Journal: Nucleic Acids Research

Article Title: Hi-BDiSCO: folding 3D mesoscale genome structures from Hi-C data using brownian dynamics

doi: 10.1093/nar/gkad1121

Figure Lengend Snippet: Our chromatin nucleosome-resolution mesoscale model ( , ). A linear 100-nucleosome chromatin fiber at bottom with the enlarged basic unit (chromatosome) at top, from a side view. The Nucleosome core is represented by the Discrete Surface Charge Optimization (DiSCO) model shown at right as an irregular surface and 300 distributed charge beads. Histone tails are shown as green (H3), yellow (H2A), red (H2B) and blue (H4) beads. Linker histones are shown as orange (globular head) and cyan (C-terminal domain) beads. Linker DNA units are shown as red beads.

Article Snippet: Here we present a Brownian Dynamics (BD) approach termed Hi-BDiSCO for producing 3D genome structures from Hi-C and Micro-C data using our mesoscale-resolution chromatin model based on the Discrete Surface Charge Optimization (DiSCO) model. Our approach integrates reconstruction with chromatin simulations at nucleosome resolution with appropriate biophysical parameters.

Techniques:

Journal: Stem Cell Research & Therapy

Article Title: Image-based crosstalk analysis of cell–cell interactions during sprouting angiogenesis using blood-vessel-on-a-chip

doi: 10.1186/s13287-022-03223-1

Figure Lengend Snippet: Conceptual sketch of this study to analyze angiogenic effects of MSC co-cultured on the microvessel-on-a-chip system. A Experimental procedure of microvessel fabrication. MSCs were embedded in the collagen gels to achieve the microvessel-on-a-chip surrounded by MSCs. Analyses of cell-to-cell crosstalk between microvessels and MSCs during sprouting angiogenesis are performed. B Analytical overview to evaluate the morphological maturation of angiogenic sprouts using surface curvature. Color bars represent the mean curvature calculated on the 3D model surfaces. Gradient color bars with blue, white, and red indicate convex surface, flat surface, and concave surface, respectively

Article Snippet: Using the open-source software, MeshLab, we estimated spatial curvature distributions on the 3D discrete surface models generated using IMARIS (Fig. A).

Techniques: Cell Culture

Journal: Stem Cell Research & Therapy

Article Title: Image-based crosstalk analysis of cell–cell interactions during sprouting angiogenesis using blood-vessel-on-a-chip

doi: 10.1186/s13287-022-03223-1

Figure Lengend Snippet: Three-dimensional reconstruction, segmentation, and characterization of microvessel morphologies when co-cultured with MSCs for 10 days. The visualization of immunostained, binarized, and segmented vascular structures from confocal laser microscopy and 3D image processing (see Additional file : Figs. S2 and S3; Additional file : Video S1; Additional file : Video S3). HUVECs were double-stained red with UEA I-fluorophore conjugate and immunostaining using Alexa Fluor 555-conjugated secondary antibody against CD31 marker. MSCs were labeled with GFP in green. Nuclei were stained with Hoechst 33,342 in blue. Image processing using IMARIS (Bitplane) allowed the reconstruction of 3D surface models, consisting of triangular meshes with vertices and edges. Surfaces of the 3D microvessel models were classified into “Sprouts” or “Parent vessel” (see “ ” section). Scale bars: 200 μm. B Segmentation of the entire surface of the 3D microvessel in ( A ) into “MSC-covered” surfaces (green) or “Uncovered” (red). Panels (i), (ii), and (iii) focus on representative MSC-binding sites as shown in white dashed boxes. Scale bars: 200 μm or 50 μm in pictures of entire or local vascular structures, respectively. C Segmentation of “sprout” surfaces in ( A ) into “MSC-covered” surfaces (green), “Uncovered” (red), or parent vessel (gray). Scale bars: 200 μm. D Segmentation of “parent vessel” surfaces in ( A ) into “MSC-covered” surfaces (green), “Uncovered” (red), or sprouts (gray). Scale bars: 200 μm. E Quantitative analyses of microvessel morphology. a Correlation analysis between red intensity (HUVECs) and green intensity (MSCs) using a single 3D image shown in ( A ). Pearson’s correlation coefficient, r , was calculated as high (> 0.6). b Comparison of sprout ranges between monoculture ( n = 4) and co-culture ( n = 5). Data are shown as box plots to compare the median values with the Mann–Whitney U test and are recognized as significantly different when the p value < 0.05. c Comparison of surface roughness on the sprouts between monoculture ( n = 4) and co-culture ( n = 5). The index “surface roughness” was defined as the unit surface area per volume. d Linear regression of MSC coverage ratio and sprout volume using five co-culture samples. P values in ( b ) and ( c ) were adjusted using Bonferroni’s multiple corrections

Article Snippet: Using the open-source software, MeshLab, we estimated spatial curvature distributions on the 3D discrete surface models generated using IMARIS (Fig. A).

Techniques: Cell Culture, Microscopy, Staining, Immunostaining, Marker, Labeling, Binding Assay, Comparison, Co-Culture Assay, MANN-WHITNEY