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  • Physics  (23)
  • Amino Acid Sequence
  • American Association for the Advancement of Science (AAAS)  (31)
  • American Chemical Society (ACS)
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  • 1
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-07-08
    Description: After many years of delays, the €1.7 billion Facility for Antiproton and Ion Research, an extension of the GSI Helmholtz Center for Heavy Ion Research near Darmstadt, Germany, may finally get built. At a council meeting on 27 and 28 June, the partner countries—eight European Union members plus India and Russia—concluded that they have enough money to cover a €320 million budget gap; they will now seek building permits from the German government. Still, some countries have yet to commit their share of the missing cash, including Russia, which had agreed to bear about 18% of FAIR's total construction cost, the second largest contribution after Germany's 70%. Author: Edwin Cartlidge
    Keywords: Physics
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  • 2
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-05-27
    Description: Author: Jelena Stajic
    Keywords: Physics
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  • 3
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-07-15
    Description: Author: Jelena Stajic
    Keywords: Physics
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  • 4
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-07-22
    Description: Author: Ian S. Osborne
    Keywords: Physics
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  • 5
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-04-08
    Description: Author: Jelena Stajic
    Keywords: Physics
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  • 6
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-03-25
    Description: Density functional theory (DFT) stands out from all first-principles quantum mechanical methods for the simulation of materials, as it enables very good approximations for the complicated components of electronic motion called exchange and correlation. DFT is the method of choice for many materials simulations because of the availability of general-purpose programs that can perform calculations on any material. Results obtained with one DFT program need to be reproducible by any of the other DFT programs, and this has not been straightforward up to now. On page 10.1126/science.aad3000 of this issue, Lejaeghere et al. (1) describe an extensive effort by developers of the major solid-state DFT codes to provide a unified and reproducible benchmark of precision for their calculations based on a reliable criterion, the so-called Δ gauge. Using the Δ gauge, the authors found that the level of precision that can be achieved today in DFT calculations of elemental crystalline solids is comparable to the precision of the most advanced techniques for experimental measurement of the properties of materials. The work leads to the conclusion that the DFT simulation of elemental crystalline solids is a (computationally) solved problem, but also poses the question of whether we can achieve the same levels of validation and reproducibility for more complex simulations of materials involving several elements and/or several methods. Author: Chris-Kriton Skylaris
    Keywords: Physics
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  • 7
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-07-01
    Description: The photoemission of electrons from atoms, molecules, and condensed matter provides the experimental basis of our understanding of electronic structure. During the process of photoemission, a sufficiently large quantum of electromagnetic radiation (a photon) is absorbed by matter and converted into an electronic excitation, promoting a bound electron into a final state above the vacuum energy Evac. In photoemission spectroscopy, the kinetic energy and momentum of electrons in such final states are analyzed after their propagation to a distant detector. To determine the electronic structure of the sample, the “sudden approximation” has to be fulfilled, whereby the photoelectron leaves the sample fast enough, without further interaction with the remaining electronic structure. On page 62 of this issue, Tao et al. (1) provide unprecedented insight into final-state dynamics by measuring the time a photoelectron takes to leave a solid material for characteristically different final states. By comparing an electron excited to a final state of a nickel solid Ψ Nif with one excited to a state of vacuum Ψ vacf, they establish that a photoelectron resides in the final state for 200 attoseconds (as) (2 × 10−16 s) before it leaves the nickel (see the figure). Such time scales would still allow for the electron to interact with its surroundings and, thus, are relevant for the validity of the sudden approximation. Authors: Uwe Bovensiepen, Manuel Ligges
    Keywords: Physics
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  • 8
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-06-24
    Description: Author: Jelena Stajic
    Keywords: Physics
