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Snp-snp interaction

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https://www.readbyqxmd.com/read/28800512/metabotropic-glutamate-receptors-as-emerging-research-targets-in-bipolar-disorder
#1
REVIEW
Caren J Blacker, Charles P Lewis, Mark A Frye, Marin Veldic
Glutamatergic dysregulation is implicated in the neuropathology of bipolar disorder (BD). There is increasing interest in investigating the role of metabotropic glutamate receptors (mGluRs) in BD and as a target for treatment intervention. Bipolar mGluR studies (published January 1992-April 2016) were identified via PubMed, Embase, Web of Science, and Scopus. Full-text screening, data extraction, and quality appraisal were conducted in duplicate, with strict inclusion and exclusion criteria. The initial literature search for mGluRs in BD, including non-bipolar mood disorders and primary psychotic disorders, identified 1544 articles...
July 31, 2017: Psychiatry Research
https://www.readbyqxmd.com/read/28794107/variation-in-recombination-rate-and-its-genetic-determinism-in-sheep-populations
#2
Morgane Petit, Jean-Michel Astruc, Julien Sarry, Laurence Drouilhet, Stéphane Fabre, Carole Moreno, Bertrand Servin
Recombination is a complex biological process that results from a cascade of multiple events during meiosis. Understanding the genetic determinism of recombination can help to understand if and how these events are interacting. To tackle this question, we studied the patterns of recombination in sheep, using multiple approaches and datasets. We constructed male recombination maps in a dairy breed from the south of France (the Lacaune breed) at a fine scale by combining meiotic recombination rates from a large pedigree genotyped with a 50K SNP array and historical recombination rates from a sample of unrelated individuals genotyped with a 600K SNP array...
August 9, 2017: Genetics
https://www.readbyqxmd.com/read/28792645/social-and-spatial-effects-on-genetic-variation-between-foraging-flocks-in-a-wild-bird-population
#3
Reinder Radersma, Colin J Garroway, Anna W Santure, Isabelle De Cauwer, Damien R Farine, Jon Slate, Ben C Sheldon
Social interactions are rarely random. In some instances animals exhibit homophily or heterophily, the tendency to interact with similar or dissimilar conspecifics respectively. Genetic homophily and heterophily influence the evolutionary dynamics of populations, because they potentially affect sexual and social selection. Here we investigate the link between social interactions and allele frequencies in foraging flocks of great tits (Parus major) over three consecutive years. We constructed co-occurrence networks which explicitly described the splitting and merging of 85,602 flocks through time (fission-fusion dynamics), at 60 feeding sites...
August 9, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28792098/identification-of-expression-quantitative-trait-loci-eqtls-in-human-peripheral-blood-mononuclear-cells-pbmcs-and-shared-with-liver-and-brain
#4
Pei He, Wei Xia, Lan Wang, Jian Wu, Yu-Fan Guo, Ke-Qin Zeng, Ming-Jun Wang, Peng-Fei Bing, Fang-Fei Xie, Xin Lu, Yong-Hong Zhang, Shu-Feng Lei, Fei-Yan Deng
PBMCs are essential for immunity and involved in various diseases. To identify genetic variations contributing to PBMCs transcriptome-wide gene expression, we performed a genome-wide eQTL analysis by using genome-wide SNPs data and transcriptome-wide mRNA expression data. To assess whether there are common regulation patterns shared among different tissues/organs, public datasets were utilized to identify common eQTLs shared with PBMCs in lymphoblastoid, monocytes, liver, and brain. Allelic expression imbalance (AEI) assay was employed to validate representative eQTLs identified...
August 9, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28770234/snps-linkage-disequilibrium-and-chronic-mountain-sickness-in-tibetan-chinese
#5
Norman E Buroker, Xue-Han Ning, Zhao-Nian Zhou, Kui Li, Wei-Jun Cen, Xiu-Feng Wu, Wei-Zhong Zhu, C Ronald Scott, Shi-Han Chen
Chronic mountain sickness (CMS) is estimated at 1.2% in Tibetans living at the Qinghai-Tibetan Plateau. Eighteen single-nucleotide polymorphisms (SNPs) from nine nuclear genes that have an association with CMS in Tibetans have been analyzed by using pairwise linkage disequilibrium (LD). The SNPs included are the angiotensin-converting enzyme (rs4340), the angiotensinogen (rs699), and the angiotensin II type 1 receptor (AGTR1) (rs5186) from the renin-angiotensin system. A low-density lipoprotein apolipoprotein B (rs693) SNP was also included...
