Mutational interference mapping experiment (MIME) for studying RNA structure and function.

RNA regulates many biological processes; however, identifying functional RNA sequences and structures is complex and time-consuming. We introduce a method, mutational interference mapping experiment (MIME), to identify, at single-nucleotide resolution, the primary sequence and secondary structures of an RNA molecule that are crucial for its function. MIME is based on random mutagenesis of the RNA target followed by functional selection and next-generation sequencing. Our analytical approach allows the recovery of quantitative binding parameters and permits the identification of base-pairing partners directly from the sequencing data. We used this method to map the binding site of the human immunodeficiency virus-1 (HIV-1) Pr55(Gag) protein on the viral genomic RNA in vitro, and showed that, by analyzing permitted base-pairing patterns, we could model RNA structure motifs that are crucial for protein binding.

Evaluating the effectiveness of routine water quality monitoring in Miyun reservoir based on geostatistical analysis.

This study used geographic information system techniques and geostatistics methods to evaluate the effectiveness of routine water quality monitoring in the western segment of the Miyun reservoir in Beijing. Methodologies as well as the sampling design are evaluated. The single-layer evaluation and three integrated evaluation methods including principal component analysis (PCA), ordinary kriging (OK)_Mean, and Mean_Layers were used to validate the effectiveness of evaluation methods, and the effectiveness of each sampling design was validated by comparing their errors. Results indicated that, while a single-layer evaluation only shows the trophic state of water at a specific level, an integrated evaluation synthetically analyzes and evaluates the trophic state of the entire water body. Furthermore, results of the integrated analysis show that a PCA method is more accurate and can represent the trophic state of the entire water body. The OK_Mean and Mean_Layers methods are only able to represent the mean level for trophic state of the entire water body but cannot reflect local trophic state and distribution details. Although methods used in the routine monitoring of Miyun reservoir have some similarities to the OK_Mean and Mean_Layers methods, their range of errors and uncertainty are greater because of a lack of detailed spatial continuous information. The analysis on the number of sampling points shows that, within a certain range of error, minor changes of sampling points will have no obvious impact on the monitoring results. For the routine monitoring of western Miyun reservoir, using only three to five sampling points for monitoring is inadequate. According to our analysis, it is more appropriate to use at least ten sampling points for monitoring these areas.