Project description:BACKGROUND: Human SP-A1 and SP-A2, encoded by SFTPA1 and SFTPA2 and their genetic variants differentially impact alveolar macrophage (AM) functions and regulation, including the miRNome. We investigated whether miRNome differences previously observed between AM from SP-A2 and SP-A1/SP-A2 mice are due to continued qualitative differences or a delayed response of mice carrying a single gene. METHODS: Human transgenic (hTG) mice, carrying SP-A2 or both SP-A genes and SP-A-KO mice were exposed to filtered air (FA) or O3. AM miRNA levels, target gene expression and pathways determined 18 h after O3 exposure. RESULTS: We found: (a) Differences in miRNome due to sex, SP-A genotype, and exposure; (b) miRNome of both sexes was largely downregulated by O3 ; co-ex had fewer changed (≥2X) miRNAs than either group. (c) the number and direction of expression of genes with significant changes in males and females in co-ex is almost the opposite of those in SP-A2; (iv) The same pathways were found in the studied groups; (e) O3 exposure attenuated sex differences; a higher number of genotype-dependent and genotype-independent miRNAs was common in both sexes after O3 exposure. CONCLUSION: Qualitative differences between SP-A2 and co-ex persist 18 h post-O3, and O3 attenuates sex differences.
Project description:By comparing the gene expression profiling in Anoxybacillus sp. SK 3-4 with and without aluminum exposure, the sets of gene up-regulated and down-regulated by aluminum were identified. The function of genes or proteins induced under these conditions can a reflection of the mechanism of resistance. Transcriptome profiling of Anoxybacillus sp. SK 3-4 treated by aluminum would allow a better understanding of the gene involving in tolerance and removal of aluminum. Global transcriptomic response of Anoxybacillus sp. SK 3-4 to aluminum exposure
Project description:Investigation of gene expression level changes in Gordonia sp. KTR9 and Gordonia sp. KTR9 mutant GlnR upon exposure to high and low nitrogen conditions The Gordonia sp. KTR9 strain used in this study has been previously described by Thompson KT, Crocker FH, Fredrickson HL.2005. Mineralization of the cyclic nitramine explosive hexahydro-1,3,5-trinitro-1,3,5-triazine by Gordonia and Williamsia spp. Appl Environ Microbiol. 2005 Dec;71(12):8265-72.
Project description:By comparing the gene expression profiling in Anoxybacillus sp. SK 3-4 with and without aluminum exposure, the sets of gene up-regulated and down-regulated by aluminum were identified. The function of genes or proteins induced under these conditions can a reflection of the mechanism of resistance. Transcriptome profiling of Anoxybacillus sp. SK 3-4 treated by aluminum would allow a better understanding of the gene involving in tolerance and removal of aluminum.
Project description:Investigation of gene expression level changes in Gordonia sp. KTR9 upon exposure to RDX and Nitrogen Limitation, compared to controls with no RDX. The Gordonia sp. KTR9 strain used in this study has been previously described by Thompson KT, Crocker FH, Fredrickson HL.2005. Mineralization of the cyclic nitramine explosive hexahydro-1,3,5-trinitro-1,3,5-triazine by Gordonia and Williamsia spp. Appl Environ Microbiol. 2005 Dec;71(12):8265-72.
Project description:Investigation of whole genome gene expression level in motile strain of Sphingomonas. sp A1 All flagellar genes in motile strain of Sphingomonas. sp A1 are highly transcribed.
Project description:Investigation of gene expression level changes in Gordonia sp. KTR9 and Gordonia sp. KTR9 mutant GlnR upon exposure to high and low nitrogen conditions The Gordonia sp. KTR9 strain used in this study has been previously described by Thompson KT, Crocker FH, Fredrickson HL.2005. Mineralization of the cyclic nitramine explosive hexahydro-1,3,5-trinitro-1,3,5-triazine by Gordonia and Williamsia spp. Appl Environ Microbiol. 2005 Dec;71(12):8265-72. A 12 x 135K array study using total RNA recovered from triplicate cultures of KTR9 exposed to high nitrogen conditions, triplicate cultures of KTR9 exposed to low nitrogen conditions, triplicate cultures of KTR9 mutant GlnR exposed to high nitrogen conditions, triplicate cultures of KTR9 mutant GlnR exposed to low nitrogen conditions.
Project description:This project is a proteomic comparison of Hyphomicrobium sp. MC8b grown with dichloromethane or with methanol. The datasets were obtained using the annotated genome of Hyphomicrobium sp. MC8b.
Project description:Background: Frankia sp. strains are actinobacteria that form N2-fixing root nodules on angiosperms. Several reference genome sequences are available enabling transcriptome studies in Frankia sp. Genomes from Frankia sp. strains differ markedly in size, a consequence proposed to be associated with a high number of indigenous transposases, more than 200 of which are found in Frankia sp. strain CcI3 used in this study. Because Frankia exhibits a high degree of cell heterogeneity as a consequence of its mycelial growth pattern, its transcriptome is likely to be quite sensitive to culture age. This study focuses on the behavior of the Frankia sp. strain CcI3 transcriptome as a function of nitrogen source and culture age. Results: To study global transcription in Frankia sp. CcI3 grown under different conditions, complete transcriptomes were determined using high throughput RNA deep sequencing. Samples varied by time (five days vs. three days) and by culture conditions (NH4+ added vs. N2 fixing). Assembly of millions of reads revealed more diversity of gene expression between five-day and three-day old cultures than between three day old cultures differing in nitrogen sources. Heat map analysis organized genes into groups that were expressed or repressed under the various conditions compared to median expression values. Twenty-one SNPs common to all three transcriptome samples were detected indicating culture heterogeneity in this slow-growing organism. Significantly higher expression of transposase ORFs was found in the five-day and N2-fixing cultures, suggesting that N starvation and culture aging provide conditions for on-going genome modification. Transposases have previously been proposed to participate in the creating the large number of gene duplication or deletion in host strains. Subsequent RT-qPCR experiments confirmed predicted elevated transposase expression levels indicated by the mRNA-seq data. Conclusions: The overall pattern of gene expression in aging cultures of CcI3 suggests significant cell heterogeneity even during normal growth on ammonia. The detection of abundant transcription of nif (nitrogen fixation) genes likely reflects the presence of anaerobic, N-depleted microsites in the growing mycelium of the culture, and the presence of significantly elevated transposase transcription during starvation indicates the continuing evolution of the Frankia sp. strain CcI3 genome, even in culture, especially under stressed conditions. These studies also sound a cautionary note when comparing the transcriptomes of Frankia grown in root nodules, where cell heterogeneity would be expected to be quite high.