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Sunday, May 28, 2017

Nano Fiber Feels Forces and Hears Sounds Made by Cells

Engineers at the University of California San Diego have developed a miniature device that’s sensitive enough to feel the forces generated by swimming bacteria and hear the beating of heart muscle cells.

The device is a nano-sized optical fiber that’s about 100 times thinner than a human hair. It can detect forces down to 160 femtonewtons — about ten trillion times smaller than a newton — when placed in a solution containing live Helicobacter pylori bacteria, which are swimming bacteria found in the gut. In cultures of beating heart muscle cells from mice, the nano fiber can detect sounds down to -30 decibels — a level that’s one thousand times below the limit of the human ear.

An artist’s illustration of nano optical fibers detecting femtonewton-scale forces produced by swimming bacteria. 
nano optical fibers
Credit: Rhett S. Miller/UC Regents

“This work could open up new doors to track small interactions and changes that couldn’t be tracked before,” said nanoengineering professor Donald Sirbuly at the UC San Diego Jacobs School of Engineering, who led the study.

Some applications, he envisions, include detecting the presence and activity of a single bacterium; monitoring bonds forming and breaking; sensing changes in a cell’s mechanical behavior that might signal it becoming cancerous or being attacked by a virus; or a mini stethoscope to monitor cellular acoustics in vivo.

The work is published in Nature Photonics on May 15.

The optical fiber developed by Sirbuly and colleagues is at least 10 times more sensitive than the atomic force microscope (AFM), an instrument that can measure infinitesimally small forces generated by interacting molecules. And while AFMs are bulky devices, this optical fiber is only several hundred nanometers in diameter. “It’s a mini AFM with the sensitivity of an optical tweezer,” Sirbuly said.

The device is made from an extremely thin fiber of tin dioxide, coated with a thin layer of a polymer, called polyethylene glycol, and studded with gold nanoparticles. To use the device, researchers dip the nano optical fiber into a solution of cells, send a beam of light down the fiber and analyze the light signals it sends out. These signals, based on their intensity, indicate how much force or sound the fiber is picking up from the surrounding cells.

“We’re not just able to pick up these small forces and sounds, we can quantify them using this device. This is a new tool for high resolution nanomechanical probing,” Sirbuly said.

Here’s how the device works: as light travels down the optical fiber, it interacts strongly with the gold nanoparticles, which then scatter the light as signals that can be seen with a conventional microscope. These light signals show up at a particular intensity. But that intensity changes when the fiber is placed in a solution containing live cells. Forces and sound waves from the cells hit the gold nanoparticles, pushing them into the polymer layer that separates them from the fiber’s surface. Pushing the nanoparticles closer to the fiber allows them to interact more strongly with the light coming down the fiber, thus increasing the intensity of the light signals. Researchers calibrated the device so they could match the signal intensities to different levels of force or sound.

The key to making this work is the fiber’s polymer layer. It acts like a spring mattress that’s sensitive enough to be compressed to different thicknesses by the faint forces and sound waves produced by the cells. And Sirbuly says the polymer layer can be tuned — if researchers want to measure larger forces, they can use a stiffer polymer coating; for increased sensitivity, they can use a softer polymer like a hydrogel.

Moving forward, researchers plan to use the nano fibers to measure bio-activity and the mechanical behavior of single cells. Future works also includes improving the fibers’ “listening” capabilities to create ultra-sensitive biological stethoscopes, and tuning their acoustic response to develop new imaging techniques.

Contacts and sources:
Liezel LabiosUniversity of California, San Diego

Paper title: “Nanofibre optic force transducers with sub-piconewton resolution via near-field plasmon-dielectric interactions” by Qian Huang*, Joon Lee*, Fernando Teran Arce*, Ilsun Yoon, Pavimol Angsantikul, Justin Liu, Yuesong Shi, Josh Villanueva, Soracha Thamphiwatana, Xuanyi Ma, Liangfang Zhang, Shaochen Chen, Ratnesh Lal and Donald J. Sirbuly at UC San Diego.

*These authors contributed equally to this work.

This work was supported by the National Science Foundation (ECCS 1150952) and the University of California, Office of the President (UC-LFRP 12-LR-238415). 

3-D Printed Ovaries Produce Healthy Offspring

Bioprosthetic ovaries produced mouse pups in otherwise infertile mice. 

The new world of 3-D printed organs now includes implanted ovary structures that, true to their design, actually ovulate, according to a study by Northwestern University Feinberg School of Medicine and McCormick School of Engineering.

By removing a female mouse’s ovary and replacing it with a bioprosthetic ovary, the mouse was able to not only ovulate but also give birth to healthy pups. The moms were even able to nurse their young.

The bioprosthetic ovaries are constructed of 3-D printed scaffolds that house immature eggs, and have been successful in boosting hormone production and restoring fertility in mice, which was the ultimate goal of the research.

“This research shows these bioprosthetic ovaries have long-term, durable function,” said Teresa K. Woodruff, a reproductive scientist and director of the Women’s Health Research Institute at Feinberg. “Using bioengineering, instead of transplanting from a cadaver, to create organ structures that function and restore the health of that tissue for that person, is the holy grail of bioengineering for regenerative medicine.”

The paper was published May 16, in Nature Communications.

How is this research different from other 3-D printed structures?

What sets this research apart from other labs is the architecture of the scaffold and the material, or “ink,” the scientists are using, said Ramille Shah, assistant professor of materials science and engineering at McCormick and of surgery at Feinberg.

That material is gelatin, which is a biological hydrogel made from broken-down collagen that is safe to use in humans. The scientists knew that whatever scaffold they created needed to be made of organic materials that were rigid enough to be handled during surgery and porous enough to naturally interact with the mouse’s body tissues.

Credit: Northwestern University

“Most hydrogels are very weak, since they’re made up of mostly water, and will often collapse on themselves,” Shah said. “But we found a gelatin temperature that allows it to be self-supporting, not collapse, and lead to building multiple layers. No one else has been able to print gelatin with such well-defined and self-supported geometry.”

That geometry directly links to whether or not the ovarian follicles, organized hormone-producing support cells surrounding an immature egg cell, will survive in the ovary, which was one of the bigger findings in the study.

“This is the first study that demonstrates that scaffold architecture makes a difference in follicle survival,” Shah said. “We wouldn’t be able to do that if we didn’t use a 3-D printer platform.”
How does this impact humans?

The scientists’ sole objective for developing the bioprosthetic ovaries was to help restore fertility and hormone production in women who have undergone adult cancer treatments or those who survived childhood cancer and now have increased risks of infertility and hormone-based developmental issues.

“What happens with some of our cancer patients is that their ovaries don’t function at a high enough level and they need to use hormone replacement therapies in order to trigger puberty,” said Monica Laronda, co-lead author of this research and a former post-doctoral fellow in the Woodruff lab. “The purpose of this scaffold is to recapitulate how an ovary would function. We’re thinking big picture, meaning every stage of the girl’s life, so puberty through adulthood to a natural menopause.”

Laronda is now an assistant professor at the Stanley Manne Children’s Research Institute at the Ann & Robert H. Lurie Children’s Hospital.

Additionally, the successful creation of 3-D printed implants to replace complex soft tissue could significantly impact future work in soft tissue regenerative medicine.

Technically, how does biological 3-D printing work?

3-D printing an ovary structure is similar to a child using Lincoln Logs, said Alexandra Rutz, co-lead author of the study and a former biomedical engineering graduate fellow in Shah’s Tissue Engineering and Additive Manufacturing (TEAM) lab at the Simpson Querrey Institute. Children can lay the logs at right angles to form structures. Depending on the distance between the logs, the structure changes to build a window or a door, etc.

“3-D printing is done by depositing filaments,” said Rutz, who is now a Whitaker International Postdoctoral Scholar at École Des Mines De Saint-Étienne in Gardanne, France. “You can control the distance between those filaments, as well as the advancing angle between layers, and that would give us different pore sizes and different pore geometries.”

In Northwestern’s lab, the researchers call these 3-D printed structures “scaffolds,” and liken them to the scaffolding that temporarily surrounds a building while it undergoes repairs.

“Every organ has a skeleton,” said Woodruff, who also is the Thomas J. Watkins Memorial Professor of Obstetrics and Gynecology and a member of the Robert H. Lurie Comprehensive Cancer Center of Northwestern University. “We learned what that ovary skeleton looked like and used it as model for the bioprosthetic ovary implant.”

