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  • richardmitnick 4:36 pm on October 30, 2014 Permalink | Reply
    Tags: Applied Research & Technology, ,   

    From livescience: “Ancient Stone Circles in Mideast Baffle Archaeologists” 


    October 30, 2014
    Owen Jarus

    Huge stone circles in the Middle East have been imaged from above, revealing details of structures that have been shrouded in mystery for decades.

    Archaeologists in Jordan have taken high-resolution aerial images of 11 ancient “Big Circles,” all but one of which are around 400 meters (1,312 feet) in diameter. Why they are so similar is unknown but the similarity seems “too close to be a coincidence” said researcher David Kennedy.

    The Big Circles (as archaeologists call them) were built with low stone walls that are no more than a few feet high. The circles originally contained no openings, and people would have had to hop over the walls in order to get inside.

    Their purpose is unknown, and archaeologists are unsure when these structures were built. Analysis of the photographs, as well as artifacts found on the ground, suggest the circles date back at least 2,000 years, but they may be much older. They could even have been constructed in prehistoric times, before writing was invented, scientists say.

    Though the Big Circles were first spotted by aircraft in the 1920s, little research has focused on these structures, and many scientists are not even aware of their existence, something these archaeologists hope the new aerial images will help to change.

    The “most important contribution is simply to collect and make known a large group of rather remarkable sites,” writes Kennedy, a professor at the University of Western Australia, in an article published recently in the journal Zeitschrift für Orient Archäologie.

    In addition to the 11 photographed circles, researchers have identified another similar circle in Jordan, which appears to have been only partially completed, Kennedy noted. Old satellite imagery also reveals two circles, one in Jordan and another in Syria, which have both been destroyed. The circle in Syria was destroyed within the last decade and the one in Jordan a few decades ago. A separate research team, from Durham University, investigated the Syria circle before it was completely gone.

    While there are many smaller stone circles in the Middle East, what makes these 11 Big Circles stand out is their large size and ancient age, Kennedy said.

    Kennedy has been leading the Aerial Archaeology in Jordan Project (AAJ) since 1997 and also co-directs the Aerial Photographic Archive for Archaeology in the Middle East (APAAME).

    Building the Big Circles

    The circles would not have been hard to build, Kennedy said. They were constructed mainly with local rocks, and a dozen people working hard could potentially complete a Big Circle in a week, Kennedy told Live Science in an email.

    The area near the Azraq Oasis in Jordan has hundreds of wheels, large structures made of stone that date back at least 2,000 years.

    Another cluster of wheels found near the Azraq Oasis.

    Cairns, or piles of stones, are often found associated with the wheels, sometimes circling the perimeter and other times in among the spokes.

    However, building the circles in a precise shape would have taken some planning. “In the case of those circles that [are] near-precise circles, it would have required at least one person as ‘architect,'” Kennedy said, adding that this architect could simply have tied a long rope to a post and walked in a circle, marking the ground as he or she moved around. “That would also explain the glitches [in the circles] where the land was uneven,” as the architect wouldn’t have been able to keep walking in a perfect circle at those spots.

    The purpose of the Big Circles is a mystery, Kennedy said. It seems unlikely that they were originally used as corrals, as the walls were no more than a few feet high, the circles contain no structures that would have helped maintain an animal herd and there’s no need for animal corrals to have such a precise shape, he said.

    One of the circles contains three cairns, or rock piles, on its edges that may have been used for burial. However, Kennedy said, “my inference is that the cairns [were built] later, when the enclosure was no longer significant.”

    Solving the circle mystery

    In order to solve the mystery, archaeologists must conduct more actual fieldwork, Kennedy said, noting that aerial images are helpful but can’t replace excavation.

    Archaeologists Graham Philip and Jennie Bradbury, both with Durham University in England, have examined a Big Circle they found near Homs in Syria. While the circle was “badly damaged” when the researchers found it, they completed their fieldwork before land development completely destroyed the structure.

    This Big Circle was positioned in such a way that it could give someone standing inside it a “panoramic” view of a basin that would have held crops and settlements, the researchers reported in a 2010 paper in the journal Levant. This “may have played an important part in the location of the enclosure,” the two archaeologists wrote in the Levant article.

    Recent satellite imagery shows that the circle near Homs is now virtually destroyed, Kennedy wrote.

    Megalithic landscape

    While the purpose of the Big Circles remains unknown, the research by Kennedy and his team shows that the creations were part of a landscape rich in stone structures.

    His team has found thousands of stone structures in Jordan and the broader Middle East. They come in a variety of shapes, including “Wheels” (circular structures with spokes radiating out); Kites (stone structures that forced animals to run into a kill zone); Pendants (lines of stone cairns that run from burials); and walls (mysterious structures that meander across the landscape for more than a mile — or up to several thousand meters — and have no apparent practical use).

    The aerial photography program his team is conducting, combined with satellite imagery from sites like Google Earth, has led to many discoveries, Kennedy said. “As soon as you get up a few hundred feet, it all comes into focus. You can suddenly see the shape of what you’ve been looking at,” Kennedy said in a YouTube video made by Google as part of their Search Stories series.

    See the full article, with more images, here.

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  • richardmitnick 3:48 pm on October 30, 2014 Permalink | Reply
    Tags: Applied Research & Technology, , , Paleobiology,   

    From NYT: “From Ancient DNA, a Clearer Picture of Europeans Today” 

    New York Times

    The New York Times

    OCT. 30, 2014
    Carl Zimmer

    About 50,000 years ago, humans from Africa first set foot in Europe. They hunted woolly mammoths and other big game — sometimes to extinction. Eventually, they began grazing livestock and raising crops.

