Mitochondrial DnaPub Date : 2015-06-01Epub Date: 2013-10-01DOI: 10.3109/19401736.2013.836510
Jianjun Xun, Zhenxing Li, Xiaolei Song, Xueshi Wang
{"title":"Identification of sequence polymorphisms in the D-loop region of mitochondrial DNA as risk biomarkers for malignant fibrous histiocytoma.","authors":"Jianjun Xun, Zhenxing Li, Xiaolei Song, Xueshi Wang","doi":"10.3109/19401736.2013.836510","DOIUrl":"https://doi.org/10.3109/19401736.2013.836510","url":null,"abstract":"<p><p>Single nucleotide polymorphisms (SNPs) in the mitochondrial DNA Displacement-loop (D-loop) region particularly in a highly polymorphic homopolymeric C stretch named D310 have been reported to be associated with cancer risk in several types of cancer. In order to evaluate the frequency of D-loop SNPs in a large series of malignant fibrous histiocytoma (MFH) and establish correlations with cancer risk, we sequenced the D-loop of 92 MFH patients and analyzed their use as predictive biomarkers for MFH risk. The minor alleles of nucleotides 73G, 151T were associated with an increased risk for MFH patients, whereas the alleles of nucleotides 16,298C, 152C, and insertion of C at the site 315 (located within the D310) were associated with a decreased risk for MFH patients. These results suggest that SNPs in the mitochondrial D-loop should be considered as a biomarker which may be useful for the early detection of MFH in individuals at risk of this cancer. </p>","PeriodicalId":49805,"journal":{"name":"Mitochondrial Dna","volume":"26 3","pages":"380-3"},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3109/19401736.2013.836510","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31773563","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}
Mitochondrial DnaPub Date : 2015-06-01Epub Date: 2014-06-18DOI: 10.3109/19401736.2014.926533
Zhuo Chen, Jie Zhang, Xiaofei Zhai, Yanjun Zhu, Xiaohong Chen
{"title":"Complete mitochondrial genome of the green odorous frog Odorrana margaretae (Anura: Ranidae).","authors":"Zhuo Chen, Jie Zhang, Xiaofei Zhai, Yanjun Zhu, Xiaohong Chen","doi":"10.3109/19401736.2014.926533","DOIUrl":"https://doi.org/10.3109/19401736.2014.926533","url":null,"abstract":"<p><p>The complete mitochondrial genome (mitogenome) of the green odorous frog Odorrana margaretae (Anura: Ranidae) has been studied. The 17,903 bp circular genome contains the typical complement of 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a control region. The AT content of the overall base compositon of H-strand is 56% and the length of control region is 2501 bp with 63.8% AT content. The arrangement of the protein-coding and ribosomal RNA genes was the same as that found in other anurans. The cluster of rearranged LTPF tRNA genes and the translocation of tRNA(His) gene into the D-loop region are observed. </p>","PeriodicalId":49805,"journal":{"name":"Mitochondrial Dna","volume":"26 3","pages":"487-8"},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3109/19401736.2014.926533","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32432803","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}
Mitochondrial DnaPub Date : 2015-06-01Epub Date: 2014-01-27DOI: 10.3109/19401736.2013.855734
Sujune Tsai, Jiann-Chu Chen, Emma Spikings, Jan-Jung Li, Chiahsin Lin
{"title":"Degradation of mitochondrial DNA in cryoprotectant-treated hard coral (Echinopora spp.) oocytes.","authors":"Sujune Tsai, Jiann-Chu Chen, Emma Spikings, Jan-Jung Li, Chiahsin Lin","doi":"10.3109/19401736.2013.855734","DOIUrl":"https://doi.org/10.3109/19401736.2013.855734","url":null,"abstract":"<p><p>A critical step for successful cryopreservation is to determine the optimal cryoprotectant treatment that can provide protective effects against cryoinjury during freezing and with minimal toxicity. Most cryoprotectants have chemical and osmotic effects when used at high concentrations. Cryoprotectants can damage coral mitochondrial distributions and membrane potentials, which results in reduced ATP production. As mitochondrial DNA (mtDNA) encodes for components of the electron transport chain (ETC) and plays a critical role in ATP synthesis capacity, we determined the effects of cryoprotectants on mtDNA in hard coral (Echinopora