Apr 6, 2017

Giant viruses may simply be a 'Frankenstein' of smaller viruses

Bubbling nitrifying activated sludge tank at a wastewater treatment plant in Klosterneuburg, Austria. This was the source of the sludge samples used for microcolony sorting.
Viruses have a ubiquitous presence in the world. Their population is estimated to be 1031, 10 times greater than the nonillion (1030) of microbes on the planet -- a figure that surpasses the number of stars in the Milky Way. Giant viruses are characterized by disproportionately large genomes and virions that house the viruses' genetic material. They can encode several genes potentially involved in protein biosynthesis, a unique feature which has led to diverging hypotheses about the origins of these viruses. But after discovering a novel group of giant viruses with a more complete set of translation machinery genes than any other virus known to date, scientists at the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, believe that this group (dubbed "Klosneuviruses") significantly increases our understanding of viral evolution.

The predicted hosts for the Klosneuviruses are protists (single-celled eukaryotic (nucleus-containing) microorganisms) and while their direct impacts on protists are not yet worked out, these giant viruses are thought to have a large impact on these protists that help regulate the planet's biogeochemical cycles. DOE JGI published the findings in the journal Science on April 7, 2017 with collaborators from the National Institutes of Health, University of Vienna, and CalTech.

"The discovery presents virus evolution for us in new ways, vastly expanding our understanding of how many essential host genes viruses can capture during their evolution," said National Institutes of Health evolutionary and computational biologist Eugene Koonin, a study co-author whose lab collaborated with DOE JGI on analyzing the Klosneuvirus genome. "Since protein synthesis is one of the most prominent hallmarks of cellular life, it shows that these new viruses are more 'cell-like' than any virus anyone has ever seen before."

Scientists have been fascinated by giant viruses since 2003, when a group of French biologists led by Didier Raoult discovered the Mimiviruses. Since then, a handful of other giant virus groups have been found. The unique ability among them to encode proteins involved in translation (typically DNA to RNA to protein) piqued researchers' interests as to the origin of giant viruses. Since then, two evolutionary hypotheses have emerged. One posits that giant viruses evolved from an ancient cell, perhaps one from an extinct fourth domain of cellular life. Another -- a scenario championed by Koonin -- presents the idea that giant viruses arose from smaller viruses.

The discovery of Klosneuvirus supports the latter idea, according to Tanja Woyke, DOE JGI Microbial Genomics Program lead and senior author of the paper. "In this scenario, a smaller virus infected different eukaryote hosts and picked up genes encoding translational machinery components from independent sources over long periods of time through piecemeal acquisition," she said.

At first glance, the suite of "cellular" genes in Klosneuvirus seemed to have a common origin, but when analyzing them in detail, the research team observed they came from different hosts. From the evolutionary trees the team built, they noticed that they were acquired by the viruses bit by bit, at different stages in their evolution. The Klosneuvirus genes contained aminoacyl-tRNA (transfer ribonucleic acid) enzymes with specificity for 19 out of 20 amino acids, along with more than 20 tRNAs and an array of translation factors and tRNA modifying enzymes -- an unprecedented finding among all viruses, including the previously known giant viruses.

JGI postdoctoral researcher Frederik Schulz and Woyke unearthed Klosneuvirus while analyzing microcolony sequence data from a wastewater treatment plant sample in Klosterneuburg, Austria. This data was generated under a DOE JGI Community Science Program (CSP) project focused on the diversity of nitrifying bacteria for converting ammonia to nitrate in industrial and sewage waste treatment. "We expected genome sequences of nitrifying bacteria in the microcolony sequence data," Woyke said. "Finding a giant virus genome took the project into a completely new and unexpected, yet very exciting direction."

When Schulz, the study's first author, noticed that several of the metagenomes were viral in origin, he and Woyke conducted analyses to determine their source. They found that the Klosneuvirus group came from a novel viral lineage affiliated with Mimiviruses.

"Mining sequence data in DOE JGI's Integrated Microbial Genomes & Microbiomes system, which houses thousands of metagenomes, allowed us to find evolutionary relatives of our Klosneuvirus," Schulz said. He notes that while the metagenomic discovery of Klosneuviruses helped answer important evolutionary questions, the actual biological function of the translation system genes remains elusive -- at least until these viruses are grown in the laboratory together with their hosts.

Read more at Science Daily

Hubble takes close-up portrait of Jupiter

This dazzling Hubble Space Telescope photo of Jupiter was taken when it was comparatively close to Earth, at a distance of 415 million miles. Hubble reveals the intricate, detailed beauty of Jupiter's clouds as arranged into bands of different latitudes, known as tropical regions. These bands are produced by air flowing in different directions at various latitudes. Lighter colored areas, called zones, are high-pressure where the atmosphere rises. Darker low-pressure regions where air falls are called belts. The planet's trademark, the Great Red Spot, is a long-lived storm roughly the diameter of Earth. Much smaller storms appear as white or brown-colored ovals. Such storms can last as little as a few hours or stretch on for centuries.
On April 3, 2017, as Jupiter made its nearest approach to Earth in a year, NASA's Hubble Space Telescope viewed the solar system's largest planet in all of its up-close glory. At a distance of 415 million miles (668 million kilometers) from Earth, Jupiter offered spectacular views of its colorful, roiling atmosphere, the legendary Great Red Spot, and it smaller companion at farther southern latitudes dubbed "Red Spot Jr."

The giant planet is now at "opposition," positioned directly opposite the sun from the Earth. This means that the sun, Earth and Jupiter line up, with Earth sitting between the sun and the gas giant. Opposition also marks Jupiter's closest point to us, and the planet appears brighter in the night sky than at any other time in the year.

This positioning allowed a team led by Amy Simon of NASA's Goddard Space Flight Center in Greenbelt, Maryland to observe Jupiter using Hubble's Wide Field Camera 3. Hubble photographed exquisite details in Jupiter's atmosphere, as small as about 80 miles (129 kilometers) across.

With its immense and powerful storms and hundreds of smaller vortices, the atmosphere of Jupiter is divided into several distinct, colorful bands, parallel to the equator. These bands, with alternating wind motions, are created by differences in the thickness and height of the ammonia ice clouds; the lighter bands rise higher and have thicker clouds than the darker bands. The bands are separated by winds that can reach speeds of up to 400 miles (644 kilometers) per hour.

Jupiter is best known for the Great Red Spot, an anticyclone that has raged for at least 150 years. This famous storm is larger than Earth. However, the Great Red Spot is slowly shrinking -- a trend seen since the late 1800s. The reason for this phenomenon is still unknown. Hubble will continue to observe Jupiter in hopes of solving this mysterious riddle.

The images are part of the Outer Planets Atmospheres Legacy program or OPAL. This program provides yearly Hubble global views of the outer planets to look for changes in their storms, winds, and clouds. It began in 2014 with Uranus, and has been studying Jupiter and Neptune since 2015. In 2018, it will begin viewing Saturn.

The team timed the Hubble observation to coincide with when NASA's space probe Juno would be near its closest point to Jupiter, so that scientists could get concurrent observations.

The Hubble Space Telescope is a project of international cooperation between NASA and ESA (European Space Agency). NASA's Goddard Space Flight Center in Greenbelt, Maryland, manages the telescope. The Space Telescope Science Institute (STScI) in Baltimore conducts Hubble science operations. STScI is operated for NASA by the Association of Universities for Research in Astronomy, Inc., in Washington, D.C.

From Science Daily

Married couples with common ancestry also share similar genes

When two married people appear similar, it isn't necessarily a coincidence.
When two married people appear similar, it isn't necessarily a coincidence, but may be related to the tendency to marry someone with the same ancestry; a trend that can have important effects on the genetics of different populations, report Ronnie Sebro of the University of Pennsylvania, and senior authors Josée Dupuis from the Boston University School of Public Health and Neil Risch from the University of California, San Francisco, in a study published April 6th, 2017 in PLOS Genetics.

Until recently, most people picked a spouse from within their local community, and that person often had the same ancestry. Over many generations, this affinity for similar mates has created a genetic structure in the population which has the potential to bias the results of genetic studies. In the first investigation into mating patterns across multiple generations within a U.S. population, researchers explored genetic similarity between spouses from three generations of white people in the Framingham Heart Study, an ongoing examination of heart health in the residents of Framingham, Massachusetts, which began in 1948.

Using genomic data, they characterized the ancestry of 879 participant spouse pairs and observed that individuals of Northern European, Southern European and Ashkenazi ancestry preferentially chose spouses of the same background. In each successive generation, however, individuals were less likely to choose a spouse with the same ancestry. They also showed that the mating patterns caused spouses to be more genetically similar to each other than might otherwise be expected, and that the genetic structure created by these mating patterns in the population has decreased over time.

