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  • 51. Barsh, Gregory S.
    et al.
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Evolutionary genomics: Detecting selection2013In: Nature, ISSN 0028-0836, Vol. 495, no 7441, 325-326 p.Article in journal (Other academic)
  • 52.
    Belonoshko, Anatoly B.
    et al.
    KTH, Superseded Departments, Physics.
    Ahuja, Rajeev
    KTH, Superseded Departments, Materials Science and Engineering.
    Johansson, Börje
    KTH, Superseded Departments, Materials Science and Engineering.
    Stability of the body-centred-cubic phase of iron in the Earth's inner core2003In: Nature, ISSN 0028-0836, Vol. 424, no 6952, 1032-1034 p.Article in journal (Refereed)
    Abstract [en]

    Iron is thought to be the main constituent of the Earth's core(1), and considerable efforts(2-14) have therefore been made to understand its properties at high pressure and temperature. While these efforts have expanded our knowledge of the iron phase diagram, there remain some significant inconsistencies, the most notable being the difference between the 'low' and 'high' melting curves(15). Here we report the results of molecular dynamics simulations of iron based on embedded atom models fitted to the results of two implementations of density functional theory. We tested two model approximations and found that both point to the stability of the body-centred-cubic (b.c.c.) iron phase at high temperature and pressure. Our calculated melting curve is in agreement with the 'high' melting curve, but our calculated phase boundary between the hexagonal close packed (h. c. p.) and b.c.c. iron phases is in good agreement with the 'low' melting curve. We suggest that the h.c.p.-b.c.c. transition was previously misinterpreted as a melting transition, similar to the case of xenon(16-18), and that the b.c.c. phase of iron is the stable phase in the Earth's inner core.

  • 53. Berggren, Gustav
    et al.
    Adamska, A.
    Lambertz, C.
    Simmons, T. R.
    Esselborn, J.
    Atta, M.
    Gambarelli, S.
    Mouesca, J. M.
    Reijerse, E.
    Lubitz, W.
    Happe, T.
    Artero, V.
    Fontecave, M.
    Biomimetic assembly and activation of [FeFe]-hydrogenases2013In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 499, no 7456, 66-69 p.Article in journal (Refereed)
  • 54.
    Berggren, Magnus
    et al.
    Bell Laboratories, Murray Hill, New Jersey, USA.
    Dodabalapur, A.
    Bell Laboratories, Murray Hill, New Jersey, USA.
    Slusher, R. E.
    Bell Laboratories, Murray Hill, New Jersey, USA.
    Bao, Z.
    Bell Laboratories, Murray Hill, New Jersey, USA.
    Light amplification in organic thin films using cascade energy transfer1997In: Nature, ISSN 0028-0836, Vol. 389, 466-469 p.Article in journal (Refereed)
    Abstract [en]

    There is currently renewed interest in the development of lasers using solid-state organic and polymeric materials as the gain media. These materials have a number of properties that make them good candidates for such applications — for example, emission bands that are displaced (via a Stokes shift) from absorption bands, and the ease with which the emitting species can be embedded in a suitable host material1, 2, 3, 4, 5. But despite these advantages, the threshold power densities required for light amplification that have been reported so far have been high6, 7, 8. Here we describe an approach, based on energy transfer between molecular species, that can lower the threshold for stimulated emission and laser action while improving markedly the waveguiding properties of the active material. In our materials, an initial molecular excited state is generated in the host compound by absorption of light; this state is then resonantly and non-radiatively transferred down in energy (through one or more steps) between suitably matched dye molecules dispersed in the host, so ensuring that the absorption losses at the final emission wavelengths are very small. Such composite gain media provide provide broad tunability of the emission wavelength, and also decouple the optical emission properties from the transport properties, so providing greater flexibility for the design of future electrically driven device structures.

  • 55.
    Berggren, Magnus
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Applied Physics. Linköping University, The Institute of Technology. null.
    Inganäs, Olle
    Linköping University, Department of Physics, Chemistry and Biology, Applied Physics. Linköping University, The Institute of Technology. null.
    Gustafsson, Göran
    Linköping University, Department of Physics, Chemistry and Biology, Applied Physics. Linköping University, The Institute of Technology. null.
    Rasmusson, J.
    Chalmers Tekniska Högskola.
    Andersson, Mats R.
    Chalmers Tekniska Högskola.
    Hjertberg, T.
    Chalmers Tekniska Högskola.
    Wennerström, O.
    Chalmers Tekniska Högskola.
    Light-emitting diodes with variable colours from polymer blends1994In: Nature, ISSN 0028-0836, Vol. 372, no 6505, 444-446 p.Article in journal (Refereed)
    Abstract [en]

    THE range of materials now available for polymer-based light-emitting diodes (LEDs) is such that electroluminescence can be obtained throughout the visible spectrum(1-12). Here we show that, by blending polymers with different emission and charge-transport characteristics, LEDs can be fabricated in which the emission colour varies as a function of the operating voltage. This phenomenon arises from the self-organizing properties of the blends, in which entropy drives phase separation of the constituent polymers and gives rise to submicrometre-sized domains having a range of compositions and emission characteristics. Emission from domains of different composition is controlled by the ease with which charge is injected, which in turn depends on the applied voltage.

  • 56.
    Berglund, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Animal Ecology.
    Evolutionary biology: Pregnant fathers in charge2010In: Nature, ISSN 0028-0836, Vol. 464, no 7287, 364-365 p.Article in journal (Refereed)
  • 57.
    Betsholtz, Christer
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Cancer and Vascular Biology. Institutionen för medicinsk biokemi och biofysik, Karolinska Institutet.
    Double function at the blood-brain barrier2014In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 509, no 7501, 432-433 p.Article in journal (Other academic)
  • 58.
    Betsholtz, Christer
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Vascular Biology.
    Transcriptional control of endothelial energy2016In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 529, no 7585, 160-161 p.Article in journal (Other academic)
  • 59. Bieling, Peter
    et al.
    Laan, Liedewij
    Schek, Henry
    Munteanu, E Laura
    Sandblad, Linda
    European Mol Biol Lab, Cell Biol & Biophys Unit, D-69117 Heidelberg, Germany .
    Dogterom, Marileen
    Brunner, Damian
    Surrey, Thomas
    Reconstitution of a microtubule plus-end tracking system in vitro2007In: Nature, ISSN 0028-0836, Vol. 450, no 7172, 1100-1105 p.Article in journal (Refereed)
    Abstract [en]

    The microtubule cytoskeleton is essential to cell morphogenesis. Growing microtubule plus ends have emerged as dynamic regulatory sites in which specialized proteins, called plus-end-binding proteins (+TIPs), bind and regulate the proper functioning of microtubules. However, the molecular mechanism of plus-end association by +TIPs and their ability to track the growing end are not well understood. Here we report the in vitro reconstitution of a minimal plus-end tracking system consisting of the three fission yeast proteins Mal3, Tip1 and the kinesin Tea2. Using time-lapse total internal reflection fluorescence microscopy, we show that the EB1 homologue Mal3 has an enhanced affinity for growing microtubule end structures as opposed to the microtubule lattice. This allows it to track growing microtubule ends autonomously by an end recognition mechanism. In addition, Mal3 acts as a factor that mediates loading of the processive motor Tea2 and its cargo, the Clip170 homologue Tip1, onto the microtubule lattice. The interaction of all three proteins is required for the selective tracking of growing microtubule plus ends by both Tea2 and Tip1. Our results dissect the collective interactions of the constituents of this plus-end tracking system and show how these interactions lead to the emergence of its dynamic behaviour. We expect that such in vitro reconstitutions will also be essential for the mechanistic dissection of other plus-end tracking systems.

  • 60. Birney, Ewan
    et al.
    Hudson, Thomas J.
    Green, Eric D.
    Gunter, Chris
    Eddy, Sean
    Rogers, Jane
    Harris, Jennifer R.
    Ehrlich, S. Dusko
    Apweiler, Rolf
    Austin, Christopher P.
    Berglund, Lisa
    Bobrow, Martin
    Bountra, Chas
    Brookes, Anthony J.
    Cambon-Thomsen, Anne
    Carter, Nigel P.
    Chisholm, Rex L.
    Contreras, Jorge L.
    Cooke, Robert M.
    Crosby, William L.
    Dewar, Ken
    Durbin, Richard
    Dyke, Stephanie O. M.
    Ecker, Joseph R.
    El Emam, Khaled
    Feuk, Lars
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Gabriel, Stacey B.
    Gallacher, John
    Gelbart, William M.
    Granell, Antoni
    Guarner, Francisco
    Hubbard, Tim
    Jackson, Scott A.
    Jennings, Jennifer L.
    Joly, Yann
    Jones, Steven M.
    Kaye, Jane
    Kennedy, Karen L.
    Knoppers, Bartha Maria
    Kyrpides, Nikos C.
    Lowrance, William W.
    Luo, Jingchu
    MacKay, John J.
    Martín-Rivera, Luis
    McCombie, W. Richard
    McPherson, John D.
    Miller, Linda
    Miller, Webb
    Moerman, Don
    Mooser, Vincent
    Morton, Cynthia C.
    Ostell, James M.
    Ouellette, B. F. Francis
    Parkhill, Julian
    Raina, Parminder S.
    Rawlings, Christopher
    Scherer, Steven E.
    Scherer, Stephen W.
    Schofield, Paul N.
    Sensen, Christoph W.
    Stodden, Victoria C.
    Sussman, Michael R.
    Tanaka, Toshihiro
    Thornton, Janet
    Tsunoda, Tatsuhiko
    Valle, David
    Vuorio, Eero I.
    Walker, Neil M.
    Wallace, Susan
    Weinstock, George
    Whitman, William B.
    Worley, Kim C.
    Wu, Cathy
    Wu, Jiayan
    Yu, Jun
    Prepublication data sharing2009In: Nature, ISSN 0028-0836, Vol. 461, no 7261, 168-170 p.Article in journal (Refereed)
    Abstract [en]

    Rapid release of prepublication data has served the field of genomics well. Attendees at a workshop in Toronto recommend extending the practice to other biological data sets.

