Nature Communications - 21 March 2018

Advertisement Do you have a career question?  The Naturejobs podcast features one-on-one Q&As, panel discussions and other exclusive content to help scientists with their careers. Hosted on the Naturejobs blog, the podcast is also available on iTunes and Soundcloud.  Listen today!     Weekly Content Alert Nature Communications is fully open access. Read more. 21 March 2018  Latest content: Editorial Comment Articles Author Correction Publisher Correction Advertisement Princeton University, Princeton Institute for the Science and Technology of Materials (PRISM), Nature Communications, Nature Materials, Nature Structural & Molecular Biology present: Princeton - Nature Conference: Frontiers in Electron Microscopy for the Physical and Life Sciences July 11-13, 2018, Princeton University, Princeton, NJ, USA Abstract submissions and registration is open. Register now to secure your place.    Journal homepage Recommend to library Web feed   Advertisement Innovators in Science Award Sponsored by Takeda Pharmaceutical Company Limited and administered by the Academy, this Award recognizes an Early-Career Scientist and a Senior Scientist in Regenerative Medicine for the creativity and impact of their research. Two prizes of US$200,000 will be awarded. Nominations close June 25, 2018. TakedaInnovators.com   Advertisement A new open access, multi- and interdisciplinary journal dedicated to publishing the highest quality papers on aging and age-related diseases, the journal is now open for submissions. Explore the benefits of submitting your next research.       Nature Communications - 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 Editorial       At the human-forest interface OPEN 21 March 2018 | doi: 10.1038/s41467-018-03586-1     Latest Comment       Strategically growing the urban forest will improve our world OPEN Theodore A. Endreny 21 March 2018 | doi: 10.1038/s41467-018-03622-0 Ecosystem services  Forestry      Latest Review View all Articles         Nature Communications JOBS of the week Research Position International Center for Young Scientists (ICYS) - National Institute for Materials Science (NIMS) Research Associate University of Cambridge Postdoctoral Fellow Johns Hopkins University PhD Studentship Universitätsklinikum Carl-Gustav-Carus Dresden Postdoctoral researcher / project researcher University of Eastern Finland Postdoctoral Fellowship Oslo University Hospital Preclinical Scientist Imanova Limited Research Fellowship The University of York Post Doctoral Scientist Victor Chang Cardiac Research Institute (VCCRI) Postdoctoral Researcher Weir Lab, Friedrich Miescher Laboratory More Science jobs from Nature Communications EVENT Clinical Trial Innovation Summit 2018 07.05.18 Boston, USA More science events from     Latest Articles View all Articles     RNA cytosine methylation and methyltransferases mediate chromatin organization and 5-azacytidine response and resistance in leukaemia OPEN Jason X. Cheng, Li Chen, Yuan Li, Adam Cloe, Ming Yue, Jiangbo Wei, Kenneth A. Watanabe, Jamile M. Shammo, John Anastasi, Qingxi J. Shen, Richard A. Larson, Chuan He, Michelle M. Le Beau & James W. Vardiman Resistance to chemotherapy is a serious issue that can be influenced by RNA epigenetics and chromatin structure. Here, the authors show in leukaemia cells that RNA 5-methylcytosine (RNA:m5C) and RNA:m5C methyltransferases (RCMTs) mediate chromatin structures that can modulate 5-Azacitidine response and resistance. 21 March 2018 | doi: 10.1038/s41467-018-03513-4 Haematological cancer  Oncology  Difluoromethylation of (hetero)aryl chlorides with chlorodifluoromethane catalyzed by nickel OPEN Chang Xu, Wen-Hao Guo, Xu He, Yin-Long Guo, Xue-Ying Zhang & Xingang Zhang Transformations with ClCF2H are very limited and normally involve a difluorocarbene intermediate. Here, the authors report a nickel-catalyzed difluoromethylation of aryl chlorides with chlorodifluoromethane via a difluoromethyl radical intermediate and apply the method to the synthesis of marketed pharmaceuticals. 21 March 2018 | doi: 10.1038/s41467-018-03532-1 Catalytic mechanisms  Homogeneous catalysis  Synthetic chemistry methodology  Structure of Schlafen13 reveals a new class of tRNA/rRNA- targeting RNase engaged in translational control OPEN Jin-Yu Yang , Xiang-Yu Deng, Yi-Sheng Li, Xian-Cai Ma, Jian-Xiong Feng, Bing Yu, Yang Chen, Yi-Ling Luo, Xi Wang, Mei-Ling Chen, Zhi-Xin Fang, Fu-Xiang Zheng, Yi-Ping Li, Qian Zhong, Tie-Bang Kang, Li-Bing Song, Rui-Hua Xu, Mu-Sheng Zeng, Wei Chen, Hui Zhang et al. Translation inhibition is a strategy for organisms to overcome various environmental stresses including viral infections. Here the authors show that a tRNA/rRNA-targeting RNase Schlafen13 inhibits protein synthesis by directly digesting cytoplasmic tRNA and rRNA with the ability to restrict viral propagation. 21 March 2018 | doi: 10.1038/s41467-018-03544-x Enzymes  Molecular biology  RNA  X-ray crystallography  Operando tribochemical formation of onion-like-carbon leads to macroscale superlubricity OPEN Diana Berman, Badri Narayanan, Mathew J. Cherukara, Subramanian K. R. S. Sankaranarayanan, Ali Erdemir, Alexander Zinovev & Anirudha V. Sumant Stress-induced tribochemical reactions that reduce friction at sliding interfaces typically require liquid lubricants. Here, the authors discover the nanoscale tribocatalytic formation of onion-like carbon from 2D MoS2 and nanodiamond under dry and oil-free conditions, providing superlubricity at the macroscale. 21 March 2018 | doi: 10.1038/s41467-018-03549-6 Surfaces, interfaces and thin films  Two-dimensional materials  nc886 is induced by TGF-β and suppresses the microRNA pathway in ovarian cancer OPEN Ji-Hye Ahn, Hyun-Sung Lee, Ju-Seog Lee, Yeon-Su Lee, Jong-Lyul Park, Seon-Young Kim, Jung-Ah Hwang, Nawapol Kunkeaw, Sung Yun Jung, Tae Jin Kim, Kwang-Soo Lee, Sung Ho Jeon, Inhan Lee, Betty H. Johnson, Jung-Hye Choi & Yong Sun Lee Ovarian cancers often display elevated TGF-β signaling but repressed miRNA expression. Here the authors identify that non-coding RNA nc886 expression is induced by TGF-β, which then binds to DICER and impairs miRNA maturation. 21 March 2018 | doi: 10.1038/s41467-018-03556-7 Growth factor signalling  Ovarian cancer  Small RNAs  Adsorption-induced slip inhibition for polymer melts on ideal substrates OPEN Mark Ilton, Thomas Salez, Paul D. Fowler, Marco Rivetti, Mohammed Aly, Michael Benzaquen, Joshua D. McGraw, Elie Raphaël, Kari Dalnoki-Veress & Oliver Bäumchen When modeling fluid flow over a solid surface, one must determine the slip velocity at the boundary. Here Ilton et al. perform experiments to quantify the slip length of polymer melts at a nearly ideal solid surface and capture them in a model involving the density of physically adsorbed polymer chains. 21 March 2018 | doi: 10.1038/s41467-018-03610-4 Fluid dynamics  Polymers  Reactive-site-centric chemoproteomics identifies a distinct class of deubiquitinase enzymes OPEN David S. Hewings, Johanna Heideker, Taylur P. Ma, Andrew P. AhYoung, Farid El Oualid, Alessia Amore, Gregory T. Costakes, Daniel Kirchhofer, Bradley Brasher, Thomas Pillow, Nataliya Popovych, Till Maurer, Carsten Schwerdtfeger, William F. Forrest, Kebing Yu, John Flygare, Matthew Bogyo & Ingrid E. Wertz Deubiquitinases are proteases that cleave after the C-terminus of ubiquitin to hydrolyze ubiquitin chains and cleave ubiquitin from substrates. Here the authors describe a reactive-site-centric chemoproteomics approach to studying deubiquitinase activity, and expand the repertoire of known deubiquitinases. 