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Journal articleLeong M, Consoli G, Davis G, et al., 2026,
Mapping the absorption landscape of far-red Photosystem II
, Nature Communications, ISSN: 2041-1723Far-red light photoacclimation enables some cyanobacteria to survive in white-light-depleted environments by extending the red limit of photosynthesis. In far-red Photosystem II, paralogous subunits replace their canonical counterparts, allowing the incorporation of some chlorophyll f molecules and one chlorophyll d that are red-shifted and spectrally distinct from the chlorophyll a manifold, and from each other. Here, we present a comparative study of far-red Photosystem II from Chroococcidiopsis thermalis PCC 7203 and Calothrix sp. NIES-3974. In C. thermalis, the cryo-electron microscopy structure reveals the far-red-exclusive subunit, PsbH2’, which forms part of a chlorophyll f binding site. We also assign four chlorophyll f sites using sequence comparisons and electrostatic potential analyses. In Calothrix, psbH2’ is absent, and the same analyses show that only two of these chlorophyll f sites are present. Comparative phylogenetic, structural, and spectroscopic analyses allow the assignment of specific wavelengths to all the red-shifted chlorophylls. This provides the framework needed to model excitation energy transfer in far-red Photosystem II, and to understand the conserved features that allow survival under far-red light.
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Journal articleMadhuprakash J, Toghani A, Pai H, et al., 2026,
A potato late blight pathogen effector interacts with ENTH-domain protein TOL9a and an activated helper NLR to suppress immunity.
, Sci Adv, Vol: 12Pathogens counteract central nodes of NLR immune receptor networks to suppress immunity. However, the mechanisms by which pathogens hijack helper NLR pathways are poorly understood. We show that an effector from the late blight pathogen Phytophthora infestans interacts with the host protein NbTOL9a and a helper NLR to suppress immunity. We solved the crystal structure of the RXLR-LWY effector AVRcap1b in complex with the ENTH domain of NbTOL9a. The structure revealed that, unlike other RXLR-LWY effectors, AVRcap1b has a previously unidentified L-shaped fold that defines a distinct structural family of effectors in the genus Phytophthora. We defined the AVRcap1b/NbTOL9a binding interface and designed effector mutants that do not bind NbTOL9a, impairing immune suppression. This suggests that ENTH binding is required for full virulence activity. Last, we show that AVRcap1b associates specifically with activated NbNRC2 independently of NbTOL9a binding. We propose a model in which the effector interconnects NbNRC2 with the NbTOL9a pathway. Our results illustrate a previously uncharacterized pathogen mechanism to hijack NLR pathways and suppress immunity.
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Journal articleMaretvadakethope S, Perez-Carrasco R, 2026,
Simple systems, complex dynamics: Lessons from minimal gene regulatory networks
, Current Opinion in Systems Biology, Vol: 44Small gene regulatory networks (GRNs) are well-established biological modules that underpin cellular decisions and dynamical function. Their theoretical understanding has largely been shaped by the motif idea, which links simple network wiring patterns to behaviours. This approach has been extremely influential, providing a clear and widely used language for regulatory logic, facilitating the understanding of behaviours such as bistability, ultra-sensitivity, or oscillations. However, a growing body of theoretical and experimental work now challenges the idea that circuit behaviour is fully determined by topology alone, revealing that even very small GRNs can exhibit much richer dynamics once molecular implementation, stochasticity, and upstream modulation are taken into account. Recent advances show that the timing, precision, and reversibility of cell-fate decisions depend critically on signal history, noise structure, and molecular context, even in minimal circuits. Furthermore, there is growing evidence that small GRNs support a wide range of non-canonical dynamical behaviours including mushroom and isola bifurcations, hybrid oscillatory–switching regimes, and pronounced critical slowing down, substantially expanding their functional repertoire without increasing topological complexity. Crucially, these behaviours are highly sensitive to how regulation is implemented at the molecular level: distinct promoter architectures, regulatory logics, and stochastic mechanisms—often hidden by standard Hill-function descriptions—can qualitatively reshape circuit dynamics, requiring an explicit link between abstract network structure and specific biophysical processes. Together, these results expose fundamental limits to inferring function from topology alone or to reconstructing mechanisms from expression data. Rather than simplified motifs, Small GRNs still provide a uniquely powerful setting in which to explore these open questions in order to progress
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Journal articleOkumu FO, Finda M, Odero JO, et al., 2026,
Adapting Africa's vector surveillance systems to monitor gene-drive mosquitoes in malaria control
, Trends in Parasitology, Vol: 42, Pages: 463-493, ISSN: 1471-4922Gene-drive mosquitoes could transform malaria control in Africa, but their rapid, autonomous spread requires rigorous post-release monitoring. Most malaria-endemic countries already conduct some entomological surveillance, although it is often limited, fragmented, and externally funded. Molecular diagnostics are also expanding but remain mostly research focused and ad hoc. These imperfect systems offer workable foundations for strategic upgrades to support essential gene-drive monitoring. Priority investments should strengthen field-entomology, high-throughput genotyping for drive alleles and resistance, technical expertise, and integrated data for decision-making. Fortunately, first-generation gene drives already align with common phenotyping and genotyping workflows, avoiding major infrastructure overhauls, and permit simpler evaluation metrics than conventional interventions. This feature review examines key technical and operational considerations for monitoring gene drives and recommends how countries can adapt their vector surveillance systems to effectively monitor gene-drive mosquito releases.
