Nature Communications - 29 July 2015

Weekly Content Alert Nature Communications is now fully open access. Read more. 29 July 2015  Featured image: Mann et al. show that microbial communities preferentially degrade permafrost-sourced carbon in a Siberian river basin. Latest content: Articles Corrigendum Erratum Journal homepage Recommend to library Web feed   Advertisement Nature Genetics in association with the Wellcome Trust present: THE GENOMICS OF COMMON DISEASES 2015 September 2-5, 2015 | Cambridge, UK  REGISTER NOW!     Latest Articles View all Articles     Ant groups optimally amplify the effect of transiently informed individuals OPEN Aviram Gelblum, Itai Pinkoviezky, Ehud Fonio, Abhijit Ghosh, Nir Gov and Ofer Feinerman Group conformity is crucial for collective behaviours, but may decrease overall responsiveness to external cues. Here the authors show that load-carrying ant groups function at a transition between ballistic and random motions, where the influence of informed individuals is maximized. 28 July 2015 | doi: 10.1038/ncomms8729 Biological Sciences  Applied physics  Zoology  Microbiota and host determinants of behavioural phenotype in maternally separated mice G. De Palma, P. Blennerhassett, J. Lu, Y. Deng, A. J. Park, W. Green, E. Denou, M. A. Silva, A. Santacruz, Y. Sanz, M. G. Surette, E. F. Verdu, S. M. Collins and P. Bercik There is growing evidence that the intestinal microbiota can affect host behaviour. Here, De Palma et al. show in mice that early-life stress (maternal separation) induces changes in host physiology that alter the gut microbiota, which then triggers anxiety-like and depression-like behaviour later in life. 28 July 2015 | doi: 10.1038/ncomms8735 Biological Sciences  Microbiology  Neuroscience  Antiquity of the South Atlantic Anomaly and evidence for top-down control on the geodynamo OPEN John A. Tarduno, Michael K. Watkeys, Thomas N. Huffman, Rory D. Cottrell, Eric G. Blackman, Anna Wendt, Cecilia A. Scribner and Courtney L. Wagner The rapid decay of Earth’s dipole magnetic field has recently captured the public imagination. Here, the authors present a southern hemisphere magnetic record from South African Iron Age sites using oriented samples in the floors and suggest that the anomalous field behaviour is not just a recent feature. 28 July 2015 | doi: 10.1038/ncomms8865 Earth Sciences  Geology and geophysics  Growth pattern from birth to adulthood in African pygmies of known age OPEN Fernando V. Ramirez Rozzi, Yves Koudou, Alain Froment, Yves Le Bouc and Jérémie Botton The African pygmies are known for their short stature, yet it is unclear when and how this phenotype is acquired during growth. Here the authors show that the pygmies’ small stature results primarily from slow growth during infancy. 28 July 2015 | doi: 10.1038/ncomms8672 Biological Sciences  Evolution  Evaluation of candidate vaccine approaches for MERS-CoV OPEN Lingshu Wang, Wei Shi, M. Gordon Joyce, Kayvon Modjarrad, Yi Zhang, Kwanyee Leung, Christopher R. Lees, Tongqing Zhou, Hadi M. Yassine, Masaru Kanekiyo, Zhi-yong Yang, Xuejun Chen, Michelle M. Becker, Megan Freeman, Leatrice Vogel, Joshua C. Johnson, Gene Olinger, John P. Todd, Ulas Bagci, Jeffrey Solomon et al. Unmet need exists for a vaccine against Middle East respiratory syndrome coronavirus (MERS-CoV). Here the authors report the establishment and evaluation, in mice and primates, of a series of MERS-CoV immunogens and show that they can serve as promising leads for vaccine development. 28 July 2015 | doi: 10.1038/ncomms8712 Biological Sciences  Immunology  Virology  Redefining the concept of protease-activated receptors: cathepsin S evokes itch via activation of Mrgprs Vemuri B. Reddy, Shuohao Sun, Ehsan Azimi, Sarina B. Elmariah, Xinzhong Dong and Ethan A. Lerner Sensory neurons that mediate histamine-independent itch express Mas-related G protein coupled receptors (Mrgprs). Here, Reddy et al. show that the cysteine protease cathepsin S cleaves and activates MrgpcrC11 without the generation of a tethered ligand, in contrast to other protease activated receptors. 28 July 2015 | doi: 10.1038/ncomms8864 Biological Sciences  Cell biology  Neuroscience  Aversive learning shapes neuronal orientation tuning in human visual cortex OPEN Lisa M. McTeague, L. Forest Gruss and Andreas Keil Sensory cortical tuning is shaped by experience to facilitate coding of features that are predictive of behaviourally relevant outcomes. Here the authors demonstrate that rapid behaviourally driven retuning of human visual cortex involves top–down projections as well as local inhibitory interactions. 28 July 2015 | doi: 10.1038/ncomms8823 Biological Sciences  Neuroscience  MCM8-9 complex promotes resection of double-strand break ends by MRE11-RAD50-NBS1 complex OPEN Kyung Yong Lee, Jun-Sub Im, Etsuko Shibata, Jonghoon Park, Naofumi Handa, Stephen C. Kowalczykowski and Anindya Dutta The MCM8-9 complex is required for repair of DNA double-strand breaks (DSBs). Here, the authors show that MCM8-9 is required for the nuclease activity of the MRE11-RAD50-NBS1 complex (MRN) and stabilizes its association with DNA damage sites, promoting resection of DSB ends. 28 July 2015 | doi: 10.1038/ncomms8744 Biological Sciences  Cell biology  Molecular biology  A biphasic epigenetic switch controls immunoevasion, virulence and niche adaptation in non-typeable Haemophilus influenzae OPEN John M. Atack, Yogitha N. Srikhanta, Kate L. Fox, Joseph A. Jurcisek, Kenneth L. Brockman, Tyson A. Clark, Matthew Boitano, Peter M. Power, Freda E.