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Journal articleYuen ELH, 2026,
A splicing checkpoint couples surface and intracellular plant immunity
, Phytopathology Research, Vol: 8, ISSN: 2096-5362Plant immunity operates through two interconnected layers. Pattern-triggered immunity (PTI) is initiated by cell-surface pattern-recognition receptors, whereas effector-triggered immunity (ETI) is executed by intracellular nucleotide-binding leucine-rich repeat (NLR) receptors. The two layers are known to potentiate one another, yet how a signal perceived at the plasma membrane is relayed to prime an intracellular NLR has remained unclear. In a recent study, Gao et al. (2026) show that the potato late blight resistance protein Rpi-vnt1.1 carries a self-imposed restraint, an autoinhibitory N-terminal extension encoded by an intron-retained mRNA isoform. Pathogen perception, acting through PTI, shifts the balance of alternative splicing towards an isoform that lacks this extension, producing a resistosome-competent receptor that the Phytophthora infestans effector AVRvnt1 can then activate. This work defines pre-mRNA alternative splicing as a checkpoint that couples surface and intracellular immunity, and points to a broadly conserved and engineerable mode of NLR control.
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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 articleWan Y, Wong JLC, Sanchez-Garrido J, et al., 2026,
Genomic and molecular characterisation of a KPC-producing Klebsiella pneumoniae clinical isolate resistant to meropenem-vaborbactam, imipenem-relebactam, and ceftazidime-avibactam
, BMC Genomic Data, Vol: 27, ISSN: 2730-6844Background Resistance to carbapenems and third-generation cephalosporins is increasing in Klebsiella pneumoniae globally, restricting therapeutic options. The β-lactam/β-lactamase inhibitor combinations are widely used to circumvent β-lactamase-mediated resistance. In 2021, an unusual K. pneumoniae clinical isolate, KpMVR1, was recovered from a hospitalised patient in England, exhibiting resistance to meropenem-vaborbactam, imipenem-relebactam, and ceftazidime-avibactam. To investigate this phenomenon, we characterised the genome and antimicrobial susceptibility of KpMVR1 alongside two clonally related isolates susceptible to all three β-lactam/β-lactamase inhibitor combinations: KpMVS1, collected from the same patient 42 days earlier, and KpMVS2, from another patient in the same hospital. Methods Illumina and MinION whole-genome sequencing were conducted for these three isolates, followed by hybrid genome assembly. Annotated genome assemblies were compared to identify genetic variation. Mutagenesis experiments were performed to verify predicted functional alterations. Results All isolates belonged to clone ST8134 and carried blaKPC-2 alleles (KpMVR1: blaKPC-157; KpMVS1 and KpMVS2: blaKPC-2) in plasmids predicted to be conjugative. Insertion sequence ISEc68 caused a frameshift mutation in KpMVR1’s ompK36 gene, reducing susceptibility to meropenem-vaborbactam and imipenem-relebactam. KPC-157 demonstrated decreased hydrolysis of imipenem and ceftazidime when compared with KPC-2. KpMVR1 also encoded a disrupted transcriptional repressor MarR and a destabilising mutation in AcrB, a component of the AcrAB-TolC multidrug efflux pump. An intact, iron-transporting fec operon was identified on a novel IncFII(pKP91)/IncFIB(K) plasmid unique to KpMVS2, possibly accounting for the cefiderocol resistance observed in this isolate. ConclusionsKpMVR1 carried multiple resistance-associated genetic alterations and likely developed its resistance profile
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Journal articleHui T-Y, Epopa PS, Millogo AA, et al., 2026,
Variance partitioning reveals contrasting random effect contributions to the density and species composition of malaria-transmitting mosquitoes in Western Burkina Faso
, Parasites and Vectors, Vol: 19, ISSN: 1756-3305Background Spatial-temporal variation exists in the density and species composition of malaria-carrying mosquitoes, which will in turn influence the transmission of the disease. While there has been extensive research on seasonality and other main drivers of the vector populations, the heterogeneity partitioned as random effects at various spatial-temporal scales is just as important but has not attracted the same attention. Methods To investigate the relative contributions of the between-house, between-village, and between year variations, as well as other house-level covariates such as inhabitant number and bed net usage on vector density and species composition, intensive Pyrethroid Spray Catches (PSC) sampling was conducted across a 60-month period between 2012-2019 from four villages in the Sudano-Sahelian region of Burkina Faso. Results For density, measured by female Anopheles gambiae s.l. counts, our modelling showed that the