目的探讨指甲游离缘及毛发中抽提核DNA的方法,并对抽提结果进行评估。方法采集5名健康成人志愿者指甲游离缘、发根及发干样本各30份。分别用无水乙醇和蒸馏水浸泡样本,去除外源性DNA。每份指甲游离缘样本为3mg指甲游离缘碎片;每份发根...目的探讨指甲游离缘及毛发中抽提核DNA的方法,并对抽提结果进行评估。方法采集5名健康成人志愿者指甲游离缘、发根及发干样本各30份。分别用无水乙醇和蒸馏水浸泡样本,去除外源性DNA。每份指甲游离缘样本为3mg指甲游离缘碎片;每份发根或发干样本各为3段0.3～0.5cm发根或发干。分别采用酚氯仿法、Chelex-100法和QIAamp DNA Investigator试剂盒法抽提3种样本的核DNA,并运用PCR扩增对抽提DNA进行评估。扩增片段位于不同染色体上,长度分别为188、248、300和741bp。PCR扩增产物用1.8%琼脂糖凝胶电泳检测。为探讨样本量对抽提结果的影响,任意取指甲游离缘1、3和5mg,发根及发干各1、3和5根重复实验,并比较结果。初步探讨增加Taq酶量对黑色素抑制的消除作用。结果在3种抽提方法中长度为248bp的引物扩增成功率均为最高。指甲游离缘样本使用试剂盒法抽提核DNAPCR扩增成功率显著高于酚氯仿法及Chelex-100法(P<0.05)。发干样本使用试剂盒法抽提核DNAPCR扩增成功率显著高于酚氯仿法(P<0.05)。发根样本3种方法抽提核DNAPCR扩增成功率差异无统计学意义(P>0.05)。指甲游离缘样本的PCR扩增成功率显著高于发根及发干样本(P<0.05),发根和发干样本的PCR扩增成功率差异无统计学意义。试剂盒法抽提指甲游离缘、发根和发干核DNAPCR扩增成功率随样本量增加而提高。酚氯仿法和Chelex-100法抽提发根或发干样本核DNAPCR扩增成功率随样本量增加呈下降趋势,提示可能存在黑色素抑制作用。增加Taq酶量对于消除黑色素抑制有一定作用。结论①3种抽提方法均能成功从指甲游离缘及毛发中抽提到核DNA,试剂盒法成功率最高。②指甲游离缘、发根和发干均可作为核DNA采样源,从指甲游离缘抽提DNA成功率最高。展开更多
Codon usage bias varies considerably among genomes and even within the genes of the same genome. In eukaryotic organisms, energy production in the form of oxidative phosphorylation （OXPHOS） is the only process under...Codon usage bias varies considerably among genomes and even within the genes of the same genome. In eukaryotic organisms, energy production in the form of oxidative phosphorylation （OXPHOS） is the only process under control of both nuclear and mitochondrial genomes. Although factors affecting codon usage in a single genome have been studied, this has not occurred when both interactional genomes are involved. Consequently, we investigated whether or not other factors influence codon usage of coevolved genes. We used Drosophila melanogaster as a model organism. Our χ^2 test on the number of codons of nuclear and mitochondrial genes involved in the OXPHOS system was significantly different （χ^2= 7945.16, P 〈 0.01）. A plot of effective number of codons against GC3s content of nuclear genes showed that few genes lie on the expected curve, indicating that codon usage was random. Correspondence analysis indicated a significant correlation between axis 1 and codon adaptation index （R = 0.947, P 〈 0.01） in every nuclear gene sequence. Thus, codon usage bias of nuclear genes appeared to be affected by translational selection. Correlation between axis 1 coordinates and GC content （R = 0.814, P 〈 0.01） indicated that the codon usage of nuclear genes was also affected by GC composition. Analysis of mitochondrial genes did not reveal a significant correlation between axis 1 and any parameter. Statistical analyses indicated that codon usages of both nDNA and mtDNA were subjected to context-dependent mutations.展开更多
Based on two mitochondrial genes (cyt b, ND4) and one nuclear gene (c-mos), we explored the relationships within the Asian pit viper genus Gloydius. In total, 23 samples representing 10 species were analyzed. All phyl...Based on two mitochondrial genes (cyt b, ND4) and one nuclear gene (c-mos), we explored the relationships within the Asian pit viper genus Gloydius. In total, 23 samples representing 10 species were analyzed. All phylogenetic analyses support a monophyletic Gloydius with two major clades, one comprising G. brevicaudus, G. blomhoffii, and G. ussuriensis with the sister clade consisting of G. intermedius, G. saxatilis, G. halys and G. shedaoensis. The relationships among the three montane species G. strauchi, G. qinlingensis and G. liupanensis, as well as the two monophyletic groups, are unstable, and discussed. Divergence date estimation indicates that Gloydius lineage formed 15 Ma and diversification of the genus occurred at 9.89 Ma. Issues regarding the taxonomy of this genus are discussed where necessary.展开更多
