Jun 24, 2017

Ultra-thin camera creates images without lenses

At Caltech, engineers have developed a new camera design that replaces the lenses with an ultra-thin optical phased array (OPA).
Traditional cameras -- even those on the thinnest of cell phones -- cannot be truly flat due to their optics: lenses that require a certain shape and size in order to function. At Caltech, engineers have developed a new camera design that replaces the lenses with an ultra-thin optical phased array (OPA). The OPA does computationally what lenses do using large pieces of glass: it manipulates incoming light to capture an image.

Lenses have a curve that bends the path of incoming light and focuses it onto a piece of film or, in the case of digital cameras, an image sensor. The OPA has a large array of light receivers, each of which can individually add a tightly controlled time delay (or phase shift) to the light it receives, enabling the camera to selectively look in different directions and focus on different things.

"Here, like most other things in life, timing is everything. With our new system, you can selectively look in a desired direction and at a very small part of the picture in front of you at any given time, by controlling the timing with femto-second -- quadrillionth of a second -- precision," says Ali Hajimiri, Bren Professor of Electrical Engineering and Medical Engineering in the Division of Engineering and Applied Science at Caltech, and the principal investigator of a paper describing the new camera. The paper was presented at the Optical Society of America's (OSA) Conference on Lasers and Electro-Optics (CLEO) and published online by the OSA in the OSA Technical Digest in March 2017.

"We've created a single thin layer of integrated silicon photonics that emulates the lens and sensor of a digital camera, reducing the thickness and cost of digital cameras. It can mimic a regular lens, but can switch from a fish-eye to a telephoto lens instantaneously -- with just a simple adjustment in the way the array receives light," Hajimiri says.

Phased arrays, which are used in wireless communication and radar, are collections of individual transmitters, all sending out the same signal as waves. These waves interfere with each other constructively and destructively, amplifying the signal in one direction while canceling it out elsewhere. Thus, an array can create a tightly focused beam of signal, which can be steered in different directions by staggering the timing of transmissions made at various points across the array.

A similar principle is used in reverse in an optical phased array receiver, which is the basis for the new camera. Light waves that are received by each element across the array cancel each other from all directions, except for one. In that direction, the waves amplify each other to create a focused "gaze" that can be electronically controlled.

"What the camera does is similar to looking through a thin straw and scanning it across the field of view. We can form an image at an incredibly fast speed by manipulating the light instead of moving a mechanical object," says graduate student Reza Fatemi (MS '16), lead author of the OSA paper.

Last year, Hajimiri's team rolled out a one-dimensional version of the camera that was capable of detecting images in a line, such that it acted like a lensless barcode reader but with no mechanically moving parts. This year's advance was to build the first two-dimensional array capable of creating a full image. This first 2D lensless camera has an array composed of just 64 light receivers in an 8 by 8 grid. The resulting image has low resolution. But this system represents a proof of concept for a fundamental rethinking of camera technology, Hajimiri and his colleagues say.

"The applications are endless," says graduate student Behrooz Abiri (MS '12), coauthor of the OSA paper. "Even in today's smartphones, the camera is the component that limits how thin your phone can get. Once scaled up, this technology can make lenses and thick cameras obsolete. It may even have implications for astronomy by enabling ultra-light, ultra-thin enormous flat telescopes on the ground or in space."

Read more at Science Daily

A 100-year-old physics problem has been solved

This is a wave-interference and resonant energy transfer from one source to another distant source or object, pertaining to the fundamental concept of resonances.
At EPFL, researchers challenge a fundamental law and discover that more electromagnetic energy can be stored in wave-guiding systems than previously thought. The discovery has implications in telecommunications. Working around the fundamental law, they conceived resonant and wave-guiding systems capable of storing energy over a prolonged period while keeping a broad bandwidth. Their trick was to create asymmetric resonant or wave-guiding systems using magnetic fields.

The study, which has just been published in Science, was led by Kosmas Tsakmakidis, first at the University of Ottawa and then at EPFL's Bionanophotonic Systems Laboratory run by Hatice Altug, where the researcher is now doing post-doctoral research.

This breakthrough could have a major impact on many fields in engineering and physics. The number of potential applications is close to infinite, with telecommunications, optical detection systems and broadband energy harvesting representing just a few examples.

Casting aside reciprocity

Resonant and wave-guiding systems are present in the vast majority of optical and electronic systems. Their role is to temporarily store energy in the form of electromagnetic waves and then release them. For more than 100 hundred years, these systems were held back by a limitation that was considered to be fundamental: the length of time a wave could be stored was inversely proportional to its bandwidth. This relationship was interpreted to mean that it was impossible to store large amounts of data in resonant or wave-guiding systems over a long period of time because increasing the bandwidth meant decreasing the storage time and quality of storage.

This law was first formulated by K. S. Johnson in 1914, at Western Electric Company (the forerunner of Bell Telephone Laboratories). He introduced the concept of the Q factor, according to which a resonator can either store energy for a long time or have a broad bandwidth, but not both at the same time. Increasing the storage time meant decreasing the bandwidth, and vice versa. A small bandwidth means a limited range of frequencies (or 'colors') and therefore a limited amount of data.

Until now, this concept had never been challenged. Physicists and engineers had always built resonant systems -- like those to produce lasers, make electronic circuits and conduct medical diagnoses -- with this constraint in mind.

But that limitation is now a thing of the past. The researchers came up with a hybrid resonant / wave-guiding system made of a magneto-optic material that, when a magnetic field is applied, is able to stop the wave and store it for a prolonged period, thereby accumulating large amounts of energy. Then when the magnetic field is switched off, the trapped pulse is released.

With such asymmetric and non-reciprocal systems, it was possible to store a wave for a very long period of time while also maintaining a large bandwidth. The conventional time-bandwidth limit was even beaten by a factor of 1,000. The scientists further showed that, theoretically, there is no upper ceiling to this limit at all in these asymmetric (non-reciprocal) systems.

"It was a moment of revelation when we discovered that these new structures did not feature any time-bandwidth restriction at all. These systems are unlike what we have all been accustomed to for decades, and possibly hundreds of years," says Tsakmakidis, the study's lead author. "Their superior wave-storage capacity performance could really be an enabler for a range of exciting applications in diverse contemporary and more traditional fields of research." Hatice Altug adds.

Medicine, the environment and telecommunications

One possible application is in the design of extremely quick and efficient all-optical buffers in telecommunication networks. The role of the buffers is to temporarily store data arriving in the form of light through optical fibers. By slowing the mass of data, it is easier to process. Up to now, the storage quality had been limited.

Read more at Science Daily

Seeker's Visual Guide to Solar Eclipses Throughout History

Solar eclipse at the ruins of Chichén Itzá.
It is hard to overestimate how important solar eclipses were to early humans. The names of several ancient Hawaiian leaders provide evidence of the significance of these dramatic celestial events: Keke-la (thin sun), Ku-ko-hu (appearing blotted), He-ma (to become faded) and Pa-le-na (not shining). Entire civilizations, such as the Aztec empire, were said to have begun and ended, in part, because of omens tied to solar eclipses, and their effect on viewers.

“The impact of solar eclipses on Mesoamerican culture and on virtually all other early civilizations cannot be overstated,” according to Bruce Masse, formerly of the University of Hawaii and Los Alamos National Laboratory.

In a paper published in the journal Vistas in Astronomy, he said that such celestial events pervade “cosmology, art iconography, chiefly symbols, architecture, time reckoning, and religious and chiefly rituals,” as well as myths and historical accounts.

Witnessing, and then surviving, an eclipse must have seemed like coming back from the dead.

The origin of the word “eclipse” comes from the Greek term ekleipsis, meaning an abandonment, a feeling shared by the Inca of South America. Worshippers of the sun god Inti, the Inca felt that their leader was mad at them whenever the moon obscured the sun. They rarely practiced human sacrifice, but a wave of killing would follow solar eclipses. The irony is that the leaders were desperately trying to give Inti what they were supposed to value the most.

While such a response would be unthinkable today, solar eclipses continue to captivate. From likely prehistoric gatherings at Stonehenge to anticipation of this year’s August 21 total solar eclipse, these incredible sky shows remain some of the solar system’s most compelling events.

