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  •   Vast CO2 release from Australian fires in 2019–2020 constrained by satellite
    Nature (IF 49.962) Pub Date : 2021-09-15
    Ivar R. van der Velde, Guido R. van der Werf, Sander Houweling, Joannes D. Maasakkers, Tobias Borsdorff, Jochen Landgraf, Paul Tol, Tim A. van Kempen, Richard van Hees, Ruud Hoogeveen, J. Pepijn Veefkind, Ilse Aben

    Southeast Australia experienced intensive and geographically extensive wildfires during the 2019–2020 summer season1,2. The fires released substantial amounts of carbon dioxide into the atmosphere3. However, existing emission estimates based on fire inventories are uncertain4, and vary by up to a factor of four for this event. Here we constrain emission estimates with the help of satellite observations

  •   An engineered IL-2 partial agonist promotes CD8+ T cell stemness
    Nature (IF 49.962) Pub Date : 2021-09-15
    Fei Mo, Zhiya Yu, Peng Li, Jangsuk Oh, Rosanne Spolski, Liang Zhao, Caleb R. Glassman, Tori N. Yamamoto, Yun Chen, Filip M. Golebiowski, Dalton Hermans, Sonia Majri-Morrison, Lora K. Picton, Wei Liao, Min Ren, Xiaoxuan Zhuang, Suman Mitra, Jian-Xin Lin, Luca Gattinoni, Jonathan D. Powell, Nicholas P. Restifo, K. Christopher Garcia, Warren J. Leonard

    Adoptive transfer of antigen-specific T cells represents a major advance in cancer immunotherapy, with robust clinical outcomes in some patients1. Both the number of transferred T cells and their differentiation state are critical determinants of effective responses2,3. T cells can be expanded with T cell receptor (TCR)-mediated stimulation and interleukin-2, but this can lead to differentiation into

  •   The diffuse γ-ray background is dominated by star-forming galaxies
    Nature (IF 49.962) Pub Date : 2021-09-15
    Matt A. Roth, Mark R. Krumholz, Roland M. Crocker, Silvia Celli

    The Fermi Gamma-ray Space Telescope has revealed a diffuse γ-ray background at energies from 0.1 gigaelectronvolt to 1 teraelectronvolt, which can be separated into emission from our Galaxy and an isotropic, extragalactic component1. Previous efforts to understand the latter have been hampered by the lack of physical models capable of predicting the γ-ray emission produced by the many candidate sources

  •   Structural basis of human transcription–DNA repair coupling
    Nature (IF 49.962) Pub Date : 2021-09-15
    Goran Kokic, Felix R. Wagner, Aleksandar Chernev, Henning Urlaub, Patrick Cramer

    Transcription-coupled DNA repair removes bulky DNA lesions from the genome1,2 and protects cells against ultraviolet (UV) irradiation3. Transcription-coupled DNA repair begins when RNA polymerase II (Pol II) stalls at a DNA lesion and recruits the Cockayne syndrome protein CSB, the E3 ubiquitin ligase, CRL4CSA and UV-stimulated scaffold protein A (UVSSA)3. Here we provide five high-resolution structures

  •   Structural insights into hepatitis C virus receptor binding and entry
    Nature (IF 49.962) Pub Date : 2021-09-15
    Ashish Kumar, Reafa A. Hossain, Samantha A. Yost, Wei Bu, Yuanyuan Wang, Altaira D. Dearborn, Arash Grakoui, Jeffrey I. Cohen, Joseph Marcotrigiano

    Hepatitis C virus (HCV) infection is a causal agent of chronic liver disease, cirrhosis and hepatocellular carcinoma in humans, and afflicts more than 70 million people worldwide. The HCV envelope glycoproteins E1 and E2 are responsible for the binding of the virus to the host cell, but the exact entry process remains undetermined1. The majority of broadly neutralizing antibodies block interaction

  •   Dairying enabled Early Bronze Age Yamnaya steppe expansions
    Nature (IF 49.962) Pub Date : 2021-09-15
    Shevan Wilkin, Alicia Ventresca Miller, Ricardo Fernandes, Robert Spengler, William T.-T. Taylor, Dorcas R. Brown, David Reich, Douglas J. Kennett, Brendan J. Culleton, Laura Kunz, Claudia Fortes, Aleksandra Kitova, Pavel Kuznetsov, Andrey Epimakhov, Victor F. Zaibert, Alan K. Outram, Egor Kitov, Aleksandr Khokhlov, David Anthony, Nicole Boivin

    During the Early Bronze Age, populations of the western Eurasian steppe expanded across an immense area of northern Eurasia. Combined archaeological and genetic evidence supports widespread Early Bronze Age population movements out of the Pontic–Caspian steppe that resulted in gene flow across vast distances, linking populations of Yamnaya pastoralists in Scandinavia with pastoral populations (known

  •   Resurgence of Ebola virus in 2021 in Guinea suggests a new paradigm for outbreaks
    Nature (IF 49.962) Pub Date : 2021-09-15
    Alpha Kabinet Keita, Fara R. Koundouno, Martin Faye, Ariane Düx, Julia Hinzmann, Haby Diallo, Ahidjo Ayouba, Frederic Le Marcis, Barré Soropogui, Kékoura Ifono, Moussa M. Diagne, Mamadou S. Sow, Joseph A. Bore, Sebastien Calvignac-Spencer, Nicole Vidal, Jacob Camara, Mamadou B. Keita, Annick Renevey, Amadou Diallo, Abdoul K. Soumah, Saa L. Millimono, Almudena Mari-Saez, Mamadou Diop, Ahmadou Doré,

    Seven years after the declaration of the first epidemic of Ebola virus disease in Guinea, the country faced a new outbreak—between 14 February and 19 June 2021—near the epicentre of the previous epidemic1,2. Here we use next-generation sequencing to generate complete or near-complete genomes of Zaire ebolavirus from samples obtained from 12 different patients. These genomes form a well-supported phylogenetic

  •   Acinar cell clonal expansion in pancreas homeostasis and carcinogenesis
    Nature (IF 49.962) Pub Date : 2021-09-15
    Patrick Neuhöfer, Caitlin M. Roake, Stewart J. Kim, Ryan J. Lu, Robert B. West, Gregory W. Charville, Steven E. Artandi

