RNA-Seq of Clostridium cellulovorans cultured in different carbon sources in exponential phase
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ABSTRACT: When Clostridium cellulovorans cultured in different carbon sources respectively, with pH controlled at 7.0 in the fed-batch fermentation, the main product was butyrate. In order to understand the carbon and energy flux of Clostridium cellulovorans, comparative transcriptome in exponential phase was performed.
Project description:Clostridium ljungdahlii not only utilizes CO, but also H2 as energy source during autotrophic growth. In theory, CO is a more energetically and thermodynamically favourable energy source than H2 in the gas fermentation of C. ljungdahlii. However, how C. ljungdahlii conserves energy for growth and ethanol/acetate formation grown on CO or CO2/H2 is not in great detail. In this study, C. ljungdahlii was fermented on CO and CO2/ H2 at pH 6.0 with 0.1 MPa gas pressure. C. ljungdahlii produced 27 g/L acetate, 9 g/L ethanol, 8 g/L 2,3-butanediol and traces of lactate in the presence of CO as energy source, while it produced 25.8 0.1 g/L acetate, 1.8 0.1 g/L ethanol, 0.7 0.01g/L 2,3-butanediol and trances of lactate in the same fermentation condition using H2 as energy source. Therefore, comparative transcriptomes between cells grown on CO and cells grown on H2/CO2 were performed to investigate gene expression profiles based on three biological replicates.
Project description:More than 5 g/L ethanol was detected at 84 h in the late-exponential phase with 0.1 MPa at pH 6.0 in the batch fermentation of C. ljungdahlii grown autotrophically. Interestingly, ethanol started to be reassimilated in the stationary phase. In order to understand the metabolic flux of ethanol, comparative transcriptome between exponential and stationary phases were performed.
Project description:Clostridium ljungdahlii can utilize CO as energy source during autotrophic growth. C. ljungdahlii grows sufficiently in CO and produces ethanol as the main product. In this study, C. ljungdahlii wild type and mutant were fermented on CO. C. ljungdahlii produced more ethanol than the ΔadhE1 mutant. The results showed that aldehyde dehydrogenase inactivation led to inefficient metabolism in C. ljungdahlii. Thus, comparative transcriptomes among cells grown on CO of WT and ΔadhE1 mutant were performed to investigate gene expression profiles based on three biological replicates.
Project description:Clostridium ljungdahlii not only utilizes CO, but also H2 as energy source during autotrophic growth. And C. ljungdahlii also grows in fructose fermentation. In theory, fructose is a more energetically favourable energy source than syngas in the fermentation of C. ljungdahlii. However, C. ljungdahlii grows insufficiently in fructose and produces less acetate and ethanol, compared to syngas fermentation. In this study, C. ljungdahlii wild type and mutants were fermented on fructose. C. ljungdahlii produced less ethanol than the ΔadhE1 mutant and consumed less fructose. The ΔadhE1+2 mutant cannot grow in the syngas fermentation and produced less ethanol among the three strains. The results showed that aldehyde dehydrogenase inactivation led to efficient metabolism in C. ljungdahlii and the bifunctional aldehyde/alcohol dehydrogenases inactivation led to decrease metabolism. Thus, comparative transcriptomes among cells grown on fructose of three strains were performed to investigate gene expression profiles based on three biological replicates.
Project description:Clostridium beijerinckii is an anaerobic strain and well known for acetone-ethanol-butanol (ABE) fermentation using carbohydrates derived from cellulose or starch. During ABE fermentation, various byproducts are formed, mainly including acids (acetate, butyrate and lactate) and gas (hydrogen and carbon dioxide). recently, we found that Clostridium beijerinckii is able to produce a new product that had never been reported before and tightly regulated by pH and nitrogen source.
Project description:The objective was to determine the role of Krüppel-like factor 5 (KLF5) in radiation-induced intestinal injury. Mice with intestinal-specific knockdown of KLF5 (Cre+ mice) were generated and their response to radiation was compared with controls (Cre- mice). Mice were given 15 Gy total body irradiation (TBI). The mice intestines were harvested at 6h post TBI and screened for differentially expressed genes by microarray analysis. We identified 11,004 and 2,466 differentially expressed genes in non-irradiated and irradiated mice at 6h post TBI, respectively. KLF5 knockdown down-regulated genes related to DNA damage repair pathways such as nucleotide excision repair, mismatch repair, non-homologous end joining and the Fanconi anemia pathway, which may suggest a novel function of KLF5. A four chip study using total RNA recovered from four pooled intestine tissues of four experimental groups. The four experimental groups respectively were the 6h-cre+ group, 6h-cre- group, con-cre+ group and con-cre- group. Equal mass amounts of total RNA were pooled from each small intestine to yield a sample representing RNA from 3 separate mice in each group. One pooled sample in every group were tested with one chip. Each chip measures the expression level of 44,170 genes from C57BL/6 mouse (background) with three 60-mer probe pairs per gene.
