Friday, May 7, 2010

TO HAVE OR NOT TO HAVE RIBS (A VERTEBRATE STORY)

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Like all vertebrates, snakes, mice and humans have in common a skeleton made of segments, the vertebrae. But a snake has between 200-400 ribs extending from all vertebrae, from the neck to the tail-end, whereas mice have only 13 pairs of ribs, and humans have 12 pairs, in both cases making up the ribcage. In the latest issue of Developmental Cell, researchers from the Instituto Gulbenkian de Ciência, in Portugal, reveal that, contrary to what was thought, making ribs is not the default state for vertebrates, but is actually an active process of balancing the activities of a remarkable class of genes - the Hox genes.

It was thought that the rib less region of the mouse embryo was the result of a rib-inhibiting programme, driven by Hox10 genes. Indeed, previous studies, in which Hox10 genes were inactivated in the embryo, generated mice with extra ribs. However, by forcing another class of Hox genes (Hox6) to be activated in future rib-less regions of the mouse embryo, Moises Mallo and his team bred mice that also have extra ribs, both in the neck area, and from just after the rib cage, all the way down to the tail, resembling a snake-like skeleton.

'It was an extraordinary, and clear-cut result', says Mallo, 'suggesting that these two groups of Hox genes balance each other out: one actively promotes rib formation to produce the thoracic region, while the other blocks this activity in the lumbar region. Our results have unveiled this balance.'

The researchers went on to unpick the genes involved in this process, and came up with yet another surprising finding: that the whole process relies on first hitting so-called muscle genes in the embryo, which then provide signals to switch on the 'rib' genes to make both ribs and muscle, in a coordinated process.

According to Mallo, 'Our findings reveal a more complicated process than we would have imagined, but one that makes perfect sense, from a functional and evolutionary point of view: it is no good to make ribs without muscle, so, in the embryo, the production of both ribs and their associated muscles is under the control of a single and coordinated mechanism.

(Photo: Instituto Gulbenkian de Ciência)

Instituto Gulbenkian de Ciência

PHYSICISTS CAPTURE FIRST IMAGES OF ATOMIC SPIN

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Though scientists argue that the emerging technology of spintronics may trump conventional electronics for building the next generation of faster, smaller, more efficient computers and high-tech devices, no one has actually seen the spin—a quantum mechanical property of electrons—in individual atoms until now.

In a study published as an Advance Online Publication in the journal Nature Nanotechnology, physicists at Ohio University and the University of Hamburg in Germany present the first images of spin in action.

The researchers used a custom-built microscope with an iron-coated tip to manipulate cobalt atoms on a plate of manganese. Through scanning tunneling microscopy, the team repositioned individual cobalt atoms on a surface that changed the direction of the electrons’ spin. Images captured by the scientists showed that the atoms appeared as a single protrusion if the spin direction was upward, and as double protrusions with equal heights when the spin direction was downward.

The study suggests that scientists can observe and manipulate spin, a finding that may impact future development of nanoscale magnetic storage, quantum computers and spintronic devices.

“Different directions in spin can mean different states for data storage,” said Saw-Wai Hla, an associate professor of physics and astronomy in Ohio University’s Nanoscale and Quantum Phenomena Institute and one of the primary investigators on the study. “The memory devices of current computers involve tens of thousands of atoms. In the future, we may be able to use one atom and change the power of the computer by the thousands.”

Unlike electronic devices, which give off heat, spintronic-based devices are expected to experience less power dissipation.

The experiments were conducted in an ultra-high vacuum at the low temperature of 10 Kelvin, with the use of liquid helium. Researchers will need to observe the phenomenon at room temperature before it can be used in computer hard drives.

But the new study suggests a path to that application, said study lead author Andre Kubetzka of the University of Hamburg. To image spin direction, the team not only used a new technique but also a manganese surface with a spin that, in turn, allowed the scientists to manipulate the spin of the cobalt atoms under study.

“The combination of atom manipulation and spin sensitivity gives a new perspective of constructing atomic-scale structures and investigating their magnetic properties,” Kubetzka said.

