Table of Contents

Volume 525 Number 7570 pp425-558

24 September 2015

About the cover

A flower and fruit abnormality known as ‘mantled’ can develop in some agricultural oil palm cultivars derived from tissue culture and the resulting mantled palms can become unproductive. Mantling is widely regarded as an epigenetic trait, but has not been fully explained. Meilina Ong-Abdullah et al. have undertaken a genome-wide, unbiased, DNA methylation analysis to look for loci epigenetically associated with the mantled phenotype. They find that hypomethylation of a single Karma family retrotransposon embedded in the intron of a homeotic gene is common to all mantled clones and associated with aberrant splicing and termination of the gene transcript. Loss of methylation — dubbed the Bad Karma epiallele — predicts a loss of oil palm yield and this property should enable screening for higher-performing clones at the plantlet stage. Cover: slpu9945/Thinkstock

This Week


  • In the name of beauty

    The ugly truth is that the plastic microbeads found in many skin scrubs and other personal-care products are a serious pollutant of the marine environment. They should be phased out rapidly.

  • Power play

    The replacement of mitochondria does not signal ethical problems.

  • STAP revisited

    Reanalysis of the controversy provides a strong example of the self-correcting nature of science.

World View


Seven Days


    News in Focus




    Books and Arts

    • Military science: Inventions of war

      Ann Finkbeiner assesses a study of DARPA, the agency that readies US technologies for coming conflicts.

      • Review of The Pentagon's Brain: An Uncensored History of DARPA, America's Top-Secret Military Research Agency
        Annie Jacobsen
    • Theatre: Lab's labour's lost

      Philip Ball appraises Nicole Kidman's stage turn as crystallographer Rosalind Franklin.

      • Review of Photograph 51
        Anna Ziegler





    • Trade talk: Medical liaison

      David Crosby describes how he moved from basic research to doing outreach to healthcare providers.

      • Monya Baker

    naturejobs job listings and advertising features



    Brief Communication Arising

    • Failure to replicate the STAP cell phenomenon

      • Alejandro De Los Angeles
      • Francesco Ferrari
      • Yuko Fujiwara
      • Ronald Mathieu
      • Soohyun Lee
      • Semin Lee
      • Ho-Chou Tu
      • Samantha Ross
      • Stephanie Chou
      • Minh Nguyen
      • Zhaoting Wu
      • Thorold W. Theunissen
      • Benjamin E. Powell
      • Sumeth Imsoonthornruksa
      • Jiekai Chen
      • Marti Borkent
      • Vladislav Krupalnik
      • Ernesto Lujan
      • Marius Wernig
      • Jacob H. Hanna
      • Konrad Hochedlinger
      • Duanqing Pei
      • Rudolf Jaenisch
      • Hongkui Deng
      • Stuart H. Orkin
      • Peter J. Park
      • George Q. Daley


    • Hallmarks of pluripotency

      • Alejandro De Los Angeles
      • Francesco Ferrari
      • Ruibin Xi
      • Yuko Fujiwara
      • Nissim Benvenisty
      • Hongkui Deng
      • Konrad Hochedlinger
      • Rudolf Jaenisch
      • Soohyun Lee
      • Harry G. Leitch
      • M. William Lensch
      • Ernesto Lujan
      • Duanqing Pei
      • Janet Rossant
      • Marius Wernig
      • Peter J. Park
      • George Q. Daley

      In response to the need for a defined set of criteria to assess stem-cell potency, this review proposes guidelines for the evaluation of newly derived pluripotent stem cells, from functional assays to integrative molecular analyses of transcriptional, epigenetic and metabolic states.


    • Epicardial FSTL1 reconstitution regenerates the adult mammalian heart

      • Ke Wei
      • Vahid Serpooshan
      • Cecilia Hurtado
      • Marta Diez-Cuñado
      • Mingming Zhao
      • Sonomi Maruyama
      • Wenhong Zhu
      • Giovanni Fajardo
      • Michela Noseda
      • Kazuto Nakamura
      • Xueying Tian
      • Qiaozhen Liu
      • Andrew Wang
      • Yuka Matsuura
      • Paul Bushway
      • Wenqing Cai
      • Alex Savchenko
      • Morteza Mahmoudi
      • Michael D. Schneider
      • Maurice J. B. van den Hoff
      • Manish J. Butte
      • Phillip C. Yang
      • Kenneth Walsh
      • Bin Zhou
      • Daniel Bernstein
      • Mark Mercola
      • Pilar Ruiz-Lozano

      The secreted factor follistatin-like 1 (FSTL1) becomes undetectable in the epicardium of infarcted hearts; when reconstituted using a collagen patch sutured onto an infarcted heart, FSTL1 can induce cell cycle entry and division of pre-existing cardiomyocytes, thus boosting heart function and survival in mouse and pig models of myocardial infarction.

