Mar 12, 2016
These are the so-called van der Waals forces, which are ubiquitous in nature and thought to play a crucial role in determining the structure, stability and function of a wide variety of systems throughout the fields of biology, chemistry, physics and materials science.
"To put it simply, every molecular system and every material in nature experiences these forces," said Robert A. DiStasio Jr., assistant professor of chemistry and chemical biology in the College of Arts and Sciences. "In fact, we are finding that their influence is quite extensive, and includes protein-drug interactions, the stability of the DNA double helix, and even the peculiar adhesion properties of the gecko's foot."
When compared with the covalent bond (which involves the sharing of electron pairs between atoms), van der Waals forces are relatively weak and arise from instantaneous electrostatic interactions between the fluctuating electron clouds that surround microscopic objects. However, these forces are still quantum mechanical in origin and have posed a substantial challenge for both theory and experiment to date.
In a paper in the March 11 issue of Science, DiStasio and collaborator Alexandre Tkatchenko of the University of Luxembourg and the Fritz Haber Institute have put forth a new proposition for describing van der Waals forces among objects at the nanoscale.
Generally speaking, there are two schools of thought regarding these forces. The prevailing description of van der Waals interactions among most chemists and biologists is the picture of two induced electric dipoles, similar to the N and S poles of a magnet, representing the uneven distributions of positive and negative charges. The picture espoused by many physicists, however, centers around the fact that wavelike vacuum fluctuations are responsible for the van der Waals interactions among larger macroscopic objects.
In their work, DiStasio and Tkatchenko demonstrate that these fundamental forces between nanostructures must also be described by the electrostatic interactions between wavelike (or delocalized) charge density fluctuations instead of the aforementioned particle-like (or local) induced dipoles. They believe their work could help to bridge the gap between these two belief systems, and help scientists understand and control the interactions between objects at the nanoscale.
"Our work is demonstrating that there is a much wider variety of systems, such as nanostructured systems, where you have to think about the van der Waals force in terms of interactions between waves instead of interactions between particles," Tkatchenko said.
Paul McEuen, the John A. Newman Professor of Physical Science and director of the Kavli Institute at Cornell for Nanoscale Science, sees the duo's research as an important first step in a long, complicated journey to what McEuen half-jokingly characterized as "solving biology."
"It sounds like a rather boring problem, but it's actually a deeply important problem, the way biomolecules assemble and so on," said McEuen. "It's a hugely important problem, especially for someone like me, who's a nano-guy, but it's going to take time to solve."
Read more at Science Daily
"It is like these electrons go down a rabbit hole and show up on the opposite surface," said Ali Yazdani, the Class of 1909 Professor of Physics. "You don't find anything else like this in other materials."
The research was published in the journal Science.
Yazdani and his colleagues discovered the odd behavior while studying electrons in a crystal made of layers of tantalum and arsenic. The material, called a Weyl semi-metal, behaves both like a metal, which conducts electrons, and an insulator, which blocks them. A better understanding of these and other "topological" materials someday could lead to new, faster electronic devices.
The team's experimental results suggest that the surface electrons plunge into the crystal only when traveling at a certain speed and direction of travel called the Weyl momentum, said Yazdani. "It is as if you have an electron on one surface, and it is cruising along, and when it hits some special value of momentum, it sinks into the crystal and appears on the opposite surface," he said.
These special values of momentum, also called Weyl points, can be thought of as portals where the electrons can depart from the surface and be conducted to the opposing surface. The theory predicts that the points come in pairs, so that a departing electron will make the return trip through the partner point.
The team decided to explore the behavior of these electrons following research, published in Science last year by another Princeton team and separately by two independent groups, revealing that electrons in Weyl semi-metals are quite unusual. For example, their experiments implied that while most surface electrons create a wave pattern that resembles the spreading rings that ripple out when a stone is thrown into a pond, the surface electrons in the new materials should make only a half circle, earning them the name "Fermi arcs."
To get a more direct look at the patterns of electron flow in Weyl semi-metals, postdoctoral researcher Hiroyuki Inoue and graduate student András Gyenis in Yazdani's lab, with help from graduate student Seong Woo Oh, used a highly sensitive instrument called a scanning tunneling microscope, one of the few tools that can observe electron waves on a crystal surface. They obtained the tantalum arsenide crystals from graduate student Shan Jiang and assistant professor Ni Ni at the University of California-Los Angeles.
The results were puzzling. "Some of the interference patterns that we expected to see were missing," Yazdani said.
Read more at Science Daily
Mar 11, 2016
The earthen mix turned out to be a blessing, since the cannabis played a key role in preserving the World Heritage site.
According to Manager Rajdeo Singh, an archaeological chemist of the Archaeological Survey of India’s science branch (western region), and Milind M. Sardesai, who teaches botany at Dr Babasaheb Ambedkar Marathwada University, the mixture prevented the plaster from degrading for over 1,500 years.
The Ellora caves were built between the 6th and 11th centuries, A.D. in the western state of Maharashtra. They are made up of a group of 34 temples carved out of stone and are dedicated to the three main religions of India — Buddhism, Hinduism and Jainism.
The structure runs in a north–south direction for about 1.2 miles. At the southern end are 12 Buddhist caves, in the north are six Jain caves and in between lie 17 Brahmanical caves.
“The caves are breathtaking examples of rock-cut architecture that stands testimony to the imagination and artistry of its creators,” Singh and Sardesai wrote in the journal Current Science.
They analyzed the clay plaster of Buddhist cave no. 12, a remarkable three-storied building.
Using a scanning electron microscope, infrared spectroscopy and stereomicroscopic studies, the researchers were able to isolate specimens of cannabis from the clay plaster.
The remains of cannabis, popularly known as ganja or bhang in India, suggest that it was used in the clay and lime mixture mainly as an insulating agent and to provide added strength to the plaster.
“The cannabis fiber appears to have a better quality and durability than other fibers. Moreover, the cannabis’ gum and sticky properties might have helped clay and lime to form a firm binder,” Sardesai told Discovery News.
Called hempcrete, the concrete-like substance used for plastering provided “a healthy, comfortable and aesthetically pleasing living environment to the Buddhist monks to stay,” the researchers said.
“As the hemp plaster has the ability to store heat, is fire-resistant and absorbs about 90 percent of airborne sound, a peaceful living environment for the monks has been created at Ellora Caves,” they added.
Studies in Europe have estimated that hempcrete can last 600–800 years. In the Ellora caves the life span doubled despite damaging environmental factors, such as a growing humidity inside the caves during rainy seasons.
Read more at Discovery News
An international team of scientists from Brazil and the United Kingdom has described Teyujagua paradoxa, a small quadruped just under 5 feet (1.5 meters) long, with nostrils high up on its snout and sharp teeth, reminiscent of modern crocodiles.
The sharp, pointed teeth indicate it was a carnivore that likely ate amphibians and other, smaller reptile-like fare.
The dating of the fossil, which was found in Brazil’s state of Rio Grande do Sul, is significant to the scientists. At 250 million years old, the creature’s existence falls just after the Permian-Triassic mass extinction event of 252 million years ago known as “the great dying,” in which roughly 90 percent of all living species were wiped out, for reasons not yet known with certainty.
The fossil could help scientists understand how ecosystems and animal life rebounded after that event, clarifying the evolution of a group of animals that would give rise to dinosaurs, birds, crocodiles, and pterosaurs.
