Characterization of aerosol pollution events in France using ground-based and POLDER-2 satellite data

We analyze the relationship between daily fine particle mass concentration (PM2.5) and columnar aerosol optical thickness derived from the Polarization and Directionality of Earth's Reflectances (POLDER) satellite sensor. The study is focused over France during the POLDER-2 lifetime between April and October 2003. We have first compared the POLDER derived aerosol optical thickness (AOT) with integrated volume size distribution derived from ground-based Sun Photometer observations. The good correlation (R=0.72) with sub-micron volume fraction indicates that POLDER derived AOT is sensitive to the fine aerosol mass concentration. Considering 1974 match-up data points over 28 fine particle monitoring sites, the POLDER-2 derived AOT is fairly well correlated with collocated PM2.5 measurements, with a correlation coefficient of 0.55. The correlation coefficient reaches a maximum of 0.80 for particular sites. We have analyzed the probability to find an appropriate air quality category (AQC) as defined by U.S. Environmental Protection Agency (EPA) from POLDER-2 AOT measurements. The probability can be up to 88.8% (±3.7%) for the "Good" AQC and 89.1% (±3.6%) for the "Moderate" AQC

Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops

BACKGROUND: Public databases now contain multitude of complete bacterial genomes, including several genomes of the same species. The available data offers new opportunities to address questions about bacterial genome evolution, a task that requires reliable fine comparison data of closely related genomes. Recent analyses have shown, using pairwise whole genome alignments, that it is possible to segment bacterial genomes into a common conserved backbone and strain-specific sequences called loops. RESULTS: Here, we generalize this approach and propose a strategy that allows systematic and non-biased genome segmentation based on multiple genome alignments. Segmentation analyses, as applied to 13 different bacterial species, confirmed the feasibility of our approach to discern the 'mosaic' organization of bacterial genomes. Segmentation results are available through a Web interface permitting functional analysis, extraction and visualization of the backbone/loops structure of documented genomes. To illustrate the potential of this approach, we performed a precise analysis of the mosaic organization of three E. coli strains and functional characterization of the loops. CONCLUSION: The segmentation results including the backbone/loops structure of 13 bacterial species genomes are new and available for use by the scientific community at the URL:

Direct radiative effect of the Russian wildfires and its impact on air temperature and atmospheric dynamics during August 2010

International audienceIn this study, we investigate the shortwave aerosol direct radiative forcing (ADRF) and its feedback on air temperature and atmospheric dynamics during a major fire event that occurred in Russia during August 2010. The methodology is based on an offline coupling between the CHIMERE chemistry-transport and the Weather Research and Forecasting (WRF) models. First, simulations for the period 5–12 August 2010 have been evaluated by using AERONET (AErosol RObotic NETwork) and satellite measurements of the POLarization and Directionality of the Earth's Reflectance (POLDER) and the Cloud-Aerosol LIdar with Orthogonal Polarization (CALIOP) sensors. During this period, elevated POLDER aerosol optical thickness (AOT) is found over a large part of eastern Europe, with values above 2 (at 550 nm) in the aerosol plume. According to CALIOP observations, particles remain confined to the first five kilometres of the atmospheric layer. Comparisons with satellite measurements show the ability of CHIMERE to reproduce the regional and vertical distribution of aerosols during their transport from the source region. Over Moscow, AERONET measurements indicate an important increase of AOT (340 nm) from 0.7 on 5 August to 2–4 between 6 and 10 August when the aerosol plume was advected over the city. Particles are mainly observed in the fine size mode (radius in the range 0.2–0.4 μm) and are characterized by elevated single-scattering albedo (SSA) (0.95–0.96 between 440 and 1020 nm). Comparisons of simulations with AERONET measurements show that aerosol physical–optical properties (size distribution, AOT, SSA) have been well simulated over Moscow in terms of intensity and/or spectral dependence. Secondly, modelled aerosol optical properties have been used as input in the radiative transfer code of WRF to evaluate their direct radiative impact. Simulations indicate a significant reduction of solar radiation at the ground (up to 80–150 W m−2 in diurnal averages over a large part of eastern Europe due to the presence of the aerosol plume. This ADRF causes an important reduction of the near-surface air temperature between 0.2 and 2.6° on a regional scale. Moscow has been affected by the aerosol plume, especially between 6 and 10 August. During this period, aerosol causes a significant reduction of surface shortwave radiation (up to 70–84 W m−2 in diurnal averages) with a moderate part (20–30%) due to solar absorption within the aerosol layer. The resulting feedbacks lead to a cooling of the air up to 1.6° at the surface and 0.1° at an altitude of 1500–2000 m (in diurnal averages), that contribute to stabilize the atmospheric boundary layer (ABL). Indeed, a reduction of the ABL height of 13 to 65% has been simulated during daytime in presence of aerosols. This decrease is the result of a lower air entrainment as the vertical wind speed in the ABL is shown to be reduced by 5 to 80% (at midday) when the feedback of the ADRF is taken into account. However, the ADRF is shown to have a lower impact on the horizontal wind speed, suggesting that the dilution of particles would be mainly affected by the weakening of the ABL development and associated vertical entrainment. Indeed, CHIMERE simulations driven by the WRF meteorological fields including this ADRF feedback result in a large increase in the modelled near-surface PM10 concentrations (up to 99%). This is due to their lower vertical dilution in the ABL, which tend to reduce model biases with the ground PM10 values observed over Moscow during this specific period

Arbuscular cell invasion coincides with extracellular vesicles and membrane tubules

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Assessing the Performance of Single-Copy Genes for Recovering Robust Phylogenies

