Biologists at Columbia University Vagelos College of Physicians and Surgeons have leveraged a computational method to map protein-protein interactions between all known human-infecting viruses and the cells they infect. The method, along with the data that it generated, has generated a wealth of information about how viruses manipulate the cells that they infect and cause disease. Among the study's findings are the role of estrogen receptors in regulating Zika virus infection and how human papillomavirus (HPV) causes cancer.
The study, led by Sagi Shapira, PhD, assistant professor of systems biology at Columbia University Vagelos College of Physicians and Surgeons, was published today in the journal Cell.
LIMITED UNDERSTANDING OF HOW VIRUSES WORK
At the molecular level, viruses invade cells and manipulate them to replicate, survive, and cause disease. Since they depend on human cells for their life cycle, one way viruses co-opt cellular machinery is through protein-protein interactions within their cell host. Similarly, cells respond to infection by initiating immune responses that control and limit viral replication -- these too, depend on protein-protein interactions.
To date, considerable effort has been invested in identifying these key interactions -- and many of these efforts have resulted in many fundamental discoveries, some with therapeutic implications. However, traditional methods are limited in terms of scalability, efficiency, and even access. To address this challenge, Dr. Shapira and his collaborators developed and implemented a computational framework, P-HIPSTER, that infers interactions between pathogen and human proteins -- the building blocks of viruses and cells.
Until now, our knowledge about many viruses that infect people is limited to their genome sequences. Yet for most viruses, little has been uncovered about the underlying biological interactions that drive these relationships and give rise to disease.
"There are over 1,000 unique viruses that are known to infect people," says Dr. Shapira. "Yet, despite their unquestionable public health importance, we know virtually nothing about the vast majority of them. We just know they infect human cells. The idea behind this effort was to systematically catalogue the interactions that viruses have with the cells they infect. And, by doing so, also reveal some really interesting biology and provide the scientific community with a resource that they can use to make interesting observations of their own."
Using a novel algorithm, P-HIPSTer exploits protein structural information to systematically interrogate virus-human protein-protein interactions with remarkable accuracy. Dr. Shapira and his collaborators applied P-HIPSTer to all 1,001 human-infecting viruses and the approximately 13,000 proteins they encode. The algorithm predicted roughly 280,000 likely pairs of interacting proteins that represent a comprehensive catalogue of human virus protein-protein interactions with an accuracy rate of almost 80 percent.
"This is the first step towards building a comprehensive cartography of physical interactions between different organisms," Dr. Shapira says.
ZIKA, HPV, VIRAL EVOLUTION
In addition to defining pan-viral protein interactions, P-HIPSTer has yielded new biological insights into Zika virus, HPV, and the impact of viruses in shaping human genetics.
Among their discoveries, the researchers found that Zika virus interacts with estrogen receptor, the protein that allows cells to effectively respond to the estrogen hormone. Importantly, they found estrogen receptor has potential to inhibit Zika virus replication. Says Dr. Shapira, "And, in fact, estrogen receptor inhibits viral replication even more than interferon, a protein that is the body's first line of defense to viral infection and our gold standard for anti-viral defense."
The finding is particularly relevant to clinical disease as pregnant women are most susceptible to Zika during their first trimester, which is when estrogen levels are at their lowest. This period also is when the fetus is most susceptible to Zika, a virus for which there is no vaccine or specific treatment and that can cause sever birth defects.
Dr. Shapira and his team also explored interactions between HPV, the leading cause of cervical cancer, and the cells that it infects. HPV is the most common sexually transmitted viral infection with approximately 80 percent of sexually active individuals contracting one of the 200 different types of HPV at some point in their lives. Dr. Shapira and his team used the data generated by P-HIPSTer to identify protein-protein interactions that distinguish HPV infections associated with cancer from those that are not. In addition to providing insights into how HPV may cause disease, the finding could lead to improved diagnostics for those infected with HPV, and P-HIPSTer could potentially be used to help predict whether or not any particular virus is likely to be highly pathogenic.
The researchers also examined whether the interactions mediated by viruses have impacted human genetics. The researchers found evidence of strong selection pressure for several dozen cellular proteins have been shaped by viral infection, unlocking new insights into how our genome has been impacted by viruses.
"One of the things we can do with this data is drill down and ask whether virus infection has changed the history of human genetics," notes Dr. Shapira. "That is certainly not a novel idea but to have a catalogue of what those proteins are is significant. There are a lot of areas that we can explore now that we couldn't before."
FUTURE WORK
Dr. Shapira and his team intend to apply P-HIPSTer on more complex pathogens, such as parasites and bacteria, and use it to better understand how bacteria in the human gut communicate with each other. In the future, the algorithm could also be used to explore viruses or pathogens that effect agricultural plants or livestock.
Read more at Science Daily
Aug 31, 2019
Marathoners, take your marks...and fluid and salt!
Legend states that after the Greek army defeated the invading Persian forces near the city of Marathon in 490 B.C.E., the courier Pheidippides ran to Athens to report the victory and then immediately dropped dead. The story -- and the distance Pheidippides covered -- inspired the modern marathon, a grueling 26.2-mile contest that attracts some 1.3 million runners annually to compete in the more than 800 races held worldwide.
While Pheidippides' demise was more likely brought about by a 300-mile run he reportedly made just prior to his "marathon," today's long-distance runners face a mostly short-term but still serious physical threat known as acute kidney injury, or AKI. Now, results of a new study of marathon runners led by researchers at Johns Hopkins Medicine and Yale University suggest that sweat (fluid) volume and sweat sodium losses, rather than a rise in core body temperature, are the key contributors to post-race AKI.
"We knew from a previous study that a large number of marathoners developed short-term AKI following a race, so we wanted more specifically to pin down the causes," says Chirag Parikh, Ph.D., director of the Division of Nephrology at the Johns Hopkins University School of Medicine and senior author of the new paper. "Our findings suggest that managing fluid volume and salt losses with a personalized regimen during the time period surrounding a marathon may help reduce the number or lessen the severity of AKI incidents afterward."
The researchers say they also found that runners with AKI following a marathon had increased levels of a blood serum protein known as copeptin. If the connection is confirmed with future studies, they say, copeptin could be valuable as a biomarker during training for predicting post-marathon susceptibility to AKI.
AKI, as described by the National Kidney Foundation, is a "sudden episode of kidney failure or kidney damage that happens within a few hours or a few days." It causes waste products to build up in the blood, making it hard for kidneys to maintain the correct balance of fluids in the body. Symptoms of AKI differ depending on the cause and may include: too little urine leaving the body; swelling in legs, ankles and around the eyes; fatigue; shortness of breath; confusion; nausea; chest pain; and in severe cases, seizures or coma. The disorder is most commonly seen in hospitalized patients whose kidneys are affected by medical and surgical stress and complications.
Similarly, a marathon subjects a runner to sustained physical stress, reduced blood flow to the kidneys and significant increases in the metabolic rate. Together, these events severely challenge the body's ability to keep fluid volume, electrolytes and temperature levels -- along with the regulatory responses to changes in all three -- in balance. The result, as seen in 82% of the runners evaluated by the same researchers in a 2017 Yale University study, was AKI that averaged two days in duration.
For the latest study, the goal was to better define the risk factors and mechanism for the problem by examining 23 runners, ages 22-63, who competed in the 2017 Hartford Marathon in Connecticut.
Participants were volunteers recruited through local running clubs and the marathon's registration process. Divided nearly equally between men and women, they were all experienced runners with a body mass index ranging between 18.5-24.9, and had completed at least four races longer than 20 kilometers (12.4 miles) within the previous three years.
