Stable isotope tagging of epitopes: a highly selective strategy for the identification of major histocompatibility complex class I-associated peptides induced upon viral infection.

Identification of peptides presented in major histocompatibility complex (MHC) class I molecules after viral infection is of strategic importance for vaccine development. Until recently, mass spectrometric identification of virus-induced peptides was based on comparative analysis of peptide pools isolated from uninfected and virus-infected cells. Here we report on a powerful strategy aiming at the rapid, unambiguous identification of naturally processed MHC class I-associated peptides, which are induced by viral infection. The methodology, stable isotope tagging of epitopes (SITE), is based on metabolic labeling of endogenously synthesized proteins during infection. This is accomplished by culturing virus-infected cells with stable isotope-labeled amino acids that are expected to be anchor residues (i.e. residues of the peptide that have amino acid side chains that bind into pockets lining the peptide-binding groove of the MHC class I molecule) for the human leukocyte antigen allele of interest. Subsequently these cells are mixed with an equal number of non-infected cells, which are cultured in normal medium. Finally peptides are acid-eluted from immunoprecipitated MHC molecules and subjected to two-dimensional nanoscale LC-MS analysis. Virus-induced peptides are identified through computer-assisted detection of characteristic, binomially distributed ratios of labeled and unlabeled molecules. Using this approach we identified novel measles virus and respiratory syncytial virus epitopes as well as infection-induced self-peptides in several cell types, showing that SITE is a unique and versatile method for unequivocal identification of disease-related MHC class I epitopes

Global Air Quality and COVID-19 Pandemic : Do We Breathe Cleaner Air?

The global spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has challenged most countries worldwide. It was quickly recognized that reduced activities (lockdowns) during the Coronavirus Disease of 2019 (COVID-19) pandemic produced major changes in air quality. Our objective was to assess the impacts of COVID-19 lockdowns on groundlevel PM2.5, NO2, and O-3 concentrations on a global scale. We obtained data from 34 countries, 141 cities, and 458 air monitoring stations on 5 continents (few data from Africa). On a global average basis, a 34.0% reduction in NO2 concentration and a 15.0% reduction in PM2.5 were estimated during the strict lockdown period (until April 30, 2020). Global average O-3 concentration increased by 86.0% during this same period. Individual country and continent-wise comparisons have been made between lockdown and business-as-usual periods. Universally, NO2 was the pollutant most affected by the COVID-19 pandemic. These effects were likely because its emissions were from sources that were typically restricted (i.e., surface traffic and non-essential industries) by the lockdowns and its short lifetime in the atmosphere. Our results indicate that lockdown measures and resulting reduced emissions reduced exposure to most harmful pollutants and could provide global-scale health benefits. However, the increased O-3 may have substantially reduced those benefits and more detailed health assessments are required to accurately quantify the health gains. At the same, these restrictions were obtained at substantial economic costs and with other health issues (depression, suicide, spousal abuse, drug overdoses, etc.). Thus, any similar reductions in air pollution would need to be obtained without these extensive economic and other consequences produced by the imposed activity reductions.Peer reviewe

Results of the first European Source Apportionment intercomparison for Receptor and Chemical Transport Models

In this study, the performance of the source apportionment model applications were evaluated by comparing the model results provided by 44 participants adopting a methodology based on performance indicators: z-scores and RMSEu, with pre-established acceptability criteria. Involving models based on completely different and independent input data, such as receptor models (RMs) and chemical transport models (CTMs), provided a unique opportunity to cross-validate them. In addition, comparing the modelled source chemical profiles, with those measured directly at the source contributed to corroborate the chemical profile of the tested model results. The most used RM was EPA- PMF5. RMs showed very good performance for the overall dataset (91% of z-scores accepted) and more difficulties are observed with SCE time series (72% of RMSEu accepted). Industry resulted the most problematic source for RMs due to the high variability among participants. Also the results obtained with CTMs were quite comparable to their ensemble reference using all models for the overall average (>92% of successful z-scores) while the comparability of the time series is more problematic (between 58% and 77% of the candidates’ RMSEu are accepted). In the CTM models a gap was observed between the sum of source contributions and the gravimetric PM10 mass likely due to PM underestimation in the base case. Interestingly, when only the tagged species CTM results were used in the reference, the differences between the two CTM approaches (brute force and tagged species) were evident. In this case the percentage of candidates passing the z-score and RMSEu tests were only 50% and 86%, respectively. CTMs showed good comparability with RMs for the overall dataset (83% of the z-scores accepted), more differences were observed when dealing with the time series of the single source categories. In this case the share of successful RMSEu was in the range 25% - 34%.JRC.C.5-Air and Climat