  • 61. Birney, Ewan
    et al.
    Stamatoyannopoulos, John A.
    Dutta, Anindya
    Guigó, Roderic
    Gingeras, Thomas R.
    Margulies, Elliott H.
    Weng, Zhiping
    Snyder, Michael
    Dermitzakis, Emmanouil T.
    Thurman, Robert E.
    Kuehn, Michael S.
    Taylor, Christopher M.
    Neph, Shane
    Koch, Christoph M.
    Asthana, Saurabh
    Malhotra, Ankit
    Adzhubei, Ivan
    Greenbaum, Jason A.
    Andrews, Robert M.
    Flicek, Paul
    Boyle, Patrick J.
    Cao, Hua
    Carter, Nigel P.
    Clelland, Gayle K.
    Davis, Sean
    Day, Nathan
    Dhami, Pawandeep
    Dillon, Shane C.
    Dorschner, Michael O.
    Fiegler, Heike
    Giresi, Paul G.
    Goldy, Jeff
    Hawrylycz, Michael
    Haydock, Andrew
    Humbert, Richard
    James, Keith D.
    Johnson, Brett E.
    Johnson, Ericka M.
    Frum, Tristan T.
    Rosenzweig, Elizabeth R.
    Karnani, Neerja
    Lee, Kirsten
    Lefebvre, Gregory C.
    Navas, Patrick A.
    Neri, Fidencio
    Parker, Stephen C.
    Sabo, Peter J.
    Sandstrom, Richard
    Shafer, Anthony
    Vetrie, David
    Weaver, Molly
    Wilcox, Sarah
    Yu, Man
    Collins, Francis S.
    Dekker, Job
    Lieb, Jason D.
    Tullius, Thomas D.
    Crawford, Gregory E.
    Sunyaev, Shamil
    Noble, William S.
    Dunham, Ian
    Denoeud, France
    Reymond, Alexandre
    Kapranov, Philipp
    Rozowsky, Joel
    Zheng, Deyou
    Castelo, Robert
    Frankish, Adam
    Harrow, Jennifer
    Ghosh, Srinka
    Sandelin, Albin
    Hofacker, Ivo L.
    Baertsch, Robert
    Keefe, Damian
    Dike, Sujit
    Cheng, Jill
    Hirsch, Heather A.
    Sekinger, Edward A.
    Lagarde, Julien
    Abril, Josep F.
    Shahab, Atif
    Flamm, Christoph
    Fried, Claudia
    Hackermüller, Jörg
    Hertel, Jana
    Lindemeyer, Manja
    Missal, Kristin
    Tanzer, Andrea
    Washietl, Stefan
    Korbel, Jan
    Emanuelsson, Olof
    Pedersen, Jakob S.
    Holroyd, Nancy
    Taylor, Ruth
    Swarbreck, David
    Matthews, Nicholas
    Dickson, Mark C.
    Thomas, Daryl J.
    Weirauch, Matthew T.
    Gilbert, James
    Drenkow, Jorg
    Bell, Ian
    Zhao, XiaoDong
    Srinivasan, K. G.
    Sung, Wing-Kin
    Ooi, Hong Sain
    Chiu, Kuo Ping
    Foissac, Sylvain
    Alioto, Tyler
    Brent, Michael
    Pachter, Lior
    Tress, Michael L.
    Valencia, Alfonso
    Choo, Siew Woh
    Choo, Chiou Yu
    Ucla, Catherine
    Manzano, Caroline
    Wyss, Carine
    Cheung, Evelyn
    Clark, Taane G.
    Brown, James B.
    Ganesh, Madhavan
    Patel, Sandeep
    Tammana, Hari
    Chrast, Jacqueline
    Henrichsen, Charlotte N.
    Kai, Chikatoshi
    Kawai, Jun
    Nagalakshmi, Ugrappa
    Wu, Jiaqian
    Lian, Zheng
    Lian, Jin
    Newburger, Peter
    Zhang, Xueqing
    Bickel, Peter
    Mattick, John S.
    Carninci, Piero
    Hayashizaki, Yoshihide
    Weissman, Sherman
    Hubbard, Tim
    Myers, Richard M.
    Rogers, Jane
    Stadler, Peter F.
    Lowe, Todd M.
    Wei, Chia-Lin
    Ruan, Yijun
    Struhl, Kevin
    Gerstein, Mark
    Antonarakis, Stylianos E.
    Fu, Yutao
    Green, Eric D.
    Karaöz, U.
    Siepel, Adam
    Taylor, James
    Liefer, Laura A
    Wetterstrand, Kris A.
    Good, Peter J.
    Feingold, Elise A.
    Guyer, Mark S.
    Cooper, Gregory M.
    Asimenos, George
    Dewey, Colin N.
    Hou, Minmei
    Nikolaev, Sergey
    Montoya-Burgos, Juan I.
    Löytynoja, Ari
    Whelan, Simon
    Pardi, Fabio
    Massingham, Tim
    Huang, Haiyan
    Zhang, Nancy R.
    Holmes, Ian
    Mullikin, James C.
    Ureta-Vidal, Abel
    Paten, Benedict
    Seringhaus, Michael
    Church, Deanna
    Rosenbloom, Kate
    Kent, W. James
    Stone, Eric A.
    Batzoglou, Serafim
    Goldman, Nick
    Hardison, Ross C.
    Haussler, David
    Miller, Webb
    Sidow, Arend
    Trinklein, Nathan D.
    Zhang, Zhengdong D.
    Barrera, Leah
    Stuart, Rhona
    King, David C.
    Ameur, Adam
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Enroth, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Bieda, Mark C.
    Kim, Jonghwan
    Bhinge, Akshay A.
    Jiang, Nan
    Liu, Jun
    Yao, Fei
    Vega, Vinsensius B.
    Lee, Charlie W.
    Ng, Patrick
    Shahab, Atif
    Yang, Annie
    Moqtaderi, Zarmik
    Zhu, Zhou
    Xu, Xiaoqin
    Squazzo, Sharon
    Oberley, Matthew J.
    Inman, David
    Singer, Michael A.
    Richmond, Todd A.
    Munn, Kyle J.
    Rada-Iglesias, Alvaro
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Wallerman, Ola
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Komorowski, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Fowler, Joanna C.
    Couttet, Phillippe
    Bruce, Alexander W.
    Dovey, Oliver M.
    Ellis, Peter D.
    Langford, Cordelia F.
    Nix, David A.
    Euskirchen, Ghia
    Hartman, Stephen
    Urban, Alexander E.
    Kraus, Peter
    Van Calcar, Sara
    Heintzman, Nate
    Kim, Tae Hoon
    Wang, Kun
    Qu, Chunxu
    Hon, Gary
    Luna, Rosa
    Glass, Christopher K.
    Rosenfeld, M. Geoff
    Aldred, Shelley Force
    Cooper, Sara J.
    Halees, Anason
    Lin, Jane M.
    Shulha, Hennady P.
    Zhang, Xiaoling
    Xu, Mousheng
    Haidar, Jaafar N.
    Yu, Yong
    Ruan, Yijun
    Iyer, Vishwanath R.
    Green, Roland D.
    Wadelius, Claes
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Farnham, Peggy J.
    Ren, Bing
    Harte, Rachel A.
    Hinrichs, Angie S.
    Trumbower, Heather
    Clawson, Hiram
    Hillman-Jackson, Jennifer
    Zweig, Ann S.
    Smith, Kayla
    Thakkapallayil, Archana
    Barber, Galt
    Kuhn, Robert M.
    Karolchik, Donna
    Armengol, Lluis
    Bird, Christine P.
    de Bakker, Paul I.
    Kern, Andrew D.
    Lopez-Bigas, Nuria
    Martin, Joel D.
    Stranger, Barbara E.
    Woodroffe, Abigail
    Davydov, Eugene
    Dimas, Antigone
    Eyras, Eduardo
    Hallgrí­msdóttir, Ingileif B.
    Huppert, Julian
    Zody, Michael C.
    Abecasis, G. R.
    Estivill, Xavier
    Bouffard, Gerard G.
    Guan, Xiaobin
    Hansen, Nancy F.
    Idol, Jacquelyn R.
    Maduro, Valerie V.
    Maskeri, Baishali
    McDowell, Jennifer C.
    Park, Morgan
    Thomas, Pamela J.
    Young, Alice C.
    Blakesley, Robert W.
    Muzny, Donna M.
    Sodergren, Erica
    Wheeler, David A.
    Worley, Kim C.
    Jiang, Huaiyang
    Weinstock, George M.
    Gibbs, Richard A.
    Graves, Tina
    Fulton, Robert
    Mardis, Elaine R.
    Wilson, Richard K.
    Clamp, Michele
    Cuff, James
    Gnerre, Sante
    Jaffe, David B.
    Chang, Jean L.
    Lindblad-Toh, Kerstin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Lander, Eric S.
    Koriabine, Maxim
    Nefedov, Mikhail
    Osoegawa, Kazutoyo
    Yoshinaga, Yuko
    Zhu, Baoli
    de Jong, Pieter J.
    Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project2007In: Nature, ISSN 0028-0836, Vol. 447, no 7146, 799-816 p.Article in journal (Refereed)
    Abstract [en]

    We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.

  • 62.
    Björling, Marcus
    et al.
    Luleå University of Technology, Department of Engineering Sciences and Mathematics, Machine Elements.
    Habchi, Wassim
    Bair, Scott
    Larsson, Roland
    Luleå University of Technology, Department of Engineering Sciences and Mathematics, Machine Elements.
    Marklund, Pär
    Luleå University of Technology, Department of Engineering Sciences and Mathematics, Machine Elements.
    Warm carbon coat reduces friction2014In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 505, no 7483, 264- p.Article in journal (Other academic)
    Abstract [en]

    A coating material made of carbon reduces friction not just by providing a slippery surface, but also by keeping the points of contact warm. Marcus Björling at Luleå University of Technology in Sweden and his team coated steel balls with ``diamond-like-carbon'' - a material in which carbon atoms have a bonding pattern similar to that of diamond. They rolled the balls against a metal disk with an oil lubricant in between, and showed that the carbon coating acts as an insulator, lowering the viscosity of the lubricant and thus reducing the fricion between the ball and the disk. These findings could encourage the development of lubricant coatings made from insulating materials

  • 63.
    Blix, Gunnar
    et al.
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Philosophy, Mathematics and Science Section.
    Snellman, Olle
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Philosophy, Mathematics and Science Section.
    Molecular shape land size of hyaluronic acid and chondroitinsulphuric acid1944In: Nature, ISSN 0028-0836, Vol. 153, 587-587 p.Article in journal (Refereed)
    Abstract [en]

    THE hyaluronic acid, which was first isolated from vitreous humor1, and later has been found in, for example, synovial fluid2 and navel cord tissue3 gives highly viscous solutions and is often precipitated as fibres. Its molecules have therefore been assumed to have a chain structure. The Chondroitinsulphuric acid gives less viscous solutions and is precipitated at most in small fibres of little coherence. Levene and La Forge4 tentatively expressed its structural formula as a tetrasaccharide, a view which seemed to receive support from von Fürth and Bruno5, who by the aid of Northrop’s diffusion method obtained a molecular weight of about 975.

  • 64. Boccaletti, Anthony
    et al.
    Thalmann, Christian
    Lagrange, Anne-Marie
    Janson, Markus
    Stockholm University, Faculty of Science, Department of Astronomy. Max Planck Society, Germany.
    Augereau, Jean-Charles
    Schneider, Glenn
    Milli, Julien
    Grady, Carol
    Debes, John
    Langlois, Maud
    Mouillet, David
    Henning, Thomas
    Dominik, Carsten
    Maire, Anne-Lise
    Beuzit, Jean-Luc
    Carson, Joseph
    Dohlen, Kjetil
    Engler, Natalia
    Feldt, Markus
    Fusco, Thierry
    Ginski, Christian
    Girard, Julien H.
    Hines, Dean
    Kasper, Markus
    Mawet, Dimitri
    Menard, Franois
    Meyer, Michael R.
    Moutou, Claire
    Olofsson, Johan
    Rodigas, Timothy
    Sauvage, Jean-Francois
    Schlieder, Joshua
    Schmid, Hans Martin
    Turatto, Massimo
    Udry, Stephane
    Vakili, Farrokh
    Vigan, Arthur
    Wahhaj, Zahed
    Wisniewski, John
    Fast-moving features in the debris disk around AU Microscopii2015In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 526, no 7572, 230-+ p.Article in journal (Refereed)
    Abstract [en]

    In the 1980s, excess infrared emission was discovered around main-sequence stars; subsequent direct-imaging observations revealed orbiting disks of cold dust to be the source(1). These 'debris disks' were thought to be by-products of planet formation because they often exhibited morphological and brightness asymmetries that may result from gravitational perturbation by planets. This was proved to be true for the beta Pictoris system, in which the known planet generates an observable warp in the disk(2-5). The nearby, young, unusually active late-type star AU Microscopii hosts a well-studied edge-on debris disk; earlier observations in the visible and near-infrared found asymmetric localized structures in the form of intensity variations along the midplane of the disk beyond a distance of 20 astronomical units(6-9). Here we report high-contrast imaging that reveals a series of five large-scale features in the southeast side of the disk, at projected separations of 10-60 astronomical units, persisting over intervals of 1-4 years. All these features appear to move away from the star at projected speeds of 4-10 kilometres per second, suggesting highly eccentric or unbound trajectories if they are associated with physical entities. The origin, localization, morphology and rapid evolution of these features are difficult to reconcile with current theories.

  • 65.
    Bohm, Christian
    et al.
    Stockholm University, Faculty of Science, Department of Physics. Stockholm University, Faculty of Science, The Oskar Klein Centre for Cosmo Particle Physics (OKC).
    Danninger, Matthias
    Stockholm University, Faculty of Science, Department of Physics. Stockholm University, Faculty of Science, The Oskar Klein Centre for Cosmo Particle Physics (OKC).
    Finley, Chad
    Stockholm University, Faculty of Science, Department of Physics. Stockholm University, Faculty of Science, The Oskar Klein Centre for Cosmo Particle Physics (OKC).
    Flis, Samuel
    Stockholm University, Faculty of Science, Department of Physics. Stockholm University, Faculty of Science, The Oskar Klein Centre for Cosmo Particle Physics (OKC).
    Hulth, Per-Olof
    Stockholm University, Faculty of Science, Department of Physics. Stockholm University, Faculty of Science, The Oskar Klein Centre for Cosmo Particle Physics (OKC).
    Hultqvist, Klas
    Stockholm University, Faculty of Science, Department of Physics. Stockholm University, Faculty of Science, The Oskar Klein Centre for Cosmo Particle Physics (OKC).
    Johansson, Henrik
    Stockholm University, Faculty of Science, Department of Physics. Stockholm University, Faculty of Science, The Oskar Klein Centre for Cosmo Particle Physics (OKC).
    Seo, Seon Hee
    Stockholm University, Faculty of Science, Department of Physics. Stockholm University, Faculty of Science, The Oskar Klein Centre for Cosmo Particle Physics (OKC).
    Walck, Christian
    Stockholm University, Faculty of Science, Department of Physics. Stockholm University, Faculty of Science, The Oskar Klein Centre for Cosmo Particle Physics (OKC).
    Wolf, Martin
    Stockholm University, Faculty of Science, Department of Physics. Stockholm University, Faculty of Science, The Oskar Klein Centre for Cosmo Particle Physics (OKC).
    Zoll, Marcel
    Stockholm University, Faculty of Science, Department of Physics. Stockholm University, Faculty of Science, The Oskar Klein Centre for Cosmo Particle Physics (OKC).
    An absence of neutrinos associated with cosmic-ray acceleration in gamma-ray bursts2012In: Nature, ISSN 0028-0836, Vol. 484, no 7394, 351-354 p.Article in journal (Refereed)
    Abstract [en]

    Very energetic astrophysical events are required to accelerate cosmic rays to above 10(18) electronvolts. GRBs (c-ray bursts) have been proposed as possible candidate sources(1-3). In the GRB 'fireball' model, cosmic-ray acceleration should be accompanied by neutrinos produced in the decay of charged pions created in interactions between the high-energy cosmic-ray protons and gamma-rays(4). Previous searches for such neutrinos found none, but the constraints were weak because the sensitivity was at best approximately equal to the predicted flux(5-7). Here we report an upper limit on the flux of energetic neutrinos associated with GRBs that is at least a factor of 3.7 below the predictions(4,8-10). This implies either that GRBs are not the only sources of cosmic rays with energies exceeding 10(18) electronvolts or that the efficiency of neutrino production is much lower than has been predicted.

