Processing within the anterior cingulate cortex (ACC) is crucial for the patterning of appropriate behavior, and ACC dysfunction following chronic drug use is thought to play a major role in drug addiction. However, cortical pyramidal projection neurons can be subdivided into two major types (intratelencephalic (IT) and pyramidal tract (PT)), with distinct inputs and projection targets, molecular and receptor profiles, morphologies and electrophysiological properties. Yet, how each of these cell populations modulate behavior related to addiction is unknown. We demonstrate that PT neurons regulate the positive features of a drug experience whereas IT neurons regulate the negative features. These findings support a revised theory of cortical function in addiction, with distinct cells and circuits mediating reward and aversion.

Since most variants that impact polygenic disease phenotypes localize to non-coding genomic regions, understanding the consequences of regulatory element variants will advance understanding of human disease mechanisms. Here, we report that the systemic lupus erythematosus (SLE) risk variant rs2431697 as likely causal for SLE through disruption of a regulatory element, modulating miR-146a expression. Using epigenomic analysis, genome-editing and 3D chromatin structure analysis, we show that rs2431697 tags a cell-type dependent distal enhancer specific for miR-146a that physically interacts with the miR-146a promoter. NF-kB binds the disease protective allele in a sequence-specific manner, increasing expression of this immunoregulatory microRNA. Finally, CRISPR activation-based modulation of this enhancer in the PBMCs of SLE patients attenuates type I interferon pathway activation by increasing miR-146a expression. Our work provides a strategy to define non-coding RNA functional regulatory elements using disease-associated variants and provides mechanistic links between autoimmune disease risk genetic variation and disease etiology.

Terrestrial space weather involves the transfer of energy and momentum from the solar wind into geospace. Despite recently discovered seasonal asymmetries between auroral forms and the intensity of emissions between northern and southern hemispheres, seasonally averaged energy input into the ionosphere is still generally considered to be symmetric. Here we show, using Swarm satellite data, a preference for electromagnetic energy input at 450 km altitude into the northern hemisphere, on both the dayside and the nightside, when averaged over season. We propose that this is explained by the offset of the magnetic dipole away from Earth's center. This introduces a larger separation between the magnetic pole and rotation axis in the south, creating different relative solar illumination of northern and southern auroral zones, resulting in changes to the strength of reflection of incident Alfvén waves from the ionosphere. Our study reveals an important asymmetry in seasonally averaged electromagnetic energy input to the atmosphere. Based on observed lower Poynting flux on the nightside this asymmetry may also exist for auroral emissions. Similar offsets may drive asymmetric energy input, and potentially aurora, on other planets.

Ferroelectric materials exhibit a phase transition to a paraelectric state driven by temperature - called the Curie transition. In conventional ferroelectrics, the Curie transition is caused by a change in crystal symmetry, while the material itself remains a continuous three-dimensional solid crystal. However, ferroelectric polymers behave differently. Polymeric materials are typically of semi-crystalline nature, meaning that they are an intermixture of crystalline and amorphous regions. Here, we demonstrate that the semi-crystalline morphology of the ferroelectric copolymer of vinylidene fluoride and trifluoroethylene (P(VDF-TrFE)) strongly affects its Curie transition, as not only a change in crystal symmetry but also in morphology occurs. We demonstrate, by high-resolution nanomechanical measurements, that the semi-crystalline microstructure in the paraelectric state is formed by crystalline domains embedded into a softer amorphous phase. Using in situ X-ray diffraction measurements, we show that the local electromechanical response of the crystalline domains is counterbalanced by the amorphous phase, effectively masking its macroscopic effect. Our quantitative multi-scale characterisations unite the nano- and macroscopic material properties of the ferroelectric polymer P(VDF-TrFE) through its semi-crystalline nature.

Solid-state batteries (SSBs) are considered to be the next-generation lithium-ion battery technology due to their enhanced energy density and safety. However, the high electronic conductivity of solid-state electrolytes (SSEs) leads to Li dendrite nucleation and proliferation. Uneven electric-field distribution resulting from poor interfacial contact can further promote dendritic deposition and lead to rapid short circuiting of SSBs. Herein, we propose a flexible electron-blocking interfacial shield (EBS) to protect garnet electrolytes from the electronic degradation. The EBS formed by an in-situ substitution reaction can not only increase lithiophilicity but also stabilize the Li volume change, maintaining the integrity of the interface during repeated cycling. Density functional theory calculations show a high electron-tunneling energy barrier from Li metal to the EBS, indicating an excellent capacity for electron-blocking. EBS protected cells exhibit an improved critical current density of 1.2 mA cm-2 and stable cycling for over 400 h at 1 mA cm-2 (1 mAh cm-2) at room temperature. These results demonstrate an effective strategy for the suppression of Li dendrites and present fresh insight into the rational design of the SSE and Li metal interface.

Graphene-covering is a promising approach for achieving an acid-stable, non-noble-metal-catalysed hydrogen evolution reaction (HER). Optimization of the number of graphene-covering layers and the density of defects generated by chemical doping is crucial for achieving a balance between corrosion resistance and catalytic activity. Here, we investigate the influence of charge transfer and proton penetration through the graphene layers on the HER mechanisms of the non-noble metals Ni and Cu in an acidic electrolyte. We find that increasing the number of graphene-covering layers significantly alters the HER performances of Ni and Cu. The proton penetration explored through electrochemical experiments and simulations reveals that the HER activity of the graphene-covered catalysts is governed by the degree of proton penetration, as determined by the number of graphene-covering layers.

Accurate prediction of peritoneal metastasis for gastric cancer (GC) with serosal invasion is crucial in clinic. The presence of collagen in the tumour microenvironment affects the metastasis of cancer cells. Herein, we propose a collagen signature, which is composed of multiple collagen features in the tumour microenvironment of the serosa derived from multiphoton imaging, to describe the extent of collagen alterations. We find that a high collagen signature is significantly associated with a high risk of peritoneal metastasis (P < 0.001). A competing-risk nomogram including the collagen signature, tumour size, tumour differentiation status and lymph node metastasis is constructed. The nomogram demonstrates satisfactory discrimination and calibration. Thus, the collagen signature in the tumour microenvironment of the gastric serosa is associated with peritoneal metastasis in GC with serosal invasion, and the nomogram can be conveniently used to individually predict the risk of peritoneal metastasis in GC with serosal invasion after radical surgery.

Active telomerase is essential for stem cells and most cancers to maintain telomeres. The enzymatic activity of telomerase is related but not equivalent to the expression of TERT, the catalytic subunit of the complex. Here we show that telomerase enzymatic activity can be robustly estimated from the expression of a 13-gene signature. We demonstrate the validity of the expression-based approach, named EXTEND, using cell lines, cancer samples, and non-neoplastic samples. When applied to over 9,000 tumors and single cells, we find a strong correlation between telomerase activity and cancer stemness. This correlation is largely driven by a small population of proliferating cancer cells that exhibits both high telomerase activity and cancer stemness. This study establishes a computational framework for quantifying telomerase enzymatic activity and provides new insights into the relationships among telomerase, cancer proliferation, and stemness.

Recent progress in nonlinear optical materials and microresonators has brought quantum computing with bulk optical nonlinearities into the realm of possibility. This platform is of great interest, not only because photonics is an obvious choice for quantum networks, but also as a promising route to quantum information processing at room temperature. We propose an approach for reprogrammable room-temperature photonic quantum logic that significantly simplifies the realization of various quantum circuits, and in particular, of error correction. The key element is the programmable photonic multi-mode resonator that implements reprogrammable bosonic quantum logic gates, while using only the bulk χ(2) nonlinear susceptibility. We theoretically demonstrate that just two of these elements suffice for a complete, compact error-correction circuit on a bosonic code, without the need for measurement or feed-forward control. Encoding and logical operations on the code are also easily achieved with these reprogrammable quantum photonic processors. An extrapolation of current progress in nonlinear optical materials and photonic circuits indicates that such circuitry should be achievable within the next decade.

High-resolution transmission electron microscopy (HRTEM) has been transformative to the field of polymer science, enabling the direct imaging of molecular structures. Although some materials have remarkable stability under electron beams, most HRTEM studies are limited by the electron dose the sample can handle. Beam damage of conjugated polymers is not yet fully understood, but it has been suggested that the diffusion of secondary reacting species may play a role. As such, we examine the effect of the addition of antioxidants to a series of solution-processable conjugated polymers as an approach to mitigating beam damage. Characterizing the effects of beam damage by calculating critical dose DC values from the decay of electron diffraction peaks shows that beam damage of conjugated polymers in the TEM can be minimized by using antioxidants at room temperature, even if the antioxidant does not alter or incorporate into polymer crystals. As a consequence, the addition of antioxidants pushes the resolution limit of polymer microscopy, enabling imaging of a 3.6 Å lattice spacing in poly[(5,6-difluoro-2,1,3-benzothiadiazol-4,7-diyl)-alt-(3,3″'-di(2-octyldodecyl)-2,2';5',2″;5″,2″'-quaterthiophene-5,5″'-diyl)] (PffBT4T-2OD).

Stable solid electrolyte interface (SEI) is highly sought after for lithium metal batteries (LMB) owing to its efficient electrolyte consumption suppression and Li dendrite growth inhibition. However, current design strategies can hardly endow a multifunctional SEI formation due to the non-uniform, low flexible film formation and limited capability to alter Li nucleation/growth orientation, which results in unconstrained dendrite growth and short cycling stability. Herein, we present a novel strategy to employ electrolyte additives containing catechol and acrylic groups to construct a stable multifunctional SEI by in-situ anionic polymerization. This self-smoothing and robust SEI offers multiple sites for Li adsorption and steric repulsion to constrain nucleation/growth process, leading to homogenized Li nanosphere formation. This isotropic nanosphere offers non-preferred Li growth orientation, rendering uniform Li deposition to achieve a dendrite-free anode. Attributed to these superiorities, a remarkable cycling performance can be obtained, i.e., high current density up to 10 mA cm-2, ultra-long cycle life over 8500 hrs operation, high cumulative capacity over 4.25 Ah cm-2 and stable cycling under 60 °C. A prolonged lifespan can also be achieved in Li-S and Li-LiFePO4 cells under lean electrolyte content, low N/P ratio or high temperature conditions. This facile strategy also promotes the practical application of LMB and enlightens the SEI design in related fields.

Coenzyme A (CoA) is a fundamental co-factor for all life, involved in numerous metabolic pathways and cellular processes, and its biosynthetic pathway has raised substantial interest as a drug target against multiple pathogens including Mycobacterium tuberculosis. The biosynthesis of CoA is performed in five steps, with the second and third steps being catalysed in the vast majority of prokaryotes, including M. tuberculosis, by a single bifunctional protein, CoaBC. Depletion of CoaBC was found to be bactericidal in M. tuberculosis. Here we report the first structure of a full-length CoaBC, from the model organism Mycobacterium smegmatis, describe how it is organised as a dodecamer and regulated by CoA thioesters. A high-throughput biochemical screen focusing on CoaB identified two inhibitors with different chemical scaffolds. Hit expansion led to the discovery of potent and selective inhibitors of M. tuberculosis CoaB, which we show to bind to a cryptic allosteric site within CoaB.

The immunosuppressive microenvironment that is shaped by hepatic metastatic pancreatic ductal adenocarcinoma (PDAC) is essential for tumor cell evasion of immune destruction. Neutrophils are important components of the metastatic tumor microenvironment and exhibit heterogeneity. However, the specific phenotypes, functions and regulatory mechanisms of neutrophils in PDAC liver metastases remain unknown. Here, we show that a subset of P2RX1-negative neutrophils accumulate in clinical and murine PDAC liver metastases. RNA sequencing of murine PDAC liver metastasis-infiltrated neutrophils show that P2RX1-deficient neutrophils express increased levels of immunosuppressive molecules, including PD-L1, and have enhanced mitochondrial metabolism. Mechanistically, the transcription factor Nrf2 is upregulated in P2RX1-deficient neutrophils and associated with PD-L1 expression and metabolic reprogramming. An anti-PD-1 neutralizing antibody is sufficient to compromise the immunosuppressive effects of P2RX1-deficient neutrophils on OVA-activated OT1 CD8+ T cells. Therefore, our study uncovers a mechanism by which metastatic PDAC tumors evade antitumor immunity by accumulating a subset of immunosuppressive P2RX1-negative neutrophils.

In quantum magnets, magnetic moments fluctuate heavily and are strongly entangled with each other, a fundamental distinction from classical magnetism. Here, with inelastic neutron scattering measurements, we probe the spin correlations of the honeycomb lattice quantum magnet YbCl3. A linear spin wave theory with a single Heisenberg interaction on the honeycomb lattice, including both transverse and longitudinal channels of the neutron response, reproduces all of the key features in the spectrum. In particular, we identify a Van Hove singularity, a clearly observable sharp feature within a continuum response. The demonstration of such a Van Hove singularity in a two-magnon continuum is important as a confirmation of broadly held notions of continua in quantum magnetism and additionally because analogous features in two-spinon continua could be used to distinguish quantum spin liquids from merely disordered systems. These results establish YbCl3 as a benchmark material for quantum magnetism on the honeycomb lattice.

The microtubule-binding outer kinetochore is coupled to centromeric chromatin through CENP-CMif2, CENP-TCnn1, and CENP-UAme1 linker pathways originating from the constitutive centromere associated network (CCAN) of the inner kinetochore. Here, we demonstrate the recurrent loss of most CCAN components, including certain kinetochore linkers during the evolution of the fungal phylum of Basidiomycota. By kinetochore interactome analyses in a model basidiomycete and human pathogen Cryptococcus neoformans, a forkhead-associated domain containing protein "bridgin" was identified as a kinetochore component along with other predicted kinetochore proteins. In vivo and in vitro functional analyses of bridgin reveal its ability to connect the outer kinetochore with centromeric chromatin to ensure accurate chromosome segregation. Unlike established CCAN-based linkers, bridgin is recruited at the outer kinetochore establishing its role as a distinct family of kinetochore proteins. Presence of bridgin homologs in non-fungal lineages suggests an ancient divergent strategy exists to bridge the outer kinetochore with centromeric chromatin.

Tandem organic solar cells are based on the device structure monolithically connecting two solar cells to broaden overall absorption spectrum and utilize the photon energy more efficiently. Herein, we demonstrate a simple strategy of inserting a double bond between the central core and end groups of the small molecule acceptor Y6 to extend its conjugation length and absorption range. As a result, a new narrow bandgap acceptor BTPV-4F was synthesized with an optical bandgap of 1.21 eV. The single-junction devices based on BTPV-4F as acceptor achieved a power conversion efficiency of over 13.4% with a high short-circuit current density of 28.9 mA cm-2. With adopting BTPV-4F as the rear cell acceptor material, the resulting tandem devices reached a high power conversion efficiency of over 16.4% with good photostability. The results indicate that BTPV-4F is an efficient infrared-absorbing narrow bandgap acceptor and has great potential to be applied into tandem organic solar cells.

Despite great challenges, the development of new molecular structures with multiple and even conflicting characteristics are eagerly pursued for exploring advanced applications. To develop high-performance chiral organic semiconducting molecules, a distorted π-system is required for strong coupling with circularly polarized light (CPL), whereas planar π-stacking systems are necessary for high charge-carrier mobility. To address this dilemma, in this work, we introduce a skeleton merging approach through distortion of a perylene diimide (PDI) core with four fused heteroaromatics to form an ortho-π-extended PDI double-[7]heterohelicene. PDI double helicene inherits a high dissymmetry factor from the helicene skeleton, and the extended π-planar system concurrently maintains a high level of charge transport properties. In addition, ortho-π-extension of the PDI skeleton brings about near-infrared (NIR) light absorption and ambipolar charge transport abilities, endowing the corresponding organic phototransistors with high photoresponsivity of 450 and 120 mA W-1 in p- and n-type modes respectively, along with a high external quantum efficiency (89%) under NIR light irradiations. Remarkably, these multiple characteristics enable high-performance broadband CPL detections up to NIR spectral region with chiral organic semiconductors.

While digital trace data from sources like search engines hold enormous potential for tracking and understanding human behavior, these streams of data lack information about the actual experiences of those individuals generating the data. Moreover, most current methods ignore or under-utilize human processing capabilities that allow humans to solve problems not yet solvable by computers (human computation). We demonstrate how behavioral research, linking digital and real-world behavior, along with human computation, can be utilized to improve the performance of studies using digital data streams. This study looks at the use of search data to track prevalence of Influenza-Like Illness (ILI). We build a behavioral model of flu search based on survey data linked to users' online browsing data. We then utilize human computation for classifying search strings. Leveraging these resources, we construct a tracking model of ILI prevalence that outperforms strong historical benchmarks using only a limited stream of search data and lends itself to tracking ILI in smaller geographic units. While this paper only addresses searches related to ILI, the method we describe has potential for tracking a broad set of phenomena in near real-time.

Fractionalization is a phenomenon where an elementary excitation partitions into several pieces. This picture explains non-trivial transport through a junction of one-dimensional edge channels defined by topologically distinct quantum Hall states, for example, a hole-conjugate state at Landau-level filling factor ν = 2/3. Here we employ a time-resolved scheme to identify an elementary fractionalization process; injection of charge q from a non-interaction region into an interacting and scattering region of one-dimensional channels results in the formation of a collective excitation with charge (1-r)q by reflecting fractionalized charge rq. The fractionalization factors, r = 0.34 ± 0.03 for ν = 2/3 and r = 0.49 ± 0.03 for ν = 2, are consistent with the quantized values of 1/3 and 1/2, respectively, which are expected in the disorder dominated regime. The scheme can be used for generating and transporting fractionalized charges with a well-defined time course along a well-defined path.

Erratum in Nat Commun. 2021 Feb 8;12(1):995.

Environmentally benign synthesis of graphite at low temperatures is a great challenge in the absence of transition metal catalysts. Herein, we report a green and efficient approach of synthesizing graphite from carbon dioxide at ultralow temperatures in the absence of transition metal catalysts. Carbon dioxide is converted into graphite submicroflakes in the seconds timescale via reacting with lithium aluminum hydride as the mixture of carbon dioxide and lithium aluminum hydride is heated to as low as 126 °C. Gas pressure-dependent kinetic barriers for synthesizing graphite is demonstrated to be the major reason for our synthesis of graphite without the graphitization process of amorphous carbon. When serving as lithium storage materials, graphite submicroflakes exhibit excellent rate capability and cycling performance with a reversible capacity of ~320 mAh g-1 after 1500 cycles at 1.0 A g-1. This study provides an avenue to synthesize graphite from greenhouse gases at low temperatures.

p97, also known as valosin-containing protein (VCP) or Cdc48, plays a central role in cellular protein homeostasis. Human p97 mutations are associated with several neurodegenerative diseases. Targeting p97 and its cofactors is a strategy for cancer drug development. Despite significant structural insights into the fungal homolog Cdc48, little is known about how human p97 interacts with its cofactors. Recently, the anti-alcohol abuse drug disulfiram was found to target cancer through Npl4, a cofactor of p97, but the molecular mechanism remains elusive. Here, using single-particle cryo-electron microscopy (cryo-EM), we uncovered three Npl4 conformational states in complex with human p97 before ATP hydrolysis. The motion of Npl4 results from its zinc finger motifs interacting with the N domain of p97, which is essential for the unfolding activity of p97. In vitro and cell-based assays showed that the disulfiram derivative bis-(diethyldithiocarbamate)-copper (CuET) can bypass the copper transporter system and inhibit the function of p97 in the cytoplasm by releasing cupric ions under oxidative conditions, which disrupt the zinc finger motifs of Npl4, locking the essential conformational switch of the complex.

