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Journal articleMolpeceres-García FJ, García-Miró A, Mateos-García E, et al., 2026,
Pseudomonas putida JM37 as a novel bacterial chassis for ethylene glycol upcycling
, Bioresource Technology, Vol: 443, ISSN: 0960-8524Ethylene glycol (EG), one of the main monomers of polyethylene terephthalate (PET), is an attractive target for microbial upcycling. Despite this interest, there is a limited number of described organisms that can efficiently metabolise EG. Here, we report the metabolic and biotechnological potential of Pseudomonas putida JM37 as a novel bacterial chassis for EG valorization. We show that JM37 efficiently grows on EG as the sole carbon and energy source, outperforming other Pseudomonas strains. Genome sequencing and directed mutagenesis revealed that genetic redundancies in the glyoxylate assimilation pathways underlie its robust EG metabolism. Beyond biomass generation, we demonstrated the biotechnological potential of JM37. This strain was able to accumulate medium-chain polyhydroxyalkanoates (mcl-PHAs), dominated by C10 monomers, directly from EG. Moreover, JM37 successfully expressed heterologous biosynthetic pathways, including a violacein biosynthetic operon and a PET-hydrolase which has been secreted actively into the extracellular medium. Together, our results support the use of P. putida JM37 as a versatile synthetic biology chassis for sustainable EG upcycling and as a promising platform for circular bioproduction.
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Journal articleWilliams JJ, Angelidou I, Cholvi M, et al., 2026,
Ethical and equitable approaches in AI for vector-borne disease management
, AI and Ethics, Vol: 6, ISSN: 2730-5961Artificial intelligence (AI) is increasingly being incorporated into public health strategies for vector-borne disease (VBD) management, offering several advances in surveillance, prediction, and control. At the same time however, the integration of AI technologies raises critical ethical and equity concerns, particularly in regions disproportionately affected by VBDs. Here, we explore seven key ethical and equitable challenges in the use of AI for VBD management: (1) data quality and representativeness, (2) risk of discrimination and inequality reinforcement, (3) transparency and reproducibility, (4) privacy and data protection, (5) cybersecurity, (6) fair and equitable benefit-sharing, and (7) environmental considerations. Within each of these challenges, we highlight how unaddressed ethical and equity issues can exacerbate health disparities and undermine public trust. We then propose actionable pathways forward, including inclusive data governance, transparency-enhancing tools, and environmentally-conscious AI practices. By highlighting how accounting for these ethical and equity concerns during AI development and deployment can further progress towards the United Nations Sustainable Development Goals, we advocate for a more responsible and inclusive approach to AI in VBD management.
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Journal articleXu H, Wang H, Prentice IC, et al., 2026,
Global variation in the ratio of sapwood to leaf area explained by optimality principles
, New Phytologist, ISSN: 0028-646X• The sapwood area supporting a given leaf area (Huber value, vH) reflects the coupling between carbon uptake and water transport and loss at a whole-plant level. Geographic variation in vH presumably reflect plant strategic adaptations but the lack of a general explanation for such variation hinders its representation in vegetation models and assessment of how its impact on the global carbon and water cycles. • Here we develop a simple hydraulic trait model to predict optimal vH by matching stem water supply and leaf water loss, and test its performance against two extensive plant hydraulic datasets. • We show that our eco-evolutionary optimality-based model explains nearly 60% of global vH variation in response to light, vapour pressure deficit, temperature and sapwood conductivity. Enhanced hydraulic efficiency with warmer temperatures reduces the sapwood area required to support a given leaf area, whereas high irradiance (supporting increased photosynthetic capacity) and drier air increase it. • This study thus provides a route to modelling variation in functional traits through the coordination of carbon uptake and water transport processes.
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Journal articleDeliard S, Barbieri E, Trizzino M, et al., 2026,
An EGR1-dependent cascade modulates genome architecture at the CSF1R locus
, Nucleic Acids Research, Vol: 54, ISSN: 0305-1048The organization and dynamics of chromatin are key to regulating gene expression during myeloid cell differentiation. Sequence-specific transcription factors initiate and maintain a complex network of enhancer-promoter contacts, which is supported by insulating elements and genome folding organizers such as CTCF and Cohesin. The spatial arrangement of enhancers and promoters, as well as their epigenetic state, drives cell and tissue-specific transcriptomes. Here we dissect the spatial, transcriptional, and epigenetic landscape of the colony stimulating factor 1 receptor (CSF1R) locus in monocytes and macrophages. CSF1R is a receptor tyrosine kinase that triggers the signaling cascade required for macrophage differentiation. Previous work showed that CSF1R expression is regulated by multiple enhancers, including the fms-intronic regulatory element (FIRE). Here, we find that a single EGR-1 binding motif dictates activation of CSF1R. We also discover that the CSF1R entire locus folds into a hub of gene regulation, affecting an extended network of myeloid and inflammatory genes. Globally, EGR1 may have an expanded role as a macrophage-specific boundary element, supporting enhancer-promoter looping at several genes. In sum, we describe a novel 3D chromatin network that is critical for macrophage development and function.
