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Genetic variation

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https://www.readbyqxmd.com/read/29223971/keeping-pace-with-the-red-queen-identifying-the-genetic-basis-of-susceptibility-to-infectious-disease
#1
Ailene MacPherson, Sarah P Otto, Scott L Nuismer
Genome-wide association studies are widely used to identify "disease genes" conferring resistance/susceptibility to infectious diseases. Using a combination of mathematical models and simulations we demonstrate that genetic interactions between hosts and parasites (GxG interactions) can drastically affect the results of these association scans and hamper our ability to detect genetic variation in susceptibility. When hosts and parasites coevolve, these GxG interactions often make Genome-wide association studies unrepeatable over time or across host populations...
December 9, 2017: Genetics
https://www.readbyqxmd.com/read/29223875/snakes-exhibit-tissue-specific-variation-in-cardiotonic-steroid-sensitivity-of-na-k-atpase
#2
Shabnam Mohammadi, Georg Petschenka, Susannah S French, Akira Mori, Alan H Savitzky
Toads are among several groups of organisms chemically defended with lethal concentrations of cardiotonic steroids. As a result, most predators that prey on amphibians avoid toads. However, several species of snakes have gained resistance-conferring mutations of Na+/K+-ATPase, the molecular target of cardiotonic steroids, and can feed on toads readily. Despite recent advances in our understanding of this adaptation at the genetic level, we have lacked functional evidence for how mutations of Na+/K+-ATPase account for cardiotonic steroid resistance in snake tissues...
December 6, 2017: Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology
https://www.readbyqxmd.com/read/29223463/terfenadine-metabolism-of-human-cytochrome-p450-2j2-containing-genetic-variations-g312r-p351l-and-p115l
#3
Dabin Jeong, Hyoung-Goo Park, Young-Ran Lim, Yejin Lee, Vitchan Kim, Myung-A Cho, Donghak Kim
The human cytochrome P450 2J2 is involved in several metabolic reactions, including the oxidation of important therapeutics and epoxidation of endogenous arachidonic acid. At least ten genetic variations of P450 2J2 have been identified, but their effects on enzymatic activity have not been clearly characterized. Here, we evaluated the functional effects of three genetic variations of P450 2J2 (G312R, P351L, and P115L). Recombinant enzymes of wild-type and three variant P450 2J2 were heterologously expressed in Escherichia coli and purified...
November 11, 2017: Drug Metabolism and Pharmacokinetics
https://www.readbyqxmd.com/read/29223338/molecular-cloning-and-expression-analysis-of-aquaporin-genes-in-pearl-millet-pennisetum-glaucum-l-r-br-genotypes-contrasting-in-their-transpiration-response-to-high-vapour-pressure-deficits
#4
Palakolanu Sudhakar Reddy, Murugesan Tharanya, Kaliamoorthy Sivasakthi, Mallayee Srikanth, C Tom Hash, Jana Kholova, Kiran K Sharma, Vincent Vadez
Pearl millet is a crop of the semi-arid tropics having high degree of genetic diversity and variable tolerance to drought stress. To investigate drought tolerance mechanism that possibly accounts for differences in drought tolerance, four recombinant inbred lines from a high resolution cross (HRC) were selected for variability in their transpiration rate (Tr) response to vapour pressure deficit (VPD) conditions. The differential Tr response of the genotypes to increased VPD conditions was used to classify the genotypes as sensitive or insensitive to high VPD...
