Results
- Showing results for:
- Reset all filters
Search results
-
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.
-
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>
-
Journal articleMishra V, Kozik Z, Biswas P, et al., 2026,
Rehydration rescues Il22-/- mice from lethal Citrobacter rodentium infection
, Nature Communications, Vol: 17, ISSN: 2041-1723Interleukin-22 (IL-22) is considered indispensable for host defence against Citrobacter rodentium, with 100% mortality of Il22 -/- mice. While IL-22 promotes epithelial barrier integrity and production of antimicrobial peptides, the precise mechanism underlying lethality remains unclear. Here, we show that following C. rodentium infection Il22-/- mice succumb due to dehydration, rather than failure to control bacterial burden or regenerate damaged intestinal epithelium. Proteomic and gene expression analysis reveal greater enterocyte depletion in C. rodentium-infected Il22-/- mice, resulting in significant reductions in ion transporter abundances. We show that while not reducing bacterial load, improving the gut barrier integrity, or affecting immune responses, fluid therapy (FT) fully rescues Il22-/- mice by correcting systemic dehydration. Survival is associated with locally increased Reg3b, IL-17F and IL-10 levels, suggesting activation of compensatory pathways that potentially support recovery in the absence of IL-22. Recovered Il22-/- mice exhibit epithelial cell regeneration and tissue physiology similarly to C. rodentium-infected Il22+/+ mice. These findings suggest that dehydration is the primary cause of mortality in Il22-/- mice and reveal that IL-22 prevent this outcome by preserving epithelial integrity and fluid-ion absorption. Importantly, this study underscores the necessity of incorporating supportive therapies into preclinical infection models to better reflect physiological settings and improve their relevance in modelling human disease.
-
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.
-
Journal articleWeeks TL, Walkden PA, Edwards DP, et al., 2026,
Land-use change undermines the stability of avian functional diversity
, Nature, Vol: 649, Pages: 381-387, ISSN: 0028-0836Land-use change causes widespread shifts in the composition and functional diversity of species assemblages. However, its impact on ecosystem resilience remains uncertain. The stability of ecosystem functioning may increase after land-use change because the most sensitive species are removed, which leaves more resilient survivors1,2,3. Alternatively, ecosystems may be destabilized if land-use change reduces functional redundancy, which accentuates the ecological impacts of further species loss4,5. Current evidence is inconclusive, partly because trait data have not been available to quantify functional stability at sufficient scale. Here we use morphological measurements of 3,696 bird species to estimate shifts in functional redundancy after recent anthropogenic land-use change at 1,281 sites worldwide. We then use extinction simulations to assess the sensitivity of these altered assemblages to future species loss. Although the proportion of disturbance-tolerant species increases after land-use change, we show that this does not increase stability because functional redundancy is reduced. This decline in redundancy destabilizes ecosystem function because relatively few additional extinctions lead to accelerated losses of functional diversity, particularly in trophic groups that deliver important ecological services such as seed dispersal and insect predation. Our analyses indicate that land-use change may have major undetected impacts on the resilience of key ecological functions, hindering the capacity of natural ecosystems to absorb further reductions in functionality caused by ongoing perturbations.
-
Journal articlePretorius D, Nikov G, Washio K, et al., 2026,
Designing novel solenoid proteins with in silico evolution
, Communications Chemistry, Vol: 9, ISSN: 2399-3669Solenoid proteins are elongated tandem repeat proteins with diverse biological functions, making them attractive targets for protein design. Advances in machine learning have transformed our understanding of sequence-structure relationships, enabling new approaches for de novo protein design. Here, we present an in silico evolution platform that couples a solenoid discriminator network with AlphaFold2 as an oracle within a genetic algorithm. Starting from random sequences, we design α-, β-, and αβ-solenoid backbones, generating structures that span natural and novel solenoid space. We experimentally characterise 41 solenoid designs, with α-solenoids consistently folding as intended, including one structurally validated design that closely matches the design model. All β-solenoids initially failed, reflecting the difficulty of designing β-strand majority proteins. By introducing terminal capping elements and refining designs based on earlier experimental screens, we generate two β-solenoids that have biophysical properties consistent with their designs. Our approach achieves fold-specific hallucination-based design without depending on explicit structural templates.
