Comparative genomic analysis for nucleotide, codon, and amino acid usage patterns of mycoplasmas.

The evolutionary factors in influencing the genetic characteristics of nucleotide, synonymous codon, and amino acid usage of 18 mycoplasma species were analyzed. The nucleotide usage at the 1st and 2nd codon position which determines amino acid composition of proteins has a significant correlation with the total nucleotide composition of gene population of these mycoplasma species, however, the nucleotide usage at the 3rd codon position which affects synonymous codon usage patterns has a slight correlation with either the total nucleotide composition or the nucleotide usage at the 1st and 2nd codon position. Other evolutionary factors join in the evolutionary process of mycoplasma apart from mutation pressure caused by nucleotide usage constraint based on the relationships between effective number of codons/codon adaptation index and nucleotide usage at the 3rd codon position. Although nucleotide usage of gene population in mycoplasma dominates in forming the overall codon usage trends, the relative abundance of codon with nucleotide context and amino acid usage pattern show that translation selection involved in translation accuracy and efficiency play an important role in synonymous codon usage patterns. In addition, synonymous codon usage patterns of gene population have a bigger power to represent genetic diversity among different species than amino acid usage. These results suggest that although the mycoplasmas reduce its genome size during the evolutionary process and shape the form, which is opposite to their hosts, of AT usages at high levels, this kind organism still depends on nucleotide usage at the 1st and 2nd codon positions to control syntheses of the requested proteins for surviving in their hosts and nucleotide usage at the 3rd codon position to develop genetic diversity of different mycoplasma species. This systemic analysis with 18 mycoplasma species may provide useful clues for further in vivo genetic studies on the related species.

[Drug dynamics research of salvia miltiorrhiza in rabbit plasma and aqueous humor after intravenous injection].

OBJECTIVES: To assess the permeability of Danshensu at blood-ocular barrier and its characteristics of pharmacokinetics by respectively measuring the concentrations of Danshensu in blood plasma and aqueous humor of the rabbit with the high performance liquid chromatography(HPLC). METHODS: It was an experimental study. Seventy-two white rabbits were split into three groups: control group (6 rabbits), plasma group (6 rabbits) and aqueous humor group (60 rabbits). After 0.85% salt water (control group)or salvia miltiorrhiza (1.0 g/kg) (plasma and aqueous group) was injected into the vein of auris-edge. Samples of blood and aqueous humor were obtained for analysis . The analytical column was a BDS C18 stainless steed column(5 µm, 4.6 mm× 250 mm); Precolumn:YWGC18; the mobile phase consists of acetonitrile and 0.01 mol/L KH2PO4 (8:92, adjusted to pH = 2.8 with phosphoric acid). The UV detector was set at 279 nm; the flow rate was 1.0 ml/min;and the column temperature was ordinary temperature. RESULTS: The plasma concentration-time curves of Salvia miltiorrhiza fitted three-compartment model. t1/2 ß (elimination half time): 5.661 min; Cmax (peak concentration): 727.29 mg/L; Tmax(peak time ): 0 min. The aqueous humor concentration-time curves fitted two-compartment model. t1/2 ß: 147.663 min; Cmax: 38.62 mg/L; Tmax: 25 min. CONCLUSIONS: HPLC is a sensitive, specific and accurate method that can be used in pharmacokinetics research on ocular tissue of rabbit for Danshensu, Salvia miltiorrhiza that is dissolvable in water can pass through the blood-ocular barrier after intravenous injection with a relatively stable concentration of danshensu in aqueous humor resulting from a slow rate of removal.

Photosynthetic and Morphological Responses of Sacha Inchi (Plukenetia volubilis L.) to Waterlogging Stress.

Sacha inchi (Plukenetia volubilis L.) is an important oilseed crop that is rich in fatty acids and protein. Climate-change-related stresses, such as chilling, high temperature, and waterlogging can cause severe production loss in this crop. In this study, we investigated the photosynthetic responses of sacha inchi seedlings to short-term waterlogging and their morphological changes after long-term waterlogging stress. Sacha inchi CO2 uptake, stomatal conductance, and transpiration rate are affected by temperature and light intensity. The seedlings had a high CO2 uptake (>10 µmol m-2s-1) during the daytime (08:00 to 15:00), and at 32 and 36 °C. At 32 °C, CO2 uptake peaked at irradiations of 1000 and 1500 µmol m-2s-1, and plants could still perform photosynthesis at high-intensity radiation of 2000-3000 µmol m-2s-1. However, after 5 days of waterlogging (5 DAF) sacha inchi seedlings significantly reduced their photosynthetic ability. The CO2 uptake, stomatal conductance, Fv/Fm, ETR, and qP, etc., of the susceptible genotypes, were significantly decreased and their wilting percentage was higher than 50% at 5 DAF. This led to a higher wilting percentage at 7 days post-recovery. Among the four lines assessed, Line 27 had a high photosynthetic capability and showed the best waterlogging tolerance. We screened many seedlings for long-term waterlogging tolerance and discovered that some seedlings can produce adventitious roots (AR) and survive after two weeks of waterlogging. Hence, AR could be a critical morphological adaptation to waterlogging in this crop. In summary, these results suggest that improvement in waterlogging tolerance has considerable potential for increasing the sustainable production of sacha inchi.