December 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/29222496/genome-wide-and-gene-based-association-mapping-for-rice-eating-and-cooking-characteristics-and-protein-content
#5
Xiaoqian Wang, Yunlong Pang, Jian Zhang, Zhichao Wu, Kai Chen, Jauhar Ali, Guoyou Ye, Jianlong Xu, Zhikang Li
Rice eating and cooking quality and protein content (PC) are important properties affecting consumers' preferences, nutrition and health. Linkage QTL mapping and association studies are usually applied to genetically dissect related traits, which could be further facilitated by high density SNP markers and gene annotation based on reference genome to rapid identify candidate genes associated with interested traits. Here, we carried out an association study for apparent amylose content (AC), gel consistency (GC), gelatinization temperature (GT) and PC evaluated in two environments using a diverse panel of 258 accessions from 3 K Rice Genome Project...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29222468/dissecting-the-genetic-basis-of-local-adaptation-in-soybean
#6
Nonoy B Bandillo, Justin E Anderson, Michael B Kantar, Robert M Stupar, James E Specht, George L Graef, Aaron J Lorenz
Soybean (Glycine max) is the most widely grown oilseed in the world and is an important source of protein for both humans and livestock. Soybean is widely adapted to both temperate and tropical regions, but a changing climate demands a better understanding of adaptation to specific environmental conditions. Here, we explore genetic variation in a collection of 3,012 georeferenced, locally adapted landraces from a broad geographical range to help elucidate the genetic basis of local adaptation. We used geographic origin, environmental data and dense genome-wide SNP data to perform an environmental association analysis and discover loci displaying steep gradients in allele frequency across geographical distance and between landrace and modern cultivars...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29222425/polymorphisms-in-jmjd1c-are-associated-with-pubertal-onset-in-boys-and-reproductive-function-in-men
#7
Nina Mørup, Alexander Siegfried Busch, Anne Kirstine Bang, Loa Nordkap, John E Nielsen, Ewa Rajpert-De Meyts, Anders Juul, Niels Jørgensen, Kristian Almstrup
JMJD1C, a member of the Jumonji-domain containing histone demethylases protein family, has been associated with levels of sex-hormone binding globulin (SHBG) and testosterone in men, and knock-out rodent models show age-dependent infertility. The objective of this study was to investigate whether single nucleotide polymorphisms (SNPs) nearby JMJD1C are associated with pubertal onset in boys and with male reproduction. 671 peri-pubertal boys, 1,027 young men, 315 fertile men, and 252 infertile men were genotyped for two JMJD1C SNPs (rs7910927 and rs10822184)...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29222170/imprecision-and-dna-break-repair-biased-towards-incompatible-end-joining-in-leukemia
#8
Franz Josef Gassner, Maria Schubert, Stefan Rebhandl, Karina Spandl, Nadja Zaborsky, Kemal Catakovic, Stephanie Blaimer, Daniel Hebenstreit, Richard Greil, Roland Geisberger
Cancer is a genetic disease caused by mutations and chromosomal abnormalities which contribute to uncontrolled cell growth. In addition, cancer cells can rapidly respond to conventional and targeted therapies by accumulating novel and often specific genetic lesions leading to acquired drug resistance and relapsing disease. In chronic lymphocytic leukemia (CLL), however, diverse chromosomal aberrations often occur. In many cases, improper repair of DNA double strand breaks (DSBs) is a major source for genomic abnormalities...
December 8, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29221444/genome-wide-association-study-of-coronary-artery-calcified-atherosclerotic-plaque-in-african-americans-with-type-2-diabetes
#9
Jasmin Divers, Nicholette D Palmer, Carl D Langefeld, W Mark Brown, Lingyi Lu, Pamela J Hicks, S Carrie Smith, Jianzhao Xu, James G Terry, Thomas C Register, Lynne E Wagenknecht, John S Parks, Lijun Ma, Gary C Chan, Sarah G Buxbaum, Adolfo Correa, Solomon Musani, James G Wilson, Herman A Taylor, Donald W Bowden, John Jeffrey Carr, Barry I Freedman
BACKGROUND: Coronary artery calcified atherosclerotic plaque (CAC) predicts cardiovascular disease (CVD). Despite exposure to more severe conventional CVD risk factors, African Americans (AAs) are less likely to develop CAC, and when they do, have markedly lower levels than European Americans. Genetic factors likely contribute to the observed ethnic differences. To identify genes associated with CAC in AAs with type 2 diabetes (T2D), a genome-wide association study (GWAS) was performed using the Illumina 5 M chip in 691 African American-Diabetes Heart Study participants (AA-DHS), with replication in 205 Jackson Heart Study (JHS) participants with T2D...
December 8, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29221129/long-non-coding-rna-polymorphisms-in-6p21-1-are-associated-with-atrophic-gastritis-risk-and-gastric-cancer-prognosis
#10
Zhi Lv, Liping Sun, Qian Xu, Yuehua Gong, Jingjing Jing, Chengzhong Xing, Yuan Yuan
It has been suggested that the genetic variation in human chromosome 6p21.1 has potential importance for the susceptibility to gastric cancer (GC). The study aims to explore the relationship between the long non-coding RNA (lncRNA) polymorphisms in 6p21.1 and the risk of GC as well as atrophic gastritis (AG). Genotyping for eight single nucleotide polymorphisms (SNPs) was conducted using Sequenom MassARRAY platform in a total of 2507 northern Chinese subjects, including 749 GC cases, 878 AG cases and 880 controls...
