EMBO/soda-nel huggingface dataset:
Parkin is a disease modifier in the mutant SOD1 mouse model of familial ALS (2018)
Figure 6

Figure 6. Parkin knockout delays disease progression and pathology in SOD1-G93A mice

A) Kaplan-Meier survival analysis (Log-Rank test with Holm-Sidak's correction for multiple comparisons). Mean age of death (± SEM) for G93A was 169.3 ± 2.5 days and for PKO/G93A was 185.6 ± 2.2 days, indicating that Parkin knockout prolongs lifespan of SOD1-G93A mice; n=19 for Non Tg (9 males and 10 females), n= 20 for PKO (10 males and 10 females), n= 18 for G93A (8 males and 10 females) and n= 19 for PKO/G93A (9 males and 10 females); p= 0.0000285.

B) Body weight changes over time, relative to body weight at 45 days that is set at 100% for each mouse. Parkin knockout delays body weight loss in SOD1-G93A mice. Results are expressed as mean ± SEM; n=19 for Non Tg (9 males and 10 females), n=20 for PKO (10 males and 10 females), n=18 for G93A (8 males and 10 females) and n=19 for PKO/G93A (9 males and 10 females); *p= 0.017 (at 150 days), *p= 0.004 (at 164 days), *p= 0.002 (at 171 days) and **p= 0.001 (at 178 days), by two-way ANOVA with repeated measures and with Holm-Sidak's correction for multiple comparisons.

C) Clasping score changes over time. Parkin knockout does not affect clasping onset in SOD1-G93A mice. An intermediate score of 2.5 is indicated by the dotted line. Results are expressed as mean ± SEM; n=19 for Non Tg (9 males and 10 females), n=20 for PKO (10 males and 10 females), n=18 for G93A (8 males and 10 females) and n=19 for PKO/G93A (9 males and 10 females). D) Representative images of NMJs in the soleus muscle at 130 days. Muscles were immunostained for neurofilament H (NF-H, in red) and stained with α-bungarotoxin (α-BTX, in green). Scale bar, 20 µm.

E) Quantification of the percentage of innervated NMJs at 130 days indicates that Parkin knockout decreases denervation in SOD1-G93A mice. Results are expressed as mean ± SEM and were collected from n= 6 mice per group (3 males and 3 females); n of images evaluated = 49 for Non Tg (with 483 NMJs counted), 46 for PKO (396 NMJs counted), 47 for G93A (413 NMJs assessed) and 38 for PKO/G93A (325 NMJs counted); ***p= 0.0001, by unpaired Mann-Whitney test.

F) Representative images of lumbar spinal cord sections at 130 days immunostained with ChAT. Scale bar, 200 µm.

G) Quantification of ChAT-positive MN in the spinal cord ventral horn (dotted areas) at 130 days shows that Parkin knockout decreases MN loss in the spinal cord of SOD1-G93A mice. Results are expressed as mean ± SEM; n = 10 mice per group in Non Tg, PKO and G93A (5 males and 5 females) and n= 9 for PKO/G93A (4 males and 5 females); *p=0.031, by unpaired Student's t test.

H) Representative images of lumbar spinal cords sections immunostained for GFAP at 130 days. Scale bar, 200 µm.

I) Quantification of the average GFAP staining intensity at 130 days indicates that Parkin knockout decreases spinal cord astrogliosis in SOD1-G93A mice. Results are expressed as mean ± SEM; n = 10 mice per group (5 males and 5 females); *p= 0.033, by paired Student's t test.
Parkin is a disease modifier in the mutant SOD1 mouse model of familial ALS (2018)
Figure 7

Figure 7. Parkin knockout improves mitochondrial dysfunction and delays PGC1α decline in SOD1-G93A mice

A) Citrate synthase activity in spinal cord homogenates at disease end stage. Results are expressed as mean ± SEM; n= 8 (4 males and 4 females) mice per group; *p= 0.024, by paired Student's t test. Activities are expressed as nmoles of substrate oxidized per minute per mg of protein.