International audienc

MOSAIC: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level

BACKGROUND: The recent availability of complete sequences for numerous closely related bacterial genomes opens up new challenges in comparative genomics. Several methods have been developed to align complete genomes at the nucleotide level but their use and the biological interpretation of results are not straightforward. It is therefore necessary to develop new resources to access, analyze, and visualize genome comparisons. DESCRIPTION: Here we present recent developments on MOSAIC, a generalist comparative bacterial genome database. This database provides the bacteriologist community with easy access to comparisons of complete bacterial genomes at the intra-species level. The strategy we developed for comparison allows us to define two types of regions in bacterial genomes: backbone segments (i.e., regions conserved in all compared strains) and variable segments (i.e., regions that are either specific to or variable in one of the aligned genomes). Definition of these segments at the nucleotide level allows precise comparative and evolutionary analyses of both coding and non-coding regions of bacterial genomes. Such work is easily performed using the MOSAIC Web interface, which allows browsing and graphical visualization of genome comparisons. CONCLUSION: The MOSAIC database now includes 493 pairwise comparisons and 35 multiple maximal comparisons representing 78 bacterial species. Genome conserved regions (backbones) and variable segments are presented in various formats for further analysis. A graphical interface allows visualization of aligned genomes and functional annotations. The MOSAIC database is available online at http://genome.jouy.inra.fr/mosaic

Persistencia de mediciones como apoyo a la gestión de proyectos de software

La medida de la calidad del software es una necesidad para las empresas de Software y Servicios Informáticos (SSI), porque representa una ventaja estratégica al proporcionar el conocimiento de los procesos productivos y permitir mejorar las tareas menos eficientes. La calidad del software está estrechamente vinculada con la medición del mismo. La implementación exitosa en una organización de una nueva práctica o el uso de una herramienta depende en gran medida de la automatización de la misma, a fin de no significar una pérdida de tiempo o uso de recursos adicionales. En este trabajo se presenta una línea de investigación que apunta a la elaboración de metodologías de medición de atributos, recolección de datos, y diseño e implementación de un repositorio de mediciones, que contribuya a una más eficiente gestión de proyectos de software y a la toma de decisiones en aspectos referidos a la calidad de software.Eje: Ingeniería de SoftwareRed de Universidades con Carreras en Informática (RedUNCI

Efficient 3‐Hydroxybutyrate Production by Quiescent Escherichia coli Microbial Cell Factories is Facilitated by Indole‐Induced Proteomic and Metabolomic Changes

The authors show that quiescent (Q‐Cell) Escherichia coli cultures can maintain metabolic activity in the absence of growth for up to 24 h, leading to four times greater specific productivity of a model metabolite, 3‐hydroxybutyrate (3HB), than a control. Q‐cells can be created by using the proton ionophore indole to halt cell division of an hns mutant strain. This uncouples metabolism from cell growth and allows for more efficient use of carbon feedstocks because less metabolic effort is diverted to surplus biomass production. However, the reason for the increased productivity of cells in the quiescent state was previously unknown. In this study, proteome expression patterns between wild‐type and Q‐cell cultures show that Q‐cells overexpress stress response proteins, which prime them to tolerate the metabolic imbalances incurred through indole addition. Metabolomic data reveal the accumulation of acetyl‐coenzyme A and phosphoenolpyruvate: excellent starting points for high‐value chemical production. We demonstrate the exploitation of these accumulated metabolites by engineering a simple pathway for 3HB production from acetyl‐coenzyme A. Quiescent cultures produced half the cell biomass of control cultures lacking indole, but were still able to produce 39.4 g L−1 of 3HB compared to 18.6 g L−1 in the control. Q‐cells therefore have great potential as a platform technology for the efficient production of a wide range of commodity and high value chemicals

Characterization of atmospheric aerosols at Monte Cimone, Italy, during summer 2004: Source apportionment and transport mechanisms

Atmospheric aerosols in the PM10 and PM1 fractions have been sampled at the Global Atmospheric Watch station Mount Cimone, Italy (2165 m above mean sea level) for 3 months during summer 2004, and simultaneous size distributions have been derived by means of an optical particle counter. Samples have been analyzed by X-ray fluorescence, ion chromatography, and thermal-optical methodology in order to quantify their elemental, ionic, and carbonaceous constituents. The concentration of PM10 was 16.1 \ub1 9.8 mg m3 (average and standard deviation). Source apportionment allowed us to identify, quantify and characterize the following aerosol classes: anthropogenic pollution (10 mg m3), mineral dust (4 mg m3), and sea salt (0.2 mg m3). Pollution has been further split into ammonium sulfate (44%), organic matter (42%), and other compounds (14%). The nitrate/sulfate ratio in the polluted aerosol was 0.1. Fine particles have been completely related to the polluted aerosol component, and they represented 70% in weight of pollution. Coarse particles characterized the dust and salt components, and crustal oxides have been found to be the largest responsible for the aerosol concentration variations that occurred during the campaign. Nitrate has also been found in the coarse particles, representing 10% of mineral dust. The analysis of the transport mechanisms responsible for aerosol fluctuations permitted us to identify the origin of the major aerosol components: Pollution has been ascribed to regional transport driven by boundary layer meteorology, whereas mineral dust has been related to long-range transport events originating in the Sahara and Sahel. A particularly significant Saharan episode has been identified on 10 August 2004 (PM10 daily concentration, 69.9 mg m3). Average elemental ratios for the African dust events were as follows: Si/Al = 2.31, Fe/Ca = 0.94, Ca/Al = 0.90, K/Ca = 0.44, Ti/Ca = 0.11, and Ti/Fe = 0.12