[Comparative Study on Quality of Volatile Oil of Acori Tatarinowii Rhizoma from Two Habitats].

OBJECTIVE: To compare the quality of volatile oil of Acori Tatarinowii Rhizoma from Guangxi and Sichuan. METHODS: The volatile oil was extracted from Acori Tatarinowii Rhizoma by using steam distillation method, and analyzed by GC-MS. Peak area normalization method was used for calculating the relative percentage contents of chemical constituents, and hierarchical cluster analysis was used for classifying the 20 batches of samples by their relative contents of the main components that were methyleugenol, cis-methylisoeugenol, γ-asarone, ß-asarone and α-asarone. RESULTS: The average extraction rate of 10 batches of volatile oil in Acori Tatarinowii Rhizoma from Guangxi was 1. 61%, and 10 batches of samples from Sichuan was 1. 72%. The relative percentage contents of five main components totaled 78. 19% and 88. 84%, respectively. By t-test, there was no statistical difference between samples from Guangxi and Sichuan. In the hierarchical cluster analysis,10 batches of samples from Guangxi and 10 batches of samples from Sichuan could respectively be classified into four clusters subcategories and five clusters subcategories, while the mean of samples of Guangxi and the mean of samples of Sichuan respectively analyzed with 20 batches of the two habitats that all were classified in the same clusters subcategories. The results of similarity showed that the correlation coefficients of 8 batches in 10 batches of samples from Guangxi were over 0. 9, while 1 batch was only 0. 466. The correlation coefficients of 7 batches in 10 batches of samples from Sichuan had were over 0. 9, while 1 batch was only 0. 069. The correlation coefficients between the mean of samples of Guangxi and the mean of samples of Sichuan was 0. 996. CONCLUSION: Quality of the different batches of volatile oil from Acori Tatarinowii Rhizoma have significant differences, but it has no obvious correlation with the habitats.

[Effects of volatile oil of Rhizoma Acori Tatarinowii on morphology and cell viability in cultured cardiac myocytes].

OBJECTIVE: To observe the effects of volatile oil of Rhizoma Acori Tatarinowii (VOSCP) on morphology and cell viability in cultured neonate rat cardiac myocytes. METHODS: The cardiac myocytes were cultured by trypsin under cool treatment, and the cell purity was assayed with imminocytochemistry; Morphological changes were observed under phase contrast microscope after cardiac myocytes with VOSCP of different concentration for 24h in vitro, and the cell viability was examed by MTT assay. RESULTS: The purity of cultured neonate rat cardiac myocytes was higher than 95%; VOSCP of different concentration could depress pulse frequency and 100-160 mg/L VOSCP can obviously improve the viability of cardiac myocytes. The relation of dose-effect relationship was a parabola whose peak was at the value of 140 mg/L. CONCLUSION: VOSCP of proper concentration can depress pulse frequency and improve the viability of cardiac myocytes.

[A new method for EST clustering].

We developed an EST (expressed sequence tag) clustering method, ESTClustering, to generate high-quality unique expressed sequence based on large-scale EST sequencing. The method uses consensus sequences to sequence analyze with megablast and assemble each cluster with phrap in clustering process. The clustering strategy can efficiently identify gene family and alternate splicing forms of expressed sequences. It can also reduce the adverse effects caused by sequence errors. The ESTClustering method tends to provide more expressed gene forms comparing with the UniGene clustering method of the National Center for Biotechnology Information. Analysis of the 112,256 ESTs of Arabidopsis with ESTClustering produced 23,581 EST clusters. Among these Arabidopsis EST clusters, 13,597 have corresponding genome coding sequences and this number is close to the number of genes predicted with Arabidopsis ESTs. Using this clustering method, a total of 147,191 rice ESTs were clustered into 33,896 groups.

Heterosis and polymorphisms of gene expression in an elite rice hybrid as revealed by a microarray analysis of 9198 unique ESTs.

