Mendel1 studied in detail seven pairs of contrasting traits in pea (Pisum sativum), establishing the foundational principles of genetic inheritance. Here we investigate the genetic architecture that underlies these traits and uncover previously undescribed alleles for the four characterized Mendelian genes2-7, including a rare revertant of Mendel's white-flowered a allele. Primarily, we focus on the three remaining uncharacterized traits and find that (1) an approximately 100-kb genomic deletion upstream of the Chlorophyll synthase (ChlG) gene disrupts chlorophyll biosynthesis through the generation of intergenic transcriptional fusion products, conferring the yellow pod phenotype of gp mutants; (2) a MYB gene with an upstream Ogre element insertion and a CLE peptide-encoding gene with an in-frame premature stop codon explain the v and p alleles, which disrupt secondary cell wall thickening and lignification, resulting in the parchmentless, edible-pod phenotype; and (3) a 5-bp exonic deletion in a CIK-like co-receptor kinase gene, in combination with a genetic modifier locus, is associated with the fasciated stem (fa) phenotype. Furthermore, we characterize genes and alleles associated with diverse agronomic traits, such as axil ring anthocyanin pigmentation, seed size and the 'semi-leafless' form. This study establishes a foundation for fundamental research, education in biology and genetics, and pea breeding practices.

Understanding the relationship between antibiotic use and the evolution of antimicrobial resistance is vital for effective antibiotic stewardship. Yet, animal models and in vitro experiments poorly replicate real-world conditions1. To explain how resistance evolves in vivo, we exposed 60 human participants to ciprofloxacin and used longitudinal stool samples and a new computational method to assemble the genomes of 5,665 populations of commensal bacterial species within participants. Analysis of 2.3 million polymorphic sequence variants revealed 513 populations that underwent selective sweeps. We found convergent evolution focused on DNA gyrase and evidence of dispersed selective pressure at other genomic loci. Roughly 10% of susceptible bacterial populations evolved towards resistance through sweeps that involved substitutions at a specific amino acid in gyrase. The evolution of gyrase was associated with large populations that decreased in relative abundance during exposure. Sweeps persisted for more than 10 weeks in most cases and were not projected to revert within a year. Targeted amplification showed that gyrase mutations arose de novo within the participants and exhibited no measurable fitness cost. These findings revealed that brief ciprofloxacin exposure drives the evolution of resistance in gut commensals, with mutations persisting long after exposure. This study underscores the capacity of the human gut to promote the evolution of resistance and identifies key genomic and ecological factors that shape bacterial adaptation in vivo.

Environmental thermal challenges trigger the brain to coordinate both autonomic and behavioural responses to maintain optimal body temperature1-4. It is unknown how temperature information is precisely stored and retrieved in the brain and how it is converted into a physiological response. Here we investigated whether memories could control whole-body metabolism by training mice to remember a thermal challenge. Mice were conditioned to associate a context with a specific temperature by combining thermoregulatory Pavlovian conditioning with engram-labelling technology, optogenetics and chemogenetics. We report that if mice are returned to an environment in which they previously experienced a 4 °C cold challenge, they increase their metabolic rates regardless of the actual environmental temperature. Furthermore, we show that mice have increased hypothalamic activity when they are exposed to the cold, and that a specific network emerges between the hippocampus and the hypothalamus during the recall of a cold memory. Both natural retrieval and artificial reactivation of cold-sensitive memory engrams in the hippocampus mimic the physiological responses that are seen during a cold challenge. These ensembles are necessary for cold-memory retrieval. These findings show that retrieval of a cold memory causes whole-body autonomic and behavioural responses that enable mice to maintain thermal homeostasis.

