네이처 컨텐츠

Editorials

Trial and error p.125

Italian officials should not go ahead with expensive clinical tests of an unproven stem-cell therapy that has no good scientific basis.

doi: 10.1038/499125a

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In the dark p.125

Germany’s main funding agency must specify how it will deal with false charges of misconduct.

doi: 10.1038/499125b

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Headline message p.126

Science communication is changing, but investigative reporting is still important.

doi: 10.1038/499126a

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News

Imaging hits noise barrier p.135

Physical limits mean that electron microscopy may be nearing highest possible resolution.

Eugenie Samuel Reich

doi: 10.1038/499135a

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News Features

Centre of attention p.142

Fiona Fox and her Science Media Centre are determined to improve Britain's press. Now the model is spreading around the world.

Ewen Callaway

doi: 10.1038/499142a

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News & Views

Molecular secrets of a parasite p.156

Research shows how the malaria parasite Plasmodium falciparum manipulates the expression of its var genes to avoid recognition by the host immune system. Four experts comment on the implications of these results for our understanding of gene regulation in general and the development of antimalaria vaccines. See Letter p.223

Swaminathan Venkatesh, Jerry L. Workman, Mats Wahlgren & Maria Teresa Bejarano

doi: 10.1038/nature12407

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A third way to rift continents p.157

Rifting of continents is usually explained by one of two mechanisms based on effects that originate far from the zone of rifting. Laboratory experiments show that this geodynamic process can also be caused by local effects.

W. Roger Buck

doi: 10.1038/499157a

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Trapping the light fantastic p.159

Using a material called a photonic crystal, researchers have designed a mirror that is, in a certain sense, perfect — there is in principle no light transmitted through it nor absorbed by it. See Letter p.188

A. Douglas Stone

doi: 10.1038/499159a

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A holistic approach to climate targets p.160

An assessment of allowable carbon emissions that factors in multiple climate targets finds smaller permissible emission budgets than those inferred from studies that focus on temperature change alone. See Letter p.197

Joeri Rogelj

doi: 10.1038/nature12406

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Lipid switches and traffic control p.161

Transport vesicles that bud from one cell membrane must change identity before fusing with another. During the process of clathrin-mediated endocytosis, various lipid phosphates mediate this identity change. See Letter p.233

Sandra L. Schmid & Marcel Mettlen

doi: 10.1038/nature12408

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Analysis

Oversimplifying quantum factoring p.163

Shor’s quantum factoring algorithm exponentially outperforms known classical methods. Previous experimental implementations have used simplifications dependent on knowing the factors in advance. However, as we show here, all composite numbers admit simplification of the algorithm to a circuit equivalent to flipping coins. The difficulty of a particular experiment therefore depends on the level of simplification chosen, not the size of the number factored. Valid implementations should not make use of the answer sought.

John A. Smolin, Graeme Smith & Alexander Vargo

doi: 10.1038/nature12290

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Articles

Temporal regulation of EGF signalling networks by the scaffold protein Shc1 p.166

The Shc1 scaffold mediates a switch in the signaling output of the epidermal growth factor receptor tyrosine kinase over time through recruitment of successive waves of proteins with distinct biological functions.

Yong Zheng, Cunjie Zhang, David R. Croucher, Mohamed A. Soliman, Nicole St-Denis, Adrian Pasculescu, Lorne Taylor, Stephen A. Tate, W. Rod Hardy, Karen Colwill + et al.

doi: 10.1038/nature12308

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A compendium of RNA-binding motifs for decoding gene regulation p.172

This study reports a global analysis of binding sites for over 200 RNA-binding proteins (RBPs) from 24 species; conserved RNA-binding motifs are identified, and their analysis allows prediction of interaction sites based on the sequence of the RNA-binding domain alone.

Debashish Ray, Hilal Kazan, Kate B. Cook, Matthew T. Weirauch, Hamed S. Najafabadi, Xiao Li, Serge Gueroussov, Mihai Albu, Hong Zheng, Ally Yang + et al.

doi: 10.1038/nature12311

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The Mycobacterium tuberculosis regulatory network and hypoxia p.178

Mycobacterium tuberculosis has the ability to survive within the host for months to decades in an asymptomatic state, and adaptations to hypoxia are thought to have an important role in pathogenesis; here a systems-wide reconstruction of the regulatory network provides a framework for understanding mycobacterial persistence in the host.

