Nature Communications - 19 September 2018

Weekly Content Alert Nature Communications is fully open access. Read more. 19 September 2018  Latest content: Articles Author Corrections Publisher Corrections Journal homepage Recommend to library Web feed     Latest Articles View all Articles     Sounding-rocket microgravity experiments on alumina dust OPEN Shinnosuke Ishizuka, Yuki Kimura, Itsuki Sakon, Hiroshi Kimura, Tomoya Yamazaki, Shinsuke Takeuchi & Yuko Inatomi Alumina is thought to be the main condensate to form in the gas outflow from oxygen-rich evolved stars. Here, the authors perform a condensation experiment with alumina in a low-gravity environment, and find spectroscopic evidence for a sharp feature at a wavelength of 13.55 μm. 19 September 2018 | doi: 10.1038/s41467-018-06359-y Astronomical instrumentation  Astrophysical dust  Infrared spectroscopy  Synthesis and processing  Zigzag carbon as efficient and stable oxygen reduction electrocatalyst for proton exchange membrane fuel cells OPEN Longfei Xue, Yongcheng Li, Xiaofang Liu, Qingtao Liu, Jiaxiang Shang, Huiping Duan, Liming Dai & Jianglan Shui Cost and stability of catalysts hinder widespread use of proton exchange membrane fuel cells. Here the authors synthesize zigzag-edged graphene nanoribbons for electrocatalysis of oxygen reduction. Employment of such a metal-free catalyst in a fuel cell yields remarkable power density and durability. 19 September 2018 | doi: 10.1038/s41467-018-06279-x Electrocatalysis  Electrochemistry  Fuel cells  Mechano-regulated metal–organic framework nanofilm for ultrasensitive and anti-jamming strain sensing OPEN Liang Pan, Gang Liu, Wenxiong Shi, Jie Shang, Wan Ru Leow, Yaqing Liu, Ying Jiang, Shuzhou Li, Xiaodong Chen & Run-Wei Li High performance flexible strain sensors with accurate signal detection and noise screening are key to the development of smart sensing systems. Here, the authors demonstrate metal–organic framework based strain sensors that are ultrasensitive, robust, and non-responsive to environmental noise. 19 September 2018 | doi: 10.1038/s41467-018-06079-3 Electronic devices  Sensors and biosensors  Asymmetric assembly of high-value α-functionalized organic acids using a biocatalytic chiral-group-resetting process OPEN Wei Song, Jin-Hui Wang, Jing Wu, Jia Liu, Xiu-Lai Chen & Li-Ming Liu Alpha-functionalized organic acids are building blocks of many bioactive compounds. Here, the authors developed a toolbox-like, modular set of enzymes that reset chiral groups, turning achiral glycine and simple aldehydes into stereodefined α-keto acids, α-hydroxy acids, and α-amino acids. 19 September 2018 | doi: 10.1038/s41467-018-06241-x Biocatalysis  Chemical modification  Processive chitinase is Brownian monorail operated by fast catalysis after peeling rail from crystalline chitin OPEN Akihiko Nakamura, Kei-ichi Okazaki, Tadaomi Furuta, Minoru Sakurai & Ryota Iino Processive chitinase is a linear molecular motor which moves on the surface of crystalline chitin. Here authors use single-molecule imaging, X-ray crystallography and simulations on chitinase A (SmChiA) and show that Brownian motion along the single chitin chain is rectified forward by substrate-assisted catalysis. 19 September 2018 | doi: 10.1038/s41467-018-06362-3 Computational biophysics  Single-molecule biophysics  Super-resolution microscopy  Total internal reflection microscopy  X-ray crystallography  An alternative pathway of enteric PEDV dissemination from nasal cavity to intestinal mucosa in swine OPEN Yuchen Li, Qingxin Wu, Lulu Huang, Chen Yuan, Jialu Wang & Qian Yang Outbreaks of porcine epidemic diarrhea virus (PEDV) have seriously affected pig farms around the world. Here, Li et al. show that PEDV can cause disease in piglets when inoculated by nasal spray, and provide insights into the cellular mechanisms underlying PEDV dissemination within the host. 19 September 2018 | doi: 10.1038/s41467-018-06056-w Viral host response  Viral infection  Viral transmission  Virus–host interactions  Exceptional thermoelectric properties of flexible organic−inorganic hybrids with monodispersed and periodic nanophase OPEN Liming Wang, Zimeng Zhang, Yuchen Liu, Biran Wang, Lei Fang, Jingjing Qiu, Kun Zhang & Shiren Wang The potential of flexible organic/inorganic hybrids for thermoelectrics is limited by the inability to control their microstructure. Here, the authors demonstrate polymer-nanoparticle hybrids with a monodispersed, periodic nanophase that shows high thermoelectric performance at room temperature. 19 September 2018 | doi: 10.1038/s41467-018-06251-9 Organic–inorganic nanostructures  Thermoelectrics  Apoε4 disrupts neurovascular regulation and undermines white matter integrity and cognitive function OPEN Kenzo Koizumi, Yorito Hattori, Sung Ji Ahn, Izaskun Buendia, Antonio Ciacciarelli, Ken Uekawa, Gang Wang, Abigail Hiller, Lingzhi Zhao, Henning U. Voss, Steven M. Paul, Chris Schaffer, Laibaik Park & Costantino Iadecola ApoE4 is a risk factor for small vessel disease, which can lead to cognitive impairment. Here the authors assess the microvasculature of the corpus callosum using 3-photon microscopy and find that mice expressing the ApoE4 allele are more susceptible than wild-type to white matter injury and cognitive impairment in a model of hypoperfusion-induced hypoxia. 19 September 2018 | doi: 10.1038/s41467-018-06301-2 Diseases of the nervous system  Neuro–vascular interactions  Adaptation decorrelates shape representations OPEN Marcelo G. Mattar, Maria Olkkonen, Russell A. Epstein & Geoffrey K. Aguirre Adaptation is thought to improve discrimination by pulling neural representations of similar stimuli farther apart. Here, the authors separately show that adaptation to a 3D shape class leads to better discrimination performance on similar shapes, and activity patterns diverge in object selective cortical areas. 19 September 2018 | doi: 10.1038/s41467-018-06278-y Object vision  Sensory processing  Short-term memory  Roquin targets mRNAs in a 3′-UTR-specific manner by different modes of regulation OPEN Katharina Essig, Nina Kronbeck, Joao C. Guimaraes, Claudia Lohs, Andreas Schlundt, Anne Hoffmann, Gesine Behrens, Sven Brenner, Joanna Kowalska, Cristina Lopez-Rodriguez, Jacek Jemielity, Helmut Holtmann, Kristin Reiche, Jörg Hackermüller, Michael Sattler, Mihaela Zavolan & Vigo Heissmeyer Roquin targets are known to contain two types of sequence-structure motifs, the constitutive and the alternative decay elements (CDE and ADE). Here, the authors describe a linear Roquin binding element (LBE) also involved in target recognition, and show that Roquin binding affects the translation of a subset of targeted mRNAs. 19 September 2018 | doi: 10.1038/s41467-018-06184-3 Autoimmunity  RNA decay  RNA folding  Translation  Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer OPEN Tyler Risom, Ellen M. Langer, Margaret P. Chapman, Juha Rantala, Andrew J. Fields, Christopher Boniface, Mariano J. Alvarez, Nicholas D. Kendsersky, Carl R. Pelz, Katherine Johnson-Camacho, Lacey E. Dobrolecki, Koei Chin, Anil J. Aswani, Nicholas J. Wang, Andrea Califano, Michael T. Lewis, Claire J. Tomlin, Paul T. Spellman, Andrew Adey, Joe W. Gray et al. Resistance to therapy can be driven by intratumoral heterogeneity. Here, the authors show that drug tolerant persistent cell populations emerge during treatment, and these emergent populations arise through epigenetically mediated cell state transitions rather than sub population selection. 19 September 2018 | doi: 10.1038/s41467-018-05729-w Breast cancer  Cancer therapeutic resistance  Epigenomics  Targeted therapies  Human Sox4 facilitates the development of CXCL13-producing helper T cells in inflammatory environments OPEN Hiroyuki Yoshitomi, Shio Kobayashi, Aya Miyagawa-Hayashino, Akinori Okahata, Kohei Doi, Kohei Nishitani, Koichi Murata, Hiromu Ito, Tatsuaki Tsuruyama, Hironori Haga, Shuichi Matsuda & Junya Toguchida At inflammatory sites, ectopic lymphoid-like structures (ELS) can be induced through the function of chemokine CXCL13 produced by CD4+ T cells. Here the authors show that a transcription factor, Sox4, induces the expression of CXCL13 in CD4 T cells in vitro, and is associated with ELS formation in patients with rheumatoid arthritis. 19 September 2018 | doi: 10.1038/s41467-018-06187-0 CD4-positive T cells  Chemokines  Chronic inflammation  Rheumatoid arthritis  Macroscopic helical chirality and self-motion of hierarchical self-assemblies induced by enantiomeric small molecules OPEN Yang Yang, Jie Liang, Fei Pan, Zhen Wang, Jianqi Zhang, Kamran Amin, Jin Fang, Wenjun Zou, Yuli Chen, Xinghua Shi & Zhixiang Wei Chirality transfer by chemical self-assembly has been studied intensively for years but chirality transfers along the same path remains elusive. Here the authors use a multiscale chemo-mechanical model to elucidate the mechanism underlying the chirality transfer via self-assembly in hierarchical camphorsulfonic acid doped polyaniline. 