Dec 17, 2018

Discovered: The most-distant solar system object ever observed

Solar system distances to scale showing the newly discovered 2018 VG18, nicknamed "Farout," compared to other known solar system objects.
A team of astronomers has discovered the most-distant body ever observed in our Solar System. It is the first known Solar System object that has been detected at a distance that is more than 100 times farther than Earth is from the Sun.

The new object was announced on Monday, December 17, 2018, by the International Astronomical Union's Minor Planet Center and has been given the provisional designation 2018 VG18. The discovery was made by Carnegie's Scott S. Sheppard, the University of Hawaii's David Tholen, and Northern Arizona University's Chad Trujillo.

2018 VG18, nicknamed "Farout" by the discovery team for its extremely distant location, is at about 120 astronomical units (AU), where 1 AU is defined as the distance between the Earth and the Sun. The second-most-distant observed Solar System object is Eris, at about 96 AU. Pluto is currently at about 34 AU, making 2018 VG18 more than three-and-a-half times more distant than the Solar System's most-famous dwarf planet.

2018 VG18 was discovered as part of the team's continuing search for extremely distant Solar System objects, including the suspected Planet X, which is sometimes also called Planet 9. In October, the same group of researchers announced the discovery of another distant Solar System object, called 2015 TG387 and nicknamed "The Goblin," because it was first seen near Halloween. The Goblin was discovered at about 80 AU and has an orbit that is consistent with it being influenced by an unseen Super-Earth-sized Planet X on the Solar System's very distant fringes.

The existence of a ninth major planet at the fringes of the Solar System was first proposed by this same research team in 2014 when they discovered 2012 VP113, nicknamed Biden, which is currently near 84 AU.

2015 TG387 and 2012 VP113 never get close enough to the Solar System's giant planets, like Neptune and Jupiter, to have significant gravitational interactions with them. This means that these extremely distant objects can be probes of what is happening in the Solar System's outer reaches. The team doesn't know 2018 VG18's orbit very well yet, so they have not been able to determine if it shows signs of being shaped by Planet X.

"2018 VG18 is much more distant and slower moving than any other observed Solar System object, so it will take a few years to fully determine its orbit," said Sheppard. "But it was found in a similar location on the sky to the other known extreme Solar System objects, suggesting it might have the same type of orbit that most of them do. The orbital similarities shown by many of the known small, distant Solar System bodies was the catalyst for our original assertion that there is a distant, massive planet at several hundred AU shepherding these smaller objects."

"All that we currently know about 2018 VG18 is its extreme distance from the Sun, its approximate diameter, and its color," added Tholen "Because 2018 VG18 is so distant, it orbits very slowly, likely taking more than 1,000 years to take one trip around the Sun."

The discovery images of 2018 VG18 were taken at the Japanese Subaru 8-meter telescope located atop Mauna Kea in Hawaii on November 10, 2018.

Once 2018 VG18 was found, it needed to be re-observed to confirm its very distant nature. (It takes multiple nights of observing to accurately determine an object's distance.) 2018 VG18 was seen for the second time in early December at the Magellan telescope at Carnegie's Las Campanas Observatory in Chile. These recovery observations were performed by the team with the addition of graduate student Will Oldroyd of Northern Arizona University. Over the next week, they monitored 2018 VG18 with the Magellan telescope to secure its path across the sky and obtain its basic physical properties such as brightness and color.

The Magellan observations confirmed that 2018 VG18 is around 120 AU, making it the first Solar System object observed beyond 100 AU. Its brightness suggests that it is about 500 km in diameter, likely making it spherical in shape and a dwarf planet. It has a pinkish hue, a color generally associated with ice-rich objects.

"This discovery is truly an international achievement in research using telescopes located in Hawaii and Chile, operated by Japan, as well as by a consortium of research institutions and universities in the United States," concluded Trujillo. "With new wide-field digital cameras on some of the world's largest telescopes, we are finally exploring our Solar System's fringes, far beyond Pluto."

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Saturn is losing its rings at 'worst-case-scenario' rate

An artist's impression of how Saturn may look in the next hundred million years. The innermost rings disappear as they rain onto the planet first, very slowly followed by the outer rings.
New NASA research confirms that Saturn is losing its iconic rings at the maximum rate estimated from Voyager 1 & 2 observations made decades ago. The rings are being pulled into Saturn by gravity as a dusty rain of ice particles under the influence of Saturn's magnetic field.

