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Human mtDNA

Liwen Hu, Xinyue Yao, Yi Shen
Accumulating epidemiological evidence indicates that the quantitative changes in human mitochondrial DNA (mtDNA) copy number could affect the genetic susceptibility of malignancies in a tumor-specific manner, but the results are still elusive. To provide a more precise estimation on the association between mtDNA copy number and risk of diverse malignancies, a meta-analysis was conducted by calculating the pooled odds ratios (OR) and the 95% confidence intervals (95% CI). A total of 36 case-control studies involving 11,847 cases and 15,438 controls were finally included in the meta-analysis...
October 24, 2016: Scientific Reports
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
Angie D Ambers, Jennifer D Churchill, Jonathan L King, Monika Stoljarova, Harrell Gill-King, Mourad Assidi, Muhammad Abu-Elmagd, Abdelbaset Buhmeida, Bruce Budowle
BACKGROUND: Although the primary objective of forensic DNA analyses of unidentified human remains is positive identification, cases involving historical or archaeological skeletal remains often lack reference samples for comparison. Massively parallel sequencing (MPS) offers an opportunity to provide biometric data in such cases, and these cases provide valuable data on the feasibility of applying MPS for characterization of modern forensic casework samples. In this study, MPS was used to characterize 140-year-old human skeletal remains discovered at a historical site in Deadwood, South Dakota, United States...
October 17, 2016: BMC Genomics
Mercedes Fernández-Moreno, Tamara Hermida-Gómez, M Esther Gallardo, Andrea Dalmao-Fernández, Ignacio Rego-Pérez, Rafael Garesse, Francisco J Blanco
INTRODUCTION: The generation of Rho-0 cells requires the use of an immortalization process, or tumor cell selection, followed by culture in the presence of ethidium bromide (EtBr), incurring the drawbacks its use entails. The purpose of this work was to generate Rho-0 cells using human mesenchymal stem cells (hMSCs) with reagents having the ability to remove mitochondrial DNA (mtDNA) more safely than by using EtBr. METHODOLOGY: Two immortalized hMSC lines (3a6 and KP) were used; 143B...
2016: PloS One
Bing Xu, Xiyuan Li, Miaomiao Du, Chao Zhou, Hezhi Fang, Jianxin Lyu, Yanling Yang
By using next-generation sequencing targeted to MitoExome including the entire mtDNA and exons of 1033 genes encoding the mitochondrial proteome, we described here a novel m.11240C>T mutation in the mitochondrial ND4 gene from a patient with Leigh syndrome. High mutant loads of m.11240C>T were detected in blood, urinary epithelium, oral mucosal epithelium cells, and skin fibroblasts of the patient. Decreased mitochondrial complex I activity was found in transmitochondrial cybrids containing the m.11240C>T mutation with biochemical analysis...
October 20, 2016: Journal of Human Genetics
Constanza Morén, Ingrid González-Casacuberta, Carmen Álvarez-Fernández, Maria Bañó, Marc Catalán-Garcia, Mariona Guitart-Mampel, Diana Luz Juárez-Flores, Ester Tobías, José Milisenda, Francesc Cardellach, Josep Maria Gatell, Sonsoles Sánchez-Palomino, Glòria Garrabou
To characterize mitochondrial/apoptotic parameters in chronically human immunodeficiency virus (HIV-1)-infected promonocytic and lymphoid cells which could be further used as therapeutic targets to test pro-mitochondrial or anti-apoptotic strategies as in vitro cell platforms to deal with HIV-infection. Mitochondrial/apoptotic parameters of U1 promonocytic and ACH2 lymphoid cell lines were compared to those of their uninfected U937 and CEM counterparts. Mitochondrial DNA (mtDNA) was quantified by rt-PCR while mitochondrial complex IV (CIV) function was measured by spectrophotometry...
October 18, 2016: Journal of Cellular and Molecular Medicine
Xiwei He, Peng Liu, Guolu Zheng, Huimei Chen, Wei Shi, Yibin Cui, Hongqiang Ren, Xu-Xiang Zhang
This study systematically evaluated five microbial and four mitochondrial DNA (mtDNA) markers, including sensitivities and specificities under PCR method, and fecal concentrations and decay rates in water under qPCR method. The microbial DNA markers were the three human-associated (BacH, HF183 and B.adolescentis) and two pig-associated (Pig-2-Bac and L.amylovorus), while the mtDNA ones were two human- (H-ND6 and H-ND5) and two pig-associated (P-CytB and P-ND5). All the mtDNA markers showed higher sensitivity (100%) than the microbial ones (84...
