Biology subjects

Schiller, C.

Publications and source records attributed to Schiller, C..

2 recordsLinked to original sources

bioRxiv2024

QuAPPro: An R/shiny app for Quantification and Alignment of Polysome Profiles

Polysome profiling is a powerful technique to study mRNA translation. After separation of ribosomal subunits from monosomes and polysomes by ultracentrifugation on sucrose density gradients, a UV absorbance profile is recorded during elution. This profile can be used to assess global translational activity, or reveal changes in ribosome biogenesis or translation elongation. In parallel to UV absorbance profiles, it is also possible to record fluorescence to measure the association of fluorescently tagged proteins with ribosomes or polysomes. To this end, the area under subsections of the UV/fluorescence profiles needs to be quantified carefully. In addition, alignment of profiles in one graph helps to visualize differences. With QuAPPro, we present the first interactive web app that allows quantification and alignment of polysome profiles, independently of the device or software that was used to generate the profiles. This user-friendly tool does not only speed up the analysis of polysome profiles but also facilitates reproducibility and documentation of the process.

bioinformatics↗

bioRxiv2023

Cell division tracing combined with single-cell transcriptomics reveals new cell types and differentiation paths in the regenerating mouse lung

Understanding the molecular and cellular processes involved in lung epithelial regeneration may fuel the development of new therapeutic approaches for lung diseases. We combined new mouse models that allow diphtheria toxin (DTA)-mediated depletion of specific epithelial cell types and GFP-labeling of dividing cells with single-cell transcriptomics to characterize the regeneration of the distal lung. We uncovered new cell types, some of which likely represent epithelial precursors, propose goblet cells as progenitor cells, and provide evidence that adventitial fibroblasts act as supporting cells in epithelial regeneration. We also found that DTA-expressing cells can persist in the lung, express specific inflammatory factors, and resemble a previously undescribed population in the lungs of COVID-19 patients. Our study provides a comprehensive single-cell atlas of the distal lung that characterizes early transcriptional and cellular responses to defined epithelial injury, encompassing proliferation, differentiation, and cell-to-cell interactions.

cell biology↗