Table of Contents

Volume 550 Number 7674 pp7-150

5 October 2017

About the cover

The cover is a coloured scanning electron micrograph of various oral bacteria. The oral cavity was among six key body sites that formed a major focus in the work to expand the Human Microbiome Project reported on in this issue. Published in 2012, the Human Microbiome Project sampled 18 different body sites to provide a broad overview of the human microbiome in healthy individuals. Curtis Huttenhower and his colleagues have now extended this work to present 1,631 new metagenomes and multiple time points in 265 individuals, looking in particular at six sites, including the nostrils, mouth and gut. Using a combination of strain profiling, species-level metagenomic functional profiling and longitudinal analyses, the study provides deeper insights into human microbial communities, providing an important resource to further our understanding about what constitutes a "healthy" microbiota. Image courtesy: SPL/Getty

This Week

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    Books and Arts

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    • Neuroscience: The mother lode of invention

      Dan Jones compares three studies on the origins and fruits of human creativity.

      • Review of The Origins of Creativity, The Runaway Species: How Human Creativity Remakes the World and Why?: What Makes Us Curious
        Edward O Wilson, David Eagleman, Anthony Brandt & Mario Livio
    • Health: The war on germs

      Tilli Tansey hails a history of Joseph Lister's drive to vanquish post-operative infection and putrefaction.

      • Review of The Butchering Art: Joseph Lister's Quest to Transform the Grisly World of Victorian Medicine
        Lindsey Fitzharris
    • Ornithology: All eyes on the 10,000 species

      Stuart Pimm considers the obsessive, sometimes dark side to the joyous pursuit of watching birds.

      • Review of Birdmania: A Remarkable Passion for Birds and Birding Without Borders: An Obsession, a Quest, and the Biggest Year in the World
        Bernd Brunner & Noah Strycker
    • Theoretical physics: When the doer met the dreamer

      Graham Farmelo applauds a study on the productive friendship of two very different physicists.

      • Review of The Quantum Labyrinth: How Richard Feynman and John Wheeler Revolutionized Time and Reality
        Paul Halpern
    • Technology: Into cyberia

      Li Gong weighs up three tomes on Silicon Valley's vast influence, for good or ill.

      • Review of The Four: The Hidden DNA of Amazon, Apple, Facebook, and Google World Without Mind: The Existential Threat of Big Tech The Know-It-Alls: The Rise of Silicon Valley as a Political Powerhouse and Social Wrecking Ball
        Scott GallowayFranklin Foer & Noam Cohen

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    spotlight: Big science in a small country

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    • Big science in a small country

      Switzerland's unique geography and economy put it at the centre of the world when it comes to scientific collaboration.

      • Nic Fleming

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    Review

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    • Expanding and reprogramming the genetic code

      • Jason W. Chin

      A review of the recent developments in reprogramming the genetic code of cells and organisms to include non-canonical amino acids in precisely engineered proteins.

    Articles

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    • Strains, functions and dynamics in the expanded Human Microbiome Project

      • Jason Lloyd-Price
      • Anup Mahurkar
      • Gholamali Rahnavard
      • Jonathan Crabtree
      • Joshua Orvis
      • A. Brantley Hall
      • Arthur Brady
      • Heather H. Creasy
      • Carrie McCracken
      • Michelle G. Giglio
      • Daniel McDonald
      • Eric A. Franzosa
      • Rob Knight
      • Owen White
      • Curtis Huttenhower

      Updates from the Human Microbiome Project analyse the largest known body-wide metagenomic profile of human microbiome personalization.

    • Genome editing reveals a role for OCT4 in human embryogenesis

      • Norah M. E. Fogarty
      • Afshan McCarthy
      • Kirsten E. Snijders
      • Benjamin E. Powell
      • Nada Kubikova
      • Paul Blakeley
      • Rebecca Lea
      • Kay Elder
      • Sissy E. Wamaitha
      • Daesik Kim
      • Valdone Maciulyte
      • Jens Kleinjung
      • Jin-Soo Kim
      • Dagan Wells
      • Ludovic Vallier
      • Alessandro Bertero
      • James M. A. Turner
      • Kathy K. Niakan

      Genome editing in human zygotes shows that OCT4 is required for normal development at an earlier stage in humans than in mice.

