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SESAME - Inside the world's most "impossible" science project

SESAME - Inside the world's most "impossible" science project | Amazing Science | Scoop.it

Against expectation, Israel, Iran and the Arab world are collaborating on a major new science project in the Middle East. Reporting assignments in the Middle East often involve great danger - think of Syria and Gaza. Others run into bureaucratic obstruction. But the SESAME science project in Jordan is so bizarre it presented challenges of a wholly unexpected kind. The first was the sheer difficulty of grasping that the story was not the figment of someone's imagination but was actually happening.

 

A "synchrotron" facility called SESAME - at its heart, a particle accelerator not unlike Europe's CERN - is coming together in Jordan. A news story on the SESAME project explains the science it aims to do, but that is not the striking thing about it. On the scale of surprises that take a very long while to sink in, SESAME is off the scale: common sense would scream at you that it just should not be feasible.

 

The scenario goes as follows: take one of the world's most unstable regions, pick some of the countries that are most violently opposed to each other and then bring them together under one roof to do science. An extraordinarily bold idea to plant a world-class science facility - a synchrotron light source - in the heart of the Middle East for researchers from anywhere from Cairo to Tel Aviv to Tehran”. The list of countries involved looks utterly improbable: it includes Jordan, Turkey, Bahrain and Egypt - so far so normal. But then add Iran and - amazingly - Israel too.

 

And they actually have to meet each other every year to discuss plans including the fraught question of contributions. This is SESAME in a nutshell: an extraordinarily bold idea to plant a world-class science facility - a synchrotron light source - in the heart of the Middle East for researchers from anywhere from Cairo to Tel Aviv to Tehran.

 

So the first obstacle is getting past one's own natural incredulity that anything like this could ever get off the ground. But the fact is that it has. SESAME not only has a rather grand new building, near the village of Allan in the hills northwest of Amman; it also has the first components that will generate and accelerate a flow of electrons. If all goes well, sometime around 2015, the energy from those electrons will be harnessed to help peer into the world of the microscopically small. This is no ordinary science project. Yet somehow, after a decade of huge uncertainties about funding and endless doubts about who will take part, the people making this project work have found a way of rubbing along.

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Tens of Billions of Earth-like Rocky Planets Orbit Red Dwarf Stars in Milky Way Alone

Tens of Billions of Earth-like Rocky Planets Orbit Red Dwarf Stars in Milky Way Alone | Amazing Science | Scoop.it
Data released early this year from the European Space Agency's (ESO) HARPS planet finder shows that rocky planets not much bigger than Earth are very common in the habitable zones around faint red stars. The international team estimates that there are tens of billions of such planets in the Milky Way galaxy alone, and probably about one hundred in the Sun’s immediate neighbourhood. This was the first direct measurement of the frequency of super-Earths around red dwarfs, which account for 80% of the stars in the Milky Way.

 

This first direct estimate of the number of light planets around red dwarf stars was announced early this year by an international team using observations with the HARPS spectrograph on the 3.6-metre telescope at ESO's La Silla Observatory in Chile. A prior announcement, showing that planets are ubiquitous in our galaxy used a different method that was not sensitive to this important class of exoplanets.

 

The HARPS team has been searching for exoplanets orbiting the most common kind of star in the Milky Way — red dwarf stars (also known as M dwarfs). These stars are faint and cool compared to the Sun, but very common and long-lived, and therefore account for 80% of all the stars in the Milky Way.

 

"Our new observations with HARPS mean that about 40% of all red dwarf stars have a super-Earth orbiting in the habitable zone where liquid water can exist on the surface of the planet," says Xavier Bonfils (IPAG, Observatoire des Sciences de l'Univers de Grenoble, France), the leader of the team."Because red dwarfs are so common — there are about 160 billion of them in the Milky Way — this leads us to the astonishing result that there are tens of billions of these planets in our galaxy alone."

 

The HARPS team surveyed a carefully chosen sample of 102 red dwarf stars in the southern skies over a six-year period. A total of nine super-Earths (planets with masses between one and ten times that of Earth) were found, including two inside the habitable zones of Gliese 581 and Gliese 667 C respectively. The astronomers could estimate how heavy the planets were and how far from their stars they orbited.

 

By combining all the data, including observations of stars that did not have planets, and looking at the fraction of existing planets that could be discovered, the team has been able to work out how common different sorts of planets are around red dwarfs. They find that the frequency of occurrence of super-Earths in the habitable zone is 41% with a range from 28% to 95%.

 

On the other hand, more massive planets, similar to Jupiter and Saturn in our Solar System, are found to be rare around red dwarfs. Less than 12% of red dwarfs are expected to have giant planets (with masses between 100 and 1000 times that of the Earth). As there are many red dwarf stars close to the Sun the new estimate means that there are probably about one hundred super-Earth planets in the habitable zones around stars in the neighbourhood of the Sun at distances less than about 30 light-years.

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Mysterious new SARS-like coronavirus came from bats

Mysterious new SARS-like coronavirus came from bats | Amazing Science | Scoop.it
Genetic analysis has confirmed that the cases of SARS-like viral disease that made headlines this fall—first killing a Saudi Arabian man in June and then sickening a Qatari man in September—were the result of a single coronavirus strain that made the leap from bats to humans.

 

“These two individuals were exposed to the same virus that was harbored in bats in the Saudi Arabian peninsula,” says Ralph Baric, a microbiologist at University of North Carolina–Chapel Hill who was not involved in the work.

 

A team led by Ron Fouchier, a virologist at the Erasmus Medical Center in the Netherlands, sequenced all 30,000 nucleotides of the new virus’ genome. Reporting today in mBio, the researchers found that the virus is most closely related to two coronaviruses found in bats, one from vesper bats and another from pipstrelle bats. The finding mirrors earlier discoveries that bats often serve as reservoirs and likely sources of coronaviruses for people. Fouchier and his colleagues additionally found that the isolates from the first two men infected with the virus differed by only 99 nucleotides, indicating that the two viruses are the same species. Genetic data from a third viral isolate taken from another Saudi Arabian man who earlier this month came down with what scientists think is the same coronavirus.

