Mitochondrial DNA Diversity in the Polish Roma

Mitochondrial DNA variability in the Polish Roma population has been studied by means of hypervariable segment I and II (HVS I and II) sequencing and restriction fragment‐length polymorphism analysis of the mtDNA coding region. The mtDNA haplotypes detected in the Polish Roma fall into the common Eurasian mitochondrial haplogroups (H, U3, K, J1, X, I, W, and M*). The results of complete mtDNA sequencing clearly indicate that the Romani M*‐lineage belongs to the Indian‐specific haplogroup M5, which is characterized by three transitions in the coding region, at sites 12477, 3921 and 709. Molecular variance analysis inferred from mtDNA data reveals that genetic distances between the Roma groups are considerably larger than those between the surrounding European populations. Also, there are significant differences between the Bulgarian Roma (Balkan and Vlax groups) and West European Roma (Polish, Lithuanian and Spanish groups). Comparative analysis of mtDNA haplotypes in the Roma populations shows that different haplotypes appear to demonstrate impressive founder effects: M5 and H (16261–16304) in all Romani groups; U3, I and J1 in some Romani groups. Interestingly, haplogroup K (with HVS I motif 16224‐16234‐16311) found in the Polish Roma sample seems to be specific for Ashkenazi Jewish populations.     

Y Chromosome and Mitochondrial DNA Variation in Lithuanians

The genetic composition of the Lithuanian population was investigated by analysing mitochondrial DNA hypervariable region 1, RFLP polymorphisms and Y chromosomal biallelic and STR markers in six ethnolinguistic groups of Lithuanians, to address questions about the origin and genetic structure of the present day population. There were no significant genetic differences among ethnolinguistic groups, and an analysis of molecular variance confirmed the homogeneity of the Lithuanian population. MtDNA diversity revealed that Lithuanians are close to both Slavic (Indo‐European) and Finno‐Ugric speaking populations of Northern and Eastern Europe. Y‐chromosome SNP haplogroup analysis showed Lithuanians to be closest to Latvians and Estonians. Significant differences between Lithuanian and Estonian Y chromosome STR haplotypes suggested that these populations have had different demographic histories. We suggest that the observed pattern of Y chromosome diversity in Lithuanians may be explained by a population bottleneck associated with Indo‐European contact. Different Y chromosome STR distributions in Lithuanians and Estonians might be explained by different origins or, alternatively, be the result of some period of isolation and genetic drift after the population split.     

Temporal Mitochondrial DNA Variation in the Basque Country: Influence of Post-Neolithic Events

The Basque population has been considered an outlier in a large number of genetic studies, due to its hypothesized antiquity and greater genetic isolation. The present paper deals with an analysis of the mtDNA variability of the historical population of Aldaieta (VI–VII c. AD; Basque Country) which, together with genetic data existing for other prehistoric populations of the Basque Country (4,500–5,000 YBP), permits an appraisal of the hypotheses proposed for the origin of the genetic differentiation of the Basque population. Given that this is an aDNA study, application has been made both of standard precautions, to avoid contamination, and of authentication criteria (analysis of duplicates, replication in an independent laboratory, quantification of target DNA, sequencing and cloning of PCR products). The variability of the mtDNA haplogroups of the historical population of Aldaieta falls within the range of the present‐day populations of Europe's Atlantic fringe, whereas the prehistoric populations of the Basque Country display clear differentiation in relation to all others. Consequently, we suggest that between 5,000–1,500 YBP approximately, there may have been gene flow amongst the western European populations that homogenised mtDNA lineages.     

