ALBERT

Description: How parental histone (H3-H4) 2 tetramers, the primary carriers of epigenetic modifications, are transferred onto leading and lagging strands of DNA replication forks for epigenetic inheritance remains elusive. Here we show that parental (H3-H4) 2 tetramers are assembled into nucleosomes onto both leading and lagging strands, with a slight preference for lagging strands. The lagging-strand preference increases markedly in budding yeast cells lacking Dpb3 and Dpb4, two subunits of the leading strand DNA polymerase, Pol , owing to the impairment of parental (H3-H4) 2 transfer to leading strands. Dpb3-Dpb4 binds H3-H4 in vitro and participates in the inheritance of heterochromatin. These results indicate that different proteins facilitate the transfer of parental (H3-H4) 2 onto leading versus lagging strands and that Dbp3-Dpb4 plays an important role in this poorly understood process.

Description: Metabolic reprogramming has been proposed to be a hallmark of cancer, yet a systematic characterization of the metabolic pathways active in transformed cells is currently lacking. Using mass spectrometry, we measured the consumption and release (CORE) profiles of 219 metabolites from media across the NCI-60 cancer cell lines, and integrated these data with a preexisting atlas of gene expression. This analysis identified glycine consumption and expression of the mitochondrial glycine biosynthetic pathway as strongly correlated with rates of proliferation across cancer cells. Antagonizing glycine uptake and its mitochondrial biosynthesis preferentially impaired rapidly proliferating cells. Moreover, higher expression of this pathway was associated with greater mortality in breast cancer patients. Increased reliance on glycine may represent a metabolic vulnerability for selectively targeting rapid cancer cell proliferation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3526189/" 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/PMC3526189/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jain, Mohit -- Nilsson, Roland -- Sharma, Sonia -- Madhusudhan, Nikhil -- Kitami, Toshimori -- Souza, Amanda L -- Kafri, Ran -- Kirschner, Marc W -- Clish, Clary B -- Mootha, Vamsi K -- K08 HL107451/HL/NHLBI NIH HHS/ -- K08HL107451/HL/NHLBI NIH HHS/ -- R01 DK081457/DK/NIDDK NIH HHS/ -- R01 GM026875/GM/NIGMS NIH HHS/ -- R01DK081457/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 2012 May 25;336(6084):1040-4. doi: 10.1126/science.1218595.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Broad Institute, Cambridge, MA 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22628656" target="_blank"〉PubMed〈/a〉

Description: Variations in maternal care affect the development of individual differences in neuroendocrine responses to stress in rats. As adults, the offspring of mothers that exhibited more licking and grooming of pups during the first 10 days of life showed reduced plasma adrenocorticotropic hormone and corticosterone responses to acute stress, increased hippocampal glucocorticoid receptor messenger RNA expression, enhanced glucocorticoid feedback sensitivity, and decreased levels of hypothalamic corticotropin-releasing hormone messenger RNA. Each measure was significantly correlated with the frequency of maternal licking and grooming (all r's 〉 -0.6). These findings suggest that maternal behavior serves to "program" hypothalamic-pituitary-adrenal responses to stress in the offspring.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, D -- Diorio, J -- Tannenbaum, B -- Caldji, C -- Francis, D -- Freedman, A -- Sharma, S -- Pearson, D -- Plotsky, P M -- Meaney, M J -- New York, N.Y. -- Science. 1997 Sep 12;277(5332):1659-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Developmental Neuroendocrinology Laboratory, Douglas Hospital Research Center, McGill University, Montreal, Canada H4H 1R3.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9287218" target="_blank"〉PubMed〈/a〉

