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 observations1-11. 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) satellite12 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.

During classical non-homologous end joining (cNHEJ), DNA-dependent protein kinase (DNA-PK) encapsulates free DNA ends, forming a recruitment platform for downstream end-joining factors including ligase 4 (LIG4)1. DNA-PK can also bind telomeres and regulate their resection2-4, but does not initiate cNHEJ at this position. How the end-joining process is regulated in this context-specific manner is currently unclear. Here we show that the shelterin components TRF2 and RAP1 form a complex with DNA-PK that directly represses its end-joining function at telomeres. Biochemical experiments and cryo-electron microscopy reveal that when bound to TRF2, RAP1 establishes a network of interactions with KU and DNA that prevents DNA-PK from recruiting LIG4. In mouse and human cells, RAP1 is redundant with the Apollo nuclease in repressing cNHEJ at chromosome ends, demonstrating that the inhibition of DNA-PK prevents telomere fusions in parallel with overhang-dependent mechanisms. Our experiments show that the end-joining function of DNA-PK is directly and specifically repressed at telomeres, establishing a molecular mechanism for how individual linear chromosomes are maintained in mammalian cells.

Protein misfolding diseases, including α1-antitrypsin deficiency (AATD), pose substantial health challenges, with their cellular progression still poorly understood1-3. We use spatial proteomics by mass spectrometry and machine learning to map AATD in human liver tissue. Combining Deep Visual Proteomics (DVP) with single-cell analysis4,5, we probe intact patient biopsies to resolve molecular events during hepatocyte stress in pseudotime across fibrosis stages. We achieve proteome depth of up to 4,300 proteins from one-third of a single cell in formalin-fixed, paraffin-embedded tissue. This dataset reveals a potentially clinically actionable peroxisomal upregulation that precedes the canonical unfolded protein response. Our single-cell proteomics data show α1-antitrypsin accumulation is largely cell-intrinsic, with minimal stress propagation between hepatocytes. We integrated proteomic data with artificial intelligence-guided image-based phenotyping across several disease stages, revealing a late-stage hepatocyte phenotype characterized by globular protein aggregates and distinct proteomic signatures, notably including elevated TNFSF10 (also known as TRAIL) amounts. This phenotype may represent a critical disease progression stage. Our study offers new insights into AATD pathogenesis and introduces a powerful methodology for high-resolution, in situ proteomic analysis of complex tissues. This approach holds potential to unravel molecular mechanisms in various protein misfolding disorders, setting a new standard for understanding disease progression at the single-cell level in human tissue.

Methyl-coenzyme M reductase (MCR) is the enzyme responsible for nearly all biologically generated methane1. Its active site comprises coenzyme F430, a porphyrin-based cofactor with a central nickel ion that is active exclusively in the Ni(I) state2,3. How methanogenic archaea perform the reductive activation of F430 represents a major gap in our understanding of one of the most ancient bioenergetic systems in nature. Here we purified and characterized the MCR activation complex from Methanococcus maripaludis. McrC, a small subunit encoded in the mcr operon, co-purifies with the methanogenic marker proteins Mmp7, Mmp17, Mmp3 and the A2 component. We demonstrated that this complex can activate MCR in vitro in a strictly ATP-dependent manner, enabling the formation of methane. In addition, we determined the cryo-electron microscopy structure of the MCR activation complex exhibiting different functional states with local resolutions reaching 1.8-2.1 Å. Our data revealed three complex iron-sulfur clusters that formed an electron transfer pathway towards F430. Topology and electron paramagnetic resonance spectroscopy analyses indicate that these clusters are similar to the [8Fe-9S-C] cluster, a maturation intermediate of the catalytic cofactor in nitrogenase. Altogether, our findings offer insights into the activation mechanism of MCR and prospects on the early evolution of nitrogenase.

Impaired differentiation is a hallmark of myeloid malignancies1,2. Therapies that enable cells to circumvent the differentiation block, such as all-trans retinoic acid (ATRA) and arsenic trioxide (ATO), are by and large curative in acute promyelocytic leukaemia3, but whether 'differentiation therapy' is a generalizable therapeutic approach for acute myeloid leukaemia (AML) and beyond remains incompletely understood. Here we demonstrate that simultaneous inhibition of the histone demethylase LSD1 (LSD1i) and the WNT pathway antagonist GSK3 kinase4 (GSK3i) robustly promotes therapeutic differentiation of established AML cell lines and primary human AML cells, as well as reducing tumour burden and significantly extending survival in a patient-derived xenograft mouse model. Mechanistically, this combination promotes differentiation by activating genes in the type I interferon pathway via inducing expression of transcription factors such as IRF7 (LSD1i) and the co-activator β-catenin (GSK3i), and their selective co-occupancy at targets such as STAT1, which is necessary for combination-induced differentiation. Combination treatment also suppresses the canonical, pro-oncogenic WNT pathway and cell cycle genes. Analysis of datasets from patients with AML suggests a correlation between the combination-induced transcription signature and better prognosis, highlighting clinical potential of this strategy. Collectively, this combination strategy rewires transcriptional programs to suppress stemness and to promote differentiation, which may have important therapeutic implications for AML and WNT-driven cancers beyond AML.

