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  • A rooted phylogeny resolves early bacterial evolution
    Science (IF 41.845) Pub Date : 2021-05-07
    Gareth A. Coleman, Adrián A. Davín, Tara A. Mahendrarajah, Lénárd L. Szánthó, Anja Spang, Philip Hugenholtz, Gergely J. Szöllősi, Tom A. Williams

    A rooted bacterial tree is necessary to understand early evolution, but the position of the root is contested. Here, we model the evolution of 11,272 gene families to identify the root, extent of horizontal gene transfer (HGT), and the nature of the last bacterial common ancestor (LBCA). Our analyses root the tree between the major clades Terrabacteria and Gracilicutes and suggest that LBCA was a free-living

  • Sex chromosome transformation and the origin of a male-specific X chromosome in the creeping vole
    Science (IF 41.845) Pub Date : 2021-05-07
    Matthew B. Couger, Scott W. Roy, Noelle Anderson, Landen Gozashti, Stacy Pirro, Lindsay S. Millward, Michelle Kim, Duncan Kilburn, Kelvin J. Liu, Todd M. Wilson, Clinton W. Epps, Laurie Dizney, Luis A. Ruedas, Polly Campbell

    The mammalian sex chromosome system (XX female/XY male) is ancient and highly conserved. The sex chromosome karyotype of the creeping vole (Microtus oregoni) represents a long-standing anomaly, with an X chromosome that is unpaired in females (X0) and exclusively maternally transmitted. We produced a highly contiguous male genome assembly, together with short-read genomes and transcriptomes for both

  • The early origin of a birdlike inner ear and the evolution of dinosaurian movement and vocalization
    Science (IF 41.845) Pub Date : 2021-05-07
    Michael Hanson, Eva A. Hoffman, Mark A. Norell, Bhart-Anjan S. Bhullar

    Reptiles, including birds, exhibit a range of behaviorally relevant adaptations that are reflected in changes to the structure of the inner ear. These adaptations include the capacity for flight and sensitivity to high-frequency sound. We used three-dimensional morphometric analyses of a large sample of extant and extinct reptiles to investigate inner ear correlates of locomotor ability and hearing

  • Evolution of vision and hearing modalities in theropod dinosaurs
    Science (IF 41.845) Pub Date : 2021-05-07
    Jonah N. Choiniere, James M. Neenan, Lars Schmitz, David P. Ford, Kimberley E. J. Chapelle, Amy M. Balanoff, Justin S. Sipla, Justin A. Georgi, Stig A. Walsh, Mark A. Norell, Xing Xu, James M. Clark, Roger B. J. Benson

    Owls and nightbirds are nocturnal hunters of active prey that combine visual and hearing adaptations to overcome limits on sensory performance in low light. Such sensory innovations are unknown in nonavialan theropod dinosaurs and are poorly characterized on the line that leads to birds. We investigate morphofunctional proxies of vision and hearing in living and extinct theropods and demonstrate deep

  • Reversible fusion and fission of graphene oxide–based fibers
    Science (IF 41.845) Pub Date : 2021-05-07
    Dan Chang, Jingran Liu, Bo Fang, Zhen Xu, Zheng Li, Yilun Liu, Laurence Brassart, Fan Guo, Weiwei Gao, Chao Gao

    Stimuli-responsive fusion and fission are widely observed in both bio-organizations and artificial molecular assemblies. However, the design of a system with structure and property persistence during repeated fusion and fission remains challenging. We show reversible fusion and fission of wet-spun graphene oxide (GO) fibers, in which a number of macroscopic fibers can fuse into a thicker one and can

  • Interfacial toughening with self-assembled monolayers enhances perovskite solar cell reliability
    Science (IF 41.845) Pub Date : 2021-05-07
    Zhenghong Dai, Srinivas K. Yadavalli, Min Chen, Ali Abbaspourtamijani, Yue Qi, Nitin P. Padture

    Iodine-terminated self-assembled monolayer (I-SAM) was used in perovskite solar cells (PSCs) to achieve a 50% increase of adhesion toughness at the interface between the electron transport layer (ETL) and the halide perovskite thin film to enhance mechanical reliability. Treatment with I-SAM also increased the power conversion efficiency from 20.2% to 21.4%, reduced hysteresis, and improved operational

  • Direct observation of deterministic macroscopic entanglement
    Science (IF 41.845) Pub Date : 2021-05-07
    Shlomi Kotler, Gabriel A. Peterson, Ezad Shojaee, Florent Lecocq, Katarina Cicak, Alex Kwiatkowski, Shawn Geller, Scott Glancy, Emanuel Knill, Raymond W. Simmonds, José Aumentado, John D. Teufel

    Quantum entanglement of mechanical systems emerges when distinct objects move with such a high degree of correlation that they can no longer be described separately. Although quantum mechanics presumably applies to objects of all sizes, directly observing entanglement becomes challenging as masses increase, requiring measurement and control with a vanishingly small error. Here, using pulsed electromechanics

  • Quantum mechanics–free subsystem with mechanical oscillators
    Science (IF 41.845) Pub Date : 2021-05-07
    Laure Mercier de Lépinay, Caspar F. Ockeloen-Korppi, Matthew J. Woolley, Mika A. Sillanpää

    Quantum mechanics sets a limit for the precision of continuous measurement of the position of an oscillator. We show how it is possible to measure an oscillator without quantum back-action of the measurement by constructing one effective oscillator from two physical oscillators. We realize such a quantum mechanics–free subsystem using two micromechanical oscillators, and show the measurements of two

  • Reversible oxygen migration and phase transitions in hafnia-based ferroelectric devices
    Science (IF 41.845) Pub Date : 2021-05-07
    Pavan Nukala, Majid Ahmadi, Yingfen Wei, Sytze de Graaf, Evgenios Stylianidis, Tuhin Chakrabortty, Sylvia Matzen, Henny W. Zandbergen, Alexander Björling, Dan Mannix, Dina Carbone, Bart Kooi, Beatriz Noheda

