Nature Communications - 21 November 2018

Weekly Content Alert Nature Communications is fully open access. Read more. 21 November 2018  Latest content: Editorial Review Articles Correspondence Author Corrections Publisher Corrections Journal homepage Recommend to library Web feed     Latest Editorial     Unsung heroes of the scientific record deserve credit OPEN 20 November 2018 | doi: 10.1038/s41467-018-07336-1     Latest Review View all Articles     Ecology and evolution of facilitation among symbionts OPEN Flore Zélé, Sara Magalhães, Sonia Kéfi & Alison B. Duncan Facilitation is a well-known ecological interaction among free-living species, but symbionts residing in or on a host can also positively affect other symbiont species. Here, the authors review examples of facilitation among symbionts, revealing how facilitation theory can improve understanding of these interactions. 19 November 2018 | doi: 10.1038/s41467-018-06779-w Community ecology  Evolutionary ecology  Evolutionary theory  Microbial ecology        Latest Articles View all Articles     Apparent self-heating of individual upconverting nanoparticle thermometers OPEN Andrea D. Pickel, Ayelet Teitelboim, Emory M. Chan, Nicholas J. Borys, P. James Schuck & Chris Dames Nanoparticles are often used as nanothermometers by measuring their luminescence from upconverted energy under illumination. The authors uncover the artificial appearance of a temperature rise at high excitation intensities due to effects involving higher energy states. 21 November 2018 | doi: 10.1038/s41467-018-07361-0 Characterization and analytical techniques  Nanoparticles  Sensors  Tuning the balance between dispersion and entropy to design temperature-responsive flexible metal-organic frameworks OPEN J. Wieme, K. Lejaeghere, G. Kresse & V. Van Speybroeck Rational design of metal organic frameworks (MOFs) with shape-memory nanopores is a formidable challenge. Here the authors use an accurate theoretical approach to design thermo-responsive MOFs based on a balance of van der Waals and entropy contributions. 21 November 2018 | doi: 10.1038/s41467-018-07298-4 Electronic properties and materials  Electronic structure  Phase transitions and critical phenomena  Defining human cardiac transcription factor hierarchies using integrated single-cell heterogeneity analysis OPEN Jared M. Churko, Priyanka Garg, Barbara Treutlein, Meenakshi Venkatasubramanian, Haodi Wu, Jaecheol Lee, Quinton N. Wessells, Shih-Yu Chen, Wen-Yi Chen, Kashish Chetal, Gary Mantalas, Norma Neff, Eric Jabart, Arun Sharma, Garry P. Nolan, Nathan Salomonis & Joseph C. Wu Human induced pluripotent stem cell derived cardiomyocytes are a powerful model for cardiogenesis and disease in vitro. Here the authors comprehensively map cardiac differentiation using multiple modalities, including single-cell RNA seq and CyTOF, in cells with a gain  or loss of function in key cardiac transcription factors. 21 November 2018 | doi: 10.1038/s41467-018-07333-4 Induced pluripotent stem cells  RNA sequencing  Determination of the two-dimensional distributions of gold nanorods by multiwavelength analytical ultracentrifugation OPEN Simon E. Wawra, Lukas Pflug, Thaseem Thajudeen, Carola Kryschi, Michael Stingl & Wolfgang Peukert Characterization of nanoparticles is a complex and important problem for the vast number of applications that require them. Here, the authors present a method to uncover the two-dimensional distribution of length and diameter of anisotropic nanoparticles like gold nanorods with a single measurement by combining spectroscopic and sedimentation data. 21 November 2018 | doi: 10.1038/s41467-018-07366-9 Characterization and analytical techniques  Nanoparticles  Hedgehog stimulates hair follicle neogenesis by creating inductive dermis during murine skin wound healing OPEN Chae Ho Lim, Qi Sun, Karan Ratti, Soung-Hoon Lee, Ying Zheng, Makoto Takeo, Wendy Lee, Piul Rabbani, Maksim V. Plikus, Jason E. Cain, David H. Wang, D. Neil Watkins, Sarah Millar, M. Mark Taketo, Peggy Myung, George Cotsarelis & Mayumi Ito On wounding, scar formation in mammals arises causing no hair follicle regeneration, but it is unclear if scarring precludes regeneration. Here, the authors show that if Sonic hedgehog signaling is activated in the wound, an inductive dermal niche forms, enabling regeneration and hair follicle formation. 21 November 2018 | doi: 10.1038/s41467-018-07142-9 Cell signalling  Gene regulation  Morphogenesis  Structural snapshot of a bacterial phytochrome in its functional intermediate state OPEN Andrea Schmidt, Luisa Sauthof, Michal Szczepek, Maria Fernandez Lopez, Francisco Velazquez Escobar, Bilal M. Qureshi, Norbert Michael, David Buhrke, Tammo Stevens, Dennis Kwiatkowski, David von Stetten, Maria Andrea Mroginski, Norbert Krauß, Tilman Lamparter, Peter Hildebrandt & Patrick Scheerer Phytochromes are photoreceptors that are present in plants, bacteria and fungi. Here the authors present crystal structures of the phytochrome Agp2 from Agrobacterium fabrum in the parent Pfr state as well as a functional Meta-F intermediate and discuss mechanistic implications for photoconversion. 21 November 2018 | doi: 10.1038/s41467-018-07392-7 Molecular conformation  X-ray crystallography  Resolving orbital pathways for intermolecular electron transfer OPEN Cameron W. Kellett, Wesley B. Swords, Michael D. Turlington, Gerald J. Meyer & Curtis P. Berlinguette It is known that intermolecular interactions impact electron transfer rates, but the mechanisms involved are challenging to define experimentally. Here, the authors have developed a platform that enables atomic orbital resolution of electron transfer through an explicit intermolecular interaction. 21 November 2018 | doi: 10.1038/s41467-018-07263-1 Electron transfer  Reaction kinetics and dynamics  Photocatalysis  Hydrodynamic assembly of two-dimensional layered double hydroxide nanostructures OPEN Nicholas A. Jose, Hua Chun Zeng & Alexei A. Lapkin While liquid-phase synthesis of 2D materials presents opportunities for large-scale production, achieving precise control over product quality, size and morphology remains challenging. Here, the authors show that hydrodynamic manipulation of nanoparticle assembly enables control over crystallinity, size and aspect ratio. 21 November 2018 | doi: 10.1038/s41467-018-07395-4 Synthesis and processing  Two-dimensional materials  Electrochemical surface passivation of LiCoO2 particles at ultrahigh voltage and its applications in lithium-based batteries OPEN Jiawei Qian, Lei Liu, Jixiang Yang, Siyuan Li, Xiao Wang, Houlong L. Zhuang & Yingying Lu LiCoO2 is a cathode material widely used in lithium-ion batteries but suffers from solubilization of cobalt and structural disorder when the voltage is increased to release more capacity. Here the authors show a ternary Li, Al and F-modified LiCoO2 and battery cells with stable cycling behavior over 4.55 V. 21 November 2018 | doi: 10.1038/s41467-018-07296-6 Engineering  Materials for energy and catalysis  Materials science  A single Gal4-like transcription factor activates the Crabtree effect in Komagataella phaffii OPEN Özge Ata, Corinna Rebnegger, Nadine E. Tatto, Minoska Valli, Teresa Mairinger, Stephan Hann, Matthias G. Steiger, Pınar Çalık & Diethard Mattanovich Aerobic ethanol production, a phenomenon referred as Crabtree effect, allows yeast to outcompete other microorganisms in sugar rich environments. Here, the authors show that overexpression of a Gal4-like transcription factor can transform Komagataella phaffii from Crabtree effect negative to positive. 21 November 2018 | doi: 10.1038/s41467-018-07430-4 Gene regulation  Industrial microbiology  Microbiology  A time-resolved multi-omic atlas of the developing mouse stomach OPEN Xianju Li, Chunchao Zhang, Tongqing Gong, Xiaotian Ni, Jin'e Li, Dongdong Zhan, Mingwei Liu, Lei Song, Chen Ding, Jianming Xu, Bei Zhen, Yi Wang & Jun Qin The mammalian stomach is a complex organ with diverse roles in health and disease. Here, the authors integrate proteomics and transcriptomics to analyze the mouse stomach at 15 time points during development, providing molecular level insights into system-wide developmental changes. 21 November 2018 | doi: 10.1038/s41467-018-07463-9 Gastric cancer  Organogenesis  Proteomics  Transcriptomics  Integrative epigenetic taxonomy of primary prostate cancer OPEN Suzan Stelloo, Ekaterina Nevedomskaya, Yongsoo Kim, Karianne Schuurman, Eider Valle-Encinas, João Lobo, Oscar Krijgsman, Daniel Simon Peeper, Seiwon Laura Chang, Felix Yi-Chung Feng, Lodewyk Frederik Ary Wessels, Rui Henrique, Carmen Jerónimo, Andries Marinus Bergman & Wilbert Zwart The Androgen Receptor (AR) is the main driver of prostate cancer and functions in conjunction with chromatin modifications. Here, the authors comprehensively profile 100 primary prostate carcinomas by sequencing RNA transcripts in combination with ChIP-sequencing for AR and the active histone marks H3K27ac, H3K4me3 and repressive mark H3K27me3. 21 November 2018 | doi: 10.1038/s41467-018-07270-2 Cancer genomics  Chromatin  Data integration  Prostate cancer  Transcriptomics  The essential genome of the crenarchaeal model Sulfolobus islandicus OPEN Changyi Zhang, Alex P. R. Phillips, Rebecca L. Wipfler, Gary J. Olsen & Rachel J. Whitaker Sulfolobus islandicus is a model organism within the TACK superphylum of the Archaea. Here, the authors perform a genome-wide analysis of essential genes in this organism, show that the proteinaceous S-layer is not essential, and explore potential stages of evolution of the essential gene repertoire in Archaea. 21 November 2018 | doi: 10.1038/s41467-018-07379-4 Archaeal biology  Archaeal evolution  Archaeal genomics  Evolutionary genetics  Integrated mapping of pharmacokinetics and pharmacodynamics in a patient-derived xenograft model of glioblastoma OPEN Elizabeth C. Randall, Kristina B. Emdal, Janice K. Laramy, Minjee Kim, Alison Roos, David Calligaris, Michael S. Regan, Shiv K. Gupta, Ann C. Mladek, Brett L. Carlson, Aaron J. Johnson, Fa-Ke Lu, X. Sunney Xie, Brian A. Joughin, Raven J. Reddy, Sen Peng, Walid M. Abdelmoula, Pamela R. Jackson, Aarti Kolluri, Katherine A. Kellersberger et al. Despite major drug discovery efforts, the therapeutic options for glioblastoma (GBM) remain inadequate. Here they analyze patient-derived xenograft model of GBM to quantitatively map distribution and cellular response to the EGFR inhibitor erlotinib, and report heterogeneous erlotinib delivery to intracranial tumors to be inadequate to inhibit EGFR signaling. 