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https://www.readbyqxmd.com/read/29332336/downregulation-of-guanine-nucleotide-binding-protein-beta-1-gnb1-is-associated-with-worsened-prognosis-of-clearcell-renal-cell-carcinoma-and-is-related-to-vegf-signaling-pathway
#1
C Chen, H Chi, L Min, Z Junhua
PURPOSE: Clear-cell renal cell carcinoma (ccRCC) is characterized by genetic abnormalities, while the role of Guanine Nucleotide-Binding Protein Beta 1 (GNB1) in ccRCC has not been studied. We thus aimed to evaluate the expression and prognostic value of GNB1 in ccRCC. METHODS: A two-stage study (exploration and validation) was conducted using in silico and immunohistochemical (IHC) scoring of ccRCC samples from our institute, to evaluate the association between GNB1 expression and clinicopathological parameters of ccRCC patients...
November 2017: Journal of B.U.ON.: Official Journal of the Balkan Union of Oncology
https://www.readbyqxmd.com/read/29331962/splicing-variant-of-wdfy4-augments-mda5-signalling-and-the-risk-of-clinically-amyopathic-dermatomyositis
#2
Yuta Kochi, Yoichiro Kamatani, Yuya Kondo, Akari Suzuki, Eiryo Kawakami, Ryosuke Hiwa, Yukihide Momozawa, Manabu Fujimoto, Masatoshi Jinnin, Yoshiya Tanaka, Takashi Kanda, Robert G Cooper, Hector Chinoy, Simon Rothwell, Janine A Lamb, Jiří Vencovský, Heřman Mann, Koichiro Ohmura, Keiko Myouzen, Kazuyoshi Ishigaki, Ran Nakashima, Yuji Hosono, Hiroto Tsuboi, Hidenaga Kawasumi, Yukiko Iwasaki, Hiroshi Kajiyama, Tetsuya Horita, Mariko Ogawa-Momohara, Akito Takamura, Shinichiro Tsunoda, Jun Shimizu, Keishi Fujio, Hirofumi Amano, Akio Mimori, Atsushi Kawakami, Hisanori Umehara, Tsutomu Takeuchi, Hajime Sano, Yoshinao Muro, Tatsuya Atsumi, Toshihide Mimura, Yasushi Kawaguchi, Tsuneyo Mimori, Atsushi Takahashi, Michiaki Kubo, Hitoshi Kohsaka, Takayuki Sumida, Kazuhiko Yamamoto
OBJECTIVES: Idiopathic inflammatory myopathies (IIMs) are a heterogeneous group of rare autoimmune diseases in which both genetic and environmental factors play important roles. To identify genetic factors of IIM including polymyositis, dermatomyositis (DM) and clinically amyopathic DM (CADM), we performed the first genome-wide association study for IIM in an Asian population. METHODS: We genotyped and tested 496 819 single nucleotide polymorphism for association using 576 patients with IIM and 6270 control subjects...
January 13, 2018: Annals of the Rheumatic Diseases
https://www.readbyqxmd.com/read/29331751/comprehensive-genomic-profiling-of-head-and-neck-squamous-cell-carcinoma-reveals-fgfr1-amplifications-and-tumour-genomic-alterations-burden-as-prognostic-biomarkers-of-survival
#3
C Dubot, V Bernard, M P Sablin, S Vacher, W Chemlali, A Schnitzler, G Pierron, K Ait Rais, N Bessoltane, E Jeannot, J Klijanienko, O Mariani, T Jouffroy, V Calugaru, C Hoffmann, M Lesnik, N Badois, F Berger, C Le Tourneau, M Kamal, I Bieche
BACKGROUND: We aimed at identifying deleterious genomic alterations from untreated head and neck squamous cell carcinoma (HNSCC) patients, and assessing their prognostic value. PATIENTS AND METHODS: We retrieved 122 HNSCC patients who underwent primary surgery. Targeted NGS was used to analyse a panel of 100 genes selected among the most frequently altered genes in HNSCC and potential therapeutic targets. We selected only deleterious (activating or inactivating) single nucleotide variations, and copy number variations for analysis...