Partial solar eclipse visible through rocks that form the monument Stonehenge in Wiltshire, Southwest England.
Construction of the megalith Stonehenge, located in England, began in 3100 BC. While historians still debate the monument’s underlying meanings, there is consensus that astronomical alignments inspired much of its design. For example, lines of it point to either sunrise at the summer solstice or sunset at the winter solstice. Some scholars believe that eclipses can be predicted via various methods involving study of Stonehenge. As photographer Ben Stansall shows, portions of the monument can frame certain solar eclipses.

People use protective glasses to catch a glimpse of a solar eclipse in front of the Pyramids of Giza and the Sphinx on March 20, 2015, in Giza, Egypt.
Pyramids and temples of ancient Egypt show stellar alignments, some of which are attested in inscriptions. A 25-year solar-lunar calendar, dating to 1257 BC during the reign of Ramses II, reveals how astronomers at the time were attempting to understand sun and moon cycles. How the pyramids fit into that process remains a mystery, but viewing solar eclipses at or near these monuments often provides some of the most striking visuals.

Babylonian clay tablet that records eclipses between 518 and 465 BC.
The earliest records of specific solar eclipses are found on clay tablets. The oldest known mention is a description of a total solar eclipse said to have occurred on May 3, 1375 BC. Modern assessment of the event — recorded on a clay tablet from the ancient city of Ugarit, in what is now Syria — determined that the eclipse actually happened on March 5, 1223. In a paper published in Nature, authors T. De Jong and W. H. Van Soldt wrote, “This new date implies that the secular deceleration of the Earth’s rotation has changed very little during the past 3,000 years.”

Solar eclipse at the ruins of Chichén Itzá.
Chichén Itzá, a massive Mayan step pyramid dating to about 600 AD, is a masterpiece of astronomical special effects. On the spring equinox, light and shadows on the Temple of Kukulcán make it look as though a feathered serpent god is crawling down the side of the pyramid. From certain angles during a solar eclipse, the darkened orb can look as though it is ascending the temple’s steps.

Read more at Discovery News

Jun 22, 2017

Select memories can be erased, leaving others intact

Two Aplysia sensory neurons with synaptic contacts on the same motor neuron in culture after isolation from the nervous system of Aplysia. The motor neuron has been injected with a fluorescent molecule that blocks the activity of a specific Protein Kinase M molecule.
Different types of memories stored in the same neuron of the marine snail Aplysia can be selectively erased, according to a new study by researchers at Columbia University Medical Center (CUMC) and McGill University and published today in Current Biology.

The findings suggest that it may be possible to develop drugs to delete memories that trigger anxiety and post-traumatic stress disorder (PTSD) without affecting other important memories of past events.

During emotional or traumatic events, multiple memories can become encoded, including memories of any incidental information that is present when the event occurs. In the case of a traumatic experience, the incidental, or neutral, information can trigger anxiety attacks long after the event has occurred, say the researchers.

"The example I like to give is, if you are walking in a high-crime area and you take a shortcut through a dark alley and get mugged, and then you happen to see a mailbox nearby, you might get really nervous when you want to mail something later on," says Samuel Schacher, PhD, a professor of neuroscience in the Department of Psychiatry at CUMC and co-author of the paper. In the example, fear of dark alleys is an associative memory that provides important information -- e.g., fear of dark alleys -- based on a previous experience. Fear of mailboxes, however, is an incidental, non-associative memory that is not directly related to the traumatic event.

"One focus of our current research is to develop strategies to eliminate problematic non-associative memories that may become stamped on the brain during a traumatic experience without harming associative memories, which can help people make informed decisions in the future -- like not taking shortcuts through dark alleys in high-crime areas," Dr. Schacher adds.

Brains create long-term memories, in part, by increasing the strength of connections between neurons and maintaining those connections over time. Previous research suggested that increases in synaptic strength in creating associative and non-associative memories share common properties. This suggests that selectively eliminating non-associative synaptic memories would be impossible, because for any one neuron, a single mechanism would be responsible for maintaining all forms of synaptic memories.

The new study tested that hypothesis by stimulating two sensory neurons connected to a single motor neuron of the marine snail Aplysia; one sensory neuron was stimulated to induce an associative memory and the other to induce a non-associative memory.

By measuring the strength of each connection, the researchers found that the increase in the strength of each connection produced by the different stimuli was maintained by a different form of a Protein Kinase M (PKM) molecule (PKM Apl III for associative synaptic memory and PKM Apl I for non-associative). They found that each memory could be erased -- without affecting the other -- by blocking one of the PKM molecules.

In addition, they found that specific synaptic memories may also be erased by blocking the function of distinct variants of other molecules that either help produce PKMs or protect them from breaking down.

The researchers say that their results could be useful in understanding human memory because vertebrates have similar versions of the Aplysia PKM proteins that participate in the formation of long-term memories. In addition, the PKM-protecting protein KIBRA is expressed in humans, and mutations of this gene produce intellectual disability.

"Memory erasure has the potential to alleviate PTSD and anxiety disorders by removing the non-associative memory that causes the maladaptive physiological response," says Jiangyuan Hu, PhD, an associate research scientist in the Department of Psychiatry at CUMC and co-author of the paper. "By isolating the exact molecules that maintain non-associative memory, we may be able to develop drugs that can treat anxiety without affecting the patient's normal memory of past events."

"Our study is a 'proof of principle' that presents an opportunity for developing strategies and perhaps therapies to address anxiety," said Dr. Schacher. "For example, because memories are still likely to change immediately after recollection, a therapist may help to 'rewrite' a non-associative memory by administering a drug that inhibits the maintenance of non-associative memory."

Read more at Science Daily

How pythons regenerate their organs and other secrets of the snake genome

A Burmese python superimposed on an analysis of gene expression that uncovers how the species changes in its organs upon feeding.
Evolution takes eons, but it leaves marks on the genomes of organisms that can be detected with DNA sequencing and analysis.

As methods for studying and comparing genetic data improve, scientists are beginning to decode these marks to reconstruct the evolutionary history of species, as well as how variants of genes give rise to unique traits.

A research team at the University of Texas at Arlington led by assistant professor of biology Todd Castoe has been exploring the genomes of snakes and lizards to answer critical questions about these creatures' evolutionary history. For instance, how did they develop venom? How do they regenerate their organs? And how do evolutionarily-derived variations in genes lead to variations in how organisms look and function?

"Some of the most basic questions drive our research. Yet trying to understand the genetic explanations of such questions is surprisingly difficult considering most vertebrate genomes, including our own, are made up of literally billions of DNA bases that can determine how an organism looks and functions," says Castoe. "Understanding these links between differences in DNA and differences in form and function is central to understanding biology and disease, and investigating these critical links requires massive computing power."

To uncover new insights that link variation in DNA with variation in vertebrate form and function, Castoe's group uses supercomputing and data analysis resources at the Texas Advanced Computing Center or TACC, one of the world's leading centers for computational discovery.

Recently, they used TACC's supercomputers to understand the mechanisms by which Burmese pythons regenerate their organs -- including their heart, liver, kidney, and small intestines -- after feeding.

Burmese pythons (as well as other snakes) massively downregulate their metabolic and physiological functions during extended periods of fasting. During this time their organs atrophy, saving energy. However, upon feeding, the size and function of these organs, along with their ability to generate energy, dramatically increase to accommodate digestion.

Within 48 hours of feeding, Burmese pythons can undergo up to a 44-fold increase in metabolic rate and the mass of their major organs can increase by 40 to 100 percent.

Writing in BMC Genomics in May 2017, the researchers described their efforts to compare gene expression in pythons that were fasting, one day post-feeding and four days post-feeding. They sequenced pythons in these three states and identified 1,700 genes that were significantly different pre- and post-feeding. They then performed statistical analyses to identify the key drivers of organ regeneration across different types of tissues.

What they found was that a few sets of genes were influencing the wholesale change of pythons' internal organ structure. Key proteins, produced and regulated by these important genes, activated a cascade of diverse, tissue-specific signals that led to regenerative organ growth.

Intriguingly, even mammalian cells have been shown to respond to serum produced by post-feeding pythons, suggesting that the signaling function is conserved across species and could one day be used to improve human health.

