Nature Communications - 16 August 2018

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October 15-17, 2018 | Shanghai, China REGISTER NOW >> Journal homepage Recommend to library Web feed     Latest Review View all Articles     Resolution of chronic inflammatory disease: universal and tissue-specific concepts OPEN Georg Schett & Markus F. Neurath Inflammation is a component of many chronic inflammatory diseases and yet it is understudied in medicine. Here, the authors review novel insights in to inflammation and how impairment of its resolution can lead to diseases. 15 August 2018 | doi: 10.1038/s41467-018-05800-6 Cytokines  Gastroenterology  Inflammation  Rheumatology        Latest Articles View all Articles     Gene essentiality landscape and druggable oncogenic dependencies in herpesviral primary effusion lymphoma OPEN Mark Manzano, Ajinkya Patil, Alexander Waldrop, Sandeep S. Dave, Amir Behdad & Eva Gottwein Our understanding of the genetics and treatment options for primary effusion lymphoma (PEL) is lacking. Here the authors performed in vitro CRISPR/Cas9 knock-out screens to identify 210 PEL-specific oncogenic genes and report strategies for therapeutic intervention. 15 August 2018 | doi: 10.1038/s41467-018-05506-9 Cancer  Microbiology  Inhibition of IRE1 RNase activity modulates the tumor cell secretome and enhances response to chemotherapy OPEN Susan E. Logue, Eoghan P. McGrath, Patricia Cleary, Stephanie Greene, Katarzyna Mnich, Aitor Almanza, Eric Chevet, Róisín M. Dwyer, Anup Oommen, Patrick Legembre, Florence Godey, Emma C. Madden, Brian Leuzzi, Joanna Obacz, Qingping Zeng, John B. Patterson, Richard Jäger, Adrienne M. Gorman & Afshin Samali IRE1/XBP-1 activation has a major role in Triple negative breast cancer (TNBC). Here, the authors show that inhibition of IRE1’s RNase activity attenuates autocrine and paracrine signaling of pro-tumorigenic cytokines and synergizes with paclitaxel to confer potent anti-tumor effects in TNBC. 15 August 2018 | doi: 10.1038/s41467-018-05763-8 Breast cancer  Cancer stem cells  Ohmic transition at contacts key to maximizing fill factor and performance of organic solar cells OPEN Jun-Kai Tan, Rui-Qi Png, Chao Zhao & Peter K. H. Ho The importance of ohmic contacts for organic solar cells has been recognized, but how the transition to ohmic behavior occurs is unknown. Tan et al. show that this transition happens separately beyond Fermi-level pinning, when the interfacial contact resistivity becomes sufficiently low. 15 August 2018 | doi: 10.1038/s41467-018-05200-w Electronic devices  Green photonics  Molecular electronics  The first transmembrane region of complement component-9 acts as a brake on its self-assembly OPEN Bradley A. Spicer, Ruby H. P. Law, Tom T. Caradoc-Davies, Sue M. Ekkel, Charles Bayly-Jones, Siew-Siew Pang, Paul J. Conroy, Georg Ramm, Mazdak Radjainia, Hariprasad Venugopal, James C. Whisstock & Michelle A. Dunstone The Complement component 9 (C9) is the pore-forming component of the Membrane Attack Complex which targets pathogens. Here authors use structural biology to compare monomeric C9 to C9 within the polymeric assembly and identify the element which inhibits C9 self-assembly in the absence of the target membrane. 15 August 2018 | doi: 10.1038/s41467-018-05717-0 Biochemistry  Complement cascade  Electron microscopy  Immunology  Structural biology  21st-century modeled permafrost carbon emissions accelerated by abrupt thaw beneath lakes OPEN Katey Walter Anthony, Thomas Schneider von Deimling, Ingmar Nitze, Steve Frolking, Abraham Emond, Ronald Daanen, Peter Anthony, Prajna Lindgren, Benjamin Jones & Guido Grosse Permafrost carbon feedback modeling has focused on gradual thaw of near-surface permafrost leading to greenhouse gas emissions that accelerate climate change. Here the authors show that deeper, abrupt thaw beneath lakes will more than double radiative forcing from permafrost-soil carbon fluxes this century. 15 August 2018 | doi: 10.1038/s41467-018-05738-9 Carbon cycle  Cryospheric science  Limnology  Distributed natural gas venting offshore along the Cascadia margin OPEN M. Riedel, M. Scherwath, M. Römer, M. Veloso, M. Heesemann & G. D. Spence Methane venting is a widespread phenomenon at the Cascadia margin, however a comprehensive database of methane vents at this margin is lacking. Here the authors show that the margin-wide average methane flow-rate ranges from ~4 × 106 to ~1590 × 106 kg y−1 and is on average around 88 ± 6 × 106 kg y−1. 15 August 2018 | doi: 10.1038/s41467-018-05736-x Carbon cycle  Geophysics  Ocean sciences  Genome‐wide mapping of plasma protein QTLs identifies putatively causal genes and pathways for cardiovascular disease OPEN Chen Yao, George Chen, Ci Song, Joshua Keefe, Michael Mendelson, Tianxiao Huan, Benjamin B. Sun, Annika Laser, Joseph C. Maranville, Hongsheng Wu, Jennifer E. Ho, Paul Courchesne, Asya Lyass, Martin G. Larson, Christian Gieger, Johannes Graumann, Andrew D. Johnson, John Danesh, Heiko Runz, Shih-Jen Hwang et al. Genetic variation can influence levels of disease-related plasma proteins and, thus, contribute to the pathogenesis of complex diseases. Here, the authors perform genome-wide QTL analysis for 71 plasma proteins to identify causal proteins for coronary heart disease and provide a molecular QTL browser. 15 August 2018 | doi: 10.1038/s41467-018-05512-x Cardiovascular genetics  Genetic variation  Proteome  Quantitative trait  Decoding topologically associating domains with ultra-low resolution Hi-C data by graph structural entropy OPEN Angsheng Li, Xianchen Yin, Bingxiang Xu, Danyang Wang, Jimin Han, Yi Wei, Yun Deng, Ying Xiong & Zhihua Zhang Accurate detection of TADs requires ultra-deep sequencing and sophisticated normalisation procedures, which limits the analysis of Hi-C data. Here the authors develop a normalisation-free method to decode the domains of chromosomes (deDoc) that utilizes structural entropy to predict TADs with ultra-low sequencing data. 15 August 2018 | doi: 10.1038/s41467-018-05691-7 Chromatin structure  Computational biology and bioinformatics  Genome informatics  Modularity  Confined small-sized cobalt catalysts stimulate carbon-chain growth reversely by modifying ASF law of Fischer–Tropsch synthesis OPEN Qingpeng Cheng, Ye Tian, Shuaishuai Lyu, Na Zhao, Kui Ma, Tong Ding, Zheng Jiang, Lihua Wang, Jing Zhang, Lirong Zheng, Fei Gao, Lin Dong, Noritatsu Tsubaki & Xingang Li Fischer–Tropsch synthesis (FTS) is theoretically limited by Anderson–Schulz–Flory (ASF) law. Here, the authors successfully tune the selectivity of products from diesel-range hydrocarbons to gasoline-range hydrocarbons in FTS by controlling the crystallite sizes of confined cobalt, and modify the ASF law. 14 August 2018 | doi: 10.1038/s41467-018-05755-8 Catalyst synthesis  Chemical physics  Heterogeneous catalysis  Materials for energy and catalysis  Nanoscale materials  Fast and powerful genome wide association of dense genetic data with high dimensional imaging phenotypes OPEN Habib Ganjgahi, Anderson M. Winkler, David C. Glahn, John Blangero, Brian Donohue, Peter Kochunov & Thomas E. Nichols Genome-wide association studies (GWAS) of neuroimaging data pose a significant computational burden because of the need to correct for multiple testing in both the genetic and the imaging data. Here, Ganjgahi et al. develop WLS-REML which significantly reduces computation running times in brain imaging GWAS. 14 August 2018 | doi: 10.1038/s41467-018-05444-6 Genome-wide association studies  Magnetic resonance imaging  Statistical methods  Statistics  Engineering the spin couplings in atomically crafted spin chains on an elemental superconductor OPEN A. Kamlapure, L. Cornils, J. Wiebe & R. Wiesendanger Magnetic atomic chains assembled on the surface of superconductors are a potential platform for engineering topological superconducting phases. Here the authors step towards this by manipulating magnetic atoms at interstitial sites to tune interatomic interactions and control the Yu-Shiba-Rusinov states that form. 14 August 2018 | doi: 10.1038/s41467-018-05701-8 Magnetic properties and materials  Superconducting properties and materials  A novel probabilistic forecast system predicting anomalously warm 2018-2022 reinforcing the long-term global warming trend OPEN Florian Sévellec & Sybren S. Drijfhout Accurate near-term predictions of global temperatures are required to determine some of the key impacts of climate change. Here the authors develop a novel probabilistic forecast system that shows anomalously warm temperatures for the next years with increased risk of extreme warming. 