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  • Journal article
    Kenna D, Graystock P, Gill R, 2023,

    Toxic temperatures: bee behaviours exhibit divergent pesticide toxicity relationships with warming

    , Global Change Biology, Vol: 29, Pages: 2981-2998, ISSN: 1354-1013

    Climate change and agricultural intensification are exposing insect pollinators to temperature extremes and increasing pesticide usage. Yet, we lack good quantification of how temperature modulates the sublethal effects of pesticides on behaviours vital for fitness and pollination performance. Consequently, we are uncertain if warming decreases or increases the severity of different pesticide impacts, and whether separate behaviours vary in the direction of response. Quantifying these interactive effects is vital in forecasting pesticide risk across climate regions and informing pesticide application strategies and pollinator conservation. This multi-stressor study investigated the responses of six functional behaviours of bumblebees when exposed to either a neonicotinoid (imidacloprid) or a sulfoximine (sulfoxaflor) across a standardised low, mid, and high temperature. We found the neonicotinoid had a significant effect on five of the six behaviours, with a greater effect at the lower temperature(s) when measuring responsiveness, the likelihood of movement, walking rate, and food consumption rate. In contrast, the neonicotinoid had a greater impact on flight distance at the higher temperature. Our findings show that different organismal functions can exhibit divergent thermal responses, with some pesticide-affected behaviours showing greater impact as temperatures dropped, and others as temperatures rose. We must therefore account for environmental context when determining pesticide risk. Moreover, we found evidence of synergistic effects, with just a 3°C increase causing a sudden drop in flight performance, despite seeing no effect of pesticide at the two lower temperatures. Our findings highlight the importance of multi-stressor studies to quantify threats to insects, which will help to improve dynamic evaluations of population tipping points and spatiotemporal risks to biodiversity across different climate regions.

  • Journal article
    Weeks TL, Betts MG, Pfeifer M, Wolf C, Banks-Leite C, Barbaro L, Barlow J, Cerezo A, Kennedy CM, Kormann UG, Marsh CJ, Olivier PI, Phalan BT, Possingham HP, Wood EM, Tobias JAet al., 2023,

    Climate-driven variation in dispersal ability predicts responses to forest fragmentation in birds

    , Nature Ecology and Evolution, Vol: 7, Pages: 1079-1091, ISSN: 2397-334X

    Species sensitivity to forest fragmentation varies latitudinally, peaking in the tropics. A prominent explanation for this pattern is that historical landscape disturbance at higher latitudes has removed fragmentation-sensitive species or promoted the evolution of more resilient survivors. However, it is unclear whether this so-called extinction filter is the dominant driver of geographic variation in fragmentation sensitivity, particularly because climatic factors may also cause latitudinal gradients in dispersal ability, a key trait mediating sensitivity to habitat fragmentation. Here we combine field survey data with a morphological proxy for avian dispersal ability (hand-wing index) to assess responses to forest fragmentation in 1,034 bird species worldwide. We find that fragmentation sensitivity is strongly predicted by dispersal limitation and that other factors—latitude, body mass and historical disturbance events—have relatively limited explanatory power after accounting for species differences in dispersal. We also show that variation in dispersal ability is only weakly predicted by historical disturbance and more strongly associated with intra-annual temperature fluctuations (seasonality). Our results suggest that climatic factors play a dominant role in driving global variation in the impacts of forest fragmentation, emphasizing the need for more nuanced environmental policies that take into account local context and associated species traits.

  • Journal article
    Baier F, Gauye F, Perez-Carrasco R, Payne JL, Schaerli Yet al., 2023,

    Environment-dependent epistasis increases phenotypic diversity in gene regulatory networks

    , SCIENCE ADVANCES, Vol: 9, ISSN: 2375-2548
  • Journal article
    Winterhalter C, Pelliciari S, Stevens D, Fenyk S, Marchand E, Cronin NB, Soultanas P, Costa TRD, Ilangovan A, Murray Het al., 2023,

    The DNA replication initiation protein DnaD recognises a specific strand of the Bacillus subtilis chromosome origin

