Improved resolution of fibronectin mRNA expression in the inner ear using laser scanning confocal microscopy

We describe a modified in sim hybridization protocol for localizing and quantifying fibronectin gene expression at the cellular level in paraffin sections of rat temporal bone. When combined with a novel analytical approach using laser scanning confocal microscopy (LSCM), this protocol significantly improved the resolution, sensitivity, and specificity of existing procedures for evaluating fibronectin synthesis in developing inner ear, For simultaneous viewing of cochlear anatomy and the autoradiographic signal, transmitted light images of the cochlea were collected separately from LSCM reflected light images of the autoradiographic silver grains and then the two images were electronically merged. Within the first 2 mu m below the surface of the emulsion, silver grains were clustered specifically over hybridized cells. In contrast, nonspecific silver grain development (i.e., background noise) was confined primarily to the lower 5 mu m of the emulsion adjacent to the tissue section. Limiting the volume of the emulsion examined in the LSCM analysis, i.e., restricting the range of optical sectioning to the first 2 mu m below the surface of the emulsion, effectively minimized nonspecific background noise and maximized the specificity of the hybridization signal. The improvements offered by the described methodological approaches are equally appropriate for non-calcified tissues.