Volume 497 Issue 7447, 2 May 2013

Editorial

  • Editorial |

    The White House urgently needs to set out a clear plan for how it intends to monitor the state of Earth.

  • Editorial |

    Research on transgenic crops must be done outside industry if it is to fulfil its early promise.

  • Editorial |

    The reform of English libel law is a victory, even if it doesn’t achieve everything that was hoped.

World View

  • World View |

    The Australian Academy of Science must take urgent steps to address the lack of gender equality among its elected fellows, warns Douglas Hilton.

    • Douglas Hilton

Research Highlights

Correction

Seven Days

  • Seven Days |

    The week in science: Bee-harming pesticides banned in Europe, North Korea atomic bomb detected, and chemist goes to trial over lab accident.

News

Correction

News Feature

Comment

  • Comment |

    Policy-makers in developing countries should not be swayed by the politicized arguments dominant in Europe, say Christopher J. M. Whitty and colleagues.

    • Christopher J. M. Whitty
    • , Monty Jones
    • , Alan Tollervey
    •  & Tim Wheeler

  • Comment |

    China's scientists are using a variety of approaches to boost crop yields and limit environmental damage, say Fusuo Zhang, Xinping Chen and Peter Vitousek.

    • Fusuo Zhang
    • , Xinping Chen
    •  & Peter Vitousek

Books & Arts

Correspondence

News & Views

  • News & Views |

    Hippocampal place cells encode information about an animal's spatial world. A study now finds that these same neurons envisage a future journey moments before a rat sets off. See Article p.74

    • Brandy Schmidt
    •  & A. David Redish

  • News & Views |

    Fresh evidence shows that the iron isotopic composition of Earth's silicate component does not, as was previously thought, reflect the formation of the planet's core at high pressure nor losses of material to space.

    • Alex N. Halliday

  • News & Views |

    Arrestin proteins regulate cellular signalling cascades initiated by ubiquitous G-protein-coupled receptors. Crystal structures reveal that two arrestins undergo similar structural changes on activation. See Letters p.137 & p.142

    • Valentin Borshchevskiy
    •  & Georg Büldt

  • News & Views |

    The spin state of a single erbium atom in a tiny silicon transistor has been probed using laser light. The finding opens a path towards a hybrid spin–photon quantum-computing architecture. See Letter p.91

    • Christoph D. Weis
    •  & Thomas Schenkel

  • News & Views |

    An elegant combination of electronics and elastic materials has been used to construct a small visual sensor that closely resembles an insect's eye. The device paves the way for autonomous navigation of tiny aerial vehicles. See Letter p.95

    • Alexander Borst
    •  & Johannes Plett

  • News & Views |

    A genomic analysis of yeast reveals that individual genes produce a rich complexity of RNA molecules with differing start and end sequences. The variation in these transcripts reflects the diversity of gene-regulation mechanisms. See Letter p.127

    • B. Franklin Pugh

  • News & Views |

    Reversible oxidation of amino-acid residues can directly regulate the activity of cellular enzymes. This principle has now been extended to deubiquitinating enzymes, with implications for cell signalling and protein turnover.

    • Michael J. Clague

Correction

Perspective

  • Perspective |

    Strongly connected and interdependent networks create risks of global-scale catastrophic failure; to make networked risks more manageable, it is suggested to establish a ‘Global Systems Science’.

    • Dirk Helbing

  • Perspective |

    This Perspective discusses the emerging advances in plant membrane transporters, which can be used to improve crop yields, nutritional value, and environmental stress resistance.

    • Julian I. Schroeder
    • , Emmanuel Delhaize
    • , Wolf B. Frommer
    • , Mary Lou Guerinot
    • , Maria J. Harrison
    • , Luis Herrera-Estrella
    • , Tomoaki Horie
    • , Leon V. Kochian
    • , Rana Munns
    • , Naoko K. Nishizawa
    • , Yi-Fang Tsay
    •  & Dale Sanders

Article

  • Article | | Open Access

    An integrative genomic analysis of several hundred endometrial carcinomas shows that a minority of tumour samples carry copy number alterations or TP53 mutations and many contain key cancer-related gene mutations, such as those involved in canonical pathways and chromatin remodelling; a reclassification of endometrial tumours into four distinct types is proposed, which may have an effect on patient treatment regimes.