    Pancreatic ductal adenocarcinoma (PDAC) is one of the leading causes of cancer deaths worldwide1. Studies in human tissues and in mouse models have suggested that for many cancers, stem cells sustain early mutations driving tumour development2,3. For the pancreas, however, mechanisms underlying cellular renewal and initiation of PDAC remain unresolved. Here, using lineage tracing from the endogenous

  •   Structural basis for tRNA methylthiolation by the radical SAM enzyme MiaB
    Nature (IF 49.962) Pub Date : 2021-09-15
    Olga A. Esakova, Tyler L. Grove, Neela H. Yennawar, Arthur J. Arcinas, Bo Wang, Carsten Krebs, Steven C. Almo, Squire J. Booker

    Numerous post-transcriptional modifications of transfer RNAs have vital roles in translation. The 2-methylthio-N6-isopentenyladenosine (ms2i6A) modification occurs at position 37 (A37) in transfer RNAs that contain adenine in position 36 of the anticodon, and serves to promote efficient A:U codon–anticodon base-pairing and to prevent unintended base pairing by near cognates, thus enhancing translational

  •   Widespread phytoplankton blooms triggered by 2019–2020 Australian wildfires
    Nature (IF 49.962) Pub Date : 2021-09-15
    Weiyi Tang, Joan Llort, Jakob Weis, Morgane M. G. Perron, Sara Basart, Zuchuan Li, Shubha Sathyendranath, Thomas Jackson, Estrella Sanz Rodriguez, Bernadette C. Proemse, Andrew R. Bowie, Christina Schallenberg, Peter G. Strutton, Richard Matear, Nicolas Cassar

    Droughts and climate-change-driven warming are leading to more frequent and intense wildfires1,2,3, arguably contributing to the severe 2019–2020 Australian wildfires4. The environmental and ecological impacts of the fires include loss of habitats and the emission of substantial amounts of atmospheric aerosols5,6,7. Aerosol emissions from wildfires can lead to the atmospheric transport of macronutrients

  •   Directed assembly of layered perovskite heterostructures as single crystals
    Nature (IF 49.962) Pub Date : 2021-09-15
    Michael L. Aubrey, Abraham Saldivar Valdes, Marina R. Filip, Bridget A. Connor, Kurt P. Lindquist, Jeffrey B. Neaton, Hemamala I. Karunadasa

    The precise stacking of different two-dimensional (2D) structures such as graphene and MoS2 has reinvigorated the field of 2D materials, revealing exotic phenomena at their interfaces1,2. These unique interfaces are typically constructed using mechanical or deposition-based methods to build a heterostructure one monolayer at a time2,3. By contrast, self-assembly is a scalable technique, where complex

  •   Structure-based classification predicts drug response in EGFR-mutant NSCLC
    Nature (IF 49.962) Pub Date : 2021-09-15
    Jacqulyne P. Robichaux, Xiuning Le, R. S. K. Vijayan, J. Kevin Hicks, Simon Heeke, Yasir Y. Elamin, Heather Y. Lin, Hibiki Udagawa, Ferdinandos Skoulidis, Hai Tran, Susan Varghese, Junqin He, Fahao Zhang, Monique B. Nilsson, Lemei Hu, Alissa Poteete, Waree Rinsurongkawong, Xiaoshan Zhang, Chenghui Ren, Xiaoke Liu, Lingzhi Hong, Jianjun Zhang, Lixia Diao, Russell Madison, Alexa B. Schrock, Jennifer

    Epidermal growth factor receptor (EGFR) mutations typically occur in exons 18–21 and are established driver mutations in non-small cell lung cancer (NSCLC)1,2,3. Targeted therapies are approved for patients with ‘classical’ mutations and a small number of other mutations4,5,6. However, effective therapies have not been identified for additional EGFR mutations. Furthermore, the frequency and effects

  •   Quantum criticality in twisted transition metal dichalcogenides
    Nature (IF 49.962) Pub Date : 2021-09-15
    Augusto Ghiotto, En-Min Shih, Giancarlo S. S. G. Pereira, Daniel A. Rhodes, Bumho Kim, Jiawei Zang, Andrew J. Millis, Kenji Watanabe, Takashi Taniguchi, James C. Hone, Lei Wang, Cory R. Dean, Abhay N. Pasupathy

    Near the boundary between ordered and disordered quantum phases, several experiments have demonstrated metallic behaviour that defies the Landau Fermi paradigm1,2,3,4,5. In moiré heterostructures, gate-tuneable insulating phases driven by electronic correlations have been recently discovered6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23. Here, we use transport measurements to characterize metal–insulator

  •   Multicomponent alkene azido-arylation by anion-mediated dual catalysis
    Nature (IF 49.962) Pub Date : 2021-09-13
    Ala Bunescu, Yusra Abdelhamid, Matthew J. Gaunt

    β-Arylethylamine-containing molecules display important indications in the modulation of pain, treatment of neurological disorders and management of opioid addiction, amongst others, making it a privileged scaffold in drug discovery1,2. De novo methods for their assembly are reliant on transformations that convert a small class of feedstocks into the target compounds via time consuming multi-step syntheses3–5

  •   Virus-induced senescence is driver and therapeutic target in COVID-19
    Nature (IF 49.962) Pub Date : 2021-09-13
    Soyoung Lee, Yong Yu, Jakob Trimpert, Fahad Benthani, Mario Mairhofer, Paulina Richter-Pechanska, Emanuel Wyler, Dimitri Belenki, Sabine Kaltenbrunner, Maria Pammer, Lea Kausche, Theresa C. Firsching, Kristina Dietert, Michael Schotsaert, Carles Martínez-Romero, Gagandeep Singh, Séverine Kunz, Daniela Niemeyer, Riad Ghanem, Helmut J. F. Salzer, Christian Paar, Michael Mülleder, Melissa Uccellini, Edward

