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Journal articleBermúdez-Puga S, Dias M, Lima Reis I, et al., 2024,
Microscopic and metabolomics analysis of the anti-Listeria activity of natural and engineered cruzioseptins.
, Biochimie, Vol: 225, Pages: 168-175Listeria monocytogenes is a human opportunistic foodborne pathogen that produces life-threatening infections with a high mortality rate. The control of Listeria in the food production environment and effective clinical management of human listeriosis are challenging due to the emergence of antibiotic resistance. Hence we evaluate the in vitro anti-Listeria activity of two synthetic cruzioseptins reproducing their natural sequences CZS-9, and CZS-12, and one engineered sequence based on CZS-1, named [K4K15]CZS-1. The assessment of the in vitro potential of cruzioseptins, highlighted the promising antibacterial effect of [K4K15]CZS-1 in very low concentrations (0.91 μM) and its thermal stability at high-temperature conditions, is compatible with the food industry. Microscopic and metabolomic analyses suggest cruzioseptin induces anti-Listeria bioactivity through membrane disruption and changes in the intracellular metabolome. We also report that [K4K15]CZS-1 is not resistant to peptidases/proteases emphasizing a key advantage for their use as a food preservative. However, there is a need for further structural and functional optimisations for the potential clinical application as an antibiotic. In conclusion, [K4K15]CZS-1 stand out as membrane-active peptides with the ability to induce shifts in the bacteria metabolome and inspire the development of strategies for the prevention of L. monocytogenes emergence and dissemination.
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Journal articleLiu Y, Murphy K, Fernandes N, et al., 2024,
Transition metal homeostasis is key to metabolism and drug tolerance of Mycobacterium abscessus
, npj Antimicrobials and Resistance, Vol: 2, ISSN: 2731-8745Antimicrobial resistance (AMR) is one of the major challenges humans are facing this century. Understanding the mechanisms behind the rise of AMR is therefore crucial to tackle this global threat. The presence of transition metals is one of the growth-limiting factors for both environmental and pathogenic bacteria, and the mechanisms that bacteria use to adapt to and survive under transition metal toxicity resemble those correlated with the rise of AMR. A deeper understanding of transition metal toxicity and their potential as antimicrobial agents will expand our knowledge of AMR and assist the development of therapeutic strategies. In this study, we investigate the antimicrobial effect of two transition metal ions, namely cobalt (Co2+) and nickel (Ni2+), on the non-tuberculous environmental mycobacterium and the opportunistic human pathogen Mycobacterium abscessus. The minimum inhibitory concentrations of Co2+ and Ni2+ on M. abscessus were first quantified and their impact on the bacterial intracellular metallome was investigated. A multi-omics strategy that combines transcriptomics, bioenergetics, metabolomics and phenotypic assays was designed to further investigate the mechanisms behind the effects of transition metals. We show that transition metals induced growth defect and changes in transcriptome and carbon metabolism in M. abscessus, while the induction of the glyoxylate shunt and the WhiB7 regulon in response to metal stresses could be the key response that led to higher AMR levels. Meanwhile, transition metal treatment alters the bacterial response to clinically relevant antibiotics, and enhance the uptake of clarithromycin into bacterial cells, leading to increased efficacy. This work provides insights into the tolerance mechanisms of M. abscessus to transition metal toxicity and demonstrates the possibility of using transition metals to adjuvate the efficacy of currently using antimicrobials against M. abscessus infections.
