A linear CO chemistry parameterization in a chemistry-transport model: evaluation and application to data assimilation

This paper presents an evaluation of a new linear parameterization valid for the troposphere and the stratosphere, based on a first order approximation of the carbon monoxide (CO) continuity equation. This linear scheme (hereinafter noted LINCO) has been implemented in the 3-D Chemical Transport Model (CTM) MOCAGE (MOdèle de Chimie Atmospherique Grande Echelle). First, a one and a half years of LINCO simulation has been compared to output obtained from a detailed chemical scheme output. The mean differences between both schemes are about ±25 ppbv (part per billion by volume) or 15% in the troposphere and ±10 ppbv or 100% in the stratosphere. Second, LINCO has been compared to diverse observations from satellite instruments covering the troposphere (Measurements Of Pollution In The Troposphere: MOPITT) and the stratosphere (Microwave Limb Sounder: MLS) and also from aircraft (Measurements of ozone and water vapour by Airbus in-service aircraft: MOZAIC programme) mostly flying in the upper troposphere and lower stratosphere (UTLS). In the troposphere, the LINCO seasonal variations as well as the vertical and horizontal distributions are quite close to MOPITT CO observations. However, a bias of ~−40 ppbv is observed at 700 Pa between LINCO and MOPITT. In the stratosphere, MLS and LINCO present similar large-scale patterns, except over the poles where the CO concentration is underestimated by the model. In the UTLS, LINCO presents small biases less than 2% compared to independent MOZAIC profiles. Third, we assimilated MOPITT CO using a variational 3D-FGAT (First Guess at Appropriate Time) method in conjunction with MOCAGE for a long run of one and a half years. The data assimilation greatly improves the vertical CO distribution in the troposphere from 700 to 350 hPa compared to independent MOZAIC profiles. At 146 hPa, the assimilated CO distribution is also improved compared to MLS observations by reducing the bias up to a factor of 2 in the tropics. This study confirms that the linear scheme is able to simulate reasonably well the CO distribution in the troposphere and in the lower stratosphere. Therefore, the low computing cost of the linear scheme opens new perspectives to make free runs and CO data assimilation runs at high resolution and over periods of several years

Midlatitude stratosphere - troposphere exchange as diagnosed by MLS O3 and MOPITT CO assimilated fields

International audienceThis paper presents a comprehensive characterization of a very deep stratospheric intrusion which occurred over the British Isles on 15 August 2007. The signature of this event is diagnosed using ozonesonde measurements over Lerwick, UK (60.14 N, 1.19 W) and is also well characterized using meteorological analyses from the global operational weather prediction model of Météo-France, ARPEGE. Modelled as well as assimilated fields of both ozone (O3) and carbon monoxide (CO) have been used in order to better document this event. O3 and CO from Aura/MLS and Terra/MOPITT instruments, respectively, are assimilated into the three-dimensional chemical transport model MOCAGE of Météo-France using a variational 3-DFGAT (First Guess at Appropriate Time) method. The validation of O3 and CO assimilated fields is done using selfconsistency diagnostics and by comparison with independent observations such as MOZAIC (O3 and CO), AIRS (CO) and OMI (O3). It particularly shows in the upper troposphere and lower stratosphere region that the assimilated fields are closer to MOZAIC than the free model run. The O3 bias between MOZAIC and the analyses is −11.5 ppbv with a RMS of 22.4 ppbv and a correlation coefficient of 0.93, whereas between MOZAIC and the free model run, the corresponding values are 33 ppbv, 38.5 ppbv and 0.83, respectively. In the same way, for CO, the bias, RMS and correlation coefficient between MOZAIC and the analyses are −3.16 ppbv, 13 ppbv and 0.79, respectively, whereas between MOZAIC and the free model run, the corresponding values are 33 ppbv, 38.5 ppbv and 0.83, respectively. In the same way, for CO, the bias, RMS and correlation coefficient between MOZAIC and the analyses are −3.16 ppbv, 13 ppbv and 0.79, respectively, whereas between MOZAIC and the free model they are 6.3 ppbv, 16.6 ppbv and 0.71, respectively. The paper also presents a demonstration of the capability of O3 and CO assimilated fields to better describe a stratosphere-troposphere exchange (STE) event in comparison with the free run modelled O3 and CO fields. Although the assimilation of MLS data improves the distribution of O3 above the tropopause compared to the free model run, it is not sufficient to reproduce the STE event well. Assimilated MOPITT CO allows a better qualitative description of the stratospheric intrusion event. The MOPITT CO analyses appear more promising than the MLS O3 analyses in terms of their ability to capture a deep STE event. Therefore, the results of this study open the perspectives for using MOPITT CO in the STE studies

