Nature Communications - 15 July 2015

Weekly Content Alert Nature Communications is now fully open access. Read more. 15 July 2015  Featured image: Ravisio et al. show that how epithelia choose to close a wound depends on the local geometry of the wound. Latest content: Articles Corrigenda Errata Advertisement Ready for a glimpse of tomorrow? Visit KAUST Discovery today KAUST Discovery highlights the cutting-edge research, technologies and innovations emerging from the King Abdullah University of Science and Technology.   http://discovery.kaust.edu.sa Journal homepage Recommend to library Web feed   Advertisement Nature Genetics: Genomes of Icelanders The largest-ever set of human genomes from a single population and the consequent insights into mutation, evolution, gene function and disease predisposition are reported in four linked papers.  Access the Web Focus free online.  Produced with support from Illumina       Nature Communications - now fully open access All new submissions, if accepted, will be published open access and an article processing charge (APC) will apply. For more information visit the website. Visit our open access funding page or contact openaccess@nature.com to learn more about APC funding.       Latest Articles View all Articles     Self-organizing human cardiac microchambers mediated by geometric confinement OPEN Zhen Ma, Jason Wang, Peter Loskill, Nathaniel Huebsch, Sangmo Koo, Felicia L. Svedlund, Natalie C. Marks, Ethan W. Hua, Costas P. Grigoropoulos, Bruce R. Conklin and Kevin E. Healy Organogenesis is orchestrated by biochemical and biophysical stimuli. Here, Ma et al. generate a micro-patterned surface that provides mechanical cues which, when combined with biochemical signals, drive human pluripotent stem cells’ differentiation into beating cardiac microchambers resembling primitive hearts. 14 July 2015 | doi: 10.1038/ncomms8413 Biological Sciences  Bioengineering  Biophysics  Developmental biology  The evolution of human and ape hand proportions OPEN Sergio Almécija, Jeroen B. Smaers and William L. Jungers The human hand can be distinguished from that of apes by its long thumb relative to fingers. Here the authors show that hand proportions vary greatly among ape species and that the human hand evolved from an ancestor that was more similar to humans than to chimpanzees. 14 July 2015 | doi: 10.1038/ncomms8717 Biological Sciences  Evolution  Palaeontology  Gut microbiota mediate caffeine detoxification in the primary insect pest of coffee OPEN Javier A. Ceja-Navarro, Fernando E. Vega, Ulas Karaoz, Zhao Hao, Stefan Jenkins, Hsiao Chien Lim, Petr Kosina, Francisco Infante, Trent R. Northen and Eoin L. Brodie The coffee berry borer, the main insect pest of coffee, feeds and lives on the caffeine-rich beans despite caffeine’s toxic effects. Here Ceja-Navarro et al. show that certain microbes, including Pseudomonas species, mediate caffeine detoxification in the insect’s gut. 14 July 2015 | doi: 10.1038/ncomms8618 Biological Sciences  Ecology  Microbiology  Zoology  Spatial and temporal changes in cumulative human impacts on the world’s ocean OPEN Benjamin S. Halpern, Melanie Frazier, John Potapenko, Kenneth S. Casey, Kellee Koenig, Catherine Longo, Julia Stewart Lowndes, R. Cotton Rockwood, Elizabeth R. Selig, Kimberly A. Selkoe and Shaun Walbridge Human pressure on the ocean is thought to be increasing globally, yet the magnitude and patterns of these changes are largely unknown. Here, the authors produce a global map of change in cumulative human pressures over the past 5 years, and show that ∼66% of the ocean has experienced elevated human impact. 14 July 2015 | doi: 10.1038/ncomms8615 Earth Sciences  Ecology  Oceanography  Climate-induced variations in global wildfire danger from 1979 to 2013 OPEN W. Matt Jolly, Mark A. Cochrane, Patrick H. Freeborn, Zachary A. Holden, Timothy J. Brown, Grant J. Williamson and David M. J. S. Bowman Global wildfires can have severe societal implications and economic cost and have been strongly linked to climate. Here, the authors analyse daily global wildfire trends and show that, during the past 35 years, wildfire season length has increased by 18.7% over more than a quarter of the Earth’s surface. 14 July 2015 | doi: 10.1038/ncomms8537 Earth Sciences  Climate science  Laser chimeras as a paradigm for multistable patterns in complex systems OPEN Laurent Larger, Bogdan Penkovsky and Yuri Maistrenko Chimera states are a class of self-organized solutions of high-dimensional networks with non-local and symmetry breaking coupling. Here the authors study the chimera patterns generated in a non-linear optical setup and uncover the transition between chimera orders as a pattern across clusters of chaoticity. 14 July 2015 | doi: 10.1038/ncomms8752 Physical Sciences  Applied physics  Optical physics  Theoretical physics  The key role of the scaffold on the efficiency of dendrimer nanodrugs OPEN Anne-Marie Caminade, Séverine Fruchon, Cédric-Olivier Turrin, Mary Poupot, Armelle Ouali, Alexandrine Maraval, Matteo Garzoni, Marek Maly, Victor Furer, Valeri Kovalenko, Jean-Pierre Majoral, Giovanni M. Pavan and Rémy Poupot The biological properties of dendrimers are thought to be largely dependent on the chemical nature of their surface. Here, the authors show that the internal scaffold of dendritic nanodrugs strongly influences their bioactivity, based on convergent information from biology and computation results. 