Nature Communications - 26 September 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. 26 September 2018  Latest content: Articles Author Corrections Publisher Corrections Advertisement   Nature Index 2018 Rising Stars Creative minds drive the scientific enterprise. This supplement profiles up-and-coming researchers in the natural sciences who have achieved excellence in the Nature Index, and have demonstrated the passion, ambition and resilience to rise even higher in the competitive world of academia. Read the full supplement Journal homepage Recommend to library Web feed   Advertisement USCAP 2019 ANNUAL MEETING ABSTRACT SUBMISSIONS!  USCAP's 2019 Annual Meeting at National Harbor, Maryland, is the magnet for global pathologists to come together to think out loud about what's new, exciting and relevant in translational research and anatomic/molecular diagnostics. It's the forum for intellectual stimulation, information exchange, and social interaction. The 2019 program is designed to exceed your expectations and expose you to contemporary and vibrant pathology education at its best.  Submit your abstract now! (Deadline September 27th)     Advertisement Nature Outline: Retinal repair The retina is crucial for vision, but damage to this light-sensing part of the eye cannot yet be repaired. Growing and then transplanting healthy retinal cells, or building entire retinas from stem cells, might offer a solution for the millions of people worldwide who are affected by retinal degeneration.  Access now >         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 Articles View all Articles     Genome-wide association study of 23,500 individuals identifies 7 loci associated with brain ventricular volume OPEN Dina Vojinovic, Hieab H. Adams, Xueqiu Jian, Qiong Yang, Albert Vernon Smith, Joshua C. Bis, Alexander Teumer, Markus Scholz, Nicola J. Armstrong, Edith Hofer, Yasaman Saba, Michelle Luciano, Manon Bernard, Stella Trompet, Jingyun Yang, Nathan A. Gillespie, Sven J. van der Lee, Alexander Neumann, Shahzad Ahmad, Ole A. Andreassen et al. An increase in the volume of the brain lateral ventricles is a sign of normal aging, but can also be associated with neurological and psychiatric disorders. Here, Vojinovic et al. identify seven genetic loci in a GWA study for ventricular volume in 23,500 individuals and find correlation with thalamus volume. 26 September 2018 | doi: 10.1038/s41467-018-06234-w Genetics of the nervous system  Genome-wide association studies  Heritable quantitative trait  A distal centriolar protein network controls organelle maturation and asymmetry OPEN Lei Wang, Marion Failler, Wenxiang Fu & Brian D. Dynlacht Removal of daughter centriole-specific/enriched proteins (DCPs) and assembly of distal appendages (DA) are important for centrosome asymmetry. Here, the authors report that a centriolar distal end protein network regulates DCP removal, DA assembly, and ciliary vesicle docking. 26 September 2018 | doi: 10.1038/s41467-018-06286-y Neurodevelopmental disorders  Organelles  Chiral self-sorted multifunctional supramolecular biocoordination polymers and their applications in sensors OPEN Xiaobo Shang, Inho Song, Gwan Yeong Jung, Wanuk Choi, Hiroyoshi Ohtsu, Jeong Hyeon Lee, Jin Young Koo, Bo Liu, Jaeyong Ahn, Masaki Kawano, Sang Kyu Kwak & Joon Hak Oh Chiral supramolecules may be used in chiral recognition, sensing and catalysis. Here the authors selectively synthesized homochiral and heterochiral supramolecular biocoordination polymers of naphthalene diimide ligands with alanine termini and Zn ions. 26 September 2018 | doi: 10.1038/s41467-018-06147-8 Polymer synthesis  Polymers  Supramolecular polymers  Mitochondrial uncoupling reveals a novel therapeutic opportunity for p53-defective cancers OPEN R. Kumar, L. Coronel, B. Somalanka, A. Raju, O. A. Aning, O. An, Y. S. Ho, S. Chen, S. Y. Mak, P. Y. Hor, H. Yang, M. Lakshmanan, H. Itoh, S. Y. Tan, Y. K. Lim, A. P. C. Wong, S. H. Chew, T. H. Huynh, B. C. Goh, C. Y. Lim et al. Several challenges are involved in direct targeting of mutant p53, while targeting altered fitness of cells with loss of wild type p53 is an alternative approach. Here they identify niclosamide to be selectively toxic to p53 deficient cells through a previously unknown mitochondrial uncoupling mechanism. 26 September 2018 | doi: 10.1038/s41467-018-05805-1 Cancer metabolism  Cancer screening  Chemotherapy  Drug development  Oncology  Magnetized fast isochoric laser heating for efficient creation of ultra-high-energy-density states OPEN Shohei Sakata, Seungho Lee, Hiroki Morita, Tomoyuki Johzaki, Hiroshi Sawada, Yuki Iwasa, Kazuki Matsuo, King Fai Farley Law, Akira Yao, Masayasu Hata, Atsushi Sunahara, Sadaoki Kojima, Yuki Abe, Hidetaka Kishimoto, Aneez Syuhada, Takashi Shiroto, Alessio Morace, Akifumi Yogo, Natsumi Iwata, Mitsuo Nakai et al. It is desirable to deposit more energy in the dense plasma core to trigger the fusion ignition. Here the authors demonstrate enhanced energy coupling from laser to plasma core by using solid targets and guiding the transport of relativistic electron beam with external magnetic field. 26 September 2018 | doi: 10.1038/s41467-018-06173-6 Laser-produced plasmas  Plasma physics  Probing ultrafast spin-relaxation and precession dynamics in a cuprate Mott insulator with seven-femtosecond optical pulses OPEN T. Miyamoto, Y. Matsui, T. Terashige, T. Morimoto, N. Sono, H. Yada, S. Ishihara, Y. Watanabe, S. Adachi, T. Ito, K. Oka, A. Sawa & H. Okamoto Understanding the dynamics of cuprates following photoexcitation can provide insights into the complex coupling mechanisms that underlie their exotic equilibrium behaviour. Here the authors use pump-probe reflection spectroscopy to investigate the nonequilibrium spin dynamics of Mott-insulating Nd2CuO4. 26 September 2018 | doi: 10.1038/s41467-018-06312-z Electronic properties and materials  Magnetic properties and materials  UBL3 modification influences protein sorting to small extracellular vesicles OPEN Hiroshi Ageta, Natsumi Ageta-Ishihara, Keisuke Hitachi, Ozge Karayel, Takanori Onouchi, Hisateru Yamaguchi, Tomoaki Kahyo, Ken Hatanaka, Koji Ikegami, Yusuke Yoshioka, Kenji Nakamura, Nobuyoshi Kosaka, Masashi Nakatani, Akiyoshi Uezumi, Tomihiko Ide, Yutaka Tsutsumi, Haruhiko Sugimura, Makoto Kinoshita, Takahiro Ochiya, Matthias Mann et al. Exosomes mediate cell-to-cell communication by transporting proteins, mRNAs, and miRNAs but the mechanisms of protein sorting to exosomes are poorly understood. Here, the authors uncover that ubiquitin-like 3 (UBL3) regulates protein sorting to exosomes by acting as a posttranslational modification. 26 September 2018 | doi: 10.1038/s41467-018-06197-y Multivesicular bodies  Post-translational modifications  A bioinspired multilegged soft millirobot that functions in both dry and wet conditions OPEN Haojian Lu, Mei Zhang, Yuanyuan Yang, Qiang Huang, Toshio Fukuda, Zuankai Wang & Yajing Shen Despite the enormous potential of magnetically-guided soft robots for various applications, challenges related to inefficient locomotion in harsh environments hinder its development. Here, the authors demonstrate a multi-legged millirobot with excellent locomotion capability in harsh environments. 26 September 2018 | doi: 10.1038/s41467-018-06491-9 Actuators  Bioinspired materials  Mechanical engineering  Two-component latency distributions indicate two-step vesicular release at simple glutamatergic synapses OPEN Takafumi Miki, Yukihiro Nakamura, Gerardo Malagon, Erwin Neher & Alain Marty Traditionally, synaptic release latency has been viewed as constant. Here, at parallel fiber-interneuron  synapses, authors see that with sustained release emerges a slow component of increased latencies, which can be simulated with a 2-step model comprised of vesicle docking followed by release. 26 September 2018 | doi: 10.1038/s41467-018-06336-5 Biophysics  Neuroscience  The MinDE system is a generic spatial cue for membrane protein distribution in vitro OPEN Beatrice Ramm, Philipp Glock, Jonas Mücksch, Philipp Blumhardt, Daniela A. García-Soriano, Michael Heymann & Petra Schwille The E. coli MinCDE system oscillates between cell poles to position the main division protein FtsZ. Here authors use in vitro reconstitution to show that MinDE oscillations also regulate unrelated membrane proteins spatiotemporally into patterns and gradients by forming a moving physical barrier. 26 September 2018 | doi: 10.1038/s41467-018-06310-1 Molecular biophysics  Synthetic biology  Physics-based forecasting of man-made earthquake hazards in Oklahoma and Kansas OPEN Cornelius Langenbruch, Matthew Weingarten & Mark D. Zoback Reinjection of saltwater, co-produced with oil, has the potential to trigger damaging earthquakes. Here, using Oklahoma and Kansas as an example, the authors present a new physics-based methodology to forecast future probabilities of potentially damaging induced-earthquakes in space and time. 26 September 2018 | doi: 10.1038/s41467-018-06167-4 Energy and society  Hydrology  Seismology  Strobilurin biosynthesis in Basidiomycete fungi OPEN Risa Nofiani, Kate de Mattos-Shipley, Karen E. Lebe, Li-Chen Han, Zafar Iqbal, Andrew M. Bailey, Christine L. Willis, Thomas J. Simpson & Russell J. Cox Strobilurins are fungal metabolites that inspired the creation of β-methoxyacrylate agricultural fungicides. Here, Nofiani et al. identify the strobilurin biosynthesis gene cluster, encoding a polyketide synthase as well as an FAD-dependent oxygenase for an oxidative rearrangement leading to β-methoxyacrylate formation. 26 September 2018 | doi: 10.1038/s41467-018-06202-4 Biosynthesis  Natural product synthesis  Reaction mechanisms  Structure elucidation  A bidentate Polycomb Repressive-Deubiquitinase complex is required for efficient activity on nucleosomes OPEN Martina Foglizzo, Adam J. Middleton, Abigail E. Burgess, Jennifer M. Crowther, Renwick C. J. Dobson, James M. Murphy, Catherine L. Day & Peter D. Mace The Polycomb Repressive-Deubiquitinase (PR-DUB) complex is responsible for the removal of the ubiquitin epigenetic modification from Histone 2A. Here the authors describe the structure of the Drosophila PR-DUB complex, providing new insight into its regulation and how cancer-associated mutations disrupt PR-DUB activity. 26 September 2018 | doi: 10.1038/s41467-018-06186-1 Deubiquitylating enzymes  Epigenetics  Structural biology  Structural analysis of HTL and D14 proteins reveals the basis for ligand selectivity in Striga OPEN Yuqun Xu, Takuya Miyakawa, Shohei Nosaki, Akira Nakamura, Ying Lyu, Hidemitsu Nakamura, Umeharu Ohto, Hanako Ishida, Toshiyuki Shimizu, Tadao Asami & Masaru Tanokura HTL and D14 receptors perceive the structurally similar signaling compounds karrikin and strigolactone. Here, the authors show that ShD14 and a divergent clade of ShHTLs from Strigae capable of recognizing strigolact are capable of recognizing strigolactone and provide structural insights into the evolution of ligand specificity. 