 

Although it’s still too early to make definitive statements, Baric says that the novel coronavirus—dubbed HCoV EMC/2012—does not appear to be transmissible between people, which distinguishes it from the virus responsible for severe acute respiratory syndrome (SARS) that spread between thousands of people a decade ago, killing around 10% of those infected. “If it were as transmissible as SARS, it would be much more dangerous,” he says.

 

Baric and his team have created a new vaccine strategy, that he believes would work to protect people from the novel coronavirus. The vaccine knocks out a key proofreading enzyme in the SARS viral genome, which cripples the virus and enables it to trigger an immune reaction in mice without causing disease. All coronaviruses, including HCoV EMC/2012, have this proofreading enzyme, Baric says. So, with modifications, the same approach should work for the newly emerging strain. However, Matthew Frieman, a microbiologist at the University of Maryland School of Medicine in Baltimore, worries that the new virus may not receive significant amounts of researchers’ attention. On 4 December, SARS will become a select agent, as I reported last week. “Everyone who wants to work on SARS is changing their labs over right now,” notes Frieman. With the deadline looming, researchers “may be too busy right now to even think about working on other viruses,” he says.

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NASA Mars Rover Fully Analyzes First Soil Samples

NASA Mars Rover Fully Analyzes First Soil Samples | Amazing Science | Scoop.it
NASA's Mars Curiosity rover has used its full array of instruments to analyze Martian soil for the first time, and found a complex chemistry within the Martian soil. Water and sulfur and chlorine-containing substances, among other ingredients, showed up in samples Curiosity's arm delivered to an analytical laboratory inside the rover.

Detection of the substances during this early phase of the mission demonstrates the laboratory's capability to analyze diverse soil and rock samples over the next two years. Scientists also have been verifying the capabilities of the rover's instruments.

 

Curiosity is the first Mars rover able to scoop soil into analytical instruments. The specific soil sample came from a drift of windblown dust and sand called "Rocknest." The site lies in a relatively flat part of Gale Crater still miles away from the rover's main destination on the slope of a mountain called Mount Sharp. The rover's laboratory includes the Sample Analysis at Mars (SAM) suite and the Chemistry and Mineralogy (CheMin) instrument. SAM used three methods to analyze gases given off from the dusty sand when it was heated in a tiny oven. One class of substances SAM checks for is organic compounds -- carbon-containing chemicals that can be ingredients for life.

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New lighting technology (FIPEL) won't flicker, shatter or burn out

New lighting technology (FIPEL) won't flicker, shatter or burn out | Amazing Science | Scoop.it
The lighting, based on field-induced polymer electroluminescent (FIPEL) technology, also gives off soft, white light – not the yellowish glint from fluorescents or bluish tinge from LEDs.

 

"People often complain that fluorescent lights bother their eyes, and the hum from the fluorescent tubes irritates anyone sitting at a desk underneath them," said David Carroll, the scientist leading the development of this technology at Wake Forest. "The new lights we have created can cure both of those problems and more."

 

The team uses a nano-engineered polymer matrix to convert the charge into light. This allows the researchers to create an entirely new light bulb – overcoming one of the major barriers in using plastic lights in commercial buildings and homes. The research supporting the technology is described in a study appearing online in advance of publication in the peer-reviewed journal Organic Electronics.

 

The device is made of three layers of moldable white-emitting polymer blended with a small amount of nanomaterials that glow when stimulated to create bright and perfectly white light similar to the sunlight human eyes prefer. However, it can be made in any color and any shape – from 2x4-foot sheets to replace office lighting to a bulb with Edison sockets to fit household lamps and light fixtures.

 

This new lighting solution is at least twice as efficient as compact fluorescent (CFL) bulbs and on par with LEDs, but these bulbs won't shatter and contaminate a home like CFLs or emit a bluish light like LED counterparts.

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Iridescence - a wide-spread phenomenon in nature

Iridescence - a wide-spread phenomenon in nature | Amazing Science | Scoop.it

Some natural surfaces can produce complex optical effects like rain droplets or a glass prism by selectively reflecting light of specific wavelengths and, therefore, specific colors. One optical effect, in particular, the one called iridescence, produces some of the most intense colorations in nature such as the rainbow-like coloration of soap bubbles, the inside of some shells, and the bright colors of the exoskeleton of some insects. The word iridescence originates from the Greek iris, which means ‘rainbow’, and refers to the optical property of some surfaces to change color and its intensity with the illumination or the viewing angle. Iridescent surfaces are uniquely structured in a way that causes the reflected light waves to interact physically with each other. The crests and troughs of the reflected light waves sometimes align (they are ‘in phase’) and reinforce each other, thus increasing the intensity of the reflected color. By contrast, if the reflected light waves are out of phase, they can cancel each other out and those particular colors never manifest. The final effect of this optical interference is the production of one or more predominant colors, the type and intensity changing with the angle of illumination and/or observation. Thus, iridescent colors are ‘structural’: they do not result from pigmentation but from physical interactions between light and surfaces.