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Journal articleGan W, Alizadeh N, Best M, et al., 2026,
An eco-evolutionary optimality model explains the acclimated temperature response of photosynthesis
, New Phytologist, Vol: 250, Pages: 2884-2899, 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 articleSilvar-Viladomiu P, Cavan EL, Martin AH, et al., 2026,
Estimating the contribution of the Irish Sea fish community to carbon sink potential
, ICES Journal of Marine Science, Vol: 83, ISSN: 1054-3139The marine biological carbon cycle plays a crucial role in the sinking and sequestration of atmospheric carbon and in regulating the global climate. Most existing research on biological carbon sequestration has focused on the role of oceanic (off-shelf) species and processes. We know little about how species living on continental shelves contribute to and influence carbon sinks due to the complex dynamics of biological and physical transport processes. However, continental shelves often have high levels of carbon productivity and a high potential for disturbance from human activities such as fishing, which strongly impact fish communities. Fish are important components of ecosystems that interact with the biological carbon cycle. Here, we used an Ecopath with Ecosim food web model of the Irish Sea coupled with biogeochemical equations to provide a novel quantitative assessment of the contribution of the fish community to the annual carbon reaching the continental-shelf seafloor over a four-decade simulation (1973–2016). Similar to the open ocean, faecal pellets dominated estimates of fish-mediated carbon flux in the Irish Sea. Our simulations imply that pelagic fish contribute more than half of the fish-mediated carbon, equivalent to approximately 2% of the plankton-mediated carbon deposited on the seafloor. Our results provide the first quantitative assessment and early insights into the relationship between fish species and the biological carbon sink in a shelf ecosystem.
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Journal articleMaia R, Barbosa M, Negreiros D, et al., 2026,
Satellite hindcasts of foliar traits reveal a subtle but consistent relaxation of conservativeness in a biodiverse mountain grassland over the last four decades
, Ecography, Vol: 2026, ISSN: 0906-7590Projected warming and drying raise concerns about the resilience of stress-adapted ecosystems, including the Brazilian Campo Rupestre, an exceptionally biodiverse mountaintop grassland mosaic on ancient, nutrient-poor substrates. Here, we combine field-based trait data and long-term remote sensing to assess the functional structure and temporal dynamics of these communities. Using foliar trait measurements from 247 vegetation plots across five contrasting habitats, we 1) quantify contemporary community-level functional structure, 2) evaluate how edaphic and climatic filters shape spatial variation in community-weighted foliar traits, and 3) reconstruct multi-decadal trait trajectories by hindcasting from long-term Landsat reflectance (1984–2022). Contemporary communities occupy a narrow and predominantly conservative region of the leaf-economic trait spectrum, yet habitats differ in their functional positions within CSR strategy space, indicating non-uniform trait coordination despite overall conservatism. Soil texture and acidity define the primary conservative–acquisitive axis of trait variation, while climatic water balance acts as a secondary modulator; together, these predictors explain 39% of the spatial variation in community-weighted traits. Contrary to expectations of increasing conservatism under progressive climatic stress, Landsat-based hindcasts reveal only modest temporal reorganisation. Specific leaf area and leaf area increase across habitats, while leaf dry matter content declines slightly, indicating a subtle relaxation of conservative trait expression. Temporal changes are small relative to the pronounced spatial differentiation, suggesting strong functional inertia in this OCBIL system. Overall, Campo Rupestre communities persist within a conservative functional domain while exhibiting fine-scale, habitat-dependent differentiation structured by enduring soil and water-balance gradients.