26 September 2018 | doi: 10.1038/s41467-018-06452-2 Evolution  Plant sciences  Structural biology  Crystal structure of the red light-activated channelrhodopsin Chrimson OPEN Kazumasa Oda, Johannes Vierock, Satomi Oishi, Silvia Rodriguez-Rozada, Reiya Taniguchi, Keitaro Yamashita, J. Simon Wiegert, Tomohiro Nishizawa, Peter Hegemann & Osamu Nureki Channelrhodopsins are light-activated ion channels that mediate cation permeation across cell membranes upon light absorption. Here, the authors report the crystal structure of the most red-shifted channelrhodopsin from the algae Chlamydomonas noctigama at 2.6 Å resolution. 26 September 2018 | doi: 10.1038/s41467-018-06421-9 Neuroscience  X-ray crystallography  Structural basis for broad neutralization of ebolaviruses by an antibody targeting the glycoprotein fusion loop OPEN Benjamin M. Janus, Nydia van Dyk, Xuelian Zhao, Katie A. Howell, Cinque Soto, M. Javad Aman, Yuxing Li, Thomas R. Fuerst & Gilad Ofek The Ebola virus glycoprotein is a target for cross-protective antibodies. Here, Janus et al. report the crystal structure of the antigen-binding fragment of a pan-reactive antibody bound to a conserved epitope of the glycoprotein, facilitating rational design of cross-protective vaccines and therapeutics. 26 September 2018 | doi: 10.1038/s41467-018-06113-4 Ebola virus  X-ray crystallography  Asymmetric remote C-H borylation of internal alkenes via alkene isomerization OPEN Xu Chen, Zhaoyang Cheng, Jun Guo & Zhan Lu Sequential alkene isomerization/functionalization enables enantioselective transformations of remote C–H bonds. Here, the authors report a chiral cobalt catalytic system for the highly enantioselective, remote C–H borylation of internal alkenes via an isomerization/hydroboration sequence. 26 September 2018 | doi: 10.1038/s41467-018-06240-y Asymmetric synthesis  Homogeneous catalysis  Stereochemistry  Mapping protein selectivity landscapes using multi-target selective screening and next-generation sequencing of combinatorial libraries OPEN Si Naftaly, Itay Cohen, Anat Shahar, Alexandra Hockla, Evette S. Radisky & Niv Papo Characterizing the binding selectivity landscape of interacting proteins is crucial in protein engineering. Here the authors use multi-target selective library screening and in silico next-generation sequencing to map the binding landscape of proteins and produce improved proteases inhibitors. 26 September 2018 | doi: 10.1038/s41467-018-06403-x High-throughput screening  Next-generation sequencing  Proteases  Protein design  A scalable online tool for quantitative social network assessment reveals potentially modifiable social environmental risks OPEN Amar Dhand, Charles C. White, Catherine Johnson, Zongqi Xia & Philip L. De Jager An individual’s social network—their friends, family, and acquaintances—is important for their health, but existing tools for assessing social networks have limitations. Here, the authors introduce a quantitative social network assessment tool on a secure open-source web platform and show its utility in a nation-wide study. 26 September 2018 | doi: 10.1038/s41467-018-06408-6 Human behaviour  Interdisciplinary studies  Multiple sclerosis  Social behaviour  Identification of small-molecule ion channel modulators in C. elegans channelopathy models OPEN Qiang Jiang, Kai Li, Wen-Jing Lu, Shuang Li, Xin Chen, Xi-Juan Liu, Jie Yuan, Qiurong Ding, Feng Lan & Shi-Qing Cai Mutations in the voltage-gated K+ channel human ether-a-go-go-related gene (hERG) lead to Long-QT syndrome, causing life-threatening cardiac arrhythmia. Here the authors use C. elegans as a platform to run a channelopathy drug screen, identifying drugs to target hERG mutants. 26 September 2018 | doi: 10.1038/s41467-018-06514-5 Arrhythmias  Drug discovery  Ion channels in the nervous system  Microenvironmental niche divergence shapes BRCA1-dysregulated ovarian cancer morphological plasticity OPEN Andreas Heindl, Adnan Mujahid Khan, Daniel Nava Rodrigues, Katherine Eason, Anguraj Sadanandam, Cecilia Orbegoso, Marco Punta, Andrea Sottoriva, Stefano Lise, Susana Banerjee & Yinyin Yuan Cancer cells can actively engage in overcoming microenvironmental constraints such as tissue stiffness through adapting their shapes; however it is unclear how microenvironmental cells shape cancer nuclear morphology in human tumors in situ. Here the authors merge machine learning, digital pathology and spatial statistics to study this issue; furthermore the authors identify decreased immune infiltration in the surrounding of diversified cancer cells in a subset of ovarian tumors. 25 September 2018 | doi: 10.1038/s41467-018-06130-3 Ecology  Ovarian cancer  Predicting nutrient content of ray-finned fishes using phylogenetic information OPEN Bapu Vaitla, David Collar, Matthew R. Smith, Samuel S. Myers, Benjamin L. Rice & Christopher D. Golden Humans increasingly depend on seafood for nutrition, but nutrient content is unknown for the vast majority of fish species. Here, the authors use phylogenetic analyses and data imputation to predict the nutrient content of fish that are under-studied but that could be of future dietary importance. 25 September 2018 | doi: 10.1038/s41467-018-06199-w Evolutionary biology  Nutrition disorders  Phylogenetics  Lnk/Sh2b3 deficiency restores hematopoietic stem cell function and genome integrity in Fancd2 deficient Fanconi anemia OPEN Joanna Balcerek, Jing Jiang, Yang Li, Qinqin Jiang, Nicholas Holdreith, Brijendra Singh, Vemika Chandra, Kaosheng Lv, Jian-gang Ren, Krasimira Rozenova, Weihua Li, Roger A. Greenberg & Wei Tong Loss of Fancd2 leads to replication stress intolerance and Fanconi Anemia, where haematopoietic stem cell (HSC) function is compromised. Here, the authors show that Lnk/Sh2b3 loss restores HSC proliferation and survival in Fancd2 knockout mice and ameliorates replication stress in a cytokine/JAK2 signaling dependent manner. 25 September 2018 | doi: 10.1038/s41467-018-06380-1 Haematopoietic stem cells  Stalled forks  Analysis of extracellular mRNA in human urine reveals splice variant biomarkers of muscular dystrophies OPEN Layal Antoury, Ningyan Hu, Leonora Balaj, Sudeshna Das, Sofia Georghiou, Basil Darras, Tim Clark, Xandra O. Breakefield & Thurman M. Wheeler Patients with myotonic dystrophy need to undergo invasive muscle biopsies to monitor disease progression and response to therapy. Here, the authors show that extracellular RNAs in human urine can be used as biomarkers to differentiate patients from unaffected controls, and to monitor exon skipping in patients with Duchenne muscular dystrophy taking the drug eteplirsen. 25 September 2018 | doi: 10.1038/s41467-018-06206-0 Biomarkers  Neuromuscular disease  A germanium hole spin qubit OPEN Hannes Watzinger, Josip Kukučka, Lada Vukušić, Fei Gao, Ting Wang, Friedrich Schäffler, Jian-Jun Zhang & Georgios Katsaros Germanium’s electronic structure and large, tunable spin-orbit coupling makes it a good material for constructing hole-based quantum devices. Here the authors demonstrate the fabrication and two-axis control of a hole spin qubit in a germanium double quantum dot. 25 September 2018 | doi: 10.1038/s41467-018-06418-4 Nanowires  Quantum dots  Qubits  Human hippocampal replay during rest prioritizes weakly learned information and predicts memory performance OPEN Anna C. Schapiro, Elizabeth A. McDevitt, Timothy T. Rogers, Sara C. Mednick & Kenneth A. Norman The hippocampus is known to 'replay' experiences and memories during rest periods, but it is unclear how particular memories are prioritized for replay. Here, the authors show that information that is remembered less well is replayed more often, suggesting that weaker memories are selected for replay. 25 September 2018 | doi: 10.1038/s41467-018-06213-1 Cognitive neuroscience  Consolidation  Hippocampus  Replay  Plasmodium co-infection protects against chikungunya virus-induced pathologies OPEN Teck-Hui Teo, Fok-Moon Lum, Khairunnisa Ghaffar, Yi-Hao Chan, Siti Naqiah Amrun, Jeslin J. L. Tan, Cheryl Y. P. Lee, Tze-Kwang Chua, Guillaume Carissimo, Wendy W. L. Lee, Carla Claser, Ravisankar Rajarethinam, Laurent Rénia & Lisa F. P. Ng Chikungunya virus (CHIKV) and Plasmodium co-infections have been reported in humans, but effects of the two pathogens on each other are unclear. Here, Teo et al. show in mice that Plasmodium infection affects CHIKV-specific T and B cell responses, leading to reduced joint inflammation. 25 September 2018 | doi: 10.1038/s41467-018-06227-9 Interferons  Malaria  Viral host response  Viral infection  One-step generation of multiple gene knock-outs in the diatom Phaeodactylum tricornutum by DNA-free genome editing OPEN Manuel Serif, Gwendoline Dubois, Anne-Laure Finoux, Marie-Ange Teste, Denis Jallet & Fayza Daboussi The manipulation of diatom genomes is essential for industrial applications based on their metabolic abilities. Here the authors present an efficient multiplex DNA-free gene editing method using CRISPR-Cas9 and counter-selectable markers. 25 September 2018 | doi: 10.1038/s41467-018-06378-9 Biotechnology  CRISPR-Cas systems  Genetics  Plant sciences  Vibrio parahaemolyticus RhsP represents a widespread group of pro-effectors for type VI secretion systems OPEN Nan Jiang, Le Tang, Ruiqiang Xie, Zhi Li, Brianne Burkinshaw, Xiaoye Liang, Dylan Sosa, L. Aravind, Tao Dong, Dapeng Zhang & Jun Zheng It is unclear how Rhs toxins lacking a PAAR motif are secreted by Type VI secretion systems. Here, the authors show for one of these proteins that the mechanism requires removal of an N-terminal fragment by auto-proteolysis, followed by interaction with a PAAR protein and then secretion. 25 September 2018 | doi: 10.1038/s41467-018-06201-5 Bacteriology  Pathogens  Caspase-1 inhibition alleviates cognitive impairment and neuropathology in an Alzheimer’s disease mouse model OPEN Joseph Flores, Anastasia Noël, Bénédicte Foveau, Jeffrey Lynham, Clotilde Lecrux & Andréa C. LeBlanc Caspase-1, activated by stress in immune cells and in CNS human neurons, may contribute to neuronal degeneration. Here, the authors investigate the therapeutic potential of a Caspase-1 inhibitor in a mouse model of Alzheimer’s disease. 