"Teyujagua is a really important discovery because it helps us understand the origins of a group of vertebrates called archosauriforms,” study co-author Richard Butler, of the University of Birmingham, explained in a press release.
“Archosauriforms are spectacularly diverse and include everything from hummingbirds and crocodiles to giant dinosaurs like Tyrannosaurus rex and Brachiosaurus. Teyujagua fills an evolutionary gap between archosauriforms and more primitive reptiles and helps us understand how the archosauriform skull first evolved,” Butler added.
The Teyujagua in the new reptile's name translates to “fierce lizard,” from the South American Guarani language, and references a mythological lizard with a dog’s head.
The team’s findings have just been published in the journal Scientific Reports.
From Discovery News
The report – Attribution of Extreme Weather Events in the Context of Climate Change – notes that asking “Did climate change cause X?” fails to recognize the context in which extreme weather events take place.
Such events, of course, have always occurred, and would be doing so now even if human activity wasn’t affecting the climate. They also require multiple contributory factors, but they do not occur in a vacuum: All weather, extreme or otherwise, is a function of the prevailing climate. So the picture can, depending on how you approach it, sometimes appear muddied.
For example, in the summer of 2010, Russia baked in a heatwave that saw daytime temperatures in Moscow surge past 100F, higher than any temperature listed in records that date back to 1879. One study reviewing that heat wave argued that it was largely natural because the temperature anomalies were greatly in excess of those explainable by long-term warming trends; another, in contrast, concluded that the anthropogenic influence was significant because long-term climate change, though small, greatly increased the probability of exceeding specified temperature thresholds.
Retired Rear Adm. David W. Titley of Penn State chaired the committee that wrote the report. He noted in a press briefing today that there are better questions to ask than “Did climate change cause this?” He suggested instead: “Are events of this severity becoming more or less likely because of climate change?” or “To what extent was this event more or less intense because of climate change?” That may seem less satisfying, but it allows the subject to be framed more accurately.
Marshall Shepherd, director of the University of Georgia’s Atmospheric Sciences Program, a past president of the American Meteorological Society, and a co-author of the new report, uses a sporting analogy to describe the difference: “Home run frequency and length varied naturally in Major League Baseball, but after the steroid era the influence was seen in the home run statistics. But was a certain baseball player’s 300th home run caused by steroids? That’s an ill-posed question.”
The new report argues that, while the causation question may be unhelpful, climate science has, in the words of co-author Adam Sobel of Columbia University, “reached the point where we can look for the human influence on climate in single weather events, and sometimes find it.”
Scientists are developing the ability to do this, says the report, by analyzing two worlds: the real one, in which atmospheric carbon dioxide levels are rising as a result of human activity, and an imaginary one in which the Industrial Revolution never happened and the climate is only influenced by solar and volcanic activity. By running computer simulations for both worlds, they are able to gain a sense of how much more likely a particular drought or flooding event is to occur in one world or the other.
To do so accurately requires what Titley called the “three legs of a stool:” sound physical principles — a clear understanding of how a changing climate might affect a particular type of event — consistent observational evidence and the ability for numerical models to replicate the event. By using those criteria as benchmarks, the report found that science was far better at assessing the links between climate and some types of events than others.
In general, the report concluded, the case is easiest to make with events that are most directly related to temperature, such as extreme heat, because, Sobel noted in the Washington Post, “the chain of causality from global warming to the event is shortest and simplest.” That Moscow heatwave, for example, which might have occurred once in a lifetime in the fictional world, is now what Titley called a “once in a mortgage event,” which could be expected every 30 years or so.
Such things as drought and extreme rainfall are more complicated, whether because of a shorter observational record, less reliable models or a less robust understanding of the physics — or some combination of the above. As report co-author Heidi Cullen of Climate Central wrote in the New York Times on Friday, the ongoing California drought is an example of this complexity: “While we now know that higher temperatures resulting from global warming are worsening the drought, current evidence indicates that the lack of precipitation in the state is not primarily a result of climate change.”
Confidence is low or non-existent in making the climate connection with tornadoes because, observed Sobel, “our models don’t yet have enough resolution to simulate them — like a digital camera with too few pixels to see someone’s face from far away — their relation to temperature is indirect, and not enough research has been done for us even to be sure how they should be changing.”
Read more at Discovery News
Even more surprising, the delicate limestone spires were uncovered nearly 165 feet (50 meters) below the water’s surface. The discovery may mark the first time scientists have uncovered limestone pillars, called sea stacks, below the water’s surface. (Most of these sea stacks form on the coastline, above the water line.)
“Sea stacks are always eroding, as we saw with the one that collapsed in 2005, so it is hugely surprising that any could be preserved at that depth of water,” David Kennedy, a geographer at the University of Melbourne in Australia, said in a statement.
Kennedy was referring to one of the shoreline spires, which toppled spectacularly in 2005.
The limestone spires were formed through a process similar to the one that carved the famous tourist attraction of the Twelve Apostles, a handful of limestone stacks that jut out from the coastline of Victoria, Australia. These impressive sea stacks occur only when conditions are just right so that water and wind can erode a slab of rock into a steep, vertical column or columns: Rocks such as granite are too hard to erode quickly enough, while softer clay cliffs cannot support the weight of the overlying piles of rock. Limestone provides the perfect medium because it is soft but maintains a high compressive strength, the researchers wrote in the paper, which was published in the Journal of Coastal Research and will be presented today (March 10) at the International Coastal Symposium in Sydney.
Kennedy and his colleagues were surveying the seafloor to map the reefs around Victoria, which are home to abalone and rock lobster hunted by commercial fishermen. While mapping the ocean floor with sonar beams, Rhiannon Bezore, a doctoral candidate in geography at the University of Melbourne, found a series of short sea stacks next to some drowned cliffs.
Read more at Discovery News
Scientists from the Department of Earth Sciences at Royal Holloway, University of London, have found the oldest pine tree fossils yet to be discovered, in a rock quarry in the Canadian province of Nova Scotia.
Interestingly, the fossils appear to be charred from a fire. When the tree was alive, the atmosphere had high oxygen levels,and the temperature was high. That created prime conditions for fires. Pine trees actually have evolved to burn and spread forest fires, so that their pine cones can germinate on the charred forest floor without competition.
“The fossils show that wildfires raged through the earliest pine forests and probably shaped the evolution of this important tree,” researcher Howard Falcon-Lang said in a press release.
The specimens, which are described in Geology journal, were preserved as charcoal within rocks from a quarry.
“It was only when I digested (the samples) in acid that these beautiful fossils fell out,” Dr Falcon-Lang told BBC News.
From Discovery News
Mar 10, 2016
The spider, dolomedes briangreenei, had a public debut of sorts, Mashable Australia reports, when it was presented to its namesake, physicist Brian Greene, at the World Science Festival in Brisbane, Australia.
Dolomedes briangreenei lives among the fresh-water streams in Brisbane and makes note of waves on the surface of the water that tell it prey is nearby. It will swim out on the water to make a meal out of insects, fish, and toads, hauling its prey back to shore to devour it.
D. briangreenei isn't the only spider that works in water worlds. In 2014, DNews reported findings that showed semi-aquatic spiders are distributed worldwide. Check out this gallery to see more of them.
