Coordinate systems and structural features of rod photoreceptors important for analyzing molecular motion. (A) Coordinate systems. (Top) The cylindrical coordinate system used in the 3-D model of diffusion in the OS and IS compartments. (Bottom) Coordinates used in the 1-D model of intercompartment diffusion (see Theory). (B) Transmission EM of a rod. A thin section along the central axis of a rod cell isolated from salamander retina showing the axial variation in the density of structures within the major rod compartments. OS, outer segment; IS, inner segment; E, mitochondria-filled ellipsoid; M, myoid; N, nucleus; ST, synaptic terminal; CC, connecting cilium (approximate position). The distal outer segment was truncated in this image. Bar, 10 µm. (CC inset; left) Cross section of a rat rod CC showing the 9 + 0 microtubule motif and the close juxtaposition of the plasma membrane, reproduced from Besharse et al. (1985) with permission. Bar, 0.3 µm. (Right) Longitudinal section of a frog rod CC (reproduced from Peters et al., 1983 with permission). Bar, 1.0 µm. (OS discs inset) Detail showing the stack of membranous discs orthogonal to the axis of the rod. Bar, 1 µm. The isolated rod and the OS disc inset are from Townes-Anderson et al. (1985). (C) Effect of suboptical resolution structures on fluorescence intensity. The presence of structural inhomogeneities of rods in the volume of the psf result in variation in recorded GFP fluorescence, even when the aqueous concentration (green color) of the protein is uniform. Red circles in the top panel illustrate a cross section of the psf in an x–y image plane of a rod that is occupied to varying degrees by different densities of subcellular structures. The bottom panel illustrates the expected variation in fluorescence (F) (compare Peet et al., 2004).