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Journal articleCreedy TJ, Ding Y, Gregory KM, et al., 2026,
Bioinformatics of combined nuclear and mitochondrial phylogenomics to define key nodes for the classification of Coleoptera
, Systematic Biology, Vol: 75, Pages: 445-467, ISSN: 1063-5157Nuclear genome sequencing for phylogenetics is resource-intensive while mitochondrial genomes can be sequenced and analyzed with relative ease for building densely sampled phylogenetic trees of the most species-rich lineages of animals. Here, we develop a conceptual approach and bioinformatics workflow for combining nuclear single-copy orthologs with less informative but densely sampled mitochondrial genomes, for a detailed tree of Coleoptera (beetles). Basal relationships of Coleoptera were first inferred from > 2,000 BUSCO loci mined from GenBank’s Short Read Archive for 119 exemplars of all major lineages under various substitution models and levels of matrix completion, to reveal universally supported nodes. Second, the corresponding mitogenomes were extracted and combined with an additional 373 species selected for broad taxonomic and biogeographic coverage, roughly in proportion to the known global species diversity of Coleoptera. Bioinformatic processing of mitogenomes was conducted with a novel pipeline for rapid, accurate annotation of protein-coding genes. Finally, phylogenetic trees from all 491 mitogenomes were generated under a backbone constraint from the universal basal nodes, which produced a well-supported tree of the major lineages at the family and superfamily level. Being genetically unlinked and showing unique character variation, mitogenomes provide a unique perspective of the phylogeny. Comparison with 3 recent nuclear phylogenomic studies resulted in the recognition of > 80 nodes universally present across all analyses. These may now support the higher classification of Coleoptera and serve as backbone of further studies, as numerous full mitogenomes and mitochondrial DNA barcodes are added to an increasingly complete phylogenetic tree of this super-diverse insect order.
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Journal articleSavolainen V, Roberts B, Collins T, et al., 2026,
Rethinking intensification: biodiversity-inclusive management sustains coconut yields
, Plants, People, Planet, ISSN: 2572-2611 -
Journal articleBailey AJ, Vlachou D, Christophides GK, 2026,
Oocyst: knowns and unknowns about the lengthiest life stage of the malaria parasite
, Open Biology, Vol: 16<jats:title>Abstract</jats:title> <jats:p>The oocyst is the longest life stage of Plasmodium, the causative agent of malaria, one of the most persistent and devastating infectious diseases of humankind. Following ingestion during blood feeding, parasites reproduce sexually and traverse the mosquito midgut epithelium to differentiate into oocysts on the basal lamina, where they undergo prolonged development, ultimately giving rise to thousands of sporozoites capable of infecting a new human host. Oocyst formation represents a severe population bottleneck, resulting in the lowest parasite numbers observed across the parasite life cycle. Given its extended duration and pronounced numerical vulnerability, it is striking that the oocyst remains one of the least explored stages of Plasmodium development. Major gaps persist in our understanding of the molecular and cellular processes governing oocyst growth and differentiation, including transcriptional and epigenetic regulation, nutrient acquisition and metabolic remodelling, cell cycle control and interactions with the mosquito immune system and physiology. Recent technological advances and renewed interest in mosquito-stage biology provide an opportunity to dissect these processes at unprecedented resolution. In this review, we synthesize knowledge of oocyst biology, highlight key unresolved questions and discuss how deeper insight into this critical stage could inform the development of next-generation transmission-blocking strategies and accelerate progress towards malaria elimination.</jats:p>
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Journal articleMajumdar A, Upadhyay MK, Ojha M, et al., 2026,
Corrigendum to "A critical review on the organo-metal(loid)s pollution in the environment: Distribution, remediation and risk assessment" [Sci. Total Environ., 951, (2024) 175531].
