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Additional file 1: Table S1. Concentration of glucose in various medium. Table S2. Primers used in this study. Table S3. Concentration of amino acids in various medium (expressed as mM). Figure S1. M9-yeast extract medium supplemented with (A) blank, (B) 10 mM glucose, or (C) 50 mM glucose was incubated by E. coli DH10B for 1–26.5 hours, and the amino acid concentrations were compared. Values are given as mean ± SD (n = 3).

Pathway analysis of glycolysis. Glycolysis pathway was constructed from KEGG. White box indicates the fold change of each protein relative to glucose at the same time point, and gray box indicates temporal profile of each protein relative to TP1 in each carbon sources. Each line indicates fold change or temporal profile (cellulose, red; xylan, purple; green, galactomannan; pectin, blue) (PDF 563 kb)

Pathway analysis of tricarboxylic acid cycle. Tricarboxylic acid cycle was constructed from KEGG. White box indicates the fold change of each protein relative to glucose at the same time point, and gray box indicates temporal profile of each protein relative to TP1 in each carbon source. Each line indicates fold change or temporal profile (cellulose, red; xylan, purple; galactomannan, green; pectin, blue) (PDF 708 kb)

Pathway analysis of xylan degradation and metabolism. Pathway of xylan degradation and metabolism was constructed from KEGG. White box indicates the fold change of each protein relative to glucose at the same time point, and gray box indicates temporal profile of each protein relative to TP1 in each carbon source. Each line indicates fold change or temporal profile (cellulose, red; xylan, purple; galactomannan, green; pectin, blue) (PDF 344 kb)

Pathway analysis of galactomannan degradation and metabolism. (a) Pathway of mannan degradation and metabolism; (b) galactose degradation and metabolism pathway A. Each pathway was constructed from KEGG. White box indicates the fold change of each protein relative to glucose at the same time point, and gray box indicates temporal profile of each protein relative to TP1 in each carbon source. Each line indicates fold change or temporal profile (cellulose, red; xylan, purple; galactomannan, green; pectin, blue) (PDF 699 kb)

Pathway analysis of pectin degradation and metabolism. Pathway of pectin degradation and metabolism was constructed from KEGG. White box indicates the fold change of each protein relative to glucose at the same time point, and gray box indicates temporal profile of each protein relative to TP1 in each carbon source. Each line indicates fold change or temporal profile (cellulose, red; xylan, purple; galactomannan, green; pectin, blue) (PDF 656 kb)

Hypoxia has critical effects on the physiology of organisms. In the yeast Saccharomyces cerevisiae, glycolytic enzymes, including enolase (Eno2p), formed cellular foci under hypoxia. Here, we investigated the regulation and biological functions of these foci. Focus formation by Eno2p was inhibited temperature independently by the addition of cycloheximide or rapamycin or by the single substitution of alanine for the Val22 residue. Using mitochondrial inhibitors and an antioxidant, mitochondrial reactive oxygen species (ROS) production was shown to participate in focus formation. Focus formation was also inhibited temperature dependently by an SNF1 knockout mutation. Interestingly, the foci were observed in the cell even after reoxygenation. The metabolic turnover analysis revealed that [U-(13)C]glucose conversion to pyruvate and oxaloacetate was accelerated in focus-forming cells. These results suggest that under hypoxia, S. cerevisiae cells sense mitochondrial ROS and, by the involvement of SNF1/AMPK, spatially reorganize metabolic enzymes in the cytosol via de novo protein synthesis, which subsequently increases carbon metabolism. The mechanism may be important for yeast cells under hypoxia, to quickly provide both energy and substrates for the biosynthesis of lipids and proteins independently of the tricarboxylic acid (TCA) cycle and also to fit changing environments.

Additional file 1: Fig S1. Oligosaccharide assimilation by C. cellulovorans. C. cellulovorans was grown in media containing 6 g/L glucose, 6 g/L cellobiose, and 6 g/L xylooligosaccharides mixture (a), 10 g/L glucose and 10 g/L xylooligosaccharides (b), 10 g/L cellobiose and 10 g/L xylooligosaccharides (c). Residual sugar amount was normalized to that of 0 h (set to 100%). Closed circles, glucose; open triangles, cellobiose; open squares, xylooligosaccharide. All points were measured in triplicate. Error bars represent means Âą SEs.

Additional file 1. List of primers used in this study (Table S1). Box plots showing the ratio of sum of pixel values for (A) rabbit, (B) chicken, (C) horse, and (D) swine erythrocytes (Fig. S1). Sequence alignment of hHAsÎą2,6 and hHAsÎą2,6* (Fig. S2).

