Mitochondrial DNA polymorphisms and extraversion.

Mitochondria is the major site of energy production in cells, therefore, mitochondrial abnormality may affect functions of organs including the brain, which constantly requires high levels of energy consumption. Previous studies have suggested a role of mitochondria and their DNA polymorphisms in neuro-psychiatric disorders, including Alzheimer's disease, Parkinson's disease, schizophrenia and bipolar mood disorder. Thus, we hypothesized that mitochondrial DNA polymorphisms might be related with the development of personality. The present study investigated a role of two mitochondrial DNA polymorphisms, the C5178A and A10398G, in personality traits evaluated using the NEO PI-R scores in 238 healthy Japanese volunteers. Subjects with the 5178A genotype showed significantly higher extraversion score than those with the 5178C genotype (P = 0.027), while no significant association was observed between the C5178A polymorphism and other scores. No significant association was found between the A10398G polymorphism and any scores. Regarding the 5178-10398 haplotype, the score of extraversion, not other scores, was significantly associated with the A-G haplotype (P = 0.042). Although further studies are recommended for the confirmation, the result may suggest a role of the mitochondrial DNA polymorphism in the personality trait.     

Mitochondrial DNA analysis: polymorphisms and pathogenicity

The investigation of mtDNA disease can be relatively straightforward if a person has a recognisable phenotype and if it is possible to identify a known pathogenic mtDNA mutation. The difficulties arise when no known mtDNA defect can be found, or when the clinical abnormalities are complex and not easily matched to those of the more common mitochondrial disorders. We will describe here the difficulties that can be encountered during the identification of pathogenic mtDNA mutations and the approaches that can be used to confirm, or eliminate, a likely pathogenic role, in either single gene diseases or in multifactorial disorders.     

Mitochondrial DNA polymorphisms in Thailand

Nucleotide sequences of the D-loop region of human mitochondrial DNA from six small ethnic groups of Thailand i.e., Hill tribes (Lisu and Mussur), Phuthai, Lao Song, Chong, and aboriginal Sakai, were analyzed. The sequences were compared with those of native Thai populations from two provinces, Chiang Mai and Khon Kaen. Based on a comparison of the 563-bp sequences in 215 Thai individuals, 137 different sequence types were observed. Of these, 124 were unique to their respective populations, whereas 13 were shared between two to five populations. The intergenic COII/tRNA^Lys 9-bp deletion was observed in every Thai population examined, except for the Sakai, with varying frequencies ranging from 18% to 40%. The D-loop sequences variation, and phylogenetic analysis, suggested that the 9-bp deletion had occurred in a very ancient ancestry of Southeast Asians, although multiple origins of the deletion cannot be ruled out. Genetic distances, based on net nucleotide diversities, between populations revealed that the Sakai were distantly related to the other Thai populations, while the Lao Song and Chong were closely related to each other. Close genetic affinities were also observed among the Hill tribes, Phuthai, and native northeast Thai (Khon Kaen), indicating that they may share some degree of the common ancestral maternal lineages. Received: October 23, 2000 / Accepted: December 4, 2000     

Mitochondrial DNA polymorphisms in bipolar disorder

BACKGROUND: Previous studies suggested mitochondrial abnormality in bipolar disorder: (1) possible contribution of parent-of-origin effect in transmission of bipolar disorder; (2) abnormal brain phosphorus metabolism detected by phosphorus-31 magnetic resonance spectroscopy; (3) comorbidity of affective disorders in patients with mitochondrial encephalopathy; (4) increased levels of the 4977bp deletion of mitochondrial DNA (mtDNA) in the postmortem brains. We investigated mtDNA polymorphisms in association with bipolar disorder. METHODS: Twelve PCR fragments including all tRNA genes were examined by the single-strand conformation polymorphism method in 43 bipolar patients. All observed polymorphisms were sequenced. Association of these polymorphisms with bipolar disorder was examined by restriction fragment length polymorphism method in 135 bipolar patients and 187 controls. RESULTS: In total, we found 28 polymorphisms including 14 polymorphisms that have not been reported previously. The A10398G polymorphism was significantly associated with bipolar disorder (10398A genotype: 33.1% in bipolar, 22.2% in the control, P<0.05). Although this difference was not significant after Bonferroni correction, the CA haplotype of the 5178 and 10398 polymorphisms was still significantly associated with bipolar disorder (CA haplotype: 33.6% in bipolar, 16.8% in control, P<0.001). Three rare mutations substituting evolutionary conserved bases; A5539G in tRNA(Trp) gene, A5747G in the origin of L-strand replication, and A8537G in ATPase subunit-6 and -8 genes, were found in patients with family history in which maternal transmission was suspected. DISCUSSION: The 5178C/10398A haplotype in mtDNA may be a risk factor of bipolar disorder (odds ratio, 2.4). Pathophysiological significance of rare mtDNA mutations needs to be verified in the future. This finding may imply the pathophysiological significance of mtDNA in bipolar disorder.     