James E. Galagan, Kyle Minch, Matthew Peterson, Anna Lyubetskaya, Elham Azizi, Linsday Sweet, Antonio Gomes, Tige Rustad, Gregory Dolganov, Irina Glotova + et al.

doi: 10.1038/nature12337

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Letters

Formation of sharp eccentric rings in debris disks with gas but without planets p.184

‘Debris disks’ around young stars (analogues of the Kuiper Belt in our Solar System) show a variety of non-trivial structures attributed to planetary perturbations and used to constrain the properties of those planets. However, these analyses have largely ignored the fact that some debris disks are found to contain small quantities of gas, a component that all such disks should contain at some level. Several debris disks have been measured with a dust-to-gas ratio of about unity, at which the effect of hydrodynamics on the structure of the disk cannot be ignored. Here we report linear and nonlinear modelling that shows that dust–gas interactions can produce some of the key patterns attributed to planets. We find a robust clumping instability that organizes the dust into narrow, eccentric rings, similar to the Fomalhaut debris disk. The conclusion that such disks might contain planets is not necessarily required to explain these systems.

W. Lyra & M. Kuchner

doi: 10.1038/nature12281

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Observation of trapped light within the radiation continuum p.188

The ability to confine light is important both scientifically and technologically. Many light confinement methods exist, but they all achieve confinement with materials or systems that forbid outgoing waves. These systems can be implemented by metallic mirrors, by photonic band-gap materials, by highly disordered media (Anderson localization) and, for a subset of outgoing waves, by translational symmetry (total internal reflection) or by rotational or reflection symmetry. Exceptions to these examples exist only in theoretical proposals. Here we predict and show experimentally that light can be perfectly confined in a patterned dielectric slab, even though outgoing waves are allowed in the surrounding medium. Technically, this is an observation of an ‘embedded eigenvalue’—namely, a bound state in a continuum of radiation modes—that is not due to symmetry incompatibility. Such a bound state can exist stably in a general class of geometries in which all of its radiation amplitudes vanish simultaneously as a result of destructive interference. This method to trap electromagnetic waves is also applicable to electronic and mechanical waves.

Chia Wei Hsu, Bo Zhen, Jeongwon Lee, Song-Liang Chua, Steven G. Johnson, John D. Joannopoulos & Marin Soljačić

doi: 10.1038/nature12289

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Metal-free oxidation of aromatic carbon–hydrogen bonds through a reverse-rebound mechanism p.192

Methods for carbon–hydrogen (C–H) bond oxidation have a fundamental role in synthetic organic chemistry, providing functionality that is required in the final target molecule or facilitating subsequent chemical transformations. Several approaches to oxidizing aliphatic C–H bonds have been described, drastically simplifying the synthesis of complex molecules. However, the selective oxidation of aromatic C–H bonds under mild conditions, especially in the context of substituted arenes with diverse functional groups, remains a challenge. The direct hydroxylation of arenes was initially achieved through the use of strong Brønsted or Lewis acids to mediate electrophilic aromatic substitution reactions with super-stoichiometric equivalents of oxidants, significantly limiting the scope of the reaction. Because the products of these reactions are more reactive than the starting materials, over-oxidation is frequently a competitive process. Transition-metal-catalysed C–H oxidation of arenes with or without directing groups has been developed, improving on the acid-mediated process; however, precious metals are required. Here we demonstrate that phthaloyl peroxide functions as a selective oxidant for the transformation of arenes to phenols under mild conditions. Although the reaction proceeds through a radical mechanism, aromatic C–H bonds are selectively oxidized in preference to activated –H bonds. Notably, a wide array of functional groups are compatible with this reaction, and this method is therefore well suited for late-stage transformations of advanced synthetic intermediates. Quantum mechanical calculations indicate that this transformation proceeds through a novel addition–abstraction mechanism, a kind of ‘reverse-rebound’ mechanism as distinct from the common oxygen-rebound mechanism observed for metal–oxo oxidants. These calculations also identify the origins of the experimentally observed aryl selectivity.

