BACKGROUND The overexpression of key enzymes in a metabolic pathway is a frequently used genetic engineering strategy for strain improvement. Metabolic control analysis has been proposed to quantitatively determine key enzymes. However, the lack of quality data often makes it difficult to correctly identify key enzymes through control analysis. Here, we proposed a method combining in vitro meta...

Rheumatoid arthritis is a classic autoimmune disease, the pathogenesis of which closely linked to auto-reactivity immune cells and joint inflammation. Three cell types, namely T cells, macrophages fibroblast-like synoviocytes (FLS), play an important role in RA. Numerous studies have pointed metabolic reprogramming FLS RA arthritis, with alterations different pathways mainly producing shift fro...

Introducing structural modifications into biomolecules represents a powerful approach to dissect their functions and roles in biological processes. Bacterial polysaccharides, despite their rich structural information and essential roles in bacterium-host interactions and bacterial virulence, have largely been unexplored for in vivo structural modifications. In this study, we demonstrate the inc...

Enormous amounts of data result from genome sequencing projects and new experimental methods. Within this tremendous amount of genomic data 30-40 per cent of the genes being identified in an organism remain unknown in terms of their biological function. As a consequence of this lack of information the overall schema of all the biological functions occurring in a specific organism cannot be prop...

EcoCyc is an organism-specific Pathway/Genome Database that describes the metabolic and signal-transduction pathways of Escherichia coli, its enzymes, and-a new addition-its transport proteins. MetaCyc is a new metabolic-pathway database that describes pathways and enzymes of many different organisms, with a microbial focus. Both databases are queried using the Pathway Tools graphical user inte...

A method to measure the polyol pathway metabolic flux in the intact rabbit lens by 13C nuclear magnetic resonance spectroscopy is described. In the lens exposed to 35.5 mM glucose, the polyol pathway accounts for 1/3 of the total glucose turnover. The high metabolic activity of the pathway suggests a significant alteration in the reduced to oxidized pyridine nucleotide ratio in the lens exposed...

Over 100 genome-scale metabolic networks (GSMNs) have been published in recent years and widely used for phenotype prediction and pathway design. However, GSMNs for a specific organism reconstructed by different research groups usually produce inconsistent simulation results, which makes it difficult to use the GSMNs for precise optimal pathway design. Therefore, it is necessary to compare and ...

Metabolic pathway databases such as KEGG contain information on thousands of enzymatic reactions drawn from the biomedical literature. Ensuring consistency of such large metabolic pathways is essential to their proper use. In this paper, we develop an efficient method to determine consistency of an important class of enzymatic reactions, and test the method on the latest release of the KEGG LIG...

Improvements in biological data acquisition and genomes sequencing now allow to reconstruct entire metabolic networks of many living organisms. The size and complexity of these networks prohibit manual drawing and thereby urge the need of dedicated visualization techniques. An efficient representation of such a network should preserve the topological information of metabolic pathways while resp...

In the last few years, the Life Sciences domain has experienced a rapid growth in the amount of available biological databases. The heterogeneity of these databases makes data integration a challenging issue. Some integration challenges are locating resources, relationships, data formats, synonyms or ambiguity. The Linked Data approach partially solves the heterogeneity problems by introducing ...