Biology subjects

Watson, H.

Publications and source records attributed to Watson, H..

11 recordsLinked to original sources

bioRxiv2026

Broad scale environmental conditions, not urbanisation, explain geographic variation in great tit feather microstructure

Urbanisation imposes novel environmental conditions that can shape phenotypic traits including plumage, yet, its effects on characteristics beyond colouration remain poorly understood. Feather microstructure plays an important role in thermoregulation, protection from solar radiation and waterproofing, and its expression is sensitive to environmental conditions. Here, we quantified feather barbule density, a key component of feather microstructure, in great tits (Parus major) from five urban-rural paired populations across Europe to assess its association with urbanisation, temperature and elevation. We found no significant effects of the urban environment or temperature. However, feather microstructure significantly varied between the studied areas and was positively associated with elevation and ultraviolet B (UV-B) radiation, suggesting a potential adaptive response to variation in solar radiation.

ecology↗

bioRxiv2026

Interleaved multi-magnification cryo-electron tomography bridges cellular and structural biology

Cryo-electron tomography (cryo-ET) enables in situ structural analysis of macromolecular complexes within native cellular environments. However, the limited field of view required for high-resolution structure determination necessarily restricts a wider assessment of the broader cellular context. We present a multi-magnification cryo-ET acquisition strategy that integrates low- and high-magnification information from coincident sample regions during the same tilt-series. By interleaving acquisition of the magnifications at each tilt angle, this strategy enables simultaneous collection of large field-of-view, low-resolution tomograms and high-resolution, small field-of-view tomograms while minimising the impact of the increased electron dose. We demonstrate that we can capture cellular organisation across tens of microns, while still enabling subtomogram averaging to resolutions below 4 [A]. This integrated acquisition framework establishes a practical route to multi-scale cryo-ET, bridging molecular and cellular scales for more comprehensive biological insight.

biochemistry↗

bioRxiv2025

Isolation of functional supramolecular attack particles (SMAPs)

High density cultures of the GMP compatible NK-92 natural killer cell line release heterogeneous extracellular particles (EP), notably extracellular vesicles (EV) and non-vesicular extracellular particles (NVEP). The NVEP include a small proportion of supramolecular attack particles (SMAPs), the direct cytotoxic potential of which suggests therapeutic promise, yet scalable enrichment and functional evaluation alongside other extracellular particles (EPs) have been lacking. Here, we develop a high-resolution serial size-exclusion liquid chromatography (SELC) workflow that resolves EPs into 4 fractions F1-F4, in which EV are enriched in F2 and SMAPs are enriched in F3. Multi-modal characterization using Nanoparticle Tracking Analysis (NTA), Nano Flow Cytometry (Nano FCM), Transmission Electron Microscopy (TEM), Total Internal Reflection Microscopy (TIRFM) and Proteomics) demonstrated that F2 NK-92 EVs are [~]130-150 nm particles enriched for complement proteins, whereas SMAPs (F3) are 100-110 nm particles enriched for cytotoxic proteins (PRF1, GZMB) and SMAP shell components (e.g., THBS1, THBS4). Functionally, Ca2+-stabilized SMAPs (F3) trigger caspase-3-dependent apoptosis in tumor cell lines with robust dose responses, while F2 lacks direct cytotoxicity in vitro. Ex vivo, F3 SMAPs kill patient-derived breast cancer and chronic lymphocytic leukaemia cells (CLL) in a concentration-dependent manner. In NSG mice, intra-tumoral treatment with SMAPs (F3) restrains the growth of aggressive B16F10 melanoma and PANC-1 pancreatic cancer, confirming in vivo functionality. These results establish a scalable method to isolate and compare NK-derived particle classes and provide a foundation for targeted SMAP engineering as a promising approach for treatment of solid tumours. Significance StatementCell therapies face barriers in solid tumours, including lack of entry and suppression. NK cells release extracellular particles (EPs), including supramolecular attack particles (SMAPs), that can traffic into tumour tissue. We define a practical, scalable chromatography process that resolves NK-derived SMAPs from other EPs and demonstrate that SMAPs induce caspase mediated apoptosis in vitro and engage in cytotoxic lymphocyte independent anti-tumour activity in vivo. These insights open a route to engineering and testing SMAP-based therapeutics to overcome limitations of whole-cell approaches in solid cancers.

