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At least 1,009 records · Page 56Linked to original sources
PubMed1995

MtDNA-encoded histocompatibility antigens.

Mitochondrially encoded H antigens are by-products of a system that has evolved in vertebrates to present peptides from intracellular pathogens on the cell surface for detection by CTLs, which can lyse the infected cell. CTL lines and clones with defined specificity against mitochondrial H antigens, which can be maintained in culture for long periods, offer a unique tool in mitochondrial genetics. Expression of polymorphic mitochondrial H antigens depends on both the presence and the activity of the corresponding mitochondrial genome, and CTLs can provide strong selection against cells displaying their cognate antigen.

Animals↗
PubMed1992

Lipid peroxidation and mtDNA degeneration. A hypothesis.

End-products of lipid peroxidation accumulate during the life of somatic cells. It is hypothesized that genotoxic intermediates of lipid peroxidation may have a role in causing age-associated DNA mutations. Such mutations are likely to accrue in the mitochondrial genome because it, unlike nuclear DNA, is not protected by histones and repair systems. In addition, it is located near the mitochondrial membrane where lipid peroxidation can be initiated by free radicals produced by the mitochondrial electron transport system. This idea is supported by in vitro experiments which show that mitochondrial DNA is damaged when mitochondria undergo lipid peroxidation.

Animals↗
PubMed1991

A new mtDNA mutation associated with mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS).

In 3 of 40 MELAS patients, a new common mutation, a T-to-C transition at nucleotide position 3271 in the mitochondrial tRNA(Leu(UUR] gene was recognized and was very near to the most common mutation site at 3243. With a simple detection method using polymerase chain reaction with a mismatch primer, none of 46 patients with other mitochondrial diseases and 50 controls had this mutation.

Acidosis, Lactic↗
PubMed2003

STR genotyping and mtDNA sequencing of latent fingerprint on paper.

A systematic study was conducted to investigate whether DNA can be successfully extracted from latent fingerprints deposited on ordinary paper and analysed using short tandem repeat profiling and mitochondrial DNA sequencing. In order to evaluate the performance of latent fingerprint analysis in a criminal case, experiments with varying conditions were carried out to improve our understanding of low copy number (LCN) DNA typing. After optimising the extraction methods to achieve increased sensitivity, the examination of touched paper can routinely yield the STR profile of the individual who has touched it. A fingerprint can therefore be considered as a potential source of DNA for genetic identification. Nevertheless, the findings of our "after enhancement experiment" (using chemically or physically pre-treated fingerprints), and our "mixture experiment" (using fingerprints from three to four people on the same sheet of paper) help to define the limitations of the low copy number PCR technique in forensic casework.

Alleles↗
PubMed2005

mtDNA HVI length heteroplasmic profile in different tissues of maternally related members.

Sequencing of the homopolymeric tract of cytosines (C-stretch) in human mitochondrial HVI region usually results in a blurred pattern beyond it when a T/C transition at nt 16189 occurs: it depends on a length heteroplasmy probably arising through a replication slippage. This study aims to investigate the distribution of heteroplasmic length variants within three related individuals along maternal lineage by cloning approach. Sequencing of multiple independent clones (12--14) is sufficient to yield heteroplasmic profiles. In addition, we illustrate a direct correlation between expansion of heteroplasmy modal length and reduction of the number of adenines preceding the homopolymeric tract; this association may be useful in pedigree analysis and in forensic field for tissues comparison, single hair sample included.

Complementarity Determining Regions↗
PubMed2004

The evolutionary origin of long-crowing chicken: its evolutionary relationship with fighting cocks disclosed by the mtDNA sequence analysis.

