Volume 505 Issue 7482, 9 January 2014

The elephant shark (Callorhinchus milii) is a cartilaginous fish native to the temperate waters off southern Australia and New Zealand, living at depths of 200 to 500 metres and migrating into shallow waters during spring for breeding. The genome sequence is published in this issue of Nature. Comparison with other vertebrate genomes shows that it is the slowest evolving genome of all known vertebrates � coelacanth included. Genome analysis points to an unusual adaptive immune system lacking the CD4 receptor and some associated cytokines, indicating that cartilaginous fishes possess a primordial gnathostome adaptive immune system. Also absent are genes encoding secreted calcium-binding phosphoproteins, in line with the absence of bone in cartilaginous fish. Cover: Rudie Kuiter/OceanwideImages.com

Editorial

  • Editorial |

    As public pressure builds for drug companies to make more results available from clinical trials, the industry should not forget that it relies on collective goodwill to test new therapies.

  • Editorial |

    Teams aimed at preventing violence on campus can offer a lifeline to those in crisis.

  • Editorial |

    How two world wars affected scientific research, and vice versa.

World View

  • World View |

    After his polar vessel became trapped in shifting sea ice, Chris Turney defends the scientific basis of the expedition.

    • Chris Turney

Research Highlights

Seven Days

  • Seven Days |

    The week in science: China crushes seized ivory, smuggled dinosaur skull recovered, and incoming asteroid spotted.

News

  • News |

    Tensions as open-access initiative goes live — without the field’s leading journal.

    • Richard Van Noorden
  • News |

    Swarms of small satellites set to deliver close to real-time imagery of swathes of the planet.

    • Declan Butler
  • News |

    Reforms to commercial and academic research systems still needed despite reaching spending milestone, say scientists.

    • Richard Van Noorden

News Feature

  • News Feature |

    Violent incidents at academic institutions have spurred universities to adopt formal procedures designed to keep campuses safer. But do the tactics work?

    • Brendan Maher

Comment

  • Comment |

    Practical, interdisciplinary ways of working forged during the Second World War had a lasting impact on a generation of physicists and their findings, says David Kaiser.

    • David Kaiser

Books & Arts

  • Books & Arts |

    David Adam applauds the autobiography of a high-flyer confronting his own nervous suffering head-on.

    • David Adam
  • Books & Arts |

    Ben Sheldon relishes a study of the broad-ranging impact of ornithology on modern biology.

    • Ben Sheldon
  • Books & Arts |

    Sound artist Daniel Fishkin tries to convey the experience of tinnitus. As the latest incarnation of his installation series Composing the Tinnitus Suites opens in Brooklyn, New York, he talks about building a mechanical model of the inner ear.

    • Jascha Hoffman

Correspondence

News & Views

  • News & Views |

    Wnt signalling molecules are thought to direct the development of an organism by spreading through tissues. But flies grow with almost normal appendages even when their main Wnt protein cannot move. Two scientists discuss the implications of this finding for our understanding of development. See Article p.180

    • Ginés Morata
    •  & Gary Struhl
  • News & Views |

    In flow batteries, energy is produced by passing solutions of 'electroactive' materials — often, metal salts — through an electrochemical cell. A non-metallic electroactive material opens the way to large-scale energy storage. See Letter p.195

    • Grigorii L. Soloveichik
  • News & Views |

    Patients differ in their requirement for, and response to, various drug doses. A general platform that allows continuous monitoring of drug levels in the blood of rats may open the door to patient-specific dosing.

    • Richard M. Crooks
  • News & Views |

    Superconducting quantum circuits are the core technology behind the most sensitive magnetometers. An analogous device has now been implemented using a gas of ultracold atoms, with possible applications for rotation sensing.

