Monday, February 18, 2019

20,000 Year Old Events Affecting Disease Transmission Today

When the last Ice Age reached its maximum size, events were happening in Africa, that affect us today. 

A genomic analysis suggests African hunting and gathering groups diverged from a common ancestry, and underscores the role of infectious disease and diet as drivers of local adaptation

Languages that involve "clicks" are relatively rare worldwide but are spoken by several groups in Africa. The Khoisan language family includes a handful of these click languages, spoken by hunter-gatherer groups in southern and eastern Africa. But the grouping of these populations into a single language family has been controversial, with some linguists convinced that a few of the languages are too different to be classified together.

With the help of a local translator, Simon Thompson from Sarah Tishkoff's lab (University of Pennsylvania) and Dawit Wolde-Meskel (collaborator from Addis Ababa University) explain the research project on African population genetics to the Argobba population, Ethiopia. After the project is presented, the researchers answer any questions.

Credit: Tishkoff lab


A genomic study of 50 African populations led by researchers at the University of Pennsylvania adds some clarity to the relationships between these click-speaking groups and many others. The results point to a relatively recent shared ancestry for a few of the click-speaking hunter-gatherer populations, indicating they are more closely related to one another than to their neighbors that practice other subsistence lifestyles, such as farming or animal herding.

The analysis, one of the most extensive of its kind of ethnically diverse populations in Africa, also demonstrates the importance of infectious disease, immunity, and diet in shaping the diversity of popluations across Africa. The work is published in the journal Proceedings of the National Academy of Sciences.

"It's very rare to have a study of this many groups that are genetically different in terms of ancestry, in their susbsistence patterns, and are geographicaly dispersed as well," says Sarah Tishkoff, a geneticist and Penn Integrates Knowledge Professor who was the senior author on the paper. "This allows us to characterize population structure and demographic history as well as to look at signatures of natural selection acting on these populations."

The analysis builds upon decades of work by the Tishkoff lab and African collaborators to explore African genetic diversity. The research, says Tishkoff, facilitates genomics research overall by examining populations that have been otherwise understudied, and it can play a role in identifying genetic variants that influence health and disease in Africa and around the world.

This study probes deeply into the genomic landscape of 840 Africans, identifying 621,000 separate nucleotides in the DNA of each participant.

The 50 groups surveyed are spread across sub-Saharan Africa and include almost all groups that practice a hunting-and-gathering lifestyle, or have until recently.

Tishkoff, Scheinfeldt, and colleagues were particularly interested in what these study participants' genomes would reveal about ancient relationships among hunter-gatherer populations, particularly those speaking languages that had been classified as Khoisan. East Africa's Hadza and Sandawe hunter-gatherers had been labeled Khoisan by some linguistic analyses, grouped with southern Africa's San hunter-gatherers.

"Some linguists say it's not correct to place all of these into the Khoisan family, arguing that the Hadza and Sandawe languages are so different from each other and from the San that they really should be in separate language classifications," says Tishkoff.

The researchers also included study participants from the Dahalo of Ethiopia, who have never been studied genetically but speak a language with remnant clicks. "It's an ongoing question in linguistics and genetics," Tishkoff says, "and we wanted to ask the question, 'Do these groups with click phonemes have a common genetic ancestry?'"

They were also curious to know whether a shared subsistence lifestyle practice--that of hunting and gathering--indicated a shared ancestry. Among the 16 hunter-gatherer populations they studied was a group called the Sabue who live in southwestern Ethiopia, surrounded by pastoralist groups. The Sabue had never before participated in genomic research and speak a language that is thus far unclassified.

Using the genetic information they obtained to map out the populations' likely relationships to one another, the researchers unexpectedly found that four hunter-gatherer populations--the Hadza, Sandawe, Dahalo, and Sabue, each of whom dwell in distinct areas of eastern Africa--clustered together.

"Typically what we see is that populations cluster by geography, but here we're seeing an exception to that," Tishkoff says. "Here you have three groups that either speak a click language, have remnant clicks, or have an unclassified language, and they're showing a common ancestry even though they're spread across different countries."

Although the researchers could not identify a uniquely shared ancestry between these four groups of eastern African Khoisan hunter-gatherers and the southern African San people, who also speak a language with clicks, they did observe shared ancestry between the San and rainforest hunter-gatherers from Central Africa, despite being geographically far apart.

In contrast, other hunter-gatherer groups, such as the Wata, El Molo, and Yaaku, appeared more genetically similar to neighboring agriculturalist and pastorlist groups.

The common ancestry for the four East Africa hunter-gatherer groups dates back more than 20,000 years ago, according to the team's analysis, around the beginning of the last glacial maximum, when ice covered extensive portions of Earth and the climate was much different than it is today.

"The idea is that this may have changed environmental conditions and introduced a barrier between populations," says Laura Scheinfeldt, the lead author who was a research associate in Tishkoff's lab, and is now with the Coriell Institute for Medical Research.

The researchers' techniques also allowed for a better understanding of the forces that have acted to differentiate the groups they studied.

"What we found was the strongest signatures of adaptation tended to be population-specific," says Scheinfeldt. In other words, targets of natural selection were different in the different groups and may well have contributed to the uniqueness of each.

Despite these individual differences, the categories of the genes that were selected were shared among populations, the researchers discovered.

"Genes involved in immune responses, diet, and metabolism were the broad categories that we saw coming up over and over again," Scheinfeldt notes. "We know infectious disease in general is a very strong pressure, and, when you look solely at how prevalent malaria is, that also explains some of the patterns we see in adaptive signatures. Just that one disease is a very strong selective pressure."

In future studies, Tishkoff and colleagues will be zooming in to see how particular genetic variants may affect physical traits in the people who possess them, studies that could shed light on genetic causes of disease susceptibility. They'll also be using powerful whole-genome sequencing techniques to further illuminate the relationships among Africa's diverse populations.

Tishkoff and Scheinfeldt's coauthors on the study were Penn's Sameer Soi, Charla Lambert, Wen-Ya Ko, Aoua Coulibaly, Alessia Ranciaro, Simon Thompson, Jibril Hirbo, William Beggs, and Junhyong Kim; the University of Khartoum's Muntaser Ibrahim; St. Joseph University College of Health Sciences' Thomas Nyambo; the Kenya Medical Research Institute's Sabah Omar; Addis Ababa University's Dawit Woldemeskel and Gurja Belay; and the Musée de l'Homme's Alain Froment.

The research was supported by the Lewis and Clark Fund, University of Pennsylvania, Leakey Foundation, National Institutes of Health (grants AI007532, ES022577, DK104339, and ES019851), and National Science Foundation (Grant 1540432).

Sarah Tishkoff is the David and Lyn Silfen University Professor and a Penn Integrates Knowledge Professor at the University of Pennsylvania, with appointments in the Department of Genetics in the Perelman School of Medicine and in the Department of Biology in the School of Arts and Sciences.

Laura Scheinfeldt is the principal investigator of the National Institutes of Neurological Disorders and Stroke's Human Genetic Resource Center at the Coriell Institute for Medical Research. She was formerly a research associate in the Tishkoff laboratory at the University of Pennsylvania.


Contacts and sources:
Katherine Unger Baillie
University of Pennsylvania



A Trillion New Trees to Save Us All

A trillion trees is what we need, says a climate scientist. Reshape forests on a global scale is what needs to be done.  So on a local scale hug a tree-hugger or plant a few trees.

Thomas Crowther identifies long-disappeared forests available for restoration across the world. He will describe how there is room for an additional 1.2 trillion new trees around the world that could absorb more carbon than human emissions each year. Crowther also describes data from thousands of soil samples collected by local scientists that reveal the world's Arctic and sub-Arctic regions store most of the world's carbon. But the warming of these ecosystems is causing the release of this soil carbon, a process that could accelerate climate change by 17%. This research is revealing that the restoration of vegetation and soil carbon is by far our best weapon in the fight against climate change.

Data enables understanding of carbon cycle feedbacks to predict climate change at a large scale.

 Credit: Andrew Coelho, Unsplash Photography


The living parts of the planet make it unique from all other parts of the solar system, and they drive every aspect of biogeochemical cycling. It is essential that we represent these living processes into our understanding of current and future biogeochemical cycles in order to understand and predict climate change.

In their research, the Crowther Lab uses the largest global dataset of forest inventory data (the Global Forest Biodiversity Initiative), measured by people on the ground in over 1.2 million locations around the world combined with satellite observations, to get a mechanistic understanding of the global forest system. The lab also uses an equivalent database for below-ground ecology - the Global Soil Biodiversity Initiative. This initiative, with tens of thousands of soil samples that describe the global patterns in the biomass and the diversity of the global soil microbiome, paired with satellite data generates a first glimpse at the billions of below-ground species that determine soil fertility, atmospheric composition and the climate.

Using this combination of above ground and below ground data the research team can identify regions of high priority for biodiversity conservation. Additionally, they can finally start to understand the feedbacks that determine atmospheric carbon concentrations over the rest of the century. They now understand that, as the soil warms, carbon emissions from the soil will increase, particularly in the high-latitude arctic and sub-arctic regions.

Under a business-as-usual climate scenario the Crowther lab model suggests that warming would drive the loss of ~55 gigatons of carbon from the upper soil horizons by 2050. This value is around 12-17 per cent of the expected anthropogenic emissions over this period. These are the 'climate change feed-backs' that Crowther discusses in his session, and understanding these processes is critical to effectively managing natural systems in order to combat climate change.

