DNA RNA DEMAGE AND DNA REPAİR

Searching for Spin Liquids: Much-Sought Exotic Quantum State of Matter Can Exist

2011-09-06T19:37:00.000-07:00

The world economy is becoming ever more reliant on high tech electronics such as computers featuring fingernail-sized microprocessors crammed with billions of transistors. For progress to continue, for Moore's Law -- according to which the number of computer components crammed onto microchips doubles every two years, even as the size and cost of components halves -- to continue, new materials and new phenomena need to be discovered.Diagram depicting anti-ferromagnetic order (upper) compared to a spin liquid phase (lower). In an anti-ferromagnet, the spins are anti-aligned. A spin liquid has no order and the spins can be viewed as bobbing about like water molecules in liquid water. (Credit: E. Edwards)
Furthermore, as the sizes of electronic components shrink, soon down to the size of single atoms or molecules, quantum interactions become ever more important. Consequently, enhanced knowledge and exploitation of quantum effects is essential. Researchers at the Joint Quantum Institute (JQI) in College Park, Maryland, operated by the University of Maryland and the National Institute of Standards and Technology (NIST), and at Georgetown University have uncovered evidence for a long-sought-after quantum state of matter, a spin liquid.

The research was performed by JQI postdoctoral scientists Christopher Varney and Kai Sun, JQI Fellow Victor Galitski, and Marcos Rigol of Georgetown University. The results appear in an editor-recommended article in the 12 August issue of the journal Physical Review Letters.

You can't pour a spin liquid into a glass. It's not a material at all, at least not a material you can touch. It is more like a kind of magnetic disorder within an ordered array of atoms. Nevertheless, it has many physicists excited.

To understand this exotic state of matter, first consider the concept of spin, which is at the heart of all magnetic phenomena. For instance, a refrigerator magnet, at the microscopic level, consists of trillions of trillions of iron atoms all lined up. Each of these atoms can be thought of loosely as a tiny spinning ball. The orientation of that spin is what makes the atom into a tiny magnet. The refrigerator magnet is an example of a ferromagnet, the ferro part coming from the Latin word for iron. In a ferromagnet, all the atomic spins are lined up in the same way, producing a large cooperative magnetic effect.

Important though they may be, ferromagnets aren't the only kind of material where magnetic interactions between spins are critical. In anti-ferromagnets, for instance, the neighboring spins are driven to be anti-aligned. That is, the orientations of the spins alternate up and down (see top picture in figure). The accumulative magnetic effect of all these up and down spins is that the material has no net magnetism. The high-temperature superconducting materials discovered in the 1980s are an important example of an anti-ferromagnetic structure.

More complicated and potentially interesting magnetic arrangements are possible, which may lead to a quantum spin liquid. Imagine an equilateral triangle, with an atom (spin) at each corner. Anti-ferromagnetism in such a geometry would meet with difficulties. Suppose that one spin points up while a second spin points down. So far, so good. But what spin orientation can the third atom take? It can't simultaneously anti-align with both of the other atoms in the triangle. Physicists employ the word "frustration" to describe this baffling condition where all demands cannot be satisfied.

In everyday life frustration is, well, frustrating, and actually this condition is found throughout nature, from magnetism to neural networks. Furthermore, understanding the different manifestations of a collection of magnetically interacting spins might help in designing new types of electronic circuitry.

One compromise that a frustrated spin system makes is to simultaneously exist in many spin orientations. In a quantum system, this simultaneous existence, or superposition, is allowed.

Here's where the JQI researchers have tried something new. They have studied what happens when frustration occurs in materials with a hexagonal (six sided) unit cell lattice.

What these atoms do is interact via their respective spins. The strength of the interaction between nearest neighbor (NN) atoms is denoted by the parameter J1. Similarly, the force between next nearest neighbors (NNN) -- that is, pairs of atoms that have at least one intervening atom between them -- is denoted by J2. Letting this batch of atoms interact among themselves, even on a pretend lattice as small as this, entails an immense calculation. Varney and his colleagues have calculated what happens in an array of hexagons consisting of 30 sites where the spins are free to swing about in a two-dimensional plane (this kind of approach is called an XY model).

Christopher Varney, who has appointments at Maryland and Georgetown, said that the interactions of atoms can be represented by a matrix (essentially a two-dimensional spreadsheet) with 155 million entries on each side. This huge number corresponds to the different spin configurations that can occur on this honeycomb-structured material.

What the researchers found were a "kaleidoscope" of phases, which represent the lowest-energy states that are allowed given the magnetic interactions. Just as water can exist in different phases -- steam, liquid, and ice -- as the temperature is changed, so here a change in the strengths of the interactions among the spins (the J1 and J2 parameters) results in different phases. For example, one simple solution is an antiferromagnet (upper picture in figure).

But one phase turns out to be a true quantum spin liquid having no order at all. When J2 is between about 21% and 36% of the value of J1, frustration coaxes the spins into disorder; the entire sample co-exists in millions of quantum states simultaneously.

It's difficult for the human mind to picture a tiny two-dimensional material in so many states at the same time. JQI fellow, Victor Galitski, suggests that one shouldn't think of the spins as residing at the original atomic sites but rather as free ranging particle-like entities dubbed "spinons." These spinons bob about, just as water molecules bob about in liquid water (see lower picture in figure). Hence the name quantum spin liquid.

Another reason for using the word liquid, Galitski says, is this 'bobbing about' is analogous to what happens inside a metal. There, the outer electrons of most atoms tend to leave their home atoms and drift through the metal sample as if they constituted a fluid, called a "Fermi liquid."

Electrons in a metal are able to drift since it takes only an infinitesimal amount of energy to put them into motion. The same is true for the fluctuating spins in the hexagonal model studied by the JQI scientists. Indeed, their spin model assumes a temperature of absolute zero, where quantum effects abound.

Writing in an essay that accompanied the article in Physical Review Letters, Tameem Albash and Stephan Haas, scientists at the University of Southern California, say that the JQI/Georgetown team "present a convincing example" of the new spin liquid state.

How can this new frustration calculation be tested? The experimental verification of the spin liquid state in a 2-dimenstional hexagonal lattice, Albash and Haas suggest, "will probably be tested using cold atoms trapped in optical lattices. In the past few years, this technology has become a reliable tool to emulate quantum many body lattice systems with tunable interactions." Indeed the authors propose such an experiment.

What would such a spin liquid material be good for? It's too early to tell. But some speculations include the idea that these materials could support some exotic kind of superconductivity or would organize particle-like entities that possessed fractional electric charge.

"Kaleidoscope of Exotic Quantum Phases in a Frustrated XY Model" by Christopher N. Varney, Kai Sun, Victor Galitski, and Marcos Rigol, Physical Review Letters, 107, 077201, (12 August 2011).

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How Many Species On Earth? About 8.7 Million, New Estimate Says

2011-09-06T16:26:00.000-07:00

Eight million, seven hundred thousand species (give or take 1.3 million).
Distribution of species by kingdom. (Credit: CoML)
That is a new, estimated total number of species on Earth -- the most precise calculation ever offered -- with 6.5 million species found on land and 2.2 million (about 25 percent of the total) dwelling in the ocean depths.

Announced today by Census of Marine Life scientists, the figure is based on an innovative, validated analytical technique that dramatically narrows the range of previous estimates. Until now, the number of species on Earth was said to fall somewhere between 3 million and 100 million.

Furthermore, the study, published by PLoS Biology, says a staggering 86% of all species on land and 91% of those in the seas have yet to be discovered, described and catalogued.

Says lead author Camilo Mora of the University of Hawaii and Dalhousie University in Halifax, Canada: "The question of how many species exist has intrigued scientists for centuries and the answer, coupled with research by others into species' distribution and abundance, is particularly important now because a host of human activities and influences are accelerating the rate of extinctions. Many species may vanish before we even know of their existence, of their unique niche and function in ecosystems, and of their potential contribution to improved human well-being."

"This work deduces the most basic number needed to describe our living biosphere," says co-author Boris Worm of Dalhousie University. "If we did not know -- even by an order of magnitude (1 million? 10 million? 100 million?) -- the number of people in a nation, how would we plan for the future?"

"It is the same with biodiversity. Humanity has committed itself to saving species from extinction, but until now we have had little real idea of even how many there are."

Dr. Worm notes that the recently-updated Red List issued by the International Union for the Conservation of Nature assessed 59,508 species, of which 19,625 are classified as threatened. This means the IUCN Red List, the most sophisticated ongoing study of its kind, monitors less than 1% of world species.

The research is published alongside a commentary by Lord Robert May of Oxford, past-president of the UK's Royal Society, who praises the researchers' "imaginative new approach."

"It is a remarkable testament to humanity's narcissism that we know the number of books in the US Library of Congress on 1 February 2011 was 22,194,656, but cannot tell you -- to within an order-of-magnitude -- how many distinct species of plants and animals we share our world with," Lord May writes.

"(W)e increasingly recognize that such knowledge is important for full understanding of the ecological and evolutionary processes which created, and which are struggling to maintain, the diverse biological riches we are heir to. Such biodiversity is much more than beauty and wonder, important though that is. It also underpins ecosystem services that -- although not counted in conventional GDP -- humanity is dependent upon."

Drawing conclusions from 253 years of taxonomy since Linnaeus

Swedish scientist Carl Linnaeus created and published in 1758 the system still used to formally name and describe species. In the 253 years since, about 1.25 million species -- roughly 1 million on land and 250,000 in the oceans -- have been described and entered into central databases (roughly 700,000 more are thought to have been described but have yet to reach the central databases).

To now, the best approximation of Earth's species total was based on the educated guesses and opinions of experts, who variously pegged the figure in a range from 3 to 100 million -- wildly differing numbers questioned because there is no way to validate them.

Drs. Mora and Worm, together with Dalhousie colleagues Derek P. Tittensor, Sina Adl and Alastair G.B. Simpson, refined the estimated species total to 8.7 million by identifying numerical patterns within the taxonomic classification system (which groups forms of life in a pyramid-like hierarchy, ranked upwards from species to genus, family, order, class, phylum, kingdom and domain).

Analyzing the taxonomic clustering of the 1.2 million species today in the Catalogue of Life and the World Register of Marine Species, the researchers discovered reliable numerical relationships between the more complete higher taxonomic levels and the species level.

Says Dr. Adl: "We discovered that, using numbers from the higher taxonomic groups, we can predict the number of species. The approach accurately predicted the number of species in several well-studied groups such as mammals, fishes and birds, providing confidence in the method."

When applied to all five known eukaryote* kingdoms of life on Earth, the approach predicted:
~7.77 million species of animals (of which 953,434 have been described and cataloged)~298,000 species of plants (of which 215,644 have been described and cataloged)~611,000 species of fungi (moulds, mushrooms) (of which 43,271 have been described and cataloged)~36,400 species of protozoa (single-cell organisms with animal-like behavior, eg. movement, of which 8,118 have been described and cataloged)~27,500 species of chromista (including, eg. brown algae, diatoms, water moulds, of which 13,033 have been described and cataloged)
Total: 8.74 million eukaryote species on Earth.

(* Notes: Organisms in the eukaryote domain have cells containing complex structures enclosed within membranes. The study looked only at forms of life accorded, or potentially accorded, the status of "species" by scientists. Not included: certain micro-organisms and virus "types," for example, which could be highly numerous.)

Within the 8.74 million total is an estimated 2.2 million (plus or minus 180,000) marine species of all kinds, about 250,000 (11%) of which have been described and catalogued. When it formally concluded in October 2010, the Census of Marine Life offered a conservative estimate of 1 million+ species in the seas.

"Like astronomers, marine scientists are using sophisticated new tools and techniques to peer into places never seen before," says Australian Ian Poiner, Chair of the Census' Scientific Steering Committee. "During the 10-year Census, hundreds of marine explorers had the unique human experience and privilege of encountering and naming animals new to science. We may clearly enjoy the Age of Discovery for many years to come."

"The immense effort entering all known species in taxonomic databases such as the Catalogue of Life and the World Register of Marine Species makes our analysis possible," says co-author Derek Tittensor, who also works with Microsoft Research and the UN Environment Programme's World Conservation Monitoring Centre. "As these databases grow and improve, our method can be refined and updated to provide an even more precise estimate."

"We have only begun to uncover the tremendous variety of life around us," says co-author Alastair Simpson. "The richest environments for prospecting new species are thought to be coral reefs, seafloor mud and moist tropical soils. But smaller life forms are not well known anywhere. Some unknown species are living in our own backyards -- literally."

"Awaiting our discovery are a half million fungi and moulds whose relatives gave humanity bread and cheese," says Jesse Ausubel, Vice-President of the Alfred P. Sloan Foundation and co-founder of the Census of Marine Life. "For species discovery, the 21st century may be a fungal century!"

Mr. Ausubel notes the enigma of why so much diversity exists, saying the answer may lie in the notions that nature fills every niche, and that rare species are poised to benefit from a change of conditions.

In his analysis, Lord May says the practical benefits of taxonomic discovery are many, citing the development in the 1970s of a new strain of rice based on a cross between conventional species and one discovered in the wild. The result: 30% more grain yield, followed by efforts ever since to protect all wild varieties of rice, "which obviously can only be done if we have the appropriate taxonomic knowledge."

"Given the looming problems of feeding a still-growing world population, the potential benefits of ramping up such exploration are clear."

Based on current costs and requirements, the study suggests that describing all remaining species using traditional approaches could require up to 1,200 years of work by more than 300,000 taxonomists at an approximate cost of $US 364 billion. Fortunately, new techniques such as DNA barcoding are radically reducing the cost and time involved in new species identification.

Concludes Dr. Mora: "With the clock of extinction now ticking faster for many species, I believe speeding the inventory of Earth's species merits high scientific and societal priority. Renewed interest in further exploration and taxonomy could allow us to fully answer this most basic question: What lives on Earth?"

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From a Flat Mirror, Designer Light: Bizarre Optical Phenomena Defies Laws of Reflection and Refraction

2011-09-06T14:20:00.000-07:00

Top, clockwise from left: Patrice Genevet, Nanfang Yu, Federico Capasso, Zeno Gaburro, and Mikhail A. Kats. Bottom: A simulation of the image that would appear in a large mirror patterned with the team's new phase mirror technology. (Credit: Photos by Eliza Grinnell and Nanfang Yu)
The discovery, published this week in Science, has led to a reformulation of the mathematical laws that predict the path of a ray of light bouncing off a surface or traveling from one medium into another -- for example, from air into glass.

"Using designer surfaces, we've created the effects of a fun-house mirror on a flat plane," says co-principal investigator Federico Capasso, Robert L. Wallace Professor of Applied Physics and Vinton Hayes Senior Research Fellow in Electrical Engineering at SEAS. "Our discovery carries optics into new territory and opens the door to exciting developments in photonics technology."

It has been recognized since ancient times that light travels at different speeds through different media. Reflection and refraction occur whenever light encounters a material at an angle, because one side of the beam is able to race ahead of the other. As a result, the wavefront changes direction.

The conventional laws, taught in physics classrooms worldwide, predict the angles of reflection and refraction based only on the incident (incoming) angle and the properties of the two media.

While studying the behavior of light impinging on surfaces patterned with metallic nanostructures, the researchers realized that the usual equations were insufficient to describe the bizarre phenomena observed in the lab.

The new generalized laws, derived and experimentally demonstrated at Harvard, take into account the Capasso group's discovery that the boundary between two media, if specially patterned, can itself behave like a third medium.

"Ordinarily, a surface like the surface of a pond is simply a geometric boundary between two media, air and water," explains lead author Nanfang Yu (Ph.D. '09), a research associate in Capasso's lab at SEAS. "But now, in this special case, the boundary becomes an active interface that can bend the light by itself."

The key component is an array of tiny gold antennas etched into the surface of the silicon used in Capasso's lab. The array is structured on a scale much thinner than the wavelength of the light hitting it. This means that, unlike in a conventional optical system, the engineered boundary between the air and the silicon imparts an abrupt phase shift (dubbed "phase discontinuity") to the crests of the light wave crossing it.

Each antenna in the array is a tiny resonator that can trap the light, holding its energy for a given amount of time before releasing it. A gradient of different types of nanoscale resonators across the surface of the silicon can effectively bend the light before it even begins to propagate through the new medium.

The resulting phenomenon breaks the old rules, creating beams of light that reflect and refract in arbitrary ways, depending on the surface pattern.

In order to generalize the textbook laws of reflection and refraction, the Harvard researchers added a new term to the equations, representing the gradient of phase shifts imparted at the boundary. Importantly, in the absence of a surface gradient, the new laws reduce to the well-known ones.

"By incorporating a gradient of phase discontinuities across the interface, the laws of reflection and refraction become designer laws, and a panoply of new phenomena appear," says Zeno Gaburro, a visiting scholar in Capasso's group who was co-principal investigator for this work. "The reflected beam can bounce backward instead of forward. You can create negative refraction. There is a new angle of total internal reflection."

Moreover, the frequency (color), amplitude (brightness), and polarization of the light can also be controlled, meaning that the output is in essence a designer beam.

The researchers have already succeeded at producing a vortex beam (a helical, corkscrew-shaped stream of light) from a flat surface. They also envision flat lenses that could focus an image without aberrations.

Yu, Capasso, and Gaburro's co-authors included Patrice Genevet, Mikhail A. Kats, Francesco Aieta, and Jean-Philippe Tetienne.

Story Source: The above story is reprinted (with editorial adaptations) from materials provided by Harvard University, via EurekAlert!, a service of AAAS.

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Biologists Discovery May Force Revision of Biology Textbooks: Novel Chromatin Particle Halfway Between DNA and a Nucleosome

2011-09-06T10:48:00.000-07:00

Basic biology textbooks may need a bit of revising now that biologists at UC San Diego have discovered a never-before-noticed component of our basic genetic material.Biologists have discovered a novel chromatin
particle halfway between DNA and a nucleosome.
While it looks like a nucleosome, it is in fact a
distinct particle of its own, researchers say.
(Credit: James Kadonaga, UC San Diego)
According to the textbooks, chromatin, the natural state of DNA in the cell, is made up of nucleosomes. And nucleosomes are the basic repeating unit of chromatin.

When viewed by a high powered microscope, nucleosomes look like beads on a string. But in the Aug. 19 issue of the journal Molecular Cell, UC San Diego biologists report their discovery of a novel chromatin particle halfway between DNA and a nucleosome. While it looks like a nucleosome, they say, it is in fact a distinct particle of its own.

"This novel particle was found as a precursor to a nucleosome," said James Kadonaga, a professor of biology at UC San Diego who headed the research team and calls the particle a "pre-nucleosome." "These findings suggest that it is necessary to reconsider what chromatin is. The pre-nucleosome is likely to be an important player in how our genetic material is duplicated and used."

The biologists say that while the pre-nucleosome may look something like a nucleosome under the microscope, biochemical tests have shown that it is in reality halfway between DNA and a nucleosome.

These pre-nucleosomes, the researchers say, are converted into nucleosomes by a motor protein that uses the energy molecule ATP.

"The discovery of pre-nucleosomes suggests that much of chromatin, which has been generally presumed to consist only of nucleosomes, may be a mixture of nucleosomes and pre-nucleosomes," said Kadonaga. "So, this discovery may be the beginning of a revolution in our understanding of what chromatin is."

"The packaging of DNA with histone proteins to form chromatin helps stabilize chromosomes and plays an important role in regulating gene activities and DNA replication," said Anthony Carter, who oversees chromatin grants at the National Institute of General Medical Sciences of the National Institutes of Health, which funded the research. "The discovery of a novel intermediate DNA-histone complex offers intriguing insights into the nature of chromatin and may help us better understand how it impacts these key cellular processes."

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Holograms Reveal Brain's Inner Workings: Microscopy Technique Used to Observe Activity of Neurons Like Never Before

2011-09-06T07:45:00.000-07:00

Like far away galaxies, powerful tools are required to bring the minute inner workings of neurons into focus. Borrowing a technique from materials science, a team of neurobiologists, psychiatrists, and advanced imaging specialists from Switzerland's EPLF and CHUV report in The Journal of Neuroscience how Digital Holographic Microscopy (DHM) can now be used to observe neuronal activity in real-time and in three dimensions -- with up to 50 times greater resolution than ever before. The application has immense potential for testing out new drugs to fight neurodegenerative diseases such as Alzheimer's and Parkinson's.This is a 3-D image of living neuron taken by DHM
technology. (Credit: Courtesy of Lyncée Tec)
Neurons come in various shapes and are transparent. To observe them in a Petri dish, scientists use florescent dyes that change the chemical composition and can skew results. Additionally, this technique is time consuming, often damages the cells, and only allows researchers to examine a few neurons at a time. But these newly published results show how DHM can bypass the limitations of existing techniques.

"DHM is a fundamentally novel application for studying neurons with a slew of advantages over traditional microscopes," explains Pierre Magistretti of EPFL's Brain Mind Institute and a lead author of the paper. "It is non-invasive, allowing for extended observation of neural processes without the need for electrodes or dyes that damage cells."

Senior team member Pierre Marquet adds, "DHM gives precious information not only about the shape of neurons, but also about their dynamics and activity, and the technique creates 3D navigable images and increases the precision from 500 nanometers in traditional microscopes to a scale of 10 nanometers."

A good way to understand how DHM works is to imagine a large rock in an ocean of perfectly regular waves. As the waves deform around the rock and come out the other side, they carry information about the rock's shape. This information can be extracted by comparing it to waves that did not smash up against the rock, and an image of the rock can be reconstructed. DHM does this with a laser beam by pointing a single wavelength at an object, collecting the distorted wave on the other side, and comparing it to a reference beam. A computer then numerically reconstructs a 3D image of the object -- in this case neurons -- using an algorithm developed by the authors. In addition, the laser beam travels through the transparent cells and important information about their internal composition is obtained.