Oryza rufipogon, the wild progenitor of Asian cultivated rice Oryza sativa, is an important resource for rice breeding1. Here we present a wild-cultivated rice pangenome based on 145 chromosome-level assemblies, comprising 129 genetically diverse O. rufipogon accessions and 16 diverse varieties of O. sativa. This pangenome contains 3.87 Gb of sequences that are absent from the O. sativa ssp. japonica cv. Nipponbare reference genome. We captured alternate assemblies that include heterozygous information missing in the primary assemblies, and identified a total of 69,531 pan-genes, with 28,907 core genes and 13,728 wild-rice-specific genes. We observed a higher abundance and a significantly greater diversity of resistance-gene analogues in wild rice than in cultivars. Our analysis indicates that two cultivated subpopulations, intro-indica and basmati, were generated through gene flows among cultivars in South Asia. We also provide strong evidence to support the theory that the initial domestication of all Asian cultivated rice occurred only once. Furthermore, we captured 855,122 differentiated single-nucleotide polymorphisms and 13,853 differentiated presence-absence variations between indica and japonica, which could be traced to the divergence of their respective ancestors and the existence of a larger genetic bottleneck in japonica. This study provides reference resources for enhancing rice breeding, and enriches our understanding of the origins and domestication process of rice.

Despite the widespread use of mRNA vaccines against COVID-19, little is known about the metabolism of therapeutic RNAs. Here we use nanopore sequencing1-3 to analyse individual therapeutic mRNA molecules, focusing on their poly(A) tails. We show that the Moderna mRNA-1273 vaccine4 has a poly(A) tail of around 100 nucleotides, followed by an mΨCmΨAG sequence. In cell lines, mRNA-1273 undergoes rapid degradation initiated by mΨCmΨAG removal, followed by CCR4-NOT-mediated deadenylation. However, in medically relevant preclinical models, particularly in macrophages, mRNA-1273 poly(A) tails are extended to up to 200 nucleotides by the TENT5A poly(A) polymerase5-7, which is induced by the vaccine. Re-adenylation, which stabilizes target mRNAs, is consistently observed in synthetic mRNAs that encode proteins targeted to the endoplasmic reticulum, such as ovalbumin or antigens from Zika virus8 or the malaria parasite9. The extent of re-adenylation varies: the BioNTech-Pfizer BNT162b2 vaccine10 shows less potent re-adenylation than mRNA-1273, which correlates with a smaller proportion of membrane-associated BNT162b2. This highlights the crucial role of spatial accessibility to ER-resident TENT5A in determining re-adenylation efficiency. In vivo, TENT5A is expressed in immune cells that take up mRNA vaccine, and TENT5A deficiency reduces specific immunoglobulin production for mRNA vaccines after immunization in mice. Overall, our findings reveal a principle for enhancing the efficacy of therapeutic mRNAs, paving the way for improvement.

Potatoes were first brought to Europe in the sixteenth century1,2. Two hundred years later, one of the species had become one of the most important food sources across the entire continent and, later, even the entire world3. However, its highly heterozygous, autotetraploid genome has complicated its improvement since then4-7. Here we present the pan-genome of European potatoes generated from phased genome assemblies of ten historical potato cultivars, which includes approximately 85% of all haplotypes segregating in Europe. Sequence diversity between the haplotypes was extremely high (for example, 20× higher than in humans), owing to numerous introgressions from wild potato species. By contrast, haplotype diversity was very low, in agreement with the population bottlenecks caused by domestication and transition to Europe. To illustrate a practical application of the pan-genome, we converted it into a haplotype graph and used it to generate phased, megabase-scale pseudo-genome assemblies of commercial potatoes (including the famous French fries potato 'Russet Burbank') using cost-efficient short reads only. In summary, we present a nearly complete pan-genome of autotetraploid European potato, we describe extraordinarily high sequence diversity in a domesticated crop, and we outline how this resource might be used to accelerate genomics-assisted breeding and research.