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  • 9
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-08-16
    Description: When a multibillion-dollar physics experiment is canceled, it's tempting to look for lessons that can be applied to future megascience projects. A new book on the rise and fall of the Superconducting Supercollider (SSC) by a trio of science historians takes on that challenge. And while the authors do an excellent job of describing what occurred in the decade from its inception to its demise, they stumble when trying to assign blame. Author: Jeffrey Mervis
    Keywords: Physics
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  • 10
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-05-20
    Description: Standard superconductors consist of a condensate of paired electrons, called Cooper pairs. The transport behavior of these pairs at junctions can produce exotic effects that are of fundamental and practical interest. When two superconductors are in contact via a normal metal, the pairs must convert to single-particle states to traverse between superconductors. This occurs by the Andreev process, whereby a low-energy electron in the normal metal injects a Cooper pair into the superconductor and generates a hole that reflects back into the metal; coherent, opposite-momentum electron-hole pairs then carry the supercurrent across the metallic junction (1) (see the figure, panel A). In the case of superconductors connected to a quantum Hall state, there are only one-way paths along the junction edges. Here, a new type of Andreev process is predicted to occur, whereby electron and hole states on opposite sample edges carry the supercurrent. This prediction was made more than 20 years ago (2), but clear observation of the effect was frustrated by the difficulty of creating coexisting superconducting and quantum Hall states. On page 966 of this issue, Amet et al. (3) report on the interplay between these two states, finding evidence for the unconventional Andreev process. Their results confirm new physics that appears when two correlated states are connected, and opens the door to a range of novel excitations and exotic devices. Author: Nadya Mason
    Keywords: Physics
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  • 11
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-03-11
    Description: Grappling with our desire to understand nature, we construct models of the specific systems that we wish to study. Unsurprisingly, such models are generally highly tailored to the system of interest. But are all these models really that distinct? Or, could there be a universal model that can somehow describe the behavior of any system we could think of? On page 1180 of this issue, De las Cuevas and Cubitt (1) venture out to weave ideas from physics and computer science in an attempt to answer this question for all classical spin models. Author: Stephanie Wehner
    Keywords: Physics
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  • 12
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-03-18
    Description: The recent report of superconductivity in hydrogen sulfide (H2S) by Drozdov et al. (1) at a record high superconducting critical temperature Tc of 203 K and at high pressure (153 GPa) triggered excitement from both a fundamental and technological perspective. On page 1303 of this issue, Troyan et al. (2) confirm the finding by using an elegant and unexpected implementation of the Mössbauer technique at the third-generation synchrotron facility in Grenoble, France. They measured the Meissner effect (3)—the expulsion of magnetic field from the sample—thereby unequivocally confirming the existence of superconductivity. The new superconductor is believed to have a simple chemical formula, H3S. The superconductivity in H3S was predicted theoretically by Duan et al. (4) before the first experimental findings were reported. The technique has great potential for future studies of tiny samples squeezed to extremely high pressure. This experimental advance paves the road to probing superconductivity in metallic hydrogen, which is expected to be a room-temperature superconductor above 500 GPa (5). Author: Viktor Struzhkin
    Keywords: Physics
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  • 13
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-03-04
    Description: Turn a switch and the light goes on. The layman's perception is that this is like opening a tap so that the water starts running. But this analogy is misleading. The flow of water is governed by the theory of hydrodynamics, whereby the behavior of the fluid does not require knowledge of the motions of individual molecules. Electrical currents in solids, however, are formed from electrons. In metals, these do not collide with each other, but they do scatter from lattice imperfections. The resulting “Knudsen flow” of electrons is reminiscent of the avalanche of balls cascading through a dense forest of pins, as in a Pachinko machine. On pages 1058, 1055, and 1061 of this issue, evidence is presented that electrons can actually yield to the laws of hydrodynamics (1–3). What is additionally surprising is that these observations are in agreement with mathematical techniques borrowed from string theory (4). These techniques have been applied to describe strongly interacting forms of quantum matter, predicting that they should exhibit hydrodynamic flows (5). Author: Jan Zaanen
