Although the green revolution adapted a handful of crops to homogeneous and high-input industrialized agriculture, much of the global population still relies on the local production of variable crop cultivars by low-input smallholder farms. This diversity of unhomogenized crops1, like that of the grain and bioenergy crop sorghum2-5, offers raw materials for genetic gain and cultivar improvement. However, breeding efforts can be constrained by highly specialized traits and breeding targets6. Here, to bridge this diversity, we constructed a 33-member pangenome reference and a diversity panel across 1,984 cultivars and landraces. We leveraged these resources to explore the complex interplay among historical contingency, ongoing adaptation and previously uncharacterized structural diversity. Specifically, our analyses conclusively demonstrated multiple nested and deeply diverged structural variants in the domestication gene SHATTERING1, which distinguish the previously established multicentric origin of sorghum. We then applied landscape genomics to reveal how gene flow and secondary contact created the complex genetic mosaic in contemporary breeding networks. As proof of concept for pangenome-accelerated trait discovery, we connected biosynthetic gene cluster structural variation to phenotypic leaf concentration of the cyanogenic glucoside dhurrin. Combined, these approaches will accelerate breeding and trait discovery and provide a framework for similar applications in other crops.

Immune responses to parasite infection involve the increased production of basophils and eosinophils. These two myeloid cell types have key roles in type 2 anti-parasite immunity1 and rely on GATA family transcription factors for their specification2,3. The first committed step in basophil and eosinophil production is generation of basophil-eosinophil-mast cell progenitors (BEMPs) from oligopotent erythroid-primed multipotent progenitors (EMPPs). However, it is not well established how immune responses act on progenitors to initiate type 2 myelopoiesis. Here we show that infection with the helminth Heligmosomoides polygyrus increases EMPP commitment to myeloid fate at the expense of erythropoiesis. Upon infection with H. polygyrus, the IL-33 alarmin accumulated in the bone marrow, causing EMPPs to upregulate the GATA co-factor LMO4 and preferentially differentiate into myeloid cells. LMO4 was sufficient to instruct myeloid fate in EMPPs by interacting with GATA2, displacing the FOG1 co-factor and redistributing GATA binding from megakaryocyte-erythroid-specific to basophil, eosinophil and mast cell (BEM)-specific chromatin. Accordingly, mice carrying a GATA2 mutation that selectively impairs the LMO4-GATA2 interaction were deficient in GATA factor allocation to BEM chromatin, myeloid lineage commitment, basophil and eosinophil production, and parasite control. This identifies LMO4 as an IL-33-regulated master regulator of type 2 myelopoiesis, and transcription factor reallocation as a mechanism of lineage commitment.

Globally, as many as 12 million girls marry before the age of 18 every year; in northern Nigeria, 80% of girls marry before 18 (refs. 1,2). Although such marriages may be deemed the best available option by many girls and parents, numerous studies suggest that, when delayed marriage is made possible, it benefits educational attainment, improves health by reducing maternal mortality and morbidity, and leads to many other benefits to girls' lives3-8. Despite this, little is known about what reduces child marriage, and successful interventions tend to have an impact of just a few percentage points. We use a paired cluster-randomized trial in 18 communities to rigorously evaluate a locally tailored big-push intervention called Pathways to Choice in northern Nigeria. We show that Pathways decreases rates of marriage among adolescent girls from 86% in the control group to only 21% in the treatment group-just over an 80% decrease. Although a key part of Pathways' effect is a significant increase in girls re-enrolling in school, education alone cannot explain its effects on child marriage. We argue that Pathways' whole-community focus reduces the likelihood of social backlash and contributes meaningfully to its success. Our results demonstrate that a big push can significantly alter entrenched, normative behaviour around child marriage, and that bundled interventions may be greater than the sum of their parts.

Immune imprinting1 or original antigenic sin2 is a phenomenon whereby the immune system preferentially recalls its initial response to a related, often evolving pathogen after subsequent exposure. Despite its important implications for vaccine development, the causes of imprinting remain unclear. Here, to understand the basis and impact of imprinting by influenza A viruses, we characterized the B cell responses of young children after consecutive first infections with divergent H1N1 and H3N2 strains of influenza. Children had a primary but otherwise similar B cell response to that of adults. Adult B cells commonly cross-reacted with past strains using more stereotyped and mutated immunoglobulin genes, indicating substantial homosubtypic imprinting. In children, after consecutive heterosubtypic primary infections, up to 6% of memory B cells are H1/H3 cross-reactive and bind to the highly conserved central stalk epitope-a lead target for broadly protective vaccine candidates. Over 90% of these B cells had a higher affinity for the imprinting H3N2 strain, resulting in reduced breadth and neutralization potency against H1N1 strains. Mechanistically, the imprinting H3 strains and affected H1 strains shared a residue change in the stalk epitope (D46N) that was central to the nearly universal shift in reactivity, despite differing by only a single atomic group. In conclusion, imprinting by influenza viruses can cause a deleterious shift of nearly the entire memory recall response against key, conserved epitopes.