The swimming arachnid can be seen here, in a tweet from the World Science Festival, as physicist Greene displays the spider that bears his name. (The spider, dubbed “little Brian,” will ultimately live at Queensland Museum.)
From Discovery News
An excavation uncovered dozens of other artifacts, including plates and bowls, three ovens, and the base of a millstone that was likely used for grinding flour, the researchers said.
The finding is a valuable one, said study co-researcher Benjamin Luley, a visiting assistant professor of anthropology and classics at Gettysburg College in Pennsylvania. Before the Romans invaded the south of France, in 125 B.C., a culture speaking the Celtic language lived there and practiced its own customs.
These Celtic people lived in densely settled, fortified sites during the Iron Age (750 B.C. to 125 B.C.), trading with cultures near and far, the researchers said. But after the Roman invasion, the Celtic culture at this location changed socially and economically, Luley said.
For instance, the new findings suggest that some people under the Romans stopped preparing their own meals and began eating at communal places, such as taverns.
“Rome had a big impact on southern France,” Luley told Live Science. “We don’t see taverns before the Romans arrive.”
The newly excavated tavern is located at Lattara, an archaeological site that’s been known to modern researchers since the early 1980s. But Luley and his colleague Gae?l Pique?s, a researcher at the French National Center for Scientific Research, were specifically looking for artifacts dating to the end of the Iron Age, when the Romans arrived, the archaeologists said.
The researchers were in luck: The site they uncovered dates to about 125 B.C. to 75 B.C., spanning the period following the Roman conquest, and was located at the intersection of two important streets, the scientists said.
At first, the researchers weren’t sure what to make of it. But a number of clues suggested the site was once a bustling tavern, one that likely served fish, flatbread, and choice cuts of cows and sheep, Luley said.
The excavated area includes a courtyard and two large rooms; one was dedicated to cooking and making flour, and the other was likely reserved for serving patrons, the researchers said.
There are three large bread ovens on one end of the kitchen, which indicates that “this isn’t just for one family,” but likely an establishment for serving many people, Luley said. On the other side of the kitchen, the researchers found a row of three stone piles, likely bases for a millstone that helped people grind flour, Luley said.
“One side, they’re making flour. On the other side, they’re making flatbread,” Luley said. “And they’re also probably using the ovens for other things as well.” For example, the archaeologists found lots of fish bones and scales that someone had cut off during food preparation, Luley added. [Photos: Mosaic Glass Dishes and Bronze Jugs from Roman England]
The other room was likely a dining room, the researchers said. The archaeologists uncovered a large fireplace and a bench along three of the walls that would have accommodated Romans, who reclined when they ate, Luley said. Moreover, the researchers found different kinds of animal bones, such as wishbones and fish vertebra, which people simply threw on the floor. (At that time, people didn’t have the same level of cleanliness as some do now, Luley noted.)
The dining room also had “an overrepresentation of drinking bowls,” used for serving wine — more than would typically be seen in a regular house, he said.
Read more at Discovery News
Over 1.1 million square miles, from the eastern Mediterranean Sea to what is now Siberia, were blanketed.
Blowing up from the Campi Flegrei, or Phlegrean Fields, on the Bay of Naples, the eruption created a four-mile-wide caldera and produced the cliffs on which the Camaldoli monastery now stands.
The long-term global impacts were so intense that they slowed the westward migration of modern hominid groups in Europe.
“It was the largest volcanic eruption of the past 200,00 years in Europe,” Antonio Costa, a researcher of geophysics at the National Institute of Geophysics and Volcanology (INGV) said.
Costa and colleagues detailed their findings in the journal Scientific Reports. They analyzed more than 100 geological deposits from the dispersal area up to Russia, and found the samples featured two different grain size, one coarser and the other finer.
“Such bimodal grain size distributions indicate two distinct phases of the eruption,” Costa told Discovery News.
He noted that previous computational studies wrongly characterized the eruption as a single-phase event.
Computer models created in collaboration with Barcelona Supercomputing Center (BSC) reconstructed the terrifying scenario in detail.
Just like the eruption of nearby Mount Vesuvius that in 79 A.D. obliterated the city of Pompeii, the eruption of the “hidden” and still active supervolcano of the Phlegrean Fields began with a Plinian explosive phase.
In this phase, a mushroom cloud of fragmented rocks and gas raised up to 27 miles into the sky, injecting volcanic gas and ash into the stratosphere, which is the layer of the atmosphere above the one we live.
The fallout consisted of nearly 13 cubic miles of fallen deposits across over 500 thousand square miles, with lapilli and coarse ash covering what is now southern Italy.
Right after, a column made of fine ash particles separated from the devastating pyroclastic flows (fast-moving currents of hot gas and rock) raced up 23 miles high.
Rivers of superheated rock fragments, ash and gas spread up to 43 miles from the eruption site. About 37 cubic miles of finer particles were dispersed in this second phase.
Overall, the super‐eruption covered an area of over 1.1 million square miles. The largest and thickest build‐ups of ash were in modern Macedonia, Bulgaria and Romania; in areas of the eastern Mediterranean layers up to 4 inches accumulated.
The huge eruption also injected large quantities of aerosols into the stratosphere, inducing a “volcanic winter” — with a cooling effect of up to 16.2 degrees Fahrenheit (9 degrees Celsius) in Eastern Europe and northern Asia.
Temperatures fell by about 7.2 degrees Fahrenheit (4 degrees Celsius) in Western Europe, and 1.8- 3.6 degrees Fahrenheit (1–2 degrees Celsius) globally.
“The effects were even more intense as the volcanic winter occurred during a glacial period, the Heinrich Event 4, which was already characterized by extreme condition and climate,” Costa said.
Read more at Discovery News
The court heard testimony earlier this week that the parents treated the boy with home remedies such as olive leaf extract and whey protein, according to the CBC, in an effort to boost their son’s immune system during the illness.
Eventually a nurse told the couple that Ezekiel likely had viral meningitis and that he should see a doctor immediately. The parents instead took their son to the nearby city of Lethbridge to visit a naturopathic alternative medicine practitioner. They increased the number of holistic and natural remedies they were giving the child, saying that if he didn’t get better they would take him to the hospital. Sadly, they didn’t get the chance; the toddler stopped breathing the next day, and only then did the Stephans seek medical help.
Ezekiel Stephan did indeed have viral meningitis, which began as an untreated lung infection and got progressively worse. The boy died five days after being admitted to Alberta Children’s Hospital.
Illusions of Improvement
Why didn’t the Stephans seek medical attention sooner? One reason is that, according to statements they made to police, Ezekiel seemed to be responding well to some of their treatments. Psychology, however, offers an explanation for why the parents may have made this fatal mistake.
The perceived improvement in their son following the various treatments was an illusion. It is what statisticians call “regression to the mean,” in which two variables — in this case, ingredients given to the child and the child’s health — appear to be correlated but are not. People tend to seek (and parents tend to provide) treatment when the symptoms are at their worst. But just because symptoms subside soon after a substance is ingested doesn’t necessarily mean that it helped.
Why? Because the severity of symptoms may come and go on their own with or without any treatment. During any prolonged sickness some days will be better than others, even if the condition is getting progressively worse.
