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A comprehensive analysis of three Asiatic black bear mitochondrial genomes (subspecies ussuricus, formosanus and mupinensis), with emphasis on the complete mtDNA sequence of Ursus thibetanus ussuricus (Ursidae) 3个亚洲黑熊(乌苏里亚种、福尔摩沙亚种和穆普尼亚种)线粒体基因组的综合分析,重点研究了熊科熊科熊(Ursus thibetanus ussuricus)线粒体dna的全序列。
Pub Date : 2008-01-01 DOI: 10.1080/19401730802389525
Dae-sik Hwang, Jang‐Seu Ki, D. Jeong, Boa Kim, Bae-Keun Lee, Sang-Hoon Han, Jae-seong Lee
In the present paper, we describe the mitochondrial genome sequence of the Asiatic black bear (Ursus thibetanus ussuricus) with particular emphasis on the control region (CR), and compared with mitochondrial genomes on molecular relationships among the bears. The mitochondrial genome sequence of U. thibetanus ussuricus was 16,700 bp in size with mostly conserved structures (e.g. 13 protein-coding, two rRNA genes, 22 tRNA genes). The CR consisted of several typical conserved domains such as F, E, D, and C boxes, and a conserved sequence block. Nucleotide sequences and the repeated motifs in the CR were different among the bear species, and their copy numbers were also variable according to populations, even within F1 generations of U. thibetanus ussuricus. Comparative analyses showed that the CR D1 region was highly informative for the discrimination of the bear family. These findings suggest that nucleotide sequences of both repeated motifs and CR D1 in the bear family are good markers for species discriminations.
本文描述了亚洲黑熊(Ursus thibetanus ussuricus)的线粒体基因组序列,重点介绍了控制区(CR),并与线粒体基因组比较了熊之间的分子关系。家鼠线粒体基因组序列大小为16700 bp,大部分结构保守(13个蛋白编码基因、2个rRNA基因、22个tRNA基因)。CR由F、E、D、C盒等典型保守结构域和一个保守序列块组成。在不同的熊种中,CR的核苷酸序列和重复基序是不同的,它们的拷贝数也随着种群的不同而变化,即使在U. thibetanus ussuricus的F1代内也是如此。对比分析表明,CR D1区对熊科的鉴别具有较高的信息性。这些发现表明,熊科中重复基序和CR D1的核苷酸序列是物种区分的良好标记。
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引用次数: 53
Genetic diversity analysis of Macaca thibetana based on mitochondrial DNA control region sequences 基于线粒体DNA控制区序列的猕猴遗传多样性分析
Pub Date : 2008-01-01 DOI: 10.1080/19401730802449196
Deming Li, Longqing Fan, J. Ran, H. Yin, Hongxing Wang, Shaobin Wu, B. Yue
Macaca thibetana is a threatened primate species endemic to China. Genetic diversities based on a 476-bp fragment at the 5′-end of the mitochondrial DNA control region HVSI were assessed. Haplotype diversity is high (0.8521), but nucleotide diversity among all haplotypes is only 0.0574. No haplotype was shared between Sichuan (SC) and Huangshan Mountain (HS) populations. Phylogenetic trees, analysis of molecular variance and network analysis consistently indicated that the SC and HS populations are significantly different. They should therefore be conserved as different units, with priority and more attention given to the HS populations.
猕猴是中国特有的濒危灵长类动物。基于线粒体DNA控制区HVSI 5 '端476 bp片段的遗传多样性进行了评估。单倍型多样性较高(0.8521),但各单倍型间核苷酸多样性仅为0.0574。四川(SC)种群与黄山(HS)种群间无单倍型共享。系统进化树、分子变异分析和网络分析一致表明,SC和HS群体存在显著差异。因此,它们应作为不同的单位保存,优先并更多地注意卫生系统人口。
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引用次数: 17
Mito-communications Mito-communications
Pub Date : 2008-01-01 DOI: 10.1080/19401730802308830
R. DeSalle
The correlation of mitochondrial (mt) anomalies with human disease in general, and neurodegenerative disorders in particular, is extensive. Here, we summarize the work of one particularly interesting study utilizing human mtDNA variants to examine neurodegenerative disorders. Blohkin et al. (2008) ask whether mt copy number anomalies are pathology-related to multiple sclerosis (MS). Previous work had determined that there is an age-dependent effect on the mtDNA copy number in cells that are cytochrome oxidase negative (COX 2). In the study reported in the Journal of Molecular Neurosciences the authors examined the correlation of mtDNA copy number with tissue degeneration associated with inflammatory demyelination of COX 2 and COX þ single glial cells associatedwithMS.Theyused real-time PCR of an ND1/18s rDNA amplification system (the 18S rDNA component of the amplification serves as a control or calibrator) to quantify the copy number of mtDNA molecules in several types of postmortem tissues. The tissues examined were normal-appearing gray matter (NAGM) and normalappearing white matter (NAWM) regions and chronic active plaques of MS patients. The authors determined that there is a significantly higher mtDNA copy number in neurons of NAGM than in cells of other MS brain regions.Anage-related decline inmtDNAcopynumber was also observed in neurons of both MS patients and controls. The results of the study exclude a change in copy number as a factor in plaque formation in MS patients. However, the authors suggest that a compensatory replication ofmtDNAormt biosynthesis occurs with neuroaxonal loss in MS. The authors suggest that some features of late-onset MS may be explained by the age-related decline of mtDNA copy number. We direct the reader to Yang et al. (2008) for a recent review of the role of mtDNA anomalies in neurodegenerative disorders.
