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https://www.readbyqxmd.com/read/28346566/gene-gene-interaction-between-pparg-and-apoe-gene-on-late-onset-alzheimer-s-disease-a-case-control-study-in-chinese-han-population
#1
S Wang, L Guan, D Luo, J Liu, H Lin, X Li, X Liu
AIMS: The aim was to investigate the impact of PPARG and APOE gene single nucleotide polymorphisms (SNPs) and additional gene- gene interaction on late-onset Alzheimer's disease (LOAD) risk based on Chinese Han population. METHODS: A total of 928 participants (466 males, 462 females), with a mean age of 81.3 ± 16.4 years old, were included in the study, including 460 LOAD patients and 468 normal controls participants. Logistic regression was performed to investigate association between SNP and LOAD risk and generalized multifactor dimensionality reduction (GMDR) was used to analysis the gene-gene interaction...
2017: Journal of Nutrition, Health & Aging
https://www.readbyqxmd.com/read/28346242/genetic-variation-in-gabr%C3%AE-1-and-the-risk-for-developing-alcohol-dependence
#2
William A McCabe, Michael J Way, Kush Ruparelia, Susanne Knapp, M Adam Ali, Quentin M Anstee, Howard C Thomas, Andrew McQuillin, Marsha Y Morgan
Associations between the γ-aminobutyric acid type-A receptors (GABAA) and alcohol dependence risk have been reported, although the receptor subunit driving the association is unclear. Recent work in mice has highlighted a possible role for variants in the Gabr β1 subunit (Gabrβ1) in alcohol dependence risk, although this gene does not contain any common nonsynonymous variants in humans. However, the GABAA receptor is a heteropentamer so multiple potential variants within the gene complex could generate the alcohol dependence phenotype...
March 24, 2017: Psychiatric Genetics
https://www.readbyqxmd.com/read/28345992/evaluation-of-a-hypervariable-octameric-oligonucleotide-fingerprints-assay-for-identification-of-and-discrimination-between-wild-type-and-vaccine-strains-of-brucella-melitensis
#3
Lijuan Tang, Jun Liu, Yuanzhi Wang, Hui Zhang, Chuangfu Chen
OBJECTIVE To evaluate a hypervariable octameric oligonucleotide fingerprints (HOOF-Prints) assay for identification of and discrimination between wild-type and vaccine strains of Brucella melitensis. SAMPLE Brucella melitensis vaccine strain M5 and wild-type strain M43. PROCEDURES 8 pairs of primers (alterable, octameric nucleotides) were designed on the basis of a biological analysis of 8 flanking sequences in the DNA of B melitensis. The HOOF-Prints technique was used to identify wild-type and vaccine strains of B melitensis...
April 2017: American Journal of Veterinary Research
https://www.readbyqxmd.com/read/28345916/molecular-mechanism-of-nucleotide-dependent-allosteric-regulation-in-amp-activated-protein-kinase
#4
Navjeet Ahalawat, Rajesh Kumar Murarka
The AMP-activated protein kinase (AMPK), a central enzyme in the regulation of energy homeostasis, is an important drug target for type 2 diabetes, obesity and cancer. Binding of adenosine nucleotides to the regulatory γ-subunit tightly regulates the activity of this enzyme. Though recent crystal structures of AMPK have provided important insights into the allosteric activation of AMPK, molecular details of the regulatory mechanism of AMPK activation is still elusive. Here, we have performed extensive all-atom molecular dynamics (MD) simulations and shown that the kinase domain (KD) and γ-subunit comes closer resulting in a more compact heterotrimeric AMPK complex in AMP-bound state compared to the ATP-bound state...
March 27, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28345264/blood-transcriptomes-and-de-novo-identification-of-candidate-loci-for-mating-success-in-lekking-great-snipe-gallinago-media
#5
Jacob Höglund, Biao Wang, Stein Are Saether, Mozes Pil Kyu Blom, Peder Fiske, Peter Halvarsson, Gavin J Horsburgh, Terry Burke, John Atle Kålås, Robert Ekblom
We assembled the great snipe blood transcriptome using data from fourteen lekking males, in order to de novo identify candidate genes related to sexual selection, and determined the expression profiles in relation to mating success. The three most highly transcribed genes were encoding different haemoglobin subunits. All tended to be overexpressed in males with high mating success. We also called Single Nucleotide Polymorphisms (SNPs) from the transcriptome data and found considerable genetic variation for many genes expressed during lekking...
