Volume 504 Issue 7480, 19 December 2013

In Nature Ten� we take stock of the highs, lows and newsmakers of the past twelve months as part of our year-end round up of 2013. Image: Bryan Christie Design/PHOTODISC.

Editorial

  • Editorial |

    In the public interest, the Italian health minister should resolve the ongoing uncertainty over a government trial of a controversial therapy.

  • Editorial |

    A rethink on monitoring land-use change is needed to estimate effects on global warming.

  • Editorial |

    Can you tell a sci-fi tale in just 200 characters? Then the Nature Futures competition is for you.

World View

  • World View |

    The revelation that US and British spy agencies have undermined a commonly used encryption code should alarm researchers, says Charles Arthur.

    • Charles Arthur

Research Highlights

Seven Days

  • Seven Days |

    The week in science: China lands rover on the Moon, Israel joins CERN, and the number of animals used for scientific purposes in the European Union falls.

News

  • News |

    Failure to impose a ban on deep-sea fishing jeopardizes the future of vulnerable ecosystems, say researchers.

    • Daniel Cressey
  • News |

    Researchers ponder whether Eastern Europe’s large areas of abandoned land should be replanted or left as a carbon sink.

    • Quirin Schiermeier
  • News |

    Foundations increasingly fund biomedical research, but are reluctant to pay overhead costs.

    • Sara Reardon
  • News |

    From the US shutdown to breakthroughs in stem-cell therapies, the past 12 months have seen fluctuating fortunes for science.

    • Richard Van Noorden
    • , Jeff Tollefson
    • , Erika Check Hayden
    • , Lauren Morello
    • , Helen Shen
    • , Declan Butler
    • , Heidi Ledford
    • , Alexandra Witze
    • , Eugenie Samuel Reich
    • , Quirin Schiermeier
    •  & David Cyranoski

News Feature

Comment

Books & Arts

  • Books & Arts |

    Harold McGee surveys a seething array of microbially transformed treats — from beard beer and grasshopper sauce to extreme herring and armpit cheese.

    • Harold McGee
  • Books & Arts |

    Melanie Keene revisits two Victorian children's science primers that harnessed interest in the supernatural.

    • Melanie Keene

Correspondence

Obituary

News & Views

  • News & Views |

    The thermal history of thousands of rock samples convincingly confirms the idea that climate cooling accelerates the rate of erosion at Earth's surface — and implicates glaciers in particular. See Letter p.423

    • David Lundbek Egholm
  • News & Views |

    Large panels of human cancer cell lines have been profiled at the DNA, RNA and pharmacological levels to accelerate the search for cancer therapies. But two of those large data sets show only partial concordance. See Analysis p.389

    • John N. Weinstein
    •  & Philip L. Lorenzi
  • News & Views |

    A marriage between satellite observations and modelling has shown that acceleration of electrons in the magnetosphere can be explained by scattering of these particles by plasma oscillations known as chorus waves. See Letter p.411

    • Mary K. Hudson
  • News & Views |

    The discovery of a protein that is targeted for degradation by the 'witch' hormones called strigolactones reveals a mechanism by which shoot architecture is controlled in rice plants. See Articles p.401 & p.406

    • Steven M. Smith

Analysis

  • Analysis |

    This Analysis compares two large-scale pharmacogenomic data sets that catalogued the sensitivity of a large number of cancer cell lines to approved and potential drugs, and finds that whereas the gene expression data are largely concordant between the two studies, the reported drug sensitivity measures and subsequently their association with genomic features are highly discordant.

    • Benjamin Haibe-Kains
    • , Nehme El-Hachem
    • , Nicolai Juul Birkbak
    • , Andrew C. Jin
    • , Andrew H. Beck
    • , Hugo J. W. L. Aerts
    •  & John Quackenbush

Article

  • Article |

    This study describes comprehensive synaptic engulfment by astrocytes, mediating synapse elimination in an activity-dependent manner; this elimination process involves the MEGF10 and MERTK phagocytic pathways and persists into adulthood, with mutant mice that lack these pathways in astrocytes exhibiting a failure to refine retinogeniculate connections during development.

    • Won-Suk Chung
    • , Laura E. Clarke
    • , Gordon X. Wang
    • , Benjamin K. Stafford
    • , Alexander Sher
    • , Chandrani Chakraborty
    • , Julia Joung
    • , Lynette C. Foo
    • , Andrew Thompson
    • , Chinfei Chen
    • , Stephen J. Smith
    •  & Ben A. Barres
  • Article |

    Strigolactones (SLs), key regulators of plant growth, are believed to mediate their responses through a proposed receptor (D14) that interacts with an F-box protein (D3) to form a D14–SCFD3 protein complex; here the perception of SLs by the D14–SCFD3 complex and the control of gene expression are linked by the finding that DWARF 53, a repressor protein of SL signalling, interacts with the D14–SCFD3 complex and is ubiquitinated and degraded in a SL-dependent manner.

