Sea Urchin Yields Key Secret Of Biomineralization

Sea urchin. The teeth and bones of mammals, the protective shells of mollusks, and the needle-sharp spines of sea urchins and other marine creatures are made-from-scratch wonders of nature. (Credit: iStockphoto/Ronald Fernandez)

ScienceDaily (Nov. 1, 2008) — The teeth and bones of mammals, the protective shells of mollusks, and the needle-sharp spines of sea urchins and other marine creatures are made-from-scratch wonders of nature.

Used to crush food, for structural support and for defense, the materials of which shells, teeth and bones are composed are the strongest and most durable in the animal world, and scientists and engineers have long sought to mimic them.

Now, harnessing the process of biomineralization may be closer to reality as an international team of scientists has detailed a key and previously hidden mechanism to transform amorphous calcium carbonate into calcite, the stuff of seashells. The new insight promises to inform the development of new, superhard materials, microelectronics and micromechanical devices.

In a report Oct. 27 in the Proceedings of the National Academy of Sciences, a group led by University of Wisconsin-Madison physicist Pupa Gilbert describes how the lowly sea urchin transforms calcium carbonate — the same material that forms "lime" deposits in pipes and boilers — into the crystals that make up the flint-hard shells and spines of marine animals. The mechanism, the authors write, could "well represent a common strategy in biomineralization…."

"If we can harness these mechanisms, it will be fantastically important for technology," argues Gilbert, a UW-Madison professor of physics. "This is nature's bottom-up nanofabrication. Maybe one day we will be able to use it to build microelectronic or micromechanical devices."

Gilbert, who worked with colleagues from Israel's Weizmann Institute of Science, the University of California at Berkeley and the Lawrence Berkeley National Laboratory, used a novel microscope that employs the soft-X-rays produced by synchrotron radiation to observe how the sea urchin builds its spicules, the sharp crystalline "bones" that constitute the animal's endoskeleton at the larval stage.

Similar to teeth and bones, the sea urchin spicule is a biomineral, a composite of organic material and mineral components that the animal synthesizes from scratch, using the most readily available elements in sea water: calcium, oxygen and carbon. The fully formed spicule is composed of a single crystal with an unusual morphology. It has no facets and within 48 hours of fertilization assumes a shape that looks very much like the Mercedes-Benz logo.

These crystal shapes, as those of tooth enamel, eggshells or snails, are very different from the familiar faceted crystals grown through non-biological processes in nature. "To achieve such unusual — and presumably more functional — morphologies, the organisms deposit a disordered amorphous mineral phase first, and then let it slowly transform into a crystal, in which the atoms are neatly aligned into a lattice with a specific and regular orientation, while maintaining the unusual morphology," Gilbert notes.

The question the Wisconsin physicist and her colleagues sought to answer was how this amorphous-to-crystalline transition occurs. The sea urchin larval spicule is a model system for biominerals, and the first one in which the amorphous calcium carbonate precursor was discovered in 1997 by the same Israeli group co-authoring the current PNAS paper. A similar amorphous-to-crystalline transition has since been observed in adult sea urchin spines, in mollusk shells, in zebra fish bones and in tooth enamel. The resulting biominerals are extraordinarily hard and fracture resistant, compared to the minerals of which they are made.

"The amorphous minerals are deposited and they are completely disordered," Gilbert explains. "So the question we addressed is 'how does crystallinity propagate through the amorphous mineral?'"

To answer it, Gilbert and her colleagues observed spicule development in 2- to 3-day-old sea urchin larvae. The sea urchin spicule is formed inside a clump of specialized cells and begins as the animal lays down a single crystal of calcite in the form of a rhombohedral seed, from which the rest of the spicule is formed. Starting from the crystalline center, three arms extend at 120 degrees from each other, as in the hood ornament of a Mercedes-Benz. The three radii are initially amorphous calcium carbonate, but slowly convert to calcite.

"We tried to find evidence of a massive crystal growth, with a well defined growth front, propagating from the central crystal through the amorphous material, but we never observed anything like that," Gilbert says. "What we found, instead, is that 40-100 nanometer amorphous calcium carbonate particles aggregate into the final morphology. One starts converting to crystalline calcite, then another immediately adjacent converts as well, and another, and so on in a three-dimensional domino effect. The pattern of crystallinity, however, is far from straight. It resembles a random walk, or a fractal, like lightning in the sky or water percolating through a porous medium," explains Gilbert.

The new work, according to Gilbert, brings science a key step closer to a thorough understanding of how biominerals form and transform. Knowing the step-by-step process may permit researchers to develop new crystal structures that can be used in applications ranging from new microelectronic devices to medical applications.

The new study was funded by the National Science Foundation and the U.S. Department of Energy.

---

Adapted from materials provided by University of Wisconsin-Madison.

NIST's modified field-effect transistor can count single photons, or particles of light. When light enters through the transmission window (see electron micrograph of top of device), it penetrates the gallium arsenide absorbing layer and separates electrons from the ‘holes’ they formerly occupied. Quantum dots (red dots) trap the positively charged holes, while electrons flow into the channel (green Xs). By measuring the channel current, researchers can determine the number of photons absorbed. (Credit: NIST)

ScienceDaily (Oct. 15, 2007) — A transistor containing quantum dots that can count individual photons (the smallest particles of light) has been designed and demonstrated at the National Institute of Standards and Technology (NIST). The semiconductor device could be integrated easily into electronics and may be able to operate at higher temperatures than other single-photon detectors--practical advantages for applications such as quantum key distribution (QKD) for "unbreakable" encryption using single photons.