25 September 2018 | doi: 10.1038/s41467-018-06449-x Alzheimer's disease  Microglia  The evolution of multiple active site configurations in a designed enzyme OPEN Nan-Sook Hong, Dušan Petrović, Richmond Lee, Ganna Gryn’ova, Miha Purg, Jake Saunders, Paul Bauer, Paul D. Carr, Ching-Yeh Lin, Peter D. Mabbitt, William Zhang, Timothy Altamore, Chris Easton, Michelle L. Coote, Shina C. L. Kamerlin & Colin J. Jackson Generation and iterative optimization of designed enzymes can provide valuable insights for a more efficient catalysis. Here the authors have followed the iterative improvement of a designed Kemp eliminase and show that remote point mutations could remodel the designed active site via substantial conformational reorganization. 25 September 2018 | doi: 10.1038/s41467-018-06305-y Computational models  Synthetic chemistry methodology  Molecular conformation  Quantifying climate sensitivity and climate-driven change in North American amphibian communities OPEN David A. W. Miller, Evan H. Campbell Grant, Erin Muths, Staci M. Amburgey, Michael J. Adams, Maxwell B. Joseph, J. Hardin Waddle, Pieter T. J. Johnson, Maureen E. Ryan, Benedikt R. Schmidt, Daniel L. Calhoun, Courtney L. Davis, Robert N. Fisher, David M. Green, Blake R. Hossack, Tracy A. G. Rittenhouse, Susan C. Walls, Larissa L. Bailey, Sam S. Cruickshank, Gary M. Fellers et al. Amphibians have seen large population declines, but the key drivers are hard to establish. Here, Miller et al. investigate trends of occupancy for 81 species of amphibians across North America and find greater sensitivity to water availability during breeding and winter conditions than mean climate. 25 September 2018 | doi: 10.1038/s41467-018-06157-6 Climate-change ecology  Community ecology  Conservation biology  Population dynamics  Lineage dynamics of murine pancreatic development at single-cell resolution OPEN Lauren E. Byrnes, Daniel M. Wong, Meena Subramaniam, Nathaniel P. Meyer, Caroline L. Gilchrist, Sarah M. Knox, Aaron D. Tward, Chun J. Ye & Julie B. Sneddon Coordinated proliferation and differentiation of diverse cell populations drive pancreatic epithelial and mesenchymal development. Here, the authors profile cell type dynamics in the developing mouse pancreas using single-cell RNA sequencing, identifying mesenchymal subtypes and undescribed endocrine progenitors. 25 September 2018 | doi: 10.1038/s41467-018-06176-3 Differentiation  Gene expression  Pancreas  Sex and species specific hearing mechanisms in mosquito flagellar ears OPEN Matthew P. Su, Marta Andrés, Nicholas Boyd-Gibbins, Jason Somers & Joerg T. Albert Auditory processing is an important component of mosquito behaviour including mating. Here the authors demonstrate substantial sex- and also species-specific variation in mosquito auditory transduction, amplification and gain control. 25 September 2018 | doi: 10.1038/s41467-018-06388-7 Auditory system  Evolutionary ecology  Sexual dimorphism  Systemic signaling contributes to the unfolded protein response of the plant endoplasmic reticulum OPEN Ya-Shiuan Lai, Giovanni Stefano, Starla Zemelis-Durfee, Cristina Ruberti, Lizzie Gibbons & Federica Brandizzi The unfolded protein response (UPR) maintains cellular function under ER stress. While typically considered cell autonomous, here Lai et al. show that in Arabidopsis the UPR also has a systemic component triggered by intercellular movement of at least one bZIP transcription factor. 25 September 2018 | doi: 10.1038/s41467-018-06289-9 Protein trafficking in plants  Stress signalling  Fine mapping of MHC region in lung cancer highlights independent susceptibility loci by ethnicity OPEN Aida Ferreiro-Iglesias, Corina Lesseur, James McKay, Rayjean J. Hung, Younghun Han, Xuchen Zong, David Christiani, Mattias Johansson, Xiangjun Xiao, Yafang Li, David C. Qian, Xuemei Ji, Geoffrey Liu, Neil Caporaso, Ghislaine Scelo, David Zaridze, Anush Mukeriya, Milica Kontic, Simona Ognjanovic, Jolanta Lissowska et al. The basis for associations between lung cancer and major histocompatibility complex genes is not completely understood. Here the authors further consider genetic variation within the MHC region in lung cancer patients and identify independent associations within HLA genes that explain MHC lung cancer associations in Europeans and Asian populations. 25 September 2018 | doi: 10.1038/s41467-018-05890-2 Epidemiology  Genetics research  Neonatally imprinted stromal cell subsets induce tolerogenic dendritic cells in mesenteric lymph nodes OPEN Joern Pezoldt, Maria Pasztoi, Mangge Zou, Carolin Wiechers, Michael Beckstette, Guilhem R. Thierry, Ehsan Vafadarnejad, Stefan Floess, Panagiota Arampatzi, Manuela Buettner, Janina Schweer, Diana Fleissner, Marius Vital, Dietmar H. Pieper, Marijana Basic, Petra Dersch, Till Strowig, Mathias Hornef, André Bleich, Ulrike Bode et al. Induction of tolerance in the gut relies on immunomodulatory functions of mesenteric lymph nodes (mLN). Here the authors show that mLN stromal cells receive early microbiota imprinting in the neonatal phase to exhibit long-term, location-specific transcriptional programs for the induction of regulatory T cells and peripheral tolerance. 25 September 2018 | doi: 10.1038/s41467-018-06423-7 Immunology  Lymph node  Mucosal immunology  Peripheral tolerance  Regulatory T cells  Simulation of slip transients and earthquakes in finite thickness shear zones with a plastic formulation OPEN Xinyue Tong & Luc L. Lavier Differences in energy partitioning between fast earthquakes and slow slip events (SSEs) remain unclear. Here, the authors present a new numerical technique and plastic formulation to model and provide a first-order attempt at quantifying the partitioning elastic energy release in fault zones. 25 September 2018 | doi: 10.1038/s41467-018-06390-z Geodynamics  Geophysics  Tectonics  Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica OPEN Timothy Paape, Roman V. Briskine, Gwyneth Halstead-Nussloch, Heidi E. L. Lischer, Rie Shimizu-Inatsugi, Masaomi Hatakeyama, Kenta Tanaka, Tomoaki Nishiyama, Renat Sabirov, Jun Sese & Kentaro K. Shimizu Despite the prevalence of genome duplication in plants, little is known about the evolutionary patterns of entire subgenomes. Here the authors resequence allopolyploid Arabidopsis kamchatica genome to estimate diversity, linkage disequilibrium and strengths of both positive and purifying selection. 25 September 2018 | doi: 10.1038/s41467-018-06108-1 Evolutionary genetics  Genome evolution  Natural variation in plants  An OB-fold complex controls the repair pathways for DNA double-strand breaks OPEN Shengxian Gao, Sumin Feng, Shaokai Ning, Jingyan Liu, Huayu Zhao, Yixi Xu, Jinfeng Shang, Kejiao Li, Qing Li, Rong Guo & Dongyi Xu How repair pathway selection occurs is still a matter of debate and many factors have been associated to this function. Here the authors provide insight into the role of FAM35A and C20ORF196, two REV7-interacting proteins, which are recruited at double-strand breaks to promote non-homologous end joining repair. 25 September 2018 | doi: 10.1038/s41467-018-06407-7 Double-strand DNA breaks  Non-homologous-end joining  Persistent repair intermediates induce senescence OPEN F. M. Feringa, J. A. Raaijmakers, M. A. Hadders, C. Vaarting, L. Macurek, L. Heitink, L. Krenning & R. H. Medema Cells with damaged DNA can permanently exit the cell cycle during the G2 phase or recover spontaneously entering mitosis. Here the authors reveal that the decision to exit from the cell cycle in G2 is dependent on the presence of repair intermediates associated with homologous recombination. 25 September 2018 | doi: 10.1038/s41467-018-06308-9 Cell-cycle exit  DNA damage and repair  DNA damage checkpoints  Chirality amplification by desymmetrization of chiral ligand-capped nanoparticles to nanorods quantified in soft condensed matter OPEN Ahlam Nemati, Sasan Shadpour, Lara Querciagrossa, Lin Li, Taizo Mori, Min Gao, Claudio Zannoni & Torsten Hegmann The mechanisms by which molecular chirality is amplified through space and across length scales is of great interest. Here the authors show how gold nanorods covered in chiral dopants are more efficient in transducing chiral information compared to other gold nanoparticles decorated with chiral ligands. 25 September 2018 | doi: 10.1038/s41467-018-06400-0 Liquid crystals  Nanoparticles  LUBAC prevents lethal dermatitis by inhibiting cell death induced by TNF, TRAIL and CD95L OPEN TNF mediated inflammation is critical in autoimmune mediated pathology, however many patients are refractory to current anti-TNF therapeutics. Here the authors show induction of several death ligands, in addition to TNF is sufficient to cause fatal dermatitis in a LUBAC deficient murine model of disease. 25 September 2018 | doi: 10.1038/s41467-018-06155-8 Apoptosis  Chronic inflammation  Necroptosis  Tumour-necrosis factors  Ubiquitylation  Skin color-specific and spectrally-selective naked-eye dosimetry of UVA, B and C radiations OPEN Wenyue Zou, Ana González, Deshetti Jampaiah, Rajesh Ramanathan, Mohammad Taha, Sumeet Walia, Sharath Sriram, Madhu Bhaskaran, José M. Dominguez-Vera & Vipul Bansal Current ultraviolet (UV) sensors cannot differentiate between UVA, B and C, each of which has a remarkably different impact on human health. Here the authors show spectrally-selective colorimetric monitoring of ultraviolet radiations by developing a photoelectrochromic ink that consists of a multiredox polyoxometalate and an e– donor. 25 September 2018 | doi: 10.1038/s41467-018-06273-3 Light harvesting  Natural hazards  Optical sensors  Gender differences in individual variation in academic grades fail to fit expected patterns for STEM OPEN R. E. O’Dea, M. Lagisz, M. D. Jennions & S. Nakagawa Men are over-represented in the STEM (science, technology, engineering and mathematics) workforce even though girls outperform boys in these subjects at school. Here, the authors cast doubt on one leading explanation for this paradox, the ‘variability hypothesis’. 25 September 2018 | doi: 10.1038/s41467-018-06292-0 Education  Intelligence  Psychology  Social sciences  Loss of PRC1 induces higher-order opening of Hox loci independently of transcription during Drosophila embryogenesis OPEN Thierry Cheutin & Giacomo Cavalli Loss of Polycomb repressive complex 1 (PRC1) proteins usually results in both chromatin unfolding and ectopic transcription. Here, the authors analyze the temporal function of two PRC1 proteins during Drosophila embryogenesis and provide evidence that PRC1 maintains gene silencing by folding chromatin domains. 