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Kiwoung Yang, Ujjal Kumar Nath, Manosh Kumar Biswas, Md Abdul Kayum, Go-Eun Yi, Jonghoon Lee, Tae-Jin Yang, Ill-Sup Nou
Plant mitochondrial genomes (mtDNAs) vary in sequence structure. We assembled the Brassica oleracea var. capitata mtDNA using a mean coverage depth of 25X whole genome sequencing (WGS) and confirmed the presence of eight contigs/fragments by BLASTZ using the previously reported KJ820683 and AP012988 mtDNA as reference. Assembly of the mtDNA sequence reads resulted in a circular structure of 219,975 bp. Our assembled mtDNA, NCBI acc. no. KU831325, contained 34 protein-coding genes, 3 rRNA genes, and 19 tRNA genes with similarity to the KJ820683 and AP012988 reference mtDNA...
2018: PloS One
Naoki Yahata, Yuji Matsumoto, Minoru Omi, Naoki Yamamoto, Ryuji Hata
A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
March 13, 2018: Scientific Reports
Chamara Arachchighe Lahiru Weerasinghe, Bich-Hong Thi Bui, Thu Thi Vu, Hong-Loan Thi Nguyen, Bao-Khanh Phung, Van-Minh Nguyen, Van-Anh Pham, Vu-Hung Cao, Tuan-Nghia Phan
Leigh syndrome is a rare inherited, heterogeneous and progressive neurometabolic disorder that is mainly caused by specific mutations in nuclear DNA (nDNA) or mitochondrial DNA (mtDNA). The present study reported a case of childhood Leigh syndrome with a point mutation at bp 8,993 in the mitochondrial ATPase6 gene. A 21‑month‑old male child had developed epilepsy, muscular weakness and vomiting, which was accompanied by high fever. Magnetic resonance imaging indicated typical characteristics of Leigh syndrome, including a symmetric abnormal signal in the dorsal medulla oblongata and Sylvian fissure enlargement in association with an abnormal signal in the periventricular white matter and in the putamina and caudate heads...
March 1, 2018: Molecular Medicine Reports
Mark A Tarnopolsky, Arun N E Sundaram, John Provias, Lauren Brady, Bekim Sadikovic
Two patients with an m.8340G>A mitochondrial DNA variant have been reported with one patient showing ptosis, ophthalmoparesis and myopathy at 53% heteroplasmy and another with pigmentary retinopathy, cataracts and sensory neural deafness and slightly higher heteroplasmy (65%). Here we report that higher muscle mutant heteroplasmy (93%) for m.8340G>A is associated with ptosis, ophthalmoparesis and mitochondrial myopathy, thus confirming the initial phenotypic association and showing that heteroplasmy per se does not explain the phenotypic spectrum of disease associated with the m...
February 28, 2018: Mitochondrion
S Taheri, S James, V Roy, T Decaëns, B W Williams, F Anderson, R Rougerie, C-H Chang, G Brown, L Cunha, D W G Stanton, E Da Silva, J-H Chen, A R Lemmon, E Moriarty Lemmon, M Bartz, D Baretta, I Barois, E Lapied, M Coulis, L Dupont
Pontoscolex corethrurus is the most widespread earthworm species in tropical and sub-tropical zones and one of the most studied in soil science. Although, ecological interactions of P. corethrurus with its environment are well documented, the taxonomic status of the species remains unclear. In this study, we investigated phylogenetic relationships within the genus Pontoscolex, in particular focusing on morphologically indistinguishable (i.e., cryptic) lineages. A total of 792 specimens collected from 25 different countries and islands all over the world were analyzed using two mitochondrial (COI and 16S rDNA) and two nuclear (internal transcribed spacers 2 and 28S rDNA) markers, and a total of 11 morphological characters both internal and external were investigated in all genetically characterized lineages...
February 28, 2018: Molecular Phylogenetics and Evolution
Mitchell M Holland, Kateryna D Makova, Jennifer A McElhoe
Abstract : Distinguishing between maternal relatives through mitochondrial (mt) DNA sequence analysis has been a longstanding desire of the forensic community. Using a deep-coverage, massively parallel sequencing (DCMPS) approach, we studied the pattern of mtDNA heteroplasmy across the mtgenomes of 39 mother-child pairs of European decent; haplogroups H, J, K, R, T, U, and X. Both shared and differentiating heteroplasmy were observed on a frequent basis in these closely related maternal relatives, with the minor variant often presented as 2-10% of the sequencing reads...
February 26, 2018: Genes
Egija Zole, Renāte Ranka
In the last decades, studies about ageing have become more essential as our population grows older. The incidence of age-related diseases increases, which pose challenges both for societies and individuals in terms of life quality and economic impact. Understanding ageing and ageing-related processes will help us to slow down or even prevent these diseases and provide opportunities for healthy ageing; additionally, we all want to live longer. Ageing is a consequence of the interaction between processes that occur over time and genetics interacting with various disease states and an individual's lifestyle...
