Tryptophan (Trp) is an essential amino acid that can be metabolized via endogenous and exogenous pathways, including the Kynurenine Pathway, 5-Hydroxyindole Pathway (also Serotonin pathway), Microbial pathway. Of these, Trp metabolic pathways in gut have recently been extensively studied for their production of bioactive molecules. The microbiota plays important role host metabolism immunity, m...

Metabolic networks reconstructed from sequenced genomes or transcriptomes can help visualize and analyze large-scale experimental data, predict metabolic phenotypes, discover enzymes, engineer metabolic pathways, and study metabolic pathway evolution. We developed a general approach for reconstructing metabolic pathway complements of plant genomes. Two new reference databases were created and a...

The estimation of parameters in even moderately large biological systems is a significant challenge. This challenge is greatly exacerbated if the mathematical formats of appropriate process descriptions are unknown. To address this challenge, the method of dynamic flux estimation (DFE) was proposed for the analysis of metabolic time series data. Under ideal conditions, the first phase of DFE yi...

MetaCyc is a metabolic-pathway database (DB) that describes 445 pathways and 1115 enzymes occurring in 158 organisms. As a general reference source on metabolic pathways, MetaCyc serves several purposes in metabolic engineering. It provides an encyclopedic listing of enzymes and their properties to allow a metabolic engineer to find an enzyme whose characteristics solve an engineering problem a...

The comparison of metabolic pathway in different species is important in detecting a missing gene. There are many visualization tools for metabolic pathway. However, biologists need not only visualization of one pathway but also visualization for comparison among pathways. K-Viz is a tool for visualization of metabolic pathway based on KEGG. To compare among pathways in different species, K-Viz...

taxol is used to treatment of variety cancers including ovarian, breast, lung, head and neck carcinomas and the aids-related karposi’s carcinoma, and was originally obtained from bark of taxus brevifolia. however the amount of extracted taxol from taxus is extremely low and cannot be considered as a suitable commercial source and it has led to studies for finding new sources of taxol. in 1998, ...

introduction: intranodal pathways of atrioventricular (av) node play a vital role in the delay of conduction time in response to various atrial inputs. the present study was aimed to determine the frequency-dependent electrophysiological properties of concealed slow pathway according to a functional model of isolated rabbit atrioventricular node preparation after fast pathway ablation. methods:...

Terpenoids are a large class of lipid molecules with important biological functions and diverse industrial medicinal applications. Metabolic engineering for terpene production has been hindered by the low-flux distribution to its biosynthesis pathway.