In a building, the scaffolding supports the materials needed to repair the building until it’s eventually removed. What’s left is a structure capable of holding itself up. Similarly, the 3-D printed “scaffold” or “skeleton” is implanted into a female and its pores can be used to optimize how follicles, or immature eggs, get wedged within the scaffold. The scaffold supports the survival of the mouse’s immature egg cells and the cells that produce hormones to boost production. The open structure also allows room for the egg cells to mature and ovulate, as well as blood vessels to form within the implant enabling the hormones to circulate within the mouse bloodstream and trigger lactation after giving birth.

The all-female McCormick-Feinberg collaboration for this research was “very fruitful,” Shah said, adding that it was motivational to be part of an all-female team doing research towards finding solutions to female health issues.

“What really makes a collaboration work are the personalities and being able to find the humor in the research,” Shah said. “Teresa and I joked that we’re grandparents of these pups.”

Contacts and sources: 
Kristin Samuelson
Northwestern University

Baboons at the Leading Edge of a Pack, Eat First, Take the Most Risks

Are you the kind of person who, at a party, tends to be surrounded by friends in the middle of the crowd, or do you prefer to find a quiet corner where you can sit and talk? Recent work by scientists at University of California Davis shows that wild baboons behave similarly to humans — with some animals consistently found in the vanguard of their troop while others crowd to the center or lag in the rear.

An adult male baboon and an adult female with clinging infant forage for food. Adult male baboons are larger than females and have impressive weaponry (i.e. larger teeth). This means that they are not only socially dominant but also less vulnerable to predators, influencing the costs and benefits of being on the edge of the group versus the center.
Photo by Margaret Crofoot

Using high-resolution GPS tracking, UC Davis Assistant Professor Margaret Crofoot and her team of researchers continuously monitored the movements of nearly an entire baboon troop in central Kenya to discover how interactions among group-mates influenced where in the troop individuals tended to be found.

“How animals position themselves within their social group can have life or death consequences,” explained Crofoot, an anthropologist. “Individuals at the front of their group may get the first crack at any food their group encounters, but they are also more vulnerable to being picked off by predators.”

Interestingly, the team’s work suggests that very simple behavioral rules may explain baboons’ apparent preferences for particular spatial positions. “Animals who pay attention to more of their group-mates when deciding where to move will inevitably end up at the center of their group,” said Crofoot. Differences in social sensitivity may therefore explain why younger baboons end up in the safest positions at the center of their troop, while adult males find themselves exposed on the leading edge.

Researchers have long noted that spatial positioning has important fitness implications, but where an animal is positioned in its group depends not only on its own behavior, but also on the behavior of its group-mates. “How natural selection shapes such emergent properties is fundamental to understanding the evolutionary dynamics of social organisms,” Crofoot said.

The findings were published in April in the journal Proceedings of the Royal Society.

The study was funded by the National Science Foundation, Office of Naval Research, Army Research Office and Human Frontiers Science Program.
More information

Contacts and sources:
Karen Nikos-Rose/Andy Fell
University of California Davis  (UC Davis)

Read the study

Baboons on the Move Practice Democracy

Interactive Touchscreen for Dolphins Created, They Play Games Like Whack-a-Mole with Training

Dolphins are highly intelligent and social animals, but can they use a smartphone built just for them? Yes, scientists have discovered—they can even play games like Whack-a-Mole with little training.

Researchers at Rockefeller University and Hunter College, working with the National Aquarium in Baltimore, MD, have developed a touchpad for dolphins, the first of its kind, using optical technology. The system, essentially an underwater computer touchscreen through which dolphins are able to interact and make choices, will be used to investigate dolphin intelligence and communication by providing them choice and control over a number of activities.

Observing dolphins interact with a specially-made touchscreen could open new windows into dolphin cognition. 
Dolphin eye
Credit: The M2C2 Research Collaborative

The eight-foot underwater touchscreen features specialized dolphin-friendly “apps” and a symbolic keyboard to provide the dolphins with opportunities to interact with the system. To make the system safe for the dolphins, the touchscreen has been installed outside an underwater viewing window, so that no parts of the device are in the pool: the animals’ touch is detected optically. 

 While the research is still in its early stages, the team has embarked on studies aimed at understanding dolphin vocal learning and communication, their capacity for symbolic communication, and what patterns of behavior may emerge when the animals have the ability to request items, videos, interactions, and images.

A dolphin’s version of touchscreen Whack-a-Mole.

 Credit: The M2C2 Research Collaborative

The interdisciplinary research team is comprised of biophysicist Marcelo Magnasco, professor and head of the Laboratory of Integrative Neuroscience at Rockefeller University, and Diana Reiss, a dolphin cognition and communication research scientist and professor in the department of psychology at Hunter College. Also involved are Ana Hocevar, a postdoctoral research scientist; and Sean Woodward, a doctoral student, both in Magnasco’s lab.

“It was surprisingly difficult to find an elegant solution that was absolutely safe for the dolphins, but it has been incredibly rewarding to work with these amazing creatures and see their reactions to our system,” says Magnasco. “It has always been hard to keep up with dolphins, they are so smart; a fully interactive and programmable system will help us follow them in any direction they take us.”

In addition to the touchscreen itself, the dolphin’s habitat at the National Aquarium has been outfitted with equipment to record their behavior and vocalizations as they encounter and begin to use the technology.

“We hope this technologically-sophisticated touchscreen will be enriching for the dolphins and also enrich our science by opening a window into the dolphin mind,” says Reiss. “Giving dolphins increased choice and control allows them to show us reflections of their way of thinking and may help us decode their vocal communication.”

Already, the scientists have begun to introduce the dolphins to some of the system’s interactive apps, so the animals can explore on their own how touching the screen results in specific contingencies. Without any explicit training or encouragement, one of the younger dolphins, Foster, spontaneously showed immediate interest and expertise in playing a dolphin version of Whack-a-Mole, in which he tracks and touches moving fish on the touchscreen.

The researchers believe this technology will help extend the high-throughput revolution in biology that has brought us whole genome sequencing and the BRAIN project, into the field of animal cognition. They also hope that the information gleaned from this research will result in increased empathy toward dolphins and inspire global policies for their protection.

Contacts and sources:
Katherine Fenz
Rockefeller University

In a Drought, Over-Irrigated Lawns Lose 70 Billion Gallons of Water a Year

In the summer of 2010, Los Angeles lost about 100 gallons of water per person per day to the atmosphere through evaporation, mostly from overwatering of lawns and trees.

Lawns accounted for 70 percent of the water loss, while trees accounted for 30 percent, according to a study published today in the journal Water Resources Research. The research was funded by the National Science Foundation (NSF) and conducted by Diane Pataki and Elizaveta Litvak of the University of Utah.

The scientists found that 70 percent of Los Angeles' evapotranspiration comes from irrigated lawns.
The scientists found that 70 percent of Los Angeles' evapotranspiration comes from irrigated lawns.
Credit: Diane Pataki

The results, based on measurements taken before Los Angeles mandated watering restrictions in 2014, show a pattern of systemic overwatering of the city's lawns, and a surprising water efficiency of its tree cover. The researchers also found a correlation between water loss and household income.

The water loss that Pataki and Litvak measured is called evapotranspiration (ET), the evaporation of water from the soil and the transpiration, or release of water vapor, from plants. ET rates depend on several factors, including plant type, temperature, humidity and the amount of water in the soil.

According to the scientists' measurements, Los Angeles' soils were an abundant source of water during the drought, largely a result of lawn overwatering. Imagine placing a soaking wet towel out to dry on a hot summer day: it's a thoroughly wet surface, and should evaporate quickly. Water loss from an over-irrigated lawn is similar because transpiration from the grass pumps water from the soil to the atmosphere.

For the study, the researchers took measurements in the urban tree canopy throughout Los Angeles.

Credit: Diane Pataki

"California's recent drought highlights the need for urban water conservation," says Tom Torgersen, program director in the Division of Earth Sciences in NSF's Geosciences Directorate, which funded the research. NSF's directorates for Biological Sciences and Social, Behavioral and Economic Sciences also funded the research.

Torgersen says that for Los Angeles, the greatest ET was due to turf grass and seed-producing trees. Palm trees made very small contributions.

"Both provide an alleviation of the urban heat island effect and reduce the need for air conditioning," Torgersen says. "However, the benefit is not evenly shared. The higher the median income, the greater the local ET, with cooler temperatures in wealthier areas and higher temperatures in poorer sections of the city."

To measure ET from lawns, Litvak devised a shoebox-size chamber that measured rapid changes of the temperature and humidity above the grass.

Pataki, Litvak and their colleagues traveled around Los Angeles in the summer of 2010 and the winter of 2011 taking measurements to develop a mathematical model of ET rates from lawns under different conditions.