The findings from this study reflect demographic patterns and how they have changed during the past 60 years in Framingham, Massachusetts. Genetic similarity within a population can be important to consider in genomic studies because it can lead to false positives when identifying gene regions that are associated with a disease, and affect estimates of the degree to which a disease is passed on through one's genes.

From Science Daily

Archaeologists Discover Remains of 3,700-Year-Old Egyptian Pyramid

The remains of an Egyptian pyramid built around 3,700 years ago have been discovered near the well-known "bent pyramid" of King Snefru, the antiquities ministry announced on Monday.

The pyramid from the 13th dynasty was found in Dahshur's royal necropolis, some 30 kilometers (20 miles) south of Cairo, it said.

"An alabaster... block engraved with 10 vertical hieroglyphic lines" was among the finds, the ministry said, citing Adel Okasha, director general at the necropolis.

It said granite lintel and stone blocks were discovered that would show more "about the internal structure of the pyramid.”

Excavation is still in its early stages and the size of the pyramid has not yet been established.

Blocks of stone and the beginning of a corridor which was discovered can be seen in photos provided by the ministry.

The corridor "leads to the interior of the pyramid, extended by a ramp and the entrance to a room,"the ministry said.

"All the discovered parts of the pyramid are in very good condition and further excavation is to take place to reveal more parts," it said.

Egypt, home of one of the world's earliest civilizations, boasts 123 ancient pyramids, Zahi Hawass, former head of the Supreme Council of Antiquities, told AFP.

Hawass, who took part in the last discovery of a new pyramid in Egypt in 2008 at Saqqara, just south of Cairo, said the remnants in Dahshur appeared to indicate that the monument belonged to "a queen buried near her husband or her son."

"The hope now is to find any inscription which can reveal the identity of the owner of this pyramid," the archaeologist said. “To find the name of a previously unknown queen would be an addition to history.”

Egypt's ancient treasures include the world-famous Pyramids of Giza, constructed around 4,500 years ago.

The Khufu pyramid, or Great Pyramid, is the largest of the three in Giza, standing at 146 meters (480 feet) tall, and the only surviving structure of the seven wonders of the ancient world.

Khufu and Khafre in Giza along with the Bent and Red pyramids in Dahshur are part of Operation ScanPyramids, with teams scanning the structures in search of hidden rooms and cavities.

The project to unearth still hidden secrets of the pyramids applies a mix of infrared thermography, radiographic imaging and 3D simulation — all of which the researchers say are non-invasive and non-destructive.

In October last year, the team announced that two additional cavities had been found in the Great Pyramid after another scan a year earlier found several thermal anomalies.

Read more at Discovery News

Early Human Cannibals Didn’t Eat Each Other for the Calories

When early humans, including our species, ate their own kind, it was more likely for ritual purposes than for a nourishing meal, according to an unusual study released Thursday.

Carving up the human body to calculate the caloric value of each part, the study argues that prehistoric cannibalism — while less rare than widely assumed — was a dangerous undertaking offering relatively meagre nutritional rewards.

Kilo for kilo, a wild horse, bear, or boar had more than three times the calories in fat and protein than our lean-and-mean human ancestors, who were mostly skin, muscle, and bone, according to the research, published in the journal Scientific Reports.

Moreover, human prey — as wily as the hunter — would surely put up a good fight before being sliced up into filets.

"I did the study because I wanted to know how nutritional we are compared to these other animals," explained James Cole, a senior lecturer in archaeology at the University of Brighton in England.

"That might tell us whether we, and other human species, were doing it for the calories, or if there is some other explanation," he told AFP.

The findings help flesh out the idea that cannibalism among homo sapiens — as well as Neanderthals, homo erectus and other hominins — was suffused with cultural meaning.

Recent scholarship suggests our ancestors, including Neanderthals, had rich cultures, evidenced by artifacts, jewelry and perhaps language.

"It seems unreasonable to think that early humans wouldn't have had as complex an attitude to cannibalism as we modern humans," Cole said. "They may have had as many reasons to consume each other as we do."

"It's not just about the meat," he added.

Sucking the marrow from a leg bone or gnawing on a spleen might have been a way to affirm territorial control and pay homage to deceased family members, Cole said.

"The consumption of the food in that scenario is a kind of bonus," he pointed out.

More broadly, the study suggests that our cave- or savannah-dwelling cousins were probably far more sophisticated than we suspect.

'Brain matter'
A review of the fossil record, along with recent genetic research, shows that cannibalism among hominin species, or early man, was fairly common.

"We don't have a lot of human remains," Cole said. "But even within that small sample, we still see quite a lot of evidence of human modification on those remains — butchery, cut marks on the bone — consistent with cannibalism."

Bones with cut marks at the tendon joints to remove filets of muscle; long arm and leg bones that have been cracked to access the marrow; human teeth marks — all are telltale signs of humans feasting on humans.

The earliest confirmed case of human cannibalism — found in a cave in Spain — features the species homo antecessor and dates back nearly one million years.    

Other research has shown that prehistoric humans developed some immunity to diseases, known as transmissible spongiform encephalopathies (TSE), that are spread by eating infected brain matter.

"The only reason an evolutionary adaptation would develop is if you are over-exposed to the pathogens," Cole said.

That could have arisen when a human ate, say, a lion that had consumed a bovine brain.

The human variant of mad cow disease that erupted in the 1990s spread when people ate beef from cows that had been fed the brains of infected animals.

"Or it comes from eating the brain matter of members of our own species," as is thought to have occurred with the Fore people of Papua New Guinea, who practiced cannibalism.

A wide range of motivations are used to explain modern-day cannibalism, ranging from psychosis (think of the liver-and-fava-bean loving Hannibal Lecter), to warfare, medicine or funerary ritual. Shipwreck and plane crashes can also lead to survival cannibalism.

Read more at Discovery News

Apr 5, 2017

Neptune's journey during early planet formation was 'smooth and calm'

Artist's conception of a loosely tethered binary planetoid pair like those studied by Fraser et al. in this work which led to the conclusion that Neptune's shepherding of them to the Kuiper Belt as gradual and gentle in nature.
Dr Wes Fraser from Queen's led an international research project 'Colours of the Outer Solar Systems Origins Survey' Col-OSSOS, which uses data collected from the Frederick C. Gillett Gemini North Telescope and Canada-France-Hawaii Telescope (CFHT) both on Maunakea in Hawaii. By simultaneously using two world class telescopes, Dr Fraser's team was able to produce unique research with a global impact.

The study focused on the Kuiper Belt -- a region of space beyond the gas giant Neptune. The area holds more than 1,700 known icy objects, which are remnants of the early Solar System. Normally objects that are formed in this area are red in colour.

However, during his research Dr Fraser identified a small number of 'oddball' objects, which stand out as uniquely blue and are zipping around in binary pairs that orbit around each other, like the moon orbits Earth.

Astronomers have always thought that these objects formed in the heart of the Kuiper Belt but Dr Fraser's findings, which have been published in Nature Astronomy, suggest that the blue binaries actually formed in a region much closer to the Sun and were then shepherded by Neptune's gravitational nudges onto their current orbits in the distant Kuiper Belt several billions of years ago.

Dr Fraser's research indicates that when Neptune moved from 20 AU to its current location at 30 AU, this was a very slow and calm movement, which allowed the fragile and loosely bound binaries to be pushed out a similar distance to where they are found currently without being disrupted into two separate single objects.

Discussing the significance of the findings, Dr Fraser said: "This research has opened the window to new aspects of understanding the early stages of planet growth. We now have a solid handle on how and where these blue binaries originated.

"There has been some evidence around how Neptune moved outwards to 30 AU. Our hypothesis about how these blue binaries came to be where they are requires that Neptune's migration was largely a smooth and calm movement.

"This novel programme uses two world-class telescopes: the Gemini-North and Canada-France-Hawaii telescopes, simultaneously. In doing so, we are able to gather comprehensive spectral information spanning the ultra-violet, optical, and near-infrared wavelength ranges. Without this programme and the partners involved, this major research breakthrough would not have been possible."

Meg Schwamb, astronomer at the Gemini Observatory, commented: "Working closely together, Gemini North and the Canada-France-Hawaii telescopes coordinated their movements to observe the Col-OSSOS Kuiper belt objects at nearly the same time."

"These simultaneous observations on Maunakea allowed us to measure the light from the same side of the Kuiper Belt object, removing one of the main challenges in studying Solar System bodies that rotate."

Todd Burdullis, QSO operations specialist at CFHT who helped to co-ordinate the observations, commented: "Facilitating the simultaneous observations with the Col-OSSOS team and Gemini Observatory was challenging, but paved the way for a greater understanding of the origins of these blue binaries.

