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voronoi tessellation analysis  (MathWorks Inc)


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    MathWorks Inc voronoi tessellation analysis
    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 <t>Voronoi</t> 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 .
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    Images

    1) Product Images from "Herpes simplex virus type 1 reshapes host chromatin architecture via transcription machinery hijacking"

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

    Journal: Nature Communications

    doi: 10.1038/s41467-025-60534-6

    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 .
    Figure Legend 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 .

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

    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 .
    Figure Legend 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 .

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

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    ANSYS inc fluent voronoi tessellation
    In this scheme, flagellated soil bacteria navigate the soil by swimming through flooded pores between soil particles and grains (left semicircle). To visualize its swimming through a complex geometry with different degrees of confinement, transparent chambers with microchannels of different widths were used (right semicircle, showing a microchannel network of 20 μ m channel width). Microfluidic devices, as sketched at the right, were fabricated based on <t>Voronoi</t> tessellations (see Materials and Methods), with channel widths of increasing confinement (20 μ m, 10 μ m and 5 μ m). Three different strains of Bradyrhizobium diazoefficiens were inoculated in the devices, a wild type (WT) with two flagellar systems and two mutants, one lacking the lateral flagellar system (Δ lafA ) and the other lacking the subpolar one (Δ fliC ) depicted as light-brown, violet, and blue bacteria, respectively. Credit for the real soil image (left semicircle): Katelyn Solbakk, Mikroliv .
    Fluent Voronoi Tessellation, supplied by ANSYS inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    voronoi tessellation  (Okabe Co Ltd)
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    In this scheme, flagellated soil bacteria navigate the soil by swimming through flooded pores between soil particles and grains (left semicircle). To visualize its swimming through a complex geometry with different degrees of confinement, transparent chambers with microchannels of different widths were used (right semicircle, showing a microchannel network of 20 μ m channel width). Microfluidic devices, as sketched at the right, were fabricated based on <t>Voronoi</t> tessellations (see Materials and Methods), with channel widths of increasing confinement (20 μ m, 10 μ m and 5 μ m). Three different strains of Bradyrhizobium diazoefficiens were inoculated in the devices, a wild type (WT) with two flagellar systems and two mutants, one lacking the lateral flagellar system (Δ lafA ) and the other lacking the subpolar one (Δ fliC ) depicted as light-brown, violet, and blue bacteria, respectively. Credit for the real soil image (left semicircle): Katelyn Solbakk, Mikroliv .
    Voronoi Tessellation, supplied by Okabe Co Ltd, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    In this scheme, flagellated soil bacteria navigate the soil by swimming through flooded pores between soil particles and grains (left semicircle). To visualize its swimming through a complex geometry with different degrees of confinement, transparent chambers with microchannels of different widths were used (right semicircle, showing a microchannel network of 20 μ m channel width). Microfluidic devices, as sketched at the right, were fabricated based on <t>Voronoi</t> tessellations (see Materials and Methods), with channel widths of increasing confinement (20 μ m, 10 μ m and 5 μ m). Three different strains of Bradyrhizobium diazoefficiens were inoculated in the devices, a wild type (WT) with two flagellar systems and two mutants, one lacking the lateral flagellar system (Δ lafA ) and the other lacking the subpolar one (Δ fliC ) depicted as light-brown, violet, and blue bacteria, respectively. Credit for the real soil image (left semicircle): Katelyn Solbakk, Mikroliv .
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    centroidal voronoi tessellations: applications and algorithms  (Applica Consumer Products)
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    In this scheme, flagellated soil bacteria navigate the soil by swimming through flooded pores between soil particles and grains (left semicircle). To visualize its swimming through a complex geometry with different degrees of confinement, transparent chambers with microchannels of different widths were used (right semicircle, showing a microchannel network of 20 μ m channel width). Microfluidic devices, as sketched at the right, were fabricated based on <t>Voronoi</t> tessellations (see Materials and Methods), with channel widths of increasing confinement (20 μ m, 10 μ m and 5 μ m). Three different strains of Bradyrhizobium diazoefficiens were inoculated in the devices, a wild type (WT) with two flagellar systems and two mutants, one lacking the lateral flagellar system (Δ lafA ) and the other lacking the subpolar one (Δ fliC ) depicted as light-brown, violet, and blue bacteria, respectively. Credit for the real soil image (left semicircle): Katelyn Solbakk, Mikroliv .
    Centroidal Voronoi Tessellations: Applications And Algorithms, supplied by Applica Consumer Products, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    functionality for polydisperse voronoi tessellation  (OVITO GmbH)
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    In this scheme, flagellated soil bacteria navigate the soil by swimming through flooded pores between soil particles and grains (left semicircle). To visualize its swimming through a complex geometry with different degrees of confinement, transparent chambers with microchannels of different widths were used (right semicircle, showing a microchannel network of 20 μ m channel width). Microfluidic devices, as sketched at the right, were fabricated based on <t>Voronoi</t> tessellations (see Materials and Methods), with channel widths of increasing confinement (20 μ m, 10 μ m and 5 μ m). Three different strains of Bradyrhizobium diazoefficiens were inoculated in the devices, a wild type (WT) with two flagellar systems and two mutants, one lacking the lateral flagellar system (Δ lafA ) and the other lacking the subpolar one (Δ fliC ) depicted as light-brown, violet, and blue bacteria, respectively. Credit for the real soil image (left semicircle): Katelyn Solbakk, Mikroliv .
    Functionality For Polydisperse Voronoi Tessellation, supplied by OVITO GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    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 .

