Computer Simulations Indicate Calcium Carbonate Has a Dense Liquid Phase

 Computer simulations conducted at the U.S. Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab) could help scientists make sense of a recently observed and puzzling wrinkle in one of nature's most important chemical processes. It turns out that calcium carbonate -- the ubiquitous compound that is a major component of seashells, limestone, concrete, antacids and myriad other naturally and industrially produced substances -- may momentarily exist in liquid form as it crystallizes from solution.

Calcium carbonate is a huge player in the planet's carbon cycle, so any new insight into how it behaves is potentially big news. The prediction of a dense liquid phase during the conversion of calcium carbonate to a solid could help scientists understand the response of marine organisms to changes in seawater chemistry due to rising atmospheric CO₂ levels. It could also help them predict the extent to which geological formations can act as carbon storage reservoirs, among other examples.

The research is published in the August 23 issue of the journalScience. It was performed in support of the Center for Nanoscale Control of Geologic CO₂, an Energy Frontier Research Center established at Berkeley Lab by the U.S. Department of Energy.

The research may also reconcile some confounding experimental observations. For more than a century, scientists believed that crystals nucleate from solution by overcoming an energy barrier. But recent studies of calcium carbonate revealed the presence of nanoscopic clusters which, under certain conditions, appear to circumvent the barrier by following an alternative aggregation-based crystallization pathway.

"Because nucleation is ubiquitous in both natural and synthetic systems, those findings have forced diverse scientific communities to reevaluate their longstanding view of this process," says the study's co-corresponding author Jim De Yoreo, formerly of Berkeley Lab and now a scientist at Pacific Northwest National Laboratory.

The Berkeley Lab-led team used molecular dynamics simulations to study the onset of calcium carbonate formation. The simulations predict that in sufficiently supersaturated calcium carbonate solutions, nanoscale dense liquid droplets can spontaneously form. These droplets then coalesce to form an amorphous solid prior to crystallization.

The findings support the aggregation-based mechanism of calcium carbonate formation. They also indicate that the presence of the nanoscale phase is consistent with a process called liquid-liquid separation, which is well known in alloys and polymers, but unexpected for salt solutions.

"Our simulations suggest the existence of a dense liquid form of calcium carbonate," says co-corresponding author Adam Wallace. He conducted the research while a post-doctoral researcher in Berkeley Lab's Earth Sciences Division, and is now an assistant professor in the Department of Geological Sciences at the University of Delaware.

"This is important because it is an as-yet unappreciated component of the carbon cycle," adds Wallace. "It also provides a means of explaining the unusual presence of nanoscale clusters in solution within the context of established physical mechanisms."

This research was supported by the U.S. Department of Energy's Office of Science through the Energy Frontier Research Center program established in 2009. The work was conducted at Berkeley Lab's Molecular Foundry, a Department of Energy national user facility. The research also used resources of the Department of Energy's National Energy Research Scientific Computing Center, which is located at Berkeley Lab.

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Wolves Howl Because They Care: Social Relationship Can Explain Variation in Vocal Production

 When a member of the wolf pack leaves the group, the howling by those left behind isn't a reflection of stress but of the quality of their relationships. So say researchers based on a study of nine wolves from two packs living at Austria's Wolf Science Center that appears in Current Biology, a Cell Press publication, on August 22.

The findings shed important light on the degree to which animal vocal production can be considered as voluntary, the researchers say.

"Our results suggest the social relationship can explain more of the variation we see in howling behavior than the emotional state of the wolf," says Friederike Range of the Messerli Research Institute at the University of Veterinary Medicine Vienna. "This suggests that wolves, to a certain extent, may be able to use their vocalizations in a flexible way."

Scientists have known very little about why animals make the sounds that they do. Are they uncontrollable emotional responses? Or do animals have the ability to change those vocalizations based on their own understanding of the social context?

At the Wolf Science Center, human handlers typically take individual wolves out for walks on a leash, one at a time. On those occasions, they knew, the remaining pack mates always howl.