B) Cytochrome oxidase (COX) activity at end stage. Results are expressed as mean ± SEM; n = 8 (4 males and 4 females) mice per group; *p= 0.032, by paired Student's t test. Activities are expressed as nmoles of substrate oxidized per minute per mg of protein.

C) qPCR (fold change) of PGC1α mRNA normalized by β-actin mRNA at 130 days of age. Results are expressed as mean ± SEM and as fold change of the Non Tg; n= 8 (4 males and 4 females). No statistically significant differences were found between G93A and PKO/G93A (p= 0.250 by paired Wilcoxon's test); *p= 0.035 paired Friedman's test with Dunn's correction (Non Tg vs. G93A). No other statistically significant differences were found.

D) qPCR (fold change) of PGC1α mRNA normalized by β-actin mRNA at end stage. Results are expressed as mean ± SEM and as fold change of the Non Tg; n= 8 (4 males and 4 females). No statistically significant differences were found between G93A and PKO/G93A (p= 0.613 by paired Student's t test). **p= 0.0058 by paired Friedman's test with Dunn's correction (for Non Tg vs. G93A comparison) and ***p<0.0001 by paired one-way ANOVA with Tukey's correction (for PKO vs. PKO/G93A comparison). Parkin knockout improves PGC1α expression at 130 days (C) but the effect is lost at end stage (D).

E, F) Representative Western blots (E) and quantification (F) of PARIS at disease end stage. Protein levels are normalized by β-actin and results are expressed as mean ± SEM and as percent of Non Tg; n= 8 (4 males and 4 females). No statistically significant differences were found between G93A and PKO/G93A by paired Wilcoxon's test (p= 0.99). PARIS levels are unchanged in SOD1-G93A mice relative to Non Tg at disease end stage.
E2/E3-independent ubiquitin-like protein conjugation by Urm1 is directly coupled to persulfidation (2022)
Figure 7

Figure 7. Trans-sulfuration and Uba4-Urm1 are independent pathways for protein thiolation

TBH cytotoxicity assay in vivo. Basic growth and the synthetic effect in wild type, ahp1Δ, urm1Δ, tum1Δ, ncs6Δ, cys3Δ, cys4Δ, cys3Δ urm1Δ, and cys4Δ urm1Δ strains was monitored without or with 1 mM TBH.

H2S production using Biggy agar plates- Wild type, ahp1Δ, urm1Δ, tum1Δ, ncs6Δ, cys3Δ, cys4Δ, cys3Δ urm1Δ, and cys4Δ urm1Δ strains were grown on Biggy medium, and H2S production was recorded as indicated in the material and methods section.

In vivo Ahp1 conjugation analyses with protein extracts obtained from the indicated yeast strains expressing HA-URM1. Unconjugated Urm1 and Urm1-Ahp1 conjugates were detected by anti-HA (top panels) Western blots. Anti-Ahp1 blots (middle) detect unmodified Ahp1. Anti-Cdc19 (bottom panels) served as loading control.

Northern-blot analysis for thiolation levels of tRNAUUCGlu in the genetic background of the indicated yeast strains. Total tRNA was resolved on denaturing PAGE supplemented with APM to retard the migration of thiolated tRNAUUCGlu. APM: ([N-Acryloyl-amino] phenyl) mercuric chloride. (bottom) Quantified thiolation levels from 3 independent biological replicates.

Scheme of sulfur source for thiolation. Sulfur released as H2S from transsulfuration enzymes Cys4 and Cys3 is used for protein persulfidation, scavenging free radicals metabolic signaling/stimulation. The sulfur from the Uba4-Urm1 pathway is directed to tRNA thiolation and to persulfidation of specific cysteine of target proteins.