, Sci Total Environ, Vol: 1026 -
Journal articleQiao S, Harrison SP, Prentice IC, et al., 2026,
Adaptive sowing helps mitigate future wheat losses globally
, Earth's Future, ISSN: 2328-4277The escalating effect of climate change on crop yields necessitates urgent adaptation measures. Shifting sowing dates is emerging as one cost-effective adaptation strategy. However, the implications for global wheat yields are unclear. Here we use an optimality-based model, assuming farmers select sowing dates to maximise yields, to quantify changes in wheat sowing dates and potential grain yields by the 2090s under two climatic scenarios (SSP126, SSP370). We find that the optimal wheat sowing dates are affected by climate change, primarily driven by temperature norms and warming trends. Global warming prompts earlier sowing (10-20 days) and even a switch from spring to winter wheat in cold areas, while strong warming delays sowing (20-40 days). Scenario modelling shows climate change is projected to negatively impact wheat potential yields under both moderate (–2.4%, SSP126) and strong (–7.8%, SSP370) warming scenarios. Adaptive sowing dates coupled with CO2 fertilization could mitigate these losses and even enhance yields, resulting in a +5.6% increase in potential yield for SSP126 and a +12.4% for SSP370. However, the benefits are not uniformly distributed across regions, with hotter and less developed regions—such as sub-Saharan Africa and Latin America—facing heightened risks of yield decline. Our findings suggest that simple adaptation strategies could help address the challenges posed by climate change for agricultural production and emphasize the need for region-specific adaptation policies to ensure equitable climate resilience in agriculture.
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Journal articleBeis K, 2026,
Shared structural mechanisms of alternating access between the secondary peptide transporter SbmA and ABC transporters
, Nature Communications, ISSN: 2041-1723SbmA is a membrane transporter from Escherichia coli that imports antimicrobial peptides. SbmA belongs to the SbmA-like peptide transporter (SLiPT) family. Although the protein is a secondary active transporter that is energized by the proton gradient, it is structurally related to the transmembrane domain (TMD) of ATP-binding cassette (ABC) transporters. SbmA therefore bridges the structural divide between primary and 61 secondary transporters. However, it remains unclear, if SbmA also shares the mechanism of alternating access with ABC transporters, because only a single (outward-open) state is resolved. Here, we show by sequence analysis that SbmA is likely evolved from the TMD of an early ancestor of the ABC transporter YddA. We determine the cryogenic electron microscopy structures of SbmA in occluded and inward-facing states. These conformations closely resemble equivalent states found in ABC trans- porters, indicating a shared structural mechanism of transport. In contrast to ABC transporters, where nucleotide binding, hydrolysis and release steer conformational changes necessary for substrate translocation, electron paramagnetic resonance (EPR) spectroscopy and molecular dynamics (MD) simulations reveal how pH changes induce conformational transitions in SbmA, consistent with a mechanism of substrate internalization that utilizes the transmembrane proton gradient.
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Journal articleSchlenker P, Lamberton J, Lan N, et al., 2026,
Ancestral iconicity: the dance language of bees revisited.
, Biol Rev Camb Philos SocThe waggle dance of bees has given rise to some of the most striking and detailed studies of animal communication. But because of its gradient character, the waggle dance has widely been taken to have properties that are wholly distinct from those of human language. We argue that this is mistaken, and that the waggle dance represents the oldest instantiation of an iconic system also found in human language, notably in sign language. The waggle dance helps bees locate a food source through four properties: (1) food distance is conveyed through the duration of the waggling phase; and (2) food direction is conveyed through the orientation of the waggle run. In addition, (3) while in bees that dance horizontally, the waggle run points towards the food source, in bees that dance vertically the information involves transposition: the angle of the dance relative to 'upwards' is interpreted as the angle of the food direction relative to the sun. Finally, (4) the number of waggle runs increases with food quality. We show that properties 1 and 2 are instantiated in sign language classifier predicates, highly iconic constructions that produce visual animations of the orientation and movement of an entity. Furthermore, classifier movement (property 3) can be interpreted either directly or with 'viewpoint shift', a more flexible version of transposition. Property 4 seems to be instantiated more generally in the pragmatics of human and animal communication, as repetition can convey intensification and/or excitement (e.g. Go, go, go!). We further show experimentally that properties 1-3 are instantiated in some gestures understood by non-signers. Thus the waggle dance is a primitive form of a semantic system also found (through convergent evolution) in human language. It is remarkably ancient, at least 20 million years old according to phylogenetic reconstructions. While the horizontal dance (without transposition) is usually thought to be ancestral, a closer look at extant phyloge
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Journal articleGrilli S, Vertsimakha O, Marston L, et al., 2026,
Sex distorter male drive for resistance-resilient population control of the human malaria vector Anopheles gambiae
, Nature Communications, ISSN: 2041-1723Progress in malaria control has plateaued, prompting the exploration of additional tools. Here, we characterise two germline-specific promoters, spo11 and vasa1, in the malaria vector Anopheles gambiae. These promoters display distinct temporal and spatial expression patterns, making them well-suited for potential applications in CRISPR-based gene drives and sex ratio distortion systems. Leveraging these unique promoter features, we developed a Sex Distorter Male Drive (SDMD) technology that generates a highly male-biased progeny while spreading through super-Mendelian inheritance. This approach greatly simplifies previous genetic construct designs, potentially improving genetic stability and resilience against the development of target site resistance, a major challenge for the efficacy of genetic strategies. Our findings position SDMD as a promising and potentially resistance-resilient tool for the population suppression of Anopheles mosquitoes in malaria-endemic regions.
