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1.
Hum Mol Genet ; 31(21): 3643-3651, 2022 10 28.
Article in English | MEDLINE | ID: mdl-35357430

ABSTRACT

Obesity has a highly complex genetic architecture, making it difficult to understand the genetic mechanisms, despite the large number of discovered loci via genome-wide association studies (GWAS). Omics techniques have provided a better resolution to view this problem. As a proxy of cell-level biology, extracellular vesicles (EVs) are useful for studying cellular regulation of complex phenotypes such as obesity. Here, in a well-established Scottish cohort, we utilized a novel technology to detect surface proteins across millions of single EVs in each individual's plasma sample. Integrating the results with established obesity GWAS, we inferred 78 types of EVs carrying one or two of 12 surface proteins to be associated with adiposity-related traits such as waist circumference. We then verified that particular EVs' abundance is negatively correlated with body adiposity, while no association with lean body mass. We also revealed that genetic variants associated with protein-specific EVs capture 2-4-fold heritability enrichment for blood cholesterol levels. Our findings provide evidence that EVs with specific surface proteins have phenotypic and genetic links to obesity and blood lipids, respectively, guiding future EV biomarker research.


Subject(s)
Extracellular Vesicles , Obesity , Humans , Extracellular Vesicles/genetics , Genome-Wide Association Study , Membrane Proteins/genetics , Obesity/genetics , Phenotype
2.
Heredity (Edinb) ; 133(1): 11-20, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38822132

ABSTRACT

Genome-wide association study (GWAS) is a powerful tool to identify genomic loci underlying complex traits. However, the application in natural populations comes with challenges, especially power loss due to population stratification. Here, we introduce a bivariate analysis approach to a GWAS dataset of Arabidopsis thaliana. We demonstrate the efficiency of dual-phenotype analysis to uncover hidden genetic loci masked by population structure via a series of simulations. In real data analysis, a common allele, strongly confounded with population structure, is discovered to be associated with late flowering and slow maturation of the plant. The discovered genetic effect on flowering time is further replicated in independent datasets. Using Mendelian randomization analysis based on summary statistics from our GWAS and expression QTL scans, we predicted and replicated a candidate gene AT1G11560 that potentially causes this association. Further analysis indicates that this locus is co-selected with flowering-time-related genes. The discovered pleiotropic genotype-phenotype map provides new insights into understanding the genetic correlation of complex traits.


Subject(s)
Arabidopsis , Flowers , Genome-Wide Association Study , Phenotype , Quantitative Trait Loci , Arabidopsis/genetics , Genome-Wide Association Study/methods , Flowers/genetics , Polymorphism, Single Nucleotide , Genotype , Models, Genetic , Genetics, Population , Computer Simulation , Alleles , Genome, Plant , Mendelian Randomization Analysis
3.
Circulation ; 145(18): 1398-1411, 2022 05 03.
Article in English | MEDLINE | ID: mdl-35387486

ABSTRACT

BACKGROUND: SARS-CoV-2, the causal agent of COVID-19, enters human cells using the ACE2 (angiotensin-converting enzyme 2) protein as a receptor. ACE2 is thus key to the infection and treatment of the coronavirus. ACE2 is highly expressed in the heart and respiratory and gastrointestinal tracts, playing important regulatory roles in the cardiovascular and other biological systems. However, the genetic basis of the ACE2 protein levels is not well understood. METHODS: We have conducted the largest genome-wide association meta-analysis of plasma ACE2 levels in >28 000 individuals of the SCALLOP Consortium (Systematic and Combined Analysis of Olink Proteins). We summarize the cross-sectional epidemiological correlates of circulating ACE2. Using the summary statistics-based high-definition likelihood method, we estimate relevant genetic correlations with cardiometabolic phenotypes, COVID-19, and other human complex traits and diseases. We perform causal inference of soluble ACE2 on vascular disease outcomes and COVID-19 severity using mendelian randomization. We also perform in silico functional analysis by integrating with other types of omics data. RESULTS: We identified 10 loci, including 8 novel, capturing 30% of the heritability of the protein. We detected that plasma ACE2 was genetically correlated with vascular diseases, severe COVID-19, and a wide range of human complex diseases and medications. An X-chromosome cis-protein quantitative trait loci-based mendelian randomization analysis suggested a causal effect of elevated ACE2 levels on COVID-19 severity (odds ratio, 1.63 [95% CI, 1.10-2.42]; P=0.01), hospitalization (odds ratio, 1.52 [95% CI, 1.05-2.21]; P=0.03), and infection (odds ratio, 1.60 [95% CI, 1.08-2.37]; P=0.02). Tissue- and cell type-specific transcriptomic and epigenomic analysis revealed that the ACE2 regulatory variants were enriched for DNA methylation sites in blood immune cells. CONCLUSIONS: Human plasma ACE2 shares a genetic basis with cardiovascular disease, COVID-19, and other related diseases. The genetic architecture of the ACE2 protein is mapped, providing a useful resource for further biological and clinical studies on this coronavirus receptor.


