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Journal articleLiu M, Prentice IC, Menviel L, et al., 2025,
Correction to: Past rapid warmings as a constraint on greenhouse-gas climate feedbacks (Communications Earth & Environment, (2022), 3, 1, (196), 10.1038/s43247-022-00536-0)
, Communications Earth and Environment, Vol: 6Correction to:Communications Earth & Environmenthttps://doi.org/10.1038/s43247-022-00536-0, published online 30 August 2022 In the version of this article originally published, three estimates of equilibrium climate sensitivity (ECS) derived from different sources were used to convert feedback strength into the unitless measure – gain – on the assumption that these were independent. In fact, these were not independent, and so combining them yields a too-narrow uncertainty range. The authors decided to only use the “very likely” (instead of “likely”) range from IPCC WG1 AR6 and treat it as a 90% confidence interval. Additionally, the gain is not normally distributed but is highly asymmetric, as it is the negative of the ratio of two approximately normally distributed variables, feedback strength (c) and the net feedback parameter (α<inf>net</inf>), with a non-zero centre. There is no standard way to derive confidence intervals from standard error for such a variable. Therefore, in the correct version, only the standard error of the gain is provided, instead of giving confidence intervals. Besides, since calculating standard error by the error propagation rule requires the input variables to be at least approximately normally distributed, the gain was calculated directly from the net feedback parameter (α<inf>net</inf>, which is assumed to be normally distributed) corresponding to ECS (which is not normally distributed). The changes implemented have no impact on the calculated feedback strengths, but they do have an impact on the estimated gains. Since confidence intervals are no longer provided for the gains, the comparison is focused on the feedback strengths. The authors would like to thank Dr. B. B. Cael from the National Oceanography Centre for bringing this issue to their attention with advice about the choice of ECS and how the very likely range should be interpreted into confidence int
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Journal articleHerzog MK-M, Peters A, Shayya N, et al., 2025,
Comparing Campylobacter jejuni to three other enteric pathogens in OligoMM12 mice reveals pathogen-specific host and microbiota responses.
, Gut Microbes, Vol: 17Campylobacter jejuni, non-typhoidal Salmonella spp., Listeria monocytogenes and enteropathogenic/enterohemorrhagic Escherichia coli (EPEC/EHEC) are leading causes of food-borne illness worldwide. Citrobacter rodentium has been used to model EPEC and EHEC infection in mice. The gut microbiome is well-known to affect gut colonization and host responses to many food-borne pathogens. Recent progress has established gnotobiotic mice as valuable models to study how microbiota affect the enteric infections by S. Typhimurium, C. rodentium and L. monocytogenes. However, for C. jejuni, we are still lacking a suitable gnotobiotic mouse model. Moreover, the limited comparability of data across laboratories is often negatively affected by variations between different research facilities or murine microbiotas. In this study, we applied the standardized gnotobiotic OligoMM12 microbiota mouse model and compared the infections in the same facility. We provide evidence of robust colonization and significant pathological changes in OligoMM12 mice following infection with these pathogens. Moreover, we offer insights into pathogen-specific host responses and metabolite signatures, highlighting the advantages of a standardized mouse model for direct comparisons of factors influencing the pathogenesis of major food-borne pathogens. Notably, we reveal for the first time that C. jejuni stably colonizes OligoMM12 mice, triggering inflammation. Additionally, our comparative approach successfully identifies pathogen-specific responses, including the detection of genes uniquely associated with C. jejuni infection in humans. These findings underscore the potential of the OligoMM12 model as a versatile tool for advancing our understanding of food-borne pathogen interactions.
