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https://www.readbyqxmd.com/read/28542625/the-identification-of-switch-like-alternative-splicing-exons-among-multiple-samples-with-rna-seq-data
#1
Zhiyi Qin, Xuegong Zhang
Alternative splicing is an ubiquitous phenomenon in most human genes and has important functions. The switch-like exon is the type of exon that has a high level of usage in some tissues, but has a low level of usage in the other tissues. They usually undergo strong tissue-specific regulations. There is still a lack a systematic method to identify switch-like exons from multiple RNA-seq samples. We proposed a novel method called iterative Tertile Absolute Deviation around the mode (iTAD) to profile the distribution of exon relative usages among multiple samples and to identify switch-like exons and other types of exons using a robust statistic estimator...
2017: PloS One
https://www.readbyqxmd.com/read/28542129/adar1-mediated-3-utr-editing-and-expression-control-of-antiapoptosis-genes-fine-tunes-cellular-apoptosis-response
#2
Chang-Ching Yang, Yi-Tung Chen, Yi-Feng Chang, Hsuan Liu, Yu-Ping Kuo, Chieh-Tien Shih, Wei-Chao Liao, Hui-Wen Chen, Wen-Sy Tsai, Bertrand Chin-Ming Tan
Adenosine-to-inosine RNA editing constitutes a crucial component of the cellular transcriptome and critically underpins organism survival and development. While recent high-throughput approaches have provided comprehensive documentation of the RNA editome, its functional output remains mostly unresolved, particularly for events in the non-coding regions. Gene ontology analysis of the known RNA editing targets unveiled a preponderance of genes related to apoptosis regulation, among which proto-oncogenes XIAP and MDM2 encode two the most abundantly edited transcripts...
May 25, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28533011/effect-of-surface-treatments-on-repair-with-composite-resin-of-a-partially-monoclinic-phase-transformed-yttrium-stabilized-tetragonal-zirconia
#3
Beatriz Regalado Galvão Ribeiro, Marilia Regalado Galvão Rabelo Caldas, Antonio Alves Almeida, Renata Garcia Fonseca, Gelson Luis Adabo
STATEMENT OF PROBLEM: Studies of composite resin repairs of yttrium-tetragonal zirconia polycrystal (Y-TZP) are usually performed in its tetragonal phase, but it may be partially transformed into a monoclinic phase in a clinical fracture. PURPOSE: The purpose of this in vitro study was to evaluate the effect of airborne-particle abrasion (APA) and a bonding agent on the shear bond strength (SBS) between a composite resin and hydrothermally aged Y-TZP. MATERIAL AND METHODS: Specimens (7...
May 20, 2017: Journal of Prosthetic Dentistry
https://www.readbyqxmd.com/read/28513612/insertion-of-alu-elements-at-a-pten-hotspot-in-cowden-syndrome
#4
Louise Crivelli, Virginie Bubien, Natalie Jones, Jennifer Chiron, Françoise Bonnet, Emmanuelle Barouk-Simonet, Patrice Couzigou, Nicolas Sevenet, Frédéric Caux, Michel Longy
Cowden syndrome (CS) is an inherited autosomal dominant disorder associated with germline pathogenic variants of the PTEN tumor suppressor gene. Its phenotypical expression is highly variable and the existence of patients with a CS suggestive phenotype without pathogenic PTEN variant may be related to genetic heterogeneity. In order to explore this hypothesis through the detection of potentially deleterious variants enabling us to identify a new candidate gene, we performed whole-exome sequencing (WES) in a series of 22 CS patients without detectable PTEN pathogenic variant using conventional methods for mutation screening...
May 17, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28502204/alu-insertion-polymorphisms-in-the-african-sahel-and-the-origin-of-fulani-pastoralists
#5
Martina Čížková, Zuzana Hofmanová, Mohammed G Mokhtar, Václav Janoušek, Issa Diallo, Pavel Munclinger, Viktor Černý
BACKGROUND: The origin of Western African pastoralism, represented today by the Fulani nomads, has been a highly debated issue for the past decades, and has not yet been conclusively resolved. AIM: In this study, we focused on Alu polymorphisms in sedentary and nomadic populations across the African Sahel to investigate patterns of diversity that can complement the existing results and contribute to resolving issues concerning the origin of West African pastoralism...