    They chopped down forests and drained swamps, turning villages into towns, then cities and capitals of empires. But even as they altered the Continent, Europeans changed, too.

    Their skin and hair grew lighter. They gained genetic traits particular to the regions in which they lived: Northern Europeans, for example, grew taller than Southern Europeans.

    Up till now, scientists have learned about evolution on the Continent mostly by looking at living Europeans. But advances in biotechnology have made it possible to begin extracting entire DNA from the bones of ancestors who lived thousands of years ago. Their genomes are like time machines, allowing scientists to see bits of European history playing out over thousands of years.

    Recently David Reich, a geneticist at Harvard Medical School, and his colleagues analyzed the genomes of nine ancient Europeans. Eight belonged to hunter-gatherers who lived about 8,000 years ago, seven in what is now Sweden and one in Luxembourg. The ninth came from a farmer who lived 7,000 years ago in present-day Germany.

    The scientists compared these genomes with those of living Europeans. As they reported last month in Nature, the study revealed something scientists never knew: Europeans today have genes from three very different populations.

    The oldest of these populations were the first Europeans, who appear to have lived as hunter-gatherers. The second were farmers who expanded into Europe about 8,500 years ago from the Near East.

    But most living Europeans also carry genes from a third population, which appears to have arrived more recently. Dr. Reich and his colleagues found the closest match in DNA taken from a 24,000-year-old individual in Siberia, suggesting that the third wave of immigrants hailed from north Eurasia. The ancient Europeans that the scientists studied did not share this North Eurasian DNA. They concluded that this third wave must have moved into Europe after 7,000 years ago.

    Last week, another team of scientists based at University College Dublin reported data from an even bigger haul of ancient European genomes — 13, all told. While Dr. Reich and his colleagues studied ancient Europeans separated by hundreds of miles, the Dublin team focused on just one region in Central Europe called the Great Hungarian Plain.

    The people whose genomes the scientists retrieved lived on the plain at various times between 7,700 years ago and 2,800 years ago.

    “What’s really exciting here is to have a transect through time,” said Johannes Krause, a co-director of the Max Planck Institute for History and the Sciences in Jena, Germany, who was not involved in the study. “It’s the first time that’s been done.”

    Archaeological digs have revealed evidence of farming on the plain as long as 8,000 years ago. People there raised crops like barley, and raised cattle and other livestock. Shards of pottery show that they consumed milk.

    The oldest genomes retrieved from human remains in the area — one from a man and one from a woman — date back to the dawn of agriculture on the plain. The woman’s DNA showed that she belonged to the ancient farming population documented by Dr. Reich and his colleagues.

    The man, however, did not have the genes of a farmer. He belonged to the oldest population of hunter-gatherers.

    “The archaeological information isn’t enough to say whether he was married to a local farmer,” said Ron Pinhasi, an archaeologist at University College Dublin and a co-author of the new study. It may even be that the man’s skull was a trophy of some sort, Dr. Pinhasi added.

    Archaeologists have found that early farming culture didn’t change drastically for the next 3,700 years. But about 4,000 years ago, the Bronze Age arrived. People started using bronze tools, trading over longer networks and moving into fortified towns.

    Dr. Pinhasi and his colleagues found that the era also brought a sudden shift in human DNA. A new population arrived on the Great Hungarian Plain, and Dr. Reich believes he knows who they were: the northern Eurasians.

    “It’s very exciting,” he said. “It documents that by this time in Central Europe, this Eastern influence had already arrived.”

    At the start of the Bronze Age, life settled down on the plain for a thousand years. But then came the Iron Age, bringing another shift in culture — and genes.

    People began traveling across the plain by horse-drawn chariots and wagons, and the genomes from 2,800 years ago show that the people of the Bronze Age had begun to be supplanted by a new Iron Age population. These are the people most closely related to living Hungarians.

    In the new study, Dr. Pinhasi and his colleagues also surveyed individual genes known to have changed over the course of European history.

    Today, for example, people in Hungary tend to have light skin and light brown hair, and half of them carry a mutation that lets them digest milk as adults. It took thousands of years for the genes for these traits to appear on the Great Hungarian Plain, the scientists found.

    The hunter-gatherer that lived 7,700 years ago, for example, probably had black hair and dark skin, along with blue eyes. His genes suggest that he also probably couldn’t digest milk — not surprising, since he came from a population that didn’t raise livestock.

    The ancient farmer woman, on the other hand, probably had dark brown hair and brown eyes. But like the hunter-gatherers, she lacked the genetic mutation for digesting milk.

    A 7,700-year-old skeleton of a woman found in Hungary has yielded DNA. Scientists have found that she belonged to a wave of early farmers who moved into Europe from the Near East. Credit Ron Pinhasi

    It is not until 6,400 years ago that the scientists find the first genetic evidence on the Great Hungarian Plain for light brown hair. And the milk mutation appeared even later, just 3,100 years ago.

    It is possible that these new genes and others were brought to the plain by successive waves of immigrants. But natural selection probably played a role in making these genes pervasive.

    Genetic mutations that enable people to drink milk as adults, for example, could have helped them survive famines. In cow-herding cultures, scientists have found, the milk-drinking mutation led to a 10 percent increase in the number of children.

    If that’s true, then for 4,600 years people on the Great Hungarian Plain were milking cows but lacked the ability to digest milk. Dr. Pinhasi suggested that they only used milk at first to make cheese and yogurt, which would have been easier to digest.

