Modeled and observed ozone sensitivity to mobile-source emissions in Mexico City

The emission characteristics of mobile sources in the Mexico City Metropolitan Area (MCMA) have changed significantly over the past few decades in response to emission control policies, advancements in vehicle technologies and improvements in fuel quality, among others. Along with these changes, concurrent non-linear changes in photochemical levels and criteria pollutants have been observed, providing a unique opportunity to understand the effects of perturbations of mobile emission levels on the photochemistry in the region using observational and modeling approaches. The observed historical trends of ozone (O3), carbon monoxide (CO) and nitrogen oxides (NOx) suggest that ozone production in the MCMA has changed from a low to a high VOC-sensitive regime over a period of 20 years. Comparison of the historical emission trends of CO, NOx and hydrocarbons derived from mobile-source emission studies in the MCMA from 1991 to 2006 with the trends of the concentrations of CO, NOx, and the CO/NOx ratio during peak traffic hours also indicates that fuel-based fleet average emission factors have significantly decreased for CO and VOCs during this period whereas NOx emission factors do not show any strong trend, effectively reducing the ambient VOC/NOx ratio. This study presents the results of model analyses on the sensitivity of the observed ozone levels to the estimated historical changes in its precursors. The model sensitivity analyses used a well-validated base case simulation of a high pollution episode in the MCMA with the mathematical Decoupled Direct Method (DDM) and the standard Brute Force Method (BFM) in the 3-D CAMx chemical transport model. The model reproduces adequately the observed historical trends and current photochemical levels. Comparison of the BFM and the DDM sensitivity techniques indicates that the model yields ozone values that increase linearly with NOx emission reductions and decrease linearly with VOC emission reductions only up to 30% from the base case. We further performed emissions perturbations from the gasoline fleet, diesel fleet, all mobile (gasoline plus diesel) and all emission sources (anthropogenic plus biogenic). The results suggest that although large ozone reductions obtained in the past were from changes in emissions from gasoline vehicles, currently significant benefits could be achieved with additional emission control policies directed to regulation of VOC emissions from diesel and area sources that are high emitters of alkenes, aromatics and aldehydes.National Science Foundation (U.S.) (ATM-0528227)Mexico. Comisión Ambiental Metropolitan

Discovering antiviral restriction factors and pathways using genetic screens

Research in the Hughes lab is supported by a grant from the Academy of Medical Sciences (SFB003/1028), a grant from Tenovus Scotland (T20/63), and The Wellcome Trust Institutional Strategic Support Fund (ISSF). Research in the Gray lab is supported Medical Research Council (MR/N001796/1) and the Biotechnology and Biological Sciences Research Council (BBS/E/D/20002172). C. E. J. is supported by a University of St Andrews Ph.D. scholarship.Viral infections activate the powerful interferon (IFN) response that induces the expression of several hundred IFN stimulated genes (ISGs). The principal role of this extensive response is to create an unfavourable environment for virus replication and to limit spread; however, untangling the biological consequences of this large response is complicated. In addition to a seemingly high degree of redundancy, several ISGs are usually required in combination to limit infection as individual ISGs often have low to moderate antiviral activity. Furthermore, what ISG or combination of ISGs are antiviral for a given virus is usually not known. For these reasons, and that the function(s) of many ISGs remains unexplored, genome-wide approaches are well placed to investigate what aspects of this response results in an appropriate, virus-specific phenotype. This review discusses the advances screening approaches have provided for the study of host defence mechanisms, including CRISPR/Cas9, ISG expression libraries and RNAi technologies.Publisher PDFPeer reviewe

Formation of semivolatile inorganic aerosols in the Mexico City Metropolitan Area during the MILAGRO campaign