"We're interested in understanding the molecular basis of this phenomenon to see what genes are regulated related to the feeding response," says Daren Card, a doctoral student in Castoe's lab and one of the authors of the study. "Our hope is that we can leverage our understanding of how snakes accomplish organ regeneration to one day help treat human diseases."

Making Evolutionary Sense of Secondary Contact

Castoe and his team used a similar genomic approach to understand gene flow in two closely related species of western rattlesnakes with an intertwined genetic history.

The two species live on opposite sides of the Continental Divide in Mexico and the U.S. They were separated for thousands of years and evolved in response to different climates and habitat. However, over time their geographic ranges came back together to the point that the rattlesnakes began to crossbreed, leading to hybrids, some of which live in a region between the two distinct climates.

The work was motivated by a desire to understand what forces generate and maintain distinct species, and how shifts in the ranges of species (for example, due to global change) may impact species and speciation.

The researchers compared thousands of genes in the rattlesnakes' nuclear DNA to study genomic differentiation between the two lineages. Their comparisons revealed a relationship between genetic traits that are most important in evolution during isolation and those that are most important during secondary contact, with greater-than-expected overlap between genes in these two scenarios.

However, they also found regions of the rattlesnake genome that are important in only one of these two scenarios. For example, genes functioning in venom composition and in reproductive differences -- distinct traits that are important for adaptation to the local habitat -- likely diverged under selection when these species were isolated. They also found other sets of genes that were not originally important for diversification of form and function, that later became important in reducing the viability of hybrids. Overall, their results provide a genome-scale perspective on how speciation might work that can be tested and refined in studies of other species.

The team published their results in the April 2017 issue of Ecology and Evolution.

The Role of Supercomputing in Genomics Research

The studies performed by members of the Castoe lab rely on advanced computing for several aspects of the research. First, they use advanced computing to create genome assemblies -- putting millions of small chunks of DNA in the correct order.

"Vertebrate genomes are typically on the larger side, so it takes a lot of computational power to assemble them," says Card. "We use TACC a lot for that."

Next, the researchers use advanced computing to compare the results among many different samples, from multiple lineages, to identify subtle differences and patterns that would not be distinguishable otherwise.

Castoe's lab has their own in-house computers, but they fall short of what is needed to perform all of the studies the group is interested in working on.

"In terms of genome assemblies and the very intensive analyses we do, accessing larger resources from TACC is advantageous," Card says. "Certain things benefit substantially from the general output from TACC machines, but they also allow us to run 500 jobs at the same time, which speeds up the research process considerably."

A third computer-driven approach lets the team simulate the process of genetic evolution over millions of generations using synthetic biological data to deduce the rules of evolution, and to identify genes that may be important for adaptation.

For one such project, the team developed a new software tool called GppFst that allows researchers to differentiate genetic drift -- a neutral process whereby genes and gene sequences naturally change due to random mating within a population -- from genetic variations that are indicative of evolutionary changes caused by natural selection.

The tool uses simulations to statistically determine which changes are meaningful and can help biologists better understand the processes that underlie genetic variation. They described the tool in the May 2017 issue of Bioinformatics.

Lab members are able to access TACC resources through a unique initiative, called the University of Texas Research Cyberinfrastructure, which gives researchers from the state's 14 public universities and health centers access to TACC's systems and staff expertise.

"It's been integral to our research," said Richard Adams, another doctoral student in Castoe's group and the developer of GppFst. "We simulate large numbers of different evolutionary scenarios. For each, we want to have hundreds of replicates, which are required to fully vet our conclusions. There's no way to do that on our in-house systems. It would take 10 to 15 years to finish what we would need to do with our own machines -- frankly, it would be impossible without the use of TACC systems."

Though the roots of evolutionary biology can be found in field work and close observation, today, the field is deeply tied to computing, since the scale of genetic material -- tiny but voluminous -- cannot be viewed with the naked eye or put in order by an individual.

"The massive scale of genomes, together with rapid advances in gathering genome sequence information, has shifted the paradigm for many aspects of life science research," says Castoe.

Read more at Science Daily

Fossil holds new insights into how fish evolved onto land

University of Calgary Professor Jason Anderson, right, and doctoral student Jason Pardo published a paper in Nature about new insights into the ancient Scottish fossil called Lethiscus stocki.
"It's like a snake on the outside, but a fish on the inside."

The fossil of an early snake-like animal -- called Lethiscus stocki -- has kept its evolutionary secrets for the last 340-million years.

Now, an international team of researchers, led by the University of Calgary, has revealed new insights into the ancient Scottish fossil that dramatically challenge our understanding of the early evolution of tetrapods, or four-limbed animals with backbones.

Their findings have just been published in the research journal Nature. "It forces a radical rethink of what evolution was capable of among the first tetrapods," said project lead Jason Anderson, a paleontologist and Professor at the University of Calgary Faculty of Veterinary Medicine (UCVM).

Before this study, ancient tetrapods -- the ancestors of humans and other modern-day vertebrates -- were thought to have evolved very slowly from fish to animals with limbs.

"We used to think that the fin-to-limb transition was a slow evolution to becoming gradually less fish like," he said. "But Lethiscus shows immediate, and dramatic, evolutionary experimentation. The lineage shrunk in size, and lost limbs almost immediately after they first evolved. It's like a snake on the outside but a fish on the inside."

Lethicus' secrets revealed with 3D medical imaging

Using micro-computer tomography (CT) scanners and advanced computing software, Anderson and study lead author Jason Pardo, a doctoral student supervised by Anderson, got a close look at the internal anatomy of the fossilized Lethiscus. After reconstructing CT scans its entire skull was revealed, with extraordinary results.

"The anatomy didn't fit with our expectations," explains Pardo. "Many body structures didn't make sense in the context of amphibian or reptile anatomy." But the anatomy did make sense when it was compared to early fish.

"We could see the entirety of the skull. We could see where the brain was, the inner ear cavities. It was all extremely fish-like," explains Pardo, outlining anatomy that's common in fish but unknown in tetrapods except in the very first. The anatomy of the paddlefish, a modern fish with many primitive features, became a model for certain aspects of Lethiscus' anatomy.

Changing position on the tetrapod 'family tree'

When they included this new anatomical information into an analysis of its relationship to other animals, Lethiscus moved its position on the 'family tree', dropping into the earliest stages of the fin-to-limb transition. "It's a very satisfying result, having them among other animals that lived at the same time," says Anderson.

Read more at Science Daily

Lizard Penises Are Being Sold Online as Fake Mystical Plant Roots

Goodbye snake oil, hello lizard penis.

If you’ve bought a mythical Indian plant root recently, we’ve got bad news for you. Investigators and scientists from the London-based wildlife advocacy group World Animal Protection released a statement this week declaring that they have discovered hundreds of dessicated monitor lizard penises that scammers are passing off as prized tantric plant roots known as Hatha Jodi.

Hatha Jodi is found only in remote parts of Nepal and Central India. Because it is rare and supposedly very powerful, one root can retail for hundreds of dollars on Amazon, Etsy, and other major online retailers. Known for its distinctive shape that looks like two human hands clasped in prayer, the root reputedly offers mystical benefits to those who possess it, and is used in rituals to promote luck, happiness, and wealth.

But unwitting customers may in fact be praying to a less holy object. It appears that the anatomical features of the lizard's hemipenis, which features a bifurcation into a pair of sexual organs, resembles the two branches of Hatha Jodi — enabling one of the most peculiar frauds in the illicit animal trade.

“We were shocked at the sheer audacity and scale of this illegal wildlife trade,” Dr. Neil D’Cruze of the World Animal Protection remarked in the statement. “Deceitful dealers claiming to sell holy plant root labelled as ‘Hatha Jodi’ are in fact peddling dried lizard penis to their unwitting customers.”

The investigators also found that some supposed roots were just moldings made from the lizard’s penises. (Why not moldings made from the root itself? We may never know.)

In case you were wondering, the monitor lizards don’t survive the penis harvesting, according to the researchers. They are being illegally poached in contravention of the Indian Wildlife Protection Act, trapped and killed gruesomely before their penises are removed. The very unlucky ones are left alive for the removal process — though they don’t stay living for long.  

These lizards don’t exactly have a lot of penis to spare. All monitor lizards are a protected species in India, where killing and selling any part of the reptile is against the law. The yellow monitor and Bengal monitor species are also both listed under the Convention on the International Trade in Endangered Species of Flora and Fauna (CITES).

