complex interplay of historical, environmental, and ecological factors structuring the 16,000-species Amazonian tree flora remains a focus of the team's work.

Read more at Science Daily

Mar 1, 2017

Shedding new light on the evolution of the squid

Belemnoteuthis antiquus NHM OR25966, a 166 million year old exceptionally preserved extinct squid-relative was found near Bristol (Christian Malford). These ancient cephalopods with their large internal shell were not as fast as their recently evolved relatives, which survived until today's squid and cuttlefish.
Octopus, cuttlefish and squid are well known in the invertebrate world. With their ink-squirting decoy technique, ability to change colour, bizarre body plan and remarkable intelligence they highlight that lacking a back-bone doesn't always mean lacking sophistication.

Examining their deep evolutionary past, researchers have been spoiled by their generous fossil record, as demonstrated by drawer after drawer of ammonites and belemnites in every natural history museum shop. But, the mostly shell-less modern cephalopods have been less easy to understand.

Now a new study, led by researchers from the University of Bristol, has found out how these remarkable creatures evolved by comparing their fossil records with the evolutionary history chronicled in their gene sequences to shed light on their origins.

Published in Proceedings of the Royal Society B, it shows that the cephalopods diversified into the familiar modern octopuses, cuttlefish and squid during a time of great change in the marine world, known as the Mesozoic Marine Revolution, 160 to 100 million years in the past.

Lead author, Al Tanner, a PhD student at the University of Bristol's School of Biological Sciences, is a molecular biologist and bioinformatician at the Bristol Palaeobiology Research Group -- a world leading evolutionary research group.

He said: "On land this was the time of the dinosaurs, but beneath the seas, ecologies were changing rapidly. Fish, squid and their predators were locked in evolutionary 'arms-races', leading to increasingly speedy and agile predators and prey.

"The cephalopods are now known to have also been caught up in this major transition, evolving to lose the shells of their ancestors and develop as dynamic and uniquely adapted marine animals."

The researchers used a technique called molecular clocks to investigate the timing of when the groups split from each other. Bristol co-author, Professor Davide Pisani, added: "Complex Bayesian models take all sorts of information into account to build a tree of evolutionary time.

"The key element of molecular clocks though is the fact that mutations steadily accumulate in genetic material over time -- so by figuring out how many mutations per million years you find, and how it may vary between different groups, we can estimate evolutionary time."

Al Tanner said: "The molecular clock results can be compared to the fossil record. What we see is that while there is some uncertainty in molecular clock estimates, octopuses and squid appear during the Mesozoic Marine Revolution and the two lines of evidence come together to tell the tale of evolution."

Co-author Dr Jakob Vinther said: "By having a reduced internal skeleton compared to their ancient relatives, the modern squids and octopuses could compress their body and more efficiently jet away leaving a baffling cloud of ink with the attacking predator. Before the predator realises what has happened and gains clear view again, the squid is far out of sight."

Read more at Science Daily

Stars regularly ripped apart by black holes in colliding galaxies

Black hole
Astronomers based at the University of Sheffield have found evidence that stars are ripped apart by supermassive black holes 100 times more often than previously thought.

Until now, such stellar cannibalism -- known as Tidal Distruption Events, or TDEs -- had only been found in surveys which observed many thousands of galaxies, leading astronomers to believe they were exceptionally rare: only one event every 10,000 to 100,000 years per galaxy.

However, the pioneering study conducted by leading scientists from the University's Department of Physics and Astronomy, recorded a star being destroyed by a supermassive black hole in a survey of just 15 galaxies -- an extremely small sample size by astronomy standards.

"Each of these 15 galaxies is undergoing a 'cosmic collision' with a neighbouring galaxy," said Dr James Mullaney, Lecturer in Astronomy and co-author of the study.

"Our surprising findings show that the rate of TDEs dramatically increases when galaxies collide. This is likely due to the fact that the collisions lead to large numbers of stars being formed close to the central supermassive black holes in the two galaxies as they merge together."

The supermassive black holes that lurk in the hearts of all large galaxies can be elusive. This is because they don't shine in a conventional sense due to their gravity being so strong that nothing can escape, not even light itself. However, the release of energy as stars are ripped apart when they move close to the black holes leads to dramatic flares. The galaxies' nuclei can then appear as bright as all the billions of stars in a typical galaxy combined. In this way, TDEs can be used to locate otherwise dim black holes and study their strong gravity and how they accrete matter.

"Our team first observed the 15 colliding galaxies in the sample in 2005, during a previous project," said Rob Spence, University of Sheffield PhD student and co-author of the study.