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Journal articleCretois B, Rosten CM, Wiel J, et al., 2026,
TABMON: Design and deployment of a transnational passive acoustic monitoring network for European birds
, Methods in Ecology and Evolution, Vol: 17, Pages: 1867-1879Ecological surveys are often fragmented, costly and limited in scale, leading to large and long-standing knowledge gaps which threaten our ability to properly safeguard biodiversity. Passive acoustic monitoring (PAM) has promised to deliver automated biodiversity monitoring, but networks are rarely deployed on scales that can offer truly novel insights due to scalability and standardization challenges around collecting, managing, analysing and sharing data. Here we present the Transnational Acoustic Biodiversity Monitoring Network (TABMON), a standardized deployment of 108 autonomous sensors across Norway, the Netherlands, France and Spain along a continental bird migration route. Audio is recorded continuously, uploaded in near real-time and processed through an automated analysis pipeline designed to support expert validation and the generation of datasets for deriving Essential Biodiversity Variables (EBVs). TABMON provides a methodological blueprint for transnational, networked PAM deployments and highlights both the opportunities and current limitations of near real-time acoustic biodiversity monitoring at continental scales.
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Journal articleRosenzweig I, Wisden W, 2026,
A New Branch on a Deep-Rooted Tree.
, J Sleep Res, Vol: 35 -
Journal articleLian X, JiJi J, Fang J, et al., 2026,
Leaf temperature and its departure from ambient air temperature.
, Nat Plants, Vol: 12, Pages: 1189-1202Leaf temperature (Tl), the temperature at which leaf-air exchanges of carbon and water occur, varies with ambient air temperature (Ta), regulated by microclimate and species' energy balance traits. Ground and satellite thermal measurements of the Tl-Ta relationship are widely used to infer plants' thermoregulation capacity. On the basis of a global synthesis of observations across diverse climates and biomes, we show that reported thermoregulation patterns vary primarily along temperature gradients. Megathermy (dTl/dTa > 1) is particularly prevalent in warm tropical regions and in sun-exposed canopy-top leaves owing to ineffective dissipation of the often excessively accumulated solar radiation, while limited homeothermy (dTl/dTa < 1) and poikilothermy (dTl/dTa = 1) are reported mostly for cold ecosystems or sub-canopy leaves. Under heat-stressed conditions, some warm-adapted species can abate rapid Tl surge through active stomatal control, unless critical temperature thresholds are exceeded, above which Tl might increase non-linearly as a warning sign of damaging stress. This thermal consideration of stomatal regulation is currently missing in mechanistic models as a source of bias in estimated photosynthetic rates. We highlight the pressing need to develop new stomatal theories that tackle a triple-target optimization between carbon gain, water loss and thermal regulation.
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Journal articleKeskin Erdogan Z, Desai K, Baldwin GS, et al., 2026,
Coexistence and collaboration: engineering encapsulation for whole-cell biosensors.
, Trends Biotechnol, Vol: 44, Pages: 1576-1588The emerging field of biosensors exploits the abilities of cells to identify specific molecules, presenting improved sensitivity, specificity, and limit of detection. Whole-cell biosensors (WCB) are organisms specifically engineered to detect a target analyte and express a reporter in response. In biomanufacturing, they can be used for monitoring of key substrate and metabolite concentrations or strain engineering, while in medicine, they can be used to diagnose disease or report on human-microbe interactions. Many applications require WCB to coexist with mammalian cells where a key challenge is to keep separate cell populations viable while still allowing them to interact. In this review, we highlight key considerations when encapsulating WCB to engineer controlled microenvironments that enable collaboration and coexistence of different populations.
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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 Phytol, Vol: 250, Pages: 3247-3263The 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 articleEndres RG, 2026,
Robust chemotaxis beyond sensing limits: signal, noise, and strategy.