14 July 2015 | doi: 10.1038/ncomms8722 Chemical Sciences  Medicinal chemistry  Organic chemistry  DNA methylation of oestrogen-regulated enhancers defines endocrine sensitivity in breast cancer OPEN Andrew Stone, Elena Zotenko, Warwick J. Locke, Darren Korbie, Ewan K. A. Millar, Ruth Pidsley, Clare Stirzaker, Peter Graham, Matt Trau, Elizabeth A. Musgrove, Robert I. Nicholson, Julia M. W. Gee and Susan J. Clark The molecular factors influencing patient response to endocrine therapy are poorly understood. Here Stone et al. characterize the DNA methylome of endocrine response and show that methylation of oestrogen receptor-associated enhancers underpins endocrine sensitivity in human breast cancer. 14 July 2015 | doi: 10.1038/ncomms8758 Biological Sciences  Cancer  Genetics  A novel UCS memory retrieval-extinction procedure to inhibit relapse to drug seeking OPEN Yi-xiao Luo, Yan-xue Xue, Jian-feng Liu, Hai-shui Shi, Min Jian, Ying Han, Wei-li Zhu, Yan-ping Bao, Ping Wu, Zeng-bo Ding, Hao-wei Shen, Jie Shi, Yavin Shaham and Lin Lu Cue-based therapies for treating drug addiction have proven to be only partially effective. Here the authors demonstrate a new memory retrieval based treatment protocol for drug addiction that results in long-lasting inhibition of drug seeking behavior in rodents. 14 July 2015 | doi: 10.1038/ncomms8675 Biological Sciences  Neuroscience  9-O-Acetylation of sialic acids is catalysed by CASD1 via a covalent acetyl-enzyme intermediate OPEN Anna-Maria T. Baumann, Mark J. G. Bakkers, Falk F. R. Buettner, Maike Hartmann, Melanie Grove, Martijn A. Langereis, Raoul J. de Groot and Martina Mühlenhoff 9-O-Acetylation is one of the most common modifications of sialic acids, implicated in sialoglycan recognition and ganglioside biology. Here, the authors show that the key enzyme for the biosynthesis of 9-O-acetylated sialoglycans is CASD1, which uses CMP-activated sialic acid as acceptor substrate. 14 July 2015 | doi: 10.1038/ncomms8673 Biological Sciences  Biochemistry  Cell biology  Observations of discrete harmonics emerging from equatorial noise OPEN Michael A. Balikhin, Yuri Y. Shprits, Simon N. Walker, Lunjin Chen, Nicole Cornilleau-Wehrlin, Iannis Dandouras, Ondrej Santolik, Christopher Carr, Keith H. Yearby and Benjamin Weiss Since the 1970s space missions have observed `equatorial noise' — noise-like plasma waves closely confined to the magnetic equatorial region of Earth s magnetosphere. Here, the authors uncover their structured and periodic frequency pattern, revealing that they are generated by proton distributions. 14 July 2015 | doi: 10.1038/ncomms8703 Physical Sciences  Astronomy  Planetary sciences  Continental flood basalts derived from the hydrous mantle transition zone Xuan-Ce Wang, Simon A. Wilde, Qiu-Li Li and Ya-Nan Yang The Earth’s mantle transition zone may play a key role in large-scale intraplate magmatism and plate tectonics. Here, the authors provide evidence for the origin of continental flood basalts in this zone, by combining oxygen isotope and geochemical evidence from the late Cenozoic Chifeng volcanics of East Asia. 14 July 2015 | doi: 10.1038/ncomms8700 Earth Sciences  Geology and geophysics  Persistent drying in the tropics linked to natural forcing Amos Winter, Davide Zanchettin, Thomas Miller, Yochanan Kushnir, David Black, Gerrit Lohmann, Allison Burnett, Gerald H. Haug, Juan Estrella-Martínez, Sebastian F. M. Breitenbach, Luc Beaufort, Angelo Rubino and Hai Cheng Accurate forecasting of tropical precipitation is dependent on our understanding of the hydrological cycle. Here, the authors present a speleothem-derived record of Mesoamerican precipitation variability since the 1930s, and show that multi-decadal declines in rainfall coincide with major volcanic eruptions. 14 July 2015 | doi: 10.1038/ncomms8627 Earth Sciences  Atmospheric science  Climate science  A highly selective biosynthetic pathway to non-natural C50 carotenoids assembled from moderately selective enzymes OPEN Maiko Furubayashi, Mayu Ikezumi, Shinichi Takaichi, Takashi Maoka, Hisashi Hemmi, Takuya Ogawa, Kyoichi Saito, Alexander V Tobias and Daisuke Umeno Synthetic engineering of complex pathways is often hindered by pathway branching and generation of non-target compounds. Here, the authors show that by judicious combination of moderately selective enzyme variants, a non-natural C50 carotenoid can be generated in bacteria with minimal production of unwanted compounds. 14 July 2015 | doi: 10.1038/ncomms8534 Biological Sciences  Biotechnology  Microbiology  RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway OPEN Yasuhiro Murakawa, Michael Hinz, Janina Mothes, Anja Schuetz, Michael Uhl, Emanuel Wyler, Tomoharu Yasuda, Guido Mastrobuoni, Caroline C. Friedel, Lars Dölken, Stefan Kempa, Marc Schmidt-Supprian, Nils Blüthgen, Rolf Backofen, Udo Heinemann, Jana Wolf, Claus Scheidereit and Markus Landthaler The RNA-binding protein RC3H1/ROQUIN1 promotes the degradation of mRNA by binding to a consensus CDE present in the 3′UTR. Here the authors expand the set of consensus sequences through which RCH31 binds and regulates mRNA encoding members of the DNA damage response and IKK/NF-κB pathway. 14 July 2015 | doi: 10.1038/ncomms8367 Biological Sciences  Bioinformatics  Cell biology  MicroRNA-31 negatively regulates peripherally derived regulatory T-cell generation by repressing retinoic acid-inducible protein 3 OPEN Lingyun Zhang, Fang Ke, Zhaoyuan Liu, Jing Bai, Jinlin Liu, Sha Yan, Zhenyao Xu, Fangzhou Lou, Hong Wang, Huiyuan Zhu, Yang Sun, Wei Cai, Yuanyuan Gao, Qun Li, Xue-Zhong Yu, Youcun Qian, Zichun Hua, Jiong Deng, Qi-Jing Li and Honglin Wang et al. Peripherally derived regulatory T cells (pTreg) exhibit immunosuppressive capacity. Here, the authors show that microRNA-31 acting through inhibiting its direct target Gprc5a negatively regulates pTreg generation and promotes the development of experimental autoimmune encephalomyelitis. 