    Unconventional ferroelectricity exhibited by hafnia-based thin films—robust at nanoscale sizes—presents tremendous opportunities in nanoelectronics. However, the exact nature of polarization switching remains controversial. We investigated a La0.67Sr0.33MnO3/Hf0.5Zr0.5O2 capacitor interfaced with various top electrodes while performing in situ electrical biasing using atomic-resolution microscopy with

  • The impact of population-wide rapid antigen testing on SARS-CoV-2 prevalence in Slovakia
    Science (IF 41.845) Pub Date : 2021-05-07
    Martin Pavelka, Kevin Van-Zandvoort, Sam Abbott, Katharine Sherratt, Marek Majdan, CMMID COVID-19 working group†, Inštitút Zdravotných Analýz†, Pavol Jarčuška, Marek Krajčí, Stefan Flasche, Sebastian Funk

    Slovakia conducted multiple rounds of population-wide rapid antigen testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in late 2020, combined with a period of additional contact restrictions. Observed prevalence decreased by 58% (95% confidence interval: 57 to 58%) within 1 week in the 45 counties that were subject to two rounds of mass testing, an estimate that remained robust

  • X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease
    Science (IF 41.845) Pub Date : 2021-05-07
    Sebastian Günther, Patrick Y. A. Reinke, Yaiza Fernández-García, Julia Lieske, Thomas J. Lane, Helen M. Ginn, Faisal H. M. Koua, Christiane Ehrt, Wiebke Ewert, Dominik Oberthuer, Oleksandr Yefanov, Susanne Meier, Kristina Lorenzen, Boris Krichel, Janine-Denise Kopicki, Luca Gelisio, Wolfgang Brehm, Ilona Dunkel, Brandon Seychell, Henry Gieseler, Brenna Norton-Baker, Beatriz Escudero-Pérez, Martin Domaracky

    The coronavirus disease (COVID-19) caused by SARS-CoV-2 is creating tremendous human suffering. To date, no effective drug is available to directly treat the disease. In a search for a drug against COVID-19, we have performed a high-throughput x-ray crystallographic screen of two repurposing drug libraries against the SARS-CoV-2 main protease (Mpro), which is essential for viral replication. In contrast

  • Extreme altitudes during diurnal flights in a nocturnal songbird migrant
    Science (IF 41.845) Pub Date : 2021-05-07
    Sissel Sjöberg, Gintaras Malmiga, Andreas Nord, Arne Andersson, Johan Bäckman, Maja Tarka, Mikkel Willemoes, Kasper Thorup, Bengt Hansson, Thomas Alerstam, Dennis Hasselquist

    Billions of nocturnally migrating songbirds fly across oceans and deserts on their annual journeys. Using multisensor data loggers, we show that great reed warblers (Acrocephalus arundinaceus) regularly prolong their otherwise strictly nocturnal flights into daytime when crossing the Mediterranean Sea and the Sahara Desert. Unexpectedly, when prolonging their flights, they climbed steeply at dawn,

  • Unearthing Neanderthal population history using nuclear and mitochondrial DNA from cave sediments
    Science (IF 41.845) Pub Date : 2021-05-07
    Benjamin Vernot, Elena I. Zavala, Asier Gómez-Olivencia, Zenobia Jacobs, Viviane Slon, Fabrizio Mafessoni, Frédéric Romagné, Alice Pearson, Martin Petr, Nohemi Sala, Adrián Pablos, Arantza Aranburu, José María Bermúdez de Castro, Eudald Carbonell, Bo Li, Maciej T. Krajcarz, Andrey I. Krivoshapkin, Kseniya A. Kolobova, Maxim B. Kozlikin, Michael V. Shunkov, Anatoly P. Derevianko, Bence Viola, Steffi

    Bones and teeth are important sources of Pleistocene hominin DNA, but are rarely recovered at archaeological sites. Mitochondrial DNA (mtDNA) has been retrieved from cave sediments but provides limited value for studying population relationships. We therefore developed methods for the enrichment and analysis of nuclear DNA from sediments and applied them to cave deposits in western Europe and southern

  • Fossil apes and human evolution
    Science (IF 41.845) Pub Date : 2021-05-07
    Sergio Almécija, Ashley S. Hammond, Nathan E. Thompson, Kelsey D. Pugh, Salvador Moyà-Solà, David M. Alba

    Humans diverged from apes (chimpanzees, specifically) toward the end of the Miocene ~9.3 million to 6.5 million years ago. Understanding the origins of the human lineage (hominins) requires reconstructing the morphology, behavior, and environment of the chimpanzee-human last common ancestor. Modern hominoids (that is, humans and apes) share multiple features (for example, an orthograde body plan facilitating

  • The coding and long noncoding single-cell atlas of the developing human fetal striatum
    Science (IF 41.845) Pub Date : 2021-05-07
    Vittoria Dickinson Bocchi, Paola Conforti, Elena Vezzoli, Dario Besusso, Claudio Cappadona, Tiziana Lischetti, Maura Galimberti, Valeria Ranzani, Raoul J. P. Bonnal, Marco De Simone, Grazisa Rossetti, Xiaoling He, Kenji Kamimoto, Ira Espuny-Camacho, Andrea Faedo, Federica Gervasoni, Romina Vuono, Samantha A. Morris, Jian Chen, Dan Felsenfeld, Giulio Pavesi, Roger A. Barker, Massimiliano Pagani, Elena

    Deciphering how the human striatum develops is necessary for understanding the diseases that affect this region. To decode the transcriptional modules that regulate this structure during development, we compiled a catalog of 1116 long intergenic noncoding RNAs (lincRNAs) identified de novo and then profiled 96,789 single cells from the early human fetal striatum. We found that D1 and D2 medium spiny

