plustiptracker for matlab  (MathWorks Inc)

Journal: Clinical cancer research : an official journal of the American Association for Cancer Research

Article Title: Microtubule Engagement with Taxane Is Altered in Taxane-Resistant Gastric Cancer

doi: 10.1158/1078-0432.CCR-19-3018

Figure Lengend Snippet: Differential gene expression analysis of sensitive and resistant cells reveals coordinated modulation of kinesin family is differentially modulated in docetaxel (DTX)-sensitive and docetaxel-resistant DIF-GC cells, which display characteristic microtubule dynamicity. A, Venn diagram representing the DEGs after docetaxel treatment in docetaxel-sensitive (AZ521 and TMK1) and docetaxel-resistant (SCH and MKN7) gastric cancer cell lines. B, Bar graph representing the microtubule-related pathways identified by Reactome pathway analysis of the 84 common DEGs, ranked by significance. C, mRNA expression of the five kinesins was assessed in biopsies obtained from 12 patients with gastric cancer at baseline, with nine matching on-treatment (cabazitaxel) samples. Fold change of on-treatment versus baseline mRNA expression levels was calculated and correlated to response to treatment. D, Computational analysis of microtubule dynamic parameters by direct detection and tracking of GFP-EB1 comets using the MATLAB-based plusTipTracker algorithm. Graphic display of the microtubule growth speed (μm × per minute) in TMK1 and HS746T cell lines at baseline and after 1 hour treatment with increasing concentrations of docetaxel. Mann–Whitney test was used for statistical analysis (*, P < 0.05; **, P < 0.01; n.s., not significant; Ctr, control).

Article Snippet: Image analysis was performed using the MATLAB-based plusTipTracker algorithm, as described previously ( 21 ).

Techniques: Expressing, MANN-WHITNEY

Journal: Molecular Biology of the Cell

Article Title: Spatial regulation of astral microtubule dynamics by Kif18B in PtK cells

doi: 10.1091/mbc.E16-04-0254

Figure Lengend Snippet: Kif18B knockdown causes an increase in the lifetime of astral MTs and a decrease in MT growth rate in general. (A, B) First frame of EB1-GFP image series of spindles in PtK1 cells transfected with (A) control or (B) Kif18B-2 siRNA. Scale bar, 10 μm. (C, D) The plusTipTracker software was used to detect and link EB1 comets from time-lapse images of spindles in A and B. Tracked comets were divided into three subspindle regions and color coded accordingly: astral MTs to the left and right of spindle poles (aster_lr) are in magenta, astral MTs in the top and bottom region of the spindle body (aster_tb) are in green, and MTs in the central region of the spindle body are in cyan (Spindle_midzone). (E) Lifetime of EB1 tracks in the three subspindle regions was fit with a one-phase exponential decay to determine the rate constant K (s −1 ), and the average lifetime (τ) was determined from K −1 . Data represent mean ± 95% confidence interval from the fit (see also Supplemental Figure S2) for 11 spindles for the control with 1045 tracks in aster_lr region, 1063 tracks in aster_tb region, and 4030 tracks in spindle_midzone region and 16 Kif18B RNAi spindles with 3605 tracks in aster_lr region, 2295 tracks in aster_tb region, and 7828 tracks in spindle_midzone region. (F) Histograms of EB1 track velocity in the entire spindle of control and Kif18B knockdowns graphed with the fitting curve of a Gaussian distribution. The mean and SD derived from each fit is indicated. Control RNAi, 11 spindles with 7782 tracks; Kif18B RNAi, 16 spindles with 16414 tracks.

Article Snippet: EB1 comets were automatically detected and frame-to-frame linked using the plusTipTracker MATLAB software package (MathWorks, Natick, MA; Applegate et al. , 2011 ).

Techniques: Knockdown, Transfection, Control, Software, Derivative Assay