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  • richardmitnick 1:49 pm on September 3, 2014 Permalink | Reply
    Tags: , , , Lawrence Berkeley National laboratory, , Peptoids   

    From LBL: “Peptoid Nanosheets at the Oil/Water Interface” 

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    Berkeley Lab

    September 3, 2014
    Lynn Yarris (510) 486-5375

    From the people who brought us peptoid nanosheets that form at the interface between air and water, now come peptoid nanosheets that form at the interface between oil and water. Scientists at the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) have developed peptoid nanosheets – two-dimensional biomimetic materials with customizable properties – that self-assemble at an oil-water interface. This new development opens the door to designing peptoid nanosheets of increasing structural complexity and chemical functionality for a broad range of applications, including improved chemical sensors and separators, and safer, more effective drug delivery vehicles.

    Supramolecular assembly at an oil-water interface is an effective way to produce 2D nanomaterials from peptoids because that interface helps pre-organize the peptoid chains to facilitate their self-interaction,” says Ron Zuckermann, a senior scientist at the Molecular Foundry, a DOE nanoscience center hosted at Berkeley Lab. “This increased understanding of the peptoid assembly mechanism should enable us to scale-up to produce large quantities, or scale- down to screen many different nanosheets for novel functions.”

    nano
    Peptoid nanosheets are among the largest and thinnest free-floating organic crystals ever made, with an area-to-thickness equivalent of a plastic sheet covering a football field. Peptoid nanosheets can be engineered to carry out a wide variety of functions.
    two
    Ron Zuckerman and Geraldine Richmond led the development of peptoid nanosheets that form at the interface between oil and water, opening the door to increased structural complexity and chemical functionality for a broad range of applications.

    Zuckermann, who directs the Molecular Foundry’s Biological Nanostructures Facility, and Geraldine Richmond of the University of Oregon are the corresponding authors of a paper reporting these results in the Proceedings of the National Academy of Sciences (PNAS). The paper is titled Assembly and molecular order of two-dimensional peptoid nanosheets at the oil-water interface. Co-authors are Ellen Robertson, Gloria Olivier, Menglu Qian and Caroline Proulx.

    Peptoids are synthetic versions of proteins. Like their natural counterparts, peptoids fold and twist into distinct conformations that enable them to carry out a wide variety of specific functions. In 2010, Zuckermann and his group at the Molecular Foundry discovered a technique to synthesize peptoids into sheets that were just a few nanometers thick but up to 100 micrometers in length. These were among the largest and thinnest free-floating organic crystals ever made, with an area-to-thickness equivalent of a plastic sheet covering a football field. Just as the properties of peptoids can be chemically customized through robotic synthesis, the properties of peptoid nanosheets can also be engineered for specific functions.

    “Peptoid nanosheet properties can be tailored with great precision,” Zuckermann says, “and since peptoids are less vulnerable to chemical or metabolic breakdown than proteins, they are a highly promising platform for self-assembling bio-inspired nanomaterials.”

    In this latest effort, Zuckermann, Richmond and their co-authors used vibrational sum frequency spectroscopy to probe the molecular interactions between the peptoids as they assembled at the oil-water interface. These measurements revealed that peptoid polymers adsorbed to the interface are highly ordered, and that this order is greatly influenced by interactions between neighboring molecules.

    “We can literally see the polymer chains become more organized the closer they get to one another,” Zuckermann says.

    ft
    Peptoid polymers adsorbed to the oil-water interface are highly ordered thanks to interactions between neighboring molecules.

    The substitution of oil in place of air creates a raft of new opportunities for the engineering and production of peptoid nanosheets. For example, the oil phase could contain chemical reagents, serve to minimize evaporation of the aqueous phase, or enable microfluidic production.

    “The production of peptoid nanosheets in microfluidic devices means that we should soon be able to make combinatorial libraries of different functionalized nanosheets and screen them on a very small scale,” Zuckermann says. “This would be advantageous in the search for peptoid nanosheets with the molecular recognition and catalytic functions of proteins.”

    Zuckermann and his group at the Molecular Foundry are now investigating the addition of chemical reagents or cargo to the oil phase, and exploring their interactions with the peptoid monolayers that form during the nanosheet assembly process.

    “In the future we may be able to produce nanosheets with drugs, dyes, nanoparticles or other solutes trapped in the interior,” he says. “These new nanosheets could have a host of interesting biomedical, mechanical and optical properties.”

    This work was primarily funded by the DOE Office of Science and the Defense Threat Reduction Agency. Part of the research was performed at the Molecular Foundry and the Advanced Light Source, which are DOE Office of Science User Facilities.

    See the full article here.

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  • richardmitnick 1:41 pm on August 29, 2014 Permalink | Reply
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    From LBL: “Going to Extremes for Enzymes” 

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    Berkeley Lab

    August 29, 2014
    Lynn Yarris (510) 486-5375

    In the age-old nature versus nurture debate, Douglas Clark, a faculty scientist with Berkeley Lab and the University of California (UC) Berkeley, is not taking sides. In the search for enzymes that can break lignocellulose down into biofuel sugars under the extreme conditions of a refinery, he has prospected for extremophilic microbes and engineered his own cellulases.

    ext
    Extremophiles thriving in thermal springs where the water temperature can be close to boiling can be a rich source of enzymes for the deconstruction of lignocellulose.

    Speaking at the national meeting of the American Chemical Society (ACS) in San Francisco, Clark discussed research for the Energy Biosciences Institute (EBI) in which he and his collaborators are investigating ways to release plant sugars from lignin for the production of liquid transportation fuels. Sugars can be fermented into fuels once the woody matter comprised of cellulose, hemicellulose, and lignin is broken down, but lignocellulose is naturally recalcitrant.

