Read by QxMD icon Read

mitochondrial copy number detect

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, Bert 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...
October 21, 2016: Genetics
Xingyun Su, Weibin Wang, Guodong Ruan, Min Liang, Jing Zheng, Ye Chen, Huiling Wu, Thomas J Fahey, Minxin Guan, Lisong Teng
Nuclear genetic alterations have been widely investigated in papillary thyroid cancer (PTC), however, the characteristics of the mitochondrial genome remain uncertain. We sequenced the entire mitochondrial genome of 66 PTCs, 16 normal thyroid tissues and 376 blood samples of healthy individuals. There were 2508 variations (543 sites) detected in PTCs, among which 33 variations were novel. Nearly half of the PTCs (31/66) had heteroplasmic variations. Among the 31 PTCs, 28 specimens harbored a total of 52 somatic mutations distributed in 44 sites...
October 10, 2016: International Journal of Molecular Sciences
Clara Valero, María José Buitrago, Maud Gits-Muselli, Marion Benazra, Aude Sturny-Leclère, Samia Hamane, Nicolas Guigue, Stéphane Bretagne, Alexandre Alanio
Pneumocystis jirovecii is an unculturable fungus and the causative agent of Pneumocystis pneumonia, a life-threatening opportunistic infection. Although molecular diagnosis is often based on the detection of mtLSU rRNA mitochondrial gene, the number of copies of mitochondrial genes had not been investigated. We developed and optimized six real-time PCR assays in order to determine the copy number of four mitochondrial genes (mtSSU rRNA, mtLSU rRNA, NAD1, and CYTB) in comparison to nuclear genome (DHPS and HSP70) and tested 84 bronchoalveolar fluids of patients at different stages of the infection...
2016: Frontiers in Microbiology
Ruxian Li, Yushuang Liu, Nan Chen, Yitong Zhang, Ge Song, Zhongling Zhang
BACKGROUND Migraine is a chronic disease that interferes with life quality and work productivity. Valproate shows protective effects against migraine, yet the underlying mechanisms are unclear. This study aimed to evaluate the potential effect of valproate on migraine using a rat model of nitroglycerin-induced trigeminovascular activation, as well as to explore the underlying mechanism. MATERIAL AND METHODS Intraperitoneal injection of nitroglycerin was conducted to induce trigeminovascular activation in rats...
2016: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
Fatemeh Bahreini, Massoud Houshmand, Mohammad Hossein Modaresi, Hassan Tonekaboni, Shahriar Nafissi, Ferdoss Nazari, Seyed Mohammad Akrami
OBJECTIVE: Pompe disease is a rare neuromuscular genetic disorder and is classified into two forms of early and late-onset. Over the past two decades, mitochondrial abnor- malities have been recognized as an important contributor to an array of neuromuscular diseases. We therefore aimed to compare mitochondrial copy number and mitochondrial displacement-loop sequence variation in infantile and adult Pompe patients. MATERIALS AND METHODS: In this retrospective study, the mitochondrial D-loop sequence was analyzed by polymerase chain reaction (PCR) and direct sequencing to detect pos- sible variation in 28 Pompe patients (17 infants and 11 adults)...
2016: Cell Journal
Bin He, Huiduo Guo, Yabin Gong, Ruqian Zhao
Lipopolysaccharide (LPS) has been reported to exert detrimental effects on boar sperm viability. In the present study, LPS was detected in boar semen samples at an average level of 0.62 ± 0.14 μg/mL. We treated boar sperm with 1 μg/mL LPS for 6 hours and examined alterations in sperm motility and apoptosis, together with mitochondrial functionality and mitochondrial reactive oxygen species generation. The expression and the location of toll-like receptor 4 (TLR4) and mitochondrial transcription factor A (TFAM) were determined to reveal possible mechanisms...
August 4, 2016: Theriogenology
Toshifumi Minamoto, Kimiko Uchii, Teruhiko Takahara, Takumi Kitayoshi, Tsuji Satsuki, Hiroki Yamanaka, Hideyuki Doi
The recently developed environmental DNA (eDNA) analysis has been used to estimate the distribution of aquatic vertebrates by using mitochondrial DNA (mtDNA) as a genetic marker. However, mtDNA markers have certain drawbacks such as variable copy number and maternal inheritance. In this study, we investigated the potential of using nuclear DNA (ncDNA) as a more reliable genetic marker for eDNA analysis by using common carp (Cyprinus carpio). We measured the copy numbers of cytochrome b (CytB) gene region of mtDNA and internal transcribed spacer 1 (ITS1) region of ribosomal DNA of ncDNA in various carp tissues and then compared the detectability of these markers in eDNA samples...
