Nature Communications - 13 April 2016

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Latest content: Review Articles Corrigendum Advertisement   Need recombinant protein?  1mg custom made protein for just $1499 Search your protein now     Journal homepage Recommend to library Web feed   Advertisement Read the latest key research on aging and age-related diseases from npj Aging and Mechanisms of Disease, a new open access journal published in partnership with the Japanese Society of Anti-Aging Medicine (JAAM):  Yeast longevity: Living longer with heavy isotopes   Heterochronic microRNAs in temporal specification of neural stem cells: application toward rejuvenation      Latest Review View all Reviews     Coupling carbon nanomaterials with photochromic molecules for the generation of optically responsive materials OPEN Xiaoyan Zhang, Lili Hou and Paolo Samorì The marriage of photochromic molecules with the rapidly expanding portfolio of nanocarbons is providing new multifunctional and responsive nanomaterials. Here, the authors review recent progress in such materials' fabrication and their possible implementations, and suggest future directions of study. 12 April 2016 | doi: 10.1038/ncomms11118 Chemical Sciences  Materials science  Nanotechnology        Latest Articles View all Articles     Disease dynamics and costly punishment can foster socially imposed monogamy OPEN Chris T. Bauch and Richard McElreath Many human societies transitioned from polygyny to socially imposed monogamy as group sizes increased. Using a simulation model, the authors show that sexually transmitted infections impose heavier fitness penalties on polygynists as group size grows, enabling monogamists who punish polygyny to thrive in large groups. 12 April 2016 | doi: 10.1038/ncomms11219 Biological Sciences  Ecology  Evolution  Viviparity stimulates diversification in an order of fish OPEN Andrew J. Helmstetter, Alexander S. T. Papadopulos, Javier Igea, Tom J. M. Van Dooren, Armand M. Leroi and Vincent Savolainen Live birth and an annual life cycle potentially enable access to new ecological niches and subsequent species diversification. Here, Helmstetter et al. build the phylogeny for fish in the order Cyprinodontiformes and find that, though live birth and annualism have each evolved multiple times, only live birth is associated with increased diversification. 12 April 2016 | doi: 10.1038/ncomms11271 Biological Sciences  Evolution  Zoology  Microtubule-dependent balanced cell contraction and luminal-matrix modification accelerate epithelial tube fusion OPEN Kagayaki Kato, Bo Dong, Housei Wada, Miho Tanaka-Matakatsu, Yoshimasa Yagi and Shigeo Hayashi During tracheal tube fusion in Drosophila, a pair of tip cells form an adherens junction and then fuse their plasma membranes. Here the authors show that a balanced pulling force mediated by myosin and microtubules, as well as localized deposition of matrix, promotes plasma membrane fusion. 12 April 2016 | doi: 10.1038/ncomms11141 Biological Sciences  Cell biology  FNDC4 acts as an anti-inflammatory factor on macrophages and improves colitis in mice OPEN Madeleen Bosma, Marco Gerling, Jenny Pasto, Anastasia Georgiadi, Evan Graham, Olga Shilkova, Yasunori Iwata, Sven Almer, Jan Söderman, Rune Toftgård, Fredrik Wermeling, Elisabeth Almer Boström and Pontus Almer Boström FDNC4 is a poorly characterized homologue of FNDC5/irisin, a myokine induced by exercise. Here the authors show that FDNC4 increases macrophage survival in growth factor deprivation, inhibits phagocytosis and transcriptional responses to M1 and M2 polarizing stimuli, and protects mice from DSS-induced colitis. 12 April 2016 | doi: 10.1038/ncomms11314 Biological Sciences  Immunology  Entropy-driven formation of chiral nematic phases by computer simulations OPEN Simone Dussi and Marjolein Dijkstra The entropy-driven formation of cholesteric liquid crystal, one of the widely used liquid crystal phase, has not yet been addressed in simulations due to large unit cells. Here, Dussi and Dijkstra overcome this problem by introducing a hard-particle model and show that shape alone can stabilize a chiral nematic phase. 12 April 2016 | doi: 10.1038/ncomms11175 Physical Sciences  Condensed matter  Materials science  Pathological lymphangiogenesis is modulated by galectin-8-dependent crosstalk between podoplanin and integrin-associated VEGFR-3 OPEN Wei-Sheng Chen, Zhiyi Cao, Satoshi Sugaya, Maria J. Lopez, Victor G. Sendra, Nora Laver, Hakon Leffler, Ulf J. Nilsson, Jianxin Fu, Jianhua Song, Lijun Xia, Pedram Hamrah and Noorjahan Panjwani Pathological lymphangiogenesis is associated with various eye diseases. Here the authors show that a carbohydrate-binding protein, galectin-8, promotes pathological lymphangiogenesis in the eye by regulating the crosstalk among VEGF-C, podoplanin and integrin pathways, and thus may represent a useful therapeutic target. 