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  • richardmitnick 4:40 pm on November 21, 2014 Permalink | Reply
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    From SLAC: “Robotics Meet X-ray Lasers in Cutting-edge Biology Studies” 


    SLAC Lab

    November 21, 2014

    Platform Brings Speed, Precision in Determining 3-D Structure of Challenging Biological Molecules

    Scientists at the Department of Energy’s SLAC National Accelerator Laboratory are combining the speed and precision of robots with one of the brightest X-ray lasers on the planet for pioneering studies of proteins important to biology and drug discovery.

    The new system uses robotics and other automated components to precisely maneuver delicate samples for study with the X-ray laser pulses at SLAC’s Linac Coherent Light Source (LCLS). This will speed efforts to map the 3-D structures of nanoscale crystallized proteins, which are important for designing targeted drugs and synthesizing natural systems and processes.

    s
    This illustration shows an experimental setup used in crystallography experiments at SLAC’s Linac Coherent Light Source X-ray laser. The drum-shaped container at left stores supercooled crystal samples that are fetched by a robotic arm and delivered to another device, called a goniometer. The goniometer moves individual crystals through the X-ray beam, which travels from the pipe at upper left toward the lower right. A detector, right, captures X-ray diffraction patterns produced as the X-rays pass through the crystal samples. (SLAC National Accelerator Laboratory)

    i
    Equipment used in a highly automated X-ray crystallography system at SLAC’s Linac Coherent Light Source X-ray laser. The metal drum at lower left contains liquid nitrogen for cooling crystallized samples studied with LCLS’s intense X-ray pulses. (SLAC National Accelerator Laboratory)

    SLAC LCLS
    SLAC LCLS

    A New Way to Study Biology

    “This is an efficient, highly reliable and automated way to obtain high-resolution 3-D structural information from small sizes and volumes of samples, and from samples that are too delicate to study using other X-ray sources and techniques,” said Aina Cohen, who oversaw the development of the platform in collaboration with staff at LCLS and at SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL), both DOE Office of Science User Facilities.

    SLAC SSRL
    SLAC SSRL

    She is co-leader of the Macromolecular Crystallography group in the Structural Molecular Biology (SMB) program at SSRL, which has used robotic sample-handling systems to run remote-controlled experiments for a decade.

    The new setup at LCLS is described in the Oct. 31 edition of Proceedings of the National Academy of Sciences. It includes a modified version of a “goniometer,” a sample-handling device in use at SSRL and many other synchrotrons, as well as a custom version of an SSRL-designed software package that pinpoints the position of crystals in arrays of samples.

    LCLS, with X-ray pulses a billion times brighter than more conventional sources, has already allowed scientists to explore biological samples too small or fragile to study in detail with other tools. The new system provides added flexibility in the type of samples and sample-holders that can be used in experiments.

    Rather than injecting millions of tiny, randomly tumbling crystallized samples into the path of the pulses in a thin liquid stream – common in biology experiments at LCLS – the goniometer-based system places crystals one at a time into the X-ray pulses. This greatly reduces the number of crystals needed for structural studies on rare and important samples that require a more controlled approach.

    Early Successes

    “This system adapts common synchrotron techniques for use at LCLS, which is very important,” said Henrik Lemke, staff scientist at LCLS. “There is a large community of scientists who are familiar with the goniometer technique.”

    The system has already been used to provide a complete picture of a protein’s structure in about 30 minutes using only five crystallized samples of an enzyme, moved one at a time into the X-rays for a sequence of atomic-scale “snapshots.”

    It has also helped to determine the atomic-scale structures of an oxygen-binding protein found in muscles, and another protein that regulates heart and other muscle and organ functions.

    “We have shown that this system works, and we can further automate it,” Cohen said. “Our goal is to make it easy for everyone to use.”

    Many biological experiments at LCLS are conducted in air-tight chambers. The new setup is designed to work in the open air and can also be used to study room-temperature samples, although most of the samples used in the system so far have been deeply chilled to preserve their structure. One goal is to speed up the system so it delivers samples and measures the resulting diffraction patterns as fast as possible, ideally as fast as LCLS delivers pulses: 120 times a second.

    The goniometer setup is the latest addition to a large toolkit of systems that deliver a variety of samples to the LCLS beam, and a new experimental station called MFX that is planned at LCLS will incorporate a permanent version.

    Team Effort

    Developed through a collaboration of SSRL’s Structural Molecular Biology program and the Stanford University School of Medicine, the LCLS goniometer system reflects increasing cooperation in the science of SSRL and LCLS, Cohen said, drawing upon key areas of expertise for SSRL and the unique capabilities of LCLS. “The combined effort of staff at both experimental facilities was key in this success,” she said.

    In addition to staff at SLAC’s SSRL and LCLS and at Stanford University’s School of Medicine, researchers from SLAC’s Photon Science Directorate, the University of Pittsburgh School of Medicine, Howard Hughes Medical Institute, Montana State University, Lawrence Berkeley National Laboratory and the University of California, San Francisco also participated in this effort.

    The work was supported by the Department of Energy Office of Basic Energy Sciences, the SSRL Structural Molecular Biology Program via the DOE Office of Biological and Environmental Research, and the Biomedical Technology Research Resources program at the National Institute of General Medical Sciences, National Institutes of Health.

    See the full article here.

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    SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.
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  • richardmitnick 4:24 pm on November 18, 2014 Permalink | Reply
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    From BNL: “Organic Crystal Film Grown on New Substrate Breaks Performance Record” 

    Brookhaven Lab

    November 18, 2014
    Laura Mgrdichian

    The study is an important step toward realizing mainstream organic electronic devices

    Many future electronic devices may be based not on standard conductors and semiconductors but rather on small organic (carbon-based) molecules and polymers. These organic electronics will have several advantages over conventional electronics, including being cheaper to fabricate, physically bendable and flexible, and, in some cases, can be created using printing methods – perhaps even in your own home.

