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    The DOE Science News Source is a Newswise initiative to promote research news from the Office of Science of the DOE to the public and news media.
    • 2020-02-14 12:30:31
    • Article ID: 726780

    January Science Snapshots

    • Credit: Boatman et al. and Smithsonian Institute

      In order to take these mesmerizing microscopy images, the team carefully demineralized small bits of T. rex bone to liberate the preserved vessel tissue inside. The sample used in this study came from the femur of the famous, nearly complete fossil specimen known as “the Nation’s T. rex,” which is currently on display at the Smithsonian National Museum of Natural History.

    • Credit: Zosia Rostomian/Berkeley Lab

    • Credit: ClaudioVentrella/iStock

    Berkeley Lab Helps Reveal How Dinosaur Blood Vessels Can Preserve Through the Ages

    --By Aliyah Kovner 

    A team of scientists led by Elizabeth Boatman at the University of Wisconsin Stout used X-ray imaging and spectromicroscopy performed at Berkeley Lab’s Advanced Light Source (ALS) to demonstrate how soft tissue structures may be preserved in dinosaur bones – countering the long-standing scientific dogma that protein-based body parts cannot survive more than 1 million years.

    In their paper, now published in Scientific Reports, the team analyzed a sample from a 66-million-year-old Tyrannosaurus rex tibia to provide evidence that vertebrate blood vessels – collagen and elastin structures that don’t fossilize like mineral-based bone – may persist across geologic time through two natural, protein-fusing “cross-linking” processes called Fenton chemistry and glycation.

    First, the scientists used imaging, diffraction, spectroscopy, and immunohistochemistry to establish that structures present in the sample are indeed the animal’s original collagen-based tissue. Then, Berkeley Lab co-authors Hoi-Ying Holman and Sirine Fakra respectively performed synchrotron radiation-based Fourier-transform infrared spectromicroscopy (SR-FTIR) to examine how the cross-linked collagen molecules were arranged, and X-ray fluorescence (XRF) mapping to analyze the distribution and types of metal present in T. rex vessels.

    “SR-FTIR takes images and spectra of the same sample, and so you can reveal the distribution of protein-folding patterns, which helps to identify the possible cross-linking mechanisms,” said Holman, a senior scientist in the Molecular Biophysics & Integrated Bioimaging Division.

    Fenton chemistry and glycation are both non-enzymatic reactions – meaning they can occur in deceased organisms – that are driven by the iron present in the body. “The XRF microprobe revealed the presence of finely crystalline goethite, a very stable iron oxyhydroxide mineral, on the vessels that likely contributed to the preservation of organic molecules,” said Fakra, an ALS research scientist.

    The authors believe that the cross-linking reactions they found evidence of, combined with the protection offered from being surrounded by dense mineralized bone, can explain how original soft tissues persist.

    Read more about this research

    Joint Genome Institute Study Reveals Diversity of Giant Viruses Worldwide

    --By Aliyah Kovner 

    A team led by the U.S. Department of Energy Joint Genome Institute (JGI) at Berkeley Lab has reconstructed the genomes of 2,074 large and giant viruses found across the globe, drastically increasing the number of known viruses and providing a resource for future studies on this poorly understood group of viruses, called nucleocytoplasmic large DNA viruses (NCLDVs).

    The work, recently published in Nature, drew from more than 8,500 publicly available metagenome datasets generated from samples of microbial communities, many of which were from freshwater ecosystems. (A metagenome is the entire collection of genetic information captured in a sample.)

    The genomes of the large and giant viruses – which carry between 10 and 100 times more genes than most well-studied viruses – were digitally extracted from the other genetic information by filtering for a NCLDV-specific protein and then organized into distinct genomes known as metagenome-assembled genomes (MAGs). This process was performed, in part, using capabilities of the National Energy Research Scientific Computing Center (NERSC), also located at Berkeley Lab.

    “This is the first study to take a more global look at giant viruses by capturing genomes of uncultivated giant viruses from environmental sequences across the globe, then using these sequences to make inferences about the biogeographic distribution of these viruses in the various ecosystems, their diversity, their predicted metabolic features and putative hosts,” said Tanja Woyke, senior author of the study and head of JGI’s Microbial Genomics Program.

    After analyzing the genes identified in the viral MAGs, Woyke and her colleagues found that NCLDVs have evolved strategies to alter the metabolism of their host organisms (primarily single-celled eukaryotes, but also multicellular eukaryotic organisms) in order to optimize conditions for viral replication. Because eukaryotic microbes are known to play a big part in biogeochemical processes such as carbon and nitrogen cycling, the findings suggest that NCLDVs are a key part of understanding how ecosystems function.

