Nature contents: 11 July 2013

Can't view this email? Click here to view in your browser.     Volume 499 Number 7457      nature •Visit Nature homepage •Subscribe to Nature •View Table of Contents The science that matters. Every week.                 Jump to the content that matters to you View Table of Contents ▶ ▼ News & Comment   ▼ Biological Sciences   ▼ Chemical Sciences   ▼ Physical Sciences   ▼ Earth & Environmental Sciences   ▼ Careers & Jobs       This week's highlights     Physical Sciences More Physical sciences ▼   Formation of sharp eccentric rings in debris disks with gas but without planets   Structures seen in debris disks around young stars are usually taken as evidence for the gravitational influence of unseen planets. Wladimir Lyra and Marc Kuchner demonstrate that interactions between dust and gas alone can account for rings and other features thought diagnostic of planets. Previous analyses largely ignored the fact that debris disks contain small quantities of gas. This model may explain why a pair of planets predicted in the debris disk around the nearby star Fomalhaut have not been found: if the system contains gas, the planets may not be here.       Earth & Environmental Sciences More Earth & Environmental sciences ▼   Allowable carbon emissions lowered by multiple climate targets   Current climate negotiations concentrate on managing emissions of greenhouse gases in order to keep warming at no more than 2º C above preindustrial levels. But temperature is just one aspect of climate change. Marco Steinacher et al. consider several additional variables - sea level rise, ocean acidification and net primary production - and set plausible thresholds for each. With this combination of goals in place the allowable level of greenhouse gas emissions is much lower than for a temperature threshold alone.       Biological Sciences More Biological sciences ▼   Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome   Bacteriophages - virus-like particles that infect bacteria - naturally coexist in abundance with their hosts in the mammalian gut. This comparative metagenomics study of gut phage populations in mice shows that exposure to antibiotics enriches phage-encoded genes linked antibiotic resistance - and that phage from antibiotic-treated mice can increase resistance in a bacterial population.       Podcast & Video     In this week's podcast: This week, the deadly effect of species population drops, how plants have become better at using water as carbon dioxide rises, and putting personality into synthesized voices.         News & Comment Read daily news coverage▶ ▲top               THIS WEEK           Editorials                   Trial and error ▶     Italian officials should not go ahead with expensive clinical tests of an unproven stem-cell therapy that has no good scientific basis.             In the dark ▶     Germany's main funding agency must specify how it will deal with false charges of misconduct.             Headline message ▶     Science communication is changing, but investigative reporting is still important.             World View                   A slippery slope to human germline modification ▶     The United Kingdom's decision to trial the technique of mitochondrial replacement is premature and ill-conceived, says Marcy Darnovsky.             Seven Days                   Seven days: 5–11 July 2013 ▶             NEWS IN FOCUS           Teething troubles at huge telescope ▶     The Large Binocular Telescope gets off to a sluggish start.             Deal boosts blind's access to texts ▶     Global copyright agreement will increase availability of scientific texts in accessible formats.             Imaging hits noise barrier ▶     Physical limits mean that electron microscopy may be nearing highest possible resolution.             Outcry over plans for 'Japanese NIH' ▶     Researchers fear reforms will bring cuts to basic science.             US research firms put under pressure to sell ▶     Commercialization rules threaten to curtail SBIR grants.             Features                   Climate change: The forecast for 2018 is cloudy with record heat ▶     Efforts to predict the near-term climate are taking off, but their record so far has been patchy.             Science media: Centre of attention ▶     Fiona Fox and her Science Media Centre are determined to improve Britain's press. Now the model is spreading around the world.             COMMENT           Energy: The smart-grid solution ▶     Massoud Amin outlines how the United States should make its electricity infrastructure self-healing to avoid massive power failures.             