13 July 2015 | doi: 10.1038/ncomms8639 Biological Sciences  Immunology  Single-step fabrication of quantum funnels via centrifugal colloidal casting of nanoparticle films OPEN Jin Young Kim, Valerio Adinolfi, Brandon R. Sutherland, Oleksandr Voznyy, S. Joon Kwon, Tae Wu Kim, Jeongho Kim, Hyotcherl Ihee, Kyle Kemp, Michael Adachi, Mingjian Yuan, Illan Kramer, David Zhitomirsky, Sjoerd Hoogland and Edward H. Sargent Centrifugal casting is widely used to fabricate functional materials that exhibit built-in spatial gradients due to the variation in material density. Kim et al. use this method to prepare colloidal quantum dot films for the first time, based on which photodetectors with gradient bandgap are built. 13 July 2015 | doi: 10.1038/ncomms8772 Physical Sciences  Materials science  Nanotechnology  A phosphorylation switch controls the spatiotemporal activation of Rho GTPases in directional cell migration OPEN Xuan Cao, Tomonori Kaneko, Jenny S. Li, An-Dong Liu, Courtney Voss and Shawn S. C. Li Directed cell migration requires spatially regulated activity of GTPases Rac1 and RhoA. Here Cao et al. show that growth factor stimulation promotes phosphorylation of tensin-3 and phosphatase and tensin homologue (PTEN) and their association with PI 3-kinase and deleted in liver cancer 1 (DLC1) to regulate GTPase activity. 13 July 2015 | doi: 10.1038/ncomms8721 Biological Sciences  Cell biology  Self-assembled two-dimensional nanofluidic proton channels with high thermal stability Jiao-Jing Shao, Kalyan Raidongia, Andrew R. Koltonow and Jiaxing Huang Two-dimensional materials can be used to construct nanofluidic channels to study molecular transport. Here the authors report a lamellar membrane constructed from exfoliated layers of a clay mineral, which exhibits high proton conductivity and extraordinary thermal stability. 13 July 2015 | doi: 10.1038/ncomms8602 Chemical Sciences  Nanotechnology  Physical chemistry  Distinguishing between plasmon-induced and photoexcited carriers in a device geometry OPEN Bob Y. Zheng, Hangqi Zhao, Alejandro Manjavacas, Michael McClain, Peter Nordlander and Naomi J. Halas Plasmonic excitations of electrons in metallic nanostructures are promising for the enhanced conversion of light in semiconductor solar cells. Here, the authors are able to experimentally distinguish the absorption phenomena of plasmonic carrier generation and excitation of carriers by light absorption. 13 July 2015 | doi: 10.1038/ncomms8797 Physical Sciences  Nanotechnology  Optical physics  Subcycle-resolved probe retardation in strong-field pumped dielectrics OPEN Aseem Prakash Pati, Imam Setiawan Wahyutama and Adrian Nikolaus Pfeiffer At the ultrafast timescale the propagation of light pulses through a dielectric material is not only determined by the envelope, but also by nonlinear interactions that evolve within one optical cycle. Here, the authors demonstrate a method to determine the subcycle-resolved delay to a probe pulse in ultrafast, high-field pump–probe experiments. 13 July 2015 | doi: 10.1038/ncomms8746 Physical Sciences  Optical physics  An itinerant antiferromagnetic metal without magnetic constituents OPEN E. Svanidze, Jiakui K. Wang, T. Besara, L. Liu, Q. Huang, T. Siegrist, B. Frandsen, J. W. Lynn, Andriy H. Nevidomskyy, Monika B. Gamża, M. C. Aronson, Y. J. Uemura and E. Morosan Sc3In and ZrZn2 are the only two known itinerant ferromagnets that form from non-magnetic constituents. Now, Svanidze et al., evidence itinerant antiferromagnetism in TiAu below 36 K using thermodynamic, transport, muon-based and neutron-based measurements, and density functional analysis. 13 July 2015 | doi: 10.1038/ncomms8701 Physical Sciences  Applied physics  Condensed matter  Critical role for syndecan-4 in dendritic cell migration during development of allergic airway inflammation Tobias Polte, Susanne Petzold, Jessica Bertrand, Nicole Schütze, Denise Hinz, Jan C. Simon, Irina Lehmann, Frank Echtermeyer, Thomas Pap and Marco Averbeck Syndecan-4 is a surface protein implicated in the regulation of cytoskeleton, adhesion and migration. Here the authors show that blocking syndecan-4 prevents dendritic cell migration into the lung and inhibits the development of allergic airway inflammation in mice. 13 July 2015 | doi: 10.1038/ncomms8554 Biological Sciences  Immunology  Landau level splitting in Cd3As2 under high magnetic fields OPEN Junzhi Cao, Sihang Liang, Cheng Zhang, Yanwen Liu, Junwei Huang, Zhao Jin, Zhi-Gang Chen, Zhijun Wang, Qisi Wang, Jun Zhao, Shiyan Li, Xi Dai, Jin Zou, Zhengcai Xia, Liang Li and Faxian Xiu Dirac semimetals have been proposed as parent materials for other topologically non-trivial phases such as Weyl semimetals, achieved by the breaking of time reversal symmetry. Here the authors use transport measurements to evidence such behaviour in single crystal Cd3As2 under an applied magnetic field. 13 July 2015 | doi: 10.1038/ncomms8779 Physical Sciences  Applied physics  Condensed matter  Quantitative operando visualization of the energy band depth profile in solar cells OPEN Qi Chen, Lin Mao, Yaowen Li, Tao Kong, Na Wu, Changqi Ma, Sai Bai, Yizheng Jin, Dan Wu, Wei Lu, Bing Wang and Liwei Chen The energy band alignment of solar cell materials is highly relevant to the device performance, but its measurement is challenging. Here, the authors report direct visualization of energy band alignment in operating organic photovoltaic devices using scanning Kelvin probe microscopy imaging. 13 July 2015 | doi: 10.1038/ncomms8745 Physical Sciences  Applied physics  Materials science  Evidence of liquid–liquid transition in glass-forming La50Al35Ni15 melt above liquidus temperature OPEN Wei Xu, Magdalena T. Sandor, Yao Yu, Hai-Bo Ke, Hua-Ping Zhang, Mao-Zhi Li, Wei-Hua Wang, Lin Liu and Yue Wu Non-density driven liquid-liquid transition has been predicted in theories, but direct experimental verification is challenging because liquid often remains metastable at transition temperature. Here, Xu et al. provide evidence in a lanthanum-based metallic glass above its liquidus temperature. 