One of the most challenging tasks for chemical transport models (CTMs) is the prediction of the formation and partitioning of the major semi-volatile inorganic aerosol components (nitrate, chloride, ammonium) between the gas and particulate phases. In this work the PMCAMx-2008 CTM, which includes the recently developed aerosol thermodynamic model ISORROPIA-II, is applied in the Mexico City Metropolitan Area in order to simulate the formation of the major inorganic aerosol components. The main sources of SO2 (such as the Miguel Hidalgo Refinery and the Francisco Perez Rios Power Plant) in the Mexico City Metropolitan Area (MCMA) are located in Tula, resulting in high predicted PM1 (particulate matter with diameter less than 1 µm) sulfate concentrations (over 25 µg m-3) in that area. The average predicted PM1 nitrate concentrations are up to 3 µg m-3 (with maxima up to 11 µg m-3) in and around the urban center, mostly produced from local photochemistry. The presence of calcium coming from the Tolteca area (7 µg m-3) as well as the rest of the mineral cations (1 µg m-3 potassium, 1 µg m-3 magnesium, 2 µg m-3 sodium, and 3 µg m-3 calcium) from the Texcoco Lake resulted in the formation of a significant amount of aerosol nitrate in the coarse mode with concentrations up to 3 µg m-3 over these areas. PM1-10 (particulate matter with diameter between 1 and 10 µm) chloride is also high and its concentration exceeds 2 µg m-3 in Texcoco Lake. PM1 ammonium concentrations peak at the center of Mexico City (2 µg m-3) and the Tula vicinity (2.5 µg m-3). The performance of the model for the major inorganic PM components (sulfate, ammonium, nitrate, chloride, sodium, calcium, and magnesium) is encouraging. At the T0 measurement site, located in the Mexico City urban center, the average measured values of PM1 sulfate, nitrate, ammonium, and chloride are 3.5 µg m-3, 3.5 µg m-3, 2.1 µg m-3, and 0.36 µg m-3, respectively. The corresponding predicted values are 3.7 µg m-3, 2.7 µg m-3, 1.7 µg m-3, and 0.25 µg m-3. High sulfate concentrations are associated with the transport of sulfate from the Tula vicinity, while in periods where southerly winds are dominant; the concentrations of sulfate are low. The underprediction of nitrate can be attributed to the underestimation of OH levels by the model during the early morning. Ammonium is sensitive to the predicted sulfate concentrations and the nitrate levels. The performance of the model is also evaluated against measurements taken from a suburban background site (T1) located north of Mexico City. The average predicted PM2.5 (particulate matter with diameter less than 2.5 µm) sulfate, nitrate, ammonium, chloride, sodium, calcium, and magnesium are 3.3, 3.2, 1.4, 0.5, 0.3, 1.2, and 0.15 µg m-3, respectively. The corresponding measured concentrations are 3.7, 2.9, 1.5, 0.3, 0.4, 0.6, and 0.15 µg m-3. The overprediction of calcium indicates a possible overestimation of its emissions and affects the partitioning of nitric acid to the aerosol phase resulting occasionally in an overprediction of nitrate. Additional improvements are possible by improving the performance of the model regarding the oxidant levels, and revising the emissions and the chemical composition of the fugitive dust. The hybrid approach in which the mass transfer to the fine aerosol is simulated using the bulk equilibrium assumption and to the remaining aerosol sections using a dynamic approach, is needed in order to accurately simulate the size distribution of the inorganic aerosols. The bulk equilibrium approach fails to reproduce the observed coarse nitrate and overpredicts the fine nitrate. Sensitivity tests indicate that sulfate concentration in Tula decreases by up to 0.5 µg m-3 after a 50% reduction of SO2 emissions while it can increase by up to 0.3 µg m-3 when NOx emissions are reduced by 50%. Nitrate concentration decreases by up to 1 µg m-3 after the 50% reduction of NOx or NH3 emissions. Ammonium concentration decreases by up to 1 µg m-3, 0.3 µg m-3, and 0.1 µg m-3 after the 50% reduction of NH3, NOx, and SO2 emissions, respectively.Seventh Framework Programme (European Commission) (MEGAPOLI Grant agreement no.: 212520)National Institutes of Health (U.S.) (NSF (ATM-0528227