    The field of organic electronics is still in its infancy, however, and scientists have much to learn before organic electronic devices are part of our everyday lives. One obstacle researchers have faced is how to successfully grow high-quality crystals of an organic molecule on top of a conventional substrate – without using a complex growth process or chemically modifying the substrate first. Solving this problem is the necessary first step to creating organic electronic circuits and devices.

    im
    Organic two-dimensional heterostructure of rubrene/h-BN

    Recently, a research group made some significant headway. Working in part at the National Synchrotron Light Source (NSLS), scientists from Columbia University, Harvard University, Brookhaven Lab, and Japan’s National Institute for Materials Science grew a high-quality, high-performing film of rubrene, an organic semiconductor, onto a substrate of hexagonal boron nitride, a layered crystalline material with hexagonally shaped molecular units (similar to graphite carbon). Their work, which they discuss in the May 14, 2014, edition of the journal Advanced Materials, is notable both due to the high-quality crystalline nature of the film and because the substrate is a new player in the field of organic electronics development.

    “The interface between the substrate and the molecular film is very important. It governs the initial nucleation during the growth of the film and also has a big impact on how the film will carry charge,” says Columbia researcher Phillip Kim, one of the paper’s authors. “Our film/substrate heterostructure yielded the highest mobility observed yet in similar systems. It is comparable to those of free-standing single crystals and represents a record for organic films grown on any substrates.”

    When paired with organic materials, conventional substrates like silicon oxide, glass, and plastic are too disordered at the molecular level and also don’t have molecular structures that are similar enough to the organic compounds. In materials science terms, they lack an “epitaxial” relationship. This discourages proper film growth and results in lower-quality films that lack long-range order. In everyday terms, this is kind of like trying to build a layer of Lego bricks on Lego board that doesn’t have an ordered grid of nubs.

    Kim and his colleagues showed that hexagonal boron nitride (h-BN) has many advantages as a substrate for organic electronics. Using an approach called “van der Waals epitaxy,” a method that takes advantage of the weak van der Waals force between molecules, the group grew rubrene films varying from 5 to 1000 nanometers thick. They studied each sample’s structure and charge-carrying ability using several methods.

    Atomic force microscopy (AFM) and transmission electron microscopy (TEM) images suggested that the film was formed of large single-crystal domains. Selected area electron diffraction (SAED), which can be performed inside a transmission electron microscope, also confirmed this. But because SAED provides only local structural information, the group used grazing x-ray diffraction at NSLS beamline X9 to get a broader “view” of the structure. The x-ray data showed sharp, intense peaks, indicating that the sample contained a high-quality crystal structure.

    To study how the film carries charge, graphene electrical contacts were incorporated into the growth process, resulting in a field-effect transistor structure. Measuring the current across it showed that electrons traveling within it are highly mobile, meaning they don’t run into too many barriers caused by a “choppy” molecular structure.

    “Our study highlights the advantages of h-BN and similar materials over commonly used substrates to achieve high-performance organic electronic devices,” said Kim. “More generally, this approach to film growth – van der Waals epitaxy – could be used to fabricate organic/inorganic structures that can be readily expanded to numerous other organic and layered materials for various electronic applications.”

    This research was supported by: the Center for Redefining Photovoltaic Efficiency Through Molecule Scale Control, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences; the FAME Center, one of six centers of STARnet, a Semiconductor Research Corporation program sponsored by MARCO and DARPA; the Nano Material Technology Development Program through the National Research Foundation of Korea funded by the Ministry of Science, ICT and Future Planning; the Basic Science Research Program through the National Research Foundation of Korea; the U.S. Department of Energy, Office of Basic Energy Sciences, under the Extreme Science and Engineering Discovery Environment, supported by the National Science Foundation.

    See the full article here.

    BNL Campus

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    One of ten national laboratories overseen and primarily funded by the Office of Science of the U.S. Department of Energy (DOE), Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. The Laboratory’s almost 3,000 scientists, engineers, and support staff are joined each year by more than 5,000 visiting researchers from around the world.Brookhaven is operated and managed for DOE’s Office of Science by Brookhaven Science Associates, a limited-liability company founded by Stony Brook University, the largest academic user of Laboratory facilities, and Battelle, a nonprofit, applied science and technology organization.
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  • richardmitnick 7:25 pm on November 17, 2014 Permalink | Reply
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    From SLAC: “SLAC X-ray Laser Brings Key Cell Structures into Focus” 


    SLAC Lab

    November 17, 2014

    Experiment is Important Step Toward Atomic-Scale Imaging of Intact Biological Particles

    Scientists have made high-resolution X-ray laser images of an intact cellular structure much faster and more efficiently than ever possible before. The results are an important step toward atomic-scale imaging of intact biological particles, including viruses and bacteria.

    The technique was demonstrated at the Linac Coherent Light Source (LCLS) at the Department of Energy’s SLAC National Accelerator Laboratory and reported in the Nov. 17 issue of Nature Photonics.

    art
    A 20-sided structure from a bacterial cell, called a carboxysome, is struck by an X-ray pulse (purple) at SLAC’s Linac Coherent Light Source. (SLAC National Accelerator Laboratory)

    An international team of scientists used LCLS, a DOE Office of Science User Facility, to produce tens of thousands of high-resolution images of the tiniest individual biological particles yet studied there – 20-sided structures called carboxysomes that are found in some bacterial cells and play a major role in Earth’s life-sustaining carbon cycle. Although these structures have been studied for years, much remains unknown about their inner workings.

    New Views of Bacteria’s Carbon-conversion Engines

    “In an experiment lasting only 12 minutes, we collected many high-quality images using a very small amount of sample,” said Janos Hajdu, a professor of biophysics at Uppsala University in Sweden, which led the research. “In the future you could conceivably get results within minutes that used to take five days for certain types of samples. We showed that with the right type of instruments and detectors, you can increase the throughput of X-ray lasers by a huge amount.”

    The results bolster the aims of the LCLS Single-Particle Imaging initiative, formally launched at SLAC in October in cooperation with the international scientific community, said Christoph Bostedt, a SLAC senior staff scientist who leads the initiative with staff scientist Andy Aquila. The initiative is working toward atomic-scale imaging for many types of biological samples by identifying and addressing technical challenges at LCLS.

    “As this work demonstrates, we are already achieving imaging of single particles today, and we are working to improve upon these capabilities,” Aquila said.