14 August 2018 | doi: 10.1038/s41467-018-05442-8 Applied mathematics  Climate sciences  Projection and prediction  Revealing circadian mechanisms of integration and resilience by visualizing clock proteins working in real time OPEN Tetsuya Mori, Shogo Sugiyama, Mark Byrne, Carl Hirschie Johnson, Takayuki Uchihashi & Toshio Ando The circadian clock proteins KaiA, KaiB, and KaiC reconstitute a circa-24 h oscillation of KaiC phosphorylation in vitro. Here the authors use high-speed atomic force microscopy to visualize in real time and quantify the dynamic interactions of KaiA with KaiC on the sub-second timescale to discover mechanisms of oscillatory resilience. 14 August 2018 | doi: 10.1038/s41467-018-05438-4 Atomic force microscopy  Enzyme mechanisms  Phosphorylation  Single-molecule biophysics  The tyrosine phosphatase SHP2 controls TGFβ-induced STAT3 signaling to regulate fibroblast activation and fibrosis OPEN Ariella Zehender, Jingang Huang, Andrea-Hermina Györfi, Alexandru-Emil Matei, Thuong Trinh-Minh, Xiaohan Xu, Yi-Nan Li, Chih-Wei Chen, Jianping Lin, Clara Dees, Christian Beyer, Kolja Gelse, Zhong-Yin Zhang, Christina Bergmann, Andreas Ramming, Walter Birchmeier, Oliver Distler, Georg Schett & Jörg H. W. Distler Hyperactivation of TGFβ signaling is a common feature of fibrotic diseases. Here the authors show that genetic or pharmacologic inactivation of the tyrosine phosphatase SHP2 prevents TGFβ-induced JAK2/STAT3 signaling, inhibits fibroblast activation and exerts potent anti-fibrotic effects. 14 August 2018 | doi: 10.1038/s41467-018-05768-3 Connective tissue diseases  Transforming growth factor beta  Chromatin regulates IL-33 release and extracellular cytokine activity OPEN Jared Travers, Mark Rochman, Cora E. Miracle, Jeff E. Habel, Michael Brusilovsky, Julie M. Caldwell, Jeffrey K. Rymer & Marc E. Rothenberg Interleukin-33 (IL-33) can be released as a cytokine or transported into the nucleus, but the significance of this nuclear shuttling is not fully understood. Here the authors show that chromatin-binding of IL-33 alters, unexpectedly, the activity of IL-33 both in alarmin release kinetics and receptor signaling capacity. 14 August 2018 | doi: 10.1038/s41467-018-05485-x Cell death and immune response  Gene regulation in immune cells  Inflammation  Interleukins  Sleep loss causes social withdrawal and loneliness OPEN Eti Ben Simon & Matthew P. Walker Loneliness markedly increases mortality and morbidity, yet the factors triggering loneliness remain largely unknown. This study shows that sleep loss leads to a neurobehavioral phenotype of human social separation and loneliness, one that is transmittable to non-sleep-deprived individuals. 14 August 2018 | doi: 10.1038/s41467-018-05377-0 Sleep deprivation  Social behaviour  Social neuroscience  A possible candidate for triply degenerate point fermions in trigonal layered PtBi2 OPEN Wenshuai Gao, Xiangde Zhu, Fawei Zheng, Min Wu, Jinglei Zhang, Chuanying Xi, Ping Zhang, Yuheng Zhang, Ning Hao, Wei Ning & Mingliang Tian Triply degenerate point (TP) fermions have been reported in MoP but the TPs are far below the Fermi level. Here, Guo et al. predict and verify the possible existence of TP fermions in trigonal layered PtBi2, where the TP points are close to the Fermi level. 14 August 2018 | doi: 10.1038/s41467-018-05730-3 Electronic properties and materials  Topological insulators  Spatially similar surface energy flux perturbations due to greenhouse gases and aerosols OPEN Geeta G. Persad, Yi Ming, Zhaoyi Shen & V. Ramaswamy Anthropogenic aerosol and greenhouse gas concentrations are spatially uncorrelated, but the climate response to each shows a similar spatial pattern. Here the authors show that two-thirds of the spatial similarity in the full response manifests through fast-acting atmosphere and land surface processes alone. 14 August 2018 | doi: 10.1038/s41467-018-05735-y Atmospheric dynamics  Attribution  Climate and Earth system modelling  Projection and prediction  A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots OPEN Daniel J. Lawson, Lucy van Dorp & Daniel Falush Clustering methods such as STRUCTURE and ADMIXTURE are widely used in population genetic studies to investigate ancestry. Here, the authors provide a tutorial on how to interpret results of these analyses and a tool to test the goodness of fit of the model. 14 August 2018 | doi: 10.1038/s41467-018-05257-7 Genetic variation  Population genetics  Non-linear response of summertime marine productivity to increased meltwater discharge around Greenland OPEN M. J. Hopwood, D. Carroll, T. J. Browning, L. Meire, J. Mortensen, S. Krisch & E. P. Achterberg Discharge from Greenland is known to deliver nutrients to the marine environment. Here, the authors show that the majority of the nutrients fueling summertime productivity downstream of Greenland’s glaciers seemingly originate from entrainment in subglacial discharge plumes rather than from meltwater itself. 14 August 2018 | doi: 10.1038/s41467-018-05488-8 Biogeochemistry  Ocean sciences  Gating mechanism of the extracellular entry to the lipid pathway in a TMEM16 scramblase OPEN Byoung-Cheol Lee, George Khelashvili, Maria Falzone, Anant K. Menon, Harel Weinstein & Alessio Accardi Some TMEM16 family members are Ca2+-dependent phospholipid scramblases, which also mediate non-selective ion transport; however, the mechanism how lipids permeate through the TMEM16 remains poorly understood. Here, the authors combine biochemical assays and simulations to identify the key steps regulating lipid movement through the membrane-exposed groove. 14 August 2018 | doi: 10.1038/s41467-018-05724-1 Ion transport  Membrane proteins  Molecular modelling  Permeation and transport  Phospholipids  Charge carrier-selective contacts for nanowire solar cells OPEN Sebastian Z. Oener, Alessandro Cavalli, Hongyu Sun, Jos E. M. Haverkort, Erik P. A. M. Bakkers & Erik C. Garnett Balancing the carrier selectivity and extraction by the selective contacts is of vital importance to the performance of the nanowire solar cells. Here Oener et al. employ a permanent local gate to overcome this tradeoff and substantially increase the open-circuit voltage by 335 mV. 14 August 2018 | doi: 10.1038/s41467-018-05453-5 Electronic devices  Nanowires  Photovoltaics  Spin and orbital structure of the first six holes in a silicon metal-oxide-semiconductor quantum dot OPEN S. D. Liles, R. Li, C. H. Yang, F. E. Hudson, M. Veldhorst, A. S. Dzurak & A. R. Hamilton For solid state qubits, silicon MOS structures offer great scalability, while hole spins promise high performance qubit operation. Liles et al. have combined these two features in a planar silicon quantum dot device that operates as an artificial atom down to the single-hole limit. 14 August 2018 | doi: 10.1038/s41467-018-05700-9 Quantum dots  Quantum information  Spintronics  Two-dimensional type-II Dirac fermions in layered oxides OPEN M. Horio, C. E. Matt, K. Kramer, D. Sutter, A. M. Cook, Y. Sassa, K. Hauser, M. Månsson, N. C. Plumb, M. Shi, O. J. Lipscombe, S. M. Hayden, T. Neupert & J. Chang Many predicted topological quasi-particles still await experimental discovery. Here, Horio et al. reveal the existence of two-dimensional type-II Dirac fermions in the high-temperature superconductor La1.77Sr0.23CuO4, promoting layered oxides as promising topological materials. 14 August 2018 | doi: 10.1038/s41467-018-05715-2 Electronic properties and materials  Topological insulators  Two-dimensional materials  Identification of susceptibility pathways for the role of chromosome 15q25.1 in modifying lung cancer risk OPEN Xuemei Ji, Yohan Bossé, Maria Teresa Landi, Jiang Gui, Xiangjun Xiao, David Qian, Philippe Joubert, Maxime Lamontagne, Yafang Li, Ivan Gorlov, Mariella de Biasi, Younghun Han, Olga Gorlova, Rayjean J. Hung, Xifeng Wu, James McKay, Xuchen Zong, Robert Carreras-Torres, David C. Christiani, Neil Caporaso et al. The chromosome 15q25.1 locus is a leading susceptibility region for lung cancer. Here, the authors interrogate three GWAS cohorts with 42,901 individuals to investigate potential pathological pathways such as gated channel activity and neuroactive ligand receptor interaction in lung cancer etiology. 