May 14, 2017: Annals of Human Biology
https://www.readbyqxmd.com/read/28502002/pcr-identification-of-genetic-polymorphisms
#6
Amanda M Harbison, Jenny Ngoc Tran Nguyen
Polymerase chain reaction (PCR) enables the amplification of a specific sequence of deoxyribonucleic acid (DNA) through the process of three main steps: template DNA denaturation, annealing of the primers to complementary sequences, and primer extension to synthesize DNA strands. By using this method, the target sequence will be copied and amplified at an exponential rate. PCR provides a qualitative method for identifying DNA from fresh or dried cells/body fluids, formalin-fixed archival tissue specimens, and ancient specimens...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28500844/cell-free-circulating-dna-integrity-is-an-independent-predictor-of-impending-breast-cancer-recurrence
#7
Jie Cheng, Katarina Cuk, Jörg Heil, Michael Golatta, Sarah Schott, Christof Sohn, Andreas Schneeweiss, Barbara Burwinkel, Harald Surowy
Non-invasive blood-based molecule markers are evaluated as promising biomarkers these days. Here we investigated the potential of cell-free circulating DNA Integrity (cfDI) as blood-based marker for the prediction of recurrence during the follow-up of breast cancer patients within a prospective study cohort. cfDI was determined in plasma of 212 individuals, by measuring ALU and LINE1 repetitive DNA elements using quantitative PCR. A significant decrease of cfDI in recurrent breast cancer patients was observed...
April 24, 2017: Oncotarget
https://www.readbyqxmd.com/read/28489894/analysis-of-global-dna-methylation-changes-in-primary-human-fibroblasts-in-the-early-phase-following-x-ray-irradiation
#8
Anna Maierhofer, Julia Flunkert, Marcus Dittrich, Tobias Müller, Detlev Schindler, Indrajit Nanda, Thomas Haaf
Epigenetic alterations may contribute to the generation of cancer cells in a multi-step process of tumorigenesis following irradiation of normal body cells. Primary human fibroblasts with intact cell cycle checkpoints were used as a model to test whether X-ray irradiation with 2 and 4 Gray induces direct epigenetic effects (within the first cell cycle) in the exposed cells. ELISA-based fluorometric assays were consistent with slightly reduced global DNA methylation and hydroxymethylation, however the observed between-group differences were usually not significant...
2017: PloS One
https://www.readbyqxmd.com/read/28488140/characterization-of-a-new-brca1-rearrangement-in-an-italian-woman-with-hereditary-breast-and-ovarian-cancer-syndrome
#9
Paola Concolino, Roberta Rizza, Karl Hackmann, Ida Paris, Angelo Minucci, Elisa De Paolis, Giovanni Scambia, Cecilia Zuppi, Evelin Schrock, Ettore Capoluongo
BACKGROUND: We report a novel BRCA1 LGR, involving the complete duplication of exon 3, in an Italian patient with a strong family history of breast and ovarian cancer. Our purpose is to provide an effective characterization of this LGR using a combination of different methods able to establish the exact breakpoints of the duplication. METHODS: MAQ assay was used as primary screening method in LGRs detection. Array CGH, RT-PCR, and Long-PCR were used for a careful characterization of rearrangement and breakpoint regions...
May 9, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28484492/relationships-between-global-dna-methylation-in-circulating-white-blood-cells-and-breast-cancer-risk-factors
#10
REVIEW
Nayha Chopra-Tandon, Haotian Wu, Kathleen F Arcaro, Susan R Sturgeon
It is not yet clear whether white blood cell DNA global methylation is associated with breast cancer risk. In this review we examine the relationships between multiple breast cancer risk factors and three markers of global DNA methylation: LINE-1, 5-mdC, and Alu. A literature search was conducted using Pubmed up to April 1, 2016, using combinations of relevant outcomes such as "WBC methylation," "blood methylation," "blood LINE-1 methylation," and a comprehensive list of known and suspected breast cancer risk factors...
2017: Journal of Cancer Epidemiology
https://www.readbyqxmd.com/read/28481278/combining-low-temperature-fluorescence-dna-hybridization-immunostaining-and-super-resolution-localization-microscopy-for-nano-structure-analysis-of-alu-elements-and-their-influence-on-chromatin-structure
#11
Matthias Krufczik, Aaron Sievers, Annkathrin Hausmann, Jin-Ho Lee, Georg Hildenbrand, Wladimir Schaufler, Michael Hausmann
Immunostaining and fluorescence in situ hybridization (FISH) are well established methods for specific labelling of chromatin in the cell nucleus. COMBO-FISH (combinatorial oligonucleotide fluorescence in situ hybridization) is a FISH method using computer designed oligonucleotide probes specifically co-localizing at given target sites. In combination with super resolution microscopy which achieves spatial resolution far beyond the Abbe Limit, it allows new insights into the nano-scaled structure and organization of the chromatin of the nucleus...