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Journal articleMoulick D, Santra SC, Majumdar A, et al., 2025,
Efficacy of Seed Priming Technology in Ameliorating Metals and Metalloids Toxicity in Crops: Prospective and Issues
, REVIEWS OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY, Vol: 263, ISSN: 0179-5953 -
Journal articleBermúdez-Puga S, Mendes B, Ramos-Galarza JP, et al., 2025,
Revolutionizing agroindustry: towards the industrial application of antimicrobial peptides against pathogens and pests
, Biotechnology Advances, Vol: 82, ISSN: 0734-9750Antibiotics are essential chemicals for medicine and agritech. However, all antibiotics are small molecules that pathogens evolve antimicrobial resistance (AMR). Alternatively, antimicrobial peptides (AMPs) offer potential to overcome or evade AMR. AMPs provide broad-spectrum activity, favourable biosafety profiles, and a rapid and efficient mechanism of action with low resistance incidence. These properties have driven innovative applications, positioning AMPs as promising contributors to advancements in various industrial sectors. This review evaluates the multifaceted nature of AMPs and their biotechnological applications in underexplored sectors. In the food industry, the application of AMPs helps to suppress the growth of microorganisms, thereby decreasing foodborne illnesses, minimizing food waste, and prolonging the shelf life of products. In animal husbandry and aquaculture, incorporating AMPs into the diet reduces the load of pathogenic microorganisms and enhances growth performance and survival rates. In agriculture, AMPs provide an alternative to decrease the use of chemical pesticides and antibiotics. We also review current methods for obtaining AMPs, including chemical synthesis, recombinant DNA technology, cell-free protein synthesis, and molecular farming, are also reviewed. Finally, we look to the peptide market to assess its status, progress, and transition from the discovery stage to benefits for society and high-quality products. Overall, our review exemplifies the other side of the coin of AMPs and how these molecules provide similar benefits to conventional antibiotics and pesticides in the agritech sector.
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Journal articleMathews DH, Casadio R, Sternberg MJE, 2025,
Computational Resources for Molecular Biology 2025
, Journal of Molecular Biology, Vol: 437, ISSN: 0022-2836 -
Journal articleOno M, 2025,
GatingTree: pathfinding analysis of group-specific effects in cytometry data
, Cytometry Part A, ISSN: 1552-4922Advancements in cytometry technologies have led to a remarkable increase in the number of markers thatcan be analyzed simultaneously, presenting significant challenges in data analysis. Traditional approaches,such as dimensional reduction techniques and computational clustering, although popular, often face reproducibility challenges due to their heavy reliance on inherent data structures. This reliance prevents thedirect translation of their outputs into gating strategies for downstream experiments. Here, we propose thenovel Gating Tree methodology, a pathfinding approach that investigates the multidimensional data landscape to unravel group-specific features without the use of dimensional reduction. This method employsnovel measures, including enrichment scores and gating entropy, to effectively identify group-specific featureswithin high-dimensional cytometric datasets. Our analysis, applied to both simulated and real cytometricdatasets, demonstrates that the Gating Tree not only identifies group-specific features comprehensively butalso produces outputs that are immediately usable as gating strategies for pinpointing key cell populations.Furthermore, by integrating machine learning methods, including Random Forest, we have benchmarkedGating Tree against existing methods, demonstrating its superior performance. A range of supervised andunsupervised methods implemented in Gating Tree thus provides effective visualization and output data,which can be immediately used as successive gating strategies for downstream study.
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Journal articleLuo X, Zhao R, Chu H, et al., 2025,
Global variation in vegetation carbon use efficiency inferred from eddy covariance observations
, Nature Ecology & Evolution, ISSN: 2397-334XTerrestrial ecosystems have been serving as a strong carbon sink that offsets one-quarter of anthropogenic CO2 emissions. Carbon use efficiency (CUE), the percentage of photosynthesized carbon that is available for biomass production and other secondary carbon products, is one factor determining the carbon sink size. The global variation in CUE remains unclear, however, as recent reports disagree over the responses of CUE to temperature, dryness, forest types and stand age, and there are limited direct observations to constrain the related uncertainty. Here, we propose to infer CUE from spatially distributed observations of land–atmosphere CO2 exchange from global eddy covariance sites based on the degree of ecosystem respiration–photosynthesis coupling. Across 2,737 site-years, CUE derived from eddy covariance observations is 0.43 ± 0.12, consistent with previous inventory-based estimates (0.47 ± 0.12, n = 301) but with a better representation of spatial–temporal variation in CUE. We find that CUE consistently decreases with temperature, precipitation, light availability and stand age, with a substantial difference in the baseline CUE among biomes. Importantly, CUE of deciduous forests is typically 15% higher than that of evergreen forests, suggesting that over the long-term deciduous forests are more efficient in using photosynthate. Our study advances the understanding of the global variation in CUE and provides insights to guide best practices of forest conservation, management and restoration for carbon sequestration.