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Journal articleBueno AS, Mendenhall CD, Anciães M, et al., 2026,
High-quality surrounding landscapes mitigate avian extirpations from forest remnants.
, Proc Natl Acad Sci U S A, Vol: 123The species-area relationship (SAR) has long been used to predict extirpation rates from habitat loss, but these rates depend not only on habitat area but also on the surrounding landscape and species' habitat specialization. We collated global data from forest islands created by river damming and forest fragments resulting from clear-cut deforestation to examine the effects of matrix type (aquatic or terrestrial) and tree cover on avian SARs. Unlike oceanic islands, which are often millions of years old, anthropogenic forest islands provide a contemporary analog to forest fragments to understand matrix effects on SARs and serve as a baseline for worst-case scenarios of forest fragmentation. Our database comprises 50 datasets from 45 studies conducted in tropical and subtropical regions, totaling 1,954 bird species detected through 39,197 incidence records from 336 forest islands and 669 forest fragments. We found that bird extirpation rates were lower in fragments than on islands, especially for forest-dependent species compared to all species. Species losses were further reduced by increasing tree cover around forest remnants at local landscape scales of 300 m, highlighting the importance of small-scale conservation strategies. Moreover, even small forest fragments with greater nearby tree cover held high conservation value, emphasizing the crucial role of the surrounding landscape in mitigating avian extirpations from forest remnants. Beyond protecting forest remnants themselves, area-based conservation efforts would therefore be greatly enhanced by improving matrix quality and expanding tree cover in otherwise hostile landscapes.
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Journal articleCreedy T, Lee S, Ounjay S, et al., 2026,
2,366 new mitochondrial genomes with preliminary identification and phylogeny of >5,500 putative species of beetles
, Scientific Data, ISSN: 2052-4463Mitochondrial genomes are a powerful marker for phylogenetics and biodiversity studies, but remain to be sequenced for the great majority of invertebrate species. We provide a reference set of newly sequenced mitogenomes and corresponding high-resolution images for 2,366 morphospecies from an inventory of beetles in two tropical forest sites in Panama and Malaysia. These sequences were combined with publicly available mitogenomes and edited and re-annotated according to standardised criteria. The final set of 5,527 mitochondrial genomes, mostly representing separate species of 5,518 Coleoptera and 9 outgroups, was used to generate a phylogenetic tree under binary RY coding and using a backbone constraint from nuclear genomes. The tree recovered deep relationships that closely matched previous coleopteran phylogenomic studies, and many lower-level relationships were also largely congruent with earlier lineage-specific works. Furthermore, the expanded taxon sampling provides preliminary insights into shallow-level relationships for several poorly studied lineages. This enhanced resource will serve as a foundation for a comprehensive Coleoptera tree-of-life and support taxonomy, ecology and conservation biology of poorly known tropical lineages.
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Journal articleMansfield TM, Zarsav A, Cox F, et al., 2026,
Ecological and genomic variation in ectomycorrhizal fungal exploration types.
, New PhytolEctomycorrhizal fungi (EMF) produce mycelia with variable extension and complexity, which can be classified according to soil 'exploration types' (ETs). ETs have received attention as one of the few mycorrhizal trait frameworks, but without an empirical classification of ET functional diversity and environmental preferences, understanding and interpreting EMF biogeographic patterns has been difficult. We conducted a synthesis combining: comparative EMF genomics to describe functional divergence in decomposition and nutrient cycling genes across ETs; and EMF trait distribution modeling across continental Europe, pairing soil and root EMF surveys to establish biogeographic ET niche profiles. We demonstrate a signature of ETs encoded in EMF genomes, which is independent from phylogeny and linked to biomass production strategies. EMF ET relative abundances were separated by soil, root, and dominant tree leaf type habitats and exhibited unique correlations with forest biotic (e.g. plant productivity and plant pathogen densities) and abiotic (e.g. nitrogen deposition and soil pH) conditions. These findings support a theory that EMF niche partitioning can be partially explained by extraradical mycelial traits, with underlying variation in ET biogeography likely arising from distinct decomposition and nutrient cycling potentials. We also identify important limitations to this trait framework and provide a guided outlook for future research.