12 April 2016 | doi: 10.1038/ncomms11302 Biological Sciences  Cell biology  Medical research  Extortion can outperform generosity in the iterated prisoner’s dilemma OPEN Zhijian Wang, Yanran Zhou, Jaimie W. Lien, Jie Zheng and Bin Xu The zero-determinant (ZD) strategies discovered by Press and Dyson overturned several decades of consensus about the iterated prisoner's dilemma. Here, the authors provide the first empirical evidence in support of Press and Dyson’s theory, by showing that knowledge of the opponent and the length of the interaction can facilitate the Generous and Extortionate ZD strategies as predicted. 12 April 2016 | doi: 10.1038/ncomms11125 Biological Sciences  Evolution  Neuroscience  Clec4A4 is a regulatory receptor for dendritic cells that impairs inflammation and T-cell immunity OPEN Tomofumi Uto, Tomohiro Fukaya, Hideaki Takagi, Keiichi Arimura, Takeshi Nakamura, Naoya Kojima, Bernard Malissen and Katsuaki Sato Clec4A4 is a C-type lectin receptor highly expressed by CD8α− dendritic cells. Here the authors show that its loss of function results in enhanced T cell responses and exacerbated autoimmunity, implicating Clec4A4 in limiting activation of the CD8α− dendritic cells. 12 April 2016 | doi: 10.1038/ncomms11273 Biological Sciences  Immunology  Fimbrin phosphorylation by metaphase Cdk1 regulates actin cable dynamics in budding yeast OPEN Yansong Miao, Xuemei Han, Liangzhen Zheng, Ying Xie, Yuguang Mu, John R. Yates and David G. Drubin Metaphase cells preferentially promote actin cable assembly through cyclin-dependent kinase 1 (Cdk1) activity. Here the authors identify fimbrin as one of the main metaphase Cdk1 targets for cell cycle regulation of actin cable assembly in budding yeast. 12 April 2016 | doi: 10.1038/ncomms11265 Biological Sciences  Cell biology  Parathyroid hormone receptor signalling in osterix-expressing mesenchymal progenitors is essential for tooth root formation OPEN Wanida Ono, Naoko Sakagami, Shigeki Nishimori, Noriaki Ono and Henry M. Kronenberg How the parathyroid hormone-related protein receptor (PPR) and its ligand act in root formation and tooth eruption is unclear. Here, the authors identify osterix-expressing dental mesenchymal cells as progenitors for root formation and that PPR signalling mediates their differentiation and tooth eruption. 12 April 2016 | doi: 10.1038/ncomms11277 Biological Sciences  Cell biology  Developmental biology  Dynamic information routing in complex networks OPEN Christoph Kirst, Marc Timme and Demian Battaglia Flexible information routing underlies the function of many biological and artificial networks. Here, the authors present a theoretical framework that shows how information can be flexibly routed across networks using collective reference dynamics and how local changes may induce remote rerouting. 12 April 2016 | doi: 10.1038/ncomms11061 Physical Sciences  Theoretical physics  A mutation in the atrial-specific myosin light chain gene (MYL4) causes familial atrial fibrillation OPEN Nathan Orr, Rima Arnaout, Lorne J. Gula, Danna A. Spears, Peter Leong-Sit, Qiuju Li, Wadea Tarhuni, Sven Reischauer, Vijay S. Chauhan, Matthew Borkovich, Shaheen Uppal, Arnon Adler, Shaun R. Coughlin, Didier Y. R. Stainier and Michael H. Gollob Here, Michael Gollob and colleagues perform a whole exome sequencing study to identify a mutation in the atrial-specific myosin light chain gene MYL4 in a small family with autosomal dominant familial atrial fibrillation. They also test the functionality of this MYL4 mutation in zebrafish cardiac function and recapitulate disease-related phenotypes. 12 April 2016 | doi: 10.1038/ncomms11303 Biological Sciences  Genetics  MicroRNA 139-5p coordinates APLNR-CXCR4 crosstalk during vascular maturation OPEN Irinna Papangeli, Jongmin Kim, Inna Maier, Saejeong Park, Aram Lee, Yujung Kang, Keiichiro Tanaka, Omar F. Khan, Hyekyung Ju, Yoko Kojima, Kristy Red-Horse, Daniel G. Anderson, Arndt F. Siekmann and Hyung J. Chun G protein-coupled receptors APLNR and CXCR4 are crucial for vascular development. Here, the authors show that these two signaling pathways communicate and that in response to blood flow APLNR signaling induces a decrease in CXCR4 expression via miR-139-5p, thereby restricting CXCR4 expression to the non-flow exposed tip cells in the retinal vasculature. 