Subject(s)
Angiotensin-Converting Enzyme 2 , COVID-19 , Angiotensin-Converting Enzyme 2/genetics , COVID-19/genetics , Cross-Sectional Studies , Genome-Wide Association Study , Humans , Receptors, Coronavirus , SARS-CoV-2
4.
Am J Hum Genet ; 101(6): 903-912, 2017 Dec 07.
Article in English | MEDLINE | ID: mdl-29198721

ABSTRACT

In recent years, as a secondary analysis in genome-wide association studies (GWASs), conditional and joint multiple-SNP analysis (GCTA-COJO) has been successful in allowing the discovery of additional association signals within detected loci. This suggests that many loci mapped in GWASs harbor more than a single causal variant. In order to interpret the underlying mechanism regulating a complex trait of interest in each discovered locus, researchers must assess the magnitude of allelic heterogeneity within the locus. We developed a penalized selection operator for jointly analyzing multiple variants (SOJO) within each mapped locus on the basis of LASSO (least absolute shrinkage and selection operator) regression derived from summary association statistics. We found that, compared to stepwise conditional multiple-SNP analysis, SOJO provided better sensitivity and specificity in predicting the number of alleles associated with complex traits in each locus. SOJO suggested causal variants potentially missed by GCTA-COJO. Compared to using top variants from genome-wide significant loci in GWAS, using SOJO increased the proportion of variance prediction for height by 65% without additional discovery samples or additional loci in the genome. Our empirical results indicate that human height is not only a highly polygenic trait, but also has high allelic heterogeneity within its established hundreds of loci.


Subject(s)
Body Height/genetics , Multifactorial Inheritance/genetics , Polymorphism, Single Nucleotide/genetics , Alleles , Body Mass Index , Genome-Wide Association Study , Humans , Quantitative Trait Loci
5.
Med Sci Monit ; 22: 969-76, 2016 Mar 24.
Article in English | MEDLINE | ID: mdl-27009380

ABSTRACT

BACKGROUND: Risk of venous thromboembolism (VTE), including deep vein thrombosis (DVT) and pulmonary embolism (PE), may be increased in liver cirrhosis. We conducted a single-center study to explore the epidemiology, risk factors, and in-hospital mortality of VTE in Chinese patients with liver cirrhosis. MATERIAL/METHODS: All patients with liver cirrhosis who were consecutively admitted to our hospital between January 2011 and December 2013 were retrospectively included. RESULTS: Of 2006 patients with liver cirrhosis included, 9 patients were diagnosed with or developed VTE during hospitalization, including 5 patients with a previous history of DVT, 1 patient with either a previous history of DVT or new onset of PE, and 3 patients with new onset of VTE (PE, n=1; DVT, n=2). Risk factors for VTE included a significantly higher proportion of hypertension and significantly higher red blood cells, hemoglobin, alanine aminotransferase, aspartate aminotransferase, prothrombin time (PT), international normalized ratio (INR), D-dimer, and Child-Pugh scores. The in-hospital mortality was significantly higher in patients with VTE than those without VTE (33.3% [3/9] versus 3.4% [67/1997], P<0.001). CONCLUSIONS: VTE was observed in 0.4% of patients with liver cirrhosis during hospitalization and it significantly increased the in-hospital mortality. Elevated PT/INR aggravated the risk of VTE.