21 November 2018 | doi: 10.1038/s41467-018-07334-3 Biological techniques  Cancer  Chemistry  Drug discovery  Neuroscience  Graphene controlled Brewster angle device for ultra broadband terahertz modulation OPEN Zefeng Chen, Xuequan Chen, Li Tao, Kun Chen, Mingzhu Long, Xudong Liu, Keyou Yan, Rayko I. Stantchev, Emma Pickwell-MacPherson & Jian-Bin Xu Low-dimensional materials show promise for applications in imaging, spectroscopy and ultra-broadband communications. Here, the authors report an effect of Brewster angle control at graphene-quartz interface for applications in terahertz modulation over a broadband range from 0.5 to 1.6 THz. 21 November 2018 | doi: 10.1038/s41467-018-07367-8 Graphene  Optical properties and devices  Terahertz optics  Terahertz rectification in ring-shaped quantum barriers OPEN Taehee Kang, R. H. Joon-Yeon Kim, Geunchang Choi, Jaiu Lee, Hyunwoo Park, Hyeongtag Jeon, Cheol-Hwan Park & Dai-Sik Kim Many experiments have been performed that study rectification by exciting electrons to tunnel across a single quantum barrier. Here, the authors take a 2-dimensional approach by combining 2D closed-loop tunneling barriers with broken symmetry to enable geometrically controllable rectification of THz fields. 21 November 2018 | doi: 10.1038/s41467-018-07365-w Nanophotonics and plasmonics  Sub-wavelength optics  Metabolic engineering of Escherichia coli for de novo biosynthesis of vitamin B12 OPEN Huan Fang, Dong Li, Jie Kang, Pingtao Jiang, Jibin Sun & Dawei Zhang Vitamin B12 is an essential nutrient with limited natural sources. Here the authors transfer 28 pathway synthesis genes from several bacteria including R. capsulatus to E. coli and, using metabolic engineering and optimised fermentation conditions, achieve high yields. 21 November 2018 | doi: 10.1038/s41467-018-07412-6 Industrial microbiology  Metabolic engineering  Detecting heritable phenotypes without a model using fast permutation testing for heritability and set-tests OPEN Regev Schweiger, Eyal Fisher, Omer Weissbrod, Elior Rahmani, Martina Müller-Nurasyid, Sonja Kunze, Christian Gieger, Melanie Waldenberger, Saharon Rosset & Eran Halperin Standard approaches for heritability and set testing in statistical genetics rely on parametric models that might not hold in reality and give inflated p-values. Here, the authors develop a fast method for permutation-based testing of marker sets and of heritability that does not suffer from model misspecification. 21 November 2018 | doi: 10.1038/s41467-018-07276-w Epigenetics  Genetics  Genomics  Observation of bound state self-interaction in a nano-eV atom collider OPEN Ryan Thomas, Matthew Chilcott, Eite Tiesinga, Amita B. Deb & Niels Kjærgaard Self-interaction of a bound state through its coupling to the continuum is a phenomenon that is very difficult to observe. Here, the authors optically collide atomic clouds of rubidium and potassium to observe the self-interaction energy through precise measurements of magnetically tunable Feshbach resonances. 20 November 2018 | doi: 10.1038/s41467-018-07375-8 Atomic and molecular collision processes  Matter waves and particle beams  Optical manipulation and tweezers  Ultracold gases  Bimodal sensing of guidance cues in mechanically distinct microenvironments OPEN Erdem D. Tabdanov, Vikram V. Puram, Zaw Win, Ashab Alamgir, Patrick W. Alford & Paolo P. Provenzano Invasive cells respond to contact guidance cues during migration. Here, using micro- and nanopatterning with different ligands and varying stiffness, the authors find that cells can make cellular protrusions through both contractility-dependent and contractility-independent means. 20 November 2018 | doi: 10.1038/s41467-018-07290-y Breast cancer  Motility  A third generation of radical fluorinating agents based on N-fluoro-N-arylsulfonamides OPEN Daniel Meyer, Harish Jangra, Fabian Walther, Hendrik Zipse & Philippe Renaud Common radical fluorination reagents, such as Selectofluor®, are penalized by the need for metal catalysts and possible oxidation side reactions. Here, the authors reported the synthesis and application of N-fluoro-N-arylsulfonamides (NFASs) as third generation of radical fluorinating reagents to overcome those limitations. 20 November 2018 | doi: 10.1038/s41467-018-07196-9 Chemical tools  Synthetic chemistry methodology  Stereochemistry  Using single nucleotide variations in single-cell RNA-seq to identify subpopulations and genotype-phenotype linkage OPEN Olivier Poirion, Xun Zhu, Travers Ching & Lana X. Garmire Identification of cell subpopulations using transcript abundance is noisy. Here, the authors developed a linear modeling framework, SSrGE, which utilizes effective and expressed nucleotide variations from single-cell RNA-seq to identify tumor subpopulations. 20 November 2018 | doi: 10.1038/s41467-018-07170-5 Computational models  Statistical methods  Design of an inherently-stable water oxidation catalyst OPEN Biswarup Chakraborty, Gal Gan-Or, Manoj Raula, Eyal Gadot & Ira A. Weinstock A current challenge in the development of molecular water oxidation catalysts is to overcome their inherent susceptibilities to oxidative or hydrolytic degradation under turnover conditions in water. Here, the authors design an inherently-stable water oxidation catalyst using oxidatively-inert ligands to harness a reactive metal oxide. 20 November 2018 | doi: 10.1038/s41467-018-07281-z Coordination chemistry  Photocatalysis  Autapses enhance bursting and coincidence detection in neocortical pyramidal cells OPEN Luping Yin, Rui Zheng, Wei Ke, Quansheng He, Yi Zhang, Junlong Li, Bo Wang, Zhen Mi, Yue-sheng Long, Malte J. Rasch, Tianfu Li, Guoming Luan & Yousheng Shu While autapses are synapses made by a neuron onto itself, its functional significance in pyramidal cells are not clear. Here, the authors show that in the mammalian neocortex, autapses of pyramidal cells can enhance burst firing and coincidence detection from other inputs. 20 November 2018 | doi: 10.1038/s41467-018-07317-4 Excitability  Neurophysiology  Early childhood investment impacts social decision-making four decades later OPEN Yi Luo, Sébastien Hétu, Terry Lohrenz, Andreas Hula, Peter Dayan, Sharon Landesman Ramey, Libbie Sonnier-Netto, Jonathan Lisinski, Stephen LaConte, Tobias Nolte, Peter Fonagy, Elham Rahmani, P. Read Montague & Craig Ramey Early childhood educational intervention has positive outcomes in adulthood, including higher education attainment, economic status, and overall health. This study shows that adults who underwent such intervention have greater enforcement of equality norm during social decision-making, potentially motivated by future planning. 20 November 2018 | doi: 10.1038/s41467-018-07138-5 Decision making  Human behaviour  The structure and function of the global citrus rhizosphere microbiome OPEN Jin Xu, Yunzeng Zhang, Pengfan Zhang, Pankaj Trivedi, Nadia Riera, Yayu Wang, Xin Liu, Guangyi Fan, Jiliang Tang, Helvécio D. Coletta-Filho, Jaime Cubero, Xiaoling Deng, Veronica Ancona, Zhanjun Lu, Balian Zhong, M. Caroline Roper, Nieves Capote, Vittoria Catara, Gerhard Pietersen, Christian Vernière et al. Research on plant root-associated microbial communities may help develop more efficient or sustainable crop production methods. Here the authors analyse the citrus rhizosphere microbiome, using both amplicon and deep shotgun metagenomic sequencing of samples collected across six continents. 20 November 2018 | doi: 10.1038/s41467-018-07343-2 Metagenomics  Microbial ecology  Microbiome  Soil microbiology  Crossover from positive to negative optical torque in mesoscale optical matter OPEN Fei Han, John A. Parker, Yuval Yifat, Curtis Peterson, Stephen K. Gray, Norbert F. Scherer & Zijie Yan Negative optical torque has been predicted theoretically, but experimental demonstrations have been scarce. Here, the authors show that the optical torque in a mesoscopic optical matter array can be reversed depending on number, separation and configuration of nanoparticles in a circularly polarized optical trap. 20 November 2018 | doi: 10.1038/s41467-018-07376-7 Nanoparticles  Optical manipulation and tweezers  Hybrid perovskite light emitting diodes under intense electrical excitation OPEN Hoyeon Kim, Lianfeng Zhao, Jared S. Price, Alex J. Grede, Kwangdong Roh, Alyssa N. Brigeman, Mike Lopez, Barry P. Rand & Noel C. Giebink Hybrid perovskite semiconductors are promising for wavelength-tunable laser diodes but their behavior under intense electrical excitation remains unexplored. Kim et al. investigate perovskite light emitting diodes at current densities nearing 1 kA cm−2 and suggest that a laser diode is within reach. 20 November 2018 | doi: 10.1038/s41467-018-07383-8 Diode lasers  Inorganic LEDs  Organic LEDs  Quantitative metaproteomics of medieval dental calculus reveals individual oral health status OPEN Rosa R. Jersie-Christensen, Liam T. Lanigan, David Lyon, Meaghan Mackie, Daniel Belstrøm, Christian D. Kelstrup, Anna K. Fotakis, Eske Willerslev, Niels Lynnerup, Lars J. Jensen, Enrico Cappellini & Jesper V. Olsen Mineralized plaque, or dental calculus, is a valuable reservoir of the ancient oral microbiome. Here, the authors use quantitative metaproteomics to analyze the dental calculus of 21 individuals from a medieval cemetery, identifying human and microbial proteins that shed light on their oral health status. 20 November 2018 | doi: 10.1038/s41467-018-07148-3 Anthropology  Archaeology  Microbiome  Proteomics  The spread of low-credibility content by social bots OPEN Chengcheng Shao, Giovanni Luca Ciampaglia, Onur Varol, Kai-Cheng Yang, Alessandro Flammini & Filippo Menczer Online misinformation is a threat to a well-informed electorate and undermines democracy. Here, the authors analyse the spread of articles on Twitter, find that bots play a major role in the spread of low-credibility content and suggest control measures for limiting the spread of misinformation. 20 November 2018 | doi: 10.1038/s41467-018-06930-7 Complex networks  Politics  Society  Technology  Tailoring atomic layer growth at the liquid-metal interface OPEN Hai Cao, Deepali Waghray, Stefan Knoppe, Wim Dehaen, Thierry Verbiest & Steven De Feyter Ultrathin metallic films are most often fabricated by atomic or molecular beam epitaxy under ultrahigh vacuum conditions, where it is difficult to control deposition and growth. Here, the authors describe a wet deposition method, using solution-borne gold nanocluster precursors, to regulate growth of atomically flat gold nanoislands on a surface. 