Aug 25, 2018

Genetic analysis of Florida's invasive pythons reveals a tangled family tree

Burmese python in Everglades National Park.
A new genetic analysis of invasive pythons captured across South Florida finds the big constrictors are closely related to one another. In fact, most of them are genetically related as first or second cousins, according to a study by wildlife genetics experts at the U.S. Geological Survey.

The study also found that at least a few of the snakes in the invasive South Florida population are not 100 percent Burmese pythons. Instead, the genetic evidence shows at least 13 snakes out of about 400 studied are a cross between two separate species: Burmese pythons, which mostly inhabit wetlands, and Indian pythons, which prefer higher ground. The interbreeding between Burmese and Indian pythons probably took place before the animals became established in the South Florida environment, and may have given them greater adaptability in their new habitats.

The South Florida pythons spring from a tangled family tree, with consequences for the species' future spread that are hard to predict, the USGS scientists said.

"The snakes in South Florida are physically identifiable as Burmese pythons, but genetically, there seems to be a different, more complicated story," said Margaret Hunter, a USGS research geneticist and lead author on the study published in the journal Ecology and Evolution.

Burmese pythons have been reproducing in the Everglades since the 1980s, and have caused important environmental changes including the decline of small-mammal populations in South Florida.

The researchers analyzed tail tissue from about 400 Burmese pythons captured across a wide area, from southwest Florida and the Big Cypress National Preserve to the Everglades, southeast Miami-Dade County and the Florida Keys, between 2001 and 2012.

The researchers looked at nuclear DNA, which contains genetic material from both parents, to determine how much each animal had in common with others in the population. To express family relationships in statistical terms, they used a common type of calculation known as a relatedness value. For all snakes in the study, the average relatedness value was about midway between first and second cousins. That close kinship means the population as a whole is experiencing inbreeding, the researchers concluded.

When the researchers tested genetic material from a different part of the snakes' cells-mitochondrial DNA, inherited solely from the mother-they were surprised to find genetic signatures from the Indian python in 13 snakes.

Sometimes interbreeding between related species "can lead to hybrid vigor, that is, the best traits of two species are passed onto their offspring," Hunter said. "Hybrid vigor can potentially lead to a better ability to adapt to environmental stressors and changes. In an invasive population like the Burmese pythons in South Florida, this could result in a broader or more rapid distribution."

In the wild, related species typically avoid interbreeding by using different habitats. In their native Asia, Burmese pythons prefer wet habitats, while Indian pythons tend to stick to drier ones. In previous studies, scientists have observed South Florida's Burmese pythons in both wet and dry habitat types.

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Mutations in this molecule may have helped mammoths tolerate the cold

This is an image of human TRPV3 in the closed and open states viewed from outside the cell. Location of the region (N647) that is mutated in mammoths is highlighted.
Columbia University biomedical researchers have captured close-up views of TRPV3, a skin-cell ion channel that plays important roles in sensing temperature, itch, and pain.

In humans, defects in the protein can lead to skin diseases such as atopic dermatitis (a type of eczema), vitiligo (uneven skin coloration), skin cancer, and rosacea.

All vertebrate DNA, including the woolly mammoth genome, contains the TRPV3 gene. Though the mammoths lived in extremely cold environments, they descended from elephants that lived in the tropics. Researchers think that changes in the TRPV3 genes of mammoths may have helped them withstand lower temperatures.

Alexander Sobolevsky's lab at Columbia University Irving Medical Center used a powerful imaging technique called cryo-electron microscopy to take pictures of TRPV3 molecules. Initial 2D images were collected by freezing the molecules in an extremely thin, clear layer of ice and bombarding them with electrons. The researchers then used computational tools to convert the 2D images into detailed molecular 3D models.

Image of human TRPV3 in the closed and open states viewed from outside the cell. Location of the region (N647) that is mutated in mammoths is highlighted. Images: Alexander Sobolevsky / CUIMC

This is the first time scientists have gotten a glimpse of TRPV3 in atomic detail. The researchers were able to get images of the protein in two states, revealing how the channel opens and closes to let ions flow into skin cells.

This exchange of ions prompts the body to react to sensations such as pain, itchiness, and changes in temperature. The group also discovered how a small molecule with anti-cancer properties called 2-APB interacts with and controls the function of this channel.

The structures in this study provide clues about how mutations in TRPV3 affect the channel's ability to sense temperature and show that lipids -- molecules that make up most of the cell membrane -- contact the channel in several regions. Mammoth TRPV3 contains a mutation in one of these lipid-touching regions.

"Temperature affects the interaction of lipids and proteins," Sobolevsky says. "A mutation in the woolly mammoth channel would most likely affect this interaction and could explain how these animals adapted to their cold environment."

Researchers will use the structure to investigate how atomic changes to the protein cause it to malfunction in human diseases. "This study gives scientists a template they can use to design more effective drugs for treating these skin-related illnesses," said Appu Singh, PhD, a postdoctoral fellow in the Sobolevsky lab and a first author of the paper.

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Aug 24, 2018

Genetically engineered virus spins gold into beads

Electron microscope image of M13 spheroid-templated spiky gold nanobead with corresponding graphical illustration.
The race is on to find manufacturing techniques capable of arranging molecular and nanoscale objects with precision.

Engineers at the University of California, Riverside, have altered a virus to arrange gold atoms into spheroids measuring a few nanometers in diameter. The finding could make production of some electronic components cheaper, easier, and faster.

"Nature has been assembling complex, highly organized nanostructures for millennia with precision and specificity far superior to the most advanced technological approaches," said Elaine Haberer, a professor of electrical and computer engineering in UCR's Marlin and Rosemary Bourns College of Engineering and senior author of the paper describing the breakthrough. "By understanding and harnessing these capabilities, this extraordinary nanoscale precision can be used to tailor and build highly advanced materials with previously unattainable performance."

Viruses exist in a multitude of shapes and contain a wide range of receptors that bind to molecules. Genetically modifying the receptors to bind to ions of metals used in electronics causes these ions to "stick" to the virus, creating an object of the same size and shape. This procedure has been used to produce nanostructures used in battery electrodes, supercapacitors, sensors, biomedical tools, photocatalytic materials, and photovoltaics.

The virus' natural shape has limited the range of possible metal shapes. Most viruses can change volume under different scenarios, but resist the dramatic alterations to their basic architecture that would permit other forms.

The M13 bacteriophage, however, is more flexible. Bacteriophages are a type of virus that infects bacteria, in this case, gram-negative bacteria, such as Escherichia coli, which is ubiquitous in the digestive tracts of humans and animals. M13 bacteriophages genetically modified to bind with gold are usually used to form long, golden nanowires.

Studies of the infection process of the M13 bacteriophage have shown the virus can be converted to a spheroid upon interaction with water and chloroform. Yet, until now, the M13 spheroid has been completely unexplored as a nanomaterial template.

Haberer's group added a gold ion solution to M13 spheroids, creating gold nanobeads that are spiky and hollow.

"The novelty of our work lies in the optimization and demonstration of a viral template, which overcomes the geometric constraints associated with most other viruses," Haberer said. "We used a simple conversion process to make the M13 virus synthesize inorganic spherical nanoshells tens of nanometers in diameter, as well as nanowires nearly 1 micron in length."

The researchers are using the gold nanobeads to remove pollutants from wastewater through enhanced photocatalytic behavior.

The work enhances the utility of the M13 bacteriophage as a scaffold for nanomaterial synthesis. The researchers believe the M13 bacteriophage template transformation scheme described in the paper can be extended to related bacteriophages.

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Dramatic development of immune system after birth

As soon as a baby is born, its immune system starts to change dramatically in response to the bacteria, viruses and so forth in its new environment, a phenomenon that is common to all babies, researchers from Karolinska Institutet in Sweden write in a paper published in Cell. The study was made possible using new techniques of immune cell analysis.

Examining how the neonatal immune system changes has been difficult since the analyses are made from samples taken from the umbilical cord directly after delivery. Researchers have now exploited a new technique of immune cell analysis to monitor how babies develop for the first few weeks of life outside the womb.

"This is the first time we've pinned down how the human immune system adapts itself to birth and the new environment," says Petter Brodin, doctor and researcher at the Science for Life Laboratory (SciLifeLab) and the Department of Women's and Children's Health, Karolinska Institutet. "We saw drastic changes in the babies' immune system between each sampling, which shows that it is highly dynamic early in life."

The study compared blood samples from 100 babies, both premature and full-term, taken during the first, fourth and twelfth week. The comparison was achieved using an advanced technique of immune cell analysis: mass cytometry in combination with extensive plasma protein analyses.

