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Mitochondrial DNA

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https://www.readbyqxmd.com/read/28545148/mitochondrial-genome-evolution-in-alismatales-size-reduction-and-extensive-loss-of-ribosomal-protein-genes
#1
Gitte Petersen, Argelia Cuenca, Athanasios Zervas, Gregory T Ross, Sean W Graham, Craig F Barrett, Jerrold I Davis, Ole Seberg
The order Alismatales is a hotspot for evolution of plant mitochondrial genomes characterized by remarkable differences in genome size, substitution rates, RNA editing, retrotranscription, gene loss and intron loss. Here we have sequenced the complete mitogenomes of Zostera marina and Stratiotes aloides, which together with previously sequenced mitogenomes from Butomus and Spirodela, provide new evolutionary evidence of genome size reduction, gene loss and transfer to the nucleus. The Zostera mitogenome includes a large portion of DNA transferred from the plastome, yet it is the smallest known mitogenome from a non-parasitic plant...
2017: PloS One
https://www.readbyqxmd.com/read/28545030/mitochondrial-dna-sequencing-and-large-scale-genotyping-identifies-mt-nd4-gene-mutation-m-11696g-a-associated-with-idiopathic-oligoasthenospermia
#2
Juan Ji, Miaofei Xu, Zhenyao Huang, Lei Li, Hongxiang Zheng, Shuping Yang, Shilin Li, Li Jin, Xiufeng Ling, Yankai Xia, Chuncheng Lu, Xinru Wang
Genetic variants of mitochondrial DNA (mtDNA) were implicated to be associated with male infertility. Our previous whole mitochondrial genome sequencing and association study has identified two susceptibility mtDNA variants for oligoasthenospermia in Han Chinese men. In this study, we tested promising associations in an extended validation using 670 idiopathic oligoasthenospermia cases and 793 healthy controls to identify additional risk variants. We found that the genetic variant of m.11696G>A showed significantly higher frequency in the case group than that in the control group (odds ratio (OR) 2...
May 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28544378/concise-review-induced-pluripotent-stem-cell-based-drug-discovery-for-mitochondrial-disease
#3
REVIEW
Gizem Inak, Carmen Lorenz, Pawel Lisowski, Annika Zink, Barbara Mlody, Alessandro Prigione
High attrition rates and loss of capital plague the drug discovery process. This is particularly evident for mitochondrial disease that typically involves neurological manifestations and is caused by nuclear or mitochondrial DNA defects. This group of heterogeneous disorders is difficult to target because of the variability of the symptoms among individual patients and the lack of viable modeling systems. The use of induced pluripotent stem cells (iPSCs) might significantly improve the search for effective therapies for mitochondrial disease...
May 22, 2017: Stem Cells
https://www.readbyqxmd.com/read/28544375/proteomic-analysis-of-hair-shafts-from-monozygotic-twins-expression-profiles-and-genetically-variant-peptides
#4
Pei-Wen Wu, Katelyn E Mason, Blythe P Durbin-Johnson, Michelle Salemi, Brett S Phinney, David M Rocke, Glendon J Parker, Robert H Rice
Forensic association of hair shaft evidence with individuals is currently assessed by comparing mitochondrial DNA haplotypes of reference and casework samples, primarily for exclusionary purposes. Present work tests and validates more recent proteomic approaches to extract quantitative transcriptional and genetic information from hair samples of monozygotic twin pairs, which would be predicted to partition away from unrelated individuals if the datasets contain identifying information. Protein expression profiles and polymorphic, genetically variant hair peptides were generated from 10 pairs of monozygotic twins...