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Journal articleIrie N, Takeda N, Satou Y, et al., 2025,
Machine learning-assisted decoding of temporal transcriptional dynamics via fluorescent timer
, Nature Communications, ISSN: 2041-1723Investigating the temporal dynamics of gene expression is crucial for understanding gene regulation across various biological processes. Using the Fluorescent Timer protein, the Timer-of-cell-kinetics-and-activity system enables analysis of transcriptional dynamics at the single-cell level. However, the complexity of Timer fluorescence data has limited its broader application. Here, we introduce an integrative approach combining molecular biology and machine learning to elucidate Foxp3 transcriptional dynamics through flow cytometric Timer analysis. We have developed a convolutional neural network-based method that incorporates image conversion and class-specific feature visualisation for class-specific feature identification at the single-cell level. Biologically, we developed a novel CRISPR mutant of Foxp3 fluorescent Timer reporter mice lacking the enhancer Conserved Non-coding Sequence 2, which revealed new roles of this enhancer in regulating Foxp3 transcription frequency under specific conditions. Furthermore, analysis of wild-type Foxp3 fluorescent Timer reporter mice at different ages uncovered distinct patterns of Foxp3 expression from neonatal to aged mice, highlighting prominent thymus-like features of neonatal splenic Foxp3+ T cells. In conclusion, our study uncovers previously unrecognised Foxp3 transcriptional dynamics, establishing a proof-of-concept for integrating CRISPR, single-cell dynamics analysis, and machine learning methods as advanced techniques to understand transcriptional dynamics in vivo.
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Journal articleMehta H, Jimenez J, Ledesma-Amaro R, et al., 2025,
Investigating the Potential of Division of Labor in Synthetic Bacterial Communities for the Production of Violacein
, ACS Synthetic Biology, ISSN: 2161-5063 -
Journal articleLamy B, Laurent F, Simoes Da Silva CJ, et al., 2025,
Acquisition of daptomycin resistance in patients results in decreased virulence in <i>Drosophila</i>
, Infection and Immunity, Vol: 93, ISSN: 0019-9567<jats:title>ABSTRACT</jats:title> <jats:sec> <jats:title/> <jats:p> <jats:italic toggle="yes">Staphylococcus aureus</jats:italic> can acquire antimicrobial resistance, which in turn may affect its pathogenic potential. Using a panel of paired clinical isolates collected before and after daptomycin resistance acquisition, most frequently through a single <jats:italic toggle="yes">mprF</jats:italic> mutation, we show a relationship between increasing daptomycin minimum inhibitory concentration and reduced virulence in a <jats:italic toggle="yes">Drosophila</jats:italic> systemic infection model. Analyzing toxin production, <jats:italic toggle="yes">in vitro</jats:italic> bacterial growth characteristics, and cell surface properties, we failed to link daptomycin resistance-related attenuated virulence to either reduced virulence factor production, reduced fitness, or any of the cell surface characteristics investigated. Competition assays in <jats:italic toggle="yes">Drosophila</jats:italic> also did not support any altered ability in immune evasion. Instead, using a panel of mutant flies defective for various immune components, we show that this daptomycin resistance-related attenuated virulence is mostly explained by greater susceptibility to the activity of <jats:italic toggle="yes">Drosophila</jats:italic> prophenoloxidase, a tyrosinase involved in melanization, but not to antimicrobial peptides or Bomanin antimicrobial effectors. Further investigation could not link daptomycin resistance-related attenuation of virulence to differential susceptibility to reactive oxygen species or quinones prominently associated with pheno
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Journal articleConsoli G, Leong HF, Davis GA, et al., 2025,
Structure of a stripped-down and tuned-up far-red phycobilisome
, Communications Biology, Vol: 8, ISSN: 2399-3642A diverse subset of cyanobacteria can transiently modify their photosynthetic machinery during far-red light photoacclimation to drive photosynthesis with less energetic photons (700 nm–800 nm). To achieve this, all the main light-driven components of the photosynthetic apparatus, including their allophycocyanin antenna, are replaced with red-shifted paralogues. Recent studies based on the structure of an incomplete complex provided some insights into the tuning of the far-red phycobiliproteins. Here, we solved the structure of the intact bicylindrical allophycocyanin complex from the cyanobacterium Chroococcidiopsis thermalis PCC 7203 at a resolution of 2.51 Å determined by Cryo-electron microscopy single particle analysis. A comparison between conserved structural features in far-red and white light allophycocyanin cores provides insight on the evolutionary adaptations needed to optimize excitation energy transfer in the far-red light adapted photosynthetic apparatus. The reduction in antenna size in far-red photosynthesis suggests a need to optimize membrane packing to increase the number of photosystems and tune the ratio between chlorophyll f molecules and bilin pigments, while the wider spread in the absorption range of the bilins suggests faster and more efficient excitation energy transfer to far-red Photosystem II by limiting backflow of excitation from the reaction centres to the far-red bilin pigments.
