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Genetic variation

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https://www.readbyqxmd.com/read/29679879/polygenic-risk-score-of-serpina6-serpina1-associates-with-diurnal-and-stress-induced-hpa-axis-activity-in-children
#1
Siddheshwar Utge, Katri Räikkönen, Eero Kajantie, Jari Lipsanen, Sture Andersson, Timo Strandberg, Rebecca M Reynolds, Johan G Eriksson, Jari Lahti
PURPOSE: Corticosteroid-binding globulin (CBG) transports glucocorticoids in blood. Variation in genes SERPINA6 encoding for CBG, SERPINA2 and SERPINA1 (serpin family A member 6, 2, and 1) have been shown to influence morning plasma cortisol and CBG in adults. However, association of this genetic variation with diurnal and stress-induced salivary cortisol remain unknown. This study aims to investigate the effect of genetic variation in SERPINA6/2/1 loci on diurnal and stress-induced salivary cortisol in children...
April 13, 2018: Psychoneuroendocrinology
https://www.readbyqxmd.com/read/29679714/population-genetics-phylogenomics-and-hybrid-speciation-of-juglans-in-china-determined-from-whole-chloroplast-genomes-transcriptomes-and-genotyping-by-sequencing-gbs
#2
Peng Zhao, Hui-Juan Zhou, Daniel Potter, Yi-Heng Hu, Xiao-Jia Feng, Meng Dang, Li Feng, Saman Zulfiqar, Wen-Zhe Liu, Guifang Zhao, Keith Woeste
Genomic data are a powerful tool for elucidating the processes involved in the evolution and divergence of species. The speciation and phylogenetic relationships among Chinese Juglans remain unclear. Here, we used results from phylogenomic and population genetic analyses, transcriptomics, Genotyping-By-Sequencing (GBS), and whole chloroplast genomes (Cp genome) data to infer processes of lineage formation among the five native Chinese species of the walnut genus (Juglans, Juglandaceae), a widespread, economically important group...
April 18, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29679645/sequencing-of-pt5282-ctxm-p13190-kpc-and-p30860-nr-and-comparative-genomics-analysis-of-incx8-plasmids
#3
Haihong Fang, Jiao Feng, Yuanhong Xu, Ying Zhang, Zhe Zhan, Zhe Yin, Xiongbo Duan, Bo Gao, Yigang Tong, Jinglin Wang, Yanping Luo, Erhei Dai, Dongsheng Zhou
This study proposed a replicon-based scheme for typing IncX into nine separately clustering subgroups, including IncX1α, IncX1β and IncX2-8. The complete nucleotide sequences of three IncX8 plasmids, namely pT5282-CTXM and p30860-NR from Enterobacter cloacae and p13190-KPC from Klebsiella pneumoniae, were determined and compared with all the other two previously sequenced IncX8 plasmids pCAV1043-58 and pCAV1741-16. These five plasmids possessed conserved IncX8 backbones with limited genetic variations with respect to gene content and organization, and each of them carried one or three accessory modules that harbored resistance markers and metabolic gene clusters as well as transposons, insertion sequence (IS)-based transposition units and miniature inverted repeat transposable elements, indicating that the relatively small IncX8 backbones were able to integrate various foreign genetic contents...
April 18, 2018: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/29679388/somatic-slc35a2-variants-in-the-brain-are-associated-with-intractable-neocortical-epilepsy
#4
Melodie R Winawer, Nicole G Griffin, Jorge Samanamud, Evan H Baugh, Dinesh Rathakrishnan, Senthilmurugan Ramalingam, David Zagzag, Catherine A Schevon, Patricia Dugan, Manu Hegde, Sameer A Sheth, Guy M McKhann, Werner K Doyle, Gerald A Grant, Brenda E Porter, Mohamad A Mikati, Carrie R Muh, Colin D Malone, Ann Marie R Bergin, Jurriaan M Peters, Danielle K McBrian, Alison M Pack, Cigdem I Akman, Christopher M LaCoursiere, Katherine M Keever, Joseph R Madsen, Edward Yang, Hart G W Lidov, Catherine Shain, Andrew S Allen, Peter Canoll, Peter B Crino, Annapurna H Poduri, Erin L Heinzen
OBJECTIVE Somatic variants are a recognized cause of epilepsy-associated focal malformations of cortical development (MCD). We hypothesized that somatic variants may underlie a wider range of focal epilepsy, including non-lesional focal epilepsy (NLFE). Through genetic analysis of brain tissue, we evaluated the role of somatic variation in focal epilepsy with and without MCD. METHODS We identified somatic variants through high-depth exome and ultra-high-depth candidate gene sequencing of DNA from epilepsy surgery specimens and leukocytes from 18 individuals with NLFE and 38 with focal MCD...