20 November 2018 | doi: 10.1038/s41467-018-07381-w Molecular self-assembly  Scanning probe microscopy  Surface assembly  Retroactive and graded prioritization of memory by reward OPEN Erin Kendall Braun, G. Elliott Wimmer & Daphna Shohamy Rewarding events are prioritized in memory, but to support adaptive decision-making memory should also be prioritized for the events leading up to a reward. Here, the authors show that reward retroactively prioritizes memory for proximal, neutral events that precede the reward. 20 November 2018 | doi: 10.1038/s41467-018-07280-0 Consolidation  Human behaviour  Customizing supercontinuum generation via on-chip adaptive temporal pulse-splitting OPEN Benjamin Wetzel, Michael Kues, Piotr Roztocki, Christian Reimer, Pierre-Luc Godin, Maxwell Rowley, Brent E. Little, Sai T. Chu, Evgeny A. Viktorov, David J. Moss, Alessia Pasquazi, Marco Peccianti & Roberto Morandotti Controlling complex properties of optical systems, like the output of nonlinear light sources, is increasingly important for applications. Here, Wetzel et al. use an actively-controlled photonic chip to prepare patterns of femtosecond laser pulses used for tailoring supercontinuum generation. 20 November 2018 | doi: 10.1038/s41467-018-07141-w Fibre optics and optical communications  Integrated optics  Nonlinear optics  BAFopathies' DNA methylation epi-signatures demonstrate diagnostic utility and functional continuum of Coffin–Siris and Nicolaides–Baraitser syndromes OPEN Erfan Aref-Eshghi, Eric G. Bend, Rebecca L. Hood, Laila C. Schenkel, Deanna Alexis Carere, Rana Chakrabarti, Sandesh C. S. Nagamani, Sau Wai Cheung, Philippe M. Campeau, Chitra Prasad, Victoria Mok Siu, Lauren Brady, Mark A. Tarnopolsky, David J. Callen, A. Micheil Innes, Susan M. White, Wendy S. Meschino, Andrew Y. Shuen, Guillaume Paré, Dennis E. Bulman et al. Mutations in genes encoding subunits of the BAF complex can cause Coffin–Siris and Nicolaides–Baraitser syndromes. Here the authors identify overlapping DNA methylation signatures in individuals with subtypes of these two syndromes that suggest a functional link and can be used to diagnose subjects with unclear clinical presentations. 20 November 2018 | doi: 10.1038/s41467-018-07193-y Clinical genetics  Epigenomics  Medical genetics  Tamoxifen therapy in a murine model of myotubular myopathy OPEN Nika Maani, Nesrin Sabha, Kamran Rezai, Arun Ramani, Linda Groom, Nadine Eltayeb, Faranak Mavandadnejad, Andrea Pang, Giulia Russo, Michael Brudno, Volker Haucke, Robert T. Dirksen & James J. Dowling Myotubular myopathy is a severe muscle disease for which no effective treatment exists. Here, the authors show that tamoxifen ameliorates pathology and extends survival in a mouse model of the disease, and that the effect is mediated via estrogen receptor signaling and involves modulation of DNM2 expression. 19 November 2018 | doi: 10.1038/s41467-018-07057-5 Hormone receptors  Neuromuscular disease  Target identification  Signal peptide represses GluK1 surface and synaptic trafficking through binding to amino-terminal domain OPEN Gui-Fang Duan, Yaxin Ye, Sha Xu, Wucheng Tao, Shiping Zhao, Tengchuan Jin, Roger A. Nicoll, Yun Stone Shi & Nengyin Sheng The two kainate receptors GluK1 and GluK2 show different surface expression and synaptic trafficking. Here authors engineer chimeric GluK1-GluK2 receptors and decipher a role how the signal peptide of GluK1 behaves as a ligand of GluK1 and modifies surface expression and trafficking. 19 November 2018 | doi: 10.1038/s41467-018-07403-7 Cellular neuroscience  Ion channels in the nervous system  Membrane biophysics  Molecular neuroscience  Synaptic transmission  Two-dimensional tessellation by molecular tiles constructed from halogen–halogen and halogen–metal networks OPEN Fang Cheng, Xue-Jun Wu, Zhixin Hu, Xuefeng Lu, Zijing Ding, Yan Shao, Hai Xu, Wei Ji, Jishan Wu & Kian Ping Loh Molecular tessellations of complex tilings are difficult to design and construct. Here, the authors show that molecular tessellations can be formed from a single building block that gives rise to two distinct supramolecular phases, whose self-similar subdomains serve as tiles in the periodic tessellations. 19 November 2018 | doi: 10.1038/s41467-018-07323-6 Materials chemistry  Self-assembly  Surface chemistry  Hydrogen production by Sulfurospirillum species enables syntrophic interactions of Epsilonproteobacteria OPEN Stefan Kruse, Tobias Goris, Martin Westermann, Lorenz Adrian & Gabriele Diekert Epsilonproteobacteria, such as Sulfurospirillum, can use molecular hydrogen as an electron donor for respiration. Here, the authors show that Sulfurospirillum can, in addition, release hydrogen during fermentation, allowing metabolic interactions with other hydrogen-consuming microorganisms. 19 November 2018 | doi: 10.1038/s41467-018-07342-3 Bacterial physiology  Bacteriology  Proteomics  Symbiosis  Competitive repopulation of an empty microglial niche yields functionally distinct subsets of microglia-like cells OPEN Harald Lund, Melanie Pieber, Roham Parsa, Jinming Han, David Grommisch, Ewoud Ewing, Lara Kular, Maria Needhamsen, Alexander Espinosa, Emma Nilsson, Anna K. Överby, Oleg Butovsky, Maja Jagodic, Xing-Mei Zhang & Robert A. Harris Brain microglial cells can be replenished by blood-derived monocytes, but many aspects of this repopulation remain unclear. Here the authors show that the brain microglial niche can be replaced both by proliferating, residential microglia as well as differentiated Ly6Chi monocytes, with the latter having overlapping but distinct characteristics. 19 November 2018 | doi: 10.1038/s41467-018-07295-7 Gene regulation in immune cells  Microglial cells  Neuroimmunology  Neuroscience  Wnt/β-catenin signaling regulates VE-cadherin-mediated anastomosis of brain capillaries by counteracting S1pr1 signaling OPEN Kathleen Hübner, Pauline Cabochette, Rodrigo Diéguez-Hurtado, Cora Wiesner, Yuki Wakayama, Kathrin S. Grassme, Marvin Hubert, Stefan Guenther, Heinz-Georg Belting, Markus Affolter, Ralf H. Adams, Benoit Vanhollebeke & Wiebke Herzog Wnt signaling is known to regulate the formation of the blood-brain barrier. Here Hübner et al. dissect the underlying mechanisms using high resolution live imaging in zebrafish, and find that Wnt regulates anastomosis of angiogenic sprouts in the brain by counteracting sphingosine-1-phosphate receptor signaling. 19 November 2018 | doi: 10.1038/s41467-018-07302-x Angiogenesis  Blood–brain barrier  Zebrafish  Sumoylation of RORγt regulates TH17 differentiation and thymocyte development OPEN Zhiheng He, Jing Zhang, Zhaofeng Huang, Qian Du, Ning Li, Qiang Zhang, Yuan Chen & Zuoming Sun The transcription factor RORγt is essential for the differentiation of TH17 cells, thymocyte development and lymphoid organogenesis. Here the authors show that the function of RORγt is regulated by PIAS4-mediated sumoylation that stabilize the interaction with SRC1 and KAT2A, to enhance the transcriptional activity of RORγt. 19 November 2018 | doi: 10.1038/s41467-018-07203-z Gene regulation in immune cells  Lymphocyte differentiation  Sumoylation  T-helper 17 cells  Single cell RNA-seq and ATAC-seq analysis of cardiac progenitor cell transition states and lineage settlement OPEN Guangshuai Jia, Jens Preussner, Xi Chen, Stefan Guenther, Xuejun Yuan, Michail Yekelchyk, Carsten Kuenne, Mario Looso, Yonggang Zhou, Sarah Teichmann & Thomas Braun Cardiac progenitor cells (CPCs) form cardiomyocytes, pericytes, smooth muscle and endothelial cells during embryonic development. Here, the authors characterize mouse CPCs marked by Nkx2.5 and Isl1 from E7.5 to E9.5 by single cell RNA-seq and ATAC-seq, showing fate transitions involve distinct open chromatin state. 19 November 2018 | doi: 10.1038/s41467-018-07307-6 Differentiation  Functional clustering  Stem cells  RIG-I like receptor sensing of host RNAs facilitates the cell-intrinsic immune response to KSHV infection OPEN Yang Zhao, Xiang Ye, William Dunker, Yu Song & John Karijolich RIG-I and MDA5, are cytosolic restriction factors and receptors for RNA viruses. Here the authors show during KSHV lytic infection that substrates for recognition by RIG-I and MDA5 are misprocessed RNAs derived from noncoding host RNA molecules, suggesting antiviral immunity can be engaged by sensing of misprocessed cellular RNAs. 19 November 2018 | doi: 10.1038/s41467-018-07314-7 Pathogens  RIG-I-like receptors  Viral host response  Viral infection  Age-related declines in α-Klotho drive progenitor cell mitochondrial dysfunction and impaired muscle regeneration OPEN A. Sahu, H. Mamiya, S. N. Shinde, A. Cheikhi, L. L. Winter, N. V. Vo, D. Stolz, V. Roginskaya, W. Y. Tang, C. St. Croix, L. H. Sanders, M. Franti, B. Van Houten, T. A. Rando, A. Barchowsky & F. Ambrosio While young muscle faithfully regenerates damaged myofibers, aged muscle is impaired. Here the authors show the "anti-aging" protein α-Klotho is upregulated in young muscle after damage via promoter demethylation and this regulation is lost in aging, resulting in mitochondrial damage and an impaired healing response. 19 November 2018 | doi: 10.1038/s41467-018-07253-3 Ageing  DNA methylation  Translation of non-standard codon nucleotides reveals minimal requirements for codon-anticodon interactions OPEN Thomas Philipp Hoernes, Klaus Faserl, Michael Andreas Juen, Johannes Kremser, Catherina Gasser, Elisabeth Fuchs, Xinying Shi, Aaron Siewert, Herbert Lindner, Christoph Kreutz, Ronald Micura, Simpson Joseph, Claudia Höbartner, Eric Westhof, Alexander Hüttenhofer & Matthias David Erlacher The recognition of the mRNA codon by the tRNA anticodon is crucial for protein synthesis. Here the authors introduce non-standard nucleotides in bacterial and eukaryotic mRNA to reveal the minimal hydrogen bond requirement of codon-anticodon interaction for efficient and accurate translation. 19 November 2018 | doi: 10.1038/s41467-018-07321-8 Chemical modification  Nucleic acids  Ribozymes  RNA  Invasive Salmonella exploits divergent immune evasion strategies in infected and bystander dendritic cell subsets OPEN Anna Aulicino, Kevin C. Rue-Albrecht, Lorena Preciado-Llanes, Giorgio Napolitani, Neil Ashley, Adam Cribbs, Jana Koth, B. Christoffer Lagerholm, Tim Ambrose, Melita A. Gordon, David Sims & Alison Simmons Salmonella employ a range of strategies to counter host defences during infection. Here, Aulicino et al. use single-cell RNA-sequencing to examine the effects of invasive and non-invasive strains of Salmonella, revealing discrete and divergent immune evasion strategies in infected and bystander dendritic cells. 