Contacts and sources:



Citation:


Iron Man Suit Technology Becoming Reality, New Hyper-Compact Mechanisms



Real science has finally caught up to the science fiction of Iron Man’s transforming exoskeleton suit.

In a paper published today in Science Robotics, engineers at Brigham Young University detail new technology that allows them to build complex mechanisms into the exterior of a structure without taking up any actual space below the surface.

Credit: BYU

This new class of mechanisms, called “developable mechanisms,” get their name from developable surfaces, or materials that can take on 3-D shapes from flat conformations without tearing or stretching, like a sheet of paper or metal. They reside in a curved surface (like, say, the arms of Iron Man’s suit) and can transform or morph when deployed to serve unique functions. When not in use, they can fold back into the surface of the structure seamlessly.


Credit: BYU

“These new discoveries make it possible to build complex machines that integrate with surfaces to be very compact, but can deploy and do complex tasks,” said researcher Larry Howell, professor of mechanical engineering at BYU. “It opens up a whole new world of potential devices that have more functions, but are still very compact.”

Credit: BYU

Making hyper-compact mechanisms is something increasingly important as manufacturers across medical, space and military industries are constantly working to get more complex functionality in less space. Potential applications of developable mechanisms include:
Medical: Surgical instruments that can both cut materials and deploy lights simultaneously during minimally-invasive surgery
Vehicles and airplanes: Storage components that could deploy from the inner surface of the fuselage and be completely out of the way when not in use
Military: Quad-rotor drones that have adjustable wing spans for fitting in tight spaces
Space: Wheels that could deploy claws for rock crawling, which could be especially useful to an interplanetary rover.
Credit: BYU

This new class of mechanical structures evolved from Howell and colleague Spencer Magleby’s work on origami-based engineering, done in collaboration with origami artist Robert Lang. From solar arrays for NASA to bulletproof barriers for police officers, their work has generated national and international coverage. As the group of researchers moved to curved origami principles, the mathematics revealed a new way of doing more complex machines.

“Origami was a stepping stone to this,” Magleby said. “The art of Origami has inspired us to do things that don’t even look like Origami, yet it is the core of much of this new engineering.”


Credit: BYU

The new line of research is sponsored by the National Science Foundation and includes researchers at BYU, the University of Southern Indiana and Lang Origami.

“It’s pretty cool to accomplish things that have merely been science fiction in the past,” Howell said. “These are discoveries that will enable us to do things that no one has ever been able to do before. And we hope that other engineers, as they build on these discoveries, will apply them in ways that will help make the world a better place.



Contacts and sources:
Todd Hollingshead
Brigham Young University

Citation: Developable mechanisms on developable surfaces.
Todd G. Nelson, Trent K. Zimmerman, Spencer P. Magleby, Robert J. Lang, Larry L. Howell. Science Robotics, 2019; 4 (27): eaau5171 DOI: 10.1126/scirobotics.aau5171


Are They Eating Off the Floor? Toxins Found in Children from Flooring Chemicals

Kids are getting more than their fill of chemical toxins from floors, according to chemical sleuths at Duke University.  This is some unlucky yucky.  They can lead to neurodevelopmental delays, obesity, endocrine and thyroid disruption, cancer and other diseases.

Children living in homes with all vinyl flooring or flame-retardant chemicals in the sofa have significantly higher concentrations of potentially harmful semi-volatile organic compounds (SVOCs) in their blood or urine than children from homes where these materials are not present, according to a new Duke University-led study.

Environmental Chemist Heather led a three-year study of in-home exposures to semi-volatile organic compounds (SVOCs) among 203 children from 190 families.
Credit: Duke University

The researchers presented their findings Sunday, Feb. 17 at the annual meeting of the American Association for the Advancement of Science in Washington, D.C.

They found that children living in homes where the sofa in the main living area contained flame-retardant polybrominated diphenyl ethers (PBDEs) in its foam had a six-fold higher concentration of PBDEs in their blood serum.

Exposure to PBDEs has been linked in laboratory tests to neurodevelopmental delays, obesity, endocrine and thyroid disruption, cancer and other diseases.

Children from homes that had vinyl flooring in all areas were found to have concentrations of benzyl butyl phthalate metabolite in their urine that were 15 times higher than those in children living with no vinyl flooring.

Benzyl butyl phthalate has been linked to respiratory disorders, skin irritations, multiple myeolma and reproductive disorders.

"SVOCs are widely used in electronics, furniture and building materials and can be detected in nearly all indoor environments," said Heather Stapleton, an environmental chemist at Duke's Nicholas School of the Environment, who led the research. "Human exposure to them is widespread, particularly for young children who spend most of their time indoors and have greater exposure to chemicals found in household dust."

"Nonetheless, there has been little research on the relative contribution of specific products and materials to children's overall exposure to SVOCs," she noted.

To address that gap, in 2014 Stapleton and colleagues from Duke, the Centers for Disease Control & Prevention, and Boston University began a three-year study of in-home exposures to SVOCs among 203 children from 190 families.

"Our primary goal was to investigate links between specific products and children's exposures, and to determine how the exposure happened -- was it through breathing, skin contact or inadvertent dust inhalation," Stapleton said.

To that end, the team analyzed samples of indoor air, indoor dust and foam collected from furniture in each of the children's homes, along with a handwipe sample, urine and blood from each child.

"We quantified 44 biomarkers of exposure to phthalates, organophosphate esters, brominated flame retardants, parabens, phenols, antibacterial agents and perfluoroalkyl and polyfluoroalkyl substances (PFAS)," Stapleton said.

Stapleton presented her team's findings at AAAS as part of the scientific session, "Homes at the Center of Chemical Exposure: Uniting Chemists, Engineers and Health Scientists."

She conducted the study with Kate Hoffman, assistant research professor in environmental sciences and policy; research assistant Emina Hodzic; and PhD students Jessica Levasseur, Stephanie Hammel and Allison Phillips, all of Duke.


Other members of the research team were Xiaoyun Ye, Antonia M. Calafat and Andreas Sjodin of the Centers for Disease Control & Prevention, and Thomas F. Webster of Boston University's School of Public Health.

Stapleton is the Dan and Bunny Gabel Associate Professor of Environmental Health at Duke's Nicholas School.



Contacts and sources:
Tim Lucas
Duke University




Citation: "Children's Exposure to Chemicals Emitted from the Home Environment," Heather M. Stapleton, Kate Hoffman, Jessica Levasseur, Emina Hodzic, Allison Phillips, Xiaoyun Ye, Antonia M. Calafat, Andreas Sjodin and Thomas F. Webster. Presented at AAAS Annual Meeting, Feb. 17, 2019.



Stormy Stagnation or Stagnating Storminess: Summer Is Going To Be a Mess Predict Scientists

Summers may be getting stranger.

Climate change is shifting the energy in the atmosphere that fuels summertime weather, which may lead to stronger thunderstorms and more stagnant conditions for midlatitude regions of the Northern Hemisphere, including North America, Europe, and Asia, a new MIT study finds.

Scientists report that rising global temperatures, particularly in the Arctic, are redistributing the energy in the atmosphere: More energy is available to fuel thunderstorms and other local, convective processes, while less energy is going toward summertime extratropical cyclones — larger, milder weather systems that circulate across thousands of kilometers. These systems are normally associated with winds and fronts that generate rain.
File:Chaparral Supercell 2.JPG
Credit: Greg Lundeen/ U.S. National Weather Service/ Wikimedia

“Extratropical cyclones ventilate air and air pollution, so with weaker extratropical cyclones in the summer, you’re looking at the potential for more poor air-quality days in urban areas,” says study author Charles Gertler, a graduate student in MIT’s Department of Earth, Atmospheric and Planetary Sciences (EAPS). “Moving beyond air quality in cities, you have the potential for more destructive thunderstorms and more stagnant days with perhaps longer-lasting heat waves.”

Gertler and his co-author, Associate Professor Paul O’Gorman of EAPS, are publishing their results this week in the Proceedings of the National Academy of Sciences.

A shrinking gradient

In contrast to more violent tropical cyclones such as hurricanes, extratropical cyclones are large weather systems that occur poleward of the Earth’s tropical zone. These storm systems generate rapid changes in temperature and humidity along fronts that sweep across large swaths of the United States. In the winter, extratropical cyclones can whip up into Nor’easters; in the summer, they can bring everything from general cloudiness and light showers to heavy gusts and thunderstorms.

Extratropical cyclones feed off the atmosphere’s horizontal temperature gradient — the difference in average temperatures between northern and southern latitudes. This temperature gradient and the moisture in the atmosphere produces a certain amount of energy in the atmosphere that can fuel weather events. The greater the gradient between, say, the Arctic and the equator, the stronger an extratropical cyclone is likely to be.

In recent decades, the Arctic has warmed faster than the rest of the Earth, in effect shrinking the atmosphere’s horizontal temperature gradient. Gertler and O’Gorman wondered whether and how this warming trend has affected the energy available in the atmosphere for extratropical cyclones and other summertime weather phenomena.

They began by looking at a global reanalysis of recorded climate observations, known as the ERA-Interim Reanalysis, a project that has been collecting available satellite and weather balloon measurements of temperature and humidity around the world since the 1970s. From these measurements, the project produces a fine-grained global grid of estimated temperature and humidity, at various altitudes in the atmosphere.

