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BACKGROUND Recent advances with high-throughput methods in life-science research have increased the need for automatized data analysis and visual exploration techniques. Sophisticated bioinformatics tools are essential to deduct biologically meaningful interpretations from the large amount of experimental data, and help to understand biological processes.(More)
BACKGROUND The elucidation of whole-cell regulatory, metabolic, interaction and other biological networks generates the need for a meaningful ranking of network elements. Centrality analysis ranks network elements according to their importance within the network structure and different centrality measures focus on different importance concepts. Central(More)
The accumulation of storage compounds is an important aspect of cereal seed metabolism. Due to the agronomical importance of the storage reserves of starch, protein, and oil, the understanding of storage metabolism is of scientific interest, with practical applications in agronomy and plant breeding. To get insight into storage patterning in developing(More)
MOTIVATION Because of the complexity of metabolic networks and their regulation, formal modelling is a useful method to improve the understanding of these systems. An essential step in network modelling is to validate the network model. Petri net theory provides algorithms and methods, which can be applied directly to metabolic network modelling and(More)
After the completion of the genomic sequencing of model organisms, numerous post-genomic studies, integrating transcriptome and metabolome data, are aimed at developing a more complete understanding of cell physiology. Here, we measure in vivo metabolic fluxes by steady state labeling, and in parallel, the activity of enzymes in central metabolism in(More)
It has recently been proposed that acetaldehyde is the physiological inducer of the alc gene system and hence indirectly the activator of the AlcA promoter in Aspergillus nidulans. Here we show that this chemical induces expression of a GUS (beta-D-glucuronidase) reporter under the control of the alc gene system in transgenic potato tubers more rapidly than(More)
MetaCrop is a manually curated repository of high-quality data about plant metabolism, providing different levels of detail from overview maps of primary metabolism to kinetic data of enzymes. It contains information about seven major crop plants with high agronomical importance and two model plants. MetaCrop is intended to support research aimed at the(More)
Transient expression of chimaeric genes (neomycin phosphotransferase fused to four different promoters) was detected in suspension culture derived protoplasts of maize, barley and rice, in mesophyll protoplasts of maize, rice, rye, and root protoplasts of maize. The introduction and expression of foreign genes could be performed with both dividing and(More)
Polyhydroxyalkanoates (PHAs) are polyoxoesters that are produced by diverse bacteria and that accumulate as intracellular granules. Phasins are granule-associated proteins that accumulate to high levels in strains that are producing PHAs. The accumulation of phasins has been proposed to be dependent on PHA production, a model which is now rigorously tested(More)
Seeds are complex structures composed of several maternal and filial tissues which undergo rapid changes during development. In this review, the barley grain is taken as a cereal seed model. Following a brief description of the developing grain, recent progress in grain development modeling is described. 3-D/4-D models based on histological sections or(More)