(Photo: Saw-Wai Hla, Ohio University)

Ohio University

ANCIENT ARTIFACTS REVEALED AS NORTHERN ICE PATCHES MELT

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High in the Mackenzie Mountains, scientists are finding a treasure trove of ancient hunting tools being revealed as warming temperatures melt patches of ice that have been in place for thousands of years.

Tom Andrews, an archaeologist with the Prince of Wales Northern Heritage Centre in Yellowknife and lead researcher on the International Polar Year Ice Patch Study, is amazed at the implements being discovered by researchers.

"We're just like children opening Christmas presents. I kind of pinch myself," says Andrews.

Ice patches are accumulations of annual snow that, until recently, remained frozen all year. For millennia, caribou seeking relief from summer heat and insects have made their way to ice patches where they bed down until cooler temperatures prevail. Hunters noticed caribou were, in effect, marooned on these ice islands and took advantage.

"I'm never surprised at the brilliance of ancient hunters anymore. I feel stupid that we didn't find this sooner," says Andrews.

Ice patch archeology is a recent phenomenon that began in Yukon. In 1997, sheep hunters discovered a 4,300-year-old dart shaft in caribou dung that had become exposed as the ice receded. Scientists who investigated the site found layers of caribou dung buried between annual deposits of ice. They also discovered a repository of well-preserved artifacts.

Andrews first became aware of the importance of ice patches when word about the Yukon find started leaking out. "We began wondering if we had the same phenomenon here."

In 2000, he cobbled together funds to buy satellite imagery of specific areas in the Mackenzie Mountains and began to examine ice patches in the region. Five years later, he had raised enough to support a four-hour helicopter ride to investigate two ice patches. The trip proved fruitful.

"Low and behold, we found a willow bow." That discovery led to a successful application for federal International Polar Year funds which have allowed an interdisciplinary team of researchers to explore eight ice patches for four years.

The results have been extraordinary. Andrews and his team have found 2400-year-old spear throwing tools, a 1000-year-old ground squirrel snare, and bows and arrows dating back 850 years. Biologists involved in the project are examining dung for plant remains, insect parts, pollen and caribou parasites. Others are studying DNA evidence to track the lineage and migration patterns of caribou. Andrews also works closely with the Shutaot'ine or Mountain Dene, drawing on their guiding experience and traditional knowledge.

"The implements are truly amazing. There are wooden arrows and dart shafts so fine you can't believe someone sat down with a stone and made them."

Andrews is currently in a race against time. His IPY funds have run out and he is keenly aware that each summer, the patches continue to melt. In fact, two of the eight original patches have already disappeared.

"We realize that the ice patches are continuing to melt and we have an ethical obligation to collect these artifacts as they are exposed," says Andrews. If left on the ground, exposed artifacts would be trampled by caribou or dissolved by the acidic soils. "In a year or two the artifacts would be gone."

University of Calgary

HOW A CELL MOTOR GETS PUSHY

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A University of Utah researcher helped discover how a "wimpy" protein motor works with two other proteins to gain the strength necessary to move nerve cells and components inside them. The findings shed light on brain development and provide clues to a rare brain disorder that often kills babies within months of birth.

"It's like the 'Transformers' films: You start with this puny little car and it becomes a big robot capable of moving big things," says biophysicist Michael Vershinin, a coauthor of a new study to be published Friday, April 16 in the journal Cell.

Vershinin, an assistant professor of physics, and his colleagues in New York and California uncovered details of how two proteins - named LIS1 and NudE (for nuclear displacement protein E).- bind to and strengthen another protein named dynein, which serves as a motor to move components around inside cells and, at times, to move the cells themselves. A cell contains hundreds to thousands of these microscopic motors.

"We found these two proteins, NudE and LIS1, make a special arrangement with dynein," Vershinin says. "All three can bind together, and NudE and LIS1 conspire to get dynein to move heavy objects like the nucleus more efficiently in the cell. Dynein is kind of wimpy. If you pull on it hard enough, it tends to give up pretty easily. With NudE and LIS1 in place, it doesn't."

Mutant LIS1 has been linked previously to the classic form of lissencephaly, a devastating brain malformation due to defective migration of nerve cells within the developing brain. The disorder occurs in about one in 100,000 live births.