From this grid of estimates, the team focused on the Northern Hemisphere, and regions between 20 and 80 degrees latitude. They took the average summertime temperature and humidity in these regions, between June, July, and August for each year from 1979 to 2017. They then fed each yearly summertime average of temperature and humidity into an algorithm, developed at MIT, that estimates the amount of energy that would be available in the atmosphere, given the corresponding temperature and humidity conditions.

“We can see how this energy goes up and down over the years, and we can also separate how much energy is available for convection, which would manifest itself as thunderstorms for example, versus larger-scale circulations like extratropical cyclones,” O’Gorman says.

Seeing changes now

Since 1979, they found the energy available for large-scale extratropical cyclones has decreased by 6 percent, whereas the energy that could fuel smaller, more local thunderstorms has gone up by 13 percent.

Their results mirror some recent evidence in the Northern Hemisphere, suggesting that summer winds associated with extratropical cyclones have decreased with global warming. Observations from Europe and Asia have also shown a strengthening of convective rainfall, such as from thunderstorms.

“Researchers are finding these trends in winds and rainfall that are probably related to climate change,” Gertler says. “But this is the first time anyone has robustly connected the average change in the atmosphere, to these subdaily timescale events. So we’re presenting a unified framework that connects climate change to this changing weather that we’re seeing.”

The researchers’ results estimate the average impact of global warming on summertime energy of the atmosphere over the Northern Hemisphere. Going forward, they hope to be able to resolve this further, to see how climate change may affect weather in more specific regions of the world.

“We’d like to work out what’s happening to the available energy in the atmosphere, and put the trends on a map to see if it’s, say, going up in North America, versus Asia and oceanic regions,” O’Gorman says. “That’s something that needs to be studied more.”

This research was supported by the National Science Foundation.

Contacts and sources:
Jennifer Chu
Massachusetts Institute of Technology

Citation:


A River of Stars Flowing Not Far from Earth Discovered


At the galactic south pole, not far from Earth, a river of stars flow across the southern hemisphere

Astronomy & Astrophysics publishes the work of researchers from the University of Vienna, who have found a river of stars, a stellar stream in astronomical parlance, covering most of the southern sky. The stream is relatively nearby and contains at least 4000 stars that have been moving together in space since they formed, about 1 billion years ago.

Due to its proximity to Earth, this stream is a perfect workbench on which to test the disruption of clusters, measure the gravitational field of the Milky Way, and learn about coeval extrasolar planet populations with upcoming planet-finding missions. For their search, the authors used data from the ESA Gaia satellite.

Fig. 1. Night sky centered on the south Galactic pole in a so-called stereographic projection. In this special projection, the Milky Way curves around the entire image in an arc. The stars in the stream are displayed in red and cover almost the entire southern Galactic hemisphere, thereby crossing many well-known constellations

. Background image: Gaia DR2 skymap.

Our own host galaxy, the Milky Way, is home to star clusters of variable sizes and ages. We find many baby clusters within molecular clouds, fewer middle-age and old age clusters in the Galactic disk, and even fewer massive, old globular clusters in the halo. These clusters, regardless of their origin and age, are all subject to tidal forces along their orbits in the Galaxy. Given enough time, the Milky Way gravitational forces relentlessly pull them apart, dispersing their stars into the collection of stars we know as the Milky Way.

“Most star clusters in the Galactic disk disperse rapidly after their birth as they do not contain enough stars to create a deep gravitational potential well, or in other words, they do not have enough glue to keep them together. Even in the immediate solar neighborhood, there are, however, a few clusters with sufficient stellar mass to remain bound for several hundred million years. So, in principle, similar, large, stream-like remnants of clusters or associations should also be part of the Milky Way disk.“ says Stefan Meingast, lead author of the paper published in Astronomy & Astrophysics.

Thanks to the precision of the Gaia measurements, the authors could measure the 3D motion of stars in space. When carefully looking at the distribution of nearby stars moving together, one particular group of stars, as yet unknown and unstudied, immediately caught the eye of the researchers. It was a group of stars that showed precisely the expected characteristics of a cluster of stars born together but being pulled apart by the gravitational field of the Milky Way.

"Identifying nearby disk streams is like looking for the proverbial needle in a haystack. Astronomers have been looking at, and through, this new stream for a long time, as it covers most of the night sky, but only now realize it is there, and it is huge, and shockingly close to the Sun” says João Alves, second author of the paper. "Finding things close to home is very useful, it means they are not too faint nor too blurred for further detailed exploration, as astronomers dream."

Due to sensitivity limitations of the Gaia observations, their selection only contained about 200 sources. An extrapolation beyond these limits suggests the stream should have at least 4000 stars, thereby making the structure more massive than most know clusters in the immediate solar neighborhood. The authors also determined the stream’s age to be around one billion years. As such, it already has completed four full orbits around the Galaxy, enough time to develop the stream-like structure as a consequence of gravitational interaction with the Milky Way disk.

“As soon as we investigated this particular group of stars in more detail, we knew that we had found what we were looking for: A coeval, stream-like structure, stretching for hundreds of parsecs across a third of the entire sky.” Says Verena Fürnkranz, co-author and Masters student at the University of Vienna. "It was so thrilling to be part of a new discovery" she adds.

This newly discovered nearby system can be used as a valuable gravity probe to measure the mass of the Galaxy. With follow-up work, this stream can tell us how galaxies get their stars, test the gravitational field of the Milky Way, and, because of its proximity, become a wonderful target for planet-finding missions. The authors hope to unravel even more such structures in the future with the help of the rich Gaia database.



Contacts and sources: 
Jennifer Martin
Astronomy & Astrophysics

Dr. Stefan Meingast
Department of Astrophysics
University of Vienna

Citation:' "Extended stellar systems in the solar neighborhood. II. Discovery of a nearby 120° stellar stream in Gaia DR2",  by Stefan Meingast, João Alves, and Verena Fürnkranz,

Published in Astronomy & Astrophysics, 2019, A&A, 622, L13
Free access to the article

How Getting Enough Sleep Reduces Cardiovascular Disease Risk


A sleep-modulating hormone called hypocretin was found to also control production of inflammatory cells.

Getting enough sleep is key to good health, and studies have shown that insufficient sleep increases the risk of serious problems, including cardiovascular disease. Now Massachusetts General Hospital (MGH) investigators have discovered one way that sleep protects against the buildup of arterial plaques called atherosclerosis. In their paper receiving advance online publication in Nature, they describe the mechanism by which insufficient sleep increases production of inflammatory white blood cells known to be major contributors to atherosclerosis. 

Sleeping girl 
File:Albert Moore - A Sleeping Girl - Google Art Project.jpg
Credit: Albert Joseph Moore (4 September 1841 – 25 September 1893) / Wikimedia

“We have discovered that sleep helps to regulate the production in the bone marrow of inflammatory cells and the health of blood vessels and that, conversely, sleep disruption breaks down control of inflammatory cell production, leading to more inflammation and more heart disease,” says Filip Swirski, PhD, of the MGH Center for Systems Biology, senior author of the Nature paper. “We also have identified how a hormone in the brain known to control wakefulness controls processes in the bone marrow and protects against cardiovascular disease.”

To investigate how insufficient sleep increases atherosclerosis, Swirski’s team subjected mice genetically programmed to develop atheroslcerosis to repeated interruptions of their sleep, similar to the experience of someone constantly waking up because of noise or discomfort. While there were no changes in weight, cholesterol levels or glucose tolerance in the sleep-deprived mice, compared to animals from the same strain allowed to sleep normally, those subjected to sleep fragmentation developed larger arterial plaques and had higher levels of monocytes and neutrophils – inflammatory cells that contribute to atherosclerosis – in their blood vessels.

Further experiments revealed that the sleep-deprived mice had a nearly two-fold increase in the production in their bone marrow of stem cells that give rise to white blood cells. A hormone called hypocretin, produced in the brain structure called the hypothalamus and known to have a role in the regulation of sleep, was found to play an unexpected role in controlling white blood cell production. While normally produced at high levels when animals – including humans – are awake, hypocretin levels were significantly reduced in the sleep-deprived mice.

The MGH team found that hypocretin regulates production of white blood cells through interaction with neutrophil progenitors in the bone marrow. Neutrophils, they discovered, induce monocyte production through release of a factor called CSF-1, and experiments with mice lacking the gene for hypocretin revealed that the hormone controls CSF-1 expression, monocyte production and the development of arterial plaques. In sleep-deprived animals, the drop in hypocretin led to increased CSF-1 production by neutrophils, elevated monocyte production and accelerated atherosclerosis.

“This is a direct demonstration that hypocretin is also an important inflammatory mediator,” says Swirski, an associate professor of Radiology at Harvard Medical School. “We now need to study this pathway in humans, explore additional mechanisms by which proper sleep maintains vascular health and further explore this newly identified neuro-immune axis.”

