Table of Contents

Volume 510 Number 7505 pp312-436

19 June 2014

About the cover

Water droplets cooling rapidly in vacuum are probed by an intense pulse from a femtosecond X-ray laser before they turn to ice, providing Jonas Sellberg et al. with unique structural information on the deeply supercooled liquid phase in the so-called ‘no-man’s land’, where water’s anomalous properties become strongly enhanced, but where ice forms too quickly for normal measurement techniques to cope. In a second paper Jeremy Palmer et al. explore water in this regime with advanced simulation methods, finding a phase transition between two structurally distinct liquids that could explain many water anomalies. Cover: Gregory Stewart, SLAC National Accelerator Laboratory.

This Week

Editorials

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  • Present danger

    There is much hype about predicting and preventing future pandemics, but not enough is being done about a threat sitting under our noses.

  • Quanundrum

    Does reality exist? Fifty years on, Bell’s theorem still divides (and confuses) physicists.

  • Summer skills

    A fledgling neuroscience programme is a rare beacon of research excellence in Romania.

World View

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Seven Days

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  • Seven days: 13–19 June 2014

    The week in science: Chile axes giant hydroelectric dams; calls to dismantle RIKEN’s centre for developmental biology; and Europe’s medicines agency frees data on drug trials.

News in Focus

Features

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  • Scientific publishing: The inside track

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    Members of the US National Academy of Sciences have long enjoyed a privileged path to publication in the body's prominent house journal. Meet the scientists who use it most heavily.

    • Peter Aldhous

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  • Stem cells: Taking a stand against pseudoscience

    Elena Cattaneo and Gilberto Corbellini are among the academics working to protect patients from questionable stem-cell therapies. Here, they share their experiences and opinions of the long, hard fight for evidence to prevail.

  • Regulation: Sell help not hope

    Stem cells are being used as a wedge in calls to allow unproven medical interventions onto the market, warn Paolo Bianco and Douglas Sipp.

Books and Arts

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  • Evolution: The complexity chronicles

    Nancy Moran enjoys a treatise on symbiosis — the intimate association of species that transformed life and Earth.

    • Review of One Plus One Equals One: Symbiosis and the Evolution of Complex Life
      John Archibald

Correspondence

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Careers

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Futures

research

Articles

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  • The genome of Eucalyptus grandisOpen

    • Alexander A. Myburg
    • Dario Grattapaglia
    • Gerald A. Tuskan
    • Uffe Hellsten
    • Richard D. Hayes
    • Jane Grimwood
    • Jerry Jenkins
    • Erika Lindquist
    • Hope Tice
    • Diane Bauer
    • David M. Goodstein
    • Inna Dubchak
    • Alexandre Poliakov
    • Eshchar Mizrachi
    • Anand R. K. Kullan
    • Steven G. Hussey
    • Desre Pinard
    • Karen van der Merwe
    • Pooja Singh
    • Ida van Jaarsveld
    • Orzenil B. Silva-Junior
    • Roberto C. Togawa
    • Marilia R. Pappas
    • Danielle A. Faria
    • Carolina P. Sansaloni
    • Cesar D. Petroli
    • Xiaohan Yang
    • Priya Ranjan
    • Timothy J. Tschaplinski
    • Chu-Yu Ye
    • Ting Li
    • Lieven Sterck
    • Kevin Vanneste
    • Florent Murat
    • Marçal Soler
    • Hélène San Clemente
    • Naijib Saidi
    • Hua Cassan-Wang
    • Christophe Dunand
    • Charles A. Hefer
    • Erich Bornberg-Bauer
    • Anna R. Kersting
    • Kelly Vining
    • Vindhya Amarasinghe
    • Martin Ranik
    • Sushma Naithani
    • Justin Elser
    • Alexander E. Boyd
    • Aaron Liston
    • Joseph W. Spatafora
    • Palitha Dharmwardhana
    • Rajani Raja
    • Christopher Sullivan
    • Elisson Romanel
    • Marcio Alves-Ferreira
    • Carsten Külheim
    • William Foley
    • Victor Carocha
    • Jorge Paiva
    • David Kudrna
    • Sergio H. Brommonschenkel
    • Giancarlo Pasquali
    • Margaret Byrne
    • Philippe Rigault
    • Josquin Tibbits
    • Antanas Spokevicius
    • Rebecca C. Jones
    • Dorothy A. Steane
    • René E. Vaillancourt
    • Brad M. Potts
    • Fourie Joubert
    • Kerrie Barry
    • Georgios J. Pappas
    • Steven H. Strauss
    • Pankaj Jaiswal
    • Jacqueline Grima-Pettenati
    • Jérôme Salse
    • Yves Van de Peer
    • Daniel S. Rokhsar
    • Jeremy Schmutz

    The Eucalyptus grandis genome has been sequenced, revealing the greatest number of tandem duplications of any plant genome sequenced so far, and the highest diversity of genes for specialized metabolites that act as chemical defence and provide unique pharmaceutical oils; genome sequencing of the sister species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding depression.

  • Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

    • Alex K. Shalek
    • Rahul Satija
    • Joe Shuga
    • John J. Trombetta
    • Dave Gennert
    • Diana Lu
    • Peilin Chen
    • Rona S. Gertner
    • Jellert T. Gaublomme
    • Nir Yosef
    • Schraga Schwartz
    • Brian Fowler
    • Suzanne Weaver
    • Jing Wang
    • Xiaohui Wang
    • Ruihua Ding
    • Raktima Raychowdhury
    • Nir Friedman
    • Nir Hacohen
    • Hongkun Park
    • Andrew P. May
    • Aviv Regev

    Large-scale single-cell RNA-seq of stimulated primary mouse bone-marrow-derived dendritic cells highlights positive and negative intercellular signalling pathways that promote and restrain cellular variation.

  • The mitochondrial deubiquitinase USP30 opposes parkin-mediated mitophagy

    • Baris Bingol
    • Joy S. Tea
    • Lilian Phu
    • Mike Reichelt
    • Corey E. Bakalarski
    • Qinghua Song
    • Oded Foreman
    • Donald S. Kirkpatrick
    • Morgan Sheng

    Damaged mitochondria are removed by mitophagy, and defects in mitophagy are linked to Parkinson’s disease; here it is shown that USP30, a deubiquitinase localized to mitochondria, antagonizes mitophagy by removing the ubiquitin tags put in place by Parkin, USP30 inhibition is therefore potentially beneficial for Parkinson’s disease by promoting mitochondrial clearance and quality control.

    See also

Letters

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  • Ultrafast X-ray probing of water structure below the homogeneous ice nucleation temperature

    • J. A. Sellberg
    • C. Huang
    • T. A. McQueen
    • N. D. Loh
    • H. Laksmono
    • D. Schlesinger
    • R. G. Sierra
    • D. Nordlund
    • C. Y. Hampton
    • D. Starodub
    • D. P. DePonte
    • M. Beye
    • C. Chen
    • A. V. Martin
    • A. Barty
    • K. T. Wikfeldt
    • T. M. Weiss
    • C. Caronna
    • J. Feldkamp
    • L. B. Skinner
    • M. M. Seibert
    • M. Messerschmidt
    • G. J. Williams
    • S. Boutet
    • L. G. M. Pettersson
    • M. J. Bogan
    • A. Nilsson

    Femtosecond X-ray laser pulses are used to probe the structure of liquid water in micrometre-sized droplets that have been cooled below the homogeneous ice nucleation temperature, revealing the existence of metastable bulk liquid water down to temperatures of 227kelvin.

  • Metastable liquid–liquid transition in a molecular model of water

    • Jeremy C. Palmer
    • Fausto Martelli
    • Yang Liu
    • Roberto Car
    • Athanassios Z. Panagiotopoulos
    • Pablo G. Debenedetti

    A stable crystal phase and two metastable liquid phases of the ST2 model of water exist at the same deeply supercooled condition, and the two liquids undergo a first-order liquid–liquid transition that meets stringent thermodynamic criteria.

  • Possible control of subduction zone slow-earthquake periodicity by silica enrichment

    • Pascal Audet
    • Roland Bürgmann

    Seismic data from subduction zones that exhibit slow earthquakes reveal that the ratio of compressional-wave to shear-wave velocity of the overriding forearc crust is linearly related to the average recurrence time of slow earthquakes and that this may be associated with quartz enrichment within the forearc crust.

  • mTORC1 controls the adaptive transition of quiescent stem cells from G0 to GAlert

    • Joseph T. Rodgers
    • Katherine Y. King
    • Jamie O. Brett
    • Melinda J. Cromie
    • Gregory W. Charville
    • Katie K. Maguire
    • Christopher Brunson
    • Namrata Mastey
    • Ling Liu
    • Chang-Ru Tsai
    • Margaret A. Goodell
    • Thomas A. Rando

    A mouse study reveals that the stem cell quiescent state is composed of two distinct phases, G0 and GAlert; stem cells reversibly transition between these two phases in response to systemic environmental stimuli acting through the mTORC1 pathway.

  • The metabolite α-ketoglutarate extends lifespan by inhibiting ATP synthase and TOR

    • Randall M. Chin
    • Xudong Fu
    • Melody Y. Pai
    • Laurent Vergnes
    • Heejun Hwang
    • Gang Deng
    • Simon Diep
    • Brett Lomenick
    • Vijaykumar S. Meli
    • Gabriela C. Monsalve
    • Eileen Hu
    • Stephen A. Whelan
    • Jennifer X. Wang
    • Gwanghyun Jung
    • Gregory M. Solis
    • Farbod Fazlollahi
    • Chitrada Kaweeteerawat
    • Austin Quach
    • Mahta Nili
    • Abby S. Krall
    • Hilary A. Godwin
    • Helena R. Chang
    • Kym F. Faull
    • Feng Guo
    • Meisheng Jiang
    • Sunia A. Trauger
    • Alan Saghatelian
    • Daniel Braas
    • Heather R. Christofk
    • Catherine F. Clarke
    • Michael A. Teitell
    • Michael Petrascheck
    • Karen Reue
    • Michael E. Jung
    • Alison R. Frand
    • Jing Huang

    Ageing in the worm Caenorhabditis elegans is shown to be delayed by supplementation with α-ketoglutarate, an effect that is probably mediated by ATP synthase—which is identified as a direct target of α-ketoglutarate—and target of rapamycin (TOR).

