gfp mapper  (Addgene inc)

Journal: Nature Communications

Article Title: FidlTrack: high-fidelity structure-aware single particle tracking resolves intracellular molecular motion in organelles sensing APP processing

doi: 10.1038/s41467-026-69067-y

Figure Lengend Snippet: a Time-averaged TIRF images of a Hela cell expressing a SEC61B::GFP ER marker (grayscale) with knock-in SEC13::SNAP (stained with cpSNAP-JF549) ER exit site marker (cyan). b Reconstructed Halo ER (ER-targeted HaloTag with KDEL retention signal, stained with PA-JF646) trajectories (individually colour-coded) reconstructed without (left) or with FidlTrack (right). c Percentage of ambiguous displacements for the trajectories reconstructed without or with FidlTrack. d Trajectories (individually colour-coded) visiting an ERES (spending at least 10 frames in ERES) found without (left) or with FidlTrack (right) overlaid on top of the averaged ER structure (grayscale) and ERES positions (cyan). e Blow up on the two regions highlighted in ( d ) showing how ERES act as attractors to local trajectories without FidlTrack (left), a problem mostly corrected when using FidlTrack (right). f Number of trajectories at ERES (spending at least 2 points close to an ERES) without and with FidlTrack. g , Average amount of time spent by trajectories close to ERES versus close to random ERES-like sites (see Fig. ). h Amount of the time spent in ERES by trajectories spending at least 5 frames at an ERES with a cutoff at 500 ms. The red line corresponds to a fit of the distribution to a biexponential function of parameters \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$a=156$$\end{document} a = 156 , \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\tau 1=10$$\end{document} τ 1 = 10 ms, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$b=29$$\end{document} b = 29 , \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\tau 2=56$$\end{document} τ 2 = 56 ms and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${R}^{2}=0.997$$\end{document} R 2 = 0.997 . i Example of a trajectory flying-by (passing without stopping) an ERES (left) and quantification of its distance to the ERES (right, top) and instantaneous displacement length (right, bottom) showing no sign of association with the ERES. j Same as ( i ) but for a trajectory visiting for some frames and then exiting an ERES. k Same as ( j ) but for a trajectory dwelling for a long time in an ERES (until bleaching). l Ratio of visiting to flyby trajectories per exit site. m Exit sites colour-coded by their visiting to flyby trajectory ratio as presented in ( l ). n Example of two exit sites exhibiting different behaviours, the left one is “sticky” with a high ratio of visiting trajectories while the right one has mostly flyby trajectories. Source data are provided as a Source Data file.

Article Snippet: 1014 , pcDNA3.1_GFP-SEC61B , SEC61B:: GFP , SEC61B fused to GFP , Fig. , Addgene #121159.

Techniques: Expressing, Marker, Knock-In, Staining

Journal: Nature Communications

Article Title: FidlTrack: high-fidelity structure-aware single particle tracking resolves intracellular molecular motion in organelles sensing APP processing

