After the death of the animals and enucleation of the eyes, retinas were rapidly dissected and frozen in liquid N2, then crushed using a tissue pulverizer (Beckman, Fullerton, CA) on dry ice. The retinas were solubilized in 9 M urea, 4% Nonidet P-40, and 2% 2-mercaptoethanol (pH 9.5). Protease inhibitor cocktail (P8340, Sigma) consisting of 4-(2-aminoethyl) benzenesulfonyl fluoride, pepstatin A, bestatin, leupeptin, E-64, and aprotinin was added to prevent protease activity. Samples were centrifuged 10 minutes at 14,000g. The supernatant was used for SDS-PAGE and the pellet discarded. Protein concentration was determined with a modified Bradford assay (Bio-Rad, Hercules, CA).
Equal amounts of retinal protein per lane (40 μg) were diluted with SDS sample buffer and loaded onto gels for SDS-PAGE (4%–20% gradient; Invitrogen, San Diego, CA). Proteins were electroblotted to polyvinylidene difluoride membranes (Immobilon-P; Millipore, Bedford, MA) and the efficiency of transfer was confirmed by staining the membrane with ponceau S red (Sigma). Gel retention was assessed by staining with Coomassie blue (Pierce, Rockford, IL). Nonspecific binding was blocked with 5% nonfat dry milk in Tween-Tris-buffered saline (TTBS). Membranes were incubated overnight at 4°C with antibodies to caspase-2 (rabbit polyclonal IgG, 1:1000; Stressgen, Victoria, BC, Canada), caspase-3 (rabbit polyclonal IgG, clone CM1, 1:3000; BD-Pharmingen, San Diego, CA), bax (rabbit polyclonal IgG, 1:1000, BD-Pharmingen), and PARP (mouse monoclonal IgG, clone C-2-10, 1:500; Biomol, Plymouth Meeting, PA). Membranes were incubated similarly with anti-phospho-p44/p42 MAPK (P-ERK, rabbit polyclonal IgG, Thr202/Tyr204, 1:2000, Cell Signaling, Beverly, MA), anti-diphosphorylated p38 (rabbit polyclonal IgG, 1:2000, Promega, Madison, WI), and anti-diphosphorylated JNK (rabbit polyclonal IgG, 1:1000, Cell Signaling). All the antibodies were prepared in 5% nonfat dry milk solution in TTBS.
Actin was used to verify equal loading of protein. The anti-actin antibody (mouse monoclonal IgM, clone JLA 20, 1:200) developed by J. J.-C. Lin, PhD, was obtained from the National Institute of Child Health and Human Development (NICHD)–supported Developmental Studies Hybridoma Bank, University of Iowa (Iowa City, IA). Appropriate horseradish (HRP)–conjugated secondary antibodies, which were anti-rabbit (goat IgG; Jackson ImmunoResearch, West Grove, PA), or anti-mouse (sheep IgG, Amersham, Arlington Heights, IL) were applied at 1:20,000. Negative controls were performed without primary antibody. Chemiluminescence was developed with a kit (Super Signal West Pico; Pierce). Protein bands were visualized digitally with an imaging system (CCDBIO 16SC; Hitachi Genetic Systems/MiraiBio, Alameda, CA), and quantitated by densitometry (Gene Tools and Gene Snap software; Hitachi).