Validation of Aura Microwave Limb Sounder O-3 and CO observations in the upper troposphere and lower stratosphere

International audienceGlobal satellite observations of ozone and carbon monoxide from the Microwave Limb Sounder (MLS) on the EOS Aura spacecraft are discussed with emphasis on those observations in the 215–100 hPa region (the upper troposphere and lower stratosphere). The precision, resolution and accuracy of the data produced by the MLS “version 2.2” processing algorithms are discussed and quantified. O3 accuracy is estimated at ~40 ppbv +5% (~20 ppbv +20% at 215 hPa) while the CO accuracy is estimated at ~30 ppbv +30% for pressures of 147 hPa and less. Comparisons with expectations and other observations show good agreements for the O3 product, generally consistent with the systematic errors quoted above. In the case of CO, a persistent factor of ~2 high bias is seen at 215 hPa. However, the morphology is shown to be realistic, consistent with raw MLS radiance data, and useful for scientific study. The MLS CO data at higher altitudes are shown to be consistent with other observations

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

KRAB–Zinc Finger Proteins and KAP1 Can Mediate Long-Range Transcriptional Repression through Heterochromatin Spreading

Krüppel-associated box domain-zinc finger proteins (KRAB–ZFPs) are tetrapod-specific transcriptional repressors encoded in the hundreds by the human genome. In order to explore their as yet ill-defined impact on gene expression, we developed an ectopic repressor assay, allowing the study of KRAB–mediated transcriptional regulation at hundreds of different transcriptional units. By targeting a drug-controllable KRAB–containing repressor to gene-trapping lentiviral vectors, we demonstrate that KRAB and its corepressor KAP1 can silence promoters located several tens of kilobases (kb) away from their DNA binding sites, with an efficiency which is generally higher for promoters located within 15 kb or less. Silenced promoters exhibit a loss of histone H3-acetylation, an increase in H3 lysine 9 trimethylation (H3K9me3), and a drop in RNA Pol II recruitment, consistent with a block of transcriptional initiation following the establishment of silencing marks. Furthermore, we reveal that KRAB–mediated repression is established by the long-range spreading of H3K9me3 and heterochromatin protein 1 β (HP1β) between the repressor binding site and the promoter. We confirm the biological relevance of this phenomenon by documenting KAP1–dependent transcriptional repression at an endogenous KRAB–ZFP gene cluster, where KAP1 binds to the 3′ end of genes and mediates propagation of H3K9me3 and HP1β towards their 5′ end. Together, our data support a model in which KRAB/KAP1 recruitment induces long-range repression through the spread of heterochromatin. This finding not only suggests auto-regulatory mechanisms in the control of KRAB–ZFP gene clusters, but also provides important cues for interpreting future genome-wide DNA binding data of KRAB–ZFPs and KAP1

Role of the Epigenetic Regulator HP1γ in the Control of Embryonic Stem Cell Properties

The unique properties of embryonic stem cells (ESC) rely on long-lasting self-renewal and their ability to switch in all adult cell type programs. Recent advances have shown that regulations at the chromatin level sustain both ESC properties along with transcription factors. We have focused our interest on the epigenetic modulator HP1γ (Heterochromatin Protein 1, isoform γ) that binds histones H3 methylated at lysine 9 (meH3K9) and is highly plastic in its distribution and association with the transcriptional regulation of specific genes during cell fate transitions. These characteristics of HP1γ make it a good candidate to sustain the ESC flexibility required for rapid program changes during differentiation. Using RNA interference, we describe the functional role of HP1γ in mouse ESC. The analysis of HP1γ deprived cells in proliferative and in various differentiating conditions was performed combining functional assays with molecular approaches (RT-qPCR, microarray). We show that HP1γ deprivation slows down the cell cycle of ESC and decreases their resistance to differentiating conditions, rendering the cells poised to differentiate. In addition, HP1γ depletion hampers the differentiation to the endoderm as compared with the differentiation to the neurectoderm or the mesoderm. Altogether, our results reveal the role of HP1γ in ESC self-renewal and in the balance between the pluripotent and the differentiation programs

Modulation of functional pendant chains within poly(ethylene glycol) hydrogels for refined control of protein release

