네이처 컨텐츠

Editorials

Fishy limits p.435

The European Union has set a worrying trend by ignoring scientific advice on overfishing. It must put long-term sustainability plans ahead of short-term political gains.

doi: 10.1038/528435a

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Quantum leap p.435

Physicists can better study the quantum behaviour of objects on the atomic scale.

doi: 10.1038/528435b

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Light relief p.436

Nature digs into the rumours about the effect of festive illuminations on wireless fidelity.

doi: 10.1038/528436a

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News

The science events that shaped 2015 p.448

Gene-editing, climate change and Pluto are among the year’s top stories.

Monya Baker, Ewen Callaway, Davide Castelvecchi, Lauren Morello, Sara Reardon, Quirin Schiermeier & Alexandra Witze

doi: 10.1038/528448a

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News Features

News & Views

Autophagy is not the answer p.482

The cellular process of autophagy has been proposed to help kill Mycobacterium tuberculosis. But although the autophagy gene Atg5 is key to host immunity, other autophagy genes do not affect the outcome of tuberculosis. See Letter p.565

Samuel M. Behar & Eric H. Baehrecke

doi: 10.1038/nature16324

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Silicon chips lighten up p.483

Microprocessor communications have received a boost from the integration of electronics and photonics in silicon — a first step towards low power consumption and efficient computing systems. See Letter p.534

Laurent Vivien

doi: 10.1038/528483a

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A personal forecast p.484

Machine learning, applied to complex multidimensional data, is shown to provide personalized dietary recommendations to control blood glucose levels. This is a step towards integrating the gut microbiome into personalized medicine.

Erica D. Sonnenburg & Justin L. Sonnenburg

doi: 10.1038/528484a

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Strength ceiling smashed for light metals p.486

Nanoscale particles have been uniformly dispersed in a magnesium alloy, yielding composites with record-breaking strengths — and raising the prospect of using magnesium as a lightweight metal for structural applications. See Letter p.539

Maria Teresa Pérez Prado & Carmen M. Cepeda-Jiménez

doi: 10.1038/528486a

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A division of labour combined p.487

The discovery of microorganisms that can oxidize ammonia all the way to nitrate refutes the century-old paradigm that this nitrification process requires the activity of two types of microbe. See Article p.504 & Letter p.555

Marcel M. M. Kuypers

doi: 10.1038/528487a

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Innate immunity repairs gut lining p.488

It emerges that innate immune cells called group 3 innate lymphoid cells signal directly to intestinal stem cells to promote the replacement of damaged epithelial cells lining the gut. See Letter p.560

Konrad Gronke & Andreas Diefenbach

doi: 10.1038/nature16325

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Articles

Network-analysis-guided synthesis of weisaconitine D and liljestrandinine p.493

Network analysis to determine the maximally bridged ring (or rings) of molecules is used as part of a strategy for the syntheses of architecturally complex natural chemicals; this strategy is demonstrated via the synthesis of the diterpenoid alkaloids weisaconitine D and liljestrandinine.

C. J. Marth, G. M. Gallego, J. C. Lee, T. P. Lebold, S. Kulyk, K. G. M. Kou, J. Qin, R. Lilien & R. Sarpong

doi: 10.1038/nature16440

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Genome-wide patterns of selection in 230 ancient Eurasians p.499

The first genome-wide scan for selection using ancient DNA, based on data from 230 West Eurasians dating between to 6500 and 300 BC and including new data from 163 individuals among which are 26 Neolithic Anatolians, provides a direct view of selection on loci associated with diet, pigmentation and immunity.

Iain Mathieson, Iosif Lazaridis, Nadin Rohland, Swapan Mallick, Nick Patterson, Songül Alpaslan Roodenberg, Eadaoin Harney, Kristin Stewardson, Daniel Fernandes, Mario Novak + et al.

doi: 10.1038/nature16152

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Complete nitrification by Nitrospira bacteria p.504

Until now, the oxidation steps necessary for complete nitrification have always been observed to occur in two separate microorganisms in a cross-feeding interaction; here, together with the study by van Kessel et al., Daims et al. report the enrichment and characterization of Nitrospira species that encode all of the enzymes necessary to catalyse complete nitrification, a phenotype referred to as 'comammox' (for complete ammonia oxidation).