Cameron McAlpine, PhD, of the MGH Center for Systems Biology is lead author of the Nature paper. The Swirski lab (@SwirskiLab) also collaborated on the study with Máté Kiss, MS, and Christoph Binder, MD, PhD, Medical University of Vienna; Peter Libby, MD, Brigham and Women’s Hospital; Anne Vassalli, PhD, and Mehdi Tafti, PhD, University of Lausanne; Thomas Scammell, MD, Beth Israel Deaconess Medical Center, and Matthias Nahrendorf, MD, MGH Radiology. Support for the study includes National Institutes of Health grants R35 HL135752, R01 HL128264 and P01 HL131478 and the American Heart Association Established Investigator Award. Swirski is the Patricia and Scott Eston MGH Research Scholar.

Contacts and sources:
Julie Cunningham
Massachusetts General Hospital

Citation: Sleep modulates haematopoiesis and protects against atherosclerosis.
McAlpine CS, Kiss MG, Rattik S, He S, Vassalli A, Valet C, Anzai A, Chan CT, Mindur JE, Kahles F, Poller WC, Frodermann V, Fenn AM, Gregory AF, Halle L, Iwamoto Y, Hoyer FF, Binder CJ, Libby P, Tafti M, Scammell TE, Nahrendorf M, Swirski FK. Nature, 2019 DOI: 10.1038/s41586-019-0948-2


Saturday, February 16, 2019

New Titanosaur Dinosaur That Wears Its “Heart” On Its Tail



A new dinosaur that wears its “heart” on its tail provides new clues to how ecosystems evolved on the African continent during the Cretaceous period according to researchers at Ohio University.

The OHIO team identified and named the new species of dinosaur in an article published this week in PLOS ONE . The new dinosaur, the third now described from southwestern Tanzania by the NSF-funded team, is yet another member of the large, long-necked titanosaur sauropods. The partial skeleton was recovered from Cretaceous-age (~100 million years ago) rocks exposed in a cliff surface in the western branch of the great East African Rift System.

The new dinosaur is named Mnyamawamtuka moyowamkia (Mm-nya-ma-wah-mm-too-ka mm-oh-yo-wa-mm-key-ah), a name derived from Swahili for “animal of the Mtuka (with) a heart-shaped tail” in reference to the name of the riverbed (Mtuka) in which it was discovered and due to the unique shape of its tail bones.

This is an illustration depicting Mnyamawamtuka in its environmental setting. 
Credit: Mark Witton

The initial discovery of Mnyamawamtuka took place in 2004, when part of the skeleton was discovered high in a cliff wall overlooking the seasonally dry Mtuka riverbed, with annual excavations continuing through 2008.

“Although titanosaurs became one of the most successful dinosaur groups before the infamous mass extinction capping the Age of Dinosaurs, their early evolutionary history remains obscure, and Mnyamawamtuka helps tell those beginnings, especially for their African-side of the story,” said lead author Dr. Eric Gorscak, a recent Ph.D. graduate of Ohio University, current research associate at the Field Museum of Natural History (Chicago) and new assistant professor at the Midwestern University in Downers Grove, just outside of Chicago. “The wealth of information from the skeleton indicates it was distantly related to other known African titanosaurs, except for some interesting similarities with another dinosaur, Malawisaurus, from just across the Tanzania–Malawi border,” noted Dr. Gorscak.

Titanosaurs are best known from Cretaceous-age rocks in South America, but other efforts by the team include new species discovered in Tanzania, Egypt, and other parts of the African continent that reveal a more complex picture of dinosaurian evolution on the planet. “The discovery of dinosaurs like Mnyamawamtuka and others we have recently discovered is like doing a four-dimensional connect the dots,” said Dr. Patrick O’Connor, professor of anatomy at Ohio University and Gorscak’s advisor during his Ph.D. research. “Each new discovery adds a bit more detail to the picture of what ecosystems on continental Africa were like during the Cretaceous, allowing us to assemble a more holistic view of biotic change in the past.”

MynamawamtukaScheme.jpg
Credit: Ohio University

The excavation process spanned multiple years, and included field teams suspended by ropes and large-scale mechanical excavators to recover one of the more complete specimens from this part of the sauropod dinosaur family tree. “Without the dedication of several field teams, including some whose members donned climbing gear for the early excavations, the skeleton would have eroded away into the river during quite intense wet seasons in this part of the East African Rift System,” added O’Connor.

“This latest discovery is yet another fine example of how Ohio University researchers work the world over in their pursuit of scientific research,” Ohio University President M. Duane Nellis said. “This team has turned out a number of notable discoveries which collectively contribute significantly to our understanding of the natural world.”

Mnyamawamtuka and the other Tanzanian titanosaurs are not the only animals discovered by the research team. Remains of bizarre relatives of early crocodiles, the oldest evidence for “insect farming,” and tantalizing clues about the early evolution of monkeys and apes have been discovered in recent years. Such findings from the East African Rift provide a crucial glimpse into ancient ecosystems of Africa and provide the impetus for future work elsewhere on the continent.

“This new dinosaur gives us important information about African fauna during a time of evolutionary change,” said Judy Skog, a program director in the National Science Foundation’s Division of Earth Sciences, which funded the research. “The discovery offers insights into paleogeography during the Cretaceous. It’s also timely information about an animal with heart-shaped tail bones during this week of Valentine’s Day.”

Recent findings by the research team in the Rukwa Rift Basin include:
Shingopana songwensis – titanosaurian sauropod dinosaur, Rukwa Rift Basin
Rukwatitan bisepultus – titanosaurian sauropod dinosaur, Rukwa Rift Basin
Pakasuchus kapilimai —mammal-like crocodile, Rukwa Rift Basin
Early evidence for monkey-ape split, Rukwa Rift Basin Project
Early evidence of insect farming—Fossil Termite Nests, Rukwa Rift Basin

“The Tanzanian story is far from over but we know enough to start asking what paleontological and geological similarities and dissimilarities there are with nearby rock units. Revisiting Malawi is my top priority to address these broader, regional questions,” said Gorscak, who also participates in ongoing projects in Egypt and Kenya. “With Mnyamawamtuka and other discoveries, I’m not sure to view it as writing or reading the next chapters in the paleontological book of Africa. I’m just excited to see where this story is going to take us.”

Photos/artistic renderings of Mnyamawamtuka can be found here.

The study was funded by the National Science Foundation, the National Geographic Society, the Jurassic Foundation, The Paleontological Society, Ohio University Student Enhancement Award, Ohio University Original Work Grant, the Ohio University Heritage College of Osteopathic Medicine, and the Ohio University Office of the Vice President for Research and Creative Activity.


Contacts and sources:
Jim Sabin
Ohio University

Citation: A new African Titanosaurian Sauropod Dinosaur from the middle Cretaceous Galula Formation (Mtuka Member), Rukwa Rift Basin, Southwestern Tanzania.
Eric Gorscak, Patrick M. O’Connor.PLOS ONE, 2019; 14 (2): e0211412 DOI: 10.1371/journal.pone.0211412

To Tool or Not To Tool? That Is the Question

Orangutans make complex economic decisions about tool use depending on the current 'market' situation

Flexible tool use is closely associated to higher mental processes such as the ability to plan actions. Now a group of cognitive biologists and comparative psychologists from the University of Vienna, the University of St Andrews and the University of Veterinary Medicine Vienna that included Isabelle Laumer and Josep Call, has studied tool related decision-making in a non-human primate species – the orangutan. 

They found that the apes carefully weighed their options: eat an immediately available food reward or wait and use a tool to obtain a better reward instead? To do so the apes considered the details such as differences in quality between the two food rewards and the functionality of the available tools in order to obtain a high quality food reward, even when multidimensional task components had to be assessed simultaneously.

Female orangutan
Credit: © Alice Auersperg

Tool-use in animals is a rare and often quickly rated as intelligent due to its striking nature. For instance, antlions throw small pebbles at potential prey, archer fish down prey by spitting water at them, and sea otters use stones to crack open shells. Nevertheless, most types of tool use are quite inflexible, typically applied to one situation and tightly controlled by processes that are a part of the respective animal’s inborn behavioural repertoire. In contrast, intelligent tool use requires the integration of multiple sources of information to flexibly adapt to quickly changing environmental conditions.

Orangutans share 97 percent of their DNA with us and are among the most intelligent and most endangered primates. They have human-like long-term memory, routinely use a variety of sophisticated tools in the wild and construct elaborate sleeping nests each night from foliage and branches. In their natural habitat, the evergreen rainforests of Borneo and Sumatra, orangutans have to consider several factors simultaneously, such as the predictability to find ripe fruits, the distance and reachability of food as well as the available tools to open extractable food sources. So far it was unknown how orangutans adapt their decisions when the use of a tool is involved and how many factors they can process at the same time in order to make profitable decisions.

Adult male uses a stick tool

Credit: © Alice Auersperg

Researchers from the University of Vienna, the University of Veterinary Medicine Vienna and the University of St Andrews investigated for the first time how orangutans adapt their decisions when the use of a tool is involved and how many factors they can process at the same time in order to make profitable decisions at the Wolfgang Koehler Primate Research Center in Leipzig.

The researchers used two different types of food items: Banana-pellets, which are the orangutans' most favourite food type, and apple pieces which they like but disregard if banana-pellets are available. They could extract these items from two different apparatuses: an apparatus required probing with a stick tool to obtain the food item while the other required dropping a ball inside it. Each apparatus could only be operated with the respective tool. During testing, orang-utans were confronted with either one or two baited apparatus/es and a choice between two items (usually a food item and a tool). Once the apes had picked one item the other was immediately removed.

