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https://www.readbyqxmd.com/read/29161613/molecular-characterization-of-urothelial-carcinoma-of-the-bladder-and-upper-urinary-tract
#1
Ji Yun Lee, Kyung Kim, Hyun Hwan Sung, Hwang Gyun Jeon, Byong Chang Jeong, Seong Il Seo, Seong Soo Jeon, Hyun Moo Lee, Han-Yong Choi, Ghee-Young Kwon, Kyoung-Mee Kim, Jeeyun Lee, Ho Yeong Lim, Se Hoon Park
PURPOSE: A better understanding of the molecular basis of urothelial carcinoma (UC) is needed to refine the clinical decision-making process. METHODS AND MATERIALS: We performed next-generation sequencing to investigate the mutational and transcriptional profiles of commonly mutated genes in UC using Ampliseq v2. Copy number variations (CNVs) were detected with nCounter assay. Genetic alterations between upper tract UC (UTUC) and urinary bladder UC (UBUC) were compared...
November 18, 2017: Translational Oncology
https://www.readbyqxmd.com/read/29161423/partial-bisulfite-conversion-for-unique-template-sequencing
#2
Vijay Kumar, Julie Rosenbaum, Zihua Wang, Talitha Forcier, Michael Ronemus, Michael Wigler, Dan Levy
We introduce a new protocol, mutational sequencing or muSeq, which uses sodium bisulfite to randomly deaminate unmethylated cytosines at a fixed and tunable rate. The muSeq protocol marks each initial template molecule with a unique mutation signature that is present in every copy of the template, and in every fragmented copy of a copy. In the sequenced read data, this signature is observed as a unique pattern of C-to-T or G-to-A nucleotide conversions. Clustering reads with the same conversion pattern enables accurate count and long-range assembly of initial template molecules from short-read sequence data...
November 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29161231/epigenetic-regulation-mechanisms-of-microrna-expression
#3
Sara Morales, Mariano Monzo, Alfons Navarro
MicroRNAs (miRNAs) are single-stranded RNAs of 18-25 nucleotides that regulate gene expression at the post-transcriptional level. They are involved in many physiological and pathological processes, including cell proliferation, apoptosis, development and carcinogenesis. Because of the central role of miRNAs in the regulation of gene expression, their expression needs to be tightly controlled. Here, we summarize the different mechanisms of epigenetic regulation of miRNAs, with a particular focus on DNA methylation and histone modification...
November 21, 2017: Biomolecular Concepts
https://www.readbyqxmd.com/read/29160870/engineering-high-performance-hairpin-stacking-circuits-for-logic-gate-operation-and-highly-sensitive-biosensing-assay-of-microrna
#4
Yueli Xing, Xinmin Li, Taixian Yuan, Wei Cheng, Dandan Li, Tianxiao Yu, Xiaojuan Ding, Shijia Ding
Recently, hairpin stacking circuits (HSC) based on toehold-mediated strand displacement have been engineered to detect nucleic acids and proteins. However, the three metastable hairpins in a HSC system can potentially react non-specifically in the absence of a catalyst, limiting its practical application. Here, we developed a unique hairpin design guideline to eliminate circuit leakage of HSC, and the high-performance HSC was successfully implemented on logic gate building and biosensing. We began by analyzing the sources of circuit leakage and optimizing the toehold lengths of hairpins in the HSC system based on the surface plasmon resonance (SPR) technique...
November 21, 2017: Analyst
https://www.readbyqxmd.com/read/29160859/the-role-of-rnf213-4810g-a-and-4950g-a-variants-in-patients-with-moyamoya-disease-in-korea
#5
Young Seok Park, Hui Jeong An, Jung Oh Kim, Won Seop Kim, In Bo Han, Ok Joon Kim, Nam Keun Kim, Dong-Seok Kim
Although a founder variant of RNF213 4810G>A is a major genetic risk factor for moyamoya disease (MMD) in East Asians, the frequency and disease susceptibility of RNF213 variants remain largely unknown. This study investigated the mutation analysis of RNF213 (4448, 4810, 4863, and 4950) between Korean MMD and healthy controls. We performed a polymerase chain reaction-restriction fragment length polymorphism analysis. To identify the association between RNF213 gene polymorphisms and MMD disease, we performed statistical analyses such as multivariable logistic regression and Fisher's exact test...