Table 1 Data collection and refinement statistics (molecular replacement)

CtAhp1 wt

PDB ID 7Q68

CtAhp1C30S (Pre)

PDB ID 7Q69

CtAhp1C30S (unreacted)

PDB ID 7Q6A

CtAhp1C30S-Urm1

PDB ID 7Q5N

Zn peak

Zn HR

$$\dagger R_{\text{meas}} = \sum_{\text{hkl}}^{}{\lbrack\frac{N}{N - 1}\rbrack}^{1/2}\sum_{i}^{}{|I_{i}\left( \text{hkl} \right) - \ \overline{I(hkl)}}|/\sum_{\text{hkl}}^{}{\sum_{i}^{}I_{i}}(hkl) $$

Expanded View Figures
A splicing isoform of GPR56 mediates microglial synaptic refinement via phosphatidylserine binding (2020)
Figure 1

Fig. 1. PS flags RGC inputs for removal by microglia during early dLGN development.
(A) A schematic drawing of experimental procedure where CTB488 is intraocularly injected, followed by intracranial injection of PSvue550 to dLGN border.

(B) A schematic diagram shows the timeline of procedures for ex vivo imaging and engulfment analysis.

(C) Top panel: Representative images show PS labeling in the WT dLGN at P6 and P13. RGC inputs were labeled with CTB488. Bottom panel: Enlarged images of the boxed region in top panels. Circles indicate PS+ RGC inputs. Arrows point to the enlarged PS+ RGC inputs in the insets. Scale bar, 5 µm.

(D) Quantification of the percentage of PS+ RGC inputs in total RGC inputs at P6 and P13. N = 4, ****p < 0.0001. Student's t-test.

(E) Co-labeling of vGlut2 and PSVue in the dLGN at P6. Circles indicate colocalized vGlut2 and PSVue.

(F) Co-labeling of Homer1 and PSVue in the dLGN at P6. Circles indicate colocalized Homer1 and PSVue. Scare bar, 5 µm.

(G) Orthogonal sections showed a triple positive PS+/CTB488+/CD68+ RGC inputs inside of microglia. Scare bar, 5 µm.

(H) Orthogonal sections showed a triple positive PS+/vGlut2+/CD68+ synapse inside of microglia. Scare bar, 5 µm.

(I) A representative image of microglia (upper-left) is surface rendered (bottom-left). The white arrow points to cells which might be apoptotic cells labeled by PSVue. RGC inputs and PSVue outside or inside of microglia are shown in the two right panels. Scare bar, 20 µm.(J) Quantification of the percentage of PS+ and PS- RGC inputs outside of microglia in total inputs. N = 4.

(K) Quantification of the percentage of engulfed PS+ and PS- RGC inputs in total engulfed inputs. N=4.

Data information: Data are presented as mean ± SD.
A splicing isoform of GPR56 mediates microglial synaptic refinement via phosphatidylserine binding (2020)
Figure 2

Fig. 2. GPR56 binds to PS.
(A) A schematic drawing of GPR56 protein structure, with a N-terminal fragment (NTF), a seven transmembrane domain (7-TM) and a C-terminal fragment (CTF).

(B) A diagram shows the hFc tag was added to the c-terminal of GPR56-NTF (NTF-hFC) or GAIN domain (GAIN-hFc).

(C) A flow chart showing the experimental design of flow cytometry analysis. Briefly, Ba/F3 cells are treated with A23187 to externalize PS. For the binding assay, Alexa Fluor 647-conjugated hFc, GAIN-hFc, or NTF-hFc were incubated with PS-externalized Ba/F3 cells. For the competition assay, Alexa Fluor 647-conjugated hFc, GAIN-hFc, or NTF-hFc were used to compete with FITC-conjugated Annexin V binding.

(D) The binding experiment using flow cytometry show that only the GAIN domain binds to PS, similar as Annexin V binding.

(E) In the competition experiment, AF647 channel shows that GAIN domain binds 60.1% of the PS+ Ba/F3 cells (left). Correspondingly, FITC channel reveals 39.7% Annexin V binding to PS+ Ba/F3 cells (right).

