Transcriptome analysis of Corynebacterium glutamicum in response to furfural presence
ABSTRACT: To understrand the altered global gene expression levels in C. glutamicum wild type in presence of furfural, transcriptome profiling was performed. Transcriptome profiles of the wild type grown in CgXII medium without furfural and with furfural stresses (each 6.5 mM, 13 mM, and 20 mM) were compared by using the samples taken at the OD600 of 6 (for the control and experiments). Each experiment was performed with a duplicate.
Project description:Transcriptional profiling of Acinetobacter baumannii ATCC17978 cells comparing treated ethanol cells with oleanolic acid treated. Based on the gene expression, we performed experiments to confirm the therapeutic effect and mechanism of OA in A. baumannii. We performed a transcriptome anaylsis of 2 samples that are OA and ethanol treatment, respectively.
Project description:RGS protein encoding genes gprK and rgsC deletion mutant microarray To identify the function of RGSs of A. fumigatus Biological replicates: WT vs. three deletion mutants, independently grown and harvested. One replicate per array
Project description:Transcriptional profiling of dark-grown Arabidopsis seedlings comparing SCR:PIF1/pifQ transgenic plant with pif1pif3pif4pif5 quadruple mutant (pifQ). Seedlings were grown under dark condition for 2.5 days. Goal was to determine the effects of endodermal PIF1 in dark-grown seedlings. Two-condition experiment, SCR:PIF1/pifQ vs. pifQ Biological replicates: 3 pifQ replicates, 3 SCR:PIF1 replicates.
Project description:We performed that comprehensive identification of genes responsible for stress tolerance by analyzing the whole-genome expression profiles of poplar (Populus alba × P. glandulosa) leaves exposed to drought and salt stresses. Examination at the molecular level how this tree species responds to drought and salt stresses by regulating the expression of genes involved in signal transduction, transcriptional regulation, and stress responses. Genome-wide analysis was conducted in poplar leaves exposed to drought and salt stresses.The plants were acclimated in soil and grown for 6 weeks in controlled conditions in a growth room (16 h light; light intensity, 150 μmol m-2sec-1; 24°C). Plants with a height of about 15 cm were separately exposed to either drought or salt stress. Up- and down-regulated genes were identified, and their putative functions are discussed.
Project description:Adapted tolerant yeast strain Y-50049 is able to in situ detoxify furfural and HMF while the wild type control Y-12632 repressed to loss function under challenges of 20 mM each of furfural and HMF A time course study during the lag phase with cells harvested at 18, 24, 28, and 42 h after 20 mM furfural and 20 mM HMF treatment
Project description:Viruses transmitted by small mammals and arthropods serve as global threats to humans. Most emergent and re-emergent viral agents are transmitted by these groups; therefore, the development of high-throughput screening methods for the detection and surveillance of such viruses is of great interest. In this study, we describe a DNA microarray platform that can be used for screening all viruses transmitted by small mammals and arthropods (SMAvirusChip) with nucleotide sequences that have been deposited in the GenBank. SMAvirusChip was designed with more than 15,000 oligonucleotide probes (60-mers), including viral and control probes. Two SMAvirusChip versions were designed: SMAvirusChip v1 contains 4209 viral probes for the detection of 409 viruses, while SMAvirusChip v2 contains 4943 probes for the detection of 416 viruses. SMAvirusChip was evaluated with 20 laboratory reference-strain viruses. These viruses could be specifically detected when alone in a sample or when artificially mixed within a single sample. The sensitivity of SMAvirusChip was evaluated using 10-fold serial dilutions of dengue virus (DENV). The results showed a detection limit as low as 2.6E3 RNA copies/mL. Additionally, the sensitivity was one log10 lower (2.6E2 RNA copies/mL) than quantitative real-time RT-PCR and sufficient to detect viral genomes in clinical samples. The detection of DENV in serum samples of DENV-infected patients (n= 6) and in a whole blood sample spiked with DENV confirmed the applicability of SMAvirusChip for the detection of viruses in clinical samples. In addition, in a pool of mosquito samples spiked with DENV, the virus was also detectable. SMAvirusChip was able to specifically detect viruses in cell cultures, serum samples, total blood samples and a pool of mosquitoes, confirming that cellular RNA/DNA did not interfere with the assay. Therefore, SMAvirusChip may represent an innovative surveillance method for the rapid identification of viruses transmitted by small mammals and arthropods. The SMAvirusChip v2 microarray includes more than 15,000 oligonucleotide probes (60-mers long) for the detection of viruses transmitted by small mammals and arthropods. The sequences of 4943 viral probes for the detection of 416 viruses (112 viruses transmitted by small mammals and 304 arboviruses) were included in this platform. Positive and negative control oligonucleotide probes were also included in the design.