-C. Jen, Alastair G. McEwan, Sean M. Grimmond, Arnold L. Smith, Stephen J. Barenkamp, Jonas Korlach, Lauren O. Bakaletz and Michael P. Jennings Non-typeable Haemophilus influenzae, which causes ear and lung infections, has a DNA methyltransferase encoded by alternative alleles that are subject to random ON/OFF switching. Here, Atack et al. show that this epigenetic switch controls the expression of key proteins involved in virulence. 28 July 2015 | doi: 10.1038/ncomms8828 Biological Sciences  Genetics  Microbiology  A molecular propeller effect for chiral separation and analysis OPEN Jonathon B. Clemens, Osman Kibar and Mirianas Chachisvilis Separation and analysis of enantiomers is a difficult task due to the normally identical physical properties they display. Here, the authors show how chiral molecules with non-zero dipoles can be propelled in opposite directions under the influence of a rotating electric field. 28 July 2015 | doi: 10.1038/ncomms8868 Chemical Sciences  Analytical chemistry  Atomic and molecular physics  Physical chemistry  The iBeetle large-scale RNAi screen reveals gene functions for insect development and physiology OPEN Christian Schmitt-Engel, Dorothea Schultheis, Jonas Schwirz, Nadi Ströhlein, Nicole Troelenberg, Upalparna Majumdar, Van Anh Dao, Daniela Grossmann, Tobias Richter, Maike Tech, Jürgen Dönitz, Lizzy Gerischer, Mirko Theis, Inga Schild, Jochen Trauner, Nikolaus D. B. Koniszewski, Elke Küster, Sebastian Kittelmann, Yonggang Hu, Sabrina Lehmann et al. Unbiased screening for insect gene function has been largely restricted to Drosophila. Here, Schmitt-Engel et al. perform an unbiased large-scale RNAi screen in the red flour beetle Tribolium castaneum to identify putative gene functions. 28 July 2015 | doi: 10.1038/ncomms8822 Biological Sciences  Developmental biology  Genetics  Stabilization of 4H hexagonal phase in gold nanoribbons OPEN Zhanxi Fan, Michel Bosman, Xiao Huang, Ding Huang, Yi Yu, Khuong P. Ong, Yuriy A. Akimov, Lin Wu, Bing Li, Jumiati Wu, Ying Huang, Qing Liu, Ching Eng Png, Chee Lip Gan, Peidong Yang and Hua Zhang Noble metals typically crystallize with the face-centered cubic structure. Here, the authors report the synthesis of gold nanoribbons in the 4H hexagonal polytype, a previously unreported, metastable phase of gold, and use it to stabilize 4H hexagonal phases of silver, palladium and platinum. 28 July 2015 | doi: 10.1038/ncomms8684 Chemical Sciences  Inorganic chemistry  Materials science  Nanotechnology  Observation of non-Markovian micromechanical Brownian motion OPEN S. Gröblacher, A. Trubarov, N. Prigge, G. D. Cole, M. Aspelmeyer and J. Eisert All quantum systems are connected to their environment, and this reduces their quantumness through decoherence. Here, the authors show that the interaction between a macroscale quantum system—a micromechanical oscillator—and its environment leads to non-Markovian Brownian motion 28 July 2015 | doi: 10.1038/ncomms8606 Physical Sciences  Theoretical physics  Phytochrome diversity in green plants and the origin of canonical plant phytochromes OPEN Fay-Wei Li, Michael Melkonian, Carl J. Rothfels, Juan Carlos Villarreal, Dennis W. Stevenson, Sean W. Graham, Gane Ka-Shu Wong, Kathleen M. Pryer and Sarah Mathews Phytochromes are red-light photoreceptors in plants that regulate key life cycle processes, yet their evolutionary origins are not well understood. Using transcriptomic and genomic data, Li et al. find that canonical plant phytochromes originated in a common ancestor of land plants and charophyte algae. 28 July 2015 | doi: 10.1038/ncomms8852 Biological Sciences  Evolution  Genetics  Plant sciences  Infrared nanospectroscopy characterization of oligomeric and fibrillar aggregates during amyloid formation OPEN F. S. Ruggeri, G. Longo, S. Faggiano, E. Lipiec, A. Pastore and G. Dietler The onset of neurodegenerative disorders is associated at the molecular level with insoluble protein aggregates, named amyloids. Here, the authors characterize by infrared nanospectroscopy and nanomechanical studies, the amyloid aggregation at the individual species scale. 28 July 2015 | doi: 10.1038/ncomms8831 Biological Sciences  Biochemistry  Biophysics  Observation of optical solitons in PT-symmetric lattices OPEN Martin Wimmer, Alois Regensburger, Mohammad-Ali Miri, Christoph Bersch, Demetrios N. Christodoulides and Ulf Peschel Parity–time symmetry can impose a stable energy flow in photonic systems with simultaneous amplification and attenuation. Here, Wimmer et al. demonstrate optical solitons belonging to a continuous parametric family of solutions in a parity–time-symmetric lattice and observe saturable absorber action. 28 July 2015 | doi: 10.1038/ncomms8782 Physical Sciences  Optical physics  Mutations in CDCA7 and HELLS cause immunodeficiency–centromeric instability–facial anomalies syndrome OPEN Peter E. Thijssen, Yuya Ito, Giacomo Grillo, Jun Wang, Guillaume Velasco, Hirohisa Nitta, Motoko Unoki, Minako Yoshihara, Mikita Suyama, Yu Sun, Richard J. L. F. Lemmers, Jessica C. de Greef, Andrew Gennery, Paolo Picco, Barbara Kloeckener-Gruissem, Tayfun Güngör, Ismail Reisli, Capucine Picard, Kamila Kebaili, Bertrand Roquelaure et al. Immunodeficiency-centromeric instability-facial anomalies syndrome is a life threatening autosomal recessive disorder caused by mutations in DNMT3B and ZBTB24. Here Thijssen et al. identify mutations in CDCA7 and HELLS in previously unexplained cases. 28 July 2015 | doi: 10.1038/ncomms8870 Biological Sciences  Genetics  Quantum Monte Carlo study of the phase diagram of solid molecular hydrogen at extreme pressures OPEN N. D. Drummond, Bartomeu Monserrat, Jonathan H. Lloyd-Williams, P. López Ríos, Chris J. Pickard and R. J. Needs Experimental studies of hydrogen at high pressure are challenging, so theory is central to understanding its phase behaviour; however, computed phase diagrams do not agree with previous measurements. Here, the authors use a quantum Monte Carlo method and present results in qualitative agreement with experiment. 