To ensure the completion of DNA replication and maintenance of genome integrity, DNA repair factors protect stalled replication forks upon replication stress. Previous studies have identified a critical role for the tumor suppressors BRCA1 and BRCA2 in preventing the degradation of nascent DNA by the MRE11 nuclease after replication stress. Here we show that depletion of SMARCAL1, a SNF2-family DNA translocase that remodels stalled forks, restores replication fork stability and reduces the formation of replication stress-induced DNA breaks and chromosomal aberrations in BRCA1/2-deficient cells. In addition to SMARCAL1, other SNF2-family fork remodelers, including ZRANB3 and HLTF, cause nascent DNA degradation and genomic instability in BRCA1/2-deficient cells upon replication stress. Our observations indicate that nascent DNA degradation in BRCA1/2-deficient cells occurs as a consequence of MRE11-dependent nucleolytic processing of reversed forks generated by fork remodelers. These studies provide mechanistic insights into the processes that cause genome instability in BRCA1/2-deficient cells.
Software for automatic general image analysis. It provides fully automatic analysis of 1-D gels including lane creation, background subtraction, band detection, molecular weight calibration, quantity calibration, and normalization. Editing tools are provided for cropping, rotating, and filtering images.
CellProfiler cell image analysis software is free and open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. It counts cells and also measures the size, shape, intensity and texture of every cell (and every labeled subcellular compartment) in every image. It was designed for high throughput screening but can perform automated image analysis for images from time-lapse movies and low-throughput experiments. CellProfiler has an increasing number of algorithms to identify and measure properties of neuronal cell types.
It is an open source image processing Java program designed for scientific multidimensional images. This open platform for scientific image analysis is used in life sciences.
Image J has been transformed to ImageJ2 application.
This new application improves ImageJ data engine to be sufficient to analyze modern datasets and makes the addition of new functionality possible and provides a framework for interoperability between a plethora of external image visualization and analysis programs.
ImageJ2 strengthens ImageJ’s utility by: 1) generalizing the ImageJ data model; 2) introducing a robust architecture instrumental in building bridges across a range of other image processing tools; 3) remaining open source and cross-platform with permissive licensing, enabling continued widespread adoption and extension; 4) building on the huge collection of existing ImageJ plugins while enabling the creation of new plugins with more powerful features; and 5) leveraging a correspondingly large and diverse community to foster a collaborative and interdisciplinary project that facilitates the collective advancement of science.
Statistical software package for data analysis, hypothesis testing, and modeling. The software can capable perform mathematical calculations (including biostatistics) and graphical plotting such as curve fitting (nonlinear regression) and scientific graphing.
Software environment and programming language for statistical computing and graphics that provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, etc) and graphical techniques. R is an integrated suite of software facilities for data manipulation, calculation and graphical display.
SciCrunch is a data sharing and display platform. Anyone can create a custom portal where they can select searchable subsets of hundreds of data sources, brand their web pages and create their community. SciCrunch will push data updates automatically to all portals on a weekly basis. User communities can also add their own data to SciCrunch, however this is not currently a free service.