    • Douglas A. Levine
    • , Gad Getz
    • , Stacey B. Gabriel
    • , Kristian Cibulskis
    • , Eric Lander
    • , Andrey Sivachenko
    • , Carrie Sougnez
    • , Mike Lawrence
    • , Cyriac Kandoth
    • , David Dooling
    • , Robert Fulton
    • , Lucinda Fulton
    • , Joelle Kalicki-Veizer
    • , Michael D. McLellan
    • , Michelle O’Laughlin
    • , Heather Schmidt
    • , Richard K. Wilson
    • , Kai Ye
    • , Li Ding
    • , Elaine R. Mardis
    • , Adrian Ally
    • , Miruna Balasundaram
    • , Inanc Birol
    • , Yaron S. N. Butterfield
    • , Rebecca Carlsen
    • , Candace Carter
    • , Andy Chu
    • , Eric Chuah
    • , Hye-Jung E. Chun
    • , Noreen Dhalla
    • , Ranabir Guin
    • , Carrie Hirst
    • , Robert A. Holt
    • , Steven J. M. Jones
    • , Darlene Lee
    • , Haiyan I. Li
    • , Marco A. Marra
    • , Michael Mayo
    • , Richard A. Moore
    • , Andrew J. Mungall
    • , Patrick Plettner
    • , Jacqueline E. Schein
    • , Payal Sipahimalani
    • , Angela Tam
    • , Richard J. Varhol
    • , A. Gordon Robertson
    • , Andrew D. Cherniack
    • , Itai Pashtan
    • , Gordon Saksena
    • , Robert C. Onofrio
    • , Steven E. Schumacher
    • , Barbara Tabak
    • , Scott L. Carter
    • , Bryan Hernandez
    • , Jeff Gentry
    • , Helga B. Salvesen
    • , Kristin Ardlie
    • , Gad Getz
    • , Wendy Winckler
    • , Rameen Beroukhim
    • , Stacey B. Gabriel
    • , Matthew Meyerson
    • , Angela Hadjipanayis
    • , Semin Lee
    • , Harshad S. Mahadeshwar
    • , Peter Park
    • , Alexei Protopopov
    • , Xiaojia Ren
    • , Sahil Seth
    • , Xingzhi Song
    • , Jiabin Tang
    • , Ruibin Xi
    • , Lixing Yang
    • , Dong Zeng
    • , Raju Kucherlapati
    • , Lynda Chin
    • , Jianhua Zhang
    • , J. Todd Auman
    • , Saianand Balu
    • , Tom Bodenheimer
    • , Elizabeth Buda
    • , D. Neil Hayes
    • , Alan P. Hoyle
    • , Stuart R. Jefferys
    • , Corbin D. Jones
    • , Shaowu Meng
    • , Piotr A. Mieczkowski
    • , Lisle E. Mose
    • , Joel S. Parker
    • , Charles M. Perou
    • , Jeff Roach
    • , Yan Shi
    • , Janae V. Simons
    • , Mathew G. Soloway
    • , Donghui Tan
    • , Michael D. Topal
    • , Scot Waring
    • , Junyuan Wu
    • , Katherine A. Hoadley
    • , Stephen B. Baylin
    • , Moiz S. Bootwalla
    • , Phillip H. Lai
    • , Timothy J. Triche Jr
    • , David J. Van Den Berg
    • , Daniel J. Weisenberger
    • , Peter W. Laird
    • , Hui Shen
    • , Lynda Chin
    • , Jianhua Zhang
    • , Gad Getz
    • , Juok Cho
    • , Daniel DiCara
    • , Scott Frazer
    • , David Heiman
    • , Rui Jing
    • , Pei Lin
    • , Will Mallard
    • , Petar Stojanov
    • , Doug Voet
    • , Hailei Zhang
    • , Lihua Zou
    • , Michael Noble
    • , Mike Lawrence
    • , Sheila M. Reynolds
    • , Ilya Shmulevich
    • , B. Arman Aksoy
    • , Yevgeniy Antipin
    • , Giovanni Ciriello
    • , Gideon Dresdner
    • , Jianjiong Gao
    • , Benjamin Gross
    • , Anders Jacobsen
    • , Marc Ladanyi
    • , Boris Reva
    • , Chris Sander
    • , Rileen Sinha
    • , S. Onur Sumer
    • , Barry S. Taylor
    • , Ethan Cerami
    • , Nils Weinhold
    • , Nikolaus Schultz
    • , Ronglai Shen
    • , Stephen Benz
    • , Ted Goldstein
    • , David Haussler
    • , Sam Ng
    • , Christopher Szeto
    • , Joshua Stuart
    • , Christopher C. Benz
    • , Christina Yau
    • , Wei Zhang
    • , Matti Annala
    • , Bradley M. Broom
    • , Tod D. Casasent
    • , Zhenlin Ju
    • , Han Liang
    • , Guoyan Liu
    • , Yiling Lu
    • , Anna K. Unruh
    • , Chris Wakefield
    • , John N. Weinstein
    • , Nianxiang Zhang
    • , Yuexin Liu
    • , Russell Broaddus
    • , Rehan Akbani
    • , Gordon B. Mills
    • , Christopher Adams