The diversity reflected by >100 different neural cell types fundamentally contributes to brain function and a central idea is that neuronal identity can be inferred from genetic information. Recent large-scale transcriptomic assays seem to confirm this hypothesis, but a lack of morphological information has limited the identification of several known cell types. In this study, we used single-cell RNA-seq in morphologically identified parvalbumin interneurons (PV-INs), and studied their transcriptomic states in the morphological, physiological, and developmental domains. Overall, we find high transcriptomic similarity among PV-INs, with few genes showing divergent expression between morphologically different types. Furthermore, PV-INs show a uniform synaptic cell adhesion molecule (CAM) profile, suggesting that CAM expression in mature PV cells does not reflect wiring specificity after development. Together, our results suggest that while PV-INs differ in anatomy and in vivo activity, their continuous transcriptomic and homogenous biophysical landscapes are not predictive of these distinct identities.

There is a vital need for authentic COVID-19 animal models to enable the pre-clinical evaluation of candidate vaccines and therapeutics. Here we report a dose titration study of SARS-CoV-2 in the ferret model. After a high (5 × 106 pfu) and medium (5 × 104 pfu) dose of virus is delivered, intranasally, viral RNA shedding in the upper respiratory tract (URT) is observed in 6/6 animals, however, only 1/6 ferrets show similar signs after low dose (5 × 102 pfu) challenge. Following sequential culls pathological signs of mild multifocal bronchopneumonia in approximately 5-15% of the lung is seen on day 3, in high and medium dosed groups. Ferrets re-challenged, after virus shedding ceased, are fully protected from acute lung pathology. The endpoints of URT viral RNA replication & distinct lung pathology are observed most consistently in the high dose group. This ferret model of SARS-CoV-2 infection presents a mild clinical disease.

Citrullination is a post-translational modification (PTM) of arginine that is crucial for several physiological processes, including gene regulation and neutrophil extracellular trap formation. Despite recent advances, studies of protein citrullination remain challenging due to the difficulty of accessing proteins homogeneously citrullinated at a specific site. Herein, we report a technology that enables the site-specific incorporation of citrulline (Cit) into proteins in mammalian cells. This approach exploits an engineered E. coli-derived leucyl tRNA synthetase-tRNA pair that incorporates a photocaged-citrulline (SM60) into proteins in response to a nonsense codon. Subsequently, SM60 is readily converted to Cit with light in vitro and in living cells. To demonstrate the utility of the method, we biochemically characterize the effect of incorporating Cit at two known autocitrullination sites in Protein Arginine Deiminase 4 (PAD4, R372 and R374) and show that the R372Cit and R374Cit mutants are 181- and 9-fold less active than the wild-type enzyme. This technology possesses the potential to decipher the biology of citrullination.

Scanning photoelectron microscopy (SPEM) and photoemission electron microscopy (PEEM) allow local surface analysis and visualising ongoing reactions on a µm-scale. These two spatio-temporal imaging methods are applied to polycrystalline Rh, representing a library of well-defined high-Miller-index surface structures. The combination of these techniques enables revealing the anisotropy of surface oxidation, as well as its effect on catalytic hydrogen oxidation. In the present work we observe, using locally-resolved SPEM, structure-sensitive surface oxide formation, which is summarised in an oxidation map and quantitatively explained by the novel step density (SDP) and step edge (SEP) parameters. In situ PEEM imaging of ongoing H2 oxidation allows a direct comparison of the local reactivity of metallic and oxidised Rh surfaces for the very same different stepped surface structures, demonstrating the effect of Rh surface oxides. Employing the velocity of propagating reaction fronts as indicator of surface reactivity, we observe a high transient activity of Rh surface oxide in H2 oxidation. The corresponding velocity map reveals the structure-dependence of such activity, representing a direct imaging of a structure-activity relation for plenty of well-defined surface structures within one sample.

In Bacteroidetes, one of the dominant phyla of the mammalian gut, active uptake of large nutrients across the outer membrane is mediated by SusCD protein complexes via a "pedal bin" transport mechanism. However, many features of SusCD function in glycan uptake remain unclear, including ligand binding, the role of the SusD lid and the size limit for substrate transport. Here we characterise the β2,6 fructo-oligosaccharide (FOS) importing SusCD from Bacteroides thetaiotaomicron (Bt1762-Bt1763) to shed light on SusCD function. Co-crystal structures reveal residues involved in glycan recognition and suggest that the large binding cavity can accommodate several substrate molecules, each up to ~2.5 kDa in size, a finding supported by native mass spectrometry and isothermal titration calorimetry. Mutational studies in vivo provide functional insights into the key structural features of the SusCD apparatus and cryo-EM of the intact dimeric SusCD complex reveals several distinct states of the transporter, directly visualising the dynamics of the pedal bin transport mechanism.

Elegant asymmetric synthesis of hasubanan alkaloids have been developed over the past decades. However, a divergent approach leading to all three sub-classes of this family of natural products remains unknown. We report herein the realization of such an endeavor by accomplishing enantioselective total syntheses of four representative members. The synthesis is characterized by catalytic enantioselective construction of the tricyclic compounds from which three different intramolecular C-N bond forming processes leading to three topologically different hasubanan alkaloids are developed. An aza-Michael addition is used for the construction of the aza-[4.4.3]-propellane structure of (-)-cepharamine, whereas an oxidation/double deprotection/intramolecular hemiaminal forming sequence is developed to forge the bridged 6/6/6/6 tetracycle of (-)-cepharatines A and C and a domino bromination/double deprotection/cyclization sequence allows the build-up of the 6/6/5/5 fused tetracyclic structure of (-)-sinoracutine.

The dynamics of three-dimensional (3D) dissipative solitons originated from spatiotemporal interactions share many common characteristics with other multi-dimensional phenomena. Unveiling the dynamics of 3D solitons thus permits new routes for tackling multidisciplinary nonlinear problems and exploiting their instabilities. However, this remains an open challenge, as they are multi-dimensional, stochastic and non-repeatable. Here, we report the real-time speckle-resolved spectral-temporal dynamics of a 3D soliton laser using a single-shot multispeckle spectral-temporal technology that leverages optical time division multiplexing and photonic time stretch. This technology enables the simultaneous observation on multiple speckle grains to provide long-lasting evolutionary dynamics on the planes of cavity time (t) - roundtrip and spectrum (λ) - roundtrip. Various non-repeatable speckly-diverse spectral-temporal dynamics are discovered in both the early and established stages of the 3D soliton formation.

Protein-ligand complexes with catch bonds exhibit prolonged lifetimes when subject to tensile force, which is a desirable yet elusive attribute for man-made nanoparticle interfaces and assemblies. Most designs proposed so far rely on macromolecular linkers with complicated folds rather than particles exhibiting simple dynamic shapes. Here, we establish a scissor-type X-shaped particle design for achieving intrinsic catch bonding ability with tunable force-enhanced lifetimes under thermal excitations. Molecular dynamics simulations are carried out to illustrate equilibrium self-assembly and force-enhanced bond lifetime of dimers and fibers facilitated by secondary interactions that form under tensile force. The non-monotonic force dependence of the fiber breaking kinetics is well-estimated by an analytical model. Our design concepts for shape-changing particles illuminates a path towards novel nanoparticle or colloidal assemblies that have the passive ability to tune the strength of their interfaces with applied force, setting the stage for self-assembling materials with novel mechanical functions and rheological properties.

Environmental triggers have important functions in multiple sclerosis (MS) susceptibility, phenotype, and trajectory. Exposure to early life trauma (ELT) has been associated with higher relapse rates in MS patients; however, the underlying mechanisms are not well-defined. Here we show ELT induces mechanistic and phenotypical alterations during experimental autoimmune encephalitis (EAE). ELT sustains downregulation of immune cell adrenergic receptors, which can be attributed to chronic norepinephrine circulation. ELT-subjected mice exhibit interferon-β resistance and neurodegeneration driven by lymphotoxin and CXCR2 involvement. These phenotypic changes are observed in control EAE mice treated with β1 adrenergic receptor antagonist. Conversely, β1 adrenergic receptor agonist treatment to ELT mice abrogates phenotype changes via restoration of immune cell β1 adrenergic receptor function. Our results indicate that ELT alters EAE phenotype via downregulation of β1 adrenergic signaling in immune cells. These results have implications for the effect of environmental factors in provoking disease heterogeneity and might enable prediction of long-term outcomes in MS.

Update of medRxiv. 2020 May 25;:

Identifying novel drug targets to overcome resistance to tyrosine kinase inhibitors (TKIs) and eradicating leukemia stem/progenitor cells are required for the treatment of chronic myelogenous leukemia (CML). Here, we show that ubiquitin-specific peptidase 47 (USP47) is a potential target to overcome TKI resistance. Functional analysis shows that USP47 knockdown represses proliferation of CML cells sensitive or resistant to imatinib in vitro and in vivo. The knockout of Usp47 significantly inhibits BCR-ABL and BCR-ABLT315I-induced CML in mice with the reduction of Lin-Sca1+c-Kit+ CML stem/progenitor cells. Mechanistic studies show that stabilizing Y-box binding protein 1 contributes to USP47-mediated DNA damage repair in CML cells. Inhibiting USP47 by P22077 exerts cytotoxicity to CML cells with or without TKI resistance in vitro and in vivo. Moreover, P22077 eliminates leukemia stem/progenitor cells in CML mice. Together, targeting USP47 is a promising strategy to overcome TKI resistance and eradicate leukemia stem/progenitor cells in CML.

IL11 is important for fibrosis in non-alcoholic steatohepatitis (NASH) but its role beyond the stroma in liver disease is unclear. Here, we investigate the role of IL11 in hepatocyte lipotoxicity. Hepatocytes highly express IL11RA and secrete IL11 in response to lipid loading. Autocrine IL11 activity causes hepatocyte death through NOX4-derived ROS, activation of ERK, JNK and caspase-3, impaired mitochondrial function and reduced fatty acid oxidation. Paracrine IL11 activity stimulates hepatic stellate cells and causes fibrosis. In mouse models of NASH, hepatocyte-specific deletion of Il11ra1 protects against liver steatosis, fibrosis and inflammation while reducing serum glucose, cholesterol and triglyceride levels and limiting obesity. In mice deleted for Il11ra1, restoration of IL11 cis-signaling in hepatocytes reconstitutes steatosis and inflammation but not fibrosis. We found no evidence for the existence of IL6 or IL11 trans-signaling in hepatocytes or NASH. These data show that IL11 modulates hepatocyte metabolism and suggests a mechanism for NAFLD to NASH transition.

Trafficking of mitochondria into dendrites and axons plays an important role in the physiology and pathophysiology of neurons. Mitochondrial outer membrane protein Miro and adaptor proteins TRAKs/Milton link mitochondria to molecular motors. Here we show that metaxins MTX-1 and MTX-2 contribute to mitochondrial transport into both dendrites and axons of C. elegans neurons. MTX1/2 bind to MIRO-1 and kinesin light chain KLC-1, forming a complex to mediate kinesin-1-based movement of mitochondria, in which MTX-1/2 are essential and MIRO-1 plays an accessory role. We find that MTX-2, MIRO-1, and TRAK-1 form another distinct adaptor complex to mediate dynein-based transport. Additionally, we show that failure of mitochondrial trafficking in dendrites causes age-dependent dendrite degeneration. We propose that MTX-2 and MIRO-1 form the adaptor core for both motors, while MTX-1 and TRAK-1 specify each complex for kinesin-1 and dynein, respectively. MTX-1 and MTX-2 are also required for mitochondrial transport in human neurons, indicative of their evolutionarily conserved function.

Colloidal gold nanoparticles (GNPs) serve as promising contrast agents in photoacoustic (PA) imaging, yet their utility is limited due to their absorption peak in the visible window overlapping with that of hemoglobin. To overcome such limitation, this report describes an ultrapure chain-like gold nanoparticle (CGNP) clusters with a redshift peak wavelength at 650 nm. The synthesized CGNP show an excellent biocompatibility and photostability. These nanoparticles are conjugated with arginine-glycine-aspartic acid (RGD) peptides (CGNP clusters-RGD) and validated in 12 living rabbits to perform multimodal photoacoustic microscopy (PAM) and optical coherence tomography (OCT) for visualization of newly developed blood vessels in the sub-retinal pigment epithelium (RPE) space of the retina, named choroidal neovascularization (CNV). The PAM system can achieve a 3D PAM image via a raster scan of 256 × 256 pixels within a time duration of 65 s. Intravenous injection of CGNP clusters-RGD bound to CNV and resulted in up to a 17-fold increase in PAM signal and 176% increase in OCT signal. Histology indicates that CGNP clusters could disassemble, which may facilitate its clearance from the body.

Enterohemorrhagic Escherichia coli (EHEC) induces changes to the intestinal cell cytoskeleton and formation of attaching and effacing lesions, characterized by the effacement of microvilli and then formation of actin pedestals to which the bacteria are tightly attached. Here, we use a Caenorhabditis elegans model of EHEC infection to show that microvillar effacement is mediated by a signalling pathway including mitotic cyclin-dependent kinase 1 (CDK1) and diaphanous-related formin 1 (CYK1). Similar observations are also made using EHEC-infected human intestinal cells in vitro. Our results support the use of C. elegans as a host model for studying attaching and effacing lesions in vivo, and reveal that the CDK1-formin signal axis is necessary for EHEC-induced microvillar effacement.

Western diet (WD) is one of the major culprits of metabolic disease including type 2 diabetes (T2D) with gut microbiota playing an important role in modulating effects of the diet. Herein, we use a data-driven approach (Transkingdom Network analysis) to model host-microbiome interactions under WD to infer which members of microbiota contribute to the altered host metabolism. Interrogation of this network pointed to taxa with potential beneficial or harmful effects on host's metabolism. We then validate the functional role of the predicted bacteria in regulating metabolism and show that they act via different host pathways. Our gene expression and electron microscopy studies show that two species from Lactobacillus genus act upon mitochondria in the liver leading to the improvement of lipid metabolism. Metabolomics analyses revealed that reduced glutathione may mediate these effects. Our study identifies potential probiotic strains for T2D and provides important insights into mechanisms of their action.

Histones control gene expression by regulating chromatin structure and function. The posttranslational modifications (PTMs) on the side chains of histones form the epigenetic landscape, which is tightly controlled by epigenetic modulator enzymes and further recognized by so-called reader domains. Histone microarrays have been widely applied to investigate histone-reader interactions, but not the transient interactions of Zn2+-dependent histone deacetylase (HDAC) eraser enzymes. Here, we synthesize hydroxamic acid-modified histone peptides and use them in femtomolar microarrays for the direct capture and detection of the four class I HDAC isozymes. Follow-up functional assays in solution provide insights into their suitability to discover HDAC substrates and inhibitors with nanomolar potency and activity in cellular assays. We conclude that similar hydroxamic acid-modified histone peptide microarrays and libraries could find broad application to identify class I HDAC isozyme-specific substrates and facilitate the development of isozyme-selective HDAC inhibitors and probes.

In recent years, advances in cryoEM have dramatically increased the resolution of reconstructions and, with it, the number of solved atomic models. It is widely accepted that the quality of cryoEM maps varies locally; therefore, the evaluation of the maps-derived structural models must be done locally as well. In this article, a method for the local analysis of the map-to-model fit is presented. The algorithm uses a comparison of two local resolution maps. The first is the local FSC (Fourier shell correlation) between the full map and the model, while the second is calculated between the half maps normally used in typical single particle analysis workflows. We call the quality measure "FSC-Q", and it is a quantitative estimation of how much of the model is supported by the signal content of the map. Furthermore, we show that FSC-Q may be helpful to detect overfitting. It can be used to complement other methods, such as the Q-score method that estimates the resolvability of atoms.

RAC1 activity is critical for intestinal homeostasis, and is required for hyperproliferation driven by loss of the tumour suppressor gene Apc in the murine intestine. To avoid the impact of direct targeting upon homeostasis, we reasoned that indirect targeting of RAC1 via RAC-GEFs might be effective. Transcriptional profiling of Apc deficient intestinal tissue identified Vav3 and Tiam1 as key targets. Deletion of these indicated that while TIAM1 deficiency could suppress Apc-driven hyperproliferation, it had no impact upon tumourigenesis, while VAV3 deficiency had no effect. Intriguingly, deletion of either gene resulted in upregulation of Vav2, with subsequent targeting of all three (Vav2-/- Vav3-/- Tiam1-/-), profoundly suppressing hyperproliferation, tumourigenesis and RAC1 activity, without impacting normal homeostasis. Critically, the observed RAC-GEF dependency was negated by oncogenic KRAS mutation. Together, these data demonstrate that while targeting RAC-GEF molecules may have therapeutic impact at early stages, this benefit may be lost in late stage disease.

Natural enzymes exhibit unparalleled selectivity due to the microenvironment around the active sites, but how to design artificial catalysts to achieve similar performance is a formidable challenge for the catalysis community. Herein, we report that a less selective platinum catalyst becomes highly active and selective for industrially relevant hydrosilylation of a broad range of substrates when a porous cage ligand is used for confinement around the catalytic active site. The catalyst is more than ten times more active than Karstedt's catalyst while being recyclable. Properties such as size-selective catalysis and Michaelis-Menten kinetics support the proposed enzyme-like model. This biomimetic catalyst exhibits remarkable site-selectivity through the cage's confining effect, which amplifies small steric differences into dramatic reactivity changes for similar functional groups within a molecule.

The realisation of fast-charging lithium-ion batteries with long cycle lifetimes is hindered by the uncontrollable plating of metallic Li on the graphite anode during high-rate charging. Here we report that surface engineering of graphite with a cooperative biphasic MoOx-MoPx promoter improves the charging rate and suppresses Li plating without compromising energy density. We design and synthesise MoOx-MoPx/graphite via controllable and scalable surface engineering, i.e., the deposition of a MoOx nanolayer on the graphite surface, followed by vapour-induced partial phase transformation of MoOx to MoPx. A variety of analytical studies combined with thermodynamic calculations demonstrate that MoOx effectively mitigates the formation of resistive films on the graphite surface, while MoPx hosts Li+ at relatively high potentials via a fast intercalation reaction and plays a dominant role in lowering the Li+ adsorption energy. The MoOx-MoPx/graphite anode exhibits a fast-charging capability (<10 min charging for 80% of the capacity) and stable cycling performance without any signs of Li plating over 300 cycles when coupled with a LiNi0.6Co0.2Mn0.2O2 cathode. Thus, the developed approach paves the way to the design of advanced anode materials for fast-charging Li-ion batteries.