between-house variation was the largest variance component, followed by the between year then between-village variation, after accounting for seasonality and other covariates. Density increased with the number of inhabitants within a household but was uncorrelated with bed net presence. A subset of female mosquitoes was genotyped for species identification, and the composition of An. coluzzii and An. gambiae, the two dominant vectors in the region, varied markedly across villages without an overall trend. The between-village variance contributed up to 76% of the total random variation in species composition, followed by the between-year variance. The between-house variation was statistically insignificant. Neither household size nor bed net usage had any impact on species composition. Conclusions Interestingly, the between-house component of variation was the largest contributor when measuring mosquito density, but it was the least important for species composition. For between-village variation the converse was found. Together with
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Journal articleDe Lorm TA, Heon SP, Bernard H, et al., 2026,
Bird and mammal communities transform without collapsing in response to oil palm replanting
, Forest Ecology and Management, Vol: 619, ISSN: 0378-1127Replanting a tree plantation - that is, clearing old trees and replacing these with young plants - drastically alters its habitat structure and microclimate, leading to changes in its biodiversity. Nevertheless, we lack an understanding of how the replanting of oil palm plantations - the most prominent oil crop globally - affects mammals and birds, while the amount of area replanted will increase exponentially over the next decades. We therefore studied how the bird and mammal community of an oil palm plantation in Malaysian Borneo changed in response to replanting. Using camera traps for mammals, and acoustic recordings and BirdNET for birds, we show that both communities are transformed. Mammal species richness slightly dropped, because of the absence from replanted plantations of long- and pig-tailed macaques (Macaca fascicularis and M. nemestrina), both endangered primate species. Bird species richness did not significantly differ between replanted and mature plantations. However, the detection frequency of most species changed, as the bird community shifted from forest and woodland species towards open-habitat species. The detection frequency and species richness of different trophic niches stayed largely constant, indicating that birds will still be able to perform similar high-level ecological functions in replanted plantations. Overall, our results show that replanting reshaped mammal and bird communities, but that their diversity and abundance does not collapse. These findings stress the importance of staggered replanting, as opposed to replanting large stretches of plantation in one go, to bolster landscape level biodiversity, and underscore that tree plantations are temporally dynamic habitats.
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Journal articleBourne A, Amatiello FG, Elger K, et al., 2026,
Feeding the disease: The impact of nutritional supplementation on Nosema (Vairimorpha) infection in honey bees (Apis mellifera).
, J Invertebr Pathol, Vol: 219Honey bees (Apis mellifera) experience variable colony losses across regions and years, with infectious diseases representing a key component of colony health challenges. Among the most prevalent pathogens are the microsporidian parasites Nosema apis and Nosema ceranae, whose impacts on host survival and transmission vary widely depending on context. While nutritional supplementation is commonly used to support honey bee health, its effects on Nosema infection outcomes remain unclear. Here, we experimentally tested whether dietary enrichment alters survival and infection intensity following exposure to a mixed Nosema inoculum. Newly emerged worker bees were challenged with Nosema spores and maintained on either a basic sucrose diet or the same diet supplemented with a commercial pollen substitute. Dietary enrichment significantly increased both mortality risk and infection intensity in Nosema-infected bees, while having no detectable effect on survival in uninfected controls. These results indicate that supplementation can, counter intuitively, exacerbate nosemosis by promoting parasite replication rather than enhancing host resistance. Our findings highlight the importance of distinguishing nutritional effects on host tolerance versus resistance, and caution that interventions intended to improve bee nutrition may inadvertently increase pathogen production and transmission potential under certain conditions.
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Journal articleMoffett ER, Gayford JH, Chen L, et al., 2026,
Biodiversity safeguards ecosystem services and functions worldwide.
