News in Brief: Atom & Cosmos

By Science News Staff
Web edition : 2:58 pm

Sun snot
Someone should teach the Sun some manners. When it sneezed on June 7, the sun blew an enormous glob of dark plasma into space — and NASA’s Solar Dynamics Observatory caught it on tape. The 20,000-degree Celsius eruption — actually rather chilly by solar standards — can be seen raining back onto the sun’s surface in blobs and streamers. Some of the material made a beeline for sunspots hundreds of thousands of kilometers from the eruption site. Scientists say an unstable magnetic filament triggered the eruption, which sent shock waves halfway around the star and blew around 4 trillion kilograms of charged particles away from the sun — one of the largest events of its type measured so far. Gesundheit. —Nadia Drake

Death of a comet
For the first time, astronomers have spotted the final death throes of a comet heading into the sun. Scientists have watched plenty of comets come close to the sun and then vanish, but witnessing the actual destruction is tough, John Brown of the University of Glasgow in Scotland and colleagues report online July 10 at Their new calculations suggest that lightweight comets explode high above the sun; only comets with nuclei heavier than about 100 billion metric tons manage to reach the surface to die. The Solar Dynamics Observatory photographed such a cometary plunge in early July. —Alexandra Witze

Hottest known planet
Welcome to Hades, a.k.a. WASP-33b. Astronomers have identified this planet, which orbits a star in the constellation Andromeda, as the hottest known. Its surface is a scalding 3,350 degrees Celsius, thanks to the inherent heat of its parent star and the fact that the planet is so close to it, orbiting just once every 1.22 days. A team led by Alexis Smith of Keele University in England reported the finding online July 8 in the Monthly Notices of the Royal Astronomical Society. —Alexandra Witze

Galactic menopause
Both the Milky Way and its neighbor, the Andromeda galaxy, could be in the midst of a midlife crisis. Astronomers have used computer models and galaxy surveys to assess how far the two galaxies have come in their life cycle, as measured by the color of their stars. Both appear to be roughly halfway between young blue stars and red older stars, a team from Swinburne University of Technology in Hawthorn, Australia report in the August 1 Astrophysical Journal. Scientists may thus be able to examine an important galactic life change as it happens. —Alexandra Witze

Antimatter Tevatron mystery gains ground

US particle physicists are inching closer to determining why the Universe exists in its current form, made overwhelmingly of matter.

Physics suggests equal amounts of matter and antimatter should have been made in the Big Bang.

In 2010, researchers at the Tevatron accelerator claimed preliminary results showing a small excess of matter over antimatter as particles decayed.

The team has submitted a paper showing those results are on a firmer footing.

Each of the fundamental particles known has an antimatter cousin, with identical properties but opposite electric charge.

When a particle encounters its antiparticle, they “annihilate” each other, disappearing in a high-energy flash of light.

The question remains: why did this not occur in the early Universe with the equal amounts of matter and antimatter, resulting in a Universe devoid of both?

New physics?
The Tevatron results come from a shower of particles produced at the facility when smashing protons into their antimatter counterparts, antiprotons.

The proton-antiproton collisions in turn create a number of different particles, and the team operating the Tevatron’s DZero detector first noticed a discrepancy in the decay of particles called B mesons.

These decayed into pairs of particles called muons alongside pairs of their antimatter versions, antimuons. But, as the team reported in May 2010 in a paper published in Physical Review Letters, there was a notable 1% excess of the matter particles.

However, unpicking important events in the soup of interactions created in particle physics experiments meant that those measurements were associated with a level of uncertainty – reflecting the probability that the effect they see is a random statistical occurrence, rather than new physics.

The researchers now have 50% more data to work with, and have tried to establish that their earlier result in fact came from the particle decays that they first proposed.

As they reported this Thursday, they have now reduced the uncertainty in their experiment to a level of “3.9 sigma”, or 3.9 standard deviations – equivalent to a 0.005% probability that the effect is a fluke.