Urine and blood samples were collected from the participants at three time points: 24 hours prior to the marathon, within 30 minutes of completing the race and 24 hours after. The researchers evaluated the samples for sodium levels; key biomolecules such as creatine phosphokinase, hemoglobin, urine protein and copeptin; and biomarkers associated with kidney injury such as interleukin-18 and kidney injury molecule-1.
Sweat collection patches were placed on the runners prior to the marathon and recovered at the 5-mile mark (because they became too saturated further in the race). Blood pressure, heart rate and weight were measured at all three time points, while a bioharness worn during the marathon continually recorded body temperature.
Twelve of the 23 runners (55%) developed AKI after the race, while 17 (74%) tested positive for markers indicating some injury to the renal tubules, the tiny portals in the kidneys where blood is filtered.
In the runners with post-race AKI, the researchers observed distinct sodium and fluid volume losses. The median salt loss was 2.3 grams, with some losing as much as 7 grams.
Fluid volume loss via sweat had a midpoint level of 2.5 liters (5.2 pints), up to a maximum of 6.8 liters (14.4 pints). For comparison, a 155-pound (70-kilogram) body contains about 42 liters (85 pints) of fluid.
Core body temperature, while significantly elevated throughout a marathon, was basically the same for all runners and therefore, was not considered a causal factor for AKI. However, the researchers say that the combination of high-body temperature along with fluid and salt losses may add to the development of kidney injury.
"Putting the sodium and fluid volume loss numbers into perspective, the median salt loss for the AKI runners was about 1 1/4 teaspoons, or the entire daily amount recommended by the American Heart Association," Parikh says. "Their median fluid volume loss was equivalent to sweating out slightly more than a 2-liter soda bottle. Beyond that, we had evidence that runners weren't adequately keeping up with those depletions."
In turn, Parikh says, that failure to balance the sodium and fluid losses during a marathon may account for the new study's other relevant finding: the higher levels of copeptin seen in runners with post-race AKI.
Copeptin is a precursor to the release of vasopressin, a hormone secreted by the pituitary gland in response to reduced blood volume. It tells our kidneys and blood vessels to hold on to water, preventing a sudden drop in blood pressure and physical collapse.
"In the runners who developed AKI, we found copeptin levels as much as 20 times higher than those who did not," Parikh says. "This is biological evidence that the AKI sufferers were severely volume down."
Because vasopressin reduces blood flow to the kidneys, and decreases renal filtration and urine output, he adds, it also may induce inflammation and injury to the kidney tissues if secreted for an extended period of time. This may explain why a large number of marathon runners get AKI while those competing at shorter distances do not.
Parikh says future studies, using larger samples, will need to evaluate whether optimizing fluid and salt volumes in marathon runners lowers rates or reduces the severity of post-race AKI. Additionally, he says, the researchers would like to follow runners who participate in multiple marathons to look for any cumulative kidney damage.
Read more at Science Daily
While Pheidippides' demise was more likely brought about by a 300-mile run he reportedly made just prior to his "marathon," today's long-distance runners face a mostly short-term but still serious physical threat known as acute kidney injury, or AKI. Now, results of a new study of marathon runners led by researchers at Johns Hopkins Medicine and Yale University suggest that sweat (fluid) volume and sweat sodium losses, rather than a rise in core body temperature, are the key contributors to post-race AKI.
"We knew from a previous study that a large number of marathoners developed short-term AKI following a race, so we wanted more specifically to pin down the causes," says Chirag Parikh, Ph.D., director of the Division of Nephrology at the Johns Hopkins University School of Medicine and senior author of the new paper. "Our findings suggest that managing fluid volume and salt losses with a personalized regimen during the time period surrounding a marathon may help reduce the number or lessen the severity of AKI incidents afterward."
The researchers say they also found that runners with AKI following a marathon had increased levels of a blood serum protein known as copeptin. If the connection is confirmed with future studies, they say, copeptin could be valuable as a biomarker during training for predicting post-marathon susceptibility to AKI.
AKI, as described by the National Kidney Foundation, is a "sudden episode of kidney failure or kidney damage that happens within a few hours or a few days." It causes waste products to build up in the blood, making it hard for kidneys to maintain the correct balance of fluids in the body. Symptoms of AKI differ depending on the cause and may include: too little urine leaving the body; swelling in legs, ankles and around the eyes; fatigue; shortness of breath; confusion; nausea; chest pain; and in severe cases, seizures or coma. The disorder is most commonly seen in hospitalized patients whose kidneys are affected by medical and surgical stress and complications.
Similarly, a marathon subjects a runner to sustained physical stress, reduced blood flow to the kidneys and significant increases in the metabolic rate. Together, these events severely challenge the body's ability to keep fluid volume, electrolytes and temperature levels -- along with the regulatory responses to changes in all three -- in balance. The result, as seen in 82% of the runners evaluated by the same researchers in a 2017 Yale University study, was AKI that averaged two days in duration.
For the latest study, the goal was to better define the risk factors and mechanism for the problem by examining 23 runners, ages 22-63, who competed in the 2017 Hartford Marathon in Connecticut.
Participants were volunteers recruited through local running clubs and the marathon's registration process. Divided nearly equally between men and women, they were all experienced runners with a body mass index ranging between 18.5-24.9, and had completed at least four races longer than 20 kilometers (12.4 miles) within the previous three years.
Urine and blood samples were collected from the participants at three time points: 24 hours prior to the marathon, within 30 minutes of completing the race and 24 hours after. The researchers evaluated the samples for sodium levels; key biomolecules such as creatine phosphokinase, hemoglobin, urine protein and copeptin; and biomarkers associated with kidney injury such as interleukin-18 and kidney injury molecule-1.
Sweat collection patches were placed on the runners prior to the marathon and recovered at the 5-mile mark (because they became too saturated further in the race). Blood pressure, heart rate and weight were measured at all three time points, while a bioharness worn during the marathon continually recorded body temperature.
Twelve of the 23 runners (55%) developed AKI after the race, while 17 (74%) tested positive for markers indicating some injury to the renal tubules, the tiny portals in the kidneys where blood is filtered.
In the runners with post-race AKI, the researchers observed distinct sodium and fluid volume losses. The median salt loss was 2.3 grams, with some losing as much as 7 grams.
Fluid volume loss via sweat had a midpoint level of 2.5 liters (5.2 pints), up to a maximum of 6.8 liters (14.4 pints). For comparison, a 155-pound (70-kilogram) body contains about 42 liters (85 pints) of fluid.
Core body temperature, while significantly elevated throughout a marathon, was basically the same for all runners and therefore, was not considered a causal factor for AKI. However, the researchers say that the combination of high-body temperature along with fluid and salt losses may add to the development of kidney injury.
"Putting the sodium and fluid volume loss numbers into perspective, the median salt loss for the AKI runners was about 1 1/4 teaspoons, or the entire daily amount recommended by the American Heart Association," Parikh says. "Their median fluid volume loss was equivalent to sweating out slightly more than a 2-liter soda bottle. Beyond that, we had evidence that runners weren't adequately keeping up with those depletions."
In turn, Parikh says, that failure to balance the sodium and fluid losses during a marathon may account for the new study's other relevant finding: the higher levels of copeptin seen in runners with post-race AKI.
Copeptin is a precursor to the release of vasopressin, a hormone secreted by the pituitary gland in response to reduced blood volume. It tells our kidneys and blood vessels to hold on to water, preventing a sudden drop in blood pressure and physical collapse.