January 10, 2018: European Journal of Cancer
https://www.readbyqxmd.com/read/29329304/a-novel-method-to-test-associations-between-a-weighted-combination-of-phenotypes-and-genetic-variants
#4
Huanhuan Zhu, Shuanglin Zhang, Qiuying Sha
Many complex diseases like diabetes, hypertension, metabolic syndrome, et cetera, are measured by multiple correlated phenotypes. However, most genome-wide association studies (GWAS) focus on one phenotype of interest or study multiple phenotypes separately for identifying genetic variants associated with complex diseases. Analyzing one phenotype or the related phenotypes separately may lose power due to ignoring the information obtained by combining phenotypes, such as the correlation between phenotypes. In order to increase statistical power to detect genetic variants associated with complex diseases, we develop a novel method to test a weighted combination of multiple phenotypes (WCmulP)...
2018: PloS One
https://www.readbyqxmd.com/read/29328361/logistic-regression-analysis-for-the-identification-of-the-metastasis-associated-signaling-pathways-of-osteosarcoma
#5
Yang Liu, Wei Sun, Xiaojun Ma, Yuedong Hao, Gang Liu, Xiaohui Hu, Houlai Shang, Pengfei Wu, Zexue Zhao, Weidong Liu
Osteosarcoma (OS) is the most common histological type of primary bone cancer. The present study was designed to identify the key genes and signaling pathways involved in the metastasis of OS. Microarray data of GSE39055 were downloaded from the Gene Expression Omnibus database, which included 19 OS biopsy specimens before metastasis (control group) and 18 OS biopsy specimens after metastasis (case group). After the differentially expressed genes (DEGs) were identified using the Linear Models for Microarray Analysis package, hierarchical clustering analysis and unsupervised clustering analysis were performed separately, using orange software and the self-organization map method...
January 2, 2018: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29325827/efficient-oligo-nucleotide-mediated-crispr-cas9-gene-editing-in-aspergilli
#6
Christina S Nødvig, Jakob B Hoof, Martin E Kogle, Zofia D Jarczynska, Jan Lehmbeck, Dorte K Klitgaard, Uffe H Mortensen
CRISPR-Cas9 technologies are revolutionizing fungal gene editing. Here we show that survival of specific Cas9/sgRNA mediated DNA double strand breaks (DSBs) depends on the non-homologous end-joining, NHEJ, DNA repair pathway and we use this observation to develop a tool to assess protospacer efficiency in Aspergillus nidulans. Moreover, we show that in NHEJ deficient strains, highly efficient marker-free gene targeting can be performed. Indeed, we show that even single-stranded oligo nucleotides efficiently works as repair templates of specific Cas9/sgRNA induced DNA DSBs in A...
January 8, 2018: Fungal Genetics and Biology: FG & B
https://www.readbyqxmd.com/read/29325772/the-association-of-snp276g-t-at-adiponectin-gene-with-insulin-resistance-and-circulating-adiponectin-in-response-to-two-different-hypocaloric-diets
#7
Daniel Antonio de Luis, Olatz Izaola, David Primo, R Aller, A Ortola, E Gómez, J J Lopez
BACKGROUND: Several adiponectin gene (ADIPOQ) single nucleotide polymorphisms (SNPS) have been related with adiponectin levels and risk for obesity. OBJECTIVE: The aim of our study was to analyze the effect of rs1501299 ADIPOQ gene polymorphism and dietary intake on total adiponectin levels and insulin resistance after two hypocaloric diets in obese subjects. MATERIAL AND METHODS: A Caucasian population of 284 obese patients was enrolled in a randomized clinical trial with two hypocaloric diets (I: moderate carbohydrates vs II: low fat)...
January 8, 2018: Diabetes Research and Clinical Practice
https://www.readbyqxmd.com/read/29325733/associations-of-gbp2-gene-copy-number-variations-with-growth-traits-and-transcriptional-expression-in-chinese-cattle
#8
REVIEW
Gui-Min Zhang, Li Zheng, Hua He, Cheng-Chuang Song, Zi-Jing Zhang, Xiu-Kai Cao, Chu-Zhao Lei, Xian-Yong Lan, Xing-Lei Qi, Hong Chen, Yong-Zhen Huang
Copy number variations (CNVs) recently have been recognized as another important genetic variability followed single nucleotide polymorphisms (SNPs). The guanylate binding protein 2 (GBP2) gene plays an important role in cell proliferation. This study was performed to determine the presence of GBP2 CNV (relative to Angus cattle) in 466 individuals representing six main cattle breeds from China, identify its relationship with growth, and explore the biological effects of gene expression. There were two CNV regions in the GBP2 gene, for three types, CNV1 loss type (relative to Angus cattle) was more frequent in XN than other breeds, and CNV2 loss type (relative to Angus cattle) was more frequent in XN and CDM than other breeds...
