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https://www.readbyqxmd.com/read/29143920/distinguishing-the-disease-associated-snps-based-on-composition-frequency-analysis
#1
Wenling Li, Menglong Li, Xuemei Pu, Yanzhi Guo
Single-nucleotide polymorphism (SNP) is a basical variation in genome. When SNPs occur at the binding sites of microRNA, they can influence the binding efficiency, cause a fluctuation of the mRNA in vivo, and thus arouse posttranscriptional level abnormality. Therefore, SNP has a strong correlation with diseases. Although enormous SNPs have been experimentally identified, only a tiny proportion of them are truly disease-associated SNPs (dSNPs) that relate to microRNA modification and then are involved in disease causing process...
November 16, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29143663/dirofilaria-immitis-jyd-34-isolate-whole-genome-analysis
#2
Catherine Bourguinat, Francois Lefebvre, Johanna Sandoval, Brenda Bondesen, Yovany Moreno, Roger K Prichard
BACKGROUND: Macrocyclic lactone (ML) anthelmintics are used for chemoprophylaxis for heartworm infection in dogs and cats. Cases of dogs becoming infected with heartworms, despite apparent compliance to recommended chemoprophylaxis with approved preventives, has led to such cases being considered as suspected lack of efficacy (LOE). Recently, microfilariae collected from a small number of LOE isolates were used as a source of infection of new host dogs and confirmed to have reduced susceptibility to ML in controlled efficacy studies using L3 challenge in dogs...
November 9, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/29143598/gwas-for-plant-growth-stages-and-yield-components-in-spring-wheat-triticum-aestivum-l-harvested-in-three-regions-of-kazakhstan
#3
Yerlan Turuspekov, Aida Baibulatova, Kanat Yermekbayev, Laura Tokhetova, Vladimir Chudinov, Grigoriy Sereda, Martin Ganal, Simon Griffiths, Saule Abugalieva
BACKGROUND: Spring wheat is the largest agricultural crop grown in Kazakhstan with an annual sowing area of 12 million hectares in 2016. Annually, the country harvests around 15 million tons of high quality grain. Despite environmental stress factors it is predicted that the use of new technologies may lead to increases in productivity from current levels of 1.5 to up to 3 tons per hectare. One way of improving wheat productivity is by the application of new genomic oriented approaches in plant breeding projects...
November 14, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29142105/the-nde1-genomic-locus-can-affect-treatment-of-psychiatric-illness-through-gene-expression-changes-related-to-microrna-484
#4
Nicholas J Bradshaw, Liisa Ukkola-Vuoti, Maiju Pankakoski, Amanda B Zheutlin, Alfredo Ortega-Alonso, Minna Torniainen-Holm, Vishal Sinha, Sebastian Therman, Tiina Paunio, Jaana Suvisaari, Jouko Lönnqvist, Tyrone D Cannon, Jari Haukka, William Hennah
Genetic studies of familial schizophrenia in Finland have observed significant associations with a group of biologically related genes, DISC1, NDE1, NDEL1, PDE4B and PDE4D, the 'DISC1 network'. Here, we use gene expression and psychoactive medication use data to study their biological consequences and potential treatment implications. Gene expression levels were determined in 64 individuals from 18 families, while prescription medication information has been collected over a 10-year period for 931 affected individuals...
November 2017: Open Biology
https://www.readbyqxmd.com/read/29141648/polymorphisms-at-microrna-binding-sites-of-ara-c-and-anthracyclines-metabolic-pathway-genes-are-associated-with-outcome-of-acute-myeloid-leukemia-patients
#5
Hai-Xia Cao, Chao-Feng Miao, Liang Yan, Ping Tang, Li-Rong Zhang, Ling Sun
BACKGROUND: Gene polymorphisms at microRNA-binding sites (poly-miRTS) may affect gene transcription and expression through miRNA regulation, which is associated with cancer susceptibility, sensitivity to chemotherapy and prognosis. This study investigated the association between poly-miRTS of Ara-C/anthracycline metabolic pathways genes and the outcome of acute myeloid leukemia (AML) in Chinese patients after Ara-C-based chemotherapy. METHODS: A total of 17 poly-miRTS were selected from the SNPinfo Web Server and genotyped in 206 Chinese Han non-FAB-M3 AML patients using the SEQUENOM Mass-ARRAY system...