-
PatentJung U, Ali S, Mathias S, et al., 2026,
Genetic constructs for improved aav titers and potency
, WO2026003353A1The present invention relates to a rep plasmid comprising at least one long adeno-associated virus replication protein coding sequence encoding at least one long functional rep protein, at least one short adeno-associated virus replication protein coding sequence encoding at least one short functional rep protein, and at least one heterologous element, wherein following translation the at least one heterologous element results in a ratio of long adeno-associated virus rep protein to short adeno-associated virus rep protein of about 1:5 to about 1:5000.
-
Journal articleChapman ASA, Adanu SK, Dalin C, et al., 2026,
Assessing trade-off risk between crop production and vertebrate biodiversity in three African countries
, People and NatureGovernments worldwide are committed to eliminating hunger and conserving biodiversity, reflected in United Nations Sustainable Development Goals 2 (Zero Hunger) and 15 (Life on Land). Expanding agricultural lands to meet growing food demands often threatens biodiversity, creating potential trade-offs between these objectives. To understand the potential trade-off risks, we need to determine the extent to which croplands are located in areas that are also species-rich and which crops pose the greatest biodiversity risk. We identify areas where there is a trade-off risk between vertebrate biodiversity and crop production important for food and livelihoods across Ethiopia, Ghana, and Zambia. We evaluate trade-off risk via three metrics: (i) the footprint, mapping the overlap between crop production and ecological priority areas; (ii) two measures of trade-off risk based on the number of species potentially impacted: one measuring average local species richness affected per unit area used to grow a crop or crop group—domestic or traded (trade-off risk intensity), and a second measuring this average local species richness impacted but summed across the total area used to grow the crop/crop group (trade-off risk potential); and (iii) the hotspots where crops are grown in regions especially rich in vertebrates. Trade-off risk varies more among crop types and regions, and relatively little, on average, between crops grown for international trade versus crops grown primarily for domestic consumption. The crops with the greatest total risk potential are wheat in Ethiopia, cocoa in Ghana, and maize in Zambia. In all three countries, coffee poses the greatest trade-off risk intensity to threatened species and bananas exceed the expected trade-off risk intensity. Trade-off risks are context-dependent and optimal management will therefore be both country- and crop-specific. As there is not just one crop posing a consistently high risk of trade-off for biodiversity, and many
-
Journal articleSayol F, NeateClegg MHC, Sheard C, et al., 2026,
AVONICHE: a global dataset of dietary and foraging niches for birds
, Global Ecology and Biogeography, Vol: 35, ISSN: 1466-822XMotivationThe 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 ContainedSpecies-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 GrainGlobal.Time Period and GrainPresent.Major Taxa and Level of MeasurementAll 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 FormatSpreadsheet (.csv).
-
Journal articleLoft T, Oliveras Menor I, Stevens N, et al., 2026,
Energy flows reveal declining ecosystem functions by animals across Africa
, Nature, Vol: 649, Pages: 104-112, ISSN: 0028-0836A key challenge for ecological science is to understand how biodiversity loss is changing ecosystem structure and function at scales that are relevant for policy1. Almost all biodiversity metrics are challenging to disaggregate into animal-mediated ecosystem functions such as pollination, seed and nutrient dispersal, and predation. Here we adopt an ecosystem energetics approach2 as a physically meaningful method of translating animal species composition into a suite of ecosystem functions. Drawing on new datasets that estimate biodiversity intactness and species population densities3,4,5, we quantify historical changes to energy flows through mammal- and bird-mediated ecosystem functions across sub-Saharan Africa. In total, trophic energy flows have decreased by more than one-third. The pattern of decreasing function varies by historical biome, driven by arboreal birds and primates in forests, terrestrial herbivores in grassy systems, and burrowing mammals in arid systems. Functions performed by megafauna in particular have collapsed outside protected areas. Compared with other biodiversity metrics, an energetics approach highlights the ecological importance of smaller animals and keystone species. The results can help practitioners conserve and restore functionally diverse, energetically intact ecosystems across land uses and biomes. By relating biodiversity intactness to energy and material flows, ecosystem energetics can also advance efforts to integrate animal-driven functions into biosphere and earth system models, helping us to understand possible regional or planetary boundaries6 for biodiversity.