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Journal articleJimenez Zarco J, 2026,
Engineering whole-cell catalysts to use plastic waste as a feedstock
, Current Opinion in Biotechnology, ISSN: 0958-1669The extensive production, durability and waste mismanagement of plastic polymers have led to a highly concerning environmental problem. Recycling methods aim to reduce the amount of plastic pollution and, among them, biological processes have emerged as an interesting alternative for the management of plastic waste that is difficult to collect or can not be recycled by other methods. While there has been significant progress in the field, in particular related to the enzymatic hydrolysis of polyesters, most biological methods rely on the use of enzymes in vitro, using collected plastics. In this review we explore the status of technologies using whole-cell catalysts that could be used for in vivo upcycling of plastic waste – with plastic becoming a microbial feedstock – and for the development of biodegradation strategies in relevant environments. We have identified a number of barriers related to polymer bioavailability, enzyme activity and secretion, and the use of strains and microbial communities that need to be overcome to materialise a much-needed solution to plastic pollution.
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Journal articleHassan A, Prentice IC, Liang X, 2026,
Insights into evapotranspiration partitioning based on hydrological observations using the generalized proportionality hypothesis
, Hydrology and Earth System Sciences, Vol: 30, Pages: 317-341<jats:p>Abstract. Evapotranspiration comprises transpiration, soil evaporation, and interception. The partitioning of evapotranspiration is challenging due to the lack of direct measurements and uncertainty of existing evapotranspiration partitioning methods. We propose a novel method to estimate long-term mean transpiration to evapotranspiration (Et/E) ratios based on the generalized proportionality hypothesis using long-term mean hydrological observations at the watershed scale. We tested the method using 648 watersheds in the United States classified into six vegetation types. We mitigated impacts of the variability associated with different Ep data products by rescaling their original Ep values using the product E/Ep ratios in combination with the observed E calculated from watershed water balance. With Ep thus rescaled, our method produced consistent Et/E across six widely used Ep products. Shrubs (0.33) and grasslands (0.32) showed lower mean Et/E than croplands (0.48) and forests (respectively 0.69, 0.60, and 0.70 for evergreen needleleaf, deciduous broadleaf, and mixed forests). Et/E showed significant dependence on aridity, leaf area index, and other hydrological and environmental conditions. Using Et/E estimates, we calculated transpiration to precipitation ratios (Et/P) ratios and revealed a bell-shaped curve at the watershed scale, which conformed to the bell-shaped relationship with the aridity index (AI) observed at the field and remote-sensing scales (Good et al., 2017). This relationship peaked at an Et/P between 0.5 and 0.6, corresponding to an AI between 2 and 3 depending on the Ep dataset used. These results strengthen our understanding of the interactions between plants and water and provide a new perspective on a long-standing challenge for hydrology and ecosystem science.</jats:p>
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Journal articleNeu CT, Antonopoulos A, Dell A, et al., 2026,
Gne-Depletion in C2C12 Myoblasts Leads to Alterations in Glycosylation and Myopathogene Expression
, Cells, Vol: 15, Pages: 199-199<jats:p>GNE myopathy is a rare genetic neuromuscular disorder caused by mutations in the GNE gene. The respective gene product, UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase (GNE), is a bifunctional enzyme that initiates endogenous sialic acid biosynthesis. Sialic acids are important building blocks for the glycosylation machinery of cells and are typically found at the terminal ends of glycoprotein N- and O-glycans. The exact pathomechanism of GNE myopathy remains elusive, and a better understanding of the disease is urgently needed for the development of therapeutic strategies. The purpose of this study was to examine the effects of hyposialylation on glycan structures and subsequent downstream effects in the C2C12 Gne knockout cell model. No overall remodeling of N-glycans was observed in the absence of Gne, but differences in glycosaminoglycan expression and O-GlcNAcylation were detected. Expression analysis of myopathogenes revealed concomitant down-regulation of muscle-specific genes. Among the top candidates were the sodium channel protein type 4 subunit α (Scn4a), voltage-dependent L-type calcium channel subunit α-1s (Cacna1s), ryanodine receptor 1 (Ryr1), and glycogen phosphorylase (Pygm), which are associated with excitation-contraction coupling and energy metabolism. The results suggest that remodeling of the glycome could have detrimental effects on intracellular signaling, excitability of skeletal muscle tissue, and glucose metabolism.</jats:p>
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Journal articleMeccariello A, 2026,
Generating cisgenic sexing strains in insect pests
, Communications Biology, ISSN: 2399-3642 -
Journal articleCui Y, Peng S, Delgado-Baquerizo M, et al., 2026,
Productivity-driven decoupling of microbial carbon use efficiency and respiration across global soils.