Read more at Science Daily

10,000 years of genetic continuity in northwest North America, study reveals

Researchers are analyzing DNA from ancient individuals found in southeast Alaska, coastal British Columbia, Washington state and Montana. A new genetic analysis of some of these human remains finds that many of today's indigenous peoples living in the same regions are descendants of ancient individuals dating to at least 10,300 years ago.
A study of the DNA in ancient skeletal remains adds to the evidence that indigenous groups living today in southern Alaska and the western coast of British Columbia are descendants of the first humans to make their home in northwest North America more than 10,000 years ago.

"Our analysis suggests that this is the same population living in this part of the world over time, so we have genetic continuity from 10,000 years ago to the present," said University of Illinois anthropology professor Ripan Malhi, who led the study with University of Chicago postdoctoral researcher John Lindo; Penn State University biology professor Michael DeGiorgio; Rosita Worl, the director of the Sealaska Heritage Institute in Juneau, Alaska; and University of Oklahoma anthropology professor Brian M. Kemp.

The findings, reported in the Proceedings of the National Academy of Sciences, also suggest that these early American peoples had a complex population history, the researchers report.

The new work comes on the heels of earlier studies of ancient Americans that focused on mitochondrial DNA, which occurs outside the nucleus of cells and is passed only from mothers to their offspring.

"Mitochondrial DNA just traces the maternal line -- your mother's mother's lineage -- so, you're missing information about all of these other ancestors," said Lindo, the first author on the paper. "We wanted to analyze the nuclear genome so we could get a better assessment of the population history of this region."

The team looked at genomic data from Shuká Káa (Tlingit for "Man Before Us"), an ancient individual whose remains -- found in a cave in southeastern Alaska -- date to about 10,300 years ago. They also analyzed the genomes of three more individuals from the nearby coast of British Columbia whose remains date to between 6,075 and 1,750 years ago.

"Interestingly, the mitochondrial type that Shuká Káa belonged to was also observed from another ancient skeleton dated to about 6,000 years ago," Kemp said. "It seems to disappear after that. The nuclear DNA suggests that this is probably not about population replacement, but rather chance occurrence through time. If a female has no children or only sons, the mitochondrial DNA is not passed to the next generation. As a male, Shuká Káa could not have passed on his own mitochondrial DNA; he must have had some maternal relatives that did so."

The researchers turned their attention to nuclear DNA, which offers a more comprehensive record of a person's ancestry.

"DNA from the mitochondria and Y chromosome provide unique yet sometimes conflicting stories, but the nuclear genome provides a more comprehensive view of past events," DeGiorgio said.

"The data suggest that there were multiple genetic lineages in the Americas from at least 10,300 years ago," Malhi said.

The descendants of some of those lineages are still living in the same region today, and a few are co-authors on the new study. Their participation is the result of a long-term collaboration between the scientists and several native groups who are embracing genomic studies as a way to learn from their ancestors, said Worl, who is Tlingit, Ch'áak' (Eagle) moiety of the Shangukeidí (Thunderbird) Clan from the Kawdliyaayi Hít (House Lowered From the Sun) in Klukwan, Alaska.

Read more at Science Daily

Bionic Leaf That ‘Bottles Sunlight’ Could Spur the Next Green Revolution

Harvard researchers have invented a so-called “bionic leaf” that produces fertilizer directly in farm soil, an innovation that could one day allow impoverished rural farmers in developing countries to make their own fertilizer on-site, significantly boosting crop yields.

The invention could be used to fight global hunger as populations expand in places like sub-Saharan Africa over the coming decades.

The researchers have already tapped their invention to grow radishes 50 percent larger than control crops raised without fertilizer, according to Dr. Daniel Nocera, who presented the findings at a press conference in San Francisco.

“I’m not saying this is an industry that’s ready to go next week,” Nocera told journalists during the annual meeting of the American Chemical Society. “I just wanted to find out if we could actually do it. And the answer is ‘Yes.’ Sometimes when you’re doing science, you just want to get to the top of the mountain to prove it can be done.”

Nocera’s current work stems from his earlier innovation unveiled six years ago: an artificial leaf that can break water down into hydrogen and oxygen using sunlight.

The new invention builds on that device. After splitting oxygen from hydrogen, it deploys a special bacteria that combines the hydrogen with carbon dioxide from the environment to create a bio-plastic. The bacteria then stores the bio-plastic as fuel internally.

“We’ve basically bottled sunlight in the form of this bio-plastic,” Nocera said.

The radishes on the right were grown with the help of a bionic leaf that produces fertilizer with bacteria, sunlight, water, and air.
Once the bio-plastic formed by the bacteria is placed in soil, it pulls nitrogen from the air to make ammonia, which acts as a fertilizing agent.

Advances in fertilizer played a key role in population growth during the 20th century, and commercial fertilizer now accounts for 30-50 percent of crop yields worldwide, according to various estimates.

Producing significant amounts of fertilizer typically requires large, expensive industrial facilities. In poor countries with underdeveloped infrastructure, there is a further need for distribution methods to transport the nutrient-rich substance to remote rural areas where subsistence farmers live.

“I’ve always felt the only importance of my research is, ‘Can I do the things that you already do in this society at large industrial scales with distribution systems, but in the back yard for the poor?’” Nocera said.

Read more at Discovery News

The Mystery of How Black Holes Collide and Merge Is Beginning to Unravel

An illustration of two supermassive black holes about to merge, with jets of superheated gas being emitted from their edges.
Last year, scientists announced that they had finally observed gravitational waves, the elusive and long sought-after ripples in the fabric of spacetime that were first posited by Albert Einstein. The waves came from a catastrophic event — the collision of two black holes located about 1.3 billion light years away from Earth — and the released energy undulated across the universe, much like ripples in a pond.

The detection by the upgraded Laser Interferometer Gravitational-Wave Observatory (Advanced LIGO), along with two subsequent gravitational wave discoveries, confirmed a major prediction of Einstein’s 1915 general theory of relativity and heralded a new era in physics, allowing scientists to study the universe in a new way by using gravity instead of light.

But a fundamental question remains unanswered: How and why do black holes collide and merge?

In order for the black holes to merge, they must start out very close together by astronomical standards, no more than about a fifth of the distance between the Earth and the Sun. But only stars with very large masses can become black holes, and during the course of their lives, these stars expand to become even larger.  

A new study published in Nature Communications uses a model called COMPAS (Compact Object Mergers: Population Astrophysics and Statistics) in an attempt to answer how large binary stars that would eventually become black holes fit within a very small orbit. COMPAS allows the researchers to pursue a kind of “paleontology” for gravitational waves.

“A paleontologist, who has never seen a living dinosaur, can figure out how the dinosaur looked and lived from its skeletal remains,” said Ilya Mandel from the University of Birmingham in the UK, senior author of a paper, in a statement. “In a similar way, we can analyze the mergers of black holes, and use these observations to figure out how those stars interacted during their brief but intense lives."

What they found was that even two widely separated “progenitor” stars can interact when they expand, engaging in several episodes of mass transfer.

The researchers started by analyzing the three gravitational wave events that were detected by LIGO and attempted to see if all three black hole collisions evolved in the same way, which they call “classical isolated binary evolution via a common-envelope phase.”

It starts with two massive progenitor stars at quite wide separations. As the stars expand, once they come so close that they cannot escape each other's gravity, they begin to interact and engage in several episodes of mass transfer. This results in a very rapid, dynamically unstable event that envelops both stellar cores in a dense cloud of hydrogen gas.

“Ejecting this gas from the system takes energy away from the orbit,” the team said. “This brings the two stars sufficiently close together for gravitational-wave emission to be efficient, right at the time when they are small enough that such closeness will no longer put them into contact.”

It actually takes few million years to form two black holes, with a possible subsequent delay of billions of years before the black holes merge and form a single, larger black hole. But that merger event itself can be quick and violent.

The researchers said the simulations with COMPAS have also helped the team to understand the typical properties of the binary stars that can go on to form such pairs of merging black holes and the environments where this can happen.

For example, the team found that a merger of two black holes with significantly unequal masses would be a strong indication that the stars formed almost entirely from hydrogen and helium — called low-metallicity stars — with other elements contributing fewer than 0.1 percent of stellar matter (for comparison, this fraction is about 2 percent in our Sun). They were able to determine that all three events detected by LIGO could have formed in low-metallicity environments.

"The beauty of COMPAS is that it allows us to combine all of our observations and start piecing together the puzzle of how these black holes merge, sending these ripples in spacetime that we were able to observe at LIGO," said Simon Stevenson, a Ph.D. candidate at the University of Birmingham and the paper’s lead author.

