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Heteroplasmy

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https://www.readbyqxmd.com/read/28087770/article-discoveries
#1
Anke Konrad, Owen Thompson, Robert H Waterston, Donald G Moerman, Peter D Keightley, Ulfar Bergthorsson, Vaishali Katju
Mitochondrial genomes of metazoans, given their elevated rates of evolution, have served as pivotal markers for phylogeographic studies and recent phylogenetic events. In order to determine the dynamics of spontaneous mitochondrial mutations in small populations in the absence and presence of selection, we evolved mutation accumulation (MA) lines of Caenorhabditis elegans in parallel over 409 consecutive generations at three varying population sizes of N = 1, 10 and 100 hermaphrodites. The N =1 populations should have a minimal influence of natural selection to provide the spontaneous mutation rate and the expected rate of neutral evolution, whereas larger population sizes should experience increasing intensity of selection...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28078444/mps-analysis-of-the-mtdna-hypervariable-regions-on-the-miseq-with-improved-enrichment
#2
Mitchell M Holland, Laura A Wilson, Sarah Copeland, Gloria Dimick, Charity A Holland, Robert Bever, Jennifer A McElhoe
The non-coding displacement (D) loop of the human mitochondrial (mt) genome contains two hypervariable regions known as HVR1 and HVR2 that are most often analyzed by forensic DNA laboratories. The massively parallel sequencing (MPS) protocol from Illumina (Human mtDNA D-Loop Hypervariable Region protocol) utilizes four sets of established PCR primer pairs for the initial amplification (enrichment) step that span the hypervariable regions. Transposase adapted (TA) sequences are attached to the 5'-end of each primer, allowing for effective library preparation prior to analysis on the MiSeq, and AmpliTaq Gold DNA polymerase is the enzyme recommended for amplification...
January 11, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/27994972/pursuing-the-quest-for-better-understanding-the-taxonomic-distribution-of-the-system-of-doubly-uniparental-inheritance-of-mtdna
#3
Arthur Gusman, Sophia Lecomte, Donald T Stewart, Marco Passamonti, Sophie Breton
There is only one exception to strict maternal inheritance of mitochondrial DNA (mtDNA) in the animal kingdom: a system named doubly uniparental inheritance (DUI), which is found in several bivalve species. Why and how such a radically different system of mitochondrial transmission evolved in bivalve remains obscure. Obtaining a more complete taxonomic distribution of DUI in the Bivalvia may help to better understand its origin and function. In this study we provide evidence for the presence of sex-linked heteroplasmy (thus the possible presence of DUI) in two bivalve species, i...
2016: PeerJ
https://www.readbyqxmd.com/read/27988613/early-diverging-bumblebees-from-across-the-roof-of-the-world-the-high-mountain-subgenus-i-mendacibombus-i-revised-from-species-gene-coalescents-and-morphology-hymenoptera-apidae
#4
Paul H Williams, Jiaxing Huang, Pierre Rasmont, Jiandong An
The bumblebees of the subgenus Mendacibombus of the genus Bombus are the sister group to all other extant bumblebees and are unusual among bees for specialising in some of the highest elevation habitats with entomophilous plants on Earth. Most named taxa in this group (24 available names, from a total of 49 published names) were described originally from small differences in the colour pattern of the hair, many as parts (e.g. subspecies) of just one species. Subsequent taxonomic treatments recognised multiple species, but have described very few morphological characters, most of which are in the male genitalia...
December 1, 2016: Zootaxa
https://www.readbyqxmd.com/read/27955616/the-ability-of-human-nuclear-dna-to-cause-false-positive-low-abundance-heteroplasmy-calls-varies-across-the-mitochondrial-genome
#5
Levent Albayrak, Kamil Khanipov, Maria Pimenova, George Golovko, Mark Rojas, Ioannis Pavlidis, Sergei Chumakov, Gerardo Aguilar, Arturo Chávez, William R Widger, Yuriy Fofanov
BACKGROUND: Low-abundance mutations in mitochondrial populations (mutations with minor allele frequency ≤ 1%), are associated with cancer, aging, and neurodegenerative disorders. While recent progress in high-throughput sequencing technology has significantly improved the heteroplasmy identification process, the ability of this technology to detect low-abundance mutations can be affected by the presence of similar sequences originating from nuclear DNA (nDNA). To determine to what extent nDNA can cause false positive low-abundance heteroplasmy calls, we have identified mitochondrial locations of all subsequences that are common or similar (one mismatch allowed) between nDNA and mitochondrial DNA (mtDNA)...