  • PTEN action in leukaemia dictated by the tissue microenvironment

    • Cornelius Miething
    • Claudio Scuoppo
    • Benedikt Bosbach
    • Iris Appelmann
    • Joy Nakitandwe
    • Jing Ma
    • Gang Wu
    • Laura Lintault
    • Martina Auer
    • Prem K. Premsrirut
    • Julie Teruya-Feldstein
    • James Hicks
    • Helene Benveniste
    • Michael R. Speicher
    • James R. Downing
    • Scott W. Lowe

    A mouse model of T-cell leukaemia is used to test whether PTEN loss is required for tumour maintenance as well as initiation; although it had little effect on tumour load in haematopoietic organs, PTEN reactivation reduced the CCR9-dependent tumour dissemination to the intestine that was amplified on PTEN loss, exposing the importance of tumour microenvironment in PTEN-deficient settings.

  • Inactivation of PI(3)K p110δ breaks regulatory T-cell-mediated immune tolerance to cancer

    • Khaled Ali
    • Dalya R. Soond
    • Roberto Piñeiro
    • Thorsten Hagemann
    • Wayne Pearce
    • Ee Lyn Lim
    • Hicham Bouabe
    • Cheryl L. Scudamore
    • Timothy Hancox
    • Heather Maecker
    • Lori Friedman
    • Martin Turner
    • Klaus Okkenhaug
    • Bart Vanhaesebroeck

    The kinase PI(3)Kδ is shown to be required for the immunosuppressive function of regulatory Tcells; inactivation of PI(3)Kδ in these cells leads to enhanced cytotoxic T-cell function and restricts tumour growth and metastasis in a variety of mouse tumour models.

    See also
  • CFIm25 links alternative polyadenylation to glioblastoma tumour suppression

    • Chioniso P. Masamha
    • Zheng Xia
    • Jingxuan Yang
    • Todd R. Albrecht
    • Min Li
    • Ann-Bin Shyu
    • Wei Li
    • Eric J. Wagner

    CFIm25 is identified as a factor that prevents messenger RNAs being shortened due to altered 3′ polyadenylation, which typically occurs when cells undergo high proliferation and correlates with increased tumorigenic activity in glioblastoma tumours.

  • Persistent gut microbiota immaturity in malnourished Bangladeshi children

    • Sathish Subramanian
    • Sayeeda Huq
    • Tanya Yatsunenko
    • Rashidul Haque
    • Mustafa Mahfuz
    • Mohammed A. Alam
    • Amber Benezra
    • Joseph DeStefano
    • Martin F. Meier
    • Brian D. Muegge
    • Michael J. Barratt
    • Laura G. VanArendonk
    • Qunyuan Zhang
    • Michael A. Province
    • William A. Petri Jr
    • Tahmeed Ahmed
    • Jeffrey I. Gordon

    Bacterial species whose representation defines healthy postnatal assembly of the gut microbiota in Bangladeshi children during their first 2 years are identified, and a model is constructed to compare healthy children to those with severe acute malnutrition (SAM); results show that SAM is associated with microbiota immaturity that is only partially ameliorated by existing nutritional interventions.

    See also
  • Ribosomal oxygenases are structurally conserved from prokaryotes to humans

    • Rasheduzzaman Chowdhury
    • Rok Sekirnik
    • Nigel C. Brissett
    • Tobias Krojer
    • Chia-hua Ho
    • Stanley S. Ng
    • Ian J. Clifton
    • Wei Ge
    • Nadia J. Kershaw
    • Gavin C. Fox
    • Joao R. C. Muniz
    • Melanie Vollmar
    • Claire Phillips
    • Ewa S. Pilka
    • Kathryn L. Kavanagh
    • Frank von Delft
    • Udo Oppermann
    • Michael A. McDonough
    • Aidan J. Doherty
    • Christopher J. Schofield

    Crystal structures of human and prokaryotic ribosomal oxygenases reported here, with and without their ribosomal protein substrates, support their assignments as hydroxylases, and provide insights into the evolution of the JmjC-domain-containing hydroxylases and demethylases.

  • Co-opting sulphur-carrier proteins from primary metabolic pathways for 2-thiosugar biosynthesis

    • Eita Sasaki
    • Xuan Zhang
    • He G. Sun
    • Mei-Yeh Jade Lu
    • Tsung-lin Liu
    • Albert Ou
    • Jeng-yi Li
    • Yu-hsiang Chen
    • Steven E. Ealick
    • Hung-wen Liu

    How sulphur is incorporated into sulphur-containing secondary metabolites is poorly understood; here, the bacterium Amycolatopsis orientalis is shown to co-opt sulphur-carrier proteins from primary metabolic pathways to facilitate the biosynthesis of sulphur-containing natural products.

Corrigenda

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