Read more at Discovery News

Jun 21, 2017

Ten near-Earth size planets in habitable zone of their star

NASA's Kepler space telescope team has identified 219 new planet candidates, 10 of which are near-Earth size and in the habitable zone of their star.
NASA's Kepler space telescope team has released a mission catalog of planet candidates that introduces 219 new planet candidates, 10 of which are near-Earth size and orbiting in their star's habitable zone, which is the range of distance from a star where liquid water could pool on the surface of a rocky planet.

This is the most comprehensive and detailed catalog release of candidate exoplanets, which are planets outside our solar system, from Kepler's first four years of data. It's also the final catalog from the spacecraft's view of the patch of sky in the Cygnus constellation.

With the release of this catalog, derived from data publicly available on the NASA Exoplanet Archive, there are now 4,034 planet candidates identified by Kepler. Of which, 2,335 have been verified as exoplanets. Of roughly 50 near-Earth size habitable zone candidates detected by Kepler, more than 30 have been verified.

Additionally, results using Kepler data suggest two distinct size groupings of small planets. Both results have significant implications for the search for life. The final Kepler catalog will serve as the foundation for more study to determine the prevalence and demographics of planets in the galaxy, while the discovery of the two distinct planetary populations shows that about half the planets we know of in the galaxy either have no surface, or lie beneath a deep, crushing atmosphere -- an environment unlikely to host life.

The findings were presented at a news conference Monday at NASA's Ames Research Center in California's Silicon Valley.

"The Kepler data set is unique, as it is the only one containing a population of these near Earth-analogs -- planets with roughly the same size and orbit as Earth," said Mario Perez, Kepler program scientist in the Astrophysics Division of NASA's Science Mission Directorate. "Understanding their frequency in the galaxy will help inform the design of future NASA missions to directly image another Earth."

The Kepler space telescope hunts for planets by detecting the minuscule drop in a star's brightness that occurs when a planet crosses in front of it, called a transit.

This is the eighth release of the Kepler candidate catalog, gathered by reprocessing the entire set of data from Kepler's observations during the first four years of its primary mission. This data will enable scientists to determine what planetary populations -- from rocky bodies the size of Earth, to gas giants the size of Jupiter -- make up the galaxy's planetary demographics.

To ensure a lot of planets weren't missed, the team introduced their own simulated planet transit signals into the data set and determined how many were correctly identified as planets. Then, they added data that appear to come from a planet, but were actually false signals, and checked how often the analysis mistook these for planet candidates. This work told them which types of planets were overcounted and which were undercounted by the Kepler team's data processing methods.

"This carefully-measured catalog is the foundation for directly answering one of astronomy's most compelling questions -- how many planets like our Earth are in the galaxy?" said Susan Thompson, Kepler research scientist for the SETI Institute in Mountain View, California, and lead author of the catalog study.

One research group took advantage of the Kepler data to make precise measurements of thousands of planets, revealing two distinct groups of small planets. The team found a clean division in the sizes of rocky, Earth-size planets and gaseous planets smaller than Neptune. Few planets were found between those groupings.

Using the W. M. Keck Observatory in Hawaii, the group measured the sizes of 1,300 stars in the Kepler field of view to determine the radii of 2,000 Kepler planets with exquisite precision.

"We like to think of this study as classifying planets in the same way that biologists identify new species of animals," said Benjamin Fulton, doctoral candidate at the University of Hawaii in Manoa, and lead author of the second study. "Finding two distinct groups of exoplanets is like discovering mammals and lizards make up distinct branches of a family tree."

It seems that nature commonly makes rocky planets up to about 75 percent bigger than Earth. For reasons scientists don't yet understand, about half of those planets take on a small amount of hydrogen and helium that dramatically swells their size, allowing them to "jump the gap" and join the population closer to Neptune's size.

The Kepler spacecraft continues to make observations in new patches of sky in its extended mission, searching for planets and studying a variety of interesting astronomical objects, from distant star clusters to objects such as the TRAPPIST-1 system of seven Earth-size planets, closer to home.

Read more at Science Daily

Massive dead disk galaxy challenges theories of galaxy evolution

This artist's concept shows what the young, dead, disk galaxy MACS2129-1, right, would look like when compared with the Milky Way galaxy, left. Although three times as massive as the Milky Way, it is only half the size. MACS2129-1 is also spinning more than twice as fast as the Milky Way. Note that regions of Milky Way are blue from bursts of star formation, while the young, dead galaxy is yellow, signifying an older star population and no new star birth.
By combining the power of a "natural lens" in space with the capability of NASA's Hubble Space Telescope, astronomers made a surprising discovery -- the first example of a compact yet massive, fast-spinning, disk-shaped galaxy that stopped making stars only a few billion years after the big bang.

Finding such a galaxy early in the history of the universe challenges the current understanding of how massive galaxies form and evolve, say researchers.

When Hubble photographed the galaxy, astronomers expected to see a chaotic ball of stars formed through galaxies merging together. Instead, they saw evidence that the stars were born in a pancake-shaped disk.

This is the first direct observational evidence that at least some of the earliest so-called "dead" galaxies -- where star formation stopped -- somehow evolve from a Milky Way-shaped disk into the giant elliptical galaxies we see today.

This is a surprise because elliptical galaxies contain older stars, while spiral galaxies typically contain younger blue stars. At least some of these early "dead" disk galaxies must have gone through major makeovers. They not only changed their structure, but also the motions of their stars to make a shape of an elliptical galaxy.

"This new insight may force us to rethink the whole cosmological context of how galaxies burn out early on and evolve into local elliptical-shaped galaxies," said study leader Sune Toft of the Dark Cosmology Center at the Niels Bohr Institute, University of Copenhagen, Denmark. "Perhaps we have been blind to the fact that early "dead" galaxies could in fact be disks, simply because we haven't been able to resolve them."

Previous studies of distant dead galaxies have assumed that their structure is similar to the local elliptical galaxies they will evolve into. Confirming this assumption in principle requires more powerful space telescopes than are currently available. However, through the phenomenon known as "gravitational lensing," a massive, foreground cluster of galaxies acts as a natural "zoom lens" in space by magnifying and stretching images of far more distant background galaxies. By joining this natural lens with the resolving power of Hubble, scientists were able to see into the center of the dead galaxy.

The remote galaxy is three times as massive as the Milky Way but only half the size. Rotational velocity measurements made with the European Southern Observatory's Very Large Telescope (VLT) showed that the disk galaxy is spinning more than twice as fast as the Milky Way.

Using archival data from the Cluster Lensing And Supernova survey with Hubble (CLASH), Toft and his team were able to determine the stellar mass, star-formation rate, and the ages of the stars.

Why this galaxy stopped forming stars is still unknown. It may be the result of an active galactic nucleus, where energy is gushing from a supermassive black hole. This energy inhibits star formation by heating the gas or expelling it from the galaxy. Or it may be the result of the cold gas streaming onto the galaxy being rapidly compressed and heated up, preventing it from cooling down into star-forming clouds in the galaxy's center.

But how do these young, massive, compact disks evolve into the elliptical galaxies we see in the present-day universe? "Probably through mergers," Toft said. "If these galaxies grow through merging with minor companions, and these minor companions come in large numbers and from all sorts of different angles onto the galaxy, this would eventually randomize the orbits of stars in the galaxies. You could also imagine major mergers. This would definitely also destroy the ordered motion of the stars."

The findings are published in the June 22 issue of the journal Nature. Toft and his team hope to use NASA's upcoming James Webb Space Telescope to look for a larger sample of such galaxies.

The Hubble Space Telescope is a project of international cooperation between NASA and ESA (European Space Agency). NASA's Goddard Space Flight Center in Greenbelt, Maryland, manages the telescope. The Space Telescope Science Institute (STScI) in Baltimore, Maryland, conducts Hubble science operations. STScI is operated for NASA by the Association of Universities for Research in Astronomy, Inc., in Washington, D.C.

Read more at Science Daily

Star's birth may have triggered another star birth, astronomers say

Protostar FIR 3 (HOPS 370) with outflow that may have triggered the formation of younger protostar FIR 4 (HOPS 108, location marked with red dot), in the Orion star-forming region. (au = astronomical unit, the distance from the Earth to the Sun, about 93 million miles.)
Astronomers using the National Science Foundation's Karl G. Jansky Very Large Array (VLA) have found new evidence suggesting that a jet of fast-moving material ejected from one young star may have triggered the formation of another, younger protostar.