-
Journal articleLearmonth R, Brearley FQ, Clark A, et al., 2026,
Drivers of individual plant species contributions to β-diversity are scale-dependent
, Oikos, ISSN: 0030-1299Species introductions and local extinctions of native species are driving biotic homogenisation in plant communities by reducing β-diversity. Individual species vary in their contributions to β-diversity (species contribution to β-diversity; species-β), yet our understanding of how species characteristics shape these contributions remains limited. Additionally, although the ecological processes influencing β-diversity are known to vary with spatial scale, we lack understanding of how species contributions, or their underlying determinants, change across scales. Here, we modelled how plant functional traits, phylogenetic relatedness, and introduction status influence their contributions to β-diversity using plant community data from 429 plots surveyed from 2017 to 2023 across three nested spatial scales (up to 1 km<sup>2</sup>) in nine sites spanning four countries. We extended the analysis to broader spatial extents (100 km<sup>2</sup> to the entire UK) using GBIF occurrence data. We found that functional traits associated with competitive ability influenced species-β, but the direction and strength of their effects varied with scale. Likewise, increasing phylogenetic distance increased species-β at small scales but reduced it at larger ones. After accounting for traits and phylogeny, introduced species consistently contributed less to β-diversity than native species – especially at broader spatial extents. These results demonstrate that species' ecological and evolutionary characteristics shape their contributions to β-diversity, but that these effects are scale-dependent. Our findings highlight the importance of scale-explicit approaches in understanding both the determinants of β-diversity, and how we can combat its loss to mitigate biotic homogenisation.
-
Journal articleMartello F, Aguirre-Gutierrez J, Andrino CO, et al., 2026,
Multitaxa functional diversity increases the resilience of biological natural capital in the Amazon
, Journal of Applied Ecology, Vol: 63, ISSN: 0021-8901The resilience of biological natural capital in the Amazon is strongly influenced by the functional diversity of multitaxa, which promotes the stability and sustainability of the ecosystem. However, biological natural capital, driven by multiple dimensions of biodiversity, is often underestimated by focusing on the taxonomic dimension, such as richness and abundance. We applied a multitaxa and trait-based approach to assess how functional diversity supports natural capital. By using a dataset including woody plants, bees, frugivorous butterflies and songbirds, we created two indices: Biological Natural Capital Resilience (BNCR), the proportion of biological assets needed to maintain natural capital integrity, and Biological Natural Capital Uniqueness (BNCU), the proportion of natural capital sustained by species' functional uniqueness. BNCR results show that, in general, more than 80% of biological assets to maintain the integrity of natural capital, and that the BNCR index reached the highest value when all taxonomical groups are combined. These results reveal that natural capital strongly depends on biological assets and underscore the importance of multitaxa approaches for assessing ecosystem resilience. BNCU values show that a substantial portion of natural capital integrity (from 46.22% to 64.23%) depends on a small subset of functionally unique species, indicating that the loss of few species, which play irreplaceable ecological roles, rapidly reduces ecosystem functioning. Synthesis and applications. This study presents a trait-based framework integrating functional diversity into biological natural capital accounting, capturing both ecosystem resilience and species uniqueness across multiple taxa. It provides ecologically grounded, standardized and reproducible indicators that move beyond single-taxon or purely taxonomic approaches. By embedding these indicators into natural capital accounts, the framework supports conservation prioritization, restoration pl
-
Journal articleWen B, Dowell R, Steyaert M, et al., 2026,
Environmental DNA as a Tool for the Assessment of Coral (Anthozoa) Composition in the Chagos Archipelago
, Environmental DNA, Vol: 8Human-induced global warming has triggered a persistent decline in the health of marine ecosystems, particularly coral reefs, which are experiencing increasingly frequent and severe bleaching and mortality events. Refining cost-effective and precise monitoring tools, such as environmental DNA (eDNA) metabarcoding, is essential to supplement future coral reef monitoring programs, with ongoing efforts focused on improving methods, validating results, and understanding limitations. Although eDNA has been widely used in aquatic ecosystem studies, its application to corals (Anthozoa) remains underexplored. Here, we investigate the use of eDNA metabarcoding with molecular markers targeting the ITS2 region of Anthozoa for monitoring coral communities in a remote and relatively undisturbed atoll system. We integrate three mainstream taxonomic assignment approaches (IDTAXA, BLAST Top Hits, and BLAST LCA), retaining only consensus identifications across methods for downstream analyses. This conservative strategy ensures highly robust and reliable taxonomic resolution, with over 90% of the sequences classified within