A toddler, of course, cannot give feedback on how he or she is feeling and the parents had to rely on their own subjective interpretation of his behavior. Since the Stephans believed—and wanted to believe—that they were helping him, they had a strong emotional and cognitive bias in interpreting any calming as signs of his recovery.
Ironically the eclectic nature of the treatments they gave him may have sealed his fate: Even if one or more of the home remedies were helping him, there would be no way to know which ones worked, and whether some of the ingredients may have had dangerous side effects or even counteracted the benefits of the others. This is why drug researchers work to isolate and identify active ingredients in medications: to determine which substances work and in what effective doses.
Read more at Discovery News
“Comet Siding Spring plunged the magnetic field around Mars into chaos,” said Jared Espley, of NASA’s Goddard Space Flight Center in Greenbelt, Md. and science team member of NASA’s Mars Atmosphere and Volatile Evolution (MAVEN) spacecraft, in a NASA press release. “We think the encounter blew away part of Mars’ upper atmosphere, much like a strong solar storm would.”
Although Mars’ magnetic field is weak and patchy (unlike Earth’s strong, global magnetosphere), MAVEN’s sensitive magnetometer detected a huge upheaval in orbit as Siding Spring’s own magnetism rattled the planet’s magnetic field.
The comet’s nucleus may only be a third of a mile wide, but the atmosphere surrounding the nucleus (known as the coma) was as wide as 600,000 miles when it encountered Mars. (The coma is formed through solar heating — the ices contained within a comet’s nucleus sublimate into space, pumping the coma with gas.) Through interactions with the solar wind, comets also generate their own magnetic fields that loop their way through the coma. So when Siding Spring buzzed Mars, coming as close as 87,000 miles, the cometary magnetism punched Mars’ weak magnetic field, sending it into violent turmoil for several hours.
MAVEN scientists likened the effect as a magnetic curtain flapping in the wind.
“The main action took place during the comet’s closest approach,” said Espley, “but the planet’s magnetosphere began to feel some effects as soon as it entered the outer edge of the comet’s coma.”
These magnetic observations were very lucky as MAVEN had only just arrived in Mars orbit weeks before the close encounter. Although most of the spacecraft’s instruments were powered down at that time (to protect them from possible damage by comet dust), the magnetometer remained on for the duration, carrying out unique observations of two magnetic fields slamming into one another.
Read more at Discovery News
Mar 9, 2016
The dolphin-like animals died out some 30 million years before the mass dinosaur extinction at the end of the Cretaceous 66 million years ago.
Vertebrate palaeontologist Dr Valentin Fischer, who led the research, published today in Nature Communications, said that the extinction of ichthyosaurs, which were extremely well adapted to oceanic life, was a long-standing enigma.
A number of hypotheses have previously been proposed to explain the ancient marine reptiles disappearance, including increased competition from other marine reptiles and fish and the decline of their main food source, squid-like belemnites, said Dr Fischer of the University of Oxford.
Over time, these pressures would have reduced species diversity, allowing relatively minor events to tip them into extinction.
“These theories were at odds with the recent understanding of the ichthyosaur fossil record, which suggests they were actually quite diverse prior to their extinction,” he said.
“We wanted to analyse this extinction thoroughly and look for possible alternative drivers.”
The researchers analysed teeth from museum collections as well as a number of newly discovered fossils from Russia.
They then correlated their results with geological evidence of sea surface temperatures and other environmental indicators to estimate ichthyosaur diversity over a 150-million year period.
“We found they were in fact very diverse during the last part of their reign; their extinction was thus a profound, rather abrupt event in the history of a successful group,” said Dr Fischer.
Instead, their demise was associated with strong fluctuations in sea levels and temperatures during what is known as the Cenomanian stage of the upper Cretaceous period, 100 million to 94 million years ago.
“It seems that a large part of the marine biosphere was affected by an event or a series of rapid events that profoundly modified marine ecosystems,” he added.
“These events coincided with profound climatic changes: fast-moving continents, intense volcanism, ice-free poles and episodes of anoxia (lack of oxygen) on the sea floor.”
During this turbulent period, Dr Fischer said ichthyosaurs failed to take advantage of the novel opportunities presented by their rapidly changing world, by evolving new species.
Changes in food availability, migratory routes, competitors, or the lack of safe birthing places may all have contributed to their downfall.
“Some groups evolved to take advantage of these new, highly fluctuating conditions while others, like ichthyosaurs, did not.”
But Australian ichthyosaur researcher Dr Benjamin Kear was cautious about the study’s conclusion, which was based on the description of various new ichthyosaur species, mainly from European deposits.
Read more at Discovery News
The team, reporting today in the journal Frontiers in Ecology and Evolution, said a butterfly known as the common bluebottle (Graphium sarpendon), has no less than 15 classes of these vision cells, known as photoreceptors.
“To date, the highest number of photoreceptor classes in any one insect was nine,” said Professor Kentaro Arikawa of Sokendai (the Graduate University of Advanced Studies) in Hayama, Japan, who is an expert in the neuroscience behind insect vision.
“Fifteen is the record.”
“All the photoreceptors are used at the same time, sensing colour, brightness, movement and shape.”
Humans have four classes of photoreceptors, including three types for colour vision (cones) and those specialised for seeing shape, movement and changes in light and dark (rods).
The large compound eyes possessed by butterflies cannot see as clearly as human eyes, but are better at seeing a wide panorama, fast movement, polarisation and grades of colour.
Professor Arikawa and colleagues discovered that a particular subspecies of the common bluebottle butterfly (G. s. nipponum) has seven different cells for identifying colour alone — including ultraviolet, blue, red and two types of cells optimised for picking up green.
By studying the genetic material expressed by these cells, the researchers found that each colour photoreceptor produced one or more of five opsin pigments. Each pigment is stimulated by some wavelengths, and less, or not at all, by other wavelengths.
“This is one mechanism to make a variety of photoreceptors,” said Professor Arikawa.
The team used dye to mark the location of the cells, and found that most of the color photoreceptors were on the side of the eye that faced downwards, and they believe this is likely useful for detecting nectar-rich flowers and the wing patterns of potential mates.
He and colleagues found other types of vision cells, mainly on the upper side of the eye that were sensitive to green light and especially tuned for detecting rapid movement.
This would be useful for detection of predatory birds or other butterflies, the insect might need to chase away.
“This butterfly is quite territorial. It sits on a leaf of a high tree and regards the surroundings as its own territory,” said Professor Arikawa.
Read more at Discovery News
The study, published in the journal Nature, suggests that meat and tools, and not the later advent of cooking, freed early humans to evolve smaller chewing-related features, such as smaller teeth and smaller, shorter faces. These, in turn, might have paved the evolutionary way for improved speech, thermoregulation and even the development of a bigger brain.
"No one knows for sure why hominins started to eat more meat around 2.6 million years ago, but there is abundant evidence for this behavior, including stone tools and cut marks on bones," lead author Katherine Zink of Harvard University's Department of Human Evolutionary Biology told Discovery News.
"The most common explanation is climate change," she added. "During this period, Africa became more open grassland, with more antelopes and other herbivores."
This early Paleo diet also included zero seafood.
She explained, "The ability to fish appears to have come much later in human evolution. Shellfish consumption also appears to be relatively recent."
