Mar 12, 2019

Meet India's starry dwarf frog, lone member of newly discovered ancient lineage

The starry dwarf frog is an expert hider. Plunging into leaf litter at the slightest disturbance, it has successfully evaded attention for millions of years -- until now.

The thumbnail-sized species was discovered in India's Western Ghats, one of the world's "hottest" biodiversity hotspots. Scientists have named the frog Astrobatrachus kurichiyana for its constellation-like markings and the indigenous people of Kurichiyarmala, the hill range where it was found.

But A. kurichiyana is not only a new species to science. It's the sole member of an ancient lineage, a long branch on the frog tree of life that researchers have classified as a new subfamily, Astrobatrachinae.

"This is an oddball frog -- it has no close sister species for maybe tens of millions of years," said David Blackburn, the associate curator of herpetology at the Florida Museum of Natural History. "With frogs, there are still ancient lineages out there awaiting discovery. This gives us one more puzzle piece to think about deep time."

Dark brown with a bright orange underbelly and speckled with pale blue dots, the frog camouflages well in wet leaf litter, and only a few individuals have been found.

"The coloration was the first thing that stood out to me, these starry patterns with a blue tinge," said Seenapuram Palaniswamy Vijayakumar, lead author of the species description and now a postdoctoral fellow at George Washington University. "We hadn't seen anything like this before."

But the starry dwarf frog nearly got overlooked in the crush of new species that Vijayakumar and his then-doctoral supervisor Kartik Shanker were finding on a series of expeditions to the Western Ghats, a 1,000-mile-long mountain range along India's southwestern coast.

Vijayakumar and Shanker, associate professor at the Indian Institute of Science, had designed a meticulous study, covering multiple elevations, habitats and hill ranges to record and map the region's frogs, lizards and snakes.

"When we started sampling, we realized we were digging up a huge treasure," Vijayakumar said. "This was one among 30 species we captured one night, and while I took photos of it, none of us paid much attention to it."

The next morning, on a chilly, wet stroll over the grasslands -- watching the ground for leeches -- Vijayakumar spotted another of the unusually patterned frogs.

"I picked it up and said, 'Hey, this is the same guy I photographed in the night,'" he said. "As a greedy researcher, I kept it, but at that point in time, it wasn't too exciting for me. I didn't realize it would become so interesting."

Years passed before Vijayakumar and Shanker could turn their attention to the unknown frog species and assemble a research team to describe it. Alex Pyron, the Robert F. Griggs associate professor of biology at George Washington University and now Vijayakumar's adviser, analyzed the frog's genetics, and Florida Museum associate scientist Edward Stanley CT scanned the frog, revealing its skeleton and other internal features.

Thanks to CT technology, the starry dwarf frog could traverse more than 8,700 miles from Pune, India, to Blackburn's computer monitor in Gainesville, Florida, in a matter of minutes.

"I've never physically seen this species we've put all this effort into describing," Blackburn said. "Once specimens are digitized, it really doesn't matter where they are. The strengths that Ed and I could contribute to the team -- comparative anatomy -- were things we were able to do digitally."

Blackburn and Stanley could instantly compare the starry dwarf frog's bone structure to other frog species from the Western Ghats that have been imaged as part of the openVertebrate project, known as oVert, an initiative to scan 20,000 vertebrates from museum collections.

"We have this deep bench of CT data that makes collections amassed over hundreds of years instantaneously available, not just to researchers, but to anyone with a computer," Stanley said.

The team found that A. kurichiyana's closest relatives are the family Nyctibatrachidae, a group of nearly 30 species native to India and Sri Lanka. But their last common ancestor could date back tens of millions of years.

"These frogs are relics. They persisted so long. This lineage could have been knocked off at any point in time," Vijayakumar said. "Irrespective of who we are, we should be celebrating the very fact that these things exist."

Scientists have found many ancient lineages of frogs in the Western Ghats, whose biodiversity stems from its history and distinct geography. India, once part of Africa, split from Madagascar about 89 million years ago and drifted northeast, eventually colliding with the Asian mainland and giving rise to the Himalayas. But its long isolation as an island provided fertile ground for the evolution of new life forms and may have sheltered species that disappeared elsewhere. This is especially true of the Western Ghats, which is much like a network of islands, Vijayakumar said. The elevated region has been cross-sectioned into separate hill ranges by millions of years of erosion and climatic changes.

"It's a perfect scenario for cooking up new species," he said.

One question he and Blackburn are interested in exploring further is whether peninsular India's frogs are the descendants of African ancestors or whether they first originated in Asia and then moved south.

Finding ancient lineages like Astrobatrachinae can help fill in in the region's distant biological past, but the starry dwarf frog maintains many mysteries of its own. Researchers still do not know its life cycle, the sound of its call or whether the species is threatened or endangered.

Read more at Science Daily

From Stone Age chips to microchips: How tiny tools may have made us human

The iconic, tear-drop shaped hand axe, which filled a human palm, required a large toolkit to produce (left), in contrast to a toolkit for tiny flakes.
Anthropologists have long made the case that tool-making is one of the key behaviors that separated our human ancestors from other primates. A new paper, however, argues that it was not tool-making that set hominins apart -- it was the miniaturization of tools.

