Potential application of a knowledgebase of iron metabolism of Acidithiobacillus ferrooxidans as an alternative platform

BACKGROUND: Acidithiobacillus ferrooxidans is a facultative anaerobe that depends on ferrous ion oxidation as well as reduced sulfur oxidation to obtain energy and is widely applied in metallurgy, environmental protection, and soil remediation. With the accumulation of experimental data, metabolic mechanisms, kinetic models, and several databases have been established. However, scattered data are not conducive to understanding A. ferrooxidans that necessitates updated information informed by systems biology. RESULTS: Here, we constructed a knowledgebase of iron metabolism of A. ferrooxidans (KIMAf) system by integrating public databases and reviewing the literature, including the database of bioleaching substrates (DBS), the database of bioleaching metallic ion-related proteins (MIRP), the A. ferrooxidans bioinformation database (Af-info), and the database for dynamics model of bioleaching (DDMB). The DBS and MIRP incorporate common bioleaching substrates and metal ion-related proteins. Af-info and DDMB integrate nucleotide, gene, protein, and kinetic model information. Statistical analysis was performed to elucidate the distribution of isolated A. ferrooxidans strains, evolutionary and metabolic advances, and the development of bioleaching models. CONCLUSIONS: This comprehensive system provides researchers with a platform of available iron metabolism-related resources of A. ferrooxidans and facilitates its application.

Potential bioactive phytochemicals, antioxidant properties and anticancer pathways of Nymphaea nouchali

Objective: To investigate bioactive phytochemicals and antioxidant activities of Nymphaea nouchali and to explore its anticancer pathways by a network pharmacology approach.Methods: Using a spectrophotometer and high-performance liquid chromatography-diode array detector (HPLC-DAD), we quantified bioactive phytochemicals in methanolic extract of Nymphaea nouchali tuber. The extracts were investigated for in vitro antioxidant properties. Targets of these bioactive phytochemicals were predicted and anticancer-associated pathways were analyzed by a network pharmacology approach. Moreover, we identified the predicted genes associated with cancer pathways and the hub genes in the protein-protein interaction network of predicted genes. Results: Quantitative results indicated the total phenolics, total flavonoids, and total proanthocyanidins in the methanolic extract of Nymphaea nouchali tuber. HPLC-DAD analysis showed rutin (39.44 mg), catechin (39.20 mg), myricetin (30.77 mg), ellagic acid (11.05 mg), gallic acid (3.67 mg), vanillic acid (0.75 mg), rosmarinic acid (4.81 mg), p-coumaric acid (3.35 mg), and quercetin (0.90 mg) in 1 g of dry extract. The extract showed the radical scavenging activities of 2, 2-diphenyl-1-picrylhydrazyl, 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) and N,N-dimethyl-p-phenylenediamine. By using network pharmacology, we predicted 130 target genes associated with cancer pathways. The top hub genes (IL6, AKT1, EGFR, JUN, PTGS2, MAPK3, CASP3, and CXCL8) were also identified, which were associated with cancer pathways and interacted with bioactive phytochemicals of the methanolic extract of Nymphaea nouchali tuber. Conclusions: Our study provides insights into the mechanism of anticancer activities of the methanolic extract of Nymphaea nouchali tuber.