Mitochondrial DNA haplogroup K is associated with a lower risk of Parkinson's disease in Italians

It has been proposed that European mitochondrial DNA (mtDNA) haplogroups J and K, and their shared 10398G single-nucleotide polymorphism (SNP) in the ND3 gene, are protective from Parkinson's disease (PD). We evaluated the distribution of the different mtDNA haplogroups in a large cohort of 620 Italian patients with adult-onset (>50, <65 years of age) idiopathic PD vs two groups of ethnic-matched controls. Neither the frequencies of haplogroup J nor that of 10398G were significantly different. However, the frequency of haplogroup K was significantly lower in PD. Stratification by sex and age indicated that the difference in the distribution of haplogroup K was more prominent in >50 year old males. In spite of the common 10398G SNP, haplogroups J and K belong to widely diverging mitochondrial clades, a consideration that may explain the different results obtained for the two haplogroups in our cohorts. Our study suggests that haplogroup K might confer a lower risk for PD in Italians, corroborating the idea that the mitochondrial oxidative phosphorylation pathway is involved in the susceptibility to idiopathic PD.     

Mitochondrial DNA polymorphisms in Yunnan nationalities in China

Nucleotide sequences of the D-loop region of human mitochondrial DNA from four Yunnan nationalities, Dai, Wa, Lahu, and Tibetan, were analyzed. Based on a comparison of 563-bp sequences in 99 people, 66 different sequence types were observed. Of these, 64 were unique to their respective populations, whereas only 2 types were shared between the Lahu and Wa nationalities. The D-loop sequence variation and phylogenetic analysis suggested that the 99 mtDNA lineages were classified into eight clusters in the phylogenetic tree. All lineages that had a 9-bp deletion in the COII/tRNA^Lys intergenic region appeared in one cluster in the D-loop tree, suggesting a single event of the deletion in the Yunnan nationalities studied. Genetic distances, based on net nucleotide diversities between populations including Han Chinese and mainland Japanese, revealed that the Dai, Wa, Lahu, and Han Chinese are closely related to each other, while Tibetan and mainland Japanese formed a single cluster. The bootstrap probabil-ity of separation between the Dai-Wa-Lahu-Chinese clade and the Tibetan-Japanese clade was 99%, indicating that there are at least two different origins among minority groups in Yunnan province. Although the genetic distance between Tibetan and Japanese within the clade is rather long, the results may shed light on the origins of mainland Japanese. Received: December 22, 2000 / Accepted: January 18, 2001     

Mitochondrial DNA haplogroup R predicts survival advantage in severe sepsis in the Han population

PurposeTo determine whether the main mitochondrial DNA (mtDNA) haplogroups of the Han people have an impact on long-term clinical outcome.MethodsWe prospectively studied 181 individuals who were sequentially admitted to the intensive care unit. Demographic and clinical data were recorded along with clinical outcome over 180 days. Follow-up was completed for all study participants. We then determined the mtDNA haplogroups of the patients and 570 healthy, age-matched Han people from Zhejiang province, Southeast China, by analyzing sequences of hypervariable mtDNA segments and testing diagnostic polymorphisms in the mtDNA coding region with DNA probes.ResultThe frequency of the main subhaplogroups of the Han population in the study cohort did not differ significantly from the control group. mtDNA haplogroup R, one of the three main mtDNA haplogroups of the Han people, was a strong independent predictor for the outcome of severe sepsis, conferring a 4.68-fold (95% CI 1.903–10.844, P = 0.001) increased chance of survival at 180 days compared with those without the haplogroup R.ConclusionIn the Han population, mtDNA haplogroup R was a strong independent predictor for the outcome of severe sepsis, conferring an increased chance of long-term survival compared with individuals without the R haplogroup.     

