Table of Contents

Volume 547 Number 7661 pp5-132

6 July 2017

About the cover

In this week’s special issue, Nature zeroes in on that most basic element of life: the cell. Technological advances are powering analyses previously impossible at the single-cell level. As a result, researchers are at last starting to chart how many different types of cell exist in complex organisms, what they do and how they change during development. Efforts to trace cell lineage are examined in a News Feature (page 20), along with a profile of Aviv Regev (page 24), who is spearheading an effort to catalogue every kind of cell in the human body. Elsewhere, researchers explore how the genome is packaged in a mouse cell throughout the division cycle (page 61) and what this might mean for examining genome interactions in 3D (page 34). And Amir Giladi and Ido Amit discuss how a focus on immune cells might aid our ability to combat diseases such as cancer (page 27). A Careers interview explores the reasons for making the move into single-cell analysis (page 129), and Toolbox takes a look at how best to probe the data being generated as the field expands (page 125). Cover illustration by Jasiek Krzysztofiak/Nature; Images: Morphart Creation/Shutterstock, Jezper/Shutterstock

This Week

Editorials

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World View

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Research Highlights

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Seven Days

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News in Focus

Features

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  • Single-cell biology

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    Analyses of life's most basic elements promise to improve therapies and provide insights into some of the most fundamental processes in biology.

  • How to build a human cell atlas

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    Aviv Regev is a maven of hard-core biological analyses. Now she is part of an effort to map every cell in the human body.

    • Anna Nowogrodzki

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  • Immunology, one cell at a time

    Analysing the DNA, RNA and protein of single cells is transforming our understanding of the immune system, say Amir Giladi and Ido Amit.

Books and Arts

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  • Cybersecurity: The cold war online

    Steven Aftergood weighs up an analysis of the fierce conflict destabilizing the Internet.

    • Review of The Darkening Web: The War for Cyberspace
      Alexander Klimburg
  • Books in brief

    Barbara Kiser reviews five of the week's best science picks.

Careers

Features

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Q&As

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naturejobs job listings and advertising features

Futures

Specials

Toolbox

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research

Brief Communications Arising

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Articles

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  • West Antarctic Ice Sheet retreat driven by Holocene warm water incursions

    • Claus-Dieter Hillenbrand
    • James A. Smith
    • David A. Hodell
    • Mervyn Greaves
    • Christopher R. Poole
    • Sev Kender
    • Mark Williams
    • Thorbjørn Joest Andersen
    • Patrycja E. Jernas
    • Henry Elderfield
    • Johann P. Klages
    • Stephen J. Roberts
    • Karsten Gohl
    • Robert D. Larter
    • Gerhard Kuhn

    During the early Holocene epoch—and since the 1940s—variations in Southern Hemisphere westerly winds controlled the upwelling of Circumpolar Deep Water and seemingly ice-sheet retreat in West Antarctica.

    See also
  • Climate change drives expansion of Antarctic ice-free habitat

    • Jasmine R. Lee
    • Ben Raymond
    • Thomas J. Bracegirdle
    • Iadine Chadès
    • Richard A. Fuller
    • Justine D. Shaw
    • Aleks Terauds

    Permanently ice-free areas, home to almost all of Antarctica’s biodiversity, are projected, in the worst case, to expand by over 17,000 km2 as a result of climate change by the end of this century, with potentially deleterious consequences for the continent’s biodiversity.

  • Recurrent and functional regulatory mutations in breast cancer

    • Esther Rheinbay
    • Prasanna Parasuraman
    • Jonna Grimsby
    • Grace Tiao
    • Jesse M. Engreitz
    • Jaegil Kim
    • Michael S. Lawrence
    • Amaro Taylor-Weiner
    • Sergio Rodriguez-Cuevas
    • Mara Rosenberg
    • Julian Hess
    • Chip Stewart
    • Yosef E. Maruvka
    • Petar Stojanov
    • Maria L. Cortes
    • Sara Seepo
    • Carrie Cibulskis
    • Adam Tracy
    • Trevor J. Pugh
    • Jesse Lee
    • Zongli Zheng
    • Leif W. Ellisen
    • A. John Iafrate
    • Jesse S. Boehm
    • Stacey B. Gabriel
    • Matthew Meyerson
    • Todd R. Golub
    • Jose Baselga
    • Alfredo Hidalgo-Miranda
    • Toshi Shioda
    • Andre Bernards
    • Eric S. Lander
    • Gad Getz

    High-depth sequencing of targeted regions in primary breast cancer identifies mutated promoter elements with recurrent mutations at specific and/or nearby bases, suggesting selection of certain non-coding events.

