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  • Author Correction: Loss of MTX2 causes mandibuloacral dysplasia and links mitochondrial dysfunction to altered nuclear morphology
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-19
    Sahar Elouej; Karim Harhouri; Morgane Le Mao; Genevieve Baujat; Sheela Nampoothiri; Hϋlya Kayserili; Nihal Al Menabawy; Laila Selim; Arianne Llamos Paneque; Christian Kubisch; Davor Lessel; Robert Rubinsztajn; Chayki Charar; Catherine Bartoli; Coraline Airault; Jean-François Deleuze; Agnes Rötig; Peter Bauer; Catarina Pereira; Abigail Loh; Nathalie Escande-Beillard; Antoine Muchir; Lisa Martino; Yosef

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

    更新日期:2020-10-19
  • Mutations associated with neuropsychiatric conditions delineate functional brain connectivity dimensions contributing to autism and schizophrenia
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-19
    Clara A. Moreau; Sebastian G. W. Urchs; Kumar Kuldeep; Pierre Orban; Catherine Schramm; Guillaume Dumas; Aurélie Labbe; Guillaume Huguet; Elise Douard; Pierre-Olivier Quirion; Amy Lin; Leila Kushan; Stephanie Grot; David Luck; Adrianna Mendrek; Stephane Potvin; Emmanuel Stip; Thomas Bourgeron; Alan C. Evans; Carrie E. Bearden; Pierre Bellec; Sebastien Jacquemont

    16p11.2 and 22q11.2 Copy Number Variants (CNVs) confer high risk for Autism Spectrum Disorder (ASD), schizophrenia (SZ), and Attention-Deficit-Hyperactivity-Disorder (ADHD), but their impact on functional connectivity (FC) remains unclear. Here we report an analysis of resting-state FC using magnetic resonance imaging data from 101 CNV carriers, 755 individuals with idiopathic ASD, SZ, or ADHD and

    更新日期:2020-10-19
  • Probing complex geophysical geometries with chattering dust
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-19
    Laura J. Pyrak-Nolte; William Braverman; Nicholas J. Nolte; Alan J. Wright; David D. Nolte

    The modern energy economy and environmental infrastructure rely on the flow of fluids through fractures in rock. Yet this flow cannot be imaged directly because rocks are opaque to most probes. Here we apply chattering dust, or chemically reactive grains of sucrose containing pockets of pressurized carbon dioxide, to study rock fractures. As a dust grain dissolves, the pockets burst and emit acoustic

    更新日期:2020-10-19
  • Pearl millet genomic vulnerability to climate change in West Africa highlights the need for regional collaboration
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-19
    Bénédicte Rhoné; Dimitri Defrance; Cécile Berthouly-Salazar; Cédric Mariac; Philippe Cubry; Marie Couderc; Anaïs Dequincey; Aichatou Assoumanne; Ndjido Ardo Kane; Benjamin Sultan; Adeline Barnaud; Yves Vigouroux

    Climate change is already affecting agro-ecosystems and threatening food security by reducing crop productivity and increasing harvest uncertainty. Mobilizing crop diversity could be an efficient way to mitigate its impact. We test this hypothesis in pearl millet, a nutritious staple cereal cultivated in arid and low-fertility soils in sub-Saharan Africa. We analyze the genomic diversity of 173 landraces

    更新日期:2020-10-19
  • A pyridinic Fe-N 4 macrocycle models the active sites in Fe/N-doped carbon electrocatalysts
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-19
    Travis Marshall-Roth; Nicole J. Libretto; Alexandra T. Wrobel; Kevin J. Anderton; Michael L. Pegis; Nathan D. Ricke; Troy Van Voorhis; Jeffrey T. Miller; Yogesh Surendranath

    Iron- and nitrogen-doped carbon (Fe-N-C) materials are leading candidates to replace platinum catalysts for the oxygen reduction reaction (ORR) in fuel cells; however, their active site structures remain poorly understood. A leading postulate is that the iron-containing active sites exist primarily in a pyridinic Fe-N4 ligation environment, yet, molecular model catalysts generally feature pyrrolic

    更新日期:2020-10-19
  • The structure of a red-shifted photosystem I reveals a red site in the core antenna
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-19
    Hila Toporik; Anton Khmelnitskiy; Zachary Dobson; Reece Riddle; Dewight Williams; Su Lin; Ryszard Jankowiak; Yuval Mazor

    Photosystem I coordinates more than 90 chlorophylls in its core antenna while achieving near perfect quantum efficiency. Low energy chlorophylls (also known as red chlorophylls) residing in the antenna are important for energy transfer dynamics and yield, however, their precise location remained elusive. Here, we construct a chimeric Photosystem I complex in Synechocystis PCC 6803 that shows enhanced

    更新日期:2020-10-19
  • A streamlined pipeline for multiplexed quantitative site-specific N-glycoproteomics
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-19
    Pan Fang; Yanlong Ji; Ivan Silbern; Carmen Doebele; Momchil Ninov; Christof Lenz; Thomas Oellerich; Kuan-Ting Pan; Henning Urlaub

    Regulation of protein N-glycosylation is essential in human cells. However, large-scale, accurate, and site-specific quantification of glycosylation is still technically challenging. We here introduce SugarQuant, an integrated mass spectrometry-based pipeline comprising protein aggregation capture (PAC)-based sample preparation, multi-notch MS3 acquisition (Glyco-SPS-MS3) and a data-processing tool