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Journal articleColonna G, Feng S, Koh H, et al., 2024,
Outstanding Reviewers for <i>Molecular Omics</i> in 2023
, MOLECULAR OMICS, Vol: 20, Pages: 504-504 -
Journal articleFarah A, Patel R, Poplawski P, et al., 2024,
A role for leucine-rich, glioma inactivated 1 in regulating pain sensitivity
, Brain, ISSN: 0006-8950<jats:title>Abstract</jats:title> <jats:p>Neuronal hyperexcitability is a key driver of persistent pain states, including neuropathic pain. Leucine-rich, glioma inactivated 1 (LGI1) is a secreted protein known to regulate excitability within the nervous system and is the target of autoantibodies from neuropathic pain patients. Therapies that block or reduce antibody levels are effective at relieving pain in these patients, suggesting that LGI1 has an important role in clinical pain.</jats:p> <jats:p>Here we have investigated the role of LGI1 in regulating neuronal excitability and pain-related sensitivity by studying the consequences of genetic ablation in specific neuron populations using transgenic mouse models.</jats:p> <jats:p>LGI1 has been well studied at the level of the brain, but its actions in the spinal cord and peripheral nervous system are poorly understood. We show that LGI1 is highly expressed in dorsal root ganglion (DRG) and spinal cord dorsal horn neurons in both mouse and human. Using transgenic mouse models, we genetically ablated LGI1, either specifically in nociceptors (LGI1fl/Nav1.8+) or in both DRG and spinal neurons (LGI1fl/Hoxb8+). On acute pain assays, we found that loss of LGI1 resulted in mild thermal and mechanical pain-related hypersensitivity when compared with littermate controls. In LGI1fl/Hoxb8+ mice, we found loss of Kv1 currents and hyperexcitability of DRG neurons. LGI1fl/Hoxb8+ mice displayed a significant increase in nocifensive behaviours in the second phase of the formalin test (not observed in LGI1fl/Nav1.8+ mice), and extracellular recordings in LGI1fl/Hoxb8+ mice revealed hyperexcitability in spinal dorsal horn neurons, including enhanced wind-up. Using the spared nerve injury model, we found that LGI1 expression was dysregulated in the spinal cord. LGI1fl/Nav1.8+ mice showed no differences in nerve injury-induced mechanical hypersensitivit
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Journal articleHutchison CDM, Perrett S, van Thor JJ, 2024,
XFEL beamline optical instrumentation for ultrafast science
, The Journal of Physical Chemistry B, Vol: 128, Pages: 8855-8868, ISSN: 1520-6106Free electron lasers operating in the soft and hard X-ray regime provide capabilities for ultrafast science in many areas, including X-ray spectroscopy, diffractive imaging, solution and material scattering, and X-ray crystallography. Ultrafast time-resolved applications in the picosecond, femtosecond, and attosecond regimes are often possible using single-shot experimental configurations. Aside from X-ray pump and X-ray probe measurements, all other types of ultrafast experiments require the synchronized operation of pulsed laser excitation for resonant or nonresonant pumping. This Perspective focuses on the opportunities for the optical control of structural dynamics by applying techniques from nonlinear spectroscopy to ultrafast X-ray experiments. This typically requires the synthesis of two or more optical pulses with full control of pulse and interpulse parameters. To this end, full characterization of the femtosecond optical pulses is also highly desirable. It has recently been shown that two-color and two-pulse femtosecond excitation of fluorescent protein crystals allowed a Tannor-Rice coherent control experiment, performed under characterized conditions. Pulse shaping and the ability to synthesize multicolor and multipulse conditions are highly desirable and would enable XFEL facilities to offer capabilities for structural dynamics. This Perspective will give a summary of examples of the types of experiments that could be achieved, and it will additionally summarize the laser, pulse shaping, and characterization that would be recommended as standard equipment for time-resolved XFEL beamlines, with an emphasis on ultrafast time-resolved serial femtosecond crystallography.
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Journal articleCrowther TW, Rappuoli R, Corinaldesi C, et al., 2024,
Scientists' call to action: Microbes, planetary health, and the Sustainable Development Goals
, CELL, Vol: 187, Pages: 5195-5216, ISSN: 0092-8674 -
Journal articleIsalan M, Armstrong A, 2024,
Engineering bacterial theranostics: from logic gates to in vivo applications
, Frontiers in Bioengineering and Biotechnology, Vol: 12, ISSN: 2296-4185Over the past two decades, rapid advances in synthetic biology have enabled the design of increasingly intricate and biologically relevant systems with broad applications in healthcare. A growing area of interest is in designing bacteria that sense and respond to endogenous diseaseassociated signals, creating engineered theranostics that function as disease surveyors for human health. In particular, engineered cells hold potential in facilitating greatly enhanced temporal and spatial control over the release of a range of therapeutics. Such systems are particularly useful for targeting challenging, under-drugged disease targets in a more nuanced manner than is currently possible. This review provides an overview of the recent advances in the design, delivery, and dynamics of bacterial theranostics to enable safe, robust, and genetically tractable therapies to treat disease. It outlines the primary challenges in theranostic clinical translation, proposes strategies to overcome these issues, and explores promising future avenues for the field.