2017: Hypoxia
https://www.readbyqxmd.com/read/28770004/discovery-and-replication-of-snp-snp-interactions-for-quantitative-lipid-traits-in-over-60-000-individuals
#6
Emily R Holzinger, Shefali S Verma, Carrie B Moore, Molly Hall, Rishika De, Diane Gilbert-Diamond, Matthew B Lanktree, Nathan Pankratz, Antoinette Amuzu, Amber Burt, Caroline Dale, Scott Dudek, Clement E Furlong, Tom R Gaunt, Daniel Seung Kim, Helene Riess, Suthesh Sivapalaratnam, Vinicius Tragante, Erik P A van Iperen, Ariel Brautbar, David S Carrell, David R Crosslin, Gail P Jarvik, Helena Kuivaniemi, Iftikhar J Kullo, Eric B Larson, Laura J Rasmussen-Torvik, Gerard Tromp, Jens Baumert, Karen J Cruickshanks, Martin Farrall, Aroon D Hingorani, G K Hovingh, Marcus E Kleber, Barbara E Klein, Ronald Klein, Wolfgang Koenig, Leslie A Lange, Winfried Mӓrz, Kari E North, N Charlotte Onland-Moret, Alex P Reiner, Philippa J Talmud, Yvonne T van der Schouw, James G Wilson, Mika Kivimaki, Meena Kumari, Jason H Moore, Fotios Drenos, Folkert W Asselbergs, Brendan J Keating, Marylyn D Ritchie
BACKGROUND: The genetic etiology of human lipid quantitative traits is not fully elucidated, and interactions between variants may play a role. We performed a gene-centric interaction study for four different lipid traits: low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), total cholesterol (TC), and triglycerides (TG). RESULTS: Our analysis consisted of a discovery phase using a merged dataset of five different cohorts (n = 12,853 to n = 16,849 depending on lipid phenotype) and a replication phase with ten independent cohorts totaling up to 36,938 additional samples...
2017: BioData Mining
https://www.readbyqxmd.com/read/28765081/intranasal-oxytocin-and-a-polymorphism-in-the-oxytocin-receptor-gene-are-associated-with-human-directed-social-behavior-in-golden-retriever-dogs
#7
Mia E Persson, Agaia J Trottier, Johan Bélteky, Lina S V Roth, Per Jensen
The oxytocin system may play an important role in dog domestication from the wolf. Dogs have evolved unique human analogue social skills enabling them to communicate and cooperate efficiently with people. Genomic differences in the region surrounding the oxytocin receptor (OXTR) gene have previously been associated with variation in dogs' communicative skills. Here we have utilized the unsolvable problem paradigm to investigate the effects of oxytocin and OXTR polymorphisms on human-directed contact seeking behavior in 60 golden retriever dogs...
July 29, 2017: Hormones and Behavior
https://www.readbyqxmd.com/read/28764923/association-of-rs1285933-single-nucleotide-polymorphism-in-clec5a-gene-with-dengue-severity-and-its-functional-effects
#8
Caroline Xavier-Carvalho, Renata Duarte da Silva Cezar, Naishe Matos Freire, Carla Mola, Victor Fiesta, Thiago Gomes de Toledo-Pinto, Luciana Gomes Fialho Torres, Rodrigo Feliciano do Carmo, Luydson Richardson Silva Vasconcelos, Marli Tenório Cordeiro, Paulo Baptista, Elzinandes Leal de Azeredo, Rivaldo Venâncio da Cunha, Luiz José de Souza, Antonio Guilherme Pacheco, Claire Fernandes Kubelka, Patrícia Moura, Milton Ozorio Moraes
Outbreaks of the Zika, dengue, and chikungunya viruses, especially in the Americas, pose a global threat due to their rapid spread and difficulty controlling the vector. Extreme phenotypes are often observed, from asymptomatic to severe clinical manifestations, which are well-studied in dengue. Host variations are also important contributors to disease outcomes, and many case-control studies have associated single nucleotide polymorphisms (SNPs) with severe dengue. Here, we found that the TC genotype and T-carriers for SNP rs1285933 in the C-type lectin superfamily member 5 (CLEC5A) gene was associated with severe dengue in a Northern Brazilian population (OR=2...
