keyword
MENU ▼
Read by QxMD icon Read
search

Nucleotide performance

keyword
https://www.readbyqxmd.com/read/29786918/novel-genes-and-insights-in-complete-asthma-remission
#1
Judith M Vonk, Maartje A E Nieuwenhuis, F Nicole Dijk, Anne Boudier, Valerie Siroux, Emmanuelle Bouzigon, Nicole Probst-Hensch, Medea Imboden, Dirk Keidel, Don Sin, Yohan Bossé, Ke Hao, Maarten van den Berge, Alen Faiz, Gerard H Koppelman, Dirkje S Postma
BACKGROUND: Asthma is a chronic respiratory disease without a cure, though there exists spontaneous remission. Genome wide association(GWA) studies have pinpointed genes associated with asthma development, but did not investigate asthma remission. OBJECTIVES: We performed a GWA study to develop insights in asthma remission. METHODS: Clinical remission (ClinR) was defined by absence of asthma treatment and wheezing in the last year and asthma attacks in the last 3 years, and complete remission (ComR) similarly but additionally with normal lung function and absence of bronchial hyperresponsiveness (BHR)...
May 22, 2018: Clinical and Experimental Allergy: Journal of the British Society for Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29785925/comparison-of-two-genotyping-methods-for-distinguishing-recrudescence-from-reinfection-in-antimalarial-drug-efficacy-effectiveness-trials
#2
Joseph R M Fulakeza, Rachel L Banda, Trancizeo R Lipenga, Dianne J Terlouw, Standwell C Nkhoma, Eva Maria Hodel
Genotyping of allelic variants of Plasmodium falciparum merozoite surface proteins 1 and 2 ( msp-1 and msp-2 ), and the glutamate-rich protein is the gold standard for distinguishing reinfections from recrudescences in antimalarial drug trials. We compared performance of the recently developed 24-single-nucleotide polymorphism (SNP) Barcoding Assay against msp-1 and msp-2 genotyping in a cluster-randomized effectiveness trial of artemether-lumefantrine and dihydroartemisinin-piperaquine in Malawi. Rates of recrudescence and reinfection estimated by the two methods did not differ significantly (Fisher's exact test; P = 0...
May 21, 2018: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/29784899/pathway-based-analysis-of-genome-wide-association-study-of-circadian-phenotypes
#3
Di-di Zhu, Jia-Min Yuan, Rui Zhu, Yao Wang, Zhi-Yong Qian, Jian-Gang Zou
Sleepiness affects normal social life, which attracts more and more attention. Circadian phenotypes contribute to obvious individual differences in susceptibility to sleepiness. We aimed to identify candidate single nucleotide polymorphisms (SNPs) which may cause circadian phenotypes, elucidate the potential mechanisms, and generate corresponding SNP-gene-pathways. A genome-wide association studies (GWAS) dataset of circadian phenotypes was utilized in the study. Then, the Identify Candidate Causal SNPs and Pathways analysis was employed to the GWAS dataset after quality control filters...
November 1, 2017: Journal of Biomedical Research
https://www.readbyqxmd.com/read/29784853/carbapenem-non-susceptible-haemophilus-influenzae-with-penicillin-binding-protein-3-containing-amino-acid-insertion
#4
Kazuki Kitaoka, Kouji Kimura, Hiromitsu Kitanaka, Hirotsugu Banno, Wanchun Jin, Jun-Ichi Wachino, Yoshichika Arakawa
Prevalence of β-lactamase-negative ampicillin-resistant Haemophilus influenzae (BLNAR) has become a clinical concern. In BLNAR, amino acid substitutions in penicillin-binding protein 3 (PBP3) are relevant to the β-lactam resistance. Carbapenem-non-susceptible H. influenzae isolates have been rarely reported. Through antimicrobial susceptibility testing and nucleotide sequence analysis of ftsI , encoding PBP3, and utilizing a collection of H. influenzae clinical isolates in our laboratory, we obtained a carbapenem-non-susceptible clinical isolate (NUBL1772) that possessed an altered PBP3 containing V525_N526insM...
May 21, 2018: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29784544/classifying-alzheimer-s-disease-with-brain-imaging-and-genetic-data-using-a-neural-network-framework
#5
Kaida Ning, Bo Chen, Fengzhu Sun, Zachary Hobel, Lu Zhao, Will Matloff, Arthur W Toga
A long-standing question is how to best use brain morphometric and genetic data to distinguish Alzheimer's disease (AD) patients from cognitively normal (CN) subjects and to predict those who will progress from mild cognitive impairment (MCI) to AD. Here, we use a neural network (NN) framework on both magnetic resonance imaging-derived quantitative structural brain measures and genetic data to address this question. We tested the effectiveness of NN models in classifying and predicting AD. We further performed a novel analysis of the NN model to gain insight into the most predictive imaging and genetics features and to identify possible interactions between features that affect AD risk...