    • , Thomas Barr
    • , Aaron D. Black
    • , Jay Bowen
    • , John Deardurff
    • , Jessica Frick
    • , Julie M. Gastier-Foster
    • , Thomas Grossman
    • , Hollie A. Harper
    • , Melissa Hart-Kothari
    • , Carmen Helsel
    • , Aaron Hobensack
    • , Harkness Kuck
    • , Kelley Kneile
    • , Kristen M. Leraas
    • , Tara M. Lichtenberg
    • , Cynthia McAllister
    • , Robert E. Pyatt
    • , Nilsa C. Ramirez
    • , Teresa R. Tabler
    • , Nathan Vanhoose
    • , Peter White
    • , Lisa Wise
    • , Erik Zmuda
    • , Nandita Barnabas
    • , Charlenia Berry-Green
    • , Victoria Blanc
    • , Lori Boice
    • , Michael Button
    • , Adam Farkas
    • , Alex Green
    • , Jean MacKenzie
    • , Dana Nicholson
    • , Steve E. Kalloger
    • , C. Blake Gilks
    • , Beth Y. Karlan
    • , Jenny Lester
    • , Sandra Orsulic
    • , Mark Borowsky
    • , Mark Cadungog
    • , Christine Czerwinski
    • , Lori Huelsenbeck-Dill
    • , Mary Iacocca
    • , Nicholas Petrelli
    • , Brenda Rabeno
    • , Gary Witkin
    • , Elena Nemirovich-Danchenko
    • , Olga Potapova
    • , Daniil Rotin
    • , Andrew Berchuck
    • , Michael Birrer
    • , Phillip DiSaia
    • , Laura Monovich
    • , Erin Curley
    • , Johanna Gardner
    • , David Mallery
    • , Robert Penny
    • , Sean C. Dowdy
    • , Boris Winterhoff
    • , Linda Dao
    • , Bobbie Gostout
    • , Alexandra Meuter
    • , Attila Teoman
    • , Fanny Dao
    • , Narciso Olvera
    • , Faina Bogomolniy
    • , Karuna Garg
    • , Robert A. Soslow
    • , Douglas A. Levine
    • , Mikhail Abramov
    • , John M. S. Bartlett
    • , Sugy Kodeeswaran
    • , Jeremy Parfitt
    • , Fedor Moiseenko
    • , Blaise A. Clarke
    • , Marc T. Goodman
    • , Michael E. Carney
    • , Rayna K. Matsuno
    • , Jennifer Fisher
    • , Mei Huang
    • , W. Kimryn Rathmell
    • , Leigh Thorne
    • , Linda Van Le
    • , Rajiv Dhir
    • , Robert Edwards
    • , Esther Elishaev
    • , Kristin Zorn
    • , Russell Broaddus
    • , Paul J. Goodfellow
    • , David Mutch
    • , Nikolaus Schultz
    • , Yuexin Liu
    • , Rehan Akbani
    • , Andrew D. Cherniack
    • , Ethan Cerami
    • , Nils Weinhold
    • , Hui Shen
    • , Katherine A. Hoadley
    • , Ari B. Kahn
    • , Daphne W. Bell
    • , Pamela M. Pollock
    • , Chen Wang
    • , David A.Wheeler
    • , Eve Shinbrot
    • , Beth Y. Karlan
    • , Andrew Berchuck
    • , Sean C. Dowdy
    • , Boris Winterhoff
    • , Marc T. Goodman
    • , A. Gordon Robertson
    • , Rameen Beroukhim
    • , Itai Pashtan
    • , Helga B. Salvesen
    • , Peter W. Laird
    • , Michael Noble
    • , Joshua Stuart
    • , Li Ding
    • , Cyriac Kandoth
    • , C. Blake Gilks
    • , Robert A. Soslow
    • , Paul J. Goodfellow
    • , David Mutch
    • , Russell Broaddus
    • , Wei Zhang
    • , Gordon B. Mills
    • , Raju Kucherlapati
    • , Elaine R. Mardis
    • , Douglas A. Levine
    • , Brenda Ayala
    • , Anna L. Chu
    • , Mark A. Jensen
    • , Prachi Kothiyal
    • , Todd D. Pihl
    • , Joan Pontius
    • , David A. Pot
    • , Eric E. Snyder
    • , Deepak Srinivasan
    • , Ari B. Kahn
    • , Kenna R. Mills Shaw
    • , Margi Sheth
    • , Tanja Davidsen
    • , Greg Eley Martin L. Ferguson
    • , John A. Demchok
    • , Liming Yang
    • , Mark S. Guyer
    • , Bradley A. Ozenberger
    • , Heidi J. Sofia
    • , Cyriac Kandoth
    • , Nikolaus Schultz
    • , Andrew D. Cherniack
    • , Rehan Akbani
    • , Yuexin Liu
    • , Hui Shen
    • , A. Gordon Robertson
    • , Itai Pashtan
    • , Ronglai Shen
    • , Christopher C. Benz
    • , Christina Yau
    • , Peter W. Laird
    • , Li Ding
    • , Wei Zhang
    • , Gordon B. Mills
    • , Raju Kucherlapati
    • , Elaine R. Mardis
    •  & Douglas A. Levine

