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TransBic: extracting bucket trend-preserving biclusters for analysis of gene expression data

<p>Datasets of TransBic: extracting bucket trend-preserving biclusters for analysis of gene expression data</p>

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Bacterial cell-size changes resulting from altering the relative expression of Min proteins

<p>E. coli single cell measurements of size changes, and FtsZ accumulation times in response to increasing minE expression. </p>

Fig. 6 in Mobilization of storage lipid reserve and expression analysis of lipase and lipoxygenase genes in rice (Oryza sativa var. Pusa Basmati 1) bran during germination

Fig. 6. Expression analysis of rice bran lipase genes using quantitative RT PCR (qRT PCR) during 2 HAI, 1, 2, 4, 6, and 8 DAI. Expression value at 0 HAI was taken as control while elongation factor 1-alpha (EF1A, accession no.: XM_015774317.2) was used as the reference gene to normalize the expression level of lipases used in this study. Bars represent means ± standard deviation (SD) of 3 biological replicates. HAI, hours after imbibition; DAI, days after imbibition.

Fig. 5 in Mobilization of storage lipid reserve and expression analysis of lipase and lipoxygenase genes in rice (Oryza sativa var. Pusa Basmati 1) bran during germination

Fig. 5. Schematic representation of the conserved motifs in (a) OsLip proteins and (b) OsLOX proteins. Each colored box represents a motif in the respective protein sequence. Motif number and color codes indicate the sequence of the conserved motif. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 1 in Mobilization of storage lipid reserve and expression analysis of lipase and lipoxygenase genes in rice (Oryza sativa var. Pusa Basmati 1) bran during germination

Fig. 1. Lipid and FA content in bran of germinating rice grains. (a) Lipid content in bran tissues (b) FA profiles of TAGs (c) FA profiles of DAGs (d) FA profiles of NEFAs and (e) FA profiles of PLs. TAG, Triacylglycerol; DAG, diacylglycerol; NEFA, non-esterified fatty acid; PL, polar lipid. Results are mean values ± SD of three replicates.

Fig. 7 in Mobilization of storage lipid reserve and expression analysis of lipase and lipoxygenase genes in rice (Oryza sativa var. Pusa Basmati 1) bran during germination

Fig. 7. Expression analysis of rice bran LOX genes using quantitative RT PCR (qRT PCR) during 2 HAI, 1, 2, 4, 6, and 8 DAI. Expression value at 0 HAI was taken as control while elongation factor 1-alpha (EF1A, accession no.: XM_015774317.2) was used as the reference gene to normalize the expression level of LOXs used in this study. Bars represent means ± standard deviation (SD) of 3 biological replicates. HAI, hours after imbibition; DAI, days after imbibition.

Fig. 4 in Mobilization of storage lipid reserve and expression analysis of lipase and lipoxygenase genes in rice (Oryza sativa var. Pusa Basmati 1) bran during germination

Fig. 4. Exon/intron organization of (a) OsLip genes [Exons (green boxes), Introns (red lines)] and (b) OsLOX genes [Exons (pink boxes), Introns (grey lines)]. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 3 in Mobilization of storage lipid reserve and expression analysis of lipase and lipoxygenase genes in rice (Oryza sativa var. Pusa Basmati 1) bran during germination

Fig. 3. Phylogenetic analysis of rice LOXs. Neighbor-joining (NJ) estimates (with 1000 bootstrap replicates) the phylogenetic relationship between rice and Arabidopsis LOX proteins. Labels are depicted in green for the 9-LOX clade, in blue for 13-LOX clade. Bootstrap values are mentioned in the branches. Branch length is indicated by the scale bar. The Arabidopsis Information Resource (TAIR) and Rice genome annotation project (RGAP) accession numbers are indicated with species names of the lipase proteins. Os, Oryza sativa; At, Arabidopsis thaliana. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 2 in Mobilization of storage lipid reserve and expression analysis of lipase and lipoxygenase genes in rice (Oryza sativa var. Pusa Basmati 1) bran during germination

Fig. 2. Phylogenetic analysis of rice lipases (Lip). Neighbor-joining (NJ) estimates (with 1000 bootstrap replicates) the phylogenetic relationship between rice and Arabidopsis lipase proteins. AtLip are depicted in green box and six OsLip candidates selected for the study based on the tree are depicted in blue box. Bootstrap values are mentioned in the branches. Branch length is indicated by the scale bar. The Arabidopsis Information Resource (TAIR) and Rice genome annotation project (RGAP) accession numbers are indicated with species names of the lipase proteins. Os, Oryza sativa; At, Arabidopsis thaliana; SDP1, sugar dependent1. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 7 in Preliminary investigations on the pathogenesis-related protein expression profile of the medicinal herb Macleaya cordata and anti-bacterial properties of recombinant proteins

Fig. 7. Antibacterial effects of a series of purified McDef1 concentration against S. aureus (A), E. coli (B), S. pullorum (C) and A. hydrophila (D). 1: 30 μg/ml, 2: 40 μg/ ml, 3: 50 μg/ml, 4: 60 μg/ml, 5: 80 μg/ml, 6: 100 μg/ml, 7: Negative control, empty vector expression supernatant; 8: Positive control, for A̢B̢C: 0.2 mg/mL Ampicillin, for D: 0.5 mg/mL Kanamycin.

