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  • 99
    LI-COR irdye 800cw
    Irdye 800cw, supplied by LI-COR, used in various techniques. Bioz Stars score: 99/100, based on 4227 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 4227 article reviews
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    irdye 800cw - by Bioz Stars, 2020-11
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    Thermo Fisher big dye terminator v3 1 cycle sequencing kit
    Big Dye Terminator V3 1 Cycle Sequencing Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 5872 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 5872 article reviews
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    big dye terminator v3 1 cycle sequencing kit - by Bioz Stars, 2020-11
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    Thermo Fisher big dye terminator cycle sequencing kit
    Big Dye Terminator Cycle Sequencing Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 4567 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 4567 article reviews
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    big dye terminator cycle sequencing kit - by Bioz Stars, 2020-11
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    Thermo Fisher sybr green dye
    Sybr Green Dye, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 5629 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    sybr green dye - by Bioz Stars, 2020-11
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    Thermo Fisher fixable viability dye efluor 780
    Gating strategies for CFSE‐labeled  C. trachomatis  bacteria and phagocytosis assay. All gatings were first set on singlet events (FSC‐A vs FSC‐H), followed by gating on target cell population (FSC‐A vs. SSC‐A).  (A)  Bacteria were then shown in APC‐A versus FITC‐A (stained either with mouse anti‐ C. trachomatis  LPS monoclonal Ab and a goat anti‐mouse‐IgG‐Alexaflour™647 secondary Ab or labeled with CFSE).  (B)  PLB‐985 cells were stained with fixable viability dye eFluor ®  780 (FvD) and gated on living cells with FSC‐A versus APC‐Cy7‐A.  (C)  CFSE‐labeled SvD bacteria were preincubated with no serum, serum from naïve rabbits, or serum from rabbits vaccinated with Hirep1 for 40 min at 37°C and incubated for 4 h with DMF‐stimulated PLB‐985 cells. CFSE‐signal was measured by flow cytometry in the FITC channel. Cells were gated on CFSE‐positive (=phagocytosing) events. Pseudo‐color dot plots show PLB‐985 cells alone or after incubation with noncoated or coated bacteria.
    Fixable Viability Dye Efluor 780, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 3073 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    fixable viability dye efluor 780 - by Bioz Stars, 2020-11
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    99
    Thermo Fisher hoechst 33342 dye
    Effect of ATM or p53 inhibition on DNA damage repair and hair cell survival 3D images of OHC nuclei taken from the basal regions of organ of Corti cultures treated with medium alone, 10 μM KU55933, 10 μM CDDP, or 10 μM CDDP in combination with 10 μM KU55933 for 1 day and immunolabeled for 53BP1 (green) and <t>Hoechst</t> 33342 (blue). Scale bar = 5 μm. Quantification analysis of 53BP1 foci number per nucleus in both IHCs (red bars) and OHCs (blue bars) for all conditions ( n = 50 nuclei per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA followed by post hoc Tukey's test (*** P ≤ 0.0004; CDDP versus control, or CDDP versus CDDP + KU55933). Confocal images showing the basal region of the organ of Corti cultures treated with medium alone, 10 μM KU55933, 10 μM CDDP, or 10 μM CDDP in combination with 10 μM KU55933 for 5 days and immunolabeled for myosin 7A (red). Scale bar = 24 μm. Histograms representing the numbers of surviving IHCs (red bars) and OHCs (blue bars) for all treatment conditions after 5 days ( n = 5 cochleae per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA test followed by post hoc Tukey's test (* P = 0.03, ** P = 0.004, *** P ≤ 0.0008; CDDP versus control, or CDDP versus CDDP + KU55933). 3D images of OHC nuclei from the basal regions of organ of Corti cultures treated with culture medium alone, 100 μM PFT‐α, 10 μM CDDP, or 10 μM CDDP in combination with 100 μM PFT‐α for 1 day and immunolabeled for 53BP1 (green) and Hoechst 33342 (blue). Scale bar = 5 μm. Quantification of 53BP1 foci number per nucleus in both IHCs (red bars) and OHCs (blue bars) for all conditions ( n = 50 nuclei per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA test followed by post hoc Tukey's test (*** P ≤ 0.0007; CDDP versus control). Data information: All experiments were performed in triplicate.
    Hoechst 33342 Dye, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 2985 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hoechst 33342 dye/product/Thermo Fisher
    Average 99 stars, based on 2985 article reviews
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    hoechst 33342 dye - by Bioz Stars, 2020-11
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    99
    Thermo Fisher genescan 500 liz size standard
    Effect of ATM or p53 inhibition on DNA damage repair and hair cell survival 3D images of OHC nuclei taken from the basal regions of organ of Corti cultures treated with medium alone, 10 μM KU55933, 10 μM CDDP, or 10 μM CDDP in combination with 10 μM KU55933 for 1 day and immunolabeled for 53BP1 (green) and <t>Hoechst</t> 33342 (blue). Scale bar = 5 μm. Quantification analysis of 53BP1 foci number per nucleus in both IHCs (red bars) and OHCs (blue bars) for all conditions ( n = 50 nuclei per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA followed by post hoc Tukey's test (*** P ≤ 0.0004; CDDP versus control, or CDDP versus CDDP + KU55933). Confocal images showing the basal region of the organ of Corti cultures treated with medium alone, 10 μM KU55933, 10 μM CDDP, or 10 μM CDDP in combination with 10 μM KU55933 for 5 days and immunolabeled for myosin 7A (red). Scale bar = 24 μm. Histograms representing the numbers of surviving IHCs (red bars) and OHCs (blue bars) for all treatment conditions after 5 days ( n = 5 cochleae per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA test followed by post hoc Tukey's test (* P = 0.03, ** P = 0.004, *** P ≤ 0.0008; CDDP versus control, or CDDP versus CDDP + KU55933). 3D images of OHC nuclei from the basal regions of organ of Corti cultures treated with culture medium alone, 100 μM PFT‐α, 10 μM CDDP, or 10 μM CDDP in combination with 100 μM PFT‐α for 1 day and immunolabeled for 53BP1 (green) and Hoechst 33342 (blue). Scale bar = 5 μm. Quantification of 53BP1 foci number per nucleus in both IHCs (red bars) and OHCs (blue bars) for all conditions ( n = 50 nuclei per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA test followed by post hoc Tukey's test (*** P ≤ 0.0007; CDDP versus control). Data information: All experiments were performed in triplicate.
    Genescan 500 Liz Size Standard, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 3071 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 3071 article reviews
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    genescan 500 liz size standard - by Bioz Stars, 2020-11
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    Thermo Fisher celltracker green cmfda
    Effect of ATM or p53 inhibition on DNA damage repair and hair cell survival 3D images of OHC nuclei taken from the basal regions of organ of Corti cultures treated with medium alone, 10 μM KU55933, 10 μM CDDP, or 10 μM CDDP in combination with 10 μM KU55933 for 1 day and immunolabeled for 53BP1 (green) and <t>Hoechst</t> 33342 (blue). Scale bar = 5 μm. Quantification analysis of 53BP1 foci number per nucleus in both IHCs (red bars) and OHCs (blue bars) for all conditions ( n = 50 nuclei per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA followed by post hoc Tukey's test (*** P ≤ 0.0004; CDDP versus control, or CDDP versus CDDP + KU55933). Confocal images showing the basal region of the organ of Corti cultures treated with medium alone, 10 μM KU55933, 10 μM CDDP, or 10 μM CDDP in combination with 10 μM KU55933 for 5 days and immunolabeled for myosin 7A (red). Scale bar = 24 μm. Histograms representing the numbers of surviving IHCs (red bars) and OHCs (blue bars) for all treatment conditions after 5 days ( n = 5 cochleae per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA test followed by post hoc Tukey's test (* P = 0.03, ** P = 0.004, *** P ≤ 0.0008; CDDP versus control, or CDDP versus CDDP + KU55933). 3D images of OHC nuclei from the basal regions of organ of Corti cultures treated with culture medium alone, 100 μM PFT‐α, 10 μM CDDP, or 10 μM CDDP in combination with 100 μM PFT‐α for 1 day and immunolabeled for 53BP1 (green) and Hoechst 33342 (blue). Scale bar = 5 μm. Quantification of 53BP1 foci number per nucleus in both IHCs (red bars) and OHCs (blue bars) for all conditions ( n = 50 nuclei per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA test followed by post hoc Tukey's test (*** P ≤ 0.0007; CDDP versus control). Data information: All experiments were performed in triplicate.