"However, when we observed the sample again in 2015, we noticed that one galaxy -- F01004-2237 -- appeared strikingly different. This led us to look at data from the Catalina Sky Survey, which monitors the brightness of objects in the sky over time. We found that in 2010, the brightness of F01004-2237 flared dramatically."

The particular combination of variability and post-flare spectrum observed in F01004-2237 -- which is 1.7 billion light years from Earth -- was unlike any known supernova or active galactic nucleus, but characteristic of TDEs.

Clive Tadhunter, Professor of Astrophysics and leader of the study, said: "Based on our results for F01004-2237, we expect that TDE events will become common in our own Milky Way galaxy when it eventually merges with the neighbouring Andromeda galaxy in about 5 billion years.

Read more at Science Daily

World's oldest fossils unearthed

Rounded-shaped laminated iron-carbonate (orange) with white chert and black oxide and silicate layers in the Nuvvuagittuq Supracrustal Belt, Québec, Canada. This outcrop may have been part of a hydrothermal vent structure.
Remains of microorganisms at least 3,770 million years old have been discovered by an international team led by UCL scientists, providing direct evidence of one of the oldest life forms on Earth.

Tiny filaments and tubes formed by bacteria that lived on iron were found encased in quartz layers in the Nuvvuagittuq Supracrustal Belt (NSB), Quebec, Canada.

The NSB contains some of the oldest sedimentary rocks known on Earth which likely formed part of an iron-rich deep-sea hydrothermal vent system that provided a habitat for Earth's first life forms between 3,770 and 4,300 million years ago. "Our discovery supports the idea that life emerged from hot, seafloor vents shortly after planet Earth formed. This speedy appearance of life on Earth fits with other evidence of recently discovered 3,700 million year old sedimentary mounds that were shaped by microorganisms," explained first author, PhD student Matthew Dodd (UCL Earth Sciences and the London Centre for Nanotechnology).

Published today in Nature and funded by UCL, NASA, Carnegie of Canada and the UK Engineering and Physical Sciences Research Council, the study describes the discovery and the detailed analysis of the remains undertaken by the team from UCL, the Geological Survey of Norway, US Geological Survey, The University of Western Australia, the University of Ottawa and the University of Leeds.

Prior to this discovery, the oldest microfossils reported were found in Western Australia and dated at 3,460 million years old but some scientists think they might be non-biological artefacts in the rocks. It was therefore a priority for the UCL-led team to determine whether the remains from Canada had biological origins.

The researchers systematically looked at the ways the tubes and filaments, made of haematite -- a form of iron oxide or 'rust' -- could have been made through non-biological methods such as temperature and pressure changes in the rock during burial of the sediments, but found all of the possibilities unlikely.

The haematite structures have the same characteristic branching of iron-oxidising bacteria found near other hydrothermal vents today and were found alongside graphite and minerals like apatite and carbonate which are found in biological matter including bones and teeth and are frequently associated with fossils.

They also found that the mineralised fossils are associated with spheroidal structures that usually contain fossils in younger rocks, suggesting that the haematite most likely formed when bacteria that oxidised iron for energy were fossilised in the rock.

"We found the filaments and tubes inside centimetre-sized structures called concretions or nodules, as well as other tiny spheroidal structures, called rosettes and granules, all of which we think are the products of putrefaction. They are mineralogically identical to those in younger rocks from Norway, the Great Lakes area of North America and Western Australia," explained study lead, Dr Dominic Papineau (UCL Earth Sciences and the London Centre for Nanotechnology).

"The structures are composed of the minerals expected to form from putrefaction, and have been well documented throughout the geological record, from the beginning until today. The fact we unearthed them from one of the oldest known rock formations, suggests we've found direct evidence of one of Earth's oldest life forms. This discovery helps us piece together the history of our planet and the remarkable life on it, and will help to identify traces of life elsewhere in the universe."

Read more at Science Daily

Astronomy: Dark matter mapped

This is a 3-D visualization of reconstructed dark matter clump distributions in a distant galaxy cluster, obtained from the Hubble Space Telescope Frontier Fields data. The unseen matter in this map is comprised of a smooth heap of dark matter on which clumps form.
A Yale-led team has produced one of the highest-resolution maps of dark matter ever created, offering a detailed case for the existence of cold dark matter -- sluggish particles that comprise the bulk of matter in the universe.

The dark matter map is derived from Hubble Space Telescope Frontier Fields data of a trio of galaxy clusters that act as cosmic magnifying glasses to peer into older, more distant parts of the universe, a phenomenon known as gravitational lensing.

