Large, "Glamorous" New Glowing Squid Species Found

A large new species of deep red, glowing squid has been discovered living near undersea mountains in the southern Indian Ocean, scientists announced Monday.

At about 28 inches (70 centimeters) long, the as yet unnamed species is relatively big—though other squid can reach as long as 65 feet (20 meters), some species are barely three quarters of an inch (1.5 centimeters).

The new species belongs to Chiroteuthidae, a group of slender squid in which light-producing organs run in the family.

"It's thought that this particular group of squid actually uses bioluminescence to lure in prey," which are thought to include small fish and crustaceans, said Alex Rogers, a conservation biologist at the University of Oxford in the U.K.

The new squid is just one of more than 70 squid species observed during a six-week research cruise that began in September 2009 but whose results are only now beginning to be released.

"In a single expedition, we sampled about a fifth of all the world's squid species that are known to date," Rogers said. "That's really a staggering diversity of squid to sample in a single trip."

Most of the squid observed were already known to science, but, in addition to the blinking beast above, a few are thought to be completely new species.

"We think we have more than one new species of squid," Rogers said. "This just happens to be the biggest and most glamorous one."

Mountains of Food for Squid and Other Species

The aim of the research cruise, led by the International Union for Conservation of Nature (IUCN), was to document the abundance of marine life associated with underwater mountains.

Scientists estimate there are tens of thousands to hundreds of thousands of seamounts—undersea mountains rising more than 0.6 mile (1 kilometer) high—scattered throughout the world's oceans.

On the single 2009 expedition alone, Rogers said, "We got a tremendous variety of ... animals, including over 200 fish species and a large collection of crustaceans as well."

One reason seamounts appear to be such biological hot spots is that the submerged peaks act as food traps for squid and other creatures living on or around them.

The undersea mountains often block the daily vertical migration of plankton and other microorganisms from the ocean's surface to its depths, Rogers explained.

"The animals," he said, "can just sit on the seamounts and feed on what drifts by."

Oldest Dinosaur Embryos Show "Big Surprises"

Oldest Embryo

Photograph courtesy Diane Scott, University of Toronto

The sharpest look yet at the oldest known dinosaur embryos (pictured, one of the eggs and its inhabitant) has revealed some "big surprises," a scientist says.

For one thing, the 190-million-year-old babies of Massospondylus—a two-legged dinosaur that preceded the well-known sauropods, such as Diplodocus—do not resemble their parents, according to study co-author Hans-Dieter Sues, a paleontologist at the National Museum of Natural History in Washington, D.C.

The 8-inch-long (20-centimeter-long) youngster, for example, had long front legs for walking on all fours, and its overall body proportion—such as a short snout—made it "look like a dwarf version of a sauropod dinosaur," the largest animals to walk Earth. (See a sauropod picture.) The babies would have lost these traits as they matured.

The discovery suggests Massospondylus had characteristics that "foreshadowed" the later look of the sauropods, he said.

Sonar Inspired by Dolphins: New Kind of Underwater Device Can Detect Objects Through Bubble Clouds

Scientists at the University of Southampton have developed a new kind of underwater sonar device that can detect objects through bubble clouds that would effectively blind standard sonar.
Just as ultrasound is used in medical imaging, conventional sonar 'sees' with sound. It uses differences between emitted sound pulses and their echoes to detect and identify targets. These include submerged structures such as reefs and wrecks, and objects, including submarines and fish shoals.

However, standard sonar does not cope well with bubble clouds resulting from breaking waves or other causes, which scatter sound and clutter the sonar image.

Professor Timothy Leighton of the University of Southampton's Institute of Soundand Vibration Research (ISVR), who led the research, explained:

"Cold War sonar was developed mainly for use in deep water where bubbles are not much of a problem, but many of today's applications involve shallow waters. Better detection and classification of targets in bubbly waters are key goals of shallow-water sonar."

Leighton and his colleagues have developed a new sonar concept called twin inverted pulse sonar (TWIPS). TWIPS exploits the way that bubbles pulsate in sound fields, which affects the characteristics of sonar echoes.

