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Journal articleMakrydaki E, Donini R, Krueger A, et al., 2024,
Immobilized enzyme cascade for targeted glycosylation
, Nature Chemical Biology, Vol: 20, Pages: 732-741, ISSN: 1552-4450Glycosylation is a critical post-translational protein modification that affects folding, half-life and functionality. Glycosylation is a non-templated and heterogeneous process because of the promiscuity of the enzymes involved. We describe a platform for sequential glycosylation reactions for tailored sugar structures (SUGAR-TARGET) that allows bespoke, controlled N-linked glycosylation in vitro enabled by immobilized enzymes produced with a one-step immobilization/purification method. We reconstruct a reaction cascade mimicking a glycosylation pathway where promiscuity naturally exists to humanize a range of proteins derived from different cellular systems, yielding near-homogeneous glycoforms. Immobilized β-1,4-galactosyltransferase is used to enhance the galactosylation profile of three IgGs, yielding 80.2-96.3% terminal galactosylation. Enzyme recycling is demonstrated for a reaction time greater than 80 h. The platform is easy to implement, modular and reusable and can therefore produce homogeneous glycan structures derived from various hosts for functional and clinical evaluation.
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Journal articlePazuki RH, Endres RG, 2024,
Robustness of Turing models and gene regulatory networks with a sweet spot
, Physical review E (statistical, nonlinear, biological, and soft matter physics), Vol: 109, ISSN: 2470-0045Traditional linear stability analysis based on matrix diagonalization is a computationally intensive process for high-dimensional systems of differential equations, posing substantial limitations for the exploration of Turing systems of pattern formation where an additional wave-number parameter needs to be investigated. In this paper, we introduce an efficient and intuitive technique that leverages Gershgorin's theorem to determine upper limits on regions of parameter space and the wave number beyond which Turing instabilities cannot occur. This method offers a streamlined avenue for exploring the phase diagrams of other complex multi-parametric models, such as those found in gene regulatory networks in systems biology. Due to its suitability for the asymptotic limit of infinitely large systems, it predicts the existence of a sweet spot in network size for maximal Jacobian stability.
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Journal articleBonnin RA, Creton E, Perrin A, et al., 2024,
Spread of carbapenemase-producing Morganella spp from 2013 to 2021: a comparative genomic study
, LANCET MICROBE, Vol: 5, Pages: e547-e558 -
Journal articleDelhaye G, van der Linde S, Bauman D, et al., 2024,
Ectomycorrhizal fungi are influenced by ecoregion boundaries across Europe
, Global Ecology and Biogeography, Vol: 33, ISSN: 1466-822XAimEcoregions 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.LocationEurope.Time Period2008–2015.Major Taxa StudiedEctomycorrhizal fungi.MethodsWe 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.ResultsEcoregions 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 ConclusionsEcoregions are useful units to investigate eco-evolutionary processes in mycorrhizal fungal communities and for conservation decision-making that includes fungi.
