Project description:Chlamydia trachomatis D serovar was grown in axenic culture with G6P or G6P with glutamine. The data reveal the early transcriptonal regulation in the bacteria.
Project description:We conducted a culture experiment by deeply submerging plants in swine wastewater in culturing Iris tectorum and co-culturing Iris tectorum and Dictyosphaerium sp., and found that the plants grew sub-normal in the plant-microalgae co-culture while the plants were dead after 21 days in the plant culture. We generated a comprehensive RNA-seq dataset from the submerged Iris tectorum leaves in both the plant culture and the plant-microalgae co-culture, aiming at providing information on the response mechanisms of the plants to waterlogging stress. Besides raw reads of the RNA-seq dataset, we used DEseq2 algorithms to detect the differently expressed genes in the plants between the different cultures. Additionally, we performed the plant disease resistance gene analysis for all the differentially expressed genes.
Project description:To provide insights into expression patterns of the genes encoding putatively secreted proteins in U. bromivora during saprophytic growth and in planta, we conducted RNA-seq analyses. To this end, we isolated RNA from axenic U. bromivora UB1 culture and from stems of twelve day old B. hybridum Bd28 plants that were spore-inoculated with U. bromivora. Among the 6756 transcripts found to be expressed in our dataset, 493 were significantly upregulated in planta compared to axenic culture (logFC > 2, adjusted p-value < 0.1), while 1138 transcripts were significantly downregulated. Notably, transcripts predicted to encode secreted proteins are significantly enriched among the upregulated transcripts compared to all annotated genes.
Project description:Coxiella burnetii, a category B select agent, is endemic worldwide, except New Zealand. It causes annually several outbreaks of the zoonotic disease Q fever predominantly in small ruminants. To date, the lipopolysaccharide (LPS), besides a type IV secretion system (T4SS), is the only defined and characterized virulence determinant of C. burnetii. This surface molecule is used to distinguish between virulent (Ph I) and low-virulent (Ph II) organisms, the latter emerge only after frequent passaging in the laboratory. As an obligate intracellular pathogen, targeted genetic modification is still not a routine and labour intensive procedure. The deeper study of novel determinants is complicated and demands not only advanced techniques for axenic and for cell culture-based cultivation but also novel approaches in the high-resolution mass spectrometry. This work is the first proteomic study comparing. C. burnetii Ph I and Ph II propagated in different axenic media and in cell culture.
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.
