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Journal articleMaia RA, Oki Y, Medina I, et al., 2026,
Atlantic forest tree enhances photoprotective and thermotolerance in soils contaminated by mining tailings
, Theoretical and Experimental Plant Physiology, Vol: 38Large-scale mining disasters in tropical regions impose long-term pressures on ecosystems by degrading soil fertility and exposing native vegetation to chemical and physical disturbances. This study investigates whether Eugenia florida, a native tree species found in both tailings-impacted and reference areas of the Rio Doce Basin in Brazil, exhibits physiological adjustments that confer resilience to combined edaphic and thermal constraints. We assessed soil properties and 16 physiological traits related to nutrient status, photosynthetic efficiency, photoprotection, and thermal tolerance. Soils in the impacted area exhibited markedly lower organic matter, cation exchange capacity, and nutrient concentrations, along with increased iron concentration. Despite a 10% reduction in nitrogen balance index, plants in the impacted area exhibited 10% more chlorophyll and 19% more flavonoids, indicating compensatory pigment production and enhanced antioxidant capacity. Photosynthetic performance remained stable across environments, but individuals in the impacted area displayed elevated regulated energy dissipation and reduced unregulated energy loss, suggesting efficient photoprotective adjustments. Transient fluorescence analyses revealed intensified excitation fluxes and greater heat dissipation per reaction centre. Thermal thresholds, defined as temperatures causing 15% and 50% reductions in photosynthetic efficiency, were significantly higher in impacted individuals. Multivariate analyses identified excitation flux traits as key predictors of thermal resilience. Physiological function in E. florida is sustained through integrated plastic responses under long-term soil degradation and thermal constraints. Its ability to modulate energy fluxes and antioxidant defences highlights its potential as a candidate species for ecological restoration in tropical regions increasingly affected by human disturbance and climate extremes.
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Journal articleDas A, Majumdar A, Thakur BK, et al., 2026,
Integrated Groundwater Management and Arsenic Mitigation in the Indo-Gangetic Plain: Aligning Strategies with Global Sustainability Goals
, Water, Air, & Soil Pollution, Vol: 237, ISSN: 0049-6979 -
Journal articleKim S, Matas-Gil A, Endres RG, 2026,
How nature discovers rare Turing islands: Exploration by common limit cycles
, Proceedings of the National Academy of Sciences, Vol: 123, ISSN: 0027-8424<jats:p>Turing patterns are a cornerstone of biological self-organization, yet their emergence typically requires finely tuned parameters occupying narrow regions of high-dimensional space. This poses a fundamental challenge: how can evolving biological systems reliably find and exploit such rare conditions? In this work, we propose that common biochemical limit cycles, such as those arising from genetic feedback loops, can act as natural explorers of Turing space. By coupling a reaction–diffusion system to an orbit that modulates some of its parameters, we show that the system can dynamically sweep through Turing-permissive regimes and generate transient spatial patterns. We use an entropy-based measure in Fourier space to quantify pattern formation and demonstrate how cycles enhance the detectability and robustness of Turing islands. We further explore how coupling to positional gradients increases reproducibility, suggesting a route from oscillatory dynamics to stable developmental programs. Our results highlight a powerful mechanism by which nature might bootstrap complex spatial structure from simple temporal motifs.</jats:p>
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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 1,2. 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 2. 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 a previously undetected, far-red exclusive subunit, PsbH2’, which forms part of a chlorophyll f binding site and could interact with the far-red allophycocyanin. We also assign four chlorophyll f sites, with one differing from previous reports 3,4, using sequence comparisons and electrostatic potential analyses. In Calothrix, psbH2’ is absent, and the same analyses show that only two of these sites are present. Comparative phylogenetic, structural, and spectroscopic analyses allow the assignment of specific wavelengths to all the red-shifted chlorophylls, which is not possible in chlorophyll-a-only photosystems due to spectral overlap. This provides the detailed 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 articleGider Yaman G, Bozkurt O, Akgun E, et al., 2026,
Neonatal Intestinal Perforations Due to IL10RB Deficiency.
, Indian J Pediatr -
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 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 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 articleSethi S, 2026,
National-scale acoustic monitoring of avian biodiversity and migration
, Communications Biology, ISSN: 2399-3642illions of birds migrate annually, triggered by endogenous behaviors but also by ecoclimatic drivers which are shifting with climate change. These dynamics play out over huge spatiotemporal scales, making monitoring of phenology challenging with traditional biodiversity survey approaches. In this study, over a complete spring migration season (April through June), we collected 37,429 hours of audio from 28 networked sensors in forests across Norway using a nationwide passive acoustic monitoring (PAM) system. We applied an open-source detection algorithm to automatically classify bird vocalizations; through expert validation we found the algorithm classified 57 species (14 full migrants) with at least 80% precision. Using these automated detections, we developed regional arrival curves for three common migratory passerines: Willow Warbler, Common Chiffchaff, and Spotted Flycatcher. We then demonstrate that PAM detections can be used to train audio species distribution models that map how species vocalization probability changes across Norway during spring migration. Lastly, we discuss how PAM can complement existing manual surveys to support the design and implementation of effective policy and conservation measures.
