Eyes were fixed in 4% paraformaldehyde in PBS at 4°C for 2 hours, rinsed in PBS, and cryoprotected overnight in 30% sucrose in PBS. Eyes were embedded in optimum cutting temperature compound (TissueTek; Sakura, Alphen aan den Rijn, The Netherlands) and frozen indirectly in isopentane cooled by liquid nitrogen. Retinas were sectioned sagittally at 20 μm using a cryostat (CM1850; Leica, North Ryde, NSW, Australia). At the appearance of the optic nerve head, sections were collected on gelatin- and poly-L-lysine–coated slides and stored at −20°C.
Sections were stained with the TUNEL technique, to detect apoptotic cells using in situ cell death detection kit (Roche, Basel, Switzerland), and were immunolabeled with antibodies against glial fibrillary acidic protein (GFAP) and the BDNF receptors NGFR, NTRK2 and SORL1.
Sections were prepared for TUNEL labeling with a 10-minute wash in terminal deoxytransferase (TdT) buffer (3 mM Trizma base, 14 mM sodium cacodylate, and 100 μM cobalt chloride), then incubated in a solution containing TdT (0.03 units/μL) and biotinylated dUTP (4 μM) for 1 hour at 37°C in TdT buffer. The reaction was terminated by a 15-minute wash in saline–sodium citrate buffer (300 mM sodium chloride, 30 mM sodium citrate). Sections were blocked with 10% goat or rabbit serum (Sigma-Aldrich Corp., St. Louis, MO, USA) in PBS for 30 minutes at room temperature. Sections were then incubated overnight at 4°C with either rabbit or mouse anti-GFAP (1:1000; Dako, Glostrup, Denmark), anti-NGFR (1:1000; Biosensis, Thebarton, SA, Australia), anti-NTRK2 (1:200; Santa Cruz Biotech, Dallas, Texas, USA), or anti-SORL1 (1:500; R&D Systems, Minneapolis, Minnesota, USA) in 1% goat or rabbit serum. The following day, sections were washed for 15 minutes in PBS prior to being incubated with a secondary antibody for 1 hour at room temperature, either goat anti-rabbit IgG Alexa 488 or rabbit anti-mouse IgG Alexa 594 (1:500; Life Technologies, Carlsbad, CA, USA) and for TUNEL labeling, Cy3-Streptavidin conjugate (1:1000, Life Technologies). After washing in PBS, sections were incubated for 2 minutes with the nuclear label bisbenzimide (1:10,000 wt/vol; Sigma-Aldrich Corp.). The slides were mounted with glycerol/gelatin (1:1; Sigma-Aldrich Corp.) and coverslipped. Negative controls were included with the substitution of primary antibody for 1% goat or rabbit serum.
For systematic measurements of retinal parameters (thickness of the outer nuclear layer [ONL], numbers of TUNEL+ cells, extent of Müller GFAP labeling), each section studied was scanned from the superior edge to the optic disc to the inferior edge, in 400-μm steps; typically there were 10 to 12 such steps from the superior edge to the disc, and another 10 to 12 from the disc to the inferior edge. At each step an image was taken using either a Zeiss Axioplan 2 deconvolution microscope (Carl Zeiss, Gottingen, Germany) or Zeiss LSM 510 confocal microscope. The criteria for identifying TUNEL+ cells have been described previously.
35 In each field we measured the thickness of the ONL as a proportion of the thickness of the retina, from the inner to the outer limiting membrane. Where the section was labeled for GFAP, we also recorded the labeled length of the Müller cells as a proportion of retinal thickness. Counts and measurements were averaged over three sections per eye for four to six animals per group.