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Random Weighting through Linear Programming into Intracellular Transporters of Rice Metabolic Network

  • Rahul Shaw
  • Sudip Kundu
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8251)

Abstract

An eukaryotic cell has different compartments which are specific to different biological activities. The total cellular metabolism is also compartmentalized. The intracellular transporters within a cell are responsible to transport some of the metabolites of one compartment to other. We formulate a model to understand the utility of different transporters. Here, we have taken a partially compartmentalized genome scale metabolic model of rice (Oryza sativa). Depending on the gene-expression, the transporters available to transport the metabolites from one compartment to other would change. We study the effect of transporter’s capacity on the overall metabolism. We find that depending on the effectiveness of transporters, the photon demand for a rice leaf’s biochemical machinery to synthesize the necessary biomass from inorganic nutrients, changes upto three fold. We also observe, interactions of mitochondrial and chloroplastid reactions are associated with this change.

Keywords

Random Weighting Linear Programming Metabolic Network Genome Scale Model Intracellular Transporter 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Rahul Shaw
    • 1
  • Sudip Kundu
    • 1
  1. 1.Department of Biophysics, Molecular Biology and BioinformaticsUniversity of CalcuttaKolkataIndia

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