    Bostedt added, “We will tackle these hurdles by working with the community. LCLS managers have committed to support this effort with dedicated experimental time.”

    Biology ‘On the Fly’

    Carboxysomes are microscopic workhorses inside cyanobacteria, which carry out photosynthesis. They pull in carbon dioxide from their surroundings and use an enzyme to convert it to forms that other living things can use. An estimated 40 percent of the organic carbon on Earth was made in these cell structures. “A better understanding of the structure and function of these cell organelles could benefit carbon-cycle research,” said Dirk Hasse of Uppsala University, one of the paper’s lead authors.

    Because they vary in size from about 90 to 140 nanometers, or billionths of a meter, in diameter, it is difficult to crystallize these tiny structures for conventional X-ray studies of their structure.

    A 2011 study by members of the same international team had studied samples of a giant virus, called Mimivirus, using a similar experimental technique that jets samples in a finely focused aerosol spray into the path of the X-ray pulses.

    In the latest study they were able to achieve better resolution, showing features as small as 18 nanometers.

    The scientists said a new design for the “aerosol injector” that shot the samples in a thin stream toward the X-ray pulses was among the key improvements that allowed them to achieve higher-resolution images. They also improved data-analysis tools that automatically sorted the 70,000 images they collected and assembled them into distinct groups. These advances lay the foundation for accurate, high-throughput structure determination for individual biological samples and other types of samples.

    The resolution achieved in this first experiment was not high enough to reveal the interior of the carboxysomes, though the team said that upgrades to higher intensity and a narrower focus of LCLS X-rays could allow far more detailed explorations of many biological samples in this size range, including small viruses. “We haven’t yet reached the limits,” said Filipe Maia of Uppsala University, who participated in the study.

    Pushing the Limits

    Max Hantke of Uppsala University, a lead author of the study, said the ultrashort pulses of X-ray lasers offer important advantages over instruments like electron microscopes that are used to study biological samples.

    For example, the X-ray laser can be used to track ultrafast processes, such as how biological samples respond to pulses of light over time. “These types of experiments are not possible with other methods,” Hantke said.

    In addition to scientists from Uppsala University and SLAC, other researchers who participated in the study were from Lawrence Berkeley National Laboratory; Kansas State University; the National University of Singapore; the University of Melbourne in Australia; University of Rome in Italy; and DESY laboratory, PNSensor, Max Planck Institute for Extraterrestrial Physics and European XFEL, all in Germany.

    This work was supported by the Swedish Research Council, the Knut and Alice Wallenberg Foundation, the European Research Council, the Röntgen-Ångström Cluster, and Stiftelsen Olle Engkvist Byggmästare. The CAMP instrument used in the experiment was funded by the Max Planck Society.

    See the full article here.

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    SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.
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  • richardmitnick 10:18 am on November 11, 2014 Permalink | Reply
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    From SLAC: “Researchers Take Snapshots of Potential ‘Kill Switch’ for Cancer” 


    SLAC Lab

    November 10, 2014

    X-ray Study Shows Protein Switch for Programmed Cell Death in Motion

    A study conducted in part at the Department of Energy’s SLAC National Accelerator Laboratory has revealed how a key human protein switches from a form that protects cells to a form that kills them – a property that scientists hope to exploit as a “kill switch” for cancer.

    The protein, called cIAP1, shields cells from programmed cell death, or apoptosis – a naturally occurring crackdown on unhealthy cells and tissues. When a cell is in trouble, a signal activates cIAP1, which rapidly transforms into a state that allows apoptosis to take place.

    cell
    The structure of cellular inhibitor-of-apoptosis protein 1 (cIAP1) in its “closed” state. The protein is a key switch for apoptosis, or programmed cell death, and is composed of four distinct domains (color coded) that rearrange depending on the position of the switch. (Allyn Schoeffler/Genentech)

    “Cancer cells produce excess amounts of cIAP1 in an attempt to shut down apoptosis and evade death,” says senior staff scientist Thomas Weiss from SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL), a DOE Office of Science User Facility, who participated in the study. “The search for drugs that would switch apoptosis back on to eradicate cancer is a very active research field.”

    The researchers used X-rays from SSRL to watch in real time how cIAP1 transitions from one state to another. The results are an important step towards becoming able to control the protein’s switching properties.

    “Our study closely ties cIAP1’s motions to its role as a switch,” says Allyn Schoeffler, a senior research associate at Genentech Inc. in South San Francisco and lead author of the study, published Nov. 10 in Nature Structural & Molecular Biology. “We now know why cIAP1 can act as a strictly controlled fail-safe for apoptosis and, at the same time, remain flexible enough to undergo rapid structural transitions.”

    Incomplete Static Model

    Earlier studies had given researchers a fairly good idea of cIAP1’s structure and general mechanism.

    In its “closed” state, which blocks apoptosis, the protein’s four parts, or domains, are tightly bound together in a rather rigid, compact structure.

    When a signal molecule binds to a specific site in cIAP1, the protein changes into its “open” state, in which the domains arrange in a more flexible, linear way. When two identical copies of this open structure partner up in what is known as a dimer, the assembly eventually self-destructs, removing the brake that blocks apoptosis and allowing cellular clean-up to carry on.

    “This model of cIAP1 action has largely been derived from static images of the protein,” Schoeffler says. “However, static pictures do not tell us the whole story.”

    Bringing Motion into the Equation

    To find out more, the research team first used a technique known as nuclear magnetic resonance spectroscopy, or NMR, to analyze how the protein domains move in the closed state, and followed up with studies at SSRL, where they observed how X-rays scatter off the transforming sample.

    scat
    Small-angle X-ray scattering models of different cIAP1 states. In its “closed” state, which blocks apoptosis, the domains are tightly bound together in a compact structure (left). Binding of a signal molecule for apoptosis switches the protein into its “open” state, in which the domains arrange in a more flexible linear way (center). When two identical copies of the open structure partner up in what is known as a dimer (right), the assembly eventually self-destructs, thereby allowing apoptosis to take place. (Allyn Schoeffler/Genentech)

    “The results showed that cIAP1 switches from ‘closed’ to ‘open’ extremely fast, within only 300 milliseconds, which we were able to determine using a technique called time-resolved small-angle X-ray scattering,” says Weiss. “The following dimer formation is even faster than that.”

    open
    Protein envelopes of cIAP1’s “open” and “closed” forms as determined by small-angle X-ray scattering (left) with detailed molecular structures modeled into them (right). For the first time, scientists have now monitored in real time how cIAP1 transitions from one state to another. (Allyn Schoeffler/Genentech)

    In addition, the scientists observed that the protein “breathes” rapidly in its closed form, with interfaces between domains opening and closing quickly.