    • Massively parallel de novo protein design for targeted therapeutics

      • Aaron Chevalier
      • Daniel-Adriano Silva
      • Gabriel J. Rocklin
      • Derrick R. Hicks
      • Renan Vergara
      • Patience Murapa
      • Steffen M. Bernard
      • Lu Zhang
      • Kwok-Ho Lam
      • Guorui Yao
      • Christopher D. Bahl
      • Shin-Ichiro Miyashita
      • Inna Goreshnik
      • James T. Fuller
      • Merika T. Koday
      • Cody M. Jenkins
      • Tom Colvin
      • Lauren Carter
      • Alan Bohn
      • Cassie M. Bryan
      • D. Alejandro Fernández-Velasco
      • Lance Stewart
      • Min Dong
      • Xuhui Huang
      • Rongsheng Jin
      • Ian A. Wilson
      • Deborah H. Fuller
      • David Baker

      A massively parallel computational and experimental approach for de novo designing and screening small hyperstable proteins targeting influenza haemagglutinin and botulinum neurotoxin B identifies new therapeutic candidates more robust than traditional antibody therapies.

    Letters

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    • A hybrid type Ia supernova with an early flash triggered by helium-shell detonation

      • Ji-an Jiang
      • Mamoru Doi
      • Keiichi Maeda
      • Toshikazu Shigeyama
      • Ken’ichi Nomoto
      • Naoki Yasuda
      • Saurabh W. Jha
      • Masaomi Tanaka
      • Tomoki Morokuma
      • Nozomu Tominaga
      • Željko Ivezić
      • Pilar Ruiz-Lapuente
      • Maximilian D. Stritzinger
      • Paolo A. Mazzali
      • Christopher Ashall
      • Jeremy Mould
      • Dietrich Baade
      • Nao Suzuki
      • Andrew J. Connolly
      • Ferdinando Patat
      • Lifan Wang
      • Peter Yoachim
      • David Jones
      • Hisanori Furusawa
      • Satoshi Miyazaki

      The detection and simulation of a type Ia supernova with an early, red flash suggests that it formed through detonation of the helium shell of a white dwarf, rather than by collision of the ejecta with a companion star or by merging with another white dwarf.

    • A spin transition mechanism for cooperative adsorption in metal–organic frameworks

      • Douglas A. Reed
      • Benjamin K. Keitz
      • Julia Oktawiec
      • Jarad A. Mason
      • Tomče Runčevski
      • Dianne J. Xiao
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      • Valentina Crocellà
      • Silvia Bordiga
      • Jeffrey R. Long

      Metal–organic frameworks that undergo a cooperative spin transition at neighbouring metal centres upon coordination to CO exhibit large CO separation capacities with only small changes in temperature.

    • Delta progradation in Greenland driven by increasing glacial mass loss

      • Mette Bendixen
      • Lars Lønsmann Iversen
      • Anders Anker Bjørk
      • Bo Elberling
      • Andreas Westergaard-Nielsen
      • Irina Overeem
      • Katy R. Barnhart
      • Shfaqat Abbas Khan
      • Jason E. Box
      • Jakob Abermann
      • Kirsty Langley
      • Aart Kroon

      Climate change has the potential to erode coastlines, but a rediscovered archive of aerial photographs from the Second World War shows that in southern Greenland, deltas have recently extended seaward.

    • Temporal coexistence mechanisms contribute to the latitudinal gradient in forest diversity

      • Jacob Usinowicz
      • Chia-Hao Chang-Yang
      • Yu-Yun Chen
      • James S. Clark
      • Christine Fletcher
      • Nancy C. Garwood
      • Zhanqing Hao
      • Jill Johnstone
      • Yiching Lin
      • Margaret R. Metz
      • Takashi Masaki
      • Tohru Nakashizuka
      • I-Fang Sun
      • Renato Valencia
      • Yunyun Wang
      • Jess K. Zimmerman
      • Anthony R. Ives
      • S. Joseph Wright

      High tree species diversity in tropical forests is driven by reduced interspecific competition relative to intraspecific competition, as a result of the asynchronous timing of tree recruitment permitted by long and stable growing seasons.

      See also
    • A reversible haploid mouse embryonic stem cell biobank resource for functional genomics

      • Ulrich Elling
      • Reiner A. Wimmer
      • Andreas Leibbrandt
      • Thomas Burkard
      • Georg Michlits
      • Alexandra Leopoldi
      • Thomas Micheler
      • Dana Abdeen
      • Sergei Zhuk
      • Irene M. Aspalter
      • Cornelia Handl
      • Julia Liebergesell
      • Maria Hubmann
      • Anna-Maria Husa
      • Manuela Kinzer
      • Nicole Schuller
      • Ellen Wetzel
      • Nina van de Loo
      • Jorge Arturo Zepeda Martinez
      • David Estoppey
      • Ralph Riedl
      • Fengtang Yang
      • Beiyuan Fu
      • Thomas Dechat
      • Zoltán Ivics
      • Chukwuma A. Agu
      • Oliver Bell
      • Dieter Blaas
      • Holger Gerhardt
      • Dominic Hoepfner
      • Alexander Stark
      • Josef M. Penninger

      The Haplobank contains over 100,000 individually reversibly mutagenized, barcoded, mouse embryonic cell lines; proof-of-principle experiments were used to search for genes that are required for rhinovirus infection and angiogenesis using forward and reverse genetic screens, respectively.