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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 articleParacuellos P, Bexter A, Patkowski JB, et al., 2026,
Molecular basis of type VI secretion system effector loading.
, Nat MicrobiolType VI secretion systems (T6SSs) are widespread bacterial nanomachines that deliver effectors into prokaryotic and eukaryotic cells. How an effector cargo is recruited and loaded into the Hcp ring assemblies that form the tube injected by the T6SS remains poorly understood. Pseudomonas aeruginosa has four T6SSs, each associated with a different Hcp protein. Here we use cryo-electron microscopy to resolve the structure of the Tce1 cargo loaded into a Hcp3 ring from the P. aeruginosa H3-T6SS. We show that a single Tce1 monomer interacts asymmetrically with, and is enclosed by, two hexameric Hcp3 rings, engaging key residues lining the inner surface of the Hcp3 disc. Our data indicate a stepwise loading mechanism, where an initial heterodimeric Hcp-cargo complex forms before ring encapsulation around the effector. Structural modelling suggests similar effector-Hcp3 interactions for a second T6SS effector, Tce2, which has antifungal activity. We propose that this mechanism enables coordinated delivery of a broad payload into target cells.
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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 articleZhu Y, Li M, Zheng J, et al., 2026,
Non-correlated variation of leaf and fine root traits in subtropical forest plants
, Ecology Letters, 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 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 articleBa W, Harding E, Nollet M, et al., 2026,
Wake-active brainstem GABA neurons signal sleep pressure by upregulating AMPA receptors to drive rebound sleep
, Current Biology, ISSN: 0960-9822How the brain compensates for sleep deprivation (SD) by generating rebound sleep (RS) is not understood. Using Ca²⁺ photometry, we identified a WAKE/REMS-active somatostatin/parvalbumin GABAergic population in the mouse brainstem oral pontine reticular nucleus (PnOVgat). Following SD, PnOVgat cells transiently switched for the first hour to higher activity during NREMS, promoting RS. Chemogenetic activation of PnOVgat neurons prolonged NREMS, whereas ablation blunted EEG delta power rebound and slowed RS accumulation. During RS, the selective switch of PnOVgat cells to having higher Ca2+ levels in NREMS correlated with elevated levels of synaptic proteins PSD95, activated CaMKII (pCaMKII T286), activated PKA (pPKA T197), and GluA1-containing AMPA receptor subunits with enhanced serine phosphorylation. All increases started during SD and persisted after the first hour of RS. Patch-clamp recordings demonstrated increased postsynaptic AMPA/NMDA receptor ratios in PnOVgat cells 1 h after RS, indicating increased excitability and greater capacity to drive RS. In contrast, an intermingled population of GABA/glycinergic neurons did not respond to SD, despite having similar baseline WAKE/REMS activities and an ability to promote NREMS. The PnO also contained an intermingled population of excitatory PnOVglut2 WAKE/REMS-active neurons; lesioning them caused hypoactivity, but sleep or WAKE amounts were unaffected. The synaptic homeostasis hypothesis (SHY) proposes that as wakefulness progresses, synaptic AMPA receptor activity is enhanced, and subsequently downregulated during NREMS to rebalance circuit function. We suggest that a variation of SHY implements catching up on lost sleep, with glutamate receptor plasticity in the PnO tracking time awake and adjusting NREMS amounts accordingly.
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Journal articleMajumdar A, Bagchi D, Kotta-Loizou I, et al., 2026,
The One Health resistome: Integrating environmental, microbial, and human antimicrobial resistance surveillance and risk analysis in the digital age.
