After euthanatization, eyes and optic nerves were immediately enucleated. Before sectioning, the dura was removed from enucleated tissue to expose the optic nerve. The retina and proximal 8 mm of optic nerve was then embedded in OCT and sectioned on a cryotome set at −30°C. To limit the potential tilting of sections, the exposed optic nerve was aligned parallel to the blade on the cryotome before cutting. Previously described measures were adopted to orientate sections and to ensure that the levels of the sections used for comparison of axonal transport and cytoskeleton studies between control and high IOP eyes were reliably matched.
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Specimens for axonal transport studies were stored immediately after sectioning and viewed under the confocal scanning laser microscope the following day. Remaining sections were either stained with Van Gieson stain to determine prelaminar and lamina cribrosa thickness or they were incubated with primary antibodies for the cytoskeleton study. Primary antibodies used to study the cytoskeleton were polyclonal antibody NF-L directed against the neurofilament light subunit (1:500, AHP286; Serotec, Oxford, United Kingdom), monoclonal antibody NF-M directed against the neurofilament medium subunit (1:200, N5264, clone NN18; Sigma-Aldrich, St. Louis, MO), monoclonal antibody NF-H directed against the phosphorylated and the nonphosphorylated neurofilament heavy subunit (1:400, N0142, clone N52; Sigma-Aldrich), monoclonal antibody NF-Hp directed against the phosphorylated neurofilament heavy subunit (1:200, N5389, clone NE14; Sigma-Aldrich), monoclonal antibody Tub directed against isotypes I and II of β-tubulin (1:200, T8535, clone JDR.3B8; Sigma-Aldrich), and anti-MAP antibody (1:200, M7273; Sigma-Aldrich). After primary antibody incubation, slides were washed and incubated with either a goat anti-mouse IgG (1:400, Alexa Fluor 488, A11001; Molecular Probes, Portland, OR) or a goat anti-rabbit IgG (1:400, Alexa Fluor 488, A11008; Molecular Probes) secondary antibody. After this, sections were washed and mounted in glycerol before study under the microscope.