Only small amounts of blood, just a few drops from each baby, are needed to analyse all the white blood cells and hundreds of proteins circulating in the blood. The researchers were also able to show that the babies who had abnormal development of the gut flora during the first weeks also demonstrated a disorder of the immune system.

"Our results are important for better understanding the infection-sensitivity of newborn babies and the risks of premature birth," says Dr Brodin. "If we can monitor the development of the immune system and steer it in different directions, we make it possible to prevent autoimmune diseases and allergies, which are partly related to the development of the immune system, and to even develop better vaccines, tailored to the neonatal immune system."

The adaptation of the immune system is thought to be triggered by the microbes, bacteria, fungi and so forth that the baby encounters outside the womb. The process begins primarily in the lungs, gut, skin and mucosa, which is to say the body's points of contact with the outside world.

"What surprised us was how similar the changes were amongst babies," says Dr Brodin. "It seems as if all babies follow one and the same pattern, with their immune systems responding with exactly the same sequence of dramatic changes. It's almost like a well-choreographed dance, a practised routine."

The researchers will now be broadening out the study to encompass more babies, all of whom will be monitored into childhood. This will enable the team to see which of them develop diabetes, allergies, asthma and inflammatory bowel disease.

"Many of these diseases can definitely be traced back to how a baby is born and how its immune system adapts to the external environment," explains Dr Brodin. "What we're bringing to the table is the specific changes in the immune system that underlie this. It's a piece of the puzzle that was formerly missing."

The study was made possible through the close collaboration of Karolinska University Hospital.

Read more at Science Daily

No safe level of alcohol, new study concludes

Bottles of assorted alcoholic beverages
A new scientific study concludes there is no safe level of drinking alcohol.

The study, published today in the international medical journal The Lancet, shows that in 2016, nearly 3 million deaths globally were attributed to alcohol use, including 12 percent of deaths in males between the ages of 15 and 49.

"The health risks associated with alcohol are massive," said Dr. Emmanuela Gakidou of the Institute for Health Metrics and Evaluation at the University of Washington and the senior author of the study. "Our findings are consistent with other recent research, which found clear and convincing correlations between drinking and premature death, cancer, and cardiovascular problems. Zero alcohol consumption minimizes the overall risk of health loss." Gakidou is a professor of health metrics sciences at the UW School of Medicine, and of global health at the UW School of Public Health.

The study does not distinguish between beer, wine, and liquor due to a lack of evidence when estimating the disease burden, Gakidou said. However, researchers used data on all alcohol-related deaths generally and related health outcomes to determine their conclusions.

Alcohol use patterns vary widely by country and by sex, the average consumption per drinker, and the attributable disease burden. Globally, more than 2 billion people were current drinkers in 2016; 63% were male.

"Average consumption" refers to a standard drink, defined in the study as 10 grams of pure alcohol, consumed by a person daily, about the equivalent of:

  • A small glass of red wine (100 ml or 3.4 fluid ounces) at 13% alcohol by volume;
  • A can or bottle of beer (375 ml or 12 fluid ounces) at 3.5% alcohol by volume; or
  • A shot of whiskey or other spirits (30 ml or 1.0 fluid ounces) at 40% alcohol by volume.

"Standard drinks" are different by country. For example, in the United Kingdom a standard drink is 8 grams of alcohol, whereas in Australia, the United States, and Japan, it is 10 grams, 14 grams, and 20 grams, respectively.

The study, part of the annual Global Burden of Disease, assesses alcohol-related health outcomes and patterns between 1990 and 2016 for 195 countries and territories and by age and sex.

It provides findings on prevalence of current drinking, prevalence of abstention, alcohol consumption among current drinkers, and deaths and overall poor health attributable to alcohol for 23 health outcomes, such as communicable and non-communicable diseases and injuries, including:

  • Cardiovascular diseases: atrial fibrillation and flutter, hemorrhagic stroke, ischemic stroke, hypertensive heart disease, ischemic heart disease, and alcoholic cardiomyopathy;
  • Cancers: breast, colorectal, liver, esophageal, larynx, lip and oral cavity, and nasal;
  • Other non-communicable diseases: cirrhosis of the liver due to alcohol use, diabetes, epilepsy, pancreatitis, and alcohol use disorders;
  • Communicable diseases: lower respiratory infections and tuberculosis;
  • Intentional injuries: interpersonal violence and self-harm;
  • Unintentional injuries: exposure to mechanical forces; poisonings; fire, heat, and hot substances; drowning; and other unintentional injuries; and
  • Transportation-related injuries.

"We now understand that alcohol is one of the major causes of death in the world today," said Lancet Editor Richard Horton. "We need to act now. We need to act urgently to prevent these millions of deaths. And we can."

This study used 694 data sources on individual and population-level alcohol consumption, along with 592 prospective and retrospective studies on the risk of alcohol use. More than 500 GBD collaborators, such as researchers, academics, and others from more than 40 nations contributed to the study, according to Max Griswold, senior researcher and lead author.

"With the largest collected evidence base to date, our study makes the relationship between health and alcohol clear -- drinking causes substantial health loss, in myriad ways, all over the world," Griswold said.

In 2016, eight of the leading 10 countries with lowest death rates attributable to alcohol use among 15- to 49-year-olds were in the Middle East: Kuwait, Iran, Palestine, Libya, Saudi Arabia, Yemen, Jordan, and Syria. The other two were Maldives and Singapore.

Conversely, seven of the leading 10 countries with highest death rates were in the Baltic, Eastern European, or Central Asian regions, specifically Russia, Ukraine, Lithuania, Belarus, Mongolia, Latvia, and Kazakhstan. The other three were Lesotho, Burundi, and Central African Republic.

Health officials in those nations, Gakidou said, would be well served by examining the study's findings to inform their policies and programs to improve the health and well-being of their constituents.

Read more at Science Daily

How sleep loss may contribute to adverse weight gain

Weight scale
In a new study, researchers at Uppsala University now demonstrate that one night of sleep loss has a tissue-specific impact on the regulation of gene expression and metabolism in humans. This may explain how shift work and chronic sleep loss impairs our metabolism and adversely affects our body composition. The study is published in the scientific journal Science Advances.

Epidemiological studies have shown that the risk for obesity and type 2 diabetes is elevated in those who suffer from chronic sleep loss or who carry out shift work. Other studies have shown an association between disrupted sleep and adverse weight gain, in which fat accumulation is increased at the same time as the muscle mass is reduced -- a combination that in and of itself has been associated with numerous adverse health consequences. Researchers from Uppsala and other groups have in earlier studies shown that metabolic functions that are regulated by e.g. skeletal muscle and adipose tissue are adversely affected by disrupted sleep and circadian rhythms. However, until now it has remained unknown whether sleep loss per se can cause molecular changes at the tissue level that can confer an increased risk of adverse weight gain.

In the new study, the researchers studied 15 healthy normal-weight individuals who participated in two in-lab sessions in which activity and meal patterns were highly standardised. In randomised order, the participants slept a normal night of sleep (over eight hours) during one session, and were instead kept awake the entire night during the other session. The morning after each night-time intervention, small tissue samples (biopsies) were taken from the participants' subcutaneous fat and skeletal muscle. These two tissues often exhibit disrupted metabolism in conditions such as obesity and diabetes. At the same time in the morning, blood samples were also taken to enable a comparison across tissue compartments of a number of metabolites. These metabolites comprise sugar molecules, as well as different fatty and amino acids.

The tissue samples were used for multiple molecular analyses, which first of all revealed that the sleep loss condition resulted in a tissue-specific change in DNA methylation, one form of mechanism that regulates gene expression. DNA methylation is a so-called epigenetic modification that is involved in regulating how the genes of each cell in the body are turned on or off, and is impacted by both hereditary as well as environmental factors, such as physical exercise.

"Our research group were the first to demonstrate that acute sleep loss in and of itself results in epigenetic changes in the so-called clock genes that within each tissue regulate its circadian rhythm. Our new findings indicate that sleep loss causes tissue-specific changes to the degree of DNA methylation in genes spread throughout the human genome. Our parallel analysis of both muscle and adipose tissue further enabled us to reveal that DNA methylation is not regulated similarly in these tissues in response to acute sleep loss," says Jonathan Cedernaes who led the study.

"It is interesting that we saw changes in DNA methylation only in adipose tissue, and specifically for genes that have also been shown to be altered at the DNA methylation level in metabolic conditions such as obesity and type 2 diabetes. Epigenetic modifications are thought to be able to confer a sort of metabolic "memory" that can regulate how metabolic programmes operate over longer time periods. We therefore think that the changes we have observed in our new study can constitute another piece of the puzzle of how chronic disruption of sleep and circadian rhythms may impact the risk of developing for example obesity," notes Jonathan Cedernaes.

