voronoi analysis  (Molecular Dynamics Inc)

Journal: Nature Communications

Article Title: Herpes simplex virus type 1 reshapes host chromatin architecture via transcription machinery hijacking

doi: 10.1038/s41467-025-60534-6

Figure Lengend Snippet: a Scheme showing hDNA labeling. A549 cells were cultured in medium supplemented with 5 µM EdC for 64 h before HSV-1 infection to ensure the complete labeling of the whole cellular DNA. Cells were infected with HSV-1 (MOI = 3), and fixed at different times post infection. Samples were then labeled with the azide-Alexa 647 (AF647). b Representative STORM density rendering images of hDNA in mock or HSV-1 infected A549 cells. Top: Whole nucleus. Scale bar: 2 µm. Bottom: Zoomed-in regions are shown in yellow boxes. Scale bar: 200 nm. Differences in DNA density follow the color scale bar; top: 0.00001 nm −2 (dark blue) to 0.01281 nm −2 (white); bottom: 0.00001 nm −2 (dark blue) to 0.02001 nm −2 (white). c Cumulative distribution of the Voronoi polygon densities for hDNA distribution in mock ( n = 29), and HSV-1 infected cells at 1 hpi ( n = 27), 3 hpi ( n = 27), and 8 hpi ( n = 45). Thick lines show the median and light colors, the interquartile range. ns, p > 0.05; **** p < 0.0001, calculated by ordinary one-way ANOVA followed by Dunnet’s multiple comparison test against mock. d Percentage of hDNA-free area per nucleus of EdC-AF647 labeled hDNA in mock ( n = 29), and HSV-1 infected cells at 1 hpi ( n = 27), 3 hpi ( n = 27), and 8 hpi ( n = 45). Mean and SD represented; ns, p > 0.05; **** p < 0.0001, calculated by ordinary one-way ANOVA followed by Dunnett’s multiple comparison test against mock. e Cropped representative STORM-PAINT images of EdC-AF647 labeled hDNA (magenta), immunolabeled ICP4 (cyan), and their merge in mock and HSV-1 infected cells. Yellow dotted line delimits the location of HC and VRCs. Scale bar: 2 µm f (Top) Cropped representative STORM-PAINT images of EdC-AF647 labeled hDNA (magenta), immunolabeled H3 (green), and their merge in mock and HSV-1 infected A549 cells. Scale bar: 2 µm. (Bottom) Zoomed-in regions are shown inside yellow boxes. Scale bar: 200 nm. g Percentage of hDNA-free and H3-free areas per nucleus quantified from SR images of mock ( n = 16), or HSV-1 infected A549 cells at 1 hpi ( n = 13), 3 hpi ( n = 16), and 8 hpi ( n = 19). Mean and SD are represented. ns, p > 0.05; ** p < 0.01; *** p < 0.001; **** p < 0.0001, calculated by ordinary one-way ANOVA followed by Dunnett’s multiple comparison test against hDNA or H3 mock, correspondingly. h Percentage of H3 clusters located in the HC over the whole nucleus at 3 hpi ( n = 16) and 8 hpi ( n = 19) in HSV-1 infected A549 cells. Mean and SD are shown. ns, p > 0.05, calculated by unpaired, two-tailed Student’s t test. i , j Dot plots showing the median number of localizations per cluster ( i ) and the median area per cluster ( j ) in mock ( n = 16), and HSV-1 infected cells at 1 hpi ( n = 13), 3 hpi ( n = 16), and 8 hpi ( n = 19). Analysis performed on H3 clusters localized in the whole nucleus for mock and 1 hpi and in the HC for 3 hpi and 8 hpi. Mean and SD are shown. ns, p > 0.05; * p < 0.05; ** p < 0.01; *** p < 0.001, calculated by ordinary one-way ANOVA followed by Dunnett’s multiple comparison test against mock. k hDNA density as a function of the distance from the center of the H3 clutch in mock ( n = 12), and HSV-1 infected cells at 1 hpi ( n = 8), 3 hpi ( n = 16), and 8 hpi (n = 18). Density is measured inside rings of increasing search radii. Mean and SD shown. l-o Dot plots showing the percentage of histone-free area ( l ), the cluster density ( m ), median localizations per cluster ( n ) and median area per cluster ( o ) for H3K27me3 in HSV-1 infected A549 cells. Mock ( n = 13), 1 hpi ( n = 11), 3 hpi ( n = 10), 4 hpi ( n = 9), 6 hpi ( n = 13), 8 hpi ( n = 12). Mean and SD are shown. ns, p > 0.05; ** p < 0.01; **** p < 0.0001, calculated by ordinary one-way ANOVA followed by Dunnett’s multiple comparison test against mock. Source data are provided as a file. p values are indicated in Supplementary Data .