Despite the significant contributions of utilizing heterosis to crop productivity worldwide, the biological mechanisms of heterosis remained largely uncharacterized. In this study, we analyzed gene expression profiles of an elite rice hybrid and the parents at three stages of young panicle development, using a cDNA microarray consisting of 9198 expressed sequence tags (ESTs), with the objective to reveal patterns of gene expression that may be associated with heterosis in yield. A total of 8422 sequences showed hybridization signals in all three genotypes in at least one stage and 5771 sequences produced detectable signals in all slides. Significant differences in expression level were detected for 438 sequences among the three genotypes in at least one of the three stages, as determined by ANOVA validated with 100 permutations at P < 0.05. Significant mid-parent heterosis was detected for 141 sequences, which demonstrated the following features: a much larger number of sequences showed negative heterosis than ones showing positive heterosis; genes functioning in DNA replication and repair tended to show positive heterosis; genes functioning in carbohydrate metabolism, lipid metabolism, energy metabolism, translation, protein degradation, and cellular information processing showed negative heterosis; both positive and negative heterosis were observed for genes in amino acid metabolism, transcription, signal transduction, plant defense and transportation. The results are indicative of the biochemical and physiological activities taking place in the hybrid relative to the parents. Identification of genes showing expression polymorphisms among different genotypes and heterotic expression in the hybrid may provide new avenues for exploring the biological mechanisms underlying heterosis.

Expression profiles of 10,422 genes at early stage of low nitrogen stress in rice assayed using a cDNA microarray.

Development of crop varieties with high nitrogen use efficiency (NUE) is imperative for sustainable agriculture. Understanding how plant genes respond to low N stress is essential for formulating approaches to manipulating genes for improving NUE. In this study we analyzed the expression profiles of an indica rice cultivar Minghui 63 at seedling stage at 20 min, 1 and 2 h after low N stress with the normal N as the control, using a microarray of 11,494 rice ESTs representing 10,422 unique genes. While no significant difference was detected in the leaf tissue, a total of 471 ESTs were detected as responsive to low N stress in the root tissue with 115 ESTs showing up-regulation and 358 ESTs showing down-regulation. The analysis of expression profiles after low N stress identified following patterns: (1) the genes involved in photosynthesis and energy metabolism were down-regulated rapidly; (2) many of the genes involved in early responses to biotic and abiotic stresses were up-regulated while many other stress responsive genes were down-regulated; (3) regulatory genes including transcription factors and ones involved in signal transduction were both up- and down-regulated; and (4) the genes known to be involved in N uptake and assimilation showed little response to the low N stress. The challenges for future studies are to characterize the functional roles of the low N stress responsive genes in N metabolisms, including the large number of genes presently with unknown functions.

Features of the expressed sequences revealed by a large-scale analysis of ESTs from a normalized cDNA library of the elite indica rice cultivar Minghui 63.

The indica subspecies of cultivated rice occupies the largest area of rice production in the world. However, a systematic analysis of cDNA sequences from the indica subspecies has not been performed. The aim of the present study was to collect and analyze the expressed sequence tags (ESTs) of indica rice on a large scale. A total of 39 208 raw sequences were generated from a normalized cDNA library prepared by use of 15 different tissues of the indica cultivar Minghui 63. After trimming, processing and analysis, 17 835 unique sequences were obtained, each of which presumably represents a unique gene. Of these sequences, 2663 were novel, and at least 70 were indica specific. Comparison of the Minghui 63 sequences with the ESTs/full-length cDNAs in GenBank revealed a large number of deletion/insertion/substitution (DIS) at both the inter- and intra-subspecific levels. The overall number of polymorphisms in the expressed sequences was higher in the inter-subspecific comparisons than in the intra-subspecific comparisons. However, the extent of DIS-based polymorphism was highly variable among different rice varieties. In total, 15 726 unique sequences, including 697 novel sequences, were assigned to regions where large numbers of quantitative trait loci (QTLs) for agronomic traits had been detected previously. These results may be useful for developing new molecular markers for genetic mapping, detecting allelic polymorphisms associated with phenotypic variations between rice varieties, and facilitating QTL cloning by providing the starting points for candidate-gene identification.

Preference of simple sequence repeats in coding and non-coding regions of Arabidopsis thaliana.

MOTIVATION: Simple sequence repeats or microsatellites have been found abundantly in many genomes. However, the significance of distribution preference has not been completely understood. Completion of the Arabidopsis genome sequencing allows us to better understand and characterize microsatellites. RESULTS: Microsatellite distribution was more abundant in 5'-flanking regions of genes compared with that expected in the whole genome, with an over-representation of AG and AAG repeats; there were clear differences from distributions in 3'-flanks and coding fractions, where triplet frequencies evidently corresponded to codon usage. We identified 1140 full-length genes that contained at least one locus of AG or AAG repeats in their upstream sequences, and whose functional characteristics were significantly associated with the repeats. This observation indicates that selective pressure markedly differed in the three transcribed regions, with positive selection of AG and AAG repeats in 5'-flanks close to those genes whose products are preferentially involved in transcription.