Normally applied to detect minute defects in materials, Magistretti, along with DHM pioneer and EPFL professor in the Advanced Photonics Laboratory, Christian Depeursinge, decided to use DHM for neurobiological applications. In the study, their group induced an electric charge in a culture of neurons using glutamate, the main neurotransmitter in the brain. This charge transfer carries water inside the neurons and changes their optical properties in a way that can be detected only by DHM. Thus, the technique accurately visualizes the electrical activities of hundreds of neurons simultaneously, in real-time, without damaging them with electrodes, which can only record activity from a few neurons at a time.

A major advance for pharmaceutical research

Without the need to introduce dyes or electrodes, DHM can be applied to High Content Screening -- the screening of thousands of new pharmacological molecules. This advance has important ramifications for the discovery of new drugs that combat or prevent neurodegenerative diseases such as Parkinson's and Alzheimer's, since new molecules can be tested more quickly and in greater numbers.

"Due to the technique's precision, speed, and lack of invasiveness, it is possible to track minute changes in neuron properties in relation to an applied test drug and allow for a better understanding of what is happening, especially in predicting neuronal death," Magistretti says. "What normally would take 12 hours in the lab can now be done in 15 to 30 minutes, greatly decreasing the time it takes for researchers to know if a drug is effective or not."

The promise of this technique for High Content Screening has already resulted in a start-up company at EPFL called LynceeTec (www.lynceetec.com).

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New Way to Measure Expansion of Universe

2011-09-06T05:01:00.000-07:00

Using a measurement of the clustering of the galaxies surveyed, plus other information derived from observations of the early universe, researchers have measured the Hubble constant with an uncertainly of less than 5 percent. The new work draws on data from a survey of more than 125,000 galaxies.The 6df Galaxy Survey data, each dot is a galaxy and
Earth is at the center of the sphere. (Credit: Image courtesy
of International Centre for Radio Astronomy Research)
A PhD student from The International Centre for Radio Astronomy Research (ICRAR) in Perth has produced one of the most accurate measurements ever made of how fast the Universe is expanding.

Florian Beutler, a PhD candidate with ICRAR at the University of Western Australia, has calculated how fast the Universe is growing by measuring the Hubble constant.

"The Hubble constant is a key number in astronomy because it's used to calculate the size and age of the Universe," said Mr Beutler.

As the Universe swells, it carries other galaxies away from ours. The Hubble constant links how fast galaxies are moving with how far they are from us.

By analysing light coming from a distant galaxy, the speed and direction of that galaxy can be easily measured. Determining the galaxy's distance from Earth is much more difficult. Until now, this has been done by observing the brightness of individual objects within the galaxy and using what we know about the object to calculate how far away the galaxy must be.

This approach to measuring a galaxy's distance from Earth is based on some well-established assumptions but is prone to systematic errors, leading Mr Beutler to tackle the problem using a completely different method.

Published July 26 in the Monthly Notices of the Royal Astronomical Society, Mr Beutler's work draws on data from a survey of more than 125,000 galaxies carried out with the UK Schmidt Telescope in eastern Australia. Called the 6dF Galaxy Survey, this is the biggest survey to date of relatively nearby galaxies, covering almost half the sky.

Galaxies are not spread evenly through space, but are clustered. Using a measurement of the clustering of the galaxies surveyed, plus other information derived from observations of the early Universe, Mr Beutler has measured the Hubble constant with an uncertainly of less than 5%.*

"This way of determining the Hubble constant is as direct and precise as other methods, and provides an independent verification of them," says Professor Matthew Colless, Director of the Australian Astronomical Observatory and one of Mr Beutler's co-authors. "The new measurement agrees well with previous ones, and provides a strong check on previous work."

The measurement can be refined even further by using data from larger galaxy surveys.

"Big surveys, like the one used for this work, generate numerous scientific outcomes for astronomers internationally," says Professor Lister Staveley-Smith, ICRAR's Deputy Director of Science.

* The new measurement of the Hubble constant is 67.0 ± 3.2 km s-1 Mpc-1

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Engineers Solve Longstanding Problem in Photonic Chip Technology: Findings Help Pave Way for Next Generation of Computer Chips

2011-09-06T01:07:00.000-07:00

Stretching for thousands of miles beneath oceans, optical fibers now connect every continent except for Antarctica. With less data loss and higher bandwidth, optical-fiber technology allows information to zip around the world, bringing pictures, video, and other data from every corner of the globe to your computer in a split second. But although optical fibers are increasingly replacing copper wires, carrying information via photons instead of electrons, today's computer technology still relies on electronic chips.Caltech engineers have developed a new way to
isolate light on a photonic chip, allowing light to
travel in only one direction. This finding can lead
to the next generation of computer-chip technology:
photonic chips that allow for faster computers
and less data loss. (Credit: Caltech/Liang Feng)
Now, researchers led by engineers at the California Institute of Technology (Caltech) are paving the way for the next generation of computer-chip technology: photonic chips. With integrated circuits that use light instead of electricity, photonic chips will allow for faster computers and less data loss when connected to the global fiber-optic network.

"We want to take everything on an electronic chip and reproduce it on a photonic chip," says Liang Feng, a postdoctoral scholar in electrical engineering and the lead author on a paper to be published in the August 5 issue of the journal Science. Feng is part of Caltech's nanofabrication group, led by Axel Scherer, Bernard A. Neches Professor of Electrical Engineering, Applied Physics, and Physics, and co-director of the Kavli Nanoscience Institute at Caltech.

In that paper, the researchers describe a new technique to isolate light signals on a silicon chip, solving a longstanding problem in engineering photonic chips.

An isolated light signal can only travel in one direction. If light weren't isolated, signals sent and received between different components on a photonic circuit could interfere with one another, causing the chip to become unstable. In an electrical circuit, a device called a diode isolates electrical signals by allowing current to travel in one direction but not the other. The goal, then, is to create the photonic analog of a diode, a device called an optical isolator. "This is something scientists have been pursuing for 20 years," Feng says.

Normally, a light beam has exactly the same properties when it moves forward as when it's reflected backward. "If you can see me, then I can see you," he says. In order to isolate light, its properties need to somehow change when going in the opposite direction. An optical isolator can then block light that has these changed properties, which allows light signals to travel only in one direction between devices on a chip.

"We want to build something where you can see me, but I can't see you," Feng explains. "That means there's no signal from your side to me. The device on my side is isolated; it won't be affected by my surroundings, so the functionality of my device will be stable."

To isolate light, Feng and his colleagues designed a new type of optical waveguide, a 0.8-micron-wide silicon device that channels light. The waveguide allows light to go in one direction but changes the mode of the light when it travels in the opposite direction.

A light wave's mode corresponds to the pattern of the electromagnetic field lines that make up the wave. In the researchers' new waveguide, the light travels in a symmetric mode in one direction, but changes to an asymmetric mode in the other. Because different light modes can't interact with one another, the two beams of light thus pass through each other.

Previously, there were two main ways to achieve this kind of optical isolation. The first way -- developed almost a century ago -- is to use a magnetic field. The magnetic field changes the polarization of light -- the orientation of the light's electric-field lines -- when it travels in the opposite direction, so that the light going one way can't interfere with the light going the other way. "The problem is, you can't put a large magnetic field next to a computer," Feng says. "It's not healthy."

The second conventional method requires so-called nonlinear optical materials, which change light's frequency rather than its polarization. This technique was developed about 50 years ago, but is problematic because silicon, the material that's the basis for the integrated circuit, is a linear material. If computers were to use optical isolators made out of nonlinear materials, silicon would have to be replaced, which would require revamping all of computer technology. But with their new silicon waveguides, the researchers have become the first to isolate light with a linear material.

Although this work is just a proof-of-principle experiment, the researchers are already building an optical isolator that can be integrated onto a silicon chip. An optical isolator is essential for building the integrated, nanoscale photonic devices and components that will enable future integrated information systems on a chip. Current, state-of-the-art photonic chips operate at 10 gigabits per second (Gbps) -- hundreds of times the data-transfer rates of today's personal computers -- with the next generation expected to soon hit 40 Gbps. But without built-in optical isolators, those chips are much simpler than their electronic counterparts and are not yet ready for the market. Optical isolators like those based on the researchers' designs will therefore be crucial for commercially viable photonic chips.

In addition to Feng and Scherer, the other authors on the Science paper, "Non-reciprocal light propagation in a silicon photonic circuit," are Jingqing Huang, a Caltech graduate student; Maurice Ayache of UC San Diego and Yeshaiahu Fainman, Cymer Professor in Advanced Optical Technologies at UC San Diego; and Ye-Long Xu, Ming-Hui Lu, and Yan-Feng Chen of the Nanjing National Laboratory of Microstructures in China. This research was done as part of the Center for Integrated Access Networks (CIAN), one of the National Science Foundation's Engineering Research Centers. Fainman is also the deputy director of CIAN. Funding was provided by the National Science Foundation, and the Defense Advanced Research Projects Agency.

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Seeing eye to eye is key to copying, say scientists

2011-09-05T23:01:00.000-07:00

Imitation may be the sincerest form of flattery but how do our brains decide when and who we should copy? Researchers from The University of Nottingham have found that the key may lie in an unspoken invitation communicated through eye contact.

In a study published this week in the Journal of Neuroscience, a team of scientists from the University's School of Psychology show that eye contact seems to act as an invitation for mimicry, triggering mechanisms in the frontal region of the brain that control imitation.

The results could be the first clues to understanding why some people, such as children with autism, struggle to grasp when they are expected to copy the actions of others in social situations.

Dr Antonia Hamilton, who led the research, said: "Many studies have looked at copying and imitation in terms of 'mirror neurons', which are believed to be specialised parts of the human brain that implement imitation. However, we also know that imitation is carefully controlled — people don't imitate everything they see, and only copy what's important.

"Our previous research has shown that when somebody makes eye contact with you, you are more likely to copy them. So eye contact seems to act as a message that says "Copy me now". This recent study aimed to see what happens to that signal in the brain."

The team of psychologists, which also included doctoral student Yin Wang and Dr Richard Ramsey, used functional magnetic resonance imaging (fMRI) to scan the brains of volunteers while they watched videos of an actress who sometimes would make eye contact with them while opening or closing her hand. The participant was told they should open their own hand whenever they saw the actress move her hand so in some trials the participant was copying the actress and in other trials they were not.

Because previous behavioural measurement such as response time revealed that the participant unconsciously copied the actress faster when the actress provided eye contact, the scientists analysed the brain imaging data to find which brain areas controlled the decision to copy. The analysis used a new mathematical method called dynamic causal modelling to compute the information processing in the brain, which has never been applied to imitation before.

The data showed that mirror neuron brain regions do play a role in the copying task. More importantly though, it revealed that these regions are controlled by the medial prefrontal cortex, an area of the brain associated with planning complex cognitive behaviours, expressing personality, decision-making and responding to social situations.

Dr Hamilton added: "Previous studies have shown that this medial prefrontal brain region is active in many social situations but responds less in people with autism, which explains why children on the autistic spectrum might not copy at the right time.

"Understanding the control of imitation has implications for many other areas of psychology too. For example, are teenagers whose prefrontal cortex is less developed more easily led to copy risky, dangerous or illegal behaviour such as imitating rioters? Could increasing the amount of eye contact between children and teachers lead to better learning by imitation? Would better control of imitation help children with autism to more effectively learn and interact? We plan further research to address these questions."

Provided by University of Nottingham

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Sun-Free Photovoltaics Powered by Heat

2011-09-05T19:16:00.000-07:00

A new photovoltaic energy-conversion system developed at MIT can be powered solely by heat, generating electricity with no sunlight at all. While the principle involved is not new, a novel way of engineering the surface of a material to convert heat into precisely tuned wavelengths of light -- selected to match the wavelengths that photovoltaic cells can best convert to electricity -- makes the new system much more efficient than previous versions.A variety of silicon chip micro-reactors developed by the MIT team. Each of these contains photonic crystals on both flat faces, with external tubes for injecting fuel and air and ejecting waste products. Inside the chip, the fuel and air react to heat up the photonic crystals. In use, these reactors would have a photovoltaic cell mounted against each face, with a tiny gap between, to convert the emitted wavelengths of light to electricity. (Credit: Photo by Justin Knight)
The key to this fine-tuned light emission, described in the journal Physical Review A, lies in a material with billions of nanoscale pits etched on its surface. When the material absorbs heat -- whether from the sun, a hydrocarbon fuel, a decaying radioisotope or any other source -- the pitted surface radiates energy primarily at these carefully chosen wavelengths.

Based on that technology, MIT researchers have made a button-sized power generator fueled by butane that can run three times longer than a lithium-ion battery of the same weight; the device can then be recharged instantly, just by snapping in a tiny cartridge of fresh fuel. Another device, powered by a radioisotope that steadily produces heat from radioactive decay, could generate electricity for 30 years without refueling or servicing -- an ideal source of electricity for spacecraft headed on long missions away from the sun.

According to the U.S. Energy Information Administration, 92 percent of all the energy we use involves converting heat into mechanical energy, and then often into electricity -- such as using fuel to boil water to turn a turbine, which is attached to a generator. But today's mechanical systems have relatively low efficiency, and can't be scaled down to the small sizes needed for devices such as sensors, smartphones or medical monitors.

"Being able to convert heat from various sources into electricity without moving parts would bring huge benefits," says Ivan Celanovic ScD '06, research engineer in MIT's Institute for Soldier Nanotechnologies (ISN), "especially if we could do it efficiently, relatively inexpensively and on a small scale."

It has long been known that photovoltaic (PV) cells needn't always run on sunlight. Half a century ago, researchers developed thermophotovoltaics (TPV), which couple a PV cell with any source of heat: A burning hydrocarbon, for example, heats up a material called the thermal emitter, which radiates heat and light onto the PV diode, generating electricity. The thermal emitter's radiation includes far more infrared wavelengths than occur in the solar spectrum, and "low band-gap" PV materials invented less than a decade ago can absorb more of that infrared radiation than standard silicon PVs can. But much of the heat is still wasted, so efficiencies remain relatively low.

An ideal match

The solution, Celanovic says, is to design a thermal emitter that radiates only the wavelengths that the PV diode can absorb and convert into electricity, while suppressing other wavelengths. "But how do we find a material that has this magical property of emitting only at the wavelengths that we want?" asks Marin Soljacic, professor of physics and ISN researcher. The answer: Make a photonic crystal by taking a sample of material and create some nanoscale features on its surface -- say, a regularly repeating pattern of holes or ridges -- so light propagates through the sample in a dramatically different way.

"By choosing how we design the nanostructure, we can create materials that have novel optical properties," Soljacic says. "This gives us the ability to control and manipulate the behavior of light."

The team -- which also includes Peter Bermel, research scientist in the Research Laboratory for Electronics (RLE); Peter Fisher, professor of physics; and Michael Ghebrebrhan, a postdoc in RLE -- used a slab of tungsten, engineering billions of tiny pits on its surface. When the slab heats up, it generates bright light with an altered emission spectrum because each pit acts as a resonator, capable of giving off radiation at only certain wavelengths.

This powerful approach -- co-developed by John D. Joannopoulos, the Francis Wright Davis Professor of Physics and ISN director, and others -- has been widely used to improve lasers, light-emitting diodes and even optical fibers. The MIT team, supported in part by a seed grant from the MIT Energy Initiative, is now working with collaborators at MIT and elsewhere to use it to create several novel electricity-generating devices.

Mike Waits, an electronics engineer at the Army Research Laboratory in Adelphi, Md., who was not involved in this work, says this approach to producing miniature power supplies could lead to lighter portable electronics, which is "critical for the soldier to lighten his load. It not only reduces his burden, but also reduces the logistics chain" to deliver those devices to the field. "There are a lot of lives at stake," he says, "so if you can make the power sources more efficient, it could be a great benefit."

The button-like device that uses hydrocarbon fuels such as butane or propane as its heat source -- known as a micro-TPV power generator -- has at its heart a "micro-reactor" designed by Klavs Jensen, the Warren K. Lewis Professor of Chemical Engineering, and fabricated in the Microsystems Technology Laboratories. While the device achieves a fuel-to-electricity conversion efficiency three times greater than that of a lithium-ion battery of the same size and weight, Celanovic is confident that with further work his team can triple the current energy density. "At that point, our TPV generator could power your smartphone for a whole week without being recharged," he says.

Celanovic and Soljacic stress that building practical systems requires integrating many technologies and fields of expertise. "It's a really multidisciplinary effort," Celanovic says. "And it's a neat example of how fundamental research in materials can result in new performance that enables a whole spectrum of applications for efficient energy conversion."

Note: The full version of the MITEI story is available at: http://web.mit.edu/mitei/research/spotlights/making-electricity-with-photovoltaics.html

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Scientists Have New Help Finding Their Way Around Brain's Nooks and Crannies

2011-09-05T15:20:00.000-07:00

Like explorers mapping a new planet, scientists probing the brain need every type of landmark they can get. Each mountain, river or forest helps scientists find their way through the intricacies of the human brain.Scientists have found a way to use MRI scanning data
to map myelin, a white sheath that covers some brain
cell branches. Such maps, previously only available via
dissection, help scientists determine precisely where they
are at in the brain. Red and yellow indicate regions with
high myelin levels; blue, purple and black areas have low
myelin levels. (Credit: David Van Essen)
Researchers at Washington University School of Medicine in St. Louis have developed a new technique that provides rapid access to brain landmarks formerly only available at autopsy. Better brain maps will result, speeding efforts to understand how the healthy brain works and potentially aiding in future diagnosis and treatment of brain disorders, the researchers report in the Journal of Neuroscience Aug. 10.

The technique makes it possible for scientists to map myelination, or the degree to which branches of brain cells are covered by a white sheath known as myelin in order to speed up long-distance signaling. It was developed in part through the Human Connectome Project, a $30 million, five-year effort to map the brain's wiring. That project is headed by Washington University in St. Louis and the University of Minnesota.

"The brain is among the most complex structures known, with approximately 90 billion neurons transmitting information across 150 trillion connections," says David Van Essen, PhD, Edison Professor and head of the Department of Anatomy and Neurobiology at Washington University. "New perspectives are very helpful for understanding this complexity, and myelin maps will give us important insights into where certain parts of the brain end and others begin."

Easy access to detailed maps of myelination in humans and animals also will aid efforts to understand how the brain evolved and how it works, according to Van Essen.

Neuroscientists have known for more than a century that myelination levels differ throughout the cerebral cortex, the gray outer layer of the brain where most higher mental functions take place. Until now, though, the only way they could map these differences in detail was to remove the brain after death, slice it and stain it for myelin.

Washington University graduate student Matthew Glasser developed the new technique, which combines data from two types of magnetic resonance imaging (MRI) scans that have been available for years.

"These are standard ways of imaging brain anatomy that scientists and clinicians have used for a long time," Glasser says. "After developing the new technique, we applied it in a detailed analysis of archived brain scans from healthy adults."

As in prior studies, Glasser's results show highest myelination levels in areas involved with early processing of information from the eyes and other sensory organs and control of movement. Many brain cells are packed into these regions, but the connections among the cells are less complex. Scientists suspect that these brain regions rely heavily on what computer scientists call parallel processing: Instead of every cell in the region working together on a single complex problem, multiple separate teams of cells work simultaneously on different parts of the problem.

Areas with less myelin include brain regions linked to speech, reasoning and use of tools. These regions have brain cells that are packed less densely, because individual cells are larger and have more complex connections with neighboring cells.

"It's been widely hypothesized that each chunk of the cerebral cortex is made up of very uniform information-processing machinery," Van Essen says. "But we're now adding to a picture of striking regional differences that are important for understanding how the brain works."

According to Van Essen, the technique will make it possible for the Connectome project to rapidly map myelination in many different research participants. Data on many subjects, acquired through many different analytical techniques including myelination mapping, will help the resulting maps cover the range of anatomic variation present in humans.

"Our colleagues are clamoring to make use of this approach because it's so helpful for figuring out where you are in the cortex, and the data are either already there or can be obtained in less than 10 minutes of MRI scanning," Glasser says.

This research was funded by the National Institutes of Health (NIH).

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How Vampire Bats Find Veins

2011-09-05T12:35:00.000-07:00

Heat-sensing protein channels in vampire bats allow the flying mammals to find the best place to sink their teeth into their prey.
Researchers have discovered an infrared-sensing protein channel that allows vampire bats to identify the hottest part of the animal—veins close to the skin’s surface that carry 38 degree-Celsius (100° F) blood, and presumably the best spot for feeding.

The channel is a variant of TRPV1, a heat-sensing protein channel that is triggered by high temperatures that could potentially cause injury, according to the study published today (August 3) in Nature, and is distinct from the heat sensor used by snakes—the only other non-insect animals that are known to detect heat by sensing infrared radiation.

“Infrared [detection] allows these guys, in pitch black, to hunt down warm-blooded prey,” said zoologist Bill Schutt, assistant professor at Long Island University, who was not involved in the research. Here, the researchers identified a modification in a common heat-sensing protein channel that lowered its temperature threshold so that it is more attuned to an animal’s body heat, he added.

The common vampire bat was appropriately named after the myth of Dracula—it feeds at night and lives solely on a diet of blood, every day or two consuming up to half its weight in the vital substance from large mammals, especially sleeping livestock. The bats first use echolocation to detect their prey, but once they are within 20 centimeters of their target, they use infrared sensors in specialized pits around their noses to zero in on the best place to feed.

In a previous study, physiologist David Julius at the University of California, San Francisco, and colleagues found that infrared detection by snakes—which, like bats, use nerves located in facial pits to detect their prey—is mediated by a cell-surface protein channel called transient receptor potential cation channel A1 (TRPA1). The channel is actually insensitive to heat in most organisms, but had evolved the capability in snakes, leading the group to suspect that a similar transformation may have given vampire bats their ability to sense infrared.

To see if this was the case, Julius and his collaborators at the University of California, San Francisco, the Venezuelan Institute of Scientific Investigation (IVIC), and the Carnegie Institution in Baltimore, Maryland, compared gene expression in vampire bats’ heat-sensing nerves, called trigeminal ganglia, with expression in a nerve cluster near the spine, called dorsal root ganglia (DRG). They also compared these expression patterns to those of the ganglia in four bat species that do not have infrared sensory abilities.

