Biology subjects

Jones, G. R.

Publications and source records attributed to Jones, G. R..

4 recordsLinked to original sources

bioRxiv2026

Refractoriness-Based Masking Yields Threshold-Specific Human Auditory Nerve Responses

Distinct auditory nerve (AN) fiber populations with varying thresholds and vulnerabilities to synaptopathy are observable in animal models, but standard non-invasive human measures lack the resolution to differentiate these groups of fibers. This fundamental limitation hinders the translation of findings in animals to human auditory pathologies. To overcome this, we developed a novel refractoriness-masking paradigm to non-invasively isolate threshold-specific AN fiber responses in humans. By presenting rapid click trains with cumulatively rising levels (45 to 105 dB peSPL) at a 250-microsecond inter-click interval, we sequentially masked lower-threshold fibers. Using a tympanic membrane electrode, we recorded compound action potentials (CAPs) in adults with normal hearing and isolated threshold-specific responses via waveform subtraction. Our results demonstrated that the isolated CAPs exhibited decreased latencies with increasing levels and a non-linear amplitude growth, plateauing at 90 dB peSPL before sharply increasing at 105 dB peSPL. This pattern reflects the sequential recruitment of AN fiber that were not effectively recruited by the preceding clicks. Validate conditions, in which the final two clicks had equal levels, produced substantially smaller CAPs, consistent with response suppression by refractoriness. Overall, this paradigm establishes a human measurement approach for characterizing level-threshold-dependent AN responses, providing a potential way to better investigate different AN pathologies, such as cochlear synaptopathy or auditory neuropathy.

neuroscience↗

bioRxiv2025

TWEAK is increased in ulcerative colitis and contributes to fibroblast-mediated monocyte activation via heterologous non-canonical NF-kB/STAT3 signalling

Background and AimsInteractions between fibroblasts and monocytes have emerged as a contributing factor in IBD pathogenesis and therapy resistance, owing to the ability of both cell types to participate in tissue inflammation and repair. We have previously shown that the TNF superfamily factor TWEAK (TNFSF12) can induce a UC-like inflammatory profile in colonic fibroblasts in vitro, in turn promoting monocyte adhesion and activation. However, the mechanisms underlying fibroblast-monocyte communication and its dysregulation in colitis are incompletely understood. MethodsHere we use co-culture models, human biopsies from ulcerative colitis (UC) patients and healthy donors, and public single-cell transcriptomics to characterise the mechanisms underlying fibroblast-mediated monocyte activation. ResultsWe show that TWEAK-treated inflammatory fibroblasts induce a transcriptional programme that resembles early monocyte/macrophage intermediates in UC and is enriched for genes associated with resistance to anti-TNF (TREM1, OSM, IL1B) and susceptibility to IBD (NOD2, ATG16L1). We find that conditioned media from TWEAK-treated fibroblast causes a sustained activation of STAT3 phosphorylation in monocytes, and that inhibition of the NF-{kappa}B Inducing Kinase (NIK) impairs the ability of inflammatory fibroblasts to activate STAT3 phosphorylation in monocytes, resulting in reduced expression of inflammatory mediators. Using tissues from UC patients, we show that the expansion of CD90+/PDPN+ inflammatory fibroblasts in UC correlates with the accumulation of TWEAK+ myeloid cells in the colonic mucosa, and that these fibroblasts co-localise with infiltrating monocytes in sites of active inflammation. ConclusionTogether, our findings suggest that the TWEAK/NF-{kappa}B/STAT3 axis represents an attractive target to tune inflammatory stroma/monocyte crosstalk.

immunology↗

bioRxiv2017

Divergence estimation in the presence of incomplete lineage sorting and migration

This paper focuses on the problem of estimating a species tree from multilocus data in the presence of incomplete lineage sorting and migration. We develop a mathematical model similar to IMa2 (Hey 2010) for the relevant evolutionary processes which allows both the the population size parameters and the migration rates between pairs of species tree branches to be integrated out. We then describe a BEAST2 package DENIM which based on this model, and which uses an approximation to sample from the posterior. The approximation is based on the assumption that migrations are rare, and it only samples from certain regions of the posterior which seem likely given this assumption. The method breaks down if there is a lot of migration. Using simulations, Leache et al 2014 showed migration causes problems for species tree inference using the multispecies coalescent when migration is present but ignored. We re-analyze this simulated data to explore DENIMs performance, and demonstrate substantial improvements over *BEAST. We also re-analyze an empirical data set. [isolation-with-migration; incomplete lineage sorting; multispecies coalescent; species tree; phylogenetic analysis; Bayesian; Markov chain Monte Carlo]

evolutionary biology↗

bioRxiv2017

Bayesian Phylogenetic Analysis For Diploid And Allotetraploid Species Networks

Allopolyploid species are formed by genome doubling after hybridization between otherwise intersterile parental species. Allopolyploidy is a common speciation mechanism in land plants. Here we describe and evaluate a Bayesian approach to the phylogenetic analysis of species relationships when both ordinary speciation and allopolyploidy are present. The approach takes incomplete lineage sorting into account using the multi-species coalescent model, and extends this to deal with the extra complications due to allopolyploidy. The number of hybridizations is not assumed, which means that the number of parameters varies and a reversible-jump MCMC algorithm is needed to sample from the posterior. The main restriction is that only diploids and allotetraploids are considered. The model is implemented in the BEAST framework and is an extension of Jones et al. (2013). Simulations show that the topology of the network can be reliably inferred along with estimates of other parameters.

evolutionary biology↗