keyword
MENU ▼
Read by QxMD icon Read
search

Nucleotides

keyword
https://www.readbyqxmd.com/read/28449554/a-study-of-single-nucleotide-polymorphisms-of-tumour-necrosis-factor-%C3%AE-1031-and-tumour-necrosis-factor-%C3%AE-252-in-chronic-rhinosinusitis
#1
Khairunnisak Misron, Suzina Sheikh Ab Hamid, Azlina Ahmad, Ramiza Ramza Ramli
Objectives: This case-controlled study aimed to identify the association of tumor necrosis factor (TNF)α-1031 and TNFβ+252 gene polymorphisms between chronic rhinosinusitis (CRS) and healthy controls. Another purpose of this study was to investigate the associations of these gene polymorphisms with factors related to CRS. Methods: All deoxyribonucleic acid (DNA) samples were genotyped for TNFα-1031 and TNFβ+252 genes by mean of polymerase chain reaction (PCR) and restriction fragment length polymorphisms (RFLP)...
April 28, 2017: Clinical and Experimental Otorhinolaryngology
https://www.readbyqxmd.com/read/28449344/endoscopic-features-and-genetic-background-of-inflammatory-bowel-disease-complicated-with-takayasu-arteritis
#2
Shintaro Akiyama, Toshimitsu Fujii, Katsuyoshi Matsuoka, Ebana Yusuke, Mariko Negi, Kento Takenaka, Masakazu Nagahori, Kazuo Ohtsuka, Mitsuaki Isobe, Mamoru Watanabe
BACKGROUND AND AIM: Takayasu arteritis (TA) is occasionally complicated with inflammatory bowel disease (IBD). This study assessed the endoscopic and genetic features of IBD complicated with TA (IBD-TA). METHODS: This study retrospectively reviewed the clinical charts of 142 TA patients (14 men and 128 women; median age 48.5 years [range, 18-97 years]). Human lymphocyte antigen (HLA) types and a single-nucleotide polymorphism rs6871626 in the IL12B gene were assessed in 101 and 81 patients with TA, respectively...
May 2017: Journal of Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/28449315/panelcn-mops-copy-number-detection-in-targeted-ngs-panel-data-for-clinical-diagnostics
#3
Gundula Povysil, Antigoni Tzika, Julia Vogt, Verena Haunschmid, Ludwine Messiaen, Johannes Zschocke, Günter Klambauer, Sepp Hochreiter, Katharina Wimmer
Targeted next-generation-sequencing (NGS) panels have largely replaced Sanger sequencing in clinical diagnostics. They allow for the detection of copy number variations (CNVs) in addition to single-nucleotide-variants and small insertions/deletions. However, existing computational CNV detection methods have shortcomings regarding accuracy, quality control, incidental findings, and user-friendliness. We developed panelcn.MOPS, a novel pipeline for detecting CNVs in targeted NGS panel data. Using data from 180 samples, we compared panelcn...
April 27, 2017: Human Mutation
https://www.readbyqxmd.com/read/28449278/seroepidemiology-and-molecular-characterization-of-hepatitis-e-virus-infection-in-swine-and-occupationally-exposed-workers-in-punjab-india
#4
M Bansal, S Kaur, D Deka, R Singh, J P S Gill
Hepatitis E virus (HEV) has two discrete epidemiological patterns: waterborne epidemics in developing countries only, caused by HEV genotype I, and sporadic zoonotic outbreaks in developing and developed countries caused by genotypes III and IV. This study was designed to investigate seroprevalence, molecular detection and the characterization of HEV by nested RT-PCR in swine as well as the occupational risk to exposed human population in Punjab state of north-western India. The occupational risk-exposed group comprised of swine farmers (organized - mixed feed feeders and unorganized - swill feeders), slaughterhouse workers, sewage workers and veterinary internes...