28 July 2015 | doi: 10.1038/ncomms8794 Physical Sciences  Condensed matter  Promotion of presynaptic filament assembly by the ensemble of S. cerevisiae Rad51 paralogues with Rad52 OPEN William A. Gaines, Stephen K. Godin, Faiz F. Kabbinavar, Timsi Rao, Andrew P. VanDemark, Patrick Sung and Kara A. Bernstein Homologous repair of DNA double strand breaks in Saccharomyces cerevisiae is dependent on several conserved Rad51 paralogs. Here the authors provide biochemical evidence that Rad55-Rad57 synergistically interacts with the Shu complex to promote Rad51 filament formation and homology directed repair. 28 July 2015 | doi: 10.1038/ncomms8834 Biological Sciences  Biochemistry  Molecular biology  Nanoscale optical positioning of single quantum dots for bright and pure single-photon emission OPEN Luca Sapienza, Marcelo Davanço, Antonio Badolato and Kartik Srinivasan Self-assembled quantum dots are good emitters, but lack emission control prior to device fabrication. Here a photoluminescence imaging technique to characterize position and emission properties of such quantum dots is demonstrated, enabling the realization of high-performance single-photon sources. 27 July 2015 | doi: 10.1038/ncomms8833 Physical Sciences  Applied physics  Nanotechnology  Optical physics  miR-218 is essential to establish motor neuron fate as a downstream effector of Isl1–Lhx3 Karen P. Thiebes, Heejin Nam, Xiaolu A. Cambronne, Rongkun Shen, Stacey M. Glasgow, Hyong-Ho Cho, Ji-sun Kwon, Richard H. Goodman, Jae W. Lee, Seunghee Lee and Soo-Kyung Lee microRNAs have emerged as important components of numerous gene regulatory networks. Here the authors demonstrate that miR-218 is an essential component of the gene regulatory network that controls motor neuron fate specification in the developing spinal cord. 27 July 2015 | doi: 10.1038/ncomms8718 Biological Sciences  Cell biology  Developmental biology  Neuroscience  Three-dimensional nanometre localization of nanoparticles to enhance super-resolution microscopy OPEN Pierre Bon, Nicolas Bourg, Sandrine Lécart, Serge Monneret, Emmanuel Fort, Jérôme Wenger and Sandrine Lévêque-Fort Tracking and stabilizing sample drifts is crucial towards realizing nanometer resolution in superresolution microscopy; metal nanoparticles can provide drift information but diffraction remains a challenge. Here, Bon et al. combine intensity and phase information to reach three-dimensional subnanometre accuracies. 27 July 2015 | doi: 10.1038/ncomms8764 Physical Sciences  Cell biology  Optical physics  How and when plume zonation appeared during the 132 Myr evolution of the Tristan Hotspot OPEN Kaj Hoernle, Joana Rohde, Folkmar Hauff, Dieter Garbe-Schönberg, Stephan Homrighausen, Reinhard Werner and Jason P. Morgan Striped geochemical zonation has been observed along parts of hotspot tracks, although its origin is not well-understood. Here, the authors present Sr–Nd–Pb–Hf isotope data and present a model that can explain the evolution of zonation in both Tristan-Gough and Hawaiian hotspots, reflecting two end members. 27 July 2015 | doi: 10.1038/ncomms8799 Earth Sciences  Geology and geophysics  Evolution of dosage compensation under sexual selection differs between X and Z chromosomes OPEN Charles Mullon, Alison E. Wright, Max Reuter, Andrew Pomiankowski and Judith E. Mank Complete sex chromosome dosage compensation is largely limited to male heterogametic species, with the majority of female heterogametic species displaying incomplete dosage compensation. Here, the authors show that sexual conflict over gene expression combined with sexual selection in males can explain this pattern. 27 July 2015 | doi: 10.1038/ncomms8720 Biological Sciences  Evolution  Genetics  Ultrafast spontaneous emission source using plasmonic nanoantennas OPEN Thang B. Hoang, Gleb M. Akselrod, Christos Argyropoulos, Jiani Huang, David R. Smith and Maiken H. Mikkelsen Typical emitters such as molecules and quantum dots have slow spontaneous emission with lifetimes of 1–10 ns. Here, Hoang et al. have fabricated a hybrid structure of plasmonic nanopatch antennas coupled to quantum dots, achieving ultrafast spontaneous emission with a lifetime of 11 ps. 27 July 2015 | doi: 10.1038/ncomms8788 Physical Sciences  Materials science  Nanotechnology  Optical physics  Tunable Fermi level and hedgehog spin texture in gapped graphene OPEN A. Varykhalov, J. Sánchez-Barriga, D. Marchenko, P. Hlawenka, P. S. Mandal and O. Rader Potential electronic applications of graphene rely on controlling its spin-dependent properties. Here, the authors use spin-resolved photoemission spectroscopy to demonstrate how Au-intercalation produces gapped one-dimensional quasi-freestanding graphene on Fe(110) with tunable Fermi surface spin texture. 27 July 2015 | doi: 10.1038/ncomms8610 Physical Sciences  Applied physics  Geologic controls on supercritical geothermal resources above magmatic intrusions OPEN Samuel Scott, Thomas Driesner and Philipp Weis Utilizing supercritical geothermal water could multiply energy production, but the abundance, location and size of such resources is unclear. Here, the authors present numerical simulations and suggest that supercritical water may play a key role in removing heat from all magmatic intrusions. 