Association algorithm to mine the rules that govern enzyme definition and to classify protein sequences

BACKGROUND: The number of sequences compiled in many genome projects is growing exponentially, but most of them have not been characterized experimentally. An automatic annotation scheme must be in an urgent need to reduce the gap between the amount of new sequences produced and reliable functional annotation. This work proposes rules for automatically classifying the fungus genes. The approach involves elucidating the enzyme classifying rule that is hidden in UniProt protein knowledgebase and then applying it for classification. The association algorithm, Apriori, is utilized to mine the relationship between the enzyme class and significant InterPro entries. The candidate rules are evaluated for their classificatory capacity. RESULTS: There were five datasets collected from the Swiss-Prot for establishing the annotation rules. These were treated as the training sets. The TrEMBL entries were treated as the testing set. A correct enzyme classification rate of 70% was obtained for the prokaryote datasets and a similar rate of about 80% was obtained for the eukaryote datasets. The fungus training dataset which lacks an enzyme class description was also used to evaluate the fungus candidate rules. A total of 88 out of 5085 test entries were matched with the fungus rule set. These were otherwise poorly annotated using their functional descriptions. CONCLUSION: The feasibility of using the method presented here to classify enzyme classes based on the enzyme domain rules is evident. The rules may be also employed by the protein annotators in manual annotation or implemented in an automatic annotation flowchart

Monascuspiloin enhances the radiation sensitivity of human prostate cancer cells by stimulating endoplasmic reticulum stress and inducing autophagy.

Prostate cancer is a very common cancer among males. Traditional treatments for prostate cancer have limited efficacy; therefore, new therapeutic strategies and/or new adjuvant drugs must be explored. Red yeast rice (RYR) is a traditional food spice made in Asia by fermenting white rice with Monascus purpureus Went yeast. Accumulating evidence indicates that RYR has antitumor activity. In this study, PC-3 cells (human prostate cancer cells) were used to investigate the anti-cancer effects of ionizing radiation (IR) combined with monascuspiloin (MP, a yellow pigment isolated from Monascus pilosus M93-fermented rice) and to determine the underlying mechanisms of these effects in vitro and in vivo. We found that IR combined with MP showed increased therapeutic efficacy when compared with either treatment alone in PC-3 cells. In addition, the combined treatment enhanced DNA damage and endoplasmic reticulum (ER) stress. The combined treatment induced primarily autophagy in PC-3 cells, and the cell death that was induced by the combined treatment was chiefly the result of inhibition of the Akt/mTOR signaling pathways. In an in vivo study, the combination treatment showed greater anti-tumor growth effects. These novel findings suggest that the combined treatment could be a potential therapeutic strategy for prostate cancer

Fuzzy Sets and Systems 118 (2001) 9–19 www.elsevier.com/locate/fss Fuzzy ARIMA model for forecasting the foreign exchange market

Considering the time-series ARIMA(p,d, q) model and fuzzy regression model, this paper develops a fuzzy ARIMA (FARIMA) model and applies it to forecasting the exchange rate of NT dollars to US dollars. This model includes interval models with interval parameters and the possibility distribution of future values is provided by FARIMA. This model makes it possible for decision makers to forecast the best- and worst-possible situations based on fewer observation

Media 1: Manipulation of micro-particles by flexible polymer-based optically-induced dielectrophoretic devices

Originally published in Optics Express on 02 January 2012 (oe-20-1-583

IR dose–response survival curves and cytotoxic effects resulting from MP and/or IR in PC-3 cells.

<p>(A) Chemical structure of MP. (B) Concentration-dependent effects of MP on the viability of PC-3 cells. Cells were treated with 5, 15, 25, 35 or 45 μM MP for 48 hrs. *, <i>p</i><0.05, MP versus control. (C) Cytotoxic effects in cells treated with IR (4 Gy) and/or MP (25 μM). #, <i>p</i><0.05, IR versus combined treatment. *, <i>p</i><0.05, MP versus combined treatment. (D) The radiation dose-response survival curves of PC-3 cells with or without MP. Data are presented as the mean ± standard deviation of three independent experiments.</p