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Journal articleHe L, Patkowski JB, Wang J, et al., 2025,
Chimeric infective particles expand species boundaries in phage-inducible chromosomal island mobilization
, Cell, ISSN: 0092-8674Some mobile genetic elements spread among unrelated bacterial species through unknown mechanisms. Recently, we discovered that identical capsid-forming phage-inducible chromosomal islands (cf-PICIs), a new family of phage satellites, are present across multiple species and genera, raising questions about their widespread dissemination. Here, we have identified and characterized a new biological entity enabling this transfer. Unlike other satellites, cf-PICIs produce their own capsids and package their DNA, relying solely on phage tails for transfer. cf-PICIs release non-infective, tailless capsids containing their DNA into the environment. These subcellular entities then interact with phage tails from various species, forming chimeric particles that inject DNA into different bacterial species depending on the tail present. Additionally, we elucidated the structure of the tailless cf-PICIs and the mechanism behind their unique capsid formation. Our findings illuminate the mechanisms used by satellites to spread in nature, contributing to bacterial evolution and the emergence of new pathogens.
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Journal articleYuen ELH, Savage Z, Pražák V, et al., 2025,
Membrane contact sites between chloroplasts and the pathogen interface underpin plant focal immune responses.
, Plant Cell, Vol: 37Communication between cellular organelles is essential for mounting effective innate immune responses. The transport of organelles to pathogen penetration sites and their assembly around the host membrane, which delineates the plant-pathogen interface, are well documented. However, whether organelles associate with these specialized interfaces, and the extent to which this process contributes to immunity, remain unknown. Here, we discovered defense-related membrane contact sites (MCS) comprising a membrane tethering complex between chloroplasts and the extrahaustorial membrane (EHM) surrounding the haustorium of the pathogen Phytophthora infestans in Nicotiana benthamiana. The assembly of this complex involves association between the chloroplast outer envelope protein CHLOROPLAST UNUSUAL POSITIONING 1 (CHUP1) and its plasma membrane-associated partner KINESIN-LIKE PROTEIN FOR ACTIN-BASED CHLOROPLAST MOVEMENT 1 (KAC1). Our biochemical assays revealed that CHUP1 and KAC1 interact, and infection cell biology assays demonstrated their co-accumulation in foci where chloroplasts contact the EHM. Genetic depletion of CHUP1 or KAC1 reduces the focal deposition of callose around the haustorium without affecting other core immune processes. Our findings suggest that the chloroplast-EHM attachment complex promotes plant focal immunity, revealing key components and their potential roles in the deposition of defense materials at the pathogen interface. These results advance our understanding of organelle-mediated immunity and highlight the significance of MCS in plant-pathogen interactions.
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Journal articlePenadés JR, Gottweis J, He L, et al., 2025,
AI mirrors experimental science to uncover a mechanism of gene transfer crucial to bacterial evolution
, Cell, ISSN: 0092-8674Artificial intelligence (AI) models have been proposed for hypothesis generation, but testing their ability to drive high-impact research is challenging since an AI-generated hypothesis can take decades to validate. Here, we challenge the ability of a recently developed large language model (LLM)-based platform, AI co-scientist, to generate high-level hypotheses by posing a question that took years to resolve experimentally but remained unpublished: how could capsid-forming phage-inducible chromosomal islands (cf-PICIs) spread across bacterial species? Remarkably, the AI co-scientist’s top-ranked hypothesis matched our experimentally confirmed mechanism: cf-PICIs hijack diverse phage tails to expand their host range. We critically assess its five highest-ranked hypotheses, showing that some opened new research avenues in our laboratories. We benchmark its performance against other LLMs and outline best practices for integrating AI into scientific discovery. Our findings suggest that AI can act not just as a tool but as a creative engine, accelerating discovery and reshaping how we generate and test scientific hypotheses.
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Journal articleBarker-Clarke RJ, Gray JM, Leither S, et al., 2025,
The balance between intrinsic and ecological fitness reveals hidden regimes in eco-evolutionary population dynamics.