      See also
    • Structure of the toxic core of α-synuclein from invisible crystals

      • Jose A. Rodriguez
      • Magdalena I. Ivanova
      • Michael R. Sawaya
      • Duilio Cascio
      • Francis E. Reyes
      • Dan Shi
      • Smriti Sangwan
      • Elizabeth L. Guenther
      • Lisa M. Johnson
      • Meng Zhang
      • Lin Jiang
      • Mark A. Arbing
      • Brent L. Nannenga
      • Johan Hattne
      • Julian Whitelegge
      • Aaron S. Brewster
      • Marc Messerschmidt
      • Sébastien Boutet
      • Nicholas K. Sauter
      • Tamir Gonen
      • David S. Eisenberg

      A short segment of α-synuclein called NACore (residues 68–78) is responsible for the formation of amyloid aggregates responsible for cytotoxicity in Parkinson disease; here the nanocrystal structure of this invisible-to-optical-microscopy segment is determined using micro-electron diffraction, offering insight into its function and simultaneously demonstrating the first use of micro-electron diffraction to solve a previously unknown protein structure.

      See also
    • Structure of mammalian eIF3 in the context of the 43S preinitiation complex

      • Amedee des Georges
      • Vidya Dhote
      • Lauriane Kuhn
      • Christopher U. T. Hellen
      • Tatyana V. Pestova
      • Joachim Frank
      • Yaser Hashem

      The cryo-electron microscopy structure of the eukaryotic initiation factor 3 (eIF3) within the larger 43S complex is determined; the improved resolution enables visualization of the secondary structures of the subunits, as well as the contacts between eIF3 and both eIF2 and DHX29.


    • The formation of submillimetre-bright galaxies from gas infall over a billion years

      • Desika Narayanan
      • Matthew Turk
      • Robert Feldmann
      • Thomas Robitaille
      • Philip Hopkins
      • Robert Thompson
      • Christopher Hayward
      • David Ball
      • Claude-André Faucher-Giguère
      • Dušan Kereš

      Submillimetre-bright galaxies at high redshift are the most luminous, heavily star-forming galaxies in the Universe, but cosmological simulations of such galaxies have so far been unsuccessful; now a cosmological hydrodynamic galaxy formation simulation is reported that can form a submillimetre galaxy that simultaneously satisfies the broad range of observed physical constraints.

      See also
    • The diurnal cycle of water ice on comet 67P/Churyumov–Gerasimenko

      • M. C. De Sanctis
      • F. Capaccioni
      • M. Ciarniello
      • G. Filacchione
      • M. Formisano
      • S. Mottola
      • A. Raponi
      • F. Tosi
      • D. Bockelée-Morvan
      • S. Erard
      • C. Leyrat
      • B. Schmitt
      • E. Ammannito
      • G. Arnold
      • M. A. Barucci
      • M. Combi
      • M. T. Capria
      • P. Cerroni
      • W.-H. Ip
      • E. Kuehrt
      • T. B. McCord
      • E. Palomba
      • P. Beck
      • E. Quirico
      • The VIRTIS Team

      Observations of water ice on the surface of comet 67P/Churyumov–Gerasimenko show the ice appearing and disappearing in a cyclic pattern that follows local illumination conditions, providing a source of localized activity and leading to cycling modification of the ice abundance on the surface.

    • Novel competitors shape species’ responses to climate change

      • Jake M. Alexander
      • Jeffrey M. Diez
      • Jonathan M. Levine

      Species’ range dynamics depend not only on their ability to track climate, but also on the migration of their competitors, and the extent to which novel and current competitors exert differing competitive effects.

    • A sexually dimorphic hypothalamic circuit controls maternal care and oxytocin secretion

      • Niv Scott
      • Matthias Prigge
      • Ofer Yizhar
      • Tali Kimchi

      Sexual dimorphism in neuronal circuits is proposed to underlie sex differences in behaviour, such as virgin female mice acting maternally toward alien pups, while males ignore or attack them; here the authors show that specific tyrosine hydroxylase-expressing neurons in the hypothalamus are more numerous in mothers than in virgin females and males, and that they control parental behaviour in a sex-specific manner.

    • Cell-fate determination by ubiquitin-dependent regulation of translation

      • Achim Werner
      • Shintaro Iwasaki
      • Colleen A. McGourty
      • Sofia Medina-Ruiz
      • Nia Teerikorpi
      • Indro Fedrigo
      • Nicholas T. Ingolia
      • Michael Rape

      This study shows that a vertebrate-specific ubiquitin ligase modulates neural crest specification in Xenopus development and human embryonic stem-cell differentiation; a proteomics approach reveals that the CUL3KBTBD8 ligase modulates translation by targeting the modulators of ribosomes production NOLC1 and its paralogue TCOF1, which is mutated in a neural-crest-associated syndrome.

