前沿速递 | NCS 集萃： 2025-04-24 期 [Up]

『Abstract』Limited color channels in fluorescence microscopy have long constrained spatial analysis in biological specimens. We introduce cycle hybridization chain reaction (cycleHCR), a method that integrates multicycle DNA barcoding with HCR to overcome this limitation. cycleHCR enables highly multiplexed imaging of RNA and proteins using a unified barcode system. Whole-embryo transcriptomics imaging achieved precise three-dimensional gene expression and cell fate mapping across a specimen depth of ~310 μm. When combined with expansion microscopy, cycleHCR revealed an intricate network of 10 subcellular structures in mouse embryonic fibroblasts. In mouse hippocampal slices, multiplex RNA and protein imaging uncovered complex gene expression gradients and cell-type–specific nuclear structural variations. cycleHCR provides a quantitative framework for elucidating spatial regulation in deep tissue contexts for research and has potential diagnostic applications.

『Abstract』Ancient Mars had surface liquid water and a dense carbon dioxide (CO 2 )–rich atmosphere. Such an atmosphere would interact with crustal rocks, potentially leaving a mineralogical record of its presence. We analyzed the composition of an 89-meter stratigraphic section of Gale crater, Mars, using data collected by the Curiosity rover. An iron carbonate mineral, siderite, occurs in abundances of 4.8 to 10.5 weight %, colocated with highly water-soluble salts. We infer that the siderite formed in water-limited conditions, driven by water-rock reactions and evaporation. Comparison with orbital data indicates that similar strata (deposited globally) sequestered the equivalent of 2.6 to 36 millibar of atmospheric CO 2 . The presence of iron oxyhydroxides in these deposits indicates that a partially closed carbon cycle on ancient Mars returned some previously sequestered CO 2 to the atmosphere.

『Abstract』Cochlear inner hair cells (IHCs) and outer hair cells (OHCs) require different transcription factors for their cell fate stabilization and survival, which suggests that separate mechanisms are involved. In this study, we found that the transcription factor Casz1 is crucial for early IHC fate consolidation and for OHC survival during mouse development. Loss of Casz1 resulted in transdifferentiation of IHCs into OHCs, without affecting OHC production. However, long-term OHC survival was compromised in Casz1 mutant mice. In addition, the transcription factor Gata3 was down-regulated in Casz1 -deleted IHCs, and overexpressing Gata3 partially rescued IHC properties, OHC numbers, and hearing in Casz1 -deleted mice. Thus, Casz1 plays critical roles in early IHC fate stabilization and OHC survival and could potentially provide a lead for therapies aimed at regenerating both IHCs and OHCs.

『Abstract』The extracellular space (apoplast) in plants is a key battleground during microbial infections. To avoid recognition, the bacterial model phytopathogen Pseudomonas syringae pv. tomato DC3000 produces glycosyrin. Glycosyrin inhibits the plant-secreted β-galactosidase BGAL1, which would otherwise initiate the release of immunogenic peptides from bacterial flagellin. Here, we report the structure, biosynthesis, and multifunctional roles of glycosyrin. High-resolution cryo–electron microscopy and chemical synthesis revealed that glycosyrin is an iminosugar with a five-membered pyrrolidine ring and a hydrated aldehyde that mimics monosaccharides. Glycosyrin biosynthesis was controlled by virulence regulators, and its production is common in bacteria and prevents flagellin recognition and alters the extracellular glycoproteome and metabolome of infected plants. These findings highlight a potentially wider role for glycobiology manipulation by plant pathogens across the plant kingdom.

『Abstract』The MYC oncogene promoter G-quadruplex (MycG4) regulates transcription and is a prevalent G4 locus in immortal cells. Nucleolin, a major MycG4-binding protein, exhibits greater affinity for MycG4 than for nucleolin recognition element (NRE) RNA. Nucleolin’s four RNA binding domains (RBDs) are essential for high-affinity MycG4 binding. We present the 2.6-angstrom crystal structure of the nucleolin-MycG4 complex, revealing a folded parallel three-tetrad G-quadruplex with two coordinating potassium ions (K ), interacting with RBD1, RBD2, and Linker12 through its 6–nucleotide (nt) central loop and 5′ flanking region. RBD3 and RBD4 bind MycG4’s 1-nt loops as demonstrated by nuclear magnetic resonance (NMR). Cleavage under targets and tagmentation sequencing confirmed nucleolin’s binding to MycG4 in cells. Our results revealed a G4 conformation-based recognition by a regulating protein through multivalent interactions, suggesting that G4s are nucleolin’s primary cellular substrates, indicating G4 epigenetic transcriptional regulation and helping G4-targeted drug discovery.

『Abstract』Synaptic plasticity underlies learning by modifying specific synaptic inputs to reshape neural activity and behavior. However, the rules governing which synapses will undergo different forms of plasticity in vivo during learning and whether these rules are uniform within individual neurons remain unclear. Using in vivo longitudinal imaging with single-synapse resolution in the mouse motor cortex during motor learning, we found that apical and basal dendrites of layer 2/3 (L2/3) pyramidal neurons showed distinct activity-dependent synaptic plasticity rules. The strengthening of apical and of basal synapses is predicted by local coactivity with nearby synapses and activity coincident with postsynaptic action potentials, respectively. Blocking postsynaptic spiking diminished basal synaptic potentiation without affecting apical plasticity. Thus, individual neurons use multiple activity-dependent plasticity rules in a compartment-specific manner in vivo during learning.

『Abstract』Differentiating between similar alkyl groups is a major challenge in asymmetric catalysis. Achieving enantiocontrol over unactivated prochiral alkyl radicals is even more difficult owing to their high reactivity and limited interactions with chiral catalysts. In this study, we report a copper-catalyzed asymmetric amination of unactivated prochiral secondary alkyl radicals, using specifically designed chiral anionic multidentate ligands in a radical substitution reaction. This approach efficiently produces highly enantioenriched α-chiral alkyl amines and facilitates the enantioselective formal synthesis of a series of important drug molecules. Mechanistic studies reveal that bulky peripheral modifications on the ligands help create a truncated cone-shaped chiral pocket, enabling precise enantiodiscrimination through steric hindrance and noncovalent interactions. This strategy holds broad potential for asymmetric transformations involving diverse unactivated prochiral alkyl radicals and nucleophiles.

『Abstract』Mutations in the ubiquitin kinase PINK1 cause early-onset Parkinson’s disease, but how PINK1 is stabilized at depolarized mitochondrial translocase complexes has remained poorly understood. We determined a 3.1-angstrom resolution cryo–electron microscopy structure of dimeric human PINK1 stabilized at an endogenous array of mitochondrial translocase of the outer membrane (TOM) and voltage-dependent anion channel (VDAC) complexes. Symmetric arrangement of two TOM core complexes around a central VDAC2 dimer is facilitated by TOM5 and TOM20, both of which also bind PINK1 kinase C-lobes. PINK1 enters mitochondria through the proximal TOM40 barrel of the TOM core complex, guided by TOM7 and TOM22. Our structure explains how human PINK1 is stabilized at the TOM complex and regulated by oxidation, uncovers a previously unknown TOM-VDAC assembly, and reveals how a physiological substrate traverses TOM40 during translocation.