October 13, 2016: Scientific Reports
Joanna Rorbach, Fei Gao, Christopher A Powell, Aaron D'Souza, Robert N Lightowlers, Michal Minczuk, Zofia M Chrzanowska-Lightowlers
The recent developments in cryo-EM have revolutionized our access to previously refractory structures. In particular, such studies of mammalian mitoribosomes have confirmed the absence of any 5S rRNA species and revealed the unexpected presence of a mitochondrially encoded tRNA (mt-tRNA) that usurps this position. Although the cryo-EM structures resolved the conundrum of whether mammalian mitoribosomes contain a 5S rRNA, they introduced a new dilemma: Why do human and porcine mitoribosomes integrate contrasting mt-tRNAs? Human mitoribosomes have been shown to integrate mt-tRNA(Val) compared with the porcine use of mt-tRNA(Phe) We have explored this observation further...
October 11, 2016: Proceedings of the National Academy of Sciences of the United States of America
Juan-Ke Xie, Qian Wang, Ting-Ting Zhang, Shen Yin, Cui-Lian Zhang, Zhao-Jia Ge
Controlled ovarian stimulation by exogenous gonadotrophins is a key procedure during the in vitro fertilization cycle to obtain a sufficient number of oocytes in humans. Previous studies demonstrated that repeated superovulation had deleterious effects on the ovaries. However, whether repeated superovulation adversely affects the mitochondrial functions of cumulus cells remains unclear. In this study, mice were divided into three groups: superovulation once (R1); superovulation three times (R3), and superovulation five times (R5)...
October 4, 2016: Scientific Reports
Mohammad Mehdi Heidari, Mehri Khatami, Amirhossein Danafar, Tahere Dianat, Ghazaleh Farahmand, Ali Reza Talebi
BACKGROUND: Several recent studies have shown that mitochondrial DNA mutations lead to major disabilities and premature death in carriers. More than 150 mutations in human mitochondrial DNA (mtDNA) genes have been associated with a wide spectrum of disorders. Varicocele, one of the causes of infertility in men wherein abnormal inflexion and distension of veins of the pampiniform plexus is observed within spermatic cord, can increase reactive oxygen species (ROS) production in semen and cause oxidative stress and sperm dysfunction in patients...
October 2016: International Journal of Fertility & Sterility
Laura M Bergner, Nicolas Dussex, Ian G Jamieson, Bruce C Robertson
Island endemic species are often vulnerable to decline and extinction following human settlement, and the genetic study of historical museum specimens can be useful in understanding these processes. The kākāpō (Strigops habroptilus) is a critically endangered New Zealand parrot that was formerly widespread and abundant. It is well established that both Polynesian and European colonization of New Zealand impacted the native avifauna, but the timeframe and severity of impacts have differed depending on species...
2016: Journal of Heredity
Ricarda Richter-Dennerlein, Silke Oeljeklaus, Isotta Lorenzi, Christin Ronsör, Bettina Bareth, Alexander Benjamin Schendzielorz, Cong Wang, Bettina Warscheid, Peter Rehling, Sven Dennerlein
Mitochondrial ribosomes translate membrane integral core subunits of the oxidative phosphorylation system encoded by mtDNA. These translation products associate with nuclear-encoded, imported proteins to form enzyme complexes that produce ATP. Here, we show that human mitochondrial ribosomes display translational plasticity to cope with the supply of imported nuclear-encoded subunits. Ribosomes expressing mitochondrial-encoded COX1 mRNA selectively engage with cytochrome c oxidase assembly factors in the inner membrane...
October 6, 2016: Cell
Jose J G Marin, Elisa Lozano, Maria J Perez
Alterations in mitochondrial DNA (mtDNA) and autophagy activation are common events in tumors. Here we have investigated the effect of mitochondrial genome depletion on chemical hypoxia-induced autophagy in liver tumor cells. Human SK-Hep-1 wild-type and mtDNA-depleted (Rho) cells were exposed to the hypoxia mimetic agents CoCl2 and deferoxamine (DFO). Up-regulation of HIF-1α, but not HIF-2α was observed. The expression of several HIF-1α target genes was also found. In human SK-Hep-1 and mouse Hepa 1-6 liver tumor cells, but not in the counterpart Rho derived lines, chemical hypoxia increased the abundance of autophagosomes and autolysosomes...
September 26, 2016: Free Radical Biology & Medicine
Linda Koshy, A L Anju, S Harikrishnan, V R Kutty, V T Jissa, Irin Kurikesu, Parvathy Jayachandran, A Jayakumaran Nair, A Gangaprasad, G M Nair, P R Sudhakaran
The extraction of genomic DNA is the crucial first step in large-scale epidemiological studies. Though there are many popular DNA isolation methods from human whole blood, only a few reports have compared their efficiencies using both end-point and real-time PCR assays. Genomic DNA was extracted from coronary artery disease patients using solution-based conventional protocols such as the phenol-chloroform/proteinase-K method and a non-phenolic non-enzymatic Rapid-Method, which were evaluated and compared vis-a-vis a commercially available silica column-based Blood DNA isolation kit...
