Nature Communications - 09 March 2016

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Journal homepage Recommend to library Web feed   Advertisement All content now free to access including archives! Nature Communications is an open access journal that publishes high-quality research from all areas of the natural sciences. Papers published by the journal represent important advances of significance to specialists within each subject area including the Earth Sciences. Visit the website to explore ALL the content available within your field.    Advertisement The Geoffrey Beene Cancer Research Center at Memorial Sloan Kettering Cancer Center, Nature, Nature Cell Biology and Nature Reviews Cancer present: CANCER AS AN EVOLVING AND SYSTEMIC DISEASE March 12-15, 2016 | New York, NY, USA REGISTER NOW!       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     Experimental evidence for compositional syntax in bird calls OPEN Toshitaka N. Suzuki, David Wheatcroft and Michael Griesser Animal vocalizations contain distinct elements, but it is not clear whether they convey combined meanings in the same way as human speech. Here, Suzuki et al. show that Japanese great tits can combine different elements of vocal signals so that they have compositional syntax. 08 March 2016 | doi: 10.1038/ncomms10986 Biological Sciences  Zoology  Stratified coastal ocean interactions with tropical cyclones OPEN S. M. Glenn, T. N. Miles, G. N. Seroka, Y. Xu, R. K. Forney, F. Yu, H. Roarty, O. Schofield and J. Kohut Accurate forecasts of hurricane intensity remain problematic. Here, using an ocean observing network to inform ocean and atmospheric model simulations, the authors show that consideration of ahead-of-eye cooling improves intensity forecasts. 08 March 2016 | doi: 10.1038/ncomms10887 Earth Sciences  Atmospheric science  Oceanography  Extinction of fish-shaped marine reptiles associated with reduced evolutionary rates and global environmental volatility OPEN Valentin Fischer, Nathalie Bardet, Roger B. J. Benson, Maxim S. Arkhangelsky and Matt Friedman The extinction of the ichthyosaurs had previously been attributed to increasing competition or to the loss of their main prey. Here, Fischer et al. analyse phylogenetic and ecological patterns of ichthyosaur diversification and extinction, and find that the decline of the group is more likely due to climatic volatility. 08 March 2016 | doi: 10.1038/ncomms10825 Biological Sciences  Evolution  Palaeontology  An extended U2AF65–RNA-binding domain recognizes the 3′ splice site signal OPEN Anant A. Agrawal, Enea Salsi, Rakesh Chatrikhi, Steven Henderson, Jermaine L. Jenkins, Michael R. Green, Dmitri N. Ermolenko and Clara L. Kielkopf The pre-mRNA splicing factor U2AF65 recognizes 3′ splice sites in human gene transcripts, but the details are not fully understood. Here, the authors report U2AF65 structures and single molecule FRET that reveal mechanistic insights into splice site recognition. 08 March 2016 | doi: 10.1038/ncomms10950 Biological Sciences  Biochemistry  Molecular biology  Tuning selectivity of electrochemical reactions by atomically dispersed platinum catalyst OPEN Chang Hyuck Choi, Minho Kim, Han Chang Kwon, Sung June Cho, Seongho Yun, Hee-Tak Kim, Karl J. J. Mayrhofer, Hyungjun Kim and Minkee Choi Atomically dispersed metal catalysts display high atom efficiency for electrocatalytic processes. Here, the authors report that sulfur-doped zeolite-templated carbon stabilizes highly dispersed platinum species, predominantly as single-atom centres, and probe its oxygen reduction selectivity. 08 March 2016 | doi: 10.1038/ncomms10922 Chemical Sciences  Catalysis  Materials science  AMPK antagonizes hepatic glucagon-stimulated cyclic AMP signalling via phosphorylation-induced activation of cyclic nucleotide phosphodiesterase 4B OPEN M. Johanns, Y.-C. Lai, M.-F. Hsu, R. Jacobs, D. Vertommen, J. Van Sande, J. E. Dumont, A. Woods, D. Carling, L. Hue, B. Viollet, M Foretz and M H Rider The diabetes drug Metformin decreases hepatic glucose production and activates AMP-activated protein kinase (AMPK). Here the authors provide evidence that AMPK activation antagonizes glucagon signalling by activating PDE4B, lowering cAMP levels and decreasing PKA activation. 08 March 2016 | doi: 10.1038/ncomms10856 Biological Sciences  Biochemistry  Cell biology  Medical research  A general approach to visualize protein binding and DNA conformation without protein labelling OPEN Dan Song, Thomas G. W. Graham and Joseph J. Loparo Single-molecule imaging of protein-DNA association requires fluorescently labelled protein, which limits the protein concentration that can be used. Here the authors exploit protein induced fluorescent enhancement of DNA sparsely labelled with Cy3 to visualize protein binding and correlate it with changes in DNA conformation. 08 March 2016 | doi: 10.1038/ncomms10976 Biological Sciences  Cell biology  Drift transport of helical spin coherence with tailored spin–orbit interactions OPEN Y. Kunihashi, H. Sanada, H. Gotoh, K. Onomitsu, M. Kohda, J. Nitta and T. Sogawa Spin-orbit effects in non-magnetic semiconductors allow for the manipulation of electronic spins in the absence of an applied magnetic field. Here, the authors exploit a persistent spin helix state in single quantum wells to enhance the coherence length of electronic drift transport. 