Orangutans flexibly adapted their decisions to different conditions: "If the apple piece (likeable food) or the banana-pellet (favourite food) was out of immediate reach inside the apparatus and the choice was between an immediate banana-pellet and a tool, they chose the food over the tool, even when the tool was functional for the respective apparatus", explains Isabelle Laumer who conducted the experiment. "However, when the orangutans could choose between the apple-piece and a tool they chose the tool but only if it worked for the available apparatus: For example when the stick and the likeable food was available but the apes faced the ball-apparatus baited with the favourite banana-pellet, they chose the apple-piece over the non-functional tool. However when the stick-apparatus with the banana-pellet inside was available they chose the stick-tool over the immediate apple-piece", she further explains. "In a final task, that required the orangutans to simultaneously focus on the two apparatuses, one baited with the banana-pellet and the other with the apple and the orangutans had to choose between the two tools they were still able to make profitable decisions by choosing the tool that enabled them to operate the apparatus with the favorite food."

These results are similar to findings in Gofffin cockatoos that have been previously tested in the same task. "Similar to the apes, the cockatoos could overcome immediate impulses in favor of future gains even if this implied tool use. "The birds were confronted with the choice between a tool to retrieve an out-of-reach food item and an immediate reward. We found that they, similar to the apes, were highly sensible to the quality of the immediate relative to the out-of-reach reward at the same time as to whether the available tool would actually work with the task at hand", explains Alice Auersperg, the head of the Goffin Lab in Austria. 

She continues: "Again, this suggests that similar cognitive abilities can evolve independently in distantly related species."Nevertheless, the cockatoos did reach their limit at the very last task in which both apparatuses baited with both possible food qualities and both tools were available at the same time."

"Optimality models suggest that orangutans should flexibly adapt their foraging decisions depending on the availability of high nutritional food sources, such as fruits", says Josep Call from the University of St Andrews. "Our study shows that orangutans can simultaneously consider multi-dimensional task components in order to maximize their gains and it is very likely that we haven´t even reached the full extent of their information processing capabilities."

"According to a 2007 survey by the United Nations Environment Program (UNEP) orangutans will be extinct in the wild within two decades if current deforestation trends continue", says Isabelle Laumer. "Habitat loss due to extensive palm-oil production is the major threat. Unfortunately palm oil is still the most widely used vegetable oil in the world. As long as there is a demand for palm oil and we keep buying products that contain palm oil, more and more of the rain-forest will be destroyed. Each of us can positively impact the survival of these extraordinary animals by making purchase decisions that may appear small, but that can collectively make a huge impact on our planet."






Contacts and sources:
Dr. Isabelle Laume
rUniversity of Vienna

Citation: Orangutans (Pongo abelii) make flexible decisions relative to reward quality and tool functionality in a multi-dimensional tool-use task.
Isabelle B. Laumer, Alice M. I. Auersperg, Thomas Bugnyar, Josep Call. . PLOS ONE, 2019; 14 (2): e0211031 DOI: 10.1371/journal.pone.0211031

Unseen Plastic Pollution from the Laundry



While the polyester leisure suit was a 1970s mistake, polyester and other synthetic fibers like nylon are still around and are a major contributor to the microplastics load in the environment, according to a Penn State materials scientist, who suggests switching to biosynthetic fibers to solve this problem.

"These materials, during production, processing and after use, break down into and release microfibers that can now be found in everything and everyone," said Melik Demirel, Lloyd and Dorothy Foehr Huck Endowed Chair in Biomimetic Materials.

Lint captured in a dryer filter consists of tiny fibers that are shed from the fabric. Modern, front-loading washers do not have lint filters.

Credit: Patrick Mansell

Unlike natural fibers like wool, cotton and silk, current synthetic fibers are petroleum-based products and are mostly not biodegradable. While natural fibers can be recycled and biodegrade, mixed fibers that contain natural and synthetic fibers are difficult or costly to recycle.

Islands of floating plastic trash in the oceans are a visible problem, but the pollution produced by textiles is invisible and ubiquitous. In the oceans, these microscopic plastic pieces become incorporated into plants and animals. Harvested fish carry these particles to market and, when people eat them, they consume microplastic particles as well.

Demirel suggested four possible approaches to solving this problem, today (Feb. 16) at the 2019 annual meeting of the American Association for the Advancement of Science in Washington, D.C. The first is to minimize the use of synthetic fibers and switch back to natural fibers such as wool, cotton, silk and linen. However, synthetic fibers are less expensive and natural fibers have other environmental costs, such as water and land-use issues.

Because much of the microfiber load that ends up in water sources comes from laundering, he suggests aftermarket filters for washing-machine outflow hoses. Clothes dryers have filters that catch lint - also microfiber waste - but current, front-loading washing machines usually do not.

"Capturing the microplastics at the source is the best filtering option," said Demirel.

He also notes that bacteria that consume plastics do exist, but are currently at the academic research phase, which takes some time to gain industrial momentum. If bacteria were used on a large scale, they could aid in biodegradation of the fibers or break the fibers down to be reused.

This is a close up of the fibers shed from fabric in a clothes dryer. These are the fibers that go down the drain and into the global water system.
Credit: Patrick Mansell

While these three options are possible, they do not solve the problem of the tons of synthetic fibers currently used in clothing around the world. Biosynthetic fibers, a fourth option, are both recyclable and biodegradable and could directly substitute for the synthetic fibers. They could also be blended with natural fibers to provide the durability of synthetic fibers but allow the blends to be recycled.

Derived from natural proteins, biosynthetic fibers also can be manipulated to have desirable characteristics. Demirel, who developed a biosynthetic fiber composed of proteins similar to silk but inspired by those found in squid ring teeth, suggests that by altering the number of tandem repeats in the sequencing of the proteins, the polymers can be altered to meet a variety of properties.

For example, material manufactured from biosynthetic squid ring-teeth proteins, called Squitex, is self-healing. Broken fibers or sections will reattach with water and a little pressure and enhance the mechanical properties of recycled cotton as a blend. Also, because the fibers are organic, they are completely biodegradable as well.

The Army Research Office, Air Force Office of Scientific Research and the Office of Naval Research supported the squid-inspired biosynthetic material. Demirel is the co-founder of a company planning to commercialize Squitex.



Contacts and sources:
A'ndrea Elyse Messer
Penn State





The Next Great Thing? Lithium-Air Batteries Can Store Energy for Cars, Houses and Industry



Growth in the offer of renewable energy sources will mean increased demand for devices optimal for energy storing; São Paulo and UK researchers presented advances in new battery development at FAPESP Week London

Current lithium ion battery technology will probably not be able to handle the coming decades' huge demand for energy. It is estimated that by 2050, electricity will make up 50% of the world's energy mix. Today that rate is 18%. But installed capacity for renewable energy production is expected to increase fourfold. This will require batteries that are more efficient, cheaper and environmentally friendly.

Growth in the offer of renewable energy sources will mean increased demand for devices optimal for energy storing said Rubens Maciel Filho, a professor at the School of Chemical Engineering of the University of Campinas (UNICAMP) during FAPESP Week London.

Credit: André Julião

One of the alternatives being studied today in many parts of the world is the lithium-air battery. Some of the Brazilian efforts in the search for such device were presented on Day Two of FAPESP Week London, held February 11-12, 2019.

"There is a lot of talk today about electric cars. Some European countries are also thinking about banning combustion engines. In addition, renewable sources like solar energy need batteries to store what is generated during the day through solar radiation," said Rubens Maciel Filho, a professor at the School of Chemical Engineering of the University of Campinas (UNICAMP).

The lithium-air battery, currently functioning only on a laboratory scale, uses ambient oxygen as a reagent. The battery stores additional energy through an electrochemical reaction that results in the formation of lithium oxide.

"It is a sustainable way to store electrical energy. With advances, it can support numerous discharge/charge cycles. It has great potential for use in transportation, in light and heavy vehicles alike. It can also work in electric power distribution networks," said the researcher.

But turning experiments into commercially viable products involves understanding the fundamentals of the electrochemical reactions that occur in the process.

"It also requires the development of new materials that allow us to leverage desirable reactions and minimize or avoid undesirable ones," said Maciel, director of the New Energy Innovation Center (CINE). With units at UNICAMP, the Nuclear Energy Research Institute (IPEN) and the São Carlos Chemistry Institute at the University of São Paulo (USP), the center is supported by FAPESP and Shell under the scope of the Engineering Research Centers Program (ERC).

He went on to explain that some of the phenomena need to be observed in operando, or in other words, in real time. "The idea is to keep track of the reactions that occur in dynamic experiments and the different chemical species that are formed, even if temporarily.

Otherwise, some of the stages in the process get lost and the battery becomes inefficient in terms of charge time and duration of charge."

To conduct these measurements, the researchers are using the National Synchrotron Light Laboratory (LNLS) at the Brazilian Center for Light Research in Energy and Materials (CNPEM), located in Campinas.

Another project presented during the session involved sulfur-air batteries. Despite not being as efficient, they are inexpensive and store energy for many hours. "They can store energy for up to 24 hours at a very low cost. Its main ingredients are sulfur and caustic soda and they are extremely inexpensive. That is why we are investing in them," said Nigel Brandon, a professor at Imperial College.

Because of these characteristics, sulfur-air batteries can be used in homes or businesses. Brandon believes, however, that their greatest potential is in charging stations for electric cars, which will become much more commonplace due to the European goal of cutting carbon emissions 80% by 2050.

