The shape of the iPSC nucleus is dynamic in time and varies across colonies; while this is likely driven in concert by many aspects of the cell state (including mitotic stage, cytoskeleton dynamics, and neighbor cell dynamics), we do not know the relative impact of the mechanisms in driving variations in nuclear shape. In this project, we aim to link our observations of nuclear shape variations to specific mechanisms by pairing data-driven analyses of observed iPSC shape variation with theory-based models predicting the dynamics driven by biophysical mechanisms. The natural, resting shape of any flexible structure determines the ways in which it is most likely to bend and stretch; modeling of these resonance-based shape variations, called “normal mode analysis (NMA),” has been applied on varying spatial scales to successfully predict the most likely conformational changes of proteins and seismological oscillations of the Earth’s surface. We begin our theoretical model of iPSC nuclear shape variation by using NMA to predict the natural resonant dynamics for our cells’ nuclei. By comparing these predicted shape variations to quantitative analysis of observed deformations of our nuclei from time-lapse microscopy, we provide an important baseline for understanding the mechanisms driving the variation of nuclear shape.
pip install git+https://github.com/jcass11/normal_mode_analysis.git
For full package documentation please visit allencellmodeling.github.io/normal_mode_analysis.
See CONTRIBUTING.md for information related to developing the code.
Free software: Allen Institute Software License