February 28, 2018: Biogerontology
Andy G X Zeng, Andy C Y Leung, Angela R Brooks-Wilson
Diffuse Large B-Cell Lymphoma (DLBCL) is an aggressive hematological cancer for which mitochondrial metabolism may play an important role. Mitochondrial DNA (mtDNA) encodes crucial mitochondrial proteins, yet the relationship between mtDNA and DLBCL remains unclear. We analyzed the functional consequences and mutational spectra of mtDNA somatic mutations and private constitutional variants in 40 DLBCL tumour-normal pairs. While private constitutional variants occurred frequently in the D-Loop, somatic mutations were randomly distributed across the mitochondrial genome...
February 26, 2018: Scientific Reports
Sonia Emperador, Mariona Vidal, Carmen Hernández-Ainsa, Cristina Ruiz-Ruiz, Daniel Woods, Ana Morales-Becerra, Jorge Arruga, Rafael Artuch, Ester López-Gallardo, M Pilar Bayona-Bafaluy, Julio Montoya, Eduardo Ruiz-Pesini
The onset of Leber hereditary optic neuropathy is relatively rare in childhood and, interestingly, the rate of spontaneous visual recovery is very high in this group of patients. Here, we report a child harboring a rare pathological mitochondrial DNA mutation, present in heteroplasmy, associated with the disease. A patient follow-up showed a rapid recovery of the vision accompanied by a decrease of the percentage of mutated mtDNA. A retrospective study on the age of recovery of all childhood-onset Leber hereditary optic neuropathy patients reported in the literature suggested that this process was probably related with pubertal changes...
2018: Frontiers in Neuroscience
Reiner A Veitia
Mitochondrial diseases may be caused by alterations of the mitochondrial genome. The pathogenic variant m.3243A>G is one of the most frequent causes of mitochondrial disease and the most common mitochondrial DNA mutation. Patients with a variant in mitochondrial DNA can have a mixture of mutated and wild-type genomes (heteroplasmy). In the case of the pathogenic variant m.3243A>G, the degree of heteroplasmy (H) correlates to some extent with the severity of the disease. Several longitudinal studies, where H is measured at two different time-points, have shown an annual decline in leukocyte H values...
February 20, 2018: Human Molecular Genetics
S Mishra, E Kacin, P Stamatiadis, S Franck, M Van der Jeught, H Mertes, G Pennings, P De Sutter, K Sermon, B Heindryckx, M Geens
The derivation of gametes from patient-specific pluripotent stem cells may provide new perspectives for genetic parenthood for patients currently facing sterility. We use current data to assess the gamete differentiation potential of patient-specific pluripotent stem cells and to determine which reprogramming strategy holds the greatest promise for future clinical applications. First, we compare the two best established somatic cell reprogramming strategies: the production of induced pluripotent stem cells (iPSC) and somatic cell nuclear transfer followed by embryonic stem cell derivation (SCNT-ESC)...
February 19, 2018: Molecular Human Reproduction
Doris G Leung, Julie S Cohen, Elizabeth Harlan Michelle, Renkui Bai, Andrew L Mammen, Lisa Christopher-Stine
We report the cases of 2 patients who presented to our Myositis Center with myalgias and elevated creatine kinase levels. Muscle biopsy showed pathological features consistent with mitochondrial myopathy. In both cases, a single large deletion in mitochondrial DNA at low-level heteroplasmy was identified by next-generation sequencing in muscle tissue. In 1 case, the deletion was identified in muscle tissue but not blood. In both cases, the deletion was only identified on next-generation sequencing of muscle mitochondrial DNA and missed on array comparative genome hybridization testing...
March 2018: Journal of Clinical Neuromuscular Disease
Edoardo Gaude, Christina Schmidt, Payam A Gammage, Aurelien Dugourd, Thomas Blacker, Sew Peak Chew, Julio Saez-Rodriguez, John S O'Neill, Gyorgy Szabadkai, Michal Minczuk, Christian Frezza
The bioenergetics and molecular determinants of the metabolic response to mitochondrial dysfunction are incompletely understood, in part due to a lack of appropriate isogenic cellular models of primary mitochondrial defects. Here, we capitalize on a recently developed cell model with defined levels of m.8993T>G mutation heteroplasmy, mTUNE, to investigate the metabolic underpinnings of mitochondrial dysfunction. We found that impaired utilization of reduced nicotinamide adenine dinucleotide (NADH) by the mitochondrial respiratory chain leads to cytosolic reductive carboxylation of glutamine as a new mechanism for cytosol-confined NADH recycling supported by malate dehydrogenase 1 (MDH1)...
February 15, 2018: Molecular Cell
Chunyu Liu, Jessica L Fetterman, Poching Liu, Yan Luo, Martin G Larson, Ramachandran S Vasan, Jun Zhu, Daniel Levy
Increasing evidence implicates mitochondrial dysfunction in aging and age-related conditions. But little is known about the molecular basis for this connection. A possible cause may be mutations in the mitochondrial DNA (mtDNA), which are often heteroplasmic-the joint presence of different alleles at a single locus in the same individual. However, the involvement of mtDNA heteroplasmy in aging and age-related conditions has not been investigated thoroughly. We deep-sequenced the complete mtDNA genomes of 356 Framingham Heart Study participants (52% women, mean age 43, mean coverage 4570-fold), identified 2880 unique mutations and comprehensively annotated them by MITOMAP and PolyPhen-2...