Dose-effect relationships of 12C6+ ions-induced dicentric plus ring chromosomes, micronucleus and nucleoplasmic bridges in human lymphocytes in vitro.

PURPOSE: The objective of this research was to explore the dose-effect relationships of dicentric plus ring (dic + r), micronucleus (MN) and nucleoplasmic bridges (NPB) induced by carbon ions in human lymphocytes. MATERIALS AND METHODS: Venous blood samples were collected from three healthy donors. 12C6+ ions beam was used to irradiate the blood samples at the energy of 330 MeV and linear energy transfer (LET) of 50 keV/µm with a dose rate of 1 Gy/min in the spread-out Bragg peak. The irradiated doses were 0 (sham irradiation), 1, 2, 3, 4, 5 and 6 Gy. Dic + r chromosomes aberrations were scored in metaphases. The cytokinesis-block micronucleus cytome (CBMN) was conducted to analyze MN and NPB. The maximum low-dose relative biological effectiveness (RBEM) values of the induction of dic + r, MN and NPB in human lymphocytes for 12C6+ ions irradiation was calculated relative to 60Co γ-rays. RESULTS: The frequencies of dic + r, MN and NPB showed significantly increases in a dose-depended manner after exposure to 12C6+ ions. The distributions of dic + r and MN exhibited overdispersion, while the distribution of NPB agreed with Poisson distribution at all doses. Linear-quadratic equations were established based on the frequencies of dic + r and MN. The dose-response curves of NPB frequencies followed a linear model. The derived RBEM values for dic + r, MN and NPB in human lymphocytes irradiated with 12C6+ ions were 8.07 ± 2.73, 2.69 ± 0.20 and 4.00 ± 2.69 in comparison with 60Co γ-rays. CONCLUSION: The dose-response curves of carbon ions-induced dic + r, MN and NPB were constructed. These results could be helpful to improve radiation risk assessment and dose estimation after exposed to carbon ions irradiation.

The analyses of relationships among nucleotide, synonymous codon and amino acid usages for E2 gene of bovine viral diarrhea virus.

In this study, the systemic analyses of nucleotide, codon and amino acid usages for E2 gene of bovine viral diarrhea virus (BVDV) were carried out for estimating its genetic features. The nucleotide usage pattern at the first codon position was strongly influenced by the overall nucleotide composition, while the nucleotide usage patterns at the second and third codon positions seemed to have little link to the overall nucleotide composition. The result indicated that the mutation pressure from nucleotide composition constraint was not the single evolutionary force for genetic features of BVDV E2 gene. Just 18 out of 59 synonymous codons were similar with synonymous codon usage patterns for E2 gene between BVDV1 and BVDV2, while all synonymous codons which contain CpG dinucleotides were selected at the low level by E2 gene, suggesting that this gene suppressed the usages of codons containing CpG dinucleotides to regulate E2 gene replicate and transcript efficiently and avoid immune response from infected hosts. Amino acid usage patterns of E2 protein were generally different between BVDV1 and BVDV2. The patterns of synonymous codon and amino acid usages for E2 gene might be caused by the equilibrium of evolutionary forces from virus and host. Our work gave new investigations into the role of host origin in the formations of synonymous codon/amino acid usages and the evolutionary trend of BVDV E2 gene. The genetic characteristics that codon/amino acid usages of E2 gene adapted to the internal environment of individual animals might assist in understanding the changes of genetics and antigenicity for newly emerging BVDV.

Analyses of nucleotide, codon and amino acids usages between peste des petits ruminants virus and rinderpest virus.