Just as tiny transistors transformed telecommunications a few decades ago, and scientists are now challenged to make them even smaller, our Stone Age ancestors felt the urge to make tiny tools. "It's a need that we've been perennially faced with and driven by," says Justin Pargeter, an anthropologist at Emory University and lead author of the paper. "Miniaturization is the thing that we do."

The journal Evolutionary Anthropology is publishing the paper -- the first comprehensive overview of prehistoric tool miniaturization. It proposes that miniaturization is a central tendency in hominin technologies going back at least 2.6 million years.

"When other apes used stone tools, they chose to go big and stayed in the forests where they evolved," says co-author John Shea, professor of anthropology at Stony Brook University. "Hominins chose to go small, went everywhere, and transformed otherwise hostile habitats to suit our changing needs."

The paper reviews how stone flakes less than an inch in length -- used for piercing, cutting and scraping -- pop up in the archeological record at sites on every continent, going back to some of the earliest known stone tool assemblages. These small stone flakes, Pargeter says, were like the disposable razor blades or paperclips of today -- pervasive, easy to make and easily replaced.

He identifies three inflection points for miniaturization in hominin evolution. The first spike occurred around two million years ago, driven by our ancestors' increasing dependence on stone flakes in place of nails and teeth for cutting, slicing and piercing tasks. A second spike occurred sometime after 100,000 years ago with the development of high-speed weaponry, such as the bow and arrow, which required light-weight stone inserts. A third spike in miniaturization occurred about 17,000 years ago. The last Ice Age was ending, forcing some humans to adapt to rapid climate change, rising sea levels and increased population densities. These changes increased the need to conserve resources, including the rocks and minerals needed to make tools.

A native of South Africa, Pargeter co-directs field work in that country along its rugged and remote Indian Ocean coastline and nearby inland mountains. He is also a post-doctoral fellow in Emory University's Center for Mind, Brain and Culture and the Department of Anthropology's Paleolithic Technology Laboratory. The lab members actually make stone tools to better understand how our ancestors learned these skills, and how that process shaped our evolution. The lab's director, Dietrich Stout, focuses on hand axes, dating back more than 500,000 years. These larger tools are considered a turning point in human biological and cognitive evolution, due to the complexity involved in making them.

Pargeter's work on tiny tools adds another facet to the investigation of human evolution. "He's exploring what may have led to the compulsion to produce these tiny instruments -- essentially the relationship between the tools and the human body, brain and the probable uses of the tools," Stout says.

When looking for a PhD thesis topic, Pargeter first focused on collections of larger implements, considered typical of the Stone Age tool kit. He pored over artifacts from a South African site called Boomplaas that were being held in storage at the Iziko Museum in Cape Town. As he rummaged through a bag labelled as waste -- containing small flakes thought to be left over from making larger tools -- something caught his eye. A sliver of crystal quartz looked like it had been shaped using a highly technical method called pressure flaking.

"It was diminutive, about the size of a small raisin, and weighed less than half a penny," he recalls. "You could literally blow it off your finger."

Pargeter examined the flake under a magnifying glass. He noticed it had a distinctive, stair-step fracture on its tip that previous experimental research showed to be associated with damage caused in hunting.

"It suddenly occurred to me that archeologists may have missed a major component of our stone tool record," Pargeter says. "In our desire to make 'big' discoveries we may have overlooked tiny, but important, details. A whole technology could lay hidden behind our methods, relegated to bags considered waste material."

So how to interpret the use of a tool so tiny that you could easily blow it off your finger?

Pargeter began thinking of this question in terms of the age of the flake -- about 17,000 years -- and the environment at the time. The last Ice Age was ending and massive melting of ice at the poles caused the global sea-level to rise. In parts of South Africa, the rising oceans swallowed an area the size of Ireland. As the coastal marshes and grasslands disappeared -- along with much of the game and aquatic life -- the hunter-gatherers living there fled inland to sites like Boomplaas, currently located about 80 kilometers inland. The mountains around Boomplaas provided permanent springs and other dependable freshwater sources.

The climate, however, was less predictable, with sudden shifts in temperature and rainfall. Vegetation was shifting dramatically, temperatures were rising and large mammals were increasingly scarce. Archaeology from Boomplaas shows that people ate small game like hares and tortoises. These small animals would have been easy to catch, but they provided limited nutritional packages.

"These are low-reward food sources, indicating a foraging stress signal," Pargeter says. "Boomplaas might have even served as a type of refugee camp, with groups of hunter-gatherers moving away from the coast, trying to survive in marginal environments as resources rapidly depleted and climate change ratcheted up."

Arrow points a little less than an inch across were already in the archaeological literature, but the Boomplaas crystal quartz flake was half that size. In order to bring down an animal, Pargeter hypothesized, the Boomplaas flake would need poison on its tip -- derived either from plants or insects -- and a high-speed delivery system, such as a bow and arrow.

Pargeter used his own extensive knowledge of prehistoric tool-making and archaeology to hypothesize that the tiny flake could have been hafted, using a plant-based resin, onto a link shaft, also likely made of a plant-based material, such as a reed. That link shaft, about the length of a finger, would in turn fit onto a light arrow shaft.

