Volume 528 Issue 7580, 3 December 2015

Tough growing conditions in polluted ground in Dhaka, Bangladesh, 4 November 2013. This issue of Nature � in recognition of what the UN Food and Agriculture Organization has designated the International Year of Soils � presents a series of Perspectives that discuss the make-up and functions of soils, their influence on the environment and human health, and how sustainable soil management might be achieved in the future. In a Comment piece, Luca Montanarella makes the case for a voluntary international agreement to protect soils worldwide. All four articles are part of ‘Soil and its sustainability� (www.nature.com/soils), a collection of articles related to soil research published in Nature Publishing Group journals during the past year. Cover: Mehedi Hasan/Demotix/Corbis

Editorial

  • Editorial |

    The number of people with science doctorates is rapidly increasing, but there are not enough academic jobs for them all. Graduate programmes should be reformed to meet students’ needs.

  • Editorial |

    Research has a part to play in identifying the factors that breed terrorism.

  • Editorial |

    Scientific innovation is being smothered by a culture of conformity.

World View

Research Highlights

Social Selection

Seven Days

News

News Feature

  • News Feature |

    There are too many PhD students for too few academic jobs — but with imagination, the problem could be solved.

    • Julie Gould
  • News Feature |

    Researchers want to wire the human body with sensors that could harvest reams of data — and transform health care.

    • Elizabeth Gibney

Comment

  • Comment |

    Extracting carbon, nitrogen and phosphorus from wastewater could generate resources and save energy, say Wen-Wei Li, Han-Qing Yu and Bruce E. Rittmann.

    • Wen-Wei Li
    • , Han-Qing Yu
    •  & Bruce E. Rittmann

Books & Arts

  • Books & Arts |

    Andrew Robinson examines three books that see seismicity as both grimly destructive and, in some contexts, culturally energizing.

    • Andrew Robinson
  • Books & Arts |

    Anthony King reviews an exhibition on the horror, and hope, posed by trauma.

    • Anthony King

Correspondence

Obituary

  • Obituary |

    Historian of science who chaired pioneering embryology regulator.

    • Anthony Grafton

News & Views

  • News & Views |

    Breakthrough calculations of collisions between two helium nuclei pave the way to a quantitative understanding of how the elements carbon and oxygen were made in stars — and to improved models of stellar evolution. See Letter p.111

    • Sofia Quaglioni
  • News & Views |

    Analysis of the temperature ranges occupied by marine species finds that the vulnerability of ecological communities to global warming may depend more on organismal physiology than on the magnitude of change. See Article p.88

    • Derek P. Tittensor
  • News & Views |

    Immune cells called regulatory T cells accumulate in fat during ageing. The anti-inflammatory activity of these cells worsens age-associated defects in metabolism, in contrast to its effect in obesity. See Letter p.137

    • Ivan Maillard
    •  & Alan R. Saltiel
  • News & Views |

    One hundred years after the first description of viruses that infect bacterial cells, the contribution of these bacteriophages to fundamental biology, biotechnology and human health continues unabated and deserves celebration.

    • Forest Rohwer
    •  & Anca M. Segall
  • News & Views |

    A property called entanglement entropy helps to describe the quantum states of interacting particles, and it has at last been measured. The findings open the door to a deeper understanding of quantum systems. See Article p.77

    • Steven Rolston
  • News & Views |

    The discovery of microtube structures that link tumour cells in some invasive brain tumours reveals how these cancers spread, and how they resist treatment. See Article p.93

    • Harald Sontheimer

Perspective

  • Perspective |

    Careful management of nitrogen fertilizer usage is required to ensure world food security while limiting environmental degradation; an analysis of historical nitrogen use efficiency reveals socio-economic factors and technological innovations that have influenced a range of past national trends and that suggest ways to improve global food production and environmental stewardship by 2050.

    • Xin Zhang
    • , Eric A. Davidson
    • , Denise L. Mauzerall
    • , Timothy D. Searchinger
    • , Patrice Dumas
    •  & Ye Shen
  • Perspective |

    Instead of containing stable and chemically unique ‘humic substances’, as has been widely accepted, soil organic matter is a mixture of progressively decomposing organic compounds; this has broad implications for soil science and its applications.