"In the runners who developed AKI, we found copeptin levels as much as 20 times higher than those who did not," Parikh says. "This is biological evidence that the AKI sufferers were severely volume down."
Because vasopressin reduces blood flow to the kidneys, and decreases renal filtration and urine output, he adds, it also may induce inflammation and injury to the kidney tissues if secreted for an extended period of time. This may explain why a large number of marathon runners get AKI while those competing at shorter distances do not.
Parikh says future studies, using larger samples, will need to evaluate whether optimizing fluid and salt volumes in marathon runners lowers rates or reduces the severity of post-race AKI. Additionally, he says, the researchers would like to follow runners who participate in multiple marathons to look for any cumulative kidney damage.
Read more at Science Daily
Aug 30, 2019
Newly discovered giant planet slingshots around its star
Astronomers have discovered a planet three times the mass of Jupiter that travels on a long, egg-shaped path around its star. If this planet were somehow placed into our own solar system, it would swing from within our asteroid belt to out beyond Neptune. Other giant planets with highly elliptical orbits have been found around other stars, but none of those worlds were located at the very outer reaches of their star systems like this one.
"This planet is unlike the planets in our solar system, but more than that, it is unlike any other exoplanets we have discovered so far," says Sarah Blunt, a Caltech graduate student and first author on the new study publishing in The Astronomical Journal. "Other planets detected far away from their stars tend to have very low eccentricities, meaning that their orbits are more circular. The fact that this planet has such a high eccentricity speaks to some difference in the way that it either formed or evolved relative to the other planets."
The planet was discovered using the radial velocity method, a workhorse of exoplanet discovery that detects new worlds by tracking how their parent stars "wobble" in response to gravitational tugs from those planets.
However, analyses of these data usually require observations taken over a planet's entire orbital period. For planets orbiting far from their stars, this can be difficult: a full orbit can take tens or even hundreds of years.
The California Planet Search, led by Caltech Professor of Astronomy Andrew W. Howard, is one of the few groups that watches stars over the decades-long timescales necessary to detect long-period exoplanets using radial velocity.
The data needed to make the discovery of the new planet were first provided by W. M. Keck Observatory in Hawaii. In 1997, the team began using the High-Resolution Echelle Spectrometer (HIRES) on the Keck I telescope to take measurements of the planet's star, called HR 5183.
"The key was persistence," said Howard. "Our team followed this star with Keck Observatory for more than two decades and only saw evidence for the planet in the past couple years! Without that long-term effort, we never would have found this planet."
In addition to Keck Observatory, the California Planet Search also used the Lick Observatory in Northern California and the McDonald Observatory in Texas.
The astronomers have been watching HR 5183 since the 1990s, but do not have data corresponding to one full orbit of the planet, called HR 5183 b, because it circles its star roughly every 45 to 100 years. The team instead found the planet because of its strange orbit.
"This planet spends most of its time loitering in the outer part of its star's planetary system in this highly eccentric orbit, then it starts to accelerate in and does a slingshot around its star," explains Howard. "We detected this slingshot motion. We saw the planet come in and now it's on its way out. That creates such a distinctive signature that we can be sure that this is a real planet, even though we haven't seen a complete orbit."
The new findings show that it is possible to use the radial velocity method to make detections of other far-flung planets without waiting decades. And, the researchers suggest, looking for more planets like this one could illuminate the role of giant planets in shaping their solar systems.
Planets take shape out of disks of material left over after stars form. That means that planets should start off in flat, circular orbits. For the newly detected planet to be on such an eccentric orbit, it must have gotten a gravitational kick from some other object.
The most plausible scenario, the researchers propose, is that the planet once had a neighbor of similar size. When the two planets got close enough to each other, one pushed the other out of the solar system, forcing HR 5183 b into a highly eccentric orbit.
"This newfound planet basically would have come in like a wrecking ball," says Howard, "knocking anything in its way out of the system."
This discovery demonstrates that our understanding of planets beyond our solar system is still evolving. Researchers continue to find worlds that are unlike anything in our solar system or in solar systems we have already discovered.
Read more at Science Daily
"This planet is unlike the planets in our solar system, but more than that, it is unlike any other exoplanets we have discovered so far," says Sarah Blunt, a Caltech graduate student and first author on the new study publishing in The Astronomical Journal. "Other planets detected far away from their stars tend to have very low eccentricities, meaning that their orbits are more circular. The fact that this planet has such a high eccentricity speaks to some difference in the way that it either formed or evolved relative to the other planets."
The planet was discovered using the radial velocity method, a workhorse of exoplanet discovery that detects new worlds by tracking how their parent stars "wobble" in response to gravitational tugs from those planets.
However, analyses of these data usually require observations taken over a planet's entire orbital period. For planets orbiting far from their stars, this can be difficult: a full orbit can take tens or even hundreds of years.
The California Planet Search, led by Caltech Professor of Astronomy Andrew W. Howard, is one of the few groups that watches stars over the decades-long timescales necessary to detect long-period exoplanets using radial velocity.
The data needed to make the discovery of the new planet were first provided by W. M. Keck Observatory in Hawaii. In 1997, the team began using the High-Resolution Echelle Spectrometer (HIRES) on the Keck I telescope to take measurements of the planet's star, called HR 5183.
"The key was persistence," said Howard. "Our team followed this star with Keck Observatory for more than two decades and only saw evidence for the planet in the past couple years! Without that long-term effort, we never would have found this planet."
In addition to Keck Observatory, the California Planet Search also used the Lick Observatory in Northern California and the McDonald Observatory in Texas.
The astronomers have been watching HR 5183 since the 1990s, but do not have data corresponding to one full orbit of the planet, called HR 5183 b, because it circles its star roughly every 45 to 100 years. The team instead found the planet because of its strange orbit.
"This planet spends most of its time loitering in the outer part of its star's planetary system in this highly eccentric orbit, then it starts to accelerate in and does a slingshot around its star," explains Howard. "We detected this slingshot motion. We saw the planet come in and now it's on its way out. That creates such a distinctive signature that we can be sure that this is a real planet, even though we haven't seen a complete orbit."
The new findings show that it is possible to use the radial velocity method to make detections of other far-flung planets without waiting decades. And, the researchers suggest, looking for more planets like this one could illuminate the role of giant planets in shaping their solar systems.
Planets take shape out of disks of material left over after stars form. That means that planets should start off in flat, circular orbits. For the newly detected planet to be on such an eccentric orbit, it must have gotten a gravitational kick from some other object.
The most plausible scenario, the researchers propose, is that the planet once had a neighbor of similar size. When the two planets got close enough to each other, one pushed the other out of the solar system, forcing HR 5183 b into a highly eccentric orbit.
"This newfound planet basically would have come in like a wrecking ball," says Howard, "knocking anything in its way out of the system."
This discovery demonstrates that our understanding of planets beyond our solar system is still evolving. Researchers continue to find worlds that are unlike anything in our solar system or in solar systems we have already discovered.
Read more at Science Daily
Hints of a volcanically active exo-moon
Jupiter's moon Io is the most volcanically active body in our solar system. Today, there are indications that an active moon outside our solar system, an exo-Io, could be hidden at the exoplanet system WASP-49b. "It would be a dangerous volcanic world with a molten surface of lava, a lunar version of close-in Super Earths like 55 Cancri-e" says Apurva Oza, postdoctoral fellow at the Physics Insitute of the University of Bern and associate of the NCCR PlanetS, "a place where Jedis go to die, perilously familiar to Anakin Skywalker." But the object that Oza and his colleagues describe in their work seems to be even more exotic than Star Wars science fiction: the possible exomoon would orbit a hot giant planet, which in turn would race once around its host star in less than three days -- a scenario 550 light years away in the inconspicuous constellation of Lepus, underneath the bright Orion constellation.