Impacts of HONO sources on the photochemistry in Mexico City during the MCMA-2006/MILAGO Campaign

The contribution of HONO sources to the photochemistry in Mexico City is investigated during the MCMA-2006/MILAGO Campaign using the WRF-CHEM model. Besides the homogeneous reaction of NO with OH, four additional HONO sources are considered in the WRF-CHEM model: secondary HONO formation from NO2 heterogeneous reaction with semivolatile organics, NO2 reaction with freshly emitted soot, NO2 heterogeneous reaction on aerosol and ground surfaces. The WRF-CHEM model with the five HONO sources performs reasonably well in tracking the observed diurnal variation of HONO concentrations. The HONO sources included are found to significantly improve the HOx (OH+HO2) simulations during daytime and the partition of NO/NO2 in the morning. The HONO sources also accelerate the accumulation of O3 concentrations in the morning by about 2 h and subsequently result in a noticeable enhancement of O3 concentrations over the course of the day with a midday average of about 6 ppb. Furthermore, these HONO sources play a very important role in the formation of secondary aerosols in the morning. They substantially enhance the secondary organic aerosol concentrations by a factor of 2 on average in the morning, although they contribute less during the rest of the day. The simulated particle-phase nitrate and ammonium are also substantially enhanced in the morning when the four HONO sources are included, in good agreement with the measurements. The impact of the HONO sources on the sulfate aerosols is negligible because of the inefficient conversion of H2SO4 from SO2 reacting with OH.National Science Foundation (U.S.) (Atmospheric Chemistry Program (ATM-0528227))Molina Center for Energy and the Environmen

Impact of primary formaldehyde on air pollution in the Mexico City Metropolitan Area

Formaldehyde (HCHO) is a radical source that plays an important role in urban atmospheric chemistry and ozone formation. The Mexico City Metropolitan Area (MCMA) is characterized by high anthropogenic emissions of HCHO (primary HCHO), which together with photochemical production of HCHO from hydrocarbon oxidation (secondary HCHO), lead to high ambient HCHO levels. The CAMx chemical transport model was employed to evaluate the impact of primary HCHO on its ambient concentration, on the ROx radical budget, and on ozone (O3) formation in the MCMA. Important radical sources, including HCHO, HONO, and O3-olefin reactions, were constrained by measurements from routine observations of the local ambient air monitoring network and the MCMA-2003 field campaign. Primary HCHO was found not only to contribute significantly to the ambient HCHO concentration, but also to enhance the radical budget and O3 production in the urban atmosphere of the MCMA. Overall in the urban area, total daytime radical production is enhanced by up to 10% and peak O3 concentration by up to 8%; moreover primary HCHO tends to make O3 both production rates and ambient concentration peak half an hour earlier. While primary HCHO contributes predominantly to the ambient HCHO concentration between nighttime and morning rush hours, significant influence on the radical budget and O3 production starts early in the morning, peaks at mid-morning and is sustained until early afternoon.Mexican Metropolitan Commission of EnvironmentNational Science Foundation (U.S.) (ATM-0528227

Sources and production of organic aerosol in Mexico City: insights from the combination of a chemical transport model (PMCAMx-2008) and measurements

