Biology subjects

Au, J.

Publications and source records attributed to Au, J..

4 recordsLinked to original sources

bioRxiv2025

The Impact of Variant Calling on Substitution Mutational Signature Inference

Identifying mutational signatures is a key component of cancer genomics studies, yet the influence of variant calling strategies on signature extraction has not been systematically evaluated. Here, we analyzed over 8,900 whole exomes from The Cancer Genome Atlas (TCGA) and over 1,800 whole genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) consortium to assess how mutation callers shape de novo single-base substitution (SBS) signatures. We found that consensus calling yielded stable de novo signatures across reference genomes and pipeline versions, whereas individual callers introduced false-positive SBSs that manifested as artifactual signatures that were reproducibly detected by three independent signatures extraction tools. A minimal consensus approach requiring agreement between only two variant calling algorithms effectively removed these artifacts while preserving true biological signal. Together, these results establish consensus variant calling as essential for robust inference of de novo SBS mutational signatures and provide practical guidelines for distinguishing genuine mutational processes from technical artifacts.

bioinformatics↗

bioRxiv2025

VasoTracker 2: An Open-source Platform for Quantitative Analysis of Vascular Reactivity and Function

VasoTracker 2 is an open-source platform for studying blood vessel dynamics, featuring versatile diameter-tracking software and complementary low-cost hardware components. This system surpasses existing tools through accessible, high-resolution analysis across multiple imaging modalities, enabling comprehensive assessment of vascular dynamics in both real-time and pre-recorded experiments. Advanced algorithms enable multi-point diameter tracking in branched vessels, automated pressure-response protocols, and reliable edge detection. The software can assess vessels imaged by brightfield microscopy, fluorescence imaging, and in ultrasound recordings, supporting diverse applications from isolated vessel studies to in vivo assessment. For ex vivo applications, VasoTracker 2 includes modular open-source hardware components that can be used to create a low-cost pressure myograph system: a confocal-compatible vessel chamber and a programmable pressure controller, VasoMoto. By combining powerful analytical capabilities with an open-access approach, VasoTracker 2 provides free software and low-cost hardware alternatives to commercial systems, democratizing access to advanced vascular research tools for scientists worldwide.

physiology↗

bioRxiv2020

A comparison of dopaminergic and cholinergic populations reveals unique contributions of VTA dopamine neurons to short-term memory

We systematically compared the contribution of two dopaminergic and two cholinergic ascending populations to a spatial short-term memory task in rats. In ventral tegmental area dopamine (VTA-DA) and nucleus basalis cholinergic (NB-ChAT) populations, trial-by-trial fluctuations in activity during the delay period related to performance with an inverted-U, despite the fact that both populations had low activity during that time. Transient manipulations revealed that only VTA-DA neurons, and not the other three populations we examined, contributed causally and selectively to short-term memory. This contribution was most significant during the delay period, when both increases or decreases in VTA-DA activity impaired short-term memory. Our results reveal a surprising dissociation between when VTA-DA neurons are most active and when they have the biggest causal contribution to short-term memory, while also providing new types of support for classic ideas about an inverted-U relationship between neuromodulation and cognition.

neuroscience↗

bioRxiv2020

Biomimetic sponges improve muscle structure and function following volumetric muscle loss

Skeletal muscle is inept in regenerating after traumatic injuries such as volumetric muscle loss (VML) due to significant loss of basal lamina and the resident satellite cells. Currently, there are no approved therapies for the treatment of muscle tissue following trauma. In this study, biomimetic sponges composed of gelatin, collagen, laminin-111, and FK-506 were used for the treatment of VML in a rodent model. We observed that biomimetic sponge treatment improved muscle structure and function while modulating inflammation and limiting the extent of fibrotic tissue deposition. Specifically, sponge treatment increased the total number of myofibers, type 2B fiber cross-sectional area, myosin: collagen ratio, myofibers with central nuclei, and peak isometric torque compared to untreated VML injured muscles. As an acellular scaffold, biomimetic sponges provide a promising "off-the-shelf" clinical therapy for VML.

bioengineering↗