25 September 2018 | doi: 10.1038/s41467-018-05945-4 Chromatin  Epigenetic memory  Gene expression  Gene silencing  RARα supports the development of Langerhans cells and langerin-expressing conventional dendritic cells OPEN Seika Hashimoto-Hill, Leon Friesen, Sungtae Park, Suji Im, Mark H. Kaplan & Chang H. Kim Langerhans cells (LC) and langerin-expressing conventional dendritic cells are made from distinct progenitors and enriched in the distinct microenvironments of the skin. Here the authors show that these immune cells are regulated by retinoic acid receptor alpha (RARα) via simultaneous induction of LC-promoting Runx3 and repression of LC-inhibiting C/EBPβ. 25 September 2018 | doi: 10.1038/s41467-018-06341-8 Antigen-presenting cells  Gene regulation in immune cells  Langerhans cells  Conventional dendritic cells  An orbitally derived single-atom magnetic memory OPEN Brian Kiraly, Alexander N. Rudenko, Werner M. J. van Weerdenburg, Daniel Wegner, Mikhail I. Katsnelson & Alexander A. Khajetoorians Single-atom storage can dramatically exceed the limit of traditional high-density memory devices but is challenging. Here the authors show the bistability in the orbital configuration of a single Co atom on black phosphorus which can be accessed, manipulated and has potential for high-temperature single-atom information storage. 25 September 2018 | doi: 10.1038/s41467-018-06337-4 Magnetic properties and materials  Spintronics  RNA editing derived epitopes function as cancer antigens to elicit immune responses OPEN Minying Zhang, Jens Fritsche, Jason Roszik, Leila J. Williams, Xinxin Peng, Yulun Chiu, Chih-Chiang Tsou, Franziska Hoffgaard, Valentina Goldfinger, Oliver Schoor, Amjad Talukder, Marie A. Forget, Cara Haymaker, Chantale Bernatchez, Leng Han, Yiu-Huen Tsang, Kathleen Kong, Xiaoyan Xu, Kenneth L. Scott, Harpreet Singh-Jasuja et al. RNA editing is a biological process that creates sequence variation. Here the authors show that peptides generated as a consequence of RNA editing are naturally presented by human leukocyte antigen (HLA) and serve as antigens to elicit anti-tumour immune responses. 25 September 2018 | doi: 10.1038/s41467-018-06405-9 Antigen processing and presentation  Cancer immunotherapy  Tumour immunology  Functional modulation of primary visual cortex by the superior colliculus in the mouse OPEN Mehran Ahmadlou, Larry S. Zweifel & J. Alexander Heimel The role of the superior colliculus (SC) in modulating V1 cortical activity is not clear. Here, the authors demonstrate the functional role of SC in modulating V1 responses through an excitatory pathway via the dorsal lateral geniculate nucleus. 25 September 2018 | doi: 10.1038/s41467-018-06389-6 Neural circuits  Visual system  Microglial dopamine receptor elimination defines sex-specific nucleus accumbens development and social behavior in adolescent rats OPEN Ashley M. Kopec, Caroline J. Smith, Nathan R. Ayre, Sean C. Sweat & Staci D. Bilbo Dopaminergic circuits in the nucleus accumbens regulate reward, including social play behavior in adolescent rodents. Here, the authors show that in male but not female rats, dopamine receptors are tagged by complement for microglial phagocytosis, thus mediating changes in social behavior. 25 September 2018 | doi: 10.1038/s41467-018-06118-z Developmental biology  Neuroscience  Cortical modulation of sensory flow during active touch in the rat whisker system OPEN Shubhodeep Chakrabarti & Cornelius Schwarz During active touch, sensory responses to object touch are gated at the level of thalamus and cortex. Here, the authors report gating at the level of the brainstem and show that an intact somatosensory cortex is essential for this response modulation. 25 September 2018 | doi: 10.1038/s41467-018-06200-6 Neural circuits  Whisker system  Estimating sources and sinks of malaria parasites in Madagascar OPEN Felana Angella Ihantamalala, Vincent Herbreteau, Feno M. J. Rakotoarimanana, Jean Marius Rakotondramanga, Simon Cauchemez, Bienvenue Rahoilijaona, Gwenaëlle Pennober, Caroline O. Buckee, Christophe Rogier, C. J. E. Metcalf & Amy Wesolowski Understanding the source of malaria outbreaks in low-transmission areas is important for controlling the disease. Here, the authors use mobile phone data to map malaria transmission in Madagascar, and are able to show that primary sources of infection in the capital city are found along populated coastal areas. 25 September 2018 | doi: 10.1038/s41467-018-06290-2 Ecological modelling  Geography  Infectious diseases  Single cell molecular alterations reveal target cells and pathways of concussive brain injury OPEN Douglas Arneson, Guanglin Zhang, Zhe Ying, Yumei Zhuang, Hyae Ran Byun, In Sook Ahn, Fernando Gomez-Pinilla & Xia Yang Traumatic brain injury (TBI) affects the hippocampus and can lead to neurological and psychiatric disorders. Here, the authors perform single-cell RNA sequencing to reveal molecular pathways across a range of cell types affected during TBI. 25 September 2018 | doi: 10.1038/s41467-018-06222-0 Brain injuries  Computational biology and bioinformatics  Gene expression analysis  Systems biology  Using both qualitative and quantitative data in parameter identification for systems biology models OPEN Eshan D. Mitra, Raquel Dias, Richard G. Posner & William S. Hlavacek Much of the data generated in biology is qualitative, but exploiting such data to inform models of biological systems remains a challenge. Here, the authors demonstrate an approach that allows use of both quantitative and qualitative data for parameterising dynamical models. 25 September 2018 | doi: 10.1038/s41467-018-06439-z Computational models  Statistical methods  Mapping of histone-binding sites in histone replacement-completed spermatozoa OPEN Keisuke Yoshida, Masafumi Muratani, Hiromitsu Araki, Fumihito Miura, Takehiro Suzuki, Naoshi Dohmae, Yuki Katou, Katsuhiko Shirahige, Takashi Ito & Shunsuke Ishii While a majority of histones are replaced by protamines during spermatogenesis, a small amount is retained in mammalian spermatozoa. Here the authors develop a method to purify histones from replacement-completed sperm (HRCS), completely solubilize histones from cross-linked HRCS without MNase digestion, and map histone-binding sites in these cells. 24 September 2018 | doi: 10.1038/s41467-018-06243-9 Biological techniques  Gene silencing  Nucleosomes  Solution-processed perovskite light emitting diodes with efficiency exceeding 15% through additive-controlled nanostructure tailoring OPEN Muyang Ban, Yatao Zou, Jasmine P. H. Rivett, Yingguo Yang, Tudor H. Thomas, Yeshu Tan, Tao Song, Xingyu Gao, Dan Credington, Felix Deschler, Henning Sirringhaus & Baoquan Sun Crystal sizes play a vital role in pushing up the efficiency of organometal halide perovskites based LEDs. Here Ban et al. incorporate a molecular additive to control the crystallite distribution and phase separation in the perovskite devices, resulting in high external quantum efficiency of 15.5%. 24 September 2018 | doi: 10.1038/s41467-018-06425-5 Electronic devices  Lasers, LEDs and light sources  Microfluidic deposition for resolving single-molecule protein architecture and heterogeneity OPEN Francesco Simone Ruggeri, Jerome Charmet, Tadas Kartanas, Quentin Peter, Sean Chia, Johnny Habchi, Christopher M. Dobson, Michele Vendruscolo & Tuomas P. J. Knowles Manual sample deposition on a substrate can introduce artifacts in quantitative AFM measurements. Here the authors present a microfluidic spray device for reliable deposition of subpicoliter droplets which dry out in milliseconds after landing on the surface, thereby avoiding protein self-assembly. 24 September 2018 | doi: 10.1038/s41467-018-06345-4 Applications of AFM  Atomic force microscopy  Microfluidics  Protein aggregation  Single-molecule biophysics  Acquired cancer resistance to combination immunotherapy from transcriptional loss of class I HLA OPEN K. G. Paulson, V. Voillet, M. S. McAfee, D. S. Hunter, F. D. Wagener, M. Perdicchio, W. J. Valente, S. J. Koelle, C. D. Church, N. Vandeven, H. Thomas, A. G. Colunga, J. G. Iyer, C. Yee, R. Kulikauskas, D. M. Koelle, R. H. Pierce, J. H. Bielas, P. D. Greenberg, S. Bhatia et al. Acquired resistance is a major problem in cancer immunotherapy. Here the authors report a study of two patients with Merkel cell carcinoma under immunotherapy treatment who develop resistance after deep responses for >1 year and identified a novel mechanism of acquired, gene-specific transcriptional suppression of HLAs. 24 September 2018 | doi: 10.1038/s41467-018-06300-3 MHC  Skin cancer  Tumour immunology  Electrical conductivity and magnetic dynamos in magma oceans of Super-Earths OPEN François Soubiran & Burkhard Militzer With the discovery of large rocky exoplanets called Super-Earths, questions have arisen regarding the properties of their interiors and their ability to produce a magnetic field. Here, the authors show that under high pressure, molten silicates are semi-metallic and that magma oceans would host a dynamo process. 24 September 2018 | doi: 10.1038/s41467-018-06432-6 Electronic properties and materials  Exoplanets  Geomagnetism  Towards exact molecular dynamics simulations with machine-learned force fields OPEN Stefan Chmiela, Huziel E. Sauceda, Klaus-Robert Müller & Alexandre Tkatchenko Simultaneous accurate and efficient prediction of molecular properties relies on combined quantum mechanics and machine learning approaches. Here the authors develop a flexible machine-learning force-field with high-level accuracy for molecular dynamics simulations. 24 September 2018 | doi: 10.1038/s41467-018-06169-2 Atomic and molecular physics  Chemical physics  Theoretical chemistry  Gas-solid reaction based over one-micrometer thick stable perovskite films for efficient solar cells and modules OPEN Zonghao Liu, Longbin Qiu, Emilio J. Juarez-Perez, Zafer Hawash, Taehoon Kim, Yan Jiang, Zhifang Wu, Sonia R. Raga, Luis K. Ono, Shengzhong (Frank) Liu & Yabing Qi Perovskite solar cells often suffer from poor uniformity and reproducibility especially in case of large area devices. Here Liu et al. developed a gas−solid reaction method that enables facile fabrication of over 1 µm thick perovskite films for solar modules with high efficiency, stability and reproducibility. 24 September 2018 | doi: 10.1038/s41467-018-06317-8 Devices for energy harvesting  Solar cells  Spatiotemporal dynamics of homologous recombination repair at single collapsed replication forks OPEN Donna R. Whelan, Wei Ting C. Lee, Yandong Yin, Dylan M. Ofri, Keria Bermudez-Hernandez, Sarah Keegan, David Fenyo & Eli Rothenberg How factors involved in homologous recombination interact and function is a matter of interest. Here the authors use super-resolution imaging to describe the spatiotemporal dynamics of proteins associated with homologous recombination DNA repair in response to replication stress. 