08 March 2016 | doi: 10.1038/ncomms10722 Physical Sciences  Condensed matter  A ligand-independent integrin β1 mechanosensory complex guides spindle orientation OPEN Nicoletta I. Petridou and Paris A. Skourides During cell division, the orientation of the mitotic spindle is sensitive to forces exerted on the cell cortex. Here Petridou and Skourides show that such cues are sensed by a mechanosensory complex established on force activated integrin β1 independent of ligand binding. 08 March 2016 | doi: 10.1038/ncomms10899 Biological Sciences  Cell biology  Cadherin-11 localizes to focal adhesions and promotes cell–substrate adhesion OPEN Rahul P. Langhe, Tetyana Gudzenko, Michael Bachmann, Sarah F. Becker, Carina Gonnermann, Claudia Winter, Genevieve Abbruzzese, Dominique Alfandari, Marie-Claire Kratzer, Clemens M. Franz and Jubin Kashef Cadherins are typically involved in cell-cell adhesion, however cadherin-11 promotes cell migration through an undefined mechanism. Langhe et al. show that cadherin-11 mediates adhesion to the cell matrix at focal adhesions through interaction with syndecan-4. 08 March 2016 | doi: 10.1038/ncomms10909 Biological Sciences  Cell biology  Using mutability landscapes of a promiscuous tautomerase to guide the engineering of enantioselective Michaelases OPEN Jan-Ytzen van der Meer, Harshwardhan Poddar, Bert-Jan Baas, Yufeng Miao, Mehran Rahimi, Andreas Kunzendorf, Ronald van Merkerk, Pieter G. Tepper, Edzard M. Geertsema, Andy-Mark W. H. Thunnissen, Wim J. Quax and Gerrit J. Poelarends The Michael-type addition reaction is used for carbon-carbon bond formation; however biocatalytic methods for this reaction are rare. Here, the authors generate and exploit mutability landscapes of 4-oxalocrotonate tautomerase to direct the redesign of this promiscuous enzyme into enantio-complementary Michaelases. 08 March 2016 | doi: 10.1038/ncomms10911 Chemical Sciences  Biochemistry  Biotechnology  Catalysis  Manipulation of prenylation reactions by structure-based engineering of bacterial indolactam prenyltransferases OPEN Takahiro Mori, Lihan Zhang, Takayoshi Awakawa, Shotaro Hoshino, Masahiro Okada, Hiroyuki Morita and Ikuro Abe Regioselective prenylation of small aromatic natural molecules is crucial for their biological activity. Here, the authors present the biochemical and structural characterisation of two prenyltransferases and a structure-based engineering strategy to modulate their substrate specificity. 08 March 2016 | doi: 10.1038/ncomms10849 Biological Sciences  Biochemistry  Biophysics  Biotechnology  Electrochemical oxygen reduction catalysed by Ni3(hexaiminotriphenylene)2 OPEN Elise M. Miner, Tomohiro Fukushima, Dennis Sheberla, Lei Sun, Yogesh Surendranath and Mircea Dincă There are numerous heterogeneous oxygen reduction reaction catalysts, although synthetic tunability is rare among these materials. Here, the authors report that a conductive metal-organic framework functions as a well-defined, tunable electrocatalyst for the oxygen reduction reaction in alkaline solution. 08 March 2016 | doi: 10.1038/ncomms10942 Chemical Sciences  Catalysis  Inorganic chemistry  Materials science  Anomalous correlation effects and unique phase diagram of electron-doped FeSe revealed by photoemission spectroscopy OPEN C. H. P. Wen, H. C. Xu, C. Chen, Z. C. Huang, X. Lou, Y. J. Pu, Q. Song, B. P. Xie, Mahmoud Abdel-Hafiez, D. A. Chareev, A. N. Vasiliev, R. Peng and D. L. Feng Electron doping is a powerful way to induce quantum phase transitions in materials and explore exotic states of matter. Here, Wen et al. present carefully-controlled potassium dosing in FeSe films and FeSe0.93S0.07 bulk, which enhances superconductivity and induces other anomalous phases, revealing a complex phase diagram. 08 March 2016 | doi: 10.1038/ncomms10840 Physical Sciences  Condensed matter  Materials science  Endothelin-1 supports clonal derivation and expansion of cardiovascular progenitors derived from human embryonic stem cells OPEN Boon-Seng Soh, Shi-Yan Ng, Hao Wu, Kristina Buac, Joo-Hye C. Park, Xiaojun Lian, Jiejia Xu, Kylie S. Foo, Ulrika Felldin, Xiaobing He, Massimo Nichane, Henry Yang, Lei Bu, Ronald A. Li, Bing Lim and Kenneth R. Chien Understanding coronary vessels development provides basis for regenerative strategies. Here, Soh et al. identify endothelin-1 as a key molecule driving long-term expansion of ISL1+ bipotent vascular progenitors derived from human embryonic stem cells, and show that these cells can regenerate coronary vessels in mice. 08 March 2016 | doi: 10.1038/ncomms10774 Biological Sciences  Developmental biology  Medical research  Inductive interactions mediated by interplay of asymmetric signalling underlie development of adult haematopoietic stem cells OPEN Céline Souilhol, Christèle Gonneau, Javier G. Lendinez, Antoniana Batsivari, Stanislav Rybtsov, Heather Wilson, Lucia Morgado-Palacin, David Hills, Samir Taoudi, Jennifer Antonchuk, Suling Zhao and Alexander Medvinsky It is unclear how the microenvironment of the aorta-gonad-mesonephros influences haematopoietic stem cell (HSC) production early in mouse development. Here, Souilhol et al. use an in vitro aggregate system as a tool to understand how several pathways, BMP, SCF and Shh, may regulate HSC production. 08 March 2016 | doi: 10.1038/ncomms10784 Biological Sciences  Cell biology  Developmental biology  Structural basis of allosteric and synergistic activation of AMPK by furan-2-phosphonic derivative C2 binding OPEN Christopher G. Langendorf, Kevin R. W. Ngoei, John W. Scott, Naomi X. Y. Ling, Sam M. A. Issa, Michael A. Gorman, Michael W. Parker, Kei Sakamoto, Jonathan S. Oakhill and Bruce E. Kemp AMPK regulates the metabolism and so drugs that activate AMPK might have potential for the treatment of metabolic disease. Here, the authors report the structure of AMPK bound to an activating compound, revealing two binding sites and indicating that dual therapy might be a good drug strategy. 