, Sci Adv, Vol: 12Despite extensive research on soil microbial carbon (C) use efficiency (CUE), its linkage to actual soil C storage remains ambiguous. A key uncertainty is that CUE estimates from short-term labeling incubations assume a linear negative relationship with respiration rates, overlooking nonlinear interactions and long-term microbial acclimation. Here, we use a stoichiometry-based approach to estimate CUE (CUEST), which links soil resource availability to microbial demand and captures microbial adaptability under resource constraints. We synthesized 1094 paired observations of CUEST and heterotrophic respiration rate (Rh) across natural ecosystems and found a nonlinear relationship between them governed by ecosystem productivity. In low-productivity arid and cold regions, CUEST declined with increasing Rh, whereas in productive tropical and temperate regions, CUEST stabilized at a low level (0.27 ± 0.11) as Rh exceeded 340 ± 10.8 grams of C per square meter per year. This shift reflects microbial trade-offs between C assimilation and stoichiometric homeostasis, revealing a decoupling of microbial growth from respiration that limits the capacity of productive ecosystems to store additional soil C.
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Journal articleCator L, 2026,
A tiger is not always a satyr: role of male mating behaviour in interspecific mating interactions between Aedes aegypti and Aedes albopictus
, Parasites and Vectors, ISSN: 1756-3305Background: Interspecific mating between Aedes aegypti and Aedes albopictus, which act as vectors of a wide range of arboviruses, is predicted to have an important influence on their future distributions and disease control efforts. While interspecific insemination has been documented in a range of laboratory and field studies, rates vary between populations. It has been suggested that the outcome of mating interactions is driven by evolved variation in both the male ability to mate interspecific females and ability of females to resist interspecific males. However, there has been relatively little dissection of the behaviours that underlie interspecific insemination rates. Methods: We compared insemination rates between sympatric, allopatric, and lab-adapted strains of Ae. aegypti (Colombia, Arizona, and Liverpool, respectively) and allopatric and sympatric strains of Ae. albopictus (Montpellier and Colombia, respectively). We then used both live observations and high-speed videography to compare intraspecific and interspecific mating interactions. Results: We found very low rates of interspecific mating across all strains used. Both behavioural observations and high-speed videography suggested that female resistance behaviours were not responsible for low interspecific mating. Interestingly, we documented male Ae. albopictus consistently aborting interspecific mating attempts. Conclusions: This study provides additional evidence for strong pre-copulatory species barriers between Ae. aegypti and Ae. albopictus species and adds male avoidance as a possible mechanism to maintain these barriers. Considering female resistance, the ability of males to overcome that resistance, and male avoidance of interspecific matings together will be important for informing understanding of how we expect interspecific mating rates to vary across populations and respond to selective pressures such as mass-release strategies.
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Journal articleLodhiya T, Palande A, Veeram A, et al., 2026,
ATP burst is the dominant driver of antibiotic lethality in Mycobacterium smegmatis.
