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https://www.readbyqxmd.com/read/28818680/clinical-validation-of-copy-number-variant-detection-from-targeted-next-generation-sequencing-panels
#1
Jennifer Kerkhof, Laila C Schenkel, Jack Reilly, Sheri McRobbie, Erfan Aref-Eshghi, Alan Stuart, C Anthony Rupar, Paul Adams, Robert A Hegele, Hanxin Lin, David Rodenhiser, Joan Knoll, Peter J Ainsworth, Bekim Sadikovic
Next-generation sequencing (NGS) technology has rapidly replaced Sanger sequencing in the assessment of sequence variations in clinical genetics laboratories. One major limitation of current NGS approaches is the ability to detect copy number variations (CNVs) greater than approximately 50bp. Since these represent a major mutational burden in many genetic disorders, parallel CNV assessment using alternate supplemental methods, along with the NGS analysis, is normally required resulting in increased labor, costs, and turnaround times...
August 14, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28818596/cardiometabolic-phenotypes-and-mitochondrial-dna-copy-number-in-two-cohorts-of-uk-women
#2
Anna L Guyatt, Kimberley Burrows, Philip A I Guthrie, Sue Ring, Wendy McArdle, Ian N M Day, Raimondo Ascione, Debbie A Lawlor, Tom R Gaunt, Santiago Rodriguez
The mitochondrial genome is present at variable copy number between individuals. Mitochondria are vulnerable to oxidative stress, and their dysfunction may be associated with cardiovascular disease. The association of mitochondrial DNA copy number with cardiometabolic risk factors (lipids, glycaemic traits, inflammatory markers, anthropometry and blood pressure) was assessed in two independent cohorts of European origin women, one in whom outcomes were measured at mean (SD) age 30 (4.3) years (N=2278) and the second at 69...
August 14, 2017: Mitochondrion
https://www.readbyqxmd.com/read/28810700/a-single-mini-barcode-test-to-screen-for-australian-mammalian-predators-from-environmental-samples
#3
Elodie Modave, Anna J MacDonald, Stephen D Sarre
Identification of species from trace samples is now possible through the comparison of diagnostic DNA fragments against reference DNA sequence databases. DNA detection of animals from non-invasive samples, such as predator faeces (scats) that contain traces of DNA from their species of origin, has proved to be a valuable tool for the management of elusive wildlife. However, application of this approach can be limited by the availability of appropriate genetic markers. Scat DNA is often degraded, meaning that longer DNA sequences, including standard DNA barcoding markers, are difficult to recover...
August 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28807237/mitochondrial-dysfunctions-in-bladder-cancer-exploring-their-role-as-disease-markers-and-potential-therapeutic-targets
#4
REVIEW
Antonella Cormio, Francesca Sanguedolce, Clara Musicco, Vito Pesce, Giuseppe Calò, Pantaleo Bufo, Giuseppe Carrieri, Luigi Cormio
Bladder cancer (BC) is a major cause of mortality worldwide as it currently lacks fully reliable markers of disease outcome and effective molecular targets for therapy. Mitochondria play a key role in cell metabolism but the role of mitochondrial dysfunctions in BC has been scarcely investigated. In this review, we explored current evidence for the potential role of mitochondrial DNA (mtDNA) alterations (point mutations and copy number) as disease markers in BC. Some germline mtDNA mutations detectable in blood could represent a non-invasive tool to predict the risk of developing BC...
September 2017: Critical Reviews in Oncology/hematology
https://www.readbyqxmd.com/read/28803790/utility-of-the-cytochrome-c-oxidase-subunit-i-gene-for-the-diagnosis-of-toxoplasmosis-using-pcr
#5
Xue Feng, Kazumi Norose, Kexin Li, Kenji Hikosaka
Toxoplasmosis is caused by the protozoan parasite Toxoplasma gondii, which belongs to the phylum Apicomplexa. Since this parasite causes severe clinical symptoms in immunocompromised patients, early diagnosis of toxoplasmosis is essential. PCR is currently used for early diagnosis, but there is no consensus regarding the most effective method for amplifying Toxoplasma DNA. In this study, we considered the utility of the cytochrome c subunit I (cox1) gene, which is encoded in the mitochondrial DNA of this parasite, as a novel target of PCR for the diagnosis of toxoplasmosis...
