Whole tissue proteomics for the comparative profiling of mdx- 4cv versus wild type brain was conducted using analytical grade reagents and materials obtained from GE Healthcare (Little Chalfont, Buckinghamshire, UK) and Bio-Rad Laboratories (Hemel-Hempstead, Hertfordshire, UK).
Preprocessing and whole-brain analyses were conducted using the AFNI (Analysis of Functional Neural Images) software (Cox, 1996).
Imaging data Inferential statistics on brain imaging data were conducted using SPM2 (Department of Cognitive Neurology, Institute of Neurology, London, UK).
Exploratory voxel-wise one-sample t-tests of whole brain contrast images were conducted using a p < .05 voxel-level probability threshold and an extent threshold of 3 voxels, with correction for multiple comparisons based on the false discovery rate (FDR) (Genovese et al. 2002).
Whole-brain fMRI analyses were conducted using XBAM software (http://www.brainmap.co.uk).
Bilateral analyses of pTH, TH, and pDARPP-32 for one brain section per region were conducted using an Olympus BX61 microscope fitted with an Olympus FV II digital camera, connected to a PC compatible computer.
In vitro experiments of bacterial adhesion on blood brain barrier (BBB) human cells were conducted using hCMEC/D3 cell line.
Both miRNA and mRNA profiles were conducted using brain tissues.
Analyses were conducted using Brain Vision Analyzer (Version 1.05, Brain Products).
Previously, in mouse embryos and newborn mice, CSF fluid dynamics based on ciliated cell activity have been examined in detail, but the observations were conducted using dissected brain tissue cut in half to expose the inner surface of the brain ventricles [ 16, 26].