Lissencephaly means smooth brain and is characterized by a lack of development of brain folds and convolutions. There are about 20 forms, including at least three caused by defective genes. Viral infections and inadequate blood flow are other causes. Mutant LIS1 is present in more than half of lissencephaly cases, Vershinin says.

Infants born with the disorder suffer severe mental retardation, seizures and early death, as well as a small head, failure to thrive and malformed fingers and toes. Newborns with lissencephaly generally live only months. Few survive into their teens.

The new study analyzed dynein, NudE and LIS1 in laboratory glassware, not in animals, so "much work remains to link our findings to the full complexity of what happens in cells," Vershinin says. "This is several layers away from any clinical advance."

Nevertheless, "I hope someday it [the new findings] will mean we can design a therapy or drug that will help," he adds. "If we understand what can possibly go wrong [with the cell motors during cell migration], then we can design a therapy."

Vershinin conducted the study with biochemist Richard McKenney, a graduate student in cell biology at Columbia University in New York; theoretical biophysicist Ambarish Kunwar, a postdoctoral researcher at the University of California, Davis; Richard Vallee, a professor of pathology and cell biology at Columbia; and biophysicist Steven Gross, a professor of developmental and cell biology at University of California, Irvine. Vershinin worked with Gross at Irvine before joining Utah's faculty.

"If you can understand the details of how motors are controlled, you can hope to understand how things get distributed and moved in cells," Vershinin says.

"By analogy, if you have a house, come in, find the lights are out and you're looking for the light switch and circuit breaker, you want to know how everything is arranged. What we had originally [in understanding cell motors] were a bunch of parts. We didn't know exactly how they were laid out and exactly what they did in the cell."

The new study "clarifies that to a certain extent," he says.

Researchers already knew the dynein motor, a protein molecule, "basically looks like two donuts with legs," Vershinin says. "They can move step by step along a 'road' [inside cells] called a microtubule."

In general, dynein motors move various cell parts along the microtubule "roadways" and toward the nucleus. Another kind of motor, known as kinesin, moves things away from the nucleus and toward the cell periphery.

Vershinin says when one cell signals another chemically, dynein pulls the incoming chemical signal from the cell membrane into the cell. When cells divide, dynein motors help them divide neatly and evenly. Dynein and kinesin help distribute energy-producing mitochondria where needed within cells.

Without molecular motors inside, "a cell is like a city without cars and trucks: dead," says Vershinin. "Moreover, it's not always about moving small things around. Sometimes a cell needs to move large things like its nucleus, and sometimes a cell itself needs to move, and such processes often need motors. If motors do not work properly that is often either the cause or a key consequence of a disease."

Previous research suggests that Alzheimer's disease, other dementias and Parkinson's disease all involve disruption of the kinesin motor, and, to a lesser extent, disruption of the dynein's ability to stay on the microtubule "road," Vershinin says.

There are different kinds of dynein motors. The new study involved cytoplasmic dynein, the motors within cells. Other kinds are found in cilia and in the flagella bacteria use to swim. Vallee's laboratory discovered cytoplasmic dynein more than a decade ago.

Vallee's team previously showed that dynein, LIS1 and NudE "worked together in very young neurons, and were key to these neurons moving into their proper positions in the developing brain" - like caterpillars using internal muscles to crawl," Vershinin says. "But the question remained: how do these proteins work together?

In the new study, "we have clarified how these proteins interact and found a few previously unknown but crucial details," Vershinin says.

Researchers previously knew that LIS1 and NudE bind to the dynein motor, but "until our study it was not clear how this binding worked," and how the three proteins interacted, he says.

"Arguably, the most important finding is that the dynein motor alone does not withstand load very well. It gives up pretty fast. So that's bad if you are trying to move large objects inside of cells and if you eventually try to move the entire cell," says Vershinin. But dynein plus the other two proteins "hang on under load much longer."

He says the study is significant because it shows "that dynein's mode of force production and motor activity can be regulated in very sophisticated ways."

