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  • Journal article
    Delhaye G, van der Linde S, Bauman D, Orme CDL, Suz LM, Bidartondo MIet al., 2024,

    Ectomycorrhizal fungi are influenced by ecoregion boundaries across Europe

    , Global Ecology and Biogeography, Vol: 33, ISSN: 1466-822X

    Aim: Ecoregions and the distance decay in community similarity are fundamental concepts in biogeography and conservation biology that are well supported across plants and animals, but not fungi. Here we test the relevance of these concepts for ectomycorrhizal (ECM) fungi in temperate and boreal regions. Location: Europe. Time Period: 2008–2015. Major Taxa Studied: Ectomycorrhizal fungi. Methods: We used a large dataset of ~24,000 ectomycorrhizas, assigned to 1350 operational taxonomic units, collected from 129 forest plots via a standardized protocol. We investigated the relevance of ecoregion delimitations for ECM fungi through complementary methodological approaches based on distance decay models, multivariate analyses and indicator species analyses. We then evaluated the effects of host tree and climate on the observed biogeographical distributions. Results: Ecoregions predict large-scale ECM fungal biodiversity patterns. This is partly explained by climate differences between ecoregions but independent from host tree distribution. Basidiomycetes in the orders Russulales and Atheliales and producing epigeous fruiting bodies, with potentially short-distance dispersal, show the best agreement with ecoregion boundaries. Host tree distribution and fungal abundance (as opposed to presence/absence only) are important to uncover biogeographical patterns in mycorrhizas. Main Conclusions: Ecoregions are useful units to investigate eco-evolutionary processes in mycorrhizal fungal communities and for conservation decision-making that includes fungi.

  • Journal article
    Rosenkranz M, Nkumama IN, Ogwang R, Kraker S, Blickling M, Mwai K, Odera D, Tuju J, Fürle K, Frank R, Chepsat E, Kapulu MC, Osier FHAet al., 2024,

    Full-length MSP1 is a major target of protective immunity after controlled human malaria infection

    , Life Science Alliance
  • Journal article
    Fecht S, Paracuellos P, Subramoni S, Tan CAZ, Ilangovan A, Costa TRD, Filloux Aet al., 2024,

    Functionality of chimeric TssA proteins in the type VI secretion system reveals sheath docking specificity within their N-terminal domains

    , Nature Communications, Vol: 15, ISSN: 2041-1723

    The genome of Pseudomonas aeruginosa encodes three type VI secretion systems, each comprising a dozen distinct proteins, which deliver toxins upon T6SS sheath contraction. The least conserved T6SS component, TssA, has variations in size which influence domain organisation and structure. Here we show that the TssA Nt1 domain interacts directly with the sheath in a specific manner, while the C-terminus is essential for oligomerisation. We built chimeric TssA proteins by swapping C-termini and showed that these can be functional even when made of domains from different TssA sub-groups. Functional specificity requires the Nt1 domain, while the origin of the C-terminal domain is more permissive for T6SS function. We identify two regions in short TssA proteins, loop and hairpin, that contribute to sheath binding. We propose a docking mechanism of TssA proteins with the sheath, and a model for how sheath assembly is coordinated by TssA proteins from this position.

  • Journal article
    Pawar S, 2024,

    Metabolic plasticity drives mismatches in physiological traits between prey and predator

    , Communications Biology, ISSN: 2399-3642
  • Journal article
    Nguyen H-TT, Zhao M, Wang T, Dang BT, Geffen AJ, Cummins SFet al., 2024,

    Sea anemone-anemonefish symbiosis: Behavior and mucous protein profiling.

    , J Fish Biol

    Fish species of the genus Amphiprion (Perciformes: Pomacentridae) seek protection from predators among the tentacles of sea anemones as their natural habitat, where they live essentially unharmed from stinging by the host's nematocysts. The skin mucus of these anemonefish has been suggested as a protective mechanism that prevents the discharge of the nematocysts upon contact. Whereas some anemonefish species seem to produce their own protective mucous coating, others may acquire mucus (or biomolecules within) from the sea anemone during an acclimation period. In controlled experiments, we show that Amphiprion ocellaris acclimated successfully to their natural host anemone species Stichodactyla gigantea, and also to Stichodactyla haddoni, and in some cases Heteractis crispa, neither of which are natural host species. No symbiosis was observed for three other anemone species tested, Entacmaea quadricolor, Macrodactyla doreensis, and Heteractis malu. We explored the skin mucous protein profile from naive and experienced A. ocellaris during their acclimation to natural and unnatural host anemones. We confidently report the presence of metabolic and structural proteins in the skin mucus of all samples, likely involved in immunological defense, molecular transport, stress response, and signal transduction. For those anemonefish that established symbiosis, there was a clear increase in ribosomal-type proteins. We additionally provide evidence for the presence of anemone proteins only in the skin mucus of individuals that established symbiosis. Our results support previous speculation of the role of skin mucous-associated proteins in anemonefish-anemone symbiosis. Further exploration of these mucosal proteins could reveal the mechanism of anemonefish acclimation to host anemones.