Peste des petits ruminants virus (PPRV) and rinderpest virus (RPV) are two causative agents of an economically important disease for ruminants (i.e., sheep, cattle and goat). In this study, the nucleotide, codon and amino acid usages for PPRV and RPV have been analyzed by multivariate statistical methods. Relative synonymous codon usage (RSCU) analysis represents that ACG for Thr and GCG for Ala are selected with under-representation in both PPRV and RPV, and AGA for Arg in PPRV and AGG for Arg in RPV are used with over-representation. The usage of nucleotide pair (CpG) tends to be removed from viral genes of the two viruses, suggesting that other evolutionary forces take part in evolutionary processes for viral genes in addition to mutation pressure from nucleotide usage at the third codon position. The overall nucleotide usage of viral gene is not major factor in shaping synonymous codon usage patterns, while the nucleotide usages at the third codon position and the nucleotide pairs play important roles in shaping synonymous codon usage patterns. Although PPRV and RPV are closely related antigenically, the codon and amino acid usage patterns for viral genes represent a significant genetic diversity between PPRV and RPV. Moreover, the overall codon usage trends for viral genes between PPRV and RPV are mainly influenced by mutation pressure from nucleotide usage at the third codon position and translation selection from hosts. Taken together, this is first comprehensive analyses for nucleotide, codon and amino acid usages of viral genes of PPRV and RPV and the findings are expected to increase our understanding of evolutionary forces influencing viral evolutionary pathway and adaptation toward hosts.

Translocator protein mediates the anxiolytic and antidepressant effects of midazolam.

The translocator protein (18 kDa) (TSPO) plays an important role in stress-related disorders, such as anxiety, depression and post-traumatic stress disorder (PTSD), caused by neurosteroids (e.g. allopregnanolone). The present study sought to evaluate the significance of TSPO in anxiolytic and antidepressant effects induced by midazolam. The animals were administrated midazolam (0.25, 0.5 and 1 mg/kg, i.p.) and subjected to behavioral tests, including Vogel-type conflict test, elevated plus-maze test, forced swimming test. Midazolam produced anxiolytic- and antidepressant-like effects Vogel-type conflict test (1 mg/kg, i.p.), elevated plus-maze test (0.5 and 1 mg/kg, i.p.), and forced swimming test (0.5 and 1 mg/kg, i.p.). These effects of Midazolam were totally blocked by the TSPO antagonist PK11195 (3 mg/kg, i.p.). To evaluate the role of allopregnanolone in the anxiolytic- and antidepressant-like effects of midazolam, the animals were decapitated at the end of the behavioral tests. The allopregnanolone levels of the prefrontal cortex and hippocampus were measured by enzyme-linked immunosorbent assay (ELISA). The allopregnanolone level of the prefrontal cortex and hippocampus was increased by midazolam (0.5, 1 mg/kg, i.p.) and the increase was reversed by PK11195 (3 mg/kg, i.p.). Overall, the results indicated that the anxiolytic- and antidepressant-like effects of midazolam were mediated by TSPO, via stimulation of allopregnanolone biosynthesis.

In situ detection of TGF betas, TGF beta receptor II mRNA and telomerase activity in rat cholangiocarcinogenesis.

AIM: Initial report on the in situ examination of the mRNA expression of transforming growth factor betas (TGFbetas), TGFbeta type II receptor (TbetaRII) and telomerase activity in the experimental rat liver tissue during cholangiocarcinogenesis. METHODS: Rat liver cholangiocarcinogenesis was induced by 3'-methyl 4-dimethylazobenzene (3'Me-DAB). In situ hybridization was used to examine the TGFbetas) and TGFbeta type II receptor (TbetaRII) mRNA, in situ TRAP was used to check the telomerase activity in the tissue samples. RESULTS: There was no TGFbetas, TbetaRII mRNA expression or telomerase activity in the control rat cholangiocytes. The expression of TGFbeta1, TbetaRII was increased in regenerative, hyperplastic, dysplastic cholangiocytes and cholangiocarcinoma (CC) cells. The expression of TGFbeta2 mRNA was observed in only a part of hyperplastic, dysplastic cholangiocytes. TGFbeta3 expression was very weak, only in hyperplastic lesion. There was positive telomerase activity in the regenerative, hyperplastic, dysplastic cholangiocytes, and CC cells. Stroma fibroblasts of these lesions also showed positive TGFbetas, TbetaRII mRNA expression and telomerase activity. CONCLUSION: There were TGFbetas, TbetaRII expression and telomerase activity in hyperplastic, dysplastic cholangiocytes, cholangiocarcinoma cells as well as in stroma fibroblasts during cholangiocarcinogenesis. Their expression or activity is important in cholangiocarcinogenesis andstroma formation.

[Establishment and application of pollutant discharge-environment quality model].