19 November 2018 | doi: 10.1038/s41467-018-07329-0 Bacterial infection  Dendritic cells  Infection  Pathogens  Nutrient supply controls particulate elemental concentrations and ratios in the low latitude eastern Indian Ocean OPEN Catherine A. Garcia, Steven E. Baer, Nathan S. Garcia, Sara Rauschenberg, Benjamin S. Twining, Michael W. Lomas & Adam C. Martiny The Indian Ocean provides a unique environmental gradient to test underlying drivers of the elemental composition of particulate organic matter. Here the authors show that nutrient supply, over temperature and biodiversity changes, controls regional variation of elemental ratios in the tropical Indian Ocean. 19 November 2018 | doi: 10.1038/s41467-018-06892-w Carbon cycle  Element cycles  Marine biology  Marine chemistry  TBX2 is a neuroblastoma core regulatory circuitry component enhancing MYCN/FOXM1 reactivation of DREAM targets OPEN Bieke Decaesteker, Geertrui Denecker, Christophe Van Neste, Emmy M. Dolman, Wouter Van Loocke, Moritz Gartlgruber, Carolina Nunes, Fanny De Vloed, Pauline Depuydt, Karen Verboom, Dries Rombaut, Siebe Loontiens, Jolien De Wyn, Waleed M. Kholosy, Bianca Koopmans, Anke H. W. Essing, Carl Herrmann, Daniel Dreidax, Kaat Durinck, Dieter Deforce et al. In high-risk neuroblastoma cases, gains in chromosome 17q are common. Here, the authors investigate the epigenomics and transcriptomics of neuroblastoma, identifying TBX2 as a core regulatory circuitry component enhancing the reactivation of DREAM targets by MYCN/FOXM1. 19 November 2018 | doi: 10.1038/s41467-018-06699-9 Biological sciences  Genetics  Effective removal of mercury from aqueous streams via electrochemical alloy formation on platinum OPEN Cristian Tunsu & Björn Wickman Removal of anthropogenic mercury from water streams is of great importance given its high toxicity and ability to spread rapidly. Here, the authors demonstrate the direct alloying of mercury with a fully recyclable platinum electrode, providing effective removal at different concentrations and pH, and in the presence of other contaminants. 19 November 2018 | doi: 10.1038/s41467-018-07300-z Electrochemistry  Nanoscale materials  Pollution remediation  Tamoxifen prolongs survival and alleviates symptoms in mice with fatal X-linked myotubular myopathy OPEN Elinam Gayi, Laurence A. Neff, Xènia Massana Muñoz, Hesham M. Ismail, Marta Sierra, Thomas Mercier, Laurent A. Décosterd, Jocelyn Laporte, Belinda S. Cowling, Olivier M. Dorchies & Leonardo Scapozza X-linked myotubular myopathy (XLMTM) is a severe muscle disease with no effective treatment. Here, the authors show that tamoxifen, a drug used to treat breast cancer, rescues the pathology in a mouse model of the disease, at least in part by normalizing expression of the disease modifier proteins DNM2 and BIN1 19 November 2018 | doi: 10.1038/s41467-018-07058-4 Neuromuscular disease  Pharmaceutics  H3K9 methyltransferases and demethylases control lung tumor-propagating cells and lung cancer progression OPEN S. P. Rowbotham, F. Li, A. F. M. Dost, S. M. Louie, B. P. Marsh, P. Pessina, C. R. Anbarasu, C. F. Brainson, S. J. Tuminello, A. Lieberman, S. Ryeom, T. M. Schlaeger, B. J. Aronow, H. Watanabe, K. K. Wong & C. F. Kim The effects of epigenetic regulators on different tumor cell populations can affect their potential as anticancer targets. In this study, the authors demonstrate that the histone methyltransferase G9a is a suppressor of lung tumor-propagating cells and tumor progression, acting through chromatin modification with MMP10 as one of its targets for metastasis regulation. 19 November 2018 | doi: 10.1038/s41467-018-07077-1 Cancer models  Cancer stem cells  Histone post-translational modifications  Non-small-cell lung cancer  Engulfing cells promote neuronal regeneration and remove neuronal debris through distinct biochemical functions of CED-1 OPEN Hui Chiu, Yan Zou, Nobuko Suzuki, Yi-Wen Hsieh, Chiou-Fen Chuang, Yi-Chun Wu & Chieh Chang It is unclear how removal of axon debris and initiation of axon regeneration following nerve injury is co-regulated. In this study, the authors show that the extracellular domain (ECD) of the engulfment receptor, CED-1, functions as an adhesion molecule to promote axonal regeneration after injury, independent of its function in phagocytosis 19 November 2018 | doi: 10.1038/s41467-018-07291-x Caenorhabditis elegans  Cell adhesion  Regeneration and repair in the nervous system  Crosstalks between mTORC1 and mTORC2 variagate cytokine signaling to control NK maturation and effector function OPEN The metabolic regulator protein family, mTOR, regulate natural killer (NK) cell development and function, but the underlying mechanism is unclear. Here, the authors show that Raptor/mTORC1 and Rictor/mTORC2 form a feedback crosstalk network to variegate cytokine and cellular signaling and modulate NK maturation and effector functions. 19 November 2018 | doi: 10.1038/s41467-018-07277-9 Gene regulation in immune cells  Innate immunity  Innate lymphoid cells  Lymphopoiesis  Cell metabolism regulates integrin mechanosensing via an SLC3A2-dependent sphingolipid biosynthesis pathway OPEN Etienne Boulter, Soline Estrach, Floriane S. Tissot, Marco L. Hennrich, Lionel Tosello, Laurence Cailleteau, Laura R. de la Ballina, Sabrina Pisano, Anne-Claude Gavin & Chloé C. Féral Mechanical and metabolic cues contribute to regulate cell and tissue homeostasis but how they are integrated is not known. Here the authors show that the amino acid transporter and integrin coreceptor CD98hc regulates mechanical signaling downstream of integrins indirectly through regulating sphingolipid availability. 19 November 2018 | doi: 10.1038/s41467-018-07268-w Integrins  Lipid signalling  Mechanotransduction  A continuous-time MaxSAT solver with high analog performance OPEN Botond Molnár, Ferenc Molnár, Melinda Varga, Zoltán Toroczkai & Mária Ercsey-Ravasz Continuous-time computation paradigm could represent a viable alternative to the standard digital one when dealing with certain classes of problems. Here, the authors propose a generalised version of a continuous-time solver and simulate its performances in solving MaxSAT and two-colour Ramsey problems. 19 November 2018 | doi: 10.1038/s41467-018-07327-2 Computational science  Computer science  Information theory and computation  Nonlinear phenomena  Orthogonal Cas9–Cas9 chimeras provide a versatile platform for genome editing OPEN Mehmet Fatih Bolukbasi, Pengpeng Liu, Kevin Luk, Samantha F. Kwok, Ankit Gupta, Nadia Amrani, Erik J. Sontheimer, Lihua Julie Zhu & Scot A. Wolfe Therapeutic genome engineering relies on the development of reliable, robust and versatile tools. Here the authors develop Cas9-Cas9 chimeras with high target site activity that generate predictable deletions. 19 November 2018 | doi: 10.1038/s41467-018-07310-x Genetic engineering  Targeted gene repair  Continuous negative-to-positive tuning of thermal expansion achieved by controlled gas sorption in porous coordination frameworks OPEN Josie E. Auckett, Arnold A. Barkhordarian, Stephen H. Ogilvie, Samuel G. Duyker, Hubert Chevreau, Vanessa K. Peterson & Cameron J. Kepert Achieving control over the thermomechanical properties of functional materials is desirable, yet remains highly challenging. Here, the authors demonstrate continuous negative-to-positive tuning of thermal expansion in two Prussian blue analogues, by varying the concentration of adsorbed CO2. 19 November 2018 | doi: 10.1038/s41467-018-06850-6 Metal–organic frameworks  Porous materials  Apoptosis of intestinal epithelial cells restricts Clostridium difficile infection in a model of pseudomembranous colitis OPEN Pedro H. V. Saavedra, Linyan Huang, Farzaneh Ghazavi, Stephanie Kourula, Tom Vanden Berghe, Nozomi Takahashi, Peter Vandenabeele & Mohamed Lamkanfi The enterotoxins TcdA and TcdB induce cytotoxicity of epithelial cells during Clostridium difficile infection. Here the authors show that bacterial induced epithelial cell death occurs via activation of caspases 3 and 7, resulting in apoptotic cell death. 19 November 2018 | doi: 10.1038/s41467-018-07386-5 Bacterial pathogenesis  Cell death and immune response  Clostridium difficile  Pathogens  Growth factor gene IGF1 is associated with bill size in the black-bellied seedcracker Pyrenestes ostrinus OPEN Bridgett M. vonHoldt, Rebecca Y. Kartzinel, Christian D. Huber, Vinh Le Underwood, Ying Zhen, Kristen Ruegg, Kirk E. Lohmueller & Thomas B. Smith Pyrenestes finches have a bill size polymorphism thought to be maintained by disruptive selection. Here, the authors identify a single candidate region, including insulin-like growth factor 1, differentiating small and large bill size morphs and a wider region differentiating the mega-billed morph. 19 November 2018 | doi: 10.1038/s41467-018-07374-9 Evolutionary biology  Evolutionary genetics  Genetic association study  Synthetic RNA-based logic computation in mammalian cells OPEN Satoshi Matsuura, Hiroki Ono, Shunsuke Kawasaki, Yi Kuang, Yoshihiko Fujita & Hirohide Saito The construction of complex RNA-delivered genetic circuits in mammalian cells is challenging, though offers advantages over DNA circuits in clinical use. Here the authors construct a set of logic gates that respond to multiple miRNAs and demonstrate an apoptosis-regulatory AND gate. 19 November 2018 | doi: 10.1038/s41467-018-07181-2 miRNAs  RNA  Synthetic biology  Flow of cerebrospinal fluid is driven by arterial pulsations and is reduced in hypertension OPEN Humberto Mestre, Jeffrey Tithof, Ting Du, Wei Song, Weiguo Peng, Amanda M. Sweeney, Genaro Olveda, John H. Thomas, Maiken Nedergaard & Douglas H. Kelley Arterial pulsations are thought to drive CSF flow through perivascular spaces (PVSs), but this has never been quantitatively shown. Using particle tracking to quantify CSF flow velocities in PVSs of live mice, the authors show that flow speeds match the instantaneous speeds of the pulsing artery walls that form the inner boundaries of the PVSs. 19 November 2018 | doi: 10.1038/s41467-018-07318-3 Fluid dynamics  Neuro–vascular interactions  Neuroscience  Sugar-based bactericides targeting phosphatidylethanolamine-enriched membranes OPEN Catarina Dias, João P. Pais, Rafael Nunes, Maria-Teresa Blázquez-Sánchez, Joaquim T. Marquês, Andreia F. Almeida, Patrícia Serra, Nuno M. Xavier, Diogo Vila-Viçosa, Miguel Machuqueiro, Ana S. Viana, Alice Martins, Maria S. Santos, Ana Pelerito, Ricardo Dias, Rogério Tenreiro, Maria C. Oliveira, Marialessandra Contino, Nicola A. Colabufo, Rodrigo F. M. de Almeida et al. Bacillus anthracis causes the infectious disease anthrax. Here, the authors synthesized deoxy glycosides that are effective against B. anthracis and related bacteria and found that these amphiphilic compounds kill bacteria via an unusual mechanism of action. 