18 September 2018 | doi: 10.1038/s41467-018-06239-5 Polymers  Self-assembly  Structural properties  Implementation and benchmarking of a novel analytical framework to clinically evaluate tumor-specific fluorescent tracers OPEN Marjory Koller, Si-Qi Qiu, Matthijs D. Linssen, Liesbeth Jansen, Wendy Kelder, Jakob de Vries, Inge Kruithof, Guo-Jun Zhang, Dominic J. Robinson, Wouter B. Nagengast, Annelies Jorritsma-Smit, Bert van der Vegt & Gooitzen M. van Dam Fluorescent tracers are being tested in clinical trials to improve detection of tumor margins, but procedures are not standardised. Here, the authors develop an analytical framework that is compatible with the workflow in the operating theatre, and show that it leads to an 88% increase in intraoperative detection of tumor margins in patients with breast cancer. 18 September 2018 | doi: 10.1038/s41467-018-05727-y Breast cancer  Clinical trials  Molecular imaging  Solvatochromic covalent organic frameworks OPEN Laura Ascherl, Emrys W. Evans, Matthias Hennemann, Daniele Di Nuzzo, Alexander G. Hufnagel, Michael Beetz, Richard H. Friend, Timothy Clark, Thomas Bein & Florian Auras Covalent organic frameworks (COFs) find increasing application as sensor material, but fast switching solvatochromism was not realized. Here the authors demonstrate that combination of electron-rich and -deficient building blocks leads to COFs which fast and reversibly change of their electronic structure depending on the surrounding atmosphere. 18 September 2018 | doi: 10.1038/s41467-018-06161-w Optical materials  Sensors and biosensors  Synthesis and processing  Quantum theory cannot consistently describe the use of itself OPEN Daniela Frauchiger & Renato Renner Quantum mechanics is expected to provide a consistent description of reality, even when recursively describing systems contained in each other. Here, the authors develop a variant of Wigner’s friend Gedankenexperiment where each of the current interpretations of QM fails in giving a consistent description. 18 September 2018 | doi: 10.1038/s41467-018-05739-8 Quantum mechanics  Theoretical physics  Water printing of ferroelectric polarization OPEN Yu Tian, Lanying Wei, Qinghua Zhang, Houbing Huang, Yuelin Zhang, Hua Zhou, Fengjie Ma, Lin Gu, Sheng Meng, Long-Qing Chen, Ce-Wen Nan & Jinxing Zhang Controlling ferroelectric polarization is conventionally achieved by applying electric fields, mechanical force or similar. Here reversible switching of the bulk polarization of a BiFeO3 thin film is demonstrated by pattering aqueous solution on to the surface enabling large-scale switching. 18 September 2018 | doi: 10.1038/s41467-018-06369-w Energy transfer  Ferroelectrics and multiferroics  A high throughput screen for next-generation leads targeting malaria parasite transmission OPEN Michael J. Delves, Celia Miguel-Blanco, Holly Matthews, Irene Molina, Andrea Ruecker, Sabrina Yahiya, Ursula Straschil, Matthew Abraham, María Luisa León, Oliver J. Fischer, Ainoa Rueda-Zubiaurre, Jochen R. Brandt, Álvaro Cortés, Anna Barnard, Matthew J. Fuchter, Félix Calderón, Elizabeth A. Winzeler, Robert E. Sinden, Esperanza Herreros, Francisco J. Gamo et al. Sexual forms of malaria parasites are responsible for transmission to the mosquito. Anti-malarial drug resistance remains a serious problem and requires advent of new drug therapies. Here, the authors present a high-throughput screen of potential antimalarial compounds, identifying seventeen drug-like molecules specifically targeting transmission. 18 September 2018 | doi: 10.1038/s41467-018-05777-2 Antimicrobials  Antiparasitic agents  Parasitology  Pkd2l1 is required for mechanoception in cerebrospinal fluid-contacting neurons and maintenance of spine curvature OPEN Jenna R. Sternberg, Andrew E. Prendergast, Lucie Brosse, Yasmine Cantaut-Belarif, Olivier Thouvenin, Adeline Orts-Del’Immagine, Laura Castillo, Lydia Djenoune, Shusaku Kurisu, Jonathan R. McDearmid, Pierre-Luc Bardet, Claude Boccara, Hitoshi Okamoto, Patrick Delmas & Claire Wyart Alteration of cerebrospinal fluid (CSF) flow and cilia defects are clinically associated with idiopathic scoliosis. This study shows that transient receptor potential channel Pkd2l1 is required for mechanosensory function of neurons detecting CSF flow and normal spine curvature development in zebrafish. 18 September 2018 | doi: 10.1038/s41467-018-06225-x Biophysics  Sensory processing  In-situ cross-linking strategy for efficient and operationally stable methylammoniun lead iodide solar cells OPEN Xiaodong Li, Wenxiao Zhang, Ying-Chiao Wang, Wenjun Zhang, Hai-Qiao Wang & Junfeng Fang The stability of perovskite solar cell remains the biggest challenge that hinders its commercialization. Here Li et al. incorporate crosslinkable molecules to form a crosslinked perovskite film and increase the device operational stability by 590 times to 400 h under standard Xenon lamp without filters. 18 September 2018 | doi: 10.1038/s41467-018-06204-2 Solar cells  Paf1 and Ctr9 subcomplex formation is essential for Paf1 complex assembly and functional regulation OPEN Ying Xie, Minying Zheng, Xinlei Chu, Yue Chen, Huisha Xu, Jiawei Wang, Hao Zhou & Jiafu Long The evolutionarily conserved multifunctional polymerase-associated factor 1 (Paf1) complex plays an essential role in gene regulation. Here, the authors report two structures of the human and yeast Ctr9/Paf1 subcomplexes, and find that this is essential for Paf1 complex assembly and function. 18 September 2018 | doi: 10.1038/s41467-018-06237-7 Histone analysis  Histone post-translational modifications  Liquid chromatography  X-ray crystallography  Biologically driven DOC release from peatlands during recovery from acidification OPEN Hojeong Kang, Min Jung Kwon, Sunghyun Kim, Seunghoon Lee, Timothy G. Jones, Anna C. Johncock, Akira Haraguchi & Chris Freeman Peatlands recovering from acidification release dissolved organic carbon (DOC), but no biological role has yet been identified in this process. Here, the authors show that pH increases enhance phenol oxidase activity, pore-water DOC concentrations and lead to greater abundances in Actinobacteria and fungi. 18 September 2018 | doi: 10.1038/s41467-018-06259-1 Carbon cycle  Environmental chemistry  Microbial ecology  Wetlands ecology  Olfactory receptor OR2AT4 regulates human hair growth OPEN Jérémy Chéret, Marta Bertolini, Leslie Ponce, Janin Lehmann, Teresa Tsai, Majid Alam, Hanns Hatt & Ralf Paus Increasing evidence suggest that olfactory receptors can carry additional functions besides olfaction. Here, Chéret et al. show that stimulation of the olfactory receptor ORT2A4 by the odorant Sandalore® stimulates growth of human scalp hair follicles ex vivo, suggesting the use of ORT2A4-targeting odorants as hair growth-promoting agents. 18 September 2018 | doi: 10.1038/s41467-018-05973-0 Cell biology  Olfactory receptors  Deep neural networks for accurate predictions of crystal stability OPEN Weike Ye, Chi Chen, Zhenbin Wang, Iek-Heng Chu & Shyue Ping Ong Crystal stability prediction is of paramount importance for novel material discovery, with theoretical approaches alternative to expensive standard schemes highly desired. Here the authors develop a deep learning approach which, just using two descriptors, provides crystalline formation energies with very high accuracy. 18 September 2018 | doi: 10.1038/s41467-018-06322-x Density functional theory  Structural properties  Theory and computation  Artemisinin kills malaria parasites by damaging proteins and inhibiting the proteasome OPEN Jessica L. Bridgford, Stanley C. Xie, Simon A. Cobbold, Charisse Flerida A. Pasaje, Susann Herrmann, Tuo Yang, David L. Gillett, Lawrence R. Dick, Stuart A. Ralph, Con Dogovski, Natalie J. Spillman & Leann Tilley Artemisinin (ART) is a widely used antimalarial drug, but its mechanism of action is poorly understood. Here, Bridgford et al. show that ART kills parasites by a two-pronged mechanism, causing protein damage and compromising proteasome function, and that accumulation of proteasome substrates activates the ER stress response. 