12 April 2016 | doi: 10.1038/ncomms11268 Biological Sciences  Developmental biology  Medical research  T-cell activation is an immune correlate of risk in BCG vaccinated infants OPEN Helen A. Fletcher, Margaret A. Snowden, Bernard Landry, Wasima Rida, Iman Satti, Stephanie A. Harris, Magali Matsumiya, Rachel Tanner, Matthew K. O’Shea, Veerabadran Dheenadhayalan, Leah Bogardus, Lisa Stockdale, Leanne Marsay, Agnieszka Chomka, Rachel Harrington-Kandt, Zita-Rose Manjaly-Thomas, Vivek Naranbhai, Elena Stylianou, Fatoumatta Darboe, Adam Penn-Nicholson et al. BCG vaccine confers only partial protection against tuberculosis. Here the authors show that the risk of tuberculosis infection and progression to disease in BCG-immunized children positively correlates with the frequency of activated HLA-DR+CD4+ T cells. 12 April 2016 | doi: 10.1038/ncomms11290 Biological Sciences  Immunology  Medical research  Alternative splicing of MALT1 controls signalling and activation of CD4+ T cells OPEN Isabel Meininger, Richard A. Griesbach, Desheng Hu, Torben Gehring, Thomas Seeholzer, Arianna Bertossi, Jan Kranich, Andrea Oeckinghaus, Andrea C. Eitelhuber, Ute Greczmiel, Andreas Gewies, Marc Schmidt-Supprian, Jürgen Ruland, Thomas Brocker, Vigo Heissmeyer, Florian Heyd and Daniel Krappmann MALT1 regulates NFκB signalling both as a scaffolding protein and as a protease. Here the authors show that during T cell activation the expression of MALT1 gene switches to an alternatively spliced variant, which increases TCR signal transduction due to enhanced TRAF6 binding. 12 April 2016 | doi: 10.1038/ncomms11292 Biological Sciences  Immunology  Molecular biology  Consistent role of weak and strong interactions in high- and low-diversity trophic food webs OPEN Gabriel Gellner and Kevin S. McCann High-and low-diversity food webs are thought to differ in their structural stability. Here, the authors use a method that bridges both levels of diversity to show that stability relationships and interaction strength can be consistent between simple and complex trophic networks. 12 April 2016 | doi: 10.1038/ncomms11180 Biological Sciences  Ecology  Local biomass burning is a dominant cause of the observed precipitation reduction in southern Africa OPEN Øivind Hodnebrog, Gunnar Myhre, Piers M. Forster, Jana Sillmann and Bjørn H. Samset Black carbon aerosols in the atmosphere absorb solar radiation and affect the hydrological cycle. Here, the authors show that local aerosol emissions from biomass burning activities are a main cause of observed decline in southern African dry season precipitation over the last century. 12 April 2016 | doi: 10.1038/ncomms11236 Earth Sciences  Atmospheric science  Climate science  A programmable synthetic lineage-control network that differentiates human IPSCs into glucose-sensitive insulin-secreting beta-like cells OPEN Pratik Saxena, Boon Chin Heng, Peng Bai, Marc Folcher, Henryk Zulewski and Martin Fussenegger Synthetic biology offers the potential for the design and implementation of rationally designed, complex genetic programmes. Here the authors design a genetic network to trigger the differentiation of patient derived IPSCs into beta-like cells. 11 April 2016 | doi: 10.1038/ncomms11247 Biological Sciences  Developmental biology  Molecular biology  Splicing misregulation of SCN5A contributes to cardiac-conduction delay and heart arrhythmia in myotonic dystrophy OPEN Fernande Freyermuth, Frédérique Rau, Yosuke Kokunai, Thomas Linke, Chantal Sellier, Masayuki Nakamori, Yoshihiro Kino, Ludovic Arandel, Arnaud Jollet, Christelle Thibault, Muriel Philipps, Serge Vicaire, Bernard Jost, Bjarne Udd, John W. Day, Denis Duboc, Karim Wahbi, Tsuyoshi Matsumura, Harutoshi Fujimura, Hideki Mochizuki et al. Patients with myotonic dystrophy (MD) suffer from severe cardiac issues of unknown aetiology. Freyermuth et al. show that fatal changes in cardiac electrophysiological properties in humans and mice with MD may arise from misregulation of the alternative splicing of the cardiac Na+ channel SCN5A transcript, resulting in expression of its fetal form. 11 April 2016 | doi: 10.1038/ncomms11067 Biological Sciences  Medical research  Unconventional endosome-like compartment and retromer complex in Toxoplasma gondii govern parasite integrity and host infection OPEN Lamba Omar Sangaré, Tchilabalo Dilezitoko Alayi, Benoit Westermann, Agnes Hovasse, Fabien Sindikubwabo, Isabelle Callebaut, Elisabeth Werkmeister, Frank Lafont, Christian Slomianny, Mohamed-Ali Hakimi, Alain Van Dorsselaer, Christine Schaeffer-Reiss and Stanislas Tomavo The retromer complex is a multi-protein component of the endosomal protein sorting machinery. Here, Sangaré et al. identify unique features in the retromer complex of the parasite Toxoplasma gondii, and show that it is crucial for the biogenesis of secretory organelles in this pathogen. 