    Collection:

  • Article |

    It is known that compressed sequences of hippocampal place cells can ‘replay’ previous navigational trajectories in linearly constrained mazes; here, rat place-cell sequences representing two-dimensional spatial trajectories were observed before navigational decisions, and predicted the immediate navigational path.

    • Brad E. Pfeiffer
    •  & David J. Foster

  • Article |

    High-resolution cryo-EM density maps are used to present the structures of Drosophila and human 80S ribosomes in complex with eEF2, E-site transfer RNA and Stm1-like proteins, and reveal the presence of two additional structural layers in the ribosomes of metazoan eukaryotes.

    • Andreas M. Anger
    • , Jean-Paul Armache
    • , Otto Berninghausen
    • , Michael Habeck
    • , Marion Subklewe
    • , Daniel N. Wilson
    •  & Roland Beckmann

Letter

  • Letter |

    Entanglement of two electron spin qubits in diamond with a spatial separation of three metres is reported; such entanglement can be combined with recently achieved initialization, readout and entanglement operations on local long-lived nuclear spin registers, and paves the way for deterministic long-distance teleportation, quantum repeaters and extended quantum networks.

    • H. Bernien
    • , B. Hensen
    • , W. Pfaff
    • , G. Koolstra
    • , M. S. Blok
    • , L. Robledo
    • , T. H. Taminiau
    • , M. Markham
    • , D. J. Twitchen
    • , L. Childress
    •  & R. Hanson

  • Letter |

    A hybrid approach to detecting individual defect spins in solids, whereby an optically induced spin change is detected electronically, offers the high fidelities required for quantum information processing devices.

    • Chunming Yin
    • , Milos Rancic
    • , Gabriele G. de Boo
    • , Nikolas Stavrias
    • , Jeffrey C. McCallum
    • , Matthew J. Sellars
    •  & Sven Rogge

  • Letter |

    Digital cameras with layouts inspired by the compound, hemispherical designs of arthropod eyes have been built by combining elastomeric optical elements with deformable arrays of thin silicon photodetectors.

    • Young Min Song
    • , Yizhu Xie
    • , Viktor Malyarchuk
    • , Jianliang Xiao
    • , Inhwa Jung
    • , Ki-Joong Choi
    • , Zhuangjian Liu
    • , Hyunsung Park
    • , Chaofeng Lu
    • , Rak-Hwan Kim
    • , Rui Li
    • , Kenneth B. Crozier
    • , Yonggang Huang
    •  & John A. Rogers

  • Letter |

    The disappearance of non-mass-dependent sulphur isotope anomalies from the rock record is thought to indicate the increase in atmospheric oxygen concentration from its initial, persistently low level; however, as a result of long-term surface recycling these anomalies may in fact survive in the sedimentary record for as long as 100 million years after an increase in atmospheric oxygen.

    • Christopher T. Reinhard
    • , Noah J. Planavsky
    •  & Timothy W. Lyons

  • Letter |

    Estimations of body shape and three-dimensional digital reconstructions of representative archosaurs along the ancestral bird line support hypotheses of a gradual, stepwise acquisition of more-crouched limb postures across much of theropod evolution but indicate that an accelerated change, rather than a discrete transition from more-upright postures, occurred within the clade Maniraptora (birds and their closest relatives, such as deinonychosaurs).

    • Vivian Allen
    • , Karl T. Bates
    • , Zhiheng Li
    •  & John R. Hutchinson

  • Letter |

    A proof of principle study shows that by exome sequencing of cell-free circulating DNA from cancer patient plasma samples, the genomic evolution of metastatic cancers and the acquisition of resistance in response to therapy can be tracked over time.