    Derailed cytokine and immune cell networks account for organ damage and clinical severity of COVID-191–4. Here we show that SARS-CoV-2, like other viruses, evokes cellular senescence as a primary stress response in infected cells. Virus-induced senescence (VIS) is indistinguishable from other forms of cellular senescence and accompanied by a senescence-associated secretory phenotype (SASP), composed

  •   The EDS1–PAD4–ADR1 node mediates Arabidopsis pattern-triggered immunity
    Nature (IF 49.962) Pub Date : 2021-09-08
    Rory N. Pruitt, Federica Locci, Friederike Wanke, Lisha Zhang, Svenja C. Saile, Anna Joe, Darya Karelina, Chenlei Hua, Katja Fröhlich, Wei-Lin Wan, Meijuan Hu, Shaofei Rao, Sara C. Stolze, Anne Harzen, Andrea A. Gust, Klaus Harter, Matthieu H. A. J. Joosten, Bart P. H. J. Thomma, Jian-Min Zhou, Jeffery L. Dangl, Detlef Weigel, Hirofumi Nakagami, Claudia Oecking, Farid El Kasmi, Jane E. Parker, Thorsten

    Plants deploy cell-surface and intracellular leucine rich-repeat domain (LRR) immune receptors to detect pathogens1. LRR receptor kinases and LRR receptor proteins at the plasma membrane recognize microorganism-derived molecules to elicit pattern-triggered immunity (PTI), whereas nucleotide-binding LRR proteins detect microbial effectors inside cells to confer effector-triggered immunity (ETI). Although

  •   Using DNA sequencing data to quantify T cell fraction and therapy response
    Nature (IF 49.962) Pub Date : 2021-09-08
    Robert Bentham, Kevin Litchfield, Thomas B. K. Watkins, Emilia L. Lim, Rachel Rosenthal, Carlos Martínez-Ruiz, Crispin T. Hiley, Maise Al Bakir, Roberto Salgado, David A. Moore, Mariam Jamal-Hanjani, Charles Swanton, Nicholas McGranahan

    The immune microenvironment influences tumour evolution and can be both prognostic and predict response to immunotherapy1,2. However, measurements of tumour infiltrating lymphocytes (TILs) are limited by a shortage of appropriate data. Whole-exome sequencing (WES) of DNA is frequently performed to calculate tumour mutational burden and identify actionable mutations. Here we develop T cell exome TREC

  •   Tunable self-assembled Casimir microcavities and polaritons
    Nature (IF 49.962) Pub Date : 2021-09-08
    Battulga Munkhbat, Adriana Canales, Betül Küçüköz, Denis G. Baranov, Timur O. Shegai

    Spontaneous formation of ordered structures—self-assembly—is ubiquitous in nature and observed on different length scales, ranging from atomic and molecular systems to micrometre-scale objects and living matter1. Self-ordering in molecular and biological systems typically involves short-range hydrophobic and van der Waals interactions2,3. Here we introduce an approach to micrometre-scale self-assembly

  •   Transmembrane transport in inorganic colloidal cell-mimics
    Nature (IF 49.962) Pub Date : 2021-09-08
    Zhe Xu, Theodore Hueckel, William T. M. Irvine, Stefano Sacanna

    A key aspect of living cells is their ability to harvest energy from the environment and use it to pump specific atomic and molecular species in and out of their system—typically against an unfavourable concentration gradient1. Active transport allows cells to store metabolic energy, extract waste and supply organelles with basic building blocks at the submicrometre scale. Unlike living cells, abiotic

  •   Positive allosteric mechanisms of adenosine A1 receptor-mediated analgesia
    Nature (IF 49.962) Pub Date : 2021-09-08
    Christopher J. Draper-Joyce, Rebecca Bhola, Jinan Wang, Apurba Bhattarai, Anh T. N. Nguyen, India Cowie-Kent, Kelly O’Sullivan, Ling Yeong Chia, Hariprasad Venugopal, Celine Valant, David M. Thal, Denise Wootten, Nicolas Panel, Jens Carlsson, Macdonald J. Christie, Paul J. White, Peter Scammells, Lauren T. May, Patrick M. Sexton, Radostin Danev, Yinglong Miao, Alisa Glukhova, Wendy L. Imlach, Arthur

    The adenosine A1 receptor (A1R) is a promising therapeutic target for non-opioid analgesic agents to treat neuropathic pain1,2. However, development of analgesic orthosteric A1R agonists has failed because of a lack of sufficient on-target selectivity as well as off-tissue adverse effects3. Here we show that [2-amino-4-(3,5-bis(trifluoromethyl)phenyl)thiophen-3-yl)(4-chlorophenyl)methanone] (MIPS521)

  •   Cells of the human intestinal tract mapped across space and time
    Nature (IF 49.962) Pub Date : 2021-09-08
    Rasa Elmentaite, Natsuhiko Kumasaka, Kenny Roberts, Aaron Fleming, Emma Dann, Hamish W. King, Vitalii Kleshchevnikov, Monika Dabrowska, Sophie Pritchard, Liam Bolt, Sara F. Vieira, Lira Mamanova, Ni Huang, Francesca Perrone, Issac Goh Kai’En, Steven N. Lisgo, Matilda Katan, Steven Leonard, Thomas R. W. Oliver, C. Elizabeth Hook, Komal Nayak, Lia S. Campos, Cecilia Domínguez Conde, Emily Stephenson

    The cellular landscape of the human intestinal tract is dynamic throughout life, developing in utero and changing in response to functional requirements and environmental exposures. Here, to comprehensively map cell lineages, we use single-cell RNA sequencing and antigen receptor analysis of almost half a million cells from up to 5 anatomical regions in the developing and up to 11 distinct anatomical

  •   Unextractable fossil fuels in a 1.5 °C world
    Nature (IF 49.962) Pub Date : 2021-09-08
    Dan Welsby, James Price, Steve Pye, Paul Ekins

    Parties to the 2015 Paris Agreement pledged to limit global warming to well below 2 °C and to pursue efforts to limit the temperature increase to 1.5 °C relative to pre-industrial times1. However, fossil fuels continue to dominate the global energy system and a sharp decline in their use must be realized to keep the temperature increase below 1.5 °C (refs. 2,3,4,5,6,7). Here we use a global energy