    更新日期:2020-10-19
  • Direct C(sp 2 )–H alkylation of unactivated arenes enabled by photoinduced Pd catalysis
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-19
    Daeun Kim; Geun Seok Lee; Dongwook Kim; Soon Hyeok Hong

    Despite the fundamental importance of efficient and selective synthesis of widely useful alkylarenes, the direct catalytic C(sp2)–H alkylation of unactivated arenes with a readily available alkyl halide remains elusive. Here, we report the catalytic C(sp2)–H alkylation reactions of unactivated arenes with alkyl bromides via visible-light induced Pd catalysis. The reaction proceeds smoothly under mild

    更新日期:2020-10-19
  • Chromosome-level genome assembly of a parent species of widely cultivated azaleas
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-19
    Fu-Sheng Yang; Shuai Nie; Hui Liu; Tian-Le Shi; Xue-Chan Tian; Shan-Shan Zhou; Yu-Tao Bao; Kai-Hua Jia; Jing-Fang Guo; Wei Zhao; Na An; Ren-Gang Zhang; Quan-Zheng Yun; Xin-Zhu Wang; Chanaka Mannapperuma; Ilga Porth; Yousry Aly El-Kassaby; Nathaniel Robert Street; Xiao-Ru Wang; Yves Van de Peer; Jian-Feng Mao

    Azaleas (Ericaceae) comprise one of the most diverse ornamental plants, renowned for their cultural and economic importance. We present a chromosome-scale genome assembly for Rhododendron simsii, the primary ancestor of azalea cultivars. Genome analyses unveil the remnants of an ancient whole-genome duplication preceding the radiation of most Ericaceae, likely contributing to the genomic architecture

    更新日期:2020-10-19
  • Single-cell transcriptomics identifies divergent developmental lineage trajectories during human pituitary development
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-19
    Shu Zhang; Yueli Cui; Xinyi Ma; Jun Yong; Liying Yan; Ming Yang; Jie Ren; Fuchou Tang; Lu Wen; Jie Qiao

    The anterior pituitary gland plays a central role in regulating various physiological processes, including body growth, reproduction, metabolism and stress response. Here, we perform single-cell RNA-sequencing (scRNA-seq) of 4113 individual cells from human fetal pituitaries. We characterize divergent developmental trajectories with distinct transitional intermediate states in five hormone-producing

    更新日期:2020-10-19
  • The ultrafast onset of exciton formation in 2D semiconductors
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-19
    Chiara Trovatello; Florian Katsch; Nicholas J. Borys; Malte Selig; Kaiyuan Yao; Rocio Borrego-Varillas; Francesco Scotognella; Ilka Kriegel; Aiming Yan; Alex Zettl; P. James Schuck; Andreas Knorr; Giulio Cerullo; Stefano Dal Conte

    The equilibrium and non-equilibrium optical properties of single-layer transition metal dichalcogenides (TMDs) are determined by strongly bound excitons. Exciton relaxation dynamics in TMDs have been extensively studied by time-domain optical spectroscopies. However, the formation dynamics of excitons following non-resonant photoexcitation of free electron-hole pairs have been challenging to directly

    更新日期:2020-10-19
  • Detection of early stage pancreatic cancer using 5-hydroxymethylcytosine signatures in circulating cell free DNA
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-19
    Gulfem D. Guler; Yuhong Ning; Chin-Jen Ku; Tierney Phillips; Erin McCarthy; Christopher K. Ellison; Anna Bergamaschi; Francois Collin; Paul Lloyd; Aaron Scott; Michael Antoine; Wendy Wang; Kim Chau; Alan Ashworth; Stephen R. Quake; Samuel Levy

    Pancreatic cancer is often detected late, when curative therapies are no longer possible. Here, we present non-invasive detection of pancreatic ductal adenocarcinoma (PDAC) by 5-hydroxymethylcytosine (5hmC) changes in circulating cell free DNA from a PDAC cohort (n = 64) in comparison with a non-cancer cohort (n = 243). Differential hydroxymethylation is found in thousands of genes, most significantly

    更新日期:2020-10-19
  • Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-19
    Malte Herold; Susana Martínez Arbas; Shaman Narayanasamy; Abdul R. Sheik; Luise A. K. Kleine-Borgmann; Laura A. Lebrun; Benoît J. Kunath; Hugo Roume; Irina Bessarab; Rohan B. H. Williams; John D. Gillece; James M. Schupp; Paul S. Keim; Christian Jäger; Michael R. Hoopmann; Robert L. Moritz; Yuzhen Ye; Sujun Li; Haixu Tang; Anna Heintz-Buschart; Patrick May; Emilie E. L. Muller; Cedric C. Laczny; Paul

    The development of reliable, mixed-culture biotechnological processes hinges on understanding how microbial ecosystems respond to disturbances. Here we reveal extensive phenotypic plasticity and niche complementarity in oleaginous microbial populations from a biological wastewater treatment plant. We perform meta-omics analyses (metagenomics, metatranscriptomics, metaproteomics and metabolomics) on

    更新日期:2020-10-19
  • Solution-processable integrated CMOS circuits based on colloidal CuInSe 2 quantum dots
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-19
    Hyeong Jin Yun; Jaehoon Lim; Jeongkyun Roh; Darren Chi Jin Neo; Matt Law; Victor I. Klimov

    The emerging technology of colloidal quantum dot electronics provides an opportunity for combining the advantages of well-understood inorganic semiconductors with the chemical processability of molecular systems. So far, most research on quantum dot electronic devices has focused on materials based on Pb- and Cd chalcogenides. In addition to environmental concerns associated with the presence of toxic

