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https://www.readbyqxmd.com/read/27914481/conserved-3-utr-stem-loop-structure-in-l1-and-alu-transposons-in-human-genome-possible-role-in-retrotransposition
#1
Daria Grechishnikova, Maria Poptsova
BACKGROUND: In the process of retrotransposition LINEs use their own machinery for copying and inserting themselves into new genomic locations, while SINEs are parasitic and require the machinery of LINEs. The exact mechanism of how a LINE-encoded reverse transcriptase (RT) recognizes its own and SINE RNA remains unclear. However it was shown for the stringent-type LINEs that recognition of a stem-loop at the 3'UTR by RT is essential for retrotransposition. For the relaxed-type LINEs it is believed that the poly-A tail is a common recognition element between LINE and SINE RNA...
December 3, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27903268/long-term-outdoor-air-pollution-and-dna-methylation-in-circulating-monocytes-results-from-the-multi-ethnic-study-of-atherosclerosis-mesa
#2
Gloria C Chi, Yongmei Liu, James W MacDonald, R Graham Barr, Kathleen M Donohue, Mark D Hensley, Lifang Hou, Charles E McCall, Lindsay M Reynolds, David S Siscovick, Joel D Kaufman
BACKGROUND: DNA methylation may mediate effects of air pollution on cardiovascular disease. The association between long-term air pollution exposure and DNA methylation in monocytes, which are central to atherosclerosis, has not been studied. We investigated the association between long-term ambient air pollution exposure and DNA methylation (candidate sites and global) in monocytes of adults (aged ≥55). METHODS: One-year average ambient fine particulate matter (PM2...
December 1, 2016: Environmental Health: a Global Access Science Source
https://www.readbyqxmd.com/read/27900322/patterns-of-transposable-element-expression-and-insertion-in-cancer
#3
Evan A Clayton, Lu Wang, Lavanya Rishishwar, Jianrong Wang, John F McDonald, I King Jordan
Human transposable element (TE) activity in somatic tissues causes mutations that can contribute to tumorigenesis. Indeed, TE insertion mutations have been implicated in the etiology of a number of different cancer types. Nevertheless, the full extent of somatic TE activity, along with its relationship to tumorigenesis, have yet to be fully explored. Recent developments in bioinformatics software make it possible to analyze TE expression levels and TE insertional activity directly from transcriptome (RNA-seq) and whole genome (DNA-seq) next-generation sequence data...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27897165/nonreciprocity-and-magnetic-free-isolation-based-on-optomechanical-interactions
#4
Freek Ruesink, Mohammad-Ali Miri, Andrea Alù, Ewold Verhagen
Nonreciprocal components, such as isolators and circulators, provide highly desirable functionalities for optical circuitry. This motivates the active investigation of mechanisms that break reciprocity, and pose alternatives to magneto-optic effects in on-chip systems. In this work, we use optomechanical interactions to strongly break reciprocity in a compact system. We derive minimal requirements to create nonreciprocity in a wide class of systems that couple two optical modes to a mechanical mode, highlighting the importance of optically biasing the modes at a controlled phase difference...
November 29, 2016: Nature Communications
https://www.readbyqxmd.com/read/27876753/metamaterials-prime-time
#5
Andrea Alù
No abstract text is available yet for this article.
November 23, 2016: Nature Materials
https://www.readbyqxmd.com/read/27868354/high-incidence-of-bscl2-intragenic-recombinational-mutation-in-peruvian-type-2-berardinelli-seip-syndrome
#6
Nelson Purizaca-Rosillo, Takayasu Mori, Yamali Benites-Cóndor, Fuki M Hisama, George M Martin, Junko Oshima
Congenital generalized lipodystrophy (CGL) is a genetically heterogeneous group of disorders characterized by the absence of functional adipose tissue. We identified two pedigrees with CGL in the community of the Mestizo tribe in the northern region of Peru. Five cases, ranging from 15 months to 7 years of age, presented with generalized lipodystrophy, muscular prominence, mild intellectual disability, and a striking aged appearance. Sequencing of the BSCL2 gene, known to be mutated in type 2 CGL (CGL2; Berardinelli-Seip syndrome), revealed a homozygous deletion of exon 3 in all five patients examined, suggesting the presence of a founder mutation...