Subject(s)
Hospital Mortality , Liver Cirrhosis/mortality , Venous Thromboembolism/mortality , Adult , Aged , Aged, 80 and over , China/epidemiology , Female , Humans , Male , Middle Aged , Multivariate Analysis , Retrospective Studies , Risk Factors
6.
Med Sci Monit ; 22: 2528-50, 2016 Jul 19.
Article in English | MEDLINE | ID: mdl-27432511

ABSTRACT

BACKGROUND Portal venous system thrombosis (PVST) is a life-threatening complication of liver cirrhosis. We conducted a retrospective study to comprehensively analyze the prevalence and risk factors of PVST in liver cirrhosis. MATERIAL AND METHODS All cirrhotic patients without malignancy admitted between June 2012 and December 2013 were eligible if they underwent contrast-enhanced CT or MRI scans. Independent predictors of PVST in liver cirrhosis were calculated in multivariate analyses. Subgroup analyses were performed according to the severity of PVST (any PVST, main portal vein [MPV] thrombosis >50%, and clinically significant PVST) and splenectomy. Odds ratios (ORs) and 95% confidence intervals (CIs) were reported. RESULTS Overall, 113 cirrhotic patients were enrolled. The prevalence of PVST was 16.8% (19/113). Splenectomy (any PVST: OR=11.494, 95%CI=2.152-61.395; MPV thrombosis >50%: OR=29.987, 95%CI=3.247-276.949; clinically significant PVST: OR=40.415, 95%CI=3.895-419.295) and higher hemoglobin (any PVST: OR=0.974, 95%CI=0.953-0.996; MPV thrombosis >50%: OR=0.936, 95%CI=0.895-0.980; clinically significant PVST: OR=0.935, 95%CI=0.891-0.982) were the independent predictors of PVST. The prevalence of PVST was 13.3% (14/105) after excluding splenectomy. Higher hemoglobin was the only independent predictor of MPV thrombosis >50% (OR=0.952, 95%CI=0.909-0.997). No independent predictors of any PVST or clinically significant PVST were identified in multivariate analyses. Additionally, PVST patients who underwent splenectomy had a significantly higher proportion of clinically significant PVST but lower MELD score than those who did not undergo splenectomy. In all analyses, the in-hospital mortality was not significantly different between cirrhotic patient with and without PVST. CONCLUSIONS Splenectomy may increase by at least 10-fold the risk of PVST in liver cirrhosis independent of severity of liver dysfunction.


Subject(s)
Liver Cirrhosis/complications , Splenectomy/adverse effects , Venous Thrombosis/etiology , Adult , Aged , Aged, 80 and over , Cohort Studies , Female , Hospital Mortality , Humans , Liver Cirrhosis/diagnostic imaging , Liver Cirrhosis/pathology , Male , Middle Aged , Portal Vein/pathology , Prevalence , Retrospective Studies , Risk Factors , Venous Thrombosis/diagnostic imaging , Venous Thrombosis/pathology
7.
Ecotoxicol Environ Saf ; 111: 1-8, 2015 Jan.
Article in English | MEDLINE | ID: mdl-25450909

ABSTRACT

Indoor environment is an important source of human exposure to several toxicants, such as brominated flame retardants. Indoor dust samples were collected in winter season in 2010, which covered 23 provinces across China, for the analysis of polybrominated diphenyl ethers (PBDEs). Concentrations of PBDEs (Σ14PBDEs) ranged from 8.92 to 37,500 ng/g, with the mean of 3520 ng/g. BDE-209 was the most dominate congener, followed by BDE-183, BDE-47 and BDE-99. PBDE concentrations and the longitude were significantly correlated (p<0.05), which was consistent with the status of social-economic development and human activities. The results of exposure to PBDEs through dust ingestion and dermal absorption indicated that the toddlers had the highest exposure dose, with the median value of 6.0 ng/kg-bw/day. According to the hazard quotients, health risk of PBDEs via dust ingestion in China is currently acceptable. Monte Carlo simulation was implemented to quantify the uncertainty and sensitivity of exposure models for determining the most influential variables. The results suggested that more specific and accurate parameters should be used for dust ingestion and dermal absorption exposure models in future.


