Science Daily — The planet's deep oceans at times may absorb enough heat to flatten the rate of global warming for periods of as long as a decade even in the midst of longer-term warming, according to a new analysis led by the National Center for Atmospheric Research (NCAR).
Tuesday, September 20, 2011
Community Mapping and Open Development in Dar Es Salaam
Community members creating maps of Tandale Ward, Dar Es Salaam
(Photo by: Mark Iliffe)
In Dar Es Salaam, one of the fastest-growing cities in the world, the local authorities, with support from the Tanzania-based World Bank urban and regional government teams, are working hard to improve urban services for the poor. Before allocating scarce resources to building roads, streetlights, solid waste collection points or roadside drainage, Tanzanian officials must first understand how a community understands its challenges and priorities for the future.
In an effort supported through a unique partnership between The World Bank andTwaweza, a regional ICT NGO, an impressive array of civic actors are leveraging information and communication technologies (ICTs) to create a new approach to this challenge in Tandale Ward, a vibrant unplanned community a few kilometres west of Dar Es Salaam’s city centre. Inspired by Map Kibera, the first community-built online map of Nairobi's largest slum, Ardhi University’s School of Urban and Regional Planning (SURP) and residents of Tandale spent much of August using GPS units to collect a wide range of public data points, from school and public toilets to health clinics and trash dumps. With the help of free and open-source software, these volunteers loaded these data onto Open Street Map (OSM), a freely accessible online map.
The effort in Tandale is an ongoing experiment in what Aleem Waljidescribes as the shift from open data to open development, where “citizen data and user-generated content [can create] opportunities for Governments to listen better to their people and be more responsive to their constituents.” The interactive map is a new information resource for the community and a powerful point of reference for government discussion and decision-making about upcoming infrastructure upgrades.
The map’s granular, community-level open data provides new opportunities for what Harvard urban economist Edward Glaeser characterises as “self-protecting urban innovation, cities’ abilities to generate the information needed to solve their own problems.” On top of this data, technologists and issue experts can build tools to help better understand and respond to the city's most pressing problems. Within days of the initial mapping, Ramani Tandale, a website that allows residents to report flooding, broken street lights and other issues to an online map, was launched. In the future, teams of developers and community leaders in Dar Es Salaam could build smartphone applications to track solid waste collection, web visualisations of drainage catchment areas, or a dashboard to help public service providers better manage citizen requests.
As we continue to draw lessons from Tandale, it is clear that a network of civic actors, encouraged by local public service providers, can use low-cost technology to create new opportunities for accountability, enable data-driven government policy-making and start a more inclusive and open development process.
Deep Oceans Can Mask Global Warming for Decade-Long Periods
"We will see global warming go through hiatus periods in the future," says NCAR's Gerald Meehl, lead author of the study. "However, these periods would likely last only about a decade or so, and warming would then resume. This study illustrates one reason why global temperatures do not simply rise in a straight line."
The study, based on computer simulations of global climate, points to ocean layers deeper than 1,000 feet (300 meters) as the main location of the "missing heat" during periods such as the past decade when global air temperatures showed little trend. The findings also suggest that several more intervals like this can be expected over the next century, even as the trend toward overall warming continues.
The research, by scientists at NCAR and the Bureau of Meteorology in Australia, is published online in Nature Climate Change. Funding for the study came from the National Science Foundation, NCAR's sponsor, and the Department of Energy.
Where the missing heat goes
The 2000s were Earth's warmest decade in more than a century of weather records. However, the single-year mark for warmest global temperature, which had been set in 1998, remained unmatched until 2010.
Yet emissions of greenhouse gases continued to climb during the 2000s, and satellite measurements showed that the discrepancy between incoming sunshine and outgoing radiation from Earth actually increased. This implied that heat was building up somewhere on Earth, according to a 2010 study published in Science by NCAR researchers Kevin Trenberth and John Fasullo.
The two scientists, who are coauthors on the new study, suggested that the oceans might be storing some of the heat that would otherwise go toward other processes, such as warming the atmosphere or land, or melting more ice and snow. Observations from a global network of buoys showed some warming in the upper ocean, but not enough to account for the global build-up of heat. Although scientists suspected the deep oceans were playing a role, few measurements were available to confirm that hypothesis.
To track where the heat was going, Meehl and colleagues used a powerful software tool known as the Community Climate System Model, which was developed by scientists at NCAR and the Department of Energy with colleagues at other organizations. Using the model's ability to portray complex interactions between the atmosphere, land, oceans, and sea ice, they performed five simulations of global temperatures.
