Create a continuous timecourse for the heart development starting from a limited number of samples acquired at different timepoints.
The algorithm is completely general and can be applied to any dataset.
All the data can be dowloaded from --> https://www.ebi.ac.uk/biostudies/studies/S-BIAD441 (folder /hearts/).
Follow the pipeline steps below to reproduce the analysis results.
- Description: can be skipped as data is ready for use. Only here for reference.
- Description: manually adjust alignment of different heart samples to a common frame
- Description: make some histograms of the scalar along some ray
- Description: more visualizations of the volume probing
- Description: probe volume and save a polydata which is a cloud of point. Files are produced to the local path. They can be visualized with command e.g.:
vedo -n -p 5 -a 0.02 -c w -x1 *2425*.vtk. If all looks OK move files todata/wtordata/ko.
- Description: plot scalar values on a specific radius shell for test:
- Description: plot the spherical harmonics expansion for the above test:
- Description: generate and save a numpy array
clm_data.npywith theClmspherical harmonic coefficients for all the time points
- Description: make 50 plots of the spherical harm coefficients visualizing the time variable for each one. Pressing return takes to the next radial shell.
- Description: plot now for each time point the reconstructed point clouds (using the sph coefficients) with a threshold to cut off points that are below some value
- Description: interpolate the above time points to generate a continous (small stepped) time course. Interpolation is done by splining all the
Clmcoefficients.
- Description: generate as many volumes as the nr of interpolated point clouds. Points in space are spatially interpolated onto the regular grid of a Volume object (made of voxels). Isosurfaces are also generated (for 3 different thresholds):
- Description: build isosurfaces for all the generated volumes using some threshold value. The absolute size is also recovered from a fit of the original sizes, to take into account the biological growth of the tissues
Ten years ago, a population of cardiac progenitor cells was identified in pharyngeal mesoderm that gives rise to a major part of the amniote heart. These multipotent progenitor cells, termed the second heart field (SHF), contribute progressively to the poles of the elongating heart tube during looping morphogenesis, giving rise to myocardium, smooth muscle, and endothelial cells.
Arid3b, a member of the conserved ARID family of transcription factors, is essential for mouse embryonic development but its precise roles are poorly understood. Arid3b is expressed in the myocardium of the tubular heart and in second heart field progenitors.
Arid3b-deficient embryos show cardiac abnormalities, including a notable shortening of the poles, absence of myocardial differentiation and altered patterning of the atrioventricular canal, which also lacks epithelial-to-mesenchymal transition. Proliferation and death of progenitors as well as early patterning of the heart appear normal.
Arid3b is thus required for heart development by regulating the motility and differentiation of heart progenitors. These findings identify Arid3b as a candidate gene involved in the aetiology of human congenital malformations.
- “Arid3b is essential for second heart field cell deployment and heart patterning”, J.J. Sanz-Esquerro et al., Development (2014) 141, 4168-4181 doi:10.1242/dev.109918
- The second heart field
- Heart Development (wikipedia).