doi: 10.1038/s41467-026-69067-y

Figure Lengend Snippet: a TIRF images of a frame from simultaneously acquired single-molecules (left) and the associated organelle geometries (right) for a mitochondria matrix targeted HaloTag probe and mNeonGreen marker (top), the mitochondria membrane protein TOMM20 and mitochondria matrix targeted mEmerald (middle), and the ER membrane protein SEC61B and ER lumen targeted mEmerald (bottom) in COS-7 cells. b Masks extracted via AI-assisted image processing from the first and last frame of the recordings for the mitochondria matrix targeted probe (top), TOMM20 (middle) and SEC61B (bottom) recordings presented in ( a ). c Stability maps, representing for each pixel the percentage of total frames in which it is part of a mask, for the mitochondria matrix targeted probe (top), TOMM20 (middle) and SEC61B (bottom) recordings presented in ( a ). d Bar plot presenting the fraction of recovered spots relative to the quantity recovered from the entire stack of masks when using the mask of either the first or last frame to perform structure-aware tracking in the different recordings presented in ( a ). e Reconstructed trajectories (individually colour-coded) from the datasets presented in ( a ) using conventional tracking (not structure-aware, top, left), structure-aware tracking using the mask from the first frame (top, right) or the whole stack of masks (bottom, left). f Plot of the displacement distributions extracted from the trajectories presented in ( e ) fitted to a mixture of two Rayleigh distributions (dashed red lines, see Methods section “Fitting of displacement lengths distributions”). g Plot of the pooled displacement distributions for structure-aware ambiguity-removed tracking of SEC61B::Halotag in COS-7 cells after 4 h of BSA or Oleic Acid treatment at 400 µM. Pooling was done over n =7/6 recordings for BSA and oleic acid, respectively, the reported statistics correspond to a two-tailed Kolmogorov–Smirnov test p < 2.2251e-308. h Bar plot of the Kolmogorov–Smirnov statistics from ( g ) for either conventional or structure-aware tracking and with or without ambiguity removal. i Temporally colour-coded mitochondria positions over 700 frames (left), trajectory of the centre of the pointed mitochondria (right, top) and the raw (black) and mitochondrion motion-corrected trajectory (red) of a TOMM20 receptor moving at the surface of the pointed mitochondrion (right, bottom). Source data are provided as a Source Data file.

Article Snippet: 1014 , pcDNA3.1_GFP-SEC61B , SEC61B:: GFP , SEC61B fused to GFP , Fig. , Addgene #121159.

Techniques: Marker, Membrane, Two Tailed Test

Journal: Nature Communications

Article Title: FidlTrack: high-fidelity structure-aware single particle tracking resolves intracellular molecular motion in organelles sensing APP processing

doi: 10.1038/s41467-026-69067-y

Figure Lengend Snippet: a Time-averaged TIRF images of a Hela cell expressing a SEC61B::GFP ER marker (grayscale) with knock-in SEC13::SNAP (stained with cpSNAP-JF549) ER exit site marker (cyan). b Reconstructed Halo ER (ER-targeted HaloTag with KDEL retention signal, stained with PA-JF646) trajectories (individually colour-coded) reconstructed without (left) or with FidlTrack (right). c Percentage of ambiguous displacements for the trajectories reconstructed without or with FidlTrack. d Trajectories (individually colour-coded) visiting an ERES (spending at least 10 frames in ERES) found without (left) or with FidlTrack (right) overlaid on top of the averaged ER structure (grayscale) and ERES positions (cyan). e Blow up on the two regions highlighted in ( d ) showing how ERES act as attractors to local trajectories without FidlTrack (left), a problem mostly corrected when using FidlTrack (right). f Number of trajectories at ERES (spending at least 2 points close to an ERES) without and with FidlTrack. g , Average amount of time spent by trajectories close to ERES versus close to random ERES-like sites (see Fig. ). h Amount of the time spent in ERES by trajectories spending at least 5 frames at an ERES with a cutoff at 500 ms. The red line corresponds to a fit of the distribution to a biexponential function of parameters \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$a=156$$\end{document} a = 156 , \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\tau 1=10$$\end{document} τ 1 = 10 ms, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$b=29$$\end{document} b = 29 , \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\tau 2=56$$\end{document} τ 2 = 56 ms and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${R}^{2}=0.997$$\end{document} R 2 = 0.997 . i Example of a trajectory flying-by (passing without stopping) an ERES (left) and quantification of its distance to the ERES (right, top) and instantaneous displacement length (right, bottom) showing no sign of association with the ERES. j Same as ( i ) but for a trajectory visiting for some frames and then exiting an ERES. k Same as ( j ) but for a trajectory dwelling for a long time in an ERES (until bleaching). l Ratio of visiting to flyby trajectories per exit site. m Exit sites colour-coded by their visiting to flyby trajectory ratio as presented in ( l ). n Example of two exit sites exhibiting different behaviours, the left one is “sticky” with a high ratio of visiting trajectories while the right one has mostly flyby trajectories. Source data are provided as a Source Data file.

Article Snippet: 1014 , pcDNA3.1_GFP-SEC61B , SEC61B:: GFP , SEC61B fused to GFP , Fig. , Addgene #121159.

Techniques: Expressing, Marker, Knock-In, Staining