, Res SqUnderstanding how populations evolve requires accounting for both intrinsic fitness, defined by genotype and environment, and ecological interactions that emerge in mixed communities. While evolutionary experiments typically assess fitness in isolation, such monoculture measures may misrepresent dynamics in realistic, interacting populations. Here, we present a game-theoretic framework that explicitly separates intrinsic and ecological contributions to fitness, allowing us to map how ecological interactions can mask, mirror, maintain, or mimic selection driven by genetic differences. We derive analytical conditions for these regimes using deterministic replicator dynamics and validate them in stochastic Wright-Fisher models with mutation and drift. Applying our model to published microbial and cancer co-culture data, we show that real systems span both intrinsic-dominant and ecology-dominant regimes, with ecological effects sometimes reversing or neutralizing intrinsic fitness advantages. These results expose a critical blind spot in experimental design and interpretation, emphasizing the need to account for ecological interactions when inferring evolutionary dynamics and designing therapeutic strategies.
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Journal articleMichael DR, John DA, Coates N, et al., 2025,
The impact of three distinct probiotic supplements on the gut microbiota and its metabolites in healthy adults
, Beneficial Microbes, ISSN: 1876-2883The effects of probiotics on the gut microbiota and microbial metabolites in healthy individuals are not well understood. Faecal and serum samples were collected at the start and end of a 3-month, double-blind, placebo-controlled, randomised study with three different probiotic formulations in free-living healthy adults. The composition of the faecal microbiota and levels of faecal and/or serum short-chain fatty acids (SCFA) and bile acids (BA) were measured and the probiotic formulations were found to impart differing effects including shifts in the composition and structure of the faecal microbiota, enhanced levels of circulating short chain fatty acids such as butyrate and propionate and elevated levels of sulphated bile acids infaeces. This was in contrast to the outcomes with the placebo population where very little change occurred over the study. These findings demonstrate that probiotic supplementation elicits formulation specific effects and that there are potential benefits for healthy individuals.
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Journal articleOjiogu AD, Patkowski JB, Kuang X, et al., 2025,
Capsid redirection mechanism of the Staphylococcus aureus pathogenicity island SaPIpT1028
, Philosophical Transactions of the Royal Society B: Biological Sciences, Vol: 380, ISSN: 0962-8436Staphylococcus aureus pathogenicity islands (SaPIs) are prototypical members of the phage-inducible chromosomal islands (PICI) family. These elements redirect helper phage capsid assembly to produce smaller capsids, accommodating the satellite genome while excluding the phage genome. This study identifies how SaPIpT1028 mediates capsid redirection through a unique gene, rcm (redirecting capsid morphogenesis). While rcm has no sequence similarity to known capsid assembly regulators, our results demonstrate that its expression is necessary and sufficient for redirecting capsid morphogenesis in S. aureus phages, such as φ7206. We show that, to do this, Rcm interacts with the φ7206 major capsid protein. Comparative evolutionary and structural analyses reveal functional parallels between Rcm and CpmB, a regulator used by other SaPIs. However, Rcm has evolved a multi-helical topology to match the multi-helical topology of the scaffold protein of φ7206. Sequence homology and AlphaFold predictions suggest that Rcm competitively interacts with the φ7206 scaffold protein, altering capsid size through a mechanism akin to CpmB. This work highlights SaPI adaptation, exemplified by Rcm's ability to exploit phages resistant to other remodellers, while inhibiting their reproduction. These findings underscore the dynamic co-evolution of phages and SaPIs, with Rcm playing a pivotal role in capsid size regulation and phage interference.This article is part of the discussion meeting issue 'The ecology and evolution of bacterial immune systems'.