Mitochondrial DNA polymorphisms in Italy I. Population data from Sardinia and Rome

The polymorphisms of human mitochondrial DNA were studied in about 150 Sardinians from Cagliari and 100 other Italians living in Rome, using total blood cell DNA and the following restriction enzymes: Hpa I , Bam HI , Hae II , Msp I , Ava II and Hinc II .
1. Seven different new morphs have been identified, one for Hae II , four for Ava II and two for Hinc II .
2. 16 and 17 mtDNA types were observed in the Sardinian and Roman samples, respectively. Of these only seven were shared by both groups. The morphs Bam HI -3, Msp I -4 and Ava II -9 were found associated at a frequency (100%) much higher than expected (0.17%).
3. Sardinians can be differentiated from the other Italians for a higher frequency of both morph Ava II-1( P < 0.05) and type 1 (2–1–1–1–1) (P0.03), and for a lower intragroup heterogeneity (0.52 v . 0.61).
4. The Italian sample on the whole can also be differentiated from the Caucasian group previously examined for a lower frequency of Bam HI morph 2 (P_Yates < 0.01), a higher frequency of Hae II morph 1 (P_Yates < 002) and for the presence at a non-negligible incidence (5 inviduals out of 229) of the new type 57–2 (2–3–1–4–13–2).
The data indicate that mtDNA polymorphisms have not only proved to be a useful tool in detecting differences among major human groups but they can also differentiate populations within the same major ethnic division.     

Mitochondrial DNA polymorphisms in Khoisan populations from Southern Africa

Mitochondrial DNA (mtDNA) restriction fragment length polymorphisms (RFLPs) were investigated in 95 individuals, consisting of 49 San ('Bushmen') and 46 Nama ('Hottentot') individuals from Namibia, using the restriction enzymes Hpa I, Bam HI, Hae II, Msp I, Ava II and Hinc II. Six of the eleven types found in the pooled Khoisan sample are shared, albeit at varying frequencies, suggesting that both the San and Nama have evolved from a recent common ancestor. However, San and Nama groups differ appreciably, in particular, type 3-2 (3-1-1–2-2-2) was found in 7/49 Sekele and 25/46 Nama (χ²_[1]= 15·3, P = 9·17 × 10^-5). In addition, type 4 makes up 428 % of the types found in the San, and is not found in the Nama group. This suggests that the San and Nama have evolved along separate lineages, with little gene flow between them, following their proposed separation from a common Khoisan ancestor. Type 7-2 (3-1-1-1-1-2), most common in Negroid populations, is found at a higher frequency in the San (20·4%) than the Nama (6·5%), suggesting that miscegenation involving Negroid females and San males is more common than that between Negroid females and Nama men. The higher frequency of type 21-2 (2-1-1-1–2-2) in the Nama (13%) than in the San (4·1%), may be attributable to gene flow from the Dama into the Nama, consistent with the consequences of enslavement of the Dama by the Nama.     

Mitochondrial DNA diversity in the Kuna Amerinds of Panama

Mitochondrial DNA (mtDNA) haplotype diversity was determinedfor 63 Chibcha-speaking Kuna Amerinds sampled widely acrosstheir geographic range in eastern Panamá. The Kuna datawere compared with mtDNA control region I sequences from twoneighboring Chibchan groups, the Ngöbé and the Huetar;two Amerind groups located at the northern and southern extremesof Amerind distribution, the Nuu-Chah Nulth of the Pacific Northwestand the Chilean Mapuche; and with a single Na-Dene group, theHaida of the Pacific Northwest. The Kuna exhibited low levelsof mitochondrial diversity as had been reported for the othertwo Chlbchan groups and, furthermore, carried only two of thefour Amerind founding lineages first reported by Schurr andcoworkers (Am. J. Hum. Genet. 1990; 46: 613–623). We positthat speakers of modern Chibchan languages (henceforth referredto as the Chibcha) passed through a popula tion bottleneck causedeither by ethnogenesls from a small founding population and/orsubsequent European conquest and colonization. Using the approachof Harpending et al. (Curr. Anthropol. 1993; 34: 483–496),we estimated a Chibchan population bottleneck and subsequentexpansion approximately 10 000 years before present, a dateconsistent with a bottleneck at the time of Chibchan ethnogenesis.The low mtDNA diversity of Kuna Amerinds, as opposed to thegenerally high levels of mtDNA variation detected in other Amerindgroups, demonstrates the need for adequate sampling of culturalor racial groups when attempting to genetically characterizehuman populations.     

