sk2  (Alomone Labs)

Journal: Environmental Microbiology Reports

Article Title: Integrated Analysis of Gene Expression, Protein Synthesis, and Epigenetic Modifications in Alcanivorax borkumensis SK2 Under Iron Limitation

doi: 10.1111/1758-2229.70106

Figure Lengend Snippet: Growth curves of A. borkumensis SK2 grown in ONR7a using 0.1% (w/v) of n‐tetradecane (Tet, circle) or 0.5% (w/v) of sodium acetate (Ac, square) as the sole carbon source, and under optimal (solid line) or iron‐limited conditions (IS, dashed line).

Article Snippet: Whole genome sequence of the strain A. borkumensis SK2 (ATCC 700651) is available at NCBI under accession number NC 008260 (Schneiker et al. ).

Techniques:

Journal: Environmental Microbiology Reports

Article Title: Integrated Analysis of Gene Expression, Protein Synthesis, and Epigenetic Modifications in Alcanivorax borkumensis SK2 Under Iron Limitation

doi: 10.1111/1758-2229.70106

Figure Lengend Snippet: PCA plotting of gene expression patterns of A. borkumensis SK2 grown on media with acetate or n‐tetradecane as sole carbon sources under iron‐limited (Fe–) and normal iron concentration (Fe+). Normalised RPKM values of gene expression were used for plotting.

Article Snippet: Whole genome sequence of the strain A. borkumensis SK2 (ATCC 700651) is available at NCBI under accession number NC 008260 (Schneiker et al. ).

Techniques: Gene Expression, Concentration Assay

Journal: Environmental Microbiology Reports

Article Title: Integrated Analysis of Gene Expression, Protein Synthesis, and Epigenetic Modifications in Alcanivorax borkumensis SK2 Under Iron Limitation

doi: 10.1111/1758-2229.70106

Figure Lengend Snippet: Adaptive gene regulation in A. borkumensis SK2 (A) growing in acetate (ABO_Ac) and (B) in n‐tetradecane (ABO_Tet) under optimal and iron limited conditions. Each coloured dot on the plot depicts one gene. Genes were plotted along X ‐axis according to their mean expression levels estimated as Log 2 (baseMean − 1). Values along Y ‐axis indicate positive or negative Log 2 (FoldChange) parameters. The genes showing statistically significant up‐regulation under iron limitation ( p ≤ 0.01 for large and 0.01 < p ≤ 0.05 for medium‐sized colour dots) are depicted by orange colour, whereas the negatively regulated genes as shown as blue dots. Regulation of genes depicted by small coloured and white dots was statistically insignificant. (C) Gene co‐regulation analysis was performed by comparison of FoldChange values obtained for the same genes under iron‐limited compared to the normal iron concentration conditions when cultures were grown on acetate and n‐tetradecane as sole carbon sources. Colour code is explained in the figure legend. Numbers of CDS falling to different sectors of the plots are shown.

Article Snippet: Whole genome sequence of the strain A. borkumensis SK2 (ATCC 700651) is available at NCBI under accession number NC 008260 (Schneiker et al. ).

Techniques: Expressing, Comparison, Concentration Assay

Journal: Environmental Microbiology Reports

Article Title: Integrated Analysis of Gene Expression, Protein Synthesis, and Epigenetic Modifications in Alcanivorax borkumensis SK2 Under Iron Limitation

doi: 10.1111/1758-2229.70106

Figure Lengend Snippet: Gene ontology enrichment – Lg(FRD) values calculated for (A) up‐regulated, and (B) down‐regulated genes of A. borkumensis SK2 under iron limitation on acetate and n‐tetradecane.

Article Snippet: Whole genome sequence of the strain A. borkumensis SK2 (ATCC 700651) is available at NCBI under accession number NC 008260 (Schneiker et al. ).

Techniques:

Journal: Environmental Microbiology Reports

Article Title: Integrated Analysis of Gene Expression, Protein Synthesis, and Epigenetic Modifications in Alcanivorax borkumensis SK2 Under Iron Limitation

doi: 10.1111/1758-2229.70106

Figure Lengend Snippet: Lambda DNA digested with crude A. borkumensis SK2 extract (line 1) and the negative control (2) with the strips of the ladder proteins on both sides.

