polyclonal rabbit anti 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: Frontiers in Pharmacology

Article Title: Compensatory attenuation of cortical apoptosis by SK2 downregulation following ketamine anesthesia

doi: 10.3389/fphar.2026.1761187

Figure Lengend Snippet: Apamin-sensitive SK2 channel-mediated mAHP currents may be linked to changes in neuronal spike frequency and adaptation at 24 h post-ketamine anesthesia. (A,B) Representative traces (A) and amplitudes (B) of the mAHP currents, treatment conditions as indicated. S1 slices from control (Ctrl) and ketamine-treated (Ket) rats were separately incubated and perfused with apamin (100 nM) or its vehicle. 22–25 neurons from 7–10 rats were used per condition. (C) Plots of spike frequency vs. current injected for layer II/III pyramidal neurons of S1. The significant differences in the spike frequency between the Ctrl and Ket groups (Ctrl: Vehicle vs. Ket: Vehicle, 80 pA, 100 pA and 110 pA, P < 0.01; 90 pA, P < 0.001) were eliminated after apamin treatment (Ctrl: Apamin vs. Ket: Apamin, P > 0.05). 20–22 neurons from 7–9 rats were recorded per condition. (D,E) Spikes in S1 layer II/III pyramidal neurons evoked for 3 s, 80 pA current injection (D) , and the adaptation index (E) was obtained by the algorithm mentioned above. 18–20 neurons from 7–9 rats were recorded per condition. (F) Quantitative analysis of SK1-3 mRNA in S1 of P8 rats. 5 rats were used per condition. P > 0.05. (G,H) Immunoblots and quantitative analysis of total (G) and membrane-bound (H) SK1-3 levels in S1 of ketamine-treated rats, normalized to corresponding levels in control rats. 8–12 rats were used per condition. * P < 0.05, ** P < 0.01, *** P < 0.001; n.s ., not significant. Data were analyzed using the Mann-Whitney U test for (F,H) and unpaired two-tailed Student’s t-tests for the other panels. Data are shown as the mean ± SEM.

Article Snippet: The following primary antibodies were used: SK1 (1:500, Alomone Labs, Cat# APC-039), SK2 (1:500, Alomone Labs, Cat# APC-028), SK3 (1:500, Alomone Labs, Cat# APC-025), β-actin (1:1,000, Millipore, Cat# A1978 ), and pan-cadherin (1:1,000, Sigma-Aldrich, Cat# SAB4500001 ).

Techniques: Control, Incubation, Injection, Western Blot, Membrane, MANN-WHITNEY, Two Tailed Test

Journal: Frontiers in Pharmacology

Article Title: Compensatory attenuation of cortical apoptosis by SK2 downregulation following ketamine anesthesia

doi: 10.3389/fphar.2026.1761187

Figure Lengend Snippet: Overexpression of SK2 reversed the increase in spike frequency and prevented the reduction in apoptosis at 24 h post-anesthesia. (A) Schematic of the experimental procedure. (B) Left panel: Schematic drawing showing the location of the AAV-injection, AAV-SK2 (pAAV-hSyn-EGFP-P2A-Kcnn2-3xFLAG-WPRE) or AAV-EGFP (pAAV-SYN-EGFP-P2A-MCS-3FLAG) were injected bilaterally into S1 at P0; Right two panels: representative images showing EGFP positive neurons (indicated the virus transfected neurons) in S1 of P8 rats. The scale bar is 100 μm. (C,D) Immunoblots and quantitation of SK2 levels from the total (C) or membrane (D) lysates in S1. Conditions as indicated. 10–11 rats were used per condition. (E,F) Representative traces (E) and amplitudes (F) of the mAHP currents, treatment conditions as indicated. AAV-EGFP- and AAV-SK2-treated rats had received PBS (Ctrl) or ketamine (Ket) at P7, and the acute brain slices containing S1 were incubated and perfused with apamin or its vehicle 24 h later. 18–24 neurons from 4 rats were used per condition. (G,H) A depolarizing current of 80 pA was injected for 3 s to induce neuronal spikes in S1 (H) , and the adaptation index of the spikes was analyzed (G) in conditions as indicated. 20–24 neurons from 4–5 rats were used per condition. (I) Plots of spike frequency evoked by graded current injections. AAV-EGFP: Ctrl vs. Ket, * P < 0.05, * *P < 0.01, *** P < 0.001; Ctrl: AAV-EGFP vs. AAV-SK2, # P < 0.05; using two-way ANOVA followed by Tukey’s multiple comparison test. 20–29 neurons from 4 rats were used per condition. (J) Representative confocal images of S1 sections labelled with CC3 (red), EGFP (green) and DAPI (blue), conditions as indicated; scale bar is 150 μm. Zoomed images of boxed regions are presented to the right of each panel; scale bar is 50 μm; CC3+ cells are indicated by white triangles. (K) Quantitation of the number of CC3 + cell per mm 3 S1, treatment conditions as indicated. 5–8 rats were used per condition. * P < 0.05, ** P < 0.01, *** P < 0.001; n.s ., not significant; using two-way ANOVA followed by Tukey’s multiple comparison tests. Data are shown as the mean ± SEM.