Read more at Discovery News

Apr 4, 2017

Steppe migrant thugs pacified by Stone Age farming women

Corded ware vessel, an axe and two discs made of amber from an early male grave.
In an earlier study Professor Kristian Kristiansen from the University of Gothenburg in Sweden and Lundbeck Foundation Professor Eske Willerslev from the Centre for GeoGenetics at the University of Copenhagen, and their research teams, showed that the large demographic changes during the first part of the Bronze Age happened as a result of massive migrations of Yamnaya people from the Pontic-Caspian steppes into Neolithic Europe. They were also able to show that plague was widespread in both Europe and Central Asia at this time.

Now Professor Kristiansen and Professor Willerslev with co-authors reveal a more detailed view of the mechanism behind the emerging culture known as the Corded Ware Culture -- the result of the encounter between the Yamnaya and the Neolithic people. Professor Kristian Kristiansen says: "We are now for the first time able to combine results from genetics, strontium isotopes on mobility and diet, and historical linguistics on language change, to demonstrate how the integration process unfolded on the ground after the Yamnaya migrations from the steppe. In our grand synthesis we argue that Yamnaya migrants were predominantly males, who married women who came from neighbouring Stone Age farming societies" These Stone Age Neolithic societies were based on large farming communities reflected in their collective burial ritual often in big stone chambers, so called megaliths. Very different from the traditions of the incoming migrants.

The origin of the Yamnaya

The Yamnaya people originated on the Caspian steppes where they lived as pastoralists and herders, using wagons as mobile homes. From burial pits archaeologists have found extensive use of thick plant mats and felt covers. Their economy was based on meat, dairy products and fish, they were tall and rather healthy with little caries in their teeth. No agriculture is documented. Barrows were aligned in groups forming lines in the landscape to mark seasonal routes and after death diseased people were put into individual graves under small family barrows. Their burial ritual thus embodied a new perception of the individual and of small monogamous family groups as the foundation of society. The continent encountered by the Yamnaya people around 3000 BC had seen a decline in the agrarian Stone Age societies, thereby allowing space for incoming migrants. This decline was probably the result of a widespread plague from Siberia to the Baltic.

"The disease dynamic here may have been comparable to the European colonization process in America after Christopher Columbus," says Kristiansen. "Perhaps Yamnaya brought plague to Europe and caused a massive collapse in the population."

"Black Youth" as migrating males and their marriage to Neolithic women

In the new synthesis article, Kristiansen and colleagues argue for a dominance of males during the early phase after the migrations, and correspond to the old Indo-European mythology of later times. These sources talk about war-bands of youths -- called "Black Youth" -- who were employed in pioneer migrations as a dynamic force. Evidence from strontium isotopic analyses, published in 2016 by Kristiansen together with Douglas Price and Karl Goran Sjogren, showed that a majority of the women in Corded Ware burials in south Germany were non-locals who had married in from Neolithic societies, since they had a Neolithic diet in their childhood. These results now form part of the new synthesis. Professor Kristian Kristiansen says: "Existing archaeological evidence of a strong 90% male dominance in the early phase of the Corded Ware/Single Grave Culture settlement in Jutland, Denmark, and elsewhere can now be explained by the old Indo-European tradition of war bands of young males who did not have any inheritance to look forward to. Therefore they were probably more willing to make a career as migrating war bands."

These Neolithic women also brought new knowledge of pottery production, and started to imitate pottery containers made of wood from the Yamnaya migrants. In this way a new pottery culture was created called Corded Ware, because of the cord impressions around the neck of the pots. They were made for beer drinking, and the new migrants also learned how to grow barley from the in-married Neolithic women in order to produce beer.

Rapid genetic changeover from Neolithic to Corded Ware cultures after 3000 BC

Eske Willerslev undertook the ancient DNA analyses together with Morten Allentoft and Martin Sikora. Professor Willerslev says:

"In our big Bronze Age study, published in 2015 we were astonished to see how strong and fast the genetic changeover was from the Neolithic to the Corded Ware. There was a heavy reduction of Neolithic DNA in temperate Europe, and a dramatic increase of the new Yamnaya genomic component that was only marginally present in Europe prior to 3000 BC. Moreover, the apparent abruptness with which this change occurred indicates that it was a large-scale migration event, rather than a slow periodic inflow of people."

New words and new Proto-Germanic dialect

The Yamnaya brought the Indo-European languages into Bronze Age Europe, but as herders, they did not have words for crops or cultivation, unlike the Neolithic farmers. As the Corded Ware Culture developed it adopted words related to farming from the indigenous Neolithic people, which they were admixing with. Guus Kroonen, a historical linguist, was able to demonstrate that these new words did not belong to the original Indo-European languages. Therefore it was possible to conclude that the Neolithic people were not speaking an Indo-European language, as did the Yamnaya migrants. Thus, the process of genetic and cultural admixture was accompanied by a process of language admixture, creating the foundations for later Germanic languages, termed Proto-Germanic.

Read more at Science Daily

Future carbon dioxide, climate warming potentially unprecedented in 420 million years

Living Ginkgo leaf (left) and fossil (right). Density of stomata in such leaves is proxy of atmospheric CO2 in past.
New research led by the University of Southampton suggests that, over the next 100 to 200 years, carbon dioxide concentrations in Earth's atmosphere will head towards values not seen since the Triassic period, 200 million years ago. Furthermore, by the 23rd century, the climate could reach a warmth not seen in 420 million years.

The study, published in Nature Communications, compiled over 1200 estimates of ancient atmospheric carbon dioxide (CO2) concentrations to produce a continuous record dating back nearly half a billion years. It concludes that if humanity burns all available fossil fuels in the future, the levels of CO2 contained in the atmosphere may have no geologically-preserved equivalent during this 420 million year period.

The researchers examined published data on fossilised plants, the isotopic composition of carbon in soils and the oceans, and the boron isotopic composition of fossil shells. Gavin Foster, lead author and Professor of Isotope Geochemistry at the University of Southampton, explains: "We cannot directly measure CO2 concentrations from millions of years ago. Instead we rely on indirect 'proxies' in the rock record. In this study, we compiled all the available published data from several different types of proxy to produce a continuous record of ancient CO2 levels."

This wealth of data shows that CO2 concentrations have naturally fluctuated on multi-million year timescales over this period, from around 200-400 parts per million (ppm) during cold 'icehouse' periods to up to 3000 ppm during intervening warm 'greenhouse' periods. Although evidence tells us our climate has fluctuated greatly in the past (with Earth currently in a colder period), it also shows the current speed of climate change is highly unusual.

Carbon dioxide is a potent greenhouse gas and in the last 150 years humanity's fossil fuel use has increased its atmospheric concentration from 280 ppm in the pre-industrialisation era to nearly 405 ppm in 2016. However, it's not just CO2 that determines the climate of our planet, ultimately it is both the strength of the greenhouse effect and the amount of incoming sunlight that is important. Changes in either parameter are able to force climate change.

"Due to nuclear reactions in stars, like our sun, over time they become brighter," adds co-author Dan Lunt, Professor of Climate Science at the University of Bristol. "This means that, although carbon dioxide concentrations were high hundreds of millions of years ago, the net warming effect of CO2 and sunlight was less. Our new CO2 compilation appears on average to have gradually declined over time by about 3-4 ppm per million years. This may not sound like much, but it is actually just about enough to cancel out the warming effect caused by the sun brightening through time, so in the long-term it appears the net effect of both was pretty much constant on average."

This interplay between carbon dioxide and the sun's brightness has fascinating implications for the history of life on Earth. Co-author Professor Dana Royer, from Wesleyan University in the US, explains: "Up until now it's been a bit of a puzzle as to why, despite the sun's output having increased slowly over time, scant evidence exists for any similar long-term warming of the climate. Our finding of little change in the net climate forcing offers an explanation for why Earth's climate has remained relatively stable, and within the bounds suitable for life for all this time."

This long-term view also offers a valuable perspective on future climate change. It is well recognised that the climate today is changing at rates well above the geological norm. If humanity fails to tackle rising CO2 and burns all the readily available fossil fuel, by AD 2250 CO2 will be at around 2000 ppm -- levels not seen since 200 million years ago.

Professor Foster adds: "However, because the Sun was dimmer back then, the net climate forcing 200 million years ago was lower than we would experience in such a high CO2 future. So not only will the resultant climate change be faster than anything Earth has seen for millions of years, the climate that will exist is likely to have no natural counterpart, as far as we can tell, in at least the last 420 million years."