(F) A diagram of membrane lipid strips spotted with fifteen different lipids. DAG, diacylglycerol; PA, phosphatidic acid; PE, phosphatidylethanolamine; PC, phosphatidylcholine; PG, phosphatidylglycerol; PI, phosphatidylinositol.

(G) Direct binding of hFc-tagged GPR56 GAIN proteins to PS and other phospholipids. HFc was used as a negative control, and GAS6 as a positive control.
A splicing isoform of GPR56 mediates microglial synaptic refinement via phosphatidylserine binding (2020)
Figure 3

Fig. 3. GPR56 S4 variant is required for synaptic refinement in the dLGN.

(A) A diagram showing Gpr56 WT, null and S4 transcripts. Solid boxes indicating exons that are transcribed. Arrowheads indicate the translation start sites.

(B) Gpr56 transcript levels in isolated microglia from Gpr56 S4 mice. N = 3, **p < 0.01 by Student's t-test.

(C) A table showing the expression status of Gpr56 WT and S4 variants in microglia of different transgenic mice.

(D) Representative images of Nissl staining of Gpr56 null and Gpr56 S4 E16.5 neocortex. Arrows indicate cortical ectopias that are shown in insets.

(E) Quantification of ectopia size per section. N = 6, p = 0.64 by Student's t-test.

(F) The distribution of ectopia from rostral to caudal cortex. N = 3, F (9, 81) = 0.65, p = 0.75 by two-way ANOVA with Bonferroni's post hoc test.

(G). Myelin basic protein (MBP) staining of corpus callosum in P28 controls, Gpr56 null and Gpr56 S4 mice. Scale bar, 100 µm.

(H) Quantification of MBP intensity in corpus callosum. N = 5, ***p < 0.001 by one-way ANOVA with Tukey's post-hoc test.

(I) Gpr56 transcript levels in WT microglia at P5 and P14. N = 4, **p < 0.01, two-way ANOVA with Sidak's multiple comparisons test.

(J) An overview of vGlut2 and Homer1 staining in dLGN at P10. The yellow outline indicates the dLGN core, and the dotted boxes show where synapses are quantified. Scale bar, 200 µm.

(K) Representative images of vGlut2/Homer1 staining in the dLGN of control, Gpr56 null, and Gpr56 S4 brains at P10. Arrows pointing to the enlarged synapse in the insets. Scale bar, 5µm.

(L) Relative vGlut2/Homer1 synapse density in dLGN. N=10 (Ctrl), N=6 (Gpr56 null), N=3 (Gpr56 S4). **p < 0.01, *** p < 0.001, one-way ANOVA with Tukey's post-hoc test. (M) A schematic representation of the in vivo engulfment assay. CTB are injected into both eyes at P4, and anterogradely trace RGC projections to the dLGN. After 24 hours, the brains are collected and analyzed at P5.

(N) Representative images and surface rendered microglia (green) in which CTB+(red) RGC inputs were engulfed. Scale bar, 10µm.

(O) Quantification of the percentage of engulfed RGC inputs in controls, Gpr56 null and Gpr56 S4 microglia. N = 4, **p < 0.01, *** p < 0.001, one-way ANOVA with Tukey's post-hoc test.

Data information: Data are presented as mean ± SEM in (F). For other statistics analysis, data are presented as mean ± SD.
A splicing isoform of GPR56 mediates microglial synaptic refinement via phosphatidylserine binding (2020)
Figure 4

Fig. 4. Microglial GPR56 is required for synaptic development in the dLGN.
(A) Gpr56 is deleted in CKO microglia. RNAscope shows Gpr56 transcripts co-localize with microglia (arrow) in controls, but not in CKO, and is absent in all cell types in the global Gpr56 KO (Gpr56 null). Arrowhead indicates non-microglia cells expressing Gpr56. RNAscope was performed in the prefrontal cortex of P30 mice. Scale bar, 20 µm.