  •   A lymphocyte–microglia–astrocyte axis in chronic active multiple sclerosis
    Nature (IF 49.962) Pub Date : 2021-09-08
    Martina Absinta, Dragan Maric, Marjan Gharagozloo, Thomas Garton, Matthew D. Smith, Jing Jin, Kathryn C. Fitzgerald, Anya Song, Poching Liu, Jing-Ping Lin, Tianxia Wu, Kory R. Johnson, Dorian B. McGavern, Dorothy P. Schafer, Peter A. Calabresi, Daniel S. Reich

    Multiple sclerosis (MS) lesions that do not resolve in the months after they form harbour ongoing demyelination and axon degeneration, and are identifiable in vivo by their paramagnetic rims on MRI scans1,2,3. Here, to define mechanisms underlying this disabling, progressive neurodegenerative state4,5,6 and foster development of new therapeutic agents, we used MRI-informed single-nucleus RNA sequencing

  •   Interface nano-optics with van der Waals polaritons
    Nature (IF 49.962) Pub Date : 2021-09-08
    Qing Zhang, Guangwei Hu, Weiliang Ma, Peining Li, Alex Krasnok, Rainer Hillenbrand, Andrea Alù, Cheng-Wei Qiu

    Polaritons are hybrid excitations of matter and photons. In recent years, polaritons in van der Waals nanomaterials—known as van der Waals polaritons—have shown great promise to guide the flow of light at the nanoscale over spectral regions ranging from the visible to the terahertz. A vibrant research field based on manipulating strong light–matter interactions in the form of polaritons, supported

  •   Inter-cellular CRISPR screens reveal regulators of cancer cell phagocytosis
    Nature (IF 49.962) Pub Date : 2021-09-08
    Roarke A. Kamber, Yoko Nishiga, Bhek Morton, Allison M. Banuelos, Amira A. Barkal, Felipe Vences-Catalán, Mingxin Gu, Daniel Fernandez, Jose A. Seoane, David Yao, Katherine Liu, Sijie Lin, Kaitlyn Spees, Christina Curtis, Livnat Jerby-Arnon, Irving L. Weissman, Julien Sage, Michael C. Bassik

    Monoclonal antibody therapies targeting tumour antigens drive cancer cell elimination in large part by triggering macrophage phagocytosis of cancer cells1,2,3,4,5,6,7. However, cancer cells evade phagocytosis using mechanisms that are incompletely understood. Here we develop a platform for unbiased identification of factors that impede antibody-dependent cellular phagocytosis (ADCP) using complementary

  •   Pollinators contribute to the maintenance of flowering plant diversity
    Nature (IF 49.962) Pub Date : 2021-09-08
    Na Wei, Rainee L. Kaczorowski, Gerardo Arceo-Gómez, Elizabeth M. O’Neill, Rebecca A. Hayes, Tia-Lynn Ashman

    Mechanisms that favour rare species are key to the maintenance of diverse communities1,2,3. One of the most critical tasks for conservation of flowering plant biodiversity is to understand how plant–pollinator interactions contribute to the maintenance of rare species4,5,6,7. Here we show that niche partitioning in pollinator use and asymmetric facilitation confer fitness advantage of rarer species

  •   Widespread woody plant use of water stored in bedrock
    Nature (IF 49.962) Pub Date : 2021-09-08
    Erica L. McCormick, David N. Dralle, W. Jesse Hahm, Alison K. Tune, Logan M. Schmidt, K. Dana Chadwick, Daniella M. Rempe

    In the past several decades, field studies have shown that woody plants can access substantial volumes of water from the pores and fractures of bedrock1,2,3. If, like soil moisture, bedrock water storage serves as an important source of plant-available water, then conceptual paradigms regarding water and carbon cycling may need to be revised to incorporate bedrock properties and processes4,5,6. Here

  •   Large metallicity variations in the Galactic interstellar medium
    Nature (IF 49.962) Pub Date : 2021-09-08
    Annalisa De Cia, Edward B. Jenkins, Andrew J. Fox, Cédric Ledoux, Tanita Ramburth-Hurt, Christina Konstantopoulou, Patrick Petitjean, Jens-Kristian Krogager

    The interstellar medium (ISM) comprises gases at different temperatures and densities, including ionized, atomic and molecular species, and dust particles1. The neutral ISM is dominated by neutral hydrogen2 and has ionization fractions of up to eight per cent3. The concentration of chemical elements heavier than helium (metallicity) spans orders of magnitudes in Galactic stars4, because they formed

  •   A roadmap for the Human Developmental Cell Atlas
    Nature (IF 49.962) Pub Date : 2021-09-08
    Muzlifah Haniffa, Deanne Taylor, Sten Linnarsson, Bruce J. Aronow, Gary D. Bader, Roger A. Barker, Pablo G. Camara, J. Gray Camp, Alain Chédotal, Andrew Copp, Heather C. Etchevers, Paolo Giacobini, Berthold Göttgens, Guoji Guo, Ania Hupalowska, Kylie R. James, Emily Kirby, Arnold Kriegstein, Joakim Lundeberg, John C. Marioni, Kerstin B. Meyer, Kathy K. Niakan, Mats Nilsson, Bayanne Olabi, Dana Pe’er

    The Human Developmental Cell Atlas (HDCA) initiative, which is part of the Human Cell Atlas, aims to create a comprehensive reference map of cells during development. This will be critical to understanding normal organogenesis, the effect of mutations, environmental factors and infectious agents on human development, congenital and childhood disorders, and the cellular basis of ageing, cancer and regenerative

  •   High-fidelity laser-free universal control of trapped ion qubits
    Nature (IF 49.962) Pub Date : 2021-09-08
    R. Srinivas, S. C. Burd, H. M. Knaack, R. T. Sutherland, A. Kwiatkowski, S. Glancy, E. Knill, D. J. Wineland, D. Leibfried, A. C. Wilson, D. T. C. Allcock, D. H. Slichter

