Modeling overview

Metabolomics is the scientific study of chemical processes involving metabolites. Specifically, metabolomics is the "systematic study of the unique chemical fingerprints that specific cellular processes leave behind", the study of their small-molecule metabolite profiles. The metabolome represents the collection of all metabolites in a biological cell, tissue, organ or organism, which are the end products of cellular processes (Jordan et al., 2009). Thus, while mRNA gene expression data and proteomic analyses do not tell the whole story of what might be happening in a cell, metabolic profiling can give an instantaneous snapshot of the physiology of that cell.

In our project, we investigate the origin of formaldehyde metabolism using computer simulation of biochemical networks in tobacco. By utilizing the genetic engineering, three pathways of formaldehyde metabolism in tobacco were taken into account and three models of regulatory mechanism were established for these pathways. There are photosynthetic formaldehyde assimilation pathway (gene HPS and PHI), folate-independent pathway (gene FALDH and FDH) and the pathway of formaldehyde which was absorbed into the stoma (gene AtAHA2). Below, let us describe all the procedures one by one.

The modeling

Photosynthetic formaldehyde assimilation pathway
Folate-independent pathway
Modeling of stoma

Reference

Jordan, K. W., J. Nordenstam, G. Y. Lauwers, D. A. Rothenberger, K. Alavi, M. Garwood and L. L. Cheng (2009). "Metabolomic characterization of human rectal adenocarcinoma with intact tissue magnetic resonance spectroscopy." Dis Colon Rectum 52(3): 520-525.