Journal: eLife

Article Title: The Wg and Dpp morphogens regulate gene expression by modulating the frequency of transcriptional bursts

doi: 10.7554/eLife.56076

Figure Lengend Snippet: ( A ) Wing discs were imaged and scored for 3D fluorescent objects using the sfGFP probe set. Discs were either from animals with two copies of the sfGFP-sens transgene and two copies of the endogenous sens E1 gene, or from animals with just two copies of the endogenous sens E1 gene. Error bars are SEM. ( B ) A representative optical section taken from a wing disc expressing the sfGFP-sens transgene and endogenous sens E1 gene. The disc was probed for sfGFP (red) and Sens (green) RNA using independent probe sets. Spots that fluoresce both green and red are presumptive sfGFP-Sens mRNAs that have annealed to both probe sets (purple arrow). Spots that only fluoresce with the Sens probe set (white arrow) are presumptive Sens mRNAs that are generated from the endogenous sens gene. Although these sens alleles are mutant for protein output, they still produce mRNA. The occasional spot (beige arrow) that only fluoresces with the sfGFP probe set are presumptive sfGFP-Sens mRNAs that failed to hybridize with the Sens probe set. These are false-negatives. Scale bar = 5 μm. ( C-E ) Pipeline for 3D segmentation of cell nuclei. ( C ) An optical section showing DAPI fluorescence. ( D ) 2D segmentation of this image. ( E ) Five contiguous z-sections of segmented nuclei are colored and viewed laterally. Note the three-dimensional ‘stack of pancakes’ nature of the nuclear objects in the wing disc 3D rendering. ( F ) 3D Voronoi tessellation of an image stack of wing disc cells. The centroids of the 3D nuclei (shown as circles) were used to tessellate the image stack, creating virtual cells. Cells are represented with different colors. Numbers in the x-y plane refer to pixel positions in the 1024 × 1024 sections. Please see the Materials and methods for a detailed description of tessellation and its meaning. ( G ) An image stack showing the centroid positions of 3D mRNA objects as circles. One tessellated cell (green) is superimposed to show the mRNA objects that reside in space occupied by the tessellated cell. These mRNAs would be assigned to that particular cell. Shown is one stripe of sfGFP-Sens expressing cells on one side of the DV boundary marked by pixel position 0.

Article Snippet: The 3D Voronoi tessellation used a polytope-bounded Voronoi diagram available for Matlab, which uses the DeLaunay triangulation to calculate the Voronoi diagram ( ).

Techniques: Expressing, Generated, Mutagenesis, Fluorescence

Journal: Scientific Reports

Article Title: Finite deformation elastography of articular cartilage and biomaterials based on imaging and topology optimization

doi: 10.1038/s41598-020-64723-9

Figure Lengend Snippet: Finite deformation elastography workflow based on image acquisition and topology optimization. ( A ) Increased tissue stiffness demands high shear wave frequency in conventional MRE . Instead, we use cyclic loading during MRI to enable large deformation imaging of stiff materials like cartilage. ( B ) Experimental setup of indentation test and undeformed and deformed morphology images; ( C ) dualMRI measured complex data from deformed tissue to extract phase maps that scale directly to displacements. Volume images were used to establish 2D and 3D mesh models. ( D ) Topology optimization was able to reconstruct a complex (e.g. bilayer) stiffness configurations by minimizing the difference of displacement between initial model and input (e.g. experimental) model.

Article Snippet: Following determination of displacements, 2D and 3D models were established using the location of each pixel in the model or sample (MATLAB), and Delaunay triangulations were created to connect each pixel.

Techniques: Shear, Imaging