Trace gas/aerosol boundary concentrations and their impacts on continental-scale AQMEII modeling domains

Copyright 2011 Elsevier B.V., All rights reserved.Over twenty modeling groups are participating in the Air Quality Model Evaluation International Initiative (AQMEII) in which a variety of mesoscale photochemical and aerosol air quality modeling systems are being applied to continental-scale domains in North America and Europe for 2006 full-year simulations for model inter-comparisons and evaluations. To better understand the reasons for differences in model results among these participating groups, each group was asked to use the same source of emissions and boundary concentration data for their simulations. This paper describes the development and application of the boundary concentration data for this AQMEII modeling exercise. The European project known as GEMS (Global and regional Earth-system Monitoring using Satellite and in-situ data) has produced global-scale re-analyses of air quality for several years, including 2006 (http://gems.ecmwf.int). The GEMS trace gas and aerosol data were made available at 3-hourly intervals on a regular latitude/longitude grid of approximately 1.9° resolution within 2 "cut-outs" from the global model domain. One cut-out was centered over North America and the other over Europe, covering sufficient spatial domain for each modeling group to extract the necessary time- and space-varying (horizontal and vertical) concentrations for their mesoscale model boundaries. Examples of the impact of these boundary concentrations on the AQMEII continental simulations are presented to quantify the sensitivity of the simulations to boundary concentrations. In addition, some participating groups were not able to use the GEMS data and instead relied upon other sources for their boundary concentration specifications. These are noted, and the contrasting impacts of other data sources for boundary data are presented. How one specifies four-dimensional boundary concentrations for mesoscale air quality simulations can have a profound impact on the model results, and hence, this aspect of data preparation must be performed with considerable care.Peer reviewedFinal Accepted Versio

Forecasts and assimilation experiments of the Antarctic ozone hole 2008

The 2008 Antarctic ozone hole was one of the largest and most long-lived in recent years. Predictions of the ozone hole were made in near-real time (NRT) and hindcast mode with the Integrated Forecast System (IFS) of the European Centre for Medium-Range Weather Forecasts (ECMWF). The forecasts were carried out both with and without assimilation of satellite observations from multiple instruments to provide more realistic initial conditions. Three different chemistry schemes were applied for the description of stratospheric ozone chemistry: (i) a linearization of the ozone chemistry, (ii) the stratospheric chemical mechanism of the Model of Ozone and Related Chemical Tracers, version 3, (MOZART-3) and (iii) the relaxation to climatology as implemented in the Transport Model, version 5, (TM5). The IFS uses the latter two schemes by means of a two-way coupled system. Without assimilation, the forecasts showed model-specific shortcomings in predicting start time, extent and duration of the ozone hole. The assimilation of satellite observations from the Microwave Limb Sounder (MLS), the Ozone Monitoring Instrument (OMI), the Solar Backscattering Ultraviolet radiometer (SBUV-2) and the SCanning Imaging Absorption spectroMeter for Atmospheric CartograpHY (SCIAMACHY) led to a significant improvement of the forecasts when compared with total columns and vertical profiles from ozone sondes. The combined assimilation of observations from multiple instruments helped to overcome limitations of the ultraviolet (UV) sensors at low solar elevation over Antarctica. The assimilation of data from MLS was crucial to obtain a good agreement with the observed ozone profiles both in the polar stratosphere and troposphere. The ozone analyses by the three model configurations were very similar despite the different underlying chemistry schemes. Using ozone analyses as initial conditions had a very beneficial but variable effect on the predictability of the ozone hole over 15 days. The initialized forecasts with the MOZART-3 chemistry produced the best predictions of the increasing ozone hole whereas the linear scheme showed the best results during the ozonehole closure

Titanite Mineralization of Microbial Bioalteration Textures in Jurassic Volcanic Glass, Coast Range Ophiolite, California