  • Environmental robustness of the global yeast genetic interaction network
    Science (IF 41.845) Pub Date : 2021-05-07
    Michael Costanzo, Jing Hou, Vincent Messier, Justin Nelson, Mahfuzur Rahman, Benjamin VanderSluis, Wen Wang, Carles Pons, Catherine Ross, Matej Ušaj, Bryan-Joseph San Luis, Emira Shuteriqi, Elizabeth N. Koch, Patrick Aloy, Chad L. Myers, Charles Boone, Brenda Andrews

    Phenotypes associated with genetic variants can be altered by interactions with other genetic variants (GxG), with the environment (GxE), or both (GxGxE). Yeast genetic interactions have been mapped on a global scale, but the environmental influence on the plasticity of genetic networks has not been examined systematically. To assess environmental rewiring of genetic networks, we examined 14 diverse

  • Role of the ionic environment in enhancing the activity of reacting molecules in zeolite pores
    Science (IF 41.845) Pub Date : 2021-05-06
    Niklas Pfriem, Peter H. Hintermeier, Sebastian Eckstein, Sungmin Kim, Qiang Liu, Hui Shi, Lara Milakovic, Yuanshuai Liu, Gary L. Haller, Eszter Baráth, Yue Liu, Johannes A. Lercher

    Tailoring the molecular environment around catalytically active site allows to enhance catalytic reactivity via a hitherto unexplored pathway. In zeolites, the presence of water creates an ionic environment via formation of hydrated hydronium ions and the negatively charged framework Al tetrahedra. The high density of cation-anion pairs determined by the aluminum concentration of a zeolite induces

  • Quantum walks on a programmable two-dimensional 62-qubit superconducting processor
    Science (IF 41.845) Pub Date : 2021-05-06
    Ming Gong, Shiyu Wang, Chen Zha, Ming-Cheng Chen, He-Liang Huang, Yulin Wu, Qingling Zhu, Youwei Zhao, Shaowei Li, Shaojun Guo, Haoran Qian, Yangsen Ye, Fusheng Chen, Chong Ying, Jiale Yu, Daojin Fan, Dachao Wu, Hong Su, Hui Deng, Hao Rong, Kaili Zhang, Sirui Cao, Jin Lin, Yu Xu, Lihua Sun, Cheng Guo, Na Li, Futian Liang, V. M. Bastidas, Kae Nemoto, W. J. Munro, Yong-Heng Huo, Chao-Yang Lu, Cheng-Zhi

    Quantum walks are the quantum mechanical analog of classical random walks and an extremely powerful tool in quantum simulations, quantum search algorithms, and even for universal quantum computing. In our work, we have designed and fabricated an 8x8 two-dimensional square superconducting qubit array composed of 62 functional qubits. We used this device to demonstrate high fidelity single and two particle

  • Structures of the human Mediator and Mediator-bound preinitiation complex
    Science (IF 41.845) Pub Date : 2021-05-06
    Xizi Chen, Xiaotong Yin, Jiabei Li, Zihan Wu, Yilun Qi, Xinxin Wang, Weida Liu, Yanhui Xu

    The 1.3-MDa transcription factor IID (TFIID) is required for preinitiation complex (PIC) assembly and RNA polymerase II (Pol II)-mediated transcription initiation on almost all genes. The 26-subunit Mediator stimulates transcription and cyclin-dependent kinase 7 (CDK7)-mediated phosphorylation of Pol II C-terminal domain (CTD). We determined the structures of human Mediator in the Tail module-extended

  • Socioeconomic status determines COVID-19 incidence and related mortality in Santiago, Chile
    Science (IF 41.845) Pub Date : 2021-05-04
    Gonzalo E. Mena, Pamela P. Martinez, Ayesha S. Mahmud, Pablo A. Marquet, Caroline O. Buckee, Mauricio Santillana

    The current COVID-19 pandemic has impacted cities particularly hard. Here, we provide an in-depth characterization of disease incidence and mortality, and their dependence on demographic and socioeconomic strata in Santiago, a highly segregated city and the capital of Chile. Our analyses show a strong association between socioeconomic status and both COVID-19 outcomes and public health capacity. People

  • Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes
    Science (IF 41.845) Pub Date : 2021-05-04
    William N. Voss, Yixuan J. Hou, Nicole V. Johnson, George Delidakis, Jin Eyun Kim, Kamyab Javanmardi, Andrew P. Horton, Foteini Bartzoka, Chelsea J. Paresi, Yuri Tanno, Chia-Wei Chou, Shawn A. Abbasi, Whitney Pickens, Katia George, Daniel R. Boutz, Dalton M. Towers, Jonathan R. McDaniel, Daniel Billick, Jule Goike, Lori Rowe, Dhwani Batra, Jan Pohl, Justin Lee, Shivaprakash Gangappa, Suryaprakash Sambhara

    The molecular composition and binding epitopes of the immunoglobulin G (IgG) antibodies that circulate in blood plasma following SARS-CoV-2 infection are unknown. Proteomic deconvolution of the IgG repertoire to the spike glycoprotein in convalescent subjects revealed that the response is directed predominantly (>80%) against epitopes residing outside the receptor-binding domain (RBD). In one subject

  • Resurgence of SARS-CoV-2: detection by community viral surveillance
    Science (IF 41.845) Pub Date : 2021-05-03
    Steven Riley, Kylie E. C. Ainslie, Oliver Eales, Caroline E. Walters, Haowei Wang, Christina Atchison, Claudio Fronterre, Peter J. Diggle, Deborah Ashby, Christl A. Donnelly, Graham Cooke, Wendy Barclay, Helen Ward, Ara Darzi, Paul Elliott

    Surveillance of the SARS-CoV-2 epidemic has mainly relied on case reporting which is biased by health service performance, test availability and test-seeking behaviors. We report a community-wide national representative surveillance program in England involving self-administered swab results from 594,000 individuals tested for SARS-CoV-2, regardless of symptoms, from May to beginning of September 2020