A global observational analysis to understand changes in air quality during exceptionally low anthropogenic emission

This global study, which has been coordinated by the World Meteorological Organization Global Atmospheric Watch (WMO/GAW) programme, aims to understand the behaviour of key air pollutant species during the COVID-19 pandemic period of exceptionally low emissions across the globe. We investigated the effects of the differences in both emissions and regional and local meteorology in 2020 compared with the period 2015–2019. By adopting a globally consistent approach, this comprehensive observational analysis focuses on changes in air quality in and around cities across the globe for the following air pollutants PM2.5, PM10, PMC (coarse fraction of PM), NO2, SO2, NOx, CO, O3 and the total gaseous oxidant (OX = NO2 + O3) during the pre-lockdown, partial lockdown, full lockdown and two relaxation periods spanning from January to September 2020. The analysis is based on in situ ground-based air quality observations at over 540 traffic, background and rural stations, from 63 cities and covering 25 countries over seven geographical regions of the world. Anomalies in the air pollutant concentrations (increases or decreases during 2020 periods compared to equivalent 2015–2019 periods) were calculated and the possible effects of meteorological conditions were analysed by computing anomalies from ERA5 reanalyses and local observations for these periods. We observed a positive correlation between the reductions in NO2 and NOx concentrations and peoples’ mobility for most cities. A correlation between PMC and mobility changes was also seen for some Asian and South American cities. A clear signal was not observed for other pollutants, suggesting that sources besides vehicular emissions also substantially contributed to the change in air quality. As a global and regional overview of the changes in ambient concentrations of key air quality species, we observed decreases of up to about 70% in mean NO2 and between 30% and 40% in mean PM2.5 concentrations over 2020 full lockdown compared to the same period in 2015–2019. However, PM2.5 exhibited complex signals, even within the same region, with increases in some Spanish cities, attributed mainly to the long-range transport of African dust and/or biomass burning (corroborated with the analysis of NO2/CO ratio). Some Chinese cities showed similar increases in PM2.5 during the lockdown periods, but in this case, it was likely due to secondary PM formation. Changes in O3 concentrations were highly heterogeneous, with no overall change or small increases (as in the case of Europe), and positive anomalies of 25% and 30% in East Asia and South America, respectively, with Colombia showing the largest positive anomaly of ~70%. The SO2 anomalies were negative for 2020 compared to 2015–2019 (between ~25 to 60%) for all regions. For CO, negative anomalies were observed for all regions with the largest decrease for South America of up to ~40%. The NO2/CO ratio indicated that specific sites (such as those in Spanish cities) were affected by biomass burning plumes, which outweighed the NO2 decrease due to the general reduction in mobility (ratio of ~60%). Analysis of the total oxidant (OX = NO2 + O3) showed that primary NO2 emissions at urban locations were greater than the O3 production, whereas at background sites, OX was mostly driven by the regional contributions rather than local NO2 and O3 concentrations. The present study clearly highlights the importance of meteorology and episodic contributions (e.g., from dust, domestic, agricultural biomass burning and crop fertilizing) when analysing air quality in and around cities even during large emissions reductions. There is still the need to better understand how the chemical responses of secondary pollutants to emission change under complex meteorological conditions, along with climate change and socio-economic drivers may affect future air quality. The implications for regional and global policies are also significant, as our study clearly indicates that PM2.5 concentrations would not likely meet the World Health Organization guidelines in many parts of the world, despite the drastic reductions in mobility. Consequently, revisions of air quality regulation (e.g., the Gothenburg Protocol) with more ambitious targets that are specific to the different regions of the world may well be required.Peer reviewedFinal Published versio

A global observational analysis to understand changes in air quality during exceptionally low anthropogenic emission conditions