Read more at Science Daily

Oldest remains of insects from bed bug genus found in Oregon

Common bed bug (Cimex lectularius) first nymph slide plate.
A cave in southern Oregon that is the site of some the oldest preserved evidence of human activity in North America was also once home to not-too-distant cousins of the common bed bug.

In research to be published next week in the Entomological Society of America's Journal of Medical Entomology, a pair of archaeologists describe remains found in caves near Paisley, Oregon, that represent the oldest specimens of insects from the genus Cimex ever found, ranging between 5,100 and 11,000 years old.

The remains were identified as relatives of the bed bug, Cimex lectularius, but they were "not the bed bug we all know and love from hotel rooms," says Martin E. Adams of Paleoinsect Research and co-author on the study with Dennis L. Jenkins of the Museum of Natural and Cultural History at the University of Oregon. The species in the Paisley Five Mile Point Caves (Cimex pilosellus, Cimex latipennis, and Cimex antennatus) are all parasites of bats.

Previously, the oldest remains of "cimicids" ever found were just 3,500 years old, found in Egypt in 1999, meaning the remains found at the Paisley Caves are the oldest Cimex specimens by a wide margin, and they raise some interesting questions for researchers about how cimicids have interacted (or not) with humans in the past.

Cimex lectularius and Cimex hemipterus are the two bed bug species that are known to parasitize humans, widely believed to have adapted to that role thousands of years ago when humans shared caves with bats in Europe, Asia, and Africa. The species found in the Oregon caves, however, never made that jump, and Adams says it's unclear why not.

"Were the cimicid populations too small to establish themselves outside the caves, or were the host populations too small?" Adams says. "Given that Paisley Caves was only a seasonal occupation area for human hunter-gatherers, did the humans move around too much, or were the bugs not able to withstand the environment outside the caves for very long? Or, were there other constraints involved? I'm working on these last few archaeological questions right now."

The identification of the three Cimex species may also offer some clues to climactic trends during the eras they were dated to, Adams says. Cimex antennatus, for instance, tends to favor the warmer climates of California and Nevada. "The presence of warm-tolerant cimicids in the caves, such as Cimex antennatus, may suggest that climatic conditions at Paisley Caves 5,100 years ago were similar to what Cimex antennatus enjoys today in its current range."

From Science Daily

The World's Most Venomous Scorpion Caught on Camera in Strike Mode

The world's most lethal scorpion, the death stalker, has been caught on high-speed camera for the first time lashing out with its lethal stinger, scientists reported Tuesday.

A comparison of half a dozen scorpion species shown in ultra-slow motion revealed an unsuspected variety of strike modes, they reported in the journal Functional Ecology.

The death stalker had the fastest lunge of all, with its venomous stinger snapping over its head like a whip at 130 centimeters (51 inches) per second.

It has a no-nonsense trajectory, moving straight towards its target before flicking upward. The emperor scorpion — the world's largest — has a similar open strike.

Other species, such as the black spitting scorpion, which can squirt venom at a distance, and various members of the hottentotta genus, strike with a more circular motion, forming an "O".

"We found that different 'tail' shapes" — some slim, some fatter — "appear to permit different strike performances," said senior author Arie van der Meijden, a professor at the University of Porto in Portugal.

To record and analyse the lightning-fast strikes, van der Meijden and his team built a small platform surrounded by mirrors on all four sides.

They filmed the scorpion strikes from above with a video camera at 500 frames per second, and then created 3D models with computers.

"Just taking them out of their container and putting them in the arena was enough to get them in stinging mood," van der Meijden said.

"All that was necessary to make them strike was touching their pincers with a thin piece of wire."

Next on the research agenda is to figure out the evolutionary forces which explain why the strike patterns are so varied.

It could be "related to the kind of predators they need to defend themselves against," van der Meijden told AFP.

The differences could also arise from the fact that some scorpions rely less on their tail stingers, and more on their pincers to ward off a threat.

Scorpions use their defensive arsenal against bats, snakes, lizards and other predators.

They also use their stinger to catch prey, and during mating.

A 2008 study in the journal Acta Tropica estimated that more than 3,000 people die every year from scorpion bites.

Read more at Discovery News

Medieval Villagers Hacked Their Dead to Pieces in Fear of Zombie Apocalypse

Composite diagram showing distribution of cut marks in the remains.
Researchers may have uncovered the first scientific evidence of a “zombie madness” that obsessed medieval England, according to a study of 137 human bones that were excavated from a deserted English village.

Dating from the 11th to 14th centuries, the skeletal remains were reduced to chopped, smashed, and burnt fragments in an apparent attempt to forestall revenants rising from the grave.

The bones were recovered in the 1960s from a pit at the site of Wharram Percy, a long-abandoned village in rural Yorkshire, but were never examined closely until now.

Gruesome evidence of extensive human activity was immediately clear.

“Some of the bones showed sharp force marks, signs of burning and perimortem breakage,” Simon Mays, human skeletal biologist at Historic England, Alistair Pike, professor of archaeological sciences at the University of Southampton, and their colleagues wrote in the Journal of Archaeological Science: Reports.

While they considered starvation cannibalism as a possible cause, the researchers said they had ruled out a scenario in which the remains were cannibalized by villagers who were enduring one of the 12 known famines that occurred in England between 1066 and 1300.

“The patterns of breakage and cut marks on the bones are not consistent with the removal of flesh for eating,” Pike told Seeker.

Rather than indicate starvation cannibalism, the breakage, burning, and knife and chop marks on the skeletal remains appear to be consistent with dismemberment and decapitation, which would reflect the dark side of medieval beliefs.

The most likely explanation, according to Mays, is that the bones are “the remains of corpses burnt and dismembered to stop them walking from their graves.”

“Belief in revenants was widespread in Medieval northern and western Europe. Revenants were usually malevolent, spreading disease and physically assaulting the living,” the researchers wrote. “Methods of dealing with the undead involved physical and/or spiritual means, with an emphasis on the former. The most usual way was to dig up the body and subject it to mutilation (particularly decapitation) and burning.”

Osteological examination of the 137 bones revealed that they belonged to at least 10 individuals, ranging in age from two to 50 years old.

Monastic documents describe the behavior of the restless undead and detail how to treat a body to prevent it from rising again.

The most common way was to dig up the corpse, which was mutilated and decapitated to destroy its integrity and burned, rendering it unrecognizable.

“Our research is the first archaeological evidence for such treatment in the UK,” Pike said. “It tells us that the fear of revenant corpses was real. People really did believe that corpses can rise from the dead.”

The Wharram Percy bones show a total of 76 sharp-force marks, mainly knife-marks, on the upper body parts. The marks were made “with a fine knife drawn across the bone,” the researchers noted.

“The knife marks can be interpreted in terms of dismemberment or other mutilation of the body, and those in the head and neck area may be associated with decapitation,” they wrote.
They added that at least 17 bones show evidence for low-temperature burning, while six long bones feature breakage that occurred at or sometime after death.

Why these 10 individuals would have been treated by the villagers in this way, or elicited such fear, remains a mystery.

“We don't know,” Pike said. “We have historical accounts of how the dead who may have been killed suddenly, or wronged in some way, come back to life and cause trouble.”

He added that no frightening diseases were detected from the bones.

“We found just a few cases of joint disease, but with a similar frequency to the individuals buried in the nearby graveyard, so there is no reason to believe these individuals were unusual,” he remarked.

Strontium isotopic analyses in the teeth suggest that the people whose corpses were mutilated likely grew up in an area close to where they were buried, possibly in the village.

“This was surprising to us, as we first wondered if the unusual treatment of the bodies might relate to their being from further afield,” Pike said.

Read more at Discovery News

Apr 3, 2017

Stretching the boundaries of neural implants

Researchers have developed a rubber-like fiber, shown here, that can flex and stretch while simultaneously delivering both optical impulses, for optoelectronic stimulation, and electrical connections, for stimulation and monitoring.
Implantable fibers have been an enormous boon to brain research, allowing scientists to stimulate specific targets in the brain and monitor electrical responses. But similar studies in the nerves of the spinal cord, which might ultimately lead to treatments to alleviate spinal cord injuries, have been more difficult to carry out. That's because the spine flexes and stretches as the body moves, and the relatively stiff, brittle fibers used today could damage the delicate spinal cord tissue.

Now, researchers have developed a rubber-like fiber that can flex and stretch while simultaneously delivering both optical impulses, for optoelectronic stimulation, and electrical connections, for stimulation and monitoring. The new fibers are described in a paper in the journal Science Advances, by MIT graduate students Chi (Alice) Lu and Seongjun Park, Professor Polina Anikeeva, and eight others at MIT, the University of Washington, and Oxford University.