Sodium gas as circumstantial evidence
Astronomers have not yet discovered a rocky moon beyond our solar system and it's on the basis of circumstantial evidence that the researchers in Bern conclude that the exo-Io exists: Sodium gas was detected at the WASP 49-b at an anomalously high-altitude. "The neutral sodium gas is so far away from the planet that it is unlikely to be emitted solely by a planetary wind," says Oza. Observations of Jupiter and Io in our solar system, by the international team, along with mass loss calculations show that an exo-Io could be a very plausible source of sodium at WASP 49-b. "The sodium is right where it should be" says the astrophysicist.
Tides keep the system stable
Already in 2006, Bob Johnson of the University of Virginia and the late Patrick Huggins at New York University, USA had shown that large amounts of sodium at an exoplanet could point to a hidden moon or ring of material, and ten years ago, researchers at Virginia calculated that such a compact system of three bodies: star, close-in giant planet and moon, can be stable over billions of years. Apurva Oza was then a student at Virginia, and after his PhD on moons atmospheres in Paris, decided to pick up the theoretical calculations of these researchers. He now publishes the results of his work together with Johnson and colleagues in the Astrophysical Journal.
"The enormous tidal forces in such a system are the key to everything," explains the astrophysicist. The energy released by the tides to the planet and its moon keeps the moon's orbit stable, simultaneously heating it up and making it volcanically active. In their work, the researchers were able to show that a small rocky moon can eject more sodium and potassium into space through this extreme volcanism than a large gas planet, especially at high altitudes. "Sodium and potassium lines are quantum treasures to us astronomers because they are extremely bright," says Oza, "the vintage street lamps that light up our streets with yellow haze, is akin to the gas we are now detecting in the spectra of a dozen exoplanets."
"We need to find more clues"
The researchers compared their calculations with these observations and found five candidate systems where a hidden exomoon can survive against destructive thermal evaporation. For WASP 49-b the observed data can be best explained by the existence of an exo-Io. However, there are other options. For example, the exoplanet could be surrounded by a ring of ionized gas, or non-thermal processes. "We need to find more clues," Oza admits. The researchers are therefore relying on further observations with ground-based and space-based instruments.
"While the current wave of research is going towards habitability and biosignatures, our signature is a signature of destruction," says the astrophysicist. A few of these worlds could be destroyed in a few billion years due to the extreme mass loss. "The exciting part is that we can monitor these destructive processes in real time, like fireworks," says Oza.
Read more at Science Daily
Sodium gas as circumstantial evidence
Astronomers have not yet discovered a rocky moon beyond our solar system and it's on the basis of circumstantial evidence that the researchers in Bern conclude that the exo-Io exists: Sodium gas was detected at the WASP 49-b at an anomalously high-altitude. "The neutral sodium gas is so far away from the planet that it is unlikely to be emitted solely by a planetary wind," says Oza. Observations of Jupiter and Io in our solar system, by the international team, along with mass loss calculations show that an exo-Io could be a very plausible source of sodium at WASP 49-b. "The sodium is right where it should be" says the astrophysicist.
Tides keep the system stable
Already in 2006, Bob Johnson of the University of Virginia and the late Patrick Huggins at New York University, USA had shown that large amounts of sodium at an exoplanet could point to a hidden moon or ring of material, and ten years ago, researchers at Virginia calculated that such a compact system of three bodies: star, close-in giant planet and moon, can be stable over billions of years. Apurva Oza was then a student at Virginia, and after his PhD on moons atmospheres in Paris, decided to pick up the theoretical calculations of these researchers. He now publishes the results of his work together with Johnson and colleagues in the Astrophysical Journal.
"The enormous tidal forces in such a system are the key to everything," explains the astrophysicist. The energy released by the tides to the planet and its moon keeps the moon's orbit stable, simultaneously heating it up and making it volcanically active. In their work, the researchers were able to show that a small rocky moon can eject more sodium and potassium into space through this extreme volcanism than a large gas planet, especially at high altitudes. "Sodium and potassium lines are quantum treasures to us astronomers because they are extremely bright," says Oza, "the vintage street lamps that light up our streets with yellow haze, is akin to the gas we are now detecting in the spectra of a dozen exoplanets."
"We need to find more clues"
The researchers compared their calculations with these observations and found five candidate systems where a hidden exomoon can survive against destructive thermal evaporation. For WASP 49-b the observed data can be best explained by the existence of an exo-Io. However, there are other options. For example, the exoplanet could be surrounded by a ring of ionized gas, or non-thermal processes. "We need to find more clues," Oza admits. The researchers are therefore relying on further observations with ground-based and space-based instruments.
"While the current wave of research is going towards habitability and biosignatures, our signature is a signature of destruction," says the astrophysicist. A few of these worlds could be destroyed in a few billion years due to the extreme mass loss. "The exciting part is that we can monitor these destructive processes in real time, like fireworks," says Oza.
Read more at Science Daily
A new way to measure how water moves
When a chemical spills in the environment, it's important to know how quickly the spill will spread. If a farmer irrigates a crop, the person will need to know how fast the water should move through the soil and be absorbed by the roots. In both cases, a good understanding of water pore structure is necessary.
A new method to measure pore structure and water flow is described in a study published in the journal Water Resources Research. With it, scientists should be able to more accurately determine how fast water, contaminants, nutrients and other liquids move through the soil -- and where they go.
The mathematical model was validated by researchers at the University of California, Davis, California State University, Northridge and University of North Carolina at Chapel Hill.
"This will open a whole new direction that will help us use our resources more efficiently and better understand the flow of water, contaminants and nutrients," said corresponding author and UC Davis assistant professor Majdi Abou Najm, who developed the model when he was at the American University of Beirut.
NOT ONE-SIZE-FITS ALL
One of the most important equations in hydrology, Darcy's law, has long been used to describe the flow of fluids through a porous medium, like rocks and soil. But that equation assumes a one-size-fits all estimation of pore size, when the reality is more complicated.
"Our model finds a middle ground between reality, which has an infinite number of pore sizes, and the current model, which represents them with one average pore size," said Abou Najm.
CHEAP AND ACCESSIBLE
The new model, which was tested on four sands for the study, has the added benefit of being relatively cheap and accessible to use in a variety of environments. The study said that most pore size measurement methods require collecting samples of limited size for lab analysis. This new method provides a simple, inexpensive approach to measuring a variety of pore sizes directly in the field using items that can be bought in a typical grocery store, such as soup thickeners or food additives.
From Science Daily
A new method to measure pore structure and water flow is described in a study published in the journal Water Resources Research. With it, scientists should be able to more accurately determine how fast water, contaminants, nutrients and other liquids move through the soil -- and where they go.
The mathematical model was validated by researchers at the University of California, Davis, California State University, Northridge and University of North Carolina at Chapel Hill.
"This will open a whole new direction that will help us use our resources more efficiently and better understand the flow of water, contaminants and nutrients," said corresponding author and UC Davis assistant professor Majdi Abou Najm, who developed the model when he was at the American University of Beirut.
NOT ONE-SIZE-FITS ALL
One of the most important equations in hydrology, Darcy's law, has long been used to describe the flow of fluids through a porous medium, like rocks and soil. But that equation assumes a one-size-fits all estimation of pore size, when the reality is more complicated.