11 April 2016 | doi: 10.1038/ncomms11191 Biological Sciences  Cell biology  Microbiology  PDE6δ-mediated sorting of INPP5E into the cilium is determined by cargo-carrier affinity OPEN Eyad Kalawy Fansa, Stefanie Kristine Kösling, Eldar Zent, Alfred Wittinghofer and Shehab Ismail PDE6δ regulates the sorting of prenylated cargo proteins. Here Fansa et al. propose that the affinity of the interaction between PDE6δ and its cargo protein determines whether they are released by cytoplasmic or cilia-specific release factors ultimately determining their subcellular localization. 11 April 2016 | doi: 10.1038/ncomms11366 Biological Sciences  Biochemistry  Cell biology  Hot super-Earths stripped by their host stars OPEN M. S. Lundkvist, H. Kjeldsen, S. Albrecht, G. R. Davies, S. Basu, D. Huber, A. B. Justesen, C. Karoff, V. Silva Aguirre, V. Van Eylen, C. Vang, T. Arentoft, T. Barclay, T. R. Bedding, T. L. Campante, W. J. Chaplin, J. Christensen-Dalsgaard, Y. P. Elsworth, R. L. Gilliland, R. Handberg et al. Theory predicts a deficit of super-Earth sized planets, which orbit close to their host star. Here, Lundkvist et al. use data from the NASA Kepler mission to show that this deficit is also seen in observations, thereby providing new insight into exoplanetary systems. 11 April 2016 | doi: 10.1038/ncomms11201 Earth Sciences  Planetary sciences  Approaching soft X-ray wavelengths in nanomagnet-based microwave technology OPEN Haiming Yu, O. d’ Allivy Kelly, V. Cros, R. Bernard, P. Bortolotti, A. Anane, F. Brandl, F. Heimbach and D. Grundler Integrating spin waves with microwave circuits is promising for microwave nanoelectronics. Here, Yu et al. demonstrate a reconfigurable microwave-to-magnon transducer by covering yttrium iron garnet with small arrays of tailored magnetic nanodisks, which transmits microwave signals via sub-100-nanometer wavelength spin waves. 11 April 2016 | doi: 10.1038/ncomms11255 Physical Sciences  Condensed matter  Materials science  Nanotechnology  Gate-controlled electromechanical backaction induced by a quantum dot OPEN Yuma Okazaki, Imran Mahboob, Koji Onomitsu, Satoshi Sasaki and Hiroshi Yamaguchi Coupling between quantum structures and mechanical resonators remains a challenge. Here, the authors couple a quantum dot and a piezoelectric microresonator and show that gate-induced single electron transport in the quantum dot enables control of the amplitude of the mechanical response. 11 April 2016 | doi: 10.1038/ncomms11132 Physical Sciences  Condensed matter  Nanotechnology  The Ku-binding motif is a conserved module for recruitment and stimulation of non-homologous end-joining proteins OPEN Gabrielle J. Grundy, Stuart L. Rulten, Raquel Arribas-Bosacoma, Kathryn Davidson, Zuzanna Kozik, Antony W. Oliver, Laurence H. Pearl and Keith W. Caldecott Werner syndrome is a progeroid disease characterised by genetic instability due to mutations to the WRN helicase/exonuclease. Here the authors define a novel Ku binding motif (KBM) and show that two such motifs facilitate the involvement of WRN in DNA double-strand break repair. 11 April 2016 | doi: 10.1038/ncomms11242 Biological Sciences  Molecular biology  Genetic and environmental influences interact with age and sex in shaping the human methylome OPEN Jenny van Dongen, Michel G. Nivard, Gonneke Willemsen, Jouke-Jan Hottenga, Quinta Helmer, Conor V. Dolan, Erik A. Ehli, Gareth E. Davies, Maarten van Iterson, Charles E. Breeze, Stephan Beck, BIOS Consortium, Peter A.C.’t Hoen, René Pool, Marleen M.J. van Greevenbroek, Coen D.A. Stehouwer, Carla J.H. van der Kallen, Casper G. Schalkwijk, Cisca Wijmenga, Sasha Zhernakova et al. Differential impact of genetic and environmental influences on DNA methylation may result in sex- and age-related physiological variation and disease susceptibility. By analysing DNA methylome of 2,603 individuals from twin families, here, the authors establish a catalogue of between-individual variation in DNA methylation. 07 April 2016 | doi: 10.1038/ncomms11115 Biological Sciences  Genetics  Molecular biology  Large-scale production of megakaryocytes from human pluripotent stem cells by chemically defined forward programming OPEN Thomas Moreau, Amanda L. Evans, Louella Vasquez, Marloes R. Tijssen, Ying Yan, Matthew W. Trotter, Daniel Howard, Maria Colzani, Meera Arumugam, Wing Han Wu, Amanda Dalby, Riina Lampela, Guenaelle Bouet, Catherine M. Hobbs, Dean C. Pask, Holly Payne, Tatyana Ponomaryov, Alexander Brill, Nicole Soranzo, Willem H. Ouwehand et al. Platelets are blood circulating corpuscles generated from megakaryocytes that initiate wound healing. Here, Moreau et al. describe a way of producing large quantities of megakaryocytes from human pluripotent stem cells in the laboratory, moving us a step closer to manufacturing transfusion products. 