    • Liang Jiang
    • , Xue Liu
    • , Guosheng Xiong
    • , Huihui Liu
    • , Fulu Chen
    • , Lei Wang
    • , Xiangbing Meng
    • , Guifu Liu
    • , Hong Yu
    • , Yundong Yuan
    • , Wei Yi
    • , Lihua Zhao
    • , Honglei Ma
    • , Yuanzheng He
    • , Zhongshan Wu
    • , Karsten Melcher
    • , Qian Qian
    • , H. Eric Xu
    • , Yonghong Wang
    •  & Jiayang Li
  • Article |

    Strigolactones (SLs), key regulators of plant growth, are believed to mediate their responses through a proposed receptor (D14) that interacts with an F-box protein (D3) to form a D14–SCFD3 protein complex; here the perception of SLs by the D14–SCFD3 complex and the control of gene expression are linked by the finding that DWARF 53, a repressor protein of SL function, interacts with the D14–SCFD3 complex and is ubiquitinated and degraded in a SL-dependent manner.

    • Feng Zhou
    • , Qibing Lin
    • , Lihong Zhu
    • , Yulong Ren
    • , Kunneng Zhou
    • , Nitzan Shabek
    • , Fuqing Wu
    • , Haibin Mao
    • , Wei Dong
    • , Lu Gan
    • , Weiwei Ma
    • , He Gao
    • , Jun Chen
    • , Chao Yang
    • , Dan Wang
    • , Junjie Tan
    • , Xin Zhang
    • , Xiuping Guo
    • , Jiulin Wang
    • , Ling Jiang
    • , Xi Liu
    • , Weiqi Chen
    • , Jinfang Chu
    • , Cunyu Yan
    • , Kotomi Ueno
    • , Shinsaku Ito
    • , Tadao Asami
    • , Zhijun Cheng
    • , Jie Wang
    • , Cailin Lei
    • , Huqu Zhai
    • , Chuanyin Wu
    • , Haiyang Wang
    • , Ning Zheng
    •  & Jianmin Wan

Letter

  • Letter |

    High-resolution measurements of electrons obtained by satellite during the geomagnetic storm of 9 October 2012 together with a data-driven global wave model are analysed to show that scattering by a magnetospheric electromagnetic emission, known as ‘chorus’, can explain the temporal evolution of the observed increase in relativistic electron flux.

    • R. M. Thorne
    • , W. Li
    • , B. Ni
    • , Q. Ma
    • , J. Bortnik
    • , L. Chen
    • , D. N. Baker
    • , H. E. Spence
    • , G. D. Reeves
    • , M. G. Henderson
    • , C. A. Kletzing
    • , W. S. Kurth
    • , G. B. Hospodarsky
    • , J. B. Blake
    • , J. F. Fennell
    • , S. G. Claudepierre
    •  & S. G. Kanekal
  • Letter |

    Engineered dissipation is used to deterministically produce and stabilize entanglement between two trapped-ion quantum bits, independently of their initial states; the entanglement is stabilized even in the presence of experimental noise and decoherence.

    • Y. Lin
    • , J. P. Gaebler
    • , F. Reiter
    • , T. R. Tan
    • , R. Bowler
    • , A. S. Sørensen
    • , D. Leibfried
    •  & D. J. Wineland
  • Letter |

    An entangled Bell state of two superconducting quantum bits can be stabilized for an arbitrary time using an autonomous feedback scheme, that is, one that does not require a complicated external error-correcting feedback loop.

    • S. Shankar
    • , M. Hatridge
    • , Z. Leghtas
    • , K. M. Sliwa
    • , A. Narla
    • , U. Vool
    • , S. M. Girvin
    • , L. Frunzio
    • , M. Mirrahimi
    •  & M. H. Devoret
  • Letter |

    To establish what effect the Late Cenozoic cooling climate shift might have had on global erosion, inverse modelling of thermochronometric ages is used to show that erosion rates are increased by cooling, especially in glaciated mountain ranges.

    • Frédéric Herman
    • , Diane Seward
    • , Pierre G. Valla
    • , Andrew Carter
    • , Barry Kohn
    • , Sean D. Willett
    •  & Todd A. Ehlers
  • Letter |

    A prospective longitudinal study identifies the earliest known indicator of social disability in human infancy: decline in attention to others’ eyes in infants who are later diagnosed with autism; the decline is evident already within the first 2 to 6 months of life, which reveals the early unfolding of the disorder but also offers a promising opportunity for the future of early intervention.