21 March 2018 | doi: 10.1038/s41467-018-03511-6 Chemical tools  Proteases  Proteomic analysis  Proteomics  The global distribution and spread of the mobilized colistin resistance gene mcr-1 OPEN Ruobing Wang, Lucy van Dorp, Liam P. Shaw, Phelim Bradley, Qi Wang, Xiaojuan Wang, Longyang Jin, Qing Zhang, Yuqing Liu, Adrien Rieux, Thamarai Dorai-Schneiders, Lucy Anne Weinert, Zamin Iqbal, Xavier Didelot, Hui Wang & Francois Balloux The recent plasmid-mediated spread of the mobilized colistin resistance gene mcr-1 poses a significant public health threat, requiring worldwide monitoring and surveillance. Here, Wang et al. compile and analyze a data set of 457 mcr-1-positive sequenced isolates to investigate the origin and global distribution of mcr-1. 21 March 2018 | doi: 10.1038/s41467-018-03205-z Antimicrobial resistance  Computational biology and bioinformatics  Microbiology  Phylogenetics  AUX1-mediated root hair auxin influx governs SCFTIR1/AFB-type Ca2+ signaling OPEN Julian Dindas, Sönke Scherzer, M. Rob G. Roelfsema, Katharina von Meyer, Heike M. Müller, K. A. S. Al-Rasheid, Klaus Palme, Petra Dietrich, Dirk Becker, Malcolm J. Bennett & Rainer Hedrich Auxin regulates multiple aspects of plant growth and development. Here Dindas et al. show that in root-hair cells, the AUX1 auxin influx carrier mediates proton-driven auxin import that is perceived by auxin receptors and coupled to Ca2+ waves that may modulate adaptive responses in the root. 21 March 2018 | doi: 10.1038/s41467-018-03582-5 Auxin  Permeation and transport  JMJD5 is a human arginyl C-3 hydroxylase OPEN Sarah E. Wilkins, Saiful Islam, Joan M. Gannon, Suzana Markolovic, Richard J. Hopkinson, Wei Ge, Christopher J. Schofield & Rasheduzzaman Chowdhury Jumonji-C domain containing protein 5 (JMJD5) is essential for animal development but its catalytic activity has remained elusive so far. Here the authors show that human JMJD5 is an arginyl-hydroxylase and present the cofactor, substrate and product bound JMJD5 crystal structures. 21 March 2018 | doi: 10.1038/s41467-018-03410-w Enzyme mechanisms  High-throughput screening  Nanocrystallography  Post-translational modifications  Proteomics  The oldest magnetic record in our solar system identified using nanometric imaging and numerical modeling OPEN Jay Shah, Wyn Williams, Trevor P. Almeida, Lesleis Nagy, Adrian R. Muxworthy, András Kovács, Miguel A. Valdez-Grijalva, Karl Fabian, Sara S. Russell, Matthew J. Genge & Rafal E. Dunin-Borkowski Magnetic fields are thought to have been influential in the formation of our solar system. Here, the authors observe thermomagnetically stable, non-uniformly magnetized kamacite grains within chondritic meteorites, and calculate the grains to retain recordings of these magnetic fields. 21 March 2018 | doi: 10.1038/s41467-018-03613-1 Early solar system  Magnetic properties and materials  Meteoritics  Palaeomagnetism  Transmission electron microscopy  Pressureless glass crystallization of transparent yttrium aluminum garnet-based nanoceramics OPEN Xiaoguang Ma, Xiaoyu Li, Jianqiang Li, Cécile Genevois, Bingqian Ma, Auriane Etienne, Chunlei Wan, Emmanuel Véron, Zhijian Peng & Mathieu Allix Transparent YAG crystals are ubiquitous in phosphors, scintillators and lasers, but are complex and costly to make. Here, the authors use a one-step pressureless crystallization of bulk glass to make a transparent biphasic YAG nanoceramic that can be doped for optical applications. 21 March 2018 | doi: 10.1038/s41467-018-03467-7 Glasses  Materials for optics  Nanoscale materials  Integrative proteomics in prostate cancer uncovers robustness against genomic and transcriptomic aberrations during disease progression OPEN Leena Latonen, Ebrahim Afyounian, Antti Jylhä, Janika Nättinen, Ulla Aapola, Matti Annala, Kati K. Kivinummi, Teuvo T. L. Tammela, Roger W. Beuerman, Hannu Uusitalo, Matti Nykter & Tapio Visakorpi Understanding of molecular events in cancer requires proteome-level characterisation. Here, proteome profiling of patient samples representing primary and progressed prostate cancer enables the authors to identify pathway alterations that are not reflected at the genomic and transcriptomic levels. 21 March 2018 | doi: 10.1038/s41467-018-03573-6 Data integration  Prostate cancer  Proteome informatics  The elusive abnormal CO2 insertion enabled by metal-ligand cooperative photochemical selectivity inversion OPEN Felix Schneck, Jennifer Ahrens, Markus Finger, A. Claudia Stückl, Christian Würtele, Dirk Schwarzer & Sven Schneider The development of molecular catalysts for the reverse water–gas shift reaction is impeded by the general selectivity of CO2 insertion into M–H bonds to formates. Here, the authors report that the selectivity of CO2 insertion into a Ni–H bond can be inverted from normal to abnormal insertion upon switching from thermal to photochemical conditions. 21 March 2018 | doi: 10.1038/s41467-018-03239-3 Catalytic mechanisms  Organometallic chemistry  Photochemistry  A spliced latency-associated VZV transcript maps antisense to the viral transactivator gene 61 OPEN Daniel P. Depledge, Werner J. D. Ouwendijk, Tomohiko Sadaoka, Shirley E. Braspenning, Yasuko Mori, Randall J. Cohrs, Georges M. G. M. Verjans & Judith Breuer Varicella-zoster virus (VZV) establishes lifelong infection in the majority of the population, but mechanisms underlying latency remain unclear. Here, the authors use ultra-deep RNA sequencing, enriched for viral RNAs, of latently infected human trigeminal ganglia and identify a spliced, latency-associated VZV mRNA. 21 March 2018 | doi: 10.1038/s41467-018-03569-2 Herpes virus  Transcriptomics  Viral pathogenesis  Placenta and appetite genes GDF15 and IGFBP7 are associated with hyperemesis gravidarum OPEN Marlena S. Fejzo, Olga V. Sazonova, J. Fah Sathirapongsasuti, Ingileif B. Hallgrímsdóttir, Vladimir Vacic, Kimber W. MacGibbon, Frederic P. Schoenberg, Nicholas Mancuso, Dennis J. Slamon & Patrick M. Mullin Hyperemesis gravidarum (HG) is a severe form of nausea and vomiting associated with unfavourable outcomes during pregnancy. Here, Fejzo et al. perform genome-wide scans for HG and pregnancy nausea and vomiting and identify genetic associations at two loci implicating the genes GDF15 and IGFBP7. 21 March 2018 | doi: 10.1038/s41467-018-03258-0 Diseases  Genetic association study  Genetics research  Dynamical origins of heat capacity changes in enzyme-catalysed reactions OPEN Marc W. van der Kamp, Erica J. Prentice, Kirsty L. Kraakman, Michael Connolly, Adrian J. Mulholland & Vickery L. Arcus Heat capacity changes affect the temperature dependence of enzyme catalysis, with implications for thermoadaptation, however their physical basis is unknown. Here the authors show that heat capacity changes are calculable by simulation, revealing distinct dynamical contributions from regions remote from the active site. 21 March 2018 | doi: 10.1038/s41467-018-03597-y Biochemistry  Catalysis  Computational biophysics  Enzymes  Elementary steps in electrical doping of organic semiconductors OPEN Max L. Tietze, Johannes Benduhn, Paul Pahner, Bernhard Nell, Martin Schwarze, Hans Kleemann, Markus Krammer, Karin Zojer, Koen Vandewal & Karl Leo Molecular doping is routinely used in organic semiconductor devices nowadays, but the physics at play remains unclarified. Tietze et al. describe it as a two-step process and show it costs little, energetically, to dissociate charge transfer complexes due to energetic disorder of organic semiconductors. 