Project description:ost-pathogen interactions are often studied in vitro using primary or immortal cell lines. This set-up avoids ethical problems of animal testing and has the additional advantage of lower costs. However, the influence of cell culture media on bacterial growth and metabolism is not considered or investigated in most cases. To address this question growth and proteome adaptation of Corynebacterium diphtheriae strain ISS3319 were investigated in this study. Bacteria were cultured in standard growth medium, cell culture medium and fetal calf serum. Mass spectrometric analyses and label-free protein quantification hint to an increased bacterial pathogenicity when grown in cell culture medium as well as an influence of the growth medium on the cell envelope.
Project description:Nitrate-reducing iron(II)-oxidizing bacteria are widespread in the environment contribute to nitrate removal and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing iron(II)-oxidizing bacteria is rarely investigated and poorly understood. The most prominent model system for this type of studies is enrichment culture KS, which originates from a freshwater sediment in Bremen, Germany. To gain insights in the metabolism of nitrate reduction coupled to iron(II) oxidation under in the absence of organic carbon and oxygen limited conditions, we performed metagenomic, metatranscriptomic and metaproteomic analyses of culture KS. Raw sequencing data of 16S rRNA amplicon sequencing, shotgun metagenomics (short reads: Illumina; long reads: Oxford Nanopore Technologies), metagenome assembly, raw sequencing data of shotgun metatranscriptomes (2 conditions, triplicates) can be found at SRA in https://www.ncbi.nlm.nih.gov/bioproject/PRJNA682552. This dataset contains proteomics data for 2 conditions (heterotrophic and autotrophic growth conditions) in triplicates.
Project description:Dictyostelium amoebae feed on bacteria, which are taken up by phagocytosis. Using DNA microarrays we have investigated gene expression during phagocytosis of Dictyostelium cells incubated with Escherichia coli. The gene expression profiles of cells incubated for a short time with bacteria were compared with cells either exposed to axenic culture medium or exponentially growing on bacteria. Transcriptional changes during exponential growth either in axenic medium or on bacteria were also compared, in order to identify genes differentially expressed during growth on bacteria. We recognized 443 and 59 genes, which are differentially regulated by phagocytosis or growth on bacteria, respectively, and 102 genes, which are common to both processes. Roughly one third of the genes is up- and two third down-regulated compared to growth in axenic medium. Functional annotation of differentially regulated genes revealed that phagocytosis induces profound changes in carbohydrate, aminoacid and lipid metabolism, in the translation machinery and in cytoskeletal components. Among the up-regulated genes are genes encoding proteins involved in transcription and translation, sterol metabolism and mitochondrial biogenesis. Very few changes were detected in genes required for endocytosis and intracellular traffic, suggesting that the intracellular traffic machinery is mostly in common between phagocytosis and pinocytosis. A few putative receptor or adhesion proteins and components of signal transduction have been identified, which could be involved in regulating phagocytosis.
Project description:Analysis of KhES-1 and H9 human ES cells in growth factors-dependent (E8) and -independent (AKIT) medium in feeder-free culture condition and KSR/bFGF medium on a feeder-layer. Results provide insight into genetic stability in different culture media/conditions.
Project description:Analysis of undifferentiated KhES-1 human embryonic stem cells in growth factors-dependent (E8) and -independent (AKIT) culture medium. Results provide insight into genes differentially expressed in pluripotent states maintained by AKIT and E8 culture medium.
Project description:The aim of this RNA-sequencing study is to measure differential gene expression in 4 intestinal bacteria (Bacteroides xylanisolvens, Bacteroides thetaiotaomicron, Subdoligranulum variabile and Roseburia intestinalis). The data highlight the coordinated action of genes within the same locus involved in the degradation of complex carbohydrates. These loci are well characterized in Bacteroidetes species and referred to as polysaccharide utilization loci. In Firmicutes species, these loci are not so clear-cut, athough the GP-PUL concept has already been proposed. Here we compare the differential gene expression in minimal culture medium supplemented with a complex carbohydrate with a minimal culture medium supplemented with glucose. This differential analysis reveals a source-specific genetic response and a coordinated expression of genes involved in carbohydrate transport, carbohydrate degradation and transcriptional activation of these complex enzymatic machineries.