13 July 2015 | doi: 10.1038/ncomms8696 Physical Sciences  Condensed matter  Materials science  Storage and retrieval of vector beams of light in a multiple-degree-of-freedom quantum memory OPEN Valentina Parigi, Vincenzo D’Ambrosio, Christophe Arnold, Lorenzo Marrucci, Fabio Sciarrino and Julien Laurat Exploiting the full structuration of light fields for storing multiple degrees of freedom holds great promise for applications in classical and quantum optics. Here, the authors demonstrate the storage of spatio-polarization-patterned beams into an optical memory, and its retrieval at the single-photon level. 13 July 2015 | doi: 10.1038/ncomms8706 Physical Sciences  Applied physics  Optical physics  Localization and topology protected quantum coherence at the edge of hot matter Yasaman Bahri, Ronen Vosk, Ehud Altman and Ashvin Vishwanath Quantum coherence should be rapidly lost in a system of many strongly coupled particles. Here, the authors show that this need not be the case in a one-dimensional magnet with impurities, allowing for a sharply defined topological phase even at high temperatures. 10 July 2015 | doi: 10.1038/ncomms8341 Physical Sciences  Theoretical physics  PGD2 deficiency exacerbates food antigen-induced mast cell hyperplasia Tatsuro Nakamura, Shingo Maeda, Kazuhide Horiguchi, Toko Maehara, Kosuke Aritake, Byung-il Choi, Yoichiro Iwakura, Yoshihiro Urade and Takahisa Murata Mast cells are major contributors to allergy. Here the authors show that prostaglandin D2-deficient mast cells produce more chemoattractants, promoting mast cell hyperplasia and exacerbating allergic responses in a mouse model of food allergy. 10 July 2015 | doi: 10.1038/ncomms8514 Biological Sciences  Immunology  Ubinuclein-1 confers histone H3.3-specific-binding by the HIRA histone chaperone complex OPEN M Daniel Ricketts, Brian Frederick, Henry Hoff, Yong Tang, David C. Schultz, Taranjit Singh Rai, Maria Grazia Vizioli, Peter D. Adams and Ronen Marmorstein Ubinuclein-1 (UBN1) is a subunit of the HIRA histone chaperone complex that deposits histone H3.3 into chromatin. Here the authors use structural and biochemical studies to show that a conserved domain in UBN1 mediates H3.3-specific binding by the HIRA complex. 10 July 2015 | doi: 10.1038/ncomms8711 Biological Sciences  Biochemistry  Collisional dynamics in a gas of molecular super-rotors OPEN Yuri Khodorkovsky, Uri Steinitz, Jean-Michel Hartmann and Ilya Sh. Averbukh Super-rotors are fast rotating molecules whose rotational–translational energy transfer is suppressed. Here the authors study the equilibration of super-rotor gases through molecular dynamics simulations, showing the emergence and explosive termination of an anisotropy in the molecular angular distribution. 10 July 2015 | doi: 10.1038/ncomms8791 Physical Sciences  Atomic and molecular physics  Dynamic structural evolution of supported palladium–ceria core–shell catalysts revealed by in situ electron microscopy OPEN Shuyi Zhang, Chen Chen, Matteo Cargnello, Paolo Fornasiero, Raymond J. Gorte, George W. Graham and Xiaoqing Pan There is currently renewed interest in the use of core–shell catalysts for methane combustion. Here, the authors perform an ex situ and in situ electron microscopy study to probe the structural evolution of palladium–cerium dioxide catalytic core–shell subunits over a wide temperature range. 10 July 2015 | doi: 10.1038/ncomms8778 Chemical Sciences  Catalysis  Materials science  Physical chemistry  Ultrastrong ductile and stable high-entropy alloys at small scales OPEN Yu Zou, Huan Ma and Ralph Spolenak Refractory high-entropy alloys show promising mechanical properties at elevated temperatures, but are generally brittle at room temperature. Here, the authors observe an improved ductility and yield strength in high-entropy alloy micropillars consisting of nanometre-sized grains that also exhibit excellent thermal stability. 10 July 2015 | doi: 10.1038/ncomms8748 Physical Sciences  Materials science  Nanotechnology  Carbon-doped BN nanosheets for metal-free photoredox catalysis OPEN Caijin Huang, Cheng Chen, Mingwen Zhang, Lihua Lin, Xinxin Ye, Sen Lin, Markus Antonietti and Xinchen Wang Metal-free semiconductors with appropriate bandgaps create photocatalytic routes to water splitting and CO2 reduction. Here the authors dope hexagonal boron nitride nanosheets with carbon via a simple method to synthesize a ternary B–C–N alloy capable of performing just this function. 10 July 2015 | doi: 10.1038/ncomms8698 Physical Sciences  Catalysis  Materials science  Physical chemistry  Telomeric G-quadruplexes are a substrate and site of localization for human telomerase OPEN Aaron L. Moye, Karina C. Porter, Scott B. Cohen, Tram Phan, Katherine G. Zyner, Natsuki Sasaki, George O. Lovrecz, Jennifer L. Beck and Tracy M. Bryan G-quadruplexes formed by four guanine bases in a square planar arrangement in telomeres may prevent extension of this region by telomerase. Here, the authors show that telomerase can localize to and partially unwind and extend G-quadruplexes, suggesting an important biological role for G-quadruplexes. 09 July 2015 | doi: 10.1038/ncomms8643 Biological Sciences  Biochemistry  Molecular biology  Two routes to senescence revealed by real-time analysis of telomerase-negative single lineages OPEN Zhou Xu, Emilie Fallet, Camille Paoletti, Steffen Fehrmann, Gilles Charvin and Maria Teresa Teixeira Erosion of telomeres eventually causes replicative senescence, but mechanisms underlying the variability and dynamics of the pathway are not known. Here, the authors examine senescence in single yeast cells with inactivated telomerase to reveal two mechanistically distinct routes to senescence. 