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Volume 507 Issue 7490, 6 March 2014

CRISPR/Cas9-based DNA targeting has quickly become a leading tool in the fields of synthetic biology and genome engineering. It exploits the ability of a bacterial endonuclease, Cas9, guided by an RNA molecule, to target virtually any matching DNA sequence of interest for binding and/or cleavage. A study published in this issue of Nature reports the use of single-molecule and bulk biochemical experiments to reveal the mechanism by which RNA-guided Cas9 locates unique 20-base-pair sequences within DNA genomes, which can be billions of base pairs long. The results highlight the role of a trinucleotide protospacer adjacent motif (PAM; yellow in the cover image) in recruiting Cas9–RNA complexes to potential DNA target sites, and in catalytically activating the nuclease (outlined in brown). Target DNA sequences are recognized via a ‘zip-up� mechanism, where the sequential formation of RNA–DNA base pairs (red) offsets the energetic cost of unwinding the DNA double helix (purple and blue). In addition to its relevance for gene manipulation, this work reveals how DNA is interrogated by Cas9–RNA in its role as an effector of adaptive immunity in bacteria. Cover: K. C. Roeyer.

Editorial

  • The authorities must take the necessary time to remedy the slapdash introduction of a database containing the medical records of the entire population of England.

    Editorial

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  • Regulatory agencies must demand conflict-of-interest statements for the research they use.

    Editorial
  • Identifiers that follow researchers’ work from grant to paper will make funding more effective.

    Editorial
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World View

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Research Highlights

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Seven Days

  • The week in science: Snow satellite launches; publishers remove computer-generated papers; and Switzerland’s access to EU research funds restricted.

    Seven Days
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News

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Correction

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News Feature

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Comment

  • Bold strategies are needed to identify the elusive particles that should make up most of the Universe's mass, say Mario Livio and Joe Silk.

    • Mario Livio
    • Joe Silk
    Comment
  • With improved breeding and cultivation, ruminant animals can yield food that is better for people and the planet, say Mark C. Eisler, Michael R. F. Lee and colleagues.

    • Mark C. Eisler
    • Michael R. F. Lee
    • Michael Winter
    Comment
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Books & Arts

  • Li Gong ponders a translation of a Chinese novel on the world of code-breaking.

    • Li Gong
    Books & Arts
  • Ewen Callaway revels in an exhibition chronicling the ebb and flow of early humanity over the British Isles.

    • Ewen Callaway
    Books & Arts
  • Materials scientist and engineer Andrea Hamilton at the University of Strathclyde in Glasgow, UK, uses chemistry research to conserve the structural and aesthetic integrity of concrete. She talks about dams, nuclear-waste storage and an artwork that explores weathering.

    • Alexandra Witze
    Books & Arts
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Correspondence

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News & Views

  • The discovery of crystallographic imperfections known as disclinations in the most profuse mineral in Earth's upper mantle has the potential to solve a problem that has vexed mineral physicists for decades. See Article p.51

    • Greg Hirth
    News & Views
  • An elastic membrane cast around a three-dimensional printed model of a specific heart allows diverse aspects of cardiac function to be monitored and modified, and paves the way to new diagnostic and therapeutic approaches.

    • Colleen E. Clancy
    • Yang K. Xiang
    News & Views
  • The protein NRT1.1 transports nitrate ions into plants over a wide range of concentrations. Two studies provide structural insight into this unusual behaviour, but give different explanations for it. See Articles p.68 & p.73

    • Yi-Fang Tsay
    News & Views
  • An optomechanical device has been designed that converts radio-frequency electrical signals into laser light. The system could allow computers to share data in a future quantum network based on optical fibres. See Letter p.81

    • Mika A. Sillanpää
    • Pertti J. Hakonen
    News & Views
  • Predicting the long-term evolution of influenza is difficult. But a model incorporating the effects of deleterious and beneficial mutations has met the more tangible goal of predicting year-to-year frequencies of viral groups. See Article p.57

    • Katia Koelle
    • David A. Rasmussen
    News & Views
  • Tumour spread is the main cause of death in patients with melanoma. Exposure of melanoma to ultraviolet radiation has now been found to cause an inflammatory response that drives the formation of distant metastases. See Letter p.109

    • Seth B. Coffelt
    • Karin E. de Visser
    News & Views
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Article

  • Using electron backscattering diffraction maps of deformed olivine to resolve the disclinations at grain boundaries, combined with a disclination-based model of a high-angle tilt boundary in olivine, reveals the missing mechanism for describing plastic flow in polycrystalline olivine: an applied shear induces grain-boundary migration through disclination motion.

    • Patrick Cordier
    • Sylvie Demouchy
    • Claude Fressengeas
    Article
  • A computational approach for predicting the future evolution of the human influenza virus, based on population-genetic data of previous strains, is presented; this model holds promise for improving vaccine strain selection for seasonal influenza.

    • Marta Łuksza
    • Michael Lässig
    Article
  • This study defines how a short DNA sequence, known as the PAM, is critical for target DNA interrogation by the CRISPR-associated enzyme Cas9 — DNA melting and heteroduplex formation initiate near the PAM and extend directionally through the remaining target sequence, and the PAM is also required to activate the catalytic activity of Cas9.

    • Samuel H. Sternberg
    • Sy Redding
    • Jennifer A. Doudna
    Article
  • In Arabidopsis thaliana the phosphorylation state of the ‘dual affinity’ transporter, NRT1.1, allows the uptake of nitrate over a wide concentration range; the crystal structure and molecular basis for this is described in this study.