    Universal control of multiple qubits—the ability to entangle qubits and to perform arbitrary individual qubit operations1—is a fundamental resource for quantum computing2, simulation3 and networking4. Qubits realized in trapped atomic ions have shown the highest-fidelity two-qubit entangling operations5,6,7 and single-qubit rotations8 so far. Universal control of trapped ion qubits has been separately

  •   Bioaccumulation of therapeutic drugs by human gut bacteria
    Nature (IF 49.962) Pub Date : 2021-09-08
    Martina Klünemann, Sergej Andrejev, Sonja Blasche, Andre Mateus, Prasad Phapale, Saravanan Devendran, Johanna Vappiani, Bernd Simon, Timothy A. Scott, Eleni Kafkia, Dimitrios Konstantinidis, Katharina Zirngibl, Eleonora Mastrorilli, Manuel Banzhaf, Marie-Therese Mackmull, Felix Hövelmann, Leo Nesme, Ana Rita Brochado, Lisa Maier, Thomas Bock, Vinita Periwal, Manjeet Kumar, Yongkyu Kim, Melanie Tramontano

    Bacteria in the gut can modulate the availability and efficacy of therapeutic drugs. However, the systematic mapping of the interactions between drugs and bacteria has only started recently1 and the main underlying mechanism proposed is the chemical transformation of drugs by microorganisms (biotransformation). Here we investigated the depletion of 15 structurally diverse drugs by 25 representative

  •   Single-cell Ribo-seq reveals cell cycle-dependent translational pausing
    Nature (IF 49.962) Pub Date : 2021-09-08
    Michael VanInsberghe, Jeroen van den Berg, Amanda Andersson-Rolf, Hans Clevers, Alexander van Oudenaarden

    Single-cell sequencing methods have enabled in-depth analysis of the diversity of cell types and cell states in a wide range of organisms. These tools focus predominantly on sequencing the genomes1, epigenomes2 and transcriptomes3 of single cells. However, despite recent progress in detecting proteins by mass spectrometry with single-cell resolution4, it remains a major challenge to measure translation

  •   SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion
    Nature (IF 49.962) Pub Date : 2021-09-06
    Petra Mlcochova, Steven Kemp, Mahesh Shanker Dhar, Guido Papa, Bo Meng, Isabella A. T. M. Ferreira, Rawlings Datir, Dami A. Collier, Anna Albecka, Sujeet Singh, Rajesh Pandey, Jonathan Brown, Jie Zhou, Niluka Goonawardane, Swapnil Mishra, Charles Whittaker, Thomas Mellan, Robin Marwal, Meena Datta, Shantanu Sengupta, Kalaiarasan Ponnusamy, Venkatraman Srinivasan Radhakrishnan, Adam Abdullahi, Oscar

    The SARS-CoV-2 B.1.617.2 (Delta) variant was first identified in the state of Maharashtra in late 2020 and spread throughout India, outcompeting pre-existing lineages including B.1.617.1 (Kappa) and B.1.1.7 (Alpha)1. In vitro, B.1.617.2 is 6-fold less sensitive to serum neutralising antibodies from recovered individuals, and 8-fold less sensitive to vaccine-elicited antibodies as compared to wild type

  •   Programmable RNA targeting with the single-protein CRISPR effector Cas7-11
    Nature (IF 49.962) Pub Date : 2021-09-06
    Ahsen Özcan, Rohan Krajeski, Eleonora Ioannidi, Brennan Lee, Apolonia Gardner, Kira S. Makarova, Eugene V. Koonin, Omar O. Abudayyeh, Jonathan S. Gootenberg

    CRISPR–Cas interference is mediated by Cas effector nucleases that are either components of multisubunit complexes—in class 1 CRISPR–Cas systems—or domains of a single protein—in class 2 systems1,2,3. Here we show that the subtype III-E effector Cas7-11 is a single-protein effector in the class 1 CRISPR–Cas systems originating from the fusion of a putative Cas11 domain and multiple Cas7 subunits that

  •   How deregulation, drought and increasing fire impact Amazonian biodiversity
    Nature (IF 49.962) Pub Date : 2021-09-01
    Xiao Feng, Cory Merow, Zhihua Liu, Daniel S. Park, Patrick R. Roehrdanz, Brian Maitner, Erica A. Newman, Brad L. Boyle, Aaron Lien, Joseph R. Burger, Mathias M. Pires, Paulo M. Brando, Mark B. Bush, Crystal N. H. McMichael, Danilo M. Neves, Efthymios I. Nikolopoulos, Scott R. Saleska, Lee Hannah, David D. Breshears, Tom P. Evans, José R. Soto, Kacey C. Ernst, Brian J. Enquist

    Biodiversity contributes to the ecological and climatic stability of the Amazon Basin1,2, but is increasingly threatened by deforestation and fire3,4. Here we quantify these impacts over the past two decades using remote-sensing estimates of fire and deforestation and comprehensive range estimates of 11,514 plant species and 3,079 vertebrate species in the Amazon. Deforestation has led to large amounts

  •   The polar oxy-metabolome reveals the 4-hydroxymandelate CoQ10 synthesis pathway
    Nature (IF 49.962) Pub Date : 2021-09-01
    Robert S. Banh, Esther S. Kim, Quentin Spillier, Douglas E. Biancur, Keisuke Yamamoto, Albert S. W. Sohn, Guangbin Shi, Drew R. Jones, Alec C. Kimmelman, Michael E. Pacold

    Oxygen is critical for a multitude of metabolic processes that are essential for human life. Biological processes can be identified by treating cells with 18O2 or other isotopically labelled gases and systematically identifying biomolecules incorporating labeled atoms. Here we labelled cell lines of distinct tissue origins with 18O2 to identify the polar oxy-metabolome, defined as polar metabolites labelled

  •   Superconductivity in rhombohedral trilayer graphene
    Nature (IF 49.962) Pub Date : 2021-09-01
    Haoxin Zhou, Tian Xie, Takashi Taniguchi, Kenji Watanabe, Andrea F. Young

    Accessing superconductivity via the electric field-effect in a clean, two-dimensional device is a central goal of nanoelectronics. Recently, superconductivity has been realized in graphene moiré heterostructures1–4, however, many of these structures are not mechanically stable, and experiments show signatures of strong disorder. Here we report the observation of superconductivity—manifesting as low-

