Accumulated evidence has shown that long non-coding RNAs (lncRNA) act as a widespread layer in gene regulatory networks and are involved in a wide range of biological processes. The dysregulation of lncRNA has been implicated in various complex human diseases. Although several computational methods have been developed to predict disease-related lncRNA, this still remains a considerable challenging task. In this study, we tried to construct an lncRNA–lncRNA crosstalk network by examining the significant co-occurrence of shared miRNA response elements on lncRNA transcripts from the competing endogenous RNAs viewpoint. As expected, functional analysis showed that lncRNA sharing significantly enriched interacting miRNAs tend to be involved in similar diseases and have more functionally related flanking gene sets. We further proposed a novel rank-based method, RWRHLD, to prioritize candidate lncRNA–disease associations by integrating three networks (miRNA-associated lncRNA–lncRNA crosstalk network, disease–disease similarity network and known lncRNA–disease association network) into a heterogeneous network and implementing a random walk with restart on this heterogeneous network. We used leave-one-out cross-validation to test the performance of this rank-based method in this study based on known experimentally verified lncRNA–disease associations and obtained a reliable AUC value of 0.871, which is much higher than RWR merely based on an lncRNA network, hypergeometric test and random situation. Furthermore, several novel lncRNA–disease associations predicted in case studies of ovarian cancer and prostate cancer have been confirmed in new studies by literature surveys.

Xanthine oxidase (XO), which can catalyze the formation of xanthine or hypoxanthine to uric acid, is the most important target of gout. To explore the conformational changes for inhibitor binding, molecular dockings and molecular dynamics simulations were performed. Docking results indicated that three inhibitors had similar pose binding to XO. Molecular dynamics simulations showed that the binding of three inhibitors influenced the secondary structure changes in XO. After binding to the inhibitor, the peptide Phe798-Leu814 formed different degrees of unhelix, while for the peptide Glu1065-Ser1075, only a partial helix region was formed when allopurinol was bound. Through the protein structure analysis in the simulation process, we found that the distance between the active residues Arg880 and Thr1010 was reduced and the distance between Glu802 and Thr1010 was increased after the addition of inhibitors. The above simulation results showed the similarities and differences of the interaction between the three inhibitors binding to the protein. MM-PBSA calculations suggested that, among three inhibitors, allopurinol had the best binding effect with XO followed by daidzin and puerarin. This finding was consistent with previous experimental data. Our results can provide some useful clues for further gout treatment research.

The donkey (Equus asinus) is an important domestic animal that provides a reliable source of protein and method of transportation for many human populations. However, the process of domestication and the dispersal routes of the Chinese donkey are still unclear, as donkey remains are sparse in the archaeological record and often confused with horse remains. To explore the maternal origins and dispersal route of Chinese donkeys, both mitochondrial DNA D-loop and cytochrome b gene fragments of 21 suspected donkey remains from four archaeological sites in China were amplified and sequenced. Molecular methods of species identification show that 17 specimens were donkeys and three samples had the maternal genetic signature of horses. One sample that dates to about 20,000 years before present failed to amplify. In this study, the phylogenetic analysis reveals that ancient Chinese donkeys have high mitochondrial DNA diversity and two distinct mitochondrial maternal lineages, known as the Somali and Nubian lineages. These results indicate that the maternal origin of Chinese domestic donkeys was probably related to the African wild ass, which includes the Nubian wild ass (Equus africanus africanus) and the Somali wild ass (Equus africanus somaliensis). Combined with historical records, the results of this study implied that domestic donkeys spread into west and north China before the emergence of the Han dynasty. The number of Chinese domestic donkeys had increased primarily to meet demand for the expansion of trade, and they were likely used as commodities or for shipping goods along the Silk Road during the Tang Dynasty, when the Silk Road reached its golden age. This study is the first to provide valuable ancient animal DNA evidence for early trade between African and Asian populations. The ancient DNA analysis of Chinese donkeys also sheds light on the dynamic process of the maternal origin, domestication, and dispersal route of ancient Chinese donkeys.