August 10, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28771582/distinct-radiation-responses-after-in-vitro-mtdna-depletion-are-potentially-related-to-oxidative-stress
#6
Marike W van Gisbergen, An M Voets, Rianne Biemans, Roland F Hoffmann, Marie-José Drittij-Reijnders, Guido R M M Haenen, Irene H Heijink, Kasper M A Rouschop, Ludwig J Dubois, Philippe Lambin
Several clinically used drugs are mitotoxic causing mitochondrial DNA (mtDNA) variations, and thereby influence cancer treatment response. We hypothesized that radiation responsiveness will be enhanced in cellular models with decreased mtDNA content, attributed to altered reactive oxygen species (ROS) production and antioxidant capacity. For this purpose BEAS-2B, A549, and 143B cell lines were depleted from their mtDNA (ρ0). Overall survival after irradiation was increased (p<0.001) for BEAS-2B ρ0 cells, while decreased for both tumor ρ0 lines (p<0...
2017: PloS One
https://www.readbyqxmd.com/read/28770830/resveratrol-alleviates-diabetic-cardiomyopathy-in-rats-by-improving-mitochondrial-function-through-pgc-1%C3%AE-deacetylation
#7
Wei-Jin Fang, Chun-Jiang Wang, Yang He, Yu-Lu Zhou, Xiang-Dong Peng, Shi-Kun Liu
Recent evidence shows that resveratrol (RSV) may ameliorate high-glucose-induced cardiac oxidative stress, mitochondrial dysfunction and myocardial fibrosis in diabetes. However, the mechanisms by which RSV regu¬lates mitochondrial function in diabetic cardiomyopathy have not been fully elucidated. Mitochondrial dysfunction contributes to cardiac dysfunction in diabetic patients, which is associated with dysregulation of peroxisome proliferator-activated receptor gamma coactivator-1α (PGC-1α). In this study we examined whether resveratrol alleviated cardiac dysfunction in diabetes by improving mitochondrial function via SIRT1-mediated PGC-1α deacetylation...
August 3, 2017: Acta Pharmacologica Sinica
https://www.readbyqxmd.com/read/28768180/increased-total-mtdna-copy-number-cures-male-infertility-despite-unaltered-mtdna-mutation-load
#8
Min Jiang, Timo Eino Sakari Kauppila, Elisa Motori, Xinping Li, Ilian Atanassov, Kat Folz-Donahue, Nina Anna Bonekamp, Sara Albarran-Gutierrez, James Bruce Stewart, Nils-Göran Larsson
Mutations of mtDNA cause mitochondrial diseases and are implicated in age-associated diseases and aging. Pathogenic mtDNA mutations are often present in a fraction of all mtDNA copies, and it has been widely debated whether the proportion of mutant genomes or the absolute number of wild-type molecules determines if oxidative phosphorylation (OXPHOS) will be impaired. Here, we have studied the male infertility phenotype of mtDNA mutator mice and demonstrate that decreasing mtDNA copy number worsens mitochondrial aberrations of spermatocytes and spermatids in testes, whereas an increase in mtDNA copy number rescues the fertility phenotype and normalizes testes morphology as well as spermatocyte proteome changes...