21 March 2018 | doi: 10.1038/s41467-018-03302-z Electronic materials  Electronic properties and materials  Semiconductors  A bright organic NIR-II nanofluorophore for three-dimensional imaging into biological tissues OPEN Hao Wan, Jingying Yue, Shoujun Zhu, Takaaki Uno, Xiaodong Zhang, Qinglai Yang, Kuai Yu, Guosong Hong, Junying Wang, Lulin Li, Zhuoran Ma, Hongpeng Gao, Yeteng Zhong, Jessica Su, Alexander L. Antaris, Yan Xia, Jian Luo, Yongye Liang & Hongjie Dai Imaging in the second near-infrared window has attracted attention due to superior penetration depth and low signal interference. Here, the authors describe a new organic nano fluorophore with high quantum yield and demonstrate its use for in vivo imaging. 21 March 2018 | doi: 10.1038/s41467-018-03505-4 3-D reconstruction  Fluorescence imaging  Nanoparticles  Visible light-driven C−H activation and C–C coupling of methanol into ethylene glycol OPEN Shunji Xie, Zebin Shen, Jiao Deng, Pu Guo, Qinghong Zhang, Haikun Zhang, Chao Ma, Zheng Jiang, Jun Cheng, Dehui Deng & Ye Wang Direct transformation of methanol into two- or multi-carbon compounds is extremely attractive but remains a challenge. Here, the authors report an efficient photocatalytic route to the transformation of methanol into ethylene glycol and hydrogen over a molybdenum disulfide nanofoam-modified cadmium sulfide nanorod catalyst. 21 March 2018 | doi: 10.1038/s41467-018-03543-y Heterogeneous catalysis  Photocatalysis  Sustainability  Catalytic mechanism and molecular engineering of quinolone biosynthesis in dioxygenase AsqJ OPEN Sophie L. Mader, Alois Bräuer, Michael Groll & Ville R. I. Kaila The catalytic activity of dioxygenase AsqJ is strictly relying on the methylation of quinolone substrates. Here, the authors apply molecular simulations, X-ray crystallography and in vitro biochemical studies to the engineering of dioxygenase AsqJ with improved catalytic activity for modified non-methylated surrogates. 21 March 2018 | doi: 10.1038/s41467-018-03442-2 Density functional theory  Enzyme mechanisms  X-ray crystallography  Inhibitory gain modulation of defense behaviors by zona incerta OPEN Xiao-lin Chou, Xiyue Wang, Zheng-gang Zhang, Li Shen, Brian Zingg, Junxiang Huang, Wen Zhong, Lukas Mesik, Li I. Zhang & Huizhong Whit Tao Zona incerta (ZI) is an inhibitory subthalamic nucleus with diverse connectivity yet its functional importance has not been extensively studied. Here the authors report that ZI receives mPFC input and can modulate both innate and learned defensive behaviors via its inhibitory projection to the PAG. 20 March 2018 | doi: 10.1038/s41467-018-03581-6 Extinction  Fear conditioning  Neural circuits  Neurophysiology  Sensory processing  Land use change and El Niño-Southern Oscillation drive decadal carbon balance shifts in Southeast Asia OPEN Masayuki Kondo , Kazuhito Ichii, Prabir K. Patra, Joseph G. Canadell, Benjamin Poulter, Stephen Sitch, Leonardo Calle, Yi Y. Liu, Albert I. J. M. van Dijk, Tazu Saeki, Nobuko Saigusa, Pierre Friedlingstein, Almut Arneth, Anna Harper, Atul K. Jain, Etsushi Kato, Charles Koven, Fang Li, Thomas A. M. Pugh, Sönke Zaehle et al. The carbon balance in Southeast Asia is highly uncertain. Here, the authors show that land use changes and occurrence of strong El Niño control decadal shifts in the carbon balance of this region. 20 March 2018 | doi: 10.1038/s41467-018-03374-x Attribution  Carbon cycle  Suppression of low-frequency charge noise in superconducting resonators by surface spin desorption OPEN S. E. de Graaf, L. Faoro, J. Burnett, A. A. Adamyan, A. Ya. Tzalenchuk, S. E. Kubatkin, T. Lindström & A. V. Danilov The performance of solid-state quantum devices is often affected by low-frequency noise that appears to arise from the presence of two-level defects. Here the authors show that surface spins that cause magnetic noise are an origin of dielectric noise in superconducting resonators. 20 March 2018 | doi: 10.1038/s41467-018-03577-2 Electronic properties and materials  Superconducting devices  Surfaces, interfaces and thin films  Spatial variation of the rain–snow temperature threshold across the Northern Hemisphere OPEN Keith S. Jennings, Taylor S. Winchell, Ben Livneh & Noah P. Molotch Land surface models often use a spatially uniform air temperature threshold when partitioning rain and snow. Here Jennings et al. show that the threshold varies significantly across the Northern Hemisphere and that threshold selection is a large source of uncertainty in snowfall simulations. 20 March 2018 | doi: 10.1038/s41467-018-03629-7 Climate change  Hydrology  Water resources  Architecture of the Saccharomyces cerevisiae NuA4/TIP60 complex OPEN Xuejuan Wang, Salar Ahmad, Zhihui Zhang, Jacques Côté & Gang Cai The NuA4 histone acetyltransferase complex is important for gene regulation, DNA repair processes and cell cycle progression. Here the authors give molecular insights into the NuA4 complex by presenting the cryo-EM structures of the NuA4 TEEAA (Tra1, Eaf1, Eaf5, actin, and Arp4) and TEEAA-piccolo NuA4 assemblies. 20 March 2018 | doi: 10.1038/s41467-018-03504-5 Cryoelectron microscopy  Histone post-translational modifications  Photonic chip-based soliton frequency combs covering the biological imaging window OPEN Maxim Karpov, Martin H. P. Pfeiffer, Junqiu Liu, Anton Lukashchuk & Tobias J. Kippenberg Dissipative Kerr solitons in optical microresonators provide excellent optical frequency comb sources for precision metrology and imaging techniques. Here, Karpov et al. demonstrate a chipscale octave-spanning soliton-based comb, operating at 1 μm wavelength that covers the biological imaging window. 20 March 2018 | doi: 10.1038/s41467-018-03471-x Frequency combs  Nonlinear optics  Solitons  Ultrafast photonics  uvCLAP is a fast and non-radioactive method to identify in vivo targets of RNA-binding proteins OPEN Daniel Maticzka, Ibrahim Avsar Ilik, Tugce Aktas, Rolf Backofen & Asifa Akhtar RNA-binding proteins have important roles in gene expression and regulation. Here the authors develop uvCLAP to purify proteins and determine their binding sites without the use of radioactivity. 20 March 2018 | doi: 10.1038/s41467-018-03575-4 Computational biology and bioinformatics  RNA metabolism  Explosive dissolution and trapping of block copolymer seed crystallites OPEN Gerald Guerin, Paul A. Rupar, Ian Manners & Mitchell A. Winnik The study of the dissolution of polymer crystals is a challenging task. Here the authors use crystallization-driven self-assembly of coil-crystalline block copolymers as a trapping technique to track the change in length of 1D seed crystallites during annealing. 