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Journal articleNg PC, Adegbite O, Li T, et al., 2025,
Structure and encapsulation of carbonic anhydrase within the α-carboxysome.
, Proc Natl Acad Sci U S A, Vol: 122Carboxysomes in cyanobacteria and certain proteobacteria enable efficient CO2 fixation by encapsulating ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and carbonic anhydrase (CA) within a semipermeable shell. Sequestered CA catalyze the rapid interconversion of CO2 and HCO3-, supplying elevated levels of CO2 to boost Rubisco carboxylation. Despite its essential role, the structure and encapsulation of CA within carboxysomes remain poorly understood. Here, we determined the molecular structure of α-carboxysomal CA from the model chemoautotrophic bacterium Halothiobacillus neapolitanus (HnCsoSCA). HnCsoSCA adopts a trimer-of-dimers oligomeric structure without the incorporation of a zinc ion at its symmetric center. Using synthetic minishells, we demonstrate that HnCsoSCA interacts with the CsoS1A shell hexamer and is incorporated into the minishells at the inner surface, independent of the CsoS2 linker protein. HnCsoSCA truncations suggest nonspecific interactions between HnCsoSCA and CsoS1A. We further show that HnCsoSCA bridges Rubisco and the shell facets. Our study offers insights into the assembly and encapsulation mechanisms of α-carboxysomes and provides the framework for reprogramming carboxysome structures for synthetic biology and biotechnological applications.
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Journal articleModiba MP, Bell T, Babalola OO, 2025,
Plant Growth-Promoting Rhizobacteria and Bacterial Biocontrol Agents in Tomato Disease Management: Mechanisms, Applications, and Omics Perspectives
, GLOBAL CHALLENGES -
Journal articleAbuhamdah R, Moore G, Djama D, et al., 2025,
Longitudinal Testing of Exploratory Behaviour in Mice Reveals Stable Cognitive Traits Across the Adult Lifespan
, AGING CELL, ISSN: 1474-9718 -
Journal articleRallis D, Tsoumani KT, Krsticevic F, et al., 2025,
Detection of sex chromosomes in Tephritid pests using R-CQ and KAMY, two computational methods to support generic pest management applications
, INSECT SCIENCE, ISSN: 1672-9609 -
Journal articleHindley HJ, Gong Z, Moradian S, et al., 2025,
Heterogeneity in responses to ribosome-targeting antibiotics mediated by bacterial RNA repair
, Nature Communications, Vol: 16, ISSN: 2041-1723RNA repair is critical for cellular function. The Rtc system maintains RNA integrity within the translational machinery of bacteria. In E. coli, Rtc expression enables cells to rescue growth and survive treatment by conferring transient resistance to ribosome-targeting antibiotics, yet the mechanisms underpinning this resistance remain obscure. Here, we present a computational model of Rtc-regulated repair of translational RNAs. Integrating model predictions with experimental validations, we uncover notable cell-to-cell heterogeneity in rtc expression that impacts on translational capacity, indicating that rtc may induce a form of heteroresistance. We moreover identify Rtc targets that may reduce the translational capacity of cells and so potentiate antibiotic effects. Our findings elucidate a complex response underpinning resistance conferred by Rtc, offering alternate routes for addressing resistance in E. coli and other relevant pathogens.
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Journal articleMacaulay SJ, 2025,
Synthesizing stressor-biodiversity relationships Freshwater ecology
, NATURE ECOLOGY & EVOLUTION, ISSN: 2397-334X -
Journal articleDavis MBE FMedSci D, 2025,
CD155 density on target cells drives divergent Natural Killer cell responses owing to DNAM-1 loss
, Journal of Immunology, ISSN: 0022-1767 -
Journal articleGrima LL, Haberkern H, Mohanta R, et al., 2025,
Foraging as an ethological framework for neuroscience
, Trends in Neurosciences, Vol: 48, Pages: 877-890, ISSN: 0166-2236The study of foraging is central to a renewed interest in naturalistic behavior in neuroscience. Applying a foraging framework grounded in behavioral ecology has enabled probing of the mechanisms underlying cognitive processes such as decision-making within a more ecological context. Yet, foraging also involves myriad other aspects, including navigation of complex environments, sensory processing, and social interactions. Here, we first provide a brief overview of the neuroscience of foraging decisions, and then combine insights from behavioral ecology and neuroscience to review the role of these additional dimensions of foraging. We conclude by highlighting four opportunities for the continued development of foraging as an ethological framework for neuroscience: integrating normative and implementation-level models, developing new tools, enabling cross-species comparisons, and fostering interdisciplinary collaboration.