18 September 2018 | doi: 10.1038/s41467-018-06221-1 Antiparasitic agents  Parasitic infection  Protein folding  Ubiquitylation  A variant NuRD complex containing PWWP2A/B excludes MBD2/3 to regulate transcription at active genes OPEN Tianyi Zhang, Guifeng Wei, Christopher J. Millard, Roman Fischer, Rebecca Konietzny, Benedikt M. Kessler, John W. R. Schwabe & Neil Brockdorff Transcription regulation requires recruitment of different epigenetic regulators to the chromatin. Here the authors provide evidence that an H3K36me3 reader PWWP2A forms a variant NuRD complex and plays a role in regulating transcription and histone acetylation dynamics. 18 September 2018 | doi: 10.1038/s41467-018-06235-9 Chromatin  Epigenetics  Control of coordinatively unsaturated Zr sites in ZrO2 for efficient C–H bond activation OPEN Yaoyuan Zhang, Yun Zhao, Tatiana Otroshchenko, Henrik Lund, Marga-Martina Pohl, Uwe Rodemerck, David Linke, Haijun Jiao, Guiyuan Jiang & Evgenii V. Kondratenko Identifying active sites and designing rationally heterogeneous catalysts are not inherently straightforward due to their complexity. Here, the authors reveal the nature of active sites for efficient C–H bond activation in C1-C4 alkanes over bare ZrO2 and provide fundamentals for controlling their concentration. 18 September 2018 | doi: 10.1038/s41467-018-06174-5 Catalytic mechanisms  Heterogeneous catalysis  Porous materials  Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism OPEN Douglas McCloskey, Sibei Xu, Troy E. Sandberg, Elizabeth Brunk, Ying Hefner, Richard Szubin, Adam M. Feist & Bernhard O. Palsson The function of metabolic genes in the context of regulatory networks is not well understood. Here, the authors investigate the adaptive responses of E. coli after knockout of metabolic genes and highlight the influence of metabolite levels in the evolution of regulatory function. 18 September 2018 | doi: 10.1038/s41467-018-06219-9 Biochemical reaction networks  Chemical biology  Experimental evolution  Metabolic pathways  Highly-sensitive optical organic vapor sensor through polymeric swelling induced variation of fluorescent intensity OPEN Xiangyu Jiang, Hanfei Gao, Xiqi Zhang, Jinhui Pang, Yunqi Li, Kan Li, Yuchen Wu, Shuzhou Li, Jia Zhu, Yen Wei & Lei Jiang Traditional optical organic vapor sensors with solvatochromic shift mechanisms have lower sensitivity due to weak intermolecular interactions. Here, the authors report a general strategy to prepare a higher sensitivity optical organic vapor sensor through polymeric swelling-induced variation of fluorescent intensity. 18 September 2018 | doi: 10.1038/s41467-018-06101-8 Fluorescent probes  Polymer synthesis  Sensors and biosensors  Alpha kinase 1 controls intestinal inflammation by suppressing the IL-12/Th1 axis OPEN Grigory Ryzhakov, Nathaniel R. West, Fanny Franchini, Simon Clare, Nicholas E. Ilott, Stephen N. Sansom, Samuel J. Bullers, Claire Pearson, Alice Costain, Alun Vaughan-Jackson, Jeremy A. Goettel, Joerg Ermann, Bruce H. Horwitz, Ludovico Buti, Xin Lu, Subhankar Mukhopadhyay, Scott B. Snapper & Fiona Powrie The Hiccs locus has been associated with susceptibility to colitis in mice. Here the authors identify a Hiccs locus gene encoding Alpha kinase 1 as a potent regulator of intestinal inflammation via modulation of the IL-12/Th1 axis. 18 September 2018 | doi: 10.1038/s41467-018-06085-5 CD4-positive T cells  Inflammatory bowel disease  Interleukins  Mucosal immunology  Transport evidence for a sliding two-dimensional quantum electron solid OPEN Pedro Brussarski, S. Li, S. V. Kravchenko, A. A. Shashkin & M. P. Sarachik At low densities, it is understood that the physics of two-dimensional electron gases becomes dominated by interactions but the nature of the state that forms remains controversial. Here the authors present transport measurements that indicate the existence of a Wigner crystal in silicon MOSFETs. 18 September 2018 | doi: 10.1038/s41467-018-06332-9 Electronic devices  Electronic properties and materials  Phase transitions and critical phenomena  A plant Bro1 domain protein BRAF regulates multivesicular body biogenesis and membrane protein homeostasis OPEN Jinbo Shen, Qiong Zhao, Xiangfeng Wang, Caiji Gao, Ying Zhu, Yonglun Zeng & Liwen Jiang The ESCRT complex contributes to selective vacuolar degradation of membrane proteins. Here, the authors show that the plant-specific BRAF protein negatively regulates intraluminal vesicle formation and membrane protein degradation by preventing FREE1 binding to the ESCRT-I complex protein Vps23. 17 September 2018 | doi: 10.1038/s41467-018-05913-y Multivesicular bodies  Protein trafficking in plants  Three-dimensional X-ray diffraction imaging of dislocations in polycrystalline metals under tensile loading OPEN Mathew J. Cherukara, Reeju Pokharel, Timothy S. O’Leary, J. Kevin Baldwin, Evan Maxey, Wonsuk Cha, Jorg Maser, Ross J. Harder, Saryu J. Fensin & Richard L. Sandberg Identifying atomic defects during deformation is crucial to understand material response but remains challenging in three dimensions. Here, the authors couple X-ray Bragg coherent diffraction imaging and atomistic simulations to correlate a strain field to a screw dislocation in a single copper grain. 17 September 2018 | doi: 10.1038/s41467-018-06166-5 Atomistic models  Imaging techniques  Mechanical properties  Metals and alloys  A key function for microtubule-associated-protein 6 in activity-dependent stabilisation of actin filaments in dendritic spines OPEN Microtubule-associated protein 6 (MAP6) is known to be important for synaptic plasticity and cognition, supposedly via interaction with microtubules. Here, the authors found that MAP6 is crucial for the stabilisation of enlarged synapses through its association with a different cytoskeletal element, actin. 17 September 2018 | doi: 10.1038/s41467-018-05869-z Actin  Cellular neuroscience  Ring synthetic chromosome V SCRaMbLE OPEN Juan Wang, Ze-Xiong Xie, Yuan Ma, Xiang-Rong Chen, Yao-Qing Huang, Bo He, Bin Jia, Bing-Zhi Li & Ying-Jin Yuan Genome structural variation can play an important functional role in phenotypic diversity. Here the authors use the SCRaMbLE system on a ring synthetic chromosome V to generate complex rearrangements distinct from a rearranged linear chromosome. 17 September 2018 | doi: 10.1038/s41467-018-06216-y Genomic engineering  Metabolic engineering  Synthetic biology  Concyclic CH-π arrays for single-axis rotations of a bowl in a tube OPEN Taisuke Matsuno, Masahiro Fujita, Kengo Fukunaga, Sota Sato & Hiroyuki Isobe The weak and directional CH-π hydrogen bond has rarely been exploited in the design of supramolecular complexes and molecular machinery. Here, the authors construct a bowl-in-tube complex stabilized solely by concyclic CH-π hydrogen bonds, and show that the guest exhibits single-axis rotational motion despite tight association with the host. 17 September 2018 | doi: 10.1038/s41467-018-06270-6 Carbon nanotubes and fullerenes  Molecular machines and motors  Supramolecular chemistry  A spin torque meter with magnetic facet domains OPEN Kyoung-Woong Moon, Changsoo Kim, Jungbum Yoon, Jun Woo Choi, Dong-Ok Kim, Kyung Mee Song, Dongseuk Kim, Byong Sun Chun & Chanyong Hwang Spin torques with different origins enable the magnetic domain wall motion, but the contributions are hard to be distinguished. Here, the authors show the method to measure both spin-magnetization transfer torque and spin–orbit torque by using mountain-shaped domains with straight domain walls. 17 September 2018 | doi: 10.1038/s41467-018-06223-z Magnetic properties and materials  Spintronics  The complex underpinnings of genetic background effects OPEN Martin N. Mullis, Takeshi Matsui, Rachel Schell, Ryan Foree & Ian M. Ehrenreich Mutations often show distinct phenotypic effects across different genetic backgrounds. Here the authors describe the genetic basis of these so-called background effects using data on genotype and growth in 10 environments from 1411 segregants from a cross of two strains of budding yeast. 17 September 2018 | doi: 10.1038/s41467-018-06023-5 Epistasis  Genetic linkage study  Anterior-posterior gradient of plasticity in primate prefrontal cortex OPEN Mitchell R. Riley, Xue-Lian Qi, Xin Zhou & Christos Constantinidis Studies of the functional organization of the prefrontal cortex have produced contradicting results depending on the task used. Here, Riley and colleagues demonstrate that prefrontal areas are specialized across the anterior posterior axis and that the effects of the task themselves impact more the anterior areas. 