Nature Communications - 16 September 2015

Advertisement To advance your research, it's critical that you see everything the tumor has to show you. With our Cancer Immunology & Immunotherapy Research Solutions, you can detect, measure, visualize, and compare multiple immune-cell phenotypes simultaneously in FFPE tissue - in the same tumor and its microenvironment.     Weekly Content Alert Nature Communications is now fully open access. Read more. 16 September 2015  Featured image: Li et al. sequence Papilio butterfly genomes and provide a method for editing them using the CRISPR/Cas9 system. Latest content: Articles Corrigendum Journal homepage Recommend to library Web feed   Advertisement Nature Energy: Call for Papers Launching in January 2016, Nature Energy is now open for submissions and inviting high-quality research from across the natural and social sciences. The journal will be dedicated to exploring all aspects of the on-going discussion of energy provision; from the generation and storage of energy, to its distribution and management, the needs and demands of the different actors, and the impacts that energy technologies and policies have on societies. Submit your next research paper to the journal.         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     Sonogenetics is a non-invasive approach to activating neurons in Caenorhabditis elegans OPEN Stuart Ibsen, Ada Tong, Carolyn Schutt, Sadik Esener and Sreekanth H. Chalasani Common optogenetic approaches require surgical procedures to deliver light of specific wavelengths to the target cells. Here the authors demonstrate the use of low-pressure ultrasound as a non-invasive trigger to activate specific neurons in Caenorhabditis elegans and find that the mechanotransduction channel TRP-4 sensitizes cells to the ultrasound stimulus. 15 September 2015 | doi: 10.1038/ncomms9264 Biological Sciences  Biotechnology  Neuroscience  Allometric growth in the extant coelacanth lung during ontogenetic development OPEN Camila Cupello, Paulo M. Brito, Marc Herbin, François J Meunier, Philippe Janvier, Hugo Dutel and Gaël Clément The presence of a pulmonary system in fossil coelacanths has only recently been identified, with little known about homologues in living species. Here, Cupello et al. confirm the presence of a lung in the extant species Latimeria chalumnae and report its growth during different stages of development. 15 September 2015 | doi: 10.1038/ncomms9222 Biological Sciences  Developmental biology  Evolution  Zoology  dNP2 is a blood–brain barrier-permeable peptide enabling ctCTLA-4 protein delivery to ameliorate experimental autoimmune encephalomyelitis OPEN Sangho Lim, Won-Ju Kim, Yeon-Ho Kim, Sohee Lee, Ja-Hyun Koo, Jung-Ah Lee, Heeseok Yoon, Do-Hyun Kim, Hong-Jai Park, Hye-Mi Kim, Hong-Gyun Lee, Ji Yun Kim, Jae-Ung Lee, Jae Hun Shin, Lark Kyun Kim, Junsang Doh, Hongtae Kim, Sang-Kyou Lee, Alfred L. M. Bothwell, Minah Suh et al. Most of the cell penetrating peptides can transport therapeutic agents across plasma membranes but barely across the blood-brain barrier. Here the authors develop a peptide that can enter the brain, and show that its fusion to immunomodulatory protein ctCTLA-4 is effective in a mouse model of multiple sclerosis. 15 September 2015 | doi: 10.1038/ncomms9244 Biological Sciences  Biotechnology  Immunology  Neuroscience  Efficient direct solar-to-hydrogen conversion by in situ interface transformation of a tandem structure OPEN Matthias M. May, Hans-Joachim Lewerenz, David Lackner, Frank Dimroth and Thomas Hannappel A future carbon-free energy economy requires an efficient photocatalytic route to hydrogen generation. Here, the authors employ surface modification techniques to raise the performance of an unassisted solar water splitting device to achieve exceptional performances. 15 September 2015 | doi: 10.1038/ncomms9286 Physical Sciences  Applied physics  Catalysis  Materials science  Covalency of hydrogen bonds in liquid water can be probed by proton nuclear magnetic resonance experiments OPEN Hossam Elgabarty, Rustam Z. Khaliullin and Thomas D. Kühne Covalency is a fundamental concept in chemical bonding, but experimentally it is not possible to measure the degree of covalency of a particular bond. Here, the authors report a model to link the covalency of hydrogen bonds in water with the anisotropy of the magnetic shielding tensor in the proton NMR. 15 September 2015 | doi: 10.1038/ncomms9318 Chemical Sciences  Physical chemistry  Solar forcing synchronizes decadal North Atlantic climate variability OPEN Rémi Thiéblemont, Katja Matthes, Nour-Eddine Omrani, Kunihiko Kodera and Felicitas Hansen While variations in solar irradiance are thought to influence North Atlantic climate variability, the direction of the forcing remains unclear. Here the authors present results from a fully coupled ocean-atmosphere model with interactive chemistry that support a top-down mechanism. 15 September 2015 | doi: 10.1038/ncomms9268 Earth Sciences  Atmospheric science  Climate science  The fatty acid elongase Bond is essential for Drosophila sex pheromone synthesis and male fertility OPEN Wan Chin Ng, Jacqueline S. R. Chin, Kah Junn Tan and Joanne Y. Yew Insect behaviours are often guided by chemical signals, but little is known about how pheromone diversity evolves. Here the authors show that loss of the gene bond in Drosophila eliminates the sex pheromone CH503, while silencing it reduces the fertility of males and their conspecific rivals. 