"It is important to underscore the fact that the different battery projects are not competing with each other but rather are complementing each other," said Geoff Rodgers of Brunel University London, session facilitator.

Sun, hydrogen and biofuels

More efficient batteries are particularly important in a scenario in which the use of solar energy is expected to increase. Peak solar radiation during the day will require the need for efficient storage of energy so it can be drawn upon at night.

Maciel also talked about a project at CINE to develop more efficient photovoltaic cells that could be used in the future to convert solar energy to electricity as well to obtain chemical products, or even hydrogen from water hydrolysis.

Liquid hydrogen is a very efficient fuel, but its production entails high-energy costs. It is one of the options being considered in the United Kingdom since biofuels are not as viable as in Brazil.

"We are looking for new bacterial enzymes for oxidation of lignin, an aromatic polymer that makes up more than 25% of plant cell walls and is part of the residue of biofuel production. The goal is to develop new products such as biofuels, new plastics and chemical products for industry," said Timothy Bugg of the University of Warwick.

CINE

With begun last year, the CINE has a research program oriented towards the conversion of methane into chemical products, a process that involves the development of catalysts and materials. The program is coordinated by Fabio Coral Fonseca (https://bv.fapesp.br/en/pesquisador/8069/fabio-coral-fonseca/) of the IPEN.

Ana Flavia Nogueira of UNICAMP's Chemistry Institute is heading up the liquid hydrogen initiative. The center also has a Computational Material Science and Chemistry Program, which uses mathematical models to enable molecular level analysis of the impact of new materials and their interactions with molecules of interest. These studies are being led by Juarez Lopes Ferreira da Silva, a professor at USP's São Carlos Chemistry Institute.


Contacts and sources:
João Carlos da SilvaSão Paulo Research Foundation (FAPESP)

Citation:



Friday, February 15, 2019

'Seeing' Tails Help Sea Snakes Avoid Predators



New research has revealed the fascinating adaptation of some Australian sea snakes that helps protect their vulnerable paddle-shaped tails from predators.

An international study led by the University of Adelaide shows that several species of Australian sea snakes can sense light on their tail skin, prompting them to withdraw their tails under shelter. The study has also produced new insights into the evolution and genetics of this rare light sense.

The researchers found that olive sea snakes (Aipysurus laevis) and other Aipysurus species move their tail away from light. They believe this is an adaptation to keep the tail hidden from sharks and other predators.

This is an olive sea snake (Aipysurus laevis) diving underwater. Sea snakes live their entire lives at sea and must come up to the sea surface to breath air.

Credit: Chris Malam

"Sea snakes live their entire lives at sea, swimming with paddle-shaped tails and resting at times during the day under coral or rocky overhangs," says study lead author Jenna Crowe-Riddell, PhD candidate in the University of Adelaide's School of Biological Sciences. "Because sea snakes have long bodies, the tail-paddle is a large distance from the head, so benefits from having a light-sense ability of its own.

"The olive sea snake was the only reptile, out of more than 10,000 reptile species, that was known to respond to light on the skin in this way."

The researchers tested for light-sensitive tails in eight species of sea snakes, but found that only three species had the light-sense ability. They concluded the unique ability probably evolved in the ancestor of just six closely related Australian species.

"There are more than 60 species of sea snake so that's less than 10% of all sea snakes," says Ms Crowe-Riddell. "We don't know why this rare sense has evolved in just a few Aipysurusspecies."

The researchers used RNA sequencing to see what genes are active in the skin of sea snakes. They discovered a gene for a light-sensitive protein called melanopsin, and several genes that are involved in converting light into information in the nervous system.

"Melanopsin is used in a range of genetic pathways that are linked to sensing overall light levels around us. It is even used by some animals, including humans, for regulating sleep cycles and in frogs to change their skin colour as a camouflage," says Ms Crowe-Riddell.

Lead scientist Dr Kate Sanders, ARC Future Fellow at the University of Adelaide, says: "We've confirmed the ability of olive sea snakes to sense light in their tails and found the same ability in two other species. We've identified a shortlist of genes that are likely to be involved in detecting light. But further study will be needed to target these genes before we can really understand the genetic pathways involved in this fascinating behavior."

Published in the journal Molecular Ecology, the study is a collaboration between the University of Adelaide, the University of Bristol, the University of Western Australia and the Natural History Museum, London.



Contacts and sources:
Ms Jenna Crowe-Riddell, PhD candidate, School of Biological Sciences,
University of Adelaide


Citation: Phototactic tails: Evolution and molecular basis of a novel sensory trait in sea snakesJenna M. Crowe‐Riddell Bruno F. Simões Julian C. Partridge David M. Hunt Steven Delean Julian G. Schwerdt James Breen Alastair Ludington David J. Gower Kate L. Sanders
http://dx.doi.org/10.1111/mec.15022



Sensor Gives Better Eyesight to Self Driving Cars



Autonomous vehicles relying on light-based image sensors often struggle to see through blinding conditions, such as fog. But MIT researchers have developed a sub-terahertz-radiation receiving system that could help steer driverless cars when traditional methods fail.

Sub-terahertz wavelengths, which are between microwave and infrared radiation on the electromagnetic spectrum, can be detected through fog and dust clouds with ease, whereas the infrared-based LiDAR imaging systems used in autonomous vehicles struggle. To detect objects, a sub-terahertz imaging system sends an initial signal through a transmitter; a receiver then measures the absorption and reflection of the rebounding sub-terahertz wavelengths. That sends a signal to a processor that recreates an image of the object.

MIT researchers have developed a chip that leverages sub-terahertz wavelengths for object recognition, which could be combined with light-based image sensors to help steer driverless cars through fog.
MIT researchers have developed a chip that leverages sub-terahertz wavelengths for object recognition, which could be combined with light-based image sensors to help steer driverless cars through fog.
Image courtesy of the researchers

But implementing sub-terahertz sensors into driverless cars is challenging. Sensitive, accurate object-recognition requires a strong output baseband signal from receiver to processor. Traditional systems, made of discrete components that produce such signals, are large and expensive. Smaller, on-chip sensor arrays exist, but they produce weak signals.

In a paper published online on Feb. 8 by the IEEE Journal of Solid-State Circuits, the researchers describe a two-dimensional, sub-terahertz receiving array on a chip that’s orders of magnitude more sensitive, meaning it can better capture and interpret sub-terahertz wavelengths in the presence of a lot of signal noise.

To achieve this, they implemented a scheme of independent signal-mixing pixels — called “heterodyne detectors” — that are usually very difficult to densely integrate into chips. The researchers drastically shrank the size of the heterodyne detectors so that many of them can fit into a chip. The trick was to create a compact, multipurpose component that can simultaneously down-mix input signals, synchronize the pixel array, and produce strong output baseband signals.

The researchers built a prototype, which has a 32-pixel array integrated on a 1.2-square-millimeter device. The pixels are approximately 4,300 times more sensitive than the pixels in today’s best on-chip sub-terahertz array sensors. With a little more development, the chip could potentially be used in driverless cars and autonomous robots.

“A big motivation for this work is having better ‘electric eyes’ for autonomous vehicles and drones,” says co-author Ruonan Han, an associate professor of electrical engineering and computer science, and director of the Terahertz Integrated Electronics Group in the MIT Microsystems Technology Laboratories (MTL). “Our low-cost, on-chip sub-terahertz sensors will play a complementary role to LiDAR for when the environment is rough.”

Joining Han on the paper are first author Zhi Hu and co-author Cheng Wang, both PhD students in in the Department of Electrical Engineering and Computer Science working in Han’s research group.

Decentralized design

The key to the design is what the researchers call “decentralization.” In this design, a single pixel — called a “heterodyne” pixel — generates the frequency beat (the frequency difference between two incoming sub-terahertz signals) and the “local oscillation,” an electrical signal that changes the frequency of an input frequency. This “down-mixing” process produces a signal in the megahertz range that can be easily interpreted by a baseband processor.

The output signal can be used to calculate the distance of objects, similar to how LiDAR calculates the time it takes a laser to hit an object and rebound. In addition, combining the output signals of an array of pixels, and steering the pixels in a certain direction, can enable high-resolution images of a scene. This allows for not only the detection but also the recognition of objects, which is critical in autonomous vehicles and robots.

Heterodyne pixel arrays work only when the local oscillation signals from all pixels are synchronized, meaning that a signal-synchronizing technique is needed. Centralized designs include a single hub that shares local oscillation signals to all pixels.

These designs are usually used by receivers of lower frequencies, and can cause issues at sub-terahertz frequency bands, where generating a high-power signal from a single hub is notoriously difficult. As the array scales up, the power shared by each pixel decreases, reducing the output baseband signal strength, which is highly dependent on the power of local oscillation signal. As a result, a signal generated by each pixel can be very weak, leading to low sensitivity. Some on-chip sensors have started using this design, but are limited to eight pixels.

The researchers’ decentralized design tackles this scale-sensitivity trade-off. Each pixel generates its own local oscillation signal, used for receiving and down-mixing the incoming signal. In addition, an integrated coupler synchronizes its local oscillation signal with that of its neighbor. This gives each pixel more output power, since the local oscillation signal does not flow from a global hub.

