Tok, S. | Search bioRxiv

bioRxiv2024

Impact of Optogenetic Activation of the Thalamic Reticular Nucleus on Sleep Architecture in Mice

Alzheimers disease (AD) is a progressive neurodegenerative disorder affecting millions worldwide and is often accompanied by significant sleep disturbances, such as sleep fragmentation, early awakenings, decreased sleep efficiency, and insomnia. It has been suggested that the alterations in activity of the thalamic reticular nucleus (TRN) are closely associated with sleep disruptions in AD. Evidence suggests that activating neurons expressing gamma-aminobutyric acid (GABA) within the TRN may enhance sleep quality and potentially ameliorate neuropathology associated with AD. However, the precise mechanisms through which TRN influences sleep disruptions and AD pathophysiology remain poorly understood. In this study, we investigated whether activating GABAergic TRN neurons could alter sleep architecture in wild-type mice. Utilizing optogenetic stimulation, we observed that activation of these neurons did not significantly alter sleep state durations or delta wave power, a key indicator of Slow Wave Sleep (SWS). Furthermore, the application of a two-virus strategy inadvertently led to non-specific opsin expression beyond the targeted TRN area. We discuss the potential factors that contributed to these outcomes, providing directions for future investigations to better delineate the role of the TRN in sleep and AD.

neuroscience↗

bioRxiv2023

Improved Resolution of Highly Pathogenic Avian Influenza Virus Haemagglutinin Cleavage Site Using Oxford Nanopore R10 Sequencing Chemistry

Highly pathogenic avian influenza viruses continue to pose global risks to One Health, including agriculture, public, and animal health. Rapid and accurate genomic surveillance is critical for monitoring viral mutations, tracing transmission, and guiding interventions in near real-time. Oxford Nanopore sequencing holds promise for real-time influenza genotyping, but data quality from R9 chemistry has limited its adoption due to challenges resolving low-complexity regions such as the biologically critical hemagglutinin cleavage site, a homopolymer of basic amino acids that distinguish highly pathogenic strains. In this study, human and avian influenza isolates (n=45) from Cambodia were sequenced using both R9.4.1 and R10.4.1 flow cells and chemistries to evaluate performance between approaches. Overall, R10.4.1 yielded increased data output with higher average quality compared to R9.4.1, producing improved consensus sequences using a reference-based bioinformatics approach. R10.4.1 had significantly lower minor population insertion and deletion frequencies, driven by improved performance in low sequence complexity regions prone to insertion and deletion errors, such as homopolymers. Within the hemagglutinin cleavage site, R10.4.1 resolved the correct motif in 90% of genomes compared to only 60% with R9.4.1. Further examination showed reduced frameshift mutations in consensus sequences generated with R10.4.1 that could result in incorrectly classified virulence. Improved consensus genome quality from nanopore sequencing approaches, especially across biologically important low-complexity regions, is critical to reduce subjective hand-curation and will improve local and global genomic surveillance responses.

genomics↗