A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1

We have constructed a collection of single-gene deletion mutants for all dispensable genes of the soil bacterium Acinetobacter baylyi ADP1. A total of 2594 deletion mutants were obtained, whereas 499 (16%) were not, and are therefore candidate essential genes for life on minimal medium. This essentiality data set is 88% consistent with the Escherichia coli data set inferred from the Keio mutant collection profiled for growth on minimal medium, while 80% of the orthologous genes described as essential in Pseudomonas aeruginosa are also essential in ADP1. Several strategies were undertaken to investigate ADP1 metabolism by (1) searching for discrepancies between our essentiality data and current metabolic knowledge, (2) comparing this essentiality data set to those from other organisms, (3) systematic phenotyping of the mutant collection on a variety of carbon sources (quinate, 2-3 butanediol, glucose, etc.). This collection provides a new resource for the study of gene function by forward and reverse genetic approaches and constitutes a robust experimental data source for systems biology approaches

Sulfur behavior in silicate glasses and melts: Implications for sulfate incorporation in nuclear waste glasses as a function of alkali cation and V2O5 content

International audiencehe presence of sulfur in radioactive waste to be incorporated in borosilicate glasses entails difficulties mainly due to the relatively low solubility of sulfates in the vitreous phase. In this work a study is presented on the effects of the ratio R = [Na2O]/[B2O3], the type of sulfate added and the addition of V2O5 on the incorporation of sulfates in borosilicate glasses. Glass samples were prepared at the laboratory scale (up to 50–100 g) by melting oxide and sulfate powders under air in Pt/Au crucibles. XRF and ICP/AES chemical analysis, SEM/EDS, microprobe WDS and Raman spectroscopy were employed to characterize the fabricated samples. The main experimental results confirm that the incorporation of sulfates in borosilicate glasses is favored by the network depolymerization, which evolves with the ratio R. The addition of V2O5 seems to accelerate the kinetics of sulfur incorporation in the glass and, probably, increase the sulfate solubility by modifying the borate network and fostering the formation of voids of shape and size compatible with the sulfur coordination polyhedron in the glassy network. The kinetics of X2SO4 incorporation in the glass seems to be slower when X = Cs

Long-listening multichannel seismic profiles in the Valencia trough (Valsis 2) and the Gulf of Lions (ECORS): A comparison

The long listening Multichannel Seismic (MCS) profiles recorded during the Valsis and ECORS experiments were analysed in order to understand the rifting processes of a young passive margin. The seismic lines were interpreted within a geological framework which is considerably improved by the results from industrial wells. The disturbed upper crust off Catalonia is tentatively connected with a Variscan front. The origin of lamellae in the lower crust beneath the Valencia shelf is discussed: a Variscan origin is rejected and a relation to a Jurassic extensional event is proposed. A companion basin to the onshore Maestrazgo basin is located off-shore of Valencia and these two basins are probably connected by the left-lateral strike-slip Castellon fault. This fault is parallel to the North Pyrenean fault, which is the trace of the rotation of Spain relative to Europe. The Castellon fault may be connected with the Asturian fault, which is located on the Atlantic side of Spain. A contour map down to the Moho has revealed some new deep features and the results are compared with the previous refraction results. The sedimentary column of the deep north Balearic-ProvenÇal basin is much thicker than that of the eastern part of the Valencia trough and this diversity in the sedimentary infilling is probably related to a difference in the subsidence processes. A comparison of the Valencia trough to the Gulf of Lions shows that the thinning of the continental crust looks similar in both regions but the crust is thinner beneath the Valencia continental shelf than that below the Gulf of Lions. In both regions the Moho rises, possibly at the expense of the continental crust, by a process as yet unexplained (petrological or/and thermal variation?). © 1992.We would like to thankt he Captainsa nd crews of .I. Charcot and R.B. Conrad. The authors would like to thanks ELF (SNEA-P), Total-CFP and particularly REPSOL for providing numerous seismic and well data. M.A. Lobos from REPSOL is greatly thanked for providing information about wells. The book, describing the Spanish boreholes, published by J.M. Lanaja (IGME), is an invaluables ource of information. We thank F. Sabat and an anonymousr eviewer for their suggestionsW. e benefitedf rom an integrated action (Number 227) for Spanish-French cooperation.T he Vaisis 2 Cruise was supported by IFREMER, INSU-CNRS and NSF. We benefited from CNRS financial support (ATP No: 1774)C. ontributionG EMCO (URA. 718,C NRS) No: 544

Tertiary sedimentary history and structure of the Valencia trough (western Mediterranean)