17 September 2018 | doi: 10.1038/s41467-018-06226-w Sensory processing  Working memory  Recurrent WNT pathway alterations are frequent in relapsed small cell lung cancer OPEN Alex H. Wagner, Siddhartha Devarakonda, Zachary L. Skidmore, Kilannin Krysiak, Avinash Ramu, Lee Trani, Jason Kunisaki, Ashiq Masood, Saiama N. Waqar, Nicholas C. Spies, Daniel Morgensztern, Jason Waligorski, Jennifer Ponce, Robert S. Fulton, Leonard B. Maggi Jr., Jason D. Weber, Mark A. Watson, Christopher J. O’Conor, Jon H. Ritter, Rachelle R. Olsen et al. Small cell lung cancer (SCLC) patients frequently relapse and become resistant to chemotherapy. Here, the authors analyse the genomic and transcriptomic landscape of primary and relapsed SCLC patients as well as in vitro models, and discover that activation of WNT signalling can drive chemotherapy resistance. 17 September 2018 | doi: 10.1038/s41467-018-06162-9 Genetics research  Small-cell lung cancer  Multi-terrane structure controls the contrasting lithospheric evolution beneath the western and central–eastern Tibetan plateau OPEN Pengpeng Huangfu, Zhong-Hai Li, Taras Gerya, Weiming Fan, Kai-Jun Zhang, Huai Zhang & Yaolin Shi The Tibetan plateau is manifested by contrasting along-strike lithospheric structures, but the correlation with multi-terrane configuration remains challenging. Here, the authors show the crucial roles of the original geometric shape of accreted terranes in regulating the lithospheric evolution of Tibetan plateau. 17 September 2018 | doi: 10.1038/s41467-018-06233-x Geodynamics  Geophysics  Tectonics  Energy cost of entanglement extraction in complex quantum systems OPEN Cédric Bény, Christopher T. Chubb, Terry Farrelly & Tobias J. Osborne Understanding the energy cost of entanglement extraction has fundamental implications, in particular for quantum field theory and condensed matter. Here, the authors analyse how the optimal energy cost scales with the number of extracted EPR pairs, when local operations and classical communication are allowed. 17 September 2018 | doi: 10.1038/s41467-018-06153-w Quantum information  Theoretical physics  Evidence for dynamic kagome ice OPEN E. Lhotel, S. Petit, M. Ciomaga Hatnean, J. Ollivier, H. Mutka, E. Ressouche, M. R. Lees & G. Balakrishnan Quantum ferromagnetic spin liquids in two dimensions, namely quantum kagome ices, yield exotic magnetic properties but their identification remains challenging. Here the authors investigate a dynamic kagome ice state in the pyrochlore oxide Nd2Zr2O7 by magnetization and neutron scattering measurements. 17 September 2018 | doi: 10.1038/s41467-018-06212-2 Magnetic properties and materials  Quantum fluids and solids  High niche diversity in Mesozoic pollinating lacewings OPEN Qing Liu, Xiumei Lu, Qingqing Zhang, Jun Chen, Xiaoting Zheng, Weiwei Zhang, Xingyue Liu & Bo Wang Kalligrammatid lacewings were among the largest Mesozoic insects. Here, Liu et al. present an assemblage of Mesozoic kalligrammatid lacewings from amber and compression fossils, highlighting diversity in traits associated with pollination, chemical communication and defense against predators. 17 September 2018 | doi: 10.1038/s41467-018-06120-5 Community ecology  Palaeoecology  Palaeontology  Hydrogen spillover through Matryoshka-type (ZIFs@)n−1ZIFs nanocubes OPEN Guowu Zhan & Hua Chun Zeng Hydrogen spillover is well-documented in hydrogenation catalysis, but its existence through metalorganic frameworks (MOFs) remains controversial. Here, the authors provide evidence of the occurrence of hydrogen spillover in microporous MOFs at elevated temperatures, and measure quantitatively the penetration depths of atomic hydrogen. 17 September 2018 | doi: 10.1038/s41467-018-06269-z Catalytic mechanisms  Heterogeneous catalysis  Metal–organic frameworks  A zeolitic vanadotungstate family with structural diversity and ultrahigh porosity for catalysis OPEN Zhenxin Zhang, Qianqian Zhu, Masahiro Sadakane, Toru Murayama, Norihito Hiyoshi, Akira Yamamoto, Shinichi Hata, Hisao Yoshida, Satoshi Ishikawa, Michikazu Hara & Wataru Ueda Zeolitic transition metal oxides provide both porosity and redox activity, thereby further expanding the diversity of porous materials, but their design and development remain rare. Here, the authors report a new class of zeolitic vanadotungstates with tunable frameworks exhibiting a large porosity and redox activity. 17 September 2018 | doi: 10.1038/s41467-018-06274-2 Catalyst synthesis  Heterogeneous catalysis  Solid-state chemistry  The shape of watersheds OPEN Timothée Sassolas-Serrayet, Rodolphe Cattin & Matthieu Ferry River networks worldwide follow the emblematic Hack’s Law, which expresses the length of a stream as a function of its watershed area. Here the authors show this law does not depend on lithology or rainfall, but on the shape of watersheds and confirms the self-similarity of river networks. 17 September 2018 | doi: 10.1038/s41467-018-06210-4 Geomorphology  Hydrology  14-3-3 proteins activate Pseudomonas exotoxins-S and -T by chaperoning a hydrophobic surface OPEN Tobias Karlberg, Peter Hornyak, Ana Filipa Pinto, Stefina Milanova, Mahsa Ebrahimi, Mikael Lindberg, Nikolai Püllen, Axel Nordström, Elinor Löverli, Rémi Caraballo, Emily V. Wong, Katja Näreoja, Ann-Gerd Thorsell, Mikael Elofsson, Enrique M. De La Cruz, Camilla Björkegren & Herwig Schüler The cellular toxicity of Pseudomonas exotoxin-S and -T depends on their activation by 14-3-3 but the underlying molecular mechanism is not fully understood. Here, the authors show that a previously unrecognized 14-3-3:exotoxin binding interface is sufficient for complex formation and toxin activation. 17 September 2018 | doi: 10.1038/s41467-018-06194-1 Bacterial toxins  Enzyme mechanisms  X-ray crystallography  The gut microbiota promotes hepatic fatty acid desaturation and elongation in mice OPEN Alida Kindt, Gerhard Liebisch, Thomas Clavel, Dirk Haller, Gabriele Hörmannsperger, Hongsup Yoon, Daniela Kolmeder, Alexander Sigruener, Sabrina Krautbauer, Claudine Seeliger, Alexandra Ganzha, Sabine Schweizer, Rosalie Morisset, Till Strowig, Hannelore Daniel, Dominic Helm, Bernhard Küster, Jan Krumsiek & Josef Ecker The role of the gut microbiota in hepatic lipid metabolism is controversial and incompletely understood. Here the authors perform multi-omics analyses of altered lipid metabolic processes in germ-free and specific pathogen-free mice, revealing how the gut microbiota affects hepatic fatty acid desaturation and elongation. 14 September 2018 | doi: 10.1038/s41467-018-05767-4 Data integration  Fat metabolism  Lipidomics  Microbiota  HUWE1 E3 ligase promotes PINK1/PARKIN-independent mitophagy by regulating AMBRA1 activation via IKKα OPEN Anthea Di Rita, Angelo Peschiaroli, Pasquale D′Acunzo, Daniela Strobbe, Zehan Hu, Jens Gruber, Mads Nygaard, Matteo Lambrughi, Gerry Melino, Elena Papaleo, Jörn Dengjel, Said El Alaoui, Michelangelo Campanella, Volker Dötsch, Vladimir V. Rogov, Flavie Strappazzon & Francesco Cecconi Mitophagy is crucial for mitochondrial quality control and maintenance of cellular homeostasis. Here the authors identify an E3 ubiquitin ligase, HUWE1, that collaborates with LC3-interacting protein AMBRA1 to induce mitochondrial clearance. 14 September 2018 | doi: 10.1038/s41467-018-05722-3 Mitophagy  Phosphorylation  Aerosol-induced intensification of cooling effect of clouds during Indian summer monsoon OPEN Chandan Sarangi, Vijay P. Kanawade, Sachchida N. Tripathi, Abin Thomas & Dilip Ganguly The invigoration of deep convective clouds in the Indian summer monsoon region is associated with high aerosol loading. Here the authors show that convective clouds from high aerosol loads in the Indian Summer Monsoon region have a cooling effect. 14 September 2018 | doi: 10.1038/s41467-018-06015-5 Atmospheric dynamics  Atmospheric science  Modular DNA strand-displacement controllers for directing material expansion OPEN Joshua Fern & Rebecca Schulman Materials which change shape in response to a trigger are of interest for soft robotics and targeted therapeutic delivery. Here, the authors report on the development of DNA-crosslinked hydrogels which can expand upon the detection of different biomolecular inputs mediated by DNA strand-displacement. 14 September 2018 | doi: 10.1038/s41467-018-06218-w DNA and RNA  DNA nanotechnology  Gels and hydrogels  Conditional and interaction gene-set analysis reveals novel functional pathways for blood pressure OPEN Christiaan A. de Leeuw, Sven Stringer, Ilona A. Dekkers, Tom Heskes & Danielle Posthuma Gene-set analysis (GSA) is widely used to infer functional and biological properties of a gene set. Here, the authors develop a conditional and interaction gene-set analysis approach that can considerably refine results from traditional GSA. 14 September 2018 | doi: 10.1038/s41467-018-06022-6 Cardiovascular genetics  Computational biology and bioinformatics  Genetic association study  Mapping a hidden terrane boundary in the mantle lithosphere with lamprophyres OPEN Arjan H. Dijkstra & Callum Hatch Lamprophyres represent hydrous alkaline mantle melts that are a unique source of information about the composition of continental lithosphere. Here the authors use isotopic compositions of lamprophyres to map a hidden terrain boundary and an unknown fragment of Armorica in the mantle lithosphere of southwest Britain. 