  • Journal article
    Ono M, Satou Y, 2024,

    Spectrum of Treg and Self-Reactive T cells: Single Cell Perspectives from Old Friend HTLV-1

    , Discovery Immunology

    <jats:title>Summary</jats:title> <jats:p>Despite extensive regulatory T cell (Treg) research, fundamental questions on in vivo dynamics remain to be answered. The current study aims to dissect several interwoven concepts in Treg biology, highlighting the ‘self-reactivity’ of Treg and their counterparts, namely naturally-arising memory-phenotype T-cells, as a key mechanism to be exploited by a human retroviral infection. We propose the novel key concept, Periodic TCR-signalled T-cells, capturing self-reactivity in a quantifiable manner using the Nr4a3-Timer-of-cell-kinetics-and-activity (Tocky) technology. Periodic and brief TCR signals in self-reactive T-cells contrast with acute TCR signals during inflammation. Thus, we propose a new two-axis model for T-cell activation by the two types of TCR signals or antigen recognition, elucidating how Foxp3 expression and acute TCR signals actively regulate Periodic TCR-signalled T-cells. Next, we highlight an underappreciated branch of immunological research on Human T-cell Leukemia Virus-1 (HTLV-1) that precedes Treg studies, illuminating the missing link between the viral infection, CD25, and Foxp3. Based on evidence by single cell analysis, we show how the viral infection exploits the regulatory mechanisms for T-cell activation and suggests a potential role of Periodic TCR signalling in infection and malignant transformation. In conclusion, the new perspectives and models in this study provide a working framework for investigating Treg within the self-reactive T-cell spectrum, expected to advance understanding of HTLV-1 infection, cancer, and immunotherapy strategies for these conditions.</jats:p>

  • Journal article
    Gayford J, Naylor GJP, Brazeau M, 2024,

    Evolutionary trends in the elasmobranch neurocranium

    , Scientific Reports, ISSN: 2045-2322
  • Journal article
    Miao A, Luo T, Hsieh B, Edge CJ, Gridley M, Wong R, Constandinou T, Wisden W, Franks Net al., 2024,

    Brain clearance is reduced during sleep and anesthesia

    , Nature Neuroscience, ISSN: 1097-6256

    It has been suggested that the function of sleep is to actively clear metabolites and toxins from the brain. Enhanced clearance is also said to occur during anesthesia. Here, we measure clearance and movement of fluorescent molecules in the brains of male mice and show that movement is, in fact, independent of sleep and wake or anesthesia. Moreover, we show that brain clearance is markedly reduced, not increased, during sleep and anesthesia.

  • Journal article
    Tica J, Chen H, LUO S, Chen M, Isalan Met al., 2024,

    Engineering tuneable, low latency spatial computation with dual input quorum sensing promoters

    , ACS Synthetic Biology, ISSN: 2161-5063
  • Journal article
    Endres R, Endres R, Pazuki R, 2024,

    Robustness of Turing models and gene regulatory networks with a sweet spot

    , Physical Review E: Statistical, Nonlinear, and Soft Matter Physics, ISSN: 1539-3755
  • Journal article
    Schroeder J, 2024,

    Not in the countryside please! Investigating UK residents’ perceptions of an introduced species, the ring-necked parakeet (Psittacula krameri)

    , NeoBiota, ISSN: 1314-2488
  • Journal article
    Sun Y, Dunning J, Taylor T, Schroeder J, Anne Zollinger Set al., 2024,

    Calls of Manx shearwater Puffinus puffinus contain individual signatures

    , Journal of Avian Biology, Vol: 2024, ISSN: 0908-8857

    Vocalisations are widely used to signal behavioural intention in animal communication, but may also carry acoustic signatures unique to the calling individual. Here, we used acoustic analysis to confirm that Manx shearwater Puffinus puffinus calls carry individual signatures, and discerned which features made the calls individual. Manx shearwater are nocturnal seabirds that breed in dense colonies, where they must recognize and locate mates among thousands of conspecifics calling in the dark. There is evidence for mate vocal recognition in two shearwater species, but quantitative data on the vocalisations are lacking. We elicited vocal responses to playback of conspecific calls in Manx shearwaters, and measured spectral and temporal parameters of the calls. We then applied linear discriminant analysis with leave-one-out cross-validation and could confirm the presence of individual vocal signatures. We then calculated among-individual repeatability of 34 features describing the vocalisation to determine the extent to which these features may contribute to individual signature coding. We found that calls cluster by individual in both temporal and spectral characteristics, suggesting these traits are contributing to Manx shearwaters' unique call signatures.