    Celltracker Green Cmfda, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 2274 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/celltracker green cmfda/product/Thermo Fisher
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    celltracker green cmfda - by Bioz Stars, 2020-11
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    Thermo Fisher rox reference dye
    Effect of ATM or p53 inhibition on DNA damage repair and hair cell survival 3D images of OHC nuclei taken from the basal regions of organ of Corti cultures treated with medium alone, 10 μM KU55933, 10 μM CDDP, or 10 μM CDDP in combination with 10 μM KU55933 for 1 day and immunolabeled for 53BP1 (green) and <t>Hoechst</t> 33342 (blue). Scale bar = 5 μm. Quantification analysis of 53BP1 foci number per nucleus in both IHCs (red bars) and OHCs (blue bars) for all conditions ( n = 50 nuclei per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA followed by post hoc Tukey's test (*** P ≤ 0.0004; CDDP versus control, or CDDP versus CDDP + KU55933). Confocal images showing the basal region of the organ of Corti cultures treated with medium alone, 10 μM KU55933, 10 μM CDDP, or 10 μM CDDP in combination with 10 μM KU55933 for 5 days and immunolabeled for myosin 7A (red). Scale bar = 24 μm. Histograms representing the numbers of surviving IHCs (red bars) and OHCs (blue bars) for all treatment conditions after 5 days ( n = 5 cochleae per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA test followed by post hoc Tukey's test (* P = 0.03, ** P = 0.004, *** P ≤ 0.0008; CDDP versus control, or CDDP versus CDDP + KU55933). 3D images of OHC nuclei from the basal regions of organ of Corti cultures treated with culture medium alone, 100 μM PFT‐α, 10 μM CDDP, or 10 μM CDDP in combination with 100 μM PFT‐α for 1 day and immunolabeled for 53BP1 (green) and Hoechst 33342 (blue). Scale bar = 5 μm. Quantification of 53BP1 foci number per nucleus in both IHCs (red bars) and OHCs (blue bars) for all conditions ( n = 50 nuclei per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA test followed by post hoc Tukey's test (*** P ≤ 0.0007; CDDP versus control). Data information: All experiments were performed in triplicate.
    Rox Reference Dye, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 2734 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rox reference dye/product/Thermo Fisher
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    rox reference dye - by Bioz Stars, 2020-11
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    Thermo Fisher bigdye terminator cycle sequencing ready reaction kit
    Effect of ATM or p53 inhibition on DNA damage repair and hair cell survival 3D images of OHC nuclei taken from the basal regions of organ of Corti cultures treated with medium alone, 10 μM KU55933, 10 μM CDDP, or 10 μM CDDP in combination with 10 μM KU55933 for 1 day and immunolabeled for 53BP1 (green) and <t>Hoechst</t> 33342 (blue). Scale bar = 5 μm. Quantification analysis of 53BP1 foci number per nucleus in both IHCs (red bars) and OHCs (blue bars) for all conditions ( n = 50 nuclei per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA followed by post hoc Tukey's test (*** P ≤ 0.0004; CDDP versus control, or CDDP versus CDDP + KU55933). Confocal images showing the basal region of the organ of Corti cultures treated with medium alone, 10 μM KU55933, 10 μM CDDP, or 10 μM CDDP in combination with 10 μM KU55933 for 5 days and immunolabeled for myosin 7A (red). Scale bar = 24 μm. Histograms representing the numbers of surviving IHCs (red bars) and OHCs (blue bars) for all treatment conditions after 5 days ( n = 5 cochleae per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA test followed by post hoc Tukey's test (* P = 0.03, ** P = 0.004, *** P ≤ 0.0008; CDDP versus control, or CDDP versus CDDP + KU55933). 3D images of OHC nuclei from the basal regions of organ of Corti cultures treated with culture medium alone, 100 μM PFT‐α, 10 μM CDDP, or 10 μM CDDP in combination with 100 μM PFT‐α for 1 day and immunolabeled for 53BP1 (green) and Hoechst 33342 (blue). Scale bar = 5 μm. Quantification of 53BP1 foci number per nucleus in both IHCs (red bars) and OHCs (blue bars) for all conditions ( n = 50 nuclei per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA test followed by post hoc Tukey's test (*** P ≤ 0.0007; CDDP versus control). Data information: All experiments were performed in triplicate.
    Bigdye Terminator Cycle Sequencing Ready Reaction Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 4685 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bigdye terminator cycle sequencing ready reaction kit/product/Thermo Fisher
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    bigdye terminator cycle sequencing ready reaction kit - by Bioz Stars, 2020-11
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    Thermo Fisher jc 1 dye
    Effect of ATM or p53 inhibition on DNA damage repair and hair cell survival 3D images of OHC nuclei taken from the basal regions of organ of Corti cultures treated with medium alone, 10 μM KU55933, 10 μM CDDP, or 10 μM CDDP in combination with 10 μM KU55933 for 1 day and immunolabeled for 53BP1 (green) and <t>Hoechst</t> 33342 (blue). Scale bar = 5 μm. Quantification analysis of 53BP1 foci number per nucleus in both IHCs (red bars) and OHCs (blue bars) for all conditions ( n = 50 nuclei per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA followed by post hoc Tukey's test (*** P ≤ 0.0004; CDDP versus control, or CDDP versus CDDP + KU55933). Confocal images showing the basal region of the organ of Corti cultures treated with medium alone, 10 μM KU55933, 10 μM CDDP, or 10 μM CDDP in combination with 10 μM KU55933 for 5 days and immunolabeled for myosin 7A (red). Scale bar = 24 μm. Histograms representing the numbers of surviving IHCs (red bars) and OHCs (blue bars) for all treatment conditions after 5 days ( n = 5 cochleae per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA test followed by post hoc Tukey's test (* P = 0.03, ** P = 0.004, *** P ≤ 0.0008; CDDP versus control, or CDDP versus CDDP + KU55933). 3D images of OHC nuclei from the basal regions of organ of Corti cultures treated with culture medium alone, 100 μM PFT‐α, 10 μM CDDP, or 10 μM CDDP in combination with 100 μM PFT‐α for 1 day and immunolabeled for 53BP1 (green) and Hoechst 33342 (blue). Scale bar = 5 μm. Quantification of 53BP1 foci number per nucleus in both IHCs (red bars) and OHCs (blue bars) for all conditions ( n = 50 nuclei per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA test followed by post hoc Tukey's test (*** P ≤ 0.0007; CDDP versus control). Data information: All experiments were performed in triplicate.
    Jc 1 Dye, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1299 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/jc 1 dye/product/Thermo Fisher
    Average 99 stars, based on 1299 article reviews
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    jc 1 dye - by Bioz Stars, 2020-11
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    Thermo Fisher big dye terminator kit