The NIST device, described in a new paper,* can accurately count 1, 2 or 3 photons at least 83 percent of the time. It is the first transistor-based detector to count numbers of photons; most other types of single-photon detectors simply "click" in response to any small number of photons. (See table for a comparison of various types of single-photon detectors used at NIST.) 

Counting requires a linear, stepwise response and low-noise operation. This capability is essential for advanced forms of precision optical metrology--a focus at NIST--and could be used both to detect photons and to evaluate single-photon sources for QKD. The new device also has the potential to be cooled electronically, at much higher temperatures than typical cryogenic photon detectors.

Dubbed QDOGFET, the new detector contains about 1,000 quantum dots, nanoscale clusters of semiconductors with unusual electronic properties. The NIST dots are custom-made to have the lowest energy of any component in the detector, like the bottom of a drain. A voltage applied to the transistor produces an internal current, or channel. Photons enter the device and their energy is transferred to electrons in a semiconductor "absorbing layer," separating the electrons from the "holes" they formerly occupied. 

As each photon is absorbed, a positively charged hole is trapped by the quantum dot drain, while the corresponding electron is swept into the channel. The amount of current flowing in the channel depends on the number of holes trapped by quantum dots. By measuring the channel response, scientists can count the detected photons. NIST measurements show that, on average, each trapped hole boosts the channel current by about one-fifth of a nanoampere. The detector has an internal quantum efficiency (percentage of absorbed photons that result in trapped holes) of 68 ± 18 percent, a record high for this type of photon detector.

The QDOGFET currently detects single photons at wavelengths of about 800 nanometers. By using different semiconductor materials, NIST researchers hope to make detectors that respond to the longer near-infrared wavelengths used in telecommunications. In addition, researchers hope to boost the external quantum efficiency (percentage of photons hitting the detector that are actually detected), now below 10 percent, and operate the device at faster speeds.

The research is supported in part by the Disruptive Technology Office. The authors include one from Los Alamos National Laboratory and one from Heriot-Watt University, Edinburgh, UK.

* E.J. Gansen, M.A. Rowe, M.B. Greene, D. Rosenberg, T.E. Harvey, M.Y. Su, R.H. Hadfield, S.W. Nam and R.P. Mirin. Photon-number-discriminating detection using a quantum dot, optically gated, field-effect transistor. Nature Photonics. 1, 585 - 588 (2007). Published on-line Oct. 1, 2007.

---

Adapted from materials provided by National Institute of Standards and Technology.

Biochemists And Engineers Create Fast-acting Pathogen Sensor

September 1, 2008 — Engineers invented a device to bring air samples into contact with genetically engineered biosensors in the effort to detect dangerous biological agents. The technology uses multiple collections of altered cell antibodies, each collection designed to respond to a specific pathogen by releasing photons of a unique wavelength upon finding it. Detectors measure the photons' wavelengths and interpret the pathogens they represent.

Anthrax, plague and small pox are some of the possible pathogens terrorists could use against us; but now, researchers say jellyfish are helping prevent these kinds of attacks.

From public transportation to federal and government buildings, experts are naming likely targets of bioterrorism.

Now, this innovative biosensor developed by scientists and engineers at Massachusetts Institute of Technology's (MIT) Lincoln Laboratory can identify harmful bacteria or viruses in the air in less than two minutes.

"It's at least ten times faster than any other automated sensor that's available," says James Harper, a biochemist and engineer at MIT.

In the lab, Todd Rider first developed the CANARY Sensor using jellyfish DNA and a high-voltage electrical charge. "I was in the lab with the electric creator," says Rider, a biologist at MIT. "I had mouse cells and the jellyfish DNA, and I frizzed my hair, said please give me life and pressed the buttons -- and the jellyfish DNA went inside the cells, and we had glowing mouse cells."

The glowing cells reveal the presence of a targeted pathogen. Still, scientists had no way to test air samples for pathogens until Harper created the PANTHER.

Scientists say operation is as simple as loading your DVD player. Disks containing sixteen chambers are loaded into the PANTHER. The machine pulls air through the disk to collect and test any pathogen that might be in the air. "That disk contains the cells that are the key to the canary technology," Harper says. "It releases those cells into the collected particles and looks for the resulting light, and gives you a sense of what's detected."

If a dangerous pathogen is detected, the sensor goes off -- alerting anyone who could be in harm's way.

Scientists and engineers say the CANARY technology can eventually be used for medical diagnostics to test patient samples. It may even be used in food processing plants to identify contaminants like E. coli or salmonella.

The technology is now licensed commercially.

WHAT IS PANTHER? The PANTHER device uses immune cells altered to act as detectors of dangerous biological agents. The device takes in air, runs it past the cells, which are gathered into groups, each designed to react to specific agent. The cells, which are engineered to respond to a specific pathogen, release photons of light when they detect their target. Other detectors recognize the release of light to indicate the pathogen that was detected. Based on the wavelengths of light that were released, the device outputs a list of dangerous pathogens that were found, about three minutes after beginning the test.

