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Genetic variation

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https://www.readbyqxmd.com/read/28732180/the-role-of-noncoding-genetic-variation-in-isolated-orofacial-clefts
#1
F Thieme, K U Ludwig
In the past decade, medical genetic research has generated multiple discoveries, many of which were obtained via genome-wide association studies (GWASs). A major GWAS finding is that the majority of risk variants for complex traits map to noncoding regions. This has resulted in a paradigm shift in terms of the interpretation of human genomic sequence variation, with more attention now being paid to what was previously termed "junk DNA." Translation of genetic findings into biologically meaningful results requires 1) large-scale and cell-specific efforts to annotate non-protein-coding regions and 2) the integration of comprehensive genomic data sets...
July 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28732062/a-drosophila-model-for-toxicogenomics-genetic-variation-in-susceptibility-to-heavy-metal-exposure
#2
Shanshan Zhou, Sarah E Luoma, Genevieve E St Armour, Esha Thakkar, Trudy F C Mackay, Robert R H Anholt
The genetic factors that give rise to variation in susceptibility to environmental toxins remain largely unexplored. Studies on genetic variation in susceptibility to environmental toxins are challenging in human populations, due to the variety of clinical symptoms and difficulty in determining which symptoms causally result from toxic exposure; uncontrolled environments, often with exposure to multiple toxicants; and difficulty in relating phenotypic effect size to toxic dose, especially when symptoms become manifest with a substantial time lag...
July 21, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28732058/the-role-of-a-fads1-polymorphism-in-the-association-of-fatty-acid-blood-levels-bmi-and-blood-pressure-in-young-children-analyses-based-on-path-models
#3
Maike Wolters, Carmen Dering, Alfonso Siani, Paola Russo, Jaakko Kaprio, Patrizia Risé, Luis A Moreno, Stefaan De Henauw, Kirsten Mehlig, Toomas Veidebaum, Denés Molnár, Michael Tornaritis, Licia Iacoviello, Yannis Pitsiladis, Claudio Galli, Ronja Foraita, Claudia Börnhorst
BACKGROUND: The recent obesity epidemic in children also showed an increase in the prevalence of hypertension. As blood pressure (BP) is associated with (long-chain) polyunsaturated fatty acids (LC PUFA), genetic variation in desaturase enzymes being involved in the synthesis of LC PUFA may be associated with BP. This study aimed to investigate the direct effects (independent of mediating variables) and indirect effects (mediated through intermediate variables) of a common variant in the FADS1 gene, rs174546, known to affect delta-5 desaturase (D5D) activity on PUFA level, body mass index (BMI) and BP...
2017: PloS One
https://www.readbyqxmd.com/read/28732049/testing-the-optimal-defense-hypothesis-in-nature-variation-for-glucosinolate-profiles-within-plants
#4
Rose A Keith, Thomas Mitchell-Olds
Plants employ highly variable chemical defenses against a broad community of herbivores, which vary in their susceptibilities to specific compounds. Variation in chemical defenses within the plant has been found in many species; the ecological and evolutionary influences on this variation, however, are less well-understood. One central theory describing the allocation of defenses in the plant is the Optimal Defense Hypothesis (ODH), which predicts that defenses will be concentrated in tissues that are of high fitness value to the plant...
2017: PloS One
https://www.readbyqxmd.com/read/28732039/abnormal-meiosis-in-an-intersectional-allotriploid-of-populus-l-and-segregation-of-ploidy-levels-in-2x-%C3%A3-3x-progeny
#5
Jun Wang, Beibei Huo, Wanting Liu, Daili Li, Ling Liao
Triploid plants are usually highly aborted owing to unbalanced meiotic chromosome segregation, but limited viable gametes can participate in the transition to different ploidy levels. In this study, numerous meiotic abnormalities were found with high frequency in an intersectional allotriploid poplar (Populus alba × P. berolinensis 'Yinzhong'), including univalents, precocious chromosome migration, lagging chromosomes, chromosome bridges, micronuclei, and precocious cytokinesis, indicating high genetic imbalance in this allotriploid...
