Metagenomics is the study of organismal DNA sequences obtained from an environmental sample. Metagenomic studies often compare samples taken from different locations (e.g., the human gut, lakes and oceans, soil) to assess significant differences in taxonomic makeup, genetic makeup, or function. Differences in function can be characterized by measuring the differential abundance of metabolic pat...

Mycobacterium tuberculosis, the main cause of tuberculosis (TB), has still remained a global health crisis especially in developing countries. Tuberculosis treatment is a laborious and lengthy process with high risk of non compliance, cytotoxicity adverse events and drug resistance in patient. Recently, there has been an alarming rise of drug resistant in TB. In this regard, it is an unmet need...

Iguratimod is a new synthetic disease-modifying antirheumatic drug intended to treat patients with rheumatoid arthritis. A new method using recombinant human CYP450s yeast cells containing c-DNA expressed P450s was applied to identify the metabolic pathways of iguratimod and to prepare its metabolite. The metabolite was isolated, and its structure was identified by quadrupole time-of-flight-mas...

There has been much interest in the structural comparison and alignment of metabolic pathways. Several techniques have been conceived to assess the similarity of metabolic pathways of different organisms. In this paper, we show that the combination of a new heuristic algorithm for the comparison of metabolic pathways together with any of three enzyme similarity measures (hierarchical, informati...

Objective(s): Hyperuricemia is a risk for cardiovascular and metabolic diseases, but the mechanism is ambiguous. Increased intestinal permeability is correlated with metabolic syndrome risk factors. Intestinal epithelial cells play a pivotal role in maintaining intestinal permeability. Uric acid is directly eliminated into intestinal lumen, however, the mechanism and e...

A major challenge in metabolic engineering and synthetic biology is to balance the flux of an engineered heterologous metabolic pathway to achieve high yield and productivity in a target organism. Here, we report a simple, efficient and programmable approach named 'customized optimization of metabolic pathways by combinatorial transcriptional engineering (COMPACTER)' for rapid tuning of gene ex...

A conventional metabolic pathway leads to a specific product. In stark contrast, there are diversity-generating metabolic pathways that naturally produce different chemicals, sometimes of great diversity. We demonstrate that for one such pathway, tru, each ensuing metabolic step is slower, in parallel with the increasing potential chemical divergence generated as the pathway proceeds. Intermedi...

To enhance the understanding of cells’ response in a specific condition, one requires information that shows the interconnected view of biological process. Broadly speaking, biological pathways fall into two functional categories: metabolic and regulatory pathways. Existing pathway databases are categorizing specific pathway types according to their own definition about their own subject. They ...

MOTIVATION Several genome-scale efforts are underway to reconstruct metabolic networks for a variety of organisms. As the resulting data accumulates, the need for analysis tools increases. A notable requirement is a pathway alignment finder that enables both the detection of conserved metabolic pathways among different species as well as divergent metabolic pathways within a species. When compa...

MetaCyc is a database of experimentally determined metabolic pathways from over 900 organisms, mostly microorganisms. The KEGG database consists of pathway maps that have hypertext links to further information on compounds, enzymes and genes. It extensively covers metabolism found in diverse organisms. The Biocatalysis/Biodegradation database is a metabolism database that focuses on catabolic p...