Project description:Caldicellulosiruptor saccharolyticus is an extremely thermophilic, Gram-positive anaerobe, which ferments cellulose-, hemicellulose- and pectin-containing biomass to acetate, CO2 and hydrogen. Its broad substrate range, high hydrogen-producing capacity, and ability to co-utilize glucose and xylose, make this bacterium an attractive candidate for microbial bioenergy production. Glycolytic pathways and an ABC-type sugar transporter were significantly up-regulated during growth on glucose and xylose, indicating that C. saccharolyticus co-ferments these sugars unimpeded by glucose-based catabolite repression. The capacity to simultaneously process and utilize a range of carbohydrates associated with biomass feedstocks represents a highly desirable feature of a lignocellulose-utilizing, biofuel-producing bacterium. Keywords: substrate response C. saccharolyticus was subcultured (overnight) 3 times on the substrate of interest in modified DSMZ 640 medium before inoculating a pH-controlled (pH = 7) 1-liter fermentor containing 4 gram substrate per liter. Cells were grown at 70 °C until mid-logarithmic phase (~OD660 = 0.3-0.4) and harvested by centrifugation and rapid cooling to 4 °C and stored at -80 °C. To elucidate the central carbon metabolic pathways and their regulation, transcriptome analysis was performed after growth on glucose, xylose and a 1:1 mixture of both substrates. L-Rhamnose, which was likely to follow another pathway, was used as a reference substrate.
Project description:Myceliophthora thermophila is a thermophilic fungus with great biotechnological characteristics for industrial applications, which can degrade and utilize all major polysaccharides in plant biomass. Nowadays, it has been developing into a platform for production of enzyme, commodity chemicals and biofuels. Therefore, an accurate genome-scale metabolic model would be an accelerator for this fungus becoming a universal chassis for biomanufacturing. Here we present a genome-scale metabolic model for M. thermophila constructed using an auto-generating pipeline with consequent thorough manual curation. Temperature plays a basic and critical role for the microbe growth. we are particularly interested in the genome wide response at metabolic layer of M. thermophilia as it is a thermophlic fungus. To study the effects of temperature on metabolic characteristics of M. thermophila growth, the fungus was cultivated under different temperature. The metabolic rearrangement predicted using context-specific GEMs integrating transcriptome data.The developed model provides new insights into thermophilic fungi metabolism and highlights model-driven strain design to improve biotechnological applications of this thermophilic lignocellulosic fungus.
Project description:Transcriptional profiling of Murine Embryonic Fibroblasts (MEFs) infected with Ad-MyD88 vs. Ad-GFP or mock infected. Three-condition experiment, Ad-MyD88 vs. Ad-GFP vs. Mock infected cells. Biological replicates: 3 Ad-MyD88, 3 Ad-GFP, 3 mock, independently grown and harvested. One replicate per array.
Project description:Transcriptional profiling of Bone-Marrow derived mouse Dendritic Cells (bmDCs) infected with Ad-MyD88 vs. Ad-GFP or mock infected Three-condition experiment, Ad-MyD88 vs. Ad-GFP vs. Mock infected cells. Biological replicates: 3 Ad-MyD88, 3 Ad-GFP, 3 mock, independently grown and harvested. One replicate per array.
Project description:The ideal microorganism for consolidated biomass processing to biofuels has the ability to breakdown of lignocellulose. This issue was examined for the H2-producing, extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus growing on lignocellulose samples as well as model hemicellulose components. Identification of the enzymes utilized by the cell in lignocellulose saccharification was done using whole-genome transcriptional response analysis and comparative genomics.
Project description:The zygomycete fungi-like Rhizomucor miehei have been extensively exploited for the production of various enzymes. As a thermophilic fungus, R. miehei is capable of growing at temperatures that approach the upper limits for all eukaryotes. In order to study the thermophilic mechanism, the transcriptional profiles of R. miehei CAU432 grown at two different temperatures (at 30°C and 50°C) were investigated by RNA-seq analysis. Approximately 35 million high-quality reads were generated from each library, and 62% reads were uniquely mapped to the genome. A high percentage of reads (67.1%) were mapped to predicted protein-coding genes, while 3.96% reads were distributed in splice junctions, 3.49% reads in antisense transcripts, 2.27% in introns, and 21.9% in other genomic regions. The frequency of reads which mapped to different genes ranged from one to over 300,000. More than 90% of predicted genes (9,680, 93% at 30°C; 9,618, 93.6% at 50°C) were detected with at least one read, while 128 genes and 190 genes were uniquely expressed at 50°C and 30°C, respectively. The results show that 2,117 genes were differently expressed (P<0.001) by the fungus with more than two-fold changes. These genes include 849 up-regulated and 1,268 down-regulated genes in mycelia grown at 50°C. These significantly differently expressed genes include many genes, putatively involved in thermophilic process, such as HSP, chaperones and proteasome.
Project description:To identify genes that may regulate distinct or overlapping functions of IRF-3 and IRF-7, primary human macrophage preparations were transduced with adenoviral vectors: Ad-GFP (control), Ad-F3 (expressing the active form of IRF-3, IRF-3 5D), or Ad-F7 (expressing the active form of IRF-7, IRF-7 D247-467) and evaluated by microarray analysis. RNA was collected 24 hours post-transduction with Ad-GFP, Ad-F3 and Ad-F7 and subjected to microarray analysis. Submited tables show the average of 7 donors.