Table of Contents

Volume 538 Number 7625 pp290-420

20 October 2016

About the cover

Xenopus laevis, also known as the African clawed frog or platanna. X. laevis is an important model organism that is used in the study of vertebrate cell and developmental biology. It is a palaeotetraploid — the product of genome duplications that occurred many millions of years ago. This makes X. laevis ideal for the study of polyploidy, but has greatly complicated genome sequencing. In this issue of Nature an international research collaboration reports the X. laevis genome sequence, and compares it to that of the related X. tropicalis. Their analyses confirm that X. laevis is an allotetraploid and distinguishes two subgenomes that evolved asymmetrically — one often retained the ancestral state and the other was subject to gene loss, deletion, rearrangement and reduced expression. The two diploid progenitor species diverged about 34 million years ago, combining to form an allotetraploid about 18 million years ago. Cover photo: Paul Starosta/Getty Images

This Week



World View


Seven Days


News in Focus




  • There is a blind spot in AI research

    Fears about the future impacts of artificial intelligence are distracting researchers from the real risks of deployed systems, argue Kate Crawford and Ryan Calo.

Books and Arts

  • Biomechanics: The wonders of whirl

    John E. Moalli and Adam P. Summers relish a book on biomechanical spin, from wheels to free-falling felines.

    • Review of Why the Wheel Is Round: Muscles, Technology, and How We Make Things Move
      Steven Vogel
  • Q&A: Lexi Jamieson Marsh and Ellen Currano: Face to face

    Outside the hall containing the posters and exhibits at last month's Geological Society of America meeting in Denver, Colorado, was a surprise. A travelling photography exhibition displayed large, black-and-white portraits of women — wearing beards. To challenge perceptions of who is and is not a scientist, the Bearded Lady Project ( has photographed more than 75 female Earth scientists; a documentary will be released in early 2017. Filmmaker and project mastermind Lexi Jamieson Marsh and palaeobotanist Ellen Currano of the University of Wyoming in Laramie, who inspired the project, talk about 'invisible women', communities of inclusivity and rocking a moustache.





  • For your information

    Sounding out people who are already working in a field that interests you is a great way to gain valuable inside knowledge during your job search, says Peter Fiske.

    • Peter Fiske

naturejobs job listings and advertising features




  • Accurate de novo design of hyperstable constrained peptides

    • Gaurav Bhardwaj
    • Vikram Khipple Mulligan
    • Christopher D. Bahl
    • Jason M. Gilmore
    • Peta J. Harvey
    • Olivier Cheneval
    • Garry W. Buchko
    • Surya V. S. R. K. Pulavarti
    • Quentin Kaas
    • Alexander Eletsky
    • Po-Ssu Huang
    • William A. Johnsen
    • Per Jr Greisen
    • Gabriel J. Rocklin
    • Yifan Song
    • Thomas W. Linsky
    • Andrew Watkins
    • Stephen A. Rettie
    • Xianzhong Xu
    • Lauren P. Carter
    • Richard Bonneau
    • James M. Olson
    • Evangelos Coutsias
    • Colin E. Correnti
    • Thomas Szyperski
    • David J. Craik
    • David Baker

    Computational methods for the de novo design of conformationally restricted peptides produce exceptionally stable short peptides stabilized by backbone cyclization and/or internal disulfide bonds that are promising starting points for a new generation of peptide-based drugs.

  • Genome evolution in the allotetraploid frog Xenopus laevisOpen

    • Adam M. Session
    • Yoshinobu Uno
    • Taejoon Kwon
    • Jarrod A. Chapman
    • Atsushi Toyoda
    • Shuji Takahashi
    • Akimasa Fukui
    • Akira Hikosaka
    • Atsushi Suzuki
    • Mariko Kondo
    • Simon J. van Heeringen
    • Ian Quigley
    • Sven Heinz
    • Hajime Ogino
    • Haruki Ochi
    • Uffe Hellsten
    • Jessica B. Lyons
    • Oleg Simakov
    • Nicholas Putnam
    • Jonathan Stites
    • Yoko Kuroki
    • Toshiaki Tanaka
    • Tatsuo Michiue
    • Minoru Watanabe
    • Ozren Bogdanovic
    • Ryan Lister
    • Georgios Georgiou
    • Sarita S. Paranjpe
    • Ila van Kruijsbergen
    • Shengquiang Shu
    • Joseph Carlson
    • Tsutomu Kinoshita
    • Yuko Ohta
    • Shuuji Mawaribuchi
    • Jerry Jenkins
    • Jane Grimwood
    • Jeremy Schmutz
    • Therese Mitros
    • Sahar V. Mozaffari
    • Yutaka Suzuki
    • Yoshikazu Haramoto
    • Takamasa S. Yamamoto
    • Chiyo Takagi
    • Rebecca Heald
    • Kelly Miller
    • Christian Haudenschild
    • Jacob Kitzman
    • Takuya Nakayama
    • Yumi Izutsu
    • Jacques Robert
    • Joshua Fortriede
    • Kevin Burns
    • Vaneet Lotay
    • Kamran Karimi
    • Yuuri Yasuoka
    • Darwin S. Dichmann
    • Martin F. Flajnik
    • Douglas W. Houston
    • Jay Shendure
    • Louis DuPasquier
    • Peter D. Vize
    • Aaron M. Zorn
    • Michihiko Ito
    • Edward M. Marcotte
    • John B. Wallingford
    • Yuzuru Ito
    • Makoto Asashima
    • Naoto Ueno
    • Yoichi Matsuda
    • Gert Jan C. Veenstra
    • Asao Fujiyama
    • Richard M. Harland
    • Masanori Taira
    • Daniel S. Rokhsar