    • Warren Jones
    •  & Ami Klin

    Special:

  • Letter |

    Two private, heterozygous mutations in two functionally related genes, GUCY1A3 and CCT7, are identified in an extended family with myocardial infarction; these genes encode proteins that work together to inhibit platelet activation after nitric oxide stimulation, suggesting a link between impaired nitric oxide signalling and myocardial infarction risk.

    • Jeanette Erdmann
    • , Klaus Stark
    • , Ulrike B. Esslinger
    • , Philipp Moritz Rumpf
    • , Doris Koesling
    • , Cor de Wit
    • , Frank J. Kaiser
    • , Diana Braunholz
    • , Anja Medack
    • , Marcus Fischer
    • , Martina E. Zimmermann
    • , Stephanie Tennstedt
    • , Elisabeth Graf
    • , Sebastian Eck
    • , Zouhair Aherrahrou
    • , Janja Nahrstaedt
    • , Christina Willenborg
    • , Petra Bruse
    • , Ingrid Brænne
    • , Markus M. Nöthen
    • , Per Hofmann
    • , Peter S. Braund
    • , Evanthia Mergia
    • , Wibke Reinhard
    • , Christof Burgdorf
    • , Stefan Schreiber
    • , Anthony J. Balmforth
    • , Alistair S. Hall
    • , Lars Bertram
    • , Elisabeth Steinhagen-Thiessen
    • , Shu-Chen Li
    • , Winfried März
    • , Muredach Reilly
    • , Sekar Kathiresan
    • , Ruth McPherson
    • , Ulrich Walter
    • , Jurg Ott
    • , Nilesh J. Samani
    • , Tim M. Strom
    • , Thomas Meitinger
    • , Christian Hengstenberg
    •  & Heribert Schunkert
  • Letter |

    Two small-molecule disruptors of the glucokinase–glucokinase-regulatory-protein complex, AMG-1694 and AMG-3969, are identified that decrease blood glucose levels in various models of hyperglycaemic rodents.

    • David J. Lloyd
    • , David J. St Jean Jr
    • , Robert J. M. Kurzeja
    • , Robert C. Wahl
    • , Klaus Michelsen
    • , Rod Cupples
    • , Michelle Chen
    • , John Wu
    • , Glenn Sivits
    • , Joan Helmering
    • , Renée Komorowski
    • , Kate S. Ashton
    • , Lewis D. Pennington
    • , Christopher Fotsch
    • , Mukta Vazir
    • , Kui Chen
    • , Samer Chmait
    • , Jiandong Zhang
    • , Longbin Liu
    • , Mark H. Norman
    • , Kristin L. Andrews
    • , Michael D. Bartberger
    • , Gwyneth Van
    • , Elizabeth J. Galbreath
    • , Steven L. Vonderfecht
    • , Minghan Wang
    • , Steven R. Jordan
    • , Murielle M. Véniant
    •  & Clarence Hale
  • Letter |

    This work shows that the Themis protein has a critical role in positive and negative thymocyte selection by dampening responses to low-affinity ligands but without affecting responses to high-affinity ligands, thus enabling positive selection of weakly self-reactive thymocytes.

    • Guo Fu
    • , Javier Casas
    • , Stephanie Rigaud
    • , Vasily Rybakin
    • , Florence Lambolez
    • , Joanna Brzostek
    • , John A. H. Hoerter
    • , Wolfgang Paster
    • , Oreste Acuto
    • , Hilde Cheroutre
    • , Karsten Sauer
    •  & Nicholas R. J. Gascoigne
  • Letter |

    The gut microbial metabolite butyrate is shown to induce the differentiation of colonic T regulatory cells in mice and to ameliorate the development of colitis; it also increases histone H3 acetylation at the Foxp3 promoter.

    • Yukihiro Furusawa
    • , Yuuki Obata
    • , Shinji Fukuda
    • , Takaho A. Endo
    • , Gaku Nakato
    • , Daisuke Takahashi
    • , Yumiko Nakanishi
    • , Chikako Uetake
    • , Keiko Kato
    • , Tamotsu Kato
    • , Masumi Takahashi
    • , Noriko N. Fukuda
    • , Shinnosuke Murakami
    • , Eiji Miyauchi
    • , Shingo Hino
    • , Koji Atarashi
    • , Satoshi Onawa
    • , Yumiko Fujimura
    • , Trevor Lockett
    • , Julie M. Clarke
    • , David L. Topping
    • , Masaru Tomita
    • , Shohei Hori
    • , Osamu Ohara
    • , Tatsuya Morita
    • , Haruhiko Koseki
    • , Jun Kikuchi
    • , Kenya Honda
    • , Koji Hase
    •  & Hiroshi Ohno
  • Letter |

    In mice, provision of butyrate—a short-chain fatty acid produced by commensal microorganisms during starch fermentation—facilitates extrathymic generation and differentiation of Foxp3+ regulatory T cells, demonstrating that metabolic by-products are sensed by cells of the immune system and affect the balance between pro- and anti-inflammatory cells.