    “The only region that is relatively rigid is the interaction site for the apoptosis signal,” says Schoeffler. “This well-defined site in the closed state allows nature to control cIAP1 very tightly. It is the critical latch that keeps the switch closed and makes sure that it does not open accidentally.”

    The rest of the protein, in contrast, is very flexible and allows cIAP1 to open instantaneously, like a spring-loaded trigger mechanism, when the proper signal is received. Once the trigger has been pulled, cell death becomes inevitable.

    Ties to Cancer Research

    The new insights could potentially benefit recent developments in cancer research. In fact, several studies are underway to explore the use of synthetic compounds that mimic nature’s signal molecules.

    “Natural and synthetic molecules are thought to interact with this protein the same way,” says Schoeffler. “Therefore, the mechanisms revealed by our study are likely to hold true in medically relevant molecules as well.”

    Research funding for the SSRL Structural Molecular Biology Program was provided by the DOE Office of Biological and Environmental Research and the National Institutes of Health, National Institute of General Medical Sciences.

    See the full article here.

    SLAC Campus
    SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.
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  • richardmitnick 1:52 pm on November 7, 2014 Permalink | Reply
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    From FNAL: “Multilaboratory collaboration brings new X-ray detector to light” 


    Fermilab is an enduring source of strength for the US contribution to scientific research world wide.

    Friday, Nov. 7, 2014
    Troy Rummler

    A collaboration blending research in DOE’s offices of High-Energy Physics (HEP) with Basic Energy Sciences (BES) will yield a one-of-a-kind X-ray detector. The device boasts Brookhaven Lab sensors mounted on Fermilab integrated circuits linked to Argonne Lab data acquisition systems. It will be used at Brookhaven’s National Synchrotron Light Source II and Argonne’s Advanced Photon Source. Lead scientists Peter Siddons, Grzegorz Deptuch and Robert Bradford represent the three laboratories.

    BNL NSLS II PhotoBNL NSLS-II Interior
    BNL NSLS II

    ANL APS
    ANL APS interior
    ANL APS

    “This partnership between HEP and BES has been a fruitful collaboration, advancing detector technology for both fields,” said Brookhaven’s Peter Siddons.

    team
    These researchers work on the VIPIC prototype. Peter Siddons of Brookhaven National Laboratory (fifth from the left), Grzegroz Deptuch of Fermilab (third from the right) and Robert Bradford of Argonne National Laboratory (far right) lead the effort. Photo courtesy of Argonne National Laboratory

    This detector is filling a need in the X-ray correlation spectroscopy (XCS) community, which has been longing for a detector that can capture dynamic processes in samples with microsecond timing and nanoscale sensitivity. Available detectors have been designed largely for X-ray diffraction crystallography and are incapable of performing on this time scale.

    det
    The 64-by-64 pixel VIPIC prototype, pictured with a sensor on the bottom and solder bump-bonding bump on top, ready to be received on the printed circuit board. Photo: Reidar Hahn

    In 2006, Fermilab’s Ray Yarema began investigating 3-D integrated chip technology, which increases circuit density, performance and functionality by vertically stacking rather than laterally arranging silicon wafers. Then in 2008 Deptuch, a member of Yarema’s group and Fermilab ASIC [Application Specific Integrated Circuit] Group leader since 2011, met with Siddons, a scientist at Brookhaven, at a medical imaging conference. They discussed applying 3-D technology to a new, custom detector project, which was later given the name VIPIC (vertically integrated photon imaging chip). Siddons was intrigued by the 3-D opportunities and has since taken the lead on leveraging Fermilab expertise toward the longstanding XCS problem. As a result, the development of the device at Fermilab — where 97 percent of research funds come through HEP — receives BES funding.

    A 64-by-64-pixel VIPIC prototype tested at Argonne this summer flaunted three essential properties: timing resolution within one microsecond; continuous new-data acquisition with simultaneous old-data read-out; and selective transmission of only pixels containing data.

    The results achieved with the prototype have attracted attention from the scientific community.

    Deptuch noted that this partnership between BES and HEP reflects the collaborative nature of such efforts at the national labs.

    “It truly is a cooperative effort, combining the expertise from three national laboratories toward one specific goal,” he said.

    The team will grow their first VIPIC prototype tiled, seamless array of chips on a sensor to form a 1-megapixel detector. The collaboration is targeting a completion date of 2017 for the basic functionality detector. Ideas for expanded capabilities are being discussed for the future.

    See the full article here.

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    Fermi National Accelerator Laboratory (Fermilab), located just outside Batavia, Illinois, near Chicago, is a US Department of Energy national laboratory specializing in high-energy particle physics.

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  • richardmitnick 7:38 pm on October 23, 2014 Permalink | Reply
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    From BNL: “National Synchrotron Light Source II Achieves ‘First Light’” 

    Brookhaven Lab

    October 23, 2014
    Chelsea Whyte, (631) 344-8671 or Peter Genzer, (631) 344-3174

    The National Synchrotron Light Source II detects its first photons, beginning a new phase of the facility’s operations. Scientific experiments at NSLS-II are expected to begin before the end of the year.

    crowd
    A crowd gathered on the experimental floor of the National Synchrotron Light Source II to witness “first light,” when the x-ray beam entered a beamline for the first time at the facility.

    The brightest synchrotron light source in the world has delivered its first x-ray beams. The National Synchrotron Light Source II (NSLS-II) at the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory achieved “first light” on October 23, 2014, when operators opened the shutter to begin commissioning the first experimental station (called a beamline), allowing powerful x-rays to travel to a phosphor detector and capture the facility’s first photons. While considerable work remains to realize the full potential of the new facility, first light counts as an important step on the road to facility commissioning.