线粒体肌病患者线粒体DNA的突变分析

目的分析线粒体肌病患者线粒体DNA的突变情况，为疾病诊断提供依据。方法用常规HE、酶组化染色和电镜检查等病理形态学方法对3例线粒体肌病疑似患者进行诊断，并用聚合酶链反应-单链构象多态和DNA测序等方法对患者线粒体DNA中全部22个tRNA基因进行突变筛查。结果3例患者均被确诊为线粒体肌病，其中例1tRNA—VaI基因发生A1627G纯合突变，例2tRNA—Val基因发生A1627G／A杂合突变，例3tRNA—Trp基因发生T5554C突变、tRNA—Arg基因发生A10412C／A杂合突变。结论线粒体DNA中的tRNA基因突变是线粒体肌病的重要病因之一。     

Mitochondrial DNA Variation in Karkar Islanders

We analyzed 375 base pairs (bp) of the first hypervariable region (HVS‐I) of the mitochondrial DNA (mtDNA) control region and intergenic COII/tRNA^Lys 9‐bp deletion from 47 Karkar Islanders (north coast of Papua New Guinea) belonging to the Waskia Papuan language group. To address questions concerning the origin and evolution of this population we compared the Karkar mtDNA haplotypes and haplogroups to those of neighbouring East Asians and Oceanic populations. The results of the phylogeographic analysis show grouping in three different clusters of the Karkar Islander mtDNA lineages: one group of lineages derives from the first Pleistocene settlers of New Guinea‐Island Melanesia, a second set derives from more recent arrivals of Austronesian speaking populations, and the third contains lineages specific to the Karkar Islanders, but still rooted to Austronesian and New Guinea‐Island Melanesia populations. Our results suggest (i) the absence of a strong association between language and mtDNA variation and, (ii) reveal that the mtDNA haplogroups F1a1, M7b1 and E1a, which probably originated in Island Southeast Asia and may be considered signatures of Austronesian population movements, are preserved in the Karkar Islanders but absent in other New Guinea‐Island Melanesian populations. These findings indicate that the Karkar Papuan speakers retained a certain degree of their own genetic uniqueness and a high genetic diversity. We present a hypothesis based on archaeological, linguistic and environmental datasets to argue for a succession of (partial) depopulation and repopulation and expansion events, under conditions of structured interaction, which may explain the variability expressed in the Karkar mtDNA.     

豚鼠线粒体DNA4568缺失与老年性聋的关系

目的 探讨豚鼠听觉器官中线粒体DNA(mitochondrial DNA, mtDNA)4568缺失与老年性聋的关系.方法 将44只豚鼠分为两组A组青年豚鼠22只;B组老年豚鼠22只.再将B组分为B1组(老年听力正常组6只)和B2组(老年聋组16只).应用听觉脑干反应(auditory brainstem response, ABR)测试豚鼠听力阈值,以左耳听阈为评判标准,并提取耳蜗螺旋器、听神经、大脑颞叶组织和外周血中的DNA,采用PCR技术检测mtDNA4568大片段缺失的情况,并与耳聋程度作比较. 结果 老年聋组(B2)豚鼠的ABR平均听阈值为(57.33±4.65)dBSPL,明显高于老年听力正常组B1[(23.00±1.43)dBSPL]和青年组[A组(15.90±1.05)dBSPL];老年组不同器官组织中mtDNA4568缺失率均明显高于青年组;老年聋组耳蜗螺旋器组织和听神经组织中mtDNA4568缺失率明显高于老年听力正常组;而大脑颞叶组织mtDNA4568缺失率在两组间差异无统计学意义;血液中仅极少数存在mtDNA缺失,未纳入统计分析.结论 豚鼠mtDNA4568缺失的发生与老龄有关;与听觉有关的耳蜗螺旋器组织和听神经组织中mtDNA4568缺失与老年性聋有关;大脑颞叶组织和外周血中mtDNA4568缺失与老年性聋的关系尚待进一步研究.     