    Daniel G. Bradley, a geneticist at University College Dublin and co-author of the new study, predicted more unexpected results would emerge as scientists gather more ancient DNA in Europe.

    “The past is going to be a different country,” he said, “and it’s going to surprise us.”

    See the full article here.

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  • richardmitnick 2:58 pm on October 30, 2014 Permalink | Reply
    Tags: Applied Research & Technology, , , ,   

    From LBL: “Lord of the Microrings” 

    Berkeley Logo

    Berkeley Lab

    October 30, 2014
    Lynn Yarris (510) 486-5375

    A significant breakthrough in laser technology has been reported by the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) and the University of California (UC) Berkeley. Scientists led by Xiang Zhang, a physicist with joint appointments at Berkeley Lab and UC Berkeley, have developed a unique microring laser cavity that can produce single-mode lasing even from a conventional multi-mode laser cavity. This ability to provide single-mode lasing on demand holds ramifications for a wide range of applications including optical metrology and interferometry, optical data storage, high-resolution spectroscopy and optical communications.

    “Losses are typically undesirable in optics but, by deliberately exploiting the interplay between optical loss and gain based on the concept of parity-time symmetry, we have designed a microring laser cavity that exhibits intrinsic single-mode lasing regardless of the gain spectral bandwidth,” says Zhang, who directs Berkeley Lab’s Materials Sciences Division and is UC Berkeley’s Ernest S. Kuh Endowed Chair Professor. “This approach also provides an experimental platform to study parity-time symmetry and phase transition phenomena that originated from quantum field theory yet have been inaccessible so far in experiments. It can fundamentally broaden optical science at both semi-classical and quantum levels”

    Xiang Zhang, director of Berkeley Lab’s Materials Sciences Division. (Photo by Roy Kaltschmidt)

    Zhang, who also directs the National Science Foundation’s Nano-scale Science and Engineering Center, and is a member of the Kavli Energy NanoSciences Institute at Berkeley, is the corresponding author of a paper in Science that describes this work. The paper is titled Single-Mode Laser by Parity-time Symmetry Breaking. Co-authors are Liang Feng, Zi Jing Wong, Ren-Min Ma and Yuan Wang.

    A laser cavity or resonator is the mirrored component of a laser in which light reflected multiple times yields a standing wave at certain resonance frequencies called modes. Laser cavities typically support multiple modes because their dimensions are much larger than optical wavelengths. Competition between modes limits the optical gain in amplitude and results in random fluctuations and instabilities in the emitted laser beams.

    “For many applications, single-mode lasing is desirable for its stable operation, better beam quality, and easier manipulation,” Zhang says. “Light emission from a single-mode laser is monochromatic with low phase and intensity noises, but creating sufficiently modulated optical gain and loss to obtain single-mode lasing has been a challenge.”
    Scanning electron microscope image of the fabricated PT symmetry microring laser cavity.

    Scanning electron microscope image of the fabricated PT symmetry microring laser cavity.

    While mode manipulation and selection strategies have been developed to achieve single-mode lasing, each of these strategies has only been applicable to specific configurations. The microring laser cavity developed by Zhang’s group is the first successful concept for a general design. The key to their success is using the concept of the breaking of parity-time (PT) symmetry. The law of parity-time symmetry dictates that the properties of a system, like a beam of light, remain the same even if the system’s spatial configuration is reversed, like a mirror image, or the direction of time runs backward. Zhang and his group discovered a phenomenon called “thresholdless parity-time symmetry breaking” that provides them with unprecedented control over the resonant modes of their microring laser cavity, a critical requirement for emission control in laser physics and applications.

    Liang Feng

    “Thresholdless PT symmetry breaking means that our light beam undergoes symmetry breaking once the gain/loss contrast is introduced no matter how large this contrast is,” says Liang Feng, lead author of the Science paper, a recent posdoc in Zhang’s group and now an assistant professor with the University at Buffalo. “In other words, the threshold for PT symmetry breaking is zero gain/loss contrast.”

    Zhang, Feng and the other members of the team were able to exploit the phenomenon of thresholdless PT symmetry breaking through the fabrication of a unique microring laser cavity. This cavity consists of bilayered structures of chromium/germanium arranged periodically in the azimuthal direction on top of a microring resonator made from an indium-gallium-arsenide-phosphide compound on a substrate of indium phosphide. The diameter of the microring is 9 micrometers.

    “The introduced rotational symmetry in our microring resonator is continuous, mimicking an infinite system,” says Feng. “The counterintuitive discovery we made is that PT symmetry does not hold even at an infinitesimal gain/loss modulation when a system is rotationally symmetric. This was not observed in previous one-dimensional PT modulation systems because those finite systems did not support any continuous symmetry operations.”

    Using the continuous rotational symmetry of their microring laser cavity to facilitate thresholdless PT symmetry breaking,

    Zhang, Feng and their collaborators are able to delicately manipulate optical gain and loss in such a manner as to ultimately yield single-mode lasing.

    “PT symmetry breaking means an optical mode can be gain-dominant for lasing, whereas PT symmetry means all the modes remain passive,” says Zi-Jing Wong, co-lead author and a graduate student in Zhang’s group. “With our microring laser cavity, we facilitate a desired mode in PT symmetry breaking, while keeping all other modes PT symmetric. Although PT symmetry breaking by itself cannot guarantee single-mode lasing, when acting together with PT symmetry for all other modes, it facilitates single-mode lasing.”