13 August 2018 | doi: 10.1038/s41467-018-05074-y Cancer genetics  Gene expression  Genetic interaction  Lung cancer  PARP2 mediates branched poly ADP-ribosylation in response to DNA damage OPEN Qian Chen, Muzaffer Ahmad Kassab, Françoise Dantzer & Xiaochun Yu PARP1 and PARP2 of the PARP family enzymes are involved in DNA damage response. Here the authors report PARP2 activation mechanisms and its role in the formation of branched poly(ADP-ribose) chains in response to DNA damage. 13 August 2018 | doi: 10.1038/s41467-018-05588-5 DNA repair enzymes  PolyADP-ribosylation  Self-organization of active particles by quorum sensing rules OPEN Tobias Bäuerle, Andreas Fischer, Thomas Speck & Clemens Bechinger Bacteria communicate and organize via quorum sensing which is determined by biochemical processes. Here the authors aim to reproduce this behaviour in a system of synthetic active particles whose motion is induced by an external beam which is in turn controlled by a feedback-loop which mimics quorum sensing. 13 August 2018 | doi: 10.1038/s41467-018-05675-7 Biological physics  Colloids  High efficiency planar-type perovskite solar cells with negligible hysteresis using EDTA-complexed SnO2 OPEN Dong Yang, Ruixia Yang, Kai Wang, Congcong Wu, Xuejie Zhu, Jiangshan Feng, Xiaodong Ren, Guojia Fang, Shashank Priya & Shengzhong (Frank) Liu The development of high efficiency planar-type perovskite solar cell has been lagging behind the mesoporous-type counterpart. Here Yang et al. modify the oxide based electron transporting layer with organic acid and obtain planar-type cells with high certified efficiency of 21.5% and decent stability. 13 August 2018 | doi: 10.1038/s41467-018-05760-x Photonic devices  Solar cells  Creating solvation environments in heterogeneous catalysts for efficient biomass conversion OPEN Qi Sun, Sai Wang, Briana Aguila, Xiangju Meng, Shengqian Ma & Feng-Shou Xiao Solvents play important roles in chemical transformations, but isolating products from solvents is cumbersome and energy-consuming. Here, the authors develop promising alternatives by anchoring the solvent moieties onto porous materials for creating solvation environments in heterogeneous catalysts for efficient biomass conversion. 13 August 2018 | doi: 10.1038/s41467-018-05534-5 Catalyst synthesis  Heterogeneous catalysis  Porous materials  Itch suppression in mice and dogs by modulation of spinal α2 and α3GABAA receptors OPEN William T. Ralvenius, Elena Neumann, Martina Pagani, Mario A. Acuña, Hendrik Wildner, Dietmar Benke, Nina Fischer, Ana Rostaher, Simon Schwager, Michael Detmar, Katrin Frauenknecht, Adriano Aguzzi, Jed Lee Hubbs, Uwe Rudolph, Claude Favrot & Hanns Ulrich Zeilhofer Chronic itch affects about 10% of the general population, however current treatments are largely ineffective. Here, the authors show that targeting of inhibitory α2 and α3GABAA receptors reduces itch in mice and in a canine model, suggesting this a potentially useful therapeutic approach. 13 August 2018 | doi: 10.1038/s41467-018-05709-0 Pharmacology  Somatosensory system  Freeze-on limits bed strength beneath sliding glaciers OPEN Colin R. Meyer, Anthony S. Downey & Alan W. Rempel Across all glaciers, ice caps, and ice sheets, the gravitational driving stress, and therefore the average basal shear stress falls in a narrow range that tops out around 1 bar. Here, the authors show that the mechanical resistance posed by heterogeneous infiltration of ice into sediments governs the peak bed strength. 13 August 2018 | doi: 10.1038/s41467-018-05716-1 Cryospheric science  Geophysics  Post-polymerisation functionalisation of conjugated polymer backbones and its application in multi-functional emissive nanoparticles OPEN Adam Creamer, Christopher S. Wood, Philip D. Howes, Abby Casey, Shengyu Cong, Adam V. Marsh, Robert Godin, Julianna Panidi, Thomas D. Anthopoulos, Claire H. Burgess, Tingman Wu, Zhuping Fei, Iain Hamilton, Martyn A. McLachlan, Molly M. Stevens & Martin Heeney Functionalisation of conjugated polymers is essential for performance in many applications, yet there are limited approaches to achieve this. Here the authors developed a method for the direct postpolymerisation modification of the aromatic backbone of conjugated polymers and used them to create multifunctional semiconducting nanoparticles. 13 August 2018 | doi: 10.1038/s41467-018-05381-4 Nanoparticles  Polymer synthesis  Light-induced mechanical response in crosslinked liquid-crystalline polymers with photoswitchable glass transition temperatures OPEN Youfeng Yue, Yasuo Norikane, Reiko Azumi & Emiko Koyama Energy conversion of light into mechanical work is of fundamental interest for a wide range of applications, but the development of efficient light responsive polymers is challenging. Here the authors demonstrate photoswitchable  glass transition temperatures contribute to the photomechanical bending in a crosslinked azobenzene polymer. 13 August 2018 | doi: 10.1038/s41467-018-05744-x Organic molecules in materials science  Polymer characterization  Polymers  Single-molecule detection with a millimetre-sized transistor OPEN Eleonora Macchia, Kyriaki Manoli, Brigitte Holzer, Cinzia Di Franco, Matteo Ghittorelli, Fabrizio Torricelli, Domenico Alberga, Giuseppe Felice Mangiatordi, Gerardo Palazzo, Gaetano Scamarcio & Luisa Torsi The sensing capability of nanometric transducers designed for label-free single molecule detection has been limited by the small number of recognition elements. Here, the authors demonstrate a millimetre-sized field effect transistor capable of selective single-molecule Immunoglobulin-G detection. 13 August 2018 | doi: 10.1038/s41467-018-05235-z Sensors  Sensors and biosensors  Universal holonomic quantum gates over geometric spin qubits with polarised microwaves OPEN Kodai Nagata, Kouyou Kuramitani, Yuhei Sekiguchi & Hideo Kosaka Holonomic quantum gates represent a promising route to noise-tolerant quantum operations. Here, the authors use polarised microwaves to implement nonadiabatic holonomic quantum gates at room temperature and zero magnetic field on NV centers, both on single-qubit and between electron and nuclear spins. 13 August 2018 | doi: 10.1038/s41467-018-05664-w Quantum information  Quantum optics  Qubits  Uphill production of dihydrogen by enzymatic oxidation of glucose without an external energy source OPEN Emmanuel Suraniti, Pascal Merzeau, Jérôme Roche, Sébastien Gounel, Andrew G. Mark, Peer Fischer, Nicolas Mano & Alexander Kuhn Most chemical reactions proceed downhill without external energy input. Here, authors employ an electronic flyback and a boost converter to store energy and spontaneously drive an uphill reaction. The concept is exhibited by an enzymatic biofuel cell, driving water splitting in a single compartment. 13 August 2018 | doi: 10.1038/s41467-018-05704-5 Electrical and electronic engineering  Electrocatalysis  Fuel cells  Post-eruptive mobility of lithium in volcanic rocks OPEN B. S. Ellis, D. Szymanowski, T. Magna, J. Neukampf, R. Dohmen, O. Bachmann, P. Ulmer & M. Guillong Lithium, an increasingly economically important element, is also used to trace the cycling of materials through the Earth system. Here the authors show that post-eruptive processes such as degassing and groundmass crystallisation control the inventory of lithium in volcanic deposits. 