  • Prior SARS-CoV-2 infection rescues B and T cell responses to variants after first vaccine dose
    Science (IF 41.845) Pub Date : 2021-04-30
    Catherine J. Reynolds, Corinna Pade, Joseph M. Gibbons, David K. Butler, Ashley D. Otter, Katia Menacho, Marianna Fontana, Angelique Smit, Jane E. Sackville-West, Teresa Cutino-Moguel, Mala K. Maini, Benjamin Chain, Mahdad Noursadeghi, UK COVIDsortium Immune Correlates Network‡, Tim Brooks, Amanda Semper, Charlotte Manisty, Thomas A. Treibel, James C. Moon, UK COVIDsortium Investigators‡, Ana M. Valdes

    SARS-CoV-2 vaccine rollout has coincided with the spread of variants of concern. We investigated if single dose vaccination, with or without prior infection, confers cross protective immunity to variants. We analyzed T and B cell responses after first dose vaccination with the Pfizer/BioNTech mRNA vaccine BNT162b2 in healthcare workers (HCW) followed longitudinally, with or without prior Wuhan-Hu-1

  • Widespread reforestation before European influence on Amazonia
    Science (IF 41.845) Pub Date : 2021-04-30
    M. B. Bush, M. N. Nascimento, C. M. Åkesson, G. M. Cárdenes-Sandí, S. Y. Maezumi, H. Behling, A. Correa-Metrio, W. Church, S. N. Huisman, T. Kelly, F. E. Mayle, C. N. H. McMichael

    An estimated 90 to 95% of Indigenous people in Amazonia died after European contact. This population collapse is postulated to have caused decreases in atmospheric carbon dioxide concentrations at around 1610 CE, as a result of a wave of land abandonment in the wake of disease, slavery, and warfare, whereby the attendant reversion to forest substantially increased terrestrial carbon sequestration.

  • The human dimension of biodiversity changes on islands
    Science (IF 41.845) Pub Date : 2021-04-30
    Sandra Nogué, Ana M. C. Santos, H. John B. Birks, Svante Björck, Alvaro Castilla-Beltrán, Simon Connor, Erik J. de Boer, Lea de Nascimento, Vivian A. Felde, José María Fernández-Palacios, Cynthia A. Froyd, Simon G. Haberle, Henry Hooghiemstra, Karl Ljung, Sietze J. Norder, Josep Peñuelas, Matthew Prebble, Janelle Stevenson, Robert J. Whittaker, Kathy J. Willis, Janet M. Wilmshurst, Manuel J. Steinbauer

    Islands are among the last regions on Earth settled and transformed by human activities, and they provide replicated model systems for analysis of how people affect ecological functions. By analyzing 27 representative fossil pollen sequences encompassing the past 5000 years from islands globally, we quantified the rates of vegetation compositional change before and after human arrival. After human

  • Equids engineer desert water availability
    Science (IF 41.845) Pub Date : 2021-04-30
    Erick J. Lundgren, Daniel Ramp, Juliet C. Stromberg, Jianguo Wu, Nathan C. Nieto, Martin Sluk, Karla T. Moeller, Arian D. Wallach

    Megafauna play important roles in the biosphere, yet little is known about how they shape dryland ecosystems. We report on an overlooked form of ecosystem engineering by donkeys and horses. In the deserts of North America, digging of ≤2-meter wells to groundwater by feral equids increased the density of water features, reduced distances between waters, and, at times, provided the only water present

  • Electric field control of natural optical activity in a multiferroic helimagnet
    Science (IF 41.845) Pub Date : 2021-04-30
    Ryoji Masuda, Yoshio Kaneko, Yoshinori Tokura, Youtarou Takahashi

    Controlling the chiral degree of freedom in matter has long been an important issue for many fields of science. The spin-spiral order, which exhibits a strong magnetoelectric coupling, gives rise to chirality irrespective of the atomic arrangement of matter. Here, we report the resonantly enhanced natural optical activity on the electrically active magnetic excitation, that is, electromagnon, in multiferroic

  • Atomic-scale ion transistor with ultrahigh diffusivity
    Science (IF 41.845) Pub Date : 2021-04-30
    Yahui Xue, Yang Xia, Sui Yang, Yousif Alsaid, King Yan Fong, Yuan Wang, Xiang Zhang

    Biological ion channels rapidly and selectively gate ion transport through atomic-scale filters to maintain vital life functions. We report an atomic-scale ion transistor exhibiting ultrafast and highly selective ion transport controlled by electrical gating in graphene channels around 3 angstroms in height, made from a single flake of reduced graphene oxide. The ion diffusion coefficient reaches two

  • A risk-based approach for managing hydraulic fracturing–induced seismicity
    Science (IF 41.845) Pub Date : 2021-04-30
    Ryan Schultz, Gregory C. Beroza, William L. Ellsworth

    Risks from induced earthquakes are a growing concern that needs effective management. For hydraulic fracturing of the Eagle Ford shale in southern Texas, we developed a risk-informed strategy for choosing red-light thresholds that require immediate well shut-in. We used a combination of datasets to simulate spatially heterogeneous nuisance and damage impacts. Simulated impacts are greater in the northeast

  • Parity-preserving and magnetic field–resilient superconductivity in InSb nanowires with Sn shells
    Science (IF 41.845) Pub Date : 2021-04-30
    M. Pendharkar, B. Zhang, H. Wu, A. Zarassi, P. Zhang, C. P. Dempsey, J. S. Lee, S. D. Harrington, G. Badawy, S. Gazibegovic, R. L. M. Op het Veld, M. Rossi, J. Jung, A.-H. Chen, M. A. Verheijen, M. Hocevar, E. P. A. M. Bakkers, C. J. Palmstrøm, S. M. Frolov