Mitochondrial DNA and Y-chromosome variation in five eastern Aleut communities: Evidence for genetic substructure in the Aleut population

Since Russian contact in 1741, the Aleut communities of southwestern Alaska have undergone a series of demographic upheavals stemming from forced relocations, disease epidemics, population bottlenecks, and pervasive admixture with European populations. This study investigates the impact of key historical events on the genetic structure of the Aleut population through analysis of mitochondrial and Y-chromosome DNA variation in five eastern Aleut communities. Results from HVS-I sequencing and Y-chromosome typing reveal patterns of variability that exhibit east–west geographic differentiation for the major Aleut haplogroups. This finding is underscored by SAMOVA and Monmonier analyses that identify genetic discontinuities between eastern and western Aleut populations. The majority of Aleut Y-chromosomes were characterized to haplogroups of mostly Russian, Scandinavian and Western European origin (approximately 85%), which is in stark contrast to the 3.6% of Aleut mtDNA lineages identified as non-Native American, and thus indicating a large degree of asymmetrical gene flow between European men and Aleut women. Overall, this study identifies a significant relationship between geography and genetic variation in the Aleut population, with a distinct substructure along an east–west axis that reflects the combined effects of founder events in aggregate island communities, male-biased gene flow from European populations, and the original peopling of the Aleutian Archipelago.     

Population Structure in Contemporary Sweden—A Y-Chromosomal and Mitochondrial DNA Analysis

A population sample representing the current Swedish population was analysed for maternally and paternally inherited markers with the aim of characterizing genetic variation and population structure. The sample set of 820 females and 883 males were extracted and amplified from Guthrie cards of all the children born in Sweden during one week in 2003. 14 Y-chromosomal and 34 mitochondrial DNA SNPs were genotyped. The haplogroup frequencies of the counties closest to Finland, Norway, Denmark and the Saami region in the north exhibited similarities to the neighbouring populations, resulting from the formation of the Swedish nation during the past millennium. Moreover, the recent immigration waves of the 20th century are visible in haplogroup frequencies, and have led to increased diversity and divergence of the major cities. Signs of genetic drift can be detected in several counties in northern as well as in southern Sweden. With the exception of the most drifted subpopulations, the population structure in Sweden appears mostly clinal. In conclusion, our study yielded valuable information of the structure of the Swedish population, and demonstrated the usefulness of biobanks as a source of population genetic research. Our sampling strategy, nonselective on the current population rather than stratified according to ancestry, is informative for capturing the contemporary variation in the increasingly panmictic populations of the world.     

中国朝鲜族群体mtDNA编码区3954-4506nt序列多态性

目的 了解中国朝鲜族群体线粒体DNA(mitochondrial DNA,mtDNA)编码区3954-4506nt的序列多态性.方法 采用PCR产物直接测序方法 对198名吉林省延边朝鲜族自治州朝鲜族无关个体进行单倍型分布调查.结果 在198名无关个体中,共分出21种单倍型.遗传变异度为0.5906,偶合概率为0.4124.测序结果 与Anderson序列比较,共检测出19个变异位点,14个与MITOMAP收录的基因突变相同,5个未见收录.结论 mtDNA编码区多态性位点作为mtDNA控制区多态性位点的补充,联合应用可以提高mtDNA的个体识别能力,为mtDNA在中国朝鲜族法医学鉴定提供了基础数据.     

Mitochondrial DNA Portrait of Latvians: Towards the Understanding of the Genetic Structure of Baltic-Speaking Populations

Mitochondrial DNA (mtDNA) variation was investigated in a sample of 299 Latvians, a Baltic-speaking population from Eastern Europe. Sequencing of the first hypervariable segment (HVS-I) in combination with analysis of informative coding region markers revealed that the vast majority of observed mtDNAs belong to haplogroups (hgs) common to most European populations. Analysis of the spatial distribution of mtDNA haplotypes found in Latvians, as well as in Baltic-speaking populations in general, revealed that they share haplotypes with all neighbouring populations irrespective of their linguistic affiliation. Hence, the results of our mtDNA analysis show that the previously described sharp difference between the Y-chromosomal hg N3 distribution in the paternally inherited gene pool of Baltic-speaking populations and of other European Indo-European speakers does not have a corresponding maternal counterpart.     