"Our model finds a middle ground between reality, which has an infinite number of pore sizes, and the current model, which represents them with one average pore size," said Abou Najm.
CHEAP AND ACCESSIBLE
The new model, which was tested on four sands for the study, has the added benefit of being relatively cheap and accessible to use in a variety of environments. The study said that most pore size measurement methods require collecting samples of limited size for lab analysis. This new method provides a simple, inexpensive approach to measuring a variety of pore sizes directly in the field using items that can be bought in a typical grocery store, such as soup thickeners or food additives.
From Science Daily
Entanglement sent over 50 km of optical fiber
For the first time, a team has sent a light particle entangled with matter over 50 km of optical fiber. This paves the way for the practical use of quantum networks and sets a milestone for a future quantum internet.
The quantum internet promises absolutely tap-proof communication and powerful distributed sensor networks for new science and technology. However, because quantum information cannot be copied, it is not possible to send this information over a classical network. Quantum information must be transmitted by quantum particles, and special interfaces are required for this. The Innsbruck-based experimental physicist Ben Lanyon, who was awarded the Austrian START Prize in 2015 for his research, is researching these important intersections of a future quantum Internet. Now his team at the Department of Experimental Physics at the University of Innsbruck and at the Institute of Quantum Optics and Quantum Information of the Austrian Academy of Sciences has achieved a record for the transfer of quantum entanglement between matter and light. For the first time, a distance of 50 kilometers was covered using fiber optic cables. "This is two orders of magnitude further than was previously possible and is a practical distance to start building inter-city quantum networks," says Ben Lanyon.
Converted photon for transmission
Lanyon's team started the experiment with a calcium atom trapped in an ion trap. Using laser beams, the researchers write a quantum state onto the ion and simultaneously excite it to emit a photon in which quantum information is stored. As a result, the quantum states of the atom and the light particle are entangled. But the challenge is to transmit the photon over fiber optic cables. "The photon emitted by the calcium ion has a wavelength of 854 nanometers and is quickly absorbed by the optical fiber," says Ben Lanyon. His team therefore initially sends the light particle through a nonlinear crystal illuminated by a strong laser. Thereby the photon wavelength is converted to the optimal value for long-distance travel: the current telecommunications standard wavelength of 1550 nanometers. The researchers from Innsbruck then send this photon through a 50-kilometer-long optical fiber line. Their measurements show that atom and light particle are still entangled even after the wavelength conversion and this long journey.
Even greater distances in sight
As a next step, Lanyon and his team show that their methods would enable entanglement to be generated between ions 100 kilometers apart and more. Two nodes send each an entangled photon over a distance of 50 kilometers to an intersection where the light particles are measured in such a way that they lose their entanglement with the ions, which in turn would entangle them. With 100-kilometer node spacing now a possibility, one could therefore envisage building the world's first intercity light-matter quantum network in the coming years: only a handful of trapped ion-systems would be required on the way to establish a quantum internet between Innsbruck and Vienna, for example.
From Science Daily
The quantum internet promises absolutely tap-proof communication and powerful distributed sensor networks for new science and technology. However, because quantum information cannot be copied, it is not possible to send this information over a classical network. Quantum information must be transmitted by quantum particles, and special interfaces are required for this. The Innsbruck-based experimental physicist Ben Lanyon, who was awarded the Austrian START Prize in 2015 for his research, is researching these important intersections of a future quantum Internet. Now his team at the Department of Experimental Physics at the University of Innsbruck and at the Institute of Quantum Optics and Quantum Information of the Austrian Academy of Sciences has achieved a record for the transfer of quantum entanglement between matter and light. For the first time, a distance of 50 kilometers was covered using fiber optic cables. "This is two orders of magnitude further than was previously possible and is a practical distance to start building inter-city quantum networks," says Ben Lanyon.
Converted photon for transmission
Lanyon's team started the experiment with a calcium atom trapped in an ion trap. Using laser beams, the researchers write a quantum state onto the ion and simultaneously excite it to emit a photon in which quantum information is stored. As a result, the quantum states of the atom and the light particle are entangled. But the challenge is to transmit the photon over fiber optic cables. "The photon emitted by the calcium ion has a wavelength of 854 nanometers and is quickly absorbed by the optical fiber," says Ben Lanyon. His team therefore initially sends the light particle through a nonlinear crystal illuminated by a strong laser. Thereby the photon wavelength is converted to the optimal value for long-distance travel: the current telecommunications standard wavelength of 1550 nanometers. The researchers from Innsbruck then send this photon through a 50-kilometer-long optical fiber line. Their measurements show that atom and light particle are still entangled even after the wavelength conversion and this long journey.
Even greater distances in sight
As a next step, Lanyon and his team show that their methods would enable entanglement to be generated between ions 100 kilometers apart and more. Two nodes send each an entangled photon over a distance of 50 kilometers to an intersection where the light particles are measured in such a way that they lose their entanglement with the ions, which in turn would entangle them. With 100-kilometer node spacing now a possibility, one could therefore envisage building the world's first intercity light-matter quantum network in the coming years: only a handful of trapped ion-systems would be required on the way to establish a quantum internet between Innsbruck and Vienna, for example.
From Science Daily
Aug 29, 2019
Busy older stars outpace stellar youngsters
The oldest stars in our Galaxy are also the busiest, moving more rapidly than their younger counterparts in and out of the disk of the Milky Way, according to new analysis carried out at the University of Birmingham.
The findings provide fresh insights into the history of our Galaxy and increase our understanding of how stars form and evolve.
Researchers calculate that the old stars are moving more quickly in and out of the disc -- the pancake-shaped mass at the heart of the Galaxy where most stars are located.
A number of theories could explain this movement -- it all depends where the star is in the disc. Stars towards the outskirts could be knocked by gravitational interactions with smaller galaxies passing by. Towards the inner parts of the disc, the stars could be disturbed by massive gas clouds which move along with the stars inside the disc. They could also be thrown out of the disc by the movement of its spiral structure.
Dr Ted Mackereth, a galactic archaeologist at the University of Birmingham, is lead author on the paper. He explains: "The specific way that the stars move tells us which of these processes has been dominant in forming the disc we see today. We think older stars are move active because they have been around the longest, and because they were formed during a period when the Galaxy was a bit more violent, with lots of star formation happening and lots of disturbance from gasses and smaller satellite galaxies. There are lots of different processes at work, and untangling all these helps us to build up a picture of the history of our Galaxy."
The study uses data from the Gaia satellite, currently working to chart the movements of around 1 billion stars in the Milky Way. It also takes information from APOGEE, an experiment run by the Sloan Digital Sky Survey that uses spectroscopy to measure the distribution of elements in stars, as well as images from the recently-retired Kepler space telescope.
Measurements provided by Kepler show how the brightness of stars varies over time, which gives insights into how they vibrate. In turn, that yields information about their interior structure, which enables scientists to calculate their age.
The Birmingham team, working with colleagues at the University of Toronto and teams involved with the Sloan Digital Sky Survey, were able to take these different data strands and calculate the differences in velocity between different sets of stars grouped by age.
They found that the older stars were moving in many different directions with some moving very quickly out from the galactic disk. Younger stars move closely together at much slower speeds out from the disc, although they are faster than the older stars as they rotate around the Galaxy within the disc.
Read more at Science Daily
The findings provide fresh insights into the history of our Galaxy and increase our understanding of how stars form and evolve.
Researchers calculate that the old stars are moving more quickly in and out of the disc -- the pancake-shaped mass at the heart of the Galaxy where most stars are located.