Holger Daims, Elena V. Lebedeva, Petra Pjevac, Ping Han, Craig Herbold, Mads Albertsen, Nico Jehmlich, Marton Palatinszky, Julia Vierheilig, Alexandr Bulaev + et al.

doi: 10.1038/nature16461

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∆F508 CFTR interactome remodelling promotes rescue of cystic fibrosis p.510

A new deep proteomic analysis method is used to identify proteins that interact with wild-type cystic fibrosis transmembrane conductance regulator (CFTR) and its mutant version that is the major cause of cystic fibrosis.

Sandra Pankow, Casimir Bamberger, Diego Calzolari, Salvador Martínez-Bartolomé, Mathieu Lavallée-Adam, William E. Balch & John R. Yates

doi: 10.1038/nature15729

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DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions p.517

The ability of the DEAD-box RNA helicase DDX5 to interact with master transcription factor RORγt is dependent on binding of the long noncoding RNA Rmrp; the DDX5–RORγt complex coordinates transcription of selective TH17 genes and is required for the pathogenicity of TH17 cells.

Wendy Huang, Benjamin Thomas, Ryan A. Flynn, Samuel J. Gavzy, Lin Wu, Sangwon V. Kim, Jason A. Hall, Emily R. Miraldi, Charles P. Ng, Frank W. Rigo + et al.

doi: 10.1038/nature16193

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Letters

Dense magnetized plasma associated with a fast radio burst p.523

Fast radio burst FRB 110523, discovered in archival data, reveals Faraday rotation and scattering that suggests dense magnetized plasma near the source; this means that to infer the source of the burst, models should involve young stellar populations such as magnetars.

Kiyoshi Masui, Hsiu-Hsien Lin, Jonathan Sievers, Christopher J. Anderson, Tzu-Ching Chang, Xuelei Chen, Apratim Ganguly, Miranda Jarvis, Cheng-Yu Kuo, Yi-Chao Li + et al.

doi: 10.1038/nature15769

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A dynamic magnetic tension force as the cause of failed solar eruptions p.526

Coronal mass ejections are driven by a sudden release of magnetic energy stored in flux ropes in the Sun’s corona, but when the ambient magnetic field that runs toroidally along an unstable flux rope is strong enough to prevent the flux rope from kinking, a dynamic magnetic tension force halts the eruption.

Clayton E. Myers, Masaaki Yamada, Hantao Ji, Jongsoo Yoo, William Fox, Jonathan Jara-Almonte, Antonia Savcheva & Edward E. DeLuca

doi: 10.1038/nature16188

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Quantum superposition at the half-metre scale p.530

Matter-wave interferometers provide an opportunity to measure whether quantum superpositions exist at macroscopic length scales or only at microscopically small scales; now such instruments have demonstrated quantum interference of wave packets separated by 54 cm.

T. Kovachy, P. Asenbaum, C. Overstreet, C. A. Donnelly, S. M. Dickerson, A. Sugarbaker, J. M. Hogan & M. A. Kasevich

doi: 10.1038/nature16155

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Single-chip microprocessor communicating directly using light p.534

An electronic–photonic microprocessor chip manufactured using a conventional microelectronics foundry process is demonstrated; the chip contains 70 million transistors and 850 photonic components and directly uses light to communicate to other chips.

Chen Sun, Mark T. Wade, Yunsup Lee, Jason S. Orcutt, Luca Alloatti, Michael S. Georgas, Andrew S. Waterman, Jeffrey M. Shainline, Rimas R. Avizienis, Sen Lin + et al.

doi: 10.1038/nature16454

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Processing and properties of magnesium containing a dense uniform dispersion of nanoparticles p.539

Magnesium is light but not very strong; here the addition of silicon carbide nanoparticles uniformly dispersed to 14 per cent by volume, achieved through a nanoparticle self-stabilization mechanism in a molten metal alloy, yields improved strength, stiffness, plasticity and high-temperature stability.

