Development of a bioinformatic tool for integration of transcriptomics, proteomics and physiology using sorghum and sugarcane as model systems

• Grant number: 13/24205-0
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: December 01, 2013
• End date: March 31, 2017
• Field of knowledge: Interdisciplinary Subjects
• Agreement: Microsoft Research
• Principal Investigator: Marcos Silveira Buckeridge
• Grantee: Amanda Rusiska Piovezani
• Host Institution: Instituto de Biociências (IB). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Company: Universidade de São Paulo (USP). Instituto de Biociências (IB)
• Associated research grant: 11/52065-3 - Using systems biology approach to develop a model for whole plant functioning, AP.PITE

Abstract

By the fact of plants being sessiles, they are unable to get away looking for areas with better conditions for their adaptation. For this reason, the plants respond to the environment through various mechanisms that have been selected during evolution. These mechanisms are dependent on systemic responses ranging from gene expression to a physiological response. The plant responses to the environment are strongly related to the flexibility of their genetic programs, as well as metabolic flexibility that the tissues present at the cellular level. The way that these genic and metabolic patterns redundant in other cells, generating reactions orchestrated to reflect a pattern of behavior at different organizational levels (tissue, organ and whole plant) are also extremely important for the plant response to the environment. Although several techniques have been developed for the understanding of how the gene expression interacting between them and between proteins or metabolites, there are no techniques that enable these organizational levels interact with the morphological and physiological level in plants. Thus, this project aims to develop a bioinformatics tool for integration of scales of gene transcription, proteomics and physiology using sorghum and sugarcane as model systems. Will be used data from transcriptome (RNAseq), proteome (quantitative proteomics), biochemical (enzymatic activities) and data on the changes that occur in the cell walls existing in the laboratory on the development of the roots of sugarcane to integrate the gene expression patterns and protein expression in order to gain predictability between different scales. Subsequently, this tool will be tested from data of transcriptome, proteome, metabolome and physiology of sorghum. Thus, it is expected to be possible to use it to understand the systemic integration in plants in order to obtain estimates of physiological behavior - at least for certain subsystems - that advance the ability to forecast responses of plants to environmental variations.Keywords : Integration of scales, plant subsystems. (AU)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

PIOVEZANI, Amanda Rusiska. Systems Integration Tool: an integration and visualization tool for big data and their application on sugarcane. 2017. Doctoral Thesis - Universidade de São Paulo (USP). Instituto de Matemática e Estatística (IME/SBI) São Paulo.