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Volume 488 Issue 7409, 2 August 2012

The association between a land plant and the soil microbes of the root microbiome is important for the plant’s well-being. A deeper understanding of these microbial communities will offer opportunities to control plant growth and susceptibility to pathogens, particularly in sustainable agricultural regimes. Two groups, working separately but developing best-practice protocols in parallel, have characterized the root microbiota of the model plant Arabidopis thaliana. Working on two continents and with five different soil types, they reach similar general conclusions. The bacterial communities in each root compartment — the rhizosphere immediately surrounding the root and the endophytic compartment within the root — are most strongly influenced by soil type, and to a lesser degree by host genotype. In natural soils, Arabidopsis plants are preferentially colonized by Actinobacteria, Proteobacteria, Bacteroidetes and Chloroflexi species. And — an important point for future work  Arabidopsis root selectivity for soil bacteria under controlled environmental conditions mimics that of plants grown in a natural environment. Cover: Tim Robberts/Getty Images

Editorial

  • Scientists must remember that however irrelevant their involvement in industry might seem to them, others will see it differently — only full disclosure will avert the taint of scandal.

    Editorial

    Advertisement

  • Scientists unhappy with policy are right to take to the streets.

    Editorial
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World View

  • After a generation of denial, research leaders are finally treating scientific fraud with the seriousness it deserves, says Colin Macilwain.

    • Colin Macilwain
    World View
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Research Highlights

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Seven Days

  • The week in science: Nine physicists net $3 million each in new prize; India curbs tiger tourism; and Uganda suffers an outbreak of ebolavirus

    Seven Days
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News

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Correction

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News Feature

  • Physicists, chemists and mathematicians in the United Kingdom are furious about funding reforms that they say threaten blue-skies research.

    • Ananyo Bhattacharya
    News Feature
  • Advocates of 'cliodynamics' say that they can use scientific methods to illuminate the past. But historians are not so sure.

    • Laura Spinney
    News Feature
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Comment

  • NASA must put more of its money into thrifty missions led by principal investigators, says Daniel N. Baker.

    • Daniel N. Baker
    Comment
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Books & Arts

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Correspondence

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News & Views

  • A complete insect fossil from the Devonian period has long been sought. The finding of a candidate may improve our patchy understanding of when winged insects evolved. See Letter p.82

    • William A. Shear
    News & Views
  • Careful analysis reveals that the global uptake of anthropogenic carbon dioxide emissions by carbon sinks has doubled during the past 50 years — but the fractions of this absorbed by land and by sea remain unclear. See Letter p.70

    • Ingeborg Levin

    Special:

    News & Views
  • A mutant repeating DNA sequence produces a toxic RNA molecule that causes the neuromuscular disorder myotonic dystrophy type 1. An ‘antisense’ therapy that targets this RNA in cell nuclei shows promise in mice. See Letter p.111

    • Peter K. Todd
    • Henry L. Paulson
    News & Views
  • A rare gene variant has been found that decreases the peptide deposition seen in the brains of people with Alzheimer's disease. The mutation may also slow the normal cognitive decline that occurs with age. See Letter p.96

    • Bart De Strooper
    • Thierry Voet
    News & Views
  • A fine marriage between atomic and optical physics has produced a medium that is transparent to single photons but opaque to multiple photons. The finding heralds the development of devices such as single-photon switches. See Letter p.57

    • Thad G. Walker
    News & Views
  • The small genomes of some bacteria could provide the first complete understanding of a biological system. A new computer model brings this goal closer, by calculating every process in a dividing Mycoplasma cell.

    • Mark Isalan
    News & Views
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Article

  • Whole-genome sequencing of medulloblastoma samples reveals several recurrent mutations in genes not previously implicated in the disease, many of which affect components of the epigenetic machinery in different disease subgroups.

    • Giles Robinson
    • Matthew Parker
    • Richard J. Gilbertson
    Article Open Access
  • Medulloblastoma is the most common malignant brain tumour in children; having assembled over 1,000 samples the authors report that somatic copy number aberrations are common in medulloblastoma, in particular a tandem duplication of SNCAIP, a gene associated with Parkinson’s disease, which is restricted to subgroup 4α, and translocations of PVT1, which are restricted to Group 3.

    • Paul A. Northcott
    • David J. H. Shih
    • Michael D. Taylor
    Article Open Access
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Letter

  • An extremely large, negative refractive index is produced in a two-dimensional electron gas by exploiting its kinetic inductance, which is a manifestation of acceleration of the electrons by electromagnetic fields.

    • Hosang Yoon
    • Kitty Y. M. Yeung
    • Donhee Ham
    Letter
  • The fossil of a complete insect from the Late Devonian period (approximately 365 million years ago) is presented; it was terrestrial, but its features suggest that modern winged insects had already started to diversify at that early date.

    • Romain Garrouste
    • Gaël Clément
    • André Nel
    Letter
  • Sequencing of the Arabidopsis thaliana root microbiome shows that its composition is strongly influenced by location, inside or outside the root, and by soil type.

    • Derek S. Lundberg
    • Sarah L. Lebeis
    • Jeffery L. Dangl
    Letter
  • Roots of land plants are populated by a specific microbiota capable of modulating plant growth and development; here large-scale sequencing analysis shows that the bacterial community inhabiting Arabidopsis roots is influenced by soil type and plant genotype, and that plant cell-wall features serve as colonization cue for a subcommunity of the root microbiota.

    • Davide Bulgarelli
    • Matthias Rott
    • Paul Schulze-Lefert
    Letter
  • Medulloblastoma is the most common brain tumour in children; using whole-genome sequencing of tumour samples the authors show that the clinically challenging Group 3 and 4 tumours can be tetraploid, and reveal the expression of the first medulloblastoma fusion genes identified.

    • David T. W. Jones
    • Natalie Jäger
    • Peter Lichter
    Letter Open Access
  • Medulloblastoma is the most common brain tumour in children; using exome sequencing of tumour samples the authors show that these cancers have low mutation rates and identify 12 significantly mutated genes, among them the gene encoding RNA helicase DDX3X.

    • Trevor J. Pugh
    • Shyamal Dilhan Weeraratne
    • Yoon-Jae Cho
    Letter
  • Nuclear-retained transcripts containing expanded repeats are shown to be sensitive to antisense silencing, and in a transgenic mouse model of myotonic dystrophy type 1, systemic administration of ASOs causes a rapid knockdown of the toxic RNA in skeletal muscle, correcting some hallmark features of the disease.

    • Thurman M. Wheeler
    • Andrew J. Leger
    • Charles A. Thornton
    Letter
  • A genomic map of nearly 300,000 potential cis-regulatory sequences determined from diverse mouse tissues and cell types reveals active promoters, enhancers and CCCTC-binding factor sites encompassing 11% of the mouse genome and significantly expands annotation of mammalian regulatory sequences.

    • Yin Shen
    • Feng Yue
    • Bing Ren
    Letter
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Column

  • Mentors should understand what causes misconduct among trainees — and keep in mind some possible remedies, argues William Neaves.

    • William Neaves
    Column
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Career Brief

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Futures

  • Interactive art.

    • Polenth Blake
    Futures
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Brief Communications Arising

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