Genetic Analysis Of Mitochondrial DNA Research Articles

Genetic analysis of mitochondrial DNA from ancient Equus caballus bones found at archaeological site of Joseon dynasty period capital area.

ObjectiveTo understand the domestication and spread of horses in history, genetic information is essential. However, mitogenetic traits of ancient or medieval horses have yet to be comprehensively revealed, especially for East Asia. This study thus set out to reveal the maternal lineage of skeletal horse remains retrieved from a 15th century archaeological site (Gongpyeongdong) at Old Seoul City in South Korea.MethodsWe extracted DNA from the femur of Equus caballus (SNU-A001) from Joseon period Gongpyeongdong site. Mitochondrial (mt) DNA (HRS 15128-16116) of E. caballus was amplified by polymerase chain reaction. Cloning and sequencing were conducted for the mtDNA amplicons. The sequencing results were analyzed by NCBI/BLAST and phylogenetic tool of MEGA7 software.ResultsBy means of mtDNA cytochrome b and D-loop analysis, we found that the 15th century Korean horse belonged to haplogroup Q representing those horses that have historically been raised widely in East Asia.ConclusionThe horse is unique among domesticated animals for the remarkable impact it has on human civilization in terms of transportation and trade. Utilizing the Joseon-period horse remains, we can obtain clues to reveal the genetic traits of Korean horse that existed before the introduction of Western horses.

Mitochondrial DNA in forensic use.

Genetic analysis of mitochondrial DNA (mtDNA) has always been a useful tool for forensic geneticists, mainly because of its ubiquitous presence in biological material, even in the absence of nuclear DNA. Sequencing, however, is not a skill that is part of the routine forensic analysis because of the relative rarity of requests, and the need for retention of necessary skill sets and associated accreditation issues. While standard Sanger sequencing may be relatively simple, many requests are made in the face of compromised biological samples. Newer technologies, provided through massively parallel sequencing (MPS), will increase the opportunity for scientists to include this tool in their routine, particularly for missing person investigations. MPS has also enabled a different approach to sequencing that can increase sensitivity in a more targeted approach. In these circumstances it is likely that only a laboratory that specialises in undertaking forensic mtDNA analysis will be able to take these difficult cases forward, more so because reviews of the literature have revealed significantly high levels of typing errors in publications reporting mtDNA sequences. The forensic community has set out important guidelines, not only in the practical aspects of analysis, but also in the interpretation of that sequence to ensure that accurate comparisons can be made. Analysis of low-level, compromised and ancient DNA is not easy, however, as contamination is extremely difficult to eliminate and circumstances leading to sequencing errors are all too easily introduced. These problems, and solutions, are discussed in the article in relation to several historic cases.

Clinical examination methods and investigation into the occurrence of endoparasites, Borna disease virus and genetic variability in the garden dormouse, Eliomys quercinus

Facing the ongoing decline in garden dormice (Eliomys quercinus) in large parts of Europe, data about genetic diversity, weight, size, and parasite burden were collected from live individuals (n = 156) from Hesse and Rhineland-Palatinate, Germany. Blood was collected under Isoflurane-oxygen-anaesthesia from the anterior vena cava or jugular vein, respectively. Sex, weight, tibiotarsal and tail length of all animals were recorded. Genetic analysis (n = 64) using hair samples, viral examinations of oral, ocular and anal swabs (n = 156) and parasitological examination of faecal samples (n = 57) were performed. Genetic analysis of mitochondrial DNA revealed three haplotypes in the study area (WE4, WE4-3, WE5). Microsatellite analysis demonstrated a comparably high genetic diversity with 66 % overlap of alleles, a low genetic distance (DJost 5.6 %) and a low index of differentiation (FST = 0.02) between individuals from Hesse and Rhineland-Palatinate. All swab samples were negative for Borna disease virus. In 47 % of the faecal samples Entamoeba sp. cysts, Eimeria sp. oocysts, and eggs of trematodes, cestodes (Hymenolepis spp.) and nematodes (Capillaria spp., Strongylida) were detected. To our knowledge, this is the first report of inhalation anaesthesia, clinical examination, blood collection and assessment of Borna disease virus in living garden dormice.

