Journal: EMBO Reports

Article Title: Kinesin-1 mediates proper ER folding of the Ca V 1.2 channel and maintains mouse glucose homeostasis

doi: 10.1038/s44319-024-00246-y

Figure Lengend Snippet: Reagents and tools table

Article Snippet: The movements of insulin granules were subjected to MSD analysis using the MSD Analyzer plugin ( https://tinevez.github.io/msdanalyzer/ ) on the MATLAB platform (Tarantino et al, ).

Techniques: Knock-Out, Recombinant, Plasmid Preparation, Knockdown, Expressing, Transduction, Sequencing, Software, Enzyme-linked Immunosorbent Assay, Blocking Assay, Transfection, Isolation, Western Blot

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: Methods in enzymology

Article Title: Direct Quantitative Monitoring of Homology-Directed DNA Repair of Damaged Telomeres

doi: 10.1016/bs.mie.2017.11.010

Figure Lengend Snippet: (A) Equation of mean square displacement (MSD) during Δt intervals for a particle i traveling in a 2D plane. (B) MSD plots of different classes of mobility. The equation, MSD= Γ tα, is used to provide a best fit curve for the MSD trajectories. Coefficient Γ indicates the magnitude of travel, while α is a time-dependence coefficient which indicates the type of movement the particle exhibits. (i) α Values of less than 1 indicate subdiffusion resulting from restriction to diffusion which would occur during molecular crowding in the nucleus. (ii) α Values of 1 indicate Brownian diffusion. (iii) α Values of greater than 1 indicate superdiffusive mobility. An α value of 2 would be characteristic of a particle traveling in a directed manner (Guigas & Weiss, 2008; Marshall et al., 1997; Zajac, Goldman, Holzbaur, & Ostap, 2013).

Article Snippet: DMEM cell culture medium with GlutaMAX (ThermoFisher), supplemented with 10% bovine calf serum and 1% Penicillin/Streptomycin (Gibco) 6-Well culture plates (Sarstedt) LipoD293 transfection reagent (Signagen) 22×22mm No 1.5 cover glass (Electron Microscopy Sciences) Incubator, 37°C and 5% CO 2 Leibovitz’s L-15 medium with l -glutamine, without phenol red (ThermoFisher) 4-Hydroxytamoxifen (Sigma) at 1m M stock concentration Shield-1 ligand (Clontech) at 0.5m M stock concentration Inverted fluorescence microscope (DM6000, Leica Microsystems), equipped with a charge-coupled device camera (QuantEM 512C, Photometrics), a 100×1.4 NA objective, automated XYZ stage (Ludl Electronic Products), an X-LIGHT Confocal Imager (Crisel Electrooptical Systems), and a SPECTRA X Light Engine (Lumencor) Stagetop heating incubator (Tokai Hit) Magnetic coverslip mounting chamber (Chamlide CM-S22–1, LCI) MetaMorph software (Molecular Devices) ImageJ Fiji (NIH, http://fiji.sc/ ) TrackMate plugin ( http://imagej.net/TrackMate ) StackReg plugin (Dr. Philippe Théevenaz, EPFL) MATLAB software (MathWorks) Mean square displacement (MSD) analyzer scripts (Dr. Jean-Yves Tinevez, Institut Pasteur) importTrackMateTracks ( https://github.com/fiji/TrackMate/blob/master/scripts/importTrackMateTracks.m ) MSD analyzer ( https://github.com/tinevez/msdanalyzer )

Techniques: Diffusion-based Assay