Results
- Showing results for:
- Reset all filters
Search results
-
Journal articleTong Jia Ming S, Tan Yi Jun K, Carissimo G, 2024,
Pathogenicity and virulence of O’nyong-nyong virus: A less studied <i>Togaviridae</i> with pandemic potential
, Virulence, Vol: 15, ISSN: 2150-5594 -
Journal articleCheong B, Tang W, Kostrzewa M, et al., 2024,
Use of stable isotope combined with intact cell lipidomic by routine MALDI mass spectrometry analysis for rapid drug susceptibility assay in mycobacteria.
, Rapid Commun Mass Spectrom, Vol: 38RATIONALE: Rapid, accurate, and easy-to-perform diagnostic assays are required to address the current need for the diagnosis of resistant pathogens. That is particularly the case for mycobacteria, such as the human pathogen Mycobacterium tuberculosis, which requires up to 2 weeks for the determination of the drug susceptibility profile using the conventional broth microdilution method. To address this challenge, we investigated the incorporation of deuterium, the stable isotope of hydrogen, into lipids as a read out of the drug susceptibility profile. METHODS: Deuterium is incorporated into newly synthesized proteins or lipids in place of hydrogen as bacterial cells grow, increasing the mass of the macromolecules, which can then be observed via matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS). As proof-of-concept, we used the non-pathogenic Mycobacterium smegmatis mc2155 strain, which is susceptible to the aminoglycoside antibiotic kanamycin, and M. smegmatis mc2155 containing the empty vector pVV16, which is kanamycin-resistant. Bacteria were incubated in a culture medium containing 50% of deuterium oxide (D2O) and either 1 or 2 times the minimal inhibitory concentration (MIC50) of kanamycin. Lipids were then analyzed using the MBT lipid Xtract matrix combined with routine MALDI mass spectrometry in the positive ion mode to evaluate the changes in the lipid profile. RESULTS: Using this approach, we were able to distinguish susceptible from resistant bacteria in less than 5 h, a process that would take 72 h using the conventional broth microdilution method. CONCLUSIONS: We therefore propose a solution for the rapid determination of drug susceptibility profiles using a phenotypic assay combining D2O stable isotope labelling and lipid analysis by routine MALDI mass spectrometry.
-
Journal articleChen W, Park Y-K, Studená L, et al., 2024,
Synthetic, marine, light-driven, autotroph-heterotroph co-culture system for sustainable β-caryophyllene production
, Bioresource Technology, Vol: 410, ISSN: 0960-8524Applying low-cost substrate is critical for sustainable bioproduction. Co-culture of phototrophic and heterotrophic microorganisms can be a promising solution as they can use CO2 and light as feedstock. This study aimed to create a light-driven consortium using a marine cyanobacterium Synechococcus sp. PCC 7002 and an industrial yeast Yarrowia lipolytica. First, the cyanobacterium was engineered to accumulate and secrete sucrose by regulating the expression of genes involved in sucrose biosynthesis and transport, resulting in 4.0 g/L of sucrose secretion. Then, Yarrowia lipolytica was engineered to efficiently use sucrose and produce β-caryophyllene that has various industrial applications. Then, co- and sequential-culture were optimized with different induction conditions and media compositions. A maximum β-caryophyllene yield of 14.1 mg/L was obtained from the co-culture. This study successfully established an artificial light-driven consortium based on a marine cyanobacterium and Y. lipolytica, and provides a foundation for sustainable bioproduction from CO2 and light through co-culture systems.
-
Book chapterGrob A, Enrico Bena C, Redwood-Sawyerr C, et al., 2024,
Simultaneous Plate-Reader Characterization of Promoter Activity and Cell Growth in Engineered Mammalian Cells
, Synthetic Promoters Methods and Protocols, Editors: Marchisio, Publisher: Humana, ISBN: 9781071640623Automated high-throughput methods that support tracking of mammalian cell growth are currently needed to advance cell line characterization and identification of desired genetic components required for cell engineering. Here, we describe a high-throughput noninvasive assay based on plate reader measurements. The assay relies on the change in absorbance of the pH indicator phenol red. We show that its basic and acidic absorbance profiles can be converted into a cell growth index consistent with cell count profiles, and that, by adopting a computational pipeline and calibration measurements, it is possible to identify a conversion that enables prediction of cell numbers from plate measurements alone. The assay is suitable for growth characterization of both suspension and adherent cell lines when these are grown under different environmental conditions and treated with chemotherapeutic drugs. The method also supports characterization of stably engineered cell lines and identification of desired promoters based on fluorescence output.