    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

    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 .

    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

    In this scheme, flagellated soil bacteria navigate the soil by swimming through flooded pores between soil particles and grains (left semicircle). To visualize its swimming through a complex geometry with different degrees of confinement, transparent chambers with microchannels of different widths were used (right semicircle, showing a microchannel network of 20 μ m channel width). Microfluidic devices, as sketched at the right, were fabricated based on Voronoi tessellations (see Materials and Methods), with channel widths of increasing confinement (20 μ m, 10 μ m and 5 μ m). Three different strains of Bradyrhizobium diazoefficiens were inoculated in the devices, a wild type (WT) with two flagellar systems and two mutants, one lacking the lateral flagellar system (Δ lafA ) and the other lacking the subpolar one (Δ fliC ) depicted as light-brown, violet, and blue bacteria, respectively. Credit for the real soil image (left semicircle): Katelyn Solbakk, Mikroliv .

    Journal: Communications Biology

    Article Title: Soil-mimicking microfluidic devices reveal restricted flagellar motility of Bradyrhizobium diazoefficiens under microconfinement

    doi: 10.1038/s42003-025-07811-8

    Figure Lengend Snippet: In this scheme, flagellated soil bacteria navigate the soil by swimming through flooded pores between soil particles and grains (left semicircle). To visualize its swimming through a complex geometry with different degrees of confinement, transparent chambers with microchannels of different widths were used (right semicircle, showing a microchannel network of 20 μ m channel width). Microfluidic devices, as sketched at the right, were fabricated based on Voronoi tessellations (see Materials and Methods), with channel widths of increasing confinement (20 μ m, 10 μ m and 5 μ m). Three different strains of Bradyrhizobium diazoefficiens were inoculated in the devices, a wild type (WT) with two flagellar systems and two mutants, one lacking the lateral flagellar system (Δ lafA ) and the other lacking the subpolar one (Δ fliC ) depicted as light-brown, violet, and blue bacteria, respectively. Credit for the real soil image (left semicircle): Katelyn Solbakk, Mikroliv .

    Article Snippet: The network was designed in Matlab as a Voronoi tessellation, obtained from N = 3000 seed points within a region of A = 2 × 1 (arbitrary units) , .

    Techniques: Bacteria