, Nat Ecol EvolBiodiversity loss threatens ecosystem services on which humanity depends, yet the strength, form and context-dependency of biodiversity-ecosystem service and biodiversity-ecosystem function relationships remain poorly quantified. Here we synthesize 423 studies to determine how biodiversity affects ecosystem functioning and service delivery. We show that regulating services, including water quality and pollination, often exhibit linear relationships, suggesting an additive role for diversity. While biodiversity enhances most functions and services, our effect-size analysis shows that oceanic 'blue carbon' sequestration is exceptionally sensitive, revealing how critical marine biodiversity is for climate mitigation. Conversely, services such as hazard regulation appear relatively insensitive to biodiversity, instead depending on a few functionally unique foundational species whose persistence nonetheless is interdependent on the wider community. Our new synthesis enables the forecasting of impacts, for example, that biodiversity loss will reduce pest regulation in countries experiencing population growth and intensive development, and it also highlights how ecosystem services might be used to anticipate future problems.
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Journal articleWiddicombe B, Barritt JD, Pipatpadungsin N, et al., 2026,
Cryo-EM Analysis of Adenovirus Vector Reveals Purification Conditions Leading to Loss of Viral Fiber Proteins and Reduced Infectivity.
, Biotechnol BioengVaccines and gene therapies require efficient delivery of genetic material to host cells. Viral vectors leverage viruses' ability to enter host cells to achieve this. Following the SARS-CoV-2 vaccine and novel gene therapies that utilize adenovirus vectors, there has been an increase in the demand for large-scale production of vectors. A benefit of adenovirus vectors is that they can act as a "plug and play" tool for any future emerging diseases for the development of vaccines. A key obstacle was the heterogeneity that is found in the final product. This can reduce the functionality of the vector and affect immune responses. A possible origin of heterogeneity is the downstream processing, specifically the bind and elute steps of anion exchange chromatography (AEX), which is widely used at scale. To better understand the heterogeneity that AEX could elicit on the adenovirus capsid, cryogenic-electron tomography was used to assess the capsid integrity after a variety of chromatography conditions in comparison to a cesium chloride (CsCl) gradient ultracentrifugation purified control. To investigate the effect of absorption time during chromatography, AEX conditions with a 5, 10, and 20 min on-resin absorption periods were evaluated. Following AEX binding at pH 6.5, samples showed a reduction from 17% in the CsCl purified control to 10% infectious particles. When examined using electron microscopy, the virions exhibited aggregation and a decrease from 70% to 54% in fiber occupancy. After a 20 min AEX hold at pH 6.5 there was almost complete loss of infectivity and fiber occupancy decreased from ~70% to below 30%. Samples run at pH 8 did not show the same loss in infectivity when held bound for 20 min. This suggests that purification conditions can cause removal of the fiber protein, which was likely causing the decrease in infectivity, due to the fiber's role in cell entry. We hypothesize that fiber removal was caused by a combination of h
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Journal articlePerren L, Livernois W, Woloszyn K, et al., 2026,
Topology-enforced synthesis of atomically precise silver nanoclusters in 3D DNA lattices.
, Sci Adv, Vol: 12DNA nanotechnology leverages the molecular design resolution of the DNA double helix to fold and tile matter into designer architectures. Recent advances in bioinorganic chemistry have exploited DNA/Ag+ affinity to carry out the templated reduction of silver nanoclusters. Here, we develop a unified method that leverages the topology of DNA triangles with embedded silver base pairs to nucleate controlled cluster growth in a mesoporous 3D lattice. Use of confocal fluorescence microscopy allows for the direct observation of reaction kinetics and reconstruction of the optical bandgap. These crystals yield molecular structures of Ag4 and Ag6 by x-ray diffraction in varying pyrimidine:pyrimidine pairs. Intercluster distances of less than 2 nanometers show observable electronic coupling, with red shifting observed relative to literature standards. A thorough computational investigation establishes a theoretical basis for our observed behavior and establishes the interplay between cluster size, charge, geometry, and resonance. We anticipate that these results will yield advances in materials synthesis, DNA-based plasmonic crystals, and optically active nanoelectronics.
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Journal articleMeramveliotakis E, Ntatsopoulos K, Vogler AP, et al., 2026,
Association with dynamic habitats disrupts speciation and reduces the efficacy of purifying selection in flightless beetles.