  • 66.
    Boisvert, Catherine
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Evolutionary Organism Biology.
    Mark-Kurik, Elga
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Evolutionary Organism Biology.
    The pectoral fin of Panderichthys and the origin of digits2008In: Nature, ISSN 0028-0836, Vol. 456, no 7222, 636-638 p.Article in journal (Refereed)
    Abstract [en]

    One of the identifying characteristics of tetrapods (limbed vertebrates) is the presence of fingers and toes. Whereas the proximal part of the tetrapod limb skeleton can easily be homologized with the paired fin skeletons of sarcopterygian (lobe-finned) fish, there has been much debate about the origin of digits. Early hypotheses1 interpreted digits as derivatives of fin radials, but during the 1990s the idea gained acceptance that digits are evolutionary novelties without direct equivalents in fish fin skeletons. This was partly based on developmental genetic data2, but also substantially on the pectoral fin skeleton of the elpistostegid (transitional fish/tetrapod) Panderichthys, which appeared to lack distal digit-like radials3. Here we present a CT scan study of an undisturbed pectoral fin of Panderichthys demonstrating that the plate-like 'ulnare' of previous reconstructions is an artefact and that distal radials are in fact present. This distal portion is more tetrapod-like than that found in Tiktaalik 4 and, in combination with new data about fin development in basal actinopterygians5, sharks6 and lungfish7, makes a strong case for fingers not being a novelty of tetrapods but derived from pre-existing distal radials present in all sarcopterygian fish.

  • 67. Borry, Pascal
    et al.
    Rusu, Olivia
    Howard, Heidi C
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Public Health and Caring Sciences, Centre for Research Ethics and Bioethics.
    Genetic testing: anonymity of sperm donors under threat.2013In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 496, no 7444, 169- p.Article in journal (Refereed)
  • 68. Botella, Hector
    et al.
    Blom, Henning
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Evolutionary Organism Biology.
    Dorka, Markus
    Ahlberg, Per Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Evolutionary Organism Biology.
    Janvier, Philippe
    Jaws and teeth of the earliest bony fishes2007In: Nature, ISSN 0028-0836, Vol. 448, no 7153, 583-586 p.Article in journal (Refereed)
    Abstract [en]

    Extant jawed vertebrates, or gnathostomes, fall into two major monophyletic groups, namely chondrichthyans (cartilaginous fishes) and osteichthyans (bony fishes and tetrapods). Fossil representatives of the osteichthyan crown group are known from the latest Silurian period, 418 million years (Myr) ago, to the present. By contrast, stem chondrichthyans and stem osteichthyans are still largely unknown. Two extinct Palaeozoic groups, the acanthodians and placoderms, may fall into these stem groups or the common stem group of gnathostomes, but their relationships and monophyletic status are both debated. Here we report unambiguous evidence for osteichthyan characters in jaw bones referred to the late Silurian (423–416-Myr-old) fishes Andreolepis hedei and Lophosteus superbus, long known from isolated bone fragments, scales and teeth, and whose affinities to, or within, osteichthyans have been debated1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11. The bones are a characteristic osteichthyan maxillary and dentary, but the organization of the tooth-like denticles they bear differs from the large, conical teeth of crown-group osteichthyans, indicating that they can be assigned to the stem group. Andreolepis and Lophosteus are thus not only the oldest but also the most phylogenetically basal securely identified osteichthyans known so far.

  • 69. Boussemart, Lise
    et al.
    Malka-Mahieu, Hélène
    Girault, Isabelle
    Allard, Delphine
    Hemmingsson, Oskar
    Umeå University, Faculty of Medicine, Department of Surgical and Perioperative Sciences, Surgery. Inserm UMR981, F-94805 Villejuif, France.
    Tomasic, Gorana
    Thomas, Marina
    Basmadjian, Christine
    Ribeiro, Nigel
    Thuaud, Frédéric
    Mateus, Christina
    Routier, Emilie
    Kamsu-Kom, Nyam
    Agoussi, Sandrine
    Eggermont, Alexander M
    Désaubry, Laurent
    Robert, Caroline
    Vagner, Stéphan
    eIF4F is a nexus of resistance to anti-BRAF and anti-MEK cancer therapies2014In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 513, no 7516, 105-109 p.Article in journal (Refereed)
    Abstract [en]

    In BRAF(V600)-mutant tumours, most mechanisms of resistance to drugs that target the BRAF and/or MEK kinases rely on reactivation of the RAS-RAF-MEK-ERK mitogen-activated protein kinase (MAPK) signal transduction pathway, on activation of the alternative, PI(3)K-AKT-mTOR, pathway (which is ERK independent) or on modulation of the caspase-dependent apoptotic cascade. All three pathways converge to regulate the formation of the eIF4F eukaryotic translation initiation complex, which binds to the 7-methylguanylate cap (m(7)G) at the 5' end of messenger RNA, thereby modulating the translation of specific mRNAs. Here we show that the persistent formation of the eIF4F complex, comprising the eIF4E cap-binding protein, the eIF4G scaffolding protein and the eIF4A RNA helicase, is associated with resistance to anti-BRAF, anti-MEK and anti-BRAF plus anti-MEK drug combinations in BRAF(V600)-mutant melanoma, colon and thyroid cancer cell lines. Resistance to treatment and maintenance of eIF4F complex formation is associated with one of three mechanisms: reactivation of MAPK signalling, persistent ERK-independent phosphorylation of the inhibitory eIF4E-binding protein 4EBP1 or increased pro-apoptotic BCL-2-modifying factor (BMF)-dependent degradation of eIF4G. The development of an in situ method to detect the eIF4E-eIF4G interactions shows that eIF4F complex formation is decreased in tumours that respond to anti-BRAF therapy and increased in resistant metastases compared to tumours before treatment. Strikingly, inhibiting the eIF4F complex, either by blocking the eIF4E-eIF4G interaction or by targeting eIF4A, synergizes with inhibiting BRAF(V600) to kill the cancer cells. eIF4F not only appears to be an indicator of both innate and acquired resistance but also is a promising therapeutic target. Combinations of drugs targeting BRAF (and/or MEK) and eIF4F may overcome most of the resistance mechanisms arising in BRAF(V600)-mutant cancers.

  • 70. Brawand, David
    et al.
    Wagner, Catherine E.
    Li, Yang I.
    Malinsky, Milan
    Keller, Irene
    Fan, Shaohua
    Simakov, Oleg
    Ng, Alvin Y.
    Lim, Zhi Wei
    Bezault, Etienne
    Turner-Maier, Jason
    Johnson, Jeremy
    Alcazar, Rosa
    Noh, Hyun Ji
    Russell, Pamela
    Aken, Bronwen
    Alfoeldi, Jessica
    Amemiya, Chris
    Azzouzi, Naoual
    Baroiller, Jean-Francois
    Barloy-Hubler, Frederique
    Berlin, Aaron
    Bloomquist, Ryan
    Carleton, Karen L.
    Conte, Matthew A.
    D'Cotta, Helena
    Eshel, Orly
    Gaffney, Leslie
    Galibert, Francis
    Gante, Hugo F.
    Gnerre, Sante
    Greuter, Lucie
    Guyon, Richard
    Haddad, Natalie S.
    Haerty, Wilfried
    Harris, Rayna M.
    Hofmann, Hans A.
    Hourlier, Thibaut
    Hulata, Gideon
    Jaffe, David B.
    Lara, Marcia
    Lee, Alison P.
    MacCallum, Iain
    Mwaiko, Salome
    Nikaido, Masato
    Nishihara, Hidenori
    Ozouf-Costaz, Catherine
    Penman, David J.
    Przybylski, Dariusz
    Rakotomanga, Michaelle
    Renn, Suzy C. P.
    Ribeiro, Filipe J.
    Ron, Micha
    Salzburger, Walter
    Sanchez-Pulido, Luis
    Santos, M. Emilia
    Searle, Steve
    Sharpe, Ted
    Swofford, Ross
    Tan, Frederick J.
    Williams, Louise
    Young, Sarah
    Yin, Shuangye
    Okada, Norihiro
    Kocher, Thomas D.
    Miska, Eric A.
    Lander, Eric S.
    Venkatesh, Byrappa
    Fernald, Russell D.
    Meyer, Axel
    Ponting, Chris P.
    Streelman, J. Todd
    Lindblad-Toh, Kerstin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Seehausen, Ole
    Di Palma, Federica
    The genomic substrate for adaptive radiation in African cichlid fish2014In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 513, no 7518, 375-381 p.Article in journal (Refereed)
    Abstract [en]

    Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand themolecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.

  • 71.
    Brazeau, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Evolutionary Organism Biology.
    The braincase and jaws of a Devonian “acanthodian” and modern gnathostome origins2009In: Nature, ISSN 0028-0836, Vol. 457, no 7227, 305-308 p.Article in journal (Refereed)
    Abstract [en]

    Modern gnathostomes ( jawed vertebrates) emerged in the early Palaeozoic era(1), but this event remains unclear owing to a scant early fossil record. The exclusively Palaeozoic 'acanthodians' are possibly the earliest(2,3) gnathostome group and exhibit amosaic of shark- and bony fish- like characters that has long given them prominence in discussions of early gnathostome evolution(1). Their relationships with modern gnathostomes have remained mysterious, partly because their un- mineralized endoskeletons rarely fossilized. Here I present the first- known braincase of an Early Devonian (approximately 418-412 Myr BP) acanthodian, Ptomacanthus anglicus(4), and re- evaluate the interrelationships of basal gnathostomes. Acanthodian braincases have previously been represented by a single genus, Acanthodes(5), which occurs more than 100 million years later in the fossil record. The braincase of Ptomacanthus differs radically from the osteichthyan- like braincase of Acanthodes(5) in exhibiting several plesiomorphic features shared with placoderms(6,7) and some early chondrichthyans(8,9). Most striking is its extremely short sphenoid region and its jaw suspension, which displays features intermediate between some Palaeozoic chondrichthyans and osteichthyans. Phylogenetic analysis resolves Ptomacanthus as either the most basal chondrichthyan or as the sister group of all living gnathostomes. These new data alter earlier conceptions of basal gnathostome phylogeny and thus help to provide a more detailed picture of the acquisition of early gnathostome characters.

  • 72. Brinkhuis, H
    et al.
    Schouten, S
    Collinson, M E
    Sluijs, A
    Damste, J S S
    Dickens, G R
    Huber, M
    Cronin, T M
    Onodera, J
    Takahashi, K
    Bujak, J P
    Stein, R
    van der Burgh, J
    Eldrett, J S
    Harding, I C
    Lotter, A F
    Sangiorgi, F
    Cittert, H V V
    de Leeuw, J W
    Matthiessen, J
    Backman, J
    Moran, K
    Jakobsson, M
    Episodic fresh surface waters in the Eocene Arctic Ocean2006In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 441, no 7093, 606-609 p.Article in journal (Refereed)
    Abstract [en]

    It has been suggested, on the basis of modern hydrology and fully coupled palaeoclimate simulations, that the warm greenhouse conditions(1) that characterized the early Palaeogene period (55-45 Myr ago) probably induced an intensified hydrological cycle(2) with precipitation exceeding evaporation at high latitudes(3). Little field evidence, however, has been available to constrain oceanic conditions in the Arctic during this period. Here we analyse Palaeogene sediments obtained during the Arctic Coring Expedition, showing that large quantities of the free-floating fern Azolla grew and reproduced in the Arctic Ocean by the onset of the middle Eocene epoch (similar to 50 Myr ago). The Azolla and accompanying abundant freshwater organic and siliceous microfossils indicate an episodic freshening of Arctic surface waters during an similar to 800,000-year interval. The abundant remains of Azolla that characterize basal middle Eocene marine deposits of all Nordic seas(4-7) probably represent transported assemblages resulting from freshwater spills from the Arctic Ocean that reached as far south as the North Sea(8). The termination of the Azolla phase in the Arctic coincides with a local sea surface temperature rise from similar to 10 degrees C to 13 degrees C, pointing to simultaneous increases in salt and heat supply owing to the influx of waters from adjacent oceans. We suggest that onset and termination of the Azolla phase depended on the degree of oceanic exchange between Arctic Ocean and adjacent seas.