  • Journal article
    Mwima R, Hui T-YJ, Kayondo JK, Burt Aet al., 2024,

    The population genetics of partial diapause, with applications to the aestivating malaria mosquito Anopheles coluzzii.

    , Mol Ecol Resour, Vol: 24

    Diapause, a form of dormancy to delay or halt the reproductive development during unfavourable seasons, has evolved in many insect species. One example is aestivation, an adult-stage diapause enhancing malaria vectors' survival during the dry season (DS) and their re-establishment in the next rainy season (RS). This work develops a novel genetic approach to estimate the number or proportion of individuals undergoing diapause, as well as the breeding sizes of the two seasons, using signals from temporal allele frequency dynamics. Our modelling shows the magnitude of drift is dampened at early RS when previously aestivating individuals reappear. Aestivation severely biases the temporal effective population size ( N e $$ {N}_e $$ ), leading to overestimation of the DS breeding size by 1 / 1 - α 2 $$ 1/{\left(1-\alpha \right)}^2 $$ across 1 year, where α $$ \alpha $$ is the aestivating proportion. We find sampling breeding individuals in three consecutive seasons starting from an RS is sufficient for parameter estimation, and perform extensive simulations to verify our derivations. This method does not require sampling individuals in the dormant state, the biggest challenge in most studies. We illustrate the method by applying it to a published data set for Anopheles coluzzii mosquitoes from Thierola, Mali. Our method and the expected evolutionary implications are applicable to any species in which a fraction of the population diapauses for more than one generation, and are difficult or impossible to sample during that stage.

  • Journal article
    Lewis-Brown E, Jennings N, Mills M, Ewers Ret al., 2024,

    Comparison of carbon management and emissions of universities that did and did not adopt voluntary carbon offsets

    , Climate Policy, Vol: 24, Pages: 706-722, ISSN: 1469-3062

    The urgent need to reduce greenhouse gas emissions, remove carbon from the atmosphere and stabilize natural carbon sinks has led to the development of many carbon management measures, increasingly including voluntary carbon offsets (VCOs). We studied carbon management in universities, institutions with large carbon footprints and considerable influence in climate science and policy fora. However, concerns that VCOs may deter adopters (including universities) from adopting other carbon reduction measures and limit emissions reductions, for example, through moral hazard, have been raised but understudied. We compared the carbon management characteristics (priorities, policies, practices and emissions) of universities that did and did not adopt VCOs. We found adopters measured carbon emissions for longer, and had set targets to reach net zero earlier than had non-adopters. Adopters of VCOs also undertook more carbon management practices in both 2010 and 2020 than non-adopters. We also found that both adopters and non-adopters significantly increased their carbon management practices over the decade studied, but with no difference between groups. Gross CO2 emissions were reduced significantly over time by adopters of VCOs but not by non-adopters, whereas carbon intensity and percentage annual emissions reductions did not relate to adoption status. Consequently, our study showed no indication of mitigation deterrence due to adoption of VCOs at the universities studied. Rather, greater emissions reductions correlated with earlier net zero target dates, and a higher number of policies and carbon management practices. However, our study was constrained to universities that were affiliated with a national environmental network, so research beyond these organizations, and with individuals, would be useful. The survey was voluntary, exposing the study to potential self-selection bias so the findings may not be generalized beyond the study group. Finally, we found the carbon ac

  • Journal article
    Pereira HM, Martins IS, Rosa IMD, Kim H, Leadley P, Popp A, van Vuuren DP, Hurtt G, Quoss L, Arneth A, Baisero D, Bakkenes M, Chaplin-Kramer R, Chini L, Di Marco M, Ferrier S, Fujimori S, Guerra CA, Harfoot M, Harwood TD, Hasegawa T, Haverd V, Havlík P, Hellweg S, Hilbers JP, Hill SLL, Hirata A, Hoskins AJ, Humpenöder F, Janse JH, Jetz W, Johnson JA, Krause A, Leclère D, Matsui T, Meijer JR, Merow C, Obersteiner M, Ohashi H, De Palma A, Poulter B, Purvis A, Quesada B, Rondinini C, Schipper AM, Settele J, Sharp R, Stehfest E, Strassburg BBN, Takahashi K, Talluto MV, Thuiller W, Titeux N, Visconti P, Ware C, Wolf F, Alkemade Ret al., 2024,

    Global trends and scenarios for terrestrial biodiversity and ecosystem services from 1900 to 2050.