, Elife, Vol: 13Antibiotic-tolerant bacteria, due to their unique physiology, are refractory to antimicrobial killing and pose challenges for infection control. Incomplete knowledge of how bactericidal antibiotics work limits our understanding of partial resistance due to phenotypic tolerance in mycobacteria, a driver for developing genetic resistance. Using proteomics, 13C isotopomer analysis, genetic and biochemical assays, we investigated the physiological response of M. smegmatis challenged with aminoglycoside and fluoroquinolone antibiotics. Two distinct classes of antibiotics elicited remarkably similar responses and increased flux through the TCA cycle, causing enhanced respiration, ROS generation, and ATP burst. We observed that excessive ATP levels and not ROS dominantly contribute to cidality, which may in part be conferred by sequestration of divalent metal ions by ATP. Consequently, 13C isotope tracing indicated TCA cycle flux deviation from its oxidative arm as a bacterial adaptive mechanism, which also included activated intrinsic resistance and a higher propensity to develop antibiotic resistance. Our study provides a new understanding of the intricate mechanisms of antibiotic-induced cell death and expands the current paradigm for antibiotic action.
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Journal articleLodhiya T, Palande A, Veeram A, et al., 2026,
ATP burst is the dominant driver of antibiotic lethality in Mycobacterium smegmatis
, eLife, Vol: 13<jats:p> Antibiotic-tolerant bacteria, due to their unique physiology, are refractory to antimicrobial killing and pose challenges for infection control. Incomplete knowledge of how bactericidal antibiotics work limits our understanding of partial resistance due to phenotypic tolerance in mycobacteria, a driver for developing genetic resistance. Using proteomics, <jats:sup>13</jats:sup> C isotopomer analysis, genetic and biochemical assays, we investigated the physiological response of <jats:italic>M. smegmatis</jats:italic> challenged with aminoglycoside and fluoroquinolone antibiotics. Two distinct classes of antibiotics elicited remarkably similar responses and increased flux through the TCA cycle, causing enhanced respiration, ROS generation, and ATP burst. We observed that excessive ATP levels and not ROS dominantly contribute to cidality, which may in part be conferred by sequestration of divalent metal ions by ATP. Consequently, <jats:sup>13</jats:sup> C isotope tracing indicated TCA cycle flux deviation from its oxidative arm as a bacterial adaptive mechanism, which also included activated intrinsic resistance and a higher propensity to develop antibiotic resistance. Our study provides a new understanding of the intricate mechanisms of antibiotic-induced cell death and expands the current paradigm for antibiotic action. </jats:p>
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Journal articleCoxshall C, Nesbit M, Hodge J, et al., 2026,
Ecological and social pressures drive same-sex sexual behaviour in non-human primates
, Nature Ecology and Evolution, ISSN: 2397-334XSame-sex sexual behaviour (SSB) is widespread across animal species; however, its evolutionary origins and ecological underpinnings remain poorly understood. In social animals, SSB is likely shaped by both genetic and environmental factors. For instance, a recent study in rhesus macaques indicate that while SSB is partially heritable and genetically based, it is also strongly influenced by environmental and social conditions. Here, we compiled species-level data on 491 non-human primate species, documenting SSB occurrence and prevalence in 59 species, and examined its associations with 15 environmental, life history, and social traits using phylogenetic regression and structural equation modelling. SSB occurrence was more likely in species inhabiting drier environments with increased food scarcity and predation pressure, in species with greater size dimorphism and longer lifespans, and in those with more complex social structures and hierarchies. Structural equation modelling further indicated that environmental and life history traits influence SSB mainly indirectly, whereas social complexity directly promotes its occurrence. Together, these findings highlight SSB as a context-dependent behaviour shaped by interactions among ecological, life history, and social factors, offering insights into the sexual diversity and social evolution of primates.
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Journal articleHabtewold T, Lwetoijera DW, Hoermann A, et al., 2026,
Gene-drive-capable mosquitoes suppress patient-derived malaria in Tanzania
, Nature, Vol: 649, Pages: 442-448, ISSN: 0028-0836Gene drive technology presents a transformative approach to combatting malaria by introducing genetic modifications into wild mosquito populations to reduce their vectorial capacity. Although effective modifications have been developed, these efforts have been confined to laboratories in the global north. We previously demonstrated that modifying Anopheles gambiae to express two exogenous antimicrobial peptides inhibits the sporogonic development of laboratory-cultured Plasmodium falciparum, with models predicting substantial contributions to malaria elimination in Africa when integrated with gene drive1,2,3. However, the effectiveness of this modification against genetically diverse, naturally circulating parasite isolates remained unknown. To address this critical gap, we adapted our technology for an African context by establishing infrastructural and research capacity in Tanzania, enabling the engineering of local A. gambiae under containment. Here we report the generation of a transgenic strain equipped with non-autonomous gene drive capabilities that robustly inhibits genetically diverse P. falciparum isolates obtained from naturally infected children. These genetic modifications were efficiently inherited by progeny when supplemented with Cas9 endonuclease provided by another locally engineered strain. Our work brings gene drive technology a critical step closer to application, providing a locally tailored and powerful tool for malaria eradication through the targeted dissemination of beneficial genetic traits in wild mosquito populations.