    See also
  • Single-molecule analysis of ligand efficacy in β2AR–G-protein activation

    • G. Glenn Gregorio
    • Matthieu Masureel
    • Daniel Hilger
    • Daniel S. Terry
    • Manuel Juette
    • Hong Zhao
    • Zhou Zhou
    • Jose Manuel Perez-Aguilar
    • Maria Hauge
    • Signe Mathiasen
    • Jonathan A. Javitch
    • Harel Weinstein
    • Brian K. Kobilka
    • Scott C. Blanchard

    Single-molecule FRET imaging provides insights into the allosteric link between the ligand-binding and G-protein nucleotide-binding pockets of the β2 adrenergic receptor (β2AR) and improved understanding of the G-protein activation mechanism.

Letters

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  • Quantifiable predictive features define epitope-specific T cell receptor repertoires

    • Pradyot Dash
    • Andrew J. Fiore-Gartland
    • Tomer Hertz
    • George C. Wang
    • Shalini Sharma
    • Aisha Souquette
    • Jeremy Chase Crawford
    • E. Bridie Clemens
    • Thi H. O. Nguyen
    • Katherine Kedzierska
    • Nicole L. La Gruta
    • Philip Bradley
    • Paul G. Thomas

    The authors characterize epitope-specific T cell repertoires, identify shared and recognizable features of TCRs, and develop tools to classify antigen specificity on the basis of sequence analysis.

    See also
    See also
  • Identifying specificity groups in the T cell receptor repertoire

    • Jacob Glanville
    • Huang Huang
    • Allison Nau
    • Olivia Hatton
    • Lisa E. Wagar
    • Florian Rubelt
    • Xuhuai Ji
    • Arnold Han
    • Sheri M. Krams
    • Christina Pettus
    • Nikhil Haas
    • Cecilia S. Lindestam Arlehamn
    • Alessandro Sette
    • Scott D. Boyd
    • Thomas J. Scriba
    • Olivia M. Martinez
    • Mark M. Davis

    The authors devise an algorithm that can cluster T cell receptor (TCR) sequences sharing the same specificity, predict the HLA restriction of these TCR clusters on the basis of subjects’ genotypes and help to identify specific peptide major histocompatibility complex ligands.

    See also
    See also
  • Tracing the origins of relapse in acute myeloid leukaemia to stem cells

    • Liran I. Shlush
    • Amanda Mitchell
    • Lawrence Heisler
    • Sagi Abelson
    • Stanley W. K. Ng
    • Aaron Trotman-Grant
    • Jessie J. F. Medeiros
    • Abilasha Rao-Bhatia
    • Ivana Jaciw-Zurakowsky
    • Rene Marke
    • Jessica L. McLeod
    • Monica Doedens
    • Gary Bader
    • Veronique Voisin
    • ChangJiang Xu
    • John D. McPherson
    • Thomas J. Hudson
    • Jean C. Y. Wang
    • Mark D. Minden
    • John E. Dick

    Identification of the cell types from which relapse arises in acute myeloid leukaemia, by following leukaemia propagation from patient-derived leukaemia samples.