"To catch prey, some dolphins make bubble nets in which the best man-made sonar would not work. It occurred to me that either dolphins were blinding their sonar when making such nets, or else they have a better sonar system. There were no recordings of the type of sonar that dolphins use in bubble nets, so instead of producing a bio-inspired sonar by copying dolphin signals, I sat down and worked out what pulse I would use if I were a dolphin," said Leighton.

As its name suggests, TWIPS uses trains of twinned pairs of sound pulses. The first pulse of each pair has a waveform that is an inverted replica of that of its twin. The first pulse is emitted a fraction of a second before its inverted twin.

Leighton's team first showed theoretically that TWIPS might be able to enhance scatter from the target while simultaneously suppressing clutter from bubbles. In principle, it could therefore be used to distinguish echoes from bubble clouds and objects that would otherwise remain hidden.

In their latest study, the researchers set out to see whether TWIPS would work in practice. Using a large testing tank, they showed experimentally that TWIPS outperformed standard sonar at detecting a small steel disc under bubbly conditions resembling those found under oceanic breaking waves.

Encouraged by their findings, they next conducted trials at sea aboard the University of Southampton's coastal research vessel the RV Bill Conway. They compared the ability of TWIPS and standard sonar to discern the seabed in Southampton Water, which handles seven per cent of the UK's entire seaborne trade. The seabed in this area varies in depth between 10 and 20 metres.

"TWIPS outperformed standard sonar in the wake of large vessels such as passenger ferries," said co-author Dr Justin Dix of the University of Southampton's School of Ocean and Earth Science (SOES) based at the National Oceanography Centre, Southampton.

Possible future marine applications for TWIPS include harbour protection and the detection of bubbles in marine sediments and manufacturing. Technologies based on the same basic principles could be used in medical ultrasound imaging, which was already using pairs of inverted pulses to enhance (rather than suppress) contrast agents injected into the body. The TWIPS principle would work with other sensors such as in Magnetic resonance imaging(MRI), and Leighton has proposed TWIPR (Twin Inverted Pulse Radar) for the detection of improvised explosive devices or covert circuitry.

But what about the original inspiration for the research -- do dolphins and other echolocating animals use TWIPS?

"Key ingredients of a TWIPS system appear in separate species but they have never been found all together in a single species," said Leighton. "There is currently no evidence that dolphins use TWIPS processing, although no-one has yet taken recordings of the signals from animals hunting with bubble nets in the wild. How they successfully detect prey in bubbly water remains a mystery that we are working to solve. I have to pay credit to the team -- students Daniel Finfer and Gim-Hwa Chua of ISVR, and Paul White (ISVR) and Justin Dix of SOES. Our applications for funding this work were repeatedly turned down, and it took real grit and determination to keep going for the five years it took us to get this far."

Antimatter Atoms Stored for the First Time

Atoms of antimatter have been trapped and stored for the first time by the ALPHA collaboration, an international team of scientists working at CERN, the European Organization for Nuclear Research near Geneva, Switzerland. Scientists from the U.S. Department of Energy's Lawrence Berkeley National Laboratory and the University of California at Berkeley have made key contributions to the ongoing international effort.

ALPHA stored atoms of antihydrogen, consisting of a single negatively charged antiproton orbited by a single positively charged anti-electron (positron). While the number of trapped anti-atoms is far too small to fuel the Starship Enterprise's matter-antimatter reactor, this advance brings closer the day when scientists will be able to make precision tests of the fundamental symmetries of nature. Measurements of anti-atoms may reveal how the physics of antimatter differs from that of the ordinary matter that dominates the world we know today.

Large quantities of antihydrogen atoms were first made at CERN eight years ago by two other teams. Although they made antimatter they couldn't store it, because the anti-atoms touched the ordinary-matter walls of the experiments within millionths of a second after forming and were instantly annihilated -- completely destroyed by conversion to energy and other particles.

"Trapping antihydrogen proved to be much more difficult than creating antihydrogen," says ALPHA team member Joel Fajans, a scientist in Berkeley Lab's Accelerator and Fusion Research Division (AFRD) and a professor of physics at UC Berkeley. "ALPHA routinely makes thousands of antihydrogen atoms in a single second, but most are too 'hot'" -- too energetic -- "to be held in the trap. We have to be lucky to catch one."