Application of Cochlear Implant for Two Cases of Maternally Inherited Diabetes and Deafness

Maternally inherited diabetes and deafness (MIDD) is a rare subtype form of diabetes caused by a mitochondrial DNA defect associated with m.3243A>G mutation. More than 90% of MIDD cases suffer from bilateral progressive sensorineural hearing loss. Here, we report two cases of MIDD with bilateral profound hearing loss that were successfully treated with cochlear implantation. Case 1 was a 61-year-old man who complained of bilateral progressive hearing loss since the age of 40 years old and who visited our department seeking treatment. He was diagnosed as having MIDD based on a genetic analysis of mitochondrial DNA that revealed a 3243 A to G substitution. Cochlear implantation (CI) was performed for the right ear, which exhibited profound hearing loss. At 5 years after the CI, the patient had acquired hearing function enabling more than 90% of spoken words to be discriminated. Case 2 was a 44-year-old woman who had suffered from diabetes and deafness since the age of 24 years and who had a 3243 A to G substitution in her mitochondrial DNA. She visited our department for cochlear implantation because hearing aids had never improved her hearing. At 6 years after the CI, she had acquired good speech discrimination. We suggest that CI might be a useful treatment for profound hearing loss in patients with MIDD.

Chronic Progressive External Ophthalmoplegia Ptosis: Problems with Diagnostics and Treatment

Ptosis is often the first symptom of chronic progressive external ophthalmoplegia (CPEO), a rare muscle disorder. As the disease progresses, it can lead to ocular motility defects. Ptosis is present in the early stages of the disease and can be corrected by levator surgery. Due to the rarity of CPEO (< 1% of ptosis patients), further diagnostic steps with muscle biopsy and genetic analysis of mitochondrial DNA are usually not considered in the early phase. Intraoperative abnormal observations during ptosis surgery and postoperative motility problems are signs of CPEO. If CPEO is confirmed, alternative surgical methods can correct the ptosis, like frontalis suspension.

Occurrence of invasive lionfish (Pterois volitans) larvae in the northern Gulf of Mexico: characterization of dispersal pathways and spawning areas

Here we document for the first time the presence of invasive lionfish larvae (Pterois volitans) in the Gulf of Mexico. Three lionfish larvae (standard length: 3.9–5.9 mm) were collected during summer ichthyoplankton surveys in the northern Gulf of Mexico in 2011, with species identification confirmed through the genetic analysis of mitochondrial DNA. Pigmentation patterns of these larvae are described and compared with published lionfish descriptions. Otolith microstructure analysis revealed that larvae were 14–17 days old and that spawning occurred in June and July. A biophysical dispersal model was used to backtrack larvae to their potential spawning locations and results indicated that spawning occurred in the southern Gulf of Mexico near the Yucatan Peninsula, suggesting that these larvae may have been transported into the northern Gulf of Mexico by the Loop Current. Here we provide useful information for identifying lionfish larvae and offer insight into lionfish spawning and larval dispersal pathways.

Novel mitochondrial tRNAIle m.4282A>G gene mutation leads to chronic progressive external ophthalmoplegia plus phenotype

Background/aimTo investigate the underlying pathomechanism in a 33-year-old female Caucasian patient presenting with chronic progressive external ophthalmoplegia (CPEO) plus symptoms.MethodsHistochemical anaylsis of skeletal muscle and biochemical measurements of individual oxidative...

Mitochondrial DNA of a late neolithic woman from Kaminnaia cave (Gorny Altai)

The results of molecular genetic analysis of mitochondrial DNA of a Late Neolithic woman (middle of the 4th millennium BC) from Kaminnaia cave (Gorny Altai) are presented. It was determined that the studied sample belongs to the East Eurasian A4 haplogroup. A phylogeographic analysis indicates an informativity of the A4 variants for the reconstruction of early stages of ethnogenetic processes on the south of Western and Eastern Siberia.