『Abstract』Strongly coupled electron-hole bilayers can host quantum states of interlayer excitons, such as high-temperature exciton condensates at zero magnetic field. This state is predicted to feature perfect Coulomb drag, where a current in one layer is accompanied by an equal but opposite current in the other. We used an optical technique to probe the electrical transport of correlated electron-hole bilayers based on MoSe 2 /hBN/WSe 2 heterostructures. We observed perfect Coulomb drag in the excitonic insulator phase at low temperatures; the counterflow resistance of interlayer excitons remained finite. These results indicate the formation of an exciton gas that does not condense into a superfluid. Our work demonstrates that dynamic optical spectroscopy provides a powerful tool for probing exciton transport behavior in correlated electron-hole fluids.

『Abstract』Structural elements are widespread across genomes, but their complexity and role in repeatedly driving local adaptation remain unclear. In this work, we use phased genome assemblies to show that adaptive divergence in cryptic color pattern in a stick insect is repeatedly underlain by structural variation, but not a simple chromosomal inversion. We found that color pattern in populations of stick insects on two mountains is associated with translocations that have also been inverted. These translocations differ in size and origin on each mountain, but they overlap partially and involve some of the same gene regions. Moreover, this structural variation is subject to divergent selection and arose without introgression between species. Our results show how the origin of structural variation provides a mechanism for repeated bouts of adaptation.

『Abstract』Excitonic insulators (EIs) are a solid-state prototype for bosonic phases of matter that can support charge-neutral exciton currents. However, demonstration of exciton transport in EIs is difficult. In this work, we show that the strong interlayer excitonic correlation at equal electron and hole densities in MoSe 2 /WSe 2 double layers separated by a 2-nanometer barrier yields perfect Coulomb drag under zero magnetic field: A charge current in one layer induces an equal but opposite drag current in the other layer at low temperatures. The drag current ratio remains above 0.9 up to about 20 kelvin. As exciton density increases above the Mott density, the excitons dissociate into an electron-hole plasma abruptly, and only frictional drag is observed. Our experiment may lead to the realization of exciton circuitry and superfluidity.

『Abstract』Solid-state lithium metal batteries (SSBs) are promising for electric vehicles because of their potential to provide high energy density and enhanced safety. However, these batteries face short-circuit challenges caused by uncontrolled lithium dendrite growth during cycling. Using operando scanning electron microscopy and phase-field simulations, we determined that failure of SSBs is closely linked to the fatigue of the lithium metal anode, which markedly contributes to interface degradation and dendrite growth in SSBs. This fatigue follows the Coffin-Manson equation in mechanics, indicating that it is an innate characteristic. Clarifying the essential role of fatigue provides a physical basis for understanding failures of SSBs and paves the way to extending their lifespan.

『Abstract』The design of enzymes with complex active sites that mediate multistep reactions remains an outstanding challenge. With serine hydrolases as a model system, we combined the generative capabilities of RFdiffusion with an ensemble generation method for assessing active site preorganization at each step in the reaction to design enzymes starting from minimal active site descriptions. Experimental characterization revealed catalytic efficiencies ( k cat / K m ) up to 2.2 × 10 M s and crystal structures that closely match the design models (Cα root mean square deviations <1 angstrom). Selection for structural compatibility across the reaction coordinate enabled identification of new catalysts remove with five different folds distinct from those of natural serine hydrolases. Our de novo approach provides insight into the geometric basis of catalysis and a roadmap for designing enzymes that catalyze multistep transformations.

『Abstract』Toxic metal pollution is ubiquitous in soils, yet its worldwide distribution is unknown. We analyzed a global database of soil pollution by arsenic, cadmium, cobalt, chromium, copper, nickel, and lead at 796,084 sampling points from 1493 regional studies and used machine learning techniques to map areas with exceedance of agricultural and human health thresholds. We reveal a previously unrecognized high-risk, metal-enriched zone in low-latitude Eurasia, which is attributed to influential climatic, topographic, and anthropogenic conditions. This feature can be regarded as a signpost for the Anthropocene era. We show that 14 to 17% of cropland is affected by toxic metal pollution globally and estimate that between 0.9 and 1.4 billion people live in regions of heightened public health and ecological risks.

『Abstract』Gene expression and complex phenotypes are determined by the activity of cis-regulatory elements. However, an understanding of how extant genetic variants affect cis regulation remains limited. Here, we investigated the consequences of cis-regulatory diversity using single-cell genomics of more than 0.7 million nuclei across 172 Zea mays (maize) inbreds. Our analyses pinpointed cis-regulatory elements distinct to domesticated maize and revealed how historical transposon activity has shaped the cis-regulatory landscape. Leveraging population genetics principles, we fine-mapped about 22,000 chromatin accessibility–associated genetic variants with widespread cell type–specific effects. Variants in TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR–binding sites were the most prevalent determinants of chromatin accessibility. Finally, integrating chromatin accessibility–associated variants, organismal trait variation, and population differentiation revealed how local adaptation has rewired regulatory networks in unique cellular contexts to alter maize flowering.

『Abstract』Habitat fragmentation generally reduces biodiversity at the patch scale (α diversity) . However, there is ongoing debate about whether such negative effects can be alleviated at the landscape scale (γ diversity) if among-patch diversity (β diversity) increases as a result of fragmentation . This controversial view has not been rigorously tested. Here we use a dataset of 4,006 taxa across 37 studies from 6 continents to test the effects of fragmentation on biodiversity across scales by explicitly comparing continuous and fragmented landscapes. We find that fragmented landscapes consistently have both lower α diversity and lower γ diversity. Although fragmented landscapes did tend to have higher β diversity, this did not translate into higher γ diversity. Our findings refute claims that habitat fragmentation can increase biodiversity at landscape scales, and emphasize the need to restore habitat and increase connectivity to minimize biodiversity loss at ever-increasing scales.

『Abstract』Cancer cells have been shown to exploit neurons to modulate their survival and growth, including through the establishment of neural circuits within the central nervous system . Here we report a distinct pattern of cancer–nerve interactions between the peripheral nervous system and gastric cancer. In multiple mouse models of gastric cancer, nociceptive nerves demonstrated the greatest degree of nerve expansion in an NGF-dependent manner. Neural tracing identified CGRP peptidergic neurons as the primary gastric sensory neurons. Three-dimensional co-culture models showed that sensory neurons directly connect with gastric cancer spheroids. Chemogenetic activation of sensory neurons induced the release of calcium into the cytoplasm of cancer cells, promoting tumour growth and metastasis. Pharmacological ablation of sensory neurons or treatment with CGRP inhibitors suppressed tumour growth and extended survival. Depolarization of gastric tumour membranes through in vivo optogenetic activation led to enhanced calcium flux in jugular nucleus complex and CGRP release, defining a cancer cell–peptidergic neuronal circuit. Together, these findings establish the functional connectivity between cancer and sensory neurons, identifying this pathway as a potential therapeutic target.