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Journal articleSchäfer RB, Baikova D, Bayat HS, et al., 2025,
Effects of biodiversity loss on freshwater ecosystem functions increase with the number of stressors
, Global Change Biology, Vol: 31, ISSN: 1354-1013A multitude of anthropogenic stressors drive biodiversity loss and alter ecosystem functioning. Freshwaters, which contribute disproportionally to global biodiversity and biogeochemical cycles, are particularly threatened. Although the relationship between biodiversity and ecosystem functions (BEF) is generally well-established, especially in terrestrial ecosystems, the role of multiple, co-occurring stressors in modulating the relationship remains unclear. We conducted a meta-analysis to address this knowledge gap by assessing the effect of multiple stressors on the relationship between taxon richness and four measures of ecosystem function. The relationship was generally positive, with the slope becoming steeper as the number of stressors increased, suggesting that exposure to multiple stressors exacerbates impacts of biodiversity loss on ecosystem function. Multiple stressor effects on both taxon richness and ecosystem functions were largely predictable from individual stressor effects, although antagonistic effects on ecosystem functions emerged in 14% of the considered cases. The type of stressor and ecosystem function, along with taxonomic group, exerted no influence on the BEF relationship, contrary to our expectations. Microbial production and biomass declined most strongly in response to stressors, despite notable variability. Overall, our findings imply that functional consequences of freshwater biodiversity loss are more severe under multifaceted environmental change than previously assumed.
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Journal articleBannister K, Patel R, Hughes S, 2025,
The descending modulation of pain
, PAIN, Vol: 166, Pages: S55-S59, ISSN: 0304-3959 -
Journal articleGranville NR, Pigot AL, Howes B, et al., 2025,
Soft Range Limits Shape Sensitivity to Forest Cover More Strongly Than Hard Range Limits
, GLOBAL ECOLOGY AND BIOGEOGRAPHY, Vol: 34, ISSN: 1466-822X -
Journal articleChan Wah Hak C, Patin EC, Patrikeev A, et al., 2025,
Xevinapant plus Chemoradiotherapy Negatively Sculpts the Tumor-Immune Microenvironment in Head and Neck Cancer
, CANCER RESEARCH COMMUNICATIONS, Vol: 5, Pages: 2079-2091 -
Journal articleJones SEI, Freeman BG, Tobias JA, et al., 2025,
Testing the thermal physiology, habitat and competition hypotheses for elevational range limits in four tropical songbirds
, PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 292, ISSN: 0962-8452 -
Journal articleReynolds JJ, Koufopanou V, Burt A, 2025,
Identifying Single-Origin Rare Variants in Population Genomic Data
, MOLECULAR BIOLOGY AND EVOLUTION, Vol: 42, ISSN: 0737-4038 -
Journal articleLopez-Cobollo R, Altmann S, Thorpe P, et al., 2025,
A novel chitinase-like family of candidate effectors unique to aphids
, Molecular Plant-Microbe Interactions, ISSN: 0894-0282Molecular interactions between aphids and plants include delivery of salivary effector proteins into host cells, acting as virulence factors to suppress host immunity, or as avirulence functions triggering immune activation. However, understanding of virulence and avirulence mechanisms in aphid-plant systems is currently limited. Here, we report discovery of an effector candidate family that is unique to aphids. Using functional genomics data on divergent pea aphid (Acyrthosiphon pisum) genotypes and their F1 progeny, we filtered for differentially expressed saliva proteins that co-segregated with virulence or avirulence phenotypes. LOC100575698 (ACPISUM_029930), annotated as an uncharacterized protein, was the sole candidate effector for which RNA-Seq and saliva proteomics data showed significantly different expression both between avirulent and virulent parents and between their segregating F1 progeny, with this gene upregulated in avirulent genotypes. BLASTP searches revealed multiple divergent homologs only in genomes of the Aphidomorpha infra-order, suggesting a hitherto undefined ancient aphid-specific gene family. AlphaFold models indicate strong structural similarities but weak sequence homology to chitinases. Because the aphid-specific clade all lack canonical DxxDxDxE motifs for catalytic activity, we designate the proteins as a novel CHitinase-Like (CHL) family. Association of ACPISUM_029930 (ApCHL1) with avirulence was further supported by co-segregating SNPs and a genotype-specific alternatively spliced isoform. We hypothesise that CHL proteins may function similarly to phylogenetically unrelated chitin-binding fungal effectors that sequester chitin, also present in aphid stylets, potentially preventing defence activation through plant chitin receptors and/or blocking chitin degradation by host-secreted chitinases.