    , Science, Vol: 384, Pages: 458-465

    Based on an extensive model intercomparison, we assessed trends in biodiversity and ecosystem services from historical reconstructions and future scenarios of land-use and climate change. During the 20th century, biodiversity declined globally by 2 to 11%, as estimated by a range of indicators. Provisioning ecosystem services increased several fold, and regulating services decreased moderately. Going forward, policies toward sustainability have the potential to slow biodiversity loss resulting from land-use change and the demand for provisioning services while reducing or reversing declines in regulating services. However, negative impacts on biodiversity due to climate change appear poised to increase, particularly in the higher-emissions scenarios. Our assessment identifies remaining modeling uncertainties but also robustly shows that renewed policy efforts are needed to meet the goals of the Convention on Biological Diversity.

  • Journal article
    Fallesen T, Amerteifio S, Pruessner G, Jensen H, Sena Get al., 2024,

    Intermittent cell division dynamics in regenerating Arabidopsis roots reveals complex long-range interactions

    , Quantitative Plant Biology, ISSN: 2632-8828
  • Journal article
    Endres R, Matas-Gil A, 2024,

    Unraveling biochemical spatial patterns: machine learning approaches to the inverse problem of stationary Turing patterns

    , iScience, ISSN: 2589-0042
  • Journal article
    Guerrero P, Perez-Carrasco R, 2024,

    Choice of friction coefficient deeply affects tissue behaviour in stochastic epithelial vertex models.

    , Philos Trans R Soc Lond B Biol Sci, Vol: 379

    To understand the mechanisms that coordinate the formation of biological tissues, the use of numerical implementations is necessary. The complexity of such models involves many assumptions and parameter choices that result in unpredictable consequences, obstructing the comparison with experimental data. Here, we focus on vertex models, a family of spatial models used extensively to simulate the dynamics of epithelial tissues. Usually, in the literature, the choice of the friction coefficient is not addressed using quasi-static deformation arguments that generally do not apply to realistic scenarios. In this manuscript, we discuss the role that the choice of friction coefficient has on the relaxation times and consequently in the conditions of cell cycle progression and division. We explore the effects that these changes have on the morphology, growth rate and topological transitions of the tissue dynamics. These results provide a deeper understanding of the role that an accurate mechanical description plays in the use of vertex models as inference tools. This article is part of a discussion meeting issue 'Causes and consequences of stochastic processes in development and disease'.

  • Journal article
    Yuen ELH, Leary AY, Clavel M, Tumtas Y, Mohseni A, Zhao J, Picchianti L, Jamshidiha M, Pandey P, Duggan C, Cota E, Dagdas Y, Bozkurt TOet al., 2024,

    A RabGAP negatively regulates plant autophagy and immune trafficking.

    , Curr Biol

    Plants rely on autophagy and membrane trafficking to tolerate stress, combat infections, and maintain cellular homeostasis. However, the molecular interplay between autophagy and membrane trafficking is poorly understood. Using an AI-assisted approach, we identified Rab3GAP-like (Rab3GAPL) as a key membrane trafficking node that controls plant autophagy negatively. Rab3GAPL suppresses autophagy by binding to ATG8, the core autophagy adaptor, and deactivating Rab8a, a small GTPase essential for autophagosome formation and defense-related secretion. Rab3GAPL reduces autophagic flux in three model plant species, suggesting that its negative regulatory role in autophagy is conserved in land plants. Beyond autophagy regulation, Rab3GAPL modulates focal immunity against the oomycete pathogen Phytophthora infestans by preventing defense-related secretion. Altogether, our results suggest that Rab3GAPL acts as a molecular rheostat to coordinate autophagic flux and defense-related secretion by restraining Rab8a-mediated trafficking. This unprecedented interplay between a RabGAP-Rab pair and ATG8 sheds new light on the intricate membrane transport mechanisms underlying plant autophagy and immunity.

  • Journal article
    Saranholi BH, França FM, Vogler AP, Barlow J, Vaz de Mello FZ, Maldaner ME, Carvalho E, Gestich CC, Howes B, Banks-Leite C, Galetti PMet al., 2024,

    Testing and optimizing metabarcoding of iDNA from dung beetles to sample mammals in the hyperdiverse Neotropics.