This report has also been produced thanks to a generous grant from the Camille and Henry Dreyfus Foundation, Inc.

Ancient Mummy, The Tyrolean Iceman, Has No Modern Children

Tyrolean Ice Man. (Credit: Professor Franco Rollo, University of Camerino)

ScienceDaily (Nov. 1, 2008) — The 5,300 year old human mummy – dubbed Öetzi or 'the Tyrolean Iceman' – is highly unlikely to have modern day relatives, according to new research.

A team comprising scientists from Italy and the UK has sequenced Öetzi's entire mitochondrial DNA (mtDNA) genome - which is passed down through the maternal line – and found that he belonged to a genetic lineage that is either extremely rare, or that has died out.

Published in this month's issue of Current Biology, the research has generated the oldest complete Homo sapiens mtDNA genome to date, and overturns previous research conducted in 1994 on a small section of Öetzi's mtDNA, which suggested that relatives of Öetzi may still exist in Europe.

"Changes arise only gradually in mitochondrial DNA as it is passed down the generations," says co-author Professor Martin Richards of the University of Leeds' Faculty of Biological Sciences, "and so it provides an effective way of tracking ancestry through the female line across many thousands of years, as well as examining evolutionary relatedness across human populations."

The team, led by Professor Franco Rollo at the University of Camerino and Dr Luca Ermini working at both Camerino and Leeds, used powerful new technologies to sequence Öetzi's mtDNA and match it with a modern day haplogroup – in genetic terms, a group that shares a common ancestral DNA sequence. He belonged to a branch of haplogroup K1, which is still common throughout Europe today. However, almost all members of K1 sampled from modern Europeans belong to one of three sub-lineages, whereas Öetzi's lineage was completely distinct.

After death DNA begins to degrade immediately, so ancient DNA is very fragmented and any study of it has to be completed in hundreds of sections. For this research the team tested around 250 fragments, each of which had to be sequenced many times to ensure the results were not distorted.

"Our analysis confirms that Öetzi belonged to a previously unidentified lineage of K1 that has not been seen to date in modern European populations. The frequency of genetic lineages tends to change over time, due to random variations in the number of children people have - a process known as 'genetic drift' - and as a result, some variants die out. Our research suggests that Öetzi's lineage may indeed have become extinct," says Prof Richards.

"We'll only know for sure by sampling intensively in the Alpine valleys where Öetzi was born. However, our results do suggest that studies of ancient samples can fill in gaps in our knowledge left open simply because many genetic lineages died out thousands of years ago. The techniques we've used here are potentially applicable to many other ancient remains."

Öetzi's mummified remains were discovered in September 1991 in the Eastern Alps near the Austro-Italian border. He was approximately 46 years old when he died, and examinations revealed that he had been severely wounded by an arrow and possibly finished off with a mace blow to the face. He is estimated to have lain undiscovered for approximately 5,300 years. His body was almost wholly preserved, together with an array of clothes and weapons, providing an unprecedented insight into the Late Neolithic or Copper Age in Europe. Since 1998 he has been on display at the South Tyrol Museum of Archaeology in Bolzano, Italy.

The research was funded by global pharmaceutical company Eli Lilly and Co.

---

Journal reference:

1. Luca Ermini, Cristina Olivieri, Ermanno Rizzi, Giorgio Corti, Raoul Bonnal, Pedro Soares, Stefania Luciani, Isolina Marota, Gianluca De Bellis, Martin B. Richards, and Franco Rollo. The Complete Mitochondrial Genome Sequence of the Tyrolean Iceman. Current Biology, Online October 30, 2008 [link]

Adapted from materials provided by University of Leeds.

Extinct Sabertooth Cats Were Social, Found Strength In Numbers, Study Shows

A reconstructed scene in the Pleistocene of western North America, showing a group of sabertooth cats of the species Smilodon fatalis, with several adults and cubs. (Credit: Artwork by Mauricio Antón)

ScienceDaily (Oct. 31, 2008) — The sabertooth cat (Smilodon fatalis), one of the most iconic extinct mammal species, was likely to be a social animal, living and hunting like lions today, according to new scientific research. The species is famous for its extremely long canine teeth, which reached up to seven inches in length and extended below the lower jaw.

Instead of relying on the bones and teeth of the sabertooths to make their findings, scientists from UCLA and the Zoological Society of London concluded that the sabertooth cat was social by using a novel technique: They compared numbers of present-day carnivores competing for kills in Africa with those of mainly extinct species found in a North American fossil deposit.

The research is published in the current issue of the Royal Society's journal Biology Letters (Oct. 28). Co-authors also included scientists from South Africa's Tshwane University of Technology and University of Pretoria.

Smilodon existed in North and South America between 1.8 million and 10,000 years ago and is one of the most common species preserved at the Rancho La Brea tar pits of Los Angeles, a fossil deposit in which dying herbivores trapped in sticky asphalt attracted numerous dire wolves and sabertooth cats, some of which also died there.

Because most living cats are solitary, controversy has persisted over the social life of Smilodon.