27 July 2015 | doi: 10.1038/ncomms8837 Earth Sciences  Geology and geophysics  A phospholipid uptake system in the model plant Arabidopsis thaliana Lisbeth R. Poulsen, Rosa L. López-Marqués, Pai R. Pedas, Stephen C. McDowell, Elizabeth Brown, Reinhard Kunze, Jeffrey F. Harper, Thomas G. Pomorski and Michael Palmgren P4-type ATPases flip lipids from one side of a membrane to the other. Here Poulsen et al. show that ALA10, a P4 ATPase from Arabidopsis thaliana, internalizes phospholipids from the outside of plant cells and suggest that this uptake may be physiologically important for lipid signalling events. 27 July 2015 | doi: 10.1038/ncomms8649 Biological Sciences  Plant sciences  Investigating Alfvénic wave propagation in coronal open-field regions OPEN R. J. Morton, S. Tomczyk and R. Pinto Alfvénic waves are oscillations that occur in a plasma threaded by a magnetic field and their propagation, reflection and dissipation is believed to be partly responsible for the solar wind. Here, the authors observe the counter-propagating Alfvénic waves that most models require for solar-wind acceleration. 27 July 2015 | doi: 10.1038/ncomms8813 Physical Sciences  Astronomy  Fluids and plasma physics  Genetic, molecular and physiological basis of variation in Drosophila gut immunocompetence OPEN Maroun S. Bou Sleiman, Dani Osman, Andreas Massouras, Ary A. Hoffmann, Bruno Lemaitre and Bart Deplancke Animals rely on a multitude of resistance and tolerance mechanisms to resist harmful gut microbes. Here, the authors explore the genetic, molecular and physiological basis underlying the remarkable phenotypic variation in resistance to enteric bacterial infection in Drosophila melanogaster. 27 July 2015 | doi: 10.1038/ncomms8829 Biological Sciences  Genetics  Immunology  Microbiology  Mechanism of potassium ion uptake by the Na+/K+-ATPase OPEN Juan P. Castillo, Huan Rui, Daniel Basilio, Avisek Das, Benoît Roux, Ramon Latorre, Francisco Bezanilla and Miguel Holmgren During transport by the Na+/K+-ATPase, Na+ and K+ ions become occluded between intra- and extracellular gates. Here Castillo et al. measure transient electrical signals arising from K+ occlusion and use molecular simulations to describe a K+ gating mechanism fundamentally different to that of Na+. 24 July 2015 | doi: 10.1038/ncomms8622 Biological Sciences  Biophysics  Structural prerequisites for G-protein activation by the neurotensin receptor OPEN Brian E. Krumm, Jim F. White, Priyanka Shah and Reinhard Grisshammer The structural basis of how G-protein coupled receptors respond to unique stimuli remains poorly understood. Here, Krumm et al. present new structures of the neurotensin receptor and reveal insights into how ligand binding is linked to structural rearrangements associated with receptor activation. 24 July 2015 | doi: 10.1038/ncomms8895 Biological Sciences  Biochemistry  Neuroscience  Fgf and Esrrb integrate epigenetic and transcriptional networks that regulate self-renewal of trophoblast stem cells OPEN Paulina A. Latos, Angela Goncalves, David Oxley, Hisham Mohammed, Ernest Turro and Myriam Hemberger The transcription factor estrogen-related receptor beta, Esrrb, regulates pluripotency genes in embryonic stem cells, but how it acts in trophoblast stem (TS) cells is unclear. Here, the authors identify Esrrb as a primary target of Fgf/Mek signaling and outline a unique TS cell-specific interactome to sustain stemness. 24 July 2015 | doi: 10.1038/ncomms8776 Biological Sciences  Cell biology  Developmental biology  Molecular biology  Unusual fast secondary relaxation in metallic glass OPEN Q. Wang, S.T. Zhang, Y. Yang, Y.D. Dong, C.T. Liu and J. Lu Mechanical relaxation processes in glasses can provide information on the structural and mechanical properties of glasses. Here, the authors observe a fast secondary relaxation process in La-based metallic glasses, providing information on the inelasticity of metallic glasses. 24 July 2015 | doi: 10.1038/ncomms8876 Physical Sciences  Materials science  The water catalysis at oxygen cathodes of lithium–oxygen cells OPEN Fujun Li, Shichao Wu, De Li, Tao Zhang, Ping He, Atsuo Yamada and Haoshen Zhou The main challenges in lithium-oxygen batteries are the low round-trip efficiency and decaying cycle life. Here, the authors present that a trace amount of water in electrolytes facilitates oxygen cathode reactions, enabling the batteries to be operated with small overpotential and good cycling stability. 24 July 2015 | doi: 10.1038/ncomms8843 Chemical Sciences  Materials science  Physical chemistry  Utilization of ancient permafrost carbon in headwaters of Arctic fluvial networks OPEN Paul J. Mann, Timothy I. Eglinton, Cameron P. McIntyre, Nikita Zimov, Anna Davydova, Jorien E. Vonk, Robert M. Holmes and Robert G. M. Spencer The climatic impact of ancient carbon released during the thawing of Arctic permafrost depends on the degree to which it is degraded. Here, the authors show that permafrost-sourced carbon is preferentially metabolized by microbial communities during transit in high-latitude rivers. 24 July 2015 | doi: 10.1038/ncomms8856 Earth Sciences  Biogeochemistry  Climate science  Highly condensed chromatins are formed adjacent to subtelomeric and decondensed silent chromatin in fission yeast OPEN Atsushi Matsuda, Yuji Chikashige, Da-Qiao Ding, Chizuru Ohtsuki, Chie Mori, Haruhiko Asakawa, Hiroshi Kimura, Tokuko Haraguchi and Yasushi Hiraoka The level of chromatin condensation and gene expression is believed to be inversely correlated. Here the authors show that the transcriptionally silent telomere regions are flanked by highly condensed chromatin, and are less condensed than euchromatin in the interphase of Schizosaccharomyces pombe. 