Analysis and Prediction of Translation Rate Based on Sequence and Functional Features of the mRNA

Protein concentrations depend not only on the mRNA level, but also on the translation rate and the degradation rate. Prediction of mRNA's translation rate would provide valuable information for in-depth understanding of the translation mechanism and dynamic proteome. In this study, we developed a new computational model to predict the translation rate, featured by (1) integrating various sequence-derived and functional features, (2) applying the maximum relevance & minimum redundancy method and incremental feature selection to select features to optimize the prediction model, and (3) being able to predict the translation rate of RNA into high or low translation rate category. The prediction accuracies under rich and starvation condition were 68.8% and 70.0%, respectively, evaluated by jackknife cross-validation. It was found that the following features were correlated with translation rate: codon usage frequency, some gene ontology enrichment scores, number of RNA binding proteins known to bind its mRNA product, coding sequence length, protein abundance and 5′UTR free energy. These findings might provide useful information for understanding the mechanisms of translation and dynamic proteome. Our translation rate prediction model might become a high throughput tool for annotating the translation rate of mRNAs in large-scale

Mining for Candidate Genes Related to Pancreatic Cancer Using Protein-Protein Interactions and a Shortest Path Approach

Pancreatic cancer (PC) is a highly malignant tumor derived from pancreas tissue and is one of the leading causes of death from cancer. Its molecular mechanism has been partially revealed by validating its oncogenes and tumor suppressor genes; however, the available data remain insufficient for medical workers to design effective treatments. Large-scale identification of PC-related genes can promote studies on PC. In this study, we propose a computational method for mining new candidate PC-related genes. A large network was constructed using protein-protein interaction information, and a shortest path approach was applied to mine new candidate genes based on validated PC-related genes. In addition, a permutation test was adopted to further select key candidate genes. Finally, for all discovered candidate genes, the likelihood that the genes are novel PC-related genes is discussed based on their currently known functions

Petroleum ether extractive of the hips of Rosa multiflora ameliorates collagen-induced arthritis in rats

Ethnopharmacological Relevance: The hip of Rosa multiflora Thunb. (HRM) has been traditionally used as a dietary supplement and a herbal remedy for the treatment of various diseases, including inflammation, osteoarthritis, rheumatoid arthritis and chronic pain, in China. The current study was to evaluate the therapeutic efficacy of the petroleum ether extractive of HRM (PEE) on type II collagen-induced rheumatoid arthritis (CIA) in male Wistar rats. In addition, the anti-inflammatory mechanism(s) of PEE on type II CIA was explored. Materials and Methods: Rheumatoid arthritis (RA) was induced by intradermal injection of bovine type II collagen on Day 1 and Day 8. Starting from Day 13, normal rats were treated with vehicle (serving as the control group); the CIA rats were treated with vehicle (CIA group), dexamethasone (0.25 mg/kg bw per day, p.o.) (a positive control), lei-gong-teng (LGT: 10 mg/kg bw per day, p.o.) (a clinically used Chinese patent medicine in RA therapy) or PEE (12, 36 or 120 mg/kg bw per day, p.o.) for 28 days. Results and Conclusions: PEE (120 mg/kg bw per day) efficiently attenuated the severity of arthritis in the CIA rats by reducing the mean arthritis severity scores and the fore/hind paw swelling as well as reduced histological changes by decreasing the cartilage surface erosion and cartilage proteoglan depletion. PEE׳s therapeutic effect in RA may involve the inhibition of pro-inflammatory cytokines, such as TNF-α, IL-1β and IL-6, in serum and/or the elevation of the activities of hepatic anti-oxidative enzymes including SOD, CAT and GSH-Px. However, the detailed anti-inflammatory mechanism, the main effective components and the interaction between different ingredients in PEE are still not clear and require more studies

Petroleum ether extractive of the hips of Rosa multiflora ameliorates collagen-induced arthritis in rats

Ethnopharmacological relevance The hip of Rosa multiflora Thunb. (HRM) has been traditionally used as a dietary supplement and a herbal remedy for the treatment of various diseases, including inflammation, osteoarthritis, rheumatoid arthritis and chronic pain, in China. The current study was to evaluate the therapeutic efficacy of the petroleum ether extractive of HRM (PEE) on type II collagen-induced rheumatoid arthritis (CIA) in male Wistar rats. In addition, the anti-inflammatory mechanism(s) of PEE on type II CIA was explored.Materials and methods Rheumatoid arthritis (RA) was induced by intradermal injection of bovine type II collagen on Day 1 and Day 8. Starting from Day 13, normal rats were treated with vehicle (serving as the control group); the CIA rats were treated with vehicle (CIA group), dexamethasone (0.25 mg/kg bw per day, p.o.) (a positive control), lei-gong-teng (LGT: 10 mg/kg bw per day, p.o.) (a clinically used Chinese patent medicine in RA therapy) or PEE (12, 36 or 120 mg/kg bw per day, p.o.) for 28 days.Results and conclusions PEE (120 mg/kg bw per day) efficiently attenuated the severity of arthritis in the CIA rats by reducing the mean arthritis severity scores and the fore/hind paw swelling as well as reduced histological changes by decreasing the cartilage surface erosion and cartilage proteoglan depletion. PEE's therapeutic effect in RA may involve the inhibition of pro-inflammatory cytokines, such as TNF-α, IL-1β and IL-6, in serum and/or the elevation of the activities of hepatic anti-oxidative enzymes including SOD, CAT and GSH-Px. However, the detailed anti-inflammatory mechanism, the main effective components and the interaction between different ingredients in PEE are still not clear and require more studies.Department of Applied Biology and Chemical Technolog