July 29, 2017: Human Immunology
https://www.readbyqxmd.com/read/28761931/unc5c-variants-are-associated-with-cerebral-amyloid-angiopathy
#9
Hyun-Sik Yang, Charles C White, Lori B Chibnik, Hans-Ulrich Klein, Julie A Schneider, David A Bennett, Philip L De Jager
OBJECTIVE: To determine whether common genetic variants in UNC5C, a recently identified late-onset Alzheimer disease (LOAD) dementia susceptibility gene, are associated with AD susceptibility or AD-related clinical/pathologic phenotypes. METHODS: We used data from deceased individuals of European descent who participated in the Religious Orders Study or the Rush Memory and Aging Project (n = 1,288). We examined whether there were associations between single nucleotide polymorphisms (SNPs) within ±100 kb of the UNC5C gene and a diagnosis of AD dementia, global cognitive decline, a pathologic diagnosis of AD, β-amyloid load, neuritic plaque count, diffuse plaque count, paired helical filament tau density, neurofibrillary tangle count, and cerebral amyloid angiopathy (CAA) score...
August 2017: Neurology. Genetics
https://www.readbyqxmd.com/read/28755387/bdnf-genotype-is-associated-with-hippocampal-volume-in-mild-traumatic-brain-injury
#10
J P Hayes, A Reagan, M W Logue, S M Hayes, N Sadeh, D R Miller, M Verfaellie, E J Wolf, R E McGlinchey, W P Milberg, A Stone, S A Schichman, M W Miller
The negative long-term effects of mild traumatic brain injury (mTBI) have been a growing concern in recent years, with accumulating evidence suggesting that mTBI combined with additional vulnerability factors may induce neurodegenerative-type changes in the brain. However, the factors instantiating risk for neurodegenerative disease following mTBI are unknown. This study examined the link between mTBI and brain derived neurotrophic factor (BDNF) genotype, which has previously been shown to regulate processes involved in neurodegeneration including synaptic plasticity and facilitation of neural survival through its expression...
July 28, 2017: Genes, Brain, and Behavior
https://www.readbyqxmd.com/read/28750074/dpp4-gene-variation-affects-glp-1-secretion-insulin-secretion-and-glucose-tolerance-in-humans-with-high-body-adiposity
#11
Anja Böhm, Robert Wagner, Fausto Machicao, Jens Juul Holst, Baptist Gallwitz, Norbert Stefan, Andreas Fritsche, Hans-Ulrich Häring, Harald Staiger
OBJECTIVE: Dipeptidyl-peptidase 4 (DPP-4) cleaves and inactivates the insulinotropic hormones glucagon-like peptide 1 (GLP-1) and gastric inhibitory polypeptide, collectively termed incretins. DPP-4 inhibitors entered clinical practice as approved therapeutics for type-2 diabetes in 2006. However, inter-individual variance in the responsiveness to DPP-4 inhibitors was reported. Thus, we asked whether genetic variation in the DPP4 gene affects incretin levels, insulin secretion, and glucose tolerance in participants of the TÜbingen Family study for type-2 diabetes (TÜF)...