    , Nucleic Acids Research, Vol: 51, Pages: 4322-4340, ISSN: 0305-1048

    Genome replication is a fundamental biological activity shared by all organisms. Chromosomal replication proceeds bidirectionally from origins, requiring the loading of two helicases, one for each replisome. However, the molecular mechanisms underpinning helicase loading at bacterial chromosome origins (oriC) are unclear. Here we investigated the essential DNA replication initiation protein DnaD in the model organism Bacillus subtilis. A set of DnaD residues required for ssDNA binding was identified, and photo-crosslinking revealed that this ssDNA binding region interacts preferentially with one strand of oriC. Biochemical and genetic data support the model that DnaD recognizes a new single-stranded DNA (ssDNA) motif located in oriC, the DnaD Recognition Element (DRE). Considered with single particle cryo-electron microscopy (cryo-EM) imaging of DnaD, we propose that the location of the DRE within oriC orchestrates strand-specific recruitment of helicase during DNA replication initiation. These findings significantly advance our mechanistic understanding of bidirectional replication from a bacterial chromosome origin.

  • Journal article
    Malik A, Sayed AA, Han P, Tan MMH, Watt E, Constantinescu-Bercu A, Cocker ATH, Khoder A, Saputil RC, Thorley EV, Teklemichael A, Ding Y, Hart ACJ, Zhang H, Mitchell WA, Imami N, Crawley JTB, Salles-Crawley II, Bussel JB, Zehnder JL, Adams SP, Zhang BM, Cooper Net al., 2023,

    The role of CD8+ T cell clones in immune thrombocytopenia

    , Blood, Vol: 141, Pages: 2417-2429, ISSN: 0006-4971

    Immune thrombocytopenia (ITP) is traditionally considered an antibody-mediated disease. However, a number of features suggest alternative mechanisms of platelet destruction. In this study, we use a multi-dimensional approach to explore the role of cytotoxic CD8+ T cells in ITP. We characterised patients with ITP and compared them to age-matched controls using immunophenotyping, next-generation sequencing of T cell receptor (TCR) genes, single-cell RNA sequencing, and functional T cell and platelet assays. We found that adults with chronic ITP have increased polyfunctional, terminally differentiated effector memory CD8+ T cells (CD45RA+CD62L-) expressing intracellular interferon-g, tumour necrosis factor-a, and Granzyme B defining them as TEMRA cells. These TEMRA cells expand when the platelet count falls and show no evidence of physiological exhaustion. Deep sequencing of the T cell receptor showed expanded T cell clones in patients with ITP. T cell clones persisted over many years, were more prominent in patients with refractory disease, and expanded when the platelet count was low. Combined single-cell RNA and TCR sequencing of CD8+ T cells confirmed that the expanded clones are TEMRA cells. Using in vitro model systems, we show that CD8+ T cells from patients with ITP form aggregates with autologous platelets, release interferon-g and trigger platelet activation and apoptosis through TCR-mediated release of cytotoxic granules. These findings of clonally expanded CD8+ T cells causing platelet activation and apoptosis provide an antibody-independent mechanism of platelet destruction, indicating that targeting specific T-cell clones could be a novel therapeutic approach for patients with refractory ITP.

  • Journal article
    Abubakkar-Waziri H, Kalaiarasan G, Wawman R, Hobbs F, Adcock I, Dilliway C, Fang F, Pain C, Porter A, Bhavsar PK, Ransome E, Savolainen V, Kumar P, Chung KFet al., 2023,