14 September 2018 | doi: 10.1038/s41467-018-06253-7 Geochemistry  Geology  Tectonics  A conserved glycine harboring disease-associated mutations permits NMDA receptor slow deactivation and high Ca2+ permeability OPEN Johansen B. Amin, Xiaoling Leng, Aaron Gochman, Huan-Xiang Zhou & Lonnie P. Wollmuth Little is known about the impact of de novo and inherited missense mutations in the NMDA receptor M4 transmembrane helices. In this study, the authors use functional and computational approaches to demonstrate how mutations to conserved glycine sites within this region cause structural rearrangement, altered receptor deactivation and calcium permeability. 14 September 2018 | doi: 10.1038/s41467-018-06145-w Ion channels in the nervous system  Macrophage-secreted interleukin-35 regulates cancer cell plasticity to facilitate metastatic colonization OPEN Chih-Chan Lee, Jiunn-Chang Lin, Wei-Lun Hwang, Ying-Ju Kuo, Hung-Kai Chen, Shyh-Kuan Tai, Chun-Chi Lin & Muh-Hwa Yang Tumor microenvironment varies between primary and metastatic sites. Here they report tumor-associated macrophages from metastatic sites to be predominantly M2 type, and secrete IL-35 to promote metastasis through activation of JAK2–STAT6–GATA3 signaling. 14 September 2018 | doi: 10.1038/s41467-018-06268-0 Cancer microenvironment  Metastasis  Autophagy differentially regulates TNF receptor Fn14 by distinct mammalian Atg8 proteins OPEN Hila Winer, Milana Fraiberg, Adi Abada, Tali Dadosh, Bat-Chen Tamim-Yecheskel & Zvulun Elazar The TNF receptor Fn14 is a short-lived protein. Here the authors show that Fn14 turnover is regulated by selective autophagy, with different ATG8 proteins having distinct roles during the process. 14 September 2018 | doi: 10.1038/s41467-018-06275-1 Lysosomes  Macroautophagy  Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits OPEN Yara Seif, Erol Kavvas, Jean-Christophe Lachance, James T. Yurkovich, Sean-Paul Nuccio, Xin Fang, Edward Catoiu, Manuela Raffatellu, Bernhard O. Palsson & Jonathan M. Monk Salmonella serovars colonize a wide range of hosts but the underlying genetic determinants remain poorly understood. Here, Seif et al. use a network-based computational analysis to link specific metabolic capabilities with host range and nutritional niche. 14 September 2018 | doi: 10.1038/s41467-018-06112-5 Biochemical networks  Infection  Nanomaterials design for super-degenerate electronic state beyond the limit of geometrical symmetry OPEN Naoki Haruta, Takamasa Tsukamoto, Akiyoshi Kuzume, Tetsuya Kambe & Kimihisa Yamamoto No substances with greater degrees of degeneracy than spherical atoms are known, due to geometrical limitations. In this work the authors combine density functional theory and tight-binding models to predict metal clusters with higher-fold degeneracies than spherical atoms, which are ascribed to dynamical symmetry. 14 September 2018 | doi: 10.1038/s41467-018-06244-8 Computational chemistry  Electronic structure of atoms and molecules  Nanoparticles  Chromatin swelling drives neutrophil extracellular trap release OPEN Elsa Neubert, Daniel Meyer, Francesco Rocca, Gökhan Günay, Anja Kwaczala-Tessmann, Julia Grandke, Susanne Senger-Sander, Claudia Geisler, Alexander Egner, Michael P. Schön, Luise Erpenbeck & Sebastian Kruss Neutrophilic granulocytes release their own DNA (NETosis) as neutrophil extracellular traps to capture pathogens. Here, the authors use time-resolved fluorescence and atomic force microscopy and reveal that NETosis is highly organized into three distinct phases with a clear point of no return defined by chromatin status. 14 September 2018 | doi: 10.1038/s41467-018-06263-5 Biological physics  Biophysics  Cell death  Chromatin  Neutrophils  Med23 serves as a gatekeeper of the myeloid potential of hematopoietic stem cells OPEN Xufeng Chen, Jingyao Zhao, Chan Gu, Yu Cui, Yuling Dai, Guangrong Song, Haifeng Liu, Hao Shen, Yuanhua Liu, Yuya Wang, Huayue Xing, Xiaoyan Zhu, Pei Hao, Fan Guo & Xiaolong Liu Hematopoietic stem cells (HSCs) in the bone marrow are quiescent, but are activated in response to stress. Here, the authors show that loss of Med23 leads to greater activation and enhanced myeloid potential of HSCs in response to stress, also Med23 maintains stemness gene expression and suppresses myeloid genes. 14 September 2018 | doi: 10.1038/s41467-018-06282-2 Haematopoietic stem cells  Stem-cell differentiation  Proteomics reveals signal peptide features determining the client specificity in human TRAP-dependent ER protein import OPEN Duy Nguyen, Regine Stutz, Stefan Schorr, Sven Lang, Stefan Pfeffer, Hudson H. Freeze, Friedrich Förster, Volkhard Helms, Johanna Dudek & Richard Zimmermann While Sec61 enables ER import of all polypeptides with N-terminal signal peptides, only selected clients are accepted for TRAP-assisted ER import. Here, the authors use a proteomics approach to characterize TRAP-dependent clients, identifying signal peptide features that govern recognition by TRAP. 14 September 2018 | doi: 10.1038/s41467-018-06188-z Endoplasmic reticulum  Protein translocation  Proteomics  Selective reduction and homologation of carbon monoxide by organometallic iron complexes OPEN Helen R. Sharpe, Ana M. Geer, Laurence J. Taylor, Benjamin M. Gridley, Toby J. Blundell, Alexander J. Blake, E. Stephen Davies, William Lewis, Jonathan McMaster, David Robinson & Deborah L. Kays Metal-mediated activation of CO for C-C coupling reactions is a valuable approach to carbon monoxide valorization. Here, the authors use low-coordinate iron(II) complexes for the selective scission and homologation of CO affording unusual squaraines and iron carboxylates under mild conditions. 14 September 2018 | doi: 10.1038/s41467-018-06242-w Ligands  Organocatalysis  The ZZ-type zinc finger of ZZZ3 modulates the ATAC complex-mediated histone acetylation and gene activation OPEN Wenyi Mi, Yi Zhang, Jie Lyu, Xiaolu Wang, Qiong Tong, Danni Peng, Yongming Xue, Adam H. Tencer, Hong Wen, Wei Li, Tatiana G. Kutateladze & Xiaobing Shi Histones are recognized by epigenetic readers, which play essential roles in regulation of chromatin and transcription. Here the authors provide evidence that the ZZ-type zinc finger domain of ZZZ3 functions as a reader of histone H3, which is required for the ATAC complex-mediated maintenance of histone acetylation and gene activation. 14 September 2018 | doi: 10.1038/s41467-018-06247-5 Acetylation  Histone post-translational modifications  Solution-state NMR  Transcription  All carbon materials pn diode OPEN Xiaojing Feng, Xing Zhao, Liu Yang, Mengyao Li, Fengxiang Qie, Jiahui Guo, Yuchun Zhang, Tiehu Li, Wenxia Yuan & Yong Yan Chemically functionalized graphene oxide-based pn junction diodes have potential for future electronic device applications. Here, the authors report an all carbon pn diode with graphene oxide and carbon nanotubes electrodes showing excellent current rectification and efficient logic gates. 14 September 2018 | doi: 10.1038/s41467-018-06150-z Electronic devices  Electronic properties and devices  Autosomal genetic variation is associated with DNA methylation in regions variably escaping X-chromosome inactivation OPEN René Luijk, Haoyu Wu, Cavin K Ward-Caviness, Eilis Hannon, Elena Carnero-Montoro, Josine L. Min, Pooja Mandaviya, Martina Müller-Nurasyid, Hailiang Mei, Silvere M. van der Maarel, Marian Beekman, Ruud van der Breggen, Joris Deelen, Nico Lakenberg, Matthijs Moed, H. Eka D. Suchiman, Wibowo Arindrarto, Peter van’t Hof, Marc Jan Bonder, Patrick Deelen et al. DNA methylation is critically involved in X chromosome inactivation (XCI) and dosage compensation, yet some X-chromosomal genes escape XCI. Here, Lujik et al. identify three autosomal genetic loci that associate with differential DNA methylation near genes that variably escape XCI in females. 14 September 2018 | doi: 10.1038/s41467-018-05714-3 DNA methylation  Dosage compensation  Epigenomics  Genome-wide association studies  UPF1-like helicase grip on nucleic acids dictates processivity OPEN Joanne Kanaan, Saurabh Raj, Laurence Decourty, Cosmin Saveanu, Vincent Croquette & Hervé Le Hir UPF1 is a highly processive helicase that plays an essential role in nonsense-mediated mRNA decay. Here the authors use single molecule binding assays to establish a functionally important relationship between helicase grip to nucleic acids, binding lifetime and the duration of translocation. 