But particle physics has a strict definition for what may be called a discovery – the “five sigma” level of certainty, or about a 0.00003% chance that the effect is not real – which the team must show before they can claim to have solved the long-standing matter/antimatter mystery.

Statistics of a ‘discovery’
Particle physics has an accepted definition for a “discovery”: a five-sigma level of certainty. The number of sigmas (or standard deviations) is a measure of how unlikely it is that an experimental result is simply down to chance rather than a real effect. Similarly, tossing a coin and getting a number of heads in a row may just be chance, rather than a sign of a “loaded” coin. The “three sigma” level represents about the same likelihood of tossing more than eight heads in a row. Five sigma, on the other hand, would correspond to tossing more than 20 in a row. A five-sigma result is highly unlikely to happen by chance, and thus an experimental result becomes an accepted discovery.

Tiny snails survive digestion by birds

By Ella Davies
Reporter, BBC Nature

Snails are able to survive intact after being eaten by birds, according to scientists.

Japanese white-eyes on the island of Hahajima, Japan feast on tiny land snails.

Researchers found that 15% of the snails eaten survived digestion and were found alive in the birds’ droppings.

This evidence suggests that bird predation could be a key factor in how snail populations spread.

It is well known that plant seeds are dispersed by birds that eat fruit.

But in findings published in the Journal of Biogeography, researchers from Tohoku University, Japan investigated whether invertebrates could also spread in this way.

Previous research has shown that pond snails can survive being eaten by fish but the same was not known for land snails.

Studies of the diets of birds on the island of Hahajima identified the Japanese white-eye’s preference for the tiny land snail Tornatellides boeningi.

In the lab scientists fed the birds with the snails to find out whether any survived the digestive process.

“We were surprised that a high rate, about 15 percent, of snails were still alive after passing through the gut of [the] birds,” explained researcher Shinichiro Wada.

They also studied the genetic differences of T. boeningi populations found across the island and discovered considerable variation.

Rather than only mating with nearby snails, these results suggested that different populations made contact despite their geographical isolation.

“Biogeography of wingless terrestrial invertebrates, in particular snails, is often faced with mysterious long distance dispersal patterns that can only be explained by hand waving arguments involving birds’ feet or guts or cyclones,” said Mr Wada.

“This is the first study showing that birds can indeed transport a substantial [number of] micro land snails in their gut alive.”

One snail in particular helped researchers identify how numerous snails could travel over distances via bird droppings.

“One of the snails fed to the bird gave birth to juveniles just after passing through the gut,” Mr Wada told the BBC.

The main factor allowing the snails to survive being eaten is their small size, according to the scientists.

At an average of 2.5mm the micro snails fared much better than larger species in previous studies whose shells were severely damaged when eaten by birds.

Mr Wada and his colleagues said further study is required to find out whether the tiny snails have other adaptations that allow them to survive.

Hahajima lies 1000km south of Tokyo in the Bonin Islands archipelago, known as the Ogasawara Group in Japan.

The islands were recently added to the UNESCO World Heritage List “for the wealth of their ecosystems which reflect a wide range of evolutionary processes”.

Genetic Switch for Limbs and Digits Found in Primitive Fish: Before Animals First Walked On Land, Fish Carried Gene Program for Limbs

ScienceDaily (July 11, 2011) —

A genetic switch taken from the skate activates a marker gene in the distal limb of the mouse embryo. (Credit: Igor Schneider, University of Chicago)

Genetic instructions for developing limbs and digits were present in primitive fish millions of years before their descendants first crawled on to land, researchers have discovered.

Genetic switches control the timing and location of gene activity. When a particular switch taken from fish DNA is placed into mouse embryos, the segment can activate genes in the developing limb region of embryos, University of Chicago researchers report in Proceedings of the National Academy of Sciences. The successful swap suggests that the recipe for limb development is conserved in species separated by 400 million years of evolution.