    • Nicholas Arpaia
    • , Clarissa Campbell
    • , Xiying Fan
    • , Stanislav Dikiy
    • , Joris van der Veeken
    • , Paul deRoos
    • , Hui Liu
    • , Justin R. Cross
    • , Klaus Pfeffer
    • , Paul J. Coffer
    •  & Alexander Y. Rudensky
  • Letter |

    The O-glycosylation enzyme Galnt11 has an important role in heterotaxy, a disorder of left–right body patterning or laterality: Galnt11 modulates Notch signalling which alters cilia types at the embryonic left–right organizer, therefore determining laterality.

    • Marko T. Boskovski
    • , Shiaulou Yuan
    • , Nis Borbye Pedersen
    • , Christoffer Knak Goth
    • , Svetlana Makova
    • , Henrik Clausen
    • , Martina Brueckner
    •  & Mustafa K. Khokha
  • Letter |

    This study establishes an important role for the enzyme Tet1 in erasing genomic imprinting in vivo — mice with a knockout of paternal Tet1 give rise to progeny with imprinting defects and associated growth and development defects, which leads to early embryonic lethality; furthermore, analysis of the DNA methylation dynamics in reprogramming primordial germ cells (PGCs) suggests that Tet1 is required at a late stage of the reprogramming process, in the second wave of DNA demethylation in PGCs.

    • Shinpei Yamaguchi
    • , Li Shen
    • , Yuting Liu
    • , Damian Sendler
    •  & Yi Zhang
  • Letter |

    During mammalian X-chromosome inactivation, the Xist long noncoding RNA coats the future inactive X chromosome and recruits polycomb repressive complex 2 to a nucleation site, but how Xist spreads silencing across the entire X chromosome is unclear; here high-resolution maps of Xist binding sites across the X chromosome are generated and show that Xist does not spread across the inactive X chromosome uniformly but in two steps, initially targeting gene-rich islands before later spreading to intervening gene-poor domains.

    • Matthew D. Simon
    • , Stefan F. Pinter
    • , Rui Fang
    • , Kavitha Sarma
    • , Michael Rutenberg-Schoenberg
    • , Sarah K. Bowman
    • , Barry A. Kesner
    • , Verena K. Maier
    • , Robert E. Kingston
    •  & Jeannie T. Lee

Retraction

Corrigendum

Feature

Career Brief

  • Career Brief |

    Dearth of high-ranking women in UK academia misrepresents faculty members and students, says report.

  • Career Brief |

    Basic research increasingly targets societal outcomes, finds study.

  • Career Brief |

    Professors are entitled to speak out and publish on social media, argues report.

Futures

Outlook

  • Outlook |

    Increased understanding of immune- and tumour-cell biology has led to an explosion of research into potential ways to harness the immune system to kill cancer. By Emily Elert.

    • Emily Elert
  • Outlook |

    William Coley found a way to prompt the immune system to fight cancer over a century ago. After years of neglect, scientists are now seeking to replicate his success.

    • Sarah DeWeerdt
  • Outlook |

    Tumours can put a brake on the immune system, but new therapies work by removing these brakes. Now, researchers have to figure out how to use them most effectively.

    • Karen Weintraub
  • Outlook |

    Immunologist Karolina Palucka, at the Baylor Institute for Immunology Research in Dallas, Texas, helped treat Nobel prizewinner Ralph Steinman's pancreatic cancer with dendritic cells — the cells he co-discovered. Here she explains the use of dendritic cells in cancer immunotherapy.

    • Karolina Palucka
  • Outlook |

    Using a variety of creative imaging techniques, researchers are tracking the dynamic interactions of immune and cancer cells. Their results will guide drug development.

    • Katherine Bourzac
  • Outlook |

    An experimental vaccine implanted beneath the skin could usher in biomaterial-based immunotherapies for cancer.

    • Elie Dolgin

Nature Outlook

  • Nature Outlook |

    Cancer immunotherapy

    A groundswell of research on the immune system is yielding a deeper understanding of how cancer progresses and offering new ways to stop it. As a result of these efforts, a range of cancer therapies are under development that work by turning our own immune cells against tumours.

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