Urban areas are large sources of organic aerosols and their precursors. Nevertheless, the contributions of primary (POA) and secondary organic aerosol (SOA) to the observed particulate matter levels have been difficult to quantify. In this study the three-dimensional chemical transport model PMCAMx-2008 is used to investigate the temporal and geographic variability of organic aerosol in the Mexico City Metropolitan Area (MCMA) during the MILAGRO campaign that took place in the spring of 2006. The organic module of PMCAMx-2008 includes the recently developed volatility basis-set framework in which both primary and secondary organic components are assumed to be semi-volatile and photochemically reactive and are distributed in logarithmically spaced volatility bins. The MCMA emission inventory is modified and the POA emissions are distributed by volatility based on dilution experiments. The model predictions are compared with observations from four different types of sites, an urban (T0), a suburban (T1), a rural (T2), and an elevated site in Pico de Tres Padres (PTP). The performance of the model in reproducing organic mass concentrations in these sites is encouraging. The average predicted PM[subscript 1] organic aerosol (OA) concentration in T0, T1, and T2 is 18 μg m[superscript −3], 11.7 μg m[superscript −3], and 10.5 μg m[superscript −3] respectively, while the corresponding measured values are 17.2 μg m[superscript −3], 11 μg m[superscript −3], and 9 μg m[superscript −3]. The average predicted locally-emitted primary OA concentrations, 4.4 μg m[superscript −3] at T0, 1.2 μg m[superscript −3] at T1 and 1.7 μg m[superscript −3] at PTP, are in reasonably good agreement with the corresponding PMF analysis estimates based on the Aerosol Mass Spectrometer (AMS) observations of 4.5, 1.3, and 2.9 μg m[superscript −3] respectively. The model reproduces reasonably well the average oxygenated OA (OOA) levels in T0 (7.5 μg m[superscript −3] predicted versus 7.5 μg m[superscript −3] measured), in T1 (6.3 μg m[superscript −3] predicted versus 4.6 μg m[superscript −3] measured) and in PTP (6.6 μg m[superscript −3] predicted versus 5.9 μg m[superscript −3] measured). The rest of the OA mass (6.1 μg m[superscript −3] and 4.2 μg m[superscript −3] in T0 and T1 respectively) is assumed to originate from biomass burning activities and is introduced to the model as part of the boundary conditions. Inside Mexico City (at T0), the locally-produced OA is predicted to be on average 60 % locally-emitted primary (POA), 6 % semi-volatile (S-SOA) and intermediate volatile (I-SOA) organic aerosol, and 34 % traditional SOA from the oxidation of VOCs (V-SOA). The average contributions of the OA components to the locally-produced OA for the entire modelling domain are predicted to be 32 % POA, 10 % S-SOA and I-SOA, and 58 % V-SOA. The long range transport from biomass burning activities and other sources in Mexico is predicted to contribute on average almost as much as the local sources during the MILAGRO period.European UnionSeventh Framework Programme (European Commission) (Grant agreement no.: 212520)National Science Foundation (U.S.) (ATM 0732598)Molina Center for Energy and the EnvironmentNational Science Foundation (U.S.) (ATM 0528227)National Science Foundation (U.S.) (ATM 0810931

GARP and EARP are required for efficient BoHV-1 replication as identified by a genome wide CRISPR knockout screen

The advances in gene editing bring unprecedented opportunities in high throughput functional genomics to animal research. Here we describe a genome wide CRISPR knockout library, btCRISPRko.v1, targeting all protein coding genes in the cattle genome. Using it, we conducted genome wide screens during Bovine Herpes Virus type 1 (BoHV-1) replication and compiled a list of pro-viral and anti-viral candidates. These candidates might influence multiple aspects of BoHV-1 biology such as viral entry, genome replication and transcription, viral protein trafficking and virion maturation in the cytoplasm. Some of the most intriguing examples are VPS51, VPS52 and VPS53 that code for subunits of two membrane tethering complexes, the endosome-associated recycling protein (EARP) complex and the Golgi-associated retrograde protein (GARP) complex. These complexes mediate endosomal recycling and retrograde trafficking to the trans Golgi Network (TGN). Simultaneous loss of both complexes in MDBKs resulted in greatly reduced production of infectious BoHV-1 virions. We also found that viruses released by these deficient cells severely lack VP8, the most abundant tegument protein of BoHV-1 that are crucial for its virulence. In combination with previous reports, our data suggest vital roles GARP and EARP play during viral protein packaging and capsid re-envelopment in the cytoplasm. It also contributes to evidence that both the TGN and the recycling endosomes are recruited in this process, mediated by these complexes. The btCRISPRko.v1 library generated here has been controlled for quality and shown to be effective in host gene discovery. We hope it will facilitate efforts in the study of other pathogens and various aspects of cell biology in cattle.</p

