Journal: Journal of Translational Medicine

Article Title: From injury to recovery: transcriptomic dynamics in zebrafish brain regeneration

doi: 10.1186/s12967-025-07400-7

Figure Lengend Snippet: Transcriptomic and pathway insights into zebrafish brain regeneration. A ) Gene Ontology (GO) enrichment analysis of biological processes (BP), molecular functions (MF), and cellular components (CC) across the three regenerative stages (1, 4, and 7 days post-lesion; dpl). The vertical axis lists the enriched GO terms, while the horizontal bars represent the gene ratios associated with each term. The depth of the color indicates the adjusted p-value, and the circle size corresponds to gene counts contributing to each term. B ) heatmap showing the expression levels of key cell cycle-related genes at 1, 4, and 7 dpl. Stage-specific activation patterns, such as peak expression of proliferation markers (aurka, aurkb, wdr76, etc.) at 4 dpl and sustained expression of MCM proteins, reflect dynamic cellular processes during brain regeneration. C ) overview of KEGG pathways enriched across the three regeneration stages. The visualization underscores the pathways driving key biological processes during zebrafish brain regeneration. D ) heatmaps showing the expression of genes related to the MAPK signaling pathway: i ) upregulated genes and ii ) downregulated genes, across the three stages, emphasizing the dynamic regulation of this critical pathway. E ) immunoblot analysis showing the levels of phosphorylated (active) and total p38α MAPK protein during zebrafish brain regeneration. F ) immunoblot analysis showing the levels of phosphorylated (active) and total MK2 and Hsp27 along with c-Jun protein during zebrafish brain regeneration. β-actin was used as the loading control for both E-F panels. G ) quantification of phosphorylated (active) and total p38α MAPK levels during regeneration is shown as a bar graph ( n = 3). H ) quantification of phosphorylated (active) and total MK2 levels during regeneration is shown as a bar graph ( n = 3). I ) quantification of c-Jun levels during regeneration is shown as a bar graph ( n = 3). J ) quantification of phosphorylated (active) and total HSP27 levels during regeneration is shown as a bar graph ( n = 3). Significance is represented as n.s. for p-value > 0.05, * for p-value < 0.05, ** for p-value < 0.01 and *** for p-value < 0.001. dpl: days post-lesion

Article Snippet: Rabbit monoclonal Phospho p38 MAPK (1:1000; 4511S; Cell Signaling Technology), rabbit polyclonal total p38 MAPK (1:1000; 9212S; Cell Signaling Technology), rabbit monoclonal Phospho HSP27 (1:1000; 9709S; Cell Signaling Technology), mouse monoclonal Total HSP27 (1:500; CPTC-HSPB1-2; Developmental Studies Hybridoma Bank), rabbit monoclonal Phospho MK2 (1:1000; 3007S; Cell Signaling Technology), Total MK2 (1:1000; EB11929; Everest Biotech), rabbit monoclonal c-Jun (1:1000; 9165S; Cell Signaling Technology), mouse monoclonal β-catenin (1:1000; 610153; BD Biosciences), Phospho AKT (1:1000; 4058S; Cell Signaling Technology), Total AKT (1:1000; 2920S; Cell Signaling Technology), mouse monoclonal β-actin (1:1000; sc47778; Santa Cruz).

Techniques: Expressing, Activation Assay, Western Blot, Control

Journal: Journal of Translational Medicine

Article Title: From injury to recovery: transcriptomic dynamics in zebrafish brain regeneration

doi: 10.1186/s12967-025-07400-7

Figure Lengend Snippet: BIRB796-mediated inhibition of MAPK14a pathway impairs the regenerative response post traumatic brain injury. A ) schematic showing BIRB796 treatment after zebrafish brain injury and the brains harvested at 4 dpl. Treatment regimen: animals were immersed in system water containing 0.5 μM or 1 μM BIRB796 (or vehicle control: 0.1% DMSO) immediately after lesion induction and maintained until sacrifice at 4 dpl. B ) immunoblot analysis showing the levels of phosphorylated (active) and total p38α MAPK protein upon BIRB796 treatment at 4 dpl;. *represents the band for p38α MAPK. C ) quantification of phosphorylated (active) and total p38α MAPK levels in control regenerating (4 dpl DMSO) brain and BIRB796 treated regenerating (4 dpl) brain is shown as a bar graph ( n = 3). D ) immunoblot analysis showing the levels of phosphorylated (active) and total Hsp27 protein upon BIRB796 treatment at 4 dpl E ) quantification of phosphorylated (active) and total Hsp27 levels in control regenerating (4 dpl DMSO) brain and BIRB796 treated regenerating (4 dpl) brain is shown as a bar graph ( n = 3). F ) immunoblot analysis showing the levels of phosphorylated (active) and total MK2 and c-Jun protein upon BIRB796 treatment at 4 dpl. G ) quantification of phosphorylated (active)and total MK2 levels in control regenerating (4 dpl DMSO) brain and BIRB796 treated regenerating (4 dpl) brain is shown as a bar graph ( n = 3). H ) quantification of c-Jun levels in control regenerating (4 dpl DMSO) brain and BIRB796 treated regenerating (4 dpl) brain is shown as a bar graph ( n = 3). Significance is represented as n.s. for p-value > 0.05, * for p-value < 0.05, ** for p-value < 0.01 and *** for p-value < 0.001. ( I ) Immunofluorescence staining on 4 dpl zebrafish brains treated with DMSO (control) or 1 μM BIRB796. Panels show staining with the following markers: PCNA (red), HuC/D (red), GFAP (green), and S100B (green), with DAPI used to label nuclei. ( A - D ) DMSO control, (A’-D’) BIRB796 treatment. Scale bar denotes 10 μm. The following anatomical regions are indicated: Dc (central zone of the dorsal telencephalic area), Dm (medial zone of dorsal telencephalic area), Dl (lateral zone of dorsal telencephalic area), Vd (dorsal nucleus of ventral telencephalic area). ( J - M ) quantification of immunostaining wherein injured hemisphere of 4 dpl regenerating brain has been compared to that of 4 dpl BIRB796 treated regenerating brain ( n = 3). Significance is represented as n.s. for p-value > 0.05, * for p-value < 0.05, ** for p-value < 0.01 and *** for p-value < 0.001. cntrl: control; dpl: days post-lesion

Article Snippet: Rabbit monoclonal Phospho p38 MAPK (1:1000; 4511S; Cell Signaling Technology), rabbit polyclonal total p38 MAPK (1:1000; 9212S; Cell Signaling Technology), rabbit monoclonal Phospho HSP27 (1:1000; 9709S; Cell Signaling Technology), mouse monoclonal Total HSP27 (1:500; CPTC-HSPB1-2; Developmental Studies Hybridoma Bank), rabbit monoclonal Phospho MK2 (1:1000; 3007S; Cell Signaling Technology), Total MK2 (1:1000; EB11929; Everest Biotech), rabbit monoclonal c-Jun (1:1000; 9165S; Cell Signaling Technology), mouse monoclonal β-catenin (1:1000; 610153; BD Biosciences), Phospho AKT (1:1000; 4058S; Cell Signaling Technology), Total AKT (1:1000; 2920S; Cell Signaling Technology), mouse monoclonal β-actin (1:1000; sc47778; Santa Cruz).

Techniques: Inhibition, Control, Western Blot, Immunofluorescence, Staining, Immunostaining