24 July 2015 | doi: 10.1038/ncomms8753 Biological Sciences  Cell biology  Molecular biology  Developmental disruptions underlying brain abnormalities in ciliopathies OPEN Jiami Guo, Holden Higginbotham, Jingjun Li, Jackie Nichols, Josua Hirt, Vladimir Ghukasyan and E.S. Anton Primary cilia are essential conveyors of signals underlying major cellular functions but their role in brain development is not completely understood. Here the authors compiled a shRNA library targeting ciliopathy genes known to cause brain disorders, and used it to query how ciliopathy genes affect distinct stages of mouse cortical development. 24 July 2015 | doi: 10.1038/ncomms8857 Biological Sciences  Developmental biology  Neuroscience  Intrinsically disordered proteins drive membrane curvature OPEN David J. Busch, Justin R. Houser, Carl C. Hayden, Michael B. Sherman, Eileen M. Lafer and Jeanne C. Stachowiak Proteins that bend membranes often contain curvature-promoting structural motifs such as wedges or crescent-shaped domains. Busch et al. report that intrinsically disordered domains can also drive membrane curvature and provide evidence that steric pressure driven by protein crowding mediates this effect. 24 July 2015 | doi: 10.1038/ncomms8875 Biological Sciences  Biophysics  Cell biology  MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA–DNA triplex structures OPEN Tanmoy Mondal, Santhilal Subhash, Roshan Vaid, Stefan Enroth, Sireesha Uday, Björn Reinius, Sanhita Mitra, Arif Mohammed, Alva Rani James, Emily Hoberg, Aristidis Moustakas, Ulf Gyllensten, Steven J.M. Jones, Claes M Gustafsson, Andrew H Sims, Fredrik Westerlund, Eduardo Gorab and Chandrasekhar Kanduri Long noncoding RNAs (lncRNAs) regulate gene expression by association with chromatin. Here, the authors show that lncRNA MEG3 regulates the TGF-β pathway by bridging the interactions between polycomb repressive complex 2 and the distal regulatory elements of the TGF-β pathway genes via formation of RNA–DNA triplexes. 24 July 2015 | doi: 10.1038/ncomms8743 Biological Sciences  Cell biology  Molecular biology  Perinuclear tethers license telomeric DSBs for a broad kinesin- and NPC-dependent DNA repair process Daniel K.C. Chung, Janet N.Y. Chan, Jonathan Strecker, Wei Zhang, Sasha Ebrahimi-Ardebili, Thomas Lu, Karan J. Abraham, Daniel Durocher and Karim Mekhail Damaged DNA is often targeted to nuclear pore complexes for repair. Here, the authors show that kinesin-14 mediates this process ensuring error-prone repair, while perinuclear telomere attachment licenses damaged telomeric loci for this repair and kinesin-14 blocks senescence in the absence of telomerase. 24 July 2015 | doi: 10.1038/ncomms8742 Biological Sciences  Cell biology  Molecular biology  Plasmodium falciparum full life cycle and Plasmodium ovale liver stages in humanized mice OPEN Valérie Soulard, Henriette Bosson-Vanga, Audrey Lorthiois, Clémentine Roucher, Jean- François Franetich, Gigliola Zanghi, Mallaury Bordessoulles, Maurel Tefit, Marc Thellier, Serban Morosan, Gilles Le Naour, Frédérique Capron, Hiroshi Suemizu, Georges Snounou, Alicia Moreno-Sabater and Dominique Mazier Mice engrafted with human cells are useful models for research on human malaria parasites. Here the authors show that the complete life cycle of Plasmodium falciparum and the liver stages of Plasmodium ovale can be studied in mice doubly engrafted with human primary hepatocytes and red blood cells. 24 July 2015 | doi: 10.1038/ncomms8690 Biological Sciences  Microbiology  Engineering a dirhodium artificial metalloenzyme for selective olefin cyclopropanation OPEN Poonam Srivastava, Hao Yang, Ken Ellis-Guardiola and Jared C. Lewis Artificial metalloenzymes (ArMs) have the potential to improve transition metal reactivity in complex media. Here, the authors link a dirhodium catalyst to a prolyl oligopeptidase to create an ArM that catalyzes enantioselective olefin cyclopropanation in aqueous solution. 24 July 2015 | doi: 10.1038/ncomms8789 Biological Sciences  Biochemistry  Chemical biology  Structural and dynamic insights into the energetics of activation loop rearrangement in FGFR1 kinase OPEN Tobias Klein, Navratna Vajpai, Jonathan J. Phillips, Gareth Davies, Geoffrey A. Holdgate, Chris Phillips, Julie A. Tucker, Richard A. Norman, Andrew D. Scott, Daniel R. Higazi, David Lowe, Gary S. Thompson and Alexander L. Breeze Receptor tyrosine kinases are key mediators of cell proliferation that have been implicated in several disease states for which they represent promising drug targets. Here the authors determine the thermodynamic basis for the low propensity of FGFR1 to access the DFG-Phe-out conformation required to bind type-II inhibitors. 23 July 2015 | doi: 10.1038/ncomms8877 Biological Sciences  Biochemistry  Biophysics  Chemical biology  Condensin targets and reduces unwound DNA structures associated with transcription in mitotic chromosome condensation OPEN Takashi Sutani, Toyonori Sakata, Ryuichiro Nakato, Koji Masuda, Mai Ishibashi, Daisuke Yamashita, Yutaka Suzuki, Tatsuya Hirano, Masashige Bando and Katsuhiko Shirahige Chromosome condensation is a prerequisite for faithful segregation of chromosomes to daughter cells. Here, the authors show that the condensin complex binds to protein-coding genes in a transcription-dependent manner during condensation, and reduces unwound DNA segments generated by transcription. 23 July 2015 | doi: 10.1038/ncomms8815 Biological Sciences  Molecular biology  Single-photon emitting diode in silicon carbide A. Lohrmann, N. Iwamoto, Z. Bodrog, S. Castelletto, T. Ohshima, T.J. Karle, A. Gali, S. Prawer, J.C. McCallum and B.C. Johnson Single-photon emitters are required for quantum cryptography and computation and single-photon metrology. Here, Lohrmann et al. fabricate electrically driven, single-photon emitting diodes in silicon carbide with a fully polarized output, high emission rates and stability at room temperature. 