"We estimate that this 'ring rain' drains an amount of water products that could fill an Olympic-sized swimming pool from Saturn's rings in half an hour," said James O'Donoghue of NASA's Goddard Space Flight Center in Greenbelt, Maryland. "From this alone, the entire ring system will be gone in 300 million years, but add to this the Cassini-spacecraft measured ring-material detected falling into Saturn's equator, and the rings have less than 100 million years to live. This is relatively short, compared to Saturn's age of over 4 billion years." O'Donoghue is lead author of a study on Saturn's ring rain appearing in Icarus December 17.

Scientists have long wondered if Saturn was formed with the rings or if the planet acquired them later in life. The new research favors the latter scenario, indicating that they are unlikely to be older than 100 million years, as it would take that long for the C-ring to become what it is today assuming it was once as dense as the B-ring. "We are lucky to be around to see Saturn's ring system, which appears to be in the middle of its lifetime. However, if rings are temporary, perhaps we just missed out on seeing giant ring systems of Jupiter, Uranus and Neptune, which have only thin ringlets today!" O'Donoghue added.

Various theories have been proposed for the ring's origin. If the planet got them later in life, the rings could have formed when small, icy moons in orbit around Saturn collided, perhaps because their orbits were perturbed by a gravitational tug from a passing asteroid or comet.

The first hints that ring rain existed came from Voyager observations of seemingly unrelated phenomena: peculiar variations in Saturn's electrically charged upper atmosphere (ionosphere), density variations in Saturn's rings, and a trio of narrow dark bands encircling the planet at northern mid-latitudes. These dark bands appeared in images of Saturn's hazy upper atmosphere (stratosphere) made by NASA's Voyager 2 mission in 1981.

In 1986, Jack Connerney of NASA Goddard published a paper in Geophysical Research Letters that linked those narrow dark bands to the shape of Saturn's enormous magnetic field, proposing that electrically charged ice particles from Saturn's rings were flowing down invisible magnetic field lines, dumping water in Saturn's upper atmosphere where these lines emerged from the planet. The influx of water from the rings, appearing at specific latitudes, washed away the stratospheric haze, making it appear dark in reflected light, producing the narrow dark bands captured in the Voyager images.

Saturn's rings are mostly chunks of water ice ranging in size from microscopic dust grains to boulders several yards (meters) across. Ring particles are caught in a balancing act between the pull of Saturn's gravity, which wants to draw them back into the planet, and their orbital velocity, which wants to fling them outward into space. Tiny particles can get electrically charged by ultraviolet light from the Sun or by plasma clouds emanating from micrometeoroid bombardment of the rings. When this happens, the particles can feel the pull of Saturn's magnetic field, which curves inward toward the planet at Saturn's rings. In some parts of the rings, once charged, the balance of forces on these tiny particles changes dramatically, and Saturn's gravity pulls them in along the magnetic field lines into the upper atmosphere.

Once there, the icy ring particles vaporize and the water can react chemically with Saturn's ionosphere. One outcome from these reactions is an increase in the lifespan of electrically charged particles called H3+ ions, which are made up of three protons and two electrons. When energized by sunlight, the H3+ ions glow in infrared light, which was observed by O'Donoghue's team using special instruments attached to the Keck telescope in Mauna Kea, Hawaii.

Their observations revealed glowing bands in Saturn's northern and southern hemispheres where the magnetic field lines that intersect the ring plane enter the planet. They analyzed the light to determine the amount of rain from the ring and its effects on Saturn's ionosphere. They found that the amount of rain matches remarkably well with the astonishingly high values derived more than three decades earlier by Connerney and colleagues, with one region in the south receiving most of it.

The team also discovered a glowing band at a higher latitude in the southern hemisphere. This is where Saturn's magnetic field intersects the orbit of Enceladus, a geologically active moon that is shooting geysers of water ice into space, indicating that some of those particles are raining onto Saturn as well. "That wasn't a complete surprise," said Connerney. "We identified Enceladus and the E-ring as a copious source of water as well, based on another narrow dark band in that old Voyager image." The geysers, first observed by Cassini instruments in 2005, are thought to be coming from an ocean of liquid water beneath the frozen surface of the tiny moon. Its geologic activity and water ocean make Enceladus one of the most promising places to search for extraterrestrial life.

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'Treasure trove' of dinosaur footprints found in southern England

Two large iguanodontian footprints with skin and claw impressions.
More than 85 well-preserved dinosaur footprints -- made by at least seven different species -- have been uncovered in East Sussex, representing the most diverse and detailed collection of these trace fossils from the Cretaceous Period found in the UK to date.