Chickens with exceptionally long crow are often favored all over the world, and connoisseur breeders have bred certain types of chicken exclusively for this trait. In Japan, three chicken varieties have been specifically bred to develop an exceptionally long crow of over 15 s. Although these three long-crowing chickens, Naganakidori, are honored as heritage varieties of Japan, the domestication process and genealogical origin of long-crowing chickens remain unclear. The purpose of this study is to clarify these issues using nucleotide sequences of the mitochondrial DNA D-loop region. Blood samples from a total of nine long-crowing chickens and 74 chickens from 11 Japanese native varieties were collected. DNA sequence data of two Junglefowl species were also collected from the International DNA database (DDBJ /EMBL/GenBank) for use as the outgroup. A phylogenetic tree was then constructed revealing that all three Naganakidori varieties were monophyletic and originated from a fighting cock, a Shamo, for cockfighting. These results suggest that these three long-crowing chickens share a common origin in spite of their conspicuously different characters, and that human cultures favoring long-crowing chickens might have been preceded by a tradition of cockfighting. Moreover, these long-crowing varieties first separated from the fighting cocks of Okinawa, which is geographically closer to Southern China and Indochina than Mainland Japan (Honshu/Kyushu). This implies that Japanese long-crowing chickens were first brought to Mainland Japan as fighting cocks from the surrounding regions of Southern China or Indochina and through Okinawa.

Aggression↗
PubMed2005

The mitochondrial genome organization of the rice frog, Fejervarya limnocharis (Amphibia: Anura): a new gene order in the vertebrate mtDNA.

The mitochondrial DNA of the rice frog, Fejervarya limnocharis (Amphibia, Anura), was obtained using long-and-accurate polymerase chain reaction (LA-PCR) combining with subcloning method. The complete nucleotide sequence (17,717 bp) of mitochondrial genome was determined subsequently. This mitochondrial genome is characterized by four distinctive features: the translocation of ND5 gene, a cluster of rearranged tRNA genes (tRNAThr, tRNAPro, tRNA(Leu CUN)), a tandem duplication of tRNAMet gene, and eight large 89-bp tandem repeats in the control region, as well as three short noncoding regions containing two repeated motifs existing in the gene cluster of ND5/tRNAThr/tRNAPro/tRNALeu/tRNAPhe. The tandem duplication of gene regions followed by deletions of supernumerary genes can be invoked to explain the shuffling of tRNAMet and a cluster of tRNA and ND5 genes, as observed in this study. Both ND5 gene translocation and tandem duplication of tRNAMet were first observed in the vertebrate mitochondrial genomes.

Animals↗
PubMed2005

Evolutionary analysis of a large mtDNA translocation (numt) into the nuclear genome of the Panthera genus species.

Translocation of cymtDNA into the nuclear genome, also referred to as numt, has been reported in many species, including several closely related to the domestic cat (Felis catus). We describe the recent transposition of 12,536 bp of the 17 kb mitochondrial genome into the nucleus of the common ancestor of the five Panthera genus species: tiger, P. tigris; snow leopard, P. uncia; jaguar, P. onca; leopard, P. pardus; and lion, P. leo. This nuclear integration, representing 74% of the mitochondrial genome, is one of the largest to be reported in eukaryotes. The Panthera genus numt differs from the numt previously described in the Felis genus in: (1) chromosomal location (F2-telomeric region vs. D2-centromeric region), (2) gene make up (from the ND5 to the ATP8 vs. from the CR to the COII), (3) size (12.5 vs. 7.9 kb), and (4) structure (single monomer vs. tandemly repeated in Felis). These distinctions indicate that the origin of this large numt fragment in the nuclear genome of the Panthera species is an independent insertion from that of the domestic cat lineage, which has been further supported by phylogenetic analyses. The tiger cymtDNA shared around 90% sequence identity with the homologous numt sequence, suggesting an origin for the Panthera numt at around 3.5 million years ago, prior to the radiation of the five extant Panthera species.

Animals↗
PubMed2005

Human mitochondrial pyrophosphatase: cDNA cloning and analysis of the gene in patients with mtDNA depletion syndromes.