Researchers estimated the flow of water vapor from the soil to the atmosphere in Los Angeles landscapes.

Credit: Diane Pataki

They tested the hypothesis that wealthier neighborhoods had more plant cover and cooler temperatures than poorer areas.

ET rates in the wealthiest neighborhoods, they found, were roughly twice those of poorer neighborhoods. That's probably due to a variety of factors, Pataki and Litvak say, including the larger lot sizes of more expensive properties.

Trees emerged as the water-saving heroes of the study, using far less water than grassy lawns.

Trees have a much lower leaf surface area and don't directly irrigate their leaves, so they are less prone to evaporation. Also, trees regulate their transpiration rate in response to the surrounding humidity. Under dry conditions, trees will rein in transpiration so they can retain water.

"It's surprising that we can maintain the tree canopy of L.A. with relatively little water," Pataki says. "There's this assumption that we need abundant irrigation to support trees. But we can drastically reduce water use and still have trees."

This spring, Los Angeles' watering restrictions were lifted after California's very wet winter.

Pataki says it's too early to tell whether Los Angeles residents' watering patterns and landscaping choices will return to pre-drought excesses.

"Whether the drought changed people's landscape preferences in a lasting way, that's something we still need to find out," she says.

Contacts and sources:
Cheryl Dybas, National Science Foundation (NSF)
Paul Gabrielsen, University of Utah

World’s Most Sensitive Dark Matter Detector Releases First Results

Scientists behind XENON1T, the largest dark matter experiment of its kind ever built, are encouraged by early results, describing them as the best so far in the search for dark matter.

Dark matter is one of the basic constituents of the universe, five times more abundant than ordinary matter. Several astronomical measurements have corroborated the existence of dark matter, leading to an international effort to observe it directly. Scientists are trying to detect dark matter particle interacting with ordinary matter through the use of extremely sensitive detectors. Such interactions are so feeble that they have escaped direct detection to date, forcing scientists to build detectors that are more and more sensitive and have extremely low levels of radioactivity.

On May 18, the XENON Collaboration released results from a first, 30-day run of XENON1T, showing the detector has a record low radioactivity level, many orders of magnitude below surrounding material on earth.

XENON1T installation in the underground hall of Laboratori Nazionali del Gran Sasso. The three story building on the right houses various auxiliary systems. The cryostat containing the LXeTPC is located inside the large water tank on the left.
XENON1T Installation
Photo by Roberto Corrieri and Patrick De Perio

“The care that we put into every single detail of the new detector is finally paying back,” said Luca Grandi, assistant professor in physics at the University of Chicago and member of the XENON Collaboration. “We have excellent discovery potential in the years to come because of the huge dimension of XENON1T and its incredibly low background. These early results already are allowing us to explore regions never explored before.”

The XENON Collaboration consists of 135 researchers from the United States, Germany, Italy, Switzerland, Portugal, France, the Netherlands, Israel, Sweden and the United Arab Emirates, who hope to one day confirm dark matter’s existence and shed light on its mysterious properties.

Located deep below a mountain in central Italy, XENON1T features a 3.2-ton xenon dual-phase time projection chamber. This central detector sits fully submersed in the middle of the water tank, in order to shield it from natural radioactivity in the cavern. A cryostat helps keep the xenon at a temperature of minus-95 degrees Celsius without freezing the surrounding water. The mountain above the laboratory further shields the detector, preventing it from being perturbed by cosmic rays.

But shielding from the outer world is not enough, since all materials on Earth contain tiny traces of natural radioactivity. Thus extreme care was taken to find, select and process the materials making up the detector to achieve the lowest possible radioactive content. This allowed XENON1T to achieve record “silence” necessary to detect the very weak output of dark matter.

A particle interaction in the one-ton central core of the time projection chamber leads to tiny flashes of light. Scientists record and study these flashes to infer the position and the energy of the interacting particle—and whether it might be dark matter.

Scientists assembling the XENON1T time projection chamber.
Photo by Enrico Sacchetti

Despite the brief 30-day science run, the sensitivity of XENON1T has already overcome that of any other experiment in the field probing unexplored dark matter territory.

“For the moment we do not see anything unexpected, so we set new constraints on dark matter properties,” Grandi said. “But XENON1T just started its exciting journey and since the end of the 30-day science run, we have been steadily accumulating new data.”
UChicago central to international collaboration

Grandi’s group is very active within XENON1T, and it is contributing to several aspects of the program. After its initial involvement in the preparation, assembly and early operations of the liquid xenon chamber, the group shifted its focus in the last several months to the development of the computing infrastructure and to data analysis.

“Despite its low background, XENON1T is producing a large amount of data that needs to be continuously processed,” said Evan Shockley, a graduate student working with Grandi. “The raw data from the detector are directly transferred from Gran Sasso Laboratory to the University of Chicago, serving as the unique distribution point for the entire collaboration.”

The framework, developed in collaboration with a group led by Robert Gardner, senior fellow at the Computation Institute, allows for the processing of data, both on local and remote resources belonging to the Open Science Grid. The involvement of UChicago’s Research Computing Center including Director Birali Runesha allows members of the collaboration all around the world to access processed data for high-level analyses.

Grandi’s group also has been heavily involved in the analysis that led to this first result. Christopher Tunnell, a fellow at the Kavli Institute for Cosmological Physics, is one of the two XENON1T analysis coordinators and corresponding author of the result. Recently, UChicago hosted about 25 researchers for a month to perform the analyses that led to the first results.

“It has been a large, concentrated effort and seeing XENON1T back on the front line makes me forget the never-ending days spent next to my colleagues to look at plots and distributions,“ Tunnell said. “There is no better thrill than leading the way in our knowledge of dark matter for the coming years.”

U.S. federal funding for the research comes from the National Science Foundation.

Contacts and sources:
University of Chicago

The Lively Garden of the Ediacaran 635 to 540 Million Years Ago

The Garden of the Ediacaran was a period in the ancient past when Earth’s shallow seas were populated with a bewildering variety of enigmatic, soft-bodied creatures. Scientists have pictured it as a tranquil, almost idyllic interlude that lasted from 635 to 540 million years ago. But a new interdisciplinary study suggests that the organisms living at the time may have been much more dynamic than experts have thought.

Artist’s conception of a scene from the Garden of the Ediacaran. The new study suggests a number of these strange species which predate animals may have been capable of moving about 
Credit: Franz Anthony / Studio 252MYA

Scientists have found It extremely difficult to fit these Precambrian species into the tree of life. That is because they lived in a time before organisms developed the ability to make shells or bones. As a result, they didn’t leave much fossil evidence of their existence behind, and even less evidence that they moved around. So, experts have generally concluded that virtually all of the Ediacarans—with the possible exception of a few organisms similar to jellyfish that floated about—were stationary and lived out their adult lives fixed in one place on the sea floor.

Fossil imprint of Parvancorina, which may have been the first species capable of orienting itself to face into an ocean current.

Credit: Masahiro Miyasaka / Wikimedia Commons

The new findings concern one of the most enigmatic of the Ediacaran genera, a penny-sized organism called Parvancorina, which ischaracterized by a series of ridges on its back that form the shape of a tiny anchor. By analyzing the way in which water flows around Parvancorina’s body, an international team of researchers has concluded that these ancient creatures must have been mobile: specifically, they must have had the ability to orient themselves to face into the current flowing around them. That would make them the oldest species known to possess this capability, which scientists call rheotaxis.

“Our analysis shows that the amount of drag produced with the current flowing from front to back is substantially less than that flowing from side to side,” said Simon Darroch, assistant professor of earth and environmental sciences at Vanderbilt University, who headed the study. “In the strong currents characteristic of shallow ocean environments, that means Parvancorina would have benefited greatly from adjusting its position to face the direction of the flow.”

Simon Darroch 
Credit: Steve Green / Vanderbilt

The analysis, which used a technique borrowed from engineering called computational fluid dynamics (CFD), also showed that when Parvancorina faced into the current, its shape created eddy currents that were directed to several specific locations on its body. “This would be very beneficial to Parvancorina if it was a suspension feeder as we suspect because it would have concentrated the suspended organic material making it easier to consume,” Darroch said.

Details of the analysis are described in a paper titled “Inference of facultative mobility in the enigmatic Ediacaran organismParvancorina” published online May 17 by the Royal Society journal Biology Letters.

These conclusions are reinforced by an independent study performed by a team of Australian researchers published March 30 in the journal Scientific Reports. Analyzing an Ediacaran site in South Australia, they found that the Parvancorina fossils were preferentially aligned in the direction of the prevailing current and determined that this alignment was not passive but represented a rheotactic response at some point in the organism’s life history.