"I wanted to create a multimodal interface with mechanical properties compatible with tissues, for neural stimulation and recording," as a tool for better understanding spinal cord functions, says Lu. But it was essential for the device to be stretchable, because "the spinal cord is not only bending but also stretching during movement." The obvious choice would be some kind of elastomer, a rubber-like compound, but most of these materials are not adaptable to the process of fiber drawing, which turns a relatively large bundle of materials into a thread that can be narrower than a hair.

The spinal cord "undergoes stretches of about 12 percent during normal movement," says Anikeeva, who is the Class of 1942 Career Development Professor in the Department of Materials Science and Engineering. "You don't even need to get into a 'downward dog' [yoga position] to have such changes." So finding a material that can match that degree of stretchiness could potentially make a big difference to research. "The goal was to mimic the stretchiness and softness and flexibility of the spinal cord," she says. "You can match the stretchiness with a rubber. But drawing rubber is difficult -- most of them just melt," she says.

"Eventually, we'd like to be able to use something like this to combat spinal cord injury. But first, we have to have biocompatibility and to be able to withstand the stresses in the spinal cord without causing any damage," she says.

The team combined a newly developed transparent elastomer, which could act as a waveguide for optical signals, and a coating formed of a mesh of silver nanowires, producing a conductive layer for the electrical signals. To process the transparent elastomer, the material was embedded in a polymer cladding that enabled it to be drawn into a fiber that proved to be highly stretchable as well as flexible, Lu says. The cladding is dissolved away after the drawing process.

After the entire fabrication process, what's left is the transparent fiber with electrically conductive, stretchy nanowire coatings. "It's really just a piece of rubber, but conductive," Anikeeva says. The fiber can stretch by at least 20 to 30 percent without affecting its properties, she says.

The fibers are not only stretchable but also very flexible. "They're so floppy, you could use them to do sutures and deliver light at the same time," she says.

"We're the first to develop something that enables simultaneous electrical recording and optical stimulation in the spinal cords of freely moving mice," Lu says. "So we hope our work opens up new avenues for neuroscience research." Scientists doing research on spinal cord injuries or disease usually must use larger animals in their studies, because the larger nerve fibers can withstand the more rigid wires used for stimulus and recording. While mice are generally much easier to study and available in many genetically modified strains, there was previously no technology that allowed them to be used for this type of research, she says.

"There are many different types of cells in the spinal cord, and we don't know how the different types respond to recovery, or lack of recovery, after an injury," she says. These new fibers, the researchers hope, could help to fill in some of those blanks.

Read more at Science Daily

Surprise discovery of Europe's first cave fish

This photograph shows a male cave loach of 8.5 cm body length.
Researchers reporting in Current Biology on April 3 have discovered the first European cave fish. A hobby cave diver first sighted the fish, a loach in the genus Barbatula, living in a hard-to-reach, underground water system in South Germany.

"The cave fish was found surprisingly far in the north in Southern Germany," says Jasminca Behrmann-Godel of Germany's University of Konstanz. "This is spectacular as it was believed before that the Pleistocene glaciations had prevented fish from colonizing subterranean habitats so far north."

Their genetic studies of the fish together with knowledge on the geological history of the region suggest that the cave loach arose recently, within the last 20,000 years.

"It was only when the glaciers retreated that the system first became a suitable habitat for fish," says Arne Nolte from the University of Oldenburg/Max Planck Institute for Evolutionary Biology, Plön.

Despite that relatively short period of evolutionary time, the fish already show adaptations characteristic of "real" cave fish. As Jörg Freyhof from the Leibniz Institute for Freshwater Ecology and Inland Fisheries (IGB) Berlin explains, their eyes are much smaller, appearing almost as if curved inwards, and their color has all but disappeared. The fish also have elongated whisker-like barbels on their heads and larger nostrils than related fish living closer to the surface.

Joachim Kreiselmaier first sighted the loaches in August 2015 while exploring the deepest parts of the Danube-Aach system, which can only be reached under particularly dry conditions in summer and fall. Noticing that the fish were "strange looking" to him, he snapped some photos and showed them to the hobby geologist and co-author Roland Berka, who contacted Behrmann-Godel, knowing her from former work. Study co-author and fish taxonomist Freyhof later confirmed that the fish could be showing cave adaptations.

"It took someone with the 'right eye' to realize that this might be something special and I believe that, on top of the right conditions and the difficult trip, this discovery depended on an exceptional diver like Joachim to realize in the first place that the fish might be special," Behrmann-Godel says.

"No more than 30 divers have ever reached the place where the fish have been found," Kreiselmaier says. "Due to the usually bad visibility, strong current, cold temperature, and a labyrinth at the entrance, most divers do not come back again for diving."

But that didn't stop Kreiselmaier. In November 2015, on another dive, Kreiselmaier succeeded in catching a live specimen, which allowed the researchers to study its features in greater detail. The following year, he caught four more fish, enabling further study of the loach's form and genetics. Based on morphological and genetic comparison to surface fish caught upstream and downstream of the cave, the researchers report that the cave loaches are indeed an isolated population and the first known European cave fish.

The findings show that adaptation to subterranean habitats can be fast -- requiring only a few thousand years. They also come as reminder that "wonders of nature can turn up anywhere, even in your own backyard," Freyhof notes.

Read more at Science Daily

New indications of gradual decline of dinosaurs before the end of the cretaceous period

Landscape in the Paredon area: There the researchers encountered fossil imprints while conducting paleontological research.
According to the latest research results of a German-Mexican team of geoscientists, the gradual decline of the dinosaurs and pterosaurs presumably came before the impact of the Chicxulub asteroid and the global mass extinction at the end of the Cretaceous Period. Studies under the direction of Prof. Dr Wolfgang Stinnesbeck of Heidelberg University and Prof. Dr Eberhard Frey of the State Museum of Natural History Karlsruhe also indicate that bird species spread and diversified at the same time the dinosaurs disappeared. Their results were published in the journal Geological Society of America Bulletin.

While conducting paleontological research in northeastern Mexico, the scientists came upon sedimentary rock deposited toward the end of the Cretaceous Period that evidenced an enormous diversity of fossils, including the tracks of birds, dinosaurs and pterosaurs. "Most of the imprints come from at least five different species of birds; dinosaur tracks, however, are rare. Only a single footprint comes from a predatory dinosaur," explains Prof. Stinnesbeck. The finds therefore indicate a gradual decline of the dinosaurs with a simultaneous increase in the diversity of birds even before the end of the Cretaceous Period. "Until now, it was generally assumed that the dinosaurs died out first and bird species diversified afterward," states the researcher. "Our data, however, substantiate the theory that birds ascended before dinosaurs became extinct."

Fossil analysis also showed that the decline of the dinosaurs occurred gradually, with probably only a few species surviving until the end of the Cretaceous Period. The extinction of the dinosaurs is therefore not -- as science frequently assumes -- due to the impact of the Chicxulub asteroid that struck Earth more than 65 million years ago. "For most of the dinosaurs and pterosaurs, this strike no longer had any effect," explains Prof. Stinnesbeck. Even the group of cephalopods, the so-called ammonites, was not annihilated by the asteroid strike at the end of the Cretaceous Period. According to Prof. Stinnesbeck, fossil finds of the Sphenodiscus pleurisepta ammonite show their successive decline beyond the Cretaceous Period. "The effects of the Chicxulub impact were therefore not the cause of a global mass extinction, which probably came about considerably less catastrophically than previously assumed," states the Heidelberg researcher.

From Science Daily

Mutant lifestyles: Researchers uncover a potent genetic element in Earth's smallest life forms

An ultra-small bacterial cell (scale bar is 100 nanometers) is thought to be a relative of the microorganisms that encode diversity-generating retroelements.
It's the stuff of science fiction, though there's nothing fiction about it: Researchers have discovered a multitude of previously unidentified microorganisms possess a genetic element that enables them to self-mutate.

What's more, these organisms are so great in number that they dramatically expand the diversity of the tree of life.

"These microorganisms can be 500 times smaller than bacteria like E. Coli," said UC Santa Barbara microbiologist David Valentine. "They also do unusual things to some of the key genes used for identification, like splitting them into pieces small enough to render them invisible to scientific surveillance. This combined with their ultra-small size explains why they were missed until recently."

To pinpoint these miniscule organisms -- tiny enough to pass through filters that capture traditional microbes -- the scientists turned to groundwater samples from a Colorado aquifer. Analyzing numerous genomes therein, they detected a prevalence of an unusual genetic element they had encountered once before: diversity-generating retroelements (DGRs). The new findings appear in the journal Nature Microbiology.