Hydrogels are highly attractive delivery vehicles for therapeutic proteins. Their innate biocompatibility, hydrophilicity and aqueous permeability allow stable encapsulation and release of proteins. The release rates also can be controlled simply by altering the crosslinking density of the polymeric network. However, the crosslinking density also influences the mechanical properties of hydrogels, generally opposite to the permeability. In addition, the release of larger proteins may be hindered below critically diminished porosity determined by the crosslinking density. Herein, the physical properties of the hydrogels are tuned by presenting functional pendant chains, independent of crosslinking density. Heterobifunctional poly(ethylene glycol) monomethacrylate (PEGMA) with various end functional groups is synthesized and copolymerized with PEG dimethacrylate (PEGDA) to engineer PEG hydrogels with pendant PEG chains. The pendant chains of the PEG hydrogels consisting of sulfonate, trimethylammonium chloride, and phenyl groups are utilized to provide negative charge, positive charge and hydrophobicity, respectively, to the hydrogels. The release rates of proteins with different isoelectric points are controlled in a wide range by the type and the density of functional pendant chains via electrostatic and hydrophobic interactions

Maïdo observatory: a new high-altitude station facility at Reunion Island (21° S, 55° E) for long-term atmospheric remote sensing and in situ measurements

Since the nineties, atmospheric measurement systems have been deployed at Reunion Island, mainly for monitoring the atmospheric composition in the framework of NDSC/NDACC (Network for the Detection of <i>Stratospheric</i> Change/Network for the Detection of Atmospheric Composition Change). The location of Reunion Island presents a great interest because there are very few multi-instrumented stations in the tropics and particularly in the southern hemisphere. In 2012, a new observatory was commissioned in Maïdo at 2200 m above sea level: it hosts various instruments for atmospheric measurements, including lidar systems, spectro-radiometers and in situ gas and aerosol measurements. <br><br> This new high-altitude Maïdo station provides an opportunity:<br> 1. to improve the performance of the optical instruments above the marine boundary layer, and to open new perspectives on upper troposphere and lower stratosphere studies;<br> 2. to develop in situ measurements of the atmospheric composition for climate change surveys, in a reference site in the tropical/subtropical region of the southern hemisphere;<br> 3. to offer trans-national access to host experiments or measurement campaigns for focused process studies

Destabilization of nucleophosmin mRNA by the HuR/KSRP complex is required for muscle fibre formation

HuR promotes myogenesis by stabilizing the MyoD, myogenin and p21 mRNAs during the fusion of muscle cells to form myotubes. Here we show that HuR, via a novel mRNA destabilizing activity, promotes the early steps of myogenesis by reducing the expression of the cell cycle promoter nucleophosmin (NPM). Depletion of HuR stabilizes the NPM mRNA, increases NPM protein levels and inhibits myogenesis, while its overexpression elicits the opposite effects. NPM mRNA destabilization involves the association of HuR with the decay factor KSRP as well as the ribonuclease PARN and the exosome. The C terminus of HuR mediates the formation of the HuR-KSRP complex and is sufficient for maintaining a low level of the NPM mRNA as well as promoting the commitment of muscle cells to myogenesis. We therefore propose a model whereby the downregulation of the NPM mRNA, mediated by HuR, KSRP and its associated ribonucleases, is required for proper myogenesis

Reduced levels of two modifiers of epigenetic gene silencing, Dnmt3a and Trim28, cause increased phenotypic noise

Background: Inbred individuals reared in controlled environments display considerable variance in many complex traits but the underlying cause of this intangible variation has been an enigma. Here we show that two modifiers of epigenetic gene silencing play a critical role in the process.Results: Inbred mice heterozygous for a null mutation in DNA methyltransferase 3a (Dnmt3a) or tripartite motif protein 28 (Trim28) show greater coefficients of variance in body weight than their wild-type littermates. Trim28 mutants additionally develop metabolic syndrome and abnormal behavior with incomplete penetrance. Genome-wide gene expression analyses identified 284 significantly dysregulated genes in Trim28 heterozygote mutants compared to wild-type mice, with Mas1, which encodes a G-protein coupled receptor implicated in lipid metabolism, showing the greatest average change in expression (7.8-fold higher in mutants). This gene also showed highly variable expression between mutant individuals.Conclusions: These studies provide a molecular explanation of developmental noise in whole organisms and suggest that faithful epigenetic control of transcription is central to suppressing deleterious levels of phenotypic variation. These findings have broad implications for understanding the mechanisms underlying sporadic and complex disease in humans