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Monier, B.

Publications and source records attributed to Monier, B..

3 recordsLinked to original sources

Physical and functional cell-matrix uncoupling in a developing tissue under tension

Tissue mechanics play a crucial role in organ development. It relies on cells and extracellular matrix (ECM) mechanical properties, but also on their reciprocal interaction. The relative physical contribution of cells and ECM to morphogenesis is poorly understood. Here, we dissected the mechanics of the envelope of the Drosophila developing leg, an epithelium submitted to a number of mechanical stresses: first stretched, it is then torn apart and withdrawn to free the leg. During stretching, we found that mechanical tension is entirely borne by the ECM at first, then by the cellular monolayer as soon as they detach themselves from one another. Then, each envelope layer is removed by an independent mechanism: while ECM withdraws following local proteolysis, cellular monolayer withdrawal is independent of ECM degradation and driven by an autonomous myosin-II-dependent contraction. These results reveal a physical and functional cell-matrix uncoupling that could timely control tissue dynamics during development.

cell biology

IRIS-DGE: An integrated RNA-seq data analysis and interpretation system for differential gene expression

MotivationNext-Generation Sequencing has made available much more large-scale genomic and transcriptomic data. Studies with RNA-sequencing (RNA-seq) data typically involve generation of gene expression profiles that can be further analyzed, many times involving differential gene expression (DGE). This process enables comparison across samples of two or more factor levels. A recurring issue with DGE analyses is the complicated nature of the comparisons to be made, in which a variety of factor combinations, pairwise comparisons, and main or blocked main effects need to be tested.\n\nResultsHere we present a tool called IRIS-DGE, which is a server-based DGE analysis tool developed using Shiny. It provides a straightforward, user-friendly platform for performing comprehensive DGE analysis, and crucial analyses that help design hypotheses and to determine key genomic features. IRIS-DGE integrates the three most commonly used R-based DGE tools to determine differentially expressed genes (DEGs) and includes numerous methods for performing preliminary analysis on user-provided gene expression information. Additionally, this tool integrates a variety of visualizations, in a highly interactive manner, for improved interpretation of preliminary and DGE analyses.\n\nAvailabilityIRIS-DGE is freely available at http://bmbl.sdstate.edu/IRIS/.\n\nContactqin.ma@sdstate.edu\n\nSupplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics

ViDGER: An R package for integrative interpretation of differential gene expression results of RNA-seq data

Differential gene expression (DGE) is one of the most common applications of RNA-sequencing (RNA-seq) data. This process allows for the elucidation of differentially expressed genes (DEGs) across two or more conditions. Interpretation of the DGE results can be non-intuitive and time consuming due to the variety of formats based on the tool of choice and the numerous pieces of information provided in these results files. Here we present an R package, ViDGER (Visualization of Differential Gene Expression Results using R), which contains nine functions that generate information-rich visualizations for the interpretation of DGE results from three widely-used tools, Cuffdiff, DESeq2, and edgeR.

bioinformatics