To better understand why, Range and her colleagues measured the wolves' stress hormone levels. They also collected information on the wolves' dominance status in the pack and their preferred partners. As they took individual wolves out for long walks, they recorded the reactions of each of their pack mates.

Those observations show that wolves howl more when a wolf they have a better relationship with leaves the group and when that individual is of high social rank. The amount of howling did not correspond to higher levels of the stress hormone cortisol.

"Our data suggest that howling is not a simple stress response to being separated from close associates but instead may be used more flexibly to maintain contact and perhaps to aid in reuniting with allies," Range says.

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Space Slinky: Jet of Superheated Gas -- 5,000 Light-Years Long -- Ejected from Supermassive Black Hole

 More than thirteen years of observations from NASA's Hubble Space Telescope have allowed astronomers to assemble time-lapse movies of a 5,000-light-year-long jet of superheated gas being ejected from a supermassive black hole in the center of the giant elliptical galaxy M87.

The movies promise to give astronomers a better understanding of how active black holes shape galaxy evolution. While matter drawn completely into a black hole cannot escape its enormous gravitational pull, most infalling material drawn toward it first joins an orbiting region known as an accretion disk encircling the black hole. Magnetic fields surrounding the black hole are thought to entrain some of this ionized gas, ejecting it as very high-velocity jets.

"Central supermassive black holes are a key component in all big galaxies," said Eileen T. Meyer of the Space Telescope Science Institute (STScI) in Baltimore, Md., the Hubble study's lead author. "Most of these black holes are believed to have gone through an active phase, and black-hole-powered jets from this active phase play a key role in the evolution of galaxies. By studying the details of this process in the nearest galaxy with an optical jet, we can hope to learn more about galaxy formation and black hole physics in general."

The Hubble movies reveal for the first time that the jet's river of plasma travels in a spiral motion. This motion is considered strong evidence that the plasma may be traveling along a magnetic field, which the team thinks is coiled like a helix. The magnetic field is believed to arise from a spinning accretion disk of material around a black hole. Although the magnetic field cannot be seen, its presence is inferred by the confinement of the jet along a narrow cone emanating from the black hole.

"We analyzed several years' worth of Hubble data of a relatively nearby jet, which allowed us to see lots of details," Meyer said. "The only reason you see the distant jet in motion at all over just a few years is because it is traveling very fast."

Meyer found evidence for the magnetic field's suspected helical structure in several locations along the jet. In the outer part of the M87 jet, for example, one bright gas clump, called knot B, appears to zigzag, as if it were moving along a spiral path. Several other gas clumps along the jet also appear to loop around an invisible structure. "Past observations of black hole jets couldn't distinguish between radial motion and side-to-side motion, so they didn't provide us with detailed information of the jet's behavior," Meyer explained.

M87 resides at the center of the neighboring Virgo cluster of roughly 2,000 galaxies, located 50 million light-years away. The galaxy's monster black hole is several billion times more massive than our Sun.

In addition, the Hubble data provided information on why the jet is composed of a long string of gas blobs, which appear to brighten and dim over time.

"The jet structure is very clumpy. Is this a ballistic effect, like cannonballs fired sequentially from a cannon?" Meyer asked. "Or, is there some particularly interesting physics going on, such as a shock that is magnetically driven?"

Meyer's team found evidence for both scenarios. "We found things that move quickly," Meyer said. "We found things that move slowly. And, we found things that are stationary. This study shows us that the clumps are very dynamic sources."

The research team spent eight months analyzing 400 observations from Hubble's Wide Field Planetary Camera 2 and Advanced Camera for Surveys. The observations were taken from 1995 to 2008. Several team members, however, have been observing M87 for 20 years. Only Hubble's sharp vision allowed the research team to measure the jet's slight motion in the sky over 13 years. Meyer's team also measured features in the hot plasma as small as 20 light-years wide.

It's too soon to tell whether all black-hole-powered jets behave like the one in M87. That's why Meyer plans to use Hubble to study three more jets. "It's always dangerous to have exactly one example because it could be a strange outlier," Meyer said. "The M87 black hole is justification for looking at more jets."

The team's results will appear Aug. 22 in the online issue of The Astrophysical Journal Letters.