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Journal articleBick A, Bakkestuen V, Pedersen M, et al., 2025,
Exploring the spatiotemporal influence of climate on American avian migration with random forests
, Scientific Reports, ISSN: 2045-2322Birds have adapted to climatic and ecological cycles to inform their Spring and Fall migration timings, but anthropogenic global warming has affected these long-establish cycles. Understanding these dynamics is critical for conservation during a changing climate. Here, we employ a modeling approach to explore how climate spatiotemporally affects bird occurrence on eBird surveys. Specifically, we train an ensemble of multivariate and multi-response random forest models on North and South American climate data, then predict eBird survey occurrence rates for 41 migrating passerine bird species in a Northeastern American ecoregion from 2008-2018. In October, when many passerines have begun their southward winter migration, we achieve more accurate predictions of bird occurrence using lagged climate features alone to predict occurrence. These results suggest that analyses of machine learning model metrics may be useful for identifying spatiotemporal climatic cues that affect migratory behavior. Lastly, we explore the application and limitations of random forests for prediction of future bird occurrence using 2021-2040 climate projections.
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Journal articleLarrouy-Maumus G, 2025,
Performance of direct detection of Mycobacterium tuberculosis within Mycobacterium tuberculosis complex by routine MALDI-ToF for the diagnosis using species-specific lipid fingerprint
, Microbiology Spectrum, ISSN: 2165-0497 -
Journal articleLarrouy-Maumus G, 2025,
Performance of direct detection of Mycobacterium tuberculosis within Mycobacterium tuberculosis complex by routine MALDI-ToF for the diagnosis using species-specific lipid fingerprint
, Microbiology Spectrum, ISSN: 2165-0497 -
Journal articleAlexandre YO, Potemkin N, Schienstock D, et al., 2025,
Splenic fibroblastic reticular cells orchestrate dendritic cell maturation and facilitate CD8 <sup>+</sup> T cell priming and protective memory
, Science Advances, Vol: 11<jats:p> Fibroblastic reticular cells (FRCs) are specialized fibroblasts that construct secondary lymphoid organs where they provide crucial signals for immune cell homeostasis and migration. While splenic FRCs are thought to support antiviral T cell responses, their role remains unclear. Here, we found that ablation of splenic FRCs impaired virus-specific CD8 <jats:sup>+</jats:sup> T cell responses during lymphocytic choriomeningitis virus (LCMV) infection. Immunofluorescence imaging revealed that FRCs promote CD8 <jats:sup>+</jats:sup> T cell clustering with type 1 conventional dendritic cells (cDC1) in the T cell zone before migration to the infected marginal zone. Without FRCs, T cells instead clustered with cDC1 and virus-infected cells in the marginal zone, leading to suboptimal priming. Mechanistically, FRCs coordinated early viral replication and the inflammatory milieu for optimal DC activation, and an intact FRC network was crucial for generating effector T cells and maintaining protective memory T cells. Thus, splenic FRCs provide essential lymphoid niches for antiviral T cell responses. </jats:p>
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Journal articleTajadura-Ortega V, Chai W, Roberts LA, et al., 2025,
Identification and characterisation of vaginal bacteria-glycan interactions implicated in reproductive tract health and pregnancy outcomes
, Nature Communications, Vol: 16, ISSN: 2041-1723Lactobacillus displacement from the vaginal microbiome associates with adverse health outcomes and is linked to increased risk of preterm birth. Glycans mediate bacterial adhesion events involved in colonisation and infection. Using customised glycan microarrays, we establish glycan interaction profiles of vaginal bacteria implicated in reproductive health. Glycan binding signatures of the opportunistic pathogens Escherichia coli, Fusobacterium nucleatum and Streptococcus agalactiae to oligomannose N-glycans, galactose-terminating glycans and hyaluronic acid, respectively are highly distinct from Lactobacillus commensals. Binding to sulphated glycosaminoglycans by vaginal bacteria is pH dependent, as is binding to neutral and sialic acid-terminating glycans by F. nucleatum. Adhesion of Lactobacillus crispatus, Lactobacillus iners, Gardnerella vaginalis, S. agalactiae and F. nucleatum to vaginal epithelial cells is partially mediated by chondroitin sulphate. S. agalactiae binding to chondroitin sulphate C oligosaccharides is inhibited by L. crispatus. This study highlights glycans as mediators of vaginal bacterial binding events involved in reproductive health and disease.