, Phys Biol, Vol: 23Bacterial chemotaxis has long been viewed as operating near the physical limits of sensing, as originally articulated by Berg and Purcell. Recent information-theoretic analyses challenge this view, suggesting thatEscherichia coliuses only a small fraction of the information available in ligand arrival statistics to bias its motion. How should such low information efficiency be interpreted at the level of behavior? Here, I argue that chemotactic performance is shaped not only by information transmission and noise, but by the strategy of movement itself. Using simple scaling arguments and minimal models, I show how run-and-tumble chemotaxis can remain robust to noise through symmetry and temporal averaging, even when internal information processing is inefficient. Comparing bacterial and eukaryotic chemotaxis highlights how different sensing strategies convert physical limits into observable behavior. These considerations suggest that low information efficiency need not imply poor performance, but may instead reflect an evolved balance between robustness, simplicity, and function.
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Journal articleGrimaldi A, Hobbs B, Stofella M, et al., 2026,
Amide Hydrogen-Deuterium Exchange in Isotopically Mixed Water.
, ACS Phys Chem Au, Vol: 6, Pages: 446-450Hydrogen-deuterium exchange (HDX) of protein backbone amides provides a powerful probe of conformational dynamics. However, when experiments are performed in H2O/D2O mixtures, quantitative interpretation is hindered by back exchange and isotope effects not captured by the classical Linderstro̷m-Lang (LL) model. We introduce a generalized Linderstro̷m-Lang (GLL) framework that explicitly accounts for forward and reverse exchange and for changes in protection upon isotopic substitution. Analytical solutions describe equilibrium enrichment (fractionation) and protection factors in mixtures, reducing to the LL model in pure D2O. Application to HDX/NMR of the molecular chaperone DNAJB1 in 50% D2O demonstrates that the GLL model recovers protection factors at 100% D2O. Ignoring back exchange (i.e., using the LL model), protection factors are systematically underestimated. A particularly powerful feature of our approach is that a single HDX experiment in a mixture (e.g., 50% D2O) simultaneously provides protection factors that report on conformational dynamics and local stability and fractionation factors that are sensitive to the local hydrogen-bonding environment.
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Journal articleSandoval Calle D, Flo V, Morfopoulos C, et al., 2026,
Environmental influences on the maximum quantum yield of terrestrial primary production
, New Phytologist, ISSN: 0028-646XHistorically, terrestrial biosphere models (TBMs) have assigned the intrinsic (maximum) quantum yield of photosynthesis (𝜑) a constant value for each plant functional type. However, experimental studies have shown that 𝜑 – when measured on light adapted leaves – depends on temperature. It is unclear whether this dependence is universal or biome-specific; how it is manifested at the ecosystem level; and how it should be represented in TBMs. By fitting empirical light-response curves to a global set of eddy-covariance CO2 flux measurements and correcting for photorespiration, we inferred apparent, ecosystem level 𝜑values and their temperature responses across a wide range of environments. The temperature response of apparent ecosystem-level 𝜑 follows a universal bell shaped curve. The shape of this curve does not markedly differ among biomes, but the maximum value of 𝜑 decreases with increasing aridity, its temperature optimum increases with increasing growth temperature, and its sensitivity to temperature increases as growth temperature declines. Our model for 𝜑(𝑇) aligns with recent theory highlighting the role of cytochrome b6f in regulating the light reactions of photosynthesis. If implemented in TBMs, this model should allow better predictions of the responses of terrestrial ecosystem function to a warming climate.
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Journal articleNguyen P-K, Froldi F, McMullen JPD, et al., 2026,
Chinmo defines the region-specific oncogenic competence in the Drosophila central nervous system.
, Proc Natl Acad Sci U S A, Vol: 123While genetic mutations can promote hyperplastic growth, they do not always result in oncogenic outcomes. We and others have previously identified the transcription factors Nerfin-1 and Lola as inhibitors of dedifferentiation. Here, we investigate how the oncogenic potential of dedifferentiation varies across different neural lineages in the Drosophila central nervous system. We found that Nerfin-1 inactivation causes tumorigenic phenotypes in the central brain and the ventral nerve cord but not the optic lobes (OLs). In contrast, Lola inactivation leads to tumor overgrowth specifically in the OLs. We identify Chinmo, a temporal transcription factor, and its regulation by ecdysone signaling as key determinants of the oncogenic competence in different regions of the brain, influencing the tumorigenic outcome of dedifferentiation. This study provides a fundamental framework to understand how oncogenic competence arises beyond genetic mutations.
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Journal articleYang J, Arvind C, Barber RA, et al., 2026,
Song complexity in suboscine birds: evolutionary drivers and ecological constraints.