To their surprise, they did not observe any differences in transcription of the TRPA1-coding gene, nor of any other genes. Instead, they discovered that the protein TRPV1—a heat-sensing protein channel normally triggered by temperatures over 43° C (110° F)—existed in two different isoforms—an approximately 850-amino-acid version and one that was 62 amino acids shorter. The short form, which resulted from alternative splicing of the transcribed mRNA, made up as much as half of the TRPV1 found in the trigeminal ganglia of vampire bats, whereas it comprised only a small percentage of the TRPV1 in the DRG. It was similarly low in both types of nerve clusters in the other bat species, suggesting that the short form may play a role in infrared detection.

To test this hypothesis, the researchers expressed one of the two TRPV1 isoforms in human kidney cells and in frog oocytes grown in vitro, and measured their temperature sensitivity using calcium imaging and electrophysiological assays, respectively. As expected, cells producing the long isoform were activated at 40 degrees Celsius (104° F). Cells producing the short isoform, on the other hand, were activated at just 30 degrees (86° F)—a drop that allows the protein to respond to the warmth of the vampire bats’ prey.

“This is a big jump in understanding how these animals locate their prey,” said Brock Fenton, a biology professor at the University of Western Ontario and author of an accompanying Nature News and Views article. While the longer isoform maintains its normal function of detecting potentially harmful high temperatures, the shorter isoform in the trigeminal nerves of the common vampire bat allows the animals to detect lower temperatures, such as the body heat of their mammalian prey.

“Basically, evolution tweaked a system in vampires bats that was already being used to sense temperatures,” said Schutt, author of the 2008 book Dark Banquet: Blood and the Curious Lives of Blood-Feeding Creatures, turning it into a useful hunting tool.

This is in contrast to the pit viper, whose infrared-sensing ability evolved from a different type of channel not involved in heat detection, but in the detection of noxious smells, added Fenton. The different evolutionary strategies employed by these two lineages “is an example of how plastic our sensory systems can be,” he said.

Posted in: bat,dorsal root ganglia,heat sensing,Infrared,ion channel,membrane proteins,nerves,Neuroscience,physiology,pit viper,snake,trigeminal ganglia,TRPA,TRPV,TRPV1,vampire,Vampire bat

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Engineers Reverse E. Coli Metabolism for Quick Production of Fuels, Chemicals

2011-09-05T09:00:00.000-07:00

In a biotechnological tour de force, Rice University engineering researchers this week unveiled a new method for rapidly converting simple glucose into biofuels and petrochemical substitutes. In a paper published online in Nature, Rice's team described how it reversed one of the most efficient of all metabolic pathways -- the beta oxidation cycle -- to engineer bacteria that produce biofuel at a breakneck pace.

Rice University engineering researchers Ramon Gonzalez (left) and
Clementina Dellomonaco reversed one of the most efficient of all
metabolic pathways -- the beta oxidation cycle -- to engineer bacteria
that make biofuels at a breakneck pace. (Credit: Jeff Fitlow/Rice
University)

Just how fast are Rice's single-celled chemical factories? On a cell-per-cell basis, the bacteria produced the butanol, a biofuel that can be substituted for gasoline in most engines, about 10 times faster than any previously reported organism.

"That's really not even a fair comparison because the other organisms used an expensive, enriched feedstock, and we used the cheapest thing you can imagine, just glucose and mineral salts," said Ramon Gonzalez, associate professor of chemical and biomolecular engineering at Rice and lead co-author of the Nature study.

Gonzalez's laboratory is in a race with hundreds of labs around the world to find green methods for producing chemicals like butanol that have historically come from petroleum.

"We call these 'drop-in' fuels and chemicals, because their structure and properties are very similar, sometimes identical, to petroleum-based products," he said. "That means they can be 'dropped in,' or substituted, for products that are produced today by the petrochemical industry."

Butanol is a relatively short molecule, with a backbone of just four carbon atoms. Molecules with longer carbon chains have been even more troublesome for biotech producers to make, particularly molecules with chains of 10 or more carbon atoms. Gonzalez said that's partly because researchers have focused on ramping up the natural metabolic processes that cells use to build long-chain fatty acids. Gonzalez and students Clementina Dellomonaco, James Clomburg and Elliot Miller took a completely different approach.

"Rather than going with the process nature uses to build fatty acids, we reversed the process that it uses to break them apart," Gonzalez said. "It's definitely unconventional, but it makes sense because the routes nature has selected to build fatty acids are very inefficient compared with the reversal of the route it uses to break them apart."

The beta oxidation process is one of biology's most fundamental, Gonzalez said. Species ranging from single-celled bacteria to human beings use beta oxidation to break down fatty acids and generate energy.

In the Nature study, Gonzalez's team reversed the beta oxidation cycle by selectively manipulating about a dozen genes in the bacteria Escherichia coli. They also showed that selective manipulations of particular genes could be used to produce fatty acids of particular lengths, including long-chain molecules like stearic acid and palmitic acid, which have chains of more than a dozen carbon atoms.

"This is not a one-trick pony," Gonzalez said. "We can make many kinds of specialized molecules for many different markets. We can also do this in any organism. Some producers prefer to use industrial organisms other than E. coli, like algae or yeast. That's another advantage of using reverse-beta oxidation, because the pathway is present in almost every organism."

The research was funded by Rice University.

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Etch-a-sketch with superconductors

2011-09-05T05:16:00.000-07:00

Reporting in Nature Materials this week, researchers from the London Centre for Nanotechnology and the Physics Department of Sapienza University of Rome have discovered a technique to 'draw' superconducting shapes using an X-ray beam. This ability to create and control tiny superconducting structures has implications for a completely new generation of electronic devices.
In future, X-ray beams could be used to write superconducting circuits, such as those depicted in the image. Here, solid lines indicate electrical connections while semicircles denote superconducting junctions, whose states are indicated by red arrows. Credit: UCL Press Office
Superconductivity is a special state where a material conducts electricity with no resistance, meaning absolutely zero energy is wasted.

The research group has shown that they can manipulate regions of high temperature superconductivity, in a particular material which combines oxygen, copper and a heavier, 'rare earth' element called lanthanum. Illuminating with X-rays causes a small scale re-arrangement of the oxygen atoms in the material, resulting in high temperature superconductivity, of the type originally discovered for such materials 25 years ago by IBM scientists. The X-ray beam is then used like a pen to draw shapes in two dimensions.

A well as being able to write superconductors with dimensions much smaller than the width of a human hair, the group is able to erase those structures by applying heat treatments. They now have the tools to write and erase with high precision, using just a few simple steps and without the chemicals ordinarily used in device fabrication. This ability to re-arrange the underlying structure of a material has wider applications to similar compounds containing metal atoms and oxygen, ranging from fuel cells to catalysts.

Prof. Aeppli, Director of the London Centre for Nanotechnology and the UCL investigator on the project, said: "Our validation of a one-step, chemical-free technique to generate superconductors opens up exciting new possibilities for electronic devices, particularly in re-writing superconducting logic circuits. Of profound importance is the key to solving the notorious 'travelling salesman problem', which underlies many of the world's great computational challenges. We want to create computers on demand to solve this problem, with applications from genetics to logistics. A discovery like this means a paradigm shift in computing technology is one step closer."

Prof Bianconi, the leader of the team from Sapienza, added: "It is amazing that in a few simple steps, we can now add superconducting 'intelligence' directly to a material consisting mainly of the common elements copper and oxygen."

More information: The X-ray experiments were performed at the Elettra (Trieste) synchrotron radiation facility. The work is published in Nature Materials, 21 August 2011 (doi:1038/nmat3088) and follows on from previous discovery of fractal-like structures in superconductors (doi:10.1038/nature09260).

Provided by University College London

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Inexpensive catalyst that makes hydrogen gas 10 times faster than natural enzyme

2011-09-05T02:26:00.000-07:00

Looking to nature for their muse, researchers have used a common protein to guide the design of a material that can make energy-storing hydrogen gas. The synthetic material works 10 times faster than the original protein found in water-dwelling microbes, the researchers report in the August 12 issue of the journal Science, clocking in at 100,000 molecules of hydrogen gas every second.The part of the catalyst that cranks out 100,000
molecules of hydrogen gas a second packs electrons
into chemical bonds between hydrogen atoms, possibly
hijacked from water. Credit: PNNL
This step is just one part of a series of reactions to split water and make hydrogen gas, but the researchers say the result shows they can learn from nature how to control those reactions to make durable synthetic catalysts for energy storage, such as in fuel cells.

In addition, the natural protein, an enzyme, uses inexpensive, abundant metals in its design, which the team copied. Currently, these materials -- called catalysts, because they spur reactions along -- rely on expensive metals such as platinum.

"This nickel-based catalyst is really very fast," said coauthor Morris Bullock of the Department of Energy's Pacific Northwest National Laboratory. "It's about a hundred times faster than the previous catalyst record holder. And from nature, we knew it could be done with abundant and inexpensive nickel or iron."

Stuffing Bonds

Electrical energy is nothing more than electrons. These same electrons are what tie atoms together when they are chemically bound to each other in molecules such as hydrogen gas. Stuffing electrons into chemical bonds is one way to store electrical energy, which is particularly important for renewable, sustainable energy sources like solar or wind power. Converting the chemical bonds back into flowing electricity when the sun isn't shining or the wind isn't blowing allows the use of the stored energy, such as in a fuel cell that runs on hydrogen.

Electrons are often stored in batteries, but Bullock and his colleagues want to take advantage of the closer packing available in chemicals.

"We want to store energy as densely as possible. Chemical bonds can store a huge amount of energy in a small amount of physical space," said Bullock, director of the Center for Molecular Electrocatalysis at PNNL, one of DOE's Energy Frontier Research Centers. The team also included visiting researcher Monte Helm from Fort Lewis College in Durango, Colo.

Biology stores energy densely all the time. Plants use photosynthesis to store the sun's energy in chemical bonds, which people use when they eat food. And a common microbe stores energy in the bonds of hydrogen gas with the help of a protein called a hydrogenase.

Because the hydrogenases found in nature don't last as long as ones that are built out of tougher chemicals (think paper versus plastic), the researchers wanted to pull out the active portion of the biological hydrogenase and redesign it with a stable chemical backbone.

Two Plus Two Equals One

In this study, the researchers looked at only one small part of splitting water into hydrogen gas, like fast-forwarding to the end of a movie. Of the many steps, there's a part at the end when the catalyst has a hold of two hydrogen atoms that it has stolen from water and snaps the two together.

The catalyst does this by completely dismantling some hydrogen atoms from a source such as water and moving the pieces around. Due to the simplicity of hydrogen atoms, those pieces are positively charged protons and negatively charged electrons. The catalyst arranges those pieces into just the right position so they can be put together correctly. "Two protons plus two electrons equals one molecule of hydrogen gas," says Bullock.

In real life, the protons would come from water, but since the team only examined a portion of the reaction, the researchers used water stand-ins such as acids to test their catalyst.

"We looked at the hydrogenase and asked what is the important part of this?" said Bullock. "The hydrogenase moves the protons around in what we call a proton relay. Where the protons go, the electrons will follow."

A Bauble for Energy

Based on the hydrogenase's proton relay, the experimental catalyst contained regions that dangled off the main structure and attracted protons, called "pendant amines." A pendant amine moves a proton into position on the edge of the catalyst, while a nickel atom in the middle of the catalyst offers a hydrogen atom with an extra electron (that's a proton and two electrons for those counting).

The pendant amine's proton is positive, while the nickel atom is holding on to a negatively charged hydrogen. Positioned close to each other, the opposites attract and the conglomerate solidifies into a molecule, forming hydrogen gas.

With that plan in mind, the team built potential catalysts and tested them. On their first try, they put a bunch of pendant amines around the nickel center, thinking more would be better. Testing their catalyst, they found it didn't work very fast. An analysis of how the catalyst was moving protons and electrons around suggested too many pendant amines got in the way of the perfect reaction. An overabundance of protons made for a sticky catalyst, which pinched it and slowed the hydrogen-gas-forming reaction down.

Like good gardeners, the team trimmed a few pendant amines off their catalyst, leaving only enough to make the protons stand out, ready to accept a negatively charged hydrogen atom.

Fastest Cat in the West

Testing the trimmed catalyst, the team found it performed much better than anticipated. At first they used conditions in which no water was present (remember, they used water stand-ins), and the catalyst could create hydrogen gas at a rate of about 33,000 molecules per second. That's much faster than their natural inspiration, which clocks in at around 10,000 per second.

However, most real-life applications will have water around, so they added water to the reaction to see how it would perform. The catalyst ran three times as fast, creating more than 100,000 hydrogen molecules every second. The researchers think the water might help by moving protons to a more advantageous spot on the pendant amine, but they are still studying the details.

Their catalyst has a drawback, however. It's fast, but it's not efficient. The catalyst runs on electricity -- after all, it needs those electrons to stuff into the chemical bonds -- but it requires more electricity than practical, a characteristic called the overpotential.

Bullock says the team has some ideas on how to reduce the inefficiency. Also, future work will require assembling a catalyst that splits water in addition to making hydrogen gas. Even with a high overpotential, the researchers see high potential for this catalyst.

More information: Monte L. Helm, Michael P. Stewart, R. Morris Bullock, M. Rakowski DuBois, Daniel L. DuBois, A Synthetic Nickel Electrocatalyst With a Turnover Frequency Above 100,000 s-1 for H2 Production, Science, August 12, 2011, DOI:10.1126/science.1205864

Provided by Pacific Northwest National Laboratory

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Word Association: Study Matches Brain Scans With Complex Thought

2011-09-05T00:21:00.000-07:00

In an effort to understand what happens in the brain when a person reads or considers such abstract ideas as love or justice, Princeton researchers have for the first time matched images of brain activity with categories of words related to the concepts a person is thinking about. The results could lead to a better understanding of how people consider meaning and context when reading or thinking.

Princeton researchers developed a method to determine the
probability of various words being associated with the object a person
thought about during a brain scan. They produced color-coded figures
that illustrate the probability of words within the Wikipedia article
about the object the participant saw during the scan actually being
associated with the object. The more red a word is, the more likely a
person is to associate it, in this case, with "cow." On the other hand,
bright blue suggests a strong correlation with "carrot." Black and grey
"neutral" words had no specific association or were not considered at
all. (Credit: Illustration courtesy of Francisco Pereira)
The researchers report in the journal Frontiers in Human Neuroscience that they used functional magnetic resonance imaging (fMRI) to identify areas of the brain activated when study participants thought about physical objects such as a carrot, a horse or a house. The researchers then generated a list of topics related to those objects and used the fMRI images to determine the brain activity that words within each topic shared. For instance, thoughts about "eye" and "foot" produced similar neural stirrings as other words related to body parts.

Once the researchers knew the brain activity a topic sparked, they were able to use fMRI images alone to predict the subjects and words a person likely thought about during the scan. This capability to put people's brain activity into words provides an initial step toward further exploring themes the human brain touches upon during complex thought.

"The basic idea is that whatever subject matter is on someone's mind -- not just topics or concepts, but also, emotions, plans or socially oriented thoughts -- is ultimately reflected in the pattern of activity across all areas of his or her brain," said the team's senior researcher, Matthew Botvinick, an associate professor in Princeton's Department of Psychology and in the Princeton Neuroscience Institute.

"The long-term goal is to translate that brain-activity pattern into the words that likely describe the original mental 'subject matter,'" Botvinick said. "One can imagine doing this with any mental content that can be verbalized, not only about objects, but also about people, actions and abstract concepts and relationships. This study is a first step toward that more general goal.

"If we give way to unbridled speculation, one can imagine years from now being able to 'translate' brain activity into written output for people who are unable to communicate otherwise, which is an exciting thing to consider. In the short term, our technique could be used to learn more about the way that concepts are represented at the neural level -- how ideas relate to one another and how they are engaged or activated."

The research, which was published Aug. 23, was funded by a grant from the National Institute of Neurological Disease and Stroke, part of the National Institutes of Health.

Depicting a person's thoughts through text is a "promising and innovative method" that the Princeton project introduces to the larger goal of correlating brain activity with mental content, said Marcel Just, a professor of psychology at Carnegie Mellon University. The Princeton researchers worked from brain scans Just had previously collected in his lab, but he had no active role in the project.

"The general goal for the future is to understand the neural coding of any thought and any combination of concepts," Just said. "The significance of this work is that it points to a method for interpreting brain activation patterns that correspond to complex thoughts."

Tracking the brain's 'semantic threads'

Largely designed and conducted in Botvinick's lab by lead author and Princeton postdoctoral researcher Francisco Pereira, the study takes a currently popular approach to neuroscience research in a new direction, Botvinick said. He, Pereira and coauthor Greg Detre, who earned his Ph.D. from Princeton in 2010, based their work on various research endeavors during the past decade that used brain-activity patterns captured by fMRI to reconstruct pictures that participants viewed during the scan.

"This 'generative' approach -- actually synthesizing something, an artifact, from the brain-imaging data -- is what inspired us in our study, but we generated words rather than pictures," Botvinick said.

"The thought is that there are many things that can be expressed with language that are more difficult to capture in a picture. Our study dealt with concrete objects, things that are easy to put into a picture, but even then there was an interesting difference between generating a picture of a chair and generating a list of words that a person associates with 'chair.'"

Those word associations, lead author Pereira explained, can be thought of as "semantic threads" that can lead people to think of objects and concepts far from the original subject matter yet strangely related.

"Someone will start thinking of a chair and their mind wanders to the chair of a corporation then to Chairman Mao -- you'd be surprised," Pereira said. "The brain tends to drift, with multiple processes taking place at the same time. If a person thinks about a table, then a lot of related words will come to mind, too. And we thought that if we want to understand what is in a person's mind when they think about anything concrete, we can follow those words."

Pereira and his co-authors worked from fMRI images of brain activity that a team led by Just and fellow Carnegie Mellon researcher Tom Mitchell, a professor of computer science, published in the journal Science in 2008. For those scans, nine people were presented with the word and picture of five concrete objects from 12 categories. The drawing and word for the 60 total objects were displayed in random order until each had been shown six times. Each time an image and word appeared, participants were asked to visualize the object and its properties for three seconds as the fMRI scanner recorded their brain activity.

Matching words and brain activity with related topics

Separately, Pereira and Detre constructed a list of topics with which to categorize the fMRI data. They used a computer program developed by Princeton Associate Professor of Computer Science David Blei to condense 3,500 articles about concrete objects from the online encyclopedia Wikipedia into all the topics the articles covered. The articles included a broad array of subjects, such as an airplane, heroin, birds and manual transmission. The program came up with 40 possible topics -- such as aviation, drugs, animals or machinery -- with which the articles could relate. Each topic was defined by the words most associated with it.

The computer ultimately created a database of topics and associated words that were free from the researchers' biases, Pereira said.

"We let the software discern the factors that make up meaning rather than stipulating it ourselves," he said. "There is always a danger that we could impose our preconceived notions of the meaning words have. Plus, I can identify and describe, for instance, a bird, but I don't think I can list all the characteristics that make a bird a bird. So instead of postulating, we let the computer find semantic threads in an unsupervised manner."

The topic database let the researchers objectively arrange the fMRI images by subject matter, Pereira said. To do so, the team searched the brain scans of related objects for similar activity to determine common brain patterns for an entire subject, Pereira said. The neural response for thinking about "furniture," for example, was determined by the common patterns found in the fMRI images for "table," "chair," "bed," "desk" and "dresser." At the same time, the team established all the words associated with "furniture" by matching each fMRI image with related words from the Wikipedia-based list.

Based on the similar brain activity and related words, Pereira, Botvinick and Detre concluded that the same neural response would appear whenever a person thought of any of the words related to furniture, Pereira said. And a scientist analyzing that brain activity would know that person was thinking of furniture. The same would follow for any topic.

Using images to predict the words on a person's mind
Finally, to ensure their method was accurate, the researchers conducted a blind comparison of each of the 60 fMRI images against each of the others. Without knowing the objects the pair of scans pertained to, Pereira and his colleagues estimated the presence of certain topics on a participant's mind based solely on the fMRI data. Knowing the applicable Wikipedia topics for a given brain image, and the keywords for each topic, they could predict the most likely set of words associated with the brain image.

The researchers found that they could confidently determine from an fMRI image the general topic on a participant's mind, but that deciphering specific objects was trickier, Pereira said. For example, they could compare the fMRI scan for "carrot" against that for "cow" and safely say that at the time the participant had thought about vegetables in the first example instead of animals. In turn, they could say that the person most likely thought of other words related to vegetables, as opposed to words related to animals.

On the other hand, when the scan for "carrot" was compared to that for "celery," Pereira and his colleagues knew the participant had thought of vegetables, but they could not identify related words unique to either object.

One aim going forward, Pereira said, is to fine-tune the group's method to be more sensitive to such detail. In addition, he and Botvinick have begun performing fMRI scans on people as they read in an effort to observe the various topics the mind accesses.

"Essentially," Pereira said, "we have found a way to generally identify mental content through the text related to it. We can now expand that capability to even further open the door to describing thoughts that are not amenable to being depicted with pictures."

Story Source:
The above story is reprinted (with editorial adaptations) from materials provided by Princeton University.

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Researchers develop prototype to detect fake websites

2011-09-04T20:56:00.000-07:00

Do you go online to pay bills, shop, transfer funds, sign up for classes, send email or instant messages or search for medical information? If so, then this pertains to you.It seems logical that a more Internet-driven world would translate into a heightened awareness of fake websites. But it isn't so. The vast majority of people still are unable to determine the authenticity of websites, resulting in tremendous monetary loses. That is what is driving the work of UA Artificial Intelligence Lab members who, along with a UA alumnus, have earned a top honor from MIS Quarterly for their research.
Members of a University of Arizona Eller College of Management team and a UA alumnus developed a prototype system to detect fake websites. When tested against other existing commercial systems, the team found that its system resulted in effective and more accurate detections of spoof sites – better than a human can.