In addition to Eileen Meyer, other members of the science team are William Sparks, John Biretta, Jay Anderson, Sangmo Tony Sohn, and Roeland van der Marel of STScI; Colin Norman of Johns Hopkins University, Baltimore, Md.; and Masanori Nakamura of Academia Sinica, Taipei, Taiwan.

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Mending a Broken Heart? Scientists Transform Non-Beating Human Cells Into Heart-Muscle Cells

In the aftermath of a heart attack, cells within the region most affected shut down. They stop beating. And they become entombed in scar tissue. But now, scientists at the Gladstone Institutes have demonstrated that this damage need not be permanent -- by finding a way to transform the class of cells that form human scar tissue into those that closely resemble beating heart cells.

Last year, these scientists transformed scar-forming heart cells, part of a class of cells known as fibroblasts, into beating heart-muscle cells in live mice. And in the latest issue of Stem Cell Reports, researchers in the laboratory of Gladstone Cardiovascular and Stem Cell Research Director Deepak Srivastava, MD, reveal that they have done the same to human cells in a petri dish.

"Fibroblasts make up about 50% of all cells in the heart and therefore represent a vast pool of cells that could one day be harnessed and reprogrammed to create new muscle," said Dr. Srivastava, who is also a professor at the University of California, San Francisco, with which Gladstone is affiliated. "Our findings here serve as a proof of concept that human fibroblasts can be reprogrammed successfully into beating heart cells."

In 2012, Dr. Srivastava and his team reported in the journalNature that fibroblasts could be reprogrammed into beating heart cells by injecting just three genes, together known as GMT, into the hearts of live mice that had been damaged by a heart attack. They reasoned that the same three genes could have the same effect on human cells. But initial experiments on human fibroblasts from three sources -- fetal heart cells, embryonic stem cells and neonatal skin cells -- revealed that the GMT combination alone was not sufficient.

"When we injected GMT into each of the three types of human fibroblasts, nothing happened -- they never transformed -- so we went back to the drawing board to look for additional genes that would help initiate the transformation," said Gladstone Staff Scientist Ji-dong Fu, PhD, the study's lead author. "We narrowed our search to just 16 potential genes, which we then screened alongside GMT, in the hopes that we could find the right combination."

The research team began by injecting all candidate genes into the human fibroblasts. They then systematically removed each one to see which were necessary for reprogramming, and which were dispensable. In the end, the team found that injecting a cocktail of five genes -- the 3-gene GMT mix plus the genes ESRRG and MESP1 -- were sufficient to reprogram the fibroblasts into heart-like cells. They then found that with the addition of two more genes, called MYOCD and ZFPM2, the transformation was even more complete. To help things along, the team initiated a chemical reaction known as the TGF-ß signaling pathway during the early stages of reprogramming, which further improved reprogramming success rates.

"While almost all the cells in our study exhibited at least a partial transformation, about 20% of them were capable of transmitting electrical signals -- a key feature of beating heart cells," said Dr. Fu. "Clearly, there are some yet-to-be-determined barriers preventing a more complete transformation for many of the cells. For example, success rates might be improved by transforming the fibroblasts within living hearts rather than in a dish -- something we also observed during our initial experiments in mice."

The immediate next steps are to test the five-gene cocktail in hearts of larger mammals, such as pigs. Eventually, the team hopes that a combination of small, drug-like molecules could be developed to replace the cocktail, offering a safer and easier method of delivery.

"With more than five million heart attack survivors in the United States, who have hearts that are no longer able to beat at full capacity, our findings -- along with recently published findings from our colleagues -- come at a critical time," added Dr. Srivastava. "We've now laid a solid foundation for developing a way to reverse the damage -- something previously thought impossible -- and changing the way that doctors may treat heart attacks in the future."

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Sea Ice Decline Spurs the Greening of the Arctic

Sea ice decline and warming trends are changing the vegetation in nearby arctic coastal areas, according to two University of Alaska Fairbanks scientists.