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Journal articleHui T-Y, Epopa PS, Millogo AA, et al., 2026,
Variance partitioning reveals contrasting random effect contributions to the density and species composition of malaria-transmitting mosquitoes in Western Burkina Faso
, Parasites and Vectors, ISSN: 1756-3305Background Spatial-temporal variation exists in the density and species composition of malaria-carrying mosquitoes, which will in turn influence the transmission of the disease. While there has been extensive research on seasonality and other main drivers of the vector populations, the heterogeneity partitioned as random effects at various spatial-temporal scales is just as important but has not attracted the same attention. Methods To investigate the relative contributions of the between-house, between-village, and between year variations, as well as other house-level covariates such as inhabitant number and bed net usage on vector density and species composition, intensive Pyrethroid Spray Catches (PSC) sampling was conducted across a 60-month period between 2012-2019 from four villages in the Sudano-Sahelian region of Burkina Faso. Results For density, measured by female Anopheles gambiae s.l. counts, our modelling showed that the between-house variation was the largest variance component, followed by the between year then between-village variation, after accounting for seasonality and other covariates. Density increased with the number of inhabitants within a household but was uncorrelated with bed net presence. A subset of female mosquitoes was genotyped for species identification, and the composition of An. coluzzii and An. gambiae, the two dominant vectors in the region, varied markedly across villages without an overall trend. The between-village variance contributed up to 76% of the total random variation in species composition, followed by the between-year variance. The between-house variation was statistically insignificant. Neither household size nor bed net usage had any impact on species composition. Conclusions Interestingly, the between-house component of variation was the largest contributor when measuring mosquito density, but it was the least important for species composition. For between-village variation the converse was found. Together with
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Journal articleGan W, Alizadeh N, Best M, et al., 2026,
An eco-evolutionary optimality model explains theacclimated temperature response of photosynthesis
, New Phytologist, ISSN: 0028-646XThe optimal temperature of net photosynthesis (Topt) generally increases with plant growth temperature. Changes in Topt are associated with changes in the maximum carboxylation capacity at 25 °C (Vcmax25) and the maximum electron transport rate at 25 °C (Jmax25). The ratio between Jmax25 and Vcmax25 declines with warming. Accurate representation of leaf-level photosynthetic responses to temperature is essential for realistic projections of the terrestrial carbon cycle and its response to ongoing climate changes. However, many land-surface models incorporate thermal acclimation through empirical approaches and through assigning distinct but static parameter values to plant functional types (PFTs). Eco-evolutionary optimality approaches provide a simpler way of modelling photosynthesis without recourse to PFTs. Here we use the sub-daily P model, an eco-evolutionary optimality-based model of photosynthesis that explicitly separates the instantaneous and acclimated responses of photosynthetic parameters to temperature to investigate how optimal temperature changes with growth temperature, as represented by leaf or air temperature. We show that the simulated responses are consistent with observations from both controlled experiments and eddy-covariance flux tower data. We show that changes in Topt, and in the assimilation rate at Topt, are caused by changes in carboxylation capacity and electron transport rate that follow directly from the hypotheses underlying the model.
