Nature Communications - 27 January 2016

Advertisement Nature Index 2015 China The 2015 Nature Index supplement dedicated to China reveals the country's output of high quality science continues to grow - a trend that shows no signs of slowing.  Access now for free.       Weekly Content Alert Nature Communications is now fully open access. Read more. 27 January 2016  Featured image: Alexander et al. show that hippocampal CA2 neurons globally remap their place fields in response to social and novel stimuli. Latest content: Articles Corrigendum Erratum Journal homepage Recommend to library Web feed   Advertisement NPG Asia Materials is proud to present a web focus on Magnetic materials for spintronic devices. This web focus features a selection of articles that are related to magnetic materials for potential application in magnetoelectronic and spintronic devices. Such materials include artificial multiferroics, half metallic Heusler alloys, topological insulators, Dirac semimetals, manganites, nanofibers, and spin wave materials, as well as molecular interfaces.  Access the Web Focus today!        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     Modelling the Tox21 10 K chemical profiles for in vivo toxicity prediction and mechanism characterization OPEN Ruili Huang, Menghang Xia, Srilatha Sakamuru, Jinghua Zhao, Sampada A. Shahane, Matias Attene-Ramos, Tongan Zhao, Christopher P. Austin and Anton Simeonov Large-scale in vitro assays may reduce the number of toxicological tests carried out in animals. Here, Huang et al. report a large dataset containing results of in vitro tests of approximately 10,000 chemicals, and use these data to create models that can potentially predict toxicity in humans. 26 January 2016 | doi: 10.1038/ncomms10425 Biological Sciences  Chemical biology  Medical research  Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children OPEN Katri Korpela, Anne Salonen, Lauri J. Virta, Riina A. Kekkonen, Kristoffer Forslund, Peer Bork and Willem M. de Vos The impact of antibiotics on the microbiome and health of children is poorly understood. Here, Korpela et al. study the gut microbiome of 142 children and show that the use of macrolides, but not penicillins, is associated with long-lasting shifts in microbiota composition and increased risk of asthma and overweight. 26 January 2016 | doi: 10.1038/ncomms10410 Biological Sciences  Medical research  Microbiology  Intracellular repair of oxidation-damaged α-synuclein fails to target C-terminal modification sites OPEN Andres Binolfi, Antonio Limatola, Silvia Verzini, Jonas Kosten, Francois-Xavier Theillet, Honor May Rose, Beata Bekei, Marchel Stuiver, Marleen van Rossum and Philipp Selenko α-synuclein is a protein linked to the occurrence of Parkinson's disease. Here, the authors use time-resolved in-cell NMR spectroscopy to study the repair of methionine-oxidized α-synuclein by endogenous cellular enzymes. 25 January 2016 | doi: 10.1038/ncomms10251 Biological Sciences  Biochemistry  Neuroscience  Evolutionary signals of selection on cognition from the great tit genome and methylome OPEN Veronika N. Laine, Toni I. Gossmann, Kyle M. Schachtschneider, Colin J. Garroway, Ole Madsen, Koen J. F. Verhoeven, Victor de Jager, Hendrik-Jan Megens, Wesley C. Warren, Patrick Minx, Richard P. M. A. Crooijmans, Pádraic Corcoran, null null, Frank Adriaensen, Eduardo Belda, Andrey Bushuev, Mariusz Cichon, Anne Charmantier, Niels Dingemanse, Blandine Doligez et al. The great tit (Parus major) is known for its complex social-cognitive behaviour. Here, the authors sequence genomes of the great tit and show genes related to learning and cognition in regions under positive selection, as well as neuronal non-CpG methylation patterns similar to those observed in mammals. 25 January 2016 | doi: 10.1038/ncomms10474 Biological Sciences  Genetics  Confinement-deconfinement transition due to spontaneous symmetry breaking in quantum Hall bilayers OPEN D. I. Pikulin, P. G. Silvestrov and T. Hyart Electronic systems with inverted band structures can support exotic topological insulator and exciton condensate states. Here, the authors demonstrate the formation of a helical exciton condensate in quantum Hall bilayers, and a quark-like quasiparticle confinement-deconfinement transition. 25 January 2016 | doi: 10.1038/ncomms10462 Physical Sciences  Condensed matter  Persistent order due to transiently enhanced nesting in an electronically excited charge density wave OPEN L. Rettig, R. Cortés, J.-H. Chu, I. R. Fisher, F. Schmitt, R. G. Moore, Z.-X. Shen, P. S. Kirchmann, M. Wolf and U. Bovensiepen Whilst excited electronic states may exhibit unique non-equilibrium behavior, order is inhibited by fluctuations. Here, the authors use femtosecond photoemission spectroscopy to demonstrate transient stabilization of charge density wave order in rare earth tritellurides after near-infrared excitation. 25 January 2016 | doi: 10.1038/ncomms10459 Physical Sciences  Condensed matter  Functional annotation of rare gene aberration drivers of pancreatic cancer OPEN Yiu Huen Tsang, Turgut Dogruluk, Philip M. Tedeschi, Joanna Wardwell-Ozgo, Hengyu Lu, Maribel Espitia, Nikitha Nair, Rosalba Minelli, Zechen Chong, Fengju Chen, Qing Edward Chang, Jennifer B. Dennison, Armel Dogruluk, Min Li, Haoqiang Ying, Joseph R. Bertino, Marie-Claude Gingras, Michael Ittmann, John Kerrigan, Ken Chen et al. Next generation sequencing allows the identification of oncogenic driver genes in pancreatic cancer. Here, in an effort to identify additional causal genes, the authors develop a high throughput in vivo screen and identify genes that whilst infrequently mutated in pancreatic cancer contribute to tumour formation. 