SV40 trafficking is inhibited by an elevation of the vacuolar pH (see also Movies S5 and S6 in the supplemental material). (A, C, and D) SV40-AF647 was incubated with cells transfected with XFP-tagged proteins, and 100 nM bafilomycin A1 (Baf), 20 mM NH4Cl, or 10 μM monensin was added; cells were imaged by confocal microscopy at different time points postwarming. Note that NH4Cl and monensin cause a swelling of endosomes and lysosomes, and Baf leads to a loss of the round appearance of endosomes. (B) Percentage of viruses colocalizing with the markers Rab7-EGFP and Rab5-mRFP at different time points postwarming in the presence of 100 nM Baf, calculated from images such as those shown in A. Error bars are SEM of data from each time point for 5 to 15 cells from three independent experiments, with an average of 50 to 100 particles per cell.