The footprints were identified by University of Cambridge researchers between 2014 and 2018, following periods of coastal erosion along the cliffs near Hastings. Many of the footprints -- which range in size from less than 2 cm to over 60 cm across -- are so well-preserved that fine detail of skin, scales and claws is easily visible.

The footprints date from the Lower Cretaceous epoch, between 145 and 100 million years ago, with prints from herbivores including Iguanodon, Ankylosaurus, a species of stegosaur, and possible examples from the sauropod group (which included Diplodocus and Brontosaurus); as well as meat-eating theropods. The results are reported in the journal Palaeogeography, Palaeoclimatology, Palaeoecology.

Over the past 160 years, there have been sporadic reports of fossilised dinosaur footprints along the Sussex coast, but no new major discoveries have been described for the past quarter century and the earlier findings were far less varied and detailed than those described in the current research.

The area around Hastings is one of the richest in the UK for dinosaur fossils, including the first known Iguanodon in 1825, and the first confirmed example of fossilised dinosaur brain tissue in 2016. However, trace fossils such as footprints, which can help scientists learn more about the composition of dinosaur communities, are less common in the area.

"Whole body fossils of dinosaurs are incredibly rare," said Anthony Shillito, a PhD student in Cambridge's Department of Earth Sciences and the paper's first author. "Usually you only get small pieces, which don't tell you a lot about how that dinosaur may have lived. A collection of footprints like this helps you fill in some of the gaps and infer things about which dinosaurs were living in the same place at the same time."

The footprints described in the current study, which Shillito co-authored with Dr Neil Davies, were uncovered during the past four winters, when strong storms and storm surges led to periods of collapse of the sandstone and mudstone cliffs.

In the Cretaceous Period, the area where the footprints were found was likely near a water source, and in addition to the footprints, a number of fossilised plants and invertebrates were also found.

"To preserve footprints, you need the right type of environment," said Davies. "The ground needs to be 'sticky' enough so that the footprint leaves a mark, but not so wet that it gets washed away. You need that balance in order to capture and preserve them."

"As well as the large abundance and diversity of these prints, we also see absolutely incredible detail," said Shillito. "You can clearly see the texture of the skin and scales, as well as four-toed claw marks, which are extremely rare.

"You can get some idea about which dinosaurs made them from the shape of the footprints -- comparing them with what we know about dinosaur feet from other fossils lets you identify the important similarities. When you also look at footprints from other locations you can start to piece together which species were the key players."

As part of his research, Shillito is studying how dinosaurs may have affected the flows of rivers. In modern times, large animals such as hippopotamuses or cows can create small channels, diverting some of the river's flow.

"Given the sheer size of many dinosaurs, it's highly likely that they affected rivers in a similar way, but it's difficult to find a 'smoking gun', since most footprints would have just washed away," said Shillito. "However, we do see some smaller-scale evidence of their impact; in some of the deeper footprints you can see thickets of plants that were growing. We also found evidence of footprints along the banks of river channels, so it's possible that dinosaurs played a role in creating those channels."

Read more at Science Daily

Dec 16, 2018

New techniques better determine how ancient viral DNA influences human genes

New laboratory techniques can identify which of our genes are influenced by DNA snippets that are left behind in our genetic code by viruses, a new study finds.

Viruses have long been known to reproduce by using the genetic machinery of the cells they invade. As part of that process over time, these microorganisms have left behind thousands of DNA sequences, called transposons, throughout the genetic material (genomes) in many lifeforms, including mice and humans, say the study authors. Studies established decades ago the idea that a few of these viral insertions have come to play a role in the action of genes.

Determining which transposons regulate which genes, however, has proven to be a challenge, as transposons may influence a nearby gene or one that is located far away in the DNA molecular chain.

Published online December 13 in Genome Biology, the new study describes methods that capture more information on the location and influence of viral insertions in genomes, identifying genes potentially controlled by active transposons (most are silenced by our cells' defense mechanisms).

"One of the interesting findings from our study is that a single transposon may control more than one gene and that one gene can be regulated by more than one transposon, increasing the complexity of the potential impact of transposons on health and disease," says senior study author Jane Skok, PhD, the Sandra and Edward H. Meyer Professor of Radiation Oncology at NYU Langone Health's Perlmutter Cancer Center. "Furthermore, viral insertions from the same family preferentially interact with each other, possibly reinforcing their impact on genetic activity."