    “Lignocellulose is designed by nature to stand tall and resist being broken down, and lignin in particular acts like a molecular glue to help hold it together” said Clark, who holds appointments with Berkeley Lab’s Physical Biosciences Division and UC Berkeley’s Chemical and Biomolecular Engineering Department where he currently serves as dean of the College of Chemistry. “Consequently, lignocellulosic biomass must undergo either chemical or enzymatic deconstruction to release the sugars that can be fermented to biofuels.”

    dc
    Douglas Clark holds joint appointments with Berkeley Lab and UC Berkeley and is a principal investigator with the Energy Biosciences Institute. (Photo by Roy Kaltschmidt)

    For various chemical reasons, all of which add up to cost-competitiveness, biorefineries could benefit if the production of biofuels from lignocellulosic biomass is carried out at temperatures between 65 and 70 degrees Celsius. The search by Clark and his EBI colleagues for cellulases that can tolerate these and even harsher conditions led them to thermal springs near Gerlach, Nevada, where the water temperature can be close to boiling. There they discovered a consortium of three hyperthermophilic Archaea that could grow on crystalline cellulose at 90 degrees Celsius.

    “This consortium represents the first instance of Archaea able to deconstruct lignocellulose optimally above 90°C,” Clark said.

    Following metagenomic studies on the consortium, the most active high-temperature cellulase was identified and named EBI-244.

    “The EBI-244 cellulase is active at temperatures as high as 108 degrees Celsius, the most extremely heat-tolerant enzyme ever found in any cellulose-digesting microbe,” Clark said.

    The most recent expedition of Clark and his colleagues was to thermal hot springs in Lassen Volcanic National Park, where they found an enzyme active on cellulose up to 100°C under highly acidic conditions – pH approximately 2.2.

    “The Lassen enzyme is the most acidothermophilic cellulase yet discovered,” Clark said. “The final products that it forms are similar to those produced by EBI244.”

    three
    A consortium of three hyperthermophilic Archaea that could grow on crystalline cellulose at 90 degrees Celsius yielded EBI-244, the most active high-temperature cellulase ever identified.

    In addition to bioprospecting for heat tolerant enzymes, Clark and his colleagues have developed a simple and effective mutagenesis method to enhance the properties of natural enzymes. Most recently they used this technique to increase the optimal temperature and enhance the thermostability of Ce17A, a fungal cellulase that is present in high concentrations in commercial cellulase cocktails. They engineered yeast to produce this enzyme with encouraging results.

    “The yeast Saccharomyces cerevisiae has often been used both in the engineering and basic study of Cel7A; however, Cel7A enzymes recombinantly expressed in yeast are often less active and less stable than their native counterparts,” Clark said. “We discovered that an important post-translational modification that was sometimes absent in the yeast-expressed enzyme was the underlying cause of this disparity and successfully carried out the post-translational modification in vitro. After this treatment, the properties of Cel7A recombinantly expressed in yeast were improved to match those of the native enzyme.”

    Collaborators in this research include Harvey Blanch, who also holds joint appointments with Berkeley Lab and UC Berkeley, and Frank Robb from the University of Maryland.

    EBI, which provided the funding for this research, is a collaborative partnership between BP, the funding agency, UC Berkeley, Berkeley Lab and the University of Illinois at Urbana-Champaign.

    See the full article here.

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  • richardmitnick 8:06 pm on August 27, 2014 Permalink | Reply
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    From Berkeley Lab: “Encyclopedia of How Genomes Function Gets Much Bigger” 

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    Berkeley Lab

    August 27, 2014
    Dan Krotz 510-486-4019

    A big step in understanding the mysteries of the human genome was unveiled today in the form of three analyses that provide the most detailed comparison yet of how the genomes of the fruit fly, roundworm, and human function.

    The research, appearing August 28 in in the journal Nature, compares how the information encoded in the three species’ genomes is “read out,” and how their DNA and proteins are organized into chromosomes.

    The results add billions of entries to a publicly available archive of functional genomic data. Scientists can use this resource to discover common features that apply to all organisms. These fundamental principles will likely offer insights into how the information in the human genome regulates development, and how it is responsible for diseases.

    mod
    Berkeley Lab scientists contributed to an NHGRI effort that provides the most detailed comparison yet of how the genomes of the fruit fly, roundworm, and human function. (Credit: Darryl Leja, NHGRI)

    The analyses were conducted by two consortia of scientists that include researchers from the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab). Both efforts were funded by the National Institutes of Health’s National Human Genome Research Institute.

    One of the consortiums, the “model organism Encyclopedia of DNA Elements” (modENCODE) project, catalogued the functional genomic elements in the fruit fly and roundworm. Susan Celniker and Gary Karpen of Berkeley Lab’s Life Sciences Division led two fruit fly research groups in this consortium. Ben Brown, also with the Life Sciences Division, participated in another consortium, ENCODE, to identify the functional elements in the human genome.

    The consortia are addressing one of the big questions in biology today: now that the human genome and many other genomes have been sequenced, how does the information encoded in an organism’s genome make an organism what it is? To find out, scientists have for the past several years studied the genomes of model organisms such as the fruit fly and roundworm, which are smaller than our genome, yet have many genes and biological pathways in common with humans. This research has led to a better understanding of human gene function, development, and disease.

    Comparing Transcriptomes

    In all organisms, the information encoded in genomes is transcribed into RNA molecules that are either translated into proteins, or utilized to perform functions in the cell. The collection of RNA molecules expressed in a cell is known as its transcriptome, which can be thought of as the “read out” of the genome.

    In the research announced today, dozens of scientists from several institutions looked for similarities and differences in the transcriptomes of human, roundworm, and fruit fly. They used deep sequencing technology and bioinformatics to generate large amounts of matched RNA-sequencing data for the three species. This involved 575 experiments that produced more than 67 billion sequence reads.

    A team led by Celniker, with help from Brown and scientists from several other labs, conducted the fruit fly portion of this research. They mapped the organism’s transcriptome at 30 time points of its development. They also explored how environmental perturbations such as heavy metals, herbicides, caffeine, alcohol and temperature affect the fly’s transcriptome. The result is the finest time-resolution analysis of the fly genome’s “read out” to date—and a mountain of new data.

    “We went from two billion reads in research we published in 2011, to 20 billion reads today,” says Celniker. “As a result, we found that the transcriptome is much more extensive and complex than previously thought. It has more long non-coding RNAs and more promoters.”

