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Biology subjects

Lawson, J.

Publications and source records attributed to Lawson, J..

17 recordsLinked to original sources

Functional modelling of human infertility-associated genetic variants using C. elegans and mice

Infertility affects one in six couples worldwide and has a significant genetic component. Genome sequencing efforts have identified increasing numbers of potentially pathogenic variants, including in conserved meiotic genes. However, the lack of functional validation remains a major barrier to establishing variant pathogenicity and clinical diagnoses. Here, we establish an experimental pipeline integrating C. elegans and mouse in vivo models with in silico protein structure predictions to functionally validate potentially pathogenic infertility-associated variants. Using CRISPR-Cas9 we generated worm and mouse models of a homozygous missense variant (P638L) in MSH4, a mismatch repair protein essential for meiotic recombination, identified in a patient with non-obstructive azoospermia (NOA). Homozygous msh-4P546L worms exhibited severe meiotic defects including an absence of chiasmata, accumulation of DNA damage, and loss of crossover markers. Comparable defects were observed in spermatocytes of homozygous Msh4P660L/P660L mice, while Msh4P660L/P660L ovaries lacked oocyte-containing follicles, demonstrating that this variant causes infertility in both sexes. Together, these findings support a model in which the MSH4 P638L substitution disrupts the conversion of early recombination events into crossovers, leading to NOA in men and primary ovarian insufficiency in women. Further worm modelling of human MSH4 genetic variants identified exclusively in heterozygosity (G649R) or also in homozygosity (Y589C) demonstrates the potential of worm models to predict the pathogenicity of missense variants in meiotic proteins found in the human population. We propose that this integrated worm-mouse pipeline provides a powerful framework for accelerating the genetic diagnosis of infertility and informing the clinical management of affected individuals.

cell biology↗

PAMalytics: a no-code application for structured validation of bioacoustic detections

1. Passive acoustic monitoring (PAM) is increasingly used for ecological research, biodiversity monitoring, assessment, and reporting. Automated species classifiers make it feasible to process large audio datasets but generate numerous detections that often need validation before use in downstream analyses or formal outputs. 2. Method development in PAM has focused on classifier building and downstream models that account for imperfect detection, yet the practical step between these - post-classification validation - remains weakly supported and is often implemented through ad hoc workflows. This increases manual handling, creates scope for transcription or consolidation errors, limits transparency and makes it difficult to document what was reviewed. 3. We introduce PAMalytics, an open-source, no-code, local browser-based application to support post-classification validation as a standardised workflow stage. PAMalytics ingests detections from any classifier, allows users to define how detections are sampled for review, and presents selected detections alongside their spectrograms with audio playback in one unified interface. Sampling strategy and review decisions are tracked alongside reviewer identity improving traceability and reproducibility across the validation workflow. 4. Case studies with Conservation International Cambodia and Imperial College London demonstrate PAMalytics in two validation settings. In Cambodia, gibbon predictions from a large, uneven dataset were sampled within sites, with likely classifier errors prioritised for validation. At Imperial, Amazon bird detections were sampled across each species classifier-confidence range before biodiversity metrics were derived. In both cases, PAMalytics reduced manual handling and validation time. By turning an ad hoc step into an accessible, structured workflow for conservation practitioners, PAMalytics fills a practical gap in the PAM bioacoustics pipeline and strengthens the link between automated detections and evidence used in biodiversity monitoring and reporting.

ecology↗

Automated Monitoring of Insects system: Building a non-lethal and scalable solution for monitoring of nocturnal insects

There is growing evidence that human-induced climate change and habitat loss are having negative impacts on insect populations. New technologies have a vital role in improving and expanding global biodiversity monitoring capacity to understand where change is happening and to support restoration. Monitoring of insects traditionally needs entomologists in the field, but insect camera traps powered by AI are emerging as a scalable approach to monitoring semi-autonomously. These systems attract, detect, and identify insects using AI algorithms and are being developed by a network of researchers across the world, notably in Europe and North America. The first version of a system for monitoring nocturnal insects was developed by Bjerge et al. 2021. An Automated Light Trap to Monitor Moths (Lepidoptera) Using Computer Vision-Based Tracking and Deep Learning. Here we describe the second generation of the system as an open-source solution. This paper aims to enable anyone to build their own system, and to iterate and improve the design for their needs. This system captures images at set intervals or based on motion detection to monitor insects that are attracted to lights at night. The UKCEH Automated Monitoring of Insects System (UKCEH AMI-system) is an insect camera trap designed using a single board computer, USB camera and attractant lights as the primary components along with peripheral accessories to make an autonomous system capable of long-term deployment in the field. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/704388v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@17ccdc4org.highwire.dtl.DTLVardef@a92179org.highwire.dtl.DTLVardef@1d4aaf8org.highwire.dtl.DTLVardef@1248d07_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