Top and side views produced by computer simulations show how water flows around the body of Parvancorina when the current is coming from the front (a), side (b) and rear (c). The arrows show the direction of the water flow and the colors represent its velocity (red and yellow are fast, blue and green are slow). It demonstrates that the flow patterns differ dramatically with each orientation. This implies that the organism had to have been mobile to feed effectively.
Credit: Simon Darroch / Vanderbilt

This is only the second time that CFD has been applied to study Ediacarans. In 2015, the same team of researchers applied this technique to analyze flow patterns around an organism called Tribrachidium heraldicum. This is a disk-shaped organism characterized by three spiraling ridges on its back. In this case, their analysissupported the conclusion that it was the oldest known suspension feeder, dating back to 555 million years.

“We decided to stop trying to figure out where these species fit in the tree of life and to try to determine how they were shaped by evolutionary forces,” said Darroch. “We wanted to understand how their weird architectures affected how they ate, reproduced and moved. Because they lived in a shallow sea environment, strong currents must have played a major role in their evolution. So computational fluid dynamics is the perfect tool for addressing this question.”

According to team member Imran Rahman, research fellow at the Oxford University Museum of Natural History, CFD has been used to analyze the design and optimize the performance of a wide variety of structures and machines, ranging from nuclear reactors to aircraft, but it is only in the last few years that they have begun applying it to study the fossil record: “CFD has the potential to transform our understanding of how ancient organisms fed and moved, so I would anticipate that many more paleontologists will start making use of the method in coming years.”

“When you sit back and think about it, we are virtually recreating ancient oceans, and populating them with digital representations of long extinct organisms that have defied our understanding for over 50 years in order to gain insight on how they lived their day to day lives,” added co-author Marc Laflamme, assistant professor of earth science at the University of Toronto Mississauga. “This kind of work would not have been feasible even a decade ago, and I believe it represents the direction that modern paleontology is forging.”

Model of a Parvancorina organism.

Credit: Matteo De Stefano/MUSE/Wikimedia Commons

“The fact that we have now established that one Ediacaran species could move around suggests that our picture of this period may be fundamentally wrong,” said Darroch. “There may have been a lot more movement going on than we thought and we intend to apply this technique to other Ediacaran fossils to determine if that was the case.”

Vanderbilt graduate student Brandt Gibson and Rachel Racicot at the Natural History Museum of Los Angeles County also contributed to the study.

CThe research was supported by National Science Foundation grants DEB 1331980 and PLR 134175 and by National Science and Engineering Research Council of Canada grant RGPIN 435402.

Contacts and sources:  
David Salisbury 
Vanderbilt University

Saturday, May 27, 2017

Life on Terra Firma Began with an Invasion from the Sea

Life on terra firma began with an invasion

Scientists are now confident animal life on solid ground started with a few short bursts of marine creatures making the leap from the oceans.

New research at the University of Portsmouth also paints a clear picture of how animals rapidly spread out and changed once they made the leap.

Trackways of modern arthropods on a desert dune. Examples like these, found preserved as fossils from millions of years ago, form the data in this study.

Credit: University of Portsmouth

The research, led by Dr Nicholas Minter of the University’s School of Earth and Environmental Sciences, is published in Nature Ecology and Evolution.

The first study to use trace fossils – the footprints of animal behaviour such as tracks and burrows – shows how a major evolutionary step for the Earth, the colonisation of land, took place.

The initial invasion happened across the world, from the fringes between land and oceans, followed by expansion later into floodplains, rivers, deserts and lakes.

It is the first time such a pattern has been identified using trace fossils to track the evolution of animal behaviour, their modes of life, and the ways in which they interacted with their new environments.

Dr Minter said: “When the first animals emerged from the oceans they had a blank canvas, there were no other animals there and so they diversified rapidly both in how they behaved and in the ecological roles, or the part they played, in the theatre of life.”

This evolutionary step-change – an early burst of rapidly adapting and diversifying to new environments, followed by a long period of little change – has been seen in the shapes and sizes of animals but this is the first time it has been shown for their behaviour.

The creatures which made the leap to land represent just a handful of the marine population, with spiders coming from the same group as crabs, and slugs and snails coming from the same group as squid and cuttlefish, for example.

“Not many from any one group, or Phylum, made the transition from sea to land or fresh water,” said Dr Minter.

“What’s surprising is the leaps in evolution follow the same pattern – an early evolutionary burst of rapid diversification and a long period of relative calm – each time animals conquered new habitats, first the margins between sea and land, then floodplains, followed by rivers, deserts and lakes.

“Each burst was an evolutionary experiment, yet the results are very similar.

“As scientists, we know experiments tend to have different outcomes if you change the parameters, but in this case, there is a consistency which suggests a fundamental constraint on the behavioural and ecological roles fulfilled by animals on land.”

The exhaustive study – a seven-year-long analysis of all known trace fossil data spanning a 200 million year period of Earth history – has the potential to tell us about our future, too, he said.

“We now have a framework we can use to apply to other questions and allows us to compare ancient and living communities. This framework may help us understand if modern communities are undergoing fundamental changes, as ancient ones have in the past, for example, in response to climate change.”

Trace fossils tell us a great deal about animal life, including who was there, when and how they behaved. Although Dr Minter’s research included examining reports of hundreds of trace fossils from hundreds of rock formations around the globe, the planet has not given up all its secrets.

He said: “This is not necessarily the final word. Another major step-change that took place was the evolution of social insects, such as ants and termites, which worked together to build complex structures and societies. More recently too, in the evolution of animals was the emergence of intelligent life – animals which could make and use tools, including humans and our ancestors, apes. We are yet to investigate how animals diversified and modified their environments during these events and how this shaped our planet.”

Contacts and sources:
University of Portsmouth 

Nation's Beekeepers Lost 33% of Bees in 2016-17

Beekeepers across the United States lost 33 percent of their honey bee colonies during the year spanning April 2016 to April 2017, according to the latest preliminary results of an annual nationwide survey. Rates of both winter loss and summer loss—and consequently, total annual losses—improved compared with recent years.

“While it is encouraging that losses are lower than in the past, I would stop short of calling this ‘good’ news,” said Dennis vanEngelsdorp, an assistant professor of entomology at the University of Maryland and project director for the Bee Informed Partnership. “Colony loss of more than 30 percent over the entire year
is high. It’s hard to imagine any other agricultural sector being able to stay in business with such consistently high losses.”

This summary chart shows the results of an 11-year annual survey that tracks honey bee colony losses in the United States, spanning 2006-2017.

Credit: University of Maryland/Bee Informed Partnership

The survey, which is conducted each year by the nonprofit Bee Informed Partnership in collaboration with the Apiary Inspectors of America, found total annual losses in 2016-17 were the lowest since 2011-12, when the survey recorded less than 29 percent of colonies lost throughout the year. Winter losses last year were the lowest recorded since the survey began in 2006-07. 

According to vanEngelsdorp, the primary reason for the drop in colony loss appears to be that efforts by beekeepers to control varroa mite infestations were more successful during the past year. Among the many different factors that contribute to colony losses, the lethal varroa mite parasite is considered to be at the top of the list.

In the fall months of 2016, varroa mite levels across the country were noticeably lower in most beekeeping operations compared with past years. The researchers said this is likely due to increased vigilance on the part of beekeepers, a greater availability of mite control products and environmental conditions that favored the use of timely and effective mite control measures. For example, some mite control products contain essential oils that break down at high temperatures, but many parts of the country experienced relatively mild temperatures in the spring and early summer of 2016.

Beekeepers who responded to the 2015-16 survey lost a total of 33.2 percent of their colonies over the course of the year. This marks a decrease of 7.3 percentage points over the previous study year (2015-16), when loss rates were found to be 40.5 percent. Winter loss rates decreased from 26.9 percent in the previous winter to 21.1 percent this past winter, while summer loss rates decreased from 23.6 percent to 18.1 percent.

The survey asks both commercial and small-scale beekeepers to track the survival rates of their honey bee colonies. Survey results for this year and all previous years are publicly available on the Bee Informed website.

“This is a complex problem,” said Kelly Kulhanek, a graduate student in the UMD Department of Entomology who helped with the survey. “Lower losses are a great start, but it’s important to remember that 33 percent is still much higher than beekeepers deem acceptable. There is still much work to do.”

In addition to the varroa mite, factors contributing to colony losses include other parasites, such as the gut parasite Nosema, and viral and bacterial diseases. Poor nutrition (due in part to loss of natural foraging habitat) and pesticide exposure also take a toll, especially among commercial beekeepers. These and other stressors are likely to synergize with each other to compound the problem, the researchers said.