  • 73.
    Budd, Graham E.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Palaeontology: Cambrian nervous wrecks2012In: Nature, ISSN 0028-0836, Vol. 490, no 7419, 180-181 p.Article in journal (Other academic)
  • 74.
    Budd, Graham E.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences.
    Telford, Maximilian J.
    The origin and evolution of arthropods2009In: Nature, ISSN 0028-0836, Vol. 457, no 7231, 812-817 p.Article, review/survey (Refereed)
    Abstract [en]

    The past two decades have witnessed profound changes in our understanding of the evolution of arthropods. Many of these insights derive from the adoption of molecular methods by systematists and developmental biologists, prompting a radical reordering of the relationships among extant arthropod classes and their closest non- arthropod relatives, and shedding light on the developmental basis for the origins of key characteristics. A complementary source of data is the discovery of fossils from several spectacular Cambrian faunas. These fossils form well- characterized groupings, making the broad pattern of Cambrian arthropod systematics increasingly consensual.

  • 75.
    Buitink, S.
    et al.
    Vrije Universiteit Brussel, Belgium ; Radboud University Nijmegen, The Netherlands.
    Corstanje, A.
    Radboud University Nijmegen, The Netherlands.
    Falcke, H.
    Radboud University Nijmegen, The Netherlands ; ASTRON, The Netherlands ; Science Park Amsterdam, The Netherlands ; Max-Planck-Institut für Radioastronomie, Germany.
    Hörandel, J. R.
    Radboud University Nijmegen, The Netherlands ; Science Park Amsterdam, The Netherlands.
    Huege, T.
    Karlsruhe Institute of Technology (KIT), Germany.
    Nelles, A.
    University of California Irvine, USA.
    Rachen, J. P.
    Radboud University Nijmegen, The Netherlands.
    Rossetto, L.
    Radboud University Nijmegen, The Netherlands.
    Schellart, P.
    Radboud University Nijmegen, The Netherlands.
    Scholten, O.
    University of Groningen, The Netherlands ; Vrije Universiteit Brussel, Belgium.
    Ter Veen, S.
    Thoudam, Satyendra
    Radboud University Nijmegen, The Netherlands.
    Trinh, T. N. G.
    Anderson, J.
    Asgekar, A.
    Avruch, I. M.
    Bell, M. E.
    Bentum, M. J.
    Bernardi, G.
    Best, P.
    Bonafede, A.
    Breitling, F.
    Broderick, J. W.
    Brouw, W. N.
    Brüggen, M.
    Butcher, H. R.
    Carbone, D.
    Ciardi, B.
    Conway, J. E.
    de Gasperin, F.
    de Geus, E.
    Deller, A.
    Dettmar, R. -J
    van Diepen, G.
    Duscha, S.
    Eislöffel, J.
    Engels, D.
    Enriquez, J. E.
    Fallows, R. A.
    Fender, R.
    Ferrari, C.
    Frieswijk, W.
    Garrett, M. A.
    Grießmeier, J. M.
    Gunst, A. W.
    van Haarlem, M. P.
    Hassall, T. E.
    Heald, G.
    Hessels, J. W. T.
    Hoeft, M.
    Horneffer, A.
    Iacobelli, M.
    Intema, H.
    Juette, E.
    Karastergiou, A.
    Kondratiev, V. I.
    Kramer, M.
    Kuniyoshi, M.
    Kuper, G.
    van Leeuwen, J.
    Loose, G. M.
    Maat, P.
    Mann, G.
    Markoff, S.
    McFadden, R.
    McKay-Bukowski, D.
    McKean, J. P.
    Mevius, M.
    Mulcahy, D. D.
    Munk, H.
    Norden, M. J.
    Orru, E.
    Paas, H.
    Pandey-Pommier, M.
    Pandey, V. N.
    Pietka, M.
    Pizzo, R.
    Polatidis, A. G.
    Reich, W.
    Röttgering, H. J. A.
    Scaife, A. M. M.
    Schwarz, D. J.
    Serylak, M.
    Sluman, J.
    Smirnov, O.
    Stappers, B. W.
    Steinmetz, M.
    Stewart, A.
    Swinbank, J.
    Tagger, M.
    Tang, Y.
    Tasse, C.
    Toribio, M. C.
    Vermeulen, R.
    Vocks, C.
    Vogt, C.
    van Weeren, R. J.
    Wijers, R. A. M. J.
    Wijnholds, S. J.
    Wise, M. W.
    Wucknitz, O.
    Yatawatta, S.
    Zarka, P.
    Zensus, J. A.
    A large light-mass component of cosmic rays at 1017–1017.5 electronvolts from radio observations2016In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 531, no 7592, 70-73 p.Article in journal (Refereed)
    Abstract [en]

    Cosmic rays are the highest-energy particles found in nature. Measurements of the mass composition of cosmic rays with energies of 1017–1018 electronvolts are essential to understanding whether they have galactic or extragalactic sources. It has also been proposed that the astrophysical neutrino signal1 comes from accelerators capable of producing cosmic rays of these energies2. Cosmic rays initiate air showers—cascades of secondary particles in the atmosphere—and their masses can be inferred from measurements of the atmospheric depth of the shower maximum3 (Xmax; the depth of the air shower when it contains the most particles) or of the composition of shower particles reaching the ground4. Current measurements5 have either high uncertainty, or a low duty cycle and a high energy threshold. Radio detection of cosmic rays6, 7, 8 is a rapidly developing technique9 for determining Xmax (refs 10, 11) with a duty cycle of, in principle, nearly 100 per cent. The radiation is generated by the separation of relativistic electrons and positrons in the geomagnetic field and a negative charge excess in the shower front6, 12. Here we report radio measurements of Xmax with a mean uncertainty of 16 grams per square centimetre for air showers initiated by cosmic rays with energies of 1017–1017.5 electronvolts. This high resolution in Xmax enables us to determine the mass spectrum of the cosmic rays: we find a mixed composition, with a light-mass fraction (protons and helium nuclei) of about 80 per cent. Unless, contrary to current expectations, the extragalactic component of cosmic rays contributes substantially to the total flux below 1017.5 electronvolts, our measurements indicate the existence of an additional galactic component, to account for the light composition that we measured in the 1017–1017.5 electronvolt range.

  • 76.
    Byass, Peter
    Umeå University, Faculty of Medicine, Department of Public Health and Clinical Medicine, Epidemiology and Global Health.
    Global health estimated over two decades2017In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 545, no 7655, 421-422 p.Article in journal (Refereed)
  • 77.
    Cabello, Adán
    Stockholm University, Faculty of Science, Department of Physics.
    Quantum physics: Correlations without parts2011In: Nature, ISSN 0028-0836, Vol. 474, no 7352, 456-458 p.Article in journal (Refereed)
  • 78. Cabral, Rita A.
    et al.
    Jackson, Matthew G.
    Rose-Koga, Estelle F.
    Koga, Kenneth T.
    Whitehouse, Martin J.
    Stockholm University, Faculty of Science, Department of Geological Sciences. Swedish Museum Nat Hist, Stockholm, Sweden.
    Antonelli, Michael A.
    Farquhar, James
    Day, James M. D.
    Hauri, Erik H.
    Anomalous sulphur isotopes in plume lavas reveal deep mantle storage of Archaean crust2013In: Nature, ISSN 0028-0836, Vol. 496, no 7446, 490-+ p.Article in journal (Refereed)
    Abstract [en]

    Basaltic lavas erupted at some oceanic intraplate hotspot volcanoes are thought to sample ancient subducted crustal materials(1,2). However, the residence time of these subducted materials in the mantle is uncertain and model-dependent(3), and compelling evidence for their return to the surface in regions of mantle upwelling beneath hotspots is lacking. Here we report anomalous sulphur isotope signatures indicating mass-independent fractionation (MIF) in olivine-hosted sulphides from 20-million-year-old ocean island basalts from Mangaia, Cook Islands (Polynesia), which have been suggested to sample recycled oceanic crust(3,4). Terrestrial MIF sulphur isotope signatures (in which the amount of fractionation does not scale in proportion with the difference in the masses of the isotopes) were generated exclusively through atmospheric photochemical reactions until about 2.45 billion years ago(5-7). Therefore, the discovery of MIF sulphur in these young plume lavas suggests that sulphur-probably derived from hydrothermally altered oceanic crust-was subducted into the mantle before 2.45 billion years ago and recycled into the mantle source of Mangaia lavas. These new data provide evidence for ancient materials, with negative Delta S-33 values, in the mantle source for Mangaia lavas. Our data also complement evidence for recycling of the sulphur content of ancient sedimentary materials to the subcontinental lithospheric mantle that has been identified in diamond-hosted sulphide inclusions(8,9). This Archaean age for recycled oceanic crust also provides key constraints on the length of time that subducted crustal material can survive in the mantle, and on the timescales of mantle convection from subduction to upwelling beneath hotspots.

  • 79. Cao, Yi
    et al.
    Kulkarni, S. R.
    Howell, D. Andrew
    Gal-Yam, Avishay
    Kasliwal, Mansi M.
    Valenti, Stefano
    Johansson, Joel
    Stockholm University, Faculty of Science, Department of Physics. Stockholm University, Faculty of Science, The Oskar Klein Centre for Cosmo Particle Physics (OKC).
    Amanullah, Rahman
    Stockholm University, Faculty of Science, Department of Physics. Stockholm University, Faculty of Science, The Oskar Klein Centre for Cosmo Particle Physics (OKC).
    Goobar, Ariel
    Stockholm University, Faculty of Science, Department of Physics. Stockholm University, Faculty of Science, The Oskar Klein Centre for Cosmo Particle Physics (OKC).
    Sollerman, Jesper
    Stockholm University, Faculty of Science, Department of Astronomy. Stockholm University, Faculty of Science, The Oskar Klein Centre for Cosmo Particle Physics (OKC).
    Taddia, Francesco
    Stockholm University, Faculty of Science, Department of Astronomy. Stockholm University, Faculty of Science, The Oskar Klein Centre for Cosmo Particle Physics (OKC).
    Horesh, Assaf
    Sagiv, Ilan
    Cenko, S. Bradley
    Nugent, Peter E.
    Arcavi, Iair
    Surace, Jason
    Wozniak, P. R.
    Moody, Daniela I.
    Rebbapragada, Umaa D.
    Bue, Brian D.
    Gehrels, Neil
    A strong ultraviolet pulse from a newborn type Ia supernova2015In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 521, no 7552, 328-+ p.Article in journal (Refereed)
    Abstract [en]

    Type Ia supernovae(1) are destructive explosions of carbon-oxygen white dwarfs(2,3). Although they are used empirically to measure cosmological distances(4-6), the nature of their progenitors remains mysterious(3). One of the leading progenitor models, called the single degenerate channel, hypothesizes that a white dwarf accretes matter from a companion star and the resulting increase in its central pressure and temperature ignites thermonuclear explosion(3,7,8). Here we report observations with the Swift Space Telescope of strong but declining ultraviolet emission from a type Ia supernova within four days of its explosion. This emission is consistent with theoretical expectations of collision between material ejected by the supernova and a companion star(9), and therefore provides evidence that some type Ia supernovae arise from the single degenerate channel.

  • 80.
    Carlsbecker, Annelie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Lee, Ji-Young
    Roberts, Christina J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Dettmer, Jan
    Lehesranta, Satu
    Zhou, Jing
    Lindgren, Ove
    Moreno-Risueno, Miguel A.
    Vatén, Anne
    Thitamadee, Siripong
    Campilho, Ana
    Sebastian, Jose
    Bowman, John L.
    Helariutta, Yka
    Benfey, Philip N.
    Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate2010In: Nature, ISSN 0028-0836, Vol. 465, no 7296, 316-321 p.Article in journal (Refereed)
    Abstract [en]

    A key question in developmental biology is how cells exchange positional information for proper patterning during organ development. In plant roots the radial tissue organization is highly conserved with a central vascular cylinder in which two water conducting cell types, protoxylem and metaxylem, are patterned centripetally. We show that this patterning occurs through crosstalk between the vascular cylinder and the surrounding endodermis mediated by cell-to-cell movement of a transcription factor in one direction and microRNAs in the other. SHORT ROOT, produced in the vascular cylinder, moves into the endodermis to activate SCARECROW. Together these transcription factors activate MIR165a and MIR166b. Endodermally produced microRNA165/6 then acts to degrade its target mRNAs encoding class III homeodomain-leucine zipper transcription factors in the endodermis and stele periphery. The resulting differential distribution of target mRNA in the vascular cylinder determines xylem cell types in a dosage-dependent manner.

