Biology subjects

Bray, J.

Publications and source records attributed to Bray, J..

5 recordsLinked to original sources

bioRxiv2025

Ancestral neuronal receptors are bacterial accessory toxins

Symbiosis and horizontal gene transfer events were crucial in the emergence of eukaryotic and multicellular life. A striking example is the acquisition of Teneurins, putative surface-exposed toxins in bacteria that function as cell adhesion receptors in metazoan neuronal development. Here, we demonstrate the evolutionary relationships between metazoan and bacterial Teneurins. We show that bacterial Teneurins are accessory proteins, that harbour diverse encapsulated toxins. They predominate in species with complex social behaviours, suggesting roles in both cell-to-cell competition and cooperation. Metazoan Teneurins are therefore repurposed bacterial toxins central to cell-to-cell communication in nervous systems. Their acquisition was a foundational event in the evolution of metazoans.

biochemistry↗

bioRxiv2024

Castanet: a pipeline for rapid analysis of targeted multi-pathogen genomic data

MotivationTarget enrichment strategies generate genomic data from multiple pathogens in a single process, greatly improving sensitivity over metagenomic sequencing and enabling cost-effective, high throughput surveillance and clinical applications. However, uptake by research and clinical laboratories is constrained by an absence of computational tools that are specifically designed for the analysis of multi-pathogen enrichment sequence data. Here we present the Castanet pipeline: an analysis pipeline for end-to-end processing and consensus sequence generation for use with multi-pathogen enrichment sequencing data. Castanet is designed to work with short-read data produced by existing targeted enrichment strategies, but can be readily deployed on any BAM file generated by another methodology. It is packaged with usability features, including graphical interface and installer script. ResultsIn addition to genome reconstruction, Castanet reports method-specific metrics that enable quantification of capture efficiency, estimation of pathogen load, differentiation of low-level positives from contamination, and assessment of sequencing quality. Castanet can be used as a traditional end-to-end pipeline for consensus generation, but its strength lies in the ability to process a flexible, pre-defined set of pathogens of interest directly from multi-pathogen enrichment experiments. In our tests, Castanet consensus sequences were accurate reconstructions of reference sequences, including in instances where multiple strains of the same pathogen were present. Castanet performs effectively on standard laptop computers and can process the entire output of a 96-sample enrichment sequencing run (50M reads) using a single batch process command, in < 2 h. Availability and ImplementationSource code freely available under GPL-3 license at https://github.com/MultipathogenGenomics/castanet, implemented in Python 3.10 and supported in Ubuntu Linux 22.04 and other Bash-like environments. The data for this study have been deposited in the European Nucleotide Archive (ENA) at EMBL-EBI under accession number PRJEB77004.

bioinformatics↗

bioRxiv2024

Mouse Exploratory behaviour in the open field with and without NAT-1 EEG device: Effects of MK801 and scopolamine

AbstractOne aspect of reproducibility in preclinical research that is frequently overlooked is the physical condition in which physiological, pharmacological or behavioural recordings are conducted. In this study, the physical conditions of mice were altered through the attachments of wireless electrophysiological recording devices (Neural Activity Tracker-1, NAT-1). NAT-1 devices are miniaturised multichannel devices with on-board memory for direct high-resolution recording of brain activity for >48 hrs. Such devices may limit the mobility of animals and affect their behavioural performance due to the added weight (total weight of approximately 3.4 g). Mice were additionally treated with saline (control), N-methyl-D-aspartate (NMDA) receptor antagonist MK801 (0.85 mg/kg), or the muscarinic acetylcholine receptor blocker scopolamine (0.65 mg/kg) to allow exploration of the effect of NAT-1 attachments in pharmacologically treated mice. We found only minimal differences in behavioural outcomes with NAT-1 attachments in standard parameters of locomotor activity widely reported for the open field test between drug-treatments. Hypoactivity was globally observed as a consistent outcome in MK801-treated subjects and hyperactivity in scopolamine groups regardless of NAT-1 attachments. These data collectively confirm the reproducibility for combined behavioural, pharmacological and physiological endpoints even in the presence of lightweight wireless data loggers. The NAT-1 therefore constitutes a pertinent tool for investigating brain activity in e.g. drug discovery, models of neuropsychiatric and/or neurodegenerative diseases with minimal effects on pharmacological and behavioural outcomes.

neuroscience↗

bioRxiv2020

Evolution of ST-4821 clonal complex hyperinvasive and quinolone-resistant meningococci: the next meningococcal pandemic?

The expansion of quinolone-resistant Neisseria meningitidis clone ChinaCC4821-R1-C/B from ST-4821 clonal complex (cc4821) caused a serogroup shift from serogroup A to C in invasive meningococcal disease (IMD) in China. To establish the relationship among globally distributed cc4821 meningococci, we analysed whole genome sequence data from 173 cc4821 meningococci isolated in four continents from 1972-2019. These meningococci clustered into four sub-lineages (1-4), with sub-lineage 1 primarily comprising serogroup C IMD isolates (82%, 41/50). Most isolates from outside China formed a distinct sub-lineage (81.6%, 40/49, the Europe-USA cluster), with the typical strain designation B:P1.17-6,23:F3-36:ST-3200(cc4821) and harbouring mutations in penicillin-binding protein 2. These data show that the quinolone-resistant clone ChinaCC4821-R1-C/B has expanded to other countries. The increasing global distribution of B:cc4821 meningococci raises concern that cc4821 has the potential to cause a global pandemic and, this would be challenging to control though there is indirect evidence that Trumenba(R) vaccine might afford some protection.

bioinformatics↗

bioRxiv2019

Environmental, social, management and health factors associated with within- and between-individual variability in fecal glucocorticoid metabolite concentrations in zoo-housed Asian and African elephants

Identifying links between environmental, social, management, and health factors as they relate to physiological stress in captive elephants is crucial for the improvement of welfare and husbandry practices in North American zoos. Studies have examined the effects of short-term and chronic elevations in glucocorticoids in small groups of elephants, but few have examined adrenal activity on a large scale. This study evaluated 106 Asian (Elephas maximus) and 131 African (Loxodonta africana) elephants housed at 64 accredited facilities across North America. Fecal samples were collected every other week for 12 months and analyzed for glucocorticoid metabolite (FGM) concentrations. Risk factors for mean and individual variability (CV) in FGM were subjected to univariate and multivariable analyses using epidemiological methods. Independent variables that included individual traits, social environment, housing and management factors were chosen based on their identification as risk factors in previously published models for the same North American population of elephants. Results indicate that African elephants are more responsive to social stressors than Asians, and that poor joint health is a stress-related welfare problem for Asian, but not African elephants. For both species, higher FGM concentrations were associated with zoos located at more northern latitudes and having free access to indoor/outdoor spaces, whereas spending more time in managed interactions with staff were associated with lower FGM concentrations. Also important for captive management, elephants having diverse enrichment options and belonging to compatible social groups exhibited lower mean and reduced intra-individual variability in FGM. Our findings show that aspects of the zoo environment can be potential sources of stress for captive elephants, and that there are management activities that can facilitate coping and adapting to zoo conditions. Given species differences in factors that affected FGM, targeted, species-specific management approaches likely are needed to ensure good welfare for all elephants.

zoology↗