Yale astrophysicist Priyamvada Natarajan led an international team of researchers that analyzed the Hubble images. "With the data of these three lensing clusters we have successfully mapped the granularity of dark matter within the clusters in exquisite detail," Natarajan said. "We have mapped all of the clumps of dark matter that the data permit us to detect, and have produced the most detailed topological map of the dark matter landscape to date."

Scientists believe dark matter -- theorized, unseen particles that neither reflect nor absorb light, but are able to exert gravity -- may comprise 80% of the matter in the universe. Dark matter may explain the very nature of how galaxies form and how the universe is structured. Experiments at Yale and elsewhere are attempting to identify the dark matter particle; the leading candidates include axions and neutralinos.

"While we now have a precise cosmic inventory for the amount of dark matter and how it is distributed in the universe, the particle itself remains elusive," Natarajan said.

Dark matter particles are thought to provide the unseen mass that is responsible for gravitational lensing, by bending light from distant galaxies. This light bending produces systematic distortions in the shapes of galaxies viewed through the lens. Natarajan's group decoded the distortions to create the new dark matter map.

Significantly, the map closely matches computer simulations of dark matter theoretically predicted by the cold dark matter model; cold dark matter moves slowly compared to the speed of light, while hot dark matter moves faster. This agreement with the standard model is notable given that all of the evidence for dark matter thus far is indirect, said the researchers.

Read more at Science Daily

'Habitable' Exoplanets Might Not Be Very Earth-Like After All

One of the most exciting moments in exoplanet science came in late February, when NASA's Spitzer Space Telescope announced the discovery of seven rocky planets orbiting in or near the habitable zone of their parent star, TRAPPIST-1, which lies 40 light years away from Earth.

"The discovery sets a new record for greatest number of habitable-zone planets found around a single star outside our solar system," NASA said in a statement. "All of these seven planets could have liquid water — key to life as we know it — under the right atmospheric conditions, but the chances are highest with the three in the habitable zone."

Comparing the habitability of our own planet to the conditions on newly-discovered exoplanets, however, could be misleading, according to the authors of a commentary in the journal Nature Astronomy. They argue that even though scientists have found hundreds of Earth-sized planets, there is no available technology to show us if their surfaces are remotely Earth-like.

Lead author Elizabeth Tasker said the language used by NASA and others can be "unnecessary and dangerous," in the sense that the public could get overly hopeful that life exists on these other planets.

Tasker, who is an associate professor in the department of solar system science at the Japan Aerospace Exploration Agency, was not involved in the TRAPPIST-1 discovery.

Artist's impression of Gliese 832 c, which some scientists consider a potentially habitable exoplanet, shown to scale with Earth. The announcement of Gliese 832 c was an impeteus for a new paper that criticizes habitability metrics used by exoplanet scientists.
In studying the data, however, she noted that the team found that many of the planets orbit in resonant configurations, meaning that one planet's orbit is a direct ratio of another. In other words: The inner planet in the TRAPPIST-1 system, for example, orbits eight times in the period it takes the outer planet to orbit two.

Tasker said this probably suggests these worlds formed further out from the star and over the years, their mutual gravitational attraction pulled them in closer. "They may not be terrestrial planets, but maybe the cores of gas giants because they formed in a similar region to our own solar system," she said.

Tasker's interest in the habitability of new-found planets sprung from the announcement of Gliese 832c in 2014. In the scientific paper announcing the discovery of the planet, the authors cautioned that this "super-Earth" is more likely a "super-Venus" with a massive atmosphere. On Venus, the surface roasts at oven temperatures and can crush unprotected spacecraft in moments. Yet, Tasker said that many of the media stories fawned over Gliese 832c as a potentially habitable world.

Tasker said the oversimplification of comparing exoplanets to our own planet arises from something called the Earth similarity index. The index uses four parameters: the radius of the planet, the radius of Earth, the stellar flux (or radiation) of the exoplanet's star, and the solar flux of our own sun. This metric is used by entities such as the Planetary Habitability Laboratory at the University of Puerto Rico at Arecibo, which ranks planets on a habitability index.

"In practice, these [parameters] aren't independent," Tasker said. For example, the flux coming from the star gives equilibrium temperature, which is different from planetary surface temperature — and doesn't take into account how much radiation the planet receives, she said.

Read more at Discovery News

Feb 28, 2017

Newfound primate teeth take a big bite out of the evolutionary tree of life

The new species Ramadapis sahnii existed 11 to 14 million years ago and is a member of the ancient Sivaladapidae primate family. It consumed leaves and was about the size of a house cat.
Fossil hunters have found part of an ancient primate jawbone related to lemurs -- the primitive primate group distantly connected to monkeys, apes and humans, a USC researcher said.