24 September 2018 | doi: 10.1038/s41467-018-06435-3 DNA  DNA replication  Double-strand DNA breaks  Homologous recombination  OCP–FRP protein complex topologies suggest a mechanism for controlling high light tolerance in cyanobacteria OPEN Nikolai N. Sluchanko, Yury B. Slonimskiy, Evgeny A. Shirshin, Marcus Moldenhauer, Thomas Friedrich & Eugene G. Maksimov Cyanobacterial photoprotection is controlled by OCP and FRP proteins, but their dynamic interplay is not fully understood. Here, the authors combine protein engineering, disulfide trapping and structural analyses to provide mechanistic insights into the transient OCP-FRP interaction. 24 September 2018 | doi: 10.1038/s41467-018-06195-0 Light responses  Non-photochemical quenching  Proteins  SAXS  Identifying the missing link in catalyst transfer polymerization OPEN Weiying He, Brian O. Patrick & Pierre Kennepohl The mechanism for nickel-catalyzed catalyst transfer polycondensation of thiophenes to polythiophenes. Here the authors show experimental and computational evidence of structurally characterized square planar η2-Ni(0)–thiophene species and their relevance to the mechanism of catalyst transfer polycondensation. 24 September 2018 | doi: 10.1038/s41467-018-06324-9 Catalytic mechanisms  Chemical bonding  Cross-coupling reactions  Homogeneous catalysis  Modulating the hierarchical fibrous assembly of Au nanoparticles with atomic precision OPEN Qi Li, Jake C. Russell, Tian-Yi Luo, Xavier Roy, Nathaniel L. Rosi, Yan Zhu & Rongchao Jin Constructing nanoparticle assemblies with atomic precision remains a major challenge in nanoscience. Here, the authors realize atomic‐level control over the 1D, 2D and hierarchical 3D assembly of Au nanoparticles by modulating the site‐specific surface ligands and associated counterions. 24 September 2018 | doi: 10.1038/s41467-018-06395-8 Materials chemistry  Nanoscale materials  Self-assembly  Natural variation at XND1 impacts root hydraulics and trade-off for stress responses in Arabidopsis OPEN Ning Tang, Zaigham Shahzad, Fabien Lonjon, Olivier Loudet, Fabienne Vailleau & Christophe Maurel Soil water uptake is a major determinant of plant performance and stress tolerance. Here the authors show that, by affecting xylem formation in the root, natural variation at the Arabidopsis XND1 locus has contrasting effects on root hydraulics and drought tolerance versus pathogen resistance. 24 September 2018 | doi: 10.1038/s41467-018-06430-8 Genome-wide association studies  Natural variation in plants  Plant stress responses  Targeting PFKFB3 radiosensitizes cancer cells and suppresses homologous recombination OPEN Nina M. S. Gustafsson, Katarina Färnegårdh, Nadilly Bonagas, Anna Huguet Ninou, Petra Groth, Elisee Wiita, Mattias Jönsson, Kenth Hallberg, Jemina Lehto, Rosa Pennisi, Jessica Martinsson, Carina Norström, Jessica Hollers, Johan Schultz, Martin Andersson, Natalia Markova, Petra Marttila, Baek Kim, Martin Norin, Thomas Olin et al. Targeting the glycolytic PFKFB3 enzyme is being studied as a therapeutic strategy against cancer. Here the authors identify PFKFB3 as being involved in homologous recombination (HR) repair of DNA double strand breaks (DSBs) and present a PFKFB3 inhibitor. 24 September 2018 | doi: 10.1038/s41467-018-06287-x Cancer metabolism  Cancer therapy  DNA damage and repair  DNA replication  Neurogenetic profiles delineate large-scale connectivity dynamics of the human brain OPEN Ibai Diez & Jorge Sepulcre Attractor dynamics have been discovered in neural circuits, but it is not clear if they exist at the level of whole-brain activity. Here, the authors show that certain brain regions act as nodes in which many activity ‘streams’ converge, regardless of brain state. These regions show distinctive gene expression. 24 September 2018 | doi: 10.1038/s41467-018-06346-3 Cognitive neuroscience  Genetics of the nervous system  Network models  Neuroscience  Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements OPEN Katariina Pärnänen, Antti Karkman, Jenni Hultman, Christina Lyra, Johan Bengtsson-Palme, D. G. Joakim Larsson, Samuli Rautava, Erika Isolauri, Seppo Salminen, Himanshu Kumar, Reetta Satokari & Marko Virta The infant gut microbiota has a high abundance of antibiotic resistance genes (ARGs) even in the absence of antibiotic exposure. Here, Pärnänen et al. analyse breast milk as well as infant and maternal gut microbiomes, and show that some of the infant gut ARGs are transferred from the mothers. 24 September 2018 | doi: 10.1038/s41467-018-06393-w Computational biology and bioinformatics  Microbiology  Regulation of the terminal maturation of iNKT cells by mediator complex subunit 23 OPEN Yu Xu, Yang Sun, Hao Shen, Yuling Dai, Haifeng Liu, Ronghong Li, Hongdao Zhang, Ligang Wu, Xiaoyan Zhu & Xiaolong Liu Invariant Natural Killer T cells (iNKT) rapidly exert effector functions upon activation, but the mechanisms of their functional maturation remain to be determined. Here, Xu and colleagues show that the mediator subunit Med23 is a transcriptional regulator controlling iNKT cell terminal maturation. 24 September 2018 | doi: 10.1038/s41467-018-06372-1 Cell death and immune response  Differentiation  Gene regulation in immune cells  NKT cells  Circuit quantum electrodynamics of granular aluminum resonators OPEN N. Maleeva, L. Grünhaupt, T. Klein, F. Levy-Bertrand, O. Dupre, M. Calvo, F. Valenti, P. Winkel, F. Friedrich, W. Wernsdorfer, A. V. Ustinov, H. Rotzinger, A. Monfardini, M. V. Fistul & I. M. Pop The electrodynamics of superconducting devices make them suitable for applications as detectors, amplifiers, and qubits. Here the authors show that resonators made from granular aluminum, which naturally realizes a network of Josephson junctions, have practically useful impedances and nonlinearities. 24 September 2018 | doi: 10.1038/s41467-018-06386-9 Superconducting devices  Superconducting properties and materials  PAXX and its paralogs synergistically direct DNA polymerase λ activity in DNA repair OPEN Andrew Craxton, Deeksha Munnur, Rebekah Jukes-Jones, George Skalka, Claudia Langlais, Kelvin Cain & Michal Malewicz PAXX functions as part of the nonhomologous end-joining pathway to repair double-strand DNA breaks. Here the authors show PAXX and its paralogs interact with polymerase lambda to promote joining of incompatible ends. 24 September 2018 | doi: 10.1038/s41467-018-06127-y DNA  DNA-binding proteins  Double-strand DNA breaks  Non-homologous-end joining  Plant neighbor detection and allelochemical response are driven by root-secreted signaling chemicals OPEN Chui-Hua Kong, Song-Zhu Zhang, Yong-Hua Li, Zhi-Chao Xia, Xue-Fang Yang, Scott J. Meiners & Peng Wang Plant growth and physiology respond to the presence of neighboring plants. Here the authors show that the chemicals (-)-loliolide and jasmonic acid, which were present in the root exudates of a range of plant species, can be detected by wheat and induce allelochemical production. 24 September 2018 | doi: 10.1038/s41467-018-06429-1 Agriculture  Ecology  Plant sciences  Structure of Type-I Mycobacterium tuberculosis fatty acid synthase at 3.3 Å resolution OPEN Nadav Elad, Szilvia Baron, Yoav Peleg, Shira Albeck, Jacob Grunwald, Gal Raviv, Zippora Shakked, Oren Zimhony & Ron Diskin The type-I fatty acid synthase (FAS-I) complex is essential for Mycobacterium tuberculosis (Mtb) and mediates the production of C26 fatty acids that are precursors for the synthesis of mycolic acids. Here the authors present the 3.3 Å resolution cryo-EM structure of Mtb FAS-I, which is of interest for tuberculosis drug development. 24 September 2018 | doi: 10.1038/s41467-018-06440-6 Cryoelectron microscopy  Electron microscopy  Pathogens  Structural biology  Griffithsin carrageenan fast dissolving inserts prevent SHIV HSV-2 and HPV infections in vivo OPEN Nina Derby, Manjari Lal, Meropi Aravantinou, Larisa Kizima, Patrick Barnable, Aixa Rodriguez, Manshun Lai, Asa Wesenberg, Shweta Ugaonkar, Keith Levendosky, Olga Mizenina, Kyle Kleinbeck, Jeffrey D. Lifson, M. Melissa Peet, Zachary Lloyd, Michael Benson, Walid Heneine, Barry R O’Keefe, Melissa Robbiani, Elena Martinelli et al. Safety and efficacy remain important challenges for non-antiretroviral-based microbicides. Here, Derby et al. show that a Griffithsin-Carrageenan fast dissolving vaginal insert provides on-demand protection against SHIV infections in macaques, paving the way for the development of pre-exposure prophylaxis on-demand products. 24 September 2018 | doi: 10.1038/s41467-018-06349-0 Antivirals  Experimental models of disease  Human papilloma virus  Preclinical research  Retrovirus  Contrasting effects on deep convective clouds by different types of aerosols OPEN Jonathan H. Jiang, Hui Su, Lei Huang, Yuan Wang, Steven Massie, Bin Zhao, Ali Omar & Zhien Wang Aerosol effects on convection have been debated for decades when all types of aerosols are lumped together in the analyses. Using NASA satellite measurements, the authors find strong evidence that smoke inhibits convection but polluted continental aerosols invigorate convection. 24 September 2018 | doi: 10.1038/s41467-018-06280-4 Atmospheric science  Climate sciences  A room-temperature sodium–sulfur battery with high capacity and stable cycling performance OPEN Xiaofu Xu, Dong Zhou, Xianying Qin, Kui Lin, Feiyu Kang, Baohua Li, Devaraj Shanmukaraj, Teofilo Rojo, Michel Armand & Guoxiu Wang Sodium–sulfur batteries operating at a high temperature between 300 and 350°C have been used commercially, but the safety issue hinders their wider adoption. Here the authors report a “cocktail optimized” electrolyte system that enables higher electrochemical performance and room-temperature operation. 24 September 2018 | doi: 10.1038/s41467-018-06443-3 Batteries  Electrochemistry  BRWD1 orchestrates epigenetic landscape of late B lymphopoiesis OPEN Malay Mandal, Mark Maienschein-Cline, Patrick Maffucci, Margaret Veselits, Domenick E. Kennedy, Kaitlin C. McLean, Michael K. Okoreeh, Sophiya Karki, Charlotte Cunningham-Rundles & Marcus R. Clark B-cell development is tightly regulated by transcription programs that are coordinated by transcription factors (TF) and locus accessibility. Here the authors show that, in mice and humans, the epigenetic reader BRWD1 inhibits and promotes the accessibility of enhancers for early and late B lymphopoiesis, respectively. 