spp.) oocytes using quantitative real-time PCR. Our results showed that an insult from a cryoprotectant may be compensated for by the genetic defense mechanisms of these cells. Methanol was found to have the least effect on coral oocytes with regard to their energy status. A single oocyte without cryoprotectant treatment produced an average of 4,220,645 ± 169,990 mtDNA copies, which was greater than that in mammals. However, relatively lower mtDNA copy numbers (<2,000,000) were observed when oocytes were treated with dimethyl sulfoxide (DMSO), propylene glycol (PG), ethylene glycol (EG), or glycerol at a concentration of 3 M for 20 min. These results provide direct evidence that hard coral (Echinopora spp.) oocytes are extremely susceptible to cryoprotectants and support the concerns with regard to the adverse effects of cryoprotectants. </p>","PeriodicalId":49805,"journal":{"name":"Mitochondrial Dna","volume":"26 3","pages":"420-5"},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3109/19401736.2013.855734","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32058056","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}
Mitochondrial DnaPub Date : 2015-06-01Epub Date: 2015-01-30DOI: 10.3109/19401736.2014.1003821
Xiaoyang Wang, Yuan Huang, Nian Liu, Jing Yang, Fumin Lei
{"title":"Seven complete mitochondrial genome sequences of bushtits (Passeriformes, Aegithalidae, Aegithalos): the evolution pattern in duplicated control regions.","authors":"Xiaoyang Wang, Yuan Huang, Nian Liu, Jing Yang, Fumin Lei","doi":"10.3109/19401736.2014.1003821","DOIUrl":"https://doi.org/10.3109/19401736.2014.1003821","url":null,"abstract":"<p><p>The control region (CR) of the mitochondrial DNA exhibits important functions in replication and transcription, and duplications of the CR have been reported in a wide range of animal groups. In most cases, concerted evolution is expected to explain the high similarity of duplicated CRs. In this paper, we present seven complete mitochondrial genome sequences from the bushtits (genus Aegithalos), in which we discovered two duplicated CRs, and try to survey the evolution pattern of these duplicated CRs. We also found that the duplicated CRs within one individual were almost identical, and variations were concentrated in two sections, one located between a poly-C site and a potential TAS (termination associated sequence) element, the other one located at the 3' end of the duplicated CRs. The phylogenetic analyses of paralogous CRs showed that the tree topology were depending on whether the two high variable regions at the upstream of TAS element and the 3'end of duplicated CRs: when they were concluded, the orthologous copies were closely related; when they were excluded, the paralogous copies in the same lineages were closely related. This may suggest the role of recombination in the evolution of duplicated CRs. Consequently, the recombination was detected, and the breakpoints were found at ∼120 bp (the upstream of the potential TAS element) and ∼1150 bp of the alignment of duplicated CRs. According to these results, we supposed that homologous recombination occurred between paralogous CRs from different mtDNA molecule was proposed as the most suitable mechanism for concerted evolution of the duplicated CRs, and the recombination took place in every replication cycle, so that most part of the duplicated regions remain identical within an individual, while the 5' and 3'end of the duplicated CRs were not involved in recombination, and evolved independently. </p>","PeriodicalId":49805,"journal":{"name":"Mitochondrial Dna","volume":"26 3","pages":"350-6"},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3109/19401736.2014.1003821","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33012675","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}
Mitochondrial DnaPub Date : 2015-06-01Epub Date: 2013-09-19DOI: 10.3109/19401736.2013.834427
Yijing Liu, Luqi Xing, Jianqiang Mi, Lan Chen, Yanxiao Tian