20 March 2018 | doi: 10.1038/s41467-018-03528-x Nanowires  Polymers  Self-assembly  Microscopic mechanisms of deformation transfer in high dynamic range branched nanoparticle deformation sensors OPEN Shilpa N. Raja, Xingchen Ye, Matthew R. Jones, Liwei Lin, Sanjay Govindjee & Robert O. Ritchie Tetrapod quantum dots are promising nanoscale stress sensors because of their non-invasive sensing technique, but sensor versatility has not yet been assessed. Here the authors show that tetrapod quantum dots exhibit a large dynamic range and excellent sensing versatility in a multitude of polymers. 20 March 2018 | doi: 10.1038/s41467-018-03396-5 Mechanical properties  Nanoparticles  Polymers  Crystal structure of an intramembranal phosphatase central to bacterial cell-wall peptidoglycan biosynthesis and lipid recycling OPEN Sean D. Workman, Liam J. Worrall & Natalie C. J. Strynadka Undecaprenyl pyrophosphate phosphatase (UppP) recycles the lipid carrier essential for bacterial cell wall synthesis. Here authors present the crystal structure of UppP from E. coli at 2.0 Å resolution, which sheds light on its phosphatase mechanism and indicates a potential flippase role for UppP. 20 March 2018 | doi: 10.1038/s41467-018-03547-8 Microbiology  X-ray crystallography  The human cortex possesses a reconfigurable dynamic network architecture that is disrupted in psychosis OPEN Jenna M. Reinen, Oliver Y. Chén, R. Matthew Hutchison, B. T. Thomas Yeo, Kevin M. Anderson, Mert R. Sabuncu, Dost Öngür, Joshua L. Roffman, Jordan W. Smoller, Justin T. Baker & Avram J. Holmes Temporal changes in brain dynamics are linked with cognitive abilities, but neither their stability nor relationship to psychosis is clear. Here, authors describe the dynamic neural architecture in healthy controls and patients with psychosis and find that they are stable over time and can predict psychotic symptoms. 20 March 2018 | doi: 10.1038/s41467-018-03462-y Cognitive neuroscience  Human behaviour  Psychosis  The genomic and functional landscapes of developmental plasticity in the American cockroach OPEN Sheng Li, Shiming Zhu, Qiangqiang Jia, Dongwei Yuan, Chonghua Ren, Kang Li, Suning Liu, Yingying Cui, Haigang Zhao, Yanghui Cao, Gangqi Fang, Daqi Li, Xiaoming Zhao, Jianzhen Zhang, Qiaoyun Yue, Yongliang Fan, Xiaoqiang Yu, Qili Feng & Shuai Zhan The American cockroach (Periplaneta americana) is an hemimetabolous insect with rapid growth, high fecundity, and remarkable tissue-regeneration capability. Here Li et al sequence its 3.38-Gb genome and perform the functional studies, yielding insights into its environmental adaptation and developmental plasticity. 20 March 2018 | doi: 10.1038/s41467-018-03281-1 Evolutionary biology  Genome evolution  RNAi  ZFR coordinates crosstalk between RNA decay and transcription in innate immunity OPEN Nazmul Haque, Ryota Ouda, Chao Chen, Keiko Ozato & J. Robert Hogg Type I interferon signaling is critical for the control of infection. Here the authors show that zinc finger RNA-binding protein (ZFR) can control type I interferon responses, and that this control is itself regulated by distinct ZFR truncation patterns that differ between monocytes and macrophages. 20 March 2018 | doi: 10.1038/s41467-018-03326-5 Alternative splicing  Innate immunity  RNA decay  Industrial brewing yeast engineered for the production of primary flavor determinants in hopped beer OPEN Charles M. Denby, Rachel A. Li, Van T. Vu, Zak Costello, Weiyin Lin, Leanne Jade G. Chan, Joseph Williams, Bryan Donaldson, Charles W. Bamforth, Christopher J. Petzold, Henrik V. Scheller, Hector Garcia Martin & Jay D. Keasling Production of aromatic monoterpene molecules in hop flowers is affected by genetic, environmental, and processing factors. Here, the authors engineer brewer’s yeast for the production of linalool and geraniol, and show pilot-scale beer produced by engineered strains reconstitutes some qualities of hop flavor. 20 March 2018 | doi: 10.1038/s41467-018-03293-x Applied microbiology  Metabolic engineering  Neighbourhood interactions drive overyielding in mixed-species tree communities OPEN Andreas Fichtner, Werner Härdtle, Helge Bruelheide, Matthias Kunz, Ying Li & Goddert von Oheimb Though biodiversity is expected to be important in productivity in tree communities, there is little empirical evidence of this at local scales. Here, Fichtner et al. show that higher neighbourhood species richness increased tree growth, explaining over half of the variation in community productivity. 20 March 2018 | doi: 10.1038/s41467-018-03529-w Biodiversity  Community ecology  Forest ecology  Robustness of anthropogenically forced decadal precipitation changes projected for the 21st century OPEN Honghai Zhang & Thomas L. Delworth Decadal precipitation changes are dominated by random natural variability, posing a challenge for projecting anthropogenic impacts. Here the authors use large suites of model simulations to show that human-induced future decadal shifts in regional precipitation can be distinguished from natural variability. 20 March 2018 | doi: 10.1038/s41467-018-03611-3 Atmospheric dynamics  Attribution  Environmental impact  Hydrology  Projection and prediction  Structure of the activated Edc1-Dcp1-Dcp2-Edc3 mRNA decapping complex with substrate analog poised for catalysis OPEN Jeffrey S. Mugridge, Ryan W. Tibble, Marcin Ziemniak, Jacek Jemielity & John D. Gross The decapping enzyme Dcp2 removes the 5′ eukaryotic cap from mRNA transcripts and acts in concert with its essential activator Dcp1 and various coactivators. Here the authors present the structure of the fully-activated mRNA decapping complex, which reveals how Dcp2 recognizes the cap substrate and coactivators Edc1 and Edc3 activate catalysis. 20 March 2018 | doi: 10.1038/s41467-018-03536-x RNA  RNA decay  Structural biology  X-ray crystallography  Memory effects can make the transmission capability of a communication channel uncomputable OPEN David Elkouss & David Pérez-García In information theory one is interested in how much information can be reliably sent over noisy communication channels. Here the authors show that for channels with memory the optimal rate of information transmission is uncomputable. 20 March 2018 | doi: 10.1038/s41467-018-03428-0 Computer science  Information theory and computation  Understanding and tailoring ligand interactions in the self-assembly of branched colloidal nanocrystals into planar superlattices OPEN Andrea Castelli, Joost de Graaf, Sergio Marras, Rosaria Brescia, Luca Goldoni, Liberato Manna & Milena P. Arciniegas The self-organization of nanocrystals into complex superlattices involves the interplay of different interactions. Here, the authors systematically reveal the effects of particle shape and ligand coverage on the assembly behavior of branched octapods into planar superlattices. 20 March 2018 | doi: 10.1038/s41467-018-03550-z Self-assembly  Surface chemistry  Synthesis and processing  Redefining the ancestral origins of the interleukin-1 superfamily OPEN Jack Rivers-Auty, Michael J. D. Daniels, Isaac Colliver, David L. Robertson & David Brough The IL-1 evolutionary history is essential in our understanding of function and development. Here the authors use molecular phylogenetic analysis to probe the IL-1 family in a range of species, suggesting disparate phylogenetic association of IL-18 and IL-33 proteins within the IL-1 family. 