January 8, 2018: Gene
https://www.readbyqxmd.com/read/29325547/paracrine-and-epigenetic-control-of-caf-induced-metastasis-the-role-of-hotair-stimulated-by-tgf-%C3%A3-1-secretion
#9
Yu Ren, Huan-Huan Jia, Yi-Qi Xu, Xuan Zhou, Xiao-Hui Zhao, Yun-Fei Wang, Xin Song, Zhi-Yan Zhu, Ting Sun, Yan Dou, Wei-Ping Tian, Xiu-Lan Zhao, Chun-Sheng Kang, Mei Mei
BACKGROUND: The communication between carcinoma associated fibroblasts (CAFs) and cancer cells facilitate tumor metastasis. In this study, we further underlying the epigenetic mechanisms of CAFs feed the cancer cells and the molecular mediators involved in these processes. METHODS: MCF-7 and MDA-MB-231 cells were treated with CAFs culture conditioned medium, respectively. Cytokine antibody array, enzyme-linked immunosorbent assay, western blotting and immunofluorescence were used to identify the key chemokines...
January 11, 2018: Molecular Cancer
https://www.readbyqxmd.com/read/29325309/-association-of-crohn-s-disease-with-aryl-hydrocarbon-receptor-gene-polymorphisms-and-haplotypes
#10
C Q Wu, S G Cao, X P Xia, C L Xu, S L Xia, X Q Lin, J Jin, R Ding, Y Jiang
Objective: To explore the relationship of Crohn's disease (CD) susceptibility to aryl hydrocarbon receptor (AhR) polymorphisms and haplotypes in Han population in Wenzhou city, China. Methods: A total of 310 CD patients and 573 age- and sex-matched healthy controls were enrolled in our study. Three single nucleotide polymorphisms (SNPs) of AhR(rs10249788,rs2158041,rs2066853) were determined by the improved multiple ligase detection reaction technique. Unconditional logistic regression analyses was applied to analyze the allelic and genotypic differences of each SNP between CD patients and controls, as well as their influence on the clinicopathologic characteristics in CD patients...
January 1, 2018: Zhonghua Nei Ke za Zhi [Chinese Journal of Internal Medicine]
https://www.readbyqxmd.com/read/29324778/genetic-diversity-and-recombination-of-enterovirus-g-strains-in-japanese-pigs-high-prevalence-of-strains-carrying-a-papain-like-cysteine-protease-sequence-in-the-enterovirus-g-population
#11
Shinobu Tsuchiaka, Yuki Naoi, Ryo Imai, Tsuneyuki Masuda, Mika Ito, Masataka Akagami, Yoshinao Ouchi, Kazuo Ishii, Shoichi Sakaguchi, Tsutomu Omatsu, Yukie Katayama, Mami Oba, Junsuke Shirai, Yuki Satani, Yasuhiro Takashima, Yuji Taniguchi, Masaki Takasu, Hiroo Madarame, Fujiko Sunaga, Hiroshi Aoki, Shinji Makino, Tetsuya Mizutani, Makoto Nagai
To study the genetic diversity of enterovirus G (EV-G) among Japanese pigs, metagenomics sequencing was performed on fecal samples from pigs with or without diarrhea, collected between 2014 and 2016. Fifty-nine EV-G sequences, which were >5,000 nucleotides long, were obtained. By complete VP1 sequence analysis, Japanese EV-G isolates were classified into G1 (17 strains), G2 (four strains), G3 (22 strains), G4 (two strains), G6 (two strains), G9 (six strains), G10 (five strains), and a new genotype (one strain)...