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Journal articleKientega M, Clarkson CS, Traoré N, et al., 2024,
Whole-genome sequencing of major malaria vectors reveals the evolution of new insecticide resistance variants in a longitudinal study in Burkina Faso
, Malaria Journal, Vol: 23, ISSN: 1475-2875BACKGROUND: Intensive deployment of insecticide based malaria vector control tools resulted in the rapid evolution of phenotypes resistant to these chemicals. Understanding this process at the genomic level is important for the deployment of successful vector control interventions. Therefore, longitudinal sampling followed by whole genome sequencing (WGS) is necessary to understand how these evolutionary processes evolve over time. This study investigated the change in genetic structure and the evolution of the insecticide resistance variants in natural populations of Anopheles gambiae over time and space from 2012 to 2017 in Burkina Faso. METHODS: New genomic data have been generated from An. gambiae mosquitoes collected from three villages in the western part of Burkina Faso between 2012 and 2017. The samples were whole-genome sequenced and the data used in the An. gambiae 1000 genomes (Ag1000G) project as part of the Vector Observatory. Genomic data were analysed using the analysis pipeline previously designed by the Ag1000G project. RESULTS: The results showed similar and consistent nucleotide diversity and negative Tajima's D between An. gambiae sensu stricto (s.s.) and Anopheles coluzzii. Principal component analysis (PCA) and the fixation index (FST) showed a clear genetic structure in the An. gambiae sensu lato (s.l.) species. Genome-wide FST and H12 scans identified genomic regions under divergent selection that may have implications in the adaptation to ecological changes. Novel voltage-gated sodium channel pyrethroid resistance target-site alleles (V402L, I1527T) were identified at increasing frequencies alongside the established alleles (Vgsc-L995F, Vgsc-L995S and N1570Y) within the An. gambiae s.l. POPULATIONS: Organophosphate metabolic resistance markers were also identified, at increasing frequencies, within the An. gambiae s.s. populations from 2012 to 2017, including the SNP Ace1-G280S and its associated duplication. Variants simultaneously identifi
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Journal articleMataranyika PN, Bez C, Venturi V, et al., 2024,
Rhizospheric, seed, and root endophytic-associated bacteria of drought-tolerant legumes grown in arid soils of Namibia
, Heliyon, Vol: 10, ISSN: 2405-8440Plant growth-promoting bacteria (PGPB) are of increased interest as they offer sustainable alternatives to the more common chemical fertilisers. Research, however, has increased into the use of PGPB as bioinoculants to improve yields. Legumes are known to interact with diazotroph PGPB which increase nutrient uptake, prevent pathogenic infections, and actively fix nitrogen. This study aimed to comprehensively describe PGPB associated with legumes grown in Namibia through analysis of the site-specific bacterial microbiomes. In the present study, we used the 16S rRNA sequencing approach to determine the structure of rhizosphere, root, and seed endosphere microbiomes of five drought-tolerant legume species: Macrotyloma uniflorum, Vigna radiata, Vigna aconitifolia, Vigna unguiculata and Lablab purpureus. Several important phyla were identified including Actinobacteriota, Bacteroidota, Firmicutes, Proteobacteria and Verrucomicrobiota. Overall, Proteobacteria was the most abundant phylum followed by Actinobacteria. The most important genera identified were Bacillus, Mesorhizobium, Pseudomonas, Bradyrhizobium and the Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium group. The relative abundance of these genera varied across sample types and legume species. This study identified important diazotrophs across all the legume species. Bacillus, an important PGPB, was found to be the most abundant genus among all the niches analysed and legume species, while Rhizobium spp. was particularly enriched in roots. This study ultimately provides previously undescribed information on legume-associated bacterial communities in Namibia.