November 15, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/29141248/association-of-functional-genetic-variants-of-hotair-with-hepatocellular-carcinoma-hcc-susceptibility-in-a-chinese-population
#6
Hao Li, Xian-Mei Tang, Yangchen Liu, Weizhen Li, Qiaoyun Chen, Yan Pan
BACKGROUND/AIMS: The HOX transcript antisense intergenic RNA (HOTAIR), a long non-coding RNA (lncRNA), plays an important role in the pathogenesis and progression of multiple tumors. The aim of the present study was to evaluate whether common single nucleotide polymorphisms (SNPs) in HOTAIR are related to hepatocellular carcinoma (HCC) susceptibility in a Chinese population. METHODS: We genotyped three SNPs of HOTAIR in a hepatocellular carcinoma (HCC) case-control study, including 482 cases and 520 control subjects...
November 15, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29141033/transcriptome-profiling-of-claw-muscle-of-the-mud-crab-scylla-paramamosain-at-different-fattening-stages
#7
Qingling Jiang, Chenchang Bao, Ya'nan Yang, An Liu, Fang Liu, Huiyang Huang, Haihui Ye
In crustaceans, muscle growth and development is complicated, and to date substantial knowledge gaps exist. In this study, the claw muscle, hepatopancreas and nervous tissue of the mud crab (Scylla paramamosain) were collected at three fattening stages for sequence by the Illumina sequencing. A total of 127.87 Gb clean data with no less than 3.94 Gb generated for each sample and the cycleQ30 percentages were more than 86.13% for all samples. De Bruijn assembly of these clean data produced 94,853 unigenes, thereinto, 50,059 unigenes were found in claw muscle...
2017: PloS One
https://www.readbyqxmd.com/read/29140524/noncodev5-a-comprehensive-annotation-database-for-long-non-coding-rnas
#8
ShuangSang Fang, LiLi Zhang, JinCheng Guo, YiWei Niu, Yang Wu, Hui Li, LianHe Zhao, XiYuan Li, XueYi Teng, XianHui Sun, Liang Sun, Michael Q Zhang, RunSheng Chen, Yi Zhao
NONCODE (http://www.bioinfo.org/noncode/) is a systematic database that is dedicated to presenting the most complete collection and annotation of non-coding RNAs (ncRNAs), especially long non-coding RNAs (lncRNAs). Since NONCODE 2016 was released two years ago, the amount of novel identified ncRNAs has been enlarged by the reduced cost of next-generation sequencing, which has produced an explosion of newly identified data. The third-generation sequencing revolution has also offered longer and more accurate annotations...
November 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29140467/genomic-prediction-in-a-nuclear-population-of-layers-using-single-step-models
#9
Yiyuan Yan, Guiqin Wu, Aiqiao Liu, Congjiao Sun, Wenpeng Han, Guangqi Li, Ning Yang
Single-step genomic prediction method has been proposed to improve the accuracy of genomic prediction by incorporating information of both genotyped and ungenotyped animals. The objective of this study is to compare the prediction performance of single-step model with a 2-step models and the pedigree-based models in a nuclear population of layers. A total of 1,344 chickens across 4 generations were genotyped by a 600 K SNP chip. Four traits were analyzed, i.e., body weight at 28 wk (BW28), egg weight at 28 wk (EW28), laying rate at 38 wk (LR38), and Haugh unit at 36 wk (HU36)...
November 11, 2017: Poultry Science
https://www.readbyqxmd.com/read/29140435/hmdb-4-0-the-human-metabolome-database-for-2018
#10
David S Wishart, Yannick Djoumbou Feunang, Ana Marcu, An Chi Guo, Kevin Liang, Rosa Vázquez-Fresno, Tanvir Sajed, Daniel Johnson, Carin Li, Naama Karu, Zinat Sayeeda, Elvis Lo, Nazanin Assempour, Mark Berjanskii, Sandeep Singhal, David Arndt, Yonjie Liang, Hasan Badran, Jason Grant, Arnau Serra-Cayuela, Yifeng Liu, Rupa Mandal, Vanessa Neveu, Allison Pon, Craig Knox, Michael Wilson, Claudine Manach, Augustin Scalbert
The Human Metabolome Database or HMDB (www.hmdb.ca) is a web-enabled metabolomic database containing comprehensive information about human metabolites along with their biological roles, physiological concentrations, disease associations, chemical reactions, metabolic pathways, and reference spectra. First described in 2007, the HMDB is now considered the standard metabolomic resource for human metabolic studies. Over the past decade the HMDB has continued to grow and evolve in response to emerging needs for metabolomics researchers and continuing changes in web standards...