View of Genetic Reality

For decades after the discovery of DNA, researchers mostly thought of genetics in terms of genes, the pieces or sequences of DNA that encode instructions for building proteins in cells. Then scientists discovered that genes make up just 2 percent of our DNA and that most genetic complexity stems from the vast non-gene code, which influences when genes are turned on or off. Further, half of that non-gene code was found to come from insertions of viral DNA. Consequently, say the authors, genetic variation, and the potential for disease-causing mistakes, occurs in transposons as well as in genes.

The current results are based on the discovery that pieces of DNA, called enhancers, control gene activity. These enhancers may be separated from their target genes by a long distance on a linear DNA chain but can curl around in 3D space to interact with another section of the chain by forming loops. Evidence then emerged that some of these looping enhancers may be parts of viral transposon sequences.

But those trying to understand the role of these enhancers faced a problem.

Transposon insertions occur at many sites and are therefore repeats of the same DNA code (not unique). However, popular genome-wide association studies rely on finding a link between a single, unique piece of DNA and risk for a disease. Thus, repeat sequences are typically ignored because it is not clear which of these multiple insertion sites is interacting with a particular disease-related gene.

Experimental evidence supports the idea that to exert influence, enhancers must make physical contact with their target genes through loop formation. Identifying such interactions between different pieces of DNA became possible in 2002 with the development of a technique called chromosome conformation capture.

The current study describes two variations on this technology, collectively called 4TRAN, which take advantage of the repetitive nature of transposons to capture their interactions. The techniques provide direct evidence that some transposons exert long-range control of genes by looping.

One of the new techniques, 4TRAN-PCR, proved to be capable of finding all interactions involving members of a transposon family that contain a particular DNA sequence, enabling the researchers to count the hundreds or thousands of places where such transposons occur. The method demonstrated that transposons are more likely to interact with DNA within local neighborhoods (topologically associating domains), but also that they take part in long-range interactions determined by the activation status of the compartments they are in.

The second technique, Capture 4TRAN, attached probes to each member of a viral family that, in combination with other tricks, enabled the team to determine the influence of any single transposon copy on a specific gene or genes. For example, the study showed that a few of the 7,200 copies of repetitive DNA left behind by the viral MER41 family, which infected our primate ancestors 60 million years ago, now serve as enhancers that turn on immune system genes via long-range DNA contacts by looping. Ironically the target genes in this case act to combat, of all things, viruses.

Read more at Science Daily

Oldest known plant virus found at ancient settlement

Ancient inhabitants of the Antelope House ruin, in Arizona's Canyon de Chelly National Monument, grew crops such as maize, beans and squash.
Researchers studying ancient corncobs found at a Native American archeological site have recovered a 1,000-year-old virus, the oldest plant virus ever reported.

Only a few RNA viruses had been discovered previously from archaeological samples, the oldest dating from about 750 years ago. The new discovery came as the research team examined ancient plant material from Antelope House, an Ancestral Puebloan ruin located at Canyon de Chelly National Monument, Arizona.

The Ancestral Puebloans who lived in the canyon planted crops such as maize, beans and squash. During the excavation of Antelope House by the National Park Service in the 1970s, more than two tons of plant refuse, in highly recognizable form, were recovered.

"It's clear from these remains that maize was a major food source for the inhabitants," said lead researcher Marilyn Roossinck, professor of plant pathology and environmental microbiology, College of Agricultural Sciences, Penn State. "The maize remnants recovered at Antelope House consisted of cobs, ears with kernels, individual kernels, husks, leaves, shanks, stem portions and tassels."

Using carbon 14 dating, researchers confirmed that the age of the ancient samples was about 1,000 years old. While analyzing cobs, the scientists isolated three nearly complete genomes of a previously unknown virus of the family Chrysoviridae, which infect plants and fungi.

The researchers, who report their findings in the current issue of the Journal of Virology, noted that chrysoviruses are persistent plant viruses that are transmitted from generation to generation through seeds and can remain in their hosts for very long time periods. Persistent viruses typically do not cause disease and rarely are detected. This is the first chrysovirus described from maize, Roossinck noted.

"When we analyzed modern corn samples, we found the same chrysovirus with only about 3 percent divergence from the ancient samples," she said. "Most RNA viruses, with short generation times and error-prone replication, evolve rapidly. However, persistent viruses have very stable genomes."

Roossinck said the most interesting aspect of the findings for the team is that the virus has been maintained in corn for so long.