May 22, 2017: Proteomics
https://www.readbyqxmd.com/read/28543871/tropical-specialist-versus-climate-generalist-diversification-and-demographic-history-of-sister-species-of-carlia%C3%A2-skinks-from-northwestern-australia
#5
Ana C Afonso Silva, Jason G Bragg, Sally Potter, Carlos Fernandes, Maria Manuela Coelho, Craig Moritz
Species endemic to the tropical regions are expected to be vulnerable to future climate change due in part to their relatively narrow climatic niches. In addition, these species are more likely to have responded strongly to past climatic change, and this can be explored through phylogeographic analyses. To test the hypothesis that tropical specialists are more sensitive to climate change than climate generalists, we generated and analyze sequence data from mtDNA and ~2500 exons to compare scales of historical persistence and population fluctuation in two sister species of Australian rainbow skinks: the tropical specialist Carlia johnstonei and the climate generalist C...
May 24, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28543759/abrus-agglutinin-promotes-irreparable-dna-damage-by-triggering-ros-generation-followed-by-atm-p73-mediated-apoptosis-in-oral-squamous-cell-carcinoma
#6
Niharika Sinha, Prashanta Kumar Panda, Prajna Paramita Naik, Durgesh Nandini Das, Subhadip Mukhopadhyay, Tapas K Maiti, Muthu K Shanmugam, Arunachalam Chinnathambi, M E Zayed, Sulaiman Ali Alharbi, Gautam Sethi, Rajesh Agarwal, Sujit K Bhutia
Oral cancer, a type of head and neck cancer, is ranked as one of the top most malignancies in India. Herein, we evaluated the anticancer efficacy of Abrus agglutinin (AGG), a plant lectin, in oral squamous cell carcinoma. AGG selectively inhibited cell growth, and caused cell cycle arrest and mitochondrial apoptosis through a reactive oxygen species (ROS)-mediated ATM-p73 dependent pathway in FaDu cells. AGG-induced ROS accumulation was identified as the major mechanism regulating apoptosis, DNA damage and DNA-damage response, which were significantly reversed by ROS scavenger N-acetylcysteine (NAC)...
May 23, 2017: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/28542832/integrated-transcriptomic-and-metabolomic-analysis-reveals-adaptive-changes-of-hibernating-retinas
#7
Yizhao Luan, Jingxing Ou, Vincent P Kunze, Fengyu Qiao, Yan Wang, Lai Wei, Wei Li, Zhi Xie
Hibernation is a seasonally adaptive strategy that allows hibernators to live through extremely cold conditions. Despite the profound reduction of blood flow to the retinas, hibernation causes no lasting retinal injury. Instead, hibernators show an increased tolerance to ischemic insults during the hibernation period. To understand the molecular changes of the retinas in response to hibernation, we applied an integrative transcriptome and metabolome analysis to explore changes in gene expression and metabolites of 13-lined ground squirrel retinas during hibernation...
May 25, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/28542490/repeated-bouts-of-exhaustive-exercise-increase-circulating-cell-free-nuclear-and-mitochondrial-dna-without-development-of-tolerance-in-healthy-men
#8
Robert Stawski, Konrad Walczak, Piotr Kosielski, Pawel Meissner, Tomasz Budlewski, Gianluca Padula, Dariusz Nowak
OBJECTIVE: Acute single strenuous exercise increases circulating cell free DNA (cf DNA). We tested whether three repeated bouts of exhaustive exercise induced the cf DNA response without development of tolerance in healthy men. METHODS: Eleven average-trained men (age 34.0±5.2 years, body mass index 26.2±3.1 kg/m2, maximal oxygen consumption-VO2max 49.6±4.5 ml/kg*min) performed three treadmill exercise tests to exhaustion at speed corresponding to 70% VO2max separated by 72 hours of resting...
2017: PloS One
https://www.readbyqxmd.com/read/28542447/exploratory-plasma-proteomic-analysis-in-a-randomized-crossover-trial-of-aspirin-among-healthy-men-and-women
#9
Xiaoliang Wang, Ali Shojaie, Yuzheng Zhang, David Shelley, Paul D Lampe, Lisa Levy, Ulrike Peters, John D Potter, Emily White, Johanna W Lampe
Long-term use of aspirin is associated with lower risk of colorectal cancer and other cancers; however, the mechanism of chemopreventive effect of aspirin is not fully understood. Animal studies suggest that COX-2, NFκB signaling and Wnt/β-catenin pathways may play a role, but no clinical trials have systematically evaluated the biological response to aspirin in healthy humans. Using a high-density antibody array, we assessed the difference in plasma protein levels after 60 days of regular dose aspirin (325 mg/day) compared to placebo in a randomized double-blinded crossover trial of 44 healthy non-smoking men and women, aged 21-45 years...