Simulations of organic aerosol concentrations in Mexico City using the WRF-CHEM model during the MCMA-2006/MILAGRO campaign

Organic aerosol concentrations are simulated using the WRF-CHEM model in Mexico City during the period from 24 to 29 March in association with the MILAGRO-2006 campaign. Two approaches are employed to predict the variation and spatial distribution of the organic aerosol concentrations: (1) a traditional 2-product secondary organic aerosol (SOA) model with non-volatile primary organic aerosols (POA); (2) a non-traditional SOA model including the volatility basis-set modeling method in which primary organic components are assumed to be semi-volatile and photochemically reactive and are distributed in logarithmically spaced volatility bins. The MCMA (Mexico City Metropolitan Area) 2006 official emission inventory is used in simulations and the POA emissions are modified and distributed by volatility based on dilution experiments for the non-traditional SOA model. The model results are compared to the Aerosol Mass Spectrometry (AMS) observations analyzed using the Positive Matrix Factorization (PMF) technique at an urban background site (T0) and a suburban background site (T1) in Mexico City. The traditional SOA model frequently underestimates the observed POA concentrations during rush hours and overestimates the observations in the rest of the time in the city. The model also substantially underestimates the observed SOA concentrations, particularly during daytime, and only produces 21% and 25% of the observed SOA mass in the suburban and urban area, respectively. The non-traditional SOA model performs well in simulating the POA variation, but still overestimates during daytime in the urban area. The SOA simulations are significantly improved in the non-traditional SOA model compared to the traditional SOA model and the SOA production is increased by more than 100% in the city. However, the underestimation during daytime is still salient in the urban area and the non-traditional model also fails to reproduce the high level of SOA concentrations in the suburban area. In the non-traditional SOA model, the aging process of primary organic components considerably decreases the OH levels in simulations and further impacts the SOA formation. If the aging process in the non-traditional model does not have feedback on the OH in the gas-phase chemistry, the SOA production is enhanced by more than 10% compared to the simulations with the OH feedback during daytime, and the gap between the simulations and observations in the urban area is around 3 μg m[superscript −3] or 20% on average during late morning and early afternoon, within the uncertainty from the AMS measurements and PMF analysis. In addition, glyoxal and methylglyoxal can contribute up to approximately 10% of the observed SOA mass in the urban area and 4% in the suburban area. Including the non-OH feedback and the contribution of glyoxal and methylglyoxal, the non-traditional SOA model can explain up to 83% of the observed SOA in the urban area, and the underestimation during late morning and early afternoon is reduced to 0.9 μg m[superscript −3] or 6% on average. Considering the uncertainties from measurements, emissions, meteorological conditions, aging of semi-volatile and intermediate volatile organic compounds, and contributions from background transport, the non-traditional SOA model is capable of closing the gap in SOA mass between measurements and models.National Science Foundation (U.S.). Atmospheric Chemistry Program (ATM-0528227)National Science Foundation (U.S.). Atmospheric Chemistry Program (ATM-0810931)Molina Center for Energy and the Environmen

Ozone response to emission changes: a modeling study during the MCMA-2006/MILAGRO Campaign

