Biology subjects

Owen, C.

Publications and source records attributed to Owen, C..

11 recordsLinked to original sources

bioRxiv2026

Hypoxia versus immune depletion - immune profiling and treatment cessation provide mechanistic insights and considerations for translation in Leigh syndrome

Genetic mitochondrial diseases (GMDs) are major challenges to human health accounting for a significant fraction of heritable neurologic diseases, myopathies, and inborn errors of metabolism. Leigh syndrome (LS) is the most common clinical presentation of GMD in pediatric patients. LS is a severe and complex disease for which effective clinical therapies are currently lacking. Preclinical therapies identified in the Ndufs4(-/-) mouse model of LS include immune-targeting interventions and chronic mild hypoxia (11% oxygen). Immune-targeting interventions include rapamycin and high-dose pexidartinib, the latter appearing to fully suppress disease. The mechanisms underlying the benefits of hypoxia remain unclear, and the relationship between hypoxia and immune interventions have not been assessed. Here, we report the immune profile of brainstem of the Ndufs4(-/-) mouse model prior to and after disease onset and the impact of pexidartinib treatment. We provide evidence that macrophages/monocytes drive pathology, consistent with recent genetic studies. We additionally find that pre-disease onset animals lack signs of inflammation, and that the elimination of leukocytes fully suppresses the molecular signature of disease. Finally, using distinct post-developmental periods of treatment, we find pexidartinib and rapamycin provide benefits which persist long beyond treatment cessation, while cessation of hypoxia results in rapid disease onset and an acceleration of disease progression. These findings are consistent with hypoxia acting upstream of immune cell activation and have major implications for the therapeutic translation of both hypoxia and immune targeting interventions. Our findings establish hypoxia-cessation as a novel method for synchronizing inflammatory disease onset in the Ndufs4(-/-) model which will be useful in future mechanistic studies.

pathology↗

bioRxiv2026

Systematic prediction and functional analysis of amino acid residues determining product specificity in the plant oxidosqualene cyclase superfamily

Oxidosqualene cyclases (OSCs) catalyse one of natures most intricate enzyme reactions, converting the linear precursor 2,3-oxidosqualene into an array of cyclic triterpene scaffolds through sequential carbocation cascades. Predicting OSC function based on sequence is challenging beyond broad family-level classification. Here, we develop a structure-based computational framework to identify amino acid determinants of OSC product specificity. Using 169 functionally characterised OSCs, we deploy a multifaceted approach combining differential conservation along with structural information, physico-chemical properties of amino acids and binding pocket electrostatics in order to understand the determinants of product specificity. Using Arabidopsis thaliana cycloartenol synthase AtCAS as a model, we then validate our predictions through targeted mutagenesis, achieving stepwise reprogramming towards the protosteryl-type products cucurbitadienol and lanosterol, including complete product switches. Molecular dynamics simulations support a mechanism in which subtle pocket remodelling alters active-site volume, water access and proton-elimination chemistry. These findings provide a blueprint for OSC engineering.

plant biology↗

bioRxiv2026

Diverse Diterpenoid Phytoalexins Shape Wheat Chemical Defenses

Cereal crops rely on a wide array of specialized metabolites to defend themselves against microbial pathogens. Here, using a combination of genome-wide analysis, heterologous pathway reconstruction, structural elucidation and in planta validation, we identify two pathogen-induced diterpenoid pathways in wheat that produce diterpenoids: the new glycosylated diterpenes aspisoside A and aspisoside B, and the diterpene alcohols scutenol A and scutenol B. The pathogen-responsive nature of these pathways, together with their antimicrobial activity are consistent with a likely defensive role in wheat. These compounds are produced by two biosynthetic gene clusters, each encoding a discrete pathway, so revealing organizational separation of wheat diterpenoid-based chemical defenses. The aspisoside-producing gene cluster is syntenic with diterpenoid phytoalexin-producing clusters in rice and barley, for momilactone and hordedane biosynthesis, respectively, yet gives rise to structurally distinct phytoalexins in wheat. The scutenol cluster is syntenic with currently uncharacterized predicted biosynthetic gene clusters in barley, oat, and Brachypodium. These findings establish diterpene glycosides as a previously unrecognized component of wheat defense chemistry and provide new insights into the chemical diversification of defense-related biosynthetic gene clusters within the Poaceae.