, Evolution, Vol: 80, Pages: 2171-2186Association with temporally dynamic habitats has been proposed as a strong predictor of effective population size (Ne) and speciation rates, and thus also potentially of molecular evolution rates, but empirical insights remain limited. We use a genomic dataset of over 2,000 single-copy orthologs to evaluate how habitat association shapes molecular evolution in closely related flightless beetle lineages (Coleoptera: Tenebrionidae: Eutagenia), co-distributed across Eastern Mediterranean islands. The focal taxa occupy either dynamic coastal sand dunes or stable compact-soil habitats but share uniform life-history traits and morphology. Species delimitation analyses identified a single widespread coastal dune species, whereas the stable-habitat clade has diversified into nine allopatric species across the same geographic space and timeframe. Despite its wide distribution, the dynamic-habitat lineage exhibits the lowest long-term Ne and accordingly the highest median nonsynonymous-to-synonymous substitution rate ratio (dN/dS), yet its total substitution rate is not significantly higher. We propose that recurrent local population extinction in dynamic habitats hinders the completion of speciation and reduces the efficacy of purifying selection, thus elevating the dN/dS ratio. More broadly, these findings indicate that diversification and molecular evolution rates may become decoupled under recurrent population turnover, a hypothesis that requires further empirical and theoretical investigation.
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Journal articleSouthworth-Davies RJ, Murray JW, Carmichael I, et al., 2026,
Separating the effects of temperature and absorbed X-ray dose on unit-cell volume.
, Acta Crystallogr D Struct BiolThe behaviour of the unit-cell volume of crystals of the iron-storage molecule ferritin, both in the apo and the holo form, and of influenza A virus subtype N9 neuraminidase at 100 K and over a controlled cryo-temperature series was investigated. The purpose of this study was to separate out the effects of dose and temperature on the protein by assessing the changes in the unit-cell volume. Over the wide range of X-ray doses examined in this work, the irreversible effect of dose on the unit-cell volume could be distinguished from the reversible (below 160 K) temperature-induced effects. Specific structural damage effects were not reversible.
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Journal articleRutter-Locher Z, Norton S, Menon B, et al., 2026,
Centrally mediated pain features predict persistent pain in early inflammatory arthritis: a 2-year prospective study.
, Pain, Vol: 167, Pages: 2365-2374Patients with inflammatory arthritis (IA) often report pain not necessarily coupled to active inflammation. We previously demonstrated that a significant subset of patients with newly diagnosed IA report features of centrally mediated pain. In this prospective study following the same IA cohort, we tracked the relative contributions of inflammatory/noninflammatory mechanisms to pain over 2 years. We used patient-reported outcome measures (PROMs), clinical data (including ultrasound), and standardised quantitative sensory testing. Mixed-effects regression models examined longitudinal associations. We recruited 66 patients. At 6, 12, and 24 months, 62%, 57%, and 49% of individuals, respectively, reported persistent pain (numerical rating scale ≥3). Using factor-derived composite scores, baseline and longitudinal inflammation was not associated with subsequent pain ( b -0.05, P = 0.87), whereas higher centrally mediated pain markers predicted less pain reduction ( b 1.41, 95%, P < 0.001). Baseline PROMs of centrally mediated pain (fibromyalgia severity average marginal effect [AME]: 0.94, P < 0.001, painDETECT AME: 1.03, P < 0.001) and mental health (eg, Generalised Anxiety Disorder-7 AME: 1.08, P < 0.001) were the strongest predictors of persistent pain. Baseline trapezius pressure pain threshold (PPT) and conditioned pain modulation (CPM) pain detection threshold (PDT) effect showed modest association (trapezius PPT AME: -0.51, P = 0.054, CPM PDT effect AME: -0.49, P = 0.051) whereas temporal summation of pain (AME: 0.09, P = 0.756) and CPM pain tolerance threshold effect (AME: -0.01, P = 0.964) did not. In our cohort, persistent pain was associated with higher baseline and longitudinal scores for centrally mediated pain according to PROMs rather than inflammation according to joint ultrasound. In IA, early identification and treatment of features of centrally mediated pain may improve pain-related outcomes.
