Journal: Molecular Systems Biology

Article Title: Coupling traction force patterns and actomyosin wave dynamics reveals mechanics of cell motion

doi: 10.15252/msb.202110505

Figure Lengend Snippet: Sequence of snapshots of the LimE‐GFP distribution and stress T for an oscillatory cell together with snapshots of the GFP‐myo distribution for a separate oscillatory cell. Corresponding speeds are 7.0 and 4.6 µm/min. The sequences show an entire cycle of oscillation (spreading and contraction). White arrows represent the direction of motion before the cell spreads and contracts during which no net motion exists. Top: Basal area (black line) and LimE fluorescent intensity (green line) as a function of time, for the same cell as in (A). Inset: Temporal CF of the area and the LimE fluorescent intensity (blue) and of the area change rate and the LimE fluorescent intensity (magenta). Bottom: Kymograph of the LimE‐GFP intensity along the cell outline. Top: Basal area (black line) and myosin fluorescent intensity (green line) as a function of time for a separate cell. Inset: Temporal CF of the area and the myosin fluorescent intensity (blue) and the area change rate and the myosin fluorescent intensity (magenta). Bottom: Kymograph of the GFP‐myo intensity along the cell outline. Top: Basal area (black line) and total force F (blue line) as a function of time, for the same cell as in (A). Inset: Temporal cross‐correlation function (CF) of the area and F (blue) and of the area change rate and F (magenta). Bottom: Kymograph of T along the cell outline. Median shift in the CF of the area and F (33.8 (22.5/42.2) s; N = 45 biological replicates), the area and the LimE‐GFP intensity (−11.2 [−19.6/−10.3] s; N = 21 biological replicates), and the area and the GFP‐myo intensity (52.5 [41.3/62.8] s; N = 11 biological replicates). Median shift in the CF of the area change rate and F (−3.7 [−11.2/3.8] s; N = 42 biological replicates), the area change rate and the LimE‐GFP intensity (16.9 [7.5/30.0] s; N = 20 biological replicates), and the area change rate and the GFP‐myo intensity (3.8 [0/7.5] s; N = 11 biological replicates). Data bellow the dashed line indicate cells for which no significant correlation was found. Time‐averaged total force F as a function of the cell area A. Data information: (B–D) The peaks in the CF are indicated by star symbols, the 95% confidence interval is gray‐shaded, and the sign of the peak in the CF defined whether the quantities were correlated (largest peak occurred for positive CF values) or were anticorrelated (largest peak occurred for negative CF values; see ). (E, F) P ‐values higher than 0.05 are considered not significant, * P < 0.05, ** P < 0.01, and **** P < 0.0001 as determined by the Wilcoxon–Mann–Whitney test using the rank sum function in MATLAB. All scale bars in the figure: 10 μm.

Article Snippet: The cell outline was determined using the MATLAB function bwboundaries, from which we constructed kymographs of fluorescent intensity and forces and computed the cell's center of mass.

Techniques: Sequencing, MANN-WHITNEY

Journal: Molecular Systems Biology

Article Title: Coupling traction force patterns and actomyosin wave dynamics reveals mechanics of cell motion

doi: 10.15252/msb.202110505

Figure Lengend Snippet: A Sequence of snapshots of the LimE‐GFP distribution and stress T for an amoeboid cell and the GFP‐myo distribution for a separate amoeboid cell. Corresponding speeds are 7.4 and 4.5 µm/min. The sequences show both the phases of protrusion and retraction. White arrows represent the direction of motion. B Spatially averaged LimE‐GFP intensity as a function of time (green line), together with the basal area (black line) for the first cell in (A). Inset: CF of the area and LimE‐GFP intensity (blue) and of the area change rate and the LimE‐GFP intensity (magenta). C Basal area (black line) and total force F (blue line) as a function of time corresponding to the first cell in (A). Inset: Temporal cross‐correlation function (CF) of the area and the total force F (blue) and of the area change rate and F (magenta). The correlation within the shaded region is below the 95% confidence interval. D Median shift in the CF of the area and F (blue symbols, N = 66 biological replicates), the LimE‐GFP intensity (brown symbols, N = 18 biological replicates), and the GFP‐myo intensity (yellow symbols, N = 7 biological replicates). Values of these shifts were determined as 11.3 (3.8/15) s, −11.2 (−15.0/‐7.5) s, and 7.5 (1.9/12.2) s. E Median shift in the CF of the area change rate and F (blue symbols, N = 52 biological replicates), the LimE‐GFP intensity (brown symbols, N = 17 biological replicates), and the GFP‐myo intensity (yellow symbols, N = 7 biological replicates). Data below the dashed line indicate cells for which no significant correlation was found. Shift values are −11.2 (−15.0/‐9.4) s, 11.3 (7.5/11.3) s, and −26.3 (−30.0/‐14.1) s. F–H Kymographs for LimE‐GFP intensity, T , and edge velocity along the cell outlines for the first cell of (A). I–K Kymographs for GFP‐myo intensity, T , and edge velocity along the cell outlines for the second cell of (A). L, M Time‐averaged total force F as a function of the cell's area and time‐averaged F y as a function of time‐averaged F x (slope of fit shown as a dashed line: 0.86, r 2 = 0.94). Markers indicate the different strains: AX2 LimE‐GFP (>), AX2 GFP‐myo (<), AX2 lifeAct‐GFP (^), and engineered cells (o). Data information: (B, C) The peaks in the CF are indicated by star symbols, the 95% confidence interval is gray‐shaded, and the sign of the peak in the CF defined whether the quantities were correlated (largest peak occurred for positive CF values) or were anticorrelated (largest peak occurred for negative CF values; see ). (D, E) P ‐values higher than 0.05 are considered not significant, * P < 0.05 and **** P < 0.0001 as determined by the Wilcoxon–Mann–Whitney test using the rank sum function in MATLAB. All scale bars in the figure: 10 μm. Arrows indicate direction of motion.