November 21, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29160852/the-complete-chloroplast-genome-sequences-of-aconitum-pseudolaeve-and-aconitum-longecassidatum-and-development-of-molecular-markers-for-distinguishing-species-in-the-aconitum-subgenus-lycoctonum
#6
Inkyu Park, Sungyu Yang, Goya Choi, Wook Jin Kim, Byeong Cheol Moon
Aconitum pseudolaeve Nakai and Aconitum longecassidatum Nakai, which belong to the Aconitum subgenus Lycoctonum, are distributed in East Asia and Korea. Aconitum species are used in herbal medicine and contain highly toxic components, including aconitine. A. pseudolaeve, an endemic species of Korea, is a commercially valuable material that has been used in the manufacture of cosmetics and perfumes. Although Aconitum species are important plant resources, they have not been extensively studied, and genomic information is limited...
November 21, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29160623/saddlebags-a-software-interface-for-submitting-full-length-hla-allele-sequences-to-the-embl-ena-nucleotide-database
#7
B M Matern, M Groeneweg, C E M Voorter, M G J Tilanus
Submission of full-length HLA allele sequences presents a unique challenge, both for high-throughput sequencing laboratories, and smaller diagnostic laboratories. HLA's extensive polymorphism means that accurate representation and annotation of allele sequence is of critical importance, and curators of nucleotide databases must establish submission formats to ensure high-quality data, and prevent ambiguities. The IPD-IMGT/HLA database is established as the standard repository for HLA sequences, and it is a major goal of the 17th International HLA and Immunogenetics Workshop to fill the IPD-IMGT/HLA database with full-length HLA sequences...
November 21, 2017: HLA
https://www.readbyqxmd.com/read/29160618/deciphering-the-fine-nucleotide-diversity-of-full-hla-class-i-and-class-ii-genes-in-a-well-documented-population-from-sub-saharan-africa
#8
Thomas Goeury, Lisa Creary, Lydie Brunet, Maxime Galan, Maeva Pasquier, Barbara Kervaire, André Langaney, Jean-Marie Tiercy, Marcelo A Fernández-Viña, José Manuel Nunes, Alicia Sanchez-Mazas
With the aim to understand how NGS improves both our assessment of genetic variation within populations and our knowledge on HLA molecular evolution, we sequenced and analysed 8 HLA loci in a well-documented population from sub-Saharan Africa (Mandenka). The results of full-gene NGS-MiSeq sequencing compared to those obtained by traditional typing techniques or limited sequencing strategies showed that segregating sites located outside exon 2 are crucial to describe not only class I, but also class II population diversity...
November 21, 2017: HLA
https://www.readbyqxmd.com/read/29160508/detection-and-genotyping-of-human-adenovirus-and-sapovirus-in-children-with-acute-gastroenteritis-in-bel%C3%A3-m-par%C3%A3-between-1990-and-1992-first-detection-of-gi-7-and-gv-2-sapoviruses-in-brazil
#9
Larissa Cristina Prado das Neves Costa, Jones Anderson Monteiro Siqueira, Thayara Morais Portal, Edivaldo Costa Sousa, Alexandre da Costa Linhares, Yvone Benchimol Gabbay, Hugo Reis Resque
INTRODUCTION: Acute gastroenteritis (AGE) is one of the most common causes of morbidity and mortality, especially among children from developing countries. Human adenovirus (HAdV) and sapovirus (SaV) are among the agents that cause AGE. The present study aimed to detect and genotype HAdV and SaV in 172 fecal samples from children with AGE, collected during a surveillance study carried out in a low-income community in Belém, Pará, between 1990 and 1992. METHODS: HAdV was detected by nested PCR, using primers Hex1deg/Hex2deg and NeHex3deg/NeHex4deg...
September 2017: Revista da Sociedade Brasileira de Medicina Tropical
https://www.readbyqxmd.com/read/29160302/role-of-cyp24a1-vdr-and-gc-gene-polymorphisms-on-deferasirox-pharmacokinetics-and-clinical-outcomes
#10
S Allegra, J Cusato, S De Francia, A Arduino, F Longo, E Pirro, D Massano, A De Nicolò, A Piga, A D'Avolio
β-Thalassemia patients develop deficiency in vitamin D absorption and liver hydroxylation, resulting in extremely low calcitriol levels. We explored the role of single-nucleotide polymorphisms (SNPs) involved in vitamin D metabolism, transport and activity on deferasirox pharmacokinetics and outcomes (effectiveness trough levels (Ctrough) and the area under the curve (AUC) cutoffs of 20 μg ml(-1) and 360 μg ml(-1) h(-1), respectively; nonresponse AUC limit of 250 μg ml(-1) h(-1)). Ninety-nine β-thalassemic patients were enrolled...