    Effect of ATM or p53 inhibition on DNA damage repair and hair cell survival 3D images of OHC nuclei taken from the basal regions of organ of Corti cultures treated with medium alone, 10 μM KU55933, 10 μM CDDP, or 10 μM CDDP in combination with 10 μM KU55933 for 1 day and immunolabeled for 53BP1 (green) and <t>Hoechst</t> 33342 (blue). Scale bar = 5 μm. Quantification analysis of 53BP1 foci number per nucleus in both IHCs (red bars) and OHCs (blue bars) for all conditions ( n = 50 nuclei per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA followed by post hoc Tukey's test (*** P ≤ 0.0004; CDDP versus control, or CDDP versus CDDP + KU55933). Confocal images showing the basal region of the organ of Corti cultures treated with medium alone, 10 μM KU55933, 10 μM CDDP, or 10 μM CDDP in combination with 10 μM KU55933 for 5 days and immunolabeled for myosin 7A (red). Scale bar = 24 μm. Histograms representing the numbers of surviving IHCs (red bars) and OHCs (blue bars) for all treatment conditions after 5 days ( n = 5 cochleae per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA test followed by post hoc Tukey's test (* P = 0.03, ** P = 0.004, *** P ≤ 0.0008; CDDP versus control, or CDDP versus CDDP + KU55933). 3D images of OHC nuclei from the basal regions of organ of Corti cultures treated with culture medium alone, 100 μM PFT‐α, 10 μM CDDP, or 10 μM CDDP in combination with 100 μM PFT‐α for 1 day and immunolabeled for 53BP1 (green) and Hoechst 33342 (blue). Scale bar = 5 μm. Quantification of 53BP1 foci number per nucleus in both IHCs (red bars) and OHCs (blue bars) for all conditions ( n = 50 nuclei per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA test followed by post hoc Tukey's test (*** P ≤ 0.0007; CDDP versus control). Data information: All experiments were performed in triplicate.
    Big Dye Terminator Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 3331 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/big dye terminator kit/product/Thermo Fisher
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    big dye terminator kit - by Bioz Stars, 2020-11
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    Thermo Fisher alexa fluor dyes
    Effect of ATM or p53 inhibition on DNA damage repair and hair cell survival 3D images of OHC nuclei taken from the basal regions of organ of Corti cultures treated with medium alone, 10 μM KU55933, 10 μM CDDP, or 10 μM CDDP in combination with 10 μM KU55933 for 1 day and immunolabeled for 53BP1 (green) and <t>Hoechst</t> 33342 (blue). Scale bar = 5 μm. Quantification analysis of 53BP1 foci number per nucleus in both IHCs (red bars) and OHCs (blue bars) for all conditions ( n = 50 nuclei per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA followed by post hoc Tukey's test (*** P ≤ 0.0004; CDDP versus control, or CDDP versus CDDP + KU55933). Confocal images showing the basal region of the organ of Corti cultures treated with medium alone, 10 μM KU55933, 10 μM CDDP, or 10 μM CDDP in combination with 10 μM KU55933 for 5 days and immunolabeled for myosin 7A (red). Scale bar = 24 μm. Histograms representing the numbers of surviving IHCs (red bars) and OHCs (blue bars) for all treatment conditions after 5 days ( n = 5 cochleae per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA test followed by post hoc Tukey's test (* P = 0.03, ** P = 0.004, *** P ≤ 0.0008; CDDP versus control, or CDDP versus CDDP + KU55933). 3D images of OHC nuclei from the basal regions of organ of Corti cultures treated with culture medium alone, 100 μM PFT‐α, 10 μM CDDP, or 10 μM CDDP in combination with 100 μM PFT‐α for 1 day and immunolabeled for 53BP1 (green) and Hoechst 33342 (blue). Scale bar = 5 μm. Quantification of 53BP1 foci number per nucleus in both IHCs (red bars) and OHCs (blue bars) for all conditions ( n = 50 nuclei per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA test followed by post hoc Tukey's test (*** P ≤ 0.0007; CDDP versus control). Data information: All experiments were performed in triplicate.
    Alexa Fluor Dyes, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1864 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    alexa fluor dyes - by Bioz Stars, 2020-11
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    96
    Thermo Fisher sypro orange dye
    Effect of ATM or p53 inhibition on DNA damage repair and hair cell survival 3D images of OHC nuclei taken from the basal regions of organ of Corti cultures treated with medium alone, 10 μM KU55933, 10 μM CDDP, or 10 μM CDDP in combination with 10 μM KU55933 for 1 day and immunolabeled for 53BP1 (green) and <t>Hoechst</t> 33342 (blue). Scale bar = 5 μm. Quantification analysis of 53BP1 foci number per nucleus in both IHCs (red bars) and OHCs (blue bars) for all conditions ( n = 50 nuclei per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA followed by post hoc Tukey's test (*** P ≤ 0.0004; CDDP versus control, or CDDP versus CDDP + KU55933). Confocal images showing the basal region of the organ of Corti cultures treated with medium alone, 10 μM KU55933, 10 μM CDDP, or 10 μM CDDP in combination with 10 μM KU55933 for 5 days and immunolabeled for myosin 7A (red). Scale bar = 24 μm. Histograms representing the numbers of surviving IHCs (red bars) and OHCs (blue bars) for all treatment conditions after 5 days ( n = 5 cochleae per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA test followed by post hoc Tukey's test (* P = 0.03, ** P = 0.004, *** P ≤ 0.0008; CDDP versus control, or CDDP versus CDDP + KU55933). 3D images of OHC nuclei from the basal regions of organ of Corti cultures treated with culture medium alone, 100 μM PFT‐α, 10 μM CDDP, or 10 μM CDDP in combination with 100 μM PFT‐α for 1 day and immunolabeled for 53BP1 (green) and Hoechst 33342 (blue). Scale bar = 5 μm. Quantification of 53BP1 foci number per nucleus in both IHCs (red bars) and OHCs (blue bars) for all conditions ( n = 50 nuclei per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA test followed by post hoc Tukey's test (*** P ≤ 0.0007; CDDP versus control). Data information: All experiments were performed in triplicate.
    Sypro Orange Dye, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 96/100, based on 1490 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    sypro orange dye - by Bioz Stars, 2020-11
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    Millipore trypan blue dye
    Effect of ATM or p53 inhibition on DNA damage repair and hair cell survival 3D images of OHC nuclei taken from the basal regions of organ of Corti cultures treated with medium alone, 10 μM KU55933, 10 μM CDDP, or 10 μM CDDP in combination with 10 μM KU55933 for 1 day and immunolabeled for 53BP1 (green) and <t>Hoechst</t> 33342 (blue). Scale bar = 5 μm. Quantification analysis of 53BP1 foci number per nucleus in both IHCs (red bars) and OHCs (blue bars) for all conditions ( n = 50 nuclei per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA followed by post hoc Tukey's test (*** P ≤ 0.0004; CDDP versus control, or CDDP versus CDDP + KU55933). Confocal images showing the basal region of the organ of Corti cultures treated with medium alone, 10 μM KU55933, 10 μM CDDP, or 10 μM CDDP in combination with 10 μM KU55933 for 5 days and immunolabeled for myosin 7A (red). Scale bar = 24 μm. Histograms representing the numbers of surviving IHCs (red bars) and OHCs (blue bars) for all treatment conditions after 5 days ( n = 5 cochleae per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA test followed by post hoc Tukey's test (* P = 0.03, ** P = 0.004, *** P ≤ 0.0008; CDDP versus control, or CDDP versus CDDP + KU55933). 3D images of OHC nuclei from the basal regions of organ of Corti cultures treated with culture medium alone, 100 μM PFT‐α, 10 μM CDDP, or 10 μM CDDP in combination with 100 μM PFT‐α for 1 day and immunolabeled for 53BP1 (green) and Hoechst 33342 (blue). Scale bar = 5 μm. Quantification of 53BP1 foci number per nucleus in both IHCs (red bars) and OHCs (blue bars) for all conditions ( n = 50 nuclei per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA test followed by post hoc Tukey's test (*** P ≤ 0.0007; CDDP versus control). Data information: All experiments were performed in triplicate.
    Trypan Blue Dye, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 1045 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    trypan blue dye - by Bioz Stars, 2020-11
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    Thermo Fisher fixable viability dye efluor 506