April 20, 2018: Annals of Neurology
https://www.readbyqxmd.com/read/29679021/systematic-evaluation-of-rna-quality-microarray-data-reliability-and-pathway-analysis-in-fresh-fresh-frozen-and-formalin-fixed-paraffin-embedded-tissue-samples
#5
Isabella Wimmer, Anna R Tröscher, Florian Brunner, Stephen J Rubino, Christian G Bien, Howard L Weiner, Hans Lassmann, Jan Bauer
Formalin-fixed paraffin-embedded (FFPE) tissues are valuable resources commonly used in pathology. However, formalin fixation modifies nucleic acids challenging the isolation of high-quality RNA for genetic profiling. Here, we assessed feasibility and reliability of microarray studies analysing transcriptome data from fresh, fresh-frozen (FF) and FFPE tissues. We show that reproducible microarray data can be generated from only 2 ng FFPE-derived RNA. For RNA quality assessment, fragment size distribution (DV200) and qPCR proved most suitable...
April 20, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29678917/genomic-inference-of-recombination-mediated-evolution-in-xanthomonas-euvesicatoria-and-x-perforans
#6
Mustafa O Jibrin, Neha Potnis, Sujan Timilsina, Gerald V Minsavage, Gary E Vallad, Pamela D Roberts, Jeffrey B Jones, Erica M Goss
Recombination is a major driver of evolution in bacterial populations because it can spread and combine independently evolved beneficial mutations. Recombinant lineages of plant bacterial pathogens are typically associated with colonization of novel hosts and emergence of new diseases. Here, we show that recombination between evolutionarily and phenotypically distinct plant pathogenic lineages generated recombinant lineages with unique combinations of pathogenicity and virulence factors. X. euvesicatoria ( Xe ) and X...
April 20, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29678862/natural-variation-within-a-species-for-traits-underpinning-c4-photosynthesis
#7
Gregory Reeves, Pallavi Singh, Timo A Rossberg, Deedi Sogbohossou, M Eric Schranz, Julian M Hibberd
Engineering C4 photosynthesis into C3 crops could substantially increase their yield by alleviating photorespiratory losses. This objective is challenging because the C4 pathway involves complex modifications to the biochemistry, cell biology and anatomy of leaves. Forward genetics has provided limited insight into the mechanistic basis of these properties, and there have been no reports of significant quantitative intra-specific variation of C4 attributes that would allow trait mapping. Here, we show that accessions of the C4 species Gynandropsis gynandra collected from locations across Africa and Asia exhibit natural variation in key characteristics of C4 photosynthesis...
April 20, 2018: Plant Physiology
https://www.readbyqxmd.com/read/29678289/pathophysiology-of-melanocortin-receptors-and-their-accessory-proteins
#8
REVIEW
T V Novoselova, L F Chan, A J L Clark
The melanocortin receptors (MCRs) and their accessory proteins (MRAPs) are involved in regulation of a diverse range of endocrine pathways. Genetic variants of these components result in phenotypic variation and disease. The MC1R is expressed in skin and variants in the MC1R gene are associated with ginger hair color. The MC2R mediates the action of ACTH in the adrenal gland to stimulate glucocorticoid production and MC2R mutations result in familial glucocorticoid deficiency (FGD). MC3R and MC4R are involved in metabolic regulation and their gene variants are associated with severe pediatric obesity, whereas the function of MC5R remains to be fully elucidated...
April 2018: Best Practice & Research. Clinical Endocrinology & Metabolism
https://www.readbyqxmd.com/read/29678141/evolving-in-the-highlands-the-case-of-the-neotropical-lerma-live-bearing-poeciliopsis-infans-woolman-1894-cyprinodontiformes-poeciliidae-in-central-mexico
#9
Rosa Gabriela Beltrán-López, Omar Domínguez-Domínguez, Rodolfo Pérez-Rodríguez, Kyle Piller, Ignacio Doadrio
BACKGROUND: Volcanic and tectonic activities in conjunction with Quaternary climate are the main events that shaped the geographical distribution of genetic variation of many lineages. Poeciliopsis infans is the only poeciliid species that was able to colonize the temperate highlands of central Mexico. We inferred the phylogenetic relationships, biogeographic history, and historical demography in the widespread Neotropical species P. infans and correlated this with geological events and the Quaternary glacial-interglacial climate in the highlands of central Mexico, using the mitochondrial genes Cytochrome b and Cytochrome oxidase I and two nuclear loci, Rhodopsin and ribosomal protein S7...