20 March 2018 | doi: 10.1038/s41467-018-03362-1 Computational biology and bioinformatics  Immunology  Interleukins  Phylogenetics  Wnt ligands influence tumour initiation by controlling the number of intestinal stem cells OPEN D. J. Huels, L. Bruens, M. C. Hodder, P. Cammareri, A. D. Campbell, R. A. Ridgway, D. M. Gay, M. Solar-Abboud, W. J. Faller, C. Nixon, L. B. Zeiger, M. E. McLaughlin, E. Morrissey, D. J. Winton, H. J. Snippert, J. van Rheenen & O. J. Sansom Wnt ligands are essential for intestinal homoeostasis and stem cell maintenance. Here, the authors show that reduction in Wnt secretion reduces the number of intestinal stem cells; this results in rapid fixation of mutated stem cells and accelerated adenoma formation due to lack of cell competition. 19 March 2018 | doi: 10.1038/s41467-018-03426-2 Colorectal cancer  Intestinal stem cells  Biomimetic artificial organelles with in vitro and in vivo activity triggered by reduction in microenvironment OPEN T. Einfalt, D. Witzigmann, C. Edlinger, S. Sieber, R. Goers, A. Najer, M. Spulber, O. Onaca-Fischer, J. Huwyler & C. G. Palivan The efficacy of stimuli-responsive enzyme delivery systems is usually limited to in vitro applications. Here the authors form artificial organelles by inserting stimuli-responsive protein gates in membranes of polymersomes loaded with enzymes and obtain a triggered functionality both in vitro and in vivo. 19 March 2018 | doi: 10.1038/s41467-018-03560-x Bioinspired materials  Supramolecular assembly  Phase nucleation through confined spinodal fluctuations at crystal defects evidenced in Fe-Mn alloys OPEN A. Kwiatkowski da Silva, D. Ponge, Z. Peng, G. Inden, Y. Lu, A. Breen, B. Gault & D. Raabe Solid-state phase transitions often involve nucleation of the new phase on defects but a detailed mechanistic understanding has not been established. Here the authors observe spinodal fluctuations at dislocations and grain boundaries in an iron alloy, which may be precursors in a multistep nucleation process. 19 March 2018 | doi: 10.1038/s41467-018-03591-4 Metals and alloys  Phase transitions and critical phenomena  Meridional heat transport variability induced by mesoscale processes in the subpolar North Atlantic OPEN Jian Zhao, Amy Bower, Jiayan Yang & Xiaopei Lin The oceanic heat transport is traditionally believed to be determined by the large-scale ocean circulation. New findings suggest that the energetic mesoscale processes in the Iceland Basin profoundly modulate the oceanic heat transport variability on time scales from intra-seasonal to interannual. 19 March 2018 | doi: 10.1038/s41467-018-03134-x Physical oceanography  Peli1 negatively regulates noncanonical NF-κB signaling to restrain systemic lupus erythematosus OPEN Junli Liu , Xinfang Huang, Shumeng Hao, Yan Wang, Manman Liu, Jing Xu, Xingli Zhang, Tao Yu, Shucheng Gan, Dongfang Dai, Xuan Luo, Qingyan Lu, Chaoming Mao, Yanyun Zhang, Nan Shen, Bin Li, Mingzhu Huang, Xiaodong Zhu, Jin Jin, Xuhong Cheng et al. Systemic lupus erythematosus (SLE) is an autoimmune disorder mediated by excessive autoantibodies. Here the authors show that an E3 ubiquitin ligase, Peli1, negatively modulates noncanonical NF-κB signaling to restrain lupus-like symptoms in mice, and that Peli1 expression inversely correlates with SLE severity in humans. 19 March 2018 | doi: 10.1038/s41467-018-03530-3 Antibodies  Autoimmunity  NF-kappaB  Ubiquitylation  Nitrogen-rich organic soils under warm well-drained conditions are global nitrous oxide emission hotspots OPEN Jaan Pärn , Jos T. A. Verhoeven, Klaus Butterbach-Bahl, Nancy B. Dise, Sami Ullah, Anto Aasa, Sergey Egorov, Mikk Espenberg, Järvi Järveoja, Jyrki Jauhiainen, Kuno Kasak, Leif Klemedtsson, Ain Kull, Fatima Laggoun-Défarge, Elena D. Lapshina, Annalea Lohila, Krista Lõhmus, Martin Maddison, William J. Mitsch, Christoph Müller et al. In a global field survey across a wide range of organic soils, the authors find that N2O flux can be predicted by models incorporating soil nitrate concentration (NO3–), water content and temperature. N2O emission increases with NO3– and temperature and follows a bell-shaped distribution with water content. 19 March 2018 | doi: 10.1038/s41467-018-03540-1 Element cycles  Spatially heterogeneous dynamics in a metallic glass forming liquid imaged by electron correlation microscopy OPEN Pei Zhang, Jason J. Maldonis, Ze Liu, Jan Schroers & Paul M. Voyles Glass forming liquids near the glass transition exhibit spatially heterogeneous dynamics, but it remains challenging to study their dynamics and structural origin on an atomic scale. Zhang et al. visualize liquid dynamics at a sub-nanometer and millisecond resolution using electron correlation microscopy. 19 March 2018 | doi: 10.1038/s41467-018-03604-2 Glasses  Structure of solids and liquids  Copper-surface-mediated synthesis of acetylenic carbon-rich nanofibers for active metal-free photocathodes OPEN Tao Zhang, Yang Hou, Volodymyr Dzhagan, Zhongquan Liao, Guoliang Chai, Markus Löffler, Davide Olianas, Alberto Milani, Shunqi Xu, Matteo Tommasini, Dietrich R. T. Zahn, Zhikun Zheng, Ehrenfried Zschech, Rainer Jordan & Xinliang Feng While photoelectrochemical devices combine light-absorption with fuel and electricity generation, their implementation is hampered by high costs and low output. Here, the authors synthesized acetylene-rich carbon fibers by copper-mediated polymerization for high-activity, metal-free photocathodes. 19 March 2018 | doi: 10.1038/s41467-018-03444-0 Conjugated polymers  Devices for energy harvesting  Heterogeneous catalysis  Photocatalysis  Surface assembly  The MerR-like protein BldC binds DNA direct repeats as cooperative multimers to regulate Streptomyces development OPEN Maria A. Schumacher, Chris D. den Hengst, Matthew J. Bush, T. B. K. Le, Ngat T. Tran, Govind Chandra, Wenjie Zeng, Brady Travis, Richard G. Brennan & Mark J. Buttner BldC regulates the onset of differentiation in Streptomycetes by a yet unknown molecular mechanism. Using a combination of structural, biochemical and in vivo approaches, the authors show that BldC controls the transcription of several developmental regulators and unravel its DNA binding mode. 19 March 2018 | doi: 10.1038/s41467-018-03576-3 Bacterial transcription  DNA-binding proteins  Transcription factors  X-ray crystallography  Glycogen synthase kinase 3 controls migration of the neural crest lineage in mouse and Xenopus OPEN Sandra G. Gonzalez Malagon, Anna M. Lopez Muñoz, Daniel Doro, Triòna G. Bolger, Evon Poon, Elizabeth R. Tucker, Hadeel Adel Al-Lami, Matthias Krause, Christopher J. Phiel, Louis Chesler & Karen J. Liu Defects in neural crest development cause neurocristopathies and cancer, but what regulates this is unclear. Here, the authors show that glycogen synthase kinase 3 (GSK3) regulates migration of neural crest cells, as shown on genetic deletion of GSK3 in the mouse, and that this acts via anaplastic lymphoma kinase. 19 March 2018 | doi: 10.1038/s41467-018-03512-5 Cell lineage  CNS cancer  Development of the nervous system  Lamellipodia  Predator-secreted sulfolipids induce defensive responses in C. elegans OPEN Zheng Liu, Maro J. Kariya, Christopher D. Chute, Amy K. Pribadi, Sarah G. Leinwand, Ada Tong, Kevin P. Curran, Neelanjan Bose, Frank C. Schroeder, Jagan Srinivasan & Sreekanth H. Chalasani Defensive behavioral responses can be triggered by predator-released odors. Here, the authors identified the relevant Pristionchus pacificus-released sulfolipid molecules and dissected the neural circuits underlying C. elegans response to this predator. 