The Liver is an Inflammatory Mediator of Pulmonary Arterial Hypertension

The livers contribution to pulmonary arterial hypertension (PAH) pathogenesis remains unclear. We hypothesized that the liver promotes inflammatory injury to the pulmonary endothelium. PAH patients without liver disease with pulmonary artery endothelial cell (PAEC) biopsies were included. Liver serologies and imaging were analyzed by unsupervised classification and regression tree (CART) to identify subclinical liver dysfunction clusters. Two machine-learning models predicted cluster assignment and informed differential expression. PAEC transcriptomes were compared to liver and lung data from monocrotaline and Sugen-Hypoxia rats. Liver fibrosis was assessed in rat and human PAH livers. Among 25 PAH patients (76% female, median age 61 [30 - 84] years), CART identified clusters distinguished by Model for End-Stage Liver Disease Sodium (MELD-Na) [≥]12, predicting higher pulmonary vascular resistance ({beta}=0.5 Wood units per point increase in MELD-Na, 95% CI 0.2-0.8, p=0.005) after adjustment for right atrial pressure. Subjects with MELD-Na [≥]12 had decreased 6-minute walk distance (353 [120 - 576] m vs. 411[300 - 600] m, p=0.03), with upregulation of apelin, beta-catenin, and immune signaling. Rat lung ECs demonstrated survival and hepatic growth-factor signaling, while rat livers showed immune activation. Rat (20.8 vs 16.6 % area stained, p=0.09) and human PAH livers revealed fibrosis despite absent right ventricular failure, supporting a pathogenic lung-liver axis in PAH.

cell biology↗

H2AK119ub Safeguards Against Ectopic Transcription Factor Mediated Gene Activation in the Developing Forebrain

The PRC1 complex regulates developmental gene expression in mammals by ubiquitinating histones (H2AK119ub) and nucleating repressive chromatin interactions. Human genetic data and functional experimentation have demonstrated that H2AK119ub is required for cortical development, however the molecular mechanism for this remains unknown. Here, we show that mouse embryos expressing catalytically deficient RING1B exhibit intact early neurogenesis but display impaired neuroectodermal fate restriction. Using in vivo, primary, and in vitro models, we demonstrate that reduced H2AK119ub leads to ectopic activation of lineage-inappropriate transcriptional programmes, including mesodermal and endodermal gene expression during neural differentiation. This transcriptional deregulation is not solely attributable to H2AK119ub or H3K27me3 loss but instead reflects sensitisation of PRC1 target genes to inappropriate transcription factor (TF)-mediated activation. Synthetic induction of candidate TFs, including GATA6, SOX7, and SNAI1, phenocopies the fate-skewing effects of PRC1 catalytic dysfunction, confirming their causal role. Our results uncover a buffering role for PRC1-catalysed H2AK119ub in safeguarding neural progenitor identity by preventing inappropriate TF-driven transcription and provides a mechanistic framework for understanding the cellular heterogeneity and phenotypic variability observed in Polycomb-associated neurodevelopmental disorders.

molecular biology↗

Robotics-assisted acoustic surveys could deliver reliable, landscape-level biodiversity insights

Terrestrial remote sensing approaches, such as acoustic monitoring, deliver finely resolved and reliable biodiversity data. However, the scalability of surveys is often limited by the effort, time and cost needed to deploy, maintain and retrieve sensors. Autonomous unmanned aerial vehicles (UAVs, or drones) are emerging as a promising tool for fully autonomous data collection, but there is considerable scope for their further use in ecology. In this study, we explored whether a novel approach to UAV-based acoustic monitoring could detect biodiversity patterns across a varied tropical landscape in Costa Rica. We simulated surveys of UAVs employing intermittent locomotion-based sampling strategies on an existing dataset of 26,411 hours of audio recorded from 341 static sites, with automated detections of 19 bird species (n = 1,819) and spider monkey (n = 2,977) vocalisations. We varied the number of samplers deployed in a single survey (sampling intensity) and whether the samplers move between sites randomly, in a pre-determined route to minimise travel time, or by adaptively responding to real-time detections (sampling strategy) and measured the impact on downstream ecological analyses. We found that observed avian species richness and spider monkey occupancy was not impacted by sampling strategy, but that sampling intensity had a strong influence on downstream metrics. Whilst our simulated UAV surveys were effective in capturing broad biodiversity trends, such as spider monkey occupancy and avian habitat associations, they were less suited for exhaustive species inventories, with rare species often missed at low sampling intensities. As autonomous UAV systems and acoustic AI analyses become more reliable and accessible, our study shows that combining these technologies could deliver valuable biodiversity data at scale.