Subject(s)
Air Pollution, Indoor/analysis , Dust/analysis , Environmental Exposure/analysis , Flame Retardants/analysis , Halogenated Diphenyl Ethers/analysis , Adolescent , Adult , Child , Child, Preschool , China , Humans , Infant , Young Adult
8.
Aging (Albany NY) ; 16(12): 10424-10434, 2024 06 14.
Article in English | MEDLINE | ID: mdl-38885061

ABSTRACT

Microbial infection-induced sepsis causes excessive inflammatory response and multiple organ failure. An effective strategy for the treatment of sepsis-related syndromes is still needed. Rosuvastatin, a typical ß-hydroxy ß-methylglutaryl-CoA reductase inhibitor licensed for reducing the levels of low-density lipoprotein cholesterol in patients with hyperlipidemia, has displayed anti-inflammatory capacity in different types of organs and tissues. However, its effects on the development of sepsis are less reported. Here, we found that the administration of Rosuvastatin reduced the mortality of sepsis mice and prevented body temperature loss. Additionally, it inhibited the production of inflammatory cytokines such as tumor necrosis factor (TNF-α), Interleukin-6 (IL-6), interleukin-1ß (IL-1ß), and migration inhibitory factor (MIF) in peritoneal lavage supernatants of animals. The increased number of mononuclear cells in the peritoneum of sepsis mice was reduced by Rosuvastatin. Interestingly, it ameliorated lung inflammation and improved the hepatic and renal function in the sepsis animals. Further in vitro experiments show that Rosuvastatin inhibited lipopolysaccharide (LPS)-induced production of proinflammatory cytokines in RAW 264.7 macrophages by preventing the activation of nuclear factor kappa-B (NF-κB). Our findings demonstrate that the administration of Rosuvastatin hampered organ dysfunction and mitigated inflammation in a relevant model of sepsis.


Subject(s)
Inflammation , Rosuvastatin Calcium , Sepsis , Animals , Rosuvastatin Calcium/pharmacology , Rosuvastatin Calcium/therapeutic use , Sepsis/drug therapy , Mice , RAW 264.7 Cells , Inflammation/drug therapy , Inflammation/metabolism , Cytokines/metabolism , Male , Hydroxymethylglutaryl-CoA Reductase Inhibitors/pharmacology , Hydroxymethylglutaryl-CoA Reductase Inhibitors/therapeutic use , NF-kappa B/metabolism , Lipopolysaccharides , Mice, Inbred C57BL , Anti-Inflammatory Agents/pharmacology , Anti-Inflammatory Agents/therapeutic use , Disease Models, Animal
9.
Arch Environ Contam Toxicol ; 65(3): 611-8, 2013 Oct.
Article in English | MEDLINE | ID: mdl-23744051

ABSTRACT

Parabens are widely used as preservatives in foods, cosmetics, and pharmaceuticals. However, recent studies have indicated that high and systemic exposure to parabens can be harmful to human health. Although a few studies have reported urinary paraben levels in western countries, studies on paraben exposure in the Chinese population are limited. China is currently a major producer of parabens in the world. In this study, 109 urine samples collected from Chinese young adults (approximately 20 years old) were analyzed for five parabens (methyl-, ethyl-, propyl-, butyl-, and benzyl-parabens) by high-performance liquid chromatography-tandem mass spectrometry. Methyl-, propyl-, and ethyl-parabens were the three major paraben analogues found in all (100%) samples. The concentration of the sum of the five parabens ranged from 0.82 to 728 ng/mL with a geometric mean value of 17.4 ng/mL. Urinary concentration of parabens was 2-fold greater in females than in males. Based on the measured urinary concentrations, daily intake of parabens by the Chinese young adults was estimated and compared with those reported for United States adults. The estimated daily intakes (EDIurine) of parabens were 18.4 and 40.8 µg/kg bw/day for Chinese males and females, respectively, values that were lower than those reported for United States adults (74.7 µg/kg bw/day). Based on the reported concentrations of parabens in foods from China and the United States, the contribution of dietary intake to EDIurine was estimated to be 5.5, 2.6, and 0.42% for Chinese males, Chinese females, and United States adults, respectively, which indicates the significance of nondietary sources of parabens to human exposures.