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Journal articleLi J, Prentice IC, 2024,
Global patterns of plant functional traits and their relationships to climate
, Communications Biology, Vol: 7, ISSN: 2399-3642Plant functional traits (FTs) determine growth, reproduction and survival strategies of plants adapted to their growth environment. Exploring global geographic patterns of FTs, their covariation and their relationships to climate are necessary steps towards better-founded predictions of how global environmental change will affect ecosystem composition. We compile an extensive global dataset for 16 FTs and characterise trait-trait and trait-climate relationships separately within non-woody, woody deciduous and woody evergreen plant groups, using multivariate analysis and generalised additive models (GAMs). Among the six major FTs considered, two dominant trait dimensions—representing plant size and the leaf economics spectrum (LES) respectively—are identified within all three groups. Size traits (plant height, diaspore mass) however are generally higher in warmer climates, while LES traits (leaf mass and nitrogen per area) are higher in drier climates. Larger leaves are associated principally with warmer winters in woody evergreens, but with wetter climates in non-woody plants. GAM-simulated global patterns for all 16 FTs explain up to three-quarters of global trait variation. Global maps obtained by upscaling GAMs are broadly in agreement with iNaturalist citizen-science FT data. This analysis contributes to the foundations for global trait-based ecosystem modelling by demonstrating universal relationships between FTs and climate.
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Journal articleShrestha D, Bahasoan Y, Eggeling C, 2024,
Cellular Output and Physicochemical Properties of the Membrane-Derived Vesicles Depend on Chemical Stimulants
, ACS APPLIED MATERIALS & INTERFACES, Vol: 16, Pages: 48982-48992, ISSN: 1944-8244 -
Journal articleCavan EL, Mackay N, Hill SL, et al., 2024,
Antarctic krill sequester similar amounts of carbon to key coastal blue carbon habitats
, Nature Communications, Vol: 15, ISSN: 2041-1723The carbon sequestration potential of open-ocean pelagic ecosystems is vastly under-reported compared to coastal vegetation ‘blue carbon’ systems. Here we show that just a single pelagic harvested species, Antarctic krill, sequesters a similar amount of carbon through its sinking faecal pellets as marshes, mangroves and seagrass. Due to their massive population biomass, fast-sinking faecal pellets and the modest depths that pellets need to reach to achieve sequestration (mean is 381 m), Antarctic krill faecal pellets sequester 20 MtC per productive season (spring to early Autumn). This is equates USD$ 4 − 46 billion depending on the price of carbon, with krill pellet carbon stored for at least 100 years and with some reaching as far as the North Pacific. Antarctic krill are being impacted by rapid polar climate change and an expanding fishery, thus krill populations and their habitat warrant protection to preserve this valuable carbon sink.
