Protocadherin-19 (PCDH19) mutations cause early-onset seizures and cognitive impairment. The PCDH19 gene is on the X-chromosome. Unlike most X-linked disorders, PCDH19 mutations affect heterozygous females (PCDH19HET) but not hemizygous males (PCDH19HEMI); however, the reason why remains to be elucidated. We demonstrate that PCDH19, a cell-adhesion molecule, is enriched at hippocampal mossy fiber synapses. Pcdh19HET but not Pcdh19HEMI mice show impaired mossy fiber synaptic structure and physiology. Consistently, Pcdh19HET but not Pcdh19HEMI mice exhibit reduced pattern completion and separation abilities, which require mossy fiber synaptic function. Furthermore, PCDH19 appears to interact with N-cadherin at mossy fiber synapses. In Pcdh19HET conditions, mismatch between PCDH19 and N-cadherin diminishes N-cadherin–dependent signaling and impairs mossy fiber synapse development; N-cadherin overexpression rescues Pcdh19HET phenotypes. These results reveal previously unknown molecular and cellular mechanisms underlying the female-specific PCDH19 disorder phenotype.

Measuring the dynamics of neural processing across time scales requires following the spiking of thousands of individual neurons over milliseconds and months. To address this need, we introduce the Neuropixels 2.0 probe together with newly designed analysis algorithms. The probe has more than 5000 sites and is miniaturized to facilitate chronic implants in small mammals and recording during unrestrained behavior. High-quality recordings over long time scales were reliably obtained in mice and rats in six laboratories. Improved site density and arrangement combined with newly created data processing methods enable automatic post hoc correction for brain movements, allowing recording from the same neurons for more than 2 months. These probes and algorithms enable stable recordings from thousands of sites during free behavior, even in small animals such as mice.

Animals in the wild are able to subsist on pathogen-infected and poisonous food and show immunity to various diseases. These may be due to their microbiota, yet we have a poor understanding of animal microbial diversity and function. We used metagenomics to analyze the gut microbiota of more than 180 species in the wild, covering diverse classes, feeding behaviors, geographies, and traits. Using de novo metagenome assembly, we constructed and functionally annotated a database of more than 5000 genomes, comprising 1209 bacterial species of which 75% are unknown. The microbial composition, diversity, and functional content exhibit associations with animal taxonomy, diet, activity, social structure, and life span. We identify the gut microbiota of wild animals as a largely untapped resource for the discovery of therapeutics and biotechnology applications.

Ray et al. (Reports, 14 February 2020, p. 800) report apparent transcriptional circadian rhythms in mouse tissues lacking the core clock component BMAL1. To better understand these surprising results, we reanalyzed the associated data. We were unable to reproduce the original findings, nor could we identify reliably cycling genes. We conclude that there is insufficient evidence to support circadian transcriptional rhythms in the absence of Bmal1.

Trapped atoms and ions, which are among the best-controlled quantum systems, find widespread applications in quantum science. For molecules, a similar degree of control is currently lacking owing to their complex energy-level structure. Quantum-logic protocols in which atomic ions serve as probes for molecular ions are a promising route for achieving this level of control, especially for homonuclear species that decouple from blackbody radiation. Here, a quantum-nondemolition protocol on single trapped molecules is demonstrated. The spin-rovibronic state of the molecule is detected with >99% fidelity, and a spectroscopic transition is measured without destroying the quantum state. This method lays the foundations for new approaches to molecular spectroscopy, state-to-state chemistry, and the implementation of molecular qubits.

Spin ices are exotic phases of matter characterized by frustrated spins obeying local "ice rules," in analogy with the electric dipoles in water ice. In two dimensions, one can similarly define ice rules for in-plane Ising-like spins arranged on a kagome lattice. These ice rules require each triangle plaquette to have a single monopole and can lead to different types of orders and excitations. Using experimental and theoretical approaches including magnetometry, thermodynamic measurements, neutron scattering, and Monte Carlo simulations, we establish HoAgGe as a crystalline (i.e., nonartificial) system that realizes the kagome spin ice state. The system features a variety of partially and fully ordered states and a sequence of field-induced phases at low temperatures, all consistent with the kagome ice rule.

Cluster of differentiation 20 (CD20) is a B cell membrane protein that is targeted by monoclonal antibodies for the treatment of malignancies and autoimmune disorders but whose structure and function are unknown. Rituximab (RTX) has been in clinical use for two decades, but how it activates complement to kill B cells remains poorly understood. We obtained a structure of CD20 in complex with RTX, revealing CD20 as a compact double-barrel dimer bound by two RTX antigen-binding fragments (Fabs), each of which engages a composite epitope and an extensive homotypic Fab:Fab interface. Our data suggest that RTX cross-links CD20 into circular assemblies and lead to a structural model for complement recruitment. Our results further highlight the potential relevance of homotypic Fab:Fab interactions in targeting oligomeric cell-surface markers.