, Proc Biol Sci, Vol: 293Acoustic signal complexity varies widely in animals, from single notes to highly sophisticated vocal displays. In birds, vocal complexity can evolve as an honest signal of individual quality driven by sexual selection. However, this hypothesis is rarely explored in conjunction with alternative drivers, including competition for ecological resources (social selection) and intra-group communication, both of which may favour increased signal complexity. Using Bayesian phylogenetic models, we test whether these alternative mechanisms predict the complexity of innate songs in 1288 species of suboscine passerine birds, while accounting for ecological constraints on sound production, transmission and detection. We found that overall song complexity was reduced by sexual selection (estimated from mating systems) and declined with body size and vegetation density. Conversely, note count and song length increased in territorial species, particularly those using song to defend year-round territories during the non-breeding season. These findings challenge the common assumption that sexual selection is the main driver of increased signal complexity and highlight the role of social selection via territorial competition as a factor increasing the temporal complexity of songs. Our results suggest that signal complexity depends on social, cultural and ecological contexts, reflecting a combination of multiple inter-related drivers and constraints.
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Journal articleGrover M, Ippolito D, Barkoulas M, 2026,
Worming out defence strategies: mechanisms of immunity through the lens of genetic screens in C. elegans
, Heredity, ISSN: 0018-067XSince Sydney Brenner's foundational work in 1974, Caenorhabditis elegans has served as an impactful model for biological discovery primarily driven by genetic approaches, including mutagenesis-based screens and RNAi-based functional genomics. We discuss here how genetic screens in C. elegans have advanced our understanding of innate immunity mechanisms by comparing signalling pathways and responses to a wide range of bacteria, viruses, and eukaryotic pathogens including oomycetes, and microsporidia. Screens have uncovered both evolutionarily conserved pathways and species-specific mechanisms of nematode immunity across multiple functional categories. These include mediators of pathogen recognition that specifically detect microbial patterns or infection-associated damage, surveillance immunity systems that sense pathogen-induced cellular dysfunction, and regulatory mechanisms that control the activation of immune signalling or balance it with physiological costs. A major theme emerging from these studies is the importance of cross tissue immune communication, as C. elegans coordinates responses between multiple tissues including neurons, intestine, and epidermis through complex signalling networks. Powerful genetic approaches, coupled with the continued development of new tools in the community, position C. elegans as an attractive whole-animal model for understanding fundamental principles of host-pathogen interactions and the evolutionary origins of innate immunity.
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Journal articleCastets J, Buridan M, Toboso Moreno I, et al., 2026,
A dual phospholipase system instructs membrane hydrolysis during the final stages of plant autophagy.
, Nat Commun, Vol: 17Autophagy is a conserved intracellular catabolic process, critical for plant stress tolerance. Upon their delivery in the vacuole, how autophagic bodies containing cargo are hydrolyzed to warrant autophagy degradation remains unclear in multicellular organisms. Here, we found that two Arabidopsis phospholipases, LCAT4 and LCAT3, traffic to the vacuolar lumen and converge on autophagic bodies through fundamentally different routes. While LCAT4 directly binds ATG8 and uses autophagy as a transport system to reach the vacuole prepackaged within autophagosomes, LCAT3 traffics to the lytic compartment independently of autophagosome formation. Knocking out both genes causes an accumulation of autophagic bodies accompanied with a reduction in autophagy degradation. In vivo reconstitution demonstrated that LCAT3 can hydrolyse the membrane of autophagic bodies, enabling the activity of LCAT4 to enhance this process. Together, this work sheds light on the vacuolar stages of autophagy, showing that plants have evolved a multi-component pathway for the efficient disruption of autophagosomal membranes as a critical step for the completion of the autophagy pathway.
