Modélisation de l'évolution thermique saisonnière du lac du Bourget

Le lac du Bourget, l'un des principaux lacs alpins situé en France, a fait l'objet en 1981 d'importants travaux d'aménagement en vue de ta restauration de la qualité de ses eaux. Une campagne de mesure portant sur les années 1988-89 a été mise en place afin de faire le point sur l'évolution du lac depuis la fin des travaux.Un modèle thermique et biogéochimique (phosphore, oxygène, azote) sera utilisé pour synthétiser les connaissances, prévoir l'évolution de la qualité des eaux du lac ainsi que l'influence d'éventuels aménagements complémentaires. Les résultats présentés ici concernent la première étape du projet d'études, la modélisation thermique du lac du Bourget.Le modèle utilisé est un modèle unidimensionnel, vertical, basé sur l'équation d'advection-diffusion.L'expression des coefficients de dispersion selon la profondeur reprend celle d'un modèle du lac Léman (Tassin, 1986). Les équations utilisées distinguent l'épilimnion, le métalimnion et l'hypolimnion.Les résultats présentés montrent que le modèle décrit de façon satisfaisante le cycle thermique annuel et l'évolution inter-annuelle des températures dans le lac du Bourget.Les profils et les valeurs des coefficients de dispersion calculés sur le lac du Bourget sont proches de ceux obtenus sur d'autres lacs à partir de mesures fines de température ou de concentrations d'isotopes naturels.Les coefficients de dispersion obtenus pourront donc être utilisés dans la modélisation des substances dissoutes dans le lac.In 1981, important works including the diversion of the main sewers entering Lake Bourget (one of the largest French alpine lakes) were undertaken in order to restore acceptable water quality standards. A detailed water quality survey will be performed in 1988-89 to complete the data base which already covers ten years. It should help in quantifying the evolution of the lake since the 1981 restoration works. The following activities will be undertaken as part of the survey : measurements within the water column, a study of the bottom sediments, the setting-up of sediment traps and the coupling of Landsat satellite images with measurements performed at some stations at the lake surface. A thermal and biogeochemical (phosphorus, oxygen, nitrogen) model will be used to summarise the information available and to forecast the evolution of water quality and the effect of other restoration measures. This paper reports on the first part of the study : the thermal modelling of Lake Bourget. A one-dimensional, vertical model based on the advection-diffusion equation is used. This equation is solved using a finite difference, semi-implicit method. The resolution grid has 145 layers (1 meter high) and the time step is 3 hours.The heat fluxes at the air-water interface are computed with the three-hourly meteorological data collected at the Chambéry airport station, at the south end of the lake. The formulas are empirical and well established in the literature.The expression for the eddy diffusion coefficients is based on a model of the lake of Geneva (Tassin, 1986). Different equations are used for the epilimnion, metalimnion and hypolimnion. In the epilimnion, the eddy diffusion coefficient expresses, by the Richardson gradients number, the interaction between the shear stress of the wind and the water column stability. It depends on the value of the eddy diffusion in neutral conditions and on a stability function which includes the Richardson number. The vertical profile of the horizontal number. The vertical profile of the horizontal currents is computed following Ekman (1905) and Simons (1981) and is approximated by a gradient which decays exponentially.In the metalimnion and the hypolimnion, the water layer stability is characterised by the Brünt-Väisälä frequency. In the hypolimnion, the eddy diffusion coefficient includes a corrective term, which is a function of depth; this term serves to reduce the dispersion near the bottom of the lake.The thermal model also includes the mixing of the first layers by waves, the vertical advective transport induced by rivers inflows into the lake and by surface water withdrawal, as well as the thermal convection induced by local instabilities of the water column.The eight parameters occurring in the heat flux equations and the eddy diffusion coefficients were estimated using data from 1981. The model has been validated over an 8 years period 1976-1983).Results of the model agree with the observed seasonal and long-term evolutions of temperature in Lake Bourget. The main characteristics of the annual cycle are reproduced : set-up of the thermocline in spring, depth of the epilimnion, thermocline and metalimnion, value of the temperature gradient in the metalimnion, deepening of the thermocline in fall and winter overturn. Significant differences between observed and simulated temperatures occur in the metalimnion and they may be partially explained by internal waves which are dominant features at this level during summer stratification. This kind of mechanism cannot be accounted for in a one-dimensional vertical model.Profiles and values of eddy diffusion coefficients calculated for Lake Bourget show a good agreement with those obtained in other large takes from measurements of temperature or natural isotopes concentrations.In general, the thermal model gives a good account of heat transport mechanisms in Lake Bourget. Accordingly, it provides acceptable dispersion coefficients which can be used to model the distribution of dissolved species in the lake

Explicit modelling of SOA formation from α-pinene photooxidation: sensitivity to vapour pressure estimation