23 July 2015 | doi: 10.1038/ncomms8783 Physical Sciences  Applied physics  Optical physics  High-resolution optical spectroscopy using multimode interference in a compact tapered fibre Noel H. Wan, Fan Meng, Tim Schröder, Ren-Jye Shiue, Edward H. Chen and Dirk Englund While desirable for compact solutions, the miniaturization of spectrometers comes at the cost of spectral resolution and operating range. Here, Wan et al. propose a tapered fibre multimode interference spectrometer exhibiting high spectral resolution from the visible to the near infrared in a compact configuration. 23 July 2015 | doi: 10.1038/ncomms8762 Physical Sciences  Applied physics  Optical physics  Controllable synthesis of molybdenum tungsten disulfide alloy for vertically composition-controlled multilayer OPEN Jeong-Gyu Song, Gyeong Hee Ryu, Su Jeong Lee, Sangwan Sim, Chang Wan Lee, Taejin Choi, Hanearl Jung, Youngjun Kim, Zonghoon Lee, Jae-Min Myoung, Christian Dussarrat, Clement Lansalot-Matras, Jusang Park, Hyunyong Choi and Hyungjun Kim The band gap modulation of two-dimensional transition metal dichalcogenide alloy is essential for successful applications. Here, we show a controllable synthesis of Mo1−xWxS2 alloy and vertically composition-controlled Mo1−xWxS2 multilayer, which is promising as a photoactive material. 23 July 2015 | doi: 10.1038/ncomms8817 Chemical Sciences  Materials science  Physical chemistry  Conserved nematode signalling molecules elicit plant defenses and pathogen resistance OPEN Patricia Manosalva, Murli Manohar, Stephan H. von Reuss, Shiyan Chen, Aline Koch, Fatma Kaplan, Andrea Choe, Robert J. Micikas, Xiaohong Wang, Karl-Heinz Kogel, Paul W. Sternberg, Valerie M. Williamson, Frank C. Schroeder and Daniel F. Klessig Plants are able to induce defense responses following recognition of certain pathogen derived molecules at the cell surface. Here, Manosalva et al. show that plants respond to ascarosides, a conserved class of nematode pheromones, providing the first example of plant recognition of an animal-derived signalling molecule. 23 July 2015 | doi: 10.1038/ncomms8795 Biological Sciences  Plant sciences  Arabidopsis AZI1 family proteins mediate signal mobilization for systemic defence priming Nicolás M. Cecchini, Kevin Steffes, Michael R. Schläppi, Andrew N. Gifford and Jean T. Greenberg Azelaic acid (AZA) is a mobile signal that is thought to induce defence responses in plants in tissues distal from the initial infection site. Here, Cecchini et al. propose that AZI1, a plastid-targeted lipid transfer protein that is necessary for the movement and priming functions of AZA. 23 July 2015 | doi: 10.1038/ncomms8658 Biological Sciences  Plant sciences  Superconductivity emerging from a suppressed large magnetoresistant state in tungsten ditelluride OPEN Defen Kang, Yazhou Zhou, Wei Yi, Chongli Yang, Jing Guo, Youguo Shi, Shan Zhang, Zhe Wang, Chao Zhang, Sheng Jiang, Aiguo Li, Ke Yang, Qi Wu, Guangming Zhang, Liling Sun and Zhongxian Zhao Tungsten ditelluride has been recently discovered to possess very large and unsaturated magnetoresistance, which opens interesting perspectives for potential applications. Here the authors show suppression of the magnetoresistance and emergence of superconductivity at high pressure. 23 July 2015 | doi: 10.1038/ncomms8804 Physical Sciences  Condensed matter  Pressure-driven dome-shaped superconductivity and electronic structural evolution in tungsten ditelluride OPEN Xing-Chen Pan, Xuliang Chen, Huimei Liu, Yanqing Feng, Zhongxia Wei, Yonghui Zhou, Zhenhua Chi, Li Pi, Fei Yen, Fengqi Song, Xiangang Wan, Zhaorong Yang, Baigeng Wang, Guanghou Wang and Yuheng Zhang Tungsten ditelluride has been recently discovered to possess very large and unsaturated magnetoresistance, up to 60 T. Here the authors apply high pressure on this material and observe a dome-shaped superconducting phase transition. 23 July 2015 | doi: 10.1038/ncomms8805 Physical Sciences  Condensed matter  Repression of arterial genes in hemogenic endothelium is sufficient for haematopoietic fate acquisition OPEN Carlos O. Lizama, John S. Hawkins, Christopher E. Schmitt, Frank L. Bos, Joan P. Zape, Kelly M. Cautivo, Hugo Borges Pinto, Alexander M. Rhyner, Hui Yu, Mary E. Donohoe, Joshua D. Wythe and Ann C. Zovein The first haematopoietic stem and progenitor cells arise from the hemogenic endothelium of arterial vascular beds. Here the authors describe the mechanism that regulates the endothelial-to-haematopoietic transition and show that Sox17 and Notch1, genes critical to arterial endothelium identity, are also crucial repressors of haematopoietic fate. 23 July 2015 | doi: 10.1038/ncomms8739 Biological Sciences  Cell biology  Constraints on soluble aerosol iron flux to the Southern Ocean at the Last Glacial Maximum OPEN T.M. Conway, E.W. Wolff, R. Röthlisberger, R. Mulvaney and H.E. Elderfield Elevated deposition of bioavailable atmospheric iron may have enhanced carbon storage in the glacial Southern Ocean. Conway et al. apply a novel rapid-filtration technique to iron trapped in Antarctic ice cores and show that glacial soluble iron deposition was an order of magnitude greater than the modern. 23 July 2015 | doi: 10.1038/ncomms8850 Earth Sciences  Climate science  Oceanography  Thrombin-dependent intravascular leukocyte trafficking regulated by fibrin and the platelet receptors GPIb and PAR4 Zane S. Kaplan, Alessandro Zarpellon, Imala Alwis, Yuping Yuan, James McFadyen, Mehran Ghasemzadeh, Simone M. Schoenwaelder, Zaverio M. Ruggeri and Shaun P. Jackson Thrombin is a key proinflammatory protease regulating leukocyte trafficking at sites of vascular injury. Here the authors show that balanced thrombin interactions with platelet proteins PAR4, GPIbα and fibrin plays a major role in regulating this process. 