This global study, which has been coordinated by the World Meteorological Organization Global Atmospheric Watch (WMO/GAW) programme, aims to understand the behaviour of key air pollutant species during the COVID-19 pandemic period of exceptionally low emissions across the globe. We investigated the effects of the differences in both emissions and regional and local meteorology in 2020 compared with the period 2015–2019. By adopting a globally consistent approach, this comprehensive observational analysis focuses on changes in air quality in and around cities across the globe for the following air pollutants PM2.5, PM10, PMC (coarse fraction of PM), NO2, SO2, NOx, CO, O3 and the total gaseous oxidant (OX = NO2 + O3) during the pre-lockdown, partial lockdown, full lockdown and two relaxation periods spanning from January to September 2020. The analysis is based on in situ ground-based air quality observations at over 540 traffic, background and rural stations, from 63 cities and covering 25 countries over seven geographical regions of the world. Anomalies in the air pollutant concentrations (increases or decreases during 2020 periods compared to equivalent 2015–2019 periods) were calculated and the possible effects of meteorological conditions were analysed by computing anomalies from ERA5 reanalyses and local observations for these periods. We observed a positive correlation between the reductions in NO2 and NOx concentrations and peoples’ mobility for most cities. A correlation between PMC and mobility changes was also seen for some Asian and South American cities. A clear signal was not observed for other pollutants, suggesting that sources besides vehicular emissions also substantially contributed to the change in air quality. As a global and regional overview of the changes in ambient concentrations of key air quality species, we observed decreases of up to about 70% in mean NO2 and between 30% and 40% in mean PM2.5 concentrations over 2020 full lockdown compared to the same period in 2015–2019. However, PM2.5 exhibited complex signals, even within the same region, with increases in some Spanish cities, attributed mainly to the long-range transport of African dust and/or biomass burning (corroborated with the analysis of NO2/CO ratio). Some Chinese cities showed similar increases in PM2.5 during the lockdown periods, but in this case, it was likely due to secondary PM formation. Changes in O3 concentrations were highly heterogeneous, with no overall change or small increases (as in the case of Europe), and positive anomalies of 25% and 30% in East Asia and South America, respectively, with Colombia showing the largest positive anomaly of ~70%. The SO2 anomalies were negative for 2020 compared to 2015–2019 (between ~25 to 60%) for all regions. For CO, negative anomalies were observed for all regions with the largest decrease for South America of up to ~40%. The NO2/CO ratio indicated that specific sites (such as those in Spanish cities) were affected by biomass burning plumes, which outweighed the NO2 decrease due to the general reduction in mobility (ratio of ~60%). Analysis of the total oxidant (OX = NO2 + O3) showed that primary NO2 emissions at urban locations were greater than the O3 production, whereas at background sites, OX was mostly driven by the regional contributions rather than local NO2 and O3 concentrations. The present study clearly highlights the importance of meteorology and episodic contributions (e.g., from dust, domestic, agricultural biomass burning and crop fertilizing) when analysing air quality in and around cities even during large emissions reductions. There is still the need to better understand how the chemical responses of secondary pollutants to emission change under complex meteorological conditions, along with climate change and socio-economic drivers may affect future air quality. The implications for regional and global policies are also significant, as our study clearly indicates that PM2.5 concentrations would not likely meet the World Health Organization guidelines in many parts of the world, despite the drastic reductions in mobility. Consequently, revisions of air quality regulation (e.g., the Gothenburg Protocol) with more ambitious targets that are specific to the different regions of the world may well be required.World Meteorological Organization Global Atmospheric Watch programme is gratefully acknowledged for initiating and coordinating this study and for supporting this publication. We acknowledge the following projects for supporting the analysis contained in this article: Air Pollution and Human Health for an Indian Megacity project PROMOTE funded by UK NERC and the Indian MOES, Grant reference number NE/P016391/1; Regarding project funding from the European Commission, the sole responsibility of this publication lies with the authors. The European Commission is not responsible for any use that may be made of the information contained therein. This project has received funding from the European Commission’s Horizon 2020 research and innovation program under grant agreement No 874990 (EMERGE project). European Regional Development Fund (project MOBTT42) under the Mobilitas Pluss programme; Estonian Research Council (project PRG714); Estonian Research Infrastructures Roadmap project Estonian Environmental Observatory (KKOBS, project 2014-2020.4.01.20-0281). European network for observing our changing planet project (ERAPLANET, grant agreement no. 689443) under the European Union’s Horizon 2020 research and innovation program, Estonian Ministry of Sciences projects (grant nos. P180021, P180274), and the Estonian Research Infrastructures Roadmap project Estonian Environmental Observatory (3.2.0304.11-0395). Eastern Mediterranean and Middle East—Climate and Atmosphere Research (EMME-CARE) project, which has received funding from the European Union’s Horizon 2020 Research and Innovation Programme (grant agreement no. 856612) and the Government of Cyprus. INAR acknowledges support by the Russian government (grant number 14.W03.31.0002), the Ministry of Science and Higher Education of the Russian Federation (agreement 14.W0331.0006), and the Russian Ministry of Education and Science (14.W03.31.0008). We are grateful to to the following agencies for providing access to data used in our analysis: A.M. Obukhov Institute of Atmospheric Physics Russian Academy of Sciences; Agenzia Regionale per la Protezione dell’Ambiente della Campania (ARPAC); Air Quality and Climate Change, Parks and Environment (MetroVancouver, Government of British Columbia); Air Quality Monitoring & Reporting, Nova Scotia Environment (Government of Nova Scotia); Air Quality Monitoring Network (SIMAT) and Emission Inventory, Mexico City Environment Secretariat (SEDEMA); Airparif (owner & provider of the Paris air pollution data); ARPA Lazio, Italy; ARPA Lombardia, Italy; Association Agr´e´ee de Surveillance de la Qualit´e de l’Air en ˆIle-de- France AIRPARIF / Atmo-France; Bavarian Environment Agency, Germany; Berlin Senatsverwaltung für Umwelt, Verkehr und Klimaschutz, Germany; California Air Resources Board; Central Pollution Control Board (CPCB), India; CETESB: Companhia Ambiental do Estado de S˜ao Paulo, Brazil. China National Environmental Monitoring Centre; Chandigarh Pollution Control Committee (CPCC), India. DCMR Rijnmond Environmental Service, the Netherlands. Department of Labour Inspection, Cyprus; Department of Natural Resources Management and Environmental Protection of Moscow. Environment and Climate Change Canada; Environmental Monitoring and Science Division Alberta Environment and Parks (Government of Alberta); Environmental Protection Authority Victoria (Melbourne, Victoria, Australia); Estonian Environmental Research Centre (EERC); Estonian University of Life Sciences, SMEAR Estonia; European Regional Development Fund (project MOBTT42) under the Mobilitas Pluss programme; Finnish Meteorological Institute; Helsinki Region Environmental Services Authority; Haryana Pollution Control Board (HSPCB), IndiaLondon Air Quality Network (LAQN) and the Automatic Urban and Rural Network (AURN) supported by the Department of Environment, Food and Rural Affairs, UK Government; Madrid Municipality; Met Office Integrated Data Archive System (MIDAS); Meteorological Service of Canada; Minist`ere de l’Environnement et de la Lutte contre les changements climatiques (Gouvernement du Qu´ebec); Ministry of Environment and Energy, Greece; Ministry of the Environment (Chile) and National Weather Service (DMC); Moscow State Budgetary Environmental Institution MOSECOMONITORING. Municipal Department of the Environment SMAC, Brazil; Municipality of Madrid public open data service; National institute of environmental research, Korea; National Meteorology and Hydrology Service (SENAMHI), Peru; New York State Department of Environmental Conservation; NSW Department of Planning, Industry and Environment; Ontario Ministry of the Environment, Conservation and Parks, Canada; Public Health Service of Amsterdam (GGD), the Netherlands. Punjab Pollution Control Board (PPCB), India. R´eseau de surveillance de la qualit´e de l’air (RSQA) (Montr´eal); Rosgydromet. Mosecomonitoring, Institute of Atmospheric Physics, Russia; Russian Foundation for Basic Research (project 20–05–00254) SAFAR-IITM-MoES, India; S˜ao Paulo State Environmental Protection Agency, CETESB; Secretaria de Ambiente, DMQ, Ecuador; Secretaría Distrital de Ambiente, Bogot´a, Colombia. Secretaria Municipal de Meio Ambiente Rio de Janeiro; Mexico City Atmospheric Monitoring System (SIMAT); Mexico City Secretariat of Environment, Secretaría del Medio Ambiente (SEDEMA); SLB-analys, Sweden; SMEAR Estonia station and Estonian University of Life Sciences (EULS); SMEAR stations data and Finnish Center of Excellence; South African Weather Service and Department of Environment, Forestry and Fisheries through SAAQIS; Spanish Ministry for the Ecological Transition and the Demographic Challenge (MITECO); University of Helsinki, Finland; University of Tartu, Tahkuse air monitoring station; Weather Station of the Institute of Astronomy, Geophysics and Atmospheric Science of the University of S˜ao Paulo; West Bengal Pollution Control Board (WBPCB).http://www.elsevier.com/locate/envintam2023Geography, Geoinformatics and Meteorolog