 

Although iridescence is a widespread phenomenon in nature, I was genuinely surprised to read a recent paper by Eric Rosenfeld’s group published in Applied and Environmental Microbiology reporting that several bacteria, including some well-known laboratory strains of Pseudomonas aeruginosa and Haemophilus influenzae, are iridescent. The paper begins with a fine introduction about what is known in the field. Bacterial iridescence was first reported in 1904 but has been loosely and poorly described thereafter. Many reports used (or misused) epithets such as “shine,” “sheen,” “glistening”, “metallic effect,” “bright”, “luster,” “glow,” “glisten,” or “rainbow-like” For example, the authors showed that the ‘metallic iridescence’ previously reported for some strains of P. aeruginosa is not angle-dependent. Thus, these colonies are not truly iridescent. In some cases, fluorescence was mistaken as iridescence. I must admit that I have used some of these terms loosely in the past, blissfully ignorant of what I was observing.The researchers unified these epithets employing a rigorous classification of bacterial iridescence by using two microscopic techniques: epi-illumination (where illumination and detection take place on the same side of the sample) and trans-illumination (which detects the light transmitted through the sample). They investigated and described in detail the iridescent properties of colonies of several strains, including an iridescent strain (strain BK) of the marine bacterium Cellulophaga lytica (formerly known as Cytophaga lytica). This strain was isolated from the surface of a red anemone and grew into colonies displaying a glitter-like green coloration under direct epi-illumination. Other strains of C. lytica available in pure culture, including the only sequenced strain of the group (DSM7489), were either non-iridescent or exhibited low-intensity iridescence. In fact, the intense green iridescence displayed by C. lytica strain BK is described by the authors as ‘unmatched in the bacterial kingdom’ and to rival that observed in some insects and vertebrates.

 

Research article:

"Iridescence of a Marine Bacterium and Classification of Prokaryotic Structural Colors"

http://dx.crossref.org/10.1128%2FAEM.07339-11

 


Via Cesar Sanchez
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Inefficiently burning kerosene lamps release around 270 Billion tons carbon particles into atmosphere

Inefficiently burning kerosene lamps release around 270 Billion tons carbon particles into atmosphere | Amazing Science | Scoop.it

Kerosene lamps glow nightly in communities across the developing world. New research shows that these tiny lights have a greater impact than expected on climate. Inefficient lamps burning kerosene release about 270 gigatons of black carbon particulate matter into the atmosphere every year, the researchers estimate. This level of emissions is similar to that of the shipping industry.


When kerosene or other hydrocarbons combust inefficiently, they produce tiny soot particles called black carbon that absorb heat from sunlight because of their dark color. Black carbon absorbs heat to a greater extent than greenhouse gases can, despite the fact the particles don’t last as long in the atmosphere as the gases do. One ton of black carbon in the atmosphere can warm the climate as much as 700 tons of carbon dioxide over a century, according to previous estimates.

 

Nicholas Lam of the University of California, Berkeley, Tami Bond of the University of Illinois, Urbana-Champaign, and their colleagues thought kerosene lamps in the developing world could be one of the missing sources. They formed this hypothesis after speaking with people about the large amount of soot produced from kerosene lamps in their homes. To test the idea, the team decided to determine exactly how much black carbon these lamps released. Teaming with scientists in India and Uganda, Bond and Lam’s team measured black carbon produced when burning different kerosene fuels. They tested simple wick lamps typically found in Uganda and elsewhere that consist of a wick or rope dipped in fuel. Using electrochemical and nondispersive infrared sensors, the scientists burned the lamps and monitored real-time levels of black carbon in people’s homes. To confirm their measurements, team members studied similar lamps in their lab in Illinois. They measured black carbon levels using the same methods, along with collecting particulate matter from the lamps on filters in flow chambers.


The team found that on average, 1 kg of kerosene fuel burned in these lamps produced 90 g of black carbon. Based on the team’s estimates of the amount of kerosene used in home lamps in the developing world, the researchers calculated that the lamps produce about 3% of the black carbon found in the atmosphere.

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Scientists report new dark matter finding from merging galaxy cluster

Scientists report new dark matter finding from merging galaxy cluster | Amazing Science | Scoop.it
Astronomers were puzzled earlier this year when NASA's Hubble Space Telescope spotted an overabundance of dark matter in the heart of the merging galaxy cluster Abell 520. This observation was surprising because dark matter and galaxies should be anchored together, even during a collision between galaxy clusters.

 

Astronomers have abundant evidence that an as-yet-unidentified form of matter is responsible for 90 percent of the gravity within galaxies and clusters of galaxies. Because it is detected via its gravity and not its light, they call it "dark matter." Now, a new observation of Abell 520 from another team of astronomers using a different Hubble camera finds that the core does not appear to be over-dense in dark matter after all. The study findings were published in The Astrophysical Journal.

 

"The earlier result presented a mystery. In our observations we didn't see anything surprising in the core," said study leader Douglas Clowe, an associate professor of physics and astronomy at Ohio University. "Our measurements are in complete agreement with how we would expect dark matter to behave."

 

Hubble observations announced earlier this year by astronomers using Hubble's Wide Field Planetary Camera 2 suggested that a clump of dark matter was left behind during a clash between massive galaxies clusters in Abell 520, located 2.4 billion light-years away. The dark matter collected into a "dark core" that contained far fewer galaxies than would be expected if the dark and luminous matter were closely connected, which is generally found to be the case. Because dark matter is not visible, its presence and distribution is found indirectly through its gravitational effects. The gravity from both dark and luminous matter warps space, bending and distorting light from galaxies and clusters behind it like a giant magnifying glass. Astronomers can use this effect, called gravitational lensing, to infer the presence of dark matter in massive galaxy clusters. Both teams used this technique to map the dark matter in the merging cluster.

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Fully 3D Printable Gun ('Wiki Weapon') Waiting on Firearms License

Fully 3D Printable Gun ('Wiki Weapon') Waiting on Firearms License | Amazing Science | Scoop.it
Prototypes of what would be the world's first fully 3D-printable plastic weapon could go into testing before the end of the year, the organization behind the controversial project has claimed.

"We're ready," said Cody Wilson, a spokesman for Defense Distributed, the company that hopes to manufacture the "Wiki Weapon". "We're sitting on the logistics, time, resources and money. We're just waiting on a little piece of paper."