13 August 2018 | doi: 10.1038/s41467-018-05688-2 Geochemistry  Petrology  Volcanology  Iridophores as a source of robustness in zebrafish stripes and variability in Danio patterns OPEN Alexandria Volkening & Björn Sandstede Iridophores interact with other cells to give zebrafish their stripes, but what drives their form shifts is unknown. Here, modelling allows the authors to identify robust cues that may specify iridophore form and to find changes to these cues that likely account for altered patterns on related fish. 13 August 2018 | doi: 10.1038/s41467-018-05629-z Multicellular systems  Pattern formation  Zebrafish  Pan-cancer deconvolution of tumour composition using DNA methylation OPEN Ankur Chakravarthy, Andrew Furness, Kroopa Joshi, Ehsan Ghorani, Kirsty Ford, Matthew J. Ward, Emma V. King, Matt Lechner, Teresa Marafioti, Sergio A. Quezada, Gareth J. Thomas, Andrew Feber & Tim R. Fenton Determining the extent of immune cell infiltration into solid tumours is essential for adequate therapeutic response. Here the authors develop a DNA methylation-based approach for tumour cell fraction deconvolution and analyse tumour composition and genomics across a wide spectrum of solid cancers. 13 August 2018 | doi: 10.1038/s41467-018-05570-1 Cancer genomics  Cancer microenvironment  Epigenomics  Predictive medicine  Apparent bias toward long gene misregulation in MeCP2 syndromes disappears after controlling for baseline variations OPEN Ayush T. Raman, Amy E. Pohodich, Ying-Wooi Wan, Hari Krishna Yalamanchili, William E. Lowry, Huda Y. Zoghbi & Zhandong Liu Recent studies have suggested that long genes (>100 kb) are more likely to be misregulated in some neurological diseases, such as autism and Rett syndrome. Here the authors find that the apparent length-dependent trends previously observed in MeCP2 microarray and RNA-sequencing datasets disappeared after controlling for baseline variations. 13 August 2018 | doi: 10.1038/s41467-018-05627-1 Gene expression  Gene regulation  Neurodevelopmental disorders  Sequencing  Visual and modular detection of pathogen nucleic acids with enzyme–DNA molecular complexes OPEN Nicholas R. Y. Ho, Geok Soon Lim, Noah R. Sundah, Diana Lim, Tze Ping Loh & Huilin Shao Rapid, visual detection of pathogens is important for point-of-care diagnostics. Here the authors present enVision, which uses enzyme-DNA complexes to detect pathogen nucleic acids and provide a rapid, smartphone compatible readout. 13 August 2018 | doi: 10.1038/s41467-018-05733-0 Biomedical engineering  Nanobiotechnology  Quantum confined peptide assemblies with tunable visible to near-infrared spectral range OPEN Kai Tao, Zhen Fan, Leming Sun, Pandeeswar Makam, Zhen Tian, Mark Ruegsegger, Shira Shaham-Niv, Derek Hansford, Ruth Aizen, Zui Pan, Scott Galster, Jianjie Ma, Fan Yuan, Mingsu Si, Songnan Qu, Mingjun Zhang, Ehud Gazit & Junbai Li Quantum confined (QC) materials have favorable photoluminescent properties, yet are less bioavailable. Here, the authors developed aromatic cyclo-dipeptides that assemble into quantum dots and organize into biocompatible QC supramolecular structures suitable for in vivo imaging and optoelectronics. 13 August 2018 | doi: 10.1038/s41467-018-05568-9 Nanoparticles  Peptides  Quantum dots  Self-assembly  Revealing the mechanism for covalent inhibition of glycoside hydrolases by carbasugars at an atomic level OPEN Weiwu Ren, Robert Pengelly, Marco Farren-Dai, Saeideh Shamsi Kazem Abadi, Verena Oehler, Oluwafemi Akintola, Jason Draper, Michael Meanwell, Saswati Chakladar, Katarzyna Świderek, Vicent Moliner, Robert Britton, Tracey M. Gloster & Andrew J. Bennet Mechanism-based inhibitors of glycoside hydrolases are useful probes for basic research and represent potential drug candidates. Here, the authors present a series of mechanism-based covalent α-galactosidase inhibitors and elucidate the kinetic and structural basis of their inhibitory activity. 13 August 2018 | doi: 10.1038/s41467-018-05702-7 Carbohydrates  Enzyme mechanisms  Hydrolases  X-ray crystallography  Climatic modulation of surface acidification rates through summertime wind forcing in the Southern Ocean OPEN Liang Xue, Wei-Jun Cai, Taro Takahashi, Libao Gao, Rik Wanninkhof, Meng Wei, Kuiping Li, Lin Feng & Weidong Yu The Southern Annular Mode is a dominant climate variability mode in the Southern Ocean. Using observational data, the authors show a strong climatic modulation of ocean acidification via Southern Annular Mode -related winds. 13 August 2018 | doi: 10.1038/s41467-018-05443-7 Carbon cycle  Marine chemistry  Learning auditory discriminations from observation is efficient but less robust than learning from experience OPEN Gagan Narula, Joshua A. Herbst, Joerg Rychen & Richard H. R. Hahnloser Many animals can learn, not just by direct experience, but by observing another animal performing a task. Here, the authors show in zebra finches that observer learning is efficient, but differs from direct learning in that it is less generalizable to novel stimuli. 13 August 2018 | doi: 10.1038/s41467-018-05422-y Animal behaviour  Learning algorithms  Sensory processing  Social behaviour  Combining spectroscopic and isotopic techniques gives a dynamic view of phosphorus cycling in soil OPEN Julian Helfenstein, Federica Tamburini, Christian von Sperber, Michael S. Massey, Chiara Pistocchi, Oliver A. Chadwick, Peter M. Vitousek, Ruben Kretzschmar & Emmanuel Frossard Our understanding of phosphorus (P) cycling in soils, a basis for many ecosystem services, has been limited by the complexity of P forms and processes. Here the authors use spectroscopic and isotopic techniques to estimate turnover times of P pools and tease apart biologically-driven and geochemically-driven P fluxes. 13 August 2018 | doi: 10.1038/s41467-018-05731-2 Biogeochemistry  Element cycles  Environmental sciences  Optical emission near a high-impedance mirror OPEN Majid Esfandyarpour, Alberto G. Curto, Pieter G. Kik, Nader Engheta & Mark L. Brongersma Light emission of molecules can be largely impacted (enhanced or quenched) by nearby surfaces. Here, Esfandyarpour et al. engineer a high-impedance mirror that increases light emission of adjacent molecules by enhancing the coupling between the molecule and free space. 13 August 2018 | doi: 10.1038/s41467-018-05505-w Characterization and analytical techniques  Metamaterials  Nanophotonics and plasmonics  Neonatal brain injury causes cerebellar learning deficits and Purkinje cell dysfunction OPEN Aaron Sathyanesan, Srikanya Kundu, Joseph Abbah & Vittorio Gallo Premature infants are vulnerable to hypoxia and thus white matter injury, especially in the cerebellum, which develops during late gestation. Here, the authors test the effects of perinatal hypoxia on motor performance and rescue behavioral deficits using the GABA reuptake inhibitor Tiagabine. 13 August 2018 | doi: 10.1038/s41467-018-05656-w Cerebellum  Developmental disorders  Strong negative nonlinear friction from induced two-phonon processes in vibrational systems OPEN X. Dong, M. I. Dykman & H. B. Chan Negative linear friction is known to lead to self-sustained vibrations in many systems. Here, the authors show that when nonlinear negative friction in an electromechanical oscillator becomes larger than its positive linear counterpart such self-sustained vibrations require activation. 13 August 2018 | doi: 10.1038/s41467-018-05246-w NEMS  Optomechanics  Emergence of winner-takes-all connectivity paths in random nanowire networks OPEN Hugh G. Manning, Fabio Niosi, Claudia Gomes da Rocha, Allen T. Bellew, Colin O’Callaghan, Subhajit Biswas, Patrick F. Flowers, Benjamin J. Wiley, Justin D. Holmes, Mauro S. Ferreira & John J. Boland Nanowire networks with memristive properties are promising for neuromorphic applications. Here, the authors observe the formation of a preferred conduction pathway which uses the lowest possible energy to get through the network and could be exploited for the design of optimal brain-inspired devices. 13 August 2018 | doi: 10.1038/s41467-018-05517-6 Computational nanotechnology  Electronic devices  Electronic properties and materials  Nanowires  Growth tradeoffs produce complex microbial communities on a single limiting resource OPEN Michael Manhart & Eugene I. Shakhnovich Higher-order interactions occur when one species mediates the interaction between two others. Here, the authors model microbial growth and competition to show that higher-order interactions can arise from tradeoffs in growth traits, leading to neutral coexistence and other complex dynamics. 