The study was prompted, in part, by a paradox that has puzzled researchers for years. By the time of Homo erectus about 2 million years ago, humans had evolved bigger brains, bodies and presumably appetites, but their teeth and gut were smaller than those of earlier ancestors. Zink and co-author Daniel Lieberman suspected that mechanical processing of food, as well as the addition of red meat into the diet, could explain the seeming paradox.
To test this out, the researchers fed adult test subjects samples of goat meat (one of the chewier red meats) and jewel yams, carrots and beetroots (to stand in for the starchy plant storage organs that early humans ate). They measured the muscular effort required for chewing and how well the food was broken up before swallowing.
The scientists found that pounding the plant material with stone tools and eating a diet composed of one-third sliced red meat reduced the need to chew by 17 percent and lowered needed force by 26 percent.
Zink and Lieberman point out that prior archaeological evidence indicates early humans fabricated stone tools by 3.3 million years ago, but did not learn to control fire until around 1 million years ago. Evidence for cooking on a regular basis dates to at least 500,000 years ago, long after evolutionary selection for smaller human teeth began.
"During this time," Lieberman said, "many of the forests thinned and transitioned into more open grasslands."
He and Zink added that starchy underground plants are much more plentiful in grasslands than the fruit/tree-based foods of most chimpanzees, and possibly also of the last common ancestor of chimps and humans.
Anthropologist David Strait of Washington University in St. Louis told Discovery News that the study inspires many follow-up questions, such as how tooth mechanics affect the processing of meat, tubers, bulbs and corms. Strait also wonders if particular tooth shapes, sizes and configurations are better able to resist being fractured when eating such foods.
Matt Sponheimer, an anthropologist at the University of Colorado at Boulder and director of the Nutritional and Isotopic Ecology Lab, believes the new paper "does a nice job broadening the recent debate about changes in the masticatory morphology (anatomy related to chewing) of Homo erectus by moving beyond the effects of cooking, and by taking a deeper look at mechanical processing -- slicing, pounding, etc. -- of foods."
"That mechanical processing of foods can lead to a net energetic benefit should be intuitively appealing to most people, or at least to people who have spent much time in the kitchen!" Sponheimer added. "I'm more of a microwave guy myself, but as we process foods in my lab and in the field all the time, this is pretty obvious."
Read more at Discovery News
In fact, as DNews' Jennifer Viegas reports today, food processing plays an important role in our evolution, according to new research from Harvard University published in the journal Nature.
Between 2 million and 3 million years ago, human ancestors worked with stone tools to process their meals, pounding or slicing their food to break it down before chewing. Around this time, early humans began adding meat to their diets, a high-calorie food difficult to chew effectively when it’s raw or in big chunks. Processing food -- even just cutting it into smaller pieces -- outsources some of the work of digestion so more energy can be extracted from meals.
Thanks to cooking and other means of food preparation, it’s easy to take for granted just how much time and energy food processing saves us.
Consider the efforts other mammals go through simply to chew their food. Our closest relatives, chimpanzees, spend much of their day chomping away at their food, and with much greater bite force at that. Most mammals eat a lower-quality diet and take their time with their meals. Other animals, like reptiles, put even more work into each meal because they swallow their food whole.
Testing how much of a difference in effort was required with chewing raw vs. primitively processed food proved a decidedly unappetizing challenge for the study’s participants. Volunteers sampled a small buffet of foods inspired by Paleolithic Era cuisine, which included raw, sliced, pounded and cooked goat as well as a selection of vegetables. Goat was chosen by the researchers because of its similar texture to game. With special devices meant to measure the effort involved, the volunteers chewed until they would normally swallow and then spat each morsel out.
According to the researchers’ data, the muscular effort and number of chews required by processed food was almost 20 percent less than its raw counterparts over the course of an entire day.
Time and energy expenditure aside, cooking or otherwise processing food comes with other benefits as well. Processed food can be consumed in smaller, more digestible pieces, providing an extra nutrition boost thanks to a higher surface area to volume ratio.
Over time, food processing began to have an impact on human physiology. “Eating meat and using stone tools to process food apparently made possible key reductions in the jaws, teeth and chewing muscles that occurred during human evolution,” study author Katie Zink said in a statement.
Read more at Discovery News
The spacecraft missed its launch opportunity this month due to a small leak in its primary science instrument, a seismometer that is designed to study the deep interior of Mars.
NASA grounded the mission for review in late December after a vacuum chamber housing the seismometer’s sensors failed a leak test.
“The quest to understand the interior of Mars has been a longstanding goal of planetary scientists,” John Grunsfeld, NASA’s associate administrator for science, said in a statement. “We’re excited to be back on the path for a launch.”
The agency said it was reviewing how much the repair and launch delay would cost, but the project scientist estimates it will be about $150 million.
NASA said it should know the final tab in August after it selects a new launch vehicle. The Atlas 5 rocket that was being prepared to fly Insight was re-assigned to another spacecraft.
InSight will be put into storage near Denver while the seismometer’s vacuum chamber is re-designed, said spacecraft builder Lockheed-Martin.
From Discovery News
Mar 8, 2016
That’s what a research team from Wake Forest University found when it investigated how drumming — the term used for the sound made by pecking woodpeckers — from territorial interlopers impacts woodpecker breeding pairs’ behavior.
“When you walk through the woods and you hear a woodpecker, most people think they are looking for food, but that’s actually a social signal they use,” explained study lead Matthew Fuxjager in a press release.
The pecking bird might be announcing its availability to mates or it might be staking a claim to the area.
To find out what kind of response the social signal elicited, the researchers recorded the drumming sounds of male woodpeckers and then manipulated them as they were played back in the wild for downy woodpecker breeding pairs that already held a given territory.
It turned out that when the downy breeding pairs — known for their territoriality — heard longer drumming sounds, they perceived the drummer as a tough customer that would require their coordination in order to attack.
Shorter-lasting drum sounds, meanwhile, made the breeding pairs think, “Eh, pushover,” and the duo did not even bother to mount a coordinated response.
“Partners will actually coordinate or cooperate with how they fight depending on who they are fighting. They size up their opponent and decide whether they need to work together,” Fuxjager said.
“In short,” he said, “it means an intruder woodpecker with a short drum is perceived as wimpier, while a long drum signifies a tough-guy intruder.”
Findings from the study have been published in the journal Behavioral Ecology and Sociobiology.
From Discovery News
The discovery is a breakthrough in understanding animal vocalizations. Before, it was difficult to prove that any animal created its own complex, structured language, but Japanese great tits appear to have done just that.
“We now have good evidence that animal communication systems share many of the basic properties of human language,” said Toshitaka Suzuki, lead author of the study appearing in Nature. “For example, mammals and birds can use specific call types to denote specific objects, and Japanese great tits can combine different ‘words’ to send a compound message.”
Suzuki is a postdoctoral fellow in the Department of Evolutionary Studies at Japan’s Graduate University for Advanced Studies. Previously, he determined that Japanese great tits created distinct alarm calls to refer to two of their main nest predators: jungle crows and Japanese rat snakes.
For the new study, he and colleagues David Wheatcroft and Michael Griesser focused on a few of the Japanese great tit’s different note types, which are named A, B, C and D. Prior research found that when A,B, and C are produced together in that order, the call instructs listeners to “scan for danger.” The “D” note instructs listeners to “approach the caller.”