    Keywords: Physics
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  • 14
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-05-20
    Description: The 20th-century philosopher Wilfrid Sellars characterized the aim of philosophy as "to understand how things in the broadest possible sense of the term hang together in the broadest possible sense of the term." This is also physicist Sean Carroll's aim in his new book, The Big Picture. He sets out to show how various phenomena, including thought, choice, conscioussness, and value, hang together with the scientific account of reality that has been developed in physics in the past 100 years. He attempts to do all this without relying on specialized jargon from philosophy and physics, and succeeds spectacularly in achieving both aims. Author: Barry Loewer
    Keywords: Physics
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  • 15
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-04-22
    Description: An inherent aspect of any two-dimensional (2D) sheet is that all atoms in the material lie on the surface. This leads to a concept of 2D crystals as a “canvas,” where different chemical groups or “ink” on the surface can lead to a palette of distinct materials properties. The most well-studied 2D crystal is graphene, a one-atom-thick sheet of carbon atoms arranged in a honeycomb lattice. Although graphene's superlative materials properties and novel physical phenomena have led to a variety of applications (1), better tunability of these properties is still required. Toward this end, hydrogenated graphene (graphane) was predicted to have a wide band gap and exhibit magnetic order (2–4), in contrast to graphene, which is (semi)metallic and diamagnetic. The chemical stability of graphene makes hydrogenation difficult to control, and this has hampered efforts to tune its electronic or magnetic properties. On page 437 of this issue, González-Herrero et al. (5) report direct evidence that hydrogen atoms on graphene do indeed yield a magnetic moment and that these moments can order ferromagnetically over relatively large distances. If these methods can be extended to industrial scales, then one can imagine storing information at unprecedented densities by painting magnetic bits on graphene canvases (see the figure). Authors: S. M. Hollen, J. A. Gupta
    Keywords: Physics
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  • 16
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-04-15
    Description: Storing information in an ensemble of single-atom magnets represents the ultimate miniaturization of data storage technology, in which two specific orientations of each atomic magnetic moment represent a bit (a 0 or 1) of information (see the figure, panel A). The inherent dilemma in using a single-atom magnet is keeping it magnetized—or, in other words, being able to hold the information in one of the bit states without an external magnetic field for a useful amount of time and at practical temperatures (1, 2). This phenomenon of magnetic remanence is dif cult to realize from a single atom, in part because diminished robustness against fluctuations from the environment can unintentionally flip the magnetic state, thus wiping out the magnetic memory. A recent attempt to observe remanence in a single atom (3) proved premature, as the results were incompatible with the magnetic ground state of that system (4) and could not be reproduced (4, 5). Hence, the question of whether this defining property of a single-atom magnet can actually be achieved has remained an open question until now. On page 318 of this issue, Donati et al. (6) demonstrate that single holmium atoms exhibit magnetic remanence up to temperatures of 40 K, much higher than previous records of atomic-scale magnets composed of 3 to 12 atoms (1, 2, 5)—a record in both size and stability for any magnet. Authors: Alexander Ako Khajetoorians, Andreas J. Heinrich
    Keywords: Physics
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  • 17
    Publication Date: 2016-01-23
    Description: Mono-ubiquitination of Fancd2 is essential for repairing DNA interstrand cross-links (ICLs), but the underlying mechanisms are unclear. The Fan1 nuclease, also required for ICL repair, is recruited to ICLs by ubiquitinated (Ub) Fancd2. This could in principle explain how Ub-Fancd2 promotes ICL repair, but we show that recruitment of Fan1 by Ub-Fancd2 is dispensable for ICL repair. Instead, Fan1 recruitment--and activity--restrains DNA replication fork progression and prevents chromosome abnormalities from occurring when DNA replication forks stall, even in the absence of ICLs. Accordingly, Fan1 nuclease-defective knockin mice are cancer-prone. Moreover, we show that a Fan1 variant in high-risk pancreatic cancers abolishes recruitment by Ub-Fancd2 and causes genetic instability without affecting ICL repair. Therefore, Fan1 recruitment enables processing of stalled forks that is essential for genome stability and health.