That little piece of paper is a federal firearms license , the permit that is needed to legally make and manufacture firearms in the United States. Barring an unexpected issue, Wilson expects the license will be granted within the next two or three weeks. Initially, the group planned to create prototypes without a license, but after the media discovered the Wiki Weapon, the group has been under increased scrutiny and several problems have threatened to derail the project.

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Research model suggests moons of some planets developed from rings

Research model suggests moons of some planets developed from rings | Amazing Science | Scoop.it

French researchers Sébastien Charnoz and Aurélien Crida have proposed in a paper published in the journal Science that moons that orbit some of the planets in our solar system came about due to accretion from material in rings that used to surround the planets, rather than as entities that took shape while their host planets were forming.

 

Space researchers have long proposed that moons circulating planets generally came to exist in one of three ways: as entities that formed on their own as their host was developing, as clumps that coalesced from material shed from a planet struck by some other body, or by being captured as they passed by. In this new research, Charnoz and Crida propose a fourth possibility – that the moons were formed from material in rings that surrounded their host planet.

In attempting to explain how moons orbiting planets such as Uranus, Neptune and Pluto, came about, the researchers created mathematical models that could predict moon formation from material surrounding a planet. Their models suggest that when material in a ring reaches a certain critical point at some distance from the host, called the Roche radius, the gravity from the host planet is offset by the gravitational pull that each piece exerts on others in the ring. Because of this, material in the ring begins to coalesce with some pieces eventually accreting enough material to form a moon. They add that the speed at which material in the ring orbits the host may account for the number of moons that form. Slow moving material might result in the formation of several small moons, while fast moving material may result in just one, as might have been the case with Earth and its single moon. Their model explains, they suggest, why all of the moons orbiting planets (except for Jupiter) in our solar system grow in size as they orbit farther from the host planet. Jupiter they say, is an exception, with its moons likely originating in tandem with the planet birth itself. The researchers concede that their models can't explain how the rings themselves came to exist, but suggest it's possible that they came about due to collisions with other bodies moving through space.

 

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Spider silk makes music at MIT

Pound for pound, spider silk is one of the strongest materials known: Research by MIT's Markus Buehler has helped explain that this strength arises from silk's unusual hierarchical arrangement of protein building blocks.

 

Now Buehler — together with David Kaplan of Tufts University and Joyce Wong of Boston University — has synthesized new variants on silk's natural structure, and found a method for making further improvements in the synthetic material. And an ear for music, it turns out, might be a key to making those structural improvements.

 

Read more: http://web.mit.edu/newsoffice/2012/the-music-of-the-silks-1128.html

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Rules devised for building artificial protein molecules from scratch

Rules devised for building artificial protein molecules from scratch | Amazing Science | Scoop.it

By following certain rules, scientists can prepare architectural plans for building artificial protein molecules not found in the real world. Based on these computer renditions, previously non-existent proteins can be produced from scratch in the lab. The principles to make this happen have now been elucidated in detail.


Dr. Nobuyasu Koga and Dr. Rie Tatsumi-Koga, a husband-and-wife scientific team in Dr. David Baker's lab at the University of Washington Protein Design Institute led the effort. The project benefited from hundreds of thousands of computer enthusiasts around the world who adopted Rosetta@home for simulating designed proteins. In this project, protein molecules start as an unstable, high energy chain of amino acids. This chain then begins folding into various shapes to try to achieve a stable, low energy state. The end result is its distinctive molecular structure.

 

Rosetta@home volunteers helped the project team to plot this energy landscape from protein structure predictions. "The structural options become fewer as the interactions that stabilize the protein selectively favor one folding pattern over others," explained Koga. "This decline in conformation options to eventually achieve a unique, ordered structure is called a funnel-shaped energy landscape," he said, drawing a tornado-like figure on a whiteboard. The researchers came up with guidelines for robustly generating this type of energy landscape.

 

According to Tatsumi-Koga, these rules require the interactions among the residues in the protein's amino acid chain to consistently favor the same folded conformation in forming its molecular shape. This is made possible, for example, by defining whether a specific unit will form a "right-handed" orientation or its mirror image, and disfavor others. The researchers, she said, synthesized the proteins they had originally designed and tested "in silico" (on the computer) and physically characterized them through "in vitro" (laboratory test tube) experiments. They also compared the molecular structures of the computer models with these laboratory-derived proteins to see how well they matched. Koga stressed that the project looked strictly at protein structure. He smiled as he said his group was striving toward a "platonic ideal," a reference to Plato's theory of perfect forms. During this project, the researchers achieved a library of five ideal structures, but since filing their report have added several more. To make them accessible to other scientists, the designs have been deposited in the Research Collaboratory for Structural Bioinformatics and the lab analysis of their chemical structure was put in the Biological Magnetic Resonance Database.


The team was not attempting to create specific new proteins that could carry out particular activities. However, their design principles and methods, according to their report, should allow the ready creation of a wide range of robust, stable, building blocks for the next generation of engineered functional proteins. Such proteins would be custom-made for the task, instead of repurposed from proteins with unrelated functions. The hope is that engineered proteins will be useful for drug and vaccine development, especially for formidable viruses like HIV or rapidly changing ones, like the flu. Proteins designed to exact specifications might also prove therapeutically useful in cleaving mutated genes, and for speeding up chemical reactions important in industry and environmental reclamation.

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DNA directly imaged with electron microscope for the first time

DNA directly imaged with electron microscope for the first time | Amazing Science | Scoop.it

It's the most famous corkscrew in history. Now an electron microscope has captured the famous Watson-Crick double helix in all its glory, by imaging threads of DNA resting on a silicon bed of nails. The technique will let researchers see how proteins, RNA and other biomolecules interact with DNA.

 

The structure of DNA was originally discovered using X-ray crystallography. This involves X-rays scattering off atoms in crystallised arrays of DNA to form a complex pattern of dots on photographic film. Interpreting the images requires complex mathematics to figure out what crystal structure could give rise to the observed patterns.