Mitochondrial DNA repair: a critical player in the response of cells of the CNS to genotoxic insults

Cells of the CNS are constantly exposed to agents which damage DNA. Although much attention has been paid to the effects of this damage on nuclear DNA, the nucleus is not the only organelle containing DNA. Within each cell, there are hundreds to thousands of mitochondria. Within each mitochondrion are multiple copies of the mitochondrial genome. These genomes are extremely vulnerable to insult and mutations in mitochondrial DNA (mtDNA) have been linked to several neurodegenerative diseases, as well as the normal process of aging. The principal mechanism utilized by cells to avoid DNA mutations is DNA repair. Multiple pathways of DNA repair have been elucidated for nuclear DNA. However, it appears that only base excision repair is functioning in mitochondria. This repair pathway is responsible for the removal of most endogenous damage including alkylation damage, depurination reactions and oxidative damage. Within the rat CNS, there are cell-specific differences mtDNA repair. Astrocytes exhibit efficient repair, whereas, other glial cell types and neuronal cells exhibit a reduced ability to remove lesions from mtDNA. Additionally, a correlation was observed between those cells with reduced mtDNA repair and an increase in the induction of apoptosis. To demonstrate a causative relationship, a strategy of targeting DNA repair proteins to mitochondria to enhance mtDNA repair capacity was employed. Enhancement of mtDNA repair in oligodendrocytes provided protection from reactive oxygen species- and cytokine-induced apoptosis. These experiments provide a novel strategy for protecting sensitive CNS cells from genotoxic insults and thus provide new treatment options for neurodegenerative diseases.     

2型糖尿病患者线粒体基因8个突变位点的研究

目的：探讨线粒体DNA tRNA Leu (UUR)基因及其相邻的ND1基因8个位点的突变与2型糖尿病的关系。 方法： 采用聚合酶链反应-限制性片段长度多态性（PCR-RFLP）的分析方法，对174例2型糖尿病患者和207名健康对照的mtDNA的3 243、3 256、3 290、3 316、3 394、3 421、3 426、3 460和3 593共9个已报道的突变位点同时进行筛选，并采用测序、反向斑点杂交和基因芯片进行方法学比较和确证，对检出的突变位点采用DNASTAR和Antherprot软件进行分析。 结果： 糖尿病组检出3 316(G→A) 突变5例(2.9%)，其中2例为多个位点突变：1例伴随3 256(C→T)和3 688(G→C)，另1例伴随3 606(A→G)；3 394(T→C)突变4例(2.3%)，3 593(T→C)、3 290(T→C)和3 618(T→C)突变各1例(0.6%)； 其中3 606(A→G)、3 618(T→C)和3 688(G→C) 为新突变位点，GenBank登录号为DQ092356；对照组只检出3 316(G→A)突变1例(0.5%)。两组间仅3 394(T→C) 突变率差异显著(P<0.05)。以上8个突变位点的测序、反向斑点杂交和基因芯片检测结果完全一致。3 606(A→G)为Leu的无意义突变，3 618(T→C)为Phe的无意义突变，3 688(G→C)为有意义突变，Ala→Pro,导致ND1蛋白的二级结构发生改变。 结论： 线粒体DNA ND1基因3 316(G→A)突变伴随3 688(G→C)突变，3 394(T→C) 突变可能与2型糖尿病发病有关。     

Mitochondrial DNA amplification in senescent cultures of Podospora anserina: Variability between the retained,amplified sequences

Summary The non-nuclear DNA of a number of independent senescent cultures of Podospora anserina was extracted and studied. In all cases, a specific repetitive DNA (SEN-DNA) arranged in multimeric sets of circular molecules, was identified. Depending on the senescent culture, the SEN-DNA was found either in a band of about same density as the mitochondrial DNA from young mycelia (1.694 g/cm³) or in a band of higher density (1.699 g/cm³). Electron microscopy, restriction enzyme analysis and Southern hybridization experiments allowed us to establish that: (1) SEN-DNAs obtained from independent senescent cultures, both from the same strain and from different strains, can differ in the size of their monomer unit (from 2.5 to 6.3 kb). (2) All SEN-DNAs hybridize with mitochondrial DNA of a young culture and not with nuclear DNA. (3) These SEN-DNAs belong to two classes which hybridize with two non-overlapping regions of the mitochondrial chromosome.     