Mitochondrial oxidation-induced cell death, a physiological process triggered by various cancer therapeutics to induce oxidative stress on tumours, has been challenging to investigate owing to the difficulties in generating mitochondria-specific oxidative stress and monitoring mitochondrial responses simultaneously. Accordingly, to the best of our knowledge, the relationship between mitochondrial protein oxidation via oxidative stress and the subsequent cell death-related biological phenomena has not been defined. Here, we developed a multifunctional iridium(III) photosensitiser, Ir-OA, capable of inducing substantial mitochondrial oxidative stress and monitoring the corresponding change in viscosity, polarity, and morphology. Photoactivation of Ir-OA triggers chemical modifications in mitochondrial protein-crosslinking and oxidation (i.e., oxidative phosphorylation complexes and channel and translocase proteins), leading to microenvironment changes, such as increased microviscosity and depolarisation. These changes are strongly related to cell death by inducing mitochondrial swelling with excessive fission and fusion. We suggest a potential mechanism from mitochondrial oxidative stress to cell death based on proteomic analyses and phenomenological observations.

Gene flow is predicted to impede parallel adaptation via de novo mutation, because it can introduce pre-existing adaptive alleles from population to population. We test this using Hawaiian crickets (Teleogryllus oceanicus) in which 'flatwing' males that lack sound-producing wing structures recently arose and spread under selection from an acoustically-orienting parasitoid. Morphometric and genetic comparisons identify distinct flatwing phenotypes in populations on three islands, localized to different loci. Nevertheless, we detect strong, recent and ongoing gene flow among the populations. Using genome scans and gene expression analysis we find that parallel evolution of flatwing on different islands is associated with shared genomic hotspots of adaptation that contain the gene doublesex, but the form of selection differs among islands and corresponds to known flatwing demographics in the wild. We thus show how parallel adaptation can occur on contemporary timescales despite gene flow, indicating that it could be less constrained than previously appreciated.

Efficient and stable perovskite solar cells with a simple active layer are desirable for manufacturing. Three-dimensional perovskite solar cells are most efficient but need to have improved environmental stability. Inclusion of larger ammonium salts has led to a trade-off between improved stability and efficiency, which is attributed to the perovskite films containing a two-dimensional component. Here, we show that addition of 0.3 mole percent of a fluorinated lead salt into the three-dimensional methylammonium lead iodide perovskite enables low temperature fabrication of simple inverted solar cells with a maximum power conversion efficiency of 21.1%. The perovskite layer has no detectable two-dimensional component at salt concentrations of up to 5 mole percent. The high concentration of fluorinated material found at the film-air interface provides greater hydrophobicity, increased size and orientation of the surface perovskite crystals, and unencapsulated devices with increased stability to high humidity.

Recent advances in deep learning have been providing non-intuitive solutions to various inverse problems in optics. At the intersection of machine learning and optics, diffractive networks merge wave-optics with deep learning to design task-specific elements to all-optically perform various tasks such as object classification and machine vision. Here, we present a diffractive network, which is used to shape an arbitrary broadband pulse into a desired optical waveform, forming a compact and passive pulse engineering system. We demonstrate the synthesis of various different pulses by designing diffractive layers that collectively engineer the temporal waveform of an input terahertz pulse. Our results demonstrate direct pulse shaping in terahertz spectrum, where the amplitude and phase of the input wavelengths are independently controlled through a passive diffractive device, without the need for an external pump. Furthermore, a physical transfer learning approach is presented to illustrate pulse-width tunability by replacing part of an existing network with newly trained diffractive layers, demonstrating its modularity. This learning-based diffractive pulse engineering framework can find broad applications in e.g., communications, ultra-fast imaging and spectroscopy.

With the advent of the big data era, applications are more data-centric and energy efficiency issues caused by frequent data interactions, due to the physical separation of memory and computing, will become increasingly severe. Emerging technologies have been proposed to perform analog computing with memory to address the dilemma. Ferroelectric memory has become a promising technology due to field-driven fast switching and non-destructive readout, but endurance and miniaturization are limited. Here, we demonstrate the α-In2Se3 ferroelectric semiconductor channel device that integrates non-volatile memory and neural computation functions. Remarkable performance includes ultra-fast write speed of 40 ns, improved endurance through the internal electric field, flexible adjustment of neural plasticity, ultra-low energy consumption of 234/40 fJ per event for excitation/inhibition, and thermally modulated 94.74% high-precision iris recognition classification simulation. This prototypical demonstration lays the foundation for an integrated memory computing system with high density and energy efficiency.

Long nanopore reads are advantageous in de novo genome assembly. However, nanopore reads usually have broad error distribution and high-error-rate subsequences. Existing error correction tools cannot correct nanopore reads efficiently and effectively. Most methods trim high-error-rate subsequences during error correction, which reduces both the length of the reads and contiguity of the final assembly. Here, we develop an error correction, and de novo assembly tool designed to overcome complex errors in nanopore reads. We propose an adaptive read selection and two-step progressive method to quickly correct nanopore reads to high accuracy. We introduce a two-stage assembler to utilize the full length of nanopore reads. Our tool achieves superior performance in both error correction and de novo assembling nanopore reads. It requires only 8122 hours to assemble a 35X coverage human genome and achieves a 2.47-fold improvement in NG50. Furthermore, our assembly of the human WERI cell line shows an NG50 of 22 Mbp. The high-quality assembly of nanopore reads can significantly reduce false positives in structure variation detection.

Erratum in Nat Commun. 2021 Jan 18;12(1):533.

The development of single-cell methods for capturing different data modalities including imaging and sequencing has revolutionized our ability to identify heterogeneous cell states. Different data modalities provide different perspectives on a population of cells, and their integration is critical for studying cellular heterogeneity and its function. While various methods have been proposed to integrate different sequencing data modalities, coupling imaging and sequencing has been an open challenge. We here present an approach for integrating vastly different modalities by learning a probabilistic coupling between the different data modalities using autoencoders to map to a shared latent space. We validate this approach by integrating single-cell RNA-seq and chromatin images to identify distinct subpopulations of human naive CD4+ T-cells that are poised for activation. Collectively, our approach provides a framework to integrate and translate between data modalities that cannot yet be measured within the same cell for diverse applications in biomedical discovery.

Erratum in Nat Commun. 2021 Feb 10;12(1):1048.

Despite proteotoxic stress and heat shock being implicated in diverse pathologies, currently no methodology to inflict defined, subcellular thermal damage exists. Here, we present such a single-cell method compatible with laser-scanning microscopes, adopting the plasmon resonance principle. Dose-defined heat causes protein damage in subcellular compartments, rapid heat-shock chaperone recruitment, and ensuing engagement of the ubiquitin-proteasome system, providing unprecedented insights into the spatiotemporal response to thermal damage relevant for degenerative diseases, with broad applicability in biomedicine. Using this versatile method, we discover that HSP70 chaperone and its interactors are recruited to sites of thermally damaged proteins within seconds, and we report here mechanistically important determinants of such HSP70 recruitment. Finally, we demonstrate a so-far unsuspected involvement of p97(VCP) translocase in the processing of heat-damaged proteins. Overall, we report an approach to inflict targeted thermal protein damage and its application to elucidate cellular stress-response pathways that are emerging as promising therapeutic targets.

For over two decades photoacoustic imaging has been tested clinically, but successful human trials have been limited. To enable quantitative clinical spectroscopy, the fundamental issues of wavelength-dependent fluence variations and inter-wavelength motion must be overcome. Here we propose a real-time, spectroscopic photoacoustic/ultrasound (PAUS) imaging approach using a compact, 1-kHz rate wavelength-tunable laser. Instead of illuminating tissue over a large area, the fiber-optic delivery system surrounding an US array sequentially scans a narrow laser beam, with partial PA image reconstruction for each laser pulse. The final image is then formed by coherently summing partial images. This scheme enables (i) automatic compensation for wavelength-dependent fluence variations in spectroscopic PA imaging and (ii) motion correction of spectroscopic PA frames using US speckle tracking in real-time systems. The 50-Hz video rate PAUS system is demonstrated in vivo using a murine model of labelled drug delivery.

p53 mutations with single amino acid changes in cancer often lead to dominant oncogenic changes. Here, we have developed a mouse model of gain-of-function (GOF) p53-driven lung cancer utilizing conditionally active LSL p53-R172H and LSL K-Ras-G12D knock-in alleles that can be activated by Cre in lung club cells. Mutation of the p53 transactivation domain (TAD) (p53-L25Q/W26S/R172H) eliminating significant transactivation activity resulted in loss of tumorigenicity, demonstrating that transactivation mediated by or dependent on TAD is required for oncogenicity by GOF p53. GOF p53 TAD mutations significantly reduce phosphorylation of nearby p53 serine 20 (S20), which is a target for PLK3 phosphorylation. Knocking out PLK3 attenuated S20 phosphorylation along with transactivation and oncogenicity by GOF p53, indicating that GOF p53 exploits PLK3 to trigger its transactivation capability and exert oncogenic functions. Our data show a mechanistic involvement of PLK3 in mutant p53 pathway of oncogenesis.

Extinction spectroscopy is a powerful tool for demonstrating the coupling of a single quantum emitter to a photonic structure. However, it can be challenging in all but the simplest of geometries to deduce an accurate value of the coupling efficiency from the measured spectrum. Here we develop a theoretical framework to deduce the coupling efficiency from the measured transmission and reflection spectra without precise knowledge of the photonic environment. We then consider the case of a waveguide interrupted by a transverse cut in which an emitter is placed. We apply that theory to a silicon nitride waveguide interrupted by a gap filled with anthracene that is doped with dibenzoterrylene molecules. We describe the fabrication of these devices, and experimentally characterise the waveguide coupling of a single molecule in the gap.

Methyl-specific isotope labeling is a powerful tool to study the structure, dynamics and interactions of large proteins and protein complexes by solution-state NMR. However, widespread applications of this methodology have been limited by challenges in obtaining confident resonance assignments. Here, we present Methyl Assignments Using Satisfiability (MAUS), leveraging Nuclear Overhauser Effect cross-peak data, peak residue type classification and a known 3D structure or structural model to provide robust resonance assignments consistent with all the experimental inputs. Using data recorded for targets with known assignments in the 10-45 kDa size range, MAUS outperforms existing methods by up to 25,000 times in speed while maintaining 100% accuracy. We derive de novo assignments for multiple Cas9 nuclease domains, demonstrating that the methyl resonances of multi-domain proteins can be assigned accurately in a matter of days, while reducing biases introduced by manual pre-processing of the raw NOE data. MAUS is available through an online web-server.

Across the evolutionary history of insects, the shift from nitrogen-rich carnivore/omnivore diets to nitrogen-poor herbivorous diets was made possible through symbiosis with microbes. The herbivorous turtle ants Cephalotes possess a conserved gut microbiome which enriches the nutrient composition by recycling nitrogen-rich metabolic waste to increase the production of amino acids. This enrichment is assumed to benefit the host, but we do not know to what extent. To gain insights into nitrogen assimilation in the ant cuticle we use gut bacterial manipulation, 15N isotopic enrichment, isotope-ratio mass spectrometry, and 15N nuclear magnetic resonance spectroscopy to demonstrate that gut bacteria contribute to the formation of proteins, catecholamine cross-linkers, and chitin in the cuticle. This study identifies the cuticular components which are nitrogen-enriched by gut bacteria, highlighting the role of symbionts in insect evolution, and provides a framework for understanding the nitrogen flow from nutrients through bacteria into the insect cuticle.

Mitochondrial complex I is central to the pathological reactive oxygen species (ROS) production that underlies cardiac ischemia-reperfusion (IR) injury. ND6-P25L mice are homoplasmic for a disease-causing mtDNA point mutation encoding the P25L substitution in the ND6 subunit of complex I. The cryo-EM structure of ND6-P25L complex I revealed subtle structural changes that facilitate rapid conversion to the "deactive" state, usually formed only after prolonged inactivity. Despite its tendency to adopt the "deactive" state, the mutant complex is fully active for NADH oxidation, but cannot generate ROS by reverse electron transfer (RET). ND6-P25L mitochondria function normally, except for their lack of RET ROS production, and ND6-P25L mice are protected against cardiac IR injury in vivo. Thus, this single point mutation in complex I, which does not affect oxidative phosphorylation but renders the complex unable to catalyse RET, demonstrates the pathological role of ROS production by RET during IR injury.

We report the development of a platform of dual targeting Fab (DutaFab) molecules, which comprise two spatially separated and independent binding sites within the human antibody CDR loops: the so-called H-side paratope encompassing HCDR1, HCDR3 and LCDR2, and the L-side paratope encompassing LCDR1, LCDR3 and HCDR2. Both paratopes can be independently selected and combined into the desired bispecific DutaFabs in a modular manner. X-ray crystal structures illustrate that DutaFabs are able to bind two target molecules simultaneously at the same Fv region comprising a VH-VL heterodimer. In the present study, this platform is applied to generate DutaFabs specific for VEGFA and PDGF-BB, which show high affinities, physico-chemical stability and solubility, as well as superior efficacy over anti-VEGF monotherapy in vivo. These molecules exemplify the usefulness of DutaFabs as a distinct class of antibody therapeutics, which is currently being evaluated in patients.

Electron sources are a critical component in a wide range of applications such as electron-beam accelerator facilities, photomultipliers, and image intensifiers for night vision. We report efficient, regenerative and low-cost electron sources based on solution-processed halide perovskites thin films when they are excited with light with energy equal to or above their bandgap. We measure a quantum efficiency up to 2.2% and a lifetime of more than 25 h. Importantly, even after degradation, the electron emission can be completely regenerated to its maximum efficiency by deposition of a monolayer of Cs. The electron emission from halide perovskites can be tuned over the visible and ultraviolet spectrum, and operates at vacuum levels with pressures at least two-orders higher than in state-of-the-art semiconductor electron sources.

Endothelial cells play a critical role in the adaptation of tissues to injury. Tissue ischemia induced by infarction leads to profound changes in endothelial cell functions and can induce transition to a mesenchymal state. Here we explore the kinetics and individual cellular responses of endothelial cells after myocardial infarction by using single cell RNA sequencing. This study demonstrates a time dependent switch in endothelial cell proliferation and inflammation associated with transient changes in metabolic gene signatures. Trajectory analysis reveals that the majority of endothelial cells 3 to 7 days after myocardial infarction acquire a transient state, characterized by mesenchymal gene expression, which returns to baseline 14 days after injury. Lineage tracing, using the Cdh5-CreERT2;mT/mG mice followed by single cell RNA sequencing, confirms the transient mesenchymal transition and reveals additional hypoxic and inflammatory signatures of endothelial cells during early and late states after injury. These data suggest that endothelial cells undergo a transient mes-enchymal activation concomitant with a metabolic adaptation within the first days after myocardial infarction but do not acquire a long-term mesenchymal fate. This mesenchymal activation may facilitate endothelial cell migration and clonal expansion to regenerate the vascular network.

Erratum in Nat Commun. 2021 Feb 23;12(1):1373.

Lima bean (Phaseolus lunatus L.), one of the five domesticated Phaseolus bean crops, shows a wide range of ecological adaptations along its distribution range from Mexico to Argentina. These adaptations make it a promising crop for improving food security under predicted scenarios of climate change in Latin America and elsewhere. In this work, we combine long and short read sequencing technologies with a dense genetic map from a biparental population to obtain the chromosome-level genome assembly for Lima bean. Annotation of 28,326 gene models show high diversity among 1917 genes with conserved domains related to disease resistance. Structural comparison across 22,180 orthologs with common bean reveals high genome synteny and five large intrachromosomal rearrangements. Population genomic analyses show that wild Lima bean is organized into six clusters with mostly non-overlapping distributions and that Mesomerican landraces can be further subdivided into three subclusters. RNA-seq data reveal 4275 differentially expressed genes, which can be related to pod dehiscence and seed development. We expect the resources presented here to serve as a solid basis to achieve a comprehensive view of the degree of convergent evolution of Phaseolus species under domestication and provide tools and information for breeding for climate change resiliency.

The mechanisms underlying gene repression and silencers are poorly understood. Here we investigate the hypothesis that H3K27me3-rich regions of the genome, defined from clusters of H3K27me3 peaks, may be used to identify silencers that can regulate gene expression via proximity or looping. We find that H3K27me3-rich regions are associated with chromatin interactions and interact preferentially with each other. H3K27me3-rich regions component removal at interaction anchors by CRISPR leads to upregulation of interacting target genes, altered H3K27me3 and H3K27ac levels at interacting regions, and altered chromatin interactions. Chromatin interactions did not change at regions with high H3K27me3, but regions with low H3K27me3 and high H3K27ac levels showed changes in chromatin interactions. Cells with H3K27me3-rich regions knockout also show changes in phenotype associated with cell identity, and altered xenograft tumor growth. Finally, we observe that H3K27me3-rich regions-associated genes and long-range chromatin interactions are susceptible to H3K27me3 depletion. Our results characterize H3K27me3-rich regions and their mechanisms of functioning via looping.

Coronary artery calcium is an accurate predictor of cardiovascular events. While it is visible on all computed tomography (CT) scans of the chest, this information is not routinely quantified as it requires expertise, time, and specialized equipment. Here, we show a robust and time-efficient deep learning system to automatically quantify coronary calcium on routine cardiac-gated and non-gated CT. As we evaluate in 20,084 individuals from distinct asymptomatic (Framingham Heart Study, NLST) and stable and acute chest pain (PROMISE, ROMICAT-II) cohorts, the automated score is a strong predictor of cardiovascular events, independent of risk factors (multivariable-adjusted hazard ratios up to 4.3), shows high correlation with manual quantification, and robust test-retest reliability. Our results demonstrate the clinical value of a deep learning system for the automated prediction of cardiovascular events. Implementation into clinical practice would address the unmet need of automating proven imaging biomarkers to guide management and improve population health.

Skeletal muscle has remarkable regeneration capabilities, mainly due to its resident muscle stem cells (MuSCs). In this review, we introduce recently developed technologies and the mechanistic insights they provide to the understanding of MuSC biology, including the re-definition of quiescence and Galert states. Additionally, we present recent studies that link MuSC function with cellular heterogeneity, highlighting the complex regulation of self-renewal in regeneration, muscle disorders and aging. Finally, we discuss MuSC metabolism and its role, as well as the multifaceted regulation of MuSCs by their niche. The presented conceptual advances in the MuSC field impact on our general understanding of stem cells and their therapeutic use in regenerative medicine.