『Abstract』Photons can carry angular momentum, which is conventionally attributed to two constituents—spin angular momentum (SAM), which is an intrinsic property related to the polarization, and orbital angular momentum (OAM), which is related to the photon spatial distribution. In paraxial optics, these two forms of angular momentum are separable , such that entanglement can be induced between the SAM and the OAM of a single photon or of different photons in a multi-photon state . In nanophotonic systems, however, the SAM and the OAM of a photon are inseparable , so only the total angular momentum (TAM) serves as a good quantum number . Here we present the observation of non-classical correlations between two photons in the near-field regime, giving rise to entanglement related to the TAM. We entangle those nanophotonic states by coupling photon pairs to plasmonic modes and use quantum imaging techniques to measure their correlations. We observe that entanglement in TAM leads to a completely different structure of quantum correlations of photon pairs, compared with entanglement related to the two constituent angular momenta. This work paves the way for on-chip quantum information processing using the TAM of photons as the encoding property for quantum information.

『Abstract』Ocean submesoscale (1–100 km) processes and their substantial impact on Earth’s climate system have been increasingly emphasized in recent decades by high-resolution numerical models and regional observations . However, the dynamics and energy associated with these processes, including submesoscale eddies and nonlinear internal waves, have never been observed from a global perspective. Where, when and how much do these submesoscale processes contribute to the large-scale ocean circulation and climate system? Here we show data from the recently launched Surface Water and Ocean Topography (SWOT) satellite that not only confirm the characteristics of submesoscale eddies and waves but also suggest that their potential impacts on ocean energetics, the marine ecosystem, atmospheric weather and Earth’s climate system are much larger than anticipated. SWOT ushers in a new era of global ocean observing, placing submesoscale ocean dynamics as a critical element of the Earth’s climate system.

『Abstract』The development of new synthetic methodologies is instrumental for enabling the discovery of new medicines. The methods that provide efficient access to structural alternatives for aromatic compounds (that is, saturated arene bioisosteres) have become highly coveted . The incorporation of these bioisosteres typically leads to favourable drug-like properties and represents an emerging field of research. Here we report a new synthetic method that furnishes a coveted motif, the bicyclo[2.1.1]hexane scaffold , using mild reaction conditions and an operationally simple protocol. The methodology proceeds through the uncommon coupling of two strained fragments: transiently generated cyclic allenes and bicyclo[1.1.0]butanes, which possess considerable strain energies of about 30 kcal mol (ref. ) and about 60 kcal mol (ref. ), respectively. The reaction is thought to proceed by a σ-bond insertion through a diradical pathway. However, rather than requiring an external stimulus to generate radical species, reactivity is thought to arise as a result of innate diradical character present in each reactant. This diradicaloid character , an underused parameter in reaction design, arises from the severe geometric distortions of each reactant. Our studies provide a means to access functionalized bicyclo[2.1.1]hexanes of value for drug discovery, underscore how geometric distortion of reactants can be used to enable uncommon modes of reactivity and should encourage the further exploration and strategic use of diradicaloids in chemical synthesis.

『Abstract』In a subset of children and adolescents, SARS-CoV-2 infection induces a severe acute hyperinflammatory shock termed multisystem inflammatory syndrome in children (MIS-C) at four to eight weeks after infection. MIS-C is characterized by a specific T cell expansion and systemic hyperinflammation . The pathogenesis of MIS-C remains largely unknown. Here we show that acute MIS-C is characterized by impaired reactivation of virus-reactive memory T cells, which depends on increased serum levels of the cytokine TGFβ resembling those that occur during severe COVID-19 (refs. ). This functional impairment in T cell reactivity is accompanied by the presence of TGFβ-response signatures in T cells, B cells and monocytes along with reduced antigen-presentation capabilities of monocytes, and can be reversed by blocking TGFβ. Furthermore, T cell receptor repertoires of patients with MIS-C exhibit expansion of T cells expressing TCRVβ21.3, resembling Epstein–Barr virus (EBV)-reactive T cell clones capable of eliminating EBV-infected B cells. Additionally, serum TGFβ in patients with MIS-C can trigger EBV reactivation, which is reversible with TGFβ blockade. Clinically, the TGFβ-induced defect in T cell reactivity correlates with a higher EBV seroprevalence in patients with MIS-C compared with age-matched controls, along with the occurrence of EBV reactivation. Our findings establish a connection between SARS-CoV-2 infection and COVID-19 sequelae in children, in which impaired T cell cytotoxicity triggered by TGFβ overproduction leads to EBV reactivation and subsequent hyperinflammation.

『Abstract』Water is the third most abundant molecule in the universe and a key component in the interiors of icy moons, giant planets and Uranus- and Neptune-like exoplanets . Owing to its distinct molecular structure and flexible hydrogen bonds that readily adapt to a wide range of pressures and temperatures, water forms numerous crystalline and amorphous phases . Most relevant for the high pressures and temperatures of planetary interiors is ice VII (ref. ), and simulations have identified along its melting curve the existence of a so-called plastic phase in which individual molecules occupy fixed positions as in a solid yet are able to rotate as in a liquid. Such plastic ice has not yet been directly observed in experiments. Here we present quasi-elastic neutron scattering measurements, conducted at temperatures between 450 and 600 K and pressures up to 6 GPa, that reveal the existence of a body-centred cubic structure, as found in ice VII, with water molecules showing picosecond rotational dynamics typical for liquid water. Comparison with molecular dynamics simulations indicates that this plastic ice VII does not conform to a free rotor phase but rather shows rapid orientational jumps, as observed in jump-rotor plastic crystals . We anticipate that our observation of plastic ice VII will affect our understanding of the geodynamics of icy planets and the differentiation processes of large icy moons.

『Abstract』Autologous chimeric antigen receptor (CAR) T cells are a genetically engineered therapy that is highly effective against B cell malignancies and multiple myeloma . However, the length and cost of personalized manufacturing limits access and leaves patients vulnerable to disease progression. Allogeneic cell therapies have the potential to increase patient access and improve treatment outcomes but are limited by immune rejection . To devise a strategy to protect allogeneic CAR T cells from host immune cells, we turned to lymphotropic viruses that have evolved integrated mechanisms for immune escape of virus-infected lymphocytes . We find that viral evasins that partially reduce human leukocyte antigen class I expression can shelter CAR T cells from mismatched CD8 T cells without triggering ‘missing-self’ rejection by natural killer cells. However, this protection alone is insufficient to sustain effective allogeneic CAR T cell therapy. HIV-1 Nef uniquely also acts through the serine/threonine kinase Pak2 to abate activation-induced cell death and promote survival of CAR T cells in vivo. Thus, virus-like immune escape can harness several mechanisms that act in concert to enhance the therapeutic efficacy of allogeneic CAR T cells.