Biren Patel, an associate professor of clinical cell and neurobiology at the Keck School of Medicine of USC, has been digging for fossils in a paleontologically rich area of Kashmir in northern India for six years. Although paleontologists have scoured this region for a century, relics of small extinct primates were rarely found or studied.

Scientists named the new species Ramadapis sahnii and said that it existed 11 to 14 million years ago. It is a member of the ancient Sivaladapidae primate family, consumed leaves and was about the size of a house cat, said Patel, co-author of the new study in the Journal of Human Evolution.

"Among the primates, the most common ones in the Kashmir region are from a genus called Sivapithecus, which were ancestral forms of orangutans," Patel said. "The fossil we found is from a different group on the primate family tree -- one that is poorly known in Asia. We are filling an ecological and biogeographical gap that wasn't really well documented. Every little step adds to the understanding of our human family tree because we're also primates."

The last primate found in the area was 38 years ago. So, in addition to being a new species, this is the first primate fossil found in the area in decades.

"In the past, people were interested in searching for big things -- things they could show off to other people," Patel said. "A lot of the small fossils were not on their radar."

The inch-and-a-quarter partial mandible belongs to a primate weighing less than 11 pounds that had outlived its other adapidae cousins found in North America, Europe and Africa by millions of years.

"New primates are always a hot topic, and this one is the first of its kind from its area in Asia, which has significant consequences for understanding primate evolution in the Old World," said Michael Habib, an assistant professor of clinical cell and neurobiology at the Keck School of Medicine who was not involved in the study.

The question that remains is how the ecosystem in northern India supported this species when its relatives elsewhere were disappearing or had already gone extinct. Future fieldwork and recovering more fossil primates will help answer this question.

"People want to know about human origins, but to fully understand human origins, you need to understand all of primate origins, including the lemurs and these Sivaladapids," Patel said. "Lemurs and sivaladapids are sister groups to what we are -- the anthropoids -- and we are all primates."

Read more at Science Daily

Scientists reach back in time to discover some of the most power-packed galaxies

In the heart of an active galaxy, matter falling toward a supermassive black hole generates jets of particles traveling near the speed of light.
When the universe was young, a supermassive black hole -- bloated to the bursting point with stupendous power -- heaved out a jet of particle-infused energy that raced through the vastness of space at nearly the speed of light.

Billions of years later, a trio of Clemson University scientists, led by College of Science astrophysicist Marco Ajello, has identified this black hole and four others similar to it that range in age from 1.4 billion to 1.9 billion years old. These objects emit copious gamma rays, light of the highest energy, that are billions of times more energetic than light that is visible to the human eye.

The previously known earliest gamma-ray blazars -- a type of galaxy whose intense emission is powered by extremely powerful relativistic jets launched by monstrous black holes -- were more than 2 billion years old. Currently, the universe is estimated to be approximately 14 billion years old.

"The discovery of these supermassive black holes, which launch jets that emit more energy in one second than our sun will produce in its entire lifetime, was the culmination of a yearlong research project," said Ajello, who has spent much of his career studying the evolution of distant galaxies. "Our next step is to increase our understanding of the mechanisms involved in the formation, development and activities of these amazing objects, which are the most powerful accelerators in the universe. We can't even come close to replicating such massive outputs of energy in our laboratories. The complexities we're attempting to unravel seem almost as mysterious as the black holes themselves."

Ajello conducted his research in conjunction with Clemson post-doc Vaidehi Paliya and Ph.D candidate Lea Marcotulli. The trio worked closely with the Fermi-Large Area Telescope collaboration, which is an international team of scientists that includes Roopesh Ojha, an astronomer at NASA's Goddard Space Flight Center in Greenbelt, Maryland; and Dario Gasparrini of the Italian Space Agency.

The Clemson team's breakthroughs were made possible by recently juiced-up software on NASA's Fermi Gamma-ray Telescope. The refurbished software significantly boosted the orbiting telescope's sensitivity to a level that made these latest discoveries possible.

"People are calling it the cheapest refurbishment in history," Ajello said. "Normally, for the Hubble Space Telescope, NASA had to send someone up to space to physically make these kinds of improvements. But in this case, they were able to do it remotely from an Earth-bound location. And of equal importance, the improvements were retroactive, which meant that the previous six years of data were also entirely reprocessed. This helped provide us with the information we needed to complete the first step of our research and also to strive onward in the learning process."

Using Fermi data, Ajello and Paliya began with a catalog of 1.4 million quasars, which are galaxies that harbor at their centers active supermassive black holes. Over the course of a year, they narrowed their search to 1,100 objects. Of these, five were finally determined to be newly discovered gamma-ray blazars that were the farthest away -- and youngest -- ever identified.

