Jollivet P.,CEA Marcoule Nuclear Site |
Gin S.,CEA Marcoule Nuclear Site |
Schumacher S.,Andra Inc
Chemical Geology | Year: 2012
This study describes the influence of neutral or slightly basic clay-equilibrated groundwater on the forward dissolution rate of nuclear borosilicate glasses. The forward rate measured for the SON68 glass, a 26-oxide glass of nuclear interest, is about five times higher in clay-equilibrated groundwater than in deionized water. The corresponding apparent activation energy, measured between 30°C and 90°C, is similar for both media, indicating that glass dissolution is likely controlled by the hydrolysis of Si-O bonds in both solutions. The specific effect of clay-equilibrated groundwater appears to be related to a surface phenomenon; aluminum-oxygen and zirconium-oxygen bonds appear to be less impacted by clay-equilibrated groundwater than silicon-oxygen bonds. More particularly, this work shows that the influence of clay-equilibrated groundwater on the forward dissolution rate is due to its ionic strength with cations predominating over anions, although not all tested cations have the same effect. The effect is due mainly to calcium ions, although the concentration of sodium ions in the clay-equilibrated water tested was four times higher than that of calcium ions. The specific influence of alkali metal (Li +, Na +, K +, Rb +, Cs +) and alkaline earth (Mg 2+, Ca 2+, Sr 2+, Ba 2+) ions shows that all cations do not have the same effect on the forward glass dissolution rate and that the rate increases with the mole fraction of surface metal sites. The presence of calcium in the glass does not prevent this particular effect. © 2012 Elsevier B.V.
Duvail M.,CEA Marcoule Nuclear Site |
Guilbaud P.,CEA Marcoule Nuclear Site
Physical Chemistry Chemical Physics | Year: 2011
Coordination of nitrate anions with lanthanoid cations (Ln3+) in water, methanol and octanol-1 has been studied by means of molecular dynamics simulations with explicit polarization. Potential of mean force (PMF) profiles have been calculated for a mono-complex of lanthanoid nitrate (Ln(NO 3)2+) in these solvents using umbrella-sampling molecular dynamics. In pure water, no difference in the nitrato coordination to lanthanoids (Nd3+, Eu3+ and Dy3+) is observed, i.e. the nitrate anion prefers the monodentate coordination, which promotes the salt dissociation. Then, the influence of the nature of the solvating molecules on the nitrato coordination to Eu3+ has been investigated. PMF profiles point out that both monodenate and bidentate coordinations are stable in neat methanol, while in neat octanol, only the bidentate one is. MD simulations of Eu(NO3)3 in water-octanol mixtures with different concentrations of water have been then performed and confirm the importance of the water molecules' presence on the nitrate ion's coordination mode. © the Owner Societies. 2011.
Christie-Oleza J.A.,CEA Marcoule Nuclear Site
Molecular & cellular proteomics : MCP | Year: 2012
Roseobacters are generalist bacteria abundantly found in the oceans. Because little is known on how marine microorganisms interact in association or competition, we focused our attention on the microbial exoproteome, a key component in their interaction with extracellular milieu. Here we present a comparative analysis of the theoretically encoded exoproteome of twelve members of the Roseobacter group validated by extensive comparative proteogenomics. In silico analysis revealed that 30% of the encoded proteome of these microorganisms could be exported. The ratio of the different protein categories varied in accordance to the ecological distinctness of each strain, a trait reinforced by quantitative proteomics data. Despite the interspecies variations found, the most abundantly detected proteins by shotgun proteomics were from transporter, adhesion, motility, and toxin-like protein categories, defining four different plausible adaptive strategies within the Roseobacter group. In some strains the toxin-secretion strategy was over-represented with repeats-in-toxin-like proteins. Our results show that exoproteomes strongly depend on bacterial trophic strategy and can slightly change because of culture conditions. Simulated natural conditions and the effect of the indigenous microbial community on the exoproteome of Ruegeria pomeroyi DSS-3 were also assayed. Interestingly, we observed a significant depletion of the toxin-like proteins usually secreted by R. pomeroyi DSS-3 when grown in presence of a natural community sampled from a Mediterranean Sea port. The significance of this specific fraction of the exoproteome is discussed.