    • Johannes Lehmann
    •  & Markus Kleber

Article

  • Article |

    Entanglement, which describes non-local correlations between quantum objects, is very difficult to measure, especially in systems of itinerant particles; here spatial entanglement is measured for ultracold bosonic atoms in optical lattices.

    • Rajibul Islam
    • , Ruichao Ma
    • , Philipp M. Preiss
    • , M. Eric Tai
    • , Alexander Lukin
    • , Matthew Rispoli
    •  & Markus Greiner

Analysis

  • Analysis |

    In panels of cancer cell lines analysed for their response to drug libraries, some studies have proposed distinct pharmacological sensitivities for some cell lines while other studies have not seen the same trends; here the data in the Cancer Cell Line Encyclopedia and the Genomics of Drug Sensitivity in Cancer are reassessed, and the authors report a stronger degree of concordance between the two data sets than that in a previous study.

    • Nicolas Stransky
    • , Mahmoud Ghandi
    • , Gregory V. Kryukov
    • , Levi A. Garraway
    • , Joseph Lehár
    • , Manway Liu
    • , Dmitriy Sonkin
    • , Audrey Kauffmann
    • , Kavitha Venkatesan
    • , Elena J. Edelman
    • , Markus Riester
    • , Jordi Barretina
    • , Giordano Caponigro
    • , Robert Schlegel
    • , William R. Sellers
    • , Frank Stegmeier
    • , Michael Morrissey
    • , Arnaud Amzallag
    • , Iulian Pruteanu-Malinici
    • , Daniel A. Haber
    • , Sridhar Ramaswamy
    • , Cyril H. Benes
    • , Michael P. Menden
    • , Francesco Iorio
    • , Michael R. Stratton
    • , Ultan McDermott
    • , Mathew J. Garnett
    •  & Julio Saez-Rodriguez

Article

  • Article |

    How marine communities will respond to climate change depends on the thermal sensitivities of existing communities; existing reef communities do not show a perfect fit between current temperatures and the thermal niches of the species within them and this thermal bias is a major contributor to projected local species loss.

    • Rick D. Stuart-Smith
    • , Graham J. Edgar
    • , Neville S. Barrett
    • , Stuart J. Kininmonth
    •  & Amanda E. Bates
  • Article |

    Brain tumours are difficult to treat because of their propensity to infiltrate brain tissue; here long processes, or tumour microtubes, extended by astrocytomas are shown to promote brain infiltration and to create an interconnected network that enables multicellular communication and that protects the tumours from radiotherapy-induced cell death, suggesting that disruption of the network could be a new therapeutic approach.

    • Matthias Osswald
    • , Erik Jung
    • , Felix Sahm
    • , Gergely Solecki
    • , Varun Venkataramani
    • , Jonas Blaes
    • , Sophie Weil
    • , Heinz Horstmann
    • , Benedikt Wiestler
    • , Mustafa Syed
    • , Lulu Huang
    • , Miriam Ratliff
    • , Kianush Karimian Jazi
    • , Felix T. Kurz
    • , Torsten Schmenger
    • , Dieter Lemke
    • , Miriam Gömmel
    • , Martin Pauli
    • , Yunxiang Liao
    • , Peter Häring
    • , Stefan Pusch
    • , Verena Herl
    • , Christian Steinhäuser
    • , Damir Krunic
    • , Mostafa Jarahian
    • , Hrvoje Miletic
    • , Anna S. Berghoff
    • , Oliver Griesbeck
    • , Georgios Kalamakis
    • , Olga Garaschuk
    • , Matthias Preusser
    • , Samuel Weiss
    • , Haikun Liu
    • , Sabine Heiland
    • , Michael Platten
    • , Peter E. Huber
    • , Thomas Kuner
    • , Andreas von Deimling
    • , Wolfgang Wick
    •  & Frank Winkler
  • Article |

    Using experimental proteomics and modelling in E. coli, the amount of protein needed to run respiration (per ATP produced) is shown to be twice as much as that needed to run fermentation; results demonstrate that overflow metabolism (known as the Warburg effect in cancer cells) is a necessary outcome of optimal bacterial growth, governed by a global resource allocation program, and that the methodology is directly applicable to synthetic biology and cancer research.