The present study is in agreement with the hypothesis that the variation of ecological conditions in three rivers in northern Israel—the Dan, Hasbani and Hermon Rivers—affects the genetic variations of the species C...The present study is in agreement with the hypothesis that the variation of ecological conditions in three rivers in northern Israel—the Dan, Hasbani and Hermon Rivers—affects the genetic variations of the species Capoeta damascina. Using mitochondrial DNA (mtDNA), cytochrome b gene (Cytb), 16S and nuclear DNA (nDNA), and Random Amplified Polymorphic DNA (RAPD), four different clusters were found in the Cytb of the Hasbani and Hermon Rivers and only two in the Dan River. Moreover, the clusters in the Hasbani River differed from those found in the Hermon River. A similar result was found when an analysis was made of a different sequence from five different haplotype frequencies using the MegAlign program, the lowest being in the Dan River (only two haplotypes) and the highest in the Hasbani River (four haplotypes). The analysis of molecular variance of Cytb and 16S (AMOVA) for individuals of C. damascina from eight populations in northern Israel showed significant differences between the rivers and the populations. The analysis by mitochondrial 16S of haplotype frequencies of C. damascina populations in the rivers in northern Israel was very low compared to Ctb. Sixteen different haplotypes were found in the different rivers: eight in the Hasbani River, seven in the Dan River and only five in the Hermon River.展开更多
文摘目的探讨指甲游离缘及毛发中抽提核DNA的方法,并对抽提结果进行评估。方法采集5名健康成人志愿者指甲游离缘、发根及发干样本各30份。分别用无水乙醇和蒸馏水浸泡样本,去除外源性DNA。每份指甲游离缘样本为3mg指甲游离缘碎片;每份发根或发干样本各为3段0.3～0.5cm发根或发干。分别采用酚氯仿法、Chelex-100法和QIAamp DNA Investigator试剂盒法抽提3种样本的核DNA,并运用PCR扩增对抽提DNA进行评估。扩增片段位于不同染色体上,长度分别为188、248、300和741bp。PCR扩增产物用1.8%琼脂糖凝胶电泳检测。为探讨样本量对抽提结果的影响,任意取指甲游离缘1、3和5mg,发根及发干各1、3和5根重复实验,并比较结果。初步探讨增加Taq酶量对黑色素抑制的消除作用。结果在3种抽提方法中长度为248bp的引物扩增成功率均为最高。指甲游离缘样本使用试剂盒法抽提核DNAPCR扩增成功率显著高于酚氯仿法及Chelex-100法(P<0.05)。发干样本使用试剂盒法抽提核DNAPCR扩增成功率显著高于酚氯仿法(P<0.05)。发根样本3种方法抽提核DNAPCR扩增成功率差异无统计学意义(P>0.05)。指甲游离缘样本的PCR扩增成功率显著高于发根及发干样本(P<0.05),发根和发干样本的PCR扩增成功率差异无统计学意义。试剂盒法抽提指甲游离缘、发根和发干核DNAPCR扩增成功率随样本量增加而提高。酚氯仿法和Chelex-100法抽提发根或发干样本核DNAPCR扩增成功率随样本量增加呈下降趋势,提示可能存在黑色素抑制作用。增加Taq酶量对于消除黑色素抑制有一定作用。结论①3种抽提方法均能成功从指甲游离缘及毛发中抽提到核DNA,试剂盒法成功率最高。②指甲游离缘、发根和发干均可作为核DNA采样源,从指甲游离缘抽提DNA成功率最高。
基金supported by the National Natural Science Foundation of China (No.30770302 and 30570970)the Program of Ministry of Science and Technology of the Republic of China (No.2006FY110500)partially by the National Science Fund for Fostering Talents in Basic Research (NSFC-J0630964/J0109)
