Nature
29 Sep 2022
Volume 609 | Issue 7929
1. Galaxy clusters enveloped by vast volumes of relativistic electrons 
下载原文
First/Corresponding author:
Affiliations:
Hamburger Sternwarte, University of Hamburg, Hamburg, Germany
INAF – Istituto di Radioastronomia, Bologna, Italy
Abstract:
The central regions of galaxy clusters are permeated by magnetic fields and filled with relativistic electrons. When clusters merge, the magnetic fields are amplified and relativistic electrons are re-accelerated by turbulence in the intracluster medium. These electrons reach energies of 1–10GeV and, in the presence of magnetic fields, produce diffuse radio halos that typically cover an area of around1Mpc2. Here we report observations of four clusters whose radio halos are embedded in much more extended, diffuse radio emission, filling a volume 30 times larger than that of radio halos. The emissivity in these larger features is about 20 times lower than the emissivity in radio halos. We conclude that relativistic electrons and magnetic fields extend far beyond radio halos, and that the physical conditions in the outer regions of the clusters are quite different from those in the radio halos
2. Observations of a Magellanic Corona 下载原文
First/Corresponding author:
Dhanesh Krishnarao
Affiliations:
Space Telescope Science Institute, Baltimore, MD, USA
William H. Miller III Department of Physics & Astronomy, Johns Hopkins University, Baltimore, MD, USA
Department of Physics, Colorado College, Colorado Springs, CO, USA
Abstract:
The Large Magellanic Cloud (LMC) and the Small Magellanic Cloud (SMC) are the closest massive satellite galaxies of the Milky Way. They are probably on their first passage on an infalling orbit towards our Galaxy and trace the continuing dynamics of the Local Group. Recent measurements of a high mass for the LMC (Mhalo≈1011.1–11.4M⊙) imply that the LMC should host a Magellanic Corona: a collisionally ionized, warm-hot gaseous halo at the virial temperature (105.3–5.5K) initially extending out to the virial radius (100–130kiloparsecs (kpc)). Such a corona would have shaped the formation of the Magellanic Stream7, a tidal gas structure extending over 200° across the sky that is bringing in metal-poor gas to the Milky Way. Here we show evidence for this Magellanic Corona with a potential direct detection in highly ionized oxygen (O+5) and indirectly by means of triply ionized carbon and silicon, seen in ultraviolet (UV) absorption towards background quasars. We find that the Magellanic Corona is part of a pervasive multiphase Magellanic circumgalactic medium (CGM) seen in many ionization states with a declining projected radial profile out to at least 35kpc from the LMC and a total ionized CGM mass of log10(MHII,CGM/M⊙)≈9.1±0.2. The evidence for the Magellanic Corona is a crucial step forward in characterizing the Magellanic group and its nested evolution with the Local Group.
3. Universal control of a six-qubit quantum processor in silicon 下载原文
First author:
Stephan G. J. Philips①
Corresponding author:
Lieven M. K. Vandersypen②
Affiliation:
QuTech and the Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands ①②
Abstract:
Future quantum computers capable of solving relevant problems will require a large number of qubits that can be operated reliably. However, the requirements of having a large qubit count and operating with high fidelity are typically conflicting. Spins in semiconductor quantum dots show long-term promise but demonstrations so far use between one and four qubits and typically optimize the fidelity of either single- or two-qubit operations, or initialization and readout. Here, we increase the number of qubits and simultaneously achieve respectable fidelities for universal operation, state preparation and measurement. We design, fabricate and operate a six-qubit processor with a focus on careful Hamiltonian engineering, on a high level of abstraction to program the quantum circuits, and on efficient background calibration, all of which are essential to achieve high fidelities on this extended system. State preparation combines initialization by measurement and real-time feedback with quantum-non-demolition measurements. These advances will enable testing of increasingly meaningful quantum protocols and constitute a major stepping stone towards large-scale quantum computers.