The simulations, which were based on projections of future greenhouse gas emissions from human activities, indicated that temperatures would rise by several degrees during this century. But each simulation also showed periods in which temperatures would stabilize for about a decade before climbing again. For example, one simulation showed the global average rising by about 2.5 degrees Fahrenheit (1.4 degrees Celsius) between 2000 and 2100, but with two decade-long hiatus periods during the century.
During these hiatus periods, simulations showed that extra energy entered the oceans, with deeper layers absorbing a disproportionate amount of heat due to changes in oceanic circulation. The vast area of ocean below about 1,000 feet (300 meters) warmed by 18% to 19% more during hiatus periods than at other times. In contrast, the shallower global ocean above 1,000 feet warmed by 60% less than during non-hiatus periods in the simulation.
"This study suggests the missing energy has indeed been buried in the ocean," Trenberth says. "The heat has not disappeared, and so it cannot be ignored. It must have consequences."
A pattern like La Niña
The simulations also indicated that the oceanic warming during hiatus periods has a regional signature. During a hiatus, average sea-surface temperatures decrease across the tropical Pacific, while they tend to increase at higher latitudes, especially around 30°S and 30°N in the Pacific and between 35°N and 40°N in the Atlantic, where surface waters converge to push heat into deeper oceanic layers.
These patterns are similar to those observed during a La Niña event, according to Meehl. He adds that El Niño and La Niña events can be overlaid on top of a hiatus-related pattern. Global temperatures tend to drop slightly during La Niña, as cooler waters reach the surface of the tropical Pacific, and they rise slightly during El Niño, when those waters are warmer.
"The main hiatus in observed warming has corresponded with La Niña conditions, which is consistent with the simulations," Trenberth says.
The simulations were part of NCAR's contribution to the Coupled Model Intercomparison Project Phase 5 (CMIP5). They were run on supercomputers at NCAR's National Science Foundation-supported Climate Simulation Laboratory, and on supercomputers at Oak Ridge Leadership Computing Facility and the National Energy Research Scientific Computing Center, both supported by the Office of Science of the U.S. Department of Energy.
Black Hole, Star Collisions May Illuminate Universe's Dark Side
Princeton and New York University researchers have simulated the effect of a primordial black hole passing through a star. Primordial black holes are among the objects hypothesized to make up dark matter -- the invisible substance thought to constitute much of the universe -- and astronomers could use the researchers' model to finally observe the elusive black holes. This image illustrates the resulting vibration waves as a primordial black hole (white dots) passes through the center of a star. The different colors correspond to the density of the primordial black hole and strength of the vibration. (Credit: Image by Tim Sandstrom)
Science Daily — Scientists looking to capture evidence of dark matter -- the invisible substance thought to constitute much of the universe -- may find a helpful tool in the recent work of researchers from Princeton University and New York University.
Postdoctoral researchers Shravan Hanasoge of Princeton's Department of Geosciences and Michael Kesden of NYU's Center for Cosmology and Particle Physics simulated the visible result of a primordial black hole passing through a star. Theoretical remnants of the Big Bang, primordial black holes possess the properties of dark matter and are one of various cosmic objects thought to be the source of the mysterious substance, but they have yet to be observed.
The team unveiled in a report in the journal Physical Review Letters this month a ready-made method for detecting the collision of stars with an elusive type of black hole that is on the short list of objects believed to make up dark matter. Such a discovery could serve as observable proof of dark matter and provide a much deeper understanding of the universe's inner workings.
If primordial black holes are the source of dark matter, the sheer number of stars in the Milky Way galaxy -- roughly 100 billion -- makes an encounter inevitable, the authors report. Unlike larger black holes, a primordial black hole would not "swallow" the star, but cause noticeable vibrations on the star's surface as it passes through.
Thus, as the number of telescopes and satellites probing distant stars in the Milky Way increases, so do the chances to observe a primordial black hole as it slides harmlessly through one of the galaxy's billions of stars, Hanasoge said. The computer model developed by Hanasoge and Kesden can be used with these current solar-observation techniques to offer a more precise method for detecting primordial black holes than existing tools.
"If astronomers were just looking at the sun, the chances of observing a primordial black hole are not likely, but people are now looking at thousands of stars," Hanasoge said.
"There's a larger question of what constitutes dark matter, and if a primordial black hole were found it would fit all the parameters -- they have mass and force so they directly influence other objects in the universe, and they don't interact with light. Identifying one would have profound implications for our understanding of the early universe and dark matter."