Research management: What would you cut? ▶     Four insiders explain how they would make the savings in US science required by the budget sequester.             Summer Books                   Summer books ▶     With the yearly exodus from labs and lecture theatres imminent, Nature's regular reviewers and editors share some tempting holiday reads.             Correspondence                   History: Don't glorify Arab astronomy Carlo Rovelli | Shale gas: Pollution fears in China Hong Yang, Roger J. Flower, Julian R. Thompson | Shale gas: Surface water also at risk Guangming Zeng, Ming Chen, Zhuotong Zeng | Policy: Badger-cull statistics carry uncertainty Christl Donnelly             Correction                   Correction ▶                     Biological Sciences ▲top             RESEARCH           Latest Online                   Bacteriology: Toxins in tandem ▶     C. Erec Stebbins             RNA biophysics: A three-state balancing act ▶     Ronald Micura             Biogeochemistry: Carbon dioxide and water use in forests ▶     Belinda Medlyn, Martin De Kauwe             Myc-driven endogenous cell competition in the early mammalian embryo ▶     Cristina Clavería, Giovanna Giovinazzo, Rocío Sierra et al.     An in vivo genetic approach to generate mosaic expression of Myc in the mouse epiblast reveals evidence of cell competition, a tissue homeostasis mechanism first described in Drosophila by which viable but suboptimal cells are eliminated from metazoan tissues; during normal development Myc expression levels in the epiblast are heterogeneous, and endogenous cell competition refines the epiblast cell population through the apoptotic elimination of cells with low relative Myc levels.             High frequency of functional extinctions in ecological networks ▶     Torbjörn Säterberg, Stefan Sellman, Bo Ebenman     A modelling study of the mechanisms of extinction within ecological networks reveals how even a small reduction in the population size of a species may lead to the loss of its ecological functionality—that is, to its functional extinction—by causing extinction of other organisms in the food web, often only indirectly connected to the focal species, revealing the value of conservation strategies that target a broader ecological network.             Increase in forest water-use efficiency as atmospheric carbon dioxide concentrations rise ▶     Trevor F. Keenan, David Y. Hollinger, Gil Bohrer et al.     Present-day forests use water more efficiently, probably owing to the effect of increased atmospheric carbon dioxide on leaf stomata, which partially close to maintain a near-constant level of carbon dioxide inside the leaves despite increasing atmospheric levels.             Reshaping of the conformational search of a protein by the chaperone trigger factor ▶     Alireza Mashaghi, Günter Kramer, Philipp Bechtluft et al.     The bacterial chaperone named trigger factor is found to stabilize protein folding intermediates that eventually convert to the native state, suggesting that chaperones play a direct role in instructing protein folding.             Generation of inner ear sensory epithelia from pluripotent stem cells in 3D culture ▶     Karl R. Koehler, Andrew M. Mikosz, Andrei I. Molosh et al.     A new approach has been developed in order to achieve the stepwise differentiation of inner ear sensory epithelia from mouse embryonic stem cells in a three-dimensional culture: this process, which mimics normal development and produces cells that have functional characteristics of mechanosensitive hair cells, is hoped to provide further insights into inner ear development and disorder.             Molecular basis of binding between novel human coronavirus MERS-CoV and its receptor CD26 ▶     Guangwen Lu, Yawei Hu, Qihui Wang et al.     MERS-CoV is a newly emerged coronavirus that is related to SARS-CoV and has proven fatal in half of the people it has infected to date: here the crystal structure of the MERS-CoV receptor binding domain is presented in complex with its receptor on human cells, CD26.             Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota ▶     Koji Atarashi, Takeshi Tanoue, Kenshiro Oshima et al.     This study identifies 17 strains of human-derived Clostridia capable of inducing the accumulation and functional maturation of regulatory T cells; it is suggested that these strains may be useful candidates for the future development of oral bacterial therapeutics to treat human inflammatory disorders.             