2017: PloS One
https://www.readbyqxmd.com/read/28731899/current-perspectives-on-invasive-nontyphoidal-salmonella-disease
#6
Andrea H Haselbeck, Ursula Panzner, Justin Im, Stephen Baker, Christian G Meyer, Florian Marks
PURPOSE OF REVIEW: We searched PubMed for scientific literature published in the past 2 years for relevant information regarding the burden of invasive nontyphoidal Salmonella disease and host factors associated with nontyphoidal Salmonella infection and discuss current knowledge on vaccine development. The following search terms were used: Salmonella, non typhoidal/nontyphoidal, NTS, disease, bloodstream infection, invasive, sepsis/septicaemia/septicemia, bacteraemia/bacteremia, gastroenteritis, incidence, prevalence, morbidity, mortality, case fatality, host/risk factor, vaccination, and prevention/control...
July 20, 2017: Current Opinion in Infectious Diseases
https://www.readbyqxmd.com/read/28731798/most-colorful-example-of-genetic-assimilation-exploring-the-evolutionary-destiny-of-recurrent-phenotypic-accommodation
#7
Alexander V Badyaev, Ahva L Potticary, Erin S Morrison
Evolution of adaptation requires both generation of novel phenotypic variation and retention of a locally beneficial subset of this variation. Such retention can be facilitated by genetic assimilation, the accumulation of genetic and molecular mechanisms that stabilize induced phenotypes and assume progressively greater control over their reliable production. A particularly strong inference into genetic assimilation as an evolutionary process requires a system where it is possible to directly evaluate the extent to which an induced phenotype is progressively incorporated into preexisting developmental pathways...
August 2017: American Naturalist
https://www.readbyqxmd.com/read/28731797/quantitative-genetic-variation-in-and-environmental-effects-on-pathogen-resistance-and-temperature-dependent-disease-severity-in-a-wild-trout
#8
Paul Vincent Debes, Riho Gross, Anti Vasemägi
Health after pathogen contact varies among individuals because of differences in pathogen load (which is limited by resistance) and disease severity in response to pathogen load (which is limited by tolerance). To understand pathogen-induced host evolution, it is critical to know not only the relative contributions of nongenetic and genetic variation to resistance and tolerance but also how they change environmentally. We quantified nongenetic and genetic variation in parasite load and the associated temperature-dependent disease among trout siblings from two rivers...
August 2017: American Naturalist
https://www.readbyqxmd.com/read/28731545/genome-scale-data-reveals-that-endemic-poecilia-populations-from-small-sulfidic-springs-display-no-evidence-of-inbreeding
#9
Anthony P Brown, Ryan Greenway, Samuel Morgan, Corey R Quackenbush, Luca Giordani, Lenin Arias-Rodriguez, Michael Tobler, Joanna L Kelley
Populations with limited ranges can be highly vulnerable to changes in their environment and are, thus, of high conservation concern. Populations that experience human-induced range reductions are often highly inbred and lack genetic diversity, but it is unknown whether this is also the case for populations with naturally small ranges. The fishes Poecilia sulphuraria (listed as critically endangered) and Poecilia thermalis, which are endemic to small hydrogen sulfide rich springs in southern Mexico, are examples of such populations with inherently small habitats...
July 21, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28731472/high-abundance-and-expression-of-transposases-in-bacteria-from-the-baltic-sea
#10
Theoden Vigil-Stenman, Karolina Ininbergs, Birgitta Bergman, Martin Ekman
Transposases are mobile genetic elements suggested to have an important role in bacterial genome plasticity and host adaptation but their transcriptional activity in natural bacterial communities is largely unexplored. Here we analyzed metagenomes and -transcriptomes of size fractionated (0.1-0.8, 0.8-3.0 and 3.0-200 μm) bacterial communities from the brackish Baltic Sea, and adjacent marine waters. The Baltic Sea transposase levels, up to 1.7% of bacterial genes and 2% of bacterial transcripts, were considerably higher than in marine waters and similar to levels reported for extreme environments...