2018: PloS One
https://www.readbyqxmd.com/read/29324742/functional-characterization-of-adaptive-variation-within-a-cis-regulatory-element-influencing-drosophila-melanogaster-growth
#12
Amanda Glaser-Schmitt, John Parsch
Gene expression variation is a major contributor to phenotypic diversity within species and is thought to play an important role in adaptation. However, examples of adaptive regulatory polymorphism are rare, especially those that have been characterized at both the molecular genetic level and the organismal level. In this study, we perform a functional analysis of the Drosophila melanogaster CG9509 enhancer, a cis-regulatory element that shows evidence of adaptive evolution in populations outside the species' ancestral range in sub-Saharan Africa...
January 11, 2018: PLoS Biology
https://www.readbyqxmd.com/read/29324738/population-structure-analysis-of-the-neglected-parasite-thelazia-callipaeda-revealed-high-genetic-diversity-in-eastern-asia-isolates
#13
Xi Zhang, Ya Li Shi, Lu Lu Han, Chen Xiong, Shi Qi Yi, Peng Jiang, Zeng Xian Wang, Ji Long Shen, Jing Cui, Zhong Quan Wang
BACKGROUND: Thelazia callipaeda is the causative agent of thelaziasis in canids, felids and humans. However, the population genetic structure regarding this parasite remains unclear. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we first explored the genetic variation of 32 T. callipaeda clinical isolates using the following multi-molecular markers: cox1, cytb, 12S rDNA, ITS1 and 18S rDNA. The isolates were collected from 13 patients from 11 geographical locations in China...
January 11, 2018: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29323246/modulediscoverer-identification-of-regulatory-modules-in-protein-protein-interaction-networks
#14
Sebastian Vlaic, Theresia Conrad, Christian Tokarski-Schnelle, Mika Gustafsson, Uta Dahmen, Reinhard Guthke, Stefan Schuster
The identification of disease-associated modules based on protein-protein interaction networks (PPINs) and gene expression data has provided new insights into the mechanistic nature of diverse diseases. However, their identification is hampered by the detection of protein communities within large-scale, whole-genome PPINs. A presented successful strategy detects a PPIN's community structure based on the maximal clique enumeration problem (MCE), which is a non-deterministic polynomial time-hard problem. This renders the approach computationally challenging for large PPINs implying the need for new strategies...
January 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29321653/integrated-sequencing-of-exome-and-mrna-of-large-sized-single-cells
#15
Lily Yan Wang, Jiajie Guo, Wei Cao, Meng Zhang, Jiankui He, Zhoufang Li
Current approaches of single cell DNA-RNA integrated sequencing are difficult to call SNPs, because a large amount of DNA and RNA is lost during DNA-RNA separation. Here, we performed simultaneous single-cell exome and transcriptome sequencing on individual mouse oocytes. Using microinjection, we kept the nuclei intact to avoid DNA loss, while retaining the cytoplasm inside the cell membrane, to maximize the amount of DNA and RNA captured from the single cell. We then conducted exome-sequencing on the isolated nuclei and mRNA-sequencing on the enucleated cytoplasm...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29321585/site-specific-randomization-of-the-endogenous-genome-by-a-regulatable-crispr-cas9-piggybac-system-in-human-cells
#16
Kentaro Ishida, Huaigeng Xu, Noriko Sasakawa, Mandy Siu Yu Lung, Julia Alexandra Kudryashev, Peter Gee, Akitsu Hotta
Randomized mutagenesis at an endogenous chromosomal locus is a promising approach for protein engineering, functional assessment of regulatory elements, and modeling genetic variations. In mammalian cells, however, it is challenging to perform site-specific single-nucleotide substitution with single-stranded oligodeoxynucleotide (ssODN) donor templates due to insufficient homologous recombination and the infeasibility of positive selection. Here, we developed a DNA transposon based CRISPR-Cas9 regulated transcription and nuclear shuttling (CRONUS) system that enables the stable transduction of CRISPR-Cas9/sgRNA in broad cell types, but avoids undesired genome cleavage in the absence two chemical inducing molecules...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29321346/mutational-screening-of-pkd2-gene-in-the-north-indian-polycystic-kidney-disease-patients-revealed-28-genetic-variations
#17
Sonam Raj, Rana Gopal Singh, Parimal Das
Polycystic kidney disease (PKD) is a systemic disorder which adds majority of renal patients to end stage renal disease. Autosomal dominant polycystic kidney disease (ADPKD) is more prevalent and leading cause of dialysis and kidney transplant. Linkage analysis revealed some closely linked loci, two of which are identified as PKD1, PKD2 and an unidentified locus to ADPKD. This study was performed using PCR and automated DNA sequencing in 84 cases and 80 controls to test potential candidature of PKD2 as underlying cause of PKD by in silico and statistical analyses...
