Synonymous codon selection in the hepatitis B virus translation initiation region.

Hepatitis B virus (HBV) infection is a major health problem worldwide. This virus and its hosts are often fated to continual co-evolutionary interactions. Codon usage analysis has significance for studies of co-evolution between viruses, their hosts, and mRNA translation. Adaptation of the overall codon usage pattern of HBV to that of humans is estimated using the synonymous codon usage value (RSCU), and the synonymous codon usage biases for the translation initiation region (TIR) of HBV are analyzed by calculation of the usage fluctuation of each synonymous codon along the TIR (the first 50 codon sites of the whole coding sequence of HBV). With respect to synonymous codon usage, our results demonstrated that HBV had no significant tendency to select over-represented codons, but had a significant tendency to select certain under-represented codons in the viral genome. Within the three common HBV hosts, 14 of 59 codons had a similar usage pattern, suggesting that mutation pressure from this DNA virus played an important role in the formation of virus synonymous codon usage. In addition, there was no obvious trend for the codons with relatively low energy to be highly selected in the TIR of HBV, suggesting that the synonymous codon usage patterns for the TIR might not be affected by the nucleotide sequence secondary structure; however, synonymous codon usage in the TIR of HBV was influenced by the overall codon usage patterns of the hosts to some degree. Our results suggest that mutation pressure from HBV plays an important role in the formation of synonymous codon usage of the viral genome, while translation selection from the hosts contributes to virus translational fine-tuning.

Overall codon usage pattern of enterovirus 71.

Hand, foot, and mouth disease (HFMD) is a systemic illness in children and is usually caused by enterovirus 71 (EV71). To provide new insights into the genetic features of EV71 and the relationship between the overall codon usage pattern of this virus and that of humans, values for relative synonymous codon usage (RSCU), effective number of codons (ENC), codon adaptation index (CAI), and nucleotide composition were calculated and analyzed. The relationship between ENC values and (G+C)3% suggests that, although nucleotide composition plays an important role in shaping the overall codon usage pattern of this virus, other factors also affect this pattern. In addition, the negative correlation between the CAI value and (G+C)3% suggests that the secondary structure of the EV71 coding sequence caused by its nucleotide composition can affect gene expression. Moreover, there was no significant correlation between ENC and CAI, suggesting that gene expression does not play a role in shaping the overall codon usage pattern of EV71. The overall codon usage pattern of the EV71 virus is only partly similar to the general codon pattern of human, suggesting that, although EV71 has co-evolved with humans for extended periods, mutation pressure played an important role in shaping the virus's overall codon usage pattern. These results revealed that the EV71 virus has developed a subtle strategy during evolution for adapting to environmental changes in its host cells solely by means of mutation pressure.

The decrease of endothelial progenitor cells caused by high altitude may lead to coronary heart disease.

OBJECTIVE: The purpose of this study was to explore the relationship between the number of endothelial progenitor cells (EPCs) and coronary heart disease (CHD). PATIENTS AND METHODS: A total of 24 patients with CHD were chosen from Lanzhou City and Xianyang City, and then, 24 healthy controls who matched the CHD group in gender, age and address were chosen as control group. C-reactive protein (CRP) and c-reaction protein (hs-CRP) were detected. The levels of interleukin-8 (IL-8), vascular endothelial growth factor (VEGF), homocysteine (Hcy), hypoxia-inducible factor-1 (HIF-1α) and stromal cell-derived factor 1 (SDF-1α) were detected. RESULTS: The number of EPCs in control groups was both increased compared with CHD group (p<0.05). The number of EPCs in Xianyang control group was increased compared with Lanzhou control group (p<0.05). Compared with the control group, the levels of TC, LDL and CRP in the CHD group were higher (p<0.05). Compared with Lanzhou control group, Hcy level was decreased in Lanzhou CHD group (p<0.05). Compared with Xianyang control group, the levels of IL-8 and VEGF were increased, but the levels of HIF-1α and Hcy were decreased in the Xianyang CHD group (p<0.05). The expressions of IL-8, VEGF, Hcy and HIF-1α were increased in Lanzhou control group than the Xianyang control group (p<0.05). In Lanzhou CHD group, Spearman correlation analysis showed that the number of EPCs was negatively related to hs-CRP content (r=-0.631, p<0.05). CONCLUSIONS: The decrease of EPCs caused by high altitude may increase the expressions of various cytokines, leading to the occurrence of CHD.

[Protective effects and mechanism of keratinocyte growth factor combined with hypoxia inducible factor-1α on intestinal crypt epithelial cells of rats with hypoxia stress].