When the birds tweet ABC-D together and in that order, there is a compound meaning that essentially translates to: scan for danger and come here. Suzuki and his team played the recorded calls to 21 adult Japanese great tits in the wild and the listening birds did exactly as the calls commanded, with the birds scanning the horizon and approaching the loudspeaker. When the researchers reversed the order of the notes to D-ABC, the listeners did not respond.
The study reveals that the birds are capable of a skill known as compositional syntax — meaning they combine distinct elements of their vocalizations and extract a compound meaning from them. Before, only humans were thought to have this ability.
The talent could be common among many different songbird species.
“There is no evidence showing that non-human primates, even chimpanzees, use compositional syntax,” Suzuki said, adding that “combinations of sounds are very common in tits and chickadees, and are also found in other species of passerines (perching birds).”
The birds seem to learn their various calls over time, with nestlings only emitting a limited number of call types associated with begging and distress. As they grow up, they copy their fathers’ mating songs and may learn their vocalizations in other ways, too.
Save for a handful of talented “polyphonic overtone” singers who can sing two notes at the same time, people are usually limited to producing one sound at a time with their vocal cords. Birds, on the other hand, “can control the two sides of their syrinx independently, allowing them to produce two different sounds simultaneously,” Suzuki said.
It is known that Japanese great tits have AC, BC, AC-D and BC-D calls, as well as probably many others, all of which are not yet understood by researchers.
Robert Magrath, a professor of behavioral ecology at the Australian National University, says the research “is interesting in showing that the specific order of notes in a call can change its meaning for listeners.”
Read more at Discovery News
The unusual process involves changes to the hydra’s mouth skin cells that allow the creature to stretch and split apart these cells in a dramatic deformation. The findings are published in the latest issue of the Biophysical Journal.
“The fact that the cells are able to stretch to accommodate the mouth opening, which is sometimes wider than the body, was really astounding,” senior author Eva-Marie Collins said in a press release. “When you watch the shapes of the cells, it looks like even the cell nuclei are deformed.”
Collins, who is a biophysicist at the University of California, San Diego, and her team genetically engineered hydra so that the animals’ two layers of tissues would light up, revealing how their mouths and bodies work on a cellular level.
Hydra measure less than one half an inch long. They look like a column with a ring of tentacles at the end. In the wild, the other end adheres to a rock or some other kind of surface, keeping the hydra in place while it waits for unsuspecting prey to swim by.
When a potential victim, such as a small shrimp, brushes against the hydra’s tentacles, the predator shoots out poisoned barbs to sting and paralyze its prey. Once the hydra contracts its tentacles, a special group of cells splits apart to display the black interior of its mouth, and the hydra sucks the prey in.
When the meal is digested, the hydra rips open its mouth to spit out any leftover materials. It then seals it back up into a continuous sheet of tissue, and waits for the next shrimp or other victim to swim by.
In the below video, a hydra in a lab eats a small crustacean, showing what the hunting and feasting look like from farther away:
“We can try to understand what look like very complicated processes in the living animal with relatively simple physics,” Collins said.
She and her team next determined that once triggered, radially oriented fibers in the hydra’s tissue contract to stretch the cells apart, similar to how muscles in the iris contract to open our pupils. When the researchers added magnesium chloride to act as a muscle relaxant, the hydras couldn’t open their mouths at all.
Read more at Discovery News
The grave in the Holy Trinity Church in Shakespeare’s birthplace of Stratford upon Avon is a place of pilgrimage for fans and has an inscription on it with a curse against anyone planning to tamper with it.
“Bleste be the man that spares these stones, And curst be he that moves my bones,” the inscription reads.
The survey could help researchers learn more about Shakespeare’s life and family, helping to detect unmarked or previously unknown graves and items buried within the coffins, the Telegraph reported.
“We can confirm a scan has been completed. The results of the scan will be revealed as part of a Channel 4 documentary later in the spring,” a spokesman for the church was quoted as saying.
A Channel 4 spokeswoman confirmed the report to AFP.
Shakespeare’s wife Anne Hathaway and daughter Suzanna as well as other members of his extended family are buried in graves around his own.
The pre-eminent British writer, who lived between 1564 and 1616, is believed to have written around 38 plays — although the precise authorship of some works has been disputed — and 154 sonnets.
Britain is marking the anniversary of his death on April 23 with a series of performances and academic workshops as well as a planned candlelit vigil in the Holy Trinity Church itself on the day.
From Discovery News
Phobos is the nearer and stranger of Mars' two moons — in the 1950s and 1960s, some scientists thought that its unusual orbit, spiraling inward, suggested that it might be a hollow, artificial body. The little moon has long, shallow grooves along its sides, likely caused by the pull of Mars, and it moves about 6.6 feet (2 meters) closer to the Red Planet every hundred years, NASA officials have said.
In fact, Phobos is the closest moon to its planet in the solar system, circling Mars at just 3,700 miles (6,000 kilometers) above its surface. It's so close that it orbits within the sphere of Mars' thin atmosphere — the blue pixels that form the new portrait's background are the ultraviolet light scattered from hydrogen gas in Mars' extended upper atmosphere. The orange comes from longer ultraviolet wavelengths of sunlight reflected from the moon's surface.
NASA's MAVEN (short for Mars Atmosphere and Volatile Evolution) mission snapped the shot with its Imaging Ultraviolet Spectrograph in December 2015 as its orbit crossed paths with Phobos', and researchers are hoping MAVEN's measurements will help determine what the moon is made of, where it came from and whether it has organic molecules on its surface. (A previous measurement, by the Mars Express spacecraft, found evidence of such organic molecules.)
"The images will allow MAVEN scientists to better assess the composition of this enigmatic object, whose origin is unknown," NASA officials said in a statement.
Original article on Space.com. Copyright 2016 SPACE.com, a Purch company. All rights reserved. This material may not be published, broadcast, rewritten or redistributed.
From Discovery News
Mar 7, 2016
Found in a large ancient building in the City of David, in the Jerusalem Walls National Park, the seal dates back to the era of the First Temple, which, according to the Hebrew Bible, was constructed by King Solomon in the 10th century B.C. and then destroyed 400 years later.
"Finding seals that bear names from the time of the First Temple is hardly a commonplace occurrence, and finding a seal that belonged to a woman is an even rarer phenomenon," excavation directors Doron Ben-Ami, Yana Tchekhanovets and Salome Cohen, said in a statement.
The seal, made of semi-precious stone, bears the mirror-writing of "to Elihana bat Gael" carved in ancient Hebrew letters. It means "Elihana daughter of Gael."
Such seals were used for signing documents, and were frequently inlaid as part of a ring that was worn by the owner.
"In antiquity they designated the identity, genealogy and status of the owner of the seal," the archaeologists said.
The name Elihana does not appear in the Bible, and there is no other information regarding the identity of the woman, but the fact that she owned a seal shows her high social status.
"She was exceptional compared to other women of the First Temple period: she had legal status which allowed her to conduct business and possess property," the archaeologists said.
Hagai Misgav, from the Hebrew University of Jerusalem's Institute of Archaeology, noted that most of the women's seal that are known today bear the name of the father rather than that of the husband.
"Here, as in other cases, this might indicate the relatively elevated status of Elihana, which depended on her original family, and not on her husband's family," Misgav said.
"It seems that Elihana maintained her right to property and financial independence even after her marriage and therefore her father's name was retained; however, we do not have sufficient information about the law in Judah during this period," he added.