immunology↗

bioRxiv2025

Developmental PBDE exposure impairs histamine release dynamics in adult male and female mice via disrupted granule maturation and calcium mobilization

Polybrominated diphenyl ethers (PBDEs) are synthetic flame retardants once widely used in furniture, electronics, and other consumer products. Although phased out in the early 2000s, their persistence and recycling into new materials have led to continued environmental contamination and widespread human exposure --particularly through diet and indoor dust. Developing individuals face the highest exposure due to placental transfer, breastfeeding, and behavior, and are especially vulnerable to long-term effects. While developmental PBDE exposure has been linked to neurobehavioral, endocrine, and metabolic disruptions, effects on the immune system remain underexplored. To address this, we focused on mast cells--long-lived, tissue-resident innate immune cells enriched at barrier surfaces and perivascular sites throughout the body, including the brain. Their strategic positioning, broad receptor repertoire, and ability to rapidly release bioactive mediators suggest a key role in mediating multisystemic effects of developmental exposures. Here we show that maternal exposure to [~]87Lg/kg/day of PBDE throughout pregnancy and lactation--a dose aligned with the lower end known to affect metabolic and neurobehavioral outcomes in preclinical models--leads to persistent dysfunction in mast cell mediator release in adult male and female offspring. This was evidenced by blunted anaphylaxis-associated hypothermia and plasma histamine release in vivo. These deficits were not due to changes in tissue-resident mast cell numbers, but rather to an impaired capacity to sustain histamine release over time. In vitro studies of mast cells derived from adult bone marrow revealed that histamine synthesis was intact, but granule maturation and stimulus-induced calcium mobilization were disrupted, in association with downregulation of genes such as IGF2R, ITGA4, ITGB6, and NGFR. These results identify a novel mechanism by which developmental PBDE exposure impairs mast cell function, with implications for broader immune and physiological dysfunctions. This is particularly concerning for developing individuals, who not only accumulate the highest levels via placental transfer, breastfeeding, and behavioral factors, but are also especially vulnerable to long-term effects. Despite well-documented impacts of developmental PBDE exposure on neurobehavioral, endocrine, and metabolic systems, the effects on the immune system remain comparatively underexplored. To begin addressing this gap, we focused on mast cells--innate immune cells well-positioned to contribute to the multisystemic effects of developmental exposures. Mast cells are long-lived, tissue-resident cells enriched at barrier surfaces and perivascular sites throughout the body, including the brain. Their widespread distribution, extensive receptor repertoire, and unique ability to store and rapidly release bioactive mediators from cytoplasmic granules position them as key modulators of immune, endocrine, and nervous system function. Using oral exposure to two doses of a PBDE mixture throughout pregnancy and lactation in mice, here we show that maternal exposure to [~]87Lg/kg/day--aligned with the lower end of doses known to affect metabolic and neurobehavioral outcomes in preclinical models, and within 10-fold of levels measured in human serum and placenta--leads to persistent dysfunction in mast cell mediator release in adult male and female offspring. This was evidenced by blunted anaphylaxis-associated hypothermia and plasma histamine release in vivo. These deficits were not due to changes in tissue-resident mast cell numbers, but rather to an impaired capacity to sustain histamine release over time. Studies in bone marrow-derived mast cells (BMMCs) revealed that histamine synthesis was intact, but granule maturation and stimulus-induced calcium mobilization were disrupted, in association with downregulation of genes such as IGF2R, ITGA4, ITGB6, and NGFR. Given that the bone marrow is the primary postnatal source of mast cells, these findings suggest that PBDEs induce lasting reprogramming at the level of hematopoietic progenitors--with broad implications not only for mast cell function across tissues, but potentially for other immune cell lineages as well. In sum, this study provides the first evidence that developmental exposure to PBDEs induces long-lasting impairments in mast cell functions, suggesting a previously unrecognized mechanism by which early-life exposure to environmental toxicants could contribute to persistent physiological and behavioral dysfunctions

