Rhubarb has been widely used for the treatment of hyperlipidemia and blood stasis. We conducted an ultra performance liquid chromatography-quadrupole time-of-flight high-definition mass spectrometry-based urinary metabolomic study on the diet-induced hyperlipidemic rats to present new insights into hyperlipidemia and the therapeutic effect of rhubarb. Coupled with blood biochemistry results, a significant difference in metabolic profiles among control, diet-induced hyperlipidemic and rhubarb-treated hyperlipidemic groups by partial least squares-discriminate analysis demonstrated that alterations in global urinary metabolites occurred significantly. Twenty-nine metabolites were identified as potential biomarkers by the accurate mass, isotopic pattern and MSE fragments information in both positive and negative ion modes. Significantly higher levels of octadecanamide, 3-methyluridine, oleamide, ascorbalamic acid, 1-methylnicotinamide, phenylacetylglycine, xanthine, aspartic acid, ribothymidine, 4-aminohippuric acid, methylhippuric acid, arginine and hippuric acid as well as significantly lower levels of 3-O-methyldopa, trimethyltridecanoic acid, S-cysteinosuccinic acid, indole-3-carboxylic acid, creatinine, carnitine, phenylalanine, 2-pyrroloylglycine, phytosphingosine, cyclohexanecarboxylic acid, propionylcarnitine, N-acetylneuraminic acid, cytidine, phenylpropionylglycine, palmitic acid and ribonic acid were observed in the diet-induced hyperlipidemic rats compared with the control rats. However, tendencies of these metabolites were obviously reversed in the rhubarb-treated hyperlipidemic rats. Changes of these metabolites were mainly associated with the perturbations of fatty acid metabolism, amino acid metabolism and nucleoside metabolism. The results indicated the amelioration and the therapeutic effect of rhubarb for hyperlipidemia, and further provided new insights into hyperlipidemia and the therapeutic effect of rhubarb.

Urine metabolomics reveals new insights into hyperlipidemia and the therapeutic effect of rhubarb

TCM grammar systems: an approach to aid the interpretation of the molecular interactions in Chinese herbal medicine.

Because of the complexity of the components in Traditional Chinese Medicine formula (TCM formula), it is still a challenge to identify its effective components, to elucidate the mechanism of the components, and to discover the relationship between components and therapy objectives. In this paper, a method called directed TCM grammar systems (dTGS) for effective component identification was proposed using entity grammar systems (EGS) as the theoretical framework. The component-disease relationship of a TCM formula (i.e., Bai-Hu decoction plus Wasting-Thirsting formula, BHDWT) and one disease (i.e., type 2 diabetes mellitus) treated with it was studied, and the effective component groups (ECGs) were identified. 19 compounds were found acting on 20 proteins in type 2 diabetes mellitus (T2D) disease network, and 15 compounds were determined as the candidate effective components. Results indicated that this method can be used to identify the effective components and provide an innovative way to elucidate the molecular mechanism of TCM formulas.

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dTGS: Method for Effective Components Identification from Traditional Chinese Medicine Formula and Mechanism Analysis

https://info.pharm.bucm.edu.cn/docs/20160114210024437420.pdf

Exploration of the mechanism of pattern-specific treatments in coronary heart disease with network pharmacology approach

A new algorithm is presented for vocabulary analysis (word detection) in texts of human origin. It performs at 60%-70% overall accuracy and greater than 80% accuracy for longer words, and approximately 85% sensitivity on Alice in Wonderland, a considerable improvement on previous methods. When applied to protein sequences, it detects short sequences analogous to words in human texts, i.e. intolerant to changes in spelling (mutation), and relatively context- independent in their meaning (function). Some of these are homonyms of up to 7 amino acids, which can assume different structures in different proteins. Others are ultra-conserved stretches of up to 18 amino acids within proteins of less than 40% overall identity, refl ecting extreme constraint or convergent evolution. Different species are found to have qualitatively different major peptide vocabularies, e.g. some are dominated by large gene families, while others are rich in simple repeats or dominated by internally repetitive proteins. This suggests the possibility of a peptide vocabulary signature, analogous to genome signatures in DNA. Homonyms may be useful in detecting convergent evolution and positive selection in protein evolution. Ultra-conserved words may be useful in identifying structures intolerant to substitution over long periods of evolutionary time.

/pdf/peptide-vocabulary-analysis-reveals-ultra-conservation-and-4y0au4fswr.pdf

Yun Wang

Papers

Entity grammar systems: a grammatical tool for studying the hierarchal structures of biological systems