    BNL NSLS II
    BNL NSLS-II Interior
    NSLS-II at BNL

    “This is a significant milestone for Brookhaven Lab, for the Department of Energy, and for the nation,” said Harriet Kung, DOE Associate Director of Science for Basic Energy Sciences. “The National Synchrotron Light Source II will foster new discoveries and create breakthroughs in crucial areas of national need, including energy security and the environment. This new U.S. user facility will advance the Department’s mission and play a leadership role in enabling and producing high-impact research for many years to come.”

    At 10:32 a.m. on October 23, a crowd of scientists, engineers, and technicians gathered around the Coherent Soft X-ray Scattering (CSX) beamline at NSLS-II, expectantly watching the video feed from inside a lead-lined hutch where the x-ray beam eventually struck the detector. As the x-rays hit the detector, cheers and applause rang out across the experimental hall for a milestone many years in the making.

    team
    The team of scientists, engineers, and technicians at the Coherent Soft X-ray Scattering (CSX) beamline gathered around the control station to watch as group leader Stuart Wilkins (seated, front) opened the shutter between the beamline and the storage ring, allowing x-rays to enter the first optical enclosure for the first time.

    “This achievement begins an exciting new chapter of synchrotron science at Brookhaven, building on the remarkable legacy of NSLS, and leading us in new directions we could not have imagined before,” said Laboratory Director Doon Gibbs. “It’s a great illustration of the ways that national labs continually evolve and grow to meet national needs, and it’s a wonderful time for all of us. Everyone at the Lab, in every role, supports our science, so we can all share in the sense of excitement and take pride in this accomplishment.”

    beam
    NSLS-II first x-rays
    Inside the beamline enclosure, a phosphor detector (the rectangle at right) captured the first x-rays (in white) which hit the mark dead center.

    In the heart of the 590,000 square foot facility, an electron gun emits packets of the negatively charged particles, which travel down a linear accelerator into a booster ring. There, the electrons are brought to nearly the speed of light, and then steered into the storage ring, where powerful magnets guide the beam on a half-mile circuit around the NSLS-II storage ring. As the electrons travel around the ring, they emit extremely intense x-rays, which are delivered and guided down beamlines into experimental end stations where scientists will carry out experiments for scientific research and discovery. NSLS-II accelerator operators have previously stored beam in the storage ring, but they hadn’t yet opened the shutters to allow x-ray light to reach a detector until today’s celebrated achievement.

    “We have been eagerly anticipating this culmination of nearly a decade of design, construction, and testing and the sustained effort and dedication of hundreds of individuals who made it possible,” said Steve Dierker, Associate Laboratory Director for Photon Sciences. ‘We have more work to do, but soon researchers from around the world will start using NSLS-II to advance their research on everything from new energy storage materials to developing new drugs to fight disease. I’m very much looking forward to the discoveries that NSLS-II will enable, and to the continuing legacy of groundbreaking synchrotron research at Brookhaven.”

    NSLS-II, a third-generation synchrotron light source, will be the newest and most advanced synchrotron facility in the world, enabling research not possible anywhere else. As a DOE Office of Science User Facility, it will offer researchers from academia, industry, and national laboratories new ways to study material properties and functions with nanoscale resolution and exquisite sensitivity by providing state-of-the-art capabilities for x-ray imaging, scattering, and spectroscopy.

    Currently 30 beamlines are under development to take advantage of the high brightness of the x-rays at NSLS-II. Commissioning of the first group of seven beamlines will begin in the coming months, with first experiments beginning at the CSX beamline before the end of 2014.

    At the NSLS-II beamlines, scientists will be able to generate images of the structure of materials such as lithium-ion batteries or biological proteins at the nanoscale level—research expected to advance many fields of science and impact people’s quality of life in the years to come.

    NSLS-II will support the Department of Energy’s scientific mission by providing the most advanced tools for discovery-class science in condensed matter and materials science, physics, chemistry, and biology—science that ultimately will enhance national and energy security and help drive abundant, safe, and clean energy technologies.

    Media Contacts:
    Karen McNulty Walsh, 631 344-8350 or kmcnulty@bnl.gov
    Chelsea Whyte, 631 344-8671 or cwhyte@bnl.gov

    See the full article here.

    BNL Campus

    One of ten national laboratories overseen and primarily funded by the Office of Science of the U.S. Department of Energy (DOE), Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. The Laboratory’s almost 3,000 scientists, engineers, and support staff are joined each year by more than 5,000 visiting researchers from around the world.Brookhaven is operated and managed for DOE’s Office of Science by Brookhaven Science Associates, a limited-liability company founded by Stony Brook University, the largest academic user of Laboratory facilities, and Battelle, a nonprofit, applied science and technology organization.
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  • richardmitnick 1:22 pm on October 7, 2014 Permalink | Reply
    Tags: , , X-ray Technology   

    From SLAC: “Five Years of Scientific Discoveries with SLAC’s LCLS” 


    SLAC Lab

    October 7, 2014

    From ‘Hollow’ Atoms to Structures Inside Living Cells, SLAC’s Laser Continues to Explore Science at the Extremes

    Five years ago, on the eve of the first X-ray laser experiment at the Department of Energy’s SLAC National Accelerator Laboratory, Linda Young summed up her role in leading this inaugural exploration: “Wow … Quite an honor, quite a responsibility.”

    SLAC LCLS
    SLAC LCLS Inside
    LCLS at SLAC

    Young, who studies interactions of light and matter at the scale of atoms and molecules, is director of the X-ray Science Division at Argonne National Laboratory. She chronicled her team’s pioneering experiment at the Linac Coherent Light Source (LCLS), a DOE Office of Science User Facility, in a series of blog posts in October 2009.

    pulse
    This illustration shows how the first experiment at SLAC’s Linac Coherent Light Source X-ray laser, conducted in October 2009, stripped away electrons from neon atoms. (SLAC National Accelerator Laboratory)

    That first group of scientists studied what happens when intense X-ray pulses from LCLS, a billion times brighter than previous X-ray sources used for research, hit neon atoms. The researchers learned how to precisely tune the pulses to peel away atoms’ outer electrons or carve out their inner electrons, creating temporarily “hollow” atoms. This process had never been explored in such detail.

    team
    Some members of the first experimental team at SLAC’s LCLS X-ray laser: (standing, left to right) Elliot Kanter, Robin Santra, Phay Ho, Stephen Pratt, Stefan Pabst and Anne-Marie March; (sitting, left to right) Linda Young, Stephen Southworth, Bertold Kraessig. (Argonne National Laboratory)

    see
    Scientists in a control room monitor the first experiment at SLAC’s Linac Coherent Light Source. (Argonne National Laboratory)

    poster

    These and other results from early experiments provided a basic understanding of the extent and speed at which LCLS X-rays can damage or destroy samples – knowledge that is especially critical for producing accurate 3-D images of complex molecular structures.