25 January 2016 | doi: 10.1038/ncomms10500 Biological Sciences  Cancer  Genetics  A novel mechanism for the biogenesis of outer membrane vesicles in Gram-negative bacteria OPEN Sandro Roier, Franz G. Zingl, Fatih Cakar, Sanel Durakovic, Paul Kohl, Thomas O. Eichmann, Lisa Klug, Bernhard Gadermaier, Katharina Weinzerl, Ruth Prassl, Achim Lass, Günther Daum, Joachim Reidl, Mario F. Feldman and Stefan Schild Bacteria release outer membrane vesicles (OMVs) that play important roles in pathogenesis and intercellular interactions. Here, Roier et al. provide evidence supporting that phospholipid accumulation in the outer leaflet of the outer membrane participates in OMV formation in Gram-negative bacteria. 25 January 2016 | doi: 10.1038/ncomms10515 Biological Sciences  Cell biology  Microbiology  Structures of the E. coli translating ribosome with SRP and its receptor and with the translocon OPEN Ahmad Jomaa, Daniel Boehringer, Marc Leibundgut and Nenad Ban The co-translational insertion of proteins into membranes requires interaction between a ribosome-bound signal recognition particle (SRP) and a membrane-bound translocon. Here the authors use cryo-EM and single particle reconstructions to obtain a comprehensive view of the co-translational protein targeting process. 25 January 2016 | doi: 10.1038/ncomms10471 Biological Sciences  Biochemistry  Biophysics  Molecular biology  Understanding of multimetallic cluster growth OPEN Stefan Mitzinger, Lies Broeckaert, Werner Massa, Florian Weigend and Stefanie Dehnen Elucidation of formation mechanisms of inorganic cluster compounds is challenging due to the high coordination flexibility of the atoms involved. Here, the authors combine crystallographic and quantum-chemical studies to probe the energy hypersurface of a series of multimetallic clusters. 25 January 2016 | doi: 10.1038/ncomms10480 Chemical Sciences  Inorganic chemistry  Materials science  Shugoshin forms a specialized chromatin domain at subtelomeres that regulates transcription and replication timing OPEN Sanki Tashiro, Tetsuya Handa, Atsushi Matsuda, Takuto Ban, Toru Takigawa, Kazumi Miyasato, Kojiro Ishii, Kazuto Kugou, Kunihiro Ohta, Yasushi Hiraoka, Hisao Masukata and Junko Kanoh A chromosome is composed of structurally and functionally distinct domains. Here, Tashiro et al. report that the conserved centromeric protein Sgo2 localizes at the subtelomeres preferentially during G2 phase and is essential for the formation of a highly condensed subtelomeric chromatin body “knob”. 25 January 2016 | doi: 10.1038/ncomms10393 Biological Sciences  Cell biology  Molecular biology  Quantum algorithms for topological and geometric analysis of data OPEN Seth Lloyd, Silvano Garnerone and Paolo Zanardi Persistent homology allows identification of topological features in data sets, allowing the efficient extraction of useful information. Here, the authors propose a quantum machine learning algorithm that provides an exponential speed up over known algorithms for topological data analysis. 25 January 2016 | doi: 10.1038/ncomms10138 Physical Sciences  Theoretical physics  The architecture of the Schizosaccharomyces pombe CCR4-NOT complex OPEN Marta Ukleja, Jorge Cuellar, Aleksandra Siwaszek, Joanna M. Kasprzak, Mariusz Czarnocki-Cieciura, Janusz M. Bujnicki, Andrzej Dziembowski and Jose M. Valpuesta CCR4-NOT is a protein complex involved in a variety of important genetic processes. Here, the authors report the mid-resolution structure of this complex, and model the positions and contacts between the subunits, providing structural support for the previously reported functions of the complex. 25 January 2016 | doi: 10.1038/ncomms10433 Biological Sciences  Biochemistry  Molecular biology  Membrane potential shapes regulation of dopamine transporter trafficking at the plasma membrane OPEN Ben D. Richardson, Kaustuv Saha, Danielle Krout, Elizabeth Cabrera, Bruce Felts, L. Keith Henry, Jarod Swant, Mu-Fa Zou, Amy Hauck Newman and Habibeh Khoshbouei The dopaminergic system has important roles in a number of cognitive process. Here, the authors use detailed analysis of dopamine transporter trafficking to show its levels at the cell surface are sensitive to changes in membrane potential. 25 January 2016 | doi: 10.1038/ncomms10423 Biological Sciences  Biochemistry  Neuroscience  Electropolymerization on wireless electrodes towards conducting polymer microfibre networks OPEN Yuki Koizumi, Naoki Shida, Masato Ohira, Hiroki Nishiyama, Ikuyoshi Tomita and Shinsuke Inagi Electropolymerization of aromatic monomers on bipolar electrodes is emerging as promising route to the surface modification of conductive objects. Here, the authors discover that some conducting polymers propagate as fibres, opening up the possibility of growing conductive polymer networks via a wireless process. 25 January 2016 | doi: 10.1038/ncomms10404 Chemical Sciences  Materials science  Physical chemistry  Mapping multidimensional electronic structure and ultrafast dynamics with single-element detection and compressive sensing OPEN Austin P. Spencer, Boris Spokoyny, Supratim Ray, Fahad Sarvari and Elad Harel Many spectral regions lack the sensitive pixel array detectors needed for multidimensional spectroscopy. Here, the authors report a method for rapidly collecting multidimensional optical spectra without an array detector, instead utilizing spatial encoding and a single-element detector. 25 January 2016 | doi: 10.1038/ncomms10434 Chemical Sciences  Optical physics  Physical chemistry  Social and novel contexts modify hippocampal CA2 representations of space OPEN Georgia M. Alexander, Shannon Farris, Jason R. Pirone, Chenguang Zheng, Laura L. Colgin and Serena M. Dudek Recent work has implicated hippocampal subfield CA2 in encoding social and contextual memory yet the neural mechanisms are not known. Here, Alexander and colleagues demonstrate that, compared to CA1 neurons, CA2 neurons modify their place fields when presented with social or novel stimuli. 