Although dark matter has not been observed directly, galaxies are thought to reside in extended dark-matter halos based on documented gravitational effects of these halos on galaxies' visible stars and gas. Like other proposed dark-matter candidates, primordial black holes are difficult to detect because they neither emit nor absorb light, stealthily traversing the universe with only subtle gravitational effects on nearby objects.
Because primordial black holes are heavier than other dark-matter candidates, however, their interaction with stars would be detectable by existing and future stellar observatories , Kesden said. When crossing paths with a star, a primordial black hole's gravity would squeeze the star, and then, once the black hole passed through, cause the star's surface to ripple as it snaps back into place.
"If you imagine poking a water balloon and watching the water ripple inside, that's similar to how a star's surface appears," Kesden said. "By looking at how a star's surface moves, you can figure out what's going on inside. If a black hole goes through, you can see the surface vibrate."
Eyeing the sun's surface for hints of dark matter
Kesden and Hanasoge used the sun as a model to calculate the effect of a primordial black hole on a star's surface. Kesden, whose research includes black holes and dark matter, calculated the masses of a primordial black hole, as well as the likely trajectory of the object through the sun. Hanasoge, who studies seismology in the sun, Earth and stars, worked out the black hole's vibrational effect on the sun's surface.
Video simulations of the researchers' calculations were created by NASA's Tim Sandstrom using the Pleiades supercomputer at the agency's Ames Research Center in California. One clip shows the vibrations of the sun's surface as a primordial black hole -- represented by a white trail -- passes through its interior. A second movie portrays the result of a black hole grazing the Sun's surface.
Marc Kamionkowski, a professor of physics and astronomy at Johns Hopkins University, said that the work serves as a toolkit for detecting primordial black holes, as Hanasoge and Kesden have provided a thorough and accurate method that takes advantage of existing solar observations. A theoretical physicist well known for his work with large-scale structures and the universe's early history, Kamionkowski had no role in the project, but is familiar with it.
"It's been known that as a primordial black hole went by a star, it would have an effect, but this is the first time we have calculations that are numerically precise," Kamionkowski said.
"This is a clever idea that takes advantage of observations and measurements already made by solar physics. It's like someone calling you to say there might be a million dollars under your front doormat. If it turns out to not be true, it cost you nothing to look. In this case, there might be dark matter in the data sets astronomers already have, so why not look?"
One significant aspect of Kesden and Hanasoge's technique, Kamionkowski said, is that it narrows a significant gap in the mass that can be detected by existing methods of trolling for primordial black holes .
The search for primordial black holes has thus far been limited to masses too small to include a black hole, or so large that "those black holes would have disrupted galaxies in heinous ways we would have noticed," Kamionkowski said. "Primordial black holes have been somewhat neglected and I think that's because there has not been a single, well-motivated idea of how to find them within the range in which they could likely exist."
The current mass range in which primordial black holes could be observed was set based on previous direct observations of Hawking radiation -- the emissions from black holes as they evaporate into gamma rays -- as well as of the bending of light around large stellar objects, Kesden said. The difference in mass between those phenomena, however, is enormous, even in astronomical terms. Hawking radiation can only be observed if the evaporating black hole's mass is less than 100 quadrillion grams. On the other end, an object must be larger than 100 septillion (24 zeroes) grams for light to visibly bend around it. The search for primordial black holes covered a swath of mass that spans a factor of 1 billion, Kesden explained -- similar to searching for an unknown object with a weight somewhere between that of a penny and a mining dump truck .
He and Hanasoge suggest a technique to give that range a much-needed trim and established more specific parameters for spotting a primordial black hole. The pair found through their simulations that a primordial black hole larger than 1 sextillion (21 zeroes) grams -- roughly the mass of an asteroid -- would produce a noticeable effect on a star's surface.
"Now that we know primordial black holes can produce detectable vibrations in stars, we could try to look at a larger sample of stars than just our own sun," Kesden said.
"The Milky Way has 100 billion stars, so about 10,000 detectable events should be happening every year in our galaxy if we just knew where to look."
This research was funded by grants from NASA and by the James Arthur Postdoctoral Fellowship at New York University.
Brightest Gamma Ray On Earth -- For a Safer, Healthier World
Science Daily — The brightest gamma ray beam ever created -- more than a thousand billion times more brilliant than the sun -- has been produced in research led at the University of Strathclyde, and could open up new possibilities for medicine.