    Improving materials used to make qubits is crucial to further progress in quantum information processing. Of particular interest are semiconductor-superconductor heterostructures that are expected to form the basis of topological quantum computing. We grew semiconductor indium antimonide nanowires that were coated with shells of tin of uniform thickness. No interdiffusion was observed at the interface

  • A widespread pathway for substitution of adenine by diaminopurine in phage genomes
    Science (IF 41.845) Pub Date : 2021-04-30
    Yan Zhou, Xuexia Xu, Yifeng Wei, Yu Cheng, Yu Guo, Ivan Khudyakov, Fuli Liu, Ping He, Zhangyue Song, Zhi Li, Yan Gao, Ee Lui Ang, Huimin Zhao, Yan Zhang, Suwen Zhao

    DNA modifications vary in form and function but generally do not alter Watson-Crick base pairing. Diaminopurine (Z) is an exception because it completely replaces adenine and forms three hydrogen bonds with thymine in cyanophage S-2L genomic DNA. However, the biosynthesis, prevalence, and importance of Z genomes remain unexplored. Here, we report a multienzyme system that supports Z-genome synthesis

  • A third purine biosynthetic pathway encoded by aminoadenine-based viral DNA genomes
    Science (IF 41.845) Pub Date : 2021-04-30
    Dona Sleiman, Pierre Simon Garcia, Marion Lagune, Jerome Loc’h, Ahmed Haouz, Najwa Taib, Pascal Röthlisberger, Simonetta Gribaldo, Philippe Marlière, Pierre Alexandre Kaminski

    Cells have two purine pathways that synthesize adenine and guanine ribonucleotides from phosphoribose via inosylate. A chemical hybrid between adenine and guanine, 2-aminoadenine (Z), replaces adenine in the DNA of the cyanobacterial virus S-2L. We show that S-2L and Vibrio phage PhiVC8 encode a third purine pathway catalyzed by PurZ, a distant paralog of succinoadenylate synthase (PurA), the enzyme

  • Noncanonical DNA polymerization by aminoadenine-based siphoviruses
    Science (IF 41.845) Pub Date : 2021-04-30
    Valerie Pezo, Faten Jaziri, Pierre-Yves Bourguignon, Dominique Louis, Deborah Jacobs-Sera, Jef Rozenski, Sylvie Pochet, Piet Herdewijn, Graham F. Hatfull, Pierre-Alexandre Kaminski, Philippe Marliere

    Bacteriophage genomes harbor the broadest chemical diversity of nucleobases across all life forms. Certain DNA viruses that infect hosts as diverse as cyanobacteria, proteobacteria, and actinobacteria exhibit wholesale substitution of aminoadenine for adenine, thereby forming three hydrogen bonds with thymine and violating Watson-Crick pairing rules. Aminoadenine-encoded DNA polymerases, homologous

  • Structural impact on SARS-CoV-2 spike protein by D614G substitution
    Science (IF 41.845) Pub Date : 2021-04-30
    Jun Zhang, Yongfei Cai, Tianshu Xiao, Jianming Lu, Hanqin Peng, Sarah M. Sterling, Richard M. Walsh, Sophia Rits-Volloch, Haisun Zhu, Alec N. Woosley, Wei Yang, Piotr Sliz, Bing Chen

    Substitution for aspartic acid (D) by glycine (G) at position 614 in the spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) appears to facilitate rapid viral spread. The G614 strain and its recent variants are now the dominant circulating forms. Here, we report cryo–electron microscopy structures of a full-length G614 S trimer, which adopts three distinct prefusion conformations

  • Toxin-antitoxin RNA pairs safeguard CRISPR-Cas systems
    Science (IF 41.845) Pub Date : 2021-04-30
    Ming Li, Luyao Gong, Feiyue Cheng, Haiying Yu, Dahe Zhao, Rui Wang, Tian Wang, Shengjie Zhang, Jian Zhou, Sergey A. Shmakov, Eugene V. Koonin, Hua Xiang

    CRISPR-Cas systems provide RNA-guided adaptive immunity in prokaryotes. We report that the multisubunit CRISPR effector Cascade transcriptionally regulates a toxin-antitoxin RNA pair, CreTA. CreT (Cascade-repressed toxin) is a bacteriostatic RNA that sequesters the rare arginine tRNAUCU (transfer RNA with anticodon UCU). CreA is a CRISPR RNA–resembling antitoxin RNA, which requires Cas6 for maturation

  • Structural insights into preinitiation complex assembly on core promoters
    Science (IF 41.845) Pub Date : 2021-04-30
    Xizi Chen, Yilun Qi, Zihan Wu, Xinxin Wang, Jiabei Li, Dan Zhao, Haifeng Hou, Yan Li, Zishuo Yu, Weida Liu, Mo Wang, Yulei Ren, Ze Li, Huirong Yang, Yanhui Xu

    Transcription factor IID (TFIID) recognizes core promoters and supports preinitiation complex (PIC) assembly for RNA polymerase II (Pol II)–mediated eukaryotic transcription. We determined the structures of human TFIID–based PIC in three stepwise assembly states and revealed two-track PIC assembly: stepwise promoter deposition to Pol II and extensive modular reorganization on track I (on TATA–TFIID-binding

  • Stepwise pathogenic evolution of Mycobacterium abscessus
    Science (IF 41.845) Pub Date : 2021-04-30
    Josephine M. Bryant, Karen P. Brown, Sophie Burbaud, Isobel Everall, Juan M. Belardinelli, Daniela Rodriguez-Rincon, Dorothy M. Grogono, Chelsea M. Peterson, Deepshikha Verma, Ieuan E. Evans, Christopher Ruis, Aaron Weimann, Divya Arora, Sony Malhotra, Bridget Bannerman, Charlotte Passemar, Kerra Templeton, Gordon MacGregor, Kasim Jiwa, Andrew J. Fisher, Tom L. Blundell, Diane J. Ordway, Mary Jackson