How long-lived memories withstand molecular turnover is a fundamental question. Aggregates of a prion-like RNA-binding protein, cytoplasmic polyadenylation element–binding (CPEB) protein, is a putative substrate of long-lasting memories. We isolated aggregated Drosophila CPEB, Orb2, from adult heads and determined its activity and atomic structure, at 2.6-angstrom resolution, using cryo–electron microscopy. Orb2 formed ~75-nanometer-long threefold-symmetric amyloid filaments. Filament formation transformed Orb2 from a translation repressor to an activator and "seed" for further translationally active aggregation. The 31–amino acid protofilament core adopted a cross-β unit with a single hydrophilic hairpin stabilized through interdigitated glutamine packing. Unlike the hydrophobic core of pathogenic amyloids, the hydrophilic core of Orb2 filaments suggests how some neuronal amyloids could be a stable yet regulatable substrate of memory.

Radiometric dating of glacial terminations over the past 640,000 years suggests pacing by Earth’s climatic precession, with each glacial-interglacial period spanning four or five cycles of ~20,000 years. However, the lack of firm age estimates for older Pleistocene terminations confounds attempts to test the persistence of precession forcing. We combine an Italian speleothem record anchored by a uranium-lead chronology with North Atlantic ocean data to show that the first two deglaciations of the so-called 100,000-year world are separated by two obliquity cycles, with each termination starting at the same high phase of obliquity, but at opposing phases of precession. An assessment of 11 radiometrically dated terminations spanning the past million years suggests that obliquity exerted a persistent influence on not only their initiation but also their duration.

In neurons, the loading of neurotransmitters into synaptic vesicles uses energy from proton-pumping vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases). These membrane protein complexes possess numerous subunit isoforms, which complicates their analysis. We isolated homogeneous rat brain V-ATPase through its interaction with SidK, a Legionella pneumophila effector protein. Cryo–electron microscopy allowed the construction of an atomic model, defining the enzyme’s ATP:proton ratio as 3:10 and revealing a homolog of yeast subunit f in the membrane region, which we tentatively identify as RNAseK. The c ring encloses the transmembrane anchors for cleaved ATP6AP1/Ac45 and ATP6AP2/PRR, the latter of which is the (pro)renin receptor that, in other contexts, is involved in both Wnt signaling and the renin-angiotensin system that regulates blood pressure. This structure shows how ATP6AP1/Ac45 and ATP6AP2/PRR enable assembly of the enzyme’s catalytic and membrane regions.

Chiral cations have been used extensively as organocatalysts, but their application to rendering transition metal–catalyzed processes enantioselective remains rare. This is despite the success of the analogous charge-inverted strategy in which cationic metal complexes are paired with chiral anions. We report here a strategy to render a common bipyridine ligand anionic and pair its iridium complexes with a chiral cation derived from quinine. We have applied these ion-paired complexes to long-range asymmetric induction in the desymmetrization of the geminal diaryl motif, located on a carbon or phosphorus center, by enantioselective C–H borylation. In principle, numerous common classes of ligand could likewise be amenable to this approach.

The sensitivity of river discharge to climate-system warming is highly uncertain, and the processes that govern river discharge are poorly understood, which impedes climate-change adaptation. A prominent exemplar is the Colorado River, where meteorological drought and warming are shrinking a water resource that supports more than 1 trillion dollars of economic activity per year. A Monte Carlo simulation with a radiation-aware hydrologic model resolves the longstanding, wide disparity in sensitivity estimates and reveals the controlling physical processes. We estimate that annual mean discharge has been decreasing by 9.3% per degree Celsius of warming because of increased evapotranspiration, mainly driven by snow loss and a consequent decrease in reflection of solar radiation. Projected precipitation increases likely will not suffice to fully counter the robust, thermodynamically induced drying. Thus, an increasing risk of severe water shortages is expected.

T cells maintain a quiescent state prior to activation. As inappropriate T cell activation can cause disease, T cell quiescence must be preserved. Despite its importance, the mechanisms underlying the "quiescent state" remain elusive. Here, we identify BTG1 and BTG2 (BTG1/2) as factors responsible for T cell quiescence. BTG1/2-deficient T cells show an increased proliferation and spontaneous activation due to a global increase in messenger RNA (mRNA) abundance, which reduces the threshold to activation. BTG1/2 deficiency leads to an increase in polyadenylate tail length, resulting in a greater mRNA half-life. Thus, BTG1/2 promote the deadenylation and degradation of mRNA to secure T cell quiescence. Our study reveals a key mechanism underlying T cell quiescence and suggests that low mRNA abundance is a crucial feature for maintaining quiescence.