November 21, 2017: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/29160301/new-insights-into-the-pharmacogenomics-of-antidepressant-response-from-the-gendep-and-star-d-studies-rare-variant-analysis-and-high-density-imputation
#11
C Fabbri, K E Tansey, R H Perlis, J Hauser, N Henigsberg, W Maier, O Mors, A Placentino, M Rietschel, D Souery, G Breen, C Curtis, L Sang-Hyuk, S Newhouse, H Patel, M Guipponi, N Perroud, G Bondolfi, M O'Donovan, G Lewis, J M Biernacka, R M Weinshilboum, A Farmer, K J Aitchison, I Craig, P McGuffin, R Uher, C M Lewis
Genome-wide association studies have generally failed to identify polymorphisms associated with antidepressant response. Possible reasons include limited coverage of genetic variants that this study tried to address by exome genotyping and dense imputation. A meta-analysis of Genome-Based Therapeutic Drugs for Depression (GENDEP) and Sequenced Treatment Alternatives to Relieve Depression (STAR*D) studies was performed at the single-nucleotide polymorphism (SNP), gene and pathway levels. Coverage of genetic variants was increased compared with previous studies by adding exome genotypes to previously available genome-wide data and using the Haplotype Reference Consortium panel for imputation...
November 21, 2017: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/29160202/re-classification-of-clavibacter-michiganensis-subspecies-on-the-basis-of-whole-genome-and-multi-locus-sequence-analyses
#12
Xiang Li, James Tambong, Kat Xiaoli Yuan, Wen Chen, Huimin Xu, C André Lévesque, Solke H De Boer
Although the genus Clavibacter was originally proposed to accommodate all phytopathogenic coryneform bacteria containing B2γ diaminobutyrate in the peptidoglycan, reclassification of all but one species into other genera has resulted in the current monospecific status of the genus. The single species in the genus, Clavibacter michiganensis, has multiple subspecies, which are all highly host-specific plant pathogens. Whole genome analysis based on average nucleotide identity and digital DNA-DNA hybridization as well as multi-locus sequence analysis (MLSA) of seven housekeeping genes support raising each of the C...
November 21, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29160200/methylobacterium-frigidaeris-sp-nov-isolated-from-an-air-conditioning-system
#13
Yunho Lee, Che Ok Jeon
A reddish pink-pigmented, Gram-stain-negative, aerobic and methylotrophic bacterial strain, designated strain IER25-16(T), was isolated from a laboratory air conditioning system in the Republic of Korea. Cells were motile rods showing catalase- and oxidase-positive reactions. Strain IER25-16(T) grew at 10-40 °C (optimum, 30 °C), at pH 4.0-7.0 (optimum, pH 5.0-7.0) and in the presence of 0-1.0 % (w/v) NaCl (optimum, 0 %). The major respiratory quinone was ubiquinone-10 and ubiquinone-9 was also detected as the minor respiratory quinone...
November 21, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29159995/multiple-abc-glucoside-transporters-mediate-sugar-stimulated-growth-in-the-heterocyst-forming-cyanobacterium-anabaena-sp-strain-pcc-7120
#14
Mercedes Nieves-Morión, Enrique Flores
Cyanobacteria are generally capable of photoautotrophic growth and are widely distributed on Earth. The model filamentous, heterocyst-forming strain Anabaena sp. PCC 7120 has been long considered a strict photoautotroph but is now known to be able to assimilate fructose. We have previously described two components of ABC glucoside uptake transporters from Anabaena that are involved in uptake of the sucrose analog esculin: GlsC (a nucleotide-binding domain subunit [NBD]) and GlsP (a transmembrane component [TMD])...
November 21, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/29159877/crystalline-structure-of-pulverized-dental-calculus-induces-cell-death-in-oral-epithelial-cells
#15
S M Ziauddin, A Yoshimura, J L Montenegro Raudales, Y Ozaki, K Higuchi, T Ukai, T Kaneko, T Miyazaki, E Latz, Y Hara
BACKGROUND AND OBJECTIVE: Dental calculus is a mineralized deposit attached to the tooth surface. We have shown that cellular uptake of dental calculus triggers nucleotide-binding oligomerization domain-like receptor family pyrin domain-containing 3 (NLRP3) inflammasome activation, leading to the processing of the interleukin-1β precursor into its mature form in mouse and human phagocytes. The activation of the NLRP3 inflammasome also induced a lytic form of programmed cell death, pyroptosis, in these cells...