08 March 2016 | doi: 10.1038/ncomms10912 Biological Sciences  Biochemistry  High-performance thermoelectric nanocomposites from nanocrystal building blocks OPEN Maria Ibáñez, Zhishan Luo, Aziz Genç, Laura Piveteau, Silvia Ortega, Doris Cadavid, Oleksandr Dobrozhan, Yu Liu, Maarten Nachtegaal, Mona Zebarjadi, Jordi Arbiol, Maksym V. Kovalenko and Andreu Cabot Nanomaterials provide a route to efficient solid-state conversion between thermal and electrical energy. Here, the authors demonstrate that a combination of metal and semiconductor colloidal nanocrystals can produce thermoelectric nanocomposites with high performance. 07 March 2016 | doi: 10.1038/ncomms10766 Physical Sciences  Applied physics  Nanotechnology  Slow-moving and far-travelled dense pyroclastic flows during the Peach Spring super-eruption OPEN O. Roche, D. C. Buesch and G. A. Valentine Pyroclastic flows of the 18.8 Ma Peach Spring Tuff super-eruption travelled >170 km and entrained substrate blocks up to ∼1 m diameter. Here, the authors show that these flows had a dense base and speeds of ∼5-20 m s−1, fed by an eruption discharging magma at rates up to ∼107-108 m3 s−1 for at least 2.5-10 h. 07 March 2016 | doi: 10.1038/ncomms10890 Earth Sciences  Geology and geophysics  Seeking a geochemical identifier for authigenic carbonate OPEN Ming-Yu Zhao, Yong-Fei Zheng and Yan-Yan Zhao Distinguishing between authigenic carbonate and primary marine carbonate is fundamental to our understanding of Earth’s carbon, oxygen and calcium cycles. Here, the authors show that a combination of uranium concentration and carbon isotope composition is able to distinguish between the two carbonate sinks. 07 March 2016 | doi: 10.1038/ncomms10885 Earth Sciences  Biogeochemistry  Geology and geophysics  Osteoclast-derived exosomal miR-214-3p inhibits osteoblastic bone formation OPEN Defang Li, Jin Liu, Baosheng Guo, Chao Liang, Lei Dang, Cheng Lu, Xiaojuan He, Hilda Yeuk-Siu Cheung, Liang Xu, Changwei Lu, Bing He, Biao Liu, Atik Badshah Shaikh, Fangfei Li, Luyao Wang, Zhijun Yang, Doris Wai-Ting Au, Songlin Peng, Zongkang Zhang, Bao-Ting Zhang et al. In previous studies the authors discovered that miR-214 inhibits osteoblastic bone formation. Here they extend on these findings, using ovariectomized mice and samples from patients with bone fractures, to show that miR-214 is a mediator of osteoclast-osteoblast crosstalk. 07 March 2016 | doi: 10.1038/ncomms10872 Biological Sciences  Medical research  Data publication with the structural biology data grid supports live analysis OPEN Peter A. Meyer, Stephanie Socias, Jason Key, Elizabeth Ransey, Emily C. Tjon, Alejandro Buschiazzo, Ming Lei, Chris Botka, James Withrow, David Neau, Kanagalaghatta Rajashankar, Karen S. Anderson, Richard H. Baxter, Stephen C. Blacklow, Titus J. Boggon, Alexandre M. J. J. Bonvin, Dominika Borek, Tom J. Brett, Amedeo Caflisch, Chung-I Chang et al. The validation and analysis of X-ray crystallographic data is essential for reproducibility and the development of crystallographic methods. Here, the authors describe a repository for crystallographic datasets and demonstrate some of the ways it could serve the crystallographic community. 07 March 2016 | doi: 10.1038/ncomms10882 Biological Sciences  Biochemistry  Rule learning enhances structural plasticity of long-range axons in frontal cortex OPEN Carolyn M. Johnson, Hannah Peckler, Lung-Hao Tai and Linda Wilbrecht The orbitofrontal cortex is associated with foraging behaviour yet the structural changes underlying such rule-based learning remain unclear. Here, the authors imaged OFC axons throughout a digging-based odour discrimination task and found correlations between the rate of bouton turnover and the behavioural strategies of individual mice. 07 March 2016 | doi: 10.1038/ncomms10785 Biological Sciences  Neuroscience  Microglial P2Y12 is necessary for synaptic plasticity in mouse visual cortex OPEN G. O. Sipe, R. L. Lowery,, M-È Tremblay, E. A. Kelly, C. E. Lamantia and A. K. Majewska Microglia play key roles during early neurodevelopment. Here the authors show that microglia are important mediators of ocular dominance plasticity (ODP). Microglia respond to monocular deprivation during the visual critical period, and disrupting microglial P2Y12 purinergic receptor abrogates ODP. 07 March 2016 | doi: 10.1038/ncomms10905 Biological Sciences  Neuroscience  Selectively enhanced photocurrent generation in twisted bilayer graphene with van Hove singularity OPEN Jianbo Yin, Huan Wang, Han Peng, Zhenjun Tan, Lei Liao, Li Lin, Xiao Sun, Ai Leen Koh, Yulin Chen, Hailin Peng and Zhongfan Liu Graphene has the high carrier mobility and short photoresponse time required for efficient photodetection, but broad and weak optical absorption are severe drawbacks. Here, the authors show that twisted bilayer graphene with van Hove singularities exhibits a strong light-matter interaction and selectively enhanced photocurrent generation. 