April 27, 2017: Zoonoses and Public Health
https://www.readbyqxmd.com/read/28449123/capturing-a-mammalian-dna-polymerase-extending-from-an-oxidized-nucleotide
#5
Amy M Whitaker, Mallory R Smith, Matthew A Schaich, Bret D Freudenthal
The oxidized nucleotide, 8-oxo-7,8-dihydro-2΄-deoxyguanosine (8-oxoG), is one of the most abundant DNA lesions. 8-oxoG plays a major role in tumorigenesis and human disease. Biological consequences of 8-oxoG are mediated in part by its insertion into the genome, making it essential to understand how DNA polymerases handle 8-oxoG. Insertion of 8-oxoG is mutagenic when opposite adenine but not when opposite cytosine. However, either result leads to DNA damage at the primer terminus (3΄-end) during the succeeding insertion event...
April 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28449067/using-high-throughput-barcode-sequencing-to-efficiently-map-connectomes
#6
Ian D Peikon, Justus M Kebschull, Vasily V Vagin, Diana I Ravens, Yu-Chi Sun, Eric Brouzes, Ivan R Corrêa, Dario Bressan, Anthony M Zador
The function of a neural circuit is determined by the details of its synaptic connections. At present, the only available method for determining a neural wiring diagram with single synapse precision-a 'connectome'-is based on imaging methods that are slow, labor-intensive and expensive. Here, we present SYNseq, a method for converting the connectome into a form that can exploit the speed and low cost of modern high-throughput DNA sequencing. In SYNseq, each neuron is labeled with a unique random nucleotide sequence-an RNA 'barcode'-which is targeted to the synapse using engineered proteins...
April 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28449057/the-streptomyces-master-regulator-bldd-binds-c-di-gmp-sequentially-to-create-a-functional-bldd2-c-di-gmp-4-complex
#7
Maria A Schumacher, Wenjie Zeng, Kim C Findlay, Mark J Buttner, Richard G Brennan, Natalia Tschowri
Streptomyces are ubiquitous soil bacteria that undergo a complex developmental transition coinciding with their production of antibiotics. This transition is controlled by binding of a novel tetrameric form of the second messenger, 3΄-5΄ cyclic diguanylic acid (c-di-GMP) to the master repressor, BldD. In all domains of life, nucleotide-based second messengers allow a rapid integration of external and internal signals into regulatory pathways that control cellular responses to changing conditions. c-di-GMP can assume alternative oligomeric states to effect different functions, binding to effector proteins as monomers, intercalated dimers or, uniquely in the case of BldD, as a tetramer...
April 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28449042/long-noncoding-rna-a-crosslink-in-biological-regulatory-network
#8
Yuwei Zhang, Yang Tao, Qi Liao
Long noncoding RNAs (lncRNAs) had been defined as a novel class of functional RNAs longer than 200 nucleotides around a decade ago. It is widely acknowledged that lncRNAs play a significant role in regulation of gene expression, but the biological and molecular mechanisms are diverse and complex, and remain to be determined. Especially, the regulatory network of lncRNAs associated with other biological molecules is still a controversial matter, thus becoming a new frontier of the studies on transcriptome. Recent advance in high-throughput sequencing technologies and bioinformatics approaches may be an accelerator to lift the mysterious veil...
