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Mitochondrial DNA

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https://www.readbyqxmd.com/read/28448897/a-performance-evaluation-of-nextera-xt-and-kapa-hyperplus-for-rapid-illumina-library-preparation-of-long-range-mitogenome-amplicons
#1
Joseph D Ring, Kimberly Sturk-Andreaggi, Michelle A Peck, Charla Marshall
Next-generation sequencing (NGS) facilitates the rapid and high-throughput generation of human mitochondrial genome (mitogenome) data to build population and reference databases for forensic comparisons. To this end, long-range amplification provides an effective method of target enrichment that is amenable to library preparation assays employing DNA fragmentation. This study compared the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA) and the KAPA HyperPlus Library Preparation Kit (Kapa Biosystems, Wilmington, MA) for enzymatic fragmentation and indexing of ∼8500bp mitogenome amplicons for Illumina sequencing...
April 5, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28445781/mitochondrial-ros-control-of-cancer
#2
REVIEW
María Del Pilar Sosa Idelchik, Ulrike Begley, Thomas J Begley, J Andrés Melendez
Mitochondria serve a primary role in energy maintenance but also function to govern levels of mitochondria-derived reactive oxygen species (mROS). ROS have long been established to play a critical role in tumorigenesis and are now considered to be integral to the regulation of diverse signaling networks that drive proliferation, tumor cell survival and malignant progression. mROS can damage DNA, activate oncogenes, block the function of tumor suppressors and drive migratory signaling. The mitochondrion's oxidant scavenging systems including SOD2, Grx2, GPrx, Trx and TrxR are key of the cellular redox tone...
April 23, 2017: Seminars in Cancer Biology
https://www.readbyqxmd.com/read/28445089/genetic-and-morphological-differentiation-of-the-semiterrestrial-crab-armases-angustipes-brachyura-sesarmidae-along-the-brazilian-coast
#3
Murilo Zanetti Marochi, Setuko Masunari, Christoph D Schubart
The genetic and morphometric population structures of the semiterrestrial crab Armases angustipes from along the Brazilian coast were examined. The influence of the Central South Equatorial Current on larval dispersal of A. angustipes also was evaluated. Six populations were sampled from estuarine areas in São Luis do Maranhão, Maranhão; Natal, Rio Grande do Norte; Maceió, Alagoas; Ilhéus, Bahia; Aracruz, Espírito Santo; and Guaratuba, Paraná. Patterns of genetic differentiation were assessed using DNA sequence data corresponding to parts of the mitochondrial cytochrome c oxidase subunit 1...
February 2017: Biological Bulletin
https://www.readbyqxmd.com/read/28444389/smithrnas-could-mitochondria-bend-nuclear-regulation
#4
Andrea Pozzi, Federico Plazzi, Liliana Milani, Fabrizio Ghiselli, Marco Passamonti
Typically, animal mitochondria have very compact genomes, with few short intergenic regions, and no introns. Hence, it may seem that there is little space for unknown functions in mitochondrial DNA (mtDNA). However, mtDNA can also operate through RNA interference, as small non coding RNAs (sncRNAs) produced by mtDNA have already been proposed for humans. We sequenced sncRNA libraries from isolated mitochondria of Ruditapes philippinarum (Mollusca Bivalvia) gonads, a species with doubly uniparental inheritance of mitochondria (DUI), and identified several putative sncRNAs of mitochondrial origin...
April 21, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28444372/quantifying-the-number-of-independent-organelle-dna-insertions-in-genome-evolution-and-human-health
#5
Einat Hazkani-Covo, William F Martin
Fragments of organelle genomes are often found as insertions in nuclear DNA. These fragments of mitochondrial DNA (numts) and plastid DNA (nupts) are ubiquitous components of eukaryotic genomes. They are, however, often edited out during the genome assembly process, leading to systematic underestimation of their frequency. Numts and nupts, once inserted, can become further fragmented through subsequent insertion of mobile elements or other recombinational events that disrupt the continuity of the inserted sequence relative to the genuine organelle DNA copy...