{"title":"Mitochondrial DNA mutations may not be frequent in patients with oral cancer.","authors":"Yijing Liu, Luqi Xing, Jianqiang Mi, Lan Chen, Yanxiao Tian","doi":"10.3109/19401736.2013.834427","DOIUrl":"https://doi.org/10.3109/19401736.2013.834427","url":null,"abstract":"Dear Sir,We read with great interest the report by Mondal & Ghosh (2013) concerning the role of mitochondrial DNA (mtDNA) mutations in tobacco-related oral cancer from Northeast of India. On the ba...","PeriodicalId":49805,"journal":{"name":"Mitochondrial Dna","volume":"26 3","pages":"331-3"},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3109/19401736.2013.834427","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31742206","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}
Mitochondrial DnaPub Date : 2015-06-01Epub Date: 2013-09-23DOI: 10.3109/19401736.2013.830298
Ying-Xiong Hu, Qiao Zhou, Yong Song, Da-Qing Chen, Yun Li
{"title":"Complete mitochondrial genome of the smallscale yellowfin, Plagiognathops microlepis (Teleostei: Cypriniformes: Cyprinidae).","authors":"Ying-Xiong Hu, Qiao Zhou, Yong Song, Da-Qing Chen, Yun Li","doi":"10.3109/19401736.2013.830298","DOIUrl":"https://doi.org/10.3109/19401736.2013.830298","url":null,"abstract":"<p><p>The smallscale yellowfin, Plagiognathops microlepis is the only one species in the genus Plagiognathops. In this study, we sequenced the complete mitochondrial genome of the P. microlepis. The complete mitogenome was 16,623 bp in size, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and 1 control region. It has the typical circular molecule structure of vertebrate's mitochondrial genome. The whole base composition was estimated to be 30.60% A, 25.19% T, 27.32% C and 16.89% G with AT bias of 55.79%. The complete mitogenome of P. microlepis provides the basis for preservation of genetic resources and genetic breeding studies on this species. </p>","PeriodicalId":49805,"journal":{"name":"Mitochondrial Dna","volume":"26 3","pages":"463-4"},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3109/19401736.2013.830298","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31753409","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}
Mitochondrial DnaPub Date : 2015-06-01Epub Date: 2013-09-25DOI: 10.3109/19401736.2013.836509
Hengxing Ba, Fuhe Yang, Xiumei Xing, Chunyi Li
{"title":"Classification and phylogeny of sika deer (Cervus nippon) subspecies based on the mitochondrial control region DNA sequence using an extended sample set.","authors":"Hengxing Ba, Fuhe Yang, Xiumei Xing, Chunyi Li","doi":"10.3109/19401736.2013.836509","DOIUrl":"https://doi.org/10.3109/19401736.2013.836509","url":null,"abstract":"<p><p>To further refine the classification and phylogeny of sika deer subspecies, the well-annotated sequences of the complete mitochondrial DNA (mtDNA) control region of 13 sika deer subspecies from GenBank were downloaded, aligned and analyzed in this study. By reconstructing the phylogenetic tree with an extended sample set, the results revealed a split between Northern and Southern Mainland Asia/Taiwan lineages, and moreover, two subspecies, C.n.mantchuricus and C.n.hortulorum, were existed in Northern Mainland Asia. Unexpectedly, Dybowskii's sika deer that was thought to originate from Northern Mainland Asia joins the Southern Mainland Asia/Taiwan lineage. The genetic divergences were ranged from 2.1% to 4.7% between Dybowskii's sika deer and all the other established subspecies at the mtDNA sequence level, which suggests that the maternal lineage of uncertain sika subspecies in Europe had been maintained until today. This study also provides a better understanding for the classification, phylogeny and phylogeographic history of sika deer subspecies. </p>","PeriodicalId":49805,"journal":{"name":"Mitochondrial Dna","volume":"26 3","pages":"373-9"},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3109/19401736.2013.836509","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31756395","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}
Mitochondrial DnaPub Date : 2015-06-01Epub Date: 2013-10-09DOI: 10.3109/19401736.2013.840591
Derek C Johnson, Sadeep Shrestha, Howard W Wiener, Robert Makowsky, Ashish Kurundkar, Craig M Wilson, Brahim Aissani