Further analyses of e.g. gene and protein expression demonstrated that the response as a result of wakefulness differed between skeletal muscle and adipose tissue. The researchers say that the period of wakefulness simulates the overnight wakefulness period of many shift workers assigned to nightwork. A possible explanation for why the two tissues respond in the observed manner could be that overnight wakefulness periods exert a tissue-specific effect on tissues' circadian rhythm, resulting in misalignment between these rhythms. This is something that the researchers found preliminary support for also in this study, as well as in an earlier similar but smaller study.

"In the present study we observed molecular signatures of increased inflammation across tissues in response to sleep loss. However, we also saw specific molecular signatures that indicate that the adipose tissue is attempting to increase its capacity to store fat following sleep loss, whereas we instead observed signs indicating concomitant breakdown of skeletal muscle proteins in the skeletal muscle, in what's also known as catabolism. We also noted changes in skeletal muscle levels of proteins involved handling blood glucose, and this could help explain why the participants' glucose sensitivity was impaired following sleep loss. Taken together, these observations may provide at least partial mechanistic insight as to why chronic sleep loss and shift work can increase the risk of adverse weight gain as well as the risk of type 2 diabetes," says Jonathan Cedernaes.

The researchers have only studied the effect of one night of sleep loss, and therefore do not know how other forms of sleep or disruption of circadian misalignment would have affected the participants' tissue metabolism.

Read more at Science Daily

Aug 23, 2018

Bird feared extinct rediscovered in the Bahamas

One of the rarest birds in the western hemisphere, the Bahama Nuthatch, has been rediscovered by research teams searching the island of Grand Bahama. The finding is particularly significant because the species had been feared extinct following the catastrophic damage caused by Hurricane Matthew in 2016, and had not been found in subsequent searches. But it is feared that there could only be two left -- placing the species on the verge of extinction and certainly among the world's most critically endangered birds.
One of the rarest birds in the western hemisphere, the Bahama Nuthatch, has been rediscovered by research teams searching the island of Grand Bahama.

The finding is particularly significant because the species had been feared extinct following the catastrophic damage caused by Hurricane Matthew in 2016, and had not been found in subsequent searches.

But it is feared that there could only be two left -- placing the species on the verge of extinction and certainly among the world's most critically endangered birds.

The Bahama Nuthatch is an endangered species, only known from a small area of native pine forest on Grand Bahama Island, which lies approximately 100 miles off Palm Beach, Florida.

University of East Anglia masters students Matthew Gardner and David Pereira set out on a three-month expedition to find this and other endemic Caribbean pine forest bird species.

They made their way through dense forest with thick 'poisonwood' understorey -- the layer of vegetation growing beneath the main forest canopy -- in what is thought to be one of the most exhaustive searches of the island.

They worked in partnership with Nigel Collar and David Wege from Birdlife International and the Bahamas National Trust, the organisation which works to protect the habitats and species of The Bahama Islands.

Meanwhile a second team of Bahamian students, led by Zeko McKenzie of the University of The Bahamas-North and supported by the American Bird Conservancy, also searched for the bird.

The Bahama Nuthatch has a long bill, a distinctive high-pitched squeaky call, and nests only in mature pine trees. There had been a sharp decline in its population crashing from an estimated 1,800 in 2004 to just 23 being seen in a survey in 2007. The decline likely began in the 1950s due to habitat loss due to timber removal, and more recently due to hurricane damage, storm surges having killed large areas native forest.

Both teams made Nuthatch sightings in May, and the UEA team were lucky enough to capture the elusive bird on film.

Dr Diana Bell, from UEA's School of Biological Sciences, said: "The Bahama Nuthatch is a critically endangered species, threatened by habitat destruction and degradation, invasive species, tourist developments, fires and hurricane damage.

"Our researchers looked for the bird across 464 survey points in 34,000 hectares of pine forest. It must have been like looking for a needle in a hay stack. They played out a recording of the bird's distinctive call in order to attract it.

"As well as searching for the elusive bird, they also collected environmental data to better understand its habitat preferences and surveyed the extent of hurricane and fire damage," she added."

Matthew Gardner said: "We were the first to undertake such an exhaustive search through 700km of forest on foot.

"We had been scouring the forest for about six weeks, and had almost lost hope. At that point we'd walked about 400km. Then, I suddenly heard its distinctive call and saw the unmistakable shape of a Nuthatch descending towards me. I shouted with joy, I was ecstatic!"

The UEA team made six Nuthatch sightings in total, and McKenzie's team independently made five sightings, using different methods, in the same small area of forest -- including a sighting of what they believe to be two birds together.

Mr Gardner said: "During three months of intensive searching we made six Bahama Nuthatch sightings. Our search was extremely thorough but we never saw two birds together, so we had thought there might only be one left in existence."

"The other team have reported seeing two together so that is promising. However, these findings place the species on the verge of extinction and certainly amongst the world's most critically endangered birds."

"We also don't know the sex of the birds. In many cases when birds dwindle to such small numbers, any remaining birds are usually male."

"The photographs clearly show this distinctive species and cannot be anything else" said Michael Parr, President of American Bird Conservancy and a UEA alumnus.

"Fortunately this is not a hard bird to identify, but it was certainly a hard bird to find," he added.

The Nuthatch was spotted in a small area known as Lucaya Estates. During the research project, birds were seen and heard in three distinct but nearby locations within this area.

Researcher Zeko McKenzie said: "Although the Bahama Nuthatch has declined precipitously, we are encouraged by the engagement of conservation scientists who are now looking for ways to save and recover the species."

The UEA team however are less optimistic as the exact drivers of the precipitous decline of the bird are still unclear.

Dr Diana Bell said: "Sadly, we think that the chances of bringing this bird back from the brink of extinction are very slim -- due to the very low numbers left, and because we are not sure of the precise drivers for its decline.

"But it is still absolutely crucial that conservation efforts in the native Caribbean pine forest do not lapse as it is such an important habitat for other endemic birds including the Bahama Swallow, Bahama Warbler and Bahama Yellowthroat.

"The habitat is also incredibly important for North American migrants including the Kirtlands Warbler," she added.

Ellsworth Weir, Grand Bahama Parks Manager at the Bahamas National Trust, said: "It has been a pleasure for The Bahamas National Trust to host both Matthew and David as they conducted this very important research on Grand Bahama."

"Their work has taken them across the length and breadth of the island in what was likely the most in depth search to be conducted. Their research, which was inclusive of bird and habitat surveys, has helped to answer questions that some residents have been asking for some time."

Read more at Science Daily

Evidence of matter-matter coupling

Rice University scientists observed Dicke cooperativity in a magnetic crystal in which two types of spins, in iron (blue arrows) and erbium (red arrows), interacted with each other. The iron spins were excited to form a wave-like object called a spin wave; the erbium spins precessing in a magnetic field (B) behaved like two-level atoms.
After their recent pioneering experiments to couple light and matter to an extreme degree, Rice University scientists decided to look for a similar effect in matter alone. They didn't expect to find it so soon.

Rice physicist Junichiro Kono, graduate student Xinwei Li and their international colleagues have discovered the first example of Dicke cooperativity in a matter-matter system, a result reported in Science this week.

The discovery could help advance the understanding of spintronics and quantum magnetism, Kono said. On the spintronics side, he said the work will lead to faster information processing with lower power consumption and will contribute to the development of spin-based quantum computing. The team's findings on quantum magnetism will lead to a deeper understanding of the phases of matter induced by many-body interactions at the atomic scale.

Instead of using light to trigger interactions in a quantum well, a system that produced new evidence of ultrastrong light-matter coupling earlier this year, the Kono lab at Rice used a magnetic field to prompt cooperativity among the spins within a crystalline compound made primarily of iron and erbium.

"This is an emerging subject in condensed matter physics," Kono said. "There's a long history in atomic and molecular physics of looking for the phenomenon of ultrastrong cooperative coupling. In our case, we'd already found a way to make light and condensed matter interact and hybridize, but what we're reporting here is more exotic."

Dicke cooperativity, named for physicist Robert Dicke, happens when incoming radiation causes a collection of atomic dipoles to couple, like gears in a motor that don't actually touch. Dicke's early work set the stage for the invention of lasers, the discovery of cosmic background radiation in the universe and the development of lock-in amplifiers used by scientists and engineers.

