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Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library.
J Vis Exp
January 2025
State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University;
The extent of functional sequences within the human genome is a pivotal yet debated topic in biology. Although high-throughput reverse genetic screens have made strides in exploring this, they often limit their scope to known genomic elements and may introduce non-specific effects. This underscores the urgent need for novel functional genomics tools that enable a deeper, unbiased understanding of genome functionality.
View Article and Find Full Text PDFFibroblast transcriptomics uncovers pathogenic genomic variants in individuals with exome-negative childhood onset epilepsy.
Epilepsia
January 2025
Applied Translational Neurogenomics Group, Vlaams Instituut voor Biotechnology (VIB) Center for Molecular Neurology, VIB, Antwerp, Belgium.
Objective: This study aims to improve genetic diagnosis in childhood onset epilepsy with neurodevelopmental problems by utilizing RNA sequencing of fibroblasts to identify pathogenic variants that may be missed by exome sequencing and copy number variation analysis.
Methods: We enrolled 41 individuals with childhood onset epilepsy and neurodevelopmental problems who previously had inconclusive genetic testing. Fibroblast samples were cultured and analyzed using RNA sequencing to detect aberrant expression, aberrant splicing, and monoallelic expression using the Detection of RNA Outlier Pipeline (DROP) pipeline.
Evidence that staphylococcal superantigens promote within-patient bacterial persistence following post-operative surgical site infection.
Infect Immun
January 2025
Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada.
is a predominant cause of post-operative surgical site infections and persistent bacteremia. Here, we describe a patient who experienced three episodes of infection over a period of 4 months following a total knee arthroplasty. The initial bloodstream isolate (SAB-0429) was a clonal complex 5 (CC5) and methicillin-resistant (MRSA), whereas two subsequent isolates (SAB-0485 and SAB-0495) were CC5 isolates but methicillin-sensitive .
View Article and Find Full Text PDFPathogen genomic surveillance and the AI revolution.
J Virol
January 2025
MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom.
The unprecedented sequencing efforts during the COVID-19 pandemic paved the way for genomic surveillance to become a powerful tool for monitoring the evolution of circulating viruses. Herein, we discuss how a state-of-the-art artificial intelligence approach called protein language models (pLMs) can be used for effectively analyzing pathogen genomic data. We highlight examples of pLMs applied to predicting viral properties and evolution and lay out a framework for integrating pLMs into genomic surveillance pipelines.
View Article and Find Full Text PDFPersistent cross-species transmission systems dominate Shiga toxin-producing O157:H7 epidemiology in a high incidence region: A genomic epidemiology study.
Elife
January 2025
Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Canada.
Several areas of the world suffer a notably high incidence of Shiga toxin-producing . To assess the impact of persistent cross-species transmission systems on the epidemiology of O157:H7 in Alberta, Canada, we sequenced and assembled O157:H7 isolates originating from collocated cattle and human populations, 2007-2015. We constructed a timed phylogeny using BEAST2 using a structured coalescent model.
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