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Journal articleCalderón-Morales E, Werden LK, Smith-Martin CM, et al., 2025,
Physiological and Growth Responses of Tropical Dry Forest Tree Seedlings to Water and Nutrient Additions: Comparisons Between Nitrogen Fixers and Non-Fixers
, Biotropica, Vol: 57, ISSN: 0006-3606Belowground resources are key determinants of seedling growth and survival in tropical forests. Nutrients and light may limit plant growth the most in tropical wet forests, whereas water may limit plant growth more in tropical dry forests. Nitrogen (N)-fixing species play an important role in the nitrogen and carbon cycles across tropical dry forests. However, studies investigating the joint effects of water and nutrients on the physiology and performance of N-fixing species are scarce. We implemented a full factorial shade house experiment that manipulated water and nutrients (NPK 20:20:20 and complete micronutrients) using eight tree species representing N-fixing and non-fixing tree species in the tropical dry forest of Costa Rica to determine: (1) How plant responses to water and nutrient availability vary between N-fixing and non-fixing tree species?; and (2) How nutrient and/or water availability influences seedling water- and nutrient-use traits? We found that growth and physiological responses to water and nutrient addition depended directly on the capacity of species to fix atmospheric N<inf>2</inf>. N-fixing species responded more strongly to nutrient addition, accumulating 67% more total biomass on average (approximately double that of non-fixing taxa) and increasing average height growth rate by 41%. N-fixing species accumulated more biomass without compromising water-use efficiency, taking full advantage of the increased nutrient availability. Interestingly, results from our experiment show that increased water availability rarely influenced tropical dry forest seedling performance, whereas nutrient availability had a strong effect on biomass and growth. Overall, our results highlight the ability of N-fixing seedlings to take advantage of local soil resource heterogeneity, which may help to explain the dominance of N-fixing trees in tropical dry forests.
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Journal articleBeaghton PJ, Burt A, 2025,
Natural selection of synthetic gene drives for population suppression can favor an intermediate strength of drive
, The American Naturalist, Vol: 206, Pages: 206-217, ISSN: 0003-0147Synthetic gene drives are being investigated as tools to suppress pest populations, and it is important to understand how natural selection will act on variant drivers that may either arise by de novo mutation or are intentionally released. In this study we extend previous spatially implicit stochastic models to examine the evolutionary dynamics of synthetic driving Y chromosomes in patchy environments when population size is responding dynamically to the spread of the driver, and derive conditions for the existence of an evolutionarily stable strategy (ESS) for drive strength. Under broad conditions an intermediate drive strengthemerges as the ESS, capable of outcompeting both stronger and weaker variants. Additionally, we show how the intentional release of two drivers straddling the ESS can help stabilize population dynamics. Finally, inbreeding depression has the effect of expanding the range ofconditions under which no intermediate ESS exists, with ever stronger drive being selected until the population is eliminated. These results provide insights into the expected evolutionary trajectories of gene drive systems, with important implications for the design and release of gene drives for pest and vector control.
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Journal articleAlkemade JA, Hawkins NJ, Baraldi E, et al., 2025,
Learning from fungicide resistance: Evolutionary insights to guide RNAi-based control of fungal crop pathogens
, Fungal Biology Reviews, Vol: 53, ISSN: 1749-4613Crop protection against fungal pathogens is essential to prevent crop losses and maintain food security. Current crop protection relies heavily on chemical fungicides. However, rapid evolution of fungicide resistance, the constant appearance of new pathogens, and legislation against chemical pesticides due to concerns regarding their impact on human health and the environment, mean new crop protection strategies are urgently required. One elegant solution is double-stranded RNA-based crop protection, which aims to silence selected genes in the pathogen to reduce crop damage. This technology brings the promise of targeting specific genes, which could be chosen to maximise protection, minimize off-target effects and reduce the risk of resistance evolution. Here we discuss strategies for successful use of this novel technology based on lessons learned from fungicide resistance and recent discoveries in fungal evolution derived from genome-sequencing.
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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 articleYordanova M, Zhang X, Torres CB, et al., 2025,
Friend or foe? Concentration of a commensal microbe induces distinct responses in developing honey bees exposed to field-realistic pesticide concentrations
, FEMS MICROBIOLOGY ECOLOGY, Vol: 101, ISSN: 0168-6496 -
Journal articleDaniel O, Heon SP, Donnelly CA, et al., 2025,
Rapid spread of African Swine Fever across Borneo
, Animals, Vol: 15, ISSN: 2076-2615African Swine Fever (ASF) reached the island of Borneo at the end of 2020. The first mortalities were recorded in wild bearded pigs (Sus barbatus) in Sabah, north-east Borneo. The virus then began to spread across the island but due to COVID-19 lockdowns the spread was difficult to monitor on the ground. With the urgent need to track this epidemic, and in the absence of traditional monitoring, the Babi Hutan Project was launched in April 2021 to gather data on pig sightings using citizen science. Any sightings of bearded pigs were requested via the website, social media and a WhatsApp hotline. Here we bring together the data from this project and other online sources to show how the virus spread across almost the entire island within a one-year period. The speed of spread appeared to increase with time following an exponential model: we estimate an average speed of spread of 0.89 km/day after 100 days since the first observation and at 4.28 km/day after 400 days. Our key recommendations are: that existing hunting bans on bearded pigs remain in place; that urgent biosecurity measures should be put in place if outbreaks occur in areas with backyard (domestic) pigs; that surviving pigs are tested for resistance; that the disease dynamics are modelled and that the International Union for Conservation of Nature (IUCN) urgently re-evaluates the bearded pig’s status.