    Effect of ATM or p53 inhibition on DNA damage repair and hair cell survival 3D images of OHC nuclei taken from the basal regions of organ of Corti cultures treated with medium alone, 10 μM KU55933, 10 μM CDDP, or 10 μM CDDP in combination with 10 μM KU55933 for 1 day and immunolabeled for 53BP1 (green) and <t>Hoechst</t> 33342 (blue). Scale bar = 5 μm. Quantification analysis of 53BP1 foci number per nucleus in both IHCs (red bars) and OHCs (blue bars) for all conditions ( n = 50 nuclei per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA followed by post hoc Tukey's test (*** P ≤ 0.0004; CDDP versus control, or CDDP versus CDDP + KU55933). Confocal images showing the basal region of the organ of Corti cultures treated with medium alone, 10 μM KU55933, 10 μM CDDP, or 10 μM CDDP in combination with 10 μM KU55933 for 5 days and immunolabeled for myosin 7A (red). Scale bar = 24 μm. Histograms representing the numbers of surviving IHCs (red bars) and OHCs (blue bars) for all treatment conditions after 5 days ( n = 5 cochleae per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA test followed by post hoc Tukey's test (* P = 0.03, ** P = 0.004, *** P ≤ 0.0008; CDDP versus control, or CDDP versus CDDP + KU55933). 3D images of OHC nuclei from the basal regions of organ of Corti cultures treated with culture medium alone, 100 μM PFT‐α, 10 μM CDDP, or 10 μM CDDP in combination with 100 μM PFT‐α for 1 day and immunolabeled for 53BP1 (green) and Hoechst 33342 (blue). Scale bar = 5 μm. Quantification of 53BP1 foci number per nucleus in both IHCs (red bars) and OHCs (blue bars) for all conditions ( n = 50 nuclei per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA test followed by post hoc Tukey's test (*** P ≤ 0.0007; CDDP versus control). Data information: All experiments were performed in triplicate.
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    Biotium evagreen dye
    Enhanced abiotic ligation afforded by the condensation of DNA into LC domains. ( a ) DNA oligomer duplexes having end-to-end attraction order into LC phases that in turn stabilize their linear aggregates. ( b ) Molecules used in this study are as follows: the self-complementary 12-mer D1p, the partially self-complementary 14-mer D2TTp, the flexible water-soluble polymer PEG (molecular weight=8,000) and the water-soluble carbodiimide EDC used as ligating agent. Both DNA oligomer have a 3′ phosphate terminus. The two sequences are chosen not to form mixed D1p/D2TTp duplexes. ( c ) Mechanisms of autocatalysis and ligation. LC-stabilized end-to-end interaction holds the 3′ phosphate and the 5′ hydroxyl terminals in physical contact. Inset is adopted from ref. 8 . EDC activates the phosphate terminal first, yielding an active intermediate that can react with the hydroxyl terminal to yield a native phosphodiester link, with isourea as by-product. ( d ) Phase behaviour and ligation in D1p/PEG/EDC/water mixtures. ( e ) At low PEG concentration, the mixture is a uniform isotropic solution. ( f ) For c PEG > 400 g l −1 , the mixture phase separates into COL droplets of linearly aggregated duplexed DNA surrounded by an isotropic solution of PEG, as shown in the pictures above of the same 20-μm-thick flat cell in polarized and in fluorescence microscopy (duplexes are selectively marked by <t>EvaGreen</t> dye). ( g ) Fifteen per cent polyacrylamide gel stained by ethidium bromide. Three electrophoretic runs are shown as follows: c PEG =200 g l −1 (uniform solution), c PEG =300 g l −1 (few small COL domains) and c PEG =400 g l −1 (COL domains). Correspondingly, the product distribution is greatly modified. ( h ) Agarose gel (3.5%) runs of the c PEG =400 g l −1 sample recorded at two different run times. The picture of the 60-min run gel has been compressed and shifted to match the band position and spacing of the 40-min run gel, according to the band analysis described in Supplementary Methods . Numbers along the lanes indicate the oligomer lengths expressed in number of bases ( N b ) and the polymerization number ( n ). In both gels, the ladder contains DNA oligomers 12, 24, 36 and 48 bases long, synthesized by repetition of D1p sequence. The straight line is a guide for the eyes marking the condition of N b =120 ( n =10). Full gel images are shown in Supplementary Figs 14 and 15 .
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    Thermo Fisher trypan blue dye
    Enhanced abiotic ligation afforded by the condensation of DNA into LC domains. ( a ) DNA oligomer duplexes having end-to-end attraction order into LC phases that in turn stabilize their linear aggregates. ( b ) Molecules used in this study are as follows: the self-complementary 12-mer D1p, the partially self-complementary 14-mer D2TTp, the flexible water-soluble polymer PEG (molecular weight=8,000) and the water-soluble carbodiimide EDC used as ligating agent. Both DNA oligomer have a 3′ phosphate terminus. The two sequences are chosen not to form mixed D1p/D2TTp duplexes. ( c ) Mechanisms of autocatalysis and ligation. LC-stabilized end-to-end interaction holds the 3′ phosphate and the 5′ hydroxyl terminals in physical contact. Inset is adopted from ref. 8 . EDC activates the phosphate terminal first, yielding an active intermediate that can react with the hydroxyl terminal to yield a native phosphodiester link, with isourea as by-product. ( d ) Phase behaviour and ligation in D1p/PEG/EDC/water mixtures. ( e ) At low PEG concentration, the mixture is a uniform isotropic solution. ( f ) For c PEG > 400 g l −1 , the mixture phase separates into COL droplets of linearly aggregated duplexed DNA surrounded by an isotropic solution of PEG, as shown in the pictures above of the same 20-μm-thick flat cell in polarized and in fluorescence microscopy (duplexes are selectively marked by <t>EvaGreen</t> dye). ( g ) Fifteen per cent polyacrylamide gel stained by ethidium bromide. Three electrophoretic runs are shown as follows: c PEG =200 g l −1 (uniform solution), c PEG =300 g l −1 (few small COL domains) and c PEG =400 g l −1 (COL domains). Correspondingly, the product distribution is greatly modified. ( h ) Agarose gel (3.5%) runs of the c PEG =400 g l −1 sample recorded at two different run times. The picture of the 60-min run gel has been compressed and shifted to match the band position and spacing of the 40-min run gel, according to the band analysis described in Supplementary Methods . Numbers along the lanes indicate the oligomer lengths expressed in number of bases ( N b ) and the polymerization number ( n ). In both gels, the ladder contains DNA oligomers 12, 24, 36 and 48 bases long, synthesized by repetition of D1p sequence. The straight line is a guide for the eyes marking the condition of N b =120 ( n =10). Full gel images are shown in Supplementary Figs 14 and 15 .
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    Enhanced abiotic ligation afforded by the condensation of DNA into LC domains. ( a ) DNA oligomer duplexes having end-to-end attraction order into LC phases that in turn stabilize their linear aggregates. ( b ) Molecules used in this study are as follows: the self-complementary 12-mer D1p, the partially self-complementary 14-mer D2TTp, the flexible water-soluble polymer PEG (molecular weight=8,000) and the water-soluble carbodiimide EDC used as ligating agent. Both DNA oligomer have a 3′ phosphate terminus. The two sequences are chosen not to form mixed D1p/D2TTp duplexes. ( c ) Mechanisms of autocatalysis and ligation. LC-stabilized end-to-end interaction holds the 3′ phosphate and the 5′ hydroxyl terminals in physical contact. Inset is adopted from ref. 8 . EDC activates the phosphate terminal first, yielding an active intermediate that can react with the hydroxyl terminal to yield a native phosphodiester link, with isourea as by-product. ( d ) Phase behaviour and ligation in D1p/PEG/EDC/water mixtures. ( e ) At low PEG concentration, the mixture is a uniform isotropic solution. ( f ) For c PEG > 400 g l −1 , the mixture phase separates into COL droplets of linearly aggregated duplexed DNA surrounded by an isotropic solution of PEG, as shown in the pictures above of the same 20-μm-thick flat cell in polarized and in fluorescence microscopy (duplexes are selectively marked by <t>EvaGreen</t> dye). ( g ) Fifteen per cent polyacrylamide gel stained by ethidium bromide. Three electrophoretic runs are shown as follows: c PEG =200 g l −1 (uniform solution), c PEG =300 g l −1 (few small COL domains) and c PEG =400 g l −1 (COL domains). Correspondingly, the product distribution is greatly modified. ( h ) Agarose gel (3.5%) runs of the c PEG =400 g l −1 sample recorded at two different run times. The picture of the 60-min run gel has been compressed and shifted to match the band position and spacing of the 40-min run gel, according to the band analysis described in Supplementary Methods . Numbers along the lanes indicate the oligomer lengths expressed in number of bases ( N b ) and the polymerization number ( n ). In both gels, the ladder contains DNA oligomers 12, 24, 36 and 48 bases long, synthesized by repetition of D1p sequence. The straight line is a guide for the eyes marking the condition of N b =120 ( n =10). Full gel images are shown in Supplementary Figs 14 and 15 .
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    Image Search Results