    SARS-CoV2 in public spaces in West London UK during COVID-19 pandemic

    , BMJ Open Respiratory Research, Vol: 10, ISSN: 2052-4439

    Background: Spread of SARS-CoV2 by aerosol is considered an important mode of transmission over distances >2 m, particularly indoors.Objectives: We determined whether SARS-CoV2 could be detected in the air of enclosed/semi-enclosed public spaces.Methods and analysis: Between March 2021 and December 2021 during the easing of COVID-19 pandemic restrictions after a period of lockdown, we used total suspended and size-segregated particulate matter (PM) samplers for the detection of SARS-CoV2 in hospitals wards and waiting areas, on public transport, in a university campus and in a primary school in West London.Results: We collected 207 samples, of which 20 (9.7%) were positive for SARS-CoV2 using quantitative PCR. Positive samples were collected from hospital patient waiting areas, from hospital wards treating patients with COVID-19 using stationary samplers and from train carriages in London underground using personal samplers. Mean virus concentrations varied between 429 500 copies/m3 in the hospital emergency waiting area and the more frequent 164 000 copies/m3 found in other areas. There were more frequent positive samples from PM samplers in the PM2.5 fractions compared with PM10 and PM1. Culture on Vero cells of all collected samples gave negative results.Conclusion: During a period of partial opening during the COVID-19 pandemic in London, we detected SARS-CoV2 RNA in the air of hospital waiting areas and wards and of London Underground train carriage. More research is needed to determine the transmission potential of SARS-CoV2 detected in the air.

  • Report
    Kirkpatrick L, Adjiman C, ApSimon H, Berry A, de Nazelle A, Mijic A, Myers R, Woodward G, Workman Met al., 2023,

    Systems thinking for the transition to zero pollution

    , Systems thinking for the transition to zero pollution, www.imperial.ac.uk/grantham, Publisher: Grantham Institute, 40

    Systems approaches are vital for coordinating decision-making in the face of complex issues because they provide the whole picture view needed to avoid negative unintended consequences and to generate genuine benefits. This paper explains how systems thinking can be used to address environmental pollution and support decision-makers in finding solutions.

  • Journal article
    Terlau JF, Brose U, Boy T, Pawar S, Pinsky M, Hirt MRet al., 2023,

    Predicting movement speed of beetles from body size and temperature

    , MOVEMENT ECOLOGY, Vol: 11, ISSN: 2051-3933
  • Journal article
    Alexander J, Posma J, Scott A, Poynter L, Mason S, Herendi L, Roberts L, McDonald J, Cameron S, Darzi A, Goldin R, Takats Z, Marchesi J, Teare J, Kinross Jet al., 2023,

    Pathobionts in the tumour microbiota predict survival following resection for colorectal cancer

    , Microbiome, Vol: 11, Pages: 1-14, ISSN: 2049-2618

    Background and aimsThe gut microbiota is implicated in the pathogenesis of colorectal cancer (CRC). We aimed to map the CRC mucosal microbiota and metabolome and define the influence of the tumoral microbiota on oncological outcomes.MethodsA multicentre, prospective observational study was conducted of CRC patients undergoing primary surgical resection in the UK (n = 74) and Czech Republic (n = 61). Analysis was performed using metataxonomics, ultra-performance liquid chromatography-mass spectrometry (UPLC-MS), targeted bacterial qPCR and tumour exome sequencing. Hierarchical clustering accounting for clinical and oncological covariates was performed to identify clusters of bacteria and metabolites linked to CRC. Cox proportional hazards regression was used to ascertain clusters associated with disease-free survival over median follow-up of 50 months.ResultsThirteen mucosal microbiota clusters were identified, of which five were significantly different between tumour and paired normal mucosa. Cluster 7, containing the pathobionts Fusobacterium nucleatum and Granulicatella adiacens, was strongly associated with CRC (PFDR = 0.0002). Additionally, tumoral dominance of cluster 7 independently predicted favourable disease-free survival (adjusted p = 0.031). Cluster 1, containing Faecalibacterium prausnitzii and Ruminococcus gnavus, was negatively associated with cancer (PFDR = 0.0009), and abundance was independently predictive of worse disease-free survival (adjusted p = 0.0009). UPLC-MS analysis revealed two major metabolic (Met) clusters. Met 1, composed of medium chain (MCFA), long-chain (LCFA) and very long-chain (VLCFA) fatty acid species, ceramides and lysophospholipids, was negatively associated with CRC (PFDR = 2.61 × 10−11); Met 2, composed of phosphatidylcholine species, nucleosides and amino acids, was strongly associated with CRC (PFDR&