09 July 2015 | doi: 10.1038/ncomms8680 Biological Sciences  Cell biology  TD-60 links RalA GTPase function to the CPC in mitosis OPEN Diana Papini, Lars Langemeyer, Maria A. Abad, Alastair Kerr, Itaru Samejima, Patrick A. Eyers, A. Arockia Jeyaprakash, Jonathan M. G. Higgins, Francis A. Barr and William C. Earnshaw TD-60 (RCC2) structurally resembles a guanine nucleotide exchange factor (GEF), but its target GTPase was unknown. Here Papini et al. show that TD-60 is a GEF for RalA, and that RalA helps to regulate the chromosomal passenger complex and kinetochore–microtubule interactions in mitosis. 09 July 2015 | doi: 10.1038/ncomms8678 Biological Sciences  Cell biology  Rapid neodymium release to marine waters from lithogenic sediments in the Amazon estuary OPEN Tristan C. C. Rousseau, Jeroen E. Sonke, Jérôme Chmeleff, Pieter van Beek, Marc Souhaut, Geraldo Boaventura, Patrick Seyler and Catherine Jeandel Neodymium isotopes are tracers for past and present ocean circulation and biogeochemistry. Here, the authors combine observations of neodymium and radium isotopes in the Amazon estuary and show that the rapid release of neodymium from river suspended sediments leaves a strong imprint on coastal sea water. 09 July 2015 | doi: 10.1038/ncomms8592 Earth Sciences  Biogeochemistry  Oceanography  Aharonov–Bohm oscillations in a quasi-ballistic three-dimensional topological insulator nanowire Sungjae Cho, Brian Dellabetta, Ruidan Zhong, John Schneeloch, Tiansheng Liu, Genda Gu, Matthew J. Gilbert and Nadya Mason A three-dimensional topological insulator nanowire is predicted to display gapped one-dimensional surface transport properties. Here, the authors demonstrate this experimentally, observing characteristic quantum oscillations in conductance in (Bi1.33Sb0.67)Se3 nanowires under an applied magnetic field. 09 July 2015 | doi: 10.1038/ncomms8634 Physical Sciences  Applied physics  Condensed matter  Significant radiative impact of volcanic aerosol in the lowermost stratosphere OPEN Sandra M. Andersson, Bengt G. Martinsson, Jean-Paul Vernier, Johan Friberg, Carl A. M. Brenninkmeijer, Markus Hermann, Peter F. J. van Velthoven and Andreas Zahn The role played by volcanic-induced cooling in the recent warming hiatus is not accurately described in the latest phase of the Coupled Model Intercomparison Project. Here, the authors use satellite and aircraft data to investigate the radiative impact of volcanic aerosols in the lowermost stratosphere since the year 2000. 09 July 2015 | doi: 10.1038/ncomms8692 Earth Sciences  Atmospheric science  Climate science  CEP63 deficiency promotes p53-dependent microcephaly and reveals a role for the centrosome in meiotic recombination Marko Marjanović, Carlos Sánchez-Huertas, Berta Terré, Rocío Gómez, Jan Frederik Scheel, Sarai Pacheco, Philip A. Knobel, Ana Martínez-Marchal, Suvi Aivio, Lluís Palenzuela, Uwe Wolfrum, Peter J. McKinnon, José A. Suja, Ignasi Roig, Vincenzo Costanzo, Jens Lüders and Travis H. Stracker CEP63 is a centrosomal protein that is mutated in the microcephaly disease Seckel syndrome. Here the authors disrupt Cep63 in the mouse and find that neural progenitor cells undergo p53-dependent cell death, and uncover a role for CEP63 in ensuring correct meiotic recombination in male gametes. 09 July 2015 | doi: 10.1038/ncomms8676 Biological Sciences  Cell biology  Neuroscience  New streams and springs after the 2014 Mw6.0 South Napa earthquake OPEN Chi-Yuen Wang and Michael Manga Following the Mw6 South Napa earthquake in California, previously dry streams and springs began to flow. Here, the authors present data from repeated stream surveys and laboratory measurements and suggest that the new flows originated from groundwater in the mountains and were released by the earthquake. 09 July 2015 | doi: 10.1038/ncomms8597 Earth Sciences  Geology and geophysics  Lansoprazole is an antituberculous prodrug targeting cytochrome bc1 OPEN Jan Rybniker, Anthony Vocat, Claudia Sala, Philippe Busso, Florence Pojer, Andrej Benjak and Stewart T. Cole Tuberculosis control is threatened by the continued emergence of drug-resistant strains. Here, Rybniker et al. screen a library of FDA-approved drugs and identify a gastric proton pump inhibitor that also has antituberculosis activity and targets the bacterial cytochrome bc1 complex. 09 July 2015 | doi: 10.1038/ncomms8659 Biological Sciences  Microbiology  A drug-specific nanocarrier design for efficient anticancer therapy Changying Shi, Dandan Guo, Kai Xiao, Xu Wang, Lili Wang and Juntao Luo Telodendrimers are versatile and robust nanoparticle-based drug carriers. From a screen of potential small-molecule building blocks, Shi et al. identify rhein-containing telodendrimers as stable and effective nanocarriers of doxorubicin for treating a xenograft Raji lymphoma model. 09 July 2015 | doi: 10.1038/ncomms8449 Biological Sciences  Cancer  Nanotechnology  Ubiquitous healthy diatoms in the deep sea confirm deep carbon injection by the biological pump OPEN S. Agusti, J. I. González-Gordillo, D. Vaqué, M. Estrada, M. I. Cerezo, G. Salazar, J. M. Gasol and C. M. Duarte Sinking of organic matter represents the dominant mechanism for sequestration of anthropogenic CO2 in the deep sea. Here, the authors report the presence of healthy photosynthetic cells in the deep dark ocean, implying the fast injection of fresh organic carbon at depth across the global oligotrophic ocean. 09 July 2015 | doi: 10.1038/ncomms8608 Earth Sciences  Biogeochemistry  Oceanography  A palette of fluorescent proteins optimized for diverse cellular environments Lindsey M. Costantini, Mikhail Baloban, Michele L. Markwardt, Mark Rizzo, Feng Guo, Vladislav V. Verkhusha and Erik L. Snapp Quantitative live cell imaging of protein trafficking suffers from misfolding and inappropriate disulphide bond formation of fluorescent proteins in the secretory pathway. Here, the authors present an optimized collection of fluorescent proteins suitable for use in oxidizing subcellular compartments. 