Journal: Journal of Pineal Research

Article Title: Melatonin ameliorates PM 2.5 ‐induced cardiac perivascular fibrosis through regulating mitochondrial redox homeostasis

doi: 10.1111/jpi.12686

Figure Lengend Snippet: Melatonin alleviated PM 2.5 ‐induced cardiac mitochondrial oxidative damage. A, The level of 3′‐NT. B, The level of 4‐HNE. C, The level of GSH/GSSG. D, Representative pictures of myocardial tissue by transmission electron microscope. The blow panels are high magnification (scale bar: 0.2 μm) images corresponding to the upper panels (scale bar: 0.5 μm). E, MitoSOX staining of heart tissues (scale bar: 100 μm). F, Mean fluorescence intensities of heart. G, Representative Western blot pictures. H, The quantitative analysis of SIRT3 protein levels. I, The activity of SIRT3. J, The quantitative analysis of SOD2 acetylation. K, The activity of SOD2. Data are expressed as the means ± SD; n = 6 in each group. * P < .05

Article Snippet: The deacetylase activity of SIRT3 was measured by a SIRT3 Fluorimetric Activity Assay Kit (BPS bioscience) following the manufacturer's protocol.

Techniques: Transmission Assay, Microscopy, Staining, Fluorescence, Western Blot, Activity Assay

Journal: Journal of Pineal Research

Article Title: Melatonin ameliorates PM 2.5 ‐induced cardiac perivascular fibrosis through regulating mitochondrial redox homeostasis

doi: 10.1111/jpi.12686

Figure Lengend Snippet: PM 2.5 regulated cardiac myofibroblast conversion via increased mitochondrial reactive oxygen levels and SOD2 acetylation, decreased SIRT3 expression and activity. A, Cardiac fibroblast cell viability after PM 2.5 ‐ treated. B, Quantification analysis of fluorescence intensity obtained from flow cytometry. C, Representative images of cardiac fibroblast α‐SMA and Vimentin immunostaining. D, Representative Western blot pictures. E, The quantitative analysis of collagen‐I, collagen‐III, and α‐SMA protein levels. F, The quantitative analysis of SIRT3 protein levels. G, The activity of SIRT3. H, The quantitative analysis of SOD2 acetylation. I, The activity of SOD2. Data are expressed as the means ± SD from three independent experiments. * P < 0.05 compared to control group

Article Snippet: The deacetylase activity of SIRT3 was measured by a SIRT3 Fluorimetric Activity Assay Kit (BPS bioscience) following the manufacturer's protocol.

Techniques: Expressing, Activity Assay, Fluorescence, Flow Cytometry, Immunostaining, Western Blot

Journal: Journal of Pineal Research

Article Title: Melatonin ameliorates PM 2.5 ‐induced cardiac perivascular fibrosis through regulating mitochondrial redox homeostasis

doi: 10.1111/jpi.12686

Figure Lengend Snippet: Mitochondrial‐derived ROS mediated PM 2.5 ‐induced cardiac myofibroblast conversion. A, Quantification analysis of fluorescence intensity obtained from flow cytometry. B, The quantitative analysis of α‐SMA protein levels. C, Representative Western blot pictures. D, The quantitative analysis of SIRT3 protein levels. E, The activity of SIRT3. F, The quantitative analysis of SOD2 acetylation. G, The activity of SOD2. Data are expressed as the means ± SD from three independent experiments. * P < .05 compared to control group; # P < .05 compared to PM 2.5 ‐treated group

Article Snippet: The deacetylase activity of SIRT3 was measured by a SIRT3 Fluorimetric Activity Assay Kit (BPS bioscience) following the manufacturer's protocol.