"The link shaft goes into the animal, sacrificing the small blade, but the arrow shaft pops out so you can retain this more costly component," he says. "Our ancestors were masters of aerodynamics and acted like engineers, rather than what we think of as 'cave people.' They built redundancy into their technological systems, allowing them to easily repair their tools and to reduce the impact of errors."

Our ancestors were also connoisseurs of the type of fine-grained rocks needed for tool-making.

Supplies of such vital toolmaking raw materials, however, were likely diminished as the rising oceans consumed land and people became more crowded together, driving them to more carefully conserve what they could find on the landscape.

As paleoanthropologists are faced with more than three million years of hominin "stuff," one of the perennial questions they keep seeking to answer is, what makes us humans unique? "We've typically said that tool use makes us human, but that's kind of buckled under," Pargeter says, as evidence of tool use by other animals accumulates.

Macaques, for example, use rocks to smash apart oysters. Chimpanzees use rocks as hammers and anvils to crack nuts and they modify sticks to dig and fish for termites. These tools, however, are large. "The hands of other primates are not evolved for repeated fine manipulation in high-force tasks," Pargeter says. "We've evolved a unique precision grip that ratchets up our ability for miniaturized technology."

Read more at Science Daily

What scientists found after sifting through dust in the solar system

In this illustration, several dust rings circle the sun. These rings form when planets' gravities tug dust grains into orbit around the sun. Recently, scientists have detected a dust ring at Mercury's orbit. Others hypothesize the source of Venus' dust ring is a group of never-before-detected co-orbital asteroids.
Just as dust gathers in corners and along bookshelves in our homes, dust piles up in space too. But when the dust settles in the solar system, it's often in rings. Several dust rings circle the Sun. The rings trace the orbits of planets, whose gravity tugs dust into place around the Sun, as it drifts by on its way to the center of the solar system.

The dust consists of crushed-up remains from the formation of the solar system, some 4.6 billion years ago -- rubble from asteroid collisions or crumbs from blazing comets. Dust is dispersed throughout the entire solar system, but it collects at grainy rings overlying the orbits of Earth and Venus, rings that can be seen with telescopes on Earth. By studying this dust -- what it's made of, where it comes from, and how it moves through space -- scientists seek clues to understanding the birth of planets and the composition of all that we see in the solar system.

Two recent studies report new discoveries of dust rings in the inner solar system. One study uses NASA data to outline evidence for a dust ring around the Sun at Mercury's orbit. A second study from NASA identifies the likely source of the dust ring at Venus' orbit: a group of never-before-detected asteroids co-orbiting with the planet.

"It's not every day you get to discover something new in the inner solar system," said Marc Kuchner, an author on the Venus study and astrophysicist at NASA's Goddard Space Flight Center in Greenbelt, Maryland. "This is right in our neighborhood."

Another Ring Around the Sun

Guillermo Stenborg and Russell Howard, both solar scientists at the Naval Research Laboratory in Washington, D.C., did not set out to find a dust ring. "We found it by chance," Stenborg said, laughing. The scientists summarized their findings in a paper published in The Astrophysical Journal on Nov. 21, 2018.

They describe evidence of a fine haze of cosmic dust over Mercury's orbit, forming a ring some 9.3 million miles wide. Mercury -- 3,030 miles wide, just big enough for the continental United States to stretch across -- wades through this vast dust trail as it circles the Sun.

Ironically, the two scientists stumbled upon the dust ring while searching for evidence of a dust-free region close to the Sun. At some distance from the Sun, according to a decades-old prediction, the star's mighty heat should vaporize dust, sweeping clean an entire stretch of space. Knowing where this boundary is can tell scientists about the composition of the dust itself, and hint at how planets formed in the young solar system.

So far, no evidence has been found of dust-free space, but that's partly because it would be difficult to detect from Earth. No matter how scientists look from Earth, all the dust in between us and the Sun gets in the way, tricking them into thinking perhaps space near the Sun is dustier than it really is.

Stenborg and Howard figured they could work around this problem by building a model based on pictures of interplanetary space from NASA's STEREO satellite -- short for Solar and Terrestrial Relations Observatory.

Ultimately, the two wanted to test their new model in preparation for NASA's Parker Solar Probe, which is currently flying a highly elliptic orbit around the Sun, swinging closer and closer to the star over the next seven years. They wanted to apply their technique to the images Parker will send back to Earth and see how dust near the Sun behaves.

Scientists have never worked with data collected in this unexplored territory, so close to the Sun. Models like Stenborg and Howard's provide crucial context for understanding Parker Solar Probe's observations, as well as hinting at what kind of space environment the spacecraft will find itself in -- sooty or sparkling clean.

Two kinds of light show up in STEREO images: light from the Sun's blazing outer atmosphere -- called the corona -- and light reflected off all the dust floating through space. The sunlight reflected off this dust, which slowly orbits the Sun, is about 100 times brighter than coronal light.