25 January 2016 | doi: 10.1038/ncomms10300 Biological Sciences  Neuroscience  Single-ion adsorption and switching in carbon nanotubes OPEN Adam W. Bushmaker, Vanessa Oklejas, Don Walker, Alan R. Hopkins, Jihan Chen and Stephen B. Cronin Single ion detection is typically performed with large devices rather than microelectronic devices. Here, the authors report the electrical detection of gaseous ions on single isolated carbon nanotubes, with a mechanism proposed based on ion-induced charge depletion in the nanostructures. 25 January 2016 | doi: 10.1038/ncomms10475 Physical Sciences  Applied physics  Condensed matter  Nanotechnology  Ultralow-power switching via defect engineering in germanium telluride phase-change memory devices OPEN Pavan Nukala, Chia-Chun Lin, Russell Composto and Ritesh Agarwal Phase change memories involve crystalline-to-amorphous transformations which require high current densities. Here, the authors introduce extended defects in GeTe crystals, reduce the current densities necessary for amorphization and obtain low-power, scalable memories with multiple resistance states. 25 January 2016 | doi: 10.1038/ncomms10482 Physical Sciences  Applied physics  Materials science  Nanotechnology  Complex disease and phenotype mapping in the domestic dog OPEN Jessica J. Hayward, Marta G. Castelhano, Kyle C. Oliveira, Elizabeth Corey, Cheryl Balkman, Tara L. Baxter, Margret L. Casal, Sharon A. Center, Meiying Fang, Susan J. Garrison, Sara E. Kalla, Pavel Korniliev, Michael I. Kotlikoff, N. S. Moise, Laura M. Shannon, Kenneth W. Simpson, Nathan B. Sutter, Rory J. Todhunter and Adam R. Boyko The domestic dog is an important model organism for our understanding of cancer and other diseases. Here the authors conduct a genome-wide association study across multiple breeds and identify novel loci significantly associated with several complex diseases and morphological traits. 22 January 2016 | doi: 10.1038/ncomms10460 Biological Sciences  Genetics  Dopant-specific unzipping of carbon nanotubes for intact crystalline graphene nanostructures OPEN Joonwon Lim, Uday Narayan Maiti, Na-Young Kim, Rekha Narayan, Won Jun Lee, Dong Sung Choi, Youngtak Oh, Ju Min Lee, Gil Yong Lee, Seok Hun Kang, Hyunwoo Kim, Yong-Hyun Kim and Sang Ouk Kim Atomic level engineering of graphene-based materials is highly demanded for the customized structures and properties. Here, the authors show heteroatom dopant-specific unzipping of carbon nanotubes as a reliable and controllable route to customized 'intact crystalline' graphene-based nanostructures. 22 January 2016 | doi: 10.1038/ncomms10364 Physical Sciences  Materials science  Nanotechnology  Genetic basis for glandular trichome formation in cotton OPEN Dan Ma, Yan Hu, Changqing Yang, Bingliang Liu, Lei Fang, Qun Wan, Wenhua Liang, Gaofu Mei, Lingjian Wang, Haiping Wang, Linyun Ding, Chenguang Dong, Mengqiao Pan, Jiedan Chen, Sen Wang, Shuqi Chen, Caiping Cai, Xiefei Zhu, Xueying Guan, Baoliang Zhou et al. Cotton plants are characterized by the presence of darkly pigmented glands that accumulate metabolites that contribute to plant defence but limit the use of cottonseed as food. Here, Ma et al. provide evidence that GoPGF, a bHLH transcription factor, is responsible for gland formation. 22 January 2016 | doi: 10.1038/ncomms10456 Biological Sciences  Genetics  Plant sciences  Water-walled microfluidics for high-optical finesse cavities OPEN Shai Maayani, Leopoldo L. Martin and Tal Carmon Micrometre-sized spheres of water can trap light, but they quickly evaporate and the light is lost. Here, the authors create water-droplet microcavities that can contain light for one million circulations by replenishing the evaporating fluid from a reservoir. 22 January 2016 | doi: 10.1038/ncomms10435 Physical Sciences  Optical physics  A kagome map of spin liquids from XXZ to Dzyaloshinskii–Moriya ferromagnet OPEN Karim Essafi, Owen Benton and L.D.C. Jaubert Spin systems on the frustrated kagome lattice exhibit classical and quantum spin liquids. Here, the authors present an anisotropic nearest-neighbour model with time-reversal symmetry which incorporates all known spin liquids, as well as promising chiral phases, into a wider unified network. 22 January 2016 | doi: 10.1038/ncomms10297 Physical Sciences  Condensed matter  LSD1 co-repressor Rcor2 orchestrates neurogenesis in the developing mouse brain OPEN Yixuan Wang, Qian Wu, Peng Yang, Chenfei Wang, Jing Liu, Wenyu Ding, Wensu Liu, Ye Bai, Yuanyuan Yang, Hong Wang, Shaorong Gao and Xiaoqun Wang Epigenetic regulation plays a key role in cortical development. Here the authors show that Rcor2, a co-repressor of the histone demethylase LSD1/KDM1A complex, regulates neural progenitor cell proliferation and cortical neurogenesis by repressing sonic hedgehog signaling. 22 January 2016 | doi: 10.1038/ncomms10481 Biological Sciences  Developmental biology  Neuroscience  Controlling molecular transport in minimal emulsions OPEN Philipp Gruner, Birte Riechers, Benoît Semin, Jiseok Lim, Abigail Johnston, Kathleen Short and Jean-Christophe Baret Emulsion droplets have many biotechnological applications, such as parallelized single cell analysis. Here, Gruner et al. introduce the concept of the minimal emulsions in a microfluidic device that allows full control of molecular transport between emulsion droplets. 22 January 2016 | doi: 10.1038/ncomms10392 Physical Sciences  Applied physics  Fluids and plasma physics  The lack of the Celf2a splicing factor converts a Duchenne genotype into a Becker phenotype OPEN J. Martone, F. Briganti, I. Legnini, M. Morlando, E. Picillo, O. Sthandier, L. Politano and I. Bozzoni Muscular Dystrophy can be caused by mutations in the dystrophin gene, causing the severe Duchenne form or the mild Becker form depending on if the transcript is in or out-of-frame. Here the authors identify a Duchenne-type mutation that gives a Becker-like phenotype due to skipping of exon 45. 