The ideal electrolyte for the widely used LiNi0.8Mn0.1Co0.1O2 (NMC811)||graphite lithium-ion batteries is expected to have the capability of supporting higher voltages (≥4.5 volts), fast charging (≤15 minutes), charging/discharging over a wide temperature range (±60 degrees Celsius) without lithium plating, and non-flammability1-4. No existing electrolyte simultaneously meets all these requirements and electrolyte design is hindered by the absence of an effective guiding principle that addresses the relationships between battery performance, solvation structure and solid-electrolyte-interphase chemistry5. Here we report and validate an electrolyte design strategy based on a group of soft solvents that strikes a balance between weak Li+-solvent interactions, sufficient salt dissociation and desired electrochemistry to fulfil all the aforementioned requirements. Remarkably, the 4.5-volt NMC811||graphite coin cells with areal capacities of more than 2.5 milliampere hours per square centimetre retain 75 per cent (54 per cent) of their room-temperature capacity when these cells are charged and discharged at -50 degrees Celsius (-60 degrees Celsius) at a C rate of 0.1C, and the NMC811||graphite pouch cells with lean electrolyte (2.5 grams per ampere hour) achieve stable cycling with an average Coulombic efficiency of more than 99.9 per cent at -30 degrees Celsius. The comprehensive analysis further reveals an impedance matching between the NMC811 cathode and the graphite anode owing to the formation of similar lithium-fluoride-rich interphases, thus effectively avoiding lithium plating at low temperatures. This electrolyte design principle can be extended to other alkali-metal-ion batteries operating under extreme conditions.

Cell identity is governed by the complex regulation of gene expression, represented as gene-regulatory networks1. Here we use gene-regulatory networks inferred from single-cell multi-omics data to perform in silico transcription factor perturbations, simulating the consequent changes in cell identity using only unperturbed wild-type data. We apply this machine-learning-based approach, CellOracle, to well-established paradigms-mouse and human haematopoiesis, and zebrafish embryogenesis-and we correctly model reported changes in phenotype that occur as a result of transcription factor perturbation. Through systematic in silico transcription factor perturbation in the developing zebrafish, we simulate and experimentally validate a previously unreported phenotype that results from the loss of noto, an established notochord regulator. Furthermore, we identify an axial mesoderm regulator, lhx1a. Together, these results show that CellOracle can be used to analyse the regulation of cell identity by transcription factors, and can provide mechanistic insights into development and differentiation.

The potential of climate change to substantially alter human history is a pressing concern, but the specific effects of different types of climate change remain unknown. This question can be addressed using palaeoclimatic and archaeological data. For instance, a 300-year, low-frequency shift to drier, cooler climate conditions around 1200 BC is frequently associated with the collapse of several ancient civilizations in the Eastern Mediterranean and Near East1-4. However, the precise details of synchronized climate and human-history-scale associations are lacking. The archaeological-historical record contains multiple instances of human societies successfully adapting to low-frequency climate change5-7. It is likely that consecutive multi-year occurrences of rare, unexpected extreme climatic events may push a population beyond adaptation and centuries-old resilience practices5,7-10. Here we examine the collapse of the Hittite Empire around 1200 BC. The Hittites were one of the great powers in the ancient world across five centuries11-14, with an empire centred in a semi-arid region in Anatolia with political and socioeconomic interconnections throughout the ancient Near East and Eastern Mediterranean, which for a long time proved resilient despite facing regular and intersecting sociopolitical, economic and environmental challenges. Examination of ring width and stable isotope records obtained from contemporary juniper trees in central Anatolia provides a high-resolution dryness record. This analysis identifies an unusually severe continuous dry period from around 1198 to 1196 (±3) BC, potentially indicating a tipping point, and signals the type of episode that can overwhelm contemporary risk-buffering practices.