Hartmann E.M.,CEA Marcoule Nuclear Site |
Armengaud J.,CEA Marcoule Nuclear Site
Environmental Microbiology | Year: 2014
Chlorinated congeners of dibenzo-p-dioxin and dibenzofuran are widely dispersed pollutants that can be treated using microorganisms, such as the Sphingomonas wittichiiRW1 bacterium, able to transform some of them into non-toxic substances. The enzymes of the upper pathway for dibenzo-p-dioxin degradation in S.wittichiiRW1 have been biochemically and genetically characterized, but its genome sequence indicated the existence of a tremendous potential for aromatic compound transformation, with 56 ring-hydroxylating dioxygenase subunits, 34 extradiol dioxygenases and 40 hydrolases. To further characterize this enzymatic arsenal, new methodological approaches should be employed. Here, a large shotgun proteomic survey was performed on cells grown on dibenzofuran, dibenzo-p-dioxin and 2-chlorodibenzo-p-dioxin, and compared with growth on acetate. Changes in the proteome were monitored over time. In total, 502 proteins were observed and quantified using a label-free mass spectrometry-based approach; all data were deposited to the ProteomeXchange (PXD000403). Our results confirmed the roles of the dioxin dioxygenase DxnA1A2, trihydroxybiphenyl dioxygenase DbfB, meta-cleavage product hydrolase DxnB and reductase RedA2, and corroborated the proposed involvement of the Swit_3046 dioxygenase and DxnB2 hydrolase. Trends across substrates and over the course of growth do not support concerted pathway regulation and suggest the involvement of an additional hydrolase and several TonB-dependent receptors. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.
Chen S.-W.W.,CEA Marcoule Nuclear Site |
Pellequer J.-L.,CEA Marcoule Nuclear Site
BMC Structural Biology | Year: 2011
Background: Atomic force microscopy (AFM) is a relatively recently developed technique that shows a promising impact in the field of structural biology and biophysics. It has been used to image the molecular surface of membrane proteins at a lateral resolution of one nanometer or less. An immediate obstacle of characterizing surface features in AFM images is stripe noise. To better interpret structures at a sub-domain level, pre-processing of AFM images for removing stripe noises is necessary. Noise removal can be performed in either spatial or frequency domain. However, denoising processing in the frequency domain is a better solution for preserving edge sharpness. Results: We have developed a denoising protocol, called DeStripe, for AFM bio-molecular images that are contaminated with heavy and fine stripes. This program adopts a divide-and-conquer approach by dividing the Fourier spectrum of the image into central and off-center regions for noisy pixels detection and intensity restoration; it is also applicable to other images interfered with high-density stripes such as those acquired by the scanning electron microscope. The denoising effect brought by DeStripe provides better visualization for image objects without introducing additional artifacts into the restored image. Conclusions: The DeStripe denoising effect on AFM images is illustrated in the present work. It allows extracting extended information from the topographic measurements and implicitly enhances the molecular features in the image. All the presented images were processed by DeStripe with the raw image as the only input without any requirement for other prior information. A web service, http://biodev.cea.fr/destripe, is available for running DeStripe. © 2011 Chen and Pellequer; licensee BioMed Central Ltd.
