Arabidodopsis thaliana

Predicting plant behaviour through mathematical modeling

It is one of the few computational models which, by reproducing the activity of several genetic networks, is able to make predictions actually verifiable at a later stage. The study, coordinated by the Department of Biology and Biotechnology "Charles Darwin" of Sapienza University in collaboration with Utrecht University, has been published on Developmental Cell journal

Organ growth is an articulate process where cell and tissue activities must be thoroughly regulated to guarantee a final shape and size compatible with the organ’s function. This is also true for plants. The mechanisms underlying the formation of organs such as roots, trunks and leaves, are still not widely known.

In the last few years, through modern full-spectrum molecular analysis, scientists have been able to gather a vast amount of data, biologically relevant. However, the ability to integrate it into a model which can predict the behaviour depending on a few parameters remains very limited. 

A new study, coordinated by Sabrina Sabatini of the Department of Biology and Biotechnologies "Charles Darwin" of Sapienza University in collaboration with the Department of Computational Biology of Utrecht University, has created a computational model able to reproduce in detail the growth stages of the root of Arabidopsis thaliana. By integrating experimental evidence with computational biology, the program can predict the plant's behaviour in vivo and under various environmental conditions. Research has been published on Developmental Cell journal.

To obtain such results, the researchers identified some of the central molecular circuits in the root growth and, subsequently, used them as parameters for the development of the model.

"This work – explains Sabrina Sabatini – is an example of how we can model a complex regulative system and predict the outcome starting with the key parameters. By using a computational model we could establish, for instance, how the PLETHORA (PLT) protein, a large amount of which can be found in the stem cell niche of the root, is gradually diluted after cell division is activated and distributed into new generation undifferentiated cells, where it reaches minimum levels of concentration."

From this premise, the researchers identified the active networks in cell differentiation and their functioning mechanisms: how the mutual inhibiting action of some molecules controls the number of the root's undifferentiated cells and how this process is interrupted, 5 days after germination, by a hormone that facilitates the differentiation and guarantees a consistent growth of the organ. 

"Ours – concludes Sabatini – is one of the few dynamic models that incorporate the activity of several genetic networks able to reproduce root growth in silico. It can be used to make testable in vivo predictions, experimentally."



A self-organized plt/auxin/arr-b network controls the dynamics of root zonation development in arabidopsis thaliana Elena Salvi, Jaap Rutten, Riccardo Di Mambro, Laura Polverari, Valerio Licursi, Rodolfo Negri, Raffaele Dello Ioio, Sabrina Sabatini & Kirsten Ten Tusscher - Developmental Cell


Further Information

Sabrina Sabatini
Department of Biology and Biotechnology "Charles Darwin"

Monday, 18 May 2020

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