Cancers arise through the accumulation of genetic and epigenetic alterations that enable cells to evade telomere-based proliferative barriers and achieve immortality. One such barrier is replicative crisis-an autophagy-dependent program that eliminates checkpoint-deficient cells with unstable telomeres and other cancer-relevant chromosomal aberrations1,2. However, little is known about the molecular events that regulate the onset of this important tumour-suppressive barrier. Here we identified the innate immune sensor Z-DNA binding protein 1 (ZBP1) as a regulator of the crisis program. A crisis-associated isoform of ZBP1 is induced by the cGAS-STING DNA-sensing pathway, but reaches full activation only when associated with telomeric-repeat-containing RNA (TERRA) transcripts that are synthesized from dysfunctional telomeres. TERRA-bound ZBP1 oligomerizes into filaments on the outer mitochondrial membrane of a subset of mitochondria, where it activates the innate immune adapter protein mitochondrial antiviral-signalling protein (MAVS). We propose that these oligomerization properties of ZBP1 serve as a signal amplification mechanism, where few TERRA-ZBP1 interactions are sufficient to launch a detrimental MAVS-dependent interferon response. Our study reveals a mechanism for telomere-mediated tumour suppression, whereby dysfunctional telomeres activate innate immune responses through mitochondrial TERRA-ZBP1 complexes to eliminate cells destined for neoplastic transformation.

The APOBEC3 (A3) proteins are host antiviral cellular proteins that hypermutate the viral genome of diverse viral families. In retroviruses, this process requires A3 packaging into viral particles1-4. The lentiviruses encode a protein Vif that antagonizes A3 family members by targeting them for degradation. Diversification of A3 allows host escape from Vif whereas adaptations in Vif enable cross-species transmission of primate lentiviruses. How this molecular arms race plays out at the structural level is unknown. Here, we report the cryogenic electron microscopy structure of human APOBE3G (A3G) bound to HIV-1 Vif and hijacked cellular proteins that promote ubiquitin mediated proteolysis. A small surface explains the molecular arms race, including a cross-species transmission event that led to the birth of HIV-1. Unexpectedly, we find RNA is a molecular glue for the Vif-A3G interaction, enabling Vif to repress A3G by ubiquitin dependent and independent mechanisms. Our results suggest a model where Vif antagonizes A3G by intercepting it in its most dangerous form for the virus, when bound to RNA and on pathway to packaging, to prevent viral restriction. By engaging essential surfaces required for restriction, Vif exploits a vulnerability in A3G, suggesting a general mechanism where RNA binding helps position key residues necessary for viral antagonism of a host antiviral gene.

In all organisms, innate immune pathways sense infection and rapidly activate potent immune responses while avoiding inappropriate activation (autoimmunity). In humans, the innate immune receptor cyclic GMP-AMP synthase (cGAS) detects viral infection to produce the nucleotide second messenger cyclic GMP-AMP (cGAMP), which initiates stimulator of interferon genes (STING)-dependent antiviral signalling1. Bacteria encode evolutionary predecessors of cGAS called cGAS/DncV-like nucleotidyltransferases2 (CD-NTases), which detect bacteriophage infection and produce diverse nucleotide second messengers3. How bacterial CD-NTase activation is controlled remains unknown. Here we show that CD-NTase-associated protein 2 (Cap2) primes bacterial CD-NTases for activation through a ubiquitin transferase-like mechanism. A cryo-electron microscopy structure of the Cap2-CD-NTase complex reveals Cap2 as an all-in-one ubiquitin transferase-like protein, with distinct domains resembling eukaryotic E1 and E2 proteins. The structure captures a reactive-intermediate state with the CD-NTase C terminus positioned in the Cap2 E1 active site and conjugated to AMP. Cap2 conjugates the CD-NTase C terminus to a target molecule that primes the CD-NTase for increased cGAMP production. We further demonstrate that a specific endopeptidase, Cap3, balances Cap2 activity by cleaving CD-NTase-target conjugates. Our data demonstrate that bacteria control immune signalling using an ancient, minimized ubiquitin transferase-like system and provide insight into the evolution of the E1 and E2 machinery across domains of life.

Temperature is a fundamental sensory modality separate from touch, with dedicated receptor channels and primary afferent neurons for cool and warm1-3. Unlike for other modalities, however, the cortical encoding of temperature remains unknown, with very few cortical neurons reported that respond to non-painful temperature, and the presence of a 'thermal cortex' is debated4-8. Here, using widefield and two-photon calcium imaging in the mouse forepaw system, we identify cortical neurons that respond to cooling and/or warming with distinct spatial and temporal response properties. We observed a representation of cool, but not warm, in the primary somatosensory cortex, but cool and warm in the posterior insular cortex (pIC). The representation of thermal information in pIC is robust and somatotopically arranged, and reversible manipulations show a profound impact on thermal perception. Despite being positioned along the same one-dimensional sensory axis, the encoding of cool and that of warm are distinct, both in highly and broadly tuned neurons. Together, our results show that pIC contains the primary cortical representation of skin temperature and may help explain how the thermal system generates sensations of cool and warm.

