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Projects / Programmes source: ARIS

Deciphering structural and dynamical properties of plant response mechanisms with systems biology approaches

Research activity

Code Science Field Subfield
4.06.05  Biotechnical sciences  Biotechnology  Plant biotechnology 
2.07.00  Engineering sciences and technologies  Computer science and informatics   

Code Science Field
B110  Biomedical sciences  Bioinformatics, medical informatics, biomathematics biometrics 

Code Science Field
4.04  Agricultural and Veterinary Sciences  Agricultural biotechnology 
1.02  Natural Sciences  Computer and information sciences 
Keywords
Arabidopsis, potato, stress, immune signaling, systems biology, network biology, mathematical modelling, motifs, modules
Evaluation (rules)
source: COBISS
Researchers (1)
no. Code Name and surname Research area Role Period No. of publicationsNo. of publications
1.  34502  PhD Živa Ramšak  Biology  Head  2019 - 2022  118 
Organisations (1)
no. Code Research organisation City Registration number No. of publicationsNo. of publications
1.  0105  National Institute of Biology  Ljubljana  5055784  13,258 
Abstract
Plants are continuously challenged by changes in their environment and different pathogenic agents. To ensure durable and environmentally friendly plant protection systems, we must continuously improve our understanding of plant stress-mitigating mechanisms. At the root of these lies an expansive signaling network, combining several phytohormones, whose concerted actions lead to specific outcomes, beneficial either for the plant or its stressor. To understand these reponses, we must analyse both the structural and dynamic properties of the signaling network, as only their conjuction will offer us a complete picture of the observed system. We propose to achieve that using a multidisciplinary systems biology approach, applied to publically available knowledge for both the model plant Arabidopsis (Arabidopsis thaliana) and crop potato (Solanum tuberosum). With the application of graph theory approaches on networks, we will examine the structural properties of networks (degrees, motifs) for both plants and be able predict novel links within the networks. Results of these structural analyses will be complemented with examinations of network dynamics by mathematical modelling (parameter estimation and genome-scale metabolic networks). To test the predictive value of hypotheses that our combined approach will generate, we will also design appropriate experiments on the observed system. Results of this integrated approach will for one (1) offer significant novel insights into the complex inner workings of complex plant responses and (2) increase the translation potential from model plants to crops, which will bring us one step closer to counteracting the sustainability challenges humanity is facing in the current century.
Significance for science
Project results will generate deeper insights into stress-mitigating mechanisms that plants use in response to various environmental stimuli. As biotic and abiotic stress adaptation in plants is under the control of a complex signaling network, its analysis will shed novel insights on the mechanisms that govern its ability to orchestrate massive changes in gene expression and extensive metabolism reprogramming. While Arabidopsis research can provide significant insights in terms of plant adaptation to its environment, inclusion of a crop species will ease the translation of new-found knowledge to help answer agronomically important questions, particularly those related to breeding for higher performance under field conditions. The proposed multidisciplinary systems biology approach will allow us to incorporate the very important time scale component, by which we will be able to observe and analyse the emergent properties of our examined system. Our better understanding of the dynamical properties of the system will in turn lead to a breakhrough towards understanding signaling mechanisms in plant stress responses, and would lead increased opportunities in direct manipulation of these processes for specific environmental adaptations to achieve increased yield performances, which is needed, in order to avert the negative impact of climate change and pests on crop productivity via breeding more resilient crops.
Significance for the country
Project results will generate deeper insights into stress-mitigating mechanisms that plants use in response to various environmental stimuli. As biotic and abiotic stress adaptation in plants is under the control of a complex signaling network, its analysis will shed novel insights on the mechanisms that govern its ability to orchestrate massive changes in gene expression and extensive metabolism reprogramming. While Arabidopsis research can provide significant insights in terms of plant adaptation to its environment, inclusion of a crop species will ease the translation of new-found knowledge to help answer agronomically important questions, particularly those related to breeding for higher performance under field conditions. The proposed multidisciplinary systems biology approach will allow us to incorporate the very important time scale component, by which we will be able to observe and analyse the emergent properties of our examined system. Our better understanding of the dynamical properties of the system will in turn lead to a breakhrough towards understanding signaling mechanisms in plant stress responses, and would lead increased opportunities in direct manipulation of these processes for specific environmental adaptations to achieve increased yield performances, which is needed, in order to avert the negative impact of climate change and pests on crop productivity via breeding more resilient crops.
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