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  • Journal article
    Yuen ELH, 2026,

    A splicing checkpoint couples surface and intracellular plant immunity

    , Phytopathology Research, Vol: 8, ISSN: 2096-5362

    Plant 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.
  • Journal article
    Maia RA, Oki Y, Medina I, Figueiredo JCG, Barbosa M, Pereira EG, Aguirre-Gutiérrez J, Fernandes GWet al., 2026,

    Atlantic forest tree enhances photoprotective and thermotolerance in soils contaminated by mining tailings

    , Theoretical and Experimental Plant Physiology, Vol: 38

    Large-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.
  • Journal article
    Wan Y, Wong JLC, Sanchez-Garrido J, Low WW, Turton JF, Morecchiato F, Baccani I, Dodgson K, Rossolini GM, Woodford N, Frankel G, Jauneikaite E, Meunier D, Hopkins KLet 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: 2730-6844

    Background 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
  • Journal article
    Hui T-Y, Epopa PS, Millogo AA, Yao FA, Koulmaga D, Noulin F, Diabate A, Burt Aet 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: 1756-3305

    Background 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
  • Journal article
    De Lorm TA, Heon SP, Bernard H, Ewers RMet al., 2026,

    Bird and mammal communities transform without collapsing in response to oil palm replanting

    , Forest Ecology and Management, Vol: 619, ISSN: 0378-1127

    Replanting 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.
  • Journal article
    Bourne A, Amatiello FG, Elger K, Roberts KE, Evison SEF, Graystock P, Hughes WOHet al., 2026,

    Feeding the disease: The impact of nutritional supplementation on Nosema (Vairimorpha) infection in honey bees (Apis mellifera).

    , J Invertebr Pathol, Vol: 219

    Honey 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.
  • Journal article
    Southworth-Davies RJ, Murray JW, Carmichael I, Rudiño-Piñera E, Weik M, Garman EFet al., 2026,

    Separating the effects of temperature and absorbed X-ray dose on unit-cell volume.

    , Acta Crystallogr D Struct Biol

    The 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.
  • Journal article
    Mullin V, Hana M, Gill R, Ian Bet 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 article
    Ellis HR, Behrends V, Larrouy-Maumus G, McQuail J, Wigneshweraraj Set al., 2026,

    Correction for Ellis et al., "Glutathione impacts Hfq condensation in nitrogen-starved Escherichia coli".

    , J Bacteriol, Vol: 208
  • Journal article
    Zhao H, Pye R, Walker G, Tran W, Simmonds O, Tsitsa I, Islam S, Hanna G, David Aet al., 2026,

    Missense3D-PTMdb: a web tool for visualising and exploring human genetic variants and post-translational modification sites using alphafold models

    , Journal of Molecular Biology, Vol: 438, ISSN: 0022-2836

    Only a fraction of the >11 million missense variants identified in humans has a known clinical significance. Post-translational modifications (PTMs), such as phosphorylation, glycosylation and ubiquitination, are key regulators of protein function and structure. PTMs depend on correct protein folding and the recognition and binding of enzymes to specific amino acid motifs near modification sites. AlphaFold models provide an unprecedented opportunity to explore variants on 3D structures, enabling systematic identification of amino acid substitutions that could affect PTMs and should be further investigated experimentally.We present Missense3D-PTMdb, a “one-stop-shop” interactive web tool that provides a user-friendly sequence-structure mapping of 20,235 human proteins, 11,5 million naturally occurring human missense variants, >60 PTM types and 203,775 PTM residues and their neighbours in sequence and 3D structure space using AlphaFold models of the human proteome. The resource also supports visualisation of novel variants not in the database. Missense3D-PTMdb is freely available at https://missense3d.bc.ic.ac.uk/ptmdb.
  • Journal article
    Casadio R, Lu ZJ, Mathews DH, Sternberg MJEet al., 2026,

    Computational Resources for Molecular Biology 2026.