10 August 2018 | doi: 10.1038/s41467-018-05703-6 Experimental evolution  Microbial ecology  Population dynamics  Theoretical ecology  Iron-based trinuclear metal-organic nanostructures on a surface with local charge accumulation OPEN Cornelius Krull, Marina Castelli, Prokop Hapala, Dhaneesh Kumar, Anton Tadich, Martina Capsoni, Mark T. Edmonds, Jack Hellerstedt, Sarah A. Burke, Pavel Jelinek & Agustin Schiffrin Polynuclear metal-organic coordination complexes are often inaccessible by traditional synthetic chemistry methods. Here, the authors use on-surface supramolecular chemistry to form a planar trinuclear Fe complex, in which an accumulation of electrons around the positive mixed-valence polynuclear centre suggests a catalytically active core. 10 August 2018 | doi: 10.1038/s41467-018-05543-4 Coordination chemistry  Materials for energy and catalysis  Molecular self-assembly  Organic–inorganic nanostructures  Targeting AURKA-CDC25C axis to induce synthetic lethality in ARID1A-deficient colorectal cancer cells OPEN Changjie Wu, Junfang Lyu, Eun Ju Yang, Yifan Liu, Baoyuan Zhang & Joong Sup Shim ARID1A is highly inactivated in cancer. Here, the authors show that ARID1A has a synthetic lethal interaction with AURKA in colorectal cancer cells and that ARID1A deficiency activates the AURKA target CDC25C, whose inhibitors also cause cell death in the ARID1A-deficient cell lines. 10 August 2018 | doi: 10.1038/s41467-018-05694-4 Cancer  Chemical biology  Drug discovery  Molecular medicine  N2 activation on a molybdenum–titanium–sulfur cluster OPEN Yasuhiro Ohki, Keisuke Uchida, Mizuki Tada, Roger E. Cramer, Takashi Ogura & Takehiro Ohta Nitrogenase—whose cofactor consists of a metal–sulfur cluster—catalyzes the production of NH3 from N2, but designing metal–sulfur complexes capable of promoting this conversion remains challenging. Here, the authors report on the activation of N2 by a metal–sulfur cluster containing [Mo3S4Ti] cubes, demonstrating NH3 and N2H4 production. 10 August 2018 | doi: 10.1038/s41467-018-05630-6 Bioinorganic chemistry  Organometallic chemistry  Chemical synthesis  Notch3-dependent β-catenin signaling mediates EGFR TKI drug persistence in EGFR mutant NSCLC OPEN Rajeswara Rao Arasada, Konstantin Shilo, Tadaaki Yamada, Jianying Zhang, Seiji Yano, Rashelle Ghanem, Walter Wang, Shinji Takeuchi, Koji Fukuda, Nobuyuki Katakami, Keisuke Tomii, Fumitaka Ogushi, Yasuhiko Nishioka, Tiffany Talabere, Shrilekha Misra, Wenrui Duan, Paolo Fadda, Mohammad A. Rahman, Patrick Nana-Sinkam, Jason Evans et al. Treatment of EGFR mutant non-small cell lung cancer (NSCLC) often develops resistance to EGFR TKIs. In this study, the authors discover a non-canonical activation of β-catenin signaling through Notch3 as a mechanism of adaptation to and resistance to EGFR TKI treatment in NSCLC. 10 August 2018 | doi: 10.1038/s41467-018-05626-2 Cancer  Lung cancer  Non-small-cell lung cancer  Elongator mutation in mice induces neurodegeneration and ataxia-like behavior OPEN Marija Kojic, Monika Gaik, Bence Kiska, Anna Salerno-Kochan, Sarah Hunt, Angelo Tedoldi, Sergey Mureev, Alun Jones, Belinda Whittle, Laura A. Genovesi, Christelle Adolphe, Darren L. Brown, Jennifer L. Stow, Kirill Alexandrov, Pankaj Sah, Sebastian Glatt & Brandon J. Wainwright Elp6 is a component of the Elongator complex that regulates tRNAs and translation. Here the authors identify a mutation in the Elp6 gene that contributes to the cerebellar ataxia-like phenotype in a mutant mouse. 10 August 2018 | doi: 10.1038/s41467-018-05765-6 Cerebellum  Neurodegeneration  Spinocerebellar ataxia  tRNAs  Programmed cell removal by calreticulin in tissue homeostasis and cancer OPEN Mingye Feng, Kristopher D. Marjon, Fangfang Zhu, Rachel Weissman-Tsukamoto, Aaron Levett, Katie Sullivan, Kevin S. Kao, Maxim Markovic, Paul A. Bump, Hannah M. Jackson, Timothy S. Choi, Jing Chen, Allison M. Banuelos, Jie Liu, Phung Gip, Lei Cheng, Denong Wang & Irving L. Weissman Macrophage-mediated programmed cell removal (PrCR) allows clearance of living cells. Here the authors show that, in mouse models, activated macrophages create an “eat me” signal via calreticulin secretion on neutrophils during peritonitis and on cancer cells, determining in both cases clearance by PrCR. 10 August 2018 | doi: 10.1038/s41467-018-05211-7 Innate immunity  Tumour immunology  A dormant TIL phenotype defines non-small cell lung carcinomas sensitive to immune checkpoint blockers OPEN S. N. Gettinger, J. Choi, N. Mani, M. F. Sanmamed, I. Datar, Ryan Sowell, Victor Y. Du, E. Kaftan, S. Goldberg, W. Dong, D. Zelterman, K. Politi, P. Kavathas, S. Kaech, X. Yu, H. Zhao, J. Schlessinger, R. Lifton, D. L. Rimm, L. Chen et al. Immune checkpoint blockade (ICB) only induces tumour response in a subset of non-small cell lung carcinomas (NSCLC). Here the authors do whole genome sequencing and multiplexed quantitative immunofluorescence on patient samples and identify a “dormant” T-cell signature associated with sensitivity to ICB. 10 August 2018 | doi: 10.1038/s41467-018-05032-8 Immunosurveillance  Non-small-cell lung cancer  Long-term deep-supercooling of large-volume water and red cell suspensions via surface sealing with immiscible liquids OPEN Haishui Huang, Martin L. Yarmush & O. Berk Usta Supercooled water is susceptible to spontaneous freezing, and preventing this process is a challenge. Here, the authors use surface sealing with immiscible liquids to eliminate primary ice nucleation at the water/air interface, enabling deep supercooling of large volumes of water and red cell suspensions for long time periods. 10 August 2018 | doi: 10.1038/s41467-018-05636-0 Applied physics  Biophysical methods  Chemical engineering  Physical chemistry  Lensfree OLEDs with over 50% external quantum efficiency via external scattering and horizontally oriented emitters OPEN Jinouk Song, Kwon-Hyeon Kim, Eunhye Kim, Chang-Ki Moon, Yun-Hi Kim, Jang-Joo Kim & Seunghyup Yoo Light extraction approaches based on a macroscopic lens in organic light-emitting diodes (OLEDs) enables competitive performance, but compromise on the technology’s key benefits. Here, the authors demonstrate ultrahigh efficiency OLEDs via a device strategy based on forward light scattering. 10 August 2018 | doi: 10.1038/s41467-018-05671-x Integrated optics  Organic LEDs  Understanding the apparent fractional charge of protons in the aqueous electrochemical double layer OPEN Leanne D. Chen, Michal Bajdich, J. Mark P. Martirez, Caroline M. Krauter, Joseph A. Gauthier, Emily A. Carter, Alan C. Luntz, Karen Chan & Jens K. Nørskov A detailed atomic-scale description of the electrochemical interface is essential to the understanding of electrochemical energy transformations. Here, the authors investigate the solvated proton at the electrochemical interface and show that it unexpectedly carries a fractional charge. 10 August 2018 | doi: 10.1038/s41467-018-05511-y Computational chemistry  Density functional theory  Electrocatalysis  Energy  Nuclear-resident RIG-I senses viral replication inducing antiviral immunity OPEN GuanQun Liu, Yao Lu, Sathya N. Thulasi Raman, Fang Xu, Qi Wu, Zhubing Li, Robert Brownlie, Qiang Liu & Yan Zhou RIG-I senses cytoplasmic viral RNA, resulting in induction of an antiviral response. Here, the authors identify nuclear RIG-I and show that it binds nuclear influenza A virus RNA, resulting in a cooperative interferon induction along with its cytoplasmic counterpart. 