  • 81. Carvalhais, Nuno
    et al.
    Forkel, Matthias
    Khomik, Myroslava
    Bellarby, Jessica
    Jung, Martin
    Migliavacca, Mirco
    Mu, Mingquan
    Saatchi, Sassan
    Santoro, Maurizio
    Thurner, Martin
    Weber, Ulrich
    Ahrens, Bernhard
    Beer, Christian
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM). Max Planck Society, Germany.
    Cescatti, Alessandro
    Randerson, James T.
    Reichstein, Markus
    Global covariation of carbon turnover times with climate in terrestrial ecosystems2014In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 514, no 7521, 213-+ p.Article in journal (Refereed)
    Abstract [en]

    The response of the terrestrial carbon cycle to climate change is among the largest uncertainties affecting future climate change projections(1,2). The feedback between the terrestrial carbon cycle and climate is partly determined by changes in the turnover time of carbon in land ecosystems, which in turn is an ecosystem property that emerges from the interplay between climate, soil and vegetation type(3-6). Here we present a global, spatially explicit and observation-based assessment of whole-ecosystem carbon turnover times that combines new estimates of vegetation and soil organic carbon stocks and fluxes. We find that the overall mean global carbon turnover time is 23(4)(+7) years (95 per cent confidence interval). Onaverage, carbon resides in the vegetation and soil near the Equator for a shorter time than at latitudes north of 75 degrees north (mean turnover times of 15 and 255 years, respectively). We identify a clear dependence of the turnover time on temperature, as expected from our present understanding of temperature controls on ecosystem dynamics. Surprisingly, our analysis also reveals a similarly strong association between turnover time and precipitation. Moreover, we find that the ecosystem carbon turnover times simulated by state-of-the-art coupled climate/carbon-cycle models vary widely and that numerical simulations, on average, tend to underestimate the global carbon turnover time by 36 per cent. The models show stronger spatial relationships with temperature than do observation-based estimates, but generally do not reproduce the strong relationships with precipitation and predict faster carbon turnover in many semiarid regions. Our findings suggest that future climate/carbon-cycle feedbacks may depend more strongly on changes in the hydrological cycle than is expected at present and is considered in Earth system models.

  • 82.
    Castroviejo-Fisher, Santiago
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Population and Conservation Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    De la Riva, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Vilà, Carles
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Population and Conservation Biology.
    Transparent frogs show potential of natural world2007In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 449, no 7165, 972-972 p.Article in journal (Refereed)
  • 83.
    Cederström, Björn
    et al.
    KTH, Superseded Departments, Physics.
    Cahn, R. N.
    Danielsson, Mats
    KTH, Superseded Departments, Physics.
    Lundqvist, M.
    Nygren, D. R.
    Focusing hard X-rays with old LPs2000In: Nature, ISSN 0028-0836, Vol. 404, no 6781, 951-951 p.Article in journal (Refereed)
  • 84. Cederwall, B.
    et al.
    Moradi, F. Ghazi
    Back, T.
    Johnson, A.
    Blomqvist, J.
    Clement, E.
    de France, G.
    Wadsworth, R.
    Andgren, K.
    Lagergren, K.
    Dijon, A.
    Jaworski, G.
    Liotta, R.
    Qi, C.
    Nyako, B. M.
    Nyberg, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Nuclear Physics.
    Palacz, M.
    Al-Azri, H.
    Algora, A.
    de Angelis, G.
    Atac, A.
    Bhattacharyya, S.
    Brock, T.
    Brown, J. R.
    Davies, P.
    Di Nitto, A.
    Dombradi, Zs.
    Gadea, A.
    Gal, J.
    Hadinia, B.
    Johnston-Theasby, F.
    Joshi, P.
    Juhasz, K.
    Julin, R.
    Jungclaus, A.
    Kalinka, G.
    Kara, S. O.
    Khaplanov, A.
    Kownacki, J.
    La Rana, G.
    Lenzi, S. M.
    Molnar, J.
    Moro, R.
    Napoli, D. R.
    Singh, B. S. Nara
    Persson, A.
    Recchia, F.
    Sandzelius, M.
    Scheurer, J. -N
    Sletten, G.
    Sohler, D.
    Söderström, Pär-Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Taylor, M. J.
    Timar, J.
    Valiente-Dobon, J. J.
    Vardaci, E.
    Williams, S.
    Evidence for a spin-aligned neutron-proton paired phase from the level structure of Pd-922011In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 469, no 7328, 68-71 p.Article in journal (Refereed)
    Abstract [en]

    Shell structure and magic numbers in atomic nuclei were generally explained by pioneering work(1) that introduced a strong spin-orbit interaction to the nuclear shell model potential. However, knowledge of nuclear forces and the mechanisms governing the structure of nuclei, in particular far from stability, is still incomplete. In nuclei with equal neutron and proton numbers (N = Z), enhanced correlations arise between neutrons and protons (two distinct types of fermions) that occupy orbitals with the same quantum numbers. Such correlations have been predicted to favour an unusual type of nuclear superfluidity, termed isoscalar neutron-proton pairing(2-6), in addition to normal isovector pairing. Despite many experimental efforts, these predictions have not been confirmed. Here we report the experimental observation of excited states in the N = Z = 46 nucleus Pd-92. Gamma rays emitted following the Ni-58(Ar-36,2n)Pd-92 fusion-evaporation reaction were identified using a combination of state-of-the-art high-resolution c-ray, charged-particle and neutron detector systems. Our results reveal evidence for a spin-aligned, isoscalar neutron-proton coupling scheme, different from the previous prediction(2-6). We suggest that this coupling scheme replaces normal superfluidity (characterized by seniority coupling(7,8)) in the ground and low-lying excited states of the heaviest N = Z nuclei. Such strong, isoscalar neutron-proton correlations would have a considerable impact on the nuclear level structure and possibly influence the dynamics of rapid proton capture in stellar nucleosynthesis.

  • 85.
    Cederwall, Bo
    et al.
    KTH, School of Engineering Sciences (SCI), Physics, Nuclear Physics.
    Ghazi Moradi, Farnaz
    KTH, School of Engineering Sciences (SCI), Physics, Nuclear Physics.
    Bäck, Torbjörn
    KTH, School of Engineering Sciences (SCI), Physics, Nuclear Physics.
    Johnson, Arne
    KTH, School of Engineering Sciences (SCI), Physics, Nuclear Physics.
    Blomqvist, Jan-Erik
    KTH, School of Engineering Sciences (SCI), Physics, Nuclear Physics.
    Clément, E.
    Grand Accélérateur National d´lons Lourds, Cean Cedex, France.
    de France, G.
    Grand Accélérateur National d´lons Lourds, Cean Cedex, France.
    Wadsworth, R.
    Department of Physics, University of York, UK.
    Andgren, Karin
    KTH, School of Engineering Sciences (SCI), Physics, Nuclear Physics.
    Lagergren, Karin
    KTH, School of Engineering Sciences (SCI), Physics, Nuclear Physics.
    Dijon, A.
    Grand Accélérateur National d´lons Lourds, Cean Cedex, France.
    Jaworski, G.
    Heavy Ion Laboratory, Univeristy of Warsaw, Warsaw, Poland.
    Liotta, Roberto
    KTH, School of Engineering Sciences (SCI), Physics, Particle and Astroparticle Physics.
    Qi, Chong
    KTH, School of Engineering Sciences (SCI), Physics, Nuclear Physics.
    Nyakó, B. M.
    Institute of Nuclear Research of the Hungarian Academy of Sciences, Debrecen, Hungary.
    Nyberg, J.
    Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden.
    Palacz, M.
    Heavy Ion Laboratory, Univeristy of Warsaw, Warsaw, Poland.
    Al-Azri, H.
    Department of Physics, University of York, UK.
    Algora, A.
    IFIC, CSIC University of Valencia, Valencia, Spain.
    de Angelis, G.
    Instituto Nazionael di Fisica Nucleare, Laboratori Nazionali di Legnaro, Legnaro, Italy.
    Atac, Ayse
    KTH, School of Engineering Sciences (SCI).
    Bhattacharyya, S.
    Grand Accélérateur National d´lons Lourds, Cean Cedex, France.
    Brock, T.
    Department of Physics, University of York, York, UK.
    Brown, J. R.
    Department of Physics, University of York, York, UK.
    Davies, P.
    Department of Physics, University of York, York, UK.
    Di Nitto, A.
    Dipartimento di Scienze Fisiche, Universitá di Napoli and Instituto Nazionale di Fisica Nucleare, Napoli, Italy.
    Dombrádi, Zs.
    Institute of Nuclear Research of the Hungarian Academy of Science, Debrecen, Hungary.
    Gadea, A.
    IFIC, CSIC, University of Valencia, Valencia, Spain.
    Gál, J.
    Institute of Nuclear Research of the Hungarian Academy of Science, Debrecen, Hungary.
    Hadinia, Baharak
    KTH, School of Engineering Sciences (SCI), Physics.
    Johnston-Theasby, F.
    Department of Physics, University of York, York, UK.
    Joshi, P.
    Department of Physics, University of York, York, UK.
    Juhász, K.
    Department of Information Technology, Universty of Debrecen, Debrecen, Hungary.
    Julin, R.
    Department of Physics, University of Jyväskylä, Jyväskylä, Finland.
    Jungclaus, A.
    Instituto de Estructura de la Materia, Madrid, Spain .
    Kalinka, G.
    Institute of Nuclear Research of the Hungarian Academy of Sciences, Debrecen, Hungary.
    Kara, S. O.
    Department of Physics, Ankara University, Tandogan Ankarar, Turkey.
    Khaplanov, Anton
    KTH, School of Engineering Sciences (SCI), Physics, Nuclear Physics.
    Kownacki, J.
    Heavy Ion Laboratory, Universty of Warsaw, Warsaw, Poland.
    La Rana, G.
    Dipartimento di Scienze Fisiche, Universitá di Napoli and Instituto Nazionale di Fisica Nucleare, Napoli, Italy.
    Lenzi, S. M.
    Dipartimento di Fisica dell'Universitá di Padova and Instituto Nazionale di Fisica Nucleare, Sezione di Padova, Padova, Italy.
    Molnár, J.
    Institute of Nuclear Research of the Hungarian Academy of Sciences, Debrecen, Hungary.
    Moro, R.
    Dipartimento di Scienze Fisiche, Universitá di Napoli and Instituto Nazionale di Fisica Nucleare, Napoli, Italy.
    Napoli, D. R.
    Instituto Nazionale di Fisica Nucleare, Laboratori Natzionali di Legnaro, Legnaro, Italy.
    Nara Singh, B. S.
    Department of Physics, University of York, York, UK.
    Persson, Andreas
    KTH, School of Engineering Sciences (SCI), Physics, Nuclear Physics.
    Recchia, F.
    Dipartimento di Fisica dell'Universitá di Padova and Instituto Nazionale di Fisica Nucleare, Sezione di Padova, Padova, Italy.
    Sandzelius, Mikael
    KTH, School of Engineering Sciences (SCI), Physics.
    Scheurer, J. -N
    Université Bordeaux, Centre d'Etudes Nucléaires de Bordeaux Gradignan, Gradignan, France.
    Sletten, G.
    The Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark.
    Sohler, D.
    Institute of Nuclear Research of the Hungarian Academy of Sciences, Debrecen, Hungary.
    Söderström, P. -A
    Department of Physics and Astromony, Uppsala University, Uppsala, Sweden.
    Taylor, M. J.
    Department of Physics, University of York, York, UK.
    Timár, J.
    Institute of Nuclear Research of the Hungarian Academy of Sciences, Debrecen, Hungary.
    Valiente-Dobón, J. J.
    instituto Nazionale di Fisica Nucleare, Laboratori Nazionali di Legnaro, Legnaro, Italy.
    Vardaci, E.
    Dipartimento di Scienze Fisiche, Universitá di Napoli and Instituto Nazionale di Fisica Nucleare, Napoli, Italy.
    Williams, S.
    TRIUMF, Vancouver, British Columbia, Canada.
    Evidence for a spin-aligned neutron-proton paired phase from the level structure of 92Pd2011In: Nature, ISSN 0028-0836, Vol. 469, no 7328, 68-71 p.Article in journal (Refereed)
    Abstract [en]

    Shell structure and magic numbers in atomic nuclei were generally explained by pioneering work(1) that introduced a strong spin-orbit interaction to the nuclear shell model potential. However, knowledge of nuclear forces and the mechanisms governing the structure of nuclei, in particular far from stability, is still incomplete. In nuclei with equal neutron and proton numbers (N = Z), enhanced correlations arise between neutrons and protons (two distinct types of fermions) that occupy orbitals with the same quantum numbers. Such correlations have been predicted to favour an unusual type of nuclear superfluidity, termed isoscalar neutron-proton pairing(2-6), in addition to normal isovector pairing. Despite many experimental efforts, these predictions have not been confirmed. Here we report the experimental observation of excited states in the N = Z = 46 nucleus Pd-92. Gamma rays emitted following the Ni-58(Ar-36,2n)Pd-92 fusion-evaporation reaction were identified using a combination of state-of-the-art high-resolution c-ray, charged-particle and neutron detector systems. Our results reveal evidence for a spin-aligned, isoscalar neutron-proton coupling scheme, different from the previous prediction(2-6). We suggest that this coupling scheme replaces normal superfluidity (characterized by seniority coupling(7,8)) in the ground and low-lying excited states of the heaviest N = Z nuclei. Such strong, isoscalar neutron-proton correlations would have a considerable impact on the nuclear level structure and possibly influence the dynamics of rapid proton capture in stellar nucleosynthesis.