Subject(s)
Cosmetics/metabolism , Environmental Exposure , Environmental Pollutants/urine , Food Preservatives/metabolism , Parabens/metabolism , Preservatives, Pharmaceutical/metabolism , China , Chromatography, High Pressure Liquid , Diet , Environmental Monitoring , Female , Humans , Male , Sex Characteristics , Tandem Mass Spectrometry , Young Adult
10.
Bull Environ Contam Toxicol ; 91(6): 640-4, 2013 Dec.
Article in English | MEDLINE | ID: mdl-24045861

ABSTRACT

Fourteen indoor dust samples were collected in 2010 winter from four cities in Heilongjiang Province, China. Fourteen polybrominated diphenyl ethers (PBDEs) were identified and quantified. Concentration of the total 14 PBDEs ranged from 240 to 9,270 ng/g, with the median of 2,520 ng/g. BDE209 was the dominant congener with concentrations ranged from 234 to 9,190 ng/g, accounting for 97.2 % of the total concentration. Positive correlations (r > 0.8, p < 0.005) were found between the group of BDE17, 28, 66, 47 and the group of BDE85, 99, 100, between BDE153 and BDE154, between BDE209 and BDE183, indicating the similar sources and/or pathways in indoor environment. Principal component analysis showed that the major sources of PBDEs were commercial Penta-BDEs and Deca-BDEs. Human exposure analysis showed that children of 1-5 years old had the highest exposure to PBDEs.


Subject(s)
Air Pollution, Indoor/analysis , Dust/analysis , Environmental Exposure/analysis , Halogenated Diphenyl Ethers/analysis , Air Pollution, Indoor/statistics & numerical data , China , Environmental Exposure/statistics & numerical data , Environmental Monitoring , Humans , Principal Component Analysis
11.
Environ Sci Pollut Res Int ; 30(25): 66936-66946, 2023 May.
Article in English | MEDLINE | ID: mdl-37099107

ABSTRACT

Phthalic acid esters (PAEs), a class of typical endocrine disruptors, have received considerable attention due to their widespread applications and adverse effects on biological health. In this study, 30 water samples, along the mainstream of the Yangtze River (YR), were collected from Chongqing (upper stream) to Shanghai (estuary) from May to June in 2019. The total concentrations of 16 targeted PAEs ranged from 0.437 to 20.5 µg/L, with an average of 1.93 µg/L, where dibutyl phthalate (DBP, 0.222-20.2 µg/L), bis (2-ethylhexyl) phthalate (DEHP, 0.254-7.03 µg/L), and diisobutyl phthalate (DIBP, 0.0645-0.621 µg/L) were the most abundant PAEs. According to the pollution level in the YR to assess the ecological risk posed by PAEs, the results showed medium risk level of PAEs in the YR, among which DBP and DEHP posed a high ecological risk to aquatic organisms. The optimal solution for DBP and DEHP is found in ten fitting curves. The PNECSSD of them is 2.50 µg/L and 0.34 µg/L, respectively.


Subject(s)
Diethylhexyl Phthalate , Water Pollutants, Chemical , Water , China , Esters , Water Pollutants, Chemical/analysis , Risk Assessment
12.
Front Genet ; 13: 798269, 2022.
Article in English | MEDLINE | ID: mdl-35444688

ABSTRACT

Integrating genome-wide association studies (GWAS) with transcriptomic data, human complex traits and diseases have been linked to relevant tissues and cell types using different methods. However, different results from these methods generated confusion while no gold standard is currently accepted, making it difficult to evaluate the discoveries. Here, applying three methods on the same data source, we estimated the sensitivity and specificity of these methods in the absence of a gold standard. We established a more specific tissue-trait association atlas by combining the information captured by different methods. Our triangulation strategy improves the performance of existing methods in establishing tissue-trait associations. The results provide better etiological and functional insights for the tissues underlying different human complex traits and diseases.