10 August 2018 | doi: 10.1038/s41467-018-05745-w Influenza virus  RIG-I-like receptors  Viral host response  Viral infection  Commensal microflora-induced T cell responses mediate progressive neurodegeneration in glaucoma OPEN Huihui Chen, Kin-Sang Cho, T. H. Khanh Vu, Ching-Hung Shen, Mandeep Kaur, Guochun Chen, Rose Mathew, M. Lisa McHam, Ahad Fazelat, Kameran Lashkari, Ngan Pan Bennett AU, Joyce Ka Yu TSE, Yingqian Li, Honghua Yu, Lanbo Yang, Joan Stein-Streilein, Chi Him Eddie Ma, Clifford J. Woolf, Mark T. Whary, Martine J. Jager et al. Glaucoma is a neurodegenerative disease of which the etiology is still unclear. Here the authors show that elevation of intraocular pressure induces T cell infiltration in the eyes. Furthermore, they show that T cell cross-reactivity between endogenous and commensal antigens contributes to disease onset in mice. 10 August 2018 | doi: 10.1038/s41467-018-05681-9 Mucosal immunology  Neuroimmunology  Retina  T cells  Beneficial effects of climate warming on boreal tree growth may be transitory OPEN Loïc D’Orangeville, Daniel Houle, Louis Duchesne, Richard P. Phillips, Yves Bergeron & Daniel Kneeshaw The productivity of boreal forests in Eastern North America is predicted to increase with warming under sufficient moisture supply. Here D’Orangeville et al. study seven tree species and predict that growth enhancements may be seen up to 2 °C warming, but would decline if temperatures exceed this. 10 August 2018 | doi: 10.1038/s41467-018-05705-4 Climate-change ecology  Forest ecology  The silicon cycle impacted by past ice sheets OPEN Jon R. Hawkings, Jade E. Hatton, Katharine R. Hendry, Gregory F. de Souza, Jemma L. Wadham, Ruza Ivanovic, Tyler J. Kohler, Marek Stibal, Alexander Beaton, Guillaume Lamarche-Gagnon, Andrew Tedstone, Mathis P. Hain, Elizabeth Bagshaw, Jennifer Pike & Martyn Tranter The role ice sheets play in the silica cycle over glacial−interglacial timescales remains unclear. Here, based on the measurement of silica isotopes in Greenland meltwater and a nearby marine sediment core, the authors suggest expanding ice sheets considerably increased isotopically light silica in the oceans. 10 August 2018 | doi: 10.1038/s41467-018-05689-1 Carbon cycle  Element cycles  Geochemistry  Marine chemistry  Multiple timescales of normalized value coding underlie adaptive choice behavior OPEN Jan Zimmermann, Paul W. Glimcher & Kenway Louie Previous work has shown that the neural representation of value adapts to the recent history of rewards. Here, the authors report that a computational model based on divisive normalization over multiple timescales can explain changes in value coding driven by changes in the reward statistics. 10 August 2018 | doi: 10.1038/s41467-018-05507-8 Computational neuroscience  Reward  Maximal viral information recovery from sequence data using VirMAP OPEN Nadim J Ajami, Matthew C. Wong, Matthew C. Ross, Richard E. Lloyd & Joseph F. Petrosino Viral taxonomic characterization from metagenomic data suffers from high background noise and signal crosstalk. Here, the authors develop VirMAP, a novel pipeline for analyses of metagenomic data that classifies viral reconstructions independent of genome coverage or read overlap. 10 August 2018 | doi: 10.1038/s41467-018-05658-8 Classification and taxonomy  Metagenomics  Virology  Capacitive neural network with neuro-transistors OPEN Zhongrui Wang, Mingyi Rao, Jin-Woo Han, Jiaming Zhang, Peng Lin, Yunning Li, Can Li, Wenhao Song, Shiva Asapu, Rivu Midya, Ye Zhuo, Hao Jiang, Jung Ho Yoon, Navnidhi Kumar Upadhyay, Saumil Joshi, Miao Hu, John Paul Strachan, Mark Barnell, Qing Wu, Huaqiang Wu et al. Though memristors can potentially emulate neuron and synapse functionality, useful signal energy is lost to Joule heating. Here, the authors demonstrate neuro-transistors with a pseudo-memcapacitive gate that actively process signals via energy-efficient capacitively-coupled neural networks. 10 August 2018 | doi: 10.1038/s41467-018-05677-5 Computer science  Electronic devices  Nanoparticles  Biology and genome of a newly discovered sibling species of Caenorhabditis elegans OPEN Natsumi Kanzaki, Isheng J. Tsai, Ryusei Tanaka, Vicky L. Hunt, Dang Liu, Kenji Tsuyama, Yasunobu Maeda, Satoshi Namai, Ryohei Kumagai, Alan Tracey, Nancy Holroyd, Stephen R. Doyle, Gavin C. Woodruff, Kazunori Murase, Hiromi Kitazume, Cynthia Chai, Allison Akagi, Oishika Panda, Huei-Mien Ke, Frank C. Schroeder et al. Caenorhabditis nematodes are important model organisms. Here, the authors report the biology and genome of Caenorhabditis inopinata, a first sibling species of C. elegans, and develop genetic and molecular techniques for C. inopinata. 10 August 2018 | doi: 10.1038/s41467-018-05712-5 Evolution  Genome  Genome evolution  A balance between aerodynamic and olfactory performance during flight in Drosophila OPEN Chengyu Li, Haibo Dong & Kai Zhao In addition to their aerodynamic properties, insect wings also move odor plumes closer to sensory organs. Li et al. show that Drosophila wings may trade optimal aerodynamic performance for improved olfactory function during flight. 10 August 2018 | doi: 10.1038/s41467-018-05708-1 Biomechanics  Engineering  Entomology  Post-drought decline of the Amazon carbon sink OPEN Yan Yang, Sassan S. Saatchi, Liang Xu, Yifan Yu, Sungho Choi, Nathan Phillips, Robert Kennedy, Michael Keller, Yuri Knyazikhin & Ranga B. Myneni Forests of the Amazon Basin have experienced frequent and severe droughts in recent years with significant impacts on their carbon cycling. Here, using satellite LiDAR samples from 2003 to 2008, the authors show the long-term legacy of these droughts with persistent loss of carbon stocks after the 2005 drought. 09 August 2018 | doi: 10.1038/s41467-018-05668-6 Carbon cycle  Climate change  Environmental impact  T cell-intrinsic IL-1R signaling licenses effector cytokine production by memory CD4 T cells OPEN Aakanksha Jain, Ran Song, Edward K. Wakeland & Chandrashekhar Pasare CD4 T cell polarizations and functions are regulated by cytokines from innate cells. Here the authors show that IL-1 deficiency does not impair the differentiation of Th1, Th2 and Th17, but IL-1 signaling is required for maintaining the expressions of their respective key cytokines to ‘license’ the functions of these T cell subsets. 09 August 2018 | doi: 10.1038/s41467-018-05489-7 CD4-positive T cells  Immunological memory  Lymphokines  T-helper 17 cells  Dual stimuli-responsive rotaxane-branched dendrimers with reversible dimension modulation OPEN Xu-Qing Wang, Wei Wang, Wei-Jian Li, Li-Jun Chen, Rui Yao, Guang-Qiang Yin, Yu-Xuan Wang, Ying Zhang, Junlin Huang, Hongwei Tan, Yihua Yu, Xiaopeng Li, Lin Xu & Hai-Bo Yang Mechanically interlocked molecules are extensively applied as artificial molecular machines but rotaxane-branched dendrimers are rarely explored because of synthetic challenges. Here the authors present the construction of dual stimuli-responsive rotaxane-branched dendrimer which can be stimulated by DMSO or acetate ions. 09 August 2018 | doi: 10.1038/s41467-018-05670-y Interlocked molecules  Self-assembly  Supramolecular polymers  Structure of the essential peptidoglycan amidotransferase MurT/GatD complex from Streptococcus pneumoniae OPEN Cécile Morlot, Daniel Straume, Katharina Peters, Olav A. Hegnar, Nolwenn Simon, Anne-Marie Villard, Carlos Contreras-Martel, Francisco Leisico, Eefjan Breukink, Christine Gravier-Pelletier, Laurent Le Corre, Waldemar Vollmer, Nicolas Pietrancosta, Leiv Sigve Håvarstein & André Zapun The amidotransferase MurT/GatD complex catalyzes peptidoglycan precursor amidation in some Gram-positive bacteria. Here the authors present the crystal structure of the Streptococcus pneumoniae MurT/GatD complex and provide mechanistic insights, which are of interest for drug development. 09 August 2018 | doi: 10.1038/s41467-018-05602-w Bacteriology  Enzyme mechanisms  X-ray crystallography  High-resolution visualization of H3 variants during replication reveals their controlled recycling OPEN Camille Clément, Guillermo A. Orsi, Alberto Gatto, Ekaterina Boyarchuk, Audrey Forest, Bassam Hajj, Judith Miné-Hattab, Mickaël Garnier, Zachary A. Gurard-Levin, Jean-Pierre Quivy & Geneviève Almouzni Epigenetic modifications are a key contributor to cell identity, and their propagation is crucial for proper development. Here the authors use a super-resolution microscopy approach to reveal how histone variants are faithfully transmitted during genome duplication, and reveal an important role for the histone chaperone ASF1 in the redistribution of parental histones. 09 August 2018 | doi: 10.1038/s41467-018-05697-1 DNA replication  Epigenetics  Histone variants  Arsenic targets Pin1 and cooperates with retinoic acid to inhibit cancer-driving pathways and tumor-initiating cells OPEN Shingo Kozono, Yu-Min Lin, Hyuk-Soo Seo, Benika Pinch, Xiaolan Lian, Chenxi Qiu, Megan K. Herbert, Chun-Hau Chen, Li Tan, Ziang Jeff Gao, Walter Massefski, Zainab M. Doctor, Brian P. Jackson, Yuanzhong Chen, Sirano Dhe-Paganon, Kun Ping Lu & Xiao Zhen Zhou Arsenic trioxide and all-trans retinoic acid combination safely cures human acute promyelocytic leukemia. Here, the authors show that this combination has potent anticancer activity in triple negative breast cancer by cooperatively targeting Pin1, a master  regulator of oncogenic signaling networks, to eliminate cancer stem cells. 