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4770513/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4770513/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lachaud, Christophe -- Moreno, Alberto -- Marchesi, Francesco -- Toth, Rachel -- Blow, J Julian -- Rouse, John -- WT096598MA/Wellcome Trust/United Kingdom -- Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2016 Feb 19;351(6275):846-9. doi: 10.1126/science.aad5634. Epub 2016 Jan 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, Sir James Black Centre, University of Dundee, Dundee DD1 5EH, Scotland, UK. ; Centre for Gene Regulation and Expression, College of Life Sciences, Sir James Black Centre, University of Dundee, Dundee DD1 5EH, Scotland, UK. ; School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden Road, Glasgow G61 1QH, UK. ; Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, Sir James Black Centre, University of Dundee, Dundee DD1 5EH, Scotland, UK. j.rouse@dundee.ac.uk.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26797144" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; *Chromosome Aberrations ; DNA Repair ; *DNA Replication ; Endodeoxyribonucleases/genetics/*metabolism ; Fanconi Anemia Complementation Group D2 Protein/genetics/*metabolism ; Female ; Gene Knock-In Techniques ; Genetic Predisposition to Disease ; Genomic Instability/*genetics ; Liver Neoplasms/genetics/pathology ; Lung Neoplasms/genetics/pathology ; Lymphoma/genetics/pathology ; Male ; Mice ; Mice, Inbred C57BL ; Molecular Sequence Data ; Pancreatic Neoplasms/*genetics ; *Ubiquitination
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  • 18
    Publication Date: 2016-04-02
    Description: The recent rapid spread of Zika virus and its unexpected linkage to birth defects and an autoimmune neurological syndrome have generated worldwide concern. Zika virus is a flavivirus like the dengue, yellow fever, and West Nile viruses. We present the 3.8 angstrom resolution structure of mature Zika virus, determined by cryo-electron microscopy (cryo-EM). The structure of Zika virus is similar to other known flavivirus structures, except for the ~10 amino acids that surround the Asn(154) glycosylation site in each of the 180 envelope glycoproteins that make up the icosahedral shell. The carbohydrate moiety associated with this residue, which is recognizable in the cryo-EM electron density, may function as an attachment site of the virus to host cells. This region varies not only among Zika virus strains but also in other flaviviruses, which suggests that differences in this region may influence virus transmission and disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4845755/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4845755/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sirohi, Devika -- Chen, Zhenguo -- Sun, Lei -- Klose, Thomas -- Pierson, Theodore C -- Rossmann, Michael G -- Kuhn, Richard J -- R01 AI073755/AI/NIAID NIH HHS/ -- R01 AI076331/AI/NIAID NIH HHS/ -- R01AI073755/AI/NIAID NIH HHS/ -- R01AI076331/AI/NIAID NIH HHS/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2016 Apr 22;352(6284):467-70. doi: 10.1126/science.aaf5316. Epub 2016 Mar 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Markey Center for Structural Biology and Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA. ; Viral Pathogenesis Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27033547" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Cryoelectron Microscopy ; Glycosylation ; Humans ; Molecular Sequence Data ; Protein Structure, Tertiary ; Viral Envelope Proteins/chemistry/ultrastructure ; Viral Matrix Proteins/chemistry/ultrastructure ; Zika Virus/*chemistry/*ultrastructure
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  • 19
    Publication Date: 2016-04-16
    Description: The nuclear pore complex (NPC) controls the transport of macromolecules between the nucleus and cytoplasm, but its molecular architecture has thus far remained poorly defined. We biochemically reconstituted NPC core protomers and elucidated the underlying protein-protein interaction network. Flexible linker sequences, rather than interactions between the structured core scaffold nucleoporins, mediate the assembly of the inner ring complex and its attachment to the NPC coat. X-ray crystallographic analysis of these scaffold nucleoporins revealed the molecular details of their interactions with the flexible linker sequences and enabled construction of full-length atomic structures. By docking these structures into the cryoelectron tomographic reconstruction of the intact human NPC and validating their placement with our nucleoporin interactome, we built a composite structure of the NPC symmetric core that contains ~320,000 residues and accounts for ~56 megadaltons of the NPC's structured mass. Our approach provides a paradigm for the structure determination of similarly complex macromolecular assemblies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lin, Daniel H -- Stuwe, Tobias -- Schilbach, Sandra -- Rundlet, Emily J -- Perriches, Thibaud -- Mobbs, George -- Fan, Yanbin -- Thierbach, Karsten -- Huber, Ferdinand M -- Collins, Leslie N -- Davenport, Andrew M -- Jeon, Young E -- Hoelz, Andre -- 5 T32 GM07616/GM/NIGMS NIH HHS/ -- ACB-12002/PHS HHS/ -- AGM-12006/PHS HHS/ -- R01 GM111461/GM/NIGMS NIH HHS/ -- R01-GM111461/GM/NIGMS NIH HHS/ -- T32 GM007616/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2016 Apr 15;352(6283):aaf1015. doi: 10.1126/science.aaf1015. Epub 2016 Apr 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA. ; Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA. hoelz@caltech.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27081075" target="_blank"〉PubMed〈/a〉
