Plant systems biology: insights, advances and challenges

Abstract

Plants dwelling at the base of biological food chain are of fundamental significance in providing solutions to some of the most daunting ecological and environmental problems faced by our planet. The reductionist views of molecular biology provide only a partial understanding to the phenotypic knowledge of plants. Systems biology offers a comprehensive view of plant systems, by employing a holistic approach integrating the molecular data at various hierarchical levels. In this review, we discuss the basics of systems biology including the various 'omics' approaches and their integration, the modeling aspects and the tools needed for the plant systems research. A particular emphasis is given to the recent analytical advances, updated published examples of plant systems biology studies and the future trends.

Insect Gallers and Their Plant Hosts: From Omics Data to Systems Biology

“…A great deal of omics data has been generated by researchers investigating plant development as well as responses to biotic and abiotic stresses. One of the primary goals of current researchers is to generate a comprehensive model of the plant system through integration of data [7,60]. One recent example of this approach is provided by Dong et al [56] who integrated heterogeneous omics data to investigate the crosstalk between different branches of the A. thaliana immune system.…”

“…The field is defined by an iterative cycle of multi-layered omics data generation and modelling of data that generates new hypotheses that are tested in the laboratory and used to refine the model (Figure 1b) [60,75]. Biological systems models are frequently displayed as networks, which is a useful way of understanding how the system is organised [76].…”

“…Systems biology approaches can be categorised as bottom-up and top-down, where the bottom describes the molecular interactions of molecules and the top is the holistic view of the system which is generally created by genome-wide analysis of omics data [75]. Integrating information from various datasets and types, for example gene expression and protein-protein interaction data, is a powerful method of capturing the dynamics, complexity, and emergent properties of a system [56,60]. …”

Labeling Maize (Zea mays L.) Leaves with 15NH4+ and Monitoring Nitrogen Incorporation into Amino Acids by GC/MS Analysis

“…Using systems biology approaches, attempts have been made to integrate the different “omics” studies in order to distinguish regulatory networks. Ultimately, this has allowed the identification of certain biological components involved in the control of plant productivity, notably vegetative biomass and grain yield, as well as resistance to biotic and abiotic stresses (Cañas et al., ; Fukushima, Kanaya, & Nishida, ; Sheth & Thaker, ).…”

LETTER TO THE EDITORThe energy flux theory celebrates 40 years: toward a systems biology concept?

“…The TEFB has enabled Prof. Strasser to establish the theoretical background and experimental framework for developing sophisticated fluorescence analysis methods like the JIP-test, an interpretation of fast fluorescence induction kinetics (fast Kautsky's curves) (Tsimilli-Michael and Strasser 2013). However, biological systems showing emergent properties (nonlinear interactions among the network of their components) (Mazzocchi 2008, Lüttge 2013, Sheth and Thaker 2014, Souza and Lüttge 2015, suggest that living organisms should not be considered as a simply conglomeration of elements, but as a complex system that has integration and organization of its parts (Amzallag 2001, Souza et al 2016.…”