Co-author Valentine, a professor in UCSB's Department of Earth Science, along with postdoctoral scholar Blair Paul and co-authors from UC Berkeley, UC San Diego and UCLA, show that these DGRs are active in sprawling lineages of recently discovered phyla: two classes of archaea -- primitive, single-celled, bacteria-like microorganisms -- and among potential new bacterial candidates in the biological tree of life. These new biological classes appear to disproportionately harbor DGRs, which enable them to target their own genes for accelerated mutation.

Lead author Paul analyzed more than 500 genomes out of a pool of 2,500 and found that the majority of a certain class of archaea, as well as a yet-to-be-characterized phyla closely related to bacteria, appear to have DGRs. In fact, many possess multiple DGRs.

"These microorganisms are so small they have minimized the amount of information they can code, so they are probably not totally self-reliant," said Valentine, also a professor in UCSB's Marine Science Institute. "This means that they engage in some form of either symbiosis or parasitism. If a microorganism shrinks down its genome and its cell to this very minimal lifestyle, it has to have mechanisms that allow it to evolve new capabilities but also to shed unneeded ones."

Valentine noted that the DGR mechanism might allow these organisms to do both. Or perhaps, he posited, they optimize to the point where it's no longer beneficial to mutate and have to rid themselves of the capability.

"The finding that DGRs are relatively widespread in tiny bacteria with symbiotic lifestyles is of great interest because these elements likely contribute to the incredible diversity of protein sequences found in these organisms," said co-author Jill Banfield, a professor of earth and planetary sciences at UC Berkeley.

While very little is known about how DGRs self-regulate, scientists are finding that these elements are able to guide and target specific sites for mutation. By examining DNA sequence from the genomes, the researchers saw recent mutation activity and observed the mechanism in action by virtue of its RNA being transcribed.

"One of the reasons we were able to see the pattern of mutations in the DNA was because the data set recovered such a depth of genomes that we could see the variability within them," Paul said.

The mechanism targets only one of the four different nucleotides (A, C, G, T) that form the basic structure of nucleic acids such as DNA. Nucleic acid synthesis and degradation require enzymes to facilitate either process. In fact, a biochemical artifact of an enzyme was what first revealed this mechanism to the UCSB investigators. A distinctive signature and location as well as only A mutations are hallmarks of this mechanism.

"There are similar proteins that don't mutate only A but are error prone," Paul explained. "We think that this enzyme is similarly prone to creating mutations."

Because the scientists are dealing with new organisms, they have not yet been able to determine what the vast majority of the diversified proteins do.

"An important question is whether these mutations alter the proteins that the genes encode or are they meant to interrupt the genes themselves and target them for removal from the genome?" Paul asked. "If this mechanism forces mutations that cause some genes to go defunct, it could be associated with evolutionary benefits."

"This discovery reveals how rapid evolution happens in some of Earth's smallest and most common, yet least-known, microbes," says Mike Sieracki of National Science Foundation's Division of Ocean Sciences, and a director for the Dimensions of Biodiversity program, which sponsored the research.

Read more at Science Daily

Tyrannosaurs show their sensitive side

A team of researchers, including UNM Honors College Professor Jason R. Moore, has found a new species of tyrannosaur dinosaur -- the most popular of the prehistoric creatures. After the fossils were pulled out of the muddy banks of a Montana river, the team was able to analyze the texture of the facial bones of the new species. The findings suggest that the face of tyrannosaurs was covered in a scaly protective layer with a high degree of tactile sensitivity, similar to crocodiles.
A team of researchers, including UNM Honors College Professor Jason R. Moore, has found a new species of tyrannosaur dinosaur -- the most popular of the prehistoric creatures.

After the fossils were pulled out of the muddy banks of a Montana river, the team was able to analyze the texture of the facial bones of the new species. The findings suggest that the face of tyrannosaurs was covered in a scaly protective layer with a high degree of tactile sensitivity, similar to crocodiles.

"Being a tyrannosaur, they had really small arms," says Moore. "They wouldn't be able to interact with their environment with their hands the way mammals do -- find food, build nests, tend to eggs and young. In order to do these things, Daspletosaurus needed to use its feet or head. The discovery and analysis of the tyrannosaur shows that the dinosaur had a developed face sensitivity similar to the sensitivity in our finger tips, suggesting it could use its snout for all those complex ecological interactions, similar to the way crocodiles do today."

An investigation by a team of scientists from Wisconsin, Australia, Louisiana, Montana and New Mexico has identified and named the new species of the tyrannosaur clan: Daspletosaurus horneri -- "Horner's Frightful Lizard."

The species is named for the renowned dinosaur paleontologist, John "Jack" R. Horner, formerly curator at the Museum of the Rockies (MOR) in Bozeman, Montana. The tyrannosaur's name honors his discoveries of numerous dinosaur fossils and his mentorship of so many students that launched them on to accomplished scientific careers. The name-bearing specimens are stored in the research collections of the MOR.

The fossil resources of Montana, where the new tyrannosaur was found, are central to studies of dinosaur evolution.

"Montana, similar to many Rocky Mountain states, has lots of rock exposed at the right time and right environment to contain dinosaurs," says Moore. "The fossils are found preserved in ancient river channels and flood plains. If you know what you're looking for, they are widespread."

The research is led by Thomas Carr of Carthage College's Department of Biology in Wisconsin, an expert on the evolution and growth of Tyrannosaurus rex and its closest relatives, collectively called tyrannosaurs.

The family tree

In addition to adding a new species to the tyrannosaur family tree, the team's research provides new information about the mode of evolution and life appearance of tyrannosaurs, specifically the face.

This latest study, published in Nature Publishing Group's Scientific Reports, found evidence for a rare, nonbranching type of evolution in tyrannosaurs and that tyrannosaurs had scaly, lipless faces and a highly touch-sensitive snout.

"Daspletosaurus horneri was the youngest, and last, of its lineage that lived after its closest relative, D. torosus, which is found in Alberta, Canada," says Carr. "The geographic proximity of these species and their sequential occurrence suggests that they represent a single lineage where D. torosus has evolved into D. horneri."

Moore elaborated, "One of the difficulties in demonstrating this style of evolution is establishing that the different species don't overlap in time. The new radiometric dates we measured help support this temporal separation between D. torosus and D. horneri."

The research confirms that the ages of the two species shows that the evolution of the dinosaur was slow -- happening over a span of 2.3 million years.

The team's work literally changes the face of tyrannosaurs, which they found was covered by a lipless 'mask' of large flat scales and extensive patches of armor-like skin. This conclusion results from comparison of tyrannosaur skulls with those of crocodylians, birds and mammals, and earlier work by other researchers who had matched bone texture with different types of skin covering.

Jayc Sedlmayr, professor at the Louisiana State University Health Sciences Center New Orleans, explained, "Much of our research ... was generated from lab based comparative anatomy, where you get arms deep in 'blood and guts' dissecting birds -- living dinosaurs and crocodilians -- their closest living relatives."

The crocodile connection

"It turns out that tyrannosaurs are identical to crocodylians in that the bones of their snouts and jaws are rough, except for a narrow band of smooth bone along the tooth row," explained Carr. "We did not find any evidence for lips in tyrannosaurs: the rough texture covered by scales extends nearly to the tooth row, providing no space for lips."

"However, we did find evidence for other types of skin on the face, including areas of extremely coarse bone that supported armor-like skin on the snout and on the sides of the lower jaws. The armor-like skin would have protected tyrannosaurs from abrasions, perhaps sustained when hunting and feeding."

The researchers found that, like in crocodylians, the snout and jaws of the tyrannosaurs are penetrated by numerous small nerve openings, allowing hundreds of branches of nerves to innervate the skin, producing a sensitivity similar to that of human fingertips.

Read more at Science Daily

Apr 2, 2017

A badger can bury a cow by itself

This is a camera trap image of a badger burying a calf carcass in Utah's Grassy Mountains, January 2016.
While studying scavenger behavior in Utah's Great Basin Desert, University of Utah biologists observed an American badger do something that no other scientists had documented before: bury an entire calf carcass by itself.

Watch a video of the badger here: https://www.youtube.com/watch?v=dsHiOwR7cfc&feature=youtu.be

While badgers and their relatives are known to cache food stores, this is the first known instance of a badger burying an animal larger than itself. The finding suggests that badgers may have no limit to the size of animal they can cache, and that they may play an important role in sequestering large carcasses, which could benefit cattle ranchers in the West. The study is published in Western North American Naturalist.

"We know a lot about badgers morphologically and genetically, but behaviorally there's a lot of blank spaces that need to be filled," says senior Ethan Frehner, first author on the paper documenting the badger behavior. "This is a substantial behavior that wasn't at all known about."

The work was funded by a National Science Foundation Graduate Research Fellowship to doctoral candidate Evan Buechley.