24 September 2018 | doi: 10.1038/s41467-018-06165-6 B cells  Epigenetics in immune cells  Lymphocyte differentiation  Systems analysis  Eosinophil recruitment is dynamically regulated by interplay among lung dendritic cell subsets after allergen challenge OPEN Shuying Yi, Jing Zhai, Rui Niu, Guangming Zhu, Meixiang Wang, Jianguo Liu, Hua Huang, Yaping Wang, Xiuli Jing, Li Kang, Wengang Song, Yufang Shi & Hua Tang Eosinophils are important mediators of allergic responses, but how they are recruited to the inflamed site is still unclear. Here the authors show that CD103+ cDC1 cells secrete CCL17 and CCL22 for eosinophil recruitment, with this process promoted by CD24−CD11b+ DC2s in the early phase but suppressed by CD24+ cDC2s in the late phase. 24 September 2018 | doi: 10.1038/s41467-018-06316-9 Eosinophils  Inflammatory diseases  Mucosal immunology  Conventional dendritic cells  Direct electric field imaging of graphene defects OPEN Ryo Ishikawa, Scott D. Findlay, Takehito Seki, Gabriel Sánchez-Santolino, Yuji Kohno, Yuichi Ikuhara & Naoya Shibata Imaging chemical bonding states in defective graphene is important to determine its functional properties. Here, the authors report triangular and rectangular atomic electric fields in monolayer graphene induced by silicon as imaged by differential phase contrast STEM. 24 September 2018 | doi: 10.1038/s41467-018-06387-8 Catalysis  Graphene  Atom-hybridization for synthesis of polymetallic clusters OPEN Takamasa Tsukamoto, Tetsuya Kambe, Aiko Nakao, Takane Imaoka & Kimihisa Yamamoto Multimetallic clusters are difficult to synthesize with control over elemental composition and organization. Here, the authors use dendrimers to precisely template the formation of five-element sub-nanoclusters, providing an elegant route to otherwise-inaccessible multinary compounds. 24 September 2018 | doi: 10.1038/s41467-018-06422-8 Inorganic chemistry  Materials chemistry  Nanoparticles  Beaming random lasers with soliton control OPEN Sreekanth Perumbilavil, Armando Piccardi, Raouf Barboza, Oleksandr Buchnev, Martti Kauranen, Giuseppe Strangi & Gaetano Assanto Owing to their lack of a conventional cavity, random lasers typically do not emit a defined beam in a specific direction. Here, the authors combine spatial solitons and collinear pumping to achieve light-confined random lasing with a smooth output profile and a controllable direction of emission. 21 September 2018 | doi: 10.1038/s41467-018-06170-9 Lasers, LEDs and light sources  Liquid crystals  Solitons  Cryo-EM analysis of the T3S injectisome reveals the structure of the needle and open secretin OPEN J. Hu, L. J. Worrall, C. Hong, M. Vuckovic, C. E. Atkinson, N. Caveney, Z. Yu & N. C. J. Strynadka The bacterial type III secretion system of Gram-negative bacteria uses its core, the needle complex, to penetrate through the infected host cell membrane. Here authors show a near-atomic resolution structure of a needle complex which sheds light on the assembly and function of this nanomachine. 21 September 2018 | doi: 10.1038/s41467-018-06298-8 Cryoelectron microscopy  Pathogens  Gallium nitride nanowire as a linker of molybdenum sulfides and silicon for photoelectrocatalytic water splitting OPEN Baowen Zhou, Xianghua Kong, Srinivas Vanka, Sheng Chu, Pegah Ghamari, Yichen Wang, Nick Pant, Ishiang Shih, Hong Guo & Zetian Mi Sunlight-harvesting materials require the clean integration of light-absorbing and catalytic components to be efficient. Here, authors link silicon photoelectrodes and molybdenum sulfide catalysts with defect-free gallium nitride nanowire to improve photoelectrochemical hydrogen evolution. 21 September 2018 | doi: 10.1038/s41467-018-06140-1 Light harvesting  Nanowires  Photocatalysis  Solar fuels  Structures of insect Imp-L2 suggest an alternative strategy for regulating the bioavailability of insulin-like hormones OPEN Nikolaj Kulahin Roed, Cristina M. Viola, Ole Kristensen, Gerd Schluckebier, Mathias Norrman, Waseem Sajid, John D. Wade, Asser Sloth Andersen, Claus Kristensen, Timothy R. Ganderton, Johan P. Turkenburg, Pierre De Meyts & Andrzej M. Brzozowski Insulin-like polypeptide binding proteins (IBPs) from insects can bind diverse insulin-like proteins (ILPs) including human insulin and IGFs. Here, the authors present structures of a Drosophila IBP in its free and ILP-bound forms, providing insights into the regulation of ILP bioavailability by insect IBPs. 21 September 2018 | doi: 10.1038/s41467-018-06192-3 Insect hormones  Insulin signalling  X-ray crystallography  Discovering human diabetes-risk gene function with genetics and physiological assays OPEN Heshan Peiris, Sangbin Park, Shreya Louis, Xueying Gu, Jonathan Y. Lam, Olof Asplund, Gregory C. Ippolito, Rita Bottino, Leif Groop, Haley Tucker & Seung K. Kim The function of genes linked to type 2 diabetes is poorly characterized. Here the authors combine Drosophila genetics and physiology with human islet biology to identify new regulators of insulin secretion including BCL11A. 21 September 2018 | doi: 10.1038/s41467-018-06249-3 Biological models  Diabetes  Endocrinology  Genetic techniques  Genetics  Alpha-enolase regulates the malignant phenotype of pulmonary artery smooth muscle cells via the AMPK-Akt pathway OPEN Jingbo Dai, Qiyuan Zhou, Jiwang Chen, Megan L. Rexius-Hall, Jalees Rehman & Guofei Zhou Metabolic reprogramming of smooth muscle cells (SMCs) plays an important role in the pathogenesis of pulmonary arterial hypertension (PAH). Here, Dai et al. show that the glycolytic enzyme alpha-enolase contributes to this reprogramming, and that its inhibition limits SMC proliferation and disease progression in animal models of PAH. 21 September 2018 | doi: 10.1038/s41467-018-06376-x Hypertension  Metabolism  A cocoon silk chemistry strategy to ultrathin N-doped carbon nanosheet with metal single-site catalysts OPEN Youqi Zhu, Wenming Sun, Jun Luo, Wenxing Chen, Tai Cao, Lirong Zheng, Juncai Dong, Jian Zhang, Maolin Zhang, Yunhu Han, Chen Chen, Qing Peng, Dingsheng Wang & Yadong Li Single-site catalysts supported by ultrathin two-dimensional (2D) porous matrix are desirable for catalytic reactions, yet their synthesis remains a great challenge. Herein the authors report a cocoon silk chemistry strategy to synthesize isolated metal single-site catalysts embedded in ultrathin 2D porous N-doped carbon nanosheets. 21 September 2018 | doi: 10.1038/s41467-018-06296-w Catalyst synthesis  Heterogeneous catalysis  Two-dimensional materials  Reconfiguring surface functions using visible-light-controlled metal-ligand coordination OPEN Chaoming Xie, Wen Sun, Hao Lu, Annika Kretzschmann, Jiahui Liu, Manfred Wagner, Hans-Jürgen Butt, Xu Deng & Si Wu Configuring surfaces on-demand for desired functionalities is an ongoing challenge. Here, diverse and tailorable modifications of quartz and porous silica surfaces that are rapidly and reversibly switchable by the use of visible light are achieved via ruthenium-thioether coordination. 21 September 2018 | doi: 10.1038/s41467-018-06180-7 Chemical bonding  Organic molecules in materials science  Sensors and biosensors  Surface chemistry  Spatiotemporal segregation of human marginal zone and memory B cell populations in lymphoid tissue OPEN Yuan Zhao, Mohamed Uduman, Jacqueline H. Y. Siu, Thomas J. Tull, Jeremy D. Sanderson, Yu-Chang Bryan Wu, Julian Q. Zhou, Nedyalko Petrov, Richard Ellis, Katrina Todd, Konstantia-Maria Chavele, William Guesdon, Anna Vossenkamper, Wayel Jassem, David P. D’Cruz, David J. Fear, Susan John, Dagmar Scheel-Toellner, Claire Hopkins, Estefania Moreno et al. Human memory and marginal zone B cells share some features including CD27 expression and somatic hypermutation, but their lineage relationship is still unclear. Here the authors use mass cytometry and sequential clustering methods to show that, despite their shared features, memory and marginal zone B cells represent distinct lineage choices. 21 September 2018 | doi: 10.1038/s41467-018-06089-1 Adaptive immunity  B cells  Immunological memory  Lymphocyte differentiation  Influence of PEDOT:PSS crystallinity and composition on electrochemical transistor performance and long-term stability OPEN Seong-Min Kim, Chang-Hyun Kim, Youngseok Kim, Nara Kim, Won-June Lee, Eun-Hak Lee, Dokyun Kim, Sungjun Park, Kwanghee Lee, Jonathan Rivnay & Myung-Han Yoon The lack of understanding of mixed transport in ion-permeable conjugated polymer films hinders the advance of organic electrochemical transistors for bioelectronics. Here, the authors elucidate the structure-property-performance relationships for conventional and crystallized PEDOT:PSS films. 21 September 2018 | doi: 10.1038/s41467-018-06084-6 Electronic devices  Sensors and biosensors  Ancient and modern anticonvulsants act synergistically in a KCNQ potassium channel binding pocket OPEN Rían W. Manville & Geoffrey W. Abbott In some countries, leaves of the shrub Mallotus oppositifolius have been used to treat epilepsy. Here, authors look at the structural and molecular basis for how chemical components of M. oppositifolius have their anticonvulsant effects, via modulation of potassium channel activity. 21 September 2018 | doi: 10.1038/s41467-018-06339-2 Molecular medicine  Physiology  Cerebello-thalamo-cortical hyperconnectivity as a state-independent functional neural signature for psychosis prediction and characterization OPEN Hengyi Cao, Oliver Y. Chén, Yoonho Chung, Jennifer K. Forsyth, Sarah C. McEwen, Dylan G. Gee, Carrie E. Bearden, Jean Addington, Bradley Goodyear, Kristin S. Cadenhead, Heline Mirzakhanian, Barbara A. Cornblatt, Ricardo E. Carrión, Daniel H. Mathalon, Thomas H. McGlashan, Diana O. Perkins, Aysenil Belger, Larry J. Seidman, Heidi Thermenos, Ming T. Tsuang et al. Brain function alterations in schizophrenia and other psychotic disorders remain poorly understood. Here, the authors discover that increased neural connectivity in the cerebello-thalamo-cortical circuitry predicts psychosis in those at high risk, and is present in people with schizophrenia. 21 September 2018 | doi: 10.1038/s41467-018-06350-7 Cognitive neuroscience  Diagnostic markers  Predictive markers  Psychosis  Complex strain evolution of polar and magnetic order in multiferroic BiFeO3 thin films OPEN Zuhuang Chen, Zhanghui Chen, Chang-Yang Kuo, Yunlong Tang, Liv R. Dedon, Qian Li, Lei Zhang, Christoph Klewe, Yen-Lin Huang, Bhagwati Prasad, Alan Farhan, Mengmeng Yang, James D. Clarkson, Sujit Das, Sasikanth Manipatruni, A. Tanaka, Padraic Shafer, Elke Arenholz, Andreas Scholl, Ying-Hao Chu et al. To fully exploit the potential of multiferroic materials the control of their intrinsic degrees of freedom is a prerequisite. Here, the control of spin orientation in strained BiFeO3 films is demonstrated elucidating the microscopic mechanism of the complex interplay of polar and magnetic order. 