The neuropathological analysis was conducted in a sham-treated control group and animals at 1, 3, 7 or 21 day(s) post-blast (
n = 3 for each time point). Animals were euthanized by CO
2 asphyxiation and perfused transcardially with ice-cold 0.9% saline followed by 10% formalin for a total of 10 min. The brains were dissected and placed in fresh 10% formalin for 72 h. Brains were block-sectioned into 5 coronal slabs, paraffin-embedded, and serially sectioned at 5 μm at Bregma level of 2.20, 1.00, − 2.80, − 7.30 and − 11.30 mm. Standard protocols were utilized for staining with hematoxylin and eosin (H&E; Leica, Cat # 3801570) [
15] and Fluoro-Jade B (FJB, Millipore Corporation, Cat # AG310-30MG) [
16]. For the immunohistochemical analysis, paraffin-embedded sections were labeled with SMI-31 to detect phosphorylated neurofilaments (1:500; Covance, Emeryville, CA), glial fibrillary acidic protein (GFAP) to detect astrocyte activation (1:1200; Chemicon) and ionized Ca
2+-binding adapter molecule (Iba1) to detect microglial activation (1:1000; Wako) and visualized by immunoperoxidase method [
17]. Briefly, 5 μm sections were deparaffinized, subjected to microwave antigen retrieval (citrate buffer, pH 6.0; BioGenex, Cat # HK086-9 K), permeabilized with 0.3% (vol/vol) Triton, quenched free of endogenous peroxidases, and blocked with a cocktail of normal goat serums (2.5% (vol/vol) each) prior to overnight incubation of primary antibodies at 4 °C. Bound primary antibodies were detected by sequential incubation with biotinylated secondary antisera and streptavidin-peroxidase, diaminobenzidine chromagen was used to detect immunoperoxidase signal (Vector; anti-mouse IgG kit, Cat # MP-7602, anti-rabbit kit, Cat # MP-7601). Quantification of GFAP-positive astrocytes was conducted using semi-stereology and the optical fractionator technique as previously described [
6]. GFAP-positive astrocytes were quantitated in brain regions, including cortex (GFAP-positive cells counted in squares of 100 × 100 μm;
n = 53–77 squares), striatum (
n = 32–53 squares) and hippocampus (
n = 19–34 squares). Semi-quantitative analysis of the immunohistochemical signal of the activated microglia marker, Iba1, and phospho-specific anti-neurofilament antibody, SMI-31 was performed using the open source image processing package FIJI (
http://www.fiji.sc). Images were captured on an epifluorescence microscope (Nikon) in TIFF format. Following standardized color deconvolution and thresholding of images, the signal was quantified on 2–3 slides from 3 individual rats for each treatment group. Iba1 was quantified in brain regions, including cortex (% area of signal;
n = 12–17 regions of interest), striatum (
n = 11–15 regions of interest) and hippocampus (
n = 8–12 regions of interest).