  • Journal article
    Lopez-Romero FA, Stumpf S, Kamminga P, Boehmer C, Pradel A, Brazeau MD, Kriwet Jet al., 2023,

    Shark mandible evolution reveals patterns of trophic and habitat-mediated diversification

    , Communications Biology, Vol: 6, ISSN: 2399-3642

    Environmental controls of species diversity represent a central research focus in evolutionary biology. In the marine realm, sharks are widely distributed, occupying mainly higher trophic levels and varied dietary preferences, mirrored by several morphological traits and behaviours. Recent comparative phylogenetic studies revealed that sharks present a fairly uneven diversification across habitats, from reefs to deep-water. We show preliminary evidence that morphological diversification (disparity) in the feeding system (mandibles) follows these patterns, and we tested hypotheses linking these patterns to morphological specialisation. We conducted a 3D geometric morphometric analysis and phylogenetic comparative methods on 145 specimens representing 90 extant shark species using computed tomography models. We explored how rates of morphological evolution in the jaw correlate with habitat, size, diet, trophic level, and taxonomic order. Our findings show a relationship between disparity and environment, with higher rates of morphological evolution in reef and deep-water habitats. Deep-water species display highly divergent morphologies compared to other sharks. Strikingly, evolutionary rates of jaw disparity are associated with diversification in deep water, but not in reefs. The environmental heterogeneity of the offshore water column exposes the importance of this parameter as a driver of diversification at least in the early part of clade history.

  • Journal article
    Sethi S, Ewers RM, Balakrishnan R, 2023,

    Ecology: correct the digital data divide

    , NATURE, Vol: 617, Pages: 35-35, ISSN: 0028-0836
  • Journal article
    Contreras MP, Pai H, Selvaraj M, Toghani A, Lawson DM, Tumtas Y, Duggan C, Yuen ELH, Stevenson CEM, Harant A, Maqbool A, Wu C-H, Bozkurt TO, Kamoun S, Derevnina Let al., 2023,

    Resurrection of plant disease resistance proteins via helper NLR bioengineering

    , SCIENCE ADVANCES, Vol: 9, ISSN: 2375-2548
  • Journal article
    Hailu E, Cantillon D, Madrazo C, Rose G, Wheeler PR, Golby P, Adnew B, Gagneux S, Aseffa A, V Gordon S, Comas I, Young DB, Waddell SJ, Larrouy-Maumus G, Berg Set al., 2023,

    Lack of methoxy- mycolates characterizes the geographically restricted lineage 7 of<i> Mycobacterium</i><i> tuberculosis</i> complex

    , MICROBIAL GENOMICS, Vol: 9, ISSN: 2057-5858
  • Conference paper
    Alexander JL, Posma JM, Scott A, Poynter L, Mason S, Doria L, Roberts L, McDonald JA, Cameron S, Hughes D, Liska V, Susova S, Soucek P, Horneffer V, Gomez-Romero M, Herendi L, Lewis M, Hoyles L, Woolston A, Cunningham D, Darzi A, Gerlinger M, Goldin R, Takats Z, Marchesi J, Teare JP, Kinross JMet al., 2023,

    NETWORKS OF PATHOBIONTS IN THE TUMOUR MUCOSAL NICHE PREDICT SURVIVAL FOLLOWING COLORECTAL CANCER RESECTION

    , Digestive Disease Week (DDW), Publisher: W B SAUNDERS CO-ELSEVIER INC, Pages: S469-S470, ISSN: 0016-5085
  • Journal article
    Osborne OG, Dobreva MP, Papadopulos AST, de Moura MSB, Brunello AT, de Queiroz LP, Pennington RT, Lloyd J, Savolainen Vet al., 2023,

    Mapping the root systems of individual trees in a natural community using genotyping-by-sequencing