plant biology↗

bioRxiv2025

plantiSMASH 2.0: improvements to detection, annotation, and prioritization of plant biosynthetic gene clusters

Plants produce bioactive compounds as part of their specialized metabolism, with applications in medicine, agriculture, and nutrition. The biosynthesis of a growing number of these specialized metabolites has been found to be encoded in biosynthetic gene clusters (BGCs), creating increasing demand for genome mining tools to automate their detection. plantiSMASH enables the identification of putative plant BGCs through a rule-based approach, available via both command-line and web interfaces. Here, we present plantiSMASH 2.0 (https://plantismash.bioinformatics.nl/), a major update that expands and improves the original framework with revised and additional BGC detection rules (now supporting 12 BGC types), substrate prediction for selected enzyme families, and regulatory analysis through transcription factor binding site detection. The updated plantiSMASH 2.0 database includes 30,423 putative BGCs across 430 genomes. Together, these improvements make plantiSMASH 2.0 a powerful and comprehensive platform for the detection and characterization of plant biosynthetic pathways, supporting and accelerating research in plant specialized metabolism and plant natural product discovery.

bioinformatics↗

bioRxiv2024

Identification of methylation-sensitive human transcription factors using meSMiLE-seq

Transcription factors (TFs) are key players in eukaryotic gene regulation, but the DNA binding specificity of many TFs remains unknown. Here, we assayed 284 mostly poorly characterized, putative human TFs using selective microfluidics-based ligand enrichment followed by sequencing (SMiLE-seq), revealing 72 new DNA binding motifs. To investigate whether some of the 158 TFs for which we did not find motifs preferably bind epigenetically modified DNA (i.e. methylated CG dinucleotides), we developed methylation-sensitive SMiLE-seq (meSMiLE-seq). This microfluidic assay simultaneously probes the affinity of a protein to methylated and unmethylated DNA, augmenting the capabilities of the original method to infer methylation-aware binding sites. We assayed 114 TFs with meSMiLE-seq and identified DNA-binding models for 48 proteins, including the known methylation-sensitive binding modes for POU5F1 and RFX5. For 11 TFs, binding to methylated DNA was preferred or resulted in the discovery of alternative, methylation-dependent motifs (e.g. PRDM13), while aversion towards methylated sequences was found for 13 TFs (e.g. USF3). Finally, we uncovered a potential role for ZHX2 as a putative binder of Z-DNA, a left-handed helical DNA structure which is adopted more frequently upon CpG methylation. Altogether, our study significantly expands the human TF codebook by identifying DNA binding motifs for 98 TFs, while providing a versatile platform to quantitatively assay the impact of DNA modifications on TF binding.

genomics↗

bioRxiv2022

Complex scaffold remodeling in plant triterpene biosynthesis

Triterpenes with complex scaffold modifications are widespread in plants yet little is known regarding biosynthesis. Limonoids are an exemplary family that includes the bitter taste in citrus (e.g., limonin) and the active constituents in neem oil, a widely used bioinsecticide (e.g., azadirachtin). Despite limonoid commercial value, a complete biosynthetic route has not been described. Here, we report the discovery of 22 enzymes that catalyze 12 unique reactions including the 4-carbon scission and furan installation that are a signature of the limonoid family and a pair of sterol isomerases previously unknown in plants. This gene set is then used for the total biosynthesis of kihadalactone A and azadirone in a heterologous plant. These results enable access to valuable limonoids and provide a template for discovery and reconstitution of triterpene biosynthetic pathways in plants that require multiple skeletal rearrangements and oxidations.