-
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.
-
Journal articleStocker B, Dong N, Perkowski EA, et al., 2024,
Empirical evidence and theoretical understanding ofecosystem carbon and nitrogen cycle interactions
, New Phytologist, ISSN: 0028-646X -
Journal articleHaslam S, 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, ISSN: 2045-2322 -
Journal articleIsalan M, Armstrong A, 2024,
Engineering bacterial theranostics: from logic gates to in vivo applications
, Frontiers in Bioengineering and Biotechnology, 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.
-
Journal articleOgwang R, Osoti V, Wamae K, et al., 2024,
A retrospective analysis of P. falciparum drug resistance markers detects an early (2016/17) high prevalence of the k13 C469Y mutation in asymptomatic infections in Northern Uganda.
, Antimicrob Agents Chemother, Vol: 68The emergence of drug-resistant Plasmodium falciparum parasites in sub-Saharan Africa will substantially challenge malaria control. Here, we evaluated the frequency of common drug resistance markers among adolescents from Northern Uganda with asymptomatic infections. We used an established amplicon deep sequencing strategy to screen dried blood spot samples collected from 2016 to 2017 during a reported malaria epidemic within the districts of Kitgum and Pader in Northern Uganda. We screened single-nucleotide polymorphisms within: kelch13 (Pfk13), dihydropteroate synthase (Pfdhps), multidrug resistance-1 (Pfmdr1), dihydrofolate reductase (Pfdhfr), and apical membrane antigen (Pfama1) genes. Within the study population, the median age was 15 years (14.3-15.0, 95% CI), and 54.9% (78/142) were Plasmodium positive by 18S rRNA qPCR, which were subsequently targeted for sequencing analysis. We observed a high frequency of resistance markers particularly for sulfadoxine-pyrimethamine (SP), with no wild-type-only parasites observed for Pfdhfr (N51I, C59R, and S108N) and Pfdhps (A437G and K540E) mutations. Within Pfmdr1, mixed infections were common for NF/NY (98.5%). While for artemisinin resistance, in kelch13, there was a high frequency of C469Y (34%). Using the pattern for Pfama1, we found a high level of polygenomic infections with all individuals presenting with complexity of infection greater than 2 with a median of 6.9. The high frequency of the quintuple SP drug-resistant parasites and the C469Y artemisinin resistance-associated mutation in asymptomatic individuals suggests an earlier high prevalence than previously reported from symptomatic malaria surveillance studies (in 2016/2017). Our data demonstrate the urgency for routine genomic surveillance programs throughout Africa and the value of deep sequencing.
-
Journal articleKourelis J, Schuster M, Demir F, et al., 2024,
Bioengineering secreted proteases converts divergent Rcr3 orthologs and paralogs into extracellular immune co-receptors.
, Plant Cell, Vol: 36, Pages: 3260-3276Secreted immune proteases "Required for Cladosporium resistance-3" (Rcr3) and "Phytophthora-inhibited protease-1" (Pip1) of tomato (Solanum lycopersicum) are both inhibited by Avirulence-2 (Avr2) from the fungal plant pathogen Cladosporium fulvum. However, only Rcr3 acts as a decoy co-receptor that detects Avr2 in the presence of the Cf-2 immune receptor. Here, we identified crucial residues in tomato Rcr3 that are required for Cf-2-mediated signaling and bioengineered various proteases to trigger Avr2/Cf-2-dependent immunity. Despite substantial divergence in Rcr3 orthologs from eggplant (Solanum melongena) and tobacco (Nicotiana spp.), minimal alterations were sufficient to trigger Avr2/Cf-2-mediated immune signaling. By contrast, tomato Pip1 was bioengineered with 16 Rcr3-specific residues to initiate Avr2/Cf-2-triggered immune signaling. These residues cluster on one side of the protein next to the substrate-binding groove, indicating a potential Cf-2 interaction site. Our findings also revealed that Rcr3 and Pip1 have distinct substrate preferences determined by two variant residues and that both are suboptimal for binding Avr2. This study advances our understanding of Avr2 perception and opens avenues to bioengineer proteases to broaden pathogen recognition in other crops.
-
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.
-
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.