August 4, 2016: Molecular Ecology Resources
Argelia Cuenca, T Gregory Ross, Sean W Graham, Craig F Barrett, Jerrold I Davis, Ole Seberg, Gitte Petersen
Loss of introns in plant mitochondrial genes is commonly explained by retroprocessing. Under this model, an mRNA is reverse transcribed and integrated back into the genome, simultaneously affecting the contents of introns and edited sites. To evaluate the extent to which retroprocessing explains intron loss, we analyzed patterns of intron content and predicted RNA editing for whole mitochondrial genomes of 30 species in the monocot order Alismatales. In this group, we found an unusually high degree of variation in the intron content, even expanding the hitherto known variation among angiosperms...
2016: Genome Biology and Evolution
Youjin Deng, Qihui Zhang, Ray Ming, Longji Lin, Xiangzhi Lin, Yiying Lin, Xiao Li, Baogui Xie, Zhiqiang Wen
Hypomyces aurantius is a mycoparasite that causes cobweb disease, a most serious disease of cultivated mushrooms. Intra-species identification is vital for disease control, however the lack of genomic data makes development of molecular markers challenging. Small size, high copy number, and high mutation rate of fungal mitochondrial genome makes it a good candidate for intra and inter species differentiation. In this study, the mitochondrial genome of H. H.a0001 was determined from genomic DNA using Illumina sequencing...
2016: International Journal of Molecular Sciences
Megan E Schreeg, Henry S Marr, Emily H Griffith, Jaime L Tarigo, David M Bird, Mason V Reichard, Leah A Cohn, Michael G Levy, Adam J Birkenheuer
Cytauxzoon felis is a tick-transmitted protozoan parasite that infects felids. Clinical disease caused by acute C. felis infection rapidly progresses in domestic cats, leading to high morbidity and mortality. Accurately diagnosing cytauxzoonosis as soon as possible during acute infection would allow for earlier initiation of antiprotozoal therapy which could lead to higher survival rates. Molecular detection of parasite rRNA genes (18S) by PCR has previously been shown to be a sensitive method of diagnosing C...
July 30, 2016: Veterinary Parasitology
Jennifer Harmon, Whitney Gibbs, Ryan Whitaker, Rick Schnellmann, DeAnna Lynn Adkins
Traumatic brain injury (TBI) results in oxidative stress and calcium dysregulation in mitochondria. However, little work has examined perturbations of mitochondrial homeostasis in peri-injury tissue. We examined mitochondrial homeostasis after a unilateral controlled cortical impact (CCI) over the sensorimotor cortex in adult male rats. There was a significant reduction in PGC-1α mRNA at post-injury days 3 and 6 and a transient reduction in mtDNA copy number at 3 days post-injury that recovered by 6 days in the ipsi-injury striatum...
June 18, 2016: Journal of Neurotrauma
Markus Böhm, Helene Z Hill
Alpha-melanocyte-stimulating hormone (alpha-MSH) increases melanogenesis and protects from UV-induced DNA damage. However, its effect on mitochondrial DNA (mtDNA) damage is unknown. We have addressed this issue in a pilot study using human epidermal keratinocytes and melanocytes incubated with alpha-MSH and irradiated with UVB. Real-time touchdown PCR was used to quantify total and deleted mtDNA. The deletion detected encompassed the common deletion but was more sensitive to detection. There were 4.4 times more mtDNA copies in keratinocytes than in melanocytes...
2016: F1000Research
David Wragg, Maria Marti-Marimon, Benjamin Basso, Jean-Pierre Bidanel, Emmanuelle Labarthe, Olivier Bouchez, Yves Le Conte, Alain Vignal
Four main evolutionary lineages of A. mellifera have been described including eastern Europe (C) and western and northern Europe (M). Many apiculturists prefer bees from the C lineage due to their docility and high productivity. In France, the routine importation of bees from the C lineage has resulted in the widespread admixture of bees from the M lineage. The haplodiploid nature of the honeybee Apis mellifera, and its small genome size, permits affordable and extensive genomics studies. As a pilot study of a larger project to characterise French honeybee populations, we sequenced 60 drones sampled from two commercial populations managed for the production of honey and royal jelly...
2016: Scientific Reports
Yuan Gao, Hong-jing Nie, Dong Yang, Cheng-shi Ding, Min Jin, Zhi-qiang Chen, Zhi-gang Qiu, Xuan Guo, Zhao-lila Chen, Jun-wen Li
OBJECTIVE: To investigate the relationship between the changes of the copy numbers of mtDNA in peripheral blood mono-nucle- ar cell(PBMC) and the disordered of antioxidant capacity of hepatocellular carcinoma (HCC) patients. METHODS: The Ficoll Hypaque method was used to isolate the PBMC from blood specimens. The ND1 gene of the mitochondrial was amplified by real-time PCR; meantime β-actin was served as a quantitative standard marker; the difference of mtDNA copy number in PBMC was compared between HCC and healthy control group...