(B) Quantification of Gpr56 fluorescence signals in (A). N = 20-50 cells for each.

(C) Confocal images of vGlut2 (green) labeling retinal ganglion cell (RGC) presynaptic terminals and Homer1 (red) for post-synapses in the dLGN of CKO and controls at P10. Overlapped vGlut2 and Homer1 are quantified as synapses, indicated by white circles. Arrows pointing to the synapse enlarged in the upper right-hand inset. Scale bar, 5 µm.

(D) A time course of dLGN synapse density (vGlut2+/Homer1+) between WT and controls. N = 3 for P0, N = 4 for P5, N=3 for P10.

(E) Representative super-resolution images and 3D-reconstructed images of vGlut2 and Homer1 staining of P8 dLGN. Green objects represent surface rendering of vGlut2+ presynaptic terminals. Red spots are rendered Homer1+ post-synapses. Magenta spots represent Homer1+ post-synapses within a distance of 300nm from the nearest vGlut2+ surface. Scale bar, 2 µm.

(F) Quantification of Homer1+ spots adjacent to vGlut2 surface within 100nm, 200nm, and 300nm, respectively. N = 3.

(G) Western blot of vGlut2 and Homer1 using microdissected dLGN tissue from P8 mice.

(H, I) Quantification of vGlut2 and Homer1 expression in CKOs and controls. N = 3, *p = 0.027.

(J) Quantification of synapse density (vGlut2+/Homer1+) in the dLGN of both male and female iCKO mice at P10. N = 3 for male, N = 4 for female.

(K) An overview of vGlut1 and Homer1 staining in dLGN at P10. The yellow outline indicates the dLGN core, and the dotted boxes show where synapses are quantified. Scale bar, 200 µm.

(L) Representative images of vGlut1+ (green) presynaptic terminals and Homer1+ (red) postsynapses in the dLGN of CKO and controls at P10. Arrows pointing to the synapse enlarged in inset. Scale bar, 5 µm.

(M) Quantification of synapse density (vGlut1/homer1) at P10 in the dLGN of CKO mice and controls. N=3 (WT), N=5 (CKO), p = 0.053.

Data information: *p < 0.05, **p < 0.01, ****p < 0.0001 using Student's t-test (F, H, I and M) or two-way ANOVA followed by Bonferroni's post hoc test (B, D and J). Data are presented as mean ± SD.
A splicing isoform of GPR56 mediates microglial synaptic refinement via phosphatidylserine binding (2020)
Figure 5

Fig. 5. Microglial GPR56 is required for synaptic development in the hippocampus.
(A) Representative images show hippocampal vGlut2 and Homer1 immunostaining. White box outlines the region of interest and yellow box shows the regions where confocal images were taken. Scale bar, 500 µm.

(B) Confocal images of synaptic immunostaining in CA1 striatum lacunosum-moleculare (str. lac/mol) at P10. Arrows pointing to the enlarged synapse in the insets. Scale bar, 5 µm.

(C, D) Quantification of synapse density in CA1 str. lac/mol in iCKO versus control at P10 (C), and CKO versus control at P21 (D). At P10, N(Ctrl) = 4, N(iCKO) = 3, p = 0.02. At P21, N = 8, p = 0.005.

(E) Representative images show hippocampal vGlut1 and Homer1 immunostaining.

(F) Confocal images of synaptic immunostaining in CA1 striatum radiatum at P10.

(G, H) Quantification of synapse density in CA1 striatum radiatum in iCKO versus control at P10 (G), and CKO versus control at P21 (H). At P10, N = 5, p = 0.83. At P21, N = 5, p = 0.89.

Data information: *p < 0.05, **p < 0.01, Student's t-test. All data are presented as mean ± SD.
A splicing isoform of GPR56 mediates microglial synaptic refinement via phosphatidylserine binding (2020)
Figure 6

Fig. 6. Microglial Gpr56 deficiency leads to impaired retinogeniculate circuit organization and function.
(A) A diagram of eye-specific segregation assay at P30.

