Biology subjects

Gagnon, S.

Publications and source records attributed to Gagnon, S..

3 recordsLinked to original sources

bioRxiv2025

Telomere-to-telomere assembly detects genomic diversity in Canadian strains of Borrelia burgdorferi

Borrelia burgdorferi, the bacteria causing Lyme disease, has a complex genome comprising a linear chromosome and a combination of linear and circular plasmids. The atypical hairpin structure at the telomere of linear replicons and the highly paralogous plasmids make the genome assembly challenging. We developed a genome assembly pipeline using Oxford Nanopore Technologies (ONT) long read and Illumina short read to overcome these challenges. Using ONT reads enabled us to completely assemble the hairpin telomeres of the linear replicons along with a novel lp28 subtype plasmid and the complete circular plasmids of nine B. burgdorferi strains from five geographical regions in Canada. Although these strains are highly similar across the conserved genomic regions, variability was observed predominantly at the right telomeric ends. Comparative analyses revealed that all nine strains carry a [~]2-10 kb right telomeric end identical to the linear plasmid lp28-1, which leads to variability in the telomere length and the gene content. Additionally, we observed diversity at the hairpin telomeric sequences of the linear chromosomes. Further analysis showed that the nine strains belong to seven ospC types and have diverse plasmid profile, highlighting the genomic diversity among the strains from the same geographical locations. Overall, these findings suggest that even the B. burgdorferi strains from close geographical locations can carry substantial genomic variation, especially at the telomeres and with respect to their plasmid content, emphasizing it to be a possible mechanism of rapid evolution within these Canadian strains.

genomics↗

bioRxiv2024

Impact of liver specific survival motor neuron (SMN) depletion on peripheral and central nervous system tissue pathology

Spinal muscular atrophy (SMA) is an inherited neuromuscular disorder stemming from deletions or mutations in the Survival Motor Neuron 1 (SMN1) gene, leading to decreased levels of SMN protein, and subsequent motor neuron death and muscle atrophy. While traditionally viewed as a disorder predominantly affecting motor neurons, recent research suggests the involvement of various peripheral organs in SMA pathology. Notably, the liver has emerged as a significant focus due to the observed fatty liver phenotype and dysfunction in both SMA mouse models and SMA patients. Despite these findings, it remains unclear whether intrinsic depletion of SMN protein in the liver contributes to pathology in the peripheral or central nervous systems. To address this knowledge gap, we developed a mouse model with a liver-specific depletion of SMN by utilizing an Alb-Cre transgene together with one Smn2B allele and one Smn exon 7 allele flanked by loxP sites. Initially, we evaluated phenotypic changes in these mice at postnatal day 19 (P19), a time when the severe model of SMA, the Smn2B/-mice, typically exhibit many symptoms of the disease. Our findings indicate that liver-specific SMN depletion does not induce motor neuron death, neuromuscular pathology or muscle atrophy, characteristics typically observed in the Smn2B/- mouse at P19. However, mild liver steatosis was observed at this time point, although no changes in liver function were detected. Notably, pancreatic alterations resembled that of Smn2B/-mice, with a decrease in insulin-producing {beta}-cells and an increase in glucagon-producing -cells, accompanied by a reduction in blood glucose and an increase in plasma glucagon and glucagon-like peptide (GLP-1) levels. Moreover, these changes were transient, as P60 mice exhibited recovery of liver and pancreatic function. While the mosaic pattern of the Cre-mediated excision precludes definitive conclusions regarding the contribution of liver-specific SMN depletion to overall tissue pathology, our findings highlight an intricate connection between liver function and pancreatic abnormalities in SMA, adding a nuanced layer to our understanding of the diseases complexities.

genetics↗

bioRxiv2021

Impact of cobas PCR Media Freezing on SARS-CoV-2 Viral RNA Integrity and Whole Genome Sequencing Analyses

SARS-CoV-2 whole genome sequencing is an important molecular biology tool performed to support many aspects of the response to the pandemic. Freezing of primary clinical nasopharyngeal swab samples and shipment to reference laboratories is usually required since RNA sequencing is rarely available in routine clinical microbiology laboratories where initial diagnosis and support to outbreak investigations occur. The cobas PCR Media transport medium developed by Roche facilitates high throughput analyses on cobas multianalyzer PCR platforms. There is no data on the stability of SARS-CoV-2 RNA after freezing and thawing of clinical samples in this transport medium, but potential denaturing of the molecular template could impair test results. Our objective was to compare the quality and results of SARS-CoV-2 genomic sequencing when performed on fresh or frozen samples in cobas PCR Media. Viral whole genome sequencing was performed using Oxford Nanopore Technologies MinION platform. Genomic coverage and sequencing depth did not significantly differ between fresh and frozen samples (n=10). For samples with lower viral inoculum and PCR cycle threshold above 30, sequencing quality scores and detection of single nucleotide polymorphisms did not differ either. Freezing of cobas PCR Media does not negatively affect the quality of SARS-CoV-2 RNA sequencing results and it is therefore a suitable transport medium for outsourcing sequencing analyses to reference laboratories. Those results support secondary use of diagnostic nasopharyngeal swab material for viral sequencing without requirement for additional clinical samples.

molecular biology↗