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Computational materials scienceSubstitution with vision p.674

A method has been developed for predicting the stability and elasticity of certain alloys for millions of atomic configurations of the materials. This approach should help to identify materials with optimized properties. See Letter p.740

Gus L. W. Hart

doi: 10.1038/nature11755

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Plant ecologyForests on the brink p.675

An analysis of the physiological vulnerability of different trees to drought shows that forests around the globe are at equally high risk of succumbing to increases in drought conditions. See Letter p.752

Bettina M. J. Engelbrecht

doi: 10.1038/nature11756

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Earth scienceMagma chambers on a slow burner p.677

An assessment of crystallization processes occurring in magma chambers in the ocean floor finds an unexpected enrichment in trace elements, reviving an old theory of the cycling of magma in these chambers. See Article p.698

Albrecht W. Hofmann

doi: 10.1038/491677a

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GenomicsDecoding our daily bread p.678

The wheat genome is large and complex, and has defied complete sequencing. But the most comprehensive analysis so far of the plant's genes will support efforts to optimize the supply of this vital food crop. See Letter p.705

Peter Langridge

doi: 10.1038/491678a

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ImmunologyVitamins prime immunity p.680

The finding that derivatives of vitamin B can bind to an antigen-presenting protein that stimulates specialized immune cells suggests a novel mechanism by which the immune system detects microbial infections. See Article p.717

Wei-Jen Chua & Ted H. Hansen

doi: 10.1038/491680a

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Quantum physicsStrongly correlated transport p.681

The field-effect transistor underlies microprocessor technology. A version of it has been demonstrated that tunes particle transport from an incoherent regime to a strongly correlated superfluid one. See Letter p.736

Lincoln D. Carr & Mark T. Lusk

doi: 10.1038/491681a

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Perspectives

Articles

The global pattern of trace-element distributions in ocean floor basalts p.698

The magmatic layers of the oceanic crust are created at constructive plate margins by partial melting of the mantle as it wells up. The chemistry of ocean floor basalts, the most accessible product of this magmatism, is studied for the insights it yields into the compositional heterogeneity of the mantle and its thermal structure. However, before eruption, parental magma compositions are modified at crustal pressures by a process that has usually been assumed to be fractional crystallization. Here we show that the global distributions of trace elements in ocean floor basalts describe a systematic pattern that cannot be explained by simple fractional crystallization alone, but is due to cycling of magma through the global ensemble of magma chambers. Variability in both major and incompatible trace-element contents about the average global pattern is due to fluctuations in the magma fluxes into and out of the chambers, and their depth, as well as to differences in the composition of the parental magmas.

Hugh St C. O’Neill & Frances E. Jenner

doi: 10.1038/nature11678

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Analysis of the bread wheat genome using whole-genome shotgun sequencing p.705

Bread wheat (Triticum aestivum) is a globally important crop, accounting for 20 per cent of the calories consumed by humans. Major efforts are underway worldwide to increase wheat production by extending genetic diversity and analysing key traits, and genomic resources can accelerate progress. But so far the very large size and polyploid complexity of the bread wheat genome have been substantial barriers to genome analysis. Here we report the sequencing of its large, 17-gigabase-pair, hexaploid genome using 454 pyrosequencing, and comparison of this with the sequences of diploid ancestral and progenitor genomes. We identified between 94,000 and 96,000 genes, and assigned two-thirds to the three component genomes (A, B and D) of hexaploid wheat. High-resolution synteny maps identified many small disruptions to conserved gene order. We show that the hexaploid genome is highly dynamic, with significant loss of gene family members on polyploidization and domestication, and an abundance of gene fragments. Several classes of genes involved in energy harvesting, metabolism and growth are among expanded gene families that could be associated with crop productivity. Our analyses, coupled with the identification of extensive genetic variation, provide a resource for accelerating gene discovery and improving this major crop.