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Journal articleLerch A, Small ST, Hui TJ, et al., 2026,
Estimation of Adult Census Size From Close‐Kin Dyads in the Malaria Mosquito <i>Anopheles gambiae</i>
, Evolutionary Applications, Vol: 19, ISSN: 1752-4571<jats:title>ABSTRACT</jats:title> <jats:p> Accurate estimates of adult mosquito abundance are central to the design and evaluation of vector control strategies, yet they are difficult to obtain from natural populations. Conventional mark‐recapture methods for estimating adult mosquito census size pose logistical and other challenges. A recently developed close‐kin mark‐recapture (CKMR) approach is a promising alternative. However, application of CKMR has been largely confined to long‐lived vertebrates. Validation on empirical data from short‐lived, highly fecund insects is lacking. Here, we apply CKMR to a natural population of <jats:styled-content style="fixed-case"> <jats:italic>Anopheles gambiae</jats:italic> </jats:styled-content> , the primary African malaria mosquito, sampled from a small island in Lake Victoria, Uganda. Using a high‐diversity amplicon panel of genome‐wide markers, we genotyped 714 adult mosquitoes collected over a 20‐day period. We classified pairs to close‐kin categories by implementing probabilistic latent‐kinship estimation rather than using a deterministic threshold‐based framework. We observe numerous full‐sibling pairs but no parent‐offspring pairs, a pattern consistent with extreme variance in reproductive success owing to frequent failure of mosquito egg clutches to produce adults. Building on existing CKMR theory tailored to mosquito life history, we fit an extended model that included the possibility of clutch failure. By incorporating probabilities of both parent‐offspring and full‐sibling relationships, we estimate an adult female census size of 26,887 (95% credible interval: 6979–146,011), and a clutch failure probability of 97.6% (CrI: 91.3%–99.6%). We use these estimates to calculate the predicted variance in reproductive success and effective populatio
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Journal articleGranville NR, Williams JJ, Groner VP, et al., 2026,
Temperature mediates variation in avian sensitivity to forest cover.
, Nat Ecol Evol, Vol: 10, Pages: 1914-1926Emerging evidence shows that responses to deforestation can differ both across species and among populations of the same species. The reasons underlying these complex patterns are unclear, and this lack of clarity is a barrier to accurate monitoring and prediction of biodiversity change. Using data from 2,262 bird species across 7,326 sites from all forested continents, we show that between-species and within-species variations in responses to forest cover are mediated by temperature. Populations in warmer macroclimates tend to decline in incidence in deforested landscapes because hotter microclimates push them closer to their species' realized upper thermal tolerance limits. By contrast, populations in cooler macroclimates tend to be less affected by or even benefit from deforestation, as microclimatic temperatures are pushed closer to more optimal temperatures. Our findings offer an empirically grounded framework for biodiversity models that move beyond fixed species responses and incorporate interactions between temperature and land-use change.
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Journal articleHe D, Brazeau MD, Zhu M, et al., 2026,
Reappraisal of the opercular anatomy in the ‘maxillate placoderms’ <i>Entelognathus primordialis</i> and <i>Qilinyu rostrata</i>
, Royal Society Open Science, Vol: 13<jats:title>Abstract</jats:title> <jats:p>The Silurian ‘maxillate placoderms’ Entelognathus primordialis and Qilinyu rostrata were previously described as possessing a single dermal operculum, suspended by either an opercular cartilage or an antiarch-like dermal articulation, respectively. Here, we reinvestigate the holotypes of these taxa using synchrotron and micro-CT scanning data, revealing opercular morphologies distinct from prior descriptions. Instead of a single opercular plate as in other ‘placoderms’, Entelognathus possesses two dermal opercular plates arranged anteroposteriorly. The larger posterior plate bears a pronounced anterodorsal process, which was previously identified as the opercular cartilage. Both plates are extensively overlapped by the skull roof. The opercular morphology of Qilinyu, although consisting of a single opercular plate, shares features with that of Entelognathus, including a pronounced anterodorsal process and an extensive overlap by the skull roof. A comparison of the gill-covering structures in various early gnathostomes indicates that the described character combination is unique to the maxillate placoderms. The skull roof overlap suggests that the opercula of both taxa could slide along the visceral surface of the skull roof. Two new phylogenetic characters and several revised characters related to the operculum are proposed for an updated phylogenetic analysis of early jawed vertebrates. The Adams consensus tree from our analysis identifies phylogenetic signal for the monophyly of at least some of the maxillate placoderms.</jats:p>
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Journal articleLiu Z, Feng T, Guo L, et al., 2026,
Host-mediated insecticide sequestration in target-site-resistant pests impacts parasitoid fitness and evolution.