"The orientation of the jet, the speed of its material, and the distance all are right for this scenario," said Mayra Osorio, of the Astrophysical Institute of Andalucia (IAA-CSIC) in Spain. Osorio is the lead author of a paper reporting the findings in the Astrophysical Journal.

The scientists studied a giant cloud of gas some 1,400 light-years from Earth in the constellation Orion, where numerous new stars are being formed. The region has been studied before, but Osorio and her colleagues carried out a series of VLA observations at different radio frequencies that revealed new details.

Images of the pair show that the younger protostar, called HOPS (Herschel Orion Protostar Survey) 108, lies in the path of the outflow from the older, called HOPS 370. This alignment led Yoshito Shimajiri and collaborators to suggest in 2008 that the shock of the fast-moving material hitting a clump of gas had triggered the clump's collapse into a protostar.

"We found knots of material within this outflow and were able to measure their speeds," said Ana K. Diaz-Rodriguez also of IAA-CSIC.

The new measurements gave important support to the idea that the older star's outflow had triggered the younger's star's formation process.

The scientists suggest that the jet from HOPS 370 (also known as FIR 3) began to hit the clump of gas about 100,000 years ago, starting the process of collapse that eventually led to the formation of HOPS 108 (also known as FIR 4). Four other young stars in the region also could be the result of similar interactions, but the researchers found evidence for shocks only in the case of HOPS 108.

While the evidence for this triggering scenario is strong, one fact appears to contradict it. The younger star seems to be moving rapidly in a way that indicates it should have been formed elsewhere, apart from the region impacted by the older star's outflow.

Read more at Science Daily

A wooden toe: Swiss Egyptologists study 3000-year-old prosthesis

Toe prosthesis of a female burial from the Theban tomb TT95, early first millennium BC. Egyptian Museum Cairo, JE100016a.
It is likely to be one of the oldest prosthetic devices in human history: Together with other experts, Egyptologists from the University of Basel have reexamined an artificial wooden big toe. The find is almost 3000 years old and was discovered in a female burial from the necropolis of Sheikh ´Abd el-Qurna close to Luxor. This area is currently being studied using state-of-the-art methods.

The international team investigated the one-of-a-kind prosthesis using modern microscopy, X-ray technology, and computer tomography. They were able to show that the wooden toe was refitted several times to the foot of its owner, a priest's daughter. The researchers also newly classified the used materials and identified the method with which the highly developed prosthesis was produced and utilized. Experts from the Egyptian Museum in Cairo -- where the prosthetic device was brought to after it had been found -- and the Institute of Evolutionary Medicine at the University of Zurich were also involved in this study.

The artificial toe from the early first millennium BC testifies to the skills of an artisan who was very familiar with the human physiognomy. The technical know-how can be seen particularly well in the mobility of the prosthetic extension and the robust structure of the belt strap. The fact that the prosthesis was made in such a laborious and meticulous manner indicates that the owner valued a natural look, aesthetics and wearing comfort and that she was able to count on highly qualified specialists to provide this.

Life histories of a burial ground

The prosthesis from the Early Iron Age was found in a plundered shaft tomb that was cut into the bedrock of an older, long time idle burial chapel at the graveyard hill of Sheikh ´Abd el-Qurna to the west of Luxor. This chapel belongs to a group of monumental rock-cut tombs from the late 15th century BC which were built for a small upper class that was close to the royal family. Since the end of 2015, the University of Basel has been studying this ancient Egyptian elite cemetery, its long history of usage, and surroundings.

For this project, funded by the Swiss National Science Foundation, microanalytic, scientifically oriented methods, as well as precision technology for surveying and photography were used. The researchers are looking into the materiality of archaeological remains and are thus gaining insight into the life histories of building structures and objects. These material biographies can provide information about the manufacturing practices, usages, personal skills, habits and preferences of people who were in contact with these objects.

A necropolis in 3-D

The oldest known tombs from Sheikh ´Abd el-Qurna date back to the early second millennium BC. The cemetery saw its heyday in the 15th century BC. However, many of these rock-cut structures were reused and in parts remodeled several times for burials during the first millennium BC. Much later, they served as dwellings mostly for locals -- a process that began with the early Christian hermits and only ended in the early 20th century.

Read more at Science Daily

Reconstruction of ancient chromosomes offers insight into mammalian evolution

Numbers on red branches from the first eutherian ancestor to Homo sapiens are the numbers of breakpoints in reconstructed ancestral chromosome fragments. Breakpoints are locations where a chromosome broke open, allowing for rearrangements. The number of breakpoints per million years is in parentheses. A total of 162 chromosomal breakpoints were identified between the eutherian ancestor and the formation of humans as a species.
What if researchers could go back in time 105 million years and accurately sequence the chromosomes of the first placental mammal? What would it reveal about evolution and modern mammals, including humans?

In a study published this week in Proceedings of the National Academy of Sciences, researchers have gone back in time, at least virtually, computationally recreating the chromosomes of the first eutherian mammal, the long-extinct, shrewlike ancestor of all placental mammals.

"The revolution in DNA sequencing has provided us with enough chromosome-scale genome assemblies to permit the computational reconstruction of the eutherian ancestor, as well as other key ancestors along the lineage leading to modern humans," said Harris Lewin, a lead author of the study and a professor of evolution and ecology and Robert and Rosabel Osborne Endowed Chair at the University of California, Davis.

"We now understand the major steps of chromosomal evolution that led to the genome organization of more than half the existing orders of mammals. These studies will allow us to determine the role of chromosome rearrangements in the formation of new mammal species and how such rearrangements result in adaptive changes that are specific to the different mammalian lineages," said Lewin.

The findings also have broad implications for understanding how chromosomal rearrangements over millions of years may contribute to human diseases, such as cancer.

"By gaining a better understanding of the relationship between evolutionary breakpoints and cancer breakpoints, the essential molecular features of chromosomes that lead to their instability can be revealed," said Lewin. "Our studies can be extended to the early detection of cancer by identifying diagnostic chromosome rearrangements in humans and other animals, and possibly novel targets for personalized therapy."

Descrambling chromosomes

To recreate the chromosomes of these ancient relatives, the team began with the sequenced genomes of 19 existing placental mammals -- all eutherian descendants -- including human, goat, dog, orangutan, cattle, mouse and chimpanzee, among others.

The researchers then utilized a new algorithm they developed called DESCHRAMBLER. The algorithm computed ("descrambled") the most likely order and orientation of 2,404 chromosome fragments that were common among the 19 placental mammals' genomes.

"It is the largest and most comprehensive such analysis performed to date, and DESCHRAMBLER was shown to produce highly accurate reconstructions using data simulation and by benchmarking it against other reconstruction tools," said Jian Ma, the study's co-senior author and an associate professor of computational biology at Carnegie Mellon University in Pittsburgh.

In addition to the eutherian ancestor, reconstructions were made for the six other ancestral genomes on the human evolutionary tree: boreoeutherian, euarchontoglires, simian (primates), catarrhini (Old World monkeys), great apes and human-chimpanzee. The reconstructions give a detailed picture of the various chromosomal changes -- translocations, inversions, fissions and other complex rearrangements -- that have occurred over the 105 million years between the first mammal and Homo sapiens.

Rates of evolution vary

One discovery is that the first eutherian ancestor likely had 42 chromosomes, four less than humans. Researchers identified 162 chromosomal breakpoints -- locations where a chromosome broke open, allowing for rearrangements -- between the eutherian ancestor and the formation of humans as a species.

The rates of evolution of ancestral chromosomes differed greatly among the different mammal lineages. But some chromosomes remained extremely stable over time. For example, six of the reconstructed eutherian ancestral chromosomes showed no rearrangements for almost 100 million years until the appearance of the common ancestor of human and chimpanzee.

Orangutan chromosomes were found to be the slowest evolving of all primates and still retain eight chromosomes that have not changed much with respect to gene order orientation as compared with the eutherian ancestor. In contrast, the lineage leading to chimpanzees had the highest rate of chromosome rearrangements among primates.