July 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28730912/rhd-specific-microrna-for-regulation-of-the-del-blood-group-integration-of-computational-and-experimental-approaches
#11
J Thongbut, U Kerdpin, T Sakuldamrongpanich, C Issarankura-Na-Ayudhya, P Nuchnoi
OBJECTIVE: The discovery of specific microRNAs (miRNA) mediates a better understanding of molecular mechanisms, diagnosis and prognosis of complex phenotypes. Synthesis of the RhD blood group involves multiple factors causing variation in the expression of RHD antigens. The mechanism underlying the extremely weak expression of RHD antigen associated with the RHD variant called DEL (D-elute) is incompletely understood. Down-regulation of gene expression through miRNA is a guide to the potential involvement of miRNAs in the DEL blood group...
July 21, 2017: British Journal of Biomedical Science
https://www.readbyqxmd.com/read/28730464/genome-wide-association-mapping-of-canopy-wilting-in-diverse-soybean-genotypes
#12
Avjinder S Kaler, Jeffery D Ray, William T Schapaugh, C Andy King, Larry C Purcell
Genome-wide association analysis identified 61 SNP markers for canopy wilting, which likely tagged 51 different loci. Based on the allelic effects of the significant SNPs, the slowest and fastest wilting genotypes were identified. Drought stress is a major global constraint for crop production, and slow canopy wilting is a promising trait for improving drought tolerance. The objective of this study was to identify genetic loci associated with canopy wilting and to confirm those loci with previously reported canopy wilting QTLs...
July 20, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28730343/age-at-maturation-has-sex-and-temperature-specific-effects-on-telomere-length-in-a-fish
#13
Kristina Noreikiene, Anna Kuparinen, Juha Merilä
Telomeres are highly conserved nucleoprotein structures which protect genome integrity. The length of telomeres is influenced by both genetic and environmental factors, but relatively little is known about how different hereditary and environmental factors interact in determining telomere length. We manipulated growth rates and timing of maturation by exposing full-sib nine-spined sticklebacks (Pungitius pungitius) to two different temperature treatments and quantified the effects of temperature treatments, sex, timing of maturation, growth rate and family (genetic influences) on telomere length...
July 20, 2017: Oecologia
https://www.readbyqxmd.com/read/28729877/genetic-diversity-population-structure-and-linkage-disequilibrium-of-an-association-mapping-panel-revealed-by-genome-wide-snp-markers-in-sesame
#14
Chengqi Cui, Hongxian Mei, Yanyang Liu, Haiyang Zhang, Yongzhan Zheng
The characterization of genetic diversity and population structure can be used in tandem to detect reliable phenotype-genotype associations. In the present study, we genotyped a set of 366 sesame germplasm accessions by using 89,924 single-nucleotide polymorphisms (SNPs). The number of SNPs on each chromosome was consistent with the physical length of the respective chromosome, and the average marker density was approximately 2.67 kb/SNP. The genetic diversity analysis showed that the average nucleotide diversity of the panel was 1...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28729876/genetic-architecture-of-flooding-tolerance-in-the-dry-bean-middle-american-diversity-panel
#15
Ali Soltani, Samira MafiMoghaddam, Katelynn Walter, Daniel Restrepo-Montoya, Sujan Mamidi, Stephan Schroder, Rian Lee, Phillip E McClean, Juan M Osorno
Flooding is a devastating abiotic stress that endangers crop production in the twenty-first century. Because of the severe susceptibility of common bean (Phaseolus vulgaris L.) to flooding, an understanding of the genetic architecture and physiological responses of this crop will set the stage for further improvement. However, challenging phenotyping methods hinder a large-scale genetic study of flooding tolerance in common bean and other economically important crops. A greenhouse phenotyping protocol was developed to evaluate the flooding conditions at early stages...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28729864/synechococcus-assemblages-across-the-salinity-gradient-in-a-salt-wedge-estuary
#16
Xiaomin Xia, Wang Guo, Shangjin Tan, Hongbin Liu