    When the scientists compared transcriptome data from all three species, they discovered 16 gene-expression modules corresponding to processes such as transcription and cell division that are conserved in the three animals. They also found a similar pattern of gene expression at an early stage of embryonic development in all three organisms.

    This work is described in a Nature article entitled “Comparative analysis of the transcriptome across distant species.”

    Comparing chromatin

    Another group, also consisting of dozens of scientists from several institutions, analyzed chromatin, which is the combination of DNA and proteins that organize an organism’s genome into chromosomes. Chromatin influences nearly every aspect of genome function.

    Karpen led the fruit fly portion of this work, with Harvard Medical School’s Peter Park contributing on the bioinformatics side, and scientists from several other labs also participating. The team mapped the distribution of chromatin proteins in the fruit fly genome. They also learned how chemical modifications to chromatin proteins impact genome functions.

    Their results were compared with results from human and roundworm chromatin research. In all, the group generated 800 new chromatin datasets from different cell lines and developmental stages of the three species, bringing the total number of datasets to more than 1400. These datasets are presented in a Nature article entitled “Comparative analysis of metazoan chromatin organization.”

    Here again, the scientists found many conserved chromatin features among the three organisms. They also found significant differences, such as in the composition and locations of repressive chromatin.

    But perhaps the biggest scientific dividend is the data itself.

    “We found many insights that need follow-up,” says Karpen. “And we’ve also greatly increased the amount of data that others can access. These datasets and analyses will provide a rich resource for comparative and species-specific investigations of how genomes, including the human genome, function.”

    See the full article here.

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  • richardmitnick 1:46 pm on August 26, 2014 Permalink | Reply
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    From Berkeley Lab: “Competition for Graphene” 

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    Berkeley Lab

    August 26, 2014
    Lynn Yarris (510) 486-5375

    A new argument has just been added to the growing case for graphene being bumped off its pedestal as the next big thing in the high-tech world by the two-dimensional semiconductors known as MX2 materials. An international collaboration of researchers led by a scientist with the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) has reported the first experimental observation of ultrafast charge transfer in photo-excited MX2 materials. The recorded charge transfer time clocked in at under 50 femtoseconds, comparable to the fastest times recorded for organic photovoltaics.

    “We’ve demonstrated, for the first time, efficient charge transfer in MX2 heterostructures through combined photoluminescence mapping and transient absorption measurements,” says Feng Wang, a condensed matter physicist with Berkeley Lab’s Materials Sciences Division and the University of California (UC) Berkeley’s Physics Department. “Having quantitatively determined charge transfer time to be less than 50 femtoseconds, our study suggests that MX2 heterostructures, with their remarkable electrical and optical properties and the rapid development of large-area synthesis, hold great promise for future photonic and optoelectronic applications.”

    fw
    Feng Wang is a condensed matter physicist with Berkeley Lab’s Materials Sciences Division and UC Berkeley’s Physics Department. (Photo by Roy Kaltschmidt)

    Wang is the corresponding author of a paper in Nature Nanotechnology describing this research. The paper is titled Ultrafast charge transfer in atomically thin MoS2/WS2 heterostructures. Co-authors are Xiaoping Hong, Jonghwan Kim, Su-Fei Shi, Yu Zhang, Chenhao Jin, Yinghui Sun, Sefaattin Tongay, Junqiao Wu and Yanfeng Zhang.

    MX2 monolayers consist of a single layer of transition metal atoms, such as molybdenum (Mo) or tungsten (W), sandwiched between two layers of chalcogen atoms, such as sulfur (S). The resulting heterostructure is bound by the relatively weak intermolecular attraction known as the van der Waals force. These 2D semiconductors feature the same hexagonal “honeycombed” structure as graphene and superfast electrical conductance, but, unlike graphene, they have natural energy band-gaps. This facilitates their application in transistors and other electronic devices because, unlike graphene, their electrical conductance can be switched off.

    “Combining different MX2 layers together allows one to control their physical properties,” says Wang, who is also an investigator with the Kavli Energy NanoSciences Institute (Kavli-ENSI). “For example, the combination of MoS2 and WS2 forms a type-II semiconductor that enables fast charge separation. The separation of photoexcited electrons and holes is essential for driving an electrical current in a photodetector or solar cell.”

    In demonstrating the ultrafast charge separation capabilities of atomically thin samples of MoS2/WS2 heterostructures, Wang and his collaborators have opened up potentially rich new avenues, not only for photonics and optoelectronics, but also for photovoltaics.

    photo
    Photoluminescence mapping of a MoS2/WS2 heterostructure with the color scale representing photoluminescence intensity shows strong quenching of the MoS2 photoluminescence. (Image courtesy of Feng Wang group)

    “MX2 semiconductors have extremely strong optical absorption properties and compared with organic photovoltaic materials, have a crystalline structure and better electrical transport properties,” Wang says. “Factor in a femtosecond charge transfer rate and MX2 semiconductors provide an ideal way to spatially separate electrons and holes for electrical collection and utilization.”

    Wang and his colleagues are studying the microscopic origins of charge transfer in MX2 heterostructures and the variation in charge transfer rates between different MX2 materials.

    “We’re also interested in controlling the charge transfer process with external electrical fields as a means of utilizing MX2 heterostructures in photovoltaic devices,” Wang says.

    This research was supported by an Early Career Research Award from the DOE Office of Science through UC Berkeley, and by funding agencies in China through the Peking University in Beijing.

    See the full article here.

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  • richardmitnick 12:30 pm on August 22, 2014 Permalink | Reply
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    From Berkeley Lab: “Shaping the Future of Nanocrystals” 

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    Berkeley Lab

    August 21, 2014
    Lynn Yarris

    The first direct observations of how facets form and develop on platinum nanocubes point the way towards more sophisticated and effective nanocrystal design and reveal that a nearly 150 year-old scientific law describing crystal growth breaks down at the nanoscale.

    Researchers with the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) used highly sophisticated transmission electron microscopes and an advanced high-resolution, fast-detection camera to capture the physical mechanisms that control the evolution of facets – flat faces – on the surfaces of platinum nanocubes formed in liquids. Understanding how facets develop on a nanocrystal is critical to controlling the crystal’s geometric shape, which in turn is critical to controlling the crystal’s chemical and electronic properties.