 

The new images are much more obvious, as they are a direct picture of the DNA strands, albeit seen with electrons rather than X-ray photons. The trick used by Enzo di Fabrizio at the University of Genoa, Italy, and his team was to snag DNA threads out of a dilute solution and lay them on a bed of nanoscopic silicon pillars.

 

The team developed a pattern of pillars that is extremely water-repellent, causing the moisture to evaporate quickly and leave behind strands of DNA stretched out and ready to view. The team also drilled tiny holes in the base of the nanopillar bed, through which they shone beams of electrons to make their high-resolution images. The results reveal the corkscrew thread of the DNA double helix, clearly visible. With this technique, researchers should be able to see how single molecules of DNA interact with other biomolecules.

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Deficiency for the Ubiquitin Ligase UBE3B in a Blepharophimosis-Ptosis-Intellectual Disability Syndrome

Deficiency for the Ubiquitin Ligase UBE3B in a Blepharophimosis-Ptosis-Intellectual Disability Syndrome | Amazing Science | Scoop.it

Studies in mice confirm that mutations in the gene, UBE3B, cause a rare genetic disorder in children.

 

Researchers have defined the gene responsible for a rare developmental disorder in children. The team showed that rare variation in a gene involved in brain development causes the disorder. This is the first time that this gene, UBE3B, has been linked to a disease. By using a combination of research in mice and sequencing the DNA of four patients with the disorder, the team showed that disruption of this gene causes symptoms including brain abnormalities and reduced growth, highlighting the power of mouse models for understanding the biology behind rare diseases.

 

"Ubiquitination, the biological pathway UBE3B is involved in, is crucial in neurodevelopment," says Dr Guntram Borck, lead author from the University of Ulm. "We have studied several patients with this rare condition, and by sequencing the coding regions of the genome of these patients we found mutations implicating the gene UBE3B. This result was confirmed by studies performed in mice by our collaborators at the Sanger Institute. At the Sanger researchers deleted the gene in mice and found that they had symptoms that were quite similar to those in the patients with UBE3B mutations including; reduced body weight and size, and reduced size of the brain.

 

The studies in mice also uncovered other defects underlying the disorder. Mice with the gene deletion had reduced cholesterol levels, a symptom that was seen by the team in three of the patients. This observation suggests that a defect in cholesterol metabolism is associated with this syndrome. "Both techniques, DNA sequencing and deleting the gene in mice, support the finding that disruption of UBE3B causes this syndrome," says Dr David Adams, lead author from the Wellcome Trust Sanger Institute. "We can now learn much more about this syndrome by studying these mice. They also represent a pre-clinical model in which we may trial potential new therapies.

 

"This is the first time that this gene has been implicated in any disorder." DNA sequencing has greatly improved the identification of variants associated with developmental disorders. But the challenge still remains for researchers to identify which of these variants, there are usually several hundred identified in each patient, cause the disorder. Animal models are a complementary approach for determining the causal gene and for understanding the biology behind genetic disorders.

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Sangamo tries to use engineered zinc finger transcriptional repressors to cure Huntington’s disease

Sangamo tries to use engineered zinc finger transcriptional repressors to cure Huntington’s disease | Amazing Science | Scoop.it
At the root of Huntington’s disease is a specific type of mutation, called a trinucleotide repeat expansion, in the Huntingtin (Htt) gene. The normal Htt gene contains up to 28 copies of the nucleotide sequence CAG, but this expands to more than 40 copies in the disease-causing allele. As a result of the expanded repeat, insoluble clumps of the Huntingtin protein accumulate inside neurons, causing cell death that leads to uncontrollable movements, dementia and, ultimately, death. Patients with between 28 and 35 repeats are unaffected, while those with between 36 and 40 have a form of the disease with reduced penetrance.

 

In animal models, reducing mutant Htt protein levels prevents disease progression and reverses some symptoms. However, most therapeutic approaches in development lower both versions of the huntingtin protein (the one produced by the normal gene, and the one made by the mutated gene). This has raised concerns about their safety for human use, because the normal protein has important, albeit as yet unknown, cellular function. To overcome this, Sangamo researchers have developed zinc finger transcriptional repressors that specifically target the mutant Htt allele and block its expression while preserving near-normal expression levels of the normal allele. Zinc fingers are naturally occurring protein segments that recognize and bind to specific DNA sequences, typically regulating the output of a given gene. Using genetic engineering, the Sangamo researchers designed zinc finger proteins containing a DNA-binding site that recognizes the prolonged tricnucleotide repeat found in the mutant Htt gene. They then fused this binding site to a protein domain that recruits other molecules that zip closed the chromosomal region containing the Htt gene with the expanded repeat—thus hindering production of mutated huntingtin protein.

 

In a recent experiment in a lab dish, the group added the engineered zinc fingers to fibroblast cells obtained from six people with Huntington’s disease. This lowered production of the mutant protein by more than 90%, while reducing the amount of the normal protein by just 10% or less, the researchers reported at the annual meeting of the Society for Neuroscience, held here this week. “There was very potent discrimination between the mutant and normal alleles in cells from all six patients, even though each contained mutant alleles of different lengths,” explains Phillip Gregory*, chief scientific officer at Sangamo BioSciences. “The next step is to make that sure they operate at a broad range of doses, and then we need to move into animal studies of efficacy and safety.”

 

This is the first attempt to apply the zinc finger approach to Huntington’s disease, and the researchers eventually aim to deliver genes for the zinc finger proteins directly into the brain using adeno-associated viral vectors*, which are already being used to successfully deliver therapeutic genes into the brains of people with Parkinson’s disease in clinical trials.