Source apportionment of ambient PM collected at three sites in an urban-industrial area with multi-time resolution factor analyses.

Chemical speciation data for PM10, collected for annual trend analyses of health-relevant species, at three receptor sites in a highly industrialized area (IJmond) in the Netherlands were used in a multi-time resolution receptor model (ME-2) to identify the PM10 sources in this area. Despite the available data not being optimized for receptor modelling, five-factor solutions were obtained for all sites based on independent PMF analysis on PM10 data from the three sites (IJM, WAZ and BEV). Four factors were common to all three sites: nitrate-sulphate (average percentage contributions to PM10: IJM: 35.3 %, WAZ: 37.7 %, and BEV: 36.3 %); sea salt (20.2 %, 23.7 %, 15.2 %); industrial (8.1 %, 11.0 %, 18.1 %) and brake wear/traffic (31.4 %, 21.2 %, 20.6 %). At WAZ, a local/site-specific factor containing most of the PAH measurements was found (6.4 %) while a crustal matter factor was resolved at IJM (7.6 %) and BEV (9.8 %). Additionally, sludge-drying was a potential source of the marker species in the industrial factor at WAZ. Bootstrapping (BS) and factor displacement (DISP) were applied to the factor profiles in this work for error estimation. In general, the factor profiles at all three sites had very small intervals from both BS and DISP methods. To our knowledge, this is the first time DISP was applied in a complex model such as the multi-time resolution model. Most of the measured metal and PAH concentrations found in the IJmond area during the 2017-2019 period had local sources, with significant contributions from several processes related to the steel industry. This study shows that available detailed PM10 chemical speciation data, although primarily collected for annual trend analyses of health-relevant species, could also be used in receptor modelling by applying a multi-time framework. We propose general recommendations for the optimization of the measurement strategy for source apportionment of PM in areas with similar urban-industrial land use

Source apportionment of ambient PM collected at three sites in an urban-industrial area with multi-time resolution factor analyses.

Chemical speciation data for PM10, collected for annual trend analyses of health-relevant species, at three receptor sites in a highly industrialized area (IJmond) in the Netherlands were used in a multi-time resolution receptor model (ME-2) to identify the PM10 sources in this area. Despite the available data not being optimized for receptor modelling, five-factor solutions were obtained for all sites based on independent PMF analysis on PM10 data from the three sites (IJM, WAZ and BEV). Four factors were common to all three sites: nitrate-sulphate (average percentage contributions to PM10: IJM: 35.3 %, WAZ: 37.7 %, and BEV: 36.3 %); sea salt (20.2 %, 23.7 %, 15.2 %); industrial (8.1 %, 11.0 %, 18.1 %) and brake wear/traffic (31.4 %, 21.2 %, 20.6 %). At WAZ, a local/site-specific factor containing most of the PAH measurements was found (6.4 %) while a crustal matter factor was resolved at IJM (7.6 %) and BEV (9.8 %). Additionally, sludge-drying was a potential source of the marker species in the industrial factor at WAZ. Bootstrapping (BS) and factor displacement (DISP) were applied to the factor profiles in this work for error estimation. In general, the factor profiles at all three sites had very small intervals from both BS and DISP methods. To our knowledge, this is the first time DISP was applied in a complex model such as the multi-time resolution model. Most of the measured metal and PAH concentrations found in the IJmond area during the 2017-2019 period had local sources, with significant contributions from several processes related to the steel industry. This study shows that available detailed PM10 chemical speciation data, although primarily collected for annual trend analyses of health-relevant species, could also be used in receptor modelling by applying a multi-time framework. We propose general recommendations for the optimization of the measurement strategy for source apportionment of PM in areas with similar urban-industrial land use

Source apportionment of ambient PM in an industrialized city using dispersion-normalized, multi-time resolution factor analyses.