The sensitivity of the formation of secondary organic aerosol (SOA) to the estimated vapour pressures of the condensable oxidation products is explored. A highly detailed reaction scheme was generated for α-pinene photooxidation using the Generator for Explicit Chemistry and Kinetics of Organics in the Atmosphere (GECKO-A). Vapour pressures (P^(vap)) were estimated with three commonly used structure activity relationships. The values of P^(vap) were compared for the set of secondary species generated by GECKO-A to describe α-pinene oxidation. Discrepancies in the predicted vapour pressures were found to increase with the number of functional groups borne by the species. For semi-volatile organic compounds (i.e. organic species of interest for SOA formation), differences in the predicted Pvap range between a factor of 5 to 200 on average. The simulated SOA concentrations were compared to SOA observations in the Caltech chamber during three experiments performed under a range of NO_x conditions. While the model captures the qualitative features of SOA formation for the chamber experiments, SOA concentrations are systematically overestimated. For the conditions simulated, the modelled SOA speciation appears to be rather insensitive to the P^vap estimation method

Modeling SOA formation from the oxidation of intermediate volatility <i>n</i>-alkanes

The chemical mechanism leading to SOA formation and ageing is expected to be a multigenerational process, i.e. a successive formation of organic compounds with higher oxidation degree and lower vapor pressure. This process is here investigated with the explicit oxidation model GECKO-A (Generator of Explicit Chemistry and Kinetics of Organics in the Atmosphere). Gas phase oxidation schemes are generated for the C₈–C₂₄ series of <i>n</i>-alkanes. Simulations are conducted to explore the time evolution of organic compounds and the behavior of secondary organic aerosol (SOA) formation for various preexisting organic aerosol concentration (<i>C</i>_OA). As expected, simulation results show that (i) SOA yield increases with the carbon chain length of the parent hydrocarbon, (ii) SOA yield decreases with decreasing <i>C</i>_OA, (iii) SOA production rates increase with increasing <i>C</i>_OA and (iv) the number of oxidation steps (i.e. generations) needed to describe SOA formation and evolution grows when <i>C</i>_OA decreases. The simulated oxidative trajectories are examined in a two dimensional space defined by the mean carbon oxidation state and the volatility. Most SOA contributors are not oxidized enough to be categorized as highly oxygenated organic aerosols (OOA) but reduced enough to be categorized as hydrocarbon like organic aerosols (HOA), suggesting that OOA may underestimate SOA. Results show that the model is unable to produce highly oxygenated aerosols (OOA) with large yields. The limitations of the model are discussed

Estimation of mechanistic parameters in the gas-phase reactions of ozone with alkenes for use in automated mechanism construction

Reaction with ozone is an important atmospheric removal process for alkenes. The ozonolysis reaction produces carbonyls and carbonyl oxides (Criegee intermediates, CI), which can rapidly decompose to yield a range of closed shell and radical products, including OH radicals. Consequently, it is essential to accurately represent the complex chemistry of Criegee intermediates in atmospheric models in order to fully understand the impact of alkene ozonolysis on atmospheric composition. A mechanism construction protocol is presented which is suitable for use in automatic mechanism generation. The protocol defines the critical parameters for describing the chemistry following the initial reaction, namely the primary carbonyl/CI yields from the primary ozonide fragmentation, the amount of stabilisation of the excited CI, the unimolecular decomposition pathways, rates and products of the CI, and the bimolecular rates and products of atmospherically important reactions of the stabilised CI (SCI). This analysis implicitly predicts the yield of OH from the alkene–ozone reaction. A comprehensive database of experimental OH, SCI and carbonyl yields has been collated using reported values in the literature and used to assess the reliability of the protocol. The protocol provides estimates of OH, SCI and carbonyl yields with root mean square errors of 0.13 and 0.12 and 0.14, respectively. Areas where new experimental and theoretical data would improve the protocol and its assessment are identified and discussed

Nucleosome occupancy reveals regulatory elements of the CFTR promoter

Access to regulatory elements of the genome can be inhibited by nucleosome core particles arranged along the DNA strand. Hence, sites that are accessible by transcription factors may be located by using nuclease digestion to identify the relative nucleosome occupancy of a genomic region. In order to define novel cis regulatory elements in the ∼2.7-kb promoter region of the cystic fibrosis transmembrane conductance regulator (CFTR) gene, we define its nucleosome occupancy. This profile reveals the precise positions of nucleosome-free regions (NFRs), both cell-type specific and others apparently unrelated to CFTR-expression level and offer the first high-resolution map of the chromatin structure of the entire CFTR promoter in relevant cell types. Several of these NFRs are strongly bound by nuclear factors in a sequence-specific manner, and directly influence CFTR promoter activity. Sequences within the NFR1 and NFR4 elements are highly conserved in many human gene promoters. Moreover, NFR1 contributes to promoter activity of another gene, angiopoietin-like 3 (ANGPTL3), while NFR4 is constitutively nucleosome-free in promoters genome wide. Conserved motifs within NFRs of the CFTR promoter also show a high level of protection from DNase I digestion genome-wide, and likely have important roles in the positioning of nucleosome core particles more generally