Mitochondrial DNA polymorphisms in the human pathogenic fungus Cryptococcus neoformans

This study examined mitochondrial DNA (mtDNA) restriction site polymorphisms among 416 strains of the human pathogenic yeast Cryptococcus neoformans from the United States and Japan. The strains included 378 serotype A, 14 serotype D, 18 serotype AD, two serotype B, and two strains whose serotype could not be determined using current commercial monoclonal antibodies. Portions of two genes were examined: (1) the mitochondrial large ribosomal RNA gene (mtLrRNA) and (2) the NADH dehydrogenase subunit 2 ( ND2). To screen for polymorphisms among the 416 strains, the endonuclease MaeIII was used to digest the PCR-amplified mtLrRNA gene fragment and three endonucleases ( BanI, AluI, MseI) were used to digest the PCR-amplified ND2 gene fragment. Four mtDNA haplotypes were identified among these strains. All strains of serotype A had mtDNA haplotype I, strains of serotype D had haplotype II, and strains of serotype B had haplotypes III and IV. Of the two non-typable strains, one was haplotype I while the other was haplotype II. Among the strains of serotype AD, 14 were haplotype I and the other four were haplotype II. These results were discussed in the context of recent findings regarding the origins of serotype AD strains and the observed uniparental mtDNA inheritance in laboratory crosses between strains of serotypes A and D.     

Mitochondrial DNA polymorphisms in Italy; III. Population data from Sicily: a possible quantitation of maternal African ancestry

mtDNA polymorphisms were studied in a sample of 90 individuals of the Sicilian population using six restriction enzymes: Hpa I, Bam HI, Hae II, Msp I, Ava II and Hinc II.
(1) Three new patterns, for Msp I, Ava II and Hinc II, have been detected.
(2) At least two different mutations were found to account for both the Ava II morph 3 and the Ava II morph 9 as in many other Caucasian groups so far examined.
(3) Seventeen types were found; of these six are new.
The frequency (54.5%) of type 1–2 (2.1.1.1.1.2) is lower than in the rest of Italy whereas those of type 6-2 (2.1.2.1.1.2) (10.0%) and type 18-2 (2.3.1.4.9*.2) (12.2%) lie at the upper level of the Italian range.
The 18-derivative, type 57-2 (2.3.1.4.13*.2), which is consistently found in all Italian samples, is present also among Sicilians with an incidence of 2.2%.
(4) Of particular interest is that the Hpa I-3/ Ava II-3 complex, which is unique to groups of African ancestry, was found in Sicily at a frequency of 4.4%. For the first time an estimate of the amount of gene flow from Blacks to the Sicilian gene pool could be obtained.     

Mitochondrial DNA and Y chromosome diversity and the peopling of the Americas: evolutionary and demographic evidence.