文摘Codon usage bias varies considerably among genomes and even within the genes of the same genome. In eukaryotic organisms, energy production in the form of oxidative phosphorylation （OXPHOS） is the only process under control of both nuclear and mitochondrial genomes. Although factors affecting codon usage in a single genome have been studied, this has not occurred when both interactional genomes are involved. Consequently, we investigated whether or not other factors influence codon usage of coevolved genes. We used Drosophila melanogaster as a model organism. Our χ^2 test on the number of codons of nuclear and mitochondrial genes involved in the OXPHOS system was significantly different （χ^2= 7945.16, P 〈 0.01）. A plot of effective number of codons against GC3s content of nuclear genes showed that few genes lie on the expected curve, indicating that codon usage was random. Correspondence analysis indicated a significant correlation between axis 1 and codon adaptation index （R = 0.947, P 〈 0.01） in every nuclear gene sequence. Thus, codon usage bias of nuclear genes appeared to be affected by translational selection. Correlation between axis 1 coordinates and GC content （R = 0.814, P 〈 0.01） indicated that the codon usage of nuclear genes was also affected by GC composition. Analysis of mitochondrial genes did not reveal a significant correlation between axis 1 and any parameter. Statistical analyses indicated that codon usages of both nDNA and mtDNA were subjected to context-dependent mutations.
基金partially funded by the National Natural Science Foundation of China(NSFC 30870290,NSFC 30970334,NSFC 31071892)the Program for New Century Excellent Talents in University(NCET-08-0908)
文摘Based on two mitochondrial genes (cyt b, ND4) and one nuclear gene (c-mos), we explored the relationships within the Asian pit viper genus Gloydius. In total, 23 samples representing 10 species were analyzed. All phylogenetic analyses support a monophyletic Gloydius with two major clades, one comprising G. brevicaudus, G. blomhoffii, and G. ussuriensis with the sister clade consisting of G. intermedius, G. saxatilis, G. halys and G. shedaoensis. The relationships among the three montane species G. strauchi, G. qinlingensis and G. liupanensis, as well as the two monophyletic groups, are unstable, and discussed. Divergence date estimation indicates that Gloydius lineage formed 15 Ma and diversification of the genus occurred at 9.89 Ma. Issues regarding the taxonomy of this genus are discussed where necessary.
文摘The present study is in agreement with the hypothesis that the variation of ecological conditions in three rivers in northern Israel—the Dan, Hasbani and Hermon Rivers—affects the genetic variations of the species Capoeta damascina. Using mitochondrial DNA (mtDNA), cytochrome b gene (Cytb), 16S and nuclear DNA (nDNA), and Random Amplified Polymorphic DNA (RAPD), four different clusters were found in the Cytb of the Hasbani and Hermon Rivers and only two in the Dan River. Moreover, the clusters in the Hasbani River differed from those found in the Hermon River. A similar result was found when an analysis was made of a different sequence from five different haplotype frequencies using the MegAlign program, the lowest being in the Dan River (only two haplotypes) and the highest in the Hasbani River (four haplotypes). The analysis of molecular variance of Cytb and 16S (AMOVA) for individuals of C. damascina from eight populations in northern Israel showed significant differences between the rivers and the populations. The analysis by mitochondrial 16S of haplotype frequencies of C. damascina populations in the rivers in northern Israel was very low compared to Ctb. Sixteen different haplotypes were found in the different rivers: eight in the Hasbani River, seven in the Dan River and only five in the Hermon River.
