9 research outputs found
Modulation of host cell processes by T3SS effectors
Two of the enteric Escherichia coli pathotypes-enteropathogenic E. coli (EPEC) and enterohaemorrhagic E. coli (EHEC)-have a conserved type 3 secretion system which is essential for virulence. The T3SS is used to translocate between 25 and 50 bacterial proteins directly into the host cytosol where they manipulate a variety of host cell processes to establish a successful infection. In this chapter, we discuss effectors from EPEC/EHEC in the context of the host proteins and processes that they target-the actin cytoskeleton, small guanosine triphosphatases and innate immune signalling pathways that regulate inflammation and cell death. Many of these translocated proteins have been extensively characterised, which has helped obtain insights into the mechanisms of pathogenesis of these bacteria and also understand the host pathways they target in more detail. With increasing knowledge of the positive and negative regulation of host signalling pathways by different effectors, a future challenge is to investigate how the specific effector repertoire of each strain cooperates over the course of an infection
Modeling regional air quality and climate: Improving organic aerosol and aerosol activation processes in WRF/Chem version 3.7.1
Air quality and climate influence each other through the uncertain processes of aerosol formation and cloud droplet activation. In this study, both processes are improved in the Weather, Research and Forecasting model with Chemistry (WRF/Chem) version 3.7.1. The existing Volatility Basis Set (VBS) treatments for organic aerosol (OA) formation in WRF/Chem are improved by considering the following: the secondary OA (SOA) formation from semi-volatile primary organic aerosol (POA), a semi-empirical formulation for the enthalpy of vaporization of SOA, and functionalization and fragmentation reactions for multiple generations of products from the oxidation of VOCs. Over the continental US, 2-month-long simulations (May to June 2010) are conducted and results are evaluated against surface and aircraft observations during the Nexus of Air Quality and Climate Change (CalNex) campaign. Among all the configurations considered, the best performance is found for the simulation with the 2005 Carbon Bond mechanism (CB05) and the VBS SOA module with semivolatile POA treatment, 25% fragmentation, and the emissions of semi-volatile and intermediate volatile organic compounds being 3 times the original POA emissions. Among the three gas-phase mechanisms (CB05, CB6, and SAPRC07) used, CB05 gives the best performance for surface ozone and PM2.5 concentrations. Differences in SOA predictions are larger for the simulations with different VBS treatments (e.g., nonvolatile POA versus semivolatile POA) compared to the simulations with different gas-phase mechanisms. Compared to the simulation with CB05 and the default SOA module, the simulations with the VBS treatment improve cloud droplet number concentration (CDNC) predictions (normalized mean biases from -40.8% to a range of -34.6 to -27.7%), with large differences between CB05-CB6 and SAPRC07 due to large differences in their OH and HO2 predictions. An advanced aerosol activation parameterization based on the Fountoukis and Nenes (2005) series reduces the large negative CDNC bias associated with the default Abdul Razzak and Ghan (2000) parameterization from -35.4% to a range of -0.8 to 7.1%. However, it increases the errors due to overpredictions of CDNC, mainly over the northeastern US. This work indicates a need to improve other aerosol-cloud-radiation processes in the model, such as the spatial distribution of aerosol optical depth and cloud condensation nuclei, in order to further improve CDNC predictions. © Author(s) 2017
Decadal evaluation of regional climate, air quality, and their interactions over the continental US and their interactions using WRF/Chem version 3.6.1
The Weather Research and Forecasting model with Chemistry (WRF/Chem) v3.6.1
with the Carbon Bond 2005 (CB05) gas-phase mechanism is evaluated for its
first decadal application during 2001–2010 using the Representative
Concentration Pathway 8.5 (RCP 8.5) emissions to assess its capability and
appropriateness for long-term climatological simulations. The initial and
boundary conditions are downscaled from the modified Community Earth System
Model/Community Atmosphere Model (CESM/CAM5) v1.2.2. The meteorological
initial and boundary conditions are bias-corrected using the National Center
for Environmental Protection's Final (FNL) Operational Global Analysis data.
Climatological evaluations are carried out for meteorological, chemical, and
aerosol–cloud–radiation variables against data from surface networks and
satellite retrievals. The model performs very well for the 2 m temperature
(T2) for the 10-year period, with only a small cold bias of
−0.3 °C. Biases in other meteorological variables including
relative humidity at 2 m, wind speed at 10 m, and precipitation tend to be
site- and season-specific; however, with the exception of T2, consistent
annual biases exist for most of the years from 2001 to 2010. Ozone mixing
ratios are slightly overpredicted at both urban and rural locations with a
normalized mean bias (NMB) of 9.7 % but underpredicted at rural locations
with an NMB of −8.8 %. PM<sub>2.5</sub> concentrations are moderately
overpredicted with an NMB of 23.3 % at rural sites but slightly
underpredicted with an NMB of −10.8 % at urban/suburban sites. In
general, the model performs relatively well for chemical and meteorological
variables, and not as well for aerosol–cloud–radiation variables.