Somatosensory neurons encode detailed information about touch and temperature and are the peripheral drivers of pain1,2. Here by combining functional imaging with multiplexed in situ hybridization3, we determined how heat and mechanical stimuli are encoded across neuronal classes and how inflammation transforms this representation to induce heat hypersensitivity, mechanical allodynia and continuing pain. Our data revealed that trigeminal neurons innervating the cheek exhibited complete segregation of responses to gentle touch and heat. By contrast, heat and noxious mechanical stimuli broadly activated nociceptor classes, including cell types proposed to trigger select percepts and behaviours4-6. Injection of the inflammatory mediator prostaglandin E2 caused long-lasting activity and thermal sensitization in select classes of nociceptors, providing a cellular basis for continuing inflammatory pain and heat hypersensitivity. We showed that the capsaicin receptor TRPV1 (ref. 7) has a central role in heat sensitization but not in spontaneous nociceptor activity. Unexpectedly, the responses to mechanical stimuli were minimally affected by inflammation, suggesting that tactile allodynia results from the continuing firing of nociceptors coincident with touch. Indeed, we have demonstrated that nociceptor activity is both necessary and sufficient for inflammatory tactile allodynia. Together, these findings refine models of sensory coding and discrimination at the cellular and molecular levels, demonstrate that touch and temperature are broadly but differentially encoded across transcriptomically distinct populations of sensory cells and provide insight into how cellular-level responses are reshaped by inflammation to trigger diverse aspects of pain.

Glacial cycles significantly influenced Earth's surface processes throughout the Quaternary, impacting the climate, sea level, and seismic and magmatic activity1-3. However, the effects of glaciation and deglaciation (that is, glacial forcing) on lithospheric motion are unknown. To study these effects, we formulated high-resolution numerical models with realistic lithospheric structures, including weak plate margins, lithospheric thickness variations and crustal structure. Our results show that glacial forcing significantly altered lithospheric motion and the spreading rates of mid-ocean ridges situated near major ice sheets in the last glacial cycle. For example, deglaciation-induced motion in the North American plate had a rotational part that was up to around 25% of its tectonic plate motion over 10,000-year timescales. The deglaciation in Greenland and Fennoscandia caused up to 40% fluctuations in the spreading rates of the Iceland Ridge between 12,000 and 6,000 years ago, which may explain the Holocene volcanism in Iceland. Our modelling also indicates increased (decreased) rates of global sea-floor production during the deglaciation (glaciation) periods with implications for mantle degassing rates. These results underscore the critical dynamic interplay between glacial cycles, lithospheric motion, ridge spreading and climate during ice ages.

Patients with treatment-refractory pancreatic cancer often succumb to systemic metastases1-3; however, the transcriptomic heterogeneity that underlies therapeutic recalcitrance remains understudied, particularly in a spatial context. Here we construct high-resolution maps of lineage states, clonal architecture and the tumour microenvironment (TME) using spatially resolved transcriptomics from 55 samples of primary tumour and metastases (liver, lung and peritoneum) collected from rapid autopsies of 13 people. We observe discernible transcriptomic shifts in cancer-cell lineage states as tumours transition from primary sites to organ-specific metastases, with the most pronounced intra-patient distinctions between liver and lung. Phylogenetic trees constructed from inferred copy number variations in primary and metastatic loci in each patient highlight diverse patient-specific evolutionary trajectories and clonal dissemination. We show that multiple tumour lineage states co-exist in each tissue, including concurrent metastatic foci in the same organ. Agnostic to tissue site, lineage states correlate with distinct TME features, such as the spatial proximity of TGFB1-expressing myofibroblastic cancer-associated fibroblasts (myCAFs) to aggressive 'basal-like' cancer cells, but not to cells in the 'classical' or 'intermediate' states. These findings were validated through orthogonal and cross-species analyses using mouse tissues and patient-derived organoids. Notably, basal-like cancer cells aligned with myCAFs correlate with plasma-cell exclusion from the tumour milieu, and neighbouring cell analyses suggest that CXCR4-CXCL12 signalling is the underlying basis for observed immune exclusion. Collectively, our findings underscore the profound transcriptomic heterogeneity and microenvironmental dynamics that characterize treatment-refractory pancreatic cancer.