April 24, 2018: Neurobiology of Aging
https://www.readbyqxmd.com/read/29783948/expansion-of-the-sos-regulon-of-vibrio-cholerae-through-extensive-transcriptome-analysis-and-experimental-validation
#6
Evelyne Krin, Sebastian Aguilar Pierlé, Odile Sismeiro, Bernd Jagla, Marie-Agnès Dillies, Hugo Varet, Oihane Irazoki, Susana Campoy, Zoé Rouy, Stéphane Cruveiller, Claudine Médigue, Jean-Yves Coppée, Didier Mazel
BACKGROUND: The SOS response is an almost ubiquitous response of cells to genotoxic stresses. The full complement of genes in the SOS regulon for Vibrio species has only been addressed through bioinformatic analyses predicting LexA binding box consensus and in vitro validation. Here, we perform whole transcriptome sequencing from Vibrio cholerae treated with mitomycin C as an SOS inducer to characterize the SOS regulon and other pathways affected by this treatment. RESULTS: Comprehensive transcriptional profiling allowed us to define the full landscape of promoters and transcripts active in V...
May 21, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29783161/candidate-gene-analysis-in-the-s%C3%A3-o-paulo-epidemiologic-sleep-study-episono-shows-an-association-of-variant-in-pde4d-and-sleepiness
#7
Victoria M Pak, Diego R Mazzotti, Brendan T Keenan, Camila Hirotsu, Philip Gehrman, Lia Bittencourt, Allan I Pack, Sergio Tufik
INTRODUCTION: Sleepiness and cardiovascular disease share common molecular pathways; thus, genetic risk factors for sleepiness may also predict cardiovascular disease risk. This study explored the associations between subjective sleepiness and single-nucleotide polymorphisms (SNPs) in candidate genes within oxidative stress, inflammatory, and neuronal pathways, which may contribute to sleepiness and downstream cardiovascular disease risk: Cytochrome B-245, Alpha Polypeptide (CYBA), Cytochrome B-245, Beta Polypeptide (CYBB), Neutrophil Cytosolic Factor (NCF2), Tumor Necrosis Factor-Alpha (TNFA), and Phosphodiesterase 4D (PDE4D)...
January 12, 2018: Sleep Medicine
https://www.readbyqxmd.com/read/29782494/ubiquitin-dependent-proteolysis-of-cxcl7-leads-to-posterior-longitudinal-ligament-ossification
#8
Michiyo Tsuru, Atsushi Ono, Hideaki Umeyama, Masahiro Takeuchi, Kensei Nagata
Ossification of the posterior longitudinal ligament (OPLL), a spinal ligament, reduces the range of motion in limbs. No treatment is currently available for OPLL, which is why therapies are urgently needed. OPLL occurs in obesity, is more common in men, and has an onset after 40 years of age. The mechanisms underlying OPLL remain unclear. In this study, we performed a serum proteomic analysis in both OPLL patients and healthy subjects to identify factors potentially involved in the development of OPLL, and found reduced levels of a protein that might underlie the pathology of OPLL...
2018: PloS One
https://www.readbyqxmd.com/read/29781987/retrospective-microrna-sequencing-complementary-dna-library-preparation-protocol-using-formalin-fixed-paraffin-embedded-rna-specimens
#9
Olivier Loudig, Christina Liu, Thomas Rohan, Iddo Z Ben-Dov
-Archived, clinically classified formalin-fixed paraffin-embedded (FFPE) tissues can provide nucleic acids for retrospective molecular studies of cancer development. By using non-invasive or pre-malignant lesions from patients who later develop invasive disease, gene expression analyses may help identify early molecular alterations that predispose to cancer risk. It has been well described that nucleic acids recovered from FFPE tissues have undergone severe physical damage and chemical modifications, which make their analysis difficult and generally requires adapted assays...
May 5, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29781737/genetic-association-study-between-the-col11a1-and-col18a1-genes-and-high-myopia-in-a-han-chinese-population
#10
Haiyan Wu, Lingxi Jiang, Rui Zheng, Dongyan Luo, Xiaoqi Liu, Fang Hao, Zhilin Jiang, Bo Gong, Zhenglin Yang, Yi Shi
PURPOSE: To evaluate the association between high myopia (HM) and single nucleotide polymorphisms (SNPs) in collagen, type XI, alpha 1 (COL11A1) and collagen, type XVIII, alpha 1 (COL18A1) genes in a Han Chinese population. MATERIALS AND METHODS: A total of 869 patients with HM and 804 controls were recruited for this study. The genotyping of five SNPs in COL11A1 and COL18A1 was performed using the SNaPshot method. The genotyping data were analyzed using the χ2 test, and the linkage disequilibrium block structure was calculated and examined by Haploview software...