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Journal articleWu G, Grassi P, Molina BG, et al., 2024,
Glycomics of cervicovaginal fluid from women at risk of preterm birth reveals immuno-regulatory epitopes that are hallmarks of cancer and viral glycosylation
, Scientific Reports, Vol: 14, ISSN: 2045-2322During pregnancy the immune system needs to maintain immune tolerance of the foetus while also responding to infection, which can cause premature activation of the inflammatory pathways leading to the onset of labour and preterm birth. The vaginal microbiome is an important modifier of preterm birth risk, with Lactobacillus dominance during pregnancy associated with term delivery while high microbial diversity is associated with an increased risk of preterm birth. Glycans on glycoproteins along the lower female reproductive tract are fundamental to microbiota-host interactions and the mediation of inflammatory responses. However, the specific glycan epitopes involved in these processes are not well understood. To address this, we conducted glycomic analyses of cervicovaginal fluid (CVF) from 36 pregnant women at high risk of preterm birth and 4 non-pregnant women. Our analysis of N- and O-glycans revealed a rich CVF glycome. While O-glycans were shown to be the main carriers of ABO blood group epitopes, the main features of N-glycans were the presence of abundant paucimannose and high mannose glycans, and a remarkable diversity of complex bi-, tri-, and tetra-antennary glycans decorated with fucose and sialic acid. We identified immuno-regulatory epitopes, such as Lewis antigens, and found that fucosylation was negatively correlated to pro-inflammatory factors, such as IL-1β, MMP-8, C3a and C5a, while glycans with only sialylated antennae were mainly positively correlated to those. Similarly, paucimannose glycans showed a positive correlation to pro-inflammatory factors. We revealed a high abundance of glycans which have previously been identified as hallmarks of cancer and viral glycosylation, such as Man8 and Man9 high mannose glycans. Although each pregnant woman had a unique glycomic profile, longitudinal studies showed that the main glycosylation features were consistent throughout pregnancy in women who delivered at term, whereas women who experienced ext
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Journal articleHaas O, Keeping T, Gomez-Dans J, et al., 2024,
The global drivers of wildfire
, Frontiers in Environmental Science, Vol: 12, ISSN: 2296-665XChanges in wildfire regimes are of growing concern and raise issues about how well we can model risks in a changing climate. Process-based coupled fire-vegetation models, used to project future wildfire regimes, capture many aspects of wildfire regimes poorly. However, there is now a wealth of information from empirical studies on the climate, vegetation, topography and human activity controls on wildfire regimes. The measures used to quantify these controls vary among studies, but certain variables consistently emerge as the most important: gross primary production as a measure of fuel availability, vegetation cover as a measure of fuel continuity, and atmospheric humidity as a measure of fuel drying. Contrary to popular perception, ignitions are generally not a limiting factor for wildfires. In this review, we describe how empirical fire models implement wildfire processes, synthesise current understanding of the controls on wildfire extent and severity, and suggest ways in which fire modelling could be improved.• Empirical analyses of the controls on wildfires consistently identify vegetation properties associated with fuel availability and continuity and climate factors associated with fuel drying as the most important influences on wildfire extent and severity. • Ignitions, whether anthropogenic or natural, are generally not limiting.• Fire size, burnt area and fire intensity are influenced by different factors; current relationships between these aspects of wildfire could become decoupled in an altered climate. • Some hypotheses embedded in 'process-based' fire-vegetation models are inconsistent with empirical evidence, implying a need for a re-design.
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Journal articleOgwang R, Osoti V, Wamae K, et al., 2024,
A retrospective analysis of <i>P. falciparum</i> drug resistance markers detects an early (2016/17) high prevalence of the k13 C469Y mutation in asymptomatic infections in Northern Uganda
, ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, Vol: 68, ISSN: 0066-4804 -
Journal articleFallesen T, Amerteifio S, Pruessner G, et al., 2024,
Intermittent cell division dynamics in regenerating Arabidopsis roots reveals complex long-range interactions
, Quantitative Plant Biology, Vol: 5, ISSN: 2632-8828In this work, we present a quantitative comparison of the cell division dynamics between populations of intact and regenerating root tips in the plant model system Arabidopsis thaliana. To achieve the required temporal resolution and to sustain it for the duration of the regeneration process, we adopted a live imaging system based on light-sheet fluorescence microscopy, previously developed in the laboratory. We offer a straightforward quantitative analysis of the temporal and spatial patterns of cell division events showing a statistically significant difference in the frequency of mitotic events and spatial separation of mitotic event clusters between intact and regenerating roots.
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Journal articleCasadio R, Mathews DH, Sternberg MJE, 2024,
Computational Resources for Molecular Biology 2024.