April 21, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28443516/synergistic-effect-of-graphene-oxide-coated-nanotised-apigenin-with-paclitaxel-go-na-ptx-a-ros-dependent-mitochondrial-mediated-apoptosis-in-ovarian-cancer
#6
Manish Kumar Pal, Shyam Pyari Jaiswar, Ashish Dwivedi, Shruti Goyal, Vinay Nand Dwivedi, Anumesh Kumar Pathak, Vinod Kumar, Pushp Lata Sankhwar, Ratan Singh Ray
Ovarian cancer is most lethal among all gynecologic malignancies. Paclitaxel (PTX) is well used chemotherapeutic regimen for cancer control; however its undesired toxicity has been always a matter of concern for clinicians. Here we used the graphene oxide coated nanotised apigenin (GO-NA) as chemo sensitizing agent to enhance the efficacy of paclitaxel to overcome the limitations of chemotherapy. GO and GO-Apigenin was prepared by modified Hummers method and the nanoparticles were characterized by dynamic light scattering and transmission electron microscopy Human ovarian adenocarcinomas (SKOV-3) cells was treated by DMSO, Group I (Control)-McCoy's 5A Medium, Group II-Paclitaxel (5nM) alone, Group III- Nanotised Apigenin (GO-NA-10μM) Group IV- Paclitaxel (5nM) + GO-NA (10μM)...
April 24, 2017: Anti-cancer Agents in Medicinal Chemistry
https://www.readbyqxmd.com/read/28442719/chlamydia-trachomatis-neither-exerts-deleterious-effects-on-spermatozoa-nor-impairs-male-fertility
#7
Jenniffer Puerta Suarez, Leonardo R Sanchez, Florencia C Salazar, Hector A Saka, Rosa Molina, Andrea Tissera, Virginia E Rivero, Walter D Cardona Maya, Ruben D Motrich
Chlamydia trachomatis is the most prevalent sexually transmitted bacterial infection. However, whether Chlamydia trachomatis has a negative impact on sperm quality and male fertility is still controversial. Herein, we report the effects on sperm quality of the in vitro exposure of spermatozoa to Chlamydia trachomatis, and also the effects of male genital infection on male fertility using an animal model. Human and mouse sperm were obtained from healthy donors and cauda epididimys from C57BL/6 mice, respectively...
April 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28442264/mitochondrial-lon-protease-dependent-degradation-of-cytochrome-c-oxidase-subunits-under-hypoxia-and-myocardial-ischemia
#8
Naresh B V Sepuri, Rajesh Angireddy, Satish Srinivasan, Manti Guha, Joseph Spear, Bin Lu, Hindupur K Anandatheerthavarada, Carolyn K Suzuki, Narayan G Avadhani
The mitochondrial ATP dependent matrix protease, Lon, is involved in the maintenance of mitochondrial DNA nucleoids and degradation of abnormal or misfolded proteins. The Lon protease regulates mitochondrial Tfam (mitochondrial transcription factor A) level and thus modulates mitochondrial DNA (mtDNA) content. We have previously shown that hypoxic stress induces the PKA-dependent phosphorylation of cytochrome c oxidase (CcO) subunits I, IVi1, and Vb and a time-dependent reduction of these subunits in RAW 264...
April 22, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28442045/lower-dietary-n-6-n-3-ratio-and-high-dose-vitamin-e-supplementation-improve-sperm-morphology-and-oxidative-stress-in-boars
#9
Qing Liu, Yuanfei Zhou, Runjia Duan, Hongkui Wei, Siwen Jiang, Jian Peng
A 2×2 factorial experiment (10 boars per treatment) was conducted for 16 weeks to evaluate the effects of the dietary n-6:n-3 ratio (14:1 vs 6:1) and vitamin E (200 vs 400mg kg(-1)) on boar sperm morphology and oxidative stress. Sperm mitochondrial membrane potential (MMP), reactive oxygen species (ROS), DNA damage (8-hydroxydeoxyguanosine; 8-OHdG), seminal lipoperoxidation (malondialdehyde; MDA) and antioxidant capacity in the serum, spermatozoa and seminal plasma were assessed as indicators of oxidative stress...
April 2017: Reproduction, Fertility, and Development
https://www.readbyqxmd.com/read/28441938/mitors-a-method-for-high-throughput-sensitive-and-accurate-detection-of-mitochondrial-dna-heteroplasmy
#10
Julien Marquis, Gregory Lefebvre, Yiannis A I Kourmpetis, Mohamed Kassam, Frédéric Ronga, Umberto De Marchi, Andreas Wiederkehr, Patrick Descombes
BACKGROUND: Mitochondrial dysfunction is linked to numerous pathological states, in particular related to metabolism, brain health and ageing. Nuclear encoded gene polymorphisms implicated in mitochondrial functions can be analyzed in the context of classical genome wide association studies. By contrast, mitochondrial DNA (mtDNA) variants are more challenging to identify and analyze for several reasons. First, contrary to the diploid nuclear genome, each cell carries several hundred copies of the circular mitochondrial genome...