23 July 2015 | doi: 10.1038/ncomms8835 Biological Sciences  Cell biology  Medical research  Observation of universal strong orbital-dependent correlation effects in iron chalcogenides OPEN M. Yi, Z-K Liu, Y. Zhang, R. Yu, J.-X. Zhu, J.J. Lee, R.G. Moore, F.T. Schmitt, W. Li, S.C. Riggs, J.-H. Chu, B. Lv, J. Hu, M. Hashimoto, S.-K. Mo, Z. Hussain, Z.Q. Mao, C.W. Chu, I.R. Fisher, Q. Si et al. A proper theoretical description for unconventional superconductivity in iron-based compounds remains elusive. Here, the authors, to capture the electron correlation strength and the role of Fermi surfaces, report ARPES measurements of three iron chalcogenide superconductors to establish universal features. 23 July 2015 | doi: 10.1038/ncomms8777 Physical Sciences  Condensed matter  Dominant oceanic bacteria secure phosphate using a large extracellular buffer OPEN Mikhail V. Zubkov, Adrian P. Martin, Manuela Hartmann, Carolina Grob and David J. Scanlan Oceanic SAR11 Alphaproteobacteria and Prochlorococcus cyanobacteria are abundant in phosphate-poor regions, despite it being vital for growth. Here, Zubkov et al. show these bacterioplankton exploit an extracellular buffer of labile phosphate to reduce their dependency on bioavailable ambient phosphate. 22 July 2015 | doi: 10.1038/ncomms8878 Biological Sciences  Biogeochemistry  Ecology  Oceanography  Genome-wide association study identifies variants at 16p13 associated with survival in multiple myeloma patients Elad Ziv, Eric Dean, Donglei Hu, Alessandro Martino, Daniel Serie, Karen Curtin, Daniele Campa, Blake Aftab, Paige Bracci, Gabriele Buda, Yi Zhao, Jennifer Caswell-Jin, Robert Diasio, Charles Dumontet, Marek Dudziński, Laura Fejerman, Alexandra Greenberg, Scott Huntsman, Krzysztof Jamroziak, Artur Jurczyszyn et al. Multiple myeloma is an incurable blood cancer with family history being a strong contributing risk factor. Here Ziv et al. perform a genome-wide association study for genetic variation associated with myeloma survival, identifying FOPNL variants associated with worse clinical outcomes. 22 July 2015 | doi: 10.1038/ncomms8539 Biological Sciences  Cancer  Genetics  STAT3 regulated ARF expression suppresses prostate cancer metastasis OPEN Jan Pencik, Michaela Schlederer, Wolfgang Gruber, Christine Unger, Steven M. Walker, Athena Chalaris, Isabelle J. Marié, Melanie R. Hassler, Tahereh Javaheri, Osman Aksoy, Jaine K. Blayney, Nicole Prutsch, Anna Skucha, Merima Herac, Oliver H. Krämer, Peter Mazal, Florian Grebien, Gerda Egger, Valeria Poli, Wolfgang Mikulits et al. IL6-STAT3 signaling is activated in prostate cancer, however inhibiting this pathway has not lead to a survival advantage in patients. Here, Pencik et al. show that loss of the IL6-STAT3 axis in mice and humans leads to metastasis due to loss of ARF, unravelling STAT3 and ARF as potential prognostic markers in prostate cancer. 22 July 2015 | doi: 10.1038/ncomms8736 Biological Sciences  Cancer  Cell biology  Medical research  Interaction-induced decay of a heteronuclear two-atom system OPEN Peng Xu, Jiaheng Yang, Min Liu, Xiaodong He, Yong Zeng, Kunpeng Wang, Jin Wang, D. J. Papoular, G. V. Shlyapnikov and Mingsheng Zhan Understanding the behaviour of trapped two-atom systems is interesting for engineering quantum gases, and one of the key quantities to determine is the inelastic relaxation time from hyperfine states. Here, the authors measure this quantity for heteronuclear systems of 87Rb and 85Rb in a micro optical trap. 22 July 2015 | doi: 10.1038/ncomms8803 Physical Sciences  Atomic and molecular physics  HDAC6 and RhoA are novel players in Abeta-driven disruption of neuronal polarity Hanako Tsushima, Marco Emanuele, Alice Polenghi, Alessandro Esposito, Massimo Vassalli, Andrea Barberis, Francesco Difato and Evelina Chieregatti Retracted neurites and disorganized actin filaments are major components of senile plaques and neurofibrillary tangles—hallmarks of Alzheimer's disease. Here the authors show that soluble ß-amyloid impairs action potential firing by disrupting actin and microtubule filaments through the inhibition of HDAC6 and activation of RhoA. 22 July 2015 | doi: 10.1038/ncomms8781 Biological Sciences  Cell biology  Neuroscience  Snf1/AMP-activated protein kinase activates Arf3p to promote invasive yeast growth via a non-canonical GEF domain OPEN Jia-Wei Hsu, Kuan-Jung Chen and Fang-Jen S. Lee Snf1p is the yeast homologue of AMP-activated protein kinase, a key regulator of cellular energy homeostasis. Here, Hsu et al. identify Snf1p as a non-canonical guanine nucleotide-exchange factor for the Arf3p GTPase, regulating the yeast invasive response to glucose depletion. 22 July 2015 | doi: 10.1038/ncomms8840 Biological Sciences  Cell biology  A draft network of ligand–receptor-mediated multicellular signalling in human OPEN Jordan A. Ramilowski, Tatyana Goldberg, Jayson Harshbarger, Edda Kloppman, Marina Lizio, Venkata P. Satagopam, Masayoshi Itoh, Hideya Kawaji, Piero Carninci, Burkhard Rost and Alistair R. R. Forrest Cell-to-cell communication relies upon interactions between secreted ligands and cell surface receptors. Here, Ramilowski et al. present a draft cell-to-cell communication network based on expression of ligand-receptor pairs in 144 different human cell types. 