"After using our filters and other devices, we were left with about 1,100 sources. And then we did the diagnostics for all of these and were able to narrow them down to 25 to 30 sources," Paliya said. "But we still had to confirm that what we had detected was scientifically authentic. So we performed a number of other simulations and were able to derive properties such as black hole mass and jet power. Ultimately, we confirmed that these five sources were guaranteed to be gamma-ray blazars, with the farthest one being about 1.4 billion years old from the beginning of time."

Marcotulli, who joined Ajello's group as a Ph.D student in 2016, has been studying the blazars' mechanisms by using images and data delivered from another orbiting NASA telescope, the Nuclear Spectroscopic Telescope Array (NuSTAR). At first, Marcotulli's role was to understand the emission mechanism of gamma-ray blazars closer to us. Now she is turning her attention toward the most distant objects in a quest to understand what makes them so powerful.

"We're trying to understand the full spectrum of the energy distribution of these objects by using physical models," Marcotulli said. "We are currently able to model what's happening far more accurately than previously devised, and eventually we'll be able to better understand what processes are occurring in the jets and which particles are radiating all the energy that we see. Are they electrons? Or protons? How are they interacting with surrounding photons? All these parameters are not fully understood right now. But every day we are deepening our understanding."

All galaxies have black holes at their centers -- some actively feeding on the matter surrounding them, others lying relatively dormant. Our own galaxy has at its center a super-sized black hole that is currently dormant. Ajello said that only one of every 10 black holes in today's universe are active. But when the universe was much younger, it was closer to a 50-50 ratio.

The supermassive black holes at the center of the five newly discovered blazar galaxies are among the largest types of black holes ever observed, on the order of hundreds of thousands to billions of times the mass of our own sun. And their accompanying accretion disks -- rotating swirls of matter that orbit the black holes -- emit more than two trillion times the energy output of our sun.

One of the most surprising elements of Ajello's research is how quickly -- by cosmic measures -- these supersized black holes must have grown in only 1.4 billion years. In terms of our current knowledge of how black holes grow, 1.4 billion years is barely enough time for a black hole to reach the mass of the ones discovered by Ajello's team.

Read more at Science Daily

Spontaneous 'dust traps:' Astronomers discover a missing link in planet formation

An image of a protoplanetary disk, made using results from the new model, after the formation of a spontaneous dust trap, visible as a bright dust ring. Gas is depicted in blue and dust in red.
Planets are thought to form in the disks of dust and gas found around young stars. But astronomers have struggled to assemble a complete theory of their origin that explains how the initial dust develops into planetary systems. A French-UK-Australian team now think they have the answer, with their simulations showing the formation of 'dust traps' where pebble-sized fragments collect and stick together, to grow into the building blocks of planets. They publish their results in Monthly Notices of the Royal Astronomical Society.

Our Solar system, and other planetary systems, began life with disks of gas and dust grains around a young star. The processes that convert these tiny grains, each a few millionths of a metre (a micron) across, into aggregates a few centimetres in size, and the mechanism for making kilometre-sized 'planetesimals' into planetary cores, are both well understood.

The intermediate stage, taking pebbles and joining them together into objects the size of asteroids, is less clear, but with more than 3,500 planets already found around other stars, the whole process must be ubiquitous.

Dr Jean-Francois Gonzalez, of the Centre de Recherche Astrophysique de Lyon, in France, led the new work. He comments: "Until now we have struggled to explain how pebbles can come together to form planets, and yet we've now discovered huge numbers of planets in orbit around other stars. That set us thinking about how to solve this mystery."

There are two main barriers that need to be overcome for pebbles to become planetesimals. Firstly the drag of gas on dust grains in a disk makes them drift rapidly towards the central star, where they are destroyed, leaving no material to form planets. The second challenge is that growing grains can be broken up in high-speed collisions, breaking them into a large number of smaller pieces and reversing the aggregation process.

The only locations in planet forming disks where these problems can be overcome are so-called 'dust traps'. In these high-pressure regions, the drift motion slows, allowing dust grains to accumulate. With their reduced velocity, the grains can also avoid fragmentation when they collide.

Until now, astronomers thought that dust traps could only exist in very specific environments, but the computer simulations run by the team indicate that they are very common. Their model pays particular attention to the way the dust in a disk drags on the gas component. In most astronomical simulations, gas causes the dust to move, but sometimes, in the dustiest settings, the dust acts more strongly on the gas.

This effect, known as aerodynamic drag back-reaction, is usually negligible, so up to now has been ignored in studies of growing and fragmenting grains. But its effects become important in dust rich environments, like those found where planets are forming.