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Journal articleSalis A, Ryder RJ, Molina A, et al., 2025,
Birds combined calls more than 11 million years ago
, Scientific Reports, ISSN: 2045-2322Multiple members of the tit and chickadee (= Parid) family combine two classes of calls, F and D, in a rigid order FD. In Japanese tits, FD has been argued on the basis of multiple experiments to involve syntax and non-trivial compositionality. How ancient are these call combinations? We show that FD combinations (as well as individual F and D calls) are present in nearly all Parid species, and almost absent in their closest relatives, the Remizidae and Stenostiridae. Using phylogenetic tools and ancestral reconstruction methods, we infer that FD combinations very likely emerged between 11 and 26 million years ago in the eastern Himalayas. This result contributes to evolutionary animal linguistics using a comparative phylogenetic approach to reconstruct the evolution of call combinations.
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Journal articleCarpenter FL, Vogler AP, 2025,
If the tape were played again: convergent evolution of clade sizes and taxonomic composition in two tropical assemblages of Coleoptera
, Ecography, Vol: 2025, ISSN: 0906-7590Communities of insects around the world consist of unique sets of species that have evolved under different historical processes of assembly and lineage diversification. Whole-community phylogenetics can partition the shared and uniquely derived evolutionary history across sites. We used mitochondrial genome sequences of > 1000 species each from two assemblages of Coleoptera (beetles) in distantly situated tropical lowland rainforests of Malaysia and Panama for phylogenetic reconstruction and community ecological analysis. Assemblages were entirely distinct at the species level but were surprisingly similar at the family level in their overall composition and relative species richness. This pattern, coupled with a high degree of phylogenetic clustering, suggests that lineage-specific tendencies have driven evolutionarily independent yet parallel diversification across distinct regions. The inclusion of species-poor lineages reduced the level of community clustering in parallel in both sites, indicating the role of lineage-specific factors in shaping species richness and local community composition. Our findings reveal a strong connection between relative species richness in local communities and global clade sizes, and consistent phylogenetic patterns across assemblages. While biotic exchange in deep time likely played a secondary role, the primary driver appears to be the intrinsic diversification rates unique to each clade (family). Such dynamics make assembly composition more predictable, i.e. replaying the ‘evolutionary tape' would yield similar outcomes wherever a new assemblage of tropical-forest Coleoptera arises.
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Journal articleSugata K, Rahman A, Niimura K, et al., 2025,
Intragenic viral silencer element regulates HTLV-1 latency via RUNX complex recruitment
, Nature Microbiology, Vol: 10, Pages: 1447-1462Retroviruses integrate their genetic material into the host genome, enabling persistent infection. Human T cell leukaemia virus type 1 (HTLV-1) and human immunodeficiency virus type 1 (HIV-1) share similarities in genome structure and target cells, yet their infection dynamics differ drastically. While HIV-1 leads to high viral replication and immune system collapse, HTLV-1 establishes latency, promoting the survival of infected cells and, in some cases, leading to leukaemia. The mechanisms underlying this latency preference remain unclear. Here we analyse blood samples from people with HTLV-1 and identify an open chromatin region within the HTLV-1 provirus that functions as a transcriptional silencer and regulates transcriptional burst. The host transcription factor RUNX1 binds to this open chromatin region, repressing viral expression. Mutation of this silencer enhances HTLV-1 replication and immunogenicity, while its insertion into HIV-1 suppresses viral production. These findings reveal a strategy by which HTLV-1 ensures long-term persistence, offering potential insights into retroviral evolution and therapeutic targets.