-
Journal articleMorales-Castilla I, Davies TJ, Legault G, et al., 2024,
Phylogenetic estimates of species-level phenology improve ecological forecasting
, Nature Climate Change, Vol: 14, Pages: 989-995, ISSN: 1758-678XThe ability to adapt to climate change requires accurate ecological forecasting. Current forecasts, however, have failed to capture important variability in biological responses, especially across species. Here we present a new method using Bayesian hierarchical phylogenetic models and show that species-level differences are larger than the average differences between cues. Applying our method to phenological experiments manipulating temperature and day length we show an underlying phylogenetic structure in plant phenological responses to temperature cues, whereas responses to photoperiod appear weaker, more uniform across species and less phylogenetically constrained. We thus illustrate how a focus on certain clades can bias prediction, but that predictions may be improved by integrating information on phylogeny to better estimate species-level responses. Our approach provides an advance in ecological forecasting, with implications for predicting the impacts of climate change and other anthropogenic forces on ecosystems.
-
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.
-
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
-
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
-
Journal articleLingche H, Miguel-Romero L, Patkowski JB, et al., 2024,
Tail assembly interference is a common strategy in bacterial antiviral defenses
, Nature Communications, Vol: 15, ISSN: 2041-1723Many bacterial immune systems recognize phage structural components to activate antiviral responses, without inhibiting the function of the phage component. These systems can be encoded in specific chromosomal loci, known as defense islands, and in mobile genetic elements such as prophages and phage-inducible chromosomal islands (PICIs). Here, we identify a family of bacterial immune systems, named Tai (for ‘tail assembly inhibition’), that is prevalent in PICIs, prophages and P4-like phage satellites. Tai systems protect their bacterial host population from other phages by blocking the tail assembly step, leading to the release of tailless phages incapable of infecting new hosts. To prevent autoimmunity, some Tai-positive phages have an associated counter-defense mechanism that is expressed during the phage lytic cycle and allows for tail formation. Interestingly, the Tai defense and counter-defense genes are organized in a non-contiguous operon, enabling their coordinated expression.
-
Journal articleJaramillo V, Hebron H, Wong S, et al., 2024,
Closed-loop auditory stimulation targeting alpha and theta oscillations during REM sleep induces phase-dependent power and frequency changes.
, SleepSTUDY OBJECTIVES: Alpha and theta oscillations characterize the waking human electroencephalogram (EEG) and can be modulated by closed-loop auditory stimulation (CLAS). These oscillations also occur during rapid eye movement (REM) sleep, but their function here remains elusive. CLAS represents a promising tool to pinpoint how these brain oscillations contribute to brain function in humans. Here we investigate whether CLAS can modulate alpha and theta oscillations during REM sleep in a phase-dependent manner. METHODS: We recorded high-density EEG during an extended overnight sleep period in 18 healthy young adults. Auditory stimulation was delivered during both phasic and tonic REM sleep in alternating 6 s ON and 6 s OFF windows. During the ON windows, stimuli were phase-locked to four orthogonal phases of ongoing alpha or theta oscillations detected in a frontal electrode. RESULTS: The phases of ongoing alpha and theta oscillations were targeted with high accuracy during REM sleep. Alpha and theta CLAS induced phase-dependent changes in power and frequency at the target location. Frequency-specific effects were observed for alpha trough (speeding up) and rising (slowing down) and theta trough (speeding up) conditions. CLAS-induced phase-dependent changes were observed during both REM sleep substages, even though auditory evoked potentials were very much reduced in phasic compared to tonic REM sleep. CONCLUSIONS: This study provides evidence that faster REM sleep rhythms can be modulated by CLAS in a phase-dependent manner. This offers a new approach to investigate how modulation of REM sleep oscillations affects the contribution of this vigilance state to brain function.
-
Journal articleMoratto E, Tang Z, Bozkurt T, et al., 2024,
Reduction of Phytophthora palmivora plant root infection in weak electric fields
, Scientific Reports, Vol: 14, ISSN: 2045-2322The global food security crisis is partly caused by significant crop losses due to pests and pathogens, leading to economic burdens. Phytophthora palmivora, an oomycete pathogen, affects many plantation crops and costs over USD 1 billion each year. Unfortunately, there is currently no prevention plan in place, highlighting the urgent need for an effective solution. P. palmivora produces motile zoospores that respond to weak electric fields. Here, we show that external electric fields can be used to reduce root infection in two plant species. We developed two original essays to study the effects of weak electric fields on the interaction between P. palmivora’s zoospores and roots of Arabidopsis thaliana and Medicago truncatula. In the first configuration, a global artificial electric field is set up to induce ionic currents engulfing the plant roots while, in the second configuration, ionic currents are induced only locally and at a distance from the roots. In both cases, we found that weak ionic currents (250–550 μA) are sufficient to reduce zoospore attachment to Arabidopsis and Medicago roots, without affecting plant health. Moreover, we show that the same configurations decrease P. palmivora mycelial growth in Medicago roots after 24 h. We conclude that ionic currents can reduce more than one stage of P. palmivora root infection in hydroponics. Overall, our findings suggest that weak external electric fields can be used as a sustainable strategy for preventing P. palmivora infection, providing innovative prospects for agricultural crop protection.