May 7, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28473128/transcatheter-aortic-valve-implantation-within-degenerated-aortic-surgical-bioprostheses-partner-2-valve-in-valve-registry
#12
John G Webb, Michael J Mack, Jonathon M White, Danny Dvir, Philipp Blanke, Howard C Herrmann, Jonathon Leipsic, Susheel K Kodali, Raj Makkar, D Craig Miller, Philippe Pibarot, Augusto Pichard, Lowell F Satler, Lars Svensson, Maria C Alu, Rakesh M Suri, Martin B Leon
BACKGROUND: Early experience with transcatheter aortic valve replacement (TAVR) within failed bioprosthetic surgical aortic valves has shown that valve-in-valve (VIV) TAVR is a feasible therapeutic option with acceptable acute procedural results. OBJECTIVES: The authors examined 30-day and 1-year outcomes in a large cohort of high-risk patients undergoing VIV TAVR. METHODS: Patients with symptomatic degeneration of surgical aortic bioprostheses at high risk (≥50% major morbidity or mortality) for reoperative surgery were prospectively enrolled in the multicenter PARTNER (Placement of Aortic Transcatheter Valves) 2 VIV trial and continued access registries...
May 9, 2017: Journal of the American College of Cardiology
https://www.readbyqxmd.com/read/28472756/development-and-validation-of-innoquant-%C3%A2-hy-a-system-for-quantitation-and-quality-assessment-of-total-human-and-male-dna-using-high-copy-targets
#13
Andrew Loftus, Gina Murphy, Hiromi Brown, Anne Montgomery, Jonathan Tabak, James Baus, Marion Carroll, André Green, Suresh Sikka, Sudhir Sinha
The development and validation of InnoQuant(®) HY, a real-time PCR system containing four DNA targets-two RE autosomal targets of different sizes, male specific targets, and an internal positive control target-are described herein. The ratio of the two autosomal targets provides a Degradation Index, or a quantitative value of a sample's degradation state. The male specific targets are multi-copy targets located on the Y chromosome, which provides information about a sample's male DNA composition. The experimental results demonstrate InnoQuant HY as a robust qPCR method producing accurate DNA quantitation results even at low dynamic ranges, with reproducibility among population groups...
April 17, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28465436/structural-variants-caused-by-alu-insertions-are-associated-with-risks-for-many-human-diseases
#14
Lindsay M Payer, Jared P Steranka, Wan Rou Yang, Maria Kryatova, Sibyl Medabalimi, Daniel Ardeljan, Chunhong Liu, Jef D Boeke, Dimitri Avramopoulos, Kathleen H Burns
Interspersed repeat sequences comprise much of our DNA, although their functional effects are poorly understood. The most commonly occurring repeat is the Alu short interspersed element. New Alu insertions occur in human populations, and have been responsible for several instances of genetic disease. In this study, we sought to determine if there are instances of polymorphic Alu insertion variants that function in a common variant, common disease paradigm. We cataloged 809 polymorphic Alu elements mapping to 1,159 loci implicated in disease risk by genome-wide association study (GWAS) (P < 10(-8))...
May 16, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28459195/impact-of-viral-and-host-dna-methylations-on-hpv16-related-cervical-cancer-pathogenesis
#15
Shrinka Sen, Paramita Mandal, Amrapali Bhattacharya, Sudip Kundu, Rahul Roy Chowdhury, Nidhu Ranjan Mondal, Tanmay Chatterjee, Biman Chakravarty, Sudipta Roy, Sharmila Sengupta
Epigenetic alterations within human papillomavirus (HPV) and host cellular genomes are known to occur during cervical carcinogenesis. Our objective was to analyse the influence of (1) methylation within two immunostimulatory CpG motifs within HPV16 E6 and E7 genes around the viral late promoter and their correlation, if any, with expression deregulation of host receptor (TLR9) and DNA methyltransferases (DNMT1, DNMT3A and DNMT3B) and (2) global DNA methylation levels within CpGs of the repetitive Alu sequences, on cervical cancer (CaCx) pathogenesis...