Anthozoa, encompassing 18 genera and 15 genera of hard corals (Scleractinia). A considerable overlap in coral identification is observed between eDNA and traditional benthic transect surveys, giving support to the ability of eDNA to identify the community composition of Anthozoan taxa. Importantly, cryptic genera, such as Cycloseris, Cyphastrea, Merulina, Oxypora, and Turbinaria were identified by the eDNA approach but not the traditional surveys. Conversely, genera such as Alveopora, Astreopora, Caulastrea, Fungia, Galaxea, Halomitra, Herpolitha, Leptastrea, Platygyra, Plerogyra, and Stylophora were identified by the traditional surveys but not the eDNA approach, likely due to primer bias, taxonomic resolution or incomplete reference databases, supporting the complementary use of both methods. We also observe that the eDNA metabarcoding may capture differences in
-
Journal articleBarber RA, Underwood BC, Clarkson JJ, et al., 2026,
Ectomycorrhizal community composition and extramatrical hyphal proportion predict soil carbon stocks at the landscape scale
, Functional Ecology, ISSN: 0269-8463While fungal composition has been linked to soil carbon at global scales, these patterns are often difficult to disentangle from broad climatic gradients and species range limits. To address this constraint, we tested which aspects of ectomycorrhizal community structure explain soil carbon variation within a single temperate woodland landscape, where climate and species pools are relatively constant. Across 189 plots, we identified fungi from over 3500 ectomycorrhizal roots, and characterised composition, diversity, abundance, and morphological traits (hyphae and rhizomorphs). We related these to soil carbon stocks using single-predictor models (fungi alone) and a multiple-predictor model that adjusted for soil chemistry, topography and woodland type. Community composition and extramatrical hyphal proportion—rather than diversity or abundance—showed the strongest and most consistent associations with carbon. In single-predictor models, conifer-associated ectomycorrhizal communities were correlated with larger carbon stocks, consistent with continental-scale patterns. However, after accounting for soil chemistry, topography and vegetation, this relationship reversed: broadleaf-associated communities emerged as positively associated with soil carbon stocks, alongside greater extramatrical hyphal proportion. Specific ectomycorrhizal fungi, notably Russula ochroleuca and Lactarius tabidus, also emerged as indicators of carbon-rich soils, offering finer resolution than broad woodland type classifications. The reversal between single and multiple-predictor models suggests that the relationship between conifer-associated communities and soil carbon observed at broader scales may partially reflect correlated environmental conditions rather than direct fungal effects and that the independent contribution of ectomycorrhizal fungi to carbon storage may be stronger in broadleaf systems. Our findings demonstrate that ectomycorrhizal community composition predicts soi
-
Journal articleMatias MG, Gravel D, Chase JM, et al., 2026,
PondNet – towards a global network of experiments on the effects of climate change on aquatic ecosystems
, Ecography, ISSN: 0906-7590Global change is reshaping the distribution of biodiversity and the functioning of ecosystems. Predicting the long-term consequences of such changes remains a challenge due to a need for a clear understanding of the mechanisms underpinning ecosystem-level responses, as well as the role of geographical and environmental contingencies. We propose that these gaps can be addressed for freshwater ecosystems using a globally distributed experiment with standardized observations and disturbances. Specifically, this paper outlines the structure of PondNet – a globally distributed network of pond mesocosm experiments – designed to investigate how aquatic food webs respond to environmental change across broad geographical gradients. Pond mesocosms are affordable, low maintenance and easily replicated model ecosystems, with broadly predictable trophic architectures and community size-structure. PondNet would implement state-of-the-art environmental DNA biodiversity assessments for standardized taxonomic identification across biogeographical regions. A major operational bottleneck for developing a global understanding of environmental change effects on ecosystem functioning is the current lack of standardized experiments across coordinated infrastructures. We propose that by building on existing distributed experiments, we can assemble a modular participation scheme that ensures broad biogeographical coverage whilst accounting for varying levels of resource commitments from local hosts. PondNet aims to answer two overarching questions: 1) how general are community, food web and ecosystem-level responses to climate change across scales (i.e. local environmental gradients to biogeographical regions)?, and 2) to what extent are such responses contingent on local climate, environment, and regional species pools? PondNet will contribute to developing predictive models that can be adaptively improved from testing with data from globally replicated experiments and monitori
-
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.
-
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
-
Journal articlede Lima RB, da Silva DAS, Nunes MH, et al., 2026,
Mapping the density of giant trees in the Amazon.