15 September 2015 | doi: 10.1038/ncomms9263 Biological Sciences  Evolution  Genetics  Zoology  How Leiomodin and Tropomodulin use a common fold for different actin assembly functions OPEN Malgorzata Boczkowska, Grzegorz Rebowski, Elena Kremneva, Pekka Lappalainen and Roberto Dominguez Leiomodins and Tropomodulins are related, but have different functions; actin filament nucleation and pointed end capping, respectively. Here, the authors use structural, biochemical and cellular approaches to show how these different activities have evolved based on a common protein fold. 15 September 2015 | doi: 10.1038/ncomms9314 Biological Sciences  Biochemistry  Cell biology  Differential genomic imprinting regulates paracrine and autocrine roles of IGF2 in mouse adult neurogenesis OPEN S. R. Ferrón, E. J. Radford, A. Domingo-Muelas, I. Kleine, A. Ramme, D. Gray, I. Sandovici, M. Constancia, A. Ward, T. R. Menheniott and A. C. Ferguson-Smith Selective biallelic expression of certain genes through genomic imprinting are known to play a role in controlling neurogenesis in the adult mammalian brain. Here the authors investigate the role of imprinting in the dosage control of Igf2 and its relevance for the function of IGF2 as a neurogenic regulator in the mouse brain. 15 September 2015 | doi: 10.1038/ncomms9265 Biological Sciences  Developmental biology  Genetics  Neuroscience  Junctional and allele-specific residues are critical for MERS-CoV neutralization by an exceptionally potent germline-like antibody OPEN Tianlei Ying, Ponraj Prabakaran, Lanying Du, Wei Shi, Yang Feng, Yanping Wang, Lingshu Wang, Wei Li, Shibo Jiang, Dimiter S. Dimitrov and Tongqing Zhou m336 is an exceptionally potent germline-like antibody against the emerging MERS-CoV virus. Here, the authors solve the structure of m336 in complex with MERS-CoV receptor-binding domain and use it to reveal a role of junctional and allele-specific residues in the interaction and suggest implications for vaccine development. 15 September 2015 | doi: 10.1038/ncomms9223 Biological Sciences  Biochemistry  Virology  A predictive structural model for bulk metallic glasses OPEN K. J. Laws, D. B. Miracle and M. Ferry The atomic structure of metallic glasses is related to their properties such as the ability of materials to form glasses. Here, the authors develop a new approach to model the atomic structure of metallic glasses, to enable a better connection between atomic structure and glass properties. 15 September 2015 | doi: 10.1038/ncomms9123 Physical Sciences  Materials science  V1 neurons respond differently to object motion versus motion from eye movements OPEN Xoana G. Troncoso, Michael B. McCamy, Ali Najafian Jazi, Jie Cui, Jorge Otero-Millan, Stephen L. Macknik, Francisco M. Costela and Susana Martinez-Conde A key question in neuroscience is understanding how the brain distinguishes self-generated motion from motion in the external world. Here the authors demonstrate that the response of primary visual cortical neurons to a moving stimulus depends on whether the motion was self- or externally generated. 15 September 2015 | doi: 10.1038/ncomms9114 Biological Sciences  Neuroscience  Direct exfoliation and dispersion of two-dimensional materials in pure water via temperature control OPEN Jinseon Kim, Sanghyuk Kwon, Dae-Hyun Cho, Byunggil Kang, Hyukjoon Kwon, Youngchan Kim, Sung O. Park, Gwan Yeong Jung, Eunhye Shin, Wan-Gu Kim, Hyungdong Lee, Gyeong Hee Ryu, Minseok Choi, Tae Hyeong Kim, Junghoon Oh, Sungjin Park, Sang Kyu Kwak, Suk Wang Yoon, Doyoung Byun, Zonghoon Lee et al. The hydrophobic surfaces of many two-dimensional (2D) materials prevents direct exfoliation in water without the use of chemical, surfactant, or surface treatments. Here, the authors exfoliate and disperse 2D materials in pure water via simple control of the temperature of the sonication bath and storage. 15 September 2015 | doi: 10.1038/ncomms9294 Physical Sciences  Materials science  Nanotechnology  Unambiguous detection of nitrated explosive vapours by fluorescence quenching of dendrimer films OPEN Yan Geng, Mohammad A. Ali, Andrew J. Clulow, Shengqiang Fan, Paul L. Burn, Ian R. Gentle, Paul Meredith and Paul E. Shaw Selective standoff detection of explosives is challenging due to the presence of volatile interferents. Here, the authors report dendrimer thin films that display distinct fluorescence responses when exposed to explosives as opposed to common interferents, allowing selective detection of nitrated explosives. 15 September 2015 | doi: 10.1038/ncomms9240 Chemical Sciences  Analytical chemistry  Materials science  Physical chemistry  Saccadic modulation of stimulus processing in primary visual cortex OPEN James M. McFarland, Adrian G. Bondy, Richard C. Saunders, Bruce G. Cumming and Daniel A. Butts Primates acquire visual information through rapid saccadic eye movements, although little is known about their effects on neural processing of visual inputs. Here the authors demonstrate that saccades produce modulations of visual cortical processing that likely originate in the thalamus. 15 September 2015 | doi: 10.1038/ncomms9110 Biological Sciences  Neuroscience  Multivariate selection drives concordant patterns of pre- and postcopulatory sexual selection in a livebearing fish OPEN Alessandro Devigili, Jonathan P. Evans, Andrea Di Nisio and Andrea Pilastro In species in which females mate with multiple partners, sexual selection acts on male traits involved in mating and fertilization. Here, the authors show that selection acting before and after mating explains a significant component of variance in male reproductive fitness in a livebearing fish. 15 September 2015 | doi: 10.1038/ncomms9291 Biological Sciences  Ecology  Evolution  Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel OPEN Jie Huang, Bryan Howie, Shane McCarthy, Yasin Memari, Klaudia Walter, Josine L. Min, Petr Danecek, Giovanni Malerba, Elisabetta Trabetti, Hou-Feng Zheng, null null, Saeed Al Turki, Antoinette Amuzu, Carl A. Anderson, Richard Anney, Dinu Antony, María Soler Artigas, Muhammad Ayub, Senduran Bala, Jeffrey C. Barrett et al. Imputation uses genotype information from SNP arrays to infer the genotypes of missing markers. Here, the authors show that an imputation reference panel derived from whole-genome sequencing of 3,781 samples from the UK10K project improves the imputation accuracy and coverage of low frequency variants compared to existing methods. 