“The genetic switches that drive the expression of genes in the digits of mice are not only present in fish, but the fish sequence can actually activate the expression in mice,” said Igor Schneider, PhD, postdoctoral researcher in the Department of Organismal Biology and Anatomy at the University of Chicago and lead author on the paper. “This tells us how the antecedents of the limb go back in time at every level, from fossils to genes.”

The genetic hunt was inspired by a famous fossil find — the 2004 discovery of the transitional fossil Tiktaalik in the Canadian Arctic by a team led by Neil Shubin of the University of Chicago. A transitional species between fish and the four-legged tetrapods, Tiktaalik possessed fins containing a skeletal structure similar to the limbs of later land-dwelling animals.

Those similarities — particularly the wrist and hand-like compartments present in the fins of Tiktaalik and its peers — inspired a laboratory experiment to look at the homology, or shared physical and genetic traits, of fish and limbed animals.

“This is really a case where knowing something about the fossils and the morphology led us to think about genetic experiments,” said Shubin, PhD, the Robert R. Bensley Professor of Organismal Biology and Anatomy and senior author of the study. “Tiktaalik and its cousins showed us that this limb compartment is not an utter novelty in tetrapods, as was thought for a long time. So an antecedent of that program must exist.”

The research team compared a genetic switch region called CsB, known to regulate limb development in humans, with similar regions in mice, chickens, frogs, and two fish species: the zebrafish and the skate. Because the last common ancestor of all these species pre-dates Tiktaalik-like “fishapods,” the comparison offered a glimpse at biology before animals made their first steps on land.

Schneider and colleagues compared the CsB regions from all five species and found that certain sequences were shared between the fish species and the tetrapods. The conservation allowed the researchers to try swapping switch sequences between species to see if they could still drive gene expression in the fin or limb. Remarkably, mouse CsB could turn on gene expression at the outer edge of the developing fin region of zebrafish, and both skate and zebrafish CsB were capable of activating gene expression in the wrist and proximal digits of the mouse limb.

“These sequences function in these organisms despite 400 million years of separation,” Schneider said. “The homologies that are perhaps not evident by morphology — just comparing a hand and a fin — can be traced back to the genome, where you find that the regulatory regions that control the making of those structures are actually present and shared between these organisms.”

The results contradict a previous finding that a developmental switch from pufferfish DNA was not capable of gene expression in the limbs of mice, suggesting that tetrapods evolved a novel developmental system. But the new experiments suggest that the genetic switch controlling limb development was in fact present deep in Earth’s evolutionary tree.

“There previously was the idea that these switches had to be generated from scratch de novo, but no, they already existed, they were already there,” said Marcelo Nobrega, MD, PhD, assistant professor of human genetics at the University of Chicago Medical Center and another author of the study. “Maybe the key was expressing a gene earlier or later or in a specific territory, but it was just a modification of a program that was already encoded in the genomes of fish almost half a billion years ago and remains there to this day.”

“These new results are actually in line with both the fossil data and the expression data,” Schneider said. “So now we can tell a story where the fossils and gene expression make sense in light of the genetic regulation.”

Future experiments will focus more closely on how the gene regulation system functions, examining the differences between the segments in fish and tetrapods that control development of either a fin or a limb. Subtle changes in the timing or location of gene expression may produce the dramatic differences in anatomy that first allowed animal life on Earth to explore land.

“There is a whole universe of questions that are opened up by this discovery,” Shubin said.

The paper, “Appendage expression driven by the Hoxd global control region is an ancient gnathostome feature,” will be published online the week of July 11 by the Proceedings of the National Academy of Sciences. In addition to Shubin, Schneider, and Nobrega, authors include Ivy Aneas and Andrew R. Gehrke of the University of Chicago, and Randall D. Dahn of Mount Desert Island Biological Lab.

Funding for the research was provided by the American Heart Association and the University of Chicago Biological Sciences Division.