"When chromosomes rearrange, new genes and regulatory elements may form that alter the regulation of expression of hundreds of genes, or more. At least some of these events may be responsible for the major phenotypic differences we observe between the mammal orders," said Denis Larkin, co-senior author of the study and a reader in comparative genomics at the Royal Veterinary College at the University of London.

Read more at Science Daily

Jun 19, 2017

Cells that make blood vessels can also make tumors and enable their spread

Dr. Lan Ko, cancer biologist in the Department of Pathology at MCG at Augusta University and Dr. Ali S. Arbab, a tumor angiogenesis expert at the Georgia Cancer Center and the MCG Department of Biochemistry and Molecular Biology, was a major collaborator.
While it's widely held that tumors can produce blood vessels to support their growth, scientists now have evidence that cells key to blood vessel formation can also produce tumors and enable their spread.

"Today we actually propose that blood vessels can form tumors and then the whole picture becomes a cycle," said Dr. Lan Ko, cancer biologist in the Department of Pathology at the Medical College of Georgia at Augusta University.

Ko is corresponding author of the study in the journal Oncotarget that provides some of the first evidence of the vicious cycle that appears to support cancer but also provides a potential new target for interference.

Dr. Ali S. Arbab, a tumor angiogenesis expert at the Georgia Cancer Center and the MCG Department of Biochemistry and Molecular Biology, was a major collaborator.

Pericytes are strong contractile cells that form the initial outer layer that gives shape and strength to a developing blood vessel. They also are stem-cell like in that they can make many different kinds of tissue. GT198 is a gene normally expressed in low levels in our bodies and known for its natural ability to repair DNA and regulate stem cells, but can become an oncogene when mutated.

Scientists have now found abnormally high levels of GT198 in the pericytes of the vascular network supporting a wide variety of human tumors. When activated, GT198 was also oddly located in the pericytes' cytoplasm rather than the nucleus.

They documented these high GT198-expressing pericytes in 14 different human cancers, including brain, lung, kidney, thyroid, prostate and bladder cancers. They documented their presence as well in six different animal models of a variety of cancers.

They also noted an additional and dangerous role for these malignant pericytes.

In human oral cancer, for example, they found malignant pericytes were abnormally thick and abundant in the blood vessel walls. Pericytes also proliferated into tumor cells and even detached from blood vessels apparently to enable the cancer's spread, the scientists report.

"Blood vessels can actually make tumors," Ko said. "This is a bit of a new idea that does not negate the fact that tumors also make blood vessels. But we believe instead provides the other half of the story."

Even in advanced tumors, the pericytes continued to make tumor cells. In this scenario, the highest level of GT198 expression was associated with decreased patient survival in the 40 patients whose tissues and clinical outcomes they examined. By contrast, GT198 expression was essentially nonexistent in normal oral cavity tissue that did not have this abnormal proliferation of blood vessels.

In an animal model of the aggressive brain tumor glioblastoma, they saw malignant pericytes from human tumors wrap around endothelial cells, as they would to form blood vessels, but they also formed tumors.

Malignant pericytes made a huge number of blood vessels as they captured the normal endothelial cells, and then prompted the endothelial cells to keep growing as well. Some of the small vessels or capillaries became larger tumor-lined blood vessels and then tumors. The scientists noted the passageway, or lumen, of the former blood vessels were still visible in some tumors. In a normal scenario, pericytes actually help control growth, Ko noted.

When they gave what was essentially a vaccine against GT198, it delayed tumor growth and prolonged mouse survival.

Together the new findings point toward GT198 as an efficient and effective cancer treatment target, said Ko. She is looking further at existing cancer drugs, which she has found directly target GT198, and exploring natural new ones.

Read more at Science Daily

The Family Tree of Exoplanets Has Just Divided Into Two Branches

This sketch illustrates a family tree of exoplanets. Planets are born out of swirling disks of gas and dust called protoplanetary disks. The disks give rise to giant planets like Jupiter as well as smaller planets mostly between the sizes of Earth and Neptune. Researchers using data from the W. M. Keck Observatory and NASA's Kepler mission discovered that the smaller planets can be cleanly divided into two size groups: the rocky Earth-like planets and super-Earths, and the gaseous mini-Neptunes.
Scientists have reorganized the exoplanetary tree of life into two distinct branches. Most exoplanets discovered so far are close in size to Earth or either Neptune, according to a new study led by the California Institute of Technology. But astronomers are puzzled as to why there is a gap between these two planetary sizes.

The work, which is based on an analysis of thousands of known exoplanets, shows that planets in our galaxy overwhelmingly fall into two groups. The first includes rocky planets up to 1.75 times the size of Earth, and the second group is made up of gaseous Neptune-like worlds between 2 to 3.5 times the size of Earth. (Neptune, by comparison, is roughly 4 times the size of Earth.)

The work includes data from NASA’s Kepler space telescope, which searches for Earth-like worlds in the habitable zones of their stars, and the W. M. Keck Observatory, which detects planets using the High Resolution Echelle Spectrometer (HIRES) on the Keck I telescope. The researchers attempted to classify these planets similarly to how biologists classify animal species.

“This is a major new division in the family tree of planets, analogous to discovering that mammals and lizards are distinct branches on the tree of life,” said Andrew Howard, professor of astronomy at Caltech and principal investigator of the new research, in a statement.

“In the solar system, there are no planets with sizes between Earth and Neptune,” added Erik Petigura, co-author of the study and a Hubble postdoctoral fellow at Caltech. “One of the great surprises from Kepler is that nearly every star has at least one planet larger than Earth but smaller than Neptune. We’d really like to know what these mysterious planets are like and why we don’t have them in our own solar system.”

A study based on the research will be published in The Astronomical Journal and a preprint version is available now in preprint version on Arxiv. The study itself is led by B.J. Fulton, a graduate student in Howard’s group who works at both Caltech and the Institute of Astronomy at the University of Hawaii.

“Astronomers like to put things in buckets,” Fulton remarked. “In this case, we have found two very distinct buckets for the majority of the Kepler planets.”

Classifying planets

The first planet around a sun-like star was discovered in the mid-1990s. Today, there are nearly 3,500 confirmed exoplanets, with thousands more yet to be confirmed. Most of these were found by Kepler, which began its mission by staring at a fixed spot in the Cygnus constellation. Kepler monitored the stars for telltale dips of light as planets passed in front of the stars.

After the mission was no longer able to point consistently due to failing gyroscopes, Kepler began a new mission in 2013 called “K2”, where it rotates its view several times a year. It still is discovering exoplanets, but at a lower rate than before.

The Kepler catalog mostly includes planets that are very close in to their stars. Previously, the planets discovered by Kepler were known to be between the size of Earth and Neptune – but no distinct groups were known until data from the Keck telescope was used.

In general, as a planet passes in front of a star, the size of the “dip” in starlight is correlated with the size of the planet. However, to understand the size of the planet, astronomers must also know the size of the parent stars. Obtaining that information required the services of Keck, which obtained spectral data on the parent stars. The spectral data provided measurements of the stars’ sizes, which in turn, yielded more precise sizes for the planets passing in front of each star.

“Before, sorting the planets by size was like trying to sort grains of sand with your naked eye,” said Fulton. “Getting the spectra from Keck is like going out and grabbing a magnifying glass. We could see details that we couldn’t before.”

Minding the gap

The information from Keck yielded the sizes of these planets with four times more precision than what was available before. The new distribution revealed a gap between rocky Earths and mini-Neptunes. While scientists are still investigating what causes the gap in planetary sizes, they have two possible explanations.

One explanation could be that many planets are naturally Earth-sized and remain at their original size, while other ones — for reasons that are still poorly understood — acquire a lot of gassy mas.

“A little bit of hydrogen and helium gas goes a very long way. So, if a planet acquires only 1 percent of hydrogen and helium in mass, that’s enough to jump the gap,” said Howard. “These planets are like rocks with big balloons of gas around them. The hydrogen and helium that’s in the balloon doesn’t really contribute to the mass of the system as a whole, but it contributes to the volume in a tremendous way, making the planets a lot bigger in size.”

Alternatively, the gap may exist because planets that are between super-Earth and mini-Neptune size see their gas burned off when they are exposed to radiation from their parent star.