Changxia Yuan, Yong Liang, Taylor Hernandez, Adrian Berriochoa, Kendall N. Houk & Dionicio Siegel

doi: 10.1038/nature12284

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Allowable carbon emissions lowered by multiple climate targets p.197

Climate targets are designed to inform policies that would limit the magnitude and impacts of climate change caused by anthropogenic emissions of greenhouse gases and other substances. The target that is currently recognized by most world governments places a limit of two degrees Celsius on the global mean warming since preindustrial times. This would require large sustained reductions in carbon dioxide emissions during the twenty-first century and beyond. Such a global temperature target, however, is not sufficient to control many other quantities, such as transient sea level rise, ocean acidification and net primary production on land. Here, using an Earth system model of intermediate complexity (EMIC) in an observation-informed Bayesian approach, we show that allowable carbon emissions are substantially reduced when multiple climate targets are set. We take into account uncertainties in physical and carbon cycle model parameters, radiative efficiencies, climate sensitivity and carbon cycle feedbacks along with a large set of observational constraints. Within this framework, we explore a broad range of economically feasible greenhouse gas scenarios from the integrated assessment community to determine the likelihood of meeting a combination of specific global and regional targets under various assumptions. For any given likelihood of meeting a set of such targets, the allowable cumulative emissions are greatly reduced from those inferred from the temperature target alone. Therefore, temperature targets alone are unable to comprehensively limit the risks from anthropogenic emissions.

Marco Steinacher, Fortunat Joos & Thomas F. Stocker

doi: 10.1038/nature12269

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Characterization and implications of intradecadal variations in length of day p.202

Variations in Earth's rotation (defined in terms of length of day) arise from external tidal torques, or from an exchange of angular momentum between the solid Earth and its fluid components. On short timescales (annual or shorter) the non-tidal component is dominated by the atmosphere, with small contributions from the ocean and hydrological system. On decadal timescales, the dominant contribution is from angular momentum exchange between the solid mantle and fluid outer core. Intradecadal periods have been less clear and have been characterized by signals with a wide range of periods and varying amplitudes, including a peak at about 6 years (refs 2, 3, 4). Here, by working in the time domain rather than the frequency domain, we show a clear partition of the non-atmospheric component into only three components: a decadally varying trend, a 5.9-year period oscillation, and jumps at times contemporaneous with geomagnetic jerks. The nature of the jumps in length of day leads to a fundamental change in what class of phenomena may give rise to the jerks, and provides a strong constraint on electrical conductivity of the lower mantle, which can in turn constrain its structure and composition.

R. Holme & O. de Viron

doi: 10.1038/nature12282

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Gene expression in the deep biosphere p.205

Scientific ocean drilling has revealed a deep biosphere of widespread microbial life in sub-seafloor sediment. Microbial metabolism in the marine subsurface probably has an important role in global biogeochemical cycles, but deep biosphere activities are not well understood. Here we describe and analyse the first sub-seafloor metatranscriptomes from anaerobic Peru Margin sediment up to 159 metres below the sea floor, represented by over 1 billion complementary DNA (cDNA) sequence reads. Anaerobic metabolism of amino acids, carbohydrates and lipids seem to be the dominant metabolic processes, and profiles of dissimilatory sulfite reductase (dsr) transcripts are consistent with pore-water sulphate concentration profiles. Moreover, transcripts involved in cell division increase as a function of microbial cell concentration, indicating that increases in sub-seafloor microbial abundance are a function of cell division across all three domains of life. These data support calculations and models of sub-seafloor microbial metabolism and represent the first holistic picture of deep biosphere activities.

William D. Orsi, Virginia P. Edgcomb, Glenn D. Christman & Jennifer F. Biddle

doi: 10.1038/nature12230

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Pan genome of the phytoplankton Emiliania underpins its global distribution OPEN p.209

Coccolithophores have influenced the global climate for over 200 million years. These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems. They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space. Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean. Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions.

Betsy A. Read, Jessica Kegel, Mary J. Klute, Alan Kuo, Stephane C. Lefebvre, Florian Maumus, Christoph Mayer, John Miller, Adam Monier, Asaf Salamov + et al.

doi: 10.1038/nature12221

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Mutational heterogeneity in cancer and the search for new cancer-associated genes p.214