The ALPHA collaboration succeeded by using a specially designed magnetic bottle called a Minimum Magnetic Field Trap. The main component is an octupole (eight-magnetic-pole) magnet whose fields keep anti-atoms away from the walls of the trap and thus prevent them from annihilating. Fajans and his colleagues in AFRD and at UC proposed, designed, and tested the octupole magnet, which was fabricated at Brookhaven. ALPHA team member Jonathan Wurtele of AFRD, also a professor of physics at UC Berkeley, led a team of Berkeley Lab staff members and visiting scientists who used computer simulations to verify the advantages of the octupole trap.

In a forthcoming issue of Nature now online, the ALPHA team reports the results of 335 experimental trials, each lasting one second, during which the anti-atoms were created and stored. The trials were repeated at intervals never shorter than 15 minutes. To form antihydrogen during these sessions, antiprotons were mixed with positrons inside the trap. As soon as the trap's magnet was "quenched," any trapped anti-atoms were released, and their subsequent annihilation was recorded by silicon detectors. In this way the researchers recorded 38 antihydrogen atoms, which had been held in the trap for almost two-tenths of a second.

"Proof that we trapped antihydrogen rests on establishing that our signal is not due to a background," says Fajans. While many more than 38 antihydrogen atoms are likely to have been captured during the 335 trials, the researchers were careful to confirm that each candidate event was in fact an anti-atom annihilation and was not the passage of a cosmic ray or, more difficult to rule out, the annihilation of a bare antiproton.

To discriminate among real events and background, the ALPHA team used computer simulations based on theoretical calculations to show how background events would be distributed in the detector versus how real antihydrogen annihilations would appear. Fajans and Francis Robicheaux of Auburn University contributed simulations of how mirror-trapped antiprotons (those confined by magnet coils around the ends of the octupole magnet) might mimic anti-atom annihilations, and how actual antihydrogen would behave in the trap.

Learning from antimatter

Before 1928, when anti-electrons were predicted on theoretical grounds by Paul Dirac, the existence of antimatter was unsuspected. In 1932 anti-electrons (positrons) were found in cosmic ray debris by Carl Anderson. The first antiprotons were deliberately created in 1955 at Berkeley Lab's Bevatron, the highest-energy particle accelerator of its day.

At first physicists saw no reason why antimatter and matter shouldn't behave symmetrically, that is, obey the laws of physics in the same way. But if so, equal amounts of each would have been made in the big bang -- in which case they should have mutually annihilated, leaving nothing behind. And if somehow that fate were avoided, equal amounts of matter and antimatter should remain today, which is clearly not the case.

In the 1960s, physicists discovered subatomic particles that decayed in a way only possible if the symmetry known as charge conjugation and parity (CP) had been violated in the process. As a result, the researchers realized, antimatter must behave slightly differently from ordinary matter. Still, even though some antiparticles violate CP, antiparticles moving backward in time ought to obey the same laws of physics as do ordinary particles moving forward in time. CPT symmetry (T is for time) should not be violated.

One way to test this assumption would be to compare the energy levels of ordinary electrons orbiting an ordinary proton to the energy levels of positrons orbiting an antiproton, that is, compare the spectra of ordinary hydrogen and antihydrogen atoms. Testing CPT symmetry with antihydrogen atoms is a major goal of the ALPHA experiment.

How to make and store antihydrogen

To make antihydrogen, the accelerators that feed protons to the Large Hadron Collider (LHC) at CERN divert some of these to make antiprotons by slamming them into a metal target; the antiprotons that result are held in CERN's Antimatter Decelerator ring, which delivers bunches of antiprotons to ALPHA and another antimatter experiment.

Wurtele says, "It's hard to catch p-bars" -- the symbol for antiproton is a small letter p with a bar over it -- "because you have to cool them all the way down from a hundred million electron volts to fifty millionths of an electron volt."

In the ALPHA experiment the antiprotons are passed through a series of physical barriers, magnetic and electric fields, and clouds of cold electrons, to further cool them. Finally the low-energy antiprotons are introduced into ALPHA's trapping region.