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Journal articleMerali N, Chouari T, Sardar P, et al., 2026,
The bile microbiome is a surrogate for the intratumoral microbiome in pancreatic ductal adenocarcinoma and is associated with oncological outcomes: a cohort study
, International Journal of Surgery, ISSN: 1743-9191Background: The bile microbiome has been shown to be associated with the development of pancreatic ductal adenocarcinoma (PDAC). However, the utility of bile fluid as a potential source of microbial biomarkers remains unknown. We aimed to characterize the bile microbial composition in PDAC compared to benign and malignant pancreatico–biliary disease, as well as correlate our findings with the pancreatic intratumoral and neighboring adjacent tissue (NAT) microbiome.Methods: Prospective matched pancreatic tumor, NAT, and bile samples were obtained from 54 patients who underwent surgery for a head of pancreas mass at Royal Surrey NHS Hospital Trust. Full-length 16S rRNA (V1-V9) gene sequencing was performed on the Oxford Nanopore MinION™ platform. The cohort consisted of 30 PDAC, 14 biliary tract cancers, and 10 benign cases.Results: We identified biliary microbial biomarkers Streptococcus (false discovery rate [FDR] = 0.0047), Klebsiella (FDR = 0.0095), Enterobacter (FDR = 9.68 × 10−7), and Veillonella (FDR = 0.0140) that were found both in the bile and tumor in patients having surgery for PDAC. These bacterial genera were significantly more abundant in PDAC tumors compared to matched NAT and benign disease. We detected a negligible number of microbial reads in the NAT samples. Our microbial signature was highly predictive of PDAC within tissue (AUC = 0.9233) and bile (AUC = 0.8101). Positive bile cultures in the PDAC cohort increased the risk of deep-seated surgical site infections (SSIs), delayed gastric emptying, and post-operative pancreatic fistula. Biliary stenting did not affect microbial composition, and the abundance of specific genera significantly correlated with overall survival and disease-free survival in PDAC.Conclusion: We have shown that the normal pancreas is a relatively sterile organ, whilst the PDAC tumor and bile are colonized with specific genera. In fact, 71% of the tumor microbiome is shared with the bile microbiome in
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Journal articleForest F, Brown R, Buerki S, et al., 2026,
High risk of extinction across the flowering plant tree of life.
, Science, Vol: 392, Pages: 655-659Global biodiversity policies recognize the necessity to preserve evolutionary lineages, as their diversity underpins current and future benefits to people and the future of life on Earth. Plants are largely absent from global biodiversity assessments, resulting in a taxonomic imbalance that has undermined their conservation for decades. We present a tree of life and extinction risk estimates for all species of flowering plants (angiosperms), representing a global assessment of their threatened evolutionary history. We estimate that 21.2% of angiosperm evolutionary history is at risk of extinction and identify 9945 priority species that disproportionately account for total threatened evolutionary history. These prioritizations serve to redress imbalances between plants and animals, monitor conservation effectiveness, and optimize resource allocation in the face of increasing human pressures on biodiversity.
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Conference paperChen J, Leung VCH, Wang R, et al., 2026,
Masked Projection Modelling for Sparse-view cryo-EM Reconstruction
, ICASSP 2026 - 2026 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), Publisher: IEEE, Pages: 11567-11571 -
Journal articleMurray JW, 2026,
Recent advances in the structural biology of photosystem II
, The Plant Journal, Vol: 126, ISSN: 0960-7412Photosystem II (PSII) is the membrane protein-pigment complex responsible for the light-driven oxidation of water to molecular oxygen, a reaction that enables the aerobic biosphere and powers biological carbon fixation. Over the past two decades, structural biology has transformed our understanding of PSII from low-resolution outlines of its protein chains and cofactors to near-atomic resolution models. Early X-ray crystallographic structures from thermophilic cyanobacteria established the architecture of the reaction centre and the Mn4CaO5 oxygen-evolving complex (OEC), defining the protein ligands and cofactor network that support charge separation and water oxidation. The advent of high-resolution single-particle cryo-EM microscopy has expanded structural coverage across taxa, assembly and repair intermediates, and PSII–antenna supercomplexes that are beyond crystallisation. CryoEM now routinely achieves sub-2.5 Å resolution. In situ cryo-EM tomography further bridges atomic models to the native thylakoid membrane environment, exposing the supramolecular organisation of PSII in cells. X-ray free electron laser (XFEL) pump–probe experiments provide time-resolved snapshots of the Kok S-state cycle, revealing substrate water insertion, metal–oxo rearrangements and approaches O–O bond formation. Despite these advances, key challenges remain, including unambiguous assignment of manganese oxidation states, direct localisation of hydrogen atoms and complete structural characterisation of transient S-state intermediates. Integration of structural methods with spectroscopy, computation and emerging protein design approaches promises not only deeper mechanistic insight into biological water oxidation, but also guidance for the development of robust, earth-abundant catalysts.