4.Topological Chern vectors in three-dimensional photonic crystals 下载原文
First author:
Gui-Geng Liu①
Corresponding authors:
Peiheng Zhou②, Yihao Yang③, Yidong Chong④, Baile Zhang⑤
Affiliations:
Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore①④⑤
National Engineering Research Center of Electromagnetic Radiation Control Materials, Key Laboratory of Multi-spectral Absorbing Materials and Structures of Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China②
Interdisciplinary Center for Quantum Information, State Key Laboratory of Modern Optical Instrumentation, ZJU-Hangzhou Global Science and Technology Innovation Center, College of Information Science and Electronic Engineering, ZJU-UIUC Institute, Zhejiang University, Hangzhou, China③
Abstract:
The paradigmatic example of a topological phase of matter, the two-dimensional Chern insulator, is characterized by a topological invariant consisting of a single integer, the scalar Chern number. Extending the Chern insulator phase from two to three dimensions requires generalization of the Chern number to a three-vector, similar to the three-dimensional (3D) quantum Hall effect. Such Chern vectors for 3D Chern insulators have never been explored experimentally. Here we use magnetically tunable 3D photonic crystals to achieve the experimental demonstration of Chern vectors and their topological surface states. We demonstrate Chern vector magnitudes of up to six, higher than all scalar Chern numbers previously realized in topological materials. The isofrequency contours formed by the topological surface states in the surface Brillouin zone form torus knots or links, whose characteristic integers are determined by the Chern vectors. We demonstrate a sample with surface states forming a (2, 2) torus link or Hopf link in the surface Brillouin zone, which is topologically distinct from the surface states of other 3D topological phases. These results establish the Chern vector as an intrinsic bulk topological invariant in 3D topological materials, with surface states possessing unique topological characteristics.
5. Photonic topological insulator induced by a dislocation in three dimensions 下载原文
First author:
Eran Lustig①
Corresponding author:
Mordechai Segev②
Affiliation:
Physics Department and Solid-State Institute, Technion – Israel Institute of Technology, Haifa, Israel①②
Abstract:
The hallmark of topological insulators (TIs) is the scatter-free propagation of waves in topologically protected edge channels. This transport is strictly chiral on the outer edge of the medium and therefore capable of bypassing sharp corners and imperfections, even in the presence of substantial disorder. In photonics, two-dimensional (2D) topological edge states have been demonstrated on several different platforms and are emerging as a promising tool for robust lasers, quantum devices and other applications. More recently, 3D TIs were demonstrated in microwavesand acoustic waves, where the topological protection in the latter is induced by dislocations. However, at optical frequencies, 3D photonic TIs have so far remained out of experimental reach. Here we demonstrate a photonic TI with protected topological surface states in three dimensions. The topological protection is enabled by a screw dislocation. For this purpose, we use the concept of synthetic dimensions in a 2D photonic waveguide arrayby introducing a further modal dimension to transform the system into a 3D topological system. The lattice dislocation endows the system with edge states propagating along 3D trajectories, with topological protection akin to strong photonic TIs. Our work paves the way for utilizing 3D topology in photonic science and technology.
6. Anomalous slip in body-centred cubic metals 下载原文
First author:
Daniel Caillard①
Corresponding author:
Emmanuel Clouet②
Affiliation:
Université Paris-Saclay, CEA, Service de Recherches de Métallurgie Physique, Gif-sur-Yvette, France①②
Abstract:
Crystal strength and plastic flow are controlled by the motion and interaction of dislocations, the line defects carrying atomic shear increments. Whereas, in most crystals, deformation develops in the crystallographic planes in which the glide force acting on dislocations is maximum, plasticity in body-centred cubic metals is more complex. Slip systems in which the resolved shear stress is not the highest can dominate at low temperature, leading to anomalous slip. Using in situ tensile tests in a transmission electron microscope we show that anomalous slip arises from the high mobility of multi-junctions, that is, junctions between more than two dislocations, which glide at a velocity several orders of magnitude larger than single dislocations. These multi-junctions result from the interaction of a simple binary junction with a gliding dislocation. Although elasticity theory predicts that these binary junctions should be unstable in crystals with a weak elastic anisotropy such as tungsten, both experiments and atomistic simulations reveal that such junctions can be created under dynamic conditions, in agreement with the existence of anomalous slip in almost all body-centred cubic metals, including tungsten.
7. Tracking single adatoms in liquid in a transmission electron microscope 下载原文
First author:
Nick Clark①
Corresponding authors:
Roman Gorbachev② Sarah J. Haigh③
Affiliations:
Department of Materials, University of Manchester, Manchester, UK①②③
National Graphene Institute, University of Manchester, Manchester, UK①②③
Abstract:
Single atoms or ions on surfaces affect processes from nucleation to electrochemical reactionsand heterogeneous catalysis. Transmission electron microscopy is a leading approach for visualizing single atoms on a variety of substrates. It conventionally requires high vacuum conditions, but has been developed for in situ imaging in liquid and gaseous environments with a combined spatial and temporal resolution that is unmatched by any other method—notwithstanding concerns about electron-beam effects on samples. When imaging in liquid using commercial technologies, electron scattering in the windows enclosing the sample and, in the liquid, generally limits the achievable resolution to a few nanometers. Graphene liquid cells, on the other hand, have enabled atomic-resolution imaging of metal nanoparticles in liquids. Here we show that a double graphene liquid cell, consisting of a central molybdenum disulfide monolayer separated by hexagonal boron nitride spacers from the two enclosing graphene windows, makes it possible to monitor, with atomic resolution, the dynamics of platinum adatoms on the monolayer in an aqueous salt solution. By imaging more than 70,000 single adatom adsorption sites, we compare the site preference and dynamic motion of the adatoms in both a fully hydrated and a vacuum state. We find a modified adsorption site distribution and higher diffusivities for the adatoms in the liquid phase compared with those in vacuum. This approach paves the way for in situ liquid-phase imaging of chemical processes with single-atom precision.