Polycomb repressive complex 2 (PRC2) is a histone methyltransferase critical for maintaining gene silencing during eukaryotic development. In mammals, PRC2 activity is regulated in part by the selective incorporation of one of two paralogs of the catalytic subunit, EZH1 or EZH2. Each of these enzymes has specialized biological functions that may be partially explained by differences in the multivalent interactions they mediate with chromatin. Here, we present two cryo-EM structures of PRC2:EZH1, one as a monomer and a second one as a dimer bound to a nucleosome. When bound to nucleosome substrate, the PRC2:EZH1 dimer undergoes a dramatic conformational change. We demonstrate that mutation of a divergent EZH1/2 loop abrogates the nucleosome-binding and methyltransferase activities of PRC2:EZH1. Finally, we show that PRC2:EZH1 dimers are more effective than monomers at promoting chromatin compaction, and the divergent EZH1/2 loop is essential for this function, thereby tying together the methyltransferase, nucleosome-binding, and chromatin-compaction activities of PRC2:EZH1. We speculate that the conformational flexibility and the ability to dimerize enable PRC2 to act on the varied chromatin substrates it encounters in the cell.

Biological organic-inorganic materials remain a popular source of inspiration for bioinspired materials design and engineering. Inspired by the self-assembling metal-reinforced mussel holdfast threads, we tested if metal-coordinate polymer networks can be utilized as simple composite scaffolds for direct in situ crosslink mineralization. Starting with aqueous solutions of polymers end-functionalized with metal-coordinating ligands of catechol or histidine, here we show that inter-molecular metal-ion coordination complexes can serve as mineral nucleation sites, whereby significant mechanical reinforcement is achieved upon nanoscale particle growth directly at the metal-coordinate network crosslink sites.

Dynamic assembly and disassembly of primary cilia controls embryonic development and tissue homeostasis. Dysregulation of ciliogenesis causes human developmental diseases termed ciliopathies. Cell-intrinsic regulatory mechanisms of cilia disassembly have been well-studied. The extracellular cues controlling cilia disassembly remain elusive, however. Here, we show that lysophosphatidic acid (LPA), a multifunctional bioactive phospholipid, acts as a physiological extracellular factor to initiate cilia disassembly and promote neurogenesis. Through systematic analysis of serum components, we identify a small molecular-LPA as the major driver of cilia disassembly. Genetic inactivation and pharmacological inhibition of LPA receptor 1 (LPAR1) abrogate cilia disassembly triggered by serum. The LPA-LPAR-G-protein pathway promotes the transcription and phosphorylation of cilia disassembly factors-Aurora A, through activating the transcription coactivators YAP/TAZ and calcium/CaM pathway, respectively. Deletion of Lpar1 in mice causes abnormally elongated cilia and decreased proliferation in neural progenitor cells, thereby resulting in defective neurogenesis. Collectively, our findings establish LPA as a physiological initiator of cilia disassembly and suggest targeting the metabolism of LPA and the LPA pathway as potential therapies for diseases with dysfunctional ciliogenesis.

Measurements of the transverse Hall resistance are widely used to investigate electron transport, magnetization phenomena, and topological quantum states. Owing to the difficulty of probing transient changes of the transverse resistance, the vast majority of Hall effect experiments are carried out in stationary conditions using either dc or ac. Here we present an approach to perform time-resolved measurements of the transient Hall resistance during current-pulse injection with sub-nanosecond temporal resolution. We apply this technique to investigate in real-time the magnetization reversal caused by spin-orbit torques in ferrimagnetic GdFeCo dots. Single-shot Hall effect measurements show that the current-induced switching of GdFeCo is widely distributed in time and characterized by significant activation delays, which limit the total switching speed despite the high domain-wall velocity typical of ferrimagnets. Our method applies to a broad range of current-induced phenomena and can be combined with non-electrical excitations to perform pump-probe Hall effect measurements.

In lead-halide perovskites, antibonding states at the valence band maximum (VBM)-the result of Pb 6s-I 5p coupling-enable defect-tolerant properties; however, questions surrounding stability, and a reliance on lead, remain challenges for perovskite solar cells. Here, we report that binary GeSe has a perovskite-like antibonding VBM arising from Ge 4s-Se 4p coupling; and that it exhibits similarly shallow bulk defects combined with high stability. We find that the deep defect density in bulk GeSe is ~1012 cm-3. We devise therefore a surface passivation strategy, and find that the resulting GeSe solar cells achieve a certified power conversion efficiency of 5.2%, 3.7 times higher than the best previously-reported GeSe photovoltaics. Unencapsulated devices show no efficiency loss after 12 months of storage in ambient conditions; 1100 hours under maximum power point tracking; a total ultraviolet irradiation dosage of 15 kWh m-2; and 60 thermal cycles from -40 to 85 °C.

Mechanical systems are one of the promising platforms for classical and quantum information processing and are already widely-used in electronics and photonics. Cavity optomechanics offers many new possibilities for information processing using mechanical degrees of freedom; one of them is storing optical signals in long-lived mechanical vibrations by means of optomechanically induced transparency. However, the memory storage time is limited by intrinsic mechanical dissipation. More over, in-situ control and manipulation of the stored signals processing has not been demonstrated. Here, we address both of these limitations using a multi-mode cavity optomechanical memory. An additional optical field coupled to the memory modifies its dynamics through time-varying parametric feedback. We demonstrate that this can extend the memory decay time by an order of magnitude, decrease its effective mechanical dissipation rate by two orders of magnitude, and deterministically shift the phase of a stored field by over 2π. This further expands the information processing toolkit provided by cavity optomechanics.

TiO2-based powder materials have been widely studied as efficient photocatalysts for water splitting due to their low cost, photo-responsivity, earthly abundance, chemical and thermal stability, etc. In particular, the recent breakthrough of nitrogen-doped TiO2, which enhances the presence of structural defects and dopant impurities at elevated temperatures, exhibits an impressive visible-light absorption for photocatalytic activity. Although their electronic and optical properties have been extensively studied, the structure-activity relationship and photocatalytic mechanism remain ambiguous. Herein, we report an in-depth structural study of rutile, anatase and mixed phases (commercial P25) with and without nitrogen-doping by variable-temperature synchrotron X-ray powder diffraction. We report that an unusual anisotropic thermal expansion of the anatase phase can reveal the intimate relationship between sub-surface oxygen vacancies, nitrogen-doping level and photocatalytic activity. For highly doped anatase, a new cubic titanium oxynitride phase is also identified which provides important information on the fundamental shift in absorption wavelength, leading to excellent photocatalysis using visible light.

Liquid crystalline network (LCN) actuator normally deforms upon thermally or optically induced order-disorder phase transition, switching once between two shapes (shape 1 in LC phase and shape 2 in isotropic state) for each stimulation on/off cycle. Herein, we report an LCN actuator that deforms from shape 1 to shape 2 and then reverses the deformation direction to form shape 3 on heating or under light only, thus completing the shape switch twice for one stimulation on/off cycle. The deformation reversal capability is obtained with a monolithic LCN actuator whose two sides are made to start deforming at different temperatures and exerting different reversible strains, by means of asymmetrical crosslinking and/or asymmetrical stretching. This desynchronized actuation strategy offers possibilities in developing light-fueled LCN soft robots. In particular, the multi-stage bidirectional shape change enables multimodal, light-driven locomotion from the same LCN actuator by simply varying the light on/off times.

The FtsZ protein is a central component of the bacterial cell division machinery. It polymerizes at mid-cell and recruits more than 30 proteins to assemble into a macromolecular complex to direct cell wall constriction. FtsZ polymers exhibit treadmilling dynamics, driving the processive movement of enzymes that synthesize septal peptidoglycan (sPG). Here, we combine theoretical modelling with single-molecule imaging of live bacterial cells to show that FtsZ's treadmilling drives the directional movement of sPG enzymes via a Brownian ratchet mechanism. The processivity of the directional movement depends on the binding potential between FtsZ and the sPG enzyme, and on a balance between the enzyme's diffusion and FtsZ's treadmilling speed. We propose that this interplay may provide a mechanism to control the spatiotemporal distribution of active sPG enzymes, explaining the distinct roles of FtsZ treadmilling in modulating cell wall constriction rate observed in different bacteria.

Self-repairable materials strive to emulate curable and resilient biological tissue; however, their performance is currently insufficient for commercialization purposes because mending and toughening are mutually exclusive. Herein, we report a carbonate-type thermoplastic polyurethane elastomer that self-heals at 35 °C and exhibits a tensile strength of 43 MPa; this elastomer is as strong as the soles used in footwear. Distinctively, it has abundant carbonyl groups in soft-segments and is fully amorphous with negligible phase separation due to poor hard-segment stacking. It operates in dual mechano-responsive mode through a reversible disorder-to-order transition of its hydrogen-bonding array; it heals when static and toughens when dynamic. In static mode, non-crystalline hard segments promote the dynamic exchange of disordered carbonyl hydrogen-bonds for self-healing. The amorphous phase forms stiff crystals when stretched through a transition that orders inter-chain hydrogen bonding. The phase and strain fully return to the pre-stressed state after release to repeat the healing process.

Although various methods have been developed for sequencing cytosine modifications, it is still challenging for specific and quantitative sequencing of individual modification at base-resolution. For example, to obtain both true 5-methylcytosine (5mC) and true 5-hydroxymethylcytosine (5hmC) information, the two major epigenetic modifications, it usually requires subtraction of two methods, which increases noise and requires high sequencing depth. Recently, we developed TET-assisted pyridine borane sequencing (TAPS) for bisulfite-free direct sequencing of 5mC and 5hmC. Here we demonstrate that two sister methods, TAPSβ and chemical-assisted pyridine borane sequencing (CAPS), can be effectively used for subtraction-free and specific whole-genome sequencing of 5mC and 5hmC, respectively. We also demonstrate pyridine borane sequencing (PS) for whole-genome profiling of 5-formylcytosine and 5-carboxylcytosine, the further oxidized derivatives of 5mC and 5hmC. This work completes the set of versatile borane reduction chemistry-based methods as a comprehensive toolkit for direct and quantitative sequencing of all four cytosine epigenetic modifications.

The blood-brain barrier (BBB) is critical for neural function. We report here circadian regulation of the BBB in mammals. Efflux of xenobiotics by the BBB oscillates in mice, with highest levels during the active phase and lowest during the resting phase. This oscillation is abrogated in circadian clock mutants. To elucidate mechanisms of circadian regulation, we profiled the transcriptome of brain endothelial cells; interestingly, we detected limited circadian regulation of transcription, with no evident oscillations in efflux transporters. We recapitulated the cycling of xenobiotic efflux using a human microvascular endothelial cell line to find that the molecular clock drives cycling of intracellular magnesium through transcriptional regulation of TRPM7, which appears to contribute to the rhythm in efflux. Our findings suggest that considering circadian regulation may be important when therapeutically targeting efflux transporter substrates to the CNS.

Reversibility of an electrode reaction is important for energy-efficient rechargeable batteries with a long battery life. Additional oxygen-redox reactions have become an intensive area of research to achieve a larger specific capacity of the positive electrode materials. However, most oxygen-redox electrodes exhibit a large voltage hysteresis >0.5 V upon charge/discharge, and hence possess unacceptably poor energy efficiency. The hysteresis is thought to originate from the formation of peroxide-like O22- dimers during the oxygen-redox reaction. Therefore, avoiding O-O dimer formation is an essential challenge to overcome. Here, we focus on Na2-xMn3O7, which we recently identified to exhibit a large reversible oxygen-redox capacity with an extremely small polarization of 0.04 V. Using spectroscopic and magnetic measurements, the existence of stable O-• was identified in Na2-xMn3O7. Computations reveal that O-• is thermodynamically favorable over the peroxide-like O22- dimer as a result of hole stabilization through a (σ + π) multiorbital Mn-O bond.

Genome sequences have been determined for many model organisms; however, repetitive regions such as centromeres, telomeres, and subtelomeres have not yet been sequenced completely. Here, we report the complete sequences of subtelomeric homologous (SH) regions of the fission yeast Schizosaccharomyces pombe. We overcame technical difficulties to obtain subtelomeric repetitive sequences by constructing strains that possess single SH regions of a standard laboratory strain. In addition, some natural isolates of S. pombe were analyzed using previous sequencing data. Whole sequences of SH regions revealed that each SH region consists of two distinct parts with mosaics of multiple common segments or blocks showing high variation among subtelomeres and strains. Subtelomere regions show relatively high frequency of nucleotide variations among strains compared with the other chromosomal regions. Furthermore, we identified subtelomeric RecQ-type helicase genes, tlh3 and tlh4, which add to the already known tlh1 and tlh2, and found that the tlh1-4 genes show high sequence variation with missense mutations, insertions, and deletions but no severe effects on their RNA expression. Our results indicate that SH sequences are highly polymorphic and hot spots for genome variation. These features of subtelomeres may have contributed to genome diversity and, conversely, various diseases.

Neural recording technologies increasingly enable simultaneous measurement of neural activity from multiple brain areas. To gain insight into distributed neural computations, a commensurate advance in experimental and analytical methods is necessary. We discuss two opportunities towards this end: the manipulation and modeling of neural population dynamics.

Genome editing critically relies on selective recognition of target sites. However, despite recent progress, the underlying search mechanism of genome-editing proteins is not fully understood in the context of cellular chromatin environments. Here, we use single-molecule imaging in live cells to directly study the behavior of CRISPR/Cas9 and TALEN. Our single-molecule imaging of genome-editing proteins reveals that Cas9 is less efficient in heterochromatin than TALEN because Cas9 becomes encumbered by local searches on non-specific sites in these regions. We find up to a fivefold increase in editing efficiency for TALEN compared to Cas9 in heterochromatin regions. Overall, our results show that Cas9 and TALEN use a combination of 3-D and local searches to identify target sites, and the nanoscopic granularity of local search determines the editing outcomes of the genome-editing proteins. Taken together, our results suggest that TALEN is a more efficient gene-editing tool than Cas9 for applications in heterochromatin.

The importance of discovering the true catalytically active species involved in photocatalytic systems allows for a better and more general understanding of photocatalytic processes, which eventually may help to improve their efficiency. Bi2O3 has been used as a heterogeneous photocatalyst and is able to catalyze several synthetically important visible-light-driven organic transformations. However, insight into the operative catalyst involved in the photocatalytic process is hitherto missing. Herein, we show through a combination of theoretical and experimental studies that the perceived heterogeneous photocatalysis with Bi2O3 in the presence of alkyl bromides involves a homogeneous BinBrm species, which is the true photocatalyst operative in the reaction. Hence, Bi2O3 can be regarded as a precatalyst which is slowly converted in an active homogeneous photocatalyst. This work can also be of importance to mechanistic studies involving other semiconductor-based photocatalytic processes.

In strongly correlated systems the strength of Coulomb interactions between electrons, relative to their kinetic energy, plays a central role in determining their emergent quantum mechanical phases. We perform resonant x-ray scattering on Bi2Sr2CaCu2O8+δ, a prototypical cuprate superconductor, to probe electronic correlations within the CuO2 plane. We discover a dynamic quasi-circular pattern in the x-y scattering plane with a radius that matches the wave vector magnitude of the well-known static charge order. Along with doping- and temperature-dependent measurements, our experiments reveal a picture of charge order competing with superconductivity where short-range domains along x and y can dynamically rotate into any other in-plane direction. This quasi-circular spectrum, a hallmark of Brazovskii-type fluctuations, has immediate consequences to our understanding of rotational and translational symmetry breaking in the cuprates. We discuss how the combination of short- and long-range Coulomb interactions results in an effective non-monotonic potential that may determine the quasi-circular pattern.

Zika virus (ZIKV) emerged from obscurity in 2013 to spread from Asia to the South Pacific and the Americas, where millions of people were infected, accompanied by severe disease including microcephaly following congenital infections. Phylogenetic studies have shown that ZIKV evolved in Africa and later spread to Asia, and that the Asian lineage is responsible for the recent epidemics in the South Pacific and Americas. However, the reasons for the sudden emergence of ZIKV remain enigmatic. Here we report evolutionary analyses that revealed four mutations, which occurred just before ZIKV introduction to the Americas, represent direct reversions of previous mutations that accompanied earlier spread from Africa to Asia and early circulation there. Our experimental infections of Aedes aegypti mosquitoes, human cells, and mice using ZIKV strains with and without these mutations demonstrate that the original mutations reduced fitness for urban, human-amplifed transmission, while the reversions restored fitness, increasing epidemic risk. These findings include characterization of three transmission-adaptive ZIKV mutations, and demonstration that these and one identified previously restored fitness for epidemic transmission soon before introduction into the Americas. The initial mutations may have followed founder effects and/or drift when the virus was introduced decades ago into Asia.

Topological order can be found in a wide range of physical systems, from crystalline solids, photonic meta-materials and even atmospheric waves to optomechanic, acoustic and atomic systems. Topological systems are a robust foundation for creating quantized channels for transporting electrical current, light, and atmospheric disturbances. These topological effects are quantified in terms of integer-valued 'invariants', such as the Chern number, applicable to the quantum Hall effect, or the [Formula: see text] invariant suitable for topological insulators. Here, we report the engineering of Rashba spin-orbit coupling for a cold atomic gas giving non-trivial topology, without the underlying crystalline structure that conventionally yields integer Chern numbers. We validated our procedure by spectroscopically measuring both branches of the Rashba dispersion relation which touch at a single Dirac point. We then measured the quantum geometry underlying the dispersion relation using matter-wave interferometry to implement a form of quantum state tomography, giving a Berry's phase with magnitude π. This implies that opening a gap at the Dirac point would give two dispersions (bands) each with half-integer Chern number, potentially implying new forms of topological transport.

Symmetrical protein complexes are ubiquitous in biology. Many have been re-engineered for chemical and medical applications. Viral capsids and their assembly are frequent platforms for these investigations. A means to create asymmetric capsids may expand applications. Here, starting with homodimeric Hepatitis B Virus capsid protein, we develop a heterodimer, design a hierarchical assembly pathway, and produce asymmetric capsids. In the heterodimer, the two halves have different growth potentials and assemble into hexamers. These preformed hexamers can nucleate co-assembly with other dimers, leading to Janus-like capsids with a small discrete hexamer patch. We can remove the patch specifically and observe asymmetric holey capsids by cryo-EM reconstruction. The resulting hole in the surface can be refilled with fluorescently labeled dimers to regenerate an intact capsid. In this study, we show how an asymmetric subunit can be used to generate an asymmetric particle, creating the potential for a capsid with different surface chemistries.