April 24, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28449029/a-genome-wide-association-study-identifies-nucleotide-variants-at-siglec5-and-defa1a3-as-risk-loci-for-periodontitis
#9
Matthias Munz, Christina Willenborg, Gesa M Richter, Yvonne Jockel-Schneider, Christian Graetz, Ingmar Staufenbiel, Jürgen Wellmann, Klaus Berger, Bastian Krone, Per Hoffmann, Nathalie van der Velde, André G Uitterlinden, Lisette C P G M de Groot, Amr Sawalha, Haner Direskeneli, Güher Saruhan-Direskeneli, Esra Guzeldemir-Akcakanat, Gencay Keceli, Matthias Laudes, Barbara Noack, Alexander Teumer, Birte Holtfreter, Thomas Kocher, Peter Eickholz, Jörg Meyle, Christof Doerfer, Corinna Bruckmann, Wolfgang Lieb, Andre Franke, Stefan Schreiber, Rahime M Nohutcu, Jeanette Erdmann, Bruno G Loos, Soeren Jepsen, Henrik Dommisch, Arne S Schaefer
Periodontitis is one of the most common inflammatory diseases, with a prevalence of 11% worldwide for the severe forms and an estimated heritability of 50%. The disease is characterized by destruction of the alveolar bone due to an aberrant host inflammatory response to a dysbiotic oral microbiome. Previous genome-wide association studies (GWAS) have reported several suggestive susceptibility loci. Here, we conducted a GWAS using a German and Dutch case-control sample of aggressive periodontitis (AgP, 896 cases, 7,104 controls), a rare but highly severe and early-onset form of periodontitis, validated the associations in a German sample of severe forms of the more moderate phenotype chronic periodontitis (CP) (993 cases, 1,419 controls)...
April 25, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28448737/involvement-of-arhgef10-gef-for-rhoa-in-rab6-rab8-mediating-membrane-traffic
#10
Satoshi Shibata, Yui Teshima, Kenta Niimi, Shinobu Inagaki
Small GTPases play crucial roles in the maintenance of a homeostatic environment and appropriate movements of the cell. In these processes, the direct or indirect interaction between distinct small GTPases could be required for regulating mutual signaling pathways. In our recent study, ARHGEF10, known as a guanine nucleotide exchange factor (GEF) for RhoA, was indicated to interact with Rab6A and Rab8A, which are known to function in the exocytotic pathway, and colocalized with these Rabs at exocytotic vesicles...
April 27, 2017: Small GTPases
https://www.readbyqxmd.com/read/28448145/coarse-grained-molecular-dynamics-model-of-double-stranded-dna-for-dna-nanostructure-design
#11
Hiromasa Yagyu, Jae-Young Lee, Do-Nyun Kim, Osamu Tabata
A new coarse-grained molecular dynamics double-stranded DNA model (nCG-dsDNA model) using an improved beads-spring model was proposed. In this model, nucleotide comprising phosphate, sugar, and base group were replaced by a single bead. The double stranded model with 202 base pairs was created to tune the parameters of the bond, the non-bond, stack, angle bending, and electrostatic interaction. The average twisted angle and the persistence length of the model without electrostatic interaction were calculated at 35...
April 27, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28448128/total-chemical-synthesis-and-folding-of-all-l-and-all-d-variants-of-oncogenic-kras-g12v
#12
Adam Marc Levinson, John H McGee, Andrew G Roberts, Gardner Creech, Ting Wang, Michael T Peterson, Ronald C Hendrickson, Gregory L Verdine, Samuel J Danishefsky
The Ras proteins are essential GTPases involved in the regulation of cell proliferation and survival. Mutated oncogenic forms of Ras alter effector binding and innate GTPase activity, leading to deregulation of downstream signal transduction. Mutated forms of Ras are involved in approximately 30% of human cancers. Despite decades of effort to develop direct Ras inhibitors, Ras has long been considered 'undruggable' due to its high affinity for GTP and its lack of hydrophobic binding pockets. Herein, we report a total chemical synthesis of all-L- and all-D-amino acid biotinylated variants of oncogenic mutant KRas(G12V)...
April 27, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28448034/using-a-fluorescent-pcr-capillary-gel-electrophoresis-technique-to-genotype-crispr-cas9-mediated-knockout-mutants-in-a-high-throughput-format
#13
Muhammad Khairul Ramlee, Jing Wang, Alice M S Cheung, Shang Li
The development of programmable genome-editing tools has facilitated the use of reverse genetics to understand the roles specific genomic sequences play in the functioning of cells and whole organisms. This cause has been tremendously aided by the recent introduction of the CRISPR/Cas9 system-a versatile tool that allows researchers to manipulate the genome and transcriptome in order to, among other things, knock out, knock down, or knock in genes in a targeted manner. For the purpose of knocking out a gene, CRISPR/Cas9-mediated double-strand breaks recruit the non-homologous end-joining DNA repair pathway to introduce the frameshift-causing insertion or deletion of nucleotides at the break site...