The coupling between electrons and phonons is one of the fundamental interactions in solids, underpinning a wide range of phenomena, such as resistivity, heat conductivity and superconductivity. However, direct measurements of this coupling for individual phonon modes remain a substantial challenge. In this work, we introduce a new technique for mapping phonon dispersions and electron-phonon coupling (EPC) in van der Waals (vdW) materials. By generalizing the quantum twisting microscope1 (QTM) to cryogenic temperatures, we demonstrate its capability to map not only electronic dispersions through elastic momentum-conserving tunnelling but also phononic dispersions through inelastic momentum-conserving tunnelling. Crucially, the inelastic tunnelling strength provides a direct and quantitative measure of the momentum and mode-resolved EPC. We use this technique to measure the phonon spectrum and EPC of twisted bilayer graphene (TBG) with twist angles larger than 6°. Notably, we find that, unlike standard acoustic phonons, whose coupling to electrons diminishes as their momentum tends to zero, TBG exhibits a low-energy mode whose coupling increases with decreasing twist angle. We show that this unusual coupling arises from the modulation of the interlayer tunnelling by a layer-antisymmetric 'phason' mode of the moiré system. The technique demonstrated here opens the way for examining a large variety of other neutral collective modes that couple to electronic tunnelling, including plasmons2, magnons3 and spinons4 in quantum materials.

Beneath oceanic spreading centres, the lithosphere-asthenosphere boundary (LAB) acts as a permeability barrier that focuses the delivery of melt from deep within the mantle towards the spreading axis1. At intermediate-spreading to fast-spreading ridge crests, the multichannel seismic reflection technique has imaged a nearly flat, 1-2-km-wide axial magma lens (AML)2 that defines the uppermost section of the LAB3, but the nature of the LAB deeper into the crust has been more elusive, with some clues gained from tomographic images, providing only a diffuse view of a wider halo of lower-velocity material seated just beneath the AML4. Here we present 3D seismic reflection images of the LAB extending deep (5-6 km) into the crust beneath Axial volcano, located at the intersection of the Juan de Fuca Ridge and the Cobb-Eickelberg hotspot. The 3D shape of the LAB, which is coincident with a thermally controlled magma assimilation front, focuses hotspot-related and mid-ocean-spreading-centre-related magmatism towards the centre of the volcano, controlling both eruption and hydrothermal processes and the chemical composition of erupted lavas5. In this context, the LAB can be viewed as the upper surface of a 'magma domain', a volume within which melt bodies reside (replacing the concept of a single 'magma reservoir')6. Our discovery of a funnel-shaped, crustal LAB suggests that thermally controlled magma assimilation could be occurring along this surface at other volcanic systems, such as Iceland.

Intrinsically disordered regions within proteins drive specific molecular functions despite lacking a defined structure1,2. Although disordered regions are integral to controlling mRNA stability and translation, the mechanisms underlying these regulatory effects remain unclear3. Here we reveal the molecular determinants of this activity using high-throughput functional profiling. Systematic mutagenesis across hundreds of regulatory disordered elements, combined with machine learning, reveals a complex pattern of molecular features important for their activity. The presence and arrangement of aromatic residues strongly predicts the ability of seemingly diverse protein sequences to influence mRNA stability and translation. We further show how many of these regulatory elements exert their effects by engaging core mRNA decay machinery. Our results define molecular features and biochemical pathways that explain how disordered regions control mRNA expression and shed light on broader principles within functional, unstructured proteins.

Clonal haematopoiesis of indeterminate potential (CHIP) involves the gradual expansion of mutant pre-leukaemic haematopoietic cells, which increases with age and confers a risk for multiple diseases, including leukaemia and immune-related conditions1. Although the absolute risk of leukaemic transformation in individuals with CHIP is very low, the strongest predictor of progression is the accumulation of mutant haematopoietic cells2. Despite the known associations between CHIP and increased all-cause mortality, our understanding of environmental and regulatory factors that underlie this process during ageing remains rudimentary. Here we show that intestinal alterations, which can occur with age, lead to systemic dissemination of a microbial metabolite that promotes pre-leukaemic cell expansion. Specifically, ADP-D-glycero-β-D-manno-heptose (ADP-heptose), a biosynthetic bi-product specific to Gram-negative bacteria3-5, is uniquely found in the circulation of older individuals and favours the expansion of pre-leukaemic cells. ADP-heptose is also associated with increased inflammation and cardiovascular risk in CHIP. Mechanistically, ADP-heptose binds to its receptor, ALPK1, triggering transcriptional reprogramming and NF-κB activation that endows pre-leukaemic cells with a competitive advantage due to excessive clonal proliferation. Collectively, we identify that the accumulation of ADP-heptose represents a direct link between ageing and expansion of rare pre-leukaemic cells, suggesting that the ADP-heptose-ALPK1 axis is a promising therapeutic target to prevent progression of CHIP to overt leukaemia and immune-related conditions.