『Abstract』More than ten ergot alkaloids comprising both natural and semi-synthetic products are used to treat various diseases . The central C ring forms the core pharmacophore for ergot alkaloids, giving them structural similarity to neurotransmitters, thus enabling their modulation of neurotransmitter receptors . The haem catalase chanoclavine synthase (EasC) catalyses the construction of this ring through complex radical oxidative cyclization . Unlike canonical catalases, which catalyse H 2 O 2 disproportionation , EasC and its homologues represent a broader class of catalases that catalyse O 2 -dependent radical reactions . We have elucidated the structure of EasC by cryo-electron microscopy, revealing a nicotinamide adenine dinucleotide phosphate (reduced) (NADPH)-binding pocket and a haem pocket common to all haem catalases, with a unique homodimeric architecture that is, to our knowledge, previously unobserved. The substrate prechanoclavine unprecedentedly binds in the NADPH-binding pocket, instead of the previously suspected haem-binding pocket, and two pockets were connected by a slender tunnel. Contrary to the established mechanisms, EasC uses superoxide rather than the more generally used transient haem iron–oxygen complexes (such as compounds I, II and III) , to mediate substrate transformation through superoxide-mediated cooperative catalysis of the two distant pockets. We propose that this reactive oxygen species mechanism could be widespread in metalloenzyme-catalysed reactions.

『Abstract』Chronic stress can change how we learn and, thus, how we make decisions . Here we investigated the neuronal circuit mechanisms that enable this. Using a multifaceted systems neuroscience approach in male and female mice, we reveal a dual-pathway, amygdala–striatal neuronal circuit architecture by which a recent history of chronic stress disrupts the action–outcome learning underlying adaptive agency and promotes the formation of inflexible habits. We found that the projection from the basolateral amygdala to the dorsomedial striatum is activated by rewarding events to support the action–outcome learning needed for flexible, goal-directed decision-making. Chronic stress attenuates this to disrupt action–outcome learning and, therefore, agency. Conversely, the projection from the central amygdala to the dorsomedial striatum mediates habit formation. Following stress, this pathway is progressively recruited to learning to promote the premature formation of inflexible habits. Thus, stress exerts opposing effects on two amygdala–striatal pathways to disrupt agency and promote habit. These data provide neuronal circuit insights into how chronic stress shapes learning and decision-making, and help understanding of how stress can lead to the disrupted decision-making and pathological habits that characterize substance use disorders and mental health conditions.

『Abstract』Who the first inhabitants of Western Europe were, what their physical characteristics were, and when and where they lived are some of the pending questions in the study of the settlement of Eurasia during the Early Pleistocene epoch. The available palaeoanthropological information from Western Europe is limited and confined to the Iberian Peninsula . Here we present most of the midface of a hominin found at the TE7 level of the Sima del Elefante site (Sierra de Atapuerca, Spain), dated to between 1.4 million and 1.1 million years ago. This fossil (ATE7-1) represents the earliest human face of Western Europe identified thus far. Most of the morphological features of the midface of this hominin are primitive for the Homo clade and they do not display the modern-like aspect exhibited by Homo antecessor found at the neighbouring Gran Dolina site, also in the Sierra de Atapuerca, and dated to between 900,000 and 800,000 years ago . Furthermore, ATE7-1 is more derived in the nasoalveolar region than the Dmanisi and other roughly contemporaneous hominins. On the basis of the available evidence, it is reasonable to assign the new human remains from TE7 level to Homo aff. erectus . From the archaeological, palaeontological and palaeoanthropological information obtained in the lower levels of the Sima del Elefante and Gran Dolina sites , we suggest a turnover in the human population in Europe at the end of the Early Pleistocene.

『Abstract』The nuclear pore complex (NPC) mediates nucleocytoplasmic exchange, catalysing a massive flux of protein and nucleic acid material in both directions . Distinct trafficking pathways for import and export would be an elegant solution to avoid unproductive collisions and opposing movements. However, the three-dimensional (3D) nanoscale spatiotemporal dynamics of macromolecules traversing the NPC remains challenging to visualize on the timescale of millisecond-scale transport events. Here we used 3D MINFLUX to identify the nuclear pore scaffold and then to simultaneously monitor both nuclear import and nuclear export, thereby establishing that both transport processes occur in overlapping regions of the central pore. Whereas translocation-arrested import complexes bound at the pore periphery, tracks of translocating complexes within the central pore region revealed a preference for an approximately 40- to 50-nm diameter annulus with minimal circumferential movement, indicating activity-dependent confinement within the permeability barrier. Movement within the pore was approximately 1,000-fold slower than in solution and was interspersed with pauses, indicating a highly restricted environment with structural constraints and/or transient binding events during transport. These results demonstrate that high spatiotemporal precision with reduced photobleaching is a major advantage of MINFLUX tracking, and that the NPC permeability barrier is divided into annular rings with distinct functional properties.

『Abstract』T cell exhaustion limits effector T cell function in chronic infection and tumours . The development of these hypofunctional T cells and of their precursors was considered to require stimulatory conditions that are met only after persistent exposure to antigen and inflammation. Here we show, however, that similar T cell populations exist in the early phase of acute infections . At that stage, the early developing TCF1 precursor population exhibits an unexpected diversity; it includes precursors of normal memory T cells, but also cells with phenotypic, gene-expression and epigenetic profiles that resemble those of precursors of exhausted T cells found in chronic infections. We show that high ligand affinity promotes and PD-1 signalling restricts the development of these precursors. Although the exhausted precursors are at first found frequently, they decline without being completely lost in infections that the immune system resolves. We therefore conclude that precursor T cells with at least two distinct phenotypes are pre-emptively generated irrespective of the outcome of an infection.

『Abstract』Numerous natural products and drugs contain flexible alkyl chains. The resulting conformational motion can create challenges in obtaining single crystals and thus determining their molecular structures by single-crystal X-ray diffraction (SCXRD) . Here we demonstrate that by using pillar[5]arene-incorporated metal–organic frameworks (MOFs) and taking advantage of pillar[5]arene−alkyl chain host−guest recognition , it is possible to reduce this motion and bring order to alkyl-chain-containing molecules as the result of docking within accessible pillar[5]arene units present in an overall MOF. This has allowed the single-crystal structures of 48 alkyl-chain-containing molecules, including 6 natural products, 2 approved drugs and 18 custom-made compounds collected from 16 research groups, to be determined using standard SCXRD instrumentation. The structures of alkyl-chain-containing molecules derived from crude reaction products can also be determined directly by SCXRD analyses without further purification. The simplicity, high efficiency and apparent generality of the present pillar[5]arene-incorporated MOF-based supramolecular docking approach suggest that it could emerge as a new tool for the analyses of natural products and drugs that might not be amenable to traditional SCXRD-based structure determination.