(B) CTB-labeled dLGN shows reduced eye-segregation at P30 in CKO mice. The left column shows contralateral dLGN labeled with CTB488 (green), and the middle one is ipsilateral dLGN with CTB647 (magenta). The right column represents the dLGN pseudocolored according to the R-value for each pixel (R = log(Fipsi/Fcontra)). Scale bar, 200 µm.

(C) A histogram distribution chart of R-value for all pixels within dLGN represents the degree of eye-specific segregation. When R is 0, it means equal ipsilateral and contralateral fluorescence intensity at a pixel. A greater R-value means a bigger difference of ipsi-to-contraleteral fluorescence intensity. The narrower distribution of CKO in the inset indicates reduced segregation.

(D) The variance of R distributions in P30 control and CKO mice. N = 4 (Ctrl), N = 6 (CKO), p = 0.004, mean ± SD.

(E) A schematic diagram of electrophysiological recording in a parasagittal dLGN.

(F) Maximal NMDAR mediated currents measured in the dLGN of P28~P34 mice, p = 0.03, N = 14 (Ctrl), 23 (CKO) cells from 5, 7 mice, respectively. Mean ± SEM.

(G) Western blot of NMDAR1 using microdissected dLGN tissue from P30 mice.

(H) Quantification of NMDAR1 expression in CKO mice and control. N = 3, p = 0.007, mean ± SD.

(I) Maximal AMPAR mediated currents measured in the dLGN of P28~P34 mice. P=0.302, N = 13 (Ctrl), 17 (CKO) cells from 5, 7 mice, respectively. Mean ± SEM.

(J) Western blot of GluR1 with microdissected P30 dLGN tissue.

(K) Quantification of GluR1 expression in CKO mice and controls. N = 3, p = 0.40, mean ± SD.

Data information: *p < 0.05, **p < 0.01, Student's t-test.
Stimulation of glycolysis promotes cardiomyocyte proliferation after injury in adult zebrafish. (2020)
Figure 1

Figure 1 - Glycolysis and pyruvate metabolism play an important role following cardiac injury.

(a) 30 and 150 days post fertilization (dpf) zebrafish ventricles were isolated and relative protein levels determined (n = 3).

(b) KEGG over-representation analysis for selected categories or upregulated proteins in 150 dpf hearts compared to 30 dpf hearts.

(c) qPCR analysis of mRNA levels of glycolytic enzyme genes in 5 dpci remote and wound border cardiac tissue (n = 2-3 technical replicates using pooled cDNA from 10 ventricles for each condition (n = 2 for pkmb and pdk4, and n = 3 for the other genes)).

(d, e) Immunostaining of heart sections for PCNA and MEF2 (d) or N2.261 and MEF2 (e) in 5 dpci animals treated with PBS, 2-DG or DCA; magnified view of area in white boxes shown below; white dashed lines mark the wound border; arrowheads point to PCNA+ (d) or N2.261+ (e) CMs; percentage of PCNA+ or N2.261+ CMs in the border zone shown on the right (n = 4-5 ventricles).

Data information: Error bars, s.e.m.; P values were calculated by Bayesian-moderated t-testing (limma) (a, b), two-tailed unpaired t-test (c) or ordinary one-way ANOVA with Dunnett's multiple comparisons test (d, e). Scale bars, 50 μm.
Stimulation of glycolysis promotes cardiomyocyte proliferation after injury in adult zebrafish. (2020)
Figure 2

Figure 2 - Loss of pkma2 and ppargc1a affects cardiomyocyte dedifferentiation and proliferation following cardiac injury.

