PMC

(a) Stokes images at the beginning, middle, end of the 16-minute clearing. The black scale bar is 500 microns; (b) mapping the Stokes vector on the Poincare sphere; (c) The boxplot of s₁, s₂, s₃ at the beginning, middle, end of the 16-minutes clearing; (d) Stokes elements, DoLP and DoCP’ changes with clearing time.

(A) In stop flow experiments, preformed Rad51 filaments were rapidly mixed with Srs2^CΔ276. In the absence of Srs2, Rad51 filaments are stable (blue trace), but when challenged with Srs2 (1.5 μM post-mixing) Rad51 filaments are cleared (red trace). (B) Srs2^CΔ276 concentration dependence of Rad51 clearing was measured with increasing concentrations of Srs2^CΔ276 (0 - 1.5 μM post-mixing, shown as insert). The relative change in fluorescence amplitude is plotted as a function of Srs2 concentration and yields a K_1/2 = 0.38 ± 0.04 μM for Rad51 filament clearing by Srs2^CΔ276. (C) The Rad51 filament clearing experiment in A was repeated with 5′Cy3 ssDNA of varying lengths (dT_n, n = 59-124 nt). Rad51 (2 μM post-mixing) was used in all the experiments to maintain sub-saturating Rad51-DNA filament forming conditions. The clearing rate observed for each DNA length in the presence of Srs2 (1.5 μM post-mixing) is plotted as a function of DNA length. The red dotted line is the expected trend for the clearing rate if a continuous Rad51-DNA filament is formed under these sub-saturating Rad51 concentrations. (D) The Rad51-DNA filament clearing experiment described in C was repeated with saturating concentrations of Rad51 (10 μM post-mixing). The clearing rates observed under these conditions are plotted as a function of DNA length. The red dotted line represents the expected trend for the clearing rate if Srs2 initiates clearing only at the 3′ end of the Rad51-DNA filament. Deviation from the predicted trend suggests that Srs2 can invade a Rad51 filament at multiple points and initiate clearing. (E) and (F) depict schematic representations of expected Rad51-DNA filaments formed under limiting or saturating concentrations of Rad51, and potential Srs2 loading or invading sites on the respective filaments.

Optical images obtained via OCT showing the eye (A) undamaged (control), (B) immediately after NaOH damage, (C) after NaOH damage and flushing, (D) during the beginning of P-ECT clearing, (E) in the middle of P-ECT clearing, and (F) at the end of P-ECT clearing.

Mouse brain tissue incubated in hydrogel (A4B5P4), cleared using SDS and RI matched using 85% glycerol. (A) Mouse brain prior to tissue clearing, (B) 2 mm section showing the end point of clearing, (C) Cleared whole brain.