"Dicke was an unusually productive physicist," Kono said. "He had many high-impact papers and accomplishments in almost all areas of physics. The particular Dicke phenomenon that's relevant to our work is related to superradiance, which he introduced in 1954. The idea is that if you have a collection of atoms, or spins, they can work together in light-matter interaction to make spontaneous emission coherent. This was a very strange idea.

"When you stimulate many atoms within a small volume, one atom produces a photon that immediately interacts with another atom in the excited state," Kono said. "That atom produces another photon. Now you have coherent superposition of two photons.

"This happens between every pair of atoms within the volume and produces macroscopic polarization that eventually leads to a burst of coherent light called superradiance," he said. Taking light out of the equation meant the Kono lab had to find another way to excite the material's dipoles, the compass-like magnetic force inherent in every atom, and prompt them to align. Because the lab is uniquely equipped for such experiments, when the test material showed up, Kono and Li were ready.

"The sample was provided by my colleague (and co-author) Shixun Cao at Shanghai University," Kono said. Characterization tests with a small or no magnetic field performed by another co-author, Dmitry Turchinovich of the University of Duisburg-Essen, drew little response.

"But Dmitry is a good friend, and he knows we have a special experimental setup that combines terahertz spectroscopy, low temperatures and high magnetic field," Kono said. "He was curious to know what would happen if we did the measurements."

"Because we have some experience in this field, we got our initial data, identified some interesting details in it and thought there was something more we could explore in depth," Li added. "But we certainly didn't predict this," Kono said.

Li said that to show cooperativity, the magnetic components of the compound had to mimic the two essential ingredients in a standard light-atom coupling system where Dicke cooperativity was originally proposed: one a species of spins that can be excited into a wave-like object that simulates the light wave, and another with quantum energy levels that would shift with the applied magnetic field and simulate the atoms.

"Within a single orthoferrite compound, on one side the iron ions can be triggered to form a spin wave at a particular frequency," Li said. "On the other side, we used the electron paramagnetic resonance of the erbium ions, which forms a two-level quantum structure that interacts with the spin wave."

While the lab's powerful magnet tuned the energy levels of the erbium ions, as detected by the terahertz spectroscope, it did not initially show strong interactions with the iron spin wave at room temperature. But the interactions started to appear at lower temperatures, seen in a spectroscopic measurement of coupling strength known as vacuum Rabi splitting.

Chemically doping the erbium with yttrium brought it in line with the observation and showed Dicke cooperativity in the magnetic interactions. "The way the coupling strength increased matches in an excellent manner with Dicke's early predictions," Li said. "But here, light is out of the picture and the coupling is matter-matter in nature."

Read more at Science Daily

Tracking the evolution and transmission of yellow fever

Preparing the testing kit, including DNA sequencing.
A pioneering Oxford University research collaboration into yellow fever virus (YFV) has shed new light on the exceptional recent outbreak in Brazil and how the virus spreads. The findings have implications for monitoring viral transmission and could potentially contribute to a strategy for eliminating YFV worldwide.

Published in Science, the international collaboration coordinated by scientists from Oxford University and FIOCRUZ Rio de Janeiro, uses modern genomic and epidemiology techniques to investigate in detail the mode of transmission of South America's largest yellow fever virus outbreak in recent history. Techniques such as portable DNA sequencing and computational analysis allowed the team to understand the virus's genetic make-up and analyse the age, sex and spatial distribution of human cases.

Yellow fever virus is transmitted by mosquitoes in one of two ways, via sylvatic (forest) or urban (city) transmission. Most recent cases of YFV in Brazil have been traced back to forest dwelling primates and mosquitos -- a pattern characteristic of sylvatic transmission. But historical outbreaks in Brazil, and a recent outbreak of the virus in Angola, Africa, arose from urban transmission -- a mode of infection that could cause a great number infections in cities. Although a very effective vaccine for YFV exists, stocks are limited and it is not given to everyone in Brazil; until recently the vaccine was given only to people living bordering forest areas thought to be at 'high risk' of infection.

The 2016 yellow fever outbreak was the largest outbreak in Brazil for >100 years. There were concerns that the sheer scale of the outbreak could indicate that YFV had begun to spread via urban transmission -- increasing the likelihood of dangerous outbreaks in the megacites of Sao Paulo and Rio de Janeiro, where vaccination coverage is lower.

Analyses of YFV cases combined with genomic data, generated locally from affected states including Minas Gerais, revealed that the virus lineage had spread through a sylvatic cycle of transmission in primates, which grew unnoticed during 2016, before spilling over into human populations in early 2017.

Dr Nuno Faria, Sir Henry Dale Research Fellow in the Department of Zoology at Oxford University, said: 'Ultimately, the combination of epidemiological and genomic data tells us that the YFV outbreak in Brazil was driven by sylvatic transmission. Although the conditions for urban transmission seem to be there, that fortunately didn't happen.'

Further analyses confirmed that 85% of both human and primate YFV cases were male and aged between 35-54 years old -- a tell-tale sign of sylvatic transmission and a technique that could be applied rapidly to evaluate transmission in YFV epidemics across the world.

Professor Oliver Pybus, Professor of Evolution & Infectious Disease in Oxford's Department of Zoology said: 'Yellow Fever virus has affected humanity for hundreds of years. It comes in waves from an animal reservoir, so we may never completely eliminate it. The problem is that we don't understand enough yet about the complex behaviour of the virus in animal populations. We need this information to control future outbreaks -to vaccinate the right people, in the right place, at the right time'.

Professor Luiz Alcantara, Senior Scientific Researcher of reference laboratory in Flavivirus of the Brazilian Ministry of Health in Oswaldo Cruz Foundation (FIOCRUZ-RJ), Brazil, said: 'In 48 hours we were able to generate the first genomes from the epicentre of the outbreak in Minas Gerais. As part of the ZiBRA project, in which we tracked the spread of the Zika virus using gene sequencing, have now trained dozens of researchers in Brazil. In just a couple of weeks, using new portable sequencing methods, we were able to triple the amount of yellow fever virus genomes from Brazil.'

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Rare intermediate fossils give researchers insight into evolution of bird-like dinosaur

Xiyunykus bones in the lab before their removal from the rock.
An international team of researchers discovered a new species of dinosaur, Xiyunykus pengi, during an expedition to Xinjiang, China. The discovery is the latest stemming from a partnership between the George Washington University and the Chinese Academy of Sciences. The findings were published today in Current Biology along with the description of a second new intermediate species, Bannykus wulatensis.

Xiyunykus and Bannykus are both alvarezsaurs, an enigmatic group of dinosaurs that share many characteristics with birds. Their bodies are slender, with a bird-like skull and many small teeth instead of the usual large, sharp cutting teeth of their meat-eating relatives.

"When we described the first well-known alvarezsaur, Mononykus, in 1993, we were amazed at the contrast between its mole-like arms and its roadrunner-like body, but there were few fossils connecting it back to other theropod groups," James Clark, the Ronald Weintraub Professor of Biology at the GW Columbian College of Arts and Sciences, said.

However, alvarezsaurs did not always look this way. Early members of the group had relatively long arms with strong-clawed hands and typical meat-eating teeth. Over time, the alvarezsaurs evolved into dinosaurs with mole-like arms and a single claw. The discovery of the new specimens allowed the researchers to uncover an important shift in how the specialized features of the alvarezsaurs evolved.

"It can be hard to pin down the relationships of highly specialized animals. But fossil species with transitional features, like Xiyunykus and Bannykus, are tremendously helpful because they link bizarre anatomical features to more typical ones," Jonah Choiniere, an associate professor at Wits University and member of the research team, said.

The fossils were discovered during an expedition co-led by Dr. Clark and Xing Xu of the Institute of Vertebrate Paleontology and Paleoanthropology at the Chinese Academy of Sciences. Xiyunykus pengi is the ninth species of dinosaur identified by the partnership between GW and the academy.

"Our international field teams have been tremendously productive over the years," Dr. Xu said. "This research showcases just some of our incredible discoveries."

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Macaws may communicate visually with 'blushing,' ruffled feathers

This is a 'Blushing' macaw (left) compared to a 'non-blushing' macaw (right).
Parrots -- highly intelligent and highly verbal -- may also ruffle their head feathers and blush to communicate visually, according to a new study published August 22 in the open-access journal PLOS ONE by Aline Bertin of the INRA Centre Val de Loire, France and colleagues. The study extends the understanding of the complex social lives of these remarkable birds.

The authors studied five hand-reared captive blue-and-yellow macaws (Ara ararauna) interacting with one another and with their human caretakers. They assessed the feather position (ruffled or sleeked) on the crown, nape, and cheek, as well as the presence or absence of blushing on the bare skin of the cheek. They found that feather ruffling was more common when the birds were not in motion, such as during social interactions and resting periods. Crown feather ruffling and blushing were both more common when the human caretaker was actively interacting with the parrot by talking and maintaining eye contact than when the keeper was in the room but ignoring and turning their backs to the bird. Together, these results suggest that head feather ruffling is associated with states of lower arousal and positive social interactions, the authors concluded.