Volcanic glasses are rarely preserved in the rock record, and the quality of preservation generally declines with increasing age. Records preserved in ancient basaltic glasses therefore provide important links between processes operating in the distant past, and those that are active on the Earth today. Microbial colonization has been linked to the formation of characteristic structures in basaltic glass, including tubules and granule-filled tubules, which are thought to be produced by microbially mediated glass dissolution. Structures of similar occurrence and morphology but filled almost entirely with fine-grained titanite have been documented in some ancient metabasalts. It has been suggested that the ancient titanite-mineralized structures are mineralized equivalents of hollow tubules in modern glassy basaltic rocks, but a direct link has not been firmly established. We report the discovery of tubular bioalteration structures in fresh and minimally altered basaltic glasses of middle Jurassic (164 Ma) age from the Stonyford Volcanic Complex (SFVC), Coast Range Ophiolite, California. Tubular structures hosted in unaltered basaltic glass are typically hollow, whilst those in zones of zeolitic alteration are mineralized by titanite. Tubules are continuous across zeolite-glass interfaces, which mark an abrupt change from titanite-filled to hollow tubules, demonstrating that titanite growth occurs preferentially within pre-existing tubular structures. Titanite mineralization in the SFVC represent a link between tubular structures in modern basaltic glass and titanite-mineralized features of similar morphology and spatial distribution in ancient metabasalts. Our observations support a link between textures in modern glassy basaltic rocks and some of the oldest-known putative ichnofossils

Global model simulations of air pollution during the 2003 European heat wave

Three global Chemistry Transport Models - MOZART, MOCAGE, and TM5 - as well as MOZART coupled to the IFS meteorological model including assimilation of ozone (O-3) and carbon monoxide (CO) satellite column retrievals, have been compared to surface measurements and MOZAIC vertical profiles in the troposphere over Western/Central Europe for summer 2003. The models reproduce the meteorological features and enhancement of pollution during the period 2-14 August, but not fully the ozone and CO mixing ratios measured during that episode. Modified normalised mean biases are around -25% (except similar to 5% for MOCAGE) in the case of ozone and from -80% to -30% for CO in the boundary layer above Frankfurt. The coupling and assimilation of CO columns from MOPITT overcomes some of the deficiencies in the treatment of transport, chemistry and emissions in MOZART, reducing the negative biases to around 20%. The high reactivity and small dry deposition velocities in MOCAGE seem to be responsible for the overestimation of O-3 in this model. Results from sensitivity simulations indicate that an increase of the horizontal resolution to around 1 degrees x1 degrees and potential uncertainties in European anthropogenic emissions or in long-range transport of pollution cannot completely account for the underestimation of CO and O-3 found for most models. A process-oriented TM5 sensitivity simulation where soil wetness was reduced results in a decrease in dry deposition fluxes and a subsequent ozone increase larger than the ozone changes due to the previous sensitivity runs. However this latest simulation still underestimates ozone during the heat wave and overestimates it outside that period. Most probably, a combination of the mentioned factors together with underrepresented biogenic emissions in the models, uncertainties in the modelling of vertical/horizontal transport processes in the proximity of the boundary layer as well as limitations of the chemistry schemes are responsible for the underestimation of ozone (overestimation in the case of MOCAGE) and CO found in the models during this extreme pollution event

Global model simulations of air pollution during the 2003 European heat wave

Three global Chemistry Transport Models – MOZART, MOCAGE, and TM5 – as well as MOZART coupled to the IFS meteorological model including assimilation of ozone (O<sub>3</sub>) and carbon monoxide (CO) satellite column retrievals, have been compared to surface measurements and MOZAIC vertical profiles in the troposphere over Western/Central Europe for summer 2003. The models reproduce the meteorological features and enhancement of pollution during the period 2–14 August, but not fully the ozone and CO mixing ratios measured during that episode. Modified normalised mean biases are around −25% (except ~5% for MOCAGE) in the case of ozone and from −80% to −30% for CO in the boundary layer above Frankfurt. The coupling and assimilation of CO columns from MOPITT overcomes some of the deficiencies in the treatment of transport, chemistry and emissions in MOZART, reducing the negative biases to around 20%. The high reactivity and small dry deposition velocities in MOCAGE seem to be responsible for the overestimation of O<sub>3</sub> in this model. Results from sensitivity simulations indicate that an increase of the horizontal resolution to around 1°×1° and potential uncertainties in European anthropogenic emissions or in long-range transport of pollution cannot completely account for the underestimation of CO and O<sub>3</sub> found for most models. A process-oriented TM5 sensitivity simulation where soil wetness was reduced results in a decrease in dry deposition fluxes and a subsequent ozone increase larger than the ozone changes due to the previous sensitivity runs. However this latest simulation still underestimates ozone during the heat wave and overestimates it outside that period. Most probably, a combination of the mentioned factors together with underrepresented biogenic emissions in the models, uncertainties in the modelling of vertical/horizontal transport processes in the proximity of the boundary layer as well as limitations of the chemistry schemes are responsible for the underestimation of ozone (overestimation in the case of MOCAGE) and CO found in the models during this extreme pollution event

