Project description:Microcosms made of filtered seawater innoculated with Enterococcus faecalis v583 were exposed to artificial sunlight to investigate photoinactivation mechanisms. Microcosms exposed to artificial sunlight were compared to dark controls. Three experiments were done on three separate days. During every experiment, the light and dark microcosms were samples at the begining (time = 0 hours) and then at 2, 6, 12 and 24 hours.
Project description:It has been performed a genome-wide analysis of gene expression of the root-colonizing bacterium Pseudomonas putida KT2440 in the rhizosphere of corn (Zea mays var. Girona. To identify reliable rhizosphere differentially expressed genes, rhizosphere populations of P. putida bacteria cells were compared with three alternative controls: i) planktonic cells growing exponentially in rich medium (LB), ii) planktonic cells in stationary phase in LB, and iii) sessile populations established in sand microcosms, under the same conditions used to grow inoculated corn plants.
Project description:This project provides tandem mass spectrometry data of leaf proteins extracted from samples of Populus x canadensis (hybrid of P. nigra x P. deltoides) grown in soil microcosms spiked with phenanthrene at different nominal concentration (0-100–200–400–700– 1000–1500–2000 mg PHE kg−1 dry weight.
Project description:This project provides tandem mass spectrometry data of root proteins extracted from samples of Populus x canadensis (hybrid of P. nigra x P. deltoides) grown in soil microcosms spiked with phenanthrene at different nominal concentration (0-100–200–400–700– 1000–1500–2000 mg PHE kg−1 dry weight.
Project description:Chronic lymphocytic leukemia (CLL) is characterized by substantial clinical heterogeneity, despite relatively few genetic alterations. To provide a basis for studying epigenome deregulation in CLL, we established genome-wide chromatin accessibility maps for 88 CLL samples from 55 patients using the ATAC-seq assay, and we also performed ChIPmentation and RNA-seq profiling for ten representative samples. Based on the resulting dataset, we devised and applied a bioinformatic method that links chromatin profiles to clinical annotations. Our analysis identified sample-specific variation on top of a shared core of CLL regulatory regions. IGHV mutation status – which distinguishes the two major subtypes of CLL – was accurately predicted by the chromatin profiles, and gene regulatory networks inferred for IGHV-mutated vs. IGHV-unmutated samples identified characteristic differences between these two disease subtypes. In summary, we found widespread heterogeneity in the CLL chromatin landscape, established a community resource for studying epigenome deregulation in leukemia, and demonstrated the feasibility of chromatin accessibility mapping in cancer cohorts and clinical research.