Salt-Loving Microbe Provides New Enzymes for the Production of Next-Generation Biofuels

ScienceDaily (July 10, 2011) —
In order to realize the full potential of advanced biofuels that are derived from non-food sources of lignocellulosic biomass — e.g., agricultural, forestry, and municipal waste, and crops such as poplar, switchgrass and miscanthus — new technologies that can efficiently and cost-effectively break down this biomass into simple sugars are required. Existing biomass pretreatment technologies are typically derived from the pulp and paper industry and rely on dilute acids and bases to break down the biomass. The treated biomass product is then exposed to biological catalysts, or enzymes, to liberate the sugars.

A new class of solvents, referred to as ionic liquids, have been reported to be much more efficient in treating the biomass and enhancing the yield of sugars liberated from it. While ionic liquids are useful for breaking down biomass, they can also hinder the ability of the cellulases (usually derived from fungi) used to produce sugars after pretreatment. Ionic liquids are a liquid form of salt that will inactivate enzymes by interfering with the folding of polypeptides — the building-blocks of proteins. To help identify new enzymes that are tolerant of ionic liquids, researchers from the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) and the Joint BioEnergy Institute (JBEI) at DOE’s Lawrence Berkeley National Laboratory are turning to those found in the complete genome sequences of halophilic (salt-tolerant) organisms.

As a test of this bioenergy-related application of DNA sequencing and enzyme discovery, researchers led by the Director of the DOE JGI, Eddy Rubin, and the Vice-President of the JBEI Deconstruction Division, Blake Simmons, employed a cellulose-degrading enzyme from a salt-tolerant microbe that was isolated from the Great Salt Lake. The microbe in question, Halorhabdus utahensis, is from the branch of the tree of life known as Archaea; H. utahensis was isolated from the natural environment at the Great Salt Lake and sequenced at the DOE JGI as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) project.

“This is one of the only reports of salt-tolerant cellulases, and the only one that represents a true ‘genome-to-function’ relevant to ionic liquids from a halophilic environment,” said Simmons of the study published June 30, 2011 in Green Chemistry. “This strategy enhances the possibility of identifying true obligatory halophilic enzymes.” Such salt-tolerant enzymes, particularly cellulases, offer significant advantages for industrial utility over conventional enzymes.

In collaboration with Jerry Eichler from Ben Gurion University of the Negev in Israel they cloned and expressed a gene from H. utahensis in another haloarchaeal microbe, and were able to identify a salt-dependent enzyme that can tolerate high temperatures and is resistant to ionic liquids. “This project has established a very important link between genomic science and the realization of enzymes that can handle very demanding chemical environments, such as those present in a biorefinery,” said Simmons.

The group plans to expand this research to develop a full complement of enzymes that is tailored for the ionic liquid process technology with the goal of demonstrating a complete biomass-to-sugar process, one they hope can enable the commercial viability of advanced biofuels.

Other contributors to the project include Tao Zhang, Natalia Ivanova, Seth Axen, Cheryl Kerfeld, Feng Chen, Nikos Kyrpides, Jan-Fang Cheng of the DOE JGI along with Philip Hugenholtz now with The University of Queensland, and Supratim Datta and Kenneth Sale of JBEI.

Pigeons Recognize Human Faces

by Remy Melina
Date: 03 July 2011 Time: 10:47 AM ET

If you shoo a pigeon, that bird is likely to remember you and know to stay out of your way the next time you cross paths, according to a new study. Researchers found that wild, untrained pigeons can recognize individual people’s faces and are not fooled by a change of clothes.

Previous research in this arena had only focused on the perception abilities of pigeons that were trained in a lab environment, but the new study was conducted on untrained feral pigeons. At a park in Paris, two researchers of similar build and skin color, but wearing different-colored lab coats, fed a group of pigeons.

One researcher ignored the pigeons after feeding them, allowing them to eat the food, while the other was hostile and chased them away. This was followed by a second session when neither researcher chased away the pigeons.

