Project description:Only recently, the natural gut microbiome of the model organism Caenorhabditis elegans has been described. C. elegans harbors a distinct gut microbiome that is shaped by environmental conditions, age, and host genotype. However, there is not much known about the genetic factors on the molecular level that the worm employs in order to keep its microbiota at bay. Previously, we have shown that TGFβ/BMP immune signaling is able to control the gut microbiome of C. elegans in particular in regards to Enterobacter species. We now aimed to identify the downstream targets of TGFβ/BMP immune signaling that implement the changes in microbiome composition. Hence, we exposed TGFβ mutants, dbl-1(nk3) and sma-3(e491), overexpression strain ctIs40 [dbl-1(+) + sur-5::GFP], and wild-type N2 to a synthetic microbiota community, CeMbio, and an E. coli OP50 control, and performed RNAseq. CeMbio is a collection of 12 diverse bacterial strains, previously isolated from wild C. elegans, C. elegans grown in microcosms, or substrates with C. elegans. Using the R packages edgeR and limma we are currently analyzing the data to understand the involvement of TGFβ/BMP signaling in host-microbiome interaction.
Project description:To identify key genes in the regulation of salt tolerance in the mangrove plant Bruguiera gymnorhiza, the transcriptome profiling under salt stress was carried out. Main roots and lateral roots were collected from the mangrove plants at 0, 1, 3, 6, 12 and 24 h, 3 6 and 12 days after NaCl-treatment. Keywords: time course, stress response, root type comparison
Project description:To identify key genes in the regulation of salt tolerance in the mangrove plant Bruguiera gymnorhiza, the transcriptome profiling under salt stress was carried out. Main roots and lateral roots were collected from the mangrove plants at 0, 1, 3, 6, 12 and 24 h, 3 6 and 12 days after NaCl-treatment. Samples were collected from each set of three trees at 0, 1, 3, 6, 12 and 24 h, 3 6 and 12 days after NaCl-treatment, that is 27 trees were used in total. RNA was extracted from mixture of the samples from 3 trees to average genotypes of 3 trees.
Project description:We performed DNase-seq on 7-day-old seedlings from four A. thaliana accessions: Bur-0, Tsu-0, Bay-0, Est-1 using INTACT constructs (Deal and Henikoff, Developmental Cell, 2010) driven by the UBQ10 promoter. Chromatin accessibility profiling (Dnase I-seq) of 7-day-old seedlings of A. thaliana accessions: Bur-0, Tsu-0, Bay-0 & Est-1 grown in LD conditions (16hr light 22°C, 8hr dark 20°C).