May 21, 2018: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/29781024/the-owl-sensor-a-fragile-dna-nanostructure-for-the-analysis-of-single-nucleotide-variations
#11
Rebekah J Karadeema, Maria Stancescu, Tyler P Steidl, Sophia C Bertot, Dmitry M Kolpashchikov
Analysis of single nucleotide variations (SNVs) in DNA and RNA sequences is instrumental in healthcare for the detection of genetic and infectious diseases and drug-resistant pathogens. Here we took advantage of the developments in DNA nanotechnology to design a hybridization sensor, named the 'owl sensor', which produces a fluorescence signal only when it complexes with fully complementary DNA or RNA analytes. The novelty of the owl sensor operation is that the selectivity of analyte recognition is, at least in part, determined by the structural rigidity and stability of the entire DNA nanostructure rather than exclusively by the stability of the analyte-probe duplex, as is the case for conventional hybridization probes...
May 21, 2018: Nanoscale
https://www.readbyqxmd.com/read/29780830/the-cd40-rs1883832-polymorphism-affects-sepsis-susceptibility-and-scd40l-levels
#12
Zuo-Liang Liu, Jing Hu, Xue-Fei Xiao, Yue Peng, Shang-Ping Zhao, Xian-Zhong Xiao, Ming-Shi Yang
Sepsis is a severe and progressive disease characterized by systemic inflammatory response syndrome (SIRS). CD40 serves as a vital link between immune response and inflammation. This study was designed to investigate the potential association between a functional single-nucleotide polymorphism (SNP) of CD40 (rs1883832) and susceptibility to sepsis. We first performed a case-control study to explore the relationship between the CD40 rs1883832 polymorphism and sepsis. CD40 mRNA expression and protein expression were determined by real-time PCR and western blotting, respectively, in peripheral blood mononuclear cells (PBMCs) from sepsis patients and healthy controls...
2018: BioMed Research International
https://www.readbyqxmd.com/read/29780373/regulation-mechanism-mediated-by-trans-encoded-srna-nc117-in-short-chain-alcohols-tolerance-in-synechocystis-sp-pcc-6803
#13
Yanqi Bi, Guangsheng Pei, Tao Sun, Zixi Chen, Lei Chen, Weiwen Zhang
Microbial small RNAs (sRNAs) play essential roles against many stress conditions in cyanobacteria. However, little is known on their regulatory mechanisms on biofuels tolerance. In our previous sRNA analysis, a trans -encoded sRNA Nc117 was found involved in the tolerance to ethanol and 1-butanol in Synechocystis sp. PCC 6803. However, its functional mechanism is yet to be determined. In this study, functional characterization of sRNA Nc117 was performed. Briefly, the exact length of the trans -encoded sRNA Nc117 was determined to be 102 nucleotides using 3' RACE, and the positive regulation of Nc117 on short chain alcohols tolerance was further confirmed...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29779773/reverse-line-probe-assay-for-cheap-detection-of-single-nucleotide-polymorphisms-in-mycobacterium-tuberculosis
#14
Memona Yasmin, Guislaine Refregier, Rubina Tabassum Siddiqui, Rizwan Iqbal, Shahid Ahmad Abbasi, Sabira Tahseen
More and more Single Nucleotide Polymosrphisms of interest among pathogenic organisms are described with the advent of Whole Genome Sequencing but WGS approach is still too expensive, time consuming, and relying on bioinformatical means that are not available in many developing countries. This study presents a low-cost reverse hybridization line probe technique for detecting SNPs in Mycobacterium tuberculosis. The proposed test is able to detect mutations in the RRDR of rpoB gene in M. tuberculosis with specificity and sensitivity of 98% and 100%, respectively and for an average cost of less than €3 per sample...
May 2018: Tuberculosis
https://www.readbyqxmd.com/read/29779728/association-between-aldehyde-dehydrogenase-2-glu504lys-polymorphism-and-alcoholic-liver-disease
#15
Binxia Chang, Shuli Hao, Longyu Zhang, Miaomiao Gao, Ying Sun, Ang Huang, Guangju Teng, Baosen Li, David W Crabb, Praveen Kusumanchi, Li Wang, Suthat Liangpunsakul, Zhengsheng Zou
BACKGROUND: Only a subset of patients with excessive alcohol use develop alcoholic liver disease (ALD), though the exact mechanism is not completely understood. Once ingested, alcohol is metabolized by 2 key oxidative enzymes, alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH). There are 2 major ALDH isoforms, cytosolic and mitochondrial, encoded by the aldehyde ALDH1 and ALDH2 genes, respectively. The ALDH2 gene was hypothesized to alter genetic susceptibility to alcohol dependence and alcohol-induced liver diseases...