April 8, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28447726/a-three-caller-pipeline-for-variant-analysis-of-cancer-whole-exome-sequencing-data
#14
Ze-Kun Liu, Yu-Kui Shang, Zhi-Nan Chen, Huijie Bian
Rapid advancements in next generation sequencing (NGS) technologies, coupled with the dramatic decrease in cost, have made NGS one of the leading approaches applied in cancer research. In addition, it is increasingly used in clinical practice for cancer diagnosis and treatment. Somatic (cancer‑only) single nucleotide variants and small insertions and deletions (indels) are the simplest classes of mutation, however, their identification in whole exome sequencing data is complicated by germline polymorphisms, tumor heterogeneity and errors in sequencing and analysis...
March 16, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28447585/metabolic-profiles-of-individuals-switched-to-second-line-antiretroviral-therapy-after-failing-standard-first-line-therapy-for-treatment-of-hiv-1-infection-in-a-randomized-controlled-trial
#15
Amanda H Yao, Cecilia L Moore, Poh Lian Lim, Jean-Michel Molina, Juan Sierra Madero, Stephen Kerr, Paddy Wg Mallon, Sean Emery, David A Cooper, Mark A Boyd
BACKGROUND: To investigate metabolic changes associated with second-line antiretroviral therapy (ART) following virological failure of first-line ART. METHODS: SECOND-LINE was an open-label randomized controlled trial. Participants were randomized 1:1 to receive ritonavir-boosted lopinavir (LPV/r) with 2-3 nucleoside/nucleotide reverse transcriptase inhibitors (N(t)RTI-group) or raltegravir (RAL-group) Two hundred and ten participants had a dual energy X-ray absorptiometry (DXA)-scan at baseline, week 48 and 96...
April 27, 2017: Antiviral Therapy
https://www.readbyqxmd.com/read/28447211/paclitaxel-induced-sensory-peripheral-neuropathy-is-associated-with-an-abcb1-single-nucleotide-polymorphism-and-older-age-in-japanese
#16
Yuko Tanabe, Chikako Shimizu, Akinobu Hamada, Kenji Hashimoto, Kazutaka Ikeda, Daisuke Nishizawa, Junko Hasegawa, Akihiko Shimomura, Yukinori Ozaki, Nobuko Tamura, Harukaze Yamamoto, Mayu Yunokawa, Kan Yonemori, Toshimi Takano, Hidetaka Kawabata, Kenji Tamura, Yasuhiro Fujiwara
PURPOSE: Whether age and inter-individual variability of pharmacogenetics are risk factors for paclitaxel-induced peripheral neuropathy (PIPN) is inconclusive. This study was conducted to evaluate the influence of previously investigated single nucleotide polymorphisms (SNPs) and age, using genotype data from a prospective study of paclitaxel-related toxicity in Japanese patients with breast cancer. METHODS: Peripheral blood mononuclear cells from 127 Japanese women with breast cancer who received weekly adjuvant paclitaxel were used to genotypes SLCO1B3 T334G (rs4149117), CYP2C8 A1196G (rs10509681), ABCB1 C1236T (rs1128503), ABCB1 G2677T/A (rs2032582), and ABCB1 C3435T (rs1045642)...
