| miRNAs (MicroRNAs) are small noncoding RNA gene products about 22 nt long that are found in multicellular organisms, including animals and plants. The researchers further found that it is relevant to gene expression,cell cycle and ontogeny course. So it is very important for gene function, human disease and biological evolution. But, miRNAs still have many questions to be clarified, such as their function of gene expression and other cases. Nowadays, most miRNAs are found by Northern bloting. But such method can not identify miRNA efficiently, as miRNAs are too short. A more serious challenge is to open the spatial and temporal patterns of miRNA expression. So, finding new miRNAs become the most important part of miRNA research. Several Bioinformatics methods were developed to find miRNAs, most of which were base on the homology search. Such methods could find many new miRNA homologues, but can not discover many species-special miRNAs. During our research, we developed a new method to more effectively identify miRNAs in Plant Genomes. Using it, we found 136 possible miRNAs which cover 41 of the already known miRNAs and some of them were conserved in Arabidopsis and other species.This computational approach mainly based on combination of EST filter with comparative characteristic feature of sequences between miRNA candidates and known miRNA precursors. The target analyzing was used to confirm miRNAs. Finally, we got new miRNAs by comparing our results with known miRNA candidates. About the novel miRNAs we found that they had less conservation than the known miRNAs. Moreover, we found the miRNA targets can code varies proteins, such as transcription factor, transposon, fatty acid enzyme, etc. As the experimental verification, 3 out of 5 candidates were detected by realtime-PCR. Addition to EST filters in our identification processing confirmes that our miRNA can be expressed in rice plants. Hence, the computational identicfication method of plant miRNAs established here is effective and reliable. Otherhand, the results shows us every species may have their own special miRNA which can produce various mutation in the evolution, this provide a path for the system classification. Same real miRNAs might miss since they did not appear in the EST library.Additionally, we developed a rapid and effective RNA extraction method from soil. Proteins including RNase, humic acids, polysaccharides, and polyphenols were effectively removed with Mg2+-K+-Na+-bentonite, phenol, chloroform, high concentrations of KI, and 2-butoxyethanol during RNA extraction from three different soil types. This method extracted up to 8～12μg of total RNA from 0.2 g of soil. The A260/A230 and A260/A280 ratios of RNA were 1.5～1.6 and 1.8～1.9, respectively. Reverse transcription-PCR amplification (16S rRNA gene) indicates that extracted RNA can be used to study gene expression and function in soil microorganisms. The whole extraction process can be completed within a few hours. Therefore a rapid, effective and economical method for RNA extraction from soils has been developed. This method can isolate RNA from a small amount of soil and is beneficial for soil RNA gene expression and function analysis.
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