线粒体(mt)异常与一般人类疾病,特别是神经退行性疾病的相关性是广泛的。在这里,我们总结了一项特别有趣的研究工作,利用人类mtDNA变异来检查神经退行性疾病。Blohkin等人(2008)询问mt拷贝数异常是否与多发性硬化症(MS)病理相关。先前的研究已经确定,细胞色素氧化酶阴性(COX 2)的细胞中mtDNA拷贝数存在年龄依赖性影响。在《分子神经科学杂志》上发表的研究中,作者研究了mtDNA拷贝数与组织变性(与COX 2和COX þ单个胶质细胞的炎症脱髓鞘相关)的相关性。他们使用ND1/18s rDNA扩增系统的实时PCR(扩增的18S rDNA成分作为对照或校准)来量化几种类型死后组织中mtDNA分子的拷贝数。检查的组织是MS患者的正常灰质(NAGM)和正常白质(NAWM)区域和慢性活动性斑块。作者确定NAGM神经元的mtDNA拷贝数明显高于MS脑其他区域的细胞。在MS患者和对照组的神经元中,mtdnacopynumber也观察到与年龄相关的下降。该研究的结果排除了拷贝数变化作为MS患者斑块形成的一个因素。然而,作者认为mtdnaormt生物合成的代偿性复制发生在多发性硬化症的神经轴突丧失中。作者认为,迟发性多发性硬化症的一些特征可能与mtDNA拷贝数的年龄相关下降有关。我们引导读者去看Yang等人(2008)最近关于mtDNA异常在神经退行性疾病中的作用的综述。
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引用次数: 1
Mitochondrial DNA inaugural issue 线粒体DNA首刊
Pub Date : 2008-01-01 DOI: 10.1080/19401730802306032
R. DeSalle
Since their discovery as integral parts of eukaryotic cells, mitochondria have played a primary role in how scientists understand the organic world. These tiny entities are not only the “power houses” of the cell, but they have also been a “power player” in the human endeavor of biological study for several decades. Most of this prominence can be attributed to the genomes of these organelles. The small size of animal mitochondrial genomes (mt-genomes) and the compact nature of both plant and animal mt-genomes make them desirable subjects of study in the biological sciences. As if that was not enough, the “extra value added” quality of mt-genomes being easily manipulated experimentally also makes them excellent and highly desirable tools in the biological sciences.
