mRNA active transport in oocyte-early embryo: 3D agent-based modeling

Marat A. Sabirov; Ekaterina M. Myasnikova; Alexander V. Spirov

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arXiv · 2301.05006

mRNA active transport in oocyte-early embryo: 3D agent-based modeling

Marat A. Sabirov·Ekaterina M. Myasnikova·Alexander V. Spirov

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Abstract

Axes of polarity (and primary morphogenetic gradients) are established in the oocyte - early embryo through active transport and localization of maternal factors. It is the oocyte - syncytial embryo of Drosophila (D. melanogaster) that is a model object for studying the molecular machinery of such transport systems. The attention of researchers is focused on the processes of formation, maintenance, and functioning of active transport systems of maternal mRNAs and proteins that are key for early Drosophila embryogenesis. Here we develop an approach for agent-based 3D modeling of the key components of transport by molecular motors (by elements of the cytoskeleton) of the Drosophila oocyte-syncytial embryo. The models were developed using Skeledyne software developed by Odell and Foe [Odell and Foe, 2008]. We start with the results of modeling transport along oriented microtubule (MT) bundles in the oocyte. This is a model of transport systems in the Drosophila oocyte, where three maternal mRNAs (bicoid (bcd), oskar, and gurken) that are key to embryonic polarity are transported along their oriented MT bundles. Then we consider models of oriented MT networks in the volume of a cell (oocyte) generated by a single microtubule organization center (or a pair of the centers). This model reproduces the formation of bcd mRNA intrusions deep into the cytoplasm in the head half of the early syncytial embryo. Finally, we consider models for the active transport of bcd mRNA in a syncytial embryo along a randomized network of many short MT strands. In conclusion, we consider the prospects for the implementation of cytoplasmic fountain flows in the active transport model.

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Marat A. Sabirov, Ekaterina M. Myasnikova, Alexander V. Spirov. 2023-01-10. mRNA active transport in oocyte-early embryo: 3D agent-based modeling. https://arxiv.org/abs/2301.05006

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