Marburgviruses (MBVs) cause severe haemorrhagic fever with higher fatality rates than Ebola virus (EBOV)1-4. Here we show that the MBV glycoprotein (GP) mediates viral entry more efficiently than EBOV GP. Using cryo-EM, we determined structures of MBV GP in three states: (1) unbound; (2) bound to its endosomal receptor NPC1; and (3) complexed with a neutralizing nanobody. The glycan cap shields the receptor-binding site from NPC1 but only partially from the nanobody, enabling limited immune evasion. After glycan cap cleavage, NPC1 binds to MBV GP in a distinct orientation compared with EBOV GP, providing an additional anchor and enhancing receptor affinity. NPC1 engagement also induces substantial conformational changes in MBV GP, probably facilitating membrane fusion. Furthermore, MBV GP is susceptible to the neutralizing nanobody, which mimics NPC1 at the receptor-binding site. Together, our findings reveal MBV GP as a highly efficient entry mediator and suggest structural mechanisms that may contribute to its enhanced entry efficiency.

G-protein-coupled receptors (GPCRs) are capable of signalling through four families of G protein α subunits. Although hundreds of nucleotide-free GPCR-G protein complex structures have been solved, the mechanism of G protein subtype selectivity remains poorly understood, with recent studies suggesting a role for dynamic nucleotide-bound intermediate states1,2. Here we use time-resolved cryo-electron microscopy to visualize the GTP-induced activation of Gαi1βγ and Gα11βγ heterotrimers bound to the neurotensin receptor 1 (NTSR1), which has been demonstrated to be highly promiscuous in G protein coupling and to possess unusual conformations in the nucleotide-free complex. We resolve ensembles of states along the G protein activation pathway, with differences in the structures and their relative populations between Gαi1 and Gα11. Structural analysis reveals a key role for several motifs, including intracellular loop 2 (ICL2) and ICL3, in stabilizing the observed intermediate states. Our results are supported by molecular dynamics simulations and kinetic bioluminescence resonance energy transfer experiments, which reveal that the stability of these intermediate states and the signalling of various G proteins are correlated with ICL2 and ICL3 sequences. Single-molecule fluorescence assays of GTP-induced NTSR1-G protein complex dissociation reveal that NTSR1 is liberated significantly faster from Gα11, consistent with the relative lack of stable Gα11-GTP intermediate states compared with Gαi1. These findings highlight that transient intermediate-state complexes along the G protein activation pathway have an important role in G protein selection that cannot be explained by nucleotide-free states alone.

Supratentorial ependymomas are aggressive childhood brain cancers that retain features of neurodevelopmental cell types1 and segregate into molecularly and clinically distinct subgroups2,3, suggesting different developmental roots. The developmental signatures, as well as microenvironmental factors, underlying aberrant cellular transformation and behaviour across each supratentorial ependymoma subgroup are unclear. Here we integrated single-cell and spatial transcriptomics, as well as in vitro and in vivo live-cell imaging, to define supratentorial ependymoma cell states, spatial organization and dynamic behaviour within the neural microenvironment. We find that individual tumour subgroups have two distinct progenitor-like cell states-neuroepithelial-like and embryonic-like-that are reminiscent of early human brain development and diverge in the extent of their neuronal or ependymal differentiation. We further identify several modes of spatial organization of these tumours, including a high-order architecture that is influenced by mesenchymal and hypoxia signatures, and local neighbourhood structures. Finally, we identify a role for brain-resident cells in shifting supratentorial ependymoma cellular heterogeneity towards neuronal-like cells that co-opt immature neuronal morphology and migratory mechanisms, and a subset of neuroepithelial-like cells that are both proliferative and highly migratory. Collectively, these findings provide a multidimensional framework to integrate transcriptional and phenotypic characterization of tumour heterogeneity in supratentorial ependymoma and its potential clinical implications.