"We're not really dust people," said Howard, who is also the lead scientist for the cameras on STEREO and Parker Solar Probe that take pictures of the corona. "The dust close to the Sun just shows up in our observations, and generally, we have thrown it away." Solar scientists like Howard -- who study solar activity for purposes such as forecasting imminent space weather, including giant explosions of solar material that the Sun can sometimes send our way -- have spent years developing techniques to remove the effect of this dust. Only after removing light contamination from dust can they clearly see what the corona is doing.

The two scientists built their model as a tool for others to get rid of the pesky dust in STEREO -- and eventually Parker Solar Probe -- images, but the prediction of dust-free space lingered in the back of their minds. If they could devise a way of separating the two kinds of light and isolate the dust-shine, they could figure out how much dust was really there. Finding that all the light in an image came from the corona alone, for example, could indicate they'd found dust-free space at last.

Mercury's dust ring was a lucky find, a side discovery Stenborg and Howard made while they were working on their model. When they used their new technique on the STEREO images, they noticed a pattern of enhanced brightness along Mercury's orbit -- more dust, that is -- in the light they'd otherwise planned to discard.

"It wasn't an isolated thing," Howard said. "All around the Sun, regardless of the spacecraft's position, we could see the same five percent increase in dust brightness, or density. That said something was there, and it's something that extends all around the Sun."

Scientists never considered that a ring might exist along Mercury's orbit, which is maybe why it's gone undetected until now, Stenborg said. "People thought that Mercury, unlike Earth or Venus, is too small and too close to the Sun to capture a dust ring," he said. "They expected that the solar wind and magnetic forces from the Sun would blow any excess dust at Mercury's orbit away."

With an unexpected discovery and sensitive new tool under their belt, the researchers are still interested in the dust-free zone. As Parker Solar Probe continues its exploration of the corona, their model can help others reveal any other dust bunnies lurking near the Sun.

Asteroids Hiding in Venus' Orbit

This isn't the first time scientists have found a dust ring in the inner solar system. Twenty-five years ago, scientists discovered that Earth orbits the Sun within a giant ring of dust. Others uncovered a similar ring near Venus' orbit, first using archival data from the German-American Helios space probes in 2007, and then confirming it in 2013, with STEREO data.

Since then, scientists determined the dust ring in Earth's orbit comes largely from the asteroid belt, the vast, doughnut-shaped region between Mars and Jupiter where most of the solar system's asteroids live. These rocky asteroids constantly crash against each other, sloughing dust that drifts deeper into the Sun's gravity, unless Earth's gravity pulls the dust aside, into our planet's orbit.

At first, it seemed likely that Venus' dust ring formed like Earth's, from dust produced elsewhere in the solar system. But when Goddard astrophysicist Petr Pokorny modeled dust spiraling toward the Sun from the asteroid belt, his simulations produced a ring that matched observations of Earth's ring -- but not Venus'.

This discrepancy made him wonder if not the asteroid belt, where else does the dust in Venus' orbit come from? After a series of simulations, Pokorny and his research partner Marc Kuchner hypothesized it comes from a group of never-before-detected asteroids that orbit the Sun alongside Venus. They published their work in The Astrophysical Journal Letters on March 12, 2019.

"I think the most exciting thing about this result is it suggests a new population of asteroids that probably holds clues to how the solar system formed," Kuchner said. If Pokorny and Kuchner can observe them, this family of asteroids could shed light on Earth and Venus' early histories. Viewed with the right tools, the asteroids could also unlock clues to the chemical diversity of the solar system.

Because it's dispersed over a larger orbit, Venus' dust ring is much larger than the newly detected ring at Mercury's. About 16 million miles from top to bottom and 6 million miles wide, the ring is littered with dust whose largest grains are roughly the size of those in coarse sandpaper. It's about 10 percent denser with dust than surrounding space. Still, it's diffuse -- pack all the dust in the ring together, and all you'd get is an asteroid two miles across.

Using a dozen different modeling tools to simulate how dust moves around the solar system, Pokorny modeled all the dust sources he could think of, looking for a simulated Venus ring that matched the observations. The list of all the sources he tried sounds like a roll call of all the rocky objects in the solar system: Main Belt asteroids, Oort Cloud comets, Halley-type comets, Jupiter-family comets, recent collisions in the asteroid belt.

"But none of them worked," Kuchner said. "So, we started making up our own sources of dust."

Perhaps, the two scientists thought, the dust came from asteroids much closer to Venus than the asteroid belt. There could be a group of asteroids co-orbiting the Sun with Venus -- meaning they share Venus' orbit, but stay far away from the planet, often on the other side of the Sun. Pokorny and Kuchner reasoned a group of asteroids in Venus' orbit could have gone undetected until now because it's difficult to point earthbound telescopes in that direction, so close to the Sun, without light interference from the Sun.

Co-orbiting asteroids are an example of what's called a resonance, an orbital pattern that locks different orbits together, depending on how their gravitational influences meet. Pokorny and Kuchner modeled many potential resonances: asteroids that circle the Sun twice for every three of Venus' orbits, for example, or nine times for Venus' ten, and one for one. Of all the possibilities, one group alone produced a realistic simulation of the Venus dust ring: a pack of asteroids that occupies Venus's orbit, matching Venus' trips around the Sun one for one.