    Gating strategies for CFSE‐labeled  C. trachomatis  bacteria and phagocytosis assay. All gatings were first set on singlet events (FSC‐A vs FSC‐H), followed by gating on target cell population (FSC‐A vs. SSC‐A).  (A)  Bacteria were then shown in APC‐A versus FITC‐A (stained either with mouse anti‐ C. trachomatis  LPS monoclonal Ab and a goat anti‐mouse‐IgG‐Alexaflour™647 secondary Ab or labeled with CFSE).  (B)  PLB‐985 cells were stained with fixable viability dye eFluor ®  780 (FvD) and gated on living cells with FSC‐A versus APC‐Cy7‐A.  (C)  CFSE‐labeled SvD bacteria were preincubated with no serum, serum from naïve rabbits, or serum from rabbits vaccinated with Hirep1 for 40 min at 37°C and incubated for 4 h with DMF‐stimulated PLB‐985 cells. CFSE‐signal was measured by flow cytometry in the FITC channel. Cells were gated on CFSE‐positive (=phagocytosing) events. Pseudo‐color dot plots show PLB‐985 cells alone or after incubation with noncoated or coated bacteria.

    Journal: Cytometry

    Article Title: A flow cytometry‐based assay to determine the phagocytic activity of both clinical and nonclinical antibody samples against Chlamydia trachomatis

