Project description:We isolated an efficient doxycycline degrading strain Chryseobacterium sp. WX1. To investigate gene expression patterns during doxycyclinedegradation by strain WX1, we conducted a comparative transcriptomic analysis using cultures of strain WX1 with and without doxycycline addition. The RNA-Seq data revealed that 90.44-96.56% of the reads mapped to the genome of Chryseobacterium sp. WX1 across all samples. Differentially expressed genes (DEGs) analysis (|log2FC| >2; p < 0.01) showed that 693 genes were significantly up-regulated and 592 genes were significantly down-regulated.
Project description:Investigation of whole genome gene expression level changes in a Gluconacetobacter xylinus NBRC 3288 delta-fnrG mutant, compared to the wild-type strain.
Project description:Purpose:The goals of this study are to clarify the B. subtilis NBRC 16449 response to soybeans. Methods: B. subtilis NBRC 16449 cells were aerobically cultured in liquid LB, LB solidified with agar, or on surface of boiled soybeans to logarithmic growth phase. Total RNAs were extracted from bacterial cells by Hot-Phenol method. Samples for RNA-seq were prepared according to Illmina protocol available from the manufacture. The sequence reads that passed quality filters were analyzed at the transcript isoform level with bowtie v0.11.2. Results: Using an optimized data analysis workflow, we mapped around 15 million sequence reads per sample to the whole genome of B. subtilis BEST195 and identified 4271 transcripts in B. subtilis NBRC 16449 with Bowtie aligner. Read count per genome was extracted from known gene annotations with HTSeq program. Compared the transcriptomes of B. subtilis NBRC 16449 grown on LB solidified with agar to that grown on surface of boiled soybeans, about 5% of genes showed the different expression levels.
Project description:In this study, we isolated a potent doxycycline-degrading bacterium, Chryseobacterium sp. WX1, from environmental samples. To elucidate the molecular mechanisms underlying doxycycline degradation by strain WX1, we assessed and interpreted the proteomic profiles of Chryseobacterium sp. WX1 under conditions both with and without doxycycline exposure.