, Proc Natl Acad Sci U S A, Vol: 123Insecticide resistance poses a major challenge to global pest management, yet its cascading effects on ecological networks remain poorly understood. Here, we show that target-site-resistant herbivorous insects can accumulate unmetabolized insecticides and inadvertently function as "toxic prey," impairing the fitness of their natural enemies. Using neonicotinoid- and spinosyn-resistant Myzus persicae and genetically modified Drosophila melanogaster, we demonstrate that resistant hosts surviving high-dose insecticide exposure retain substantial poison residues that are transferred to developing parasitoids. This host-mediated exposure leads to reduced parasitoid emergence, shortened adult lifespan, and smaller body size, even persisting across generations. Moreover, we identify parallel evolution of resistance-conferring Rdl (resistance to dieldrin) mutations in multiple distantly related parasitoid species that target cyclodiene- and fipronil-resistant hosts. This mirrors the coevolutionary arms race seen in natural systems, where the same genetic mutations that allow herbivores to tolerate plant toxins also enable their predators to overcome those defenses. By uncovering a consequential route of insecticide exposure via trophic transfer, and the resulting coadaptation in higher trophic levels, our study offers critical insights into the ecological costs of resistance and highlights the need for pest management strategies that integrate both chemical and biological control sustainably.
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Journal articleZhou B, Prentice CI, 2026,
Optimal biomass allocation to leaves across global terrestrial ecosystems
, Global Change Biology, ISSN: 1354-1013Leaves influence global climate and water resources by regulating the flows of CO₂, energy, and water between the atmosphere and land. Here we developed a theoretical framework that predicts the optimal annual fraction of biomass production allocated to the production of new leaves (ηf) as the product of the optimal leaf area index(LAI) and the optimal ratio of leaf mass–per–area to the leaf life cycle (LMA/LC), divided by annual total biomass production (BP). All quantities depend on local environmental variables, with different solutions (embedding a climatic aridity effect on optimal LMA/LC) for evergreen and deciduous plants. Using a global compilation of ηf data, we show that this theory predicts the emergent responses of ηf to growing–season temperature and aridity. These responses arise from the trade–offs among the environmental sensitivities of LMA/LC, LAI, and BP. It is predicted that the rising CO₂ is steadily reducing the fraction of biomass production allocated to leaves.
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Journal articleYamaguchi H, Isalan M, 2026,
Loop engineering and activity improvement of TEV protease by a phagemid-based selection system
, Scientific Reports, ISSN: 2045-2322Loop engineering of enzymes remains challenging due to high flexibility and conformational complexity, posing a bottleneck for deep-learning-based design. Here, we constructed mutant libraries for three loops of TEV protease to assess combining directed evolution with deep learning. Using an M13 phagemid-based selection system, the three libraries were screened, resulting in a Loop 1 variant (HyperTEV60/L1) that significantly enhanced the Miichaelis constant (Km) of the HyperTEV60 scaffold, a highly active mutant identified byProteinMPNN. Structural modeling suggested that a single-residue deletion and substitution in Loop 1 expands the substrate binding pocket, accounting for the improved Km. Although the catalytic efficiency kcat/Km of HyperTEV60/L1 was only marginally higher than HyperTEV60, due to a kcat decrease, our results reveal that the phagemid-based selection system tended to find variants optimizing Km. This study demonstrates that combining deep- learning-based global optimization with localized directed evolution maximizes the probability of discovering distinct, high-performance enzyme variants.
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Journal articleKnüsel S, Benninger M, Versluis DM, et al., 2026,
Chemotactic responses of Trypanosoma brucei procyclic forms to proline and other metabolites.
, Mol Biochem Parasitol, Vol: 268Many protozoan parasites have complex life cycles entailing migration through different organs in their hosts, but the cues guiding them remain poorly understood. Using a semi-solid plate motility assay, we show that early procyclic forms of Trypanosoma brucei, the first stage to develop in the tsetse fly midgut, perceive several metabolites - including glucose, glycerol and proline - as chemoattractants, while the glycolytic end-product succinate acts as a repellent. During adaptation in the fly, T. brucei switches from glucose/glycerol to proline as its primary energy source. We show that the parasite's chemotactic response towards proline requires adenylate cyclase ACP5 and the cyclic AMP response protein CARP3, two components of a signalling pathway involved in pH sensing. These results are consistent with a role for T. brucei's expanded repertoire of adenylate cyclases as environmental sensors, providing a tractable system for future studies on how trypanosomes navigate through the host.