    Although almost all mycobacterial species are saprophytic environmental organisms, a few, such as Mycobacterium tuberculosis, have evolved to cause transmissible human infection. By analyzing the recent emergence and spread of the environmental organism M. abscessus through the global cystic fibrosis population, we have defined key, generalizable steps involved in the pathogenic evolution of mycobacteria

  • Chronoculture, harnessing the circadian clock to improve crop yield and sustainability
    Science (IF 41.845) Pub Date : 2021-04-30
    Gareth Steed, Dora Cano Ramirez, Matthew A. Hannah, Alex A. R. Webb

    Human health is dependent on a plentiful and nutritious supply of food, primarily derived from crop plants. Rhythmic supply of light as a result of the day and night cycle led to the evolution of circadian clocks that modulate most plant physiology, photosynthesis, metabolism, and development. To regulate crop traits and adaptation, breeders have indirectly selected for variation at circadian genes

  • Modulation of MHC-E transport by viral decoy ligands is required for RhCMV/SIV vaccine efficacy
    Science (IF 41.845) Pub Date : 2021-04-30
    Marieke C. Verweij, Scott G. Hansen, Ravi Iyer, Nessy John, Daniel Malouli, David Morrow, Isabel Scholz, Jennie Womack, Shaheed Abdulhaqq, Roxanne M. Gilbride, Colette M. Hughes, Abigail B. Ventura, Julia C. Ford, Andrea N. Selseth, Kelli Oswald, Rebecca Shoemaker, Brian Berkemeier, William J. Bosche, Michael Hull, Jason Shao, Jonah B. Sacha, Michael K. Axthelm, Paul T. Edlefsen, Jeffrey D. Lifson

    Strain 68-1 rhesus cytomegalovirus (RhCMV) vectors expressing simian immunodeficiency virus (SIV) antigens elicit CD8+ T cells recognizing epitopes presented by major histocompatibility complex II (MHC-II) and MHC-E but not MHC-Ia. These immune responses mediate replication arrest of SIV in 50 to 60% of monkeys. We show that the peptide VMAPRTLLL (VL9) embedded within the RhCMV protein Rh67 promotes

  • Dynamic remodeling of host membranes by self-organizing bacterial effectors
    Science (IF 41.845) Pub Date : 2021-04-29
    Ting-Sung Hsieh, Victor A. Lopez, Miles H. Black, Adam Osinski, Krzysztof Pawłowski, Diana R. Tomchick, Jen Liou, Vincent S. Tagliabracci

    During infection Legionella bacteria translocate a variety of effectors into host cells that modify host cell membrane trafficking for the benefit of the intracellular pathogen. Here we found a self-organizing system consisting of a bacterial phosphoinositide kinase and its opposing phosphatase that formed spatiotemporal patterns, including traveling waves, to remodel host cellular membranes. The Legionella

  • Household COVID-19 risk and in-person schooling
    Science (IF 41.845) Pub Date : 2021-04-29
    Justin Lessler, M. Kate Grabowski, Kyra H. Grantz, Elena Badillo-Goicoechea, C. Jessica E. Metcalf, Carly Lupton-Smith, Andrew S. Azman, Elizabeth A. Stuart

    In-person schooling has proved contentious and difficult to study throughout the SARS-CoV-2 pandemic. Data from a massive online survey in the United States indicates an increased risk of COVID-19-related outcomes among respondents living with a child attending school in-person. School-based mitigation measures are associated with significant reductions in risk, particularly daily symptoms screens

  • Extreme oxidant amounts produced by lightning in storm clouds
    Science (IF 41.845) Pub Date : 2021-04-29
    W. H. Brune, P. J. McFarland, E. Bruning, S. Waugh, D. MacGorman, D. O. Miller, J. M. Jenkins, X. Ren, J. Mao, J. Peischl

    Lightning increases the atmosphere’s ability to cleanse itself by producing nitric oxide (NO), leading to atmospheric chemistry that forms ozone (O3) and the atmosphere’s primary oxidant, the hydroxyl radical (OH). Our analysis of a 2012 airborne study of deep convection and chemistry demonstrates that lightning also directly generates the oxidants OH and the hydroperoxyl radical (HO2). Extreme amounts

  • Transformative climate adaptation in the United States: Trends and prospects
    Science (IF 41.845) Pub Date : 2021-04-29
    Linda Shi, Susanne Moser

    As climate change intensifies, civil society is increasingly calling for transformative adaptation that redresses drivers of climate vulnerability. We review trends in how U.S. federal government, private industry and civil society are planning for climate adaptation. We find growing divergence in their approaches and impacts. This incoherence increases maladaptive investment in climate-blind infrastructure

  • Imaging translation dynamics in live embryos reveals spatial heterogeneities
    Science (IF 41.845) Pub Date : 2021-04-29
    Jeremy Dufourt, Maelle Bellec, Antonio Trullo, Matthieu Dejean, Sylvain De Rossi, Cyril Favard, Mounia Lagha

    Much is known about the factors involved in the translation of mRNA into protein; however, this multi-step process has not been imaged in living multicellular organisms. Here, we deploy the SunTag method to visualize and quantify the timing, location, and kinetics of the translation of single mRNAs in living Drosophila embryos. By focusing on the translation of the conserved major epithelial-mesenchymal

  • Noncanonical crRNAs derived from host transcripts enable multiplexable RNA detection by Cas9
    Science (IF 41.845) Pub Date : 2021-04-27
    Chunlei Jiao, Sahil Sharma, Gaurav Dugar, Natalia L. Peeck, Thorsten Bischler, Franziska Wimmer, Yanying Yu, Lars Barquist, Christoph Schoen, Oliver Kurzai, Cynthia M. Sharma, Chase L. Beisel