Scavenger bait

The team didn't originally intend to study badgers. In January 2016, Buechley set out seven calf carcasses in Utah's Grassy Mountains, west of Salt Lake City. Each carcass was staked down and equipped with a camera trap to document what scavengers visited which carcasses. Buechley, who studies vultures and other avian scavengers, hoped to learn more about the ecology of scavengers in the Great Basin during the winter.

Buechley went out to check on the carcasses after a week, and found that one was missing.

"When I first got there I was bummed because it's hard to get these carcasses, to haul them out and set them up," he says. "I thought 'Oh, well we've lost one after a week.'"

He searched around the area, thinking that perhaps a coyote or mountain lion had dragged the carcass away, but after finding nothing, returned to the site and realized the ground where the carcass had been was disturbed. "Right on the spot I downloaded the photos," he says, "We didn't go out to study badgers specifically, but the badger declared itself to us."

A happy badger

Little was previously known about badger behavior, Frehner says. "They're an enigmatic species. A substantial amount of their lifetime is spent either underground or a lot of nocturnal behavior, so it's hard to directly observe that." Camera traps, a relatively new tool for researchers, made it possible to observe more natural behaviors.

In the photos, Buechley saw the badger dig around and beneath the carcass, which disappeared into the cavity created by the excavation. "Watching badgers undertake this massive excavation around and underneath is impressive," Frehner says. "It's a lot of excavation engineering they put into accomplishing this."

Camera trap records show that the badger completely buried the roughly 50-pound carcass over the course of five days, and then spent around two weeks in his underground burrow before leaving and intermittently returning to the burrow for the next few weeks until early March. According to the researchers, badgers cache food to isolate it from other scavengers and to keep it in an environment where it will last longer. "Like putting it in the fridge," Buechley says. Previously, biologists saw badgers caching rodents and rabbits, but never an animal larger than itself.

Senior Tara Christensen assembled a time-lapse video of the burial, which shows the badger sitting contently atop the burrow. Buechley says, "Not to anthropomorphize too much, but he looks like a really really happy badger, rolling in the dirt and living the high life."

Badgers' ecological role

Another badger, at another site in the same study, also attempted to bury a calf carcass, suggesting that the behavior is likely widespread for badgers. It's unclear whether badger relatives, called mustelids, can also cache such large animals. Other mustelids such as weasels, wolverines and martens aren't as specialized for digging as badgers are, but one account does document a fisher caching a black bear carcass under branches and bracken.

Buechley says that large-animal caching could have a large impact in the harsh and sparse ecosystem of the Great Basin. "There's not a lot of resources out there," he says. "A large dead ungulate can provide a ton of resources. So far on the carcasses we've put out, we've had turkey vultures, golden eagles, many ravens, bobcats, kit fox and coyote, so there's a lot of animals that could be using this resource, and the badger just monopolizes it."

The badger could also provide an ecological service to ranchers. Many ranchers see badgers as pests, because they dig burrows through rangeland and can eat chickens. But if badgers can bury a calf, they may bury other carrion before any diseases incubating in the carcass can infect other cows. "It's not beneficial to have rotting carcasses out among your other cattle because of disease vectors," Frehner says. Christensen adds, "Keeping large predators away is a big deal for a lot of ranchers. You could argue that if the carcasses are being buried, they're not going to be attracting large predators."

Both Frehner and Christensen participated in this study as undergraduates, an experience that gave them an early insight into the research process. "Doing research and getting involved in a lab is a great way to see how science is done," Christensen says. "I've learned a lot in the last few months about data analysis and using these things to find real results."

Frehner adds, "Writing the paper has been a substantial learning experience for me that I don't think I would have gotten any other way."

Read more at Science Daily

Massive, computer-analyzed geological database reveals chemistry of ancient ocean

Julia Wilcots, a Madison native who was then at Princeton University, at a rock quarry in Shorewood Hills, Wisconsin. The layers at her head and chest level are both composed of different types of stromatolites.
A study that used a new digital library and machine reading system to suck the factual marrow from millions of geologic publications dating back decades has unraveled a longstanding mystery of ancient life: Why did easy-to-see and once-common structures called stromatolites essentially cease forming over the long arc of earth history?

Stromatolites are contorted layers of sediment formed by microbes, and they are often found in limestone and other ancient sedimentary rocks deposited beneath oceans.

"Geologists have known for a long time that stromatolites were abundant in shallow marine environments during the Precambrian, before the emergence of multi-cellular life" more than 560 million years ago, says Jon Husson, a post-doctoral researcher and co-author of a study now online in the journal Geology. "But, stromatolites are rare in the ocean today."

The new study measures the slide in stromatolite prevalence based on descriptions of rocks sifted from more than 3 million scientific publications.

"Paleontologists have largely attributed the decline in stromatolites to the evolution of animals, starting some 560 million years ago," says Shanan Peters, a professor of geoscience at University of Wisconsin-Madison and study first author. "Many multi-cellular animals, like snails, eat microbes. The evolution of these big microbe-grazing animals hit 'reset' on the stromatolite's world. Or so the story has gone."

The new study found a weak correlation between stromatolite occurrence and the diversity of animals, but a stronger link to seawater chemistry.

"The best predictor of stromatolite prevalence, both before and after the evolution of animals, is the abundance of dolomite in shallow marine sediments," says Husson. Dolomite is a high-magnesium variety of carbonate, the type of sediment that forms limestone. Dolomite is harder to make than low-magnesium carbonate and it forms today in only a narrow range of marine environments.

When the ocean water is super-saturated with carbonate, "that can make it easier for things like stromatolites to form," says Husson. "In Lake Tanganyika [Africa], there are stromatolites forming today, even though there are animals everywhere, snails and fish. The lake is super-saturated with carbonate, and it's begging to be precipitated. The microbes come along and help it to precipitate, and the result is an abundance of stromatolites." Elevated carbonate saturation can also help the formation of dolomite, thereby driving the correlation with stromatolites found in this study.

Measuring the prevalence of stromatolites through all Earth history is difficult because counting the number of stromatolites alone is not sufficient. You must also know how many rocks could potentially have stromatolites, but do not.

The big innovation of this study is the interplay of a new type of digital library and machine reading system called GeoDeepDive with a geological database called Macrostrat. Both were spearheaded by Peters at UW-Madison.

GeoDeepDive is a digital library built on high throughput computing technology that can "read" millions of papers and siphon off specific information. To date, the GeoDeepDive library contains more than 3 million scientific publications from all scientific disciplines; some 10,000 new published papers are added daily.

Macrostrat is a database describing the known geological properties of North America's upper crust, at different times and depths.

The massive computing capacity at UW-Madison's Center for High Throughput Computing and HTCondor system, the brainchild of UW-Madison computer scientist Miron Livny, powers GeoDeepDive. Combining the digital library with the geological database allowed the researchers to estimate, at different time periods, the percentage of shallow marine rocks that actually have stromatolites.

The study began in the summer of 2015, when the third author, Julia Wilcots, a Madison-native who was then an undergraduate at Princeton, asked Peters for a summer project. "In my typical fashion I gave Julia a few options," Peters says. "She picked stromatolites, so I said, 'Okay, go do it!' With minimal help from us, she developed a working application to discover and extract every mention of stromatolites from our library."

Among 10,200 papers that mentioned stromatolites, "our program was able to extract 1,013 with a name of a rock unit, which enabled us to link stromatolite occurrences to Macrostrat," says Husson.

Wilcots did not have to travel to see stromatolites, Peters says. "In Madison, we are sitting on top of rocks recording one of the biggest rises in stromatolite abundance -- at least during the age of animals."

Scientists long ago observed that stromatolites started a long decline just before the start of the Cambrian era, but that decline represented a "fundamental question of paleobiology," Husson says. "Stromatolites are the oldest fossils that are visible to the naked eye. If you look at rock that is a billion years old, the chance for seeing evidence of life equals the chance of seeing stromatolites."

Beyond answering a fundamental question of Earth's history, the new study "allows us to do the kind of analyses that scientists used to only dream about, Peters says: 'If we could just compile all the published information on... anything!'

"Doing this study without GeoDeepDive would be all but impossible," Peters adds. "Reading thousands of papers to pick out references to stromatolites, and then linking them to a certain rock unit and geologic period, would take an entire career, even with Google Scholar. Here we got started with a talented undergrad working on a summer project. GeoDeepDive has greatly lowered the barrier to compiling literature data in order to answer many questions."

Another beauty of the big data, machine-reading approach is the baked-in capability for replication and improvement. "Now that this study has been done, we can run the stromatolite application again and again. We can refine the searches, and they will evaluate the new data that is being published all the time," Peters says. "So a rerun could make a better study, with minimal effort."

Read more at Science Daily