    , New Phytologist, Vol: 238, Pages: 1305-1317, ISSN: 0028-646X

    •The architecture of root systems is an important driver of plant fitness, competition and ecosystem processes. However, the methodological difficulty of mapping roots hampers the study of these processes. Existing approaches to match individual plants to belowground samples are low throughput and species specific. Here, we developed a scalable sequencing-based method to map the root systems of individual trees across multiple species. We successfully applied it to a tropical dry forest community in the Brazilian Caatinga containing 14 species. • We sequenced all 42 individual shrubs and trees in a 14 × 14 m plot using double-digest restriction site-associated sequencing (ddRADseq). We identified species-specific markers and individual-specific haplotypes from the data. We matched these markers to the ddRADseq data from 100 mixed root samples from across the centre (10 × 10 m) of the plot at four different depths using a newly developed R package. • We identified individual root samples for all species and all but one individual. There was a strong significant correlation between belowground and aboveground size measurements, and we also detected significant species-level root-depth preference for two species. • The method is more scalable and less labour intensive than the current techniques and is broadly applicable to ecology, forestry and agricultural biology.

  • Journal article
    Avendano R, Munoz-Montero S, Rojas-Gatjens D, Fuentes-Schweizer P, Vieto S, Montenegro R, Salvador M, Frew R, Kim J, Chavarria M, Jimenez JIIet al., 2023,

    Production of selenium nanoparticles occurs throughan interconnected pathway of sulphur metabolism andoxidative stress response in Pseudomonas putida KT2440

    , Microbial Biotechnology, Vol: 16, Pages: 931-946, ISSN: 1751-7907

    The soil bacterium Pseudomonas putida KT2440 has been shown to produce selenium nanoparticles aerobically from selenite; however, the molecular actors involved in this process are unknown. Here, through a combination of genetic and analytical techniques, we report the first insights into selenite metabolism in this bacterium. Our results suggest that the reduction of selenite occurs through an interconnected metabolic network involving central metabolic reactions, sulphur metabolism, and the response to oxidative stress. Genes such as sucA, D2HGDH and PP_3148 revealed that the 2-ketoglutarate and glutamate metabolism is important to convert selenite into selenium. On the other hand, mutations affecting the activity of the sulphite reductase decreased the bacteria's ability to transform selenite. Other genes related to sulphur metabolism (ssuEF, sfnCE, sqrR, sqr and pdo2) and stress response (gqr, lsfA, ahpCF and sadI) were also identified as involved in selenite transformation. Interestingly, suppression of genes sqrR, sqr and pdo2 resulted in the production of selenium nanoparticles at a higher rate than the wild-type strain, which is of biotechnological interest. The data provided in this study brings us closer to understanding the metabolism of selenium in bacteria and offers new targets for the development of biotechnological tools for the production of selenium nanoparticles.

  • Journal article
    Dvorak P, Galvao TC, Pflueger-Grau K, Banks AM, de Lorenzo V, Jimenez JIet al., 2023,

    Water potential governs the effector specificity of the transcriptional regulator XylR of Pseudomonas putida

    , Environmental Microbiology, Vol: 25, Pages: 1041-1054, ISSN: 1462-2912

    The biodegradative capacity of bacteria in their natural habitats is affected by water availability. In this work, we have examined the activity and effector specificity of the transcriptional regulator XylR of the TOL plasmid pWW0 of Pseudomonas putida mt-2 for biodegradation of m-xylene when external water potential was manipulated with polyethylene glycol PEG8000. By using non-disruptive luxCDEAB reporter technology, we noticed that the promoter activated by XylR (Pu) restricted its activity and the regulator became more effector-specific towards head TOL substrates when cells were grown under water subsaturation. Such a tight specificity brought about by water limitation was relaxed when intracellular osmotic stress was counteracted by the external addition of the compatible solute glycine betaine. With these facts in hand, XylR variants isolated earlier as effector-specificity responders to the non-substrate 1,2,4-trichlorobenzene under high matric stress were re-examined and found to be unaffected by water potential in vivo. All these phenomena could be ultimately explained as the result of water potential-dependent conformational changes in the A domain of XylR and its effector-binding pocket, as suggested by AlphaFold prediction of protein structures. The consequences of this scenario for the evolution of specificities in regulators and the emergence of catabolic pathways are discussed.