    , J Mol Biol, Vol: 438
  • Journal article
    Conev A, Islam SA, Tsitsa I, David A, Sternberg MJEet al., 2026,

    3DSeqCheck: a web-based tool for verifying sequence consistency between a 3D structure file and the corresponding UniProt entry

    , Journal of Molecular Biology, Vol: 438, ISSN: 0022-2836

    UniProt is a central repository of protein sequences and annotations, with entries being updated several times a year as new sequencing evidence is collected. By contrast, protein structure resources often evolve at a different pace. The AlphaFold database remained unchanged for four years, until September 2025, during which time nearly 3% of the associated sequences underwent revisions in UniProt. In a range of bioinformatics tasks, protein structure data is paired with sequence annotations from UniProt. Mapping annotations to outdated structure files can lead to errors in downstream analysis. While this concern has been addressed for experimental structures, efforts for the modeled structures are lacking. 3DSeqCheck is a lightweight web tool that enables quick comparison of the sequence of modeled and experimental structures to the latest UniProt entries. 3DSeqCheck provides an interactive visual panel of the alignment and the comparison of the residue numbering and can be accessed freely at: https://missense3d.bc.ic.ac.uk/3dseqcheck and https://github.ic.ac.uk/ImperialCollegeLondon/check3Dseq.
  • Journal article
    Maretvadakethope S, Aor I, Fischer MM, Pedrosa ÀP, Schaerli Y, Perez-Carrasco Ret al., 2026,

    Let there be multifunctionality: Uncovering the dynamical zoo of the AC-DC genetic circuit.

    , Cell Syst

    Gene regulatory networks (GRNs) govern many cell processes. While multistability and oscillations are common GRN dynamics, they are typically studied and engineered in isolation. Here, we challenge this separation using the AC-DC circuit, a minimal three-gene network that merges the classical toggle switch and repressilator. Using a thermodynamic formalism and Bayesian inference, we show that a single-inducer version of the circuit displays diverse multifunctional dynamics, including coexistence of oscillations and multistability. We explore robustness, classify emergent behaviors, and analyze critical slowing down. Remarkably, the AC-DC circuit can produce more than thirty topologically distinct bifurcation diagrams, results that challenge the classical view that network topology rigidly constrains dynamical outcomes. This flexibility enables synthetic capabilities coupling hysteresis with oscillations, criticality, and reversibility. By uncovering the potential of minimal genetic circuits and outlining design principles for their implementation, this work opens directions for harnessing emergent complexity using the basic building blocks of life. A record of this paper's transparent peer review process is included in the supplemental information.
  • Journal article
    Georgiou C, Liu Q, Bruno F, Mai C, Tissot FS, Fan X, Gonzalez Anton S, Birch F, Mukhopadhyay D, Kinston SJ, Chabra S, Sergi C, van Gastel N, Malanchi I, Wilson NK, Duffy KR, Pospori C, Blagborough AM, Gottgens B, Luis TC, Lo Celso Cet al., 2026,

    Rare Hematopoietic Stem Cells resilient to infection-induced stress sense yet withstand inflammation.

    , Blood

    Hematopoietic stem cells (HSCs) sustain lifelong hematopoiesis as their progeny differentiate into all blood cell lineages. Homeostatic HSCs are mostly quiescent and only rarely divide, however their proliferation and differentiation rates can be modulated by external factors. Acute and chronic infections from a wide range of pathogens are known to challenge HSCs at the population level, being forced to respond to inflammation-mediated organismal demand to replenish the myeloid cell pool. However, less is known about the degree of heterogeneity in the HSCs' response to inflammation at the single cell level. Here, using a natural murine malaria model and an NHS-ester biotin dilution assay we identify two subsets of HSCs, BiotinLo and BiotinHi, with distinct proliferation kinetics. Using combined functional, single-cell transcriptomics and phenotypic analyses, we uncover that BiotinHi HSCs remain highly functional despite expressing strong interferon response signatures. These resilient HSCs are more poised to enter cell cycle than control HSCs, but do not divide. They maintain less active mitochondria and express higher levels of CD74 and MHC-II. Additionally, they express higher levels of integrin β2/CD18, which suggest they may have specific interactions with the bone marrow microenvironment. Similar patterns of NHS-ester biotin dilution were elicited by LPS and poly (I:C) challenges. These findings highlight previously unmeasured heterogeneity in the response of HSCs to acute infection-induced inflammation and demonstrate that a likely reserve pool of HSCs remains highly functional during Plasmodium infection not because cells are shielded, but because they maintain a stemness associated metabolic profile despite effectively sensing inflammation.
  • Journal article
    Larrouy-Maumus G, 2026,

