Biomedical subjects

Wolfram Weckwerth

Publications and source records attributed to Wolfram Weckwerth.

23 records · Page 2Linked to original sources

PubMed2003

Stable isotope labeling of phosphopeptides for multiparallel kinase target analysis and identification of phosphorylation sites.

An approach for multiparallel target identification and relative quantification of in vitro kinase activities in two different biological samples, using liquid chromatography/mass spectrometry (LC/MS), is described. Synthetic target peptides, containing the putative regulatory phosphorylation sites of sucrose-phosphate synthase (SPS) isoenzymes from Arabidopsis thaliana, were simultaneously in vitro phosphorylated and their phosphorylation states determined. Quantification was achieved by stable isotope labeling of the phosphoserine moiety with ethanethiol and [(2)D(5)]-ethanethiol. This revealed different kinase activities in extracts of wild-type (WT) plants and mutant plants lacking plastidic phosphoglucomutase (PGM). The multiparallel assay allowed the determination of favored substrate specificities among the putative phosphorylation sites in SPS. Additionally, we extended the method to unambiguously identify phosphorylation sites in peptides via differential labeling.

Amino Acid Sequence↗

PubMed2003

Deciphering metabolic networks.

All higher organisms divide major biochemical steps into different cellular compartments and often use tissue-specific division of metabolism for the same purpose. Such spatial resolution is accompanied with temporal changes of metabolite synthesis in response to environmental stimuli or developmental needs. Although analyses of primary and secondary gene products, i.e. transcripts, proteins, and metabolites, regularly do not cope with this spatial and temporal resolution, these gene products are often observed to be highly coregulated forming complex networks. Methods to study such networks are reviewed with respect to data acquisition, network statistics, and biochemical interpretation.

Animals↗

PubMed2003

Metabolomics in systems biology.

The primary aim of "omic" technologies is the nontargeted identification of all gene products (transcripts, proteins, and metabolites) present in a specific biological sample. By their nature, these technologies reveal unexpected properties of biological systems. A second and more challenging aspect of omic technologies is the refined analysis of quantitative dynamics in biological systems. For metabolomics, gas and liquid chromatography coupled to mass spectrometry are well suited for coping with high sample numbers in reliable measurement times with respect to both technical accuracy and the identification and quantitation of small-molecular-weight metabolites. This potential is a prerequisite for the analysis of dynamic systems. Thus, metabolomics is a key technology for systems biology. The aim of this review is to (a) provide an in-depth overview about metabolomic technology, (b) explore how metabolomic networks can be connected to the underlying reaction pathway structure, and (c) discuss the need to investigate integrative biochemical networks.

Models, Biological↗

PubMed2002

Can we discover novel pathways using metabolomic analysis?

Metabolomic analysis aims at the identification and quantitation of all metabolites in a given biological sample. Current data acquisition and network analysis strategies are classified on the basis of pathway elucidation and characteristics of theoretical networks. The development of metabolomic methods and tools is progressing rapidly, but an understanding of the resulting data is limited owing to a fundamental lack of biochemical and physiological knowledge about network organization in plants.

Chromatography↗

PubMedDate not supplied

The role of mass spectrometry in plant systems biology.

Large-scale analyses of proteins and metabolites are intimately bound to advancements in MS technologies. The aim of these non-targeted "omic" technologies is to extend our understanding beyond the analysis of only parts of the system. Here, metabolomics and proteomics emerged in parallel with the development of novel mass analyzers and hyphenated techniques such as gas chromatography coupled to time-of-flight mass spectrometry (GC-TOF-MS) and multidimensional liquid chromatography coupled to mass spectrometry (LC-MS). The analysis of (i) proteins (ii) phosphoproteins, and (iii) metabolites is discussed in the context of plant physiology and environment and with a focus on novel method developments. Recently published studies measuring dynamic (quantitative) behavior at these levels are summarized; for these works, the completely sequenced plants Arabidopsis thaliana and Oryza sativa (rice) have been the primary models of choice. Particular emphasis is given to key physiological processes such as metabolism, development, stress, and defense. Moreover, attempts to combine spatial, tissue-specific resolution with systematic profiling are described. Finally, we summarize the initial steps to characterize the molecular plant phenotype as a corollary of environment and genotype.

Mass Spectrometry↗