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Assessing spatial sequencing and imaging approaches to capture the molecular and pathological heterogeneity of archived cancer tissues.
J Pathol
January 2025
The Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia.
Spatial transcriptomics (ST) offers enormous potential to decipher the biological and pathological heterogeneity in precious archival cancer tissues. Traditionally, these tissues have rarely been used and only examined at a low throughput, most commonly by histopathological staining. ST adds thousands of times as many molecular features to histopathological images, but critical technical issues and limitations require more assessment of how ST performs on fixed archival tissues.
View Article and Find Full Text PDFSearching and Using MobiDB Resource 6 to Explore Predictions and Annotations for Intrinsically Disordered Proteins.
Curr Protoc
December 2024
Department of Biomedical Sciences, University of Padova, Padova, Italy.
Intrinsically disordered proteins (IDPs) make up around 30% of eukaryotic proteomes and play a crucial role in cellular processes and in pathological conditions such as neurodegenerative disorders and cancers. However, IDPs exhibit dynamic conformational ensembles and are often involved in the formation of biomolecular condensates. Understanding the function of IDPs is critical to research in many areas of science.
View Article and Find Full Text PDFUsing Vesicular Stomatitis Virus as a Platform for Directed Protease Evolution.
Curr Protoc
December 2024
Institute of Virology, Medical University of Innsbruck, Innsbruck, Austria.
Antiviral drugs are essential medications to save the lives of infected people. However, they are under constant threat to become ineffective as viruses evolve quickly. Studying the development of resistance is therefore paramount to understand the impact of mutations on pharmacological treatment and to make informed decisions.
View Article and Find Full Text PDFGEDI: An R Package for Integration of Transcriptomic Data from Multiple Platforms for Bioinformatics Applications.
Curr Protoc
October 2024
Department of Applied Mathematics and Computer Science, Technical University of Denmark, Lyngby, Denmark.
Transcriptomic data is often expensive and difficult to generate in large cohorts relative to genomic data; therefore, it is often important to integrate multiple transcriptomic datasets from both microarray- and next generation sequencing (NGS)-based transcriptomic data across similar experiments or clinical trials to improve analytical power and discovery of novel transcripts and genes. However, transcriptomic data integration presents a few challenges including reannotation and batch effect removal. We developed the Gene Expression Data Integration (GEDI) R package to enable transcriptomic data integration by combining existing R packages.
View Article and Find Full Text PDFDisease-modifying therapies for Parkinson disease: lessons from multiple sclerosis.
Nat Rev Neurol
December 2024
Division of Neurology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada.
Article Synopsis
- * Recently, there have been great breakthroughs for MS, with new medications being approved, but people with PD still have not gotten new treatments and only have old ones that don't work as well.
- * Experts from around the world gathered in Toronto to discuss how to improve treatment for PD by learning from what worked for MS, focusing on things like better clinical trials and understanding the diseases better.
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