 

“This is very promising and exciting work,” says Sarah Tabrizi, a professor at the Institute of Neurology in London, who was not involved in the study, “but it’s still at a very early and exploratory stage, and it’s a big jump going from cells in culture to the human brain.” One challenge is that targeting viral vectors to specified brain areas and then ensuring their proper distribution is difficult, and this is further complicated by the fact that Huntington’s disease begins in deep brain structures before spreading to the cerebral cortex. “Distributing the vector will be a challenge,” Tabrizi says, “but I don’t think it’s insurmountable.”

 

Read more about ZFN and TALENs ("Editing the genome, here, there and everywhere"): http://tinyurl.com/ccdhao5

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A Spoonful of Medicine: Drug approval and rejection highlights from 2012

A Spoonful of Medicine: Drug approval and rejection highlights from 2012 | Amazing Science | Scoop.it

Another year, another round of approvals, mixed reviews and high-profile failures. We look back on which medicines made the headlines.

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NASA Voyager 1 Encounters New Region in Deep Space

NASA Voyager 1 Encounters New Region in Deep Space | Amazing Science | Scoop.it
NASA's Voyager 1 spacecraft has entered a new region at the far reaches of our solar system that scientists feel is the final area the spacecraft has to cross before reaching interstellar space.

 

Scientists refer to this new region as a magnetic highway for charged particles because our sun's magnetic field lines are connected to interstellar magnetic field lines. This connection allows lower-energy charged particles that originate from inside our heliosphere -- or the bubble of charged particles the sun blows around itself -- to zoom out and allows higher-energy particles from outside to stream in. Before entering this region, the charged particles bounced around in all directions, as if trapped on local roads inside the heliosphere.

 

The Voyager team infers this region is still inside our solar bubble because the direction of the magnetic field lines has not changed. The direction of these magnetic field lines is predicted to change when Voyager breaks through to interstellar space. The new results were described at the American Geophysical Union meeting in San Francisco on Monday.

 

"Although Voyager 1 still is inside the sun's environment, we now can taste what it's like on the outside because the particles are zipping in and out on this magnetic highway," said Edward Stone, Voyager project scientist based at the California Institute of Technology, Pasadena. "We believe this is the last leg of our journey to interstellar space. Our best guess is it's likely just a few months to a couple years away. The new region isn't what we expected, but we've come to expect the unexpected from Voyager."

 

Since December 2004, when Voyager 1 crossed a point in space called the termination shock, the spacecraft has been exploring the heliosphere's outer layer, called the heliosheath. In this region, the stream of charged particles from the sun, known as the solar wind, abruptly slowed down from supersonic speeds and became turbulent. Voyager 1's environment was consistent for about five and a half years. The spacecraft then detected that the outward speed of the solar wind slowed to zero.

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Most powerful black hole blast discovered - 100 times the energy of whole Milky Way ejected

Most powerful black hole blast discovered - 100 times the energy of whole Milky Way ejected | Amazing Science | Scoop.it

Astronomers analysed the energy being carried away from a huge quasar – the bright centres of distant galaxies which are powered by supermassive black holes and spew out vast amounts of matter.

 

Scientists have long claimed that extraordinarily powerful quasars must exist and play a key role in the formation of new galaxies, but until now none had been discovered which came close to their predictions.


Now measurements of a quasar known as SDSS J1106+1939 have established that it releases energy with about two million million times the power output of the Sun – the type of very high energy proposed by theorists. The team of scientists, who made their observations using the European Southern Observatory's Very Large Telescope (VLT), calculated that a mass equivalent to 400 Suns is given off by the quasar each year, at a speed of 800km per second. Dr. Nahum Arav of Virginia Tech University, who led the study, said: “We have discovered the most energetic quasar outflow known to date ... I’ve been looking for something like this for a decade, so it’s thrilling to finally find one of the monster outflows that have been predicted."


Theorists claim that the existence of quasars with such a powerful outflow of energy could solve a number of unanswered questions in cosmology, such as how the central black hole mass of galaxies helps determine the overall mass of the galaxy, and why the universe has so few very large galaxies.


Until now it was unclear whether quasars were powerful enough to produce such vast galaxies as some seen in the distant universe, but the researchers established that both SDSS J1106+1939 and one other quasar each have tremendous outflows.

 

They are now studying a further 12 similar quasars to determine whether the same is true of other luminous quasars spread across the universe.

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Individual Brains Synchronize When Musicians Play Together

Individual Brains Synchronize When Musicians Play Together | Amazing Science | Scoop.it
Researchers from the Max Planck Institute for Human Development in Berlin have shown that synchronization emerges between brains when making music together, and even when musicians play different voices. In a study published in Frontiers in Neuroscience, Johanna Sanger and her team used electrodes to record the brain waves of guitarists while they played different voices of the same duet. The results point to brain synchronicity that cannot be explained away by similitudes in external stimulation but can be attributed to a more profound interpersonal coordination.

 

Scientists working with Ulman Lindenberger at the Max Planck Institute in Berlin already discovered synchronous brain activity between musicians playing the same piece in 2009. The current study goes one step further by examining the brain activity of guitar players performing a piece of music with two different parts. Their aim was to find out whether musicians' brains would synchronize if the two guitarists were not playing exactly the same notes, but instead played different voices of the same song.

 

To test their hypothesis, the psychologists arranged 32 experienced guitarists in duet pairs, and recorded electrical activity in different brain regions of each musician. They were then asked to play a sequence from the "Sonata in G Major" by Christian Gottlieb Scheidler a total of 60 times, and the duet partners were given slightly different tasks: each musician had to play a different voice, and one of the two was responsible for ensuring that they started at the same time and held the same tempo. Thus, one person took the lead and the other followed. The duet's brain activities showed coordinated brain oscillations, even when playing different voices of the same duet. Called phase coherence, this synchronous activity suggests a direct neural basis for interpersonal coordination.