    Keywords: Active Transport, Cell Nucleus ; Amino Acid Sequence ; Cryoelectron Microscopy ; Crystallography, X-Ray ; Cytoplasm/metabolism ; Electron Microscope Tomography ; Fungal Proteins/chemistry/genetics/metabolism ; Humans ; Molecular Sequence Data ; Nuclear Pore/chemistry/*metabolism/*ultrastructure ; Nuclear Pore Complex Proteins/chemistry/genetics/*metabolism ; *Protein Interaction Maps ; Protein Structure, Tertiary ; Protein Subunits/chemistry/genetics/metabolism
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  • 20
    Publication Date: 2016-02-26
    Description: T cell-mediated destruction of insulin-producing beta cells in the pancreas causes type 1 diabetes (T1D). CD4 T cell responses play a central role in beta cell destruction, but the identity of the epitopes recognized by pathogenic CD4 T cells remains unknown. We found that diabetes-inducing CD4 T cell clones isolated from nonobese diabetic mice recognize epitopes formed by covalent cross-linking of proinsulin peptides to other peptides present in beta cell secretory granules. These hybrid insulin peptides (HIPs) are antigenic for CD4 T cells and can be detected by mass spectrometry in beta cells. CD4 T cells from the residual pancreatic islets of two organ donors who had T1D also recognize HIPs. Autoreactive T cells targeting hybrid peptides may explain how immune tolerance is broken in T1D.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Delong, Thomas -- Wiles, Timothy A -- Baker, Rocky L -- Bradley, Brenda -- Barbour, Gene -- Reisdorph, Richard -- Armstrong, Michael -- Powell, Roger L -- Reisdorph, Nichole -- Kumar, Nitesh -- Elso, Colleen M -- DeNicola, Megan -- Bottino, Rita -- Powers, Alvin C -- Harlan, David M -- Kent, Sally C -- Mannering, Stuart I -- Haskins, Kathryn -- 1K01DK094941/DK/NIDDK NIH HHS/ -- 1R01DK081166/DK/NIDDK NIH HHS/ -- 5U01DK89572/DK/NIDDK NIH HHS/ -- DK104211/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 2016 Feb 12;351(6274):711-4. doi: 10.1126/science.aad2791.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Immunology and Microbiology, University of Colorado School of Medicine, Denver, Anschutz Medical Campus, Aurora, CO 80045, USA. thomas.delong@ucdenver.edu katie.haskins@ucdenver.edu. ; Department of Immunology and Microbiology, University of Colorado School of Medicine, Denver, Anschutz Medical Campus, Aurora, CO 80045, USA. ; Pharmaceutical Sciences, University of Colorado School of Medicine, Aurora, CO 80045, USA. ; Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065, Australia. ; Department of Medicine, Diabetes Division, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA. ; Institute of Cellular Therapeutics, Allegheny-Singer Research Institute, Allegheny Health Network, Pittsburgh, PA, USA. ; Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, and Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN, USA. VA Tennessee Valley Healthcare System, Nashville, TN, USA. ; Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065, Australia. University of Melbourne, Department of Medicine, St. Vincent's Hospital, Fitzroy, Victoria 3065, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26912858" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; C-Peptide/chemistry/*immunology ; CD4-Positive T-Lymphocytes/*immunology ; Clone Cells ; Diabetes Mellitus, Experimental/*immunology/pathology ; Diabetes Mellitus, Type 1/*immunology/pathology ; Epitopes/*immunology ; Immune Tolerance ; Insulin-Secreting Cells/*immunology/pathology ; Mice ; Mice, Inbred NOD ; Molecular Sequence Data ; Peptides/chemistry/immunology
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  • 21
    Publication Date: 2016-02-26
    Description: With functions that range from cell envelope structure to signal transduction and transport, lipoproteins constitute 2 to 3% of bacterial genomes and play critical roles in bacterial physiology, pathogenicity, and antibiotic resistance. Lipoproteins are synthesized with a signal peptide securing them to the cytoplasmic membrane with the lipoprotein domain in the periplasm or outside the cell. Posttranslational processing requires a signal peptidase II (LspA) that removes the signal peptide. Here, we report the crystal structure of LspA from Pseudomonas aeruginosa complexed with the antimicrobial globomycin at 2.8 angstrom resolution. Mutagenesis studies identify LspA as an aspartyl peptidase. In an example of molecular mimicry, globomycin appears to inhibit by acting as a noncleavable peptide that sterically blocks the active site. This structure should inform rational antibiotic drug discovery.