    • Muhammed Murtaza
    • , Sarah-Jane Dawson
    • , Dana W. Y. Tsui
    • , Davina Gale
    • , Tim Forshew
    • , Anna M. Piskorz
    • , Christine Parkinson
    • , Suet-Feung Chin
    • , Zoya Kingsbury
    • , Alvin S. C. Wong
    • , Francesco Marass
    • , Sean Humphray
    • , James Hadfield
    • , David Bentley
    • , Tan Min Chin
    • , James D. Brenton
    • , Carlos Caldas
    •  & Nitzan Rosenfeld

  • Letter |

    In Drosophila, olfactory sensory neurons project to spatially invariant loci (glomeruli) and stereotyped circuitry is maintained in projections to a brain centre thought to mediate innate behaviours; here it is shown that neurons of the mushroom body, a centre that translates olfactory information into learned behaviours, integrate input from an apparently random combination of glomeruli, which could allow the fly to contextualize novel sensory experiences.

    • Sophie J. C. Caron
    • , Vanessa Ruta
    • , L. F. Abbott
    •  & Richard Axel

  • Letter |

    The current model to explain accurate chromosome segregation after DNA replication holds that kinetochore–microtubule attachments exert tension across the centromere and are stabilized by spatial separation from inner centromere-localized Aurora B; here an alternative model is presented, wherein active Aurora B produced by clustering is sufficient to ensure biorientation through a mechanism that is intrinsic to the kinetochore.

    • Christopher S. Campbell
    •  & Arshad Desai

  • Letter |

    The CXXC domains of TET2 (encoded by the distinct gene IDAX) and TET3 are found to have previously unknown roles in the regulation of TET proteins through the activation of caspases and subsequent reduction in TET catalytic activity; this regulation is dependent on DNA binding through the CXXC domain.

    • Myunggon Ko
    • , Jungeun An
    • , Hozefa S. Bandukwala
    • , Lukas Chavez
    • , Tarmo Äijö
    • , William A. Pastor
    • , Matthew F. Segal
    • , Huiming Li
    • , Kian Peng Koh
    • , Harri Lähdesmäki
    • , Patrick G. Hogan
    • , L. Aravind
    •  & Anjana Rao

  • Letter |

    Variation among RNA transcript isoforms can be generated from alternative start and polyadenylation sites, and results in RNAs and proteins with different properties being generated from the same genomic sequence; here a new method termed transcript isoform sequencing is described in yeast, and the method allows a fuller exploration of transcriptome diversity across the compact yeast genome.

    • Vicent Pelechano
    • , Wu Wei
    •  & Lars M. Steinmetz

  • Letter |

    A mechanism is proposed for the formation of methane by bacteria, through the cleavage of a highly unreactive carbon–phosphorus bond in methyl phosphonate by PhnJ in the bacterial C–P lyase complex.

    • Siddhesh S. Kamat
    • , Howard J. Williams
    • , Lawrence J. Dangott
    • , Mrinmoy Chakrabarti
    •  & Frank M. Raushel

  • Letter |

    The crystal structure of β-arrestin-1 in complex with a fully phosphorylated 29-amino-acid carboxy-terminal peptide derived from the V2 vasopressin receptor is reported; the structure of the complex shows striking conformational differences in β-arrestin-1 when compared with its inactive conformation.

    • Arun K. Shukla
    • , Aashish Manglik
    • , Andrew C. Kruse
    • , Kunhong Xiao
    • , Rosana I. Reis
    • , Wei-Chou Tseng
    • , Dean P. Staus
    • , Daniel Hilger
    • , Serdar Uysal
    • , Li-Yin Huang
    • , Marcin Paduch
    • , Prachi Tripathi-Shukla
    • , Akiko Koide
    • , Shohei Koide
    • , William I. Weis
    • , Anthony A. Kossiakoff
    • , Brian K. Kobilka
    •  & Robert J. Lefkowitz

  • Letter |

    The crystal structure of arrestin-1 is reported, in which the activation step is mimicked by C-tail truncation; the structure of this pre-activated arrestin is markedly different from the basal state and gives an insight into the activation mechanism.

    • Yong Ju Kim
    • , Klaus Peter Hofmann
    • , Oliver P. Ernst
    • , Patrick Scheerer
    • , Hui-Woog Choe
    •  & Martha E. Sommer

Feature

  • Feature |

    With careful planning and tuned expectations, researchers can supplement their project support with donations from the public.

    • Karen Kaplan

Q&A

  • Q&A |

    Microbiologist changes career paths and learns the nuances of microscopy and management.

    • Katharine Sanderson

Futures

  • Futures |

    Reports from the battlefield.

    • Vaughan Stanger
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