22 January 2016 | doi: 10.1038/ncomms10488 Biological Sciences  Genetics  Molecular biology  Large deglacial shifts of the Pacific Intertropical Convergence Zone OPEN A. W. Jacobel, J. F. McManus, R. F. Anderson and G. Winckler The extent to which the location of the Intertropical Convergence Zone (ITCZ)—a primary influence over tropical hydrology—varied in the past remains uncertain. Here, the authors use a transect of marine sediment cores to quantify latitudinal migrations of the ITCZ during the penultimate deglaciation. 22 January 2016 | doi: 10.1038/ncomms10449 Earth Sciences  Biogeochemistry  Climate science  Subwavelength nonlinear phase control and anomalous phase matching in plasmonic metasurfaces OPEN Euclides Almeida, Guy Shalem and Yehiam Prior The fundamental issue of phase-matching across metasurfaces has not been thoroughly addressed. Here, Almeida et al. show full phase control by introducing a spatially varying phase response of a metallic metasurface consisting of subwavelength nanoantennas and demonstrate metasurface-phase-matching. 22 January 2016 | doi: 10.1038/ncomms10367 Physical Sciences  Nanotechnology  Optical physics  Broadband single-molecule excitation spectroscopy OPEN Lukasz Piatkowski, Esther Gellings and Niek F. van Hulst In single-molecule spectroscopy typically only emission spectra are recorded. Here, the authors develop a technique to record single-molecule excitation spectra under ambient conditions, which is robust against blinking and bleaching, and reveals a large distribution of spectra across the molecule ensemble. 22 January 2016 | doi: 10.1038/ncomms10411 Physical Sciences  Nanotechnology  Optical physics  Physical chemistry  Octanol-assisted liposome assembly on chip OPEN Siddharth Deshpande, Yaron Caspi, Anna E. C. Meijering and Cees Dekker A broad application of liposomes calls for high throughout techniques to produce them in a controlled and fast manner. Here, Deshpande et al. show a microfluidic approach using alcohol-based lipid-carrying material to generate monodisperse and unilamellar liposomes within a just few minutes. 22 January 2016 | doi: 10.1038/ncomms10447 Biological Sciences  Biotechnology  Fluids and plasma physics  Unexpected seasonality in quantity and composition of Amazon rainforest air reactivity OPEN A. C. Nölscher, A. M. Yañez-Serrano, S. Wolff, A. Carioca de Araujo, J. V. Lavrič, J. Kesselmeier and J. Williams The degree to which biogenic volatile organic compounds released by the Amazon canopy impact oxidation capacity remains uncertain. Here, the authors evaluate the vertical distribution of total hydroxyl radical reactivity and individual trace gases in the Amazon rainforest, and determine seasonal variations. 22 January 2016 | doi: 10.1038/ncomms10383 Earth Sciences  Atmospheric science  Biogeochemistry  Climate science  Multilayer block copolymer meshes by orthogonal self-assembly OPEN Amir Tavakkoli K. G., Samuel M. Nicaise, Karim R. Gadelrab, Alfredo Alexander-Katz, Caroline A. Ross and Karl K. Berggren Block copolymer self-assembly can successfully generate monolayers of complex nanopatterns. Here, the authors orthogonally self-assemble 2 or 3 layers of distinct molecular weight block copolymers, and fabricate complex nanomesh structures without alignment or high-resolution lithographic templating. 22 January 2016 | doi: 10.1038/ncomms10518 Physical Sciences  Materials science  Nanotechnology  p38γ and δ promote heart hypertrophy by targeting the mTOR-inhibitory protein DEPTOR for degradation OPEN Bárbara González-Terán, Juan Antonio López, Elena Rodríguez, Luis Leiva, Sara Martínez-Martínez, Juan Antonio Bernal, Luis Jesús Jiménez-Borreguero, Juan Miguel Redondo, Jesús Vazquez and Guadalupe Sabio mTOR signalling pathway is a critical regulator of cardiac hypertrophy. Here the authors show that two kinases, p38γ and p38δ, control heart growth by promoting mTOR activity via phosphorylation and consequent proteasome degradation of mTOR inhibitor DEPTOR, extending our knowledge of cardiac hypertrophy regulation. 22 January 2016 | doi: 10.1038/ncomms10477 Biological Sciences  Cell biology  Medical research  Functional profiles of orphan membrane transporters in the life cycle of the malaria parasite OPEN Sanketha Kenthirapalan, Andrew P. Waters, Kai Matuschewski and Taco W. A. Kooij The functions of many putative membrane transport proteins of malaria parasites are unknown. Here, Kenthirapalan et al. use mutant strains carrying targeted gene deletions to study the functions of 35 such proteins during the life cycle of Plasmodium berghei in mosquito and mouse hosts. 22 January 2016 | doi: 10.1038/ncomms10519 Biological Sciences  Cell biology  Genetics  Microbiology  Nanoscale manipulation of the Mott insulating state coupled to charge order in 1T-TaS2 OPEN Doohee Cho, Sangmo Cheon, Ki-Seok Kim, Sung-Hoon Lee, Yong-Heum Cho, Sang-Wook Cheong and Han Woong Yeom Controlled switching between states in materials with strong electronic correlations can form the basis for functional devices. Here, the authors use a scanning tunnelling microscope tip to switch between a Mott insulator state and a metallic state with charge-density-wave domains in 1T-TaS2. 22 January 2016 | doi: 10.1038/ncomms10453 Physical Sciences  Condensed matter  Producing air-stable monolayers of phosphorene and their defect engineering OPEN Jiajie Pei, Xin Gai, Jiong Yang, Xibin Wang, Zongfu Yu, Duk-Yong Choi, Barry Luther-Davies and Yuerui Lu It has been a long-standing challenge to produce air-stable few- or monolayer phosphorene. Here, the authors demonstrate a new highly controllable method for fabricating high quality, air-stable mono- and few-layer phosphorene films, enabling precise defect engineering in monolayer phosphorene. 22 January 2016 | doi: 10.1038/ncomms10450 Physical Sciences  Materials science  Nanotechnology  Recent increases in Arctic freshwater flux affects Labrador Sea convection and Atlantic overturning circulation OPEN Qian Yang, Timothy H. Dixon, Paul G. Myers, Jennifer Bonin, Don Chambers and M. R. van den Broeke Labrador Sea convection and the Atlantic overturning circulation are sensitive to surface freshening of the North Atlantic. Here, the authors show that the recent increases in Arctic freshwater flux can directly weaken Labrador Sea convection and potentially affect the overturning circulation. 