Ambient fine particulate matter (PM2.5) data were collected in the lower City of Hamilton, Ontario to apportion the sources of this pollutant over an 18-month period. Hamilton has complex topographical features that may result in worsened air pollution within the lower city, thus, dispersion-normalized, multi-time resolution factor analysis (DN-MT-FA) was used to identify and quantify contributions of factors in a manner that reduced the influence of local meteorology. These factors were secondary organic aerosols type 1 (SOA_1), particulate nitrate (pNO3), particulate sulphate (pSO4), primary traffic organic matter (PTOM), Steel/metal processing and vehicular road dust emissions (Steel & Mobile) and, secondary organic aerosols type 2 (SOA_2) with origins ranging from mainly regional to mainly local. Factors that were mainly local (PTOM, Steel & Mobile, SOA_2) contributed up to 17% of the average PM2.5 mass while mixed local/regional factors (pNO3, pSO4) made up 43% on average, indicating the potential for further reduction of harmful PM concentrations locally. Of particular interest from a health protection perspective, was the composition of PM2.5 on days when an exceedance of the 24-hr WHO air quality guideline for this pollutant was observed. In general, SOA_1 was found to drive summer exceedances while pNO3 dominated in the winter. During the summer period, SOA_1 was attributable to wildfires in the northern parts of Canada while local traffic sources in winter contributed to the high levels of pNO3. While local, industrial factors only had minor relative mass contributions during exceedances, they are high in highly oxidized organic species (SOA_2) and toxic metals (Steel & Mobile). Thus, they are likely to have more impacts on human health. The methods and results described in this work will be useful in understanding prevalent sources of particulate matter pollution in the ambient air in the presence of complex topography and meteorological effects

Improvements in air quality in the Netherlands during the corona lockdown based on observations and model simulations

The lockdown measures in response to the SARS-CoV-2 virus outbreak in 2020 have resulted in reductions in emissions of air pollutants and corresponding ambient concentrations. In the Netherlands, the most stringent lockdown measures were in effect from March to May 2020. These measures coincided with a period of unusual meteorological conditions with wind from the north-east and clear-sky conditions, which complicates the quantification of the effect of the lockdown measures on the air quality. Here we quantify the lockdown effects on the concentrations of nitrogen oxides (NOx and NO2), particulate matter (PM10 and PM2.5) and ozone (O3) in the Netherlands, by analyzing observations and simulations with the atmospheric chemistry-transport model EMEP/MSC-W in its EMEP4NL configuration, after eliminating the effects of meteorological conditions during the lockdown. Based on statistical analyses with a Random Forest method, we estimate that the lockdown reduced observed NO2 concentrations by 30% (95% confidence interval 25–35%), 26% (21–32%), and 18% (10–25%) for traffic, urban, and rural background locations, respectively. Slightly smaller reductions of 8–28% are found with the EMEP4NL simulations for urban and regional background locations based on estimates in reductions in economic activity and emissions of traffic and industry in the Netherlands and other European countries. Reductions in observed PM2.5 concentrations of about 20% (10–25%) are found for all locations, which is somewhat larger than the estimates of 5–16% based on the model simulations. A comparison of the calculated NO2 traffic contributions with observations shows a substantial drop of about 35% in traffic contributions during the lockdown period, which is similar to the estimated reductions in mobility data as reported by Apple and Google. Since the largest health effects related to air pollution in the Netherlands are associated with exposure to PM10 and PM2.5, the lockdown measures in spring of 2020 have temporarily improved the air quality in the Netherlands. The concentrations of the most health relevant compounds have only been reduced by about 10–25%