    doi: 10.1002/cyto.a.23353

    Figure Lengend Snippet: Gating strategies for CFSE‐labeled C. trachomatis bacteria and phagocytosis assay. All gatings were first set on singlet events (FSC‐A vs FSC‐H), followed by gating on target cell population (FSC‐A vs. SSC‐A). (A) Bacteria were then shown in APC‐A versus FITC‐A (stained either with mouse anti‐ C. trachomatis LPS monoclonal Ab and a goat anti‐mouse‐IgG‐Alexaflour™647 secondary Ab or labeled with CFSE). (B) PLB‐985 cells were stained with fixable viability dye eFluor ® 780 (FvD) and gated on living cells with FSC‐A versus APC‐Cy7‐A. (C) CFSE‐labeled SvD bacteria were preincubated with no serum, serum from naïve rabbits, or serum from rabbits vaccinated with Hirep1 for 40 min at 37°C and incubated for 4 h with DMF‐stimulated PLB‐985 cells. CFSE‐signal was measured by flow cytometry in the FITC channel. Cells were gated on CFSE‐positive (=phagocytosing) events. Pseudo‐color dot plots show PLB‐985 cells alone or after incubation with noncoated or coated bacteria.

    Article Snippet: The PBS was removed and the cells were resuspended in 50 µl fixable viability dye eFluor® 780 (Thermofischer Scientific; Cat. 65–0865‐14).

    Techniques: Labeling, Phagocytosis Assay, Staining, Incubation, Flow Cytometry, Cytometry

    Effect of ATM or p53 inhibition on DNA damage repair and hair cell survival 3D images of OHC nuclei taken from the basal regions of organ of Corti cultures treated with medium alone, 10 μM KU55933, 10 μM CDDP, or 10 μM CDDP in combination with 10 μM KU55933 for 1 day and immunolabeled for 53BP1 (green) and Hoechst 33342 (blue). Scale bar = 5 μm. Quantification analysis of 53BP1 foci number per nucleus in both IHCs (red bars) and OHCs (blue bars) for all conditions ( n = 50 nuclei per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA followed by post hoc Tukey's test (*** P ≤ 0.0004; CDDP versus control, or CDDP versus CDDP + KU55933). Confocal images showing the basal region of the organ of Corti cultures treated with medium alone, 10 μM KU55933, 10 μM CDDP, or 10 μM CDDP in combination with 10 μM KU55933 for 5 days and immunolabeled for myosin 7A (red). Scale bar = 24 μm. Histograms representing the numbers of surviving IHCs (red bars) and OHCs (blue bars) for all treatment conditions after 5 days ( n = 5 cochleae per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA test followed by post hoc Tukey's test (* P = 0.03, ** P = 0.004, *** P ≤ 0.0008; CDDP versus control, or CDDP versus CDDP + KU55933). 3D images of OHC nuclei from the basal regions of organ of Corti cultures treated with culture medium alone, 100 μM PFT‐α, 10 μM CDDP, or 10 μM CDDP in combination with 100 μM PFT‐α for 1 day and immunolabeled for 53BP1 (green) and Hoechst 33342 (blue). Scale bar = 5 μm. Quantification of 53BP1 foci number per nucleus in both IHCs (red bars) and OHCs (blue bars) for all conditions ( n = 50 nuclei per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA test followed by post hoc Tukey's test (*** P ≤ 0.0007; CDDP versus control). Data information: All experiments were performed in triplicate.

    Journal: EMBO Molecular Medicine

    Article Title: Reversible p53 inhibition prevents cisplatin ototoxicity without blocking chemotherapeutic efficacy

    doi: 10.15252/emmm.201606230

    Figure Lengend Snippet: Effect of ATM or p53 inhibition on DNA damage repair and hair cell survival 3D images of OHC nuclei taken from the basal regions of organ of Corti cultures treated with medium alone, 10 μM KU55933, 10 μM CDDP, or 10 μM CDDP in combination with 10 μM KU55933 for 1 day and immunolabeled for 53BP1 (green) and Hoechst 33342 (blue). Scale bar = 5 μm. Quantification analysis of 53BP1 foci number per nucleus in both IHCs (red bars) and OHCs (blue bars) for all conditions ( n = 50 nuclei per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA followed by post hoc Tukey's test (*** P ≤ 0.0004; CDDP versus control, or CDDP versus CDDP + KU55933). Confocal images showing the basal region of the organ of Corti cultures treated with medium alone, 10 μM KU55933, 10 μM CDDP, or 10 μM CDDP in combination with 10 μM KU55933 for 5 days and immunolabeled for myosin 7A (red). Scale bar = 24 μm. Histograms representing the numbers of surviving IHCs (red bars) and OHCs (blue bars) for all treatment conditions after 5 days ( n = 5 cochleae per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA test followed by post hoc Tukey's test (* P = 0.03, ** P = 0.004, *** P ≤ 0.0008; CDDP versus control, or CDDP versus CDDP + KU55933). 3D images of OHC nuclei from the basal regions of organ of Corti cultures treated with culture medium alone, 100 μM PFT‐α, 10 μM CDDP, or 10 μM CDDP in combination with 100 μM PFT‐α for 1 day and immunolabeled for 53BP1 (green) and Hoechst 33342 (blue). Scale bar = 5 μm. Quantification of 53BP1 foci number per nucleus in both IHCs (red bars) and OHCs (blue bars) for all conditions ( n = 50 nuclei per condition and per time point). Data are expressed as mean ± SEM. One‐way ANOVA test followed by post hoc Tukey's test (*** P ≤ 0.0007; CDDP versus control). Data information: All experiments were performed in triplicate.

    Article Snippet: The Hoechst 33342 dye (0.002% wt:vol in PBS 1×, Thermo Fisher Scientific, #62249) was used to stain chromatin.