The sensitivity of ozone production to precursor emissions was investigated under five different meteorological conditions in the Mexico City Metropolitan Area (MCMA) during the MCMA-2006/MILAGRO field campaign using the gridded photochemical model CAMx driven by observation-nudged WRF meteorology. Precursor emissions were constrained by the comprehensive data from the field campaign and the routine ambient air quality monitoring network. Simulated plume mixing and transport were examined by comparing with measurements from the G-1 aircraft during the campaign. The observed concentrations of ozone precursors and ozone were reasonably well reproduced by the model. The effects of reducing precursor emissions on urban ozone production were performed for three representative emission control scenarios. A 50% reduction in VOC emissions led to 7 to 22 ppb decrease in daily maximum ozone concentrations, while a 50% reduction in NOx [NO subscript x] emissions leads to 4 to 21 ppb increase, and 50% reductions in both NOx [NO subscript x] and VOC emission decrease the daily maximum ozone concentrations up to 10 ppb. These results along with a chemical indicator analysis using the chemical production ratios of H2O2 [H subscript 2 O subscript 2] to HNO3 [HNO subscript 3] demonstrate that the MCMA urban core region is VOC-limited for all meteorological episodes, which is consistent with the results from MCMA-2003 field campaign; however the degree of the VOC-sensitivity is higher during MCMA-2006 due to lower VOCs, lower VOC reactivity and moderately higher NOx [NO subscript x] emissions. Ozone formation in the surrounding mountain/rural area is mostly NOx-limited [NO subscript x - limited], but can be VOC-limited, and the range of the NOx-limited [NO subscript x - limited] or VOC-limited areas depends on meteorology.United States. Dept. of Energy. Office of Biological and Environmental Research. Atmospheric Science Program (DE-FG02-05ER63980)National Science Foundation (U.S.). Atmospheric Chemistry Program (ATM-0528227)National Science Foundation (U.S.). Atmospheric Chemistry Program (ATM-810931)Mexico. Comisión Ambiental MetropolitanaMolina Center for Energy and the Environmen

Evaluation of the volatility basis-set approach for the simulation of organic aerosol formation in the Mexico City metropolitan area

New primary and secondary organic aerosol modules have been added to PMCAMx, a three dimensional chemical transport model (CTM), for use with the SAPRC99 chemistry mechanism based on recent smog chamber studies. The new modeling framework is based on the volatility basis-set approach: both primary and secondary organic components are assumed to be semivolatile and photochemically reactive and are distributed in logarithmically spaced volatility bins. This new framework with the use of the new volatility basis parameters for low-NOx [low - NO subscript x] and high-NOx [high - NO subscript x] conditions tends to predict 4–6 times higher anthropogenic SOA concentrations than those predicted with older generation of models. The resulting PMCAMx-2008 was applied in Mexico City Metropolitan Area (MCMA) for approximately a week during April of 2003. The emission inventory, which uses as starting point the MCMA 2004 official inventory, is modified and the primary organic aerosol (POA) emissions are distributed by volatility based on dilution experiments. The predicted organic aerosol (OA) concentrations peak in the center of Mexico City reaching values above 40 μg [mu g] m−3 [m superscript -3]. The model predictions are compared with Aerosol Mass Spectrometry (AMS) observations and their Positive Matrix Factorization (PMF) analysis. The model reproduces both Hydrocarbon-like Organic Aerosol (HOA) and Oxygenated Organic Aerosol (OOA) concentrations and diurnal profiles. The small OA underprediction during the rush hour periods and overprediction in the afternoon suggest potential improvements to the description of fresh primary organic emissions and the formation of the oxygenated organic aerosols respectively, although they may also be due to errors in the simulation of dispersion and vertical mixing. However, the AMS OOA data are not specific enough to prove that the model reproduces the organic aerosol observations for the right reasons. Other combinations of contributions of primary, aged primary, and secondary organic aerosol production rates may lead to similar results. The model results suggest strongly that during the simulated period transport of OA from outside the city was a significant contributor to the observed OA levels. Future simulations should use a larger domain in order to test whether the regional OA can be predicted with current SOA parameterizations. Sensitivity tests indicate that the predicted OA concentration is especially sensitive to the volatility distribution of the emissions in the lower volatility bins.Seventh Framework Programme (European Commission)European UnionMEGAPOLI (Project) (Grant agreement no. 212520)Molina Center for Energy and the EnvironmentUnited States. National Oceanic and Atmospheric Administration. Office of Global Programs (Grant NA08OAR4310565)National Science Foundation (U.S.) (Grant ATM-0528634)National Science Foundation (U.S.) (Grant ATM-0528227)United States. Dept. of Energy. Office of Biological and Environmental Research. Atmospheric Science Program (DEFG0208ER64627