Article Snippet: The following primary antibodies were used: SK1 (1:500, Alomone Labs, Cat# APC-039), SK2 (1:500, Alomone Labs, Cat# APC-028), SK3 (1:500, Alomone Labs, Cat# APC-025), β-actin (1:1,000, Millipore, Cat# A1978 ), and pan-cadherin (1:1,000, Sigma-Aldrich, Cat# SAB4500001 ).

Techniques: Over Expression, Injection, Virus, Transfection, Western Blot, Quantitation Assay, Membrane, Incubation, Comparison

Journal: Frontiers in Pharmacology

Article Title: Compensatory attenuation of cortical apoptosis by SK2 downregulation following ketamine anesthesia

doi: 10.3389/fphar.2026.1761187

Figure Lengend Snippet: SK2 downregulation recapitulated neuronal hyperexcitability and further reduced the number of apoptotic neurons at 24 h post-anesthesia. (A) Schematic of the experimental procedure. (B) Left panel: Schematic drawing showing the location of the AAV injection, shRNA-SK2 [pAAV-CBG-EGFP-3xFLAG-WPRE-H1-shRNA (Kcnn2)] or shRNA-Ctrl (pAKD-CMV-bGlobin-eGFP-H1-shRNA-NC) were injected bilaterally into S1 at P0; Right two panels: representative images showing EGFP positive neurons (the virus transfected neurons) in S1 of P8 rats. The scale bar is 100 μm. (C,D) Immunoblots and quantitation of SK2 from the total (C) or membrane (D) lysates of S1 on P8. Conditions as indicated. 8 rats were used per condition. (E,F) Representative traces (E) and the amplitude (F) of the mAHP currents, treatment conditions as indicated. 20–23 neurons from 4 rats were used per condition. (G,H) A depolarizing current of 80 pA was injected for 3 s to induce neuronal spikes in S1 (H) , and the adaptation index of the spikes was analyzed (G) using the mentioned methods. 18–20 neurons from 4–5 rats were used per condition. (I) Plots of spike frequency evoked by stepping current injections. No significant difference was found between Ctrl and Ket groups following shRNA-SK2 virus transfection ( P > 0.05). (shRNA-Ctrl: Ctrl vs. Ket): 80 pA, 90 pA, and 120 pA, P < 0.05; 100 pA and 110 pA, P < 0.01; using two-way ANOVA followed by Tukey’s multiple comparison test. 20–21 neurons from 4–5 rats were used per condition. (J) Representative confocal images of S1 sections labelled with CC3 (red), EGFP (green) and DAPI (blue), conditions as indicated; scale bar is 150 μm. Zoomed images of boxed regions are presented to the right of each panel; scale bar is 50 μm; CC3 + cells are indicated by white triangles. (K) Quantitation of the number of CC3 + cell per mm 3 S1, treatment conditions as indicated. 3–4 rats were used per condition. * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001; n.s ., not significant; using two-way ANOVA followed by Tukey’s multiple comparison test. Data are shown as the mean ± SEM.

Article Snippet: The following primary antibodies were used: SK1 (1:500, Alomone Labs, Cat# APC-039), SK2 (1:500, Alomone Labs, Cat# APC-028), SK3 (1:500, Alomone Labs, Cat# APC-025), β-actin (1:1,000, Millipore, Cat# A1978 ), and pan-cadherin (1:1,000, Sigma-Aldrich, Cat# SAB4500001 ).