Techniques: Derivative Assay, Fluorescence, Flow Cytometry, Western Blot, Activity Assay

Journal: Journal of Pineal Research

Article Title: Melatonin ameliorates PM 2.5 ‐induced cardiac perivascular fibrosis through regulating mitochondrial redox homeostasis

doi: 10.1111/jpi.12686

Figure Lengend Snippet: Melatonin alleviated the oxidative stress, SIRT3 impairment after PM 2.5 treatment in vitro. A, Cardiac fibroblast cell viability after melatonin ‐ treated. B, Quantification analysis of fluorescence intensity obtained from flow cytometry. C, The quantitative analysis of α‐SMA protein levels. D, Representative Western blot pictures. E, The quantitative analysis of SIRT3 protein levels. F, The activity of SIRT3. G, The quantitative analysis of SOD2 acetylation. H, The activity of SOD2. Data are expressed as the means ± SD from three independent experiments. * P < .05 compared to control group; # P < .05 compared to PM 2.5 ‐treated group

Article Snippet: The deacetylase activity of SIRT3 was measured by a SIRT3 Fluorimetric Activity Assay Kit (BPS bioscience) following the manufacturer's protocol.

Techniques: In Vitro, Fluorescence, Flow Cytometry, Western Blot, Activity Assay

Journal: Journal of Pineal Research

Article Title: Melatonin ameliorates PM 2.5 ‐induced cardiac perivascular fibrosis through regulating mitochondrial redox homeostasis

doi: 10.1111/jpi.12686

Figure Lengend Snippet: 3‐TYP pretreatment abolished the melatonin‐suppressed cardiac myofibroblast conversion induced by PM 2.5 treatment. A, Quantification analysis of fluorescence intensity obtained from flow cytometry. B, The quantitative analysis of α‐SMA protein levels. C, Representative Western blot pictures. D, The quantitative analysis of SIRT3 protein levels. E, The activity of SIRT3. F, The quantitative analysis of SOD2 acetylation. G, The activity of SOD2. Data are expressed as the means ± SD from three independent experiments. * P < .05 compared to PM 2.5 ‐treated group; # P < .05 compared to melatonin pretreatment group; ∆ P < .05 compared to 3‐TYP pretreatment group

Article Snippet: The deacetylase activity of SIRT3 was measured by a SIRT3 Fluorimetric Activity Assay Kit (BPS bioscience) following the manufacturer's protocol.

Techniques: Fluorescence, Flow Cytometry, Western Blot, Activity Assay

Journal: Immunity

Article Title: Innate immune training restores pro-reparative myeloid functions to promote remyelination in the aged central nervous system.