8.Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape 下载原文
First author:
Yatish Turakhia①
Corresponding author:
Russell Corbett-Detig②
Affiliations:
Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA①②
Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA①②
Department of Electrical and Computer Engineering, University of California, San Diego, San Diego, CA, USA①
Abstract:
Accurate and timely detection of recombinant lineages is crucial for interpreting genetic variation, reconstructing epidemic spread, identifying selection and variants of interest, and accurately performing phylogenetic analyses. During the SARS-CoV-2 pandemic, genomic data generation has exceeded the capacities of existing analysis platforms, thereby crippling real-time analysis of viral evolution. Here, we use a new phylogenomic method to search a nearly comprehensive SARS-CoV-2 phylogeny for recombinant lineages. In a 1.6 million sample tree from May 2021, we identify 589 recombination events, which indicate that around 2.7% of sequenced SARS-CoV-2 genomes have detectable recombinant ancestry. Recombination breakpoints are inferred to occur disproportionately in the 3' portion of the genome that contains the spike protein. Our results highlight the need for timely analyses of recombination for pinpointing the emergence of recombinant lineages with the potential to increase transmissibility or virulence of the virus. We anticipate that this approach will empower comprehensive real-time tracking of viral recombination during the SARS-CoV-2 pandemic and beyond.
9. CLN3 is required for the clearance of glycerophosphodiesters from lysosomes 下载原文
First author:
Nouf N. Laqtom①
Corresponding authors:
David M. Sabatini/Monther Abu-Remaileh②
Affiliations:
Department of Chemical Engineering, Stanford University, Stanford, CA, USA①②
Department of Genetics, Stanford University, Stanford, CA, USA①②
The Institute for Chemistry, Engineering & Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA①②
Abstract:
Lysosomes have many roles, including degrading macromolecules and signalling to the nucleus. Lysosomal dysfunction occurs in various human conditions, such as common neurodegenerative diseases and monogenic lysosomal storage disorders (LSDs). For most LSDs, the causal genes have been identified but, in some, the function of the implicated gene is unknown, in part because lysosomes occupy a small fraction of the cellular volume so that changes in lysosomal contents are difficult to detect. Here we develop the LysoTag mouse for the tissue-specific isolation of intact lysosomes that are compatible with the multimodal profiling of their contents. We used the LysoTag mouse to study CLN3, a lysosomal transmembrane protein with an unknown function. In children, the loss of CLN3 causes juvenile neuronal ceroid lipofuscinosis (Batten disease), a lethal neurodegenerative LSD. Untargeted metabolite profiling of lysosomes from the brains of mice lacking CLN3 revealed a massive accumulation of glycerophosphodiesters (GPDs)—the end products of glycerophospholipid catabolism. GPDs also accumulate in the lysosomes of CLN3-deficient cultured cells and we show that CLN3 is required for their lysosomal egress. Loss of CLN3 also disrupts glycerophospholipid catabolism in the lysosome. Finally, we found elevated levels of glycerophosphoinositol in the cerebrospinal fluid of patients with Batten disease, suggesting the potential use of glycerophosphoinositol as a disease biomarker. Our results show that CLN3 is required for the lysosomal clearance of GPDs and reveal Batten disease as a neurodegenerative LSD with a defect in glycerophospholipid metabolism.
10. Living material assembly of bacteriogenic protocells 下载原文
First author:
Can Xu①
Corresponding authors:
Mei Li②, Stephen Mann③
Affiliations:
Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, Bristol, UK①②③
School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, P. R. China②③
Max Planck-Bristol Centre for Minimal Biology, School of Chemistry, University of Bristol, Bristol, United Kingdom③
Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, Shanghai, P. R. China③
Abstract:
Advancing the spontaneous bottom-up construction of artificial cells with high organizational complexity and diverse functionality remains an unresolved issue at the interface between living and non-living matter1,2,3,4. Here, to address this challenge, we developed a living material assembly process based on the capture and on-site processing of spatially segregated bacterial colonies within individual coacervate microdroplets for the endogenous construction of membrane-bounded, molecularly crowded, and compositionally, structurally and morphologically complex synthetic cells. The bacteriogenic protocells inherit diverse biological components, exhibit multifunctional cytomimetic properties and can be endogenously remodelled to include a spatially partitioned DNA–histone nucleus-like condensate, membranized water vacuoles and a three-dimensional network of F-actin proto-cytoskeletal filaments. The ensemble is biochemically energized by ATP production derived from implanted live Escherichia coli cells to produce a cellular bionic system with amoeba-like external morphology and integrated life-like properties. Our results demonstrate a bacteriogenic strategy for the bottom-up construction of functional protoliving microdevices and provide opportunities for the fabrication of new synthetic cell modules and augmented living/synthetic cell constructs with potential applications in engineered synthetic biology and biotechnology.