, J Mol Biol, Vol: 436 -
Journal articleCioccolo S, Barritt JD, Pollock N, et al., 2024,
The mycobacterium lipid transporter MmpL3 is dimeric in detergent solution, SMALPs and reconstituted nanodiscs
, RSC Chemical Biology, Vol: 5, Pages: 901-913, ISSN: 2633-0679The mycobacterial membrane protein large 3 (MmpL3) transports key precursor lipids to the outer membrane of Mycobacterium species. Multiple structures of MmpL3 from both M. tuberculosis and M. smegmatis in various conformational states indicate that the protein is both structurally and functionally monomeric. However, most other resistance, nodulation and cell division (RND) transporters structurally characterised to date are either dimeric or trimeric. Here we present an in depth biophysical and computational analysis revealing that MmpL3 from M. smegmatis exists as a dimer in a variety of membrane mimetic systems (SMALPs, detergent-based solution and nanodiscs). Sucrose gradient separation of MmpL3 populations from M. smegmatis, reconstituted into nanodiscs, identified monomeric and dimeric populations of the protein using laser induced liquid bead ion desorption (LILBID), a native mass spectrometry technique. Preliminary cryo-EM analysis confirmed that MmpL3 forms physiological dimers. Untargeted lipidomics experiments on membrane protein co-purified lipids revealed PE and PG lipid classes were predominant. Molecular dynamics simulations, in the presence of physiologically-relevant lipid compositions revealed the likely dimer interface.
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Conference paperMazza T, Roumeliotis TI, Garitta E, et al., 2024,
Unveiling the Modulation of MRP2 Activity: Insights from Phosphorylation and Drug Interactions
, 22nd European Bioenergetics Conference (EBEC), Publisher: ELSEVIER, Pages: 84-85, ISSN: 0005-2728 -
Conference paperZhao Z, Vercellino I, Nixon PJ, et al., 2024,
Structural analysis of dimeric photosystem II complexes
, 22nd European Bioenergetics Conference (EBEC), Publisher: ELSEVIER, Pages: 52-52, ISSN: 0005-2728 -
Journal articleFlo V, Joshi J, Sabot M, et al., 2024,
Incorporating photosynthetic acclimation improves stomatal optimisation models
, Plant, Cell and Environment, Vol: 47, Pages: 3478-3493, ISSN: 0140-7791Stomatal 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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Journal articleJeong S, Ryu Y, Gentine P, et al., 2024,
Persistent global greening over the last four decades using novel long-term vegetation index data with enhanced temporal consistency
, Remote Sensing of Environment, Vol: 311, ISSN: 0034-4257Advanced Very High-Resolution Radiometer (AVHRR) satellite observations have provided the longest global daily records from 1980s, but the remaining temporal inconsistency in vegetation index datasets has hindered reliable assessment of vegetation greenness trends. To tackle this, we generated novel global long-term Normalized Difference Vegetation Index (NDVI) and Near-Infrared Reflectance of vegetation (NIRv) datasets derived from AVHRR and Moderate Resolution Imaging Spectroradiometer (MODIS). We addressed residual temporal inconsistency through three-step post processing including cross-sensor calibration among AVHRR sensors, orbital drifting correction for AVHRR sensors, and machine learning-based harmonization between AVHRR and MODIS. After applying each processing step, we confirmed the enhanced temporal consistency in terms of detrended anomaly, trend and interannual variability of NDVI and NIRv at calibration sites. Our refined NDVI and NIRv datasets showed a persistent global greening trend over the last four decades (NDVI: 0.0008 yr−1; NIRv: 0.0003 yr−1), contrasting with those without the three processing steps that showed rapid greening trends before 2000 (NDVI: 0.0017 yr−1; NIRv: 0.0008 yr−1) and weakened greening trends after 2000 (NDVI: 0.0004 yr−1; NIRv: 0.0001 yr−1). These findings highlight the importance of minimizing temporal inconsistency in long-term vegetation index datasets, which can support more reliable trend analysis in global vegetation response to climate changes.