 

"When people coordinate their own actions, small networks between brain regions are formed. But we also observed similar network properties between the brains of the individual players, especially when mutual coordination is very important; for example at the joint onset of a piece of music," says Johanna Sänger. The difference between leader and follower was also reflected in the results of the measurement of electrical activity captured by electrodes: "In the player taking the lead, the internal synchronization of an individual's brain waves was stronger and, importantly, was present already before the duet started to play," says Johanna Sänger. "This could be a reflection of the leading player's decision to begin playing at a certain moment in time," she added.

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Taiwan engineers defeat limits of flash memory

Taiwan engineers defeat limits of flash memory | Amazing Science | Scoop.it
Taiwan-based Macronix has found a solution for a weakness in flash memory fadeout. A limitation of flash memory is simply that eventually it cannot be used; the more cells in the memory chips are erased, the less useful to store data. The write-erase cycles degrade insulation; eventually the cell fails. "Flash wears out after being programmed and erased about 10,000 times," said the IEEE Spectrum. Engineers at Macronix have a solution that moves flash memory over to a new life. They propose a "self-healing" NAND flash memory solution that can survive over 100 million cycles.

 

News of their findings appears in the IEEE Spectrum, discussing flash memory's limitations and the Taiwan company's solution. Macronix is a manufacturer in the Non-Volatile Memory (NVM) market, with a NOR Flash, NAND Flash, and ROM products. Before their solution announcement, though, many engineers inside and outside of Macronix were aware of a life-giving workaround: heat. The snag is that applying heat was not found to be practical. As the Macronix team put it, the "long baking time is impractical for real time operation." Although subjecting the cells to high heat could return memory, the process was problematic; the entire memory chip would need heating for hours at around 250 °C. They redesigned a flash memory chip to include onboard heaters to anneal small groups of memory cells. Applying a brief jolt of heat to a very restricted area within the chip (800 degrees C) returns the cell to a "good" state. They said that the process does not have to be run all that often. According to project member Hang‑Ting Lue, the annealing can be done infrequently and on one sector at a time while the device is inactive but still connected to the power source. It would not drain a cellphone battery, he added.

 

Macronix estimates that the flash memory cells could beat the 10,000 cycle limit by lasting for as much as for 100 million cycles but a commercial product is not imminent. Instead, Macronix will present their approach—very high temperature in a very short time— this month at the IEEE International Electron Devices Meeting (IEDM) from December 10 to 12 in San Francisco. This is the forum for presenting breakthroughs in semiconductor and electronic device technology. Lue observed that in coming up with the approach, his team would not be able to lay claim to any new physics principle. "We could have done this ten years ago." He said it took merely a leap of imagination into a different "regime." For their upcoming IEEE presentation, they said they propose and demonstrate a novel self-healing flash, where a high temperature (>800°C), and short time annealing are generated by a built-in heater. "We discover that a BE-SONOS charge-trapping NAND Flash device can be quickly annealed within a few milliseconds," they said.

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Animal vision evolved 700 million years ago

Animal vision evolved 700 million years ago | Amazing Science | Scoop.it

Gaze deep into any animal eye and you will find opsin, the protein through which we see the world. Every ray of light that you perceive was caught by an opsin first. Without opsin there would be no blue, no red, no green. The entire visible spectrum would be.. just another spectrum.

 

But opsins haven’t always been the sensitive light detectors that they are today. There is one critter, obscure and small, carries opsins that are blind to light. These opsins aren’t broken, like they are in some cave dwelling species. They never worked to begin with. They are the relics of a distant past, a time in which our ancestors still dwelt in darkness.

 

Opsin is a member of large family of detector proteins, called the ‘G-protein coupled receptors’ (GPCRs). Like a needle and thread, all GPCRs wind themselves through the outer membrane of the cell seven times. Halfway between cell and outside world, these tiny sensors are perfectly positioned to monitor the surroundings of the cell. Most GPCRs detect the presence of certain molecules. When a certain hormone or neurotransmitter docks their outward facing side they become activated and release signalling molecules on the inside of the cell. But opsin is different. It doesn’t bind molecules physically. Instead, it senses the presence of a more delicate and ephemeral particle: the photon itself, the particles (and waves) that light is made of.

Opsins trap photons with a small molecule in the heart of their architecture, called retinal. In its resting state retinal has a bent and twisted tail. But as soon as light strikes retinal, its tail unbends. This molecular stretching exercise forces the opsin to change shape as well. The opsin is now activated and eventually will cause a nearby nerve to fire, which will relay its message to the brain: light!.

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Precisely engineering 3-D brain tissues - New design technique for personalized medicine

Precisely engineering 3-D brain tissues - New design technique for personalized medicine | Amazing Science | Scoop.it
Borrowing from microfabrication techniques used in the semiconductor industry, MIT and Harvard Medical School (HMS) engineers have developed a simple and inexpensive way to create three-dimensional brain tissues in a lab dish.

 

The new technique yields tissue constructs that closely mimic the cellular composition of those in the living brain, allowing scientists to study how neurons form connections and to predict how cells from individual patients might respond to different drugs. The work also paves the way for developing bioengineered implants to replace damaged tissue for organ systems, according to the researchers.

 

Brain tissue includes many types of neurons, including inhibitory and excitatory neurons, as well as supportive cells such as glial cells. All of these cells occur at specific ratios and in specific locations. To mimic this architectural complexity in their engineered tissues, the researchers embedded a mixture of brain cells taken from the primary cortex of rats into sheets of hydrogel. They also included components of the extracellular matrix, which provides structural support and helps regulate cell behavior.

 

Those sheets were then stacked in layers, which can be sealed together using light to crosslink hydrogels. By covering layers of gels with plastic photomasks of varying shapes, the researchers could control how much of the gel was exposed to light, thus controlling the 3-D shape of the multilayer tissue construct. This type of photolithography is also used to build integrated circuits onto semiconductors — a process that requires a photomask aligner machine, which costs tens of thousands of dollars. However, the team developed a much less expensive way to assemble tissues using masks made from sheets of plastic, similar to overhead transparencies, held in place with alignment pins.

