Achieving the in Silico Plant. Systems Biology and the Future of Plant Biological Research

Minorsky, Peter V.

doi:10.1104/pp.900076

Cited by 72 publications

(8 citation statements)

References 12 publications

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“…Systems biology provides a framework for assembling models of biological systems-using computational analysis-from systematic measurements obtained by experimental analysis such as genomics, transcriptomics, proteomics or other high-throughput methods. 11 Since systems biology was first introduced a decade ago, considerable progress has been made in technologies for global experimental measurement as well as in computational analyses of these data to map and model the studied functions. 12 Another principle emerging from the systems biology research is that not only the physical components and interactions of a system can be evidenced, but also it can map how the information propagates through this system in response to perturbations.…”

Section: Introductionmentioning

confidence: 99%

Transcriptomics and systems biology analysis in identification of specific pathways involved in cacao resistance and susceptibility to witches' broom disease

et al. 2012

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This study reports on expression analysis associated with molecular systems biology of cacao-Moniliophthora perniciosa interaction. Gene expression data were obtained for two cacao genotypes (TSH1188, resistant; Catongo, susceptible) challenged or not with the fungus M. perniciosa and collected at three time points through disease. Using expression analysis, we identified 154 and 227 genes that are differentially expressed in TSH1188 and Catongo, respectively. The expression of some of these genes was confirmed by RT-qPCR. Physical protein-protein interaction (PPPI) networks of Arabidopsis thaliana orthologous proteins corresponding to resistant and susceptible interactions were obtained followed by cluster and gene ontology analyses. The integrated analysis of gene expression and systems biology allowed designing a general scheme of major mechanisms associated with witches' broom disease resistance/susceptibility. In this sense, the TSH1188 cultivar shows strong production of ROS and elicitors at the beginning of the interaction with M. perniciosa followed by resistance signal propagation and ROS detoxification. On the other hand, the Catongo genotype displays defense mechanisms that include the synthesis of some defense molecules but without success in regards to elimination of the fungus. This phase is followed by the activation of protein metabolism which is achieved with the production of proteasome associated with autophagy as a precursor mechanism of PCD. This work also identifies candidate genes for further functional studies and for genetic mapping and marker assisted selection.

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Section: Introductionmentioning

confidence: 99%

Transcriptomics and systems biology analysis in identification of specific pathways involved in cacao resistance and susceptibility to witches' broom disease

et al. 2012

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“…The unique ability of microfluidic devices to produce concentration gradients coupled with advances in fluorescent substrates offers simplified solutions for studying enzyme reactions on a wide variety of plant responses. 90,91 The major hurdle in structural biology studies involving ultra small volume screening of protein crystallization conditions was solved by a scalable microfluidic scheme called barrier interface metering (BIM). 90 The developed chip with BIM scheme had picolitre accuracy, negligible sample waste and complete insensitivity to the fluid properties.…”

Section: Microfluidics For Plant Productionmentioning

confidence: 99%

Microfluidics for food, agriculture and biosystems industries

et al. 2011

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Microfluidics, a rapidly emerging enabling technology has the potential to revolutionize food, agriculture and biosystems industries. Examples of potential applications of microfluidics in food industry include nano-particle encapsulation of fish oil, monitoring pathogens and toxins in food and water supplies, micro-nano-filtration for improving food quality, detection of antibiotics in dairy food products, and generation of novel food structures. In addition, microfluidics enables applications in agriculture and animal sciences such as nutrients monitoring and plant cells sorting for improving crop quality and production, effective delivery of biopesticides, simplified in vitro fertilization for animal breeding, animal health monitoring, vaccination and therapeutics. Lastly, microfluidics provides new approaches for bioenergy research. This paper synthesizes information of selected microfluidics-based applications for food, agriculture and biosystems industries.

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“…The notion of a virtual or in silico plant suitable for this purpose has occupied the thinking of molecular biologists (Minorsky 2003) and wholeplant physiologists (Hammer et al , 2004Tardieu 2003;Yin et al 2004). The former suggest a path integrating from the gene and gene function level up to the organism phenotype (i.e.…”

Section: Introductionmentioning

confidence: 99%

Trait physiology and crop modelling as a framework to link phenotypic complexity to underlying genetic systems

Hammer

Chapman

Oosterom

et al. 2005

Aust. J. Agric. Res.

145

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New tools derived from advances in molecular biology have not been widely adopted in plant breeding for complex traits because of the inability to connect information at gene level to the phenotype in a manner that is useful for selection. In this study, we explored whether physiological dissection and integrative modelling of complex traits could link phenotype complexity to underlying genetic systems in a way that enhanced the power of molecular breeding strategies. A crop and breeding system simulation study on sorghum, which involved variation in 4 key adaptive traits-phenology, osmotic adjustment, transpiration efficiency, stay-green-and a broad range of production environments in north-eastern Australia, was used. The full matrix of simulated phenotypes, which consisted of 547 location-season combinations and 4235 genotypic expression states, was analysed for genetic and environmental effects. The analysis was conducted in stages assuming gradually increased understanding of gene-to-phenotype relationships, which would arise from physiological dissection and modelling. It was found that environmental characterisation and physiological knowledge helped to explain and unravel gene and environment context dependencies in the data. Based on the analyses of gene effects, a range of marker-assisted selection breeding strategies was simulated. It was shown that the inclusion of knowledge resulting from trait physiology and modelling generated an enhanced rate of yield advance over cycles of selection. This occurred because the knowledge associated with component trait physiology and extrapolation to the target population of environments by modelling removed confounding effects associated with environment and gene context dependencies for the markers used. Developing and implementing this gene-to-phenotype capability in crop improvement requires enhanced attention to phenotyping, ecophysiological modelling, and validation studies to test the stability of candidate genetic regions.

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Achieving the in Silico Plant. Systems Biology and the Future of Plant Biological Research

Cited by 72 publications

References 12 publications

Transcriptomics and systems biology analysis in identification of specific pathways involved in cacao resistance and susceptibility to witches' broom disease

Transcriptomics and systems biology analysis in identification of specific pathways involved in cacao resistance and susceptibility to witches' broom disease

Microfluidics for food, agriculture and biosystems industries

Trait physiology and crop modelling as a framework to link phenotypic complexity to underlying genetic systems

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