11.A mechanism for oxidative damage repair at gene regulatory elements 下载原文
First author:
Corresponding author:
Sherif F. El-Khamisy②
Affiliations:
School of Biosciences, University of Sheffield, Sheffield, UK①
The Healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK①②
School of Life and Environmental Sciences, Department of Life Sciences, University of Lincoln, Lincoln, UK①
Institute of Cancer Therapeutics, School of Pharmacy and Medical Sciences, University of Bradford, Bradford, UK
Abstract:
Oxidative genome damage is an unavoidable consequence of cellular metabolism. It arises at gene regulatory elements by epigenetic demethylation during transcriptional activation. Here we show that promoters are protected from oxidative damage via a process mediated by the nuclear mitotic apparatus protein NuMA (also known as NUMA1). NuMA exhibits genomic occupancy approximately 100bp around transcription start sites. It binds the initiating form of RNA polymerase II, pause-release factors and single-strand break repair (SSBR) components such as TDP1. The binding is increased on chromatin following oxidative damage, and TDP1 enrichment at damaged chromatin is facilitated by NuMA. Depletion of NuMA increases oxidative damage at promoters. NuMA promotes transcription by limiting the polyADP-ribosylation of RNA polymerase II, increasing its availability and release from pausing at promoters. Metabolic labelling of nascent RNA identifies genes that depend on NuMA for transcription including immediate–early response genes. Complementation of NuMA-deficient cells with a mutant that mediates binding to SSBR, or a mitotic separation-of-function mutant, restores SSBR defects. These findings underscore the importance of oxidative DNA damage repair at gene regulatory elements and describe a process that fulfils this function.
12.Columnar structure of human telomeric chromatin 下载原文
First author:
Corresponding authors:
Daniela Rhodes②, Lars Nordenskiöld③
Affiliations:
School of Biological Sciences, Nanyang Technological University, Singapore, Singapore①②③
NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore②③
Medical Research Council, Laboratory of Molecular Biology, Cambridge, UK②
Abstract:
Telomeres, the ends of eukaryotic chromosomes, play pivotal parts in ageing and cancer and are targets of DNA damage and the DNA damage response. Little is known about the structure of telomeric chromatin at the molecular level. Here we used negative stain electron microscopy and single-molecule magnetic tweezers to characterize 3-kbp-long telomeric chromatin fibres. We also obtained the cryogenic electron microscopy structure of the condensed telomeric tetranucleosome and its dinucleosome unit. The structure displayed close stacking of nucleosomes with a columnar arrangement, and an unusually short nucleosome repeat length that comprised about 132bp DNA wound in a continuous superhelix around histone octamers. This columnar structure is primarily stabilized by the H2A carboxy-terminal and histone amino-terminal tails in a synergistic manner. The columnar conformation results in exposure of the DNA helix, which may make it susceptible to both DNA damage and the DNA damage response. The conformation also exists in an alternative open state, in which one nucleosome is unstacked and flipped out, which exposes the acidic patch of the histone surface. The structural features revealed in this work suggest mechanisms by which protein factors involved in telomere maintenance can access telomeric chromatin in its compact form.
13. Methotrexate recognition by the human reduced folate carrier SLC19A1 下载原文
First author:
Corresponding author:
Seok-Yong Lee②
Affiliation:
Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA①②
Abstract:
Folates are essential nutrients with important roles as cofactors in one-carbon transfer reactions, being heavily utilized in the synthesis of nucleic acids and the metabolism of amino acids during cell division. Mammals lack de novo folate synthesis pathways and thus rely on folate uptake from the extracellular milieu. The human reduced folate carrier (hRFC, also known as SLC19A1) is the major importer of folates into the cell, as well as chemotherapeutic agents such as methotrexate. As an anion exchanger, RFC couples the import of folates and antifolates to anion export across the cell membrane and it is a major determinant in methotrexate (antifolate) sensitivity, as genetic variants and its depletion result in drug resistance. Despite its importance, the molecular basis of substrate specificity by hRFC remains unclear. Here we present cryo-electron microscopy structures of hRFC in the apo state and captured in complex with methotrexate. Combined with molecular dynamics simulations and functional experiments, our study uncovers key determinants of hRFC transport selectivity among folates and antifolate drugs while shedding light on important features of anion recognition by hRFC.