07 April 2016 | doi: 10.1038/ncomms11208 Biological Sciences  Biotechnology  Cell biology  4D Visualization of replication foci in mammalian cells corresponding to individual replicons OPEN V. O. Chagin, C. S. Casas-Delucchi, M. Reinhart, L. Schermelleh, Y. Markaki, A. Maiser, J. J. Bolius, A. Bensimon, M. Fillies, P. Domaing, Y. M. Rozanov, H. Leonhardt and M. C. Cardoso Whether replication happens at individual replicons or in replication factories is a controversial debate. Here the authors use super-resolution microscopy and analysis of replication fork speed to present evidence in favour of replicons. 07 April 2016 | doi: 10.1038/ncomms11231 Biological Sciences  Molecular biology  Atlas of prostate cancer heritability in European and African-American men pinpoints tissue-specific regulation OPEN Alexander Gusev, Huwenbo Shi, Gleb Kichaev, Mark Pomerantz, Fugen Li, Henry W. Long, Sue A. Ingles, Rick A. Kittles, Sara S. Strom, Benjamin A. Rybicki, Barbara Nemesure, William B. Isaacs, Wei Zheng, Curtis A. Pettaway, Edward D. Yeboah, Yao Tettey, Richard B. Biritwum, Andrew A. Adjei, Evelyn Tay, Ann Truelove et al. Over one hundred loci have been identified to be associated with the familial risk of prostate cancer but the functional effects are poorly understood. Here the authors use single-nucleotide variant and epigentic data to show an underlying genetic architecture marked by histone modification. 07 April 2016 | doi: 10.1038/ncomms10979 Biological Sciences  Cancer  Genetics  Chemical ordering suppresses large-scale electronic phase separation in doped manganites OPEN Yinyan Zhu, Kai Du, Jiebin Niu, Lingfang Lin, Wengang Wei, Hao Liu, Hanxuan Lin, Kai Zhang, Tieying Yang, Yunfang Kou, Jian Shao, Xingyu Gao, Xiaoshan Xu, Xiaoshan Wu, Shuai Dong, Lifeng Yin and Jian Shen In oxide materials, cation doping strongly influences the electronic correlations which promote diverse phenomena such as colossal magnetoresistance and superconductivity. Here, the authors use magnetic microscopy to image the effects of spatially ordered doping on electronic phase separation in oxide superlattices. 07 April 2016 | doi: 10.1038/ncomms11260 Physical Sciences  Condensed matter  3D replicon distributions arise from stochastic initiation and domino-like DNA replication progression OPEN D. Löb, N. Lengert, V. O. Chagin, M. Reinhart, C. S. Casas-Delucchi, M. C. Cardoso and B. Drossel DNA replication in higher eukaryotes is a complex process occurring in a complex genome environment. Here the authors present a model of DNA replication that incorporates random loop chromatin folding and domino-like fork progression reproducing the spatial and temporal characteristics of S-phase. 07 April 2016 | doi: 10.1038/ncomms11207 Biological Sciences  Molecular biology  Akt1-mediated Gata3 phosphorylation controls the repression of IFNγ in memory-type Th2 cells OPEN Hiroyuki Hosokawa, Tomoaki Tanaka, Yusuke Endo, Miki Kato, Kenta Shinoda, Akane Suzuki, Shinichiro Motohashi, Masaki Matsumoto, Keiichi I. Nakayama and Toshinori Nakayama Although IFNγ is a Th1 signature cytokine and is repressed in Th2 cells, it is reactivated in a subset of memory Th2 cells. Here the authors show that Hdac2 is released from Gata3 by Akt-mediated phosphorylation, leading to transcriptional derepression of Tbx21 and IFNγ in these cells. 07 April 2016 | doi: 10.1038/ncomms11289 Biological Sciences  Immunology  Molecular biology  Giant spin-torque diode sensitivity in the absence of bias magnetic field OPEN Bin Fang, Mario Carpentieri, Xiaojie Hao, Hongwen Jiang, Jordan A. Katine, Ilya N. Krivorotov, Berthold Ocker, Juergen Langer, Kang L. Wang, Baoshun Zhang, Bruno Azzerboni, Pedram Khalili Amiri, Giovanni Finocchio and Zhongming Zeng Nanomagnetic materials allow for the emission and detection of microwave radiation in technological applications by spin excitation. Here, the authors present sensitive room-temperature microwave detectors based on nanoscale magnetic tunnel junctions, enabled via spin torque and injection locking. 07 April 2016 | doi: 10.1038/ncomms11259 Physical Sciences  Condensed matter  Real-time imaging of glutamate clearance reveals normal striatal uptake in Huntington disease mouse models OPEN Matthew P. Parsons, Matthieu P. Vanni, Cameron L. Woodard, Rujun Kang, Timothy H. Murphy and Lynn A. Raymond Huntington disease (HD) has been linked via biochemical uptake assays to impaired glutamate clearance and resultant excitotoxicity. Here, utilizing a fluorescent reporter, the authors measure real-time glutamate dynamics in mouse model HD brain slices and find normal or even accelerated glutamate clearance. 