Rachel Brenchley, Manuel Spannagl, Matthias Pfeifer, Gary L. A. Barker, Rosalinda D’Amore, Alexandra M. Allen, Neil McKenzie, Melissa Kramer, Arnaud Kerhornou, Dan Bolser + et al.

doi: 10.1038/nature11650

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A physical, genetic and functional sequence assembly of the barley genome p.711

Barley (Hordeum vulgare L.) is among the world’s earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 ‘high-confidence’ genes with homology support from other plant genomes. Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement.

doi: 10.1038/nature11543

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MR1 presents microbial vitamin B metabolites to MAIT cells p.717

Antigen-presenting molecules, encoded by the major histocompatibility complex (MHC) and CD1 family, bind peptide- and lipid-based antigens, respectively, for recognition by T cells. Mucosal-associated invariant T (MAIT) cells are an abundant population of innate-like T cells in humans that are activated by an antigen(s) bound to the MHC class I-like molecule MR1. Although the identity of MR1-restricted antigen(s) is unknown, it is present in numerous bacteria and yeast. Here we show that the structure and chemistry within the antigen-binding cleft of MR1 is distinct from the MHC and CD1 families. MR1 is ideally suited to bind ligands originating from vitamin metabolites. The structure of MR1 in complex with 6-formyl pterin, a folic acid (vitamin B9) metabolite, shows the pterin ring sequestered within MR1. Furthermore, we characterize related MR1-restricted vitamin derivatives, originating from the bacterial riboflavin (vitamin B2) biosynthetic pathway, which specifically and potently activate MAIT cells. Accordingly, we show that metabolites of vitamin B represent a class of antigen that are presented by MR1 for MAIT-cell immunosurveillance. As many vitamin biosynthetic pathways are unique to bacteria and yeast, our data suggest that MAIT cells use these metabolites to detect microbial infection.

Lars Kjer-Nielsen, Onisha Patel, Alexandra J. Corbett, Jérôme Le Nours, Bronwyn Meehan, Ligong Liu, Mugdha Bhati, Zhenjun Chen, Lyudmila Kostenko, Rangsima Reantragoon + et al.

doi: 10.1038/nature11605

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Visualizing transient low-populated structures of RNA p.724

The visualization of RNA conformational changes has provided fundamental insights into how regulatory RNAs carry out their biological functions. The RNA structural transitions that have been characterized so far involve long-lived species that can be captured by structure characterization techniques. Here we report the nuclear magnetic resonance visualization of RNA transitions towards ‘invisible’ excited states (ESs), which exist in too little abundance (2–13%) and for too short a duration (45–250 μs) to allow structural characterization by conventional techniques. Transitions towards ESs result in localized rearrangements in base-pairing that alter building block elements of RNA architecture, including helix–junction–helix motifs and apical loops. The ES can inhibit function by sequestering residues involved in recognition and signalling or promote ATP-independent strand exchange. Thus, RNAs do not adopt a single conformation, but rather exist in rapid equilibrium with alternative ESs, which can be stabilized by cellular cues to affect functional outcomes.

Elizabeth A. Dethoff, Katja Petzold, Jeetender Chugh, Anette Casiano-Negroni & Hashim M. Al-Hashimi

doi: 10.1038/nature11498

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Letters

Global convergence in the vulnerability of forests to drought p.752

Brendan Choat, Steven Jansen, Tim J. Brodribb, Hervé Cochard, Sylvain Delzon, Radika Bhaskar, Sandra J. Bucci, Taylor S. Feild, Sean M. Gleason, Uwe G. Hacke + et al.

doi: 10.1038/nature11688

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Impaired intrinsic immunity to HSV-1 in human iPSC-derived TLR3-deficient CNS cells p.769

Fabien G. Lafaille, Itai M. Pessach, Shen-Ying Zhang, Michael J. Ciancanelli, Melina Herman, Avinash Abhyankar, Shui-Wang Ying, Sotirios Keros, Peter A. Goldstein, Gustavo Mostoslavsky + et al.

doi: 10.1038/nature11583

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