Lian-Yi Chen, Jia-Quan Xu, Hongseok Choi, Marta Pozuelo, Xiaolong Ma, Sanjit Bhowmick, Jenn-Ming Yang, Suveen Mathaudhu & Xiao-Chun Li

doi: 10.1038/nature16445

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Thermal vesiculation during volcanic eruptions p.544

A textural examination of volcanic ash erupted from Santiaguito volcano in Guatemala coupled with an analysis of the geophysical signals indicates that rapid heating during fault friction can cause melting and vesiculation (development of bubbles) of hydrated silicic magma, thus strongly affecting magma strength and eruptive behaviour.

Yan Lavallée, Donald B. Dingwell, Jeffrey B. Johnson, Corrado Cimarelli, Adrian J. Hornby, Jackie E. Kendrick, Felix W. von Aulock, Ben M. Kennedy, Benjamin J. Andrews, Fabian B. Wadsworth + et al.

doi: 10.1038/nature16153

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Neonicotinoid pesticide exposure impairs crop pollination services provided by bumblebees p.548

Despite substantial evidence that neonicotinoid pesticides can have negative effects on bees, there have been no reports that this leads to problems with pollination; here bumblebee colonies exposed to a neonicotinoid are shown to provide reduced pollination services to apple trees, leading to a reduction in seed number.

Dara A. Stanley, Michael P. D. Garratt, Jennifer B. Wickens, Victoria J. Wickens, Simon G. Potts & Nigel E. Raine

doi: 10.1038/nature16167

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Complete nitrification by a single microorganism p.555

Until now, the oxidation steps necessary for complete nitrification had always been observed to occur in two separate microorganisms in a cross-feeding interaction; here, together with the study by Daims et al., van Kessel et al. report the enrichment and characterization of Nitrospira species that encode all of the enzymes necessary to catalyse complete nitrification, a phenotype referred to as ‘comammox’ (for complete ammonia oxidation).

Maartje A. H. J. van Kessel, Daan R. Speth, Mads Albertsen, Per H. Nielsen, Huub J. M. Op den Camp, Boran Kartal, Mike S. M. Jetten & Sebastian Lücker

doi: 10.1038/nature16459

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Interleukin-22 promotes intestinal-stem-cell-mediated epithelial regeneration p.560

Innate lymphoid cells increase the growth of mouse intestinal organoids via IL-22 production; recombinant IL-22 promotes growth of both mouse and human organoids, and promotes mouse intestinal stem cell (ISC) expansion and ISC-driven organoid growth via a STAT3-dependent pathway and independently of Paneth cells; IL-22 treatment in vivo enhances the recovery of ISCs from intestinal injury.

Caroline A. Lindemans, Marco Calafiore, Anna M. Mertelsmann, Margaret H. O’Connor, Jarrod A. Dudakov, Robert R. Jenq, Enrico Velardi, Lauren F. Young, Odette M. Smith, Gillian Lawrence + et al.

doi: 10.1038/nature16460

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Unique role for ATG5 in neutrophil-mediated immunopathology during M. tuberculosis infection p.565

Genetic engineering in mice reveals that autophagy is not an essential mechanism in myeloid cells for controlling Mycobacterium tuberculosis infection, and that autophagy factor ATG5 protects organisms by regulating neutrophil influx and tissue damage.

Jacqueline M. Kimmey, Jeremy P. Huynh, Leslie A. Weiss, Sunmin Park, Amal Kambal, Jayanta Debnath, Herbert W. Virgin & Christina L. Stallings

doi: 10.1038/nature16451

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Germline variant FGFR4  p.G388R exposes a membrane-proximal STAT3 binding site p.570