ecology↗

High-Sensitivity Top-Down Proteomics Reveals Enhanced Maturation of Micropatterned Induced Pluripotent Stem Cell-Derived Cardiomyocytes

Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) are increasingly used for disease modeling, drug discovery, and precision medicine, yet their utility is often limited by their immature phenotype. One promising maturation strategy involves using micropatterned substrates that mimic native cardiomyocytes organizational growth and stiffness. However, the molecular maturity of this model has not yet been assessed, and there is currently no method to extract proteins from micropatterned hiPSC-CMs for top-down proteomic analysis. Herein, we present a high-sensitivity, surfactant-free protein extraction protocol for the top-down proteomic analysis of hiPSC-CMs. Through this method, we assessed the maturation of micropatterned hiPSC-CMs compared to traditional unstructured monoculture and co-culture monolayers at the proteoform level. We found that micropatterned hiPSC-CMs display molecular signatures of cardiomyocyte maturations including increased expression of ventricular myosin light chain isoforms, reduced expression of the fetal troponin T isoform, and decreased phosphorylation of alpha-tropomyosin. This surfactant-free, high-sensitivity approach enables robust top-down proteomics from limited, heterogeneous cell populations, and identifies the micropattern hiPSC-CM as a more adult-like CM model, broadening the utility of structured culture systems for cardiac disease modeling and translational research.

molecular biology↗

A novel dataset of 2,362 equine fecal microbiomes from eight veterinary teaching hospital on three continents reveals dominant effects of geography, breed, and disease

Horses and other equids are reliant on the gut microbiome for health, and studies have reported associations between certain clinical conditions and features of the fecal microbiome. However, research to date on the equine fecal microbiome has often relied on small sample sizes collected from single and relatively localized geographic regions. Previous work largely employs single timepoint analyses, or horses selected based on limited health criteria. To address these issues and expand our understanding of the core microbiome in health, and the changes associated with adverse outcomes, the Equine Gut Group (EGG) has collected and performed 16S rRNA sequencing on 2,362 fecal samples from 1,190 healthy and affected horses. Here we present the EGG database and demonstrate its utility in characterizing the equine microbiome in health and acute gastrointestinal disease. The EGG 16S rRNA database is a valuable resource to study the equine microbiome and its role in equine health.

microbiology↗

Automatic vocalisation detection delivers reliable, multi-faceted, and global avian biodiversity monitoring

Tracking biodiversity and its dynamics at scale is essential if we are to solve global environmental challenges. Detecting animal vocalisations in passively recorded audio data offers a highly automatable, inexpensive, and taxonomically broad way to monitor biodiversity. However, uptake is slow due to the expertise and labour required to label new data and fine-tune algorithms for each deployment. In this study, we applied an off-the-shelf bird vocalisation detection model, BirdNET, to 152,376 hours of audio comprising of datasets from Norway, Taiwan, Costa Rica, and Brazil. We manually listened to a subset of detections for each species in each dataset and found precisions of over 80% for 89 of the 139 species (100% for 57 species). Whilst 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 on diel (Brazil) and seasonal (Taiwan) temporal scales, as well as landscape (Costa Rica) and national (Norway) spatial scales. Our findings demonstrate that, with a relatively fast validation step, a single vocalisation detection model can deliver multi-faceted community and species level insight across highly diverse datasets; unlocking the scale at which acoustic monitoring can deliver immediate applied impact.