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Journal articleSalis A, Molina A, Mephane-Montel L, et al., 2025,
No effect of note order on the response of coal tits to conspecific, heterospecific and artificial mobbing calls
, Ethology, Vol: 131, ISSN: 0179-1613Most Parid species produce specific, order-constrained mobbing calls. These calls elicit responses from both conspecifics and heterospecifics, with evidence indicating that such responses occur only when the calls are organised in this specific order. One notable exception is the coal tit (Periparus ater), a species that employs similar types of notes, yet does not exhibit clear order constraints within its mobbing sequences. Despite this apparent absence of order constraints, a recent experiment has demonstrated that coal tits may be sensitive to the order of notes in heterospecific calls. Therefore, the relative significance of note order in conspecific and heterospecific communication among coal tits remains unclear. We conducted a playback experiment to examine the effects of note order (natural coal tit order, typical Parid order and reversed order) and species identity (conspecific, familiar heterospecific—the great tit, Parus major, or artificial notes) on coal tit mobbing responses. Our findings indicate that coal tits exhibited a strong response to conspecific calls, regardless of the order of the notes; conversely, they displayed little to no response to heterospecific calls and artificial notes, irrespective of note order. A similar pattern was observed when assessing the general community response. This unexpectedly low response to familiar heterospecific calls may be attributable to a reduced density of great tits in the area we tested: ecological factors, such as community composition, may influence heterospecific mobbing behaviours and the subsequent biological interpretations of playback experiments. This study also underscores the necessity of conducting comparative research on closely related species to evaluate the potential generality of findings, such as strong order constraints recently observed in great tits and Japanese tits.
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Journal articleSchulte to Bühne H, Tobias JA, Durant SM, et al., 2025,
Land use configuration shapes climate change vulnerability of gallery forests in a savannah ecosystem
, Global Ecology and Conservation, Vol: 59, ISSN: 2351-9894Interactions between anthropogenic pressures make it difficult to predict biodiversity change and plan conservation interventions. Climate change is expected to drive widespread ecological change in the tropics over the coming decades, but it is unclear where and when these changes are going to intensify, or reduce, the impacts of additional pressures from human land use. To address this uncertainty, we apply a novel vulnerability assessment framework to show how land use configuration modifies the extent of potential harms arising from climate change to gallery forests, an important vegetation type in tropical savannahs. We highlight how the spatial distribution of climate change (specifically, change in annual rainfall) interacts with the spatial distribution of land use (specifically, cropland), as well as the biophysical context of the study site (the W-Arly-Pendjari transboundary protected area in West Africa), to shape the vulnerability of gallery forests to changes in rainfall in the region. Due to the pathways by which rainfall change and land use interact, vulnerability is especially elevated in core protected areas, warranting particular attention from conservation managers. Overall, our work illustrates how unexpected patterns in potential negative consequences can arise through interactions between pressures on biodiversity, highlighting the importance of considering mechanistic pathways for predicting biodiversity outcomes under multifaceted global environmental change.
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Journal articleCabral A, Bender IMA, Couvreur TLP, et al., 2025,
Seed‐dispersing vertebrates and the abiotic environment shape functional diversity of the pantropical Annonaceae
, New Phytologist, Vol: 246, Pages: 2263-2279, ISSN: 0028-646XMutualistic interactions between fruiting plants and frugivorous animals are shaped by interaction-relevant functional traits. However, it is unclear whether ‘trait matching’ underlies broad-scale relationships in plant and frugivore species and their functional diversity.We integrated novel trait data and global occurrences for c. 1900 species in a major tropical plant family (Annonaceae) with data for 7607 bird and mammal species, including 1418 frugivores, alongside data on the abiotic environment. We applied structural equation models to evaluate the direct and indirect drivers of global and continental variation in frugivory-related functional diversity in Annonaceae, and assessed frugivory-exclusive drivers through comparisons with non-frugivores.We show that global variation in Annonaceae frugivory-related functional diversity is influenced by species richness (SRic) and trait matching with co-occurring frugivorous mammals. Frugivorous birds and mammals indirectly influenced Annonaceae functional diversity at continental scales by affecting Annonaceae SRic. We found that climate, elevation, and seed dispersers jointly shaped Annonaceae diversity globally.Our results suggest that seed dispersal interactions with mammals are particularly important for shaping global variation in Annonaceae diversity, possibly through mutualistic co-evolutionary dynamics. However, distinct effects of frugivores on Annonaceae diversity across biogeographical realms suggest that biogeography modulates how mutualistic interactions promote diversity.