"How birds use facial displays and whether they communicate their inner subjective feelings is a question that is crucial to deepening our understanding of bird sentience," say Bertin et al. "Although caution must be exercised when interpreting these data due to the small sample size, we argue that crown ruffling and skin color variation may provide facial indicators of birds' inner subjective feelings. On a practical level, parrots are popular companion animals, with millions of parrots being kept as pets, and understanding visual communication in parrots may help to assess their well-being in captive conditions."

Bertin summarizes: "Blushing may not be a characteristic unique to humans: the featherless cheek of the blue-and-yellow macaw parrot reveals rapid skin color changes in situations associated with emotion. The macaw's particularly complex face may enable communication of emotion via color and feather displays."

From Science Daily

Aug 22, 2018

Laser breakthrough has physicists close to cooling down antimatter

Ti:Sapphire laser system built at the University of British Columbia.
For the first time, physicists at CERN have observed a benchmark atomic energy transition in anithydrogen, a major step toward cooling and manipulating the basic form of antimatter.

"The Lyman-alpha transition is the most basic, important transition in regular hydrogen atoms, and to capture the same phenomenon in antihydrogen opens up a new era in antimatter science," said Takamasa Momose, the University of British Columbia chemist and physicist who led the development of the laser system used to manipulate the anithydrogen.

"This approach is a gateway to cooling down antihydrogen, which will greatly improve the precision of our measurements and allow us test how antimatter and gravity interact, which is still a mystery."

The results were published today in Nature.

Antimatter, annihilated on impact with matter, is notoriously tricky to capture and work with. But its study is key to solving one of the great mysteries of the universe: why anti-matter, which should have existed in equal amounts to matter at the time of the Big Bang, has all but disappeared.

"This gets us just a bit closer to answering some of these big questions in physics," said Makoto Fujiwara, Canada's spokesperson for CERN's ALPHA antihydrogen research collaboration, and a physicist with TRIUMF, Canada's particle accelerator centre. "Over the past decades, scientists have been able to revolutionize atomic physics using optical manipulation and laser cooling, and with this result we can begin applying the same tools to probing the mysteries of antimatter."

An antihydrogen atom, consisting of an antiproton and positron, is the antimatter counterpart of a hydrogen atom, made of a single proton with an orbiting electron.

The so-called Lyman-alpha transition, first seen in hydrogen more than 100 years ago, is measured as a series of ultraviolet emissions when a hydrogen atom's electron is prompted to shift from a low orbital to a high orbital. Using laser pulses lasting nano seconds, Momose, Fujiwara, Canadian colleagues, and the international ALPHA collaboration at CERN, were able to achieve the same transition in several hundred antihydrogen atoms magnetically trapped in a vacuum.

Aside from the very real challenge of trapping that many antihydrogen atoms long enough to work with them, fine-tuning the laser system components took years.

"You can't actually see the laser pulses you're using to excite the antihydrogen and shift the orbitals," says Momose. "So, our team was essentially working and trouble-shooting the laser system in the blind!"

The team's next step is to use the laser innovation to help produce cold and dense sample of anti-atoms for precision spectroscopy and gravity measurements.

Read more at Science Daily

New genetic regulators of regeneration identified

The zebrafish, a common aquarium fish, is one of nature's champions of regeneration. Scientists Viravuth P. Yin, Ph.D., of the MDI Biological Laboratory and Benjamin L. King, Ph.D., of the University of Maine discovered genetic material in the cell that likely plays a part in regulating genetic circuits responsible for regeneration in highly regenerative animals by studying the early stages of heart regeneration in the zebrafish.
Scientists at the MDI Biological Laboratory and the University of Maine have discovered that genetic material in the cell that was previously thought to be "junk" because of its apparent lack of function likely plays a part in regulating genetic circuits responsible for regeneration in highly regenerative animals.

Viravuth P. Yin, Ph.D., of the MDI Biological Laboratory and Benjamin L. King, Ph.D., of the University of Maine identified these "long noncoding RNAs" by studying genomic data from highly regenerative animals included in a RegenDbase (Comparative Models of Regeneration Database) developed by the MDI Biological Laboratory.

The discovery of these novel long noncoding RNAs and their role in regulating regeneration may lead to an answer to the paramount question that is being examined by scientists at the MDI Biological Laboratory: If highly regenerative animals such as zebrafish and salamanders can regenerate tissues and organs, why we can't we?

The answer could one day lead to the development of drugs to trigger humans' dormant pathways for regeneration. Like most other mammals, the capacity for regeneration in adult humans is limited.

The paper describing the scientists' findings was published in a recent issue of npj Regenerative Medicine.

"Many chronic and degenerative diseases are characterized by a limited capacity to repair and regenerate damaged tissues," said Yin. "By advancing our understanding of the genetic regulation of regeneration in highly regenerative animals, we may one day be able to trigger regeneration in humans with drugs that manipulate these pathways."

The role of noncoding RNAs

In particular, the scientists looked at the role of noncoding RNAs, or RNAs that were formerly considered "junk" because they do not make proteins, in the early stages of heart regeneration in the zebrafish, a common aquarium fish that is one of nature's champions of regeneration.

RNA, or ribonucleic acid, typically acts as a messenger that transports instructions from the DNA, the carrier of genetic information, to the machinery in the cell that manufactures proteins involved in biological functions.

"One of the secrets to decoding why zebrafish can regenerate their hearts while adult humans cannot may lie with these noncoding RNAs," said King, the paper's lead author. "The protein-coding genes in zebrafish and humans are more or less the same -- what's different is how they are regulated during regeneration by noncoding RNAs."

The discoveries of Yin and King -- as well as other recent advances in the field of regenerative biology -- have been enabled by the introduction of sophisticated genomic tools that scientists can use to identify the networks of genes responsible for orchestrating the complex process of regeneration in highly regenerative animals.

Applying these tools, the authors defined a comprehensive regeneration gene expression atlas for zebrafish heart regeneration and anchored the data as a point of reference for comparison with other models. Using computational analysis, they identified shared and unique patterns of gene expression in genomic data from various species.

"The biological role of more than 90 percent of the genetic material in the cell is unknown, which raises the question: Why is it there?" said Hermann Haller, M.D., president of the MDI Biological Laboratory. "This extraordinary discovery demonstrates the power of computational biology to map this uncharted genetic landscape."

Yin and King studied the roles of two types of noncoding RNAs -- microRNAs and long noncoding RNAs -- in zebrafish heart regeneration.

In addition to further elucidating the role of microRNAs, which are known to play a regulatory role in heart regeneration, the scientists also characterized the role of known and previously unknown long noncoding RNAs and the genes they potentially regulate through genetic proximity searches that King called "guilt by association."

The next step is to conduct studies of a select group of long noncoding RNAs in vertebrates with varying capacities for regeneration to validate the functions of the target gene networks that the scientists have identified and to test the extent to which these long noncoding RNAs are responsible for regulating these networks.

The RegenDbase: a 'Rosetta Stone' for regeneration

The paper also introduced the RegenDbase, a new database that allows scientists to compare and contrast gene regulatory pathways within and across tissues and research models, with a focus on noncoding RNAs.

The database was created using a new dataset for heart regeneration in zebrafish created at the MDI Biological Laboratory, as well as existing data on multiple types of injured tissues from various species. The utility of the database, which is available to the public, is expected to grow as more data is added, including from human tissues.

Yin compares the database to the Rosetta Stone, which in 1799 allowed linguists to decipher Egyptian hieroglyphs because the information inscribed on it was also presented in ancient Greek, a known language. Similarly, the new database is helping scientists translate the genetic code for regeneration from one species to another.

"Everything in biology comes with an instruction manual," said Yin, explaining the analogy. "If the manual for regeneration is in ancient Egyptian for zebrafish and in Greek for mammals, we can use the database to translate the codes into the same language so we can identify the components that are lacking in mammals."

The RegenDbase was created by the MDI Biological Laboratory under its Center of Biomedical Research Excellence (COBRE) program grant award. The institution was designated as a center of excellence in research on the comparative biology of tissue repair, regeneration and aging in 2013, a designation that was recently renewed.