The study reported in Biology Letters took a new approach to the question by comparing data from the La Brea fossil record and data obtained from "playbacks" used in Africa, in which the recorded calls of distressed prey and the sounds of lions and hyenas are used to attract carnivores. This technique has been used by scientists to estimate carnivore densities in eastern and southern Africa.

Results showed that large social species made up a far larger proportion of the animals attracted than one would expect, considering their population size compared to other carnivores. Large social carnivores were, in fact, found to attend approximately 60 times more often than expected on the basis of relative abundance. When these results were compared with the records at the tar pits of California, the scientists found that the proportion of Smilodon records matched the proportion of the large social carnivores in the playbacks.

"It absolutely makes sense that social species will predominate at carcasses, both now and in the past," said Blaire Van Valkenburgh, UCLA professor of ecology and evolutionary biology and senior author on the paper. "Why approach a situation where you are likely to encounter dangerous competitors without having a few friends along?"

The same social advantage, she said, would apply to all scavengers, including early humans, who began consuming more meat about 2 million year ago, some of which they probably scavenged.

Although commonly called the "sabertoothed tiger," the species is actually not closely related to the tiger, which is part of a different subfamily. However, the sabertooth cat was large and muscular, similar in size to a modern-day tiger.

"The extinct sabertooth cat, Smilodon fatalis, has been something of an enigma, with almost nothing known of its behavior," said Chris Carbone, a senior research fellow at the Zoological Society of London and lead author of the paper. "This research allowed us to use the behavior of its present-day relatives to conclude that this extinct cat was more likely to roam in formidable gangs than as a secretive, solitary animal."

---

Adapted from materials provided by University of California - Los Angeles.

Clues To Planets' Birth Discovered In Meteorites

A picture of the first discovered (and therefore eponymous) angrite "Angra dos Reis"; which was observed to fall from the sky in 1869 near the town of Angra dos Reis in Brazil. The black; shiny face was produced from melting of the meteorite's surface during passage through Earth's atmosphere. Scale bar is in centimeters. (Credit: Photo courtesy / Maria Zucolotto (Museu Nacional; Brasil))

ScienceDaily (Oct. 31, 2008) — Meteorites that are among the oldest rocks ever found have provided new clues about the conditions that existed at the beginning of the solar system, solving a longstanding mystery and overturning some accepted ideas about the way planets form.

The ancient meteorites, like disk drives salvaged from an ancient computer, still contain magnetic records about the very early history of planets, according to research by MIT planetary scientist Benjamin P. Weiss.

Weiss, the Victor P. Starr Career Development Assistant Professor of Planetary Sciences in the Department of Earth, Atmospheric and Planetary Sciences, and his five co-authors examined pieces of three meteorites called angrites, which are among the most ancient rocks known. The results of their study are being published in Science on Oct. 31.

The analysis showed that surprisingly, during the formation of the solar system, when dust and rubble in a disk around the sun collided and stuck together to form ever-larger rocks and eventually the planets we know today, even objects much smaller than planets — just 160 kilometers across or so — were large enough to melt almost completely.

This total melting of the planet-forming chunks of rock, called planetesimals, caused their constituents to separate out, with lighter materials including silicates floating to the surface and eventually forming a crust, while heavier iron-rich material sank down to the core, where it began swirling around to produce a magnetic dynamo. The researchers were able to study traces of the magnetic fields produced by that dynamo, now recorded in the meteorites that fell to Earth.

"The magnetism in meteorites has been a longstanding mystery," Weiss said, and the realization that such small bodies could have melted and formed magnetic dynamos is a major step toward solving that riddle.

Until relatively recently, it was commonly thought that the planetesimals — similar to the asteroids seen in the solar system today — that came together to build planets were "just homogenous, unmelted rocky material, with no large-scale structure," Weiss said. "Now we're realizing that many of the things that were forming planets were mini-planets themselves, with crusts and mantles and cores."

That could change theorists' picture of how the planets themselves took shape. If the smaller bodies were already molten as they slammed together to build up larger planet-sized bodies, that could "significantly change our understanding" of the processes that took place in the early years of the nascent planets, as their internal structures were forming, Weiss said. This could have implications for how different minerals are distributed in the Earth's crust, mantle and core today, for example.

"In the last five or 10 years," Weiss said, "our understanding of the early history of the solar system has undergone a sort of mini-revolution, driven by analytical advances in geochemistry. In this study we used a geophysical technique to independently test many of these new ideas. "

"Events happened surprisingly fast at the beginning of the solar system," he said. Some of the angrite meteorites in this study formed just 3 million years after the birth of the solar system itself, 4,568 million years ago, and show signs that their parent body had a magnetic field that was 20 to 40 percent as strong as Earth's today. "We are used to thinking of dynamo magnetic fields in rocky bodies as uncommon phenomena today. But it may be that short-lived planetesimal dynamos were widespread in the early solar system."

The paper was co-authored by Mitsui Career Development Assistant Professor of Geology Linda Elkins-Tanton, research scientist Eduardo A. Lima, postdoctoral researcher Laurent Carpozen, student James S. Berdahl, and Sabine Stanley, assistant professor of physics at the University of Toronto. The work was supported by a grant from the National Science Foundation's Instrumentation and Facilities Program.

---

Adapted from materials provided by Massachusetts Institute of Technology.