    , Mol Ecol Resour

    Over the past few years, insects have been used as samplers of vertebrate diversity by assessing the ingested-derived DNA (iDNA), and dung beetles have been shown to be a good mammal sampler given their broad feeding preference, wide distribution and easy sampling. Here, we tested and optimized the use of iDNA from dung beetles to assess the mammal community by evaluating if some biological and methodological aspects affect the use of dung beetles as mammal species samplers. We collected 403 dung beetles from 60 pitfall traps. iDNA from each dung beetle was sequenced by metabarcoding using two mini-barcodes (12SrRNA and 16SrRNA). We assessed whether dung beetles with different traits related to feeding, nesting and body size differed in the number of mammal species found in their iDNA. We also tested differences among four killing solutions in preserving the iDNA and compared the effectiveness of each mini barcode to recover mammals. We identified a total of 50 mammal OTUs (operational taxonomic unit), including terrestrial and arboreal species from 10 different orders. We found that at least one mammal-matching sequence was obtained from 70% of the dung beetle specimens. The number of mammal OTUs obtained did not vary with dung beetle traits as well as between the killing solutions. The 16SrRNA mini-barcode recovered a higher number of mammal OTUs than 12SrRNA, although both sets were partly non-overlapping. Thus, the complete mammal diversity may not be achieved by using only one of them. This study refines the methodology for routine assessment of tropical mammal communities via dung beetle 'samplers' and its universal applicability independently of the species traits of local beetle communities.

  • Journal article
    Merckx VSFT, Gomes SIF, Wang D, Verbeek C, Jacquemyn H, Zahn FE, Gebauer G, Bidartondo MIet al., 2024,

    Mycoheterotrophy in the wood-wide web

    , Nature Plants, ISSN: 2055-026X

    The prevalence and potential functions of common mycorrhizal networks, or the 'wood-wide web', resulting from the simultaneous interaction of mycorrhizal fungi and roots of different neighbouring plants have been increasingly capturing the interest of science and society, sometimes leading to hyperbole and misinterpretation. Several recent reviews conclude that popular claims regarding the widespread nature of these networks in forests and their role in the transfer of resources and information between plants lack evidence. Here we argue that mycoheterotrophic plants associated with ectomycorrhizal or arbuscular mycorrhizal fungi require resource transfer through common mycorrhizal networks and thus are natural evidence for the occurrence and function of these networks, offering a largely overlooked window into this methodologically challenging underground phenomenon. The wide evolutionary and geographic distribution of mycoheterotrophs and their interactions with a broad phylogenetic range of mycorrhizal fungi indicate that common mycorrhizal networks are prevalent, particularly in forests, and result in net carbon transfer among diverse plants through shared mycorrhizal fungi. On the basis of the available scientific evidence, we propose a continuum of carbon transfer options within common mycorrhizal networks, and we discuss how knowledge on the biology of mycoheterotrophic plants can be instrumental for the study of mycorrhizal-mediated transfers between plants.

  • Journal article
    Blackford K, Kasoar M, Burton C, Burke E, Prentice IC, Voulgarakis Aet al., 2024,

    INFERNO-peat v1.0.0: a representation of northern high latitude peat fires in the JULES-INFERNO global fire model

    , Geoscientific Model Development, Vol: 17, Pages: 3063-3079, ISSN: 1991-959X

    Peat fires in the northern high latitudes have the potential to burn vast amounts of carbon-rich organic soil, releasing large quantities of long-term stored carbon to the atmosphere. Due to anthropogenic activities and climate change, peat fires are increasing in frequency and intensity across the high latitudes. However, at present they are not explicitly included in most fire models. Here we detail the development of INFERNO-peat, the first parameterization of peat fires in the JULES-INFERNO (Joint UK Land Environment Simulator INteractive Fire and Emission algoRithm for Natural envirOnments) fire model. INFERNO-peat utilizes knowledge from lab and field-based studies on peat fire ignition and spread to be able to model peat burnt area, burn depth, and carbon emissions, based on data of the moisture content, inorganic content, bulk density, soil temperature, and water table depth of peat. INFERNO-peat improves the representation of burnt area in the high latitudes, with peat fires simulating on average an additional 0.305×106 km2 of burn area each year, emitting 224.10 Tg of carbon. Compared to Global Fire Emissions Database version 5 (GFED5), INFERNO-peat captures ∼ 20 % more burnt area, whereas INFERNO underestimated burning by 50 %. Additionally, INFERNO-peat substantially improves the representation of interannual variability in burnt area and subsequent carbon emissions across the high latitudes. The coefficient of variation in carbon emissions is increased from 0.071 in INFERNO to 0.127 in INFERNO-peat, an almost 80 % increase. Therefore, explicitly modelling peat fires shows a substantial improvement in the fire modelling capabilities of JULES-INFERNO, highlighting the importance of representing peatland systems in fire models.