    更新日期:2020-10-19
  • Automated microfluidic platform for dynamic and combinatorial drug screening of tumor organoids
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-19
    Brooke Schuster; Michael Junkin; Sara Saheb Kashaf; Isabel Romero-Calvo; Kori Kirby; Jonathan Matthews; Christopher R. Weber; Andrey Rzhetsky; Kevin P. White; Savaş Tay

    Three-dimensional (3D) cell culture technologies, such as organoids, are physiologically relevant models for basic and clinical applications. Automated microfluidics offers advantages in high-throughput and precision analysis of cells but is not yet compatible with organoids. Here, we present an automated, high-throughput, microfluidic 3D organoid culture and analysis system to facilitate preclinical

    更新日期:2020-10-19
  • Hsc70/Stub1 promotes the removal of individual oxidatively stressed peroxisomes
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-19
    Bo-Hua Chen; Yao-Jen Chang; Steven Lin; Wei Yuan Yang

    Peroxisomes perform beta-oxidation of branched and very-long chain fatty acids, which leads to the formation of reactive oxygen species (ROS) within the peroxisomal lumen. Peroxisomes are therefore prone to ROS-mediated damages. Here, using light to specifically and acutely induce ROS formation within the peroxisomal lumen, we find that cells individually remove ROS-stressed peroxisomes through ubiquitin-dependent

    更新日期:2020-10-19
  • Structural basis of heterotetrameric assembly and disease mutations in the human cis -prenyltransferase complex
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-19
    Michal Lisnyansky Bar-El; Pavla Vaňková; Adva Yeheskel; Luba Simhaev; Hamutal Engel; Petr Man; Yoni Haitin; Moshe Giladi

    The human cis-prenyltransferase (hcis-PT) is an enzymatic complex essential for protein N-glycosylation. Synthesizing the precursor of the glycosyl carrier dolichol-phosphate, mutations in hcis-PT cause severe human diseases. Here, we reveal that hcis-PT exhibits a heterotetrameric assembly in solution, consisting of two catalytic dehydrodolichyl diphosphate synthase (DHDDS) and inactive Nogo-B receptor

    更新日期:2020-10-19
  • Antibodies targeting epitopes on the cell-surface form of NS1 protect against Zika virus infection during pregnancy
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-19
    Alex W. Wessel; Nurgun Kose; Robin G. Bombardi; Vicky Roy; Warangkana Chantima; Juthathip Mongkolsapaya; Melissa A. Edeling; Christopher A. Nelson; Irene Bosch; Galit Alter; Gavin R. Screaton; David H. Fremont; James E. Crowe; Michael S. Diamond

    There are no licensed therapeutics or vaccines available against Zika virus (ZIKV) to counteract its potential for congenital disease. Antibody-based countermeasures targeting the ZIKV envelope protein have been hampered by concerns for cross-reactive responses that induce antibody-dependent enhancement (ADE) of heterologous flavivirus infection. Nonstructural protein 1 (NS1) is a membrane-associated

    更新日期:2020-10-19
  • Author Correction: The Seminavis robusta genome provides insights into the evolutionary adaptations of benthic diatoms
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Cristina Maria Osuna-Cruz; Gust Bilcke; Emmelien Vancaester; Sam De Decker; Atle M. Bones; Per Winge; Nicole Poulsen; Petra Bulankova; Bram Verhelst; Sien Audoor; Darja Belisova; Aikaterini Pargana; Monia Russo; Frederike Stock; Emilio Cirri; Tore Brembu; Georg Pohnert; Gwenael Piganeau; Maria Immacolata Ferrante; Thomas Mock; Lieven Sterck; Koen Sabbe; Lieven De Veylder; Wim Vyverman; Klaas Vandepoele

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

    更新日期:2020-10-17
  • The future of low-temperature carbon dioxide electrolysis depends on solving one basic problem
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Joshua A. Rabinowitz; Matthew W. Kanan

    Carbonate formation is the primary source of energy and carbon losses in low-temperature carbon dioxide electrolysis. Realigning research priorities to address the carbonate problem is essential if this technology is to become a viable option for renewable chemical and fuel production. Low-temperature carbon dioxide electrolysis is an attractive process for sustainable fuel synthesis, but current systems

    更新日期:2020-10-17
  • The human microbiome in the 21 st century
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Elze Rackaityte; Susan V. Lynch

    The human body supports a thriving diversity of microbes which comprise a dynamic, ancillary, functional system that synergistically develops in lock-step with physiological development of its host. The human microbiome field has transitioned from cataloging this rich diversity to dissecting molecular mechanisms by which microbiomes influence human health. Early life microbiome development trains immune

    更新日期:2020-10-17
  • Xenon iron oxides predicted as potential Xe hosts in Earth’s lower mantle
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Feng Peng; Xianqi Song; Chang Liu; Quan Li; Maosheng Miao; Changfeng Chen; Yanming Ma

    An enduring geological mystery concerns the missing xenon problem, referring to the abnormally low concentration of xenon compared to other noble gases in Earth’s atmosphere. Identifying mantle minerals that can capture and stabilize xenon has been a great challenge in materials physics and xenon chemistry. Here, using an advanced crystal structure search algorithm in conjunction with first-principles

    更新日期:2020-10-17
  • Metal chalcogenide hollow polar bipyramid prisms as efficient sulfur hosts for Na-S batteries
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Muhammad Kashif Aslam; Ieuan D. Seymour; Naman Katyal; Sha Li; Tingting Yang; Shu-juan Bao; Graeme Henkelman; Maowen Xu