'Living Fossil' Tree Contains Genetic Imprints Of Rain Forests Under Climate Change

The distinctive trunk and aerial roots of the tropical tree Symphonia globulifera in a rain forest in Panama. (Credit: Rolando Pérez, Smithsonian Tropical Research Institute)

ScienceDaily (Oct. 31, 2008) — A "living fossil" tree species is helping a University of Michigan researcher understand how tropical forests responded to past climate change and how they may react to global warming in the future.

The research appears in the November issue of the journal Evolution.

Symphonia globulifera is a widespread tropical tree with a history that goes back some 45 million years in Africa, said Christopher Dick, an assistant professor of ecology and evolutionary biology who is lead author on the paper. It is unusual among tropical trees in having a well-studied fossil record, partly because the oil industry uses its distinctive pollen fossils as a stratigraphic tool.

About 15 to 18 million years ago, deposits of fossil pollen suggest, Symphonia suddenly appeared in South America and then in Central America. Unlike kapok, a tropical tree with a similar distribution that Dick also has studied, Symphonia isn't well-suited for traveling across the ocean—its seeds dry out easily and can't tolerate saltwater. So how did Symphonia reach the neotropics? Most likely the seeds hitched rides from Africa on rafts of vegetation, as monkeys did, Dick said. Even whole trunks, which can send out shoots when they reach a suitable resting place, may have made the journey. Because Central and South American had no land connection at the time, Symphonia must have colonized each location separately.

Once Symphonia reached its new home, it spread throughout the neotropical rain forests. By measuring genetic diversity between existing populations, Dick and coworker Myriam Heuertz of the Université Libre de Bruxelles were able to reconstruct environmental histories of the areas Symphonia colonized.

"For Central America, we see a pattern in Symphonia that also has been found in a number of other species, with highly genetically differentiated populations across the landscape," Dick said. "We think the pattern is the result of the distinctive forest history of Mesoamerica, which was relatively dry during the glacial period 10,000 years ago. In many places the forests were confined to hilltops or the wettest lowland regions. What we're seeing in the patterns of genetic diversity is a signature of that forest history."

In the core Amazon Basin, which was moist throughout the glacial period, allowing for more or less continuous forest, less genetic diversity is found among populations, Dick said. "There's less differentiation across the whole Amazon Basin than there is among sites in lower Central America."

The study is the first to make such comparisons of genetic diversity patterns in Central and South America. "We think similar patterns will be found in other widespread species," Dick said.

Learning how Symphonia responded to past climate conditions may be helpful for predicting how forests will react to future environmental change, Dick said.

"Under scenarios of increased warmth and drying, we can see that populations are likely to be constricted, particularly in Central America, but also that they're likely to persist, because Symphonia has persisted throughout Central America and the Amazon basin. That tells us that some things can endure in spite of a lot of forest change. However, past climate changes were not combined with deforestation, as is the case today. That combination of factors could be detrimental to many species—especially those with narrow ranges—in the next century."

The researchers received funding from the National Science Foundation and the National Fund for Scientific Research of Belgium.

---

Adapted from materials provided by University of Michigan.

Ultrafast Lasers Show Snapshot Of Electrons In Action

A laser beam first excites dinitrogen tetraoxide molecules, or N2O4, inducing large vibrations. A second laser beam then generates X-rays from the vibrating molecules. (Credit: Image courtesy of University of Colorado at Boulder)

ScienceDaily (Oct. 31, 2008) — In the quest to slow down and ultimately understand chemistry at the level of atoms and electrons, University of Colorado at Boulder and Canadian scientists have found a new way to peer into a molecule that allows them to see how its electrons rearrange as the molecule changes shape.

Understanding how electrons rearrange during chemical reactions could lead to breakthroughs in materials research and in fields like catalysis and alternative energy, according to CU-Boulder physics professors and JILA fellows Margaret Murnane and Henry Kapteyn, who led the research efforts with scientist Albert Stolow of the Canadian National Research Council's Steacie Institute for Molecular Sciences.

"The Holy Grail in molecular sciences would be to be able to look at all aspects of a chemical reaction and to see how atoms are moving and how electrons are rearranging themselves as this happens," Murnane said. "We're not there yet, but this is a big step toward that goal."

To be able to chart a chemical reaction, scientists need to be able to see how bonds are formed or broken between atoms in a molecule during chemical reactions. But only extremely limited tools are available to view the rapidly changing electron cloud that surrounds a molecule as the atoms move around, Murnane said. Changes in the electron cloud can happen on timescales of less than a femtosecond, or one quadrillionth of a second, representing some of the fastest processes in the natural world.

In a paper to appear in the Oct. 30 issue of Science Express, the online version of the journal Science, the CU team describes how they shot a molecule of dinitrogen tetraoxide, or N2O4, with a short burst of laser light to induce very large oscillations within the molecule. They then used a second laser to produce an X-ray, which was used to map the electron energy levels of the molecule, and most importantly, to understand how these electron energy levels rearrange as the molecule changes its shape, according to Kapteyn.

"This is a fundamentally new way of looking at molecules," Kapteyn said. "This process allowed us to freeze the motion of electrons in a system, and to capture their dizzying dance."