Objective: To investigate the protective effects and mechanism of keratinocyte growth factor (KGF) combined with hypoxia inducible factor-1α (HIF-1α) on intestinal crypt epithelial cells (IEC-6) of rats with hypoxia stress. Methods: (1) The routinely cultured IEC-6 of rats were collected and divided into normoxia blank group, normoxia KGF group, normoxia HIF-1α group, and normoxia combine group, according to the random number table, and then the previous mediums were respectively replaced with dulbecco's modified eagle medium (DMEM), medium with 0.5 ng/mL KGF, medium with 10.0 ng/mL HIF-1α, and medium with 0.5 ng/mL KGF and 30.0 ng/mL HIF-1α. And the cells were cultured in cell incubator with oxygen volume fraction of 21% for 24 hours. (2) Another batch of routinely cultured IEC-6 were collected and divided into normoxia control group, hypoxia control group, hypoxia KGF group, hypoxia HIF-1α group, and hypoxia combine group, according to the random number table. The previous mediums were replaced with DMEM, DMEM, medium with 0.5 ng/mL KGF, medium with 10.0 ng/mL HIF-1α, and medium with 0.5 ng/mL KGF and 30.0 ng/mL HIF-1α respectively. And then, the cells in normoxia control group were cultured routinely for 24 hours, and cells in the other 4 groups were cultured in cells incubator of 3 gases, with oxygen volume fraction of 5% for 24 hours. Cells cultured in normoxic and hypoxic incubators were collected, with 3 samples in each group, and morphological changes of cells were observed with optical microscope. Cells cultured in normoxic and hypoxic incubators were collected, with 3 samples in each group, and survival rates of cells were detected by cell count kit 8. Cells in normoxia control group and cells cultured in hypoxic incubator were collected, with 3 samples in each group. The cell cycle changes and apoptosis rates were detected by flow cytometer, the content of adenosine triphosphate (ATP) was detected by ultraviolet spectrophotometer, and protein expression of p53 was detected by Western blotting. Data were processed with one-way analysis of variance and least significant difference test. Results: (1) After being cultured for 24 h, cells cultured in normoxic incubator grew well with oval or round shapes and clear cytoplasm, and cells cultured in hypoxic incubator showed irregular shapes such as fusiform or starlike shape, with black particle in cytoplasm. (2) After being cultured for 24 h, cell survival rates of normoxia blank group, normoxia KGF group, normoxia HIF-1α group, and normoxia combine group were (107.4±8.7)%, (109.8±2.9)%, (115.8±7.4)%, and (112.8±10.6)% respectively. There was no significantly statistical difference in general comparison of cell survival rates among the above groups (F=0.685, P=0.586). After being cultured for 24 h, cell survival rates of hypoxia control group, hypoxia KGF group, hypoxia HIF-1α group, and hypoxia combine group were (35.1±4.6)%, (52.9±6.8)%, (56.2±3.1)%, and (71.2±9.6)% respectively, which were significantly lower than (106.3±12.3)% of normoxia control group (P<0.001). Survival rates of cells in hypoxia KGF group, hypoxia HIF-1α group, and hypoxia combine group were significantly higher than the rate of cells in hypoxia control group (P=0.023, 0.009, <0.001). Survival rate of cells in hypoxia combine group was significantly higher than the rates of cells in hypoxia KGF group and hypoxia HIF-1α group (P=0.017, 0.045). (3) After being cultured for 24 h, percentage of cells in G1 phase in hypoxia control group was significantly higher than that of cells in normoxia control group (P=0.030), percentages of cells in S phase in hypoxia control group, hypoxia KGF group, and hypoxia HIF-1α group were obviously lower than the percentage of cells in normoxia control group (P=0.020, 0.031, 0.026), and percentages of cells in different phases in other groups were close to those of cells in normoxia control group (P=0.516, 0.107, 0.052, 0.985, 0.637, 0.465, 0.314, 0.591). After being cultured for 24 h, percentages of cells in G1 phase in hypoxia control group, hypoxia KGF group, and hypoxia HIF-1α group were obviously higher than the percentage of cells in hypoxia combine group (P=0.001, 0.030, 0.014), and percentages of cells in S phase in the above 3 groups were obviously lower than the percentage of cells in hypoxia combine group (P=0.001, 0.012, 0.010). (4) After being cultured for 24 h, compared with that of cells in normoxia control group, apoptosis rate of cells in hypoxia control group obviously increased (P=0.018), and apoptosis rate of cells in hypoxia combine group obviously decreased (P=0.008). After being cultured for 24 h, compared with that of cells in hypoxia control group, apoptosis rates of cells in hypoxia KGF group and hypoxia combine group obviously decreased (P=0.004, 0.001). Apoptosis rate of cells in hypoxia combine group was obviously lower than those of cells in hypoxia KGF group and hypoxia HIF-1α group (P=0.032, 0.002). (5) After being cultured for 24 h, compared with that of cells in normoxia control group, the content of ATP of cells in hypoxia combine group changed unobviously (P=0.209), and content of ATP of cells in the other groups obviously decreased (P= <0.001, 0.001, 0.002). Content of ATP of cells in hypoxia HIF-1α group and hypoxia combine group was obviously higher than that of cells in hypoxia control group (P=0.044, 0.001). Content of ATP of cells in hypoxia combine group was obviously higher than that of cells in hypoxia KGF group and hypoxia HIF-1α group (P=0.011, 0.020). (6) After being cultured for 24 h, protein expressions of p53 of cells in hypoxia control group, hypoxia KGF group, and hypoxia HIF-1α group were obviously higher than that of cells in normoxia control group (P<0.001), and protein expression of p53 of cells in hypoxia combine group was obviously lower than those of cells in hypoxia control group, hypoxia KGF group, and hypoxia HIF-1α group (P=0.001, 0.001, 0.002). Conclusions: KGF combined with HIF-1α have significant protective effects on IEC-6 of rats with hypoxia stress, and can improve its survival in hypoxic environment by inhibiting cell cycle arrest, reducing the level of apoptosis, and increasing level of energy metabolism.