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Journal articleYang H, Yuen FW, Ryan MJ, et al., 2026,
Pathogenicity of Fusarium xylarioides, the Causal Pathogen of Coffee Wilt Disease, in Coffee Seedlings and an Alternate Host, Tomato Fruit
, Plant Pathology, Vol: 75, ISSN: 0032-0862Widespread crop cultivation has offered more opportunity for pathogens to evolve resulting in the emergence of new virulence and lifestyle patterns. Alternate hosts surrounding a crop field can also help pathogens survive, spread and provide inoculum for subsequent growing seasons. Examining pathogen hosts under laboratory conditions can explain disease emergence mechanisms. Here, we studied four strains of Fusarium xylarioides, a soil-borne, vascular fungal pathogen that causes coffee wilt disease collected over several decades and preserved in the CABI culture collection. We observed that these fungi can colonise tomato fruits as an alternate host to coffee and used these to test the pathogenicity of historic F. xylarioides and F. oxysporum f. sp. lycopersici strains. Expression of effector genes in F. xylarioides was compared in both the primary (coffee) and an alternate plant host (tomato). We used pathogenicity assays on coffee seedlings and tomato fruits by fungal staining, diagnostic end-point PCRs and real-time quantitative PCRs to verify the infection of both plant hosts. Passaging through coffee seedlings (infection followed by re-isolation of the pathogen) resulted in increased effector gene expression and enhanced pathogenicity. These findings indicate that alternate hosts may act as reservoirs for the pathogen, with implications for disease persistence and spread. A clearer understanding of plant disease cycles is therefore essential for the development of effective management strategies aimed at mitigating impacts on global food production.
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Journal articleBernard KS, Tarling GA, Atkinson A, et al., 2026,
Ecological roles, climate-driven responses, and critical knowledge gaps of krill in the global ocean
, ICES Journal of Marine Science, Vol: 83, ISSN: 1054-3139Human-induced global climate change and other anthropogenic stressors are fundamentally altering our oceans. Understanding the ecological and societal implications of these changes is critical for developing mitigation strategies and conservation measures. However, major components of the marine pelagic ecosystem remain poorly understood. This is true for euphausiids (“krill”), which are a crucial part of marine food webs and play an important role in elemental cycling, including in the biological carbon pump, but for which we know surprisingly little. In this review, we first provide an overview of the ecological and socio-economic value of krill, highlighting their function in marine food webs and biogeochemical cycling. Next, we describe what is currently known regarding the response of krill to climate change and other anthropogenic stressors, focusing on changes in their biogeography, physiology, life history, as well as the impacts of krill fishing and their association with pathogens and parasites. We identify five key gaps in our current knowledge of krill: (1) the effects of krill on food web dynamics and stability, (2) the effects of changing predator and/or prey communities on krill populations, (3) the identification of important krill habitats, (4) the understanding of vertical and horizontal range shifts, and (5) the combined effects of multiple climate change and other anthropogenic stressors on krill. We also highlight the krill species, regions, and habitats that are understudied. Finally, we propose strategies to improve our understanding of this ecologically important taxonomic group, including the sustained funding for time series; implementation of novel research technologies; expanding research on understudied species and regions; and creating a global community of krill researchers.
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Journal articleZhu Y, Li M, Zheng J, et al., 2026,
Non-correlated variation of leaf and fine root traits in subtropical forest plants
, Ecology Letters, Vol: 29, ISSN: 1461-023XPlants employ multiple strategies to adapt to their growth environment. Characterizing key dimensions in plant trait space is important for understanding functional diversity within ecosystems. Leaf and root functional traits have been studied in the context of resource economics, but whether they covary, and through which mechanisms, is still debated. We investigated this in subtropical forests by sampling root and leaf traits on individuals of coexisting species in two communities with different resource availability. We found largely non-correlated variation between leaf and fine root traits both across- and within-communities, and a clear decoupling between leaf economic spectrum and root economic space, independent of evolutionary history. Our results suggest that leaf-root trait relationships are shaped by an interplay between microenvironmental heterogeneity that drives decoupling, and shared selection pressures promoting covariation. The interplay explains the weak observed coordination and highlights the importance of environmental context in predicting above- and below-ground plant functions.