  • Journal article
    Oliver T, Kim TD, Trinugroho JP, Cordon-Preciado V, Wijayatilake N, Bhatia A, Rutherford AW, Cardona Londono Tet al., 2023,

    The evolution and evolvability of photosystem II

    , Annual Review of Plant Biology, Vol: 74, ISSN: 1040-2519

    Photosystem II is the water-oxidizing and O2 -evolving enzyme of photosynthesis. How and when this remarkable enzyme arose are fundamental questions in the history of life that have remained difficult to answer. Here, recent advances in our understanding of the origin andevolution of photosystem II are reviewed and discussed in detail. The evolution of photosystem II indicates that water oxidation originated early in the history of life, long before the diversification of cyanobacteria and other major groups of prokaryotes, challenging and transforming current paradigms on the evolution of photosynthesis. We show that photosystem II has remained virtually unchanged for well over three billion years, and yet the nonstop duplication process of the D1 subunit of photosystem II, which controls photochemistry and catalysis, has enabled the enzyme to become adaptable to variable environmental conditions, and even to innovate enzymatic functions beyond water oxidation. It is suggested that this evolvability can be exploited to develop novel light-powered enzymes with the capacity to carry out complex multi-step oxidative transformations for sustainable biocatalysis.

  • Patent
    Kourelis J, Marchal C, Kamoun S, 2023,

    MODIFYING THE IMMUNE RESPONSE IN PLANTS

    , EP4170039A1

    Chimeric proteins comprising a binding molecule, preferably a single chain antibody, linked to a plant immune receptor protein, are disclosed.

  • Journal article
    Huang Z, Lai PF, Cocker ATH, Haslam SM, Dell A, Brady HJM, Johnson MRet al., 2023,

    Roles of N-linked glycosylation and glycan-binding proteins in placentation: trophoblast infiltration, immunomodulation, angiogenesis, and pathophysiology

    , Biochemical Society Transactions, Vol: 51, Pages: 639-653, ISSN: 0300-5127

    Protein N-linked glycosylation is a structurally diverse post-translational modification that stores biological information in a larger order of magnitude than other post-translational modifications such as phosphorylation, ubiquitination and acetylation. This gives N-glycosylated proteins a diverse range of properties and allows glyco-codes (glycan-related information) to be deciphered by glycan-binding proteins (GBPs). The intervillous space of the placenta is richly populated with membrane-bound and secreted glycoproteins. Evidence exists to suggest that altering the structural nature of their N-glycans can impact several trophoblast functions, which include those related to interactions with decidual cells. This review summarizes trophoblast-related activities influenced by N-glycan-GBP recognition, exploring how different subtypes of trophoblasts actively adapt to characteristics of the decidualized endometrium through cell-specific expression of N-glycosylated proteins, and how these cells receive decidua-derived signals via N-glycan-GBP interactions. We highlight work on how changes in N-glycosylation relates to the success of trophoblast infiltration, interactions of immunomodulators, and uterine angiogenesis. We also discuss studies that suggest aberrant N-glycosylation of trophoblasts may contribute to the pathogenesis of pregnancy complications (e.g. pre-eclampsia, early spontaneous miscarriages and hydatidiform mole). We propose that a more in-depth understanding of how N-glycosylation shapes trophoblast phenotype during early pregnancy has the potential to improve our approach to predicting, diagnosing and alleviating poor maternal/fetal outcomes associated with placental dysfunction.

  • Journal article
    Cornford R, Spooner F, McRae L, Purvis A, Freeman Ret al., 2023,

    Ongoing over-exploitation and delayed responses to environmental change highlight the urgency for action to promote vertebrate recoveries by 2030

    , PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 290, ISSN: 0962-8452
  • Journal article
    Low WW, Seddon C, Beis K, Frankel Get al., 2023,

    The Interaction of the F-Like Plasmid-Encoded TraN Isoforms with Their Cognate Outer Membrane Receptors

    , JOURNAL OF BACTERIOLOGY, Vol: 205, ISSN: 0021-9193
  • Journal article
    Chen T, Hojka M, Davey P, Sun Y, Dykes GF, Zhou F, Lawson T, Nixon PJ, Lin Y, Liu L-Net al., 2023,