The team's subsequent article, “Detecting Fake Websites: The Contribution of Statistical Learning Theory" was published last year in an issue of MIS Quarterly, or MISQ. A preeminent peer-reviewed journal in the field of management information systems, MISQ has since been named the article its top paper for 2010.

"Even to get into MISQ is very difficult, and this is probably the first technical paper to receive the Best Paper award," said Hsinchun Chen, the UA Artificial Intelligence Lab director, one of the paper's five authors.

MISQ will formally honor the researchers in Shanghai, China later this year during the International Conference on Information Systems.

"The topic of detecting fake websites and also our computational approach are both considered major contributions. This topic has great relevance to the industry, the society and the citizens in general," said Chen, also the McClelland Professor of Management Information Systems.

"This award is not something just for me, or my lab, but also for our department," he said, adding that the team's eventual goal is technology transfer.

UA alumnus Ahmed Abbasi, now a University of Virginia assistant professor of information technology, is lead author on the paper. Chen served as his dissertation adviser. Other co-authors are UA Eller College's department of management information systems faculty members Zhu Zhang and Jay F. Nunamaker Jr.; and David Zimbra, a doctoral student in the Artificial Intelligence Lab.

For the research, the team used the prototype and several other detection systems to evaluate the authenticity of 900 websites.

It is easy to pick up on a site's authenticity by checking whether the URL contains "http" when it should read "https," when it was last updated, if a security key is missing or if images appear strangely pixelated.

The team found that its system – founded on statistical learning technology, which evaluates a large accumulation of data – was more apt to detect imitation sites and those that were entirely concocted, said Abbasi, who earned his doctoral degree in management information systems from the UA in 2008.

The major difference between the authors’ prototype and the other systems? Their system relied on a tremendously rich set of fraud cues.

The team developed five categories with thousands of cues, finding that the best results were attained when utilizing thousands of highly visible and also deeply embedded cues, such as placement, URL length, the number of links, characters types on the site and how thorough the site's "frequently asked questions" section is detailed, among other features.

The project's origins were born out of the Artificial Intelligence Lab, where Abbasi developed the mathematical formula the team eventually used while working as a project lead and research associate. He continued the work after having taken a faculty position at the University of Wisconsin-Milwaukee.

"It creates a greater awareness for a problem that has been around for a while yet still remains an issue as we increasingly move to the Internet for everything – online banking, online health initiatives and medical information," Abbasi said.

Given the pervasive nature of online phishing scams, being able to readily and frequently detect a site's validity is crucial, Abbasi said, also noting research that indicates people are less than 60 percent accurate in detecting fake sites, and other security issues.

"The problem we're looking at is quite big. Fake websites constitute much of the Internet fraud's multi-billion dollar industry, and that is monetary loss…we can’t even quantify the social ramifications," Abbasi said. "That's the whole motivation. It is so profitable for fraudsters, and it is slipping through the cracks."

Today, Chen and more than one dozen of his collaborators are continuing to investigate fake sites. Meanwhile, Abbasi is undertaking an investigation of peoples' abilities to detect fake sites through a grant funded by the National Science Foundation.

Today, Chen and more than one dozen of his collaborators are continuing to investigate fake sites. Meanwhile, Abbasi is undertaking an investigation of users and peoples' abilities to detect fake sites.

Abbasi said developing better detection systems requires improved statistical learning technology that utilize larger quantities of cues. It also is important to dismiss long-held perceptions about how fake sites might and should appear.

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Scientists Discover Tipping Point for the Spread of Ideas

2011-09-04T17:18:00.000-07:00

Scientists at Rensselaer Polytechnic Institute have found that when just 10 percent of the population holds an unshakable belief, their belief will always be adopted by the majority of the society. The scientists, who are members of the Social Cognitive Networks Academic Research Center (SCNARC) at Rensselaer, used computational and analytical methods to discover the tipping point where a minority belief becomes the majority opinion. The finding has implications for the study and influence of societal interactions ranging from the spread of innovations to the movement of political ideals.
In this visualization, we see the tipping point where minority opinion (shown in red) quickly becomes majority opinion. Over time, the minority opinion grows. Once the minority opinion reached 10 percent of the population, the network quickly changes as the minority opinion takes over the original majority opinion (shown in green). (Credit: SCNARC/Rensselaer Polytechnic Institute)
"When the number of committed opinion holders is below 10 percent, there is no visible progress in the spread of ideas. It would literally take the amount of time comparable to the age of the universe for this size group to reach the majority," said SCNARC Director Boleslaw Szymanski, the Claire and Roland Schmitt Distinguished Professor at Rensselaer. "Once that number grows above 10 percent, the idea spreads like flame."

As an example, the ongoing events in Tunisia and Egypt appear to exhibit a similar process, according to Szymanski. "In those countries, dictators who were in power for decades were suddenly overthrown in just a few weeks."

The findings were published in the July 22, 2011, early online edition of the journal Physical Review E in an article titled "Social consensus through the influence of committed minorities."

An important aspect of the finding is that the percent of committed opinion holders required to shift majority opinion does not change significantly regardless of the type of network in which the opinion holders are working. In other words, the percentage of committed opinion holders required to influence a society remains at approximately 10 percent, regardless of how or where that opinion starts and spreads in the society.

To reach their conclusion, the scientists developed computer models of various types of social networks. One of the networks had each person connect to every other person in the network. The second model included certain individuals who were connected to a large number of people, making them opinion hubs or leaders. The final model gave every person in the model roughly the same number of connections. The initial state of each of the models was a sea of traditional-view holders. Each of these individuals held a view, but were also, importantly, open minded to other views.

Once the networks were built, the scientists then "sprinkled" in some true believers throughout each of the networks. These people were completely set in their views and unflappable in modifying those beliefs. As those true believers began to converse with those who held the traditional belief system, the tides gradually and then very abruptly began to shift.

"In general, people do not like to have an unpopular opinion and are always seeking to try locally to come to consensus. We set up this dynamic in each of our models," said SCNARC Research Associate and corresponding paper author Sameet Sreenivasan. To accomplish this, each of the individuals in the models "talked" to each other about their opinion. If the listener held the same opinions as the speaker, it reinforced the listener's belief. If the opinion was different, the listener considered it and moved on to talk to another person. If that person also held this new belief, the listener then adopted that belief.

"As agents of change start to convince more and more people, the situation begins to change," Sreenivasan said. "People begin to question their own views at first and then completely adopt the new view to spread it even further. If the true believers just influenced their neighbors, that wouldn't change anything within the larger system, as we saw with percentages less than 10."

The research has broad implications for understanding how opinion spreads. "There are clearly situations in which it helps to know how to efficiently spread some opinion or how to suppress a developing opinion," said Associate Professor of Physics and co-author of the paper Gyorgy Korniss. "Some examples might be the need to quickly convince a town to move before a hurricane or spread new information on the prevention of disease in a rural village."

The researchers are now looking for partners within the social sciences and other fields to compare their computational models to historical examples. They are also looking to study how the percentage might change when input into a model where the society is polarized. Instead of simply holding one traditional view, the society would instead hold two opposing viewpoints. An example of this polarization would be Democrat versus Republican.

The research was funded by the Army Research Laboratory (ARL) through SCNARC, part of the Network Science Collaborative Technology Alliance (NS-CTA), the Army Research Office (ARO), and the Office of Naval Research (ONR).

The research is part of a much larger body of work taking place under SCNARC at Rensselaer. The center joins researchers from a broad spectrum of fields -- including sociology, physics, computer science, and engineering -- in exploring social cognitive networks. The center studies the fundamentals of network structures and how those structures are altered by technology. The goal of the center is to develop a deeper understanding of networks and a firm scientific basis for the newly arising field of network science. More information on the launch of SCNARC can be found at http://news.rpi.edu/update.do?artcenterkey=2721&setappvar=page(1)

Szymanski, Sreenivasan, and Korniss were joined in the research by Professor of Mathematics Chjan Lim, and graduate students Jierui Xie (first author) and Weituo Zhang.

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Brain Cap Technology Turns Thought Into Motion; Mind-Machine Interface Could Lead to New Life-Changing Technologies for Millions of People

2011-09-04T13:46:00.000-07:00

"Brain cap" technology being developed at the University of Maryland allows users to turn their thoughts into motion. Associate Professor of Kinesiology José 'Pepe' L. Contreras-Vidal and his team have created a non-invasive, sensor-lined cap with neural interface software that soon could be used to control computers, robotic prosthetic limbs, motorized wheelchairs and even digital avatars.University of Maryland associate professor of
kinesiology Jose "Pepe" Contreras-Vidal wears his
Brain Cap, a noninvasive, sensor-lined cap with neural
interface software that soon could be used to control
computers, robotic prosthetic limbs, motorized
wheelchairs and even digital avatars. (Credit: John
Consoli, University of Maryland)
"We are on track to develop, test and make available to the public- within the next few years -- a safe, reliable, noninvasive brain computer interface that can bring life-changing technology to millions of people whose ability to move has been diminished due to paralysis, stroke or other injury or illness," said Contreras-Vidal of the university's School of Public Health.

The potential and rapid progression of the UMD brain cap technology can be seen in a host of recent developments, including a just published study in the Journal of Neurophysiology, new grants from the National Science Foundation (NSF) and National Institutes of Health, and a growing list of partners that includes the University of Maryland School of Medicine, the Veterans Affairs Maryland Health Care System, the Johns Hopkins University Applied Physics Laboratory, Rice University and Walter Reed Army Medical Center's Integrated Department of Orthopaedics & Rehabilitation.

"We are doing something that few previously thought was possible," said Contreras-Vidal, who is also an affiliate professor in Maryland's Fischell Department of Bioengineering and the university's Neuroscience and Cognitive Science Program. "We use EEG [electroencephalography] to non-invasively read brain waves and translate them into movement commands for computers and other devices.

Peer Reviewed

Contreras-Vidal and his team have published three major papers on their technology over the past 18 months, the latest a just released study in the Journal of Neurophysiology in which they successfully used EEG brain signals to reconstruct the complex 3-D movements of the ankle, knee and hip joints during human treadmill walking. In two earlier studies they showed (1) similar results for 3-D hand movement and (2) that subjects wearing the brain cap could control a computer cursor with their thoughts.

Alessandro Presacco, a second-year doctoral student in Contreras-Vidal's Neural Engineering and Smart Prosthetics Lab, Contreras-Vidal and co-authors write that their Journal of Neurophysiology study indicated "that EEG signals can be used to study the cortical dynamics of walking and to develop brain-machine interfaces aimed at restoring human gait function."

There are other brain computer interface technologies under development, but Contreras-Vidal notes that these competing technologies are either very invasive, requiring electrodes to be implanted directly in the brain, or, if noninvasive, require much more training to use than does UMD's EEG-based, brain cap technology.

Partnering to Help Sufferers of Injury and Stroke

Contreras-Vidal and his team are collaborating on a rapidly growing cadre projects with researchers at other institutions to develop thought-controlled robotic prosthetics that can assist victims of injury and stroke. Their latest partnership is supported by a new $1.2 million NSF grant. Under this grant, Contreras-Vidal's Maryland team is embarking on a four-year project with researchers at Rice University, the University of Michigan and Drexel University to design a prosthetic arm that amputees can control directly with their brains, and which will allow users to feel what their robotic arm touches.

"There's nothing fictional about this," said Rice University co-principal investigator Marcia O'Malley, an associate professor of mechanical engineering. "The investigators on this grant have already demonstrated that much of this is possible. What remains is to bring all of it -- non-invasive neural decoding, direct brain control and [touch] sensory feedback -- together into one device."

In a NIH-supported project underway, Contreras-Vidal and his colleagues are pairing their brain cap's EEG-based technology with a DARPA-funded next-generation robotic arm designed by researchers at the Johns Hopkins Applied Physics Laboratory to function like a normal limb. And the UMD team is developing a new collaboration with the New Zealand's start-up Rexbionics, the developer of a powered lower-limb exoskeleton called Rex that could be used to restore gait after spinal cord injury.

Two of the earliest partnerships formed by Contreras-Vidal and his team are with the University of Maryland School of Medicine in Baltimore and the Veterans Affairs Medical Center in Baltimore. A particular focus of this research is the use of the brain cap technology to help stroke victims whose brain injuries affect their motor-sensory control. Originally funded by a seed grant from the University of Maryland, College Park and the University of Maryland, Baltimore, the work now also is supported by a VA merit grant (anklebot BMI) and an NIH grant (Stroke).

"There is a big push in brain science to understand what exercise does in terms of motor learning or motor retraining of the human brain," says Larry Forrester, an associate professor of physical therapy and rehabilitation science at the University of Maryland School of Medicine.

For the more than a year, Forrester and the UMD team have tracked the neural activity of people on a treadmill doing precise tasks like stepping over dotted lines. The researchers are matching specific brain activity recorded in real time with exact lower-limb movements.

This data could help stroke victims in several ways, Forrester says. One is a prosthetic device, called an "anklebot," or ankle robot, that stores data from a normal human gait and assists partially paralyzed people. People who are less mobile commonly suffer from other health issues such as obesity, diabetes or cardiovascular problems, Forrester says, "so we want to get [stroke survivors] up and moving by whatever means possible."

The second use of the EEG data in stroke victims is more complex, yet offers exciting possibilities. "By decoding the motion of a normal gait," Contreras-Vidal says, "we can then try and teach stroke victims to think in certain ways and match their own EEG signals with the normal signals." This could "retrain" healthy areas of the brain in what is known as neuroplasticity.

One potential method for retraining comes from one of the Maryland research team's newest members, Steve Graff, a first-year bioengineering doctoral student. He envisions a virtual reality game that matches real EEG data with on-screen characters. "It gives us a way to train someone to think the right thoughts to generate movement from digital avatars. If they can do that, then they can generate thoughts to move a device," says Graff, who brings a unique personal perspective to the work. He has congenital muscular dystrophy and uses a motorized wheelchair. The advances he's working on could allow him to use both hands -- to put on a jacket, dial his cell phone or throw a football while operating his chair with his mind.

No Surgery Required

During the past two decades a great deal of progress has been made in the study of direct brain to computer interfaces, most of it through studies using monkeys with electrodes implanted in their brains. However, for use in humans such an invasive approach poses many problems, not the least of which is that most people don't' want holes in their heads and wires attached to their brains. "EEG monitoring of the brain, which has a long, safe history for other applications, has been largely ignored by those working on brain-machine interfaces, because it was thought that the human skull blocked too much of the detailed information on brain activity needed to read thoughts about movement and turn those readings into movement commands for multi-functional high-degree of freedom prosthetics," said Contreras-Vidal. He is among the few who have used EEG, MEG or other sensing technologies to develop non-invasive neural interfaces, and the only one to have demonstrated decoding results comparable to those achieved by researchers using implanted electrodes.

A paper Contreras-Vidal and colleagues published in the Journal of Neuroscience in March 2010 showed the feasibility of Maryland's EEG-based technology to infer multidimensional natural movement from noninvasive measurements of brain activity. In their two latest studies, Contreras-Vidal and his team have further advanced the development of their EEG brain interface technology, and provided powerful new evidence that it can yield brain computer interface results as good as or better than those from invasive studies, while also requiring minimal training to use.

In a paper published in April in the Journal of Neural Engineering, the Maryland team demonstrated that people wearing the EEG brain cap, could after minimal training control a computer cursor with their thoughts and achieve performance levels comparable to those by subjects using invasive implanted electrode brain computer interface systems. Contreras-Vidal and his co-authors write that this study also shows that compared to studies of other noninvasive brain control interface systems, training time with their system was substantially shorter, requiring only a single 40-minute session.

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Speaking and Understanding Speech Share the Same Parts of the Brain

2011-09-04T11:45:00.000-07:00

The brain has two big tasks related to speech: making it and understanding it. Psychologists and others who study the brain have debated whether these are really two separate tasks or whether they both use the same regions of the brain. Now, a new study, published in the August issue of Psychological Science, a journal of the Association for Psychological Science, finds that speaking and understanding speech share the same parts of the brain, with one difference: we don't need the brain regions that control the movements of lips, teeth, and so on to understand speech.
New research finds that speaking and understanding
speech share the same parts of the brain.
(Credit: © Artsem Martysiuk / Fotolia)
Most studies of how speech works in the brain focuses on comprehension. That's mostly because it's easier to image the brains of people who are listening quietly; talking makes the head move, which is a problem when you're measuring the brain. But now, the Donders Institute at the Radboud University Nijmegen, where the study was conducted, has developed technology that allows recording from a moving brain.

Laura Menenti, a Postdoctoral Research Associate at the University of Glasgow, co-wrote the paper along with Peter Hagoort of Radboud University Nijmegen and the Max Planck Institute for Psycholinguistics, Sarah Gierhan and Katrien Segaert. Menenti was initially interested in how the brain produces grammatical sentences and wanted to track the process of producing a sentence in its entirety; looking not only at its grammatical structure but also at its meaning. "What made this particularly exciting to us was that no one had managed to perform such a study before, meaning that we could explore an almost completely new topic," says Menenti.

The authors used functional MRI technology to measure brain activity in people who were either listening to sentences or speaking sentences. The other problem with measuring brain activity in people who are speaking is that you have to get them to say the right kind of sentence. The authors accomplished this with a picture of an action -- a man strangling a woman, say -- with one person colored green and one colored red to indicate their order in the sentence. This prompted people to say either "The man is strangling the woman" or "The woman is strangled by the man." (The experiments were all carried out in Dutch.)

From this, the researchers were able to tell where in the brain three different speech tasks (computing meaning, coming up with the words, and building a grammatical sentence) -- were taking place. They found that the same areas were activated for each of these tasks in people who were speaking and people who were listening to sentences. However, although some studies have suggested that while people are listening to speech, they silently articulate the words in order to understand them, the authors found no involvement of motor regions when people were listening.

According to Menenti, though the study was largely designed to answer a specific theoretical question, it also points towards some useful avenues for treatment of people with language-related problems. It suggests that while it sometimes seems that people with comprehension problems may have intact production, and vice versa, this may not necessarily be the case. According to Menenti, "Our data suggest that these problems would be expected to always at least partly coincide. On the other, our data confirm the idea that many different processes in the language system, such as understanding meaning or grammar, can at least partly, be damaged independently of each other."

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Glowing, Blinking Bacteria Reveal How Cells Synchronize Biological Clocks

2011-09-04T08:12:00.000-07:00

Biologists have long known that organisms from bacteria to humans use the 24 hour cycle of light and darkness to set their biological clocks. But exactly how these clocks are synchronized at the molecular level to perform the interactions within a population of cells that depend on the precise timing of circadian rhythms is less well understood.Green fluorescent protein causes the E. coli to glow
when the cells' clock is activated. (Credit: UC San Diego)
To better understand that process, biologists and bioengineers at UC San Diego created a model biological system consisting of glowing, blinking E. coli bacteria. This simple circadian system, the researchers report in the September 2 issue of Science, allowed them to study in detail how a population of cells synchronizes their biological clocks and enabled the researchers for the first time to describe this process mathematically.

"The cells in our bodies are entrained, or synchronized, by light and would drift out of phase if not for sunlight," said Jeff Hasty, a professor of biology and bioengineering at UC San Diego who headed the research team. "But understanding the phenomenon of entrainment has been difficult because it's difficult to make measurements. The dynamics of the process involve many components and it's tricky to precisely characterize how it works. Synthetic biology provides an excellent tool for reducing the complexity of such systems in order to quantitatively understand them from the ground up. It's reductionism at its finest."

To study the process of entrainment at the genetic level, Hasty and his team of researchers at UC San Diego's Biocircuits Institute combined techniques from synthetic biology, microfluidic technology and computational modeling to build a microfluidic chip with a series of chambers containing populations of E. coli bacteria. Within each bacterium, the genetic machinery responsible for the biological clock oscillations was tied to green fluorescent protein, which caused the bacteria to periodically fluoresce.

To simulate day and night cycles, the researchers modified the bacteria to glow and blink whenever arabinose -- a chemical that triggered the oscillatory clock mechanisms of the bacteria -- was flushed through the microfluidic chip. In this way, the scientists were able to simulate periodic day-night cycles over a period of only minutes instead of days to better understand how a population of cells synchronizes its biological clocks.

Hasty said a similar microfluidic system in principal could be constructed with mammalian cells to study how human cells synchronize with light and darkness. Such genetic model systems would have important future applications since scientists have discovered that problems with the biological clock can result in many common medical problems from diabetes to sleep disorders.

Other members of Hasty's team included Lev Tsimring, associate director of the BioCircuits Institute, and bioengineering graduate students Octavio Mondragon, Tal Danino and Jangir Selimkhanov. Their research was supported by grants from the National Institutes of Health and General Medicine and the San Diego Center for Systems Biology.

Story Source: The above story is reprinted (with editorial adaptations) from materials provided by University of California - San Diego.

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New Depiction of Light Aids Telecommunications

2011-09-04T05:36:00.000-07:00

Physicists with the Institute of Ultrafast Spectroscopy and Lasers (IUSL) at The City College of New York have presented a new way to map spiraling light that could help harness untapped data channels in optical fibers. Increased bandwidth would ease the burden on fiber-optic telecommunications networks taxed by an ever-growing demand for audio, video and digital media. The new model, developed by graduate student Giovanni Milione, Professor Robert Alfano and colleagues, could even spur enhancements in quantum computing and other applications.

Higher Order Poincare Sphere model developed by physicists with the
Institute of Ultrafast Spectroscopy and Lasers tracks movement of
complex forms of light. (Credit: Image courtesy of City College of New
York)
"People now can detect (light in) the ground channel, but this gives us a way to detect and measure a higher number of channels," says Mr. Milione. With such heavy traffic funneled through a single channel, there is great interest in exploiting others that can be occupied by complex forms of light, he explains.

The team published their work in the July 25 issue of Physical Review Letters. Mr. Milione will present it at the Optical Society of America's "Frontiers in Optics 2011" conference, October 16-20 in San Jose, Calif.

Polarization is everything to a physicist tracking light in an optical fiber or laser. More than a way to cut glare with sunglasses, polarization refers to a specific direction and orientation of the light's movement and electric field -- when it isn't going every which way as it does when emanating from a light bulb, for example.