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Journal articleBonnin RA, Jacquemin A, Pizzato J, et al., 2025,
MALDI-TOF lipidomics rapidly detects modification of 2-hydroxymyristate lipid A, a potential virulence trait in Enterobacter bugandensis
, Microbiology Spectrum, Vol: 13Enterobacter cloacae complex (ECC) comprises numerous species that can be difficult to identify. Among these species, Enterobacter bugandensis is recognized as a threat in neonatal intensive care units due to its involvement in septic shock. A potential virulence factor responsible for its virulence is the modification of the lipid A of the lipopolysaccharide (LPS). This modification corresponds to a hydroxylation of the myristate component of lipid A. A collection of 168 ECC, including 10 E. bugandensis and one isolate involved in fatal septic shock in the neonatal intensive care unit, were tested for the presence of 2-hydroxymyristate. All isolates were sequenced to determine the genetic diversity of this collection and detect the presence of the lpxO gene responsible for this hydroxylation. matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF) analysis revealed that only a fraction (4/11) of E. bugandensis were able to modify their lipid A, which correlates with the presence of the lpxO gene. Genomic analysis of E. bugandensis revealed that only half of the genomes carried the lpxO gene. Lpxo-negative isolates exhibited a deletion of 1,094 bp encompassing the lpxO gene. Lipid A analysis also revealed that hydroxylation of myristate was not specific to E. bugandensis since this modification was systematically found in several species including Enterobacter chengduensis, Enterobacter chuandaensis, or Enterobacter cloacae subsp cloacae. Here, we provide a simple detection test allowing the rapid identification of hydroxymyristate of lipid A involved in the virulence of E. bugandensis. Rapid identification of lipid A modification might help clinicians to adapt procedures when an Enterobacter spp. is identified in newborns.
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Journal articleDorigatti I, Gaythorpe KAM, Cox VM, et al., 2025,
Priorities for modelling arbovirus transmission under climate change
, Trends in Molecular Medicine, ISSN: 1471-4914 -
Journal articleGroner VP, Cook J, Orme CDL, et al., 2025,
Harmonizing nature’s timescales in ecosystem models
, Trends in Ecology & Evolution, Vol: 40, Pages: 575-585, ISSN: 0169-5347 -
Journal articleHobbs B, Limmer N, Ossa F, et al., 2025,
A low-complexity linker as a driver of intra- and intermolecular interactions in DNAJB chaperones
, Nature Communications, Vol: 16, ISSN: 2041-1723J-domain proteins ( JDPs) act as major regulators of the proteostasis network by driving the specificity of the Hsp70 machine. Their important functions are mediated by a low-complexity glycine-/phenylalanine-rich region (GF-linker) that links the folded J-domain with the substrate binding domain. Recently, we and others have shown that in an autoinhibited JDP state, an α-helix formed within the GF-linker blocks the Hsp70 binding site on the J-domain. However, the role of the disordered GF-linker in autoinhibition and how the latter is released, are still not understood. Here, using autoinhibited DNAJB1 and DNAJB6 constructs, we show that in combination with the J-domain, the GF-linker creates a hydrophobic, partially collapsed cluster that shows a remarkable degree of long-range structural communication, disruption of which can lead to destabilisation of autoinhibition. Apart from this crucial intramolecular role, we reveal that the GF-linker can also be recognised by the substrate-binding domain of Hsp70 and dictate the lifetime of the entire JDP–Hsp70 complex. Strikingly, the GF-linkers of DNAJB1 and DNAJB6 display distinct structural properties that lead to different Hsp70 binding kinetics, showing that the behaviour of the GF-linker can vary dramatically even within the same class of JDPs.