The effect of the back-reaction is to slow the inward drift of the grains, which gives them time to grow in size. Once large enough, the grains are their own masters, and the gas can no longer govern their motion. The gas, under the influence of this back-reaction, will be pushed outwards and form a high-pressure region: the dust trap. These spontaneous traps then concentrate the grains coming from the outer disk regions, creating a very dense ring of solids, and giving a helping hand to the formation of planets.

Gonzalez concludes: "We were thrilled to discover that, with the right ingredients in place, dust traps can form spontaneously, in a wide range of environments. This is a simple and robust solution to a long standing problem in planet formation."

Read more at Science Daily

Volcanic hydrogen spurs chances of finding exoplanet life

Night sky.
Hunting for habitable exoplanets now may be easier: Cornell University astronomers report that hydrogen pouring from volcanic sources on planets throughout the universe could improve the chances of locating life in the cosmos.

Planets located great distances from stars freeze over. "On frozen planets, any potential life would be buried under layers of ice, which would make it really hard to spot with telescopes," said lead author Ramses Ramirez, research associate at Cornell's Carl Sagan Institute. "But if the surface is warm enough -- thanks to volcanic hydrogen and atmospheric warming -- you could have life on the surface, generating a slew of detectable signatures."

Combining the greenhouse warming effect from hydrogen, water and carbon dioxide on planets sprinkled throughout the cosmos, distant stars could expand their habitable zones by 30 to 60 percent, according to this new research. "Where we thought you would only find icy wastelands, planets can be nice and warm -- as long as volcanoes are in view," said Lisa Kaltenegger, Cornell professor of astronomy and director of the Carl Sagan Institute.

Their research, "A Volcanic Hydrogen Habitable Zone," published in the Astrophysical Journal Letters.

The idea that hydrogen can warm a planet is not new, but an Earth-like planet cannot hold onto its hydrogen for more than a few million years. Volcanoes change the concept. "You get a nice big warming effect from volcanic hydrogen, which is sustainable as long as the volcanoes are intense enough," said Ramirez, who suggested the possibility that these planets may sustain detectable life on their surface.

A very light gas, hydrogen also "puffs up" planetary atmospheres, which will likely help scientists detect signs of life. "Adding hydrogen to the air of an exoplanet is a good thing if you're an astronomer trying to observe potential life from a telescope or a space mission. It increases your signal, making it easier to spot the makeup of the atmosphere as compared to planets without hydrogen," said Ramirez.

In our solar system, the habitable zone extends to 1.67 times the Earth-sun distance, just beyond the orbit of Mars. With volcanically sourced hydrogen on planets, this could extend the solar system's habitable zone reach to 2.4 times the Earth-sun distance -- about where the asteroid belt is located between Mars and Jupiter. This research places a lot of planets that scientists previously thought to be too cold to support detectable life back into play.

"We just increased the width of the habitable zone by about half, adding a lot more planets to our 'search here' target list," said Ramirez.

Atmospheric biosignatures, such as methane in combination with ozone -- indicating life -- will likely be detected by the forthcoming, next-generation James Webb Space Telescope, launching in 2018, or the approaching European Extremely Large Telescope, first light in 2024.

Last week, NASA reported finding seven Earth-like planets around the star Trappist-1. "Finding multiple planets in the habitable zone of their host star is a great discovery because it means that there can be even more potentially habitable planets per star than we thought," said Kaltenegger. "Finding more rocky planets in the habitable zone -- per star -- increases our odds of finding life."

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Feb 27, 2017

Saturn's rings viewed in the mid-infrared show bright Cassini division

A three-color composite of the mid-infrared images of Saturn on Jan. 23, 2008 captured with COMICS on the Subaru Telescope. The Cassini Division and the C ring appear bright. Color differences reflect the temperatures; the warmer part is blue, the cooler part is red.
A team of researchers has succeeded in measuring the brightnesses and temperatures of Saturn's rings using the mid-infrared images taken by the Subaru Telescope in 2008. The images are the highest resolution ground-based views ever made. They reveal that, at that time, the Cassini Division and the C ring were brighter than the other rings in the mid-infrared light and that the brightness contrast appeared to be the inverse of that seen in the visible light. The data give important insights into the nature of Saturn's rings.

The beautiful appearance of Saturn and its rings has always fascinated people. The rings consist of countless numbers of ice particles orbiting above Saturn's equator. However, their detailed origin and nature remain unknown. Spacecraft- and ground-based telescopes have tackled that mystery with many observations at various wavelengths and methods. The international Cassini mission led by NASA has been observing Saturn and its rings for more than 10 years, and has released a huge number of beautiful images.