Meanwhile low-energy positrons, originating from decays in a radioactive sodium source, are brought into the trap from the opposite end. Being charged particles, both positrons and antiprotons can be held in separate sections of the trap by a combination of electric and magnetic fields -- a cloud of positrons in an "up well" in the center and the antiprotons in a "down well" toward the ends of the trap.

To join the positrons in their central well, the antiprotons must be carefully nudged by an oscillating electric field, which increases their velocity in a controlled way through a phenomenon called autoresonance.

"It's like pushing a kid on a playground swing," says Fajans, who credits his former graduate student Erik Gilson and Lazar Friedland, a professor at Hebrew University and visitor at Berkeley, with early development of the technique. "How high the swing goes doesn't have as much to do with how hard you push or how heavy the kid is or how the long the chains are, but instead with the timing of your pushes."

The novel autoresonance technique turned out to be essential for adding energy to antiprotons precisely, in order to form relatively low energy anti-atoms. The newly formed anti-atoms are neutral in charge, but because of their spin and the distribution of the opposite charges of their components, they have a magnetic moment; provided their energy is low enough, they can be captured in the octupole magnetic field and mirror fields of the Minimum Magnetic Field Trap.

Of the thousands of antihydrogen atoms made in each one-second mixing session, most are too energetic to be held and annihilate themselves against the trap walls.

Setting the ALPHA 38 free

After mixing and trapping -- plus the "clearing" of the many bare antiprotons that have not formed antihydrogen -- the superconducting magnet that produces the confining field is abruptly turned off -- within a mere nine-thousandths of a second. This causes the magnet to "quench," a quick return to normal conductivity that results in fast heating and stress.

"Millisecond quenches are almost unheard of," Fajans says. "Deliberately turning off a superconducting magnet is usually done thousands of times more slowly, and not with a quench. We did a lot of experiments at Berkeley Lab to make sure the ALPHA magnet could survive multiple rapid quenches."

From the start of the quench the researchers allowed 30-thousandths of a second for any trapped antihydrogen to escape the trap, as well as any bare antiprotons that might still be in the trap. Cosmic rays might also wander through the experiment during this interval. By using electric fields to sweep the trap of charged particles or steer them to one end of the detectors or the other, and by comparing the real data with computer simulations of candidate antihydrogen annihilations and look-alike events, the researchers were able to unambiguously identify 38 antihydrogen atoms that had survived in the trap for at least 172 milliseconds -- almost two-tenths of a second.

Says Fajans, "Our report in Nature describes ALPHA's first successes at trapping antihydrogen atoms, but we're constantly improving the number and length of time we can hold onto them. We're getting close to the point where we can do some classes of experiments on antimatter atoms. The first attempts will be crude, but no one has ever done anything like them before."

Scientists Identify Antivirus System

Viruses have led scientists at Washington University School of Medicine in St. Louis to the discovery of a security system in host cells. Viruses that cause disease in animals beat the security system millennia ago. But now that researchers are aware of it, they can explore the possibility of bringing the system back into play in the fight against diseases such as sudden acute respiratory syndrome (SARS), West Nile virus, dengue and yellow fever.

The findings, published in Nature, solve a 35-year-old mystery that began when National Institutes of Health researcher Bernard Moss, MD, PhD, noticed that poxviruses put chemical "caps" on particular spots in every piece of genetic material transcribed from their DNA. That transcribed material is RNA; to reproduce, viruses need to trick the host cell into making viral proteins from this RNA.

Noting evidence that the host cell puts caps on its own RNA in identical positions, Moss theorized that the caps might be a way for cells to distinguish between their RNA and that of an invader. He guessed the caps might serve as a sort of fake identification badge for the virus' RNA, allowing it to bypass host cell security systems primed to attack any RNA lacking the caps.

Since Moss's study, scientists have learned that some viruses have strategies for stealing RNA caps from host cells and putting them on their own RNA. Several disease-causing viruses have to make their own caps, including:

* poxviruses, which cause smallpox
* flaviviruses, which cause West Nile encephalitis, yellow fever and dengue;
* rhabdoviruses, which cause rabies;
* coronaviruses, which cause SARS;
* reoviruses, which cause mild respiratory distress or diarrhea.