    • Charles A. Sackett
  • News & Views |

    Two crystal structures reveal that the Vif and Vpx proteins of human and simian immunodeficiency viruses mediate evasion of host defences by reprogramming the cellular protein-degradation machinery. See Letters p.229 & p.234

    • Michael H. Malim

Correction

Article

  • Article |

    Examination of demographic age trajectories for species from a wide range of taxonomic groups shows that these species have very diverse life-history patterns; mortality and reproduction vary greatly with age for both long- and short-lived species, and the relationships between ageing, mortality and reproduction are clearly complex.

    • Owen R. Jones
    • , Alexander Scheuerlein
    • , Roberto Salguero-Gómez
    • , Carlo Giovanni Camarda
    • , Ralf Schaible
    • , Brenda B. Casper
    • , Johan P. Dahlgren
    • , Johan Ehrlén
    • , María B. García
    • , Eric S. Menges
    • , Pedro F. Quintana-Ascencio
    • , Hal Caswell
    • , Annette Baudisch
    •  & James W. Vaupel
  • Article | | Open Access

    Whole-genome analysis of the elephant shark, a cartilaginous fish, shows that it is the slowest evolving of all known vertebrates, lacks critical bone formation genes and has an unusual adaptive immune system.

    • Byrappa Venkatesh
    • , Alison P. Lee
    • , Vydianathan Ravi
    • , Ashish K. Maurya
    • , Michelle M. Lian
    • , Jeremy B. Swann
    • , Yuko Ohta
    • , Martin F. Flajnik
    • , Yoichi Sutoh
    • , Masanori Kasahara
    • , Shawn Hoon
    • , Vamshidhar Gangu
    • , Scott W. Roy
    • , Manuel Irimia
    • , Vladimir Korzh
    • , Igor Kondrychyn
    • , Zhi Wei Lim
    • , Boon-Hui Tay
    • , Sumanty Tohari
    • , Kiat Whye Kong
    • , Shufen Ho
    • , Belen Lorente-Galdos
    • , Javier Quilez
    • , Tomas Marques-Bonet
    • , Brian J. Raney
    • , Philip W. Ingham
    • , Alice Tay
    • , LaDeana W. Hillier
    • , Patrick Minx
    • , Thomas Boehm
    • , Richard K. Wilson
    • , Sydney Brenner
    •  & Wesley C. Warren
  • Article |

    Replacement of the wingless (wg) gene in Drosophila with one that expresses a membrane-tethered form of Wg results in viable flies with normally patterned appendages of nearly the right size; early wg transcription and memory of signalling ensure continued target-gene expression in the absence of Wg release, even though the spread of Wg could boost cell proliferation.

    • Cyrille Alexandre
    • , Alberto Baena-Lopez
    •  & Jean-Paul Vincent

Letter

  • Letter |

    Observations of local galaxy I Zw 18 imply that the dust mass in star-forming, metal-poor environments is much lower than expected, and, therefore, that the amount of dust in young galaxies of the early Universe, such as redshift-6.6 galaxy Himiko, is probably a factor of about 100 less than previously thought.

    • David B. Fisher
    • , Alberto D. Bolatto
    • , Rodrigo Herrera-Camus
    • , Bruce T. Draine
    • , Jessica Donaldson
    • , Fabian Walter
    • , Karin M. Sandstrom
    • , Adam K. Leroy
    • , John Cannon
    •  & Karl Gordon
  • Letter |

    High-quality graphene is grown on copper and then transferred to the underlying substrate, typically silicon oxide or quartz, by simply etching away the copper; the graphene is held in place during etching by capillary bridges.

    • Libo Gao
    • , Guang-Xin Ni
    • , Yanpeng Liu
    • , Bo Liu
    • , Antonio H. Castro Neto
    •  & Kian Ping Loh
  • Letter |

    Flow batteries, in which the electro-active components are held in fluid form external to the battery itself, are attractive as a potential means for regulating the output of intermittent renewable sources of electricity; an aqueous flow battery based on inexpensive commodity chemicals is now reported that also has the virtue of enabling further improvement of battery performance through organic chemical design.