07 April 2016 | doi: 10.1038/ncomms11251 Biological Sciences  Neuroscience  Omnivory in birds is a macroevolutionary sink OPEN Gustavo Burin, W. Daniel Kissling, Paulo R. Guimarães Jr, Çağan H. Şekercioğlu and Tiago B. Quental Diet is known to influence speciation, but much less is known about how this process operates at macroevolutionary scales. Using a global dietary database of birds, Burin et al. show that omnivory is associated with higher extinction and lower speciation rates compared to other guilds. 07 April 2016 | doi: 10.1038/ncomms11250 Biological Sciences  Ecology  Evolution  Groundwater–surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover OPEN James C. Stegen, James K. Fredrickson, Michael J. Wilkins, Allan E. Konopka, William C. Nelson, Evan V. Arntzen, William B. Chrisler, Rosalie K. Chu, Robert E. Danczak, Sarah J. Fansler, David W. Kennedy, Charles T. Resch and Malak Tfaily Groundwater-surface water mixing zones link critical ecosystem domains, but attendant microbe-biogeochemistry-hydrology interactions are poorly known. Here, the authors show that groundwater-surface water mixing stimulates respiration, alters carbon composition, and shifts the ecology from stochastic to deterministic. 07 April 2016 | doi: 10.1038/ncomms11237 Earth Sciences  Biogeochemistry  Ecology  Light-enhanced liquid-phase exfoliation and current photoswitching in graphene–azobenzene composites OPEN Markus Döbbelin, Artur Ciesielski, Sébastien Haar, Silvio Osella, Matteo Bruna, Andrea Minoia, Luca Grisanti, Thomas Mosciatti, Fanny Richard, Eko Adi Prasetyanto, Luisa De Cola, Vincenzo Palermo, Raffaello Mazzaro, Vittorio Morandi, Roberto Lazzaroni, Andrea C. Ferrari, David Beljonne and Paolo Samorì Photochemical isomerisation can engender large conformational rearrangements, giving rise to switchable physical and electronic properties. Here, the authors use azo-benzene derivatives as addressable surfactants to facilitate the exfoliation of graphene and provide light activated modulation. 07 April 2016 | doi: 10.1038/ncomms11090 Chemical Sciences  Materials science  Nanotechnology  Physical chemistry  Meta-analysis of gene–environment-wide association scans accounting for education level identifies additional loci for refractive error OPEN Qiao Fan, Virginie J. M. Verhoeven, Robert Wojciechowski, Veluchamy A. Barathi, Pirro G. Hysi, Jeremy A. Guggenheim, René Höhn, Veronique Vitart, Anthony P. Khawaja, Kenji Yamashiro, S Mohsen Hosseini, Terho Lehtimäki, Yi Lu, Toomas Haller, Jing Xie, Cécile Delcourt, Mario Pirastu, Juho Wedenoja, Puya Gharahkhani, Cristina Venturini et al. This report by the Consortium for Refractive Error and Myopia uses gene-environment-wide interaction study (GEWIS) to identify genetic loci that affect environmental influence in myopia development, and identifies ethnic specific genetic loci that attribute to eye refractive errors. 06 April 2016 | doi: 10.1038/ncomms11008 Biological Sciences  Genetics  Experience-dependent hippocampal pattern differentiation prevents interference during subsequent learning OPEN Serra E. Favila, Avi J. H. Chanales and Brice A. Kuhl There is limited evidence linking learning related changes in hippocampal representations and memory interference. Here Favila and colleagues demonstrate that learning reduces overlap in hippocampal activity patterns corresponding to similar events, which benefits subsequent learning by preventing interference. 06 April 2016 | doi: 10.1038/ncomms11066 Biological Sciences  Neuroscience  FOXE3 contributes to Peters anomaly through transcriptional regulation of an autophagy-associated protein termed DNAJB1 OPEN Shahid Y. Khan, Shivakumar Vasanth, Firoz Kabir, John D. Gottsch, Arif O. Khan, Raghothama Chaerkady, Mei-Chong W. Lee, Carmen C. Leitch, Zhiwei Ma, Julie Laux, Rafael Villasmil, Shaheen N. Khan, Sheikh Riazuddin, Javed Akram, Robert N. Cole, C. Conover Talbot, Nader Pourmand, Norann A. Zaghloul, J. Fielding Hejtmancik and S. Amer Riazuddin Peter's Anomaly is a developmental disorder of the eye and has been linked to mutations in a range of genes, including the transcription factor FOXE3. Here the authors use next-generation RNA sequencing and mass spectrometry to identify an autophagy-associated protein, DNAJB1 as the transcriptional target of FOXE3. 