22 July 2015 | doi: 10.1038/ncomms8866 Biological Sciences  Bioinformatics  Cell biology  Assembly-driven activation of the AIM2 foreign-dsDNA sensor provides a polymerization template for downstream ASC OPEN Seamus R. Morrone, Mariusz Matyszewski, Xiong Yu, Michael Delannoy, Edward H. Egelman and Jungsan Sohn The AIM2 inflammasome complex is essential for defence against a number of human pathogens but how it assembles upon recognition of foreign DNA remains incompletely understood. Here Morrone et al. suggest the AIM2 pyrin domain acts in both DNA binding and filament assembly to generate a structural template for complex assembly. 22 July 2015 | doi: 10.1038/ncomms8827 Biological Sciences  Biophysics  Immunology  Predicting the stability of large structured food webs OPEN Stefano Allesina, Jacopo Grilli, György Barabás, Si Tang, Johnatan Aljadeff and Amos Maritan Understanding the dynamics of empirical food webs is of central importance for predicting the stability of ecological communities. Here Allesina et al. derive an approximation to accurately predict the stability of large food webs whose structure is built using the cascade model. 22 July 2015 | doi: 10.1038/ncomms8842 Biological Sciences  Ecology  Modulating protein activity using tethered ligands with mutually exclusive binding sites OPEN Alberto Schena, Rudolf Griss and Kai Johnsson Designing proteins whose activities can be switched on and off by effector molecules is a central challenge in protein engineering. Here, the authors use tethered chemical ligands with two mutually exclusive binding sites as a general method to modulate protein activity in response to specific effectors. 22 July 2015 | doi: 10.1038/ncomms8830 Biological Sciences  Biochemistry  Chemical biology  Patterned arrays of lateral heterojunctions within monolayer two-dimensional semiconductors OPEN Masoud Mahjouri-Samani, Ming-Wei Lin, Kai Wang, Andrew R. Lupini, Jaekwang Lee, Leonardo Basile, Abdelaziz Boulesbaa, Christopher M. Rouleau, Alexander A. Puretzky, Ilia N. Ivanov, Kai Xiao, Mina Yoon and David B. Geohegan Lateral heterojunctions between two-dimensional semiconductor crystals are essential building blocks for electronic devices. Here, the authors utilize electron-beam lithography and selective conversion to simultaneously fabricate arrays of molybdenum diselenide–molybdenum disulfide heterojunctions. 22 July 2015 | doi: 10.1038/ncomms8749 Physical Sciences  Materials science  Nanotechnology  DOT1L cooperates with the c-Myc-p300 complex to epigenetically derepress CDH1 transcription factors in breast cancer progression OPEN Min-Hyung Cho, Ji-Hye Park, Hee-Joo Choi, Mi-Kyung Park, Hee-Young Won, Yeon-Ji Park, Chang Hoon Lee, Seung-Hyun Oh, Young-Soo Song, Hyun Sung Kim, Young-Ha Oh, Jeong-Yeon Lee and Gu Kong DOT1L is an anti-cancer therapeutic target in leukaemia but has a poorly understood role in solid tumours. Here the authors show that DOT1L expression is associated with poor survival and aggressive cancers by helping to epigenetically activate the epithelial-mesenchymal transition during breast cancer progression. 22 July 2015 | doi: 10.1038/ncomms8821 Biological Sciences  Cancer  Molecular biology  Observation of vibrational overtones by single-molecule resonant photodissociation OPEN Ncamiso B. Khanyile, Gang Shu and Kenneth R. Brown Studying the spectra of molecules typically requires large samples, which can be difficult to achieve for hard-to-generate ions. Here, the authors obtain spectra from single CaH+ molecules in a three-ion Columbic crystal, observing new molecular transitions. 22 July 2015 | doi: 10.1038/ncomms8825 Chemical Sciences  Atomic and molecular physics  Physical chemistry  Structures of FolT in substrate-bound and substrate-released conformations reveal a gating mechanism for ECF transporters OPEN Qin Zhao, Chengcheng Wang, Chengyuan Wang, Hui Guo, Zhihao Bao, Minhua Zhang and Peng Zhang Substrate specificity of ECF transporters is determined by the transmembrane EcfS protein subunit. Here Zhao et al. present substrate-bound and substrate-released structures of a bacterial folate transporter EcfS and suggest a gating mechanism for ECF transporters. 22 July 2015 | doi: 10.1038/ncomms8661 Biological Sciences  Biochemistry  Biophysics  Combined crystal structure prediction and high-pressure crystallization in rational pharmaceutical polymorph screening OPEN M. A. Neumann, J. van de Streek, F. P. A. Fabbiani, P. Hidber and O. Grassmann Crystal polymorphism can lead to substances with vastly differing physicochemical properties, which has serious implications in the pharmaceutical industry. Here, the authors use in silico polymorph screening to accurately predict the resulting structures under set crystallisation environments. 22 July 2015 | doi: 10.1038/ncomms8793 Chemical Sciences  Materials science  Organic chemistry  Physical chemistry    Nature Communications JOBS of the week Early Stage Researcher Queen's University Belfast Project Leader Cancer Research UK Postdoc Fellow, Institut Pasteur Institut Pasteur Research Associate The University of Manchester Postdoctoral Position - Postdoctoral Fellow University of Tennessee Health Science Center Postdoctoral Fellow Brigham & Women's Hospital - Harvard Medical School Postdoctoral Associate The Scripps Research Institute Postdoctoral Researcher John Innes Centre (JIC) Postdoctoral Position Markus Stoffel / ETH Zürich Senior Research Scientist Lodz University of Technology More Science jobs from Nature Communications EVENT Cancer Diagnostics Conference 16.11.15 San Francisco, USA More science events from       Latest Corrigendum     Corrigendum: Rethinking Indian monsoon rainfall prediction in the context of recent global warming Bin Wang, Baoqiang Xiang, Juan Li, Peter J. 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