14 September 2015 | doi: 10.1038/ncomms9111 Biological Sciences  Genetics  Oxidation of the alarmin IL-33 regulates ST2-dependent inflammation OPEN E. Suzanne Cohen, Ian C. Scott, Jayesh B. Majithiya, Laura Rapley, Benjamin P. Kemp, Elizabeth England, D. Gareth Rees, Catherine L. Overed-Sayer, Joanne Woods, Nicholas J. Bond, Christel Séguy Veyssier, Kevin J. Embrey, Dorothy A. Sims, Michael R. Snaith, Katherine A. Vousden, Martin D. Strain, Denice T. Y. Chan, Sara Carmen, Catherine E. Huntington, Liz Flavell et al. IL-33, released by epithelial cells in response to stress, is a potent activator of inflammation. Here Cohen et al. show that secreted IL-33 is rapidly inactivated by disulfide bond formation that prevents binding to its receptor, and that IL-33-related cytokines are susceptible to similar oxidation. 14 September 2015 | doi: 10.1038/ncomms9327 Biological Sciences  Biochemistry  Immunology  A porous proton-relaying metal-organic framework material that accelerates electrochemical hydrogen evolution OPEN Idan Hod, Pravas Deria, Wojciech Bury, Joseph E. Mondloch, Chung-Wei Kung, Monica So, Matthew D. Sampson, Aaron W. Peters, Cliff P. Kubiak, Omar K. Farha and Joseph T. Hupp Hydrogen evolution technologies for a future carbon-free energy economy require efficient catalysts which can be implemented on a large scale. Here, the authors prepare a composite electrode from readily available elements, whereby a metal-organic framework boosts catalytic performance by enabling rapid proton transport. 14 September 2015 | doi: 10.1038/ncomms9304 Chemical Sciences  Catalysis  Inorganic chemistry  Materials science  Seismic evidence of a two-layer lithospheric deformation in the Indian Ocean Yanfang Qin and Satish C Singh The Central Indian Ocean Basin is one of the most active intra-plate deformation zones on Earth; such areas and their associated earthquakes are poorly understood. Here, the authors show very deep reflectors in the oceanic mantle, suggesting that the lithospheric mantle deformation can be divided into two layers. 14 September 2015 | doi: 10.1038/ncomms9298 Earth Sciences  Geology and geophysics  Proteomics of yeast telomerase identified Cdc48-Npl4-Ufd1 and Ufd4 as regulators of Est1 and telomere length OPEN Kah-Wai Lin, Karin R. McDonald, Amanda J. Guise, Angela Chan, Ileana M. Cristea and Virginia A. Zakian Regulating telomere length and telomerase activity are critical biological processes implicated in ageing and cancer. Here the authors use mass spectrometry to identify the Cdc48-Npl4-Ufd1 complex, which targets proteins for degradation, as a novel regulator of the yeast telomerase Est1. 14 September 2015 | doi: 10.1038/ncomms9290 Biological Sciences  Biochemistry  Molecular biology  LRRK2 G2019S mutation attenuates microglial motility by inhibiting focal adhesion kinase OPEN Insup Choi, Beomsue Kim, Ji-Won Byun, Sung Hoon Baik, Yun Hyun Huh, Jong-Hyeon Kim, Inhee Mook-Jung, Woo Keun Song, Joo-Ho Shin, Hyemyung Seo, Young Ho Suh, Ilo Jou, Sang Myun Park, Ho Chul Kang and Eun-Hye Joe In response to brain injury, microglia extend processes to isolate the lesion. Here Choi et al. show that microglia expressing a pathogenic mutation in the Parkinson’s disease-associated LRRK2 gene show reduced motility and delayed lesion isolation in vitro and in vivo due to attenuated focal adhesion kinase activity. 14 September 2015 | doi: 10.1038/ncomms9255 Biological Sciences  Cell biology  Neuroscience  GITR subverts Foxp3+ Tregs to boost Th9 immunity through regulation of histone acetylation OPEN Xiang Xiao, Xiaomin Shi, Yihui Fan, Xiaolong Zhang, Minhao Wu, Peixiang Lan, Laurie Minze, Yang-Xin Fu, Rafik M. Ghobrial, Wentao Liu and Xian Chang Li Glucocorticoid-induced TNFR-related protein (GITR), a costimulatory protein expressed by T cells, has immunostimulatory effect but the underlying mechanism is not clear. Here the authors show that GITR ligation inhibits the induction of Foxp3 expression and diverts CD4 T cells towards Th9 differentiation instead of iTreg. 14 September 2015 | doi: 10.1038/ncomms9266 Biological Sciences  Immunology  Calcium-controlled conformational choreography in the N-terminal half of adseverin OPEN Sakesit Chumnarnsilpa, Robert C. Robinson, Jonathan M. Grimes and Cedric Leyrat The calcium-regulated gelsolin family of actin-binding proteins includes adseverin. Here, the authors report the X-ray crystal structure of the N-terminal portion of adseverin and use small-angle scattering and molecular dynamics simulations to examine the calcium-dependent function of this protein. 14 September 2015 | doi: 10.1038/ncomms9254 Biological Sciences  Biochemistry  Biophysics  Coordination tuning of cobalt phosphates towards efficient water oxidation catalyst OPEN Hyunah Kim, Jimin Park, Inchul Park, Kyoungsuk Jin, Sung Eun Jerng, Sun Hee Kim, Ki Tae Nam and Kisuk Kang The role of metal-coordination environment on the effectiveness of water oxidation catalysts is relatively unexplored. Here, the authors study a range of cobalt phosphate catalysts with varying coordination environments and observe high activity and stability for a distorted tetrahedral cobalt system. 