August 1, 2017: Cell Metabolism
https://www.readbyqxmd.com/read/28767123/complete-mitochondrial-genome-of-the-lappet-moth-kunugia-undans-lepidoptera-lasiocampidae-genomic-comparisons-among-macroheteroceran-superfamilies
#9
Min Jee Kim, Jun Seong Jeong, Jong Seok Kim, Su Yeon Jeong, Iksoo Kim
The mitochondrial genome (mitogenome) characteristics of the monotypic Lasiocampoidea are largely unknown, because only limited number of mitogenomes is available from this superfamily. In this study, we sequenced the complete mitogenome of the lappet moth, Kunugia undans (Lepidoptera: Lasiocampidae) and compared it to those of Lasiocampoidea and macroheteroceran superfamilies (59 species in six superfamilies). The 15,570-bp K. undans genome had one additional trnR that was located between trnA and trnN loci and this feature was unique in Macroheterocera, including Lasiocampoidea...
July 31, 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28756741/modulation-of-mitochondrial-dna-copy-number-to-induce-hepatocytic-differentiation-of-human-amniotic-epithelial-cells
#10
Vijesh Vaghjiani, Jason E Cain, William Lee, Vijayaganapathy Vaithilingam, Bernard E Tuch, Justin St John
Mitochondrial DNA (mtDNA) copy number is tightly regulated during pluripotency and differentiation. There is increased demand of cellular ATP during differentiation for energy intensive cell types such as hepatocytes and neurons to meet the cell's functional requirements. During hepatocyte differentiation, mtDNA copy number must be synchronously increased to generate sufficient ATP through oxidative phosphorylation. Unlike bone marrow mesenchymal cells (BM-MSC), mtDNA copy number failed to increase by 28 days of differentiation of Human Amniotic Epithelial Cells (hAEC) into Hepatocyte-Like Cells (HLC) despite their expression of some end stage hepatic markers...
July 29, 2017: Stem Cells and Development
https://www.readbyqxmd.com/read/28754700/segregation-of-mitochondrial-dna-mutations-in-the-human-placenta-implication-for-prenatal-diagnosis-of-mtdna-disorders
#11
Pauline Vachin, Elodie Adda-Herzog, Gihad Chalouhi, Caroline Elie, Marlène Rio, Sophie Rondeau, Nadine Gigarel, Fabienne Jabot Hanin, Sophie Monnot, Roxana Borghese, Joana Bengoa, Yves Ville, Agnes Rotig, Arnold Munnich, Jean-Paul Bonnefont, Julie Steffann
BACKGROUND: Mitochondrial DNA (mtDNA) disorders have a high clinical variability, mainly explained by variation of the mutant load across tissues. The high recurrence risk of these serious diseases commonly results in requests from at-risk couples for prenatal diagnosis (PND), based on determination of the mutant load on a chorionic villous sample (CVS). Such procedures are hampered by the lack of data regarding mtDNA segregation in the placenta.The objectives of this report were to determine whether mutant loads (1) are homogeneously distributed across the whole placentas, (2) correlate with those in amniocytes and cord blood cells and (3) correlate with the mtDNA copy number...
July 28, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/28751712/activation-of-mitophagy-leads-to-decline-in-mfn2-and-loss-of-mitochondrial-mass-in-fuchs-endothelial-corneal-dystrophy
#12
Anne-Sophie Benischke, Shivakumar Vasanth, Takashi Miyai, Kishore Reddy Katikireddy, Tomas White, Yuming Chen, Adna Halilovic, Marianne Price, Francis Price, Paloma B Liton, Ula V Jurkunas
Human corneal endothelial cells (HCEnCs) are terminally differentiated cells that have limited regenerative potential. The large numbers of mitochondria in HCEnCs are critical for pump and barrier function required for corneal hydration and transparency. Fuchs Endothelial Corneal Dystrophy (FECD) is a highly prevalent late-onset oxidative stress disorder characterized by progressive loss of HCEnCs. We previously reported increased mitochondrial fragmentation and reduced ATP and mtDNA copy number in FECD. Herein, carbonyl cyanide m-chlorophenyl hydrazone (CCCP)-induced mitochondrial depolarization decreased mitochondrial mass and Mfn2 levels, which were rescued with mitophagy blocker, bafilomycin, in FECD...