Description: Rapid induction of type I interferon expression, a central event in establishing the innate antiviral response, requires cooperative activation of numerous transcription factors. Although signaling pathways that activate the transcription factors nuclear factor kappaB and ATF-2/c-Jun have been well characterized, activation of the interferon regulatory factors IRF-3 and IRF-7 has remained a critical missing link in understanding interferon signaling. We report here that the IkappaB kinase (IKK)-related kinases IKKepsilon and TANK-binding kinase 1 are components of the virus-activated kinase that phosphorylate IRF-3 and IRF-7. These studies illustrate an essential role for an IKK-related kinase pathway in triggering the host antiviral response to viral infection.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sharma, Sonia -- tenOever, Benjamin R -- Grandvaux, Nathalie -- Zhou, Guo-Ping -- Lin, Rongtuan -- Hiscott, John -- New York, N.Y. -- Science. 2003 May 16;300(5622):1148-51. Epub 2003 Apr 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Lady Davis Institute for Medical Research-Jewish General Hospital, Departments of Microbiology and Immunology and Medicine, McGill University, Montreal, Quebec H3T 1E2, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12702806" target="_blank"〉PubMed〈/a〉

Description: With the use of synthetic biology, we reduced the Escherichia coli K-12 genome by making planned, precise deletions. The multiple-deletion series (MDS) strains, with genome reductions up to 15%, were designed by identifying nonessential genes and sequences for elimination, including recombinogenic or mobile DNA and cryptic virulence genes, while preserving good growth profiles and protein production. Genome reduction also led to unanticipated beneficial properties: high electroporation efficiency and accurate propagation of recombinant genes and plasmids that were unstable in other strains. Eradication of stress-induced transposition evidently stabilized the MDS genomes and provided some of the new properties.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Posfai, Gyorgy -- Plunkett, Guy 3rd -- Feher, Tamas -- Frisch, David -- Keil, Gunther M -- Umenhoffer, Kinga -- Kolisnychenko, Vitaliy -- Stahl, Buffy -- Sharma, Shamik S -- de Arruda, Monika -- Burland, Valerie -- Harcum, Sarah W -- Blattner, Frederick R -- GM35682/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 May 19;312(5776):1044-6. Epub 2006 Apr 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Biochemistry, Biological Research Center, H-6726 Szeged, Hungary. posfaigy@nucleus.szbk.u-szeged.hu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16645050" target="_blank"〉PubMed〈/a〉

Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sharma, S -- Mehta, S -- Morgan, J -- Maizel, A -- New York, N.Y. -- Science. 1996 Oct 25;274(5287):631b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17759702" target="_blank"〉PubMed〈/a〉

Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sharma, S -- Maizel, A -- Jackson, J R -- New York, N.Y. -- Science. 1994 Aug 19;265(5175):1111.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17832904" target="_blank"〉PubMed〈/a〉