2017: PloS One
https://www.readbyqxmd.com/read/28542338/a-technique-for-setting-analytical-thresholds-in-massively-parallel-sequencing-based-forensic-dna-analysis
#10
Brian Young, Jonathan L King, Bruce Budowle, Luigi Armogida
Amplicon (targeted) sequencing by massively parallel sequencing (PCR-MPS) is a potential method for use in forensic DNA analyses. In this application, PCR-MPS may supplement or replace other instrumental analysis methods such as capillary electrophoresis and Sanger sequencing for STR and mitochondrial DNA typing, respectively. PCR-MPS also may enable the expansion of forensic DNA analysis methods to include new marker systems such as single nucleotide polymorphisms (SNPs) and insertion/deletions (indels) that currently are assayable using various instrumental analysis methods including microarray and quantitative PCR...
2017: PloS One
https://www.readbyqxmd.com/read/28541756/genetic-diversity-of-mtdna-d-loop-sequences-in-four-native-chinese-chicken-breeds
#11
H W Guo, C Li, X N Wang, Z J Li, G R Sun, G X Li, X J Liu, X T Kang, R L Han
1. To explore the genetic diversity of Chinese indigenous chicken breeds, a 585 bp fragment of the mitochondrial DNA (mtDNA) region was sequenced in 102 birds from the Xichuan Black-bone chicken, Yunyang Black-bone chicken and Lushi chicken. In addition, 30 mtDNA D-loop sequences of Silkie fowls were downloaded from NCBI. The mtDNA D-loop sequence polymorphism and maternal origin of 4 chicken breeds were analysed in this study. 2. The results showed that a total of 33 mutation sites and 28 haplotypes were detected in the 4 chicken breeds...
May 25, 2017: British Poultry Science
https://www.readbyqxmd.com/read/28541477/mitochondrial-retroprocessing-promoted-functional-transfers-of-rpl5-to-the-nucleus-in-grasses
#12
Zhiqiang Wu, Daniel B Sloan, Colin W Brown, Mónica Rosenblueth, Jeffrey D Palmer, Han Chuan Ong
Functional gene transfers from the mitochondrion to the nucleus are ongoing in angiosperms and have occurred repeatedly for all 15 ribosomal protein genes, but it is not clear why some of these genes are transferred more often than others nor what the balance is between DNA- and RNA-mediated transfers. Although direct insertion of mitochondrial DNA into the nucleus occurs frequently in angiosperms, case studies of functional mitochondrial gene transfer have implicated an RNA-mediated mechanism that eliminates introns and RNA editing sites, which would otherwise impede proper expression of mitochondrial genes in the nucleus...
May 25, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28540166/inhibition-of-protein-kinases-by-anticancer-dna-intercalator-4-butylaminopyrimido-4-5-4-5-thieno-2-3-b-quinoline
#13
HeggoduG Rohit Kumar, Chethan S Kumar, Hulihalli N Kiran Kumar, Gopal M Advi Rao
Targeting protein kinases (PKs) has been a promising strategy in treating cancer, as PKs are key regulators of cell survival and proliferation. Here in this study, we studied the ability of pyrimido[4',5':4,5]thieno(2,3-b)quinolines (PTQ) to inhibit different PKs by performing computational docking and in vitro screening. Docking studies revealed that 4-butylaminopyrimido[4',5':4,5]thieno(2,3-b)quinoline (BPTQ) has a higher order of interaction with the kinase receptors than other PTQ derivatives. In vitro screening confirms that BPTQ inhibits VEGFR1 and CHK2, with the IC50 values of 0...