The researchers describe their process of stretching the N2O4 molecule as being similar to pulling on a Slinky toy and then letting it go and watching it vibrate. They used the N2O4 molecule because it vibrates more slowly compared to other molecules, allowing them to observe the physical processes under way.

In many ways, molecules are like tiny masses connected by tiny springs of differing strengths, Murnane said. These springs are the chemical bonds, made up of shared electrons, which hold all matter together. In this experiment they used ultrafast laser pulses to "twang" these springs, making the nanoscale molecular Slinkies vibrate. However, unlike real springs, when researchers vibrate the molecules their properties can change, she said.

Being able to watch and understand why the electrons did what they did is very useful in fields like alternative energy, according to the researchers.

"If we understand the nature of these processes, in the future we can then translate that knowledge into better technology, such as creating more efficient light-harvesting molecules or catalysis or perhaps even solar cells," Stolow said.

The research was completed by an international team with JILA Research Associate Wen Li as the paper's corresponding author. He worked with CU-Boulder physics graduate students Xibin Zhou and Robynne Lock as well as Serguei Patchkovskii and Stolow of the Steacie Institute for Molecular Sciences in Ottawa, Canada.

---

Adapted from materials provided by University of Colorado at Boulder.

Brain's 'Hate Circuit' Identified

New research has found that people who view pictures of someone they hate display activity in distinct areas of the brain that, together, may be thought of as a 'hate circuit.' (Credit: iStockphoto/Valentin Casarsa)

ScienceDaily (Oct. 29, 2008) — People who view pictures of someone they hate display activity in distinct areas of the brain that, together, may be thought of as a 'hate circuit', according to new research by scientists at UCL (University College London).

The study, by Professor Semir Zeki and John Romaya of the Wellcome Laboratory of Neurobiology at UCL, examined the brain areas that correlate with the sentiment of hate and shows that the 'hate circuit' is distinct from those related to emotions such as fear, threat and danger – although it shares a part of the brain associated with aggression. The circuit is also quite distinct from that associated with romantic love, though it shares at least two common structures with it.

The results are an extension of previous studies on the brain mechanisms of romantic and maternal love from the same laboratory. Explaining the idea behind the research, Professor Zeki said: "Hate is often considered to be an evil passion that should, in a better world, be tamed, controlled, and eradicated. Yet to the biologist, hate is a passion that is of equal interest to love. Like love, it is often seemingly irrational and can lead individuals to heroic and evil deeds. How can two opposite sentiments lead to the same behaviour?"

To compare their present results with their previous ones on romantic love, Zeki and Romaya specifically studied hate directed against an individual. Seventeen subjects, both female and male, had their brains scanned while viewing pictures of their hated person as well as that of neutral faces with which they were familiar. Viewing a hated person showed activity in distinct areas of the brain that, together, may be thought of as a 'hate circuit'.

The 'hate circuit' includes structures in the cortex and in the sub-cortex and has components that are important in generating aggressive behaviour, and translating this into action through motor planning, as if the brain becomes mobilised to take some action. It also involves a part of the frontal cortex that has been considered critical in predicting the actions of others, probably an important feature when one is confronted by a hated person.

The subcortical activity involves two distinct structures, the putamen and insula. The former, which has been implicated in the perception of contempt and disgust, may also be part of the motor system that is mobilised to take action, since it is known to contain nerve cells that are active in phases preparatory to making a move.

Professor Zeki added: "Significantly, the putamen and insula are also both activated by romantic love. This is not surprising. The putamen could also be involved in the preparation of aggressive acts in a romantic context, as in situations when a rival presents a danger. Previous studies have suggested that the insula may be involved in responses to distressing stimuli, and the viewing of both a loved and a hated face may constitute such a distressing signal.

"A marked difference in the cortical pattern produced by these two sentiments of love and hate is that, whereas with love large parts of the cerebral cortex associated with judgment and reasoning become de-activated, with hate only a small zone, located in the frontal cortex, becomes de-activated. This may seem surprising since hate can also be an all-consuming passion, just like love. But whereas in romantic love, the lover is often less critical and judgmental regarding the loved person, it is more likely that in the context of hate the hater may want to exercise judgment in calculating moves to harm, injure or otherwise extract revenge.

"Interestingly, the activity in some of these structures in response to viewing a hated face is proportional in strength to the declared intensity of hate, thus allowing the subjective state of hate to be objectively quantified. This finding may have legal implications in criminal cases, for example."

Unlike romantic love, which is directed at one person, hate can be directed against entire individuals or groups, as is the case with racial, political, or gender hatred. Professor Zeki said that these different varieties of hate will be the subject of future studies from his laboratory.

---

Journal reference:

1. Zeki et al. Neural Correlates of Hate. PLoS ONE, 2008; 3 (10): e3556 DOI: 10.1371/journal.pone.0003556

Adapted from materials provided by University College London, via EurekAlert!, a service of AAAS.

Second Life: 'Second China' Offers Foreign Service Workers First Impression

Second China. A hostess introduces a visitor to a teahouse in Second China, a virtual city aimed and educating and preparing foreign service or other government professionals for their first visit to China. Accessible through the popular online world Second Life, Second China offers an array of virtual experiences to users who want to familiarize themselves with the sights and experiences they will encounter as first-time visitors. These include meetings, visits to teahouses and other Chinese cultural institutions, even a taxi cab ride. (Credit: Image courtesy of Paul Fishwick/University of Florida)

ScienceDaily (Oct. 29, 2008) — Diplomats or military envoys making their first trip to China may soon have a chance to visit a Chinese office building, stop in at a traditional teahouse or hop a cab — all before they board a plane.