Pyrophosphatases (PPases) catalyze the hydrolysis of inorganic pyrophosphate generated in several cellular enzymatic reactions. A novel human pyrophosphatase cDNA encoding a 334-amino-acid protein approximately 60% identical to the previously identified human cytosolic PPase was cloned and characterized. The novel enzyme, named PPase-2, was enzymatically active and catalyzed hydrolysis of pyrophosphate at a rate similar to that of the previously identified PPase-1. A functional mitochondrial import signal sequence was identified in the N-terminus of PPase-2, which targeted the enzyme to the mitochondrial matrix. The human pyrophosphatase 2 gene (PPase-2) was mapped to chromosome 4q25 and the 1.4-kb mRNA was ubiquitously expressed in human tissues, with highest levels in muscle, liver, and kidney. The yeast homologue of the mitochondrial PPase-2 is required for mitochondrial DNA maintenance and yeast cells lacking the enzyme exhibit mitochondrial DNA depletion. We sequenced the PPA2 gene in 13 patients with mitochondrial DNA depletion syndromes (MDS) of unknown cause to determine if mutations in the PPA2 gene of these patients were associated with this disease. No pathogenic mutations were identified in the PPA2 gene of these patients and we found no evidence that PPA2 gene mutations are a common cause of MDS in humans.

Amino Acid Sequence↗
PubMed2004

MtDNA sequencing from zooplankton after long-term preservation in buffered formalin.

Molecular genetic analysis of zooplankton has been slowed by the usual practice of preservation and storage of samples in dilute formalin solutions, which are not always adequately buffered for pH. We report here the determination of DNA sequences for Meganyctiphanes norvegica (Crustacea, Euphausiacea) preserved and stored in buffered formalin for up to 25 years. Specifically designed molecular protocols for DNA extraction and PCR amplification yielded valid sequence data for short (approximately 100-200 bp) regions of the mitochondrial cytochrome b (mtCYB) gene for individual euphausiids. Critical aspects of our approach include: extended extraction and proteinase-K digestion to maximize DNA yield; use of protocols requiring short DNA fragments; design of species-specific PCR primers to minimize risks of contamination by exogenous DNA; and comparison with published DNA sequences for the same gene and species. We conclude that the yield of DNA and the success of subsequent molecular analyses depend primarily on the length of time the tissue has been exposed to formalin and the pH of the solution. Zooplankton samples intended for molecular analysis should preferably be preserved and maintained in ethanol or deep-frozen, but long-term storage in buffered formalin does not preclude some types of molecular genetic analysis.

Animals↗
PubMed2004

MtDNA phylogeny and biogeography of Copelatinae, a highly diverse group of tropical diving beetles (Dytiscidae).

Copelatinae is a diverse lineage of diving beetles (Dytiscidae) frequently encountered in wet tropical and subtropical forests, but phylogenetic relationships are very poorly understood. We performed a phylogenetic and biogeographic analysis of this worldwide distributed group based on 50 species including a representative sample of major taxonomic groups and biogeographical regions. DNA sequences were obtained for the mitochondrial genes cytochrome oxidase I, cytochrome b, and 16S rRNA, for a total of 1575 aligned nucleotide positions. We found Copelatinae to be monophyletic, placed in a derived position and not sister to all remaining dytiscids, as had been suggested by earlier authors. The largest genus, Copelatus with some 460 known species was paraphyletic with respect to the smaller genera Lacconectus and Aglymbus. Among the major lineages of Copelatus, the subgenus Papuadytes was consistently recovered as sister to all other species (including Lacconectus and Aglymbus) with the possible exception of two western Palearctic taxa. We propose that the subgenus Papuadytes is removed from Copelatus and assigned generic status. Likewise, the two western Palearctic Copelatus are removed from this genus, and assigned the available genus name Liopterus. Our best phylogenetic hypothesis retrieved Afrotropical and New Guinean plus Australian species of Copelatus as monophyletic. Asian species were paraphyletic with respect to a species from Sulawesi which grouped with the species from New Guinea. Asian species were also paraphyletic with respect to Oriental Lacconectus, which was grouped with a clade of Neotropical species. Neotropical Copelatus form at least two separate lineages. The biogeographical evolution of Papuadytes is consistent with the relative age of the landmasses in the Austral region. Basal species are Australian, and successively derived ones are from New Caledonia and New Guinea. One species apparently dispersed from New Caledonia to China. Assuming a molecular clock and using a standard calibration of 2% divergence/MY the origin of Copelatinae is estimated to be between 85 and 95 MY.