November 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29138870/insig2-rs7566605-single-nucleotide-variant-and-global-dna-methylation-index-levels-are-associated-with-weight-loss-in-a-personalized-weight-reduction-program
#11
Francesca Pirini, Sebastian Rodriguez-Torres, Bola Grace Ayandibu, María Orera-Clemente, Alberto Gonzalez-de la Vega, Fahcina Lawson, Roland J Thorpe, David Sidransky, Rafael Guerrero-Preston
Single nucleotide polymorphisms associated with lipid metabolism and energy balance are implicated in the weight loss response caused by nutritional interventions. Diet‑induced weight loss is also associated with differential global DNA methylation. DNA methylation has been proposed as a predictive biomarker for weight loss response. Personalized biomarkers for successful weight loss may inform clinical decisions when deciding between behavioral and surgical weight loss interventions. The aim of the present study was to investigate the association between global DNA methylation, genetic variants associated with energy balance and lipid metabolism, and weight loss following a non‑surgical weight loss regimen...
November 14, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29138689/clarifying-sub-genomic-positions-of-qtls-for-flowering-habit-and-fruit-quality-in-u-s-strawberry-fragaria%C3%A3-ananassa-breeding-populations-using-pedigree-based-qtl-analysis
#12
Sujeet Verma, Jason D Zurn, Natalia Salinas, Megan M Mathey, Beatrice Denoyes, James F Hancock, Chad E Finn, Nahla V Bassil, Vance M Whitaker
The cultivated strawberry (Fragaria×ananassa) is consumed worldwide for its flavor and nutritional benefits. Genetic analysis of commercially important traits in strawberry are important for the development of breeding methods and tools for this species. Although several quantitative trait loci (QTL) have been previously detected for fruit quality and flowering traits using low-density genetic maps, clarity on the sub-genomic locations of these QTLs was missing. Recent discoveries in allo-octoploid strawberry genomics led to the development of the IStraw90 single-nucleotide polymorphism (SNP) array, enabling high-density genetic maps and finer resolution QTL analysis...
2017: Horticulture Research
https://www.readbyqxmd.com/read/29138579/association-of-gemin4-gene-polymorphism-and-the-risk-of-cancer-a-meta-analysis
#13
Nan Wu, Xiaowei Zhang, Jinlong Tian, Shuang Yu, Ying Qiao
Gem-associated protein 4 (GEMIN4) gene is a key regulator for the miRNA biogenesis processes. Recent studies have demonstrated that some single-nucleotide polymorphisms (SNPs) in GEMIN4 gene are associated with the risk of cancer, but the results are still controversial. Therefore, we conducted a meta-analysis to analyze the association between three major SNPs (rs2740348, rs7813, and rs3744741) in the GEMIN4 gene and the risk of cancer. Relevant articles were searched in Web of Science, PubMed, Cochrane Library, Chinese Wan Fang, and Chinese National Knowledge Infrastructure databases...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/29135487/update-on-endocrine-aspects-of-childhood-obesity
#14
Charumathi Baskaran, Nurgun Kandemir
PURPOSE OF REVIEW: Although childhood obesity has leveled off in the last decade, 'severe obesity' continues to be on the rise. Various genetic, environmental and hormonal factors contribute to obesity. This article reviews the most current understanding of obesity's multifactorial origin and recent recommendations for its management in childhood and adolescence. RECENT FINDINGS: Epigenetics plays a key role in transmitting obesity risk to offspring. Single-nucleotide polymorphisms at genetic loci for adipokines and their receptors are associated with obesity...
November 11, 2017: Current Opinion in Endocrinology, Diabetes, and Obesity
https://www.readbyqxmd.com/read/29135014/25-years-and-still-going-strong-2-o-pyren-1-yl-methylribonucleotides-versatile-building-blocks-for-applications-in-molecular-biology-diagnostics-and-materials-science
#15
REVIEW
Patrick J Hrdlicka, Saswata Karmakar
Oligonucleotides (ONs) modified with 2'-O-(pyren-1-yl)methylribonucleotides have been explored for a range of applications in molecular biology, nucleic acid diagnostics, and materials science for more than 25 years. The first part of this review provides an overview of synthetic strategies toward 2'-O-(pyren-1-yl)methylribonucleotides and is followed by a summary of biophysical properties of nucleic acid duplexes modified with these building blocks. Insights from structural studies are then presented to rationalize the reported properties...