    Engineering α-carboxysomes into chloroplasts to support autotrophic photosynthesis

    , Nature Communications, ISSN: 2041-1723
  • Journal article
    Shen Y, Cai W, Prentice IC, Harrison SPet al., 2023,

    Community abundance of resprouting in woody plants reflects fire return time, intensity, and type

    , Forests, Vol: 14, Pages: 1-13, ISSN: 1999-4907

    Plants in fire-prone ecosystems have evolved a variety of mechanisms to resist or adapt to fire. Post-fire resprouting is a key adaptation that promotes rapid ecosystem recovery and hence has a major impact on the terrestrial carbon cycle. However, our understanding of how the incidence of resprouting varies in different fire regimes is largely qualitative. The increasing availability of plant trait data and plot-based species cover data provides an opportunity to quantify the relationships between fire-related traits and fire properties. We investigated the quantitative relationship between fire frequency (expressed as the fire return time) and the proportion of resprouters in woody plants using plot data on species cover from Australia and Europe. We also examined the relationship between the proportion of resprouters and gross primary production (GPP) and grass cover, where GPP was assumed to reflect fuel loads and hence fire intensity, while grass cover was considered to be an indicator of the likelihood of ground fire and the speed of fire spread, using generalised linear modelling. The proportion of resprouting species decreased significantly as the fire return time increased. When the fire return time was considered along with other aspects of the fire regime, the proportion of resprouters had significant negative relationships with the fire return time and grass cover and a significant positive relationship with GPP. These findings demonstrate that plants with the ability to resprout occur more often where fire regimes are characterised by high-frequency and high-intensity crown fires. Establishing quantitative relationships between the incidence of resprouting and the fire return time and fire type provides a basis for modelling resprouting as a consequence of the characteristics of the fire regime, which in turn makes it possible to model the consequences of changing fire regimes on ecosystem properties.

  • Journal article
    van Thor JJ, Champion PM, 2023,

    Photoacid dynamics in the green fluorescent protein

    , Annual Review of Physical Chemistry, Vol: 74, Pages: 1-22, ISSN: 0066-426X

    The photoacid dynamics of fluorescent proteins include both electronic excited- and ground-state mechanisms of proton transfer. The associated characteristic timescales of these reactions range over many orders of magnitude, and the tunneling, barrier crossing, and relevant thermodynamics have in certain cases been linked to coherent nuclear motion. We review the literature and summarize the experiments and theory that demonstrate proton tunneling in the electronic ground state of the green fluorescent protein (GFP). We also discuss the excited-state proton-transfer reaction of GFP that takes place on the picosecond timescale. Although this reaction has been investigated using several vibrational spectroscopic methods, the interpretation remains unsettled. We discuss recent advances as well as remaining questions, in particular those related to the vibrational mode couplings that involve low-frequency modulations of chromophore vibrations on the timescale of proton transfer.

  • Journal article
    Ghani L, Zhang X, Munk CF, Hariharan P, Lan B, Yun HS, Byrne B, Guan L, Loland CJ, Liu X, Chae PSet al., 2023,

    Tris(hydroxymethyl)aminomethane linker-bearing triazine-based triglucosides for solubilization and stabilization of membrane proteins

    , Bioconjugate Chemistry, Vol: 34, Pages: 739-747, ISSN: 1043-1802

    High-resolution membrane protein structures are essential for a fundamental understanding of the molecular basis of diverse cellular processes and for drug discovery. Detergents are widely used to extract membrane-spanning proteins from membranes and maintain them in a functional state for downstream characterization. Due to limited long-term stability of membrane proteins encapsulated in conventional detergents, development of novel agents is required to facilitate membrane protein structural study. In the current study, we designed and synthesized tris(hydroxymethyl)aminomethane linker-bearing triazine-based triglucosides (TTGs) for solubilization and stabilization of membrane proteins. When these glucoside detergents were evaluated for four membrane proteins including two G protein-coupled receptors, a few TTGs including TTG-C10 and TTG-C11 displayed markedly enhanced behaviors toward membrane protein stability relative to two maltoside detergents [DDM (n-dodecyl-β-d-maltoside) and LMNG (lauryl maltose neopentyl glycol)]. This is a notable feature of the TTGs as glucoside detergents tend to be inferior to maltoside detergents at stabilizing membrane proteins. The favorable behavior of the TTGs for membrane protein stability is likely due to the high hydrophobicity of the lipophilic groups, an optimal range of hydrophilic–lipophilic balance, and the absence of cis–trans isomerism.