    “For years, predictions of the equilibrium shape of a nanocrystal have been based on the surface energy minimization proposal by Josiah Willard Gibbs in the 1870s to describe the equilibrium shape of a water droplet,” says Haimei Zheng, a staff scientist in Berkeley Lab’s Materials Sciences Division who led this study. “For nanocrystals, the idea is that during crystal growth, high-energy facets will grow at a higher rate than low-energy facets and eventually disappear, resulting in a nanocrystal whose shape is configured to minimize surface energy.”

    The research of Zheng and her collaborators showed that at the molecular level, the geometric shape of nanocrystals during synthesis in solution is actually driven by differences in the mobility of ligands across the surfaces of different facets.

    “By choosing ligands that selectively bind on the facets, we should be able to control the shape of the nanocrystal as it grows,” she says. “This would provide a new way to design nanomaterials for advanced applications, including nanostructures for bio-imaging, catalysts for solar conversion, and energy storage.”

    two
    Haimei Zheng and Hong-Gang Liao used TEMs at the National Center for Electron Microscopy and a K2-IS camera to record the first direct observations facet formation in platinum nanocubes. (Photo by Kelly Owen)

    Zheng is the corresponding author of a paper in Science titled Facet Development During Platinum Nanocube Growth. Hong-Gang Liao is the lead author. Co-authors are Danylo Zherebetskyy, Huolin Xin, Cory Czarnik, Peter Ercius, Hans Elmlund, Ming Pan and Lin-Wang Wang.

    The performance of nanocrystals in such surface-enhanced applications as catalysis, sensing and photo-optics is strongly influenced by shape. While significant advances have been made in the synthesis of nanocrystals featuring a variety of shapes – cube, octahedron, tetrahedron, decahedron, icosahedron, etc., – controlling these shapes is often difficult and unpredictable.

    “A major roadblock has been that the atomic pathways of facet development in nanocrystals are mostly unknown due to the lack of direct observation,” Zheng says. “It has been assumed that commonly used surfactants modify the energy of specific facets through preferential adsorption, thereby influencing the relative growth rate of different facets and the shape of the final nanocrystal. However, this assumption was based on post-reaction characterizations that did not account for how facet dynamics evolve during crystal growth.”

    As a crystal undergoes growth, its constituent atoms or molecules fan out along specific directional planes whose coordinates are denoted by a three-digit system called the Miller Index. Facets form when the surfaces along different planes grow at different rates. Three of the most critical facets for determining a crystal’s geometric shape are the so-called “low index facets,” which are designated under the Miller Index as {100}, {110} and {111}.

    image
    Berkeley Lab researchers found that differences in ligand mobility during crystallization cause the low index facets – {100}, {110} and {111} – to stop growing at different times, resulting in the crystal’s final cubic shape. (Image courtesy of Haimei Zheng group)

    Working with platinum, one of the most effective industrial catalysts in use today, Zheng and her collaborators initiated the growth of nanocubes in a thin layer of liquid sandwiched between two silicon nitride membranes. This microfabricated liquid cell can encapsulate and maintain the liquid inside the high vacuum of a transmission electron microscope (TEM) for an extended period of time, enabling in situ observations of single nanoparticle growth trajectories.

    “With the liquid cells, we’re able to use TEMs to observe the growth of nanocrystals that remarkably resemble nanocrystals synthesized in flasks,” Zheng says. “We found that the growth rates of all low index facets are similar until the {100} facets stop growing. The {110} facets will continue to grow until they reach two neighboring {100} facets, at which point they form the edge of a cube whose corners will be filled in by the continued growth of {111} facets. The arrested growth of the {100} facets that triggers this process is determined by ligand mobility on the {100} facets, which is much lower than on the {110} and {111} facets.”

    For their observations, Zeng and her collaborators were able to use several of the TEMs at Berkeley Lab’s National Center for Electron Microscopy (NCEM), a DOE Office of Science user facility, including the TEAM 0.5 instrument, the world’s most powerful TEM. In addition, they were able to use a K2-IS camera from Gatan, Inc., which can capture electron images directly onto a CMOS sensor at 400 frames per second (fps) with 2K-by-2K pixel resolution.

    “The K2-IS camera can also be configured to capture images at up to 1600 fps with appropriate scaling of the field of view, which is critical for observing particles that are moving dynamically in the field of view,” says lead author Liao, a member of Zheng’s research group. “The elimination of the traditional scintillation process during image detection results in significant improvement in both sensitivity and resolution. High resolution imaging is also facilitated by the thin silicon nitride membranes of our liquid cell window, which is about 10 nanometers thick per membrane.”

    The lower ligand mobility and arrested growth of selected facets experimentally observed by Zheng and Liao, were supported by ab initio calculations carried out under the leadership of co-author Wang, a senior scientist with the Materials Sciences Division who heads the Computational Material Science and Nano Science group.

    “At first, we thought the continued growth in the {111} direction might be a result of higher surface energy on the {111} plane,” says co-author Zherebetskyy, a member of Wang’s group. “The experimental observations forced us to consider alternative mechanisms and our calculations show that the relatively low energy barrier on the {111} plane allow the ligand molecules on that plane to be very mobile.”

    Says Wang, “Our collaboration with Haimei Zheng’s group showcases how ab initio calculations can be combined with experimental observations to shed new light on hidden molecular processes.”

    Zheng and her group are now in the process of determining whether the ligand mobility in platinum that shaped the formation of cube-shaped nanocrystals also applies to ligands in other nanomaterials and the formation of nanocrystals in other geometric shapes.

    This research was supported by the DOE Office of Science.

    See the full article here.

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  • richardmitnick 4:09 pm on August 21, 2014 Permalink | Reply
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    From Berkeley Lab: “Researchers Map Quantum Vortices Inside Superfluid Helium Nanodroplets” 

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    Berkeley Lab

    August 21, 2014
    Kate Greene

    Scientists have, for the first time, characterized so-called quantum vortices that swirl within tiny droplets of liquid helium. The research, led by scientists at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab), the University of Southern California, and SLAC National Accelerator Laboratory, confirms that helium nanodroplets are in fact the smallest possible superfluidic objects and opens new avenues for studying quantum rotation.