May 2017: Acta Pharmaceutica Sinica. B
https://www.readbyqxmd.com/read/28539631/phylogeography-of-the-tyrrhenian-red-deer-cervus-elaphus-corsicanus-resolved-using-ancient-dna-of-radiocarbon-dated-subfossils
#14
K Doan, F E Zachos, B Wilkens, J-D Vigne, N Piotrowska, A Stanković, B Jędrzejewska, K Stefaniak, M Niedziałkowska
We present ancient mitochondrial DNA analyses of 31 complete cytochrome b gene sequences from subfossil red deer remains from the Tyrrhenian islands (Corsica and Sardinia) and mainland Italy in a European-wide phylogeographic framework. Tyrrhenian and North African red deer, both going back to human introductions, were previously the only red deer to harbour the mitochondrial B lineage whose origin, however, remained unknown. Our ancient Italian samples from the central part of the peninsula that were radiocarbon-dated to an age of ca...
May 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28539470/the-src-c-abl-pathway-is-a-potential-therapeutic-target-in-amyotrophic-lateral-sclerosis
#15
Keiko Imamura, Yuishin Izumi, Akira Watanabe, Kayoko Tsukita, Knut Woltjen, Takuya Yamamoto, Akitsu Hotta, Takayuki Kondo, Shiho Kitaoka, Akira Ohta, Akito Tanaka, Dai Watanabe, Mitsuya Morita, Hiroshi Takuma, Akira Tamaoka, Tilo Kunath, Selina Wray, Hirokazu Furuya, Takumi Era, Kouki Makioka, Koichi Okamoto, Takao Fujisawa, Hideki Nishitoh, Kengo Homma, Hidenori Ichijo, Jean-Pierre Julien, Nanako Obata, Masato Hosokawa, Haruhiko Akiyama, Satoshi Kaneko, Takashi Ayaki, Hidefumi Ito, Ryuji Kaji, Ryosuke Takahashi, Shinya Yamanaka, Haruhisa Inoue
Amyotrophic lateral sclerosis (ALS), a fatal disease causing progressive loss of motor neurons, still has no effective treatment. We developed a phenotypic screen to repurpose existing drugs using ALS motor neuron survival as readout. Motor neurons were generated from induced pluripotent stem cells (iPSCs) derived from an ALS patient with a mutation in superoxide dismutase 1 (SOD1). Results of the screen showed that more than half of the hits targeted the Src/c-Abl signaling pathway. Src/c-Abl inhibitors increased survival of ALS iPSC-derived motor neurons in vitro...
May 24, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/28539260/phylogenetic-relationships-of-the-tribe-toxotrypanini-diptera-tephritidae-based-on-molecular-characters
#16
Ximo Mengual, Peter Kerr, Allen L Norrbom, Norman B Barr, Matthew L Lewis, Anna M Stapelfeldt, Sonja J Scheffer, Patrick Woods, Md-Sajedul Islam, Cheslavo A Korytkowski, Keiko Uramoto, Erick J Rodriguez, Bruce D Sutton, Norma Nolazco, Gary J Steck, Stephen Gaimari
Current hypotheses of relationship among the species of the fruit fly genera Anastrepha and Toxotrypana are tested using sequence data from six DNA regions: the mitochondrial regions 16S, CAD, and COI, and the nuclear regions EF1a, PER, and PGD. DNA sequences were obtained from 146 species of Anastrepha, representing 19 of the 21 species groups as well as five of the six clades of the robusta group, and four species of Toxotrypana in addition to species of Hexachaeta, Pseudophorellia, Alujamyia, and 13 other tephritid genera used as outgroups...