Read more at Science Daily

Dec 15, 2018

Physical activity in the evening does not cause sleep problems

Moderate intensity exercise shortly before bedtime does not negatively affect sleep. At most, vigorous exercise close to bedtime might have a negative effect. Each symbol in this overview represents one set of experimental data.
Even among sleep researchers, it is a widely held belief that sleep quality can be improved by avoiding exercise in the evening. However, as researchers from the Institute of Human Movement Sciences and Sport at ETH Zurich have demonstrated, it is not generally true.

The scientists combed through the literature on the subject and analysed all 23 studies that met their quality requirements. They concluded that doing exercise in the four hours before going to bed does not have a negative effect on sleep. "If doing sport in the evening has any effect on sleep quality at all, it's rather a positive effect, albeit only a mild one," says Christina Spengler, head of the Exercise Physiology Lab at ETH Zurich.

By combining the data from the different studies, the researchers showed that in the night after study participants had done some sport in the evening, they spent 21.2 percent of their sleeping time in deep sleep. Following an evening without exercise, the average figure was 19.9 percent. While the difference is small, it is statistically significant. Deep sleep phases are especially important for physical recovery.

Intensive training late in the evening: an exception to the rule

Vigorous training within an hour before bedtime is an exception to the rule. According to this analysis, it is the only type of evening exercise that may have a negative effect on sleep. "However, this preliminary observation is based on just one study," Spengler says.

"As a rule of thumb, vigorous training is defined as training in which a person is unable to talk. Moderate training is physical activity of an intensity high enough that a person would no longer be able to sing, but they could speak," Spengler says. One example of vigorous training is the kind of high-intensity interval training that competitive athletes often perform. In many cases, though, a longer endurance run or a longer ride on a racing bike would fall into the moderate training category.

As the analysis showed, it took study participants who completed an intensive training session shortly before bedtime longer to fall asleep. The study also provided insight into why this is the case: the test subjects were not able to recover sufficiently in the hour before they went to bed. Their hearts were still beating more than 20 beats per minute faster than their resting heart rate.

Possible sleep problems are no excuse

According to the official recommendations of sport physicians, people should do at least 150 minutes of moderate exercise each week. Many may ask themselves: should I exercise in the evening if I didn't have time during the day, or will that have a negative effect on my sleep? "People can do exercise in the evening without hesitation. The data shows that moderate exercise in the evening is no problem at all," says Jan Stutz, a doctoral student in Spengler's research group and lead author of the analysis, which was published in the journal Sports Medicine. Moderate exercise did not cause sleep problems in any of the studies examined, not even when the training session ended just 30 minutes before bedtime. "However, vigorous training or competitions should be scheduled earlier in the day, if possible," Stutz says.

Stutz and Spengler point out that they examined average values over the course of their analysis, which made only general statements possible. "Not everyone reacts to exercise in the same way, and people should keep listening to their bodies. If they notice they are having problems falling asleep after doing sport, they should try to work out a little earlier," Stutz says.

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Biologists turn eavesdropping viruses into bacterial assassins

These E. coli bacteria harbor proteins from the eavesdropping virus. One of the viral proteins has been tagged with a red marker. When the virus is in the 'stay' mode (left), the bacteria grow and the red protein is spread throughout each cell. When the virus overhears that its hosts have achieved a quorum (right), the kill-stay decision protein is flipped to 'kill' mode. A second viral protein binds the red protein and sends it to the cell poles (yellow dots). All the cells in the right panel will soon die.
Princeton molecular biologist Bonnie Bassler and graduate student Justin Silpe have identified a virus, VP882, that can listen in on bacterial conversations -- and then, in a twist like something out of a spy novel, they found a way to use that to make it attack bacterial diseases like E. coli and cholera.

"The idea that a virus is detecting a molecule that bacteria use for communication -- that is brand-new," said Bassler, the Squibb Professor of Molecular Biology. "Justin found this first naturally occurring case, and then he re-engineered that virus so that he can provide any sensory input he chooses, rather than the communication molecule, and then the virus kills on demand." Their paper will appear in the Jan. 10 issue of the journal Cell.

A virus can only ever make one decision, Bassler said: Stay in the host or kill the host. That is, either remain under the radar inside its host or activate the kill sequence that creates hundreds or thousands of offspring that burst out, killing the current host and launching themselves toward new hosts.