February 8, 2018: Human Genetics
Michelle A Peck, Kimberly Sturk-Andreaggi, Jacqueline T Thomas, Robert S Oliver, Suzanne Barritt-Ross, Charla Marshall
Generating mitochondrial genome (mitogenome) data from reference samples in a rapid and efficient manner is critical to harnessing the greater power of discrimination of the entire mitochondrial DNA (mtDNA) marker. The method of long-range target enrichment, Nextera XT library preparation, and Illumina sequencing on the MiSeq is a well-established technique for generating mitogenome data from high-quality samples. To this end, a validation was conducted for this mitogenome method processing up to 24 samples simultaneously along with analysis in the CLC Genomics Workbench and utilizing the AQME (AFDIL-QIAGEN mtDNA Expert) tool to generate forensic profiles...
January 16, 2018: Forensic Science International. Genetics
Lauren Brady, Bekim Sadikovic, C Anthony Rupar, Mark A Tarnopolsky
Mitochondrial DNA (mtDNA) mutations have been implicated in a wide variety of neurological conditions and are maternally inherited through a complex process which is not fully understood. Genetic counselling for mitochondrial conditions secondary to a mtDNA mutation can be challenging as it is not currently possible to accurately predict the mutational load/heteroplasmy of the mutation which could be passed to the offspring. In general, one expects that the higher the level of heteroplasmy the more likely that the same mtDNA mutation will be seen in the offspring...
February 1, 2018: Mitochondrion
Mengqin Duan, Jing Tu, Zuhong Lu
The co-existence of wild-type and mutated mitochondrial DNA (mtDNA) molecules termed heteroplasmy becomes a research hot point of mitochondria. In this review, we listed several methods of mtDNA heteroplasmy research, including the enrichment of mtDNA and the way of calling heteroplasmic variations. At the present, while calling the novel ultra-low level heteroplasmy, high-throughput sequencing method is dominant while the detection limit of recorded mutations is accurate to 0.01% using the other quantitative approaches...
February 3, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Rubi N Meza-Lázaro, Chantal Poteaux, Natalia J Bayona-Vásquez, Michael G Branstetter, Alejandro Zaldívar-Riverón
We assembled mitogenomes from 21 ant workers assigned to four morphospecies (E. ruidum spp. 1-4) and putative hybrids of the Ectatomma ruidum complex (E. ruidum spp. 2x3), and to E. tuberculatum using NGS data. Mitogenomes from specimens of E. ruidum spp. 3, 4 and 2 × 3 had a high proportion of polymorphic sites. We investigated whether polymorphisms in mitogenomes are due to nuclear mt paralogues (numts) or due to the presence of more than one mitogenome within an individual (heteroplasmy). We did not find loss of function signals in polymorphic protein-coding genes, and observed strong evidence for purifying selection in two haplotype-phased genes, which indicate the presence of two functional mitochondrial genomes coexisting within individuals instead of numts...
January 31, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Sarbast Ihsan Mustafa, Trude Schwarzacher, J S Heslop-Harrison
The geographical centre of domestication and species diversity for sheep (Ovis aries) lies around the Kurdistan region of Northern Iraq, within the 'Fertile Crescent'. From whole genome sequence reads, we assembled the mitochondrial genomes (mtDNA or mitogenome) of five animals of the two main Kurdistani sheep breeds Hamdani and Karadi and found they fitted into known sheep haplogroups (or matrilineages), with some SNPs. Haplotyping 31 animals showed presence of the main Asian (hpgA) and European (hpgB) haplogroups, as well as the rarer Anatolian haplogroup hpgC...
January 31, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Oliver M Russell, Isabelle Fruh, Pavandeep K Rai, David Marcellin, Thierry Doll, Amy Reeve, Mitchel Germain, Julie Bastien, Karolina A Rygiel, Raffaele Cerino, Andreas W Sailer, Majlinda Lako, Robert W Taylor, Matthias Mueller, Robert N Lightowlers, Doug M Turnbull, Stephen B Helliwell
We generated induced pluripotent stem cells (iPSCs) from patient fibroblasts to yield cell lines containing varying degrees of heteroplasmy for a m.13514 A > G mtDNA point mutation (2 lines) and for a ~6 kb single, large scale mtDNA deletion (3 lines). Long term culture of the iPSCs containing a single, large-scale mtDNA deletion showed consistent increase in mtDNA deletion levels with time. Higher levels of mtDNA heteroplasmy correlated with increased respiratory deficiency. To determine what changes occurred in deletion level during differentiation, teratomas comprising all three embryonic germ layers were generated from low (20%) and intermediate heteroplasmy (55%) mtDNA deletion clones...
January 29, 2018: Scientific Reports
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