The outbreak of a novel coronavirus (2019-nCoV) represents a pandemic threat that has been declared a public health emergency of international concern. The CoV spike (S) glycoprotein is a key target for vaccines, therapeutic antibodies, and diagnostics. To facilitate medical countermeasure development, we determined a 3.5-angstrom-resolution cryo–electron microscopy structure of the 2019-nCoV S trimer in the prefusion conformation. The predominant state of the trimer has one of the three receptor-binding domains (RBDs) rotated up in a receptor-accessible conformation. We also provide biophysical and structural evidence that the 2019-nCoV S protein binds angiotensin-converting enzyme 2 (ACE2) with higher affinity than does severe acute respiratory syndrome (SARS)-CoV S. Additionally, we tested several published SARS-CoV RBD-specific monoclonal antibodies and found that they do not have appreciable binding to 2019-nCoV S, suggesting that antibody cross-reactivity may be limited between the two RBDs. The structure of 2019-nCoV S should enable the rapid development and evaluation of medical countermeasures to address the ongoing public health crisis.

In most human cancers, only a few genes are mutated at high frequencies; most are mutated at low frequencies. The functional consequences of these recurrent but infrequent "long tail" mutations are often unknown. We focused on 484 long tail genes in head and neck squamous cell carcinoma (HNSCC) and used in vivo CRISPR to screen for genes that, upon mutation, trigger tumor development in mice. Of the 15 tumor-suppressor genes identified, ADAM10 and AJUBA suppressed HNSCC in a haploinsufficient manner by promoting NOTCH receptor signaling. ADAM10 and AJUBA mutations or monoallelic loss occur in 28% of human HNSCC cases and are mutually exclusive with NOTCH receptor mutations. Our results show that oncogenic mutations in 67% of human HNSCC cases converge onto the NOTCH signaling pathway, making NOTCH inactivation a hallmark of HNSCC.

Stroke affects millions each year. Poststroke brain edema predicts the severity of eventual stroke damage, yet our concept of how edema develops is incomplete and treatment options remain limited. In early stages, fluid accumulation occurs owing to a net gain of ions, widely thought to enter from the vascular compartment. Here, we used magnetic resonance imaging, radiolabeled tracers, and multiphoton imaging in rodents to show instead that cerebrospinal fluid surrounding the brain enters the tissue within minutes of an ischemic insult along perivascular flow channels. This process was initiated by ischemic spreading depolarizations along with subsequent vasoconstriction, which in turn enlarged the perivascular spaces and doubled glymphatic inflow speeds. Thus, our understanding of poststroke edema needs to be revised, and these findings could provide a conceptual basis for development of alternative treatment strategies.

The measured nitrogen-to-carbon ratio in comets is lower than for the Sun, a discrepancy which could be alleviated if there is an unknown reservoir of nitrogen in comets. The nucleus of comet 67P/Churyumov-Gerasimenko exhibits an unidentified broad spectral reflectance feature around 3.2 micrometers, which is ubiquitous across its surface. On the basis of laboratory experiments, we attribute this absorption band to ammonium salts mixed with dust on the surface. The depth of the band indicates that semivolatile ammonium salts are a substantial reservoir of nitrogen in the comet, potentially dominating over refractory organic matter and more volatile species. Similar absorption features appear in the spectra of some asteroids, implying a compositional link between asteroids, comets, and the parent interstellar cloud.

At the body surface, skin’s stratified squamous epithelium is challenged by environmental extremes. The surface of the skin is composed of enucleated, flattened surface squames. They derive from underlying, transcriptionally active keratinocytes that display filaggrin-containing keratohyalin granules (KGs) whose function is unclear. Here, we found that filaggrin assembles KGs through liquid-liquid phase separation. The dynamics of phase separation governed terminal differentiation and were disrupted by human skin barrier disease–associated mutations. We used fluorescent sensors to investigate endogenous phase behavior in mice. Phase transitions during epidermal stratification crowded cellular spaces with liquid-like KGs whose coalescence was restricted by keratin filament bundles. We imaged cells as they neared the skin surface and found that environmentally regulated KG phase dynamics drive squame formation. Thus, epidermal structure and function are driven by phase-separation dynamics.