『Abstract』Single-atom catalysts (SACs) with maximized metal use and discrete energy levels hold promise for broad applications in heterogeneous catalysis, energy conversion, environmental science and biomedicine . The activity and stability of SACs are governed by the pair of metal–adsorbate and metal–support interactions . However, the understanding of these interactions with their catalytic performance in nature is challenging. Correlations of activity with the charge state of metal atoms have frequently reached controversial conclusions . Here we report that the activity of palladium (Pd 1 ) SACs exhibits a linear scaling relationship with the positions of the lowest unoccupied molecular orbital (LUMO) of oxide supports across 14 types of semiconductor. Elevation of the LUMO position by reducing the support particle size to a few nanometres boosts a record high activity along with excellent stability in the semi-hydrogenation of acetylene. We show that the elevated LUMO of support reduces its energy gap with the highest occupied molecular orbital (HOMO) of Pd 1 atoms, which promotes Pd 1 –support orbital hybridizations for high stability and further amends the LUMO of anchored Pd 1 atoms to enhance Pd 1 –adsorbate interactions for high activity. These findings are consistent with the frontier molecular orbital theory and provide a general descriptor for the rational selection of metal–support pairs with predictable activity.

『Abstract』The crypt–villus structure of the small intestine serves as an essential protective barrier. The integrity of this barrier is monitored by the complex sensory system of the gut, in which serotonergic enterochromaffin (EC) cells play an important part . These rare sensory epithelial cells surveil the mucosal environment for luminal stimuli and transmit signals both within and outside the gut . However, whether EC cells in crypts and villi detect different stimuli or produce distinct physiological responses is unknown. Here we address these questions by developing a reporter mouse model to quantitatively measure the release and propagation of serotonin from EC cells in live intestines. Crypt EC cells exhibit a tonic low-level mode that activates epithelial serotonin 5-HT 4 receptors to modulate basal ion secretion and a stimulus-induced high-level mode that activates 5-HT 3 receptors on sensory nerve fibres. Both these modes can be initiated by the irritant receptor TRPA1, which is confined to crypt EC cells. The activation of TRPA1 by luminal irritants is enhanced when the protective mucus layer is compromised. Villus EC cells also signal damage through a distinct mechanism, whereby oxidative stress activates TRPM2 channels, which leads to the release of both serotonin and ATP and consequent excitation of sensory nerve fibres. This topological segregation of EC cell functionality along the mucosal architecture constitutes a mechanism for the surveillance, maintenance and protection of gut integrity under diverse physiological conditions.

『Abstract』This study examines the origin and differentiation of stem-like CD8 T cells that are essential for sustained T cell immunity in chronic viral infections and cancer and also have a key role in PD-1 directed immunotherapy . These PD-1 TCF-1 TOX stem-like CD8 T cells (also known as precursors of exhausted T cells ) have a distinct program that enables them to adapt to chronic antigen stimulation. Here, using the mouse model of chronic lymphocytic choriomeningitis virus (LCMV) infection, we find that virus-specific stem-like CD8 T cells are generated early (day 5) during chronic infection, suggesting that this crucial fate commitment occurs irrespective of the infection outcome. Indeed, we find that nearly identical populations of stem-like CD8 T cells were generated early during acute or chronic LCMV infection, and that antigen was essential for maintaining the stem-like phenotype. We performed reciprocal adoptive transfer experiments to determine the fate of these early stem-like CD8 T cells after viral clearance versus persistence. After transfer of day 5 stem-like CD8 T cells from chronically infected mice into acutely infected mice, these cells downregulated canonical markers of the chronic stem-like CD8 T cells and expressed markers (CD127 and CD62L) associated with central memory CD8 T cells. Reciprocally, when day 5 stem-like cells from acutely infected mice were transferred into chronically infected mice, these CD8 T cells functioned like chronic resource cells and responded effectively to PD-1 therapy. These findings highlight the ability of these early PD-1 TCF-1 TOX stem-like CD8 T cells to adapt their differentiation trajectory to either an acute or a chronic viral infection. Importantly, our study shows that the host is prepared a priori to deal with a potential chronic infection.

『Abstract』The global spread of multidrug-resistant pathogenic fungi presents a serious threat to human health, necessitating the discovery of antifungals with unique modes of action . However, conventional activity-based screening for previously undescribed antibiotics has been hampered by the high-frequency rediscovery of known compounds and the lack of new antifungal targets . Here we report the discovery of a polyene antifungal antibiotic, mandimycin, using a phylogeny-guided natural-product discovery platform. Mandimycin is biosynthesized by the mand gene cluster, has evolved in a distinct manner from known polyene macrolide antibiotics and is modified with three deoxy sugars. It has demonstrated potent and broad-spectrum fungicidal activity against a wide range of multidrug-resistant fungal pathogens in both in vitro and in vivo settings. In contrast to known polyene macrolide antibiotics that target ergosterol, mandimycin has a unique mode of action that involves targeting various phospholipids in fungal cell membranes, resulting in the release of essential ions from fungal cells. This unique ability to bind multiple targets gives it robust fungicidal activity as well as the capability to evade resistance. The identification of mandimycin using the phylogeny-guided natural-product discovery strategy represents an important advancement in uncovering antimicrobial compounds with distinct modes of action, which could be developed to combat multidrug-resistant fungal pathogens.

『Abstract』Developing a general algorithm that learns to solve tasks across a wide range of applications has been a fundamental challenge in artificial intelligence. Although current reinforcement-learning algorithms can be readily applied to tasks similar to what they have been developed for, configuring them for new application domains requires substantial human expertise and experimentation . Here we present the third generation of Dreamer, a general algorithm that outperforms specialized methods across over 150 diverse tasks, with a single configuration. Dreamer learns a model of the environment and improves its behaviour by imagining future scenarios. Robustness techniques based on normalization, balancing and transformations enable stable learning across domains. Applied out of the box, Dreamer is, to our knowledge, the first algorithm to collect diamonds in Minecraft from scratch without human data or curricula. This achievement has been posed as a substantial challenge in artificial intelligence that requires exploring farsighted strategies from pixels and sparse rewards in an open world . Our work allows solving challenging control problems without extensive experimentation, making reinforcement learning broadly applicable.

『Abstract』The discovery of Ruddlesden–Popper (RP) bilayer nickelate superconductors under high pressure has opened a new chapter in high-transition-temperature superconductivity . However, the high-pressure conditions and presence of impurity phases have hindered comprehensive investigations into their superconducting properties and potential applications. Here we report ambient-pressure superconductivity onset above the McMillan limit (40 K) in RP bilayer nickelate epitaxial thin films. Three-unit-cell-thick La 2.85 Pr 0.15 Ni 2 O 7 pure-phase single-crystal films are grown using the gigantic-oxidative atomic layer-by-layer epitaxy on SrLaAlO 4 substrates . Resistivity measurements and magnetic field responses indicate onset transition temperature of 45 K. The transition to zero resistance shows characteristics consistent with a Berezinskii–Kosterlitz–Thouless (BKT) behaviour, with T BKT = 9 K. The Meissner diamagnetic effect is observed at 8 K by using a mutual inductance setup, in agreement with the BKT-like transition. In- and out-of-plane critical magnetic fields show anisotropy. Scanning transmission electron microscopy images and X-ray reciprocal space mappings reveal that the RP bilayer nickelate films adopt a tetragonal phase under roughly 2% coherent epitaxial compressive strain in the NiO 2 planes relative to the bulk. Our findings pave the way for comprehensive investigations of nickelate superconductors under ambient pressure conditions and for exploring superconductivity at higher transition temperatures through strain engineering in heterostructures.