, New Phytol, Vol: 249, Pages: 152-168Tall trees (height ≥ 60 m) are keystone elements of tropical forests, strongly influencing biodiversity, carbon storage, and ecosystem resilience. Yet, their density and spatial distribution remain poorly quantified, especially in remote Amazonian regions, limiting our understanding of their ecological roles and contribution to forest-climate interactions. We combined airborne LiDAR data from 900 transects across the Brazilian Amazon with environmental predictors to model tall-tree density. Spatial extrapolations allowed us to generate regional distribution estimates and assess associations with climate, topography, and disturbance regimes. Our model predicts that tall trees are unevenly distributed, with c. 14% of the estimated density concentrated in c. 1% of the Amazon and c. 50% within c. 11%. The highest densities occur in Roraima and the Guiana Shield provinces, where water availability is high and lightning or storm incidence is low. Modeled density strongly correlates with aboveground biomass, highlighting the disproportionate contribution of tall trees to carbon stocks. We estimate c. 55.5 million tall trees across the Brazilian Amazon. These findings demonstrate that tall-tree distribution is a crucial but underused predictor for biomass models. Understanding their ecological and spatial dynamics is vital for forest conservation and climate-resilience strategies under increasing anthropogenic pressures.
-
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.
-
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
-
Journal articleCakin I, Millington R, Pawar S, et al., 2026,
A novel method to simultaneously estimate bacterial respiration and growth from oxygen dynamics.
, ISME Commun, Vol: 6Bacterial growth and respiration are fundamental metabolic processes that drive energy transformation and allocation within organisms and impact carbon sequestration at the ecosystem scale. However, these traits are usually measured independently; bacterial growth is quantified with endpoint biomass measurements, while respiration is determined by monitoring oxygen or carbon dioxide. Because the two physiological traits are collected at different temporal and volumetric scales (hours-to-days for growth versus minutes-to-hours for respiration), reconciling them is challenging and often introduces scale-mismatch bias, obscuring causal links between metabolism and environmental drivers. In this study, we develop a novel method for quantifying the rates of bacterial growth and respiration from a single dissolved-oxygen time series. Our approach introduces a model that couples exponential biomass growth with biomass-specific respiration, enabling simultaneous inference of growth rate and respiration rate from each oxygen trajectory. We applied our high-throughput method to 15 bacterial taxa isolated from natural environments. Our approach yielded growth estimates in close agreement with measurements based on popular methods using optical density or flow cytometry ([Formula: see text] > 0.9) with no evidence of taxon-specific bias. We also tested our approach in quantifying the effects of temperature on respiration, growth, and carbon use-efficiency in Pseudomonas sp. Our method yielded typical unimodal thermal response curves for growth and respiration where rates were highest at moderate temperatures, while carbon use efficiency increased with temperature, peaked around the growth thermal optimum (∼30°C-35°C), and declined at the highest temperature. By quantifying respiration and growth within a single assay and in high throughput, our approach effectively enables measurement of microbial metabolic strategies and adaptations to stress. It offers a noninv
-
Journal articleHarpenslager SF, Randall K, Zhu Y, et al., 2026,
A fixed methane filter maximizes freshwater emissions under warming.
, Nat Clim Chang, Vol: 16, Pages: 704-711, ISSN: 1758-678XApproximately half of all methane (CH4) emissions come from freshwaters, where they are regulated by the microbial 'CH4 filter' whose efficiency describes the fraction of CH4 produced that is subsequently oxidized back to CO2 (methanotrophy) before emission. How the CH4 filter efficiency responds to natural warming over centuries or millennia remains unknown. Here we address this question using a natural experiment comprising high-latitude, geothermally warmed streams in five regions spanning the Northern Hemisphere. CH4 production becomes more efficient with warming, linked to increased abundance of methanogens and underpinned by community shifts. In contrast, while CH4 oxidation activity increases, its process-level efficiency does not, and methanotrophs shift towards less efficient taxa. Consequently, the system-level CH4 filter efficiency remains fixed, and CH4 emissions increase. If this fixed CH4 filter efficiency under warming is common to freshwaters worldwide (wetlands, lakes and rivers), then an upward trajectory for CH4 emissions through future climate change appears inevitable.
-
Journal articleSharkey MJ, Mutanen M, Baker A, et al., 2026,
Toward scalable species descriptions for dark taxa: the role of molecular data.