Many disease pathologies can be understood through the elucidation of localized biomolecular networks, or microenvironments. To this end, enzymatic proximity labeling platforms are broadly applied for mapping the wider spatial relationships in subcellular architectures. However, technologies that can map microenvironments with higher precision have long been sought. Here, we describe a microenvironment-mapping platform that exploits photocatalytic carbene generation to selectively identify protein-protein interactions on cell membranes, an approach we term MicroMap (μMap). By using a photocatalyst-antibody conjugate to spatially localize carbene generation, we demonstrate selective labeling of antibody binding targets and their microenvironment protein neighbors. This technique identified the constituent proteins of the programmed-death ligand 1 (PD-L1) microenvironment in live lymphocytes and selectively labeled within an immunosynaptic junction.

Wide–band gap metal halide perovskites are promising semiconductors to pair with silicon in tandem solar cells to pursue the goal of achieving power conversion efficiency (PCE) greater than 30% at low cost. However, wide–band gap perovskite solar cells have been fundamentally limited by photoinduced phase segregation and low open-circuit voltage. We report efficient 1.67–electron volt wide–band gap perovskite top cells using triple-halide alloys (chlorine, bromine, iodine) to tailor the band gap and stabilize the semiconductor under illumination. We show a factor of 2 increase in photocarrier lifetime and charge-carrier mobility that resulted from enhancing the solubility of chlorine by replacing some of the iodine with bromine to shrink the lattice parameter. We observed a suppression of light-induced phase segregation in films even at 100-sun illumination intensity and less than 4% degradation in semitransparent top cells after 1000 hours of maximum power point (MPP) operation at 60°C. By integrating these top cells with silicon bottom cells, we achieved a PCE of 27% in two-terminal monolithic tandems with an area of 1 square centimeter.

The mechanism by which psychological stress elicits various physiological responses is unknown. We discovered a central master neural pathway in rats that drives autonomic and behavioral stress responses by connecting the corticolimbic stress circuits to the hypothalamus. Psychosocial stress signals from emotion-related forebrain regions activated a VGLUT1-positive glutamatergic pathway from the dorsal peduncular cortex and dorsal tenia tecta (DP/DTT), an unexplored prefrontal cortical area, to the dorsomedial hypothalamus (DMH), a hypothalamic autonomic center. Genetic ablation and optogenetics revealed that the DP/DTT->DMH pathway drives thermogenic, hyperthermic, and cardiovascular sympathetic responses to psychosocial stress without contributing to basal homeostasis. This pathway also mediates avoidance behavior from psychosocial stressors. Given the variety of stress responses driven by the DP/DTT->DMH pathway, the DP/DTT can be a potential target for treating psychosomatic disorders.

The genome versus experience dichotomy has dominated understanding of behavioral individuality. By contrast, the role of nonheritable noise during brain development in behavioral variation is understudied. Using Drosophila melanogaster, we demonstrate a link between stochastic variation in brain wiring and behavioral individuality. A visual system circuit called the dorsal cluster neurons (DCN) shows nonheritable, interindividual variation in right/left wiring asymmetry and controls object orientation in freely walking flies. We show that DCN wiring asymmetry instructs an individual’s object responses: The greater the asymmetry, the better the individual orients toward a visual object. Silencing DCNs abolishes correlations between anatomy and behavior, whereas inducing DCN asymmetry suffices to improve object responses.

Topological structures are effective descriptors of the nonequilibrium dynamics of diverse many-body systems. For example, motile, point-like topological defects capture the salient features of two-dimensional active liquid crystals composed of energy-consuming anisotropic units. We dispersed force-generating microtubule bundles in a passive colloidal liquid crystal to form a three-dimensional active nematic. Light-sheet microscopy revealed the temporal evolution of the millimeter-scale structure of these active nematics with single-bundle resolution. The primary topological excitations are extended, charge-neutral disclination loops that undergo complex dynamics and recombination events. Our work suggests a framework for analyzing the nonequilibrium dynamics of bulk anisotropic systems as diverse as driven complex fluids, active metamaterials, biological tissues, and collections of robots or organisms.

Single-atom impurities and other atomic-scale defects can notably alter the local vibrational responses of solids and, ultimately, their macroscopic properties. Using high-resolution electron energy-loss spectroscopy in the electron microscope, we show that a single substitutional silicon impurity in graphene induces a characteristic, localized modification of the vibrational response. Extensive ab initio calculations reveal that the measured spectroscopic signature arises from defect-induced pseudo-localized phonon modes—that is, resonant states resulting from the hybridization of the defect modes and the bulk continuum—with energies that can be directly matched to the experiments. This finding realizes the promise of vibrational spectroscopy in the electron microscope with single-atom sensitivity and has broad implications across the fields of physics, chemistry, and materials science.