April 26, 2017: Cancer Chemotherapy and Pharmacology
https://www.readbyqxmd.com/read/28447075/sofosbuvir-velpatasvir-fixed-dose-combination-for-the-treatment-of-chronic-hepatitis-c-virus-infection
#17
V Nehra, S A Rizza, Z Temesgen
The fixed-dose combination of sofosbuvir, a nucleotide analogue NS5B polymerase inhibitor, and velpatasvir, a second-generation NS5A inhibitor, has been approved by the United States Food and Drug Administration and the European Medicines Agency for the treatment of adult patients with chronic hepatitis C virus (HCV) genotype 1, 2, 3, 4, 5 or 6 infection. This combination, administered over 12 weeks as a single-tablet regimen, has resulted in high cure rates in all 6 HCV genotypes and in a variety of patient populations, including patients without cirrhosis, patients with compensated cirrhosis and patients with HIV coinfection...
March 2017: Drugs of Today
https://www.readbyqxmd.com/read/28447043/comparative-genomics-of-human-stem-cell-factor-scf
#18
Moein Dehbashi, Elahe Kamali, Sadeq Vallian
Stem cell factor (SCF) is a critical protein with key roles in the cell such as hematopoiesis, gametogenesis and melanogenesis. In the present study a comparative analysis on nucleotide sequences of SCF was performed in Humanoids using bioinformatics tools including NCBI-BLAST, MEGA6, and JBrowse. Our analysis of nucleotide sequences to find closely evolved organisms with high similarity by NCBI-BLAST tools and MEGA6 showed that human and Chimpanzee (Pan troglodytes) were placed into the same cluster. By using JBrowse, we found that SCF in Neanderthal had a single copy number similar to modern human and partly conserved nucleotide sequences...
March 2017: Molecular Biology Research Communications
https://www.readbyqxmd.com/read/28446908/association-of-ctla-4-gene-variants-with-response-to-therapy-and-long-term-survival-in-metastatic-melanoma-patients-treated-with-ipilimumab-an-italian-melanoma-intergroup-study
#19
Paola Queirolo, Beatrice Dozin, Anna Morabito, Barbara Banelli, Patrizia Piccioli, Cristiana Fava, Claudio Leo, Roberta Carosio, Stefania Laurent, Vincenzo Fontana, Pier Francesco Ferrucci, Chiara Martinoli, Emilia Cocorocchio, Angelo Battaglia, Paolo A Ascierto, Mariaelena Capone, Ester Simeone, Federica De Galitiis, Elena Pagani, Gian Carlo Antonini Cappellini, Paolo Marchetti, Michele Guida, Stefania Tommasi, Mario Mandalà, Barbara Merelli, Pietro Quaglino, Paolo Fava, Massimo Guidoboni, Massimo Romani, Francesco Spagnolo, Maria Pia Pistillo
Ipilimumab (IPI) blocks CTLA-4 immune checkpoint resulting in T cell activation and enhanced antitumor immunity. IPI improves overall survival (OS) in 22% of patients with metastatic melanoma (MM). We investigated the association of CTLA-4 single nucleotide variants (SNVs) with best overall response (BOR) to IPI and OS in a cohort of 173 MM patients. Patients were genotyped for six CTLA-4 SNVs (-1661A>G, -1577G>A, -658C>T, -319C>T, +49A>G, and CT60G>A). We assessed the association between SNVs and BOR through multinomial logistic regression (MLR) and the prognostic effect of SNVs on OS through Kaplan-Meier method...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28446855/eosinophilic-granuloma-in-jaw-bone-a-pare-pediatric-case-report
#20
Karthiga Kannan, Naif Alwithanani, Mohamed Salama, Manoj Kumar, Roshan Uthappa, Mazood Ahamed
BACKGROUND: Eosinophilic granuloma (EG), one of the three clinical forms of Langerhans cell histiocytosis (LCH), is a benign inflammatory reaction to an unknown etiologic agent. It most commonly occurs in children and young adults. The most frequently involved bones are the skull, the ribs and the femurs. Alongside the cranium, the maxilla and mandible can also be affected. CASE DETAILS: Herein, we report a case of eosinophilic granuloma in a ten years old boy involving posterior quadrants upper and lower jaws as a destructive lesion involving gingiva, periodontium and alveolar bone...
September 2016: Ethiopian Journal of Health Sciences
keyword
keyword
77251
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"