July 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28734953/estimating-relative-mitochondrial-dna-copy-number-using-high-throughput-sequencing-data
#13
Pan Zhang, Brian D Lehmann, David C Samuels, Shilin Zhao, Ying-Yong Zhao, Yu Shyr, Yan Guo
We hypothesize that the relative mitochondria copy number (MTCN) can be estimated by comparing the abundance of mitochondrial DNA to nuclear DNA reads using high throughput sequencing data. To test this hypothesis, we examined relative MTCN across 13 breast cancer cell lines using the RT-PCR based NovaQUANT Human Mitochondrial to Nuclear DNA Ratio Kit as the gold standard. Six distinct computational approaches were used to estimate the relative MTCN in order to compare to the RT-PCR measurements. The results demonstrate that relative MTCN correlates well with the RT-PCR measurements using exome sequencing data, but not RNA-seq data...
July 19, 2017: Genomics
https://www.readbyqxmd.com/read/28726777/humanin-g-hng-protects-age-related-macular-degeneration-amd-transmitochondrial-arpe-19-cybrids-from-mitochondrial-and-cellular-damage
#14
Sonali Nashine, Pinchas Cohen, Marilyn Chwa, Stephanie Lu, Anthony B Nesburn, Baruch D Kuppermann, M Cristina Kenney
Age-related macular degeneration (AMD) ranks third among the leading causes of visual impairment with a blindness prevalence rate of 8.7%. Despite several treatment regimens, such as anti-angiogenic drugs, laser therapy, and vitamin supplementation, being available for wet AMD, to date there are no FDA-approved therapies for dry AMD. Substantial evidence implicates mitochondrial damage and retinal pigment epithelium (RPE) cell death in the pathogenesis of AMD. However, the effects of AMD mitochondria and Humanin G (HNG), a more potent variant of the mitochondrial-derived peptide (MDP) Humanin, on retinal cell survival have not been elucidated...
July 20, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28722338/hdr-del-a-tool-based-on-hamming-distance-for-prioritizing-pathogenic-chromosomal-deletions-in-exome-sequencing
#15
Atsuko Imai, Masakazu Kohda, Kaori Kobayashi, Tomoko Hirata, Yasushi Sakata, Kei Murayama, Akira Ohtake, Yasushi Okazaki, Akihiro Nakaya, Jurg Ott
High-density oligonucleotide arrays have been widely used to detect pathogenic chromosomal deletions. In addition to high-density oligonucleotide arrays, programs using whole exome sequencing have become available for estimating copy number variations using depth of coverage. Here we propose a new statistical method, HDR-del, to prioritize pathogenic chromosomal deletions based on Hamming distance in exome sequencing. In vcf (Variant Call Format) files generated from exome sequencing, hemizygous chromosomal deletion regions lack heterozygous variants and lead to apparent long runs of homozygosity (ROH)...