Evaluation of protein quantification; The standard sample was combined at a ratio of 0.5:1:2 by volume. After labeling with TMT reagents, the three samples were mixed in a single tube and injected into nonoLCâ MS/MS. Relative intensity of reporter ion ratios were obtained by dividing the intensity of reporter ions from the 0.5-sample and the 2-sample by that from the 1-sample.

In this research, 2D and 3D FEM models are composed for the clarification of the effect of initial thickness distribution on its distribution after drawing and the residual stresses. In the 2D FEM, the minimum bare element numberwas determined in terms on both residual stress precision and calculation time. Based on the results of 2D FEM, the element numberin3D FEM wasdetermined. Using the obtained 3D FEM, the effect of initial thickness distribution was clarified with the combination of thicknessreduction. It was revealed that light reduction in thickness in plug drawing sometimes lead to increase of thickness deviation, against intuitiveprediction based on tube drawing without plug.On the other hand, increase of thickness reduction resulted in decrease of thickness deviation. The mechanism of thickness change was also examined.

Levels of TNF-α secreted by macrophages upon interaction with C. albicans; Data are represented as mean ± standard deviation (SD) from three independent experiments.

Biaxial loading and reverse loading tests were performed using seamless carbon steel tubes. Biaxial stress components in the axial and circumferential directions were applied to the tubular specimens using a servo-controlled multiaxial tube expansion testing machine developed by Kuwabara and Sugawara (2013). The tubular specimens were loaded under linear tensile stress paths. Contours of plastic work were measured in the principal stress space, and the differential hardening (DH) behavior was observed; the shapes of the contours of plastic work changed with an increase in plastic work. In addition, small uniaxial tensile specimens were fabricated from the mother tube wall in axial and hoop directions, and tension–compression reverse loading tests were performed to quantitatively evaluate the Bauschinger effect of the test material. Moreover, bilinear stress path experiments were performed to investigate the effects of axial prestraining on the change in the Bauschinger effect; compressive preloading in the axial direction (first loading) was followed by the application of linear stress paths in the first quadrant of the principal stress space (second loading). The measured Bauschinger effect in the second loading was different from those measured in the uniaxial reverse loading tests for the as-received material. The material model will be utilized to improve the accuracy in the numerical analyses of the cold working processes for fabricating steel tubes.

Large amounts of fossil fuels are consumed every day in spite of increasing environmental problems. To preserve the environment and construct a sustainable society, the use of biofuels derived from different kinds of biomass is being practiced worldwide. Although bioethanol has been largely produced, it commonly requires food crops such as corn and sugar cane as substrates. To develop a sustainable energy supply, cellulosic biomass should be used for bioethanol production instead of grain biomass. For this purpose, cell surface engineering technology is a very promising method. In biobutanol and biodiesel production, engineered host fermentation has attracted much attention; however, this method has many limitations such as low productivity and low solvent tolerance of microorganisms. Despite these problems, biofuels such as bioethanol, biobutanol, and biodiesel are potential energy sources that can help establish a sustainable society.

The homogenization method considering crystal plasticity was taken as a prediction method of mechanical properties after metal forming. Copper and low carbon steel were taken as raw materials. It was experimentally clarified that low carbon steel showed stronger Bauschinger effect than copper. At the first trial of analysis, the homogenization method considering crystal plasticity showed a similar behavior to that of copper of single phase metal rather than low carbon steel. However, addition of small amount of carbide in low carbon steel inside the crystals, just as in the actual steel, significantly improved the prediction accuracy.

Clostridium cellulovorans, an anaerobic and mesophilic bacterium, degrades native substrates in soft biomass such as corn fibre and rice straw efficiently by producing an extracellular enzyme complex called the cellulosome. Recently, we have reported the whole-genome sequence of C. cellulovorans comprising 4220 predicted genes in 5.10 Mbp [Y. Tamaru et al., (2010) J. Bacteriol., 192: 901–902]. As a result, the genome size of C. cellulovorans was about 1 Mbp larger than that of other cellulosome-producing clostridia, mesophilic C. cellulolyticum and thermophilic C. thermocellum. A total of 57 cellulosomal genes were found in the C. cellulovorans genome, and they coded for not only carbohydrate-degrading enzymes but also a lipase, peptidases and proteinase inhibitors. Interestingly, two novel genes encoding scaffolding proteins were found in the genome. According to KEGG metabolic pathways and their comparison with 11 Clostridial genomes, gene expansion in the C. cellulovorans genome indicated mainly non-cellulosomal genes encoding hemicellulases and pectin-degrading enzymes. Thus, by examining genome sequences from multiple Clostridium species, comparative genomics offers new insight into genome evolution and the way natural selection moulds functional DNA sequence evolution. Our analysis, coupled with the genome sequence data, provides a roadmap for constructing enhanced cellulosome-producing Clostridium strains for industrial applications such as biofuel production.