Mouse BIRN Projects
We have chosen mouse models for three devastating and common human neurological diseases—multiple sclerosis, Alzheimer’s disease, and Parkinson’s disease. These models provide a well-delimited workspace for our collaboration and maintain firm linkage to the two active Human BIRN test-beds and the BIRN-CC. All three diseases have mixed genetic and environmental etiologies and are sufficiently complex to be challenging from a bioinformatics perspective.
The Projects
These models came into the mouse BIRN project as part of collaborative mechanisms and act to drive development of an open data sharing infrastructure. Our collaborators include:
- Dr. Joanna Jankowsky at Caltech for the Alzheimer’s disease model (APP)
- Dr. Rhonda Voskuhl at UCLA for the multiple sclerosis model (EAE)
- Dr. Eliezer Masliah at UCSD for the Parkinson’s disease model (alpha synuclein-SNCA)
Information about the Projects can be found here.
These individuals are leaders in the field of neurodegenerative diseases, and all have substantial practical experience managing, exploiting, and interpreting results generated using these three models. Other models from the community will be integrated as they appear and the project evolves. This architecture and its component tools are meant to be open and generally available to the scientific community.
Methods
Data Collection:
MBIRN is developing multi-scale databases for these models that will support integration of 3-dimensional images ranging from the whole brain to cellular, subcellular, and supramolecular elements. More specifically, images are being integrated from:
- 3-dimensional magnetic resonance imaging and microscopy (MRI and MRM)
- Cryosectioned whole mouse brains
- Conventional optical histology and localized gene expression registered with the MRM and optical images
- 3D cellular and subcellular data with protein localization data from laser confocal and multiphoton imaging
- Supramolecular image data from transmission electron microscopy (TEM) and intermediate high voltage electron microscopic tomography (IVEM Tomo) to provide annotated representations from selected areas
Multi-scale linkage of these data will allow the investigators a comprehensive basis for interpretation of the signals from the whole brain images relative to the tissue and cellular alterations occurring in these animal models. An example of this data collected from a single animal is shown in the figure below (this figure is from the common specimen study in the news section).
Genes of Interest
Genes of Interest in relation to the mouse BIRN three disease models are listed in this file (courtesy of Rob Williams). There are 177 genes with data sets that overlap in both GENSAT and the GeneNetwork. The genes names are listed for both human and mouse and play a role in at least one of the three disease models of the mouse BIRN; Alzheimer's Disease, Parkinsons' Disease, or Multiple Sclerosis.
- MouseBIRNGeneLists.xls: Excel spreadsheet with these genes
- MouseBIRNGeneLists.pdf: pdf of just overlapping genes