This is the 11th year of the winter loss survey, and the seventh year to include summer and annual losses. More than 4,900 beekeepers from all 50 states and the District of Columbia responded to this year’s survey. All told, these beekeepers manage about 13 percent of the nation’s estimated 2.78 million honey bee colonies.

The survey is part of a larger research effort to understand why honey bee colonies are in such poor health, and what can be done to manage the situation. Some crops, such as almonds, depend entirely on honey bees for pollination. Honey bees pollinate an estimated $15 billion worth of crops in the U.S. annually.

“Bees are good indicators of the health of the landscape as a whole,” said Nathalie Steinhauer, a graduate student in the UMD Department of Entomology who leads the data collection efforts for the annual survey. “Honey bees are strongly affected by the quality of their environment, including flower diversity, contaminants and pests. To keep healthy bees, you need a good environment and you need your neighbors to keep healthy bees. Honey bee health is a community matter.”

2016-2017 survey results as well as previous years’ results are publicly available on the Bee Informed Partnership’s website.

Contacts and sources:
Matthew Wright
University of Maryland

Bacteria with Multicolor Vision

MIT researchers have engineered bacteria with “multicolor vision” — E. coli that recognize red, green, or blue (RGB) light and, in response to each color, express different genes that perform different biological functions.

Red, green, and blue light can be used to control gene expression in engineered E. coli.

To showcase the technology, the researchers produced several colored images on culture plates — one of which spells out “MIT” — by using RGB lights to control the pigment produced by the bacteria. Outside of the lab, the technology could also prove useful for commercial, pharmaceutical, and other applications.

Researchers produced colored images on culture plates by using red, green, and blue lights to control the pigment produced by bacteria with “multicolor vision.” The image has been color-corrected in Photoshop to improve contrast.
Researchers produced colored images on culture plates by using red, green, and blue lights to control the pigment produced by bacteria with “multicolor vision.”  The image has been color-corrected in Photoshop to improve contrast. Image: Felix Moser
The E. coli is programmed with a protein- and enzyme-based system, analogous to a computer chip, with several different modules to process the light input and produce a biological output. In computing terms, a “sensor array” first becomes activated in the presence of either red, green, or blue light, and a “circuit” processes the signal. Then, a “resource allocator” connects the processed information to “actuators” that implement the corresponding biological function.

Think of the new E. coli as microbial marionettes, with colored light instead of puppet strings making the bacteria act in a certain way, says MIT professor of biological engineering Chris Voigt, co-author of a paper in Nature describing the technology. “Using different colors, we can control different genes that are being expressed,” he says.

The paper’s co-authors are former postdocs Jesus Fernandez-Rodriguez, Felix Moser, and Miryoung Song.

Synthetic-biology innovation comes together

In 2005, Voigt, who co-directs the Synthetic Biology Center at MIT, and other researchers pioneered a “bacterial camera” by programming a light sensor into a strain of E. coli, along with a gene that produced black pigment. When light shone through a stencil onto a bacteria-coated plate, the microbes formed black-and-white images. At the time, this feat required only four genes and three promoters — regions of DNA that initiate gene transcription — to get the job done.

New synthetic biology tools, such as the genome-editing system CRISPR, have cropped up since then, opening broader possibilities to researchers. In contrast to the 2005 system, the new RGB system — the first to use three colors — consists of 18 genes and 14 promoters, among other parts, as well as 46,000 base pairs of DNA.

But with greater complexity come greater challenges. Because the researchers were dealing with a sensor array that could detect three separate colors, for instance, they had to include in the microbial program a protein that prevents gene transcription of the two unused sensors.

Colored images (insets) were projected onto plates of bacteria containing the RGB system to spell “MIT.” The image has been color-corrected in Photoshop to improve contrast.
Colored images (insets) were projected onto plates of bacteria containing the RGB system to spell “MIT.” The image has been color-corrected in Photoshop to improve contrast.
Image: Felix Moser

In computing terms, this is called a “NOT gate,” a circuit that produces an output signal — in this case, gene repression — only when there is not a signal on its input. With bacteria under a red light, for instance, the NOT gate would unleash that gene-repressing protein on the green and blue sensors, turning them off.

About five years ago, Voigt led a team that engineered microbes to respond to red and green light. Adding a third sensor was a major challenge of the new research. “Inside the cell, all the new protein sensors you add interfere with each other, because it’s all molecules bumping around the cell, and they all require keeping the cell alive and happy. With every additional sensor you add, that gets exponentially harder,” he says.

In that regard, Voigt adds, the system’s resource allocator, a new feature, also acts as a circuit breaker, shutting down the sensors if all three turn on at once, overloading the cell.

From a genetic engineering perspective, the four-subsystem configuration was “the biggest impact of this work,” Voigt says. Each subsystem — the sensor array, circuits, resource actuators, and actuators — was designed, built, and optimized in isolation before being assembled into a final structure. This simplified, modular process could pave the way for more complex biological programming in the future, according to the researchers.

Generally speaking, Voigt sees the new system as a culmination of a decade of synthetic-biology innovations. “It’s a representation of where we are currently, and all the pieces that needed to come together over the last decade to create systems of this scale and complexity,” he says.

Making “disco bacteria”

To make the new color images, the researchers programmed bacteria to produce the same pigment as the red, green, or blue light shone upon them. In an incubator, the researchers coated a petri dish with bacteria that are genetically identical. “You can think of it like undeveloped film, where you have the petri dish with bacteria on it,” Voigt says, “and the camera is the incubator.”

At the top of the incubator is a hole, where a stenciled image is projected onto the plate. Over time, the bacteria grow, producing an enzyme that produces a pigment corresponding to whichever RBG color they’re illuminated by. In addition to the MIT logo, the researchers produced images of various patterns, multicolored fruit, and the video game character Super Mario.

The engineered bacteria could also be used to rapidly start and stop the chemical reactions of microbes in industrial fermentation processes, which are used to make pharmaceuticals and other products. Today, controlling such chemical reactions requires dumping different chemical additives into large fermenting vats, which is time-consuming and inefficient.

In their paper, the researchers demonstrated this “chemicals on-demand” concept on a small scale. Using CRISPR gene-editing tools, they modified three genes that produce acetate — a sometimes-unwanted byproduct of various bioprocesses — to produce less of the chemical in response to RGB lights.

“Individually, and in combination with one another, the different colors of light reduce acetate production without sacrificing biomass accumulation,” the researchers wrote in their paper.

Voigt has coined an amusing name for these industrial microbes. “I refer to them as ‘disco bacteria,’” he says, “because different colored lights are flashing inside the fermenter and controlling the cells.”

A future application, Voigt adds, could be in controlling cells to form various materials and structures. Researchers, including some at MIT, have started programming cells to assemble into living materials that one day could be used to design solar cells, self-healing materials, or diagnostic sensors.

“It’s amazing when you look at the world and see all the different materials,” Voigt says. “Things like cellulose, silk proteins, metals, nanowires, and living materials like organs — all these different things in nature we get from cells growing into different patterns. You can imagine using different colors of light to tell the cells how they should be growing as part of building that material.”

The research was funded by the National Science Foundation’s Synthetic Biology Engineering Research Center, the Office of Naval Research’s Multidisciplinary University Research Initiative, and the National Institutes of Health.

Contacts and sources:
Rob MathesonMassachusetts Institute of Technology (MIT)

Conch Shell Secrets May Provide "Best-Ever" Helmets, Body Armor

The shells of marine organisms take a beating from impacts due to storms and tides, rocky shores, and sharp-toothed predators. But as recent research has demonstrated, one type of shell stands out above all the others in its toughness: the conch.

Now, researchers at MIT have explored the secrets behind these shells’ extraordinary impact resilience. And they’ve shown that this superior strength could be reproduced in engineered materials, potentially to provide the best-ever protective headgear and body armor.

Researchers at MIT have explored the secrets behind the conch shell’s extraordinary impact resilience. The findings are reported in a new study by MIT graduate student Grace Gu (right), postdoc Mahdi Takaffoli (left), and McAfee Professor of Engineering Markus Buehler.
Researchers at MIT have explored the secrets behind the conch shell’s extraordinary impact resilience. The findings are reported in a new study by MIT graduate student Grace Gu (right), postdoc Mahdi Takaffoli (left), and McAfee Professor of Engineering Markus Buehler.
Photo: Melanie Gonick/MIT

The findings are reported in the journal Advanced Materials, in a paper by MIT graduate student Grace Gu, postdoc Mahdi Takaffoli, and McAfee Professor of Engineering Markus Buehler.