Animals↗
PubMed2004

Molecular phylogeny and taxonomy of wood mice (genus Apodemus Kaup, 1829) based on complete mtDNA cytochrome b sequences, with emphasis on Chinese species.

Phylogenetic relationships among 15 species of wood mice (genus Apodemus) were reconstructed to explore some long-standing taxonomic problems. The results provided support for the monophyly of the genus Apodemus, but could not reject the hypothesis of paraphyly for this genus. Our data divided the 15 species into four major groups: (1) the Sylvaemus group (A. sylvaticus, A. flavicollis, A. alpicola, and A. uralensis), (2) the Apodemus group (A. peninsulae, A. chevreri, A. agrarius, A. speciosus, A. draco, A. ilex, A. semotus, A. latronum, and A. mystacinus), (3) A. argenteus, and (4) A. gurkha. Our results also suggested that orestes should be a valid subspecies of A. draco rather than an independent species; in contrast, A. ilex from Yunnan may be regarded as a separate species rather than a synonym of orestes or draco. The species level status of A. latronum, tscherga as synonyms of A. uralensis, and A. chevrieri as a valid species and the closest sibling species of A. agrarius were further corroborated by our data. Applying a molecular clock with the divergences of Mus and Rattus set at 12 million years ago (Mya) as a calibration point, it was estimated that five old lineages (A. mystacinus and four major groups above) diverged in the late Miocene (7.82-12.74 Mya). Then the Apodemus group (excluding A. mystacinus) split into two subgroups: agrarius and draco, at about 7.17-9.95 Mya. Four species of the Sylvaemus group were estimated to diverge at about 2.92-5.21 Mya. The Hengduan Mountains Region was hypothesized to have played important roles in Apodemus evolutionary histories since the Pleistocene.

Animals↗
PubMed2005

Phylogenetic analysis of the genus Thymallus (grayling) based on mtDNA control region and ATPase 6 genes, with inferences on control region constraints and broad-scale Eurasian phylogeography.

We present first insights into the molecular phylogeny of the grayling genus Thymallus (Salmonidae) using sequences from the mitochondrial control region and ATPase6 genes. A suite of analytical approaches were applied for each gene separately and for the combined data. The ATPase6 gene is shown to have a mean divergence rate across the genus of 2.46 times faster than the complete control region. Based on the combined data, four major (internal) clades, presumably originating in the Pliocene, were resolved with high support in all analyses and represented two distinct lineages in the Amur basin, one lineage in all remaining Siberian and Mongolian drainages, and one lineage corresponding to European grayling Thymallus thymallus. The resolution of multiple lineages, from both additional internal and terminal clades, within each major drainage basin underscores the complexity and effects that Pleistocene hydrological dynamics have had on the distribution of biodiversity in Siberia.

Animals↗
PubMed2005

A phylogenetic framework for the terns (Sternini) inferred from mtDNA sequences: implications for taxonomy and plumage evolution.

We sequenced 2800 bp of mitochondrial DNA from each of 33 species and 2 subspecies (35 taxa) of terns (Sternini), and employed Bayesian methods to derive a phylogeny with good branch support based on posterior probabilities. The resulting tree confirmed many of the generally accepted taxonomic groups, and led us to suggest a revision of the terns that recognizes 12 genera, 11 of which correspond to a distinct clade on the tree or a highly divergent species (1 genus was not represented in the phylogeny). As an example of how the molecular phylogeny reflects similarities in morphology and behavior among the terns, we used the phylogeny to examine the evolution of the breeding (alternate) head plumage patterns among the terns to test the hypothesis that this character is phylogenetically informative. The three basic types of head plumage (white crown, black cap, and black cap with a white blaze on the forehead) were highly conserved within clades, with notable exceptions in two white-crowned species that evolved independently among the black-capped terns. Based on the appearance of the close relatives of these exceptional species, their white crowns appear to be due to the retention of either winter (basic) plumage characteristics or perhaps juvenile characteristics when the birds molt into their breeding plumage. Examination of the evolutionary history of head plumage indicated that the white-crowned species such as the noddies (Anous) and the white tern (Gygis alba) are probably most representative of ancestral terns.

Animals↗