December 12, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27937010/high-occurrence-of-length-heteroplasmy-in-domestic-bactrian-camel-camelus-bactrianus
#6
Xiaohong He, Xiaofei Chen, Wenbin Zhang, Yabin Pu, Shen Song, Jianlin Han, Kunzhe Dong, Qianjun Zhao, Weijun Guan, Yuehui Ma, Lin Jiang
Heteroplasmy is the presence of more than one mitochondrial DNA (mtDNA) variant within a cell, tissue, or individual. In this study, sequence variation was investigated in the control region (CR) of mitochondrial DNA (mtDNA) from 135 individuals belonging to five primary domestic Bactrian camel breeds in China and Mongolia. Due to variation of the repeat unit G(T/C)(AC)n, length heteroplasmy was detected within each camel by direct sequencing and fragment analysis. A high occurrence of mtDNA heteroplasmy, up to 100 percentages was observed in five camel populations...
December 10, 2016: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/27919073/mitochondrial-replacement-in-human-oocytes-carrying-pathogenic-mitochondrial-dna-mutations
#7
Eunju Kang, Jun Wu, Nuria Marti Gutierrez, Amy Koski, Rebecca Tippner-Hedges, Karen Agaronyan, Aida Platero-Luengo, Paloma Martinez-Redondo, Hong Ma, Yeonmi Lee, Tomonari Hayama, Crystal Van Dyken, Xinjian Wang, Shiyu Luo, Riffat Ahmed, Ying Li, Dongmei Ji, Refik Kayali, Cengiz Cinnioglu, Susan Olson, Jeffrey Jensen, David Battaglia, David Lee, Diana Wu, Taosheng Huang, Don P Wolf, Dmitry Temiakov, Juan Carlos Izpisua Belmonte, Paula Amato, Shoukhrat Mitalipov
Maternally inherited mitochondrial (mt)DNA mutations can cause fatal or severely debilitating syndromes in children, with disease severity dependent on the specific gene mutation and the ratio of mutant to wild-type mtDNA (heteroplasmy) in each cell and tissue. Pathogenic mtDNA mutations are relatively common, with an estimated 778 affected children born each year in the United States. Mitochondrial replacement therapies or techniques (MRT) circumventing mother-to-child mtDNA disease transmission involve replacement of oocyte maternal mtDNA...
December 8, 2016: Nature
https://www.readbyqxmd.com/read/27908228/detection-of-mutations-in-mitochondrial-dna-by-droplet-digital-pcr
#8
REVIEW
J K Sofronova, Y Y Ilinsky, K E Orishchenko, E G Chupakhin, E A Lunev, I O Mazunin
Mutations in mitochondrial DNA (mtDNA) may result in various pathological processes. Detection of mutant mtDNAs is a problem for diagnostic practice that is complicated by heteroplasmy - a phenomenon of the inferring presence of at least two allelic variants of the mitochondrial genome. Also, the level of heteroplasmy largely determines the profile and severity of clinical manifestations. Here we discuss detection of mutations in heteroplasmic mtDNA using up-to-date methods that have not yet been introduced as routine clinical assays...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27899967/heteroplasmy-of-mutant-mitochondrial-dna-a10398g-and-analysis-of-its-prognostic-value-in-non-small-cell-lung-cancer
#9
Yuexiao Qi, Yuehua Wei, Qiaoli Wang, Hui Xu, You Wang, Anqi Yao, Hui Yang, Yan Gao, Fuxiang Zhou
Mitochondrial dysfunction is associated with pathogenic mitochondrial (mt)DNA mutations. The majority of mtDNA point mutations have a heteroplasmic status, which is defined as the coexistence of wild-type and mutated DNA within a cell or tissue. Previous findings demonstrated that certain mtDNA heteroplasmic mutations contribute to widely spread chronic diseases, including cancer, and alterations in the heteroplasmy level are associated with the clinical phenotype and severity of cancer. In the present study, the proportions of mutant mtDNA 10398G were assessed using amplification-refractory mutation system-quantitative polymerase chain reaction (PCR) assay in 129 non-small cell lung cancer (NSCLC) tissue samples...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27896131/case-report-5%C3%A2-year-follow-up-of-adult-late-onset-mitochondrial-encephalomyopathy-with-lactic-acid-and-stroke-like-episodes-melas
#10
Kiri Sunde, Patrick R Blackburn, Anvir Cheema, Jennifer Gass, Jessica Jackson, Sarah Macklin, Paldeep S Atwal
Mitochondrial encephalomyopathy with lactic acid and stroke-like episodes (MELAS) is a multisystem mitochondrial disorder that typically presents in childhood. We describe the follow-up of a patient who was diagnosed with late-onset MELAS at the age of 49. Her clinical course includes sensorineural hearing loss, seizures, and multiple episodes of stroke-like metabolic crises. Molecular genetic testing on whole blood revealed 31% heteroplasmy of a m.3243A > G variant in the mtDNA, the causative variant in approximately 80% of MELAS cases...
