Biology subjects

Walsh, C.

Publications and source records attributed to Walsh, C..

4 recordsLinked to original sources

bioRxiv2018

Multifaceted integration - memory for faces is subserved by widespread connections between visual, memory, social and auditory networks

Face memory abilities are at the core of human social interaction, yet these vary widely within the general population, ranging from developmental prosopagnosia to \"super-recognizers\". Previous work has focused mainly on the contribution of the well described face network to this variance. However, given the nature of the face memory task, and the social context in which it takes place, we were interested in exploring how the collaboration between different networks outside the face network (measured through resting state connectivity) affects performance on face memory tasks. We discovered that face recognition memory is supported by a wide network of connections between the face patches, memory regions, auditory regions and social networks. Moreover, this network was selective for memory for faces, and did not predict memory for other visual objects, such as cars.

neuroscience↗

bioRxiv2018

Arginine to glutamine mutation in olfactomedin-like 3 (OLFML3) is a candidate for severe goniodysgenesis and glaucoma in the Border Collie dog breed.

Goniodysgenesis is a developmental abnormality of the anterior chamber of the eye. It is generally considered to be congenital in dogs (Canis lupus familiaris), and has been associated with glaucoma and blindness. Goniodysgenesis and early-onset glaucoma initially emerged in Border Collies in Australia in the late 1990s and has subsequently been found in Europe and the USA. The objective of the present study was to determine the genetic basis of goniodysgenesis in Border Collies. Clinical diagnosis was based on results of examinations by veterinary ophthalmologists of affected and unaffected dogs from eleven different countries. Genotyping using the Illumina high density canine SNP chip and whole genome sequencing were used to identify candidate genetic regions. Expression profiles and evolutionary conservation of candidate genes were assessed using public databases. Analysis of pedigree information was consistent with an autosomal recessive mode of inheritance for severe goniodysgenesis (potentially leading to glaucoma) in this breed. There was a highly significant peak of association over chromosome 17, with a p-value of 2 x 10-13. Whole genome sequences of three dogs with glaucoma, three severely affected and three unaffected dogs identified a missense variant in the olfactomedin like 3 (OLFML3) gene in all six affected animals. This was homozygous in all nine cases with glaucoma and 12 of 14 other severely affected animals. Of 67 reportedly unaffected animals, only one (offspring of two homozygous affected parents) was homozygous for this variant. The identification of a candidate genetic region and putative causative mutation will aid breeders to reduce the frequency of goniodysgenesis and the risk of glaucoma in the Border Collie population.

genetics↗

bioRxiv2017

The bovine alveolar macrophage DNA methylome is resilient to infection with Mycobacterium bovis

DNA methylation is pivotal in orchestrating gene expression patterns in various mammalian biological processes. Perturbation of the bovine alveolar macrophage (bAM) transcriptome, due to Mycobacterium bovis (M. bovis) infection, has been well documented; however, the impact of this intracellular pathogen on the bAM epigenome has not been determined. Here, whole genome bisulfite sequencing (WGBS) was used to assess the effect of M. bovis infection on the bAM DNA methylome. The methylomes of bAM infected with M. bovis were compared to those of non-infected bAM 24 hours post-infection (hpi). No differences in DNA methylation (CpG or non-CpG) were observed. Analysis of DNA methylation at proximal promoter regions uncovered >250 genes harbouring intermediately methylated (IM) promoters (average methylation of 33-66%). Gene ontology analysis, focusing on genes with low, intermediate or highly methylated promoters, revealed that genes with IM promoters were enriched for immune-related GO categories; this enrichment was not observed for genes in the high or low methylation groups. Targeted analysis of genes in the IM category confirmed the WGBS observation. This study is the first in cattle examining genome-wide DNA methylation at single nucleotide resolution in an important bovine cellular host-pathogen interaction model, providing evidence for IM promoter methylation in bAM.

genomics↗

bioRxiv2017

PaSD-qc: Quality control for single cell whole-genome sequencing data using power spectral density estimation

Single cell whole-genome sequencing (scWGS) is providing novel insights into the nature of genetic heterogeneity in normal and diseased cells. However, scWGS introduces DNA amplification-related biases that can confound downstream analysis. Here we present a statistical method, with an accompanying package PaSD-qc (Power Spectral Density-qc), that evaluates the quality of single cell libraries. It uses a modified power spectral density to assess amplification uniformity, amplicon size distribution, autocovariance, and inter-sample consistency as well as identifies aberrantly amplified chromosomes. We demonstrate the usefulness of this tool in evaluating scWGS protocols and in selecting high-quality libraries from low-coverage data for deep sequencing.

bioinformatics↗