"Being able to follow polarization and other changes as light travels gives you insight into the material it travels through, " explains Milione. This helps control the light and can essentially give a fingerprint of the material being analyzed.

Detecting the polarization also lets users finely tune a laser. Such control can allow a laser to burn away one layer of material while leaving the other layers it passes through intact.

Until now, only the simplest form of light, the ground state, could be mapped and controlled. Multiple higher channels in an optical fiber, which could be occupied by more complex light, were left sitting idle.

A globe-shaped model, called the Poincaré Sphere, has long been used to map such simple light. This light has peaks and troughs, like waves on the ocean, and moves or vibrates in "plane waves." One maps how light intersects the sphere in the same way one pinpoints a location on Earth using longitude and latitude.

But complex light moves with both spin and orbital angular momentum, more or less like the movement of our moon as it spins on its axis and orbits Earth.

Such light twists like a tornado as it travels through space and takes the form of what are called vector beams and vortices. To map these vortices the researchers expanded the existing sphere to develop their Higher Order Poincaré Sphere (HOPS).

The team studies even more complex patterns of light, such as star-shaped forms. Their model uses the HOPS to reduce what could be pages of mathematics to single equations. These are the mathematical tools that will harness the complex light for use in technology.

"The sphere facilitates understanding, showing phase vortices are on poles and vector beams are on the equator," explains Milione. "It organizes the relationship between these vortices of light."

"This kind of organization on the higher level Poincaré Sphere could clear the path to a number of novel physics and engineering efforts such as quantum computing and optical transitions; could greatly expand the sensitivity of spectroscopy and the complexity of computer cryptography; and might further push the boundaries what can be 'seen'," said Dr. Alfano.

The research was funded in part by Corning Inc. and the Army Research Office.

View the original article here

Supergene is key to copycat butterflies

2011-09-04T03:01:00.000-07:00

"We were blown away by what we found," said Mathieu Joron of France's National Museum of Natural History, who led the probe into what is being called a "supergene".

"These butterflies are the 'transformers' of the insect world," said Joron.

"But instead of being able to turn from a car into a robot with the flick of a switch, a single genetic switch allows these insects to morph into several different mimetic forms.

"It is amazing, and the stuff of science fiction. Now we are starting to understand how this switch can have such a pervasive effect."

The trick, known as Muellerian mimicry, was investigated by French and British scientists, who focussed on a species of Amazonian rainforest butterfly, Heliconius numata.

It is able to copy the colour patterns of several species of the Melinaea butterfly which are unpalatable to birds.

The "supergene" comprises a tightly packed region of genes on a single chromosome which control different elements of the wing pattern.

"By changing just one gene, the butterfly is able to fool its predators," explained Richard ffrench-Constant of the University of Exeter, southwestern England.

Even more astonishing is that three versions of the chromosome exist within this species, with each version controlling distinct wing-pattern forms.

Even though the butterflies look quite different from each other, they have the same DNA.

The supergene apparently transmits in a block from generation to generation, rather than go through recombination -- the mingling of genes from both parents.

The "supergene" also appears important in other species, say the authors.

One such species, the peppered moth, developped black wings in 19th-century Britain as a means of gaining camouflage in the sooty industrial environment.

"It's a gene that really packs an evolutionary punch," said ffrench-Constant. The paper is published online by the British science journal Nature.

View the original article here

Southampton engineers fly the world's first 'printed' aircraft

2011-09-03T23:51:00.000-07:00

Engineers at the University of Southampton have designed and flown the world's first 'printed' aircraft, which could revolutionise the economics of aircraft design.SULSA is the world's first "printed" aircraft.
Credit: University of Southampton
The SULSA (Southampton University Laser Sintered Aircraft) plane is an unmanned air vehicle (UAV) whose entire structure has been printed, including wings, integral control surfaces and access hatches. It was printed on an EOS EOSINT P730 nylon laser sintering machine, which fabricates plastic or metal objects, building up the item layer by layer.

No fasteners were used and all equipment was attached using 'snap fit' techniques so that the entire aircraft can be put together without tools in minutes.

The electric-powered aircraft, with a 2-metres wingspan, has a top speed of nearly 100 miles per hour, but when in cruise mode is almost silent. The aircraft is also equipped with a miniature autopilot developed by Dr Matt Bennett, one of the members of the team.

Laser sintering allows the designer to create shapes and structures that would normally involve costly traditional manufacturing techniques. This technology allows a highly-tailored aircraft to be developed from concept to first flight in days. Using conventional materials and manufacturing techniques, such as composites, this would normally take months. Furthermore, because no tooling is required for manufacture, radical changes to the shape and scale of the aircraft can be made with no extra cost.

This project has been led by Professors Andy Keane and Jim Scanlan from the University's Computational Engineering and Design Research group.

Professor Scanlon says: "The flexibility of the laser sintering process allows the design team to re-visit historical techniques and ideas that would have been prohibitively expensive using conventional manufacturing. One of these ideas involves the use of a Geodetic structure. This type of structure was initially developed by Barnes Wallis and famously used on the Vickers Wellington bomber which first flew in 1936. This form of structure is very stiff and lightweight, but very complex. If it was manufactured conventionally it would require a large number of individually tailored parts that would have to be bonded or fastened at great expense."

Professor Keane adds: "Another design benefit that laser sintering provides is the use of an elliptical wing planform. Aerodynamicists have, for decades, known that elliptical wings offer drag benefits. The Spitfire wing was recognised as an extremely efficient design but it was notoriously difficult and expensive to manufacture. Again laser sintering removes the manufacturing constraint associated with shape complexity and in the SULSA aircraft there is no cost penalty in using an elliptical shape."

SULSA is part of the EPSRC-funded DECODE project, which is employing the use of leading edge manufacturing techniques, such as laser sintering, to demonstrate their use in the design of UAVs.

The University of Southampton has been at the forefront of UAV development since the early 1990s, when work began on the Autosub programme at its waterfront campus at the National Oceanography Centre, Southampton. A battery powered submarine travelled under sea ice in more than 300 voyages to map the North Sea, and assess herring stocks.

Now, the University is launching a groundbreaking course which enables students to take a Master's Degree in unmanned autonomous vehicle (UAV) design.

Provided by University of Southampton

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New Invisibility Cloak Hides Objects from Human View

2011-09-03T20:47:00.000-07:00

For the first time, scientists have devised an invisibility cloak material that hides objects from detection using light that is visible to humans. The new device is a leap forward in cloaking materials, according to a report in the ACS journal Nano Letters.A real-life invisibility cloak, shown in this cross- sectional
illustration, can hide objects from human view. (Credit: ACS)
Xiang Zhang and colleagues note that invisibility cloaks, which route electromagnetic waves around an object to make it undetectable, "are still in their infancy." Most cloaks are made of materials that can only hide things using microwave or infrared waves, which are just below the threshold of human vision. To remedy this, the researchers built a reflective "carpet cloak" out of layers of silicon oxide and silicon nitride etched in a special pattern. The carpet cloak works by concealing an object under the layers, and bending light waves away from the bump that the object makes, so that the cloak appears flat and smooth like a normal mirror.

Although the study cloaked a microscopic object roughly the diameter of a red blood cell, the device demonstrates that it may be "capable of cloaking any object underneath a reflective carpet layer. In contrast to the previous demonstrations that were limited to infrared light, this work makes actual invisibility for the light seen by the human eye possible," the scientists write.

The authors acknowledge funding from the U.S. Army Research Office, the Natural Sciences and Engineering Research Council of Canada, and the NSF Graduate Research Fellowship Program.

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World-Record Pulsed Magnetic Field Achieved; Lab Moves Closer to 100-Tesla Mark

2011-09-03T17:22:00.000-07:00

Researchers at the National High Magnetic Field Laboratory's Pulsed Field Facility at Los Alamos National Laboratory have set a new world record for the strongest
magnetic field produced by a nondestructive magnet.
Yates Coulter, left, and Mike Gordon of Los Alamos National Laboratory make final preparations before successfully achieving a world-record for the strongest magnetic field produced by a nondestructive magnet. Working at the National High Magnetic Field Laboratory's Pulsed Field Facility at Los Alamos, a team of researchers achieved a field of 97.4 tesla, which is nearly 100 times stronger than the magnetic field found in giant electromagnets used in metal scrap yards. (Credit: Image courtesy of DOE/Los Alamos National Laboratory)The scientists achieved a field of 92.5 tesla on Thursday, August 18, taking back a record that had been held by a team of German scientists and then, the following day, surpassed their achievement with a whopping 97.4-tesla field. For perspective, Earth's magnetic field is 0.0004 tesla, while a junk-yard magnet is 1 tesla and a medical MRI scan has a magnetic field of 3 tesla.

The ability to create pulses of extremely high magnetic fields nondestructively (high-power magnets routinely rip themselves to pieces due to the large forces involved) provides researchers with an unprecedented tool for studying fundamental properties of materials, from metals and superconductors to semiconductors and insulators. The interaction of high magnetic fields with electrons within these materials provides valuable clues for scientists about the properties of materials. With the recent record-breaking achievement, the Pulsed Field Facility at LANL, a national user facility, will routinely provide scientists with magnetic pulses of 95 tesla, enticing the worldwide user community to Los Alamos for a chance to use this one-of-a-kind capability.

The record puts the Los Alamos team within reach of delivering a magnet capable of achieving 100 tesla, a goal long sought by researchers from around the world, including scientists working at competing magnet labs in Germany, China, France, and Japan.

Such a powerful nondestructive magnet could have a profound impact on a wide range of scientific investigations, from how to design and control material functionality to research into the microscopic behavior of phase transitions. This type of magnet allows researchers to carefully tune material parameters while perfectly reproducing the non-invasive magnetic field. Such high magnetic fields confine electrons to nanometer scale orbits, thereby helping to reveal the fundamental quantum nature of a material.

Thursday's experiment was met with as much excitement as trepidation by the group of condensed matter scientists, high-field magnet technicians, technologists, and pulsed-magnet engineers who gathered to witness the NHMFL-PFF retake the world record. Crammed into the tight confines of the Magnet Lab's control room, they gathered, lab notebooks or caffeine of choice in hand. Their conversation reflected a giddy sense of anticipation tempered with nervousness.

With Mike Gordon commanding the controls that draw power off of a massive 1.4-gigawatt generator system and directs it to the magnet, all eyes and ears were keyed to video monitors showing the massive 100 tesla Multishot Magnet and the capacitor bank located in the now eerily empty Large Magnet Hall next door. The building had been emptied as a standard safety protocol.

Scientists heard a low warping hum, followed by a spine-tingling metallic screech signaling that the magnet was spiking with a precisely distributed electric current of more than 100 megajoules of energy. As the sound dissipated and the monitors confirmed that the magnet performed perfectly, attention turned to data acquired during the shot through two in-situ measurements -- proof positive that the magnet had achieved 92.5 tesla, thus yanking back from a team of German scientists a record that Los Alamos had previously held for five years.

The next day's even higher 97.4-tesla achievement was met with high-fives and congratulatory pats on the back. Later, researchers Charles Mielke, Neil Harrison, Susan Seestrom, and Albert Migliori certified with their signatures the data that would be sent to the Guiness Book of World Records.

The NHMFL is sponsored primarily by the National Science Foundation, Division of Materials Research, with additional support from the State of Florida and the DOE. These recent successes were enabled by long-term support from the U.S. Department of Energy's Office of Basic Energy Sciences, and the National Science Foundation's 100 Tesla Multi-Shot magnet program.

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American Genes Don’t Exist

2011-09-03T13:57:00.000-07:00

Congratulations to Meb Keflezighi of Eritrean descent, who won the New York City Marathon last Sunday and was the first Yankee to try to to so since 1982!

Why did I mention that he was born in Eritrea? As a result of critics say that an immigrant like Keflezighi who moved to the U.S. at age twelve isn’t a legitimate American.

A post on Letsrun.com said:

Provide us all a break. It’s just another African marathon winner.

How about creating that African-Yank?

Silly me. I thought that naturalized Yankee voters equal American citizens at birth with the identical rights and privileges (with the exception of obtaining to be the President of the United States). Leaving that debate aside, however, the idea that East Africans are genetically endowed for marathon running has conjointly clouded Keflezighi’s celebration.

The success of distance runners from Kenya and Ethiopia has fostered a lore of East Africans as genetically gifted, unbeatable, dominant because of their biology. Scientists have searched for - however not found - genes specific to East Africans that could account for his or her distance ability, said John Hoberman, a professor at the University of Texas at Austin who studies race and sports.

Truly Yank? Dialogue Dogs a Triumph in the Marathon - NYTimes.com

Little question Keflezighi has genes which enhance his physiological capabilities for endurance and different traits found in winning marathoners. This does not mean that Keflezighi is any a lot of or less Yankee than alternative non-East African runners who have the same genes.

The Oxford English Dictionary defines “nationality” in 2 components:

nationality

noun (pl. nationalities) one the status of belonging to a explicit nation. 2 an ethnic cluster forming a half of one or more political nations.

While ethnic groups are mentioned, the U.S. is clearly a rustic of many ethnic groups thus genes ought to not be part of the talk when discussing whether someone is Yankee or not.

Quite frankly, I’m not even sure what makes an individual Yankee and I don’t assume anyone else does either. I hold an Yankee passport and spent the years between ages half dozen and 26 within the U.S. I’ve lived in six different countries in the past 10 years and hence, my national identity is slightly muddled. My son is even additional confused. He holds an Yank passport similarly however has never lived in the U.S although he’s lived in four totally different countries in his seven years. He was born in Japan thus some days he says that he’s Japanese and now that he lives in Singapore, he typically says he’s Singaporean. I’m sure some people would say he’s not American at all.

It might be less complicated to mention we’re global citizens with ties to a lot of than one country. Truth be told, I’m proud to mention I’m Chinese-Yank with the accent to prove it.

Edited to add this video of Meb Keflezighi on David Letterman:

Data about Genetic Risk is Power or is it Concern?

2011-09-03T10:53:00.000-07:00

A little over two years ago, I confessed that I was “just a little fearful of genetic testing.” I actually have two young kids and almost every day I see traits in them that I’m pretty positive they inherited from me whether or not via genes or behavior. If you’re a parent, I’m sure you'll imagine that there’s a lot of self-blame happening in our house.

Thus when it involves genetic testing, I ought to want to understand but I don’t. A minimum of not right this minute. Haven’t I got enough to fret concerning?

From Middletown Journal’s month-long series on the battle against cancer - Many with cancer gene don’t want to know.

There is a crowd of out there who could not wish to know. There’s a subset of individuals who if they knew would act on the knowledge and profit and there are others who would rather bury their heads within the sand.

~Dr. Michael Watson, director of the Yankee School of Medical Genetics

NIH Director Francis Collins, however, falls squarely in the camp of people who not solely want to understand, they act on the info. Well done!

Collins hits the gym following genetic testing from The Nice Beyond, Nature blog

Maybe if a genetic test could motivate me to go to the gym and lose weight, it would be price it

Murderer Gets Reduced Sentence Because His Genes Made Him Do It

2011-09-03T07:28:00.000-07:00

Hey criminals! Here’s how you get out of taking full responsibility for your dastardly actions:

Pretend your DNA sampleBlame it on your identical twin See if you have got the genes that predispose you to whatever crime you’ve committed
Murderer Abdelmalek Bayout and his attorneys selected possibility three. Bayout admitted in 2007 to stabbing and killing Walter Felipe Novoa Perez in Italy. During the first sentencing, he was found to be mentally ill. This year, neuroscientists additionally found abnormalities in brain-imaging scans and five genes linked to violent behavior, including MAOA.

Although there have been numerous cases since 1994 in which the defense argued for leniency based on MAOA deficiency, this is often the first case in that this tactic has been successful. Based on the scans and genetic testing results, the decide reduced Bayout’s sentence by another year.

Not everyone agrees with the choose’s decision.

"We have a tendency to don’t know how the whole genome functions and therefore the [possible] protective effects of other genes," says Giuseppe Novelli, a forensic scientist and geneticist at the University Tor Vergata in Rome. Tests for single genes such as MAOA are "useless and expensive", he adds.

Even worse, this verdict might open the floodgates to claims of all sorts the more we have a tendency to know about genetic influences on behavior. That list on top of is just regarding to induce longer.

Source: Scientific Yankee

Image: “Structural (left) and practical (right) MRI scan knowledge shows that subjects with the violence-connected version of the MAO-A gene (MAOA-L) had reduced volume and activity of the anterior cingulate cortex (blue area in front part of brain at left and corresponding yellow space in at right), that is considered the hub of a circuit responsible for regulating impulsive aggression. The color-coded areas show where subjects with the L gene kind differed from subjects with the H gene type.”

NIMH Clinical Brain Disorders Branch

Video: Knome’s Ari Kiirikki Speaks with Medgadget

2011-09-03T04:24:00.000-07:00

via Medgadget

AKPC_IDS += "1410,";Comments Off

Southampton engineers fly the world's first 'printed' aircraft

2011-09-03T00:59:00.000-07:00

No fasteners were used and all equipment was attached using 'snap fit' techniques so that the entire aircraft can be put together without tools in minutes.

This project has been led by Professors Andy Keane and Jim Scanlan from the University's Computational Engineering and Design Research group.

SULSA is part of the EPSRC-funded DECODE project, which is employing the use of leading edge manufacturing techniques, such as laser sintering, to demonstrate their use in the design of UAVs.

Now, the University is launching a groundbreaking course which enables students to take a Master's Degree in unmanned autonomous vehicle (UAV) design.

Provided by University of Southampton

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New Way to Measure Expansion of Universe

2011-09-02T22:14:00.000-07:00

Florian Beutler, a PhD candidate with ICRAR at the University of Western Australia, has calculated how fast the Universe is growing by measuring the Hubble constant.

"The Hubble constant is a key number in astronomy because it's used to calculate the size and age of the Universe," said Mr Beutler.

As the Universe swells, it carries other galaxies away from ours. The Hubble constant links how fast galaxies are moving with how far they are from us.

The measurement can be refined even further by using data from larger galaxy surveys.

"Big surveys, like the one used for this work, generate numerous scientific outcomes for astronomers internationally," says Professor Lister Staveley-Smith, ICRAR's Deputy Director of Science.

* The new measurement of the Hubble constant is 67.0 ± 3.2 km s-1 Mpc-1

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Engineers Reverse E. Coli Metabolism for Quick Production of Fuels, Chemicals

2011-09-02T18:39:00.000-07:00

Gonzalez's laboratory is in a race with hundreds of labs around the world to find green methods for producing chemicals like butanol that have historically come from petroleum.

The research was funded by Rice University.

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Brain Cap Technology Turns Thought Into Motion; Mind-Machine Interface Could Lead to New Life-Changing Technologies for Millions of People

2011-09-02T16:08:00.000-07:00

Peer Reviewed

Partnering to Help Sufferers of Injury and Stroke

No Surgery Required

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Holograms Reveal Brain's Inner Workings: Microscopy Technique Used to Observe Activity of Neurons Like Never Before

2011-09-02T12:19:00.000-07:00

A major advance for pharmaceutical research

The promise of this technique for High Content Screening has already resulted in a start-up company at EPFL called LynceeTec (www.lynceetec.com).

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Biologists Discovery May Force Revision of Biology Textbooks: Novel Chromatin Particle Halfway Between DNA and a Nucleosome

2011-09-02T09:24:00.000-07:00

The biologists say that while the pre-nucleosome may look something like a nucleosome under the microscope, biochemical tests have shown that it is in reality halfway between DNA and a nucleosome.

These pre-nucleosomes, the researchers say, are converted into nucleosomes by a motor protein that uses the energy molecule ATP.

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Supergene is key to copycat butterflies

2011-09-02T07:15:00.000-07:00

Since Charles Darwin, biologists have pondered the mystery of "mimicry butterflies", which survive by copying the wing patterns of other butterflies that taste horrible to their predators, birds.

This undated handout photo released by the CNRS shows butterflies, Melinaea mneme (top) and Heliconius numata. The mystery of how a butterfly has changed its wing patterns to mimic neighbouring species and avoid being eaten by birds has been solved by a team of European scientists.
The answer, according to a study released on Friday, lies in an astonishing cluster of about 30 genes in a single chromosome.

"We were blown away by what we found," said Mathieu Joron of France's National Museum of Natural History, who led the probe into what is being called a "supergene".

"These butterflies are the 'transformers' of the insect world," said Joron.

"But instead of being able to turn from a car into a robot with the flick of a switch, a single genetic switch allows these insects to morph into several different mimetic forms.

"It is amazing, and the stuff of science fiction. Now we are starting to understand how this switch can have such a pervasive effect."

The trick, known as Muellerian mimicry, was investigated by French and British scientists, who focussed on a species of Amazonian rainforest butterfly, Heliconius numata.

It is able to copy the colour patterns of several species of the Melinaea butterfly which are unpalatable to birds.

The "supergene" comprises a tightly packed region of genes on a single chromosome which control different elements of the wing pattern.

"By changing just one gene, the butterfly is able to fool its predators," explained Richard ffrench-Constant of the University of Exeter, southwestern England.

Even more astonishing is that three versions of the chromosome exist within this species, with each version controlling distinct wing-pattern forms.

Even though the butterflies look quite different from each other, they have the same DNA.

The supergene apparently transmits in a block from generation to generation, rather than go through recombination -- the mingling of genes from both parents.

The "supergene" also appears important in other species, say the authors.

One such species, the peppered moth, developped black wings in 19th-century Britain as a means of gaining camouflage in the sooty industrial environment.