Read more at Science Daily

Air pollution leads to cardiovascular diseases

Fine dust from industry, road and air traffic, and agriculture pollutes the air and leads to cardiovascular diseases.
Air pollution, and fine dust in particular, is responsible for more than four million deaths each year. Almost 60 per cent of deaths occur as a result of cardiovascular diseases. Scientists around Professor Thomas Münzel, Director of Cardiology I at the Department of Cardiology at the Medical Center of Johannes Gutenberg University Mainz (JGU), reviewed the mechanisms responsible for vascular damage from air pollution together with scientists from the UK and the USA. Their findings have been published in the latest issue of the European Heart Journal.

The large percentage of deaths from cardiovascular disease has prompted an international group of experts from Germany, England, and the USA to analyze the negative effects of air pollution on vascular function in a review article. Key research questions focused on components of air pollution (particulate matter, ozone, nitrogen dioxide, carbon monoxide, and sulfur dioxide) that are particularly damaging to the cardiovascular system and mechanisms that damage the vessels.

"This report in the latest issue of the European Heart Journal is another important contribution from our Working Group on Environment and Cardiovascular Disease. In summary, it can be said that in relation to the vascular damaging effect of air pollution, particulate matter plays a prominent role," commented Professor Thomas Münzel. "We are especially worried about ultrafine dust. These particles have the size of a virus. When ultrafine matter is inhaled, it immediately enters the bloodstream through the lungs, is taken up by the vessels, and causes local inflammation. Ultimately, this causes more atherosclerosis (vascular calcification) and thus leads to more cardiovascular diseases such as myocardial infarction, acute myocardial infarction, heart failure, and cardiac arrhythmias. Of particular interest is the fact that with regard to the much-discussed diesel exhaust emissions, particulate matter and not nitrogen dioxide (NO2), both of which are produced by burning diesel fuel, have a negative effect on vascular function," Münzel continued.

Other participants in the expert group include the particulate matter researcher Professor Sanjay Rajagopalan of the UH Cleveland Medical Center, the vascular researcher and cardiologist Professor John Deanfield of the Institute of Cardiovascular Science at University College London, Professor Andreas Daiber, Head of Molecular Cardiology at the Mainz University Medical Center, and Professor Jos Lelieveld from the Max Planck Institute for Chemistry (MPIC) in Mainz.

"The fine dust particles are chemically formed mainly in the atmosphere from emissions from traffic, industry, and agriculture. In order to achieve low, harmless concentrations, emissions from all these sources need to be reduced," commented Professor Jos Lelieveld.

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Fossil turtle didn't have a shell yet, but had the first toothless turtle beak

Illustration showing what Eorhynchochelys would have looked like in life.
There are a couple of key features that make a turtle a turtle: its shell, for one, but also its toothless beak. A newly-discovered fossil turtle that lived 228 million years ago is shedding light on how modern turtles developed these traits. It had a beak, but while its body was Frisbee-shaped, its wide ribs hadn't grown to form a shell like we see in turtles today.

"This creature was over six feet long, it had a strange disc-like body and a long tail, and the anterior part of its jaws developed into this strange beak," says Olivier Rieppel, a paleontologist at Chicago's Field Museum and one of the authors of a new paper in Nature. "It probably lived in shallow water and dug in the mud for food."

The new species has been christened Eorhynchochelys sinensis -- a mouthful, but with a straightforward meaning. Eorhynchochelys ("Ay-oh-rink-oh-keel-is") means "dawn beak turtle" -- essentially, first turtle with a beak -- while sinensis, meaning "from China," refers to the place where it was found by the study's lead author, Li Chun of China's Institute of Vertebrate Paleontology and Paleoanthropology.

Eorhynchochelys isn't the only kind of early turtle that scientists have discovered -- there is another early turtle with a partial shell but no beak. Until now, it's been unclear how they all fit into the reptile family tree. "The origin of turtles has been an unsolved problem in paleontology for many decades," says Rieppel. "Now with Eorhynchochelys, how turtles evolved has become a lot clearer."

The fact that Eorhynchochelys developed a beak before other early turtles but didn't have a shell is evidence of mosaic evolution -- the idea that traits can evolve independently from each other and at a different rate, and that not every ancestral species has the same combination of these traits. Modern turtles have both shells and beaks, but the path evolution took to get there wasn't a straight line. Instead, some turtle relatives got partial shells while others got beaks, and eventually, the genetic mutations that create these traits occurred in the same animal.

"This impressively large fossil is a very exciting discovery giving us another piece in the puzzle of turtle evolution," says Nick Fraser, an author of the study from National Museums Scotland. "It shows that early turtle evolution was not a straightforward, step-by-step accumulation of unique traits but was a much more complex series of events that we are only just beginning to unravel."

Fine details in the skull of Eorhynchochelys solved another turtle evolution mystery. For years, scientists weren't sure if turtle ancestors were part of the same reptile group as modern lizards and snakes -- diapsids, which early in their evolution had two holes on the sides of their skulls -- or if they were anapsids that lack these openings. Eorhynchochelys's skull shows signs that it was a diapsid. "With Eorhynchochelys's diapsid skull, we know that turtles are not related to the early anapsid reptiles, but are instead related to evolutionarily more advanced diapsid reptiles. This is cemented, the debate is over," says Rieppel.

The study's authors say that their findings, both about how and when turtles developed shells and their status as diapsids, will change how scientists think about this branch of animals. "I was surprised myself," says Rieppel. "Eorhynchochelys makes the turtle family tree make sense. Until I saw this fossil, I didn't buy some of its relatives as turtles. Now, I do."

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Neanderthal mother, Denisovan father! Hybrid fossil

This bone fragment ('Denisova 11') was found in 2012 at Denisova Cave in Russia by Russian archaeologists and represents the daughter of a Neanderthal mother and a Denisovan father.
Together with their sister group the Neanderthals, Denisovans are the closest extinct relatives of currently living humans. "We knew from previous studies that Neanderthals and Denisovans must have occasionally had children together," says Viviane Slon, researcher at the MPI-EVA and one of three first authors of the study. "But I never thought we would be so lucky as to find an actual offspring of the two groups."

The ancient individual is only represented by a single small bone fragment. "The fragment is part of a long bone, and we can estimate that this individual was at least 13 years old," says Bence Viola of the University of Toronto. The bone fragment was found in 2012 at Denisova Cave (Russia) by Russian archaeologists. It was brought to Leipzig for genetic analyses after it was identified as a hominin bone based on its protein composition.

"An interesting aspect of this genome is that it allows us to learn things about two populations -- the Neanderthals from the mother's side, and the Denisovans from the father's side," explains Fabrizio Mafessoni from the MPI-EVA who co-authored the study. The researchers determined that the mother was genetically closer to Neanderthals who lived in western Europe than to a Neanderthal individual that lived earlier in Denisova Cave. This shows that Neanderthals migrated between western and eastern Eurasia tens of thousands of years before their disappearance.

Analyses of the genome also revealed that the Denisovan father had at least one Neanderthal ancestor further back in his family tree. "So from this single genome, we are able to detect multiple instances of interactions between Neanderthals and Denisovans," says Benjamin Vernot from the MPI-EVA, the third co-author of the study.

"It is striking that we find this Neanderthal/Denisovan child among the handful of ancient individuals whose genomes have been sequenced," adds Svante Pääbo, Director of the Department of Evolutionary Genetics at the MPI-EVA and lead author of the study. "Neanderthals and Denisovans may not have had many opportunities to meet. But when they did, they must have mated frequently -- much more so than we previously thought."

From Science Daily

Aug 21, 2018

How do muscles know what time it is?

The 'circadian clock' of muscle cells (shown here is the transverse section of a muscle fiber) controls an entire metabolic network.
How do muscle cells prepare for the particular metabolic challenges of the day? Scientists at Helmholtz Zentrum München and Ludwig-Maximilians-Universität München (LMU), members of the German Center for Diabetes Research (DZD), have investigated this question and published their results in 'PLOS Biology'. The study has uncovered a metabolic network which is, contrary to expectations, not controlled by the brain but rather by the 'circadian clock' of muscle cells.

Circadian clocks are present in all cells of the body, and have a pervasive influence on all aspects of human physiology. This is because they regulate homeostasis by anticipating rhythmic changes in behavior and nutritional state, and by compartmentalizing incompatible metabolic pathways within precise temporal windows. "This applies, for example, to the use of nutrients such as fats and carbohydrates," explains Professor Henriette Uhlenhaut. She is group leader at the Institute for Diabetes and Obesity of Helmholtz Zentrum München (IDO) and the Gene Center of LMU. "If the body's internal clock gets out of synch, however, it can have serious consequences for the body's metabolism. For example, it is known that shift workers are particularly susceptible to metabolic diseases such as diabetes."