Techniques: Injection, shRNA, Virus, Transfection, Western Blot, Quantitation Assay, Membrane, Comparison

Journal: Frontiers in Pharmacology

Article Title: Compensatory attenuation of cortical apoptosis by SK2 downregulation following ketamine anesthesia

doi: 10.3389/fphar.2026.1761187

Figure Lengend Snippet: The ubiquitination level of SK2 channels in S1 significantly increased at 24 h post-ketamine anesthesia. (A) Immunoprecipitation was performed with anti-SK2 antibodies or control IgG antibodies in PBS (Ctrl) and ketamine (Ket) treated rats, and western blots were labelled with anti-SK2 (left panel) or anti-ubiquitin (Ub) (right panel) antibodies. (B) The column graph shows a significant increase in ubiquitination of SK2 in S1 at 24 h after ketamine exposure. * P < 0.05, unpaired two-tailed Student’s t-tests. 7 rats were used per condition. (C) Input protein levels examined by Western blot probed with SK2 and β-actin antibodies, conditions as indicated. Data are shown as the mean ± SEM.

Article Snippet: The following primary antibodies were used: SK1 (1:500, Alomone Labs, Cat# APC-039), SK2 (1:500, Alomone Labs, Cat# APC-028), SK3 (1:500, Alomone Labs, Cat# APC-025), β-actin (1:1,000, Millipore, Cat# A1978 ), and pan-cadherin (1:1,000, Sigma-Aldrich, Cat# SAB4500001 ).

Techniques: Ubiquitin Proteomics, Immunoprecipitation, Control, Western Blot, Two Tailed Test

Journal: Frontiers in Pharmacology

Article Title: Compensatory attenuation of cortical apoptosis by SK2 downregulation following ketamine anesthesia

doi: 10.3389/fphar.2026.1761187

Figure Lengend Snippet: MG132 normalized neuronal spike frequency and abolished the compensatory reduction in apoptosis by restoring SK2 protein levels. (A,B) Immunoblots and quantitation of SK2 from the total (A) or membrane (B) lysates of S1 with conditions as indicated. 11 rats were used per condition. (C,D) Representative traces (C) and the amplitude (D) of the mAHP currents, treatment conditions as indicated. 18–22 neurons from 4–5 rats were used per condition. (E) Plots of spike frequency evoked by stepping current injections. MG132 pre-treatment eliminated the increase in neuronal spike frequency caused by ketamine. 20–26 neurons from 4–5 rats were used per condition. (F) Plots of spike frequency vs. current injections. The effects of MG132 on neuronal spike frequency were abolished by apamin. 21–22 neurons from 4 - 6 rats were used per condition. (Vehicle: Ctrl) vs. (Apamin: Ctrl), * P < 0.05, ** P < 0.01, *** P < 0.001; (Vehicle: Ctrl) vs. (Apamin: Ket), ## P < 0.01, ### P < 0.001; Vehicle: Ctrl vs. Ket, and Apamin: Ctrl vs. Ket, P > 0.05; using two-way ANOVA followed by Tukey’s multiple comparison test. (G,H) A depolarizing current of 80 pA was injected for 3 s to induce neuronal spikes of S1 pyramidal neurons (G) , and the adaptation index of the spikes was analyzed (H) using the same algorithm mentioned. 20–21 neurons from 4–5 rats were used per condition. (I) The bar graph showed the effects of MG132 on spike adaptation were prevented by apamin. 17–22 neurons from 4–5 rats were used per condition. Ctrl: Vehicle vs. Apamin, * P < 0.05; Ket: Vehicle vs. Apamin, # P < 0.05; using two-way ANOVA followed by Tukey’s multiple comparison test. (J) Representative confocal images of S1 sections labelled with CC3 (red) and DAPI (blue), conditions as indicated; scale bar is 150 μm. Zoomed images of boxed regions are presented to the right of each panel; scale bar is 50 μm; CC3 + cells are indicated by white triangles. (K) Quantitation of the number of CC3 + cell per mm 3 S1, treatment conditions as indicated. 4–7 rats were used per condition. * P < 0.05, ** P < 0.01, *** P < 0.001; n.s ., not significant; using two-way ANOVA followed by Tukey’s multiple comparison test. Data are shown as the mean ± SEM.

Article Snippet: The following primary antibodies were used: SK1 (1:500, Alomone Labs, Cat# APC-039), SK2 (1:500, Alomone Labs, Cat# APC-028), SK3 (1:500, Alomone Labs, Cat# APC-025), β-actin (1:1,000, Millipore, Cat# A1978 ), and pan-cadherin (1:1,000, Sigma-Aldrich, Cat# SAB4500001 ).

Techniques: Western Blot, Quantitation Assay, Membrane, Comparison, Injection

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