-
Journal articleLi J, Prentice IC, 2024,
Global patterns of plant functional traits and their relationships to climate
, Communications Biology, ISSN: 2399-3642 -
Journal articleCoathup M, Savolainen V, 2024,
Ecological speciation in sympatric palms: 5. Evidence for pleiotropic speciation genes using gene knockout and high-throughput phenotyping
, Evolutionary Journal of the Linnean SocietyTheoretical models predict that sympatric, ecological speciation may be facilitated more readily when so-called ‘magic traits’ are present, linking traits under divergent selection with assortative mating. Such traits might be encoded by pleiotropic genes, that is, genes that affect multiple, apparently unrelated, phenotypes. However, few convincing examples of sympatric speciation exist, and empirical evidence for the role of magic traits in driving such speciation is rare. One of the strongest cases of sympatric speciation is the Howea palms of Lord Howe Island, Australia, comprising the sister species H. belmoreana and H. forsteriana, which have diverged due to soil substrate preferences and flowering time displacement. By carrying out high-throughput phenotyping experiments using 1,830 Arabidopsis thaliana plants with knockouts of candidate Howea ‘speciation genes’, here we investigate the role that pleiotropy may have played in the speciation process. We identify several genes that show signatures of adaptive divergence between the Howea species and demonstrate pleiotropic roles in soil stress tolerance and flowering time, consistent with the Howea speciation scenario – notably, Howea orthologs of the A. thaliana loci At2-MMP, DCL1, RCD1, SAL1, and SIZ1. Empirical evidence is provided, therefore, for a range of pleiotropic genes with the potential to have driven sympatric speciation by generating magic traits which link divergent selection to non-random mating.
-
Journal articleBarnada SM, Giner de Gracia A, Morenilla-Palao C, et al., 2024,
ARID1A-BAF coordinates ZIC2 genomic occupancy for epithelial-to-mesenchymal transition in cranial neural crest specification.
, Am J Hum GenetThe BAF chromatin remodeler regulates lineage commitment including cranial neural crest cell (CNCC) specification. Variants in BAF subunits cause Coffin-Siris syndrome (CSS), a congenital disorder characterized by coarse craniofacial features and intellectual disability. Approximately 50% of individuals with CSS harbor variants in one of the mutually exclusive BAF subunits, ARID1A/ARID1B. While Arid1a deletion in mouse neural crest causes severe craniofacial phenotypes, little is known about the role of ARID1A in CNCC specification. Using CSS-patient-derived ARID1A+/- induced pluripotent stem cells to model CNCC specification, we discovered that ARID1A-haploinsufficiency impairs epithelial-to-mesenchymal transition (EMT), a process necessary for CNCC delamination and migration from the neural tube. Furthermore, wild-type ARID1A-BAF regulates enhancers associated with EMT genes. ARID1A-BAF binding at these enhancers is impaired in heterozygotes while binding at promoters is unaffected. At the sequence level, these EMT enhancers contain binding motifs for ZIC2, and ZIC2 binding at these sites is ARID1A-dependent. When excluded from EMT enhancers, ZIC2 relocates to neuronal enhancers, triggering aberrant neuronal gene activation. In mice, deletion of Zic2 impairs NCC delamination, while ZIC2 overexpression in chick embryos at post-migratory neural crest stages elicits ectopic delamination from the neural tube. These findings reveal an essential ARID1A-ZIC2 axis essential for EMT and CNCC delamination.
-
Journal articleGeffen AJ, Nash RDM, Fox CJ, 2024,
How well do connectivity tools agree over the full life cycle? A case study of Irish Sea plaice Pleuronectes platessa Linnaeus, 1758.