April 26, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28441753/coq10-deficiency-may-indicate-mitochondrial-dysfunction-in-cr-vi-toxicity
#11
Xiali Zhong, Xing Yi, Rita de Cássia da Silveira E Sá, Yujing Zhang, Kaihua Liu, Fang Xiao, Caigao Zhong
To investigate the toxic mechanism of hexavalent chromium Cr(VI) and search for an antidote for Cr(VI)-induced cytotoxicity, a study of mitochondrial dysfunction induced by Cr(VI) and cell survival by recovering mitochondrial function was performed. In the present study, we found that the gene expression of electron transfer flavoprotein dehydrogenase (ETFDH) was strongly downregulated by Cr(VI) exposure. The levels of coenzyme 10 (CoQ10) and mitochondrial biogenesis presented by mitochondrial mass and mitochondrial DNA copy number were also significantly reduced after Cr(VI) exposure...
April 24, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28441466/biomonitoring-of-marine-vertebrates-in-monterey-bay-using-edna-metabarcoding
#12
Elizabeth A Andruszkiewicz, Hilary A Starks, Francisco P Chavez, Lauren M Sassoubre, Barbara A Block, Alexandria B Boehm
Molecular analysis of environmental DNA (eDNA) can be used to assess vertebrate biodiversity in aquatic systems, but limited work has applied eDNA technologies to marine waters. Further, there is limited understanding of the spatial distribution of vertebrate eDNA in marine waters. Here, we use an eDNA metabarcoding approach to target and amplify a hypervariable region of the mitochondrial 12S rRNA gene to characterize vertebrate communities at 10 oceanographic stations spanning 45 km within the Monterey Bay National Marine Sanctuary (MBNMS)...
2017: PloS One
https://www.readbyqxmd.com/read/28441108/novel-clades-of-the-hu-ihf-superfamily-point-to-unexpected-roles-in-the-eukaryotic-centrosome-chromosome-partitioning-and-biologic-conflicts
#13
A Maxwell Burroughs, Gurmeet Kaur, Dapeng Zhang, L Aravind
The HU superfamily of proteins, with a unique DNA-binding mode, has been extensively studied as the primary chromosome-packaging protein of the bacterial superkingdom. Representatives also play a role in DNA-structuring during recombination events and in eukaryotic organellar genome maintenance. However, beyond these well-studied roles, little is understood of the functional diversification of this large superfamily. Using sensitive sequence and structure analysis methods we identify multiple novel clades of the HU superfamily...
April 25, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28440425/mitochondrial-transcription-factor-a-tfam-is-upregulated-in-glioma
#14
Hyunji Lee, Jisoo Park, Quangdon Tran, Dohoon Kim, Youngeun Hong, Hyeonjeong Cho, So Hee Kwon, Derek Brazil, Seon-Hwan Kim, Jongsun Park
Mitochondrial transcription factor A (TFAM), which was initially discovered as a transcription factor for mitochondrial DNA, has known to be critical for the regulation of mitochondrial DNA. However the possible involvement of TFAM in cancer is largely unknown. In this study, we have provided some evidence that TFAM may have a potential role in brain tumor. Western blot analysis with anti‑TFAM antibody indicated that TFAM is overexpressed in glioblastoma cell lines including U87MG and U251MG. Transcriptome profiling of U87MG and U251MG cells by using deep‑sequencing revealed that TFAM transcripts were upregulated in these cells compared to its of cerebral cortex...
April 12, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28439972/mitochondrial-biogenesis-and-pgc-1%C3%AE-gene-expression-in-male-broilers-from-ascites-susceptible-and-resistant-lines
#15
N Khodambashi Emami, A Golian, M Danesh Mesgaran, N B Anthony, D D Rhoads
Ascites is a cardiovascular metabolic disease characterized by accumulation of fluid around the heart and in the abdominal cavity that eventually leads to death. This syndrome is the end-point result of a series of metabolic incidents that are generally caused by impaired oxygen availability. Mitochondria are the major sites of oxygen consumption, therefore major contributors to oxidative stress. Genetic, metabolic and dietary factors can influence variations in mitochondrial biogenesis (mitochondrial size, number and mass) that might have an effect on oxygen consumption and reactive oxygen species production...