November 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29220522/meta-analysis-of-genome-wide-association-studies-identifies-8-novel-loci-involved-in-shape-variation-of-human-head-hair
#11
Fan Liu, Yan Chen, Gu Zhu, Pirro G Hysi, Sijie Wu, Kaustubh Adhikari, Krystal Breslin, Ewelina Pospiech, Merel A Hamer, Fuduan Peng, Charanya Muralidharan, Victor Acuna-Alonzo, Samuel Canizales-Quinteros, Gabriel Bedoya, Carla Gallo, Giovanni Poletti, Francisco Rothhammer, Maria Catira Bortolini, Rolando Gonzalez-Jose, Changqing Zeng, Shuhua Xu, Li Jin, André G Uitterlinden, M Arfan Ikram, Cornelia M van Duijn, Tamar Nijsten, Susan Walsh, Wojciech Branicki, Sijia Wang, Andrés Ruiz-Linares, Timothy D Spector, Nicholas G Martin, Sarah E Medland, Manfred Kayser
Shape variation of human head hair shows striking variation within and between human populations, while its genetic basis is far from being understood. We performed a series of genome-wide association studies (GWASs) and replication studies in a total of 28,964 subjects from 9 cohorts from multiple geographic origins. A meta-analysis of three European GWASs identified 8 novel loci (1p36.23 ERRFI1/SLC45A1, 1p36.22 PEX14, 1p36.13 PADI3, 2p13.3 TGFA, 11p14.1 LGR4, 12q13.13 HOXC13, 17q21.2 KRTAP, and 20q13.33 PTK6), and confirmed 4 previously known ones (1q21...
December 6, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/29220507/assessing-the-heterogeneity-of-in-silico-plasmid-predictions-based-on-whole-genome-sequenced-clinical-isolates
#12
Cedric C Laczny, Valentina Galata, Achim Plum, Andreas E Posch, Andreas Keller
High-throughput next-generation shotgun sequencing of pathogenic bacteria is growing in clinical relevance, especially for chromosomal DNA-based taxonomic identification and for antibiotic resistance prediction. Genetic exchange is facilitated for extrachromosomal DNA, e.g. plasmid-borne antibiotic resistance genes. Consequently, accurate identification of plasmids from whole-genome sequencing (WGS) data remains one of the major challenges for sequencing-based precision medicine in infectious diseases. Here, we assess the heterogeneity of four state-of-the-art tools (cBar, PlasmidFinder, plasmidSPAdes and Recycler) for the in silico prediction of plasmid-derived sequences from WGS data...
December 5, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29220491/cnvcaller-highly-efficient-and-widely-applicable-software-for-detecting-copy-number-variations-in-large-populations
#13
Xihong Wang, Zhuqing Zheng, Yudong Cai, Ting Chen, Chao Li, Weiwei Fu, Yu Jiang
Background: The increasing amount of sequencing data available for a wide variety of species can be theoretically used for detecting copy number variations (CNVs) at the population level. However, the growing sample sizes and the divergent complexity of non-human genomes challenge the efficiency and robustness of current human-oriented CNV detection methods. Results: Here, we present CNVcaller, a read-depth method for discovering CNVs in population sequencing data...
December 4, 2017: GigaScience
https://www.readbyqxmd.com/read/29220485/funricegenes-dataset-for-comprehensive-understanding-and-application-of-rice-functional-genes
#14
Wen Yao, Guangwei Li, Yiming Yu, Yidan Ouyang
Background: As a main staple food, rice is also a model plant for functional genomic studies of monocots. Decoding of every DNA element of the rice genome is essential for genetic improvement to address increasing food demands. The past 15 years have witnessed extraordinary advances in rice functional genomics. Systematic characterization and proper deposition of every rice gene are vital for both functional studies and crop genetic improvement. Findings: We built a comprehensive and accurate dataset of ∼2,800 functionally characterized rice genes and ∼5,000 members of different gene families, by integrating data from available databases and reviewing of every publication on rice functional genomic studies...
December 4, 2017: GigaScience
https://www.readbyqxmd.com/read/29220389/association-of-genetic-variations-in-foxo3-gene-with-susceptibility-to-noise-induced-hearing-loss-in-a-chinese-population
#15
Haoran Guo, Enmin Ding, Ying Bai, Hengdong Zhang, Huanxi Shen, Jun Wang, Xianping Song, Wenyan Cai, Jiadi Guo, Baoli Zhu
Noise induced hearing loss (NIHL), a multifactorial disease involving both genetic and environmental factors, is one of the most important occupational health hazards. Nonetheless, the influence of FOXO3 variants on NIHL risk have not been illuminated. This research was conducted to explore the effects of FOXO3 polymorphisms on individual susceptibility to NIHL. A total of 2689 industrial workers from one textile factory of east China were recruited to participate in the current research. Venous blood was collected, questionnaire and pure-tone audiometry (PTA) was conducted by specialist physicians...