July 19, 2017: Human Mutation
https://www.readbyqxmd.com/read/28720802/a-novel-adoa-associated-opa1-mutation-alters-the-mitochondrial-function-membrane-potential-ros-production-and-apoptosis
#16
Juanjuan Zhang, Xiaoling Liu, Xiaoyang Liang, Yuanyuan Lu, Ling Zhu, Runing Fu, Yanchun Ji, Wenlu Fan, Jie Chen, Bing Lin, Yimin Yuan, Pingping Jiang, Xiangtian Zhou, Min-Xin Guan
Autosomal dominant optic atrophy (ADOA) is a dominantly inherited optic neuropathy, affecting the specific loss of retinal ganglion cells (RGCs). The majority of affected cases of ADOA are associated with mutations in OPA1 gene. Our previous investigation identified the c.1198C > G (p.P400A) mutation in the OPA1 in a large Han Chinese family with ADOA. In this report, we performed a functional characterization using lymphoblostoid cell lines derived from affected members of this family and control subjects...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28717105/ephedrine-induced-mitophagy-via-oxidative-stress-in-human-hepatic-stellate-cells
#17
Ah Young Lee, Yoonjeong Jang, Seong-Ho Hong, Seung-Hee Chang, Sungjin Park, Sanghwa Kim, Kyung-Sun Kang, Ji-Eun Kim, Myung-Haing Cho
The herb Ephedra sinica (also known as Chinese ephedra or Ma Huang), used in traditional Chinese medicine, contains alkaloids identical to ephedrine and pseudoephedrine as its principal active constituents. Recent studies have reported that ephedrine has various side effects in the cardiovascular and nervous systems. In addition, herbal Ephedra, a plant containing many pharmacologically active alkaloids, principally ephedrine, has been reported to cause acute hepatitis. Many studies reported clinical cases, however, the cellular mechanism of liver toxicity by ephedrine remains unknown...
2017: Journal of Toxicological Sciences
https://www.readbyqxmd.com/read/28716668/incomplete-penetrance-in-mitochondrial-optic-neuropathies
#18
Leonardo Caporali, Alessandra Maresca, Mariantonietta Capristo, Valentina Del Dotto, Francesca Tagliavini, Maria Lucia Valentino, Chiara La Morgia, Valerio Carelli
Incomplete penetrance characterizes the two most frequent inherited optic neuropathies, Leber's Hereditary Optic Neuropathy (LHON) and dominant optic atrophy (DOA), due to genetic errors in the mitochondrial DNA (mtDNA) and the nuclear DNA (nDNA), respectively. For LHON, compelling evidence has accumulated on the complex interplay of mtDNA haplogroups and environmental interacting factors, whereas the nDNA remains essentially non informative. However, a compensatory mechanism of activated mitochondrial biogenesis and increased mtDNA copy number, possibly driven by a permissive nDNA background, is documented in LHON; when successful it maintains unaffected the mutation carriers, but in some individuals it might be hampered by tobacco smoking or other environmental factors, resulting in disease onset...
July 14, 2017: Mitochondrion
https://www.readbyqxmd.com/read/28714949/aspartate-%C3%AE-hydroxylase-disrupts-mitochondrial-dna-stability-and-function-in-hepatocellular-carcinoma
#19
C Tang, Y Hou, H Wang, K Wang, H Xiang, X Wan, Y Xia, J Li, W Wei, S Xu, Z Lei, T M Pawlik, H Wang, M Wu, F Shen
The mechanism of aberrant mitochondrial genome and function in hepatocellular carcinoma (HCC) remains largely unknown. Our previous study demonstrated an increased expression of aspartate β-hydroxylase (ASPH) in HCC tissues, which was associated with tumor invasiveness and a worse prognosis. Currently, we unexpectedly observed the presence of ASPH in purified mitochondrial protein fraction. In addition, immunostaining of both exogenously and endogenously expressed ASPH showed a colocalization with mitochondrial biomarkers...
July 17, 2017: Oncogenesis
https://www.readbyqxmd.com/read/28712868/salicylates-promote-mitochondrial-biogenesis-by-regulating-the-expression-of-pgc-1%C3%AE-in-murine-3t3-l1-pre-adipocytes
#20
Yimin Yan, Xiaohong Yang, Tao Zhao, Yi Zou, Rui Li, Yancheng Xu
Mitochondrial dysfunction has been associated with insulin resistance and diabetes. Decreased mitochondrial density and mitochondrial copy numbers have been found in insulin-resistant individuals. Restoration of the number of mitochondria and normal mitochondrial function has become an important therapeutic target of diabetes. Salicylate, the main active ingredient in aspirin, has been in medicinal use since ancient times. Little information regarding the effects of salicylate on mitochondrial function has been reported...
July 13, 2017: Biochemical and Biophysical Research Communications
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