In the fundamental laws of physics, gauge fields mediate the interaction between charged particles. An example is the quantum theory of electrons interacting with the electromagnetic field, based on U(1) gauge symmetry. Solving such gauge theories is in general a hard problem for classical computational techniques. Although quantum computers suggest a way forward, large-scale digital quantum devices for complex simulations are difficult to build. We propose a scalable analog quantum simulator of a U(1) gauge theory in one spatial dimension. Using interspecies spin-changing collisions in an atomic mixture, we achieve gauge-invariant interactions between matter and gauge fields with spin- and species-independent trapping potentials. We experimentally realize the elementary building block as a key step toward a platform for quantum simulations of continuous gauge theories.

Episodic memory retrieval is thought to rely on the replay of past experiences, yet it remains unknown how human single-unit activity is temporally organized during episodic memory encoding and retrieval. We found that ripple oscillations in the human cortex reflect underlying bursts of single-unit spiking activity that are organized into memory-specific sequences. Spiking sequences occurred repeatedly during memory formation and were replayed during successful memory retrieval, and this replay was associated with ripples in the medial temporal lobe. Together, these data demonstrate that human episodic memory is encoded by specific sequences of neural activity and that memory recall involves reinstating this temporal order of activity.

Stacking solar cells with decreasing band gaps to form tandems presents the possibility of overcoming the single-junction Shockley-Queisser limit in photovoltaics. The rapid development of solution-processed perovskites has brought perovskite single-junction efficiencies >20%. However, this process has yet to enable monolithic integration with industry-relevant textured crystalline silicon solar cells. We report tandems that combine solution-processed micrometer-thick perovskite top cells with fully textured silicon heterojunction bottom cells. To overcome the charge-collection challenges in micrometer-thick perovskites, we enhanced threefold the depletion width at the bases of silicon pyramids. Moreover, by anchoring a self-limiting passivant (1-butanethiol) on the perovskite surfaces, we enhanced the diffusion length and further suppressed phase segregation. These combined enhancements enabled an independently certified power conversion efficiency of 25.7% for perovskite-silicon tandem solar cells. These devices exhibited negligible performance loss after a 400-hour thermal stability test at 85°C and also after 400 hours under maximum power point tracking at 40°C.

Ribosome profiling has revealed pervasive but largely uncharacterized translation outside of canonical coding sequences (CDSs). In this work, we exploit a systematic CRISPR-based screening strategy to identify hundreds of noncanonical CDSs that are essential for cellular growth and whose disruption elicits specific, robust transcriptomic and phenotypic changes in human cells. Functional characterization of the encoded microproteins reveals distinct cellular localizations, specific protein binding partners, and hundreds of microproteins that are presented by the human leukocyte antigen system. We find multiple microproteins encoded in upstream open reading frames, which form stable complexes with the main, canonical protein encoded on the same messenger RNA, thereby revealing the use of functional bicistronic operons in mammals. Together, our results point to a family of functional human microproteins that play critical and diverse cellular roles.

Mycobacterium tuberculosis has an unusual outer membrane that lacks canonical porin proteins for the transport of small solutes to the periplasm. We discovered that 3,3-bis-di(methylsulfonyl)propionamide (3bMP1) inhibits the growth of M. tuberculosis, and resistance to this compound is conferred by mutation within a member of the proline-proline-glutamate (PPE) family, PPE51. Deletion of PPE51 rendered M. tuberculosis cells unable to replicate on propionamide, glucose, or glycerol. Growth was restored upon loss of the mycobacterial cell wall component phthiocerol dimycocerosate. Mutants in other proline-glutamate (PE)/PPE clusters, responsive to magnesium and phosphate, also showed a phthiocerol dimycocerosate–dependent growth compromise upon limitation of the corresponding substrate. Phthiocerol dimycocerosate determined the low permeability of the mycobacterial outer membrane, and the PE/PPE proteins apparently act as solute-specific channels.

The regulation of messenger RNA levels in mammalian cells can be achieved by the modulation of synthesis and degradation rates. Metabolic RNA-labeling experiments in bulk have quantified these rates using relatively homogeneous cell populations. However, to determine these rates during complex dynamical processes, for instance during cellular differentiation, single-cell resolution is required. Therefore, we developed a method that simultaneously quantifies metabolically labeled and preexisting unlabeled transcripts in thousands of individual cells. We determined synthesis and degradation rates during the cell cycle and during differentiation of intestinal stem cells, revealing major regulatory strategies. These strategies have distinct consequences for controlling the dynamic range and precision of gene expression. These findings advance our understanding of how individual cells in heterogeneous populations shape their gene expression dynamics.