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Journal articleChao KW, Wong L, Oqua AI, et al., 2026,
Human class B1 GPCR modulation by plasma membrane lipids
, Communications Biology, ISSN: 2399-3642The class B1 G protein-coupled receptor (GPCR) subfamily is a class of receptors known for their regulatory roles in metabolism and neuronal activity and as important drug targets. Lipids play key functional roles in modulation of GPCR signalling, yet our understanding of the molecular level detail of specific lipid interactions with class B1 GPCRs remains limited. Here we present coarse-grained molecular dynamics (MD) simulations of the active and inactive states of 15 human class B1 family members and use aiida-gromacs to capture full provenance for the set-up of simulations in complex plasma membranes. Receptors exhibit state-dependent lipid interactions with the regulatory sterol cholesterol and phospholipid phosphatidylinositiol-3,4-bisphosphate (PIP2) at defined locations on the receptor surface. Global analysis of trends across the subfamily reveals conserved patterns of lipid interaction dynamics. The glycosphingolipid GM3 exerts a modulatory influence on the dynamics of class B1 extracellular domains in both simulations and in vitro time-resolved FRET assays.
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Journal articlevan Thor J, 2026,
Coherent two dimensional electronic-X-ray spectroscopy
, Journal of Chemical Physics, ISSN: 0021-9606Ultrafast pump-probe time resolved X-ray spectroscopy carries information on the valence-core dynamics of molecular systems. Here, a coherent two-dimensional nonlinear electronic-X-ray spectroscopy (2DEX) application is proposed in order to reveal the frequency-frequency correlations for the valence and the core transition excitations. 2DEX is in the class of extreme-cross peak correlation spectroscopy and is experimentally straightforward to measure as an adaptation of the conventional optical pump – X-ray probe technique by creating a phase-locked pulse pair of the ultrafast laser for the valence excitation. Theoretical evaluation of the coherences and populations for several applications of ultrafast valence-core spectroscopy experiments is shown. Using a response function approach, 2DEX four wave signals are calculated and evaluated with respect to frequency separation in the electronic and X-ray ranges as well as the lineshape characteristics. It is shown that stationary and oscillatory contributions to the rephasing, non-rephasing and absorptive signals can be resolved depending on pulse shaping and phase cycling, phase matching, X-ray spectrometer and material response parameters. Calculations are shown for examples that include the valence-core coherences for a vibrational monomer and for Frenkel and charge transfer (CT)electronic exciton states, which in the X-ray absorption near-edge structure (XANES) spectral region have the potential to resolve the population and coherence contributions in the atomic localised basis.
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Journal articleBurton GP, Ceci P, MacKinnon L, et al., 2026,
Phylogenetics and evolution of Digitaria grasses, including cereal crops fonio, raishan, and Polish millet
, Annals of Botany, Vol: 137, Pages: 141-157, ISSN: 0305-7364Background and Aims Millet crops in the grass genus Digitaria include white and black fonio (D. exilis and D. iburua), raishan (D. compacta) and Polish millet (D. sanguinalis), cultivated across West Africa, India, and Europe. Fonio and raishan crops are important to supporting food security and subsistence agricultural systems in rural communities, while D. sanguinalis is no longer cultivated. These crops are resilient to challenging climates. We aim to produce an integrated study of these crops: a phylogeny of the Digitaria genus including all four food species, to identify key crop wild relatives (CWRs); time-calibrated biogeographic analysis, to investigate the history and evolution of Digitaria; and morphological study to assess the transition between wild and domesticated species. Methods We use the Angiosperm 353 target-enrichment sequencing approach to produce maximum likelihood and coalescent model nuclear phylogenies for 46 Digitaria species, and Bayesian methods to propose an evolutionary and biogeographic history for the genus. Morphology of wild and cultivated species is investigated for spikelets and growth habits using microscopy and SEM imaging.Key Results Four distinct evolutionary lineages are found for the Digitaria crops, and we identify new close crop wild relatives D. fuscescens, D. atrofusca, D. setigera and D. radicosa, and D. ciliaris. South and eastern Africa is proposed as a likely origin of early Digitaria divergence, with crop lineages diverging from wild relatives around 2-6mya. Incomplete domestication traits are observed, including the loss of trichomes, but no clear change in appearance for spikelet or abscission zone morphologies.Conclusions The knowledge produced in this study about Digitaria CWRs will be useful in improving crop traits through targeted breeding and physiological studies; and we also highlight the need for conservation of seed material through programmes working with local partners, for these important climate-tole