A team of University of Florida computer engineers and scholars has used the popular online world Second Life to create a virtual Chinese city, one that hands a key to users who want to familiarize themselves with the sights and experiences they will encounter as first-time visitors. The goal of the federally funded research project: To educate and prepare foreign service or other government professionals to arrive in the country prepared and ready to work.

“I think what we hope is that this kind of environment can provide a bridge between knowledge alone and actually being in the real-life environment,” said Julie Henderson, an international program specialist at the UF College of Pharmacy and co-principal investigator and project designer for the effort.

People have long prepared for international travel with language and cultural instruction, role-playing and, in recent years, distance-learning experiences. The “Second China Project” seeks to add another element: Simulated experiences aimed at introducing users not only to typical sights and the Chinese language, but also to expectations of politeness, accepted business practices and cultural norms.

It may not be the real thing, but it’s a lot easier to get there.

As with all Second Life worlds, users’ avatars simply “teleport” in to Second China, a city with both old and new buildings that looks surprisingly similar to some of China’s fastest growing metropolises. There, they can try a number of different activities — including, for example, visiting an office building for a conference.

“We’ve built an environment around learning objectives,” said Paul Fishwick, lead investigator and a professor of computer and information science and engineering.

In the office simulation, the user’s avatar chooses appropriate business attire and a gift, greets a receptionist, and is guided to a conference room to be seated, among other activities. With each scenario, the user gains understanding or awareness: the Chinese formal greeting language and procedure, that it’s traditional to bring a gift to a first meeting, that guests typically are seated facing the door in a Chinese meeting room, and so on.

Supplementing the visual experience: A Web-based tutorial that the user can click on as he or she navigates Second China. The tutorial has much more detail about every experience. For example, it lists appropriate as well as inappropriate gifts — such as clocks, which in China are considered bad luck when presented as gifts.

In the teahouse simulation, a greeter shows the visitor photos of well-known personalities who have visited as patrons, a typical practice in many establishments in China. However, in the simulation the photos include, for example, a photo of Hu Jintao, the president of China. The accompanying Web tutorial provides biographical background on Hu and the other well-known Chinese personalities in the photos.

“It’s important to be able to go to China already familiar with the important historic and political figures,” said Henderson.

In Second Life, users typically control avatars. But in Second China, the teahouse greeter and other avatars in the various scenarios are controlled by computer software. This allows users to enter Second China anytime they wish, while also ensuring that all users have similar experiences, an important trait for an educational tool.

None of the information in Second China is exclusive to the Second Life simulation — it could also be presented in books or other traditional media.

But Fishwick and Henderson think that allowing users to place themselves within Second China’s virtual world may make the information more memorable and pique users’ curiosity and urge to explore. They’ll know more soon: After spending a year developing the project, they’ll spend the next year testing it on users to gauge its effectiveness.

“In terms of knowledge and empathy toward the culture, we don’t yet know the answer to the question of where one medium succeeds and another one fails,” Fishwick said.

The Second China project has been funded with a $1.25 million federal grant. Other co-principal investigators at UF are Elinore Fresh, a senior lecturer in Chinese and Franz Futterknecht, a professor of Germanic and Slavic studies. Amy Jo Coffey and Rasha Kamhawi, both assistant professors of journalism and communications in the department of telecommunication, will participate in the assessment phase.

---

Adapted from materials provided by University of Florida.

Scientists Unwrap The Elements Of Life

New research has shown that to ensure a copper and a manganese protein wrap around the correct metal atoms they do this in different parts of the cell, in zones which contain different metals. Therefore, which protein attaches to which metal is determined by where the folding action takes place in the cell. (Credit: Image courtesy of Newcastle University)

ScienceDaily (Oct. 28, 2008) — Researchers at Newcastle University have taken a step forward in our understanding of how the fundamental building blocks of life are put together.

In a paper published in Nature, the team led by Professor Nigel Robinson have revealed a mechanism that ensures the right metal goes to the right protein. Proteins are essential and involved in just about every process in living cells.

Life, microbe, plant or human, is a painstaking assembly of trillions of atoms. The atoms include metals such as copper and manganese which act as catalysts in proteins. The proteins wrap around the metal atoms.

The research team has shown that to ensure a copper and a manganese protein wrap around the correct metal atoms, they do this in different parts of the cell, in zones which contain different metals. Therefore, which protein attaches to which metal is determined by where the folding action takes place in the cell.

Previously, a common view was that the right metals were simply those which were most attracted to the protein, but in this work that is not the case.

Professor Nigel Robinson at Newcastle University who led the research says: "This has taken us one step closer to understanding why metals and proteins assemble in the ways they do."

"One motive behind the work is pure curiosity, but as so many proteins need metals this type of work has many potential uses - for example, in synthetic biology which is striving to produce green power from bacteria by using energy from sunlight to produce hydrogen gas, a process which needs nickel and iron.

