Methods applications and concepts of metabolite profiling Primary metabolism

Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 PotsdamGolm, Germany In the 1990s the concept of a comprehensive analysis of the metabolic complement in biological systems, termed metabolomics or alternately metabonomics, was established as the last of four cornerstones for phenotypic studies in the post-genomic era. With genomic, transcriptomic, and proteomic technologies in place and metabolomic phenotyping under rapid development all necessary tools appear to be...

Reverse genetics strategies in plants

Several genome-wide gene targeting techniques have been widely developed in plants. In the absence of efficient and routine methods for homologous recombina tion in plants, insertional mutatagenesis using transferred DNA (T-DNA) from Agrobacterium or transposable elements has been the method of choice for genome size reverse genetics approaches in the model plants Arabidopsis and rice. Several populations of tens of thousand of mutagenised plants have been created with the objective to reach...

Methods applications and concepts of metabolite profiling Secondary metabolism

Huhman, Ewa Urbanczyk-Wochniak and Zhentian Lei Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA Plants manufacture a vast array of secondary metabolites natural products for protection against biotic or abiotic environmental challenges. These compounds provide increased fitness due to their antimicrobial, anti-herbivory, and or alleopathic activities. Secondary metabolites also serve fundamental roles as key...

Examples of systems biology research1

3bpga Structure

One aspect of systems biology is the analysis of the structure of the molecular networks and its consequences for the cell. In much the same way as genome sequencing has lead to the emergence of the theoretical analysis of genomes (bioinformatics), has the availability of the entire metabolic, signaling, and gene networks of cells led to the development of theoretical analyses of networks 6, 54 . Many interesting properties of molecular networks haven been discovered 54-56 . Most noticeably are...

Info

Example of a MS-survey scan of 18O labeled and non-labeled peptide. A zoom in from a MS-survey scan of a singly charged peptide is shown which has been digested in the presence of normal water (804.3908 Da) and 18O labeled water (808.3994). The double incorporation of oxygen reveals the distinct difference of 4 Da. The ratio of the relative intensity of the different peptides is used for the relative protein peptide quantification. Figure 6. Example of a MS-survey scan of 18O labeled...

Tilling

TILLING is a general reverse-genetics strategy first described by McCallum et al. 108 who used this method for allele discovery for chromomethylase gene in Arabidopsis 113 . This method combines random chemical mutagenesis by EMS (ethylmethanesulfonate) with PCR-based methods for detecting unknown point mutations in regions of interest in target genes. Since the early description of the method, which was then performed by using heteroduplex analysis with dHPLC 108 , the method has been refined...

References

Rensink WA, Lee Y, Liu J, Iobst S, Ouyang S, Buell RC 2005 Comparative analyses of six solanaceous transcriptomes reveal a high degree of sequence conservation and species-specific transcripts. BMC Genomics 6 124 2. Dievart A, Clark SE 2003 Using mutant alleles to determine the structure and function of leucine-rich repeat receptor-like kinases. Curr Opin Plant Biol 6 507-516 3. Tanksley SD, Ganal MW, Martin GB 1995 Chromosome landing - a paradigm for map-based gene cloning in plants with...

B

RI-offset between GC-EI-MS systems operated with an identical stationary GC column phase. Authenticated MSTs from pure reference substances exhibit good RI linearity between different GC-EI-MS systems A and in general a constant elution sequence B . Metabolites of identical compound classes exhibit strict repeatability of elution. In contrast, the RI sequence may locally differ between compound classes, for examples refer to allantoin and hexoses, aspartic and pyroglutamic acid, or...

List of contributors

Ana-Paula Alonso, Department of Plant Biology, Michigan State University. 166 Plant Biology Building, East Lansing, MI 48824, USA Christian H. Ahrens, Functional Genomics Center Z rich, Winterthurerstrasse 190, Y32H66, 8057 Z rich, Switzerland e-mail christian.ahrens fgcz.ethz.ch Simon Barkow, Computer Engineering and Networks Laboratory, Swiss Federal Institute of Technology ETH , Gloriastrasse 35, 8092 Z rich, Switzerland Stefan Bleuler, Computer Engineering and Networks Laboratory, Swiss...