A number of theories could explain this movement -- it all depends where the star is in the disc. Stars towards the outskirts could be knocked by gravitational interactions with smaller galaxies passing by. Towards the inner parts of the disc, the stars could be disturbed by massive gas clouds which move along with the stars inside the disc. They could also be thrown out of the disc by the movement of its spiral structure.
Dr Ted Mackereth, a galactic archaeologist at the University of Birmingham, is lead author on the paper. He explains: "The specific way that the stars move tells us which of these processes has been dominant in forming the disc we see today. We think older stars are move active because they have been around the longest, and because they were formed during a period when the Galaxy was a bit more violent, with lots of star formation happening and lots of disturbance from gasses and smaller satellite galaxies. There are lots of different processes at work, and untangling all these helps us to build up a picture of the history of our Galaxy."
The study uses data from the Gaia satellite, currently working to chart the movements of around 1 billion stars in the Milky Way. It also takes information from APOGEE, an experiment run by the Sloan Digital Sky Survey that uses spectroscopy to measure the distribution of elements in stars, as well as images from the recently-retired Kepler space telescope.
Measurements provided by Kepler show how the brightness of stars varies over time, which gives insights into how they vibrate. In turn, that yields information about their interior structure, which enables scientists to calculate their age.
The Birmingham team, working with colleagues at the University of Toronto and teams involved with the Sloan Digital Sky Survey, were able to take these different data strands and calculate the differences in velocity between different sets of stars grouped by age.
They found that the older stars were moving in many different directions with some moving very quickly out from the galactic disk. Younger stars move closely together at much slower speeds out from the disc, although they are faster than the older stars as they rotate around the Galaxy within the disc.
Read more at Science Daily
Biological 'rosetta stone' brings scientists closer to deciphering how the body is built
Every animal, from an ant to a human, contains in their genome pieces of DNA called Hox genes. Architects of the body, these genes are keepers of the body's blueprints; they dictate how embryos grown into adults, including where a developing animal puts its head, legs and other body parts.
Scientists have long searched for ways to decipher how Hox genes create this body map; a key to decoding how we build our bodies.
Now an international group of researchers from Columbia University and the Spanish National Research Council (CSIC) based at the Universidad Pablo de Olavide in Seville, Spain have found one such key: a method that can systematically identify the role each Hox gene plays in a developing fruit fly. Their results, reported recently in Nature Communications, offer a new path forward for researchers hoping to make sense of a process that is equal parts chaotic and precise, and that is critical to understanding not only growth and development but also aging and disease.
"The genome, which contains thousands of genes and millions of letters of DNA, is the most complicated code ever written," said Richard Mann, PhD, principal investigator at Columbia's Mortimer B. Zuckerman Mind Brain Behavior Institute and the paper's co-senior author. "Deciphering this code has proven so difficult because evolution wrote it in fits and starts over hundreds of millions of years. Today's study offers a key to cracking that code, bringing us closer than ever to understanding how Hox genes build a healthy body, or how this process gets disrupted in disease."
Hox genes are ancient; they can be found across all animal species. Even primitive jellyfish have them. Each type of organism has different combinations of these genes. Fruit flies have eight Hox genes, while humans have 39.
These genes work by producing special proteins called transcription factors, which work together with similar proteins called Hox cofactors to bind to different segments of DNA and turn many other genes on and off at just the right time -- a Rube Goldberg machine of microscopic proportions.
"Because these genes are intricately involved in many aspects of development, it has proven incredibly challenging to isolate individual Hox genes and trace their activity over time," said James Castelli-Gair Hombría, PhD, a principal investigator at the Centro Andaluz de Biologi?a del Desarrollo at the Universidad Pablo de Olavide and the paper's co-senior author. "We had this incredibly complex equation to solve but too many unknowns to make significant progress."
Recently, Dr. Hombría and his team hit upon a bit of luck. While examining genetic activity in a developing fruit fly, they stumbled upon a small piece of regulatory DNA, called vvI1+2, that had an unusual -- and surprising -- attribute. Although it was active in cells across the fruit fly's entire developing body, it appeared to be regulated by all of the fruit fly's eight Hox genes.
"The ubiquity of the vvI1+2 DNA segment across the entire developing fruit fly, combined with the fact that every Hox gene touches it, made it an ideal system by which to study the Hox gene family," said Carlos Sánchez-Higueras, PhD, a postdoctoral researcher in the Hombría lab and the paper's first author. "In this single piece of DNA, we had the perfect tool; we could now devise a method to systematically manipulate vvI1+2 activity to see how each Hox gene functioned."
First, Dr. Sánchez-Higueras teamed up with Dr. Mann at Columbia's Zuckerman Institute and used a sophisticated computer algorithm called No Read Left Behind, or NRLB. NRLB was recently developed by Dr. Mann, his lab, and his collaborators, including Columbia systems biology professor Harmen Bussemaker, PhD. This powerful algorithm pinpoints the locations where transcription factors bind to a stretch of DNA, even if these binding sites are very weak and difficult to capture. For this study, the researchers focused on the Hox transcription factors and Hox cofactors that bind to vvI1+2.
"Our analyses provided a precise road map of Hox binding sites in vvI1+2, which we could then apply to a living fruit fly," said Dr. Mann, who is also the Higgins Professor of Biochemistry and Molecular Biophysics (in Systems Biology) at Columbia's Vagelos College of Physicians and Surgeons.
By employing a combination of elegant genetic manipulations in living, or in vivo, fly embryos, together with advanced biochemical and computational analysis, the researchers could then systematically manipulate Hox target activity with an unprecedented level of precision.
"We now had a starting point from which to systematically decode Hox gene regulation," said Dr. Hombría, "a kind of Rosetta Stone to help us decipher the genetics of body development."
The researchers' findings are especially promising because they can be applied to the entire genome. The steps that Hox genes undergo to regulate vvI1+2 can inform how Hox genes regulate other DNA, not just in fruit flies but beyond -- including in vertebrates, such as mammals, and even humans.
Read more at Science Daily
Scientists have long searched for ways to decipher how Hox genes create this body map; a key to decoding how we build our bodies.
Now an international group of researchers from Columbia University and the Spanish National Research Council (CSIC) based at the Universidad Pablo de Olavide in Seville, Spain have found one such key: a method that can systematically identify the role each Hox gene plays in a developing fruit fly. Their results, reported recently in Nature Communications, offer a new path forward for researchers hoping to make sense of a process that is equal parts chaotic and precise, and that is critical to understanding not only growth and development but also aging and disease.
"The genome, which contains thousands of genes and millions of letters of DNA, is the most complicated code ever written," said Richard Mann, PhD, principal investigator at Columbia's Mortimer B. Zuckerman Mind Brain Behavior Institute and the paper's co-senior author. "Deciphering this code has proven so difficult because evolution wrote it in fits and starts over hundreds of millions of years. Today's study offers a key to cracking that code, bringing us closer than ever to understanding how Hox genes build a healthy body, or how this process gets disrupted in disease."
Hox genes are ancient; they can be found across all animal species. Even primitive jellyfish have them. Each type of organism has different combinations of these genes. Fruit flies have eight Hox genes, while humans have 39.
These genes work by producing special proteins called transcription factors, which work together with similar proteins called Hox cofactors to bind to different segments of DNA and turn many other genes on and off at just the right time -- a Rube Goldberg machine of microscopic proportions.