Article Snippet: The cell outline was determined using the MATLAB function bwboundaries, from which we constructed kymographs of fluorescent intensity and forces and computed the cell's center of mass.

Techniques: Sequencing, MANN-WHITNEY

Journal: Molecular Systems Biology

Article Title: Coupling traction force patterns and actomyosin wave dynamics reveals mechanics of cell motion

doi: 10.15252/msb.202110505

Figure Lengend Snippet: Protrusion and retraction speed for amoeboid, oscillatory, and fan‐shaped cells, defined as the average of the pixels with the 20% lowest and highest membrane speed. Ratio between the edge velocity, stress, LimE‐GFP, and GFP‐myo intensity in membrane regions identified as protrusions and retractions. Average edge velocity in regions of low and high LimE‐GFP and GFP‐myo fluorescence. High fluorescence was defined as the 20% brightest LimE‐GFP and GFP‐myo pixels in the kymographs, while low fluorescence consisted of the remaining 80% pixels. Ratio between the stress in regions of high and low LimE‐GFP and GFP‐myo fluorescence for the three modes of migration. The ratio was significantly different for all modes and was found to be much smaller in the fan‐shaped cells, which have large traction force poles at the back of the cell. Data information: P ‐values higher than 0.05 are considered not significant, * P < 0.05, ** P < 0.01, *** P < 0.001, and **** P < 0.0001 as determined by the Wilcoxon–Mann–Whitney test using the rank sum function in MATLAB. The box plots were created using the boxplot function in MATLAB, with the line indicating the median, the bottom and top edges of the box indicating the 25 th and 75 th percentiles, respectively, and the whiskers extending to the most extreme data points not considered outliers. Values and number of biological replicates are listed in Appendix Table . (B, C) The dotted line indicates a ratio equal to 1.

Article Snippet: The cell outline was determined using the MATLAB function bwboundaries, from which we constructed kymographs of fluorescent intensity and forces and computed the cell's center of mass.

Techniques: Membrane, Fluorescence, Migration, MANN-WHITNEY

Journal: Cardiovascular Research

Article Title: Ultrastructure of the intercellular space in adult murine ventricle revealed by quantitative tomographic electron microscopy

doi: 10.1093/cvr/cvv182

Figure Lengend Snippet: Operational workflow applied to tomographic EM images of the adult ID. (A) Gallery view of virtual XY slices along the Z-axis of a small region cropped from a tomogram (down-sampled here for simplicity). (B) The membranes of each apposing cell were manually traced on each slice to create a binary 3D mask. (C) Intercellular volume binary masks were generated by virtually filling the space located between the two segmented membranes. (D) Mask of the contours of the membranes generated by applying an edge detection algorithm. (E) 2D projection along the Z-axis of mask in B. (F) Virtually filled space located between the two most external lines. (G) Skeletonized 2D representation of the ID obtained by mathematically extracting the central line of the white region shown in F. (H) A representation of the skeletonized ID whose ends (red dots) have been automatically detected. (I) A virtual slice of the 3D binary mask of the contours generated in D. (J) Boundaries automatically detected in I. Each colour represents the membrane of a different cell. (K) For each boundary point, the closest point in the opposite boundary was found and the corresponding distance was calculated (in green). (L) Close-up of the region inside the dashed square in K. Original contours (white), boundaries (blue and red), and distances (green) are visible.

Article Snippet: For each virtual slice of the 3D binary mask, the membranes of the two apposing cells were defined as two boundaries (b1 and b2; Matlab function ‘bwboundaries’; Figure I and J ), and for each point in one boundary, we identified the shortest distance to the opposing one ( Figure K and L ).

Techniques: Generated, Membrane