    • Brian Huskinson
    • , Michael P. Marshak
    • , Changwon Suh
    • , Süleyman Er
    • , Michael R. Gerhardt
    • , Cooper J. Galvin
    • , Xudong Chen
    • , Alán Aspuru-Guzik
    • , Roy G. Gordon
    •  & Michael J. Aziz
  • Letter |

    A method of selectively activating both allylic carbon–hydrogen bonds and carbon–carbon bonds can furnish sophisticated molecular scaffolds with all-carbon quaternary stereogenic centres that can themselves be derivatized.

    • Ahmad Masarwa
    • , Dorian Didier
    • , Tamar Zabrodski
    • , Marvin Schinkel
    • , Lutz Ackermann
    •  & Ilan Marek
  • Letter |

    Drilling by the Integrated Ocean Drilling Program has recovered primitive, modally layered, orthopyroxene-bearing cumulate rocks from the lower plutonic crust formed at a fast-spreading ridge, leading to a better-constrained estimate of the bulk composition of fast-spreading oceanic crust.

    • Kathryn M. Gillis
    • , Jonathan E. Snow
    • , Adam Klaus
    • , Natsue Abe
    • , Álden B. Adrião
    • , Norikatsu Akizawa
    • , Georges Ceuleneer
    • , Michael J. Cheadle
    • , Kathrin Faak
    • , Trevor J. Falloon
    • , Sarah A. Friedman
    • , Marguerite Godard
    • , Gilles Guerin
    • , Yumiko Harigane
    • , Andrew J. Horst
    • , Takashi Hoshide
    • , Benoit Ildefonse
    • , Marlon M. Jean
    • , Barbara E. John
    • , Juergen Koepke
    • , Sumiaki Machi
    • , Jinichiro Maeda
    • , Naomi E. Marks
    • , Andrew M. McCaig
    • , Romain Meyer
    • , Antony Morris
    • , Toshio Nozaka
    • , Marie Python
    • , Abhishek Saha
    •  & Robert P. Wintsch
  • Letter |

    A comprehensive study into the effects of polymorphisms on gene expression dynamics during a 12-hour development period of Caenorhabditis elegans shows that both cis and trans expression quantitative trait loci (eQTLs) can increase and decrease gene expression, depending on the time point, and that trans eQTLs can act as modifiers of expression during a given period of development.

    • Mirko Francesconi
    •  & Ben Lehner
  • Letter |

    HMGA2 promotes lung cancer progression in mice and humans; in mouse and human lung cancer cells, HMGA2 competes with mRNAs like TGFBR3 for the let-7 microRNA family, and in human non-small-cell lung cancer tissue, expression levels of HMGA2 and TGFBR3 are correlated, suggesting that HMGA2 functions both as a protein-coding gene and as a non-coding RNA.

    • Madhu S. Kumar
    • , Elena Armenteros-Monterroso
    • , Philip East
    • , Probir Chakravorty
    • , Nik Matthews
    • , Monte M. Winslow
    •  & Julian Downward
  • Letter |

    Using long-term intravital photography to explore the cellular changes after compression-induced traumatic brain injury in a murine model, it is shown that parenchymal and meningeal inflammation as well as cell death can be modulated by topical treatment with purinergic receptor antagonists and glutathione.

    • Theodore L. Roth
    • , Debasis Nayak
    • , Tatjana Atanasijevic
    • , Alan P. Koretsky
    • , Lawrence L. Latour
    •  & Dorian B. McGavern
  • Letter |

    This study provides a crystal structure of the Vif–CBF-β–CUL5–ELOB–ELOC complex, which shows that Vif mimics the action of SOCS2 to interact with CUL5 and ELOC.

    • Yingying Guo
    • , Liyong Dong
    • , Xiaolin Qiu
    • , Yishu Wang
    • , Bailing Zhang
    • , Hongnan Liu
    • , You Yu
    • , Yi Zang
    • , Maojun Yang
    •  & Zhiwei Huang
  • Letter |

    The crystal structure of a ternary complex of the lentiviral accessory protein Vpx with the E3 ligase substrate adaptor DCAF1 and the HIV-1 restriction factor SAMHD1 shows how Vpx recruits SAMHD1 to the cell’s ubiquitination machinery.