Sunflower (Helianthus annuus L.) contains active ingredients, such as flavonoids, alkaloids and tannins. Nevertheless, few studies have focused on essential oil from the receptacle of sunflower (SEO). In this work, we investigated the chemical composition and antimicrobial and antioxidant activities of SEO. The yield of SEO was about 0.42% (v/w) by hydrodistillation. A total of 68 volatile components of SEO were putatively identified by gas chromatography–mass spectrometry (GC-MS). The main constituents of SEO were α-pinene (26.00%), verbenone (7.40%), terpinolene (1.69%) and α-terpineol (1.27%). The minimum inhibitory concentration (MIC) of SEO against P. aeruginosa and S. aureus was 0.2 mg/mL. The MIC of SEO against S. cerevisiae was 3.2 mg/mL. The MIC of SEO against E. coli and Candida albicans was 6.4 mg/mL. The results showed that SEO had high antibacterial and antifungal activities. Three different analytical assays (DPPH, ABTS and iron ion reducing ability) were used to determine the antioxidant activities. The results showed that SEO had antioxidant activities. To summarize, the results in this study demonstrate the possibility for the development and application of SEO in potential natural preservatives and medicines due to its excellent antimicrobial and antioxidant activities.

This study was focused on extraction, radical scavenging activities, and chemical composition identification of total flavonoids in sunflower (Helianthus annuus L.) receptacles (TFSR). We investigated the optimal extract parameters of TFSR using response surface methodology. The highest yield of TFSR was 1.04% with the ethanol concentration 58%, the material-to-liquid ratio 1:20 (v/w), the extraction time 2.6 h, and the extraction temperature 67 °C. The results of radical scavenging activities showed that ethyl acetate fraction (EAF) was the strongest by using 2-diphenyl-1-picrylhydrazyl (DPPH), 2, 2’-azino-bis (3-ethylbenzo thiazoline-6-sulfonic acid) (ABTS) and iron ion reducing analysis. The EAF had the highest flavonoids contents. Four fractions A, B, C and D were enrichment from EAF by polyamide resin. Fraction B had the highest flavonoids content. Thirteen chemical components of flavonoids in fraction B were first identified by Ultimate 3000 Nano LC System coupled to a Q Exactive HF benchtop Orbitrap mass spectrometer (UHPLC-HRMS/MS). Among of the thirteen chemical components, isoquercetin and daidzein were identified accurately by comparing with standard samples. Radical scavenging analysis showed that isoquercetin and EAF had strong activities. Therefore, sunflower receptacles can be used as a source of natural flavonoids. TFSR as a natural radical scavenger has potential applications in pharmaceutical industry.

Angiotensin-converting enzyme (ACE)-inhibitory peptides extracted from food proteins can lower blood pressure by inhibiting ACE activity. A recent study showed that the inhibitory activity of IY (Ile-Tyr, a dipeptide derived from soybean protein) against ACE was much higher than that of LL (Leu-Leu), although they had similar hydrophobic and predicted activity values. It was difficult to reveal the deep molecular mechanism underlying this phenomenon by traditional experimental methods. The Apo and two complex systems (i.e., ACE–LL and ACE–IY) were therefore subjected to 1 μs long Gaussian accelerated molecular dynamics (GaMD) simulations. The results showed that the binding of IY can cause obvious contraction of the active site of ACE, mainly manifested by a significant lateral shift of α13, α14, and α15. In addition, hinge 2 and hinge 3 were more stable in the ACE–IY system, while these phenomena were not present in the ACE–LL system. Moreover, the α10 of the IY-bound ACE kept an inward state during the simulation progress, which facilitated the ACE to remain closed. However, for the LL-bound ACE, the α10 switched between two outward states. To sum up, our study provides detailed insights into inhibitor-induced conformational changes in ACE that may help in the design of specific inhibitors targeting ACE for the treatment of hypertension.