自从作为真核细胞的组成部分被发现以来,线粒体在科学家如何理解有机世界中起着主要作用。这些微小的实体不仅是细胞的“发电厂”,而且在人类几十年来的生物学研究中也是一个“强有力的参与者”。这种突出的作用大部分可归因于这些细胞器的基因组。动物线粒体基因组(mt-基因组)的小尺寸和植物和动物线粒体基因组的紧凑性质使它们成为生物科学研究的理想对象。似乎这还不够,mt-基因组易于实验操作的“额外附加价值”特性也使它们成为生物科学中极好的、非常理想的工具。
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引用次数: 0
Complete mitochondrial DNA sequence of the yellowfin seabream Acanthopagrus latus and a genomic comparison among closely related sparid species 黄鳍海鳃棘鱼线粒体DNA全序列及近缘种间的基因组比较
Pub Date : 2008-01-01 DOI: 10.1080/19401730802350998
J. Xia, Kuai-fei Xia, Shi-gui Jiang
The complete mitochondrial genome of the yellowfin seabream Acanthopagrus latus was determined in the present study. The genome was 16,609 bp in length and contained 37 genes (2 ribosomal RNA, 22 transfer RNA and 13 protein-coding genes) and the control region (CR), with the content and order of genes being similar to those in typical teleosts. Comparisons of the 37 genes and CR among species indicate the CR was the highest divergent (0.3341), but tRNAGly possesses the lowest genetic variation (0.0542). Much greater p-genetic distances [mean = 0.1559, standard deviation (SD) = 0.0235; n = 1653] for the interspecies level with high frequency (99.4%) than those of the intraspecies level (mean = 0.0098, SD = 0.0090; n = 20) were inferred from 212 Cyt b sequence data, suggesting the Cyt b gene is conserved within Sparidae species and supporting the barcoding validity of Cyt b sequence data for Sparidae species identification. Phylogenetic analysis using amino acid sequences of 13 protein-coding genes supported that the genus Pagrus was not monophyletic, showing the need to re-evaluate the morphological characteristics of Pagrus fishes.
本研究测定了黄鳍鲷棘鱼(Acanthopagrus latus)的线粒体全基因组。该基因组全长16609 bp,包含37个基因(2个核糖体RNA、22个转移RNA和13个蛋白质编码基因)和控制区(CR),基因的含量和顺序与典型硬骨鱼相似。37个基因与种间CR比较表明,CR差异最大(0.3341),而tRNAGly遗传变异最小(0.0542)。更大的p-遗传距离[平均值= 0.1559,标准差(SD) = 0.0235;n = 1653],种间水平出现的频率(99.4%)高于种内水平(平均值= 0.0098,SD = 0.0090;n = 20),表明该基因在Sparidae种内具有保守性,支持了Sparidae种鉴定中Cyt b序列数据的条形码有效性。利用13个蛋白质编码基因的氨基酸序列进行系统发育分析,支持Pagrus属不是单系的,表明需要重新评估Pagrus鱼类的形态特征。
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引用次数: 17
Comparison of the mitochondrial genomes of East Asian Pseudolabrus fishes 东亚假柄鱼线粒体基因组比较
Pub Date : 2008-01-01 DOI: 10.1080/19401730802449204
D. Oh, Se Jae Kim, Yong-Hwan Jung
We determined the complete mitochondrial genomes of Pseudolabrus sieboldi and P. eoethinus, and analyzed the genome organization, codon usage, and transition/transversion mutation ratio of the mitochondrial genome. The mitochondrial genomes of P. sieboldi and P. eoethinus are 16,507 and 16,508 bp in length, respectively, and consisted of 37 genes (13 protein-coding genes, two ribosomal RNAs, and 22 transfer RNAs), which is typical for vertebrate mitochondrial DNA. All protein-coding genes of two species used the initiation codon ATG except the cytochrome c oxidase subunit (CO) 1, which began with GTG as an initiation codon. However, the termination codon for the NADH dehydrogenase subunit (ND) 6 gene encoded with TAA in P. sieboldi, and TAG in P. eoethinus. The 12S and 16S rRNA genes were 949 and 1694 bp, respectively, in P sieboldi, and were 948 and 1693 bp in P. eoethinus. The A+T content of the two rRNA genes were 52.9% in P. sieboldi and 52.5% in P. eoethinus, which is slightly lower than that of other labrid species. The identity of the 13 protein-coding genes ranged between 67% (ND6) and 94% (CO2 and ATP8). The G+C contents of all of the protein-coding genes of P. sieboldi were slightly higher than those of P. eoethinus. Our data contribute to the identification, and further our understanding, of the comparative genetics of Pseudolabrus species distributed in East Asia.