pharmacology and toxicology↗

bioRxiv2025

Human milk oligosaccharide metabolism by Clostridium species suppresses inflammation and pathogen growth

Gut microbiome development is strongly impacted by breastmilk and human milk oligosaccharides (HMOs), with short- and long-term health implications. HMO metabolism is best characterised within bifidobacteria, but the full range of other HMO-utilising species remains unknown. This study examined HMO-utilising bacteria that colonise preterm infants (born <32 weeks gestation), their role in microbiome modulation, and their effects on intestinal barrier function. We found that infant-derived Clostridium perfringens, and three other Clostridium species, metabolise HMOs, producing short chain fatty acids, tryptophan catabolites, and other metabolites known to improve host health. C. perfringens inhibited pathobiont growth and supressed inflammation in preterm-derived intestinal organoids. These findings suggest a previously unrecognised role for C. perfringens, specifically those lacking the perfringolysin O gene, in promoting healthy gut development during infancy.

microbiology↗

bioRxiv2024

Xenon plasma focused ion beam lamella fabrication on high-pressure frozen specimens for structural cell biology

Cryo focused ion beam lamella preparation is a potent tool for in situ structural biology, enabling the study of macromolecules in their native cellular environments. However, throughput is currently limited, especially for thicker, more biologically complex samples. We describe how xenon plasma focused ion beam milling can be used for routine bulk milling of thicker, high-pressure frozen samples during lamellae preparation with a high success rate and determine a 4.0 [A] structure of the Escherichia coli ribosome on these lamellae using sub volume averaging. We determine the effects of increased ion currents on sample integrity during bulk milling of thicker planar samples, also showing that beyond an initial region of damage, no measurable structural damage propagates beyond this. The use of xenon results in substantial structural damage to particles up to 30 nm in depth from the milled surfaces, with detectable damage observed to 45 nm. Ours results outlines how the use of high currents using xenon plasma focused ion beam milling may be integrated into FIB milling regimes for preparing thin lamellae for high-resolution in situ structural biology.

biochemistry↗

bioRxiv2022

Urbanisation impacts plumage colouration in a songbird across Europe: evidence from a correlational, experimental, and meta-analytical approach

Urbanisation is increasing at a phenomenal rate across the globe, transforming landscapes, presenting organisms with novel challenges, shaping phenotypic traits, and even impacting fitness. Among colour traits, urban individuals are widely claimed to have duller tones in carotenoid-based traits, the so-called "urban dullness" phenomenon. However, at the intra-specific level, this generalisation is surprisingly inconsistent and often based on examples from single urban/non-urban population pairs or a limited geographic area. Here, combining correlational, experimental, and meta-analytical results from a common songbird, the great tit (Parus major), we investigated carotenoid-based plumage coloration in urban and forest populations across Europe. We find that, as predicted, urban individuals are paler than forest individuals. Interestingly, we also find large population-specific differences in the magnitude of the urban-forest contrast in plumage colouration. Moreover, our meta-analysis indicates a non-significant effect of environmental pollution on carotenoid-based plumage for the species, suggesting that the observed differences across urban populations are not only driven by pollution. Finally, using one region as an example (Malmo, Sweden), we reveal population-specific processes behind plumage colouration differences, which are likely the result of variation in the spatial and temporal distribution of carotenoid-rich resources in anthropogenic environments. This is the first study to quantify the consistency of an oft-cited textbook example of the impact of urbanisation on wildlife; our results provide the most convincing evidence to date of the "urban dullness" phenomenon, but also highlight that the magnitude of the phenomenon depends on local urban characteristics.