  •   Half and quarter metals in rhombohedral trilayer graphene
    Nature (IF 49.962) Pub Date : 2021-09-01
    Haoxin Zhou, Tian Xie, Areg Ghazaryan, Tobias Holder, James R. Ehrets, Eric M. Spanton, Takashi Taniguchi, Kenji Watanabe, Erez Berg, Maksym Serbyn, Andrea F. Young

    Ferromagnetism is most common in transition metal compounds where electrons occupy highly localized d-orbitals. However, ferromagnetic order may also arise in low-density two-dimensional electron systems1–5. Here we show that gate-tuned van Hove singularities in rhombohedral trilayer graphene6 drive spontaneous ferromagnetic polarization of the electron system into one or more spin- and valley flavors

  •   Decision trees within a molecular memristor
    Nature (IF 49.962) Pub Date : 2021-09-01
    Sreetosh Goswami, Rajib Pramanick, Abhijeet Patra, Santi Prasad Rath, Martin Foltin, A. Ariando, Damien Thompson, T. Venkatesan, Sreebrata Goswami, R. Stanley Williams

    Profuse dendritic-synaptic interconnections among neurons in the neocortex embed intricate logic structures enabling sophisticated decision-making that vastly outperforms any artificial electronic analogues1,2,3. The physical complexity is far beyond existing circuit fabrication technologies: moreover, the network in a brain is dynamically reconfigurable, which provides flexibility and adaptability

  •   AIM2 forms a complex with pyrin and ZBP1 to drive PANoptosis and host defence
    Nature (IF 49.962) Pub Date : 2021-09-01
    SangJoon Lee, Rajendra Karki, Yaqiu Wang, Lam Nhat Nguyen, Ravi C. Kalathur, Thirumala-Devi Kanneganti

    Inflammasomes are important sentinels of innate immune defence, sensing pathogens and inducing cell death in infected cells1. There are several inflammasome sensors that each detect and respond to a specific pathogen- or damage-associated molecular pattern (PAMP or DAMP, respectively)1. During infection, live pathogens can induce the release of multiple PAMPs and DAMPs, which can simultaneously engage

  •   Scalable production of high-performing woven lithium-ion fibre batteries
    Nature (IF 49.962) Pub Date : 2021-09-01
    Jiqing He, Chenhao Lu, Haibo Jiang, Fei Han, Xiang Shi, Jingxia Wu, Liyuan Wang, Taiqiang Chen, Jiajia Wang, Ye Zhang, Han Yang, Guoqi Zhang, Xuemei Sun, Bingjie Wang, Peining Chen, Yonggang Wang, Yongyao Xia, Huisheng Peng

    Fibre lithium-ion batteries are attractive as flexible power solutions because they can be woven into textiles, offering a convenient way to power future wearable electronics1,2,3,4. However, they are difficult to produce in lengths of more than a few centimetres, and longer fibres were thought to have higher internal resistances3,5 that compromised electrochemical performance6,7. Here we show that

  •   Structure of Geobacter pili reveals secretory rather than nanowire behaviour
    Nature (IF 49.962) Pub Date : 2021-09-01
    Yangqi Gu, Vishok Srikanth, Aldo I. Salazar-Morales, Ruchi Jain, J. Patrick O’Brien, Sophia M. Yi, Rajesh Kumar Soni, Fadel A. Samatey, Sibel Ebru Yalcin, Nikhil S. Malvankar

    Extracellular electron transfer by Geobacter species through surface appendages known as microbial nanowires1 is important in a range of globally important environmental phenomena2, as well as for applications in bio-remediation, bioenergy, biofuels and bioelectronics. Since 2005, these nanowires have been thought to be type 4 pili composed solely of the PilA-N protein1. However, previous structural

  •   Emergent hydrodynamics in a strongly interacting dipolar spin ensemble
    Nature (IF 49.962) Pub Date : 2021-09-01
    C. Zu, F. Machado, B. Ye, S. Choi, B. Kobrin, T. Mittiga, S. Hsieh, P. Bhattacharyya, M. Markham, D. Twitchen, A. Jarmola, D. Budker, C. R. Laumann, J. E. Moore, N. Y. Yao

    Conventional wisdom holds that macroscopic classical phenomena naturally emerge from microscopic quantum laws1,2,3,4,5,6,7. However, despite this mantra, building direct connections between these two descriptions has remained an enduring scientific challenge. In particular, it is difficult to quantitatively predict the emergent ‘classical’ properties of a system (for example, diffusivity, viscosity

  •   Measuring the density structure of an accretion hot spot
    Nature (IF 49.962) Pub Date : 2021-09-01
    C. C. Espaillat, C. E. Robinson, M. M. Romanova, T. Thanathibodee, J. Wendeborn, N. Calvet, M. Reynolds, J. Muzerolle

    Magnetospheric accretion models predict that matter from protoplanetary disks accretes onto stars via funnel flows, which follow stellar magnetic field lines and shock on the stellar surfaces1,2,3, leaving hot spots with density gradients4,5,6. Previous work has provided observational evidence of varying density in hot spots7, but these observations were not sensitive to the radial density distribution

  •   Enantioselective synthesis of ammonium cations
    Nature (IF 49.962) Pub Date : 2021-09-01
    Mark P. Walsh, Joseph M. Phelps, Marc E. Lennon, Dmitry S. Yufit, Matthew O. Kitching

    Control of molecular chirality is a fundamental challenge in organic synthesis. Whereas methods to construct carbon stereocentres enantioselectively are well established, routes to synthesize enriched heteroatomic stereocentres have garnered less attention1,2,3,4,5. Of those atoms commonly present in organic molecules, nitrogen is the most difficult to control stereochemically. Although a limited number

  •   Functional HPV-specific PD-1+ stem-like CD8 T cells in head and neck cancer
    Nature (IF 49.962) Pub Date : 2021-09-01
    Christiane S. Eberhardt, Haydn T. Kissick, Mihir R. Patel, Maria A. Cardenas, Nataliya Prokhnevska, Rebecca C. Obeng, Tahseen H. Nasti, Christopher C. Griffith, Se Jin Im, Xu Wang, Dong M. Shin, Mary Carrington, Zhuo G. Chen, John Sidney, Alessandro Sette, Nabil F. Saba, Andreas Wieland, Rafi Ahmed

