Genomic Analysis of Parent-of-Origin Allelic Expression in Arabidopsis thaliana Seeds

Differential expression of maternally and paternally inherited alleles of a gene is referred to as gene imprinting, a form of epigenetic gene regulation common to flowering plants and mammals. In plants, imprinting primarily occurs in the endosperm, a seed tissue that supports the embryo during its growth and development. Previously, we demonstrated that widespread DNA demethylation at remnants of transposable elements accompanies endosperm development and that a subset of these methylation changes are associated with gene imprinting. Here we assay imprinted gene expression genome-wide by performing high-throughput sequencing of RNA derived from seeds of reciprocal intraspecific crosses. We identify more than 200 loci that exhibit parent-of-origin effects on gene expression in the endosperm, including a large number of transcription factors, hormone biosynthesis and response genes, and genes that encode regulators of epigenetic information, such as methylcytosine binding proteins, histone methyltransferases, and chromatin remodelers. The majority of these genes are partially, rather than completely, imprinted, suggesting that gene dosage regulation is an important aspect of imprinted gene expression

Centrality evolution of the charged-particle pseudorapidity density over a broad pseudorapidity range in Pb-Pb collisions at root s(NN)=2.76TeV

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Infections à vibrions non cholériques

International audienceLes vibrions sont des bactéries à Gram négatif, hôtes naturels du milieu marin, dont les variations de densité, et donc le risque sanitaire potentiel qu'ils représentent pour l'homme, sont fonction de facteurs environnementaux régulés en partie par le changement climatique. Les « vibrions non cholériques » (VNC) d'intérêt médical comprennent les souches appartenant aux sérogroupes autres que O1 ou O139 de l'espèce Vibrio cholerae (V. cholerae non-O1/non-O139) et à onze autres espèces du genre Vibrio. Ces VNC ne sont pas spécialement adaptés à l'homme et n'entraînent que des infections sporadiques, pouvant cependant être très graves, plus rarement des toxi-infections alimentaires collectives. Quatre espèces – V. cholerae, V. parahaemolyticus, V. vulnificus et V. alginolyticus – sont plus particulièrement impliquées en pathologie humaine. Deux voies d'exposition sont à l'origine des infections à VNC, l'ingestion d'aliments contaminés, fruits de mer crus ou insuffisamment cuits en particulier, et le contact direct avec l'eau de mer ou l'environnement marin. Trois grands syndromes cliniques leur sont associés, gastroentérites, infections de plaies et septicémies. Les pathologies hépatiques ont été identifiées comme un facteur de risque de septicémie primaire, que la contamination soit ou non d'origine alimentaire. Les infections les plus sévères sont associées à l'espèce V. vulnificus qui peut être à l'origine d'infections invasives rapidement évolutives qu'il est important de diagnostiquer et de traiter rapidement. Un renforcement de la surveillance environnementale et alimentaire, une prise de conscience accrue par les cliniciens leur permettant une reconnaissance précoce des infections, la mise en place d'un traitement approprié et l'information des patients à risque permettraient d'anticiper l'impact de ces infections en santé humaine

Occurrence of the tdh and trh genes in Vibrio parahaemolyticus isolates from waters and raw shellfish collected in two French coastal areas and from seafood imported into France

International audienceThe occurrence of the hemolysin genes, tdh and trh, in Vibrio parahaemolyticus strains isolated from environmental samples collected in two French coastal areas, clinical samples, and seafood products imported into France was studied. Polymerase chain reaction (PCR) with two sets of primers was used to detect the hemolysin genes. Most of the clinical isolates (91%) and 1.5% of the isolates from seafood possessed the hemolysin genes. Three and fifteen percent, respectively, of the two groups of environmental strains carried the hemolysin genes depending on the geographic site. The tdh and trh genes play important roles in virulence. Thus, our results indicate that pathogenic V. parahaemolyticus isolates are present in French coastal areas and in seafood imported into France. Furthermore, they may also be present in French seafood product