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Journal articleSauthof L, Szczepek M, Schmidt A, et al., 2025,
Serial-femtosecond crystallography reveals how a phytochrome variant couples chromophore and protein structural changes
, Science Advances, Vol: 11<jats:p>The photoreaction and commensurate structural changes of a chromophore within biological photoreceptors elicit conformational transitions of the protein promoting the switch between deactivated and activated states. We investigated how this coupling is achieved in a bacterial phytochrome variant, Agp2-PAiRFP2. Contrary to classical protein crystallography, which only allows probing (cryo-trapped) stable states, we have used time-resolved serial femtosecond x-ray crystallography (tr-SFX) and pump-probe techniques with various illumination and delay times with respect to photoexcitation of the parent Pfr state. Thus, structural data for seven time frames were sorted into groups of molecular events along the reaction coordinate. They range from chromophore isomerization to the formation of Meta-F, the intermediate that precedes the functional relevant secondary structure transition of the tongue. Structural data for the early events were used to calculate the photoisomerization pathway to complement the experimental data. Late events allow identifying the molecular switch that is linked to the intramolecular proton transfer as a prerequisite for the following structural transitions.</jats:p>
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Journal articleZhang H, Wang H, Wright IJ, et al., 2025,
Thermal acclimation of stem respiration implies a weaker carbon-climate feedback
, Science, ISSN: 0036-8075 -
Journal articleDuchêne DA, Chowdhury A-A, Yang J, et al., 2025,
Drivers of avian genomic change revealed by evolutionary rate decomposition
, Nature, Vol: 641, Pages: 1208-1216, ISSN: 0028-0836Modern birds have diversified into a striking array of forms, behaviours and ecological roles. Analyses of molecular evolutionary rates can reveal the links between genomic and phenotypic change1,2,3,4, but disentangling the drivers of rate variation at the whole-genome scale has been difficult. Using comprehensive estimates of traits and evolutionary rates across a family-level phylogeny of birds5,6, we find that genome-wide mutation rates across lineages are predominantly explained by clutch size and generation length, whereas rate variation across genes is driven by the content of guanine and cytosine. Here, to find the subsets of genes and lineages that dominate evolutionary rate variation in birds, we estimated the influence of individual lineages on decomposed axes of gene-specific evolutionary rates. We find that most of the rate variation occurs along recent branches of the tree, associated with present-day families of birds. Additional tests on axes of rate variation show rapid changes in microchromosomes immediately after the Cretaceous–Palaeogene transition. These apparent pulses of evolution are consistent with major changes in the genetic machineries for meiosis, heart performance, and RNA splicing, surveillance and translation, and correlate with the ecological diversity reflected in increased tarsus length. Collectively, our analyses paint a nuanced picture of avian evolution, revealing that the ancestors of the most diverse lineages of birds underwent major genomic changes related to mutation, gene usage and niche expansion in the early Palaeogene period.
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Journal articleKim J, Darlington A, Muñoz-Montero S, et al., 2025,
Gene expression depends on the interplay among growth, resource biogenesis, and nutrient quality
, ACS Synthetic Biology, ISSN: 2161-5063The gene expression capacity of bacteria depends on the interplay between growth and the availability of the transcriptional and translational machinery. Growth rate is accepted as the physiological parameter controlling the allocation of cellular resources. Understanding the relationship between growth and resources is key for the efficient design of genetic constructs, but it is obscured by the mutual dependence between growth and gene expression. In this work, we investigate the contributions of molecular factors, growth rate, and metabolism to gene expression by investigating the behavior of bacterial cells grown in chemostats. Using a model of the whole cell and validating it experimentally, our results show that while growth rate and molecular factors, such as the number of rRNA operons, set the abundance of transcriptional and translational machinery, it is metabolism that governs the usage of resources by tuning elongation rates. We show, using a biotechnologically relevant example, that gene expression capacity can be maximized using low growth in a high-quality medium. These findings unveil fundamental trade-offs in physiology that will inform future bioprocess optimization.
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