Quantum fluctuations give rise to Casimir forces between two parallel conducting plates, the magnitude of which increases monotonically as the separation decreases. By introducing nanoscale gratings to the surfaces, recent advances have opened opportunities for controlling the Casimir force in complex geometries. Here, we measure the Casimir force between two rectangular silicon gratings. Using an on-chip detection platform, we achieve accurate alignment between the two gratings so that they interpenetrate as the separation is reduced. Just before interpenetration occurs, the measured Casimir force is found to have a geometry dependence that is much stronger than previous experiments, with deviations from the proximity force approximation reaching a factor of ~500. After the gratings interpenetrate each other, the Casimir force becomes non-zero and independent of displacement. This work shows that the presence of gratings can strongly modify the Casimir force to control the interaction between nanomechanical components.

Understanding of charge-density wave (CDW) phases is a main challenge in condensed matter due to their presence in high-Tc superconductors or transition metal dichalcogenides (TMDs). Among TMDs, the origin of the CDW in VSe2 remains highly debated. Here, by means of inelastic x-ray scattering and first-principles calculations, we show that the CDW transition is driven by the collapse at 110 K of an acoustic mode at qCDW = (2.25 0 0.7) r.l.u. The softening starts below 225 K and expands over a wide region of the Brillouin zone, identifying the electron-phonon interaction as the driving force of the CDW. This is supported by our calculations that determine a large momentum-dependence of the electron-phonon matrix-elements that peak at the CDW wave vector. Our first-principles anharmonic calculations reproduce the temperature dependence of the soft mode and the TCDW onset only when considering the out-of-plane van der Waals interactions, which reveal crucial for the melting of the CDW phase.

The ribosome represents a promising avenue for synthetic biology, but its complexity and essentiality have hindered significant engineering efforts. Heterologous ribosomes, comprising rRNAs and r-proteins derived from different microorganisms, may offer opportunities for novel translational functions. Such heterologous ribosomes have previously been evaluated in E. coli via complementation of a genomic ribosome deficiency, but this method fails to guide the engineering of refractory ribosomes. Here, we implement orthogonal ribosome binding site (RBS):antiRBS pairs, in which engineered ribosomes are directed to researcher-defined transcripts, to inform requirements for heterologous ribosome functionality. We discover that optimized rRNA processing and supplementation with cognate r-proteins enhances heterologous ribosome function for rRNAs derived from organisms with ≥76.1% 16S rRNA identity to E. coli. Additionally, some heterologous ribosomes undergo reduced subunit exchange with E. coli-derived subunits. Cumulatively, this work provides a general framework for heterologous ribosome engineering in living cells.

Single-cell RNA sequencing in principle offers unique opportunities to improve the efficacy of contemporary T-cell based immunotherapy against cancer. The use of high-quality single-cell data will aid our incomplete understanding of molecular programs determining the differentiation and functional heterogeneity of cytotoxic T lymphocytes (CTLs), allowing for optimal therapeutic design. So far, a major obstacle to high depth single-cell analysis of CTLs is the minute amount of RNA available, leading to low capturing efficacy. Here, to overcome this, we tailor a droplet-based approach for high-throughput analysis (tDrop-seq) and a plate-based method for high-performance in-depth CTL analysis (tSCRB-seq). The latter gives, on average, a 15-fold higher number of captured transcripts per gene compared to droplet-based technologies. The improved dynamic range of gene detection gives tSCRB-seq an edge in resolution sensitive downstream applications such as graded high confidence gene expression measurements and cluster characterization. We demonstrate the power of tSCRB-seq by revealing the subpopulation-specific expression of co-inhibitory and co-stimulatory receptor targets of key importance for immunotherapy.

Nanoscale materials modified by crystal defects exhibit significantly different behaviours upon chemical reactions such as oxidation, catalysis, lithiation and epitaxial growth. However, unveiling the exact defect-controlled reaction dynamics (e.g. oxidation) at atomic scale remains a challenge for applications. Here, using in situ high-resolution transmission electron microscopy and first-principles calculations, we reveal the dynamics of a general site-selective oxidation behaviour in nanotwinned silver and palladium driven by individual stacking-faults and twin boundaries. The coherent planar defects crossing the surface exhibit the highest oxygen binding energies, leading to preferential nucleation of oxides at these intersections. Planar-fault mediated diffusion of oxygen atoms is shown to catalyse subsequent layer-by-layer inward oxide growth via atomic steps migrating on the oxide-metal interface. These findings provide an atomistic visualization of the complex reaction dynamics controlled by planar defects in metallic nanostructures, which could enable the modification of physiochemical performances in nanomaterials through defect engineering.

Transition metal nitrides are an important class of materials with applications as abrasives, semiconductors, superconductors, Li-ion conductors, and thermoelectrics. However, high oxidation states are difficult to attain as the oxidative potential of dinitrogen is limited by its high thermodynamic stability and chemical inertness. Here we present a versatile synthesis route using azide-mediated oxidation under pressure that is used to prepare the highly oxidised ternary nitride Ca4FeN4 containing Fe4+ ions. This nitridometallate features trigonal-planar [FeN3]5- anions with low-spin Fe4+ and antiferromagnetic ordering below a Neel temperature of 25 K, which are characterised by neutron diffraction, 57Fe-Mössbauer and magnetisation measurements. Azide-mediated high-pressure synthesis opens a way to the discovery of highly oxidised nitrides.

Author information: (1)The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark. ditte@biomed.au.dk. (2)Center for Genomics and Personalized Medicine, Aarhus, Denmark. ditte@biomed.au.dk. (3)Department of Biomedicine - Human Genetics, Aarhus University, Aarhus, Denmark. ditte@biomed.au.dk. (4)Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. (5)Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA. (6)The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark. (7)Center for Genomics and Personalized Medicine, Aarhus, Denmark. (8)Department of Biomedicine - Human Genetics, Aarhus University, Aarhus, Denmark. (9)Department of Psychology, Emory University, Atlanta, GA, USA. (10)Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark. (11)National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark. (12)Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain. (13)Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Catalonia, Spain. (14)Biomedical Network Research Center on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain. (15)Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain. (16)Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark. (17)GLOBE Institute, Center for GeoGenetics, University of Copenhagen, Copenhagen, Denmark. (18)Institute of Biological Psychiatry, MHC Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark. (19)Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark. (20)Copenhagen University Hospital, Mental Health Centre Copenhagen Mental Health Services in the Capital Region of Denmark, Hellerup, Denmark. (21)Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. (22)Psychosis Research Unit, Aarhus University Hospital, Aarhus, Denmark. (23)Centre for Integrated Register-Based Research, Aarhus University, Aarhus, Denmark. (24)Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain. (25)Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalonia, Spain. (26)Institut de Recerca Sant Joan de Déu (IRSJD), Esplugues de Llobregat, Barcelona, Catalonia, Spain. (27)Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA. (28)Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands. (29)Department of Psychiatry, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands. (30)Departments of Psychiatry and of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY, USA. sfaraone@childpsychresearch.org. (31)The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark. anders@biomed.au.dk. (32)Center for Genomics and Personalized Medicine, Aarhus, Denmark. anders@biomed.au.dk. (33)Department of Biomedicine - Human Genetics, Aarhus University, Aarhus, Denmark. anders@biomed.au.dk.

Elevated plasma cholesterol and type 2 diabetes (T2D) are associated with coronary artery disease (CAD). Individuals treated with cholesterol-lowering statins have increased T2D risk, while individuals with hypercholesterolemia have reduced T2D risk. We explore the relationship between lipid and glucose control by constructing network models from the STARNET study with sequencing data from seven cardiometabolic tissues obtained from CAD patients during coronary artery by-pass grafting surgery. By integrating gene expression, genotype, metabolomic, and clinical data, we identify a glucose and lipid determining (GLD) regulatory network showing inverse relationships with lipid and glucose traits. Master regulators of the GLD network also impact lipid and glucose levels in inverse directions. Experimental inhibition of one of the GLD network master regulators, lanosterol synthase (LSS), in mice confirms the inverse relationships to glucose and lipid levels as predicted by our model and provides mechanistic insights.

Timescale comparison between optical atomic clocks over ground-to-space and terrestrial free-space laser links will have enormous benefits for fundamental and applied sciences. However, atmospheric turbulence creates phase noise and beam wander that degrade the measurement precision. Here we report on phase-stabilized optical frequency transfer over a 265 m horizontal point-to-point free-space link between optical terminals with active tip-tilt mirrors to suppress beam wander, in a compact, human-portable set-up. A phase-stabilized 715 m underground optical fiber link between the two terminals is used to measure the performance of the free-space link. The active optical terminals enable continuous, cycle-slip free, coherent transmission over periods longer than an hour. In this work, we achieve residual instabilities of 2.7 × 10-6 rad2 Hz-1 at 1 Hz in phase, and 1.6 × 10-19 at 40 s of integration in fractional frequency; this performance surpasses the best optical atomic clocks, ensuring clock-limited frequency comparison over turbulent free-space links.

The emergence and spread of artemisinin resistance, driven by mutations in Plasmodium falciparum K13, has compromised antimalarial efficacy and threatens the global malaria elimination campaign. By applying systems-based quantitative transcriptomics, proteomics, and metabolomics to a panel of isogenic K13 mutant or wild-type P. falciparum lines, we provide evidence that K13 mutations alter multiple aspects of the parasite's intra-erythrocytic developmental program. These changes impact cell-cycle periodicity, the unfolded protein response, protein degradation, vesicular trafficking, and mitochondrial metabolism. K13-mediated artemisinin resistance in the Cambodian Cam3.II line was reversed by atovaquone, a mitochondrial electron transport chain inhibitor. These results suggest that mitochondrial processes including damage sensing and anti-oxidant properties might augment the ability of mutant K13 to protect P. falciparum against artemisinin action by helping these parasites undergo temporary quiescence and accelerated growth recovery post drug elimination.

In Rhizobiales bacteria, such as Sinorhizobium meliloti, cell elongation takes place only at new cell poles, generated by cell division. Here, we show that the role of the FtsN-like protein RgsS in S. meliloti extends beyond cell division. RgsS contains a conserved SPOR domain known to bind amidase-processed peptidoglycan. This part of RgsS and peptidoglycan amidase AmiC are crucial for reliable selection of the new cell pole as cell elongation zone. Absence of these components increases mobility of RgsS molecules, as well as abnormal RgsS accumulation and positioning of the growth zone at the old cell pole in about one third of the cells. These cells with inverted growth polarity are able to complete the cell cycle but show partially impaired chromosome segregation. We propose that amidase-processed peptidoglycan provides a landmark for RgsS to generate cell polarity in unipolarly growing Rhizobiales.

Cardiac ischemia-reperfusion (I/R) injury is a pathological process resulting in cardiomyocyte death. The present study aims to evaluate the role of the long noncoding RNA Cardiac Injury-Related Bclaf1-Inhibiting LncRNA (lncCIRBIL) on cardiac I/R injury and delineate its mechanism of action. The level of lncCIRBIL is reduced in I/R hearts. Cardiomyocyte-specific transgenic overexpression of lncCIRBIL reduces infarct area following I/R injury. Knockout of lncCIRBIL in mice exacerbates cardiac I/R injury. Qualitatively, the same results are observed in vitro. LncCIRBIL directly binds to BCL2-associated transcription factor 1 (Bclaf1), to inhibit its nuclear translocation. Cardiomyocyte-specific transgenic overexpression of Bclaf1 worsens, while partial knockout of Bclaf1 mitigates cardiac I/R injury. Meanwhile, partial knockout of Bclaf1 abrogates the detrimental effects of lncCIRBIL knockout on cardiac I/R injury. Collectively, the protective effect of lncCIRBIL on I/R injury is accomplished by inhibiting the nuclear translocation of Bclaf1. LncCIRBIL and Bclaf1 are potential therapeutic targets for ischemic cardiac disease.

Erratum in Nat Commun. 2022 Jun 16;13(1):3474.

Single-molecule localization microscopy enables far-field imaging with lateral resolution in the range of 10 to 20 nanometres, exploiting the fact that the centre position of a single-molecule's image can be determined with much higher accuracy than the size of that image itself. However, attaining the same level of resolution in the axial (third) dimension remains challenging. Here, we present Supercritical Illumination Microscopy Photometric z-Localization with Enhanced Resolution (SIMPLER), a photometric method to decode the axial position of single molecules in a total internal reflection fluorescence microscope. SIMPLER requires no hardware modification whatsoever to a conventional total internal reflection fluorescence microscope and complements any 2D single-molecule localization microscopy method to deliver 3D images with nearly isotropic nanometric resolution. Performance examples include SIMPLER-direct stochastic optical reconstruction microscopy images of the nuclear pore complex with sub-20 nm axial localization precision and visualization of microtubule cross-sections through SIMPLER-DNA points accumulation for imaging in nanoscale topography with sub-10 nm axial localization precision.

The rectification of electromagnetic waves to direct currents is a crucial process for energy harvesting, beyond-5G wireless communications, ultra-fast science, and observational astronomy. As the radiation frequency is raised to the sub-terahertz (THz) domain, ac-to-dc conversion by conventional electronics becomes challenging and requires alternative rectification protocols. Here, we address this challenge by tunnel field-effect transistors made of bilayer graphene (BLG). Taking advantage of BLG's electrically tunable band structure, we create a lateral tunnel junction and couple it to an antenna exposed to THz radiation. The incoming radiation is then down-converted by the tunnel junction nonlinearity, resulting in high responsivity (>4 kV/W) and low-noise (0.2 pW/[Formula: see text]) detection. We demonstrate how switching from intraband Ohmic to interband tunneling regime can raise detectors' responsivity by few orders of magnitude, in agreement with the developed theory. Our work demonstrates a potential application of tunnel transistors for THz detection and reveals BLG as a promising platform therefor.

Marine low clouds play an important role in the climate system, and their properties are sensitive to cloud condensation nuclei concentrations. While new particle formation represents a major source of cloud condensation nuclei globally, the prevailing view is that new particle formation rarely occurs in remote marine boundary layer over open oceans. Here we present evidence of the regular and frequent occurrence of new particle formation in the upper part of remote marine boundary layer following cold front passages. The new particle formation is facilitated by a combination of efficient removal of existing particles by precipitation, cold air temperatures, vertical transport of reactive gases from the ocean surface, and high actinic fluxes in a broken cloud field. The newly formed particles subsequently grow and contribute substantially to cloud condensation nuclei in the remote marine boundary layer and thereby impact marine low clouds.

Investigation of neural circuit dynamics is crucial for deciphering the functional connections among regions of the brain and understanding the mechanism of brain dysfunction. Despite the advancements of neural circuit models in vitro, technologies for both precisely monitoring and modulating neural activities within three-dimensional (3D) neural circuit models have yet to be developed. Specifically, no existing 3D microelectrode arrays (MEAs) have integrated capabilities to stimulate surrounding neurons and to monitor the temporal evolution of the formation of a neural network in real time. Herein, we present a 3D high-density multifunctional MEA with optical stimulation and drug delivery for investigating neural circuit dynamics within engineered 3D neural tissues. We demonstrate precise measurements of synaptic latencies in 3D neural networks. We expect our 3D multifunctional MEA to open up opportunities for studies of neural circuits through precise, in vitro investigations of neural circuit dynamics with 3D brain models.

Accurate pathogenicity prediction of missense variants is critically important in genetic studies and clinical diagnosis. Previously published prediction methods have facilitated the interpretation of missense variants but have limited performance. Here, we describe MVP (Missense Variant Pathogenicity prediction), a new prediction method that uses deep residual network to leverage large training data sets and many correlated predictors. We train the model separately in genes that are intolerant of loss of function variants and the ones that are tolerant in order to take account of potentially different genetic effect size and mode of action. We compile cancer mutation hotspots and de novo variants from developmental disorders for benchmarking. Overall, MVP achieves better performance in prioritizing pathogenic missense variants than previous methods, especially in genes tolerant of loss of function variants. Finally, using MVP, we estimate that de novo coding variants contribute to 7.8% of isolated congenital heart disease, nearly doubling previous estimates.

Sarcomas are malignant soft tissue and bone tumours affecting adults, adolescents and children. They represent a morphologically heterogeneous class of tumours and some entities lack defining histopathological features. Therefore, the diagnosis of sarcomas is burdened with a high inter-observer variability and misclassification rate. Here, we demonstrate classification of soft tissue and bone tumours using a machine learning classifier algorithm based on array-generated DNA methylation data. This sarcoma classifier is trained using a dataset of 1077 methylation profiles from comprehensively pre-characterized cases comprising 62 tumour methylation classes constituting a broad range of soft tissue and bone sarcoma subtypes across the entire age spectrum. The performance is validated in a cohort of 428 sarcomatous tumours, of which 322 cases were classified by the sarcoma classifier. Our results demonstrate the potential of the DNA methylation-based sarcoma classification for research and future diagnostic applications.

The Rustenburg Layered Suite of the Bushveld Complex of South Africa is a vast layered accumulation of mafic and ultramafic rocks. It has long been regarded as a textbook result of fractional crystallization from a melt-dominated magma chamber. Here, we show that most units of the Rustenburg Layered Suite can be derived with thermodynamic models of crustal assimilation by komatiitic magma to form magmatic mushes without requiring the existence of a magma chamber. Ultramafic and mafic cumulate layers below the Upper and Upper Main Zone represent multiple crystal slurries produced by assimilation-batch crystallization in the upper and middle crust, whereas the chilled marginal rocks represent complementary supernatant liquids. Only the uppermost third formed via lower-crustal assimilation-fractional crystallization and evolved by fractional crystallization within a melt-rich pocket. Layered intrusions need not form in open magma chambers. Mineral deposits hitherto attributed to magma chamber processes might form in smaller intrusions of any geometric form, from mushy systems entirely lacking melt-dominated magma chambers.

Mast cells are critical effectors of allergic inflammation and protection against parasitic infections. We previously demonstrated that transcription factors GATA2 and MITF are the mast cell lineage-determining factors. However, it is unclear whether these lineage-determining factors regulate chromatin accessibility at mast cell enhancer regions. In this study, we demonstrate that GATA2 promotes chromatin accessibility at the super-enhancers of mast cell identity genes and primes both typical and super-enhancers at genes that respond to antigenic stimulation. We find that the number and densities of GATA2- but not MITF-bound sites at the super-enhancers are several folds higher than that at the typical enhancers. Our studies reveal that GATA2 promotes robust gene transcription to maintain mast cell identity and respond to antigenic stimulation by binding to super-enhancer regions with dense GATA2 binding sites available at key mast cell genes.