07 March 2016 | doi: 10.1038/ncomms10699 Physical Sciences  Materials science  Nanotechnology  Optical physics  Summer rainfall over the southwestern Tibetan Plateau controlled by deep convection over the Indian subcontinent OPEN Wenhao Dong, Yanluan Lin, Jonathon S. Wright, Yi Ming, Yuanyu Xie, Bin Wang, Yong Luo, Wenyu Huang, Jianbin Huang, Lei Wang, Lide Tian, Yiran Peng and Fanghua Xu While precipitation over the Tibetan Plateau is a vital resource for glacier mass balance, river runoff and local ecology, the controlling mechanisms are poorly understood. Here, the authors combine observations and simulations and show that convective storms over India sweep moisture up and over the plateau. 07 March 2016 | doi: 10.1038/ncomms10925 Earth Sciences  Climate science  CSF-contacting neurons regulate locomotion by relaying mechanical stimuli to spinal circuits OPEN Urs Lucas Böhm, Andrew Prendergast, Lydia Djenoune, Sophie Nunes Figueiredo, Johanna Gomez, Caleb Stokes, Sonya Kaiser, Maximilliano Suster, Koichi Kawakami, Marine Charpentier, Jean-Paul Concordet, Jean-Paul Rio, Filippo Del Bene and Claire Wyart CSF-contacting neurons are known to project to locomotor CPGs although their relevance to active locomotion is unclear. Here, the authors show that these cells constitute a mechanosensory organ relying on PKD2L1 channels to detect spinal cord curvature and modulate locomotor frequency in freely moving animals. 07 March 2016 | doi: 10.1038/ncomms10866 Biological Sciences  Cell biology  Neuroscience  Humans choose representatives who enforce cooperation in social dilemmas through extortion OPEN Manfred Milinski, Christian Hilbe, Dirk Semmann, Ralf Sommerfeld and Jochem Marotzke Social dilemmas force players to balance between personal and collective gain. Here, inspired by the negotiations for greenhouse-gas emission limitations, the authors experimentally studied a representative-based collective-risk scenario, reporting the emergence of extortionate zero-determinant (ZD) strategies. 07 March 2016 | doi: 10.1038/ncomms10915 Physical Sciences  Climate science  Theoretical physics  Designing high-performance layered thermoelectric materials through orbital engineering OPEN Jiawei Zhang, Lirong Song, Georg K. H. Madsen, Karl F. F. Fischer, Wenqing Zhang, Xun Shi and Bo B. Iversen Thermoelectric materials with enhanced performances need to be identified. Here, the authors use the crystal field splitting energy of orbitals as a descriptor to design thermoelectric materials by solid solution maps and strain engineering in layered CaAl2Si2-type Zintl compounds. 07 March 2016 | doi: 10.1038/ncomms10892 Chemical Sciences  Condensed matter  Materials science  Large-area graphene-based nanofiltration membranes by shear alignment of discotic nematic liquid crystals of graphene oxide OPEN Abozar Akbari, Phillip Sheath, Samuel T. Martin, Dhanraj B. Shinde, Mahdokht Shaibani, Parama Chakraborty Banerjee, Rachel Tkacz, Dibakar Bhattacharyya and Mainak Majumder Membranes made from graphene have ultra-fast water transport and precise molecular sieving properties. Here, the authors show how large-area membranes can be manufactured by a rapid and scalable process based on shear alignment of graphene-oxide liquid crystals for unlocking industrial applications. 07 March 2016 | doi: 10.1038/ncomms10891 Physical Sciences  Materials science  Nanotechnology  The acetyllysine reader BRD3R promotes human nuclear reprogramming and regulates mitosis OPEN Zhicheng Shao, Ruowen Zhang, Alireza Khodadadi-Jamayran, Bo Chen, Michael R. Crowley, Muhamad A. Festok, David K. Crossman, Tim M. Townes and Kejin Hu The reprogramming of fibroblasts to pluripotent stem cells has been well documented but there is interest in identifying additional factors involved. Here, the authors perform a screen of human kinases and show that the bromodomain protein, BRD3R, can promote reprogramming and suggest a role for this factor in regulating mitosis. 07 March 2016 | doi: 10.1038/ncomms10869 Biological Sciences  Cell biology  Developmental biology  Increased amyloidogenic APP processing in APOE ɛ4-negative individuals with cerebral β-amyloidosis OPEN Niklas Mattsson, Philip S. Insel, Sebastian Palmqvist, Erik Stomrud, Danielle van Westen, Lennart Minthon, Henrik Zetterberg, Kaj Blennow and Oskar Hansson Autosomal dominant Alzheimer's disease is thought to be caused by increased amyloidogenic APP processing. Mattson et al. show that association between brain Aβ and cerobrospinal fluid Aβ40 levels is stronger in APOE ɛ4 negative people, suggesting that increased processing may also underlie sporadic disease. 07 March 2016 | doi: 10.1038/ncomms10918 Biological Sciences  Neuroscience  Catch-bond mechanism of the bacterial adhesin FimH OPEN Maximilian M. Sauer, Roman P. Jakob, Jonathan Eras, Sefer Baday, Deniz Eriş, Giulio Navarra, Simon Bernèche, Beat Ernst, Timm Maier and Rudi Glockshuber Catch bonds have a role in bacterial adhesion and infection by uropathogenic E. coli. Here, the authors report crystal structures, molecular dynamics simulations, ligand binding analysis and cell tracking to characterise the catch bond interaction between the adhesin FimH and carbohydrate receptors. 07 March 2016 | doi: 10.1038/ncomms10738 Biological Sciences  Biochemistry  Microbiology  The HMGB1 protein induces a metabolic type of tumour cell death by blocking aerobic respiration OPEN Georg Gdynia, Sven W. Sauer, Jürgen Kopitz, Dominik Fuchs, Katarina Duglova, Thorsten Ruppert, Matthias Miller, Jens Pahl, Adelheid Cerwenka, Markus Enders, Heimo Mairbäurl, Marcin M. Kamiński, Roland Penzel, Christine Zhang, Jonathan C. Fuller, Rebecca C. Wade, Axel Benner, Jenny Chang-Claude, Hermann Brenner, Michael Hoffmeister et al. HMBG1 is a protein expressed in natural killer cells and is important in immunosurveillance. In this study, the authors show that HMGB1 binds to and inhibits PKM2, resulting in a block in aerobic glycolysis and ultimately cell death. 