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Journal articleCai JA, Christophides GK, 2024,
Immune interactions between mosquitoes and microbes during midgut colonization
, CURRENT OPINION IN INSECT SCIENCE, Vol: 63, ISSN: 2214-5745 -
Journal articleMoulick D, Majumdar A, Choudhury A, et al., 2024,
Emerging concern of nano-pollution in agro-ecosystem: Flip side of nanotechnology
, PLANT PHYSIOLOGY AND BIOCHEMISTRY, Vol: 211, ISSN: 0981-9428 -
Journal articleDuncan SM, Carbajo CG, Nagar R, et al., 2024,
Generation of a bloodstream form <i>Trypanosoma brucei</i> double glycosyltransferase null mutant competent in receptor-mediated endocytosis of transferrin
, PLOS PATHOGENS, Vol: 20, ISSN: 1553-7366 -
Journal articleRiva F, Haddad N, Fahrig L, et al., 2024,
Principles for area-based biodiversity conservation
, ECOLOGY LETTERS, Vol: 27, ISSN: 1461-023X -
Journal articleLuiselli J, Overcast I, Rominger A, et al., 2024,
Detecting the ecological footprint of selection
, PLoS One, Vol: 19, ISSN: 1932-6203The structure of communities is influenced by many ecological and evolutionary processes, but the way these manifest in classic biodiversity patterns often remains unclear. Here we aim to distinguish the ecological footprint of selection-through competition or environmental filtering-from that of neutral processes that are invariant to species identity. We build on existing Massive Eco-evolutionary Synthesis Simulations (MESS), which uses information from three biodiversity axes-species abundances, genetic diversity, and trait variation-to distinguish between mechanistic processes. To correctly detect and characterise competition, we add a new and more realistic form of competition that explicitly compares the traits of each pair of individuals. Our results are qualitatively different to those of previous work in which competition is based on the distance of each individual's trait to the community mean. We find that our new form of competition is easier to identify in empirical data compared to the alternatives. This is especially true when trait data are available and used in the inference procedure. Our findings hint that signatures in empirical data previously attributed to neutrality may in fact be the result of pairwise-acting selective forces. We conclude that gathering more different types of data, together with more advanced mechanistic models and inference as done here, could be the key to unravelling the mechanisms of community assembly and question the relative roles of neutral and selective processes.
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Journal articleLu Y, Duman R, Beilsten-Edmands J, et al., 2024,
Ray-tracing analytical absorption correction for X-ray crystallography based on tomographic reconstructions
, JOURNAL OF APPLIED CRYSTALLOGRAPHY, Vol: 57, Pages: 649-658, ISSN: 1600-5767 -
Journal articleManser CL, Perez-Carrasco R, 2024,
A mathematical framework for measuring and tuning tempo in developmental gene regulatory networks
, DEVELOPMENT, Vol: 151, ISSN: 0950-1991 -
Journal articlePerez-Carrasco R, 2024,
The people behind the papers - Charlotte Manser and Ruben Perez-Carrasco
, DEVELOPMENT, Vol: 151, ISSN: 0950-1991 -
Journal articleChristman ME, Spears LR, Burchfield EK, et al., 2024,
Bumble bee responses to climate and landscapes: Investigating habitat associations and species assemblages across geographic regions in the United States of America
, GLOBAL CHANGE BIOLOGY, Vol: 30, ISSN: 1354-1013 -
Journal articleBradfer-Lawrence T, Duthie B, Abrahams C, et al., 2024,
The Acoustic Index User's Guide: A practical manual for defining, generating and understanding current and future acoustic indices
, METHODS IN ECOLOGY AND EVOLUTION, ISSN: 2041-210X -
Journal articleAffinito F, Kordas RL, Matias MG, et al., 2024,
Metabolic plasticity drives mismatches in physiological traits between prey and predator
, Communications Biology, Vol: 7, ISSN: 2399-3642Metabolic rate, the rate of energy use, underpins key ecological traits of organisms, from development and locomotion to interaction rates between individuals. In a warming world, the temperature-dependence of metabolic rate is anticipated to shift predator-prey dynamics. Yet, there is little real-world evidence on the effects of warming on trophic interactions. We measured the respiration rates of aquatic larvae of three insect species from populations experiencing a natural temperature gradient in a large-scale mesocosm experiment. Using a mechanistic model we predicted the effects of warming on these taxa’s predator-prey interaction rates. We found that species-specific differences in metabolic plasticity lead to mismatches in the temperature-dependence of their relative velocities, resulting in altered predator-prey interaction rates. This study underscores the role of metabolic plasticity at the species level in modifying trophic interactions and proposes a mechanistic modelling approach that allows an efficient, high-throughput estimation of climate change threats across species pairs.