Thousands of genetic variants in protein-coding genes have been linked to disease. However, the functional impact of most variants is unknown as they occur within intrinsically disordered protein regions that have poorly defined functions1-3. Intrinsically disordered regions can mediate phase separation and the formation of biomolecular condensates, such as the nucleolus4,5. This suggests that mutations in disordered proteins may alter condensate properties and function6-8. Here we show that a subset of disease-associated variants in disordered regions alter phase separation, cause mispartitioning into the nucleolus and disrupt nucleolar function. We discover de novo frameshift variants in HMGB1 that cause brachyphalangy, polydactyly and tibial aplasia syndrome, a rare complex malformation syndrome. The frameshifts replace the intrinsically disordered acidic tail of HMGB1 with an arginine-rich basic tail. The mutant tail alters HMGB1 phase separation, enhances its partitioning into the nucleolus and causes nucleolar dysfunction. We built a catalogue of more than 200,000 variants in disordered carboxy-terminal tails and identified more than 600 frameshifts that create arginine-rich basic tails in transcription factors and other proteins. For 12 out of the 13 disease-associated variants tested, the mutation enhanced partitioning into the nucleolus, and several variants altered rRNA biogenesis. These data identify the cause of a rare complex syndrome and suggest that a large number of genetic variants may dysregulate nucleoli and other biomolecular condensates in humans.

Quantum computation (QC) features known examples of hardware acceleration for certain problems but is challenging to realize due to its susceptibility to small errors from noise or imperfect control. The principles of fault tolerance may enable computational acceleration with imperfect hardware, but they place strict requirements on the character and correlation of errors [1]. For many qubit technologies [2-21], some challenges to achieving fault tolerance can be traced to correlated errors arising from the need to control qubits by injecting microwave energy matching qubit resonances. Here we demonstrate an alternative approach to QC that utilizes energy-degenerate encoded qubit states controlled by nearest-neighbor contact interactions that partially swap the spin states of electrons with those of their neighbors. Calibrated sequences of such partial SWAPs, implemented using only voltage pulses, allow universal quantum control while bypassing microwave-associated correlated error sources [1, 22-28]. We use an array of six 28Si/SiGe quantum dots, built using a platform that is capable of extending in two dimensions following processes used in conventional microelectronics [29]. We quantify the operational fidelity of universal control of two encoded qubits using interleaved randomized benchmarking [30], finding a fidelity of 96.3 ± 0.7% for encoded controlled-NOT operations and 99.3 ± 0.5% for encoded SWAP. The quantum coherence offered by enriched silicon [5-9, 16, 18, 20, 22, 27, 29, 31-37], the all-electrical and low-crosstalk-control of partial swap operations [1, 22-28], and the configurable insensitivity of our encoding to certain error sources [28, 33, 34, 38] all combine to offer a strong pathway toward scalable fault tolerance and computational advantage.

Single-cell technologies have enabled the characterization of the tumour microenvironment at unprecedented depth and have revealed vast cellular diversity among tumour cells and their niche. Anti-tumour immunity relies on cell-cell relationships within the tumour microenvironment1,2, yet many single-cell studies lack spatial context and rely on dissociated tissues3. Here we applied imaging mass cytometry to characterize the immunological landscape of 139 high-grade glioma and 46 brain metastasis tumours from patients. Single-cell analysis of more than 1.1 million cells across 389 high-dimensional histopathology images enabled the spatial resolution of immune lineages and activation states, revealing differences in immune landscapes between primary tumours and brain metastases from diverse solid cancers. These analyses revealed cellular neighbourhoods associated with survival in patients with glioblastoma, which we leveraged to identify a unique population of myeloperoxidase (MPO)-positive macrophages associated with long-term survival. Our findings provide insight into the biology of primary and metastatic brain tumours, reinforcing the value of integrating spatial resolution to single-cell datasets to dissect the microenvironmental contexture of cancer.