March 27, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28344780/abnormal-glycosylation-in-joubert-syndrome-type-10
#6
Megan S Kane, Mariska Davids, Michelle R Bond, Christopher J Adams, Megan E Grout, Ian G Phelps, Diana R O'Day, Jennifer C Dempsey, Xeuli Li, Gretchen Golas, Gilbert Vezina, Meral Gunay-Aygun, John A Hanover, Dan Doherty, Miao He, May Christine V Malicdan, William A Gahl, Cornelius F Boerkoel
BACKGROUND: The discovery of disease pathogenesis requires systematic agnostic screening of multiple homeostatic processes that may become deregulated. We illustrate this principle in the evaluation and diagnosis of a 5-year-old boy with Joubert syndrome type 10 (JBTS10). He carried the OFD1 mutation p.Gln886Lysfs*2 (NM_003611.2: c.2656del) and manifested features of Joubert syndrome. METHODS: We integrated exome sequencing, MALDI-TOF mass spectrometry analyses of plasma and cultured dermal fibroblasts glycomes, and full clinical evaluation of the proband...
2017: Cilia
https://www.readbyqxmd.com/read/28344587/the-chloroplast-genome-of-passiflora-edulis-passifloraceae-assembled-from-long-sequence-reads-structural-organization-and-phylogenomic-studies-in-malpighiales
#7
Luiz A Cauz-Santos, Carla F Munhoz, Nathalie Rodde, Stephane Cauet, Anselmo A Santos, Helen A Penha, Marcelo C Dornelas, Alessandro M Varani, Giancarlo C X Oliveira, Hélène Bergès, Maria Lucia C Vieira
The family Passifloraceae consists of some 700 species classified in around 16 genera. Almost all its members belong to the genus Passiflora. In Brazil, the yellow passion fruit (Passiflora edulis) is of considerable economic importance, both for juice production and consumption as fresh fruit. The availability of chloroplast genomes (cp genomes) and their sequence comparisons has led to a better understanding of the evolutionary relationships within plant taxa. In this study, we obtained the complete nucleotide sequence of the P...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28343299/the-role-of-line-1-methylation-in-predicting-survival-among-colorectal-cancer-patients-a-meta-analysis
#8
Ding Ye, Danjie Jiang, Yingjun Li, Mingjuan Jin, Kun Chen
BACKGROUND: The prognostic value of long interspersed nucleotide element-1 (LINE-1) methylation in patients with colorectal cancer (CRC) remains uncertain. We have therefore performed a meta-analysis to elucidate this issue. METHODS: The PubMed and Web of Science databases were searched for studies published up to 30 June 2016 which reported on an association between LINE-1 methylation and overall survival (OS), disease-free survival (DFS), or cancer-specific survival (CSS) among CRC patients...
March 25, 2017: International Journal of Clinical Oncology
https://www.readbyqxmd.com/read/28343162/mesothelin-promoter-variants-are-associated-with-increased-soluble-mesothelin-related-peptide-levels-in-asbestos-exposed-individuals
#9
Chiara De Santi, Perla Pucci, Alessandra Bonotti, Ombretta Melaiu, Monica Cipollini, Roberto Silvestri, Veronika Vymetalkova, Elisa Barone, Elisa Paolicchi, Alda Corrado, Irene Lepori, Irene Dell'Anno, Lucia Pellè, Pavel Vodicka, Luciano Mutti, Rudy Foddis, Alfonso Cristaudo, Federica Gemignani, Stefano Landi
BACKGROUND: Soluble mesothelin-related peptide (SMRP) is a promising diagnostic biomarker for malignant pleural mesothelioma (MPM), but various confounders hinder its usefulness in surveillance programmes. We previously showed that a single nucleotide polymorphism (SNP) within the 3'untranslated region (3'UTR) of the mesothelin (MSLN) gene could affect the levels of SMRP. OBJECTIVES: To focus on SNPs located within MSLN promoter as possible critical genetic variables in determining SMRP levels...
March 25, 2017: Occupational and Environmental Medicine
https://www.readbyqxmd.com/read/28342889/heteromeric-complexes-of-aldo-keto-reductase-auxiliary-kv%C3%AE-subunits-akr6a-regulate-sarcolemmal-localization-of-kv1-5-in-coronary-arterial-myocytes
#10
Matthew A Nystoriak, Deqing Zhang, Ganapathy Jagatheesan, Aruni Bhatnagar
Redox-sensitive potassium channels consisting of the voltage-gated K(+) (KV) channel pore subunit KV1.5 regulate resting membrane potential and thereby contractility of vascular smooth muscle cells. Members of the KV1 family associate with cytosolic auxiliary β subunits, which are members of the aldo-keto reductase (AKR) superfamily (AKR6A subfamily). The Kvβ subunits have been proposed to regulate Kv1 gating via pyridine nucleotide cofactor binding. However, the molecular identity of KVβ subunits that associate with native KV1...
