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Modeling hairy root tissue growth in in vitro environments using an agent-based, structured growth model

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Abstract

An agent-based model for simulating the in vitro growth of Beta vulgaris hairy root cultures is described. The model fitting is based on experimental results and can be used as a virtual experimentator for root networks. It is implemented in the JAVA language and is designed to be easily modified to describe the growth of diverse biological root networks. The basic principles of the model are outlined, with descriptions of all of the relevant algorithms using the ODD protocol, and a case study is presented in which it is used to simulate the development of hairy root cultures of beetroot (Beta vulgaris) in a Petri dish. The model can predict various properties of the developing network, including the total root length, branching point distribution, segment distribution and secondary metabolite accumulation. It thus provides valuable information that can be used when optimizing cultivation parameters (e.g., medium composition) and the cultivation environment (e.g., the cultivation temperature) as well as how constructional parameters change the morphology of the root network. An image recognition solution was used to acquire experimental data that were used when fitting the model and to evaluate the agreement between the simulated results and practical experiments. Overall, the case study simulation closely reproduced experimental results for the cultures grown under equivalent conditions to those assumed in the simulation. A 3D-visualization solution was created to display the simulated results relating to the state of the root network and its environment (e.g., oxygen and nutrient levels).

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Abbreviations

AVL:

Adelson-Velski and Landis (tree)

CSV:

Comma separated values

MFA:

Metabolic flux analysis

MS:

Murashige & Skoog

MSL:

Mean segment length

ODE:

Ordinary differential equation

OOM:

Object oriented model

SSL:

Single segment length (mm)

SSM:

Single-way state machine

TBP:

total number of branching points

TNS:

Total number of segments

TRL:

Total root length (mm)

TRV:

Total root volume (mm3)

UML:

Unified modeling language

VERN:

Virtual experimentator for root networks

X:

Biomass (g/L)

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Acknowledgments

The authors gratefully acknowledge financial support from the European Social Fund (ESF) and the Free State of Saxony (project number 080938406).

Conflict of interest

The authors have declared no commercial or financial conflict of interest.

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Authors and Affiliations

  1. Faculty of Mechanical Science and Engineering, Institute of Food Technology and Bioprocess Engineering, Technische Universität Dresden, Dresden, Germany

    Felix Lenk, Mandy Schneider, Juliane Steingroewer & Thomas Bley

  2. Institute of Scientific Computing, Technische Universität Dresden, Dresden, Germany

    Almuth Sürmann & Patrick Oberthür

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  1. Felix Lenk
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  2. Almuth Sürmann
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  3. Patrick Oberthür
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  4. Mandy Schneider
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  5. Juliane Steingroewer
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  6. Thomas Bley
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Correspondence to Felix Lenk.

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Lenk, F., Sürmann, A., Oberthür, P. et al. Modeling hairy root tissue growth in in vitro environments using an agent-based, structured growth model. Bioprocess Biosyst Eng 37, 1173–1184 (2014). https://doi.org/10.1007/s00449-013-1088-y

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  • DOI: https://doi.org/10.1007/s00449-013-1088-y

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