ecology↗

iPSC-Astrocyte morphology reflects patient clinical markers

Human iPSCs provide powerful cellular models of Alzheimers disease (AD) and offer many advantages over non-human models, including the potential to reflect variation in individual-specific pathophysiology and clinical symptoms Previous studies have demonstrated that iPSC-neurons from individuals with Alzheimers disease (AD) reflect clinical markers, including {beta}-amyloid (A{beta}) levels and synaptic vulnerability. However, despite neuronal loss being a key hallmark of AD pathology, many risk genes are predominantly expressed in glia, highlighting them as potential therapeutic targets. In this work iPSC-derived astrocytes were generated from a cohort of individuals with high versus low levels of the inflammatory marker YKL-40, in their cerebrospinal fluid (CSF). iPSC-derived astrocytes were treated with exogenous A{beta} oligomers and high content imaging demonstrated a correlation between astrocytes that underwent the greatest morphology change from patients with low levels of CSF-YKL-40 and more protective APOE genotypes. This finding was subsequently verified using similarity learning as an unbiased approach. This study shows that iPSC-derived astrocytes from AD patients reflect key aspects of the pathophysiological phenotype of those same patients, thereby offering a novel means of modelling AD, stratifying AD patients and conducting therapeutic screens. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=93 SRC="FIGDIR/small/548687v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1df3486org.highwire.dtl.DTLVardef@f184d8org.highwire.dtl.DTLVardef@48a33dorg.highwire.dtl.DTLVardef@d53a90_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

The effects of nano'' and microplastic ingestion on the survivorship and reproduction of Aedes aegypti (L.) and Aedes albopictus (Skuse)

Microplastics (MPs) and nanoplastics (NPs) are pervasive environmental pollutants that raise concerns due to their potential impact on organisms across different trophic levels. While the effects of MPs on aquatic organisms have been extensively studied, their impacts on terrestrial organisms, mainly insects, still need to be explored. This study investigates the effects of MP and NP ingestion on the survivorship and reproduction of two medically important mosquito species, Aedes aegypti (L.), and Ae. albopictus (Skuse). Larval and pupal survivorship were not significantly affected by particle size or concentration, but there was a reduction of Ae. aegypti pupal survivorship associated with the ingestion of 0.03 {micro}m NPs. Results also suggest that ingesting 0.03 {micro}m NPs reduced egg production in both mosquito species. However, there was little impact of 0.03 NP and 1.0 {micro}m MP ingestion on adult survivorship and longevity. To further investigate the effects of MP ingestion on mosquito fitness, we also examined the effects of lab generated MPs of varying shape, size, and plastic polymer type on Ae. aegypti immature and adult survivorship. The data suggests that the polymer type and shape did not impact Ae. aegypti immature or adult survivorship. These findings highlight the potential consequences and the need to investigate further the ecological and potential public health implications of MP and NP ingestion by mosquitoes.

microbiology↗

Endothelial Caspase-9 Promotes Glial Changes, Inflammation, and Contrast Sensitivity Decline in Retinal Vascular Injury

Retinal glial cells-- microglia, astrocytes, and Muller glia--provide homeostatic support, regulate vascular blood flow, and react to injury by releasing inflammatory cytokines. Glial reactivity has been shown to be relevant for retinal vascular pathology and neuronal death. Non-apoptotic expression of endothelial caspase-9 (EC Casp9) was recently identified as a key mediator of retinal edema, hypoxic-ischemic injury, and neurodegeneration in retinal vein occlusion (RVO). In the current study we aimed to determine the glial responses that are modulated by EC Casp9 as a means to identify relevant neuro-immune mechanisms for the development of retinal edema and neurodegeneration. To this end we used a mouse model of RVO and a tamoxifen inducible EC Casp9 KO mouse line. We show that EC Casp9 leads to an increase in reactive microglia and to macrogliosis in a time-dependent manner. RVO induced an EC Casp9 dependent astroglial caspase-6 and cleavage of GFAP. Cytokine array analysis revealed that RVO increases expression of inflammatory cytokines out of which CX3CL1, IGF-1, IL-4, LIX, IL-1, M-CSF, TNF-, IL-1{beta}, IL-10, and VEGF-A, were regulated by EC Casp9. Moreover, we found that EC Casp9 deletion resulted in protection from contrast sensitivity decline one day post-RVO. These results demonstrate that caspase-9 in hypoxic endothelial cells regulates retinal inflammatory signaling in microglia, astrocytes and Muller cells and changes in visual function.

neuroscience↗

Structural maturation of SYCP1-mediated meiotic chromosome synapsis through conformational remodelling by molecular adapter SYCE3