  • Journal article
    Williams J, Pettorelli N, Hartmann A, Quinn R, Plaisance L, OMahoney M, Meyer C, Fabricius K, Knowlton N, Ransome Eet al., 2024,

    Decline of a distinct coral reef holobiont community under ocean acidification

    , Microbiome, Vol: 12, ISSN: 2049-2618

    Background: Microbes play vital roles across coral reefs both in the environment and inside and upon macrobes (holobionts), where they support critical functions such as nutrition and immune system modulation. These roles highlight the potential ecosystem-level importance of microbes, yet most knowledge of microbial functions on reefs is derived from a small set of holobionts such as corals and sponges. Declining seawater pH - an important global coral reef stressor - can cause ecosystem-level change on coral reefs, providing an opportunity to study the role of microbes at this scale. We use an in situ experimental approach to test the hypothesis that under such ocean acidification (OA) known shifts among macrobe trophic and functional groups may drive a general ecosystem-level response extending across macrobes and microbes, leading to reduced distinctness between the benthic holobiont community microbiome and the environmental microbiome. Results: We test this hypothesis using genetic and chemical data from benthic coral reef community holobionts sampled across a pH gradient from CO2 seeps in Papua New Guinea. We find support for our hypothesis: under OA the microbiome and metabolome of the benthic holobiont community become less compositionally distinct from the sediment microbiome and metabolome, suggesting that benthic macrobe communities are colonized by environmental microbes to a higher degree under OA conditions. We also find a simplification and homogenisation of the benthic photosynthetic community, and an increased abundance of fleshy macroalgae, consistent with previously observed reef microbialisation. Conclusions: We demonstrate a novel structural shift in coral reefs involving macrobes and microbes: that the microbiome of the benthic holobiont community becomes less distinct from the sediment microbiome under OA. Our findings provide evidence that microbialisation and the disruption of macrobe trophic networks are interwoven general responses to envi

  • Journal article
    Griffiths D, Anderson M, Richardson K, Inaba-Inoue S, Allen WJ, Collinson I, Beis K, Morris M, Giles K, Politis Aet al., 2024,

    Cyclic Ion Mobility for Hydrogen/Deuterium Exchange-Mass Spectrometry Applications.

    , Anal Chem, Vol: 96, Pages: 5869-5877

    Hydrogen/deuterium exchange-mass spectrometry (HDX-MS) has emerged as a powerful tool to probe protein dynamics. As a bottom-up technique, HDX-MS provides information at peptide-level resolution, allowing structural localization of dynamic changes. Consequently, the HDX-MS data quality is largely determined by the number of peptides that are identified and monitored after deuteration. Integration of ion mobility (IM) into HDX-MS workflows has been shown to increase the data quality by providing an orthogonal mode of peptide ion separation in the gas phase. This is of critical importance for challenging targets such as integral membrane proteins (IMPs), which often suffer from low sequence coverage or redundancy in HDX-MS analyses. The increasing complexity of samples being investigated by HDX-MS, such as membrane mimetic reconstituted and in vivo IMPs, has generated need for instrumentation with greater resolving power. Recently, Giles et al. developed cyclic ion mobility (cIM), an IM device with racetrack geometry that enables scalable, multipass IM separations. Using one-pass and multipass cIM routines, we use the recently commercialized SELECT SERIES Cyclic IM spectrometer for HDX-MS analyses of four detergent solubilized IMP samples and report its enhanced performance. Furthermore, we develop a novel processing strategy capable of better handling multipass cIM data. Interestingly, use of one-pass and multipass cIM routines produced unique peptide populations, with their combined peptide output being 31 to 222% higher than previous generation SYNAPT G2-Si instrumentation. Thus, we propose a novel HDX-MS workflow with integrated cIM that has the potential to enable the analysis of more complex systems with greater accuracy and speed.

  • Journal article
    Chakraborty A, Alsharqi L, Kostrzewa M, Armstrong-James D, Larrouy-Maumus Get al., 2024,

    Intact cell lipidomics using the Bruker MBT lipid Xtract assay allows the rapid detection of glycosyl-inositol-phospho-ceramides from Aspergillus fumigatus.