But the scientists couldn't just call it a day after finding a hypothetical solution that worked. "We thought we'd discovered this population of asteroids, but then had to prove it and show it works," Pokorny said. "We got excited, but then you realize, 'Oh, there's so much work to do.'"

They needed to show that the very existence of the asteroids makes sense in the solar system. It would be unlikely, they realized, that asteroids in these special, circular orbits near Venus arrived there from somewhere else like the asteroid belt. Their hypothesis would make more sense if the asteroids had been there since the very beginning of the solar system.

The scientists built another model, this time starting with a throng of 10,000 asteroids neighboring Venus. They let the simulation fast forward through 4.5 billion years of solar system history, incorporating all the gravitational effects from each of the planets. When the model reached present-day, about 800 of their test asteroids survived the test of time.

Pokorny considers this an optimistic survival rate. It indicates that asteroids could have formed near Venus' orbit in the chaos of the early solar system, and some could remain there today, feeding the dust ring nearby.

The next step is actually pinning down and observing the elusive asteroids. "If there's something there, we should be able to find it," Pokorny said. Their existence could be verified with space-based telescopes like Hubble, or perhaps interplanetary space-imagers similar to STEREO's. Then, the scientists will have more questions to answer: How many of them are there, and how big are they? Are they continuously shedding dust, or was there just one break-up event?

Read more at Science Daily

Mar 11, 2019

Genes that evolve from scratch expand protein diversity

Rice plants
One of the most important questions in biology is how rapidly new proteins evolve in organisms. Proteins are the building blocks that carry out the basic functions of life. As the genes that produce them change, the proteins change as well, introducing new functionality or traits that can eventually lead to the evolution of new species.

A new study published in Nature Ecology and Evolution led by scientists from the University of Chicago challenges one of the classic assumptions about how new proteins evolve. The research shows that random, noncoding sections of DNA can quickly evolve to produce new proteins. These de novo, or "from scratch," genes provide a new, unexplored way that proteins evolve and contribute to biodiversity.

"Using a big genome comparison, we show that noncoding sequences can evolve into completely novel proteins. That's a huge discovery," said Manyuan Long, PhD, the Edna K. Papazian Distinguished Service Professor of Ecology and Evolution at UChicago and senior author of the new study.

A third way for genes to evolve

For decades, scientists believed that there were only two ways new genes evolved: duplication and divergence or recombination. During the normal process of replication and repair, a section of DNA gets copied and creates a duplicate version of the gene. Then, one of these copies may acquire mutations that change its functionality enough that it diverges and becomes a distinct new gene. With recombination, pieces of genetic material are reshuffled to create new combinations and new genes. However, these two methods only account for a relatively small number of proteins, given the total number of possible combinations of amino acids that comprise them.

Scientists have long wondered about a third mechanism, where de novo genes could evolve from scratch. All organisms have long stretches of genetic material that do not encode proteins, sometimes up to 97 percent of the total genome. Is it possible for these noncoding sections to acquire mutations that suddenly make them functional?

This has been difficult to study because it requires high-quality reference genomes from several closely related species that show both the ancestral, noncoding sequences and subsequent new genes that evolved from them. Without this clear, visible line of evolution, there's no way to prove it's truly a de novo gene. The supposed new genes reported previously could just be an "orphaned gene" that diverged or transferred from unrelated organisms at some point, then all traces of its predecessors disappeared.

To overcome these challenges, Long's team took advantage of 13 new genomes sequenced and annotated recently from 11 closely-related species of rice plants, including Oryza sativa, the most common food crop. He worked with groups headed by Prof. Rod Wing at the University of Arizona. Prof. Yidan Ouyang from Huazhong Agricultural University, China, also led a team that cultivated their own rice plants in Hainan, a tropical island off the southern coast of China, and harvested them for proteomics sampling.

After analyzing the genomes of these plants, they detected at least 175 de novo genes. Further mass spectrometry analysis of protein activity was conducted by another group led by Prof. Siqi Liu at BGI-Shenzhen, a genome sequencing center located in Shenzhen, Guangdong, China. They found evidence that 57 percent of these genes actually translated into new proteins, including more than 300 new peptides.

With this first, large dataset of authentic de novo genes, Long's team detected a pattern in their evolution. It began with the early evolution of expression, followed by subsequent mutation into protein coding potentials for almost all de novo genes.

"This makes sense given the widely observed expression of intergenic regions in various organisms," said Li Zhang, a postdoctoral researcher at UChicago and lead author of the article.

Long says that the Oryza plants are good genomes to search for de novo genes because they are relatively young -- you can still see evidence of evolution in their existing genomes.

"The 11 species diverged from each other only about three to four million years ago, so they are all young species," he said. "For that reason, when we sequence the genomes, all the sequences are highly similar. They haven't accumulated multiple generations of changes, so all the previous non-coding sections are still there."

Long and his team next want to study the new proteins to further understand their function and evolution and see if there is something unique about their structure. If de novo genes open up an unexplored path for evolution, they could reveal mechanisms for creating new and improved cellular functions. For instance, the researchers detected evidence of natural selection acting to fix insertions and deletions in the genome to generate new protein sequences, and the sequence's evolution toward improved functions.