"It's a gene that really packs an evolutionary punch," said ffrench-Constant. The paper is published online by the British science journal Nature

Cellular Stress Can Induce Yeast to Promote Prion Formation

2011-09-02T04:05:00.000-07:00

It's a chicken and egg question. Where do the infectious protein particles called prions come from? Essentially clumps of misfolded proteins, prions cause neurodegenerative disorders, such as mad cow/Creutzfeld-Jakob disease, in humans and animals. Prions trigger the misfolding and aggregation of their properly folded protein counterparts, but they usually need some kind of "seed" to get started.
Biochemists at Emory University School of Medicine have identified a yeast protein called Lsb2 that can promote spontaneous prion formation. This unstable, short-lived protein is strongly induced by cellular stresses such as heat. Lsb2's properties also illustrate how cells have developed ways to control and regulate prion formation. Research in yeast has shown that sometimes, prions can actually help cells adapt to different conditions.

The results are published in the July 22 issue of the journal Molecular Cell. The senior author is Keith Wilkinson, PhD, professor of biochemistry at Emory University School of Medicine The first author is senior associate Tatiana Chernova, PhD.

The aggregated form of proteins connected with several other neurodegenerative diseases such as Alzheimer's, Parkinson's and Huntington's can, in some circumstances, act like prions. So the Emory team's finding provides insight into how the ways that cells deal with stress might lead to poisonous protein aggregation in human diseases.

"A direct human homolog of Lsb2 doesn't exist, but there may be a protein that performs the same function," Wilkinson says. "The mechanism may say more about other types of protein aggregates than about classical prions in humans, This mechanism of seeding and growth may be more important for aggregate formation in diseases such as Huntington's."

Lsb2 does not appear to form stable prions by itself. Rather, it seems to bind to and encourage the aggregation of another protein, Sup35, which does form prions.

"Our model is that stress induces high levels of Lsb2, which allows the accumulation of misfolded prion proteins," Wilkinson says. "Lsb2 protects enough of these newborn prion particles from the quality control machinery for a few of them to get out."

The research was supported by the National Institutes of Health.

More information: T.A. Chernova et al. Prion Induction by the Short-lived Stress Induced Protein Lsb2 Is Regulated by Ubiquitination and Association with the Actin Cytoskeleton Mol. Cell (2011).
Provided by Emory University

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Scientists Discover Tipping Point for the Spread of Ideas

2011-09-02T01:43:00.000-07:00

The findings were published in the July 22, 2011, early online edition of the journal Physical Review E in an article titled "Social consensus through the influence of committed minorities."

Szymanski, Sreenivasan, and Korniss were joined in the research by Professor of Mathematics Chjan Lim, and graduate students Jierui Xie (first author) and Weituo Zhang.

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Etch-a-sketch with superconductors

2011-09-01T23:18:00.000-07:00

Provided by University College London

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Seeing eye to eye is key to copying, say scientists

2011-09-01T20:02:00.000-07:00

The results could be the first clues to understanding why some people, such as children with autism, struggle to grasp when they are expected to copy the actions of others in social situations.

Provided by University of Nottingham

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Eat, Prey, Rain: New Model of Dynamics of Clouds and Rain Is Based On a Predator-Prey Population Model

2011-09-01T17:23:00.000-07:00

What do a herd of gazelles and a fluffy mass of clouds have in common? A mathematical formula that describes the population dynamics of such prey animals as gazelles and their predators has been used to model the relationship between cloud systems, rain and tiny floating particles called aerosols. This model may help climate scientists understand, among other things, how human-produced aerosols affect rainfall patterns. The research recently appeared in the Proceedings of the National Academy of Sciences (PNAS).A new mathematical model may help climate scientists
understand, among other things, how human-produced
aerosols affect rainfall patterns. (Credit: © Brian
Jackson / Fotolia)
Clouds are major contributors to the climate system. In particular the shallow marine stratocumulus clouds that form huge cloud decks over the subtropical oceans cool the atmosphere by reflecting part of the incoming solar energy back to space. Drs. Ilan Koren of the Weizmann Institute's Environmental Sciences and Energy Research Department (Faculty of Chemistry) and Graham Feingold of the NOAA Earth System Research Laboratory, Colorado, found that equations for modeling prey-predator cycles in the animal world were a handy analogy for cloud-rain cycles: Just as respective predator and prey populations expand and contract at the expense of one another, so too rain depletes clouds, which grow again once the rain runs out. And just as the availability of grass affects herd size, the relative abundance of aerosols -- which "feed" the clouds as droplets condense around them -- affects the shapes of those clouds. A larger supply of airborne particles gives rise to more droplets, but these droplets are smaller and thus remain high up in the cloud rather than falling as rain.

In previous research, Feingold and Koren had "zoomed in" to discover oscillations in convective cells in marine stratocumulus. Now they returned to their data, but from a "top down" angle to see if a generalized formula could reveal something about these systems. Using just three simple equations, they developed a model showing that cloud-rain dynamics mimic three known predator-prey modes. Like gazelles and lions, the two can oscillate in tandem, the "predator" rain cycle following a step behind peak cloud formation. Or the two can reach a sort of steady state in which the clouds are replenished at the same rate as they are diminished (as in a light, steady drizzle). The third option is chaos -- the crash that occurs when predator populations get out of hand or a strong rain destroys the cloud system.

The model shows that as the amounts of aerosols change, the system can abruptly shift from one state to another. It also reveals a bifurcation -- two scenarios at different ends of the aerosol scale that lend themselves to stable patterns. In the first, relatively low aerosol levels lead to clouds in which development depends heavily on aerosol concentrations. In the second, high levels produce saturation; these clouds depend solely on the initial environmental conditions.

Using this so-called systems approach, says Koren, "can open new windows to view and understand the emergent behavior of the complex relationships between clouds, rain and aerosols, giving us a more useful view of the big picture and helping us to understand how shifting aerosol levels can lead to different climate patterns."

View the original article here

New Invisibility Cloak Hides Objects from Human View

2011-09-01T13:57:00.000-07:00

The authors acknowledge funding from the U.S. Army Research Office, the Natural Sciences and Engineering Research Council of Canada, and the NSF Graduate Research Fellowship Program.

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Improving batteries' energy storage

2011-09-01T11:08:00.000-07:00

MIT researchers have found a way to improve the energy density of a type of battery known as lithium-air (or lithium-oxygen) batteries, producing a device that could potentially pack several times more energy per pound than the lithium-ion batteries that now dominate the market for rechargeable devices in everything from cellphones to cars.
The work is a continuation of a project that last year demonstrated improved efficiency in lithium-air batteries through the use of noble-metal-based catalysts. In principle, lithium-air batteries have the potential to pack even more punch for a given weight than lithium-ion batteries because they replace one of the heavy solid electrodes with a porous carbon electrode that stores energy by capturing oxygen from air flowing through the system, combining it with lithium ions to form lithium oxides.

The new work takes this advantage one step further, creating carbon-fiber-based electrodes that are substantially more porous than other carbon electrodes, and can therefore more efficiently store the solid oxidized lithium that fills the pores as the battery discharges.

"We grow vertically aligned arrays of carbon nanofibers using a chemical vapor deposition process. These carpet-like arrays provide a highly conductive, low-density scaffold for energy storage," explains Robert Mitchell, a graduate student in MIT's Department of Materials Science and Engineering (DMSE) and co-author of a paper describing the new findings in the journal Energy and Environmental Science.
This diagram depicts the essential functioning of the lithium-air battery. Ions of lithium combine with oxygen from the air to form particles of lithium oxides, which attach themselves to carbon fibers on the electrode as the battery is being used. During recharging, the lithium oxides separate again into lithium and oxygen and the process can begin again. Graphic: Courtesy of Mitchell, Gallant, and Shao-Horn
During discharge, lithium-peroxide particles grow on the carbon fibers, adds co-author Betar Gallant, a graduate student in MIT's Department of Mechanical Engineering. In designing an ideal electrode material, she says, it's important to "minimize the amount of carbon, which adds unwanted weight to the battery, and maximize the space available for lithium peroxide," the active compound that forms during the discharging of lithium-air batteries.

"We were able to create a novel carpet-like material — composed of more than 90 percent void space — that can be filled by the reactive material during battery operation," says Yang Shao-Horn, the Gail E. Kendall Professor of Mechanical Engineering and Materials Science and Engineering and senior author of the paper. The other senior author of the paper is Carl Thompson, the Stavros Salapatas Professor of Materials Science and Engineering and interim head of DMSE.

In earlier lithium-air battery research that Shao-Horn and her students reported last year, they demonstrated that carbon particles could be used to make efficient electrodes for lithium-air batteries. In that work, the carbon structures were more complex but only had about 70 percent void space.
As the battery is used, particles of
lithium peroxide form as small dots
on the sides of carbon nanofibers
(top), and eventually assume larger
toroidal (donut) shapes as the battery
continues to discharge (bottom), as
seen in these scanning electron
microscope images. Photo: Courtesy
of Mitchell, Gallant, and Shao-Horn
The gravimetric energy stored by these electrodes — the amount of power they can store for a given weight — "is among the highest values reported to date, which shows that tuning the carbon structure is a promising route for increasing the energy density of lithium-air batteries," Gallant says. The result is an electrode that can store four times as much energy for its weight as present lithium-ion battery electrodes.

In the paper published last year, the team had estimated the kinds of improvement in gravimetric efficiency that might be achieved with lithium-air batteries; this new work "realizes this gravimetric gain," Shao-Horn says. Further work is still needed to translate these basic laboratory advances into a practical commercial product, she cautions.

Because the electrodes take the form of orderly "carpets" of carbon fibers — unlike the randomly arranged carbon particles in other electrodes — it is relatively easy to use a scanning electron microscope to observe the behavior of the electrodes at intermediate states of charge. The researchers say this ability to observe the process, an advantage that they had not anticipated, is a critical step toward further improving battery performance. For example, it could help explain why existing systems degrade after many charge-discharge cycles.

Ji-Guang Zhang, a laboratory fellow in battery technology at the Pacific Northwest National Laboratory, says this is "original and high-quality work." He adds that this research "demonstrates a very unique approach to preparing high-capacity electrodes for lithium-air batteries."

This story is republished courtesy of MIT News (http://web.mit.edu/newsoffice/), a popular site that covers news about MIT research, innovation and teaching.

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World-Record Pulsed Magnetic Field Achieved; Lab Moves Closer to 100-Tesla Mark

2011-09-01T08:19:00.000-07:00

Researchers at the National High Magnetic Field Laboratory's Pulsed Field Facility at Los Alamos National Laboratory have set a new world record for the strongest magnetic field produced by a nondestructive magnet.
Yates Coulter, left, and Mike Gordon of Los Alamos National Laboratory make final preparations before successfully achieving a world-record for the strongest magnetic field produced by a nondestructive magnet. Working at the National High Magnetic Field Laboratory's Pulsed Field Facility at Los Alamos, a team of researchers achieved a field of 97.4 tesla, which is nearly 100 times stronger than the magnetic field found in giant electromagnets used in metal scrap yards. (Credit: Image courtesy of DOE/Los Alamos National Laboratory)The scientists achieved a field of 92.5 tesla on Thursday, August 18, taking back a record that had been held by a team of German scientists and then, the following day, surpassed their achievement with a whopping 97.4-tesla field. For perspective, Earth's magnetic field is 0.0004 tesla, while a junk-yard magnet is 1 tesla and a medical MRI scan has a magnetic field of 3 tesla.

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Speaking and Understanding Speech Share the Same Parts of the Brain

2011-09-01T05:01:00.000-07:00

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Sun-Free Photovoltaics Powered by Heat

2011-09-01T02:42:00.000-07:00

An ideal match

"By choosing how we design the nanostructure, we can create materials that have novel optical properties," Soljacic says. "This gives us the ability to control and manipulate the behavior of light."

Note: The full version of the MITEI story is available at: http://web.mit.edu/mitei/research/spotlights/making-electricity-with-photovoltaics.html

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Researchers develop prototype to detect fake websites

2011-09-01T00:23:00.000-07:00

MISQ will formally honor the researchers in Shanghai, China later this year during the International Conference on Information Systems.

"This award is not something just for me, or my lab, but also for our department," he said, adding that the team's eventual goal is technology transfer.

For the research, the team used the prototype and several other detection systems to evaluate the authenticity of 900 websites.

The major difference between the authors’ prototype and the other systems? Their system relied on a tremendously rich set of fraud cues.

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Searching for Spin Liquids: Much-Sought Exotic Quantum State of Matter Can Exist

2011-08-31T21:50:00.000-07:00

One compromise that a frustrated spin system makes is to simultaneously exist in many spin orientations. In a quantum system, this simultaneous existence, or superposition, is allowed.

Here's where the JQI researchers have tried something new. They have studied what happens when frustration occurs in materials with a hexagonal (six sided) unit cell lattice.

"Kaleidoscope of Exotic Quantum Phases in a Frustrated XY Model" by Christopher N. Varney, Kai Sun, Victor Galitski, and Marcos Rigol, Physical Review Letters, 107, 077201, (12 August 2011).

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Engineers Solve Longstanding Problem in Photonic Chip Technology: Findings Help Pave Way for Next Generation of Computer Chips

2011-08-31T19:02:00.000-07:00

In that paper, the researchers describe a new technique to isolate light signals on a silicon chip, solving a longstanding problem in engineering photonic chips.

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Scientists Have New Help Finding Their Way Around Brain's Nooks and Crannies

2011-08-31T15:04:00.000-07:00

Easy access to detailed maps of myelination in humans and animals also will aid efforts to understand how the brain evolved and how it works, according to Van Essen.

Washington University graduate student Matthew Glasser developed the new technique, which combines data from two types of magnetic resonance imaging (MRI) scans that have been available for years.

This research was funded by the National Institutes of Health (NIH).

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Inexpensive catalyst that makes hydrogen gas 10 times faster than natural enzyme

2011-08-31T11:10:00.000-07:00

Stuffing Bonds

Electrons are often stored in batteries, but Bullock and his colleagues want to take advantage of the closer packing available in chemicals.

Two Plus Two Equals One

In real life, the protons would come from water, but since the team only examined a portion of the reaction, the researchers used water stand-ins such as acids to test their catalyst.

A Bauble for Energy

Like good gardeners, the team trimmed a few pendant amines off their catalyst, leaving only enough to make the protons stand out, ready to accept a negatively charged hydrogen atom.

Fastest Cat in the West

Provided by Pacific Northwest National Laboratory

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How Many Species On Earth? About 8.7 Million, New Estimate Says

2011-08-31T08:34:00.000-07:00

Furthermore, the study, published by PLoS Biology, says a staggering 86% of all species on land and 91% of those in the seas have yet to be discovered, described and catalogued.

"It is the same with biodiversity. Humanity has committed itself to saving species from extinction, but until now we have had little real idea of even how many there are."

The research is published alongside a commentary by Lord Robert May of Oxford, past-president of the UK's Royal Society, who praises the researchers' "imaginative new approach."

Drawing conclusions from 253 years of taxonomy since Linnaeus

"Given the looming problems of feeding a still-growing world population, the potential benefits of ramping up such exploration are clear."

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How Vampire Bats Find Veins

2011-08-31T05:48:00.000-07:00

Posted in: bat,dorsal root ganglia,heat sensing,Infrared,ion channel,membrane proteins,nerves,Neuroscience,physiology,pit viper,snake,trigeminal ganglia,TRPA,TRPV,TRPV1,vampire,Vampire bat

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New Depiction of Light Aids Telecommunications

2011-08-31T03:13:00.000-07:00

Detecting the polarization also lets users finely tune a laser. Such control can allow a laser to burn away one layer of material while leaving the other layers it passes through intact.

But complex light moves with both spin and orbital angular momentum, more or less like the movement of our moon as it spins on its axis and orbits Earth.

"The sphere facilitates understanding, showing phase vortices are on poles and vector beams are on the equator," explains Milione. "It organizes the relationship between these vortices of light."

The research was funded in part by Corning Inc. and the Army Research Office.

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Murderer Gets Reduced Sentence Because His Genes Made Him Do It

2011-08-31T01:08:00.000-07:00

Hey criminals! Here’s how you get out of taking full responsibility for your dastardly actions:

Fake your DNA sampleBlame it on your identical twin See if you have the genes that predispose you to whatever crime you’ve committed

Murderer Abdelmalek Bayout and his attorneys chose option three. Bayout admitted in 2007 to stabbing and killing Walter Felipe Novoa Perez in Italy. During the first sentencing, he was found to be mentally ill. This year, neuroscientists also found abnormalities in brain-imaging scans and five genes linked to violent behavior, including MAOA.

Although there have been numerous cases since 1994 in which the defense argued for leniency based on MAOA deficiency, this is the first case in which this tactic has been successful. Based on the scans and genetic testing results, the judge reduced Bayout’s sentence by another year.

Not everyone agrees with the judge’s decision.

"We don’t know how the whole genome functions and the [possible] protective effects of other genes," says Giuseppe Novelli, a forensic scientist and geneticist at the University Tor Vergata in Rome. Tests for single genes such as MAOA are "useless and expensive", he adds.

Even worse, this verdict could open the floodgates to claims of all sorts the more we know about genetic influences on behavior. That list above is just about to get longer.

Source: Scientific American

Image: “Structural (left) and functional (right) MRI scan data shows that subjects with the violence-related version of the MAO-A gene (MAOA-L) had reduced volume and activity of the anterior cingulate cortex (blue area in front part of brain at left and corresponding yellow area in at right), which is thought to be the hub of a circuit responsible for regulating impulsive aggression. The color-coded areas show where subjects with the L gene type differed from subjects with the H gene type.”

NIMH Clinical Brain Disorders Branch

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DNA Network Tweet Cloud

2011-08-30T22:34:00.000-07:00
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American Genes Don’t Exist

2011-08-30T18:58:00.000-07:00

Congratulations to Meb Keflezighi of Eritrean descent, who won the New York City Marathon last Sunday and was the first American to do so since 1982!
Why did I mention that he was born in Eritrea? Because critics say that an immigrant like Keflezighi who moved to the U.S. at age 12 isn’t a legitimate American.
A post on Letsrun.com said:
Give us all a break. It’s just another African marathon winner.
How about making that African-American?
Silly me. I thought that naturalized American citizens equal American citizens at birth with the same rights and privileges (with the exception of getting to be the President of the United States). Leaving that debate aside, however, the belief that East Africans are genetically endowed for marathon running has also clouded Keflezighi’s celebration.
The success of distance runners from Kenya and Ethiopia has fostered a lore of East Africans as genetically gifted, unbeatable, dominant because of their biology. Scientists have looked for — but not found — genes specific to East Africans that could account for their distance ability, said John Hoberman, a professor at the University of Texas at Austin who studies race and sports.
Truly American? Debate Dogs a Triumph in the Marathon – NYTimes.com
No doubt Keflezighi has genes which enhance his physiological capabilities for endurance and other traits found in winning marathoners. This does not mean that Keflezighi is any more or less American than other non-East African runners who have the same genes.
The Oxford English Dictionary defines “nationality” in two parts:
nationality
noun (pl. nationalities) 1 the status of belonging to a particular nation. 2 an ethnic group forming a part of one or more political nations.
Even though ethnic groups are mentioned, the U.S. is clearly a country of many ethnic groups so genes should not be part of the debate when discussing whether someone is American or not.
Quite frankly, I’m not even sure what makes a person American and I don’t think anyone else does either. I hold an American passport and spent the years between ages 6 and 26 in the U.S. I’ve lived in six different countries in the past 10 years and as a result, my national identity is slightly muddled. My son is even more confused. He holds an American passport as well but has never lived in the U.S although he’s lived in four different countries in his seven years. He was born in Japan so some days he says that he’s Japanese and now that he lives in Singapore, he sometimes says he’s Singaporean. I’m sure some people would say he’s not American at all.
It might be simpler to say we’re global citizens with ties to more than one country. Truth be told, I’m proud to say I’m Chinese-American with the accent to prove it.
Edited to add this video of Meb Keflezighi on David Letterman:
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Genetic Genealogy on Faces of America

2011-08-30T16:46:00.000-07:00

Quite a line-up of celebrities!
Eva Longoria, Meryl Streep, Mario Batali, Stephen Colbert, Malcolm Gladwell, Yo-Yo Ma, Mike Nichols, Kristi Yamaguchi, Elizabeth Alexander, Queen Noor and Louise Erdrich have all submitted DNA tests for a new PBS television series FACES OF AMERICA.

Faces of America with Henry Louis Gates, Jr. airs on Wednesdays, February 10 – March 3, 2010 from 8-9 p.m. ET on PBS.
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Video: Knome’s Ari Kiirikki Speaks with Medgadget

2011-08-30T14:34:00.000-07:00

via Medgadget
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Knowledge about Genetic Risk is Power or is it Fear?