Biofilms contribute to bacterial infection and drug resistance and are a serious threat to global human health. Antibacterial nanomaterials have attracted considerable attention, but the inhibition of biofilms remains a major challenge. Herein, we propose a nanohole-boosted electron transport (NBET) antibiofilm concept. Unlike known antibacterial mechanisms (e.g., reactive oxygen species production and cell membrane damage), nanoholes with atomic vacancies and biofilms serve as electronic donors and receptors, respectively, and thus boost the high electron transport capacity between nanomaterials and biofilms. Electron transport effectively destroys the critical components (proteins, intercellularly adhered polysaccharides and extracellular DNA) of biofilms, and the nanoholes also significantly downregulate the expression of genes related to biofilm formation. The anti-infection capacity is thoroughly verified both in vitro (human cells) and in vivo (rat ocular and mouse intestinal infection models), and the nanohole-enabled nanomaterials are found to be highly biocompatible. Importantly, compared with typical antibiotics, nanomaterials are nonresistant and thereby exhibit high potential for use in various applications. As a proof-of-principle demonstration, these findings hold promise for the use of NBET in treatments for pathogenic bacterial infection and antibiotic drug resistance.

Thousands of human small and alternative open reading frames (smORFs and alt-ORFs, respectively) have recently been annotated. Many alt-ORFs are co-encoded with canonical proteins in multicistronic configurations, but few of their functions are known. Here, we report the detection of alt-RPL36, a protein co-encoded with human RPL36. Alt-RPL36 partially localizes to the endoplasmic reticulum, where it interacts with TMEM24, which transports the phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) precursor phosphatidylinositol from the endoplasmic reticulum to the plasma membrane. Knock-out of alt-RPL36 increases plasma membrane PI(4,5)P2 levels, upregulates PI3K-AKT-mTOR signaling, and increases cell size. Alt-RPL36 contains four phosphoserine residues, point mutations of which abolish interaction with TMEM24 and, consequently, alt-RPL36 effects on PI3K signaling and cell size. These results implicate alt-RPL36 as an upstream regulator of PI3K-AKT-mTOR signaling. More broadly, the RPL36 transcript encodes two sequence-independent polypeptides that co-regulate translation via different molecular mechanisms, expanding our knowledge of multicistronic human gene functions.

Erratum in Nat Commun. 2021 Mar 17;12(1):1840.

Erratum in Nat Commun. 2021 Feb 15;12(1):1187.

SARS-CoV-2 is the pathogen responsible for the COVID-19 pandemic. The SARS-CoV-2 papain-like cysteine protease (PLpro) has been implicated in playing important roles in virus maturation, dysregulation of host inflammation, and antiviral immune responses. The multiple functions of PLpro render it a promising drug target. Therefore, we screened a library of approved drugs and also examined available inhibitors against PLpro. Inhibitor GRL0617 showed a promising in vitro IC50 of 2.1 μM and an effective antiviral inhibition in cell-based assays. The co-crystal structure of SARS-CoV-2 PLproC111S in complex with GRL0617 indicates that GRL0617 is a non-covalent inhibitor and it resides in the ubiquitin-specific proteases (USP) domain of PLpro. NMR data indicate that GRL0617 blocks the binding of ISG15 C-terminus to PLpro. Using truncated ISG15 mutants, we show that the C-terminus of ISG15 plays a dominant role in binding PLpro. Structural analysis reveals that the ISG15 C-terminus binding pocket in PLpro contributes a disproportionately large portion of binding energy, thus this pocket is a hot spot for antiviral drug discovery targeting PLpro.

The cytoplasm in mammalian cells is considered homogeneous. In this study, we report that the cytoplasmic fluidity is regulated in the blebbing cells; the cytoplasm of rapidly expanding membrane blebs is more disordered than the cytoplasm of retracting blebs. The increase of cytoplasmic fluidity in the expanding bleb is caused by a sharp rise in the calcium concentration. The STIM-Orai1 pathway regulates this rapid and restricted increase of calcium in the expanding blebs. Conversely, activated ERM protein binds to Orai1 to inhibit the store-operated calcium entry in retracting blebs, which results in decreased in cytoplasmic calcium, rapid reassembly of the actin cortex.

Axonemal dyneins are tethered to doublet microtubules inside cilia to drive ciliary beating, a process critical for cellular motility and extracellular fluid flow. Axonemal dyneins are evolutionarily and biochemically distinct from cytoplasmic dyneins that transport cargo, and the mechanisms regulating their localization and function are poorly understood. Here, we report a single-particle cryo-EM reconstruction of a three-headed axonemal dynein natively bound to doublet microtubules isolated from cilia. The slanted conformation of the axonemal dynein causes interaction of its motor domains with the neighboring dynein complex. Our structure shows how a heterotrimeric docking complex specifically localizes the linear array of axonemal dyneins to the doublet microtubule by directly interacting with the heavy chains. Our structural analysis establishes the arrangement of conserved heavy, intermediate and light chain subunits, and provides a framework to understand the roles of individual subunits and the interactions between dyneins during ciliary waveform generation.

Erratum in Nat Commun. 2021 May 28;12(1):3302.

Complex-valued neural networks have many advantages over their real-valued counterparts. Conventional digital electronic computing platforms are incapable of executing truly complex-valued representations and operations. In contrast, optical computing platforms that encode information in both phase and magnitude can execute complex arithmetic by optical interference, offering significantly enhanced computational speed and energy efficiency. However, to date, most demonstrations of optical neural networks still only utilize conventional real-valued frameworks that are designed for digital computers, forfeiting many of the advantages of optical computing such as efficient complex-valued operations. In this article, we highlight an optical neural chip (ONC) that implements truly complex-valued neural networks. We benchmark the performance of our complex-valued ONC in four settings: simple Boolean tasks, species classification of an Iris dataset, classifying nonlinear datasets (Circle and Spiral), and handwriting recognition. Strong learning capabilities (i.e., high accuracy, fast convergence and the capability to construct nonlinear decision boundaries) are achieved by our complex-valued ONC compared to its real-valued counterpart.

Some Bacteroidetes and other human colonic bacteria can degrade arabinoxylans, common polysaccharides found in dietary fiber. Previous work has identified gene clusters (polysaccharide-utilization loci, PULs) for degradation of simple arabinoxylans. However, the degradation of complex arabinoxylans (containing side chains such as ferulic acid, a phenolic compound) is poorly understood. Here, we identify a PUL that encodes multiple esterases for degradation of complex arabinoxylans in Bacteroides species. The PUL is specifically upregulated in the presence of complex arabinoxylans. We characterize some of the esterases biochemically and structurally, and show that they release ferulic acid from complex arabinoxylans. Growth of four different colonic Bacteroidetes members, including Bacteroides intestinalis, on complex arabinoxylans results in accumulation of ferulic acid, a compound known to have antioxidative and immunomodulatory properties.

Steroid hormones are essential in stress response, immune system regulation, and reproduction in mammals. Steroids with 3-oxo-Δ4 structure, such as testosterone or progesterone, are catalyzed by steroid 5α-reductases (SRD5As) to generate their corresponding 3-oxo-5α steroids, which are essential for multiple physiological and pathological processes. SRD5A2 is already a target of clinically relevant drugs. However, the detailed mechanism of SRD5A-mediated reduction remains elusive. Here we report the crystal structure of PbSRD5A from Proteobacteria bacterium, a homolog of both SRD5A1 and SRD5A2, in complex with the cofactor NADPH at 2.0 Å resolution. PbSRD5A exists as a monomer comprised of seven transmembrane segments (TMs). The TM1-4 enclose a hydrophobic substrate binding cavity, whereas TM5-7 coordinate cofactor NADPH through extensive hydrogen bonds network. Homology-based structural models of HsSRD5A1 and -2, together with biochemical characterization, define the substrate binding pocket of SRD5As, explain the properties of disease-related mutants and provide an important framework for further understanding of the mechanism of NADPH mediated steroids 3-oxo-Δ4 reduction. Based on these analyses, the design of therapeutic molecules targeting SRD5As with improved specificity and therapeutic efficacy would be possible.

Functional CsPbI3 perovskite phases are not stable at ambient conditions and spontaneously convert to a non-perovskite δ phase, limiting their applications as solar cell materials. We demonstrate the preservation of a black CsPbI3 perovskite structure to room temperature by subjecting the δ phase to pressures of 0.1 - 0.6 GPa followed by heating and rapid cooling. Synchrotron X-ray diffraction and Raman spectroscopy indicate that this perovskite phase is consistent with orthorhombic γ-CsPbI3. Once formed, γ-CsPbI3 could be then retained after releasing pressure to ambient conditions and shows substantial stability at 35% relative humidity. First-principles density functional theory calculations indicate that compression directs the out-of-phase and in-phase tilt between the [PbI6]4- octahedra which in turn tune the energy difference between δ- and γ-CsPbI3, leading to the preservation of γ-CsPbI3. Here, we present a high-pressure strategy for manipulating the (meta)stability of halide perovskites for the synthesis of desirable phases with enhanced materials functionality.

Clostridioides difficile is a bacterial pathogen that causes a range of clinical disease from mild to moderate diarrhea, pseudomembranous colitis, and toxic megacolon. Typically, C. difficile infections (CDIs) occur after antibiotic treatment, which alters the gut microbiota, decreasing colonization resistance against C. difficile. Disease is mediated by two large toxins and the expression of their genes is induced upon nutrient depletion via the alternative sigma factor TcdR. Here, we use tcdR mutants in two strains of C. difficile and omics to investigate how toxin-induced inflammation alters C. difficile metabolism, tissue gene expression and the gut microbiota, and to determine how inflammation by the host may be beneficial to C. difficile. We show that C. difficile metabolism is significantly different in the face of inflammation, with changes in many carbohydrate and amino acid uptake and utilization pathways. Host gene expression signatures suggest that degradation of collagen and other components of the extracellular matrix by matrix metalloproteinases is a major source of peptides and amino acids that supports C. difficile growth in vivo. Lastly, the inflammation induced by C. difficile toxin activity alters the gut microbiota, excluding members from the genus Bacteroides that are able to utilize the same essential nutrients released from collagen degradation.

In terms of producing new advances in sustainable nanomaterials, cation exchange (CE) of post-processed colloidal nanocrystals (NCs) has opened new avenues towards producing non-toxic energy materials via simple chemical techniques. The main processes governing CE can be explained by considering hard/soft acid/base theory, but the detailed mechanism of CE, however, has been debated and has been attributed to both diffusion and vacancy processes. In this work, we have performed in situ x-ray absorption spectroscopy to further understand the mechanism of the CE of copper in solution phase CdSe NCs. The x-ray data indicates clear isosbestic points, suggestive of cooperative behavior as previously observed via optical spectroscopy. Examination of the extended x-ray absorption fine structure data points to the observation of interstitial impurities during the initial stages of CE, suggesting the diffusion process is the fundamental mechanism of CE in this system.

Electron and hole spins in organic light-emitting diodes constitute prototypical two-level systems for the exploration of the ultrastrong-drive regime of light-matter interactions. Floquet solutions to the time-dependent Hamiltonian of pairs of electron and hole spins reveal that, under non-perturbative resonant drive, when spin-Rabi frequencies become comparable to the Larmor frequencies, hybrid light-matter states emerge that enable dipole-forbidden multi-quantum transitions at integer and fractional g-factors. To probe these phenomena experimentally, we develop an electrically detected magnetic-resonance experiment supporting oscillating driving fields comparable in amplitude to the static field defining the Zeeman splitting; and an organic semiconductor characterized by minimal local hyperfine fields allowing the non-perturbative light-matter interactions to be resolved. The experimental confirmation of the predicted Floquet states under strong-drive conditions demonstrates the presence of hybrid light-matter spin excitations at room temperature. These dressed states are insensitive to power broadening, display Bloch-Siegert-like shifts, and are suggestive of long spin coherence times, implying potential applicability for quantum sensing.

Erratum in Nat Commun. 2021 Mar 1;12(1):1489.

Globally, flood risk is projected to increase in the future due to climate change and population growth. Here, we quantify the role of dams in flood mitigation, previously unaccounted for in global flood studies, by simulating the floodplain dynamics and flow regulation by dams. We show that, ignoring flow regulation by dams, the average number of people exposed to flooding below dams amount to 9.1 and 15.3 million per year, by the end of the 21st century (holding population constant), for the representative concentration pathway (RCP) 2.6 and 6.0, respectively. Accounting for dams reduces the number of people exposed to floods by 20.6 and 12.9% (for RCP2.6 and RCP6.0, respectively). While environmental problems caused by dams warrant further investigations, our results indicate that consideration of dams significantly affect the estimation of future population exposure to flood, emphasizing the need to integrate them in model-based impact analysis of climate change.

Drug tolerant/resistant leukemic stem cell (LSC) subpopulations may explain frequent relapses in acute myeloid leukemia (AML), suggesting that these relapse-initiating cells (RICs) persistent after chemotherapy represent bona fide targets to prevent drug resistance and relapse. We uncover that calcitonin receptor-like receptor (CALCRL) is expressed in RICs, and that the overexpression of CALCRL and/or of its ligand adrenomedullin (ADM), and not CGRP, correlates to adverse outcome in AML. CALCRL knockdown impairs leukemic growth, decreases LSC frequency, and sensitizes to cytarabine in patient-derived xenograft models. Mechanistically, the ADM-CALCRL axis drives cell cycle, DNA repair, and mitochondrial OxPHOS function of AML blasts dependent on E2F1 and BCL2. Finally, CALCRL depletion reduces LSC frequency of RICs post-chemotherapy in vivo. In summary, our data highlight a critical role of ADM-CALCRL in post-chemotherapy persistence of these cells, and disclose a promising therapeutic target to prevent relapse in AML.

There have been notable advances in the development of vaccines against active tuberculosis (TB) disease for adults and adolescents. Using mathematical models, we seek to estimate the potential impact of a post-exposure TB vaccine, having 50% efficacy in reducing active disease, on global rifampicin-resistant (RR-) TB burden. In 30 countries that together accounted for 90% of global RR-TB incidence in 2018, a future TB vaccine could avert 10% (95% credible interval: 9.7-11%) of RR-TB cases and 7.3% (6.6-8.1%) of deaths over 2020-2035, with India, China, Indonesia, Pakistan, and the Russian Federation having the greatest contribution. This impact would increase to 14% (12-16%) and 31% (29-33%) respectively, when combined with improvements in RR-TB diagnosis and treatment relative to a scenario of no vaccine and no such improvements. A future TB vaccine could have important implications for the global control of RR-TB, especially if implemented alongside enhancements in management of drug resistance.

Erratum in Nat Commun. 2021 Mar 5;12(1):1598.

Resolution and field-of-view often represent a fundamental tradeoff in microscopy. Atomic force microscopy (AFM), in which a cantilevered probe deflects under the influence of local forces as it scans across a substrate, is a key example of this tradeoff with high resolution imaging being largely limited to small areas. Despite the tremendous impact of AFM in fields including materials science, biology, and surface science, the limitation in imaging area has remained a key barrier to studying samples with intricate hierarchical structure. Here, we show that massively parallel AFM with >1000 probes is possible through the combination of a cantilever-free probe architecture and a scalable optical method for detecting probe-sample contact. Specifically, optically reflective conical probes on a comparatively compliant film are found to comprise a distributed optical lever that translates probe motion into an optical signal that provides sub-10 nm vertical precision. The scalability of this approach makes it well suited for imaging applications that require high resolution over large areas.

Erratum in Nat Commun. 2021 Mar 16;12(1):1801.

The Atlantic Niño is the leading mode of interannual sea-surface temperature (SST) variability in the equatorial Atlantic and assumed to be largely governed by coupled ocean-atmosphere dynamics described by the Bjerknes-feedback loop. However, the role of the atmospheric diabatic heating, which can be either an indicator of the atmosphere's response to, or its influence on the SST, is poorly understood. Here, using satellite-era observations from 1982-2015, we show that diabatic heating variability associated with the seasonal migration of the Inter-Tropical Convergence Zone controls the seasonality of the Atlantic Niño. The variability in precipitation, a measure of vertically integrated diabatic heating, leads that in SST, whereas the atmospheric response to SST variability is relatively weak. Our findings imply that the oceanic impact on the atmosphere is smaller than previously thought, questioning the relevance of the classical Bjerknes-feedback loop for the Atlantic Niño and limiting climate predictability over the equatorial Atlantic sector.

All-day passive radiative cooling has recently attracted tremendous interest by reflecting sunlight and radiating heat to the ultracold outer space. While some progress has been made, it still remains big challenge in fabricating highly efficient and low-cost radiative coolers for all-day and all-climates. Herein, we report a hierarchically structured polymethyl methacrylate (PMMA) film with a micropore array combined with random nanopores for highly efficient day- and nighttime passive radiative cooling. This hierarchically porous array PMMA film exhibits sufficiently high solar reflectance (0.95) and superior longwave infrared thermal emittance (0.98) and realizes subambient cooling of ~8.2 °C during the night and ~6.0 °C to ~8.9 °C during midday with an average cooling power of ~85 W/m2 under solar intensity of ~900 W/m2, and promisingly ~5.5 °C even under solar intensity of ~930 W/m2 and relative humidity of ~64% in hot and moist climate. The micropores and nanopores in the polymer film play crucial roles in enhancing the solar reflectance and thermal emittance.

Lipopolysaccharides are important components of the bacterial cell envelope that among other things act as a protective barrier against the environment and toxic molecules such as antibiotics. One of the most widely disseminated pathways of polysaccharide biosynthesis is the inner membrane bound Wzy-dependent pathway. Here we present the 3.0 Å structure of the co-polymerase component of this pathway, WzzB from E. coli solved by single-particle cryo-electron microscopy. The overall architecture is octameric and resembles a box jellyfish containing a large bell-shaped periplasmic domain with the 2-helix transmembrane domain from each protomer, positioned 32 Å apart, encircling a large empty transmembrane chamber. This structure also reveals the architecture of the transmembrane domain, including the location of key residues for the Wzz-family of proteins and the Wzy-dependent pathway present in many Gram-negative bacteria, explaining several of the previous biochemical and mutational studies and lays the foundation for future investigations.

The mega-diversity of herbivorous insects is attributed to their co-evolutionary associations with plants. Despite abundant studies on insect-plant interactions, we do not know whether host-plant shifts have impacted both genomic adaptation and species diversification over geological times. We show that the antagonistic insect-plant interaction between swallowtail butterflies and the highly toxic birthworts began 55 million years ago in Beringia, followed by several major ancient host-plant shifts. This evolutionary framework provides a valuable opportunity for repeated tests of genomic signatures of macroevolutionary changes and estimation of diversification rates across their phylogeny. We find that host-plant shifts in butterflies are associated with both genome-wide adaptive molecular evolution (more genes under positive selection) and repeated bursts of speciation rates, contributing to an increase in global diversification through time. Our study links ecological changes, genome-wide adaptations and macroevolutionary consequences, lending support to the importance of ecological interactions as evolutionary drivers over long time periods.

