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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 articleCasadio R, Lu ZJ, Mathews DH, et al., 2026,
Computational Resources for Molecular Biology 2026.
, J Mol Biol, Vol: 438 -
Journal articleZhao H, Pye R, Walker G, et 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: 0022-2836Only 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.
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Journal articleConev A, Islam SA, Tsitsa I, et 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: 0022-2836UniProt 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.
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Journal articleGeorgiou C, Liu Q, Bruno F, et al., 2026,
Rare Hematopoietic Stem Cells resilient to infection-induced stress sense yet withstand inflammation.
, BloodHematopoietic 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.
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Journal articleLarrouy-Maumus G, 2026,
Rv3400 is a phosphoglucomutase required for trehalose metabolism in Mycobacterium tuberculosis
, Journal of Bacteriology, ISSN: 0021-9193Mycobacterium 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.
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Journal articleMishra V, Biswas P, Kozik Z, et al., 2026,
EspO-mediated neutrophil accumulation drives lethality during Citrobacter rodentium infection in interleukin-22-deficient mice.
, PLoS Pathog, Vol: 22Citrobacter 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.
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Journal articleYi L, Kulik N, Shao S, et al., 2026,
The transmembrane domain is a primary determinant of the location and substrate specificity in cyanobacterial FtsH heterocomplexes
, Algal Research, Vol: 98, ISSN: 2211-9264Membrane-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.
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Journal articleFerrando-Marco M, Lin S, Garcia Del Valle B, et al., 2026,
HDAC1/2-mediated repression of Wnt receptor expression orients asymmetric division polarity in Caenorhabditis elegans.
, Development, Vol: 153Asymmetric 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.
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Journal articleGodson A, Eddie L, Schuster M, et al., 2026,
NbRD21 protease controls receptor kinase homeostasis in Nicotiana benthamiana.
, New Phytol, Vol: 251, Pages: 2741-2752RD21-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.
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Journal articleRowell J, Yanez DC, Ross S, et al., 2026,
The Thymic Microenvironment Shapes Age-Related Qualitative Changes in the TCR Repertoire.
, Aging Cell, Vol: 25Ageing 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.
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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 EvolEmerging 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 articleBrook T, Piponi K, Collins T, et al., 2026,
Genomic architecture and breeding trade-offs of coconut drought tolerance
, Plants, People, Planet, ISSN: 2572-2611Climate 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.
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Journal articleMurray JW, 2026,
Random repeats open a route into folded protein space
, Proceedings of the National Academy of Sciences, Vol: 123, ISSN: 0027-8424 -
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 -
Journal articleHarrison SP, Prentice IC, Ascoli D, et al., 2026,
Land management to mitigate the risks of future fire in the Mediterranean region: strategiesand barriers to their adoption
, Frontiers in Environmental Science, ISSN: 2296-665X -
Journal articleLiu 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: 2397-3722El 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.
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Journal articleBergum M, Martin B, Sutton M, et al., 2026,
A liquid handling platform for standardised quantification of cell-free enzymatic activity encoded by antimicrobial resistance genes
, Synthetic Biology, ISSN: 1939-7267Antimicrobial 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.
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Journal articleZhao Z, Vercellino I, Whitelegge JP, et al., 2026,
Cryo-EM structures of naturally occurring dimeric photosystem II complexes lacking the Mn₄CaO₅ cluster
, Nature Communications, Vol: 17, ISSN: 2041-1723Robust oxygenic photosynthesis requires the efficient assembly and repair of the multi-subunit oxygen-evolving photosystem II (PSII) complex. Previous cryogenic electron microscopy (cryo-EM) structures of PSII assembly/disassembly intermediates have relied on the analysis of deletion mutants or removal of PSII subunits in vitro. Here we report the cryo-EM structures of naturally occurring dimeric PSII intermediates from the cyanobacterium Thermosynechococcus vestitus at a resolution of about 2.2 Å. These intermediates contain inactive dimers lacking the oxygen-evolving complex (OEC) and semi-active dimers with the OEC present in one of the two monomers. Our structural data provide a mechanism for how assembly and disassembly of the Mn4CaO5 cluster is coordinated with the binding and release of the extrinsic proteins: restructuring of the C-terminal tail of D1 subunit during assembly or disassembly of the Mn cluster triggers conformational changes in D2, CP47 and CP43 to drive the binding/release of the extrinsic proteins. A combination of structural and mass spectrometry data also suggests that the inactive PSII complexes may include damaged complexes containing oxidized D1-His332, a monodentate ligand to one of the Mn ions of the OEC.
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Journal articleBaizurah SN, Groner VP, 2026,
Conservation: When extremes meet rarity.
, Curr Biol, Vol: 36, Pages: R919-R921A 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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Journal articleOvwemuvwose J, Prentice IC, Graven HD, 2026,
Uncertainty in land carbon fluxes simulated by CMIP6 models from treatments of crop distributions and photosynthetic pathways
, Biogeosciences, Vol: 23, Pages: 5593-5605, ISSN: 1726-4170A reliable representation of the diversity of vegetation in terrestrial ecosystems is needed for the accurate simulation of present and future biogeochemical cycling and global climate, particularly as climate change affects different vegetation types differently. We compare the distributions of crops and of C3 versus C4 photosynthetic pathways in both natural vegetation and crops across Earth System Models in the 6th Coupled Model Intercomparison Project (CMIP6). We find a large range in C3 and C4 crops, natural and total vegetation for area and gross primary production (GPP) across the models. Even though 10 of the11 models used Land Use Harmonisation (LUH2) crop areas as input data, modelled total crop area ranges from -28 to +10 % of a satellite-based estimate. The C3 and C4 crop areas were -56 to +15 % and -100 to +38 % of LUH2 for 2014, respectively. The C4 fraction of total vegetation area in the models is 9-25 %, compared to 20 ± 3 % in observation-based estimates for the year 2014. Total global GPP varies by a factor of two across the models, and the C4 fraction of GPP ranges from 12 to 27 %. Simulated trends in the fraction of GPP by C3 versus C4 vegetation type (-20 to +29 %) would have changed global stable carbon isotopic discrimination by -0.35 to +0.11 ‰ over 1975-2005, not including changes in discrimination over time within C3 and C4 vegetation, indicating that modeled changes in the fraction of GPP by C3 and C4 vegetation do not account for the +0.7 ‰ increase indicated by atmospheric data. Disparity in vegetation with these photosynthetic pathways in models contributes to uncertainty in land carbon flux simulations, and further constraints and improvements in models are needed.
