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Gene Regulatory Network Dynamical Logical Models for Plant Development

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Plant Systems Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2395))

Abstract

Mathematical and computational approaches that integrate and model the concerted action of multiple genetic and nongenetic components holding highly nonlinear interactions are fundamental for the study of developmental processes. Among these, gene regulatory network (GRN) dynamical models are very useful to understand how diverse types of regulatory constraints restrict the multigene expression patterns that characterize different cell fates. In this chapter we present a hands-on approach to model GRN dynamics, taking as a working example a well-curated and experimentally grounded GRN developmental module proposed by our group: the flower organ specification gene regulatory network (FOS-GRN). We demonstrate how to build and analyze a GRN model according to the following steps: (1) integration of molecular genetic data and formulation of logical rules specifying the dynamic behavior of each gene; (2) determination of steady states (attractors) corresponding to each cell type; (3) validation of the GRN model; and (4) extension of the deterministic model with the inclusion of stochasticity in order to model cell-state transitions dependent on noise due to fluctuations of the involved gen products. The methodologies explained here in detail can be applied to any other developmental module.

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Author information

Authors and Affiliations

  1. Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA

    José Dávila-Velderrain

  2. Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, CDMX, Coyoacán, México

    José Luis Caldú-Primo & María Elena Álvarez-Buylla Roces

  3. Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Ciudad Universitaria, CDMX, México

    José Luis Caldú-Primo & María Elena Álvarez-Buylla Roces

  4. Departamento de Control Automático, Cinvestav-IPN, CDMX, Gustavo A. Madero, México

    Juan Carlos Martínez-García

Authors
  1. José Dávila-Velderrain
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  2. José Luis Caldú-Primo
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  3. Juan Carlos Martínez-García
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  4. María Elena Álvarez-Buylla Roces
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Corresponding author

Correspondence to María Elena Álvarez-Buylla Roces .

Editor information

Editors and Affiliations

  1. DIADE, Univ Montpellier, IRD,, CIRAD, Montpellier, France

    Mikaël Lucas

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Dávila-Velderrain, J., Caldú-Primo, J.L., Martínez-García, J.C., Álvarez-Buylla Roces, M.E. (2022). Gene Regulatory Network Dynamical Logical Models for Plant Development. In: Lucas, M. (eds) Plant Systems Biology. Methods in Molecular Biology, vol 2395. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1816-5_4

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  • DOI: https://doi.org/10.1007/978-1-0716-1816-5_4

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1814-1

  • Online ISBN: 978-1-0716-1816-5

  • eBook Packages: Springer Protocols

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