March 22, 2017: Chemico-biological Interactions
https://www.readbyqxmd.com/read/28342698/targeted-exome-sequencing-and-chromosomal-microarray-for-the-molecular-diagnosis-of-nevoid-basal-cell-carcinoma-syndrome
#11
Yoshihiro Matsudate, Takuya Naruto, Yumiko Hayashi, Mitsuyoshi Minami, Mikiko Tohyama, Kenji Yokota, Daisuke Yamada, Issei Imoto, Yoshiaki Kubo
BACKGROUND: Nevoid basal cell carcinoma syndrome (NBCCS) is an autosomal dominant disorder mainly caused by heterozygous mutations of PTCH1. In addition to characteristic clinical features, detection of a mutation in causative genes is reliable for the diagnosis of NBCCS; however, no mutations have been identified in some patients using conventional methods. OBJECTIVE: To improve the method for the molecular diagnosis of NBCCS. METHODS: We performed targeted exome sequencing (TES) analysis using a multi-gene panel, including PTCH1, PTCH2, SUFU, and other sonic hedgehog signaling pathway-related genes, based on next-generation sequencing (NGS) technology in 8 cases in whom possible causative mutations were not detected by previously performed conventional analysis and 2 recent cases of NBCCS...
March 11, 2017: Journal of Dermatological Science
https://www.readbyqxmd.com/read/28341840/comparison-of-two-massively-parallel-sequencing-platforms-using-83-single-nucleotide-polymorphisms-for-human-identification
#12
Dame Loveliness T Apaga, Sheila E Dennis, Jazelyn M Salvador, Gayvelline C Calacal, Maria Corazon A De Ungria
The potential of Massively Parallel Sequencing (MPS) technology to vastly expand the capabilities of human identification led to the emergence of different MPS platforms that use forensically relevant genetic markers. Two of the MPS platforms that are currently available are the MiSeq(®) FGx™ Forensic Genomics System (Illumina) and the HID-Ion Personal Genome Machine (PGM)™ (Thermo Fisher Scientific). These are coupled with the ForenSeq™ DNA Signature Prep kit (Illumina) and the HID-Ion AmpliSeq™ Identity Panel (Thermo Fisher Scientific), respectively...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28340580/toll-like-receptors-genes-polymorphisms-and-the-occurrence-of-hcmv-infection-among-pregnant-women
#13
Wioletta Wujcicka, Edyta Paradowska, Mirosława Studzińska, Jan Wilczyński, Dorota Nowakowska
BACKGROUND: Human cytomegalovirus (HCMV) is the most common cause of intrauterine infections worldwide. The toll-like receptors (TLRs) have been reported as important factors in immune response against HCMV. Particularly, TLR2, TLR4 and TLR9 have been shown to be involved in antiviral immunity. Evaluation of the role of single nucleotide polymorphisms (SNPs), located within TLR2, TLR4 and TLR9 genes, in the development of human cytomegalovirus (HCMV) infection in pregnant women and their fetuses and neonates, was performed...
March 24, 2017: Virology Journal
https://www.readbyqxmd.com/read/28340265/association-of-runx2-and-tnfsf11-genes-with-production-traits-in-a-paternal-broiler-line
#14
N V Grupioni, N B Stafuzza, A B Carvajal, A M G Ibelli, J O Peixoto, M C Ledur, D P Munari
Intense selection for production traits has improved the genetic gain of important economic traits. However, selection for performance and carcass traits has led to the onset of locomotors problems and decreasing bone strength in broilers. Thus, genes associated with bone integrity traits have become candidates for genetic studies in order to reduce the impact of bone disorders in broilers. This study investigated the association of the RUNX2 and TNFSF11 genes with 79 traits related to performance, carcass composition, organs, and bone integrity in a paternal broiler line...
March 22, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28339749/multi-generational-genome-wide-association-studies-identify-chromosomal-regions-associated-with-ascites-phenotype
#15
K J Tarrant, S Dey, R Kinney, N B Anthony, D D Rhoads
Ascites is a multi-faceted disease commonly observed in fast growing broilers, which is initiated when the body is insufficiently oxygenated. A series of events follow, including an increase in pulmonary artery pressure, right ventricle hypertrophy, and accumulation of fluid in the abdominal cavity and pericardium. Advances in management practices along with improved selection programs have decreased ascites incidence in modern broilers. However, ascites syndrome remains an economically important disease throughout the world, causing estimated losses of $100 million per year...