Another key finding is that "LIS1 binds to dynein only at a specific time when its binding is crucial for moving large cargoes," and it helps dynein stay on the microtubule "road," he says.

Vershinin says the researchers believe NudE holds LIS1 in place so it is available to bind to dynein when needed, and so it doesn't diffuse away when not needed.

"It's like a little leash," Vershinin says of the NudE protein.

(Photo: Dave Meikle, University of Utah)

University of Utah

NEW SOLAR CONCENTRATOR DESIGN

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A new solar concentrator design from an electrical engineering Ph.D. student at the University of California, San Diego could lead to solar concentrators that are less expensive and require fewer photovoltaic cells than existing solar concentrators.

The graduate student, Jason Karp and his colleagues at the UC San Diego Jacobs School of Engineering presented the new solar concentrator in a paper in the January 2010 issue of the journal Optics Express.

On April 15, Karp and his solar concentrator won the 2010 Rudee Research Expo Outstanding Poster Award at the 29th Annual Research Expo at the UC San Diego Jacobs School of Engineering (http://www.jacobsschool.ucsd.edu/re/)

While engineers have already developed high-efficiency solar concentrators that incorporate optics to focus the sun hundreds of times and can deliver twice the power of rigid solar panels, the new design offers potential new benefits. Existing solar concentrator systems typically use arrays of individual lenses that focus directly onto independent photovoltaic cells which all need to be aligned and electrically connected. In contrast, the new solar concentrator collects sunlight with thousands of small lenses imprinted on a common sheet. All these lenses couple into a flat "waveguide" which funnels light to a single photovoltaic cell.

Karp built a working prototype with just two primary optical components, thus reducing materials, alignment and assembly. This solar concentrator is compatible with high-volume, low-cost manufacturing.

"The real reason that we are trying to do this type of concentrator is certainly for cost," said Karp in an interview after winning best poster at Research Expo 2010 at the UC San Diego Jacobs School of Engineering. Karp explained that his design minimizes the cost for the optics associated with the entire system. One path to building optics very cheaply leads engineers to existing manufacturing techniques. The new solar concentrator is compatible with existing roll-to-roll processing techniques involved in fabricating large televisions.

Karp designed and built prototypes for the new solar concentrator in the Photonic Systems Integration Laboratory led by electrical engineering professor Joseph Ford from the UC San Diego Jacobs School of Engineering.

(Photo: UC San Diego / Jason Karp)

University of California, San Diego

RECYCLING NANOPARTICLES

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Some nanoparticles are more precious than gold, so being able to recycle them would offer manufacturers important cost savings.

Professor Julian Eastoe at the University of Bristol, and colleagues, report the development of a special type of microemulsion – a mixture of oil and water (mayonnaise is an edible emulsion) – that may make it easier for manufacturers to recover, recycle, and reuse nanoparticles.

In laboratory tests using cadmium and zinc nanoparticles, they demonstrate how the oil and water in the microemulsion separated into two layers when heated. One layer contained the nanoparticles that could be recovered and the other contained none.

Importantly, the team reports, the recovered particles retain their shape and chemical properties, which is crucial for their reuse. The new method could speed application of nanotechnology in new generations of solar cells, flexible electronic displays and various other products.

Julian Eastoe said, “Recovering and recycling nanoparticles is especially difficult because they tend to form complex, hard-to-separate mixtures with other substances. We have designed a new kind of solvent which is perfectly suited to nanotechnology.

“A significant advantage of this method over more traditional approaches is that it is much milder on the particles, thereby preserving their structure and stability, and permitting recyclability. Additionally, it allows us to separate and recover the nanoparticles ‘at the flick of a switch’, simply by changing the temperature.”

This simple process may potentially find applications in cleanup and purification technologies in order to recover, redisperse and reuse valuable nanomaterials. Without this new development, manufacturing processes that take advantage of the unusual properties of nanoparticles might become prohibitively expensive.

(Photo: Julian Eastoe)

University of Bristol

DO THE BLIND HAVE A MORE ACUTE SENSE OF SMELL?

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An ongoing study by Mathilde Beaulieu-Lefebvre, a graduate student from the Université de Montréal Department of Psychology, has debunked the myth that the blind have a more acute sense of smell than the sighted. Vision loss simply makes blind people pay more attention to how they perceive smells.