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Journal articleRosindell J, Manson K, Gumbs R, et al., 2024,
Phylogenetic Biodiversity Metrics Should Account for Both Accumulation and Attrition of Evolutionary Heritage
, SYSTEMATIC BIOLOGY, Vol: 73, Pages: 158-182, ISSN: 1063-5157 -
Journal articleSandoval Calle D, Prentice IC, Nobrega R, 2024,
Simple process-led algorithms for simulating habitats (SPLASH v 2.0): robust calculations of water and energy fluxes
, Geoscientific Model Development, Vol: 17, Pages: 4229-4309, ISSN: 1991-959XThe current representation of key processes in Land Surface Models (LSM) for estimating water and energy balances still relies heavily on empirical equations that require calibration oriented to site-specific characteristics. When multiple parameters are used, different combinations of parameter values can produce equally acceptable results, leading to a risk of obtaining “right answers for wrong reasons”, compromising the reproducibility of the simulations and limiting the ecological interpretability of the results. To address this problem and reduce the need for free parameters, here we present novel formulations based on first-principles to calculate key components of water and energy balances, extending the already parsimonious SPLASHmodel v.1.0 (Davis et al. 2017, GMD). We found analytical solutions for many processes, enabling us to increase spatial resolution and include the terrain effects directly in the calculations without unreasonably inflating computational demands. This calibration-free model estimates quantities such as net radiation, evapotranspiration, condensation, soil water content,surface runoff, subsurface lateral flow and snow-water equivalent. These quantities are derived from readily meteorological data such as near-surface air temperature, precipitation and solar radiation, and soil physical properties. Whenever empirical formulations were required, e.g. pedotransfer functions and albedo-snow cover relationships, we selected and optimized thebest-performing equations through a combination of remote sensing and globally distributed terrestrial observational datasets. Simulations at global scales at different resolutions were run to evaluate spatial patterns, while simulations with point-based observations were run to evaluate seasonal patterns using data from hundreds of stations and comparisons with the VIC-3L model, demonstrating improved performance based on statistical tests and observational comparisons. In summary, our m
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Journal articleConnolly JB, Burt A, Christophides G, et al., 2024,
Considerations for first field trials of low-threshold gene drive for malaria vector control
, Malaria Journal, Vol: 23, ISSN: 1475-2875Sustainable reductions in African malaria transmission require innovative tools for mosquito control. One proposal involves the use of low-threshold gene drive in Anopheles vector species, where a 'causal pathway' would be initiated by (i) the release of a gene drive system in target mosquito vector species, leading to (ii) its transmission to subsequent generations, (iii) its increase in frequency and spread in target mosquito populations, (iv) its simultaneous propagation of a linked genetic trait aimed at reducing vectorial capacity for Plasmodium, and (v) reduced vectorial capacity for parasites in target mosquito populations as the gene drive system reaches fixation in target mosquito populations, causing (vi) decreased malaria incidence and prevalence. Here the scope, objectives, trial design elements, and approaches to monitoring for initial field releases of such gene dive systems are considered, informed by the successful implementation of field trials of biological control agents, as well as other vector control tools, including insecticides, Wolbachia, larvicides, and attractive-toxic sugar bait systems. Specific research questions to be addressed in initial gene drive field trials are identified, and adaptive trial design is explored as a potentially constructive and flexible approach to facilitate testing of the causal pathway. A fundamental question for decision-makers for the first field trials will be whether there should be a selective focus on earlier points of the pathway, such as genetic efficacy via measurement of the increase in frequency and spread of the gene drive system in target populations, or on wider interrogation of the entire pathway including entomological and epidemiological efficacy. How and when epidemiological efficacy will eventually be assessed will be an essential consideration before decisions on any field trial protocols are finalized and implemented, regardless of whether initial field trials focus exclusively on the measur
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Journal articleFecht S, Paracuellos P, Subramoni S, et 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: 2041-1723The 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.