Subaru Views Saturn

The Subaru Telescope also has observed Saturn several times over the years. Dr. Hideaki Fujiwara, Subaru Public Information Officer/Scientist, analyzed data taken in January 2008 using the Cooled Mid-Infrared Camera and Spectrometer (COMICS) on the telescope to produce a beautiful image of Saturn for public information purposes. During the analysis, he noticed that the appearance of Saturn's rings in the mid-infrared part of the spectrum was totally different from what is seen in the visible light

Saturn's main rings consist of the C, B, and A rings, each with different populations of particles. The Cassini Division separates the B and A rings. The 2008 image shows that the Cassini Division and the C ring are brighter in the mid-infrared wavelengths than the B and A rings appear to be. This brightness contrast is the inverse of how they appear in the visible light, where the B and A rings are always brighter than the Cassini Division and the C ring.

"Thermal emission" from ring particles is observed in the mid-infrared, where warmer particles are brighter. The team measured the temperatures of the rings from the images, which revealed that the Cassini Division and the C ring are warmer than the B and A rings. The team concluded that this was because the particles in the Cassini Division and C ring are more easily heated by solar light due to their sparser populations and darker surfaces.

On the other hand, in the visible light, observers see sunlight being reflected by the ring particles. Therefore, the B and A rings, with their dense populations of particles, always seem bright in the visible wavelengths, while the Cassini Division and the C ring appear faint. The difference in the emission process explains the inverse brightnesses of Saturn's rings between the mid-infrared and the visible-light views.

Changing Angles Change the Brightnesses

It turns out that the Cassini Division and the C ring are not always brighter than the B and A rings, even in the mid-infrared. The team investigated images of Saturn's rings taken in April 2005 with COMICS, and found that the Cassini Division and the C ring were fainter than the B and A rings at that time, which is the same contrast to what was seen in the visible light.

The team concluded that the "inversion" of the brightness of Saturn's rings between 2005 and 2008 was caused by the seasonal change in the ring opening angle to the Sun and Earth. Since the rotation axis of Saturn inclines compared to its orbital plane around the Sun, the ring opening angle to the Sun changes over a 15-year cycle. This makes a seasonal variation in the solar heating of the ring particles. The change in the opening angle viewed from the Earth affects the apparent filling factor of the particles in the rings. These two variations -- the temperature and the observed filling factor of the particles -- led to the change in the mid-infrared appearance of Saturn's rings.

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Mars More Earth-like than moon-like

This is a solidified lava flow over the side of a crater rim of Elysium.
Mars' mantle may be more complicated than previously thought. In a new study published in the Nature-affiliated journal Scientific Reports, researchers at LSU document geochemical changes over time in the lava flows of Elysium, a major martian volcanic province.

LSU Geology and Geophysics graduate researcher David Susko led the study with colleagues at LSU including his advisor Suniti Karunatillake, the University of Rahuna in Sri Lanka, the SETI Institute, Georgia Institute of Technology, NASA Ames, and the Institut de Recherche en Astrophysique et Planétologie in France.

They found that the unusual chemistry of lava flows around Elysium is consistent with primary magmatic processes, such as a heterogeneous mantle beneath Mars' surface or the weight of the overlying volcanic mountain causing different layers of the mantle to melt at different temperatures as they rise to the surface over time.

Elysium is a giant volcanic complex on Mars, the second largest behind Olympic Mons. For scale, it rises to twice the height of Earth's Mount Everest, or approximately 16 kilometers. Geologically, however, Elysium is more like Earth's Tibesti Mountains in Chad, the Emi Koussi in particular, than Everest. This comparison is based on images of the region from the Mars Orbiter Camera, or MOC, aboard the Mars Global Surveyor, or MGS, Mission.

Elysium is also unique among martian volcanoes. It's isolated in the northern lowlands of the planet, whereas most other volcanic complexes on Mars cluster in the ancient southern highlands. Elysium also has patches of lava flows that are remarkably young for a planet often considered geologically silent.

"Most of the volcanic features we look at on Mars are in the range of 3-4 billion years old," Susko said. "There are some patches of lava flows on Elysium that we estimate to be 3-4 million years old, so three orders of magnitude younger. In geologic timescales, 3 million years ago is like yesterday."

In fact, Elysium's volcanoes hypothetically could still erupt, Susko said, although further research is needed to confirm this. "At least, we can't yet rule out active volcanoes on Mars," Susko said. "Which is very exciting."