19 November 2018 | doi: 10.1038/s41467-018-06488-4 Bacterial infection  Deoxy sugars  Memory formation and long-term maintenance of IL-7Rα+ ILC1s via a lymph node-liver axis OPEN Xianwei Wang, Hui Peng, Jingjing Cong, Xuefu Wang, Zhexiong Lian, Haiming Wei, Rui Sun & Zhigang Tian Natural killer cells may respond better on second antigen encounters, but how this memory is induced or maintained in vivo is not clear. Here the authors show that memory NK cells expressing interleukin-7 (IL-7) receptor are induced in the lymph nodes but later recruited to liver for long term, IL-7 dependent survival and memory maintenance. 19 November 2018 | doi: 10.1038/s41467-018-07405-5 Immunological memory  Innate lymphoid cells  Interleukins  NK cells  Effective connectivity of the anterior hippocampus predicts recollection confidence during natural memory retrieval OPEN Yudan Ren, Vinh T. Nguyen, Saurabh Sonkusare, Jinglei Lv, Tianji Pang, Lei Guo, Simon B. Eickhoff, Michael Breakspear & Christine C. Guo While memory is often studied using voluntary recollection, the neural correlates of involuntary memory recall and its effect on cognition are unclear. Here, Ren and colleagues show that the effective connectivity from the anterior hippocampus to the precuneus can predict the strength of involuntary retrieval of episodic memory. 19 November 2018 | doi: 10.1038/s41467-018-07325-4 Computational neuroscience  Long-term memory  Control of spin-wave transmission by a programmable domain wall OPEN Sampo J. Hämäläinen, Marco Madami, Huajun Qin, Gianluca Gubbiotti & Sebastiaan van Dijken Magnon-based spintronic devices crucially rely on the capability of spin wave manipulation. Here the authors achieve active control of spin wave transmission by programming a pinned 90 degree Néel domain wall in a continuous CoFeB/BaTiO3 film with abrupt rotations of uniaxial magnetic anisotropy. 19 November 2018 | doi: 10.1038/s41467-018-07372-x Condensed-matter physics  Magnetic properties and materials  Downregulation of macrophage Irs2 by hyperinsulinemia impairs IL-4-indeuced M2a-subtype macrophage activation in obesity OPEN Tetsuya Kubota, Mariko Inoue, Naoto Kubota, Iseki Takamoto, Tomoka Mineyama, Kaito Iwayama, Kumpei Tokuyama, Masao Moroi, Kohjiro Ueki, Toshimasa Yamauchi & Takashi Kadowaki Obesity is associated with low-grade chronic inflammation. Here the authors show that the activation of anti-inflammatory M2a-subtype macrophages requires the IL4/Irs2/Akt pathway. Due to decreased Irs2 expression this pathway is impaired in obese mice thus leading to a defect in M2a activation. 19 November 2018 | doi: 10.1038/s41467-018-07358-9 Diseases  Immunological disorders  Metabolic disorders  Fungal spores as a source of sodium salt particles in the Amazon basin OPEN Swarup China, Susannah M. Burrows, Bingbing Wang, Tristan H. Harder, Johannes Weis, Meryem Tanarhte, Luciana V. Rizzo, Joel Brito, Glauber G. Cirino, Po-Lun Ma, John Cliff, Paulo Artaxo, Mary K. Gilles & Alexander Laskin Salt particles in the Amazon basin are typically attributed to marine aerosols transported from the Atlantic Ocean. Here the authors show the potential importance of fungal spores as a source of sodium-salt particles in the Amazon rainforest. 19 November 2018 | doi: 10.1038/s41467-018-07066-4 Atmospheric chemistry  Biogeochemistry  Environmental sciences  Locomotion modulates specific functional cell types in the mouse visual thalamus OPEN Çağatay Aydın, João Couto, Michele Giugliano, Karl Farrow & Vincent Bonin Locomotion is known to modulate neuronal firing in both the visual thalamus (LGN) and V1. Here, the authors characterize the LGN modulation in detail and report that neurons with transient ON responses for high spatial frequency stimuli show the strongest gain modulation. 19 November 2018 | doi: 10.1038/s41467-018-06780-3 Sensory processing  Visual system  A chromosome-scale assembly of the sorghum genome using nanopore sequencing and optical mapping OPEN Stéphane Deschamps, Yun Zhang, Victor Llaca, Liang Ye, Abhijit Sanyal, Matthew King, Gregory May & Haining Lin Assembly of large, repeat-rich eukaryotic genomes remains challenging. Here, the authors use BioNano Genomics DLS optical mapping and single-molecule nanopore sequencing to generate a chromosome-scale assembly of a new Sorghum bicolor accession and identify variation compared to the publicly available S. bicolor genome. 19 November 2018 | doi: 10.1038/s41467-018-07271-1 Agricultural genetics  Genome  Plant genetics  Sequencing  Molecular basis of maintaining an oxidizing environment under anaerobiosis by soluble fumarate reductase OPEN Sunghwan Kim, Chang Min Kim, Young-Jin Son, Jae Young Choi, Rahel K. Siegenthaler, Younho Lee, Tae-Ho Jang, Jaeyoung Song, Hara Kang, Chris A. Kaiser & Hyun Ho Park Soluble fumarate reductases are essential for eukaryotic cell survival under anaerobic conditions but their mechanism is not fully understood. Here, the authors present structural and enzymatic analyses of yeast fumarate reductase Osm1, elucidating the molecular basis of maintaining redox balance during anaerobiosis. 19 November 2018 | doi: 10.1038/s41467-018-07285-9 Enzyme mechanisms  Oxidoreductases  X-ray crystallography  Manipulation of the dephasing time by strong coupling between localized and propagating surface plasmon modes OPEN Jinghuan Yang, Quan Sun, Kosei Ueno, Xu Shi, Tomoya Oshikiri, Hiroaki Misawa & Qihuang Gong Strong coupling between two resonant modes is a prerequisite for many scientifically and technologically interesting effects. Here, Yang et al. demonstrate strong coupling between localized and propagating plasmon modes with a splitting energy of 144 meV and controllable dephasing times. 19 November 2018 | doi: 10.1038/s41467-018-07356-x Nanophotonics and plasmonics  Optical physics  Palladium concave nanocrystals with high-index facets accelerate ascorbate oxidation in cancer treatment OPEN Yu Chong, Xing Dai, Ge Fang, Renfei Wu, Lin Zhao, Xiaochuan Ma, Xin Tian, Sangyun Lee, Chao Zhang, Chunying Chen, Zhifang Chai, Cuicui Ge & Ruhong Zhou The therapeutic efficiency of ascorbate is limited by its slow autoxidation. Here, the authors show the application of concave-structured palladium nanocrystals for the treatment of colorectal cancer through the oxidation of ascorbate, enhancing the production of oxidative stresses specifically on cancer cells. 19 November 2018 | doi: 10.1038/s41467-018-07257-z Biophysics  Cancer  Cell biology  Chemical biology  Computational biology and bioinformatics  Hidden diversity of soil giant viruses OPEN Frederik Schulz, Lauren Alteio, Danielle Goudeau, Elizabeth M. Ryan, Feiqiao B. Yu, Rex R. Malmstrom, Jeffrey Blanchard & Tanja Woyke Current knowledge of giant virus diversity is largely based on samples from aquatic environments. Here the authors employ cultivation-independent metagenomics and mini-metagenomics on forest soil and identify 16 novel giant virus genomes, some of which representing novel lineages, including the so far largest genome in Mimiviridae. 19 November 2018 | doi: 10.1038/s41467-018-07335-2 Metagenomics  Microbiology  Virology  NUAK2 is a critical YAP target in liver cancer OPEN Wei-Chien Yuan, Brian Pepe-Mooney, Giorgio G. Galli, Michael T. Dill, Hai-Tsang Huang, Mingfeng Hao, Yumeng Wang, Han Liang, Raffaele A. Calogero & Fernando D. Camargo Hippo-YAP pathway plays an important role in cancers; however the in vivo relevance of YAP/TAZ target genes is unclear. Here, the authors show that NUAK2 is a target of YAP and participates in a feedback loop to maximize YAP activity. Inhibition of NUAK2 suppresses YAP-driven hepatomegaly and liver cancer growth, offering a new target for cancer therapy. 16 November 2018 | doi: 10.1038/s41467-018-07394-5 HIPPO signalling  Liver cancer  Targeted therapies  Barren plateaus in quantum neural network training landscapes OPEN Jarrod R. McClean, Sergio Boixo, Vadim N. Smelyanskiy, Ryan Babbush & Hartmut Neven Gradient-based hybrid quantum-classical algorithms are often initialised with random, unstructured guesses. Here, the authors show that this approach will fail in the long run, due to the exponentially-small probability of finding a large enough gradient along any direction. 16 November 2018 | doi: 10.1038/s41467-018-07090-4 Quantum information  Quantum mechanics  Dna2 processes behind the fork long ssDNA flaps generated by Pif1 and replication-dependent strand displacement OPEN Silvia Emma Rossi, Marco Foiani & Michele Giannattasio DNA2 encodes a 5′ flap DNA endonuclease involved in replication and DNA double strand break processing. Here the authors by using a conditional degron system together with electron microscopy characterize the role played by Dna2 and Pif1 helicase during unperturbed DNA replication in S. cerevisiae. 16 November 2018 | doi: 10.1038/s41467-018-07378-5 DNA synthesis  Genetics  A hPSC-based platform to discover gene-environment interactions that impact human β-cell and dopamine neuron survival OPEN Diseases such as diabetes and Parkinson's manifest based on interactions between genes and environment. Here, the authors find among a panel of cell types that propargite, a common pesticide, induces pancreatic β-cell and dopamine neuron death and that loss of the gene GSTT1 confers hypersensitivity. 16 November 2018 | doi: 10.1038/s41467-018-07201-1 Embryonic stem cells  Screening  Shockwave generates < 100 > dislocation loops in bcc iron OPEN Qing Peng, Fanjiang Meng, Yizhong Yang, Chenyang Lu, Huiqiu Deng, Lumin Wang, Suvranu De & Fei Gao Irradiating iron introduces defects such as interstitial dislocation loops, whose exact formation mechanism remains unclear. Here, the authors use large scale molecular dynamics simulations to reveal a punch out mechanism that can directly create < 100 > interstitial dislocation loops. 16 November 2018 | doi: 10.1038/s41467-018-07102-3 Atomic and molecular collision processes  Atomistic models  Metals and alloys  Cellular metabolism constrains innate immune responses in early human ontogeny OPEN Bernard Kan, Christina Michalski, Helen Fu, Hilda H. T. Au, Kelsey Lee, Elizabeth A. Marchant, Maye F. Cheng, Emily Anderson-Baucum, Michal Aharoni-Simon, Peter Tilley, Raghavendra G. Mirmira, Colin J. Ross, Dan S. Luciani, Eric Jan & Pascal M. Lavoie Little is known about developmental set points of immune responses, especially in humans. Here the authors show that the metabolic state of monocytes isolated from prematurely born infants underlies attenuated responsiveness to fungal infection via selective control of protein translation. 