    Read the full release by JGI

    X-Ray Technology Sheds New Light on Antibiotic Synthesis

    -- By Aliyah Kovner 

    Atomic-scale structural analyses performed at Berkeley Lab’s Advanced Light Source (ALS) are helping scientists understand the inner workings of the enzyme “assembly lines” that microbes use to produce an important class of compounds, many of which have uses as antibiotics, antifungals, and immunosuppressants.

    These cellular machines, known as nonribosomal peptide synthetases (NRPSs), are large, multi-enzyme clusters that synthesize compounds by passing a precursor molecule from one module to the next, with each “station” catalyzing a change in the molecule. In the past decade, researchers have learned a great deal about how individual NRPS modules work, but an understanding of how the assembly lines function as a whole has been lacking. In the hopes of eventually engineering custom NRPSs to make new and improved medicines, a team led by McGill University began investigating the bacterial NRPS that synthesizes the antibiotic gramicidin.

    The scientists used the SIBYLS X-ray scattering beamline at the ALS to validate X-ray crystallography and small-angle X-ray scattering performed at the Canadian Light Source in Saskatchewan and the Advanced Photon Source at Argonne National Laboratory. The results, published in Science, show that the modules are surprisingly physically flexible, and that the assembly line can function in many different arrangements.

    Gregory Hura, a Berkeley Lab biophysicist on the SIBYLS team and head of the Structural Biology Department in the Molecular Biophysics & Integrated Bioimaging Division, notes that the analytic capabilities of the beamline are helping decode the functionality of many important large molecules. “There is no surprise that macromolecules, responsible for the complex activities of life, are dynamic, modular, and multifaceted – but our appreciation for those dynamics has been hindered by a lack of modalities for sensing them. The newly upgraded SIBYLS beamline provides unique insights that complement crystallography and electron microscopy, and together, these technologies are helping us develop new medicines.”

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    Argonne researchers create active material out of microscopic spinning particles

    Argonne researchers create active material out of microscopic spinning particles

    Argonne researchers have created a new kind of self-healing active material out of "microspinners," which self-assemble under a magnetic field to form a lattice.

    Global Environmental Changes Leading to Shorter, Younger Trees

    Global Environmental Changes Leading to Shorter, Younger Trees

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    Researchers use ALCF resources to model the spread of COVID-19

    Researchers use ALCF resources to model the spread of COVID-19

    Argonne researchers lead highly detailed COVID-19 modeling efforts to understand how the virus spreads through populations.

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    Return of the Blob: Scientists find surprising link to troublesome turbulence at the edge of fusion plasmas

    Correlation discovered between magnetic turbulence in fusion plasmas and troublesome blobs at the plasma edge.

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    Novel insight reveals topological tangle in unexpected corner of the universe

    In a recent theoretical study, scientists discovered the presence of the Hopfion topological structure in nano-sized particles of ferroelectrics -- materials with promising applications in microelectronics and information technology.

    New insights into the dynamic edge of fusion plasmas could help capture the power that drives the sun and stars

    New insights into the dynamic edge of fusion plasmas could help capture the power that drives the sun and stars

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    Researchers capture the coordinated dance between electrons and nuclei in a light-excited molecule

    Researchers capture the coordinated dance between electrons and nuclei in a light-excited molecule

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    Untangling a key step in photosynthetic oxygen production

    Untangling a key step in photosynthetic oxygen production

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    Platinum-free catalysts could make cheaper hydrogen fuel cells

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    Electrons Break Rotational Symmetry in Exotic Low-Temp Superconductor

    Electrons Break Rotational Symmetry in Exotic Low-Temp Superconductor

    This odd behavior may promote the material's ability upon cooling to perfectly conduct electricity in a way unexplained by standard theories.


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    Lehigh University graduate student wins DOE award to conduct thesis research at PPPL

    Lehigh University graduate student wins DOE award to conduct thesis research at PPPL

    Article profiles Vincent Graber, his research interests and thesis plans.

    Lograsso named Critical Materials Institute Director

    Lograsso named Critical Materials Institute Director

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    Renowned scientist to head new research for plasma applications in industry and quantum information science

    Renowned scientist to head new research for plasma applications in industry and quantum information science

    The Princeton Plasma Physics Laboratory has appointed David Graves, an internationally known chemical engineer, to head a new research enterprise that will explore plasma applications in semiconductor manufacturing and the next generation of super-fast quantum computers.

    Argonne physicist Giulia Galli earns two top honors for outstanding research and leadership

    Argonne physicist Giulia Galli earns two top honors for outstanding research and leadership

    Galli elected to both the American Academy of Arts and Sciences and the National Academy of Sciences.

    Brookhaven Biochemist Receives Prestigious Award for Plant Lipid Research

    Brookhaven Biochemist Receives Prestigious Award for Plant Lipid Research

    Jantana Keereetaweep, a biochemistry research associate in the biology department at the U.S. Department of Energy's Brookhaven National Laboratory, has been awarded the Paul K. Stumpf Award for her research on plant lipids (fats and oils). The award, given every two years, recognizes the contributions of a promising early-career scientist in honor of Stumpf, who was a world leader and pioneer in the study of plant lipid biochemistry.

