Evaluating pathway enumeration algorithms in metabolic engineering case studies

The design of cell factories for the production of compounds involves the search for suitable heterologous pathways. Different strategies have been proposed to infer such pathways, but most are optimization approaches with specific objective functions, not suited to enumerate multiple pathways. In this work, we analyze two pathway enumeration algorithms based on graph representations: the Solution Structure Generation and the Find Path algorithms. Both are capable of enumerating exhaustively multiple pathways using network topology. We study their capabilities and limitations when designing novel heterologous pathways, by applying these methods on two case studies of synthetic metabolic engineering related to the production of butanol and vanillin

Evidence of contamination by oil and oil products in the Santos-Sao Vicente estuary, Sao Paulo, Brazil

Different components of the mixed function oxidase (MFO) system and the levels of fluorescent aromatic compounds in bile (FACs) were measured in Cathorops spixii in order to assess the impact of polycyclic aromatic hydrocarbons (PAHs). Fish were sampled in an estuary (Santos/Sao Vicente) with a history of contamination by PAHs, mainly due to the presence of the industrial complex of Cubatao city and of another of low anthropogenic influence (Cananeia) on the Brazilian coast. FACs were higher in fish from the polluted site, and the PAH 5 and 6-ring metabolites were the most frequent - with 14% and 15%, respectively. Levels of the different components of the MFO system showed the same variation profile as the FACs for both estuaries. Therefore, the values found for somatic indexes and biomarkers with data of bile PAH metabolites indicate the presence of organic contaminants, especially in the area subject to the influence of the industrial complex on the Santos/Sao Vicente estuary.CAPES (Brazilian Agency for Science and Technology); Oceanographic Institute of Sao Paulo University; Laboratory of Ecotoxicology and Environmental Chemistry of the University of Algarve; CAPES-PDEE [BEX 2176/07-6]info:eu-repo/semantics/publishedVersio