December 2017: Journal of Genetics
https://www.readbyqxmd.com/read/29321194/polygenic-hazard-score-to-guide-screening-for-aggressive-prostate-cancer-development-and-validation-in-large-scale-cohorts
#18
Tyler M Seibert, Chun Chieh Fan, Yunpeng Wang, Verena Zuber, Roshan Karunamuni, J Kellogg Parsons, Rosalind A Eeles, Douglas F Easton, ZSofia Kote-Jarai, Ali Amin Al Olama, Sara Benlloch Garcia, Kenneth Muir, Henrik Grönberg, Fredrik Wiklund, Markus Aly, Johanna Schleutker, Csilla Sipeky, Teuvo Lj Tammela, Børge G Nordestgaard, Sune F Nielsen, Maren Weischer, Rasmus Bisbjerg, M Andreas Røder, Peter Iversen, Tim J Key, Ruth C Travis, David E Neal, Jenny L Donovan, Freddie C Hamdy, Paul Pharoah, Nora Pashayan, Kay-Tee Khaw, Christiane Maier, Walther Vogel, Manuel Luedeke, Kathleen Herkommer, Adam S Kibel, Cezary Cybulski, Dominika Wokolorczyk, Wojciech Kluzniak, Lisa Cannon-Albright, Hermann Brenner, Katarina Cuk, Kai-Uwe Saum, Jong Y Park, Thomas A Sellers, Chavdar Slavov, Radka Kaneva, Vanio Mitev, Jyotsna Batra, Judith A Clements, Amanda Spurdle, Manuel R Teixeira, Paula Paulo, Sofia Maia, Hardev Pandha, Agnieszka Michael, Andrzej Kierzek, David S Karow, Ian G Mills, Ole A Andreassen, Anders M Dale
OBJECTIVES: To develop and validate a genetic tool to predict age of onset of aggressive prostate cancer (PCa) and to guide decisions of who to screen and at what age. DESIGN: Analysis of genotype, PCa status, and age to select single nucleotide polymorphisms (SNPs) associated with diagnosis. These polymorphisms were incorporated into a survival analysis to estimate their effects on age at diagnosis of aggressive PCa (that is, not eligible for surveillance according to National Comprehensive Cancer Network guidelines; any of Gleason score ≥7, stage T3-T4, PSA (prostate specific antigen) concentration ≥10 ng/L, nodal metastasis, distant metastasis)...
January 10, 2018: BMJ: British Medical Journal
https://www.readbyqxmd.com/read/29320875/characterization-of-bacteriophages-and-their-carriage-in-staphylococcus-aureus-isolated-from-broilers-in-poland
#19
A Marek, E Pyzik, D Stępień-Pyśniak, R Urban-Chmiel, A Nowaczek
1. The objective of this study was the isolation and morphological characterisation of temperate bacteriophages induced from Staphylococcus aureus strains isolated from clinical samples from broiler chickens and turkeys. 2. Eighty-five S. aureus strains were tested for susceptibility to oxacillin in order to determine which were multi-resistant. A total of 24 strains showed resistance to methicillin. 3. Thirty-one bacteriophages that were lytic against S. aureus strains were isolated and the host range of the bacteriophages was evaluated...
January 11, 2018: British Poultry Science
https://www.readbyqxmd.com/read/29320851/stringency-of-synthetic-promoter-sequences-in-clostridium-revealed-and-circumvented-by-tuning-promoter-library-mutation-rates
#20
Pawel Mordaka, John T Heap
Collections of characterized promoters of different strengths are key resources for synthetic biology, but are not well established for many important organisms, including industrially-relevant Clostridium spp. When generating promoters, reporter constructs are used to measure expression, but classical fluorescent reporter proteins are oxygen-dependent and hence inactive in anaerobic bacteria like Clostridium. We directly compared oxygen-independent reporters of different types in Clostridium acetobutylicum and found that glucuronidase (GusA) from E...
January 10, 2018: ACS Synthetic Biology
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