14 September 2015 | doi: 10.1038/ncomms9253 Chemical Sciences  Catalysis  Materials science  Cross-polarized photon-pair generation and bi-chromatically pumped optical parametric oscillation on a chip OPEN Christian Reimer, Michael Kues, Lucia Caspani, Benjamin Wetzel, Piotr Roztocki, Matteo Clerici, Yoann Jestin, Marcello Ferrera, Marco Peccianti, Alessia Pasquazi, Brent E. Little, Sai T. Chu, David J. Moss and Roberto Morandotti On-chip nonlinear optics devices find a number of applications in modern optics from spectroscopy to communications. Here, the authors increase the degrees of freedom for frequency mixing by demonstrating the nonlinear interaction of perpendicularly-polarized modes in an integrated microring resonator. 14 September 2015 | doi: 10.1038/ncomms9236 Physical Sciences  Applied physics  Optical physics  RNA regulatory networks diversified through curvature of the PUF protein scaffold OPEN Daniel Wilinski, Chen Qiu, Christopher P. Lapointe, Markus Nevil, Zachary T. Campbell, Traci M. Tanaka Hall and Marvin Wickens Members of the PUF family of RNA-binding proteins bind multiple mRNAs in vivo. Here the authors show that the S. cerevisiae Puf5p binds targets of varying lengths that correlate with biological functions. The RNA-binding sites adopt different structures to adapt to a fixed protein scaffold. 14 September 2015 | doi: 10.1038/ncomms9213 Biological Sciences  Biochemistry  Bioinformatics  Integrating regional conservation priorities for multiple objectives into national policy OPEN Maria Beger, Jennifer McGowan, Eric A. Treml, Alison L. Green, Alan T. White, Nicholas H. Wolff, Carissa J. Klein, Peter J. Mumby and Hugh P. Possingham Conservation initiatives that span multiple countries often face conflicting national priorities. Here, Beger et al. develop a framework for integrating regional priorities and national plans by identifying multi-objective and complementary conservation hotspots, and apply it to the Coral Triangle Initiative. 14 September 2015 | doi: 10.1038/ncomms9208 Biological Sciences  Ecology  Nanophotonic coherent light–matter interfaces based on rare-earth-doped crystals OPEN Tian Zhong, Jonathan M. Kindem, Evan Miyazono and Andrei Faraon Quantum light–matter interfaces connecting stationary qubits to photons are fundamental elements of future quantum optical networks. Here, the authors report a quantum interface based on highly coherent rare-earth ions—the solid-state qubits—coupled to a nanophotonic cavity fabricated in the host crystal. 14 September 2015 | doi: 10.1038/ncomms9206 Physical Sciences  Applied physics  Optical physics  Resolution of structure of PIP5K1A reveals molecular mechanism for its regulation by dimerization and dishevelled OPEN Jian Hu, Qianying Yuan, Xue Kang, Yuanbo Qin, Lin Li, Ya Ha and Dianqing Wu Type I phosphatidylinositol phosphate kinase is an important component of many cellular pathways, including Wnt signalling. Here the authors report the crystal structure of the zebrafish protein along with in vitro assays that help to elucidate the regulation and function of this kinase. 14 September 2015 | doi: 10.1038/ncomms9205 Biological Sciences  Biochemistry  Polarization-resolved spectroscopy imaging of grain boundaries and optical excitations in crystalline organic thin films OPEN Z. Pan, N. Rawat, I. Cour, L. Manning, R. L. Headrick and M. Furis In-depth understanding of organic crystalline semiconductor thin films is critical for the development of many electronic and photonic devices. Here, the authors use combined linear dichroism and polarization-resolved photoluminescence scanning microscopy to unveil the nature of excited states in such systems. 14 September 2015 | doi: 10.1038/ncomms9201 Physical Sciences  Analytical chemistry  Materials science  Direct observation shows superposition and large scale flexibility within cytoplasmic dynein motors moving along microtubules OPEN Hiroshi Imai, Tomohiro Shima, Kazuo Sutoh, Matthew L. Walker, Peter J. Knight, Takahide Kon and Stan A. Burgess Cytoplasmic dynein is a dimeric protein that steps processively along microtubules. Here Imai et al. present cryo-electron microscopy images of stepping D. discoideum dynein, revealing diverse microtubule-bound configurations including a hinge-dependent, motors side-by-side arrangement. 14 September 2015 | doi: 10.1038/ncomms9179 Biological Sciences  Biophysics  Cell biology  Structure of HCMV glycoprotein B in the postfusion conformation bound to a neutralizing human antibody OPEN Sumana Chandramouli, Claudio Ciferri, Pavel A. Nikitin, Stefano Caló, Rachel Gerrein, Kara Balabanis, James Monroe, Christy Hebner, Anders E. Lilja, Ethan C. Settembre and Andrea Carfi Cytomegalovirus is a danger to individuals with compromised immune systems and neonates infected in utero. Here the authors show the structure of a neutralizing antibody-bound viral fusion protein glycoprotein B, supporting the development of therapeutic antibodies and vaccines. 14 September 2015 | doi: 10.1038/ncomms9176 Biological Sciences  Biochemistry  Emergence of a novel prey life history promotes contemporary sympatric diversification in a top predator Jakob Brodersen, Jennifer G. Howeth and David M. Post Intraspecific variation is known to cascade evolutionary change down through food webs, although bottom-up changes are less well described. Here, Brodersen et al. show that life history change in a prey fish species, mediated through anthropogenic activity, can promote phenotypic diversification of its top predator. 14 September 2015 | doi: 10.1038/ncomms9115 Biological Sciences  Ecology  Evolution  Zoology  Monolayered Bi2WO6 nanosheets mimicking heterojunction interface with open surfaces for photocatalysis OPEN Yangen Zhou, Yongfan Zhang, Mousheng Lin, Jinlin Long, Zizhong Zhang, Huaxiang Lin, Jeffrey C.-S. Wu and Xuxu Wang Although they tend to exhibit exciting optoelectronic behaviours, the difficulty in fabricating chemically bonded two-dimensional layered heterojunctions has hindered progress in the area. Here, the authors synthesize sandwich-substructured Bi2WO6 monolayers and investigate their photocatalytic activity. 