Origins, ages and population histories: comparative phylogeography of endemic Hawaiian butterflyfishes (genus Chaetodon)

AbstractAim To investigate phylogeographic relationships, genetic connectivity and potential colonization routes for Hawaii’s endemic butterflyfishes (family Chaetodontidae).Location The Hawaiian Archipelago (central Pacific Ocean).Methods Molecular genetic analysis of mitochondrial DNA from three species of endemic Hawaiian butterflyfishes (Chaetodon multicinctus, n = 280; Chaetodon miliaris, n = 408; Chaetodon fremblii, n = 358) sampled from across the Hawaiian Archipelago was used in a suite of population genetic analyses to examine population histories and calculate coalescence times. We review a recent phylogenetic hypothesis for the Chaetodontidae and optimize ancestral distributions to nodes as a means of inferring colonization pathways to Hawaii.Results We found no evidence for population subdivisions across their ranges for any of the three endemic Hawaiian butterflyfish species (ΦST ≈ 0; P &gt; 0.05 in each case). Coalescence analyses revealed that C. multicinctus, C. miliaris and C. fremblii date to genetic bottlenecks of c. 12 ka (95% confidence interval of τ, 0–46,732 years ago), c. 74 ka (95% confidence interval of τ, 62,918–105,699 years ago) and c. 301 ka (95% confidence interval of τ, 88,981–478,495 years ago), respectively. We found that the West Pacific appears to be the ancestral source for two of three independent colonization events to Hawaii (leading to the speciation of C. miliaris and C. fremblii). The third colonization of Hawaii (leading to the divergence of C. multicinctus) is ambiguous, but may have involved island‐hopping from the South Pacific via the Line Islands.Main conclusions Our results are consistent with the growing body of data indicating that ecological specialists may be more susceptible to severe population bottlenecks during large‐scale climatic variation on evolutionary time‐scales. The isolation of the Hawaiian Archipelago presents challenges for colonization by even the most highly dispersive marine organisms, and routes of colonization by endemic butterflyfishes show a variable pattern, indicating that there may be several pathways, both spatially and temporally, for marine fauna to colonize Hawaii. Hawaiian endemic butterflyfishes appear to represent genetically homogeneous populations across the archipelago.

The phylogenetic position of “ Papio ruhei” – a unique baboon taxon from Somalia

Baboons from the lower Webi Shebelli, Somalia have been described as a distinct taxon, Papio ruhei, in 1942. The distinctiveness was later questioned and P. ruhei was classified as synonym of Papio cynocephalus ibeanus (Ibean baboon). A molecular genetic analysis of mitochondrial DNA of the type specimen supported synonymy and revealed that hybridization events between olive ( Papio anubis) and yellow baboons ( Papio c. cynocephalus) may have played a major role in the evolution of the baboons of E and NE Africa and the Arabian peninsula.

A familial case of mitochondrial disease resembling Alport syndrome

A 38-year-old man with mild sensorineural hearing loss, diabetes mellitus, proteinuria, and slight renal dysfunction was admitted to our hospital for a renal biopsy to determine the cause of kidney disease. His elder sister and mother also had sensorineural hearing loss and renal failure, suggesting the existence of a common genetic disease in this family. Although the clinical features of the patient were similar to features of Alport syndrome, renal biopsy revealed no sign of Alport syndrome. We next considered a possibility of a mitochondrial kidney disease described by Jansen in 1997. Indeed, genetic analysis of mitochondrial DNA clarified the existence of A3243G mutation in the patient and his sister. This syndrome should be recognized by nephrologists as a differential diagnosis of Alport syndrome, diabetic nephropathy, and primary glomerular diseases.