    “We’ve found out not only the basic processes that happen in atoms in response to LCLS pulses, but some of the subtleties that go along with it,” Young said, reflecting on the progress made possible by experiments at LCLS.

    Since that first experiment, the number of LCLS experimental stations has multiplied from one to six, and thousands more scientists have probed previously unreachable realms in fields from biology and chemistry to materials science and astrophysics. LCLS experiments have generated hundreds of articles in peer-reviewed scientific journals, with almost one-third of them appearing in prominent journals like Science and Nature.

    LCLS has already achieved important milestones in several fields, mapping the structure of an enzyme relevant to a disease called African sleeping sickness and a crystallized protein embedded in living bacterial cells, detailing quantum phenomena in microscopic droplets of helium, and learning how DNA guards against damage from ultraviolet light.

    Young has returned to LCLS several times, most recently last spring. It seems there is always a steady supply of new instruments and techniques to try out at LCLS, she said: “The machine scientists keep coming up with new configurations that allow us to delve a little deeper.”

    Importantly, the sensitivity of the X-ray detectors has increased, she noted, and her team is now studying more complex molecules. Young said improvements in computer-based modeling should also help scientists prepare for LCLS experiments and interpret LCLS-generated data.

    She added, “Science at LCLS is still rapidly evolving – I don’t think it has lost its flavor of being very exploratory. We’re just starting to scratch the surface.”

    See the full article here.

    Coming soon: LCLS-II
    SLAC LCLSII

    SLAC Campus
    SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.
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  • richardmitnick 6:44 pm on September 22, 2014 Permalink | Reply
    Tags: , , , , X-ray Technology   

    From Stanford: “Stanford researchers create ‘evolved’ protein that may stop cancer from spreading” 

    Stanford University Name
    Stanford University

    September 21, 2014
    Tom Abate

    Experimental therapy stopped the metastasis of breast and ovarian cancers in lab mice, pointing toward a safe and effective alternative to chemotherapy.

    A team of Stanford researchers has developed a protein therapy that disrupts the process that causes cancer cells to break away from original tumor sites, travel through the bloodstream and start aggressive new growths elsewhere in the body.

    This process, known as metastasis, can cause cancer to spread with deadly effect.

    “The majority of patients who succumb to cancer fall prey to metastatic forms of the disease,” said Jennifer Cochran, an associate professor of bioengineering who describes a new therapeutic approach in Nature Chemical Biology.

    Today doctors try to slow or stop metastasis with chemotherapy, but these treatments are unfortunately not very effective and have severe side effects.

    The Stanford team seeks to stop metastasis, without side effects, by preventing two proteins – Axl and Gas6 – from interacting to initiate the spread of cancer.

    Axl proteins stand like bristles on the surface of cancer cells, poised to receive biochemical signals from Gas6 proteins.

    When two Gas6 proteins link with two Axls, the signals that are generated enable cancer cells to leave the original tumor site, migrate to other parts of the body and form new cancer nodules.

    To stop this process Cochran used protein engineering to create a harmless version of Axl that acts like a decoy. This decoy Axl latches on to Gas6 proteins in the bloodstream and prevents them from linking with and activating the Axls present on cancer cells.

    In collaboration with Professor Amato Giaccia, co-director of the Radiation Biology Program in the Stanford Cancer Center, the researchers gave intravenous treatments of this bioengineered decoy protein to mice with aggressive breast and ovarian cancers.

    two
    Jennifer Cochran and Amato Giaccia are members of a team of researchers who have developed an experimental therapy to treat metastatic cancer.

    Mice in the breast cancer treatment group had 78 percent fewer metastatic nodules than untreated mice. Mice with ovarian cancer had a 90 percent reduction in metastatic nodules when treated with the engineered decoy protein.

    “This is a very promising therapy that appears to be effective and nontoxic in preclinical experiments,” Giaccia said. “It could open up a new approach to cancer treatment.”

    Giaccia and Cochran are scientific advisors to Ruga Corp., a biotech startup in Palo Alto that has licensed this technology from Stanford. Further preclinical and animal tests must be done before determining whether this therapy is safe and effective in humans.

    Greg Lemke, of the Molecular Neurobiology Laboratory at the Salk Institute, called this “a prime example of what bioengineering can do” to open up new therapeutic approaches to treat metastatic cancer.

    “One of the remarkable things about this work is the binding affinity of the decoy protein,” said Lemke, a noted authority on Axl and Gas6 who was not part of the Stanford experiments.

    “The decoy attaches to Gas6 up to a hundredfold more effectively than the natural Axl,” Lemke said. “It really sops up Gas6 and takes it out of action.”
    Directed evolution

    The Stanford approach is grounded on the fact that all biological processes are driven by the interaction of proteins, the molecules that fit together in lock-and-key fashion to perform all the tasks required for living things to function.

    In nature proteins evolve over millions of years. But bioengineers have developed ways to accelerate the process of improving these tiny parts using technology called directed evolution. This particular application was the subject of the doctoral thesis of Mihalis Kariolis, a bioengineering graduate student in Cochran’s lab.

    Using genetic manipulation, the Stanford team created millions of slightly different DNA sequences. Each DNA sequence coded for a different variant of Axl.

    The researchers then used high-throughput screening to evaluate over 10 million Axl variants. Their goal was to find the variant that bound most tightly to Gas6.

    Kariolis made other tweaks to enable the bioengineered decoy to remain in the bloodstream longer and also to tighten its grip on Gas6, rendering the decoy interaction virtually irreversible.