In order to explore the mutual influence between pollutant discharge and environment quality, relation models of pollutant discharge and environmental quality were established, and the relationship was divided into four types, low pollutant discharge-high environmental quality, high pollutant discharge-high environmental quality, high pollutant discharge-low environmental quality, and low pollutant discharge-low environmental quality. The evolution paths from one type into another were also discussed. The regional data in 2005 and 2010 was used to validate the pollutant discharge-environmental quality models. The results showed that most regions of China belonged to the high pollutant discharge-low environmental quality type, and the pollutant discharge- environmental quality type didn't vary too much during the 2005-2010 period. In the majority of provinces, the environmental quality index was higher than the pollutant discharge index, and the pollutant discharge quantity overflowed the environmental capacity. The reduction of pollutant discharge quantity should be the most important environmental problem in China. At present, China is in a critical period of environmental governance, and excessive disturbance from economic system to the environment system should be prevented. The results should be helpful for understanding the regional environmental quality situation, on the implementation of pollutant discharge reduction, and the improvement of environmental quality.

[Effect of economic structure adjustment on pollution emission: a case study of COD].

Economic structure adjustment is an important means to reduce the emissions of pollutants. For quantitative analysis of the effect of economic structure adjustment on the reduction of pollution emission, the country was divided into four sub-regions, eastern, northeastern, central and western, and the industry was divided into 39 sectors. Taking chemical oxygen demand (COD) as an example, the influences of regional structure and industry structure adjustment on total emission reduction and emission intensity were analyzed through building a model. The results showed that, in 2000-2010: (1) COD emissions in China were reduced from 1 445 x 10(4) t to 1 238 x 10(4) t, with a total emission of 14 950 x 10(4) t in 11 years, among which the emissions from eastern area occupied the largest proportion, accounting for 35.6%. (2) In the industrial COD emissions, emission from paper and paper products was the largest, accounting for 35.8% of the industrial COD emissions. (3) The economic structure changes in the four areas reduced the COD emissions by 420 x 10(4) t, resulting in a decrease of 1.29% in COD emission intensity. (4) Industrial internal structure changes reduced the COD emissions by 533 x 10(4) t, leading to a decrease of 3.1% in COD emission intensity. The research results have certain reference value in guiding the Chinese economic structure adjustment and achieving the targets of energy-saving and emission reduction.

[Factor decomposition and reduction effect on the changes of industrial wastewater discharge].

After describing the volume of industrial wastewater discharge, economic growth, economic space structure and industrial wastewater discharge intensity, the non-residue complete decomposition model was applied to analyze the effects of three economically factors, which were economic scale, discharge intensity and space structure, on the changes of industrial wastewater discharge quantitatively from 1981 to 2006 in China. Then industrial wastewater reduction effect was computed by use of H-P filter method. The main results could be summarized as follows: (1) The average annual growth of industrial wastewater discharge is 0.25 x 10(8) t, and the scale of economic development, the space structure and the industrial wastewater discharge intensity have different contributions to the change, being 25.9 x 10(8) t, - 25.5 x 10(8) t, -0.16 x 10(8) t respectively. (2) Accumulative quantity of industrial wastewater discharge reduction is 641.8 x 10(8) t from 1981 to 2006 in China. During this period, with the impact of macroeconomic policies, reduction gap has been fluctuating; however, total reduction gap is a positive number. It is to say that actual reduction volume is more than potential reduction one. (3) With the shift of time, potential reduction efficiency tends to increase firstly and then decline. (4) During 1982-1990 and 1997-2006, industry is high-pollution, while during 1991-1996, industry is low-pollution correspondingly.

[Noise-reduction function and its affecting factors of urban plant communities in Shanghai].

The factor analysis on the relationships between excess noise attenuation (decrement after noise propagating 30 m) and 8 structural characteristics of 19 urban plant communities in Shanghai showed that all the plant communities had notable effects on reducing noise, and the noise attenuation ability of the communities was significantly higher than that of lawn (P < 0.01). The plant communities could be divided into three groups base on their noise attenuation ability, i.e., those of > or = 10 dB(A), 6-10 dB(A), and < or = 6 dB(A). The main factors affecting the noise attenuation ability of the communities were leaf area index, average bifurcate height, average height, coverage, and average canopy diameter, and their correlation coefficients with noise attenuation were 0.343, 0.318, 0.285, 0.226 and 0.193, respectively. These five factors had a cumulative contribution rate of 65.47%, suggesting that they should be considered in stress when designing urban greenbelt for noise reduction.