Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

Understanding the dynamics of eukaryotic transcriptome is essential for studying the complexity of transcriptional regulation and its impact on phenotype. However, comprehensive studies of transcriptomes at single base resolution are rare, even for modern organisms, and lacking for rice. Here, we present the first transcriptome atlas for eight organs of cultivated rice. Using high-throughput paired-end RNA-seq, we unambiguously detected transcripts expressing at an extremely low level, as well as a substantial number of novel transcripts, exons, and untranslated regions. An analysis of alternative splicing in the rice transcriptome revealed that alternative cis-splicing occurred in similar to 33% of all rice genes. This is far more than previously reported. In addition, we also identified 234 putative chimeric transcripts that seem to be produced by trans-splicing, indicating that transcript fusion events are more common than expected. In-depth analysis revealed a multitude of fusion transcripts that might be by-products of alternative splicing. Validation and chimeric transcript structural analysis provided evidence that some of these transcripts are likely to be functional in the cell. Taken together, our data provide extensive evidence that transcriptional regulation in rice is vastly more complex than previously believed.

Phytoremediation of triazophos by Canna indica Linn. in a hydroponic system

The phytoremediation of triazophos (O, O-diethyl-O-(1-phenyl-1, 2, 4-triazole-3-base) sulfur phosphate, TAP) by Canna indica Linn. in a hydroponic system was studied. After 21 d of exposure, the removal kinetic constant (K) of TAP was 0.0229-0.0339 d(-1) and the removal percentage of TAP was 41-55% in the plant system and the K and removal percentage of TAP were about 0.002 d(-1) and 1%, respectively, in darkness and disinfected control. However, the K and removal percentage of TAP were 0.006 d(-1) and approximately 11%, respectively, in the treatment with eluate from the media of constructed wetland. The contribution of plant to the remediation of TAP was 74% and C. indica played the most important role in the hydroponic system. Under the stress of TAP and without inorganic phosphorus nutrient, the activity of phosphatase in the plant system increased and phytodegradation was observed. The production and release of phosphatase is seen as the key mechanism for C. indica to degrade TAP. C. indica, which showed the potential of phytoremediation of TAP, and is commonly used in constructed wetland, so the technique of phytoremediation of TAP from contaminated water can be developed with the combination of constructed wetland.

Isolation and characterization of polymorphic microsatellites in a sex-reversal fish, rice field eel (Monopterus albus)

The rice field eel (Monopterus albus) is a fish of economic importance in China and some Asian countries. From a (GT)(n)-enriched genomic library, 30 microsatellites were developed by employing the fast isolation by AFLP of sequences containing repeats (FIASCO) protocol. Thirteen loci exhibited polymorphism with two to 13 alleles (mean 7.9 alleles/locus) in a test population and observed heterozygosity ranged from 0.3125 to 0.9688 (mean 0.7140). These loci should provide sufficient level of genetic variation to study the fine-scale population structure and reproductive ecology of the species.

Effect of dietary supplementation of vitamins A, D-3, E, and C on yearling rice field eel, Monopterus albus: Serum indices, gonad development, and metabolism of calcium and phosphorus

The objective of this study was to determine the effect of dietary vitamins A, D-3, E, and C on the gonad development, lipid peroxidation, and immune response of yearling rice field eel, Monopterus albus. A 6-wk feeding trial was designed according to an L-16(4(5)) orthogonal design, in which four vitamins, each at four supplementation levels, were arranged. Sixteen diets were mixed with the different vitamin levels and randomly assigned to 16 groups of fish. Increasing dietary vitamin E supplementation level significantly (P <= 0.05) increased the gonadosomatic index and lowered the serum content of malondialdehyde of rice field eel. Increasing dietary vitamin A and C levels also showed similar effect, but the differences were not statistically significant. Serum immunoglobulin M content increased significantly (P <= 0.01) as dietary vitamin C supplementation levels increased. The concentrations of calcium in bones showed significant (P <= 0.05) trend with vitamin D-3 and A supplementation levels, but the bone phosphorus content was not affected by the dietary vitamin levels.

Effects of microcystins on the growth and the activity of superoxide dismutase and peroxidase of rape (Brassica napus L.) and rice (Oryza sativa L.)