Pancreatic ductal adenocarcinoma (PDAC) subsists in a nutrient-deregulated microenvironment, making it particularly susceptible to treatments that interfere with cancer metabolism1,2. For example, PDAC uses, and is dependent on, high levels of autophagy and other lysosomal processes3-5. Although targeting these pathways has shown potential in preclinical studies, progress has been hampered by the difficulty in identifying and characterizing favourable targets for drug development6. Here, we characterize PIKfyve, a lipid kinase that is integral to lysosomal functioning7, as a targetable vulnerability in PDAC. Using a genetically engineered mouse model, we established that PIKfyve is essential to PDAC progression. Furthermore, through comprehensive metabolic analyses, we found that PIKfyve inhibition forces PDAC to upregulate a distinct transcriptional and metabolic program favouring de novo lipid synthesis. In PDAC, the KRAS-MAPK signalling pathway is a primary driver of de novo lipid synthesis. Accordingly, simultaneously targeting PIKfyve and KRAS-MAPK resulted in the elimination of the tumour burden in numerous preclinical human and mouse models. Taken together, these studies indicate that disrupting lipid metabolism through PIKfyve inhibition induces synthetic lethality in conjunction with KRAS-MAPK-directed therapies for PDAC.

Understanding the human de novo mutation (DNM) rate requires complete sequence information1. Here using five complementary short-read and long-read sequencing technologies, we phased and assembled more than 95% of each diploid human genome in a four-generation, twenty-eight-member family (CEPH 1463). We estimate 98-206 DNMs per transmission, including 74.5 de novo single-nucleotide variants, 7.4 non-tandem repeat indels, 65.3 de novo indels or structural variants originating from tandem repeats, and 4.4 centromeric DNMs. Among male individuals, we find 12.4 de novo Y chromosome events per generation. Short tandem repeats and variable-number tandem repeats are the most mutable, with 32 loci exhibiting recurrent mutation through the generations. We accurately assemble 288 centromeres and six Y chromosomes across the generations and demonstrate that the DNM rate varies by an order of magnitude depending on repeat content, length and sequence identity. We show a strong paternal bias (75-81%) for all forms of germline DNM, yet we estimate that 16% of de novo single-nucleotide variants are postzygotic in origin with no paternal bias, including early germline mosaic mutations. We place all this variation in the context of a high-resolution recombination map (~3.4 kb breakpoint resolution) and find no correlation between meiotic crossover and de novo structural variants. These near-telomere-to-telomere familial genomes provide a truth set to understand the most fundamental processes underlying human genetic variation.

Bridge-like lipid-transport proteins (BLTPs) are an evolutionarily conserved family of proteins that localize to membrane-contact sites and are thought to mediate the bulk transfer of lipids from a donor membrane, typically the endoplasmic reticulum, to an acceptor membrane, such as that of the cell or an organelle1. Although BLTPs are fundamentally important for a wide array of cellular functions, their architecture, composition and lipid-transfer mechanisms remain poorly characterized. Here we present the subunit composition and the cryogenic electron microscopy structure of the native LPD-3 BLTP complex isolated from transgenic Caenorhabditis elegans. LPD-3 folds into an elongated, rod-shaped tunnel of which the interior is filled with ordered lipid molecules that are coordinated by a track of ionizable residues that line one side of the tunnel. LPD-3 forms a complex with two previously uncharacterized proteins, one of which we have named Spigot and the other of which remains unnamed. Spigot interacts with the N-terminal end of LPD-3 where lipids are expected to enter the tunnel, and experiments in multiple model systems indicate that Spigot has a conserved role in BLTP function. Our LPD-3 complex structural data reveal protein-lipid interactions that suggest a model for how the native LPD-3 complex mediates bulk lipid transport and provides a foundation for mechanistic studies of BLTPs.