『Abstract』The crab-eating macaques ( Macaca fascicularis ) and rhesus macaques ( Macaca mulatta ) are pivotal in biomedical and evolutionary research . However, their genomic complexity and interspecies genetic differences remain unclear . Here, we present a complete genome assembly of a crab-eating macaque, revealing 46% fewer segmental duplications and 3.83 times longer centromeres than those of humans . We also characterize 93 large-scale genomic differences between macaques and humans at a single-base-pair resolution, highlighting their impact on gene regulation in primate evolution. Using ten long-read macaque genomes, hundreds of short-read macaque genomes and full-length transcriptome data, we identified roughly 2 Mbp of fixed-genetic variants, roughly 240 Mbp of complex loci, 16.76 Mbp genetic differentiation regions and 110 alternative splice events, potentially associated with various phenotypic differences between the two macaque species. In summary, the integrated genetic analysis enhances understanding of lineage-specific phenotypes, adaptation and primate evolution, thereby improving their biomedical applications in human disease research.

『Abstract』At subduction zones, lithospheric material descends through the upper mantle to the mantle transition zone (MTZ), where it may continue to sink into the lower mantle or stagnate . Several factors may be important in influencing this flow, including chemical heterogeneity . However, tight constraints on these mantle flows and the exact factors that affect them have proved challenging. We use P-to-S receiver functions to image the subducting slab and the MTZ beneath the Lesser Antilles subduction zone. We image a singular, superdeep (>700 km) 660-km discontinuity over a 200-km-wide zone within the slab, accompanied by nearby double 660 discontinuity phases (normal and superdeep). Combined geodynamic and waveform modelling shows that this observation cannot be explained by temperature effects in typical mantle compositions but requires a large basalt-rich chemical anomaly, strongest in the location of the singular, deep 660. The inferred basalt signature is near the proposed location of a subducted extinct spreading ridge , where basalt is probably present in greater proportions. Our finding suggests that past tectonic events impart chemical heterogeneity into slabs, and the heterogeneities, in turn, may affect the inherent tendency of the slab to sink.

『Abstract』Substantial epigenetic resetting during early embryo development from fertilization to blastocyst formation ensures zygotic genome activation and leads to progressive cellular heterogeneities . Mapping single-cell epigenomic profiles of core histone modifications that cover each individual cell is a fundamental goal in developmental biology. Here we develop target chromatin indexing and tagmentation (TACIT), a method that enabled genome-coverage single-cell profiling of seven histone modifications across mouse early embryos. We integrated these single-cell histone modifications with single-cell RNA sequencing data to chart a single-cell resolution epigenetic landscape. Multimodal chromatin-state annotations showed that the onset of zygotic genome activation at the early two-cell stage already primes heterogeneities in totipotency. We used machine learning to identify totipotency gene regulatory networks, including stage-specific transposable elements and putative transcription factors. CRISPR activation of a combination of these identified transcription factors induced totipotency activation in mouse embryonic stem cells. Together with single-cell co-profiles of multiple histone modifications, we developed a model that predicts the earliest cell branching towards the inner cell mass and the trophectoderm in latent multimodal space and identifies regulatory elements and previously unknown lineage-specifying transcription factors. Our work provides insights into single-cell epigenetic reprogramming, multimodal regulation of cellular lineages and cell-fate priming during mouse pre-implantation development.

『Abstract』Hepatic stellate cells (HSCs) have a central pathogenetic role in the development of liver fibrosis. However, their fibrosis-independent and homeostatic functions remain poorly understood . Here we demonstrate that genetic depletion of HSCs changes WNT activity and zonation of hepatocytes, leading to marked alterations in liver regeneration, cytochrome P450 metabolism and injury. We identify R-spondin 3 (RSPO3), an HSC-enriched modulator of WNT signalling, as responsible for these hepatocyte-regulatory effects of HSCs. HSC-selective deletion of Rspo3 phenocopies the effects of HSC depletion on hepatocyte gene expression, zonation, liver size, regeneration and cytochrome P450-mediated detoxification, and exacerbates alcohol-associated and metabolic dysfunction-associated steatotic liver disease. RSPO3 expression decreases with HSC activation and is inversely associated with outcomes in patients with alcohol-associated and metabolic dysfunction-associated steatotic liver disease. These protective and hepatocyte-regulating functions of HSCs via RSPO3 resemble the R-spondin-expressing stromal niche in other organs and should be integrated into current therapeutic concepts.

『Abstract』Intratumour heterogeneity and phenotypic plasticity drive tumour progression and therapy resistance . Oncogene dosage variation contributes to cell-state transitions and phenotypic heterogeneity , thereby providing a substrate for somatic evolution. Nonetheless, the genetic mechanisms underlying phenotypic heterogeneity are still poorly understood. Here we show that extrachromosomal DNA (ecDNA) is a major source of high-level focal amplification in key oncogenes and a major contributor of MYC heterogeneity in pancreatic ductal adenocarcinoma (PDAC). We demonstrate that ecDNAs drive varying levels of MYC dosage, depending on their regulatory landscape, enabling cancer cells to rapidly and reversibly adapt to microenvironmental changes. In the absence of selective pressure, a high ecDNA copy number imposes a substantial fitness cost on PDAC cells. We also show that MYC dosage affects cell morphology and dependence of cancer cells on stromal niche factors. Our work provides a detailed analysis of ecDNAs in PDAC and describes a new genetic mechanism driving MYC heterogeneity in PDAC.

『Abstract』Recently the quest for post-silicon semiconductors has escalated owing to the inherent limitations of conventional bulk semiconductors, which are plagued by issues such as drain-induced barrier lowering, interfacial-scattering-induced mobility degradation and a constrained current on/off ratio determined by semiconductor bandwidth. These challenges have prompted the search for more advanced materials, with atomic-layer-thick two-dimensional (2D) semiconductors emerging as a potential solution. Following over a decade of research advances, recent developments in wafer-scale growth and device fabrication have led to breakthroughs in 2D semiconductor electronics. However, the level of integration remains constrained to a few hundred transistors. We describe a reduced instruction set computing architecture (RISC-V) microprocessor capable of executing standard 32-bit instructions on 5,900 MoS 2 transistors and a complete standard cell library based on 2D semiconductor technology. The library contains 25 types of logic units. In alignment with advances in silicon integrated circuits, we also co-optimized the process flow and design of the 2D logic circuits. Our combined manufacturing and design methodology has overcome the significant challenges associated with wafer-scale integration of 2D circuits and enabled a pioneering prototype of an MoS 2 microprocessor that exemplifies the potential of 2D integrated-circuit technology beyond silicon.