There's an inherent risk in choosing the kill option: "If there are no other hosts nearby, then the virus and all its kin just died," she said. VP882 has found a way to take the risk out of the decision. It listens for the bacteria to announce that they are in a crowd, upping the chances that when the virus kills, the released viruses immediately encounter new hosts. "It's brilliant and insidious!" said Bassler.

"This paper provides an entirely new perspective on the dynamic relationship between viruses and their hosts," said Graham Hatfull, the Eberly Family Professor of Biotechnology at the University of Pittsburgh, who was not involved in this research. "This study tells us for the first time … that when a phage is in the lysogenic [stay] state, it is not 'fast asleep', but rather catnapping, with one eye open and ears alert, ready to respond when it 'hears' signals that cells are getting ready to respond to changes in their environment."

Bassler, who is also the chair of molecular biology and a Howard Hughes Medical Institute Investigator, had discovered years before that bacteria can communicate and sense one another's presence and that they wait to establish a quorum before they act in concert. But she had never imagined that a virus could eavesdrop on this quorum-sensing communication.

"The bugs are getting bugged," she said with a laugh. "Plus, Justin's work shows that these quorum-sensing molecules are conveying information across kingdom boundaries." Viruses are not in the same kingdom as bacteria -- in fact, they are not in any kingdom, because they are not technically alive. But for such radically different organisms to be able to detect and interpret each other's signals is simply mind-boggling, she said. It's not like enemy nations spying on each other, or even like a human communicating with a dog -- those at least are members of the same kingdom (animal) and phylum (vertebrate).

After finding the first evidence of this cross-kingdom eavesdropping, Silpe started looking for more -- and found it.

"He just started a brand-new field," Bassler said. "The idea that there's only one example of this cross-domain communication made no sense to us. Justin discovered the first case, and then, with his discovery in hand, he went looking more deeply and he found a whole set of viruses that harbor similar capabilities. They may not all be listening in to this quorum-sensing information, but it is clear that these viruses can listen in to their hosts' information and then use that information to kill them."

Silpe said he was drawn to work in Bassler's lab because of her research on bacterial communication. "Communication seems like such an evolved trait," he said. "To hear that bacteria can do it -- her discovery -- it was just mind-blowing that organisms you think of as so primitive could actually be capable of communication. And viruses are even simpler than bacteria. The one I studied, for example, only has about 70 genes. It's really remarkable that it devotes one of those genes to quorum sensing. Communication is clearly not something higher organisms created."

Once Silpe demonstrated that VP882 was eavesdropping, he began experimenting with feeding it misinformation to trick the virus into killing on command -- to turn the predator into an assassin.

VP882 is not the first virus used as an antimicrobial treatment. Viruses that prey on bacteria are called "phages," and "phage therapy" -- targeting a bacterial disease with a phage -- is a known medical strategy. But VP882 is the first phage that uses eavesdropping to know when it is optimal to kill its targets, making Silpe's experiments with salmonella and other disease-causing bacteria the first time that phage therapy has used trans-kingdom communication.

In addition, this virus holds enormous promise as a therapeutic tool because it does not act like a typical virus, Bassler said. Most viruses can only infect a very specific type of cell. Flu viruses, for example, only infect lung cells; HIV only targets specific immune-system cells. But the virus VP882 has an "exceptionally broad host range," Bassler said. So far, Silpe has only performed "proof of principle" tests with three unrelated bacteria: Vibrio cholerae (cholera), salmonella and E. coli. Those diseases have evolved separately for hundreds of millions of years, so the fact that they are all susceptible to this bacterial assassin suggests that many, many more are as well.

Hatfull is also optimistic about the utility of this re-engineered virus for antibiotic-resistant bacteria. "Antibiotic resistance is clearly a major global health threat, and there is a clear and evident demand for new strategies and approaches to this problem," he said. "Although we have admittedly found it tricky even to reach 'first base' with basic therapeutic use of naturally occurring phages, we can envisage the possibility of a 'home run' if we can engineer phages for therapeutic use that have very specific targeting." These viral assassins might even slow down the emergence of antibiotic resistant strains, he said.

Bassler gives all credit for the discovery to Silpe. After identifying a new quorum-sensing gene in V. cholerae, he made the choice to search genome databases for that gene. It showed up in some cholera-related strains and exactly one virus. Bassler wondered if that could be a meaningless data artifact, but Silpe wanted to get a specimen of the virus and run experiments.