13.
Sci Total Environ ; 817: 152998, 2022 Apr 15.
Article in English | MEDLINE | ID: mdl-35031376

ABSTRACT

Terrestrial water storage is a crucial component in water cycle and plays an important role in flood formations process, particularly in a changing environment. In this study, we aim to examine the future variation of terrestrial water storage anomaly (TWSA) and associated flood potential in one of the most flood-prone regions, the Yangtze River basin in China. Using the Gravity Recovery and Climate Experiment (GRACE) data, we perform bias correction for seven general circulation models (GCMs) from the Coupled Model Intercomparison Project Phase 6 under three Shared Socio-economic Pathway (SSP) scenarios: SSP126, SSP245, and SSP585. The spatiotemporal characteristics of changes in future Flood Potential Index are projected and compared between the near (2031-2060) and far (2071-2100) future with reference to the historical period (1985-2014). The results show that GCMs-simulated TWSA generally agrees well with the GRACE results after downscaling and bias correction with the average correlation coefficient of 0.86, Nash-Sutcliffe efficiency of 0.73 and the root mean square error of 21.68 mm. We found that the total variance of projected TWSA is mainly sourced from the internal variability and model uncertainties, while the uncertainties in scenarios contribute relatively less. Moreover, the flood potential is projected to decline during the near future under various scenarios and even lower during the far future under SSP585 scenario. Our findings provide implications for flood control and management under climate change over high flood risk regions worldwide.


Subject(s)
Floods , Rivers , Climate Change , Water , Water Cycle
14.
Front Genet ; 12: 665252, 2021.
Article in English | MEDLINE | ID: mdl-34504513

ABSTRACT

Estimating the phenotypic correlations between complex traits and diseases based on their genome-wide association summary statistics has been a useful technique in genetic epidemiology and statistical genetics inference. Two state-of-the-art strategies, Z-score correlation across null-effect single nucleotide polymorphisms (SNPs) and LD score regression intercept, were widely applied to estimate phenotypic correlations. Here, we propose an improved Z-score correlation strategy based on SNPs with low minor allele frequencies (MAFs), and show how this simple strategy can correct the bias generated by the current methods. The low MAF estimator improves phenotypic correlation estimation, thus it is beneficial for methods and applications using phenotypic correlations inferred from summary association statistics.

15.
Sci Prog ; 104(3_suppl): 368504211054256, 2021 Sep.
Article in English | MEDLINE | ID: mdl-34851210

ABSTRACT

INTRODUCTION: Curriculum learning through the wisdom tree massive open online course platform not only gets rid of the limitations of specialty, school and region, eliminates the limitations of time and space in traditional teaching, but also effectively solves the problem of educational equity. OBJECTIVES: This paper proposes an intelligent algorithm combining decision tree, support vector machine, and simulated annealing to obtain the best classification accuracy and decision rules for university students' satisfaction with the wisdom tree massive open online course platform. METHODS: This study takes the university students in Fuzhou city information management department as the survey object, and adopts the electronic questionnaire survey method. A total of 1136 formal questionnaires were responded, and 1028 valid questionnaires were obtained after data cleaning and deleting invalid questionnaires (the effective rate was 90.49%). In this paper, the reliability and validity of the questionnaire were tested by IBM SPSS-20.0 software, and six explanatory variables including function, achievement, exercise, quality, richness, and interaction were obtained by principal component analysis. Then, the questionnaire data is converted to CSV (comma separated values) format for analysis. This paper proposes an intelligent algorithm combining decision tree, support vector machine, and simulated annealing to obtain the best classification accuracy and decision rules for university students' satisfaction with the wisdom tree massive open online course platform. In this paper, the proposed algorithm is compared with decision tree, random forest, k-nearest neighbor, and support vector machine to verify its performance. RESULTS: The experimental results show that training set classification accuracy of decision tree, random forest, k-nearest neighbor, only support vector machine and the proposed algorithm (simulated annealing + support vector machine) are 92.21%, 96.10%, 95.67%, 97.29%, and 99.58%, respectively. CONCLUSION: The proposed algorithm simulated annealing + support vector machine does increase the classification accuracy. At the same time, the 11 decision rules generated by simulated annealing + decision tree can provide useful information for decision makers.