2017: PloS One
https://www.readbyqxmd.com/read/28747474/male-female-relatedness-at-specific-snp-linkage-groups-influences-cryptic-female-choice-in-chinook-salmon-oncorhynchus-tshawytscha
#12
Cornelia Geßner, Sheri L Johnson, Paul Fisher, Shannon Clarke, Kim Rutherford, Jane Symonds, Neil J Gemmell
In a range of taxa, the relatedness between mates influences both pre- and post-mating processes of sexual selection. However, relatively little is known about the genetic loci facilitating such a bias, with the exception of the major histocompatibility complex. Here, we performed tightly controlled replicated in vitro fertilization trials to explore the impact of relatedness on two possible mechanisms of cryptic female choice (CFC) in Chinook salmon (Oncorhynchus tshawytscha). We tested (i) whether relatedness of mates, assessed using 682 single nucleotide polymorphisms (SNPs) on 29 SNP-linkage groups (LGs), biases a male's sperm velocity in ovarian fluid (a parameter previously shown to predict male fertilization success), and (ii) whether relatedness of mates governs fertilization success via other mechanisms, probably via sperm-egg interactions...
July 26, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28747436/the-alzheimer-s-disease-protective-cd33-splice-variant-mediates-adaptive-loss-of-function-via-diversion-to-an-intracellular-pool
#13
Shoib S Siddiqui, Stevan A Springer, Andrea Verhagen, Venkatasubramaniam Sundaramurthy, Frederico Alisson-Silva, Weiping Jiang, Pradipta Ghosh, Ajit Varki
The immunomodulatory receptor Siglec-3/CD33 influences risk for late-onset Alzheimers disease (LOAD), an apparently human-specific post-reproductive disease. CD33 generates two splice variants: a full-length CD33M transcript produced primarily by the LOAD-risk allele and a shorter CD33m isoform lacking the sialic acid-binding domain, produced primarily from the LOAD-protective allele. A SNP that modulates CD33 splicing to favor CD33m is associated with enhanced microglial activity. Individuals expressing more protective isoform accumulate less brain Beta-amyloid and have a lower LOAD risk...
July 26, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28747144/abcg2-c-421c-a-is-associated-with-outcomes-following-severe-traumatic-brain-injury
#14
Solomon M Adams, Yvette P Conley, Dianxu Ren, David O Okonkwo, Ava Puccio, C Edward Dixon, Robert Sb Clark, Patrick M Kochanek, Philip E Empey
Traumatic brain injury (TBI) is a leading cause of death with no pharmacologic treatments that improve outcomes. Transporter proteins participate in TBI recovery by maintaining the CNS biochemical milieu. Genetic variations in transporters that alter expression and/or function have been associated with TBI outcomes. The ATP-binding cassette transporter, ABCG2, is a uric acid (UA) transporter that effluxes UA from cells in the CNS and is responsible for systemic UA clearance. Uric acid is a CNS antioxidant and/or a biomarker that might support TBI recovery...
July 26, 2017: Journal of Neurotrauma
https://www.readbyqxmd.com/read/28744816/ace2-calm3-and-tnni3k-polymorphisms-as-potential-disease-modifiers-in-hypertrophic-and-dilated-cardiomyopathies
#15
Amit Kumar, Bindu Rani, Rajni Sharma, Gurjeet Kaur, Rishikesh Prasad, Ajay Bahl, Madhu Khullar
The marked clinical and genetic heterogeneity seen in hypertrophic (HCM) and dilated cardiomyopathies (DCM) suggests involvement of disease modifiers and environmental factors in the pathophysiology of these diseases. In the current study, we examined association of single nucleotide polymorphisms (SNPs) of three candidate genes, ACE2 (rs6632677), TNNI3K (rs49812611) and CALM3 (rs13477425) with clinical phenotypes of HCM and DCM patients of North Indian ethnicity. Prevalence of ACE2 (7160726 C>G) variant genotypes (CG and GG) was significantly higher in DCM subjects as compared to controls...
July 25, 2017: Molecular and Cellular Biochemistry
https://www.readbyqxmd.com/read/28743890/polymorphism-in-ercc1-confers-susceptibility-of-coronary-artery-disease-and-severity-of-coronary-artery-atherosclerosis-in-a-chinese-han-population
#16
Shuai Zhang, Xue-Bin Wang, Ya-di Han, Chen-Ling Xiong, Ye Zhou, Chen Wang, Ze-Jin Liu, Na Yang, Fang Zheng
Excision repair cross-complementing 1 (ERCC1) gene encodes ERCC1 protein, which is mainly responsible for the repair of DNA damage in different diseases including coronary artery atherosclerosis by acting as a rate-limiting element in nucleotide excision repair (NER). Using a three-stage case-control study with 3037 coronary artery disease (CAD) patients and 3002 controls, we investigated associations of three single nucleotide polymorphisms (SNPs) with CAD risk and severity of coronary artery atherosclerosis in Chinese Han population...