Plant nucleotide-binding leucine-rich repeat (NLR) immune receptors detect pathogen effectors and activate immunity1. Coiled-coil NLRs (CNLs) form resistosomes as Ca2+-permeable channels in the plasma membrane (PM)2-4. However, the mechanism by which resistosomes activate cell death remains unclear. Here we report that the CNL SUPPRESSOR OF mkk1 mkk2 2 (SUMM2), unlike canonical CNLs that use a MADA motif to penetrate the PM5, tethers to the PM through N-myristoylation, a common feature among many CNLs. PM targeting via N-myristoylation is essential for SUMM2-induced cell death. Upon activation, SUMM2 promotes the association of the lipase-like proteins ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1) and PHYTOALEXIN DEFICIENT 4 (PAD4) with the helper NLR-ACTIVATED DISEASE RESISTANCE 1-LIKE 1 (ADR1-L1). Furthermore, active SUMM2 induces the clustering of multiple ADR1-L1 resistosomes into a ring-like assembly colocalized with the EDS1-PAD4 complex, and the EDS1-PAD4-ADR1 module is essential for SUMM2-activated cell death. Together, these findings reveal that N-myristoylation-mediated PM targeting of SUMM2 promotes the assembly of higher-order EDS1-PAD4-ADR1-L1 resistosome clusters for cell death initiation.

Ageing is accompanied by declining memory function, with extremely heterogeneous manifestation in the human population1. Brain-extrinsic factors influencing cognitive decline, such as gastrointestinal signals, have emerged as attractive targets for peripheral interventions2-6, but the underlying mechanisms remain largely unclear. Here, by charting a high-resolution map of microbiome ageing and its functional consequences throughout the lifespan of mice, we identify a mechanism by which inhibition of gut-brain signalling during ageing results in impaired neuronal activation in the hippocampus and loss of memory encoding. Specifically, accumulation of gut bacteria that produce medium-chain fatty acids, such as Parabacteroides goldsteinii, can drive peripheral myeloid cell inflammation through GPR84 signalling. As a result, the function of vagal afferent neurons is impaired, the interoceptive signal received by the brain is weakened and hippocampal function declines. We leverage this pathway to define interventions that enhance memory in aged mice, such as phage targeting of Parabacteroides, GPR84 inhibition and restoration of vagal activity. These findings indicate a key role for interoceptive dysfunction in brain ageing and suggest that interoceptomimetics that stimulate gut-brain communication may counteract age-associated cognitive decline.

CD4+ regulatory T cells (Treg cells) are essential for immune tolerance1. Peripherally induced Treg cells (pTreg cells) complement thymic Treg cells by broadening Treg cell reactivity in response to a changing antigenic landscape2. Although both TGFβ and IL-2 synergistically promote functional pTreg cell development in vitro3-6, their combined roles in inducing pTreg cell generation in vivo have not been exploited for tolerizing immunotherapy. Here we designed an IL-2-TGFβ 'surrogate' co-agonist by creating a single-chain fusion protein between IL-2 and a low-affinity TGFβ mimic agonist derived from a helminth parasite7. This IL-2-TGFβ surrogate functions as an AND-gated co-agonist and enabled simultaneous cis-activation of IL-2-STAT5 and TGFβ-SMAD2/3 signalling specifically in T cells that express IL-2 receptors. The IL-2-TGFβ surrogate agonist robustly induced antigen-specific, functional and stable pTreg cells in vivo within peripheral lymphoid organs in mice immunized with ovalbumin (OVA) and myelin oligodendrocyte glycoprotein (MOG)35-55. The induced pTreg cells display an effector-like, actively expanding state with high RORγt expression, enabling efficient migration and suppression of intestinal inflammation. Treatment with this agonist effectively quelled immune activation in mouse models of allergen-induced allergic inflammation and self-antigen-driven autoimmune neuroinflammation, suggesting a strategy for the induction of antigen-specific pTreg cells in vivo to establish immune tolerance in inflammatory, allergic and autoimmune diseases.

Sexual reproduction is ancient and ubiquitous despite its obvious disadvantages1. Theory predicts that the reassortment of alleles that results from sex is necessary for natural selection to act effectively on individual loci; therefore, a purely clonal organism should rapidly accumulate deleterious mutations and go extinct2-4. Nevertheless, many asexual species have existed for longer than theory predicts is possible5-7, such as the Amazon molly (Poecilia formosa), a clonally reproducing fish arising from a single hybridization event more than 100,000 years ago8-10. Here we show that although the Amazon molly has accumulated mutations faster than its sexual progenitor species, this has not led to functional mutational decay, defying theoretical expectations. Instead, gene conversion facilitates both adaptive and purifying selection by generating new clonal lineages in which previous mutations are either reverted or fixed, and by resolving hybrid incompatibilities between the ancestral haplotypes. The transition to clonality altered chromatin structure, but the asexual haplotypes of the Amazon molly nonetheless maintain the divergent mutational landscapes of their progenitor species. Together, these results provide new insights into long-standing questions about the trade-offs involved in asexual reproduction.