07 March 2016 | doi: 10.1038/ncomms10764 Biological Sciences  Cancer  Medical research  Lasing in silicon–organic hybrid waveguides OPEN Dietmar Korn, Matthias Lauermann, Sebastian Koeber, Patrick Appel, Luca Alloatti, Robert Palmer, Pieter Dumon, Wolfgang Freude, Juerg Leuthold and Christian Koos On-chip light sources for silicon photonic circuits remain a challenge since the indirect bandgap of silicon prevents efficient light emission. The authors demonstrate that lasing can be achieved by combining standard silicon-on-insulator waveguides with dye-doped organic cladding materials to provide optical gain. 07 March 2016 | doi: 10.1038/ncomms10864 Physical Sciences  Applied physics  Materials science  Optical physics  Melanoma cell lysosome secretory burst neutralizes the CTL-mediated cytotoxicity at the lytic synapse OPEN Roxana Khazen, Sabina Müller, Nicolas Gaudenzio, Eric Espinosa, Marie-Pierre Puissegur and Salvatore Valitutti Cytotoxic T lymphocytes recognise and eliminate tumour cells. Here, the authors show that on contact with these immune cells melanoma cells can resist T cell cytotoxicity by modulating the trafficking of their lysosomal compartment, this results in the degradation of the T cell protein perforin by the protease cathepsin B. 04 March 2016 | doi: 10.1038/ncomms10823 Biological Sciences  Cancer  Immunology  Medical research  Two-colour live-cell nanoscale imaging of intracellular targets OPEN Francesca Bottanelli, Emil B. Kromann, Edward S. Allgeyer, Roman S. Erdmann, Stephanie Wood Baguley, George Sirinakis, Alanna Schepartz, David Baddeley, Derek K. Toomre, James E. Rothman and Joerg Bewersdorf The intracellular applications of STED microscopy are limited by the availability of dyes. Here the authors develop a two-colour labelling strategy based on SiR and ATTO590 dyes, and apply their strategy to image various subcellular membrane compartments. 04 March 2016 | doi: 10.1038/ncomms10778 Biological Sciences  Biophysics  Cell biology  Field-free magnetization reversal by spin-Hall effect and exchange bias OPEN A. van den Brink, G. Vermijs, A. Solignac, J. Koo, J. T. Kohlhepp, H. J. M. Swagten and B. Koopmans Future information storage technology may exploit electrical currents to write the states of ferromagnetic nanoelements via spin torque effects. Here, the authors demonstrate such behaviour promoted by exchange bias from an interfaced antiferromagnet, which may help overcome practical device limitations. 04 March 2016 | doi: 10.1038/ncomms10854 Physical Sciences  Condensed matter  Nanotechnology  Nuclear PTEN functions as an essential regulator of SRF-dependent transcription to control smooth muscle differentiation OPEN Henrick Horita, Christina L. Wysoczynski, Lori A. Walker, Karen S. Moulton, Marcella Li, Allison Ostriker, Rebecca Tucker, Timothy A. McKinsey, Mair E. A. Churchill, Raphael A. Nemenoff and Mary C. M. Weiser-Evans The transcription factor, serum response factor, SRF regulates critical smooth muscle (SM) contractile gene expression but what else controls SM differentiation is unclear. Here, Horita et al. demonstrate that nuclear PTEN acts with SRF at the transcriptional level to maintain the differentiated SM phenotype. 04 March 2016 | doi: 10.1038/ncomms10830 Biological Sciences  Cell biology  Developmental biology  Commensurate antiferromagnetic excitations as a signature of the pseudogap in the tetragonal high-Tc cuprate HgBa2CuO4+δ OPEN M. K. Chan, C. J. Dorow, L. Mangin-Thro, Y. Tang, Y. Ge, M. J. Veit, G. Yu, X. Zhao, A. D. Christianson, J. T. Park, Y. Sidis, P. Steffens, D. L. Abernathy, P. Bourges and M. Greven In the cuprates, antiferromagnetic correlations might be the cause of the pseudogap phenomenon. Here the authors use neutron scattering on the tetragonal cuprate HgBa2CuO4+δ revealing commensurate antiferromagnetic excitations as a signature of the pseudogap state. 04 March 2016 | doi: 10.1038/ncomms10819 Physical Sciences  Condensed matter  Elemental superdoping of graphene and carbon nanotubes OPEN Yuan Liu, Yuting Shen, Litao Sun, Jincheng Li, Chang Liu, Wencai Ren, Feng Li, Libo Gao, Jie Chen, Fuchi Liu, Yuanyuan Sun, Nujiang Tang, Hui-Ming Cheng and Youwei Du Doping of low-dimensional graphitic materials with heteroatoms can enhance their catalytic, electrochemical and magnetic properties. Here, the authors report a tunable method to ‘superdope’ these materials with high levels of nitrogen, sulfur, or boron, via a simple fluorination and annealing procedure. 04 March 2016 | doi: 10.1038/ncomms10921 Chemical Sciences  Materials science  Nanotechnology  BK channel inactivation gates daytime excitability in the circadian clock OPEN Joshua P. Whitt, Jenna R. Montgomery and Andrea L. Meredith BK potassium channels have been previously shown to mediate SCN circadian firing, although the precise mechanisms are unclear. Here, using knockout and rescue approaches, the authors find that the ß2 ‘ball-and-chain’ confers BK channel inactivation during the day, promoting SCN electrical upstate. 04 March 2016 | doi: 10.1038/ncomms10837 Biological Sciences  Cell biology  Neuroscience  A coral-on-a-chip microfluidic platform enabling live-imaging microscopy of reef-building corals OPEN Orr H. Shapiro, Esti Kramarsky-Winter, Assaf R. Gavish, Roman Stocker and Assaf Vardi Studies of coral in laboratory settings are limited by a lack of reliable methods for manipulation of the coral microenvironment and monitoring of coral processes in vitro. Here the authors develop coral-on-a-chip, a microfluidic platform to enable study of coral processes at single-cell resolution. 