November 21, 2016: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/27862296/dna-methylation-changes-in-mexican-children-exposed-to-arsenic-from-two-historic-mining-areas-in-san-luis-potos%C3%A3
#7
Jorge Alejandro Alegría-Torres, Leticia Carrizales-Yánez, Fernando Díaz-Barriga, Fernando Rosso-Camacho, Valeria Motta, Letizia Tarantini, Valentina Bollati
Arsenic is a carcinogen and epimutagen that threatens the health of exposed populations worldwide. In this study, we examined the methylation status of Alu and long interspersed nucleotide elements (LINE-1) and their association with levels of urinary arsenic in 84 Mexican children between 6 and 12 years old from two historic mining areas in the State of San Luis Potosí, Mexico. Urinary arsenic levels were determined by atomic absorption spectrophotometry and DNA methylation analysis was performed in peripheral blood leukocytes by bisulfite-pyrosequencing...
December 2016: Environmental and Molecular Mutagenesis
https://www.readbyqxmd.com/read/27861119/splicing-repression-allows-the-gradual-emergence-of-new-alu-exons-in-primate-evolution
#8
Jan Attig, Igor Ruiz de Los Mozos, Nejc Haberman, Zhen Wang, Warren Emmett, Kathi Zarnack, Julian König, Jernej Ule
Alu elements are retrotransposons that frequently form new exons during primate evolution. Here, we assess the interplay of splicing repression by hnRNPC and nonsense-mediated mRNA decay (NMD) in the quality control and evolution of new Alu-exons. We identify 3100 new Alu-exons and show that NMD more efficiently recognises transcripts with Alu-exons compared to other exons with premature termination codons. However, some Alu-exons escape NMD, especially when an adjacent intron is retained, highlighting the importance of concerted repression by splicing and NMD...
November 18, 2016: ELife
https://www.readbyqxmd.com/read/27846216/the-quality-of-selected-essential-medicines-sold-in-accredited-drug-dispensing-outlets-and-pharmacies-in-tanzania
#9
Eliangiringa Kaale, Vicky Manyanga, Mhina Chambuso, Jafary Liana, Edmund Rutta, Martha Embrey, Thomas Layloff, Keith Johnson
INTRODUCTION: The purpose of this study was to investigate the quality of a select group of medicines sold in accredited drug dispensing outlets (ADDOs) and pharmacies in different regions of Tanzania as part of an in-depth cross-sectional assessment of community access to medicines and community use of medicines. METHODS: We collected 242 samples of amoxicillin trihydrate, artemether-lumefantrine (ALu), co-trimoxazole, ergometrine maleate, paracetamol, and quinine from selected ADDOs and pharmacies in Mbeya, Morogoro, Singida, and Tanga regions...
2016: PloS One
https://www.readbyqxmd.com/read/27843499/evidence-for-l1-associated-dna-rearrangements-and-negligible-l1-retrotransposition-in-glioblastoma-multiforme
#10
Patricia E Carreira, Adam D Ewing, Guibo Li, Stephanie N Schauer, Kyle R Upton, Allister C Fagg, Santiago Morell, Michaela Kindlova, Patricia Gerdes, Sandra R Richardson, Bo Li, Daniel J Gerhardt, Jun Wang, Paul M Brennan, Geoffrey J Faulkner
BACKGROUND: LINE-1 (L1) retrotransposons are a notable endogenous source of mutagenesis in mammals. Notably, cancer cells can support unusual L1 retrotransposition and L1-associated sequence rearrangement mechanisms following DNA damage. Recent reports suggest that L1 is mobile in epithelial tumours and neural cells but, paradoxically, not in brain cancers. RESULTS: Here, using retrotransposon capture sequencing (RC-seq), we surveyed L1 mutations in 14 tumours classified as glioblastoma multiforme (GBM) or as a lower grade glioma...
2016: Mobile DNA
https://www.readbyqxmd.com/read/27843410/reciprocity-passivity-and-causality-in-willis-materials
#11
Michael B Muhlestein, Caleb F Sieck, Andrea Alù, Michael R Haberman
Materials that require coupling between the stress-strain and momentum-velocity constitutive relations were first proposed by Willis (Willis 1981 Wave Motion3, 1-11. (doi:10.1016/0165-2125(81)90008-1)) and are now known as elastic materials of the Willis type, or simply Willis materials. As coupling between these two constitutive equations is a generalization of standard elastodynamic theory, restrictions on the physically admissible material properties for Willis materials should be similarly generalized. This paper derives restrictions imposed on the material properties of Willis materials when they are assumed to be reciprocal, passive and causal...