22 January 2016 | doi: 10.1038/ncomms10525 Earth Sciences  Climate science  Oceanography  Cavity-excited Huygens’ metasurface antennas for near-unity aperture illumination efficiency from arbitrarily large apertures OPEN Ariel Epstein, Joseph P. S. Wong and George V. Eleftheriades The realization of highly-directive beams using low-profile devices has been a long-standing problem. Here, Epstein et al. demonstrate a cavity-excited Huygens’ metasurface antenna, where the single-source-fed cavity is designed to optimize aperture illumination, while the metasurface facilitates phase purity. 21 January 2016 | doi: 10.1038/ncomms10360 Physical Sciences  Applied physics  Optical physics  Manipulating Majorana zero modes on atomic rings with an external magnetic field OPEN Jian Li, Titus Neupert, B. Andrei Bernevig and Ali Yazdani Majorana fermions, particles which are their own antiparticles, are predicted to exist in systems combining superconductivity and topologically non-trivial band structure. Here, the authors propose means to create and manipulate such excitations in one-dimensional chains of adatoms on superconducting surfaces. 21 January 2016 | doi: 10.1038/ncomms10395 Physical Sciences  Condensed matter  Pin1At regulates PIN1 polar localization and root gravitropism OPEN Wanyan Xi, Ximing Gong, Qiaoyun Yang, Hao Yu and Yih-Cherng Liou Asymmetric transport of auxin allows plants to orient growth of their roots towards gravity. Here, the authors show that the peptidyl-prolyl cis/trans isomerase Pin1At contributes to root gravitropism and propose that it acts by altering the polarity of the PIN1 auxin transport protein. 21 January 2016 | doi: 10.1038/ncomms10430 Biological Sciences  Plant sciences  Imaging tumour cell heterogeneity following cell transplantation into optically clear immune-deficient zebrafish OPEN Qin Tang, John C. Moore, Myron S. Ignatius, Inês M. Tenente, Madeline N. Hayes, Elaine G. Garcia, Nora Torres Yordán, Caitlin Bourque, Shuning He, Jessica S. Blackburn, A. Thomas Look, Yariv Houvras and David M. Langenau Direct visualisation of heterogeneous cell populations in live animals has been challenging. Here, the authors optimize cell transplantation into optically clear immune-deficient zebrafish, and use intravital imaging to track and to assess functional diversity of individual cancer cells in vivo. 21 January 2016 | doi: 10.1038/ncomms10358 Biological Sciences  Cancer  Conformation and dynamics of the ligand shell of a water-soluble Au102 nanoparticle OPEN Kirsi Salorinne, Sami Malola, O. Andrea Wong, Christopher D. Rithner, Xi Chen, Christopher J. Ackerson and Hannu Häkkinen The core structure of inorganic nanoparticles, stabilized by a passivating layer of organic molecules, is often known but information about the organic layer is tougher to derive. Here, the authors use NMR and computational methods to probe the ligand disorder and visualize possible ligand conformations. 21 January 2016 | doi: 10.1038/ncomms10401 Chemical Sciences  Inorganic chemistry  Nanotechnology  Axotomy-induced HIF-serotonin signalling axis promotes axon regeneration in C. elegans OPEN Tanimul Alam, Hiroki Maruyama, Chun Li, Strahil Iv. Pastuhov, Paola Nix, Michael Bastiani, Naoki Hisamoto and Kunihiro Matsumoto The molecular mechanism of axon regeneration after injury is poorly understood. Here the authors show that in C. elegans, the HIF-1 transcription factor induces ectopic synthesis of serotonin in severed ‘non-serotonergic’ neurons and that serotonin activates downstream signaling pathways leading to axon regeneration. 21 January 2016 | doi: 10.1038/ncomms10388 Biological Sciences  Cell biology  Neuroscience  Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code OPEN Alexey Rozov, Natalia Demeshkina, Iskander Khusainov, Eric Westhof, Marat Yusupov and Gulnara Yusupova The anticodon loops of almost all tRNAs contain modifications known to be important for their function. Here the authors use crystallography to provide new mechanistic insights into how the modification at the wobble position of the E. coli tRNALysUUU assists in discrimination between cognate and near-cognate codons. 21 January 2016 | doi: 10.1038/ncomms10457 Biological Sciences  Biochemistry  Biophysics  Molecular biology  The novel tumour suppressor Madm regulates stem cell competition in the Drosophila testis OPEN Shree Ram Singh, Ying Liu, Jiangsha Zhao, Xiankun Zeng and Steven X. Hou Stem cell competition mediates the balance between tissue homeostasis and tumour formation, but how this occurs is unclear. Here, Singh et al. show that the tumour suppressor Mlfl-adaptor molecule regulates the balance between germline stem cell and somatic cyst stem cell growth in the Drosophila testis niche. 21 January 2016 | doi: 10.1038/ncomms10473 Biological Sciences  Cell biology  Developmental biology  Biochemical characterization of predicted Precambrian RuBisCO OPEN Patrick M. Shih, Alessandro Occhialini, Jeffrey C. Cameron, P John Andralojc, Martin A. J. Parry and Cheryl A. Kerfeld The enzyme RuBisCO has evolved over billions of years and catalyses reactions in plants and bacteria, although why some reactions persist is unclear. Here, the authors resurrect ancestral RuBisCO to reveal aspects of the Precambrian atmosphere and the selective pressures governing RuBisCO evolution. 21 January 2016 | doi: 10.1038/ncomms10382 Earth Sciences  Biogeochemistry  Evolution  Engineered Mott ground state in a LaTiO3+δ/LaNiO3 heterostructure OPEN Yanwei Cao, Xiaoran Liu, M. Kareev, D. Choudhury, S. Middey, D. Meyers, J.