February 21, 2017: Poultry Science
https://www.readbyqxmd.com/read/28339471/expression-quantitative-trait-loci-for-pax8-contributes-to-the-prognosis-of-hepatocellular-carcinoma
#16
Shijie Ma, Jianshui Yang, Ci Song, Zijun Ge, Jing Zhou, Guoxin Zhang, Zhibin Hu
Paired-box family member PAX8 encodes a transcription factor that has a role in cell differentiation and cell growth and may participate in the prognosis of hepatocellular carcinoma (HCC). By bioinformatics analysis, we identified several single nucleotide polymorphisms (SNPs) within a newly identified long non-coding RNA (lncRNA) AC016683.6 as expression quantitative trait loci (eQTLs) for PAX8. Hence, we hypothesized that PAX8eQTLs in lncRNA AC016683.6 may influence the HCC prognosis. We then performed a case-only study to assess the association between the two SNPs as well as the prognosis of HCC in 331 HBV-positive HCC patients without surgical treatment...
2017: PloS One
https://www.readbyqxmd.com/read/28339009/identification-of-egflam-spatc1l-and-rnase13-as-novel-susceptibility-loci-for-aortic-aneurysm-in-japanese-individuals-by-exome-wide-association-studies
#17
Yoshiji Yamada, Jun Sakuma, Ichiro Takeuchi, Yoshiki Yasukochi, Kimihiko Kato, Mitsutoshi Oguri, Tetsuo Fujimaki, Hideki Horibe, Masaaki Muramatsu, Motoji Sawabe, Yoshinori Fujiwara, Yu Taniguchi, Shuichi Obuchi, Hisashi Kawai, Shoji Shinkai, Seijiro Mori, Tomio Arai, Masashi Tanaka
We performed an exome-wide association study (EWAS) to identify genetic variants - in particular, low‑frequency or rare variants with a moderate to large effect size - that confer susceptibility to aortic aneurysm with 8,782 Japanese subjects (456 patients with aortic aneurysm, 8,326 control individuals) and with the use of Illumina HumanExome-12 DNA Analysis BeadChip or Infinium Exome-24 BeadChip arrays. The correlation of allele frequencies for 41,432 single nucleotide polymorphisms (SNPs) that passed quality control to aortic aneurysm was examined with Fisher's exact test...
March 21, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28338805/deciphering-the-genetic-control-of-fruit-texture-in-apple-by-multiple-family-based-analysis-and-genome-wide-association
#18
Mario Di Guardo, Marco C A M Bink, Walter Guerra, Thomas Letschka, Lidia Lozano, Nicola Busatto, Lara Poles, Alice Tadiello, Luca Bianco, Richard G F Visser, Eric van de Weg, Fabrizio Costa
Fruit texture is a complex feature composed of mechanical and acoustic properties relying on the modifications occurring in the cell wall throughout fruit development and ripening. Apple is characterized by a large variation in fruit texture behavior that directly impacts both the consumer's appreciation and post-harvest performance. To decipher the genetic control of fruit texture comprehensively, two complementing quantitative trait locus (QTL) mapping approaches were employed. The first was represented by a pedigree-based analysis (PBA) carried out on six full-sib pedigreed families, while the second was a genome-wide association study (GWAS) performed on a collection of 233 apple accessions...
February 24, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28337273/t-box-family-of-transcription-factor-tbx5-insights-in-development-and-disease
#19
Ting Zhu, Longwei Qiao, Qian Wang, Rui Mi, Jinnan Chen, Yaojuan Lu, Junxia Gu, Qiping Zheng
The T-box gene family refers to a group of transcription factors that share a highly conserved, sequence-specific DNA-binding domain (T-box) containing around 180-amino acids. According to HUGO gene nomenclature committee (HGNC), there are 18 T-box family members. These T-box genes have been implicated essential roles during embryogenesis and cardiac development, given their specific expression pattern in developing mammalian heart for several T-box genes, including TBX5. TBX5 is consisted of three transcriptional variants which cover 9 exons and encode two distinct isoforms that differ in N-terminus...
2017: American Journal of Translational Research
https://www.readbyqxmd.com/read/28337209/transcriptional-responses-of-chilean-quinoa-chenopodium-quinoa-willd-under-water-deficit-conditions-uncovers-aba-independent-expression-patterns
#20
Andrea Morales, Andres Zurita-Silva, Jonathan Maldonado, Herman Silva
HIGHLIGHTS R49 genotype displayed best performance on selected physiological parameters and highest tolerance to drought.R49 drought over-represented transcripts has exhibited 19% of genes (306 contigs) that presented no homology to published databases.Expression pattern for canonical responses to drought such as ABA biosynthesis and other genes induced in response to drought were assessed by qPCR. Global freshwater shortage is one of the biggest challenges of our time, often associated to misuse, increased consumption demands and the effects of climate change, paralleled with the desertification of vast areas...
2017: Frontiers in Plant Science
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