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mitochondrial dna selection

Erik Norberg, Ana Lako, Pei-Hsuan Chen, Illana A Stanley, Feng Zhou, Scott B Ficarro, Bjoern Chapuy, Linfeng Chen, Scott Rodig, Donghyuk Shin, Dong Wook Choi, Sangho Lee, Margaret A Shipp, Jarrod A Marto, Nika N Danial
Diffuse large B-cell lymphomas (DLBCLs) are a highly heterogeneous group of tumors in which subsets share molecular features revealed by gene expression profiles and metabolic fingerprints. While B-cell receptor (BCR)-dependent DLBCLs are glycolytic, OxPhos-DLBCLs rely on mitochondrial energy transduction and nutrient utilization pathways that provide pro-survival benefits independent of BCR signaling. Integral to these metabolic distinctions is elevated mitochondrial electron transport chain (ETC) activity in OxPhos-DLBCLs compared with BCR-DLBCLs, which is linked to greater protein abundance of ETC components...
October 21, 2016: Cell Death and Differentiation
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
Séverine Fourdrilis, Patrick Mardulyn, Olivier J Hardy, Kurt Jordaens, António Manuel de Frias Martins, Thierry Backeljau
We report the presence of mitochondrial DNA (mtDNA) hyperdiversity in the marine periwinkle Melarhaphe neritoides (Linnaeus, 1758), the first such case among marine gastropods. Our dataset consisted of concatenated 16S-COI-Cytb gene fragments. We used Bayesian analyses to investigate three putative causes underlying genetic variation, and estimated the mtDNA mutation rate, possible signatures of selection and the effective population size of the species in the Azores archipelago. The mtDNA hyperdiversity in M...
2016: PeerJ
Jaime Aguayo, Fabien Halkett, Claude Husson, Zoltán Á Nagy, András Szigethy, József Bakonyi, Pascal Frey, Benoit Marçais
: Assessing the process that gives rise to hybrid pathogens is central to understand the evolution of emerging plant diseases. Phytophthora ×alni, a pathogen of alder, results from the homoploid hybridization of two related species, Phytophthora uniformis and Phytophthora ×multiformis Describing genetic characteristics of P. ×alni should help understanding how reproductive mechanisms and historical processes shaped the population structure of this emerging hybrid pathogen. The population genetic structure of P...
October 7, 2016: Applied and Environmental Microbiology
Sun Jiji, Zhao Xiaoxu, Qiao Lihua, Mei Shuang, Nie Zhipeng, Zhang Qinghai, Ji Yanchun, Jiang Pingping, Guan Min-Xin
Mitochondrial DNA (mtDNA) mutations cause a variety of mitochondrial DNA-based diseases which have been studied using Lymphoblastoid cell lines (LCLs) and transmitochondrial cybrids. Individual genetic information is preserved permanently in LCLs while the development of transmitochondrial cybrids provide ex-vivo cellular platform to study molecular mechanism of mitochondrial DNA-based diseases. The cytoplasmic donor cells for previous transmitochondrial cybrids come from patient's tissue or platelet directly...
July 20, 2016: Yi Chuan, Hereditas
Christian Arstad, Paulo Refinetti, David Warren, Karl-Erik Giercksky, Per Olaf Ekstrøm
To bypass possible nuclear contamination and to exclusively amplify DNA from the mitochondrion, a set of 23 primers was selected. On the mitochondrial DNA selection fragments, a second set of fragments was used to amplify and identify mutant fractions with a detection limit of 1% . This mutation scanning method analyzed 76% of the mitochondrial genome and was used to examine 94 tumours from different tissues of origin. In all, 87 tumours had one or more mutations, leaving seven samples without observed mutations...
October 11, 2016: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Sreetama Choudhury, Sayan Ghosh, Sudeshna Mukherjee, Payal Gupta, Saurav Bhattacharya, Arghya Adhikary, Sreya Chattopadhyay
Molecular mechanisms involved in arsenic-induced toxicity are complex and elusive. Liver is one of the most favored organs for arsenic toxicity as methylation of arsenic occurs mostly in the liver. In this study, we have selected a range of environmentally relevant doses of arsenic to examine the basis of arsenic toxicity and the role of pomegranate fruit extract (PFE) in combating it. Male Swiss albino mice exposed to different doses of arsenic presented marked hepatic injury as evident from histological and electron microscopic studies...