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Journal articleGayford J, Brazeau M, Naylor GJP, 2024,
Evolutionary trends in the elasmobranch neurocranium
, Scientific Reports, Vol: 14, ISSN: 2045-2322The neurocranium (braincase) is one of the defining vertebrate characters. Housing the brain and other key sensory organs, articulating with the jaws and contributing to the shape of the anteriormost portion of the body, the braincase is undoubtedly of great functional importance. Through studying relationships between braincase shape and ecology we can gain an improved understanding of form-function relationships in extant and fossil taxa. Elasmobranchii (sharks and rays) represent an important case study of vertebrate braincase diversity as their neurocranium is simplified and somewhat decoupled from other components of the cranium relative to other vertebrates. Little is known about the associations between ecology and braincase shape in this clade. In this study we report patterns of mosaic cranial evolution in Elasmobranchii that differ significantly from those present in other clades. The degree of evolutionary modularity also differs between Selachii and Batoidea. In both cases innovation in the jaw suspension appears to have driven shifts in patterns of integration and modularity, subsequently facilitating ecological diversification. Our results confirm the importance of water depth and biogeography as drivers of elasmobranch cranial diversity and indicate that skeletal articulation between the neurocranium and jaws represents a major constraint upon the evolution of braincase shape in vertebrates.
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Journal articleYuen ELH, Leary AY, Clavel M, et al., 2024,
A RabGAP negatively regulates plant autophagy and immune trafficking
, CURRENT BIOLOGY, Vol: 34, ISSN: 0960-9822 -
Journal articleCreamer A, Lo Fiego A, Agliano A, et al., 2024,
Modular synthesis of semiconducting graft co-polymers to achieve ‘clickable’ fluorescent nanoparticles with long circulation and specific cancer targeting
, Advanced Materials, Vol: 36, Pages: 1-14, ISSN: 0935-9648Semiconducting polymer nanoparticles (SPNs) are explored for applications in cancer theranostics because of their high absorption coefficients, photostability, and biocompatibility. However, SPNs are susceptible to aggregation and protein fouling in physiological conditions, which can be detrimental for in vivo applications. Here, a method for achieving colloidally stable and low-fouling SPNs is described by grafting poly(ethylene glycol) (PEG) onto the backbone of the fluorescent semiconducting polymer, poly(9,9′-dioctylfluorene-5-fluoro-2,1,3-benzothiadiazole), in a simple one-step substitution reaction, postpolymerization. Further, by utilizing azide-functionalized PEG, anti-human epidermal growth factor receptor 2 (HER2) antibodies, antibody fragments, or affibodies are site-specifically “clicked” onto the SPN surface, which allows the functionalized SPNs to specifically target HER2-positive cancer cells. In vivo, the PEGylated SPNs are found to have excellent circulation efficiencies in zebrafish embryos for up to seven days postinjection. SPNs functionalized with affibodies are then shown to be able to target HER2 expressing cancer cells in a zebrafish xenograft model. The covalent PEGylated SPN system described herein shows great potential for cancer theranostics.
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Journal articleNguyen H-TT, Zhao M, Wang T, et al., 2024,
Sea anemone-anemonefish symbiosis: Behavior and mucous protein profiling
, JOURNAL OF FISH BIOLOGY, ISSN: 0022-1112 -
Journal articleMiao A, Luo T, Hsieh B, et al., 2024,
Brain clearance is reduced during sleep and anesthesia
, Nature Neuroscience, Vol: 27, Pages: 1046-1050, ISSN: 1097-6256It 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.