    Techniques: Inhibition, Immunolabeling

    Cochlear explant and slice preparation, and CDDP‐induced DNA damage and cell death in sensory hair cells and spiral ganglion neurons Representative images showing an organ of Corti explant and a cochlear slice (250–300 μm thickness) cultured with culture medium alone for 5 days. The explant and slice were then immunolabeled with myosin 7A (red) and NF200 (green). SG: spiral ganglion, nf: nerve fiber, SV: scala vestibuli, SM: scala media, ST: scala tympani, oC: organ of Corti. Scale bars = (A), 300 μm; (B), 60 μm. Confocal images showing the spiral ganglion neurons from the basal turns of cochlear slices treated with either culture medium alone or medium containing 10 μM CDDP for 3 days before being cultured for a further 2 days. The slices were labeled with NF200 (green) to highlight auditory nerve fibers and neurons and Hoechst 33342 dye (blue) to label chromatin. Scale bar = 20 μm. Quantification analysis of spiral ganglion neuron density in control and CDDP‐exposed cochlear slices ( n = 2–3 slices per cochlea and 5 cochleae per group, all experiments were performed in triplicate). Data are expressed as mean ± SEM. One‐way ANOVA test followed by post hoc Tukey's test ( P > 0.05). Confocal images showing the basal region of cochlear explants treated with culture medium either alone (E) or containing 10 μM CDDP for 3 days (F, G). Hair cells were identified using myosin 7A (red), phosphatidylserine sites on the cell membrane surface using fluorochrome‐labeled Annexin V (green in F), and apoptotic DNA fragmentation using a TUNEL apoptosis kit (green in G). The white arrowheads indicate cell surface Annexin V‐positive labeling and TUNEL‐positive nuclei in some CDDP‐damaged IHCs. Scale bar = 20 μm. Confocal images showing the spiral ganglion neurons from the basal turn of cochlear slice cultures treated with culture medium either alone or containing 10 μM CDDP for 1 day and immunolabeled for NF200 (red) and γH2AX (green in H), or NF200 (red) and 53BP1 (green in I). The white arrowheads indicate CDDP‐induced γH2AX and 53BP1 foci in some spiral ganglion neurons. Scale bar = 20 μm.

    Journal: EMBO Molecular Medicine

    Article Title: Reversible p53 inhibition prevents cisplatin ototoxicity without blocking chemotherapeutic efficacy

    doi: 10.15252/emmm.201606230

    Figure Lengend Snippet: Cochlear explant and slice preparation, and CDDP‐induced DNA damage and cell death in sensory hair cells and spiral ganglion neurons Representative images showing an organ of Corti explant and a cochlear slice (250–300 μm thickness) cultured with culture medium alone for 5 days. The explant and slice were then immunolabeled with myosin 7A (red) and NF200 (green). SG: spiral ganglion, nf: nerve fiber, SV: scala vestibuli, SM: scala media, ST: scala tympani, oC: organ of Corti. Scale bars = (A), 300 μm; (B), 60 μm. Confocal images showing the spiral ganglion neurons from the basal turns of cochlear slices treated with either culture medium alone or medium containing 10 μM CDDP for 3 days before being cultured for a further 2 days. The slices were labeled with NF200 (green) to highlight auditory nerve fibers and neurons and Hoechst 33342 dye (blue) to label chromatin. Scale bar = 20 μm. Quantification analysis of spiral ganglion neuron density in control and CDDP‐exposed cochlear slices ( n = 2–3 slices per cochlea and 5 cochleae per group, all experiments were performed in triplicate). Data are expressed as mean ± SEM. One‐way ANOVA test followed by post hoc Tukey's test ( P > 0.05). Confocal images showing the basal region of cochlear explants treated with culture medium either alone (E) or containing 10 μM CDDP for 3 days (F, G). Hair cells were identified using myosin 7A (red), phosphatidylserine sites on the cell membrane surface using fluorochrome‐labeled Annexin V (green in F), and apoptotic DNA fragmentation using a TUNEL apoptosis kit (green in G). The white arrowheads indicate cell surface Annexin V‐positive labeling and TUNEL‐positive nuclei in some CDDP‐damaged IHCs. Scale bar = 20 μm. Confocal images showing the spiral ganglion neurons from the basal turn of cochlear slice cultures treated with culture medium either alone or containing 10 μM CDDP for 1 day and immunolabeled for NF200 (red) and γH2AX (green in H), or NF200 (red) and 53BP1 (green in I). The white arrowheads indicate CDDP‐induced γH2AX and 53BP1 foci in some spiral ganglion neurons. Scale bar = 20 μm.

    Article Snippet: The Hoechst 33342 dye (0.002% wt:vol in PBS 1×, Thermo Fisher Scientific, #62249) was used to stain chromatin.

    Techniques: Slice Preparation, Cell Culture, Immunolabeling, Labeling, TUNEL Assay

    Enhanced abiotic ligation afforded by the condensation of DNA into LC domains. ( a ) DNA oligomer duplexes having end-to-end attraction order into LC phases that in turn stabilize their linear aggregates. ( b ) Molecules used in this study are as follows: the self-complementary 12-mer D1p, the partially self-complementary 14-mer D2TTp, the flexible water-soluble polymer PEG (molecular weight=8,000) and the water-soluble carbodiimide EDC used as ligating agent. Both DNA oligomer have a 3′ phosphate terminus. The two sequences are chosen not to form mixed D1p/D2TTp duplexes. ( c ) Mechanisms of autocatalysis and ligation. LC-stabilized end-to-end interaction holds the 3′ phosphate and the 5′ hydroxyl terminals in physical contact. Inset is adopted from ref. 8 . EDC activates the phosphate terminal first, yielding an active intermediate that can react with the hydroxyl terminal to yield a native phosphodiester link, with isourea as by-product. ( d ) Phase behaviour and ligation in D1p/PEG/EDC/water mixtures. ( e ) At low PEG concentration, the mixture is a uniform isotropic solution. ( f ) For c PEG > 400 g l −1 , the mixture phase separates into COL droplets of linearly aggregated duplexed DNA surrounded by an isotropic solution of PEG, as shown in the pictures above of the same 20-μm-thick flat cell in polarized and in fluorescence microscopy (duplexes are selectively marked by EvaGreen dye). ( g ) Fifteen per cent polyacrylamide gel stained by ethidium bromide. Three electrophoretic runs are shown as follows: c PEG =200 g l −1 (uniform solution), c PEG =300 g l −1 (few small COL domains) and c PEG =400 g l −1 (COL domains). Correspondingly, the product distribution is greatly modified. ( h ) Agarose gel (3.5%) runs of the c PEG =400 g l −1 sample recorded at two different run times. The picture of the 60-min run gel has been compressed and shifted to match the band position and spacing of the 40-min run gel, according to the band analysis described in Supplementary Methods . Numbers along the lanes indicate the oligomer lengths expressed in number of bases ( N b ) and the polymerization number ( n ). In both gels, the ladder contains DNA oligomers 12, 24, 36 and 48 bases long, synthesized by repetition of D1p sequence. The straight line is a guide for the eyes marking the condition of N b =120 ( n =10). Full gel images are shown in Supplementary Figs 14 and 15 .