11 September 2015 | doi: 10.1038/ncomms9340 Physical Sciences  Applied physics  Catalysis  Materials science  Emergent surface superconductivity in the topological insulator Sb2Te3 Lukas Zhao, Haiming Deng, Inna Korzhovska, Milan Begliarbekov, Zhiyi Chen, Erick Andrade, Ethan Rosenthal, Abhay Pasupathy, Vadim Oganesyan and Lia Krusin-Elbaum Combining the electronic properties of topological materials and superconductivity is predicted to yield exotic new transport phenomena. Here, the authors evidence surface superconductivity in the topological insulator Sb2Te3 below 9 K induced by Te vapour over-pressuring during crystal growth. 11 September 2015 | doi: 10.1038/ncomms9279 Physical Sciences  Applied physics  Condensed matter  Strong correlations elucidate the electronic structure and phase diagram of LaAlO3/SrTiO3 interface OPEN E. Maniv, M. Ben Shalom, A. Ron, M. Mograbi, A. Palevski, M. Goldstein and Y. Dagan The interface between SrTiO3 and LaAlO3 has the properties of a superconducting two-dimensional electron gas. Here, the authors study the band structure of the interface and found that the population of the mobile band and its density of states are non-monotonic functions of the chemical potential. 11 September 2015 | doi: 10.1038/ncomms9239 Physical Sciences  Applied physics  Condensed matter  Waveguide integrated superconducting single-photon detectors implemented as near-perfect absorbers of coherent radiation Mohsen K. Akhlaghi, Ellen Schelew and Jeff F. Young A large volume of active material in a single-photon detector enhances absorption efficiency at the expense of conversion efficiency, noise and speed. Here the authors overcome this tradeoff in a near-perfect absorber architecture for a waveguide-integrated superconducting nanowire single-photon detector. 11 September 2015 | doi: 10.1038/ncomms9233 Physical Sciences  Applied physics  Optical physics  Magnetic fingerprint of individual Fe4 molecular magnets under compression by a scanning tunnelling microscope OPEN Jacob A.J. Burgess, Luigi Malavolti, Valeria Lanzilotto, Matteo Mannini, Shichao Yan, Silviya Ninova, Federico Totti, Steffen Rolf-Pissarczyk, Andrea Cornia, Roberta Sessoli and Sebastian Loth The incorporation of single-molecule magnets into spintronic devices is often hindered by electronic or structural modifications. Here, the authors demonstrate how confinement of Fe4 molecules in junctions between a Cu2N substrate and a scanning microscope tip enhances intra-molecular exchange interaction. 11 September 2015 | doi: 10.1038/ncomms9216 Physical Sciences  Applied physics  Atomic and molecular physics  Condensed matter  Light-induced metal-like surface of silicon photonic waveguides OPEN Stefano Grillanda and Francesco Morichetti On the nanoscale materials exhibit surface phenomena that do not occur in the bulk. Here, Grillanda et al. demonstrate that the surface of silicon photonic waveguides change according to the intensity of the light propagating in the waveguide, underlining considerations in design of integrated optoelectronic devices. 11 September 2015 | doi: 10.1038/ncomms9182 Physical Sciences  Materials science  Nanotechnology  Optical physics  Nano-socketed nickel particles with enhanced coking resistance grown in situ by redox exsolution OPEN Dragos Neagu, Tae-Sik Oh, David N. Miller, Hervé Ménard, Syed M. Bukhari, Stephen R. Gamble, Raymond J. Gorte, John M. Vohs and John T.S. Irvine Metal particles supported on oxide surfaces are widely used catalysts, and the composites are generally formed by deposition or exsolution methods. Here, the authors show that nickel particles exsolved from the parent perovskite exhibit enhanced stability due to a stronger metal–oxide interface. 11 September 2015 | doi: 10.1038/ncomms9120 Chemical Sciences  Catalysis  Inorganic chemistry  Materials science  The positive piezoconductive effect in graphene OPEN Kang Xu, Ke Wang, Wei Zhao, Wenzhong Bao, Erfu Liu, Yafei Ren, Miao Wang, Yajun Fu, Junwen Zeng, Zhaoguo Li, Wei Zhou, Fengqi Song, Xinran Wang, Yi Shi, Xiangang Wan, Michael S. Fuhrer, Baigeng Wang, Zhenhua Qiao, Feng Miao and Dingyu Xing et al. The thinness and elastic properties of graphene make it an ideal candidate for nanoelectromechanical systems. Here, the authors demonstrate the positive piezoconductive effect in suspended bi- and multi-layer graphene, showing the most pronounced response for three layer samples. 11 September 2015 | doi: 10.1038/ncomms9119 Physical Sciences  Applied physics  Materials science  Novel PRD-like homeodomain transcription factors and retrotransposon elements in early human development OPEN Virpi Töhönen, Shintaro Katayama, Liselotte Vesterlund, Eeva-Mari Jouhilahti, Mona Sheikhi, Elo Madissoon, Giuditta Filippini-Cattaneo, Marisa Jaconi, Anna Johnsson, Thomas R. Bürglin, Sten Linnarsson, Outi Hovatta and Juha Kere Understanding human preimplantation development is invaluable for human reproduction and stem cell research. By employing single-cell RNA sequencing in oocytes, zygotes and single blastomeres, Töhönen et al. identify new regulatory factors and sequences that drive early human preimplantation development. 11 September 2015 | doi: 10.1038/ncomms9207 Biological Sciences  Developmental biology  Medical research  Transgranular liquation cracking of grains in the semi-solid state OPEN S. Karagadde, P. D. Lee, B. Cai, J. L. Fife, M. A. Azeem, K. M. Kareh, C. Puncreobutr, D. Tsivoulas, T. Connolley and R. C. Atwood To obtain superior mechanical properties of cast components, grain refinement via semi-solid deformation is desirable. Here, the authors use in situ X-ray tomography to study the response of an alloy to indentation, and present a new mechanism of transgranular liquation cracking. 