Armengaud J.,CEA Marcoule Nuclear Site |
Marie Hartmann E.,CEA Marcoule Nuclear Site |
Bland C.,CEA Marcoule Nuclear Site
Proteomics | Year: 2013
Proteogenomics sensu stricto refers to the use of proteomic data to refine the annotation of genomes from model organisms. Because of the limitations of automatic annotation pipelines, a relatively high number of errors occur during the structural annotation of genes coding for proteins. Whether putative orphan sequences or short genes encoding low-molecular-weight proteins really exist is still frequently a mystery. Whether start codons are well defined is also an open debate. These problems are exacerbated for genomes of microorganisms belonging to poorly documented genera, as related sequences are not always available for homology-guided annotation. The functional annotation of a significant proportion of genes is also another well-known issue when annotating environmental microorganisms. High-throughput shotgun proteomics has recently greatly evolved, allowing the exploration of the proteome from any microorganism at an unprecedented depth. The structural and functional annotation process may be usefully complemented with experimental data. Indeed, proteogenomic mapping has been successfully performed for a wide variety of organisms. Specific approaches devoted to systematically establishing the N-termini of a large set of proteins are being developed. N-terminomics is giving rise to datasets of experimentally proven translational start codons as well as validated peptide signals for secreted proteins. By extension, combining genomic and proteomic data is becoming routine in many research projects. The proteomic analysis of organisms with unfinished genome sequences, the so-called composite proteomics, and the search for microbial biomarkers by bottom-up and top-down combined approaches are some examples of proteogenomic-flavored studies. They illustrate the advent of a new era of environmental microbiology where proteomics and genomics are intimately integrated to answer key biological questions. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Guilbaud P.,CEA Marcoule Nuclear Site |
Zemb T.,Marcoule Institute for Separative Chemistry
ChemPhysChem | Year: 2012
Reverse micelles? The transition from weak aggregation to water-poor reverse micelles triggered by the presence of extracted ion pairs is modeled using molecular dynamics simulations (see picture). The presence of the ion induces a polar/apolar segregation and the formation of a curved film microstructure consistent with the classical inverse micelle. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Armengaud J.,CEA Marcoule Nuclear Site
Expert Review of Proteomics | Year: 2010
This review describes how intimately proteogenomics and system biology are imbricated. Quantitative cell-wide monitoring of cellular processes and the analysis of this information is the basis for systems biology. Establishing the most comprehensive protein-parts list is an essential prerequisite prior to analysis of the cell-wide dynamics of proteins, their post-translational modifications, their complex network interactions and interpretation of these data as a whole. High-quality genome annotation is, thus, a crucial basis. Proteogenomics consists of high-throughput identification and characterization of proteins by extra-large shotgun MS/MS approaches and the integration of these data with genomic data. Discovery of the remaining unannotated genes, defining translational start sites, listing signal peptide processing events and post-translational modifications, are tasks that can currently be carried out at a full-genomic scale as soon as the genomic sequence is available. Proteomics is increasingly being used at the primary stage of genome annotation and such an approach may become standard in the near future for genome projects. Advantageously, the same experimental proteomic datasets may be used to characterize the specific metabolic traits of the organism under study. Undoubtedly, comparative genomics will experience a renaissance taking into account this new dimension. Synthetic biology aimed at re-engineering living systems will also benefit from these significant progresses. © 2010 Expert Reviews Ltd.
Armengaud J.,CEA Marcoule Nuclear Site
Current Opinion in Biotechnology | Year: 2016
Environmental biotechnology relies on the exploration of novel biological systems and a thorough understanding of the underlying molecular mechanisms. Next-generation proteomics based on the latest generation of mass analyzers currently allows the recording of complete proteomes from any microorganism. Interpreting these data can be straightforward if the genome of the organism is established, or relatively easy to perform through proteogenomics approaches if a draft sequence can be obtained. However, next-generation proteomics faces new, interesting challenges when the organism is distantly related to previously characterized organisms or when mixtures of organisms have to be analyzed. New mass spectrometers and innovative bioinformatics tools are reshaping the possibilities of homology-based proteomics, proteogenomics, and metaproteomics for the characterization of biological systems. Novel time- and cost-effective screening strategies are also possible with this methodology, as exemplified by whole proteome thermal profiling and subpopulation proteomics. The complexity of environmental samples allows for unique developments of approaches and concepts. © 2016 Elsevier Ltd.
Poinssot C.,CEA Marcoule Nuclear Site |
Gin S.,CEA Marcoule Nuclear Site
Journal of Nuclear Materials | Year: 2012
High level waste (HLW) management requires being able to demonstrate the safety over geological timescales, typically 1 My. This can be made possible by using a rigorous, complex and iterative scientific approach called Long-term Behavior Science. The methodology relies on experiments and modelling. A large multi-scale approach is required and involves a mechanistic understanding of the key phenomena controlling the source term (i.e. the flux of radionuclides released from the waste as a function of time), as well as parametric studies, integrated and in situ tests. As a result, it is eventually possible to develop an operational model based on clever simplifications of a very complex reality, ensuring that predictions will always remain conservative despite conceptual and numerical uncertainties. Finally, predictive models must be validated based on the study of natural or archaeological analogues. In this paper, we show how this methodology can be applied by selecting examples of spent nuclear fuel and HLW glass. © 2011 Elsevier B.V. All rights reserved.