    The two homoeologous subgenomes in the allotetraploid frog Xenopus laevis evolved asymmetrically; one often retained the ancestral state, whereas the other experienced gene loss, deletion, rearrangement and reduced gene expression.

    See also
  • Diversity-oriented synthesis yields novel multistage antimalarial inhibitors

    • Nobutaka Kato
    • Eamon Comer
    • Tomoyo Sakata-Kato
    • Arvind Sharma
    • Manmohan Sharma
    • Micah Maetani
    • Jessica Bastien
    • Nicolas M. Brancucci
    • Joshua A. Bittker
    • Victoria Corey
    • David Clarke
    • Emily R. Derbyshire
    • Gillian L. Dornan
    • Sandra Duffy
    • Sean Eckley
    • Maurice A. Itoe
    • Karin M. J. Koolen
    • Timothy A. Lewis
    • Ping S. Lui
    • Amanda K. Lukens
    • Emily Lund
    • Sandra March
    • Elamaran Meibalan
    • Bennett C. Meier
    • Jacob A. McPhail
    • Branko Mitasev
    • Eli L. Moss
    • Morgane Sayes
    • Yvonne Van Gessel
    • Mathias J. Wawer
    • Takashi Yoshinaga
    • Anne-Marie Zeeman
    • Vicky M. Avery
    • Sangeeta N. Bhatia
    • John E. Burke
    • Flaminia Catteruccia
    • Jon C. Clardy
    • Paul A. Clemons
    • Koen J. Dechering
    • Jeremy R. Duvall
    • Michael A. Foley
    • Fabian Gusovsky
    • Clemens H. M. Kocken
    • Matthias Marti
    • Marshall L. Morningstar
    • Benito Munoz
    • Daniel E. Neafsey
    • Amit Sharma
    • Elizabeth A. Winzeler
    • Dyann F. Wirth
    • Christina A. Scherer
    • Stuart L. Schreiber

    The bicyclic azetidines, a class of potent, well-tolerated antimalarial compounds that is active against multiple stages of the Plasmodium life-cycle, has been discovered following screens against libraries of compounds reminiscent of natural products.

    See also
  • Frizzled proteins are colonic epithelial receptors for C. difficile toxin B

    • Liang Tao
    • Jie Zhang
    • Paul Meraner
    • Alessio Tovaglieri
    • Xiaoqian Wu
    • Ralf Gerhard
    • Xinjun Zhang
    • William B. Stallcup
    • Ji Miao
    • Xi He
    • Julian G. Hurdle
    • David T. Breault
    • Abraham L. Brass
    • Min Dong

    Here, a genome-wide CRISPR–Cas9 screen is used to identify the Wnt receptors frizzled as physiologically relevant Clostridium difficile toxin B receptors, providing new therapeutic targets for treating C. difficile infections.


  • Multi-petahertz electronic metrology

    • M. Garg
    • M. Zhan
    • T. T. Luu
    • H. Lakhotia
    • T. Klostermann
    • A. Guggenmos
    • E. Goulielmakis

    Investigations using single-cycle intense optical fields to drive electron motion in bulk silicon dioxide show that the light-induced electric currents extend in frequency up to about 8 petahertz.

    See also
  • A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns

    • Faiyaz Notta
    • Michelle Chan-Seng-Yue
    • Mathieu Lemire
    • Yilong Li
    • Gavin W. Wilson
    • Ashton A. Connor
    • Robert E. Denroche
    • Sheng-Ben Liang
    • Andrew M. K. Brown
    • Jaeseung C. Kim
    • Tao Wang
    • Jared T. Simpson
    • Timothy Beck
    • Ayelet Borgida
    • Nicholas Buchner
    • Dianne Chadwick
    • Sara Hafezi-Bakhtiari
    • John E. Dick
    • Lawrence Heisler
    • Michael A. Hollingsworth
    • Emin Ibrahimov
    • Gun Ho Jang
    • Jeremy Johns
    • Lars G. T. Jorgensen
    • Calvin Law
    • Olga Ludkovski
    • Ilinca Lungu
    • Karen Ng
    • Danielle Pasternack
    • Gloria M. Petersen
    • Liran I. Shlush
    • Lee Timms
    • Ming-Sound Tsao
    • Julie M. Wilson
    • Christina K. Yung
    • George Zogopoulos
    • John M. S. Bartlett
    • Ludmil B. Alexandrov
    • Francisco X. Real
    • Sean P. Cleary
    • Michael H. Roehrl
    • John D. McPherson
    • Lincoln D. Stein
    • Thomas J. Hudson
    • Peter J. Campbell
    • Steven Gallinger

    Pancreatic cancer is not caused by a specific series of genetic alterations that occur sequentially but by one, or few, catastrophic events that result in simultaneous oncogenic genetic rearrangements, giving rise to highly aggressive tumours.

