DNA SequencePub Date : 2008-01-01DOI: 10.1080/19401730802389525
Dae-sik Hwang, Jang‐Seu Ki, D. Jeong, Boa Kim, Bae-Keun Lee, Sang-Hoon Han, Jae-seong Lee
{"title":"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)","authors":"Dae-sik Hwang, Jang‐Seu Ki, D. Jeong, Boa Kim, Bae-Keun Lee, Sang-Hoon Han, Jae-seong Lee","doi":"10.1080/19401730802389525","DOIUrl":"https://doi.org/10.1080/19401730802389525","url":null,"abstract":"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.","PeriodicalId":11381,"journal":{"name":"DNA Sequence","volume":"3 1","pages":"418 - 429"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79235109","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
DNA SequencePub Date : 2008-01-01DOI: 10.1080/19401730802449196
Deming Li, Longqing Fan, J. Ran, H. Yin, Hongxing Wang, Shaobin Wu, B. Yue
{"title":"Genetic diversity analysis of Macaca thibetana based on mitochondrial DNA control region sequences","authors":"Deming Li, Longqing Fan, J. Ran, H. Yin, Hongxing Wang, Shaobin Wu, B. Yue","doi":"10.1080/19401730802449196","DOIUrl":"https://doi.org/10.1080/19401730802449196","url":null,"abstract":"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.","PeriodicalId":11381,"journal":{"name":"DNA Sequence","volume":"1 1","pages":"446 - 452"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90660249","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
DNA SequencePub Date : 2008-01-01DOI: 10.1080/19401730802308830
R. DeSalle
{"title":"Mito-communications","authors":"R. DeSalle","doi":"10.1080/19401730802308830","DOIUrl":"https://doi.org/10.1080/19401730802308830","url":null,"abstract":"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.","PeriodicalId":11381,"journal":{"name":"DNA Sequence","volume":"60 1","pages":"373 - 375"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90953814","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
DNA SequencePub Date : 2008-01-01DOI: 10.1080/19401730802306032
R. DeSalle
{"title":"Mitochondrial DNA inaugural issue","authors":"R. DeSalle","doi":"10.1080/19401730802306032","DOIUrl":"https://doi.org/10.1080/19401730802306032","url":null,"abstract":"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.","PeriodicalId":11381,"journal":{"name":"DNA Sequence","volume":"321 1","pages":"371 - 372"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76104625","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
DNA SequencePub Date : 2008-01-01DOI: 10.1080/19401730802350998
J. Xia, Kuai-fei Xia, Shi-gui Jiang
{"title":"Complete mitochondrial DNA sequence of the yellowfin seabream Acanthopagrus latus and a genomic comparison among closely related sparid species","authors":"J. Xia, Kuai-fei Xia, Shi-gui Jiang","doi":"10.1080/19401730802350998","DOIUrl":"https://doi.org/10.1080/19401730802350998","url":null,"abstract":"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.","PeriodicalId":11381,"journal":{"name":"DNA Sequence","volume":"381 1","pages":"385 - 393"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74255432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
DNA SequencePub Date : 2008-01-01DOI: 10.1080/19401730802449204
D. Oh, Se Jae Kim, Yong-Hwan Jung
{"title":"Comparison of the mitochondrial genomes of East Asian Pseudolabrus fishes","authors":"D. Oh, Se Jae Kim, Yong-Hwan Jung","doi":"10.1080/19401730802449204","DOIUrl":"https://doi.org/10.1080/19401730802449204","url":null,"abstract":"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.","PeriodicalId":11381,"journal":{"name":"DNA Sequence","volume":"310 1","pages":"453 - 460"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76443088","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
DNA SequencePub Date : 2008-01-01DOI: 10.1080/19401730802351012
W. Deng, Keming Luo, Zheng-guo Li, Yingwu Yang
{"title":"Molecular cloning and characterization of a mitochondrial dicarboxylate/tricarboxylate transporter gene in Citrus junos response to aluminum stress","authors":"W. Deng, Keming Luo, Zheng-guo Li, Yingwu Yang","doi":"10.1080/19401730802351012","DOIUrl":"https://doi.org/10.1080/19401730802351012","url":null,"abstract":"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.","PeriodicalId":11381,"journal":{"name":"DNA Sequence","volume":"7 1","pages":"376 - 384"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87604281","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
DNA SequencePub Date : 2008-01-01DOI: 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
{"title":"Content index","authors":"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","doi":"10.1080/19401730802658622","DOIUrl":"https://doi.org/10.1080/19401730802658622","url":null,"abstract":"","PeriodicalId":11381,"journal":{"name":"DNA Sequence","volume":"80 1","pages":"497 - 502"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79069475","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
DNA SequencePub Date : 2002-01-01DOI: 10.1080/10425170290030042
H. Tadros, N. Seidah, M. Chrétien, M. Mbikay
{"title":"Genetic Mapping of the Gene for SKI-1/S1P Protease (locus Symbol Mbtps 1) to Mouse Chromosome 8","authors":"H. Tadros, N. Seidah, M. Chrétien, M. Mbikay","doi":"10.1080/10425170290030042","DOIUrl":"https://doi.org/10.1080/10425170290030042","url":null,"abstract":"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.","PeriodicalId":11381,"journal":{"name":"DNA Sequence","volume":"74 1","pages":"109 - 111"},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79492280","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
DNA SequencePub Date : 2002-01-01DOI: 10.1080/10425170290019928
H. Vermeiren, V. Keijers, J. Vanderleyden
{"title":"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","authors":"H. Vermeiren, V. Keijers, J. Vanderleyden","doi":"10.1080/10425170290019928","DOIUrl":"https://doi.org/10.1080/10425170290019928","url":null,"abstract":"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.","PeriodicalId":11381,"journal":{"name":"DNA Sequence","volume":"143 1","pages":"67 - 74"},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79625449","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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