Read more at Science Daily

Palaeolithic art featuring birds and humans discovered

Image of the findings with a tracing of the engraved figures on the piece.
It is not very common to find representations of scenes instead of individual figures in Palaeolithic art, but it is even harder for these figures to be birds instead of mammals such as goats, deer or horses. So far, historians have only found three scenes of Palaeolithic art featuring humans and birds in Europe.

Now, an article published in the journal L'Anthropologie tells how University of Barcelona researchers found -in the site of Hort de la Bequera (Margalef de Montsant, Priorat)-, an artistic piece from 12,500 years ago in which humans and birds try to interact in a pictorial scene with exceptional traits: figures seem to star a narration on hunting and motherhood. Regarding the Catalan context in particular, this is an important finding regarding the few pieces of Palaeolithic art in Catalonia and it places this territory within the stream of artistic production of the upper Palaeolithic in the Mediterranean.

The piece they found is a 30-centimeter long limestone which shows two human figures and two birds, which the researchers identified as cranes. Since they found the piece in 2011, they underwent all cleaning, restoration and 3D copying procedures to study it in detail. Those figures were engraved in the stone board with a flint tool so that they created an organized composition compared to the other pieces of the same period.

"This is one of the few found scenes so far which suggest the birth of a narrative art in Europe, and this theme is unique, since it combines an image of hunting and a motherhood one: a birth with its young one," says the first signer of the article, ICREA researcher and lecturer at the UB Inés Domingo. "In the represented scene the birds catch the attention, they are copied or chased by two human figures," continues Domingo. "We do not know the meaning of the scene for prehistoric peoples, but what it says is that not only they were regarded as preys but also as a symbol for European Palaeolithic societies," she continues.

"We do not doubt this is an exceptional milestone in European Palaeolithic rock art due its singularity, its excellent conservation and the chances to study it within a general context of excavation," say the authors of the article; members of the Prehistoric Studies and Research Seminar (SERP). Apart from Domingo, other signers are the UB lecturers of Prehistory Pilar García Argüelles, Jordi Nadal, directors of the excavation in Host de la Boquera, Professor Josep Maria Fullola, director of SERP, and José L. Lerma and the researcher Miriam Cabrelles, from Universitat Politècnica de València, who worked on the 3D reproduction of this piece.

Palaeolithic art in Montsant valley

The other sites in Europe researchers had found so far with human and bird figures are rock paintings in the site of Lascauz, a perforated baton in Abri Mege (Teyjat, Dordogne), and the Great Hunter plaque in the site of Gönnersdorf (Germany).

SERP researchers have been excavating in the valley of Montsant since 1979, an exceptional area regarding findings of this period of the late upper Palaeolithic. In particular, excavations have taken place in Host de la Boquera since 1998 and it provided a great amount of flint tools and structure such as rooms for a fireplace.

The director of the excavation, Pilar García Argüelles notes that "the findings of the engraved scene are exceptional, and proves the importance of the site and the area regarding Palaeolithic art in the peninsular north-east area; where we can find nearby the only Palaeolithic cave engraving in Catalonia, the deer in the cave of Taverna (Margalef de Montsant), and about 40 kilometres away there is Molí del Salt (Vimbodí), with an interesting series of stone blocks with engraved animals and a representation of huts."

Read more at Science Daily

Teenage T. rex was already chomping on prey

Joseph Peterson, a vertebrate paleontologist at the University of Wisconsin Oshkosh, demonstrates how a T. rex takes a bite.
New research from the University of Wisconsin Oshkosh indicates that even as a teenager the Tyrannosaurus rex showed signs that it would grow up to be a ferocious predator.

In a study published last week in the peer-reviewed journal Peerj -- the Journal of Life and Environmental Sciences, UWO scientists reported evidence that a juvenile T. rex fed on a large plant-eating dinosaur, even though it lacked the bone-crushing abilities it would develop as an adult.

While studying fossils from an Edmontosaurus -- a plant-eating Hadrosaurid or duck-billed dinosaur, UWO vertebrate paleontologist Joseph Peterson noticed three large, v-shaped, bite marks on a tail bone and wondered, "Who made these?"

Peterson knew that T. rex -- a member of the meat-eating dinosaur suborder known as Theropoda -- was "a likely culprit."

"We suspected that T. rex was responsible for the bit marks, because in the upper Cretaceous rock formation, where the hadrosaur was discovered, there are only a few carnivorous dinosaurs and other reptiles in the fossil record. Crocodile fossils are found there, but such a crocodile would have left tooth marks that are round rather than the elliptical punctures we found on the vertebra," Peterson explained.

"There also were small Velociraptor-like dinosaurs, but their teeth are too small to have made the marks. Finally, an adult T. rex would have made punctures that would have been too large! That's when we started considering a juvenile tyrannosaur."

To test the hypothesis, Peterson and geology student Karsen Daus, of Suamico, coated the fossil with a silicon rubber to make a silicone peel of the puncture marks.

They found that the dimensions of the "teeth" better matched a late-stage juvenile T. rex (11 to 12 years) than an adult (approximately 30 years).

"Although this T. rex was young, it really packed a punch," Peterson said.