14 September 2018 | doi: 10.1038/s41467-018-06313-y DNA-binding proteins  Enzyme mechanisms  RNA-binding proteins  Single-molecule biophysics  Abrupt drainage basin reorganization following a Pleistocene river capture OPEN Niannian Fan, Zhongxin Chu, Luguang Jiang, Marwan A. Hassan, Michael P. Lamb & Xingnian Liu River capture acts as one river steals the neighboring headwaters, which is a dramatic natural process for mountain landscapes evolution. Here the authors show a stream piracy reversed flow in a major river resulting in waterfall formation, bedrock gorge incision, and widespread topographic disequilibrium. 14 September 2018 | doi: 10.1038/s41467-018-06238-6 Environmental sciences  Hydrology  The last-born daughter cell contributes to division orientation of Drosophila larval neuroblasts OPEN Nicolas Loyer & Jens Januschke The highly proliferative neuroblasts of the Drosophila larval brain divide over many cell cycles in a polarized manner. Here the authors show that the orientation of the axis of NB divisions is defined by the position of their last-born daughter cell. 14 September 2018 | doi: 10.1038/s41467-018-06276-0 Apicobasal polarity  Mitosis  CD69 prevents PLZFhi innate precursors from prematurely exiting the thymus and aborting NKT2 cell differentiation OPEN Motoko Y. Kimura, Akemi Igi, Koji Hayashizaki, Yukiyoshi Mita, Miho Shinzawa, Tejas Kadakia, Yukihiro Endo, Satomi Ogawa, Ryoji Yagi, Shinichiro Motohashi, Alfred Singer & Toshinori Nakayama CD69 competes with S1P1, a chemokine receptor mediating thymocyte egress, for surface expression on thymocytes, but whether CD69 is required for normal thymic development is unclear. Here the authors show that CD69 and S1P1 synergize to control type 2 natural killer (NKT2) cells differentiation by modulating the thymic egress of NKT2 precursor. 14 September 2018 | doi: 10.1038/s41467-018-06283-1 Cell migration  Lymphocyte differentiation  NKT cells  Thymus  Extremely rare variants reveal patterns of germline mutation rate heterogeneity in humans OPEN Jedidiah Carlson, Adam E. Locke, Matthew Flickinger, Matthew Zawistowski, Shawn Levy, Richard M. Myers, Michael Boehnke, Hyun Min Kang, Laura J. Scott, Jun Z. Li, Sebastian Zöllner, Devin Absher, Huda Akil, Gerome Breen, Margit Burmeister, Sarah Cohen-Woods, William G. Iacono, James A. Knowles, Lisa Legrand, Qing Lu et al. Germline mutation rate is a critical parameter in the study of genetics and evolution. Here, Carlson et al. infer fine-scale patterns of human mutation rate heterogeneity by analyzing ~36 million singleton variants from 3560 whole-genome sequences. 14 September 2018 | doi: 10.1038/s41467-018-05936-5 Computational biology and bioinformatics  Evolutionary biology  Population genetics  New suspension-feeding radiodont suggests evolution of microplanktivory in Cambrian macronekton OPEN Rudy Lerosey-Aubril & Stephen Pates Planktonic life was well established by the Cambrian, but few nektonic filter feeders have been identified. Here, the authors provide fossil evidence that Pahvantia hastata was a suspension-feeder that likely captured much smaller plankton than any other known free-swimming animals of that time. 14 September 2018 | doi: 10.1038/s41467-018-06229-7 Marine biology  Palaeoecology  Palaeontology  A self-improving triboelectric nanogenerator with improved charge density and increased charge accumulation speed OPEN Li Cheng, Qi Xu, Youbin Zheng, Xiaofeng Jia & Yong Qin The performance of triboelectric nanogenerators is impacted by charge density, which can be restricted by air breakdown. Here the authors report a self-improving triboelectric nanogenerator that overcomes the limitation, achieving increased charge density, charge accumulation speed, and output current. 14 September 2018 | doi: 10.1038/s41467-018-06045-z Devices for energy harvesting  Electronic and spintronic devices  Ketamine reduces aversion in rodent pain models by suppressing hyperactivity of the anterior cingulate cortex OPEN Haocheng Zhou, Qiaosheng Zhang, Erik Martinez, Jahrane Dale, Sile Hu, Eric Zhang, Kevin Liu, Dong Huang, Guang Yang, Zhe Chen & Jing Wang Ketamine is a short-acting analgesic that also has anti-depressant effects. Here the authors show in rat models of chronic pain that low-dose ketamine can induce an anti-aversive state that persists after the initial short term analgesia has ended. 14 September 2018 | doi: 10.1038/s41467-018-06295-x Chronic pain  Cortex  Structural determinants of Rab11 activation by the guanine nucleotide exchange factor SH3BP5 OPEN Meredith L. Jenkins, Jean Piero Margaria, Jordan T. B. Stariha, Reece M. Hoffmann, Jacob A. McPhail, David J. Hamelin, Martin J. Boulanger, Emilio Hirsch & John E. Burke Rab11 GTPases are involved in various cellular processes but their activation by guanine nucleotide exchange factors (GEFs) is not fully understood. Here, the authors present a structural and biochemical analysis of Rab11 bound to the GEF SH3BP5, providing insights how Rab-GEF specificity is achieved. 14 September 2018 | doi: 10.1038/s41467-018-06196-z GTP-binding protein regulators  Mass spectrometry  Small GTPases  X-ray crystallography  rec-YnH enables simultaneous many-by-many detection of direct protein–protein and protein–RNA interactions OPEN Jae-Seong Yang, Mireia Garriga-Canut, Nele Link, Carlo Carolis, Katrina Broadbent, Violeta Beltran-Sastre, Luis Serrano & Sebastian P. Maurer Current methods to unveil protein–protein and protein–RNA interactions often involve long, costly procedures. Here the authors present a rapid yeast 2- and 3-hybrid screening pipeline to detect interactions within protein libraries or between protein libraries and RNA fragment pools. 14 September 2018 | doi: 10.1038/s41467-018-06128-x Assay systems  High-throughput screening  Identification of multiple risk loci and regulatory mechanisms influencing susceptibility to multiple myeloma OPEN Molly Went, Amit Sud, Asta Försti, Britt-Marie Halvarsson, Niels Weinhold, Scott Kimber, Mark van Duin, Gudmar Thorleifsson, Amy Holroyd, David C. Johnson, Ni Li, Giulia Orlando, Philip J. Law, Mina Ali, Bowang Chen, Jonathan S. Mitchell, Daniel F. Gudbjartsson, Rowan Kuiper, Owen W. Stephens, Uta Bertsch et al. Multiple myeloma is a cancer of the plasma cells, and the complete aetiology of the disease is still unclear. Here the authors perform an additional GWAS analysis followed by a meta-analysis with existing GWAS and replication genotyping and identify 6 novel risk loci and utilise gene expression, epigenetic profiling and in situ Hi-C data to further our understanding of MM susceptibility. 13 September 2018 | doi: 10.1038/s41467-018-04989-w Cancer genetics  Cancer genomics  Genome-wide association studies  Myeloma  Less absorbed solar energy and more internal heat for Jupiter OPEN Radiant energy budgets and internal heat play a key role in the evolution of planets. Here, the authors analyze data from the Cassini mission to show that Jupiter’s radiant energy and internal heat budgets are significantly larger than previous estimates. 13 September 2018 | doi: 10.1038/s41467-018-06107-2 Giant planets  SNX3-retromer requires an evolutionary conserved MON2:DOPEY2:ATP9A complex to mediate Wntless sorting and Wnt secretion OPEN Ian J. McGough, Reinoud E. A. de Groot, Adam P. Jellett, Marco C. Betist, Katherine C. Varandas, Chris M. Danson, Kate J. Heesom, Hendrik C. Korswagen & Peter J. Cullen Sustained Wnt secretion requires the endosomal SNX3-retromer complex for endosome-to-trans-Golgi network transport of the internalised Wnt chaperone Wntless. Here the authors show that in both C. elegans and human cells, SNX3-retromer requires an evolutionary conserved membrane remodelling complex for Wntless sorting and Wnt secretion. 13 September 2018 | doi: 10.1038/s41467-018-06114-3 Cell biology  Morphogen signalling  Retromer  Identifying weak interdomain interactions that stabilize the supertertiary structure of the N-terminal tandem PDZ domains of PSD-95 OPEN Inna S. Yanez Orozco, Frank A. Mindlin, Junyan Ma, Bo Wang, Brie Levesque, Matheu Spencer, Soheila Rezaei Adariani, George Hamilton, Feng Ding, Mark E. Bowen & Hugo Sanabria Biologically relevant weak and transient interdomain interactions within proteins are difficult to analyze. Here, the authors combine multiscale molecular dynamics simulations and high-precision FRET experiments to characterize interactions between the tandem PDZ domains of PSD-95, revealing previously hidden conformational states. 