    Sodium sulfur batteries require efficient sulfur hosts that can capture soluble polysulfides and enable fast reduction kinetics. Herein, we design hollow, polar and catalytic bipyramid prisms of cobalt sulfide as efficient sulfur host for sodium sulfur batteries. Cobalt sulfide has interwoven surfaces with wide internal spaces that can accommodate sodium polysulfides and withstand volumetric expansion

    更新日期:2020-10-17
  • Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Alexandra Stützer; Luisa M. Welp; Monika Raabe; Timo Sachsenberg; Christin Kappert; Alexander Wulf; Andy M. Lau; Stefan-Sebastian David; Aleksandar Chernev; Katharina Kramer; Argyris Politis; Oliver Kohlbacher; Wolfgang Fischle; Henning Urlaub

    Protein–DNA interactions are key to the functionality and stability of the genome. Identification and mapping of protein–DNA interaction interfaces and sites is crucial for understanding DNA-dependent processes. Here, we present a workflow that allows mass spectrometric (MS) identification of proteins in direct contact with DNA in reconstituted and native chromatin after cross-linking by ultraviolet

    更新日期:2020-10-17
  • Photon-directed multiplexed enzymatic DNA synthesis for molecular digital data storage
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Howon Lee; Daniel J. Wiegand; Kettner Griswold; Sukanya Punthambaker; Honggu Chun; Richie E. Kohman; George M. Church

    New storage technologies are needed to keep up with the global demands of data generation. DNA is an ideal storage medium due to its stability, information density and ease-of-readout with advanced sequencing techniques. However, progress in writing DNA is stifled by the continued reliance on chemical synthesis methods. The enzymatic synthesis of DNA is a promising alternative, but thus far has not

    更新日期:2020-10-17
  • Non-dispersive infrared multi-gas sensing via nanoantenna integrated narrowband detectors
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Xiaochao Tan; Heng Zhang; Junyu Li; Haowei Wan; Qiushi Guo; Houbin Zhu; Huan Liu; Fei Yi

    Non-dispersive infrared (NDIR) spectroscopy analyzes the concentration of target gases based on their characteristic infrared absorption. In conventional NDIR gas sensors, an infrared detector has to pair with a bandpass filter to select the target gas. However, multiplexed NDIR gas sensing requires multiple pairs of bandpass filters and detectors, which makes the sensor bulky and expensive. Here,

    更新日期:2020-10-17
  • Whole-genome sequencing of acral melanoma reveals genomic complexity and diversity
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Felicity Newell; James S. Wilmott; Peter A. Johansson; Katia Nones; Venkateswar Addala; Pamela Mukhopadhyay; Natasa Broit; Carol M. Amato; Robert Van Gulick; Stephen H. Kazakoff; Ann-Marie Patch; Lambros T. Koufariotis; Vanessa Lakis; Conrad Leonard; Scott Wood; Oliver Holmes; Qinying Xu; Karl Lewis; Theresa Medina; Rene Gonzalez; Robyn P. M. Saw; Andrew J. Spillane; Jonathan R. Stretch; Robert V.

    To increase understanding of the genomic landscape of acral melanoma, a rare form of melanoma occurring on palms, soles or nail beds, whole genome sequencing of 87 tumors with matching transcriptome sequencing for 63 tumors was performed. Here we report that mutational signature analysis reveals a subset of tumors, mostly subungual, with an ultraviolet radiation signature. Significantly mutated genes

    更新日期:2020-10-17
  • A causal role for frontal cortico-cortical coordination in social action monitoring
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Taihei Ninomiya; Atsushi Noritake; Kenta Kobayashi; Masaki Isoda

    Decision-making via monitoring others’ actions is a cornerstone of interpersonal exchanges. Although the ventral premotor cortex (PMv) and the medial prefrontal cortex (MPFC) are cortical nodes in social brain networks, the two areas are rarely concurrently active in neuroimaging, inviting the hypothesis that they are functionally independent. Here we show in macaques that the ability of the MPFC to

    更新日期:2020-10-17
  • Whole blood immunophenotyping uncovers immature neutrophil-to-VD2 T-cell ratio as an early marker for severe COVID-19
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Guillaume Carissimo; Weili Xu; Immanuel Kwok; Mohammad Yazid Abdad; Yi-Hao Chan; Siew-Wai Fong; Kia Joo Puan; Cheryl Yi-Pin Lee; Nicholas Kim-Wah Yeo; Siti Naqiah Amrun; Rhonda Sin-Ling Chee; Wilson How; Stephrene Chan; Bingwen Eugene Fan; Anand Kumar Andiappan; Bernett Lee; Olaf Rötzschke; Barnaby Edward Young; Yee-Sin Leo; David Chien Lye; Laurent Renia; Lai Guan Ng; Anis Larbi; Lisa FP Ng

    SARS-CoV-2 is the novel coronavirus responsible for the current COVID-19 pandemic. Severe complications are observed only in a small proportion of infected patients but the cellular mechanisms underlying this progression are still unknown. Comprehensive flow cytometry of whole blood samples from 54 COVID-19 patients reveals a dramatic increase in the number of immature neutrophils. This increase strongly

    更新日期:2020-10-17
  • ATP hydrolysis by yeast Hsp104 determines protein aggregate dissolution and size in vivo
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Udhayabhaskar Sathyanarayanan; Marina Musa; Peter Bou Dib; Nuno Raimundo; Ira Milosevic; Anita Krisko