November 20, 2017: Journal of Periodontal Research
https://www.readbyqxmd.com/read/29159421/qtl-mapping-of-downy-and-powdery-mildew-resistances-in-pi-197088-cucumber-with-genotyping-by-sequencing-in-ril-population
#16
Yuhui Wang, Kyle VandenLangenberg, Changlong Wen, Todd C Wehner, Yiqun Weng
Host resistances in PI 197088 cucumber to downy and powdery mildew pathogens are conferred by 11 (3 with major effect) and 4 (1 major effect) QTL, respectively, and three of which are co-localized. The downy mildew (DM) and powdery mildew (PM) are the two most important foliar diseases of cucurbit crops worldwide. The cucumber accession PI 197088 exhibits high-level resistances to both pathogens. Here, we reported QTL mapping results for DM and PM resistances with 148 recombinant inbred lines from a cross between PI 197088 and the susceptible line 'Coolgreen'...
November 20, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29159324/dna-repair-after-oxidative-stress-current-challenges
#17
Bennett Van Houten, Gloria A Santa-Gonzalez, Mauricio Camargo
Reactive oxygen and nitrogen species damage cellular macromolecules including DNA. Cells have a robust base excision repair pathway to deal with this damage in both nuclear and mitochondrial genomes. However, mitochondria lack nucleotide excision repair. Evidence suggests that chronic oxidative stress can induce protective pathways lowering genotoxicity. Understanding oxidant injury to DNA and its repair is critical for our understanding the pathophysiology of a wide range of human disorders.
February 2018: Current Opinion in Toxicology
https://www.readbyqxmd.com/read/29158942/the-single-nucleotide-polymorphism-rs1014290-of-the-slc2a9-gene-is-associated-with-uric-acid-metabolism-in-parkinson-s-disease
#18
Jiangfang Miao, Jing Liu, Li Xiao, Jiedi Zheng, Chunfeng Liu, Zufu Zhu, Kai Li, Weifeng Luo
Individuals with Parkinson's disease (PD) have lower uric acid levels than those without PD, and the CC genotype and C minor allele of a single nucleotide polymorphism (SNP), rs1014290 of SLC2A9, are associated with lower uric acid levels. We investigated the association of rs1014290 with uric acid metabolism in a cohort of PD cases (220) and controls (110) in a Han Chinese population. Uric acid levels were determined and rs1014290 was assayed using a mutation-sensitive on/off switch technology. PD uric acid levels (291...
2017: Parkinson's Disease
https://www.readbyqxmd.com/read/29158878/molecular-analysis-of-rs2070744-and-rs1799983-polymorphisms-of-nos3-gene-in-iranian-patients-with-multiple-sclerosis
#19
Mohammad Mehdi Heidari, Mehri Khatami, Yaser Tahamtan
Introduction: Multiple Sclerosis (MS) is a disease of central nervous system that mainly causes lesions or plaques in the spinal cord and brain. The purpose of this study was to analyze the relation between c.-813C>T (rs2070744) and c.894G>T (rs1799983) polymorphisms of NOS3 gene and MS in Iranian patients. Methods: A total of 78 patients with MS and 80 healthy controls were screened for NOS3 (rs2070744 and rs1799983) Single Nucleotide Polymorphisms (SNPs) by tetra-primer multiplex ARMS-PCR and PCR-RFLP...
July 2017: Basic and Clinical Neuroscience
https://www.readbyqxmd.com/read/29158794/association-between-sumoylation-related-gene-rs77447679-polymorphism-and-risk-of-gastric-cancer-gc-in-a-chinese-population
#20
Ying Luo, Sihong You, Jirong Wang, Shuling Fan, Jie Shi, Ai Peng, Tingting Yu
Purpose: Sumoylation plays a critical role in gene regulation and tumorigenesis, and is hypothesized to correlate with the development of various cancers. So far, there has been no reported association between sumoylation-related genes and the risk of gastric cancer (GC). Methods: A total of 17 tagging single-nucleotide polymorphisms (tag-SNPs) in 5 sumoylation-related genes were selected and genotyped by SNaPshot in a case-control study, including 1021 GC patients and 1304 controls. Odds ratio (OR) and 95% confidential interval (CI) were computed to evaluate the genetic association of the onset of GC...
2017: Journal of Cancer
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