DevoWorm: developing the worm (and Ascidian, and graph, and digital embryo)

 

Abstract: The DevoWorm subproject is focused on understanding embryogenesis and other developmental processes in worms using a combination of simulation, the analysis of secondary data, and experimental methods. Through this combination of methods, we are contributing to models of how worms develop their adult function and structure (e.g. phenotypes). In this talk, we will discuss the latest developments in DevoWorm [1]. Having made great strides since our last report to the OpenWorm community [2], this project is now a multifaceted investigation into the mechanisms and dynamics of Nematode development. DevoWorm encompasses the application of theoretical biology, innovations in data analysis, and development of simulation. 

We are interested in emulating Caenorhabditis elegans embryogenesis, and development more generally. Advances include a software platform (Morphozoic) to model digital morphogenesis, computational and statistical analyses of secondary data (C. elegans and Ciona intestinalis) to investigate developmental dynamics across species, and the generation and modeling of primary data to investigate reproductive and developmental plasticity. 

A number of results will be presented, including proof-of-concept pattern formation in Morphozoic, alternative representations to the standard lineage tree for cellular differentiation during embryogenesis [3, 4], and the parameterization of reproduction and developmental plasticity in C. elegans.

Selected references for the talk:
[1] Project website: http://bradly-alicea.weebly.com/devoworm.html

[2] Alicea, B., McGrew, S., Gordon, R., Larson, S., Warrington, T., & Watts, M. (2014). DevoWorm: differentiation waves and computation in C. elegans embryogenesis. bioRxiv, 009993.http://www.biorxiv.org/content/biorxiv/early/2014/10/03/009993

[3] Alicea, B. and Gordon, R. (2016). Quantifying Mosaic Development: Towards an Evo-Devo Postmodern Synthesis of the Evolution of Development Via Differentiation Trees of Embryos. Biology (Special Issue: beyond the modern evolutionary synthesis). Submitted.
https://drive.google.com/file/d/0B7RsqJbITXXATWZrV2xUMVJhczA/view?usp=sharing

[4] Alicea, B. and Gordon, R.  Ciona intestinalis Embryonic Differentiation Tree (1- to 112-cell stage). doi: 10.6084/m9.figshare.2117152
https://figshare.com/articles/C_elegans_Embryonic_Differentiation_Tree_10_division_events_/2118049

Alicea, B. and Gordon, R.  Caenorhabditis elegans Embryonic Differentiation Tree (10 division events). doi:10.6084/m9. figshare.2118049.
https://figshare.com/articles/C_intestinalis_Embryonic_Differentiation_Tree_1_to_112_cell_stage_/2117152