19 March 2018 | doi: 10.1038/s41467-018-03333-6 Sensory processing  Social behaviour  A supramolecular biomimetic skin combining a wide spectrum of mechanical properties and multiple sensory capabilities OPEN Zhouyue Lei & Peiyi Wu Biomimetic skin finds wide application in robotics and smart wearable devices but materials mimicking mechanical properties of skin and responding at the same time to multiple stimuli are rarely realized. Here the authors demonstrate a biomimetic hydrogel with multiple sensory capabilities which imitates mechanical properties of natural skin. 19 March 2018 | doi: 10.1038/s41467-018-03456-w Actuators  Gels and hydrogels  Polymers  An evolutionary hotspot defines functional differences between CRYPTOCHROMES OPEN Clark Rosensweig, Kimberly A. Reynolds, Peng Gao, Isara Laothamatas, Yongli Shan, Rama Ranganathan, Joseph S. Takahashi & Carla B. Green The molecular mechanisms that define the periodicity or rate of the circadian clock are not well understood. Here the authors use a multidisciplinary approach and identify a mechanism for period regulation that depends on the affinity of the core clock proteins for one another. 19 March 2018 | doi: 10.1038/s41467-018-03503-6 Circadian rhythm signalling peptides and proteins  Transcription  CtIP fusion to Cas9 enhances transgene integration by homology-dependent repair OPEN M. Charpentier, A. H. Y. Khedher, S. Menoret, A. Brion, K. Lamribet, E. Dardillac, C. Boix, L. Perrouault, L. Tesson, S. Geny, A. De Cian, J. M. Itier, I. Anegon, B. Lopez, C. Giovannangeli & J. P. Concordet The integration of exogenous DNA into the genome using CRISPR–Cas9 often presents a challenge to researchers. Here the authors fuse CtIP to Cas9 to stimulate recombination at target loci. 19 March 2018 | doi: 10.1038/s41467-018-03475-7 CRISPR-Cas9 genome editing  Functional genomics  Gene therapy  Genetic engineering  HIV envelope V3 region mimic embodies key features of a broadly neutralizing antibody lineage epitope OPEN Daniela Fera, Matthew S. Lee, Kevin Wiehe, R. Ryan Meyerhoff, Alessandro Piai, Mattia Bonsignori, Baptiste Aussedat, William E. Walkowicz, Therese Ton, Jeffrey O. Zhou, Samuel Danishefsky, Barton F. Haynes & Stephen C. Harrison The V3 region of HIV Env elicits broadly neutralizing antibodies (bnAbs) in patients and represents a potential vaccine antigen. Here, Fera et al. show that the structure of a synthetic V3-glycopeptide closely resembles the conformation in intact HIV Env and identify amino acids in bnAbs that are important for neutralization breadth. 16 March 2018 | doi: 10.1038/s41467-018-03565-6 Antibodies  HIV infections  Structural biology  Vaccines  Intersubband plasmons in the quantum limit in gated and aligned carbon nanotubes OPEN Kazuhiro Yanagi, Ryotaro Okada, Yota Ichinose, Yohei Yomogida, Fumiya Katsutani, Weilu Gao & Junichiro Kono Quantum confinement has enabled the development of modern optoelectronic devices, including the quantum cascade laser, based on the control of intersubband plasmons. Here, Yanagi et al. observe intersubband plasmons in gated and aligned carbon nanotubes with applications in carbon-based optoelectronics and fundamental physics. 16 March 2018 | doi: 10.1038/s41467-018-03381-y Carbon nanotubes and fullerenes  Nanophotonics and plasmonics  Continuous-wave highly-efficient low-divergence terahertz wire lasers OPEN Simone Biasco, Katia Garrasi, Fabrizio Castellano, Lianhe Li, Harvey E. Beere, David A. Ritchie, Edmund H. Linfield, A. Giles Davies & Miriam S. Vitiello Quantum cascade lasers are compact sources, but simultaneously achieving cw operation, low divergence and single-mode emission has proven difficult. Here, Biasco et al. use a combination of distributed feedback and outcoupling via hole arrays, improving the performance of such a terahertz laser. 16 March 2018 | doi: 10.1038/s41467-018-03440-4 Quantum cascade lasers  Terahertz optics  Thalamocortical dysrhythmia detected by machine learning OPEN Sven Vanneste, Jae-Jin Song & Dirk De Ridder Thalamocortical dysrhythmia has been proposed to occur in a number of neurological and psychiatric disorders. Here, the authors use a data-driven approach to demonstrate thalamocortical dysrhythmia occurs in individuals with Parkinson’s disease, neuropathic pain, tinnitus, and depression. 16 March 2018 | doi: 10.1038/s41467-018-02820-0 Electroencephalography – EEG  Thalamus  Monitoring ultrafast vibrational dynamics of isotopic molecules with frequency modulation of high-order harmonics OPEN Lixin He, Qingbin Zhang, Pengfei Lan, Wei Cao, Xiaosong Zhu, Chunyang Zhai, Feng Wang, Wenjing Shi, Muzi Li, Xue-Bin Bian, Peixiang Lu & André D. Bandrauk Previous studies on high harmonic generation from molecules have been used to identify the spectral properties and orbital contributions. Here the authors measure the isotopic effects in the energy shift of the HHG spectra caused by the nuclear motion of the molecules. 16 March 2018 | doi: 10.1038/s41467-018-03568-3 Atomic and molecular collision processes  Atomic and molecular interactions with photons  Atomic and molecular physics  Scalable total synthesis and comprehensive structure–activity relationship studies of the phytotoxin coronatine OPEN Mairi M. Littleson, Christopher M. Baker, Anne J. Dalençon, Elizabeth C. Frye, Craig Jamieson, Alan R. Kennedy, Kenneth B. Ling, Matthew M. McLachlan, Mark G. Montgomery, Claire J. Russell & Allan J. B. Watson Development of comprehensive structure–activity relationships for coronatine has been a major goal in the agrochemical industry. Here, the authors report the gram-scale production and structure–activity relationship of parent coronafacic acid and ultimately rationalise the biological activity of analogues of this phytotoxin. 16 March 2018 | doi: 10.1038/s41467-018-03443-1 Diversity-oriented synthesis  Synthetic chemistry methodology  Natural product synthesis  Archimedes’ law explains penetration of solids into granular media OPEN Wenting Kang, Yajie Feng, Caishan Liu & Raphael Blumenfeld The penetration dynamics of solid objects into granular media has been described by theories that are constrained to the use of phenomenological models or empirical parameters. Here, Kang et al. propose and test a parameter-free model for the dependence of the resistance force on penetration depth. 16 March 2018 | doi: 10.1038/s41467-018-03344-3 Civil engineering  Condensed-matter physics  Fluid dynamics  Fluids  Calcineurin-mediated IL-2 production by CD11chighMHCII+ myeloid cells is crucial for intestinal immune homeostasis OPEN Andrea Mencarelli, Hanif Javanmard Khameneh, Jan Fric, Maurizio Vacca, Sary El Daker, Baptiste Janela, Jing Ping Tang, Sabrina Nabti, Akhila Balachander, Tong Seng Lim, Florent Ginhoux, Paola Ricciardi-Castagnoli & Alessandra Mortellaro Treg cells can maintain intestinal homeostasis and limit intestinal bowel disease. Here the authors use a mouse model of spontaneous colitis to show that calcineurin-NFAT-induced IL-2 production by dendritic cells regulates the balance between Treg and effector T cells in the gut lamina propria. 