Synechococcus are the most abundant and widely distributed picocyanobacteria in the ocean. The salt-wedge type of estuary possesses the complete horizontal and vertical gradient of salinity together with other physical and chemical parameters. In order to reveal whether such a complex environmental gradient harbors a high diversity of Synechococcus, we investigated the abundance, taxonomic composition and pigment genetic diversity of Synechococcus in surface and bottom waters across the salinity gradient in a salt-wedge estuary by flow cytometric analysis and pyrosequencing of the rpoC1 gene and cpcBA operon (encoding phycocyanin)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28729842/a-gene-based-analysis-of-acoustic-startle-latency
#17
Alicia K Smith, Tanja Jovanovic, Varun Kilaru, Adriana Lori, Lauren Gensler, Samuel S Lee, Seth Davin Norrholm, Nicholas Massa, Bruce Cuthbert, Bekh Bradley, Kerry J Ressler, Erica Duncan
Latency of the acoustic startle response is the time required from the presentation of startling auditory stimulus until the startle response is elicited and provides an index of neural processing speed. Latency is prolonged in subjects with schizophrenia compared to controls in some but not all studies and is 68-90% heritable in baseline startle trials. In order to determine the genetic association with latency as a potential inroad into genetically based vulnerability to psychosis, we conducted a gene-based study of latency followed by an independent replication study of significant gene findings with a single-nucleotide polymorphism (SNP)-based analysis of schizophrenia and control subjects...
2017: Frontiers in Psychiatry
https://www.readbyqxmd.com/read/28729817/ssr-marker-variations-in-brassica-species-provide-insight-into-the-origin-and-evolution-of-brassica-amphidiploids
#18
Ajay Kumar Thakur, Kunwar Harendra Singh, Lal Singh, Joghee Nanjundan, Yasin Jeshima Khan, Dhiraj Singh
BACKGROUND: Oilseed Brassica represents an important group of oilseed crops with a long history of evolution and cultivation. To understand the origin and evolution of Brassica amphidiploids, simple sequence repeat (SSR) markers were used to unravel genetic variations in three diploids and three amphidiploid Brassica species of U's triangle along with Eruca sativa as an outlier. RESULTS: Of 124 Brassica-derived SSR loci assayed, 100% cross-transferability was obtained for B...
2018: Hereditas
https://www.readbyqxmd.com/read/28729732/evidence-of-selection-on-splicing-associated-loci-in-human-populations-and-relevance-to-disease-loci-mapping
#19
Eric R Gamazon, Anuar Konkashbaev, Eske M Derks, Nancy J Cox, Younghee Lee
We performed a whole-genome scan of genetic variants in splicing regulatory elements (SREs) and evaluated the extent to which natural selection has shaped extant patterns of variation in SREs. We investigated the degree of differentiation of single nucleotide polymorphisms (SNPs) in SREs among human populations and applied long-range haplotype- and multilocus allelic differentiation-based methods to detect selection signatures. We describe an approach, sampling a large number of loci across the genome from functional classes and using the consensus from multiple tests, for identifying candidates for selection signals...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729690/functional-variation-of-shp-2-promoter-is-associated-with-preterm-birth-and-delayed-myelination-and-motor-development-in-preterm-infants
#20
So-Yeon Shim, Hye Jin Jeong, Hyo Jin Park, Eun Young Kwon, Bo Min Kim, Yang Ji Choi, Youn-Hee Choi, Su Jin Cho, Ji Ha Choi, Eun Ae Park
Src homology 2 domain-containing protein tyrosine phosphatase 2 (SHP-2) is a cytoplasmic tyrosine phosphatase that is highly expressed in hematopoietic cells and in the CNS and exerts opposite effects on signal transduction by exerting a neuroprotective or proapoptotic effect. Several mutations of SHP-2 have been found in children with myeloproliferative disorders or malignant leukemia, and some of these can affect brain development. In the present study, we aimed to identify and functionally characterize genetic variations in SHP-2 in 72 preterm and 58 full-term infants and to evaluate the effect of the variations on neurodevelopment in preterm infants...
July 20, 2017: Scientific Reports
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