  • mTORC1-dependent AMD1 regulation sustains polyamine metabolism in prostate cancer

    • Amaia Zabala-Letona
    • Amaia Arruabarrena-Aristorena
    • Natalia Martín-Martín
    • Sonia Fernandez-Ruiz
    • James D. Sutherland
    • Michelle Clasquin
    • Julen Tomas-Cortazar
    • Jose Jimenez
    • Ines Torres
    • Phong Quang
    • Pilar Ximenez-Embun
    • Ruzica Bago
    • Aitziber Ugalde-Olano
    • Ana Loizaga-Iriarte
    • Isabel Lacasa-Viscasillas
    • Miguel Unda
    • Verónica Torrano
    • Diana Cabrera
    • Sebastiaan M. van Liempd
    • Ylenia Cendon
    • Elena Castro
    • Stuart Murray
    • Ajinkya Revandkar
    • Andrea Alimonti
    • Yinan Zhang
    • Amelia Barnett
    • Gina Lein
    • David Pirman
    • Ana R. Cortazar
    • Leire Arreal
    • Ludmila Prudkin
    • Ianire Astobiza
    • Lorea Valcarcel-Jimenez
    • Patricia Zuñiga-García
    • Itziar Fernandez-Dominguez
    • Marco Piva
    • Alfredo Caro-Maldonado
    • Pilar Sánchez-Mosquera
    • Mireia Castillo-Martín
    • Violeta Serra
    • Naiara Beraza
    • Antonio Gentilella
    • George Thomas
    • Mikel Azkargorta
    • Felix Elortza
    • Rosa Farràs
    • David Olmos
    • Alejo Efeyan
    • Juan Anguita
    • Javier Muñoz
    • Juan M. Falcón-Pérez
    • Rosa Barrio
    • Teresa Macarulla
    • Jose M. Mato
    • Maria L. Martinez-Chantar
    • Carlos Cordon-Cardo
    • Ana M. Aransay
    • Kevin Marks
    • José Baselga
    • Josep Tabernero
    • Paolo Nuciforo
    • Brendan D. Manning
    • Katya Marjon
    • Arkaitz Carracedo

    mTOR complex 1 signalling regulates polyamine metabolism and thereby promotes tumorigenesis, through regulation of the stability of a key enzyme, AMD1.

  • RNase III nucleases from diverse kingdoms serve as antiviral effectors

    • Lauren C. Aguado
    • Sonja Schmid
    • Jared May
    • Leah R. Sabin
    • Maryline Panis
    • Daniel Blanco-Melo
    • Jaehee V. Shim
    • David Sachs
    • Sara Cherry
    • Anne E. Simon
    • Jean-Pierre Levraud
    • Benjamin R. tenOever

    RNase III from all three domains of life elicits RNA-targeting antiviral activity that is independent of, and possibly predates, other known eukaryotic antiviral systems.

  • Electron cryo-microscopy structure of the mechanotransduction channel NOMPC

    • Peng Jin
    • David Bulkley
    • Yanmeng Guo
    • Wei Zhang
    • Zhenhao Guo
    • Walter Huynh
    • Shenping Wu
    • Shan Meltzer
    • Tong Cheng
    • Lily Yeh Jan
    • Yuh-Nung Jan
    • Yifan Cheng

    Single-particle electron cryo-microscopy analysis of the mechanotransduction channel NOMPC reveals that it contains a bundle of four helical spring-shaped ankyrin repeat domains that undergo motion, potentially allowing mechanical movement of the cytoskeleton to be coupled to the opening of the channel.

Addendum

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  • Addendum: Immune clearance of highly pathogenic SIV infection

    • Scott G. Hansen
    • Michael Piatak
    • Abigail B. Ventura
    • Colette M. Hughes
    • Roxanne M. Gilbride
    • Julia C. Ford
    • Kelli Oswald
    • Rebecca Shoemaker
    • Yuan Li
    • Matthew S. Lewis
    • Awbrey N. Gilliam
    • Guangwu Xu
    • Nathan Whizin
    • Benjamin J. Burwitz
    • Shannon L. Planer
    • John M. Turner
    • Alfred W. Legasse
    • Michael K. Axthelm
    • Jay A. Nelson
    • Klaus Früh
    • Jonah B. Sacha
    • Jacob D. Estes
    • Brandon F. Keele
    • Paul T. Edlefsen
    • Jeffrey D. Lifson
    • Louis J. Picker