    Signs of proteostasis failure often entwine with those of metabolic stress at the cellular level. Here, we study protein sequestration during glucose deprivation-induced ATP decline in Saccharomyces cerevisiae. Using live-cell imaging, we find that sequestration of misfolded proteins and nascent polypeptides into two distinct compartments, stress granules, and Q-bodies, is triggered by the exhaustion

    更新日期:2020-10-17
  • The protein translation machinery is expressed for maximal efficiency in Escherichia coli
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Xiao-Pan Hu; Hugo Dourado; Peter Schubert; Martin J. Lercher

    Protein synthesis is the most expensive process in fast-growing bacteria. Experimentally observed growth rate dependencies of the translation machinery form the basis of powerful phenomenological growth laws; however, a quantitative theory on the basis of biochemical and biophysical constraints is lacking. Here, we show that the growth rate-dependence of the concentrations of ribosomes, tRNAs, mRNA

    更新日期:2020-10-17
  • High resolution spectral metrology leveraging topologically enhanced optical activity in fibers
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Aaron P. Greenberg; Gautam Prabhakar; Siddharth Ramachandran

    Optical rotation, a form of optical activity, is a phenomenon employed in various metrological applications and industries including chemical, food, and pharmaceutical. In naturally-occurring, as well as structured media, the integrated effect is, however, typically small. Here, we demonstrate that, by exploiting the inherent and stable spin-orbit interaction of orbital angular momentum fiber modes

    更新日期:2020-10-17
  • Structure of inhibitor-bound mammalian complex I
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Hannah R. Bridges; Justin G. Fedor; James N. Blaza; Andrea Di Luca; Alexander Jussupow; Owen D. Jarman; John J. Wright; Ahmed-Noor A. Agip; Ana P. Gamiz-Hernandez; Maxie M. Roessler; Ville R. I. Kaila; Judy Hirst

    Respiratory complex I (NADH:ubiquinone oxidoreductase) captures the free energy from oxidising NADH and reducing ubiquinone to drive protons across the mitochondrial inner membrane and power oxidative phosphorylation. Recent cryo-EM analyses have produced near-complete models of the mammalian complex, but leave the molecular principles of its long-range energy coupling mechanism open to debate. Here

    更新日期:2020-10-17
  • Fusing subnational with national climate action is central to decarbonization: the case of the United States
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Nathan E. Hultman; Leon Clarke; Carla Frisch; Kevin Kennedy; Haewon McJeon; Tom Cyrs; Pete Hansel; Paul Bodnar; Michelle Manion; Morgan R. Edwards; Ryna Cui; Christina Bowman; Jessie Lund; Michael I. Westphal; Andrew Clapper; Joel Jaeger; Arijit Sen; Jiehong Lou; Devashree Saha; Wendy Jaglom; Koben Calhoun; Kristin Igusky; James deWeese; Kareem Hammoud; J. C. Altimirano; Margaret Dennis; Chris Henderson;

    Approaches that root national climate strategies in local actions will be essential for all countries as they develop new nationally determined contributions under the Paris Agreement. The potential impact of climate action from non-national actors in delivering higher global ambition is significant. Sub-national action in the United States provides a test for how such actions can accelerate emissions

    更新日期:2020-10-17
  • A role for spindles in the onset of rapid eye movement sleep
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Mojtaba Bandarabadi; Carolina Gutierrez Herrera; Thomas C. Gent; Claudio Bassetti; Kaspar Schindler; Antoine R. Adamantidis

    Sleep spindle generation classically relies on an interplay between the thalamic reticular nucleus (TRN), thalamo-cortical (TC) relay cells and cortico-thalamic (CT) feedback during non-rapid eye movement (NREM) sleep. Spindles are hypothesized to stabilize sleep, gate sensory processing and consolidate memory. However, the contribution of non-sensory thalamic nuclei in spindle generation and the role

    更新日期:2020-10-17
  • A high-stringency blueprint of the human proteome
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Subash Adhikari; Edouard C. Nice; Eric W. Deutsch; Lydie Lane; Gilbert S. Omenn; Stephen R. Pennington; Young-Ki Paik; Christopher M. Overall; Fernando J. Corrales; Ileana M. Cristea; Jennifer E. Van Eyk; Mathias Uhlén; Cecilia Lindskog; Daniel W. Chan; Amos Bairoch; James C. Waddington; Joshua L. Justice; Joshua LaBaer; Henry Rodriguez; Fuchu He; Markus Kostrzewa; Peipei Ping; Rebekah L. Gundry; Peter

    The Human Proteome Organization (HUPO) launched the Human Proteome Project (HPP) in 2010, creating an international framework for global collaboration, data sharing, quality assurance and enhancing accurate annotation of the genome-encoded proteome. During the subsequent decade, the HPP established collaborations, developed guidelines and metrics, and undertook reanalysis of previously deposited community

    更新日期:2020-10-17
  • Non-invasive decision support for NSCLC treatment using PET/CT radiomics
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Wei Mu; Lei Jiang; JianYuan Zhang; Yu Shi; Jhanelle E. Gray; Ilke Tunali; Chao Gao; Yingying Sun; Jie Tian; Xinming Zhao; Xilin Sun; Robert J. Gillies; Matthew B. Schabath

    Two major treatment strategies employed in non-small cell lung cancer, NSCLC, are tyrosine kinase inhibitors, TKIs, and immune checkpoint inhibitors, ICIs. The choice of strategy is based on heterogeneous biomarkers that can dynamically change during therapy. Thus, there is a compelling need to identify comprehensive biomarkers that can be used longitudinally to help guide therapy choice. Herein, we