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Journal articleOno M, 2025,
TockyLocus: quantitative analysis of flow cytometric fluorescent timer data in Nr4a3-Tocky and Foxp3-Tocky mice
, Biology Methods & Protocols, ISSN: 2396-8923Fluorescent Timer proteins undergo a time-dependent shift from blue to red fluorescence after translation, providing a temporal record of transcriptional activity in Timer reporter systems. While Timer proteins are well suited for studying dynamic cellular processes such as T cell activation using the Timer of-Cell-Kinetics-and-Activity (Tocky) framework, quantitative analysis of Timer-based flow cytometry data has yet to be fully standardised.In this study, we optimise quantitative analysis methods for the key parameter within the Tocky framework, Timer Angle, and introduce TockyLocus, an open-source R package that implements a five category scheme based on biologically grounded angular intervals (designated as Tocky Loci). This approach is validated using both simulated and experimental datasets and enables downstream statistical testing and visualisation of transcriptional dynamics in flow cytometry data.Using computational modelling of Timer protein kinetics, we define transcriptional dynamics in relation to key anchoring points in Timer Angle values at 0◦, 45◦, and 90◦. Comprehensive simulations with synthetic spike-in datasets further demonstrate the robustness of the five-locus approach, which capturesthe three key points and the intermediate regions between these points. Building on the TockyPrep pre processing framework, we systematically evaluated categorisation schemes ranging from three to sevenloci on real-world datasets from Nr4a3-Tocky and Foxp3-Tocky mice. The five-locus model emerged asoptimal, showing significant advantages in balancing biological interpretability and statistical robustness.Optimised algorithms implemented in the TockyLocus package now standardise quantitative analysisof Timer Angle data, enabling reproducible interpretation without reliance on arbitrary gating or complexassumptions. In summary, the five-locus categorisation of Timer Angle data effectively links underlyingbiological dynamics to the percentage of cells in each Tocky
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Journal articleBarker-Clarke RJ, Gray JM, Leither S, et al., 2025,
The balance between intrinsic and ecological fitness reveals hidden regimes in eco-evolutionary population dynamics.
, bioRxivUnderstanding how populations evolve requires accounting for both intrinsic fitness, defined by genotype and environment, and ecological interactions that emerge in mixed communities. While evolutionary experiments typically assess fitness in isolation, such monoculture measures may misrepresent dynamics in realistic, interacting populations. Here, we present a game-theoretic framework that explicitly separates intrinsic and ecological contributions to fitness, allowing us to map how ecological interactions can mask, mirror, maintain, or mimic selection driven by genetic differences. We derive analytical conditions for these regimes using deterministic replicator dynamics and validate them in stochastic Wright-Fisher models with mutation and drift. Applying our model to published microbial and cancer co-culture data, we show that real systems span both intrinsic-dominant and ecology-dominant regimes, with ecological effects sometimes reversing or neutralizing intrinsic fitness advantages. These results expose a critical blind spot in experimental design and interpretation, emphasizing the need to account for ecological interactions when inferring evolutionary dynamics and designing therapeutic strategies.