"He was gung-ho, and I thought, 'What the heck, give this kid a little rope. If this isn't working soon, we can always move on,'" she said. "His was a crazy idea, because there's never, ever been evidence of a virus listening in on bacterial host information to decide whether to stay put or kill. But this lab was built on crazy ideas, like bacteria talking to each other, and we've kind of made a living out of it. … Of course, that's the beauty of science, and science at Princeton, that you have enough resources to play those hunches out, and see if there's a 'there' there. And this time, there was a big 'there' there."

Read more at Science Daily

Dec 14, 2018

How complexity science can quickly detect climate record anomalies

This is a segment of the West Antarctic Ice Core.
The history of our climate is written in ice. Reading it is a matter of deciphering the complex signals pulled from tens of thousands of years of accumulated isotopes frozen miles below the surface of Antarctica.

When making sense of the massive amount of information packed into an ice core, scientists face a forensic challenge: how best to separate the useful information from the corrupt.

A new paper published in the journal Entropy shows how tools from information theory, a branch of complexity science, can address this challenge by quickly homing in on portions of the data that require further investigation.

"With this kind of data, we have limited opportunities to get it right," says Joshua Garland, a mathematician at the Santa Fe Institute who works with 68,000 years of data from the West Antarctic Ice Sheet Divide ice Core. "Extracting the ice and processing the data takes hundreds of people, and tons of processing and analysis. Because of resource constraints, replicate cores are rare. "

By the time Garland and his team got ahold of the data, more than 10 years had passed from the initial drilling of the ice core to the publishing of the dataset it contained. The two-mile ice core was extracted over five seasons from 2007-2012, by teams from the multiple universities funded by the National Science Foundation. From the field camp in West Antarctica, the core was packaged, then shipped to the National Science Foundation Ice Core Facility in Colorado, and finally to the University of Colorado. At the Stable Isotope Lab at the Institute of Arctic and Alpine Research, a state-of-the-art processing facility helped scientists pull water isotope records from the ice.

The result is a highly resolved, complex dataset. Compared to previous ice core data, which allowed for analysis every 5 centimeters, the WAIS Divide core permits analysis at millimeter resolution.

"One of the exciting thing about ice core research in the last decade is we've developed these lab systems to analyze the ice in high resolution," says Tyler Jones, a paleoclimatologist at the University of Colorado Boulder. "Quite a while back we were limited in our ability to analyze climate because we couldn't get enough data points, or if we could it would take too long. These new techniques have given us millions of data points, which is rather difficult to manage and interpret without some new advances in our [data] processing."

In previous cores, Garland notes that decades, even centuries, were aggregated into a single point. The WAIS data, by contrast, sometimes gives more than forty data points per year. But as scientists move to analyze the data at shorter time scales, even small anomalies can be problematic.

"As fine-grained data becomes available, fine-grained analyses can be performed," Garland notes. "But it also makes the analysis susceptible to fine-grained anomalies."

To quickly identify which anomalies require further investigation, the team uses information theoretic techniques to measure how much complexity appears at each point in the time sequence. A sudden spike in the complexity could mean that there was either a major, unexpected climate event, like a super volcano, or that there was an issue in the data or the data processing pipeline.

"This kind of anomaly would be invisible without a highly detailed, fine-grained, point-by-point analysis of the data, which would take a human expert many months to perform," says Elizabeth Bradley, a computer scientist at the University of Colorado Boulder and External Professor at the Santa Fe Institute. "Even though information theory can't tell us the underlying cause of an anomaly, we can use these techniques to quickly flag the segments of the data set that should be investigated by paleoclimate experts."

She compares the ice core dataset to a Google search that returns a million pages. "It's not that you couldn't go through those million pages," Bradley says. "But imagine if you had a technique that could point you toward the ones that were potentially meaningful?" When analyzing large, real-world datasets, information theory can spot differences in the data that signal either a processing error or a significant climate event.

In their Entropy paper, the scientists detail how they used information theory to identify and repair a problematic stretch of data from the original ice core. Their investigation eventually prompted a resampling of the archival ice core -- the longest resampling of a high-resolution ice core to date. When that portion of the ice was resampled and reprocessed, the team was able to resolve an anomalous spike in entropy from roughly 5,000 years ago.

"It's vitally important to get this area right," Garland notes, "because it contains climate information from the dawn of human civilization."

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A young star caught forming like a planet

This is an artists impression of the disc of dust and gas surrounding the massive protostar MM 1a, with its companion MM 1b forming in the outer regions.
Astronomers have captured one of the most detailed views of a young star taken to date, and revealed an unexpected companion in orbit around it.