Cloud-aerosol variables including aerosol optical depth, cloud water path,
cloud optical thickness, and cloud droplet number concentration are generally
underpredicted on average across the continental US. Overpredictions of
several cloud variables over the eastern US result in underpredictions of
radiation variables (such as net shortwave radiation – GSW – with a mean
bias – MB – of −5.7 W m<sup>−2</sup>) and overpredictions of shortwave and
longwave cloud forcing (MBs of  ∼  7 to 8 W m<sup>−2</sup>), which are
important climate variables. While the current performance is deemed to be
acceptable, improvements to the bias-correction method for CESM downscaling
and the model parameterizations of cloud dynamics and thermodynamics, as well
as aerosol–cloud interactions, can potentially improve model performance for
long-term climate simulations
CESM/CAM5 improvement and application: comparison and evaluation of updated CB05_GE and MOZART-4 gas-phase mechanisms and associated impacts on global air quality and climate
Atmospheric chemistry plays a key role in determining the amounts and
distributions of oxidants and gaseous precursors that control the formation
of secondary gaseous and aerosol pollutants; all of those species can
interact with the climate system. To understand the impacts of different
gas-phase mechanisms on global air quality and climate predictions, in this
work, a comprehensive comparative evaluation is performed using the Community
Atmosphere Model (CAM) Version 5 with comprehensive tropospheric and
stratospheric chemistry (CAM5-chem) within the Community Earth System Model
(CESM) with the two most commonly used gas-phase chemical mechanisms: the
2005 Carbon Bond mechanism with Global Extension (CB05_GE) and the Model of
OZone and Related chemical Tracers version 4 (MOZART-4) mechanism with
additional updates (MOZART-4x). MOZART-4x and CB05_GE use different
approaches to represent volatile organic compounds (VOCs) and different
surrogates for secondary organic aerosol (SOA) precursors. MOZART-4x includes
a more detailed representation of isoprene chemistry compared to CB05_GE.
CB05_GE includes additional oxidation of SO<sub>2</sub> by O<sub>3</sub> over the
surface of dust particles, which is not included in MOZART-4x. The results
show that the two CAM5-chem simulations with CB05_GE and MOZART-4x predict
similar chemical profiles for major gases (e.g., O<sub>3</sub>, CO, and NO<sub><i>x</i></sub>)
compared to the aircraft measurements, with generally better agreement for
NO<sub><i>y</i></sub> profiles by CB05_GE than MOZART-4x. The concentrations of SOA at
four sites in the continental US (CONUS) and organic carbon (OC) over the
IMPROVE sites are well predicted by MOZART-4x (with normalized mean biases
(NMBs) of −1.9 and 2.1 %, respectively) but moderately underpredicted
by CB05_GE (with NMBs of −23.1 and −20.7 %, respectively). This is
mainly due to the higher biogenic emissions and OH levels simulated with
MOZART-4x than with CB05_GE. The concentrations of OC over Europe are
largely underpredicted by both MOZART-4x and CB05_GE, with NMBs of −73.0
and −75.1 %, respectively, indicating the uncertainties in the
emissions of precursors and primary OC and relevant model treatments such as
the oxidations of VOCs and SOA formation. Uncertainties in the emissions and
convection scheme can contribute to the large bias in the model predictions
(e.g., SO<sub>2</sub>, CO, black carbon, and aerosol optical depth). The two
simulations also have similar cloud/radiative predictions, with a slightly
better performance of domain average cloud condensation nuclei (CCN) at
supersaturation of 0.5 % by CB05_GE, but slightly better agreement with
observed CCN (at supersaturation of 0.2 %) profile over Beijing by
MOZART-4x. The two gas-phase mechanisms result in a global average difference
of 0.5 W m<sup>−2</sup> in simulated shortwave cloud radiative forcing, with
significant differences (e.g., up to 13.6 W m<sup>−2</sup>) over subtropical
regions
Development and initial application of the global-through-urban weather research and forecasting model with chemistry (GU-WRF/Chem)
A unified model framework with online-coupled meteorology and chemistry and consistent model treatments across spatial scales is required to realistically simulate chemistry-aerosol-cloud-radiation-precipitation-climate interactions. In this work, a global-through-urban WRF/Chem model (i.e., GU-WRF/Chem) has been developed to provide such a unified model framework to simulate these important interactions across a wide range of spatial scales while reducing uncertainties from the use of offline-coupled model systems with inconsistent model treatments. Evaluation against available observations shows that GU-WRF/Chem is capable of reproducing observations with comparable or superior fidelity than existing mesoscale models. The net effect of atmospheric aerosols is to decrease shortwave and longwave radiation, NO2 photolysis rate, near-surface temperature, wind speed at 10-m, planetary boundary layer height, and precipitation as well as to increase relative humidity at 2-m, aerosol optical depths, column cloud condensation nuclei, cloud optical thickness, and cloud droplet number concentrations at all scales. As expected, such feedbacks also change the abundance and lifetimes of chemical species through changing radiation, atmospheric stability, and the rates of many meteorologically- dependent chemical and microphysical processes. The use of higher resolutions in progressively nested domains from the global to local scale notably improves the model performance of some model predictions (especially for chemical predictions) and also captures spatial variability of aerosol feedbacks that cannot be simulated at a coarser grid resolution. Simulated aerosol, radiation, and cloud properties exhibit small-to-high sensitivity to various nucleation and aerosol activation parameterizations. Representing one of the few unified global-through-urban models, GU-WRF/Chem can be applied to simulate air quality and its interactions with meteorology and climate and to quantify the impact of global change on urban/regional air quality across various spatial scales. © 2012. American Geophysical Union. All Rights Reserved