    更新日期:2020-10-17
  • Resensitizing carbapenem- and colistin-resistant bacteria to antibiotics using auranofin
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Hongzhe Sun; Qi Zhang; Runming Wang; Haibo Wang; Yuen-Ting Wong; Minji Wang; Quan Hao; Aixin Yan; Richard Yi-Tsun Kao; Pak-Leung Ho; Hongyan Li

    Global emergence of Gram-negative bacteria carrying the plasmid-borne resistance genes, blaMBL and mcr, raises a significant challenge to the treatment of life-threatening infections by the antibiotics, carbapenem and colistin (COL). Here, we identify an antirheumatic drug, auranofin (AUR) as a dual inhibitor of metallo-β-lactamases (MBLs) and mobilized colistin resistance (MCRs), two resistance enzymes

    更新日期:2020-10-17
  • Increased RNA editing in maternal immune activation model of neurodevelopmental disease
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Hadas Tsivion-Visbord; Eli Kopel; Ariel Feiglin; Tamar Sofer; Ran Barzilay; Tali Ben-Zur; Orly Yaron; Daniel Offen; Erez Y. Levanon

    The etiology of major neurodevelopmental disorders such as schizophrenia and autism is unclear, with evidence supporting a combination of genetic factors and environmental insults, including viral infection during pregnancy. Here we utilized a mouse model of maternal immune activation (MIA) with the viral mimic PolyI:C infection during early gestation. We investigated the transcriptional changes in

    更新日期:2020-10-17
  • Metformin enhances anti-mycobacterial responses by educating CD8+ T-cell immunometabolic circuits
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Julia Böhme; Nuria Martinez; Shamin Li; Andrea Lee; Mardiana Marzuki; Anteneh Mehari Tizazu; David Ackart; Jessica Haugen Frenkel; Alexandra Todd; Ekta Lachmandas; Josephine Lum; Foo Shihui; Tze Pin Ng; Bernett Lee; Anis Larbi; Mihai G. Netea; Randall Basaraba; Reinout van Crevel; Evan Newell; Hardy Kornfeld; Amit Singhal

    Patients with type 2 diabetes (T2D) have a lower risk of Mycobacterium tuberculosis infection, progression from infection to tuberculosis (TB) disease, TB morality and TB recurrence, when being treated with metformin. However, a detailed mechanistic understanding of these protective effects is lacking. Here, we use mass cytometry to show that metformin treatment expands a population of memory-like

    更新日期:2020-10-17
  • Defining the impact of dietary macronutrient balance on PCOS traits
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Valentina Rodriguez Paris; Samantha M. Solon-Biet; Alistair M. Senior; Melissa C. Edwards; Reena Desai; Nicodemus Tedla; Madeleine J. Cox; William L. Ledger; Robert B. Gilchrist; Stephen J. Simpson; David J. Handelsman; Kirsty A. Walters

    Lifestyle, mainly dietary, interventions are first-line treatment for women with polycystic ovary syndrome (PCOS), but the optimal diet remains undefined. We combined a hyperandrogenized PCOS mouse model with a systematic macronutrient approach, to elucidate the impact of dietary macronutrients on the development of PCOS. We identify that an optimum dietary macronutrient balance of a low protein, medium

    更新日期:2020-10-17
  • Broadband multi-magnon relaxometry using a quantum spin sensor for high frequency ferromagnetic dynamics sensing
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Brendan A. McCullian; Ahmed M. Thabt; Benjamin A. Gray; Alex L. Melendez; Michael S. Wolf; Vladimir L. Safonov; Denis V. Pelekhov; Vidya P. Bhallamudi; Michael R. Page; P. Chris Hammel

    Development of sensitive local probes of magnon dynamics is essential to further understand the physical processes that govern magnon generation, propagation, scattering, and relaxation. Quantum spin sensors like the NV center in diamond have long spin lifetimes and their relaxation can be used to sense magnetic field noise at gigahertz frequencies. Thus far, NV sensing of ferromagnetic dynamics has

    更新日期:2020-10-17
  • DIALib-QC an assessment tool for spectral libraries in data-independent acquisition proteomics
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Mukul K. Midha; David S. Campbell; Charu Kapil; Ulrike Kusebauch; Michael R. Hoopmann; Samuel L. Bader; Robert L. Moritz

    Data-independent acquisition (DIA) mass spectrometry, also known as Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH), is a popular label-free proteomics strategy to comprehensively quantify peptides/proteins utilizing mass spectral libraries to decipher inherently multiplexed spectra collected linearly across a mass range. Although there are many spectral libraries produced worldwide

    更新日期:2020-10-17
  • Quantum chemical accuracy from density functional approximations via machine learning
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Mihail Bogojeski; Leslie Vogt-Maranto; Mark E. Tuckerman; Klaus-Robert Müller; Kieron Burke

    Kohn-Sham density functional theory (DFT) is a standard tool in most branches of chemistry, but accuracies for many molecules are limited to 2-3 kcal ⋅ mol−1 with presently-available functionals. Ab initio methods, such as coupled-cluster, routinely produce much higher accuracy, but computational costs limit their application to small molecules. In this paper, we leverage machine learning to calculate

    更新日期:2020-10-17
  • Language prediction mechanisms in human auditory cortex
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    K. J. Forseth; G. Hickok; P. S. Rollo; N. Tandon

    Spoken language, both perception and production, is thought to be facilitated by an ensemble of predictive mechanisms. We obtain intracranial recordings in 37 patients using depth probes implanted along the anteroposterior extent of the supratemporal plane during rhythm listening, speech perception, and speech production. These reveal two predictive mechanisms in early auditory cortex with distinct