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Journal articleAlzate A, Rozzi R, Velasco JA, et al., 2025,
Evolutionary age correlates with range size across plants and animals
, NATURE COMMUNICATIONS, Vol: 16 -
Journal articleHazime KS, Sheppard S, Niembro-Vivanco O, et al., 2025,
Nanoscale re-structuring of the immune synapse with an engager enhances NK cell function
, Proceedings of the National Academy of Sciences of USA, ISSN: 0027-8424 -
Journal articleClaramunt S, Sheard C, Brown JW, et al., 2025,
A new time tree of birds reveals the interplay between dispersal, geographic range size, and diversification
, CURRENT BIOLOGY, Vol: 35, ISSN: 0960-9822 -
Journal articleCambron TW, Fisher JB, Hungate B, et al., 2025,
Plant nutrient acquisition under elevated CO2 and implications for the land carbon sink
, Nature Climate Change, ISSN: 1758-678XTerrestrial ecosystems currently sequester around a third of anthropogenic carbon emitted each year, slowing the pace of climate change. However, the future of this sink under rising atmospheric CO2 concentrations remains uncertain, in part due to the impact that nutrient limitation may have on plant biomass. Here, we review plant nutrient acquisition strategies and evidence of the enhanced utilization of these strategies under experimental and real-world elevated CO2 (eCO2). Many of the strategies that are key to nutrient limitation alleviation under eCO2 are not yet well represented in Earth System Models (ESMs). A simple, data-driven analysis implies that ESMs without nutrient acquisition strategies could underestimate the land sink.
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Journal articleVarga T, Woods R, Pitsillides F, et al., 2025,
Whole genome sequencing of historical specimens from the world's largest fungal collection yields high-quality assemblies
, NEW PHYTOLOGIST, ISSN: 0028-646X -
Journal articleDonini R, Blundell P, Pleass RJ, et al., 2025,
Genetic Divergence and Antibody Expression Influence the N-Glycomes of CHO-K1 and CHO-S Cells
, BIOTECHNOLOGY AND BIOENGINEERING, ISSN: 0006-3592 -
Journal articleVerma A, Khadke L, Budakoti S, 2025,
Understanding the dynamics of 2024 extreme heat event in India: spatial variability, hydrometeorological impacts, and model evaluation
, Atmospheric Research, Vol: 322, ISSN: 0169-8095Heatwaves are becoming more intense, frequent, and prolonged due to global warming, posing significant risks to ecosystems and human societies. Despite their profound impact, detailed regional assessments of extreme heat events remain limited, particularly in India. This study addresses the gap by systematically investigating the 2024 extreme heat event in India. We evaluated the performance of various land surface schemes in simulating heat extremes using the Weather Research and Forecasting model and also assessed the accuracy of Global Forecast System (GFS) forecasts. Our analysis reveals a strong co-occurrence of drought and heat stress during the extreme heat event. This combination results in increased fire risk and negative impacts on vegetation productivity in regions affected by both drought and heat stress highlighting the severe consequences of this compound event. We compare different land surface models (RUC, Noah, Noah-MP, Noah-MP with dynamic vegetation, CLM) against India Meteorological Department (IMD) observations. We observe that Noah is optimal for reducing bias and RMSE, while Noah-MP with dynamic vegetation is most accurate for simulating extreme heat, with the highest hit rate and threat score for the 90th percentile threshold. Additionally, GFS maximum temperature forecasts for 1–3 day lead times perform well at short lead times, especially in Southern India but overestimate temperatures in heatwave-prone regions like the Indo-Gangetic Plains. Our findings highlight the importance of enhancing land surface models and forecasting systems to better predict extreme heat events, which is crucial for localized hazard and risk assessments and improving disaster management efficiency.
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Journal articleMadsen CD, Barbensi A, Zhang SY, et al., 2025,
The topological properties of the protein universe
, NATURE COMMUNICATIONS, Vol: 16 -
Journal articleKose Cetinkaya A, Sari FN, Buyuktiryaki M, et al., 2025,
Postnatal weight gain of premature small for gestational age versus appropriate for gestational age infants during NICU stay.
, J Trop Pediatr, Vol: 71To assess the feeding characteristics and postnatal weight gain of premature small for gestational age (SGA) versus appropriate for gestational age (AGA) infants during neonatal intensive care unit stay and to investigate the association between postnatal growth failure (PGF) and neonatal variables. This retrospective study was conducted on premature infants with a birth weight ≤1500 g and a gestational age <32 weeks, born between January 2013 and June 2016. The infants were categorized into two groups: SGA (n = 42) and AGA (n = 380). The groups were compared in terms of demographics, clinical characteristics, and PGF at discharge. PGF was defined as a decrease in the z-score of more than 1.34 from birth to discharge. Multiple logistic regression analysis was used to identify variables associated with PGF. SGA infants had a longer time to achieve full enteral feeding (P = .010) and a longer duration of total parenteral nutrition (P = .001). Although the frequency of feeding intolerance was higher in SGA infants, the difference was not statistically significant (P = .056). The overall prevalence of PGF at discharge was 42% and comparable between the two groups. Late-onset sepsis, hemodynamically significant patent ductus arteriosus and lower weight z-score at fourth week of life [adjusted odds ratio (aOR) = 1.69, 95% confidence interval (CI) = 1.06-2.69, P = .027; aOR = 1.75, 95% CI = 1.14-2.68, P = .01; and aOR = 1.86, 95% CI = 1.21-2.86, P = .004, respectively) were independently associated with an increased risk of PGF. SGA infants experienced more severe growth failure at discharge compared to AGA infants. However, the rate of PGF was similar between the two groups.