09 July 2015 | doi: 10.1038/ncomms8670 Biological Sciences  Cell biology  Point nodes persisting far beyond Tc in Bi2212 OPEN Takeshi Kondo, W. Malaeb, Y. Ishida, T. Sasagawa, H. Sakamoto, Tsunehiro Takeuchi, T. Tohyama and S. Shin The pairing gap of the high-T c cuprates has been expected to close at the transition temperature, similarly to the case of conventional superconductors. Here the authors perform ARPES measurements on Bi2212, and reveal a point nodal gap formation beyond T c, characterized in terms of three parameters. 09 July 2015 | doi: 10.1038/ncomms8699 Physical Sciences  Applied physics  Condensed matter  Synthesis of quasi-free-standing bilayer graphene nanoribbons on SiC surfaces OPEN Myriano H. Oliveira, Jr., Joao Marcelo J. Lopes, Timo Schumann, Lauren A. Galves, Manfred Ramsteiner, Katja Berlin, Achim Trampert and Henning Riechert Bilayer graphene nanoribbons are very promising for future nanoelectronics. Here Lopes et al. show a novel approach for the fabrication of quasi-free-standing bilayer graphene nanoribbons on SiC, based on the precise control of the layer-by-layer growth of graphene and a simple annealing step in air. 09 July 2015 | doi: 10.1038/ncomms8632 Physical Sciences  Materials science  Nanotechnology  PTEN regulates DNA replication progression and stalled fork recovery Jinxue He, Xi Kang, Yuxin Yin, K. S. Clifford Chao and Wen H. Shen PTEN plays multiple roles in genome protection and tumour suppression. Here the authors show that PTEN depletion leads to impairment of replication progression, stalled fork recovery and diminished chromatin loading of Rad51, highlighting the interplay of PTEN with Rad51 in promoting stalled fork restart. 09 July 2015 | doi: 10.1038/ncomms8620 Biological Sciences  Cell biology  Molecular biology  Epigenetic silencing of Oct4 by a complex containing SUV39H1 and Oct4 pseudogene lncRNA OPEN Michele Scarola, Elisa Comisso, Rhena Pascolo, Riccardo Chiaradia, Rosa Maria Marion, Claudio Schneider, Maria A. Blasco, Stefan Schoeftner and Roberta Benetti Pseudogene derived long non-coding RNAs (lncRNAs) can regulate the expression of their ancestral genes. Here, the authors show that the Oct4 pseudogene OctP4 lncRNA plays an important role in inducing and maintaining silencing of the ancestral Oct4 gene in differentiating mouse embryonic stem cells. 09 July 2015 | doi: 10.1038/ncomms8631 Biological Sciences  Cell biology  Molecular biology  Growth-regulating Mycobacterium tuberculosis VapC-mt4 toxin is an isoacceptor-specific tRNase Jonathan W. Cruz, Jared D. Sharp, Eric D. Hoffer, Tatsuya Maehigashi, Irina O. Vvedenskaya, Arvind Konkimalla, Robert N. Husson, Bryce E. Nickels, Christine M. Dunham and Nancy A. Woychik Toxin–antitoxin systems of the Vap class regulate the growth of several bacterial pathogens including Mycobacterium tuberculosis. Here, the authors show that toxin VapC-mt4 arrests M. tuberculosis growth by specifically cleaving three tRNAs at a single site in their anticodon stem loop, leading to translation inhibition. 09 July 2015 | doi: 10.1038/ncomms8480 Biological Sciences  Biochemistry  Microbiology  Molecular biology  Biotin starvation causes mitochondrial protein hyperacetylation and partial rescue by the SIRT3-like deacetylase Hst4p OPEN Christian T. Madsen, Kathrine B. Sylvestersen, Clifford Young, Sara C. Larsen, Jon W. Poulsen, Marianne A. Andersen, Eva A. Palmqvist, Martin Hey-Mogensen, Per B. Jensen, Jonas T. Treebak, Michael Lisby and Michael L. Nielsen Biotin is an essential vitamin in the regulation of energy metabolism. Here Madsen et al. show that biotin deficiency in yeast leads to hyperacetylation of mitochondrial proteins that is compensated for by the SIRT-like deacetylase Hst4p. 09 July 2015 | doi: 10.1038/ncomms8726 Biological Sciences  Cell biology  Crucial roles of RSK in cell motility by catalysing serine phosphorylation of EphA2 OPEN Yue Zhou, Naoki Yamada, Tomohiro Tanaka, Takashi Hori, Satoru Yokoyama, Yoshihiro Hayakawa, Seiji Yano, Junya Fukuoka, Keiichi Koizumi, Ikuo Saiki and Hiroaki Sakurai The EphA2 receptor tyrosine kinase is overexpressed in many cancers and is reported to be phosphorylated by Akt. Here, Zhou et al. show that RSK, rather than Akt, phosphorylates EphA2 on Ser-897, and this regulates cell migration and invasion of metastatic cancer cells. 09 July 2015 | doi: 10.1038/ncomms8679 Biological Sciences  Cancer  Cell biology  Vibronic origin of long-lived coherence in an artificial molecular light harvester OPEN James Lim, David Paleček, Felipe Caycedo-Soler, Craig N. Lincoln, Javier Prior, Hans von Berlepsch, Susana F. Huelga, Martin B. Plenio, Donatas Zigmantas and Jürgen Hauer Two-dimensional spectroscopy revealed oscillatory signals in photosynthesis’ exciton dynamics, but crowded spectra impede the identification of what sustains the oscillations. Here the authors probe an J-aggregate, whose uncongested response shows that vibronic coupling is responsible for the sustained coherence. 09 July 2015 | doi: 10.1038/ncomms8755 Physical Sciences  Biophysics  Theoretical physics  Inhibition of Ebola virus glycoprotein-mediated cytotoxicity by targeting its transmembrane domain and cholesterol Moritz Hacke, Patrik Björkholm, Andrea Hellwig, Patricia Himmels, Carmen Ruiz de Almodóvar, Britta Brügger, Felix Wieland and Andreas M. Ernst The GP protein of the Ebola virus is involved in the detachment of infected cells, which eventually leads to vascular leakage and contributes to haemorrhagic fever. Here Hacke et al. show that the membrane-anchored subunit of GP is sufficient to induce cell detachment, and that cholesterol contributes to this process. 