Article Snippet: Whole genome sequence of the strain A. borkumensis SK2 (ATCC 700651) is available at NCBI under accession number NC 008260 (Schneiker et al. ).

Techniques: Lambda DNA Preparation, Negative Control

Journal: Environmental Microbiology Reports

Article Title: Integrated Analysis of Gene Expression, Protein Synthesis, and Epigenetic Modifications in Alcanivorax borkumensis SK2 Under Iron Limitation

doi: 10.1111/1758-2229.70106

Figure Lengend Snippet: Distribution of methylated canonical motifs and non‐canonical modified bases across various genomic regions predicted by the program SeqWord Motif Mapper for A) GaTNNNNNGtGG motif; B) AgGCcT motif; C) modified adenines; and D) modified cytosines. Each panel represents the distribution of various canonical motifs across the chromosome of A. borkumensis SK2. The graphs, from top to bottom, depict GC‐content, GC‐skew, and the number of methylated bases within 8 kbp sliding windows moving along chromosomal sequences with a 2 kbp step. Modified base densities in the lower histograms are depicted by bars extending above and below the average density line. Chromosomal coordinates are shown at the bottom of the panels. Identified inserts of mobile genetic elements (MGEs) are indicated by pink bars. Results of statistical analysis are presented on the right side of the panels, including Spearman correlation (SP) with confidence interval (ci) values between GC‐content and GC‐skew of sliding windows and the number of modified bases within the windows; Z‐scores with standard errors and estimated p ‐values of biased distribution of modified bases across MGEs and core genomic parts, and between coding, non‐coding, and 120 bp TSC‐upstream regions.

Article Snippet: Whole genome sequence of the strain A. borkumensis SK2 (ATCC 700651) is available at NCBI under accession number NC 008260 (Schneiker et al. ).

Techniques: Methylation, Modification

Journal: Environmental Microbiology Reports

Article Title: Integrated Analysis of Gene Expression, Protein Synthesis, and Epigenetic Modifications in Alcanivorax borkumensis SK2 Under Iron Limitation

doi: 10.1111/1758-2229.70106

Figure Lengend Snippet: Distribution of canonical and non‐canonical modified adenine and cytosine residues in the A. borkumensis SK2 genomes. (A) Canonical methylated nucleotides plotted according to their local coverage values and scores of epigenetic modifications predicted by ipdSummary. (B) Plot of non‐canonical epigenetically modified nucleotides. Individual modified adenine and cytosine residues in both plots are depicted by red and green circles, respectively. (C) Heatmap showing percentages of shared and experiment‐specific (diagonal line) modified adenine residues with NucMod scores ≥ 150. (D) Heatmap of modified cytosine residues with NucMod scores ≥ 150. Total numbers of respective modified nucleotides in each sequenced genome are shown alongside the right vertical edges of the plots.

Article Snippet: Whole genome sequence of the strain A. borkumensis SK2 (ATCC 700651) is available at NCBI under accession number NC 008260 (Schneiker et al. ).

Techniques: Modification, Methylation

Journal: Environmental microbiology reports

Article Title: Integrated Analysis of Gene Expression, Protein Synthesis, and Epigenetic Modifications in Alcanivorax borkumensis SK2 Under Iron Limitation.

doi: 10.1111/1758-2229.70106

Figure Lengend Snippet: FIGURE 1 | Growth curves of A. borkumensis SK2 grown in ONR7a using 0.1% (w/v) of n-tetradecane (Tet, circle) or 0.5% (w/v) of sodium acetate (Ac, square) as the sole carbon source, and under optimal (solid line) or iron-limited conditions (IS, dashed line).

Article Snippet: The bacterial strain used in this study was A. borkumensis SK2 (ATCC 700651, Yakimov et al. 1998).

Techniques:

Journal: Environmental microbiology reports

Article Title: Integrated Analysis of Gene Expression, Protein Synthesis, and Epigenetic Modifications in Alcanivorax borkumensis SK2 Under Iron Limitation.

doi: 10.1111/1758-2229.70106

Figure Lengend Snippet: FIGURE 5 | Lambda DNA digested with crude A. borkumensis SK2 extract (line 1) and the negative control (2) with the strips of the ladder proteins on both sides.

Article Snippet: The bacterial strain used in this study was A. borkumensis SK2 (ATCC 700651, Yakimov et al. 1998).

Techniques: Lambda DNA Preparation, Negative Control