Subject(s)
Education, Distance , Algorithms , Humans , Personal Satisfaction , Reproducibility of Results , Students , Universities
16.
Nat Commun ; 12(1): 2845, 2021 05 14.
Article in English | MEDLINE | ID: mdl-33990588

ABSTRACT

Quantifying the overall magnitude of every single locus' genetic effect on the widely measured human phenome is of great challenge. We introduce a unified modelling technique that can consistently provide a total genetic contribution assessment (TGCA) of a gene or genetic variant without thresholding genetic association signals. Genome-wide TGCA in five UK Biobank phenotype domains highlights loci such as the HLA locus for medical conditions, the bone mineral density locus WNT16 for physical measures, and the skin tanning locus MC1R and smoking behaviour locus CHRNA3 for lifestyle. Tissue-specificity investigation reveals several tissues associated with total genetic contributions, including the brain tissues for mental health. Such associations are driven by tissue-specific gene expressions, which share genetic basis with the total genetic contributions. TGCA can provide a genome-wide atlas for the overall genetic contributions in each particular domain of human complex traits.


Subject(s)
Genome, Human , Models, Genetic , Biological Specimen Banks/statistics & numerical data , Computer Simulation , Genome-Wide Association Study/statistics & numerical data , Humans , Molecular Sequence Annotation/statistics & numerical data , Multifactorial Inheritance/genetics , Organ Specificity/genetics , Phenotype , Polymorphism, Single Nucleotide , Quantitative Trait Loci
17.
Front Genet ; 12: 627989, 2021.
Article in English | MEDLINE | ID: mdl-33613642

ABSTRACT

The ever-growing genome-wide association studies (GWAS) have revealed widespread pleiotropy. To exploit this, various methods that jointly consider associations of a genetic variant with multiple traits have been developed. Most efforts have been made concerning improving GWAS discovery power. However, how to replicate these discovered pleiotropic loci has yet to be discussed thoroughly. Unlike a single-trait scenario, multi-trait replication is not trivial considering the underlying genotype-multi-phenotype map of the associations. Here, we evaluate four methods for replicating multi-trait associations, corresponding to four levels of replication strength. Weak replication cannot justify pleiotropic genetic effects, whereas strong replication using our developed correlation methods can inform consistent pleiotropic genetic effects across the discovery and replication samples. We provide a protocol for replicating multi-trait genetic associations in practice. The described methods are implemented in the free and open-source R package MultiABEL.

18.
Sci Total Environ ; 769: 145218, 2021 May 15.
Article in English | MEDLINE | ID: mdl-33736268

ABSTRACT

Bisphenol A (BPA) is a well-known xenoestrogen, and UV/H2O2 advanced oxidation process (AOP) is one of the most effective technologies to remove BPA from water. Using BPA spiked tap water, a batch-scale photochemical experiment was conducted to investigate whether BPA can pose a genotoxicity concern during the medium pressure (MP) UV/H2O2 treatment and the post-chloramination. Samples at different UV exposure and post-chloramination durations were collected and analyzed by CALUX® gene reporter assays regarding estrogen receptor α (ERα) and p53 transcriptional activity. MP UV/H2O2 process did not cause extra estrogenic effects from the degradation of BPA, whereas genotoxicity occurred when the treated water was exposed with monochloramine. Seven frequently reported nitrogenous disinfection byproducts (N-DBPs) were detected, but none of them were responsible for the observed genotoxicity. Employed with gas chromatography-quadrupole time-of-flight mass spectrometry (GC-QTOF-MS), four compounds possibly contributed to the genotoxicity were tentatively identified and two of them with aminooxy- or cyano- group were considered as "new" N-DBPs. This study demonstrated that by-products differ from their parent compounds in toxicity can be formed in the UV oxidation with post-disinfection process, which should become a cause for concern.