, J Fish BiolAdult plaice in the Irish Sea have distinct traits that reflect the spawning locations that could suggest a number of different populations. However, do connectivity pathways support this concept? Different tools are directed at measuring exchange or connectivity between different life-history stages, and the challenge is to integrate the signals to obtain full life-cycle estimates. Collectively, the different methods reveal stable connectivity between known spawning and nursery grounds, with sufficient exchange to maintain a single population with weak genetic structure.
-
Journal articleHaas O, Keeping T, Gomez-Dans J, et al., 2024,
The global drivers of wildfire
, Frontiers in Environmental Science, 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.
-
Journal articleBoyle MJW, Sharp AC, Barclay MV, et al., 2024,
Tropical beetles more sensitive to impacts are less likely to be known to science
, Current Biology, Vol: 34, Pages: R770-R771, ISSN: 0960-9822Insects are posited to be declining globally. This is particularly pertinent in tropical forests, which exhibit both the highest levels of biodiversity and the highest rates of biodiversity loss. However, for the hyper-diverse tropical insects there are scant data available to evidence declines. Understanding tropical insect diversity and its response to environmental change has therefore become a challenge, but it is estimated that 80% of tropical insect species remain undescribed1. Insect biodiversity predictions are based mostly on well-studied taxa and extrapolated to other groups, but no one knows whether resilience to environmental change varies between undescribed and described species. Here, we collected staphylinid beetles from unlogged and logged tropical forests in Borneo and investigated their responses to environmental change. Out of 252 morphospecies collected, 76% were undescribed. Undescribed species showed higher community turnover, reduced abundance and decreased probability of occurrence in logged forests. Thus the unknown components of tropical insect biodiversity are likely more impacted by human-induced environmental change. If these patterns are widespread, how accurate will assessments of insect declines in the tropics be?
-
Journal articleSavolainen V, Bezeng BS, 2024,
An African perspective to biodiversity conservation in the 21st century
, Philosophical Transactions of the Royal Society B: Biological Sciences, ISSN: 0962-8436Africa boasts high biodiversity while also being home to some of the largest and fastest-growing human populations. Although the current environmental footprint of Africa is low compared to other continents, the population of Africa is estimated at around 1.5 billion inhabitants, representing nearly 18% of the world's total population. Consequently, Africa’s rich biodiversity is under threat, yet only 19% of the landscape and 17% of the seascape are under any form of protection. To effectively address this issue and align with the Convention on Biological Diversity's ambitious ‘30 by 30’ goal, which seeks to protect 30% of the world's land and oceans by 2030, substantial funding and conservation measures are urgently required. In response to this critical challenge, as scientists and conservationists working in Africa, we propose five recommendations for future directions aimed at enhancing biodiversity conservation for the betterment of African society: (i) accelerate data collection, data sharing and analytics for informed policy and decision making; (ii) innovate education and capacity building for future generations; (iii) enhance and expand protected areas, ecological networks, and foundational legal frameworks; (iv) unlock creative funding channels for cutting-edge conservation initiatives; and (v) integrate indigenous and local knowledge into forward-thinking conservation strategies. By implementing these recommendations, we believe Africa can make significant strides towards preserving its unique biodiversity, while fostering a healthier society, and contributing to global conservation efforts.
-
Journal articleMills MB, Both S, Jotan P, et al., 2024,
From tree to plot: investigating stem CO2 efflux and its drivers along a logging gradient in Sabah, Malaysian Borneo.
, New PhytolStem respiration constitutes a substantial proportion of autotrophic respiration in forested ecosystems, but its drivers across different spatial scales and land-use gradients remain poorly understood. This study quantifies and examines the impact of logging disturbance on stem CO2 efflux (EA) in Malaysian Borneo. EA was quantified at tree- and stand-level in nine 1-ha plots over a logging gradient from heavily logged to old-growth using the static chamber method. Tree-level results showed higher EA per unit stem area in logged vs old-growth plots (37.0 ± 1.1 vs 26.92 ± 1.14 g C m-2 month-1). However, at stand-level, there was no difference in EA between logged and old-growth plots (6.7 ± 1.1 vs 6.0 ± 0.7 Mg C ha-1 yr-1) due to greater stem surface area in old-growth plots. Allocation to growth respiration and carbon use efficiency was significantly higher in logged plots. Variation in EA at both tree- and stand-level was driven by tree size, growth and differences in investment strategies between the forest types. These results reflect different resource allocation strategies and priorities, with a priority for growth in response to increased light availability in logged plots, while old-growth plots prioritise maintenance and cell structure.