Conch shells “have this really unique architecture,” Gu explains. The structure makes the material 10 times tougher than nacre, commonly known as mother of pearl. This toughness, or resistance to fractures, comes from a unique configuration based on three different levels of hierarchy in the material’s internal structure.

The three-tiered structure makes it very hard for any tiny cracks to spread and enlarge, Gu says. The material has a “zigzag matrix, so the crack has to go through a kind of a maze” in order to spread, she says.

Until recently, even after the structure of the conch shell was understood, “you couldn’t replicate it that well. But now, our lab has developed 3-D printing technology that allows us to duplicate that structure and be able to test it,” says Buehler, who is the head of the Department of Civil and Environmental Engineering.

Part of the innovation involved in this project was the team’s ability to both simulate the material’s behavior and analyze its actual performance under realistic conditions. “In the past, a lot of testing [of protective materials] was static testing,” Gu explains. “But a lot of applications for military uses or sports involve highly dynamic loading,” which requires a detailed examination of how an impact’s effects spread out over time.
For this work, the researchers did tests in a drop tower that enabled them to observe exactly how cracks appeared and spread — or didn’t spread — in the first instants after an impact. “There was amazing agreement between the model and the experiments,” Buehler says.

The team 3-D printed composite materials with precisely controlled structures, and conducted tests in a drop tower that enabled them to observe exactly how cracks appeared and spread — or didn’t spread — in the first instants after an impact.
The team 3-D printed composite materials with precisely controlled structures, and conducted tests in a drop tower that enabled them to observe exactly how cracks appeared and spread — or didn’t spread — in the first instants after an impact.
Courtesy of the researchers

That’s partly because the team was able to 3-D print composite materials with precisely controlled structures, rather than using samples of real shells, which can have unpredictable variations that can complicate the analysis. By printing the samples, “we can use exactly the same geometry” as used in the computer simulations, “and we get very good agreement.” Now, in continuing the work, they can focus on making slight variations “as a basis for future optimization,” Buehler says.

To test the relative importance of the three levels of structure, the team tried making variations of the material with different levels of hierarchy. Higher levels of hierarchy are introduced by incorporating smaller length-scale features into the composite, as in an actual conch shell. Sure enough, lower-level structures proved to be significantly weaker than the highest level pursued in this study, which consisted of the cross-lamellar features inherent in natural conch shells.

Testing proved that the geometry with the conch-like, criss-crossed features was 85 percent better at preventing crack propagation than the strongest base material, and 70 percent better than a traditional fiber composite arrangement, Gu says.

Testing proved that the geometry with the conch-like, criss-crossed features (right) was substantially better at preventing crack propagation.
Testing proved that the geometry with the conch-like, criss-crossed features (right) was substantially better at preventing crack propagation.
Photo: Melanie Gonick/MIT

Protective helmets and other impact-resistant gear require a key combination of both strength and toughness, Buehler explains. Strength refers to a material’s ability to resist damage, which steel does well, for example. Toughness, on the other hand, refers to a material’s ability to dissipate energy, as rubber does. Traditional helmets use a metal shell for strength and a flexible liner for both comfort and energy dissipation. But in the new composite material, this combination of qualities is distributed through the whole material.

“This has stiffness, like glass or ceramics,” Buehler says, but it lacks the brittleness of those materials, thanks to the integration of materials with different degrees of strength and flexibility within the composite structure. Like plywood, the composite is made up of layers whose “grain,” or the internal alignment of its materials, is oriented differently from one layer to the next.

Because of the use of 3-D printing technology, this system would make it possible to produce individualized helmets or other body armor. Each helmet, for example, could be “tailored and personalized; the computer would optimize it for you, based on a scan of your skull, and the helmet would be printed just for you,” Gu says.

These researchers “ingeniously used 3-D printing and experimentation to elucidate the effect of material hierarchy on bioinspired composites,” says Horacio Espinosa, a professor of mechanical engineering and director of the Theoretical and Applied Mechanics program at Northwestern University, who was not involved in this work. “An interesting remaining question,” he says, “is the applicability of the conch shell design to curved surfaces like those one would encounter in helmets.”

The research was supported by the Office of Naval Research, a National Defense Science and Engineering Graduate Fellowship, the Defense University Research Instrumentation Program (DURIP), the Institute for Soldier Nanotechnologies (ISN), and the Natural Sciences and Engineering Research Council of Canada.

Contacts and sources:
David L. Chandler
Massachusetts Institute of Technology

Hidden World of Giant Viruses Found in Seawater

An international team of researchers including University of Tennessee faculty has discovered a hidden world of giant viruses within a teaspoon of seawater.

The findings could help scientists directly examine the genetic potential of a virus without first having to grow it in a lab. This ability would be especially helpful for researchers in environmental and medical fields as well as virologists, as it would allow them to more rapidly identify and screen the molecular biology of new viruses.

Using a newly developed technique called single virus genomics—looking at a single virus particle instead of extracting DNA from millions of viruses to sequence a genome—researchers have picked out individual virus particles from seawater collected from the Gulf of Maine and analyzed their genomes. Through their work at the world-renowned Single Cell Genomics Center at the Bigelow Laboratory for Ocean Sciences in Maine, they discovered that every giant virus they analyzed was different and previously unknown to science. Some of the genomes revealed new infection mechanisms or enzymes not previously observed in viruses.

Giant viruses are a new group of virus particles that are larger, both in size and genomic content, than traditional viruses.

File:Atomic force microscopic images of starfish-shaped features on defibered mimiviruses - journal.pbio.1000092.g004.png
Credit: Structural Studies of the Giant Mimivirus. PLoS Biol 7(4): e1000092. doi:10.1371/journal.pbio.1000092/Wikimedia Commons

The results were recently published in the International Society for Microbial Ecology Journal, a division of the Nature publishing group.

The UT team members are Steven Wilhelm, Kenneth and Blaire Mossman Professor of Microbiology; Gary LeCleir, research assistant professor; and Mohammad Moniruzzaman, a former microbiology graduate student.

Steven Wilhelm
Credit: University of Tennessee

The team also included researchers from the Bigelow Laboratory, the National Institutes of Health, and two United Kingdom-based institutions—the Sir Alister Hardy Foundation for Ocean Sciences and Plymouth University.

The use of single virus genomics is a new way to obtain genomic sequence information from aquatic viruses. The term “viral dark matter,” a reference to the unknown genetic codes associated with observed effects, is often used in conjunction with aquatic viruses. These viruses—which account for 100,000,000 particles per liter of seawater—have massive effects in the ocean but are difficult to observe and even more difficult to measure. Single virus genomics can provide scientists with a new tool that will open up a universe of possibilities in understanding viruses.

Most of the newly discovered viruses belong to a group called the mimiviruses, because they mimic bacteria to persuade their hosts to eat them. Once ingested, the mimiviruses infect their hosts.

Many of the previously characterized mimiviruses have been isolated using an easily cultivated human pathogen—an amoeba that is unlikely to be the mimiviruses’ natural host in the ocean. One challenge marine scientists still face is that of determining what the natural hosts of these marine mimiviruses actually are. With clues in the genomes of individual viruses, tools developed in the study will help to address this challenge. In addition, exploration of these genomes will identify novel and diverse metabolisms of the newly discovered viruses.

“Linking individual viruses to individual hosts in nature is challenging,” Wilhelm said. “Given the size of these viruses, just confirming what their genome contains can be a challenge. With this approach we feel reconstruction of individual giant virus genomes directly from seawater is now possible. With this data, we can then infer the numbers and kinds of viruses that inhabit a particular ecosystem.”

Contacts and sources:
Steven Wilhelm
Lola Alapo
University of Tennessee Knoxville

Some Snakes Hunt in Packs

Snakes, although as social as birds and mammals, have long been thought to be solitary hunters and eaters. A new study from University of Tennessee (UT) shows that some snakes coordinate their hunts to increase their chances of success.

Vladimir Dinets, a research assistant professor of psychology, observed the Cuban boa—the island nation’s largest native terrestrial predator—in bat caves for the study.

Credit: Wikipedia/Eduard Horak

Many Cuban caves shelter large bat colonies, and in some of them small populations of boas regularly hunt the bats as they fly out at dusk and return at dawn. Dinets noticed that the boas hung down from the ceiling of the cave entrance and grabbed passing bats in midair. He found that if more than one boa was present, the snakes coordinated their positions in such a way that they formed a wall across the entrance. This made it difficult or impossible for the bats to pass without getting within striking distance of at least one boa.