April 20, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29677476/cd4-helper-and-cd8-cytotoxic-t-cell-differentiation
#10
Ichiro Taniuchi
A fundamental question in developmental immunology is how bipotential thymocyte precursors generate both CD4+ helper and CD8+ cytotoxic T cell lineages. The MHC specificity of αβ T cell receptors (TCRs) on precursors is closely correlated with cell fate-determining processes, prompting studies to characterize how variations in TCR signaling are linked with genetic programs establishing lineage-specific gene expression signatures, such as exclusive CD4 or CD8 expression. The key transcription factors ThPOK and Runx3 have been identified as mediating development of helper and cytotoxic T cell lineages, respectively...
April 26, 2018: Annual Review of Immunology
https://www.readbyqxmd.com/read/29677403/indel-variation-in-the-regulatory-region-of-the-major-flowering-time-gene-lanftc1-is-associated-with-vernalisation-response-and-flowering-time-in-narrow-leafed-lupin-lupinus-angustifolius-l
#11
Candy M Taylor, Lars G Kamphuis, Weilu Zhang, Gagan Garg, Jens D Berger, Mahsa Mousavi-Derazmahalleh, Philipp E Bayer, David Edwards, Karam B Singh, Wallace A Cowling, Matthew N Nelson
Narrow-leafed lupin (Lupinus angustifolius L.) cultivation was transformed by two dominant vernalisation-insensitive, early flowering time loci known as Ku and Julius (Jul), which allowed expansion into shorter season environments. However, reliance on these loci has limited genetic and phenotypic diversity for environmental adaptation in cultivated lupin. We recently predicted that a 1,423 bp deletion in the cis-regulatory region of LanFTc1, a FLOWERING LOCUS T (FT) homologue, de-repressed expression of LanFTc1 and was the underlying cause of the Ku phenotype...
April 20, 2018: Plant, Cell & Environment
https://www.readbyqxmd.com/read/29677196/catechol-o-methyltransferase-moderates-effect-of-stress-mindset-on-affect-and-cognition
#12
Alia J Crum, Modupe Akinola, Bradley P Turnwald, Ted J Kaptchuk, Kathryn T Hall
There is evidence that altering stress mindset-the belief that stress is enhancing vs. debilitating-can change cognitive, affective and physiological responses to stress. However individual differences in responsiveness to stress mindset manipulations have not been explored. Given the previously established role of catecholamines in both placebo effects and stress, we hypothesized that genetic variation in catechol-O-methyltransferase (COMT), an enzyme that metabolizes catecholamines, would moderate responses to an intervention intended to alter participants' mindsets about stress...
2018: PloS One
https://www.readbyqxmd.com/read/29676071/differences-in-genetic-variations-between-treatable-and-recalcitrant-atopic-dermatitis-in-korean
#13
Myungsoo Jun, Hye Young Wang, Solam Lee, Eunhee Choi, Hyeyoung Lee, Eung Ho Choi
PURPOSE: Variations in barrier- or immune response-related genes are closely related to the development of atopic dermatitis (AD). This study was designed to identify genetic variations and clinical features to predict 'recalcitrant AD.' METHODS: AD patients were classified as treatable and recalcitrant. Treatable AD patients showed satisfactory clinical improvement with basic and topical treatments. Recalcitrant AD patients used systemic immune-suppressants for over 4 weeks as they had not shown clinical improvement with basic and topical treatments...
May 2018: Allergy, Asthma & Immunology Research
https://www.readbyqxmd.com/read/29676059/among-year-variation-in-selection-during-early-life-stages-and-the-genetic-basis-of-fitness-in-arabidopsis-thaliana
#14
Froukje M Postma, Jon Ågren
Incomplete information regarding both selection regimes and the genetic basis of fitness limits our understanding of adaptive evolution. Among-year variation in the genetic basis of fitness is rarely quantified, and estimates of selection are typically based on single components of fitness, thus potentially missing conflicting selection acting during other life-history stages. Here, we examined among-year variation in selection on a key life-history trait and the genetic basis of fitness covering the whole life cycle in the annual plant Arabidopsis thaliana...
April 19, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29676042/meta-analysis-of-chromosome-scale-crossover-rate-variation-in-eukaryotes-and-its-significance-to-evolutionary-genomics
#15
Quiterie Haenel, Telma G Laurentino, Marius Roesti, Daniel Berner
Understanding the distribution of crossovers along chromosomes is crucial to evolutionary genomics because the crossover rate determines how strongly a genome region is influenced by natural selection on linked sites. Nevertheless, generalities in the chromosome-scale distribution of crossovers have not been investigated formally. We fill this gap by synthesizing joint information on genetic and physical maps across 62 animal, plant, and fungal species. Our quantitative analysis reveals a strong and taxonomically wide-spread reduction of the crossover rate in the center of chromosomes relative to their peripheries...