evolutionary biology↗

bioRxiv2022

Inhibiting Runx1 protects heart function after myocardial infarction

Myocardial infarction is a major cause of death worldwide. Effective treatments are required that limit adverse cardiac remodelling and preserve cardiac contractility following myocardial infarction, with the aim of improving patient outcomes and preventing progression to heart failure. The perfused but hypocontractile myocardium bordering a newly created infarct is functionally distinct from the remote surviving myocardium; it is also a major determinant of adverse cardiac remodelling and whole heart contractility. Expression of the transcription factor RUNX1 is increased in the border zone at 1 day after myocardial infarction, suggesting potential for targeted therapeutic intervention. Here we demonstrate that RUNX1 drives reductions in cardiomyocyte contractility, sarcoplasmic reticulum-mediated calcium release, mitochondrial density, and the expression of genes important for oxidative phosphorylation. Antagonising RUNX1 expression via short-hairpin RNA interference preserved cardiac contractile function following myocardial infarction when delivered either via direct adenoviral delivery into the border zone or via an adeno-associated virus vector administered intravenously. Equivalent effects were obtained with a small molecule inhibitor (Ro5-3335) that reduces RUNX1 function by blocking its interaction with the essential co-factor CBF{beta}. Both tamoxifen-inducible Runx1-deficient and Cbf{beta}-deficient cardiomyocyte-specific mouse models demonstrated that antagonising RUNX1 function preserves the expression of genes important for oxidative phosphorylation following myocardial infarction. Our results confirm the translational potential of RUNX1 as a novel therapeutic target in myocardial infarction, with wider opportunities for use across a range of cardiac diseases where RUNX1 drives adverse cardiac remodelling.

pathology↗

bioRxiv2019

Correcting the coverage of credible sets in Bayesian genetic fine-mapping

Genome Wide Association Studies (GWAS) have successfully identified thousands of loci associated with human diseases. Bayesian genetic fine-mapping studies aim to identify the specific causal variants within GWAS loci responsible for each association, reporting credible sets of plausible causal variants, which are interpreted as containing the causal variant with some "coverage probability". Here, we use simulations to demonstrate that the coverage probabilities are over-conservative in most fine-mapping situations. We show that this is because fine-mapping data sets are not randomly selected from amongst all causal variants, but from amongst causal variants with larger effect sizes. We present a method to re-estimate the coverage of credible sets using rapid simulations based on the observed, or estimated, SNP correlation structure, we call this the "corrected coverage estimate". This is extended to find "corrected credible sets", which are the smallest set of variants such that their corrected coverage estimate meets the target coverage. We use our method to improve the resolution of a fine-mapping study of type 1 diabetes. We found that in 27 out of 39 associated genomic regions our method could reduce the number of potentially causal variants to consider for follow-up, and found that none of the 95% or 99% credible sets required the inclusion of more variants - a pattern matched in simulations of well powered GWAS. Crucially, our correction method requires only GWAS summary statistics and remains accurate when SNP correlations are estimated from a large reference panel. Using our method to improve the resolution of fine-mapping studies will enable more efficient expenditure of resources in the follow-up process of annotating the variants in the credible set to determine the implicated genes and pathways in human diseases. Author summaryPinpointing specific genetic variants within the genome that are causal for human diseases is difficult due to complex correlation patterns existing between variants. Consequently, researchers typically prioritise a set of plausible causal variants for functional validation - these sets of putative causal variants are called "credible sets". We find that the probabilistic interpretation that these credible sets do indeed contain the true causal variant is variable, in that the reported probabilities often underestimate the true coverage of the causal variant in the credible set. We have developed a method to provide researchers with a "corrected coverage estimate" that the true causal variant appears in the credible set, and this has been extended to find "corrected credible sets", allowing for more efficient allocation of resources in the expensive follow-up laboratory experiments. We used our method to reduce the number of genetic variants to consider as causal candidates for follow-up in 27 genomic regions that are associated with type 1 diabetes.