09 July 2015 | doi: 10.1038/ncomms8688 Biological Sciences  Cell biology  Microbiology  Virology  Gap geometry dictates epithelial closure efficiency OPEN Andrea Ravasio, Ibrahim Cheddadi, Tianchi Chen, Telmo Pereira, Hui Ting Ong, Cristina Bertocchi, Agusti Brugues, Antonio Jacinto, Alexandre J. Kabla, Yusuke Toyama, Xavier Trepat, Nir Gov, Luís Neves de Almeida and Benoit Ladoux Epithelial wound closure proceeds through both crawling into the wound and by constricting an actomyosin cable in a so-called purse-string mechanism. Here the authors show that the two mechanisms are mechanically coupled and the curvature of the wound regulates the overall dynamics of wound closure. 09 July 2015 | doi: 10.1038/ncomms8683 Biological Sciences  Cell biology  Genome-wide burden of deleterious coding variants increased in schizophrenia OPEN Loes M. Olde Loohuis, Jacob A. S. Vorstman, Anil P. Ori, Kim A. Staats, Tina Wang, Alexander L. Richards, Ganna Leonenko, James T. Walters, Joseph DeYoung, null null, René S. Kahn, Don Linszen, Jim van Os, Durk Wiersma, Richard Bruggeman, Wiepke Cahn, Lieuwe de Haan, Lydia Krabbendam, Inez Myin-Germeys, Rita M. Cantor et al. Schizophrenia is a complex disorder with high heritability but poorly understood genetics. Here Olde Loohuis et al. compare schizophrenia patients to unaffected individuals and identify an increased individual burden of rare deleterious mutations in patients. 09 July 2015 | doi: 10.1038/ncomms8501 Biological Sciences  Genetics  Stereomicroscopic 3D-pattern profiling of murine and human intestinal inflammation reveals unique structural phenotypes OPEN Alex Rodriguez-Palacios, Tomohiro Kodani, Lindsey Kaydo, Davide Pietropaoli, Daniele Corridoni, Scott Howell, Jeffry Katz, Wei Xin, Theresa T. Pizarro and Fabio Cominelli The gut epithelium is damaged in inflammatory bowel disease, but capturing such lesions by histology can be difficult. Here, the authors use stereomicroscopy to visualize different 3D inflammatory structures and associated microbes in humans and in 16 genetic mouse models relevant to intestinal inflammation. 08 July 2015 | doi: 10.1038/ncomms8577 Biological Sciences  Medical research  Causative role of left aIPS in coding shared goals during human–avatar complementary joint actions OPEN Lucia M. Sacheli, Matteo Candidi, Vanessa Era and Salvatore M. Aglioti The neural mechanisms supporting imitative motor interactions have been well studied. However, considerably less is known about the mechanisms supporting complementary interactions. Here the authors demonstrate a causal role for left anterior intraparietal sulcus in coding complementary motor goals. 08 July 2015 | doi: 10.1038/ncomms8544 Biological Sciences  Neuroscience  Constant-intensity waves and their modulation instability in non-Hermitian potentials K. G. Makris, Z. H. Musslimani, D. N. Christodoulides and S. Rotter In the presence of a Hermitian potential, a plane wave propagating in free space cannot maintain a constant intensity due to scattering. Here, Makris et al. show that in non-Hermitian potential, waves can propagate with constant intensity through linear and nonlinear inhomogeneous media with gain and loss. 08 July 2015 | doi: 10.1038/ncomms8257 Physical Sciences  Applied physics  Optical physics  Theoretical physics  The surface structure of silver-coated gold nanocrystals and its influence on shape control OPEN J. Daniel Padmos, Michelle L. Personick, Qing Tang, Paul N. Duchesne, De-en Jiang, Chad A. Mirkin and Peng Zhang Nanocrystal surface structure affects many properties but is tough to determine for halide-adsorbed materials. Here, the authors combine X-ray absorption measurements and computational modelling to elucidate the chloride metal surface structures for silver-coated gold nanocrystals with controlled shapes. 08 July 2015 | doi: 10.1038/ncomms8664 Chemical Sciences  Materials science  Nanotechnology  Discovery of intramolecular trans-sialidases in human gut microbiota suggests novel mechanisms of mucosal adaptation OPEN Louise E. Tailford, C. David Owen, John Walshaw, Emmanuelle H. Crost, Jemma Hardy-Goddard, Gwenaelle Le Gall, Willem M. de Vos, Garry L. Taylor and Nathalie Juge Mucosal sialoglycans contribute to host–microbe interactions at mucosal surfaces and impact bacterial colonization of the digestive system. Here the authors identify and characterize an intramolecular trans-sialidase produced by the gut bacterium R. gnavus ATCC 29149 that may contribute to adaptation to the mucosal environment. 08 July 2015 | doi: 10.1038/ncomms8624 Biological Sciences  Biochemistry  Biophysics  Microbiology  Natural variation in timing of stress-responsive gene expression predicts heterosis in intraspecific hybrids of Arabidopsis Marisa Miller, Qingxin Song, Xiaoli Shi, Thomas E. Juenger and Z. Jeffrey Chen The genetic distance between parents influences hybrid performance in plants. Here Miller et al. show that Arabidopsis hybrids produced from diverse parental ecotypes have reduced expression of stress responsive genes at certain times of the day and this correlates with greater biomass production. 08 July 2015 | doi: 10.1038/ncomms8453 Biological Sciences  Plant sciences  Cryo-EM structure of Hepatitis C virus IRES bound to the human ribosome at 3.9-Å resolution OPEN Nick Quade, Daniel Boehringer, Marc Leibundgut, Joop van den Heuvel and Nenad Ban The Hepatitis C virus (HCV) relies on an internal ribosome entry site (IRES) for translation of all the proteins encoded by its single-stranded RNA genome. Here the authors present a near-atomic cryo-EM structure of the HCV IRES bound to the human ribosome, shedding light on the initiation mechanism of HCV's and related IRESs. 