doi: 10.1016/j.immuni.2024.07.001

Figure Lengend Snippet: Figure 6. HDAC1/2 depletion in microglia improves remyelination in aged mice (A) Schematic representation of experimental paradigm in Cx3cr1creERT/hetHdac1fl/flHdac2fl/flaged mice. (B) Quantitative PCR analysis of Hdac1 and Hdac2 in CD11b+ cells isolated from Cre and Cre+ mice 2 weeks after tamoxifen induction. (C) Images of MAC2+IBA1+ cells in the demyelinated lesions at 4 dpi. Scale bars, 50 mm. (D) Quantification of the percentage of MAC2+IBA1+ cells over IBA1+ cells in the demyelinated lesion at 4 dpi. (E) Images of MHCII+IBA1+ cells in the demyelinated lesions at 4 dpi. Scale bars, 50 mm. (F) Quantification of the percentage of MHCII+IBA1+ cells over IBA1+ cells in the demyelinated lesion at 4 dpi. (G) Images of corpus callosum lesions in aged (12 months) Cre (control) and Cre+ (knockout) mice at 14 dpi. Scale bars, 200 mm. (H) Quantification of lesion volume and IBA1+ volume in aged (12 months) Cre (control) and Cre+ (knockout) mice at 14 dpi. (I) Quantification of CC1+OLIG2+ cells per mm2 of lesion at 14 dpi.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER High Sensitivity NGS Fragment Analysis Kit Agilent Cat# DNF-474 DNA Clear & Concentrator TM-5 kit Zymo-research Cat# D4014 IP-Star Compact Automated System Diagenode Cat# B03000002 MicroPlex Library Preparation Kit v3 /96 rxns Diagenode Cat# C05010002 Qubit dsDNA HS Assay Kit Thermofisher Scientific Cat# Q32854 HDAC1 Fluorogenic Assay Kit BPS bioscience Cat#50061 HDAC2 Fluorogenic Assay Kit BPS bioscience Cat#50062 Deposited data Raw and analyzed data This paper GEO (GSE230187, GSE230190, GSE230191, GSE230480, GSE247529) Experimental models: Organisms/strains Mouse: C57BL/6JRj JANVIER labs RRID:IMSR_RJ:C57BL-6JRJ Mouse: Cx3cr1creERT2x Hdac1,2flox Datta et al.47 N/A Oligonucleotides Primers Table S4 N/A Software and algorithms R https://www.r-project.org/ RRID:SCR_001905 R studio https://www.rstudio.com/ Version 4.2 and 4.3 LIGER Welch et al.64 RRID:SCR_018100 Cell ranger 10x genomics v(6.1.0); RRID:SCR_017344 Doublet finder McGinnis et al.65 v(2.0.2); RRID:SCR_018771 scCustomise https://doi.org/10.5281/zenodo.5706430 RRID:SCR_024675 Seurat Satija et al.66 v(4.0.6; 4.4.0); RRID:SCR_016341 Galaxy https://usegalaxy.eu/ RRID:SCR_006281 IGV Robinson et al.67 RRID:SCR_011793 Trim galore http://www.bioinformatics. babraham.ac.uk/ projects/trim_galore/ RRID:SCR_011847 Cutadapt Martin68 RRID:SCR_011841 Bowtie2 Langmead and Salzberg69 RRID:SCR_016368 BAM tools Barnett et al.70 RRID:SCR_015987 Picard tools http://broadinstitute.github.io/picard RRID:SCR_006525 Deep tools Ramı́rez et al.71 RRID:SCR_016366 MACS2 Zhang et al.72 RRID:SCR_013291 Csaw Lun and Smyth73 https://doi.org/10.1093/nar/gkv1191 FindMotifsGenome tool Heinz et al.74 http://homer.ucsd.edu/homer/motif/ STAR Dobin et al.75 RRID:SCR_004463 Feature counts Liao et al.76 RRID:SCR_012919 Deseq2 Love et al.77 RRID:SCR_015687 Gene ontology (GO) enrichment analysis http://www.geneontology.org RRID:SCR_002811 scCODA B€uttner et al.78 https://github.com/theislab/scCODA Revigo Supek et al.79 RRID:SCR_005825 Cytoscape https://cytoscape.org/ RRID:SCR_003032 Graph Pad Prism https://www.graphpad.com/ RRID:SCR_002798 Image Lab Software Bio-Rad RRID:SCR_014210 ImageJ (Fiji) Schindelin et al.80 RRID:SCR_002285 Adobe Illustrator https://www.adobe.com/ RRID:SCR_010279 Code for calculating the lesion volume Bosch-Queralt et al.81 https://github.com/lenkavaculciakova/ lesion_volume (Continued on next page) e2 Immunity 57, 1–18.e1–e8, September 10, 2024

Techniques: Real-time Polymerase Chain Reaction, Isolation, Control, Knock-Out

Journal: Current Issues in Molecular Biology

Article Title: Mechanistic Insights into Vorinostat as a Repositioned Modulator of TACE-Mediated TNF-α Signaling via MAPK and NFκB Pathways

doi: 10.3390/cimb47090720

Figure Lengend Snippet: Effect of vorinostat on TACE (ADAM17) activity and TNF-α expression. ( A ) TACE activity was evaluated using a fluorogenic ADAM17 assay in the presence of 10 nM BMS-561392 or 10 nM vorinostat. The assay mixture was incubated with each inhibitor for 1, 2, or 2.5 h. * p < 0.05 vs. control in vorinostat treated set; ## p < 0.001 vs. control in BMS-561392 treated set. ( B ) TNF-α expression was measured by ELISA following LPS stimulation (1 μg/mL, 4 h) in RAW264.7 cells pretreated with BMS-561392 or vorinostat at concentrations of 1, 10, or 100 μM. ** p < 0.001 vs. LPS alone in vorinostat treated set; ## p < 0.001 vs. LPS alone in BMS-561392 treated set. Data are presented as mean ± SD (n = 3).

Article Snippet: TACE activity was measured using the ADAM17 Fluorogenic Assay Kit (BPS Bioscience, Cat. #78000, San Diego, CA, USA) following the manufacturer’s protocol.

Techniques: Activity Assay, Expressing, Incubation, Control, Enzyme-linked Immunosorbent Assay