extracted_captions/fernandes2019cell.json

{"CAPTION FIG1.png": "'Figure 1: A quantitative treatment of TCS triggering relying on receptor dual time at phosphatase-depicted close contacts. (_A_) Top and side views of the close contact depicting contact topography (with contact radius \u201cr\u201d) and CD45 exclusion. The first box (solid line) shows the region of the cell magnified below it. The second box (dotted line) shows the region depicted in the top view on the right. (_B_) According to the model, a TCR (TCR) is triggered, i.e., phosphorylated because its residence time in the contact is >=2 s. TCR\\\\({}_{2}\\\\) is not triggered because it diffuses out of the contact in less than 2 s. (_C_) Also according to the model, a receptor (TCR) that engages ligand is likely to be held in the contact \u22652 s and become triggered. In \\\\(B\\\\) and \\\\(C\\\\), the margins of the contact are marked by the average positions of excluded CD45 molecules (green). (_D_) Snapshots from the simulation of the TCR density probability evolution in dose-contacts as they grow over time (_S_ Appendix_ _A_).\\n\\n'", "CAPTION FIG2.png": "'Figure 2: Parameterization of the model. (A) Experimental approach. High-density labeling of CD45 (Gap 8.3 Fab, Alexa Fluor 488) was used to indicate sites of close-contact formation between T cells and a rat CD2-presenting SIs (Ledt), and this was combined with simultaneous low-density labeling of CD45 (Gap 8.3 Fab, Alexa Fluor SBE), Lck (Halo tag, tetramethylrhodamine [TM&]), or TCR (Halo tag, TMR) (right) to enable TIRFM-based single-molecule tracking. (B-D, Left) TERM-based single-molecule tracking of CD45 (B), Lck (C), and TCR (D). Well-separated individual trajectories were recorded for >280 ms and colored according to position in the contact (orange in CD45-rich region and blue in CD45-depleted regions). (Right) Close-up views of trajectories in regions marked by white rectangles CD45-rich regions are shown in gray. (Scale bar, 2 \u03bcm.) Data are representative of three independent experiments with \\\\(n>10\\\\) cells.\\n\\n'", "CAPTION FIG4.png": "'\\nFig. 4: Why the TCR can be triggered in the absence of ligands. (A) Probability that a TCR remains inside a dose contact for time, \\\\(\\\\tau\\\\), for close contacts of varying fixed radius, \\\\(\\\\tau_{0}\\\\) (B) Probability that a single TCR stays inside a dose contact >2 s as a function of final close-contact radius for growing contacts. (C) Total number of TCRs that remain inside the close contact for >2 s, incorporating the estimates shown in \\\\(A\\\\), the density of TCRs in Jurkat T cells, and the degree of exclusion of the TCR from close contacts for cells interacting with rCD2-presenting SLBs. (_D_) Total contact area (region of CD45 exclusion) at the time of calcium release for T cells interacting with rCD2-presenting SLBs (13 cells, 5 independent experiments). Central lines indicate the median; small squares indicate the mean; boxes show interquartile range; whiskers indicate SD.\\n\\n'", "CAPTION FIG5.png": "'\\nFig. 5: Self-finensifel discrimination. (_A_) Probability distribution of close-contact residence times for TCRs in the presence and absence of agonist and self pMHC, for a close contact of radius \\\\(\\\\tau_{0}=220\\\\) nm, showing that discrimination of ligands is not dependent on a threshold value for \\\\(\\\\tau_{\\\\rm exc}\\\\). (_B_) Probability that at least one TCR will be triggered, i.e., stay in the contact for \\\\(\\\\tau_{0}\\\\geq 2.5\\\\), as a function of contact duration in the presence and absence of agonist pMHC with a low \\\\(k_{\\\\rm int}\\\\) (\\\\(k_{\\\\rm int}=1^{-1}\\\\), 30 pMHC\\\\(\\\\mu\\\\)m\\\\(\\\\lambda\\\\)), or a self pMHC with a larger \\\\(k_{\\\\rm int}\\\\) present at higher pMHC densities (\\\\(k_{\\\\rm int}=50\\\\)\\\\(\\\\times\\\\)\\\\(1^{-1}\\\\), 300 pMHC\\\\(\\\\mu\\\\)m\\\\(\\\\lambda\\\\)). (_C_) Comparison of the triggering probability in the absence of pMHC for close contacts of 220 and 440 nm. (_D_) Triggering probability as a function of pMHC densities and pMHC of rates for a single contact of 220 nm radius with a duration of \\\\(\\\\tau_{0}=120\\\\) s. (_F_) Triggering probability as a function of close contact radius for pMHC with varying off rates for a contact duration of \\\\(\\\\tau_{0}=120\\\\) s. (_F_) Contribution to the overall signal of TCRs that are triggered without binding to pMHC, in the presence of agonist pMHC with varying \\\\(k_{\\\\rm int}\\\\) (30 pMHC\\\\(\\\\mu\\\\)m\\\\(\\\\lambda\\\\)).\\n\\n'", "CAPTION FIG6.png": "'Figure 6: Prediction of the relative signaling potentials of well-characterized TCR ligands. Peptide-stimulation potentials (EC48 and EC5E values for IL-2 selection) for CD4\\\\({}^{+}\\\\) (Left) and CD8\\\\({}^{+}\\\\) T cells (Right) (determined elsewhere in refs. 11, 33, and 53), plotted against the probability that at least one TCR triggering event (\\\\(t_{\\\\rm{oxin}}\\\\geq 2\\\\) s) occurs at a single contact of \\\\(r_{\\\\rm{a}}=220\\\\) nm, that persists for \\\\(t_{\\\\rm{f}}=120\\\\) s.\\n\\n'", "CAPTION TAB1.png": "'\\n\\n**Table 1.** Experimental parameters used in this study.\\n\\n'"}