    Rv3400 is a phosphoglucomutase required for trehalose metabolism in Mycobacterium tuberculosis

    , Journal of Bacteriology, ISSN: 0021-9193

    Mycobacterium tuberculosis causes over one million deaths from tuberculosis (TB) every year and remains a major burden on human health. Reducing the deadly impact of TB requires a better understanding of the strategies used by M. tuberculosis to adapt its metabolism, survive and persist in the human host. Previous enzymological studies reported that the Mtb rv3400 gene encodes a β-phosphoglucomutase; however, its role in M. tuberculosis metabolism had not been investigated. Here, we show that deletion of rv3400 causes a 30-fold increase in β-D- glucose-1-phosphate, confirming its primary function as a β-phosphoglucomutase. Deletion of rv3400 also causes a growth defect when trehalose is the sole carbon source. Targeted metabolomics revealed that metabolites associated with redox homeostasis, including ergothioneine, mycothiol and mycothione, are decreased in the Mtb Δrv3400 strain compared with the wild type, indicating altered tolerance to redox stress. Consistent with this, the Δrv3400 strain showed increased susceptibility to oxidative stress induced by H2O2 and cumene hydroperoxide, conditions that Mtb encounters during infection. This work advances our understanding of trehalose metabolism in Mtb and suggests that Rv3400 may represent a target for the development of new antimicrobial therapies.
  • Journal article
    Rutter-Locher Z, Norton S, Menon B, Esterine T, Williams R, Taams LS, Kirkham BW, Bannister Ket al., 2026,

    Centrally mediated pain features predict persistent pain in early inflammatory arthritis: a 2-year prospective study.

    , Pain

    Patients 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.
  • Journal article
    Ferrando-Marco M, Lin S, Garcia Del Valle B, Hintze M, Narunsky L, Huang J, Edwards S, Barkoulas Met al., 2026,

    HDAC1/2-mediated repression of Wnt receptor expression orients asymmetric division polarity in Caenorhabditis elegans.

    , Development, Vol: 153

    Asymmetric cell division generates distinct daughter cells essential for tissue development, yet the mechanisms orienting division polarity within tissues remain incompletely understood. Here, we uncover a role for chromatin-mediated transcriptional repression in controlling polarity orientation during asymmetric division of Caenorhabditis elegans epidermal stem cells, known as the seam cells. Tissue-specific loss of the class I histone deacetylase hda-1, homologous to mammalian HDAC1/2, causes polarity reversals and reduces molecular asymmetry between daughter cells. Using Targeted DamID, we identify the Wnt receptors lin-17 (frizzled homologue) and cam-1 (Ror homologue) as key targets. Single-molecule fluorescence in situ hybridisation reveals opposing expression gradients along the body axis, with cam-1 enriched anteriorly and lin-17 posteriorly. In hda-1 mutants, both receptors are upregulated and differences between seam cells are flattened. Overexpression of either receptor alone is sufficient to reproduce the polarity reversals, while co-overexpression produces additive effects. The polarity phenotype is independent of the canonical NuRD and SIN3 complexes, suggesting that HDA-1 acts through an alternative mechanism. These findings link histone deacetylase activity to Wnt receptor expression and suggest that graded receptor expression may provide cues that orient asymmetric division polarity.
  • Journal article
    Yi L, Kulik N, Shao S, Nixon PJ, Komenda J, Krynická V, Yu J, Liu Bet al., 2026,

    The transmembrane domain is a primary determinant of the location and substrate specificity in cyanobacterial FtsH heterocomplexes

    , Algal Research, Vol: 98, ISSN: 2211-9264

    Membrane-embedded FtsH proteases play important and diverse physiological roles in prokaryotes, chloroplasts and mitochondria, but how substrates are distinguished remains unclear. The cyanobacterium Synechocystis sp. PCC 6803 contains four FtsH homologs organized into two distinct heterocomplexes and one homocomplex. The two heterocomplexes, derived from a recent gene duplication event, are the essential FtsH1/3 complex found in the cytoplasmic membrane, and the thylakoid-embedded FtsH2/3 complex, with a role in the repair of photodamaged photosystem II. Using a domain swapping approach, we demonstrate here that the transmembrane domains of FtsH1 and FtsH2 are primary determinants of the cellular location and functional differences between the FtsH1/3 and FtsH2/3 complexes, whereas the soluble AAA+ (ATPases associated with diverse cellular activities) and protease domains and the soluble linker were largely interchangeable under the conditions tested. Overall, our findings identify the transmembrane domain as an important determinant of both the location and substrate specificity of FtsH heterocomplexes and support a role for this domain in their functional evolution.
  • Journal article
    Hodges PW, Arendt-Nielsen L, Bannister K, Clauw D, Nijs J, van den Broeke E, Veasley C, Woolf CJ, Sterling Met al., 2026,

    Central sensitization: when is this the right terminology?