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Journal articleChia K-S, Kourelis J, Teulet A, et al., 2024,
The N-terminal domains of NLR immune receptors exhibit structural and functional similarities across divergent plant lineages
, PLANT CELL, Vol: 36, Pages: 2491-2511, ISSN: 1040-4651 -
Journal articlePirzio-Biroli A, Crowley SL, Siriwardena GM, et al., 2024,
Not in the countryside please! Investigating UK residents’ perceptions of an introduced species, the ring-necked parakeet (Psittacula krameri)
, NeoBiota, Vol: 93, Pages: 1-24, ISSN: 1314-2488Wildlife management can generate social conflict when stakeholder perceptions of the target species are not considered. Introduced Ring-necked Parakeets (RNP) are established in the UK and have been added to the ‘general licence’ of birds that can be killed to prevent serious economic damage. We aimed to better understand perceptions of RNPs on a nationwide scale to inform mitigation actions for potential future conflict over RNP management. We surveyed 3,947 UK residents to understand awareness of, knowledge of and attitudes towards the RNP across the UK.We found that most respondents (90.2%) were aware of the RNP. Almost half of respondents (45.9%) held negative opinions, particularly against the RNP in rural areas (64.7%), suggesting landscape contexts influence attitudes. Respondent preference for the RNP was low in local neighbourhoods (7.80%) although the species was considered aesthetically pleasing by most (83.0%). Many respondents knew the species’ name (54.9%), but underestimated current population numbers in the UK (82.6%) and few knew its full native range (10.0%). We identified respondents’ ecological interest, age, education, preference for, awareness of and knowledge of the RNP as significant factors associated with perceptions.Our findings suggest that the RNP presents a complex socio-environmental challenge, with respondent awareness, knowledge and attitudes each forming an important component of perceptions towards this species. We recommend that wildlife managers utilise our findings and cohesive approach to enhance future RNP perception research in the UK and abroad and towards the success of any proposed management initiatives under the UK general licence.
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Journal articleLo E, Nie R-E, Vogler AP, 2024,
The geographic and phylogenetic structure of public DNA barcode databases: an assessment using Chrysomelidae (leaf beetles)
, FRONTIERS IN ECOLOGY AND EVOLUTION, Vol: 12, ISSN: 2296-701X -
Journal articleCoatsworth P, Cotur Y, Asfour T, et al., 2024,
Plant-on-a-chip: continuous, soilless electrochemical monitoring of salt uptake and tolerance among different genotypes of tomato
, Sensors & Diagnostics, Vol: 3, Pages: 799-808, ISSN: 2635-0998Tomatoes (Solanum lycopersicum), a high-value crop, exhibit a unique relationship with salt, where increased levels of NaCl can enhance flavor, aroma and nutritional quality but can cause oxidative damage and reduce yields. A drive for larger, better-looking tomatoes has reduced the importance of salt sensitivity, a concern considering that the sodium content of agricultural land is increasing over time. Currently, there are no simple ways of comparing salt tolerance between plants, where a holistic approach looking at [Na+] throughout the plant typically involves destructive, single time point measurements or expensive imaging techniques. Finding methods that collect rapid information in real time could improve the understanding of salt resistance in the field. Here we investigate the uptake of NaCl by tomatoes using TETRIS (Time-resolved Electrochemical Technology for plant Root environment In situ chemical Sensing), a platform used to measure chemical signals in the root area of living plants. Low-cost, screen-printed electrochemical sensors were used to measure changes in salt concentration via electrical impedance measurements, facilitating the monitoring of the uptake of ions by roots. We not only demonstrated differences in the rate of uptake of NaCl between tomato seedlings under different growth conditions, but also showed differences in uptake between varieties of tomato with different NaCl sensitivities and the relatively salt-resistant “wild tomato” (Solanum pimpinellifolium) sister species. Our results suggest that TETRIS could be used to ascertain physiological traits of salt resistance found in adult plants but at the seedling stage of growth. This extrapolation, and the possibility to multiplex and change sensor configuration, could enable high-throughput screening of many hundreds or thousands of mutants or varieties.
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Journal articleCorti R, Piazza E, Armelloni EN, et al., 2024,
A multidisciplinary approach to describe population structure of <i>Solea solea</i> in the Mediterranean Sea
, FRONTIERS IN MARINE SCIENCE, Vol: 11 -
Journal articleLewis-Brown E, Jennings N, Mills M, et 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: 1469-3062The 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
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