04 March 2016 | doi: 10.1038/ncomms10860 Biological Sciences  Biotechnology  Microbiology  Cyclophilin A stabilizes the HIV-1 capsid through a novel non-canonical binding site OPEN Chuang Liu, Juan R. Perilla, Jiying Ning, Manman Lu, Guangjin Hou, Ruben Ramalho, Benjamin A. Himes, Gongpu Zhao, Gregory J. Bedwell, In-Ja Byeon, Jinwoo Ahn, Angela M. Gronenborn, Peter E. Prevelige, Itay Rousso, Christopher Aiken, Tatyana Polenova, Klaus Schulten and Peijun Zhang The host cell factor cyclophilin A (CypA) interacts with the HIV-1 capsid and regulates infectivity. Here the authors combine cryo-EM, solid-state NMR and all-atom MD simulations, identifying an interaction interface between CypA and the HIV capsid that stabilizes the viral capsid and regulates infectivity. 04 March 2016 | doi: 10.1038/ncomms10714 Biological Sciences  Biophysics  Virology  TRF2-RAP1 is required to protect telomeres from engaging in homologous recombination-mediated deletions and fusions OPEN Rekha Rai, Yong Chen, Ming Lei and Sandy Chang While yeast Rap1 regulates telomere length and protects telomeres from non-homologous end joining, its role in higher eukaryotes is controversial. Here the authors present evidence that in mammals, RAP1 cooperates with TRF2 to prevent homologous recombination-mediated repair of telomeres. 04 March 2016 | doi: 10.1038/ncomms10881 Biological Sciences  Molecular biology  Genetic suppression reveals DNA repair-independent antagonism between BRCA1 and COBRA1 in mammary gland development OPEN Sreejith J. Nair, Xiaowen Zhang, Huai-Chin Chiang, Md Jamiul Jahid, Yao Wang, Paula Garza, Craig April, Neeraj Salathia, Tapahsama Banerjee, Fahad S. Alenazi, Jianhua Ruan, Jian-Bing Fan, Jeffrey D. Parvin, Victor X. Jin, Yanfen Hu and Rong Li COBRA1 is a BRCA1-binding protein and, as part of the negative elongation factor, regulates RNA polymerase II pausing and transcription elongation. Here, the authors show that tissue-specific deletion of mouse Cobra1 inhibits postnatal mammary gland development and that the mammary defects can be rescued by additional deletion of Brca1 in a DNA repair-independent manner. 04 March 2016 | doi: 10.1038/ncomms10913 Biological Sciences  Cell biology  Developmental biology  Genetics  Feedback regulation of apical progenitor fate by immature neurons through Wnt7–Celsr3–Fzd3 signalling OPEN Wei Wang, Yves Jossin, Guoliang Chai, Wen-Hui Lien, Fadel Tissir and Andre M. Goffinet The switch from neurogenesis to gliogenesis in cortical development is only partially understood. Here the authors show that Wnt-Planar cell polarity signaling in immature cortical neurons activates Notch in neural progenitor cells, thereby tuning the timing of their fate decisions. 04 March 2016 | doi: 10.1038/ncomms10936 Biological Sciences  Developmental biology  Neuroscience  Protection from septic peritonitis by rapid neutrophil recruitment through omental high endothelial venules OPEN Konrad Buscher, Huiyu Wang, Xueli Zhang, Paul Striewski, Benedikt Wirth, Gurpanna Saggu, Stefan Lütke-Enking, Tanya N. Mayadas, Klaus Ley, Lydia Sorokin and Jian Song Neutrophils are critical in preventing the transition of acute peritoneal infection to sepsis. Here the authors show in three mouse models of peritonitis that neutrophils enter the abdominal cavity via high endothelial venules of the greater omentum, and characterize adhesion molecules involved. 04 March 2016 | doi: 10.1038/ncomms10828 Biological Sciences  Immunology  Temperature mapping of operating nanoscale devices by scanning probe thermometry OPEN Fabian Menges, Philipp Mensch, Heinz Schmid, Heike Riel, Andreas Stemmer and Bernd Gotsmann Thermometry using scanning probe techniques allows for the thermal imaging and characterization of devices with nanoscale resolution, however can be hindered by contact-related artefacts. Here, the authors demonstrate a thermal scanning probe approach which eliminates contact-resistance effects. 03 March 2016 | doi: 10.1038/ncomms10874 Physical Sciences  Condensed matter  Nanotechnology  EAF2 mediates germinal centre B-cell apoptosis to suppress excessive immune responses and prevent autoimmunity OPEN Yingqian Li, Yoshimasa Takahashi, Shin-ichiro Fujii, Yang Zhou, Rongjian Hong, Akari Suzuki, Takeshi Tsubata, Koji Hase and Ji-Yang Wang EAF2 has been previously known as a transcriptional elongation factor and a proapoptotic gene lost in prostate cancer. Here the authors show that EAF2 is required for apoptosis of germinal centre B cells, and that EAF2-deficient mice develop excessive antibody responses and autoimmunity. 03 March 2016 | doi: 10.1038/ncomms10836 Biological Sciences  Immunology  Itk is required for Th9 differentiation via TCR-mediated induction of IL-2 and IRF4 OPEN Julio Gomez-Rodriguez, Françoise Meylan, Robin Handon, Erika T. Hayes, Stacie M. Anderson, Martha R. Kirby, Richard M. Siegel and Pamela L. Schwartzberg The Tec family tyrosine kinase, Itk, is a component of the T-cell receptor essential for optimal Th2 responses in vivo. Here the authors show in human cells and mouse models that Itk is also needed for the production of IL-9, an important contributor to allergic asthma. 