我们测定了希伯尔假刀蛾和伊埃特诺假刀蛾的线粒体全基因组,并分析了线粒体基因组的组织结构、密码子的使用以及线粒体基因组的过渡/翻转突变率。P. sieboldi和P. eoethinus线粒体基因组长度分别为16507和16508 bp,包含37个基因(13个蛋白质编码基因、2个核糖体rna和22个转移rna),具有典型的脊椎动物线粒体DNA特征。除了细胞色素c氧化酶亚基(CO) 1以GTG为起始密码子外,两种物种的蛋白质编码基因均使用起始密码子ATG。然而,NADH脱氢酶亚基(ND) 6基因的终止密码子在P. sieboldi中编码TAA,在P. eoethinus中编码TAG。在P. sieboldi和P. eoethinus中,12S和16S rRNA基因分别为949和1694 bp和948和1693 bp。两种rRNA基因的A+T含量分别为52.9%和52.5%,略低于其他杂种。13个蛋白编码基因的同源性在67% (ND6)和94% (CO2和ATP8)之间。所有蛋白质编码基因的G+C含量均略高于P. eoethinus。我们的数据有助于鉴定和进一步了解分布在东亚的假角蕨的比较遗传学。
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引用次数: 8
Molecular cloning and characterization of a mitochondrial dicarboxylate/tricarboxylate transporter gene in Citrus junos response to aluminum stress 柑橘对铝胁迫响应的线粒体二羧酸/三羧酸转运蛋白基因的克隆与表征
Pub Date : 2008-01-01 DOI: 10.1080/19401730802351012
W. Deng, Keming Luo, Zheng-guo Li, Yingwu Yang
A mitochondrial dicarboxylate/tricarboxylate carrier gene, CjDTC, was isolated from Citrus junos by the rapid amplification of cDNA ends and the Y-shaped adaptor-dependent extension methods. It consisted of a 472-base pair (bp) upstream regulatory region and an 897-bp open reading frame encoding a protein of 299 amino acids. Homologous analysis revealed that CjDTC protein might be a plant dicarboxylate/tricarboxylate carrier protein involved in the mitochondria dicarboxylate/tricarboxylate transport. The putative light responsiveness and salicylic acid responsiveness regulatory elements were identified in the upstream regulatory region of CjDTC. Southern blot analysis demonstrated the presence of a single CjDTC gene located on the genome of citrus. As shown by northern hybridization, CjDTC was expressed in all plant tissues examined and the highest transcript level was observed in roots with significantly lower transcript amounts in leaves and stems. Moreover, real-time polymerase chain reaction analysis demonstrated that CjDTC expression was induced by aluminum treatment, suggesting that CjDTC protein might be involved in the excretion of organic acids and rhizotoxic aluminum tolerance.
利用cDNA末端快速扩增和y型接头依赖延伸方法,从柑桔中分离到线粒体二羧酸盐/三羧酸盐载体基因CjDTC。它包括一个472碱基对(bp)的上游调控区和一个897 bp的开放阅读框,编码299个氨基酸的蛋白。同源分析表明,CjDTC蛋白可能是参与线粒体二羧酸/三羧酸转运的植物二羧酸/三羧酸载体蛋白。在CjDTC上游调控区确定了光响应性调控元件和水杨酸响应性调控元件。Southern blot分析表明,在柑橘基因组中存在一个CjDTC基因。northern杂交结果显示,CjDTC在所有检测的植物组织中均有表达,其中根中转录量最高,叶和茎中转录量显著低于根。实时聚合酶链反应分析表明,铝处理诱导了CjDTC的表达,表明CjDTC蛋白可能参与有机酸的排泄和根毒性铝的耐受性。
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引用次数: 17
Content index 内容索引
Pub Date : 2008-01-01 DOI: 10.1080/19401730802658622
Shu-hong Zhang, Ji-hua Yao, Huai-Dong Song, Lu Wang, Jinging Xue, Mingying Liu, Dong Wu, N. Liu, Qing-Wen Meng, Lei-qiang Li, Shicui Zhang, Chunxin Fan, Zhenhui Liu, Lingyong Li, Xiao-liang Wang, J. Gai, G. Hawkins, D. Meyers, E. Bleecker, Jianjun Shi, D. Cai, Xue J. Chen, H. Sheng, Z. Zhong, Hao (Richard) Zhang, Meirong Bai, Jun Ni, Bo Wan, Xinya Chen, C. Ho, P. Nguyen, J. Harikrishna, R. Rahim, Guidong Yue, Zhenhua Sui, Qiang Gao, Juren Zhang, Keun-Yong Kim, Sang Yoon Lee, Y. Cho, I. Bang, D. S. Kim, Xichun Pan, Min Chen, Yan Liu, Qiang Wang, Lingjiang Zeng, Lianqiang Li, Z. Liao, Qun Shao, Chang Zhao, N. Han
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引用次数: 1
Genetic Mapping of the Gene for SKI-1/S1P Protease (locus Symbol Mbtps 1) to Mouse Chromosome 8 小鼠8号染色体SKI-1/S1P蛋白酶基因(位点符号Mbtps 1)的遗传定位
Pub Date : 2002-01-01 DOI: 10.1080/10425170290030042
H. Tadros, N. Seidah, M. Chrétien, M. Mbikay
Subtilisin/kexin isozyme-1 (SKI-1), otherwise known as Site-1 protease (S1P), is a Golgi proteinase mediating the proteolytic activation of the precursor to sterol-regulated element-binding proteins (SREBPs) 1 and 2, two transcriptional factors that regulate expression of a variety of genes involved in cholesterol and lipid metabolism. Using PCR and RFLP analysis on a panel of genomic DNA from a mouse intersubspecific backcross, we have mapped the SK1-/S1P gene (locus symbol: Mbtps 1) to the distal part of mouse chromosome 8, in a region that exhibits synteny homology to the human chromosome 16q24 region where its orthologue had been previously mapped.