We present here main results of the Common Depth Point (CDP) data acquired during the Valsis 2 Cruise in 1988 in the Valencia trough. The profiles are tied in with industrial well data and this correlation allows the sedimentary and structural history of the region to be deduced. The Valsis Cruise seismic profiles have been supplemented by a very dense grid of industrial seismic lines and these data permit us to establish an accurate depth to basement map. The formation of the initial grabens, coeval with those of the Gulf of Lions, is related to the Early Miocene opening of the northwestern Mediterranean basin and the Barcelona graben is filled by the same sedimentary layers, including evaporites, as that of the Provençal region. Nevertheless, the Valencia-Catalan grabens have been reactivated by young extensional tectonics which could be a consequence of the convergence of Africa relative to Europe. The Valencia trough is segmented by transfer faults which trend NW-SE. These faults, which have a more accentuated structural expression than the Valencia and Catalonia grabens, may act as transform faults separating the individual Balearic Islands. The transfer faults are in strike with volcanic ridges which have been sampled during the DSDP Leg 13. The dense seismic grid allows us to delineate several widespread volcanic features in the Valencia trough which have been active from the Early Miocene to the Pleistocene. However, we note that the volcanic features are mainly Miocene in age whereas the recent volcanism is restricted to a narrow zone (Columbretes Islands). The compressional tectonics which deformed the Balearic Islands does not appear to extend far towards the North. We delineate the compressional front north of Ibiza, but we failed to determine any thrust or fold north of Mallorca, whereas an extensional tectonics is evident. © 1992.The Valsis 2 Cruise was supported by NSF, IFREMER and INSU-CNRS. We benefited from CNRS financial support (ATP No: 1774). Contribution GEMCO (URA. 718, CNRS) No: 54

Specific overexpression of rheumatoid arthritis-associated HLA-DR alleles and presentation of low-affinity peptides.

International audienceObjective To compare levels of HLA–DR expression in rheumatoid arthritis (RA) patients and healthy controls for whom an ordered expression according to the DR alleles is demonstrated and to test the functional consequences of this expression on peptide presentation. Methods Using monoclonal antibodies that recognize different DRB1 alleles, DR molecules were quantitated at the surface of the peripheral blood B cells of 23 RA patients and 17 healthy subjects. The functional consequences of the level of DR surface expression was tested using a universal model of antigen presentation and mutated peptides with variable affinities for the T cell receptor. Results In healthy subjects, surface HLA–DR molecules were expressed at different levels according to allele (DR53, DR4, and DR11 less than DR1 less than DR7 less than DR15). In RA patients, this hierarchy was not conserved and, furthermore, the density of RA‐associated DR4 and DR1 molecules was enhanced in patients compared with the basal density in healthy individuals. We demonstrated that an increased expression of DR molecules at the surface of antigen‐presenting cells allowed a noteworthy presentation of low‐affinity peptides that under normal conditions are not efficient in generating a T cell response at physiologic surface density of the DR molecules. Conclusion Our results suggest that the specific overexpression of RA‐associated HLA molecules could be responsible for the presentation of low‐affinity autopeptides and therefore the activation of peripheral autoreactive T cells

Geospatial information for African agriculture: A key investment for agricultural policies

International audienceGeospatial information and its derived products, designed to contribute to public agricultural policy making, are not widely used in Africa. The infrastructure, training and skills are lacking, and research and development activities are dispersed and inadequate. More importantly, needs are not formalised and technological resources, driven by the industrialised countries, are ill-adapted to the characteristics of agricultural systems in Africa. Moreover, companies, institutions and projects require a stable environment to ensure operational services, relevant products and useful information. These co-constructed services emerge within long-term partnerships between researchers, consultancies and end users. Research thus offers new opportunities for using satellite imagery to document and explain agricultural transformation processes. Finally, lasting interdisciplinary skills networks are needed to facilitate methodological and thematic exchanges

FSAB: A new fructose-6-phosphate aldolase from Escherichia coli. Cloning, over-expression and comparative kinetic characterization with FSAA

International audienceFructose-6-phosphate aldolase B (FSAB) from Escherichia coli was successfully over-expressed as Histagged recombinant protein. A decameric protein was observed as for FSAA. Unlike FSAA, FSAB is not thermally stable at temperatures higher than 60 ◦C. The 70% identity between the two aldolases has allowed the generation of a 3D structure which has shown a high similarity of the two active sites. Full kinetic studies towards several substrates have revealed that FSAB catalytic activity is very close to FSAA activity, corroborated by the similarity of their active sites. FSAB has been able to react with three known donors (dihydroxyacetone, hydroxyacetone and glycolaldehyde) but always slightly slower than FSA

Novel metabolic features in Acinetobacter baylyi ADP1 revealed by a multiomics approach

Expansive knowledge of bacterial metabolism has been gained from genome sequencing output, but the high proportion of genes lacking a proper functional annotation in a given genome still impedes the accurate prediction of the metabolism of a cell. To access to a more global view of the functioning of the soil bacterium Acinetobacter baylyi ADP1, we adopted a multi ‘omics’ approach. Application of RNA-seq transcriptomics and LC/MS-based metabolomics, along with the systematic phenotyping of the complete collection of single-gene deletion mutants of A. baylyi ADP1 made possible to interrogate on the metabolic perturbations encountered by the bacterium upon a biotic change. Shifting the sole carbon source from succinate to quinate elicited in the cell not only a specific transcriptional response, necessary to catabolize the new carbon source, but also a major reorganization of the transcription pattern. Here, the expression of more than 12 % of the total number of genes was affected, most of them being of unknown function. These perturbations were ultimately reflected in the metabolome, in which the concentration of about 50 % of the LC/MS-detected metabolites was impacted. And the differential regulation of many genes of unknown function is probably related to the synthesis of the numerous unidentified compounds that were present exclusively in quinate-grown cells. Together, these data suggest that A. baylyi ADP1 metabolism involves unsuspected enzymatic reactions that await discovery. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11306-014-0662-x) contains supplementary material, which is available to authorized users