Several hydrogen-rich superconductors have been found to show unprecedentedly high critical temperatures1-4, stimulating investigations into the nature of the superconductivity in these materials. Although their macroscopic superconducting properties are established1,5-7, microscopic insights into the pairing mechanism remains unclear. Here we characterize the superconducting gap structure in the high-temperature superconductor H3S and its deuterium counterpart D3S by performing tunnelling spectroscopy measurements. The tunnelling spectra reveal that H3S and D3S both have a fully gapped structure, which could be well described by a single s-wave Dynes model, with gap values 2Δ of approximately 60 meV and 44 meV, respectively. Furthermore, we observed gap features of another likely H-depleted HxS superconducting phase in a poorly synthesized hydrogen sulfide sample. Our work offers direct experimental evidence for superconductivity in the hydrogen-rich superconductor H3S from a microscopic perspective. It validates the phonon-mediated mechanism of superconducting pairing and provides a foundation for further understanding the origins of high-temperature superconductivity in hydrogen-rich compounds.

Recent breakthroughs in ultrathin, single-crystalline, freestanding complex oxide systems have sparked industry interest in their potential for next-generation commercial devices1,2. However, the mass production of these ultrathin complex oxide membranes has been hindered by the challenging requirement of inserting an artificial release layer between the epilayers and substrates3,4. Here we introduce a technique that achieves atomic precision lift-off of ultrathin membranes without artificial release layers to facilitate the high-throughput production of scalable, ultrathin, freestanding perovskite systems. Leveraging both theoretical insights and empirical evidence, we have identified the pivotal role of lead in weakening the interface. This insight has led to the creation of a universal exfoliation strategy that enables the production of diverse ultrathin perovskite membranes less than 10 nm. Our pyroelectric membranes demonstrate a record-high pyroelectric coefficient of 1.76 × 10-2 C m-2 K-1, attributed to their exceptionally low thickness and freestanding nature. Moreover, this method offers an approach to manufacturing cooling-free detectors that can cover the full far-infrared spectrum, marking a notable advancement in detector technology5.

Neuroimmune interactions-signals transmitted between immune and brain cells-regulate many aspects of tissue physiology1, including responses to psychological stress2-5, which can predispose individuals to develop neuropsychiatric diseases6-9. Still, the interactions between haematopoietic and brain-resident cells that influence complex behaviours are poorly understood. Here, we use a combination of genomic and behavioural screens to show that astrocytes in the amygdala limit stress-induced fear behaviour through epidermal growth factor receptor (EGFR). Mechanistically, EGFR expression in amygdala astrocytes inhibits a stress-induced, pro-inflammatory signal-transduction cascade that facilitates neuron-glial crosstalk and stress-induced fear behaviour through the orphan nuclear receptor NR2F2 in amygdala neurons. In turn, decreased EGFR signalling and fear behaviour are associated with the recruitment of meningeal monocytes during chronic stress. This set of neuroimmune interactions is therapeutically targetable through the administration of psychedelic compounds, which reversed the accumulation of monocytes in the brain meninges along with fear behaviour. Together with validation in clinical samples, these data suggest that psychedelics can be used to target neuroimmune interactions relevant to neuropsychiatric disorders and potentially other inflammatory diseases.

The body of an animal influences how its nervous system generates behaviour1. Accurately modelling the neural control of sensorimotor behaviour requires an anatomically detailed biomechanical representation of the body. Here we introduce a whole-body model of the fruit fly Drosophila melanogaster in a physics simulator2. Designed as a general-purpose framework, our model enables the simulation of diverse fly behaviours, including both terrestrial and aerial locomotion. We validate its versatility by replicating realistic walking and flight behaviours. To support these behaviours, we develop phenomenological models for fluid and adhesion forces. Using data-driven, end-to-end reinforcement learning3,4, we train neural network controllers capable of generating naturalistic locomotion5-7 along complex trajectories in response to high-level steering commands. Furthermore, we show the use of visual sensors and hierarchical motor control8, training a high-level controller to reuse a pretrained low-level flight controller to perform visually guided flight tasks. Our model serves as an open-source platform for studying the neural control of sensorimotor behaviour in an embodied context.