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Journal articleLee S, Bai M, Zhu C-D, et al., 2025,
Rethinking Changing "Unethical" Names in Taxonomy: An Asian Perspective
, BIOSCIENCE, ISSN: 0006-3568 -
Journal articleSimmchen J, Gordon D, MacKenzie J, et al., 2025,
Perspective on interdisciplinary approaches on chemotaxis
, Angewandte Chemie International Edition, ISSN: 1433-7851Most living things on Earth – from bacteria to humans – must migrate in some way to find favourable conditions. Therefore, they nearly all use chemotaxis, in which their movement is steered by a gradient of chemicals. Chemotaxis is fundamental to many processes that control our well-being, including inflammation, neuronal patterning, wound healing, tumour spread in cancer, even embryogenesis. Understanding it is a key goal for biologists. Despite the fact that many basic principles appear to have been conserved throughout evolution, most research has focused on understanding the molecular mechanisms that control signal processing and locomotion. Cell signaling – cells responding to time-varying external signals – underlies almost all biological processes at the cellular scale. Chemotaxis of single cells provides particularly amenable model systems for quantitative cell signaling studies, even in the presence of noise and fluctuations, because the output, the cell's motility response, is directly observable. However, the different scientific disciplines involved in chemotaxis research rarely overlap, so biologists, physicists and mathematicians interact far too infrequently, methodologies and models differ and commonalities are often overlooked, such as the possible influence of physical or environmental conditions, which has been largely neglected.
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Journal articleAlvey E, Paterlini A, Williams ME, et al., 2025,
A manifesto for plant science education
, PLANTS PEOPLE PLANET -
Journal articleBozkurt O, Bagdiken EY, 2025,
Early lactate elimination trend during therapeutic hypothermia predicts acute kidney injury in hypoxic ischemic encephalopathy
, PEDIATRIC NEPHROLOGY, ISSN: 0931-041X -
Journal articleStrampelli A, Willis K, Gulliford HR, et al., 2025,
A male-drive female-sterile system for the self-limited control of the malaria mosquito Anopheles gambiae
, Nature Communications, Vol: 16, ISSN: 2041-1723Despite great leaps forward in preventing and treating malaria, several challenges, including insecticide resistance, have hindered progress in fighting the disease. Thus, there is a pressing need for new tools to control malaria, including the use of genetically modified mosquitoes (GMMs) in the field. Various genetic strategies for vector control are currently explored, ranging from self-sustaining GMMs with unrestricted geographic and temporal spread to self-limiting alternatives. Here, we describe a self-limiting gene drive strategy called Male Drive Female Sterile (MDFS) targeting Anopheles gambiae, a major malaria vector. The MDFS genetic construct causes dominant sterility in females, while transgenic males remain fertile, allowing them to transmit the female sterility trait at super-Mendelian rates. Laboratory studies show that repeated releases of MDFS can lead to elimination of caged mosquito populations. Based on these findings, modelling suggests MDFS could be a highly effective and self-limiting strategy for suppressing wild malaria mosquito populations.