biochemistry↗

bioRxiv2021

Genome Mining Uncovers Clustered Biosynthetic Pathways for Defense-Related Molecules in Bread Wheat

Wheat is one of the most widely grown food crops in the world. However, it succumbs to numerous pests and pathogens that cause substantial yield losses. A better understanding of biotic stress responses in wheat is thus of major importance. Here we identify previously unknown pathogen-induced biosynthetic pathways that produce a diverse set of molecules, including flavonoids, diterpenes and triterpenes. These pathways are encoded by six biosynthetic gene clusters and share a common regulatory network. We further identify associations with known or novel phytoalexin clusters in other cereals and grasses. Our results significantly advance the understanding of chemical defenses in wheat and open up new avenues for enhancing disease resistance in this agriculturally important crop.

plant biology↗

bioRxiv2021

A phylogeny-based metric for estimating changes in transmissibility from recurrent mutations in SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in late 2019 and spread globally to cause the COVID-19 pandemic. Despite the constant accumulation of genetic variation in the SARS-CoV-2 population, there was little evidence for the emergence of significantly more transmissible lineages in the first half of 2020. Starting around November 2020, several more contagious and possibly more virulent Variants of Concern (VoCs) were reported in various regions of the world. These VoCs share some mutations and deletions that haven arisen recurrently in distinct genetic backgrounds. Here, we build on our previous work modelling the association of mutations to SARS-CoV-2 transmissibility and characterise the contribution of individual recurrent mutations and deletions to estimated viral transmissibility. We then assess how patterns of estimated transmissibility in all SARS-CoV-2 clades have varied over the course of the COVID-19 pandemic by summing transmissibility estimates for all individual mutations carried by any sequenced genome analysed. Such an approach recovers the Delta variant (21A) as the most transmissible clade currently in circulation, followed by the Alpha variant (20I). By assessing transmissibility over the time of sampling, we observe a tendency for estimated transmissibility within clades to slightly decrease over time in most clades. Although subtle, this pattern is consistent with the expectation of a decay in transmissibility in mainly non-recombining lineages caused by the accumulation of weakly deleterious mutations. SARS-CoV-2 remains a highly transmissible pathogen, though such a trend could conceivably play a role in the turnover of different global viral clades observed over the pandemic so far. CaveatsO_LIThis work is not about the severity of disease. We do not analyse the severity of disease. We do not present any evidence that SARS-CoV-2 has decreased in severity. C_LIO_LILineage replacement dynamics are affected by many factors. The trend we recover for a decrease in inferred transmissibility of a clade over time is a small effect. We caution against over-interpretation. This result would not affect the management of the SARS-CoV-2 pandemic: for example, we make no claims about any impact on the efficacy of particular non-pharmaceutical interventions (NPIs). C_LIO_LIOur phylogeny-based method to infer changes in estimated transmissibility due to recurrent mutations and deletions makes a number of simplifying assumptions. These may not all be valid. The consistent trend for the slight decrease we report might be due to an as-yet-unidentified systematic bias. C_LI

genomics↗

bioRxiv2021

The anthropometric and physical qualities of womens rugby league Super League and international players; identifying differences in playing position and standard