    “The observation of quantum vortices is one of the most clear and unique demonstrations of the quantum properties of these microscopic objects,” says Oliver Gessner, senior scientist in the Chemical Sciences Division at Berkeley Lab. Gessner and colleagues, Andrey Vilesov of the University of Southern California and Christoph Bostedt of SLAC National Accelerator Laboratory at Stanford, led the multi-facility and multi-university team that published the work this week in Science.

    Droplet_art_fin3drop
    Illustration of analysis of superfluid helium nanodroplets. Droplets are emitted via a cooled nozzle (upper right) and probed with x-ray from the free-electron laser. The multicolored pattern (upper left) represents a diffraction pattern that reveals the shape of a droplet and the presence of quantum vortices such as those represented in the turquoise circle with swirls (bottom center). Credit: Felix P. Sturm and Daniel S. Slaughter, Berkeley Lab.

    The finding could have implications for other liquid or gas systems that contain vortices, says USC’s Vilesov. “The quest for quantum vortices in superfluid droplets has stretched for decades,” he says. “But this is the first time they have been seen in superfluid droplets.”

    Superfluid helium has long captured scientist’s imagination since its discovery in the 1930s. Unlike normal fluids, superfluids have no viscosity, a feature that leads to strange and sometimes unexpected properties such as crawling up the walls of containers or dripping through barriers that contained the liquid before it transitioned to a superfluid.

    Helium superfluidity can be achieved when helium is cooled to near absolute zero (zero kelvin or about -460 degrees F). At this temperature, the atoms within the liquid no longer vibrate with heat energy and instead settle into a calm state in which all atoms act together in unison, as if they were a single particle.

    For decades, researchers have known that when superfluid helium is rotated–in a little spinning bucket, say–the rotation produces quantum vortices, swirls that are regularly spaced throughout the liquid. But the question remained whether anyone could see this behavior in an isolated, nanoscale droplet. If the swirls were there, it would confirm that helium nanodroplets, which can range in size from tens of nanometers to microns, are indeed superfluid throughout and that the motion of the entire liquid drop is that of a single quantum object rather than a mixture of independent particles.

    But measuring liquid flow in helium nanodroplets has proven to be a serious challenge. “The way these droplets are made is by passing helium through a tiny nozzle that is cryogenically cooled down to below 10 Kelvin,” says Gessner. “Then, the nanoscale droplets shoot through a vacuum chamber at almost 200 meters-per-second. They live once for a few milliseconds while traversing the experimental chamber and then they’re gone. How do you show that these objects, which are all different from one another, have quantum vortices inside?”

    og
    Oliver Gessner, Chemical Sciences Division, Berkeley Lab. Credit: Roy Kaltschmidt

    The researchers turned to a facility at SLAC called the Linac Coherent Light Source (LCLS), a DOE Office of Science user facility that is the world’s first x-ray free-electron laser. This laser produces very short light pulses, lasting just a ten-trillionth of a second, which contain a huge number of high-energy photons. These intense x-ray pulses can effectively take snapshots of single, ultra-fast, ultra-small objects and phenomena.

    slac
    Inside the SLAC LCLS

    “With the new x-ray free electron laser, we can now image phenomenon and look at processes far beyond what we could imagine just a decade ago,” says Bostedt of SLAC. “Looking at the droplets gave us a beautiful glimpse into the quantum world. It really opens the door to fascinating sciences.”

    In the experiment, the researchers blasted a stream of helium nanodroplets across the x-ray laser beam inside a vacuum chamber; a detector caught the pattern that formed when the x-ray light diffracted off the drops.

    The diffraction patterns immediately revealed that the shape of many droplets were not spheres, as was previously assumed. Instead, they were oblate. Just as the Earth’s rotation causes it to bulge at the equator, so too do rotating nanodroplets expand around the middle and flatten at the top and bottom.

    But the vortices themselves are invisible to x-ray diffraction, so the researchers used a trick of adding xenon atoms to the droplets. The xenon atoms get pulled into the vortices and cluster together.

    “It’s similar to pulling the plug in a bathtub and watching the kids’ toys gather in the vortex,” says Gessner. The xenon atoms diffract x-ray light much stronger than the surrounding helium, making the regular arrays of vortices inside the droplet visible. In this way, the researchers confirmed that vortices in nanodroplets behave as those found in larger amounts of rotating superfluid helium.

    Armed with this new information, the researchers were able to determine the rotational speed of the nanodroplets. They were surprised to find that the nanodroplets spin up to 100,000 times faster than any other superfluid helium sample ever studied in a laboratory.

    Moreover, while normal liquid drops will change shape as they spin faster and faster–to resemble a peanut or multi-lobed globule, for instance–the researchers saw no evidence of such shapeshifting in the helium nanodroplets. “Essentially, we’re exploring a new regime of quantum rotation with this matter,” Gessner says.

    “It’s a new kind of matter in a sense because it is a self-contained isolated superfluid,” he adds. “It’s just all by itself, held together by its own surface tension. It’s pretty perfect to study these systems if one wants to understand superfluidity and isolate it as much as possible.”

    This research was supported by the DOE Office of Science, Office of Basic Energy Sciences, Chemical Sciences, Geosciences and Biosciences Division as well as the National Science Foundation.

    See the full article here.

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  • richardmitnick 2:39 pm on August 19, 2014 Permalink | Reply
    Tags: , , Lawrence Berkeley National laboratory, Nuclear magnetic resonance,   

    From Berkeley Lab: “News Center NMR Using Earth’s Magnetic Field” 

    Berkeley Logo

    Berkeley Lab

    August 19, 2014
    Rachel Berkowitz

    Earth’s magnetic field, a familiar directional indicator over long distances, is routinely probed in applications ranging from geology to archaeology. Now it has provided the basis for a technique which might, one day, be used to characterize the chemical composition of fluid mixtures in their native environments.

    Researchers from the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) conducted a proof-of-concept NMR experiment in which a mixture of hydrocarbons and water was analyzed using a high-sensitivity magnetometer and a magnetic field comparable to that of the Earth.