Uma Bhatt, an associate professor with UAF's Geophysical Institute, and Skip Walker, a professor at UAF's Institute of Arctic Biology, contributed to a recent review of research on the response of plants, marine life and animals to declining sea ice in the Arctic.

"Our thought was to see if sea ice decline contributed to greening of the tundra along the coastal areas," Bhatt said. "It's a relatively new idea."

The review appeared in a recent issue of Science magazine. It is a close, comprehensive look at how the losses of northern sea ice affect surrounding areas. Bhatt and Walker were two of ten authors.

The review team analyzed 10 years worth of data and research on the subject. The findings show that sea ice loss is changing marine and terrestrial food chains. Sea-ice disappearance means a loss of sea-ice algae, the underpinning of the marine food web. Larger plankton is thriving, replacing smaller, but more nutrient dense plankton. What that means exactly is not yet understood.

Above water, loss of sea ice has destroyed old pathways of animal migration across sea ice while opening new pathways for marine animals in others. Some animals and plants will become more isolated. In the case of the farthest north and coldest parts of the Arctic, entire biomes may be lost without the cooling effects of disappearing summer sea ice.

Walker, a plant biologist, says warming soils provide an opportunity for new vegetation to grow where less vegetation occurred previously. This contributes to a general greening of the Arctic that is visible from space. Bhatt, an atmospheric scientist, examined a 1982-2010 time series of remote sensing data to examine trends in sea ice, land-surface temperatures and changes in the vegetation abundance.

A surprise and puzzling finding shows that despite a general warming and greening of Arctic lands in North America, some areas in northern Russia and along the Bering Sea coast of Alaska are showing recent cooling trends and declines in vegetation productivity.

"We don't know why," Bhatt said.

This all illustrates the complexity of the arctic system and why scientists from different disciplines should work together to understand it, Bhatt said. The review article is one of the first steps in this direction.

"It's not a simple story here," Bhatt said. "I'm an atmospheric scientist and Skip (Walker) is a plant biologist. We have had many conversations to understand each other so we might better understand what's happening in the Arctic."

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Lab-Made Complexes Are 'Sun Sponges'

A ring of protein and pigments, half synthetic and half natural, can be used to quickly prototype light-harvesting antennas that absorb more sunlight than fully natural ones

In diagrams it looks like a confection of self-curling ribbon with bits of bling hung off the ribbon here and there. In fact it is a carefully designed ring of proteins with attached pigments that self-assembles into a structure that soaks up sunlight.

The scientists who made it call it a testbed, or platform for rapid prototyping of light-harvesting antennas-structures found in plants and photosynthesizing bacteria-that take the first step in converting sunlight into usable energy. The antennas consist of protein scaffolding that holds pigment molecules in ideal positions to capture and transfer the sun's energy. The number and variety of the pigment molecules determines how much of the sun's energy the antennas can grab and dump into an energy trap.

In the August 6, 2013 online edition of Chemical Science, a new publication of the Royal Society of Chemistry, the scientists describe two prototype antennas they've built on their testbed. One incorporated synthetic dyes called Oregon Green and Rhodamine Red and the other combined Oregon Green and a synthetic version of the bacterial pigment bacteriochlorophyll that absorbs light in the near-infrared region of the spectrum.

Both designs soak up more of the sun's spectrum than native antennas in purple bacteria that provided the inspiration and some components for the testbed. The prototypes were also far easier to assemble than synthetic antennas made entirely from scratch. In this sense they offer the best of both worlds, combining human synthetic ingenuity with the repertoire of robust chemical machinery selected by evolution.

One day a two-part system (consisting of an antenna and a second unit called a reaction center) might serve as a miniature power outlet into which photochemical modules could be plugged. The sun's energy could then be used directly to split water, generate electricity, or build molecular-scale devices.

The project was organized by the Photosynthetic Antenna Research Center (PARC) at Washington University in St. Louis, one of 46 Energy Frontier Research Centers funded by the Department of Energy in 2009. The team tapped the expertise of many PARC-affiliated scientists, including Dewey Holten and Christine Kirmaier of Washington University in St. Louis, Paul Loach and Pamela Parkes-Loach of Northwestern University, Jonathan Lindsey of North Carolina State University, David Bocian of the University of California, Riverside, and Neil Hunter of University of Sheffield in the United Kingdom.

