Project description:We characterized the bacterial diversity of chlorinated drinking water from three surface water treatment plants supplying the city of Paris, France. For this purpose, we used serial analysis of V6 ribosomal sequence tag (SARST-V6) to produce concatemers of PCR-amplified ribosomal sequence tags (RSTs) from the V6 hypervariable region of the 16S rRNA gene for sequence analysis. Using SARST-V6, we obtained bacterial profiles for each drinking water sample, demonstrating a strikingly high degree of biodiversity dominated by a large collection of low-abundance phylotypes. In all water samples, between 57.2-77.4% of the sequences obtained indicated bacteria belonging to the Proteobacteria phylum. Full-length 16S rDNA sequences were also generated for each sample, and comparison of the RSTs with these sequences confirmed the accurate assignment for several abundant bacterial phyla identified by SARST-V6 analysis, including members of unclassified bacteria, which account for 6.3-36.5% of all V6 sequences. These results suggest that these bacteria may correspond to a common group adapted to drinking water systems. The V6 primers used were subsequently evaluated with a computer algorithm to assess their hybridization efficiency. Potential errors associated with primer-template mismatches and their impacts on taxonomic group detection were investigated. The biodiversity present in all three drinking water samples suggests that the bacterial load of the drinking water leaving treatment plants may play an important role in determining the downstream community dynamics of water distribution networks. 3 different drinking water samples (Orly, Ivry, Joinville drinking water sample)
Project description:We characterized the bacterial diversity of chlorinated drinking water from three surface water treatment plants supplying the city of Paris, France. For this purpose, we used serial analysis of V6 ribosomal sequence tag (SARST-V6) to produce concatemers of PCR-amplified ribosomal sequence tags (RSTs) from the V6 hypervariable region of the 16S rRNA gene for sequence analysis. Using SARST-V6, we obtained bacterial profiles for each drinking water sample, demonstrating a strikingly high degree of biodiversity dominated by a large collection of low-abundance phylotypes. In all water samples, between 57.2-77.4% of the sequences obtained indicated bacteria belonging to the Proteobacteria phylum. Full-length 16S rDNA sequences were also generated for each sample, and comparison of the RSTs with these sequences confirmed the accurate assignment for several abundant bacterial phyla identified by SARST-V6 analysis, including members of unclassified bacteria, which account for 6.3-36.5% of all V6 sequences. These results suggest that these bacteria may correspond to a common group adapted to drinking water systems. The V6 primers used were subsequently evaluated with a computer algorithm to assess their hybridization efficiency. Potential errors associated with primer-template mismatches and their impacts on taxonomic group detection were investigated. The biodiversity present in all three drinking water samples suggests that the bacterial load of the drinking water leaving treatment plants may play an important role in determining the downstream community dynamics of water distribution networks.
Project description:We developed a novel method for the identification of SUMO sites by expression of His-tagged SUMO mutants and affinity purification of SUMOylated proteins, followed by trypsin digestion and immunocapture of peptides containing diglycine signature tags. Lab Head: Dr Pascale Cossart, pascale.cossart@pasteur.fr Institut Pasteur Unité des Interactions Bactéries-Cellules, Inserm U604, INRA USC2020 25 rue du Dr. Roux 75015 Paris France
Project description:CHQ5B primary human myoblasts obtained from Dr V. Mouly (Paris, France) have been described previously (Faulkner et al., 1999). Ankrd2 is upregulated on differentiation of myoblasts. The change in gene expression was studied in cells silenced for Ankrd2 (infected with AAV-shAnkrd2), control cells (infected with AAV-shLuc) and control cells uninfected.
Project description:Poly(A) and CUT RNA fractions are compared using 3 'Long-SAGE deep-sequencing. ArrayExpress Release Date: 2008-12-19 Publication Title: Widespread bidirectional promoters are the major source of cryptic transcripts in yeast Publication Author List: Helen Neil, Christophe Malabat, Yves d'Aubenton-Carafa, Zhenyu Xu, Lars M. Steinmetz and Alain Jacquier Person Roles: submitter Person Last Name: Malabat Person First Name: Christophe Person Mid Initials: Person Email: christophe.malabat@pasteur.fr Person Phone: Person Address: Unité de Génétique des Interactions Macromoléculaires; CNRS, URA2171,F-75015, Paris, France Person Affiliation: Institut Pasteur
Project description:786-O cells (150, 000) were treated for 24h with DMSO, 5 µM of CX4945 or AB668. Total RNA was extracted from treated cells using the MirVana PARIS kit (Thermofisher). The 3′ Bulk RNA Barcoding and sequencing (BRB-seq) experiments were performed at the Research Institute for Environmental and Occupational Health (Irset, Rennes, France) according to the published protocol (Alpern et al., 2019). Sequencing was perfomred by SiLicium.