 

The tissue cubes can be made with a precision of 10 microns, comparable to the size of a single cell body. At the other end of the spectrum, the researchers are aiming to create a cubic millimeter of brain tissue with 100,000 cells and 900 million connections. The new system is the first that includes all of the necessary features for building useful 3-D tissues: It is inexpensive, precise, and allows complex patterns to be generated, says Metin Sitti, a professor of mechanical engineering at Carnegie Mellon University. “Many people could easily use this method for creating heterogeneous, complex gel structures,” says Sitti, who was not part of the research team.

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Newly Developed Technique Creates 60-Day Lasting Bread

Newly Developed Technique Creates 60-Day Lasting Bread | Amazing Science | Scoop.it

Longer-Lasting Bread: The average loaf of grocery story bread will start to go moldy in 10 days. But a U.S. company has devised a technique that it says can extend a loaf's freshness by up to 60 days.

 

The technique developed at Texas Tech University in Lubbock involves zapping the bread in a microwave array. The microwaves kill spores inside the bread that would normally develop into mold.

 

Food waste is a huge problem in the United States, where it's estimated the average family ends up tossing out about 40 percent of the food they buy. Bread is often one of the items that ends up in the garbage due to its short shelf life.

 

The new zapping technique could not only reduce that waste, the researchers say it could also help bread manufacturers use less preservatives. Currently many bread manufacturers add preservatives to their products to extend the bread's shelf life. They then add extra chemicals to mask the taste of the preservatives. By zapping the bread, it may be possible to avoid using preservatives altogether.

The technique can also be used to extend the freshness of other foods, including fresh turkey and many fruits and vegetables.

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Can a Jellyfish Unlock the Secret of Immortality and Reversal of Aging?

Can a Jellyfish Unlock the Secret of Immortality and Reversal of Aging? | Amazing Science | Scoop.it

Christian Sommer, a German marine-biology student in his early 20s, was conducting research on hydrozoans, small invertebrates that, depending on their stage in the life cycle, resemble either a jellyfish or a soft coral. Every morning, Sommer went snorkeling in the turquoise water off the cliffs of Portofino, Italy. He scanned the ocean floor for hydrozoans, gathering them with plankton nets. Among the hundreds of organisms he collected was a tiny, relatively obscure species known to biologists as Turritopsis dohrnii. Today it is more commonly known as the immortal jellyfish. Sommer kept his hydrozoans in petri dishes and observed their reproduction habits. After several days he noticed that his Turritopsis dohrnii was behaving in a very peculiar manner, for which he could hypothesize no earthly explanation. Plainly speaking, it refused to die. It appeared to age in reverse, growing younger and younger until it reached its earliest stage of development, at which point it began its life cycle anew.

 

Sommer was baffled by this development but didn’t immediately grasp its significance. (It was nearly a decade before the word “immortal” was first used to describe the species.) But several biologists in Genoa, fascinated by Sommer’s finding, continued to study the species, and in 1996 they published a paper called “Reversing the Life Cycle.” The scientists described how the species — at any stage of its development — could transform itself back to a polyp, the organism’s earliest stage of life, “thus escaping death and achieving potential immortality.” This finding appeared to debunk the most fundamental law of the natural world — you are born, and then you die. One of the paper’s authors, Ferdinando Boero, likened the Turritopsis to a butterfly that, instead of dying, turns back into a caterpillar. Another metaphor is a chicken that transforms into an egg, which gives birth to another chicken. The anthropomorphic analogy is that of an old man who grows younger and younger until he is again a fetus. For this reason Turritopsis dohrnii is often referred to as the Benjamin Button jellyfish.

 

Some progress has been made, however, in the quarter-century since Christian Sommer’s discovery. We now know, for instance, that the rejuvenation of Turritopsis dohrnii and some other members of the genus is caused by environmental stress or physical assault. We know that, during rejuvenation, it undergoes cellular transdifferentiation, an unusual process by which one type of cell is converted into another — a skin cell into a nerve cell, for instance. (The same process occurs in human stem cells.) But we still don’t understand how it ages in reverse.

 

Immortality is, to a certain degree, a question of semantics. “That word ‘immortal’ is distracting,” says James Carlton, the professor of marine sciences at Williams. “If by ‘immortal’ you mean passing on your genes, then yes, it’s immortal. But those are not the same cells anymore. The cells are immortal, but not necessarily the organism itself.” To complete the Benjamin Button analogy, imagine the man, after returning to a fetus, being born again. The cells would be recycled, but the old Benjamin would be gone; in his place would be a different man with a new brain, a new heart, a new body. He would be a clone.

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Scientists describe the elusive replication machinery of flu viruses

Scientists describe the elusive replication machinery of flu viruses | Amazing Science | Scoop.it

Scientists at The Scripps Research Institute (TSRI) have made a major advance in understanding how flu viruses replicate within infected cells. The researchers used cutting-edge molecular biology and electron-microscopy techniques to "see" one of influenza's essential protein complexes in unprecedented detail. The images generated in the study show flu virus proteins in the act of self-replication, highlighting the virus's vulnerabilities that are sure to be of interest to drug developers.

 

Influenza virus ribonucleoprotein complexes (RNPs) are central to the viral life cycle and in adaptation to new host species. RNPs are composed of the viral genome, viral polymerase, and many copies of the viral nucleoprotein. In vitro cell expression of all RNP protein components with four of the eight influenza virus gene segments enabled structural determination of native influenza virus RNPs by cryo-EM. The cryo-EM structure reveals the architecture and organization of the native RNP, thereby defining the attributes of its largely helical structure and how polymerase interacts with NP and the viral genome. Observations of branched-RNP structures in negative stain EM and their putative identification as replication intermediates suggest a mechanism for viral replication by a second polymerase on the RNP template.

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