Designer pigments

Nature has evolved many different systems to capture the sun's energy, but they all rely on pigments, molecules that appear strongly colored because they are selectively absorbing some wavelengths, or colors, of light in the solar spectrum.

The pigment we are most familiar with is chlorophyll, the molecule that makes plants appear green. But that green color is a tipoff about the plant's solar absorption. We see plants as green because they're reflecting the green part of the spectrum and absorbing in the violet and the red parts of the spectrum instead.

Not only do plants miss the middle of the visible spectrum, they also miss light at wavelengths longer than we can see, including near-infrared photons absorbed by photosynthetic bacteria. The accessory pigments such as carotenoids that give leaves their splendid fall colors fill some gaps but large swaths of the solar spectrum pass through untouched.

"Since plant pigments actually reject a lot of the light that falls on them," Hunter said, "potentially there's a lot of light you could gather that plants don't bother with."

The team relies on Jonathan Lindsey to design and synthesize pigments that can absorb at wavelengths that will fill some of the holes in the absorption of natural systems. "It can't be done from first principles," Lindsey said, "but we have a large database of known absorbers and so drawing on that and reasoning by analogy we can design a large variety of pigments."

More than one synthetic or natural pigment can be attached to the protein scaffolding. "The prototypes in the Chemical Sciencepaper both have two but ultimately we'd like to add three or four or even more," said Lindsey. "One of our goals is to understand to what extent the protein can be derivatized with pigments."

"The effectiveness of the design depends not only on having extra pigments but also pigments able to talk to one another, so that energy that lands on any one of them is able to hop onto the next pigment and then to the next one after that. They have to work together," Hunter explained.

"The energy cascades down like a waterfall," Hunter said. "So you pour the energy at the top of the waterfall and it hits one pigment and jumps to the next and the next and finally to the pigment at the bottom, which in terms of energy is the pigment that is reddest in color."

Self assembly line

If broad spectral coverage was one goal of the project, another was to avoid the laborious synthesis typically required to make designer light-harvesting antennas.

Fortunately light-harvesting antennas from purple bacteria are modular devices that self assemble under appropriate conditions, conditions that have been worked out by team members Paul Loach and Pamela Parkes-Loach. The basic module is a pair of peptides (short proteins) called alpha and beta that in turn house two bacteriochlorophyll molecules that both absorb light and act as the trap for all the harvested energy.

Thanks to the chemical affinities of the components, they self-assemble into dyads when added together in detergent (detergent is used instead of water alone because parts of the peptides shun water). By adjusting the detergent concentration and temperature, the dyads form rings, which in native antenna contain up to 16 alpha/beta dyads and thus as many as 32 bacteriochlorophylls.

In the testbed, the scientists use peptides that have been slightly modified from the native amino acid sequence for attachment of the extra pigments to increase solar spectral coverage. The attachment sites were chosen to avoid disrupting the self assembly of the components into dyads and dyads into rings.

"This is an example of what the field would refer to as semi-synthesis," Lindsey said. "We take naturally occurring materials and combine them with synthetic ones to make something that doesn't exist in nature. By taking lots of material from nature we can make molecules that are architecturally more complex than those we can make from scratch."

Once assembled, the antenna are sent to the Holten/Kirmaier lab, where a variety of spectroscopic methods including ultra-fast laser spectroscopy are used to excite each pigment molecule and to follow the energy transfer from one pigment to the next and down to the target bacteriochlorophyll. Given the right pigments in the right locations, this transfer is extremely efficient, and little energy is lost on the way.

Samples also went to the Bocian laboratory where they are probed for structural integrity and to the Hunter laboratory where images are made of the rings, which are only 11 to 16 nanometers (a billionth of a meter) across and must be magnified tens of thousands of times to be visible.

"I've been working in photosynthesis for 50 years," said Loach, "and I can't think of many other times when there were so many good people with so many different talents coming together to try to solve problems. It's fun to be part of it and to see what comes out of the collaboration."

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