, J Hazard Mater, Vol: 513Antimicrobial resistance (AMR) and antibiotic resistance (ABR) represent one of the most pressing global health threats, driven by the complex interplay between human, animal, and environmental factors. The One Health resistome framework recognises that resistance genes circulate continuously across clinical, agricultural, and environmental compartments through horizontal gene transfer, co-selection mechanisms, and anthropogenic contamination. This comprehensive review synthesises current evidence on integrated AMR surveillance, examining how digital technologies are transforming our capacity to monitor, predict, and respond to resistance emergence. Key advances include whole-genome sequencing enabling high-resolution pathogen tracking, metagenomics revealing environmental resistome diversity, machine learning algorithms predicting resistance phenotypes with > 85% accuracy, and point-of-care diagnostics extending sophisticated testing to resource-limited settings. Geographic information systems facilitate spatial hotspot identification, while wastewater-based surveillance provides early warning capabilities, detecting resistance genes before clinical manifestation. Despite technological progress, substantial challenges persist: fragmented data streams across sectors, lack of standardised environmental monitoring methods, limited laboratory capacity in low- and middle-income countries, and chronic underfunding. Emerging technologies, portable nanopore sequencing, CRISPR-based diagnostics, artificial intelligence, and blockchain-enabled data governance promise to address these gaps. Realising comprehensive One Health resistome surveillance requires sustained investment in interoperable digital infrastructure, international standardisation, capacity building, and political commitment to cross-sectoral coordination, prioritising equitable global implementation.
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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 CommunAutophagy 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 articleEneli AA, Siu PC, Perez MF, et al., 2026,
On the use of generative models for demographic inference in malaria vectors from genomic data.
, G3 (Bethesda)Malaria in sub-Saharan Africa is transmitted by mosquitoes from the Anopheles genus. Efforts to control the spread of malaria have often focused on these vectors, but little is known about the demographic history of populations and species of Anopheles mosquitoes. Here, we adapt and apply an innovative generative deep learning algorithm to infer the joint evolutionary history of Anopheles gambiae populations sampled in Guinea and Burkina Faso. We further develop a model selection approach and discover that an evolutionary model with migration fits this pair of populations better than a model without post-split migration. For the migration model, we find that our method accurately captures population genetic differentiation. These findings demonstrate that machine learning and generative models are a valuable direction for future understanding of the evolution of malaria vectors, including the joint inference of demography and natural selection. Understanding changes in population size, migration patterns, and adaptation in hosts, vectors, and pathogens will assist malaria control interventions, with the ultimate goal of predicting nuanced outcomes from insecticide resistance to population collapse.
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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 articleMajumdar A, Kotta-Loizou I, Buck M, et al., 2026,
Temperature-dependent biofilm and sublancin production arrest soil arsenic and antibiotic resistance gene mobility.
, J Hazard Mater, Vol: 512Climate change-induced warming and arsenic soil contamination synergistically threaten agricultural sustainability by restructuring microbial communities and accelerating antimicrobial resistance dissemination. Here, through integrated greenhouse and field trials, we demonstrate that Bacillus subtilis 168-derived biofilm and sublancin, a glycosylated antimicrobial peptide, simultaneously immobilise rhizospheric arsenic and suppress horizontal transfer of antibiotic resistance genes (ARGs). Temperature-dependent biofilm formation (25-35°C) enhanced arsenic sequestration within the extracellular polymeric substance matrix, with SEM-EDX revealing a 74% increase in arsenic weight percentage at 35°C and ToF-SIMS confirming ∼14-fold and ∼9-fold increases in root-associated arsenic on biofilm-colonised surfaces in greenhouse and field trials, respectively. Sublancin production peaked at 30°C (129.72 mg L⁻¹), selectively suppressing all 12 tested pathogenic Gram-positive species by 74-86% while preserving Gram-negative communities. Bio-amendment reduced horizontal gene transfer frequency by 74.7% (p < 0.001) across all temperature regimes. Transcriptomic profiling revealed coordinated upregulation of exopolysaccharide biosynthesis (FDR ∼1.0 × 10⁻²⁷) and sublancin machinery (sunA: +3.5 log₂), alongside downregulation of conventional ARGs (vanA, blaTEM: -2.5 to -4.0 log₂). These findings establish sublancin as a dual-function, climate-adaptive soil bio-amendment simultaneously addressing arsenic bioaccumulation and antibiotic resistance gene dissemination under warming scenarios.
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Journal articleLian X, JiJi J, Fang J, et al., 2026,
Leaf temperature and its departure from ambient air temperature.
, Nat PlantsLeaf 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 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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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 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 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 articleYang H, Yuen FW, Ryan MJ, et al., 2026,
Pathogenicity of <i>Fusarium xylarioides</i> , the Causal Pathogen of Coffee Wilt Disease, in Coffee Seedlings and an Alternate Host, Tomato Fruit
, Plant Pathology, Vol: 75, ISSN: 0032-0862<jats:title>ABSTRACT</jats:title> <jats:p> Widespread 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 <jats:italic>Fusarium xylarioides</jats:italic> , 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 <jats:italic>F. xylarioides</jats:italic> and <jats:italic>F. oxysporum</jats:italic> f. sp. <jats:italic>lycopersici</jats:italic> strains. Expression of effector genes in <jats:italic>F. xylarioides</jats:italic> 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 st
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