September 6, 2016: Journal of Nutritional Biochemistry
Maria G Onyango, Nicola C Aitken, Cameron Jack, Aaron Chuah, James Oguya, Appolinaire Djikeng, Steve Kemp, Glenn A Bellis, Adrian Nicholas, Peter J Walker, Jean-Bernard Duchemin
BACKGROUND: The advent of genotyping by Next Generation Sequencing has enabled rapid discovery of thousands of single nucleotide polymorphism (SNP) markers and high throughput genotyping of large populations at an affordable cost. Genotyping by sequencing (GBS), a reduced representation library sequencing method, allows highly multiplexed sequencing of genomic subsets. This method has limitations for small organisms with low amounts of genomic DNA, such as the bluetongue virus (BTV) vectors, Culicoides midges...
September 30, 2016: BMC Genomics
Ruslan Aphasizhev, Takuma Suematsu, Liye Zhang, Inna Aphasizheva
RNA uridylation is a significant transcriptome-shaping factor in protists, fungi, metazoans, and plants. The 3' U-additions are catalyzed by terminal uridyltransferases (TUTases), a diverse group of enzymes that along with non-canonical poly(A) polymerases form a distinct group in the superfamily of DNA polymerase β-like nucleotidyl transferases. Within and across studied organisms and subcellular compartments, TUTases differ in nucleotide triphosphate selectivity, interacting partners, and RNA targets. A general premise linking RNA uridylation to 3'-5' degradation received support from several studies of small RNAs and mRNA turnover...
October 7, 2016: RNA Biology
L Ming, L Yi, F C Guo, S Siriguleng, J Jirimutu
The Bactrian camel is an important domesticated animal providing milk, meat, and other products in desert countries. In this study, 111 individuals representing 11 domestic Bactrian camel breeds from China, Mongolia, Russia, and one wild Bactrian camel group from Mongolia were selected for the preparation of mitochondrial DNA. The 1140-bp fragments of the cytochrome b gene (Cytb) were amplified by polymerase chain reaction and sequenced directly. Sequences of the 92 domestic and 19 wild Bactrian camel samples were analyzed with DNASTAR, and a phylogenic tree was constructed using MEGA...
September 19, 2016: Genetics and Molecular Research: GMR
Li-Mian Er, Ming-Li Wu, Yang Gao, Shi-Jie Wang, Yong Li
BACKGROUND: Gastroenteropancreatic neuroendocrine neoplasms (GEP-NEN) are relatively rare tumors that arise from the diffuse neuroendocrine system, and the biggest advances in molecular biology have helped in understanding these biological diversity of tumors over the past decades. It is important to determine the carcinogenesis of GEP-NEN from the perspective of genetic backgrounds. METHODS: Mitochondrial DNA (mtDNA) of peripheral blood from 66 GEP-NEN patients and from 75 healthy controls without history of any cancer were examined for single nucleotide polymorphisms (SNPs) and mutations in the displacement loop (D-loop) region...
October 5, 2016: Journal of Clinical Laboratory Analysis
Jo-Ann Chuah, Akimasa Matsugami, Fumiaki Hayashi, Keiji Numata
Human mitochondrial dysfunction can lead to severe and often deadly diseases, for which there are no known cures. Although the targeted delivery of therapeutic gene to mitochondria is a promising approach to alleviate these disorders, gene carrier systems for the selective delivery of functional DNA into the mitochondria of living mammalian cells are currently unavailable. Here we rationally developed dual-domain peptides containing DNA-condensing/cell-penetrating/endosome-disruptive and mitochondria-targeting sequences...
October 3, 2016: Biomacromolecules
T G Demarest, R A Schuh, E L Waite, J Waddell, M C McKenna, Gary Fiskum
Males are more susceptible to brain mitochondrial bioenergetic dysfunction following neonatal cerebral hypoxic-ischemia (HI) than females. Mitochondrial biogenesis has been implicated in the cellular response to HI injury, but sex differences in biogenesis following HI have not been described. We tested the hypothesis that mitochondrial biogenesis or the expression of mitochondrial electron transport chain (ETC) proteins are differentially stimulated in the brains of 8 day old male and female rats one day following HI, and promoted by treatment with acetyl-L-carnitine (ALCAR)...
September 28, 2016: Journal of Bioenergetics and Biomembranes
William J Smiles, Evelyn B Parr, Vernon G Coffey, Orly Lacham-Kaplan, John A Hawley, Donny M Camera
Alcohol ingestion decreases post-exercise rates of muscle protein synthesis, but the mechanism(s) (e.g., increased protein breakdown) underlying this observation are unknown. Autophagy is an intracellular "recycling" system required for homeostatic substrate and organelle turnover; its dysregulation may provoke apoptosis and lead to muscle atrophy. We investigated the acute effects of alcohol ingestion on autophagic cell signaling responses to a bout of concurrent (combined resistance- and endurance-based) exercise...
