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Nets-within-nets for modeling emergent patterns in ontogenetic processes.

Roberta Bardini1, Alfredo Benso1, Gianfranco Politano1

  • 1Politecnico di Torino, Control and Computer Engineering Department, Corso Duca degli Abruzzi 24, Torino 10129, Italy.

Computational and Structural Biotechnology Journal
|November 12, 2021
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Summary
This summary is machine-generated.

This study introduces a novel computational model for understanding organism development (ontogenesis) by simulating gene and epigenetic regulation. The Nets-Within-Nets approach successfully models cell specification, offering insights into developmental processes and mutations.

Keywords:
C. ElegansOntogenesisPetri netsSystems biology

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Area of Science:

  • Developmental Biology
  • Computational Biology
  • Systems Biology

Background:

  • Ontogenesis involves complex regulation of genetic and epigenetic factors to achieve phenotypic diversity from shared genomic information.
  • Understanding cellular development requires analyzing multi-level regulatory interactions and dynamic state transitions.
  • Existing models may not fully capture the hierarchical and context-dependent nature of developmental regulation.

Purpose of the Study:

  • To propose and validate a novel computational framework, Nets-Within-Nets, for modeling ontogenesis.
  • To simulate the interplay between different layers of genetic and epigenetic regulation during development.
  • To model the early stages of Vulval Precursor Cells (VPC) specification in C. elegans.

Main Methods:

  • Utilized the Nets-Within-Nets formalism, integrating Petri Nets for simulating hierarchical and context-dependent regulatory networks.
  • Developed a modeling strategy to represent critical processes in ontogenesis.
  • Applied the model to a case study of C. elegans VPC specification.

Main Results:

  • The Nets-Within-Nets model successfully simulated the emergent morphogenetic patterns of C. elegans VPC specification.
  • The model accurately reproduced developmental outcomes in both physiological conditions and simulated mutations.
  • The computational model is publicly available for further research.

Conclusions:

  • The Nets-Within-Nets formalism provides a powerful tool for studying complex developmental processes like ontogenesis.
  • This modeling approach can elucidate the mechanisms underlying cell fate determination and pattern formation.
  • The validated model serves as a foundation for further investigations into developmental biology and related fields.