-W. Kim, P. J. Ryan, J.W. Freeland and J. Chakhalian Interfaces between two dissimilar transition metal oxides can exhibit emergent strongly correlated electronic and magnetic states due to charge transfer and electronic reconfiguration. Here, the authors synthesize and investigate an exotic Mott ground state in LaTiO3+δ/LaNiO3 heterostructures. 21 January 2016 | doi: 10.1038/ncomms10418 Physical Sciences  Condensed matter  Quantum interference in heterogeneous superconducting-photonic circuits on a silicon chip OPEN C. Schuck, X. Guo, L. Fan, X. Ma, M. Poot and H. X. Tang Scaling photonic quantum information processing approaches remains challenging for integrated quantum optics. Here, Schuck et al. develop a hybrid superconducting-photonic circuit system to show how quantum interference and single-photon detectors can be combined in a scalable fashion on a silicon chip. 21 January 2016 | doi: 10.1038/ncomms10352 Physical Sciences  Nanotechnology  Optical physics  D25V apolipoprotein C-III variant causes dominant hereditary systemic amyloidosis and confers cardiovascular protective lipoprotein profile OPEN Sophie Valleix, Guglielmo Verona, Noémie Jourde-Chiche, Brigitte Nédelec, P. Patrizia Mangione, Frank Bridoux, Alain Mangé, Ahmet Dogan, Jean-Michel Goujon, Marie Lhomme, Carolane Dauteuille, Michèle Chabert, Riccardo Porcari, Christopher A. Waudby, Annalisa Relini, Philippa J. Talmud, Oleg Kovrov, Gunilla Olivecrona, Monica Stoppini, John Christodoulou et al. Decrease in Apolipoprotein C-III (ApoC-III) yields a cardioprotective lipoprotein profile. Here, Valleix et al. reveal a novel ApoC-III variant conferring low plasma ApoC-III concentration and cardioprotection despite renal insufficiency, and, unexpectedly, causing dominant hereditary systemic amyloidosis due to its fibrillogenic nature. 21 January 2016 | doi: 10.1038/ncomms10353 Biological Sciences  Medical research  Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function OPEN Cristian Pattaro, Alexander Teumer, Mathias Gorski, Audrey Y. Chu, Man Li, Vladan Mijatovic, Maija Garnaas, Adrienne Tin, Rossella Sorice, Yong Li, Daniel Taliun, Matthias Olden, Meredith Foster, Qiong Yang, Ming-Huei Chen, Tune H. Pers, Andrew D. Johnson, Yi-An Ko, Christian Fuchsberger, Bamidele Tayo et al. Reduced glomerular filtration rate (eGFR) is a hallmark of chronic kidney disease. Here, Pattaro et al. conduct a meta-analysis to discover several new loci associated with variation in eGFR and find that genes associated with eGFR loci often encode proteins potentially related to kidney development. 21 January 2016 | doi: 10.1038/ncomms10023 Biological Sciences  Genetics  Human brain networks function in connectome-specific harmonic waves OPEN Selen Atasoy, Isaac Donnelly and Joel Pearson Inter-areal oscillatory synchronization is constrained by anatomical connections, yet a fundamental principle linking functional and structural connectivity is lacking. Here, Atasoy and colleagues show that harmonic patterns in structural connectome can predict dynamics of resting state networks. 21 January 2016 | doi: 10.1038/ncomms10340 Biological Sciences  Neuroscience  4π-periodic Josephson supercurrent in HgTe-based topological Josephson junctions OPEN J. Wiedenmann, E. Bocquillon, R. S. Deacon, S. Hartinger, O. Herrmann, T. M. Klapwijk, L. Maier, C. Ames, C. Brüne, C. Gould, A. Oiwa, K. Ishibashi, S. Tarucha, H. Buhmann and L. W. Molenkamp A material weakly linking two superconductors may itself exhibit superconductivity whilst its material properties strongly influence the nature of the supercurrent. Here, the authors identify a supercurrent with p-wave symmetry in such a Josephson junction made of topologically non-trivial material. 21 January 2016 | doi: 10.1038/ncomms10303 Physical Sciences  Condensed matter  Substantial bulk photovoltaic effect enhancement via nanolayering OPEN Fenggong Wang, Steve M. Young, Fan Zheng, Ilya Grinberg and Andrew M. Rappe Spontaneous polarization in ferroelectric materials leads to their use as photovoltaic devices. Here, the authors show by first-principles calculations how nanolayering of PbTiO3 with nickel ions and oxygen vacancies can result in enhanced photocurrents due to smaller bandgaps and photocurrent alignment. 21 January 2016 | doi: 10.1038/ncomms10419 Physical Sciences  Applied physics  Materials science  Nanotechnology  Prevention of Treacher Collins syndrome craniofacial anomalies in mouse models via maternal antioxidant supplementation OPEN Daisuke Sakai, Jill Dixon, Annita Achilleos, Michael Dixon and Paul A. Trainor The TCOF1 gene is mutated in Treacher Collin's syndrome, a congenital craniofacial syndrome. Here, the authors show that Tcof1 loss-of-function results in oxidative stress induced DNA damage and neuroepithelial cell death, and addition of antioxidants to pregnant mutant mice protected against these defects. 21 January 2016 | doi: 10.1038/ncomms10328 Biological Sciences  Cell biology  Developmental biology  Bacteria increase arid-land soil surface temperature through the production of sunscreens OPEN Estelle Couradeau, Ulas Karaoz, Hsiao Chien Lim, Ulisses Nunes da Rocha, Trent Northen, Eoin Brodie and Ferran Garcia-Pichel Soil surface temperature, which affects many biogeochemical processes, depends on soil albedo. Here, Couradeau et al. show that some cyanobacteria can increase the temperature of arid-land soil surface by as much as 10 °C through the accumulation of a sunscreen metabolite. 20 January 2016 | doi: 10.1038/ncomms10373 Biological Sciences  Biogeochemistry  Ecology  Microbiology  Giant phonon anomaly associated with superconducting fluctuations in the pseudogap phase of cuprates OPEN Ye-Hua Liu, Robert M. Konik, T. M. Rice and Fu-Chun Zhang The emergence of a giant phonon anomaly in the pseudogap phase of underdoped cuprate superconductors has been assumed to be a consequence of instability towards a charge density wave state. Here, the authors present a theory suggesting the anomaly arises due to large superconducting fluctuations. 