    更新日期:2020-10-17
  • 16.8% Monolithic all-perovskite triple-junction solar cells via a universal two-step solution process
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Junke Wang; Valerio Zardetto; Kunal Datta; Dong Zhang; Martijn M. Wienk; René A. J. Janssen

    Perovskite semiconductors hold a unique promise in developing multijunction solar cells with high-efficiency and low-cost. Besides design constraints to reduce optical and electrical losses, integrating several very different perovskite absorber layers in a multijunction cell imposes a great processing challenge. Here, we report a versatile two-step solution process for high-quality 1.73 eV wide-,

    更新日期:2020-10-17
  • Spectroscopic capture of a low-spin Mn(IV)-oxo species in Ni–Mn 3 O 4 nanoparticles during water oxidation catalysis
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Sunghak Park; Kyoungsuk Jin; Hyung Kyu Lim; Jin Kim; Kang Hee Cho; Seungwoo Choi; Hongmin Seo; Moo Young Lee; Yoon Ho Lee; Sangmoon Yoon; Miyoung Kim; Hyungjun Kim; Sun Hee Kim; Ki Tae Nam

    High-valent metal-oxo moieties have been implicated as key intermediates preceding various oxidation processes. The critical O–O bond formation step in the Kok cycle that is presumed to generate molecular oxygen occurs through the high-valent Mn-oxo species of the water oxidation complex, i.e., the Mn4Ca cluster in photosystem II. Here, we report the spectroscopic characterization of new intermediates

    更新日期:2020-10-17
  • GPAHex-A synthetic biology platform for Type IV–V glycopeptide antibiotic production and discovery
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Min Xu; Wenliang Wang; Nicholas Waglechner; Elizabeth J. Culp; Allison K. Guitor; Gerard D. Wright

    Glycopeptide antibiotics (GPAs) are essential for the treatment of severe infectious diseases caused by Gram-positive bacteria. The emergence and spread of GPA resistance have propelled the search for more effective GPAs. Given their structural complexity, genetic intractability, and low titer, expansion of GPA chemical diversity using synthetic or medicinal chemistry remains challenging. Here we describe

    更新日期:2020-10-17
  • Detection of haplotype-dependent allele-specific DNA methylation in WGBS data
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    J. Abante; Y. Fang; A. P. Feinberg; J. Goutsias

    In heterozygous genomes, allele-specific measurements can reveal biologically significant differences in DNA methylation between homologous alleles associated with local changes in genetic sequence. Current approaches for detecting such events from whole-genome bisulfite sequencing (WGBS) data perform statistically independent marginal analysis at individual cytosine-phosphate-guanine (CpG) sites,

    更新日期:2020-10-17
  • Structural and functional analysis of protective antibodies targeting the threefold plateau of enterovirus 71
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Kuan-Ying A. Huang; Daming Zhou; Elizabeth E. Fry; Abhay Kotecha; Peng-Nien Huang; Shu-Li Yang; Kuo-Chien Tsao; Yhu-Chering Huang; Tzou-Yien Lin; Jingshan Ren; David I. Stuart

    Enterovirus 71 (EV71)-neutralizing antibodies correlate with protection and have potential as therapeutic agents. We isolate and characterize a panel of plasmablast-derived monoclonal antibodies from an infected child whose antibody response focuses on the plateau epitope near the icosahedral 3-fold axes. Eight of a total of 19 antibodies target this epitope and three of these potently neutralize the

    更新日期:2020-10-17
  • Repair of G1 induced DNA double-strand breaks in S-G2/M by alternative NHEJ
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Wei Yu; Chloé Lescale; Loelia Babin; Marie Bedora-Faure; Hélène Lenden-Hasse; Ludivine Baron; Caroline Demangel; José Yelamos; Erika Brunet; Ludovic Deriano

    The alternative non-homologous end-joining (NHEJ) pathway promotes DNA double-strand break (DSB) repair in cells deficient for NHEJ or homologous recombination, suggesting that it operates at all stages of the cell cycle. Here, we use an approach in which DNA breaks can be induced in G1 cells and their repair tracked, enabling us to show that joining of DSBs is not functional in G1-arrested XRCC4-deficient

    更新日期:2020-10-17
  • Single-shot stereo-polarimetric compressed ultrafast photography for light-speed observation of high-dimensional optical transients with picosecond resolution
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Jinyang Liang; Peng Wang; Liren Zhu; Lihong V. Wang

    Simultaneous and efficient ultrafast recording of multiple photon tags contributes to high-dimensional optical imaging and characterization in numerous fields. Existing high-dimensional optical imaging techniques that record space and polarization cannot detect the photon’s time of arrival owing to the limited speeds of the state-of-the-art electronic sensors. Here, we overcome this long-standing limitation

    更新日期:2020-10-17
  • Genome-wide screens identify Toxoplasma gondii determinants of parasite fitness in IFNγ-activated murine macrophages
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Yifan Wang; Lamba Omar Sangaré; Tatiana C. Paredes-Santos; Musa A. Hassan; Shruthi Krishnamurthy; Anna M. Furuta; Benedikt M. Markus; Sebastian Lourido; Jeroen P. J. Saeij

    Macrophages play an essential role in the early immune response against Toxoplasma and are the cell type preferentially infected by the parasite in vivo. Interferon gamma (IFNγ) elicits a variety of anti-Toxoplasma activities in macrophages. Using a genome-wide CRISPR screen we identify 353 Toxoplasma genes that determine parasite fitness in naїve or IFNγ-activated murine macrophages, seven of which