Major international projects are underway that are aimed at creating a comprehensive catalogue of all the genes responsible for the initiation and progression of cancer. These studies involve the sequencing of matched tumour–normal samples followed by mathematical analysis to identify those genes in which mutations occur more frequently than expected by random chance. Here we describe a fundamental problem with cancer genome studies: as the sample size increases, the list of putatively significant genes produced by current analytical methods burgeons into the hundreds. The list includes many implausible genes (such as those encoding olfactory receptors and the muscle protein titin), suggesting extensive false-positive findings that overshadow true driver events. We show that this problem stems largely from mutational heterogeneity and provide a novel analytical methodology, MutSigCV, for resolving the problem. We apply MutSigCV to exome sequences from 3,083 tumour–normal pairs and discover extraordinary variation in mutation frequency and spectrum within cancer types, which sheds light on mutational processes and disease aetiology, and in mutation frequency across the genome, which is strongly correlated with DNA replication timing and also with transcriptional activity. By incorporating mutational heterogeneity into the analyses, MutSigCV is able to eliminate most of the apparent artefactual findings and enable the identification of genes truly associated with cancer.

Michael S. Lawrence, Petar Stojanov, Paz Polak, Gregory V. Kryukov, Kristian Cibulskis, Andrey Sivachenko, Scott L. Carter, Chip Stewart, Craig H. Mermel, Steven A. Roberts + et al.

doi: 10.1038/nature12213

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Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome p.219

The mammalian gut ecosystem has considerable influence on host physiology, but the mechanisms that sustain this complex environment in the face of different stresses remain obscure. Perturbations to the gut ecosystem, such as through antibiotic treatment or diet, are at present interpreted at the level of bacterial phylogeny. Less is known about the contributions of the abundant population of phages to this ecological network. Here we explore the phageome as a potential genetic reservoir for bacterial adaptation by sequencing murine faecal phage populations following antibiotic perturbation. We show that antibiotic treatment leads to the enrichment of phage-encoded genes that confer resistance via disparate mechanisms to the administered drug, as well as genes that confer resistance to antibiotics unrelated to the administered drug, and we demonstrate experimentally that phages from treated mice provide aerobically cultured naive microbiota with increased resistance. Systems-wide analyses uncovered post-treatment phage-encoded processes related to host colonization and growth adaptation, indicating that the phageome becomes broadly enriched for functionally beneficial genes under stress-related conditions. We also show that antibiotic treatment expands the interactions between phage and bacterial species, leading to a more highly connected phage–bacterial network for gene exchange. Our work implicates the phageome in the emergence of multidrug resistance, and indicates that the adaptive capacity of the phageome may represent a community-based mechanism for protecting the gut microflora, preserving its functional robustness during antibiotic stress.

Sheetal R. Modi, Henry H. Lee, Catherine S. Spina & James J. Collins

doi: 10.1038/nature12212

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PfSETvs methylation of histone H3K36 represses virulence genes in Plasmodium falciparum p.223

The variant antigen Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1), which is expressed on the surface of P. falciparum-infected red blood cells, is a critical virulence factor for malaria. Each parasite has 60 antigenically distinct var genes that each code for a different PfEMP1 protein. During infection the clonal parasite population expresses only one gene at a time before switching to the expression of a new variant antigen as an immune-evasion mechanism to avoid the host antibody response. The mechanism by which 59 of the 60 var genes are silenced remains largely unknown. Here we show that knocking out the P. falciparum variant-silencing SET gene (here termed PfSETvs), which encodes an orthologue of Drosophila melanogaster ASH1 and controls histone H3 lysine 36 trimethylation (H3K36me3) on var genes, results in the transcription of virtually all var genes in the single parasite nuclei and their expression as proteins on the surface of individual infected red blood cells. PfSETvs-dependent H3K36me3 is present along the entire gene body, including the transcription start site, to silence var genes. With low occupancy of PfSETvs at both the transcription start site of var genes and the intronic promoter, expression of var genes coincides with transcription of their corresponding antisense long noncoding RNA. These results uncover a previously unknown role of PfSETvs-dependent H3K36me3 in silencing var genes in P. falciparum that might provide a general mechanism by which orthologues of PfSETvs repress gene expression in other eukaryotes. PfSETvs knockout parasites expressing all PfEMP1 proteins may also be applied to the development of a malaria vaccine.