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Journal articleBevan PA, BanksLeite C, Kovac M, et al., 2025,
Robotics‐assisted acoustic surveys could deliver reliable, landscape‐level biodiversity insights
, Remote Sensing in Ecology and Conservation, ISSN: 2056-3485Terrestrial remote sensing approaches, such as acoustic monitoring, deliver finely resolved and reliable biodiversity data. However, the scalability of surveys is often limited by the effort, time and cost needed to deploy, maintain and retrieve sensors. Autonomous unmanned aerial vehicles (UAVs, or drones) are emerging as a promising tool for fully autonomous data collection, but there is considerable scope for their further use in ecology. In this study, we explored whether a novel approach to UAV-based acoustic monitoring could detect biodiversity patterns across a varied tropical landscape in Costa Rica. We simulated surveys of UAVs employing intermittent locomotion-based sampling strategies on an existing dataset of 26,411 h of audio recorded from 341 static sites, with automated detections of 19 bird species (n = 1819) and spider monkey (n = 2977) vocalizations. We varied the number of UAVs deployed in a single survey (sampling intensity) and whether the UAVs move between sites randomly, in a pre-determined route to minimize travel time, or by adaptively responding to real-time detections (sampling strategy), and measured the impact on downstream ecological analyses. We found that avian species detections and spider monkey occupancy were not impacted by sampling strategy, but that sampling intensity had a strong influence on downstream metrics. Whilst our simulated UAV surveys were effective in capturing broad biodiversity trends, such as spider monkey occupancy and avian habitat associations, they were less suited for exhaustive species inventories, with rare species often missed at low sampling intensities. As autonomous UAV systems and acoustic AI analyses become more reliable and accessible, our study shows that combining these technologies could deliver valuable biodiversity data at scale.
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Journal articleAi L, Muggleton SH, Liang S-S, et al., 2025,
Boolean matrix logic programming for active learning of gene functions in genome-scale metabolic network models
, MACHINE LEARNING, Vol: 114, ISSN: 0885-6125 -
Journal articleSchlenker P, Pawlowitsch C, Arnal LH, et al., 2025,
Ancestral Meanings: a prelude to evolutionary animal linguistics
, LINGUISTICS AND PHILOSOPHY, ISSN: 0165-0157 -
Journal articleGrech J, Shinde AP, Periz J, et al., 2025,
Tepsin and AP4 mediate transport from the trans-Golgi to the plant-like vacuole in toxoplasma
, JOURNAL OF CELL BIOLOGY, Vol: 224, ISSN: 0021-9525 -
Journal articleHancock P, Hui T-Y, Epopa PS, et al., 2025,
Requirements for designing cluster randomised control trials to detect suppression of malaria vector population densities
, BMC Biology, Vol: 23, ISSN: 1741-7007BackgroundNovel interventions for mosquito-borne disease control which release modified mosquitoes that are sterilised or genetically modified to cause offspring inviability are progressing towards field applications. Cluster randomised control trials (CRCTs) could provide robust assessment of intervention efficacy in suppressing mosquito populations in field environments, but guidance on designing CRCTs to detect mosquito suppression impacts is limited.ResultsWe developed statistical models to simulate CRCTs, informed by a 5-year time series measuring densities of malaria vector species from the Anopheles gambiae complex in four villages in western Burkina Faso. We estimated requirements for parallel and step wedge designs, varying the targeted vector species, the suppression effect and the monitoring regime. For a suppression effect of 50%, 21–22 clusters were required to detect suppression with 90% power when all An. gambiae complex species were targeted, while 24–26 clusters were required when only An. coluzzii was targeted and 60–66 clusters were required when only An. gambiae was targeted. For stronger suppression effects, required trial sizes depended less on target species, with 9–10 clusters being sufficient to detect a 90% suppression effect. We investigated how reducing sampling effort, by sampling fewer houses and restricting sampling to rainy season months, affected statistical power.ConclusionsOur results provide empirically based guidance for designing CRCTs to evaluate interventions aiming to suppress malaria vector populations.