Recent critical commentaries unfavorably compare deep learning (DL) with standard machine learning (SML) approaches for brain imaging data analysis. However, their conclusions are often based on pre-engineered features depriving DL of its main advantage - representation learning. We conduct a large-scale systematic comparison profiled in multiple classification and regression tasks on structural MRI images and show the importance of representation learning for DL. Results show that if trained following prevalent DL practices, DL methods have the potential to scale particularly well and substantially improve compared to SML methods, while also presenting a lower asymptotic complexity in relative computational time, despite being more complex. We also demonstrate that DL embeddings span comprehensible task-specific projection spectra and that DL consistently localizes task-discriminative brain biomarkers. Our findings highlight the presence of nonlinearities in neuroimaging data that DL can exploit to generate superior task-discriminative representations for characterizing the human brain.

Causal inference via Mendelian randomization requires making strong assumptions about horizontal pleiotropy, where genetic instruments are connected to the outcome not only through the exposure. Here, we present causal Graphical Analysis Using Genetics (cGAUGE), a pipeline that overcomes these limitations using instrument filters with provable properties. This is achievable by identifying conditional independencies while examining multiple traits. cGAUGE also uses ExSep (Exposure-based Separation), a novel test for the existence of causal pathways that does not require selecting instruments. In simulated data we illustrate how cGAUGE can reduce the empirical false discovery rate by up to 30%, while retaining the majority of true discoveries. On 96 complex traits from 337,198 subjects from the UK Biobank, our results cover expected causal links and many new ones that were previously suggested by correlation-based observational studies. Notably, we identify multiple risk factors for cardiovascular disease, including red blood cell distribution width.

Comment in Nat Rev Rheumatol. 2021 Jun;17(6):313-314.

Bright and efficient blue emission is key to further development of metal halide perovskite light-emitting diodes. Although modifying bromide/chloride composition is straightforward to achieve blue emission, practical implementation of this strategy has been challenging due to poor colour stability and severe photoluminescence quenching. Both detrimental effects become increasingly prominent in perovskites with the high chloride content needed to produce blue emission. Here, we solve these critical challenges in mixed halide perovskites and demonstrate spectrally stable blue perovskite light-emitting diodes over a wide range of emission wavelengths from 490 to 451 nanometres. The emission colour is directly tuned by modifying the halide composition. Particularly, our blue and deep-blue light-emitting diodes based on three-dimensional perovskites show high EQE values of 11.0% and 5.5% with emission peaks at 477 and 467 nm, respectively. These achievements are enabled by a vapour-assisted crystallization technique, which largely mitigates local compositional heterogeneity and ion migration.

Resolving how Earth surface redox conditions evolved through the Proterozoic Eon is fundamental to understanding how biogeochemical cycles have changed through time. The redox sensitivity of cerium relative to other rare earth elements and its uptake in carbonate minerals make the Ce anomaly (Ce/Ce*) a particularly useful proxy for capturing redox conditions in the local marine environment. Here, we report Ce/Ce* data in marine carbonate rocks through 3.5 billion years of Earth's history, focusing in particular on the mid-Proterozoic Eon (i.e., 1.8 - 0.8 Ga). To better understand the role of atmospheric oxygenation, we use Ce/Ce* data to estimate the partial pressure of atmospheric oxygen (pO2) through this time. Our thermodynamics-based modeling supports a major rise in atmospheric oxygen level in the aftermath of the Great Oxidation Event (~ 2.4 Ga), followed by invariant pO2 of about 1% of present atmospheric level through most of the Proterozoic Eon (2.4 to 0.65 Ga).

Phosphorylated H2A.X is a critical chromatin marker of DNA damage repair (DDR) in higher eukaryotes. However, H2A.X gene expression remains relatively uncharacterised. Replication-dependent (RD) histone genes generate poly(A)- mRNA encoding new histones to package DNA during replication. In contrast, replication-independent (RI) histone genes synthesise poly(A)+ mRNA throughout the cell cycle, translated into histone variants that confer specific epigenetic patterns on chromatin. Remarkably H2AFX, encoding H2A.X, is a hybrid histone gene, generating both poly(A)+ and poly(A)- mRNA isoforms. Here we report that the selective removal of either mRNA isoform reveals different effects in different cell types. In some cells, RD H2A.X poly(A)- mRNA generates sufficient histone for deposition onto DDR associated chromatin. In contrast, cells making predominantly poly(A)+ mRNA require this isoform for de novo H2A.X synthesis, required for efficient DDR. This highlights the importance of differential H2A.X mRNA 3'-end processing in the maintenance of effective DDR.

Aberrant neural oscillations hallmark numerous brain disorders. Here, we first report a method to track the phase of neural oscillations in real-time via endpoint-corrected Hilbert transform (ecHT) that mitigates the characteristic Gibbs distortion. We then used ecHT to show that the aberrant neural oscillation that hallmarks essential tremor (ET) syndrome, the most common adult movement disorder, can be transiently suppressed via transcranial electrical stimulation of the cerebellum phase-locked to the tremor. The tremor suppression is sustained shortly after the end of the stimulation and can be phenomenologically predicted. Finally, we use feature-based statistical-learning and neurophysiological-modelling to show that the suppression of ET is mechanistically attributed to a disruption of the temporal coherence of the aberrant oscillations in the olivocerebellar loop, thus establishing its causal role. The suppression of aberrant neural oscillation via phase-locked driven disruption of temporal coherence may in the future represent a powerful neuromodulatory strategy to treat brain disorders.

Comment in J Cancer Biol. 2021;2(2):42-43.

The inhibition of Plasmodium cytosolic phenylalanine tRNA-synthetase (cFRS) by a novel series of bicyclic azetidines has shown the potential to prevent malaria transmission, provide prophylaxis, and offer single-dose cure in animal models of malaria. To date, however, the molecular basis of Plasmodium cFRS inhibition by bicyclic azetidines has remained unknown. Here, we present structural and biochemical evidence that bicyclic azetidines are competitive inhibitors of L-Phe, one of three substrates required for the cFRS-catalyzed aminoacylation reaction that underpins protein synthesis in the parasite. Critically, our co-crystal structure of a PvcFRS-BRD1389 complex shows that the bicyclic azetidine ligand binds to two distinct sub-sites within the PvcFRS catalytic site. The ligand occupies the L-Phe site along with an auxiliary cavity and traverses past the ATP binding site. Given that BRD1389 recognition residues are conserved amongst apicomplexan FRSs, this work lays a structural framework for the development of drugs against both Plasmodium and related apicomplexans.

Erratum in Nat Commun. 2021 Mar 5;12(1):1600.

Molecular sieving may occur when two molecules compete for a nanopore. In nearly all known examples, the nanopore is larger than the molecule that selectively enters the pore. Here, we experimentally demonstrate the ability of single-wall carbon nanotubes with a van der Waals pore size of 0.42 nm to separate n-hexane from cyclohexane-despite the fact that both molecules have kinetic diameters larger than the rigid nanopore. This unexpected finding challenges our current understanding of nanopore selectivity and how molecules may enter a tight channel. Ab initio molecular dynamics simulations reveal that n-hexane molecules stretch by nearly 11.2% inside the nanotube pore. Although at a relatively low probability (28.5% overall), the stretched state of n-hexane does exist in the bulk solution, allowing the molecule to enter the tight pore even at room temperature. These insights open up opportunities to engineer nanopore selectivity based on the molecular degrees of freedom.

Erratum in Nat Commun. 2021 Jun 2;12(1):3466.

The yeast protein Rad5 and its orthologs in other eukaryotes promote replication stress tolerance and cell survival using their multiple activities, including ubiquitin ligase, replication fork remodeling and DNA lesion targeting activities. Here, we present the crystal structure of a nearly full-length Rad5 protein. The structure shows three distinct, but well-connected, domains required for Rad5's activities. The spatial arrangement of these domains suggest that different domains can have autonomous activities but also undergo intrinsic coordination. Moreover, our structural, biochemical and cellular studies demonstrate that Rad5's HIRAN domain mediates interactions with the DNA metabolism maestro factor PCNA and contributes to its poly-ubiquitination, binds to DNA and contributes to the Rad5-catalyzed replication fork regression, defining a new type of HIRAN domains with multiple activities. Our work provides a framework to understand how Rad5 integrates its various activities in replication stress tolerance.

Circular RNAs (circRNAs) have emerged as an important class of functional RNA molecules. Short-read RNA sequencing (RNA-seq) is a widely used strategy to identify circRNAs. However, an inherent limitation of short-read RNA-seq is that it does not experimentally determine the full-length sequences and exact exonic compositions of circRNAs. Here, we report isoCirc, a strategy for sequencing full-length circRNA isoforms, using rolling circle amplification followed by nanopore long-read sequencing. We describe an integrated computational pipeline to reliably characterize full-length circRNA isoforms using isoCirc data. Using isoCirc, we generate a comprehensive catalog of 107,147 full-length circRNA isoforms across 12 human tissues and one human cell line (HEK293), including 40,628 isoforms ≥500 nt in length. We identify widespread alternative splicing events within the internal part of circRNAs, including 720 retained intron events corresponding to a class of exon-intron circRNAs (EIciRNAs). Collectively, isoCirc and the companion dataset provide a useful strategy and resource for studying circRNAs in human transcriptomes.

When two-dimensional crystals are brought into close proximity, their interaction results in reconstruction of electronic spectrum and crystal structure. Such reconstruction strongly depends on the twist angle between the crystals, which has received growing attention due to interesting electronic and optical properties that arise in graphene and transitional metal dichalcogenides. Here we study two insulating crystals of hexagonal boron nitride stacked at small twist angle. Using electrostatic force microscopy, we observe ferroelectric-like domains arranged in triangular superlattices with a large surface potential. The observation is attributed to interfacial elastic deformations that result in out-of-plane dipoles formed by pairs of boron and nitrogen atoms belonging to opposite interfacial surfaces. This creates a bilayer-thick ferroelectric with oppositely polarized (BN and NB) dipoles in neighbouring domains, in agreement with our modeling. These findings open up possibilities for designing van der Waals heterostructures and offer an alternative probe to study moiré-superlattice electrostatic potentials.

Rapid Auger recombination represents an important challenge faced by quasi-2D perovskites, which induces resulting perovskite light-emitting diodes' (PeLEDs) efficiency roll-off. In principle, Auger recombination rate is proportional to materials' exciton binding energy (Eb). Thus, Auger recombination can be suppressed by reducing the corresponding materials' Eb. Here, a polar molecule, p-fluorophenethylammonium, is employed to generate quasi-2D perovskites with reduced Eb. Recombination kinetics reveal the Auger recombination rate does decrease to one-order-of magnitude lower compared to its PEA+ analogues. After effective passivation, nonradiative recombination is greatly suppressed, which enables resulting films to exhibit outstanding photoluminescence quantum yields in a broad range of excitation density. We herein demonstrate the very efficient PeLEDs with a peak external quantum efficiency of 20.36%. More importantly, devices exhibit a record luminance of 82,480 cd m-2 due to the suppressed efficiency roll-off, which represent one of the brightest visible PeLEDs yet.

Erratum in Nat Commun. 2021 May 6;12(1):2753.

Field induced domain wall displacements define ferroelectric/ferroelastic hysteresis loops, which are at the core of piezoelectric, magnetoelectric and memristive devices. These collective displacements are scale invariant jumps with avalanche characteristics. Here, we analyse the spatial distribution of avalanches in ferroelectrics with different domain and transformation patterns: Pb(Mg1/3Nb2/3)O3-PbTiO3 contains complex domains with needles and junction patterns, while BaTiO3 has parallel straight domains. Nevertheless, their avalanche characteristics are indistinguishable. The energies, areas and perimeters of the switched regions are power law distributed with exponents close to predicted mean field values. At the coercive field, the area exponent decreases, while the fractal dimension increases. This fine structure of the switching process has not been detected before and suggests that switching occurs via criticality at the coercive field with fundamentally different switching geometries at and near this critical point. We conjecture that the domain switching process in ferroelectrics is universal at the coercive field.

Skeletal muscle is the protein reservoir of our body and an important regulator of glucose and lipid homeostasis. Consequently, the growth or the loss of muscle mass can influence general metabolism, locomotion, eating and respiration. Therefore, it is not surprising that excessive muscle loss is a bad prognostic index of a variety of diseases ranging from cancer, organ failure, infections and unhealthy ageing. Muscle function is influenced by different quality systems that regulate the function of contractile proteins and organelles. These systems are controlled by transcriptional dependent programs that adapt muscle cells to environmental and nutritional clues. Mechanical, oxidative, nutritional and energy stresses, as well as growth factors or cytokines modulate signaling pathways that, ultimately, converge on protein and organelle turnover. Novel insights that control and orchestrate such complex network are continuously emerging and will be summarized in this review. Understanding the mechanisms that control muscle mass will provide therapeutic targets for the treatment of muscle loss in inherited and non-hereditary diseases and for the improvement of the quality of life during ageing.

Multistep enzyme-catalyzed cascade reactions are highly efficient in nature due to the confinement and concentration of the enzymes within nanocompartments. In this way, rates are exceptionally high, and loss of intermediates minimised. Similarly, extended enzyme cascades trapped and crowded within the nanoconfined environment of a porous conducting metal oxide electrode material form the basis of a powerful way to study and exploit myriad complex biocatalytic reactions and pathways. One of the confined enzymes, ferredoxin-NADP+ reductase, serves as a transducer, rapidly and reversibly recycling nicotinamide cofactors electrochemically for immediate delivery to the next enzyme along the chain, thereby making it possible to energize, control and observe extended cascade reactions driven in either direction depending on the electrode potential that is applied. Here we show as proof of concept the synthesis of aspartic acid from pyruvic acid or its reverse oxidative decarboxylation/deamination, involving five nanoconfined enzymes.

High-throughput sequencing protocols such as RNA-seq have made it possible to interrogate the sequence, structure and abundance of RNA transcripts at higher resolution than previous microarray and other molecular techniques. While many computational tools have been proposed for identifying mRNA variation through differential splicing/alternative exon usage, challenges in its analysis remain. Here, we propose a framework for unbiased and robust discovery of aberrant RNA transcript structures using short read sequencing data based on shape changes in an RNA-seq coverage profile. Shape changes in selecting sample outliers in RNA-seq, SCISSOR, is a series of procedures for transforming and normalizing base-level RNA sequencing coverage data in a transcript independent manner, followed by a statistical framework for its analysis ( https://github.com/hyochoi/SCISSOR ). The resulting high dimensional object is amenable to unsupervised screening of structural alterations across RNA-seq cohorts with nearly no assumption on the mutational mechanisms underlying abnormalities. This enables SCISSOR to independently recapture known variants such as splice site mutations in tumor suppressor genes as well as novel variants that are previously unrecognized or difficult to identify by any existing methods including recurrent alternate transcription start sites and recurrent complex deletions in 3' UTRs.

Pemphigoid diseases refer to a group of severe autoimmune skin blistering diseases characterized by subepidermal blistering and loss of dermal-epidermal adhesion induced by autoantibody and immune cell infiltrate at the dermal-epidermal junction and upper dermis. Here, we explore the role of the immune cell-secreted serine protease, granzyme B, in pemphigoid disease pathogenesis using three independent murine models. In all models, granzyme B knockout or topical pharmacological inhibition significantly reduces total blistering area compared to controls. In vivo and in vitro studies show that granzyme B contributes to blistering by degrading key anchoring proteins in the dermal-epidermal junction that are necessary for dermal-epidermal adhesion. Further, granzyme B mediates IL-8/macrophage inflammatory protein-2 secretion, lesional neutrophil infiltration, and lesional neutrophil elastase activity. Clinically, granzyme B is elevated and abundant in human pemphigoid disease blister fluids and lesional skin. Collectively, granzyme B is a potential therapeutic target in pemphigoid diseases.

The environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) causes hepatic toxicity associated with prominent lipid accumulation in humans. Here, the authors report that the lysosomal copper transporter SLC46A3 is induced by TCDD and underlies the hepatic lipid accumulation in mice, potentially via effects on mitochondrial function. SLC46A3 was localized to the lysosome where it modulated intracellular copper levels. Forced expression of hepatic SLC46A3 resulted in decreased mitochondrial membrane potential and abnormal mitochondria morphology consistent with lower copper levels. SLC46A3 expression increased hepatic lipid accumulation similar to the known effects of TCDD exposure in mice and humans. The TCDD-induced hepatic triglyceride accumulation was significantly decreased in Slc46a3-/- mice and was more pronounced when these mice were fed a high-fat diet, as compared to wild-type mice. These data are consistent with a model where lysosomal SLC46A3 induction by TCDD leads to cytosolic copper deficiency resulting in mitochondrial dysfunction leading to lower lipid catabolism, thus linking copper status to mitochondrial function, lipid metabolism and TCDD-induced liver toxicity.

Magma from Plinian volcanic eruptions contains an extraordinarily large numbers of bubbles. Nucleation of those bubbles occurs because pressure decreases as magma rises to the surface. As a consequence, dissolved magmatic volatiles, such as water, become supersaturated and cause bubbles to nucleate. At the same time, diffusion of volatiles into existing bubbles reduces supersaturation, resulting in a dynamical feedback between rates of nucleation due to magma decompression and volatile diffusion. Because nucleation rate increases with supersaturation, bubble number density (BND) provides a proxy record of decompression rate, and hence the intensity of eruption dynamics. Using numerical modeling of bubble nucleation, we reconcile a long-standing discrepancy in decompression rate estimated from BND and independent geospeedometers. We demonstrate that BND provides a record of the time-averaged decompression rate that is consistent with independent geospeedometers, if bubble nucleation is heterogeneous and facilitated by magnetite crystals.

Bioelectrical impulses intrinsically generated within the sinoatrial node (SAN) trigger the contraction of the heart in mammals. Though discovered over a century ago, the molecular and cellular features of the SAN that underpin its critical function in the heart are uncharted territory. Here, we identify four distinct transcriptional clusters by single-cell RNA sequencing in the mouse SAN. Functional analysis of differentially expressed genes identifies a core cell cluster enriched in the electrogenic genes. The similar cellular features are also observed in the SAN from both rabbit and cynomolgus monkey. Notably, Vsnl1, a core cell cluster marker in mouse, is abundantly expressed in SAN, but is barely detectable in atrium or ventricle, suggesting that Vsnl1 is a potential SAN marker. Importantly, deficiency of Vsnl1 not only reduces the beating rate of human induced pluripotent stem cell - derived cardiomyocytes (hiPSC-CMs) but also the heart rate of mice. Furthermore, weighted gene co-expression network analysis (WGCNA) unveiled the core gene regulation network governing the function of the SAN in mice. Overall, these findings reveal the whole transcriptome profiling of the SAN at single-cell resolution, representing an advance toward understanding of both the biology and the pathology of SAN.