April 25, 2017: Journal of Animal Physiology and Animal Nutrition
https://www.readbyqxmd.com/read/28438700/further-consideration-on-the-phylogeny-of-the-ciliophora-analyses-using-both-mitochondrial-and-nuclear-data-with-focus-on-the-extremely-confused-class-phyllopharyngea
#16
Pu Wang, Yurui Wang, Chundi Wang, Tengteng Zhang, Saleh A Al-Farraj, Feng Gao
Most ciliate phylogenetic analyses have largely relied on the nuclear small subunit ribosome DNA (nSSU-rDNA) locus. However, single locus or multi-loci from the same genome or chromosome may not be sufficient enough to elucidate phylogenetic relationships among ciliate taxa. Therefore, in addition to nSSU-rDNA, the mitochondrial small subunit ribosome DNA (mtSSU-rDNA) was applied in this study. We expanded the taxon sampling especially within the class Phyllopharyngea. Phylogenetic analyses based on nSSU-rDNA and mtSSU-rDNA, independently, as well as concatenated were performed and revealed the following: (1) mtSSU-rDNA is more variable than nSSU-rDNA, and is better at elucidating relationships at lower levels, e...
April 21, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28438607/obesity-exposed-oocytes-accumulate-and-transmit-damaged-mitochondria-due-to-an-inability-to-activate-mitophagy
#17
Anna L Boudoures, Jessica Saben, Andrea Drury, Suzanne Scheaffer, Zeel Modi, Wendy Zhang, Kelle H Moley
Mitochondria are the most prominent organelle in the oocyte. Somatic cells maintain a healthy population of mitochondria by degrading damaged mitochondria via mitophagy, a specialized autophagy pathway. However, evidence from previous work investigating the more general macroautophagy pathway in oocytes suggests that mitophagy may not be active in the oocyte. This would leave the vast numbers of mitochondria - poised to be inherited by the offspring - vulnerable to damage. Here we test the hypothesis that inactive mitophagy in the oocyte underlies maternal transmission of dysfunctional mitochondria...
April 21, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28438434/connective-tissue-growth-factor-decreases-mitochondrial-metabolism-through-ubiquitin-mediated-degradation-of-mitochondrial-transcription-factor-a-in-oral-squamous-cell-carcinoma
#18
Wei-Ting Lai, Yue-Ju Li, Shi-Bei Wu, Cheng-Ning Yang, Tai-Sheng Wu, Yau-Huei Wei, Yi-Ting Deng
BACKGROUND/PURPOSE: Deregulation of metabolic pathways is one of the hallmarks of cancer progression. Connective tissue growth factor (CTGF/CCN2) acts as a tumor suppressor in oral squamous cell carcinoma (OSCC). However, the role of CTGF in modulating cancer metabolism is still unclear. METHODS: OSCC cells stably overexpressing CTGF (SAS/CTGF) and shRNA against CTGF (TW2.6/shCTGF) were established. Oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) were examined by the Seahorse XF24 analyzer...
April 21, 2017: Journal of the Formosan Medical Association, Taiwan Yi Zhi
https://www.readbyqxmd.com/read/28437554/molecular-identification-of-cetaceans-from-the-west-atlantic-using-the-e3-i5-region-of-coi
#19
L H O Falcão, A S Campos, J E P Freitas, M A A Furtado-Neto, V V Faria
Molecular identification is very useful in cases where morphology-based species identification is not possible. Examples for its application in cetaceans include the identification of carcasses of stranded animals in advanced state of decomposition and body parts that are illegally traded. One DNA region that is often used for molecular identification is the Folmer region of the mitochondrial gene cytochrome c oxidase subunit I (COI) (locus 48 to 705 bp). This locus has been used for the identification of several animal species, including whales and dolphins...
April 20, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28436451/empirical-modeling-of-physiochemical-immune-response-of-multilayer-zinc-oxide-nanomaterials-under-uv-exposure-to-melanoma-and-foreskin-fibroblasts
#20
Muhammad Fakhar-E-Alam, M Waseem Akram, Seemab Iqbal, K S Alimgeer, M Atif, K Sultana, M Willander, Zhiming M Wang
Carcinogenesis is a complex molecular process starting with genetic and epigenetic alterations, mutation stimulation, and DNA modification, which leads to proteomic adaptation ending with an uncontrolled proliferation mechanism. The current research focused on the empirical modelling of the physiological response of human melanoma cells (FM55P) and human foreskin fibroblasts cells (AG01518) to the multilayer zinc oxide (ZnO) nanomaterials under UV-A exposure. To validate this experimental scheme, multilayer ZnO nanomaterials were grown on a femtotip silver capillary and conjugated with protoporphyrin IX (PpIX)...
April 24, 2017: Scientific Reports
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