21 September 2018 | doi: 10.1038/s41467-018-06190-5 Electronic devices  Ferroelectrics and multiferroics  Magnetic properties and materials  A naturally protective epitope of limited variability as an influenza vaccine target OPEN Craig P. Thompson, José Lourenço, Adam A. Walters, Uri Obolski, Matthew Edmans, Duncan S. Palmer, Kreepa Kooblall, George W. Carnell, Daniel O’Connor, Thomas A. Bowden, Oliver G. Pybus, Andrew J. Pollard, Nigel J. Temperton, Teresa Lambe, Sarah C. Gilbert & Sunetra Gupta Current influenza vaccine approaches largely focus on highly variable epitopes with high immunogenicity or epitopes of low variability that often have low immunogenicity. Here, Thompson et al. identify a highly immunogenic epitope of limited variability in the head domain of the H1 haemagglutinin and show protection from diverse H1N1 strains in mice. 21 September 2018 | doi: 10.1038/s41467-018-06228-8 Influenza virus  Vaccines  Viral evolution  Viral immune evasion  Active particles bound by information flows OPEN Utsab Khadka, Viktor Holubec, Haw Yang & Frank Cichos Synthetic active particles with inter-particle propulsion have been served as a model system to study the collective animal behaviors. Here, Khadka et al. add complexity to the model by spatially controlling particle motions through a laser feedback loop in response to the collective dynamics of particles. 21 September 2018 | doi: 10.1038/s41467-018-06445-1 Colloids  Optical manipulation and tweezers  Statistical physics, thermodynamics and nonlinear dynamics  Towards synthetic cells using peptide-based reaction compartments OPEN Kilian Vogele, Thomas Frank, Lukas Gasser, Marisa A. Goetzfried, Mathias W. Hackl, Stephan A. Sieber, Friedrich C. Simmel & Tobias Pirzer Lipid-based membranes coupled to biochemical reaction networks can be difficult to implement in vitro. Here the authors use elastin-like peptides to create self-assembled vesicle structures containing transcription-translation systems for autonomous growth. 21 September 2018 | doi: 10.1038/s41467-018-06379-8 Biological physics  Synthetic biology  A conformational sensor based on genetic code expansion reveals an autocatalytic component in EGFR activation OPEN Martin Baumdick, Márton Gelléri, Chayasith Uttamapinant, Václav Beránek, Jason W. Chin & Philippe I. H. Bastiaens Upon ligand binding epidermal growth factor receptor (EGFR) dimerizes and activates its intrinsic kinase to auto-phosphorylate EGFR. Here, the authors engineer and image a FRET-based conformational EGFR indicator which reveals that activation loop phosphorylation induces a catalytically active conformation in EGFR monomers. 21 September 2018 | doi: 10.1038/s41467-018-06299-7 Biological techniques  Chemical biology  Molecular biology  Forward models demonstrate that repetition suppression is best modelled by local neural scaling OPEN Arjen Alink, Hunar Abdulrahman & Richard N. Henson The neural mechanisms underlying the suppression of fMRI responses to repeated stimuli are under debate. Here, the authors compare computational models to show that only a local scaling model can fit univariate and multivariate fMRI repetition effects across two paradigms and multiple brain regions. 21 September 2018 | doi: 10.1038/s41467-018-05957-0 Cognitive neuroscience  Neuroscience  Sensory processing  Visual system  Positive cardiac inotrope omecamtiv mecarbil activates muscle despite suppressing the myosin working stroke OPEN Michael S. Woody, Michael J. Greenberg, Bipasha Barua, Donald A. Winkelmann, Yale E. Goldman & E. Michael Ostap Omecamtiv mecarbil (OM) is a positive cardiac inotrope in clinical trials for the treatment of heart failure whose mechanism of action is incompletely understood. Here the authors show that OM inhibits myosin's working stroke and prolongs actomyosin attachment and propose a model that reconciles the OM-induced increase in cardiac performance in vivo with the inhibitory actions observed in vitro. 21 September 2018 | doi: 10.1038/s41467-018-06193-2 Heart failure  Single-molecule biophysics  The chromatin remodeler RSF1 controls centromeric histone modifications to coordinate chromosome segregation OPEN Ho-Soo Lee, Zhonghui Lin, Sunyoung Chae, Young-Suk Yoo, Byung-Gyu Kim, Youngsoo Lee, Jared L. Johnson, You-Sun Kim, Lewis C. Cantley, Chang-Woo Lee, Hongtao Yu & Hyeseong Cho The chromatin remodeler RSF1 is enriched at mitotic centromeres but its function there is poorly understood. Here, the authors show that RSF1 regulates H2A phosphorylation and acetylation at mitotic centromeres and contributes to chromosome stability. 21 September 2018 | doi: 10.1038/s41467-018-06377-w Chromosome segregation  Cohesion  Tunable colloid trajectories in nematic liquid crystals near wavy walls OPEN Yimin Luo, Daniel A. Beller, Giuseppe Boniello, Francesca Serra & Kathleen J. Stebe Nematic liquid crystals have a rich energy landscape which can define elastic fields to guide colloidal assembly. Here the authors show controllable trapping of colloidal particles by placing them in a system with wavy walls which are exploited to obtain stable, metastable and unstable equilibria. 21 September 2018 | doi: 10.1038/s41467-018-06054-y Colloids  Liquid crystals  Self-assembly  Controlling factor of incoming plate hydration at the north-western Pacific margin OPEN Gou Fujie, Shuichi Kodaira, Yuka Kaiho, Yojiro Yamamoto, Tsutomu Takahashi, Seiichi Miura & Tomoaki Yamada Bend faulting prior to subduction is considered to promote hydration, yet the relationship remains ambiguous. Here, via analysis of seismic surveys from the Japan and Kuril trenches junction, the authors show that pre-subduction bend faulting and post-subduction plate hydration are strongly correlated. 21 September 2018 | doi: 10.1038/s41467-018-06320-z Seismology  Tectonics  Gap junction protein Connexin-43 is a direct transcriptional regulator of N-cadherin in vivo OPEN Maria Kotini, Elias H. Barriga, Jonathan Leslie, Marc Gentzel, Verena Rauschenberger, Alexandra Schambon & Roberto Mayor Connexins are components of gap junctions that link cells and allow intercellular communication. Here, the authors show that the Connexin 43 carboxy tail interacts with basic transcription factor-3, leading to nuclear translocation and direct regulation of N-cadherin expression and neural crest migration. 21 September 2018 | doi: 10.1038/s41467-018-06368-x Cell adhesion  Cell migration  Morphogenesis  Repeated inversions within a pannier intron drive diversification of intraspecific colour patterns of ladybird beetles OPEN The harlequin ladybird beetle, Harmonia axyridis, has remarkable phenotypic diversity, with over 200 colour patterns. Here, Ando et al. show that this patterning is regulated by the transcription factor gene pannier and has diversified by repeated inversions and cis-regulatory modifications of pannier. 21 September 2018 | doi: 10.1038/s41467-018-06116-1 Evolutionary developmental biology  Evolutionary genetics  Structural variation  Hierarchical and stage-specific regulation of murine cardiomyocyte maturation by serum response factor OPEN Yuxuan Guo, Blake D. Jardin, Pingzhu Zhou, Isha Sethi, Brynn N. Akerberg, Christopher N Toepfer, Yulan Ai, Yifei Li, Qing Ma, Silvia Guatimosim, Yongwu Hu, Grigor Varuzhanyan, Nathan J. VanDusen, Donghui Zhang, David C. Chan, Guo-Cheng Yuan, Christine E. Seidman, Jonathan G. Seidman & William T. Pu The processes regulating cardiomyocyte (CM) maturation are unclear. Here, the authors show that serum response factor regulates CM maturation only in neonatal CMs through stage-specific chromatin occupancy that affects cell size, sarcomere and transverse-tubule organization, and mitochondria 21 September 2018 | doi: 10.1038/s41467-018-06347-2 Differentiation  Heart development  Transcription  A tissue-specific self-interacting chromatin domain forms independently of enhancer-promoter interactions OPEN Jill M. Brown, Nigel A. Roberts, Bryony Graham, Dominic Waithe, Christoffer Lagerholm, Jelena M. Telenius, Sara De Ornellas, A. Marieke Oudelaar, Caroline Scott, Izabela Szczerbal, Christian Babbs, Mira T. Kassouf, Jim R. Hughes, Douglas R. Higgs & Veronica J. Buckle Self-interacting chromatin domains encompass genes and their cis-regulatory elements. Here the authors use high-resolution chromosome conformation capture and super-resolution imaging to study a 70 kb domain that includes the mouse α-globin regulatory locus and find that a tissue-specific self-interacting chromatin domain forms independently of enhancer-promoter interactions. 21 September 2018 | doi: 10.1038/s41467-018-06248-4 Gene expression  Gene regulation  Nuclear organization  Super-resolution microscopy  Notch2 controls non-autonomous Wnt-signalling in chronic lymphocytic leukaemia OPEN Maurizio Mangolini, Frederik Götte, Andrew Moore, Tim Ammon, Madlen Oelsner, Gloria Lutzny-Geier, Ludger Klein-Hitpass, James C. Williamson, Paul J. Lehner, Jan Dürig, Michael Möllmann, Lívia Rásó-Barnett, Katherine Hughes, Antonella Santoro, Simón Méndez-Ferrer, Robert A. J. Oostendorp, Ursula Zimber-Strobl, Christian Peschel, Daniel J. Hodson, Marc Schmidt-Supprian et al. The Wnt pathway is one of the core de-regulated pathways in chronic lymphocytic leukaemia (CLL) and is activated in only a subset of patients; however, no universal drivers of the disease have been identified. Here the authors show that Notch2 and β-catenin pathways are the main drivers of the pro-survival bidirectional crosstalk between stromal cells and leukemic cells. 21 September 2018 | doi: 10.1038/s41467-018-06069-5 Cancer microenvironment  Chronic lymphocytic leukaemia  An interstellar synthesis of phosphorus oxoacids OPEN Andrew M. Turner, Alexandre Bergantini, Matthew J. Abplanalp, Cheng Zhu, Sándor Góbi, Bing-Jian Sun, Kang-Heng Chao, Agnes H. H. Chang, Cornelia Meinert & Ralf I. Kaiser Extraterrestrial sources may have provided prebiotic phosphorus to the early Earth. Here, the authors investigate the potential of phosphine-doped astrochemical analog ices to form phosphorus oxoacids as precursors to more complex prebiotic compounds. 21 September 2018 | doi: 10.1038/s41467-018-06415-7 Chemical origin of life  Physical chemistry  Vegetation response to exceptional global warmth during Oceanic Anoxic Event 2 OPEN Ulrich Heimhofer, Nina Wucherpfennig, Thierry Adatte, Stefan Schouten, Elke Schneebeli-Hermann, Silvia Gardin, Gerta Keller, Sarah Kentsch & Ariane Kujau The Cretaceous Oceanic Anoxic Event 2 represents one of the warmest episodes in the last 250 million years. Here, the authors present spore-pollen data and temperature estimates (TEX86) across an expanded stratigraphic section illustrating the dynamic response of vegetation during this exceptionally warm interval. 