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Journal articleSayol F, Neate-Clegg M, Sheard C, et al., 2026,
AVONICHE: A Global Dataset of Dietary and Foraging Niches for Birds
, Global Ecology and Biogeography, Vol: 35, ISSN: 1466-822XMotivation: The role of each animal species in an ecosystem is largely determined both by the resources it uses and the behaviours through which these resources are obtained. Even in well-studied vertebrate groups, like birds, quantitative data on the relative use of different food resources in the context of foraging strategies are generally lacking. Most analyses in macroecology, macroevolution and conservation biology are therefore limited to simplified dietary categories, ignoring the specific foraging behaviours and substrates used to access resources. Here we present AVONICHE, a dataset quantifying proportional membership in 32 foraging niches, representing a combination of dietary categories and associated foraging strategies used by all bird species. Main Types of Variables Contained: Species-level information on the proportional use of foraging niches, each of which is defined as a particular foraging strategy within a specific dietary category (e.g., invertebrate feeding is subdivided into 7 foraging niches based on different foraging behaviors). Spatial Location and Grain: Global. Time Period and Grain: Present. Major Taxa and Level of Measurement: All bird species (Class Aves). To allow integration with global phylogenies and other data resources published in future, we align species-level niche data with four different taxonomic treatments: BirdTree (9993 species), Clements/eBird (10,661 species), BirdLife International (10,999 species) and the new AviList taxonomy (10,981 species). Software Format: Spreadsheet (.csv).
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Journal articleEndres RG, 2026,
Bacteria may not be good at chemotaxis
, Nature Physics, Vol: 22, Pages: 8-9, ISSN: 1745-2473Bacteria appear to be masters of chemotaxis, but it is unclear how well they process chemical information. A study now argues that cells squander most sensory information, making chemotaxis far less efficient than established physical limits allow.
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Journal articleKurokawa R, Mtali CS, Daniel IJ, et al., 2026,
Dynamics of lung-infiltrating virus-specific T cells associated with age-dependent SARS-CoV-2 pneumonia severity.
, PLoS Pathog, Vol: 22Coronavirus disease 2019 (COVID-19) pneumonia is prevalent in the elderly infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); however, the mechanisms underlying its age-dependent pathogenesis remain unclear. In this study, we established a mouse-adapted SARS-CoV-2 strain infected Nr4a3-Tocky mouse model to examine T-cell dynamics associated with disease severity. Nr4a3-Tocky mice allow the analysis of the dynamics and induction of antigen-reactive T cells following antigen recognition in vivo using fluorescent Timer protein. SARS-CoV-2-infected adult mice exhibited transient body weight loss and recovery, whereas aged mice developed severe pneumonia. BALF viral RNA was comparable between 1-4 days post-inoculation (d.p.i.), but declined in adults at 5 d.p.i. Aged mice displayed stronger inflammation as indicated by scRNA-seq, and higher levels of inflammatory cytokines (TNF-α, CCL2, CXCL10 and IL-6) in BALF correlated with weight loss. Timer analysis revealed induction of antigen-reactive T cells in the adult lungs at 5 and 8 d.p.i., which inversely correlated with disease severity. Additionally, S-specific IFN-γ ⁺ CD8 ⁺ T cells were detected at 5 d.p.i. in adults, whereas detection of antigen-specific T cells was delayed in aged mice. These results suggest that the coexistence of age-related lung inflammation and delayed induction of antigen-specific T cells is linked to more severe pneumonia, while earlier T-cell responses are associated with improved viral control and milder disease. In this study, we utilized a novel mouse model enabling characterization of antigen-reactive T cells in the local tissue, and investigated inflammatory responses in the lung together with lung-infiltrating virus-specific T cells, finding the dynamics of these immunological parameters associated with the age of the mice. Our analysis provides new insights into understanding how age-related T-cell dysfunction is associated
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Journal articleMoitra T, Larrouy-Maumus G, 2026,
Integrated approaches for discovery and functional annotation of proteins of unknown function.