Digit loss in archosaur evolution and the interplay between selection and constraints ▶     Merijn A. G. de Bakker, Donald A. Fowler, Kelly den Oude et al.     Research on the Nile crocodile and five birds shows that limb evolution is shaped by an interplay between natural selection and developmental constraints, the outcome varying between different digits, and between embryos and adults.             Structure and function of the Salmonella Typhi chimaeric A2B5 typhoid toxin ▶     Jeongmin Song, Xiang Gao, Jorge E. Galán     Unlike most salmonellae, Salmonella enterica serovar Typhi causes life-threatening systemic infections known as typhoid fever, for which the molecular basis is unknown; here administration of typhoid toxin produced by S. Typhi reproduces many of the acute symptoms of typhoid fever, carbohydrates on cell surface glycoproteins are identified as receptors for typhoid toxin and the toxin's crystal structure is determined, providing insights into these interactions.             Three-state mechanism couples ligand and temperature sensing in riboswitches ▶     Anke Reining, Senada Nozinovic, Kai Schlepckow et al.     In the human pathogen Vibrio vulnificus, the riboswitch regulating gene expression of the adenosine deaminase is shown to exist in three distinct stable conformational states; this three-state mechanism allows control of gene expression over a broad temperature range, which is essential for Vibrio adaptation.             Pathogenesis and transmission of avian influenza A (H7N9) virus in ferrets and mice ▶     Jessica A. Belser, Kortney M. Gustin, Melissa B. Pearce et al.     The new H7N9 influenza virus, recently emerged in China, can replicate in human airway cells and in the respiratory tract of ferrets to a higher level than can seasonal H3N2 virus and shows higher lethality in mice than genetically related H7N9 and H9N2 viruses, but shows limited transmission in ferrets by respiratory droplets.             Characterization of H7N9 influenza A viruses isolated from humans ▶     Tokiko Watanabe, Maki Kiso, Satoshi Fukuyama et al.     Here, biological attributes of two early human isolates of the newly emerged H7N9 influenza viruses are characterized: the potential of these viruses to infect and/or transmit within various animal models is discussed, as is their relative sensitivity to neuraminidase inhibitors and experimental polymerase inhibitors compared to an H1N1 pandemic strain.             Articles and Letters                   Temporal regulation of EGF signalling networks by the scaffold protein Shc1 ▶     Yong Zheng, Cunjie Zhang, David R. Croucher et al.     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.             A compendium of RNA-binding motifs for decoding gene regulation ▶     Debashish Ray, Hilal Kazan, Kate B. Cook et al.     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.             The Mycobacterium tuberculosis regulatory network and hypoxia ▶     James E. Galagan, Kyle Minch, Matthew Peterson et al.     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.             Gene expression in the deep biosphere ▶     William D. Orsi, Virginia P. Edgcomb, Glenn D. Christman et al.     Gene expression of microbes in anaerobic sediment from the Peru Margin at depths up to 159 metres below the sea floor is analysed: anaerobic metabolism of amino acids, carbohydrates and lipids are seen to be the dominant metabolic processes, and genes associated with cell division are found to be correlated with microbial cell concentration, suggesting that ongoing cell division contributes to biomass turnover.             Pan genome of the phytoplankton Emiliania underpins its global distribution OPEN ▶     Betsy A. Read, Jessica Kegel, Mary J. Klute et al.     A reference genome from the coccolithophore Emiliania huxleyi is presented, along with sequences from 13 additional isolates, revealing a pan genome comprising core genes and genes variably distributed between strains: E. huxleyi is found to harbour extensive genetic variability under different metabolic repertoires, explaining its ability to thrive under a diverse range of environmental conditions.             Mutational heterogeneity in cancer and the search for new cancer-associated genes ▶     Michael S. Lawrence, Petar Stojanov, Paz Polak et al.     