Immune reconstitution involves defective negative selection of conventional αβT cells. (A) Detection of TCR-signaled cleaved caspase 3⁺ thymocytes undergoing negative selection in control (white dots) or in BMT mice at 28 d (d28) after transplant (black dots). Data are from three separate experiments; n = 9 for each time point. (B) Schematic for generation of BALB/c background BM chimeras, where expression of the green fluorescent protein Kaede enables identification of donor-derived cells. (C and D) Quantitation of TCRVβ3⁺, Vβ5⁺, and Vβ11⁺ SP CD4⁺TCRβ⁺ or SP CD8⁺TCRβ⁺ in thymus (left panel) or spleen (right panel) with control (white dots) or BMT mice at 28 d after transplant (black dots; C) or 56 d after transplant (D). For BMT mice in C and D, cells were pregated on Kaede⁺ cells of donor origin. Data from three separate experiments; n = 8–10 per time point. Error bars indicate SEM. *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001. SSC-A, side scatter area.