09 August 2018 | doi: 10.1038/s41467-018-05402-2 Breast cancer  Cancer  Cancer therapy  Targeted therapies  Late Cenozoic unification of East and West Antarctica OPEN Roi Granot & Jérôme Dyment The West Antarctic rift system, which divides the East and West Antarctic plates, was believed to be active until 26 Myr. Here, the authors demonstrate through new geophysical data that rifting within the West Antarctic rift system lasted until 11 Myr, providing a new interpretation on the development of Antarctica. 09 August 2018 | doi: 10.1038/s41467-018-05270-w Geodynamics  Tectonics  Identification of recurrent USP48 and BRAF mutations in Cushing’s disease OPEN Jianhua Chen, Xuemin Jian, Siyu Deng, Zengyi Ma, Xuefei Shou, Yue Shen, Qilin Zhang, Zhijian Song, Zhiqiang Li, Hong Peng, Cheng Peng, Min Chen, Cheng Luo, Dan Zhao, Zhao Ye, Ming Shen, Yichao Zhang, Juan Zhou, Aamir Fahira, Yongfei Wang et al. In this study the authors report USP48 and BRAF are frequently mutated in USP8 wild-type corticotroph adenomas, and cause Cushing’s disease mainly through promoting the promoter activity of POMC. Inhibition of BRAF may be a promising therapeutic strategy for the treatment of patients with BRAF-mutated corticotroph adenomas. 09 August 2018 | doi: 10.1038/s41467-018-05275-5 Cancer genomics  Pituitary tumours  Hybrid nanodiamond quantum sensors enabled by volume phase transitions of hydrogels OPEN Ting Zhang, Gang-Qin Liu, Weng-Hang Leong, Chu-Feng Liu, Man-Hin Kwok, To Ngai, Ren-Bao Liu & Quan Li Nitrogen-vacancy (NV) centers in diamonds are used for quantum sensing but NV centers are not sensitive to parameters such as temperature, pressure and biomolecules. Here the authors propose a scheme based on a magnetic nanoparticle docked responsive hydrogel which acts as a transducer between the particles and the diamond. 09 August 2018 | doi: 10.1038/s41467-018-05673-9 Magneto-optics  Sensors  Sensors and biosensors  Genome-wide association study identifies multiple new loci associated with Ewing sarcoma susceptibility OPEN Mitchell J. Machiela, Thomas G. P. Grünewald, Didier Surdez, Stephanie Reynaud, Olivier Mirabeau, Eric Karlins, Rebeca Alba Rubio, Sakina Zaidi, Sandrine Grossetete-Lalami, Stelly Ballet, Eve Lapouble, Valérie Laurence, Jean Michon, Gaelle Pierron, Heinrich Kovar, Nathalie Gaspar, Udo Kontny, Anna González-Neira, Piero Picci, Javier Alonso et al. Ewing sarcoma (EWS) is a rare pediatric bone cancer typically involving the EWSR1-FLI1 fusion. Here the authors perform a genome-wide association study and report three new EWS risk loci that reside near GGAA repeat sequences, and identify candidate genes (RREB1 and KIZ) from eQTL analysis. 09 August 2018 | doi: 10.1038/s41467-018-05537-2 Genome-wide association studies  Paediatric cancer  A Late Cretaceous amber biota from central Myanmar OPEN Daran Zheng, Su-Chin Chang, Vincent Perrichot, Suryendu Dutta, Arka Rudra, Lin Mu, Richard S. Kelly, Sha Li, Qi Zhang, Qingqing Zhang, Jean Wong, Jun Wang, He Wang, Yan Fang, Haichun Zhang & Bo Wang The amber deposits from Kachin, Myanmar have provided numerous insights into life in the Cretaceous ~99 million years ago. Here, Zheng and colleagues describe a new Late Cretaceous amber biota from Tilin, Myanmar, dating from ~72 million years ago and preserving a diverse insect assemblage. 09 August 2018 | doi: 10.1038/s41467-018-05650-2 Palaeoecology  Palaeontology  Small molecule inhibitors of RAS-effector protein interactions derived using an intracellular antibody fragment OPEN Camilo E. Quevedo, Abimael Cruz-Migoni, Nicolas Bery, Ami Miller, Tomoyuki Tanaka, Donna Petch, Carole J. R. Bataille, Lydia Y. W. Lee, Phillip S. Fallon, Hanna Tulmin, Matthias T. Ehebauer, Narcis Fernandez-Fuentes, Angela J. Russell, Stephen B. Carr, Simon E. V. Phillips & Terence H. Rabbitts Intracellular antibodies can inhibit disease-relevant protein interactions, but inefficient cellular uptake limits their utility. Using a RAS-targeting intracellular antibody as a screening tool, the authors here identify small molecules that inhibit RAS-effector interactions and readily penetrate cells. 09 August 2018 | doi: 10.1038/s41467-018-05707-2 Oncogene proteins  Screening  Structure-based drug design  X-ray crystallography  Single-shot condensation of exciton polaritons and the hole burning effect OPEN E. Estrecho, T. Gao, N. Bobrovska, M. D. Fraser, M. Steger, L. Pfeiffer, K. West, T. C. H. Liew, M. Matuszewski, D. W. Snoke, A. G. Truscott & E. A. Ostrovskaya The mechanism for exciton-polariton condensation in the presence of an incoherent reservoir has been long debated. Here the authors demonstrate the role of the spatial hole burning in condensation of long‐lived exciton polaritons by imaging the condensates in a single-shot excitation regime. 09 August 2018 | doi: 10.1038/s41467-018-05349-4 Bose–Einstein condensates  Quantum fluids and solids  Plant and animal functional diversity drive mutualistic network assembly across an elevational gradient OPEN Jörg Albrecht, Alice Classen, Maximilian G. R. Vollstädt, Antonia Mayr, Neduvoto P. Mollel, David Schellenberger Costa, Hamadi I. Dulle, Markus Fischer, Andreas Hemp, Kim M. Howell, Michael Kleyer, Thomas Nauss, Marcell K. Peters, Marco Tschapka, Ingolf Steffan-Dewenter, Katrin Böhning-Gaese & Matthias Schleuning Differential responses of plant and animal functional diversity to climatic variation could affect trait matching in mutualistic interactions. Here, Albrecht et al. show that network structure varies across an elevational gradient owing to bottom-up and top-down effects of functional diversity. 09 August 2018 | doi: 10.1038/s41467-018-05610-w Community ecology  Ecological networks  Ecology  Ecosystem ecology  Quantum coherence of multiple excitons governs absorption cross-sections of PbS/CdS core/shell nanocrystals OPEN Hirokazu Tahara, Masanori Sakamoto, Toshiharu Teranishi & Yoshihiko Kanemitsu Understanding the physics underlying the generation and recombination of excitons is expected to help improve the performance of solar call and photodetector devices. Here the authors demonstrate that the quantum coherence of excitons significantly affects multiexciton absorption cross-sections. 09 August 2018 | doi: 10.1038/s41467-018-05698-0 Nanoparticles  Nanophotonics and plasmonics  Control of transmembrane charge transfer in cytochrome c oxidase by the membrane potential OPEN Markus L. Björck & Peter Brzezinski Cytochrome c oxidase (CytcO) is the last enzyme of the electron transport chain, but how the electrochemical membrane potential affects CytcO is unclear. Here the authors show that proton uptake to the catalytic site of CytcO and presumably proton translocation was impaired by the potential, but electron transfer was not affected. 09 August 2018 | doi: 10.1038/s41467-018-05615-5 Bioenergetics  Enzyme mechanisms  Ion pumps  Ion transport  Metalloproteins  More replenishment than priming loss of soil organic carbon with additional carbon input OPEN Junyi Liang, Zhenghu Zhou, Changfu Huo, Zheng Shi, James R. Cole, Lei Huang, Konstantinos T. Konstantinidis, Xiaoming Li, Bo Liu, Zhongkui Luo, C. Ryan Penton, Edward A. G. Schuur, James M. Tiedje, Ying-Ping Wang, Liyou Wu, Jianyang Xia, Jizhong Zhou & Yiqi Luo The magnitudes of replenishment and priming, two important but opposing fluxes in soil organic carbon (SOC) dynamics, have not been compared. Here the authors show that the magnitude of replenishment is greater than that of priming, resulting in a net SOC accumulation after additional carbon input to soils. 