    CRISPR-Cas systems recognize foreign genetic material using CRISPR RNAs (crRNAs). In Type II systems, a trans-activating crRNA (tracrRNA) hybridizes to crRNAs to drive their processing and utilization by Cas9. While analyzing Cas9-RNA complexes from Campylobacter jejuni, we discovered tracrRNA hybridizing to cellular RNAs, leading to formation of “noncanonical” crRNAs capable of guiding DNA targeting

  • Epidemiological and evolutionary considerations of SARS-CoV-2 vaccine dosing regimes
    Science (IF 41.845) Pub Date : 2021-04-23
    Chadi M. Saad-Roy, Sinead E. Morris, C. Jessica E. Metcalf, Michael J. Mina, Rachel E. Baker, Jeremy Farrar, Edward C. Holmes, Oliver G. Pybus, Andrea L. Graham, Simon A. Levin, Bryan T. Grenfell, Caroline E. Wagner

    Given vaccine dose shortages and logistical challenges, various deployment strategies are being proposed to increase population immunity levels to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Two critical issues arise: How timing of delivery of the second dose will affect infection dynamics and how it will affect prospects for the evolution of viral immune escape via a buildup of partially

  • Replication timing maintains the global epigenetic state in human cells
    Science (IF 41.845) Pub Date : 2021-04-23
    Kyle N. Klein, Peiyao A. Zhao, Xiaowen Lyu, Takayo Sasaki, Daniel A. Bartlett, Amar M. Singh, Ipek Tasan, Meng Zhang, Lotte P. Watts, Shin-ichiro Hiraga, Toyoaki Natsume, Xuemeng Zhou, Timour Baslan, Danny Leung, Masato T. Kanemaki, Anne D. Donaldson, Huimin Zhao, Stephen Dalton, Victor G. Corces, David M. Gilbert

    The temporal order of DNA replication [replication timing (RT)] is correlated with chromatin modifications and three-dimensional genome architecture; however, causal links have not been established, largely because of an inability to manipulate the global RT program. We show that loss of RIF1 causes near-complete elimination of the RT program by increasing heterogeneity between individual cells. RT

  • Assessing China’s efforts to pursue the 1.5°C warming limit
    Science (IF 41.845) Pub Date : 2021-04-23
    Hongbo Duan, Sheng Zhou, Kejun Jiang, Christoph Bertram, Mathijs Harmsen, Elmar Kriegler, Detlef P. van Vuuren, Shouyang Wang, Shinichiro Fujimori, Massimo Tavoni, Xi Ming, Kimon Keramidas, Gokul Iyer, James Edmonds

    Given the increasing interest in keeping global warming below 1.5°C, a key question is what this would mean for China’s emission pathway, energy restructuring, and decarbonization. By conducting a multimodel study, we find that the 1.5°C-consistent goal would require China to reduce its carbon emissions and energy consumption by more than 90 and 39%, respectively, compared with the “no policy” case

  • Conserved genetic signatures parcellate cardinal spinal neuron classes into local and projection subsets
    Science (IF 41.845) Pub Date : 2021-04-23
    Peter J. Osseward, Neal D. Amin, Jeffrey D. Moore, Benjamin A. Temple, Bianca K. Barriga, Lukas C. Bachmann, Fernando Beltran, Miriam Gullo, Robert C. Clark, Shawn P. Driscoll, Samuel L. Pfaff, Marito Hayashi

    Motor and sensory functions of the spinal cord are mediated by populations of cardinal neurons arising from separate progenitor lineages. However, each cardinal class is composed of multiple neuronal types with distinct molecular, anatomical, and physiological features, and there is not a unifying logic that systematically accounts for this diversity. We reasoned that the expansion of new neuronal

  • Broadband directional control of thermal emission
    Science (IF 41.845) Pub Date : 2021-04-23
    Jin Xu, Jyotirmoy Mandal, Aaswath P. Raman

    Controlling the directionality of emitted far-field thermal radiation is a fundamental challenge. Photonic strategies enable angular selectivity of thermal emission over narrow bandwidths, but thermal radiation is a broadband phenomenon. The ability to constrain emitted thermal radiation to fixed narrow angular ranges over broad bandwidths is an important, but lacking, capability. We introduce gradient

  • C(sp3)–H methylation enabled by peroxide photosensitization and Ni-mediated radical coupling
    Science (IF 41.845) Pub Date : 2021-04-23
    Aristidis Vasilopoulos, Shane W. Krska, Shannon S. Stahl

    The “magic methyl” effect describes the change in potency, selectivity, and/or metabolic stability of a drug candidate associated with addition of a single methyl group. We report a synthetic method that enables direct methylation of C(sp3)–H bonds in diverse drug-like molecules and pharmaceutical building blocks. Visible light–initiated triplet energy transfer promotes homolysis of the O–O bond in

  • Higher-dimensional supersymmetric microlaser arrays
    Science (IF 41.845) Pub Date : 2021-04-23
    Xingdu Qiao, Bikashkali Midya, Zihe Gao, Zhifeng Zhang, Haoqi Zhao, Tianwei Wu, Jieun Yim, Ritesh Agarwal, Natalia M. Litchinitser, Liang Feng

    The nonlinear scaling of complexity with the increased number of components in integrated photonics is a major obstacle impeding large-scale, phase-locked laser arrays. Here, we develop a higher-dimensional supersymmetry formalism for precise mode control and nonlinear power scaling. Our supersymmetric microlaser arrays feature phase-locked coherence and synchronization of all of the evanescently coupled

  • Josephson junction infrared single-photon detector
    Science (IF 41.845) Pub Date : 2021-04-23
    Evan D. Walsh, Woochan Jung, Gil-Ho Lee, Dmitri K. Efetov, Bae-Ian Wu, K.-F. Huang, Thomas A. Ohki, Takashi Taniguchi, Kenji Watanabe, Philip Kim, Dirk Englund, Kin Chung Fong