Article Snippet: Voronoi tessellation analysis was performed in MATLAB 2016a as previously described .

Techniques: Labeling, Cell Culture, Infection, Comparison, Immunolabeling, Two Tailed Test

Journal: Nature Communications

Article Title: Herpes simplex virus type 1 reshapes host chromatin architecture via transcription machinery hijacking

doi: 10.1038/s41467-025-60534-6

Figure Lengend Snippet: a (Left) Cropped representative STORM-PAINT images of EdC-AF647 labeled hDNA (magenta), immunolabeled RNAP II phSer5 (green), and their merge in mock and HSV-1 infected A549 cells at 1 hpi, 3 hpi, and 8 hpi. Yellow arrowheads indicate large aggregates of RNAP II phSer5. Scale bar: 2 µm. (Right) Zoomed-in regions are shown in yellow boxes. Scale bar: 200 nm. b Percentage of RNAP II phSer5 clusters located in VRCs over the whole nucleus in HSV-1 infected A549 cells at 3 hpi ( n = 20), and 8 hpi ( n = 14). Mean and SD are shown. ** p < 0.01, calculated by unpaired, two-tailed Student’s t test. c–e Dot plots showing the median number of RNAP II phSer5 localizations per cluster ( c ), the median area per cluster ( d ) and the NND between clusters ( e ), for mock ( n = 44) and HSV-1 infected A549 cells at 1 hpi ( n = 32), 2 hpi (HC, n = 15; VRC, n = 8), 3 hpi (HC, n = 20; VRC, n = 20), and 8 hpi (HC, n = 14; VRC, n = 28). Mean and SD are shown. ns, p > 0.05; * p < 0.05; *** p < 0.001; **** p < 0.0001; calculated by ordinary one-way ANOVA followed by Dunnett’s multiple comparison test against mock. f Representative conventional images of hDNA (magenta), conventional ICP4 (cyan), and cropped STORM images of RNAP II phSer5 (green), in mock, HSV-1 infected cells and HSV-1 n12 infected cells at 3 and 8 hpi. Scale bar: 2 µm. g Representative STORM density rendering images of hDNA in mock or HSV-1 WT and HSV-1 n12 infected A549 cells. Scale bar: 2 µm. Differences in DNA density follow the color scale bar; top: 0.00001 nm −2 (dark blue) to 0.01518 nm −2 (white). h Cumulative distribution of the Voronoi polygon densities for hDNA distribution in mock, HSV-1 and HSV-1 n12 infected cells at 3 hpi and 8 hpi. Mock ( n = 24), 3 hpi WT ( n = 22), 3 hpi n12 ( n = 32), 8 hpi WT ( n = 26), 8 hpi n12 ( n = 24). Thick lines show the median and light colors, the interquartile range. ns, p > 0.05; ** p < 0.001, *** p < 0.001, calculated by ordinary one-way ANOVA followed by Dunnet’s multiple comparison test against mock. i Percentage of hDNA-free area per nucleus of EdC-AF647 labeled hDNA in mock, HSV-1 WT and HSV-1 n12 infected cells at 3 hpi and 8 hpi. Mock (n = 24), 3 hpi WT ( n = 22), 3 hpi n12 ( n = 32), 8 hpi WT ( n = 26), 8 hpi n12 ( n = 24). Mean and SD represented; ns, p > 0.05; **** p < 0.0001, calculated by ordinary one-way ANOVA followed by Dunnett’s multiple comparison test against mock. Source data are provided as a file. p -values are indicated in Supplementary Data .

Article Snippet: Voronoi tessellation analysis was performed in MATLAB 2016a as previously described .

Techniques: Labeling, Immunolabeling, Infection, Two Tailed Test, Comparison