Project description:To characterize anaerobic stress-induced expression in adhE mutants, the microarray experiment was performed with two serotypes of wild type E. coli and their adhE mutants: (1) K-12 strain, wild type; (2) B strain, wild type; (3) BW25113, adhE mutants; (4) BL21(DE3), adhE mutants. Under anaerobic growth condition in glucose-containing complex medium, the wild type strains 1 and 2 grew well whereas the mutant strains 3 and 4 experienced anaerobic stress and grew after 24 hours and 48 hours, respectively. For each of the four strains, RNA sampling was done after six hours of growth under anaerobic condition. Only one replicate was obtained for each strain.
Project description:The data explore the transcriptional response of strains LY180 and EMFR9 to 5 mM furfural under anaerobic fermentation condition The data explore the transcriptional response of strains LY180 and EMFR35 to 15 mM furfural under anaerobic fermentation condition The expression differences of polyamine transporters in LY180 vs EMFR9 and EMFR35 are further described in RD Geddes,X Wang, LP Yomano, EN Miller, H Zheng, KT Shanmugam, and LO Ingram. 2013. Selected Polyamines and Polyamine Transporters Increase Furfural Tolerance (in preparation for submission to Appl Env Microbiol) Total RNA was prepared from cultures of LY180, EMFR9 and EMFR35 immediately before and 15 min after addition of furfural (5mM and 15 mM). The Nimblegen TI83333 chip measures expression of 4,237 genes, with 5 replicates, and 18 probes average per gene. The complete dataset comprising 8 samples is linked below as a supplementary file.
Project description:We have employed whole RNA microarray expression profiling as a discovery platform to identify genes regulated by overexpression of miR-145 in U87 glioma cell. Lentivirus containing miR-145 coding sequence was infected to U87 cell to make U87 overexpressing miR-145. We did genome microarray between U87 and U87 overexpressing miR-145. Total RNAs from U87 cell or U87 overexpressing miR-145 were extracted. Whole RNA microarray expression profiling was performed between them.
Project description:Resistance of Saccharomyces cerevisiae to high furfural concentration is based on NADPH-dependent reduction by at least two oxireductases. Biofuels derived from lignocellulosic biomass hold promises for a sustainable fuel economy, but several problems hamper their economical feasibility. One important problem is the presence of toxic compounds in processed lignocellulosic hydrolysates with furfural as a key toxin. While Saccharomyces cerevisiae has some intrinsic ability to reduce furfural to the less toxic furfuryl alcohol, higher resistance is necessary for process conditions. By comparing an evolved, furfural resistant strain and its parent in micro-aerobic, glucose-limited chemostats at increasing furfural challenge, we elucidate key mechanism and the molecular basis of both natural and high-level furfural resistance. At lower furfural concentrations, NADH-dependent oxireductases are the main defence mechanism. At concentrations above 15 mM, however, [1-13C]-flux and global array-based transcript analysis demonstrated that the NADPH-generating flux through pentose-phosphate pathway increases and that NADPH-dependent oxireductases became the major resistance mechanism. The transcript analysis further revealed that iron transmembrane transport is up-regulated in response to furfural. While these responses occur in both strains, high-level resistance in the evolved strain was based on strong induction of ADH7, the uncharacterised ORF YKL071W and 4 further, likely NADPH-dependent oxireductases. By overexpressing the ADH7 gene and the ORF YKL071W, we inverse engineered significantly increased furfural resistance in the parent strain, thereby demonstrating these two enzymes to be key elements of the resistance phenotype. Experiment Overall Design: RNA levels were measured in glucose limited, micro-aerobic chemostat cultures with different concentrations of the growth inhibitor furfural. Two strains were compared: TMB3400-FT30-3 is a strain that has been evolutionary adapted to withstand high furfural concentrations. TMB3400 is its less resistant parent. Number of biological replicates: 2-3.