The ray could have several uses, such as in medical imaging, radiotherapy and radioisotope production for PET (positron emission tomography) scanning. The source could also be useful in monitoring the integrity of stored nuclear waste.
Physicists have discovered that ultra-short duration laser pulses can interact with ionised gas to give off beams that are so intense they can pass through 20 cm of lead and would take 1.5 m of concrete to be completely absorbed.
In addition, the laser pulses are short enough -- lasting a quadrillionth of a second -- to capture the response of a nucleus to stimuli, making the rays ideal for use in lab-based study of the nucleus.
The device used in the research is smaller and less costly than more conventional sources of gamma rays, which are a form of X-rays.
The experiments were carried out on the Gemini laser in the Central Laser Facility at the Science and Technology Facilities Council's Rutherford Appleton Laboratory. Strathclyde was also joined in the research by University of Glasgow and Instituto Superior Técnico in Lisbon.
Professor Dino Jaroszynski of Strathclyde, who led the research, said: "This is a great breakthrough, which could make the probing of very dense matter easier and more extensive, and so allow us to monitor nuclear fusion capsules imploding.
"To prove this we have imaged very thin wires -- 25 microns thick -- with gamma rays and produced very clear images using a new method called phase-contrast imaging. This allows very weakly absorbing material to be clearly imaged. Matter illuminated by gamma rays only cast a very weak shadow and therefore are invisible. Phase-contrast imaging is the only way to render these transparent objects visible.
"It could also act as a powerful tool in medicine for cancer therapy and there is nothing else to match the duration of the gamma ray pulses, which is also why it is so bright.
"In nature, if you accelerate charged particles, such as electrons, they radiate. We trapped particles in a cavity of ions trailing an intense laser pulse and accelerated these to high energies. Electrons in this cavity also interact with the laser and pick up energy from it and oscillate wildly -- much like a child being pushed on a swing. The large swinging motion and the high energy of the electrons allow a huge increase in the photon energy to produce gamma rays. This enabled the gamma ray photons to outshine any other earthbound source.
"The accelerator we use is a new type called a laser-plasma wakefield accelerator which uses high power lasers and ionised gas to accelerate charged particles to very high energies -- thus shrinking a conventional accelerator, which is 100m long, to one which fits in the palm of your hand."
The peak brilliance of the gamma rays was measured to be greater than 1023 photons per second, per square milliradian, per square millimetre, per 0.1% bandwidth.
The research was supported by the Engineering and Physical Sciences Research Council, the Science and Technology Facilities Council, the Laserlab-Europe Consortium and the Extreme Light Infrastructure project. It is linked to SCAPA (Scottish Centre for the Application of Plasma-based Accelerators), which is based at Strathclyde and is run through the Scottish Universities Physics Alliance.
The research has been published in the journal Nature Physics.
'Inexhaustible' Source of Hydrogen May Be Unlocked by Salt Water, Engineers Say
Science Daily — A grain of salt or two may be all that microbial electrolysis cells need to produce hydrogen from wastewater or organic byproducts, without adding carbon dioxide to the atmosphere or using grid electricity, according to Penn State engineers.
Microbial electrolysis cells that produce hydrogen are the basis of this recent work, but previously, to produce hydrogen, the fuel cells required some electrical input. Now, Logan, working with postdoctoral fellow Younggy Kim is using the difference between river water and seawater to add the extra energy needed to produce hydrogen.
"This system could produce hydrogen anyplace that there is wastewater near sea water," said Bruce E. Logan, Kappe Professor of Environmental Engineering. "It uses no grid electricity and is completely carbon neutral. It is an inexhaustible source of energy."
Their results, published Sept. 19 in the Proceedings of the National Academy of Sciences, "show that pure hydrogen gas can efficiently be produced from virtually limitless supplies of seawater and river water and biodegradable organic matter."
Logan's cells were between 58 and 64 percent efficient and produced between 0.8 to 1.6 cubic meters of hydrogen for every cubic meter of liquid through the cell each day. The researchers estimated that only about 1 percent of the energy produced in the cell was needed to pump water through the system.
The key to these microbial electrolysis cells is reverse-electrodialysis or RED that extracts energy from the ionic differences between salt water and fresh water. A RED stack consists of alternating ion exchange membranes -- positive and negative -- with each RED contributing additively to the electrical output.
"People have proposed making electricity out of RED stacks," said Logan. "But you need so many membrane pairs and are trying to drive an unfavorable reaction."