The experiment was repeated several times, with the pigeons continuously recognizing the individuals and avoiding the researcher who had first chased them away even when the participant no longer did so. Swapping lab coats during the experiments did not confuse the pigeons, and they continued to stay away from the researcher who had been initially hostile.

“It is very likely that the pigeons recognized the researchers by their faces, since the individuals were both female and of a similar age, build and skin color,” study researcher Dalila Bovet of the University of Paris Ouest Nanterre La Défense said in a statement.

“Interestingly, the pigeons, without training, spontaneously used the most relevant characteristics of the individuals (probably facial traits), instead of the lab coats that covered 90 percent of the body,” Bovet added.

The researchers noted that the birds appear to be able to differentiate between humans and are aware that clothing color is not a good way to tell humans apart. They theorize that this recognition ability may have come about over the long period of association with humans, from early domestication to many years of living in cities.

Previous research supports the findings, as the memory and recognition skills of certain bird species have been demonstrated by other studies. In May 2011, Seoul National University researcher Won Young Lee noticed that when he returned to an area where he had previously installed cameras into the nests of magpies, the birds recognized his face and began dive-bombing him.

A 2009 study showed that jackdaws, which are the smaller cousins of crows and ravens, can interpret human eye cues and even follow human gestures such as pointing. University of Oxford researchers noted that hand-raised jackdaws could find food when a familiar person’s eyes looked back and forth from the food to the bird. The birds also responded when the person pointed to the food’s location. However, the jackdaws took longer to approach food when an unfamiliar person was watching.

“I think they can generalize to human eyes somehow, and interpret human eyes as eyes,” said Auguste Bayern, a cognitive biologist at the University of Oxford and lead author of the 2009 study.

Tree Frog’s Sticky Secrets Revealed

LiveScience Staff
Date: 03 July 2011 Time: 11:16 AM ET

It must have been a wild ride for the tree frogs in the lab.

Scientists placed the frogs on a tilting, rotatable platform to measure the angles at which the frogs lost their grip. Adding dust caused them to slip sooner, but the frogs would take a few steps and regain their footing.

That ability to clean their feet so quickly, which scientists now understand, could lead to new self-cleaning surfaces and adhesives.

“When the frogs did not move the adhesive forces recovered much more slowly,” said study researcher Niall Crawford at the University of Glasgow. “This shows that just taking a step enables frogs to clean their feet and restore their adhesion ability.”

The frogs in the study, White’s tree frogs, have sticky pads on their toes. Scientists learned in 2007 that the angle of the toe pads and a secretion of mucus were involved in the frogs’ ability to stick to wet, smooth leaves, rough, dry trees and other surfaces.

The study showed that tiny hexagonal patterns allow some parts of the foot pad to remain in contact with the surface and create friction, while the channels between allow the mucus to spread throughout the pad. This mucus allows the frog to stick and then, when they move, also carries away any dirt.

If this can be translated into a man-made design it could provide a re-useable, effective adhesive. (Geckos have also been studied for their natural super adhesive.)

“Tree frog feet may provide a design for self-cleaning sticky surfaces, which could be useful for a wide range of products especially in contaminating environments – medical bandages, tire performance, and even long lasting adhesives,” Crawford explained today at the Society for Experimental Biology Annual Conference in Glasgow.

Toxins close N. Ore. beaches to mussel harvest

by Associated Press
Posted on July 2, 2011 at 1:01 PM

SALEM — Oregon Agriculture Department officials have closed recreational mussel harvesting on Oregon’s north coastal beaches due to elevated levels of marine toxins.

The closure announced Friday extends from the south jetty of the Columbia River to Cape Meares on the north Oregon coast. It includes mussels found on beaches, rocks, jetties, and bay entrances.

The closure does not affect recreational clam harvesting on the north coast. Crab are also safe to eat.

All Oregon coastal areas south of Cape Meares remain open to recreational shellfish harvesting.

Paralytic shellfish toxins can cause minor to severe illness or even death. Cooking will not destroy them. The toxins are produced by algae and the department will continue to test toxin levels.