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Journal articleR Ellis H, Behrends V, Larrouy-Maumus G, et al., 2026,
Glutathione impacts Hfq condensation in nitrogen starved Escherichia coli
, Journal of Bacteriology, Vol: 208, ISSN: 0021-9193Nitrogen (N) is essential for bacterial growth, and adaptation to N starvation involves extensive reprogramming of metabolism and gene expression. A hallmark subcellular feature in long-term N-starved Escherichia coli cells is the presence of biomolecular condensates of the major bacterial RNA regulator Hfq. The Hfq condensates, which accumulate gradually during N starvation, contribute to adaptation by modulating RNA metabolism and central metabolic pathways. Metabolites play central roles in stress responses, often acting as modulators of protein function to support survival and recovery. Glutathione (GSH), a universal stress protectant, has broad roles in bacterial stress adaptation, yet its function during N starvation remains unexplored. Using a GSH-deficient mutant (ΔgshAB), we show that GSH is required for optimal survival and recovery from prolonged N starvation. We reveal that GSH regulates the temporal dynamics of Hfq condensation and dissipation during N starvation and recovery from N starvation, respectively, via an as-yet unknown mechanism. However, the contribution of GSH to survival during and recovery from N starvation and Hfq condensation dynamics seems to be unlinked. Overall, the results point to a role for GSH in the adaptive response to N starvation, potentially extending its canonical function as a stress protectant.IMPORTANCENitrogen is a vital nutrient for bacterial growth. When nitrogen becomes scarce, bacteria must quickly adapt to survive. Escherichia coli forms tiny structures called Hfq condensates, which help manage genetic information flow and metabolism. Small molecules called metabolites aid bacteria in coping with stress, and one such molecule, glutathione (GSH), protects cells under various stress conditions. GSH’s role during nitrogen starvation is unknown. We used an E. coli mutant unable to produce GSH and found that these bacteria struggle to survive and recover from nitrogen starvation. We also discovered that GSH
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Journal articleDellavalle A, Devenish AJM, Jarrett C, et al., 2026,
Shifting baselines increase the risk of misinterpreting biodiversity trends
, Ecography, Vol: 2026, ISSN: 0906-7590Ecological studies quantifying the impact of land-use change on biodiversity may be sensitive to the choice of reference points – or baselines – particularly when sampling across human land-use gradients and other space-for-time comparisons. Much depends on whether the chosen baseline has already undergone shifts in species composition because of hunting, habitat loss and degradation. However, few studies have assessed the influence of shifting baselines on estimates of anthropogenic impacts. Using new survey data from five West African land-use gradients, we examine how habitat patch size and structure influences the estimated impact of land-use change on bird species richness and functional diversity. We show that smaller forests have already lost many forest-dependent birds, particularly those with large body size or specialised ecological niches, leading to reduced estimates of biodiversity loss after deforestation. The steepest biodiversity loss was found in mid-sized forests whereas relatively shallow declines were estimated for the most extensive forests – despite their richer taxonomic and functional diversity. In these larger forest blocks, accurate estimates of biodiversity loss may require longer transects extending beyond the biodiversity ‘shadow' caused by the more extensive spillover of forest species into the surrounding landscape, potentially linked to source–sink dynamics. These findings suggest that biodiversity assessments are highly sensitive to baseline selection and transect design, highlighting the risk of underestimating land-use impacts unless shifting baselines are carefully considered.
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Journal articleHedger G, Lyman E, Rouse SL, 2026,
Ligand-like lipid interactions with membrane proteins: simulations and machine learning
, Current Opinion in Structural Biology, Vol: 97, ISSN: 0959-440XMembrane lipids can bind to specific sites on membrane proteins in a ligand-like manner and modulate protein structure and function. Molecular dynamics simulations encompass a suite of approaches to identify, characterise, and explain the atomic-level mechanisms that underlie the functional effects of ligand-like lipids on membrane proteins. Simulations have shown good agreement with available structural data on lipid-protein interactions. Building on successes, simulations are now used to identify new interactions and mechanisms de novo for a given membrane protein. In this age of abundance, it is increasingly possible to analyse patterns across large groups of proteins and in ever more complex membrane environments. The dawn of machine learning approaches in lipid-protein cofolding holds considerable promise to synergistically capitalise on this availability of simulation data and uncover new facets of ligand-like lipid biology.
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Journal articleXu H, Wang H, Prentice IC, et al., 2026,
Global variation in the ratio of sapwood to leaf area explained by optimality principles
, New Phytologist, Vol: 250, Pages: 181-193, ISSN: 0028-646X• The sapwood area supporting a given leaf area (Huber value, vH) reflects the coupling between carbon uptake and water transport and loss at a whole-plant level. Geographic variation in vH presumably reflect plant strategic adaptations but the lack of a general explanation for such variation hinders its representation in vegetation models and assessment of how its impact on the global carbon and water cycles. • Here we develop a simple hydraulic trait model to predict optimal vH by matching stem water supply and leaf water loss, and test its performance against two extensive plant hydraulic datasets. • We show that our eco-evolutionary optimality-based model explains nearly 60% of global vH variation in response to light, vapour pressure deficit, temperature and sapwood conductivity. Enhanced hydraulic efficiency with warmer temperatures reduces the sapwood area required to support a given leaf area, whereas high irradiance (supporting increased photosynthetic capacity) and drier air increase it. • This study thus provides a route to modelling variation in functional traits through the coordination of carbon uptake and water transport processes.