Single-cell technologies have revealed the complexity of the tumour immune microenvironment with unparalleled resolution1-9. Most clinical strategies rely on histopathological stratification of tumour subtypes, yet the spatial context of single-cell phenotypes within these stratified subgroups is poorly understood. Here we apply imaging mass cytometry to characterize the tumour and immunological landscape of samples from 416 patients with lung adenocarcinoma across five histological patterns. We resolve more than 1.6 million cells, enabling spatial analysis of immune lineages and activation states with distinct clinical correlates, including survival. Using deep learning, we can predict with high accuracy those patients who will progress after surgery using a single 1-mm2 tumour core, which could be informative for clinical management following surgical resection. Our dataset represents a valuable resource for the non-small cell lung cancer research community and exemplifies the utility of spatial resolution within single-cell analyses. This study also highlights how artificial intelligence can improve our understanding of microenvironmental features that underlie cancer progression and may influence future clinical practice.

Brain anatomy provides key evidence for the relationships between ray-finned fishes1, but two major limitations obscure our understanding of neuroanatomical evolution in this major vertebrate group. First, the deepest branching living lineages are separated from the group's common ancestor by hundreds of millions of years, with indications that aspects of their brain morphology-like other aspects of their anatomy2,3-are specialized relative to primitive conditions. Second, there are no direct constraints on brain morphology in the earliest ray-finned fishes beyond the coarse picture provided by cranial endocasts: natural or virtual infillings of void spaces within the skull4-8. Here we report brain and cranial nerve soft-tissue preservation in Coccocephalus wildi, an approximately 319-million-year-old ray-finned fish. This example of a well-preserved vertebrate brain provides a window into neural anatomy deep within ray-finned fish phylogeny. Coccocephalus indicates a more complicated pattern of brain evolution than suggested by living species alone, highlighting cladistian apomorphies1 and providing temporal constraints on the origin of traits uniting all extant ray-finned fishes1,9. Our findings, along with a growing set of studies in other animal groups10-12, point to the importance of ancient soft tissue preservation in understanding the deep evolutionary assembly of major anatomical systems outside of the narrow subset of skeletal tissues13-15.

The SARS-CoV-2 RNA-dependent RNA polymerase coordinates viral RNA synthesis as part of an assembly known as the replication-transcription complex (RTC)1. Accordingly, the RTC is a target for clinically approved antiviral nucleoside analogues, including remdesivir2. Faithful synthesis of viral RNAs by the RTC requires recognition of the correct nucleotide triphosphate (NTP) for incorporation into the nascent RNA. To be effective inhibitors, antiviral nucleoside analogues must compete with the natural NTPs for incorporation. How the SARS-CoV-2 RTC discriminates between the natural NTPs, and how antiviral nucleoside analogues compete, has not been discerned in detail. Here, we use cryogenic-electron microscopy to visualize the RTC bound to each of the natural NTPs in states poised for incorporation. Furthermore, we investigate the RTC with the active metabolite of remdesivir, remdesivir triphosphate (RDV-TP), highlighting the structural basis for the selective incorporation of RDV-TP over its natural counterpart adenosine triphosphate3,4. Our results explain the suite of interactions required for NTP recognition, informing the rational design of antivirals. Our analysis also yields insights into nucleotide recognition by the nsp12 NiRAN (nidovirus RdRp-associated nucleotidyltransferase), an enigmatic catalytic domain essential for viral propagation5. The NiRAN selectively binds guanosine triphosphate, strengthening proposals for the role of this domain in the formation of the 5' RNA cap6.

Antibody responses during infection and vaccination typically undergo affinity maturation to achieve high-affinity binding for efficient neutralization of pathogens1,2. Similarly, high affinity is routinely the goal for therapeutic antibody generation. However, in contrast to naturally occurring or direct-targeting therapeutic antibodies, immunomodulatory antibodies, which are designed to modulate receptor signalling, have not been widely examined for their affinity-function relationship. Here we examine three separate immunologically important receptors spanning two receptor superfamilies: CD40, 4-1BB and PD-1. We show that low rather than high affinity delivers greater activity through increased clustering. This approach delivered higher immune cell activation, in vivo T cell expansion and antitumour activity in the case of CD40. Moreover, an inert anti-4-1BB monoclonal antibody was transformed into an agonist. Low-affinity variants of the clinically important antagonistic anti-PD-1 monoclonal antibody nivolumab also mediated more potent signalling and affected T cell activation. These findings reveal a new paradigm for augmenting agonism across diverse receptor families and shed light on the mechanism of antibody-mediated receptor signalling. Such affinity engineering offers a rational, efficient and highly tuneable solution to deliver antibody-mediated receptor activity across a range of potencies suitable for translation to the treatment of human disease.