In their recent work, the team led by Uhlenhaut turned their attention to the 24-hour metabolic rhythm of muscles. "We focused specifically on two proteins that act as master regulators, positive and negative arms of the circadian clock," says Kenneth Dyar, a scientist at the IDO and lead author of the study. "These two opposing molecules bind to DNA and trigger expression of additional proteins known to regulate lipid and protein metabolism." Using muscle cells from mice, the scientists determined the activity of the two proteins over the course of the day and night. "We measured everything, from DNA binding to gene expression and metabolites," says Kenneth Dyar, explaining the researchers' comprehensive approach. Building upon previous studies, the scientists studied the synthesis and breakdown of fats and proteins over 24 hours -- an approach that might also be interesting for athletes.

Uncovering a metabolic network

In collaboration with Italian and Austrian colleagues (from the Venetian Institute of Molecular Medicine and the Universities of Padua, Graz, and Trieste) the researchers identified certain processes that are switched on at night by the regulators of the internal clock: "They include, for example, fat storage, glucose metabolism and insulin sensitivity," explains Henriette Uhlenhaut. At the same time, opposing processes such as fatty acid oxidation and protein breakdown are throttled down, according the authors. These patterns are especially pronounced in the hours before awakening and are thought to prepare the muscles for the day ahead.

Read more at Science Daily

Carbon reserves in Central American soils still affected by ancient Mayan deforestation

This is an ancient stone carving of the Maya God Pauahtun, taken at Copan Ruinas, Honduras.
Deforestation is suspected to have contributed to the mysterious collapse of Mayan civilization more than 1,000 years ago. A new study shows that the forest-clearing also decimated carbon reservoirs in the tropical soils of the Yucatan peninsula region long after ancient cities were abandoned and the forests grew back.

The findings, published in the journal Nature Geoscience, underscore how important soils and our treatment of them could be in determining future levels of greenhouse gases in the planet's atmosphere.

The Maya began farming around 4,000 years ago, and the spread of agriculture and building of cities eventually led to widespread deforestation and soil erosion, previous research has shown. What's most surprising in the new study is that the soils in the region haven't fully recovered as carbon sinks in over a millennium of reforestation, says McGill University geochemist Peter Douglas, lead author of the new paper.

Ecosystem 'fundamentally changed'

"When you go to this area today, much of it looks like dense, old-growth rainforest," says Douglas, an Assistant Professor of Earth and Planetary Sciences at McGill. "But when you look at soil carbon storage, it seems the ecosystem was fundamentally changed and never returned to its original state."

Soil is one of the largest storehouses of carbon on Earth, containing at least twice as much carbon as today's atmosphere. Yet scientists have very little understanding of how soil carbon reservoirs change on timescales longer than a decade or so. The new study, along with other recently published research, suggests that these reservoirs can change dramatically on timescales spanning centuries or even millennia.

To investigate these long-term effects, Douglas and his co-authors examined sediment cores extracted from the bottom of three lakes in the Maya Lowlands of southern Mexico and Guatemala. The researchers used measurements of radiocarbon, an isotope that decays with time, to determine the age of molecules called plant waxes, which are usually stored in soils for a long time because they become attached to minerals. They then compared the age of wax molecules with that of plant fossils deposited with the sediments.

The team -- which included scientists from Yale University, ETH Zurich, the University of Florida and the University of Wisconsin-Superior -- found that once the ancient Maya began deforesting the landscape, the age difference between the fossils and the plant waxes went from being very large to very small. This implies that carbon was being stored in soils for much shorter periods of time.

The project stemmed from research that Douglas had done several years ago as a PhD student at Yale, using plant-wax molecules to trace past climate change affecting the ancient Maya. At the same time, work by other researchers was indicating that these molecules were a good tracer for changes in soil-carbon reservoirs. "Putting these things together, we realized there was an important data-set here relating ancient deforestation to changes in soil carbon reservoirs," Douglas explains.

Protecting old-growth tropical forests

"This offers another reason -- adding to a long list -- to protect the remaining areas of old-growth tropical forests in the world," Douglas says. "It could also have implications for how we design things like carbon offsets, which often involve reforestation but don't fully account for the long-term storage of carbon." (Carbon offsets enable companies or individuals to offset their greenhouse-gas emissions by purchasing credits from environmental projects, such as tree-planting.)

Read more at Science Daily

Ice confirmed at the moon's poles

The image shows the distribution of surface ice at the Moon's south pole (left) and north pole (right), detected by NASA's Moon Mineralogy Mapper instrument. Blue represents the ice locations, plotted over an image of the lunar surface, where the gray scale corresponds to surface temperature (darker representing colder areas and lighter shades indicating warmer zones). The ice is concentrated at the darkest and coldest locations, in the shadows of craters. This is the first time scientists have directly observed definitive evidence of water ice on the Moon's surface.
In the darkest and coldest parts of its polar regions, a team of scientists has directly observed definitive evidence of water ice on the Moon's surface. These ice deposits are patchily distributed and could possibly be ancient. At the southern pole, most of the ice is concentrated at lunar craters, while the northern pole's ice is more widely, but sparsely spread.

A team of scientists, led by Shuai Li of the University of Hawaii and Brown University and including Richard Elphic from NASA's Ames Research Center in California's Silicon Valley, used data from NASA's Moon Mineralogy Mapper (M3) instrument to identify three specific signatures that definitively prove there is water ice at the surface of the Moon.

M3, aboard the Chandrayaan-1 spacecraft, launched in 2008 by the Indian Space Research Organization, was uniquely equipped to confirm the presence of solid ice on the Moon. It collected data that not only picked up the reflective properties we'd expect from ice, but was able to directly measure the distinctive way its molecules absorb infrared light, so it can differentiate between liquid water or vapor and solid ice.

Most of the newfound water ice lies in the shadows of craters near the poles, where the warmest temperatures never reach above minus 250 degrees Fahrenheit. Because of the very small tilt of the Moon's rotation axis, sunlight never reaches these regions.

Previous observations indirectly found possible signs of surface ice at the lunar south pole, but these could have been explained by other phenomena, such as unusually reflective lunar soil.

With enough ice sitting at the surface -- within the top few millimeters -- water would possibly be accessible as a resource for future expeditions to explore and even stay on the Moon, and potentially easier to access than the water detected beneath the Moon's surface.

Learning more about this ice, how it got there, and how it interacts with the larger lunar environment will be a key mission focus for NASA and commercial partners, as we endeavor to return to and explore our closest neighbor, the Moon.

The findings were published in the Proceedings of the National Academy of Sciences on August 20, 2018.

Read more at Science Daily

Massive monumental cemetery built by Eastern Africa's earliest herders discovered in Kenya

Stone pendants and earrings from the communal cemetery of Lothagam North, Kenya, built by eastern Africa's earliest herders ~5000-4300 years ago. Megaliths, stone circles, and cairns flank the 30-m platform mound; its mortuary cavity contains an estimated several hundred individuals, tightly arranged. Most burials had highly personalized ornaments. Lothagam North demonstrates monumentality may arise among dispersed, mobile groups without strong hierarchy.
An international team, including researchers at Stony Brook University and the Max Planck Institute for the Science of Human History, has found the earliest and largest monumental cemetery in eastern Africa. The Lothagam North Pillar Site was built 5,000 years ago by early pastoralists living around Lake Turkana, Kenya. This group is believed to have had an egalitarian society, without a stratified social hierarchy. Thus their construction of such a large public project contradicts long-standing narratives about early complex societies, which suggest that a stratified social structure is necessary to enable the construction of large public buildings or monuments. The study, led by Elisabeth Hildebrand, of Stony Brook University, is published in the Proceedings of the National Academy of Sciences.

The Lothagam North Pillar Site was a communal cemetery constructed and used over a period of several centuries, between about 5,000 and 4,300 years ago. Early herders built a platform approximately 30 meters in diameter and excavated a large cavity in the center to bury their dead. After the cavity was filled and capped with stones, the builders placed large, megalith pillars, some sourced from as much as a kilometer away, on top. Stone circles and cairns were added nearby. An estimated minimum of 580 individuals were densely buried within the central platform cavity of the site. Men, women, and children of different ages, from infants to the elderly, were all buried in the same area, without any particular burials being singled out with special treatment. Additionally, essentially all individuals were buried with personal ornaments and the distribution of ornaments was approximately equal throughout the cemetery. These factors indicate a relatively egalitarian society without strong social stratification.