  • 86.
    Chabera, Pavel
    et al.
    Lund Univ, Dept Chem, Div Phys Chem, Box 124, SE-22100 Lund, Sweden..
    Liu, Yizhu
    Lund Univ, Dept Chem, CAS, Box 124, SE-22100 Lund, Sweden..
    Prakash, Om
    Lund Univ, Dept Chem, CAS, Box 124, SE-22100 Lund, Sweden..
    Thyrhaug, Erling
    Lund Univ, Dept Chem, Div Phys Chem, Box 124, SE-22100 Lund, Sweden..
    El Nahhas, Amal
    Lund Univ, Dept Chem, Div Phys Chem, Box 124, SE-22100 Lund, Sweden..
    Honarfar, Alireza
    Lund Univ, Dept Chem, Div Phys Chem, Box 124, SE-22100 Lund, Sweden..
    Essen, Sofia
    Lund Univ, Dept Chem, CAS, Box 124, SE-22100 Lund, Sweden..
    Fredin, Lisa A.
    Lund Univ, Dept Chem, Div Theoret Chem, Box 124, SE-22100 Lund, Sweden..
    Harlang, Tobias C. B.
    Lund Univ, Dept Chem, Div Phys Chem, Box 124, SE-22100 Lund, Sweden.;Tech Univ Denmark, Dept Phys, DK-2800 Lyngby, Denmark..
    Kjaer, Kasper S.
    Lund Univ, Dept Chem, Div Phys Chem, Box 124, SE-22100 Lund, Sweden.;Tech Univ Denmark, Dept Phys, DK-2800 Lyngby, Denmark..
    Handrup, Karsten
    Lund Univ, Dept Phys, Div Synchrotron Radiat Res, Box 118, SE-22100 Lund, Sweden..
    Ericson, Fredric
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Microsystems Technology.
    Tatsuno, Hideyuki
    Lund Univ, Dept Chem, Div Phys Chem, Box 124, SE-22100 Lund, Sweden..
    Morgan, Kelsey
    NIST, Boulder, CO 80305 USA..
    Schnadt, Joachim
    Lund Univ, Dept Phys, Div Synchrotron Radiat Res, Box 118, SE-22100 Lund, Sweden..
    Häggström, Lennart
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Ericsson, Tore
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Sobkowiak, Adam
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Lidin, Sven
    Lund Univ, Dept Chem, CAS, Box 124, SE-22100 Lund, Sweden..
    Huang, Ping
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Styring, Stenbjörn
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Uhlig, Jens
    Lund Univ, Dept Chem, Div Phys Chem, Box 124, SE-22100 Lund, Sweden..
    Bendix, Jesper
    Univ Copenhagen, Dept Chem, Univ Pk 5, DK-2100 Copenhagen, Denmark..
    Lomoth, Reiner
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Sundström, Villy
    Lund Univ, Dept Chem, Div Phys Chem, Box 124, SE-22100 Lund, Sweden..
    Persson, Petter
    Lund Univ, Dept Chem, Div Theoret Chem, Box 124, SE-22100 Lund, Sweden..
    Warnmark, Kenneth
    Lund Univ, Dept Chem, CAS, Box 124, SE-22100 Lund, Sweden..
    A low-spin Fe(III) complex with 100-ps ligand-to-metal charge transfer photoluminescence2017In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 543, no 7647, 695-+ p.Article in journal (Refereed)
    Abstract [en]

    Transition-metal complexes are used as photosensitizers(1), in light-emitting diodes, for biosensing and in photocatalysis(2). A key feature in these applications is excitation from the ground state to a charge-transfer state(3,4); the long charge-transfer-state lifetimes typical for complexes of ruthenium(5) and other precious metals are often essential to ensure high performance. There is much interest in replacing these scarce elements with Earth-abundant metals, with iron(6) and copper(7) being particularly attractive owing to their low cost and non-toxicity. But despite the exploration of innovative molecular designs(6,8-10), it remains a formidable scientific challenge(11) to access Earth-abundant transition-metal complexes with long-lived charge-transfer excited states. No known iron complexes are considered(12) photoluminescent at room temperature, and their rapid excited-state deactivation precludes their use as photosensitizers(13-15). Here we present the iron complex [Fe(btz)(3)](3+) (where btz is 3,3'-dimethyl-1,1'-bis(p-tolyl)-4,4'-bis(1,2,3-triazol-5-ylidene)), and show that the superior sigma-donor and pi-acceptor electron properties of the ligand stabilize the excited state sufficiently to realize a long charge-transfer lifetime of 100 picoseconds (ps) and room-temperature photoluminescence. This species is a low-spin Fe(III) d(5) complex, and emission occurs from a long-lived doublet ligand-to-metal charge-transfer ((LMCT)-L-2) state that is rarely seen for transition-metal complexes(4,16,17). The absence of intersystem crossing, which often gives rise to large excited-state energy losses in transition-metal complexes, enables the observation of spin-allowed emission directly to the ground state and could be exploited as an increased driving force in photochemical reactions on surfaces. These findings suggest that appropriate design strategies can deliver new iron-based materials for use as light emitters and photosensitizers.

  • 87. Chapman, Henry N.
    et al.
    Fromme, Petra
    Barty, Anton
    White, Thomas A.
    Kirian, Richard A.
    Aquila, Andrew
    Hunter, Mark S.
    Schulz, Joachim
    DePonte, Daniel P.
    Weierstall, Uwe
    Doak, R. Bruce
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Martin, Andrew V.
    Schlichting, Ilme
    Lomb, Lukas
    Coppola, Nicola
    Shoeman, Robert L.
    Epp, Sascha W.
    Hartmann, Robert
    Rolles, Daniel
    Rudenko, Artem
    Foucar, Lutz
    Kimmel, Nils
    Weidenspointner, Georg
    Holl, Peter
    Liang, Mengning
    Barthelmess, Miriam
    Caleman, Carl
    Boutet, Sebastien
    Bogan, Michael J.
    Krzywinski, Jacek
    Bostedt, Christoph
    Bajt, Sasa
    Gumprecht, Lars
    Rudek, Benedikt
    Erk, Benjamin
    Schmidt, Carlo
    Hoemke, Andre
    Reich, Christian
    Pietschner, Daniel
    Strueder, Lothar
    Hauser, Guenter
    Gorke, Hubert
    Ullrich, Joachim
    Herrmann, Sven
    Schaller, Gerhard
    Schopper, Florian
    Soltau, Heike
    Kuehnel, Kai-Uwe
    Messerschmidt, Marc
    Bozek, John D.
    Hau-Riege, Stefan P.
    Frank, Matthias
    Hampton, Christina Y.
    Sierra, Raymond G.
    Starodub, Dmitri
    Williams, Garth J.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Rocker, Andrea
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Jönsson, Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Stern, Stephan
    Nass, Karol
    Andritschke, Robert
    Schroeter, Claus-Dieter
    Krasniqi, Faton
    Bott, Mario
    Schmidt, Kevin E.
    Wang, Xiaoyu
    Grotjohann, Ingo
    Holton, James M.
    Barends, Thomas R. M.
    Neutze, Richard
    Marchesini, Stefano
    Fromme, Raimund
    Schorb, Sebastian
    Rupp, Daniela
    Adolph, Marcus
    Gorkhover, Tais
    Andersson, Inger
    SLU.
    Hirsemann, Helmut
    Potdevin, Guillaume
    Graafsma, Heinz
    Nilsson, Björn
    Spence, John C. H.
    Femtosecond X-ray protein nanocrystallography2011In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 470, no 7332, 73-77 p.Article in journal (Refereed)
    Abstract [en]

    X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded(1-3). It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction 'snapshots' are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source(4). We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes(5). More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (similar to 200 nm to 2 mm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes(6). This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.

  • 88. Chapman, Henry N
    et al.
    Hau-Riege, Stefan P
    Bogan, Michael J
    Bajt, Sasa
    Barty, Anton
    Boutet, Sébastien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Marchesini, Stefano
    Frank, Matthias
    Woods, Bruce W
    Benner, W Henry
    London, Richard A
    Rohner, Urs
    Szöke, Abraham
    Spiller, Eberhard
    Möller, Thomas
    Bostedt, Christoph
    Shapiro, David A
    Kuhlmann, Marion
    Treusch, Rolf
    Plönjes, Elke
    Burmeister, Florian
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bergh, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Huldt, Gösta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Femtosecond time-delay X-ray holography2007In: Nature, ISSN 0028-0836, Vol. 448, no 7154, 676-679 p.Article in journal (Refereed)
    Abstract [en]

    Extremely intense and ultrafast X-ray pulses from free-electron lasers offer unique opportunities to study fundamental aspects of complex transient phenomena in materials. Ultrafast time-resolved methods usually require highly synchronized pulses to initiate a transition and then probe it after a precisely defined time delay. In the X-ray regime, these methods are challenging because they require complex optical systems and diagnostics. Here we propose and apply a simple holographic measurement scheme, inspired by Newton's 'dusty mirror' experiment1, to monitor the X-ray-induced explosion of microscopic objects. The sample is placed near an X-ray mirror; after the pulse traverses the sample, triggering the reaction, it is reflected back onto the sample by the mirror to probe this reaction. The delay is encoded in the resulting diffraction pattern to an accuracy of one femtosecond, and the structural change is holographically recorded with high resolution. We apply the technique to monitor the dynamics of polystyrene spheres in intense free-electron-laser pulses, and observe an explosion occurring well after the initial pulse. Our results support the notion that X-ray flash imaging2, 3 can be used to achieve high resolution, beyond radiation damage limits for biological samples4. With upcoming ultrafast X-ray sources we will be able to explore the three-dimensional dynamics of materials at the timescale of atomic motion.

  • 89.
    Charpentier, Emmanuelle
    et al.
    Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS).
    Doudna, Jennifer A.
    Biotechnology: rewriting a genome2013In: Nature, ISSN 0028-0836, Vol. 495, no 7439, 50-51 p.Article in journal (Other academic)
  • 90.
    Charpentier Ljungqvist, Fredrik
    et al.
    Stockholm University, Faculty of Humanities, Department of History.
    Krusic, Paul J.
    Stockholm University, Faculty of Science, Department of Physical Geography.
    Sundqvist, Hanna S.
    Stockholm University, Faculty of Science, Department of Physical Geography.
    Zorita, Eduardo
    Brattström, Gudrun
    Stockholm University, Faculty of Science, Department of Mathematics.
    Frank, David
    Northern Hemisphere hydroclimate variability over the past twelve centuries2016In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 532, no 7597, 94-98 p.Article in journal (Refereed)
    Abstract [en]

    Accurate modelling and prediction of the local to continental-scale hydroclimate response to global warming is essential given the strong impact of hydroclimate on ecosystem functioning, crop yields, water resources, and economic security. However, uncertainty in hydroclimate projections remains large, in part due to the short length of instrumental measurements available with which to assess climate models. Here we present a spatial reconstruction of hydroclimate variability over the past twelve centuries across the Northern Hemisphere derived from a network of 196 at least millennium-long proxy records. We use this reconstruction to place recent hydrological changes and future precipitation scenarios in a long-term context of spatially resolved and temporally persistent hydroclimate patterns. We find a larger percentage of land area with relatively wetter conditions in the ninth to eleventh and the twentieth centuries, whereas drier conditions are more widespread between the twelfth and nineteenth centuries. Our reconstruction reveals that prominent seesaw patterns of alternating moisture regimes observed in instrumental data across the Mediterranean, western USA, and China have operated consistently over the past twelve centuries. Using an updated compilation of 128 temperature proxy records, we assess the relationship between the reconstructed centennial-scale Northern Hemisphere hydroclimate and temperature variability. Even though dry and wet conditions occurred over extensive areas under both warm and cold climate regimes, a statistically significant co-variability of hydroclimate and temperature is evident for particular regions. We compare the reconstructed hydroclimate anomalies with coupled atmosphere-ocean general circulation model simulations and find reasonable agreement during pre-industrial times. However, the intensification of the twentieth-century-mean hydroclimate anomalies in the simulations, as compared to previous centuries, is not supported by our new multi-proxy reconstruction. This finding suggests that much work remains before we can model hydroclimate variability accurately, and highlights the importance of using palaeoclimate data to place recent and predicted hydroclimate changes in a millennium-long context.