    , Pain, Vol: 167, Pages: 1986-1991
  • Journal article
    Mishra V, Biswas P, Kozik Z, Choudhary J, Frankel Get al., 2026,

    EspO-mediated neutrophil accumulation drives lethality during Citrobacter rodentium infection in interleukin-22-deficient mice.

    , PLoS Pathog, Vol: 22

    Citrobacter rodentium (CR) is a murine-specific enteric pathogen widely used to model infections of the attaching and effacing pathogens enteropathogenic and enterohaemorrhagic Escherichia coli. Infection induces colonic epithelial damage and inflammation that are resolved in resistant mice but result in severe disease and mortality in mice lacking interleukin-22 (IL-22). While IL-22-deficient (Il22-/-) mice succumb to CR infection due to dehydration, in part mediated by disruption of the barrier integrity by the type III secretion system (T3SS) effector EspF, the contribution of immunopathology to infection outcomes is not known. Here, using CR we tested whether dysregulated neutrophil responses drive disease progression in Il22-/- mice. We show that IL-22 deficiency is associated with progressive colonic pathology and increased neutrophil accumulation and activity in the colonic mucosa. Infection of mice with CR lacking the T3SS effector EspO, which is implicated in neutrophil recruitment, resulted in markedly reduced neutrophil accumulation and activity in Il22-/- mice without altering bacterial burden. Notably, CRΔespO infection led to reduced colonic inflammation and complete survival of Il22-/- mice. Consistent with these findings, CXCR2 antagonist treated Il22-/- mice displayed attenuated disease severity and delayed mortality. Together, we identified EspO as the second effector, alongside EspF, whose deletion results in survival of CR-infected Il22-/- mice. Moreover, these findings suggest that excessive neutrophil accumulation and activity are key drivers of lethality during CR infection in Il22-/- mice and that EspO amplifies neutrophil-dependent pathology within a vulnerable epithelial environment.
  • Journal article
    Rowell J, Yanez DC, Ross S, Lau C-I, Zhang E, Monfared A, Peña OA, Chain B, Crompton Tet al., 2026,

    The Thymic Microenvironment Shapes Age-Related Qualitative Changes in the TCR Repertoire.

    , Aging Cell, Vol: 25

    Ageing impairs immune function, increasing susceptibility to infection, autoimmunity and inflammation. The thymus undergoes involution during childhood, and thymocyte and thymic epithelial cell (TEC) numbers decline. Given that adaptive immunity depends on T-cells recognising diverse antigens via their unique T-cell receptor (TCR), the precise age-related changes in TCR repertoire composition are key to understand immunity. To investigate the influence of age on the thymic TCR repertoire we sequenced TCRα and TCRβ transcripts from developmentally defined thymocyte populations from 4-week, 12-month and 18-month-old mice, and from thymocytes recovering from hydrocortisone-treatment, and athymic recipients of RAG1-deficient thymus transplants. The 18-month thymus selected TCR repertoires with distinctive patterns of VxJ and CDR3 k-mer usage compared to young thymus, indicating it had a qualitatively different repertoire with different specificity. It also selected a less diverse TCRβ repertoire with more expanded clones than young thymus. On recovery from hydrocortisone-treatment, both 4-week and 12-month thymus showed bias towards foetal-like 3'TRAVx5'TRAJ rearrangements, but 12-month thymus also produced less diverse and evenly distributed TCRβ repertoires, with increased expansion of TCRβ clones at the CD4-CD8-CD25+CD44-intracellularTCRβ+ stage, increased TRBJ-1-cluster usage and distinctive patterns of combinatorial VxJ usage. Transplantation of athymic nude recipients with old RAG1-deficient thymus generated less diverse, less evenly distributed TCR repertoires with different combinatorial VxJ usage than those generated by young transplants. Taken together our experiments show that the old thymus generates qualitatively different TCR repertoires than young thymus and the non-lymphoid compartment of the thymus contributes strongly to these changes and to age-associated decline in TCR repertoire diversity.
  • Journal article
    Godson A, Eddie L, Schuster M, Zheng K, Toth R, Li Y, Li T, Huang J, Kaschani F, Jutras PV, Kourelis J, Kaiser M, Bozkurt T, Van der Hoorn RALet al., 2026,

    NbRD21 protease controls receptor kinase homeostasis in Nicotiana benthamiana.