"It may also help in diseases such as Alzheimers where there are unexplained links to proteins binding metals such as copper. There's also application in controlling infections by Staphylococcus aureus; a bacterium which our bodies defences succeed - or sometimes fail - in killing by removing manganese and zinc from abscesses."

The researchers have shown that the way the metals attach is identical for a protein that binds manganese to one that binds copper. In both cases the metals bind inside protein barrels with the same type of metal-attractions.

Carrying out the work in a blue-green algae, a cyanobacterium, the team has been able to show that a protein requiring copper transports to the periplasm, the outer area of the cell, where it then folds around the available metal, which is copper.

Conversely, manganese but not copper atoms are found in the cytosol, in the middle of the cell. The team has demonstrated that a protein requiring manganese folds in the cytosol. The manganese protein is then transported to the periplasm having first trapped its manganese.

The cyanobacterium organism was chosen because it has a high demand for these two metals which are required for proteins involved in photosynthesis. These metals were chosen because they lie towards opposite ends of a chemical series called the Irving-Williams series, such that selecting these metals for proteins should be especially demanding.

In the work funded by the BBSRC, the Newcastle University team first developed a new approach to discover metal-binding proteins. This is now being swiftly applied to lots of other types of living cells and other essential metals (zinc, nickel, cobalt, iron). Unexpectedly, x-ray crystal structures showed that the identified proteins, MncA for manganese and CucA for copper, were both cupins (Latin for barrels) with identical sets of atoms for binding to the metals. Consistent with the chemical series, a ten-thousand times excess of manganese over copper was needed to fill the MncA barrel with manganese when folding is done in the laboratory.

Once folded, the manganese site is buried, the metal trapped inside the protein, and so the manganese protein can subsequently co-exist with the copper protein because its' metal becomes impervious to replacement by metals further up the Irving-Williams series.

The work exemplifies a cell overcoming the metal binding preferences of proteins.

The new discipline of synthetic biology aims to engineer cells to carry out useful tasks, for example to generate valuable compounds. Because metals are the catalysts for so much of biology, knowing how to engineer a supply of the right metals to the right proteins will be important to the success of these ventures.

The work is funded by the BBSRC.

Background

Cyanobacteria are ancient organisms that changed the planet. They released di-oxygen into the atmosphere and removed CO₂. As a by-product, this changed the chemical forms of metals such as iron and copper in the environment and shifted the course of evolution. Cyanobacteria convert light into chemical forms of energy. They evolved into the chloroplasts of plants.

---

Journal reference:

1. Steve Tottey, Kevin J. Waldron, Susan J. Firbank, Brian Reale, Conrad Bessant, Katsuko Sato, Timothy R. Cheek, Joe Gray, Mark J. Banfield, Christopher Dennison & Nigel J. Robinson. Protein-folding location can regulate manganese-binding versus copper- or zinc-binding.Nature, October 22, 2008

Adapted from materials provided by Newcastle University.

Gene Against Bacterial Attack Unraveled

Burkholderia Pseudomallei. (Credit: Image courtesy of Netherlands Organization for Scientific Research)

ScienceDaily (Oct. 28, 2008) — Dutch researcher Joost Wiersinga from AMC Medical Centre in Amsterdam has unravelled a genetic defence mechanism against the lethal bacteria Burkholderia pseudomallei. The research is the next step towards a vaccine against this bacterium suitable for bioweapons.

Humans have an innate defence system against deadly bacteria. However, how the step from gene to anti-bacterial effect occurs in the body is not yet known. To date, B. Pseudomallei, a bacterium suitable for bioweapons, had managed to elude medics. It can remain hidden in the human body for many years without being detected by the immune system. The bacteria can suddenly become activated and spread throughout the body, resulting in the patient dying from blood poisoning.

AMC physician Joost Wiersinga and the Laboratory for Experimental Internal Medicine discovered which gene-protein combination renders the lethal bacteria B. pseudomallei harmless.

Immune system fooled

Wiersinga focussed on the so-called Toll-like receptors. These are the proteins that initiate the fight against pathogens. There are currently ten known Toll-like receptors which are located on the outside of immune cells, our body's defence system. The toll-like receptors jointly function as a 10-figure alarm code. Upon coming into contact with the immune cell each bacterium enters its own Toll code. For known pathogens this sets off an alarm in the immune system and the defence mechanism is activated. Yet B. pseudomallei fools the system by entering the code of a harmless bacterium. As a result the body's defence system remains on standby.

Yet some people are resistant: they become infected but not ill. Wiersinga found a genetic cause for this resistance. He discovered which toll receptor can fend off B. pseudomallei. He did this by rearing mice DNA in which the gene for Toll2 production was switched on and off. 'The group where the gene for Toll2 was switched off, survived the bacterial infection', says Wiersinga. 'The other receptor that we investigated, Toll4, had no effect - even though for the past ten years medics had regarded this as the most important receptor.' The ultimate aim of this study is to develop a vaccine.

Wiersinga and his colleagues are working together with the Wellcome Trust in Oxford and a clinic in Thailand. B. pseudomallei is endemic in Asia and claims thousands of victims each year. The research was published in PloS Medicine, and Science and Nature Reviews also ran articles on it. NWO funded the work.

---

Adapted from materials provided by Netherlands Organization for Scientific Research.