For RED technology to hydrolyze water -- split it into hydrogen and oxygen -- requires 1.8 volts, which would in practice require about 25 pairs of membrane sand increase pumping resistance. However, combining RED technology with exoelectrogenic bacteria -- bacteria that consume organic material and produce an electric current -- reduced the number of RED stacks to five membrane pairs.
Previous work with microbial electrolysis cells showed that they could, by themselves, produce about 0.3 volts of electricity, but not the 0.414 volts needed to generate hydrogen in these fuel cells. Adding less than 0.2 volts of outside electricity released the hydrogen. Now, by incorporating 11 membranes -- five membrane pairs that produce about 0.5 volts -- the cells produce hydrogen.
"The added voltage that we need is a lot less than the 1.8 volts necessary to hydrolyze water," said Logan. "Biodegradable liquids and cellulose waste are abundant and with no energy in and hydrogen out we can get rid of wastewater and by-products. This could be an inexhaustible source of energy."
Logan and Kim's research used platinum as a catalyst on the cathode, but subsequent experimentation showed that a non-precious metal catalyst, molybdenum sulfide, had a 51 percent energy efficiency. The King Abdullah University of Science and Technology supported this work.
Why Carbon Nanotubes Spell Trouble for Cells
Science Daily — It's been long known that asbestos spells trouble for human cells. Scientists have seen cells stabbed with spiky, long asbestos fibers, and the image is gory: Part of the fiber is protruding from the cell, like a quivering arrow that's found its mark.
"It's as if we would eat a lollipop that's longer than us," said Huajian Gao, professor of engineering at Brown and the paper's corresponding author. "It would get stuck."
But scientists had been unable to understand why cells would be interested in asbestos fibers and other materials at the nanoscale that are too long to be fully ingested. Now a group of researchers at Brown University explains what happens. Through molecular simulations and experiments, the team reports inNature Nanotechnology that certain nanomaterials, such as carbon nanotubes, enter cells tip-first and almost always at a 90-degree angle. The orientation ends up fooling the cell; by taking in the rounded tip first, the cell mistakes the particle for a sphere, rather than a long cylinder. By the time the cell realizes the material is too long to be fully ingested, it's too late.
The research is important because nanomaterials like carbon nanotubes have promise in medicine, such as acting as vehicles to transport drugs to specific cells or to specific locations in the human body. If scientists can fully understand how nanomaterials interact with cells, then they can conceivably design products that help cells rather than harm them.
"If we can fully understand (nanomaterial-cell dynamics), we can make other tubes that can control how cells interact with nanomaterials and not be toxic," Gao said. "We ultimately want to stop the attraction between the nanotip and the cell."
Like asbestos fibers, commercially available carbon nanotubes and gold nanowires have rounded tips that often range from 10 to 100 nanometers in diameter. Size is important here; the diameter fits well within the cell's parameters for what it can handle. Brushing up against the nanotube, special proteins called receptors on the cell spring into action, clustering and bending the membrane wall to wrap the cell around the nanotube tip in a sequence that the authors call "tip recognition." As this occurs, the nanotube is tipped to a 90-degree angle, which reduces the amount of energy needed for the cell to engulf the particle.
Once the engulfing -- endocytosis -- begins, there is no turning back. Within minutes, the cell senses it can't fully engulf the nanostructure and essentially dials 911. "At this stage, it's too late," Gao said. "It's in trouble and calls for help, triggering an immune response that can cause repeated inflammation."
The team hypothesized the interaction using coarse-grained molecular dynamic simulations and capped multiwalled carbon nanotubes. In experiments involving nanotubes and gold nanowires and mouse liver cells and human mesothelial cells, the nanomaterials entered the cells tip-first and at a 90-degree angle about 90 percent of the time, the researchers report.
"We thought the tube was going to lie on the cell membrane to obtain more binding sites. However, our simulations revealed the tube steadily rotating to a high-entry degree, with its tip being fully wrapped," said Xinghua Shi, first author on the paper who earned his doctorate at Brown and is at the Chinese Academy of Sciences in Beijing. "It is counter-intuitive and is mainly due to the bending energy release as the membrane is wrapping the tube."
The team would like to study whether nanotubes without rounded tips -- or less rigid nanomaterials such as nanoribbons -- pose the same dilemma for cells.
"Interestingly, if the rounded tip of a carbon nanotube is cut off (meaning the tube is open and hollow), the tube lies on the cell membrane, instead of entering the cell at a high-degree-angle," Shi said.