As the sample size in cancer genome studies increases, the list of genes identified as significantly mutated is likely to include more false positives; here, this problem is identified as stemming largely from mutation heterogeneity, and a new analytical methodology designed to overcome this problem is described.             Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome ▶     Sheetal R. Modi, Henry H. Lee, Catherine S. Spina et al.     By exploring the phageome in mice, antibiotic treatment is shown to lead to enrichment of phage-encoded genes that are related to antibiotic resistance.             PfSETvs methylation of histone H3K36 represses virulence genes in Plasmodium falciparum  ▶     Lubin Jiang, Jianbing Mu, Qingfeng Zhang et al.     The malaria parasite Plasmodium falciparum escapes immune detection by expressing one of 60 antigenically distinct var genes at any one time during the course of infection: here it is shown that the P. falciparum protein PfSETvs has a key role in var gene silencing through the trimethylation of histone H3K36.             Wnt activation in nail epithelium couples nail growth to digit regeneration ▶     Makoto Takeo, Wei Chin Chou, Qi Sun et al.     Nail stem cells (NSCs) reside in the proximal nail matrix, and early nail progenitors undergo Wnt-dependent differentiation into the nail; after amputation, Wnt activation is required for nail and digit regeneration, and amputations proximal to the Wnt-active nail progenitors fail to regenerate, but β-catenin stabilization in the NSC region induces regeneration.             Spatiotemporal control of endocytosis by phosphatidylinositol-3,4-bisphosphate ▶     York Posor, Marielle Eichhorn-Gruenig, Dmytro Puchkov et al.     Phosphoinositides are important regulators of intracellular membrane traffic, and although the role of PI(4,5)P2 has been well characterised, the function of PI(3,4)P2 remains unclear; here the formation of PI(3,4)P2 by the class II phosphatidylinositol-3-kinase C2α enzyme is shown to control clathrin-mediated endocytosis.             An siRNA screen for NFAT activation identifies septins as coordinators of store-operated Ca2+ entry ▶     Sonia Sharma, Ariel Quintana, Gregory M. Findlay et al.     A genome-wide RNA interference analysis identifies the septin family of cytoskeletal filaments as important regulators of store-operated Ca2+ entry into the cell; septins are shown to organize plasma membrane microdomains important in STIM1 and ORAI1 signalling, and may also be relevant in membrane microdomains underlying other signalling processes.             News & Views                   Malaria: Molecular secrets of a parasite ▶     Swaminathan Venkatesh, Jerry L. Workman, Mats Wahlgren & Maria Teresa Bejarano             Cell biology: Lipid switches and traffic control ▶     Sandra L. Schmid & Marcel Mettlen             Bacteriology: Toxins in tandem ▶     C. Erec Stebbins             RNA biophysics: A three-state balancing act ▶     Ronald Micura             Biogeochemistry: Carbon dioxide and water use in forests ▶     Belinda Medlyn, Martin De Kauwe             Brief Communications Arising                   Can ovarian follicles fossilize? ▶     Gerald Mayr, Albrecht Manegold             Zheng et al. reply ▶     Jingmai O'Connor, Xiaoting Zheng, Zhonghe Zhou             Corrigendum                   Corrigendum: Inhibition dominates sensory responses in awake cortex ▶     B. Haider, M. Häusser, M. Carandini             Research Highlights                   Anthropology: Crops ingrained in Iranian past | Neuroscience: Seeing threats in the brain | Disease research: Short telomeres, damaged hearts | Homeostasis: Fat cells that sense cold | Bioelectronics: An ear by printing         NEWS & COMMENT           Outcry over plans for 'Japanese NIH' | Summer books | Policy: Badger-cull statistics carry uncertainty | Trial and error | A slippery slope to human germline modification             More Biological Sciences ▶                 Nature Publishing Index 2012 Global  The Nature Publishing Index (NPI) ranks institutions and countries according to the number of primary research articles they publish in the Nature family of journals in a one-year period. The Nature Publishing Index 2012 Global supplement provides league tables and commentary based on articles published between 1 January 2012 and 31 December 2012.  Where does your institution rank?         Chemical Sciences ▲top             RESEARCH           Articles and Letters                   Metal-free oxidation of aromatic carbon–hydrogen bonds through a reverse-rebound mechanism ▶     Changxia Yuan, Yong Liang, Taylor Hernandez et al.     