While observing the young star, astronomers led by Dr John Ilee from the University of Leeds discovered it was not in fact one star, but two.

The main object, referred to as MM 1a, is a young massive star surrounded by a rotating disc of gas and dust that was the focus of the scientists' original investigation.

A faint object, MM 1b, was detected just beyond the disc in orbit around MM 1a. The team believe this is one of the first examples of a "fragmented" disc to be detected around a massive young star.

"Stars form within large clouds of gas and dust in interstellar space," said Dr Ilee, from the School of Physics and Astronomy at Leeds.

"When these clouds collapse under gravity, they begin to rotate faster, forming a disc around them. In low mass stars like our Sun, it is in these discs that planets can form."

"In this case, the star and disc we have observed is so massive that, rather than witnessing a planet forming in the disc, we are seeing another star being born."

By measuring the amount of radiation emitted by the dust, and subtle shifts in the frequency of light emitted by the gas, the researchers were able to calculate the mass of MM 1a and MM 1b.

Their work, published today in the Astrophysical Journal Letters, found MM 1a weighs 40 times the mass of our Sun. The smaller orbiting star MM 1b was calculated to weigh less than half the mass of our Sun.

"Many older massive stars are found with nearby companions," added Dr Ilee. "But binary stars are often very equal in mass, and so likely formed together as siblings. Finding a young binary system with a mass ratio of 80:1 is very unusual, and suggests an entirely different formation process for both objects."

The favoured formation process for MM 1b occurs in the outer regions of cold, massive discs. These "gravitationally unstable" discs are unable to hold themselves up against the pull of their own gravity, collapsing into one -- or more -- fragments.

Dr Duncan Forgan, a co-author from the Centre for Exoplanet Science at the University of St Andrews, added: "I've spent most of my career simulating this process to form giant planets around stars like our Sun. To actually see it forming something as large as a star is really exciting."

The researchers note that newly-discovered young star MM 1b could also be surrounded by its own circumstellar disc, which may have the potential to form planets of its own -- but it will need to be quick.

Dr Ilee added: "Stars as massive as MM 1a only live for around a million years before exploding as powerful supernovae, so while MM 1b may have the potential to form its own planetary system in the future, it won't be around for long."

The astronomers made this surprising discovery by using a unique new instrument situated high in the Chilean desert -- the Atacama Large Millimetre/submillimetre Array (ALMA).

Using the 66 individual dishes of ALMA together in a process called interferometry, the astronomers were able to simulate the power of a single telescope nearly 4km across, allowing them to image the material surrounding the young stars for the first time.

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Can stem cells help a diseased heart heal itself? Researcher achieves important milestone

A team of Rutgers scientists, including Leonard Lee and Shaohua Li, have taken an important step toward the goal of making diseased hearts heal themselves -- a new model that would reduce the need for bypass surgery, heart transplants or artificial pumping devices.

The study, recently published in Frontiers in Cell and Developmental Biology, involved removing connective tissue cells from a human heart, "reverse-engineering" them into heart stem cells, then "re-engineering" them into heart muscle cells.

The Rutgers team's true breakthrough, however, is that the newly created cardiac muscle cells clumped together into a single unit that visibly pumps under the microscope.

Senior author Leonard Y. Lee, chair of the Department of Surgery at Rutgers Robert Wood Johnson Medical School, said cardiac cells made in this way don't normally come together and beat as one. His team succeeded in making this happen by over-expressing, a protein in the cells called CREG.

According to Lee, fibroblasts, a cell in connective tissue, were isolated from the heart tissue and reverse-engineered -- or transformed -- into stem cells. This was done so that when the CREG protein was over expressed the stem cells would differentiate into cardiac cells.

"Heart failure has reached epidemic proportions. Right now, the only option to treat it is surgery, transplant, or connecting the patient with a blood-pumping machine," Lee said. "But transplantable hearts are in short supply and mechanical devices limit the patient's quality of life. So, we are working for ways to help hearts heal themselves."

Though still far off, Lee's ultimate goal is to be able to remove small amounts of a patient's native heart tissue, use CREG to convert the tissue into cardiac muscles that will work together cohesively, and re-introduce them into the patient's heart allowing it to heal itself.

More than six million Americans are living with heart failure, according to the American Heart Association. While most people hear the term "heart failure" and think this means the heart is no longer working at all, but it actually means that the heart is not pumping as well as it should be. People with heart failure often experience fatigue and shortness of breath and have difficulty with every day activities such as walking and climbing stairs.

From Science Daily