April 19, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29676012/further-audiovestibular-characterization-of-dfnb77-caused-by-deleterious-variants-in-loxhd1-and-investigation-into-the-involvement-of-fuchs-corneal-dystrophy
#16
M Wesdorp, V Schreur, A J Beynon, J Oostrik, J M van de Kamp, M W Elting, M-J H van den Boogaard, I Feenstra, R J C Admiraal, H P M Kunst, C B Hoyng, H Kremer, H G Yntema, R J E Pennings, M Schraders
This study focuses on further characterization of the audiovestibular phenotype and on genotype-phenotype correlations of DFNB77, an autosomal recessive type of hearing impairment (HI). DFNB77 is associated with disease-causing variants in LOXHD1, and is genetically and phenotypically highly heterogeneous. Heterozygous deleterious missense variants in LOXHD1 have been associated with late-onset Fuchs corneal dystrophy (FCD). However, up to now screening for FCD of heterozygous carriers in DFNB77 families has not been reported...
April 19, 2018: Clinical Genetics
https://www.readbyqxmd.com/read/29675902/demography-or-selection-on-linked-cultural-traits-or-genes-investigating-the-driver-of-low-mtdna-diversity-in-the-sperm-whale-using-complementary-mitochondrial-and-nuclear-genome-analyses
#17
Phillip A Morin, Andrew D Foote, C Scott Baker, Brittany L Hancock-Hanser, Kristin Kaschner, Bruce R Mate, Sarah L Mesnick, Victoria L Pease, Patricia E Rosel, Alana Alexander
Mitochondrial DNA has been heavily utilized in phylogeography studies for several decades. However, underlying patterns of demography and phylogeography may be misrepresented due to coalescence stochasticity, selection, variation in mutation rates, and cultural hitchhiking (linkage of genetic variation to culturally transmitted traits affecting fitness). Cultural hitchhiking has been suggested as an explanation for low genetic diversity in species with strong social structures, counteracting even high mobility, abundance and limited barriers to dispersal...
April 19, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29675891/association-of-the-hla-b27-antigen-and-the-ctla4-gene-ct60-rs3087243-polymorphism-with-ankylosing-spondylitis-in-algerian-population-a-case-control-study
#18
C A Dahmani, A Benzaoui, H Amroun, F Mecabih, F Z Sediki, F Zemani-Fodil, M Fodil, W Boughrara, B Mecheti, N Attal, N Mehtar, E Petit-Teixeira, A Boudjema
Ankylosing spondylitis (AS) is a complex inflammatory disease that represents a major health problem both in Algeria and worldwide. Several lines of evidence support that genetic risk factors play a role in AS etiology and the CTLA4 gene has attracted a considerable attention. In this study, we were interested in evaluating the HLA-B27 frequency and in exploring the CTLA4 gene in a sample of the North African population. The dataset of the current study is composed of 81 patients with AS and 123 healthy controls...
April 19, 2018: International Journal of Immunogenetics
https://www.readbyqxmd.com/read/29675634/investigation-of-circle-of-willis-variants-and-hemodynamic-parameters-in-twins-using-transcranial-color-coded-doppler-sonography
#19
Bianka Forgó, Ádám Domonkos Tárnoki, Dávid László Tárnoki, Levente Littvay, Corrado Fagnani, Maria Antonietta Stazi, Giorgio Meneghetti, Emanuela Medda, Filippo Farina, Claudio Baracchini
Morphological and hemodynamic variations of the circle of Willis (CW) may have an important impact on cerebrovascular events. However, the environmental and genetic influence remains unclear. For this reason we studied the variations and hemodynamic parameters of the CW in twins using transcranial color-coded sonography (TCCS). Sixty-four twins, 19 monozygotic (MZ) and 13 dizygotic (DZ) pairs from the Italian Twin Registry (average age 45.0 ± 13.7 years) underwent TCCS and risk factor assessment. We examined CW morphology and recorded peak systolic velocity (PSV), end-diastolic velocity (EDV) and pulsatility index (PI)...
April 19, 2018: International Journal of Cardiovascular Imaging
https://www.readbyqxmd.com/read/29675619/variation-in-allele-frequencies-at-the-bg112-locus-reveals-unequal-inheritance-of-nuclei-in-a-dikaryotic-isolate-of-the-fungus-rhizophagus-irregularis
#20
Frédéric G Masclaux, Tania Wyss, Ivan D Mateus-Gonzalez, Consolée Aletti, Ian R Sanders
The genetic state of the arbuscular mycorrhizal fungus species Rhizophagus irregularis differs among isolates, including both homokaryotic and dikaryotic isolates. Via the production of multi-nucleate axexual spores, siblings of dikaryotic isolates may inherit unequal frequencies of nucleotypes. Using bg112, a microsatellite marker, previous studies revealed that lines deriving from single spores of the dikaryotic R. irregularis isolate C3 differed in their proportions of different alleles. A genomic study of single nuclei of R...
April 19, 2018: Mycorrhiza
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