December 2016: Molecular Genetics and Metabolism Reports
https://www.readbyqxmd.com/read/27869334/prediction-of-long-term-prognosis-by-heteroplasmy-levels-of-the-m-3243a-g-mutation-in-patients-with-the-mitochondrial-encephalomyopathy-lactic-acidosis-and-stroke-like-episodes-syndrome
#11
A Fayssoil, P Laforêt, W Bougouin, C Jardel, A Lombès, H M Bécane, N Berber, T Stojkovic, A Béhin, B Eymard, D Duboc, K Wahbi
BACKGROUND AND PURPOSE: Our aim was to determine the prognostic value of urine and blood heteroplasmy in patients with the m.3243A>G mutation. METHODS: Adults with the m.3243A>G mutation referred to our institution between January 2000 and May 2014 were retrospectively included. The relationship between their baseline clinical characteristics, their mutation load in urine and blood, and major adverse events (MAEs) during follow-up, defined as medical complications requiring a hospitalization or complicated by death, was studied...
November 21, 2016: European Journal of Neurology: the Official Journal of the European Federation of Neurological Societies
https://www.readbyqxmd.com/read/27843288/leber-s-hereditary-optic-neuropathy-is-multiorgan-not-mono-organ
#12
REVIEW
Josef Finsterer, Sinda Zarrouk-Mahjoub
Leber's hereditary optic neuropathy (LHON) is a maternally inherited mitochondrial disorder with bilateral loss of central vision primarily due to mitochondrial DNA (mtDNA) mutations in subunits of complex I in the respiratory chain (primary LHON mutations), while other mtDNA mutations can also be causative. Since the first description, it is known that LHON is not restricted to the eyes but is a multisystem disorder additionally involving the central nervous system, ears, endocrinological organs, heart, bone marrow, arteries, kidneys, or the peripheral nervous system...
2016: Clinical Ophthalmology
https://www.readbyqxmd.com/read/27843124/evolution-of-cell-to-cell-variability-in-stochastic-controlled-heteroplasmic-mtdna-populations
#13
Iain G Johnston, Nick S Jones
Populations of physiologically vital mitochondrial DNA (mtDNA) molecules evolve in cells under control from the nucleus. The evolution of populations of mixed mtDNA types is complicated and poorly understood, and variability of these controlled admixtures plays a central role in the inheritance and onset of genetic disease. Here, we develop a mathematical theory describing the evolution of, and variability in, these stochastic populations for any type of cellular control, showing that cell-to-cell variability in mtDNA and mutant load inevitably increases with time, according to rates that we derive and which are notably independent of the mechanistic details of feedback signaling...
November 3, 2016: American Journal of Human Genetics
https://www.readbyqxmd.com/read/27816849/a-collaborative-ednap-exercise-on-snapshot%C3%A2-based-mtdna-control-region-typing
#14
N E C Weiler, K Baca, D Ballard, F Balsa, M Bogus, C Børsting, F Brisighelli, J Červenáková, L Chaitanya, M Coble, V Decroyer, S Desmyter, K J van der Gaag, K Gettings, C Haas, J Heinrich, M João Porto, A J Kal, M Kayser, A Kúdelová, N Morling, A Mosquera-Miguel, F Noel, W Parson, V Pereira, C Phillips, P M Schneider, D Syndercombe Court, M Turanska, A Vidaki, P Woliński, L Zatkalíková, T Sijen
A collaborative European DNA Profiling (EDNAP) Group exercise was undertaken to assess the performance of an earlier described SNaPshot™-based screening assay (denoted mini-mtSNaPshot) (Weiler et al., 2016) [1] that targets 18 single nucleotide polymorphism (SNP) positions in the mitochondrial (mt) DNA control region and allows for discrimination of major European mtDNA haplogroups. Besides the organising laboratory, 14 forensic genetics laboratories were involved in the analysis of 13 samples, which were centrally prepared and thoroughly tested prior to shipment...
January 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/27814659/current-strategies-towards-therapeutic-manipulation-of-mtdna-heteroplasmy
#15
Claudia V Pereira, Carlos T Moraes
Mitochondrial disease is a multifactorial disorder involving both nuclear and mitochondrial genomes. Over the past 20 years, great progress was achieved in the field of gene editing which raised the possibility of partial or complete elimination of mutant mtDNA that causes disease phenotypes. Each cell contains thousands of copies of mtDNA which can be either wild-type (WT) or mutant, a condition called heteroplasmy. As there are multiple copies of mtDNA inside a cell, the percentage of mutant mtDNA can vary and a directional shift in the heteroplasmy ratio towards an increase of WT mtDNA copies would have therapeutic value...