    Yu Rebecca Miao, a postdoctoral scholar in Giaccia’s lab, designed the testing in animals and worked with Kariolis to administer the decoy Axl to the lab mice. They also did comparison tests to show that sopping up Gas6 resulted in far fewer secondary cancer nodules.

    Irimpan Mathews, a protein crystallography expert at SLAC National Accelerator Laboratory, joined the research effort to help the team better understand the binding mechanism between the Axl decoy and Gas6.

    Protein crystallography captures the interaction of two proteins in a solid form, allowing researchers to take X-ray-like images of how the atoms in each protein bind together. These images showed molecular changes that allowed the bioengineered Axl decoy to bind Gas6 far more tightly than the natural Axl protein.
    Next steps

    Years of work lie ahead to determine whether this protein therapy can be approved to treat cancer in humans. Bioprocess engineers must first scale up production of the Axl decoy to generate pure material for clinical tests. Clinical researchers must then perform additional animal tests in order to win approval for and to conduct human trials. These are expensive and time-consuming steps.

    But these early, hopeful results suggest that the Stanford approach could become a nontoxic way to fight metastatic cancer.

    Glenn Dranoff, a professor of medicine at Harvard Medical School and a leading researcher at the Dana-Farber Cancer Institute, reviewed an advance copy of the Stanford paper but was otherwise unconnected with the research. “It is a beautiful piece of biochemistry and has some nuances that make it particularly exciting,” Dranoff said, noting that tumors often have more than one way to ensure their survival and propagation.

    Axl has two protein cousins, Mer and Tyro3, that can also promote metastasis. Mer and Tyro3 are also activated by Gas6.

    “So one therapeutic decoy might potentially affect all three related proteins that are critical in cancer development and progression,” Dranoff said.

    Erinn Rankin, a postdoctoral fellow in the Giaccia lab, carried out proof of principle experiments that paved the way for this study.

    Other co-authors on the Nature Chemical Biology paper include Douglas Jones, a former doctoral student, and Shiven Kapur, a postdoctoral scholar, both of Cochran’s lab, who contributed to the protein engineering and structural characterization, respectively.

    Cochran said Stanford’s support for interdisciplinary research made this work possible.

    Stanford ChEM-H (Chemistry, Engineering & Medicine for Human Health) provided seed funds that allowed Cochran and Mathews to collaborate on protein structural studies.

    The Stanford Wallace H. Coulter Translational Research Grant Program, which supports collaborations between engineers and medical researchers, supported the efforts of Cochran and Giaccia to apply cutting-edge bioengineering techniques to this critical medical need.

    See the full article here.

    Leland and Jane Stanford founded the University to “promote the public welfare by exercising an influence on behalf of humanity and civilization.” Stanford opened its doors in 1891, and more than a century later, it remains dedicated to finding solutions to the great challenges of the day and to preparing our students for leadership in today’s complex world. Stanford, is an American private research university located in Stanford, California on an 8,180-acre (3,310 ha) campus near Palo Alto. Since 1952, more than 54 Stanford faculty, staff, and alumni have won the Nobel Prize, including 19 current faculty members

    Stanford University Seal

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  • richardmitnick 3:27 pm on September 15, 2014 Permalink | Reply
    Tags: , , , PETRA III, , X-ray Technology   

    From DESY: “Double topping-out celebrations at DESY” 

    DESY
    DESY

    Two new experimental halls for research light source PETRA III

    Today DESY celebrates the topping-out of two large experimental halls for the research light source PETRA III.Ten additional beamlines, which will serve in the PETRA III particle accelerator’s high intensity X-ray experiments, are under construction in a space measuring approximately 6000 square meters; the facility will also include en-suite offices and laboratory spaces for scientists.The experimentation capabilities at the PETRA III synchrotron radiation source will be considerably increased due to the expansion project.The first new beamlines of the 80-million-Euro-project will be ready for operation beginning in autumn 2015.
    Zoom (17 KB)

    pit

    “With the new experimental stations, we are significantly expanding the research capabilities of PETRA III, for example, with new nanospectroscopy and materials research technologies,” says Chairman of the DESY Board of Directors Professor Helmut Dosch at the event. “At the same time, we will be fulfilling the enormous worldwide scientific demand for the best synchrotron radiation source in the world.”

    Hamburg´s Science Senator Dr. Dorothee Stapelfeldt says: “The senate’s aim is to develop Hamburg into one of the leading locations for research and innovation in Europe.In order to do so, it is essential to further raise the profiles of universities and research institutions in close dialogue with all stakeholders.Hamburg already occupies a leading position in structural research.The ground-breaking cooperation between DESY, the university and their partners at the Bahrenfeld research campus has been clearly recognized internationally.With the two new experimental halls, PETRA’s synchrotron radiation will be made available to even more researchers from all over the world in the future.”

    “With a total of ten new beamlines, the allure of Hamburg as a location for cutting-edge research will continue to increase, nationally and internationally,” says Dr. Beatrix Vierkorn-Rudolph (BMBF), Chairperson of the DESY Foundation Council. “With its excellent research opportunities, PETRA III contributes to rapidly transfering the results of basic research into application while also strengthening the innovative power of Germany.”

    DESY’s 2.3-kilometre-long PETRA III ring accelerator produces high intensity, highly collimated X-ray pulses for a diverse range of physical, biological and chemical experiments.Fourteen measuring stations, which can accommodate up to thirty experiments, already exist in an approximately 300-metre-long experimental hall.The properties of light pulses, which PETRA delivers to the different measuring stations, are thereby precisely attuned to the different research disciplines.Using the extremely brilliant X-rays, researchers study, for example, innovative solar cells, observe the dynamics of cell membranes and analyse fossilised dinosaur eggs.

    PETRA III, the world´s best X-ray source of its kind, has been heavily over-booked since it began operations in 2009.The PETRA III Extension Project was begun in December 2013 to give more scientists access to the unique experimental possibilities of this research light source and to broaden PETRA III’s research portfolio in experimental technologies:measuring approximately 6000 square meters in their entirety, the two new experimental halls house enough space for technical installations of up to ten additional beam lines, and an additional 1400 square metres provide office and laboratory space for the scientists.The beam lines and measuring instruments in the new halls are under construction in close cooperation with the future user community and are, in part, collaborative research projects.Three of the future PETRA beamlines will be constructed as an international partnership with Sweden, India and Russia.

