Retinas were lysed in cold lysis buffer (50 mM Tris-HCl pH 7.4, 150 mM NaCl, 1% Nonidet P-40, 0.1% SDS, 1 mM EDTA, 1 mM Na3VO4, protease inhibitor cocktail from Sigma) and incubated 30 minutes on ice. Tissue was disrupted with 40 strokes and centrifuged at 900g for 5 minutes at 4°C. For mitochondrial-enriched extracts, tissue was homogenized in 220 mM D-mannitol, 70 mM sucrose, 20 mM HEPES-KOH pH 7.2, 1 mM EDTA, 0.1% BSA, 1 mM Na3VO4, protease inhibitor cocktail (Sigma) and centrifuged at 500g for 10 minutes at 4°C. The low-speed supernatant was centrifuged at 10,000g for 10 minutes at 4°C. The resulting mitochondrial pellet was resuspended in washing buffer (250 mM sucrose, 20 mM HEPES-KOH pH 7.4, 1 mM EDTA, 1 mM Na3VO4, protease inhibitor cocktail) and centrifuged at 10,000g for 10 minutes at 4°C. The final mitochondrial pellet was resuspended in respiration buffer (250 mM sucrose, 50 mM HEPES pH 7.4, 10 mM KH2PO4, 2 mM MgCl2, 1 mM EDTA, 1 mM Na3VO4, protease inhibitor cocktail). The purity of enriched lysates was checked by Western blotting analysis with a mitochondrial marker (anti-cytochrome c, 1:2000; BD Biosciences, Milan, Italy) or a cytosol marker (anti-pan-actin, 1:3000; Millipore).
Equivalent amounts of protein extracts (50 μg) were used for Western blot analysis. The antibodies used for Western blotting were anti-Bax 6A7 (1:2000; Millipore), anti-Bcl2 (1:2000; Cell Signaling, Milan, Italy), anti-Calpain 1 (1:1000; Chemicon, Segrate, Italy), anti-Calpain 2 (1:3000; Abcam, Cambridge, UK), and anti-Cathepsin D (C-20 1:1000; Santa Cruz Biotechnology). Quantification was performed by densitometry analysis of scanned images using ImageJ software (National Institutes of Health, Bethesda, MD, USA), corrected by background, and plotted as protein/normalizing protein. Data are means ± SD of three blots with proteins derived from three animals from two biological replicates.