The NADH Dehydrogenase Genes of Apis mellifera, A. cerana, A. dorsata, A. laboriosa and A. florea: Sequence Comparison and Genetic Diversity

The genetic analysis of mitochondrial DNA (mtDNA) provides substantial information for evolutionary studies. A relatively small size compared with nuclear DNA, a rapid rate of sequence divergence, and maternal inheritance, make the mtDNA a useful tool for molecular phylogenetic studies. Here, we investigated and analyzed the mtDNA of five species of honeybees, Apis mellifera, A. cerana, A. dorsata, A. laboriosa and A. florea collected from Japan, Nepal, and India. A 528-bp DNA fragment of the NADH dehydrogenase subunit 4 (ND4 according to A. mellifera's mt DNA sequence) was PCR-amplified and sequenced. The DNA and deduced amino acid sequences were aligned and the phylogenetic relationships were investigated. The results indicate the genetic diversity of this functional protein among different honeybee species. For these studied species, a high A+T content (from 78.21 to 79.74%) was observed. Of the three colon positions, the third and the second positions show the most AT bias (91.93%) and the least AT bias (69.66%), respectively. The extremely high A+T content in the gene leads to high A → T and T → A transversion substitutions and the biases of colon usage. The phylogenetic trees were constructed with maximum likelihood method for the amino acid and the nucleotide sequences of ND4. For the analysis of nucleotide sequences, the first and second positions and the third position of the colons were separately investigated. All trees showed that evolutionary relationship between A. mellifera and A. cerana was close as well as between A. dorsata and A. laboriosa, while the phylogenetic position of A. florea was uncertain.

Oftalmoplejía crónica progresiva externa familiar de origen mitocondrial

The syndrome of chronic progressive external ophthalmoplegia (CPEO) is a mitochondrial disease characterized by ptosis and ophthalmoplegia has that has been associated to the presence of large deletion, single or multiple, in the mitochondrial DNA of skeletal muscle. We report a familiar case of chronic progressive external ophthalmoplegia of maternal inheritance that began at birth, and developed with slow progression but with no multisystemic involvement. Non of the affected individuals had ragged-red fibers in skeletal muscle. Genetic analysis of mitochondrial DNA revealed the presence of a single deletion of 4,977 bp that encompasses the nucleotide positions 8,482 to 13,460, flanked by a direct repeat sequence. The amount of deleted mitochondrial DNA (15%) in this patient's muscle suggests, even if the percentage of the mutation is low, that this deletion is the molecular cause of the phenotypic presentation of this patient. This is one of the few cases described in the literature of CPEO maternally inherited.

Deleción en el ADN mitocondrial de una paciente brasileña con oftalmoplejía cróncia progresiva externa

The syndrome of chronic progressive external ophthalmoplegia (CPEO) has been associated to the presence of large deletion, single or multiple, in the mitochondrial DNA of skeletal muscle. We report a sporadic case of chronic progressive external ophthalmoplegia that began at age 19 years and was associated with ragged red fibers in skeletal muscle. Genetic analysis of mitochondrial DNA revealed the presence of a single deletion of 4237 bp that encompasses the nucleotide positions 9486 to 13722, a location that has not been described before, and flanked by a direct repeat sequence. The deletion is flanked by a direct repeat. The amount of deleted mitochondrial DNA (55%) in this patient's muscle suggests that this deletion is the molecular cause of the phenotypic presentation of this patient.

Epilepsia partialis continua associated with NADH-coenzyme Q reductase deficiency

We report the clinical, neuroradiological and biochemical features of a patient with epilepsia partialis continua (EPC). MRI studies disclosed multiple cortico-subcortical areas of abnormal signal intensity. The activity of complex I of the mitochondrial respiratory chain was markedly reduced in skeletal muscle. The biochemical defect was reflected in vivo by a failure of brain and skeletal muscle bioenergetics, as shown by exercise and phosphorus magnetic resonance spectroscopy ( 31P-MRS) studies. Muscle morphology was repeatedly normal, and molecular genetic analysis of mitochondrial DNA was not informative. On the basis of in vivo and in vitro findings, the observed defect of the mitochondrial respiratory chain was considered the underlying biochemical pathogenesis of the disease. The observation of an oxidative defect in the brain and skeletal muscle of a patient with EPC emphasizes the importance of studying mitochondrial energy metabolism in patients with EPC not associated with primary CNS lesions when clinical and morphological findings suggesting a mitochondrial disorder are lacking. 31P-MRS can be a useful method to uncover deficits of CNS mitochondrial function and provide the indication for further biochemical studies.