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Journal articleDi Domenico F, Kucharczyk MW, Patel R, et al., 2026,
Perioperative pregabalin does not alter behavioural or diffuse noxious inhibitory control responses in 2 rat models of chronic pain
, PAIN Reports, Vol: 11<jats:title>Abstract</jats:title> <jats:sec> <jats:title>Introduction:</jats:title> <jats:p>Multiple mechanisms contribute to the experience of pain where the use of model organisms to dissect mechanistically sensory regulatory circuitry is a vital component of discovering underlying causes of persistent pain in disease states. Such disease states can be modelled in animals using surgical procedures that, ethically, should involve administration of analgesia. However, since basic pain researchers often wish to measure pain-related events, animals may be denied perioperative analgesia to avoid adversely influencing experimental outcomes.</jats:p> </jats:sec> <jats:sec> <jats:title>Methods:</jats:title> <jats:p>We conducted a structured review of perioperative analgesia usage in rat spinal nerve ligation (SNL) and cancer-induced bone pain (CIBP) models. Using a combination of behavioural testing and in vivo electrophysiology in the dorsal horn of the spinal cord, we assessed the impact of perioperative pregabalin on nociceptive behaviours in the acute recovery phase, and behavioural and electrophysiological experimental outcomes in the established phase, of rat SNL and CIBP models.</jats:p> </jats:sec> <jats:sec> <jats:title>Results:</jats:title> <jats:p>A literature search revealed that, for studies using rat models of SNL or CIBP, only 5.37% and 12.69%, respectively, reported the use of perioperative analgesia. We then demonstrated that the use of pregabalin as a perioperative analgesic reduced mechanical hypersensitivity in the acute period after SNL surgery, with no impact on behavioural, electrophysiological, or neuropharmacological outcomes in the established p
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Journal articleKütahya C, Pániker CC, Ly F, et al., 2026,
Masterbatch-enabled acceleration of polyolefin biodegradation under open air terrestrial environmental conditions
, npj Materials Degradation, Vol: 10, ISSN: 2397-2106Polyolefins, commonly used in packaging and single-use products, are notoriously persistent in the environment, contributing significantly to environmental pollution. In scientific literature to date, polyolefins have not been reported to fully biodegrade. This study examines the biodegradation potential of polyolefin materials, specifically polyethylene (PE) and polypropylene (PP), enhanced through the incorporation of Biotransformation Masterbatch technology. The inclusion of the Biotransformation Masterbatch accelerated and enabled the full biodegradation of PE and PP, as demonstrated by laboratory weathering, and biodegradation studies in soil at mesophilic temperatures. Ecotoxicity tests revealed no adverse effects on test organisms in both soil and water environments, while metagenomics analysis demonstrated that biodegradation of these polyolefins did not significantly change the soil microbiota composition, which showed higher metabolic activity compared to virgin plastic controls. These findings demonstrate that Biotransformation technology provides an effective solution for delivering polyolefin-based materials with reduced environmental impact. It offers a sustainable alternative to conventional plastics, preserving the performance characteristics of traditional polyolefins while addressing the problem with fugitive plastic waste in the environment.
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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 articleZhu Z, Wang H, Zhou B, et al., 2026,
Optimal canopy light-use strategy shapes global greenness dynamics
, Nature Communications, 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 articleGhosh M, Goodman D, 2026,
Partial recurrence can enable robust and efficient computation
, Communications AI and computing, Vol: 1, ISSN: 3091-292XNeural circuits are sparse and bidirectional. Meaning that signals flow from early sensory areas to later regions and back. Yet, between connected areas there exist some but not all pathways. How does this structure, somewhere between feedforward and fully recurrent, shape circuit function? To address this question, we designed a recurrent neural network model in which a set of weight matrices (i.e. pathways) can be combined to generate every network structure between feedforward and fully recurrent. We term these architectures partially recurrent neural networks (pRNNs). We trained over 25,000 pRNNs on a novel set of reinforcement learning tasks, designed to mimic multisensory navigation, and compared their performance across multiple functional metrics. Our findings reveal three key insights. First, in dense-cue environments, most pRNN architectures match or exceed the task performance, learning speed or robustness of fully recurrent networks, despite using as few as one quarter the number of parameters; in sparse-cue environments, many match but a substantial fraction underperform. These results demonstrate that partial recurrence can enable energy efficient, yet performant solutions. Second, each pathway’s functional impact is both task and circuit dependent. For instance, feedback connections enhance robustness to noise in some, but not all contexts. Third, different pRNN architectures learn solutions with distinct input sensitivities and memory dynamics, and these computational traits help to explain their functional capabilities. Overall, our results demonstrate that partial recurrence can enable robust and efficient computation- a finding that may help to explain why neural circuits are sparse and bidirectional, and shows how these principles can inform the design of artificial systems.
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