Transcriptome Analysis of Female and Male Xiphophorus maculatus Jp 163 A

Background: Xiphophorus models are important for melanoma, sex determination and differentiation, ovoviviparity and evolution. To gain a global view of the molecular mechanism(s) whereby gene expression may influence sexual dimorphism in Xiphophorus and to develop a database for future studies, we performed a large-scale transcriptome study. Methodology/Principal Findings: The 454-FLX massively parallel DNA sequencing platform was employed to obtain 742,771 and 721,543 reads from 2 normalized cDNA libraries generated from whole adult female and male X. maculatus Jp 163 A, respectively. The reads assembled into 45,538 contigs (here, a "contig" is a set of contiguous sequences), of which, 11,918 shared homology to existing protein sequences. These numbers estimate that the contigs may cover 53% of the total number of Xiphophorus transcriptome. Putative translations were obtained for 11,918 cDNA contigs, of which, 3,049 amino acid sequences contain Pfam domains and 11,064 contigs encode secretory proteins. A total of 3,898 contigs were associated with 2,781 InterPro (IPR) entries and 5,411 contigs with 132 KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways. There were 10,446 contigs annotated with 69,778 gene ontology (GO) terms and the three corresponding organizing principles. Fifty-four potential sex differentially expressed genes have been identified from these contigs. Eight and nine of these contigs were confirmed by real-time PCR as female and male predominantly expressed genes respectively. Based on annotation results, 34 contigs were predicted to be differentially expressed in male and female and 17 of them were also confirmed by real-time PCR. Conclusions/Significance: This is the first report of an annotated overview of the transcriptome of X. maculatus and identification of sex differentially expressed genes. These data will be of interest to researchers using the Xiphophorus model. This work also provides an archive for future studies in molecular mechanisms of sexual dimorphism and evolution, and can be used in comparative studies of other fish

The Enhancer of Trithorax and Polycomb Corto Interacts with Cyclin G in Drosophila

BACKGROUND: Polycomb (PcG) and trithorax (trxG) genes encode proteins involved in the maintenance of gene expression patterns, notably Hox genes, throughout development. PcG proteins are required for long-term gene repression whereas TrxG proteins are positive regulators that counteract PcG action. PcG and TrxG proteins form large complexes that bind chromatin at overlapping sites called Polycomb and Trithorax Response Elements (PRE/TRE). A third class of proteins, so-called "Enhancers of Trithorax and Polycomb" (ETP), interacts with either complexes, behaving sometimes as repressors and sometimes as activators. The role of ETP proteins is largely unknown. METHODOLOGY/PRINCIPAL FINDINGS: In a two-hybrid screen, we identified Cyclin G (CycG) as a partner of the Drosophila ETP Corto. Inactivation of CycG by RNA interference highlights its essential role during development. We show here that Corto and CycG directly interact and bind to each other in embryos and S2 cells. Moreover, CycG is targeted to polytene chromosomes where it co-localizes at multiple sites with Corto and with the PcG factor Polyhomeotic (PH). We observed that corto is involved in maintaining Abd-B repression outside its normal expression domain in embryos. This could be achieved by association between Corto and CycG since both proteins bind the regulatory element iab-7 PRE and the promoter of the Abd-B gene. CONCLUSIONS/SIGNIFICANCE: Our results suggest that CycG could regulate the activity of Corto at chromatin and thus be involved in changing Corto from an Enhancer of TrxG into an Enhancer of PcG

Context-Dependent Dual Role of SKI8 Homologs in mRNA Synthesis and Turnover

Eukaryotic mRNA transcription and turnover is controlled by an enzymatic machinery that includes RNA polymerase II and the 3′ to 5′ exosome. The activity of these protein complexes is modulated by additional factors, such as the nuclear RNA polymerase II-associated factor 1 (Paf1c) and the cytoplasmic Superkiller (SKI) complex, respectively. Their components are conserved across uni- as well as multi-cellular organisms, including yeast, Arabidopsis, and humans. Among them, SKI8 displays multiple facets on top of its cytoplasmic role in the SKI complex. For instance, nuclear yeast ScSKI8 has an additional function in meiotic recombination, whereas nuclear human hSKI8 (unlike ScSKI8) associates with Paf1c. The Arabidopsis SKI8 homolog VERNALIZATION INDEPENDENT 3 (VIP3) has been found in Paf1c as well; however, whether it also has a role in the SKI complex remains obscure so far. We found that transgenic VIP3-GFP, which complements a novel vip3 mutant allele, localizes to both nucleus and cytoplasm. Consistently, biochemical analyses suggest that VIP3–GFP associates with the SKI complex. A role of VIP3 in the turnover of nuclear encoded mRNAs is supported by random-primed RNA sequencing of wild-type and vip3 seedlings, which indicates mRNA stabilization in vip3. Another SKI subunit homolog mutant, ski2, displays a dwarf phenotype similar to vip3. However, unlike vip3, it displays neither early flowering nor flower development phenotypes, suggesting that the latter reflect VIP3's role in Paf1c. Surprisingly then, transgenic ScSKI8 rescued all aspects of the vip3 phenotype, suggesting that the dual role of SKI8 depends on species-specific cellular context