“A planet would have to get lucky to land in the gap, and then if it did, it probably wouldn’t stay there,” said Howard. “It’s unlikely for a planet to have just the right amount of gas to land in the gap. And those planets that do have enough gas can have their thin atmospheres blown off. Both scenarios likely carve out the gap in planet sizes that we observe.”

The researchers plan more study to look at the heavy elements in each planet to learn more about the worlds’ composition, which would in turn refine the predictions about how these planets are formed.

Read more at Discovery News

Massive Volcanic Eruptions Triggered the Dinosaur Age

An artists depiction of a dinosaur and other animals escaping from an erupting volcano 235 million years ago in northwestern Argentina. Around 35 million years earlier, researchers believe that volcanic eruptions triggered the dawn of dinosaurs.
Intense volcanic eruptions, along with a devastating meteor strike, likely contributed to the extinction of non-avian dinosaurs around 66.5 million years ago. Now new research shows that volcanic eruptions at the end of the Triassic period (252–201 million years ago) triggered the Dinosaur Age, meaning these animals were bookended by some of Earth’s most extreme and fiery conditions.

The new evidence for volcanism, reported in the journal Proceedings of the National Academy of Sciences, corroborates earlier studies suggesting multiple volcanic eruptions occurred over a long period approximately 200–201 million years ago.

“The total duration of the end-Triassic volcanism is at least 700,000 years, and our paper supports the hypothesis that volcanic activity occurred on-and-off over that time, rather than being continuous for 700,000 years,” lead author Lawrence Percival of the University of Oxford said.

“How long the individual mega eruptions lasted isn’t something we can really answer at this time, but it is likely, based on other studies, that they would have lasted years–decades, with groups of such mega eruptions lasting hundreds–thousands of years,” he added.

Percival, along with colleagues Micha Ruhl, Stephen Hesselbo, Hugh Jenkyns, Tamsin Mather, and Jessica Whiteside, analyzed volcanic rocks and sediments dating to the latter part of the Triassic. The materials were sourced from the UK, Austria, Argentina, Greenland, Canada, and Morocco.

The field site in Morocco, where evidence for end-Triassic volcanism was found.
While studying these rocks and sediments, which once covered a huge area spanning four continents, the scientists focused on mercury content. They explained that volcanoes give off mercury gas emissions, which accumulates in sediments.

Their investigation found that nearly all of the sediment deposits showed large increases in mercury content beginning at the end-Triassic point in history.

“The mercury concentrations are shown to be in sediments of the same age as hugely extensive lava flows, further strengthening the case for volcanism being the source of this mercury,” Percival said.

He continued that the mercury increase was found to occur in the same sediments that record increased carbon dioxide during the end of the Triassic, supporting a volcanic origin for both gases.

This period further coincides with the end-Triassic mass extinction, which was once of the largest extinctions of animal life on record. Its long casualty list, including large crocodile-like reptiles and several marine invertebrates, amounted to around 76 percent of all terrestrial and marine species. The mass extinction also caused tremendous changes to land vegetation.

On the upside, it was during this time of death and destruction that dinosaur evolution really took off. Dinosaurs, which first emerged around 230 million years ago, were able to fill ecological niches left behind by the animals that went extinct. Some early mammals and amphibians benefitted from the food chain vacancies, too.  

As for how volcanism impacted the end-Triassic environment, Percival said, “The favored model is typically a short, sharp period of intense global cooling due to the initial release of sulphur aerosols and ash into the atmosphere, partly blocking sunlight, followed by more prolonged global warming caused by long-term volcanic carbon dioxide release.”

If Triassic animals like the giant croc-resembling reptiles were not directly burned to a crisp, they would have then experienced horrific climatic conditions challenging, and then ultimately ending, their existence.

Now two big questions remain. The first is: If the non-avian dinosaurs survived the end-Triassic volcanism, why did volcanic activity at the end-Cretaceous help to wipe them out? The researchers are not sure, but believe that the meteor impact 65.5 million years ago was a game changer, and that ecological factors were different during each extinction episode.

An artist’s recreation of the extinction of dinosaurs in the Deccan Traps of Western Ghats, India.
The second question is: If widespread volcanic activity coincided with two of the worst mass extinctions on Earth, could such massive eruptions happen again?

The researchers said that most of the huge volcanic events that took place over the past 200 million years on our planet were linked to the breakup of the supercontinent Pangea. Throughout the Dinosaur Age, Pangea continued to split into the continents seen today, and almost every split shows evidence for tremendous volcanism. Africa and South America, for example, retain evidence of similar lava flows of the same age preserved on their Atlantic coasts.

Read more at Discovery News

DNA Reveals How Domestic Cats Conquered the World

Domestic cats live on all continents except Antarctica, and thrive in Earth’s most remote regions. The evolutionary success of cats is unquestioned, and yet few major differences appear to exist between these furry dynamos and their wild counterparts.

New genetic analysis of domestic cats spanning the last 9,000 years helps to explain how a few sleek wildcat lineages discovered humans, outcompeted other animals, expanded across the globe, and became the seemingly tame couch surfers common today to many homes. The findings are published in the journal Nature Ecology & Evolution.

One of first great feline achievements was to replace other species that figured out human settlements were a great source of food.

“For example, in Roman society, the weasel was quite popular, in particular as a pest control agent, but cats took over, which may be due to the fact that their hunting strategy, ambushing, is better adapted to towns,” lead author Claudio Ottoni said. “The success of cats might be linked to the evolution of their more ‘friendly’ attitude to humans, which we speculate might have evolved in the Egyptian society.”

Ottoni, a scientist specializing in biomolecular archaeology and paleogenetics at the University of Leuven, and his colleagues analyzed the DNA of 200 domestic cats representing various time periods over the last 9,000 years. The researchers focused on two purported early centers of cat domestication: the Near East and Egypt. Feline remains included in the study were found in Europe, north and east Africa, and southwest Asia.

Attempts to trace cat lineages have been made before, but co-author Thierry Grange of CNRS and Paris Diderot University said that the new large-scale study was made possible by the development in recent years of molecular biology techniques. These methods permitted the screening of large numbers of genetic samples coming from areas with climatic conditions that are not favorable for DNA preservation, such as parts of the Arabic world and Egypt.

As for why the 9000-year mark is important, senior author Eva-Maria Geigl, also from CNRS and Paris Diderot University, explained that cat remains found in earlier Paleolithic sites are scarce. She suspects that humans might have hunted wildcats (Felis silvestris) for fur or food, but it is unclear what the precise interactions were then.

The cat goddess Bastet, bronze statue. Egyptian civilisation, Saite period (XXVI Dynasty), 672-525 BC.
DNA and archaeological evidence suggest that wildcats were drawn to early human settlements tied to the dawn of agriculture. Food storage sites attracted rodents and other small mammals that, in turn, attracted predatory wildcats. What began as a commensal relationship with humans then evolved into something more complex.

“From our data, we can deduce that the cat was tamed, or at least started to live with humans, in the Near East at least 6,500 years ago,” Geigl said. “We can also deduce that there was a second [domestication] event taking place in Egypt where another cat lineage was tamed and spread in the Eastern Mediterranean during the first millennium BC.”

The researchers identified these two distinct lineages of Felis silvestris as subclade IV-A and IV-C. Intriguingly most domestic cats alive today are related to these lineages. This means that the majority of cats today have ancestry that traces back to Southwest Asia (a region consisting of Turkey, Syria, Iraq, Jordan, Saudi Arabia, and the other nations of the Arabian Peninsula) and Egypt.

The scientists also identified other lineages at lower frequencies in both early and modern cat DNA. The genetic evidence suggests that domestic cats over the years have bred with local wildcats, resulting in everything from the now-extinct Mexican hairless cat to the Siamese, which derived from a feline native to Thailand.

Key to the global spread of cats were early shipping trade routes.
The scientists found evidence for Indian cats at a Roman site in Egypt, which Geigl said “strongly suggests large distance spread of ships’ cats.” The researchers also found DNA evidence for the Egyptian feline lineage in Viking ports along the Baltic Sea. Just as felines discovered the perks of human farming settlements, they also discovered the benefits of boating life.

“It was probably the availability of fishes that attracted them to the ports, where they got embarked on ships,” Grange said. “There, they could feast on fish and rodents!”