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Journal articleGarner BH, Scott A, Vogler AP, 2026,
Beetles, barcodes and big data: A deep dive into the phylogeny of Harpalinae (Carabidae)
, Systematic Entomology, Vol: 51, ISSN: 0307-6970The ground beetles (Carabidae) are a highly species-rich lineage of the Coleoptera, with over half of their diversity concentrated in the ~20,000 described species in the subfamily Harpalinae sensu lato. As a presumed recent radiation lacking deeply distinct morphological divisions, their taxonomic classification has been challenging, while molecular studies remain limited in the number of genes and taxa sampled. Using ~450 mitochondrial genome sequences from across the Carabidae and the major biogeographic realms we investigate the tribal relationships in Harpalinae. Our phylogenetic analysis supports a revised system that broadly divides the harpalines into two major reciprocally monophyletic lineages, corresponding to a narrowly defined Harpalinae sensu novo and a distinct Lebiinae. Within Harpalinae, we recover well-supported subclades that mostly represent existing tribes (e.g., Harpalini, Pterostichini, Licinini, Platynini), while clades in Lebiinae required the recognition of three new or redefined clades: Lebiini, Agrini and Odacanthini. We also establish the polyphyletic status of the ‘Truncatipennes’ defined by truncated elytra and traditionally encompassing most ‘lebiomorphs’, which are split into the Lebiinae and at least two additional lineages, corresponding to the Dryptinae and Brachininae (bombardier beetles) branching below the Harpalinae + Lebiinae clade. The mitogenome data were extended to include ~7000 species of Carabidae by adding all available cytochrome c oxidase subunit I (COI) barcodes and other legacy sequences. The resulting phylogeny broadly concurs with the tribal boundaries defined by mitogenomes and provides a curated barcode reference library for species identification. The unprecedented scale of mitogenome sequencing, combined with dense taxon sampling of barcodes, resolves a particularly complex portion of the beetle tree-of-life.
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Journal articleKientega M, Kaboré H, Sawadogo G, et al., 2026,
Genomic insights into the spread and evolution of insecticide resistance variants in Anopheles gambiae s.l. from Burkina Faso
, Scientific Reports, Vol: 16 -
Journal articleYuen ELH, Bozkurt TO, 2026,
Autophagy in the arms race: how pathogen effectors rewire immunity in plants.
, Open Biol, Vol: 16Autophagy is an evolutionarily conserved recycling process that underpins cellular homeostasis and stress resilience in eukaryotes. In the context of plant-pathogen interactions, autophagy has emerged as a key regulatory hub linking immunity, metabolism and programmed cell death. Recent discoveries reveal that diverse virulence factors, or effectors, from a wide range of pathogens target the host autophagy machinery to manipulate cellular responses for their own benefit. On the one hand, selective autophagy functions as a critical component of plant immunity by directly eliminating intracellular pathogens and pathogen-derived molecules, while also degrading negative regulators of immune pathways, thereby strengthening host defences. On the other hand, many pathogens subvert autophagic processes through their effector arsenal: some suppress autophagic degradation to evade immune clearance or maintain host cell viability, whereas others hijack autophagic membranes and signalling components to promote replication and nutrient acquisition. Together, these findings establish autophagy as a central battleground in the molecular arms race between plants and their pathogens. Understanding how effector-autophagy interfaces shape infection outcomes will be critical for engineering disease resistance and for redefining the multifaceted roles of autophagy in plant immunity.
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Journal articleLi Z, Chawla H, Di Vagno L, et al., 2026,
Xylosyltransferase engineering to manipulate proteoglycans in mammalian cells.
, Nat Chem Biol, Vol: 22, Pages: 612-621Mammalian cells receive signaling instructions through interactions on their surfaces. Proteoglycans are critical to these interactions, carrying long glycosaminoglycans that recruit signaling molecules. Biosynthetic redundancy in the first glycosylation step by two xylosyltransferases XT1/2 complicates annotation of proteoglycans. Here we develop a chemical genetic strategy that manipulates the glycan attachment site of cellular proteoglycans. Through a bump-and-hole tactic, we engineer the two isoenzymes XT1 and XT2 to specifically transfer the chemically tagged xylose analog 6AzGlc to target proteins. The tag contains a bioorthogonal functionality, allowing to visualize and profile target proteins in mammalian cells. Unlike xylose analogs, 6AzGlc is amenable to cellular nucleotide-sugar biosynthesis, establishing the XT1/2 bump-and-hole tactic in cells. The approach allows pinpointing glycosylation sites by mass spectrometry and exploiting the chemical handle to manufacture proteoglycans with defined glycosaminoglycan chains for cellular applications. Engineered XT enzymes permit an orthogonal view into proteoglycan biology through conventional techniques in biochemistry.