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Journal articleKontopoulos D-G, Patmanidis I, Barraclough TG, et al., 2025,
Changes in flexibility but not in compactness underlie the thermal adaptation of prokaryotic adenylate kinases
, EVOLUTION LETTERS -
Journal articleTobias JA, Bullock JM, Dicks LV, et al., 2025,
Biodiversity conservation requires integration of species-centric and process-based strategies
, Proceedings of the National Academy of Sciences, Vol: 122, ISSN: 0027-8424Conservation science and policy are geared primarily toward the preservation of species and habitats, with priority often given to the rarest, most vulnerable or most charismatic forms. This pattern-based approach has broad appeal and offers a pragmatic short-cut for targeting conservation action. However, the long-term efficacy of species and landscape conservation programs remains highly uncertain, amid growing evidence that sustainable conservation action requires an increased emphasis on preserving ecological and evolutionary processes. This reframing of conservation goals was first proposed 50 y ago, but the concept has struggled to gain traction, particularly in terms of translation into policy. Nonetheless, recent events have shifted the narrative, with multiple interlinked global challenges—including biological invasions, food security, disease, and climate change—putting ecological processes firmly back on the agenda. Concurrently, conservation finance is changing rapidly, driven in part by the 2022 Kunming-Montreal Global Biodiversity Framework, which prioritized actions to enhance and restore ecosystem stability, connectivity, and resilience. These ecosystem properties are fundamentally process-driven and appear to create an operational gulf between current conservation practice and the targets of international agreements. We describe how new approaches can be used to close this gap by redirecting conservation attention toward processes at the heart of ecosystem function, including adaptation, gene flow, dispersal, and trophic interactions. Wider adoption of these approaches is urgently needed to forge a deeper connection between conservation practice and policy targets, thereby ensuring that ongoing investment in biodiversity conservation goes beyond damage limitation and instead leaves a lasting legacy of resilient ecosystems.
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Journal articleNishikawa M, Tang W, Kostrzewa M, et al., 2025,
Discrimination of Klebsiella pneumoniae and Klebsiella quasipneumoniae by MALDI-TOF mass spectrometry coupled with machine learning
, MicrobiologyOpen, Vol: 14, ISSN: 2045-8827Klebsiella species, including Klebsiella pneumoniae and Klebsiella quasipneumoniae, present significant challenges in clinical microbiology due to their genetic similarity, which complicates accurate species identification using established methods, including matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) on the protein/peptide level. Although the treatment choice for infections caused by these pathogens is often similar, precise species characterization enhances our epidemiological understanding. While whole-genome sequencing can accurately distinguish Klebsiella species accurately, those analyses are time-consuming, requiring specialized expertise, and are not currently used in routine clinical laboratories. Therefore, developing a timely and accurate pathogen characterization method is essential for effective treatment, management, and infection control measures. This study combined MALDI-TOF MS in negative ion mode with machine learning techniques to identify potential lipid biomarkers as a novel method to distinguish between K. pneumoniae and K. quasipneumoniae. Using this method, we identified discriminative features between the species, with peaks at m/z 2157, m/z 1931, m/z 1964, m/z 2042, and m/z 1407 highlighted as potential biomarkers for species identification. Our findings suggest that the lipid profiles of the species obtained from MALDI-TOF MS can serve as effective biomarkers for distinguishing Klebsiella species. Further research should focus on the structural identification of these biomarkers and expand the data set to include more isolates for each of the species. This approach holds promise for developing more cost-effective and rapid diagnostic tools in clinical microbiology, ultimately improving patient outcomes and infection control.