July 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28740106/environment-changes-genetic-effects-on-respiratory-conditions-and-allergic-phenotypes
#17
Yong Song, Michelle J Schwager, Vibeke Backer, Jing Guo, Celeste Porsbjerg, Siew-Kim Khoo, Ingrid A Laing, Eric K Moses, Peter LeSouëf, Guicheng Brad Zhang
The prevalence of asthma and allergic diseases is disproportionately distributed among different populations, with an increasing trend observed in Western countries. Here we investigated how the environment affected genotype-phenotype association in a genetically homogeneous, but geographically separated population. We evaluated 18 single nucleotide polymorphisms (SNPs) corresponding to 8 genes (ADAM33, ALOX5, LT-α, LTC4S, NOS1, ORMDL3, TBXA2R and TNF-α), the lung function and five respiratory/allergic conditions (ever asthma, bronchitis, rhinitis, dermatitis and atopy) in two populations of Inuit residing either in the westernized environment of Denmark or in the rural area of Greenland...
July 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28739304/role-of-nadphox-rho-kinase-signaling-in-the-cyclosporine-nsaids-interactions-on-blood-pressure-and-baroreflexes-in-female-rats
#18
Hanan M El-Gowelli, Karim S Ibrahim, Ahmed F El-Yazbi, Mahmoud M El-Mas
AIMS: The hypertensive effect of the immunosuppressant drug cyclosporine (CSA) is paralleled, and probably triggered, by impaired arterial baroreceptor sensitivity (BRS). Here we asked if these effects of CSA are influenced by co-administration of nonsteroidal antiinflammatory drugs (NSAIDs) and if the oxidative NADPH-oxidase (NADPHox)/Rho-kinase (ROCK) pathway mediates this interaction. MATERIALS AND METHODS: Female rats were treated for 10days with CSA (25mg/kg/day), diclofenac (DIC, COX-1/COX-2 inhibitor, 1mg/kg/day), celecoxib (COX-2 inhibitor, 10mg/kg/day), or their combinations...
July 21, 2017: Life Sciences
https://www.readbyqxmd.com/read/28738859/genes-and-pathways-underlying-susceptibility-to-impaired-lung-function-in-the-context-of-environmental-tobacco-smoke-exposure
#19
K de Jong, J M Vonk, M Imboden, L Lahousse, A Hofman, G G Brusselle, N M Probst-Hensch, D S Postma, H M Boezen
BACKGROUND: Studies aiming to assess genetic susceptibility for impaired lung function levels upon exposure to environmental tobacco smoke (ETS) have thus far focused on candidate-genes selected based on a-priori knowledge of potentially relevant biological pathways, such as glutathione S-transferases and ADAM33. By using a hypothesis-free approach, we aimed to identify novel susceptibility loci, and additionally explored biological pathways potentially underlying this susceptibility to impaired lung function in the context of ETS exposure...
July 24, 2017: Respiratory Research
https://www.readbyqxmd.com/read/28738682/prototropically-allosteric-probe-for-superbly-selective-dna-analysis
#20
Fan Lin, Yufeng Zhou, Qiusha Li, Xiaoshun Zhou, Yong Shao, Benoit Habermeyer, Hui Wang, Xinghua Shi, Zhiai Xu
Selective nucleotide recognition for biosensor evolution requires rational probe design toward the binding-pattern-susceptible readout but without serious poison in selectivity from the context sequences. In this work, we synthesized a dual-function (trihydroxyphenyl)porphyrin (POH3) to target the abasic site (AP site) in ds-DNA using the trihydroxyphenyl substituent and the tetrapyrrole macrocycle as the recognition unit (RU) and the fluorescent signal unit (SU), respectively. RU and SU are separated from each other but are prototropically allosteric...
August 11, 2017: Analytical Chemistry
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