2011-08-30T11:25:00.000-07:00

A little over two years ago, I confessed that I was “just a little scared of genetic testing.” I have two young children and almost every day I see traits in them that I’m pretty sure they inherited from me whether via genes or behavior. If you’re a parent, I’m sure you can imagine that there’s a lot of self-blame going on in our house.
So when it comes to genetic testing, I should want to know but I don’t. At least not right this minute. Haven’t I got enough to worry about?
From Middletown Journal’s month-long series on the battle against cancer – Many with cancer gene don’t want to know.
There are people out there who may not want to know. There’s a subset of people who if they knew would act on the information and benefit and there are others who would rather bury their heads in the sand.
~Dr. Michael Watson, director of the American College of Medical Genetics
NIH Director Francis Collins, however, falls squarely in the camp of those who not only want to know, they act on the info. Well done!
Collins hits the gym following genetic testing from The Great Beyond, Nature blog
Maybe if a genetic test could motivate me to go to the gym and lose weight, it would be worth it.
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DNA{wesome}

2011-08-30T09:24:00.000-07:00

That’s right, baby!
via Buzzfeed
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Genetics = Real Science

2011-08-30T06:03:00.000-07:00

Matchmaking services are adding DNA testing to their list of offers. The DNA test analyzes HLA genes of the immune system that influence a person’s body odor. The theory is that people are attracted to those whose HLA genes and body odor differ from their own so that their potential offspring have the possibility of inheriting a more varied set of HLA genes leading to enhanced health due to a stronger immune system.
In an Associated Press article, Dr. Rocio Moran, medical director of the General Genetics Clinic at the Cleveland Clinic said:
They are just trying to make a buck. That if it’s genetic, it must be real science.
That’s the kind of argument some shady companies are making about direct-to-consumer genetic testing. It reminds me of the ruckus earlier this year over companies that offer genetic testing to parents who’re interested in having their children tested for athletic prowess and other abilities.
If it’s genetic, it must be real science.
If it’s science, it must be true.
Anyone living in the real world knows that genetics and science can only carry you so far. In the end, what it comes down to is the kind of person you are in spite of your genes. That doesn’t mean a genetic test is worthless. If you’re the kind of person that thinks a DNA test holds some kind of magic then maybe you will be able to find a mate who thinks the same way. After all, there’s a lid for every pot.
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Lopez Tonight First Late-Night Show to Offer DNA Testing

2011-08-30T02:03:00.000-07:00
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Larry David’s DNA Test

2011-08-29T23:51:00.001-07:00

I’d like to know which loci they used to decide he is 37% native American!
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Did you know Drug Testing

2008-05-01T23:44:00.000-07:00
Did you know Drug Testing It is becoming more and more common for drug testing to be used during a custody dispute or evaluation. With recreational drug use increasing every year, the chance that one or both of the parents involved in a custody battle has used drugs goes up proportionately. Accusations of drug use, whether true or false, almost always result in the ordering of drug testing by the court. A drug test can be a valuable tool to assist in determining the fitness of a particular parent, but the use of this tool must be balanced against the fact that drug testing is not always accurate. Needless to say, a "false positive" result on a drug test can destroy any chance that you had for gaining custody. Should you be asked (or ordered) to take a drug test, follow the guidelines below to ensure that your rights are preserved during this process.
Do you know Drug Testing If you are asked to submit to a drug test, always say "yes", but do not commit to a test date before you consult with your attorney. Inform the person asking that you are willing to be drug tested but that you will need to consult with your attorney privately and clear it with him first. There may be valid reasons why your attorney would not want you to be tested.
If you consent to drug testing, always schedule a private test first. Pay for the test in cash, NOT with a check or credit card. Ask that the results be sent to your attorney's office- this is safer than having them sent to your home or work address. Once you have the results you can decide how to proceed. If the test comes back positive, ask that another test be performed or that another type of test be used.
Sit down and make a comprehensive list of all prescription drugs, over-the-counter medications and foods that you've taken in the last several months. Many prescription drugs, over-the-counter medications and even foods can cause "false positives" on drug tests. All drugs alter body chemistry; after all, that is why they're taken. Unfortunately, changes in body chemistry can fool some drug tests and produce inaccurate results ("false positives").
Ask the company doing the drug test to provide you with information on the kind of test that will be done. Also ask the company for a list of all prescription drugs, over-the-counter medications and foods that may interfere with the drug test results. If the company refuses to provide such a list, instruct your attorney to subpoena a list from them. You may also do your own research to find out what medicines or foods could cause the drug test to be invalid.
Request a copy of the laboratory's certification for drug testing, then investigate. What is their "false positive" rate? Has the laboratory's certification ever been suspended, revoked? Has the company ever been cited or found to be in violation of the certification? How long have they been in business? The answers may show that the company cannot be relied upon to provide accurate results.
Do you know Drug Testing If you're being asked to take a drug test, always insist that your spouse be tested too. If you're willing to do it, they should be willing to do it. Insist that the cost of the testing be split 50/50 between you.
Drinking plenty of water and juices helps rid the body of impurities. Stay away from coffee, tea and carbonated beverages if possible. Also refrain from drinking alcohol. While alcohol is being metabolized the body does little else in the way of processing other foods and ingestibles, preferring to concentrate on the alcohol because it is an extremely rich source of energy and sugars. In other words, consuming alcohol slows the body's process of clearing itself of other impurities.
Whenever possible, schedule your drug test for the afternoon, not in the morning. Chemical impurities are at higher concentrations in the body early in the day than later in the day (when your body has had some time to process them). Urine, for example, is typically most concentrated in the morning. If the testing laboratory insists that you schedule a morning drug test, agree, then call in on the day of the test and tell them that you will be late due to unforeseen circumstances (you got stuck in traffic, the car broke down, the bus was late, etc). Reassure them that you will be in to take the test as soon as you possibly can, then show up in the afternoon. If they want to reschedule you for another morning test, refuse. Tell them that you are here now, that you want to take your test now and that you don't want to have to come back again. If they refuse, insist that they give you a written note stating that they would not allow you to take the drug test at this time. Drug Test Interaction With Medicines And Foods
Be aware that certain foods and over-the-counter medications can cause you to test "positive" for various kinds of drugs.
Poppy seeds, for example, can show up on a drug test as morphine.
Cold remedies that contain codeine can also cause a positive result for morphine.
Valium reportedly can produce erroneous indications of PCP (Phencyclidine), and other cold remedies can apparently produce false reports of methamphetamine usage.
Dextromethorphan can produce a falsely positive qualitative urine opiate screening.
The widespread availability of hemp-containing products, including everything from hemp-seed oil nutritional supplements to hemp-seed candy, cookies, cheese, bread, cooking oil, and general seasoning, means that ingesting ANY of these products could potentially cause a false positive result on a test for marijuana.
Ibuprofen, contained in Advil, Nuprin, and Mortin, can make a positive result for marijauna. The EMIT test (an immunoassay test) has therefore been changed to use a different enzyme to eliminate false positives due to Ibuprofen. Ibuprofen in very high doses will still interfere with both the EMIT and the GC/MS (Gas Chromatograph/Mass Spectrometer) test. Ibuprofen: Ibuprofen is a common pain reliever that (even in low dosages) used to cause a false THC positive on the EMIT test. The EMIT has been changed to use a different enzyme to eliminate false positives due to Ibuprofen. Ibuprofen in very high doses will still interfere with both the EMIT and the GC/MS. There is some conflicting data here because some sources say that the GC/MS tests can distinguish between Ibuprofen and THC (as well as other over-the-counter drugs).
Common over the counter cold, asthma, and allergy remedies and diet pills such as Diatec, Dexatrim, Cotylenol, Triaminic, Primatene, Bronkotabs, and Nyquil can show up as positive for amphetamines.
Do you know Vicks Formula-44, Demerol, Mydol, Primatene-M and common prescription antidepressants such as Elavil and Tofanil can show up as positive for opiates such as opium and heroin.
Ephedra, also known as Ephedra Alkaloids or 'MaHuang Extract' has a chemical structure which is closely related to amphetamine, and can reportedly give a false positive for amphetamines. Often sold as an 'energy pill' it is an effective decongestant in low doses.
Valerian root is reported to cause false positives for benzodiazepines. Other herbal supplements such as Kava Kava and St Johns Wort may also affect body chemistry such that false positives are produced.
Zoloft is reported to cause false positives in urine screens, although for what specific substance isn't clear.
Do you know Primatene can also show up as positive for barbiturates, and Benadryl can show up positive for Methadone.
Some additional over the counter medicines that may cause various kinds of drug test interactions include Alka-Seltzer plus, Allerest, Bronkaid, Contac, Donnagel, Sinuntab, and Sudafed. Common Testing MethodsSeveral different methods of drug testing are available. Each has its advantages and disadvantages.
Urine TestThe most common form of drug testing is to analyze a sample of urine for traces of drugs. A positive test result only indicates that a drug was used sometime in the recent past; it does not tell whether or not the person was under the influence when giving the sample. For detecting alcohol, a urine test is accurate but is not used because it correlates poorly with blood levels when usual collection procedures are used. Blood TestA blood test measures the actual amount of alcohol or other drugs in the blood at the time of the test. Unlike the urine test, the results tell whether or not the person was under the influence at the time the test was done. Saliva and Hair TestsResearchers have begun studying the testing of hair and saliva to detect alcohol and other drug use. Early results suggest that testing saliva may be a valid testing method. The accuracy, reliability, and interpretation of hair testing have been determined to be useable in a court of law, although the actual accuracy is still open to some debate. Breath-Alcohol TestA breath test is the most common method of testing for alcohol. The results tell if the individual is under the influence of alcohol at the time the breath sample is taken. Alcohol is metabolized out of the body in a relatively short period of time; therefore, unless a person is under the influence at the time the specimen is collected, a breath test for alcohol will not detect alcohol use that occurred a day earlier.

Did you know Genetic fingerprinting

2008-04-27T22:06:00.000-07:00
Did you know genetic Fingerprinting (also called DNA testing, DNA typing, or DNA profiling) is a technique used to distinguish between individuals of the same species using only samples of their DNA. Although two individuals will have the vast majority of their DNA sequence in common, DNA profiling exploits highly variable repeat sequences called VNTRs. These loci are variable enough that two unrelated humans are unlikely to have the same alleles. The technique was first reported in 1984 by Dr. Alec Jeffreys at the University of Leicester, and is now the basis of several national DNA identification databases.
Reference samples
DNA identification must be done by an extraction of DNA from substances such as:
Personal items (e.g. toothbrush, razor, ...)
Banked samples (e.g. banked sperm or biopsy tissue)
Blood kin (biological relative)
Human remains previously identified
Reference samples are often collected using buccal swab.
Variations of VNTR allele lengths in 6 individuals.

Did you know DNA supercoil

2008-04-27T22:02:00.000-07:00

Did you know In a "relaxed" double-helical segment of DNA, the two strands twist around the helical axis once every 10.4 base pairs of sequence. Adding or subtracting twists, as some enzymes can do, imposes strain. If a DNA segment under twist strain were to be closed into a circle by joining its two ends and then it is allowed to move freely, the circular DNA would contort into new shape, such as a simple figure-eight. Such a contortion is a supercoil.
The simple figure eight is the simplest supercoil, and is the shape a circular DNA assumes to accommodate one too many or one too few helical twists. The two lobes of the figure eight will appear rotated either clockwise or counterclockwise with respect to one another, depending on whether the helix is over or underwound. For each additional helical twist being accommodated, the lobes will show one more rotation about their axis.
The noun form "supercoil" is rarely used in the context of DNA topology. Instead, global contortions of a circular DNA, such as the rotation of the figure-eight lobes above, are referred to as writhe. The above example illustrates that twist and writhe are interconvertible. "Supercoiling" is an abstract mathematical property, and represents the sum of twist and writhe. The twist is the number of helical turns in the DNA and the writhe is the number of times the double helix crosses over on itself (these are the supercoils). The relationship of twist, writhe and supercoiling is expressed as the equation:
S = T + W.
Extra helical twists are positive and lead to positive supercoiling, while subtractive twisting causes negative supercoiling. Many topoisomerase enzymes sense supercoiling and either generate or dissipate it as they change DNA topology. DNA of most organisms is negatively supercoiled.
Do you know In part because chromosomes may be very large, segments in the middle may act as if their ends are anchored. As a result, they may be unable to distribute excess twist to the rest of the chromosome or to absorb twist to recover from underwinding--the segments may become supercoiled, in other words. In response to supercoiling, they will assume an amount of writhe, just as if their ends were joined.
Supercoiled DNA forms two structures; a plectoneme or a toroid, or a combination of both. A negatively supercoiled DNA molecule will produce either a one-start left-handed helix, the toroid, or a two-start right-handed helix with terminal loops, the plectoneme. Plectonemes are typically more common in nature, and this is the shape most bacterial plasmids will take. For larger molecules it is common for hybrid structures to form - a loop on a toroid can extend into a plectoneme. If all the loops on a toroid extend then it becomes a branch point in the plectonemic structure.

Did you know DNA Data Bank

2008-04-27T22:01:00.002-07:00
Did you know a serial predator is on the loose in Reno, Nevada. He’s already murdered one young victim – 19-year-old Brianna Denison – and DNA evidence connects him to at least two other sexual assaults. As investigators worked to identify this monster, they ran into a huge roadblock. Detectives thought that there might be more attacks linked to the same suspect – and that the predator might be someone who lready has a criminal record. In Nevada, as in most states, every convicted felon must submit a DNA sample. But here’s the problem: in Washoe County, where Reno is located, an estimated 3000 DNA samples were sitting on a shelf, waiting to be analyzed and added to the database. Lack of funds to do all the work had created the backlog. Whether the killer’s DNA was among those 3000 samples – or if they contained evidence matching him to yet another case – the police had no way of knowing. Private citizens, unwilling to accept that, helped raise $160,000 so that the backlog could be cleared. Unfortunately, the answers police needed weren’t in there.
Even more unfortunately, the situation in Washoe County is far from unique. The Justice Department recently admitted that the FBI has a huge backlog of DNA from convicted criminals waiting to be tested – nearly 200,000 samples. And the backlog is growing. There’s no question that the FBI needs more funding for this important job, because I think that we need to expand the bureau’s nationwide DNA data bank, known as CODIS, even further. I’d like to see every state have mandatory collection of DNA from everybody charged with a felony, not just convicted of one. I’d like all of that information in CODIS, so that every law enforcement agency in the country has access to it.
Imagine if there was a national DNA data bank that was up-to-date, not years behind in its work. It would help solve hundreds of crimes – and it would help absolve many accused people of crimes they didn’t commit. We need to be uniformly collecting DNA profiles from both convicted AND accused criminals across the country. And we must make sure that everyone involved, from the FBI to local law enforcement, has all the resources they need to make that happen.

Did you know DNA Base Pairing Principle

2008-04-27T22:01:00.001-07:00
Did you know the Base Pairing Principle is: Complementary base pairs are: adenine and thymine (A - T )guanine and cytosine (G - C)
The base pairing is called complementary because there are specific geometry requirements in the formation of hydrogen bonds between the heterocylic amines. Heterocyclic amine base pairing is an application of the hydrogen bonding principle. In the structures for the complementary base pairs given in the graphic on the left, notice that the thymine - adenine pair interacts through two hydrogen bonds represented as (T=A) and that the cytosine-guanine pair interacts through three hydrogen bonds represented as (C=G).
Although other base pairing-hydrogen bonding combinations may be possible, they are not utilized because the bond distances do not correspond to those given by the base pairs already cited. The diameter of the helix is 20 Angstroms.

Did you know alternative double-helical structures

2008-04-27T21:57:00.000-07:00
Did you know DNA exists in many possible conformations. However, only A-DNA, B-DNA, and Z-DNA have been observed in organisms. Which conformation DNA adopts depends on the sequence of the DNA, the amount and direction of supercoiling, chemical modifications of the bases and also solution conditions, such as the concentration of metal ions and polyamines. Of these three conformations, the "B" form described above is most common under the conditions found in cells. The two alternative double-helical forms of DNA differ in their geometry and dimensions.
The A form is a wider right-handed spiral, with a shallow, wide minor groove and a narrower, deeper major groove. The A form occurs under non-physiological conditions in dehydrated samples of DNA, while in the cell it may be produced in hybrid pairings of DNA and RNA strands, as well as in enzyme-DNA complexes. Segments of DNA where the bases have been chemically-modified by methylation may undergo a larger change in conformation and adopt the Z form. Here, the strands turn about the helical axis in a left-handed spiral, the opposite of the more common B form. These unusual structures can be recognized by specific Z-DNA binding proteins and may be involved in the regulation of transcription.

Did you know Chemical differences between DNA & RNA

2008-04-27T21:55:00.000-07:00
Did you know both RNA and DNA are composed of repeated units. The repeating units of RNA are ribonucleotide monophosphates and of DNA are 2'-deoxyribonucleotide monophosphates.
Both RNA and DNA form long, unbranched polynucleotide chains in which different purine or pyrimidine bases are joined by N-glycosidic bonds to a repeating sugar-phosphate backbone.
The chains have a polarity. The sequence of a nucleic acid is customarily read from 5' to 3'. For example the sequence of the RNA molecule is AUGC and of the DNA molecule is ATGC
The base sequence carries the information, i.e. the sequence ATGC has different information that AGCT even though the same bases are involved.
Consequences of RNA/DNA chemistry
The DNA backbone is more stable, especially to alkaline conditions. The 2' OH on the RNA forms 2'3'phosphodiester intermediates under basic conditions which breaks down to a mix of 2' and 3' nucleoside monophosphates. Therefore, the RNA polynucleotide is unstable.
The 2' deoxyribose allows the sugar to assume a lower energy conformation in the backbone. This helps to increase the stability of DNA polynucleotides. The following link shows 3-D models of the DNA and RNA nucleotides.
Cytidine deamination to Uridine can be detected in DNA but not RNA because deamination of Cytidine in DNA leads to Uridine not Thymidine. Uridine bases in DNA are removed by a specific set of DNA repair enzymes and replaced with cytidine bases.

2008-04-27T21:51:00.000-07:00
Do you know Live is DNA
As fans of the “CSI” television shows know, DNA testing is an amazing tool for solving crimes. That said, the potential benefits of RNA / DNA’s ability to enhance and preserve the crime of aging makes it the most advance dynamic formula on the market today. Full Spectrum RNA/DNA HGH with IGF-1 and GHRH not only incorporates all of the elements of HBC’s renound Full Spectrum Growth Hormone Formula, but it now has recombinant DNA and RNA in multiple potencies for a broad range of activity. It will support and rapidly encourage Growth Hormone release, production, assimilation as it renews and replenishs overrall health faster than any Growth Hormone formulation on the market today.
In the body, RNA helps to transfer genetic messages from the DNA to guide the manufacture of proteins using the amino acids that are extracted from foods or created by the body. What this means in practical terms for medicine is that the RNA has the ability to direct the synthesis of proteins. This is an amazingly powerful concept. It doesn’t matter if the proteins are involved in heart disease, cholesterol metabolism, or weight management. By modulating the levels of RNA one has the ability to specifically affect the levels of any protein in the body in a specific way. This process of modifying the RNA to make changes in the protein is a naturally occurring regulatory process. This natural process of RNA regulation is used by bacteria, plants, and animals as a central regulatory system. For instance, when your body is exposed to heat, your body responds by making a group of proteins called heat shock, or stress activated proteins. The way that your body translates the information to make these proteins after the body has sensed heat, or stress is by modifying the levels of specific RNAs that are necessary to direct the synthesis of the specific proteins. The way that your body is able to respond to environmental changes is by modifying the RNA levels so that different proteins can be made in response to a situation.

Cloning DNA

2008-04-21T23:46:00.000-07:00
The word "clone" has several different meanings in biology. As a noun, a clone is an identical genetic copy of either a piece of deoxyribonucleic acid (DNA), a cell, or a whole organism. Identical twins are clones, as are two daughter cells produced by mitosis. As a verb, "to clone" means to produce identical genetic copies of either pieces of DNA, cells, or whole organisms.
DNA cloning is usually performed for one of two reasons: either to produce a lot of identical DNA for further study, or to use the DNA in an intact organism to produce useful proteins. In the first case, for example, a researcher might want to determine the DNA sequence of the gene or study the factors that control its expression (transcription). In the second case, one might want to produce large amounts of a medically useful protein, such as insulin or growth hormone.
Large quantities of identical DNA can be produced via the polymerase chain reaction (PCR), but only if the DNA pieces are rather short (less than about 40 kilobases [kb], and usually closer to 1 kb). For larger pieces, or for protein production, DNA is almost always cloned in bacteria.

Techniques for cloning change rapidly, but the overall picture is as follows, using the insulin gene as an example:
• Isolate and purify all the DNA from a sample of human cells. Break apart the cells and then wash, centrifuge, and use other purification techniques.
• Cut the DNA into millions of small fragments using restriction enzymes. Each DNA piece may be as large as 10 kb, but is more commonly 1 to 5 kb.
• Mix the DNA fragments with plasmids that have been cut with the same restriction enzymes. Add DNA ligase, an enzyme that joins the human DNA fragments to the plasmids and seals the circles up again. By using the right ratio of plasmid to fragment, a researcher can ensure that each plasmid harbors at most one human DNA fragment. With luck, one DNA fragment will contain the insulin gene.
• Cause a bacterial culture to take up the plasmids. This can be done by ionic shock. Again, adjusting the ratio can ensure one plasmid per bacterium. The plasmid used usually carries a gene for antibiotic resistance.
• Grow the bacteria on antibiotic-containing agar plates, spread very thinly. The antibiotic will kill bacteria that didn't take up the plasmid. Single bacteria give rise to colonies, which will appear as small spots on the plate. The resulting bacterial colonies are called a genomic library.
• To find which of the colonies includes the human insulin gene, use a probe. This is typically a radioactive segment of DNA whose sequence is complementary to part of the insulin gene, allowing it to bind. Apply the probe, and see where it sticks.
• Isolate that colony, and let it multiply in a rich broth. Each bacterium will replicate the insulin gene, providing many copies to work with. Including the appropriate promoters and other regulatory factors will prompt the bacteria to synthesize the human insulin protein, which can then be purified for medical use.
Several modifications of this technique allow cloning of even larger DNA fragments. Cloning into the bacterial virus bacteriophage λ allows use of fragments up to about 20 kb. In this scheme, the bacteriophage infects cultured bacteria and directs production of the gene of interest. Cosmid vectors can package about 44 kb. These are plasmids containing special sequences from bacteriophage (λ) that promote very efficient sealing of the plasmid circle. Bacterial artificial chromosomes (BACs) can contain up to 300 kb, and yeast artificial chromosomes (YACs), grown in yeast cells, can handle up to 2,000 kb, or 2 megabases.
Cloning an Animal
Since the nucleus of virtually every animal cell contains the entire genome of the animal, it might seem easy enough to clone an animal by placing the nucleus in an egg cell from which the nucleus has been removed. While this was tried many times, it was never successfully accomplished until 1996, in the creation of the sheep Dolly by Ian Wilmut and colleagues in Scotland. Dolly was the first mammal created using the nucleus from a cell of a mature adult mammal. Prior to this feat, it had been thought that normal mammalian development caused irreversible changes in some portion of the DNA that prevented it from acting as embryonic DNA does.
Amphibians have long been cloned from adult cells, but they invariably die in the tadpole stage. Adult amphibians, though, have been successfully cloned for many years from embryo nuclei. In this technique, nuclei from cells of an early embryo are extracted using a very fine glass pipette and placed in egg cells that have been shed by a female amphibian such as a frog (after removing the unfertilized egg cell nucleus). In 1998, mice were cloned from adult somatic cell nuclei, using the same technique as was used for Dolly. This technique may become especially important for producing large numbers of transgenic animals, for use in research or production of specialized proteins. However, cloned mammals are generally not very healthy. Apparently development is not quite normal when it begins with a nucleus that has already existed in another animal, compared to a genome derived from a sperm and an egg.