Lubin Jiang, Jianbing Mu, Qingfeng Zhang, Ting Ni, Prakash Srinivasan, Kempaiah Rayavara, Wenjing Yang, Louise Turner, Thomas Lavstsen, Thor G. Theander + et al.

doi: 10.1038/nature12361

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Wnt activation in nail epithelium couples nail growth to digit regeneration p.228

The tips of mammalian digits can regenerate after amputation, like those of amphibians. It is unknown why this capacity is limited to the area associated with the nail. Here we show that nail stem cells (NSCs) reside in the proximal nail matrix and that the mechanisms governing NSC differentiation are coupled directly with their ability to orchestrate digit regeneration. Early nail progenitors undergo Wnt-dependent differentiation into the nail. After amputation, this Wnt activation is required for nail regeneration and also for attracting nerves that promote mesenchymal blastema growth, leading to the regeneration of the digit. Amputations proximal to the Wnt-active nail progenitors result in failure to regenerate the nail or digit. Nevertheless, β-catenin stabilization in the NSC region induced their regeneration. These results establish a link between NSC differentiation and digit regeneration, and suggest that NSCs may have the potential to contribute to the development of novel treatments for amputees.

Makoto Takeo, Wei Chin Chou, Qi Sun, Wendy Lee, Piul Rabbani, Cynthia Loomis, M. Mark Taketo & Mayumi Ito

doi: 10.1038/nature12214

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Spatiotemporal control of endocytosis by phosphatidylinositol-3,4-bisphosphate p.233

Phosphoinositides serve crucial roles in cell physiology, ranging from cell signalling to membrane traffic. Among the seven eukaryotic phosphoinositides the best studied species is phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2), which is concentrated at the plasma membrane where, among other functions, it is required for the nucleation of endocytic clathrin-coated pits. No phosphatidylinositol other than PI(4,5)P2 has been implicated in clathrin-mediated endocytosis, whereas the subsequent endosomal stages of the endocytic pathway are dominated by phosphatidylinositol-3-phosphates(PI(3)P). How phosphatidylinositol conversion from PI(4,5)P2-positive endocytic intermediates to PI(3)P-containing endosomes is achieved is unclear. Here we show that formation of phosphatidylinositol-3,4-bisphosphate (PI(3,4)P2) by class II phosphatidylinositol-3-kinase C2α (PI(3)K C2α) spatiotemporally controls clathrin-mediated endocytosis. Depletion of PI(3,4)P2 or PI(3)K C2α impairs the maturation of late-stage clathrin-coated pits before fission. Timed formation of PI(3,4)P2 by PI(3)K C2α is required for selective enrichment of the BAR domain protein SNX9 at late-stage endocytic intermediates. These findings provide a mechanistic framework for the role of PI(3,4)P2 in endocytosis and unravel a novel discrete function of PI(3,4)P2 in a central cell physiological process.

York Posor, Marielle Eichhorn-Gruenig, Dmytro Puchkov, Johannes Schöneberg, Alexander Ullrich, André Lampe, Rainer Müller, Sirus Zarbakhsh, Federico Gulluni, Emilio Hirsch + et al.

doi: 10.1038/nature12360

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An siRNA screen for NFAT activation identifies septins as coordinators of store-operated Ca2+ entry p.238

The STIM1–ORAI1 pathway of store-operated Ca2+ entry is an essential component of cellular Ca2+ signalling. STIM1 senses depletion of intracellular Ca2+ stores in response to physiological stimuli, and relocalizes within the endoplasmic reticulum to plasma-membrane-apposed junctions, where it recruits and gates open plasma membrane ORAI1 Ca2+ channels. Here we use a genome-wide RNA interference screen in HeLa cells to identify filamentous septin proteins as crucial regulators of store-operated Ca2+ entry. Septin filaments and phosphatidylinositol-4,5-bisphosphate (also known as PtdIns(4,5)P2) rearrange locally at endoplasmic reticulum–plasma membrane junctions before and during formation of STIM1–ORAI1 clusters, facilitating STIM1 targeting to these junctions and promoting the stable recruitment of ORAI1. Septin rearrangement at junctions is required for PtdIns(4,5)P2 reorganization and efficient STIM1–ORAI1 communication. Septins are known to demarcate specialized membrane regions such as dendritic spines, the yeast bud and the primary cilium, and to serve as membrane diffusion barriers and/or signalling hubs in cellular processes such as vesicle trafficking, cell polarity and cytokinesis. Our data show that septins also organize the highly localized plasma membrane domains that are important in STIM1–ORAI1 signalling, and indicate that septins may organize membrane microdomains relevant to other signalling processes.

Sonia Sharma, Ariel Quintana, Gregory M. Findlay, Marcel Mettlen, Beate Baust, Mohit Jain, Roland Nilsson, Anjana Rao & Patrick G. Hogan

doi: 10.1038/nature12229

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