    In their Science paper, the researchers suggest that single-mode lasing through PT-symmetry breaking could pave the way to next generation optoelectronic devices for communications and computing as it enables the independent manipulation of multiple laser beams without the “crosstalk” problems that plague today’s systems. Their microring laser cavity concept might also be used to engineer optical modes in a typical multi-mode laser cavity to create a desired lasing mode and emission pattern.

    “Our microring laser cavities could also replace the large laser boxes that are routinely used in labs and industry today,” Feng says. “Moreover, the demonstrated single-mode operation regardless of gain spectral bandwidth may create a laser chip carrying trillions of informational signals at different frequencies. This would make it possible to shrink a huge datacenter onto a tiny photonic chip.”

    This research was supported by the Office of Naval Research MURI program.

    See the full article here.

    A U.S. Department of Energy National Laboratory Operated by the University of California

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  • richardmitnick 4:11 am on October 30, 2014 Permalink | Reply
    Tags: Applied Research & Technology, ,   

    From livescience: “70,000-Year-Old Mammoth Skeleton Uncovered in Idaho” 


    October 28, 2014
    Megan Gannon

    The skeleton of a mammoth was discovered this month on the banks of a reservoir in Idaho. Paleontologists have rescued part of its skull and a tusk, but there could be a lot more buried below the surface.

    Excavators raced rising water levels to unearth the exposed mammoth fossil. Credit: Bureau of Reclamation Photo by Dave Walsh

    “We may even have a complete mammoth,” said Mary Thompson, a vertebrate paleontologist and senior collections manager at the Idaho Museum of Natural History. “This is very unique for us.”

    Every year, when water levels drop in Idaho’s American Falls Reservoir, teams of paleontologists and volunteers with the Bureau of Reclamation3 walk the beaches in search of fossils. The ancient bones of camels, bison latifrons, giant ground sloths, saber-toothed cats and other extinct Ice Age beasts sometimes poke out of the freshly eroded reservoir banks.

    The fossil was discovered by a volunteer with the Bureau of Reclamation who was scanning the reservoir beaches for freshly revealed fossils. (Credit: Bureau of Reclamation Photo by Dave Walsh)

    Earlier this month, one volunteer stumbled upon the mammoth fossil on a cliff face about 30 feet (9 meters) below the reservoir’s high-water mark. Thompson said she could tell it was from a mammoth as soon as she got the pictures in her email inbox. She and a team of students and volunteers mounted a quick, two-and-a-half-day excavation to dig up the bones as they raced rising water levels.

    “I’ve been here since 1990, and we haven’t gotten anything this complete from that site since then,” Thompson told Live Science. “Out of this area, we have one other complete mammoth.”

    This photo, taken on Oct. 16, shows Idaho State University students Casey Dooms and Jeff Castro brushing the mammoth fossil clean on the edge of American Falls Reservoir in southeastern Idaho. Some pieces of the skeleton were excavated over the course of two and a half days. (Credit: Bureau of Reclamation Photo by Dave Walsh)

    The excavators used plaster casts to remove most of the mammoth’s right tusk, which was about 7.5 inches (19 centimeters) in diameter. They also found part of its skull, a chunk of its mandible and two jagged upper molars. The specimen was transferred to the Idaho Museum of Natural History at Idaho State University in Pocatello.

    From the rings in the tusk, the researchers estimated that the mammoth was 16 years old — a fully grown adult — when it died. Based on the age of the surrounding sediments, Thompson thinks the mammoth must have been buried on its right side more than 72,000 years ago.

    The unexcavated parts of the mammoth were covered up with geotextile and soil after the short dig. Thompson said she hopes to bring a team back next year with ground-penetrating radar tools to get a better idea of what actually lies below the surface. If they are dealing with a full mammoth skeleton or even a partial skeleton, the team might need to figure out a way to get a backhoe down the steep reservoir bank to help with the excavation. This month, they did all the heavy lifting and digging by hand and with shovels.

    See the full article here.

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  • richardmitnick 6:29 pm on October 29, 2014 Permalink | Reply
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    From LLNL: “Tiny carbon nanotube pores make big impact “ 

    Lawrence Livermore National Laboratory

    Oct. 29, 2014

    Anne M Stark

    A team led by the Lawrence Livermore scientists has created a new kind of ion channel consisting of short carbon nanotubes, which can be inserted into synthetic bilayers and live cell membranes to form tiny pores that transport water, protons, small ions and DNA.

    These carbon nanotube “porins” have significant implications for future health care and bioengineering applications. Nanotube porins eventually could be used to deliver drugs to the body, serve as a foundation of novel biosensors and DNA sequencing applications, and be used as components of synthetic cells.

    Researchers have long been interested in developing synthetic analogs of biological membrane channels that could replicate high efficiency and extreme selectivity for transporting ions and molecules that are typically found in natural systems. However, these efforts always involved problems working with synthetics and they never matched the capabilities of biological proteins.

    Unlike taking a pill which is absorbed slowly and is delivered to the entire body, carbon nanotubes can pinpoint an exact area to treat without harming surrounding other organs.

    “Many good and efficient drugs that treat diseases of one organ are quite toxic to another,” said Aleksandr Noy, an LLNL biophysicist who led the study and is the senior author on the paper appearing in the Oct. 30 issue of the journal, Nature. “This is why delivery to a particular part of the body and only releasing it there is much better.”

    From left: Lawrence Livermore National Laboratory scientists Aleksandr Noy, Kyunghoon Kim and Jia Geng hold up a model of a carbon nanotube that can be inserted into live cells, which can pinpoint an exact area to treat without harming other organs. Photo by Julie Russell.