Halide perovskite light-emitting diodes promise high-efficiency1-3, low-cost optoelectronics, yet their operational instability remains a critical barrier to practical deployment. Here we develop a multimodal in situ electron microscopy approach that integrates four-dimensional scanning transmission electron microscopy, energy-dispersive X-ray spectroscopy and atomic-resolution imaging to directly visualize structural and chemical evolution in a working halide perovskite light-emitting diode with nanometre precision. Our in situ biasing measurements uncover nanoscale structural and chemical transformations initiated at transport layer interfaces, including the formation of metallic lead and lead-rich secondary phases, as well as strain-driven grain fragmentation. On biasing, we observe the partial transformation of the metallic Al contact to insulating AlCl3. Crucially, whereas the bulk of the perovskite emitter remains relatively intact, our experiment shows that degradation is localized at interfaces. By comparing in situ and ex situ measurements, these results establish a mechanistic link between interfacial strain, ionic transport and electrochemical reactions in working devices, and provide a broadly applicable framework for nanoscale degradation analysis in complex multilayered optoelectronic systems using multimodal in situ biasing microscopy.

Genome-editing technologies that use recombinases to insert kilobase-scale DNA sequences into mammalian genomes canonically require large double-stranded DNA (dsDNA) donors1,2. However, dsDNA molecules evoke problematic and toxic innate immune responses, limiting integration efficiencies and generally constraining applicability to ex vivo or immune-deficient contexts. By harnessing mechanisms of integrative prokaryotic viruses and mobile genetic elements, here we demonstrate that recombinases are compatible with immune evasive circular single-stranded DNA molecules optimally bearing a partial-duplex region that reconstitutes the recombinase recognition sequence. This approach, which we term integration through nucleus-synthesized template addition of large lengths (INSTALL), is compatible with diverse protein and RNA-guided recombinases for high-fidelity kilobase-scale human genome writing. INSTALL minimizes innate immune responses in primary human cells and in mice, improving recombinase-mediated integration efficiencies and supporting systemic in vivo non-viral DNA delivery by substantially increasing tolerability and broadening the dosing range compared with lipid nanoparticle-delivered dsDNA molecules. Together, INSTALL overcomes fundamental challenges for DNA delivery and integration methods by synergizing immune-stealth nucleic acids with recombinases to enable kilobase-scale integration strategies without viral vectors.

Subtle changes in molecular structure can lead to profound changes in molecular function. However, even minor structural refinements can require the complete resynthesis of a target molecule, adding time and cost to molecular design campaigns1. Recently, editing methods have emerged targeting subtle molecular perturbations, including atomic substitution, stereocentre inversion and functional group repositioning2. These precision tools hold the potential to streamline the optimization of molecular function by fine-tuning molecular structure. Here we report an editing method that enables the migration of common alcohol functional groups to proximal sites with predictable stereo- and regiochemical outcomes. The reaction proceeds through a 1,2-acyloxy radical migration step under reversible H atom transfer catalysis conditions promoted by the excited-state decatungstate polyanion. Proximity effects arising from non-covalent interactions between substrate and reagent enable efficient radical formation at polarity-mismatched positions. Application of this tool at a late synthetic stage allows for the precise repositioning of alcohol functional groups, whereas integration with common alcohol group installation methods provides new synthetic strategies to access challenging oxygenation patterns.

Hybrid back-contact (BC) silicon solar cells1-3 combine the strengths of tunnel oxide passivated contact (TOPCon)-derived4-7 n-type contacts, silicon heterojunction (SHJ)-derived8-12 p-type contacts and interdigitated back-contact (IBC)13,14 device structures. Although high performance in the form of 27.8% efficiency has been demonstrated1, the understanding of the fundamental advantages of the hybrid BC architecture over conventional BC cells (for example, eliminating front-surface metallization shading3) remains unexplored. Here we take advantage of the design flexibility of the hybrid BC architecture to use a multifunctional front layer for both light trapping and passivation. Meanwhile, we improved carrier collection and process compatibility of the rear carrier-selective contacts. We also show that the optimal crystalline silicon (c-Si) absorber thickness is increased to 160 μm, leading to a certified efficiency of 27.62% for industrially compatible c-Si solar cells.