    , Mol Omics

    Glycosyl-inositol-phospho-ceramides (GIPCs) or glycosylphosphatidylinositol-anchored fungal polysaccharides are major lipids in plant and fungal plasma membranes and play an important role in stress adaption. However, their analysis remains challenging due to the multiple steps involved in their extraction and purification prior to mass spectrometry analysis. To address this challenge, we report here a novel simplified method to identify GIPCs from Aspergillus fumigatus using the new Bruker MBT lipid Xtract assay. A. fumigatus reference strains and clinical isolates were cultured, harvested, heat-inactivated and suspended in double-distilled water. A fraction of this fungal preparation was then dried in a microtube, mixed with an MBT lipid Xtract matrix (Bruker Daltonik, Germany) and loaded onto a MALDI target plate. Analysis was performed using a Bruker MALDI Biotyper Sirius system in the linear negative ion mode. Mass spectra were scanned from m/z 700 to m/z 2 000. MALDI-TOF MS analysis of cultured fungi showed a clear signature of GIPCs in Aspergillus fumigatus reference strains and clinical isolates. Here, we have demonstrated that routine MALDI-TOF in the linear negative ion mode combined with the MBT lipid Xtract is able to detect Aspergillus fumigatus GIPCs.

  • Journal article
    Bradley R, Simon D, Spiga L, Xiang Y, Takats Z, Williams Het al., 2024,

    Laser desorption rapid evaporative ionization mass spectrometry (LD-REIMS) demonstrates a direct impact of hypochlorous acid stress on PQS-mediated quorum sensing in Pseudomonas aeruginosa.

    , mSystems, Vol: 9

    UNLABELLED: To establish infections in human hosts, Pseudomonas aeruginosa must overcome innate immune-generated oxidative stress, such as the hypochlorous acid (HOCl) produced by neutrophils. We set out to find specific biomarkers of oxidative stress through the development of a protocol for the metabolic profiling of P. aeruginosa cultures grown in the presence of different oxidants using a novel ionization technique for mass spectrometry, laser desorption rapid evaporative ionization mass spectrometry (LD-REIMS). We demonstrated the ability of LD-REIMS to classify samples as untreated or treated with a specific oxidant with 100% accuracy and identified a panel of 54 metabolites with significantly altered concentrations after exposure to one or more of the oxidants. Key metabolic changes were conserved in P. aeruginosa clinical strains isolated from patients with cystic fibrosis lung infections. These data demonstrated that HOCl stress impacted the Pseudomonas quinolone signal (PQS) quorum sensing system. Ten 2-alkyl-4-quinolones (AHQs) associated with the PQS system were significantly lower in concentration in HOCl-stressed P. aeruginosa cultures, including 2-heptyl-3-hydroxy-4(1H)-quinolone (PQS), the most active signal molecule of the PQS system. The PQS system regulates the production of virulence factors, including pyocyanin and elastase, and their levels were markedly affected by HOCl stress. No pyocyanin was detectable and elastase concentrations were reduced by more than 75% in cultures grown with sub-lethal concentrations of HOCl, suggesting that this neutrophil-derived oxidant may disrupt the ability of P. aeruginosa to establish infections through interference with production of PQS-associated virulence factors. IMPORTANCE: This work demonstrates that a high-throughput ambient ionization mass spectrometry method can be used successfully to study a bacterial stress response. Its application to the opportunistic pathogen Pseudomonas aeruginosa led to the

  • Journal article
    Zhang-Zheng H, Adu-Bredu S, Duah-Gyamfi A, Moore S, Addo-Danso S, Amissah L, Valentini R, Djagbletey G, Anum-Adjei K, Quansah J, Sarpong B, Owusu-Afriyie K, Gvozdevaite A, Tang M, Ruiz-Jaen M, Ibrahim F, Girardin C, Rifai S, Dahlsjo C, Riutta T, Deng X, Sun Y, Prentice IC, Oliveras Menor I, Malhi Yet al., 2024,

    Contrasting carbon cycle along tropical forest aridity gradients in West Africa and Amazonia

    , Nature Communications, Vol: 15, ISSN: 2041-1723

    Tropical forests cover large areas of equatorial Africa and play a substantial role in the global carbon cycle. However, there has been a lack of biometric measurements to understand the forests’ gross and net primary productivity (GPP, NPP) and their allocation. Here we present a detailed field assessment of the carbon budget of multiple forest sites in Africa, by monitoring 14 one-hectare plots along an aridity gradient in Ghana, West Africa. When compared with an equivalent aridity gradient in Amazonia, the studied West African forests generally had higher productivity and lower carbon use efficiency (CUE). The West African aridity gradient consistently shows the highest NPP, CUE, GPP, and autotrophic respiration at a medium-aridity site, Bobiri. Notably, NPP and GPP of the site are the highest yet reported anywhere for intact forests. Widely used data products substantially underestimate productivity when compared to biometric measurements in Amazonia and Africa. Our analysis suggests that the high productivity of the African forests is linked to their large GPP allocation to canopy and semi-deciduous characteristics.