    The Lawrence Livermore team, together with colleagues at the Molecular Foundry at the Lawrence Berkeley National Laboratory, University of California Merced and Berkeley campuses, and University of Basque Country in Spain created a much more efficient, biocompatible membrane pore channel out of a carbon nanotube (CNT) — a straw-like molecule that consists of a rolled up graphene sheet.

    This research showed that despite their structural simplicity, CNT porins display many characteristic behaviors of natural ion channels: they spontaneously insert into the membranes, switch between metastable conductance states, and display characteristic macromolecule-induced blockades. The team also found that, just like in the biological channels, local channel and membrane charges could control the ionic conductance and ion selectivity of the CNT porins.

    “We found that these nanopores are a promising biomimetic platform for developing cell interfaces, studying transport in biological channels, and creating biosensors,” Noy said. “We are thinking about CNT porins as a first truly versatile synthetic nanopore that can create a range of applications in biology and materials science.”

    “Taken together, our findings establish CNT porins as a promising prototype of a synthetic membrane channel with inherent robustness toward biological and chemical challenges and exceptional biocompatibility that should prove valuable for bionanofluidic and cellular interface applications,” said Jia Geng, a postdoc who is the first co-author of the paper.

    Kyunghoon Kim, a postdoc and another co-author, added: “We also expect that our CNT porins could be modified with synthetic ‘gates’ to dramatically alter their selectivity, opening up exciting possibilities for their use in synthetic cells, drug delivery and biosensing.”

    Other LLNL researchers include Ramya Tunuguntla, Kang Rae Cho, Dayannara Munoz and Morris Wang. The team members performed some of the work at the Molecular Foundry, a DOE user facility as a part of its user project.

    See the full article here.

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    Operated by Lawrence Livermore National Security, LLC, for the Department of Energy’s National Nuclear Security
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  • richardmitnick 6:18 pm on October 29, 2014 Permalink | Reply
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    From PNNL: “New Assay Platform Detects Largest Number of Known Biotoxins Simultaneously” 

    PNNL Lab

    October 2014
    No Writer Credit

    New Assay Platform Detects Largest Number of Known Biotoxins Simultaneously

    Rapid, inexpensive microarray increases ability to identify, treat toxin exposure

    Results: The largest panel of biotoxins to be simultaneously detected to date has been achieved using an assay platform developed by scientists at Pacific Northwest National Laboratory. The enzyme-linked immunosorbent assay (ELISA) microarray simultaneously detected 10 plant and microbial toxins in buffer and clinical and environmental samples. These included ricin, botulinum neurotoxins (BoNT), shiga (STX), and staphylococcal enterotoxin B (SEB). Previously, the largest number of toxins to be simultaneously detected has been six.

    A molecule of ricin, one of the most deadly and common toxins discovered to date. An assay developed at Pacific Northwest National Laboratory can detect ricin and nine other biotoxins simultaneously, the largest panel to date.

    “Most assays to detect toxins target one or two toxins at a time, at best. In the event of a bioterrorist attack, it may not be obvious which agent was released, although this knowledge is critical for delivering appropriate medical treatment,” said Dr. Susan Varnum, a biologist at PNNL who led the study, which appears in Analyst.

    “There’s a pressing need for assays that analyze multiple toxins simultaneously so that in case of exposure, differentiation of multiple biothreat toxins can occur early enough for appropriate care to be given,” Varnum added.

    ELISAs are widely used to detect the presence of a single antigen-or biomarker-in biological samples. This new microarray ELISA platform allows the highly sensitive detection of up to 50 antigens simultaneously. Typically, commercially available antibodies are used in the development of these assays. However, to differentiate among six closely related BoNT serotypes, the scientists used high-affinity reagents generated in the laboratory of Dr. James Marks, University of California, San Francisco School of Medicine. The new, highly sensitive assay design developed by PNNL is rapid, specific, and simple enough for easy adoption by other research groups.

    Why It Matters: Protein toxins are considered to be potential biological threat agents because of their extreme toxicity, widespread availability, and ease of use. Biothreat toxins have been stockpiled for bioweapon use and even used in previous bioterrorism events. To treat exposure to these toxins, sensitive and specific detection systems that can quickly identify multiple biothreat toxins are needed. The new assay platform affords simultaneous detection of 10 biothreat toxins simultaneously in a diverse range of clinical and environmental samples, including blood, saliva, urine, stool, milk, and apple juice.

    Methods: The research team based their diagnostic assay on the antibody microarray approach. Antibody protein microarrays are miniaturized, solid-phase analytical assays for the detection of many proteins in parallel. This approach uses an array of high-affinity capture reagents, or antibodies, immobilized on a glass slide. These spatially arrayed antibodies bind a specific antigen from a sample added to the array. A second, labeled antibody that recognizes the same antigen as the first antibody then is used for detection to form a “sandwich” assay. This sandwich approach favors specificity in analyte detection.

    A Venn diagram outlining and contrasting some aspects of the fields of bio-MEMS, lab-on-a-chip, μTAS.

    The assay not only sensitively detected the biotoxins in buffer but also in complex clinical and environmental matrices at levels in the low picogram per mL-1 range and with a minimal sample volume of 20 microliters. The multiplex ELISA-based protein antibody microarray developed at PNNL demonstrates an excellent assay that can achieve some of the lowest detection limits and maintain sensitivity below the reported median lethal dose (LD50) in a wide range of biological fluids.


    Sponsors: This research was supported by the National Institute of Allergy and Infectious Diseases.

    Research Team: Kathryn Jenko, Yanfang Zhang, Yulia Kostenko, and Susan Varnum (PNNL); Yongfeng Fan, Consuelo Garcia-Rodriguez, Jianlong Lou, and James Marks (UCSF).