    T cells are important in tumour immunity but a better understanding is needed of the differentiation of antigen-specific T cells in human cancer1,2. Here we studied CD8 T cells in patients with human papillomavirus (HPV)-positive head and neck cancer and identified several epitopes derived from HPV E2, E5 and E6 proteins that allowed us to analyse virus-specific CD8 T cells using major histocompatibility

  •   RecA finds homologous DNA by reduced dimensionality search
    Nature (IF 49.962) Pub Date : 2021-09-01
    Jakub Wiktor, Arvid H. Gynnå, Prune Leroy, Jimmy Larsson, Giovanna Coceano, Ilaria Testa, Johan Elf

    Homologous recombination is essential for the accurate repair of double-stranded DNA breaks (DSBs)1. Initially, the RecBCD complex2 resects the ends of the DSB into 3′ single-stranded DNA on which a RecA filament assembles3. Next, the filament locates the homologous repair template on the sister chromosome4. Here we directly visualize the repair of DSBs in single cells, using high-throughput microfluidics

  •   Structural basis for piRNA targeting
    Nature (IF 49.962) Pub Date : 2021-09-01
    Todd A. Anzelon, Saikat Chowdhury, Siobhan M. Hughes, Yao Xiao, Gabriel C. Lander, Ian J. MacRae

    PIWI proteins use PIWI-interacting RNAs (piRNAs) to identify and silence transposable elements and thereby maintain genome integrity between metazoan generations1. The targeting of transposable elements by PIWI has been compared to mRNA target recognition by Argonaute proteins2,3, which use microRNA (miRNA) guides, but the extent to which piRNAs resemble miRNAs is not known. Here we present cryo-electron

  •   The contribution of insects to global forest deadwood decomposition
    Nature (IF 49.962) Pub Date : 2021-09-01
    Sebastian Seibold, Werner Rammer, Torsten Hothorn, Rupert Seidl, Michael D. Ulyshen, Janina Lorz, Marc W. Cadotte, David B. Lindenmayer, Yagya P. Adhikari, Roxana Aragón, Soyeon Bae, Petr Baldrian, Hassan Barimani Varandi, Jos Barlow, Claus Bässler, Jacques Beauchêne, Erika Berenguer, Rodrigo S. Bergamin, Tone Birkemoe, Gergely Boros, Roland Brandl, Hervé Brustel, Philip J. Burton, Yvonne T. Cakpo-Tossou

    The amount of carbon stored in deadwood is equivalent to about 8 per cent of the global forest carbon stocks1. The decomposition of deadwood is largely governed by climate2,3,4,5 with decomposer groups—such as microorganisms and insects—contributing to variations in the decomposition rates2,6,7. At the global scale, the contribution of insects to the decomposition of deadwood and carbon release remains

  •   Multiple hominin dispersals into Southwest Asia over the past 400,000 years
    Nature (IF 49.962) Pub Date : 2021-09-01
    Huw S. Groucutt, Tom S. White, Eleanor M. L. Scerri, Eric Andrieux, Richard Clark-Wilson, Paul S. Breeze, Simon J. Armitage, Mathew Stewart, Nick Drake, Julien Louys, Gilbert J. Price, Mathieu Duval, Ash Parton, Ian Candy, W. Christopher Carleton, Ceri Shipton, Richard P. Jennings, Muhammad Zahir, James Blinkhorn, Simon Blockley, Abdulaziz Al-Omari, Abdullah M. Alsharekh, Michael D. Petraglia

    Pleistocene hominin dispersals out of, and back into, Africa necessarily involved traversing the diverse and often challenging environments of Southwest Asia1,2,3,4. Archaeological and palaeontological records from the Levantine woodland zone document major biological and cultural shifts, such as alternating occupations by Homo sapiens and Neanderthals. However, Late Quaternary cultural, biological

  •   Lectins enhance SARS-CoV-2 infection and influence neutralizing antibodies
    Nature (IF 49.962) Pub Date : 2021-08-31
    Florian A. Lempp, Leah Soriaga, Martin Montiel-Ruiz, Fabio Benigni, Julia Noack, Young-Jun Park, Siro Bianchi, Alexandra C. Walls, John E. Bowen, Jiayi Zhou, Hannah Kaiser, Anshu Joshi, Maria Agostini, Marcel Meury, Exequiel Dellota, Stefano Jaconi, Elisabetta Cameroni, Javier Martinez-Picado, Júlia Vergara-Alert, Nuria Izquierdo-Useros, Herbert W. Virgin, Antonio Lanzavecchia, David Veesler, Lisa

    SARS-CoV-2 infection, which involves both cell attachment and membrane fusion, relies on the ACE2 receptor that is paradoxically found at low levels in the respiratory tract1–3, suggesting that additional mechanisms facilitating infection may exist. Here we show that C-type lectin receptors, DC-SIGN, L-SIGN and the sialic acid-binding Ig-like lectin 1 (SIGLEC1) function as attachment receptors by enhancing

  •   Metallaphotoredox-enabled deoxygenative arylation of alcohols
    Nature (IF 49.962) Pub Date : 2021-08-31
    Zhe Dong, David W. C. MacMillan

    Metal-catalysed cross-couplings are a mainstay of organic synthesis and are widely used for the formation of C-C bonds, particularly in the production of unsaturated scaffolds1. However, alkyl cross-couplings using native sp3-hybridized functional groups such as alcohols remain relatively underdeveloped2. In particular, a robust and general method for the direct deoxygenative coupling of alcohols would

  •   Burden and characteristics of COVID-19 in the United States during 2020
    Nature (IF 49.962) Pub Date : 2021-08-26
    Sen Pei, Teresa K. Yamana, Sasikiran Kandula, Marta Galanti, Jeffrey Shaman