Wistar大鼠不同组织线粒体DNA相对含量的测定

为了比较Wistar大鼠各组织线粒体DNA的含量,探讨其与组织功能状态的关系,本文应用定量Southern杂交法,以线粒体DNA与核18SrDNA的密度比值作为观察指标,检测Wistar大鼠骨骼肌、心肌、脑、肾及肝组织线粒体DNA的相对含量。结果表明：（1）骨骼肌的线粒体DNA相对含量最高,心、脑及肝肾依次减少（P＜0．05）;（2）肝和肾的线粒体DNA相对含量无显著性差别。说明各组织的线粒体DNA相对含量是有区别的,与其功能状态密切相关,了解各组织线粒体DNA含量的差别有助于研究氧化磷酸化疾病和衰老。同时也提供了一个较好的研究方法。     

再生障碍性贫血线粒体突变与端粒长度相关性的研究

目的：研究再生障碍性贫血患者线粒体突变及端粒长度情况,了解两者间的相关性。方法选择2010~2014年确诊为再生障碍性贫血的患者45例,留取骨髓及口腔黏膜上皮标本以进行线粒体DNA ( mitochondrial DNA, mtDNA)突变和端粒长度的检测。线粒体全测序检测到了151个突变,分布在18个基因中,其中包括了40个沉默突变及28个框移突变。同时使用HBG作为内参基因,检测了再障患者和健康志愿者端粒的相对长度( relative T/S value,端粒长度)。结果分析发现非沉默突变的mtDNA突变与白细胞数、血红蛋白水平及血小板数成负相关。端粒长度与白细胞数、血红蛋白水平及血小板数成正相关性,而且非沉默突变的mtDNA突变与端粒长度呈负相关性。结论研究提示突变导致线粒体氧化呼吸链功能紊乱及端粒的缩短是再障患者骨髓衰竭病程中的一个重要因素,而且这两者还会互相影响。     

Mitochondrial DNA Variation in Mauritania and Mali and their Genetic Relationship to Other Western Africa Populations

Mitochondrial DNA (mtDNA) variation was analyzed in Mauritania and Mali, and compared to other West African samples covering the considerable geographic, ethnic and linguistic diversity of this region. The Mauritanian mtDNA profile shows that 55% of their lineages have a west Eurasian provenance, with the U6 cluster (17%) being the best represented. Only 6% of the sub‐Saharan sequences belong to the L3A haplogroup a frequency similar to other Berber speaking groups but significantly different to the Arabic speaking North Africans. The historic Arab slave trade may be the main cause of this difference. Only one HV west Eurasian lineage has been detected in Mali but 40% of the sub‐Saharan sequences belong to cluster L3A. The presence of L0a representatives demonstrates gene flow from eastern regions. Although both groups speak related dialects of the Mande branch, significant genetic differences exist between the Bambara and Malinke groups. The West African genetic variation is well structured by geography and language, but more detailed ethnolinguistic clustering suggest that geography is the main factor responsible for this differentiation.     