    Research Area: Biological Systems Science

    Reference: Jenko K, Y Zhang, Y Kostenko, Y Fan, C Garcia-Rodriguez, J Lou, JD Marks, and SM Varnum. 2014. Development of an ELISA Microarray Assay for the Sensitive and Simultaneous Detection of Ten Biodefense Toxins. Analyst 139(20):5093-5102. DOI: 10.1039/c4an01270d.

    See the full article here.

    Pacific Northwest National Laboratory (PNNL) is one of the United States Department of Energy National Laboratories, managed by the Department of Energy’s Office of Science. The main campus of the laboratory is in Richland, Washington.

    PNNL scientists conduct basic and applied research and development to strengthen U.S. scientific foundations for fundamental research and innovation; prevent and counter acts of terrorism through applied research in information analysis, cyber security, and the nonproliferation of weapons of mass destruction; increase the U.S. energy capacity and reduce dependence on imported oil; and reduce the effects of human activity on the environment. PNNL has been operated by Battelle Memorial Institute since 1965.


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  • richardmitnick 3:20 pm on October 29, 2014 Permalink | Reply
    Tags: Applied Research & Technology, , , , ,   

    From LBL: “New Lab Startup Afingen Uses Precision Method to Enhance Plants” 

    Berkeley Logo

    Berkeley Lab

    October 29, 2014
    Julie Chao (510) 486-6491

    Imagine being able to precisely control specific tissues of a plant to enhance desired traits without affecting the plant’s overall function. Thus a rubber tree could be manipulated to produce more natural latex. Trees grown for wood could be made with higher lignin content, making for stronger yet lighter-weight lumber. Crops could be altered so that only the leaves and certain other tissues had more wax, thus enhancing the plant’s drought tolerance, while its roots and other functions were unaffected.

    By manipulating a plant’s metabolic pathways, two scientists at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab), Henrik Scheller and Dominique Loqué, have figured out a way to genetically rewire plants to allow for an exceptionally high level of control over the spatial pattern of gene expression, while at the same time boosting expression to very high levels. Now they have launched a startup company called Afingen to apply this technology for developing low-cost biofuels that could be cost-competitive with gasoline and corn ethanol.

    Henrik Scheller (left) and Dominique Loque hold a tray of Arabidopsis Thaliana plants, which they used in their research. (Berkeley Lab photo)

    “With this tool we seem to have found a way to control very specifically what tissue or cell type expresses whatever we want to express,” said Scheller. “It’s a new way that people haven’t thought about to increase metabolic pathways. It could be for making more cell wall, for increasing the stress tolerance response in a specific tissue. We think there are many different applications.”

    Cost-competitive biofuels

    Afingen was awarded a Small Business Innovation Research (SBIR) grant earlier this year for $1.72 million to engineer switchgrass plants that will contain 20 percent more fermentable sugar and 40 percent less lignin in selected structures. The grant was provided under a new SBIR program at DOE that combines an SBIR grant with an option to license a specific technology produced at a national laboratory or university through DOE-supported research.

    “Techno-economic modeling done at (the Joint BioEnergy Institute, or JBEI) has shown that you would get a 23 percent reduction in the price of the biofuel with just a 20 percent reduction in lignin,” said Loqué. “If we could also increase the sugar content and make it easier to extract, that would reduce the price even further. But of course it also depends on the downstream efficiency.”

    Scheller and Loqué are plant biologists with the Department of Energy’s Joint BioEnergy Institute (JBEI), a Berkeley Lab-led research center established in 2007 to pursue breakthroughs in the production of cellulosic biofuels. Scheller heads the Feedstocks Division and Loqué leads the cell wall engineering group.

    The problem with too much lignin in biofuel feedstocks is that it is difficult and expensive to break down; reducing lignin content would allow the carbohydrates to be released and converted into fuels much more cost-effectively. Although low-lignin plants have been engineered, they grow poorly because important tissues lack the strength and structural integrity provided by the lignin. With Afingen’s technique, the plant can be manipulated to retain high lignin levels only in its water-carrying vascular cells, where cell-wall strength is needed for survival, but low levels throughout the rest of the plant.

    The centerpiece of Afingen’s technology is an “artificial positive feedback loop,” or APFL. The concept targets master transcription factors, which are molecules that regulate the expression of genes involved in certain biosynthetic processes, that is, whether certain genes are turned “on” or “off.” The APFL technology is a breakthrough in plant biotechnology, and Loqué and Scheller recently received an R&D 100 Award for the invention.

    An APFL is a segment of artificially produced DNA coded with instructions to make additional copies of a master transcription factor; when it is inserted at the start of a chosen biosynthetic pathway—such as the pathway that produces cellulose in fiber tissues—the plant cell will synthesize the cellulose and also make a copy of the master transcription factor that launched the cycle in the first place. Thus the cycle starts all over again, boosting cellulose production.

    The process differs from classical genetic engineering. “Some people distinguish between ‘transgenic’ and ‘cisgenic.’ We’re using only pieces of DNA that are already in that plant and just rearranging them in a new way,” said Scheller. “We’re not bringing in foreign DNA.”

    Other licensees and applications

    This breakthrough technique can also be used in fungi and for a wide variety of uses in plants, for example, to increase food crop yields or to boost production of highly specialized molecules used by the pharmaceutical and chemical industries. “It could also increase the quality of forage crops, such as hay fed to cows, by increasing the sugar content or improving the digestibility,” Loqué said.