May 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28452557/time-reversal-symmetry-bounds-on-the-electromagnetic-response-of-asymmetric-structures
#16
Dimitrios L Sounas, Andrea Alù
Asymmetric structures support different field distributions and electromagnetic responses when excited from different directions. Here we show that time-reversal symmetry imposes fundamental constraints on their overall response, beyond those dictated by reciprocity. For two-port devices, the asymmetry in field distribution for opposite excitations is shown to be fundamentally bounded by the reflection at the ports, and the fields are identical everywhere in space in the case of full transmission. In multiport and open scenarios, these bounds have implications on radiation and scattering at different ports and towards different directions...
April 14, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28450901/insertion-and-deletion-polymorphisms-of-the-ancient-alus-family-in-the-human-genome
#17
Maria S Kryatova, Jared P Steranka, Kathleen H Burns, Lindsay M Payer
BACKGROUND: Polymorphic Alu elements account for 17% of structural variants in the human genome. The majority of these belong to the youngest AluY subfamilies, and most structural variant discovery efforts have focused on identifying Alu polymorphisms from these currently retrotranspositionally active subfamilies. In this report we analyze polymorphisms from the evolutionarily older AluS subfamily, whose peak activity was tens of millions of years ago. We annotate the AluS polymorphisms, assess their likely mechanism of origin, and evaluate their contribution to structural variation in the human genome...
2017: Mobile DNA
https://www.readbyqxmd.com/read/28436945/adar1-controls-apoptosis-of-stressed-cells-by-inhibiting-staufen1-mediated-mrna-decay
#18
Masayuki Sakurai, Yusuke Shiromoto, Hiromitsu Ota, Chunzi Song, Andrew V Kossenkov, Jayamanna Wickramasinghe, Louise C Showe, Emmanuel Skordalakes, Hsin-Yao Tang, David W Speicher, Kazuko Nishikura
Both p150 and p110 isoforms of ADAR1 convert adenosine to inosine in double-stranded RNA (dsRNA). ADAR1p150 suppresses the dsRNA-sensing mechanism that activates MDA5-MAVS-IFN signaling in the cytoplasm. In contrast, the biological function of the ADAR1p110 isoform, which is usually located in the nucleus, is largely unknown. Here, we show that stress-activated phosphorylation of ADAR1p110 by MKK6-p38-MSK MAP kinases promotes its binding to Exportin-5 and its export from the nucleus. After translocating to the cytoplasm, ADAR1p110 suppresses apoptosis in stressed cells by protecting many antiapoptotic gene transcripts that contain 3'-untranslated-region dsRNA structures primarily comprising inverted Alu repeats...
April 24, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28423240/biochemical-cellular-physiological-and-pathological-consequences-of-human-loss-of-n-glycolylneuraminic-acid
#19
Jonathan Okerblom, Ajit Varki
About 2-3 million years ago, Alu-mediated deletion of a critical exon in the CMAH gene became fixed in the hominin lineage ancestral to humans, possibly through a stepwise process of selection by pathogen targeting of the CMAH product (the sialic acid Neu5Gc), followed by reproductive isolation via female anti-Neu5Gc antibodies. Loss of CMAH has occurred independently in some other lineages, but is functionally intact in Old World primates, including our closest relatives, the chimpanzees. While the biophysical and biochemical ramifications of losing tens of millions of Neu5Gc hydroxyl groups at most cell surfaces remains poorly understood, there are multi-scale effects functionally relevant to both sides of the host-pathogen interface...
April 19, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28417465/effects-of-rare-sugar-d-allulose-on-heat-induced-gelation-of-surimi-prepared-from-marine-fish
#20
Masahiro Ogawa, Masaki Inoue, Shigeru Hayakawa, Siwaporn O'Charoen, Makiko Ogawa
BACKGROUND: d-Allulose (Alu), the C3-epimer of d-fructose, is a non-caloric sweetener (0.39 kcal g(-1) ) with a suppressive effect on postprandial blood glucose elevation. The aim of this study was to investigate the effects of Alu used as a sweetener and gel improver instead of sucrose on heat-induced gelation of surimi. RESULTS: The puncture test of a heat-induced surimi gel showed that with 50 g kg(-1) Alu the gel had 15% and 6% higher gel strength than the corresponding gel with sucrose (Suc) and with sorbitol (Sor), respectively...
April 18, 2017: Journal of the Science of Food and Agriculture
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