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Journal articleStewart K, Venditti C, Carmona CP, et al., 2025,
Threat reduction must be coupled with targeted recovery programmes to conserve global bird diversity
, Nature Ecology & Evolution, Vol: 9, Pages: 1499-1511, ISSN: 2397-334XAmbitious international commitments have been made to preserve biodiversity, with the goal of preventing extinctions and maintaining ecosystem resilience, yet the efficacy of large-scale protection for preventing near-term extinctions remains unclear. Here, we used a trait-based approach to show that global actions—such as the immediate abatement of all threats across at least half of species ranges for ~10,000 bird species—will only prevent half of the projected species extinctions and functional diversity loss attributable to current and future threats in the next 100 years. Nonetheless, targeted recovery programmes prioritizing the protection of the 100 most functionally unique threatened birds could avoid 68% of projected functional diversity loss. Actions targeting ‘habitat loss and degradation’ will prevent the greatest number of species extinctions and proportion of functional diversity loss relative to other drivers of extinction, whereas control of ‘hunting and collection’ and ‘disturbance and accidental mortality’ would save fewer species but disproportionately boost functional richness. These findings show that conservation of avian diversity requires action partitioned across all drivers of decline and highlight the importance of understanding and mitigating the ecological impacts of species extinctions that are predicted to occur even under optimistic levels of conservation action.
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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 articlePowell HR, Islam SA, David A, et al., 2025,
Phyre2.2: a community resource for template-based protein structure prediction
, Journal of Molecular Biology, Vol: 437, ISSN: 0022-2836Template-based modelling, also known as homology modelling, is a powerful approach to predict the structure of a protein from its amino acid sequence. The approach requires one to identify a sequence similarity between the query sequence and that of a known structure as they will adopt a similar conformation, and the known structure can be used as the template for modelling the query sequence. Recently several approaches, most notably AlphaFold, have employed enhanced machine learning and have yielded accurate models irrespective of whether there is an identifiable template. Here we report Phyre2.2 which incorporates several enhancements to our widely-used template modelling portal Phyre2. The main development is facilitating a user to submit their sequence and then Phyre2.2 identifies the most suitable AlphaFold model to be used as a template. In Phyre2.2 the user searches a template library of known structures. We have now included in our library a representative structure for every protein sequence in the protein databank (PDB). In addition, there are representatives for an apo and a holo structure if they are in the PDB. The ranking of hits has been modified to highlight to the user if there are different domains spanning the sequence. Phyre2.2 continues to support batch processing where a user can submit up to 100 sequences facilitating processing of proteomes. Phyre2.2 is freely available to all users, including commercial users, at https://www.sbg.bio.ic.ac.uk/phyre2/.
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Journal articleNikov GI, Pretorius D, Murray JW, 2025,
SOLeNNoID: a deep learning pipeline for solenoid residue detection in protein structures
, Bioinformatics, Vol: 41, ISSN: 1367-4811Motivation: Solenoid proteins, a subset of tandem repeat proteins, have structurally distinct, modular, and elongated architectures that differentiate them from globular proteins. These proteins play essential roles in diverse biological processes, including protein binding, enzymatic catalysis, ice binding, and nucleic acid interactions. Despite their biological significance and increasing commercial applications–such as in therapeutic engineered variants like DARPins and designed PPR proteins–accurate identification and annotation of solenoid structures remain challenging. Given that solenoid structures are more conserved than their sequences, recent advances in protein structure prediction suggest that structure-based solenoid detection methods are preferable to sequence-based ones.Results: We introduce SOLeNNoID, a deep-learning-based pipeline for predicting solenoid residues in protein structures. Our method employs a convolutional neural network architecture to analyse protein distance matrices, enabling accurate identification of solenoid-containing regions. SOLeNNoID covers all three solenoid subclasses: α-, α/β-, and β-solenoids. Comparative evaluation against existing structure-based methods demonstrates the superior performance of our approach. Applying SOLeNNoID to the entire Protein Data Bank led to a 71% increase in detected solenoid-containing entries compared to the gold-standard RepeatsDB database, significantly expanding the known solenoid protein repertoire.Availability and implementation: SOLeNNoID is implemented in Python and available on github at https://github.com/gnik2018/SOLeNNoID. The source code and pre-trained models are accessible under a free-software license. Training data are available on Zenodo at https://zenodo. org/records/14927497
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