    The work was conducted in the NMR laboratory of Alexander Pines, one of the world’s foremost NMR authorities, as part of a long-standing collaboration with physicist Dmitry Budker at the University of California, Berkeley, along with colleagues at the National Institute of Standards and Technology (NIST). The work will be featured on the cover of Angewandte Chemie and is published in a paper titled Ultra-Low-Field NMR Relaxation and Diffusion Measurements Using an Optical Magnetometer. The corresponding author is Paul Ganssle, who was a PhD student in Pines’ lab at the time of the work.

    “This fundamental research program seeks to answer a broad question: how can we sense the interior chemical and physical attributes of an object at a distance, without sampling it or encapsulating it?” says Vikram Bajaj, a principal investigator in Pines’ group. “A particularly beautiful aspect of magnetic resonance is its ability to gently peer within intact objects, but it’s tough to do that from far away.”

    High-field and low-field NMR

    The exquisite sensitivity of NMR for detecting chemical composition, and the spatial resolution which it can provide in medical applications, requires large and precise superconducting magnets. These magnets are expensive and immobile. Further, the sample of interest must be placed inside the magnet, such that the entire sample is exposed to a homogeneous magnetic field. This well-developed method is called high-field NMR. The sensitivity of high-field NMR is proportional to magnetic field strength.

    three
    (From left) Alex Pines, Dimitry Budker and Scott Seltzer led a proof-of-concept NMR experiment using a high-sensitivity magnetometer and a magnetic field comparable to that of the Earth. (Photo by Roy Kaltschmidt)

    But chemical characterization of objects that cannot be placed inside a magnet requires a different approach. In ex situ NMR measurements, the geometry of a typical high-field experiment is reversed such that the detector probes the sample surface, and the magnetic field is projected into the object. A main challenge with this situation is generating a homogeneous magnetic field over a sufficiently large sample area: it is not feasible to generate field strengths necessary to make conventional high-resolution NMR measurements.

    Instead of a superconducting magnet, low-field NMR measurements may rely on Earth’s magnetic field, given a sufficiently sensitive magnetometer.

    “One nice thing about Earth’s magnetic field is that it’s very homogeneous,” explains Ganssle. “The problem with its use in inductively-detected MRI [MRI – magnetic resonance imaging – is NMR’s technological sibling] is that you need a magnetic field that’s both strong and homogeneous, so you need to surround the whole subject with superconducting coils, which is not something that’s possible in an application like oil-well logging.”

    “Sensitivity of magnetic resonance depends profoundly on the magnetic field, because the field causes the detected spins to align slightly,” adds Bajaj. “The stronger the applied field, the stronger the signal, and the higher its frequency, which also contributes to the detection sensitivity.”

    pg
    Paul Ganssle is the corresponding author of a paper in Angewandte Chemie describing the ultra-low-field NMR using an optical magnetometer. (Photo by Roy Kaltschmidt)

    Earth’s magnetic field is indeed very weak, but optical magnetometers can serve as detectors for ultra-low-field NMR measurements in the ambient field alone without any permanent magnets. This means that ex-situ measurements lose chemical sensitivity due to field strength alone. But this method offers other advantages.

    Relaxation and diffusion

    In high-field NMR, the chemical properties of a sample are determined from their resonance spectrum, but this is not possible without either extremely high fields or extremely long-lived coherent signals (neither of which are possible with permanent magnets). In contrast, relaxation and diffusion measurements in low-field NMR are more than sufficient to determine bulk materials properties.

    “The approach at low-field, which you can achieve using permanent magnets or Earth’s magnetic field, is to measure spin relaxation,” explains Ganssle. Relaxation refers to the rate at which polarized spin returns to equilibrium, based on chemical and physical characteristics of the system. Additionally, NMR experiments resolve chemical compounds based on their different diffusion coefficients, which depend on the size and shape of the molecule.

    A key difference between this and conventional experiments is that the relaxation and diffusion properties are resolved through optically-detected NMR, which operates sensitively even in low magnetic fields.

    “A previous achievement of our collaboration has been the development of magnetometers for the detection of NMR,” says Bajaj. “This experiment represents the first time magnetometers have been used to make combined relaxation and diffusion measurements of multicomponent mixtures.”

    Relaxation and/or diffusion measurements are already commonly used in the oil industry for underground NMR measurements, though conventional probes use a permanent magnet to increase the local magnetic field. There were attempts to perform oil well logging starting in the 1950s using the Earth’s ambient field, but insufficient detection sensitivity led to the introduction of magnets, which are now ubiquitous in logging tools.

    “What’s novel here is that using magnetometers, we finally have technology that might be sensitive enough for efficient detection in the Earth’s field, perhaps ultimately enabling detection at longer distances,” explains Scott Seltzer, a co-author on the study.

    The design was tested in the lab by measuring relaxation coefficients first for various hydrocarbons and water by themselves, then for a heterogeneous mixture, as well as in two-dimensional correlation experiments, using a magnetometer and an applied magnetic field representative of Earth’s.

    “This proof of concept might be productively applied in the oil industry,” says Ganssle. “We mixed hydrocarbons and water, pre-polarized them with a magnet, and applied a magnetic field the same as the Earth’s. Then we made measurements with our magnetometer and determined that we had easily enough sensitivity to separate components of oil and water based on their relaxation spectra.”

    This technology could help the oil industry to characterize fluids in rocks, because water relaxes at a different rate from oil. Other applications include measuring the content of water and oil flowing in a pipeline by measuring chemical composition with time, and inspecting the quality of foods and any kind of polymer curing process such as cement curing and drying.

    The next step involves understanding the depth in a geological formation that could be imaged with this technology.

    “Our next study will be tailored to that question,” says Bajaj. “We hope that this technology will eventually peer a meter or more into the formation and elucidate the chemistry within.”

    Eventually, probes could be used to characterize entire borehole environments in this way, while current devices can only image inches deep. The combination of terrestrial magnetism and versatile sensing technology again offers an elegant solution.