"If you enter a room in which coffee is brewing, you will quickly look for the coffee machine. The blind person entering the same room will only have the smell of coffee as information," says Beaulieu-Lefebvre. "That smell will therefore become very important for their spatial representation."

The three-step study tested 25 subjects, 11 of whom were blind from birth. Participants answered a questionnaire and were subjected to two experiments: one where they had to differentiate 16 different perfumes using an olfactometer, another where they lay in a tomodensitometer to identify three smells: a rose, vanilla and butanol (a sweet alcohol).

"There is an urban legend that blind people have better smell than the sighted. We are proving this to be false," says Maurice Ptito, a professor at the Université de Montréal School of Optometry and Beaulieu-Lefebvre's thesis director. "However, the blind do set themselves apart when it comes to cognitive efforts."

Using functional imagery, the team determined that the blind use their secondary olfactory cortex more than the sighted when they smell. They also use the occipital cortex, which is normally used for vision. "That's interesting because it means the blind are recuperating that part of their brain," says Dr. Ptito. "We're not speaking of recycling per se, yet that part of the brain is reorganized and used otherwise."

This research could lead to concrete applications in the re-adaptation of the blind. "For instance, smells are very peculiar in shopping centers," says Beaulieu-Lefebvre. "A hair salon, a pharmacy and a clothing store each have their own distinctive scent. We could easily foresee developing re-adaptation programs for getting around in such places."

(Photo: U. Montreal)

Université de Montréal

HOW CHIMPS DEAL WITH DEATH: STUDIES OFFER RARE GLIMPSES

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Two studies in the April 27th issue of Current Biology, a Cell Press publication, offer rare glimpses into the ways that chimpanzees deal with the deaths of those closest to them. In one case, researchers describe the final hours and moment of death of an older female chimp living in a small group at a UK safari park as captured on video. In the other, researchers observed as two chimpanzee mothers in the wild carried their infants' mummified remains for a period of weeks after they were lost to a respiratory epidemic.

"Several phenomena have at one time or another been considered as setting humans apart from other species: reasoning ability, language ability, tool use, cultural variation, and self-awareness, for example, but science has provided strong evidence that the boundaries between us and other species are nowhere near to being as clearly defined as many people used to think," said James Anderson of the University of Stirling in reference to his observations of the safari park chimps. "The awareness of death is another such psychological phenomenon. The findings we've described, along with other observations of how chimpanzees respond to dead and dying companions, indicate that their awareness of death is probably more highly developed than is often suggested. It may be related to their sense of self-awareness, shown through phenomena such as self-recognition and empathy towards others."

Few have witnessed chimps' response at the moment a member of their group dies, Anderson said. Mother chimps have been known to carry their dead infants, he said, and some observers have seen the commotion that follows when an adult chimp is lost to some sort of sudden trauma.

"In contrast to the frenzied, noisy responses to traumatic adult deaths, the chimpanzees witnessing the female's death in our case were mostly calm," Anderson said.

In the days leading up to the chimp's death, the group was very quiet and paid close attention to her, the researchers report. Immediately before she died, she received much grooming and caressing from the others, who appeared to test her for signs of life as she died. They left her soon after, but her adult daughter returned and remained by her mother all night. When keepers removed the mother's body the next day, the chimpanzees remained calm and subdued. For several days they avoided sleeping on the platform where the female had died, even though it was normally a favored sleeping spot, and remained subdued for some time after the death.

"In general, we found several similarities between the chimpanzees' behavior toward the dying female, and their behavior after her death, and some reactions of humans when faced with the demise of an elderly group member or relative, even though chimpanzees do not have religious beliefs or rituals surrounding death," Anderson said. Whatever the reasons for the chimps' actions, he added, they suggest that chimpanzees have a highly developed awareness of death.

In the second study, Dora Biro of the University of Oxford and her colleagues witnessed the deaths of five members (including two infants) of a semi-isolated chimpanzee community that researchers have been studying for over three decades in the forests surrounding Bossou, Guinea.

