Measurement of dry deposition to bulk precipitation collectors using a novel flushing sampler

Bulk precipitation samplers, which are continuously open, also sample gases and particles deposited on the funnel surface. Wet-only samplers, which open only during precipitation, avoid this problem, but can be bulky (leading to disruption of air flow and droplet collection) and need electrical power. We describe here a simple battery-powered modification to a standard bulk sampler that allows the separate measurement of deposition to the funnel surface and wet deposition by washing the funnel surface when precipitation is detected. Comparison of this design with a standard bulk sampler over 3 months at a site in eastern Scotland showed that dry deposition to the funnel surface contributed around 20% of sulphate, 20-30% of nitrate and 20-40% of ammonium ions. There was also a significant loss of ammonium and nitrate in the modified sampler, presumably in the tubing, even though a biocide had been added to the sample bottles. This observation has implications for bulk samplers of similar design, with a sample bottle at ground level. Deposition of sea salts and calcium was greater to the flushing collectors than to the bulk collectors, implying that regular cleaning of funnel surfaces with 10% methanol solution subtly alters the capture efficiency for larger particles

Development and application of low-cost monitoring approaches for atmospheric ammonia, acid gases and ammonium aerosols

Ammonia (NH3) is the major alkaline gas in the atmosphere, with around 90 % of the total anthropogenic emissions in Europe coming from agriculture-related sources. Following emission to the atmosphere, the neutralisation reaction between NH3 and the acid gases sulfur dioxide (SO2), nitric acid (HNO3) and hydrochloric acid (HCl) produces secondary inorganic aerosols (ammonium nitrate (NH4NO3), ammonium sulfate ((NH4)2SO4) and ammonium chloride (NH4Cl)). With longer atmospheric lifetimes than the gases, the aerosols also contribute to transboundary pollution problems. The gases and aerosols are removed from the atmosphere by wet (in precipitation) or dry (direct uptake by vegetation and surfaces) deposition processes. Together, they can negatively impact the natural environment through the input of excess acidity and nutrient nitrogen and harm human health through the formation of aerosols that contributes to fine-mode particulate matter (PM2.5). They can also potentially influence climate change from the radiative forcing properties of the aerosols and the inputs of nitrogen that can alter the carbon cycle.Monitoring data are necessary for assessing the spatial and temporal extent of pollution and as evidence to detect changes in pollutant concentrations in response to current and future policies to mitigate emissions of NOx, SO2 and NH3. Combined with models, the concentration data are also used to estimate the different fractions of the total sulfur or nitrogen input and different chemical forms of the pollutants. Since the spatial and temporal patterns and atmospheric behaviours of gases and aerosols differ, measurements therefore need to distinguish between the phases. The development of simple, low-cost, time-integrated air sampling methods and their application in cost-efficient monitoring strategies to assess temporal, spatial and trends in the gas and aerosol pollutants in the UK and across Europe is described. An active diffusion denuder method (DELTA®) and a passive sampler (ALPHA®) are implemented at a large number of sites (> 70) in the UK National Ammonia Monitoring Network (NAMN, established 1996) to measure NH3 with a monthly frequency. An extension of the DELTA® method provided additional, monthly measurements of particulate NH4+ (for the NAMN) and of the acid gases (SO2, HNO3, HCl) and aerosol species (NO3 , SO42-, Cl , Na+, Ca2+, Mg2+) for the UK Acid Gas and Aerosol network (AGANet, established 1999) at a subset of NAMN sites. The close integration of the two networks demonstrated the cost-effectiveness of the DELTA® approach, which provided quality assured, concurrent speciated measurement data on multiple pollutants at multiple sites, and also simplicity of operation by a large network of site operators, some of whom have no technical or scientific background. The DELTA® approach and quality protocol developed in the UK networks was further applied to a pan-European NitroEurope (NEU) DELTA® network (20 countries: 2006 – 2010), with knowledge sharing and collaboration between multiple laboratories and research organisations. Important features in the spatial variability and seasonality in the gas and aerosol components were captured in the UK and European networks. The gases, with shorter lifetimes in the atmosphere were found to be spatially more heterogeneous, with a wider range of concentrations than their aerosol counterparts. Variations on a spatial scale were correlated with distributions and magnitude of emission sources, e.g. NH3 and NH4+ concentrations were highest in intensively farmed areas (e.g. East Anglia in eastern England, NAMN) and countries (e.g. the Netherlands, NEU DELTA®). In the UK, evidence is also presented of the contribution by long-range transboundary sources to enhancement of concentrations of NH4NO3 and (NH4)2SO4.Distinct and contrasting seasonal cycles in the gas and aerosol phase components were established, important for identifying periods of pollution and for targeting abatement measures. The observed variations were attributed to seasonal changes in emission sources, atmospheric interactions and the influence of climate on partitioning between the gases and aerosols. For NH3, peaks in concentrations occur from increased volatilisation promoted by warm, dry conditions (summer) and also from agriculture-related emissions, with a main peak in spring and a smaller peak in autumn. Concentrations of SO2 were higher in winter (increased combustion), except in Southern Europe where the peak period was in summer. HNO3 concentrations were more complex, with small peaks in the seasonal cycle related to traffic and industrial emissions, photochemistry, meteorology and the influence of climate on HNO3:NH4NO3 equilibrium. In comparison, the springtime peak in NH4NO3 was attributed to the reaction of a surplus of NH3 with HNO3 to form NH4NO3 in the aerosol phase under cooler, wetter conditions. A summertime peak in particulate SO42- was observed in Southern Europe, coinciding also with peaks in SO2, NH3 and HNO3 concentrations. While the high HNO3 concentrations suggests increased oxidative capacity for formation of H2SO4 (from SO2) and reaction with NH3 to form (NH4)2SO4, the absence of an NH4+ peak illustrates the larger influence of the more abundant NH4NO3 in controlling the seasonality of particulate NH4+.Important changes in the atmospheric concentrations and partitioning between the different gas and aerosol components were captured. The measurement data highlighted the dominance of NH3 and NH4NO3 in rural air, as the emissions of SO2 and NOx continues to fall, against a backdrop of increasing NH3 emissions in the UK and across Europe since 2013. The observed shift in the form of NH4+ aerosol from the stable (NH4)2SO4 to the semi-volatile NH4NO3 is expected to maintain a larger fraction of the NH3 and HNO3 in the gas phase. NH4NO3 can act as a reservoir and release the gases in warm weather, which may partly explain the observed non-linearity between emissions and measured concentrations of NH3 in the UK data. The current and projected trends in the emissions of the gases SO2, NOx and NH3 suggest that NH3 and NH4NO3 can be expected to continue to dominate the inorganic pollution load over the next decades