『Abstract』Understanding how proteins in different mammalian tissues are regulated is central to biology. Protein abundance, turnover, and post-translational modifications such as phosphorylation are key factors that determine tissue-specific proteome properties. However, these properties are challenging to study across tissues and remain poorly understood. Here, we present Turnover-PPT , a comprehensive resource mapping the abundance and lifetime of 11,000 proteins and 40,000 phosphosites in eight mouse tissues and various brain regions using advanced proteomics and stable isotope labeling. We reveal tissue-specific short- and long-lived proteins, strong correlations between interacting protein lifetimes, and distinct impacts of phosphorylation on protein turnover. Notably, we discover a remarkable pattern of turnover changes for peroxisome proteins in specific tissues and that phosphorylation regulates the stability of neurodegeneration-related proteins, such as Tau and α-synuclein. Thus, Turnover-PPT provides fundamental insights into protein stability, tissue dynamic proteotypes, and functional protein phosphorylation and is accessible via an interactive web-based portal at https://yslproteomics.shinyapps.io/tissuePPT .

『Abstract』Brassinosteroid hormones are positive regulators of plant organ growth, yet their function in proliferating tissues remains unclear. Here, through integrating single-cell RNA sequencing with long-term live-cell imaging of the Arabidopsis root, we reveal that brassinosteroid activity fluctuates throughout the cell cycle, decreasing during mitotic divisions and increasing during the G1 phase. The post-mitotic recovery of brassinosteroid activity is driven by the intrinsic polarity of the mother cell, resulting in one daughter cell with enhanced brassinosteroid signaling, while the other supports brassinosteroid biosynthesis. The coexistence of these distinct daughter cell states during the G1 phase circumvents a negative feedback loop to facilitate brassinosteroid production while signaling increases. Our findings uncover polarity-guided, uneven mitotic divisions in the meristem, which control brassinosteroid hormone activity to ensure optimal root growth.

『Abstract』Cytokines interact with their receptor complexes to orchestrate diverse processes—from immune responses to behavioral modulation. Interleukin-17A (IL-17A) mediates protective immune responses by binding to IL-17 receptor A (IL-17RA) and IL-17RC subunits. IL-17A also modulates social interaction, yet the role of cytokine receptors in this process and their expression in the brain remains poorly characterized. Here, we mapped the brain-region-specific expression of all major IL-17R subunits and found that in addition to IL-17RA, IL-17RB—but not IL-17RC—plays a role in social behaviors through its expression in the cortex. We further showed that IL-17E, expressed in cortical neurons, enhances social interaction by acting on IL-17RA- and IL-17RB-expressing neurons. These findings highlight an IL-17 circuit within the cortex that modulates social behaviors. Thus, characterizing spatially restricted cytokine receptor expression can be leveraged to elucidate how cytokines function as critical messengers mediating neuroimmune interactions to shape animal behaviors.

『Abstract』Patients with autoimmune or infectious diseases can develop persistent mood alterations after inflammatory episodes. Peripheral immune molecules, like cytokines, can influence behavioral and internal states, yet their impact on the function of specific neural circuits in the brain remains unclear. Here, we show that cytokines act as neuromodulators to regulate anxiety by engaging receptor-expressing neurons in the basolateral amygdala (BLA). Heightened interleukin-17A (IL-17A) and IL-17C levels, paradoxically induced from treatment with anti-IL-17 receptor A (IL-17RA) antibodies, promote anxiogenic behaviors by increasing the excitability of IL-17RA/RE-expressing BLA neurons. Conversely, the anti-inflammatory IL-10, acting on the same population of BLA neurons via its receptor, exerts opposite effects on neuronal excitability and behavior. These findings reveal that inflammatory and anti-inflammatory cytokines bidirectionally modulate anxiety by engaging their respective receptors in the same BLA population. Our results highlight the role of cytokine signaling in shaping internal states through direct modulation of specific neural substrates.

『Abstract』Pooled optical screens have enabled the study of cellular interactions, morphology, or dynamics at massive scale, but they have not yet leveraged the power of highly plexed single-cell resolved transcriptomic readouts to inform molecular pathways. Here, we present a combination of imaging spatial transcriptomics with parallel optical detection of in situ amplified guide RNAs (Perturb-FISH). Perturb-FISH recovers intracellular effects that are consistent with single-cell RNA-sequencing-based readouts of perturbation effects (Perturb-seq) in a screen of lipopolysaccharide response in cultured monocytes, and it uncovers intercellular and density-dependent regulation of the innate immune response. Similarly, in three-dimensional xenograft models, Perturb-FISH identifies tumor-immune interactions altered by genetic knockout. When paired with a functional readout in a separate screen of autism spectrum disorder risk genes in human-induced pluripotent stem cell (hIPSC) astrocytes, Perturb-FISH shows common calcium activity phenotypes and their associated genetic interactions and dysregulated molecular pathways. Perturb-FISH is thus a general method for studying the genetic and molecular associations of spatial and functional biology at single-cell resolution.

『Abstract』High-density probes allow electrophysiological recordings from many neurons simultaneously across entire brain circuits but fail to reveal cell type. Here, we develop a strategy to identify cell types from extracellular recordings in awake animals and reveal the computational roles of neurons with distinct functional, molecular, and anatomical properties. We combine optogenetics and pharmacology using the cerebellum as a testbed to generate a curated ground-truth library of electrophysiological properties for Purkinje cells, molecular layer interneurons, Golgi cells, and mossy fibers. We train a semi-supervised deep learning classifier that predicts cell types with greater than 95% accuracy based on the waveform, discharge statistics, and layer of the recorded neuron. The classifier’s predictions agree with expert classification on recordings using different probes, in different laboratories, from functionally distinct cerebellar regions, and across species. Our classifier extends the power of modern dynamical systems analyses by revealing the unique contributions of simultaneously recorded cell types during behavior.

『Abstract』Knowing whether we are moving or something in the world is moving around us is possibly the most critical sensory discrimination we need to perform. How the brain and, in particular, the visual system solves this motion-source separation problem is not known. Here, we find that motor, vestibular, and visual motion signals are used by the mouse primary visual cortex (VISp) to differentially represent the same visual flow information according to whether the head is stationary or experiencing passive versus active translation. During locomotion, we find that running suppresses running-congruent translation input and that translation signals dominate VISp activity when running and translation speed become incongruent. This cross-modal interaction between the motor and vestibular systems was found throughout the cortex, indicating that running and translation signals provide a brain-wide egocentric reference frame for computing the internally generated and actual speed of self when moving through and sensing the external world.