    • David Schwefel
    • , Harriet C. T. Groom
    • , Virginie C. Boucherit
    • , Evangelos Christodoulou
    • , Philip A. Walker
    • , Jonathan P. Stoye
    • , Kate N. Bishop
    •  & Ian A. Taylor
  • Letter |

    Saccharomyces cerevisiae bearing engineered alginate and mannitol catabolic pathways can ferment sugars from brown macroalgae to produce ethanol, potentially allowing the use of brown macroalgae as a viable feedstock for the production of biofuels and renewable chemicals.

    • Maria Enquist-Newman
    • , Ann Marie E. Faust
    • , Daniel D. Bravo
    • , Christine Nicole S. Santos
    • , Ryan M. Raisner
    • , Arthur Hanel
    • , Preethi Sarvabhowman
    • , Chi Le
    • , Drew D. Regitsky
    • , Susan R. Cooper
    • , Lars Peereboom
    • , Alana Clark
    • , Yessica Martinez
    • , Joshua Goldsmith
    • , Min Y. Cho
    • , Paul D. Donohoue
    • , Lily Luo
    • , Brigit Lamberson
    • , Pramila Tamrakar
    • , Edward J. Kim
    • , Jeffrey L. Villari
    • , Avinash Gill
    • , Shital A. Tripathi
    • , Padma Karamchedu
    • , Carlos J. Paredes
    • , Vineet Rajgarhia
    • , Hans Kristian Kotlar
    • , Richard B. Bailey
    • , Dennis J. Miller
    • , Nicholas L. Ohler
    • , Candace Swimmer
    •  & Yasuo Yoshikuni
  • Letter |

    Femtosecond crystallography with an X-ray free-electron laser is used to analyse micrometre-sized protein crystals, generating a high-resolution structure of the protein without previous knowledge of what it looks like.

    • Thomas R. M. Barends
    • , Lutz Foucar
    • , Sabine Botha
    • , R. Bruce Doak
    • , Robert L. Shoeman
    • , Karol Nass
    • , Jason E. Koglin
    • , Garth J. Williams
    • , Sébastien Boutet
    • , Marc Messerschmidt
    •  & Ilme Schlichting