January 2016: Chinese Journal of Applied Physiology
Takanori Senoo, Mayumi Yamanaka, Atori Nakamura, Tomoki Terashita, Shinji Kawano, Shogo Ikeda
Quantitative polymerase chain reaction (QPCR) has been employed to detect DNA damage and repair in mitochondrial DNA (mtDNA) of human and several model organisms. The assay also permits the quantitation of relative mtDNA copy number in cells. Here, we developed the QPCR assay primers and reaction conditions for the fission yeast Schizosaccharomyces pombe, an important model of eukaryote biology, not previously described. Under these conditions, long targets (approximately 10kb) in mtDNA were quantitatively amplified using 0...
August 2016: Journal of Microbiological Methods
Yun Wang, Shuixiang He, Xingmei Zhu, Wei Qiao, Juan Zhang
INTRODUCTION: The aim of this investigation was to determine whether alterations in mitochondrial DNA (mtDNA) copy number in colon cancer were associated with clinicopathological parameters and postsurgical outcome. METHODS: By quantitative real-time PCR assay, the mtDNA copy number was detected in a cohort of colon cancer and matched adjacent colon tissues (n = 162). RESULTS: The majority of patients had higher mtDNA content in colon cancer tissues than matched adjacent colon tissues...
May 17, 2016: International Journal of Biological Markers
Eun Hyun Ahn, Seung Hyuk Lee, Joon Yup Kim, Chia-Cheng Chang, Lawrence A Loeb
Rare stochastic mutations may accumulate during dormancy of stem-like cells, but technical limitations in DNA sequencing have limited exploring this possibility. In this study, we employed a recently established deep-sequencing method termed Duplex Sequencing to conduct a genome-wide analysis of mitochondrial (mt) DNA mutations in a human breast stem cell model that recapitulates the sequential stages of breast carcinogenesis. Using this method, we found significant differences in mtDNA among normal stem cells, immortal/preneoplastic cells, and tumorigenic cells...
August 1, 2016: Cancer Research
Riana I Wernick, Suzanne Estes, Dana K Howe, Dee R Denver
Heteroplasmy-the presence of more than one mitochondrial DNA (mtDNA) sequence type in a cell, tissue, or individual-impacts human mitochondrial disease and numerous aging-related syndromes. Understanding the trans-generational dynamics of mtDNA is critical to understanding the underlying mechanisms of mitochondrial disease and evolution. We investigated mtDNA mutation and heteroplasmy using a set of wild-type (N2 strain) and mitochondrial electron transport chain (ETC) mutant (gas-1) mutant Caenorhabditis elegans mutation-accumulation (MA) lines...
2016: Frontiers in Genetics
Nicole Y P Souren, Lisa A Gerdes, Tania Kümpfel, Pavlo Lutsik, Thomas Klopstock, Reinhard Hohlfeld, Jörn Walter
We examined the debated link between mitochondrial DNA (mtDNA) variation and multiple sclerosis (MS) using 49 monozygotic (MZ) twin pairs clinically discordant for MS, which enables to associate de novo mtDNA variants, skewed heteroplasmy, and mtDNA copy number with MS manifestation. Ultra-deep sequencing of blood-derived mtDNA revealed 25 heteroplasmic variants with potentially pathogenic features in 18 pairs. All variants were pair-specific and had low and/or similar heteroplasmy levels in both cotwins. In one pair, a confirmed pathogenic variant (m...
August 2016: Human Mutation
Johann Beghain, Anne-Claire Langlois, Eric Legrand, Laura Grange, Nimol Khim, Benoit Witkowski, Valentine Duru, Laurence Ma, Christiane Bouchier, Didier Ménard, Richard E Paul, Frédéric Ariey
BACKGROUND: In eukaryotic genomes, deletion or amplification rates have been estimated to be a thousand more frequent than single nucleotide variation. In Plasmodium falciparum, relatively few transcription factors have been identified, and the regulation of transcription is seemingly largely influenced by gene amplification events. Thus copy number variation (CNV) is a major mechanism enabling parasite genomes to adapt to new environmental changes. METHODS: Currently, the detection of CNVs is based on quantitative PCR (qPCR), which is significantly limited by the relatively small number of genes that can be analysed at any one time...
2016: Malaria Journal
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"