{"title":"Mitochondrial DNA diversity in the African American population.","authors":"Derek C Johnson, Sadeep Shrestha, Howard W Wiener, Robert Makowsky, Ashish Kurundkar, Craig M Wilson, Brahim Aissani","doi":"10.3109/19401736.2013.840591","DOIUrl":"https://doi.org/10.3109/19401736.2013.840591","url":null,"abstract":"<p><p>Genetic polymorphism along mitochondrial DNA (mtDNA) defines population-specific signatures called mtDNA haplogroups. Estimation of mtDNA haplogroup distribution may be prone to errors, notably if the study sample is not drawn from a multicenter cohort. Here, we report on mtDNA diversity in a sample of African American individuals (n = 343) enrolled in a multicenter cohort. Sequencing of the hypervariable regions I and II of the D-loop control region showed that the most common mitochondrial variants are 73G, 146C, 150T, 152C, 189G, 16278T, and 16311C. In agreement with the published data, we observed 17 common mtDNA haplogroups: L0, L1, L1b, L1c, L2, L2a, L2b, L2c, L2e, L3, L3b, L3d, L3e, L3f, L3h, L3x, and L4. The most commonly observed haplogroup is L2a (19.8%), followed by L1b (10.2%). Overall, the observed mtDNA haplogroup distribution in our study is similar to those published for the African American and the African populations. </p>","PeriodicalId":49805,"journal":{"name":"Mitochondrial Dna","volume":"26 3","pages":"445-51"},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3109/19401736.2013.840591","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31788000","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mitochondrial DnaPub Date : 2015-06-01Epub Date: 2014-01-17DOI: 10.3109/19401736.2013.873931
Chun-Hong Li, Wei Shi, Wan-Yu Shi
{"title":"Mitochondrial genome sequence of Egyptian swift Rock Pigeon (Columba livia breed Egyptian swift).","authors":"Chun-Hong Li, Wei Shi, Wan-Yu Shi","doi":"10.3109/19401736.2013.873931","DOIUrl":"https://doi.org/10.3109/19401736.2013.873931","url":null,"abstract":"<p><p>The Egyptian swift Rock Pigeon is a breed of fancy pigeon developed over many years of selective breeding. In this work, we report the complete mitochondrial genome sequence of Egyptian swift Rock Pigeon. The total length of the mitogenome was 17,239 bp and its overall base composition was estimated to be 30.2% for A, 24.0% for T, 31.9% for C and 13.9% for G, indicating an A-T (54.2%)-rich feature in the mitogenome. It contained the typical structure of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a non-coding control region (D-loop region). The complete mitochondrial genome sequence of Egyptian swift Rock Pigeon would serve as an important data set of the germplasm resources for further study. </p>","PeriodicalId":49805,"journal":{"name":"Mitochondrial Dna","volume":"26 3","pages":"479-80"},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3109/19401736.2013.873931","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32041746","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}
Mitochondrial DnaPub Date : 2015-06-01Epub Date: 2015-02-04DOI: 10.3109/19401736.2014.1003906
Rui-Hua Zhang, Wen-Xiao He, Tong Xu
{"title":"Characterization of the complete mitochondrial genome of the king pigeon (Columba livia breed king).","authors":"Rui-Hua Zhang, Wen-Xiao He, Tong Xu","doi":"10.3109/19401736.2014.1003906","DOIUrl":"https://doi.org/10.3109/19401736.2014.1003906","url":null,"abstract":"<p><p>The king pigeon is a breed of pigeon developed over many years of selective breeding primarily as a utility breed. In the present work, we report the complete mitochondrial genome sequence of king pigeon for the first time. The total length of the mitogenome was 17,221 bp with the base composition of 30.14% for A, 24.05% for T, 31.82% for C, and 13.99% for G and an A-T (54.22 %)-rich feature was detected. It harbored 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one non-coding control region (D-loop region). The arrangement of all genes was identical to the typical mitochondrial genomes of pigeon. The complete mitochondrial genome sequence of king pigeon would serve as an important data set of the germplasm resources for further study. </p>","PeriodicalId":49805,"journal":{"name":"Mitochondrial Dna","volume":"26 3","pages":"491-2"},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3109/19401736.2014.1003906","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33025940","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}