13 September 2018 | doi: 10.1038/s41467-018-06133-0 Biological fluorescence  Molecular biophysics  Proteins  Copper-catalyzed methylative difunctionalization of alkenes OPEN Xu Bao, Takayuki Yokoe, Tu M. Ha, Qian Wang & Jieping Zhu While the trifluoromethylative difunctionalization of unactivated alkenes has been largely explored, methylative difunctionalization remains underinvestigated. Here, the authors report copper-catalyzed alkoxy- and azido-methylation reactions of alkenes leading to important synthetic building blocks and valuable O- and N-heterocycles. 13 September 2018 | doi: 10.1038/s41467-018-06246-6 Catalytic mechanisms  Homogeneous catalysis  Synthetic chemistry methodology  Nonlocal electron correlations in an itinerant ferromagnet OPEN Christian Tusche, Martin Ellguth, Vitaliy Feyer, Alexander Krasyuk, Carsten Wiemann, Jürgen Henk, Claus M. Schneider & Jürgen Kirschner The consequences of electron-electron interactions are difficult to calculate reliably but this is needed to understand important physical properties such as ferromagnetism. Tusche et al. show that interaction effects in cobalt are nonlocal, presenting a challenge to future theoretical approaches. 13 September 2018 | doi: 10.1038/s41467-018-05960-5 Electronic properties and materials  Ferromagnetism  Magnetic properties and materials  Rapid functional genetics of the oligodendrocyte lineage using pluripotent stem cells OPEN Angela M. Lager, Olivia G. Corradin, Jared M. Cregg, Matthew S. Elitt, H. Elizabeth Shick, Benjamin L. L. Clayton, Kevin C. Allan, Hannah E. Olsen, Mayur Madhavan & Paul J. Tesar The isolation and propagation of oligodendroglial cells from postnatal animals can be impractical for functional genetic studies. This study highlights the potential of a new approach to rapidly generate oligodendrocytes and their progenitors from mouse embryonic and induced pluripotent stem cells, independent of mouse strain or mutational status. 13 September 2018 | doi: 10.1038/s41467-018-06102-7 Neurodevelopmental disorders  Oligodendrocyte  Pluripotent stem cells  Age structure landscapes emerge from the equilibrium between aging and rejuvenation in bacterial populations OPEN Audrey M. Proenca, Camilla Ulla Rang, Christen Buetz, Chao Shi & Lin Chao Some daughter cells inherit the maternal old pole during bacterial division, but does this correspond to aging? Here, Proenca et al. show that constant patterns of aging and rejuvenation connect distinct growth equilibria within bacterial clonal populations, providing evidence for deterministic age structures. 13 September 2018 | doi: 10.1038/s41467-018-06154-9 Bacteria  Bacterial systems biology  Experimental evolution  Lithiophilic-lithiophobic gradient interfacial layer for a highly stable lithium metal anode OPEN Huimin Zhang, Xiaobin Liao, Yuepeng Guan, Yu Xiang, Meng Li, Wenfeng Zhang, Xiayu Zhu, Hai Ming, Lin Lu, Jingyi Qiu, Yaqin Huang, Gaoping Cao, Yusheng Yang, Liqiang Mai, Yan Zhao & Hao Zhang Lithium metal batteries suffer from the dendrite growth upon electrochemical cycling. Here the authors introduce a lithiophilic-lithiophobic gradient interfacial ZnO/CNT layer, which facilitates the formation of a stable solid electrolyte interphase, and suppresses the growth of lithium dendrite. 13 September 2018 | doi: 10.1038/s41467-018-06126-z Energy science and technology  Nanoscience and technology  Influence of surface atomic structure demonstrated on oxygen incorporation mechanism at a model perovskite oxide OPEN Michele Riva, Markus Kubicek, Xianfeng Hao, Giada Franceschi, Stefan Gerhold, Michael Schmid, Herbert Hutter, Juergen Fleig, Cesare Franchini, Bilge Yildiz & Ulrike Diebold The availability of surface oxygen vacancies or electrons is often viewed as the defining factor for the reactivity of perovskite oxides. Two precisely controlled surfaces on SrTiO3(110) show strikingly different O exchange kinetics, which the authors ascribe to the flexibility of the surface polyhedra. 13 September 2018 | doi: 10.1038/s41467-018-05685-5 Fuel cells  Surfaces, interfaces and thin films  Coulomb-bound four- and five-particle intervalley states in an atomically-thin semiconductor OPEN Shao-Yu Chen, Thomas Goldstein, Takashi Taniguchi, Kenji Watanabe & Jun Yan Valleytronic devices of atomically thin transition metal dichalcogenides may benefit from high-order exciton complexes. Here, the authors present experimental evidence for four-particle biexcitons and five-particle exciton-trions in high-quality monolayer WSe2. 13 September 2018 | doi: 10.1038/s41467-018-05558-x Optical materials and structures  Two-dimensional materials  Negatively charged nanoporous membrane for a dendrite-free alkaline zinc-based flow battery with long cycle life OPEN Zhizhang Yuan, Xiaoqi Liu, Wenbin Xu, Yinqi Duan, Huamin Zhang & Xianfeng Li Dendrite accumulation is a hindrance for alkaline zinc-based flow batteries. Here the authors design a negatively charged nanoporous membrane that mitigates zinc dendrite growth by repulsion of zincate anions, leading to a zinc-based flow battery with high power density and cycling stability. 13 September 2018 | doi: 10.1038/s41467-018-06209-x Batteries  Electrochemistry  Seed-mediated atomic-scale reconstruction of silver manganate nanoplates for oxygen reduction towards high-energy aluminum-air flow batteries OPEN Jaechan Ryu, Haeseong Jang, Joohyuk Park, Youngshin Yoo, Minjoon Park & Jaephil Cho Aluminum-air batteries are lightweight and cost effective, but performance is limited by corrosion and solid by-products. Here the authors catalyze oxygen reduction with silver manganate nanoplates and develop an aluminum-air flow battery that delivers high energy density and alleviates side reactions. 13 September 2018 | doi: 10.1038/s41467-018-06211-3 Batteries  Electrochemistry  Crystal structure of TcpK in complex with oriT DNA of the antibiotic resistance plasmid pCW3 OPEN Daouda A. K. Traore, Jessica A. Wisniewski, Sarena F. Flanigan, Paul J. Conroy, Santosh Panjikar, Yee-Foong Mok, Carmen Lao, Michael D. W. Griffin, Vicki Adams, Julian I. Rood & James C. Whisstock Conjugative transfer of antibiotic resistance plasmid pCW3 in Clostridium perfringens is mediated by the tcp locus. Here, the authors identify a wHTH-type protein, TcpK, that is essential for efficient plasmid transfer and interacts with the plasmid oriT region in a unique manner. 13 September 2018 | doi: 10.1038/s41467-018-06096-2 Bacterial genetics  DNA  X-ray crystallography  Converting organosulfur compounds to inorganic polysulfides against resistant bacterial infections OPEN Zhuobin Xu, Zhiyue Qiu, Qi Liu, Yixin Huang, Dandan Li, Xinggui Shen, Kelong Fan, Juqun Xi, Yunhao Gu, Yan Tang, Jing Jiang, Jialei Xu, Jinzhi He, Xingfa Gao, Yuan Liu, Hyun Koo, Xiyun Yan & Lizeng Gao Garlic has a mild antibacterial activity due to its organosulfur content. Here, the authors develop an approach to convert natural organosulfur into iron-sulfur nanosheets, with significantly higher antibacterial activity that can be used against infections as well as biofilms. 13 September 2018 | doi: 10.1038/s41467-018-06164-7 Antimicrobials  Nanocomposites  Biexcitons in monolayer transition metal dichalcogenides tuned by magnetic fields OPEN Christopher. E. Stevens, Jagannath Paul, Timothy Cox, Prasana K. Sahoo, Humberto R. Gutiérrez, Volodymyr Turkowski, Dimitry Semenov, Steven A. McGill, Myron D. Kapetanakis, Ilias E. Perakis, David J. Hilton & Denis Karaiskaj Biexciton complexes in atomically thin transition metal dichalcogenides have unusually large binding energies. Here, the authors explore biexciton formation dynamics in monolayer MoSe2 in the presence of magnetic fields up to 25 T. 13 September 2018 | doi: 10.1038/s41467-018-05643-1 Electronic properties and materials  Quantum fluids and solids  A small molecule targeting myoferlin exerts promising anti-tumor effects on breast cancer OPEN Tao Zhang, Jingjie Li, Yuan He, Feifei Yang, Yun Hao, Wangrui Jin, Jing Wu, Zhenliang Sun, Yunqi Li, Yihua Chen, Zhengfang Yi & Mingyao Liu Improved therapeutics are needed for treating breast cancer. Here they show the druggability of myoferlin with a small molecule inhibitor in breast cancer and demonstrate its anti-breast cancer effects in vitro and in vivo. 13 September 2018 | doi: 10.1038/s41467-018-06179-0 Breast cancer  Metastasis  Target identification  Development of an antibody fragment that stabilizes GPCR/G-protein complexes OPEN Shoji Maeda, Antoine Koehl, Hugues Matile, Hongli Hu, Daniel Hilger, Gebhard F. X. Schertler, Aashish Manglik, Georgios Skiniotis, Roger J. P. Dawson & Brian K. Kobilka The determination of high resolution structures of G protein coupled receptors (GPCRs) in complex with heterotrimeric G proteins is challenging. Here authors develop an antibody fragment, mAB16, which stabilizes GPCR/G-protein complexes and facilitates the application of high resolution cryo-EM. 13 September 2018 | doi: 10.1038/s41467-018-06002-w Cryoelectron microscopy  G protein-coupled receptors  X-ray crystallography  Triboelectric microplasma powered by mechanical stimuli OPEN Jia Cheng, Wenbo Ding, Yunlong Zi, Yijia Lu, Linhong Ji, Fan Liu, Changsheng Wu & Zhong Lin Wang Gas discharge plasma sources are bulky and of limited use in remote areas with no external power supply. Here the authors create triboelectric plasma by triggering TENGs with mechanical stimuli and discuss its application as a portable plasma source. 