10 September 2015 | doi: 10.1038/ncomms9300 Physical Sciences  Materials science  Disparate ultrafast dynamics of itinerant and localized magnetic moments in gadolinium metal OPEN B. Frietsch, J. Bowlan, R. Carley, M. Teichmann, S. Wienholdt, D. Hinzke, U. Nowak, K. Carva, P. M. Oppeneer and M. Weinelt Due the strength of the intra-atomic exchange interaction, it is generally assumed that alignment of spin moments in intra-atomic orbitals is quasi-instantaneous. Here, the authors demonstrate the breakdown of this relation between the 4f and 5d electrons in gadolinium following ultrashort optical excitation. 10 September 2015 | doi: 10.1038/ncomms9262 Physical Sciences  Applied physics  Condensed matter  TORC1 controls G1–S cell cycle transition in yeast via Mpk1 and the greatwall kinase pathway OPEN Marta Moreno-Torres, Malika Jaquenoud and Claudio De Virgilio The target of rapamycin complex 1 (TORC1) pathway couples nutrient availability with cell growth and division by destabilizing the cyclin-dependent kinase (CDK) inhibitor Sic1. Here the authors show that TORC1 downregulation leads to stabilization of Sic1 via phosphorylation by the MAP kinase Mpk1 and inhibition of dephosphorylation via the greatwall kinase pathway. 10 September 2015 | doi: 10.1038/ncomms9256 Biological Sciences  Cell biology  Covalency-reinforced oxygen evolution reaction catalyst OPEN Shunsuke Yagi, Ikuya Yamada, Hirofumi Tsukasaki, Akihiro Seno, Makoto Murakami, Hiroshi Fujii, Hungru Chen, Naoto Umezawa, Hideki Abe, Norimasa Nishiyama and Shigeo Mori Perovskites are cost-effective and efficient catalysts for electrocatalytic oxygen evolution, however often lack stability. Here, the authors report a tetravalent iron based quadruple perovskite which is both active and stable, due to the covalent bonding network incorporating many of its iron and copper ions. 10 September 2015 | doi: 10.1038/ncomms9249 Chemical Sciences  Catalysis  Inorganic chemistry  Materials science  Increased COUP-TFII expression in adult hearts induces mitochondrial dysfunction resulting in heart failure OPEN San-Pin Wu, Chung-Yang Kao, Leiming Wang, Chad J. Creighton, Jin Yang, Taraka R. Donti, Romain Harmancey, Hernan G. Vasquez, Brett H. Graham, Hugo J. Bellen, Heinrich Taegtmeyer, Ching-Pin Chang, Ming-Jer Tsai and Sophia Y. Tsai Transcription factor COUP-TFII is elevated in the hearts of non-ischaemic cardiomyopathy patients, but the nature of this correlation is unknown. Here the authors show that forced cardiac expression of COUP-TFII in mice causes dilated cardiomyopathy because of altered mitochondrial function and impaired metabolic remodelling. 10 September 2015 | doi: 10.1038/ncomms9245 Biological Sciences  Cell biology  Developmental biology  Medical research  High-efficiency reprogramming of fibroblasts into cardiomyocytes requires suppression of pro-fibrotic signalling OPEN Yuanbiao Zhao, Pilar Londono, Yingqiong Cao, Emily J. Sharpe, Catherine Proenza, Rebecca O’Rourke, Kenneth L. Jones, Mark Y. Jeong, Lori A. Walker, Peter M. Buttrick, Timothy A. McKinsey and Kunhua Song Direct reprogramming of cardiac fibroblasts into cardiomyocytes is an attractive strategy for heart regeneration, but it is hampered by the low efficiency of the process. Here the authors show that mouse fibroblasts can be reprogrammed with high efficiency into functional cardiomyocytes when pro-fibrotic signaling is inhibited. 10 September 2015 | doi: 10.1038/ncomms9243 Biological Sciences  Cell biology  Developmental biology  Medical research  Helicity multiplexed broadband metasurface holograms OPEN Dandan Wen, Fuyong Yue, Guixin Li, Guoxing Zheng, Kinlong Chan, Shumei Chen, Ming Chen, King Fai Li, Polis Wing Han Wong, Kok Wai Cheah, Edwin Yue Bun Pun, Shuang Zhang and Xianzhong Chen The demonstration of visible frequency metasurfaces with broadband optical response is challenging due to plasmonic losses and non-uniform nanofabrication. Here, Wen et al. demonstrate a helicity multiplexed metasurface hologram capable of achieving high efficiency and image quality in the visible and near infrared. 10 September 2015 | doi: 10.1038/ncomms9241 Physical Sciences  Materials science  Optical physics  Single gene locus changes perturb complex microbial communities as much as apex predator loss OPEN Deirdre McClean, Luke McNally, Letal I. Salzberg, Kevin M. Devine, Sam P. Brown and Ian Donohue Some species of social bacteria can chemically modify their nutrient environments, which may influence community interactions. Here, McClean et al. show that changes at a single gene locus in a biofilm-forming bacteria can perturb community structure to the same extent as the loss of an apex predator. 10 September 2015 | doi: 10.1038/ncomms9235 Biological Sciences  Ecology  Evolution  Microbiology  Epigenetic regulation of Smad2 and Smad3 by profilin-2 promotes lung cancer growth and metastasis Yun-Neng Tang, Wei-Qiao Ding, Xiao-Jie Guo, Xin-Wang Yuan, Dong-Mei Wang and Jian-Guo Song Smad signalling has been implicated in tumour and metastases formation. Here, Tang et al. show that profilin-2 enhances Smad signalling and tumour growth via an epigenetic mechanism, and that Smad expression correlates with an unfavourable prognosis of lung cancer patients. 10 September 2015 | doi: 10.1038/ncomms9230 Biological Sciences  Cancer  Nuclear envelope-associated endosomes deliver surface proteins to the nucleus OPEN Alexandre Chaumet, Graham D. Wright, Sze Hwee Seet, Keit Min Tham, Natalia V. Gounko and Frederic Bard Endocytosis typically directs proteins on a recycling route back to the plasma membrane, transport to the Golgi apparatus or delivery to the lysosome. Here Chaumet et al. describe a population of vesicles that can fuse directly with the outer nuclear membrane and deliver cargo into the nuclear envelope, where it can be translocated into the nucleoplasm. 