    • Joanne L. Parker
    • Simon Newstead
    Article
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Letter

  • Observations of a protostellar envelope and disk (from which planets should form) in the relatively close star-forming region of the Taurus molecular cloud reveal unexpected chemistry in the gas between the envelope and the disk: the unsaturated hydrocarbon molecule cyclic-C3H2 and sulphur monoxide.

    • Nami Sakai
    • Takeshi Sakai
    • Satoshi Yamamoto
    Letter
  • Scanning tunnelling microscopy reveals that molecules of ferrocenecarboxylic acid can self-assemble into quasicrystal monolayers containing highly unusual cyclic hydrogen-bonded pentamers; this molecular framework could form the basis of a large range of supramolecular assemblies.

    • Natalie A. Wasio
    • Rebecca C. Quardokus
    • S. Alex Kandel
    Letter
  • A global analysis shows that for most tree species the largest trees are the fastest-growing trees, a finding that resolves conflicting assumptions about tree growth and that has implications for understanding forest carbon dynamics, resource allocation trade-offs within trees and plant senescence.

    • N. L. Stephenson
    • A. J. Das
    • M. A. Zavala
    Letter
  • Direct neural recordings from electrodes over bilateral cortices show that sensory–motor transformations for speech occur bilaterally; neural responses are robust during both perception and production in an overt word-repetition task, and bilateral sensory–motor responses can perform transformations between speech-perception and speech-production representations during a non-word transformation task.

    • Gregory B. Cogan
    • Thomas Thesen
    • Bijan Pesaran
    Letter
  • Generation of human induced pluripotent stem cells from patient fibroblasts containing ring chromosomes with large deletions reveals that reprogrammed cells lose the abnormal chromosome and duplicate the wild-type homologue through compensatory uniparental disomy, suggesting that cellular reprogramming may hold potential for ‘chromosome therapy’.

    • Marina Bershteyn
    • Yohei Hayashi
    • Anthony Wynshaw-Boris

    Special:

    Letter
  • This study shows that PADI4-mediated citrullination occurs during pluripotency and that citrullination of H1 results in loosening of chromatin compaction; furthermore, citrullination is shown to be important for the activation of stem-cell genes, for iPS cell reprogramming and to maintain pluripotent cells in the early mouse embryo.

    • Maria A. Christophorou
    • Gonçalo Castelo-Branco
    • Tony Kouzarides
    Letter
  • Escherichia coli K-12 performs sulphoglycolysis; heterologous expression of enzymes encoded in a ten-gene cluster present in almost all (>91%) available E. coli genomes is used to show that sulphoquinovose is catabolised through four reactions to produce dihydroxyacetone phosphate, which powers energy conservation and growth, and a sulphonate product, which is excreted.

    • Karin Denger
    • Michael Weiss
    • David Schleheck
    Letter
  • Here it is shown that T-cell receptors accumulate at the immunological synapse after stimulation with cognate antigen and are released in extracellular microvesicles by an ESCRT-dependent mechanism, the microvesicles deliver transcellular signals from CD4 T cells to antigen-presenting B cells and can induce B-cell signalling.

    • Kaushik Choudhuri
    • Jaime Llodrá
    • Michael L. Dustin
    Letter
  • In Arabidopsis, the RNA-directed DNA methylation pathway is important for establishing and maintaining DNA methylation — here Pol V is shown to depend on SUVH2 and SUVH9, where both of these proteins are proposed to bind specifically to methylated DNA to recruit Pol V, providing a self-reinforcing loop mechanism for maintenance of RNA-directed DNA methylation.

    • Lianna M. Johnson
    • Jiamu Du
    • Steven E. Jacobsen
    Letter
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Feature

  • China is luring back expatriates with generous incentives, causing many to weigh the pros and cons of returning.

    • Quirin Schiermeier
    Feature
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Column

  • Scientists should find engaging ways to present information to their target audience, says Yoshimi Rii.

    • Yoshimi Rii
    Column
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Futures

  • Reconnect with your past.

    • Coy St Clair
    Futures
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Outlook

    • Herb Brody
    Outlook
  • The advent of routine childhood vaccination has led to dramatic declines in many contagious diseases in the United States. Maintaining these gains there and spreading these successes worldwide are major public-health challenges. By Tony Scully.

    • Tony Scully
    Outlook
  • Malaria, HIV/AIDS and tuberculosis are humanity's deadliest foes, and have stymied vaccinologists for centuries. New technology and ideas could finally make a difference.

    • Katherine Bourzac
    Outlook
  • Extreme temperatures damage vaccines. Efforts are underway to find better ways to deliver the goods.

    • Neil Savage
    Outlook
  • China is poised to become a major global vaccine maker, but first it must overcome serious problems with quality control.

    • Priya Shetty
    Outlook
  • We must push harder to eliminate diseases, for everyone's benefit, say Andrew Artenstein and Gregory Poland.

    • Andrew W. Artenstein
    • Gregory A. Poland
    Outlook
  • Faced with outbreaks of preventable diseases, public-health experts need to win over parents who refuse vaccinations.

    • Michael Eisenstein
    Outlook
  • Klaus Stöhr asks whether those responsible for public health will grasp new opportunities to ensure pandemic vaccine readiness.

    • Klaus Stöhr
    Outlook
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Nature Outlook

  • Vaccination is a triumph of preventative healthcare. But the project to erect immunological shields against deadly pathogens is far from complete — some of the most lethal diseases still lack effective vaccines. Moreover, major inequities exist in the global distribution of vaccines. Despite substantial advances in vaccine production and development, global efforts to eradicate disease through inoculation still face scientific, technological and economic hurdles.

    Nature Outlook
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