"Because these genes are intricately involved in many aspects of development, it has proven incredibly challenging to isolate individual Hox genes and trace their activity over time," said James Castelli-Gair Hombría, PhD, a principal investigator at the Centro Andaluz de Biologi?a del Desarrollo at the Universidad Pablo de Olavide and the paper's co-senior author. "We had this incredibly complex equation to solve but too many unknowns to make significant progress."
Recently, Dr. Hombría and his team hit upon a bit of luck. While examining genetic activity in a developing fruit fly, they stumbled upon a small piece of regulatory DNA, called vvI1+2, that had an unusual -- and surprising -- attribute. Although it was active in cells across the fruit fly's entire developing body, it appeared to be regulated by all of the fruit fly's eight Hox genes.
"The ubiquity of the vvI1+2 DNA segment across the entire developing fruit fly, combined with the fact that every Hox gene touches it, made it an ideal system by which to study the Hox gene family," said Carlos Sánchez-Higueras, PhD, a postdoctoral researcher in the Hombría lab and the paper's first author. "In this single piece of DNA, we had the perfect tool; we could now devise a method to systematically manipulate vvI1+2 activity to see how each Hox gene functioned."
First, Dr. Sánchez-Higueras teamed up with Dr. Mann at Columbia's Zuckerman Institute and used a sophisticated computer algorithm called No Read Left Behind, or NRLB. NRLB was recently developed by Dr. Mann, his lab, and his collaborators, including Columbia systems biology professor Harmen Bussemaker, PhD. This powerful algorithm pinpoints the locations where transcription factors bind to a stretch of DNA, even if these binding sites are very weak and difficult to capture. For this study, the researchers focused on the Hox transcription factors and Hox cofactors that bind to vvI1+2.
"Our analyses provided a precise road map of Hox binding sites in vvI1+2, which we could then apply to a living fruit fly," said Dr. Mann, who is also the Higgins Professor of Biochemistry and Molecular Biophysics (in Systems Biology) at Columbia's Vagelos College of Physicians and Surgeons.
By employing a combination of elegant genetic manipulations in living, or in vivo, fly embryos, together with advanced biochemical and computational analysis, the researchers could then systematically manipulate Hox target activity with an unprecedented level of precision.
"We now had a starting point from which to systematically decode Hox gene regulation," said Dr. Hombría, "a kind of Rosetta Stone to help us decipher the genetics of body development."
The researchers' findings are especially promising because they can be applied to the entire genome. The steps that Hox genes undergo to regulate vvI1+2 can inform how Hox genes regulate other DNA, not just in fruit flies but beyond -- including in vertebrates, such as mammals, and even humans.
Read more at Science Daily
A face for Lucy's ancestor
Australopithecus anamensis is the earliest-known species of Australopithecus and widely accepted as the progenitor of 'Lucy's' species, Australopithecus afarensis. Until now, A. anamensis was known mainly from jaws and teeth. Yohannes Haile-Selassie of the Cleveland Museum of Natural History, Stephanie Melillo of the Max Planck Institute for Evolutionary Anthropology and their colleagues have discovered the first cranium of A. anamensis at the paleontological site of Woranso-Mille, in the Afar Region of Ethiopia.
The 3.8 million-year-old fossil cranium represents a time interval between 4.1 and 3.6 million years ago, when A. anamensis gave rise to A. afarensis. Researchers used morphological features of the cranium to identify which species the fossil represents. "Features of the upper jaw and canine tooth were fundamental in determining that MRD was attributable to A. anamensis," said Melillo. "It is good to finally be able to put a face to the name." The MRD cranium, together with other fossils previously known from the Afar, show that A. anamensis and A. afarensis co-existed for approximately 100,000 years. This temporal overlap challenges the widely-accepted idea of a linear transition between these two early human ancestors. Haile-Selassie said: "This is a game changer in our understanding of human evolution during the Pliocene."
Working for the past 15 years at the site, the team discovered the cranium (MRD-VP-1/1, here referred to as "MRD") in February 2016. In the years following their discovery, paleoanthropologists of the project conducted extensive analyses of MRD, while project geologists worked on determining the age and context of the specimen. The results of the team's findings are published online in two papers in the international scientific journal Nature.
Discovery of the cranium
The Woranso-Mille project has been conducting field research in the central Afar region of Ethiopia since 2004. The project has collected more than 12,600 fossil specimens representing about 85 mammalian species. The fossil collection includes about 230 fossil hominin specimens dating to between more than 3.8 and about 3.0 million years ago. The first piece of MRD, the upper jaw, was found by Ali Bereino (a local Afar worker) on February 10, 2016 at a locality known as Miro Dora, Mille district of the Afar Regional State. The specimen was exposed on the surface and further investigation of the area resulted in the recovery of the rest of the cranium. "I couldn't believe my eyes when I spotted the rest of the cranium. It was a eureka moment and a dream come true," said Haile-Selassie.
Geology and age determination
In a companion paper published in the same issue of Nature, Beverly Saylor of Case Western Reserve University and her colleagues determined the age of the fossil as 3.8 million years by dating minerals in layers of volcanic rocks nearby. They mapped the dated levels to the fossil site using field observations and the chemistry and magnetic properties of rock layers. Saylor and her colleagues combined the field observations with analysis of microscopic biological remains to reconstruct the landscape, vegetation and hydrology where MRD died.
MRD was found in the sandy deposits of a delta where a river entered a lake. The river likely originated in the highlands of the Ethiopian plateau while the lake developed at lower elevations where rift activity caused the Earth surface to stretch and thin, creating the lowlands of the Afar region. Fossil pollen grains and chemical remains of fossil plant and algae that are preserved in the lake and delta sediments provide clues about the ancient environmental conditions. Specifically they indicate that the watershed of the lake was mostly dry but that there were also forested areas on the shores of the delta or along the side the river that fed the delta and lake system. "MRD lived near a large lake in a region that was dry. We're eager to conduct more work in these deposits to understand the environment of the MRD specimen, the relationship to climate change and how it affected human evolution, if at all," said Naomi Levin, a co-author on the study from University of Michigan.
A new face in the crowd
Australopithecus anamensis is the oldest known member of the genus Australopithecus. Due to the cranium's rare near-complete state, the researchers identified never-before-seen facial features in the species. "MRD has a mix of primitive and derived facial and cranial features that I didn't expect to see on a single individual," Haile-Selassie said. Some characteristics were shared with later species, while others had more in common with those of even older and more primitive early human ancestor groups such as Ardipithecus and Sahelanthropus. "Until now, we had a big gap between the earliest-known human ancestors, which are about 6 million years old, and species like 'Lucy', which are two to three million years old. One of the most exciting aspects of this discovery is how it bridges the morphological space between these two groups," said Melillo.
Branching out
Among the most important findings was the team's conclusion that A. anamensis and its descendant species, the well-known A. afarensis, coexisted for a period of at least 100,000 years. This finding contradicts the long-held notion of an anagenetic relationship between these two taxa, instead supporting a branching pattern of evolution. Melillo explains: "We used to think that A. anamensis gradually turned into A. afarensis over time. We still think that these two species had an ancestor-descendent relationship, but this new discovery suggests that the two species were actually living together in the Afar for quite some time. It changes our understanding of the evolutionary process and brings up new questions -- were these animals competing for food or space?"
This conclusion is based on the assignment of the 3.8-million-year-old MRD to A. anamensis and the 3.9-million-year-old hominin cranial fragment commonly known as the Belohdelie frontal, to A. afarensis. The Belohdelie frontal was discovered in the Middle Awash of Ethiopia by a team of paleontologists in 1981, but its taxonomic status has been questioned in the intervening years.