Incidence rates of colorectal cancer vary geographically and have changed over time1. Notably, in the past two decades, the incidence of early-onset colorectal cancer, which affects individuals below 50 years of age, has doubled in many countries2-5. The reasons for this increase are unknown. Here we investigate whether mutational processes contribute to geographic and age-related differences by examining 981 colorectal cancer genomes from 11 countries. No major differences were found in microsatellite-unstable cancers, but variations in mutation burden and signatures were observed in the 802 microsatellite-stable cases. Multiple signatures, most with unknown aetiologies, exhibited varying prevalence in Argentina, Brazil, Colombia, Russia and Thailand, indicating geographically diverse levels of mutagenic exposure. Signatures SBS88 and ID18, caused by the bacteria-produced mutagen colibactin6,7, had higher mutation loads in countries with higher colorectal cancer incidence rates. SBS88 and ID18 were also enriched in early-onset colorectal cancers, being 3.3 times more common in individuals who were diagnosed before 40 years of age than in those over 70 years of age, and were imprinted early during colorectal cancer development. Colibactin exposure was further linked to APC driver mutations, with ID18 being responsible for about 25% of APC driver indels in colibactin-positive cases. This study reveals geographic and age-related variations in colorectal cancer mutational processes, and suggests that mutagenic exposure to colibactin-producing bacteria in early life may contribute to the increasing incidence of early-onset colorectal cancer.

Engineering and characterizing proteins can be time-consuming and cumbersome, motivating the development of generalist CRISPR-Cas enzymes1-4 to enable diverse genome-editing applications. However, such enzymes have caveats such as an increased risk of off-target editing3,5,6. Here, to enable scalable reprogramming of Cas9 enzymes, we combined high-throughput protein engineering with machine learning to derive bespoke editors that are more uniquely suited to specific targets. Through structure-function-informed saturation mutagenesis and bacterial selections, we obtained nearly 1,000 engineered SpCas9 enzymes and characterized their protospacer-adjacent motif (PAM)7 requirements to train a neural network that relates amino acid sequence to PAM specificity. By utilizing the resulting PAM machine learning algorithm (PAMmla) to predict the PAMs of 64 million SpCas9 enzymes, we identified efficacious and specific enzymes that outperform evolution-based and engineered SpCas9 enzymes as nucleases and base editors in human cells while reducing off-targets. An in silico-directed evolution method enables user-directed Cas9 enzyme design, including for allele-selective targeting of the RHOP23H allele in human cells and mice. Together, PAMmla integrates machine learning and protein engineering to curate a catalogue of SpCas9 enzymes with distinct PAM requirements, motivating a shift away from generalist enzymes towards safe and efficient bespoke Cas9 variants.

Poxviruses cause severe diseases including smallpox and mpox, which pose major threats to human health. The poxvirus core protease (CorePro) is essential for viral maturation and highly conserved in poxviruses, making it an attractive antiviral target1. However, the structure of CorePro remains unknown, hampering antiviral development. Here, we determined the structures of mpox virus (MPXV) apo-CorePro and its complex with an inhibitor aloxistatin, which is a drug candidate for muscular dystrophy2. These structures show that CorePro forms a homodimer featuring a unique "dancing-couple" fold. The catalytic intermediate state of CorePro was characterized by an aldehyde derivative from a natural substrate (I-G18). This derivative covalently binds to the catalytic cysteine 328 (Cys328), making the active site of viral protease shift from a closed conformation in the apo-form to a favorable open conformation upon substrate binding. Based on the CorePro-I-G18 complex, we then designed a series of peptidomimetic inhibitors with a nitrile warhead, which could covalently anchor with the catalytic Cys328. These compounds inhibit the CorePro with IC50 values of 44.9-100.3 nM, exhibiting potent and broad anti-poxvirus activity as well. Our studies provide the basis for designing wide-spectrum inhibitors against poxvirus infections.