Legal and financial independence for women was a rare thing in those times.
According to the Book of Proverbs, an ideal wife was responsible for providing for the needs of her household when her husband was engaged in public and legal affairs at the city gate.
"She seeks wool and flax, and works with willing hands … Her husband is known in the gates, when he sits among the elders of the land," it stated.
Read more at Discovery News
The two prehistoric big cats were infants when they died, their remains estimated to be some 12,000 years old, found in a cave in Yakutia, a part of Siberia also called the Sakha Republic.
Woo-Suk, already pursuing the resurrection of a woolly mammoth, got his samples after a dispute over tissue sample size was settled via compromise between the Korean and Siberian scientists.
Siberian cave lions (Panthera leo spelaea) would have looked roughly like modern lions. They lived during the Pleistocene and were distributed throughout Europe, Asia and northwestern North America, before going extinct about 10,000 years ago.
It’s likely they preyed on animals such as bison, young or injured mammoths, deer, and horses.
The lion cubs were estimated to be only a couple of weeks old. While the circumstances surrounding their deaths is not certain, Albert Protopopov, head of the mammoth fauna studies department of the Yakutian Academy of Sciences, told the Times he surmises the cubs were placed in the cave by their mother for protection, but then a landslide sealed the area, trapping the young animals inside.
From Discovery News
The burial ground was discovered in spring 2013 during the construction of an industrial park. In 2014 a team from the Ministry of Tourism and Antiquities of Palestine excavated some of the tombs, and in 2015 a joint Italian-Palestinian team surveyed the necropolis and created a plan for future exploration. The archaeologists found that the necropolis covered 3 hectares (more than 7 acres) and originally contained more than 100 tombs in use between roughly 2200 B.C. and 650 B.C.
Located on the side of a hill, the archaeological site — now called Khalet al-Jam’a — was likely a burial ground for a nearby settlement whose location is unknown.
The site’s “long-lasting utilization, over a millennium and a half or more, and the large number of tombs, suggest that Khalet al-Jam’a was the necropolis of a major settlement in the area, possibly a town,” Lorenzo Nigro, professor at Sapienza University of Rome, wrote in an article published recently in the journal Vicino Oriente.
Nigro said that finds from the necropolis indicate that the settlement was a wealthy place, with access to trade routes. Ancient texts refer to a “Beth-Lehem” that flourished in the area.
“Typical pieces of the burial sets are finely executed carinated bowls, small shouldered jars/bowls with everted rim, one-spouted lamps, huge and well-refined Canaanite jars with two or four handles, as well as bronze daggers and spearheads,” Nigro wrote.
Though the necropolis has been partly destroyed by looting and construction, the archaeologists were able to identify at least 30 tombs. “The necropolis of Khalet al-Jam’a is mainly characterized by shaft tombs with single or multiple rock-cut chambers,” the team wrote in another paper published in Vicino Oriente, noting that the builders enlarged and renovated natural cavities on the hillside.
In one tomb, the remains of a man, woman and child were found buried with two bronze daggers and a variety of ceramics, including twin vases attached together. Archaeologists found that the tomb dated to the Middle Bronze Age, more than 3,500 years ago.
Another tomb at Khalet al-Jam’a contained a nearly complete male skeleton buried with a ceramic lamp that had four sides folded into spouts. Archaeologists said this particular tomb may date to an earlier point in the Bronze Age more than 4,000 years ago.
Another intriguing tomb contained two Egyptian-like amulets, known as scarabs, which were mounted on rings made of bronze or gold. It’s possible that, rather than being imported from Egypt, the scarabs were made locally.
The scarabs date to the 13th dynasty of Egypt (1802 B.C. to 1640 B.C.), Nigro said. One of the scarabs contains a series of circular decorations, while the other has swirling designs and what appears to be hieroglyphic writing. Two of the hieroglyphic symbols are written within an oval circle known as a cartouche. The Egyptians often wrote royal names in cartouches, and archaeologists are studying the scarabs for these types of details.
Egyptian scarabs have been found at many other sites in the eastern Mediterranean. Ancient records say the Egyptians were very active in the region, trading for goods and, at times, conquering territory.
Read more at Discovery News
This isn’t the first time scientists have proposed that Earth’s fiery depths are filled with brimstone, another name for sulfur. That’s because the inner core is less dense than it would be if the solid metal ball were pure iron. However, the new research further confirms the idea with tests of pure iron at the extreme temperatures and pressures found in the inner core.
Researchers at Tohoku University in Sendai, Japan, mimicked the inner core in a laboratory equipped with a laser-heated diamond anvil cell. A small crumb of pure iron was squeezed between two diamond-tipped anvils to create high pressure and blasted with laser beams to boost the temperature. The experiment reached 163 gigapascals (about 1.6 million times the pressure at sea level) and about 5,000 degrees Fahrenheit (3,000 kelvins, or about 2,700 degrees Celsius).
During the experiment, the team measured how fast sound waves traveled through iron at these conditions. If the Earth’s inner core was pure iron, then the speed of sound waves traveling through the core should be similar to the experimental results.
But instead, the researchers discovered the velocity of sound waves through Earth’s actual core is lower than if it were made only of iron. The data and observations match more closely if 5 to 10 percent of the core’s weight is a mix of sulfur, hydrogen and silicon, the researchers reported in the journal Science Advances.
“This result helps us constrain the candidate elements in the core,” said lead study author Tatsuya Sakamaki, of Tohoku University. “We already know that the Earth’s core contains some amount of light elements because the density of the core is smaller than that of iron. In this study, we newly show that the velocity of the core is also smaller than that of iron,” Sakamaki told Live Science in an email interview.
Read more at Discovery News
In its final orbits, MESSENGER not only confirmed that Mercury’s dark hue is due to carbon, but also revealed that the carbon wasn’t deposited by impacting comets, as some researchers suspected.
Instead, scientists now believe they are seeing remnants of the planet’s primordial crust, which likely formed when a global ocean of super-heated magma cooled, allowing minerals to solidify.
Computer simulations and experiments show that most of these crystallized minerals would sink -- with one key exception. Graphite, the studies show, would float.
Scientists used an instrument on MESSENGER called a neutron spectrometer to make low-altitude measurements of the darkest regions on the planet’s surface, which were suspected of having the most low-reflectance material (LRM.)
“The measurements showed enhanced fluxes of thermal neutrons over three areas of LRM, so only graphite as the darkening agent fits both the spectral reflectance observations and the neutron measurements,” MESSENGER’s lead scientist Sean Solomon, with Columbia University, wrote in an email to Discovery News.
Scientists also were able to match the carbon-rich material with large impact craters, evidence that the material stemmed from deep within Mercury’s crust and was exposed after an impacting body gouged out a crater.
“Because LRM deposits on Mercury are all associated with material excavated from depth by large impact craters, they must come from the mid to lower crust,” Solomon said.
Scientists estimate the ancient crust was about .62 mile, or 1 kilometer, thick.
The crust of present-day Mercury has been bashed by impacts, covered with lava, melted and otherwise disturbed.
“The processes … would dilute any primordial crust,” physicist Patrick Peplowski, with Johns Hopkins University Applied Physics Lab, and colleagues write in a paper published this week in Nature Geoscience.