20 January 2016 | doi: 10.1038/ncomms10378 Physical Sciences  Condensed matter  Unveiling the structural arrangements responsible for the atomic dynamics in metallic glasses during physical aging OPEN V. M. Giordano and B Ruta Glass aging is one of unsolved problems during glass processing and annealing, partly due to the lack of the mechanistic understanding on microscales. Here, the authors show how local stresses and their evolution affect structural relaxation at an atomic level in a metallic glass system. 20 January 2016 | doi: 10.1038/ncomms10344 Physical Sciences  Condensed matter  Materials science  In vivo covalent cross-linking of photon-converted rare-earth nanostructures for tumour localization and theranostics OPEN Xiangzhao Ai, Chris Jun Hui Ho, Junxin Aw, Amalina Binte Ebrahim Attia, Jing Mu, Yu Wang, Xiaoyong Wang, Yong Wang, Xiaogang Liu, Huabing Chen, Mingyuan Gao, Xiaoyuan Chen, Edwin K.L. Yeow, Gang Liu, Malini Olivo and Bengang Xing Directing nanomedicines to desired locations - such as tumour sites - is difficult to achieve selectively. Here, the authors develop a method to covalently crosslink peptide-modified upconversion nanocrystals into tumour sites for photodynamic therapy and show in vivo tumour inhibition in mice. 20 January 2016 | doi: 10.1038/ncomms10432 Chemical Sciences  Chemical biology  Medicinal chemistry  Nanotechnology  Removal of the mechanoprotective influence of the cytoskeleton reveals PIEZO1 is gated by bilayer tension OPEN Charles D. Cox, Chilman Bae, Lynn Ziegler, Silas Hartley, Vesna Nikolova-Krstevski, Paul R. Rohde, Chai-Ann Ng, Frederick Sachs, Philip A. Gottlieb and Boris Martinac PIEZO1 is a mechanosensitive ion channel, but the mechanism of force transduction is unknown. Here Cox and Bae et al. disrupt the cortical cytoskeleton in HEK293 cells to show that PIEZO1 is gated directly by membrane tension. 20 January 2016 | doi: 10.1038/ncomms10366 Biological Sciences  Biophysics  Cell biology  Conversion of graded phosphorylation into switch-like nuclear translocation via autoregulatory mechanisms in ERK signalling OPEN Yuki Shindo, Kazunari Iwamoto, Kazunari Mouri, Kayo Hibino, Masaru Tomita, Hidetaka Kosako, Yasushi Sako and Koichi Takahashi While ERK signalling can produce switch-like cell behaviour, phosphorylation of ERK increases linearly with extracellular signals. Here, the authors solve this seeming contradiction by showing that nuclear translocation of ERK behaves in a switch-like manner and is controlled by ERK activity. 20 January 2016 | doi: 10.1038/ncomms10485 Biological Sciences  Cell biology  Systems biology  Nanoscale visualization of functional adhesion/excitability nodes at the intercalated disc OPEN Alejandra Leo-Macias, Esperanza Agullo-Pascual, Jose L. Sanchez-Alonso, Sarah Keegan, Xianming Lin, Tatiana Arcos, Feng-Xia-Liang, Yuri E. Korchev, Julia Gorelik, David Fenyö, Eli Rothenberg and Mario Delmar In myelinated fibres conduction and adhesion proteins aggregate at discrete foci, but it is unclear if this organization is present in other excitable cells. Using nanoscale visualization and in silico techniques, the authors show that adhesion/excitability nodes exist at the intercalated discs of adult cardiac muscle. 20 January 2016 | doi: 10.1038/ncomms10342 Biological Sciences  Medical research  Protein unfolding as a switch from self-recognition to high-affinity client binding OPEN Bastian Groitl, Scott Horowitz, Karl A. T. Makepeace, Evgeniy V. Petrotchenko, Christoph H. Borchers, Dana Reichmann, James C. A. Bardwell and Ursula Jakob Under stress conditions the molecular chaperone Hsp33 is activated to process unfolded proteins. Here, the authors use in vivo and in vitro crosslinking and 19F-NMR to elucidate the binding site for misfolded proteins and are able to propose a model for its mechanism of action. 20 January 2016 | doi: 10.1038/ncomms10357 Biological Sciences  Biochemistry  Endoplasmic reticulum stress drives proteinuria-induced kidney lesions via Lipocalin 2 OPEN Khalil El Karoui, Amandine Viau, Olivier Dellis, Alessia Bagattin, Clément Nguyen, William Baron, Martine Burtin, Mélanie Broueilh, Laurence Heidet, Géraldine Mollet, Anne Druilhe, Corinne Antignac, Bertrand Knebelmann, Gérard Friedlander, Frank Bienaimé, Morgan Gallazzini and Fabiola Terzi Proteinuria promotes chronic kidney disease progression. Karoui et al. show that proteinuria stimulates overexpression of iron transporting protein lipocalin-2 via Ca2+ release-induced ER stress, which leads to tubular apoptosis, and that inhibition of this pathway by PBA delays renal deterioration in proteinuric mice. 20 January 2016 | doi: 10.1038/ncomms10330 Biological Sciences  Cell biology  Medical research  A vacuolar iron-transporter homologue acts as a detoxifier in Plasmodium OPEN Ksenija Slavic, Sanjeev Krishna, Aparajita Lahree, Guillaume Bouyer, Kirsten K. Hanson, Iset Vera, Jon K. Pittman, Henry M. Staines and Maria M. Mota Iron is an essential nutrient but, in high concentrations, it is also toxic to cells. Here, Slavic et al. identify an iron transporter in malaria parasites that plays a major role in iron detoxification and is required for the parasite’s normal development. 