March 20, 2018: American Journal of the Medical Sciences
https://www.readbyqxmd.com/read/29779017/-xpg-rs17655-g-c-polymorphism-associated-with-cancer-risk-evidence-from-60-studies
#16
Jie Zhao, Shanshan Chen, Haixia Zhou, Ting Zhang, Yang Liu, Jing He, Jinhong Zhu, Jichen Ruan
Xeroderma pigmentosum group G (XPG), a key component in nucleotide excision repair pathway, functions to cut DNA lesions during DNA repair. Genetic variations that alter DNA repair gene expression or function may decrease DNA repair ability and impair genome integrity, thereby predisposing to cancer. The association between XPG rs17655 G>C polymorphism and cancer risk has been investigated extensively, but the results remain contradictory. To get a more accurate conclusion, we performed a comprehensive meta-analysis of 60 case-control studies, involving 27,098 cancer cases and 30,535 healthy controls...
May 20, 2018: Aging
https://www.readbyqxmd.com/read/29778907/association-of-the-fto-fat-mass-and-obesity-associated-gene-rs9939609-polymorphism-with-rewarding-value-of-food-and-eating-behavior-in-chilean-children
#17
Ana Maria Obregón Rivas, Jose L Santos, Macarena A Valladares, Jameson Cameron, Gary Goldfield
OBJECTIVES: The aim of this study was to assess the association between the single-nucleotide polymorphism rs9939609 in the FTO gene and homeostatic/non-homeostatic eating behavior patterns in Chilean children. METHODS: A cross-sectional study was conducted in 258 children (44% female; 8-14 y of age). Anthropometric measurements (weight, height, Z-score of height, body mass index, and waist circumference) were performed. Eating behavior was assessed using the Eating in Absence of Hunger Questionnaire; the Child Eating Behavior Questionnaire; the Three Factor Eating Questionnaire, and the Food Reinforcement Value Questionnaire...
March 27, 2018: Nutrition
https://www.readbyqxmd.com/read/29778843/a-synbiotic-improves-the-immunity-of-white-shrimp-litopenaeus-vannamei-metabolomic-analyses-reveal-compelling-evidence
#18
Truong-Giang Huynh, Ann-Chang Cheng, Chia-Chun Chi, Kuo-Hsun Chiu, Chun-Hung Liu
In this study, we examined the synergistic effects of a diet-administered synbiotic comprising galactooligosaccharide (GOS) and the probiotic Lactobacillus plantarum 7-40 on immune responses, immune-related gene expressions, and disease resistance to Vibrio alginolyticus in white shrimp Litopenaeus vannamei. To unravel the regulatory role of the synbiotic in activating the immune system of shrimp, 1 H nuclear magnetic resonance (NMR)-based metabolomic analyses were used to investigate hepatopancreas metabolites, then significantly altered metabolites were confirmed in both the hepatopancreas and plasma by reverse-phase high-performance liquid chromatography (RP-HPLC) and spectrophotometric analyses...
May 17, 2018: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29778183/high-genetic-diversity-of-extended-spectrum-%C3%AE-lactamases-producing-escherichia-coli-in-feces-of-horses
#19
Syndia Sadikalay, Yann Reynaud, Stéphanie Guyomard-Rabenirina, Mélanie Falord, Célia Ducat, Laetitia Fabre, Simon Le Hello, Antoine Talarmin, Séverine Ferdinand
Extended-spectrum beta-lactamases (ESBLs), especially those of the CTX-M type, represent a major public health problem throughout the world. Although the carriage of ESBL-producing Enterobacteriaceae (EPE) in feces of horses is now well recognized, little is known about the diversity of EPE after treatment of horses with antibiotics. We undertook this study to assess and follow the diversity of EP Escherichia coli isolated from horses after antibiotic treatment for an infection. Fecal samples from two horses treated and two that were untreated were tested for the presence of EPE on different days...
June 2018: Veterinary Microbiology
https://www.readbyqxmd.com/read/29777939/variation-of-genes-encoding-kat1-aadat-and-ido1-as-a-potential-risk-of-depression-development
#20
Paulina Wigner, Piotr Czarny, Ewelina Synowiec, Michał Bijak, Monika Talarowska, Piotr Galecki, Janusz Szemraj, Tomasz Sliwinski
Numerous data suggests that the disorders of tryptophan catabolites (TRYCATs) pathway, including a decreased level of tryptophan or evaluated concentration of harmful TRYCATs -kynurenine, quinolinic acid, 3-hydroxyanthranilic acid, 3-hydroxytryptophan - may cause the occurrence of DD symptoms. In this work, we assessed the relationship between single-nucleotide polymorphisms (SNPs) of KAT1, KAT2 and IDO1 gene encoding, and the risk of depression development. Our study was performed on the DNA isolated from peripheral blood of 281 depressed patients and 236 controls...
May 16, 2018: European Psychiatry: the Journal of the Association of European Psychiatrists
keyword
keyword
77354
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"