31 research outputs found

    MOESM2 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics

    No full text
    Additional file 2. Raw and processed read counts, alignment statistics, log2-fold changes in the gene expression, and K-means clusters and GO enrichment of differentially expressed genes from samples taken from C. thermocellum LL1210 cultured in chemostats at pH values 6.98, 6.48, pH 6.24, and pH 6.12 (washout conditions). Gene expression at pH 6.98 was used as a reference for differential expression at lower pH values

    MOESM4 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics

    No full text
    Additional file 4: Figure S2. Average growth (A), terminal pH (B), and remaining substrates and products at the end of C. thermocellum-mutant strain fermentations of cellobiose in MOPS-free carbon-replete medium (C). Averages were computed with data from four biological replicates. Error bars in each graph indicate standard deviation. Some error bars are too small to see. Deletion mutants are designated as LL1210 (hydrogenase maturation protein, lactate dehydrogenase, pyruvate formate lyase, phosphotransacetylase and acetate kinase), GLDH (glutamate dehydrogenase), GS (glutamine synthetase), GOGAT (glutamate synthase), GS-GOGAT (both), and NifH (nitrogenase iron protein). The parental strain designated DSM1313 has a deletion in the hypoxanthine phosphoribosyltransferase

    MOESM7 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics

    No full text
    Additional file 7. Extracellular amino acid concentrations in media from C. thermocellum LL1210 chemostats that were sampled when pH values were pH 6.48, pH 6.24, pH 6.12, and below. Demonstrations of data homoscedasticity for T tests

    MOESM3 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics

    No full text
    Additional file 3: Figure S1. Average optical density at wave-length 600nm (A and C) and average terminal pH (B and D) of C. thermocellum LL1210 cultured in 48-well plates. OD600nm readings were taken automatically every 15 min in a microplate spectrophotometer (Biotek Eon, Winooski, VT) kept in an anaerobic chamber. Only 3-h time points are shown. Nine hundred microliters of inoculated medium was mixed with 100 Îźl of uninoculated medium supplemented with spermine, spermidine, or putrescine (polyamines), or arginine (polyamine precursor) so that the final concentration was 100 ÎźM. Initial culture pH was 7.00 (A and B) or 6.75 (C and D). Averages were calculated from at least three biological replicates. Error bars indicate standard deviation and are colored the same as the amendments in the legend. Table S1. Average and standard deviation of maximum and terminal optical densities (600nm) and specific growth rate of C. thermocellum LL1210 cultured in media with and without amendments and having initial pHs of 7.00 and 6.75

    MOESM5 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics

    No full text
    Additional file 5: Figure S3. Differential expression of genes found in Clostridia sporulation cascades. pro-σE processing protease is a stage III sporulation factor. BofA is an inhibitor of the stage IV pro-σK processing protease SpoIVFB. Table S2. Percentage of spherical morphologies 144 and 216 h after inoculation. Figure S4. Substrates and products (A) and the pH (B) after 144 and 216 h of C. thermocellum-mutant fermentations on MOPS-free carbon-replete medium starting with an initial pH of 6.75. Significant differences at α = 0.001 for comparisons with DSM1313 (∆hpt) are indicated with a “*” and comparisons with DSM1313 (∆hpt) and LL1210 are indicated with “**”. Averages were calculated with six biological replicates. Error bars indicate standard deviation

    MOESM1 of Consolidated bioprocessing of Populus using Clostridium (Ruminiclostridium) thermocellum: a case study on the impact of lignin composition and structure

    No full text
    Additional file 1: Figure A.1. Carbohydrate composition of initially screened Populus biomass. Figure A.2. Fermentation products of Avicel-control CBP cultures. Figure A.3. Carbohydrate content in Populus before and after repeat autoclave sterilization. Figure A.4. Lignin content in Populus before and after repeat autoclave sterilization
    corecore