"We observed the deaths of two young infants—both from a flu-like respiratory ailment," Biro said. "In each case, our observations showed a remarkable response by chimpanzee mothers to the death of their infants: they continued to carry the corpses for weeks, even months, following death."

In that time, the corpses mummified completely, and the mothers exhibited care of the bodies reminiscent of their treatment of live infants: they carried them everywhere during their daily activities, groomed them, and took them into their day and night nests during periods of rest. Over this extended period, they also began to "let go" of the infants gradually, Biro said. They allowed other individuals within the group to handle them more and more frequently and tolerated longer periods of separation from them, including instances where other infants and juveniles were allowed to carry off and play with the corpses.

Other group members showed some interest in the bodies, but almost without exception, the other chimps showed no aversion toward the corpses. Biro noted that a member of her team made very similar observations following the death of one chimpanzee infant in Bossou back in 1992.

"Chimpanzees are humans' closest evolutionary relatives, and they have already been shown to resemble us in many of their cognitive functions: they empathize with others, have a sense of fairness, and can cooperate to achieve goals," Biro said. "How they perceive death is a fascinating question, and little data exist so far concerning chimpanzees' responses to the passing of familiar or related individuals either in captivity or in the wild. Our observations confirm the existence of an extremely powerful bond between mothers and their offspring which can persist, remarkably, even after the death of the infant, and they further call for efforts to elucidate the extent to which chimpanzees understand and are affected by the death of a close relative or group-mate. This would both have implications for our understanding of the evolutionary origins of human perceptions of death and provide insights into the way chimpanzees interpret the world around them."

Cell Press

TO LEARN BETTER, TAKE A NAP (AND DON'T FORGET TO DREAM)

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Researchers reporting online on April 22nd in Current Biology, a Cell Press publication, offer more evidence that successful study habits should include plenty of napping. They found that people who take a nap and dream about a task they've just learned perform it better upon waking than either those who don't sleep at all or those who sleep but don't report any associated dreams.

The learners in the study were asked to sit in front of a computer screen and learn the layout of a three-dimensional maze so that they could find their way to a landmark (a tree) when they were plopped down at a random location within the virtual space five hours later. Those who were allowed to take a nap and also remembered dreaming of the task found the tree in less time.

"We at first thought that dreaming must reflect the memory process that's improving performance," said Robert Stickgold of Harvard Medical School. "But when you look at the content of the dreams, it was hard to argue that."

In a couple of cases, the dreamers said they recalled just the music from the computer maze. One subject said they were dreaming that there were people at particular checkpoints in the maze, even though the real maze didn't have any people or checkpoints. Another said they dreamt about an experience they'd had tromping through bat caves and thinking that the caves were like mazes.

"We think that the dreams are a marker that the brain is working on the same problem at many levels," Stickgold said. "The dreams might reflect the brain's attempt to find associations for the memories that could make them more useful in the future."

In other words, it's not that the dreams led to better memory, but rather that they are a sign that other, unconscious parts of the brain were working hard to remember how to get through the virtual maze. The dreams are essentially a side effect of that memory process.

Stickgold said that there may still be ways to take advantage of this phenomenon for improving learning and memory. For instance, it may be better to study hard right before you go to sleep than in the afternoon, or to take a nap after a period of intense afternoon study. More generally, people might take notice of the study habits or mental processes while awake that lead them to dream about something they need to remember. Perhaps other more directed ways to guide dreams could even prove useful to make your brain work on what you want it to at night.

But, Stickgold said, the most exciting thing to him is the notion that this line of evidence might elucidate a deeper question that has seemed almost impossible to tackle: Why do we dream? What is its function?

"Some have viewed dreaming as entertainment, but this study suggests it is a by-product of memory processing," he said. Whether you have to remember your dreams to get the benefits isn't yet entirely clear, but Stickgold suspects not. After all, he said, people generally remember only a small fraction, no more than 10 to 15 percent, of their dreams.

The researchers hope to follow up their study by manipulating the learning environment in ways that boost incorporation into dreams. They also plan to study the same phenomenon following a full night of sleep as opposed to a nap.

Cell Press

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