genetics↗

bioRxiv2019

Shared Genetic Risk between Eating Disorder- and Substance-Use-Related Phenotypes: Evidence from Genome-Wide Association Studies

Eating disorders and substance use disorders frequently co-occur. Twin studies reveal shared genetic variance between liabilities to eating disorders and substance use, with the strongest associations between symptoms of bulimia nervosa (BN) and problem alcohol use (genetic correlation [rg], twin-based=0.23-0.53). We estimated the genetic correlation between eating disorder and substance use and disorder phenotypes using data from genome-wide association studies (GWAS). Four eating disorder phenotypes (anorexia nervosa [AN], AN with binge-eating, AN without binge-eating, and a BN factor score), and eight substance-use-related phenotypes (drinks per week, alcohol use disorder [AUD], smoking initiation, current smoking, cigarettes per day, nicotine dependence, cannabis initiation, and cannabis use disorder) from eight studies were included. Significant genetic correlations were adjusted for variants associated with major depressive disorder (MDD). Total sample sizes per phenotype ranged from ~2,400 to ~537,000 individuals. We used linkage disequilibrium score regression to calculate single nucleotide polymorphism-based genetic correlations between eating disorder and substance-use-related phenotypes. Significant positive genetic associations emerged between AUD and AN (rg=0.18; false discovery rate q=0.0006), cannabis initiation and AN (rg=0.23; q<0.0001), and cannabis initiation and AN with binge-eating (rg=0.27; q=0.0016). Conversely, significant negative genetic correlations were observed between three non-diagnostic smoking phenotypes (smoking initiation, current smoking, and cigarettes per day) and AN without binge-eating (rgs=-0.19 to -0.23; qs<0.04). The genetic correlation between AUD and AN was no longer significant after co-varying for MDD loci. The patterns of association between eating disorder- and substance-use-related phenotypes highlights the potentially complex and substance-specific relationships between these behaviors.

genetics↗

bioRxiv2019

RICOPILI: Rapid Imputation for COnsortias PIpeLIne

MotivationGenome-wide association study (GWAS) analyses, at sufficient sample sizes and power, have successfully revealed biological insights for several complex traits. RICOPILI, an open sourced Perl-based pipeline was developed to address the challenges of rapidly processing large scale multi-cohort GWAS studies including quality control, imputation and downstream analyses. The pipeline is computationally efficient with portability to a wide range of high-performance computing (HPC) environments.\n\nSummaryRICOPILI was created as the Psychiatric Genomics Consortium (PGC) pipeline for GWAS and has been adopted by other users. The pipeline features i) technical and genomic quality control in case-control and trio cohorts ii) genome-wide phasing and imputation iv) association analysis v) meta-analysis vi) polygenic risk scoring and vii) replication analysis. Notably, a major differentiator from other GWAS pipelines, RICOPILI leverages on automated parallelization and cluster job management approaches for rapid production of imputed genome-wide data. A comprehensive meta-analysis of simulated GWAS data has been incorporated demonstrating each step of the pipeline. This includes all of the associated visualization plots, to allow ease of data interpretation and manuscript preparation. Simulated GWAS datasets are also packaged with the pipeline for user training tutorials and developer work.\n\nAvailability and ImplementationRICOPILI has a flexible architecture to allow for ongoing development and incorporation of newer available algorithms and is adaptable to various HPC environments (QSUB, BSUB, SLURM and others). Specific links for genomic resources are either directly provided in this paper or via tutorials and external links. The central location hosting scripts and tutorials is found at this URL: https://sites.google.com/a/broadinstitute.org/RICOPILI/home\n\nContactsripke@broadinstitute.org\n\nSupplementary informationSupplementary data are available.

genetics↗