October 2016: Proceedings. Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/27829678/missing-genetic-variations-in-gne-myopathy-rearrangement-hotspots-encompassing-5-utr-and-founder-allele
#12
Wenhua Zhu, Satomi Mitsuhashi, Takahiro Yonekawa, Satoru Noguchi, Josiah Chai Yui Huei, Atchayaram Nalini, Veeramani Preethish-Kumar, Masayoshi Yamamoto, Kenji Murakata, Madoka Mori-Yoshimura, Sachiko Kamada, Hiroyuki Yahikozawa, Masato Karasawa, Seigo Kimura, Fumitada Yamashita, Ichizo Nishino
GNE myopathy is an autosomal recessive distal myopathy caused by loss-of-function mutations in the GNE gene, which encodes UDP-GlcNAc 2-epimerase/ManNAc kinase (GNE), a key enzyme in sialic-acid biosynthesis. By comprehensive screening of manifesting patients using a fine-mapped targeted next-generation sequencing (NGS), we identified copy number variations (CNVs) in 13 patients from 11 unrelated families. The nine unique CNVs largely vary in size from 0.3 to 72 kb. Over half of the cases carry different deletions spanning merely exon 2, which contains the 5' untranslated region (5'UTR) of the muscle major transcript hGNE1...
November 10, 2016: Journal of Human Genetics
https://www.readbyqxmd.com/read/27815101/cerebral-embolic-protection-during-transcatheter-aortic-valve-replacement
#13
Samir R Kapadia, Susheel Kodali, Raj Makkar, Roxana Mehran, Ronald M Lazar, Robert Zivadinov, Michael G Dwyer, Hasan Jilaihawi, Renu Virmani, Saif Anwaruddin, Vinod H Thourani, Tamim Nazif, Norman Mangner, Felix Woitek, Amar Krishnaswamy, Stephanie Mick, Tarun Chakravarty, Mamoo Nakamura, James M McCabe, Lowell Satler, Alan Zajarias, Wilson Y Szeto, Lars Svensson, Maria C Alu, Roseann M White, Carlye Kraemer, Azin Parhizgar, Martin B Leon, Axel Linke
BACKGROUND: Neurological events and brain infarction after transcatheter aortic valve replacement (TAVR) are concerns which may be reduced with transcatheter embolic protection (TEP). OBJECTIVE: Evaluate the safety and efficacy of TEP during TAVR. METHODS: Nineteen centers randomized 363 patients undergoing TAVR to safety (n=123), device imaging (n=121), and control imaging (n=119). The primary safety endpoint was major adverse cardiac and cerebrovascular events (MACCE) at 30 days and the primary efficacy endpoint was reduction in new lesion volume in protected brain territories on MRI scans at 2-7 days...
October 27, 2016: Journal of the American College of Cardiology
https://www.readbyqxmd.com/read/27807467/a-map-of-mobile-dna-insertions-in-the-nci-60-human-cancer-cell-panel
#14
John G Zampella, Nemanja Rodić, Wan Rou Yang, Cheng Ran Lisa Huang, Jane Welch, Veena P Gnanakkan, Toby C Cornish, Jef D Boeke, Kathleen H Burns
BACKGROUND: The National Cancer Institute-60 (NCI-60) cell lines are among the most widely used models of human cancer. They provide a platform to integrate DNA sequence information, epigenetic data, RNA and protein expression, and pharmacologic susceptibilities in studies of cancer cell biology. Genome-wide studies of the complete panel have included exome sequencing, karyotyping, and copy number analyses but have not targeted repetitive sequences. Interspersed repeats derived from mobile DNAs are a significant source of heritable genetic variation, and insertions of active elements can occur somatically in malignancy...
2016: Mobile DNA
https://www.readbyqxmd.com/read/27801483/molecular-data-highlight-hybridization-in-squirrel-monkeys-saimiri-cebidae
#15
Jeferson Carneiro, Luis Fernando da Silva Rodrigues-Filho, Horacio Schneider, Iracilda Sampaio
Hybridization has been reported increasingly frequently in recent years, fueling the debate on its role in the evolutionary history of species. Some studies have shown that hybridization is very common in captive New World primates, and hybrid offspring have phenotypes and physiological responses distinct from those of the "pure" parents, due to gene introgression. Here we used the TA15 Alu insertion to investigate hybridization in the genus Saimiri. Our results indicate the hybridization of Saimiri boliviensis peruviensis with S...