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vogeley, Lutz -- El Arnaout, Toufic -- Bailey, Jonathan -- Stansfeld, Phillip J -- Boland, Coilin -- Caffrey, Martin -- BB/I019855/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2016 Feb 19;351(6275):876-80. doi: 10.1126/science.aad3747.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland. ; Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK. ; School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland. martin.caffrey@tcd.ie.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26912896" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Anti-Bacterial Agents/*chemistry/pharmacology ; Aspartic Acid Endopeptidases/*antagonists & inhibitors/*chemistry/genetics ; Bacterial Proteins/*antagonists & inhibitors/*chemistry/genetics ; Catalytic Domain ; Conserved Sequence ; Crystallography, X-Ray ; Mutagenesis ; Peptides/*chemistry/pharmacology ; Protein Conformation ; Protein Processing, Post-Translational ; Pseudomonas aeruginosa/*enzymology ; Substrate Specificity
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  • 22
    Publication Date: 2016-03-12
    Description: Poly(ethylene terephthalate) (PET) is used extensively worldwide in plastic products, and its accumulation in the environment has become a global concern. Because the ability to enzymatically degrade PET has been thought to be limited to a few fungal species, biodegradation is not yet a viable remediation or recycling strategy. By screening natural microbial communities exposed to PET in the environment, we isolated a novel bacterium, Ideonella sakaiensis 201-F6, that is able to use PET as its major energy and carbon source. When grown on PET, this strain produces two enzymes capable of hydrolyzing PET and the reaction intermediate, mono(2-hydroxyethyl) terephthalic acid. Both enzymes are required to enzymatically convert PET efficiently into its two environmentally benign monomers, terephthalic acid and ethylene glycol.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yoshida, Shosuke -- Hiraga, Kazumi -- Takehana, Toshihiko -- Taniguchi, Ikuo -- Yamaji, Hironao -- Maeda, Yasuhito -- Toyohara, Kiyotsuna -- Miyamoto, Kenji -- Kimura, Yoshiharu -- Oda, Kohei -- New York, N.Y. -- Science. 2016 Mar 11;351(6278):1196-9. doi: 10.1126/science.aad6359.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Applied Biology, Faculty of Textile Science, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan. Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan. ; Department of Applied Biology, Faculty of Textile Science, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan. ; Life Science Materials Laboratory, ADEKA, 7-2-34 Higashiogu, Arakawa-ku, Tokyo 116-8553, Japan. ; Department of Polymer Science, Faculty of Textile Science, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan. ; Ecology-Related Material Group Innovation Research Institute, Teijin, Hinode-cho 2-1, Iwakuni, Yamaguchi 740-8511, Japan. ; Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26965627" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Betaproteobacteria/*enzymology ; Environmental Restoration and Remediation ; Enzymes/classification/genetics/metabolism ; Hydrolysis ; Microbial Consortia ; Molecular Sequence Data ; Phthalic Acids/metabolism ; Phylogeny ; Plastics/*metabolism ; Polyethylene Terephthalates/*metabolism ; Recycling
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  • 23
    Publication Date: 2016-02-06
    Description: SH3 and multiple ankyrin repeat domains 3 (SHANK3) haploinsufficiency is causative for the neurological features of Phelan-McDermid syndrome (PMDS), including a high risk of autism spectrum disorder (ASD). We used unbiased, quantitative proteomics to identify changes in the phosphoproteome of Shank3-deficient neurons. Down-regulation of protein kinase B (PKB/Akt)-mammalian target of rapamycin complex 1 (mTORC1) signaling resulted from enhanced phosphorylation and activation of serine/threonine protein phosphatase 2A (PP2A) regulatory subunit, B56beta, due to increased steady-state levels of its kinase, Cdc2-like kinase 2 (CLK2). Pharmacological and genetic activation of Akt or inhibition of CLK2 relieved synaptic deficits in Shank3-deficient and PMDS patient-derived neurons. CLK2 inhibition also restored normal sociability in a Shank3-deficient mouse model. Our study thereby provides a novel mechanistic and potentially therapeutic understanding of deregulated signaling downstream of Shank3 deficiency.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bidinosti, Michael -- Botta, Paolo -- Kruttner, Sebastian -- Proenca, Catia C -- Stoehr, Natacha -- Bernhard, Mario -- Fruh, Isabelle -- Mueller, Matthias -- Bonenfant, Debora -- Voshol, Hans -- Carbone, Walter -- Neal, Sarah J -- McTighe, Stephanie M -- Roma, Guglielmo -- Dolmetsch, Ricardo E -- Porter, Jeffrey A -- Caroni, Pico -- Bouwmeester, Tewis -- Luthi, Andreas -- Galimberti, Ivan -- New York, N.Y. -- Science. 