    Another intriguing application is for biomanufacturing. By engineering plants to grow entirely new pharmaceuticals, specialty chemicals, or polymer materials, the plant essentially becomes a “factory.” “We’re interested in using the plant itself as a host for production,” Scheller said. “Just like you can upregulate pathways in plants that make cell walls or oil, you can also upregulate pathways that make other compounds or properties of interest.”

    Separately, two other companies are using the APFL technology. Tire manufacturer Bridgestone has a cooperative research and development agreement (CRADA) with JBEI to develop more productive rubber-producing plants. FuturaGene, a Brazilian paper and biomass company, has licensed the technology for exclusive use with eucalyptus trees and several other crops; APFL can enhance or develop traits to optimize wood quality for pulping and bioenergy applications.

    “The inventors/founders of Afingen made the decision to not compete for a license in fields of use that were of interest to other companies that had approached JBEI. This allowed JBEI to move the technology forward more quickly on several fronts,” said Robin Johnston, Berkeley Lab’s Acting Deputy Chief Technology Transfer Officer. “APFL is a very insightful platform technology, and I think only a fraction of the applications have even been considered yet.”

    Afingen currently has one employee—Ai Oikawa, a former postdoctoral researcher and now the director of plant engineering—and will be hiring three more in November. It is the third startup company to spin out of JBEI. The first two were Lygos, which uses synthetic biology tools to produce chemical compounds, and TeselaGen, which makes tools for DNA synthesis and cloning.

    See the full article here.

    A U.S. Department of Energy National Laboratory Operated by the University of California

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  • richardmitnick 6:52 pm on October 28, 2014 Permalink | Reply
    Tags: Applied Research & Technology, ,   

    From PPPL: “Bob Ellis designs a PPPL first: A 3D printed mirror for microwave launchers” 


    October 28, 2014
    John Greenwald

    When scientists at the Korea Supercomputing Tokamak Advanced Research (KSTAR) facility needed a crucial new component, they turned to PPPL engineer Bob Ellis. His task: Design a water-cooled fixed mirror that can withstand high heat loads for up to 300 seconds while directing microwaves beamed from launchers to heat the plasma that fuels fusion reactions.

    Bob Ellis with a 3D-printed plastic prototype for a non-mirror part of the launcher. (Photo by Elle Starkman/PPPL Office of Communications)

    KSTAR Tokamak

    Ellis, who had designed mirrors without coolant for shorter experiments, decided to try out a novel manufacturing process called 3D printing that produces components as unified wholes with minimal need for further processing. 3D printing would enable the mirror to be built for less cost than a non-water-cooled mirror produced by conventional manufacturing, Ellis said, “and that was a very nice thing to find out about.”

    The project marked a first for PPPL, which had previously used 3D printers to build plastic models but had not employed the process for creating metal parts. “Metal came into 3D printing about five years ago and was sort of exotic then,” said Phil Heitzenroeder, who heads the Mechanical Engineering Division at PPPL. “Now 3D is beginning to drift down into real-world metal products.”

    Ellis created a CAD-CAM model of the shoebox-size mirror system and delivered it to Imperial Machine & Tool Co. to produce the stainless steel and copper component through metal 3D printing. The process puts down hair-thin layers of stainless steel powder and fuses the powder in each layer with lasers. The parts are thus built from the bottom up layer by layer — another name for 3D printing is “additive manufacturing” — and follow every twist and turn of the CAD-CAM design.

    The stainless steel granules have the consistency of talcum powder before they are fused, said Christian M. Joest, president of the 70-year-old Columbia, N.J., machining and fabricating company. The 3D process took about 20 hours to complete, Joest said.

    The process proved ideal for the water-cooled mirror, which PPPL shipped to KSTAR in early October. The part consists of a thin sheet of polished copper mounted atop a stainless steel base, with serpentine channels for water winding through the base’s center. Conventional construction could have required the base to be built in multiple pieces so that the channels could be drilled, with the pieces then welded back together. “3D printing allows you to produce components in a single piece,” Ellis said, “and that’s a huge advantage.”

    Ellis now is designing a steerable mirror for KSTAR that can be controlled by computer to direct microwaves into different parts of the plasma. Ellis dubs this mirror, to be delivered next year, “Generation 2.0,” since it will have flat cooling channels rather than the round ones on the fixed mirror. The flat channels will increase the efficiency of the coolant, he said, which will be important for shedding heat from the constantly moving steerable mirror.

    See the full article here.

    Princeton Plasma Physics Laboratory is a U.S. Department of Energy national laboratory managed by Princeton University.

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  • richardmitnick 4:26 pm on October 28, 2014 Permalink | Reply
    Tags: Applied Research & Technology, Moon Studies,   

    From NOVA: “NASA Hopes to Test Mining Moon Water for Future Manned Missions” 



    28 Oct 2014
    Bridget Reed Morawski

    Two proposed missions would scour the moon’s upper crust for deposits of ice that may support moon bases.

    We may soon be one sip of water closer to living on the moon, at least if NASA’s plans pan out. The space agency has announced their intention to send two new missions to the moon to analyze and mine pockets of frozen water. The projects, nicknamed Lunar Flashlight and Resource Prospector Mission (RPM), will launch in late 2017 and 2018, respectively.

    The lunar poles are thought to harbor massive reserves of ice.

    Scientists are seeking to determine if future manned lunar outposts could exploit the deposits as a resource for drinking water. Here’s Mike Wall reporting for Space.com:

    “If you’re going to have humans on the moon and you need water for drinking, breathing, rocket fuel, anything you want, it’s much, much cheaper to live off the land than it is to bring everything with you,” said Lunar Flashlight principal investigator Barbara Cohen, of NASA’s Marshall Space Flight Center in Huntsville, Alabama.