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Journal articleDechant B, Kattge J, Pavlick R, et al., 2024,
Intercomparison of global foliar trait maps reveals fundamental differences and limitations of upscaling approaches
, Remote Sensing of Environment, Vol: 311, ISSN: 0034-4257Foliar traits such as specific leaf area (SLA), leaf nitrogen (N), and phosphorus (P) concentrations play important roles in plant economic strategies and ecosystem functioning. Various global maps of these foliar traits have been generated using statistical upscaling approaches based on in-situ trait observations. Here, we intercompare such global upscaled foliar trait maps at 0.5° spatial resolution (six maps for SLA, five for N, three for P), categorize the upscaling approaches used to generate them, and evaluate the maps with trait estimates from a global database of vegetation plots (sPlotOpen). We disentangled the contributions from different plant functional types (PFTs) to the upscaled maps and quantified the impacts of using different plot-level trait metrics on the evaluation with sPlotOpen: community weighted mean (CWM) and top-of-canopy weighted mean (TWM). We found that the global foliar trait maps of SLA and N differ drastically and fall into two groups that are almost uncorrelated (for P only maps from one group were available). The primary factor explaining the differences between these groups is the use of PFT information combined with remote sensing-derived land cover products in one group while the other group mostly relied on environmental predictors alone. The maps that used PFT and corresponding land cover information exhibit considerable similarities in spatial patterns that are strongly driven by land cover. The maps not using PFTs show a lower level of similarity and tend to be strongly driven by individual environmental variables. Upscaled maps of both groups were moderately correlated to sPlotOpen data aggregated to the grid-cell level (R = 0.2–0.6) when processing sPlotOpen in a way that is consistent with the respective trait upscaling approaches, including the plot-level trait metric (CWM or TWM) and the scaling to the grid cells with or without accounting for fractional land cover. The impact of using TWM or CWM was relevant
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Journal articleHenson SA, Laufkotter C, Leung S, et al., 2024,
Author Correction: Uncertain response of ocean biological carbon export in a changing world (vol 4,2024, 01516)
, NATURE GEOSCIENCE, Vol: 17, Pages: 944-944, ISSN: 1752-0894 -
Journal articleRoberts C, Flintrop CM, Khachikyan A, et al., 2024,
Microplastics may reduce the efficiency of the biological carbon pump by decreasing the settling velocity and carbon content of marine snow
, LIMNOLOGY AND OCEANOGRAPHY, Vol: 69, Pages: 1918-1928, ISSN: 0024-3590 -
Journal articleMattioli M, Raele RA, Gautam G, et al., 2024,
Tuning VSV-G Expression Improves Baculovirus Integrity, Stability and Mammalian Cell Transduction Efficiency
, VIRUSES-BASEL, Vol: 16 -
Journal articleNahman-Averbuch H, Piché M, Bannister K, et al., 2024,
Involvement of propriospinal processes in conditioned pain modulation
, Pain, Vol: 165, Pages: 1907-1913, ISSN: 0304-3959 -
Journal articlePatel R, Taylor JL, Dickenson AH, et al., 2024,
A back-translational study of descending interactions with the induction of hyperalgesia by high-frequency electrical stimulation in rats and humans
, Pain, Vol: 165, Pages: 1978-1989, ISSN: 0304-3959<jats:title>Abstract</jats:title> <jats:p>In humans and animals, high-frequency electrocutaneous stimulation (HFS) induces an “early long-term potentiation-like” sensitisation, where synaptic plasticity is underpinned by an ill-defined interaction between peripheral input and central modulatory processes. The relative contributions of these processes to the initial pain or nociceptive response likely differ from those that underpin development of the heightened response. To investigate the impact of HFS-induced hyperalgesia on pain and nociception in perception and neural terms, respectively, and to explore the impact of descending inhibitory pathway activation on the development of HFS-induced hyperalgesia, we performed parallel studies utilising identical stimuli to apply HFS concurrent to (1) a conditioned pain modulation paradigm during psychophysical testing in healthy humans or (2) a diffuse noxious inhibitory controls paradigm during in vivo electrophysiological recording of spinal neurones in healthy anaesthetised rats. High-frequency electrocutaneous stimulation alone induced enhanced perceptual responses to pinprick stimuli in cutaneous areas secondary to the area of electrical stimulation in humans and increased the excitability of spinal neurones which exhibited stimulus intensity–dependent coded responses to pinprick stimulation in a manner that tracked with human psychophysics, supporting their translational validity. Application of a distant noxious conditioning stimulus during HFS did not alter perceived primary or secondary hyperalgesia in humans or the development of primary or secondary neuronal hyperexcitability in rats compared with HFS alone, suggesting that, upon HFS-response initiation in a healthy nervous system, excitatory signalling escapes inhibitory control. Therefore, in this model, dampening facilitatory mechanisms rather than augmenting top-down inhibitions could prevent pain development.&l