Humans must have quickly recognized the benefits of keeping a mouse chaser on board their ships, such that mariners then intentionally brought cats along on trips.

Some wildcats are known as “fishing cats,” but this behavior is not tied to Felis silvestris. Future analysis of feline DNA could reveal if some domestic cat lineages were exposed to a more fish-based diet than others, perhaps helping to explain why some kitties today have greater seafood cravings.

Another finding of the study is that one of the first cats bred for visual traits is the tabby, referring to domestic cats that sport distinctive stripes, dots, lines or swirling patterns, usually together with an “M” mark on the forehead. The oldest occurrence of the allele for a recessive mutation associated with domestic tabby populations was found in cat remains unearthed in the Ottoman Empire of southwest Asia. They date to the Middle Ages.

A pair of mackerel tabby cats.
Other early breeds include the Siamese and Birman, which were mentioned in writings by Buddhist monks in the 14th century. These are considered to be “natural breeds,” however, since they arose due to isolation of certain distinctive-looking local cat populations.

“Most of the domestic fancy breeds described nowadays were created by human intervention only in the 19th century,” Ottoni said. “The first exhibition of fancy breed cats took place in 1871 in London.”

He and his colleagues think that before then, cats were valued more for their behavioral traits rather than for their aesthetics. Nevertheless, the beauty and often graceful movements of cats seemed to be noticed by early artists and political leaders. Ancient Egyptians even adorned representations of felines with earrings, and connected them to the goddess Bastet. This gave felines an even greater regal appearance in statues and other objects.

Read more at Discovery News

Jun 18, 2017

Injured bones reconstructed by gene and stem cell therapies

Illustration shows the bone-tissue engineering technique developed by Cedars-Sinai investigators. "Endogenous MSCs" refers to stem cells from a patient's bone. The "BMP gene" is a gene that promotes bone repair.
A Cedars-Sinai-led team of investigators has successfully repaired severe limb fractures in laboratory animals with an innovative technique that cues bone to regrow its own tissue. If found to be safe and effective in humans, the pioneering method of combining ultrasound, stem cell and gene therapies could eventually replace grafting as a way to mend severely broken bones.

"We are just at the beginning of a revolution in orthopedics," said Dan Gazit, PhD, DMD, co-director of the Skeletal Regeneration and Stem Cell Therapy Program in the Department of Surgery and the Cedars-Sinai Board of Governors Regenerative Medicine Institute. "We're combining an engineering approach with a biological approach to advance regenerative engineering, which we believe is the future of medicine."

Gazit was the principal investigator and co-senior author of the research study, published in the journal Science Translational Medicine.

More than 2 million bone grafts, frequently necessitated by severe injuries involving traffic accidents, war or tumor removal, are performed worldwide each year. Such injuries can create gaps between the edges of a fracture that are too large for the bone to bridge on its own. The grafts require implanting pieces from either the patient's or a donor's bone into the gap.

"Unfortunately, bone grafts carry disadvantages," said Gazit, a professor of surgery at Cedars-Sinai. "There are huge unmet needs in skeleton repair."

One problem is that enough healthy bone is not always available for repairs. Surgeries to remove a bone piece, typically from the pelvis, and implant it can lead to prolonged pain and expensive, lengthy hospitalizations. Further, grafts from donors may not integrate or grow properly, causing the repair to fail.

The new technique developed by the Cedars-Sinai-led team could provide a much-needed alternative to bone grafts.

In their experiment, the investigators constructed a matrix of collagen, a protein the body uses to build bones, and implanted it in the gap between the two sides of a fractured leg bone in laboratory animals. This matrix recruited the fractured leg's own stem cells into the gap over a period of two weeks. To initiate the bone repair process, the team delivered a bone-inducing gene directly into the stem cells, using an ultrasound pulse and microbubbles that facilitated the entry of the gene into the cells.

Eight weeks after the surgery, the bone gap was closed and the leg fracture was healed in all the laboratory animals that received the treatment. Tests showed that the bone grown in the gap was as strong as that produced by surgical bone grafts, said Gadi Pelled, PhD, DMD, assistant professor of surgery at Cedars-Sinai and the study's co-senior author.

"This study is the first to demonstrate that ultrasound-mediated gene delivery to an animal's own stem cells can effectively be used to treat nonhealing bone fractures," Pelled said. "It addresses a major orthopedic unmet need and offers new possibilities for clinical translation."

The study involved six departments at Cedars-Sinai, plus investigators from Hebrew University in Jerusalem; the University of Rochester in Rochester, New York; and the University of California, Davis.

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Southern California mountain lions' genetic connectivity dangerously low

This female mountain lion, known as F52, was collared in the Santa Ana range. She later died near a busy highway of unknown causes. Mountain lions in the Santa Ana range are effectively cut off from those on the other side of I-15, which strongly contributes to their genetic decay.
If a dangerously inbred puma population in Southern California is to survive in the future, an urgent need for genetic connectivity must be met, according to two scientific papers from a team of researchers coordinated by the University of California, Davis, and involving scientists at the University of Wyoming and the University of Massachusetts-Amherst.

The first paper, published in the journal Royal Society Open Science in May, reports that the puma population of about 20 adults in the Santa Ana Mountains has the lowest genetic diversity ever reported for pumas besides the Florida panther, which nearly went extinct from genetic causes.

The pumas' isolation is primarily due to surrounding urbanization from Los Angeles and San Diego.

"The only hope for puma movements in and out of the Santa Ana Mountains is to cross I-15 -- an eight- to 10-lane interstate highway -- which poses a major barrier for pumas attempting to migrate between the Santa Ana Mountains and the rural Eastern Peninsular Mountains," said lead author Kyle Gustafson, a postdoctoral conservation geneticist from the University of Wyoming.

University of Wyoming researchers conducted genetic analyses of both radiocollared and uncollared pumas to develop a multigeneration pedigree. This showed where pumas and their offspring were born, and whether they successfully migrated and reproduced after crossing I-15, which separates the Santa Ana Mountains from other mountain ranges to the east.

The Power of One

Although seven males crossed I-15 over the past 20 years, only one -- male puma #86 (M86) -- was able to successfully produce offspring in the Santa Anas after migrating from the genetically diverse population to the east. By producing a total of 11 detected offspring, M86 rapidly disseminated unique genes into the inbred population, which reduced the level of inbreeding and significantly increased genetic diversity.

Unfortunately, M86 was hit by a car between 2014 and 2015, and more than half of his offspring are either now deceased or in captivity.

"This is consistent with mortality rates we found previously in the region," said Winston Vickers, a wildlife veterinarian from UC Davis' Karen C. Drayer Wildlife Health Center who conducted most of the field research. "Only one other migrant, named M119, remains in the Santa Ana Mountains, but whether he is alive or produced offspring is uncertain."

Senior author Holly Ernest, a wildlife population geneticist and research veterinarian at the University of Wyoming, said that by introducing new genetic material and raising the level of genetic diversity in this population, that single male mountain lion, M86, performed what amounts to a "genetic rescue."

"Our study also shows how quickly his genetics were lost by high mortality levels of his offspring," Ernest said. "A message here is that this population needs help to regain healthy genetics and persist in the Southern California landscape. That help can come in the form of just a few individuals over time adding 'new blood' to the population."

Connectivity is Key

The second paper, published this week in the journal PLOS ONE, provides a potential solution to this issue. In it, the researchers propose a conservation network for pumas spanning the Santa Ana Mountains and the Eastern Peninsular Mountains.

Using genetic data and data from GPS radio-collared pumas, this analysis identified critical habitat patches, movement corridors, and key road crossing locations across I-15 that would allow pumas to persist and increase genetic diversity.

"Without continued emigration into the Santa Ana Mountains by pumas coming from the east of I-15, eroding genetic diversity and continued inbreeding are expected to resume," said veterinarian Walter Boyce, co-director of the Wildlife Health Center's Southern California Mountain Lion Study with Vickers.

Protected areas in Southern California currently cover about 50 percent of this proposed puma conservation network. Incorporating key new areas in Orange, Riverside and San Diego counties would increase the protected areas to nearly 80 percent. Habitat protection, coupled with wildlife crossing structures and wildlife fencing, will be needed to promote the safe passage of pumas across I-15 and ensure adequate gene flow.

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