, Trends Biochem Sci, Vol: 51, Pages: 80-92, ISSN: 0968-0004Proteins of unknown function (PUFs) remain a persistent blind spot in molecular biology. Emerging evidence implicates many PUFs in crucial but poorly characterised roles in biomedical contexts, particularly cancer and infectious diseases. Here, we explore integrative strategies combining high-throughput experimental platforms with computational models to address this gap. We outline how functional insights can be derived across a molecular hierarchy, spanning individual proteins, interaction networks, and transient assemblies, and evaluate the distinct opportunities and challenges faced at each level. Framing these advances within a systems biology lens, we argue that characterising PUFs could redefine therapeutic discovery pipelines. We call for data-driven discovery methods and community efforts to support reproducible, scalable annotation of the 'dark' proteome.
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Journal articleHerzog MK-M, Peters A, Shayya N, et al., 2025,
Comparing <i>Campylobacter jejuni</i> to three other enteric pathogens in OligoMM<SUP>12</SUP> mice reveals pathogen-specific host and microbiota responses
, GUT MICROBES, Vol: 17, ISSN: 1949-0976- Cite
- Citations: 1
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Journal articleBiswas P, Sanchez-Garrido J, Kozik Z, et al., 2025,
The accessory type III secretion system effectors collectively shape intestinal inflammatory infection outcomes
, GUT MICROBES, Vol: 17, ISSN: 1949-0976 -
Journal articleMoron-Ortiz A, Ferrando-Marco M, Leon-Vaz A, et al., 2025,
Effects of lutein, phytoene and carotenoid-rich microalgal extracts on the epidermis of <i>Caenorhabditis elegans</i>
, FOOD CHEMISTRY, Vol: 497, ISSN: 0308-8146 -
Journal articleConev A, Islam SA, Tsitsa I, et al., 2025,
3DSeqCheck: A Web-based Tool for Verifying Sequence Consistency Between a 3D Structure File and the Corresponding UniProt Entry.
, J Mol BiolUniProt 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 articlePeters A, Sanchez Garrido J, Shareefdeen H, et al., 2025,
Stable coexistence of Citrobacter rodentium with a lytic bacteriophage during in vivo murine infection
, mBio, ISSN: 2161-2129Bacteriophages are ubiquitously present in bacterial communities, yet phage-bacteria interactions in complex environments like the gut remain poorly understood. While antibiotic resistance is driving a renewed interest in phage therapy, most studies have been conducted in in vitro systems, offering limited insight into the complexity of such dynamics in physiological contexts. Here, we use Citrobacter rodentium (CR), a natural mouse-restricted enteric pathogen and well-established model for human enteropathogenic and enterohaemorrhagic Escherichia coli (EPEC and EHEC) infections, to investigate phage-pathogen interactions in vivo. We isolate and characterise Eifel2, a novel lytic phage infecting CR, and generate anti-phage specific antibodies that enable the visualisation of phage infections in vitro. In a murine model of CR infection, oral administration of Eifel2 led to robust phage replication in the gut without reducing the bacterial burden or infection-associated inflammation, confirming the establishment of a stable coexistence in the gut. Despite the emergence of a sub-population of phage-resistant CR mutants in vivo, they did not undergo clonal expansion, indicating that additional selective pressures impaired their widespread dissemination in the gut. Together, our findings demonstrate that imaging approaches can capture key infection stages in vitro, while in vivo models are essential for capturing the complexity of phage-bacteria interactions. This work highlights the importance of studying phage therapy in host-pathogen contexts that include a normal microbiota and a suitable host environment, where dynamic co-existence rather than eradication may define therapeutic outcomes.
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Journal articleBrook TS, Hutton IJ, Papadopulos AST, et al., 2025,
Two new species of Currant Bush Coprosma (Rubiaceae) from an endemic radiation on Lord Howe Island
, Botanical Journal of the Linnean Society, ISSN: 0024-4074Molecular and morphological evidence provide support for the description of two new species of Coprosma (Rubiaceae) from Lord Howe Island, a remote oceanic island in the Tasman Sea. The first species, C. savolainenii sp. nov., was discovered during a plant survey, whereas the second species, C. ptotopetra sp. nov. was identified using DNA fingerprinting. Confirmation of both has recently been reconfirmed through high-throughput sequencing. We provide detailed descriptions of each new species, alongside an updated description of C. putida, a species with similar morphology to C. ptotopetra sp. nov.. We also provide phenological, distribution, and conservation data for each species. This description goes beyond a traditional species account, as it represents a unique endemic radiation occurring in sympatry on an isolated island of global conservation significance. It may also represent a rare botanical example of the syngameon hypothesis, where hybrid speciation accelerates evolutionary radiation.