May 21, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28539070/mitogenomics-data-reveal-effective-population-size-historical-bottlenecks-and-the-effects-of-hunting-on-new-zealand-fur-seals-arctocephalus-forsteri
#17
Arsalan Emami-Khoyi, Adrian M Paterson, David A Hartley, Laura J Boren, Robert H Cruickshank, James G Ross, Elaine C Murphy, Terry-Ann Else
The New Zealand fur seal (Arctocephalus forsteri) passed through a population bottleneck due to commercial sealing during the eighteenth to nineteenth centuries. To facilitate future management options, we reconstructed the demographic history of New Zealand fur seals in a Bayesian framework using maternally inherited, mitochondrial DNA sequences. Mitogenomic data suggested two separate clades (most recent common ancestor 5000 years ago) of New Zealand fur seals that survived large-scale human harvest. Mitochondrial haplotype diversity was high, with 45 singletons identified from 46 individuals although mean nucleotide diversity was low (0...
May 25, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28538623/impact-of-a-novel-pi3-kinase-inhibitor-in-preventing-mitochondrial-dna-damage-and-damage-associated-molecular-pattern-accumulation-results-from-the-biochronicity-project
#18
George E Black, Kyle K Sokol, Donald M Moe, Jon Simmons, David Muscat, Victor Pastukh, Gina Capley, Olena Gorodnya, Mykhalo Ruchko, Mark B Roth, Mark Gillespie, Matthew J Martin
BACKGROUND: Despite improvements in the management of severely injured patients, development of multiple organ dysfunction syndrome (MODS) remains a morbid complication of traumatic shock. One of the key attributes of MODS is a profound bioenergetics crisis, for which the mediators and mechanisms are poorly understood. We hypothesized that metabolic uncoupling using an experimental PI3-kinase inhibitor, LY294002 (LY), may prevent mitochondrial abnormalities that lead to the generation of mitochondrial DNA (mtDNA) damage and the release of mtDNA damage associated molecular patterns (DAMPs) METHODS: 16 swine were studied using LY294002 (LY), a non-selective PI3-KI: Animals were assigned to Trauma only (TO, N=3); LY drug only (LYO, N=3); and Experimental (N=10), trauma + drug (LY+T) groups...
May 22, 2017: Journal of Trauma and Acute Care Surgery
https://www.readbyqxmd.com/read/28537816/effect-of-vitamin-e-and-polyunsaturated-fatty-acids-on-cryopreserved-sperm-quality-in-bos-taurus-bulls-under-testicular-heat-stress
#19
João D A Losano, Daniel S R Angrimani, Andressa Dalmazzo, Carolina C Rocha, Maíra M Brito, Eduardo G A Perez, Roberta H Tsunoda, Paola A A Góes, Camilla M Mendes, Mayra E O A Assumpção, Valquiria H Barnabe, Marcilio Nichi
Taurine bulls are highly susceptible to heat stress, leading to increased oxidative stress (OS) and impaired sperm viability. Polyunsaturated fatty acids (PUFAs) supplementation can be an alternative to improve semen quality, which also results in more sperm susceptibility to lipid peroxidation. Moreover, this deleterious effect can be exacerbated in animals affected by heat stress. Vitamin E is a key antioxidant that counteracts lipid peroxidation of sperm membrane caused by OS. Thus, combining PUFAs with vitamin E may improve sperm quality...
May 24, 2017: Animal Biotechnology
https://www.readbyqxmd.com/read/28537774/association-of-sperm-mitochondrial-dna-deletions-with-male-infertility-in-an-iranian-population
#20
Elaheh Talebi, Mohammad Karimian, Hossein Nikzad
Disruptions of mitochondrial DNA (mtDNA) may affect male reproductive function. The aim of this study was to investigate the association of three deletions (4977, 7345 and 7599 bp) and two-point mutations (A73G and A3243G) of mitochondrial DNA with male infertility in an Iranian population. In a case-control study, we collected semen samples of 60 infertile men and 60 healthy controls. Detection of the mtDNA deletions and point mutations were performed by long range PCR and PCR-RFLP method, respectively. Our data revealed that 4977 and 7599 bp deletions are associated with male infertility...
May 24, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
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