10 September 2015 | doi: 10.1038/ncomms9218 Biological Sciences  Cell biology  Outbred genome sequencing and CRISPR/Cas9 gene editing in butterflies OPEN Xueyan Li, Dingding Fan, Wei Zhang, Guichun Liu, Lu Zhang, Li Zhao, Xiaodong Fang, Lei Chen, Yang Dong, Yuan Chen, Yun Ding, Ruoping Zhao, Mingji Feng, Yabing Zhu, Yue Feng, Xuanting Jiang, Deying Zhu, Hui Xiang, Xikan Feng, Shuaicheng Li et al. Butterflies are a promising system to study the genetics and evolution of morphological diversification, yet genomic and technological resources are limited. Here, the authors sequence genomes of two Papilio butterflies and develop a CRISPR/Cas9 gene editing method for these species. 10 September 2015 | doi: 10.1038/ncomms9212 Biological Sciences  Evolution  Genetics  Ultrafast isomerization initiated by X-ray core ionization Chelsea E. Liekhus-Schmaltz, Ian Tenney, Timur Osipov, Alvaro Sanchez-Gonzalez, Nora Berrah, Rebecca Boll, Cedric Bomme, Christoph Bostedt, John D. Bozek, Sebastian Carron, Ryan Coffee, Julien Devin, Benjamin Erk, Ken R. Ferguson, Robert W. Field, Lutz Foucar, Leszek J. Frasinski, James M. Glownia, Markus Gühr, Andrei Kamalov et al. Proton migration in the acetylene cation is commonly used as a model to study isomerisation dynamics. Here, the authors use X-ray pump-probe experiments to study this process, and show that isomerization occurs significantly faster than expected—within the first 12 femtoseconds following core ionization. 10 September 2015 | doi: 10.1038/ncomms9199 Physical Sciences  Atomic and molecular physics  Physical chemistry  Blood coagulation protein fibrinogen promotes autoimmunity and demyelination via chemokine release and antigen presentation OPEN Jae Kyu Ryu, Mark A. Petersen, Sara G. Murray, Kim M. Baeten, Anke Meyer-Franke, Justin P. Chan, Eirini Vagena, Catherine Bedard, Michael R. Machado, Pamela E. Rios Coronado, Thomas Prod'homme, Israel F. Charo, Hans Lassmann, Jay L. Degen, Scott S. Zamvil and Katerina Akassoglou Autoimmune brain inflammation is associated with activation of macrophages and microglia. Here the authors show that fibrinogen induces encephalitogenic T-cell activation and macrophage recruitment to the central nervous system, and promotes demyelination in a mouse model of multiple sclerosis. 10 September 2015 | doi: 10.1038/ncomms9164 Biological Sciences  Immunology  Neuroscience  Identification of a plastidial phenylalanine exporter that influences flux distribution through the phenylalanine biosynthetic network OPEN Joshua R. Widhalm, Michael Gutensohn, Heejin Yoo, Funmilayo Adebesin, Yichun Qian, Longyun Guo, Rohit Jaini, Joseph H. Lynch, Rachel M. McCoy, Jacob T. Shreve, Jyothi Thimmapuram, David Rhodes, John A. Morgan and Natalia Dudareva Phenylalanine is synthesized in plant chloroplasts and is then exported to the cytosol, where it is a precursor for various secondary metabolites. Here, the authors identify PhpCAT as a plastid phenylalanine transporter required to maintain metabolic flux in petunia. 10 September 2015 | doi: 10.1038/ncomms9142 Biological Sciences  Plant sciences  Observation of correlated spin–orbit order in a strongly anisotropic quantum wire system C. Brand, H. Pfnür, G. Landolt, S. Muff, J. H. Dil, Tanmoy Das and Christoph Tegenkamp Quantum wires offer a platform for controlling spin–orbit coupling and therefore creating exotic phases of matter. Here, the authors use high-resolution spin- and angle-resolved photoemission measurements to identify an interaction-induced spin- and orbital-entangled state in atomic lead wires. 10 September 2015 | doi: 10.1038/ncomms9118 Physical Sciences  Condensed matter  Nanotechnology  Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data OPEN Camille D. A. Terfve, Edmund H. Wilkes, Pedro Casado, Pedro R. Cutillas and Julio Saez-Rodriguez Phosphoproteomics can offer significant insight into cell signalling and how signalling is modified in response to perturbations. Here the authors develop a new tool for the analysis of high-content phosphoproteomics in the context of kinase/phosphatase-substrate knowledge, which is used to train logic models. 10 September 2015 | doi: 10.1038/ncomms9033 Biological Sciences  Biochemistry  Bioinformatics  Dynamically stabilized magnetic skyrmions OPEN Y. Zhou, E. Iacocca, A. A. Awad, R. K. Dumas, F. C. Zhang, H. B. Braun and J. Åkerman Magnetic skyrmions are particle-like spin textures with non-trivial topology which are stabilized by local magnetic interactions. Here, the authors demonstrate theoretically a class of skyrmions which are stabilized dynamically in the absence of interactions in a nanocontact spin-torque oscillator. 09 September 2015 | doi: 10.1038/ncomms9193 Physical Sciences  Condensed matter  Theoretical physics  Magnetic crystals and helical liquids in alkaline-earth fermionic gases OPEN Simone Barbarino, Luca Taddia, Davide Rossini, Leonardo Mazza and Rosario Fazio One-dimensional alkaline-earth-like fermionic gases with large nuclear spins and atomic repulsion host a hierarchy of states with intriguing properties. Here, the authors use analytical and numerical techniques to predict the emergence of magnetic ordering in gapped states and helical modes in gapless phases. 09 September 2015 | doi: 10.1038/ncomms9134 Physical Sciences  Atomic and molecular physics  Theoretical physics  Telomeres are partly shielded from ultraviolet-induced damage and proficient for nucleotide excision repair of photoproducts OPEN Dhvani Parikh, Elise Fouquerel, Connor T. Murphy, Hong Wang and Patricia L. Opresko DNA damage caused by ultraviolet irradiation is removed from the genome by nucleotide excision repair; however, it is unclear if this occurs at chromosome ends. Here the authors provide evidence indicating that telomeres are partially shielded from damage and that repair is fully functional. 