October 31, 2016: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/27798849/dusp11-activity-on-triphosphorylated-transcripts-promotes-argonaute-association-with-noncanonical-viral-micrornas-and-regulates-steady-state-levels-of-cellular-noncoding-rnas
#16
James M Burke, Rodney P Kincaid, Ryan M Nottingham, Alan M Lambowitz, Christopher S Sullivan
RNA silencing is a conserved eukaryotic gene expression regulatory mechanism mediated by small RNAs. In Caenorhabditis elegans, the accumulation of a distinct class of siRNAs synthesized by an RNA-dependent RNA polymerase (RdRP) requires the PIR-1 phosphatase. However, the function of PIR-1 in RNAi has remained unclear. Since mammals lack an analogous siRNA biogenesis pathway, an RNA silencing role for the mammalian PIR-1 homolog (dual specificity phosphatase 11 [DUSP11]) was unexpected. Here, we show that the RNA triphosphatase activity of DUSP11 promotes the RNA silencing activity of viral microRNAs (miRNAs) derived from RNA polymerase III (RNAP III) transcribed precursors...
September 15, 2016: Genes & Development
https://www.readbyqxmd.com/read/27797956/a-portrait-of-ribosomal-dna-contacts-with-hi-c-reveals-5s-and-45s-rdna-anchoring-points-in-the-folded-human-genome
#17
Shoukai Yu, Bernardo Lemos
Ribosomal rRNAs account for >60% of all RNAs in eukaryotic cells and are encoded in the ribosomal DNA (rDNA) arrays. The rRNAs are produced from two sets of loci: the 5S rDNA array resides exclusively on human chromosome 1, while the 45S rDNA array resides on the short arm of five human acrocentric chromosomes. The 45S rDNA gives origin to the nucleolus, the nuclear organelle that is the site of ribosome biogenesis. Intriguingly, 5S and 45S rDNA arrays exhibit correlated copy number variation in lymphoblastoid cells (LCLs)...
October 25, 2016: Genome Biology and Evolution
https://www.readbyqxmd.com/read/27797328/-conformational-polymorphysm-of-g-rich-fragments-of-dna-alu-repeats-i-potential-noncanonical-structures
#18
A V Sekridova, A M Varizhuk, O N Tatarinova, V V Severov, N A Barinov, I P Smirnov, V N Lazarev, D V Klinov, G E Pozmogova
In this paper, we report results of systematic studies of conformational polymorphism of G-rich DNA fragments from Alu repeats. Alu retrotransposones are primate-specific short interspersed elements. Using the Alu sequence from the prooncogen bcl2 intron and the consensus AluSx sequence as representative examples, we determined characteristic Alu sites that are capable of adopting G-quadruplex (GQ) conformations (i.e., potential quadruplex sites - PQSAlu), and demonstrated by bioinformatics methods that those sites are Alu-specific in the human genome...
July 2016: Biomedit︠s︡inskai︠a︡ Khimii︠a︡
https://www.readbyqxmd.com/read/27786608/de-novo-methylation-in-male-germ-cells-of-the-common-marmoset-monkey-occurs-during-postnatal-development-and-is-maintained-in-vitro
#19
Daniel Langenstroth-Röwer, Jörg Gromoll, Joachim Wistuba, Ina Tröndle, Sandra Laurentino, Stefan Schlatt, Nina Neuhaus
The timing of de novo DNA methylation in male germ cells during human testicular development is yet unsolved. Apart from that, the stability of established imprinting patterns in vitro is controversially discussed. This study aimed at determining the timing of DNA de novo methylation and at assessing the stability of the methylation status in vitro. We employed the marmoset monkey (Callithrix jacchus) as it is considered the best non-human primate model for human testicular development. We selected neonatal, pre-pubertal, pubertal, and adult animals (n = 3, each) and assessed germ cell global DNA methylation levels by 5-methyl cytosine staining, and Alu elements and gene-specific methylation (H19, LIT1, SNRPN, MEST, OCT4, MAGE-A4, and DDX-4) by pyrosequencing...
October 27, 2016: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27782844/transcriptome-wide-effects-of-inverted-sines-on-gene-expression-and-their-impact-on-rna-polymerase-ii-activity
#20
Mansoureh Tajaddod, Andrea Tanzer, Konstantin Licht, Michael T Wolfinger, Stefan Badelt, Florian Huber, Oliver Pusch, Sandy Schopoff, Michael Janisiw, Ivo Hofacker, Michael F Jantsch
BACKGROUND: Short interspersed elements (SINEs) represent the most abundant group of non-long-terminal repeat transposable elements in mammalian genomes. In primates, Alu elements are the most prominent and homogenous representatives of SINEs. Due to their frequent insertion within or close to coding regions, SINEs have been suggested to play a crucial role during genome evolution. Moreover, Alu elements within mRNAs have also been reported to control gene expression at different levels...
October 25, 2016: Genome Biology
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