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Journal articleSanchez-Garrido J, 2026,
Commensals join the effector game.
, Nat Immunol, Vol: 27, Pages: 649-651 -
Journal articleStadinski BD, Mills EA, Humphries PA, et al., 2026,
Author Correction: Age-dependent Zap70 expression in thymocytes regulates selection of the neonatal regulatory T cell repertoire.
, Nat Immunol, Vol: 27 -
Journal articleCooke R, Burton VJ, Brown C, et al., 2026,
Future scenarios for British biodiversity under climate and land-use change.
, Nat Commun, Vol: 17Projections of biodiversity futures are needed to translate global policies into national action. We use dissimilarity modelling to project climate change scenarios for 1002 plant, 56 butterfly, and 219 bird species across Great Britain up to 2080. Under all scenarios we find extensive community reorganisation, with the disappearance of current bioclimates and emergence of novel ones. We also explore impacts of combined climate and land-use change, finding that even optimistic scenarios could see accumulating extinction debts. Scenarios featuring reduced emissions and a more sustainable society could bend the curve of loss, reducing species heading for extinction by 32% for plants, 14% for butterflies, and 20% for birds. Scenarios differ in impact between groups, with plants showing the most severe responses to environmental change. Overall, we show that actions taken during the next 20 years are crucial to mitigate the worst effects of climate and land-use change for biodiversity in Britain.
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Journal articleWang H-Y, Yuen ELH, Chen Y-F, et al., 2026,
A hydrophobic core in the coiled-coil domain is essential for NRC resistosome function.
, New PhytolThe nucleotide-binding leucine-rich repeat protein (NLR) required for cell death (NRC) family represents a group of helper NLRs that are required by sensor NLRs to execute hypersensitive cell death during pathogen infection. NRCs contain an N-terminal coiled-coil (CC) domain essential for their function, yet our knowledge of how this domain contributes to NRC function remains limited. Using site-directed mutagenesis and transient expression in Nicotiana benthamiana, we screened conserved hydrophobic residues among NRCs and identified seven required for NRC4-mediated cell death, revealing a hydrophobic feature within the CC domain that contributes to NRC-mediated immunity. Structural analysis revealed that four of these residues form a hydrophobic core in the CC domain. This hydrophobic core is important for NRC4 subcellular localization, oligomerization, and phospholipid association, but not for NRC4 focal accumulation at the extrahaustorial membrane during Phytophthora infestans infection. Sequence analysis and functional assays revealed that this core is highly conserved in NRCs and some singleton NLRs but has degenerated in NRC-dependent sensor NLRs. Our study identifies a hydrophobic feature in the CC domain of NRCs and reveals its contribution to NLR-mediated immunity.
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Journal articleBannister K, 2026,
Peri-operative pregabalin does not alter behavioural or diffuse noxious inhibitory control responses in two rat models of chronic pain
, PAIN Reports, ISSN: 2471-2531Introduction: Multiple mechanisms contribute to the experience of pain where the use of model organisms to dissect mechanistically sensory regulatory circuitry is a vital component of discovering underlying causes of persistent pain in disease states. Such disease states can be modelled in animals using surgical procedures that, ethically, should involve administration of analgesia. However, since basic pain researchers often wish to measure pain-related events, animals may be denied peri-operative analgesia to avoid adversely influencing experimental outcomes. Methods: We conducted a structured review of peri-operative analgesia usage in rat spinal nerve ligation (SNL) and cancer-induced bone pain (CIBP) models. Using a combination of behavioural testing and in vivo electrophysiology in the dorsal horn of the spinal cord, we assessed the impact of peri-operative pregabalin on nociceptive behaviours in the acute recovery phase, and behavioural and electrophysiological experimental outcomes in the established phase, of rat SNL and CIBP models.Results: A literature search revealed that, for studies using rat models of SNL or CIBP, only 5.37 % and 12.69 % respectively reported the use of peri-operative analgesia. We then demonstrated that the use of pregabalin as a peri-operative analgesic reduced mechanical hypersensitivity in the acute period following SNL surgery, with no impact on behavioural, electrophysiological or neuropharmacological outcomes in the established phase of either model.Conclusions: This study challenges the basic science researcher’s reasoning that peri-operative analgesia confounds neurobiological outcomes. The use of peri-operative analgesia should be an important consideration to improve animal welfare in chronic models of pain.