Mitochondrial DNA Rearrangements in Health and Disease—A Comprehensive Study

Mitochondrial DNA (mtDNA) rearrangements cause a wide variety of highly debilitating and often fatal disorders and have been implicated in aging and age‐associated disease. Here, we present a meta‐analytical study of mtDNA deletions (n = 730) and partial duplications (n = 37) using information from more than 300 studies published over the last 30 years. We show that both classes of mtDNA rearrangements are unequally distributed among disorders and their breakpoints have different genomic locations. We also demonstrate that 100% of cases with sporadic mtDNA deletions and 97.3% with duplications have no breakpoints in the 16,071 breakage hotspot site, in contrast with deletions from healthy and aged tissues. Notably, most deletions removing a section of the D‐loop are found in tumors. Deleted mtDNA molecules lacking the origin of L‐strand replication (O_L) represent only 9.5% of all reported cases, whereas extra origins of replication occur in all duplications. As previously shown for deletions, imperfect stretches of homology are common in duplication breakpoints. Finally, we provide a dedicated Website with detailed information on deleted/duplicated mtDNA regions to facilitate the design of efficient methods for identification and screening of rearranged mitochondrial genomes (available at http://www.portugene.com/mtDNArearrangements.html ).     

Mitochondrial DNA mutations in a patient with sex reversal and clinical features consistent with Fraser syndrome

We describe a 20-year-old 46,XY woman, with clinical findings of Fraser syndrome and three mitochondrial DNA (mtDNA) mutations of Leber hereditary optic neuropathy. The patient had microphthalmia, blindness, widely spaced nipples, bifid ureter, syndactyly of the toes, and mental retardation. Sonography showed the presence of a uterus and intra-abdominal gonads. The proband was screened for mtDNA mutations because of chronic gastrointestinal pseudo-obstruction, urinary tract dysmotility, seizures, mental retardation and persistent macrocytosis, as well as the intermittent elevation of methylmalonic acid. Analysis of point mutations by multiplex polymerase chain reaction and allele-specific oligonucleotide dot-blot hybridization revealed three homoplasmic mtDNA mutations, T14484C, T4216C, and T3394C. This represents a unique case with sex reversal, Fraser-like syndrome, and mitochondrial disease.     

Evaluating Mitochondrial DNA Variation in Autism Spectrum Disorders

Despite the increasing speculation that oxidative stress and abnormal energy metabolism may play a role in Autism Spectrum Disorders (ASD), and the observation that patients with mitochondrial defects have symptoms consistent with ASD, there are no comprehensive published studies examining the role of mitochondrial variation in autism. Therefore, we have sought to comprehensively examine the role of mitochondrial DNA (mtDNA) variation with regard to ASD risk, employing a multi‐phase approach. In phase 1 of our experiment, we examined 132 mtDNA single‐nucleotide polymorphisms (SNPs) genotyped as part of our genome‐wide association studies of ASD. In phase 2 we genotyped the major European mitochondrial haplogroup‐defining variants within an expanded set of autism probands and controls. Finally in phase 3, we resequenced the entire mtDNA in a subset of our Caucasian samples (～400 proband‐father pairs). In each phase we tested whether mitochondrial variation showed evidence of association to ASD. Despite a thorough interrogation of mtDNA variation, we found no evidence to suggest a major role for mtDNA variation in ASD susceptibility. Accordingly, while there may be attractive biological hints suggesting the role of mitochondria in ASD our data indicate that mtDNA variation is not a major contributing factor to the development of ASD.     

Mutagenesis by Transient Misalignment in the Human Mitochondrial DNA Control Region

To study spontaneous base substitutions in human mitochondrial DNA (mtDNA), we reconstructed the mutation spectra of the hypervariable segments I and II (HVS I and II) using published data on polymorphisms from various human populations. Classification analysis revealed numerous mutation hotspots in HVS I and II mutation spectra. Statistical analysis suggested that strand dislocation mutagenesis, operating in monotonous runs of nucleotides, plays an important role in generating base substitutions in the mtDNA control region. The frequency of mutations compatible with the primer strand dislocation in the HVS I region was almost twice as high as that for template strand dislocation. Frequencies of mutations compatible with the primer and template strand dislocation models are almost equal in the HVS II region. Further analysis of strand dislocation models suggested that an excess of pyrimidine transitions in mutation spectra, reconstructed on the basis of the L‐strand sequence, is caused by an excess of both L‐strand pyrimidine transitions and H‐strand purine transitions. In general, no significant bias toward parent H‐strand‐specific dislocation mutagenesis was found in the HVS I and II regions.