Description: The diffuse interstellar bands (DIBs) are absorption lines observed in visual and near-infrared spectra of stars. Understanding their origin in the interstellar medium is one of the oldest problems in astronomical spectroscopy, as DIBs have been known since 1922. In a completely new approach to understanding DIBs, we combined information from nearly 500,000 stellar spectra obtained by the massive spectroscopic survey RAVE (Radial Velocity Experiment) to produce the first pseudo-three-dimensional map of the strength of the DIB at 8620 angstroms covering the nearest 3 kiloparsecs from the Sun, and show that it follows our independently constructed spatial distribution of extinction by interstellar dust along the Galactic plane. Despite having a similar distribution in the Galactic plane, the DIB 8620 carrier has a significantly larger vertical scale height than the dust. Even if one DIB may not represent the general DIB population, our observations outline the future direction of DIB research.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kos, Janez -- Zwitter, Tomaz -- Wyse, Rosemary -- Bienayme, Olivier -- Binney, James -- Bland-Hawthorn, Joss -- Freeman, Kenneth -- Gibson, Brad K -- Gilmore, Gerry -- Grebel, Eva K -- Helmi, Amina -- Kordopatis, Georges -- Munari, Ulisse -- Navarro, Julio -- Parker, Quentin -- Reid, Warren A -- Seabroke, George -- Sharma, Sanjib -- Siebert, Arnaud -- Siviero, Alessandro -- Steinmetz, Matthias -- Watson, Fred G -- Williams, Mary E K -- New York, N.Y. -- Science. 2014 Aug 15;345(6198):791-5. doi: 10.1126/science.1253171.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, 1000 Ljubljana, Slovenia. janez.kos@fmf.uni-lj.si. ; Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, 1000 Ljubljana, Slovenia. ; Johns Hopkins University, Homewood Campus, 3400 North Charles Street, Baltimore, MD 21218, USA. ; Observatoire astronomique de Strasbourg, Universite de Strasbourg, CNRS, 11 rue de l'Universite, F-67000 Strasbourg, France. ; Rudolf Peierls Centre for Theoretical Physics, Keble Road, Oxford OX1 3NP, UK. ; Sydney Institute for Astronomy, School of Physics A28, University of Sydney, NSW 2008, Australia. ; Research School of Astronomy and Astrophysics, Australian National University, Canberra, Australia. ; Chair, Computational Astrophysics, Jeremiah Horrocks Institute, University of Central Lancashire, Preston PR1 2HE, UK. ; Institute of Astronomy, Madingley Road, Cambridge CB3 0HA, UK. ; Astronomisches Rechen-Institut, Zentrum fur Astronomie der Universitat Heidelberg, Monchhofstrasssse 12-14, D-69120 Heidelberg, Germany. ; Kapteyn Astronomical Institute, Post Office Box 800, NL-9700 AV Groningen, Netherlands. ; Instituto Nazionale di Astrofisica Astronomical Observatory of Padova, 36012 Asiago (VI), Italy. ; University of Victoria, Victoria BC, Canada V8P 5C2. ; Department of Physics and Astronomy, Macquarie University, Sydney, NSW 2109, Australia. Centre for Astronomy, Astrophysics and Astrophotonics, Macquarie University, Sydney, NSW 2109, Australia. Australian Astronomical Observatory, Post Office Box 915, North Ryde, NSW 1670, Australia. ; Department of Physics and Astronomy, Macquarie University, Sydney, NSW 2109, Australia. Centre for Astronomy, Astrophysics and Astrophotonics, Macquarie University, Sydney, NSW 2109, Australia. ; Mullard Space Science Laboratory, University College London, Holmbury St Mary, Dorking RH5 6NT, UK. ; Department of Physics and Astronomy, Padova University, Vicolo dell'Osservatorio 2, I-35122 Padova, Italy. Leibniz-Institut fur Astrophysik Potsdam (AIP), An der Sternwarte 16, 14482 Potsdam, Germany. ; Leibniz-Institut fur Astrophysik Potsdam (AIP), An der Sternwarte 16, 14482 Potsdam, Germany. ; Australian Astronomical Observatory, Post Office Box 915, North Ryde, NSW 1670, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25124434" target="_blank"〉PubMed〈/a〉

