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

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).

Hairy Root Cultures—A Versatile Tool With Multiple Applications

“…fuzzy logicbased simulations, neural network). This type of computer modeling approaches has been used to optimize chemical culture conditions of HRCs (Lenk et al, 2014).…”

Modeling of plant in vitro cultures: Overview and estimation of biotechnological processes

“…To date, different forms of plant in vitro cultures are in the interest of research investigations (Eibl and Eibl, ) and, in some cases, profitable industrial applications (Mulabagal and Tsay, ). Several publications deal with induction (Geipel et al, ; Mustafa et al, ), cultivation (Geipel et al, ; Haas et al, ), application for products (Kolewe et al, ; Weathers et al, ), and growth modeling (Bailey et al, ; Lenk et al, ) of plant in vitro cultures. Known culture types are callus, and associated plant cell suspensions (SU), hairy roots (HR), adventitious roots, and shoots, each with different advantages and disadvantages concerning handling or cultivation requirements (Rao and Ravishankar, ).…”

“…Yan et al () focused on increased tanshinone yields in Salvia miltiorrhiza (Chinese sage) HR through elicitation and adsorption together with a corresponding model. Finally, Lenk et al () published an article concerning 3D growth measurement and modeling of Beta vulgaris (beet) HR in Petri dishes with solid medium.…”

Use of computational modeling combined with advanced visualization to develop strategies for the design of crop ideotypes to address food security

“…Recently, L-system formalisms have been modified and expanded to perform 3D modeling in an agent-based, structured growth model of beetroot hairy root cultures. 41 In this work, the Virtual Experimentator for Root Networks was developed to simulate the development of hairy root culture morphology to generate data that would help optimize media recipes and improve the design of bioreactor environments. The rationale for this study was to identify optimal bioreactor conditions for the production of secondary metabolites, such as betalains, in hairy root cultures.…”