16 March 2018 | doi: 10.1038/s41467-018-03495-3 Chronic inflammation  Mucosal immunology  Conventional dendritic cells  Physiological and therapeutic regulation of glucose homeostasis by upper small intestinal PepT1-mediated protein sensing OPEN Helen J. Dranse, T. M. Zaved Waise, Sophie C. Hamr, Paige V. Bauer, Mona A. Abraham, Brittany A. Rasmussen & Tony K. T. Lam High protein diets are known to improve metabolic parameters including adiposity and glucose homeostasis. Here the authors demonstrate that preabsorptive upper small intestinal protein-sensing mechanisms mediated by peptide transporter 1 improve glucose homeostasis by inhibiting hepatic glucose production. 16 March 2018 | doi: 10.1038/s41467-018-03490-8 Metabolism  Nutrient signalling  Pre-diabetes  A b map implying the first eastern rupture of the Nankai Trough earthquakes OPEN K. Z. Nanjo & A. Yoshida Earthquakes generated from the Nankai Trough have caused much devastation over the years. Here, the authors present a b-value map for the Nankai Trough zone, where the Eastern part of the trough has lower b-values than the West, which may help to explain why the Eastern part tends to rupture first. 16 March 2018 | doi: 10.1038/s41467-018-03514-3 Geodynamics  Natural hazards  Seismology  Clathrin-adaptor ratio and membrane tension regulate the flat-to-curved transition of the clathrin coat during endocytosis OPEN Delia Bucher, Felix Frey, Kem A. Sochacki, Susann Kummer, Jan-Philip Bergeest, William J. Godinez, Hans-Georg Kräusslich, Karl Rohr, Justin W. Taraska, Ulrich S. Schwarz & Steeve Boulant The sequence of structural and molecular events during clathrin-mediated endocytosis is unclear. Here the authors combine correlative microscopy and simple mathematical growth laws to demonstrate that the flat patch starts to curve when around 70% of the final clathrin content is reached. 16 March 2018 | doi: 10.1038/s41467-018-03533-0 Cellular imaging  Endocytosis  Membrane curvature  SUMO targets the APC/C to regulate transition from metaphase to anaphase OPEN Karolin Eifler, Sabine A. G. Cuijpers, Edwin Willemstein, Jonne A. Raaijmakers, Dris El Atmioui, Huib Ovaa, René H. Medema & Alfred C. O. Vertegaal Signal transduction by small ubiquitin-like modifier (SUMO) is important for cell cycle progression. Here the authors show that SUMOylation regulates the APC/C complex, a master orchestrator of metaphase to anaphase transition, with consequences for mitotic progression. 16 March 2018 | doi: 10.1038/s41467-018-03486-4 Chromosome segregation  Sumoylation  Ubiquitylation  A DHODH inhibitor increases p53 synthesis and enhances tumor cell killing by p53 degradation blockage OPEN Marcus J. G. W. Ladds , Ingeborg M. M. van Leeuwen, Catherine J. Drummond, Su Chu, Alan R. Healy, Gergana Popova, Andrés Pastor Fernández, Tanzina Mollick, Suhas Darekar, Saikiran K. Sedimbi, Marta Nekulova, Marijke C. C. Sachweh, Johanna Campbell, Maureen Higgins, Chloe Tuck, Mihaela Popa, Mireia Mayoral Safont, Pascal Gelebart, Zinayida Fandalyuk, Alastair M. Thompson et al. Activation of the tumor suppressor p53 is a promising approach in cancer therapy. Here, the authors discover a series of small molecule dihydroorotate dehydrogenase (DHODH) inhibitors that increase p53 synthesis and reduce tumor growth in synergy with the common mdm2 inhibitor nutlin3. 16 March 2018 | doi: 10.1038/s41467-018-03441-3 Drug development  Mechanism of action  Small molecules  Target identification  Functional architecture of reward learning in mushroom body extrinsic neurons of larval Drosophila OPEN Timo Saumweber, Astrid Rohwedder, Michael Schleyer, Katharina Eichler, Yi-chun Chen, Yoshinori Aso, Albert Cardona, Claire Eschbach, Oliver Kobler, Anne Voigt, Archana Durairaja, Nino Mancini, Marta Zlatic, James W. Truman, Andreas S. Thum & Bertram Gerber The mushroom body of Drosophila integrates sensory information with past experience to guide behaviour. Here, the authors provide an atlas of the input and output neurons of the stage 3 larval mushroom body at the single-cell level, and analyse their function in learned and innate behaviours. 16 March 2018 | doi: 10.1038/s41467-018-03130-1 Drosophila  Learning and memory  Asymmetric adhesion of rod-shaped bacteria controls microcolony morphogenesis OPEN Marie-Cécilia Duvernoy, Thierry Mora, Maxime Ardré, Vincent Croquette, David Bensimon, Catherine Quilliet, Jean-Marc Ghigo, Martial Balland, Christophe Beloin, Sigolène Lecuyer & Nicolas Desprat It is unclear how cell adhesion and elongation coordinate during formation of bacterial microcolonies. Here, Duvernoy et al. monitor microcolony formation in rod-shaped bacteria, and show that patterns of surface colonization derive from the spatial distribution of adhesive factors on the cell envelope. 16 March 2018 | doi: 10.1038/s41467-018-03446-y Biofilms  Biophysics  Cellular microbiology  Microbial ecology  Plasma dye coating as straightforward and widely applicable procedure for dye immobilization on polymeric materials OPEN Lieselot De Smet, Gertjan Vancoillie, Peter Minshall, Kathleen Lava, Iline Steyaert, Ella Schoolaert, Elke Van De Walle, Peter Dubruel, Karen De Clerck & Richard Hoogenboom Dye coating techniques for colored materials are often cost intensive or cause degradation of the material during processing. Here the authors demonstrate a fast, scalable and cost efficient plasma dye coating procedure, which allows for covalent immobilization of dye molecules on different polymer surfaces. 16 March 2018 | doi: 10.1038/s41467-018-03583-4 Design, synthesis and processing  Materials science  Organic molecules in materials science  Polymers  Estrogen receptor α drives pro-resilient transcription in mouse models of depression OPEN Zachary S. Lorsch , Yong-Hwee Eddie Loh, Immanuel Purushothaman, Deena M. Walker, Eric M. Parise, Marine Salery, Michael E. Cahill, Georgia E. Hodes, Madeline L. Pfau, Hope Kronman, Peter J. Hamilton, Orna Issler, Benoit Labonté, Ann E. Symonds, Matthew Zucker, Tie Yuan Zhang, Michael J. Meaney, Scott J. Russo, Li Shen, Rosemary C. Bagot et al. Stress resilience is accompanied by broad changes in gene expression. This study shows that estrogen receptor α (ERα) is a key upstream regulator of these changes in the nucleus accumbens, and that overexpression of ERα increases behavioral resilience via a sex-specific transcriptional mechanism. 16 March 2018 | doi: 10.1038/s41467-018-03567-4 Molecular neuroscience  Stress and resilience  PLK1 has tumor-suppressive potential in APC-truncated colon cancer cells OPEN Monika Raab, Mourad Sanhaji, Yves Matthess, Albrecht Hörlin, Ioana Lorenz, Christina Dötsch, Nils Habbe, Oliver Waidmann, Elisabeth Kurunci-Csacsko, Ron Firestein, Sven Becker & Klaus Strebhardt The overexpression of Polo-like kinase 1 (Plk1) promotes various cancers in humans; sporadic evidence suggests Plk1 could act as a tumor suppressor but the molecular basis for this effect are unclear. Here the authors show that Plk1 inhibition augments the tumorigenic capacity of a dominant-negative ∆APC mutant by increasing polyploidy and cell division. 16 March 2018 | doi: 10.1038/s41467-018-03494-4 Cancer  Colon cancer  Gastrointestinal cancer  Neural basis for categorical boundaries in the primate pre-SMA during relative categorization of time intervals OPEN Germán Mendoza, Juan Carlos Méndez, Oswaldo Pérez, Luis Prado & Hugo Merchant Grouping stimuli into categories often depends on a subjective determination of category boundaries. Here the authors report a neuronal population in pre-supplementary motor area whose peak activity predicts the categorical decision boundary between long and short time intervals on a trial-by-trial basis. 