2017: PloS One
https://www.readbyqxmd.com/read/29220109/population-transcriptomics-in-daphnia-the-role-of-thermal-selection
#16
Maike Herrmann, Suda Parimala Ravindran, Klaus Schwenk, Mathilde Cordellier
The complex interplay of forces influencing genetic divergence among populations complicates the discovery of the genetic basis underlying local adaptation. Here, we utilized for the first time a combined reverse ecology and population transcriptomic approach to assess the contribution of thermal selection to population differentiation, thereby considering transcriptome-wide variation in both gene expression profiles and DNA sequences. We compared transcriptomes among four Daphnia galeata populations and identified transcripts potentially responding to local thermal selection based on an extensive literature search for candidate genes possibly under thermal selection in arthropods...
December 8, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29220073/collective-effects-of-common-snps-and-genetic-risk-prediction-in-type-1-diabetes
#17
Y Gui, X Lei, S Huang
Type 1 diabetes (T1D) is a common autoimmune disease and may be related to multiple genetic and environmental risk factors. Previous genetic studies have focused on looking for individual polymorphic risk variants. Here we studied the overall levels of genetic diversity in T1D patients by making use of a previously published study including 1,865 cases and 2,828 reference samples with genotyping data for 500K common single nucleotide polymorphisms (SNPs). We determined the minor allele status of each SNP in the reference samples and calculated the total number of minor alleles or minor allele contents (MAC) of each individual...
December 8, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/29219063/an-insight-on-the-pathogenesis-and-treatment-of-systemic-lupus-erythematosus
#18
Murtaza Ali, Chelapram K Firoz, Nasimudeen R Jabir, Mohd Rehan, Mohd Shahnawaz Khan, Shams Tabrez
BACKGROUND AND OBJECTIVE: Systemic lupus erythematosus (SLE) is a diverse autoimmune disorder, evoked in response to self-immune system that leads to immune complex depositions and organ damage. The exact mechanism of SLE pathogenesis is still unclear but certain genetic and environmental factors have been suggested in the literature that could influence its pathogenesis. The modulation in B- and T- cell responses and genetic variations could lead to abnormal lymphocyte functions and the production of antibodies against the indigenous proteins and the immune complex depositions...
December 7, 2017: Endocrine, Metabolic & Immune Disorders Drug Targets
https://www.readbyqxmd.com/read/29219045/mitochondrial-genetic-diversity-and-phylogeography-of-mus-musculus-castaneus-in-northern-punjab-pakistan
#19
Shahnaz Bibi, Muhammad Sajid Nadeem, Andrew Stephen Wiewel, Mirza Azhar Beg, Khalid Hameed, Musarrat Jabeen, Ghazala Kaukab Raja
Regions of Iran, Afghanistan, Pakistan and northwestern India have been proposed as the place of origin of Mus musculus castaneus. But despite the fact that Pakistan encompasses an important part of its range, M. m. castaneus populations in Pakistan have not been the subject of intensive genetic and biogeographic studies, except for a very small number of samples included in past studies. We studied genetic variation in M. m. castaneus (CAS) from northern Punjab Province, Pakistan, by using cytochrome b (Cytb) analysis in a sample of 98 individuals...
December 2017: Zoological Science
https://www.readbyqxmd.com/read/29219041/potential-causative-mutation-for-melanism-in-rats-identified-in-the-agouti-signaling-protein-gene-asip-of-the-rattus-rattus-species-complex-on-okinawa-island-japan
#20
Shoichi Sasamori, Andrew S Wiewel, Vicki A Thomson, Motoko Kobayashi, Katsushi Nakata, Hitoshi Suzuki
The occurrence of black fur, or melanism, in many mammalian species is known to be linked to DNA sequence variation in the agouti signaling protein (Asip) gene, which is a major determinant of eumelanin and pheomelanin pigments in coat color. We investigated 38 agouti (i.e., banded wildtype) and four melanistic Rattus rattus species complex (RrC) lineage II specimens from Okinawa Island, Ryukyu Islands, Japan, for genetic variation in three exons and associated flanking regions in the Asip gene. On Okinawa, a predicted loss-of-function mutation caused by a cysteine to serine amino acid change at p...
December 2017: Zoological Science
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