2016 Mar 11;351(6278):1199-203. doi: 10.1126/science.aad5487. Epub 2016 Feb 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Developmental Molecular Pathways, Novartis Institutes for Biomedical Research, Basel, Switzerland. ; Friedrich Miescher Institute, Basel, Switzerland. ; Analytical Sciences and Imaging, Novartis Institutes for Biomedical Research, Basel, Switzerland. ; Neuroscience, Novartis Institutes for Biomedical Research, Cambridge, USA. ; Developmental Molecular Pathways, Novartis Institutes for Biomedical Research, Basel, Switzerland. ivan.galimberti@novartis.com.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26847545" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Autism Spectrum Disorder/*drug therapy/enzymology/genetics ; Chromosome Deletion ; Chromosome Disorders/genetics ; Chromosomes, Human, Pair 22/genetics ; Disease Models, Animal ; Down-Regulation ; Gene Knockdown Techniques ; Humans ; Insulin-Like Growth Factor I/metabolism ; Mice ; Molecular Sequence Data ; Multiprotein Complexes/metabolism ; Nerve Tissue Proteins/*genetics ; Neurons/enzymology ; Phosphorylation ; Protein Phosphatase 2/metabolism ; Protein-Serine-Threonine Kinases/*antagonists & inhibitors/metabolism ; Protein-Tyrosine Kinases/*antagonists & inhibitors/metabolism ; Proteomics ; Proto-Oncogene Proteins c-akt/genetics/metabolism ; Rats ; Signal Transduction ; TOR Serine-Threonine Kinases/metabolism
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  • 24
    Publication Date: 2016-03-26
    Description: Induction of broadly neutralizing antibodies (bnAbs) is a major HIV vaccine goal. Germline-targeting immunogens aim to initiate bnAb induction by activating bnAb germline precursor B cells. Critical unmet challenges are to determine whether bnAb precursor naive B cells bind germline-targeting immunogens and occur at sufficient frequency in humans for reliable vaccine responses. Using deep mutational scanning and multitarget optimization, we developed a germline-targeting immunogen (eOD-GT8) for diverse VRC01-class bnAbs. We then used the immunogen to isolate VRC01-class precursor naive B cells from HIV-uninfected donors. Frequencies of true VRC01-class precursors, their structures, and their eOD-GT8 affinities support this immunogen as a candidate human vaccine prime. These methods could be applied to germline targeting for other classes of HIV bnAbs and for Abs to other pathogens.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4872700/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4872700/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jardine, Joseph G -- Kulp, Daniel W -- Havenar-Daughton, Colin -- Sarkar, Anita -- Briney, Bryan -- Sok, Devin -- Sesterhenn, Fabian -- Ereno-Orbea, June -- Kalyuzhniy, Oleksandr -- Deresa, Isaiah -- Hu, Xiaozhen -- Spencer, Skye -- Jones, Meaghan -- Georgeson, Erik -- Adachi, Yumiko -- Kubitz, Michael -- deCamp, Allan C -- Julien, Jean-Philippe -- Wilson, Ian A -- Burton, Dennis R -- Crotty, Shane -- Schief, William R -- P01 AI094419/AI/NIAID NIH HHS/ -- P01 AI110657/AI/NIAID NIH HHS/ -- P41GM103393/GM/NIGMS NIH HHS/ -- R01 AI084817/AI/NIAID NIH HHS/ -- UM1 AI100663/AI/NIAID NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2016 Mar 25;351(6280):1458-63. doi: 10.1126/science.aad9195.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. ; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA. ; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. ; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. ; Program in Molecular Structure and Function, Hospital for Sick Children Research Institute, Toronto, Ontario M5G 0A4, Canada. ; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. ; Vaccine and Infectious Disease Division, Statistical Center for HIV/AIDS Research and Prevention (SCHARP), Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. ; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Program in Molecular Structure and Function, Hospital for Sick Children Research Institute, Toronto, Ontario M5G 0A4, Canada. Departments of Biochemistry and Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada. ; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. ; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02129, USA. ; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA. Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA. schief@scripps.edu shane@lji.org. ; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02129, USA. schief@scripps.edu shane@lji.org.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27013733" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines/*immunology ; Amino Acid Sequence ; Antibodies, Monoclonal/chemistry/*immunology/isolation & purification ; Antibodies, Neutralizing/chemistry/*immunology/isolation & purification ; Antibody Affinity ; B-Lymphocytes/immunology ; Cell Separation ; Combinatorial Chemistry Techniques ; Epitopes, B-Lymphocyte/chemistry/genetics/*immunology ; Germ Cells/*immunology ; HIV Antibodies/chemistry/*immunology/isolation & purification ; HIV-1/*immunology ; Humans ; Molecular Sequence Data ; Mutation ; Peptide Library ; Precursor Cells, B-Lymphoid/*immunology ; Protein Conformation
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  • 25
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-09-30