September 29, 2016: Molecular Biology Reports
François Vallée, Aurélien Luciani, Murray P Cox
Archeology, linguistics and increasingly genetics are clarifying how populations moved from mainland Asia, through Island Southeast Asia, and out into the Pacific during the farming revolution. Yet key features of this process remain poorly understood, particularly how social behaviors intersected with demographic drivers to create the patterns of genomic diversity observed across Island Southeast Asia today. Such questions are ripe for computer modeling. Here, we construct an agent-based model to simulate human mobility across Island Southeast Asia from the Neolithic period to the present, with a special focus on interactions between individuals with Asian, Papuan and mixed Asian-Papuan ancestry...
September 28, 2016: Genetics
Pere Gelabert, Marcela Sandoval-Velasco, Iñigo Olalde, Rosa Fregel, Adrien Rieux, Raül Escosa, Carles Aranda, Krijn Paaijmans, Ivo Mueller, M Thomas P Gilbert, Carles Lalueza-Fox
Phylogenetic analysis of Plasmodium parasites has indicated that their modern-day distribution is a result of a series of human-mediated dispersals involving transport between Africa, Europe, America, and Asia. A major outstanding question is the phylogenetic affinity of the malaria causing parasites Plasmodium vivax and falciparum in historic southern Europe-where it was endemic until the mid-20th century, after which it was eradicated across the region. Resolving the identity of these parasites will be critical for answering several hypotheses on the malaria dispersal...
October 11, 2016: Proceedings of the National Academy of Sciences of the United States of America
Teivi Laurimäe, Liina Kinkar, Vanessa Andresiuk, Karen Luisa Haag, Francisco Ponce-Gordo, Gerardo Acosta-Jamett, Teresa Garate, Luis Miguel Gonzàlez, Urmas Saarma
Echinococcus granulosus is a taeniid cestode and the etiological agent of an infectious zoonotic disease known as cystic echinococcosis (CE) or hydatid disease. CE is a serious public health concern in many parts of the world, including the Americas, where it is highly endemic in many regions. Echinococcus granulosus displays high intraspecific genetic variability and is divided into multiple genotypes (G1-G8, G10) with differences in their biology and etiology. Of these, genotype G1 is responsible for the majority of human and livestock infections and has the broadest host spectrum...
September 19, 2016: Infection, Genetics and Evolution
Zbigniew Borowski, Magdalena Świsłocka, Maciej Matosiuk, Paweł Mirski, Kamil Krysiuk, Magdalena Czajkowska, Anetta Borkowska, Mirosław Ratkiewicz
The trajectories of postglacial range expansions, the occurrence of lineage patches and the formation and maintenance of secondary contact between lineages may mostly reflect neutral demographic processes, including density blocking, that may leave long-lasting genetic signatures. However, a few studies have recently shown that climate may also play a role. We used red deer, a large, mobile herbivore that is assumed to be sensitive to climate change, to test hypotheses of possible selection on the mitochondrial DNA cytochrome b gene (mtDNA cytb) and competitive and/or density-blocking (using mtDNA control region)...
2016: PloS One
Krishna Kumar Ganta, Anirban Mandal, Binay Chaubey
Efavirenz is a non-nucleoside reverse transcriptase inhibitor (NNRTI) and an active constituent of the highly active antiretroviral therapy regime. It has significantly contributed in control and management of human immunodeficiency virus propagation. However, EFV administration has also led to severe adverse effects, several reports highlighted the role of EFV in mitochondrial dysfunction and toxicity but the molecular mechanism has been poorly understood. In present study, human hepatoma cells Huh 7.5 were treated with clinically relevant concentrations of EFV and parameters like cytotoxicity, mitochondrial transmembrane potential, mitochondrial morphology, cytochrome c release, mitochondria-mediated apoptosis, mtDNA and mtRNA levels and EFV distribution into mitochondrial compartment were evaluated to understand sequence of events leading to cell death in EFV-treated cells...
September 17, 2016: Cell Biology and Toxicology
Frido Welker, Mateja Hajdinjak, Sahra Talamo, Klervia Jaouen, Michael Dannemann, Francine David, Michèle Julien, Matthias Meyer, Janet Kelso, Ian Barnes, Selina Brace, Pepijn Kamminga, Roman Fischer, Benedikt M Kessler, John R Stewart, Svante Pääbo, Matthew J Collins, Jean-Jacques Hublin
In Western Europe, the Middle to Upper Paleolithic transition is associated with the disappearance of Neandertals and the spread of anatomically modern humans (AMHs). Current chronological, behavioral, and biological models of this transitional period hinge on the Châtelperronian technocomplex. At the site of the Grotte du Renne, Arcy-sur-Cure, morphological Neandertal specimens are not directly dated but are contextually associated with the Châtelperronian, which contains bone points and beads. The association between Neandertals and this "transitional" assemblage has been controversial because of the lack either of a direct hominin radiocarbon date or of molecular confirmation of the Neandertal affiliation...
October 4, 2016: Proceedings of the National Academy of Sciences of the United States of America
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