A good analogy for the new decentralized design is an irrigation system, Han says. A traditional irrigation system has one pump that directs a powerful stream of water through a pipeline network that distributes water to many sprinkler sites. Each sprinkler spits out water that has a much weaker flow than the initial flow from the pump. If you want the sprinklers to pulse at the exact same rate, that would require another control system.

The researchers’ design, on the other hand, gives each site its own water pump, eliminating the need for connecting pipelines, and gives each sprinkler its own powerful water output. Each sprinkler also communicates with its neighbor to synchronize their pulse rates. “With our design, there’s essentially no boundary for scalability,” Han says. “You can have as many sites as you want, and each site still pumps out the same amount of water … and all pumps pulse together.”

The new architecture, however, potentially makes the footprint of each pixel much larger, which poses a great challenge to the large-scale, high-density integration in an array fashion. In their design, the researchers combined various functions of four traditionally separate components — antenna, downmixer, oscillator, and coupler — into a single “multitasking” component given to each pixel. This allows for a decentralized design of 32 pixels.

“We designed a multifunctional component for a [decentralized] design on a chip and combine a few discrete structures to shrink the size of each pixel,” Hu says. “Even though each pixel performs complicated operations, it keeps its compactness, so we can still have a large-scale dense array.”

Guided by frequencies

In order for the system to gauge an object’s distance, the frequency of the local oscillation signal must be stable.

To that end, the researchers incorporated into their chip a component called a phase-locked loop, that locks the sub-terahertz frequency of all 32 local oscillation signals to a stable, low-frequency reference. Because the pixels are coupled, their local oscillation signals all share identical, high-stability phase and frequency. This ensures that meaningful information can be extracted from the output baseband signals. This entire architecture minimizes signal loss and maximizes control.

“In summary, we achieve a coherent array, at the same time with very high local oscillation power for each pixel, so each pixel achieves high sensitivity,” Hu says.

Contacts and sources:
Rob Matheson
Massachusetts Institute of Technology



Immune Stimulant Molecule Shown to Prevent Cancer



A research team at the University of Louisville has discovered that an immune checkpoint molecule they developed for cancer immunotherapy, also protects against future development of multiple types of cancer when administered by itself.

The recombinant protein molecule SA-4-1BBL has been used to enhance the therapeutic efficacy of cancer vaccines with success in pre-clinical animal models. It accomplishes this by boosting the effectiveness of CD8+ T cells, adaptive immune cells trained to target the tumor for destruction. Surprisingly, when the researchers treated normal healthy mice with SA-4-1BBL alone, the mice were protected when the researchers later exposed them to different types of tumor cells.

A confocal microscope image shows the SA-4-1BBL (green color) bound to its receptor on an immune cell (red color) to initiate an immune activation cascade to fight cancer.

Credit: University of Louisville

"The novelty we are reporting is the ability of this molecule to generate an immune response that patrols the body for the presence of rare tumor cells and to eliminate cancer before it takes hold in the body," said Haval Shirwan, Ph.D., professor in the UofL Department of Microbiology and Immunology and the UofL Institute for Cellular Therapeutics. "Generally, the immune system will need to be exposed to the tumor, recognize the tumor as dangerous, and then generate an adaptive and tumor-specific response to eliminate the tumor that it recognizes. Thus, our new finding is very surprising because the immune system has not seen a tumor, so the response is not to the presence of a tumor."

The researchers have determined that the molecule generates a tumor immune surveillance system through activation of what are known as CD4+ T cells and innate NK cells, thereby protecting the mice against various cancer types they have never had. This function is an indication of the molecule's effectiveness in cancer immunoprevention.

In the research, published today in Cancer Research, mice that had never had cancer were treated with SA-4-1BBL alone, then challenged with cervical and lung cancer tumor cells at various time intervals. The mice showed significant protection against tumor development, with the greatest protection when challenged two weeks after treatment with SA-4-1BBL. The cancer immunoprevention effect generated by SA-4-1BBL lasted more than eight weeks.

"Just giving SA-4-1BBL alone prevents the formation of tumors in animal models," Shirwan said. "To our knowledge, this is the first study to demonstrate that an immune checkpoint stimulator, known for its function for adaptive immunity, as a single agent can activate an immune system surveillance mechanism for protection against various tumor types."

Additional testing showed that CD8+ T cells were not required for the protection, but when CD4+ T and NK cells were eliminated in the mice, protection failed, indicating these two cell types were necessary to achieve the effect. The lack of necessity for CD8+ T cells indicates the process is not one of conventional acquired immunity.

Although the research, which was conducted in collaboration with FasCure Therapeutics, LLC, tested the mice for cervical and lung cancers, the protective function of SA-4-1BBL works without context of specific tumor antigens, giving it the potential to be effective in preventing any number of tumor types.

"We are very excited about the cancer immunoprevention possibilities of this molecule. Its effectiveness is not tumor specific, and as a natural ligand, it does not cause toxicity, as is found with 4-1BB agonist antibodies. Plus, the fear of autoimmunity is highly minimized, as evident from our data, because it is activating the innate immune cells," said Esma Yolcu, Ph.D., associate professor at UofL and co-author of the study.

Immune checkpoint stimulators and inhibitors are major regulators of the immune system and work in a similar fashion to the "brake" and "gas" pedals in a vehicle. Cancer evades the immune system by various means, including immune checkpoint inhibitors, which apply the brake on the immune response against a tumor. Stimulators, on the other hand, serve the accelerator function, improving immune responses against cancer.

Drugs to block the action of immune checkpoint inhibitors already have shown therapeutic efficacy for several cancer types in the clinic and are approved by the Food and Drug Administration (FDA). According to Shirwan, the focus now is on immune checkpoint stimulators.

"Several antibody molecules are in clinical testing for cancer immunotherapy as immune checkpoint stimulators. However, nothing so far is approved by the FDA that gives a positive signal to the T cells," Shirwan said. "The immune checkpoint inhibitors take the foot off the brake, so to speak. This ligand, as an immune checkpoint stimulator, puts the gas on the immune system to destroy the tumor.

"Another big surprise is that an antibody to the same receptor targeted by SA-4-1BBL did not protect against tumors, demonstrating unique and desired features of SA-4-1BBL for caner immunoprevention."

Shirwan and Yolcu plan to conduct further tests for SA-4-1BBL in cancer immunoprevention.

"Although the notion of cancer immunoprevention is an attractive one, the design of clinical trials presents a challenge with respect to the target population," Shirwan said. "However, with advances in cancer screening technologies and genetic tools to identify high-risk individuals, we ultimately are hoping to have the opportunity to test the SA-4-1BBL molecule for immunoprevention in individuals who are predisposed to certain cancers, as well as in the presence of precancerous lesions."


Contacts and sources:
Betty CoffmanUniversity of Louisville



Could Undersea Gases Superheat Our Planet Again?


Undersea carbon reservoirs have caused global warming before — and it could happen again, according to research by an international team of scientists led by USC

The world’s oceans could harbor an unpleasant surprise for global warming, based on new research that shows how naturally occurring carbon gases trapped in reservoirs atop the seafloor escaped to superheat the planet in prehistory.

Bubbles of liquid carbon dioxide float out of the seafloor at a vent on Northwest Eifuku volcano off the coast of Japan.
Undersea carbon reservoirs: Bubbles of carbon dioxide
Photo/Bob Embley, NOAA Office of Ocean Exploration

Scientists say events that began on the ocean bottom thousands of years ago so disrupted the Earth’s atmosphere that it melted away the ice age. Those new findings challenge a long-standing paradigm that ocean water alone regulated carbon dioxide in the atmosphere during glacial cycles. Instead, the study shows geologic processes can dramatically upset the carbon cycle and cause global change.

For today’s world, the findings could portend an ominous development. The undersea carbon reservoirs released greenhouse gas to the atmosphere as oceans warmed, the study shows, and today the ocean is heating up again due to manmade global warming.

If undersea carbon reservoirs are upset again, they would emit a huge new source of greenhouse gases, exacerbating climate change. Temperature increases in the ocean are on pace to reach that tipping point by the end of the century. For example, a big carbon reservoir beneath the western Pacific near Taiwan is already within a few degrees Celsius of destabilizing.
Undersea carbon reservoirs unaccounted for

Moreover, the phenomenon is a threat unaccounted for in climate model projections. Undersea carbon dioxide reservoirs are relatively recent discoveries and their characteristics and history are only beginning to be understood.

Those findings come from a new research paper produced by an international team of Earth scientists led by USC and published in January in the journal Environmental Research Letters.

“We’re using the past as a way to anticipate the future,” said Lowell Stott, professor of Earth sciences at the USC Dornsife College of Letters, Arts and Sciences and lead author of the study. “We know there are vast reservoirs of carbon gas at the bottom of the oceans. We know when they were disrupted during the Pleistocene it warmed the planet.

“We have to know if these carbon reservoirs could be destabilized again. It’s a wild card for which we need to account.”

At issue are expanses of carbon dioxide and methane accumulating underwater and scattered across the seafloor. They form as volcanic activity releases heat and gases that can congeal into liquid and solid hydrates, which are compounds stuck together in an icy slurry that encapsulates the reservoirs.
Undersea carbon reservoirs vulnerable in a warming ocean

These undersea carbon reservoirs largely stay put unless perturbed, but the new study shows the natural reservoirs are vulnerable in a warming ocean and provides proof the Earth’s climate has been affected by rapid release of geologic carbon.