    Journal: Nature Communications

    Article Title: Abiotic ligation of DNA oligomers templated by their liquid crystal ordering

    doi: 10.1038/ncomms7424

    Figure Lengend Snippet: Enhanced abiotic ligation afforded by the condensation of DNA into LC domains. ( a ) DNA oligomer duplexes having end-to-end attraction order into LC phases that in turn stabilize their linear aggregates. ( b ) Molecules used in this study are as follows: the self-complementary 12-mer D1p, the partially self-complementary 14-mer D2TTp, the flexible water-soluble polymer PEG (molecular weight=8,000) and the water-soluble carbodiimide EDC used as ligating agent. Both DNA oligomer have a 3′ phosphate terminus. The two sequences are chosen not to form mixed D1p/D2TTp duplexes. ( c ) Mechanisms of autocatalysis and ligation. LC-stabilized end-to-end interaction holds the 3′ phosphate and the 5′ hydroxyl terminals in physical contact. Inset is adopted from ref. 8 . EDC activates the phosphate terminal first, yielding an active intermediate that can react with the hydroxyl terminal to yield a native phosphodiester link, with isourea as by-product. ( d ) Phase behaviour and ligation in D1p/PEG/EDC/water mixtures. ( e ) At low PEG concentration, the mixture is a uniform isotropic solution. ( f ) For c PEG > 400 g l −1 , the mixture phase separates into COL droplets of linearly aggregated duplexed DNA surrounded by an isotropic solution of PEG, as shown in the pictures above of the same 20-μm-thick flat cell in polarized and in fluorescence microscopy (duplexes are selectively marked by EvaGreen dye). ( g ) Fifteen per cent polyacrylamide gel stained by ethidium bromide. Three electrophoretic runs are shown as follows: c PEG =200 g l −1 (uniform solution), c PEG =300 g l −1 (few small COL domains) and c PEG =400 g l −1 (COL domains). Correspondingly, the product distribution is greatly modified. ( h ) Agarose gel (3.5%) runs of the c PEG =400 g l −1 sample recorded at two different run times. The picture of the 60-min run gel has been compressed and shifted to match the band position and spacing of the 40-min run gel, according to the band analysis described in Supplementary Methods . Numbers along the lanes indicate the oligomer lengths expressed in number of bases ( N b ) and the polymerization number ( n ). In both gels, the ladder contains DNA oligomers 12, 24, 36 and 48 bases long, synthesized by repetition of D1p sequence. The straight line is a guide for the eyes marking the condition of N b =120 ( n =10). Full gel images are shown in Supplementary Figs 14 and 15 .

    Article Snippet: Fluorescent images are obtained by doping DNA with EvaGreen dye (Biotium).

    Techniques: Ligation, Molecular Weight, Concentration Assay, Fluorescence, Microscopy, Staining, Modification, Agarose Gel Electrophoresis, Synthesized, Sequencing

    Ligation in condensed LC and isotropic DNA droplets. ( a ) Sketch, bright-field and fluorescent emission microscope picture of condensed D2TTp ISO droplets in a D2TTp/PEG mixture at T =20 °C. Duplexes are selectively marked by EvaGreen dye. ( b ) Sketch and polarized microscope images (crossed and parallel polarizers) of ISO D1p droplets in a D1p/PEG/EDC mixture at T =65 °C and c PEG =300 g l −1 , respectively. ( c ) Sketch and polarized microscope images (crossed and parallel polarizers) of COL D1p droplets in a D1p/PEG/EDC mixture at T =65 °C and c PEG =400 g l −1 , respectively (identical structures are found at 20 °C). ( d ) Polyacrylamide gel (15%) comparing the ligation products in D1p and D2TTp in identical conditions. The formation of concentrated DNA domains produces in the case of D2TTp (lanes on the left-hand side of the gel) a minor increment in the product length, contrasting with the marked discontinuity in the case of D1p. ( e ) Polyacrylamide gel (15%) comparing the ligation products obtained in D1p/PEG/EDC at T =65 °C, where, depending on c PEG , the system is either uniformly mixed or it partitions into two coexisting ISO phases ( c PEG =300 g l −1 , sketch b ), or else it phase separates into coexisting COL and ISO phases ( c PEG =400 g l −1 , sketch c ). Numbers along the lanes indicate the oligomer lengths expressed in number of bases ( N b ) and the polymerization number ( n ). In both gels, the ladder contains DNA oligomers 12, 24, 36 and 48 bases long, synthesized by repetition of D1p sequence. The straight lines are a guide for the eyes, helping the identification of bands corresponding to selected N b . Full gel images are shown in Supplementary Fig. 16 .

    Journal: Nature Communications

    Article Title: Abiotic ligation of DNA oligomers templated by their liquid crystal ordering

    doi: 10.1038/ncomms7424

    Figure Lengend Snippet: Ligation in condensed LC and isotropic DNA droplets. ( a ) Sketch, bright-field and fluorescent emission microscope picture of condensed D2TTp ISO droplets in a D2TTp/PEG mixture at T =20 °C. Duplexes are selectively marked by EvaGreen dye. ( b ) Sketch and polarized microscope images (crossed and parallel polarizers) of ISO D1p droplets in a D1p/PEG/EDC mixture at T =65 °C and c PEG =300 g l −1 , respectively. ( c ) Sketch and polarized microscope images (crossed and parallel polarizers) of COL D1p droplets in a D1p/PEG/EDC mixture at T =65 °C and c PEG =400 g l −1 , respectively (identical structures are found at 20 °C). ( d ) Polyacrylamide gel (15%) comparing the ligation products in D1p and D2TTp in identical conditions. The formation of concentrated DNA domains produces in the case of D2TTp (lanes on the left-hand side of the gel) a minor increment in the product length, contrasting with the marked discontinuity in the case of D1p. ( e ) Polyacrylamide gel (15%) comparing the ligation products obtained in D1p/PEG/EDC at T =65 °C, where, depending on c PEG , the system is either uniformly mixed or it partitions into two coexisting ISO phases ( c PEG =300 g l −1 , sketch b ), or else it phase separates into coexisting COL and ISO phases ( c PEG =400 g l −1 , sketch c ). Numbers along the lanes indicate the oligomer lengths expressed in number of bases ( N b ) and the polymerization number ( n ). In both gels, the ladder contains DNA oligomers 12, 24, 36 and 48 bases long, synthesized by repetition of D1p sequence. The straight lines are a guide for the eyes, helping the identification of bands corresponding to selected N b . Full gel images are shown in Supplementary Fig. 16 .

    Article Snippet: Fluorescent images are obtained by doping DNA with EvaGreen dye (Biotium).

    Techniques: Ligation, Microscopy, Synthesized, Sequencing