-
Journal articleMajumdar A, Upadhyay MK, Ojha M, et al., 2024,
A critical review on the organo-metal(loid)s pollution in the environment: Distribution, remediation and risk assessment.
, Sci Total Environ, Vol: 951Toxic metal(loid)s, e.g., mercury, arsenic, lead, and cadmium are known for several environmental disturbances creating toxicity to humans if accumulated in high quantities. Although not discussed critically, the organo-forms of these inorganic metal(loid)s are considered a greater risk to humans than their elemental forms possibly due to physico-chemical modulation triggering redox alterations or by the involvement of biological metabolism. This extensive review describes the chemical and physical causes of organometals and organometal(loid)s distribution in the environment with ecotoxicity assessment and potential remediation strategies. Organo forms of various metal(loid)s, such as mercury (Hg), arsenic (As), lead (Pb), tin (Sn), antimony (Sb), selenium (Se), and cadmium (Cd) have been discussed in the context of their ecotoxicity. In addition, we elaborated on the transformation, speciation and transformation pathways of these toxic metal(loid)s in soil-water-plant-microbial systems. The present review has pointed out the status of toxic organometal(loid)s, which is required to make the scientific community aware of this pressing condition of organometal(loid)s distribution in the environment. The gradual disposal and piling of organometal(loid)s in the environment demand a thorough revision of the past-present status with possible remediation strategies prescribed as reflected in this review.
-
Journal articleSethi S, Bick IA, Chen M-Y, et al., 2024,
Large-scale avian vocalization detection delivers reliable global biodiversity insights
, Proceedings of the National Academy of Sciences of USA, Vol: 121, ISSN: 0027-8424Tracking biodiversity and its dynamics at scale is essential if we are to solve global environmental challenges. Detecting animal vocalizations in passively recorded audio data offers an automatable, inexpensive, and taxonomically broad way to monitor biodiversity. However, the labor and expertise required to label new data and fine-tune algorithms for each deployment is a major barrier. In this study, we applied a pretrained bird vocalization detection model, BirdNET, to 152,376 h of audio comprising datasets from Norway, Taiwan, Costa Rica, and Brazil. We manually listened to a subset of detections for each species in each dataset, calibrated classification thresholds, and found precisions of over 90% for 109 of 136 species. While some species were reliably detected across multiple datasets, the performance of others was dataset specific. By filtering out unreliable detections, we could extract species and community-level insight into diel (Brazil) and seasonal (Taiwan) temporal scales, as well as landscape (Costa Rica) and national (Norway) spatial scales. Our findings demonstrate that, with relatively fast but essential local calibration, a single vocalization detection model can deliver multifaceted community and species-level insight across highly diverse datasets; unlocking the scale at which acoustic monitoring can deliver immediate applied impact.
-
Journal articlePatin EC, Nenclares P, Chan Wah Hak C, et al., 2024,
Sculpting the tumour microenvironment by combining radiotherapy and ATR inhibition for curative-intent adjuvant immunotherapy.
, Nat Commun, Vol: 15The combination of radiotherapy/chemoradiotherapy and immune checkpoint blockade can result in poor outcomes in patients with locally advanced head and neck squamous cell carcinoma (HNSCC). Here, we show that combining ATR inhibition (ATRi) with radiotherapy (RT) increases the frequency of activated NKG2A+PD-1+ T cells in animal models of HNSCC. Compared with the ATRi/RT treatment regimen alone, the addition of simultaneous NKG2A and PD-L1 blockade to ATRi/RT, in the adjuvant, post-radiotherapy setting induces a robust antitumour response driven by higher infiltration and activation of cytotoxic T cells in the tumour microenvironment. The efficacy of this combination relies on CD40/CD40L costimulation and infiltration of activated, proliferating memory CD8+ and CD4+ T cells with persistent or new T cell receptor (TCR) signalling, respectively. We also observe increased richness in the TCR repertoire and emergence of numerous and large TCR clonotypes that cluster based on antigen specificity in response to NKG2A/PD-L1/ATRi/RT. Collectively, our data point towards potential combination approaches for the treatment of HNSCC.
This data is extracted from the Web of Science and reproduced under a licence from Thomson Reuters. You may not copy or re-distribute this data in whole or in part without the written consent of the Science business of Thomson Reuters.
Postgraduate research
Interested in studying a PhD at the Department of Life Sciences? Find out more about postgraduate research opportunties.