09 September 2015 | doi: 10.1038/ncomms9214 Biological Sciences  Molecular biology  The interactions between a small molecule and G-quadruplexes are visualized by fluorescence lifetime imaging microscopy OPEN Arun Shivalingam, M. Angeles Izquierdo, Alix Le Marois, Aurimas Vyšniauskas, Klaus Suhling, Marina K. Kuimova and Ramon Vilar Guanine-rich oligonucleotides can fold into secondary structures known as G-quadruplexes that are proposed to have various biological roles. Here, Shivalingam et al. develop a cell-permeable, low-toxicity probe that can be used to probe interactions between G-quadruplexes and small molecules in vivo. 09 September 2015 | doi: 10.1038/ncomms9178 Biological Sciences  Biotechnology  Cell biology  Robust production of recombinant phosphoproteins using cell-free protein synthesis OPEN Javin P. Oza, Hans R. Aerni, Natasha L. Pirman, Karl W. Barber, Charlotte M. ter Haar, Svetlana Rogulina, Matthew B. Amrofell, Farren J. Isaacs, Jesse Rinehart and Michael C. Jewett The inability to produce recombinant phosphoproteins has hindered research into their structure and function. Here the authors develop a cell-free protein synthesis platform to site-specifically incorporate phosphoserine into proteins at high yields, and recapitulate a MEK1 kinase signalling cascade. 09 September 2015 | doi: 10.1038/ncomms9168 Biological Sciences  Biochemistry  A flexible codon in genomically recoded Escherichia coli permits programmable protein phosphorylation OPEN Natasha L. Pirman, Karl W. Barber, Hans R. Aerni, Natalie J. Ma, Adrian D. Haimovich, Svetlana Rogulina, Farren J. Isaacs and Jesse Rinehart The effects of protein phosphorylation, a common post-translational modification, are difficult to study using recombinant proteins. Here the authors use genomically engineered E. coli to enhance translation systems that express phosphor-serine containing proteins, and use these systems to produce phosphorylated MEK1 kinase. 09 September 2015 | doi: 10.1038/ncomms9130 Biological Sciences  Biochemistry  Bioengineering  Molecular biology  A synthetic hydrogel for the high-throughput study of cell–ECM interactions OPEN Andrew D. Rape, Mikhail Zibinsky, Niren Murthy and Sanjay Kumar Multiple extracellular matrix parameters influence cellular behaviour, but it is difficult to dissect their cooperative contributions. Here the authors describe a hydrogel system in which ligand density and substrate stiffness can be tuned orthogonally to study the contribution of combinations of these parameters simultaneously. 09 September 2015 | doi: 10.1038/ncomms9129 Biological Sciences  Biotechnology  Cell biology  Sliding tethered ligands add topological interactions to the toolbox of ligand–receptor design OPEN Martin Bauer, Patrick Kékicheff, Jean Iss, Christophe Fajolles, Thierry Charitat, Jean Daillant and Carlos M. Marques Biological adhesion is mediated by specific lock and key interactions between ligand receptor pairs. Here Bauer et al. engineer tethered ligands for which spacers can slide at the anchoring point to produce versatile bio-adhesive substrates. 09 September 2015 | doi: 10.1038/ncomms9117 Biological Sciences  Biophysics  Physical chemistry  Importance of salt fingering for new nitrogen supply in the oligotrophic ocean OPEN B. Fernández-Castro, B. Mouriño-Carballido, E. Marañón, P. Chouciño, J. Gago, T. Ramírez, M. Vidal, A. Bode, D. Blasco, S.-J. Royer, M. Estrada and R. Simó The relative contribution of nitrogen fixation and nitrogen diffusion to marine biomes is presently debated. Here, the authors evaluate the contribution of these pathways across the tropics and subtropics of the global ocean and show that nitrogen diffusion, reinforced by salt fingers, is the dominant process. 09 September 2015 | doi: 10.1038/ncomms9002 Earth Sciences  Biogeochemistry  Oceanography    Nature Communications JOBS of the week Postdoctoral Scientist Medical Research Council PhD Student Position Otto-Von-Guericke University Magdeburg Tenure Track Faculty Positions University of Texas Health Science Center at San Antonio Postdoctoral Fellowship Johns Hopkins University Postdoctoral Fellow The University of Tennessee Health Science Center Bioinformatics Officer The Francis Crick Institute Postdoctoral Associate The Rockfeller University Postdoctoral Fellow - Cancer Genetics Wellcome Trust Sanger Institute Executive Dean, School of Science RMIT University Research Scientist Institute of Molecular Biology (IMB) Mainz More Science jobs from Nature Communications EVENT Ancient DNA and Human Evolution 29.04.16 La Jolla, USA More science events from       Latest Corrigendum     Corrigendum: Genome-wide association study identifies multiple loci associated with both mammographic density and breast cancer risk Sara Lindström, Deborah J. Thompson, Andrew D. Paterson, Jingmei Li, Gretchen L. Gierach, Christopher Scott, Jennifer Stone, Julie A. Douglas, Isabel dos-Santos-Silva, Pablo Fernandez-Navarro, Jajini Verghase, Paula Smith, Judith Brown, Robert Luben, Nicholas J. Wareham, Ruth J. F. Loos, John A. Heit, V. Shane Pankratz, Aaron Norman, Ellen L. Goode et al. 09 September 2015 | doi: 10.1038/ncomms9358 Biological Sciences  Cancer  Genetics      Advertisement Open for Submissions  A new open access, multi-and interdisciplinary journal dedicated to publishing the finest research on both microbial biofilms and microbiomes, the journal is now open for submissions.  Explore the benefits of submitting your next research article.    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. 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