09 August 2018 | doi: 10.1038/s41467-018-05667-7 Carbon cycle  Ecosystem ecology  PI3Kδ hyper-activation promotes development of B cells that exacerbate Streptococcus pneumoniae infection in an antibody-independent manner OPEN Anne-Katrien Stark, Anita Chandra, Krishnendu Chakraborty, Rafeah Alam, Valentina Carbonaro, Jonathan Clark, Srividya Sriskantharajah, Glyn Bradley, Alex G. Richter, Edward Banham-Hall, Menna R. Clatworthy, Sergey Nejentsev, J. Nicole Hamblin, Edith M. Hessel, Alison M. Condliffe & Klaus Okkenhaug Antibody mediated immune responses to Streptococcus pneumoniae are crucial for the immune response to infection. Here the authors show hyper-activation of PI3Kδ promotes development of a subset of B cells that exacerbate infection in an antibody-independent manner and can be reversed by therapeutic targeting in vivo. 09 August 2018 | doi: 10.1038/s41467-018-05674-8 B cells  Bacterial infection  Immunological disorders  Infection  Role of VTA dopamine neurons and neuroligin 3 in sociability traits related to nonfamiliar conspecific interaction OPEN Sebastiano Bariselli, Hanna Hörnberg, Clément Prévost-Solié, Stefano Musardo, Laetitia Hatstatt-Burklé, Peter Scheiffele & Camilla Bellone Individuals with autism spectrum disorder have alteration in social and novelty behaviors. Here, Bellone and colleagues show that chemogenetic inhibition of mouse dopamine neurons in the ventral tegmental area can blunt exploration towards unfamiliar conspecifics, and that these behavioral deficits are recapitulated in mice lacking neuroligin3 gene product. 09 August 2018 | doi: 10.1038/s41467-018-05382-3 Autism spectrum disorders  Reward  Social behaviour  Systematic identification of non-coding pharmacogenomic landscape in cancer OPEN Yue Wang, Zehua Wang, Jieni Xu, Jiang Li, Song Li, Min Zhang & Da Yang In this study the authors build lncRNA-drug response models for 265 anti-cancer agents across 27 cancer types. They report their cancer cell line based lncRNA EN-models are able to effectively predict therapeutic outcome for breast cancer, ovarian cancer, endometrial cancer and stomach cancer patients. 09 August 2018 | doi: 10.1038/s41467-018-05495-9 Cancer genomics  Machine learning  Perturbation to the nitrogen cycle during rapid Early Eocene global warming OPEN Christopher K. Junium, Alexander J. Dickson & Benjamin T. Uveges Studying the PETM, a past period of rapid warming ~56 Ma, could provide insights into ecosystem response under future warming conditions. Here, the authors present stable nitrogen isotope data that reveal a dramatic change in the marine nitrogen cycle and the emergence of anoxic conditions. 09 August 2018 | doi: 10.1038/s41467-018-05486-w Biogeochemistry  Element cycles  Palaeoceanography  Palaeoclimate  Holocene reconfiguration and readvance of the East Antarctic Ice Sheet OPEN Sarah L. Greenwood, Lauren M. Simkins, Anna Ruth W. Halberstadt, Lindsay O. Prothro & John B. Anderson Ice sheets are vulnerable to changes in the environment where ice discharges into the ocean. Here, the authors show that, in spite of widespread retreat following the last glacial maximum, a sub-sector of the East Antarctic Ice Sheet in the Ross Sea underwent sustained readvance. 09 August 2018 | doi: 10.1038/s41467-018-05625-3 Cryospheric science  Palaeoclimate  Identification of nine new susceptibility loci for endometrial cancer OPEN Tracy A. O’Mara, Dylan M. Glubb, Frederic Amant, Daniela Annibali, Katie Ashton, John Attia, Paul L. Auer, Matthias W. Beckmann, Amanda Black, Manjeet K. Bolla, Hiltrud Brauch, Hermann Brenner, Louise Brinton, Daniel D. Buchanan, Barbara Burwinkel, Jenny Chang-Claude, Stephen J. Chanock, Chu Chen, Maxine M. Chen, Timothy H. T. Cheng et al. Endometrial cancer is the most common invasive gynaecological cancer in developed countries. Here a meta-analysis identifies an additional nine novel endometrial cancer risk loci and eQTL analysis reveals risk variants associate with reduced expression of negative regulators of oncogenic signal transduction proteins. 09 August 2018 | doi: 10.1038/s41467-018-05427-7 Genome-wide association studies  Gynaecological cancer  Structural basis for reactivating the mutant TERT promoter by cooperative binding of p52 and ETS1 OPEN Xueyong Xu, Yinghui Li, Sakshibeedu R. Bharath, Mert Burak Ozturk, Matthew W. Bowler, Bryan Zong Lin Loo, Vinay Tergaonkar & Haiwei Song Incessant telomere synthesis in cancer cells depends on specific mutations in the TERT promoter, enabling its activation by transcription factors ETS1 and p52. Here, the authors elucidate the structural basis for p52/ETS1 binding to mutant TERT, suggesting a general mechanism for TERT reactivation in cancer. 09 August 2018 | doi: 10.1038/s41467-018-05644-0 Telomeres  Transcription factors  X-ray crystallography  Universal molecular structures in natural dissolved organic matter OPEN Maren Zark & Thorsten Dittmar Dissolved organic matter (DOM) in aquatic systems is among the most complex molecular mixtures known. Here the authors show that a major component in DOM is molecularly indistinguishable in marine and freshwater environments, which could reflect universal mechanisms behind long-term DOM turnover. 09 August 2018 | doi: 10.1038/s41467-018-05665-9 Carbon cycle  Marine chemistry  Reassessment of pre-industrial fire emissions strongly affects anthropogenic aerosol forcing OPEN D. S. Hamilton, S. Hantson, C. E. Scott, J. O. Kaplan, K. J. Pringle, L. P. Nieradzik, A. Rap, G. A. Folberth, D. V. Spracklen & K. S. Carslaw Several lines of evidence suggest that fire activity was much greater in the preindustrial era than currently assumed in climate models. Here the authors show that greater emission of aerosols from fires leads to a substantial reduction in the magnitude of aerosol radiative forcing over the Industrial Era. 09 August 2018 | doi: 10.1038/s41467-018-05592-9 Atmospheric chemistry  Climate and Earth system modelling  Climate change    Nature Communications JOBS of the week Post-doctoral Fellow Mercer University Postdoctoral Research Assistant Royal Veterinary College, University of London Tenure-Track Faculty position in Cancer Pharmacogenomics University of Wisconsin - Madison Research Fellow in Psychiatric Genomics / Health Informatics Cardiff University Senior Staff Scientist - Malaria Wellcome Sanger Institute Senior Research Fellow The University of Warwick Assistant / Journal Manager AIP Publishing Postdoctoral position Medical University of South Carolina Postdoctoral Fellow University of Pennsylvania Bioinformatician (Single Cell Analysis) The Earlham Institute More Science jobs from Nature Communications EVENT Microbiome Therapeutics US 05.09.18 Boston, USA More science events from     Latest Correspondence       C-C bond cleavage in biosynthesis of 4-alkyl-L-proline precursors of lincomycin and anthramycin cannot precede C-methylation OPEN Zdenek Kamenik, Radek Gazak, Stanislav Kadlcik, Lucie Steiningerova, Vit Rynd & Jiri Janata 09 August 2018 | doi: 10.1038/s41467-018-05455-3 Biosynthesis  Chemical biology  Reply to ‘C–C bond cleavage in biosynthesis of 4-alkyl-l-proline precursors of lincomycin and anthramycin cannot precede C-methylation’ OPEN Guannan Zhong, Hua Chen & Wen Liu 09 August 2018 | doi: 10.1038/s41467-018-05500-1 Biosynthesis  Hydrolases      Latest Publisher Correction       Publisher Correction: Achieving high permeability and enhanced selectivity for Angstrom-scale separations using artificial water channel membranes OPEN Yue-xiao Shen, Woochul Song, D. Ryan Barden, Tingwei Ren, Chao Lang, Hasin Feroz, Codey B. Henderson, Patrick O. Saboe, Daniel Tsai, Hengjing Yan, Peter J. Butler, Guillermo C. Bazan, William A. Phillip, Robert J. Hickey, Paul S. Cremer, Harish Vashisth & Manish Kumar 14 August 2018 | doi: 10.1038/s41467-018-05447-3 Molecular self-assembly  Self-assembly  Two-dimensional materials      Advertisement Nature Conference on Inflammation and Cancer This meeting will bring together a diverse group of researchers from the many interconnected areas of immunology and cancer to discuss how inflammation affects tumour development and metastasis. Presentations will focus on the most recent findings on the tumour-promoting and -suppressing effects of inflammation, the immune tumour environment, and therapeutic approaches. October 23-25, 2018 | Beijing, China REGISTER NOW >>   Advertisement Nature Briefing is an essential round-up of science news, opinion and analysis, free in your inbox every weekday. 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