Individuals vary widely in how they categorize novel and ambiguous phenomena. This individual variation has led influential theories in cognitive and social science to suggest that communication in large social groups introduces path dependence in category formation, which is expected to lead separate populations toward divergent cultural trajectories. Yet, anthropological data indicates that large, independent societies consistently arrive at highly similar category systems across a range of topics. How is it possible for diverse populations, consisting of individuals with significant variation in how they categorize the world, to independently construct similar category systems? Here, we investigate this puzzle experimentally by creating an online "Grouping Game" in which we observe how people in small and large populations collaboratively construct category systems for a continuum of ambiguous stimuli. We find that solitary individuals and small groups produce highly divergent category systems; however, across independent trials with unique participants, large populations consistently converge on highly similar category systems. A formal model of critical mass dynamics in social networks accurately predicts this process of scale-induced category convergence. Our findings show how large communication networks can filter lexical diversity among individuals to produce replicable society-level patterns, yielding unexpected implications for cultural evolution.

Vaccines and therapeutics are urgently needed for the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we screen human monoclonal antibodies (mAb) targeting the receptor binding domain (RBD) of the viral spike protein via antibody library constructed from peripheral blood mononuclear cells of a convalescent patient. The CT-P59 mAb potently neutralizes SARS-CoV-2 isolates including the D614G variant without antibody-dependent enhancement effect. Complex crystal structure of CT-P59 Fab/RBD shows that CT-P59 blocks interaction regions of RBD for angiotensin converting enzyme 2 (ACE2) receptor with an orientation that is notably different from previously reported RBD-targeting mAbs. Furthermore, therapeutic effects of CT-P59 are evaluated in three animal models (ferret, hamster, and rhesus monkey), demonstrating a substantial reduction in viral titer along with alleviation of clinical symptoms. Therefore, CT-P59 may be a promising therapeutic candidate for COVID-19.

The electrical Hall effect can be significantly enhanced through the interplay of the conduction electrons with magnetism, which is known as the anomalous Hall effect (AHE). Whereas the mechanism related to band topology has been intensively studied towards energy efficient electronics, those related to electron scattering have received limited attention. Here we report the observation of giant AHE of electron-scattering origin in a chiral magnet MnGe thin film. The Hall conductivity and Hall angle, respectively, reach [Formula: see text] Ω-1 cm-1 and [Formula: see text]% in the ferromagnetic region, exceeding the conventional limits of AHE of intrinsic and extrinsic origins, respectively. A possible origin of the large AHE is attributed to a new type of skew-scattering via thermally excited spin-clusters with scalar spin chirality, which is corroborated by the temperature-magnetic-field profile of the AHE being sensitive to the film-thickness or magneto-crystalline anisotropy. Our results may open up a new platform to explore giant AHE responses in various systems, including frustrated magnets and thin-film heterostructures.

Room-temperature skyrmions in magnetic multilayers are considered to be promising candidates for the next-generation spintronic devices. Several approaches have been developed to control skyrmions, but they either cause significant heat dissipation or require ultrahigh electric fields near the breakdown threshold. Here, we demonstrate electric-field control of skyrmions through strain-mediated magnetoelectric coupling in ferromagnetic/ferroelectric multiferroic heterostructures. We show the process of non-volatile creation of multiple skyrmions, reversible deformation and annihilation of a single skyrmion by performing magnetic force microscopy with in situ electric fields. Strain-induced changes in perpendicular magnetic anisotropy and interfacial Dzyaloshinskii-Moriya interaction strength are characterized experimentally. These experimental results, together with micromagnetic simulations, demonstrate that strain-mediated magnetoelectric coupling (via strain-induced changes in both the perpendicular magnetic anisotropy and interfacial Dzyaloshinskii-Moriya interaction is responsible for the observed electric-field control of skyrmions. Our work provides a platform to investigate electric-field control of skyrmions in multiferroic heterostructures and paves the way towards more energy-efficient skyrmion-based spintronics.

Stochastic fluctuations at the transcriptional level contribute to isogenic cell-to-cell heterogeneity in mammalian cell populations. However, we still have no clear understanding of the repercussions of this heterogeneity, given the lack of tools to independently control mean expression and variability of a gene. Here, we engineer a synthetic circuit to modulate mean expression and heterogeneity of transgenes and endogenous human genes. The circuit, a Tunable Noise Rheostat (TuNR), consists of a transcriptional cascade of two inducible transcriptional activators, where the output mean and variance can be modulated by two orthogonal small molecule inputs. In this fashion, different combinations of the inputs can achieve the same mean but with different population variability. With TuNR, we achieve low basal expression, over 1000-fold expression of a transgene product, and up to 7-fold induction of the endogenous gene NGFR. Importantly, for the same mean expression level, we are able to establish varying degrees of heterogeneity in expression within an isogenic population, thereby decoupling gene expression noise from its mean. TuNR is therefore a modular tool that can be used in mammalian cells to enable direct interrogation of the implications of cell-to-cell variability.

A crucial step towards engineering biological systems is the ability to precisely tune the genetic response to environmental stimuli. In the case of Escherichia coli inducible promoters, our incomplete understanding of the relationship between sequence composition and gene expression hinders our ability to predictably control transcriptional responses. Here, we profile the expression dynamics of 8269 rationally designed, IPTG-inducible promoters that collectively explore the individual and combinatorial effects of RNA polymerase and LacI repressor binding site strengths. We then fit a statistical mechanics model to measured expression that accurately models gene expression and reveals properties of theoretically optimal inducible promoters. Furthermore, we characterize three alternative promoter architectures and show that repositioning binding sites within promoters influences the types of combinatorial effects observed between promoter elements. In total, this approach enables us to deconstruct relationships between inducible promoter elements and discover practical insights for engineering inducible promoters with desirable characteristics.

Comment in Nat Commun. 2021 Jan 12;12(1):329.

3D printing offers enormous flexibility in fabrication of polymer objects with complex geometries. However, it is not suitable for fabricating large polymer structures with geometrical features at the sub-micrometer scale. Porous structure at the sub-micrometer scale can render macroscopic objects with unique properties, including similarities with biological interfaces, permeability and extremely large surface area, imperative inter alia for adsorption, separation, sensing or biomedical applications. Here, we introduce a method combining advantages of 3D printing via digital light processing and polymerization-induced phase separation, which enables formation of 3D polymer structures of digitally defined macroscopic geometry with controllable inherent porosity at the sub-micrometer scale. We demonstrate the possibility to create 3D polymer structures of highly complex geometries and spatially controlled pore sizes from 10 nm to 1000 µm. Produced hierarchical polymers combining nanoporosity with micrometer-sized pores demonstrate improved adsorption performance due to better pore accessibility and favored cell adhesion and growth for 3D cell culture due to surface porosity. This method extends the scope of applications of 3D printing to hierarchical inherently porous 3D objects combining structural features ranging from 10 nm up to cm, making them available for a wide variety of applications.

Understanding inorganic nanocrystal (NC) growth dynamic pathways under their native fabrication environment remains a central goal of science, as it is crucial for rationalizing novel nanoformulations with desired architectures and functionalities. We here present an in-situ method for quantifying, in real time, NCs' size evolution at sub-nm resolution, their concentration, and reactants consumption rate for studying NC growth mechanisms. Analyzing sequential high-resolution liquid-state 19F-NMR spectra obtained in-situ and validating by ex-situ cryoTEM, we explore the growth evolution of fluoride-based NCs (CaF2 and SrF2) in water, without disturbing the synthesis conditions. We find that the same nanomaterial (CaF2) can grow by either a particle-coalescence or classical-growth mechanism, as regulated by the capping ligand, resulting in different crystallographic properties and functional features of the fabricated NC. The ability to reveal, in real time, mechanistic pathways at which NCs grow open unique opportunities for tunning the properties of functional materials.

The complete human genome sequence is used as a reference for next-generation sequencing analyses. However, some ethnic ancestries are under-represented in the reference genome (e.g., GRCh37) due to its bias toward European and African ancestries. Here, we perform de novo assembly of three Japanese male genomes using > 100× Pacific Biosciences long reads and Bionano Genomics optical maps per sample. We integrate the genomes using the major allele for consensus and anchor the scaffolds using genetic and radiation hybrid maps to reconstruct each chromosome. The resulting genome sequence, JG1, is contiguous, accurate, and carries the Japanese major allele at most loci. We adopt JG1 as the reference for confirmatory exome re-analyses of seven rare-disease Japanese families and find that re-analysis using JG1 reduces total candidate variant calls versus GRCh37 while retaining disease-causing variants. These results suggest that integrating multiple genomes from a single population can aid genome analyses of that population.

Key questions in COVID-19 are the duration and determinants of infectious virus shedding. Here, we report that infectious virus shedding is detected by virus cultures in 23 of the 129 patients (17.8%) hospitalized with COVID-19. The median duration of shedding infectious virus is 8 days post onset of symptoms (IQR 5-11) and drops below 5% after 15.2 days post onset of symptoms (95% confidence interval (CI) 13.4-17.2). Multivariate analyses identify viral loads above 7 log10 RNA copies/mL (odds ratio [OR] of 14.7 (CI 3.57-58.1; p < 0.001) as independently associated with isolation of infectious SARS-CoV-2 from the respiratory tract. A serum neutralizing antibody titre of at least 1:20 (OR of 0.01 (CI 0.003-0.08; p < 0.001) is independently associated with non-infectious SARS-CoV-2. We conclude that quantitative viral RNA load assays and serological assays could be used in test-based strategies to discontinue or de-escalate infection prevention and control precautions.

The mobility of dislocation loops in materials is a principle factor in understanding the mechanical strength, and the evolution of microstructures due to deformation and radiation. In body-centered cubic (BCC) iron, the common belief is that <100> interstitial dislocation loops are immobile once formed. However, using self-adaptive accelerated molecular dynamics (SSAMD), a new diffusion mechanism has been discovered for <100> interstitial dislocation loops. The key aspect of the mechanism is the changing of the habit planes between the {100} plane and the {110} plane, which provides a path for the <100> loops to diffuse one-dimensionally. The migration behavior modeled with SSAMD is further confirmed by in-situ transmission electron microscopy (TEM) measurements, and represents a significant step for understanding the formation of <100> loop walls and the mechanical behavior of BCC Fe under irradiation.

Absent pharmaceutical interventions, social distancing, lock-downs and mobility restrictions remain our prime response in the face of epidemic outbreaks. To ease their potentially devastating socioeconomic consequences, we propose here an alternating quarantine strategy: at every instance, half of the population remains under lockdown while the other half continues to be active - maintaining a routine of weekly succession between activity and quarantine. This regime minimizes infectious interactions, as it allows only half of the population to interact for just half of the time. As a result it provides a dramatic reduction in transmission, comparable to that achieved by a population-wide lockdown, despite sustaining socioeconomic continuity at  ~50% capacity. The weekly alternations also help address the specific challenge of COVID-19, as their periodicity synchronizes with the natural SARS-CoV-2 disease time-scales, allowing to effectively isolate the majority of infected individuals precisely at the time of their peak infection.

Acute myeloid leukemia (AML) is a high remission, high relapse fatal blood cancer. Although mTORC1 is a master regulator of cell proliferation and survival, its inhibitors have not performed well as AML treatments. To uncover the dynamics of mTORC1 activity in vivo, fluorescent probes are developed to track single cell proliferation, apoptosis and mTORC1 activity of AML cells in the bone marrow of live animals and to quantify these activities in the context of microanatomical localization and intra-tumoral heterogeneity. When chemotherapy drugs commonly used clinically are given to mice with AML, apoptosis is rapid, diffuse and not preferentially restricted to anatomic sites. Dynamic measurement of mTORC1 activity indicated a decline in mTORC1 activity with AML progression. However, at the time of maximal chemotherapy response, mTORC1 signaling is high and positively correlated with a leukemia stemness transcriptional profile. Cell barcoding reveals the induction of mTORC1 activity rather than selection of mTORC1 high cells and timed inhibition of mTORC1 improved the killing of AML cells. These data define the real-time dynamics of AML and the mTORC1 pathway in association with AML growth, response to and relapse after chemotherapy. They provide guidance for timed intervention with pathway-specific inhibitors.

Understanding the function of surface states on photoanodes is crucial for unraveling the underlying reaction mechanisms of water oxidation. For hematite photoanodes, only one type of surface states with higher oxidative energy (S1) has been proposed and verified as reaction intermediate, while the other surface state located at lower potentials (S2) was assigned to inactive or recombination sites. Through employing rate law analyses and systematical (photo)electrochemical characterizations, here we show that S2 is an active reaction intermediate for water oxidation as well. Furthermore, we demonstrate that the reaction kinetics and dynamic interactions of both S1 and S2 depend significantly on operational parameters, such as illumination intensity, nature of the electrolyte, and applied potential. These insights into the individual reaction kinetics and the interplay of both surface states are decisive for designing efficient photoanodes.

The neural circuitry mediating taste has been mapped out from the periphery to the cortex, but genetic identity of taste-responsive neurons has remained elusive. Here, we describe a population of neurons in the gustatory region of the parabrachial nucleus that express the transcription factor Satb2 and project to taste-associated regions, including the gustatory thalamus and insular cortex. Using calcium imaging in awake, freely licking mice, we show that Satb2 neurons respond to the five basic taste modalities. Optogenetic activation of these neurons enhances taste preferences, whereas chronic inactivation decreases the magnitude of taste preferences in both brief- and long-access taste tests. Simultaneous inactivation of Satb2 and calcitonin gene-related peptide neurons in the PBN abolishes responses to aversive tastes. These data suggest that taste information in the parabrachial nucleus is conveyed by multiple populations of neurons, including both Satb2 and calcitonin gene-related peptide neurons.

While a number of human coronaviruses are believed to be originated from ancestral viruses in bats, it remains unclear if bat coronaviruses are ready to cause direct bat-to-human transmission. Here, we report the isolation of a MERS-related coronavirus, Tylonycteris-bat-CoV-HKU4, from lesser bamboo bats. Tylonycteris-bat-CoV-HKU4 replicates efficiently in human colorectal adenocarcinoma and hepatocarcinoma cells with cytopathic effects, and can utilize human-dipeptidyl-peptidase-4 and dromedary camel-dipeptidyl-peptidase-4 as the receptors for cell entry. Flow cytometry, co-immunoprecipitation and surface plasmon resonance assays show that Tylonycteris-bat-CoV-HKU4-receptor-binding-domain can bind human-dipeptidyl-peptidase-4, dromedary camel-dipeptidyl-peptidase-4, and Tylonycteris pachypus-dipeptidyl-peptidase-4. Tylonycteris-bat-CoV-HKU4 can infect human-dipeptidyl-peptidase-4-transgenic mice by intranasal inoculation with self-limiting disease. Positive virus and inflammatory changes were detected in lungs and brains of infected mice, associated with suppression of antiviral cytokines and activation of proinflammatory cytokines and chemokines. The results suggest that MERS-related bat coronaviruses may overcome species barrier by utilizing dipeptidyl-peptidase-4 and potentially emerge in humans by direct bat-to-human transmission.

Grid cells are part of a widespread network which supports navigation and spatial memory. Stable grid patterns appear late in development, in concert with extracellular matrix aggregates termed perineuronal nets (PNNs) that condense around inhibitory neurons. It has been suggested that PNNs stabilize synaptic connections and long-term memories, but their role in the grid cell network remains elusive. We show that removal of PNNs leads to lower inhibitory spiking activity, and reduces grid cells' ability to create stable representations of a novel environment. Furthermore, in animals with disrupted PNNs, exposure to a novel arena corrupted the spatiotemporal relationships within grid cell modules, and the stored representations of a familiar arena. Finally, we show that PNN removal in entorhinal cortex distorted spatial representations in downstream hippocampal neurons. Together this work suggests that PNNs provide a key stabilizing element for the grid cell network.

The emerging field of twistronics, which harnesses the twist angle between two-dimensional materials, represents a promising route for the design of quantum materials, as the twist-angle-induced superlattices offer means to control topology and strong correlations. At the small twist limit, and particularly under strain, as atomic relaxation prevails, the emergent moiré superlattice encodes elusive insights into the local interlayer interaction. Here we introduce moiré metrology as a combined experiment-theory framework to probe the stacking energy landscape of bilayer structures at the 0.1 meV/atom scale, outperforming the gold-standard of quantum chemistry. Through studying the shapes of moiré domains with numerous nano-imaging techniques, and correlating with multi-scale modelling, we assess and refine first-principle models for the interlayer interaction. We document the prowess of moiré metrology for three representative twisted systems: bilayer graphene, double bilayer graphene and H-stacked MoSe2/WSe2. Moiré metrology establishes sought after experimental benchmarks for interlayer interaction, thus enabling accurate modelling of twisted multilayers.

Realizing a long coherence time quantum memory is a major challenge of current quantum technology. Until now, the longest coherence-time of a single qubit was reported as 660 s in a single 171Yb+ ion-qubit through the technical developments of sympathetic cooling and dynamical decoupling pulses, which addressed heating-induced detection inefficiency and magnetic field fluctuations. However, it was not clear what prohibited further enhancement. Here, we identify and suppress the limiting factors, which are the remaining magnetic-field fluctuations, frequency instability and leakage of the microwave reference-oscillator. Then, we observe the coherence time of around 5500 s for the 171Yb+ ion-qubit, which is the time constant of the exponential decay fit from the measurements up to 960 s. We also systematically study the decoherence process of the quantum memory by using quantum process tomography and analyze the results by applying recently developed resource theories of quantum memory and coherence. Our experimental demonstration will accelerate practical applications of quantum memories for various quantum information processing, especially in the noisy-intermediate-scale quantum regime.

The efficient transformation of CO2 into chemicals and fuels is a key challenge for the decarbonisation of the synthetic production chain. Formic acid (FA) represents the first product of CO2 hydrogenation and can be a precursor of higher added value products or employed as a hydrogen storage vector. Bases are typically required to overcome thermodynamic barriers in the synthesis of FA, generating waste and requiring post-processing of the formate salts. The employment of buffers can overcome these limitations, but their catalytic performance has so far been modest. Here, we present a methodology utilising IL as buffers to catalytically transform CO2 into FA with very high efficiency and comparable performance to the base-assisted systems. The combination of multifunctional basic ionic liquids and catalyst design enables the synthesis of FA with very high catalytic efficiency in TONs of >8*105 and TOFs > 2.1*104 h-1.

Leishmaniasis is widely regarded as a vaccine-preventable disease, but the costs required to reach pivotal Phase 3 studies and uncertainty about which candidate vaccines should be progressed into human studies significantly limits progress in vaccine development for this neglected tropical disease. Controlled human infection models (CHIMs) provide a pathway for accelerating vaccine development and to more fully understand disease pathogenesis and correlates of protection. Here, we describe the isolation, characterization and GMP manufacture of a new clinical strain of Leishmania major. Two fresh strains of L. major from Israel were initially compared by genome sequencing, in vivo infectivity and drug sensitivity in mice, and development and transmission competence in sand flies, allowing one to be selected for GMP production. This study addresses a major roadblock in the development of vaccines for leishmaniasis, providing a key resource for CHIM studies of sand fly transmitted cutaneous leishmaniasis.

Erratum in Nat Commun. 2021 Feb 23;12(1):1372.