Such group hunts were always successful, and the more snakes were present, the less time it took each to capture a bat. But if there was only one boa, it sometimes failed to secure a meal.

These findings were recently published open-access in the journal Animal Behavior and Cognition.

To date, only a handful of snakes have been observed to hunt in groups, and coordination among them—or among any other group-hunting reptiles—has never been proven, Dinets said.

Credit: Wikimedia Commons/Sgt. Mathieu Perry

Only a few of the world’s 3,650 snake species have ever been observed hunting in the wild, so very little is known about snakes’ diverse hunting tactics.

“It is possible that coordinated hunting is not uncommon among snakes, but it will take a lot of very patient field research to find out,” Dinets said.

He added that observing the Cuban boa, although an amazing spectacle, is becoming increasingly difficult since only the most remote caves still have boas. The boas are being hunted for food and possibly pet trade.

“I suspect that if their numbers in a cave fall, they can’t hunt in groups anymore and might die out even if some of them don’t get caught by hunters,” Dinets said. “A few of these caves are in national parks, but there’s a lot of poaching everywhere.”

Contacts and sources:
Lola Alapo
Vladimir Dinets 
University of Tennessee Knoxville

Friday, May 26, 2017

The Mystery of Floating Stones Solved

It’s true — some rocks can float on water for years at a time. And now scientists know how they do it, and what causes them to eventually sink.

X-ray studies at the Department of Energy’s Lawrence Berkeley National Laboratory have helped scientists to solve this mystery by scanning inside samples of lightweight, glassy and porous volcanic rocks known as pumice stones. The X-ray experiments were performed at Berkeley Lab’s Advanced Light Source (ALS), an X-ray source known as a synchrotron.
UC Berkeley pumice
Credit: Berkeley Lab

The surprisingly long-lived buoyancy of these rocks — which can form miles-long debris patches on the ocean known as pumice rafts that can travel for thousands of miles — can help scientists discover underwater volcano eruptions.

In this 2006 satellite image, a large “raft” of floating pumice stones (beige) appears following a volcanic eruption in the Tonga Islands.

Credit: Jesse Alan/NASA Earth Observatory, Goddard Space Flight Center

And, beyond that, learning about its flotation can help us understand how it spreads species around the planet; pumice is nutrient rich and readily serves as a seafaring carrier of plant life and other organisms. Floating pumice can also be a hazard for boats, as the ashy mixture of ground-up pumice can clog engines.

“The question of floating pumice has been around the literature for a long time, and it hadn’t been resolved,” said Kristen E. Fauria, a UC Berkeley graduate student who led the study, published in Earth and Planetary Science Letters.

Pumice stones

Credit: Berkeley Lab

While scientists have known that pumice can float because of pockets of gas in its pores, it was unknown how those gases remain trapped inside the pumice for prolonged periods. If you soak up enough water in a sponge, for example, it will sink.

“It was originally thought that the pumice’s porosity is essentially sealed,” Fauria said, like a corked bottle floating in the sea. But pumice’s pores are actually largely open and connected — more like an uncorked bottle. “If you leave the cap off and it still floats … what’s going on?”

Some pumice stones have even been observed to “bob” in the laboratory — sinking during the evening and surfacing during the day.

How it works

This animation, produced from a series of X-ray microtomography images collected at Berkeley Lab’s Advanced Light Source, shows a cube-shaped sample of pumice (blue-gray) and pockets of trapped gases (other colors). The animation also shows liquid (at 18 seconds) that surrounds the gases.

Credit: Berkeley Lab, UC Berkeley

To understand what’s at work in these rocks, the team used wax to coat bits of water-exposed pumice sampled from Medicine Lake Volcano near Mount Shasta in Northern California and Santa María Volcano in Guatemala.

They then used an X-ray imaging technique at the ALS known as microtomography to study concentrations of water and gas — in detail measured in microns, or thousandths of a millimeter — within preheated and room-temperature pumice samples.

The detailed 3-D images produced by the technique are very data-intensive, which posed a challenge in quickly identifying the concentrations of gas and water present in the pumice samples’ pores.

To tackle this problem, Zihan Wei, a visiting undergraduate researcher from Peking University, used a data-analysis software tool that incorporates machine learning to automatically identify the gas and water components in the images.

Concentrations of liquid and gas in samples of pumice stones are labeled in these images, produced by X-ray microtomography at Berkeley Lab’s Advanced Light Source. The images assisted researchers in identifying the mechanisms that enable pumice to float for prolonged periods. Heated pumice (shown in images at the top right and bottom right) samples contain a smaller volume of trapped gas than room-temperature samples.

Credit: UC Berkeley, Berkeley Lab

Researchers found that the gas-trapping processes that are in play in the pumice stones relates to “surface tension,” a chemical interaction between the water’s surface and the air above it that acts like a thin skin — this allows some creatures, including insects and lizards, to actually walk on water.

“The process that’s controlling this floating happens on the scale of human hair,” Fauria said. “Many of the pores are really, really small, like thin straws all wound up together. So surface tension really dominates.”

The team also found that a mathematical formulation known as percolation theory, which helps to understand how a liquid enters a porous material, provides a good fit for the gas-trapping process in pumice. And gas diffusion — which describes how gas molecules seek areas of lower concentration — explains the eventual loss of these gases that causes the stones to sink.

Floating and sinking

Individual gas bubbles trapped in two pumice samples (labeled “ML01” and “SM01”) are shaded with different colors. The size and connectedness of the bubbles can vary widely within a sample.

Credit: UC Berkeley, Berkeley Lab

Michael Manga, a staff scientist in Berkeley Lab’s Energy Geosciences Division and a professor in the Department of Earth and Planetary Science at UC Berkeley who participated in the study, said, “There are two different processes: one that lets pumice float and one that makes it sink,” and the X-ray studies helped to quantify these processes for the first time. The study showed that previous estimates for flotation time were in some cases off by several orders of magnitude.

“Kristen had the idea that in hindsight is obvious,” Manga said, “that water is filling up only some of the pore space.” The water surrounds and traps gases in the pumice, forming bubbles that make the stones buoyant. Surface tension serves to keep these bubbles locked inside for prolonged periods. The bobbing observed in laboratory experiments of pumice floatation is explained by trapped gas expanding during the heat of day, which causes the stones to temporarily float until the temperature drops.

The X-ray work at the ALS, coupled with studies of small pieces of pumice floating in water in Manga’s UC Berkeley lab, helped researchers to develop a formula for predicting how long a pumice stone will typically float based on its size. Manga has also used an X-ray technique at the ALS called microdiffraction, which is useful for studying the origins of crystals in volcanic rocks.

Dula Parkinson, a research scientist at Berkeley Lab’s ALS who assisted with the team’s microtomography experiments, said, “I’m always amazed at how much information Michael Manga and his collaborators are able to extract from the images they collect at ALS, and how they’re able to join that information with other pieces to solve really complicated puzzles.”

These 3-D printed models show a magnified sample of pumice (black) and a large concentration of gas (white) filling interconnected pores within that pumice sample.

Credit: Berkeley Lab

The recent study triggered more questions about floating pumice, Fauria said, such as how pumice, ejected from deep underwater volcanoes, finds its way to the surface. Her research team has also conducted X-ray experiments at the ALS to study samples from so-called “giant” pumice that measured more than a meter long.

That stone was recovered from the sea floor in the area of an active underwater volcano by a 2015 research expedition that Fauria and Manga participated in. The expedition, to a site hundreds of miles north of New Zealand, was co-led by Rebecca Carey, a scientist formerly affiliated with the Lab’s ALS.

Underwater volcano eruptions are not as easy to track down as eruptions on land, and floating pumice spotted by a passenger on a commercial aircraft actually helped researchers track down the source of a major underwater eruption that occurred in 2012 and motivated the research expedition. Pumice stones spewed from underwater volcano eruptions vary widely in size but can typically be about the size of an apple, while pumice stones from volcanoes on land tend to be smaller than a golf ball.

“We’re trying to understand how this giant pumice rock was made,” Manga said. “We don’t understand well how submarine eruptions work. This volcano erupted completely different than we hypothesized. Our hope is that we can use this one example to understand the process.”

Fauria agreed that there is much to learn from underwater volcano studies, and she noted that X-ray studies at the ALS will play an ongoing role in her team’s work.

The Advanced Light Source is a DOE Office of Science User Facility. This work was supported by the U.S. National Science Foundation.