Fig. 6 in Preliminary investigations on the pathogenesis-related protein expression profile of the medicinal herb Macleaya cordata and anti-bacterial properties of recombinant proteins

Fig. 6. Antibacterial effects of recombinant yeasts with McDef1 or McDef2 fermentation supernatant on S. aureus (A), S. pullorum (B), E. coli (C) and A. hydrophila (D). 1: Fermentation supernatant of the recombinant McDef1; 2: Fermentation supernatant of the recombinant McDef2; 3: Negative control, empty vector expression supernatant; 4: Positive control, A̢B̢C: 0.2 mg/mL Ampicillin; D: 0.5 mg/mL Kanamycin.

Fig. 4 in Preliminary investigations on the pathogenesis-related protein expression profile of the medicinal herb Macleaya cordata and anti-bacterial properties of recombinant proteins

Fig. 4. Multiple sequence alignments of the mature peptides of McLTP1 homologs from different plants with ClustalW2. The target proteins McLTP1 of this study are highlighted with yellow fluorescent background. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 2 in Preliminary investigations on the pathogenesis-related protein expression profile of the medicinal herb Macleaya cordata and anti-bacterial properties of recombinant proteins

Fig. 2. Multiple sequence alignments of the McDef1 (A) and McDef2-5 (B) homologs from different plants with ClustalW2. The conserved domains α-core and γ-core are marked under the homologous sequences respectively. The target proteins McDef1 in (A) and McDef2-5 in (B) of this study are highlighted with yellow fluorescent background. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 1 in Preliminary investigations on the pathogenesis-related protein expression profile of the medicinal herb Macleaya cordata and anti-bacterial properties of recombinant proteins

Fig. 1. The alignment analysis of McDef1-5. The underlined amino acids represent the signal sequence predicted with SignalP. The cysteines are marked in yellow background and the putative disulfide bonds are also shown. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 8 in Preliminary investigations on the pathogenesis-related protein expression profile of the medicinal herb Macleaya cordata and anti-bacterial properties of recombinant proteins

Fig. 8. Antibacterial effects of a series of purified McDef2 concentration against S. aureus (A), E. coli (B), S. pullorum (C) and A. hydrophila (D). 1: 30 μg/ml, 2: 40 μg/ ml, 3: 50 μg/ml, 4: 60 μg/ml, 5: 80 μg/ml, 6: 100 μg/ml, 7: Negative control, empty vector expression supernatant; 8: Positive control, for A̢B̢C: 0.2 mg/mL Ampicillin, for D: 0.5 mg/mL Kanamycin.

Fig. 3 in Comparison of carbohydrate partitioning and expression patterns of some genes involved in carbohydrate biosynthesis pathways in annual and biennial species of Cichorium spp.

Fig. 3. Relative gene expression of SUT1-3 in different tissues of chicory and endive at S1 and S2 stages. Transcript levels were determined by qPCR and normalized against the expression of the reference gene (RPL19). Transcript levels in different organs were expressed relative to the levels of leaves of chicory at S1. Values represent the mean of three biological replicates ± SE. Different letters indicate statistical significance P <0.05 (Duncan's multiple range test).

Fig. 2 in Comparison of carbohydrate partitioning and expression patterns of some genes involved in carbohydrate biosynthesis pathways in annual and biennial species of Cichorium spp.

Fig. 2. Transcript levels of FAZY genes, 1-SST (a), 1-FFT (b), 1-FEHI (c), 1-FEHII (d) in different tissues of chicory and endive at S1 and S2 stages. Transcript levels were determined by qPCR and normalized against the expression of the reference gene (RPL19). Transcript levels in different organs were expressed relative to the levels of leaves of chicory at S1. Values represent the mean of three biological replicates ± SE. Different letters indicate statistical significance at P <0.05 (Duncan's multiple range test).

Fig. 1 in Comparison of carbohydrate partitioning and expression patterns of some genes involved in carbohydrate biosynthesis pathways in annual and biennial species of Cichorium spp.

Fig. 1. Fructose (a), glucose (b) and sucrose content (c) in different tissues of endive and chicory at two stages (S1 and S2), Values represent the mean of three biological replicates ± SE. Different letters indicate statistical significance at P <0.05 (Duncan's multiple range test). 1-kestose, nystose, inulin (D) and mDP (E) in roots of chicory at two stages (S1and S2), Values represent the mean of three biological replicates ± SE. Different letters indicate statistical significance according to the LSD at 0.01 probability level.

Fig. 4 in Comparison of carbohydrate partitioning and expression patterns of some genes involved in carbohydrate biosynthesis pathways in annual and biennial species of Cichorium spp.

Fig. 4. Relative expression analysis of SUS, VI, and CWI1-3, in different tissues of chicory and endive at S1 and S2 stages. Transcript levels were determined by qPCR and normalized against the expression of the reference gene (RPL19). Transcript levels in different organs were expressed relative to the levels of leaves of chicory at S1. Values represent the mean of three biological replicates ± SE. Different letters indicate statistical significance at P <0.05 (Duncan's multiple range test).