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Journal articleHe S, Sanchez Garrido J, Beis K, et al., 2026,
TraN variants mediate conjugation species specificity of IncA/C, IncH and Acinetobacter baumannii plasmids
, Journal of Bacteriology, ISSN: 0021-9193IncA/C and IncH plasmids commonly carry antimicrobial resistance genes, notably blaNDM-1. Although these plasmids disseminate among Gram-negative pathogens via conjugation, the mechanisms underlying mating pair stabilisation (MPS) and conjugation species specificity remain poorly understood. In IncF plasmids, MPS is mediated by interactions between outer membrane proteins (OMP) encoded by the plasmids in the donor (TraN) and by the chromosome in the recipient. Using the Plascad database, we extracted 1,436 TraN sequences from 1517 plasmids: 62.5% (898/1,436), mainly in IncF plasmids, are 550–660aa (we renamed TraN short, TraNS); 15% (216/1,436), in IncA/C plasmids, are 880–950aa (TraN medium, TraNM); and 11% (160/1,436), in IncH plasmids, are 1,050–1,070aa (TraN long, TraNL). One TraN, found in six plasmids from Acinetobacter baumannii (891aa), was designated TraN V-shaped (TraNV). Like TraNS, TraNM and TraNL contain a base and one distal tip domain essential for conjugation, whereas TraNV has a base and two distinct tip domains forming a V-shaped structure. TraNM, TraNL and TraNV determine conjugation species specificity, with TraNL cooperating with OmpA. Tip swapping reverses conjugation specificity, revealing how TraNM and TraNL diversity influence plasmid host range and AMR dissemination. Our new data reveal the molecular basis of plasmid host specificity and broaden our understanding of how conjugation drives the dissemination of antimicrobial resistance genes among clinically relevant bacteria.
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Journal articleAlonso A, Kirkegaard JB, Endres RG, 2026,
Reply to van Haastert: Local competition between Ras/actin-driven protrusions.
, Proc Natl Acad Sci U S A, Vol: 123 -
Journal articleXu V, McInnes A, Wake M, et al., 2026,
Structural basis for Rep-mediated adeno-associated virus packaging
, Cell Reports, Vol: 45, ISSN: 2211-1247Adeno-associated viruses (AAVs) are parvoviruses utilized as gene therapy vectors. However, the AAV packaging mechanism is unresolved at the molecular level, creating a bottleneck for vector manufacturing, safety, and efficacy. Here, cryo-EM structures of the Rep helicase packaging motor in complex with the packaging marker DNA (ITR) and the Rep-AAV8 capsid complex are presented. Rep-ITR complexes reveal dynamic oligomeric states on the DNA, elucidating the strand separation mechanism coupled to its ATPase cycle. We observe Rep preferentially bound to empty capsids, with a binding interface likely conserved across the virus family. This complex also unveils a cryptic capsid ATP-binding site which, alongside Rep binding, triggers structural rearrangements priming the capsid for packaging. Collectively, these findings advance the understanding of Rep-mediated packaging, with significant implications for parvovirus virology and viral vector design.
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Journal articleChen Y-F, Lin K-Y, Huang C-Y, et al., 2026,
Subcellular calcium dynamics and organelle perturbations in resistosome-mediated cell death.
, Proc Natl Acad Sci U S A, Vol: 123Plant nucleotide-binding domain leucine-rich repeat-containing (NLR) proteins act as intracellular immune receptors that assemble into resistosomes to execute immune responses. However, the subcellular processes during cell death following resistosome activation remain unclear. Here, we visualized the changes in calcium signaling and organelle behavior after activation of the NRC4 (NLR required for cell death 4) resistosome. We found that NRC4 membrane enrichment coincided with calcium influx. This is followed by sequential mitochondria and plastid disruption, endoplasmic reticulum fragmentation, and cytoskeleton depolymerization. Subsequent loss of plasma membrane integrity, nuclear shrinkage, and vacuolar collapse mark the terminal stage of cell death. Our findings reveal a spatiotemporally resolved cascade of subcellular events downstream of resistosome activation, providing mechanistic insight into the execution phase of plant immune cell death.
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