Phthaloyl peroxide functions as a selective oxidant of C–H bonds in the transformation of arenes to phenols under mild conditions, in a reaction that is compatible with a wide array of functional groups.             News & Views                   Cell biology: Lipid switches and traffic control ▶     Sandra L. Schmid & Marcel Mettlen             More Chemical Sciences ▶               Physical Sciences ▲top             RESEARCH           Latest Online                   Sequential deposition as a route to high-performance perovskite-sensitized solar cells ▶     Julian Burschka, Norman Pellet, Soo-Jin Moon et al.     A method of producing perovskite-sensitized solar cells by sequential — as opposed to single-step — deposition of the perovskite's components onto a nanoporous titanium oxide film allows for greater reproducibility of device performance and a record power conversion efficiency of 15 per cent.             Articles and Letters                   Formation of sharp eccentric rings in debris disks with gas but without planets ▶     W. Lyra, M. Kuchner     The narrow rings seen in some debris disks, thought to be evidence for hidden exoplanets, might instead be caused by gas–dust interaction and a recently identified photoelectric instability.             Observation of trapped light within the radiation continuum ▶     Chia Wei Hsu, Bo Zhen, Jeongwon Lee et al.     Theoretical and experimental studies reveal that light can be confined within a planar dielectric photonic crystal slab even though the frequency of this optical bound state is inside the continuous spectrum of extended states from the same symmetry group.             Metal-free oxidation of aromatic carbon–hydrogen bonds through a reverse-rebound mechanism ▶     Changxia Yuan, Yong Liang, Taylor Hernandez et al.     Phthaloyl peroxide functions as a selective oxidant of C–H bonds in the transformation of arenes to phenols under mild conditions, in a reaction that is compatible with a wide array of functional groups.             Oversimplifying quantum factoring ▶     John A. Smolin, Graeme Smith, Alexander Vargo     Building a device capable of factoring large numbers is a major goal of quantum computing; an algorithm for quantum factoring (Shor's algorithm) exists, and a simple coin-tossing exercise is used to illustrate the dangers of oversimplification when implementing this algorithm experimentally.             News & Views                   Optical physics: Trapping the light fantastic ▶     A. Douglas Stone             Research Highlights                   Quantum communication: Broken quantum links still work | Nanotechnology: Single-molecule electric switch         NEWS & COMMENT           Teething troubles at huge telescope | Imaging hits noise barrier | Climate change: The forecast for 2018 is cloudy with record heat | Energy: The smart-grid solution | Summer books | History: Don't glorify Arab astronomy | Deal boosts blind's access to texts             More Physical Sciences ▶               Earth & Environmental Sciences ▲top             RESEARCH           Latest Online                   Biogeochemistry: Carbon dioxide and water use in forests ▶     Belinda Medlyn, Martin De Kauwe             Increase in forest water-use efficiency as atmospheric carbon dioxide concentrations rise ▶     Trevor F. Keenan, David Y. Hollinger, Gil Bohrer et al.     Present-day forests use water more efficiently, probably owing to the effect of increased atmospheric carbon dioxide on leaf stomata, which partially close to maintain a near-constant level of carbon dioxide inside the leaves despite increasing atmospheric levels.             Articles and Letters                   Allowable carbon emissions lowered by multiple climate targets ▶     Marco Steinacher, Fortunat Joos, Thomas F. Stocker     The amount of greenhouse gas emissions that will limit the risks from such emissions has been set by the goal of keeping global warming below two degrees Celsius above preindustrial, but this study sets thresholds for sea level rise, ocean acidification and agricultural productivity as well as warming and shows that emissions need to be lowered even further.             Characterization and implications of intradecadal variations in length of day ▶     R. Holme, O. de Viron     Variations in Earth's rotation show clear signals of a 5.9-year oscillation and jumps in Earth's moment of inertia; correlation with the geomagnetic field suggests an origin in Earth's core and constrains the conductivity and thus the composition and mineralogy of the deep mantle.             