08 July 2015 | doi: 10.1038/ncomms8646 Biological Sciences  Biochemistry  Biophysics  Virology  Thickness dependence of the interfacial Dzyaloshinskii–Moriya interaction in inversion symmetry broken systems OPEN Jaehun Cho, Nam-Hui Kim, Sukmock Lee, June-Seo Kim, Reinoud Lavrijsen, Aurelie Solignac, Yuxiang Yin, Dong-Soo Han, Niels J. J. van Hoof, Henk J. M. Swagten, Bert Koopmans and Chun-Yeol You Spin-orbit effects at heavy metal/ferromagnet interfaces can give rise to the Dzyaloshinskii-Moriya interaction, promoting chiral magnetization textures applicable in thin film devices. Here, the authors use Brillouin light scattering to study the dependence of this interaction on film thickness. 08 July 2015 | doi: 10.1038/ncomms8635 Physical Sciences  Applied physics  Condensed matter  Digital quantum simulation of fermionic models with a superconducting circuit OPEN R. Barends, L. Lamata, J. Kelly, L. García-Álvarez, A. G. Fowler, A Megrant, E Jeffrey, T. C. White, D. Sank, J. Y. Mutus, B. Campbell, Yu Chen, Z. Chen, B. Chiaro, A. Dunsworth, I.-C. Hoi, C. Neill, P. J. J. O’Malley, C. Quintana, P. Roushan et al. Quantum simulation offers an unparalleled computational resource, but realizing it for fermionic systems is challenging due to their particle statistics. Here the authors report on the time evolutions of fermionic interactions implemented with digital techniques on a nine-qubit superconducting circuit. 08 July 2015 | doi: 10.1038/ncomms8654 Physical Sciences  Applied physics  Condensed matter  Theoretical physics  Netrin-1 regulates somatic cell reprogramming and pluripotency maintenance OPEN Duygu Ozmadenci, Olivier Féraud, Suzy Markossian, Elsa Kress, Benjamin Ducarouge, Benjamin Gibert, Jian Ge, Isabelle Durand, Nicolas Gadot, Michela Plateroti, Annelise Bennaceur-Griscelli, Jean-Yves Scoazec, Jesus Gil, Hongkui Deng, Agnes Bernet, Patrick Mehlen and Fabrice Lavial Reprogramming holds great promise for regenerative medicine but the molecular mechanisms governing the generation of induced pluripotent stem cells remain unclear. Here, the authors reveal functions for the axonal guidance cue Netrin-1 in constraining apoptosis at the early stage of reprogramming and in established pluripotent cells. 08 July 2015 | doi: 10.1038/ncomms8398 Biological Sciences  Cell biology  Developmental biology  Molecular biology    Nature Communications JOBS of the week Postdoctoral position New York University Medical Center Group Leader(s) in Early Detection University of Cambridge Postdoctoral Training Fellow - Frickel Lab The Francis Crick Institute Senior Scientist University of Helsinki Directorship of the ICR Centre for Evolution and Cancer Institute of Cancer Research (ICR) Post-doctoral Fellow Massachusetts General Hospital & Harvard Medical School Postdoctoral Fellow University of Connecticut Assistant or Associate Professor (3 posts available) The University of Warwick Postdoctoral Researcher NUI Galway Postdoctoral Scientist German Cancer Research Center (DKFZ) More Science jobs from Nature Communications EVENT 3rd Annual Congress of the European Society for Translational Medicine (EUSTM-2015) 01.09.15 Vienna, Austria More science events from       Latest Corrigenda     Corrigendum: PP2A and Aurora differentially modify Cdc13 to promote telomerase release from telomeres at G2/M phase Zih-Jie Shen, Pang-Hung Hsu, Yu-Tai Su, Chia-Wei Yang, Li Kao, Shun-Fu Tseng, Ming-Daw Tsai and Shu-Chun Teng 10 July 2015 | doi: 10.1038/ncomms8819 Biological Sciences  Cell biology  Molecular biology      Corrigendum: An IL-27/NFIL3 signalling axis drives Tim-3 and IL–10 expression and T-cell dysfunction Chen Zhu, Kaori Sakuishi, Sheng Xiao, Zhiyi Sun, Sarah Zaghouani, Guangxiang Gu, Chao Wang, Dewar J. Tan, Chuan Wu, Manu Rangachari, Thomas Pertel, Hyun-Tak Jin, Rafi Ahmed, Ana C. Anderson and Vijay K. Kuchroo 08 July 2015 | doi: 10.1038/ncomms8657 Biological Sciences  Immunology        Latest Errata     Erratum: MORC1 represses transposable elements in the mouse male germline William A. Pastor, Hume Stroud, Kevin Nee, Wanlu Liu, Dubravka Pezic, Sergei Manakov, Serena A. Lee, Guillaume Moissiard, Natasha Zamudio, Déborah Bourc’his, Alexei A. Aravin, Amander T. Clark and Steven E. Jacobsen 10 July 2015 | doi: 10.1038/ncomms8604 Biological Sciences  Cell biology  Molecular biology      Erratum: Photogated humidity-driven motility Lidong Zhang, Haoran Liang, Jolly Jacob and Panče Naumov 09 July 2015 | doi: 10.1038/ncomms8862 Chemical Sciences  Materials science      Advertisement An online-only, open access, multidisciplinary journal dedicated to publishing high-quality original research articles, reviews, editorials, commentaries, and hypothesis generating observations on all areas of breast cancer research. Part of the Nature Partner Journals series, published in partnership with the Breast Cancer Research Foundation. Now open for submissions.   Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. The contents of the Natureevents Directory are now live. The digital version is available here. Find the latest scientific conferences, courses, meetings and symposia on natureevents.com. For event advertising opportunities across the Nature Publishing Group portfolio please contact natureevents@nature.com  More Nature Events 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/myaccount (You will need to log in to be recognised as a nature.com registrant) For further technical assistance, please contact our registration department For other enquiries, please contact our customer feedback department Nature Publishing Group | 75 Varick Street, 9th Floor | New York | NY 10013-1917 | USA Nature Publishing Group's worldwide offices: London - Paris - Munich - New Delhi - Tokyo - Melbourne San Diego - San Francisco - Washington - New York - Boston 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.