, Zookeys, Vol: 1283, Pages: 297-322, ISSN: 1313-2989Species descriptions remain the foundation of biodiversity science, but alpha taxonomy faces a twofold challenge: accelerating the pace of species discovery while ensuring that descriptions produce data that are usable, comparable, and reproducible. This is particularly acute for "dark taxa"-small, hyperdiverse, and morphologically challenging groups-for which morphology-based workflows alone often fail to deliver scalable and reliable identifications. As a result, most species remain undescribed, and many described species are difficult or impossible to identify. We argue that species descriptions must be integrative in a way that meets the practical requirements of modern taxonomy, including scalability, reliable identification, reproducibility, and applicability across life stages. At present, standardized molecular data in the form of DNA barcoding is the only approach that consistently satisfies these criteria. Emerging approaches based on robotics, imaging and artificial intelligence may eventually provide complementary frameworks, but currently lack the standardization and interoperability required for routine application at scale. In contrast, barcode data already enable high-throughput species delimitation, straightforward identification, and direct comparability across studies, supported by global reference libraries and standardized protocols. We therefore propose that DNA barcodes be treated as a baseline component of species descriptions for invertebrates. Standardizing molecular data in taxonomy will accelerate species discovery, improve reproducibility and stability, and ensure that newly described taxa remain accessible in an increasingly DNA-based research landscape.
-
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: 1949-0976Injection of effectors via a type III secretion system (T3SS) is an infection strategy shared by various Gram-negative bacterial pathogens, many infecting mucosal surfaces. While individual T3SS effectors are well characterized, their network-level organization and the distinction between core and accessory effectors remain incompletely understood. Here, by systematically dissecting the T3SS effector network of the enteric mouse pathogen Citrobacter rodentium (CR) we identified a subset of 12 accessory effectors that, while dispensable for colonization, significantly alter infection outcomes. A strain lacking the accessory effectors (CRM12) remained virulent in susceptible mouse hosts yet resulted in reduced epithelial barrier damage, inflammation, and immune cell infiltration in resistant mice. Deep proteomic analysis specifically targeting CR-attached colonic epithelial cells revealed that, despite lacking 39% of its effector repertoire, infection with CRM12 results in similar changes to global protein expression as seen in mice infected with the wild-type strain, though key regulators of barrier integrity were differentially expressed. Using a host with impaired barrier repair (Il22− /− mice), we confirmed that accessory effectors collectively shape infection outcomes without significantly impacting virulence. This study refines the concept of core and accessory effectors, providing a basis for further studies into effector-driven host adaptation.
-
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
-
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
, Journal of Molecular Biology, 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.
-
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 is currently being obtained 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.
-
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).
-
Journal articleSomveille M, Grainger-Hull J, Ferguson N, et al., 2025,
Consistent and scalable monitoring of birds and habitats along a coffee production intensity gradient
, Remote Sensing in Ecology and Conservation, Vol: 11, Pages: 686-700, ISSN: 2056-3485Land use change associated with agricultural intensification is a leading driver of biodiversity loss in the tropics. To evaluate the habitat–biodiversity relationship in production systems of tropical agricultural commodities, birds are commonly used as indicators. However, a consistent and reliable methodological approach for monitoring tropical avian communities and habitat quality in a way that is scalable is largely lacking. In this study, we examined whether the automated analysis of audio data collected by passive acoustic monitoring, together with the analysis of remote sensing data, can be used to efficiently monitor avian biodiversity along the gradient of habitat degradation associated with the intensification of coffee production. Coffee is an important crop produced in tropical forested regions, whose production is expanding and intensifying, and coffee production systems form a gradient of ecological complexity ranging from forest-like shaded polyculture to dense sun-exposed monoculture. We used LiDAR technology to survey the habitat, together with autonomous recording units and a vocalization classifier to assess bird community composition in a coffee landscape comprising a shade-grown coffee farm, a sun coffee farm and a forest remnant, located in southern Mexico. We found that LiDAR can capture relevant variation in vegetation across the habitat gradient in coffee systems, specifically matching the generally observed pattern that the intensification of coffee production is associated with a decrease in vegetation density and complexity. We also found that bioacoustics can capture known functional signatures of avian communities across this habitat degradation gradient. Thus, we show that these technologies can be used in a robust way to monitor how biodiversity responds to land use intensification in the tropics. A major advantage of this approach is that it has the potential to be deployed cost-effectively at large scales to help design and c
This data is extracted from the Web of Science and reproduced under a licence from Thomson Reuters. You may not copy or re-distribute this data in whole or in part without the written consent of the Science business of Thomson Reuters.
Postgraduate research
Interested in studying a PhD at the Department of Life Sciences? Find out more about postgraduate research opportunties.