    ORNL's Brian Post named SME Young Engineer of the Year

    ORNL's Brian Post named SME Young Engineer of the Year

    Brian Post, a researcher in large-scale additive manufacturing at Oak Ridge National Laboratory, has been selected as a recipient of the 2020 Outstanding Young Manufacturing Engineer Award by the Society of Mechanical Engineers (SME).

    Fourth cohort of 6 innovators selected for Chain Reaction Innovations program

    Fourth cohort of 6 innovators selected for Chain Reaction Innovations program

    Six new innovators will be joining Chain Reaction Innovations (CRI), the entrepreneurship program at the U.S. Department of Energy's (DOE) Argonne National Laboratory, as part of the elite program's fourth cohort.

    Graduate student at PPPL Ian Ochs wins top Princeton University fellowship

    Graduate student at PPPL Ian Ochs wins top Princeton University fellowship

    Graduate student in plasma physics at the Princeton Plasma Physics Laboratory has won a highly selective honorific fellowship from Princeton University.

    U.S. Department of Energy's INCITE program seeks proposals for 2021

    U.S. Department of Energy's INCITE program seeks proposals for 2021

    The INCITE program is now seeking proposals for high-impact, computationally intensive research projects that require the power and scale of DOE's leadership-class supercomputers.

    Argonne's Paul Dickman honored with nuclear waste management achievement award

    Argonne's Paul Dickman honored with nuclear waste management achievement award

    Paul Dickman has been named a Waste Management Symposium Fellow for 2020.


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    Harvesting Energy from Light using Bio-inspired Artificial Cells

    Harvesting Energy from Light using Bio-inspired Artificial Cells

    Scientists designed and connected two different artificial cells to each other to produce molecules called ATP (adenosine triphosphate).

    Engineering Living Scaffolds for Building Materials

    Engineering Living Scaffolds for Building Materials

    Bone and mollusk shells are composite systems that combine living cells and inorganic components. This allows them to regenerate and change structure while also being very strong and durable. Borrowing from this amazing complexity, researchers have been exploring a new class of materials called engineered living materials (ELMs).

    Excavating Quantum Information Buried in Noise

    Excavating Quantum Information Buried in Noise

    Researchers developed two new methods to assess and remove error in how scientists measure quantum systems. By reducing quantum "noise" - uncertainty inherent to quantum processes - these new methods improve accuracy and precision.

    How Electrons Move in a Catastrophe

    How Electrons Move in a Catastrophe

    Lanthanum strontium manganite (LSMO) is a widely applicable material, from magnetic tunnel junctions to solid oxide fuel cells. However, when it gets thin, its behavior changes for the worse. The reason why was not known. Now, using two theoretical methods, a team determined what happens.

    When Ions and Molecules Cluster

    When Ions and Molecules Cluster

    How an ion behaves when isolated within an analytical instrument can differ from how it behaves in the environment. Now, Xue-Bin Wang at Pacific Northwest National Laboratory devised a way to bring ions and molecules together in clusters to better discover their properties and predict their behavior.

    Tune in to Tetrahedral Superstructures

    Tune in to Tetrahedral Superstructures

    Shape affects how the particles fit together and, in turn, the resulting material. For the first time, a team observed the self-assembly of nanoparticles with tetrahedral shapes.

    Tracing Interstellar Dust Back to the Solar System's Formation

    Tracing Interstellar Dust Back to the Solar System's Formation

    This study is the first to confirm dust particles pre-dating the formation of our solar system. Further study of these materials will enable a deeper understanding of the processes that formed and have since altered them.

    Investigating Materials that Can Go the Distance in Fusion Reactors

    Investigating Materials that Can Go the Distance in Fusion Reactors

    Future fusion reactors will require materials that can withstand extreme operating conditions, including being bombarded by high-energy neutrons at high temperatures. Scientists recently irradiated titanium diboride (TiB2) in the High Flux Isotope Reactor (HFIR) to better understand the effects of fusion neutrons on performance.

    Better 3-D Imaging of Tumors in the Breast with Less Radiation

    Better 3-D Imaging of Tumors in the Breast with Less Radiation

    In breast cancer screening, an imaging technique based on nuclear medicine is currently being used as a successful secondary screening tool alongside mammography to improve the accuracy of the diagnosis. Now, a team is hoping to improve this imaging technique.

    Microbes are Metabolic Specialists

    Microbes are Metabolic Specialists

    Scientists can use genetic information to measure if microbes in the environment can perform specific ecological roles. Researchers recently analyzed the genomes of over 6,000 microbial species.


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