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Journal articleBradshaw J, Sanchez-Garrido J, David S, et al., 2026,
PgaR is a positive regulator of the pgaABCD biosynthetic operon in Klebsiella pneumoniae.
, Infect ImmunThe biosynthetic locus encoding the exopolysaccharide poly-N-acetyl-glucosamine (PNAG) is widely conserved across bacteria, including the World Health Organization critical-priority pathogen Klebsiella pneumoniae (Kp). In Kp, PNAG synthesis is mediated by the pgaABCD operon, yet its lineage-specific regulation remains incompletely understood. Using a comparative genomics approach to interrogate the pgaABCD locus across the high-risk clonal Kp complex 258 (CC258) lineage, we identified a previously uncharacterized positive transcriptional regulator located immediately upstream of pgaA, which we designate pgaR. Phylogenetic analysis revealed recurrent evolutionary events affecting this regulatory region, including repeated deletion or truncation of pgaR and a G > A substitution upstream of the pgaR start codon. Functional characterization demonstrated that loss of pgaR abolishes pgaABCD expression and PNAG production, whereas the upstream G > A substitution drives PNAG hyperproduction. Under in vitro growth conditions, Kp produce extensive extracellular PNAG networks. Using a prototype hypervirulent strain to model the role of PNAG in vivo indicated that it is dispensable for virulence in murine pneumonia and peritonitis models. In contrast, PNAG hyper-production significantly attenuated virulence and reduced disease severity. Collectively, these findings identify PgaR as a novel upstream gene regulator of the pgaABCD operon and reveal a previously unrecognized lineage-specific layer of PNAG regulation in Kp. This demonstrates that opposing PNAG phenotypes, loss and hyper-production, have independently and repeatedly emerged among clinical CC258 isolates, highlighting selective pressures acting on this locus.
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Journal articleShen S, Zahedifard F, Agbebi EA, et al., 2026,
A luminal proteome of the endoplasmic reticulum and Golgi apparatus reveals a novel modulator of ER stress tolerance in African trypanosomes.
, Open Biol, Vol: 16African trypanosomes employ specialized mechanisms of membrane trafficking as a strategy to persist in both the mammalian host and insect vector. Their survival relies on continuous synthesis and surface delivery of extremely abundant surface coat proteins, imposing an extraordinary biosynthetic burden on the secretory pathway. Despite this, their ER and Golgi luminal proteomes remain incompletely characterized. Here, we exploit proximity biotinylation, using the abundant ER chaperone BiP as bait to map the ER proteome in bloodstream and procyclic lifecycle stages. Comparison with BiPN, a truncated secretory form of BiP that escapes the ER and transits the Golgi, provides differential compartmental labelling. Quantitative ranking of BiP labelling intensity identifies a candidate BiP interactor cohort including a divergent homologue to the mammalian BiP nucleotide exchange inhibitor MANF. Reciprocal manipulation of TbMANF abundance produces opposing shifts in cellular sensitivity to ER stress. These data are consistent with a role in regulating BiP ATPase cycling in an organism that, unlike opisthokonts, lacks a canonical unfolded protein response, making TbMANF the first regulator of BiP activity identified in kinetoplastids. Finally, proximity labelling anchored at the inner face of the nuclear pore via NUP65 extends our endomembrane map to the inner nuclear membrane, identifying candidate proteins of this specialized ER-continuous domain.
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Journal articleHarrison SP, Prentice IC, Ascoli D, et al., 2026,
Land management to mitigate the risks of future fire in the Mediterranean region: strategies and barriers to their adoption
, Frontiers in Environmental Science, Vol: 14, ISSN: 2296-665XExtreme wildfires are becoming more frequent in the Mediterranean region and already frequently exceed controllable thresholds, leading to large impacts on natural and social systems. Wildfire risk is predicted to increase in the region over the 21st century because of ongoing global climate changes. The risk of wildfires is being exacerbated by rural land abandonment, which is promoting increased landscape flammability; and by expansion of the wildland-urban interface. To address the challenges arising from fire regime changes, there is an urgent need to improve existing management strategies to reduce fire risk and to minimise the occurrence of extreme wildfires. Doing so successfully requires integrating insights across varied wildfire management paradigms, that stem from diverse disciplinary traditions and often serve competing policy priorities. Here we review the state of knowledge and practice on wildfire management in the Mediterranean region. We begin by highlighting the diversity of land management practices that deliberately or indirectly have been used for fire risk mitigation, shaping contemporary Mediterranean landscapes and fire regimes. We then summarise the evolution of policy priorities and fire management practices, and how these changes in infrastructural, economic and legal frameworks could influence landscape vulnerability to wildfire. We also examine some of the barriers that work against the adoption of management strategies to minimise wildfire risk at local and national levels. The paper brings together ecological, land-management, governance, planning and economic perspectives that are often treated separately, in order to clarify where current wildfire risk reduction strategies are supported by evidence and where important barriers remain. Finally, we integrate these different insights to identify key knowledge gaps and make recommendations for future action.