06 April 2016 | doi: 10.1038/ncomms10953 Biological Sciences  Genetics  Molecular biology  GATA3 induces human T-cell commitment by restraining Notch activity and repressing NK-cell fate OPEN Inge Van de Walle, Anne-Catherine Dolens, Kaat Durinck, Katrien De Mulder, Wouter Van Loocke, Sagar Damle, Els Waegemans, Jelle De Medts, Imke Velghe, Magda De Smedt, Bart Vandekerckhove, Tessa Kerre, Jean Plum, Georges Leclercq, Ellen V. Rothenberg, Pieter Van Vlierberghe, Frank Speleman and Tom Taghon Strong Notch signalling promotes initial T cell lineage specification of lymphoid progenitors but is also permissive for thymic natural killer (NK) cell development. Here the authors show that GATA3 directs human T-lineage commitment by modulating Notch activity and repressing the NK programme. 06 April 2016 | doi: 10.1038/ncomms11171 Biological Sciences  Immunology  Molecular biology  Cryo-EM structure of lysenin pore elucidates membrane insertion by an aerolysin family protein OPEN Monika Bokori-Brown, Thomas G. Martin, Claire E. Naylor, Ajit K. Basak, Richard W. Titball and Christos G. Savva Lysenin is member of the aerolysin family of small ß-barrel pore-forming toxins that include virulence factors from several human and animal pathogens. Here the authors determine the structure of the lysenin pore by single particle cryo- EM and propose a conserved pore formation mechanism for the aerolysin protein family. 06 April 2016 | doi: 10.1038/ncomms11293 Biological Sciences  Biophysics  Microbiology  Spatial and temporal homogeneity of driver mutations in diffuse intrinsic pontine glioma OPEN Hamid Nikbakht, Eshini Panditharatna, Leonie G. Mikael, Rui Li, Tenzin Gayden, Matthew Osmond, Cheng-Ying Ho, Madhuri Kambhampati, Eugene I. Hwang, Damien Faury, Alan Siu, Simon Papillon-Cavanagh, Denise Bechet, Keith L. Ligon, Benjamin Ellezam, Wendy J. Ingram, Caedyn Stinson, Andrew S. Moore, Katherine E. Warren, Jason Karamchandani et al. Diffuse Intrinsic Pontine Gliomas are diagnosed by sampling a small portion of the tumour. Here, using multiple samples from tumours, the authors analyse the spatial and temporal distribution of driver mutations revealing that H3K27M mutations arise first in tumorigenesis followed by a specific invariable sequence of driver mutations, which are homogeneously distributed across the tumour mass. 06 April 2016 | doi: 10.1038/ncomms11185 Biological Sciences  Cancer  Genetics  A squalene synthase-like enzyme initiates production of tetraterpenoid hydrocarbons in Botryococcus braunii Race L OPEN Hem R. Thapa, Mandar T. Naik, Shigeru Okada, Kentaro Takada, István Molnár, Yuquan Xu and Timothy P. Devarenne The green microalga Botryococcus braunii is a promising biofuel producer due to its ability to produce large amounts of hydrocarbon oils that can be converted into fuels. Here the authors implicate lycopaoctaene synthase, a squalene synthases-like enzyme, in the first step towards the biosynthesis of the C40 tetraterpenoid hydrocarbon lycopadiene. 06 April 2016 | doi: 10.1038/ncomms11198 Biological Sciences  Biochemistry  Chemical biology  Plant sciences  Near optimal graphene terahertz non-reciprocal isolator OPEN Michele Tamagnone, Clara Moldovan, Jean-Marie Poumirol, Alexey B. Kuzmenko, Adrian M. Ionescu, Juan R. Mosig and Julien Perruisseau-Carrier Optical isolators, or optical diodes, allow electromagnetic radiation to travel in one direction but not the other. Here, the authors achieve unidirectional propagation of terahertz waves by taking advantage of the non-reciprocal nature of optical conductivity in magnetostatically biased graphene. 06 April 2016 | doi: 10.1038/ncomms11216 Physical Sciences  Materials science  Optical physics  Directed elimination of senescent cells by inhibition of BCL-W and BCL-XL OPEN Reut Yosef, Noam Pilpel, Ronit Tokarsky-Amiel, Anat Biran, Yossi Ovadya, Snir Cohen, Ezra Vadai, Liat Dassa, Elisheva Shahar, Reba Condiotti, Ittai Ben-Porath and Valery Krizhanovsky The accumulation of senescent cells within tissues plays a role in numerous age-related pathologies. Yosef and Pilpel et al. demonstrate that the resistance of these cells to apoptosis is driven by upregulation of survival proteins, whose pharmacological inhibition triggers senescent cell elimination in mice. 06 April 2016 | doi: 10.1038/ncomms11190 Biological Sciences  Cell biology  Medical research  Catalytic N-radical cascade reaction of hydrazones by oxidative deprotonation electron transfer and TEMPO mediation OPEN Xiao-Qiang Hu, Xiaotian Qi, Jia-Rong Chen, Quan-Qing Zhao, Qiang Wei, Yu Lan and Wen-Jing Xiao The use of N-centred radicals is limited by the difficulties in their preparation. Here, the authors report a photoredox method for the formation of N-centred radicals on hydrazones and their use for the synthesis of heterocyclic compounds through a radical cascade reaction. 