Participation in womens rugby league has been growing since the foundation of the English womens rugby league Super League in 2017. However, the evidence base to inform womens rugby league remains sparse. This study provides the largest quantification of anthropometric and physical qualities of womens rugby league players to date, identifying differences between positions (forwards & backs) and playing standard (Womens Super League [WSL] vs. International). The height, weight, body composition, lower body strength, jump height, speed and aerobic capacity of 207 players were quantified during the pre-season period. Linear mixed models and effects sizes were used to determine differences between positions and standards. Forwards were significantly (p < 0.05) heavier (forwards: 82.5 {+/-} 14.8kg; backs: 67.7 {+/-} 9.2kg) and have a greater body fat % (forwards: 37.7 {+/-} 6.9%; backs: 30.4 {+/-} 6.3%) than backs. Backs had significantly greater lower body power measured via jump height (forwards: 23.5 {+/-} 4.4cm; backs: 27.6 {+/-} 4.9cm), speed over 10m (forwards: 2.12 {+/-} 0.14s; backs: 1.98 {+/-} 0.11s), 20m (forwards: 3.71 {+/-} 0.27s; backs: 3.46 {+/-} 0.20s), 30m (forwards: 5.29 {+/-} 0.41s; backs: 4.90 {+/-} 0.33s), 40m (forwards: 6.91 {+/-} 0.61s; backs: 6.33 {+/-} 0.46s) and aerobic capacity (forwards: 453.4 {+/-} 258.8m; backs: 665.0 {+/-} 298.2m) than forwards. Additionally, international players were found to have greater anthropometric and physical qualities in comparison to their WSL counterparts. This study adds to the limited evidence base surrounding the anthropometric and physical qualities of elite womens rugby league players. Comparative values for anthropometric and physical qualities are provided which practitioners may use to evaluate the strengths and weaknesses of players, informing training programs to prepare players for the demands of womens rugby league.

physiology↗

bioRxiv2020

Recurrent mutations in SARS-CoV-2 genomes isolated from mink point to rapid host-adaptation

SARS-CoV-2, the agent of the COVID-19 pandemic, can infect a wide range of mammals. Since its spread in humans, secondary host jumps of SARS-CoV-2 from humans to a variety of domestic and wild populations of mammals have been documented. The evolution of SARS-CoV-2 in different host species is of fundamental interest while also providing indication of how SARS-CoV-2 may have adapted to human hosts soon after the initial host jump, a time window for which there are no genome sequences available. Moreover, the study of SARS-CoV-2 circulating in animals is critical to assess the risk that the transmission of animal-adapted viral lineages back into humans (i.e., spillback) may pose. Here, we compared the genomic landscapes of SARS-CoV-2 isolated from animal species relative to that in humans, profiling the mutational biases indicative of potentially different selective pressures in animals. We focused on viral genomes collected in infected mink (Neovison vison) and white-tailed deer (Odocoileus virginianus) for which reports of multiple independent spillover events and subsequent animal-to-animal transmission are available. We identified six candidate mutations for animal-specific adaptation in mink (NSP9_G37E, Spike_F486L, Spike_N501T, Spike_Y453F, ORF3a_T229I, ORF3a_L219V), and one in deer (NSP3a_L1035F), though these mutations appear to confer minimal advantage for circulation in humans. Additionally, circulation of SARS-CoV-2 in mink and deer has not caused considerable changes to the evolutionary trajectory of SARS-CoV-2 thus far. Finally, our results suggest that minimal adaptation was required for human-to-animal spillover and subsequent onward transmission in mink and deer, highlighting the generalist nature of SARS-CoV-2 as a pathogen of mammalian hosts.

genomics↗

bioRxiv2018

Temperature is a key driver of a wildlife epidemic and future warming will increase impacts

Increasing environmental temperatures are predicted to have increasingly severe and deleterious effects on biodiversity. For the most part, the impacts of a warming environment are presumed to be direct, however some predict increasingly severe disease epidemics, primarily from vector-borne pathogens, that will have the capacity to deplete host populations. Data to support this hypothesis are lacking. Here we describe increasing severity of ranavirosis driven by increasing temperature affecting a widely distributed amphibian host. Both in vitro and in vivo experiments showed that increasing environmental temperature leads to increased propagation of ranavirus and, in the latter, increased incidence of host infection and mortality. Also, temperature was shown to be a key determinant of disease dynamics in wild amphibians, raising the odds and severity of disease incidents. The direction of this effect was highly consistent in the context of other interacting variables such as shading around ponds. Projections based on future climate indicate that changes in seasonal weather in the UK will result in the increased incidence of severe cases of ranavirosis in amphibian populations that could affect recruitment. These complementary lines of evidence present a clear case of direct environmental modulation of a host-pathogen interaction and provide information for proposing mitigation actions.

epidemiology↗