  • 91.
    Chen, Donglei
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Blom, Henning
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Sanchez, Sophie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. European Synchrotron Radiat Facil, 6 Rue Jules Horowitz, F-38043 Grenoble, France..
    Tafforeau, Paul
    European Synchrotron Radiat Facil, 6 Rue Jules Horowitz, F-38043 Grenoble, France..
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    The stem osteichthyan Andreolepis and the origin of tooth replacement2016In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 539, no 7628, 237-+ p.Article in journal (Refereed)
    Abstract [en]

    The teeth of gnathostomes (jawed vertebrates) show rigidly patterned, unidirectional replacement that may or may not be associated with a shedding mechanism. These mechanisms, which are critical for the maintenance of the dentition, are incongruently distributed among extant gnathostomes. Although a permanent tooth-generating dental lamina is present in all chondrichthyans, many tetrapods and some teleosts, it is absent in the non-teleost actinopterygians. Tooth-shedding by basal hard tissue resorption occurs in most osteichthyans (including tetrapods) but not in chondrichthyans. Here we report a three-dimensional virtual dissection of the dentition of a 424-million-year-old stem osteichthyan, Andreolepis hedei, using propagation phase-contrast synchrotron microtomography, with a reconstruction of its growth history. Andreolepis, close to the common ancestor of all extant osteichthyans, shed its teeth by basal resorption but probably lacked a permanent dental lamina. This is the earliest documented instance of resorptive tooth shedding and may represent the primitive osteichthyan mode of tooth replacement.

  • 92. Chen, Richard Z
    et al.
    Pettersson, Ulf
    Whitehead Institute for Biomedical Research, Department of Biology, Cambridge, USA.
    Beard, Caroline
    Jackson-Grusby, Laurie
    Jaenisch, Rudolf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology, Medical Genetics.
    DNA hypomethylation leads to elevated mutation rates1998In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 395, no 6697, 89-93 p.Article in journal (Refereed)
    Abstract [en]

    Genome-wide demethylation has been suggested to be a step in carcinogenesis. Evidence for this notion comes from the frequently observed global DNA hypomethylation in tumour cells, and from a recent study suggesting that defects in DNA methylation might contribute to the genomic instability of some colorectal tumour cell lines. DNA hypomethylation has also been associated with abnormal chromosomal structures, as observed in cells from patients with ICF (Immunodeficiency, Centromeric instability and Facial abnormalities) syndrome and in cells treated with the demethylating agent 5-azadeoxycytidine. Here we report that murine embryonic stem cells nullizygous for the major DNA methyltransferase (Dnmt1) gene exhibited significantly elevated mutation rates at both the endogenous hypoxanthine phosphoribosyltransferase (Hprt) gene and an integrated viral thymidine kinase (tk) transgene. Gene deletions were the predominant mutations at both loci. The major cause of the observed tk deletions was either mitotic recombination or chromosomal loss accompanied by duplication of the remaining chromosome. Our results imply an important role for mammalian DNA methylation in maintaining genome stability.

  • 93. Cho, Hae Sung
    et al.
    Deng, Hexiang
    Miyasaka, Keiichi
    Dong, Zhiyue
    Cho, Minhyung
    Neimark, Alexander V.
    Kang, Jeung Ku
    Yaghi, Omar M.
    Terasaki, Osamu
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Graduate School of Energy, Environment, Water and Sustainability, South Korea.
    Extra adsorption and adsorbate superlattice formation in metal-organic frameworks2015In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 527, no 7579, 503-U193 p.Article in journal (Refereed)
    Abstract [en]

    Metal-organic frameworks (MOFs) have a high internal surface area and widely tunable composition(1,2), which make them useful for applications involving adsorption, such as hydrogen, methane or carbon dioxide storage(3-9). The selectivity and uptake capacity of the adsorption process are determined by interactions involving the adsorbates and their porous host materials. But, although the interactions of adsorbate molecules with the internal MOF surface(10-17) and also amongst themselves within individual pores(18-22) have been extensively studied, adsorbate-adsorbate interactions across pore walls have not been explored. Here we show that local strain in the MOF, induced by pore filling, can give rise to collective and long-range adsorbate-adsorbate interactions and the formation of adsorbate superlattices that extend beyond an original MOF unit cell. Specifically, we use in situ small-angle X-ray scattering to track and map the distribution and ordering of adsorbate molecules in five members of the mesoporous MOF-74 series along entire adsorption-desorption isotherms. We find in all cases that the capillary condensation that fills the pores gives rise to the formation of 'extra adsorption domains'-that is, domains spanning several neighbouring pores, which have a higher adsorbate density than non-domain pores. In the case of one MOF, IRMOF-74-V-hex, these domains form a superlattice structure that is difficult to reconcile with the prevailing view of pore-filling as a stochastic process. The visualization of the adsorption process provided by our data, with clear evidence for initial adsorbate aggregation in distinct domains and ordering before an even distribution is finally reached, should help to improve our understanding of this process and may thereby improve our ability to exploit it practically.

  • 94. Choi, Minkee
    et al.
    Na, Kyungsu
    Kim, Jeongnam
    Sakamoto, Yasuhiro
    Terasaki, Osamu
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Ryoo, Ryong
    Stable single-unit-cell nanosheets of zeolite MFI as active and long-lived catalysts2009In: Nature, ISSN 0028-0836, Vol. 461, no 7261, 246-249 p.Article in journal (Refereed)
    Abstract [en]

    Zeolites-microporous crystalline aluminosilicates-are widely used in petrochemistry and fine-chemical synthesis(1-3) because strong acid sites within their uniform micropores enable size- and shape-selective catalysis. But the very presence of the micropores, with aperture diameters below 1 nm, often goes hand-in-hand with diffusion limitations(3-5) that adversely affect catalytic activity. The problem can be overcome by reducing the thickness of the zeolite crystals, which reduces diffusion path lengths and thus improves molecular diffusion(4,5). This has been realized by synthesizing zeolite nanocrystals(6), by exfoliating layered zeolites(7-9), and by introducing mesopores in the microporous material through templating strategies(10-17) or demetallation processes(18-22). But except for the exfoliation, none of these strategies has produced 'ultrathin' zeolites with thicknesses below 5 nm. Here we show that appropriately designed bifunctional surfactants can direct the formation of zeolite structures on themesoporous and microporous length scales simultaneously and thus yield MFI (ZSM-5, one of the most important catalysts in the petrochemical industry) zeolite nanosheets that are only 2 nm thick, which corresponds to the b-axis dimension of a single MFI unit cell. The large number of acid sites on the external surface of these zeolites renders them highly active for the catalytic conversion of large organic molecules, and the reduced crystal thickness facilitates diffusion and thereby dramatically suppresses catalyst deactivation through coke deposition during methanol-to-gasoline conversion. We expect that our synthesis approach could be applied to other zeolites to improve their performance in a range of important catalytic applications.

     