『Abstract』Microglia, essential in the central nervous system (CNS), were historically considered absent from the peripheral nervous system (PNS). Here, we show a PNS-resident macrophage population that shares transcriptomic and epigenetic profiles as well as an ontogenetic trajectory with CNS microglia. This population (termed PNS microglia-like cells) enwraps the neuronal soma inside the satellite glial cell envelope, preferentially associates with larger neurons during PNS development, and is required for neuronal functions by regulating soma enlargement and axon growth. A phylogenetic survey of 24 vertebrates revealed an early origin of PNS microglia-like cells, whose presence is correlated with neuronal soma size (and body size) rather than evolutionary distance. Consistent with their requirement for soma enlargement, PNS microglia-like cells are maintained in vertebrates with large peripheral neuronal soma but absent when neurons evolve to have smaller soma. Our study thus reveals a PNS counterpart of CNS microglia that regulates neuronal soma size during both evolution and ontogeny.

『Abstract』Koala retrovirus-A (KoRV-A) is spreading through wild koalas in a north-to-south wave while transducing the germ line, modifying the inherited genome as it transitions to an endogenous retrovirus. Previously, we found that KoRV-A is expressed in the germ line, but unspliced genomic transcripts are processed into sense-strand PIWI-interacting RNAs (piRNAs), which may provide an initial “innate” form of post-transcriptional silencing. Here, we show that this initial post-transcriptional response is prevalent south of the Brisbane River, whereas KoRV-A expression is suppressed, promoters are methylated, and sense and antisense piRNAs are equally abundant in a subpopulation of animals north of the river. These animals share a KoRV-A provirus in the MAP4K4 gene’s 3′ UTR that is spreading through northern koalas and produces hybrid transcripts that are processed into antisense piRNAs, which guide transcriptional silencing. We speculate that this provirus triggers adaptive transcriptional silencing of KoRV-A and is sweeping to fixation.

『Abstract』Long terminal repeat (LTR) retrotransposons belong to the transposable elements (TEs), autonomously replicating genetic elements that integrate into the host’s genome. Among animals, Drosophila melanogaster serves as an important model organism for TE research and contains several LTR retrotransposons, including the Ty1- copia family, which is evolutionarily related to retroviruses and forms virus-like particles (VLPs). In this study, we use cryo-focused ion beam (FIB) milling and lift-out approaches to visualize copia VLPs in ovarian cells and intact egg chambers, resolving the in situ copia capsid structure to 7.7 Å resolution by cryoelectron tomography (cryo-ET). Although cytoplasmic copia VLPs vary in size, nuclear VLPs are homogeneous and form densely packed clusters, supporting a model in which nuclear import acts as a size selector. Analyzing flies deficient in the TE-suppressing PIWI-interacting RNA (piRNA) pathway, we observe copia ’s translocation into the nucleus during spermatogenesis. Our findings provide insights into the replication cycle and cellular structural biology of an active LTR retrotransposon.

『Abstract』Social interaction is integral to animal behavior. However, lacking tools to describe it in quantitative and rigorous ways has limited our understanding of its structure, underlying principles, and the neuropsychiatric disorders, like autism, that perturb it. Here, we present a technique for high-resolution 3D tracking of postural dynamics and social touch in freely interacting animals, solving the challenging subject occlusion and part-assignment problems using 3D geometric reasoning, graph neural networks, and semi-supervised learning. We collected over 110 million 3D pose samples in interacting rats and mice, including seven monogenic autism rat lines. Using a multi-scale embedding approach, we identified a rich landscape of stereotyped actions, interactions, synchrony, and body contacts. This high-resolution phenotyping revealed a spectrum of changes in autism models and in response to amphetamine not resolved by conventional measurements. Our framework and large library of interactions will facilitate studies of social behaviors and their neurobiological underpinnings.

『Abstract』Jumbo bacteriophages of the ϕKZ-like family assemble a lipid-based early phage infection (EPI) vesicle and a proteinaceous nucleus-like structure during infection. These structures protect the phage from nucleases and may create selective pressure for immunity mechanisms targeting this specific phage family. Here, we identify “jumbo phage killer” (Juk), a two-component immune system that terminates infection of ϕKZ-like phages, suppressing the expression of early phage genes and preventing phage DNA replication and phage nucleus assembly while saving the cell. JukA (formerly YaaW) rapidly senses the EPI vesicle by binding to an early-expressed phage protein, gp241, and then directly recruits JukB. The JukB effector structurally resembles a pore-forming toxin and destabilizes the EPI vesicle. Functional anti-ϕKZ JukA homologs are found across bacterial phyla, associated with diverse effectors. These findings reveal a widespread defense system that specifically targets early events executed by ϕKZ-like jumbo phages prior to phage nucleus assembly.

『Abstract』The relationships of human diversity with biomedical phenotypes are pervasive yet remain understudied, particularly in a single-cell genomics context. Here, we present the Asian Immune Diversity Atlas (AIDA), a multi-national single-cell RNA sequencing (scRNA-seq) healthy reference atlas of human immune cells. AIDA comprises 1,265,624 circulating immune cells from 619 donors, spanning 7 population groups across 5 Asian countries, and 6 controls. Though population groups are frequently compared at the continental level, we found that sub-continental diversity, age, and sex pervasively impacted cellular and molecular properties of immune cells. These included differential abundance of cell neighborhoods as well as cell populations and genes relevant to disease risk, pathogenesis, and diagnostics. We discovered functional genetic variants influencing cell-type-specific gene expression, which were under-represented in non-Asian populations, and helped contextualize disease-associated variants. AIDA enables analyses of multi-ancestry disease datasets and facilitates the development of precision medicine efforts in Asia and beyond.

『Abstract』Chronic hepatitis B virus (HBV) infection is an incurable pathogen responsible for causing liver disease and hepatocellular carcinoma. During the genesis of infection, HBV establishes an independent minichromosome consisting of the viral covalently closed circular DNA (cccDNA) genome and host histones. The viral X gene must be expressed immediately upon infection to induce degradation of the host silencing factor, the Smc5/6 complex. However, the relationship between cccDNA chromatinization and X gene transcription remains poorly understood. By establishing a reconstituted viral minichromosome platform, we found that nucleosome occupancy in cccDNA regulates X transcription. We corroborated these findings in situ and further showed that the chromatin-destabilizing molecule CBL137 inhibits full-length X transcription and HBV infection in primary human hepatocytes. Our results shed light on a long-standing paradox and represent a potential therapeutic approach for the treatment of chronic HBV infection.

『Abstract』Efforts to use genome-wide assays or brain scans to diagnose autism have seen diminishing returns. Yet the clinical intuition of healthcare professionals, based on longstanding first-hand experience, remains the gold standard for diagnosis of autism. We leveraged deep learning to deconstruct and interrogate the logic of expert clinician intuition from clinical reports to inform our understanding of autism. After pre-training on hundreds of millions of general sentences, we finessed large language models (LLMs) on >4,000 free-form health records from healthcare professionals to distinguish confirmed versus suspected autism cases. By introducing an explainability strategy, our extended language model architecture could pin down the most salient single sentences in what drives clinical thinking toward correct diagnoses. Our framework flagged the most autism-critical DSM-5 criteria to be stereotyped repetitive behaviors, special interests, and perception-based behaviors, which challenges today’s focus on deficits in social interplay, suggesting necessary revision of long-trusted diagnostic criteria in gold-standard instruments.