  • Allogeneic transplantation of iPS cell-derived cardiomyocytes regenerates primate hearts

    • Yuji Shiba
    • Toshihito Gomibuchi
    • Tatsuichiro Seto
    • Yuko Wada
    • Hajime Ichimura
    • Yuki Tanaka
    • Tatsuki Ogasawara
    • Kenji Okada
    • Naoko Shiba
    • Kengo Sakamoto
    • Daisuke Ido
    • Takashi Shiina
    • Masamichi Ohkura
    • Junichi Nakai
    • Narumi Uno
    • Yasuhiro Kazuki
    • Mitsuo Oshimura
    • Itsunari Minami
    • Uichi Ikeda

    Allogenic induced pluripotent stem cell-derived cardiomyocytes transplanted directly into infarcted cynomolgus monkey hearts show electrical coupling with host cardiomyocytes improve cardiac contractile function after mild immunosuppression.

  • Fetal liver endothelium regulates the seeding of tissue-resident macrophages

    • Pia Rantakari
    • Norma Jäppinen
    • Emmi Lokka
    • Elias Mokkala
    • Heidi Gerke
    • Emilia Peuhu
    • Johanna Ivaska
    • Kati Elima
    • Kaisa Auvinen
    • Marko Salmi

    PLVAP selectively controls the seeding of fetal liver monocyte-derived tissue-resident macrophages, seemingly by interacting with chemotactic and adhesive molecules at the diaphragms of liver sinusoidal endothelium.

  • The epichaperome is an integrated chaperome network that facilitates tumour survival

    • Anna Rodina
    • Tai Wang
    • Pengrong Yan
    • Erica DaGama Gomes
    • Mark P. S. Dunphy
    • Nagavarakishore Pillarsetty
    • John Koren
    • John F. Gerecitano
    • Tony Taldone
    • Hongliang Zong
    • Eloisi Caldas-Lopes
    • Mary Alpaugh
    • Adriana Corben
    • Matthew Riolo
    • Brad Beattie
    • Christina Pressl
    • Radu I. Peter
    • Chao Xu
    • Robert Trondl
    • Hardik J. Patel
    • Fumiko Shimizu
    • Alexander Bolaender
    • Chenghua Yang
    • Palak Panchal
    • Mohammad F. Farooq
    • Sarah Kishinevsky
    • Shanu Modi
    • Oscar Lin
    • Feixia Chu
    • Sujata Patil
    • Hediye Erdjument-Bromage
    • Pat Zanzonico
    • Clifford Hudis
    • Lorenz Studer
    • Gail J. Roboz
    • Ethel Cesarman
    • Leandro Cerchietti
    • Ross Levine
    • Ari Melnick
    • Steven M. Larson
    • Jason S. Lewis
    • Monica L. Guzman
    • Gabriela Chiosis

    Chaperomes are dynamic assemblies of proteins that regulate cellular homeostasis but specific cellular stresses remodel chaperome components into a stable chaperome network called the epichaperome, which might offer a new cancer target.

    See also
  • Molecular basis of Lys11-polyubiquitin specificity in the deubiquitinase Cezanne

    • Tycho E. T. Mevissen
    • Yogesh Kulathu
    • Monique P.C. Mulder
    • Paul P. Geurink
    • Sarah L. Maslen
    • Malte Gersch
    • Paul R. Elliott
    • John E. Burke
    • Bianca D. M. van Tol
    • Masato Akutsu
    • Farid El Oualid
    • Masato Kawasaki
    • Stefan M.V. Freund
    • Huib Ovaa
    • David Komander

    The structures of the deubiquitinating enzyme Cezanne alone or in complex with its substrate or product are solved, showing how Cezanne specifically targets Lys11-linked polyubiquitin.

  • Atomic structure of the entire mammalian mitochondrial complex I

    • Karol Fiedorczuk
    • James A. Letts
    • Gianluca Degliesposti
    • Karol Kaszuba
    • Mark Skehel
    • Leonid A. Sazanov

    The atomic structure of ovine mitochondrial complex I is solved at 3.9 Å resolution, revealing that supernumerary subunits stabilize the complex and providing insight into the molecular basis of its function and regulation.

  • X-ray structure of the human α4β2 nicotinic receptor

    • Claudio L. Morales-Perez
    • Colleen M. Noviello
    • Ryan E. Hibbs

    Nicotinic acetylcholine receptors are ligand-gated ion channels that mediate fast chemical neurotransmission; here, the first X-ray crystal structure of a nicotinic receptor is reported, revealing how nicotine stabilizes the receptor in a non-conducting, desensitized conformation.