Mechanotransduction and growth factor signalling to engineer cellular microenvironments

Engineering cellular microenvironments involves biochemical factors, the extracellular matrix (ECM) and the interaction with neighbouring cells. This progress report provides a critical overview of key studies that incorporate growth factor (GF) signalling and mechanotransduction into the design of advanced microenvironments. Materials systems have been developed for surface-bound presentation of GFs, either covalently tethered or sequestered through physico-chemical affinity to the matrix, as an alternative to soluble GFs. Furthermore, some materials contain both GF and integrin binding regions and thereby enable synergistic signalling between the two. Mechanotransduction refers to the ability of the cells to sense physical properties of the ECM and to transduce them into biochemical signals. Various aspects of the physics of the ECM, i.e. stiffness, geometry and ligand spacing, as well as time-dependent properties, such as matrix stiffening, degradability, viscoelasticity, surface mobility as well as spatial patterns and gradients of physical cues are discussed. To conclude, various examples illustrate the potential for cooperative signalling of growth factors and the physical properties of the microenvironment for potential applications in regenerative medicine, cancer research and drug testing

The Red Sea, Coastal Landscapes, and Hominin Dispersals

This chapter provides a critical assessment of environment, landscape and resources in the Red Sea region over the past five million years in relation to archaeological evidence of hominin settlement, and of current hypotheses about the role of the region as a pathway or obstacle to population dispersals between Africa and Asia and the possible significance of coastal colonization. The discussion assesses the impact of factors such as topography and the distribution of resources on land and on the seacoast, taking account of geographical variation and changes in geology, sea levels and palaeoclimate. The merits of northern and southern routes of movement at either end of the Red Sea are compared. All the evidence indicates that there has been no land connection at the southern end since the beginning of the Pliocene period, but that short sea crossings would have been possible at lowest sea-level stands with little or no technical aids. More important than the possibilities of crossing the southern channel is the nature of the resources available in the adjacent coastal zones. There were many climatic episodes wetter than today, and during these periods water draining from the Arabian escarpment provided productive conditions for large mammals and human populations in coastal regions and eastwards into the desert. During drier episodes the coastal region would have provided important refugia both in upland areas and on the emerged shelves exposed by lowered sea level, especially in the southern sector and on both sides of the Red Sea. Marine resources may have offered an added advantage in coastal areas, but evidence for their exploitation is very limited, and their role has been over-exaggerated in hypotheses of coastal colonization

Fructooligosacharides Reduce Pseudomonas aeruginosa PAO1 Pathogenicity through Distinct Mechanisms

Pseudomonas aeruginosa is ubiquitously present in the environment and acts as an opportunistic pathogen on humans, animals and plants. We report here the effects of the prebiotic polysaccharide inulin and its hydrolysed form FOS on this bacterium. FOS was found to inhibit bacterial growth of strain PAO1, while inulin did not affect growth rate or yield in a significant manner. Inulin stimulated biofilm formation, whereas a dramatic reduction of the biofilm formation was observed in the presence of FOS. Similar opposing effects were observed for bacterial motility, where FOS inhibited the swarming and twitching behaviour whereas inulin caused its stimulation. In co-cultures with eukaryotic cells (macrophages) FOS and, to a lesser extent, inulin reduced the secretion of the inflammatory cytokines IL-6, IL-10 and TNF- a . Western blot experiments indicated that the effects mediated by FOS in macrophages are associated with a decreased activation of the NF- k B pathway. Since FOS and inulin stimulate pathway activation in the absence of bacteria, the FOS mediated effect is likely to be of indirect nature, such as via a reduction of bacterial virulence. Further, this modulatory effect is observed also with the highly virulent ptxS mutated strain. Co-culture experiments of P. aeruginosa with IEC18 eukaryotic cells showed that FOS reduces the concentration of the major virulence factor, exotoxin A, suggesting that this is a possible mechanism for the reduction of pathogenicity. The potential of these compounds as components of antibacterial and anti-inflammatory cocktails is discussed.The authors acknowledge financial support from FEDER funds and Fondo Social Europeo through grants from the Spanish Ministry of Economy and Competitiveness (grants SAF2011-22922, SAF2011-22812) the Andalusian regional government Junta de Andalucía (grant CVI-7335) and the Centre of Networked Biomedical Research on Hepatic and Digestive Diseases (CIBERehd) which is funded by the Carlos III Health Institute and the Ramón Areces Foundation, Spain