    Description: Next week, the 2016 Nobel Prize in Physics will be announced, and many scientists expect it to honor the detection of ripples in space called gravitational waves, reported in February by scientists working with the Laser Interferometer Gravitational-Wave Observatory (LIGO). If other prizes are a guide, the Nobel will go to the troika of physicists who 32 years ago conceived of LIGO: Rainer Weiss of the Massachusetts Institute of Technology in Cambridge, and Ronald Drever and Kip Thorne of the California Institute of Technology (Caltech) in Pasadena. But some influential physicists, including previous Nobel laureates, say the prize, which can be split three ways at most, should include somebody else: Barry Barish, a particle physicist at Caltech. Barish didn't invent LIGO, but he made it happen. The hardware at LIGO's two observatories in Hanford, Washington, and Livingston, Louisiana; the structure of the collaboration; even the big-science character of gravitational wave research—all were molded by Barish, who is now 80. Without Barish, some physicists say, there would have been no discovery. Author: Adrian Cho
    Keywords: Physics
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  • 26
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-11-04
    Description: Spectroscopy is the most accurate branch of science. Optical transition frequencies in isolated atoms and molecules can nowadays be measured to many-digit accuracies by applying the tools developed in the atomic physics community: ultrastable lasers, locked via frequency-comb lasers to atomic clocks, and the techniques to cool and control the motion of atoms. Precision measurements on small quantum systems can be compared with theoretical descriptions of these systems at the most fundamental level, allowing physics theories to be tested and enabling the search for physics beyond the standard model (1). On page 610 of this issue, Hori et al. (2) apply these tricks of the trade to a small atomic quantum system with a built-in antiparticle to perform precise spectroscopic measurement in antiprotonic helium (see the figure). The technique of buffer-gas cooling is demonstrated for the first time on a composite matter–antimatter particle. Author: Wim Ubachs
    Keywords: Physics
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  • 27
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-08-13
    Description: Author: Jelena Stajic
    Keywords: Physics
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  • 28
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-11-04
    Description: Author: Jelena Stajic
    Keywords: Physics
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  • 29
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-10-08
    Description: Inspired by the intriguing topological phenomena recently observed in condensed-matter systems (1), a variety of different research areas, from optical to mechanical systems, have devoted their studies to topological physics. Owing to their high level of experimental controllability, cold atomic gases offer a promising platform to simulate condensed-matter models. Their charge neutrality, however, is an apparent limitation. To overcome these constraints, new experimental techniques are currently being developed that mimic the physics of charged particles. On page 83 of this issue, Wu et al. (2) report on such a new experimental technique to simulate two-dimensional (2D) spin-orbit coupling (SOC) for neutral atoms in an optical lattice—an important ingredient to explore topological quantum states. Author: Monika Aidelsburger
    Keywords: Physics
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  • 30
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-10-08
    Description: Mathematical physicist Roger Penrose stands out as an independent thinker, who for years has been critical of a few current trends in theoretical physics and cosmology. You don't have to agree with all, or even a part, of Penrose's criticism to realize that Fashion, Faith, and Fantasy in the New Physics of the Universe represents an extremely original, rich, and thoughtful survey of today's most fashionable attempts to decipher the cosmos on its smallest and largest scales, writes reviewer Mario Livio. Author: Mario Livio
    Keywords: Physics
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  • 31
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-09-30
    Description: Is time discrete or continuous? What is the smallest measurement of time that we can make? And does time actually pass faster as we age, or is it just our perception? You may consider such questions to be metaphysical or philosophical, but in Now: The Physics of Time Richard Muller ponders these and other questions through the lens of a number of major 20th century physics discoveries. In doing so, Muller successfully introduces and describes most, if not all, of the key elements in an undergraduate physics course, masterfully connecting them with the conceptual thread of "the arrow of time." Author: Lisa Jardine-Wright
    Keywords: Physics
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