Gene expression in the deep biosphere ▶     William D. Orsi, Virginia P. Edgcomb, Glenn D. Christman et al.     Gene expression of microbes in anaerobic sediment from the Peru Margin at depths up to 159 metres below the sea floor is analysed: anaerobic metabolism of amino acids, carbohydrates and lipids are seen to be the dominant metabolic processes, and genes associated with cell division are found to be correlated with microbial cell concentration, suggesting that ongoing cell division contributes to biomass turnover.             News & Views                   Geophysics: A third way to rift continents ▶     W. Roger Buck             Earth science: A holistic approach to climate targets ▶     Joeri Rogelj             Biogeochemistry: Carbon dioxide and water use in forests ▶     Belinda Medlyn, Martin De Kauwe             Erratum                   Erratum: The importance of feldspar for ice nucleation by mineral dust in mixed-phase clouds ▶     James D. Atkinson, Benjamin J. Murray, Matthew T. Woodhouse et al.             Research Highlights                   Conservation: Nuclear bombs mark tusks and teeth | Climate science: Drought-busting cyclones         NEWS & COMMENT           Climate change: The forecast for 2018 is cloudy with record heat | Summer books | Shale gas: Pollution fears in China | Shale gas: Surface water also at risk             More Earth & Environmental Sciences ▶                 SciBX is pleased to present: SciBX Summit on Innovation in Drug Discovery and Development 2013 October 29-30, 2013 The Colonnade Hotel, Boston, MA, USA  Click here for more information or to register for this conference today!         Careers & Jobs ▲top               Networking: Real connections ▶     Meeting up in person is still the best way to make contacts and ease career moves.                   Music meets science ▶     Successful musical composition and scientific research share important traits, argues Stephane Detournay.             Careers related news & comment                   Headline message | Seven days: 5–11 July 2013 | In the dark | Outcry over plans for 'Japanese NIH' Ichiko Fuyuno | Research management: What would you cut? | Deal boosts blind's access to texts Declan Butler | US research firms put under pressure to sell Eugenie Samuel Reich               naturejobs.com Science jobs of the week       Postdoctoral Research Associate     University of Southern California            Graduate student     University of Alberta            Research Associate     University of Glasgow            Six Research Fellows     Uppsala University          No matter what your career stage, student, postdoc or senior scientist, you will find articles on naturejobs.com to help guide you in your science career. Keep up-to-date with the latest sector trends, vote in our reader poll and sign-up to receive the monthly Naturejobs newsletter.           • Natureevents Directory featured events           natureevents directory featured events         Cancer Therapeutics 2013: From Bench to Bedside     04.11.13 La Jolla, USA         Natureevents Directory is the premier resource for scientists looking for the latest scientific conferences, courses, meetings and symposia. Featured across Nature Publishing Group journals and centrally at natureevents.com it is an essential reference guide to scientific events worldwide.               Futures                   All that remains ▶     Shane D. Rhinewald                 Your email address is in the Nature mailing list. You have been sent this Table of Contents Alert because you have opted in to receive it. You can change or discontinue your e-mail alerts at any time, by modifying your preferences on your nature.com account at: www.nature.com/nams/svc/myaccount (You will need to log in to be recognised as a nature.com registrant). For further technical assistance, please contact subscriptions@nature.com For other enquiries, please contact feedback@nature.com Nature Publishing Group | 75 Varick Street, 9th floor | New York | NY 10013-1917 | USA Nature Publishing Group's offices: Principal offices: London - New York - Tokyo Worldwide offices: Basingstoke - Boston - Buenos Aires - Delhi - Hong Kong - Madrid - Melbourne - Munich - Paris - San Francisco - Seoul - Washington DC Macmillan Publishers Limited is a company incorporated in England and Wales under company number 785998 and whose registered office is located at Brunel Road, Houndmills, Basingstoke, Hampshire RG21 6XS. © 2013 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.