msd analyzer  (MathWorks Inc)

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: A responsive living material prepared by diffusion reveals extracellular enzyme activity of cyanobacteria

doi: 10.1073/pnas.2424405122

Figure Lengend Snippet: Experimental diffusion coefficient of S. elongatus cells entering NC-PNIPAm using MSD. ( A and B ) Illustrations depicting diffusion experiment. ( A ) Experimental set up where 5 µL of diluted culture of S. elongatus is pipetted onto the surface of deswelled NC-PNIPAm (20 mm × 5 mm × 0.025 mm) affixed onto a microscope slide. ( B ) Overhead view of deswelled NC-PNIPAm and droplet of S. elongatus ; the arrow indicates direction cells move as diffusion takes place. ( C ) Schematic depicting microscopic movement of S. elongatus cells diffusing through two-dimensional hydrogel matrix as the NC-PNIPAm transitions from the deswelled to reswelled state. ( D ) Fluorescent image depicts S. elongatus cells detected by chlorophyll a autofluorescence with TRITC filter immediately after pipetting culture of S. elongatus onto the surface of NC-PNIPAm (denoted as t 0 ) and 300 s after addition of culture of S. elongatus (denoted as t 0 + 300 s). Purple circles illustrate the located cells and blue lines indicate the tracked vector displacement of cells, identified by multiple particle tracking FIJI plugin, respectively. White arrows indicate the general direction that S. elongatus cells move during the diffusion process. ( E ) MSD plotted as a function of time traveled and fitted to calculate experimental diffusion coefficient. MSD of individual S. elongatus cells are represented by colored lines, and the average MSD and SD of S. elongatus cells represented by the black line and light blue shaded region, respectively.

Article Snippet: Utilizing the previous research of Tarantino et al. , the tracked cells and their vector displacement were analyzed in an MSD analyzer in MATLAB, and the tracked cells and their vector displacement were linearly fit to the MSD equation ( E ).

Techniques: Diffusion-based Assay, Microscopy, Plasmid Preparation

Journal: Communications Biology

Article Title: Microtubule polarity determines the lineage of embryonic neural precursor in zebrafish spinal cord

doi: 10.1038/s42003-024-06018-7

Figure Lengend Snippet: a Maximal z-projection of 24hpf zebrafish spinal cord between somites 6–8, showing KIF16Ba (KIF16Ba-mCherry, magenta) and Sara endosomes (GFP-Sara CRISPR Knock in, green) colocalization. b Relative pole B Sara endosomes ratio as a function of spindle-MT enrichment for control (gray, n = 61 NPs) and KIF16Ba MO (green, n = 18 NPs) datasets. Below, GMM clustering of KIF16Ba MO spindle-MT enrichment (DI = 77.8%) with symmetric (blue) and asymmetric (red) clusters. c Sum z-projection of a dividing KIF16Ba MO asymmetric NP (registered t = 75 s) showing Sara endosomes (mCherry-Sara, magenta) and spindle-MTs (GFP-DCX, green). Relative pole B Sara endosomes ratio and spindle-MT enrichment are indicated. Arrows show Sara endosomes symmetric inheritance between the poles (cell contours). a , c Scale bars, 5 μm. d Dynamic of Sara endosomes mean ratio (log scale) as a function of registered time in pole A for control asymmetric (blue; n = 21 NPs) and KIF16Ba MO asymmetric (red; n = 8 NPs) datasets. ANOVA comparison of Sara endosome mean densities as a function of registered time between pole B and pole A ( e ) or cell center and cell sides ( h ) for KIF16Ba MO asymmetric ( e ; n = 8 NPs, 1141 endosomes) and KIF16Ba MO combined datasets ( h ; n = 18 NPs, 1986 endosomes). f Weighted average mean square displacement (MSD) (weighted according to certainty, see methods) as a function of delay for control combined (blue line) and KIF16Ba MO combined (red line) datasets. Blue dashed line, quadratic fit of combined control dataset. Red dashed line, linear fit of KIF16Ba MO combined dataset. R², correlation coefficient (95% confidence). g Average percentage of Sara endosomes in the central spindle area as a function of registered time for the control combined (blue) and KIF16Ba MO combined (red) datasets. Black dashed line indicates departure. d , g , f Shades, relative standard error mean (RSEM).

Article Snippet: Afterward, MSD analyzer package was used with a custom Matlab code to generate \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$MSD(t)=\langle (\varDelta {x}^{2})\rangle +\langle (\varDelta {y}^{2})\rangle$$\end{document} M S D ( t ) = ⟨ ( Δ x 2 ) ⟩ + ⟨ ( Δ y 2 ) ⟩ of each individual track (Fig. ; ).

Techniques: CRISPR, Knock-In, Control, Comparison