  • Journal article
    Chia K-S, Kourelis J, Teulet A, Vickers M, Sakai T, Walker JF, Schornack S, Kamoun S, Carella Pet al., 2024,

    The N-terminal domains of NLR immune receptors exhibit structural and functional similarities across divergent plant lineages.

    , The Plant Cell, ISSN: 1040-4651

    Nucleotide-binding domain and leucine-rich repeat (NLR) proteins are a prominent class of intracellular immune receptors in plants. However, our understanding of plant NLR structure and function is limited to the evolutionarily young flowering plant clade. Here, we describe an extended spectrum of NLR diversity across divergent plant lineages and demonstrate the structural and functional similarities of N-terminal domains that trigger immune responses. We show that the broadly distributed coiled-coil (CC) and toll/interleukin-1 receptor (TIR) domain families of non-flowering plants retain immune-related functions through trans-lineage activation of cell death in the angiosperm Nicotiana benthamiana. We further examined a CC subfamily specific to non-flowering lineages and uncovered an essential N-terminal MAEPL motif that is functionally comparable to motifs in resistosome-forming CC-NLRs. Consistent with a conserved role in immunity, the ectopic activation of CCMAEPL in the non-flowering liverwort Marchantia polymorpha led to profound growth inhibition, defense gene activation, and signatures of cell death. Moreover, comparative transcriptomic analyses of CCMAEPL activity delineated a common CC-mediated immune program shared across evolutionarily divergent non-flowering and flowering plants. Collectively, our findings highlight the ancestral nature of NLR-mediated immunity during plant evolution that dates its origin to at least ∼500 million years ago.

  • Journal article
    Ogwang R, Murugu L, Nailain I, Nyamako L, Kai O, Mwai K, Murungi L, Idro R, Bejon P, Tuju J, Kinyanjui SM, Osier FHAet al., 2024,

    Bi-isotype immunoglobulins enhance antibody-mediated neutrophil activity against Plasmodium falciparum parasites

    , Frontiers in Immunology, Vol: 15, ISSN: 1664-3224

    Background: Malaria remains a major global health priority, and monoclonal antibodies (mAbs) are emerging as potential new tools to support efforts to control the disease. Recent data suggest that Fc-dependent mechanisms of immunity are important mediators of protection against the blood stages of the infection, but few studies have investigated this in the context of mAbs. We aimed to isolate mAbs agnostic to cognate antigens that target whole merozoites and simultaneously induce potent neutrophil activity measured by the level of reactive oxygen species (ROS) production using an antibody-dependent respiratory burst (ADRB) assay.Methods: We used samples from semi-immune adults living in coastal Kenya to isolate mAbs that induce merozoite-specific ADRB activity. We then tested whether modifying the expressed IgG1 isotype to an IgG–IgA Fc region chimera would enhance the level of ADRB activity.Results: We isolated a panel of nine mAbs with specificity to whole merozoites. mAb J31 induced ADRB activity in a dose-dependent fashion. Compared to IgG1, our modified antibody IgG–IgA bi-isotype induced higher ADRB activity across all concentrations tested. Further, we observed a negative hook effect at high IgG1 mAb concentrations (i.e., >200 µg/mL), but this was reversed by Fc modification. We identified MSP3.5 as the potential cognate target of mAb J31.Conclusions: We demonstrate an approach to engineer mAbs with enhanced ADRB potency against blood-stage parasites.

  • Journal article
    Flo V, Joshi J, Sabot M, Sandoval D, Prentice ICet al., 2024,

    Incorporating photosynthetic acclimation improves stomatal optimisation models

    , Plant, Cell and Environment, ISSN: 0140-7791

    Stomatal opening in plant leaves is regulated through a balance of carbon and water exchange under different environmental conditions. Accurate estimation of stomatal regulation is crucial for understanding how plants respond to changing environmental conditions, particularly under climate change. A new generation of optimality-based modelling schemes determines instantaneous stomatal responses from a balance of trade-offs between carbon gains and hydraulic costs, but most such schemes do not account for biochemical acclimation in response to drought. Here, we compare the performance of six instantaneous stomatal optimisation models with and without accounting for photosynthetic acclimation. Using experimental data from 37 plant species, we found that accounting for photosynthetic acclimation improves the prediction of carbon assimilation in a majority of the tested models. Photosynthetic acclimation contributed significantly to the reduction of photosynthesis under drought conditions in all tested models. Drought effects on photosynthesis could not accurately be explained by the hydraulic impairment functions embedded in the stomatal models alone, indicating that photosynthetic acclimation must be considered to improve estimates of carbon assimilation during drought.

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