A number of important insights into the peopling of the New World have been gained through molecular genetic studies of Siberian and Native American populations. While there is no complete agreement on the interpretation of the mitochondrial DNA (mtDNA) and Y chromosome (NRY) data from these groups, several generalizations can be made. To begin with, the primary migration of ancestral Asians expanded from south-central Siberia into the New World and gave rise to ancestral Amerindians. The initial migration seems to have occurred between 20,000-15,000 calendar years before present (cal BP), i.e., before the emergence of Clovis lithic sites (13,350-12,895 cal BP) in North America. Because an interior route through northern North America was unavailable for human passage until 12,550 cal BP, after the last glacial maximum (LGM), these ancestral groups must have used a coastal route to reach South America by 14,675 cal BP, the date of the Monte Verde site in southern Chile. The initial migration appears to have brought mtDNA haplogroups A-D and NRY haplogroups P-M45a and Q-242/Q-M3 to the New World, with these genetic lineages becoming widespread in the Americas. A second expansion that perhaps coincided with the opening of the ice-free corridor probably brought mtDNA haplogroup X and NRY haplogroups P-M45b, C-M130, and R1a1-M17 to North and Central America. Finally, populations that formerly inhabited Beringia expanded into northern North America after the LGM, and gave rise to Eskimo-Aleuts and Na-Dené Indians.     

Mitochondrial DNA polymorphisms among Hindus: A comparison with the Tharus of Nepal

The polymorphisms of mitochondrial DNA for the restriction enzymes Hpal, Bamill, Haell, Mspl, Avail and Hindi were studied in a sample of 79 Hindus, 45 from New Delhi (India) and 34 from Terai (Nepal), both to characterize another Caucasian population and to investigate some possible Hindu component in the genetic structure of the Tharus, a Nepalese population, the anthropological position of which is still disputed.
1. A new Bam HI polymorphism was detected; about 5 % of the Hindu mtDNAs have lost the site at 14258 bp and lack any Bam HI site. Once again a Bam HI polymorphism was found in a Caucasian population.
2. New site mutations were found to yield morphs previously described ( Msp I-7, Ava II - 18).
3. Variant morphs for two different enzymes were found due to a shared mutation (morphs Bam HI - O /Ava II - 30 and morphs Msp I-7^Hindu/ Ava II-18^Hindu).
4. Comparison between Hindu and Tharu data does not show any evidence of a specific Indian component in the Tharu genetic structure and allows us to conclude that Tharus are clearly differentiated from modern Hindus.     

Single nucleotide polymorphisms detection based on DNA microarray technology: HLA as a model

The significance of DNA variations among individuals, including single nucleotide polymorphisms (SNPs) and/or genome nucleotide mutations as well as to their detection by using new technology, will improve and facilitate the knowledge of each gene sequence. Microarray may provide information about thousands of gene simultaneously, leading to a more rapid and accurate genotyping. In this view, we developed a new methodology as an example for the detection of SNPs based on DNA microarray, using a panel of HLA alleles representative of loci A, B, DRB1. A panel of 180 oligonucleotide probes was selected to identify polymorphic positions located in exons 2 and 3 of HLA-A and B, and in exon 2 of HLA-DRB1 locus. Each oligonucleotide sequence was designed with a nucleotide mismatch located in the same position as the center of the hybridization sequence. Hybridization experiments were carried out with genomic probes constructed with an asymmetric PCR strategy. The amplified DNAs were obtained from bone marrow cells of donors previously typed for transplant. The results obtained were showing that the method was reliable thus providing a feasible technique both for HLA typing and for the investigation of other regions of genetic and clinical interest including polymorphisms correlated with different autoimmune diseases.     

Mitochondrial DNA polymorphisms in Italy II. Molecular analysis of new and rare morphs from Sardinia and Rome

A molecular analysis of morphs found in a previous survey of mtDNA restriction enzyme polymorphisms in Italy revealed that different site changes can give similar patterns and that the same mutation can yield variant morphs for apparently unrelated enzymes. 1. Alternative site variations were found to yield restriction fragment patterns resembling HpaI morph 4, HaeII morph 5 and AvaII morph 2. 2. A strong association was observed between the BamHI morph 3 (gain of site a) and the AvaII morph 9 and its derivatives (loss of site d). This association appears to result from an A to G transition at base pair (bp) 13368 which simultaneously creates a new BamHI site and abolishes an AvaII site. On the other hand, the loss of the AvaII site d, which in Italy was only found in the above-mentioned association, does not always produce a new BamHI site, as observed in other Caucasian groups. Similarly, the Bam HI morph 2 (gain of site b) was always found to be associated with AvaII morphs lacking site f. An A to G transition at bp 16391 was shown to account for both changes. As in the previous case, the converse is not true. Hence, these data show that AvaII sites d and f were lost in more than one way and one of these seems to be typical of Caucasians. 3. The variation producing BamHI-3/AvaII-9 and derivatives is preferentially associated with MspI morph 4 but this is not a product of a shared mutation. Hence, this association must be the result of the linkage disequilibrium due to the maternal inheritance of mtDNA and lack of recombination. 4. The high frequency of the combination BamHI-3/AvaII-9 and derivatives with MspI-4 found in Italy (29 subjects out of 229 analysed) can best be explained by diffusion of the relevant haplotype rather than by repeated mutational events. 5. The phylogeny trees of all mtDNA morphs so far described and of mtDNA types in Caucasians have been revised taking into account both the inter- and the intra-morph heterogeneity detected by this analysis.     