In meiosis, a supramolecular protein structure, the synaptonemal complex (SC), assembles between homologous chromosomes to facilitate their recombination. Mammalian SC formation is thought to involve hierarchical zipper-like assembly of an SYCP1 protein lattice that recruits stabilising central element (CE) proteins as it extends. Here, we combine biochemical approaches with separation-of-function mutagenesis in mice to uncover that, rather than stabilising the SYCP1 lattice, the CE protein SYCE3 actively remodels this structure during synapsis. We find that SYCP1 tetramers undergo conformational change into 2:1 heterotrimers upon SYCE3-binding, removing their assembly interfaces and disrupting the SYCP1 lattice. SYCE3 then establishes a new lattice by its self-assembly mimicking the role of the disrupted interface in tethering together SYCP1 dimers. SYCE3 also interacts with CE complexes SYCE1-SIX6OS1 and SYCE2-TEX12, providing a mechanism for their recruitment. Thus, SYCE3 remodels the SYCP1 lattice into a CE-binding integrated SYCP1-SYCE3 lattice to achieve long-range synapsis by a mature SC.

biochemistry↗

Neurons derived from individual early Alzheimer's disease patients reflect clinical vulnerability

Establishing preclinical models of Alzheimers disease that predict clinical outcomes remains a critically important, yet to date not fully realised, goal. Models derived from human cells offer considerable advantages over non-human models, including the potential to reflect some of the inter-individual differences that are apparent in patients. Here we report an approach using induced pluripotent stem cell-derived cortical neurons from people with early symptomatic Alzheimers disease where we sought a match between individual disease characteristics in cells with analogous characteristics in the people from whom they were derived. We show that the response to amyloid-{beta} burden in life, as measured by cognitive decline and brain activity levels, varies between individuals and this vulnerability rating correlates with the individual cellular vulnerability to extrinsic amyloid-{beta} in vitro as measured by synapse loss and function. Our findings indicate that patient induced pluripotent stem cell-derived cortical neurons not only present key aspects of Alzheimers disease pathology, but also reflect key aspects of the clinical phenotypes of the same patients. Cellular models that reflect an individuals in-life clinical vulnerability thus represent a tractable method of Alzheimers disease modelling using clinical data in combination with cellular phenotypes.

neuroscience↗

Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL)

The traditional model of genomic data analysis - downloading data from centralized warehouses for analysis with local computing resources - is increasingly unsustainable. Not only are transfers slow and cost prohibitive, but this approach also leads to redundant and siloed compute infrastructure that makes it difficult to ensure security and compliance of protected data. The NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL; https://anvilproject.org) inverts this model, providing a unified cloud computing environment for data storage, management, and analysis. AnVIL eliminates the need for data movement, allows for active threat detection and monitoring, and provides scalable, shared computing resources that can be acquired by researchers as needed. This presents many new opportunities for collaboration and data sharing that will ultimately lead to scientific discoveries at scales not previously possible.

bioinformatics↗

AusTraits: a curated plant trait database for the Australian flora

We introduce the AusTraits database - a compilation of measurements of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 375 traits across 29230 taxa from field campaigns, published literature, taxonomic monographs, and individual taxa descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological parameters (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual-, species- and genus-level observations coupled to, where available, contextual information on site properties. This data descriptor provides information on version 2.1.0 of AusTraits which contains data for 937243 trait-by-taxa combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data to increase our collective understanding of the Australian flora.

ecology↗

Translational activity of the splicing factor SRSF1 is required for development and cilia function

Shuttling RNA-binding proteins coordinate nuclear and cytoplasmic steps of gene expression. The SR family proteins regulate RNA splicing in the nucleus and a subset of them, including SRSF1, shuttles between the nucleus and cytoplasm affecting post-splicing processes. However, the physiological significance of this remains unclear. Here, we used genome editing to knock-in a nuclear retention signal (NRS) in Srsf1 to create a mouse model harboring an SRSF1 protein that is retained exclusively in the nucleus. Srsf1NRS/NRS mutants displayed small body size, hydrocephalus and immotile sperm, all traits associated with ciliary defects. We observed reduced translation of a subset of mRNAs and decreased abundance of proteins involved in multiciliogenesis, with disruption of ciliary ultrastructure and motility in cells derived from this mouse model. These results demonstrate that SRSF1 shuttling is used to reprogram gene expression networks in the context of high cellular demands, as observed here, during motile ciliogenesis.

molecular biology↗