November 14, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/29134637/ercc4-regulatory-variant-predict-grade-3-or-4-toxicities-in-patients-with-advanced-non-small-cell-lung-cancer-treated-by-platinum-based-therapy
#16
Ruoxin Zhang, Ming Jia, Yuan Xu, Danwen Qian, Mengyun Wang, Meiling Zhu, Menghong Sun, Jianhua Chang, Qingyi Wei
Platinum-based chemotherapy (PBC) in combination with the 3(rd) generation drugs is the first-line treatment for patients with advanced non-small cell lung cancer (NSCLC); however, the efficacy is severely hampered by grade 3-4 toxicities. Nucleotide excision repair (NER) pathway is the main mechanism of removing platinum-induced DNA adducts, contributing to the toxicity and outcome of PBC. We analyzed data from 710 Chinese NSCLC patients treated with PBC and assessed the associations of 25 potentially functional single nucleotide polymorphisms (SNPs) in eight NER core genes with overall, gastrointestinal and hematologic toxicities...
November 14, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29134240/fine-mapping-of-a-male-sterility-gene-ms-3-in-a-novel-cucumber-cucumis-sativus-l-mutant
#17
Yike Han, Fengyue Zhao, Shang Gao, Xianyun Wang, Aimin Wei, Zhengwu Chen, Nan Liu, Xueqiang Tong, Xinmeng Fu, Changlong Wen, Zhenxian Zhang, Ningning Wang, Shengli Du
The cucumber male sterility gene ms - 3 was fine mapped in a 76 kb region harboring an MMD1 -like gene Csa3M006660 that may be responsible for the male sterile in cucumber. A cucumber (Cucumis sativus L.) male sterile mutant (ms-3) in an advanced-generation inbred line was identified, and genetic analysis revealed that the male sterility trait was controlled by a recessive nuclear gene, ms-3, which was stably inherited. Histological studies suggested that the main cause of the male sterility was defective microsporogenesis, resulting in no tetrad or microspores being formed...
November 13, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29133511/which-individuals-to-choose-to-update-the-reference-population-minimizing-the-loss-of-genetic-diversity-in-animal-genomic-selection-programs
#18
S E Eynard, P Croiseau, D Laloë, S Fritz, M P L Calus, G Restoux
Genomic selection is commonly used in livestock and increasingly in plant breeding. Relying on phenotypes and genotypes of a reference population, genomic selection allows performance prediction for young individuals having only genotypes. This is expected to achieve fast high genetic gain but with a potential loss of genetic diversity. Existing methods to conserve genetic diversity depend mostly on the choice of the breeding individuals. In this study we propose a modification of the reference population composition to mitigate diversity loss...
November 13, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29132927/whole-exome-sequencing-identified-a-pathogenic-mutation-in-ryr2-in-a-chinese-family-with-unexplained-sudden-death
#19
Yubi Lin, Siqi He, Zili Liao, Ruiling Feng, Ruilin Liu, Yongzheng Peng, Nan Yu, Hang Qi, Jia Chen, Zifeng Huang, Heping Lei, Yang Liu, Fang Rao, Chunyu Deng, Yumei Xue, Guolin Zhang, Bin Zhang, Hua Yao, Shulin Wu
OBJECTIVE: This study aimed to identify the pathogenic mutation in a Chinese family with unexplained sudden death (USD) or occasional syncope. MATERIALS AND METHODS: Whole exome sequencing and target capture sequencing were respectively conducted for two related patients. The genetic data was screened using the 1000 genomes project and SNP database (PubMed), and the identified mutations were assessed for predicted pathogenicity using the SIFT and Polyphen-2 algorithms...
October 10, 2017: Journal of Electrocardiology
https://www.readbyqxmd.com/read/29130521/a-variant-in-ppp4r3a-protects-against-alzheimer-related-metabolic-decline
#20
Leigh Christopher, Valerio Napolioni, Raiyan R Khan, Summer S Han, Michael D Greicius
OBJECTIVES: A reduction in glucose metabolism in the posterior cingulate cortex (PCC) predicts conversion to Alzheimer's disease (AD) and tracks disease progression, signifying its importance in AD. We aimed to use decline in PCC glucose metabolism as a proxy for the development and progression of AD to discover common genetic variants associated with disease vulnerability. METHODS: We performed a genome-wide association study (GWAS) of decline in PCC [(18) F] FDG PET measured in Alzheimer's Disease Neuroimaging Initiative (ADNI) participants (n=606)...
November 11, 2017: Annals of Neurology
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