In most eukaryotes,oxidative phosphorylation(OXPHOS)is the main energy production process and it involves both mitochondrial and nuclear genomes.The close interaction between the two genomes is critical for the coordi...In most eukaryotes,oxidative phosphorylation(OXPHOS)is the main energy production process and it involves both mitochondrial and nuclear genomes.The close interaction between the two genomes is critical for the coordinated function of the OXPHOS process.Some bivalves show doubly uniparental inheritance(DUI)of mitochondria,where two highly divergent mitochondrial genomes,one inherited through eggs(F-type)and the other through sperm(M-type),coexist in the same individual.However,it remains a puzzle how nuclear OXPHOS genes coordinate with two divergent mitochondrial genomes in DUI species.In this study,we compared transcription,polymorphism,and synonymous codon usage in the mitochondrial and nuclear OXPHOS genes of the DUI species Ruditapes philippinarum using sex-and tissue-specific transcriptomes.Mitochondrial and nuclear OXPHOS genes showed different transcription profiles.Strong co-transcription signal was observed within mitochondrial(separate for F-and M-type)and within nuclear OXPHOS genes but the signal was weak or absent between mitochondrial and nuclear OXPHOS genes,suggesting that the coordination between mitochondrial and nuclear OXPHOS subunits is not achieved transcriptionally.McDonald-Kreitman and frequency-spectrum based tests indicated that M-type OXPHOS genes deviated significantly from neutrality,and that F-type and M-type OXPHOS genes undergo different selection patterns.Codon usage analysis revealed that mutation bias and translational selection were the major factors affecting the codon usage bias in different OXPHOS genes,nevertheless,translational selection in mitochondrial OXPHOS genes appears to be less efficient than nuclear OXPHOS genes.Therefore,we speculate that the coordination between OXPHOS genes may involve post-transcriptional/translational regulation.展开更多
In this study, 414 whole protein-coding sequences (238 004 codons) of alternatively spliced genes of human chromosome 1 have been employed to explore the patterns of codon usage bias among genes. Overall codon usage d...In this study, 414 whole protein-coding sequences (238 004 codons) of alternatively spliced genes of human chromosome 1 have been employed to explore the patterns of codon usage bias among genes. Overall codon usage data analysis indicates that G- and C-ending codons are predominant in the genes. The base usage in all three codon positions suggests a selection-mutation balance. Multivariate statistical analysis reveals that the codon usage variation has a strong positive correlation with the expressivities of the genes (r=0.5790, P<0.0001). All 27 codons identified as optimal are G- and C-ending codons. Correlation analysis shows a strong negative correlation between the gene length and codon adaptation index value (r=0.2252, P<0.0001), and a significantly positive correlation between the gene length and Nc values (r=0.1876, P<0.0001). These results suggest that the comparatively shorter genes in the genes have higher codon usage bias to maximize translational efficiency, and selection may also contribute to the reduction of highly expressed proteins.展开更多
目的系统梳理针药结合治疗哮喘的临床研究文献,利用数据挖掘探讨其潜在的临床优势与针灸选穴规律。方法检索收录在中国知网、维普资讯中文期刊服务平台、万方数据知识服务平台、中国生物医学文献数据库及PubMed、Web of Science、Embase...目的系统梳理针药结合治疗哮喘的临床研究文献,利用数据挖掘探讨其潜在的临床优势与针灸选穴规律。方法检索收录在中国知网、维普资讯中文期刊服务平台、万方数据知识服务平台、中国生物医学文献数据库及PubMed、Web of Science、Embase、Scoups等数据库中的近20年临床研究文献,建立“针药结合治疗哮喘数据库”,运用频数统计及SPSS Modeler 18.0、Gephi0.10.1软件进行文献挖掘分析。结果①针刺优势以靶器官功能与多项血生化指标(免疫功能指标、血清炎症因子)的调节为主;中药优势为能进一步增强肺通气功能;针刺与中药联合应用可显著提高哮喘患者临床疗效。②针刺治疗哮喘重要程度排名前5位的腧穴依次为肺俞、定喘、足三里、肾俞、膻中,关联规则分析显示定喘-肺俞支持度最高,其次为脾俞-肺俞;足太阳膀胱经与手太阴肺经为常用经脉。③体现针刺优势的腧穴处方重视局部选穴,循经选穴,上下配穴。结论针药结合治疗哮喘是提高疗效的主要原因,其临床优势在于局部与整体兼顾,“标本同治,从肺论治,局部选穴,远近配穴”的临床取穴规律是针刺优势的体现之一,这为针药结合的科学应用提供了新思路。展开更多
基金supported by the China Scholarship Council,Italian Ministry of Education University and Research(MIUR)FIR2013 Programme(RBFR13T97A to F.G.)MIUR SIR Programme(RBSI14G0P5 to L.M.)Canziani Bequest to F.G.,and“Ricerca Fondamentale Orientata”(RFO)from the University of Bologna to F.G.and L.M.