    更新日期:2020-10-17
  • Multivalent interactions drive nucleosome binding and efficient chromatin deacetylation by SIRT6
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Wallace H. Liu; Jie Zheng; Jessica L. Feldman; Mark A. Klein; Vyacheslav I. Kuznetsov; Craig L. Peterson; Patrick R. Griffin; John M. Denu

    The protein deacetylase SIRT6 maintains cellular homeostasis through multiple pathways that include the deacetylation of histone H3 and repression of transcription. Prior work suggests that SIRT6 is associated with chromatin and can substantially reduce global levels of H3 acetylation, but how SIRT6 is able to accomplish this feat is unknown. Here, we describe an exquisitely tight interaction between

    更新日期:2020-10-17
  • Understanding and managing new risks on the Nile with the Grand Ethiopian Renaissance Dam
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Kevin G. Wheeler; Marc Jeuland; Jim W. Hall; Edith Zagona; Dale Whittington

    When construction of the Grand Ethiopian Renaissance Dam (GERD) is completed, the Nile will have two of the world’s largest dams—the High Aswan Dam (HAD) and the GERD—in two different countries (Egypt and Ethiopia). There is not yet agreement on how these dams will operate to manage scarce water resources. We elucidate the potential risks and opportunities to Egypt, Sudan and Ethiopia by simulating

    更新日期:2020-10-17
  • Standardization and harmonization of distributed multi-center proteotype analysis supporting precision medicine studies
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Yue Xuan; Nicholas W. Bateman; Sebastien Gallien; Sandra Goetze; Yue Zhou; Pedro Navarro; Mo Hu; Niyati Parikh; Brian L. Hood; Kelly A. Conrads; Christina Loosse; Reta Birhanu Kitata; Sander R. Piersma; Davide Chiasserini; Hongwen Zhu; Guixue Hou; Muhammad Tahir; Andrew Macklin; Amanda Khoo; Xiuxuan Sun; Ben Crossett; Albert Sickmann; Yu-Ju Chen; Connie R. Jimenez; Hu Zhou; Siqi Liu; Martin R. Larsen;

    Cancer has no borders: Generation and analysis of molecular data across multiple centers worldwide is necessary to gain statistically significant clinical insights for the benefit of patients. Here we conceived and standardized a proteotype data generation and analysis workflow enabling distributed data generation and evaluated the quantitative data generated across laboratories of the international

    更新日期:2020-10-17
  • Structural basis for two metal-ion catalysis of DNA cleavage by Cas12i2
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Xue Huang; Wei Sun; Zhi Cheng; Minxuan Chen; Xueyan Li; Jiuyu Wang; Gang Sheng; Weimin Gong; Yanli Wang

    To understand how the RuvC catalytic domain of Class 2 Cas proteins cleaves DNA, it will be necessary to elucidate the structures of RuvC-containing Cas complexes in their catalytically competent states. Cas12i2 is a Class 2 type V-I CRISPR-Cas endonuclease that cleaves target dsDNA by an unknown mechanism. Here, we report structures of Cas12i2–crRNA–DNA complexes and a Cas12i2–crRNA complex. We reveal

    更新日期:2020-10-17
  • Orbital climate variability on the northeastern Tibetan Plateau across the Eocene–Oligocene transition
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Hong Ao; Guillaume Dupont-Nivet; Eelco J. Rohling; Peng Zhang; Jean-Baptiste Ladant; Andrew P. Roberts; Alexis Licht; Qingsong Liu; Zhonghui Liu; Mark J. Dekkers; Helen K. Coxall; Zhangdong Jin; Chunju Huang; Guoqiao Xiao; Christopher J. Poulsen; Natasha Barbolini; Niels Meijer; Qiang Sun; Xiaoke Qiang; Jiao Yao; Zhisheng An

    The first major build-up of Antarctic glaciation occurred in two consecutive stages across the Eocene–Oligocene transition (EOT): the EOT-1 cooling event at ~34.1–33.9 Ma and the Oi-1 glaciation event at ~33.8–33.6 Ma. Detailed orbital-scale terrestrial environmental responses to these events remain poorly known. Here we present magnetic and geochemical climate records from the northeastern Tibetan

    更新日期:2020-10-17
  • Large scale genome reconstructions illuminate Wolbachia evolution
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Matthias Scholz; Davide Albanese; Kieran Tuohy; Claudio Donati; Nicola Segata; Omar Rota-Stabelli

    Wolbachia is an iconic example of a successful intracellular bacterium. Despite its importance as a manipulator of invertebrate biology, its evolutionary dynamics have been poorly studied from a genomic viewpoint. To expand the number of Wolbachia genomes, we screen over 30,000 publicly available shotgun DNA sequencing samples from 500 hosts. By assembling over 1000 Wolbachia genomes, we provide a

    更新日期:2020-10-17
  • A bacterial endophyte exploits chemotropism of a fungal pathogen for plant colonization
    Nat. Commun. (IF 12.121) Pub Date : 2020-10-16
    Davide Palmieri; Stefania Vitale; Giuseppe Lima; Antonio Di Pietro; David Turrà

    Soil-inhabiting fungal pathogens use chemical signals released by roots to direct hyphal growth towards the host plant. Whether other soil microorganisms exploit this capacity for their own benefit is currently unknown. Here we show that the endophytic rhizobacterium Rahnella aquatilis locates hyphae of the root-infecting fungal pathogen Fusarium oxysporum through pH-mediated chemotaxis and uses them

    更新日期:2020-10-17
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