Agnes Kane, professor of pathology and laboratory medicine at Brown, is a corresponding author on the paper. Other authors include Annette von dem Bussche from the Department of Pathology and Laboratory Medicine at Brown and Robert Hurt from the Institute for Molecular and Nanoscale Innovation at Brown.
The National Science Foundation, the U.S. Department of Commerce National Institute of Standards and Technology, the National Institute of Environmental Health Sciences Superfund Research Program, and the American Recovery and Reinvestment Act funded the research.
Sequencing 'Dark Matter' of Life: Elusive Genomes of Thousands of Bacteria Species Can Now Be Decoded
Science Daily — Researchers have developed a new method to sequence and analyze the dark matter of life -- the genomes of thousands of bacteria species previously beyond scientists' reach, from microorganisms that produce antibiotics and biofuels to microbes living in the human body.
"This part of life was completely inaccessible at the genomic level," said Pavel Pevzner, a computer science professor at the Jacobs School of Engineering at UC San Diego and a pioneer of algorithms for modern DNA sequencing technology.
Scientists from UC San Diego, the J. Craig Venter Institute and Illumina Inc., published their findings in the Sept. 18 online issue of the journalNature Biotechnology. The breakthrough will enable researchers to assemble virtually complete genomes from DNA extracted from a single bacterial cell. By contrast, traditional sequencing methods require at least a billion identical cells, grown in cultures in the lab. The study opens the door to the sequencing of bacteria that cannot be cultured -- the lion's share of bacterial species living on the planet.
Pevzner, in collaboration with UC San Diego mathematics professor Glenn Tesler and computer science postdoctoral researcher Hamidreza Chitsaz, developed an algorithm that dramatically improves the performance of software used to sequence DNA produced from a single bacterial cell. These programs traditionally recover 70 percent of genes.
"The new assembly algorithm captures 90 percent of genes from a single cell. Admittedly, it is not 100 percent. But it's almost as good as it gets for modern sequencing technologies: today biologists typically capture 95 percent of genes but they need to grow a billion cells to accomplish it," said Tesler.
Bacteria play a vital role in human health. They make up about 10 percent of the weight of the human body and can be found anywhere from the stomach to the mouth. Some, like E. coli, can wreak havoc. Others help us digest. Yet others, recent studies have found, can change the way we behave by, for example, tricking us into eating more than we need. That's why it is crucial to analyze bacteria's genomes, which in turn help scientists understand bacteria's behavior.
Modern sequencing machines require DNA from one billion bacterial cells to produce a complete genome. Biologists usually grow the required amount of bacteria in cultures in the lab. That is how they obtained enough DNA to sequence E. coli. But a wide majority of bacteria -- 99.9 percent according to some estimates -- cannot be cultured in the lab because they live in specific conditions and environments that are hard to reproduce, for example in symbiosis with other bacteria or on an animal's skin.
Enter Multiple Displacement Amplification (MDA) technology, developed about a decade ago by Professor Roger Lasken, now at the Venter Institute and co-author of the Nature Biotechnology study. MDA can be used on bacteria that can't be cultured in the lab. The technology is the equivalent of a copy machine that starts from a single cell and makes copies of fragments of its genome until it produces the equivalent of one billion cells. In 2005, Lasken and colleagues used MDA to sequence DNA produced from a single cell for the first time with funding from the Department of Energy.
However, while MDA is an ingenious cellular copy machine, it gives sequencing software programs a hard time. The DNA copies that MDA makes carry various errors and are not amplified uniformly: some pieces of the genome are copied thousands of times, and others only once or twice. Modern sequencing algorithms aren't equipped to deal with these disparities. In fact, they tend to discard bits of the genome that were replicated only a few times as sequencing errors, even though they could be key to sequencing the whole genome. The algorithm developed by Pevzner's team changes that. It retains these genome pieces and uses them to improve sequencing.
Researchers sequenced a single cell of E. coli with this method to verify the accuracy of the algorithm and recovered 91 percent of its genes, doing nearly as well as conventional sequencing from cultured cells. This provides enough data to answer many important biological questions, such as what antibiotics a species of bacteria produces. It also, for the first time, enables researchers to perform in-depth studies to figure out which proteins and peptides the bacteria living in human beings use to communicate with each other and with their host.
The scientists then turned to a species of marine bacteria that had never been sequenced before -- part of the dark matter of life. They not only sequenced its genome, but also analyzed it and were able to get information about how it lives and moves. The fairly complete and annotated genome they obtained was the first genome obtained via MDA to be deposited in GenBank, the genetic sequence database at the National Institutes of Health. With the help of the new algorithm developed by Pevzner and colleagues, thousands more are set to follow.