    • Inflammasome-driven catecholamine catabolism in macrophages blunts lipolysis during ageing

      • Christina D. Camell
      • Jil Sander
      • Olga Spadaro
      • Aileen Lee
      • Kim Y. Nguyen
      • Allison Wing
      • Emily L. Goldberg
      • Yun-Hee Youm
      • Chester W. Brown
      • John Elsworth
      • Matthew S. Rodeheffer
      • Joachim L. Schultze
      • Vishwa Deep Dixit

      Lipolysis declines with age because NLRP3 inflammasome-activated adipose tissue macrophages reduce levels of noradrenaline by upregulating genes that control its degradation, such as GDF3 and MAOA.

    • CG dinucleotide suppression enables antiviral defence targeting non-self RNA

      • Matthew A. Takata
      • Daniel Gonçalves-Carneiro
      • Trinity M. Zang
      • Steven J. Soll
      • Ashley York
      • Daniel Blanco-Melo
      • Paul D. Bieniasz

      Vertebrate genomes contain fewer CG dinucleotides than would be expected by chance, and this pattern is mimicked by many viruses; HIV-1 derivatives mutated to contain more CG dinucleotides are targeted by the human antiviral protein ZAP, suggesting that CG suppression has evolved in viruses to evade recognition.

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    • Discovery of a selective catalytic p300/CBP inhibitor that targets lineage-specific tumours

      • Loren M. Lasko
      • Clarissa G. Jakob
      • Rohinton P. Edalji
      • Wei Qiu
      • Debra Montgomery
      • Enrico L. Digiammarino
      • T. Matt Hansen
      • Roberto M. Risi
      • Robin Frey
      • Vlasios Manaves
      • Bailin Shaw
      • Mikkel Algire
      • Paul Hessler
      • Lloyd T. Lam
      • Tamar Uziel
      • Emily Faivre
      • Debra Ferguson
      • Fritz G. Buchanan
      • Ruth L. Martin
      • Maricel Torrent
      • Gary G. Chiang
      • Kannan Karukurichi
      • J. William Langston
      • Brian T. Weinert
      • Chunaram Choudhary
      • Peter de Vries
      • John H. Van Drie
      • David McElligott
      • Ed Kesicki
      • Ronen Marmorstein
      • Chaohong Sun
      • Philip A. Cole
      • Saul H. Rosenberg
      • Michael R. Michaelides
      • Albert Lai
      • Kenneth D. Bromberg

      A potent and selective catalytic inhibitor of p300/CBP histone acetyltransferases suppresses tumour proliferation across multiple cell lineages, illustrating the therapeutic potential of drug-like small molecules that target histone acetyltransferases.

    • PAK signalling drives acquired drug resistance to MAPK inhibitors in BRAF-mutant melanomas

      • Hezhe Lu
      • Shujing Liu
      • Gao Zhang
      • Bin Wu
      • Yueyao Zhu
      • Dennie T. Frederick
      • Yi Hu
      • Wenqun Zhong
      • Sergio Randell
      • Norah Sadek
      • Wei Zhang
      • Gang Chen
      • Chaoran Cheng
      • Jingwen Zeng
      • Lawrence W. Wu
      • Jie Zhang
      • Xiaoming Liu
      • Wei Xu
      • Clemens Krepler
      • Katrin Sproesser
      • Min Xiao
      • Benchun Miao
      • Jianglan Liu
      • Claire D. Song
      • Jephrey Y. Liu
      • Giorgos C. Karakousis
      • Lynn M. Schuchter
      • Yiling Lu
      • Gordon Mills
      • Yusheng Cong
      • Jonathan Chernoff
      • Jun Guo
      • Genevieve M. Boland
      • Ryan J. Sullivan
      • Zhi Wei
      • Jeffrey Field
      • Ravi K. Amaravadi
      • Keith T. Flaherty
      • Meenhard Herlyn
      • Xiaowei Xu
      • Wei Guo

      BRAF-inhibition resistance in metastatic melanoma occurs through p21-activated kinase-mediated reactivation of ERK, whereas resistance to combined BRAF and MEK inhibition occurs through p21-activated kinase-mediated regulation of JNK and β-catenin phosphorylation, mTOR pathway activation and apoptosis inhibition in many patients.

    Corrigenda

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