Corrigendum

  • Corrigendum |

    • Kerstin Howe
    • , Matthew D. Clark
    • , Carlos F. Torroja
    • , James Torrance
    • , Camille Berthelot
    • , Matthieu Muffato
    • , John E. Collins
    • , Sean Humphray
    • , Karen McLaren
    • , Lucy Matthews
    • , Stuart McLaren
    • , Ian Sealy
    • , Mario Caccamo
    • , Carol Churcher
    • , Carol Scott
    • , Jeffrey C. Barrett
    • , Romke Koch
    • , Gerd-Jörg Rauch
    • , Simon White
    • , William Chow
    • , Britt Kilian
    • , Leonor T. Quintais
    • , José A. Guerra-Assunção
    • , Yi Zhou
    • , Yong Gu
    • , Jennifer Yen
    • , Jan-Hinnerk Vogel
    • , Tina Eyre
    • , Ruby Banerjee
    • , Jianxiang Chi
    • , Beiyuan Fu
    • , Elizabeth Langley
    • , Sean F. Maguire
    • , Gavin Laird
    • , David Lloyd
    • , Emma Kenyon
    • , Sarah Donaldson
    • , Harminder Sehra
    • , Jeff Almeida-King
    • , Jane Loveland
    • , Stephen Trevanion
    • , Matt Jones
    • , Mike Quail
    • , Dave Willey
    • , Adrienne Hunt
    • , John Burton
    • , Sarah Sims
    • , Kirsten McLay
    • , Bob Plumb
    • , Joy Davis
    • , Chris Clee
    • , Karen Oliver
    • , Richard Clark
    • , Clare Riddle
    • , David Elliott
    • , Glen Threadgold
    • , Glenn Harden
    • , Darren Ware
    • , Sharmin Begum
    • , Beverley Mortimore
    • , Giselle Kerry
    • , Paul Heath
    • , Benjamin Phillimore
    • , Alan Tracey
    • , Nicole Corby
    • , Matthew Dunn
    • , Christopher Johnson
    • , Jonathan Wood
    • , Susan Clark
    • , Sarah Pelan
    • , Guy Griffiths
    • , Michelle Smith
    • , Rebecca Glithero
    • , Philip Howden
    • , Nicholas Barker
    • , Christine Lloyd
    • , Christopher Stevens
    • , Joanna Harley
    • , Karen Holt
    • , Georgios Panagiotidis
    • , Jamieson Lovell
    • , Helen Beasley
    • , Carl Henderson
    • , Daria Gordon
    • , Katherine Auger
    • , Deborah Wright
    • , Joanna Collins
    • , Claire Raisen
    • , Lauren Dyer
    • , Kenric Leung
    • , Lauren Robertson
    • , Kirsty Ambridge
    • , Daniel Leongamornlert
    • , Sarah McGuire
    • , Ruth Gilderthorp
    • , Coline Griffiths
    • , Deepa Manthravadi
    • , Sarah Nichol
    • , Gary Barker
    • , Siobhan Whitehead
    • , Michael Kay
    • , Jacqueline Brown
    • , Clare Murnane
    • , Emma Gray
    • , Matthew Humphries
    • , Neil Sycamore
    • , Darren Barker
    • , David Saunders
    • , Justene Wallis
    • , Anne Babbage
    • , Sian Hammond
    • , Maryam Mashreghi-Mohammadi
    • , Lucy Barr
    • , Sancha Martin
    • , Paul Wray
    • , Andrew Ellington
    • , Nicholas Matthews
    • , Matthew Ellwood
    • , Rebecca Woodmansey
    • , Graham Clark
    • , James D. Cooper
    • , Anthony Tromans
    • , Darren Grafham
    • , Carl Skuce
    • , Richard Pandian
    • , Robert Andrews
    • , Elliot Harrison
    • , Andrew Kimberley
    • , Jane Garnett
    • , Nigel Fosker
    • , Rebekah Hall
    • , Patrick Garner
    • , Daniel Kelly
    • , Christine Bird
    • , Sophie Palmer
    • , Ines Gehring
    • , Andrea Berger
    • , Christopher Dooley
    • , Zübeyde Ersan-Ürün
    • , Cigdem Eser
    • , Horst Geiger
    • , Maria Geisler
    • , Lena Karotki
    • , Anette Kirn
    • , Judith Konantz
    • , Martina Konantz
    • , Martina Oberländer
    • , Silke Rudolph-Geiger
    • , Mathias Teucke
    • , Christa Lanz
    • , Günter Raddatz
    • , Kazutoyo Osoegawa
    • , Baoli Zhu
    • , Amanda Rapp
    • , Sara Widaa
    • , Cordelia Langford
    • , Fengtang Yang
    • , Stephan C. Schuster
    • , Nigel P. Carter
    • , Jennifer Harrow
    • , Zemin Ning
    • , Javier Herrero
    • , Steve M. J. Searle
    • , Anton Enright
    • , Robert Geisler
    • , Ronald H. A. Plasterk
    • , Charles Lee
    • , Monte Westerfield
    • , Pieter J. de Jong
    • , Leonard I. Zon
    • , John H. Postlethwait
    • , Christiane Nüsslein- Volhard
    • , Tim J. P. Hubbard
    • , Hugues Roest Crollius
    • , Jane Rogers
    •  & Derek L. Stemple

Feature

Q&A

Futures

  • Futures |

    A matter of honour.

    • Grace Tang
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