16 November 2018 | doi: 10.1038/s41467-018-07215-9 Developmental biology  Fungal pathogenesis  Immunology  Innate immunity  Pathogens  In situ synthesis of supported metal nanocatalysts through heterogeneous doping OPEN No Woo Kwak, Seung Jin Jeong, Han Gil Seo, Siwon Lee, YeonJu Kim, Jun Kyu Kim, Pilgyu Byeon, Sung-Yoon Chung & WooChul Jung Supported metal nanoparticles hold great promise for many fields, including catalysis and renewable energy. Here the authors report a novel methodology for the in-situ growth of architecturally tailored, regenerative metal nanocatalysts that is applicable to a wide range of materials. 16 November 2018 | doi: 10.1038/s41467-018-07050-y Catalyst synthesis  Heterogeneous catalysis  Nanoparticles  Surfaces, interfaces and thin films  Optogenetic dissection of Rac1 and Cdc42 gradient shaping OPEN S. de Beco, K. Vaidžiulytė, J. Manzi, F. Dalier, F. di Federico, G. Cornilleau, M. Dahan & M. Coppey A steep gradient of Cdc42 is at the front of migrating cells, whereas the active Rac1 gradient is graded. Here the authors show that Cdc42 gradients follow the distribution of GEFs and govern direction of migration, while Rac1 gradients require the activity of the GAP β2-chimaerin and control cell speed. 16 November 2018 | doi: 10.1038/s41467-018-07286-8 Cellular motility  Optogenetics  Regulatory networks  RHO signalling  Proteostasis by STUB1/HSP70 complex controls sensitivity to androgen receptor targeted therapy in advanced prostate cancer OPEN Chengfei Liu, Wei Lou, Joy C. Yang, Liangren Liu, Cameron M. Armstrong, Alan P. Lombard, Ruining Zhao, Onika D. V. Noel, Clifford G. Tepper, Hong-Wu Chen, Marc Dall'Era, Christopher P. Evans & Allen C. Gao The AR-V7 isoform is associated with anti-androgen drug resistance in prostate cancer. Here, the authors show that AR-V7 protein stability is regulated by HSP70/STUB1 complex-mediated proteostasis which confers drug resistance in late stage prostate cancer. Inhibition of HSP70 re-sensitizes resistant cells to enzalutamide therapy. 16 November 2018 | doi: 10.1038/s41467-018-07178-x Cancer  Prostate cancer  Urology  Mechanism of copper-free Sonogashira reaction operates through palladium-palladium transmetallation OPEN Martin Gazvoda, Miha Virant, Balazs Pinter & Janez Košmrlj Although the Sonogashira coupling of acetylenes and vinyl/aryl halides has been applied for decades, many mechanistic questions have remained unanswered. Here, the authors provide experimental and theoretical support for two interlinked palladium cycles operating in the debated Sonogashira coupling mechanism. 16 November 2018 | doi: 10.1038/s41467-018-07081-5 Catalytic mechanisms  Homogeneous catalysis  Reaction mechanisms  Over 1000-fold enhancement of upconversion luminescence using water-dispersible metal-insulator-metal nanostructures OPEN Ananda Das, Chenchen Mao, Suehyun Cho, Kyoungsik Kim & Wounjhang Park Upconversion nanoparticles are already used in bio-imaging but still suffer from low luminescence. Here, metal-insulator-metal nanostructures with 1-2 orders magnitude enhancement in upconversion are introduced enabling bioimaging at reduced particle or excitation power densities, respectively. 16 November 2018 | doi: 10.1038/s41467-018-07284-w Nanofabrication and nanopatterning  Nanophotonics and plasmonics  Optical materials and structures  Multi-color live-cell super-resolution volume imaging with multi-angle interference microscopy OPEN Youhua Chen, Wenjie Liu, Zhimin Zhang, Cheng Zheng, Yujia Huang, Ruizhi Cao, Dazhao Zhu, Liang Xu, Meng Zhang, Yu-Hui Zhang, Jiannan Fan, Luhong Jin, Yingke Xu, Cuifang Kuang & Xu Liu 3D super-resolution imaging of dynamic processes in live cells is still challenging, especially in a large field of view. Here the authors combine SIM with multi-angle evanescent light illumination and achieve improved lateral and axial resolution, with stack acquisition time in the range of 1–2 s. 16 November 2018 | doi: 10.1038/s41467-018-07244-4 Super-resolution microscopy  Total internal reflection microscopy  Wide-field fluorescence microscopy  A majority of HIV persistence during antiretroviral therapy is due to infected cell proliferation OPEN Daniel B. Reeves, Elizabeth R. Duke, Thor A. Wagner, Sarah E. Palmer, Adam M. Spivak & Joshua T. Schiffer HIV infected cells persist for decades in patients under ART, but the mechanisms responsible remain unclear. Here, Reeves et al. use modeling approaches adapted from ecology to show that cellular proliferation, rather than viral replication, generates a majority of infected cells during ART. 16 November 2018 | doi: 10.1038/s41467-018-06843-5 Applied mathematics  Computational models  HIV infections  Viral reservoirs  Water assisted biomimetic synergistic process and its application in water-jet rewritable paper OPEN Guan Xi, Lan Sheng, Jiahui Du, Jinyan Zhang, Minjie Li, Hongze Wang, Yufei Ma & Sean Xiao-An Zhang Water based inks used for water-jet rewritable paper (WJRP) are an environmental friendly alternative to conventional printing, but black colour in WJRP could not be realized so far. Here the authors demonstrate black as well as other colour WJRP based on binary systems containing less-sensitive acidochromic dyes and mild proton donors. 16 November 2018 | doi: 10.1038/s41467-018-07211-z Organic molecules in materials science  Sustainability  Synthesis and processing  Graphene mechanical pixels for Interferometric Modulator Displays OPEN Santiago J. Cartamil-Bueno, Dejan Davidovikj, Alba Centeno, Amaia Zurutuza, Herre S. J. van der Zant, Peter G. Steeneken & Samer Houri The electro-optical response of suspended graphene membranes measured by change in wavelength-dependent reflectance can enable interferometric modulation display (IMOD) technology. Here, the authors report suspended double layer graphene based IMOD drums with 2500 pixels per inch. 16 November 2018 | doi: 10.1038/s41467-018-07230-w Mechanical and structural properties and devices  Optical properties and devices  Reward regulation in plant–frugivore networks requires only weak cues OPEN Jörg Albrecht, Jonas Hagge, Dana G. Schabo, H. Martin Schaefer & Nina Farwig A challenge for mutualists is that partner cue reliability is often low. Here, the authors show that though fruit brightness is weakly predictive of nutritional content, the diets of birds (e.g. migrants vs. residents) are structured by fruit brightness in alignment with expected nutritional needs. 16 November 2018 | doi: 10.1038/s41467-018-07362-z Behavioural ecology  Community ecology  Ecological networks  Serotonin signals through a gut-liver axis to regulate hepatic steatosis OPEN No effective pharmacological treatments exist for nonalcoholic fatty liver disease (NAFLD). Here, the authors show that serotonin concentration in the portal blood is increased in nine human subjects and in mice fed a high-fat diet, and that local serotonin signaling ablation, either genetically or with an antagonist, prevents hepatic steatosis in mice. 16 November 2018 | doi: 10.1038/s41467-018-07287-7 Metabolic diseases  Non-alcoholic fatty liver disease  Warming assessment of the bottom-up Paris Agreement emissions pledges OPEN Yann Robiou du Pont & Malte Meinshausen The Paris Agreement includes bottom-up pledges and top-down warming threshold. Under this setting where countries effectively choose their own fairness principle, this article assesses the global warming implied by each Nationally Determined Contribution to inform the future ratcheting-up process. 16 November 2018 | doi: 10.1038/s41467-018-07223-9 Climate-change mitigation  RET rearrangements are actionable alterations in breast cancer OPEN Bhavna S. Paratala, Jon H. Chung, Casey B. Williams, Bahar Yilmazel, Whitney Petrosky, Kirstin Williams, Alexa B. Schrock, Laurie M. Gay, Ellen Lee, Sonia C. Dolfi, Kien Pham, Stephanie Lin, Ming Yao, Atul Kulkarni, Frances DiClemente, Chen Liu, Lorna Rodriguez-Rodriguez, Shridar Ganesan, Jeffrey S. Ross, Siraj M. Ali et al. Fusions of the gene RET have been described in thyroid and lung cancers. Here, the AUs identify RET gene alterations, including known fusions, novel fusions, and rearrangements in breast cancer (BC) that are involved in the tumorigenic process and show the benefit of RET therapy in a recurrent BC patient carrying the NCOA4-RET fusion. 16 November 2018 | doi: 10.1038/s41467-018-07341-4 Breast cancer  Cancer genomics  Cancer models  Cancer therapy  Tumour biomarkers  Demographic histories and genetic diversity across pinnipeds are shaped by human exploitation, ecology and life-history OPEN Historical hunting has caused documented declines in pinnipeds, but the extent to which hunting caused genetic bottlenecks among species was unknown. Here, the authors show evidence of severe bottlenecks in several pinniped species, particularly those that breed on land. 16 November 2018 | doi: 10.1038/s41467-018-06695-z Conservation biology  Ecological genetics  Evolutionary genetics  Population genetics  Multiple forest attributes underpin the supply of multiple ecosystem services OPEN María R. Felipe-Lucia, Santiago Soliveres, Caterina Penone, Peter Manning, Fons van der Plas, Steffen Boch, Daniel Prati, Christian Ammer, Peter Schall, Martin M. Gossner, Jürgen Bauhus, Francois Buscot, Stefan Blaser, Nico Blüthgen, Angel de Frutos, Martin Ehbrecht, Kevin Frank, Kezia Goldmann, Falk Hänsel, Kirsten Jung et al. Managing forests for the supply of multiple ecosystem services (ES) is key given potential trade-offs among services. Here, the authors analyse how forest stand attributes generate trade-offs among ES and the relative contribution of forest attributes and environmental factors to predict services. 16 November 2018 | doi: 10.1038/s41467-018-07082-4 Ecosystem ecology  Ecosystem services  Forest ecology  Forestry  Cross-ecosystem carbon flows connecting ecosystems worldwide OPEN Isabelle Gounand, Chelsea J. Little, Eric Harvey & Florian Altermatt Material flows between ecosystems, though the degree to which ecosystems are coupled is under investigation. Here Gounand et al. analyze cross-ecosystem carbon flows and relate them to in situ functions, and report different dependencies on spatial flows across numerous ecosystems. 16 November 2018 | doi: 10.1038/s41467-018-07238-2 Ecology  Ecosystem ecology  CYP6AE gene cluster knockout in Helicoverpa armigera reveals role in detoxification of phytochemicals and insecticides OPEN Huidong Wang, Yu Shi, Lu Wang, Shuai Liu, Shuwen Wu, Yihua Yang, René Feyereisen & Yidong Wu Cotton bollworm is an important agricultural pest with widespread resistance to insecticides. Here Wang et al. identifies CYP6AEs from cotton bollworm involved in detoxifying plant toxins and chemical insecticides through the CRISPR-Cas9-based reverse genetics approach in conjunction with in vitro metabolism. 