Variant rs351855-G/A is a commonly occurring single-nucleotide polymorphism of coding regions in exon 9 of the fibroblast growth factor receptor FGFR4 (CD334) gene (c.1162G>A). It results in an amino-acid change at codon 388 from glycine to arginine (p.Gly388Arg) in the transmembrane domain of the receptor. Despite compelling genetic evidence for the association of this common variant with cancers of the bone, breast, colon, prostate, skin, lung, head and neck, as well as soft-tissue sarcomas and non-Hodgkin lymphoma, the underlying biological mechanism has remained elusive. Here we show that substitution of the conserved glycine 388 residue to a charged arginine residue alters the transmembrane spanning segment and exposes a membrane-proximal cytoplasmic signal transducer and activator of transcription 3 (STAT3) binding site Y390-(P)XXQ393. We demonstrate that such membrane-proximal STAT3 binding motifs in the germline of type I membrane receptors enhance STAT3 tyrosine phosphorylation by recruiting STAT3 proteins to the inner cell membrane. Remarkably, such germline variants frequently co-localize with somatic mutations in the Catalogue of Somatic Mutations in Cancer (COSMIC) database. Using Fgfr4 single nucleotide polymorphism knock-in mice and transgenic mouse models for breast and lung cancers, we validate the enhanced STAT3 signalling induced by the FGFR4 Arg388-variant in vivo. Thus, our findings elucidate the molecular mechanism behind the genetic association of rs351855 with accelerated cancer progression and suggest that germline variants of cell-surface molecules that recruit STAT3 to the inner cell membrane are a significant risk for cancer prognosis and disease progression.

Vijay K. Ulaganathan, Bianca Sperl, Ulf R. Rapp & Axel Ullrich

doi: 10.1038/nature16449

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Competition between DNA methylation and transcription factors determines binding of NRF1 p.575

The relationship between DNA methylation and transcription factor binding was studied across the genome in mouse embryonic stem cells—the study reveals that the transcription factor NRF1 is methylation-sensitive and how physiological binding of NRF1 relies on local removal of DNA methylation.

Silvia Domcke, Anaïs Flore Bardet, Paul Adrian Ginno, Dominik Hartl, Lukas Burger & Dirk Schübeler

doi: 10.1038/nature16462

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Exploring the repeat protein universe through computational protein design p.580

In this study, 83 proteins containing helix–loop–helix–loop repeats were designed—with sequences unrelated to known repeat proteins—and experimentally characterized; 43 solution X-ray scattering spectra and 15 structures of the designed proteins show that these non-natural repeat proteins have a broad range of curvatures and that their overall structures are in close agreement with design models.

TJ Brunette, Fabio Parmeggiani, Po-Ssu Huang, Gira Bhabha, Damian C. Ekiert, Susan E. Tsutakawa, Greg L. Hura, John A. Tainer & David Baker

doi: 10.1038/nature16162

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Rational design of α-helical tandem repeat proteins with closed architectures p.585

Tandem repeat proteins, which are formed by repetition of modular units of protein sequence and structure, play important biological roles as macromolecular binding and scaffolding domains, enzymes, and building blocks for the assembly of fibrous materials. The modular nature of repeat proteins enables the rapid construction and diversification of extended binding surfaces by duplication and recombination of simple building blocks. The overall architecture of tandem repeat protein structures—which is dictated by the internal geometry and local packing of the repeat building blocks—is highly diverse, ranging from extended, super-helical folds that bind peptide, DNA, and RNA partners, to closed and compact conformations with internal cavities suitable for small molecule binding and catalysis. Here we report the development and validation of computational methods for de novo design of tandem repeat protein architectures driven purely by geometric criteria defining the inter-repeat geometry, without reference to the sequences and structures of existing repeat protein families. We have applied these methods to design a series of closed α-solenoid repeat structures (α-toroids) in which the inter-repeat packing geometry is constrained so as to juxtapose the amino (N) and carboxy (C) termini; several of these designed structures have been validated by X-ray crystallography. Unlike previous approaches to tandem repeat protein engineering, our design procedure does not rely on template sequence or structural information taken from natural repeat proteins and hence can produce structures unlike those seen in nature. As an example, we have successfully designed and validated closed α-solenoid repeats with a left-handed helical architecture that—to our knowledge—is not yet present in the protein structure database.

Lindsey Doyle, Jazmine Hallinan, Jill Bolduc, Fabio Parmeggiani, David Baker, Barry L. Stoddard & Philip Bradley

doi: 10.1038/nature16191

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