06 April 2016 | doi: 10.1038/ncomms11188 Chemical Sciences  Catalysis  Organic chemistry  Calcium-sensing receptors signal constitutive macropinocytosis and facilitate the uptake of NOD2 ligands in macrophages OPEN Johnathan Canton, Daniel Schlam, Christian Breuer, Michael Gütschow, Michael Glogauer and Sergio Grinstein Macropinocytosis can be induced in several cell types by growth factors to promote nutrient acquisition. Here the authors find that constitutive macropinocytosis, unique to dendritic cells and macrophages, requires the activity of calcium-sensing receptors. 06 April 2016 | doi: 10.1038/ncomms11284 Biological Sciences  Cell biology  Immunology  Superconductivity below 20 K in heavily electron-doped surface layer of FeSe bulk crystal OPEN J. J. Seo, B. Y. Kim, B. S. Kim, J. K. Jeong, J. M. Ok, Jun Sung Kim, J. D. Denlinger, S. -K. Mo, C. Kim and Y. K. Kim Thin FeSe film on SrTiO3 substrate becomes a superconductor with a transition temperature over 100 K, yet the origin remains controversial. Here, Seo et al. show superconductivity below 20 K on the electron-doped surface of an FeSe crystal, suggesting a decisive role of interfacial effects in the enhancement of superconductivity. 06 April 2016 | doi: 10.1038/ncomms11116 Physical Sciences  Condensed matter  Materials science  Mercury anomalies and the timing of biotic recovery following the end-Triassic mass extinction OPEN Alyson M. Thibodeau, Kathleen Ritterbush, Joyce A. Yager, A. Joshua West, Yadira Ibarra, David J. Bottjer, William M. Berelson, Bridget A. Bergquist and Frank A. Corsetti The association between Central Atlantic Magmatic Province (CAMP) eruption volatiles and the end-Triassic mass extinction remains ambiguous. Here, the authors present mercury and palaeontological evidence from the same archive and show that significant biotic recovery did not begin until CAMP eruptions ceased. 06 April 2016 | doi: 10.1038/ncomms11147 Earth Sciences  Biogeochemistry  Geology and geophysics  Circular RNA profiling reveals an abundant circHIPK3 that regulates cell growth by sponging multiple miRNAs OPEN Qiupeng Zheng, Chunyang Bao, Weijie Guo, Shuyi Li, Jie Chen, Bing Chen, Yanting Luo, Dongbin Lyu, Yan Li, Guohai Shi, Linhui Liang, Jianren Gu, Xianghuo He and Shenglin Huang Circular RNAs are formed from exon back-splicing, the significance of these endogenous RNAs is beginning to be unraveled. Here, the authors identify thousands of circular RNAs differentially expressed between normal and cancer tissues and show that an abundant circular RNA generated from HIPK3 regulates cell growth. 06 April 2016 | doi: 10.1038/ncomms11215 Biological Sciences  Cancer  Molecular biology  SCFSAP controls organ size by targeting PPD proteins for degradation in Arabidopsis thaliana OPEN Zhibiao Wang, Na Li, Shan Jiang, Nathalie Gonzalez, Xiahe Huang, Yingchun Wang, Dirk Inzé and Yunhai Li Organ size in plants is regulated by cell proliferation and cell expansion. Here, Wang et al. show that STERILE APETALA participates in the regulation of organ size as a component of an E3 ligase complex that promotes the degradation of negative regulators of meristemoid proliferation 06 April 2016 | doi: 10.1038/ncomms11192 Biological Sciences  Plant sciences    Nature Communications JOBS of the week 4 Doctoral Researcher Positions (m / f) International Leibniz Research School for Microbial and Biomolecular Interactions Postdoctoral Research Associate University of Liverpool Postdoctoral Research Assistant University of Dundee Laboratory Research Scientist The Francis Crick Institute Open Rank Faculty Position University of North Carolina at Chapel Hill Research Associate Indiana University Post Doctoral Research Fellow University of California - San Francisco Research Fellow (5 posts) Cardiff University Postdoctoral Research Fellow Georgia Institute of Technology Junior Group Leader Position University of Lyon More Science jobs from Nature Communications EVENT Proteins and Peptides: Structure, Function and Biotechnology 22.07.16 Genève, Switzerland More science events from       Latest Corrigendum     Corrigendum: Differential developmental requirement and peripheral regulation for dermal Vγ4 and Vγ6T17 cells in health and inflammation Yihua Cai, Feng Xue, Chris Fleming, Jie Yang, Chuanlin Ding, Yunfeng Ma, Min Liu, Huang-ge Zhang, Jie Zheng, Na Xiong and Jun Yan 11 April 2016 | doi: 10.1038/ncomms11354 Biological Sciences  Immunology      Advertisement nature.com webcasts Nature Publishing Group presents a custom webcast on: Releasable purification of monocytes for human dendritic cell generation Wednesday April 27, 2016 8AM PDT, 11AM EDT, 4PM BST, 5PM CEST Register for the webcast and live Q&A session Sponsored by: Quad Technologies     Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. 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