    • Markus Basan
    • , Sheng Hui
    • , Hiroyuki Okano
    • , Zhongge Zhang
    • , Yang Shen
    • , James R. Williamson
    •  & Terence Hwa

Letter

  • Letter |

    In the local Universe, the census of all observed baryons falls short of the estimated number by a factor of two, and simulations have indicated that the missing baryons reside throughout the filaments of the cosmic web; X-ray observations of filamentary structures associated with the galaxy cluster Abell 2744 now find that 5 to 10 per cent of the filament mass is in the form of baryonic gas.

    • Dominique Eckert
    • , Mathilde Jauzac
    • , HuanYuan Shan
    • , Jean-Paul Kneib
    • , Thomas Erben
    • , Holger Israel
    • , Eric Jullo
    • , Matthias Klein
    • , Richard Massey
    • , Johan Richard
    •  & Céline Tchernin
  • Letter |

    Persistent low-velocity baryonic jets have been detected from a supersoft X-ray source; the low velocity suggests that these jets have not been launched from a white dwarf, and the persistence speaks against the origin being a canonical black hole or neutron star, indicating that a different type of source must be implicated.

    • Ji-Feng Liu
    • , Yu Bai
    • , Song Wang
    • , Stephen Justham
    • , You-Jun Lu
    • , Wei-Min Gu
    • , Qing-Zhong Liu
    • , Rosanne Di Stefano
    • , Jin-Cheng Guo
    • , Antonio Cabrera-Lavers
    • , Pedro Álvarez
    • , Yi Cao
    •  & Shri Kulkarni
  • Letter |

    An ab initio calculation of alpha–alpha scattering is described for which the number of computational operations scales approximately quadratically with particle number and which uses lattice Monte Carlo simulations and lattice effective field theory, combined with the adiabatic projection method to reduce the eight-body system to a two-cluster system.

    • Serdar Elhatisari
    • , Dean Lee
    • , Gautam Rupak
    • , Evgeny Epelbaum
    • , Hermann Krebs
    • , Timo A. Lähde
    • , Thomas Luu
    •  & Ulf-G. Meißner
  • Letter |

    Recent work has suggested that sections of the West Antarctic ice sheet are already rapidly retreating, raising concerns about increased sea-level rise; now, an ice-sheet model is used to simulate the mass loss from the entire Antarctic ice sheet to 2200, suggesting that it could contribute up to 30 cm of sea-level rise by 2100 and 72 cm by 2200, but is unlikely to contribute more.

    • Catherine Ritz
    • , Tamsin L. Edwards
    • , Gaël Durand
    • , Antony J. Payne
    • , Vincent Peyaud
    •  & Richard C. A. Hindmarsh
  • Letter |

    It has been suggested that carbon starvation, owing to reduced availability of non-structural carbohydrates (NSCs), is an important contributor to tree mortality during drought in tropical rainforests; however, data from the world’s longest-running experimental drought study presented here show no evidence of carbon starvation, and instead the researchers conclude that impaired water hydraulic processes (involving the transport of water from soil to leaf) have a more important role in triggering tree death from long-term drought.

    • L. Rowland
    • , A. C. L. da Costa
    • , D. R. Galbraith
    • , R. S. Oliveira
    • , O. J. Binks
    • , A. A. R. Oliveira
    • , A. M. Pullen
    • , C. E. Doughty
    • , D. B. Metcalfe
    • , S. S. Vasconcelos
    • , L. V. Ferreira
    • , Y. Malhi
    • , J. Grace
    • , M. Mencuccini
    •  & P. Meir
  • Letter |

    Genetic correction of MeCP2 levels largely reversed the behavioural, molecular and physiological deficits associated with MECP2 duplication syndrome in a transgenic mouse model; similarly, reduction of MeCP2 levels using an antisense oligonucleotide strategy resulted in phenotypic rescue in adult transgenic mice, and dose-dependently corrected MeCP2 levels in cells from patients with MECP2 duplication.

    • Yehezkel Sztainberg
    • , Hong-mei Chen
    • , John W. Swann
    • , Shuang Hao
    • , Bin Tang
    • , Zhenyu Wu
    • , Jianrong Tang
    • , Ying-Wooi Wan
    • , Zhandong Liu
    • , Frank Rigo
    •  & Huda Y. Zoghbi
  • Letter |

    Inhibitory antibodies to two specific human and mouse Notch ligands, Jagged1 and Jagged2, are generated and shown to have beneficial effects in a goblet cell metaplasia asthma model; systemic Jagged1 inhibition transdifferentiates secretory cells into ciliated cells in the mouse, demonstrating that Jagged1 from ciliated cells normally holds back secretory cells to adopt the ciliated fate.