    Altogether approximately 170 metres of the PETRA tunnel and accelerator have been dismantled since February to build the new experimental halls. Since August, the accelerator, equipped with special magnets for producing X-ray radiation, has been under reconstruction within the new tunnel areas that have already been completed.After the preliminary construction phase of the experimental halls, they are to be developed further from December 2014 onward; the accelerator will at the same time resume operation.The experiments will re-start in the PETRA III experimental hall “Max von Laue” beginning in April 2015 and the first measuring stations in the new, still unnamed halls should gradually become ready for operation in autumn 2015 and the start of 2016.

    The extension’s total budget of approximately 80 million Euros stems in large part from the Helmholtz Association’s expansion funds as well as funds from the Federal Ministry of Research, the Free and Hanseatic City of Hamburg and DESY.Collaborative partners from Germany and abroad cover approximately one third of the costs.

    See the full article here.

    desi

    DESY is one of the world’s leading accelerator centres. Researchers use the large-scale facilities at DESY to explore the microcosm in all its variety – from the interactions of tiny elementary particles and the behaviour of new types of nanomaterials to biomolecular processes that are essential to life. The accelerators and detectors that DESY develops and builds are unique research tools. The facilities generate the world’s most intense X-ray light, accelerate particles to record energies and open completely new windows onto the universe. 
That makes DESY not only a magnet for more than 3000 guest researchers from over 40 countries every year, but also a coveted partner for national and international cooperations. Committed young researchers find an exciting interdisciplinary setting at DESY. The research centre offers specialized training for a large number of professions. DESY cooperates with industry and business to promote new technologies that will benefit society and encourage innovations. This also benefits the metropolitan regions of the two DESY locations, Hamburg and Zeuthen near Berlin.

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  • richardmitnick 3:43 pm on September 12, 2014 Permalink | Reply
    Tags: , , , , X-ray Technology   

    From DESY: “Researchers X-Ray Living Cancer Cells” 

    DESY
    DESY

    27.02.2014

    Nanodiffraction opens up new insights into the physics of life

    Göttingen-based scientists working at DESY’s PETRA III research light source have carried out the first studies of living biological cells using high-energy X-rays. The new method shows clear differences in the internal cellular structure between living and dead, chemically fixed cells that are often analysed. “The new method for the first time enables us to investigate the internal structures of living cells in their natural environment using hard X-rays,” emphasises the leader of the working group, Prof. Sarah Köster from the Institute for X-Ray Physics of the University of Göttingen. The researchers present their work in the scientific journal Physical Review Letters.
    Zoom (17 KB)

    c ells
    X-ray scan of chemically fixed cells. Each pixel represents a full diffraction image. The colours indicate how strong the X-rays are scattered at each individual point. Credit: Britta Weinhausen/University of Göttingen

    Thanks to analytical methods with ever-higher resolution, scientists today can study biological cells at the level of individual molecules. The cells are frequently chemically fixed before they are studied with the help of optical, X-ray or electron microscopes. The process of chemical fixation involves immersing the cells in a type of chemical preservative which fixes all of the cell’s organelles and even the proteins in place. “Minor changes to the internal structure of the cells are unavoidable in this process,” emphasises Köster. “In our studies, we were able to show these changes in direct comparison for the first time.”

    The team used cancer cells from the adrenal cortex for their analyses. They grew the cells on a silicon nitrite substrate, which is almost transparent to X-rays. In order to keep the cells alive in the experimental chamber during the experiment, they were supplied with nutrients, and their metabolic products were pumped away via fine channels just 0.5 millimetres in diameter. “The biological cells are thus located in a sample environment which very closely resembles their natural environment,” explains Dr. Britta Weinhausen from Köster’s group, the paper’s first author.

    The experiments were carried out at the Nanofocus Setup (GINIX) of PETRA III’s experimental station P10. The scientists used the brilliant X-ray beam from PETRA III to scan the cells in order to obtain information about their internal nanostructure. “Each frame was exposed for just 0.05 seconds, in order to avoid damaging the living cells too quickly”, explains co-author Dr. Michael Sprung from DESY. “Even nanometre-scale structures can be measured with the GINIX assembly, thanks to the combination of PETRA III’s high brilliance and the GINIX setup which is matched to the source.”

    The researchers studied living and chemically fixed cells using this so-called nanodiffraction technique and compared the cells’ internal structures on the basis of the X-ray diffraction images. The results showed that the chemical fixation produces noticeable differences in the cellular structure on a scale of 30 to 50 nanometres (millionths of a millimetre).

    “Thanks to the ever-greater resolution of the various investigative techniques, it is increasingly important to know whether the internal structure of the sample changes during sample preparation,” explains Köster. In future, the new technique will make it possible to study unchanged living cells at high resolution. Although other methods have an even higher resolution than X-ray scattering, they require a chemical fixation or complex and invasive preparation of the cells. Lower-energy, so-called soft X-rays have already been used for studies of living cells. However, the study of structures with sizes as small as 12 nanometres first becomes possible through the analysis of diffraction images produced using hard X-rays.

    See the full article here.

    desi

    DESY is one of the world’s leading accelerator centres. Researchers use the large-scale facilities at DESY to explore the microcosm in all its variety – from the interactions of tiny elementary particles and the behaviour of new types of nanomaterials to biomolecular processes that are essential to life. The accelerators and detectors that DESY develops and builds are unique research tools. The facilities generate the world’s most intense X-ray light, accelerate particles to record energies and open completely new windows onto the universe. 
That makes DESY not only a magnet for more than 3000 guest researchers from over 40 countries every year, but also a coveted partner for national and international cooperations. Committed young researchers find an exciting interdisciplinary setting at DESY. The research centre offers specialized training for a large number of professions. DESY cooperates with industry and business to promote new technologies that will benefit society and encourage innovations. This also benefits the metropolitan regions of the two DESY locations, Hamburg and Zeuthen near Berlin.

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