03 March 2016 | doi: 10.1038/ncomms10857 Biological Sciences  Immunology  Mechanism of intermediate filament recognition by plakin repeat domains revealed by envoplakin targeting of vimentin OPEN Claudia Fogl, Fiyaz Mohammed, Caezar Al-Jassar, Mark Jeeves, Timothy J. Knowles, Penelope Rodriguez-Zamora, Scott A. White, Elena Odintsova, Michael Overduin and Martyn Chidgey Plakin proteins link cell junctions to cytoskeletal frameworks, and their disruption within epithelial and cardiac muscle cells cause skin blistering diseases and cardiomyopathies. Here the authors use structural biology approaches to reveal the mechanism that allows plakins to recognize intermediate filaments within the cytoskeleton. 03 March 2016 | doi: 10.1038/ncomms10827 Biological Sciences  Biochemistry  Biophysics  Elimination of HIV-1-infected cells by broadly neutralizing antibodies OPEN Timothée Bruel, Florence Guivel-Benhassine, Sonia Amraoui, Marine Malbec, Léa Richard, Katia Bourdic, Daniel Aaron Donahue, Valérie Lorin, Nicoletta Casartelli, Nicolas Noël, Olivier Lambotte, Hugo Mouquet and Olivier Schwartz Broadly neutralizing antibodies (bNAbs) are promising as potential therapies targeting HIV-1 but their overall antiviral activity remains to be fully elucidated. Here the authors evaluate the ability of a panel of bNAbs to trigger antibody-dependent cellular cytotoxicity and identify the most effective antibody combinations. 03 March 2016 | doi: 10.1038/ncomms10844 Biological Sciences  Immunology  Virology  Single-cell differences in matrix gene expression do not predict matrix deposition OPEN Allison J. Cote, Claire M. McLeod, Megan J. Farrell, Patrick D. McClanahan, Margaret C. Dunagin, Arjun Raj and Robert L. Mauck Regenerative tissue engineering with mesenchymal stem cells is hampered by bulk methods of assessing differentiation status and a general assumption that expression of individual markers of stem cell differentiation correlate with functional capacity. Here the authors debunk this assumption by applying single-cell techniques to disassociate aggrecan mRNA abundance and matrix deposition. 03 March 2016 | doi: 10.1038/ncomms10865 Biological Sciences  Cell biology  Medical research  Shisa6 traps AMPA receptors at postsynaptic sites and prevents their desensitization during synaptic activity OPEN Remco V. Klaassen, Jasper Stroeder, Françoise Coussen, Anne-Sophie Hafner, Jennifer D. Petersen, Cedric Renancio, Leanne J. M. Schmitz, Elisabeth Normand, Johannes C. Lodder, Diana C. Rotaru, Priyanka Rao-Ruiz, Sabine Spijker, Huibert D. Mansvelder, Daniel Choquet and August B. Smit Auxiliary AMPA receptor subunits can affect gating and surface mobility. Here the authors show that Shisa6 traps AMPA receptors at postsynaptic sites via PSD-95, and keeps them in an activated state in the presence of glutamate, preventing full desensitization and consequently synaptic depression. 02 March 2016 | doi: 10.1038/ncomms10682 Biological Sciences  Cell biology  Neuroscience  mTORC1-mediated inhibition of polycystin-1 expression drives renal cyst formation in tuberous sclerosis complex OPEN Monika Pema, Luca Drusian, Marco Chiaravalli, Maddalena Castelli, Qin Yao, Sara Ricciardi, Stefan Somlo, Feng Qian, Stefano Biffo and Alessandra Boletta Polycystic kidney disease (PKD) is a ciliopathy resulting from defective localization of membrane proteins such as PC-1 to the primary cilium, resulting in renal cysts, and is associated with another cystic genetic disease called tuberous sclerosis complex (TSC). Here the authors use kidney-specific Tsc1 and Pkd1 mice to show that mTORC1 signalling inhibits PC-1 biogenesis as a potential mechanism of TSC/PKD contiguous gene syndrome. 02 March 2016 | doi: 10.1038/ncomms10786 Biological Sciences  Medical research  Volcanic ash melting under conditions relevant to ash turbine interactions OPEN Wenjia Song, Yan Lavallée, Kai-Uwe Hess, Ulrich Kueppers, Corrado Cimarelli and Donald B. Dingwell Volcanic ash is hazardous to jet engines, with high temperatures in turbines causing ash particles to melt and stick to the engine, adversely affecting turbine function. Here, the authors explore the spectrum of natural ash compositions and their behaviour and impact at high temperatures. 02 March 2016 | doi: 10.1038/ncomms10795 Earth Sciences  Geology and geophysics  Materials science  Observation of magnon-mediated current drag in Pt/yttrium iron garnet/Pt(Ta) trilayers OPEN Junxue Li, Yadong Xu, Mohammed Aldosary, Chi Tang, Zhisheng Lin, Shufeng Zhang, Roger Lake and Jing Shi Future spintronic devices may be based on the transport of electronic spin without an associated charge current in thin film materials. Here, the authors demonstrate the interconversion of spin current at the interface between a normal metal and magnetic insulator via magnon-mediated current drag. 02 March 2016 | doi: 10.1038/ncomms10858 Physical Sciences  Condensed matter  Nanotechnology  Topological phase transitions and chiral inelastic transport induced by the squeezing of light OPEN Vittorio Peano, Martin Houde, Christian Brendel, Florian Marquardt and Aashish A. Clerk Most known topological states of light are in the end closely analogous to fermionic states. Here, the authors show that the squeezing of light can lead to the formation of photonic topological states which do not have any fermionic counterpart yet support unusual chiral edge states. 