January 1, 2017: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/27811968/very-short-mitochondrial-dna-fragments-and-heteroplasmy-in-human-plasma
#16
Ruoyu Zhang, Kiichi Nakahira, Xiaoxian Guo, Augustine M K Choi, Zhenglong Gu
Cell free DNA (cfDNA) has received increasing attention and has been studied in a broad range of clinical conditions. However, few studies have focused on mitochondrial DNA (mtDNA) in the cell free form. We optimized DNA isolation and sequencing library preparation protocols to better retain short DNA fragments from plasma, and applied these optimized methods to plasma samples from patients with sepsis. Our methods can retain substantially shorter DNA, resulting in an average of 11.5 fold increase in short DNA fragments yield (DNA <100bp)...
November 4, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27792786/genetic-evidence-for-elevated-pathogenicity-of-mitochondrial-dna-heteroplasmy-in-autism-spectrum-disorder
#17
Yiqin Wang, Martin Picard, Zhenglong Gu
Increasing clinical and biochemical evidence implicate mitochondrial dysfunction in the pathophysiology of Autism Spectrum Disorder (ASD), but little is known about the biological basis for this connection. A possible cause of ASD is the genetic variation in the mitochondrial DNA (mtDNA) sequence, which has yet to be thoroughly investigated in large genomic studies of ASD. Here we evaluated mtDNA variation, including the mixture of different mtDNA molecules in the same individual (i.e., heteroplasmy), using whole-exome sequencing data from mother-proband-sibling trios from simplex families (n = 903) where only one child is affected by ASD...
October 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27770035/replication-errors-made-during-oogenesis-lead-to-detectable-de-novo-mtdna-mutations-in-zebrafish-oocytes-with-a-low-mtdna-copy-number
#18
Auke B C Otten, Alphons P M Stassen, Michiel Adriaens, Mike Gerards, Richard G J Dohmen, Adriana J Timmer, Sabina J V Vanherle, Rick Kamps, Iris B W Boesten, Jo M Vanoevelen, Marc Muller, Hubert J M Smeets
Of all pathogenic mitochondrial DNA (mtDNA) mutations in humans, ∼25% is de novo, although the occurrence in oocytes has never been directly assessed. We used next-generation sequencing to detect point mutations directly in the mtDNA of 3-15 individual mature oocytes and three somatic tissues from eight zebrafish females. Various statistical and biological filters allowed reliable detection of de novo variants with heteroplasmy ≥1.5%. In total, we detected 38 de novo base substitutions, but no insertions or deletions...
December 2016: Genetics
https://www.readbyqxmd.com/read/27760018/relevance-of-molecular-changes-in-the-nd4-gene-in-german-shepherd-dog-tumours
#19
B Ślaska, L Grzybowska-Szatkowska, M Bugno-Poniewierska, A Gurgul, A Śmiech, D Różańska, J Dudka
The aim of the study was to identify polymorphisms and mutations in the mitochondrial ND4 gene and to analyse the associations between the occurrence of molecular changes in mtDNA and phenotypic traits in tumours in German Shepherd dogs. Fifty samples obtained from blood and tumour tissues of German Shepherd dogs with diagnosed tumours were analysed. DNA extraction, amplification, and sequencing of the mtDNA ND4 gene, and bioinformatics, statistical, and in silico protein coding SNP analyses were performed...
September 1, 2016: Polish Journal of Veterinary Sciences
https://www.readbyqxmd.com/read/27721048/characterization-of-a-leber-s-hereditary-optic-neuropathy-lhon-family-harboring-two-primary-lhon-mutations-m-11778g-a-and-m-14484t-c-of-the-mitochondrial-dna
#20
Claudia B Catarino, Uwe Ahting, Mirjana Gusic, Arcangela Iuso, Birgit Repp, Katrin Peters, Saskia Biskup, Bettina von Livonius, Holger Prokisch, Thomas Klopstock
Leber's hereditary optic neuropathy (LHON) is an inherited mitochondrial disease that usually leads to acute or subacute bilateral central vision loss. In 95% of cases, LHON is caused by one of three primary mutations of the mitochondrial DNA (mtDNA), m.11778G>A in the MT-ND4 gene, m.14484T>C in the MT-ND6 gene, or m.3460G>A in the MT-ND1 gene. Here we characterize clinically, genetically, and biochemically a LHON family with multiple patients harboring two of these primary LHON mutations, m.11778G>A homoplasmic and m...
October 6, 2016: Mitochondrion
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