  • 95. Clack, J. A.
    et al.
    Ahlberg, Per E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Evolutionary Organism Biology.
    Finney, S. M.
    Dominguez Alonso, P.
    Robinson, J.
    Ketcham, R. A.
    A uniquely specialized ear in a very early tetrapod2003In: Nature, ISSN 0028-0836, Vol. 425, no 6953, 66-69 p.Article in journal (Refereed)
  • 96. Clark, Andrew G.
    et al.
    Eisen, Michael B.
    Smith, Douglas R.
    Bergman, Casey M.
    Oliver, Brian
    Markow, Therese A.
    Kaufman, Thomas C.
    Kellis, Manolis
    Gelbart, William
    Iyer, Venky N.
    Pollard, Daniel A.
    Sackton, Timothy B.
    Larracuente, Amanda M.
    Singh, Nadia D.
    Abad, Jose P.
    Abt, Dawn N.
    Adryan, Boris
    Aguade, Montserrat
    Akashi, Hiroshi
    Anderson, Wyatt W.
    Aquadro, Charles F.
    Ardell, David H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Arguello, Roman
    Artieri, Carlo G.
    Barbash, Daniel A.
    Barker, Daniel
    Barsanti, Paolo
    Batterham, Phil
    Batzoglou, Serafim
    Begun, Dave
    Bhutkar, Arjun
    Blanco, Enrico
    Bosak, Stephanie A.
    Bradley, Robert K.
    Brand, Adrianne D.
    Brent, Michael R.
    Brooks, Angela N.
    Brown, Randall H.
    Butlin, Roger K.
    Caggese, Corrado
    Calvi, Brian R.
    de Carvalho, A. Bernardo
    Caspi, Anat
    Castrezana, Sergio
    Celniker, Susan E.
    Chang, Jean L.
    Chapple, Charles
    Chatterji, Sourav
    Chinwalla, Asif
    Civetta, Alberto
    Clifton, Sandra W.
    Comeron, Josep M.
    Costello, James C.
    Coyne, Jerry A.
    Daub, Jennifer
    David, Robert G.
    Delcher, Arthur L.
    Delehaunty, Kim
    Do, Chuong B.
    Ebling, Heather
    Edwards, Kevin
    Eickbush, Thomas
    Evans, Jay D.
    Filipski, Alan
    Findeiss, Sven
    Freyhult, Eva
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Fulton, Lucinda
    Fulton, Robert
    Garcia, Ana C. L.
    Gardiner, Anastasia
    Garfield, David A.
    Garvin, Barry E.
    Gibson, Greg
    Gilbert, Don
    Gnerre, Sante
    Godfrey, Jennifer
    Good, Robert
    Gotea, Valer
    Gravely, Brenton
    Greenberg, Anthony J.
    Griffiths-Jones, Sam
    Gross, Samuel
    Guigo, Roderic
    Gustafson, Erik A.
    Haerty, Wilfried
    Hahn, Matthew W.
    Halligan, Daniel L.
    Halpern, Aaron L.
    Halter, Gillian M.
    Han, Mira V.
    Heger, Andreas
    Hillier, LaDeana
    Hinrichs, Angie S.
    Holmes, Ian
    Hoskins, Roger A.
    Hubisz, Melissa J.
    Hultmark, Dan
    Huntley, Melanie A.
    Jaffe, David B.
    Jagadeeshan, Santosh
    Jeck, William R.
    Johnson, Justin
    Jones, Corbin D.
    Jordan, William C.
    Karpen, Gary H.
    Kataoka, Eiko
    Keightley, Peter D.
    Kheradpour, Pouya
    Kirkness, Ewen F.
    Koerich, Leonardo B.
    Kristiansen, Karsten
    Kudrna, Dave
    Kulathinal, Rob J.
    Kumar, Sudhir
    Kwok, Roberta
    Lander, Eric
    Langley, Charles H.
    Lapoint, Richard
    Lazzaro, Brian P.
    Lee, So-Jeong
    Levesque, Lisa
    Li, Ruiqiang
    Lin, Chiao-Feng
    Lin, Michael F.
    Lindblad-Toh, Kerstin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Llopart, Ana
    Long, Manyuan
    Low, Lloyd
    Lozovsky, Elena
    Lu, Jian
    Luo, Meizhong
    Machado, Carlos A.
    Makalowski, Wojciech
    Marzo, Mar
    Matsuda, Muneo
    Matzkin, Luciano
    McAllister, Bryant
    McBride, Carolyn S.
    McKernan, Brendan
    McKernan, Kevin
    Mendez-Lago, Maria
    Minx, Patrick
    Mollenhauer, Michael U.
    Montooth, Kristi
    Mount, Stephen M.
    Mu, Xu
    Myers, Eugene
    Negre, Barbara
    Newfeld, Stuart
    Nielsen, Rasmus
    Noor, Mohamed A. F.
    O'Grady, Patrick
    Pachter, Lior
    Papaceit, Montserrat
    Parisi, Matthew J.
    Parisi, Michael
    Parts, Leopold
    Pedersen, Jakob S.
    Pesole, Graziano
    Phillippy, Adam M.
    Ponting, Chris P.
    Pop, Mihai
    Porcelli, Damiano
    Powell, Jeffrey R.
    Prohaska, Sonja
    Pruitt, Kim
    Puig, Marta
    Quesneville, Hadi
    Ram, Kristipati Ravi
    Rand, David
    Rasmussen, Matthew D.
    Reed, Laura K.
    Reenan, Robert
    Reily, Amy
    Remington, Karin A.
    Rieger, Tania T.
    Ritchie, Michael G.
    Robin, Charles
    Rogers, Yu-Hui
    Rohde, Claudia
    Rozas, Julio
    Rubenfield, Marc J.
    Ruiz, Alfredo
    Russo, Susan
    Salzberg, Steven L.
    Sanchez-Gracia, Alejandro
    Saranga, David J.
    Sato, Hajime
    Schaeffer, Stephen W.
    Schatz, Michael C.
    Schlenke, Todd
    Schwartz, Russell
    Segarra, Carmen
    Singh, Rama S.
    Sirot, Laura
    Sirota, Marina
    Sisneros, Nicholas B.
    Smith, Chris D.
    Smith, Temple F.
    Spieth, John
    Stage, Deborah E.
    Stark, Alexander
    Stephan, Wolfgang
    Strausberg, Robert L.
    Strempel, Sebastian
    Sturgill, David
    Sutton, Granger
    Sutton, Granger G.
    Tao, Wei
    Teichmann, Sarah
    Tobari, Yoshiko N.
    Tomimura, Yoshihiko
    Tsolas, Jason M.
    Valente, Vera L. S.
    Venter, Eli
    Venter, J. Craig
    Vicario, Saverio
    Vieira, Filipe G.
    Vilella, Albert J.
    Villasante, Alfredo
    Walenz, Brian
    Wang, Jun
    Wasserman, Marvin
    Watts, Thomas
    Wilson, Derek
    Wilson, Richard K.
    Wing, Rod A.
    Wolfner, Mariana F.
    Wong, Alex
    Wong, Gane Ka-Shu
    Wu, Chung-I
    Wu, Gabriel
    Yamamoto, Daisuke
    Yang, Hsiao-Pei
    Yang, Shiaw-Pyng
    Yorke, James A.
    Yoshida, Kiyohito
    Zdobnov, Evgeny
    Zhang, Peili
    Zhang, Yu
    Zimin, Aleksey V.
    Baldwin, Jennifer
    Abdouelleil, Amr
    Abdulkadir, Jamal
    Abebe, Adal
    Abera, Brikti
    Abreu, Justin
    Acer, St Christophe
    Aftuck, Lynne
    Alexander, Allen
    An, Peter
    Anderson, Erica
    Anderson, Scott
    Arachi, Harindra
    Azer, Marc
    Bachantsang, Pasang
    Barry, Andrew
    Bayul, Tashi
    Berlin, Aaron
    Bessette, Daniel
    Bloom, Toby
    Blye, Jason
    Boguslavskiy, Leonid
    Bonnet, Claude
    Boukhgalter, Boris
    Bourzgui, Imane
    Brown, Adam
    Cahill, Patrick
    Channer, Sheridon
    Cheshatsang, Yama
    Chuda, Lisa
    Citroen, Mieke
    Collymore, Alville
    Cooke, Patrick
    Costello, Maura
    D'Aco, Katie
    Daza, Riza
    De Haan, Georgius
    DeGray, Stuart
    DeMaso, Christina
    Dhargay, Norbu
    Dooley, Kimberly
    Dooley, Erin
    Doricent, Missole
    Dorje, Passang
    Dorjee, Kunsang
    Dupes, Alan
    Elong, Richard
    Falk, Jill
    Farina, Abderrahim
    Faro, Susan
    Ferguson, Diallo
    Fisher, Sheila
    Foley, Chelsea D.
    Franke, Alicia
    Friedrich, Dennis
    Gadbois, Loryn
    Gearin, Gary
    Gearin, Christina R.
    Giannoukos, Georgia
    Goode, Tina
    Graham, Joseph
    Grandbois, Edward
    Grewal, Sharleen
    Gyaltsen, Kunsang
    Hafez, Nabil
    Hagos, Birhane
    Hall, Jennifer
    Henson, Charlotte
    Hollinger, Andrew
    Honan, Tracey
    Huard, Monika D.
    Hughes, Leanne
    Hurhula, Brian
    Husby, M. Erii
    Kamat, Asha
    Kanga, Ben
    Kashin, Seva
    Khazanovich, Dmitry
    Kisner, Peter
    Lance, Krista
    Lara, Marcia
    Lee, William
    Lennon, Niall
    Letendre, Frances
    LeVine, Rosie
    Lipovsky, Alex
    Liu, Xiaohong
    Liu, Jinlei
    Liu, Shangtao
    Lokyitsang, Tashi
    Lokyitsang, Yeshi
    Lubonja, Rakela
    Lui, Annie
    MacDonald, Pen
    Magnisalis, Vasilia
    Maru, Kebede
    Matthews, Charles
    McCusker, William
    McDonough, Susan
    Mehta, Teena
    Meldrim, James
    Meneus, Louis
    Mihai, Oana
    Mihalev, Atanas
    Mihova, Tanya
    Mittelman, Rachel
    Mlenga, Valentine
    Montmayeur, Anna
    Mulrain, Leonidas
    Navidi, Adam
    Naylor, Jerome
    Negash, Tamrat
    Nguyen, Thu
    Nguyen, Nga
    Nicol, Robert
    Norbu, Choe
    Norbu, Nyima
    Novod, Nathaniel
    O'Neill, Barry
    Osman, Sahal
    Markiewicz, Eva
    Oyono, Otero L.
    Patti, Christopher
    Phunkhang, Pema
    Pierre, Fritz
    Priest, Margaret
    Raghuraman, Sujaa
    Rege, Filip
    Reyes, Rebecca
    Rise, Cecil
    Rogov, Peter
    Ross, Keenan
    Ryan, Elizabeth
    Settipalli, Sampath
    Shea, Terry
    Sherpa, Ngawang
    Shi, Lu
    Shih, Diana
    Sparrow, Todd
    Spaulding, Jessica
    Stalker, John
    Stange-Thomann, Nicole
    Stavropoulos, Sharon
    Stone, Catherine
    Strader, Christopher
    Tesfaye, Senait
    Thomson, Talene
    Thoulutsang, Yama
    Thoulutsang, Dawa
    Topham, Kerri
    Topping, Ira
    Tsamla, Tsamla
    Vassiliev, Helen
    Vo, Andy
    Wangchuk, Tsering
    Wangdi, Tsering
    Weiand, Michael
    Wilkinson, Jane
    Wilson, Adam
    Yadav, Shailendra
    Young, Geneva
    Yu, Qing
    Zembek, Lisa
    Zhong, Danni
    Zimmer, Andrew
    Zwirko, Zac
    Alvarez, Pablo
    Brockman, Will
    Butler, Jonathan
    Chin, CheeWhye
    Grabherr, Manfred
    Kleber, Michael
    Mauceli, Evan
    MacCallum, Iain
    Evolution of genes and genomes on the Drosophila phylogeny.2007In: Nature, ISSN 0028-0836, Vol. 450, no 7167, 203-218 p.Article in journal (Refereed)
    Abstract [en]

    Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

  • 97. Clutton-Brock, T. H.
    et al.
    Hodge, S. J.
    Spong, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Animal Ecology.
    Russell, A. F.
    Jordan, N. R.
    Bennett, N. C.
    Sharpe, L. L.
    Manser, M. B.
    Intrasexual competition and sexual selection in cooperative mammals2006In: Nature, ISSN 0028-0836, Vol. 444, no 7122, 1065-1068 p.Article in journal (Refereed)
    Abstract [en]

    In most animals, the sex that invests least in its offspring competes more intensely for access to the opposite sex and shows greater development of secondary sexual characters than the sex that invests most(1,2). However, in some mammals where females are the primary care-givers, females compete more frequently or intensely with each other than males(3-5). A possible explanation is that, in these species, the resources necessary for successful female reproduction are heavily concentrated and intrasexual competition for breeding opportunities is more intense among females than among males. Intrasexual competition between females is likely to be particularly intense in cooperative breeders where a single female monopolizes reproduction in each group(6). Here, we use data from a twelve-year study of wild meerkats (Suricata suricatta), where females show high levels of reproductive skew, to show that females gain greater benefits from acquiring dominant status than males and traits that increase competitive ability exert a stronger influence on their breeding success. Females that acquire dominant status also develop a suite of morphological, physiological and behavioural characteristics that help them to control other group members. Our results show that sex differences in parental investment are not the only mechanism capable of generating sex differences in reproductive competition and emphasize the extent to which competition for breeding opportunities between females can affect the evolution of sex differences and the operation of sexual selection.

  • 98. Conrad, Donald F.
    et al.
    Pinto, Dalila
    Redon, Richard
    Feuk, Lars
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Gokcumen, Omer
    Zhang, Yujun
    Aerts, Jan
    Andrews, T. Daniel
    Barnes, Chris
    Campbell, Peter
    Fitzgerald, Tomas
    Hu, Min
    Ihm, Chun Hwa
    Kristiansson, Kati
    MacArthur, Daniel G.
    MacDonald, Jeffrey R.
    Onyiah, Ifejinelo
    Pang, Andy Wing Chun
    Robson, Sam
    Stirrups, Kathy
    Valsesia, Armand
    Walter, Klaudia
    Wei, John
    Tyler-Smith, Chris
    Carter, Nigel P.
    Lee, Charles
    Scherer, Stephen W.
    Hurles, Matthew E.
    Origins and functional impact of copy number variation in the human genome2010In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 464, no 7289, 704-712 p.Article in journal (Refereed)
    Abstract [en]

    Structural variations of DNA greater than 1 kilobase in size account for most bases that vary among human genomes, but are still relatively under-ascertained. Here we use tiling oligonucleotide microarrays, comprising 42 million probes, to generate a comprehensive map of 11,700 copy number variations (CNVs) greater than 443 base pairs, of which most (8,599) have been validated independently. For 4,978 of these CNVs, we generated reference genotypes from 450 individuals of European, African or East Asian ancestry. The predominant mutational mechanisms differ among CNV size classes. Retrotransposition has duplicated and inserted some coding and non-coding DNA segments randomly around the genome. Furthermore, by correlation with known trait-associated single nucleotide polymorphisms (SNPs), we identified 30 loci with CNVs that are candidates for influencing disease susceptibility. Despite this, having assessed the completeness of our map and the patterns of linkage disequilibrium between CNVs and SNPs, we conclude that, for complex traits, the heritability void left by genome-wide association studies will not be accounted for by common CNVs.

  • 99. Constância, Miguel
    et al.
    Hemberger, Myriam
    Hughes, Jennifer
    Dean, Wendy
    Ferguson-Smith, Anne
    Fundele, Reinald
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Stewart, Francesca
    Kelsey, Gavin
    Fowden, Abigail
    Sibley, Colin
    Reik, Wolf
    Placental-specific IGF-II is a major modulator of placental and fetal growth2002In: Nature, ISSN 0028-0836, Vol. 417, no 6892, 945-8 p.Article in journal (Refereed)
  • 100. Contreras, F.-Xabier
    et al.
    Ernst, Andreas M.
    Haberkant, Per
    Björkholm, Patrik
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Lindahl, Erik
    Gönen, Basak
    Tischer, Christian
    Elofsson, Arne
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    von Heijne, Gunnar
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Thiele, Christoph
    Pepperkok, Rainer
    Wieland, Felix
    Brügger, Britta
    Molecular recognition of a single sphingolipid species by a protein’s transmembrane domain2012In: Nature, ISSN 0028-0836, Vol. 481, no 7382, 525-529 p.Article in journal (Refereed)
    Abstract [en]

    Functioning and processing of membrane proteins critically depend on the way their transmembrane segments are embedded in the membrane. Sphingolipids are structural components of membranes and can also act as intracellular second messengers. Not much is known of sphingolipids binding to transmembrane domains (TMDs) of proteins within the hydrophobic bilayer, and how this could affect protein function. Here we show a direct and highly specific interaction of exclusively one sphingomyelin species, SM 18, with the TMD of the COPI machinery protein p24 (ref. 2). Strikingly, the interaction depends on both the headgroup and the backbone of the sphingolipid, and on a signature sequence (VXXTLXXIY) within the TMD. Molecular dynamics simulations show a close interaction of SM 18 with the TMD. We suggest a role of SM 18 in regulating the equilibrium between an inactive monomeric and an active oligomeric state of the p24 protein, which in turn regulates COPI-dependent transport. Bioinformatic analyses predict that the signature sequence represents a conserved sphingolipid-binding cavity in a variety of mammalian membrane proteins. Thus, in addition to a function as second messengers, sphingolipids can act as cofactors to regulate the function of transmembrane proteins. Our discovery of an unprecedented specificity of interaction of a TMD with an individual sphingolipid species adds to our understanding of why biological membranes are assembled from such a large variety of different lipids.

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