02 March 2016 | doi: 10.1038/ncomms10779 Physical Sciences  Nanotechnology  Optical physics  Theoretical physics  A Helitron transposon reconstructed from bats reveals a novel mechanism of genome shuffling in eukaryotes OPEN Ivana Grabundzija, Simon A. Messing, Jainy Thomas, Rachel L. Cosby, Ilija Bilic, Csaba Miskey, Andreas Gogol-Döring, Vladimir Kapitonov, Tanja Diem, Anna Dalda, Jerzy Jurka, Ellen J. Pritham, Fred Dyda, Zsuzsanna Izsvák and Zoltán Ivics Helitron elements are proposed rolling-circle transposons in eukaryotic genomes, but experimental evidence for their transposition has been lacking. Here, Grabundzija et al. reconstruct an active Helitron from bats which they name Helraiser, and characterize its mechanism of transposition in cell-free reactions and in human cell cultures in vitro. 02 March 2016 | doi: 10.1038/ncomms10716 Biological Sciences  Evolution  Genetics  Molecular biology  Myocardial pathology induced by aldosterone is dependent on non-canonical activities of G protein-coupled receptor kinases OPEN Alessandro Cannavo, Daniela Liccardo, Akito Eguchi, Katherine J. Elliott, Christopher J. Traynham, Jessica Ibetti, Satoru Eguchi, Dario Leosco, Nicola Ferrara, Giuseppe Rengo and Walter J. Koch High aldosterone levels cause heart damage independently of its well-known effect on blood pressure. Here, Cannavo et al. show that aldosterone-mediated cardiac pathology involves G protein-coupled receptor (GPCR) kinase 2 (GRK2) and GRK5 that integrate signals from angiotensin II receptor (AT1R). 02 March 2016 | doi: 10.1038/ncomms10877 Biological Sciences  Medical research  Spin generation via bulk spin current in three-dimensional topological insulators OPEN Xingyue Peng, Yiming Yang, Rajiv R.P. Singh, Sergey Y. Savrasov and Dong Yu Future spintronic devices may exploit topological insulators, bulk-insulating materials possessing conductive surface states with orthogonally-locked electronic spin and momentum. Here, the authors propose a mechanism by which bulk spin currents drive surface spin accumulation in such a material. 02 March 2016 | doi: 10.1038/ncomms10878 Physical Sciences  Condensed matter  Biochemical reconstitution of TET1–TDG–BER-dependent active DNA demethylation reveals a highly coordinated mechanism OPEN Alain R. Weber, Claudia Krawczyk, Adam B. Robertson, Anna Kuśnierczyk, Cathrine B. Vågbø, David Schuermann, Arne Klungland and Primo Schär Cytosine methylation is a dynamic DNA modification with the involvement of the base excision repair pathway suspected to be involved in demethylation. Here the authors show that TET1 and TDG interact to target modified bases and coordinate BER to avoid double strand breaks. 02 March 2016 | doi: 10.1038/ncomms10806 Biological Sciences  Molecular biology  GSG1L suppresses AMPA receptor-mediated synaptic transmission and uniquely modulates AMPA receptor kinetics in hippocampal neurons OPEN Xinglong Gu, Xia Mao, Marc P. Lussier, Mary Anne Hutchison, Liang Zhou, F. Kent Hamra, Katherine W. Roche and Wei Lu The molecular mechanism controlling the trafficking and function of AMPARs at synapses are not fully understood. Here the authors show that GSG1L, a membrane protein, negatively regulates AMPAR-mediated synaptic transmission and represents a new class of AMPAR auxiliary subunit. 02 March 2016 | doi: 10.1038/ncomms10873 Biological Sciences  Cell biology  Neuroscience    Nature Communications JOBS of the week Postdoctoral Research Associate University of North Texas Health Science Center Senior Research Associate – Research Programmer University of East Anglia (UEA) Postdoctoral Fellows The University of Alabama PhD and post-doc programs Center for Integrative Biology Postdoctoral Research Scientist Cancer Research UK Beatson Institute in Glasgow Three Postdoctoral fellow positions University of Oslo Research Position (PhD) Universitatsklinikum Carl-Gustav-Carus Faculty Position Yale University Associate Research Fellow University of Exeter Tenure Track Positions University of Vienna (Universitaet Wien) More Science jobs from Nature Communications EVENT 8th Excellence in Pediatrics Conference 08.12.16 London, UK More science events from       Latest Corrigenda     Corrigendum: Notch signal strength controls cell fate in the haemogenic endothelium OPEN Leonor Gama-Norton, Eva Ferrando, Cristina Ruiz-Herguido, Zhenyi Liu, Jordi Guiu, Abul B. M. M. K. Islam, Sung-Uk Lee, Minhong Yan, Cynthia J. Guidos, Nuria López-Bigas, Takahiro Maeda, Lluis Espinosa, Raphael Kopan and Anna Bigas 04 March 2016 | doi: 10.1038/ncomms10978 Biological Sciences  Cell biology  Developmental biology      Corrigendum: DICER1 and microRNA regulation in post-traumatic stress disorder with comorbid depression OPEN Aliza P. Wingo, Lynn M. Almli, Jennifer S. Stevens, Torsten Klengel, Monica Uddin, Yujing Li, Angela C. Bustamante, Adriana Lori, Nastassja Koen, Dan J. Stein, Alicia K. Smith, Allison E. Aiello, Karestan C. Koenen, Derek E. Wildman, Sandro Galea, Bekh Bradley, Elisabeth B. Binder, Peng Jin, Greg Gibson and Kerry J. Ressler et al. 03 March 2016 | doi: 10.1038/ncomms10958 Biological Sciences  Genetics  Neuroscience      Corrigendum: Gs-coupled GPCR signalling in AgRP neurons triggers sustained increase in food intake OPEN Ken-ichiro Nakajima, Zhenzhong Cui, Chia Li, Jaroslawna Meister, Yinghong Cui, Ou Fu, Adam S. Smith, Shalini Jain, Bradford B. Lowell, Michael J. Krashes and Jürgen Wess 03 March 2016 | doi: 10.1038/ncomms11019 Biological Sciences  Molecular biology  Neuroscience      Advertisement npj Clean Water: open for submissions  An open access, online-only journal, dedicated to publishing high-quality papers that describe the significant and cutting-edge research that continues to ensure the supply of clean water to populations.  Explore the benefits of submitting your next manuscript.    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. 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