Damage To Sperm DNA Affects Older Men's Chances Of Fathering Children

2008-04-21T23:41:00.000-07:00
Do you know Dr. Sergey Moskovtsev, of the Mount Sinai Hospital, Toronto, Canada, told the conference that an increase in the average maternal and paternal ages at the time of attempted first pregnancy made this particularly significant. "Older men tend to reproduce with older women", he said, "and the combination of increased female factor infertility, increased sperm DNA damage, low levels of DNA repair, and increased abnormalities in conventional semen parameters present in this population will have a pronounced impact on their reproductive potential."
Do you know Dr. Moskovtsev and his team examined the relationship of DNA integrity, a novel semen parameter related to fertility potential, to age in 2134 men presenting for evaluation of their fertility. They identified damaged and normal sperm by means of a fluorescent dye that attaches to DNA, staining red when attached to damaged DNA and green to normal. Using 20 000 sperm per sample, they calculated DNA damage in each specimen via the ratio of red to green plus red. They found that DNA damage was significantly higher in men over 45 years old than in all younger age groups, and that the damage was doubled in those men 45 years and older compared with those less than 30 years old.
"Sperm DNA damage cannot be repaired", said Dr. Moskovtsev, "and appears to be a marker of reduced fertility potential rather than a predictor of fertility. Men with normal DNA integrity may be infertile for various reasons. We need to investigate the possibility of developing techniques to identify and select sperm without DNA damage for use in assisted reproduction techniques." IVF and ICSI cannot overcome abnormalities in DNA integrity, said Dr. Moskovtsev, who intends to follow up his work by investigating further the role of abnormalities in protamine, a protein found in sperm. This is one of the putative causes of reduced DNA integrity in sperm. He will also look at older and younger groups of men with abnormal DNA integrity to see if there are differences in the mechanism of DNA damage between the two groups.
"The effect of age on male fertility is particularly interesting because of the growth in the number of men choosing to father children at older ages", he said. "In the United States, the birth rate for fathers older than 35 years increased by almost 20% between 1980 and 1995. ESHRE has reported that there had been an increase in the number of men between 50 and 65 years of age attending andrology centres over the same time period, and our study confirms these observations -- men over 40 made up almost 25% of our patient population.
"Many of these older couples will have trouble in conceiving and resort to IVF and ICSI", he said. "This will bypass the natural selection of normal, healthy sperm and may lead to fertilisation by sperm with damaged DNA which can result in early embryonic loss or the birth of unhealthy offspring."
An assessment of DNA damage in sperm should be an essential part of any examination of the fertility potential of older men, he said.

DNA damage in infertile men's sperm

2008-04-21T23:28:00.000-07:00
The sperm of infertile men may look and behave normally, but have hidden genetic damage that could stop them producing a child.
Approximately half of all infertility is thought to be due to problems on the man's side.
However, the precise mechanism of many of these cases remains unexplained.
A team of researchers from Cleveland, Ohio in the US looked at the sperm of 92 men undergoing fertility treatment and compared it with the sperm of 16 fertile men.
Many of the infertile men had obviously defective sperm, either abnormal-looking or unable to swim normally.
However, 25% of the infertile men had normal-looking sperm.
All the sperm were genetically tested to look for signs of damaged DNA in their genetic structure.
DNA problems
As expected, the abnormal sperm had a high rate of DNA damage.
But just under half the men with normal-appearing sperm also had signs of this damage.
The finding is a concern because of pre-existing fears that a particular fertility technique might be passing genetic defects from infertile fathers to their children.
Normal in-vitro fertilisation (IVF) involves simply putting millions of sperm and a number of eggs in a dish together and hoping the sperm will perform their usual function of swimming up to the egg, penetrating its surface and triggering cell division into an embryo.
However, where sperm are few, or poor swimmers, or where IVF has failed to work, a technique called intra-cytoplasmic sperm injection (Icsi) is used.
In this, a single sperm is selected by lab workers and physically injected into the egg.
Defects
Studies have suggested a higher rate of infertility-linked birth defects among Icsi-conceived babies, and there are concerns that babies born under these circumstances will be more likely to be infertile themselves.
There are also concerns that Icsi babies might be more prone to cancer - but there is no study evidence so far to back this up.
The latest research supports those fears, by highlighting the high level of DNA damage in the sperm.
Dr Ramadan Saleh, who authored the paper in the journal Fertility and Sterility, said: "Icsi is the technique used primarily for the treatment of infertile men with very poor sperm quality.
"The use of DNA-damaged sperm to fertilise the egg may have adverse consequences such as fertilisation failure, early embryo death, miscarriage, childhood cancer and infertility in the offspring."
He suggested that infertile men might be better spotted using DNA damage analysis of their sperm rather than simply examining its physical appearance.

DNA damage in human sperm is related to urinary levels of phthalate monoester and oxidative metabolites

2008-04-21T23:27:00.001-07:00
BACKGROUND: The ubiquitous use of phthalate esters in plastics, personal care products and food packaging materials results in widespread general population exposure. In this report, we extend our preliminary study on the relationship between urinary concentrations of phthalate metabolites and sperm DNA damage among a larger sample of men and include measurements of mono-(2-ethyl-5-hydroxyhexyl) phthalate (MEHHP) and mono-(2-ethyl-5-oxohexyl) phthalate (MEOHP), two oxidative metabolites of di-(2-ethylhexyl) phthalate (DEHP). METHODS: Among 379 men from an infertility clinic, urinary concentrations of phthalate metabolites were measured using isotope-dilution high-performance liquid chromatography-tandem mass spectrometry. Sperm DNA damage measurements, assessed with the neutral comet assay, included comet extent (CE), percentage of DNA in tail (Tail%) and tail distributed moment (TDM). RESULTS: Monoethyl phthalate (MEP), a metabolite of diethyl phthalate, was associated with increased DNA damage, confirming our previous findings. Mono-(2-ethylhexyl) phthalate (MEHP), a metabolite of DEHP, was associated with DNA damage after adjustment for the oxidative DEHP metabolites. After adjustment for MEHHP, for an interquartile range increase in urinary MEHP, CE increased 17.3% [95% confidence interval (CI) = 8.7-25.7%], TDM increased 14.3% (95% CI = 6.8-21.7%) and Tail% increased 17.5% (95% CI = 3.5-31.5%). CONCLUSIONS: Sperm DNA damage was associated with MEP and with MEHP after adjusting for DEHP oxidative metabolites, which may serve as phenotypic markers of DEHP metabolism to ‘less toxic’ metabolites. The urinary levels of phthalate metabolites among these men were similar to those reported for the US general population, suggesting that exposure to some phthalates may affect the population distribution of sperm DNA damage.

Oxidative Stress/DNA Damage and DNA Repair

2008-04-21T23:22:00.000-07:00
Oxidative stress is produced in cells by oxygen-derived species resulting from cellular metabolism and from interaction with cells of exogenous sources such as carcinogenic compounds, redox-cycling drugs and ionizing radiations. DNA damage caused by oxygen-derived species including free radicals is the most frequent type encountered by aerobic cells. DNA damage caused by oxygen-derived species including free radicals is the most frequent type encountered by aerobic cells. When this type of damage occurs to DNA, it is called oxidative DNA damage and it can produce a multiplicity of modifications in DNA including base and sugar lesions, strand breaks, DNA-protein cross-links and base-free sites. Accurate measurement of these modifications is essential for understanding of mechanisms of oxidative DNA damage and its biological effects. Numerous DNA lesions have been identified in cells and tissues at steady-state levels and upon exposure to free radical-generating systems. Data accumulated over many years clearly show that oxidative DNA damage plays an important role in a number of disease processes. Thus, oxidative DNA damage is implicated in carcinogenesis and neurodegenerative diseases such as Alzheimer’s disease. There is also strong evidence for the role of this type of DNA damage in the aging process. The accumulation of oxidative DNA damage in non-dividing cells is thought to contribute to age-associated diseases. DNA damage is countered in cells by DNA repair, which is a basic and universal process to protect the genetic integrity of organisms. The genomes of organisms encode DNA repair enzymes that continuously monitor chromosomes to correct DNA damage. Multiple processes such as base- and nucleotide-excision pathways exist to repair the wide range of DNA damages. If left unrepaired, oxidative DNA damage can lead to detrimental biological consequences in organisms, including cell death, mutations and transformation of cells to malignant cells. Therefore, DNA repair is regarded as one of the essential events in all life forms. There is an increasing awareness of the importance of oxidative DNA damage and its repair to human health. Thus, it becomes exceedingly important to understand, at the fundamental level, the mechanisms of oxidative DNA damage, and its processing by DNA repair enzymes as well as how unrepaired DNA lesions may lead to cytotoxicity, mutagenesis and eventually to diseases and aging. More detailed knowledge of mechanisms of DNA damage and repair might allow us to modulate DNA repair. This could lead to drug developments and clinical applications including the improvement of cancer therapy by inhibiting DNA repair in drug- or radiation-resistant tumors and/or the increase in the resistance of normal cells to DNA damage by over-expressing DNA repair genes.

Watercress Reduce DNA Damages Leading to Cancer

2008-04-21T23:19:00.000-07:00

Did you know that daily consumption– about 85g daily– of fresh watercress can significantly reduce DNA damage to blood cells due to free radicals, and thus reduce cancer risks? Watercress is a rich source of phytochemicals called glucosinolates, and also contains phenolic compounds and flavonoids.
According to a study published in this month’s American Journal of Clinical Nutrition, a watercress diet resulted to
significant reduction in DNA damage to lymphocytes (white blood cells), by 22.9 per cent.
reduction in DNA damage to lymphocytes (white blood cells) when a sample was challenged with the free radical generating chemical hydrogen peroxide, by 9.4%
reduction in blood triglyceride levels, by an average of 10%
significant increase in blood levels of lutein and beta-carotene, which have antioxidant activity, by 100% and 33% respectively (higher intakes of lutein have also been associated with a lower incidence of eye diseases such as cataract and age-related macular degeneration).

Repair of clustered uracil DNA damages in Escherichia coli

2008-04-21T23:18:00.000-07:00
Multiply damaged sites (MDS) are defined as greater than/equal to two lesions within 10–15 bp and are generated in DNA by ionizing radiation. In vitro repair of closely opposed base damages =" src="http://nar.oxfordjournals.org/math/ge.gif" border=0>2 bp apart results in a double strand break (DSB). This work extends the in vitro studies by utilizing clusters of uracil DNA damage as model lesions to determine whether MDS are converted to DSBs in bacteria. Lesions were positioned within the firefly luciferase coding region, transformed into bacteria (wild-type, uracil DNA glycosylase-deficient, ung–, or exonuclease III and endonuclease IV-deficient, xth–nfo–) and luciferase activity measured following repair. DSB formation was expected to decrease activity. Two closely opposed uracils separated by 7 bp decreased luciferase activity in wild-type and xth–nfo–, but not ung– bacteria. Growth of bacteria to obtain plasmid-containing colonies demonstrated that the plasmid was destroyed following the mis-repair of two uracils positioned 7 bp apart. This study indicates a DSB is formed when uracil DNA glycosylase initiates repair of two closely opposed uracils 7 bp apart, even in the absence of the major apurinic endonucleases. This work supports the in vitro studies and demonstrates that DNA repair is not always advantageous to cells.

Diabetes Damages DNA In Men's Sperm And May Affect Fertility

2008-04-21T23:16:00.000-07:00
Scientists have found that sperm from diabetic men have greater levels of DNA damage than sperm from men who do not have the disease. They warn that such DNA damage might affect a man's fertility. In the first study [1] to compare the quality of DNA in sperm from diabetic and non-diabetic men, the researchers from Belfast, Northern Ireland showed that the DNA in the nuclei of the sperm cells had greater levels of fragmentation in diabetic men (52%, versus 32% in non-diabetic men), and that there were more deletions of DNA in the tiny, energy-generating structures in the cells called mitochondria (4 versus 3). Dr Ishola Agbaje, who undertook the research published online today (Thursday 3 May) in the journal Human Reproduction, said: "As far as we know, this is the first report of the quality of DNA in the nucleus and mitochondria of sperm in diabetes. Our study identifies important evidence of increased DNA fragmentation of nuclear DNA and mitochondrial DNA deletions in sperm from diabetic men. These findings cause concern, as they may have implications for fertility." The incidence of type 1 and type 2 diabetes is increasing rapidly worldwide. While diet and obesity are known to be key factors in the increase of type 2 (or late onset) diabetes, type 1 diabetes which is usually diagnosed in childhood or adolescence, is increasing by three per cent a year in European children, although the reason for this is not entirely clear. Genetic factors that make people more susceptible, or environmental factors such as viruses that may trigger the onset of type 1 diabetes, could play a role. Dr Agbaje, a research fellow in the Reproductive Medicine Research Group at Queen's University, Belfast, said: "If the increasing trend in the incidence of type I diabetes continues, this will result in a 50% increase over the next ten years. As a consequence, diabetes will affect many more men prior to and during their reproductive years. Infertility is already a major health problem in both the developed and developing world, with up to one in six couples requiring specialist investigation or treatment in order to conceive. Moreover, the last 50 years have seen an apparent decline in semen quality. Sperm disorders are thought to cause or contribute to infertility in 40-50% of infertile couples. The increasing incidence of systemic diseases such as diabetes may further exacerbate this decline in male fertility. However, it is not clear to what extent clinics consider information about the diabetic status of their patients when investigating fertility problems." [2] Dr Agbaje and his colleagues examined sperm from 27 diabetic men, with an average age of 34, and 29 non-diabetic men with an average age of 33. They found that although semen volume was significantly less in diabetic men (2.6 versus 3.3 ml), there were no significant differences in sperm concentration, total sperm output, form and structure of the sperm or their ability to move. When they measured DNA damage they found that the percentage of fragmented nuclear DNA was significantly higher in sperm from the diabetic men and that the number of deletions in mitochondrial DNA was also higher - the number of deletions ranged from three to six (average four) in the diabetic men and from one to four (average three) in the non-diabetic men. Professor Sheena Lewis, scientific director of the Reproductive Medicine Research Group, said: "Our study shows increased levels of sperm DNA damage in diabetic men. From a clinical perspective this is important, particularly given the overwhelming evidence that sperm DNA damage impairs male fertility and reproductive health. Other studies have already shown that, while the female egg has a limited ability to repair damaged sperm DNA, fragmentation beyond this threshold may result in increased rates of embryonic failure and pregnancy loss. In the context of spontaneous conception, sperm DNA quality has been found to be poorer in couples with a history of miscarriages." However, Prof Lewis said that it was not possible to say from this current study whether the DNA damage caused by diabetes would have the same effect on men's fertility and the health of future children as DNA damage caused by other factors such as smoking. "This is just one, relatively small study that highlights a possible concern. Further studies need to be carried out in order to understand the precise nature of the diabetes-related damage, the causal mechanisms and the clinical significance. Given the global rise in the prevalence of diabetes, it is also vital to examine the reproductive outcomes of pregnancies fathered by diabetic men, and the prevalence of diabetes amongst men attending for infertility treatment," she concluded.----------------------------Article adapted by Medical News Today from original press release.---------------------------- [1] Insulin dependent diabetes mellitus: implications for male reproductive function. Human Reproduction. doi:10.1093/humrep/dem077. [2] Studies have estimated the prevalence of diabetes in sub-fertile men as 1% - three times more than expected (0.3%), given the prevalence of diabetes and male infertility in the general population. This suggests that diabetes is having a significant impact on male fertility.

DNA Repair

2008-04-20T10:27:00.001-07:00
Damage can occur to all cellular molecules. If RNAs or proteins are damaged, they can be degraded and newly synthesized via transcription and translation using DNA as the template (later).
However, because DNA is the genetic material, changes in its structure can result in mutations (in the change of the base sequence). Although mutations can sometimes be beneficial, the overwhelming majority is not.
Mutations in DNA can result from incorporation of incorrect bases during replication or DNA may undergo chemical changes either spontaneously (Fig. 12.23) or as a result of exposure to chemicals (Fig. 12.22) or radiation (Fig. 12.28).
As we will see, some chemical changes occur with an extraordinary frequency. The resulting huge frequency of mutations would be devastating for the survival of the cell and overwhelm any beneficial mutation that might have ocurred among them.
Cells had to evolve mechanisms to repair damaged DNA:
Classes of repair mechanisms:
1) direct reversal of damage reaction 2) removal of damaged bases and replacement with newly synthesized DNAAlso, mechanisms to cope with damage if it cannot be repaired.
Direct reversal:
Only a few types of damage are repaired in this way although it is probably the most energy efficient. Especially the formation of pyrimidine dimers, which is the major type of damage induced by UV light. Pyrimidine dimers are formed between adjacent pyrimidines (particularly thymines) on the same strand of DNA by the formation of a cyclobutane ring resulting from saturation of the double bonds in their ring structure (Fig. 12.25).
Pyrimidine dimers distort the double helical structure of DNA and block transcription or replication past the damaged site. Recognition of distortions in the double helix is the major way that DNA damage is generally recognized in the cell.
One mechanism of repair (there are several others) is through direct reversal of the dimerization reaction. The process is called photoreactivation because the energy to break the cyclobutane ring is derived from visible light. Therefore, in this kind of repair mechanism the original pyrimidine bases are restored and remain in the DNA.
The repair of pyrimidine dimers by photoreactivation by the enzyme photolyase, is common to many prokaryotes and eukaryotes (E. coli, yeast, and several species of plants and animals). However, photoreactivation is not universal. Many species (including humans) lack this kind of repair mechanism. But humans have other kinds of repair mechanisms that directly reverse certain damages.
Excision repair (movie)
Most important repair mechanism. Damaged DNA is recognized, removed either as free bases or as nucleotides, and the gap is filled by synthesis of new DNA using the complementary strand as a template (Fig. 12.26).
Types of excision repair: 1) base excision repair 2) nucleotide excision repair 3) mismatch repair
One example for base excision repair is the removal of uracil from DNA. Most uracil in DNA arises from the deamination of cytosine which directly leads to the structure of uracil (Fig. 12.23).
In humans it occurs at a frequency of about 100 times a day in each cell.
If uracil is not repaired, it will base pair with adenine during the next round of replication and thus cause a mutation. The general use of thymine instead of uracil in DNA allows the repair system to recognize deaminated cytosine as incorrect.
In general, the excision of a base is catalyzed by DNA glycosylase, which cleaves the bond between the base and the deoxyribose (called glycosidic bond). The result is an apyrimidinic or apurinic (AP) site: a sugar with no base attached.
AP sites also form through spontaneous loss of a base. This occurs especially often with purines, for example several thousand times a day in a human cell.
Repair of AP sites by AP endonuclease: cleaves adjacent to AP site.
The deoxyribose is removed and the single base gap filled by DNA polymerase and ligase.
Nucleotide excision repair removes a whole oligonucleotide that containes the damage. Thymine-thymine dimer residues are examples of damage caused by UV radiation (Fig. 12.25).
In E. coli three genes involved (uvrA, B and C). The protein UvrA recognizes the damage, recruits UvrB and UvrC which cleave at 3' and 5' site of damage, respectively, producing an oligonucleotide of 12 or 13 bases.
Helicase necessary to remove oligonucleotide (disruption of hydrogen bonds from base pairing), DNA polymerase fills gap, ligase seals.
Nucleotide excision repair also in eukaryotes. Similar mechanism. Mismatch repair system (movie)
Recognizes mismatches resulting from replication. Scans newly replicated DNA, identifies mismatch, excises the mismatched base specifically from new strand so error can be repaired (Fig. 12.24).
How can the old strand of DNA be distinguished from the new strand after replication?
In E. coli, because new strand not yet methylated at GATC sequences as is normally the case (A of GATC methylated).
In E. coli mismatch repair is initiated by the protein MutS, which recognizes mismatch, and forms complex with MutL and MutH. Then MutH (an endonuclease) cleaves the unmethylated DNA strand at a GATC sequence.
Eukaryotes have a similar mismatch repair system, but the mechanism by which they identify the newly replicated DNA strand is not known.
If DNA contains damaged bases (like a pyrimidine dimer) that cannot be repaired, replication and transcription are blocked at this site. However, there are mechanisms to circumvent the damaged site. For example, replication can be initiated downstream of the damaged site by an Okazaki fragment. The result is a gap in the new daughter strand opposite the damage of the parental strand. Recombinational repair (Repair mechanisms for gaps) (movie)
Recombinational repair makes use of the undamaged parental strand to undergo recombination shifting the gap to the other newly synthesized DNA molecule, the one that does not contain the damage. Because the gap is now opposite an undamaged strand, it can be filled by DNA polymerase. And the damage lies now opposite a normal strand and can be dealt with later. SOS repair, Error-prone repair (movie)
In error-prone repair, the gap opposite the site of DNA damage is directly filled by newly synthesized DNA. But because of damage to the template the repair is very inacurate and leads to frequent mutations. Error-prone repair is used only in bacteria that have been subjected to potentially lethal conditions (such as extensive UV irradiation), where damage is so enormous that cell death is probably the only alternative.

DNA Molecule - Two Views

2008-04-20T10:23:00.000-07:00
DNA Molecule - Two Views
Legend:
The double helix of the DNA is shown along with details of how the bases, sugars and phosphates connect to form the structure of the molecule.
DNA is a double-stranded molecule twisted into a helix (think of a spiral staircase). Each spiraling strand, comprised of a sugar-phosphate backbone and attached bases, is connected to a complementary strand by non-covalent hydrogen bonding between paired bases. The bases are adenine (A), thymine (T), cytosine (C) and guanine (G). A and T are connected by two hydrogen bonds. G and C are connected by three hydrogen bonds.