Journal: Traffic (Copenhagen, Denmark)

Article Title: Components of the G s signaling cascade exhibit distinct changes in mobility and membrane domain localization upon β 2 -adrenergic receptor activation

doi: 10.1111/tra.12724

Figure Lengend Snippet: SMM tracking and colocalization image analysis. The original stack of images of single molecules (in this example Halo-Gγ2) undergoes the process of molecule localization detection and tracking using the Trackmate Fiji plugin. Diffusion coefficient values are calculated using @msdanalyzer MATLAB-based software. The original ensemble TIRF image of clathrin light chain-mNeonGreen (CLC-mNeonGreen) or caveolin-1-mNeonGreen (Cav1-mNeonGreen) undergoes background subtraction and channel drift correction. The image is then thresholded using Niblack’s local thresholding algorithm and cell mask creation in Fiji. All localizations outside the mask are excluded from analysis. SMM tracking results are overlaid with detected clathrin-coated structures (CCSs) or caveolae and colocalization coefficients and membrane domain residence times are determined using in-house built MATLAB scripts. Scale bar 10 μm.

Article Snippet: 41 Diffusion coefficients for individual tracks were calculated by analyzing the results of the Trackmate plugin with the MATLAB-based @msdanalyzer software.

Techniques: Diffusion-based Assay, Software, Membrane

Journal: bioRxiv

Article Title: Transcriptional activity generates chromatin motion that drives nuclear blebbing

doi: 10.1101/2025.05.20.655131

Figure Lengend Snippet: (A) Example images of wild type MEF nuclei with NLS-GFP and Cy3-dUTP used for tracking chromatin motion. Example Trackmate tracks for all measured chromatin foci domain motion tracked and example single chromatin domain foci track for untreated control (UNT, black), RNA Pol II inhibition (AAM, green), serum starved (orange), and serum add back (purple). (B) Mean squared displacement (MSD) plots of UNT, AAM, serum starved, and serum add back of >8 foci averaged per nucleus over 75 seconds, which is half of full tracking of 150 seconds, with 20 nuclei per condition, except AAM with 10 nuclei. (C) Three example mean squared displacement (MSD) plots of the same nucleus serum starved (orange) and serum added back (purple) of >8 foci averaged per nucleus over 75 seconds, which is half of full tracking of 150 seconds, for 3 nuclei. Serum starved and serum add back are paired measurements of the same nucleus before and after serum re-addition. Error bars represent standard error and statistical tests are one-way ANOVA with a post-hoc Tukey test except panel C Two-tailed paired Student’s T-test, with significance denoted by *= p<0.05, **= p<0.01, and ***=p<0.001. Scale bar =10µm.

Article Snippet: Chromatin motion tracking was achieved using both Nikon NIS Elements the FIJI plugin Trackmate.

Techniques: Control, Inhibition, Two Tailed Test

Journal: bioRxiv

Article Title: Transcriptional activity generates chromatin motion that drives nuclear blebbing

doi: 10.1101/2025.05.20.655131

Figure Lengend Snippet: (A) Mean squared displacement (MSD) plots of UNT, and BO2 of >8 foci averaged per nucleus over 75 seconds, which is half of full tracking of 150 seconds, 10 nuclei per condition. (B) Example images of wild type MEF nuclei with CY3-dUTP used for tracking chromatin motion. Example trackmate tracks for all measured chromatin foci domain motion tracked and example single chromatin domain foci track for untreated control (UNT, black) and BO2 (blue). (C) Example images of normal and blebbed MEF wild type nuclei stained with Hoechst and graph of blebbing percentage in normal (black outline), VPA (gray fill), and BO2 (blue fill). (D) Example images of a MEF nuclear bleb reabsorption and graph of the percentage of bleb reabsorption events for UNT and BO2 treated MEF cells. For C and D N=3 with n> 50 cells precondition. (E-G) Dual micropipette micromanipulation nuclear spring constant measurements for (X) short extension > 3 µm and (X) long extension < 3 µm for MEF untreated (UNT, n = 13) and B02-treated (n = 11) nuclei. Error bars represent standard error and statistical tests are two-tailed (C,D) paired or (A, F, G) unpaired Student’s t-test with significance denoted by *= p<0.05, **= p<0.01, and ***=p<0.001. Scale bar =10µm.

Article Snippet: Chromatin motion tracking was achieved using both Nikon NIS Elements the FIJI plugin Trackmate.

Techniques: Control, Staining, Micromanipulation, Two Tailed Test