    , New Phytol, Vol: 251, Pages: 2741-2752

    RD21-like proteases are papain-like cysteine proteases with a C-terminal granulin domain that are abundant and ubiquitous in angiosperms and have often been implicated in immunity. We previously found that the activity of RD21 in Nicotiana benthamiana (NbRD21) is suppressed during infection with Pseudomonas syringae. Here, we studied the role of NbRD21 in immunity and proteome processing. NbRD21 was disrupted by genome editing and rd21 mutants were subjected to disease assays and shotgun proteomics. Dipeptide substrate zLR-AMC was used in protease assays and agroinfiltration was used to transiently express NbRD21 and candidate substrates. Genome-edited lines lacking NbRD21 develop normally but have drastically reduced zLRase activity and are significantly more susceptible to P. syringae. Shotgun proteomics revealed an increased accumulation of c. 20 diverse receptor-like kinases (RLKs) in untreated rd21 knockout lines, but their transcript levels are unaltered when compared to wild-type plants. 35S-driven GFP-tagged RLKs accumulate more upon transient expression in rd21 plants than in wild-type plants. These data indicate that NbRD21 post-translationally controls RLK homeostasis, either by directly degrading RLKs or indirectly by regulating endocytic RLK recycling.
  • Journal article
    Granville NR, Williams JJ, Groner VP, Barlow J, Betts MG, Daskalova GN, Ewers RM, Dos Anjos L, Arroyo-Rodriguez V, Barbaro L, Cerezo A, Develey PF, Hatfield JH, Jactel H, Karubian J, Kormann UG, Lasky JR, Marsh CJ, Mestre LAM, Morante-Filho JC, Olivier P, Phalan BT, Pidgeon AM, Proença V, Terraube J, Uezu A, Wood EM, Pigot AL, Banks-Leite Cet al., 2026,

    Temperature mediates variation in avian sensitivity to forest cover.

    , Nat Ecol Evol

    Emerging 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.
  • Journal article
    Llewellyn T, Vogler A, 2026,

    A robust phylogenetic framework for ophiostomatoid fungi: orders Ophiostomatales and Microascales (Sordariomycetes, Ascomycota)

    , MycoKeys, ISSN: 1314-4057

    Ophiostomatoids are an ecological group of microfungi that commonly associate with bark and ambrosia beetles. In addition to being insect symbionts, they play significant ecological roles as plant pathogens and include species responsible for major forest tree diseases. Despite their ecological similarities, ophiostomatoid fungi are distributed across two distantly related orders, Microascales and Ophiostomatales, which include many additional fungi with diverse ecological lifestyles. Previous studies have typically focused on localised taxonomic issues or specific fungal ecologies. As a result, public repositories suffer from fragmented locus coverage, sequence misidentifications, and uneven taxon sampling, leaving the community without a standardised, comprehensive dataset to study these fungi at scale. To address this, all available ophiostomatoid fungal sequence data across seven widely used marker loci were curated and analysed to reconstruct densely sampled alignments and trees covering 918 concatenated Microascales sequences and 859 Ophiostomatales sequences. Evaluation of locus performance showed that whilst individual loci exhibit extreme state frequency heterogeneity, composition bias, and topological discordance, concatenated datasets produce robust, well-supported topologies consistent with published genomic studies. Integrating phylogenies with broad ecological trait data reveals a clear contrast in data distribution between the two orders, with ecological lifestyles and beetle associations being broadly uniform and stable across the Ophiostomatales tree but highly heterogeneous in the Microascales, despite comparable species richness. These macroecological data distributions are also shaped by taxonomic philosophies, whereby the fragmentation of Microascales into small, restricted genera tends to visually amplify trait variation, whereas the large, heterogeneous genera of Ophiostomatales can obscure it. This unified, fully reproducible framework establ
  • Journal article
    Brook T, Piponi K, Collins T, Savolainen Vet al., 2026,