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Journal articleVitale M, Kranjc N, Georgiades M, et al., 2026,
Sex-ratio distorters enable pre-zygotic sexing for sex-specific transcriptomics in Anopheles gambiae embryos
, Cell reports, Vol: 45, ISSN: 2211-1247The study of sex establishment at the onset of development is difficult due to the absence of early morphological differences between male and female embryos. This challenge is particularly relevant in non-model organisms such as the malaria mosquito Anopheles gambiae, where sex-determination mechanisms are not fully understood. We employed a pre-zygotic sexing (PZS) system based on synthetic sex-ratio distorters (X- and Y-shredders) to generate large-scale male- or female-biased embryo populations. Combining the PZS system with a hybrid long- and short-read RNA sequencing, we produced a comprehensive sex-specific transcriptomic dataset of early An. gambiae embryogenesis. Comparative analysis identified four sex-specific spliced genes interacting with the sex-determination network, providing candidates for future functional investigation. Together, the PZS system and sex-specific transcriptomic dataset provide a platform for dissecting early sex differences in An. gambiae, advancing both fundamental understanding of insect sex determination and informing novel vector control strategies.
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Journal articleDias J, Franco CH, Alcantara LM, et al., 2026,
The miR-744-5p/connexin 43 axis modulates Salmonella-containing vacuole association with the Golgi network
, EMBO Journal, ISSN: 0261-4189 -
Journal articleZhu Z, Wang H, Zhou B, et al., 2026,
Optimal canopy light-use strategy shapes global greenness dynamics
, Nature Communications, Vol: 17, ISSN: 2041-1723“Greenness” is a key indicator of the functional state of vegetation. However, the physiological processes behind seasonal patterns in greenness are diverse and incompletely understood, hindering the predictability of climate-driven shifts in global foliage phenology. Optimality principles suggest that plants invest in canopy architecture to maximize light capture. Therefore, we hypothesize that, irrespective of specific physiological mechanisms, greenness (fAPAR: fractional canopy light absorption) commonly tracks the seasonal dynamics of potential production (A0: theoretical canopy carbon uptake with all light absorbed). In other words, plants tend to display foliage when it is most productive. We show that observations confirm this hypothesis and develop a model predicting fAPAR from the seasonal cycle of A0, with a phenological lag that increases (from 2 weeks to 3 months) with increasing moisture. This model captures 81% of observed variations in fAPAR and shows that light and environmentally regulated biophysical constraints shape global patterns of vegetation greenness, its seasonal cycle, and its recent increase.
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Journal articleBidartondo M, 2026,
MycorrhizaTracer: a bioinformatic pipeline for fungi and plant classification of Sanger DNA sequences
, Biodiversity Data Journal, ISSN: 1314-2828 -
Journal articlePrakash S, Varela C, Walsh M, et al., 2026,
A genetically encoded local learning rule enables physical learning in engineered bacteria
, Nature Communications, ISSN: 2041-1723 -
Journal articlePrakash S, Isalan M, Varela C, 2026,
A genetically encoded local learning rule enables physical learning in engineered bacteria
, Nature Communications, ISSN: 2041-1723 -
Journal articleMullin V, Hana M, Gill R, et al., 2026,
Museum specimens reveal the genomic consequences of long-term population decline in an insect pollinator
, Molecular Biology and Evolution (MBE), ISSN: 0737-4038 -
Journal articleEllis HR, Behrends V, Larrouy-Maumus G, et al., 2026,
Correction for Ellis et al., "Glutathione impacts Hfq condensation in nitrogen-starved Escherichia coli".
, J Bacteriol, Vol: 208
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