    • Daniel Lafkas
    • , Amy Shelton
    • , Cecilia Chiu
    • , Gladys de Leon Boenig
    • , Yongmei Chen
    • , Scott S. Stawicki
    • , Christian Siltanen
    • , Mike Reichelt
    • , Meijuan Zhou
    • , Xiumin Wu
    • , Jeffrey Eastham-Anderson
    • , Heather Moore
    • , Meron Roose-Girma
    • , Yvonne Chinn
    • , Julie Q. Hang
    • , Søren Warming
    • , Jackson Egen
    • , Wyne P. Lee
    • , Cary Austin
    • , Yan Wu
    • , Jian Payandeh
    • , John B. Lowe
    •  & Christian W. Siebel
  • Letter |

    Regulatory T cells need to express a diverse T-cell-receptor repertoire to control pathogenic self-reactive T cells; here it is shown that repertoire diversification depends on the intronic Foxp3 enhancer CNS3 acting at the regulatory T-cell-precursor stage to induce T-cell-receptor responsiveness to low-strength signals.

    • Yongqiang Feng
    • , Joris van der Veeken
    • , Mikhail Shugay
    • , Ekaterina V. Putintseva
    • , Hatice U. Osmanbeyoglu
    • , Stanislav Dikiy
    • , Beatrice E. Hoyos
    • , Bruno Moltedo
    • , Saskia Hemmers
    • , Piper Treuting
    • , Christina S. Leslie
    • , Dmitriy M. Chudakov
    •  & Alexander Y. Rudensky
  • Letter |

    Fat-resident regulatory T cells (fTreg cells) accumulate in adipose tissue of mice as a function of age, but not obesity; mice without fTreg cells are protected against age-associated insulin resistance, but remain susceptible to obesity-associated insulin resistance and metabolic disease, indicating different aetiologies of age-associated versus obesity-associated insulin resistance.

    • Sagar P. Bapat
    • , Jae Myoung Suh
    • , Sungsoon Fang
    • , Sihao Liu
    • , Yang Zhang
    • , Albert Cheng
    • , Carmen Zhou
    • , Yuqiong Liang
    • , Mathias LeBlanc
    • , Christopher Liddle
    • , Annette R. Atkins
    • , Ruth T. Yu
    • , Michael Downes
    • , Ronald M. Evans
    •  & Ye Zheng
  • Letter |

    A large-scale enhancer complementation assay assessing the activating or repressing contributions of over 800 Drosophila transcription factors and cofactors to combinatorial enhancer control reveals a more complex picture than expected, with many factors having diverse regulatory functions that depend on the enhancer context.

    • Gerald Stampfel
    • , Tomáš Kazmar
    • , Olga Frank
    • , Sebastian Wienerroither
    • , Franziska Reiter
    •  & Alexander Stark

Corrigendum

  • Corrigendum |

    • Supriya K. Saha
    • , Christine A. Parachoniak
    • , Krishna S. Ghanta
    • , Julien Fitamant
    • , Kenneth N. Ross
    • , Mortada S. Najem
    • , Sushma Gurumurthy
    • , Esra A. Akbay
    • , Daniela Sia
    • , Helena Cornella
    • , Oriana Miltiadous
    • , Chad Walesky
    • , Vikram Deshpande
    • , Andrew X. Zhu
    • , Aram F. Hezel
    • , Katharine E. Yen
    • , Kimberly S. Straley
    • , Jeremy Travins
    • , Janeta Popovici-Muller
    • , Camelia Gliser
    • , Cristina R. Ferrone
    • , Udayan Apte
    • , Josep M. Llovet
    • , Kwok-Kin Wong
    • , Sridhar Ramaswamy
    •  & Nabeel Bardeesy
  • Corrigendum |