20 September 2018 | doi: 10.1038/s41467-018-06319-6 Palaeoceanography  Palaeoclimate  Sedimentology  Solid Earth sciences  Structural basis for recognition of the malaria vaccine candidate Pfs48/45 by a transmission blocking antibody OPEN Frank Lennartz, Florian Brod, Rebecca Dabbs, Kazutoyo Miura, David Mekhaiel, Arianna Marini, Matthijs M. Jore, Max M. Søgaard, Thomas Jørgensen, Willem A. de Jongh, Robert W. Sauerwein, Carole A. Long, Sumi Biswas & Matthew K. Higgins Pfs48/45 is a promising component for a transmission-blocking malaria vaccine. Here, the authors develop a system to produce full-length Pfs48/45 for immunisation, characterise a panel of monoclonal antibodies and determine the structure of a potent transmission-blocking epitope. 20 September 2018 | doi: 10.1038/s41467-018-06340-9 Antibodies  Malaria  Vaccines  X-ray crystallography  Strongly lensed repeating fast radio bursts as precision probes of the universe OPEN Zheng-Xiang Li, He Gao, Xu-Heng Ding, Guo-Jian Wang & Bing Zhang Fast radio bursts (FRBs) are likely to be gravitationally lensed by intervening galaxies. Here, the authors propose to make accurate measurements of time delays between images of lensed FRBs as a powerful probe for precision cosmology. 20 September 2018 | doi: 10.1038/s41467-018-06303-0 Cosmology  Transient astrophysical phenomena  LNMAT1 promotes lymphatic metastasis of bladder cancer via CCL2 dependent macrophage recruitment OPEN Changhao Chen, Wang He, Jian Huang, Bo Wang, Hui Li, Qingqing Cai, Feng Su, Junming Bi, Hongwei Liu, Bin Zhang, Ning Jiang, Guangzheng Zhong, Yue Zhao, Wen Dong & Tianxin Lin Mechanism of lymph node (LN) metastasis induced by tumor associated macrophages (TAMs) remains unclear. Here they demonstrate that a long noncoding RNA LNMAT1 promotes LN metastasis of bladder cancer via recruitment of TAMs through epigenetic regulation of CCL2 expression. 20 September 2018 | doi: 10.1038/s41467-018-06152-x Cancer microenvironment  Metastasis  Robust single-cell DNA methylome profiling with snmC-seq2 OPEN Chongyuan Luo, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, Joseph R. Nery, António Pinto-Duarte, Brian Bui, Conor Fitzpatrick, Carolyn O’Connor, Seth Ruga, Marc E. Van Eden, David A. Davis, Deborah C. Mash, M. Margarita Behrens & Joseph R. Ecker Single-cell DNA methylome profiling allows the study of epigenomic heterogeneity in tissues but has been impeded by library quality. Here the authors demonstrate snmC-seq2 which improves mapping, throughput and library complexity. 20 September 2018 | doi: 10.1038/s41467-018-06355-2 DNA methylation  DNA sequencing  Epigenomics  Rechargeable potassium-ion batteries with honeycomb-layered tellurates as high voltage cathodes and fast potassium-ion conductors OPEN Titus Masese, Kazuki Yoshii, Yoichi Yamaguchi, Toyoki Okumura, Zhen-Dong Huang, Minami Kato, Keigo Kubota, Junya Furutani, Yuki Orikasa, Hiroshi Senoh, Hikari Sakaebe & Masahiro Shikano The development of potassium-ion batteries requires cathode materials that can maintain the structural stability during cycling. Here the authors have developed honeycomb-layered tellurates K2M2TeO6 that afford high ionic conductivity and reversible intercalation of large K ions at high voltages. 20 September 2018 | doi: 10.1038/s41467-018-06343-6 Batteries  Ceramics  Solid-phase synthesis  Identification of active sites on supported metal catalysts with carbon nanotube hydrogen highways OPEN Nicholas M. Briggs, Lawrence Barrett, Evan C. Wegener, Leidy V. Herrera, Laura A. Gomez, Jeffrey T. Miller & Steven P. Crossley Understanding the location and nature of the catalytic active site is critical for controlling a catalyst’s activity and selectivity. Here, the authors separate the metal from the support by a controlled distance while maintaining the ability to promote defects via the use of carbon nanotube hydrogen highways. 20 September 2018 | doi: 10.1038/s41467-018-06100-9 Carbon nanotubes and fullerenes  Catalyst synthesis  Chemical engineering  Heterogeneous catalysis  Frustrated endocytosis controls contractility-independent mechanotransduction at clathrin-coated structures OPEN Francesco Baschieri, Stéphane Dayot, Nadia Elkhatib, Nathalie Ly, Anahi Capmany, Kristine Schauer, Timo Betz, Danijela Matic Vignjevic, Renaud Poincloux & Guillaume Montagnac Cells sense mechanical properties of their environment using various cellular structures including focal adhesions. Here, the authors identify flat clathrin-coated structures (CCSs) as mechanosensitive signaling platforms that form independently of contractility and in response to substrate rigidity. 20 September 2018 | doi: 10.1038/s41467-018-06367-y Cell adhesion  Cell biology  Female mice lacking Ftx lncRNA exhibit impaired X-chromosome inactivation and a microphthalmia-like phenotype OPEN Yusuke Hosoi, Miki Soma, Hirosuke Shiura, Takashi Sado, Hidetoshi Hasuwa, Kuniya Abe, Takashi Kohda, Fumitoshi Ishino & Shin Kobayashi Although Ftx lncRNA has been linked to X-chromosome inactivation, its physiological roles in vivo remain unclear. Here the authors show that deletion of mouse Ftx causes eye abnormalities similar to human microphthalmia in a subset of female mice but rarely in males and provide evidence that Ftx plays a role in gene silencing on the inactive X chromosome. 20 September 2018 | doi: 10.1038/s41467-018-06327-6 Dosage compensation  Embryology  Epigenetic memory  Epigenetics  Lung colonization by Aspergillus fumigatus is controlled by ZNF77 OPEN Sara Gago, Nicola L. D. Overton, Nagwa Ben-Ghazzi, Lilyann Novak-Frazer, Nick D. Read, David W. Denning & Paul Bowyer Aspergillus fumigatus regularly colonises the lungs but in the context of respiratory disease can be associated with increased pathology. Here the authors show mutations in ZNF77 result in altered bronchial epithelial characteristics and enhanced fungal burden. 20 September 2018 | doi: 10.1038/s41467-018-06148-7 Clinical microbiology  Fungal host response  Fungal infection  Fungi  Endogenous metabolites of vitamin E limit inflammation by targeting 5-lipoxygenase OPEN Helmut Pein, Alexia Ville, Simona Pace, Veronika Temml, Ulrike Garscha, Martin Raasch, Khaled Alsabil, Guillaume Viault, Chau-Phi Dinh, David Guilet, Fabiana Troisi, Konstantin Neukirch, Stefanie König, Rosella Bilancia, Birgit Waltenberger, Hermann Stuppner, Maria Wallert, Stefan Lorkowski, Christina Weinigel, Silke Rummler et al. Vitamin E metabolites are proposed to have signalling capacity, but how they may regulate immune responses is still unclear. Here the authors show that a vitamin E metabolite, α-T-13′-COOH, can inhibit 5-lipoxygenase and thereby suppress the synthesis of lipid mediators of immune activation and inflammatory responses. 20 September 2018 | doi: 10.1038/s41467-018-06158-5 Granulocytes  Inflammatory diseases  Lipids  Pharmacology  Copper-on-nitride enhances the stable electrosynthesis of multi-carbon products from CO2 OPEN Zhi-Qin Liang, Tao-Tao Zhuang, Ali Seifitokaldani, Jun Li, Chun-Wei Huang, Chih-Shan Tan, Yi Li, Phil De Luna, Cao Thang Dinh, Yongfeng Hu, Qunfeng Xiao, Pei-Lun Hsieh, Yuhang Wang, Fengwang Li, Rafael Quintero-Bermudez, Yansong Zhou, Peining Chen, Yuanjie Pang, Shen-Chuan Lo, Lih-Juann Chen et al. While multi-carbon (C2+) products present high-value species attainable from emitted carbon dioxide, it is challenging to prepare stable, C2+ selective catalysts. Here, authors support copper on copper nitride to improve copper’s electrocatalytic stability and selectivity toward C2+ synthesis. 20 September 2018 | doi: 10.1038/s41467-018-06311-0 Carbon capture and storage  Electrocatalysis    Nature Communications EVENT HIV Glasgow 2018 28.10.18 Glasgow, UK More science events from     Latest Author Corrections       Author Correction: An intercross population study reveals genes associated with body size and plumage color in ducks OPEN Zhengkui Zhou , Ming Li, Hong Cheng, Wenlei Fan, Zhengrong Yuan, Qiang Gao, Yaxi Xu, Zhanbao Guo, Yunsheng Zhang, Jian Hu, Hehe Liu, Dapeng Liu, Weihuang Chen, Zhuqing Zheng, Yong Jiang, Zhiguo Wen, Yongming Liu, Hua Chen, Ming Xie, Qi Zhang et al. 25 September 2018 | doi: 10.1038/s41467-018-06521-6 Animal breeding  Genome evolution  Population genetics  Author Correction: Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls OPEN Cynthia M. Kallenbach, Serita D. Frey & A. Stuart Grandy 24 September 2018 | doi: 10.1038/s41467-018-06427-3 Author Correction: 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. 20 September 2018 | doi: 10.1038/s41467-018-06428-2 Mucosal immunology  Neuroimmunology  Retina  T cells  Author Correction: MYC-driven epigenetic reprogramming favors the onset of tumorigenesis by inducing a stem cell-like state OPEN Vittoria Poli, Luca Fagnocchi, Alessandra Fasciani, Alessandro Cherubini, Stefania Mazzoleni, Sara Ferrillo, Annarita Miluzio, Gabriella Gaudioso, Valentina Vaira, Alice Turdo, Miriam Gaggianesi, Aurora Chinnici, Elisa Lipari, Silvio Bicciato, Silvano Bosari, Matilde Todaro & Alessio Zippo 20 September 2018 | doi: 10.1038/s41467-018-06480-y Breast cancer  Histone post-translational modifications  Reprogramming  Transcriptional regulatory elements  Author Correction: Molecular architecture of the multifunctional collagen lysyl hydroxylase and glycosyltransferase LH3 OPEN Luigi Scietti, Antonella Chiapparino, Francesca De Giorgi, Marco Fumagalli, Lela Khoriauli, Solomon Nergadze, Shibom Basu, Vincent Olieric, Lucia Cucca, Blerida Banushi, Antonella Profumo, Elena Giulotto, Paul Gissen & Federico Forneris 20 September 2018 | doi: 10.1038/s41467-018-06481-x Biochemistry  Enzymes  X-ray crystallography      Latest Publisher Corrections       Publisher Correction: Hypermethylation of gene body CpG islands predicts high dosage of functional oncogenes in liver cancer OPEN Maria Arechederra, Fabrice Daian, Annie Yim, Sehrish K. Bazai, Sylvie Richelme, Rosanna Dono, Andrew J. Saurin, Bianca H. Habermann & Flavio Maina 25 September 2018 | doi: 10.1038/s41467-018-06482-w Cancer models  Hepatocellular carcinoma  Publisher Correction: Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation OPEN Éadaoin Harney, Hila May, Dina Shalem, Nadin Rohland, Swapan Mallick, Iosif Lazaridis, Rachel Sarig, Kristin Stewardson, Susanne Nordenfelt, Nick Patterson, Israel Hershkovitz & David Reich 20 September 2018 | doi: 10.1038/s41467-018-06484-8 Anthropology  Population genetics      Advertisement Communications Biology: Open for Submissions Communications Biology is a new open access journal that publishes high-quality primary research articles, reviews and commentary representing significant advances and new insights to the field of biology. 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