Pevzner's team is at work on a second-generation version of the algorithm. Lasken and his team plan to continue their work on improving MDA as well.
Lasken keeps a few hundred tubes filled with unsequenced bacteria in his laboratory at the Venter Institute in La Jolla, Calif. Each represents a bacterial terra incognita that scientists soon will explore using the method developed through the combined efforts of researchers at the UC San Diego Jacobs School of Engineering, the Venter Institute and Illumina.
"It's a very big step forward," Lasken said.
The research was partially supported by grants from the National Human Genome Research Institute and the Alfred P. Sloan Foundation and by a grant from the National Institutes of Health.
Gamers Succeed Where Scientists Fail: Molecular Structure of Retrovirus Enzyme Solved, Doors Open to New AIDS Drug Design
Science Daily — Gamers have solved the structure of a retrovirus enzyme whose configuration had stumped scientists for more than a decade. The gamers achieved their discovery by playing Foldit, an online game that allows players to collaborate and compete in predicting the structure of protein molecules.
This class of enzymes, called retroviral proteases, has a critical role in how the AIDS virus matures and proliferates. Intensive research is under way to try to find anti-AIDS drugs that can block these enzymes, but efforts were hampered by not knowing exactly what the retroviral protease molecule looks like.
After scientists repeatedly failed to piece together the structure of a protein-cutting enzyme from an AIDS-like virus, they called in the Foldit players. The scientists challenged the gamers to produce an accurate model of the enzyme. They did it in only three weeks.
"We wanted to see if human intuition could succeed where automated methods had failed," said Dr. Firas Khatib of the University of Washington Department of Biochemistry. Khatib is a researcher in the protein structure lab of Dr. David Baker, professor of biochemistry.
Remarkably, the gamers generated models good enough for the researchers to refine and, within a few days, determine the enzyme's structure. Equally amazing, surfaces on the molecule stood out as likely targets for drugs to de-active the enzyme.
"These features provide exciting opportunities for the design of retroviral drugs, including AIDS drugs," wrote the authors of a paper appearing Sept. 18 in Nature Structural & Molecular Biology. The scientists and gamers are listed as co-authors.
This is the first instance that the researchers are aware of in which gamers solved a longstanding scientific problem.
Fold-it was created by computer scientists at the University of Washington Center for Game Science in collaboration with the Baker lab.
"The focus of the UW Center for Game Sciences," said director Dr. Zoran Popovic, associate professor of computer science and engineering, "is to solve hard problems in science and education that currently cannot be solved by either people or computers alone."
The solution of the virus enzyme structure, the researchers said, "indicates the power of online computer games to channel human intuition and three-dimensional pattern matching skills to solve challenging scientific problems."
With names like Foldit Contenders Group and Foldit Void Crushers Group, the gamer teams were fired up for the task of real-world molecule modeling problems. The online protein folding game captivates thousands of avid players worldwide and engages the general public in scientific discovery.
Players come from all walks of life. The game taps into their 3-D spatial abilities to rotate chains of amino acids in cyberspace. New players start at the basic level, "One Small Clash," proceed to "Swing it Around" and step ahead until reaching "Rubber Band Reversal."
Direct manipulation tools, as well as assistance from a computer program called Rosetta, encourage participants to configure graphics into a workable protein model. Teams send in their answers, and UW researchers constantly improve the design of the game and its puzzles by analyzing the players' problem-solving strategies.
Figuring out the shape and misshape of proteins contributes to research on causes of and cures for cancer, Alzheimer's, immune deficiencies and a host of other disorders, as well as to environmental work on biofuels.
Referring to this week's report of the online gamers' molecule solution opening new avenues for anti-viral drug research, Carter Kimsey, program director, National Science Foundation Division of Biological Infrastructure, observed, "After this discovery, young people might not mind doing their science homework. This is an innovative approach to getting humans and computer models to 'learn from each other' in real-time."
The researchers noted that much attention has been given to the possibilities of crowd-sourcing and game playing in scientific discovery. Their results indicate the potential for integrating online video games into real-world science.
Dr. Seth Cooper, of the UW Department of Computing Science and Engineering, is a co-creator of Foldit and its lead designer and developer. He studies human-computer exploration methods and the co-evolution of games and players.
"People have spatial reasoning skills, something computers are not yet good at," Cooper said. "Games provide a framework for bringing together the strengths of computers and humans. The results in this week's paper show that gaming, science and computation can be combined to make advances that were not possible before."