16 November 2018 | doi: 10.1038/s41467-018-07226-6 Entomology  Molecular ecology  Coherent multidimensional spectroscopy of dilute gas-phase nanosystems OPEN Lukas Bruder, Ulrich Bangert, Marcel Binz, Daniel Uhl, Romain Vexiau, Nadia Bouloufa-Maafa, Olivier Dulieu & Frank Stienkemeier Coherent multidimensional spectroscopy has greatly advanced our understanding of molecular dynamics but was so far broadly limited to complex condensed phase probes. Bruder et al. extend the method to isolated nanosystems in the gas phase and study cold molecules in a superfluid helium environment. 16 November 2018 | doi: 10.1038/s41467-018-07292-w Atomic and molecular interactions with photons  Chemical physics  Nonlinear optics  Ultrafast photonics  Endothelial cell rearrangements during vascular patterning require PI3-kinase-mediated inhibition of actomyosin contractility OPEN Ana Angulo-Urarte, Pedro Casado, Sandra D. Castillo, Piotr Kobialka, Maria Paraskevi Kotini, Ana M. Figueiredo, Pau Castel, Vinothini Rajeeve, Maria Milà-Guasch, Jaime Millan, Cora Wiesner, Helena Serra, Laia Muixi, Oriol Casanovas, Francesc Viñals, Markus Affolter, Holger Gerhardt, Stephan Huveneers, Heinz-Georg Belting, Pedro R. Cutillas et al. Angiogenesis requires dynamic endothelial rearrangements and relative position changes within the vascular tubes. Here the authors show that a PI3K/NUAK1/MYPT1/MLCP pathway regulates actomyosin contractility in endothelial cells and cellular rearrangement during vascular patterning. 16 November 2018 | doi: 10.1038/s41467-018-07172-3 Angiogenesis  Myosin  Non-obstructive intracellular nanolasers OPEN Alasdair H. Fikouras, Marcel Schubert, Markus Karl, Jothi D. Kumar, Simon J. Powis, Andrea Di Falco & Malte C. Gather While the sharp emission lines of microlasers are advantageous for cell tagging, their relatively large size can impede cell migration and behavior. Here, Fikouras et al. develop nano-sized lasers that can readily tag and track various types of cells, including through narrow constrictions. 16 November 2018 | doi: 10.1038/s41467-018-07248-0 Biophotonics  Nanocavities  Semiconductor lasers  Glucose metabolism induced by Bmp signaling is essential for murine skeletal development OPEN Seung-Yon Lee, E. Dale Abel & Fanxin Long It is unclear how metabolic regulation affects development of the skeleton. Here, the authors show that deletion of the glucose transporter Glut1 (Slc2a1) both prior to and following chondrogenesis in the mouse limb impairs chondrocyte proliferation and shortening of the limbs, modulated by BMP signaling. 16 November 2018 | doi: 10.1038/s41467-018-07316-5 Cartilage development  Developmental biology  Genetics  Organic field-effect optical waveguides OPEN Guangyao Zhao, Huanli Dong, Qing Liao, Jun Jiang, Yi Luo, Hongbing Fu & Wenping Hu Despite recent advances in organic optoelectronics development, integration of electronics and photonics in a chip remains a challenge. Here, the authors demonstrate organic field-effect optical waveguides that control propagating photons by the electric field produced in an organic transistor. 15 November 2018 | doi: 10.1038/s41467-018-07269-9 Electronic devices  Molecular electronics  Conditional deletion of Rcan1 predisposes to hypertension-mediated intramural hematoma and subsequent aneurysm and aortic rupture OPEN Silvia Villahoz, Paula Sofía Yunes-Leites, Nerea Méndez-Barbero, Katia Urso, Elena Bonzon-Kulichenko, Sagrario Ortega, J. Francisco Nistal, Jesus Vazquez, Stefan Offermanns, Juan Miguel Redondo & Miguel R. Campanero Constitutive deletion of Rcan1 has been previously shown to prevent Angiotensin II-induced aneurysm in mice. Here the authors show that tissue-specific inducible deletion of Rcan1 in vascular cell types predisposes to hypertension-mediated aortic rupture, intramural hematoma, and aneurysm, due to increased GSK-3b-mediated activation of ROCK and induction of a hypercontractile phenotype. 15 November 2018 | doi: 10.1038/s41467-018-07071-7 Aortic diseases  Hypertension  Parity transitions in the superconducting ground state of hybrid InSb–Al Coulomb islands OPEN Jie Shen, Sebastian Heedt, Francesco Borsoi, Bernard van Heck, Sasa Gazibegovic, Roy L. M. Op het Veld, Diana Car, John A. Logan, Mihir Pendharkar, Senja J. J. Ramakers, Guanzhong Wang, Di Xu, Daniël Bouman, Attila Geresdi, Chris J. Palmstrøm, Erik P. A. M. Bakkers & Leo P. Kouwenhoven Understanding the ground state (GS) phase transitions in the quantum tunneling regime of a superconducting system is important for future qubit devices. Here, Shen, Heedt and Borsoi et al. report distinct types of fermion parity GS transitions as a function of magnetic field and gate voltages in a Coulomb-blockaded InSb–Al island. 15 November 2018 | doi: 10.1038/s41467-018-07279-7 Electronic properties and materials  Superconducting devices  Superconducting properties and materials  Samarium(II) folding cascades involving hydrogen atom transfer for the synthesis of complex polycycles OPEN Mateusz P. Plesniak, Monserrat H. Garduño-Castro, Philipp Lenz, Xavier Just-Baringo & David J. Procter Diversity-oriented synthesis is a valuable strategy to construct complex molecules of medicinal interest. Here, the authors show a folding cascade strategy to convert linear substrates into polycyclic compounds with multiple stereocentres by combining the reductive chemistry of SmI2 with 1,5-hydrogen atom transfer. 15 November 2018 | doi: 10.1038/s41467-018-07194-x Diversity-oriented synthesis  Synthetic chemistry methodology  Reaction mechanisms  A diagnosis of the plasma waves responsible for the explosive energy release of substorm onset OPEN N. M. E. Kalmoni, I. J. Rae, C. E. J. Watt, K. R. Murphy, M. Samara, R. G. Michell, G. Grubbs & C. Forsyth The origin of geomagnetic substorms is still uncertain due to lack of comprehensive quantitative analyses. Here, the authors construct an observational dispersion relation of auroral forms that correspond to the explosive energy release from substorm onset. 15 November 2018 | doi: 10.1038/s41467-018-07086-0 Aurora  Magnetospheric physics  Plasma physics  Lattice-contraction triggered synchronous electrochromic actuator OPEN Kerui Li, Yuanlong Shao, Hongping Yan, Zhi Lu, Kent J. Griffith, Jinhui Yan, Gang Wang, Hongwei Fan, Jingyu Lu, Wei Huang, Bin Bao, Xuelong Liu, Chengyi Hou, Qinghong Zhang, Yaogang Li, Junsheng Yu & Hongzhi Wang Materials that exhibit synchronous color change and actuation may benefit biomimetic camouflage, but stimuli can be difficult to control. Here the authors report a composite with electricity-driven electrochromic and actuating capabilities for use in a solid-state ionic polymer-metal composite actuator. 15 November 2018 | doi: 10.1038/s41467-018-07241-7 Actuators  Nanowires  Structural properties  Perforin inhibition protects from lethal endothelial damage during fulminant viral hepatitis OPEN M. Welz, S. Eickhoff, Z. Abdullah, J. Trebicka, K. H. Gartlan, J. A. Spicer, A. J. Demetris, H. Akhlaghi, M. Anton, K. Manske, D. Zehn, B. Nieswandt, C. Kurts, J. A. Trapani, P. Knolle, D. Wohlleber & W. Kastenmüller CD8 T cells can protect the liver from viral infection, but can also result in severe liver damage and organ failure. Here, the authors develop a mouse model reflecting fulminant CD8 T cell mediated viral hepatitis, which occurs in a perforin-dependent manner that is protected by the use of perforin inhibitors. 15 November 2018 | doi: 10.1038/s41467-018-07213-x Cytotoxic T cells  Hepatology  Imaging the immune system  Viral infection  Winding around non-Hermitian singularities OPEN Qi Zhong, Mercedeh Khajavikhan, Demetrios N. Christodoulides & Ramy El-Ganainy A general description of observable effects induced by non-Hermitian singularities is complex. Here, Zhong et al. develop such a formalism, showing that loops around the same exceptional point starting from the same point in the same direction do not need to have the same outcome. 15 November 2018 | doi: 10.1038/s41467-018-07105-0 Optical physics  Theoretical physics  Metastable silica high pressure polymorphs as structural proxies of deep Earth silicate melts OPEN E. Bykova, M. Bykov, A. Černok, J. Tidholm, S. I. Simak, O. Hellman, M. P. Belov, I. A. Abrikosov, H.-P. Liermann, M. Hanfland, V. B. Prakapenka, C. Prescher, N. Dubrovinskaia & L. Dubrovinsky As silica melts are believed to be important components of the Earth's mantle, their structure should determine many of its properties. Here, the authors identify two crystalline modifications of SiO2, whose local structures closely resemble those of known melts, providing a structural model for their atomic ordering at the nanoscale. 15 November 2018 | doi: 10.1038/s41467-018-07265-z Geochemistry  Solid-state chemistry  Structure of solids and liquids  Valley coherent exciton-polaritons in a monolayer semiconductor OPEN S. Dufferwiel, T. P. Lyons, D. D. Solnyshkov, A. A. P. Trichet, A. Catanzaro, F. Withers, G. Malpuech, J. M. Smith, K. S. Novoselov, M. S. Skolnick, D. N. Krizhanovskii & A. I. Tartakovskii The short exciton life time in atomically thin transition metal dichalcogenides poses limitations to efficient control of the valley pseudospin and coherence. Here, the authors manipulate the exciton coherence in a WSe2 monolayer embedded in an optical microcavity in the strong light-matter coupling regime. 15 November 2018 | doi: 10.1038/s41467-018-07249-z Fluorescence spectroscopy  Microresonators  Two-dimensional materials  Proteolysis of histidine kinase VgrS inhibits its autophosphorylation and promotes osmostress resistance in Xanthomonas campestris OPEN Chao-Ying Deng, Huan Zhang, Yao Wu, Li-Li Ding, Yue Pan, Shu-Tao Sun, Ya-Jun Li, Li Wang & Wei Qian Bacterial histidine kinases (HKs) play key roles in the response to stimuli and are regulated by reversible phosphorylation. Here, the authors show that the activity of a HK in the plant pathogen Xanthomonas campestris is modulated by irreversible, proteolytic modification in response to osmostress. 15 November 2018 | doi: 10.1038/s41467-018-07228-4 Bacterial genes  Bacterial genetics  Kinases  A tumor-targeted trimeric 4-1BB-agonistic antibody induces potent anti-tumor immunity without systemic toxicity OPEN Marta Compte, Seandean Lykke Harwood, Ines G. Muñoz, Rocio Navarro, Manuela Zonca, Gema Perez-Chacon, Ainhoa Erce-Llamazares, Nekane Merino, Antonio Tapia-Galisteo, Angel M. Cuesta, Kasper Mikkelsen, Eduardo Caleiras, Natalia Nuñez-Prado, M. Angela Aznar, Simon Lykkemark, Jorge Martínez-Torrecuadrada, Ignacio Melero, Francisco J. Blanco, Jorge Bernardino de la Serna, Juan M. Zapata et al. Cancer therapy using systemically administrated 4-1BB-targeting antibodies is often associated with severe toxicity due to the nonspecific activation of autoreactive T cells. Here, the authors have developed a trimeric antibody targeting both 4-1BB and EGFR, which activates T cells effectively and shows negligible cytotoxicity. 