Air pollution trends in the EMEP region between 1990 and 2012

The present report synthesises the main features of the evolution over the 1990-2012 time period of the concentration and deposition of air pollutants relevant in the context of the Convention on Long-range Transboundary Air Pollution: (i) ozone, (ii) sulfur and nitrogen compounds and particulate matter, (iii) heavy metals and persistent organic pollutants. It is based on observations gathered in State Parties to the Convention within the EMEP monitoring network of regional background stations, as well as relevant modelling initiatives. Joint Report of: EMEP Task Force on Measurements and Modelling (TFMM), Chemical Co-ordinating Centre (CCC), Meteorological Synthesizing Centre-East (MSC-E), Meteorological Synthesizing Centre-West (MSC-W)

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. The consortium generated over 427 million long-read sequences from cDNA and direct RNA datasets, encompassing human, mouse, and manatee species, using different protocols and sequencing platforms. These data were utilized by developers to address challenges in transcript isoform detection and quantification, as well as de novo transcript isoform identification. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. When aiming to detect rare and novel transcripts or when using reference-free approaches, incorporating additional orthogonal data and replicate samples are advised. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis

Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis

Publisher Copyright: © 2022, The Author(s).Background: Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery. Results: To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N = 1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3–5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism. Conclusions: Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk.Peer reviewe

Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis

Abstract Background Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery. Results To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N = 1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3–5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism. Conclusions Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk

Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis

Funding GMP, PN, and CW are supported by NHLBI R01HL127564. GMP and PN are supported by R01HL142711. AG acknowledge support from the Wellcome Trust (201543/B/16/Z), European Union Seventh Framework Programme FP7/2007–2013 under grant agreement no. HEALTH-F2-2013–601456 (CVGenes@Target) & the TriPartite Immunometabolism Consortium [TrIC]-Novo Nordisk Foundation’s Grant number NNF15CC0018486. JMM is supported by American Diabetes Association Innovative and Clinical Translational Award 1–19-ICTS-068. SR was supported by the Academy of Finland Center of Excellence in Complex Disease Genetics (Grant No 312062), the Finnish Foundation for Cardiovascular Research, the Sigrid Juselius Foundation, and University of Helsinki HiLIFE Fellow and Grand Challenge grants. EW was supported by the Finnish innovation fund Sitra (EW) and Finska Läkaresällskapet. CNS was supported by American Heart Association Postdoctoral Fellowships 15POST24470131 and 17POST33650016. Charles N Rotimi is supported by Z01HG200362. Zhe Wang, Michael H Preuss, and Ruth JF Loos are supported by R01HL142302. NJT is a Wellcome Trust Investigator (202802/Z/16/Z), is the PI of the Avon Longitudinal Study of Parents and Children (MRC & WT 217065/Z/19/Z), is supported by the University of Bristol NIHR Biomedical Research Centre (BRC-1215–2001) and the MRC Integrative Epidemiology Unit (MC_UU_00011), and works within the CRUK Integrative Cancer Epidemiology Programme (C18281/A19169). Ruth E Mitchell is a member of the MRC Integrative Epidemiology Unit at the University of Bristol funded by the MRC (MC_UU_00011/1). Simon Haworth is supported by the UK National Institute for Health Research Academic Clinical Fellowship. Paul S. de Vries was supported by American Heart Association grant number 18CDA34110116. Julia Ramierz acknowledges support by the People Programme of the European Union’s Seventh Framework Programme grant n° 608765 and Marie Sklodowska-Curie grant n° 786833. Maria Sabater-Lleal is supported by a Miguel Servet contract from the ISCIII Spanish Health Institute (CP17/00142) and co-financed by the European Social Fund. Jian Yang is funded by the Westlake Education Foundation. Olga Giannakopoulou has received funding from the British Heart Foundation (BHF) (FS/14/66/3129). CHARGE Consortium cohorts were supported by R01HL105756. Study-specific acknowledgements are available in the Additional file 32: Supplementary Note. The views expressed in this manuscript are those of the authors and do not necessarily represent the views of the National Heart, Lung, and Blood Institute; the National Institutes of Health; or the U.S. Department of Health and Human Services.Peer reviewedPublisher PD

Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis

Funding Information: GMP, PN, and CW are supported by NHLBI R01HL127564. GMP and PN are supported by R01HL142711. AG acknowledge support from the Wellcome Trust (201543/B/16/Z), European Union Seventh Framework Programme FP7/2007–2013 under grant agreement no. HEALTH-F2-2013–601456 (CVGenes@Target) & the TriPartite Immunometabolism Consortium [TrIC]-Novo Nordisk Foundation’s Grant number NNF15CC0018486. JMM is supported by American Diabetes Association Innovative and Clinical Translational Award 1–19-ICTS-068. SR was supported by the Academy of Finland Center of Excellence in Complex Disease Genetics (Grant No 312062), the Finnish Foundation for Cardiovascular Research, the Sigrid Juselius Foundation, and University of Helsinki HiLIFE Fellow and Grand Challenge grants. EW was supported by the Finnish innovation fund Sitra (EW) and Finska Läkaresällskapet. CNS was supported by American Heart Association Postdoctoral Fellowships 15POST24470131 and 17POST33650016. Charles N Rotimi is supported by Z01HG200362. Zhe Wang, Michael H Preuss, and Ruth JF Loos are supported by R01HL142302. NJT is a Wellcome Trust Investigator (202802/Z/16/Z), is the PI of the Avon Longitudinal Study of Parents and Children (MRC & WT 217065/Z/19/Z), is supported by the University of Bristol NIHR Biomedical Research Centre (BRC-1215–2001) and the MRC Integrative Epidemiology Unit (MC_UU_00011), and works within the CRUK Integrative Cancer Epidemiology Programme (C18281/A19169). Ruth E Mitchell is a member of the MRC Integrative Epidemiology Unit at the University of Bristol funded by the MRC (MC_UU_00011/1). Simon Haworth is supported by the UK National Institute for Health Research Academic Clinical Fellowship. Paul S. de Vries was supported by American Heart Association grant number 18CDA34110116. Julia Ramierz acknowledges support by the People Programme of the European Union’s Seventh Framework Programme grant n° 608765 and Marie Sklodowska-Curie grant n° 786833. Maria Sabater-Lleal is supported by a Miguel Servet contract from the ISCIII Spanish Health Institute (CP17/00142) and co-financed by the European Social Fund. Jian Yang is funded by the Westlake Education Foundation. Olga Giannakopoulou has received funding from the British Heart Foundation (BHF) (FS/14/66/3129). CHARGE Consortium cohorts were supported by R01HL105756. Study-specific acknowledgements are available in the Additional file : Supplementary Note. The views expressed in this manuscript are those of the authors and do not necessarily represent the views of the National Heart, Lung, and Blood Institute; the National Institutes of Health; or the U.S. Department of Health and Human Services. Publisher Copyright: © 2022, The Author(s).Background: Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery. Results: To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N = 1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3–5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism. Conclusions: Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk.Peer reviewe

New loci and coding variants confer risk for age-related macular degeneration in East Asians

加齢黄斑変性の発症に関わるアジア人特有の遺伝子変異を発見. 京都大学プレスリリース. 2015-02-05.Updated 30 March 2015. [Corrigendum] doi:10.1038/ncomms7817Age-related macular degeneration (AMD) is a major cause of blindness, but presents differently in Europeans and Asians. Here, we perform a genome-wide and exome-wide association study on 2, 119 patients with exudative AMD and 5, 691 controls, with independent replication in 4, 226 patients and 10, 289 controls, all of East Asian descent, as part of The Genetics of AMD in Asians (GAMA) Consortium. We find a strong association between CETP Asp442Gly (rs2303790), an East Asian-specific mutation, and increased risk of AMD (odds ratio (OR)=1.70, P=5.60 × 10[-22]). The AMD risk allele (442Gly), known to protect from coronary heart disease, increases HDL cholesterol levels by 0.17mmoll-1 (P=5.82 × 10[-21]) in East Asians (n=7, 102). We also identify three novel AMD loci: C6orf223 Ala231Ala (OR=0.78, P=6.19 × 10[-18]), SLC44A4 Asp47Val (OR=1.27, P=1.08 × 10[-11]) and FGD6 Gln257Arg (OR=0.87, P=2.85 × 10[-8]). Our findings suggest that some of the genetic loci conferring AMD susceptibility in East Asians are shared with Europeans, yet AMD in East Asians may also have a distinct genetic signature