BackgroundThe mouse inbred line C57BL/6J is widely used in mouse genetics and its genome has been incorporated into many genetic reference populations. More recently large initiatives such as the International Knockout Mouse Consortium (IKMC) are using the C57BL/6N mouse strain to generate null alleles for all mouse genes. Hence both strains are now widely used in mouse genetics studies. Here we perform a comprehensive genomic and phenotypic analysis of the two strains to identify differences that may influence their underlying genetic mechanisms.ResultsWe undertake genome sequence comparisons of C57BL/6J and C57BL/6N to identify SNPs, indels and structural variants, with a focus on identifying all coding variants. We annotate 34 SNPs and 2 indels that distinguish C57BL/6J and C57BL/6N coding sequences, as well as 15 structural variants that overlap a gene. In parallel we assess the comparative phenotypes of the two inbred lines utilizing the EMPReSSslim phenotyping pipeline, a broad based assessment encompassing diverse biological systems. We perform additional secondary phenotyping assessments to explore other phenotype domains and to elaborate phenotype differences identified in the primary assessment. We uncover significant phenotypic differences between the two lines, replicated across multiple centers, in a number of physiological, biochemical and behavioral systems.ConclusionsComparison of C57BL/6J and C57BL/6N demonstrates a range of phenotypic differences that have the potential to impact upon penetrance and expressivity of mutational effects in these strains. Moreover, the sequence variants we identify provide a set of candidate genes for the phenotypic differences observed between the two strains.

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Traumatic brain injury (TBI) is caused by brain deformations resulting in the pathophysiological activation of cellular cascades which produce delayed cell damage and death. Understanding the consequences of mechanical injuries on living brain tissue continues to be a significant challenge. We have developed a reproducible tissue culture model of TBI which employs organotypic brain slice cultures to study the relationship between mechanical stimuli and the resultant biological response of living brain tissue. The device allows for the independent control of tissue strain (up to 100%) and strain rate (up to 150 s-1) so that tolerance criteria at the tissue level can be developed for the interpretation of computational simulations. The application of texture correlation image analysis algorithms to high speed video of the dynamic deformation allows for the direct calculation of substrate strain and strain rate which was found to be equi-biaxial and independent of radial position. Precisely controlled, mechanical injuries were applied to organotypic hippocampal slice cultures, and resultant cell death was quantified. Cell death was found to be dependent on both strain magnitude and rate and required several days to develop. An immunohistological examination of injured cultures with antibodies to amyloid precursor protein revealed the presence of traumatic axonal injury, suggesting that the model closely replicates in vivo TBI but with advantages gained in vitro. We anticipate that a combined in vitro approach with optical strain mapping will provide a more detailed understanding of the dependence of brain cell injury and death on strain and strain rate.

The function of the majority of genes in the mouse and human genomes remains unknown. The mouse ES cell knockout resource provides a basis for characterisation of relationships between gene and phenotype. The EUMODIC consortium developed and validated robust methodologies for broad-based phenotyping of knockouts through a pipeline comprising 20 disease-orientated platforms. We developed novel statistical methods for pipeline design and data analysis aimed at detecting reproducible phenotypes with high power. We acquired phenotype data from 449 mutant alleles, representing 320 unique genes, of which half had no prior functional annotation. We captured data from over 27,000 mice finding that 83% of the mutant lines are phenodeviant, with 65% demonstrating pleiotropy. Surprisingly, we found significant differences in phenotype annotation according to zygosity. Novel phenotypes were uncovered for many genes with unknown function providing a powerful basis for hypothesis generation and further investigation in diverse systems.

HighlightsAutomated assessment of mouse home-cage behaviour is robust and reliable.Analysis over multiple light/dark cycles improves ability to classify behaviours.Combined RFID and video analysis enables home-cage analysis in group housed animals.