    Josephson junctions are superconducting devices used as high-sensitivity magnetometers and voltage amplifiers as well as the basis of high-performance cryogenic computers and superconducting quantum computers. Although device performance can be degraded by the generation of quasiparticles formed from broken Cooper pairs, this phenomenon also opens opportunities to sensitively detect electromagnetic

  • Timing the SARS-CoV-2 index case in Hubei province
    Science (IF 41.845) Pub Date : 2021-04-23
    Jonathan Pekar, Michael Worobey, Niema Moshiri, Konrad Scheffler, Joel O. Wertheim

    Understanding when severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged is critical to evaluating our current approach to monitoring novel zoonotic pathogens and understanding the failure of early containment and mitigation efforts for COVID-19. We used a coalescent framework to combine retrospective molecular clock inference with forward epidemiological simulations to determine how

  • Global groundwater wells at risk of running dry
    Science (IF 41.845) Pub Date : 2021-04-23
    Scott Jasechko, Debra Perrone

    Groundwater wells supply water to billions of people, but they can run dry when water tables decline. Here, we analyzed construction records for ~39 million globally distributed wells. We show that 6 to 20% of wells are no more than 5 meters deeper than the water table, implying that millions of wells are at risk of running dry if groundwater levels decline by only a few meters. Further, newer wells

  • Barcoded viral tracing of single-cell interactions in central nervous system inflammation
    Science (IF 41.845) Pub Date : 2021-04-23
    Iain C. Clark, Cristina Gutiérrez-Vázquez, Michael A. Wheeler, Zhaorong Li, Veit Rothhammer, Mathias Linnerbauer, Liliana M. Sanmarco, Lydia Guo, Manon Blain, Stephanie E. J. Zandee, Chun-Cheih Chao, Katelyn V. Batterman, Marius Schwabenland, Peter Lotfy, Amalia Tejeda-Velarde, Patrick Hewson, Carolina Manganeli Polonio, Michael W. Shultis, Yasmin Salem, Emily C. Tjon, Pedro H. Fonseca-Castro, Davis

    Cell-cell interactions control the physiology and pathology of the central nervous system (CNS). To study astrocyte cell interactions in vivo, we developed rabies barcode interaction detection followed by sequencing (RABID-seq), which combines barcoded viral tracing and single-cell RNA sequencing (scRNA-seq). Using RABID-seq, we identified axon guidance molecules as candidate mediators of microglia-astrocyte

  • Cholinergic neurons constitutively engage the ISR for dopamine modulation and skill learning in mice
    Science (IF 41.845) Pub Date : 2021-04-23
    Ashley R. Helseth, Ricardo Hernandez-Martinez, Victoria L. Hall, Matthew L. Oliver, Brandon D. Turner, Zachary F. Caffall, Joseph E. Rittiner, Miranda K. Shipman, Connor S. King, Viviana Gradinaru, Charles Gerfen, Mauro Costa-Mattioli, Nicole Calakos

    The integrated stress response (ISR) maintains proteostasis by modulating protein synthesis and is important in synaptic plasticity, learning, and memory. We developed a reporter, SPOTlight, for brainwide imaging of ISR state with cellular resolution. Unexpectedly, we found a class of neurons in mouse brain, striatal cholinergic interneurons (CINs), in which the ISR was activated at steady state. Genetic

  • Preventing Engrailed-1 activation in fibroblasts yields wound regeneration without scarring
    Science (IF 41.845) Pub Date : 2021-04-23
    Shamik Mascharak, Heather E. desJardins-Park, Michael F. Davitt, Michelle Griffin, Mimi R. Borrelli, Alessandra L. Moore, Kellen Chen, Bryan Duoto, Malini Chinta, Deshka S. Foster, Abra H. Shen, Michael Januszyk, Sun Hyung Kwon, Gerlinde Wernig, Derrick C. Wan, H. Peter Lorenz, Geoffrey C. Gurtner, Michael T. Longaker

    Skin scarring, the end result of adult wound healing, is detrimental to tissue form and function. Engrailed-1 lineage–positive fibroblasts (EPFs) are known to function in scarring, but Engrailed-1 lineage–negative fibroblasts (ENFs) remain poorly characterized. Using cell transplantation and transgenic mouse models, we identified a dermal ENF subpopulation that gives rise to postnatally derived EPFs

  • Fluctuations shape plants through proprioception
    Science (IF 41.845) Pub Date : 2021-04-23
    Bruno Moulia, Stéphane Douady, Olivier Hamant

    Plants constantly experience fluctuating internal and external mechanical cues, ranging from nanoscale deformation of wall components, cell growth variability, nutating stems, and fluttering leaves to stem flexion under tree weight and wind drag. Developing plants use such fluctuations to monitor and channel their own shape and growth through a form of proprioception. Fluctuations in mechanical cues

  • Radiation-related genomic profile of papillary thyroid cancer after the Chernobyl accident
    Science (IF 41.845) Pub Date : 2021-04-22
    Lindsay M. Morton, Danielle M. Karyadi, Chip Stewart, Tetiana I. Bogdanova, Eric T. Dawson, Mia K. Steinberg, Jieqiong Dai, Stephen W. Hartley, Sara J. Schonfeld, Joshua N. Sampson, Yosi Maruvka, Vidushi Kapoor, Dale A. Ramsden, Juan Carvajal-Garcia, Charles M. Perou, Joel S. Parker, Marko Krznaric, Meredith Yeager, Joseph F. Boland, Amy Hutchinson, Belynda D. Hicks, Casey L. Dagnall, Julie M. Gastier-Foster

    The 1986 Chernobyl nuclear power plant accident increased papillary thyroid cancer (PTC) incidence in surrounding regions, particularly for 131I-exposed children. We analyzed genomic, transcriptomic, and epigenomic characteristics of 440 PTCs from Ukraine (359 with estimated childhood 131I exposure and 81 unexposed children born after 1986). PTCs displayed radiation dose-dependent enrichment of fusion

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