September 27, 2016: American Journal of Physiology. Endocrinology and Metabolism
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
Martijn Fenaux, Xiaodong Lin, Fumiaki Yokokawa, Zachary Sweeney, Oliver Saunders, Lili Xie, Siew Pheng Lim, Marianne Uteng, Kyoko Uehara, Robert Warne, Wang Gang, Christopher Jones, Satya Yendluri, Helen Gu, Keith Mansfield, Julie Boisclair, Tycho Heimbach, Alexandre Catoire, Kathryn Bracken, Margaret Weaver, Heinz Moser, Weidong Zhong
Nucleoside or nucleotide inhibitors are a highly successful class of antivirals due to selectivity, potency, broad coverage, and high barrier to resistance. Nucleosides are the backbone of combination treatments for HIV, hepatitis B and - since the FDA approval of sofosbuvir in 2013 - also for hepatitis C (HCV). However, many promising nucleotides have advanced to clinical trials only to be terminated due to unexpected toxicity. Here we describe the in vitro pharmacology of 1: , a monophosphate prodrug of a 2' -ethynyluridine developed for the treatment of HCV...
September 19, 2016: Antimicrobial Agents and Chemotherapy
Knut H Lauritzen, Md Mahdi Hasan-Olive, Christine E Regnell, Liv Kleppa, Morten Scheibye-Knudsen, Albert Gjedde, Arne Klungland, Vilhelm A Bohr, Jon Storm-Mathisen, Linda H Bergersen
Mitochondrial genome maintenance plays a central role in preserving brain health. We previously demonstrated accumulation of mitochondrial DNA damage and severe neurodegeneration in transgenic mice inducibly expressing a mutated mitochondrial DNA repair enzyme (mutUNG1) selectively in forebrain neurons. Here, we examine whether severe neurodegeneration in mutUNG1-expressing mice could be rescued by feeding the mice a ketogenic diet, which is known to have beneficial effects in several neurological disorders...
August 18, 2016: Neurobiology of Aging
Chi-Jing Choong, Hideki Mochizuki
Parkinson's disease (PD) presents a relative selective localization of pathology to substantia nigra and well-defined motor symptoms caused by dopaminergic degeneration that makes it an ideal target for gene therapy. Parallel progress in viral vector systems enables the delivery of therapeutic genes directly into brain with reasonable safety along with sustained transgene expression. To date, gene therapy for PD that has reached clinical trial evaluation is mainly based on symptomatic approach that involves enzyme replacement strategy and restorative approach that depends on the addition of neurotrophic factors...
September 16, 2016: Journal of Neural Transmission
Dan Bar-Yaacov, Idan Frumkin, Yuka Yashiro, Takeshi Chujo, Yuma Ishigami, Yonatan Chemla, Amit Blumberg, Orr Schlesinger, Philipp Bieri, Basil Greber, Nenad Ban, Raz Zarivach, Lital Alfonta, Yitzhak Pilpel, Tsutomu Suzuki, Dan Mishmar
The mitochondrial ribosome, which translates all mitochondrial DNA (mtDNA)-encoded proteins, should be tightly regulated pre- and post-transcriptionally. Recently, we found RNA-DNA differences (RDDs) at human mitochondrial 16S (large) rRNA position 947 that were indicative of post-transcriptional modification. Here, we show that these 16S rRNA RDDs result from a 1-methyladenosine (m1A) modification introduced by TRMT61B, thus being the first vertebrate methyltransferase that modifies both tRNA and rRNAs. m1A947 is conserved in humans and all vertebrates having adenine at the corresponding mtDNA position (90% of vertebrates)...
September 2016: PLoS Biology
Seikoh Saitoh, Hiroaki Aoyama, Saori Fujii, Haruki Sunagawa, Hideki Nagahama, Masako Akutsu, Naoya Shinzato, Nobuhiro Kaneko, Taizo Nakamori
We developed a novel protocol with superior quantitative analysis results for DNA metabarcoding of Collembola, a major soil microarthropod order. Degenerate PCR primers were designed for conserved regions in the mitochondrial cytochrome c oxidase subunit I (mtCOI) and 16S ribosomal RNA (mt16S) genes based on published collembolan mitogenomes. The best primer pair was selected based on its ability to amplify each gene, irrespective of the species. DNA was extracted from 10 natural communities sampled in a temperate forest (with typically 25-30 collembolan species per 10 soil samples) and 10 mock communities (with seven cultured collembolan species)...
September 2016: Genome Génome / Conseil National de Recherches Canada
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