"This is significant to paleontology because it demonstrates how T. rex -- the most popular dinosaur of all time -- may have developed changes in diet and feeding abilities while growing," he said. "This is part of a larger, ongoing research initiative by many paleontologists to better understand how T. rex grew and functioned as a living creature over 65 million years ago."

Most theropod feeding traces and bite marks are attributed to adults; juvenile tooth marks rarely have been reported in the literature, he added.

Read more at Science Daily

Massive twin star discovered snuggling close to its stellar sibling

2MASS observations (background image) revealed a highly reddened source back in 2003 indicating the massive young nature of PDS 27. PIONIER on VLTI provides 2,000 times higher angular resolution making it possible to resolve PDS 27 as a binary system for the first time in 2019.
Astronomers have discovered a binary star system with the closest high-mass young stellar objects ever measured, providing a valuable "laboratory" to test theories on high mass binary star formation.

An international team led by the University of Leeds has determined the distance between the massive young star PDS 27 and its orbiting stellar companion to be just 30 astronomical units away or 4.5 billion km. That is roughly the distance between our Sun and Neptune, making them the stellar companions with the closest proximity ever determined for young high mass stars in a binary system -- a star system with two stars in orbit around a centre of mass.

Study lead author, Dr Evgenia Koumpia, from the School of Physics and Astronomy at Leeds, said: "This is a very exciting discovery, observing and simulating massive binaries at the early stages of their formation is one of the main struggles of modern astronomy. With PDS 27 and its companion we have now found the closest, most massive young stellar objects in binaries resolved to date.

"There is a shortage of known young massive binary systems in charted space. High mass stars have comparatively short lifespans, burning out and exploding as supernovae in only a few million years, making them difficult to spot. This limits our ability to test the theories on how these stars form."

As part of their study the team has also identified a companion object for another young massive star referred to as PDS 37. The analysis revealed a distance between PDS 37 and its companion to be between 42 to 54 astronomical units -comparable to the distance between the Sun and Pluto. While further apart than PDS 27 and its companion, it is still a significant discovery given the need for confirmed massive young stellar binaries in astronomical research.

Dr Koumpia continued: "How these binary systems form is quite a controversial question with several theories having been put forward. Observational studies of binaries in their early stages are crucial to verifying the theories of their formation.

"PDS 27 and PDS 37 are rare and important laboratories that can help inform and test the theories on the formation of high mass binaries."

PDS 27 is at least 10 times more massive than our Sun, Dr Koumpia explained, and about 8,000 light years away. To determine the presence of stellar companions for PDS 27 and PDS 37, the team used the highest spatial resolution provided by the PIONIER instrument on the European Southern Observatory's Very Large Telescope Interferometer (VLTI). This instrument combines light beams from four telescopes, each of which is 8.2 metres across, and mimics a single telescope with a diameter of 130m. The resulting high spatial resolving power allowed the team to resolve such close binary systems despite their huge distance from us and their close proximity to each other.

Study co-author Professor Rene Oudmaijer, also from the School of Physics and Astronomy at Leeds, said: "The next big question -- which we have tended to avoid so far because of observational difficulties -- is why so many of these massive stars are in binary systems?"

"It has become increasingly clear to astronomers that massive stars are almost never born alone, with at least one sibling for company. But the reasons why that is the case are still rather murky.

"Massive stars exert significant influence on their cosmic environment. Their stellar winds, energy and the supernova explosions they generate in turn can impact the formation of other stars and galaxies. The evolution and fate of high-mass stars is quite complex but previous studies have shown that they can be influenced to a large degree by their binary properties.

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Kepler Space Telescope's first exoplanet candidate confirmed

Sound waves propagating through the stellar interior were used to characterize the star and the planet. Kepler-1658b, orbiting with a period of just 3.8 days, was the first exoplanet candidate discovered by Kepler nearly 10 years ago.
An international team of astronomers, led by University of Hawaii graduate student Ashley Chontos, announced the confirmation of the first exoplanet candidate identified by NASA's Kepler Mission. The result was presented at the fifth Kepler/K2 Science Conference held in Glendale, CA.

Launched almost exactly 10 years ago, the Kepler Space Telescope has discovered thousands of exoplanets using the transit method -- small dips in a star's brightness as planets cross in front of the star. Because other phenomena can mimic transits, Kepler data reveal planet candidates, but further analysis is required to confirm them as genuine planets.

Despite being the very first planet candidate discovered by NASA's Kepler Space Telescope, the object now known as Kepler-1658 b had a rocky road to confirmation. The initial estimate of the size of the planet's host star was incorrect, so the sizes of both the star and Kepler-1658 b were vastly underestimated. It was later set aside as a false positive when the numbers didn't quite make sense for the effects seen on its star for a body of that size. Fortuitously, Chontos' first year graduate research project, which focused on re-analyzing Kepler host stars, happened at just the right time.

"Our new analysis, which uses stellar sound waves observed in the Kepler data to characterize the host star, demonstrated that the star is in fact three times larger than previously thought. This in turn means that the planet is three times larger, revealing that Kepler-1658 b is actually a hot Jupiter-like planet," said Chontos. With this refined analysis, everything pointed to the object truly being a planet, but confirmation from new observations was still needed.