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Journal articleBurton VJ, Jones AG, Robinson LD, et al., 2025,
Who watches the worms? Motivation and (non-)participation in a contributory citizen science project
, BMC Ecology and Evolution, ISSN: 2730-7182BackgroundCitizen science projects rely on public participation to generate data and promote engagement with science. However, little is known about the motivations of individuals who register for citizen science projects but ultimately do not participate. Understanding non-participation is important for improving recruitment and engagement strategies. This study used Earthworm Watch, a UK-based soil biodiversity citizen science project that ran from April 2016 to August 2018, to explore the motivations of both participants and non-participants, and to examine how these relate to demographic factors and survey completion rates.ResultsA total of 1,678 participants registered for Earthworm Watch. The overall survey return rate was 12.75%, with no significant differences by age or gender. The provision of physical survey packs did not significantly affect completion rates. Direct contact with project staff was the only recruitment method associated with a significantly higher survey return rate. Significantly more registrants were female than male across all age groups. Motivations related to understanding and values were most reported, with participants often expressing a desire to learn more or to contribute to the topic, but these participants contributed fewer surveys than those without those motivations. Social motivations were mentioned less frequently but were more commonly reported by women. Younger participants were more likely to cite career-related motivations.ConclusionsThe limited impact of physical materials on participation suggests that designing projects for immediate and accessible involvement could be more cost-effective. The significant influence of meeting project members and hands-on experiences at events strengthens the case for including these activities in engagement plans. Motivations to participate in Earthworm Watch varied by demographic factors such as age and gender; however, when significant, they influenced only the number of surveys sub
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Journal articlePawar S, Kontopoulos D-G, 2025,
Toward a general understanding of thermal performance curves in biology
, Proceedings of the National Academy of Sciences, Vol: 122, ISSN: 0027-8424Temperature profoundly influences biological processes at all scales, from enzyme kinetics to ecosystem-level metabolism. Despite the enormous physiological diversity of life on Earth—from unicellular microbes to plants and animals—there is a remarkable similarity in how individual-level traits (e.g., metabolic rate, locomotion, growth rate) respond to temperature (1–3). These relationships are captured by thermal performance curves (TPCs), which describe how the rate or magnitude of a biological trait varies continuously with temperature (2, 4). TPCs are typically unimodal and left-skewed (Fig. 1), rising in an Arrhenius-like (that is, exponentially) manner with temperature up to an optimum and then declining steeply beyond a critical upper threshold (5, 6). In their new study, Arnoldi et al. (7) provide a strikingly general explanation for this ubiquitous curve shape, showing that the diversity of mechanistic TPC models and empirical data can be unified under a single, mathematically derived “Universal Thermal Performance Curve” (UTPC).
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Journal articleKeeping TR, Shepherd TG, Prentice IC, et al., 2025,
Influence of global climate modes on wildfire occurrence in the contiguous United States under recent and future climates
, Climate Dynamics, Vol: 64, ISSN: 0930-7575Predictable modes of climate variability, such as the El Niño Southern Oscillation (ENSO), have a major influence on regional weather patterns, an important control on wildfire occurrence. Although these global climate modes have been associated with historical variability in wildfire occurrence in the United States and are used to forecast seasonal wildfire risk, precise information about the spatial pattern and magnitude of their influence is lacking and the satellite record of wildfires is too short to address these issues. Here we use wildfire occurrence model with a large ensemble of 1600 simulated years from EC-Earth3 in a recent climate (2000–2009) and a future climate corresponding to + 2 °C global warming, to characterise the impact of specific climate modes on wildfire occurrence in the contiguous US. We show that ENSO, the Indian Ocean Dipole (IOD), and the 1-year lagged Tropical North Atlantic (TNA+1) have the greatest effect on annual fire occurrence—strongly contributed by the effect of these modes on hot, dry conditions in the Great Plains and precipitation in the southwestern US. El Niño is not significantly associated with wildfire occurrence in the northwestern US, contrary to expectation, but is associated with a later (earlier) wildfire season peak in the southwestern (southeastern) US. Under future warming, the AMO and PNA become a significant influence over most of the US, and the magnitude of impact of ENSO and TNA+1 increase strongly.
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