Read more at Discovery News
Mar 6, 2016
A bioinformatics group from The Children's Hospital of Philadelphia collaborated with researchers from Rutgers University on the study, which appeared online today in Science.
"The algorithms we developed enable us to tackle many questions across diverse areas of DNA and RNA biology," said study co-author Deanne M. Taylor, Ph.D., Director of Bioinformatics in the Department of Biomedical and Health Informatics at The Children's Hospital of Philadelphia (CHOP). "Understanding these fundamental processes may help in developing antimicrobial treatments to fight bacterial disease."
Taylor collaborated on the study with biochemist Bryce Nickels, Ph.D., and chemist Richard Ebright, Ph.D., both from Rutgers, the State University of New Jersey.
The research focuses on transcription--how cells read genetic information stored in DNA by first synthesizing a copy of that genetic information as RNA. The enzyme RNA polymerase is the molecular machine that carries out transcription. In the current study, the CHOP/Rutgers team determined how RNA polymerase locates the site on DNA where it starts transcription.
In particular, working in bacteria, the CHOP/Rutgers team showed that after RNA polymerase binds to DNA and partly unwinds the two strands of the DNA helix, it then continues unwinding those two strands, pulling the unwound DNA strands into itself until it engages the transcription start site (TSS). The researchers call this process--unwinding DNA and pulling strands into itself--"DNA scrunching." Nickels points out, "Scientists have known for more than three decades that transcription start sites vary, but did not previously know the mechanism."
To detect DNA scrunching during TSS selection, the researchers developed powerful new experimental approaches, called MASTER and MASTER-XL. The CHOP/Rutgers team first described MASTER (for "massively systematic transcript end readout") in a December 2015 paper in Molecular Cell.
MASTER-XL combines the MASTER technology with crosslinking--introducing artificial amino acids at specific sites on proteins to crosslink to sites in DNA. Using high-throughput algorithms, the study team was able to precisely and rapidly pinpoint those crosslinking sites in a million different DNA sequences, each carrying a distinct TSS region. In each sequence, the team identified the TSS as well as front (leading edge) and rear (trailing edge) positions where RNA polymerase attached to DNA.
Yuanchao Zhang, a graduate student working with Taylor's bioinformatics group at CHOP, developed the big-data algorithms with Taylor to analyze the sequencing data output from MASTER and MASTER-XL experiments. "Our algorithms rapidly process many millions of DNA and RNA sequence reads," said Taylor.
The rapid sequencing, plus advanced biochemical and chemical methods underlying the crosslinking, provided a key finding on how DNA scrunching occurs during transcription. As the position of the TSS changes, the position of RNA polymerase's leading edge changes in lock step, but the enzyme's trailing edge remains in the same position. This causes the DNA to scrunch: it remains fastened to RNA polymerase at its trailing edge, but RNA polymerase unwinds the adjacent DNA and pulls the unwound DNA into itself until it locates a new TSS.
"The crucial feature of our approach," explained Ebright, "is the combination of protein-DNA crosslinking with next-generation-sequencing of DNA. This enables us to perform crosslinking studies with a million different DNA sequences in the same amount of time that we previously would have needed to perform crosslinking studies with one DNA sequence." He added, "The million-fold increase in throughput allows biological problems to be solved that couldn't be solved before."
Read more at Science Daily
"Curium is an elusive element. It is one of the heaviest-known elements, yet it does not occur naturally because all of its isotopes are radioactive and decay rapidly on a geological time scale," said the study's lead author, François Tissot, UChicago PhD'15, now a W.O. Crosby Postdoctoral Fellow at the Massachusetts Institute of Technology.
And yet Tissot and his co-authors, UChicago's Nicolas Dauphas and Lawrence Grossman, have found evidence of curium in an unusual ceramic inclusion they called "Curious Marie," taken from a carbonaceous meteorite. Curium became incorporated into the inclusion when it condensed from the gaseous cloud that formed the sun early in the history of the solar system.
Curious Marie and curium are both named after Marie Curie, whose pioneering work laid the foundation of the theory of radioactivity. Curium was only discovered in 1944, by Glenn Seaborg and his collaborators at the University of California, Berkeley, who, by bombarding atoms of plutonium with alpha particles (atoms of helium) synthesized a new, very radioactive element.
To chemically, and unambiguously, identify this new element, Seaborg and his collaborators studied the energy of the particles emitted during its decay at the Metallurgical Laboratory at UChicago (which later became Argonne National Laboratory). The isotope they had synthesized was the very unstable curium-242, which decays in a half-life of 162 days.
On Earth today, curium exists only when manufactured in laboratories or as a byproduct of nuclear explosions. Curium could have been present, however, early in the history of the solar system, as a product of massive star explosions that happened before the solar system was born.
"The possible presence of curium in the early solar system has long been exciting to cosmochemists, because they can often use radioactive elements as chronometers to date the relative ages of meteorites and planets," said study co-author Nicolas Dauphas, UChicago's Louis Block Professor in Geophysical Sciences.
Indeed, the longest-lived isotope of curium (247Cm) decays over time into an isotope of uranium (235U). Therefore, a mineral or a rock formed early in the solar system, when 247Cm existed, would have incorporated more 247Cm than a similar mineral or rock that formed later, after 247Cm had decayed. If scientists were to analyze these two hypothetical minerals today, they would find that the older mineral contains more 235U (the decay product of 247Cm) than the younger mineral.
"The idea is simple enough, yet, for nearly 35 years, scientists have argued about the presence of 247Cm in the early solar system," Tissot said.
Early studies in the 1980s found large excesses of 235U in any meteoritic inclusions they analyzed, and concluded that curium was very abundant when the solar system formed. More refined experiments conducted by James Chen and UChicago alumnus Gerald Wasserburg, SB'51, SM'52, PhD'54, at the California Institute of Technology showed that these early results were spurious, and that if curium was present in the early solar system, its abundance was so low that state-of-the-art instrumentation would be unable to detect it.
Scientists had to wait until a new, higher-performance mass spectrometer was developed to successfully identify, in 2010, tiny excesses of 235U that could be the smoking gun for the presence of 247Cm in the early solar system.
"That was an important step forward but the problem is, those excesses were so small that other processes could have produced them," Tissot noted.
Models predict that curium, if present, was in low abundance in the early solar system. Therefore, the excess 235U produced by the decay of 247Cm cannot be seen in minerals or inclusions that contain large or even average amounts of natural uranium. One of the challenges was thus to find a mineral or inclusion likely to have incorporated a lot of curium but containing little uranium.
With the help of study co-author Lawrence Grossman, UChicago professor emeritus in geophysical sciences, the team was able to identify and target a specific kind of meteoritic inclusion rich in calcium and aluminum. These CAIs (calcium, aluminum-rich inclusions) are known to have a low abundance of uranium and likely to have high curium abundance. One of these inclusions--Curious Marie-- contained an extremely low amount of uranium,
"It is in this very sample that we were able to resolve an unprecedented excess of 235U," Tissot said. "All natural samples have a similar isotopic composition of uranium, but the uranium in Curious Marie has six percent more 235U, a finding that can only be explained by live 247Cm in the early solar system."
Thanks to this sample, the research team was able to calculate the amount of curium present in the early solar system and to compare it to the amount of other heavy radioactive elements such as iodine-129 and plutonium-244. They found that all these isotopes could have been produced together by a single process in stars.
Read more at Science Daily