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Journal articleXing J, Qin H, Tang C, et al., 2026,
Invasion legacy reshapes resident microbiome multifunctionality through the Matthew effect
, Journal of Applied Ecology, Vol: 63, ISSN: 0021-8901Beneficial microbial inoculation is a widely adopted strategy in agriculture for disease suppression and ecosystem service enhancement. However, the invasion and establishment of exogenous strains in soil are often uncertain. Microbial invasions are known to fundamentally alter ecosystem functioning, yet their persistent legacy effects remain inadequately characterized and could pose unintended risks to soil health. Using four taxonomically distinct bacterial inoculants with disease-suppressive traits, we conducted a longitudinal experiment to trace invasion-induced community restructuring from the invasion phase through an extended legacy period following invader extinction. Our results, through several bacterial invasions under controlled conditions with varying treatments, reveal a consistent and pronounced ‘Matthew effect’ across all four inoculants, whereby invasion reinforces the dominance of abundant taxa while suppressing rare ones, leading to persistent community polarization and functional trade-offs. This reorganization enhanced resource acquisition and nutrient cycling but reduced stress tolerance and ecosystem resilience. Mechanistically, invasion legacy accelerates the replacement of slow-growing with fast-growing taxa, shifting assembly from deterministic to stochastic processes. This ‘Matthew effect’ was modulated by carbon sources: labile carbon (glucose) intensified polarization, while recalcitrant carbon in organic fertilizer buffered the shift, preserving rare taxa and functional diversity. A supporting analysis of published invasion studies corroborates these patterns, indicating broader ecological relevance. Our findings provide a unifying framework for understanding how transient microbial invasions generate lasting ecological imbalances, cascading from community structure to ecosystem multifunctionality. Importantly, we show that organic amendments, particularly those containing recalcitrant carbon, can mitigate the &l
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Journal articleChen SYS, Marchal O, Andres M, et al., 2026,
Deep Cyclones and Benthic Storms in the Western North Atlantic: New Insights From a Regional Circulation Model
, Journal of Geophysical Research Oceans, Vol: 131, ISSN: 2169-9275Deep cyclones (DCs) are mesoscale, deep-reaching features that develop near meander troughs of large-scale currents, such as the Gulf Stream. Although, in some aspects, they could be viewed as oceanic analogs of synoptic-scale cyclones in the mid-latitude atmosphere, their dynamics and impacts are not fully understood. Notably, the roles of different vorticity sources in deep cyclogenesis and the relationship of DCs with “benthic storms” remain to be elucidated. Here we develop a regional configuration of a primitive-equation model with 1/20° horizontal resolution and 10-m vertical resolution over the entire water column to study DCs in the western North Atlantic. In our simulation, DCs form both in the Hatteras Abyssal Plain, where DCs were observed during the 1980-90s SYNOP campaign, and in the Sohm Abyssal Plain, where observations are lacking. Their spatial scales, lifetimes, pressure drops, swirl velocities, and drift speeds compare favorably with observational estimates. During deep cyclogenesis, the pressure fall at abyssal depth reflects a small imbalance between the effects of the sea level drop and of the density increase in the overlying water column within tightening meander troughs. Below 1,500 m, the main source of cyclonic vorticity is vortex stretching, associated mainly with the curvature-induced ageostrophic flow, while vortex tilting is a sink of smaller magnitude. Near-bottom currents in DCs reach speeds comparable to those observed during benthic storms and, when present, dominate the basin-scale bottom energy dissipation. Overall, the study highlights the importance of DCs for sub-annual variability and material transport in the abyssal interior.
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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 articleNoone DP, Bubeck D, 2026,
Advances in cryo-EM that have shaped mechanistic models of membrane attack complex assembly and regulation
, IUCrJ, Vol: 13, Pages: 221-227, ISSN: 2052-2525The complement system is a blood-based immune network that plays a crucial role in fighting infection and maintaining immune homeostasis. The membrane attack complex (MAC) is a pore assembled from complement proteins that creates holes in cells when the immune system is activated. Over the last 10 years, advances in cryo electron microscopy (cryo-EM) have enabled key molecular insights into how MAC assembles, remodels membranes, and is regulated. These new tools revealed the inherent flexibility of complement complexes. By adapting computational approaches that disentangle diverse conformations, these studies have provided detailed mechanisms for MAC activity that could underpin novel complement-targeted therapeutics. Now accelerated by AI-driven image analysis and advances in structural cell biology, the next revolution in cryo-EM o ers new opportunities to understand the cellular consequences of immune activation.
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