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Journal articleHuang C-Y, Huang Y-S, Sugihara Y, et al., 2024,
Subfunctionalization of NRC3 altered the genetic structure of the Nicotiana NRC network
, PLoS Genetics, Vol: 20, ISSN: 1553-7390Nucleotide-binding domain and leucine-rich repeat (NLR) proteins play crucial roles in immunity against pathogens in both animals and plants. In solanaceous plants, activation of several sensor NLRs triggers their helper NLRs, known as NLR-required for cell death (NRC), to form resistosome complexes to initiate immune responses. While the sensor NLRs and downstream NRC helpers display diverse genetic compatibility, molecular evolutionary events leading to the complex network architecture remained elusive. Here, we showed that solanaceous NRC3 variants underwent subfunctionalization after the divergence of Solanum and Nicotiana, altering the genetic architecture of the NRC network in Nicotiana. Natural solanaceous NRC3 variants form three allelic groups displaying distinct compatibilities with the sensor NLR Rpi-blb2. Ancestral sequence reconstruction and analyses of natural and chimeric variants identified six key amino acids involved in sensor-helper compatibility. These residues are positioned on multiple surfaces of the resting NRC3 homodimer, collectively contributing to their compatibility with Rpi-blb2. Upon activation, Rpi-blb2-compatible NRC3 variants form membrane-associated punctate and high molecular weight complexes, and confer resistance to the late blight pathogen Phytophthora infestans. Our findings revealed how mutations in NRC alleles lead to subfunctionalization, altering sensor-helper compatibility and contributing to the increased complexity of the NRC network.
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Journal articleHeath BE, Suzuki R, LePenru NP, et al., 2024,
Spatial ecosystem monitoring with a Multichannel Acoustic Autonomous Recording Unit (MAARU)
, Methods in Ecology and Evolution, Vol: 15, Pages: 1568-1579, ISSN: 2041-210X1. Multi-microphone recording adds spatial information to recorded audio with emerging applications in ecosystem monitoring. Specifically placing sounds in space can improve animal count accuracy, locate illegal activity like logging and poaching, track animals to monitor behaviour and habitat use and allow for ‘beamforming’ to amplify sounds from target directions for downstream classification. Studies have shown many advantages of spatial acoustics, but uptake remains limited as the equipment is often expensive, complicated, inaccessible or only suitable for short-term deployments.2. With an emphasis on enhanced uptake and usability, we present a low-cost, open-source, six-channel recorder built entirely from commercially available components which can be integrated into a solar-powered, online system. The MAARU (Multichannel Acoustic Autonomous Recording Unit) works as an independent node in long-term autonomous, passive and/or short-term deployments. Here, we introduce MAARU's hardware and software and present the results of lab and field tests investigating the device's durability and usability.3. MAARU records multichannel audio with similar costs and power demands to equivalent omnidirectional recorders. MAARU devices have been deployed in the United Kingdom and Brazil, where we have shown MAARUs can accurately localise pure tones up to 6 kHz and bird calls as far as 8 m away (±10° range, 100% and >60% of signals, respectively). Louder calls may have even further detection radii. We also show how beamforming can be used with MAARUs to improve species ID confidence scores.4. MAARU is an accessible, low-cost option for those looking to explore spatial acoustics accurately and easily with a single device, and without the formidable expenses and processing complications associated with establishing arrays. Ultimately, the added directional element of the multichannel recording provided by MAARU allows for enhanced recording
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Postgraduate research
Interested in studying a PhD at the Department of Life Sciences? Find out more about postgraduate research opportunties.