    Other authors on the Angewandte Chemie paper include Hyun Doug Shin, Micah Ledbetter, Dmitry Budker, Svenja Knappe, John Kitching, and Alexander Pines. The current publication presents some of the work for which Berkeley Lab won an R&D 100 award earlierthis year on optically-detected oil well logging by MRI.

    This research was supported by the U.S. Department of Energy’s Office of Science.

    See the full article here.

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  • richardmitnick 4:44 pm on August 18, 2014 Permalink | Reply
    Tags: , , , Lawrence Berkeley National laboratory   

    From Berkeley Lab: “Bionic Liquids from Lignin” 

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    Berkeley Lab

    August 18, 2014
    Lynn Yarris (510) 486-5375

    While the powerful solvents known as ionic liquids show great promise for liberating fermentable sugars from lignocellulose and improving the economics of advanced biofuels, an even more promising candidate is on the horizon – bionic liquids.

    Researchers at the U.S. Department of Energy’s Joint BioEnergy Institute (JBEI) have developed “bionic liquids” from lignin and hemicellulose, two by-products of biofuel production from biorefineries. JBEI is a multi-institutional partnership led by Lawrence Berkeley National Laboratory (Berkeley Lab) that was established by the DOE Office of Science to accelerate the development of advanced, next-generation biofuels.

    “What if we could turn what is now a bane to the bioenergy industry into a boon?” says Blake Simmons, a chemical engineer who is JBEI’s Chief Science and Technology Officer and heads JBEI’s Deconstruction Division. “Lignin is viewed as a waste stream that is typically burned to generate heat and electricity for the biorefinery, but if other uses for lignin could be found with higher economic value it would significantly improve the refinery’s overall economics. Our concept of bionic liquids opens the door to realizing a closed-loop process for future lignocellulosic biorefineries, and has far-reaching economic impacts for other ionic liquid-based process technologies that currently use ionic liquids synthesized from petroleum sources.”

    Simmons and Seema Singh, who directs JBEI’s biomass pretreatment program, are the corresponding authors of a paper describing this research in the Proceedings of the National Academy of Sciences (PNAS). The paper is titled Efficient biomass pretreatment using ionic liquids derived from lignin and hemicellulose. The lead author is Aaron Socha. Other co-authors are Ramakrishnan Parthasarathi, Jian Shi, Sivakumar Pattathil, Dorian Whyte, Maxime Bergeron, Anthe George, Kim Tran, Vitalie Stavila, Sivasankari Venkatachalam and Michael Hahn.

    two
    Blake Simmons and Seema Singh of the Joint BioEnergy Institute (JBEI) are leading an effort to improve the economics of biofuel production through improved deconstruction of lignocellulosic biomass.

    The cellulosic sugars stored in the biomass of grasses and other non-food crops, and in agricultural waste, can be used to make advanced biofuels that could substantially reduce the use of the fossil fuels responsible for the release of nearly 9 billion metric tons of excess carbon into the atmosphere each year. More than a billion tons of biomass are produced annually in the United States alone and fuels from this biomass could be clean, green and renewable substitutes for gasoline, diesel and jet fuel on a gallon-for-gallon basis. Unlike ethanol, “drop-in” transportation fuels derived from biomass have the potential to be directly dropped into today’s engines and infrastructures at high levels – greater than 50-percent – without negatively impacting performance.

    However, if biofuels, including cellulosic ethanol, are to be a commercial success, they must be cost-competitive with fossil fuels. This means economic technologies must be developed for extracting fermentable sugars from cellulosic biomass and synthesizing them into fuels and other valuable chemical products. A major challenge has been that unlike the simple sugars in corn grain, the complex polysaccharides in biomass are deeply embedded within a tough woody material called lignin. Researchers at JBEI have been cost-effectively deconstructing biomass into fuel sugars by pre-treating the biomass with ionic liquids – salts that are composed entirely of paired ions and are liquid at room temperature. The ionic liquids that have emerged from this JBEI effort as a benchmark for biomass processing are imidazolium-based molten salts, which are made from nonrenewable sources such as petroleum or natural gas.

    “Imidazolium-based ionic liquids effectively and efficiently dissolve biomass, and represent a remarkable platform for biomass pretreatment, but imidazolium cations are expensive and thus limited in their large-scale industrial deployment,” says Singh. “To replace them with a renewable product, we synthesized a series of tertiary amine-based ionic liquids from aromatic aldehydes in lignin and hemicellulose.”

    as
    Aaron Socha directs the Center for Sustainable Energy at the Bronx Community College in NYC.

    The JBEI researchers tested the effectiveness of their bionic liquids as a pre-treatment for biomass deconstruction on switchgrass, one of the leading potential crops for making liquid transportation fuels. After 73 hours of incubation with these new bionic liquids, sugar yields were between 90- and 95-percent for glucose, and between 70- and 75-percent for xylose. These yields are comparable to the yields obtained after pre-treatment with the best-performing imidazolium-based ionic liquids.

    “Lignin and hemicellulose are byproducts from the agricultural industry, biofuel plants and pulp mills, which not only makes these abundant polymers inexpensive, but also allows for a closed-loop bio-refinery, in which the lignin in the waste stream can be up-cycled and reused to make more bionic liquid,” says lead author Socha, who is now the Director of the Center for Sustainable Energy at the Bronx Community College in New York City.

    The current batch of bionic liquids was made using reductive amination and phosphoric acid, but Socha says the research team is now investigating the use of alternative reducing agents and acids that would be less expensive and even more environmentally benign.

    “Our results have established an important foundation for the further study of bionic liquids in biofuels as well as other industrial applications,” he says.

    This research was supported by the DOE Office of Science.

    See the full article here.

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  • richardmitnick 2:31 pm on August 15, 2014 Permalink | Reply
    Tags: , , , Lawrence Berkeley National laboratory   

    From Berkeley Lab: “Of Metal Heads and Imaging” 

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    Berkeley Lab

    August 15, 2014
    Lynn Yarris (510) 486-5375

    You don’t have to listen to heavy-metal music to be a metal head. The human brain harbors far more copper, iron and zinc than anywhere else in the body. Abnormally high levels of these metals can lead to disorders such as Alzheimer’s and Parkinson’s diseases. Chris Chang, a faculty chemist with Berkeley Lab’s Chemical Sciences Division, has spent the past several years developing new probes and techniques for imaging the molecular activity of these metals in the brain. Speaking at the national meeting of the American Chemical Society (ACS) in San Francisco, he discussed challenges and recent achievements in this area of research.

