Morphogenesis software based on epigenetic code concept

• Main Authors: Nikolay Bessonov, Oksana Butuzova, Andrey Minarsky, Robert Penner, Christophe Soulé, Alen Tosenberger, Nadya Morozova
• Format: Article
• Language: English
• Published: Elsevier 2019-01-01
• Series: Computational and Structural Biotechnology Journal
• Online Access: http://www.sciencedirect.com/science/article/pii/S2001037019301795

The process of morphogenesis is an evolution of shape of an organism together with the differentiation of its parts. This process encompasses numerous biological processes ranging from embryogenesis to regeneration following crisis such as amputation or transplantation. A fundamental theoretical question is where exactly do these instructions for (re-)construction reside and how are they implemented?We have recently proposed a set of concepts, aiming to respond to these questions and to provide an appropriate mathematical formalization of the geometry of morphogenesis [1]. First, we consider a possibility that the evolution of shape is determined by epigenetic information, responsible for realization of different types of cell events. Second, we suggest a set of rules for converting this epigenetic information into instructive signals for cell event for each cell, as well as for transforming it after each cell event. Next we give notions of cell state, determined by its epigenetic array, and cell event, which is a change of cell state, and formalize development as a graph (tree) of cell states connected by 5 types of cell events, corresponding to the processes of cell division, cell growth, cell death, cell movement and cell differentiation.Here we present a Morphogenesis software capable to simulate an evolution of a 3D embryo starting from zygote, following a set of rules, based on our theoretical assumptions, and thus to provide a proof-of-concept of the hypothesis of epigenetic code regulation. The software creates a developing embryo and a corresponding graph of cell events according to the zygotic epigenetic spectrum and chosen parameters of the developmental rules. Variation of rules influencing the resulting shape of an embryo may help elucidating the principal laws underlying pattern formation.