The formation of accessible chromatin around DNA double-strand breaks is essential for their efficient repair1. Although the linker histone H1 is known to facilitate higher-order chromatin compaction2,3, the mechanisms by which H1 modifications regulate chromatin relaxation in response to DNA damage are unclear. Here we show that CTP synthase 1 (CTPS1)-catalysed deamidation of H1 asparagine residues 76 and 77 triggers the sequential acetylation of lysine 75 following DNA damage, and this dual modification of H1 is associated with chromatin opening. Mechanistically, the histone acetyltransferase p300 showed a preference for deamidated H1 as a substrate, establishing H1 deamidation as a prerequisite for subsequent acetylation. Moreover, high expression of CTPS1 was associated with resistance to cancer radiotherapy, in both mouse xenograft models and clinical cohorts. These findings provide new insights into how linker histones regulate dynamic chromatin alterations in the DNA damage response.

The pursuit of non-volatile memory with program speeds below one nanosecond, beyond the capabilities of non-volatile flash and high-speed volatile static random-access memory, remains a longstanding challenge in the field of memory technology1. Utilizing fundamental physics innovation enabled by advanced materials, series of emerging memories2-5 are being developed to overcome the speed bottleneck of non-volatile memory. As the most extensively applied non-volatile memory, the speed of flash is limited by the low efficiency of the electric-field-assisted program, with reported speeds6-10 much slower than sub-one nanosecond. Here we report a two-dimensional Dirac graphene-channel flash memory based on a two-dimensional-enhanced hot-carrier-injection mechanism, supporting both electron and hole injection. The Dirac channel flash shows a program speed of 400 picoseconds, non-volatile storage and robust endurance over 5.5 × 106 cycles. Our results confirm that the thin-body channel can optimize the horizontal electric-field (Ey) distribution, and the improved Ey-assisted program efficiency increases the injection current to 60.4 pA μm-1 at |VDS| = 3.7 V. We also find that the two-dimensional semiconductor tungsten diselenide has two-dimensional-enhanced hot-hole injection, but with different injection behaviour. This work demonstrates that the speed of non-volatile flash memory can exceed that of the fastest volatile static random-access memory with the same channel length.

Parkinson's disease is a progressive neurodegenerative condition with a considerable health and economic burden1. It is characterized by the loss of midbrain dopaminergic neurons and a diminished response to symptomatic medical or surgical therapy as the disease progresses2. Cell therapy aims to replenish lost dopaminergic neurons and their striatal projections by intrastriatal grafting. Here, we report the results of an open-label phase I clinical trial (NCT04802733) of an investigational cryopreserved, off-the-shelf dopaminergic neuron progenitor cell product (bemdaneprocel) derived from human embryonic stem (hES) cells and grafted bilaterally into the putamen of patients with Parkinson's disease. Twelve patients were enrolled sequentially in two cohorts-a low-dose (0.9 million cells, n = 5) and a high-dose (2.7 million cells, n = 7) cohort-and all of the participants received one year of immunosuppression. The trial achieved its primary objectives of safety and tolerability one year after transplantation, with no adverse events related to the cell product. At 18 months after grafting, putaminal 18Fluoro-DOPA positron emission tomography uptake increased, indicating graft survival. Secondary and exploratory clinical outcomes showed improvement or stability, including improvement in the Movement Disorder Society Unified Parkinson's Disease Rating Scale (MDS-UPDRS) Part III OFF scores by an average of 23 points in the high-dose cohort. There were no graft-induced dyskinesias. These data demonstrate safety and support future definitive clinical studies.

Parkinson's disease is caused by the loss of dopamine neurons, causing motor symptoms. Initial cell therapies using fetal tissues showed promise but had complications and ethical concerns1-5. Pluripotent stem (PS) cells emerged as a promising alternative for developing safe and effective treatments6. In this phase I/II trial at Kyoto University Hospital, seven patients (ages 50-69) received bilateral transplantation of dopaminergic progenitors derived from induced PS (iPS) cells. Primary outcomes focused on safety and adverse events, while secondary outcomes assessed motor symptom changes and dopamine production for 24 months. There were no serious adverse events, with 73 mild to moderate events. Patients' anti-parkinsonian medication doses were maintained unless therapeutic adjustments were required, resulting in increased dyskinesia. Magnetic resonance imaging showed no graft overgrowth. Among six patients subjected to efficacy evaluation, four showed improvements in the Movement Disorder Society Unified Parkinson's Disease Rating Scale part III OFF score, and five showed improvements in the ON scores. The average changes of all six patients were 9.5 (20.4%) and 4.3 points (35.7%) for the OFF and ON scores, respectively. Hoehn-Yahr stages improved in four patients. Fluorine-18-L-dihydroxyphenylalanine (18F-DOPA) influx rate constant (Ki) values in the putamen increased by 44.7%, with higher increases in the high-dose group. Other measures showed minimal changes. This trial (jRCT2090220384) demonstrated that allogeneic iPS-cell-derived dopaminergic progenitors survived, produced dopamine and did not form tumours, therefore suggesting safety and potential clinical benefits for Parkinson's disease.