15 November 2018 | doi: 10.1038/s41467-018-07195-w Cancer  Cancer therapy  Molecular engineering  Tumour immunology  A conserved enhancer regulates Il9 expression in multiple lineages OPEN Byunghee Koh, Amina Abdul Qayum, Rajneesh Srivastava, Yongyao Fu, Benjamin J. Ulrich, Sarath Chandra Janga & Mark H. Kaplan Interleukin-9 (IL-9) is important for allergy, autoimmunity and tumor immunity, but how its expression is regulated is unclear. Here the authors show the essential function of an enhancer, CNS-25 in mouse and CNS-18 in human, for IL-9 expression, with the deletion of this enhancer severely hampering IL-9 production in mice or human cells. 15 November 2018 | doi: 10.1038/s41467-018-07202-0 Epigenetics in immune cells  Innate immune cells  Interleukins  Lymphocytes  Photoreduction of gaseous oxidized mercury changes global atmospheric mercury speciation, transport and deposition OPEN Alfonso Saiz-Lopez, Sebastian P. Sitkiewicz, Daniel Roca-Sanjuán, Josep M. Oliva-Enrich, Juan Z. Dávalos, Rafael Notario, Martin Jiskra, Yang Xu, Feiyue Wang, Colin P. Thackray, Elsie M. Sunderland, Daniel J. Jacob, Oleg Travnikov, Carlos A. Cuevas, A. Ulises Acuña, Daniel Rivero, John M. C. Plane, Douglas E. Kinnison & Jeroen E. Sonke Reduction of gaseous Hg(II) compounds drives atmospheric mercury wet and dry deposition to Earth surface ecosystems. Global Hg models assume this reduction takes place in clouds. Here the authors report a new gas-phase Hg photochemical mechanism that changes atmospheric mercury lifetime and its deposition to the surface. 15 November 2018 | doi: 10.1038/s41467-018-07075-3 Atmospheric chemistry  Element cycles  Environmental sciences  Targeting fidelity of adenine and cytosine base editors in mouse embryos OPEN Hye Kyung Lee, Michaela Willi, Shannon M. Miller, Sojung Kim, Chengyu Liu, David R. Liu & Lothar Hennighausen Understanding the risks of bystander and off-target editing is essential for genome engineering applications. Here, the authors analyze the fidelity of adenine and cytosine base editors in vivo. 15 November 2018 | doi: 10.1038/s41467-018-07322-7 CRISPR-Cas9 genome editing  Genetic engineering  Martian magmatism from plume metasomatized mantle OPEN James M. D. Day, Kimberly T. Tait, Arya Udry, Frédéric Moynier, Yang Liu & Clive R. Neal A unified model for the formation of martian rock types is required to understand Mars's formation and evolution. Here the authors show that nakhlite and chassignite meteorites originate from melting of metasomatized depleted mantle lithosphere, whereas shergottite melts originate from deep plume sources. 15 November 2018 | doi: 10.1038/s41467-018-07191-0 Geochemistry  Inner planets  Meteoritics  Atomic scale insights into structure instability and decomposition pathway of methylammonium lead iodide perovskite OPEN Shulin Chen, Xiaowei Zhang, Jinjin Zhao, Ying Zhang, Guoli Kong, Qian Li, Ning Li, Yue Yu, Ningan Xu, Jingmin Zhang, Kaihui Liu, Qing Zhao, Jian Cao, Jicai Feng, Xinzheng Li, Junlei Qi, Dapeng Yu, Jiangyu Li & Peng Gao Hybrid perovskites are highly promising for photovoltaic applications, but they are prone to decomposition. Here, the authors probe the stability of CH3NH3PbI3 films in a transmission electron microscope, defining the threshold conditions to avoid damage under the electron beam, and describing a decomposition pathway. 15 November 2018 | doi: 10.1038/s41467-018-07177-y Organic–inorganic nanostructures  Solar energy    Nature Communications EVENT 5th International Conference on Computer Science, Engineering and Information Technology (CSEIT 2018) 22.12.18 "Dubai, UAE" More science events from     Latest Correspondence     Reply to 'Flawed assumptions compromise water yield assessment' OPEN Ping Zhou, Qiang Li, Guoyi Zhou, Xiaohua Wei, Mingfang Zhang, Zhiyong Liu, Xiuzhi Chen, Xiaodong Liu, Yin Xiao, Ge Sun, David F. Scott, Shuyidan Zhou, Liusheng Han & Yongxian Su 15 November 2018 | doi: 10.1038/s41467-018-07065-5 Ecology  Forestry  Water resources      Latest Author Corrections     Author Correction: Misestimation of heritability and prediction accuracy of male-pattern baldness OPEN Chloe X. Yap, Julia Sidorenko, Riccardo E. Marioni, Loic Yengo, Naomi R. Wray & Peter M. Visscher 20 November 2018 | doi: 10.1038/s41467-018-07400-w Genetics  Heritable quantitative trait  Author Correction: Atomically precise graphene etch stops for three dimensional integrated systems from two dimensional material heterostructures OPEN Jangyup Son, Junyoung Kwon, SunPhil Kim, Yinchuan Lv, Jaehyung Yu, Jong-Young Lee, Huije Ryu, Kenji Watanabe, Takashi Taniguchi, Rita Garrido-Menacho, Nadya Mason, Elif Ertekin, Pinshane Y. Huang, Gwan-Hyoung Lee & Arend M. van der Zande 20 November 2018 | doi: 10.1038/s41467-018-07297-5 Electronic properties and devices  Molecular electronics  NEMS  Two-dimensional materials  Author Correction: Expression-based drug screening of neural progenitor cells from individuals with schizophrenia OPEN Benjamin Readhead, Brigham J. Hartley, Brian J. Eastwood, David A. Collier, David Evans, Richard Farias, Ching He, Gabriel Hoffman, Pamela Sklar, Joel T. Dudley, Eric E. Schadt, Radoslav Savić & Kristen J. Brennand 19 November 2018 | doi: 10.1038/s41467-018-07326-3 Data integration  High-throughput screening  Induced pluripotent stem cells  Author Correction: Variants in exons 5 and 6 of ACTB cause syndromic thrombocytopenia OPEN Sharissa L. Latham , Nadja Ehmke, Patrick Y. A. Reinke, Manuel H. Taft, Dorothee Eicke, Theresia Reindl, Werner Stenzel, Michael J. Lyons, Michael J. Friez, Jennifer A. Lee, Ramona Hecker, Michael C. Frühwald, Kerstin Becker, Teresa M. Neuhann, Denise Horn, Evelin Schrock, Indra Niehaus, Katharina Sarnow, Konrad Grützmann, Luzie Gawehn et al. 19 November 2018 | doi: 10.1038/s41467-018-07404-6 Disease genetics  Haematological diseases  Microtubules  Platelets  Author Correction: Non-collinear spin states in bottom-up fabricated atomic chains OPEN Manuel Steinbrecher, Roman Rausch, Khai Ton That, Jan Hermenau, Alexander A. Khajetoorians, Michael Potthoff, Roland Wiesendanger & Jens Wiebe 19 November 2018 | doi: 10.1038/s41467-018-07428-y Magnetic properties and materials  Spintronics  Author Correction: Substantiating freedom from parasitic infection by combining transmission model predictions with disease surveys OPEN Edwin Michael, Morgan E. Smith, Moses N. Katabarwa, Edson Byamukama, Emily Griswold, Peace Habomugisha, Thomson Lakwo, Edridah Tukahebwa, Emmanuel S. Miri, Abel Eigege, Evelyn Ngige, Thomas R. Unnasch & Frank O. Richards 19 November 2018 | doi: 10.1038/s41467-018-07507-0 Computational models  Developing world  Epidemiology  Parasitic infection  Author Correction: Comprehensive integrative analyses identify GLT8D1 and CSNK2B as schizophrenia risk genes OPEN Cui-Ping Yang, Xiaoyan Li, Yong Wu, Qiushuo Shen, Yong Zeng, Qiuxia Xiong, Mengping Wei, Chunhui Chen, Jiewei Liu, Yongxia Huo, Kaiqin Li, Gui Xue, Yong-Gang Yao, Chen Zhang, Ming Li, Yongbin Chen & Xiong-Jian Luo 16 November 2018 | doi: 10.1038/s41467-018-07401-9 Genetics of the nervous system  Genetics research  Genome-wide association studies  Schizophrenia  Author Correction: Dynamic intercellular transport modulates the spatial patterning of differentiation during early neural commitment OPEN Chad M. Glen, Todd C. McDevitt & Melissa L. Kemp 16 November 2018 | doi: 10.1038/s41467-018-07442-0 Computational models  Dynamic networks  Multicellular systems  Pattern formation  Stem-cell differentiation  Author Correction: Higher ambient synaptic glutamate at inhibitory versus excitatory neurons differentially impacts NMDA receptor activity OPEN Lulu Yao, Teddy Grand, Jesse E. Hanson, Pierre Paoletti & Qiang Zhou 15 November 2018 | doi: 10.1038/s41467-018-07441-1 Neuroscience  Physiology      Latest Publisher Corrections     Publisher Correction: Cytoplasmic localization of GRHL3 upon epidermal differentiation triggers cell shape change for epithelial morphogenesis OPEN Chiharu Kimura-Yoshida, Kyoko Mochida, Masa-aki Nakaya, Takeomi Mizutani & Isao Matsuo 20 November 2018 | doi: 10.1038/s41467-018-07486-2 Cell signalling  Morphogenesis  Publisher Correction: A shear-dependent NO-cGMP-cGKI cascade in platelets acts as an auto-regulatory brake of thrombosis OPEN Lai Wen, Susanne Feil, Markus Wolters, Martin Thunemann, Frank Regler, Kjestine Schmidt, Andreas Friebe, Marcus Olbrich, Harald Langer, Meinrad Gawaz, Cor de Wit & Robert Feil 20 November 2018 | doi: 10.1038/s41467-018-07409-1 Calcium signalling  Fluorescence imaging  Platelets  Thrombosis  Publisher Correction: In vivo neutralization of dendrotoxin-mediated neurotoxicity of black mamba venom by oligoclonal human IgG antibodies OPEN Andreas H. Laustsen, Aneesh Karatt-Vellatt, Edward W. Masters, Ana Silvia Arias, Urska Pus, Cecilie Knudsen, Saioa Oscoz, Peter Slavny, Daniel T. Griffiths, Alice M. Luther, Rachael A. Leah, Majken Lindholm, Bruno Lomonte, José María Gutiérrez & John McCafferty 20 November 2018 | doi: 10.1038/s41467-018-07480-8 Antibody therapy  Applied immunology  Translational research  Publisher Correction: Coordinated targeting of cold and nicotinic receptors synergistically improves obesity and type 2 diabetes OPEN Christoffer Clemmensen , Sigrid Jall, Maximilian Kleinert, Carmelo Quarta, Tim Gruber, Josefine Reber, Stephan Sachs, Katrin Fischer, Annette Feuchtinger, Angelos Karlas, Stephanie E. Simonds, Gerald Grandl, Daniela Loher, Eva Sanchez-Quant, Susanne Keipert, Martin Jastroch, Susanna M. Hofmann, Emmani B. M. Nascimento, Patrick Schrauwen, Vasilis Ntziachristos et al. 20 November 2018 | doi: 10.1038/s41467-018-07479-1 Metabolic disorders  Metabolism  Translational research  Publisher Correction: All-inorganic cesium lead iodide perovskite solar cells with stabilized efficiency beyond 15% OPEN Kang Wang, Zhiwen Jin, Lei Liang, Hui Bian, Dongliang Bai, Haoran Wang, Jingru Zhang, Qian Wang & Shengzhong Liu 19 November 2018 | doi: 10.1038/s41467-018-07485-3 Electronic devices  Materials science  Publisher Correction: Engineering bacterial vortex lattice via direct laser lithography OPEN Daiki Nishiguchi, Igor S. Aranson, Alexey Snezhko & Andrey Sokolov 19 November 2018 | doi: 10.1038/s41467-018-07443-z Bioinspired materials  Cellular motility  Self-assembly      Advertisement Nature Briefing is an essential round-up of science news, opinion and analysis, free in your inbox every weekday. With Nature Briefing, we'll keep you updated on the latest research, so you can focus on yours. 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