"We alerted Dave Latham (a senior astronomer at the Smithsonian Astrophysical Observatory, and co-author on the paper) and his team collected the necessary spectroscopic data to unambiguously show that Kepler-1658 b is a planet," said Dan Huber, co-author and astronomer at the University of Hawaii. "As one of the pioneers of exoplanet science and a key figure behind the Kepler mission, it was particularly fitting to have Dave be part of this confirmation."

Kepler-1658 is 50% more massive and three times larger than the Sun. The newly confirmed planet orbits at a distance of only twice the star's diameter, making it one of the closest-in planets around a more evolved star -- one that resembles a future version of our Sun. Standing on the planet, the star would appear 60 times larger in diameter than the Sun as seen from Earth.

Planets orbiting evolved stars similar to Kepler-1658 are rare, and the reason for this absence is poorly understood. The extreme nature of the Kepler-1658 system allows astronomers to place new constraints on the complex physical interactions that can cause planets to spiral into their host stars. The insights gained from Kepler-1658b suggest that this process happens slower than previously thought, and therefore may not be the primary reason for the lack of planets around more evolved stars.

Read more at Science Daily

Mar 10, 2019

Scientists tackle major challenges to sending astronauts to search for life on Mars

Allyson Brady examines samples of basalt rock.
An international team of researchers, which includes scientists from McMaster's School of Geography & Earth Sciences, NASA, and others, is tackling one of the biggest problems of space travel to Mars: what happens when we get there?

A series of articles published today in a special edition of the journal Astrobiology, focuses on the scientific, logistical, operational and communications challenges of sending astronauts to deep space.

It is the culmination of years of work in NASA's BASALT research program, or the Biologic Analog Science Associated with Lava Terrains, which involves geologists, microbiologists, geneticists, engineers and astrobiologists from all over the world.

One of the biggest challenges the team is investigating is how best to conduct meaningful science in such harsh and dangerous conditions -- where time and resources are highly restricted -- and how to send valuable information back to Earth to enable input from an Earth-based science support team.

Researchers simulated mission conditions on Mars in several scenarios which included conducting field work in the unforgiving, Mars-like terrain of Craters of the Moon National Park Monument and Preserve in Idaho and the Hawaii Volcanoes National Park.

These regions are rich in basalt, a fine-grained rock similar to rock found on Mars. Scientists hope samples can provide important clues in the ongoing search for life on Mars.

Supported by funding from the Canadian Space Agency, Allyson Brady, a post-doctoral fellow in McMaster's School of Geography & Earth Sciences, who is working with her advisor Greg Slater on the project, is investigating organic biomarkers of microbial life associated with the rocks.

"When astronauts finally go to Mars, we need to identify the best place to potentially find evidence of life and to target the kind of basalt rock samples which may contain a lot of organic material, for example," explains Brady. "There will be many, many limitations on Mars so we need to consider the best way to conduct research and gather samples including getting timely feedback from science experts on Earth."

Brady and NASA scientists are also considering the challenges of sharing information when teams are millions of kilometres apart. For example, they tested different forms of communications -- video and photo transmissions, voice messaging, texting using specialized software -- between field researchers, who wore communications packs as an astronaut might, and mission control.

"There can be a significant delay, as long as 20 minutes, between an astronaut on Mars and the team on earth," explains Brady. "So we are working to optimize operations so astronauts don't have idle time and the flow of information continues," she says.

From Science Daily

Blood holds key to liver regeneration

The liver is the only organ in the body that can regenerate. But some patients who undergo a liver resection, a surgery that removes a diseased portion of the organ, end up needing a transplant because the renewal process doesn't work.

A new Michigan State University study, published in the journal Blood, shows that the blood-clotting protein fibrinogen may hold the key as to why this happens.

"We discovered that fibrinogen accumulates within the remaining liver quickly after surgery and tells platelets to act as first responders, triggering the earliest phase of regeneration," said James Luyendyk, a professor of pathobiology in the College of Veterinary Medicine. "But if fibrinogen or platelets are inhibited, then regeneration is delayed."

Platelets are blood cells that help form clots and stop bleeding. When they receive information from fibrinogen, they go into action and accumulate in the remaining part of the liver to help restore it, increasing the chances of a fully functional liver and successful recovery.

Using samples from patients undergoing liver resection and a comparable model in mice, Luyendyk and his team noticed that when fibrinogen was low, the number of platelets in the liver decreased.

"This shows that fibrinogen deposits are extremely important and directly impact regeneration in both mice and humans," Luyendyk said.

According to Dafna Groeneveld, Luyendyk's co-author and post-doctoral research associate in his lab, their finding demonstrates that fibrinogen levels could be a predictive marker for doctors, too.

"Measuring this protein in liver resection patients may help us determine in advance whether the organ will regenerate successfully or if it will become dysfunctional," she said.

This could lead to new treatments that would help doctors correct low levels of the protein by using fibrinogen concentrates that can be administered during surgery.

"This type of treatment hasn't been tried in liver resection patients yet," Luyendyk said. "But once we figure out exactly how fibrinogen works in the regeneration process and test potential therapies in mice, it could eventually provide the proof we need to bring our work into the clinic and improve patient outcomes."

From Science Daily