    Genomic architecture and breeding trade-offs of coconut drought tolerance

    , Plants, People, Planet, ISSN: 2572-2611

    Climate change threatens coconut palms (Cocos nucifera), a vital tropical crop supporting millions, with yields projected to drop nearly 50%. We assessed drought tolerance in over four thousand trees from the world’s largest coconut collection in Côte d'Ivoire, using 30 years of yield and climate data. Our reaction norm modelling approach revealed substantial variation in drought tolerance and a potential trade-off with yield. Using a quantitative genomic approach, we identified a substantial heritable component, highlighting the potential for genomic selection approaches in breeding climate-resilient coconuts.
  • Journal article
    Bergum M, Martin B, Sutton M, Moore Set al., 2026,

    A liquid handling platform for standardised quantification of cell-free enzymatic activity encoded by antimicrobial resistance genes

    , Synthetic Biology, ISSN: 1939-7267

    Antimicrobial resistance (AMR) is a growing global threat to human health, and rapid methods for characterising emerging antimicrobial resistance genes (ARGs) are needed. Here, we develop a semi-automated workflow using cell-free gene expression (CFE) systems to measure the activity of two ARGs encoded on plasmid DNA that produce rifampicin-inactivating and gentamicin-inactivating enzymes. We validated the use of a small benchtop Myra liquid handling system compared to manual pipetting, with no statistical differences observed. After optimising the pre-incubation time of ARGs and dispensing protocol, expression of aac(3)-IIa increased the half-maximal inhibition concentration (IC50) of gentamicin by over 150-fold, while arr-3 increased the IC50 of rifampicin by approximately 20-fold compared to controls. This methodology for rapid, semi-automated ARG characterisation offers a strategy to combat AMR by assessing novel ARGs identified through genomic surveillance or profiling activity of new or derivative antibiotics.
  • Journal article
    Murray JW, 2026,

    Random repeats open a route into folded protein space

    , Proceedings of the National Academy of Sciences, Vol: 123, ISSN: 0027-8424
  • Journal article
    Harrison SP, Prentice IC, Ascoli D, Biffis E, Greenhalgh S, Grillakis M, Haas O, Kountouris Y, O'Kelley RM, Fernandes PM, Menor IO, Xanthopoulos G, Voulgarakis Aet 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, ISSN: 2296-665X

    Extreme 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.
  • Journal article
    Liu H, Prentice IC, Morfopoulos C, 2026,

    Tracing Vegetation Stress from Space: Isoprene Emissions Capture the Spatiotemporal Footprint of El Niño

    , npj Climate and Atmospheric Science, ISSN: 2397-3722

    El Niño events exert a profound influence on the global carbon cycle by imposing widespread heat and water stress on terrestrial ecosystems. Plant isoprene emissions respond rapidly to such stress, yet it remains unclear whether this response can track the spatiotemporal evolution of El Niño’s impacts over land. Here, we used satellite-derived global isoprene emissions for the first time to assess the west-east progression of the 2015–2016 El Niño. We observed that isoprene emissions increased by up to approximately 30% across tropical ecosystems relative to the climatological mean, with pronounced anomalies emerging during the event. The spatiotemporal evolution of these anomalies closely aligns with the El Niño progression inferred from sea surface temperature (SST) anomalies in the equatorial Pacific. In contrast, commonly used satellite vegetation products, including leaf area index (LAI) and solar-induced chlorophyll fluorescence (SIF), show weaker and spatially incoherent responses. These results demonstrate that satellite-derived isoprene provides a sensitive and mechanistically grounded tracer of ecosystem stress, offering a complementary perspective for monitoring the intensity and propagation of extreme climate events across terrestrial ecosystems.
  • Journal article
    Baizurah SN, Groner VP, 2026,

    Conservation: When extremes meet rarity.

    , Curr Biol, Vol: 36, Pages: R919-R921

    A catastrophic five-day rain triggered over 50,000 landslides across the core habitat of the critically endangered Tapanuli orangutan in Sumatra, potentially killing a significant proportion of the population and raising urgent questions about rare species' viability in a changing climate.

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