Description: The widespread popularity of density functional theory has given rise to an extensive range of dedicated codes for predicting molecular and crystalline properties. However, each code implements the formalism in a different way, raising questions about the reproducibility of such predictions. We report the results of a community-wide effort that compared 15 solid-state codes, using 40 different potentials or basis set types, to assess the quality of the Perdew-Burke-Ernzerhof equations of state for 71 elemental crystals. We conclude that predictions from recent codes and pseudopotentials agree very well, with pairwise differences that are comparable to those between different high-precision experiments. Older methods, however, have less precise agreement. Our benchmark provides a framework for users and developers to document the precision of new applications and methodological improvements.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lejaeghere, Kurt -- Bihlmayer, Gustav -- Bjorkman, Torbjorn -- Blaha, Peter -- Blugel, Stefan -- Blum, Volker -- Caliste, Damien -- Castelli, Ivano E -- Clark, Stewart J -- Dal Corso, Andrea -- de Gironcoli, Stefano -- Deutsch, Thierry -- Dewhurst, John Kay -- Di Marco, Igor -- Draxl, Claudia -- Dulak, Marcin -- Eriksson, Olle -- Flores-Livas, Jose A -- Garrity, Kevin F -- Genovese, Luigi -- Giannozzi, Paolo -- Giantomassi, Matteo -- Goedecker, Stefan -- Gonze, Xavier -- Granas, Oscar -- Gross, E K U -- Gulans, Andris -- Gygi, Francois -- Hamann, D R -- Hasnip, Phil J -- Holzwarth, N A W -- Iusan, Diana -- Jochym, Dominik B -- Jollet, Francois -- Jones, Daniel -- Kresse, Georg -- Koepernik, Klaus -- Kucukbenli, Emine -- Kvashnin, Yaroslav O -- Locht, Inka L M -- Lubeck, Sven -- Marsman, Martijn -- Marzari, Nicola -- Nitzsche, Ulrike -- Nordstrom, Lars -- Ozaki, Taisuke -- Paulatto, Lorenzo -- Pickard, Chris J -- Poelmans, Ward -- Probert, Matt I J -- Refson, Keith -- Richter, Manuel -- Rignanese, Gian-Marco -- Saha, Santanu -- Scheffler, Matthias -- Schlipf, Martin -- Schwarz, Karlheinz -- Sharma, Sangeeta -- Tavazza, Francesca -- Thunstrom, Patrik -- Tkatchenko, Alexandre -- Torrent, Marc -- Vanderbilt, David -- van Setten, Michiel J -- Van Speybroeck, Veronique -- Wills, John M -- Yates, Jonathan R -- Zhang, Guo-Xu -- Cottenier, Stefaan -- New York, N.Y. -- Science. 2016 Mar 25;351(6280):aad3000. doi: 10.1126/science.aad3000.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Molecular Modeling, Ghent University, Technologiepark 903, BE-9052 Zwijnaarde, Belgium. ; Peter Grunberg Institute and Institute for Advanced Simulation, Forschungszentrum Julich and JARA (Julich Aachen Research Alliance), D-52425 Julich, Germany. ; Department of Physics, Abo Akademi, FI-20500 Turku, Finland. Centre of Excellence in Computational Nanoscience (COMP) and Department of Applied Physics, Aalto University School of Science, Post Office Box 11100, FI-00076 Aalto, Finland. ; Institute of Materials Chemistry, Vienna University of Technology, Getreidemarkt 9/165-TC, A-1060 Vienna, Austria. ; Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA. ; Universite Grenoble Alpes, Institut Nanosciences et Cryogenie-Modeling and Material Exploration Department (INAC-MEM), Laboratoire de Simulation Atomistique (L_Sim), F-38042 Grenoble, France. Commissariat a l'Energie Atomique et aux Energies Alternatives (CEA), INAC-MEM, L_Sim, F-38054 Grenoble, France. ; Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Federale de Lausanne, CH-1015 Lausanne, Switzerland. ; Department of Physics, University of Durham, Durham DH1 3LE, UK. ; International School for Advanced Studies (SISSA) and DEMOCRITOS, Consiglio Nazionale delle Ricerche-Istituto Officina dei Materiali (CNR-IOM), Via Bonomea 265, I-34136 Trieste, Italy. ; Max-Planck-Institut fur Mikrostrukturphysik, Weinberg 2, D-06120 Halle, Germany. ; Department of Physics and Astronomy, Division of Materials Theory, Uppsala University, Post Office Box 516, SE-75120 Uppsala, Sweden. ; Institut fur Physik and Integrative Research Institute for the Sciences (IRIS)-Adlershof, Humboldt-Universitat zu Berlin, Zum Grossen Windkanal 6, D-12489 Berlin, Germany. Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany. ; Center for Atomic-Scale Materials Design, Department of Physics, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark. ; Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8553, Gaithersburg, MD 20899, USA. ; Department of Mathematics, Computer Science, and Physics, University of Udine, Via delle Scienze 206, I-33100 Udine, Italy. ; Institute of Condensed Matter and Nanosciences-Nanoscopic Physics (NAPS), Universite Catholique de Louvain, Chemin des Etoiles 8, BE-1348 Louvain-la-Neuve, Belgium. ; Institut fur Physik, Universitat Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland. ; Department of Physics and Astronomy, Division of Materials Theory, Uppsala University, Post Office Box 516, SE-75120 Uppsala, Sweden. School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA. ; Department of Computer Science, University of California-Davis, Davis, CA 95616, USA. ; Department of Physics and Astronomy, Rutgers University, Piscataway, NJ 08854-8019, USA. Mat-Sim Research, Post Office Box 742, Murray Hill, NJ 07974, USA. ; Department of Physics, University of York, Heslington, York YO10 5DD, UK. ; Department of Physics, Wake Forest University, Winston-Salem, NC 27109, USA. ; Scientific Computing Department, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot OX11 0QX, UK. ; CEA, DAM, DIF, F-91297 Arpajon, France. ; Department of Materials, University of Oxford, 16 Parks Road, Oxford OX1 3PH, UK. ; Faculty of Physics and Center for Computational Materials Science, University of Vienna, Sensengasse 8/12, A-1090 Vienna, Austria. ; LeibnizInstitut fur Festkorper- und Werkstoffforschung (IFW) Dresden, Post Office Box 270 116, D-01171 Dresden, Germany. Dresden Center for Computational Materials Science (DCMS), Technische Universitat Dresden, D-01069 Dresden, Germany. ; Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Federale de Lausanne, CH-1015 Lausanne, Switzerland. International School for Advanced Studies (SISSA) and DEMOCRITOS, Consiglio Nazionale delle Ricerche-Istituto Officina dei Materiali (CNR-IOM), Via Bonomea 265, I-34136 Trieste, Italy. ; Department of Physics and Astronomy, Division of Materials Theory, Uppsala University, Post Office Box 516, SE-75120 Uppsala, Sweden. Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands. ; Institut fur Physik and Integrative Research Institute for the Sciences (IRIS)-Adlershof, Humboldt-Universitat zu Berlin, Zum Grossen Windkanal 6, D-12489 Berlin, Germany. ; LeibnizInstitut fur Festkorper- und Werkstoffforschung (IFW) Dresden, Post Office Box 270 116, D-01171 Dresden, Germany. ; Institute for Solid State Physics, The University of Tokyo, Kashiwa 277-8581, Japan. ; Institut de Mineralogie, de Physique des Materiaux, et de Cosmochimie (IMPMC), Sorbonne Universites-Pierre and Marie Curie University Paris 06, Centre National de la Recherche Scientifique (CNRS) Unite Mixte de Recherche (UMR) 7590, Museum National d'Histoire Naturelle, Institut de Recherche pour le Developpement (IRD) Unite de Recherche 206, 4 Place Jussieu, F-75005 Paris, France. ; Department of Materials Science and Metallurgy, University of Cambridge, 27 Charles Babbage Road, Cambridge CB3 0FS, UK. ; Center for Molecular Modeling, Ghent University, Technologiepark 903, BE-9052 Zwijnaarde, Belgium. High Performance Computing Unit, Ghent University, Krijgslaan 281 S9, BE-9000 Ghent, Belgium. ; Department of Physics, Royal Holloway, University of London, Egham TW20 0EX, UK. ISIS Facility, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot OX11 0QX, UK. ; Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany. Department of Chemistry and Biochemistry and Materials Department, University of California-Santa Barbara, Santa Barbara, CA 93106-5050, USA. ; Institute for Solid State Physics, Vienna University of Technology, A-1040 Vienna, Austria. ; Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany. Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg. ; Department of Physics and Astronomy, Rutgers University, Piscataway, NJ 08854-8019, USA. ; Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA. ; Institute of Theoretical and Simulational Chemistry, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, People's Republic of China. ; Center for Molecular Modeling, Ghent University, Technologiepark 903, BE-9052 Zwijnaarde, Belgium. Department of Materials Science and Engineering, Ghent University, Technologiepark 903, BE-9052 Zwijnaarde, Belgium.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27013736" target="_blank"〉PubMed〈/a〉