Contacts and sources: 
Glenn Roberts Jr.
 Lawrence Berkeley National Laboratory

Summer Solstice Arrives for Saturn, A Once in Every 15 Years Event

NASA's Cassini spacecraft still has a few months to go before it completes its mission in September, but the veteran Saturn explorer reaches a new milestone today. Saturn's solstice -- that is, the longest day of summer in the northern hemisphere and the shortest day of winter in the southern hemisphere -- arrives today for the planet and its moons. The Saturnian solstice occurs about every 15 Earth years as the planet and its entourage slowly orbit the sun, with the north and south hemispheres alternating their roles as the summer and winter poles.

Reaching the solstice, and observing seasonal changes in the Saturn system along the way, was a primary goal of Cassini's Solstice Mission -- the name of Cassini's second extended mission.

These natural color views from Cassini show how the color of Saturn’s north-polar region changed between June 2013 and April 2017, as the northern hemisphere headed toward summer solstice.
Saturn’s north-polar region from two time periods
Credits: NASA/JPL-Caltech/SSI/Hampton Univ.

Cassini arrived at Saturn in 2004 for its four-year primary mission to study Saturn and its rings and moons. Cassini's first extended mission, from 2008 to 2010, was known as the Equinox Mission. During that phase of the mission, Cassini watched as sunlight struck Saturn's rings edge-on, casting shadows that revealed dramatic new ring structures. NASA chose to grant the spacecraft an additional seven-year tour, the Solstice Mission, which began in 2010.

"During Cassini's Solstice Mission, we have witnessed -- up close for the first time -- an entire season at Saturn," said Linda Spilker, Cassini project scientist at NASA's Jet Propulsion Laboratory, Pasadena, California. "The Saturn system undergoes dramatic transitions from winter to summer, and thanks to Cassini, we had a ringside seat."


During its Solstice Mission, Cassini watched a giant storm erupt and encircle the planet. The spacecraft also saw the disappearance of bluer hues that had lingered in the far north as springtime hazes began to form there. The hazes are part of the reason why features in Saturn's atmosphere are more muted in their appearance than those on Jupiter.

Cassini's view of Saturn during its 2009 equinox shows both the northern and southern hemispheres equally sunlit, with the north pole half in shadow. Since then, the sun has risen fully over the north, while the south has slipped into winter shadow.

Credits: NASA/JPL/Space Science Institute

Data from the mission showed how the formation of Saturn's hazes is related to the seasonally changing temperatures and chemical composition of Saturn's upper atmosphere. Cassini researchers have found that some of the trace hydrocarbon compounds there -- gases like ethane, propane and acetylene -- react more quickly than others to the changing amount of sunlight over the course of Saturn's year.

Researchers were also surprised that the changes Cassini observed on Saturn didn't occur gradually. They saw changes occur suddenly, at specific latitudes in Saturn's banded atmosphere. "Eventually a whole hemisphere undergoes change, but it gets there by these jumps at specific latitude bands at different times in the season," said Robert West, a Cassini imaging team member at JPL.


Following equinox and continuing toward northern summer solstice, the sun rose ever higher above the rings' northern face. And as the sun rises higher, its light penetrates deeper into the rings, heating them to the warmest temperatures seen there during the mission. The solstice sunlight helps reveal to Cassini's instruments how particles clump together and whether the particles buried in the middle of the ring plane have a different composition or structure than the ones in the rings' outer layers.

During its seven-year Solstice Mission, Cassini watched as a huge storm erupted and encircled Saturn. Scientists think storms like this are related, in part, to seasonal effects of sunlight on Saturn's atmosphere.

Credits: NASA/JPL/Space Science Institute

Saturn's changing angle with respect to the sun also means the rings are tipped toward Earth by their maximum amount at solstice. In this geometry, Cassini's radio signal passes more easily and cleanly through the densest rings, providing even higher-quality data about the ring particles there.


Cassini has watched Saturn's largest moon, Titan, change with the seasons, with occasional dramatic outbursts of cloud activity. After observing methane storm clouds around Titan's south pole in 2004, Cassini watched giant storms transition to Titan's equator in 2010. Although a few northern clouds have begun to appear, scientists have since been surprised at how long it has taken for cloud activity to shift to the northern hemisphere, defying climate models that had predicted such activity should have started several years earlier.

"Observations of how the locations of cloud activity change and how long such changes take give us important information about the workings of Titan's atmosphere and also its surface, as rainfall and wind patterns change with the seasons too," said Elizabeth Turtle, a Cassini imaging team associate at the Johns Hopkins University Applied Physics Laboratory in Laurel, Maryland.

Following Saturnian equinox in 2009, Cassini observed cloud activity on Titan shift from southern latitudes toward the equator, and eventually to the high north. Such observations have provided evidence of seasonal shifts in Titan's weather systems.

Credits: NASA/JPL/Space Science Institute

In 2013, Cassini observed a sudden and rapid buildup of haze and trace hydrocarbons in the south that were previously observed only in Titan's high north. This indicated to scientists that a seasonal reversal was underway, in which Titan’s main atmospheric circulation changes direction. This circulation was apparently channeling fresh hydrocarbon chemicals from closer to the equator toward the south pole, where they were safe from destruction by sunlight as that pole moved deeper into winter shadow.


For Enceladus, the most important seasonal change was the onset of winter darkness in the south. Although it meant Cassini could no longer take sunlit images of the geologically active surface, the spacecraft could more clearly observe the heat coming from within Enceladus itself. With the icy moon's south pole in shadow, Cassini scientists have been able to monitor the temperature of the terrain there without concern for the sun's influence. These observations are helping researchers to better understand the global ocean that lies beneath the surface. From the moon's south polar region, that hidden ocean sprays a towering plume of ice and vapor into space that Cassini has directly sampled.

Toward the Final Milestone

As Saturn's solstice arrives, Cassini is currently in the final phase of its long mission, called its Grand Finale. Over the course of 22 weeks from April 26 to Sept. 15, the spacecraft is making a series of dramatic dives between the planet and its icy rings. The mission is returning new insights about the interior of the planet and the origins of the rings, along with images from closer to Saturn than ever before. The mission will end with a final plunge into Saturn's atmosphere on Sept. 15.

The Cassini-Huygens mission is a cooperative project of NASA, ESA (European Space Agency) and the Italian Space Agency. NASA's Jet Propulsion Laboratory, a division of Caltech in Pasadena, California, manages the mission for NASA's Science Mission Directorate, Washington. JPL designed, developed and assembled the Cassini orbiter.

Contacts and sources:
Preston Dyches
Jet Propulsion Laboratory,

New Insights into the Origins of the Archaean Ancestors of All Complex Life

A team of scientists led by the University of Bristol has provided new insights into the origins of the Archaea, the group of simple cellular organisms that are the ancestors of all complex life.

The Archaea are one of the Earth's most genetically and ecologically diverse groups of micro-organisms.

They thrive in a bewildering variety of habitats, from the familiar - soils and oceans - to the inhospitable and bizarre, such as the boiling acid pools of Yellowstone National Park.

Artist’s impression of an Archean landscape. The earliest metabolisms of the Archaea were based on the anaerobic reduction of carbon dioxide, and likely evolved during the earliest period of Earth’s evolutionary history.
Credit: Tim Bertelink

The research provides a new evolutionary tree for the Archaea that will help to make sense of their biodiversity, and provides a new window into the early history of life on Earth that is not preserved in the fossil record.

The work is published in PNAS.

With the development of new technologies for sequencing genomes directly from the environment, many new groups of Archaea have been discovered.

Dr Tom Williams from the School of Earth Sciences, said: "But while these genomes have greatly improved our understanding of the diversity of Archaea, they have so far failed to bring clarity to the evolutionary history of the group.

"This is because, like other micro-organisms, Archaea frequently obtain DNA from distantly related organisms by lateral gene transfer, which can greatly complicate the reconstruction of evolutionary history."

However, in their new work, Dr Williams and colleagues use a new statistical approach that combines information from thousands of genes found in many different archaeal genomes to show that events of lateral gene transfer can actually be used to orient the tree in time, resolving the deepest relationships in the evolutionary tree.

By determining which genes appeared first during the evolution of the Archaea, the new tree makes clear predictions about the basic biochemistry of the earliest Archaea, cells which may have lived over 3.5 billion years ago: these cells likely made energy using the Wood-Ljungdahl pathway, a biochemical pathway that today is found not only in Archaea but also in Bacteria, another major group of micro-organisms.

Contacts and sources:
University of Bristol

Paper:'Integrative modelling of gene and genome evolution roots the archaeal tree of life' by T. Williams, G. Szollosi, A. Spang, T. Ettema, P. Foster, S. Heaps, T. Martin-Embley and B. Boussau in PNAS.