The scientists say it occurred in the distant past when the Earth was much warmer, and it’s happened more recently — about 17,000 years ago at the end of the Pleistocene epoch when glaciers advanced and receded, which is the focus on the new study. Warming was evident due to changes in atmospheric greenhouse gas concentrations, based on ice cores, marine and continental records.

But how did that happen? What forced such dramatic change in the first place? Scientists have been searching for that answer for 40 years, with focus on oceans because they’re a giant carbon sink and play a central role in carbon dioxide variations.

They soon realized that processes that regulate carbon to the ocean operated too slowly to account for the surge in atmospheric greenhouse gases that led to warming that ended the ice age. So, scientists around the world began examining the role of Earth’s hydrothermal systems and their impact on deep-ocean carbon to see how it affected the atmosphere.

The new study by scientists at USC, the Australian National University and Lund University in Sweden, focused on the Eastern Equatorial Pacific (EEP) hundreds of miles off the coast of Ecuador. The EEP is a primary conduit through which the ocean releases carbon to the atmosphere.

The scientists report evidence of deep-sea hydrothermal systems releasing greenhouse gases to the ocean and atmosphere at the end of the last ice age, just as the oceans were beginning to warm. They measured increased deposition of hydrothermal metals in ancient marine sediments. They correlated glaciation intervals with variations in atmospheric carbon dioxide with differences in marine microorganism ages. They found a four-fold increase in zinc in protozoa (foraminifera) shells, a telltale sign of widespread hydrothermal activity.

Taken together, the new data show that there were major releases of naturally occurring carbon from the EEP, which contributed to dramatic change in Earth’s temperature as the ice age was ending, the study says.

More undersea carbon reservoirs being discovered

Elsewhere around the world, more and more deep-ocean carbon reservoirs are being discovered. They mostly occur near hydrothermal vents, of which scores have been identified so far, especially in the Pacific, Atlantic and Indian oceans. They occur where the Earth’s crust spreads or collides, creating ideal conditions for the formation of deep-sea carbon dioxide reservoirs. Only about one-third of the ocean’s volcanic regions have been surveyed.

One such reservoir of undersea carbon dioxide, seen in an accompanying video, was discovered about 4,000 feet deep off the coast of Taiwan. Similar discoveries of carbon gas reservoirs have been made off the coast of Okinawa, in the Aegean Sea, in the Gulf of California and off the west coast of Canada.

“The grand challenge is we don’t have estimates of the size of these or which ones are particularly vulnerable to destabilization,” Stott said. “It’s something that needs to be determined.”

A deep-sea reservoir near Taiwan spews carbon dioxide when its slurry-like hydrate cap ruptures

. (Video/The National Academy of Sciences of the USA)

In many cases, the carbon reservoirs are bottled up by their hydrate caps. But those covers are sensitive to temperature changes. As oceans warm, the caps can melt, a development the paper warns would lead to a double wallop for climate change — a new source of geologic carbon in addition to the manmade greenhouse gases.

Oceans absorb nearly all the excess energy from the Earth’s atmosphere, and as a result they have been warming rapidly in recent decades. Over the past quarter-century, Earth’s oceans have retained 60 percent more heat each year than scientists previously had thought, other studies have shown. Throughout the marine water column, ocean heat has increased for the last 50 years. The federal government’s Climate Science Special Report projected a global increase in average sea surface temperatures of up to 5 degrees Fahrenheit by the end of the century, given current emissions rates. Temperature gains of that magnitude throughout the ocean could eventually destabilize the geologic hydrate reservoirs, Stott said.

“The last time it happened, climate change was so great it caused the end of the ice age. Once that geologic process begins, we can’t turn it off,” Stott said.

Moreover, other similar events have happened in the distant past, helping shape the Earth’s environment over and over again. In earlier research, Stott discovered a large, carbon anomaly that occurred 55 million years ago. It disrupted the ocean’s chemistry, causing extensive dissolution of marine carbonates and the extinction of many marine organisms. The ocean changes were accompanied by a rapid rise in global temperatures, an event called the Paleocene-Eocene Thermal Maxima (PETM), a period lasting less than 20,000 years during which so much carbon was released to the atmosphere that Earth’s temperatures surged to about 8 degrees Celsius hotter than today.

“Until quite recently, we had no idea these events occurred. The PETM event is a good analog for what can happen when undersea carbon escapes through the water column to the atmosphere. And now we know the PETM event was not a unique event, that this has happened more recently,” Stott said.

The study comes with some caveats. Much of the ocean floor is unexplored, so scientists don’t know the full extent of the carbon dioxide reservoirs. There is no inventory of greenhouse gases from these geologic sources. And ocean warming is not uniform, making it difficult to predict when and where the undersea carbon reservoirs will be affected. It would take much more study to answer those questions.

Undersea carbon reservoirs clearly at risk

Nonetheless, the study makes clear the undersea carbon reservoirs are at risk.

“Geologic carbon reservoirs such as these are not explicitly included in current marine carbon budgets” used to model the impacts of climate change, the study says. Yet, “even if only a small percentage of the unsampled hydrothermal systems contain separate gas or liquid carbon dioxide phases, it could change the global marine carbon budget substantially.”

Said Stott: “Discoveries of accumulations of liquid, hydrate and gaseous carbon dioxide in the ocean has not been accounted for because we didn’t know these reservoirs existed until recently, and we didn’t know they affected global change in a significant way.

“This study shows that we’ve been missing a critical component of the marine carbon budget. It shows these geologic reservoirs can release large amounts of carbon from the oceans. Our paper makes the case that this process has happened before and it could happen again.”

Contacts and sources:
 Gary Polakovic
University of Southern California
Citation:  Hydrothermal carbon release to the ocean and atmosphere from the Eastern Equatorial Pacific during the Last Glacial Termination
Lowell Douglas Stott, Kathleen M. Harazin, Nadine B. Quintana Krupinski. . Environmental Research Letters, 2019; DOI: 10.1088/1748-9326/aafe28



Phosphorus Key to Making Lithium Metal Batteries Simpler, Stronger and Safer



Rice University scientists have taken the next step toward the deployment of powerful, rechargeable lithium metal batteries by making them safer and simpler to manufacture.

The Rice lab of chemist James Tour made test cells with a coat of red phosphorus on the separator that keeps the anode and cathode electrodes apart. The phosphorus acts as a spy for management systems used to charge and monitor batteries by detecting the formation of dendrites, protrusions of lithium that can cause them to fail.

A layer of red phosphorus in rechargeable lithium metal batteries can signal when damaging dendrites threaten to create a short circuit. The technique developed at Rice University could lead to more powerful lithium metal batteries.

Credit: Tour Group/Rice University

Lithium metal anodes charge much faster and hold about 10 times more energy by volume than common lithium-ion anodes used in just about every electronic device on the market, including cellphones and electric cars. Anodes are one of two electrodes needed for battery operation.

But charging lithium-infused anodes forms dendrites that, if they reach the cathode, cause a short circuit and possibly a fire or explosion. When a dendrite reaches a red phosphorus-coated separator, the battery's charging voltage changes. That tells the battery management system to stop charging.

Unlike other proposed dendrite detectors, the Rice strategy doesn't require a third electrode.

"Manufacturing batteries with a third electrode is very hard," Tour said. "We propose a static layer that gives a spike in the voltage while the battery is charging. That spike is a signal to shut it down."

The research appears in Advanced Materials.

The red phosphorus layer had no significant effect on normal performance in experiments on test batteries by the Tour lab.

The researchers built a transparent test cell with an electrolyte (the liquid or gel-like material between the electrodes and around the separator that allows the battery to generate a current) known to accelerate aging of the cathode and encourage dendrite growth. That let them monitor the voltage while they watched dendrites grow.

Images of a half-cell lithium metal battery show dendrites approaching a red phosphorus separator. The separator delivers a signal to the battery's electronics to shut down when dendrites threaten to create a short circuit. The discovery by scientists at Rice University could help make lithium batteries safer.
Credit: Tour Group/Rice University

With an ordinary separator, they saw the dendrites contact and penetrate the separator with no change in voltage, a situation that would lead a normal battery to fail. But with the red phosphorus layer, they observed a sharp drop in voltage when the dendrites contacted the separator.

"As soon as a growing dendrite touches the red phosphorus, it gives a signal in the charging voltage," Tour said. "When the battery management system senses that, it can say, 'Stop charging, don't use.'"

Last year, the lab introduced carbon nanotube films that appear to completely halt dendrite growth from lithium metal anodes.

"By combining the two recent advances, the growth of lithium dendrites can be mitigated, and there is an internal insurance policy that the battery will shut down in the unlikely event that even a single dendrite will start to grow toward the cathode," Tour said.

"Literally, when you make a new battery, you're making over a billion of them," he said. "Might a couple of those fail? It only takes a few fires for people to get really antsy. Our work provides a further guarantee for battery safety. We're proposing another layer of protection that should be simple to implement."



Contacts and sources:
Jeff Falk
Rice University


Citation: Detecting Li Dendrites in a Two‐Electrode Battery System Tuo Wang Rodrigo Villegas Salvatierra James M. Tour First published: 13 February 2019 https://doi.org/10.1002/adma.201807405  https://onlinelibrary.wiley.com/doi/abs/10.1002/adma.201807405