Scientists also learned that one of the chemical caps added to RNA helps stabilize it, preventing the RNA from breaking down. However, despite years of research, the purpose of another cap, added near the beginning of every RNA strand in a position scientists refer to as 2' (two prime), was a persistent mystery.

The new paper from the laboratory of senior author Michael S. Diamond, MD, PhD, solves that puzzle and confirms Moss' speculation. The study used a mutant form of the West Nile virus created by Pei-Yong Shi, PhD, now a researcher at the Novartis Institute for Tropical Diseases. The mutant strain can attach the cap that keeps RNA stable but is unable to add the 2' cap. When Diamond, professor of medicine, pathology and immunology, and molecular microbiology at Washington University School of Medicine, infected mice with this mutant virus, it could not cause disease.

Next, scientists injected the mutant virus into mice lacking the receptors for interferons. These proteins are important players in defensive reactions to invading viruses within the cell, a branch of the immune system known as intrinsic immunity. The mutant virus made these mice sick, suggesting that intrinsic immunity stops the mutant viruses in normal mice, and that the 2' cap was helping normal viruses evade this part of the immune system.

Researchers recently identified a gene, IFIT2, that is activated by interferons, has mild antiviral effects against West Nile virus and seems to have potential connections to translation of RNA into proteins. When Diamond turned IFIT2 levels up in cell culture and exposed it to the mutant West Nile virus, the mutant virus could barely replicate. Tests of a mutant poxvirus and a mutant coronavirus that could not attach the 2' cap produced similar results. Knocking out a related gene in mice, IFIT1, allowed the mutant virus to evade intrinsic immunity and cause infection when it was injected into the brain.

"Now that we know what this cap is used for, we can look at the question of whether the human and viral enzymes that put the cap on are sufficiently different," says Diamond. "If they are, we may be able to design inhibitors that prevent viruses from capping their RNA and make it much harder for them to replicate once the intrinsic immune system is activated."

Months of Geologic Unrest Signaled Reawakening of Icelandic Volcano

Months of volcanic restlessness preceded the eruptions this spring of Icelandic volcano Eyjafjallajökull, providing insight into what roused it from centuries of slumber.

An international team of researchers analyzed geophysical changes in the long-dormant volcano leading up to its eruptions in March and April 2010 that suggest that magma flowing beneath the volcano may have triggered its reawakening. Their study is published in the Nov. 18 issue of the journal Nature.

"Several months of unrest preceded the eruptions, with magma moving around downstairs in the plumbing and making noise in the form of earthquakes," says study co-author Kurt Feigl, a professor of geosciences at the University of Wisconsin-Madison. "By monitoring volcanoes, we can understand the processes that drive them to erupt."

With funding from a RAPID grant from the U.S. National Science Foundation, Feigl and collaborators from Iceland, Sweden, and the Netherlands used a combination of satellite imaging and GPS surveying to watch the volcano's edifice as it deformed. They found that the volcano swelled for 11 weeks before it began to erupt in March 2010 from one flank.

"If you watch a volcano for decades, you can tell when it's getting restless," Feigl says.

In late summer 2009, a subtle shift at a GPS station on Eyjafjallajökull's flank prompted the study's lead author, Freysteinn Sigmundsson, and his colleagues to begin monitoring the mountain more closely. Then, in early January 2010, the rate of deformation and the number of earthquakes began to increase. As the deformation and seismic unrest continued, the researchers installed more GPS stations near the mountain. Just a few weeks later, the instruments detected more rapid inflation, indicating that magma was moving upwards through the "plumbing" inside the volcano.

By the time the volcano began to erupt on March 20, the volcano's flanks had expanded by more than six inches as magma flowed from deep within the Earth into shallow chambers underneath the mountain.

Surprisingly, the rapid deformation stopped as soon as the eruption began. In many cases, volcanoes deflate as magma flows out of shallow chambers during an eruption. Eyjafjallajökull, however, maintained basically the same inflated shape through mid-April, when the first eruption ended.