    Lunar Flashlight will be making approximately 80 rotations around the moon’s atmosphere, hovering a mere 12 miles over the lunar surface. The intent of the mission is to find, measure, and map pockets of ice in darkened craters within and around the lunar poles.

    NASA Lunar Flashlight
    NASA/Lunar Flashlight

    The Lunar Flashlight mission would use a solar sail to carry the spacecraft along its orbital route. According to Cohen, the device would begin to expand upon reaching space, from “the size of a cereal box” into an 860-square foot solar sail. It will take Lunar Flashlight six months to reach the moon and another year to slowly descend to the 12-mile-high research orbit.
    LCROSS, an earlier NASA mission that looked for water on the moon, was a relatively low-budget affair.

    While Lunar Flashlight will only observe easily accessible deposits of water, RPM will operate on the surface of the moon. The rover will be equipped with drills and other materials to extract samples from 3.3 feet below the moon’s surface. It will chart water concentrations with an on-board neutron spectrometer and a near-infrared spectrometer. It’ll have to work fast, though, as it’s lifespan is expected to be only one week as it crawls from the near side of the moon into permanently dark lunar territory.

    Neither the Lunar Flashlight nor RPM projects have been approved by NASA yet, but if they are accepted, the knowledge could bring us closer to greater understanding the moon’s water resources—and what we might be able to do with them should we return.

    Two proposed NASA missions would lay more groundwork for manned lunar bases.

    See the full article here.

    NOVA is the highest rated science series on television and the most watched documentary series on public television. It is also one of television’s most acclaimed series, having won every major television award, most of them many times over.

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  • richardmitnick 5:33 pm on October 27, 2014 Permalink | Reply
    Tags: Applied Research & Technology,   

    From Princeton: “What makes a tumor switch from dormant to malignant?” 

    Princeton University
    Princeton University

    October 27, 2014
    Tien Nguyen, Department of Chemistry

    Cancer constantly wages war on the human body. Battles are won, lost or sometimes end in a stalemate. This stalemate, known as tumor dormancy, is extremely difficult to study in both cellular and animal models.

    A new computational model developed in the laboratory of Salvatore Torquato, a professor of chemistry at Princeton University, offers a way to probe the conditions surrounding tumor dormancy and the switch to a malignant state. Published Oct. 16 in the journal “PLOS ONE,” the so-called cellular automaton model simulated various scenarios of tumor growth leading to tumor dormancy or proliferation.
    Researchers from Princeton University have developed a computer model that simulates the competition between tumor dormancy and proliferation under various conditions. Through a series of simulations, they generated a phase diagram, pictured here, that could be used by experimentalists to predict when the tumor will be in a proliferative or dormant state. (Image courtesy of Salvatore Torquato Lab)

    “The power of the model is that it lets people test medically realistic scenarios,” said Torquato, who is also affiliated with the Princeton Institute for the Science and Technology of Materials. In future collaborations, these scenarios could be engineered in laboratory experiments and the observed outcomes could be used to calibrate the model.

    For each scenario, a set of rules is imposed on the virtual cell population. Rules are possible interactions, such as neighboring cell death or immune system suppression, that dictate cell division through probabilities derived from past experimental data. Once the researchers programmed the rules, they watched as the simulated competition unfolded between the tumor and the environmental factors that may suppress its growth.

    “We were very surprised to observe this phenomena where the tumor all of a sudden began to rapidly divide,” said Duyu Chen, graduate student in the Torquato lab and lead author on the article. This was the first time that the emergent switch behavior, which has been observed clinically, occurred spontaneously in a model, Chen said.

    The researchers evaluated a number of factors that could affect tumor cell growth including spontaneous cell mutations, mechanical properties, and the rate and strength of suppression factors such as the immune system. One of the model’s findings was the likely suppression of tumors in harsh environments, characterized by high density and pressure.

    “The way [the researchers] built their model system is that the dormancy state is not one of cells simply sleeping, in fact it’s an active state, it’s just that the whole system is held in equilibrium or stalemate,” said Micheal Espey, program manager at the National Cancer Institute who was not involved in the research. “That’s a very interesting viewpoint.”

    The research team also predicted that if the number of actively dividing cells within the proliferative rim reached a certain critical level, the tumor was very likely to begin growing rapidly. This result could provide insight into early cancer treatment, Chen said.

    Through repeated simulations the research team constructed a phase diagram that revealed the boundary between a dormant and proliferative state. If experimental data was incorporated into the model, Espey said, researchers could predict when the tumor was in a dormant state and when it was heading toward a proliferative state. “That’s the value,” he said.

    The research was supported by the National Cancer Institute under Award No. U54CA143803.

    See the full article here.

    About Princeton: Overview

    Princeton University is a vibrant community of scholarship and learning that stands in the nation’s service and in the service of all nations. Chartered in 1746, Princeton is the fourth-oldest college in the United States. Princeton is an independent, coeducational, nondenominational institution that provides undergraduate and graduate instruction in the humanities, social sciences, natural sciences and engineering.

    As a world-renowned research university, Princeton seeks to achieve the highest levels of distinction in the discovery and transmission of knowledge and understanding. At the same time, Princeton is distinctive among research universities in its commitment to undergraduate teaching.

    Today, more than 1,100 faculty members instruct approximately 5,200 undergraduate students and 2,600 graduate students. The University’s generous financial aid program ensures that talented students from all economic backgrounds can afford a Princeton education.

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