    “Brain physiology relies on unique inorganic chemistry not found elsewhere in the body,” Chang said. “Although it accounts for only two-percent of total body mass, it is the body’s most oxidatively active organ, consuming more than 20 percent of the oxygen we breathe. This high oxygen intake combined with the brain’s high content of copper and iron can lead to oxidative damage and subsequent neuronal death when levels of these redox-active metals rise and become misregulated.”

    cc
    Chris Chang is a faculty chemist with Berkeley Lab and UC Berkeley, and an HHMI investigator. (Photo by Roy Kaltschmidt)

    Chang, who also holds faculty appointments with the University of California (UC) Berkeley’s Chemistry Department and is an investigator with the Howard Hughes Medical Institute (HHMI), described a series of small-molecule fluorescent probes he and his group developed to safely image copper levels in living cells. Their first success was Coppersensor-3 (CS3), a probe that can be used to image labile copper pools in living cells at endogenous basal levels.

    “We used CS3 in conjunction with synchrotron-based X-ray fluorescence microscopy (XRFM) to establish the first link between mobile copper and major cell signaling pathways,” Chang said. “Neuronal cells move significant pools of copper upon activation and these copper movements are dependent on calcium signaling.”

    The most recent copper probe from Chang’s group is Coppersensor 790 (CS790), a fluorescent sensor that features near-infrared excitation and emission capabilities, ideal for penetrating thicker biological specimens.

    “CS790 can be used to monitor fluctuations in exchangeable copper stores under basal conditions, as well as under copper overload or deficiency conditions,” he said.

    For monitoring iron in the brain, Chang and his group have developed Iron Probe 1 (IP1), which enables researchers to monitor changes in natural cellular iron stores.

    “IP1 is a new type of reaction-based turn-on fluorescent probe for monitoring exchangeable iron ion pools in aqueous solution and living cells,” he said. “It is sensitive enough to detect endogenous, basal labile iron pools and can identify and visualize expansions in these iron pools upon stimulation with either the hormone hepcidin or vitamin C.”

    These and other probes being developed by Chang and his group will help provide a better understanding of the contributions by metals such as copper and iron to the functioning of the brain in various stages of health and disease.

    “The brain offers a grand challenge for a molecular understanding of memory and senses such as sight, smell, and taste, as well as for developing new therapeutics for stroke, aging and neurodegenerative diseases such as Alzheimer’s and Parkinson’s,” Chang said.

    See the full article here.

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  • richardmitnick 9:30 am on August 3, 2014 Permalink | Reply
    Tags: , , Lawrence Berkeley National laboratory,   

    From BerkeleyLab: “Recently Identified Molecule Could Lead to New Way to Repair Tendons” 

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    Berkeley Lab

    July 24, 2014
    Dan Krotz

    It’s an all-too familiar scenario for many people. You sprain your ankle or twist your knee. If you’re an adult, the initial pain is followed by a long road of recovery, with no promise that the torn ligament or tendon will ever regain its full strength.

    That’s because tendon and ligament cells in adults produce little collagen, the fibrous protein that is used to build new tendon and ligament tissue. Physical therapy and surgery help, but for many people, there may always be a nagging reminder of the injury.

    But what if doctors could coax an injured tendon to regenerate itself back to its original strength? A solution along these lines may come from an unlikely, feathered source. Berkeley Lab scientists have identified a molecule that guides the formation of tendons and ligaments. And they found it in chicken embryos.

    image
    This image, which depicts a tendon-muscle junction in an adolescent chicken (approximately 4 months old), suggests a new way to repair tendons. It shows a growth plate with a large number of tendon cells stained purple. The muscle is at the top left and the tendon is at the bottom and right. The tendon, which is made up of a group of threads called fibrils, is growing so that the tendon length will match the growth of the bones. The image shows that mature tendon has very few cells.(Credit: Richard Schwarz)

    The molecule binds to the outer lipid membrane of tendon cells, and allows tendon cells to signal their presence to other cells. The molecule’s job is to orchestrate growth and collagen production. In a chicken embryo, a dense growth plate of tendon cells work together to spin out collagen and weave new tendon, which is basically a collagen rope. The more cells signaling their presence to each other, the more collagen is produced.

    The gene that expresses the protein component of this signaling molecule is highly conserved among animals, meaning a similar molecule performs the same tendon-building job in developing humans.

    “More research is needed, but our initial experiments suggest this protein-phospholipid molecule could be administered to adults who’ve had tendon injuries, to spark healthy tendon growth in the same way that happens during embryogenesis,” says Richard Schwarz of Berkeley Lab’s Life Sciences Division, a biologist who leads this research.

    Schwarz studied chickens because they’re stars when it comes to making tendons. Chicken embryos start developing tendons just eleven days before hatching, and they enter the world ready to skitter about for food.

    “Their tendon-growth process is very fast,” says Schwarz.

    The process isn’t nearly as fast in humans, but the idea is the same. When we’re growing, the tendon cells in growth plates are densely packed together, the perfect conditions for collagen production. In adults, however, the growth plates recede and the few remaining tendon cells are at low cell density. They produce enough collagen to maintain tendons, but not enough to repair an injured tendon.

    “In adults, tendon repairs are more like darning a sock—adequate, but not like new,” says Schwarz.

    Schwarz’s idea is to reignite the tendon-building capability that occurs during embryogenesis and throughout childhood.

    “If we could add back this growth factor, then we could make tendon cells believe they are at high density again—and cause them to reform this growth plate,” says Schwarz.

    Initial experiments on cell cultures have proved promising, but Schwarz says that more research is needed. For example, one big question that needs to tested in vivo is whether adult tendon can be driven to form a new growth plate—and heal the tendon or ligament in a stronger and faster manner—by injecting a tendon cell-density signal.

    See the full article here.

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