13 September 2018 | doi: 10.1038/s41467-018-06198-x Atomic and molecular collision processes  Characterization and analytical techniques  Devices for energy harvesting  Spin dynamics of the block orbital-selective Mott phase OPEN J. Herbrych, N. Kaushal, A. Nocera, G. Alvarez, A. Moreo & E. Dagotto Exploring the orbital-selective Mott phase (OSMP) addresses the central issue of electron correlations in the iron-based superconductors. Here the authors theoretically study the dynamical spin structure factor in the block-OSMP regime and unveil momentum dependent characteristics for different spin excitation modes. 13 September 2018 | doi: 10.1038/s41467-018-06181-6 Magnetic properties and materials  Superconducting properties and materials  NLRP1 restricts butyrate producing commensals to exacerbate inflammatory bowel disease OPEN Hazel Tye, Chien-Hsiung Yu, Lisa A. Simms, Marcel R. de Zoete, Man Lyang Kim, Martha Zakrzewski, Jocelyn S. Penington, Cassandra R. Harapas, Fernando Souza-Fonseca-Guimaraes, Leesa F. Wockner, Adele Preaudet, Lisa A. Mielke, Stephen A. Wilcox, Yasunori Ogura, Sinead C. Corr, Komal Kanojia, Konstantinos A. Kouremenos, David P. De Souza, Malcolm J. McConville, Richard A. Flavell et al. The inflammasome is normally activated by pathogens to induce tissue inflammation. Here the authors show that, in mouse experimental colitis models, Nlrp1 inflammasome sensor activates IL-18 to reduce beneficial colonic Clostridiales species, thereby decreasing microbial butyrate and its protective effects on colitis. 13 September 2018 | doi: 10.1038/s41467-018-06125-0 Antimicrobial responses  Inflammasome  Interleukins  NOD-like receptors  Finding any Waldo with zero-shot invariant and efficient visual search OPEN Mengmi Zhang, Jiashi Feng, Keng Teck Ma, Joo Hwee Lim, Qi Zhao & Gabriel Kreiman Visual search requires recognizing an object “invariantly”, despite changes in its appearance. Here, the authors show that humans can efficiently and invariantly search for objects in complex scenes and introduce a biologically-inspired zero-shot model that captures human eye movements during search. 13 September 2018 | doi: 10.1038/s41467-018-06217-x Attention  Computer science  Network models  Perception  Efficient generation of neutral and charged biexcitons in encapsulated WSe2 monolayers OPEN Ziliang Ye, Lutz Waldecker, Eric Yue Ma, Daniel Rhodes, Abhinandan Antony, Bumho Kim, Xiao-Xiao Zhang, Minda Deng, Yuxuan Jiang, Zhengguang Lu, Dmitry Smirnov, Kenji Watanabe, Takashi Taniguchi, James Hone & Tony F. Heinz High-order correlated states in atomically thin transition metal dichalcogenides may be facilitated by long-lived optically dark excitons. Here, the authors report experimentally the emergence of neutral and charged biexciton species at low light intensities in encapsulated WSe2 monolayers. 13 September 2018 | doi: 10.1038/s41467-018-05917-8 Nonlinear optics  Two-dimensional materials  Extreme–ultraviolet high–harmonic generation in liquids OPEN Tran Trung Luu, Zhong Yin, Arohi Jain, Thomas Gaumnitz, Yoann Pertot, Jun Ma & Hans Jakob Wörner While high–harmonic generation from gases, and more recently also from solids, has been extensively studied, there is little data on HHG from liquids. Here, Luu et al. experimentally demonstrate and study HHG up to 27th order from the bulk of liquid water and different alcohols. 13 September 2018 | doi: 10.1038/s41467-018-06040-4 High-harmonic generation  Charge-tuneable biexciton complexes in monolayer WSe2 OPEN Matteo Barbone, Alejandro R.-P. Montblanch, Dhiren M. Kara, Carmen Palacios-Berraquero, Alisson R. Cadore, Domenico De Fazio, Benjamin Pingault, Elaheh Mostaani, Han Li, Bin Chen, Kenji Watanabe, Takashi Taniguchi, Sefaattin Tongay, Gang Wang, Andrea C. Ferrari & Mete Atatüre Multi-exciton states may emerge in atomically thin transition metal dichalcogenides as a result of strong many-body interactions. Here, the authors report experimental evidence of four- and five-particle biexciton complexes in monolayer WSe2 and their electrical control. 13 September 2018 | doi: 10.1038/s41467-018-05632-4 Condensed-matter physics  Two-dimensional materials  Revealing the biexciton and trion-exciton complexes in BN encapsulated WSe2 OPEN Zhipeng Li, Tianmeng Wang, Zhengguang Lu, Chenhao Jin, Yanwen Chen, Yuze Meng, Zhen Lian, Takashi Taniguchi, Kenji Watanabe, Shengbai Zhang, Dmitry Smirnov & Su-Fei Shi Owing to strong Coulomb interactions, atomically thin transition metal dichalcogenides host strongly bound excitonic complexes. Here, the authors report charge-neutral biexciton and negatively charged trion-exciton complexes in hBN encapsulated monolayer WSe2 by employing low-temperature photoluminescence spectroscopy. 13 September 2018 | doi: 10.1038/s41467-018-05863-5 Engineering  Materials science  Nanoscience and technology  Optics and photonics  Physics  Hierarchical rupture growth evidenced by the initial seismic waveforms OPEN Takashi Okuda & Satoshi Ide The degree to which small and large earthquakes share the same rupture processes remains unknown. Here, the authors reveal earthquakes of magnitude 3–5 share almost identical growth processes shared, but while they are controlled by some characteristic structures, their final size remains unpredictable. 13 September 2018 | doi: 10.1038/s41467-018-06168-3 Natural hazards  Seismology    Nature Communications JOBS of the week Post-Doctoral Associate University of Minnesota Postdoctoral Position UPMC Hillman Cancer Center Postdoctoral Fellow Positions in Metabolism and lncRNA Temple University School of Medicine Postdoc Positions in Computational Epigenetics and Non-coding RNA Analysis Institute of Molecular Biology (IMB) Mainz Postdoctoral fellow in genetic epidemiology McGill University Open Faculty Position at Institute of Molecular Biology, Academia Sinica Academia Sinica Science Writer and Editor Rothamsted Research Faculty Positions Department of Cell and Molecular Biology St. Jude Children's Research Hospital (SJCRH) Scientist – Bioinformatics Genentech, Inc. More Science jobs from Nature Communications EVENT 4th International Conference on BioTribology (ICoBT2018) 26.09.18 Montreal, Canada More science events from     Latest Author Corrections       Author Correction: Genome‐wide mapping of plasma protein QTLs identifies putatively causal genes and pathways for cardiovascular disease OPEN Chen Yao , George Chen, Ci Song, Joshua Keefe, Michael Mendelson, Tianxiao Huan, Benjamin B. Sun, Annika Laser, Joseph C. Maranville, Hongsheng Wu, Jennifer E. Ho, Paul Courchesne, Asya Lyass, Martin G. Larson, Christian Gieger, Johannes Graumann, Andrew D. Johnson, John Danesh, Heiko Runz, Shih-Jen Hwang et al. 18 September 2018 | doi: 10.1038/s41467-018-06231-z Cardiovascular genetics  Genetic variation  Proteome  Quantitative trait  Author Correction: Eya3 partners with PP2A to induce c-Myc stabilization and tumor progression OPEN Lingdi Zhang, Hengbo Zhou, Xueni Li, Rebecca L. Vartuli, Michael Rowse, Yongna Xing, Pratyaydipta Rudra, Debashis Ghosh, Rui Zhao & Heide L. Ford 17 September 2018 | doi: 10.1038/s41467-018-06265-3     Latest Publisher Corrections       Publisher Correction: Heme enables proper positioning of Drosha and DGCR8 on primary microRNAs OPEN Alexander C. Partin, Tri D. Ngo, Emily Herrell, Byung-Cheon Jeong, Gary Hon & Yunsun Nam 18 September 2018 | doi: 10.1038/s41467-018-06426-4 Enzyme mechanisms  miRNAs  RNA  Publisher Correction: Melting conditions in the modern Tibetan crust since the Miocene OPEN Jinyu Chen, Fabrice Gaillard, Arnaud Villaros, Xiaosong Yang, Mickael Laumonier, Laurent Jolivet, Martyn Unsworth, Leїla Hashim, Bruno Scaillet & Guillaume Richard 17 September 2018 | doi: 10.1038/s41467-018-06344-5 Geodynamics  Geophysics  Petrology      Advertisement Nature Briefing is an essential round-up of science news, opinion and analysis, free in your inbox every weekday. 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