Fixation conditions for DNA and RNA in situ hybridization: a reassessment of molecular morphology dogma.

Neutral buffered formalin (NBF) (4% neutral buffered formaldehyde) has been advocated by most investigators as the primary fixative of choice for in situ hybridization (ISH), and specific anecdotal cautions interdicting the use of precipitating fixatives, which otherwise may offer certain advantages such as superior nuclear detail, are common. Few systematic studies addressing ISH fixation conditions have been published. We reasoned that heavy metals present in some precipitating fixatives may compromise duplex formation during ISH. Cell lines containing known viral gene content (CaSki, 200 to 600 human papilloma virus 16 copies/cell, and SiHa, 1 to 2 human papilloma virus 16 copies/cell) and two negative cell lines (K562 and MOLT 4) were expanded to >10(10) and pellets fixed in NBF, zinc formalin, B5, and Bouin's and Hollande's solutions, and subjected to DNA ISH using biotinylated genomic probes. Ten tissue biopsies fixed in both Hollande's and NBF solutions were also evaluated for human papilloma virus content using DNA ISH. Additionally, 17 cases of Hodgkin's disease fixed in B5 and formalin were compared for Epstein-Barr encoded RNA detection using RNA ISH with fluorescein isothiocyanate-labeled oligonucleotides. Catalyzed reporter deposition combined with Streptavidin-Nanogold staining and silver acetate autometallography (Catalyzed reporter deposition-Ng-autometallography ISH) and a conventional indirect alkaline phosphatase method were used for detection for both DNA and RNA. Contaminating heavy metals entrapped in fixed tissues were removed by two exposures to Lugol's iodine. Results for both DNA and RNA ISH comparing B5 and NBF fixatives were virtually identical. Hollande's, Bouin's, B5, and zinc formalin fixed tissue showed results indistinguishable from NBF fixed tissue in DNA ISH. Precipitating fixatives such as B5 and Hollande's solution may be used for DNA and RNA ISH under appropriate conditions.     

Mitochondrial haplogroup H correlates with ATP levels and age at onset in Huntington disease

Mitochondrial dysfunction has been implicated in the pathogenesis of Huntington disease (HD), a primarily neurodegenerative disorder that results from an expansion in the polymorphic trinucleotide CAG tract in the HD gene. In order to evaluate whether mitochondrial DNA (mtDNA) variation contributes to HD phenotype we genotyped 13 single nucleotide polymorphisms (SNPs) that define the major European mtDNA haplogroups in 404 HD patients. Genotype-dependent functional effects on intracellular ATP concentrations were assessed in peripheral leukocytes. In patients carrying the most common haplogroup H (48.3%), we demonstrate a significantly lower age at onset (AO). In combination with PGC-1alpha genotypes, 3.8% additional residual variance in HD AO can be explained. Intracellular ATP concentrations in HD patients carrying the cytochrome c oxidase subunit I (CO1) 7028C allele defining haplogroup H were significantly higher in comparison to non-H individuals (mean?±?SEM, 599?±?51.8 ng/ml, n?= 14 vs. 457.5?±?40.4 ng/ml, p?=?0.03, n?=?9). In contrast, ATP concentrations in cells of HD patients independent from mtDNA haplogroup showed no significant differences in comparison to matched healthy controls. Our data suggest that an evolutionarily advantageous mitochondrial haplogroup is associated with functional mitochondrial alterations and may modify disease phenotype in the context of neurodegenerative conditions such as HD.