Microcystins are naturally occurring hepatotoxic cyclic heptapeptides produced by some toxic freshwater cyanobacterial species. In this study, crude extract of toxic cyanobacterial blooms from Dianchi Lake in southwestern China was used to determine the effects of microcystins on rape (Brassica napus L.) and rice (Oryza sativa L.). Experiments were carried out on a range of doses of the extract (equivalent to 0, 0.024, 0.12, 0.6 and 3 mug MC-LR/ml). Investigations showed that exposure to microcystins inhibited the growth and development of both rice and rape seedlings, however, microcystins had more powerful inhibition effect on rape than rice in germination percentage of seeds and seedling height. Microcystins significantly inhibited the elongation of primary roots of rape and rice seedlings. Determination of the activities of peroxidase and superoxide dismutase demonstrated that microcystin stress was manifested as an oxidative stress. Using ELISA, microcystins were examined from the extract of exposed rape and rice seedlings, indicating that consumption of edible plants exposed to microcystins via irrigation route may have health risks. Significantly different levels of recovered microcystins between exposed rice and rape seedlings Suggested that there might be different tolerant mechanisms toward microcystins. (C) 2004 Elsevier Ltd. All rights reserved.

Effects of cadmium on chlorophyll content, photochemical efficiency, and photosynthetic intensity of Canna indica Linn.

The effects of cadmium (Cd2+) on growth status, chlorophyll (Chl) content, photochemical efficiency, and photosynthetic intensity were studied on Canna indica Linn. Plant specimens that were produced from a constructed wetland and precultivated hydroponically in 20 L of 1/10 Hoagland solution under greenhouse conditions for I week were exposed to cadmium in concentrations of 0, 0.4, 0.8, 1.6 and 3.2 mg L- Cd2+, respectively. The results show that leaves were injured in the Cd2+ solution by the third day of exposure and the injury became more serious with an increase in the applied heavy metal. Under 3.2 mg L-1 Cd2+ treatment, growth retardation, the decrease of chlorophyll content from 0.70 to 0.43 mg g(-1) FW, and a decrease in Chl a/b ratio from 2.0 to 1.2 were observed. Chl a was more sensitive than Chl b to Cd2+ stress. The decrease was the same with photochemical efficiency. Photosynthetic intensity decreased by 13.3% from 1.5X10(4) mumol m(-2)s(-1) CO2 in control to 1.3x10(4) mumol m(2)s(-1) CO2 in the treatment of 3.2 mg L-1. Because Canna species are used in heavy metal phytoremediation, these results show that C. indica can tolerate 0.4 to 0.8 mg L-1 Cd2+. Therefore, it is a potential species for phytoremediation of cadmium with some limitations only at higher concentrations.

Microcalorimetric studies on the thermogenesis of energy release of mitochondria isolated from rice

After isolation from rice mitochondria still have activity and can live for a long time by using its stored nutrients. The thermogenesis curves of energy release of the mitochondria isolated from variant strains of rice have been determined by using an LKB2277 bioactivity monitor. The differences in shape of the curves and the thermodynamic and kinetic characteristics of the thermogenesis of the mitochondria have been compared. The thermodynamic and kinetic parameters of energy release of the mitochondria in the thermogenesis increasing stage have been calculated, and the experimental thermokinetic equations of the thermogenesis have been established. (C) 2001 Elsevier Science B.V. All rights reserved.

Studies on the energy release of rice mitochondria under different conditions by means of microcalorimetry

The thermodynamic and kinetic behaviors of energy release of mitochondria isolated from rice (Oryza sative L.) were studied by using a LKB 2277 Bioactivity Monitor under different conditions. The thermogenesis curves of energy release of the rice mitochondria (which had been kept at 0-3 degreesC for 15 h and 40 day before the determination) were determined respectively at 25 and 30 degreesC, and the difference in shape of the thermogenesis curves and thermodynamic and kinetic characteristics were compared. The thermodynamic and kinetic parameters of energy release of the mitochondria in the thermogenesis increasing stage have been calculated, and the experimental thermokinetic equations of the thermogenesis have been established. The results indicated that the lower the temperature, the slower the energy release of the rice mitochondria. Both the thermogenesis and the energy release late of the rice mitochondria increased after the mitochondria was kept at lower temperature for 40 days. One can use the methods to characterize the ability of the rice mitochondria to release energy under different conditions. (C) 2001 Published by Elsevier Science B.V.