    • Matthew H. Alford
    • , Thomas Peacock
    • , Jennifer A. MacKinnon
    • , Jonathan D. Nash
    • , Maarten C. Buijsman
    • , Luca R. Centurioni
    • , Shenn-Yu Chao
    • , Ming-Huei Chang
    • , David M. Farmer
    • , Oliver B. Fringer
    • , Ke-Hsien Fu
    • , Patrick C. Gallacher
    • , Hans C. Graber
    • , Karl R. Helfrich
    • , Steven M. Jachec
    • , Christopher R. Jackson
    • , Jody M. Klymak
    • , Dong S. Ko
    • , Sen Jan
    • , T. M. Shaun Johnston
    • , Sonya Legg
    • , I-Huan Lee
    • , Ren-Chieh Lien
    • , Matthieu J. Mercier
    • , James N. Moum
    • , Ruth Musgrave
    • , Jae-Hun Park
    • , Andrew I. Pickering
    • , Robert Pinkel
    • , Luc Rainville
    • , Steven R. Ramp
    • , Daniel L. Rudnick
    • , Sutanu Sarkar
    • , Alberto Scotti
    • , Harper L. Simmons
    • , Louis C. St Laurent
    • , Subhas K. Venayagamoorthy
    • , Yu-Huai Wang
    • , Joe Wang
    • , Yiing J. Yang
    • , Theresa Paluszkiewicz
    •  & Tswen-Yung (David) Tang

Toolbox

  • Toolbox |

    Scientific publishers are forging links with an organization that wants scientists to scribble comments over online research papers.

    • Jeffrey M. Perkel

    Collection:

Correction

Column

  • Column |

    Postdocs need a level of autonomy to get the best out of their position, say Viviane Callier and Jessica Polka.

    • Viviane Callier
    •  & Jessica Polka

News

Futures

Outlook

  • Outlook |

    Genome editing uses enzymes that are targeted to sequences of DNA to make cuts. These cuts are then repaired by the cell's machinery. This technology allows scientists to disrupt or modify genes with unprecedented precision. By Amy Maxmen, infographic by Denis Mallet.

    • Amy Maxmen
  • Outlook |

    Scientists now have several tools to edit the genomes of living organisms. One of the most recent is revolutionizing research and has thrust two of its creators into the limelight.

    • Zoë Corbyn
  • Outlook |

    Genome-editing presents many opportunities. But the advent of human-germline editing brings urgency to ethical discussions, says Jennifer Doudna.

    • Jennifer Doudna
  • Outlook |

    Rather than emphasize risks that are not entirely new, talks about germline editing should focus more on the benefits, argues George Church.

    • George Church
  • Outlook |

    Although yet to complete clinical trials, genome editing has already shown promise against a globally important disease.

    • Michael Eisenstein
  • Outlook |

    The first therapeutics based on genome-editing tools will treat diseases caused by single genes, but many other factors dictate what is currently possible.

    • Virginia Gewin
  • Outlook |

    Epigeneticists are harnessing genome-editing technologies to tackle a central question hanging over the community — does their field matter?

    • Heidi Ledford
  • Outlook |

    Tim Lu's synthetic-biology research at Massachusetts Institute of Technology in Cambridge combines biological engineering with electronics and computer science to create bacteria that make structural proteins containing tiny semi-conductors called quantum dots. He explains how genome-editing techniques are furthering his research and their role in treating disease.

    • Will Tauxe
  • Outlook |

    Genome editing allows much smaller changes to be made to DNA compared with conventional genetic engineering. In terms of agriculture, this might win over public and regulator opinion.

    • Claire Ainsworth
  • Outlook |

    Despite the popularity of genome-editing techniques, researchers are still grappling with the known unknowns of the technologies. Here are four of their most pressing questions.

    • Will Tauxe

Supplement

Collections

  • Collection |

    Infectious disease control and elimination: Modelling the impact of improved diagnostics

    Diagnostic technologies play a pivotal part in understanding and addressing the burden of infectious diseases. The Diagnostics Modelling Consortium was established in 2013 to facilitate the integration of diagnostic data into models of disease transmission dynamics. In this supplement, the Consortium and its partners report on the latest research outcomes across several major diseases. The outputs demonstrate that improved, well-considered diagnostics could support the elimination of multiple diseases in the field.

  • Nature Outlook |

    Genome editing

    The term genetic engineering has been around since the 1970s, but it is only in the past few years that researchers have developed the tools to allow them to engineer the genome with the precision that they had originally envisaged. As scientists come together this December to discuss editing the human germ line, this Nature Outlooklooks at the risks and benefits of genome editing.

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