Susko's work in particular reveals that the composition of volcanoes on Mars may evolve over their eruptive history. In earlier research led by Karunatillake, assistant professor in LSU's Department of Geology and Geophysics, researchers in LSU's Planetary Science Lab, or PSL, found that particular regions of Elysium and the surrounding shallow subsurface of Mars are geochemically anomalous, strange even relative to other volcanic regions on Mars. They are depleted in the radioactive elements thorium and potassium. Elysium is one of only two igneous provinces on Mars where researchers have found such low levels of these elements so far.

"Because thorium and potassium are radioactive, they are some of the most reliable geochemical signatures that we have on Mars," Susko said. "They act like beacons emitting their own gamma photons. These elements also often couple in volcanic settings on Earth."

In their new paper, Susko and colleagues started to piece together the geologic history of Elysium, an expansive volcanic region on Mars characterized by strange chemistry. They sought to uncover why some of Elysium's lava flows are so geochemically unusual, or why they have such low levels of thorium and potassium. Is it because, as other researchers have suspected, glaciers located in this region long ago altered the surface chemistry through aqueous processes? Or is it because these lava flows arose from different parts of Mars' mantle than other volcanic eruptions on Mars?

Perhaps the mantle has changed over time, meaning that more recent volcanic eruption flows differ chemically from older ones. If so, Susko could use Elysium's geochemical properties to study how Mars' bulk mantle has evolved over geologic time, with important insights for future missions to Mars. Understanding the evolutionary history of Mars' mantle could help researchers gain a better understanding of what kinds of valuable ores and other materials could be found in the crust, as well as whether volcanic hazards could unexpectedly threaten human missions to Mars in the near future. Mars' mantle likely has a very different history than Earth's mantle because the plate tectonics on Earth are absent on Mars as far as researchers know. The history of the bulk interior of the red planet also remains a mystery.

Susko and colleagues at LSU analyzed geochemical and surface morphology data from Elysium using instruments on board NASA's Mars Odyssey Orbiter (2001) and Mars Reconnaissance Orbiter (2006). They had to account for the dust that blankets Mars' surface in the aftermath of strong dust storms, to make sure that the shallow subsurface chemistry actually reflected Elysium's igneous material and not the overlying dust.

Through crater counting, the researchers found differences in age between the northwest and the southeast regions of Elysium -- about 850 million years of difference. They also found that the younger southeast regions are geochemically different from the older regions, and that these differences in fact relate to igneous processes, not secondary processes like the interaction of water or ice with the surface of Elysium in the past.

"We determined that while there might have been water in this area in the past, the geochemical properties in the top meter throughout this volcanic province are indicative of igneous processes," Susko said. "We think levels of thorium and potassium here were depleted over time because of volcanic eruptions over billions of years. The radioactive elements were the first to go in the early eruptions. We are seeing changes in the mantle chemistry over time."

"Long-lived volcanic systems with changing magma compositions are common on Earth, but an emerging story on Mars," said James Wray, study co-author and associate professor in the School of Earth and Atmospheric Sciences at Georgia Tech.

Wray led a 2013 study that showed evidence for magma evolution at a different martian volcano, Syrtis Major, in the form of unusual minerals. But such minerals could be originating at the surface of Mars, and are visible only on rare dust-free volcanoes.

"At Elysium we are truly seeing the bulk chemistry change over time, using a technique that could potentially unlock the magmatic history of many more regions across Mars," he said.

Susko speculates that the very weight of Elysium's lava flows, which make up a volcanic province six times higher and almost four times wider than its morphological sister on Earth, Emi Koussi, has caused different depths of Mars' mantle to melt at different temperatures. In different regions of Elysium, lava flows may have come from different parts of the mantle. Seeing chemical differences in different regions of Elysium, Susko and colleagues concluded that Mars' mantle might be heterogeneous, with different compositions in different areas, or that it may be stratified beneath Elysium.

Overall, Susko's findings indicate that Mars is a much more geologically complex body than originally thought, perhaps due to various loading effects on the mantle caused by the weight of giant volcanoes.

"It's more Earth-like than moon-like," Susko said. "The moon is cut and dry. It often lacks the secondary minerals that occur on Earth due to weathering and igneous-water interactions. For decades, that's also how we envisioned Mars, as a lifeless rock, full of craters with a number of long inactive volcanoes. We had a very simple view of the red planet. But the more we look at Mars, the less moon-like it becomes. We're discovering more variety in rock types and geochemical compositions, as seen across the Curiosity Rover's traverse in Gale Crater, and more potential for viable resource utilization and capacity to sustain a human population on Mars. It's much easier to survive on a complex planetary body bearing the mineral products of complex geology than on a simpler body like the moon or asteroids."

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