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Journal articleMiles SL, Santillo D, Painter H, et al., 2025,
Enhanced virulence and stress tolerance are signatures of epidemiologically successful <i>Shigella sonnei</i>
, NATURE COMMUNICATIONS, Vol: 16 -
Journal articleZhao J, ZHOU B, Harrison SP, et al., 2025,
Eco-evolutionary modelling of global vegetation dynamics and the impact of CO2 during the late quaternary: insights from contrasting periods
, Earth System Dynamics, ISSN: 2190-4979Changes in climate have had major impacts on global vegetation during the Quaternary. However, variations in CO2 levels also play a role in shaping vegetation dynamics by influencing plant productivity and water-use efficiency, and consequently the relative competitive success of the C3 and C4 photosynthetic pathways. We use an eco-evolutionary optimality (EEO) based modelling approach to examine the impacts of climate fluctuations and CO2-induced alterations on gross primary production (GPP). We considered two contrasting periods, the Last Glacial Maximum (LGM, 21,000 years before present) and the mid-Holocene (MH, 6,000 years before present) and compared both to pre-industrial conditions (PI). The LGM, characterised by generally colder and drier climate, had a CO2 level close to the minimum for effective C3 plant operation. In contrast, the MH had warmer summers and increased monsoonal rainfall in the northern hemisphere, although with a CO2 level still below PI. We simulated vegetation primary production at the LGM and the MH compared to the PI baseline using a light-use efficiency model that simulates GPP coupled to an EEO model that simulates leaf area index (LAI) and C3/C4 competition. We found that low CO2 at the LGM was nearly as important as climate in reducing tree cover, increasing the abundance of C4 plants and lowering GPP. Global GPP in the MH was similar to the PI (although greater than the LGM), also reflecting CO2 constraints on plant growth despite the positive impacts of warmer and/or wetter climates experienced in the northern hemisphere and tropical regions. These results emphasise the importance of taking account of impacts of changing CO2 levels on plant growth to model ecosystem changes.
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Journal articleConsoli G, Tufail F, Leong HF, et al., 2025,
Locating the missing chlorophylls f in far-red photosystem I
, Science, ISSN: 0036-8075The discovery of chlorophyll f-containing photosystems, with their long-wavelength photochemistry, represented a distinct, low-energy paradigm for oxygenic photosynthesis. Structural studies on chlorophyll f-containing photosystem I could identify some chlorophylls f sites, but none among the photochemically active pigments and concluded that chlorophyll f plays no photochemical role. Here, we report two cryo-EM structures of far-red PSI from Chroococcidiopsis thermalis PCC 7203, allowing the assignment of eight chlorophylls f molecules, including the redox active A-1B. Simulations of absorption difference spectra induced by charge separation indicate that the experimental spectra can be reproduced only by considering the presence of a chlorophyll f at the A-1B site. The chlorophyll f locations, wavelength assignments, and conserved far-red-specific residues provide functional insights for efficient use of long wavelength photons.
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Journal articleHain S, Fu MS, Wigg L, et al., 2025,
Brain-infiltrating CD4 T cells drive inflammatory microglia proliferation during cryptococcal meningitis in mice
, NATURE COMMUNICATIONS, Vol: 16 -
Journal articleMitchell Z, Den Hoed J, Claassen W, et al., 2025,
The NuRD component CHD3 promotes BMP signalling during cranial neural crest cell specification
, EMBO Reports, Vol: 26, Pages: 4723-4741, ISSN: 1469-221XPathogenic genetic variants in the NuRD component CHD3 cause Snijders Blok–Campeau Syndrome, a neurodevelopmental disorder manifesting with intellectual disability and craniofacial anomalies. To investigate the role of CHD3 in craniofacial development, we differentiated control and CHD3-depleted human-induced pluripotent stem cells into cranial neural crest cells (CNCCs). In control lines, CHD3 is upregulated in early stages of CNCC specification, where it enhances the BMP signalling response by opening chromatin at BMP-responsive cis-regulatory elements and by increasing expression of BMP-responsive transcription factors, including DLX paralogs. CHD3 loss leads to repression of BMP target genes and loss of chromatin accessibility at cis-regulatory elements usually bound by BMP-responsive factors, causing an imbalance between BMP and Wnt signalling. Consequently, the CNCC specification fails, replaced by aberrant early-mesoderm identity, which can be partially rescued by titrating Wnt levels. Our findings highlight a novel role for CHD3 as a pivotal regulator of BMP signalling, essential for proper neural crest specification and craniofacial development. Moreover, these results suggest a molecular mechanism for the craniofacial anomalies of Snijders Blok–Campeau Syndrome.
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