15 March 2018 | doi: 10.1038/s41467-018-03482-8 Decision  Network models  Perception  Sensitive and frequent identification of high avidity neo-epitope specific CD8 + T cells in immunotherapy-naive ovarian cancer OPEN Sara Bobisse , Raphael Genolet, Annalisa Roberti, Janos L. Tanyi, Julien Racle, Brian J. Stevenson, Christian Iseli, Alexandra Michel, Marie-Aude Le Bitoux, Philippe Guillaume, Julien Schmidt, Valentina Bianchi, Denarda Dangaj, Craig Fenwick, Laurent Derré, Ioannis Xenarios, Olivier Michielin, Pedro Romero, Dimitri S. Monos, Vincent Zoete et al. Epithelial ovarian cancer (EOC) has low mutational load. Here the authors analyze circulating and tumor-infiltrating lymphocytes (TILs) from 19 EOC patients and report frequent recovery of neo-antigen-reactive T cells from both compartments but with distinct TCR repertoires that have higher affinity in TILs. 15 March 2018 | doi: 10.1038/s41467-018-03301-0 Cancer immunotherapy  Ovarian cancer  Tumour immunology  A common mechanism of proteasome impairment by neurodegenerative disease-associated oligomers OPEN Tiffany A. Thibaudeau, Raymond T. Anderson & David M. Smith Disruption of the ubiquitin proteasome system (UPS) is often associated with neurodegenerative diseases. Here the authors demonstrate the existence of a general mechanism of proteasomal impairment triggered by a specific protein oligomer structure, irrespective of its protein constituent. 15 March 2018 | doi: 10.1038/s41467-018-03509-0 Alzheimer's disease  Enzyme mechanisms  Proteases  Protein aggregation  A comprehensive evaluation of module detection methods for gene expression data OPEN Wouter Saelens, Robrecht Cannoodt & Yvan Saeys Modules composed of groups of genes with similar expression profiles tend to be functionally related and co-regulated. Here, Saelens et al evaluate the performance of 42 computational methods and provide practical guidelines for module detection in gene expression data. 15 March 2018 | doi: 10.1038/s41467-018-03424-4 Data mining  Gene regulatory networks  How RNA transcripts coordinate DNA recombination and repair OPEN Shane McDevitt, Timur Rusanov, Tatiana Kent, Gurushankar Chandramouly & Richard T. Pomerantz Homologous recombination (HR) typically uses DNA as a donor template to accurately repair DNA breaks. Here, the authors elucidate two mechanisms by which RAD52 uses RNA as a template for HR: one involving RNA-mediated synapsis of a homologous DNA break, and the other involving reverse transcriptase dependent RNA-to-DNA sequence transfer at DNA breaks. 15 March 2018 | doi: 10.1038/s41467-018-03483-7 DNA  DNA damage and repair  RNA  Voltage gating of mechanosensitive PIEZO channels OPEN Mirko Moroni, M. Rocio Servin-Vences, Raluca Fleischer, Oscar Sánchez-Carranza & Gary R. Lewin PIEZO proteins form mechanosensitive ion channels. Here the authors present electrophysiological measurements that show that PIEZO channels are also modulated by voltage and can switch to a purely voltage gated mode, which is an evolutionary conserved property of this channel family. 15 March 2018 | doi: 10.1038/s41467-018-03502-7 Ion channels in the nervous system  Ion transport  Mechanisms of disease  Peripheral vascular disease  Permeation and transport  Apolipoprotein AI prevents regulatory to follicular helper T cell switching during atherosclerosis OPEN Dalia E. Gaddis, Lindsey E. Padgett, Runpei Wu, Chantel McSkimming, Veronica Romines, Angela M. Taylor, Coleen A. McNamara, Mitchell Kronenberg, Shane Crotty, Michael J. Thomas, Mary G. Sorci-Thomas & Catherine C. Hedrick Regulatory T (Treg) cells contribute to the anti-inflammatory response during atherogenesis. Here Gaddis et al. show that Apolipoprotein AI prevents the conversion of Treg cells into pro-atherogenic T follicular helper cells, and thus regulates the immune response during atherogenesis. 15 March 2018 | doi: 10.1038/s41467-018-03493-5 Atherosclerosis  Follicular T-helper cells  Regulatory T cells  Amplification of heat extremes by plant CO2 physiological forcing OPEN Christopher B. Skinner, Christopher J. Poulsen & Justin S. Mankin The effect of plants on future extreme heat events under elevated carbon dioxide (CO2) is unclear. Here, the authors show that CO2 plant physiological effects lead to increases in heat waves within a suite of climate model simulations, suggesting that vegetated areas are at risk of increased heat extremes. 15 March 2018 | doi: 10.1038/s41467-018-03472-w Carbon cycle  Climate and Earth system modelling  Projection and prediction  Light-triggered enzymatic reactions in nested vesicle reactors OPEN James W. Hindley, Yuval Elani, Catriona M. McGilvery, Simak Ali, Charlotte L. Bevan, Robert V. Law & Oscar Ces Matryoshka doll-like, nested vesicles, each containing a different ingredient to a chemical reaction, can serve as microreactors. Here, the authors developed a system in which mixing of the ingredients can be induced by irradiation with ultraviolet light. 15 March 2018 | doi: 10.1038/s41467-018-03491-7 Biocatalysis  Membranes  Molecular self-assembly  Photocatalysis  Modulation of sensory prediction error in Purkinje cells during visual feedback manipulations OPEN Martha L. Streng, Laurentiu S. Popa & Timothy J. Ebner Cerebellum is thought to encode predictions about upcoming movements and provide a sensory prediction error based on the actual movement. Here the authors manipulate visual feedback during a movement-tracking task to show that both signals are carried in the lead and lag modulations of simple spikes of Purkinje cells. 15 March 2018 | doi: 10.1038/s41467-018-03541-0 Cerebellum  Sensorimotor processing      Latest Author Correction       Author Correction: Efficient green light-emitting diodes based on quasi-two-dimensional composition and phase engineered perovskite with surface passivation OPEN Xiaolei Yang, Xingwang Zhang, Jinxiang Deng, Zema Chu, Qi Jiang, Junhua Meng, Pengyang Wang, Liuqi Zhang, Zhigang Yin & Jingbi You 16 March 2018 | doi: 10.1038/s41467-018-03702-1 Materials for devices  Organic LEDs      Latest Publisher Correction       Publisher Correction: Anderson light localization in biological nanostructures of native silk OPEN Seung Ho Choi, Seong-Wan Kim, Zahyun Ku, Michelle A. Visbal-Onufrak, Seong-Ryul Kim, Kwang-Ho Choi, Hakseok Ko, Wonshik Choi, Augustine M. Urbas, Tae-Won Goo & Young L. Kim 19 March 2018 | doi: 10.1038/s41467-018-03595-0 Biomaterials  Nanoscience and technology  Photonic devices  Renewable energy      Advertisement Focal Point on Japan's Designated National University Initiative Japan's radical new program to boost just a handful of universities has precedents across the world Access free online   Advertisement nature.com webcasts Nature Research Custom presents a webcast on: Precision Health: Using Blood Biomarkers to Detect and Prevent Disease Date: Thursday, March 29, 2018  Register for FREE Sponsored by: Quanterix    Advertisement Communications Biology: now publishing content Communications Biology is a new open access journal publishing high-quality primary research articles, reviews and commentary which represent significant advances and new insights in the field of biology. 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