After a two-day pause, the volcano began to erupt again on April 22. This time, the lava broke out through a new conduit under the ice on the summit of the mountain, causing an explosive reaction as water flashed to steam and gas escaped from bubbles in the magma. The resulting "ash" plume rose high into the atmosphere, disrupting air traffic over Europe for weeks and stranding millions of travelers.

Why did Eyjafjallajökull erupt when it did? The geologic processes that trigger an actual eruption are not yet well understood, says Feigl. "We're still trying to figure out what wakes up a volcano."

To begin to answer this question, the scientists suggest that a magmatic intrusion deep within the volcano may have triggered the eruption, but this hypothesis remains to be tested at other volcanoes.

They are also studying the structures inside the volcano, such as magma chambers and intrusive conduits, by extracting information from the sensors installed around Eyjafjallajökull.

"The explosiveness of the eruption depends on the type of magma, and the type of magma depends on the depth of its source," Feigl says. "We're a long way from being able to predict eruptions, but if we can visualize the magma as it moves upward inside the volcano, then we'll improve our understanding of the processes driving volcanic activity."

Satellite radar images were obtained from TerraSAR-X, a satellite operated by the German Space Agency (DLR). Funding was provided by the National Science Foundation, Icelandic Research Fund, University of Iceland, and the Icelandic government.

Mortal Chemical Combat Typifies the World of Bacteria

Like all organisms, bacteria must compete for resources to survive, even if it means a fight to the death.

New research led by scientists from the University of North Carolina at Chapel Hill School of Medicine and the University of California, Santa Barbara, describes new complexities in the close chemical combat waged among bacteria.

And the findings from this microscopic war zone may have implications for human health and survival.

"It has been known for a long time that bacteria can produce toxins that they release into their surroundings that can kill other bacteria, sort of like throwing hand grenades at enemies," said Peggy A. Cotter, PhD, associate professor in the microbiology and immunology department at UNC. "Our data suggests that the situation is far more complex that we thought."

Cotter points out that it was in David A. Low's lab at U.C. Santa Barbara, where the discovery was made that bacteria can also produce proteins on their surface that inhibit the growth and end the life of other bacteria upon contact.

"So it appears that some bacteria participate in 'man to man' (or 'bacteria to bacteria') combat using poison-tipped swords," Cotter said. "What we have discovered is that each bacterium can have a different poison at the tip of their sword. For each poison, there is a specific protective (immunity) protein that the bacteria also make so that they don't kill themselves and are not killed by other members of their same 'family'."

The new research by senior co-authors Cotter and Low and others appear on-line November 18, 2010 in the journal Nature.

As to "swords," the metaphor lives close to reality. Bacteria use proteins to interact with a host, including disease-causing bacteria, such as Bordetella pertussis, the cause of whooping cough and Burkholderia pseudomallei, found in soil throughout Southeast Asia and a cause of a frequently fatal tropic disease.

In these and other gram-negative bacteria, large proteins appear as rods on the surface of cells. "In the soil or in humans, different bacteria bump into each other all the time and bump into their own 'family,' too. They have to touch each other and recognize each other and then one can inhibit the growth of the other, non-family, bacteria." Cotter said.

According to the UNC scientist, this system may represent a primitive form of kin selection, whereby organisms kill organisms that are genetically different but not those that are closely related.

"As an additional twist, we have found that some bacteria can have two or three (or possibly more) systems. Our data suggest that these bacteria will be protected from killing by bacteria that produce any of three types of poison swords and they will be able to kill other bacteria that lack at least one of those types of immunity proteins."

Moreover, there's evidence here that these bacteria acquire these additional systems by horizontal gene transfer from other bacteria. "In other words, it seems that they may be able to kill their enemy and then steal the poison-tipped sword and protective (immunity) protein from the dead enemy, increasing their own repertoire of weapons."

By teasing out the genetics of these bacterial close combat mysteries, it may someday be possible to "engineer an organism, a non-pathogenic variant, and by putting it out in the environment, such as soil, you can potentially get rid of other pathogens, "Cotter said. "Or you could decontaminate an area, if the new knowledge is applied to biodefense.