Somatic DNMT3A-R882 codon mutations drive the most common form of clonal haematopoiesis (CH) and are associated with increased acute myeloid leukaemia (AML) risk1,2. Preventing expansion of DNMT3A-R882-mutant haematopoietic stem/progenitor cells (HSPCs) may therefore avert progression to AML. To identify DNMT3A-R882-mutant-specific vulnerabilities, we conducted a genome-wide CRISPR screen on primary mouse Dnmt3aR882H/+ HSPCs. Among the 640 vulnerability genes identified, many were involved in mitochondrial metabolism, and metabolic flux analysis confirmed enhanced oxidative phosphorylation use in Dnmt3aR882H/+ versus Dnmt3a+/+ (WT) HSPCs. We selected citrate/malate transporter Slc25a1 and complex I component Ndufb11, for which pharmacological inhibitors are available, for downstream studies. In vivo administration of SLC25A1 inhibitor CTPI2 and complex I inhibitors IACS-010759 and metformin suppressed post-transplantation clonal expansion of Dnmt3aR882H/+, but not WT, long-term haematopoietic stem cells. The effect of metformin was recapitulated using a primary human DNMT3A-R882 CH sample. Notably, analysis of 412,234 UK Biobank participants showed that individuals taking metformin had a markedly lower prevalence of DNMT3A-R882-mutant CH, after controlling for potential confounders including glycated haemoglobin, diabetes and body mass index. Collectively, our data propose modulation of mitochondrial metabolism as a therapeutic strategy for prevention of DNMT3A-R882-mutant AML.

The gastrointestinal tract is continuously exposed to foreign antigens in food and commensal microorganisms with potential to induce adaptive immune responses. Peripherally induced T regulatory (pTreg) cells are essential for mitigating inflammatory responses to these agents1-4. Although RORγt+ antigen-presenting cells (APCs) have been shown to programme gut microbiota-specific pTreg cells5-7, their definition remains incomplete, and the APC responsible for food tolerance has remained unknown. Here we identify an APC subset that is required for differentiation of both food- and microbiota-specific pTreg cells and for establishment of oral tolerance. Development and function of these APCs require expression of the transcription factors PRDM16 and RORγt, as well as a unique Rorc(t) cis-regulatory element. Gene expression, chromatin accessibility, and surface marker analysis establish the pTreg-inducing APCs as myeloid in origin, distinct from type 3 innate lymphoid cells, and sharing epigenetic profiles with classical dendritic cells, and designate them PRDM16+RORγt+ tolerizing dendritic cells (tolDCs). Upon genetic perturbation of tolDCs, we observe a substantial increase in food antigen-specific T helper 2 cells in lieu of pTreg cells, leading to compromised tolerance in mouse models of asthma and food allergy. Single-cell analyses of freshly resected mesenteric lymph nodes from a human organ donor, as well as multiple specimens of human intestine and tonsil, reveal candidate tolDCs with co-expression of PRDM16 and RORC and an extensive transcriptome shared with tolDCs from mice, highlighting an evolutionarily conserved role across species. Our findings suggest that a better understanding of how tolDCs develop and how they regulate T cell responses to food and microbial antigens could offer new insights into developing therapeutic strategies for autoimmune and allergic diseases as well as organ transplant tolerance.

