Biology subjects

Grundy, L.

Publications and source records attributed to Grundy, L..

3 recordsLinked to original sources

bioRxiv2026

OpusTaxa: A Unified Workflow for Taxonomic Profiling, Assembly, and Functional Analysis of Shotgun Metagenomes

Shotgun metagenomics has become a cornerstone of microbiome research, yet the complexity of existing workflows remains a major barrier for life scientists without dedicated bioinformatics support. Manual database setup, detailed sample sheet preparation, and management of software dependencies can make routine analysis difficult and time-consuming. Cross-study comparisons are further hampered by inconsistent processing pipelines, database versions, and profiling strategies, limiting reproducibility and the potential for large-scale meta-analyses. We present OpusTaxa, an open-source Snakemake workflow that provides end-to-end processing of short paired-end shotgun metagenomic data with minimal configuration. Users provide either FASTQ files or Sequence Read Archive accessions; OpusTaxa automatically downloads required databases, performs quality control, removes host reads, and executes taxonomic profiling, metagenome assembly, and functional analysis. All analysis modules can be independently toggled, and per-sample outputs are automatically merged into harmonised, cross-sample tables ready for downstream exploration. Across two public datasets, we demonstrate how OpusTaxa can be used to compare consistency across complementary taxonomic profilers and to estimate microbial load in addition to standard metagenomic workflows. AvailabilityOpusTaxa is freely available at https://github.com/yenkaiC/OpusTaxa. Documentation, test data, and example configurations are included in the repository.

bioinformatics↗

bioRxiv2025

Bladder mucosal afferents detect UTI and aid pathogen clearance

The bladder is innervated by a complex network of sensory neurons that detect and transmit mechanical and chemical signals to the central nervous system, regulating both urine storage and voiding, as well as mediating sensations of bladder fullness and pain. While stretch-sensitive afferents within the bladder wall are known to monitor filling, the contribution of stretch-insensitive afferents that reside within the bladder mucosa to bladder sensation and function remains unclear. Here, we establish a novel mouse model of selective bladder mucosal afferent denervation using intravesical instillation of resiniferatoxin (RTX) to define the functional roles of these fibres in health and disease. We assessed the impact of mucosal denervation on sensory nerve activity and bladder function in healthy mice and in a model of urinary tract infection (UTI) induced by acute bacterial challenge with uropathogenic E. coli. We show that mucosa-innervating afferents do not influence bladder distension responses or voiding function under healthy conditions. In contrast, during UTI, these afferents become hypersensitive and serve as critical drivers of infection-induced pelvic pain and urinary frequency, responses that contribute to enhanced bacterial clearance. Together, these findings identify bladder mucosal afferents as key sensors of pathogenic challenge and reveal a previously unrecognised mechanism that drives behavioural responses to reduce the burden and extent of UTI.

neuroscience↗

bioRxiv2020

Activation of MrgprA3 and MrgprC11 on bladder-innervating afferents induces peripheral and central hypersensitivity to bladder distension

Understanding the sensory mechanisms innervating the bladder is paramount to developing efficacious treatments for chronic bladder hypersensitivity conditions. The contribution of Mas-gene-related G protein-coupled receptors (Mrgpr) to bladder signalling is currently unknown. Here we show in mice with single-cell RT-PCR that sub-populations of dorsal root ganglion (DRG) neurons innervating the mouse bladder express MrgprA3 (14%) and MrgprC11 (38%), either individually or in combination, with high levels of co-expression with Trpv1 (81-89%). Calcium imaging studies demonstrated MrgprA3 and MrgprC11 agonists (chloroquine, BAM8-22 and neuropeptide FF) activated sub-populations of bladder-innervating DRG neurons, showing functional evidence of co-expression between MrgprA3, MrgprC11 and TRPV1. In ex vivo bladder-nerve preparations chloroquine, BAM8-22 and neuropeptide FF all evoked mechanical hypersensitivity in sub-populations (20-41%) of bladder afferents. These effects were absent in recordings from Mrgpr-cluster{Delta}-/- mice. In vitro whole-cell patch clamp recordings showed that application of an MrgprA3/C11 agonist cocktail induced neuronal hyper-excitability in 44% of bladder-innervating DRG neurons. Finally, in vivo instillation of an MrgprA3/C11 agonist cocktail into the bladder of wild-type mice induced a significant activation of dorsal horn neurons within the lumbosacral spinal cord, as quantified by pERK-immunoreactivity. This MrgprA3/C11 agonist-induced activation was particularly apparent within the superficial dorsal horn and the sacral parasympathetic nuclei of wild-type, but not Mrgpr-cluster{Delta}-/- mice. This study demonstrates, for the first time, functional expression of MrgprA3 and MrgprC11 in bladder afferents. Activation of these receptors is not required for normal bladder function but does trigger hypersensitivity to distension, a critically valuable factor for therapeutic target development. Significance statementDetermining how bladder afferents become sensitized is the first step in finding effective treatments for common urological disorders such as overactive bladder and interstitial cystitis/bladder pain syndrome. Here we show that two of the key receptors, MrgprA3 and MrgprC11, that mediate itch from the skin are also expressed on afferents innervating the bladder. Activation of these receptors results in sensitization of bladder afferents, resulting in sensory signals being sent into the spinal cord that prematurely indicate bladder fullness. Targeting bladder afferents expressing MrgprA3 or MrgprC11 and preventing their sensitisation may provide a novel approach for treating overactive bladder and interstitial cystitis/bladder pain syndrome.

neuroscience↗