枯草素/酮蛋白同工酶-1 (SKI-1),也被称为Site-1蛋白酶(S1P),是一种高尔基蛋白酶,介导胆固醇调节元件结合蛋白(SREBPs) 1和2前体的蛋白水解活化,SREBPs 1和2是两种转录因子,调节多种参与胆固醇和脂质代谢的基因的表达。通过对小鼠亚种间回交的基因组DNA进行PCR和RFLP分析,我们将SK1-/S1P基因(位点符号:Mbtps 1)定位到小鼠8号染色体的远端部分,该区域与人类染色体16q24区域具有同源性,该区域的同源物先前已被定位。
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引用次数: 3
Isolation and Sequence Analysis of the GlnKamtB 1 amtB 2 Gene Cluster, Encoding a P II Homologue and Two Putative Ammonium Transporters, from Pseudomonas stutzeri A15 stutzeri假单胞菌A15基因GlnKamtB 1 amtB 2基因簇的分离与序列分析
Pub Date : 2002-01-01 DOI: 10.1080/10425170290019928
H. Vermeiren, V. Keijers, J. Vanderleyden
By PCR, using primers based on heterologous amtB genes, an amtB sequence of Pseudomonas stutzeri A15 was amplified. This DNA fragment was used as a probe in Southern hybridisation experiments and resulted in the isolation and sequence analysis of a 6017 u bp genomic fragment of P. stutzeri A15 containing glnKamtB 1 amtB 2. GlnK codes for a homologue of the nitrogen regulatory P II protein, amtB 1 and amtB 2 encode putative ammonium transporters. Whereas a glnKamtB gene cluster is common among bacteria, a tandem repeat of ammonium transporter genes has not been reported before. Apart from the presence of a second amtB gene, the gene organisation on this 6 u kbp fragment is very similar to a particular region in the genome of Pseudomonas aeruginosa PAO1, relatively closely related to P. stutzeri. Furthermore, the amtB 1 gene shows the highest similarity with P. aeruginosa amtB, whereas the amtB 2 gene is more closely related to cyanobacterial amtB genes, which are reported to be monocistronically transcribed and not clustered with glnK homologues. Upstream of glnK, NtrC and RpoN recognition sites can be observed. In the intergenic region of glnKamtB 1 amtB 2 no terminators nor extra promoter sequences were observed, indicating that glnKamtB 1 amtB 2 is possibly transcribed as a nitrogen regulated operon.
采用PCR方法,利用基于异源amtB基因的引物扩增出stutzeri假单胞菌A15的amtB序列。利用该DNA片段作为探针进行南方杂交实验,分离得到了含有glnKamtB 1 amtB 2的stutzeri A15基因组片段6017 u bp,并进行了序列分析。GlnK编码氮调控蛋白的同源物,amtB 1和amtB 2编码推定的铵转运蛋白。虽然glnKamtB基因簇在细菌中很常见,但铵转运体基因的串联重复以前尚未报道。除了存在第二个amtB基因外,该6u kbp片段上的基因组织与铜绿假单胞菌PAO1基因组中的特定区域非常相似,与假单胞菌stutzeri相对密切相关。此外,amtB 1基因与铜绿假单胞菌amtB的相似性最高,而amtB 2基因与蓝藻amtB基因的关系更密切,据报道,蓝藻amtB基因是单顺反转录的,不与glnK同源物聚集。glnK、NtrC和RpoN识别位点的上游可以观察到。在glnKamtB 1 amtB 2的基因间区,没有观察到终止子和额外的启动子序列,表明glnKamtB 1 amtB 2可能是作为氮调控操纵子转录的。
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引用次数: 6
期刊
DNA Sequence
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