Journal: Nature Protocols

Article Title: Multicolor two-photon imaging of in vivo cellular pathophysiology upon influenza virus infection using the two-photon IMPRESS

doi: 10.1038/s41596-019-0275-y

Figure Lengend Snippet: Comparison of fluorescent dyes for in vivo imaging using two-photon excitation microscopy

Article Snippet: Cascade Blue-conjugated dextran (10,000 molecular weight (MW); Invitrogen, cat. no. D1976) Fluorescein isothiocyanate (FITC)-conjugated dextran (4,000 MW; Sigma-Aldrich, cat. no. 46944) FITC-conjugated dextran (10,000 MW; Invitrogen, cat. no. D1820) FITC-conjugated dextran (40,000 MW; Invitrogen, cat. no. D1845) FITC-conjugated dextran (70,000 MW; Sigma-Aldrich, cat. no. 46945) Texas Red-conjugated dextran (3,000 MW; Invitrogen, cat. no. D3328) Texas Red-conjugated dextran (10,000 MW; Invitrogen, cat. no. D1863) Texas Red-conjugated dextran (70,000 MW; Invitrogen, cat. no. D1864) Qtracker 655 vascular labels (Invitrogen, cat. no. Q21021MP) Qdot 655 wheat germ agglutinin (WGA) conjugate (Invitrogen, cat. no. Q12021MP) Calcein AM solution (Sigma-Aldrich, cat. no. C1359) SYTOX Blue nucleic acid stain (Invitrogen, cat. no. S11348) SYTOX Green nucleic acid stain (Invitrogen, cat. no. S7020) SYTOX Orange nucleic acid stain (Invitrogen, cat. no. S11368) Propidium iodide (Invitrogen, cat. no. P1304MP) DAPI (4ʹ,6-diamidino-2-phenylindole, dilactate; Invitrogen, cat. no. D3571) Hoechst 33342, trihydrochloride, trihydrate (Invitrogen, cat. no. H3570) Pan caspase (FAM-VAD-FMK) in vivo probe, green (Vergent Bioscience, cat. no. 20100) CellROX Green Reagent (Invitrogen, cat. no. C10444) CellROX Orange Reagent (Invitrogen, cat. no. C10443) CellROX Deep Red Reagent (Invitrogen, cat. no. C10422) LysoTracker Blue DND-22 (Invitrogen, cat. no. L7525) LysoTracker Green DND-26 (Invitrogen, cat. no. L7526) LysoTracker Red DND-99 (Invitrogen, cat. no. L7528) LysoTracker Deep Red (Invitrogen, cat. no. L12492) MitoTracker Orange CMTMRos (Invitrogen, cat. no. M7510) MitoTracker Red CM-H 2 Xros (Invitrogen, cat. no. M7513) MitoTracker Red FM (Invitrogen, cat. no. M22425) Rhodamine 6G (Sigma-Aldrich, cat. no. 252433) Tetramethylrhodamine, ethyl ester, perchlorate (TMRE; Invitrogen, cat. no. T669) FluoSpheres polystyrene microspheres (1.0 μm, red fluorescent; Invitrogen, cat. no. F13083) SiR-actin (Cytoskeleton, cat. no. CY-SC001) SiR-tubulin (Cytoskeleton, cat. no. CY-SC002) PKH26 Red Fluorescent Cell Linker Kit (Sigma-Aldrich, cat. no. PKH26PCL) FITC-conjugated anti-mouse Ly-6G antibody (BioLegend, cat. no. 127606, RRID: AB_1236494) Alexa Fluor 488–conjugated anti-mouse Ly-6G antibody (BioLegend, cat. no. 127626, RRID: AB_2561340) DyLight 488–conjugated anti-mouse Ly-6G antibody (Leinco Technologies, cat. no. L287, RRID: AB_2810281) PE-conjugated anti-mouse Ly-6G antibody (BD Biosciences, cat. no. 551461, RRID: AB_394208) Alexa Fluor 594–conjugated anti-mouse Ly-6G antibody (BioLegend, cat. no. 127636, RRID: AB_2563207) Alexa Fluor 647–conjugated anti-mouse Ly-6G antibody (BioLegend, cat. no. 127610, RRID: AB_1134159)

Techniques: Comparison, In Vivo Imaging, Concentration Assay, Staining, In Vivo, Imaging, Labeling

Journal: Nature

Article Title: Mitochondrial double-stranded RNA triggers antiviral signalling in humans.

doi: 10.1038/s41586-018-0363-0

Figure Lengend Snippet: Fig. 1 | Mitochondria form dsRNA that is suppressed by the RNA degradosome. a, dsRNA-seq experimental approach. b, dsRNA-seq reads across the mitochondrial genome spanning protein coding region in untreated HeLa cells. H-strand genes are shown as blue bars and L-strand as red bars. Short tRNA genes are denoted with T as the first letter. Data are representative of two experiments. c, Immunostaining of dsRNA in HeLa cells with anti-dsRNA (J2) antibody. Mitochondria and nuclei are stained with MitoTracker Deep Red and Hoechst, respectively. Scale bars,

Article Snippet: ABT-737 (sc-207242, Santa Cruz), 5,6-dichloro-1-β-d-ribofuranosylbenzimidazole (DRB) (D1916, Sigma) or Act D (A1410, Sigma), digitonin (D141, sigma), MitoTracker Deep Red (M22426, Thermo Fisher Scientific), MitoTracker Red CMXRos (9082, Cell Signaling). pppIVT-RNA99nt and CIP-EMCV-RNA were provided by J.R.28.

Techniques: Immunostaining, Staining

Journal: Nature

Article Title: Mitochondrial double-stranded RNA triggers antiviral signalling in humans.

doi: 10.1038/s41586-018-0363-0

Figure Lengend Snippet: Fig. 3 | Pathological PNPT1 mutations result in mtdsRNA accumulation and activation of ISGs. a, PNPase western blot in fibroblasts from four patients with mutations in PNPT1 and a control. Quantification is shown as mean and s.d. from four experiments. b, Immunostaining of dsRNA (J2) in fibroblast cell lines from patients with PNPT1 mutations and controls. Mitochondria are stained with MitoTracker Red CMXRos and nuclei with DAPI (blue). Scale bars, 10 μm (main images) and 1 μm (expanded view). Images are representative of two experiments. c, Left, RT–qPCR analysis of cytosolic mtRNA (four loci) in cells with PNPT1 mutations versus

Article Snippet: ABT-737 (sc-207242, Santa Cruz), 5,6-dichloro-1-β-d-ribofuranosylbenzimidazole (DRB) (D1916, Sigma) or Act D (A1410, Sigma), digitonin (D141, sigma), MitoTracker Deep Red (M22426, Thermo Fisher Scientific), MitoTracker Red CMXRos (9082, Cell Signaling). pppIVT-RNA99nt and CIP-EMCV-RNA were provided by J.R.28.

Techniques: Activation Assay, Western Blot, Control, Immunostaining, Staining, Quantitative RT-PCR