    The COVID-19 pandemic disrupted health systems and economies throughout the world during 2020 and was particularly devastating for the United States, which experienced the highest numbers of reported cases and deaths during 20201–3. Many of the epidemiological features responsible for observed rates of morbidity and mortality have been reported4–8; however, the overall burden and characteristics of

  •   Photocatalytic solar hydrogen production from water on a 100 m2-scale
    Nature (IF 49.962) Pub Date : 2021-08-25
    Hiroshi Nishiyama, Taro Yamada, Mamiko Nakabayashi, Yoshiki Maehara, Masaharu Yamaguchi, Yasuko Kuromiya, Hiromasa Tokudome, Seiji Akiyama, Tomoaki Watanabe, Ryoichi Narushima, Sayuri Okunaka, Naoya Shibata, Tsuyoshi Takata, Takashi Hisatomi, Kazunari Domen

    The unprecedented impact of human activity on Earth’s climate and the ongoing increase in global energy demand have made the development of carbon-neutral energy sources ever more important. Hydrogen is an attractive and versatile energy carrier (and important and widely used chemical) obtainable from water through photocatalysis using sunlight, and through electrolysis driven by solar or wind energy1

  •   Extensive phylogenies of human development inferred from somatic mutations
    Nature (IF 49.962) Pub Date : 2021-08-25
    Tim H. H. Coorens, Luiza Moore, Philip S. Robinson, Rashesh Sanghvi, Joseph Christopher, James Hewinson, Moritz J. Przybilla, Andrew R. J. Lawson, Michael Spencer Chapman, Alex Cagan, Thomas R. W. Oliver, Matthew D. C. Neville, Yvette Hooks, Ayesha Noorani, Thomas J. Mitchell, Rebecca C. Fitzgerald, Peter J. Campbell, Iñigo Martincorena, Raheleh Rahbari, Michael R. Stratton

    Starting from the zygote, all cells in the human body continuously acquire mutations. Mutations shared between different cells imply a common progenitor and are thus naturally occurring markers for lineage tracing1,2. Here we reconstruct extensive phylogenies of normal tissues from three adult individuals using whole-genome sequencing of 511 laser capture microdissections. Reconstructed embryonic progenitors

  •   Universal pair polaritons in a strongly interacting Fermi gas
    Nature (IF 49.962) Pub Date : 2021-08-25
    Hideki Konishi, Kevin Roux, Victor Helson, Jean-Philippe Brantut

    Cavity quantum electrodynamics (QED) manipulates the coupling of light with matter, and allows several emitters to couple coherently with one light mode1. However, even in a many-body system, the light–matter coupling mechanism has so far been restricted to one-body processes. Leveraging cavity QED for the quantum simulation of complex, many-body systems has thus far relied on multi-photon processes

  •   Hypothalamic dopamine neurons motivate mating through persistent cAMP signalling
    Nature (IF 49.962) Pub Date : 2021-08-25
    Stephen X. Zhang, Andrew Lutas, Shang Yang, Adriana Diaz, Hugo Fluhr, Georg Nagel, Shiqiang Gao, Mark L. Andermann

    Transient neuromodulation can have long-lasting effects on neural circuits and motivational states1,2,3,4. Here we examine the dopaminergic mechanisms that underlie mating drive and its persistence in male mice. Brief investigation of females primes a male’s interest to mate for tens of minutes, whereas a single successful mating triggers satiety that gradually recovers over days5. We found that both

  •   Single-crystal, large-area, fold-free monolayer graphene
    Nature (IF 49.962) Pub Date : 2021-08-25
    Meihui Wang, Ming Huang, Da Luo, Yunqing Li, Myeonggi Choe, Won Kyung Seong, Minhyeok Kim, Sunghwan Jin, Mengran Wang, Shahana Chatterjee, Youngwoo Kwon, Zonghoon Lee, Rodney S. Ruoff

    Chemical vapour deposition of carbon-containing precursors on metal substrates is currently the most promising route for the scalable synthesis of large-area, high-quality graphene films1. However, there are usually some imperfections present in the resulting films: grain boundaries, regions with additional layers (adlayers), and wrinkles or folds, all of which can degrade the performance of graphene

  •   Clonal dynamics in early human embryogenesis inferred from somatic mutation
    Nature (IF 49.962) Pub Date : 2021-08-25
    Seongyeol Park, Nanda Maya Mali, Ryul Kim, Jeong-Woo Choi, Junehawk Lee, Joonoh Lim, Jung Min Park, Jung Woo Park, Donghyun Kim, Taewoo Kim, Kijong Yi, June Hyug Choi, Seong Gyu Kwon, Joo Hee Hong, Jeonghwan Youk, Yohan An, Su Yeon Kim, Soo A Oh, Youngoh Kwon, Dongwan Hong, Moonkyu Kim, Dong Sun Kim, Ji Young Park, Ji Won Oh, Young Seok Ju

    Cellular dynamics and fate decision in early human embryogenesis remain largely unknown owing to the challenges of performing studies in human embryos1. Here, we explored whole-genomes of 334 single-cell colonies and targeted deep sequences of 379 bulk tissues obtained from various anatomical locations of seven recently deceased adult human donors. Using somatic mutations as an intrinsic barcode, we

  •   Direct observation of ultrafast hydrogen bond strengthening in liquid water
    Nature (IF 49.962) Pub Date : 2021-08-25
    Jie Yang, Riccardo Dettori, J. Pedro F. Nunes, Nanna H. List, Elisa Biasin, Martin Centurion, Zhijiang Chen, Amy A. Cordones, Daniel P. Deponte, Tony F. Heinz, Michael E. Kozina, Kathryn Ledbetter, Ming-Fu Lin, Aaron M. Lindenberg, Mianzhen Mo, Anders Nilsson, Xiaozhe Shen, Thomas J. A. Wolf, Davide Donadio, Kelly J. Gaffney, Todd J. Martinez, Xijie Wang

    Water is one of the most important, yet least understood, liquids in nature. Many anomalous properties of liquid water originate from its well-connected hydrogen bond network1, including unusually efficient vibrational energy redistribution and relaxation2. An accurate description of the ultrafast vibrational motion of water molecules is essential for understanding the nature of hydrogen bonds and

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