20 January 2016 | doi: 10.1038/ncomms10403 Biological Sciences  Cell biology  Microbiology  ssODN-mediated knock-in with CRISPR-Cas for large genomic regions in zygotes OPEN Kazuto Yoshimi, Yayoi Kunihiro, Takehito Kaneko, Hitoshi Nagahora, Birger Voigt and Tomoji Mashimo CRISPR-Cas9 is a powerful genome engineering tool but gene knock-in is limited by fragment size and efficiency of recombination. Here the authors used a modified strategy employing single-strand oligonucleotides to efficiently knock-in large DNA fragments and humanise native rat loci. 20 January 2016 | doi: 10.1038/ncomms10431 Biological Sciences  Genetics  Molecular biology  The onset of visual experience gates auditory cortex critical periods OPEN Todd M. Mowery, Vibhakar C. Kotak and Dan H. Sanes Visual and auditory systems influence each other during development. Here, the authors show that the onset of eyelid opening regulates critical points during which the auditory cortex is sensitive to hearing loss or the restoration of hearing 20 January 2016 | doi: 10.1038/ncomms10416 Biological Sciences  Neuroscience  Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments OPEN Remy Chait, Adam C. Palmer, Idan Yelin and Roy Kishony Antibiotic concentrations are low in most natural environments, except around localized antibiotic sources. Here, Chait et al. show that sub-inhibitory antibiotic levels can interact with many other stresses to generate complex patterns of selection for and against resistance to the antibiotic. 20 January 2016 | doi: 10.1038/ncomms10333 Biological Sciences  Ecology  Evolution  Microbiology  CLIC4 regulates apical exocytosis and renal tube luminogenesis through retromer- and actin-mediated endocytic trafficking OPEN Szu-Yi Chou, Kuo-Shun Hsu, Wataru Otsu, Ya-Chu Hsu, Yun-Cin Luo, Celine Yeh, Syed S. Shehab, Jie Chen, Vincent Shieh, Guo-an He, Michael B. Marean, Diane Felsen, Aihao Ding, Dix P. Poppas, Jen-Zen Chuang and Ching-Hwa Sung Chloride intracellular channel (CLIC) 4 is an ion channel, localized in the cytoplasm, and first identified as an actin binding protein. Here, Chou et al. knockout CLIC4 in mice and observe tubulogenesis and renal proximal tubule dilation defects, which is caused by irregular actin and endosomal trafficking. 20 January 2016 | doi: 10.1038/ncomms10412 Biological Sciences  Cell biology  Developmental biology  Pulse-density modulation control of chemical oscillation far from equilibrium in a droplet open-reactor system OPEN Haruka Sugiura, Manami Ito, Tomoya Okuaki, Yoshihito Mori, Hiroyuki Kitahata and Masahiro Takinoue Biological systems typically operate at conditions far from chemical equilibrium. Here, the authors model and develop a microfluidic reactor allowing control over time-variable supply and dissipation of chemicals by droplet fusion and fission, allowing non-equilibrium chemical reactions to be regulated. 20 January 2016 | doi: 10.1038/ncomms10212 Chemical Sciences  Applied physics  Physical chemistry  Bcl-xL promotes metastasis independent of its anti-apoptotic activity OPEN Soyoung Choi, Zhengming Chen, Laura H. Tang, Yuanzhang Fang, Sandra J. Shin, Nicole C. Panarelli, Yao-Tseng Chen, Yi Li, Xuejun Jiang and Yi-Chieh Nancy Du Bcl-xL is an anti-apoptotic protein that has also been implicated in metastasis. In this study, the authors show that nuclear Bcl-xL promotes metastasis by regulating TGFβ signaling, which is independent of the anti-apoptotic activity of Bcl-xL. 20 January 2016 | doi: 10.1038/ncomms10384 Biological Sciences  Cancer  Cell biology  Nanometre-thick single-crystalline nanosheets grown at the water–air interface OPEN Fei Wang, Jung-Hun Seo, Guangfu Luo, Matthew B. Starr, Zhaodong Li, Dalong Geng, Xin Yin, Shaoyang Wang, Douglas G. Fraser, Dane Morgan, Zhenqiang Ma and Xudong Wang The recently discovered phenomena arising from 2D nanomaterials have led to an increased interest in the fabrication of other ultrathin materials from those typically only observed in the bulk. Here, the authors demonstrate the synthesis of micron-sized, single-crystalline ZnO nanosheets via solution based methods. 20 January 2016 | doi: 10.1038/ncomms10444 Chemical Sciences  Materials science  Nanotechnology  Quantifying the origin of metallic glass formation OPEN W. L. Johnson, J. H. Na and M. D. Demetriou The crystal formation waiting time of a homogeneous supercooled liquid exhibits a pronounced minimum depending on temperature, and this minimum is a measure of glass forming ability. Here, the authors propose an expression for this minimum for all metallic glasses that depends only on two fitting parameters. 20 January 2016 | doi: 10.1038/ncomms10313 Physical Sciences  Materials science    Nature Communications JOBS of the week Postdoctoral Research Associate The Scripps Research Institute - Florida Junior Research Group Leader positions IBEC (Institute for Bioengineering of Catalonia) Research Assistant University of Bristol Senior Laboratory Research Scientist Francis Crick Institute Institut Curie COFUND International PhD Program - 12 PhD positions in October 2016 Institut Curie Postdoctoral Research Fellow Cardiovascular Research Center - Mass General Hosp Post doctoral fellow in neuroscience Uppsala University PhD Positions Medical University Graz Research Associate University of Glasgow Research Technician University of Exeter More Science jobs from Nature Communications EVENT Techniques &Applications of Molecular Biology 11.07.16 Coventry, UK More science events from       Latest Corrigendum     Corrigendum: Impaired protein translation in Drosophila models for Charcot–Marie–Tooth neuropathy caused by mutant tRNA synthetases OPEN Sven Niehues, Julia Bussmann, Georg Steffes, Ines Erdmann, Caroline Köhrer, Litao Sun, Marina Wagner, Kerstin Schäfer, Guangxia Wang, Sophia N. Koerdt, Morgane Stum, Sumit Jaiswal, Uttam L. RajBhandary, Ulrich Thomas, Hermann Aberle, Robert W. Burgess, Xiang-Lei Yang, Daniela Dieterich and Erik Storkebaum 21 January 2016 | doi: 10.1038/ncomms10497 Biological Sciences  Molecular biology  Neuroscience  Systems biology        Latest Erratum     Erratum: Ankyrin-mediated self-protection during cell invasion by the bacterial predator Bdellovibrio bacteriovorus OPEN Carey Lambert, Ian T. Cadby, Rob Till, Nhat Khai Bui, Thomas R. Lerner, William S. Hughes, David J. Lee, Luke J. Alderwick, Waldemar Vollmer, R. Elizabeth Sockett and Andrew L. Lovering 21 January 2016 | doi: 10.1038/ncomms10483 Biological Sciences  Biochemistry  Microbiology  Molecular biology      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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