(a, b, c, d) Immunostaining of heart sections for PCNA and MEF2 (a, c) or N2.261 and MEF2 (b, d) in 5 dpci pkma2+/-; pkmb+/- and pkma2-/-; pkmb+/- (a, b) or ppargc1a+/+ and ppargc1a-/- (c, d) animals; magnified view of area in white boxes shown below; arrowheads point to PCNA+ (a, c) or N2.261+ (b, d) CMs; white dashed lines mark the wound border; percentage of PCNA+ (a, c) or N2.261+ (b, d) CMs in the border zone shown on the right (n = 4-6 ventricles of each genotype).

(e, f) AFOG staining of heart sections from 60 dpci pkma2+/-; pkmb+/- and pkma2-/-; pkmb+/- (e) or 45 dpci ppargc1a+/+ and ppargc1a-/- (f) animals; black dashed lines outline the scar area; scar area measured on the right (n = 3-5 ventricles of each genotype).

Data information: Error bars, s.e.m.; P values were calculated by two-tailed unpaired t-test. Scale bars, 50 μm.
Stimulation of glycolysis promotes cardiomyocyte proliferation after injury in adult zebrafish. (2020)
Figure 3

Figure 3 - Cardiomyocyte specific modulation of pyruvate metabolism cell-autonomously affects their dedifferentiation and proliferation following cardiac injury.

(a) Transgenic animals and experimental time course for data shown in (b-e).

(b-e) Immunostaining of heart sections for PCNA and MEF2 (b, c) or N2.261 and MEF2 (d, e) in 5 dpci animals (Tg(hsp70l:LOXP-STOP-LOXP-pdha1aSTA-T2A-mCherry) and Tg(hsp70l:LOXP-STOP-LOXP-pdk3b-T2A-mCherry) alone (control) or in combination with Tg(myl7:Cre-ERT2), all after tamoxifen and heat shock treatments); magnified view of area in white boxes shown below; arrowheads point to PCNA+ (b, c) or N2.261+ (d, e) CMs; white dashed lines mark the wound border; percentage of PCNA+ (b, c) or N2.261+ (d, e) CMs in the border zone shown on the right (n = 4-5 ventricles of each genotype).

(f, g) AFOG staining of heart sections from 60 dpci animals (Tg(hsp70l:LOXP-STOP-LOXP-pdha1aSTA-T2A-mCherry) (f) and Tg(hsp70l:LOXP-STOP-LOXP-pdk3b-T2A-mCherry) (g) alone (control) or in combination with Tg(myl7:Cre-ERT2), all after tamoxifen and heat shock treatments); black dashed lines outline the scar area; scar area measured on the right (n = 4-5 ventricles of each genotype).

Data information: Error bars, s.e.m.; P values were calculated by two-tailed unpaired t-test. Scale bars, 50 μm.
Stimulation of glycolysis promotes cardiomyocyte proliferation after injury in adult zebrafish. (2020)
Figure 4

Figure 4 - Pyruvate metabolism modulation affects the behavior of rat neonatal cardiomyocytes in culture.

(a, b) Staining for Ki67, CTNI and DNA (DAPI) in control, PDHA1STA OE or PDK3 OE RNCMs cultured in growth (a) or non-growth (b) medium; arrowheads point to Ki67+ RNCMs; percentage of Ki67+ RNCMs shown on the right (n = 4 biological replicates for each condition).

(c) Staining for CTNI and DNA (DAPI) in scratch assay using control, PDHA1STA OE or PDK3 OE RNCMs immediately or at 3 days after generating the scratch; magnified view of area in white boxes shown below; arrowheads point to membrane protrusions of RNCMs; quantification of CM membrane protrusions shown on the right (n = 4 biological replicates for each condition).

(d) Reactome over-representation analysis of differentially regulated genes in PDK3 OE RNCMs compared to control.

(e, f) Heat map of gene expression for key regulators of cell cycle (e) and DNA replication (f) in PDK3 OE vs control RNCMs.

Data information: Error bars, s.e.m.; P values were calculated by ordinary one-way ANOVA with Dunnett's multiple comparisons test (a, b, c) or Benjamini-Hochberg correction (d). Scale bars, 20 μm.

Expanded View Figure legends