    • Neutrophil ageing is regulated by the microbiome

      • Dachuan Zhang
      • Grace Chen
      • Deepa Manwani
      • Arthur Mortha
      • Chunliang Xu
      • Jeremiah J. Faith
      • Robert D. Burk
      • Yuya Kunisaki
      • Jung-Eun Jang
      • Christoph Scheiermann
      • Miriam Merad
      • Paul S. Frenette

      Neutrophil ageing, which encourages inflammation and vaso-occlusion in a mouse model of sickle-cell disease, is shown to depend on the intestinal microbiota and activation of the TLR/Myd88 signalling pathways.

    • Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm

      • Meilina Ong-Abdullah
      • Jared M. Ordway
      • Nan Jiang
      • Siew-Eng Ooi
      • Sau-Yee Kok
      • Norashikin Sarpan
      • Nuraziyan Azimi
      • Ahmad Tarmizi Hashim
      • Zamzuri Ishak
      • Samsul Kamal Rosli
      • Fadila Ahmad Malike
      • Nor Azwani Abu Bakar
      • Marhalil Marjuni
      • Norziha Abdullah
      • Zulkifli Yaakub
      • Mohd Din Amiruddin
      • Rajanaidu Nookiah
      • Rajinder Singh
      • Eng-Ti Leslie Low
      • Kuang-Lim Chan
      • Norazah Azizi
      • Steven W. Smith
      • Blaire Bacher
      • Muhammad A. Budiman
      • Andrew Van Brunt
      • Corey Wischmeyer
      • Melissa Beil
      • Michael Hogan
      • Nathan Lakey
      • Chin-Ching Lim
      • Xaviar Arulandoo
      • Choo-Kien Wong
      • Chin-Nee Choo
      • Wei-Chee Wong
      • Yen-Yen Kwan
      • Sharifah Shahrul Rabiah Syed Alwee
      • Ravigadevi Sambanthamurthi
      • Robert A. Martienssen

      The oil palm fruit ‘mantled’ abnormality is a somaclonal variant that markedly reduces yield; here, a genome-wide DNA methylation analysis finds that hypomethylation of a single Karma family retrotransposon embedded in a homeotic gene intron is common to all mantled clones and is associated with aberrant splicing and termination of the gene transcript, and that loss of methylation predicts a loss of oil palm yield.

      See also
    • BET inhibitor resistance emerges from leukaemia stem cells

      • Chun Yew Fong
      • Omer Gilan
      • Enid Y. N. Lam
      • Alan F. Rubin
      • Sarah Ftouni
      • Dean Tyler
      • Kym Stanley
      • Devbarna Sinha
      • Paul Yeh
      • Jessica Morison
      • George Giotopoulos
      • Dave Lugo
      • Philip Jeffrey
      • Stanley Chun-Wei Lee
      • Christopher Carpenter
      • Richard Gregory
      • Robert G. Ramsay
      • Steven W. Lane
      • Omar Abdel-Wahab
      • Tony Kouzarides
      • Ricky W. Johnstone
      • Sarah-Jane Dawson
      • Brian J. P. Huntly
      • Rab K. Prinjha
      • Anthony T. Papenfuss
      • Mark A. Dawson

      BET inhibitors that target bromodomain chromatin readers such as BRD4 are being explored as potential therapeutics in cancer; here, in a MLL–AF9 mouse leukaemia model, resistance to BET inhibitors is shown to emerge from leukaemia stem cells, and be partly due to increased Wnt/β-catenin signalling.

      See also
    • Transcriptional plasticity promotes primary and acquired resistance to BET inhibition

      • Philipp Rathert
      • Mareike Roth
      • Tobias Neumann
      • Felix Muerdter
      • Jae-Seok Roe
      • Matthias Muhar
      • Sumit Deswal
      • Sabine Cerny-Reiterer
      • Barbara Peter
      • Julian Jude
      • Thomas Hoffmann
      • Łukasz M. Boryń
      • Elin Axelsson
      • Norbert Schweifer
      • Ulrike Tontsch-Grunt
      • Lukas E. Dow
      • Davide Gianni
      • Mark Pearson
      • Peter Valent
      • Alexander Stark
      • Norbert Kraut
      • Christopher R. Vakoc
      • Johannes Zuber

      BET bromodomain inhibitors are being explored as potential therapeutics in cancer; here, AML cells are shown to evade sensitivity to BET inhibition through rewiring the transcriptional regulation of BRD4 target genes such as MYC in a process that is facilitated by suppression of PRC2 and WNT signalling activation.

      See also
    • Crystal structures of a double-barrelled fluoride ion channel

      • Randy B. Stockbridge
      • Ludmila Kolmakova-Partensky
      • Tania Shane
      • Akiko Koide
      • Shohei Koide
      • Christopher Miller
      • Simon Newstead

      Microorganisms can export toxic fluoride ions through highly selective channels of the Fluc family; here, the crystal structures of two bacterial Fluc homologues are presented, revealing that selectivity for small F ions may arise from the proteins’ narrow pores and unusual anion coordination.