Games like Foldit are evolving. To piece together the retrovirus enzyme structure, Cooper said, gamers used a new Alignment Tool for the first time to copy parts of know molecules and test their fit in an incomplete model.
"The ingenuity of game players," Khatib said, "is a formidable force that, if properly directed, can be used to solve a wide range of scientific problems.
According to Popovic, "Foldit shows that a game can turn novices into domain experts capable of producing first-class scientific discoveries. We are currently applying the same approach to change the way math and science are taught in school."
The other scientists involved in this project were Frank DiMaio and James Thompson, both of the UW Department of Biochemistry, and Maciej Kazmierczyk, Miroslaw Gilski, Szymon Krzywda, Helena Zabranska, and Mariusz Jaskolski, all of the Faculty of Chemistry of A. Mickiewicz University in Poznan, Poland, and Iva Pichova of the Academy of Sciences of the Czech Republic, Prague.
The project was supported by the UW Center for Game Science, the U.S. Defense Advanced Research Projects Agency (DARPA), the U.S. National Science Foundation, the Howard Hughes Medical Institute, and Microsoft Corp.
Quantum Behavior With a Flash: Laser Pulses Can Reveal Quantum Features of Large Objects
Science Daily — Just as a camera flash illuminates unseen objects hidden in darkness, a sequence of laser pulses can be used to study the elusive quantum behavior of a large "macroscopic" object. This method provides a novel tool of unprecedented performance for current experiments that push the boundaries of the quantum world to larger and larger scales.
One of the most fascinating and still open questions in physics is how far quantum phenomena extend into our everyday world. To answer that, experiments need to peer into the quantum world at a completely new scale of mass and size. This is a bumpy road: it becomes increasingly difficult to detect the genuine quantum features as mass and size are increased. A collaboration of scientists led by researchers from the Vienna Center for Quantum Science and Technology (VCQ) at the University of Vienna report this new scheme in the forthcoming issue of theProceedings of the National Academy of Sciences.Overcoming the "blur"
The research team proposes a method that uses flashes of light to observe quantum features of large objects with unprecedented resolution. The main idea is based on the fact that quantum objects, in contrast to classical objects, behave differently when they are being watched. "In current approaches, objects are constantly monitored and the possible quantum features are being washed out. This is in many ways analogous to the blurring of a photograph of a fast moving object," says Michael R. Vanner, lead author of the paper and member of the Vienna Doctoral School Complex Quantum Systems (CoQuS). "Loosely speaking, the flashes freeze the motion and create a sharp image of the quantum behavior."
How macroscopic can "quantum" be?
With this new tool, experiments will be able to peer into the quantum world at a completely new scale of mass and size. In particular, the scheme can be directly applied to the ongoing experiments that attempt to prepare quantum phenomena in micro-mechanical resonators, i.e. mechanically vibrating massive objects. "By analyzing the dynamics of such behavior, pulsed quantum optomechanics provides a path for investigating whether macroscopic mechanical objects can be used in future quantum technologies. It will also help shed light on nature's apparent division between the quantum and the classical worlds."
Nanoparticles cause brain injury in fish
Posted by Biomechanism
Scientists at the University of Plymouth have shown, for the first time in an animal, that nanoparticles have a detrimental effect on the brain and other parts of the central nervous system.
They subjected rainbow trout to titanium oxide nanoparticles which are widely used as a whitening agent in many products including paints, some personal care products, and with applications being considered for the food industry. They found that the particles caused vacuoles (holes) to form in parts of the brain and for nerve cells in the brain to die. Although some effects of nanoparticles have been shown previously in cell cultures and other in vitro systems this is the first time it has been confirmed in a live vertebrate.
The results will be presented at the “6th International meeting on the Environmental Effects on Nanoparticles and Nanomaterials” (21st – 23rd September) at the Royal Society in London.
“It is not certain at this stage of the research whether these effects are caused by the nanoparticles entering the brain or whether it is a secondary effect of nanoparticle chemistry or reactivity”, says Professor Richard Handy, lead scientist.
The results of Professor Handy’s work and that of other researchers investigating the biological effects of nanoparticles may influence policy regulations on the environmental protection and human safety of nanomaterials.
“It is worrying that the effects on the fish brain caused by these nanoparticles have some parallels with other substances like mercury poisoning, and one concern is that the materials may bioaccumulate and present a progressive or persistent hazard to wildlife and to humans”, says Professor Handy.
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