Historically, archeologists have theorized that people built permanent monuments as reminders of shared history, ideals and culture, when they had established a settled, socially stratified agriculture society with abundant resources and strong leadership. It was believed that a political structure and the resources for specialization were prerequisites to engaging in monument building. Ancient monuments have thus previously been regarded as reliable indicators of complex societies with differentiated social classes. However, the Lothagam North cemetery was constructed by mobile pastoralists who show no evidence of a rigid social hierarchy. "This discovery challenges earlier ideas about monumentality," explains Elizabeth Sawchuk of Stony Brook University and the Max Planck Institute for the Science of Human History. "Absent other evidence, Lothagam North provides an example of monumentality that is not demonstrably linked to the emergence of hierarchy, forcing us to consider other narratives of social change."

The discovery is consistent with similar examples elsewhere in Africa and on other continents in which large, monumental structures have been built by groups thought to be egalitarian in their social organization. This research has the potential to reshape global perspectives on how -- and why -- large groups of people come together to form complex societies. In this case, it appears that Lothagam North was built during a period of profound change. Pastoralism had just been introduced to the Turkana Basin and newcomers arriving with sheep, goats, and cattle would have encountered diverse groups of fisher-hunter-gatherers already living around the lake. Additionally, newcomers and locals faced a difficult environmental situation, as annual rainfall decreased during this period and Lake Turkana shrunk by as much as fifty percent. Early herders may have constructed the cemetery as a place for people to come together to form and maintain social networks to cope with major economic and environmental change.

"The monuments may have served as a place for people to congregate, renew social ties, and reinforce community identity," states Anneke Janzen also of the Max Planck Institute for the Science of Human History. "Information exchange and interaction through shared ritual may have helped mobile herders navigate a rapidly changing physical landscape." After several centuries, pastoralism became entrenched and lake levels stabilized. It was around this time that the cemetery ceased to be used.

Read more at Science Daily

Aug 20, 2018

Light from ancient quasars helps confirm quantum entanglement

This artist's impression of one of the most distant, oldest, brightest quasars ever seen is hidden behind dust. The quasar dates back to less than one billion years after the big bang.
Last year, physicists at MIT, the University of Vienna, and elsewhere provided strong support for quantum entanglement, the seemingly far-out idea that two particles, no matter how distant from each other in space and time, can be inextricably linked, in a way that defies the rules of classical physics.

Take, for instance, two particles sitting on opposite edges of the universe. If they are truly entangled, then according to the theory of quantum mechanics their physical properties should be related in such a way that any measurement made on one particle should instantly convey information about any future measurement outcome of the other particle -- correlations that Einstein skeptically saw as "spooky action at a distance."

In the 1960s, the physicist John Bell calculated a theoretical limit beyond which such correlations must have a quantum, rather than a classical, explanation.

But what if such correlations were the result not of quantum entanglement, but of some other hidden, classical explanation? Such "what-ifs" are known to physicists as loopholes to tests of Bell's inequality, the most stubborn of which is the "freedom-of-choice" loophole: the possibility that some hidden, classical variable may influence the measurement that an experimenter chooses to perform on an entangled particle, making the outcome look quantumly correlated when in fact it isn't.

Last February, the MIT team and their colleaguessignificantly constrainedthe freedom-of-choice loophole, by using 600-year-old starlight to decide what properties of two entangled photons to measure. Their experiment proved that, if a classical mechanism caused the correlations they observed, it would have to have been set in motion more than 600 years ago, before the stars' light was first emitted and long before the actual experiment was even conceived.

Now, in a paper published today in Physical Review Letters, the same team has vastly extended the case for quantum entanglement and further restricted the options for the freedom-of-choice loophole. The researchers used distant quasars, one of which emitted its light 7.8 billion years ago and the other 12.2 billion years ago, to determine the measurements to be made on pairs of entangled photons. They found correlations among more than 30,000 pairs of photons, to a degree that far exceeded the limit that Bell originally calculated for a classically based mechanism.

"If some conspiracy is happening to simulate quantum mechanics by a mechanism that is actually classical, that mechanism would have had to begin its operations -- somehow knowing exactly when, where, and how this experiment was going to be done -- at least 7.8 billion years ago. That seems incredibly implausible, so we have very strong evidence that quantum mechanics is the right explanation," says co-author Alan Guth, the Victor F. Weisskopf Professor of Physics at MIT.

"The Earth is about 4.5 billion years old, so any alternative mechanism -- different from quantum mechanics -- that might have produced our results by exploiting this loophole would've had to be in place long before even there was a planet Earth, let alone an MIT," adds David Kaiser, the Germeshausen Professor of the History of Science and professor of physics at MIT. "So we've pushed any alternative explanations back to very early in cosmic history."

Guth and Kaiser's co-authors include Anton Zeilinger and members of his group at the Austrian Academy of Sciences and the University of Vienna, as well as physicists at Harvey Mudd College and the University of California at San Diego.

A decision, made billions of years ago

In 2014, Kaiser and two members of the current team, Jason Gallicchio and Andrew Friedman,proposed an experimentto produce entangled photons on Earth -- a process that is fairly standard in studies of quantum mechanics. They planned to shoot each member of the entangled pair in opposite directions, toward light detectors that would also make a measurement of each photon using a polarizer. Researchers would measure the polarization, or orientation, of each incoming photon's electric field, by setting the polarizer at various angles and observing whether the photons passed through -- an outcome for each photon that researchers could compare to determine whether the particles showed the hallmark correlations predicted by quantum mechanics.

The team added a unique step to the proposed experiment, which was to use light from ancient, distant astronomical sources, such as stars and quasars, to determine the angle at which to set each respective polarizer. As each entangled photon was in flight, heading toward its detector at the speed of light, researchers would use a telescope located at each detector site to measure the wavelength of a quasar's incoming light. If that light was redder than some reference wavelength, the polarizer would tilt at a certain angle to make a specific measurement of the incoming entangled photon -- a measurement choice that was determined by the quasar. If the quasar's light was bluer than the reference wavelength, the polarizer would tilt at a different angle, performing a different measurement of the entangled photon.

In their previous experiment, the team used small backyard telescopes to measure the light from stars as close as 600 light years away. In their new study, the researchers used much larger, more powerful telescopes to catch the incoming light from even more ancient, distant astrophysical sources: quasars whose light has been traveling toward the Earth for at least 7.8 billion years -- objects that are incredibly far away and yet are so luminous that their light can be observed from Earth.

Tricky timing

On Jan. 11, 2018, "the clock had just ticked past midnight local time," as Kaiser recalls, when about a dozen members of the team gathered on a mountaintop in the Canary Islands and began collecting data from two large, 4-meter-wide telescopes: the William Herschel Telescope and the Telescopio Nazionale Galileo, both situated on the same mountain and separated by about a kilometer.

One telescope focused on a particular quasar, while the other telescope looked at another quasar in a different patch of the night sky. Meanwhile, researchers at a station located between the two telescopes created pairs of entangled photons and beamed particles from each pair in opposite directions toward each telescope.

In the fraction of a second before each entangled photon reached its detector, the instrumentation determined whether a single photon arriving from the quasar was more red or blue, a measurement that then automatically adjusted the angle of a polarizer that ultimately received and detected the incoming entangled photon.

"The timing is very tricky," Kaiser says. "Everything has to happen within very tight windows, updating every microsecond or so."

Demystifying a mirage

The researchers ran their experiment twice, each for around 15 minutes and with two different pairs of quasars. For each run, they measured 17,663 and 12,420 pairs of entangled photons, respectively. Within hours of closing the telescope domes and looking through preliminary data, the team could tell there were strong correlations among the photon pairs, beyond the limit that Bell calculated, indicating that the photons were correlated in a quantum-mechanical manner.

Guth led a more detailed analysis to calculate the chance, however slight, that a classical mechanism might have produced the correlations the team observed.

He calculated that, for the best of the two runs, the probability that a mechanism based on classical physics could have achieved the observed correlation was about 10 to the minus 20 -- that is, about one part in one hundred billion billion, "outrageously small," Guth says. For comparison, researchers have estimated the probability that the discovery of the Higgs boson was just a chance fluke to be about one in a billion.

"We certainly made it unbelievably implausible that a local realistic theory could be underlying the physics of the universe," Guth says.

And yet, there is still a small opening for the freedom-of-choice loophole. To limit it even further, the team is entertaining ideas of looking even further back in time, to use sources such as cosmic microwave background photons that were emitted as leftover radiation immediately following the Big Bang, though such experiments would present a host of new technical challenges.

"It is fun to think about new types of experiments we can design in the future, but for now, we are very pleased that we were able to address this particular loophole so dramatically. Our experiment with quasars puts extremely tight constraints on various alternatives to quantum mechanics. As strange as quantum mechanics may seem, it continues to match every experimental test we can devise," Kaiser says.

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