Project description:Various saprotrophic microorganisms, especially filamentous fungi, can efficiently degrade lignocellulose that is one of the most abundant natural material on earth. It consists of complex carbohydrates and aromatic polymers found in plant cell wall and thus in plant debris. Aspergillus fumigatus Z5 was isolated from compost heaps and showed highly efficient plant biomass-degradation capability.Genome analysis revealed an impressive array of genes encoding cellulases, hemicellulases, and pectinases involved in lignocellulosic biomass degradation. We sequenced the transcriptomes of Aspergillus fumigatus Z5 induced by sucrose, xylan, cellulose and rice straw, respectively. There were 444, 1711 and 1386 significantly differently (q-value ⤠0.0001 and |log2 of the ratio of the RPM values| ⥠2) expressed genes in xylan, cellulose and rice straw,respectively, relative to sucrose control. After incubation at 45 â, 145rpm for 20 hours with sucrose as the carbon source, mycelia were induced for 16 hours using xylan, cellulose and rice straw, respectively. Transcriptome induced by sucrose was used as the control when comparing the differences between other three transcriptomes (induced by xylan, cellulose and rice straw, respectively).
Project description:The miRNA microarray analysis was performed to explore the expression profiles of miRNAs using the same liver tissues of NFD-fed mice and HFD-fed mice Summary: An abstract of the experiment and the data analysis. Project Description: Sample and experiment information. Array Information: miRCURY™ LNA expression array information. Data Analysis for miRNAs: 1. Low intensity filtering and data normalization: After low intensity miRNAs filtering, raw signal intensities are normalized in Median method. (miRNAs that intensities>=30 in all samples are chosen for calculating normalization factor) 2. Quality assessment of miRNA data after filtering: Contains box plot, Correlation Matrix and scatter plot for miRNAs after normalization. 3. Differentially expressed miRNAs screening: Contains significant differentially expressed miRNAs that pass Volcano Plot filtering. (Fold Change>=1.5, P-value<=0.05) 4. Heat map and hierarchical clustering: Hierarchical clustering on the significant differentially expressed miRNAs that passed Volcano Plots filtering. Sample RNA Quality Control: Sample quality control data file from Nanodrop 1000 spectrophotometer and standard denaturing agarose gel electrophoresis. Methods: A brief introduction for microarray, experiment, and data analysis. FAQ: Frequently asked question Additional miRNA Array Analysis (charge an extra fee): Prediction Analysis for Microarrays (PAM analysis) miRNA Target Gene Prediction and Functional Analysis Additional files provided: Graphs (*.jpg) Raw Intensity File(*.xls, raw miRNAs signal intensity) Layout File (*.gal, the files contain information on the positioning of the capture probes on the array and microRNA annotations for your species of interest) Raw data files produced by GenePix Pro 6.0
Project description:The purpose of this study was to determine which genes are differentially regulated virus infection in RAW264.7 cells. Cells were infected with Vesicular Stomatitis Virus (VSV) or herpes simplex virus 1 (HSV-1) for 6h. Then the differentially regulated genes were analyzed, focusing on F-box proteins and E3 ubiquitin ligases. RAW264.7 cells were infected with Vesicular Stomatitis Virus (VSV, MOI=1) or herpes simplex virus 1 (HSV-1, MOI=5) for 6h. Equal amounts of RNA were assayed for gene expression using Affymetrix mouse 430 2.0 arrays.
Project description:The purpose of this study was to determine what are the effects of Src deficiency on innate antiviral response upon virus infection in RAW264.7 cells. Wild type and Src-/- RAW264.7 cells were infected with vesicular stomatitis virus (VSV) or herpes simplex virus 1 (HSV-1) for 6h. Then the differentially regulated genes were analyzed. Wild type and Src-/- RAW264.7 cells were infected with vesicular stomatitis virus (VSV, MOI=1) or herpes simplex virus 1 (HSV-1, MOI=5) for 6h. Equal amounts of RNA were assayed for gene expression using Affymetrix mouse 430 2.0 arrays.