  • Journal article
    Larrouy-Maumus G, 2023,

    A whole cell-based Matrix-assisted laser desorption/ionization mass spectrometry lipidomic assay for the discovery of compounds that target lipid a modifications

    , Frontiers in Microbiology, Vol: 14, Pages: 1-7, ISSN: 1664-302X

    Introduction: Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is a powerful analytical technique that has been applied to a wide variety of applications ranging from proteomics to clinical diagnostics. One such application is its use as a tool for discovery assays, such as monitoring the inhibition of purified proteins. With the global threat from antimicrobial-resistant (AMR) bacteria, new and innovative solutions are required to identify new molecules that could revert bacterial resistance and/or target virulence factors. Here, we used a whole cell-based MALDI-TOF lipidomic assay using a routine MALDI Biotyper Sirius system operating in linear negative ion mode combined with the MBT Lipid Xtract kit to discover molecules targeting bacteria that are resistant to polymyxins, which are considered last-resort antibiotics.Methods: A library of 1200 natural compounds was tested against an E. coli strain expressing mcr-1, which is known to modify lipid A by adding phosphoethanolamine (pETN), making the strain resistant to colistin.Results and Discussion: Using this approach, we identified 8 compounds that led to a decrease in this lipid A modification by MCR-1 and could potentially be employed to revert resistance. Taken together, as-proof-of-principle, the data we report here represent a new workflow based on the analysis of bacterial lipid A by routine MALDI-TOF for the discovery of inhibitors that could target bacterial viability and/or virulence.

  • Journal article
    Mielcarek M, Isalan M, 2023,

    A minimal region of the HSP90AB1 promoter is suitable for ubiquitous expression in different somatic tissues with applicability for gene therapy

    , Frontiers in Molecular Biosciences, Vol: 10, ISSN: 2296-889X

    Huntington’s disease (HD) is a multi-tissue failure disorder for which there is no cure. We have previously shown an effective therapeutic approach limited mainly to the central nervous system, based on a synthetic zinc finger (ZF) transcription repressor gene therapy, but it would be important to target other tissues as well. In this study, we identify a novel minimal HSP90AB1 promoter region that can efficiently control expression not only in the CNS but also in other affected HD tissues. This promoter-enhancer is effective in driving expression of ZF therapeutic molecules in both HD skeletal muscles and the heart, in the symptomatic R6/1 mouse model. Moreover, for the first time we show that ZF molecules repressing mutant HTT reverse transcriptional pathological remodelling in HD hearts. We conclude that this HSP90AB1 minimal promoter may be used to target multiple HD organs with therapeutic genes. The new promoter has the potential to be added to the portfolio of gene therapy promoters, for use where ubiquitous expression is needed.

  • Journal article
    Liu D, Semenchuk P, Essl F, Lenzner B, Moser D, Blackburn TM, Cassey P, Biancolini D, Capinha C, Dawson W, Dyer EE, Guenard B, Economo EP, Kreft H, Pergl J, Pysek P, van Kleunen M, Nentwig W, Rondinini C, Seebens H, Weigelt P, Winter M, Purvis A, Dullinger Set al., 2023,

    The impact of land use on non-native species incidence and number in local assemblages worldwide

    , NATURE COMMUNICATIONS, Vol: 14
  • Journal article
    Santini L, Tobias JA, Callaghan C, Gallego-Zamorano J, Benitez-Lopez Aet al., 2023,

    Global patterns and predictors of avian population density

    , GLOBAL ECOLOGY AND BIOGEOGRAPHY, ISSN: 1466-822X

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