A common behavior in natural environments is foraging for rewards. However, this is often in the presence of predators. Therefore, one of the most fundamental decisions for humans, as for other animals, is how to apportion time between reward-motivated pursuit behavior and threat-motivated checking behavior. To understand what affects how people strike this balance, we developed an ecologically inspired task and looked at both within-participant dynamics (moods) and between-participant individual differences (questionnaires about real-life behaviors) in two large internet samples (n = 374 and n = 702) in a cross-sectional design. For the within-participant dynamics, we found that people regulate task-evoked stress homeostatically by changing behavior (increasing foraging and hiding). Individual differences, even in superficially related traits (apathy-anhedonia and anxiety-compulsive checking) reliably mapped onto unique behaviors. Worse task performance, due to maladaptive checking, was linked to gender (women checked excessively) and specific anxiety-related traits: somatic anxiety (reduced self-reported checking due to worry) and compulsivity (self-reported disorganized checking). While anhedonia decreased self-reported task engagement, apathy, strikingly, improved overall task performance by reducing excessive checking. In summary, we provide a multifaceted paradigm for assessment of checking for threat in a naturalistic task that is sensitive to both moods as they change throughout the task and clinical dimensions. Thus, it could serve as an objective measurement tool for future clinical studies interested in threat, vigilance or behavior-emotion interactions in contexts requiring both reward seeking and threat avoidance.

Gender inequality substantially impacts society, disproportionately disadvantaging women, especially in the Global South. This inequality correlates with brain health outcomes for women, including a higher risk of cognitive decline and dementia. This perspective highlights how sex-linked biology and gender disparities affect women's brain health in the Global South through various pathways, such as differential exposome, health behaviors, and gender biases in research and healthcare systems. Alzheimer's disease and other brain health conditions exemplify how sex-specific risk factors and gender-related health barriers interact to influence brain health. We advocate for incorporating sex/gender considerations in research, policy, and clinical practice to improve brain health interventions in the Global South. Additionally, we propose using the patient and public involvement framework to effectively tailor health strategies that address these factors.

Existing wearable technologies rely on physical coupling to the body to establish optical1,2, fluidic3,4, thermal5,6 and/or mechanical7,8 measurement interfaces. Here we present a class of wearable device platforms that instead relies on physical decoupling to define an enclosed chamber immediately adjacent to the skin surface. Streams of vapourized molecular substances that pass out of or into the skin alter the properties of the microclimate defined in this chamber in ways that can be precisely quantified using an integrated collection of wireless sensors. A programmable, bistable valve dynamically controls access to the surrounding environment, thereby creating a transient response that can be quantitatively related to the inward and outward fluxes of the targeted species by analysing the time-dependent readings from the sensors. The systems reported here offer unique capabilities in measuring the flux of water vapour, volatile organic compounds and carbon dioxide from various locations on the body, each with distinct relevance to clinical care and/or exposure to hazardous vapours. Studies of healing processes associated with dermal wounds in models of healthy and diabetic mice and of responses in models using infected wounds reveal characteristic flux variations that provide important insights, particularly in scenarios in which the non-contact operation of the devices avoids potential damage to fragile tissues.

Mammalian neocortex contains a highly diverse set of cell types. These cell types have been mapped systematically using a variety of molecular, electrophysiological and morphological approaches1-4. Each modality offers new perspectives on the variation of biological processes underlying cell-type specialization. Cellular-scale electron microscopy provides dense ultrastructural examination and an unbiased perspective on the subcellular organization of brain cells, including their synaptic connectivity and nanometre-scale morphology. In data that contain tens of thousands of neurons, most of which have incomplete reconstructions, identifying cell types becomes a clear challenge for analysis5. Here, to address this challenge, we present a systematic survey of the somatic region of all cells in a cubic millimetre of cortex using quantitative features obtained from electron microscopy. This analysis demonstrates that the perisomatic region is sufficient to identify cell types, including types defined primarily on the basis of their connectivity patterns. We then describe how this classification facilitates cell-type-specific connectivity characterization and locating cells with rare connectivity patterns in the dataset.

The complexity of neural circuits makes it challenging to decipher the brain's algorithms of intelligence. Recent breakthroughs in deep learning have produced models that accurately simulate brain activity, enhancing our understanding of the brain's computational objectives and neural coding. However, it is difficult for such models to generalize beyond their training distribution, limiting their utility. The emergence of foundation models1 trained on vast datasets has introduced a new artificial intelligence paradigm with remarkable generalization capabilities. Here we collected large amounts of neural activity from visual cortices of multiple mice and trained a foundation model to accurately predict neuronal responses to arbitrary natural videos. This model generalized to new mice with minimal training and successfully predicted responses across various new stimulus domains, such as coherent motion and noise patterns. Beyond neural response prediction, the model also accurately predicted anatomical cell types, dendritic features and neuronal connectivity within the MICrONS functional connectomics dataset2. Our work is a crucial step towards building foundation models of the brain. As neuroscience accumulates larger, multimodal datasets, foundation models will reveal statistical regularities, enable rapid adaptation to new tasks and accelerate research.