Evaluation of Most-Probable-Number–PCR Method with Internal Amplification Control for the Counting of Total and Pathogenic Vibrio parahaemolyticus in Frozen Shrimps

International audienceThe most-probable-number (MPN) method is often time-consuming for the isolation, detection, and quantification of Vibrio parahaemolyticus from natural sources. MPN counting of V. parahaemolyticus bacteria usually involves the isolation of typical V. parahaemolyticus colonies on selective medium, with subsequent confirmation by biochemical identification. In this study, we evaluated the use of a PCR on MPN enrichment cultures (MPN-PCR) for the direct detection of total and pathogenic V. parahaemolyticus cells in frozen shrimp. This reaction targeted the R72H, tdh, and trh sequences. An internal amplification control was added to the samples before R72H amplification. There was an excellent correlation between the results of the two methods for artificially inoculated and natural shrimp samples. Of 36 natural samples, 28 tested positive for the presence of V. parahaemolyticus, with an MPN value of 2 | 10 21 to 9.2 | 10 1 per g. No pathogenic V. parahaemolyticus cells were detected. The test had a detection limit of one V. parahaemolyticus organism per g and was completed within two working days. These results support the use of the combination of PCR with MPN for the detection of total or potentially pathogenic V. parahaemolyticus cells in frozen shrimp

Total and pathogenic Vibrio parahaemolyticus in shrimp: Fast and reliable quantification by real-time PCR

International audienceVibrio parahaemolyticus is found in aquatic environments and is the leading cause of gastroenteritis due to seafood consumption worldwide. We evaluated a quantitative real-time PCR (Q-PCR) assay with hydrolysis probes, to determine whether this method could be used for the efficient counting of total, tdh and trh-positive V. parahaemolyticus in shrimps. We assessed the specificity of this assay, using 62 strains from 12 non target bacterial species of the Vibrio, Photobacterium, Shewanella and Aeromonas genera. Only V. parahaemolyticus with the appropriate target gene generated a fluorescent signal. We assessed the robustness of this assay, by analyzing spiked shrimps by Q-PCR and traditional culture methods, using most probable number (MPN)-PCR. After a 6 h enrichment period, the assay successfully detected total and pathogenic V. parahaemolyticus in shrimps samples spiked with less than 5 V. parahaemolyticus cells/g of shrimp. The Q-PCR results obtained were compared with those obtained by most probable number (MPN)-PCR format. An excellent correlation between the two methods was observed in all cases (R 2 N 0.9742). The application of this Q-PCR assay to 85 natural shrimp samples also resulted in the successful quantification of V. parahaemolyticus in this matrix, and the counts obtained were correlated with those obtained by (MPN)-PCR (P = 0.2598). Thus, this rapid and sensitive Q-PCR can be used to quantify V. parahaemolyticus in natural shrimp samples. This assay could be proposed, in response to the demands of the European Commission, as a tool for testing for the presence of vibrios in crustaceans, making it possible to legislate in this domain

Improved specific detection of Vibrio cholerae in environmental water samples by culture on selective medium and colony hybridization assay with an oligonucleotide probe

International audienceWe developed a rapid and efficient method based on culture on selective medium and colony hybridization assay for the detection of Vibrio cholerae in estuarine water samples. A 22-oligonucleotide sequence of the 16S-23S rDNA intergenic spacer region was labeled with digoxigenin and evaluated for specificity and sensitivity by dot blot and colony hybridization with collection strains and environmental and clinical isolates. No isolates of species other than V. cholerae hybridized with the oligonucleotide probe. Colony hybridization was then performed with mixed microbial populations from brackish and sea water samples isolated, after an enrichment step, on selective culture media. Plating on alkaline nutrient agar without added NaCl (modified alkaline nutrient agar, mANA) resulted in higher V. cholerae colony counts than did plating on other frequently used selective media, and favored direct detection by colony hybridization. The combined use of mANA agar and an oligonucleotide probe resulted in the specific recovery of V. cholerae and could be used for confirmation of the most-probable-number procedure usually used to count this bacterium in environmental sample