文摘In most eukaryotes,oxidative phosphorylation(OXPHOS)is the main energy production process and it involves both mitochondrial and nuclear genomes.The close interaction between the two genomes is critical for the coordinated function of the OXPHOS process.Some bivalves show doubly uniparental inheritance(DUI)of mitochondria,where two highly divergent mitochondrial genomes,one inherited through eggs(F-type)and the other through sperm(M-type),coexist in the same individual.However,it remains a puzzle how nuclear OXPHOS genes coordinate with two divergent mitochondrial genomes in DUI species.In this study,we compared transcription,polymorphism,and synonymous codon usage in the mitochondrial and nuclear OXPHOS genes of the DUI species Ruditapes philippinarum using sex-and tissue-specific transcriptomes.Mitochondrial and nuclear OXPHOS genes showed different transcription profiles.Strong co-transcription signal was observed within mitochondrial(separate for F-and M-type)and within nuclear OXPHOS genes but the signal was weak or absent between mitochondrial and nuclear OXPHOS genes,suggesting that the coordination between mitochondrial and nuclear OXPHOS subunits is not achieved transcriptionally.McDonald-Kreitman and frequency-spectrum based tests indicated that M-type OXPHOS genes deviated significantly from neutrality,and that F-type and M-type OXPHOS genes undergo different selection patterns.Codon usage analysis revealed that mutation bias and translational selection were the major factors affecting the codon usage bias in different OXPHOS genes,nevertheless,translational selection in mitochondrial OXPHOS genes appears to be less efficient than nuclear OXPHOS genes.Therefore,we speculate that the coordination between OXPHOS genes may involve post-transcriptional/translational regulation.
基金the National Natural Science Foundation of China (No. 60171038) and the Science and Technology Ministry of China (No. 2001CCA01400)
文摘In this study, 414 whole protein-coding sequences (238 004 codons) of alternatively spliced genes of human chromosome 1 have been employed to explore the patterns of codon usage bias among genes. Overall codon usage data analysis indicates that G- and C-ending codons are predominant in the genes. The base usage in all three codon positions suggests a selection-mutation balance. Multivariate statistical analysis reveals that the codon usage variation has a strong positive correlation with the expressivities of the genes (r=0.5790, P<0.0001). All 27 codons identified as optimal are G- and C-ending codons. Correlation analysis shows a strong negative correlation between the gene length and codon adaptation index value (r=0.2252, P<0.0001), and a significantly positive correlation between the gene length and Nc values (r=0.1876, P<0.0001). These results suggest that the comparatively shorter genes in the genes have higher codon usage bias to maximize translational efficiency, and selection may also contribute to the reduction of highly expressed proteins.
文摘目的系统梳理针药结合治疗哮喘的临床研究文献,利用数据挖掘探讨其潜在的临床优势与针灸选穴规律。方法检索收录在中国知网、维普资讯中文期刊服务平台、万方数据知识服务平台、中国生物医学文献数据库及PubMed、Web of Science、Embase、Scoups等数据库中的近20年临床研究文献,建立“针药结合治疗哮喘数据库”,运用频数统计及SPSS Modeler 18.0、Gephi0.10.1软件进行文献挖掘分析。结果①针刺优势以靶器官功能与多项血生化指标(免疫功能指标、血清炎症因子)的调节为主;中药优势为能进一步增强肺通气功能;针刺与中药联合应用可显著提高哮喘患者临床疗效。②针刺治疗哮喘重要程度排名前5位的腧穴依次为肺俞、定喘、足三里、肾俞、膻中,关联规则分析显示定喘-肺俞支持度最高,其次为脾俞-肺俞;足太阳膀胱经与手太阴肺经为常用经脉。③体现针刺优势的腧穴处方重视局部选穴,循经选穴,上下配穴。结论针药结合治疗哮喘是提高疗效的主要原因,其临床优势在于局部与整体兼顾,“标本同治,从肺论治,局部选穴,远近配穴”的临床取穴规律是针刺优势的体现之一,这为针药结合的科学应用提供了新思路。