Read more at Science Daily
The 3.8 million-year-old fossil cranium represents a time interval between 4.1 and 3.6 million years ago, when A. anamensis gave rise to A. afarensis. Researchers used morphological features of the cranium to identify which species the fossil represents. "Features of the upper jaw and canine tooth were fundamental in determining that MRD was attributable to A. anamensis," said Melillo. "It is good to finally be able to put a face to the name." The MRD cranium, together with other fossils previously known from the Afar, show that A. anamensis and A. afarensis co-existed for approximately 100,000 years. This temporal overlap challenges the widely-accepted idea of a linear transition between these two early human ancestors. Haile-Selassie said: "This is a game changer in our understanding of human evolution during the Pliocene."
Working for the past 15 years at the site, the team discovered the cranium (MRD-VP-1/1, here referred to as "MRD") in February 2016. In the years following their discovery, paleoanthropologists of the project conducted extensive analyses of MRD, while project geologists worked on determining the age and context of the specimen. The results of the team's findings are published online in two papers in the international scientific journal Nature.
Discovery of the cranium
The Woranso-Mille project has been conducting field research in the central Afar region of Ethiopia since 2004. The project has collected more than 12,600 fossil specimens representing about 85 mammalian species. The fossil collection includes about 230 fossil hominin specimens dating to between more than 3.8 and about 3.0 million years ago. The first piece of MRD, the upper jaw, was found by Ali Bereino (a local Afar worker) on February 10, 2016 at a locality known as Miro Dora, Mille district of the Afar Regional State. The specimen was exposed on the surface and further investigation of the area resulted in the recovery of the rest of the cranium. "I couldn't believe my eyes when I spotted the rest of the cranium. It was a eureka moment and a dream come true," said Haile-Selassie.
Geology and age determination
In a companion paper published in the same issue of Nature, Beverly Saylor of Case Western Reserve University and her colleagues determined the age of the fossil as 3.8 million years by dating minerals in layers of volcanic rocks nearby. They mapped the dated levels to the fossil site using field observations and the chemistry and magnetic properties of rock layers. Saylor and her colleagues combined the field observations with analysis of microscopic biological remains to reconstruct the landscape, vegetation and hydrology where MRD died.
MRD was found in the sandy deposits of a delta where a river entered a lake. The river likely originated in the highlands of the Ethiopian plateau while the lake developed at lower elevations where rift activity caused the Earth surface to stretch and thin, creating the lowlands of the Afar region. Fossil pollen grains and chemical remains of fossil plant and algae that are preserved in the lake and delta sediments provide clues about the ancient environmental conditions. Specifically they indicate that the watershed of the lake was mostly dry but that there were also forested areas on the shores of the delta or along the side the river that fed the delta and lake system. "MRD lived near a large lake in a region that was dry. We're eager to conduct more work in these deposits to understand the environment of the MRD specimen, the relationship to climate change and how it affected human evolution, if at all," said Naomi Levin, a co-author on the study from University of Michigan.
A new face in the crowd
Australopithecus anamensis is the oldest known member of the genus Australopithecus. Due to the cranium's rare near-complete state, the researchers identified never-before-seen facial features in the species. "MRD has a mix of primitive and derived facial and cranial features that I didn't expect to see on a single individual," Haile-Selassie said. Some characteristics were shared with later species, while others had more in common with those of even older and more primitive early human ancestor groups such as Ardipithecus and Sahelanthropus. "Until now, we had a big gap between the earliest-known human ancestors, which are about 6 million years old, and species like 'Lucy', which are two to three million years old. One of the most exciting aspects of this discovery is how it bridges the morphological space between these two groups," said Melillo.
Branching out
Among the most important findings was the team's conclusion that A. anamensis and its descendant species, the well-known A. afarensis, coexisted for a period of at least 100,000 years. This finding contradicts the long-held notion of an anagenetic relationship between these two taxa, instead supporting a branching pattern of evolution. Melillo explains: "We used to think that A. anamensis gradually turned into A. afarensis over time. We still think that these two species had an ancestor-descendent relationship, but this new discovery suggests that the two species were actually living together in the Afar for quite some time. It changes our understanding of the evolutionary process and brings up new questions -- were these animals competing for food or space?"
This conclusion is based on the assignment of the 3.8-million-year-old MRD to A. anamensis and the 3.9-million-year-old hominin cranial fragment commonly known as the Belohdelie frontal, to A. afarensis. The Belohdelie frontal was discovered in the Middle Awash of Ethiopia by a team of paleontologists in 1981, but its taxonomic status has been questioned in the intervening years.
Read more at Science Daily
Prehistoric puma feces reveals oldest parasite DNA ever recorded
 |
| Modern-day puma |
A team of Argentinian scientists from the National Council of Scientific and Technical Research (CONICET) made the discovery after studying a coprolite taken from a rock-shelter in the country's mountainous Catamarca Province, where the remains of now extinct megafauna have previously been recovered in stratigraphic excavations.
Radiocarbon dating revealed that the coprolite and thus the parasitic roundworm eggs preserved inside dated back to between 16,570 and 17,000 years ago, towards the end of the last Ice Age.
At that time, the area around the shelter at Peñas de las Trampas in the southern Andean Puna was thought to have been wetter than today, making it a suitable habitat for megafauna like giant ground sloths, and also smaller herbivores like American horses and South American camelids which the pumas may have preyed on.
Ancient mitochondrial DNA analysis was used to confirm the coprolite came from a Puma (Puma concolor) and that the eggs belonged to Toxascaris leonina, a species of roundworm still commonly found in the digestive systems of modern day cats, dogs and foxes.
The study, published in the journal Parasitology, explains that the extremely dry, cold and salty conditions which took hold at the Peñas de las Trampas site since the onset of the Holocene would have helped to reduce the breakdown of the DNA, allowing it to be preserved.
Led by Romina Petrigh and Martín Fugassa, the study was carried out by an interdisciplinary team including archaeologists and biologists and is part of a project that views ancient faeces as important paleobiological reservoirs.
Dr Petrigh, from the National University of Mar del Plata and CONICET, said: "While we have found evidence of parasites in coprolites before, those remains were much more recent, dating back only a few thousand years. The latest find shows that these roundworms were infecting the fauna of South America before the arrival of the first humans in the area around 11,000 years ago."
She added: "I was very happy when I discovered how old this DNA was. It's difficult to recover DNA of such an old age as it usually suffers damage over time. Our working conditions had to be extremely controlled to avoid contamination with modern DNA, so we used special decontaminated reagents and disposable supplies. Several experiments were performed to authenticate the DNA sequences obtained and the efforts of the team of researchers who participated was essential."
The discovery marks a number of firsts: it represents the oldest record of an ancient DNA sequence for a gastrointestinal nematode parasite of wild mammals, the oldest molecular parasite record worldwide, and also a new maximum age for the recovery of old DNA of this origin.
For Dr Petrigh, the findings also cast light on both the past and the present. She said: "This work confirms the presence of T. leonina in prehistoric times, presumably even before that of humans in the region, and it represents the oldest record in the world. The common interpretation is that the presence of T. leonina in American wild carnivores today is a consequence of their contact with domestic dogs or cats, but that should no longer be assumed as the only possible explanation.
"Our aDNA studies have also confirmed the presence of pumas in the southern Puna at the end of the Pleistocene. This has significant implications for the natural history of the region, as well as for inferring the ecological context immediately before -- as far as is known -- the first human explorers ventured into the area."
Read more at Science Daily
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