植物学技术

Steady state 13C-MFA is classically used to measure fluxes in complex metabolic networks. However, the modeling of steady state labeling allows the quantification of internal fluxes only and requires the estimation, by other methods, of the external fluxes, corresponding to substrate ...

The use of in vivo NMR within the framework of Metabolic Flux Analysis in plants is presented. In vivo NMR allows to visualize the active metabolic network, to determine metabolic and isotopic steady state and to measure metabolic fluxes which are not necessarily accessible by isotopic steady s ...

This chapter focuses on the way to build a metabolic network and how to analyze its structure. The first part of this chapter describes the methods of the network model reconstruction from biochemical data found in specialized databases and/or literature. The second part deals with metabolic ...

This volume compiles a series of chapters that cover the major aspects of plant metabolic flux analysis, such as but not limited to labeling of plant material, acquisition of labeling data, mathematical modeling of metabolic network at the cell, tissue, and plant level. A short revue, including m ...

The integration of mathematical modeling with analytical experimentation in an iterative fashion is a powerful approach to advance our understanding of the architecture and regulation of metabolic networks. Ultimately, such knowledge is highly valuable to support efforts aim ...

The importance of kinetic modeling for understanding the control and regulation of complex metabolic networks is increasingly being recognized. Kinetic models encapsulate the available kinetic information of all the enzymes in a pathway, and then calculate the complex behavior t ...

The diversity of useful compounds produced by plant secondary metabolism has stimulated broad systems biology approaches to identify the genes involved in their biosynthesis. Systems biology studies in non-model plants pose interesting but addressable challenges, and have be ...

In recent years the number of sequenced and annotated plant genomes has increased significantly, and novel approaches are required to retrieve valuable information from these data sets. The field of systems biology has accelerated the simulation and prediction of phenotypes derived ...

A genome-scale model (GSM) is an in silico metabolic model comprising hundreds or thousands of chemical reactions that constitute the metabolic inventory of a cell, tissue, or organism. A complete, accurate GSM, in conjunction with a simulation technique such as flux balance analysis (FBA), ...

In the recent years, a large number of genomes from a variety of different organisms have been sequenced. Most of the sequence data has been publicly released and can be assessed by interested users. However, this wealth of information is currently underexploited by scientists not directly inv ...

The IUBMB Enzyme List is widely used by other databases as a source for avoiding ambiguity in the recognition of enzymes as catalytic entities. However, it was not designed for metabolic pathway tracing, which has become increasingly important in systems biology. A Reactions Database has been ...

Metabolic databases such as The Plant Metabolic Network/MetaCyc and KEGG PATHWAY are publicly accessible resources providing organism-specific information on reactions and metabolites. KEGG PATHWAY depicts metabolic networks as wired, electronic circuit-like maps, wh ...

Stable isotope labeling experiments (ILE) constitute a powerful methodology for estimating metabolic fluxes. An optimal label design for such an experiment is necessary to maximize the precision with which fluxes can be determined. But often, precision gained in the determination of ...

Isotope labeling experiments (ILEs) offer a powerful methodology to perform metabolic flux analysis. However, the task of interpreting data from these experiments to evaluate flux values requires significant mathematical modeling skills. Toward this, this chapter provides b ...

Mass spectrometry (MS) offers a sensitive, reliable, and highly accurate method for measurement of isotopic labeling, which is required for generating comprehensive flux maps using metabolic flux analysis (MFA). We present protocols for assessing isotope labeling in a wide range of bi ...

Two-dimensional heteronuclear single quantum correlation (HSQC) spectroscopy nuclear magnetic resonance (NMR) is a comprehensive tool in metabolic flux analysis using 13C-labeling experiments. NMR is particularly relevant when extensive isotopomer measurements a ...

Cellular metabolites and ions can exhibit very specific spatiotemporal dynamics that are very challenging to monitor using extraction-based methods. Genetically encoded F�ster resonance energy transfer sensors afford a powerful method of measuring these dynamics in situ and ...

Plant volatiles occupy diverse roles as signaling molecules, defensive compounds, hormones, and even waste products. Exponential growth in the related literature coupled with the availability of new analytical and computational technologies has inspired novel avenues of inq ...

Single-cell analysis of metabolites by mass spectrometry (MS) is challenging due to the very limited volume and inherent molecular complexity of the sample. Quantitative metabolomic analysis of individual cells provides information on the metabolic heterogeneity of cells una ...

Polyphenolics are a chemically diverse class of plant specialized metabolites with strong antioxidant properties, and their consumption has been associated with improved human health. Metabolomic analysis of these compounds in both plant and mammalian samples has relied pred ...