Subject(s)
Water Pollutants, Chemical , Water Purification , Benzhydryl Compounds , Biological Assay , Disinfection , Hydrogen Peroxide , Phenols , Ultraviolet Rays , Water Pollutants, Chemical/analysis , Water Pollutants, Chemical/toxicity
19.
Chemosphere ; 273: 128860, 2021 Jun.
Article in English | MEDLINE | ID: mdl-33218730

ABSTRACT

The logarithm of gas/particle (G/P) partition quotient (logKP) has been found to have a linear relationship with logKOA (octanol-air partition coefficient) with slope mo and intercept bo and logPL (subcooled liquid vapor pressure) with slope mp and intercept bp. In the sister paper of the present work, analytical equations to predict the slope mo and intercept bo based on logKOA and predict the slope mp and intercept bp based on logPL are developed using steady state theory. In this work, the equations are evaluated using world-wide monitoring data (262 pairs for mo and bo values and 292 pairs for mp and bp values produced from more than 10,000 monitiring data worldwide) for selected seven groups of semi-volatile organic compounds (SVOCs), including polybrominated diphenyl ethers (PBDEs), polychlorinated dibenzo-p-dioxins and polychorinated dibenzofurans (PCDD/Fs), polyclorinated biphenyl (PCBs), polycyclic aromatic hydrocarbons (PAHs), polychlorinated naphthalenes (PCNs), organochlorinated pesticides (OCPs), novel brominated flame retardants (NBFRs), and other selected halogenated flame retardants. The slopes and intercepts predicted by the steady state equations reproduce the trends observed in monitoring regression results for the seven SVOC groups, with 44.4% of the variation of monitoring mo values accounted for by logKOA and 48.2% of the variation of monitoring mp values accounted for by logPL. Theoretically, the values of mo can be any value between 0 and 1 dependent on the values of KOA, and are not constrained to 1 as in equilibrium theory. Likewise, the values of mp can be any value between 0 and -1 dependent on the values of PL, and not constrained to -1 predicted by the equilibrium theory. The influence of sampling artifacts on the G/P partitioning of SVOCs has most likely been overemphasized by the equilibrium theory. Thus, the equilibrium approach should be abandoned in favor of the steady state approach for calculating the G/P partition quotients for SVOCs with high KOA values (>1011.38) or low PL values (<10-4.92).


Subject(s)
Air Pollutants , Polychlorinated Dibenzodioxins , Volatile Organic Compounds , Air Pollutants/analysis , Dibenzofurans , Environmental Monitoring , Halogenated Diphenyl Ethers/analysis , Octanols , Vapor Pressure , Volatile Organic Compounds/analysis
20.
Molecules ; 15(5): 3694-708, 2010 May 25.
Article in English | MEDLINE | ID: mdl-20657508

ABSTRACT

Response surface methodology was employed to optimize the conditions for alkaline extraction of polysaccharides from Ganoderma lucidum. The results indicated that the optimum conditions were an extraction temperature of 60.1 degrees C, an extraction time of 77.3 min, a sodium hydroxide (NaOH) concentration of 5.1% and a substrate/liquid ratio of 1:21.4. Immunological assays results have shown that the alkaline soluble polysaccharides have no noticeable effects on monocyte phagocytosis and immune organ (spleen, thymus) weight of immunocompromised mice at the tested dosages. However, they could restore delayed type hypersensitivity reaction to dinitrofluorobenzene (DFNB), hemolysis antibody levels at the three doses applied, and improve the natural killer cell activity at the high-dose and medium dose.


Subject(s)
Immunity/drug effects , Plant Extracts/chemistry , Polysaccharides/isolation & purification , Polysaccharides/pharmacology , Reishi/chemistry , Animals , Dose-Response Relationship, Drug , Methods , Mice , Organ Size , Phagocytosis/drug effects , Spleen/immunology , Thymus Gland/immunology
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